diff --git a/Project.toml b/Project.toml
index e6dda70..5a54922 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,15 +1,19 @@
 name = "LaMEM"
 uuid = "2e889f3d-35ce-4a77-8ea2-858aecb630f7"
 authors = ["Boris Kaus <kaus@uni-mainz.de>"]
-version = "0.1.14"
+version = "0.2.0"
 
 [deps]
+DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
+GeoParams = "e018b62d-d9de-4a26-8697-af89c310ae38"
 GeophysicalModelGenerator = "3700c31b-fa53-48a6-808a-ef22d5a84742"
 Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
 LaMEM_jll = "15d6fa20-f789-5486-b71b-22b4ac8eb1c1"
+Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
 PETSc_jll = "8fa3689e-f0b9-5420-9873-adf6ccf46f2d"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 ReadVTK = "dc215faf-f008-4882-a9f7-a79a826fadc3"
+Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 
 [compat]
 GeophysicalModelGenerator = "0.4 - 0.6"
@@ -17,11 +21,13 @@ Glob = "1"
 LaMEM_jll = "1.2.4 - 1.2.4"
 PETSc_jll = "3.16.8 - 3.16.8"
 ReadVTK = "0.1.7"
-julia = "1.6"
+Requires = "1.0, 2"
+julia = "1.9"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+
 
 [targets]
 test = ["Test"]
diff --git a/docs/build/assets/documenter.js b/docs/build/assets/documenter.js
new file mode 100644
index 0000000..6adfbbb
--- /dev/null
+++ b/docs/build/assets/documenter.js
@@ -0,0 +1,331 @@
+// Generated by Documenter.jl
+requirejs.config({
+  paths: {
+    'highlight-julia': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.5.1/languages/julia.min',
+    'headroom': 'https://cdnjs.cloudflare.com/ajax/libs/headroom/0.12.0/headroom.min',
+    'jqueryui': 'https://cdnjs.cloudflare.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min',
+    'katex-auto-render': 'https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/contrib/auto-render.min',
+    'jquery': 'https://cdnjs.cloudflare.com/ajax/libs/jquery/3.6.0/jquery.min',
+    'headroom-jquery': 'https://cdnjs.cloudflare.com/ajax/libs/headroom/0.12.0/jQuery.headroom.min',
+    'katex': 'https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min',
+    'highlight': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.5.1/highlight.min',
+    'highlight-julia-repl': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.5.1/languages/julia-repl.min',
+  },
+  shim: {
+  "highlight-julia": {
+    "deps": [
+      "highlight"
+    ]
+  },
+  "katex-auto-render": {
+    "deps": [
+      "katex"
+    ]
+  },
+  "headroom-jquery": {
+    "deps": [
+      "jquery",
+      "headroom"
+    ]
+  },
+  "highlight-julia-repl": {
+    "deps": [
+      "highlight"
+    ]
+  }
+}
+});
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery', 'katex', 'katex-auto-render'], function($, katex, renderMathInElement) {
+$(document).ready(function() {
+  renderMathInElement(
+    document.body,
+    {
+  "delimiters": [
+    {
+      "left": "$",
+      "right": "$",
+      "display": false
+    },
+    {
+      "left": "$$",
+      "right": "$$",
+      "display": true
+    },
+    {
+      "left": "\\[",
+      "right": "\\]",
+      "display": true
+    }
+  ]
+}
+
+  );
+})
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery', 'highlight', 'highlight-julia', 'highlight-julia-repl'], function($) {
+$(document).ready(function() {
+    hljs.highlightAll();
+})
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require([], function() {
+function addCopyButtonCallbacks() {
+  for (const el of document.getElementsByTagName("pre")) {
+    const button = document.createElement("button");
+    button.classList.add("copy-button", "fas", "fa-copy");
+    el.appendChild(button);
+
+    const success = function () {
+      button.classList.add("success", "fa-check");
+      button.classList.remove("fa-copy");
+    };
+
+    const failure = function () {
+      button.classList.add("error", "fa-times");
+      button.classList.remove("fa-copy");
+    };
+
+    button.addEventListener("click", function () {
+      copyToClipboard(el.innerText).then(success, failure);
+
+      setTimeout(function () {
+        button.classList.add("fa-copy");
+        button.classList.remove("success", "fa-check", "fa-times");
+      }, 5000);
+    });
+  }
+}
+
+function copyToClipboard(text) {
+  // clipboard API is only available in secure contexts
+  if (window.navigator && window.navigator.clipboard) {
+    return window.navigator.clipboard.writeText(text);
+  } else {
+    return new Promise(function (resolve, reject) {
+      try {
+        const el = document.createElement("textarea");
+        el.textContent = text;
+        el.style.position = "fixed";
+        el.style.opacity = 0;
+        document.body.appendChild(el);
+        el.select();
+        document.execCommand("copy");
+
+        resolve();
+      } catch (err) {
+        reject(err);
+      } finally {
+        document.body.removeChild(el);
+      }
+    });
+  }
+}
+
+if (document.readyState === "loading") {
+  document.addEventListener("DOMContentLoaded", addCopyButtonCallbacks);
+} else {
+  addCopyButtonCallbacks();
+}
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery', 'headroom', 'headroom-jquery'], function($, Headroom) {
+
+// Manages the top navigation bar (hides it when the user starts scrolling down on the
+// mobile).
+window.Headroom = Headroom; // work around buggy module loading?
+$(document).ready(function() {
+  $('#documenter .docs-navbar').headroom({
+    "tolerance": {"up": 10, "down": 10},
+  });
+})
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery'], function($) {
+
+// Modal settings dialog
+$(document).ready(function() {
+  var settings = $('#documenter-settings');
+  $('#documenter-settings-button').click(function(){
+    settings.toggleClass('is-active');
+  });
+  // Close the dialog if X is clicked
+  $('#documenter-settings button.delete').click(function(){
+    settings.removeClass('is-active');
+  });
+  // Close dialog if ESC is pressed
+  $(document).keyup(function(e) {
+    if (e.keyCode == 27) settings.removeClass('is-active');
+  });
+});
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery'], function($) {
+
+// Manages the showing and hiding of the sidebar.
+$(document).ready(function() {
+  var sidebar = $("#documenter > .docs-sidebar");
+  var sidebar_button = $("#documenter-sidebar-button")
+  sidebar_button.click(function(ev) {
+    ev.preventDefault();
+    sidebar.toggleClass('visible');
+    if (sidebar.hasClass('visible')) {
+      // Makes sure that the current menu item is visible in the sidebar.
+      $("#documenter .docs-menu a.is-active").focus();
+    }
+  });
+  $("#documenter > .docs-main").bind('click', function(ev) {
+    if ($(ev.target).is(sidebar_button)) {
+      return;
+    }
+    if (sidebar.hasClass('visible')) {
+      sidebar.removeClass('visible');
+    }
+  });
+})
+
+// Resizes the package name / sitename in the sidebar if it is too wide.
+// Inspired by: https://github.com/davatron5000/FitText.js
+$(document).ready(function() {
+  e = $("#documenter .docs-autofit");
+  function resize() {
+    var L = parseInt(e.css('max-width'), 10);
+    var L0 = e.width();
+    if(L0 > L) {
+      var h0 = parseInt(e.css('font-size'), 10);
+      e.css('font-size', L * h0 / L0);
+      // TODO: make sure it survives resizes?
+    }
+  }
+  // call once and then register events
+  resize();
+  $(window).resize(resize);
+  $(window).on('orientationchange', resize);
+});
+
+// Scroll the navigation bar to the currently selected menu item
+$(document).ready(function() {
+  var sidebar = $("#documenter .docs-menu").get(0);
+  var active = $("#documenter .docs-menu .is-active").get(0);
+  if(typeof active !== 'undefined') {
+    sidebar.scrollTop = active.offsetTop - sidebar.offsetTop - 15;
+  }
+})
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery'], function($) {
+
+function set_theme(theme) {
+  var active = null;
+  var disabled = [];
+  for (var i = 0; i < document.styleSheets.length; i++) {
+    var ss = document.styleSheets[i];
+    var themename = ss.ownerNode.getAttribute("data-theme-name");
+    if(themename === null) continue; // ignore non-theme stylesheets
+    // Find the active theme
+    if(themename === theme) active = ss;
+    else disabled.push(ss);
+  }
+  if(active !== null) {
+    active.disabled = false;
+    if(active.ownerNode.getAttribute("data-theme-primary") === null) {
+      document.getElementsByTagName('html')[0].className = "theme--" + theme;
+    } else {
+      document.getElementsByTagName('html')[0].className = "";
+    }
+    disabled.forEach(function(ss){
+      ss.disabled = true;
+    });
+  }
+
+  // Store the theme in localStorage
+  if(typeof(window.localStorage) !== "undefined") {
+    window.localStorage.setItem("documenter-theme", theme);
+  } else {
+    console.error("Browser does not support window.localStorage");
+  }
+}
+
+// Theme picker setup
+$(document).ready(function() {
+  // onchange callback
+  $('#documenter-themepicker').change(function themepick_callback(ev){
+    var themename = $('#documenter-themepicker option:selected').attr('value');
+    set_theme(themename);
+  });
+
+  // Make sure that the themepicker displays the correct theme when the theme is retrieved
+  // from localStorage
+  if(typeof(window.localStorage) !== "undefined") {
+    var theme =  window.localStorage.getItem("documenter-theme");
+    if(theme !== null) {
+      $('#documenter-themepicker option').each(function(i,e) {
+        e.selected = (e.value === theme);
+      })
+    } else {
+      $('#documenter-themepicker option').each(function(i,e) {
+        e.selected = $("html").hasClass(`theme--${e.value}`);
+      })
+    }
+  }
+})
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery'], function($) {
+
+// update the version selector with info from the siteinfo.js and ../versions.js files
+$(document).ready(function() {
+  // If the version selector is disabled with DOCUMENTER_VERSION_SELECTOR_DISABLED in the
+  // siteinfo.js file, we just return immediately and not display the version selector.
+  if (typeof DOCUMENTER_VERSION_SELECTOR_DISABLED === 'boolean' && DOCUMENTER_VERSION_SELECTOR_DISABLED) {
+    return;
+  }
+
+  var version_selector = $("#documenter .docs-version-selector");
+  var version_selector_select = $("#documenter .docs-version-selector select");
+
+  version_selector_select.change(function(x) {
+    target_href = version_selector_select.children("option:selected").get(0).value;
+    window.location.href = target_href;
+  });
+
+  // add the current version to the selector based on siteinfo.js, but only if the selector is empty
+  if (typeof DOCUMENTER_CURRENT_VERSION !== 'undefined' && $('#version-selector > option').length == 0) {
+    var option = $("<option value='#' selected='selected'>" + DOCUMENTER_CURRENT_VERSION + "</option>");
+    version_selector_select.append(option);
+  }
+
+  if (typeof DOC_VERSIONS !== 'undefined') {
+    var existing_versions = version_selector_select.children("option");
+    var existing_versions_texts = existing_versions.map(function(i,x){return x.text});
+    DOC_VERSIONS.forEach(function(each) {
+      var version_url = documenterBaseURL + "/../" + each;
+      var existing_id = $.inArray(each, existing_versions_texts);
+      // if not already in the version selector, add it as a new option,
+      // otherwise update the old option with the URL and enable it
+      if (existing_id == -1) {
+        var option = $("<option value='" + version_url + "'>" + each + "</option>");
+        version_selector_select.append(option);
+      } else {
+        var option = existing_versions[existing_id];
+        option.value = version_url;
+        option.disabled = false;
+      }
+    });
+  }
+
+  // only show the version selector if the selector has been populated
+  if (version_selector_select.children("option").length > 0) {
+    version_selector.toggleClass("visible");
+  }
+})
+
+})
diff --git a/docs/build/assets/search.js b/docs/build/assets/search.js
new file mode 100644
index 0000000..c133f74
--- /dev/null
+++ b/docs/build/assets/search.js
@@ -0,0 +1,267 @@
+// Generated by Documenter.jl
+requirejs.config({
+  paths: {
+    'lunr': 'https://cdnjs.cloudflare.com/ajax/libs/lunr.js/2.3.9/lunr.min',
+    'lodash': 'https://cdnjs.cloudflare.com/ajax/libs/lodash.js/4.17.21/lodash.min',
+    'jquery': 'https://cdnjs.cloudflare.com/ajax/libs/jquery/3.6.0/jquery.min',
+  }
+});
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery', 'lunr', 'lodash'], function($, lunr, _) {
+
+$(document).ready(function() {
+  // parseUri 1.2.2
+  // (c) Steven Levithan <stevenlevithan.com>
+  // MIT License
+  function parseUri (str) {
+    var  o   = parseUri.options,
+      m   = o.parser[o.strictMode ? "strict" : "loose"].exec(str),
+      uri = {},
+      i   = 14;
+
+    while (i--) uri[o.key[i]] = m[i] || "";
+
+    uri[o.q.name] = {};
+    uri[o.key[12]].replace(o.q.parser, function ($0, $1, $2) {
+      if ($1) uri[o.q.name][$1] = $2;
+    });
+
+    return uri;
+  };
+  parseUri.options = {
+    strictMode: false,
+    key: ["source","protocol","authority","userInfo","user","password","host","port","relative","path","directory","file","query","anchor"],
+    q:   {
+      name:   "queryKey",
+      parser: /(?:^|&)([^&=]*)=?([^&]*)/g
+    },
+    parser: {
+      strict: /^(?:([^:\/?#]+):)?(?:\/\/((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?))?((((?:[^?#\/]*\/)*)([^?#]*))(?:\?([^#]*))?(?:#(.*))?)/,
+      loose:  /^(?:(?![^:@]+:[^:@\/]*@)([^:\/?#.]+):)?(?:\/\/)?((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?)(((\/(?:[^?#](?![^?#\/]*\.[^?#\/.]+(?:[?#]|$)))*\/?)?([^?#\/]*))(?:\?([^#]*))?(?:#(.*))?)/
+    }
+  };
+
+  $("#search-form").submit(function(e) {
+    e.preventDefault()
+  })
+
+  // list below is the lunr 2.1.3 list minus the intersect with names(Base)
+  // (all, any, get, in, is, only, which) and (do, else, for, let, where, while, with)
+  // ideally we'd just filter the original list but it's not available as a variable
+  lunr.stopWordFilter = lunr.generateStopWordFilter([
+    'a',
+    'able',
+    'about',
+    'across',
+    'after',
+    'almost',
+    'also',
+    'am',
+    'among',
+    'an',
+    'and',
+    'are',
+    'as',
+    'at',
+    'be',
+    'because',
+    'been',
+    'but',
+    'by',
+    'can',
+    'cannot',
+    'could',
+    'dear',
+    'did',
+    'does',
+    'either',
+    'ever',
+    'every',
+    'from',
+    'got',
+    'had',
+    'has',
+    'have',
+    'he',
+    'her',
+    'hers',
+    'him',
+    'his',
+    'how',
+    'however',
+    'i',
+    'if',
+    'into',
+    'it',
+    'its',
+    'just',
+    'least',
+    'like',
+    'likely',
+    'may',
+    'me',
+    'might',
+    'most',
+    'must',
+    'my',
+    'neither',
+    'no',
+    'nor',
+    'not',
+    'of',
+    'off',
+    'often',
+    'on',
+    'or',
+    'other',
+    'our',
+    'own',
+    'rather',
+    'said',
+    'say',
+    'says',
+    'she',
+    'should',
+    'since',
+    'so',
+    'some',
+    'than',
+    'that',
+    'the',
+    'their',
+    'them',
+    'then',
+    'there',
+    'these',
+    'they',
+    'this',
+    'tis',
+    'to',
+    'too',
+    'twas',
+    'us',
+    'wants',
+    'was',
+    'we',
+    'were',
+    'what',
+    'when',
+    'who',
+    'whom',
+    'why',
+    'will',
+    'would',
+    'yet',
+    'you',
+    'your'
+  ])
+
+  // add . as a separator, because otherwise "title": "Documenter.Anchors.add!"
+  // would not find anything if searching for "add!", only for the entire qualification
+  lunr.tokenizer.separator = /[\s\-\.]+/
+
+  // custom trimmer that doesn't strip @ and !, which are used in julia macro and function names
+  lunr.trimmer = function (token) {
+    return token.update(function (s) {
+      return s.replace(/^[^a-zA-Z0-9@!]+/, '').replace(/[^a-zA-Z0-9@!]+$/, '')
+    })
+  }
+
+  lunr.Pipeline.registerFunction(lunr.stopWordFilter, 'juliaStopWordFilter')
+  lunr.Pipeline.registerFunction(lunr.trimmer, 'juliaTrimmer')
+
+  var index = lunr(function () {
+    this.ref('location')
+    this.field('title',{boost: 100})
+    this.field('text')
+    documenterSearchIndex['docs'].forEach(function(e) {
+        this.add(e)
+    }, this)
+  })
+  var store = {}
+
+  documenterSearchIndex['docs'].forEach(function(e) {
+      store[e.location] = {title: e.title, category: e.category, page: e.page}
+  })
+
+  $(function(){
+    searchresults = $('#documenter-search-results');
+    searchinfo = $('#documenter-search-info');
+    searchbox = $('#documenter-search-query');
+    searchform = $('.docs-search');
+    sidebar = $('.docs-sidebar');
+    function update_search(querystring) {
+      tokens = lunr.tokenizer(querystring)
+      results = index.query(function (q) {
+        tokens.forEach(function (t) {
+          q.term(t.toString(), {
+            fields: ["title"],
+            boost: 100,
+            usePipeline: true,
+            editDistance: 0,
+            wildcard: lunr.Query.wildcard.NONE
+          })
+          q.term(t.toString(), {
+            fields: ["title"],
+            boost: 10,
+            usePipeline: true,
+            editDistance: 2,
+            wildcard: lunr.Query.wildcard.NONE
+          })
+          q.term(t.toString(), {
+            fields: ["text"],
+            boost: 1,
+            usePipeline: true,
+            editDistance: 0,
+            wildcard: lunr.Query.wildcard.NONE
+          })
+        })
+      })
+      searchinfo.text("Number of results: " + results.length)
+      searchresults.empty()
+      results.forEach(function(result) {
+        data = store[result.ref]
+        link = $('<a class="docs-label">'+data.title+'</a>')
+        link.attr('href', documenterBaseURL+'/'+result.ref)
+        if (data.category != "page"){
+          cat = $('<span class="docs-category">('+data.category+', '+data.page+')</span>')
+        } else {
+          cat = $('<span class="docs-category">('+data.category+')</span>')
+        }
+        li = $('<li>').append(link).append(" ").append(cat)
+        searchresults.append(li)
+      })
+    }
+
+    function update_search_box() {
+      querystring = searchbox.val()
+      update_search(querystring)
+    }
+
+    searchbox.keyup(_.debounce(update_search_box, 250))
+    searchbox.change(update_search_box)
+
+    // Disable enter-key form submission for the searchbox on the search page
+    // and just re-run search rather than refresh the whole page.
+    searchform.keypress(
+      function(event){
+        if (event.which == '13') {
+          if (sidebar.hasClass('visible')) {
+            sidebar.removeClass('visible');
+          }
+          update_search_box();
+          event.preventDefault();
+        }
+      }
+    );
+
+    search_query_uri = parseUri(window.location).queryKey["q"]
+    if(search_query_uri !== undefined) {
+      search_query = decodeURIComponent(search_query_uri.replace(/\+/g, '%20'))
+      searchbox.val(search_query)
+    }
+    update_search_box();
+  })
+})
+
+})
diff --git a/docs/build/assets/themes/documenter-dark.css b/docs/build/assets/themes/documenter-dark.css
new file mode 100644
index 0000000..c94a294
--- /dev/null
+++ b/docs/build/assets/themes/documenter-dark.css
@@ -0,0 +1,7 @@
+@keyframes spinAround{from{transform:rotate(0deg)}to{transform:rotate(359deg)}}html.theme--documenter-dark .tabs,html.theme--documenter-dark .pagination-previous,html.theme--documenter-dark .pagination-next,html.theme--documenter-dark .pagination-link,html.theme--documenter-dark .pagination-ellipsis,html.theme--documenter-dark .breadcrumb,html.theme--documenter-dark .file,html.theme--documenter-dark .button,.is-unselectable,html.theme--documenter-dark .modal-close,html.theme--documenter-dark .delete{-webkit-touch-callout:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;user-select:none}html.theme--documenter-dark .navbar-link:not(.is-arrowless)::after,html.theme--documenter-dark .select:not(.is-multiple):not(.is-loading)::after{border:3px solid rgba(0,0,0,0);border-radius:2px;border-right:0;border-top:0;content:" 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+  Author: @ericwbailey
+  Maintainer: @ericwbailey
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!important}html.theme--documenter-dark .button.is-light.is-outlined[disabled],fieldset[disabled] html.theme--documenter-dark .button.is-light.is-outlined{background-color:transparent;border-color:#ecf0f1;box-shadow:none;color:#ecf0f1}html.theme--documenter-dark .button.is-light.is-inverted.is-outlined{background-color:transparent;border-color:#282f2f;color:#282f2f}html.theme--documenter-dark .button.is-light.is-inverted.is-outlined:hover,html.theme--documenter-dark .button.is-light.is-inverted.is-outlined.is-hovered,html.theme--documenter-dark .button.is-light.is-inverted.is-outlined:focus,html.theme--documenter-dark .button.is-light.is-inverted.is-outlined.is-focused{background-color:#282f2f;color:#ecf0f1}html.theme--documenter-dark .button.is-light.is-inverted.is-outlined.is-loading:hover::after,html.theme--documenter-dark .button.is-light.is-inverted.is-outlined.is-loading.is-hovered::after,html.theme--documenter-dark .button.is-light.is-inverted.is-outlined.is-loading:focus::after,html.theme--documenter-dark .button.is-light.is-inverted.is-outlined.is-loading.is-focused::after{border-color:transparent transparent #ecf0f1 #ecf0f1 !important}html.theme--documenter-dark .button.is-light.is-inverted.is-outlined[disabled],fieldset[disabled] html.theme--documenter-dark .button.is-light.is-inverted.is-outlined{background-color:transparent;border-color:#282f2f;box-shadow:none;color:#282f2f}html.theme--documenter-dark .button.is-dark,html.theme--documenter-dark .content kbd.button{background-color:#282f2f;border-color:transparent;color:#ecf0f1}html.theme--documenter-dark .button.is-dark:hover,html.theme--documenter-dark .content kbd.button:hover,html.theme--documenter-dark .button.is-dark.is-hovered,html.theme--documenter-dark .content kbd.button.is-hovered{background-color:#232829;border-color:transparent;color:#ecf0f1}html.theme--documenter-dark .button.is-dark:focus,html.theme--documenter-dark .content kbd.button:focus,html.theme--documenter-dark .button.is-dark.is-focused,html.theme--documenter-dark .content kbd.button.is-focused{border-color:transparent;color:#ecf0f1}html.theme--documenter-dark .button.is-dark:focus:not(:active),html.theme--documenter-dark .content kbd.button:focus:not(:active),html.theme--documenter-dark .button.is-dark.is-focused:not(:active),html.theme--documenter-dark .content kbd.button.is-focused:not(:active){box-shadow:0 0 0 0.125em rgba(40,47,47,0.25)}html.theme--documenter-dark .button.is-dark:active,html.theme--documenter-dark .content kbd.button:active,html.theme--documenter-dark .button.is-dark.is-active,html.theme--documenter-dark .content kbd.button.is-active{background-color:#1d2122;border-color:transparent;color:#ecf0f1}html.theme--documenter-dark .button.is-dark[disabled],html.theme--documenter-dark .content kbd.button[disabled],fieldset[disabled] html.theme--documenter-dark .button.is-dark,fieldset[disabled] html.theme--documenter-dark .content kbd.button{background-color:#282f2f;border-color:transparent;box-shadow:none}html.theme--documenter-dark .button.is-dark.is-inverted,html.theme--documenter-dark .content kbd.button.is-inverted{background-color:#ecf0f1;color:#282f2f}html.theme--documenter-dark .button.is-dark.is-inverted:hover,html.theme--documenter-dark .content kbd.button.is-inverted:hover,html.theme--documenter-dark .button.is-dark.is-inverted.is-hovered,html.theme--documenter-dark .content kbd.button.is-inverted.is-hovered{background-color:#dde4e6}html.theme--documenter-dark .button.is-dark.is-inverted[disabled],html.theme--documenter-dark .content kbd.button.is-inverted[disabled],fieldset[disabled] html.theme--documenter-dark .button.is-dark.is-inverted,fieldset[disabled] html.theme--documenter-dark .content kbd.button.is-inverted{background-color:#ecf0f1;border-color:transparent;box-shadow:none;color:#282f2f}html.theme--documenter-dark .button.is-dark.is-loading::after,html.theme--documenter-dark .content kbd.button.is-loading::after{border-color:transparent transparent #ecf0f1 #ecf0f1 !important}html.theme--documenter-dark .button.is-dark.is-outlined,html.theme--documenter-dark .content kbd.button.is-outlined{background-color:transparent;border-color:#282f2f;color:#282f2f}html.theme--documenter-dark .button.is-dark.is-outlined:hover,html.theme--documenter-dark .content kbd.button.is-outlined:hover,html.theme--documenter-dark .button.is-dark.is-outlined.is-hovered,html.theme--documenter-dark .content kbd.button.is-outlined.is-hovered,html.theme--documenter-dark .button.is-dark.is-outlined:focus,html.theme--documenter-dark .content kbd.button.is-outlined:focus,html.theme--documenter-dark .button.is-dark.is-outlined.is-focused,html.theme--documenter-dark .content kbd.button.is-outlined.is-focused{background-color:#282f2f;border-color:#282f2f;color:#ecf0f1}html.theme--documenter-dark .button.is-dark.is-outlined.is-loading::after,html.theme--documenter-dark .content kbd.button.is-outlined.is-loading::after{border-color:transparent transparent #282f2f #282f2f !important}html.theme--documenter-dark .button.is-dark.is-outlined.is-loading:hover::after,html.theme--documenter-dark .content kbd.button.is-outlined.is-loading:hover::after,html.theme--documenter-dark .button.is-dark.is-outlined.is-loading.is-hovered::after,html.theme--documenter-dark .content kbd.button.is-outlined.is-loading.is-hovered::after,html.theme--documenter-dark .button.is-dark.is-outlined.is-loading:focus::after,html.theme--documenter-dark .content kbd.button.is-outlined.is-loading:focus::after,html.theme--documenter-dark .button.is-dark.is-outlined.is-loading.is-focused::after,html.theme--documenter-dark .content kbd.button.is-outlined.is-loading.is-focused::after{border-color:transparent transparent #ecf0f1 #ecf0f1 !important}html.theme--documenter-dark .button.is-dark.is-outlined[disabled],html.theme--documenter-dark .content kbd.button.is-outlined[disabled],fieldset[disabled] html.theme--documenter-dark .button.is-dark.is-outlined,fieldset[disabled] html.theme--documenter-dark .content kbd.button.is-outlined{background-color:transparent;border-color:#282f2f;box-shadow:none;color:#282f2f}html.theme--documenter-dark .button.is-dark.is-inverted.is-outlined,html.theme--documenter-dark .content kbd.button.is-inverted.is-outlined{background-color:transparent;border-color:#ecf0f1;color:#ecf0f1}html.theme--documenter-dark .button.is-dark.is-inverted.is-outlined:hover,html.theme--documenter-dark .content kbd.button.is-inverted.is-outlined:hover,html.theme--documenter-dark .button.is-dark.is-inverted.is-outlined.is-hovered,html.theme--documenter-dark .content kbd.button.is-inverted.is-outlined.is-hovered,html.theme--documenter-dark .button.is-dark.is-inverted.is-outlined:focus,html.theme--documenter-dark .content kbd.button.is-inverted.is-outlined:focus,html.theme--documenter-dark .button.is-dark.is-inverted.is-outlined.is-focused,html.theme--documenter-dark .content kbd.button.is-inverted.is-outlined.is-focused{background-color:#ecf0f1;color:#282f2f}html.theme--documenter-dark .button.is-dark.is-inverted.is-outlined.is-loading:hover::after,html.theme--documenter-dark .content kbd.button.is-inverted.is-outlined.is-loading:hover::after,html.theme--documenter-dark .button.is-dark.is-inverted.is-outlined.is-loading.is-hovered::after,html.theme--documenter-dark .content kbd.button.is-inverted.is-outlined.is-loading.is-hovered::after,html.theme--documenter-dark .button.is-dark.is-inverted.is-outlined.is-loading:focus::after,html.theme--documenter-dark .content kbd.button.is-inverted.is-outlined.is-loading:focus::after,html.theme--documenter-dark .button.is-dark.is-inverted.is-outlined.is-loading.is-focused::after,html.theme--documenter-dark .content kbd.button.is-inverted.is-outlined.is-loading.is-focused::after{border-color:transparent transparent #282f2f #282f2f !important}html.theme--documenter-dark 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.docstring>section>a.button.is-outlined.is-hovered.docs-sourcelink,html.theme--documenter-dark .button.is-primary.is-outlined:focus,html.theme--documenter-dark .docstring>section>a.button.is-outlined.docs-sourcelink:focus,html.theme--documenter-dark .button.is-primary.is-outlined.is-focused,html.theme--documenter-dark .docstring>section>a.button.is-outlined.is-focused.docs-sourcelink{background-color:#375a7f;border-color:#375a7f;color:#fff}html.theme--documenter-dark .button.is-primary.is-outlined.is-loading::after,html.theme--documenter-dark .docstring>section>a.button.is-outlined.is-loading.docs-sourcelink::after{border-color:transparent transparent #375a7f #375a7f !important}html.theme--documenter-dark .button.is-primary.is-outlined.is-loading:hover::after,html.theme--documenter-dark .docstring>section>a.button.is-outlined.is-loading.docs-sourcelink:hover::after,html.theme--documenter-dark .button.is-primary.is-outlined.is-loading.is-hovered::after,html.theme--documenter-dark 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a.navbar-item:hover{background-color:rgba(0,0,0,0);color:#dbdee0}html.theme--documenter-dark .navbar-dropdown a.navbar-item.is-active{background-color:rgba(0,0,0,0);color:#1abc9c}.navbar.is-spaced html.theme--documenter-dark .navbar-dropdown,html.theme--documenter-dark .navbar-dropdown.is-boxed{border-radius:8px;border-top:none;box-shadow:0 8px 8px rgba(10,10,10,0.1), 0 0 0 1px rgba(10,10,10,0.1);display:block;opacity:0;pointer-events:none;top:calc(100% + (-4px));transform:translateY(-5px);transition-duration:86ms;transition-property:opacity, transform}html.theme--documenter-dark .navbar-dropdown.is-right{left:auto;right:0}html.theme--documenter-dark .navbar-divider{display:block}html.theme--documenter-dark .navbar>.container .navbar-brand,html.theme--documenter-dark .container>.navbar .navbar-brand{margin-left:-.75rem}html.theme--documenter-dark .navbar>.container .navbar-menu,html.theme--documenter-dark .container>.navbar .navbar-menu{margin-right:-.75rem}html.theme--documenter-dark .navbar.is-fixed-bottom-desktop,html.theme--documenter-dark .navbar.is-fixed-top-desktop{left:0;position:fixed;right:0;z-index:30}html.theme--documenter-dark .navbar.is-fixed-bottom-desktop{bottom:0}html.theme--documenter-dark .navbar.is-fixed-bottom-desktop.has-shadow{box-shadow:0 -2px 3px rgba(10,10,10,0.1)}html.theme--documenter-dark .navbar.is-fixed-top-desktop{top:0}html.theme--documenter-dark html.has-navbar-fixed-top-desktop,html.theme--documenter-dark body.has-navbar-fixed-top-desktop{padding-top:4rem}html.theme--documenter-dark html.has-navbar-fixed-bottom-desktop,html.theme--documenter-dark body.has-navbar-fixed-bottom-desktop{padding-bottom:4rem}html.theme--documenter-dark html.has-spaced-navbar-fixed-top,html.theme--documenter-dark body.has-spaced-navbar-fixed-top{padding-top:6rem}html.theme--documenter-dark html.has-spaced-navbar-fixed-bottom,html.theme--documenter-dark body.has-spaced-navbar-fixed-bottom{padding-bottom:6rem}html.theme--documenter-dark a.navbar-item.is-active,html.theme--documenter-dark .navbar-link.is-active{color:#1abc9c}html.theme--documenter-dark a.navbar-item.is-active:not(:focus):not(:hover),html.theme--documenter-dark .navbar-link.is-active:not(:focus):not(:hover){background-color:rgba(0,0,0,0)}html.theme--documenter-dark .navbar-item.has-dropdown:focus .navbar-link,html.theme--documenter-dark .navbar-item.has-dropdown:hover .navbar-link,html.theme--documenter-dark .navbar-item.has-dropdown.is-active .navbar-link{background-color:rgba(0,0,0,0)}}html.theme--documenter-dark .hero.is-fullheight-with-navbar{min-height:calc(100vh - 4rem)}html.theme--documenter-dark .pagination{font-size:15px;margin:-.25rem}html.theme--documenter-dark .pagination.is-small,html.theme--documenter-dark #documenter .docs-sidebar form.docs-search>input.pagination{font-size:.85em}html.theme--documenter-dark .pagination.is-medium{font-size:1.25rem}html.theme--documenter-dark .pagination.is-large{font-size:1.5rem}html.theme--documenter-dark 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.pagination-ellipsis{font-size:1em;justify-content:center;margin:.25rem;padding-left:.5em;padding-right:.5em;text-align:center}html.theme--documenter-dark .pagination-previous,html.theme--documenter-dark .pagination-next,html.theme--documenter-dark .pagination-link{border-color:#5e6d6f;color:#1abc9c;min-width:2.25em}html.theme--documenter-dark .pagination-previous:hover,html.theme--documenter-dark .pagination-next:hover,html.theme--documenter-dark .pagination-link:hover{border-color:#8c9b9d;color:#1dd2af}html.theme--documenter-dark .pagination-previous:focus,html.theme--documenter-dark .pagination-next:focus,html.theme--documenter-dark .pagination-link:focus{border-color:#8c9b9d}html.theme--documenter-dark .pagination-previous:active,html.theme--documenter-dark .pagination-next:active,html.theme--documenter-dark .pagination-link:active{box-shadow:inset 0 1px 2px rgba(10,10,10,0.2)}html.theme--documenter-dark .pagination-previous[disabled],html.theme--documenter-dark 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.panel-block{align-items:center;color:#f2f2f2;display:flex;justify-content:flex-start;padding:0.5em 0.75em}html.theme--documenter-dark .panel-block input[type="checkbox"]{margin-right:0.75em}html.theme--documenter-dark .panel-block>.control{flex-grow:1;flex-shrink:1;width:100%}html.theme--documenter-dark .panel-block.is-wrapped{flex-wrap:wrap}html.theme--documenter-dark .panel-block.is-active{border-left-color:#1abc9c;color:#17a689}html.theme--documenter-dark .panel-block.is-active .panel-icon{color:#1abc9c}html.theme--documenter-dark a.panel-block,html.theme--documenter-dark label.panel-block{cursor:pointer}html.theme--documenter-dark a.panel-block:hover,html.theme--documenter-dark label.panel-block:hover{background-color:#282f2f}html.theme--documenter-dark .panel-icon{display:inline-block;font-size:14px;height:1em;line-height:1em;text-align:center;vertical-align:top;width:1em;color:#fff;margin-right:0.75em}html.theme--documenter-dark .panel-icon 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+  Theme: Default
+  Description: Original highlight.js style
+  Author: (c) Ivan Sagalaev <maniac@softwaremaniacs.org>
+  Maintainer: @highlightjs/core-team
+  Website: https://highlightjs.org/
+  License: see project LICENSE
+  Touched: 2021
+*/pre code.hljs{display:block;overflow-x:auto}code.hljs{padding:3px 5px}.hljs{background:#F0F0F0;color:#444}.hljs-comment{color:#888888}.hljs-tag,.hljs-punctuation{color:#444a}.hljs-tag .hljs-name,.hljs-tag .hljs-attr{color:#444}.hljs-keyword,.hljs-attribute,.hljs-selector-tag,.hljs-meta .hljs-keyword,.hljs-doctag,.hljs-name{font-weight:bold}.hljs-type,.hljs-string,.hljs-number,.hljs-selector-id,.hljs-selector-class,.hljs-quote,.hljs-template-tag,.hljs-deletion{color:#880000}.hljs-title,.hljs-section{color:#880000;font-weight:bold}.hljs-regexp,.hljs-symbol,.hljs-variable,.hljs-template-variable,.hljs-link,.hljs-selector-attr,.hljs-operator,.hljs-selector-pseudo{color:#BC6060}.hljs-literal{color:#78A960}.hljs-built_in,.hljs-bullet,.hljs-code,.hljs-addition{color:#397300}.hljs-meta{color:#1f7199}.hljs-meta .hljs-string{color:#4d99bf}.hljs-emphasis{font-style:italic}.hljs-strong{font-weight:bold}
diff --git a/docs/build/assets/themeswap.js b/docs/build/assets/themeswap.js
new file mode 100644
index 0000000..c58e993
--- /dev/null
+++ b/docs/build/assets/themeswap.js
@@ -0,0 +1,66 @@
+// Small function to quickly swap out themes. Gets put into the <head> tag..
+function set_theme_from_local_storage() {
+  // Intialize the theme to null, which means default
+  var theme = null;
+  // If the browser supports the localstorage and is not disabled then try to get the
+  // documenter theme
+  if(window.localStorage != null) {
+    // Get the user-picked theme from localStorage. May be `null`, which means the default
+    // theme.
+    theme =  window.localStorage.getItem("documenter-theme");
+  }
+  // Check if the browser supports user color preference
+  var darkPreference = false;
+  // Check if the users preference is for dark color scheme
+  if(window.matchMedia('(prefers-color-scheme: dark)').matches === true) {
+    darkPreference = true;
+  }
+  // Initialize a few variables for the loop:
+  //
+  //  - active: will contain the index of the theme that should be active. Note that there
+  //    is no guarantee that localStorage contains sane values. If `active` stays `null`
+  //    we either could not find the theme or it is the default (primary) theme anyway.
+  //    Either way, we then need to stick to the primary theme.
+  //
+  //  - disabled: style sheets that should be disabled (i.e. all the theme style sheets
+  //    that are not the currently active theme)
+  var active = null; var disabled = []; var darkTheme = null;
+  for (var i = 0; i < document.styleSheets.length; i++) {
+    var ss = document.styleSheets[i];
+    // The <link> tag of each style sheet is expected to have a data-theme-name attribute
+    // which must contain the name of the theme. The names in localStorage much match this.
+    var themename = ss.ownerNode.getAttribute("data-theme-name");
+    // attribute not set => non-theme stylesheet => ignore
+    if(themename === null) continue;
+    // To distinguish the default (primary) theme, it needs to have the data-theme-primary
+    // attribute set.
+    var isprimary = (ss.ownerNode.getAttribute("data-theme-primary") !== null);
+    // Check if the theme is primary dark theme
+    var isDarkTheme = (ss.ownerNode.getAttribute("data-theme-primary-dark") !== null);
+    // If ss is for dark theme then set the value of darkTheme to the name of the theme
+    if(isDarkTheme) darkTheme = themename;
+    // If we find a matching theme (and it's not the default), we'll set active to non-null
+    if(themename === theme) active = i;
+    // Store the style sheets of inactive themes so that we could disable them
+    if(themename !== theme) disabled.push(ss);
+  }
+  if(active !== null) {
+    // If we did find an active theme, we'll (1) add the theme--$(theme) class to <html>
+    document.getElementsByTagName('html')[0].className = "theme--" + theme;
+    // and (2) disable all the other theme stylesheets
+    disabled.forEach(function(ss){
+      ss.disabled = true;
+    });
+  }
+  else if(darkTheme !== null && darkPreference === true) {
+    // If we did find an active theme, we'll (1) add the theme--$(theme) class to <html>
+    document.getElementsByTagName('html')[0].className = "theme--" + darkTheme;
+    // and (2) disable all the other theme stylesheets
+    disabled.forEach(function(ss){
+      if (ss.ownerNode.getAttribute("data-theme-name") !== darkTheme) {
+        ss.disabled = true;
+      }
+    });
+  }
+}
+set_theme_from_local_storage();
diff --git a/docs/build/index.html b/docs/build/index.html
new file mode 100644
index 0000000..19916c1
--- /dev/null
+++ b/docs/build/index.html
@@ -0,0 +1,2 @@
+<!DOCTYPE html>
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You can also use these binaries directly from your terminal, so you are not limited to julia. Gone are the days where you had to first spend hours or days to install PETSc on your system!</li><li>We provide a simple function to run LaMEM from julia (also in parallel).</li><li>We provide functions to read timesteps back into julia. </li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="man/installation.html">Installation »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Friday 14 July 2023 12:46">Friday 14 July 2023</span>. 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+<!DOCTYPE html>
+<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Grid · LaMEM.jl</title><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="../index.html">LaMEM.jl</a></span></div><form class="docs-search" action="../search.html"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../index.html">Home</a></li><li><a class="tocitem" href="installation.html">Installation</a></li><li><a class="tocitem" href="installation_HPC.html">Installation on HPC systems</a></li><li><span class="tocitem">Create LaMEM models in julia</span><ul><li><a class="tocitem" href="juliasetups.html">Overview</a></li><li class="is-active"><a class="tocitem" href="LaMEM_ModelFunctions.html">Grid</a></li></ul></li><li><a class="tocitem" href="runlamem.html">Run LaMEM</a></li><li><a class="tocitem" href="readtimesteps.html">Reading timesteps</a></li><li><a class="tocitem" href="listfunctions.html">List of functions</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li><a class="is-disabled">Create LaMEM models in julia</a></li><li class="is-active"><a href="LaMEM_ModelFunctions.html">Grid</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="LaMEM_ModelFunctions.html">Grid</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/JuliaGeodynamics/LaMEM.jl/blob/main/docs/src/man/LaMEM_ModelFunctions.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="List-functions"><a class="docs-heading-anchor" href="#List-functions">List functions</a><a id="List-functions-1"></a><a class="docs-heading-anchor-permalink" href="#List-functions" title="Permalink"></a></h1><p>These are all the functions that are provided for the LaMEM Julia Setup interface </p><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.BoundaryConditions" href="#LaMEM.LaMEM_Model.BoundaryConditions"><code>LaMEM.LaMEM_Model.BoundaryConditions</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Structure that contains the LaMEM boundary conditions information.</code></pre><ul><li><p><code>noslip::Vector{Int64}</code>: No-slip boundary flag mask (left right front back bottom top)</p></li><li><p><code>open_top_bound::Int64</code>: Stress-free (free surface/infinitely fast erosion) top boundary flag</p></li><li><p><code>temp_top::Float64</code>: Constant temperature on the top boundary</p></li><li><p><code>temp_bot::Float64</code>: Constant temperature on the bottom boundary</p></li><li><p><code>exx_num_periods::Int64</code>: number intervals of constant background strain rate (x-axis)</p></li><li><p><code>exx_time_delims::Vector{Float64}</code>: time delimiters (one less than number of intervals, not required for one interval)</p></li><li><p><code>exx_strain_rates::Vector{Float64}</code>: strain rates for each interval</p></li><li><p><code>eyy_num_periods::Int64</code></p></li><li><p><code>eyy_time_delims::Vector{Float64}</code></p></li><li><p><code>eyy_strain_rates::Vector{Float64}</code></p></li><li><p><code>exy_num_periods::Int64</code></p></li><li><p><code>exy_time_delims::Vector{Float64}</code></p></li><li><p><code>exy_strain_rates::Vector{Float64}</code></p></li><li><p><code>exz_num_periods::Int64</code></p></li><li><p><code>exz_time_delims::Vector{Float64}</code></p></li><li><p><code>exz_strain_rates::Vector{Float64}</code></p></li><li><p><code>eyz_num_periods::Int64</code></p></li><li><p><code>eyz_time_delims::Vector{Float64}</code></p></li><li><p><code>eyz_strain_rates::Vector{Float64}</code></p></li><li><p><code>bg_ref_point::Vector{Float64}</code>: background strain rate reference point (fixed)</p></li></ul></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Dike" href="#LaMEM.LaMEM_Model.Dike"><code>LaMEM.LaMEM_Model.Dike</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Defines the properties related to inserting dikes</code></pre><ul><li><p><code>ID::Int64</code>: Material phase ID</p></li><li><p><code>Mf::Float64</code>: value for dike/magma- accommodated extension, between 0 and 1, in the front of the box, for phase dike</p></li><li><p><code>Mc::Float64</code>: [optional] value for dike/magma- accommodate extension, between 0 and 1, for dike phase; M is linearly interpolated between Mf &amp; Mc and Mc &amp; Mb, if not set, Mc default is set to -1 so it is not used</p></li><li><p><code>y_Mc::Union{Nothing, Float64}</code>: [optional], location for Mc, must be between front and back boundaries of dike box, if not set, default value to 0.0, but not used</p></li><li><p><code>Mb::Union{Nothing, Float64}</code>: value for dike/magma-accommodated extension, between 0 and 1, in the back of the box, for phase dike</p></li><li><p><code>PhaseID::Union{Nothing, Int64}</code>: Phase ID</p></li><li><p><code>PhaseTransID::Union{Nothing, Int64}</code>: Phase transition ID</p></li></ul></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.FreeSurface" href="#LaMEM.LaMEM_Model.FreeSurface"><code>LaMEM.LaMEM_Model.FreeSurface</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Structure that contains the LaMEM free surface information.</code></pre><ul><li><p><code>surf_use::Int64</code>: Free surface activation flag</p></li><li><p><code>surf_corr_phase::Int64</code>: air phase ratio correction flag (phases in an element that contains are modified based on the surface position)</p></li><li><p><code>surf_level::Float64</code>: initial level of the free surface</p></li><li><p><code>surf_air_phase::Int64</code>: phase ID of sticky air layer</p></li><li><p><code>surf_max_angle::Float64</code>: maximum angle with horizon (smoothed if larger)</p></li><li><p><code>surf_topo_file::String</code>: initial topography file (redundant)</p></li><li><p><code>erosion_model::Int64</code>: erosion model [0-none (default), 1-infinitely fast, 2-prescribed rate with given level]</p></li><li><p><code>er_num_phases::Int64</code>: number of erosion phases</p></li><li><p><code>er_time_delims::Vector{Float64}</code>: erosion time delimiters (one less than number)</p></li><li><p><code>er_rates::Vector{Float64}</code>: constant erosion rates in different time periods</p></li><li><p><code>er_levels::Vector{Int64}</code>: levels above which we apply constant erosion rates in different time periods</p></li><li><p><code>sediment_model::Int64</code>: sedimentation model [0-none (dafault), 1-prescribed rate with given level, 2-cont. margin]</p></li><li><p><code>sed_num_layers::Int64</code>: number of sediment layers</p></li><li><p><code>sed_time_delims::Vector{Float64}</code>: sediment layers time delimiters (one less than number)</p></li><li><p><code>sed_rates::Vector{Float64}</code>: sediment rates in different time periods</p></li><li><p><code>sed_levels::Vector{Float64}</code>: levels below which we apply constant sediment rates in different time periods</p></li><li><p><code>sed_phases::Vector{Int64}</code>: sediment layers phase numbers in different time periods</p></li><li><p><code>marginO::Vector{Float64}</code>: lateral coordinates of continental margin - origin</p></li><li><p><code>marginE::Vector{Float64}</code>: lateral coordinates of continental margin - 2nd point</p></li><li><p><code>hUp::Float64</code>: up dip thickness of sediment cover (onshore)</p></li><li><p><code>hDown::Float64</code>: down dip thickness of sediment cover (off shore)</p></li><li><p><code>dTrans::Float64</code>: half of transition zone</p></li></ul></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Grid" href="#LaMEM.LaMEM_Model.Grid"><code>LaMEM.LaMEM_Model.Grid</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Structure that contains the LaMEM grid information</code></pre><ul><li><p><code>nmark_x::Int64</code>: number of markers/element in x-direction</p></li><li><p><code>nmark_y::Int64</code>: number of markers/element in y-direction</p></li><li><p><code>nmark_z::Int64</code>: number of markers/element in x-direction</p></li><li><p><code>nel_x::Vector{Int64}</code>: number of elements in x-direction</p></li><li><p><code>nel_y::Vector{Int64}</code>: number of elements in y-direction</p></li><li><p><code>nel_z::Vector{Int64}</code>: number of elements in z-direction</p></li><li><p><code>coord_x::Vector{Float64}</code>: coordinates in x-direction</p></li><li><p><code>coord_y::Vector{Float64}</code>: coordinates in y-direction</p></li><li><p><code>coord_z::Vector{Float64}</code>: coordinates in z-direction</p></li><li><p><code>nseg_x::Int64</code>: number of segments in x-direction (if we employ variable grid spacing in x-direction)</p></li><li><p><code>nseg_y::Int64</code>: number of segments in y-direction (if we employ variable grid spacing in y-direction)</p></li><li><p><code>nseg_z::Int64</code>: number of segments in z-direction (if we employ variable grid spacing in z-direction)</p></li><li><p><code>bias_x::Vector{Float64}</code>: bias in x-direction (if we employ variable grid spacing in x-direction)</p></li><li><p><code>bias_y::Vector{Float64}</code>: bias in y-direction (if we employ variable grid spacing in y-direction)</p></li><li><p><code>bias_z::Vector{Float64}</code>: bias in z-direction (if we employ variable grid spacing in z-direction)</p></li><li><p><code>Grid::GeophysicalModelGenerator.LaMEM_grid</code>: Contains the LaMEM Grid object</p></li><li><p><code>Phases::Array{Int32}</code>: Phases; 3D phase information</p></li><li><p><code>Temp::Array{Float64}</code>: Temp; 3D phase information</p></li></ul><p><strong>Example 1</strong></p><pre><code class="language-julia hljs">julia&gt; d=LaMEM.Grid(coord_x=[0.0, 0.7, 0.8, 1.0], bias_x=[0.3,1.0,3.0], nel_x=[10,4,2])
+LaMEM grid with 1D refinement: 
+  nel         : ([10, 4, 2], [16], [16])
+  marker/cell : (3, 3, 3)
+  x           ϵ [0.0, 0.7, 0.8, 1.0], bias=[0.3, 1.0, 3.0], nseg=3, Δmin=0.025000000000000022, Δmax=0.1499999999999999
+  y           ϵ [-10.0 : 0.0]
+  z           ϵ [-10.0 : 0.0]</code></pre><p><strong>Example 2</strong></p><pre><code class="language-julia hljs">julia&gt; d=LaMEM.Grid(nel=(10,20))
+LaMEM grid with constant Δ: 
+  nel         : ([10], [1], [20])
+  marker/cell : (3, 3, 3)
+  x           ϵ [-10.0 : 10.0]
+  y           ϵ [-10.0 : 0.0]
+  z           ϵ [-10.0 : 0.0]</code></pre></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Materials" href="#LaMEM.LaMEM_Model.Materials"><code>LaMEM.LaMEM_Model.Materials</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Structure that contains the material properties in the current simulation</code></pre><ul><li><p><code>Phases::Vector{Phase}</code>: Different Materials implemented</p></li><li><p><code>SofteningLaws::Vector{Softening}</code>: Softening laws implemented</p></li><li><p><code>PhaseTransitions::Vector{PhaseTransition}</code>: Internal Phase Transitions (that change the ID of markers) implemented</p></li><li><p><code>Dikes::Vector{Dike}</code>: Dikes implemented (mostly for MOR simulations)</p></li></ul></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Model" href="#LaMEM.LaMEM_Model.Model"><code>LaMEM.LaMEM_Model.Model</code></a> — <span class="docstring-category">Type</span></header><section><div><p>;     Model</p><p>Structure that holds all the information to create a LaMEM input file</p><ul><li><p><code>Scaling::Scaling</code>: Scaling parameters</p></li><li><p><code>Grid::Grid</code>: LaMEM Grid</p></li><li><p><code>Time::Any</code>: Time options</p></li><li><p><code>FreeSurface::Any</code>: Free surface options</p></li><li><p><code>BoundaryConditions::Any</code>: Boundary conditions</p></li><li><p><code>SolutionParams::Any</code>: Global solution parameters</p></li><li><p><code>Solver::Any</code>: Solver options and optional PETSc options</p></li><li><p><code>ModelSetup::Any</code>: Model setup</p></li><li><p><code>Output::Any</code>: Output options</p></li><li><p><code>Materials::Any</code>: Material parameters for each of the phases</p></li></ul></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Model-Tuple" href="#LaMEM.LaMEM_Model.Model-Tuple"><code>LaMEM.LaMEM_Model.Model</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">Model(args...)</code></pre><p>Allow to define a model setup by specifying some of the basic objects</p><p><strong>Example</strong></p><pre><code class="language-julia hljs">julia&gt; d = Model(Grid(nel=(10,1,20)), Scaling(NO_units()))
+LaMEM Model setup
+|
+|-- Scaling             :  GeoParams.Units.GeoUnits{GeoParams.Units.NONE}
+|-- Grid                :  nel=(10, 1, 20); xϵ(-10.0, 10.0), yϵ(-10.0, 0.0), zϵ(-10.0, 0.0) 
+|-- Time                :  nstep_max=50; nstep_out=1; time_end=1.0; dt=0.05
+|-- Boundary conditions :  noslip=[0, 0, 0, 0, 0, 0]
+|-- Solution parameters :  
+|-- Solver options      :  direct solver; superlu_dist; penalty term=10000.0
+|-- Model setup options :  Type=geom; 
+|-- Output options      :  filename=output; pvd=1; avd=0; surf=0
+|-- Materials           :  1 phases;  
+</code></pre></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Model-Tuple{}" href="#LaMEM.LaMEM_Model.Model-Tuple{}"><code>LaMEM.LaMEM_Model.Model</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">Model(;
+    Scaling=Scaling(GEO_units()),
+    Grid=Grid(), 
+    Time=Time(),
+    FreeSurface=FreeSurface(),
+    BoundaryConditions=BoundaryConditions(),
+    SolutionParams=SolutionParams(),
+    Solver=Solver(),
+    ModelSetup=ModelSetup(),
+    Output=Output(),
+    Materials=Materials()
+    )</code></pre><p>Creates a LaMEM Model setup.</p><ul><li><p><code>Scaling::Scaling</code></p></li><li><p><code>Grid::Grid</code></p></li><li><p><code>Time::Any</code></p></li><li><p><code>FreeSurface::Any</code></p></li><li><p><code>BoundaryConditions::Any</code></p></li><li><p><code>SolutionParams::Any</code></p></li><li><p><code>Solver::Any</code></p></li><li><p><code>ModelSetup::Any</code></p></li><li><p><code>Output::Any</code></p></li><li><p><code>Materials::Any</code></p></li></ul></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.ModelSetup" href="#LaMEM.LaMEM_Model.ModelSetup"><code>LaMEM.LaMEM_Model.ModelSetup</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Structure that contains the LaMEM Model Setup and Advection options</code></pre><ul><li><p><code>msetup::String</code>: Setup type - can be <code>geom</code> (phases are assigned from geometric primitives), <code>files</code> (from julia input), <code>polygons</code> (from geomIO input, which requires <code>poly_file</code> to be specified)</p></li><li><p><code>rand_noise::Int64</code>: add random noise to the particle location</p></li><li><p><code>rand_noiseGP::Int64</code>: random noise flag, subsequently applied to geometric primitives</p></li><li><p><code>bg_phase::Int64</code>: background phase ID</p></li><li><p><code>save_mark::Int64</code>: save marker to disk flag</p></li><li><p><code>mark_load_file::String</code>: marker input file (extension is .xxxxxxxx.dat), if using <code>msetup</code>=<code>files</code></p></li><li><p><code>mark_save_file::String</code>: marker output file (extension is .xxxxxxxx.dat)</p></li><li><p><code>poly_file::String</code>: polygon geometry file (redundant), if using <code>msetup</code>=<code>polygons</code></p></li><li><p><code>temp_file::String</code>: initial temperature file (redundant), if not set on markers</p></li><li><p><code>advect::String</code>: advection scheme; options=<code>none</code> (no advection); <code>basic</code> (Euler classical implementation [default]); <code>Euler</code> (Euler explicit in time); <code>rk2</code> (Runge-Kutta 2nd order in space)</p></li><li><p><code>interp::String</code>: velocity interpolation scheme; options = <code>stag</code> (trilinear interpolation from FDSTAG points), <code>minmod</code> ( MINMOD interpolation to nodes, trilinear interpolation to markers + correction), <code>stagp</code> ( STAG_P empirical approach by T. Gerya)</p></li><li><p><code>stagp_a::Float64</code>: STAG_P velocity interpolation parameter</p></li><li><p><code>mark_ctrl::String</code>: marker control type; options are <code>subgrid</code> (default; marker control enforced over fine scale grid), <code>none</code> (none), <code>basic</code> (AVD for cells + corner insertion), and <code>avd</code> (pure AVD for all control volumes)</p></li><li><p><code>nmark_lim::Vector{Int64}</code>: min/max number per cell (marker control)</p></li><li><p><code>nmark_avd::Vector{Int64}</code>: x-y-z AVD refinement factors (avd marker control)</p></li><li><p><code>nmark_sub::Int64</code>: max number of same phase markers per subcell (subgrid marker control)</p></li><li><p><code>geom_primitives::Vector</code>: Different geometric primitives that can be selected if we <code>msetup</code><code>=</code>geom<code>; see</code>geom_Sphere`</p></li></ul></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Output" href="#LaMEM.LaMEM_Model.Output"><code>LaMEM.LaMEM_Model.Output</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Structure that contains the LaMEM output options</code></pre><ul><li><p><code>out_file_name::Any</code>: output file name</p></li><li><p><code>out_dir::Any</code>: output directory</p></li><li><p><code>param_file_name::Any</code>: parameter filename</p></li><li><p><code>write_VTK_setup::Any</code>: write VTK initial model setup</p></li><li><p><code>out_pvd::Any</code>: activate writing .pvd file</p></li><li><p><code>out_phase::Any</code>: dominant phase</p></li><li><p><code>out_density::Any</code>: density</p></li><li><p><code>out_visc_total::Any</code>: total (viscoelastoplastic) viscosity</p></li><li><p><code>out_visc_creep::Any</code>: creep viscosity</p></li><li><p><code>out_velocity::Any</code>: velocity</p></li><li><p><code>out_pressure::Any</code>: (dynamic) pressure</p></li><li><p><code>out_tot_press::Any</code>: total pressure</p></li><li><p><code>out_eff_press::Any</code>: effective pressure</p></li><li><p><code>out_over_press::Any</code></p></li><li><p><code>out_litho_press::Any</code></p></li><li><p><code>out_pore_press::Any</code></p></li><li><p><code>out_temperature::Any</code>: temperature</p></li><li><p><code>out_dev_stress::Any</code>: deviatoric strain rate tensor</p></li><li><p><code>out_j2_dev_stress::Any</code>: second invariant of deviatoric stress tensor</p></li><li><p><code>out_strain_rate::Any</code>: deviatoric strain rate tensor</p></li><li><p><code>out_j2_strain_rate::Any</code>: second invariant of strain rate tensor</p></li><li><p><code>out_shmax::Any</code></p></li><li><p><code>out_ehmax::Any</code></p></li><li><p><code>out_yield::Any</code></p></li><li><p><code>out_rel_dif_rate::Any</code>: relative proportion of diffusion creep strainrate</p></li><li><p><code>out_rel_dis_rate::Any</code>: relative proportion of dislocation creep strainrate</p></li><li><p><code>out_rel_prl_rate::Any</code>: relative proportion of peierls creep strainrate</p></li><li><p><code>out_rel_pl_rate::Any</code>: relative proportion of plastic strainrate</p></li><li><p><code>out_plast_strain::Any</code>: accumulated plastic strain</p></li><li><p><code>out_plast_dissip::Any</code>: plastic dissipation</p></li><li><p><code>out_tot_displ::Any</code></p></li><li><p><code>out_moment_res::Any</code></p></li><li><p><code>out_cont_res::Any</code></p></li><li><p><code>out_energ_res::Any</code></p></li><li><p><code>out_melt_fraction::Any</code></p></li><li><p><code>out_fluid_density::Any</code></p></li><li><p><code>out_conductivity::Any</code></p></li><li><p><code>out_vel_gr_tensor::Any</code></p></li><li><p><code>out_surf::Any</code>: activate surface output</p></li><li><p><code>out_surf_pvd::Any</code>: activate writing .pvd file</p></li><li><p><code>out_surf_velocity::Any</code>: surface velocity</p></li><li><p><code>out_surf_topography::Any</code>: surface topography</p></li><li><p><code>out_surf_amplitude::Any</code>: amplitude of topography (=topo-average(topo))</p></li><li><p><code>out_mark::Any</code>: activate marker output</p></li><li><p><code>out_mark_pvd::Any</code>: activate writing .pvd file</p></li><li><p><code>out_avd::Any</code>: activate AVD phase output</p></li><li><p><code>out_avd_pvd::Any</code>: activate writing .pvd file</p></li><li><p><code>out_avd_ref::Any</code>: AVD grid refinement factor</p></li><li><p><code>out_ptr::Any</code>: activate</p></li><li><p><code>out_ptr_ID::Any</code>: ID of the passive tracers</p></li><li><p><code>out_ptr_phase::Any</code>: phase of the passive tracers</p></li><li><p><code>out_ptr_Pressure::Any</code>: interpolated pressure</p></li><li><p><code>out_ptr_Temperature::Any</code>: temperature</p></li><li><p><code>out_ptr_MeltFraction::Any</code>: melt fraction computed using P-T of the marker</p></li><li><p><code>out_ptr_Active::Any</code>: option that highlight the marker that are currently active</p></li><li><p><code>out_ptr_Grid_Mf::Any</code>: option that allow to store the melt fraction seen within the cell</p></li></ul></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Phase" href="#LaMEM.LaMEM_Model.Phase"><code>LaMEM.LaMEM_Model.Phase</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Defines the material properties for each of the phases</code></pre><ul><li><p><code>ID::Union{Nothing, Int64}</code>: Material phase ID</p></li><li><p><code>Name::Union{Nothing, String}</code>: Description of the phase</p></li><li><p><code>rho::Union{Nothing, Float64}</code>: Density [kg/m^3]</p></li><li><p><code>eta::Union{Nothing, Float64}</code>: Linear viscosity [Pas]</p></li><li><p><code>visID::Union{Nothing, Int64}</code>: material ID for phase visualization (default is ID)</p></li><li><p><code>diff_prof::Union{Nothing, String}</code>: DIFFUSION creep profile; example: &quot;Dry<em>Olivine</em>diff<em>creep-Hirth</em>Kohlstedt_2003&quot;</p></li><li><p><code>disl_prof::Union{Nothing, String}</code>: DISLOCATION creep profile; example: &quot;Granite-Tirel<em>et</em>al_2008&quot;</p></li><li><p><code>peir_prof::Union{Nothing, String}</code>: PEIERLS creep profile; example:  &quot;Olivine<em>Peierls-Kameyama</em>1999&quot;</p></li><li><p><code>rho_n::Union{Nothing, Float64}</code>: depth-dependent density model parameter</p></li><li><p><code>rho_c::Union{Nothing, Float64}</code>: depth-dependent density model parameter</p></li><li><p><code>beta::Union{Nothing, Float64}</code>: pressure-dependent density model parameter</p></li><li><p><code>G::Union{Nothing, Float64}</code>: shear modulus</p></li><li><p><code>Kb::Union{Nothing, Float64}</code>: bulk modulus</p></li><li><p><code>E::Union{Nothing, Float64}</code>: Young&#39;s modulus</p></li><li><p><code>nu::Union{Nothing, Float64}</code>: Poisson&#39;s ratio</p></li><li><p><code>Kp::Union{Nothing, Float64}</code>: pressure dependence parameter</p></li><li><p><code>Bd::Union{Nothing, Float64}</code>: DIFFUSION creep pre-exponential constant</p></li><li><p><code>Ed::Union{Nothing, Float64}</code>: activation energy</p></li><li><p><code>Vd::Union{Nothing, Float64}</code>: activation volume</p></li><li><p><code>eta0::Union{Nothing, Float64}</code>: POWER LAW reference viscosity</p></li><li><p><code>e0::Union{Nothing, Float64}</code>: reference strain rate</p></li><li><p><code>Bn::Union{Nothing, Float64}</code>: DISLOCATION creep pre-exponential constant</p></li><li><p><code>En::Union{Nothing, Float64}</code>: activation energy</p></li><li><p><code>Vn::Union{Nothing, Float64}</code>: activation volume</p></li><li><p><code>n::Union{Nothing, Float64}</code>: power law exponent</p></li><li><p><code>Bp::Union{Nothing, Float64}</code>: PEIERLS creep pre-exponential constant</p></li><li><p><code>Ep::Union{Nothing, Float64}</code>: activation energy</p></li><li><p><code>Vp::Union{Nothing, Float64}</code>: activation volume</p></li><li><p><code>taup::Union{Nothing, Float64}</code>: scaling stress</p></li><li><p><code>gamma::Union{Nothing, Float64}</code>: approximation parameter</p></li><li><p><code>q::Union{Nothing, Float64}</code>: stress-dependence parameter</p></li><li><p><code>eta_fk::Union{Nothing, Float64}</code>: reference viscosity for Frank-Kamenetzky viscosity</p></li><li><p><code>gamma_fk::Union{Nothing, Float64}</code>: gamma parameter for Frank-Kamenetzky viscosity</p></li><li><p><code>TRef_fk::Union{Nothing, Float64}</code>: reference Temperature for Frank-Kamenetzky viscosity (if not set it is 0°C)</p></li><li><p><code>ch::Union{Nothing, Float64}</code>: cohesion</p></li><li><p><code>fr::Union{Nothing, Float64}</code>: friction angle</p></li><li><p><code>eta_st::Union{Nothing, Float64}</code>: stabilization viscosity (default is eta_min)</p></li><li><p><code>rp::Union{Nothing, Float64}</code>: pore-pressure ratio</p></li><li><p><code>chSoftID::Union{Nothing, Int64}</code>: friction softening law ID</p></li><li><p><code>frSoftID::Union{Nothing, Int64}</code>: cohesion softening law ID</p></li><li><p><code>healID::Union{Nothing, Int64}</code>: healing ID, points to healTau in Softening</p></li><li><p><code>alpha::Union{Nothing, Float64}</code>: thermal expansivity</p></li><li><p><code>Cp::Union{Nothing, Float64}</code>: specific heat (capacity), J⋅K−1⋅kg−1</p></li><li><p><code>k::Union{Nothing, Float64}</code>: thermal conductivity</p></li><li><p><code>A::Union{Nothing, Float64}</code>: radiogenic heat production</p></li><li><p><code>T::Union{Nothing, Float64}</code>: optional temperature to set within the phase</p></li><li><p><code>Latent_hx::Union{Nothing, Float64}</code>: optional, used for dike heating, J/kg</p></li><li><p><code>T_liq::Union{Nothing, Float64}</code>: optional, used for dike heating, liquidus temperature of material, celsius</p></li><li><p><code>T_sol::Union{Nothing, Float64}</code>: optional, used for dike heating, solidus temperature of material, celsius</p></li><li><p><code>T_Nu::Union{Nothing, Float64}</code>: default value for thermal conductivity boundary</p></li><li><p><code>nu_k::Union{Nothing, Float64}</code>: optional parameter, Nusselt number for use with conductivity</p></li><li><p><code>rho_ph::Union{Nothing, String}</code>: name of the phase diagram you want to use (still needs rho to be defined for the initial guess of pressure)</p></li><li><p><code>rho_ph_dir::Union{Nothing, String}</code>: in case the phase diagram has a different path provide the path (without the name of the actual PD) here</p></li><li><p><code>mfc::Union{Nothing, Float64}</code>: melt fraction viscosity correction factor (positive scalar)</p></li></ul></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.PhaseTransition" href="#LaMEM.LaMEM_Model.PhaseTransition"><code>LaMEM.LaMEM_Model.PhaseTransition</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Defines phase transitions on markers (that change the Phase ID of a marker depending on some conditions)</code></pre><ul><li><p><code>ID::Int64</code>: Phase_transition law ID</p></li><li><p><code>Type::String</code>: [Constant, Clapeyron, Box]: Constant - the phase transition occurs only at a fixed value of the parameter; Clapeyron - clapeyron slope</p></li><li><p><code>Name_Clapeyron::Union{Nothing, Int64}</code>: Type of predefined Clapeyron slope, such as Mantle<em>Transition</em>660km</p></li><li><p><code>PTBox_Bounds::Union{Nothing, Vector{Float64}}</code>: box bound coordinates: [left, right, front, back, bottom, top]</p></li><li><p><code>BoxVicinity::Union{Nothing, Int64}</code>: 1: only check particles in the vicinity of the box boundaries (2: in all directions)</p></li><li><p><code>Parameter_transition::String</code>: [T = Temperature, P = Pressure, Depth = z-coord, X=x-coord, Y=y-coord, APS = accumulated plastic strain, MeltFraction, t = time] parameter that triggers the phase transition</p></li><li><p><code>ConstantValue::Union{Nothing, Float64}</code>: Value of the parameter [unit of T,P,z, APS]</p></li><li><p><code>number_phases::Union{Nothing, Int64}</code>: The number of involved phases [default=1]</p></li><li><p><code>PhaseAbove::Union{Nothing, Vector{Int64}}</code>: Above the chosen value the phase is 1, below it, the value is PhaseBelow</p></li><li><p><code>PhaseBelow::Union{Nothing, Vector{Int64}}</code></p></li><li><p><code>PhaseInside::Union{Nothing, Vector{Int64}}</code>: Phase within the box  [use -1 if you don&#39;t want to change the phase inside the box]</p></li><li><p><code>PhaseOutside::Union{Nothing, Vector{Int64}}</code>: Phase outside the box [use -1 if you don&#39;t want to change the phase outside the box. If combined with OutsideToInside, all phases that come in are set to PhaseInside]</p></li><li><p><code>PhaseDirection::String</code>: [BothWays=default; BelowToAbove; AboveToBelow] Direction in which transition works</p></li><li><p><code>ResetParam::String</code>: [APS] Parameter to reset on particles below PT or within box</p></li><li><p><code>PTBox_TempType::String</code>: # Temperature condition witin the box [none, constant, linear, halfspace]</p></li><li><p><code>PTBox_topTemp::Union{Nothing, Float64}</code>: Temp @ top of box [for linear &amp; halfspace]</p></li><li><p><code>PTBox_botTemp::Union{Nothing, Float64}</code>: Temp @ bottom of box [for linear &amp; halfspace]</p></li><li><p><code>PTBox_thermalAge::Union{Nothing, Float64}</code>: Thermal age, usually in geo-units [Myrs] [only in case of halfspace]</p></li><li><p><code>PTBox_cstTemp::Union{Nothing, Float64}</code>: Temp within box [only for constant T]</p></li><li><p><code>v_box::Union{Nothing, Float64}</code>: [optional] only for NotInAirBox, velocity with which box moves in cm/yr</p></li><li><p><code>t0_box::Union{Nothing, Float64}</code>: [optional] beginning time of movemen in Myr</p></li><li><p><code>t1_box::Union{Nothing, Float64}</code>: [optional] end time of movement in Myr</p></li></ul></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Scaling" href="#LaMEM.LaMEM_Model.Scaling"><code>LaMEM.LaMEM_Model.Scaling</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Scaling{T} is a structure that contains the scaling info, employed in the current simulation</code></pre><ul><li><code>Scaling::Any</code>: Scaling object (as in GeoParams), which can be <code>GEO_units()</code>, <code>NO_units()</code>, or <code>SI_units()</code></li></ul></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Softening" href="#LaMEM.LaMEM_Model.Softening"><code>LaMEM.LaMEM_Model.Softening</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Defines strain softening parameters</code></pre><ul><li><p><code>ID::Int64</code>: softening law ID</p></li><li><p><code>APS1::Float64</code>: Begin of softening, in units of accumulated plastic strain (APS)</p></li><li><p><code>APS2::Float64</code>: End of softening, in units of accumulated plastic strain (APS)</p></li><li><p><code>A::Float64</code>: Reduction ratio</p></li><li><p><code>Lm::Float64</code>: Material length scale (in selected units, e.g. km in geo)</p></li><li><p><code>APSheal2::Union{Nothing, Float64}</code>: APS when healTau2 activates</p></li><li><p><code>healTau::Union{Nothing, Float64}</code>: healing timescale parameter [Myr]</p></li><li><p><code>healTau2::Union{Nothing, Float64}</code>: healing timescale parameter [Myr]  starting at APS=APSheal2</p></li></ul></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.SolutionParams" href="#LaMEM.LaMEM_Model.SolutionParams"><code>LaMEM.LaMEM_Model.SolutionParams</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Structure that contains the LaMEM global solution parameters.</code></pre><ul><li><p><code>gravity::Vector{Float64}</code>: gravitational acceleration vector</p></li><li><p><code>FSSA::Float64</code>: free surface stabilization parameter [0 - 1]; The value has to be between 0 and 1</p></li></ul><ul><li><p><code>shear_heat_eff::Float64</code>: shear heating efficiency parameter   [0 - 1]</p></li><li><p><code>Adiabatic_Heat::Float64</code>: Adiabatic Heating activation flag and efficiency. <a href="man/e.g. 0.5 means that only 50% of the potential adiabatic heating affects the energy equation">0.0 - 1.0</a></p></li><li><p><code>act_temp_diff::Int64</code>: temperature diffusion activation flag</p></li><li><p><code>act_therm_exp::Int64</code>: thermal expansion activation flag</p></li><li><p><code>act_steady_temp::Int64</code>: steady-state temperature initial guess activation flag</p></li><li><p><code>steady_temp_t::Float64</code>: time for (quasi-)steady-state temperature initial guess</p></li><li><p><code>nstep_steady::Int64</code>: number of steps for (quasi-)steady-state temperature initial guess (default = 1)</p></li><li><p><code>act_heat_rech::Int64</code>: recharge heat in anomalous bodies after (quasi-)steady-state temperature initial guess (=2: recharge after every diffusion step of initial guess)</p></li><li><p><code>init_lith_pres::Int64</code>: sets initial pressure to be the lithostatic pressure (stabilizes compressible setups in the first steps)</p></li><li><p><code>init_guess::Int64</code>: create an initial guess step (using constant viscosity <code>eta_ref</code> before starting the simulation</p></li><li><p><code>p_litho_visc::Int64</code>: use lithostatic instead of dynamic pressure for creep laws</p></li><li><p><code>p_litho_plast::Int64</code>: use lithostatic pressure for plasticity</p></li><li><p><code>p_lim_plast::Int64</code>: limit pressure at first iteration for plasticity</p></li><li><p><code>p_shift::Int64</code>: add a constant value [MPa] to the total pressure field, before evaluating plasticity (e.g., when the domain is located @ some depth within the crust)</p></li><li><p><code>act_p_shift::Int64</code>: pressure shift activation flag (enforce zero pressure on average in the top cell layer); note: this overwrites p_shift above!</p></li><li><p><code>eta_min::Float64</code>: viscosity lower bound [Pas]</p></li><li><p><code>eta_max::Float64</code>: viscosity upper limit [Pas]</p></li><li><p><code>eta_ref::Float64</code>: Reference viscosity (used for the initial guess) [Pas]</p></li><li><p><code>T_ref::Float64</code>: Reference temperature [C]</p></li><li><p><code>RUGC::Float64</code>: universal gas constant (you need to change this only for non-dimensional setups)</p></li><li><p><code>min_cohes::Float64</code>: cohesion lower bound  [Pa]</p></li><li><p><code>min_fric::Float64</code>: friction lower bound  [degree]</p></li><li><p><code>tau_ult::Float64</code>: ultimate yield stress [Pa]</p></li><li><p><code>rho_fluid::Float64</code>: fluid density for depth-dependent density model</p></li><li><p><code>gw_level_type::String</code>: ground water level type for pore pressure computation (see below)</p></li><li><p><code>gw_level::Float64</code>: ground water level at the free surface (if defined)</p></li><li><p><code>biot::Float64</code>: Biot pressure parameter</p></li><li><p><code>get_permea::Float64</code>: effective permeability computation activation flag</p></li><li><p><code>rescal::Float64</code>: stencil rescaling flag (for internal constraints, for example while computing permeability)</p></li><li><p><code>mfmax::Float64</code>: maximum melt fraction affecting viscosity reduction</p></li><li><p><code>lmaxit::Int64</code>: maximum number of local rheology iterations</p></li><li><p><code>lrtol::Float64</code>: local rheology iterations relative tolerance</p></li><li><p><code>act_dike::Int64</code>: dike activation flag (additonal term in divergence)</p></li><li><p><code>useTk::Int64</code>: switch to use T-dependent conductivity, 0: not active</p></li><li><p><code>dikeHeat::Int64</code>: switch to use Behn &amp; Ito heat source in the dike</p></li><li><p><code>Compute_velocity_gradient::Int64</code>: compute the velocity gradient tensor 1: active, 0: not active. If active, it automatically activates the output in the .pvd file</p></li></ul></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Solver" href="#LaMEM.LaMEM_Model.Solver"><code>LaMEM.LaMEM_Model.Solver</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Structure that contains the LaMEM solver options</code></pre><ul><li><p><code>SolverType::String</code>: solver employed [<code>&quot;direct&quot;</code> or <code>&quot;multigrid&quot;</code>]</p></li><li><p><code>DirectSolver::String</code>: mumps/superlu_dist/pastix/umfpack  (requires these external PETSc packages to be installed!)</p></li><li><p><code>DirectPenalty::Float64</code>: penalty parameter [employed if we use a direct solver]</p></li><li><p><code>MGLevels::Int64</code>: number of MG levels [default=3]</p></li><li><p><code>MGSweeps::Int64</code>: number of MG smoothening steps per level [default=10]</p></li><li><p><code>MGSmoother::String</code>: type of smoothener used [chebyshev or jacobi]</p></li><li><p><code>MGJacobiDamp::Float64</code>: Dampening parameter [only employed for Jacobi smoothener; default=0.6]</p></li><li><p><code>MGCoarseSolver::String</code>: coarse grid solver if using multigrid [<code>&quot;direct&quot;</code> / <code>&quot;mumps&quot;</code> / <code>&quot;superlu_dist&quot;</code> or <code>&quot;redundant&quot;</code> - more options specifiable through the command-line options <code>-crs_ksp_type</code> &amp; <code>-crs_pc_type</code>]</p></li><li><p><code>MGRedundantNum::Int64</code>: How many times do we copy the coarse grid? [only employed for redundant solver; default is 4]</p></li><li><p><code>MGRedundantSolver::String</code>: The coarse grid solver for each of the redundant solves [only employed for redundant; options are <code>&quot;mumps&quot;</code>/<code>&quot;superlu_dist&quot;</code> with default <code>&quot;superlu_dist&quot;</code>]</p></li><li><p><code>PETSc_options::Vector{String}</code>: List with (optional) PETSc options</p></li></ul></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Time" href="#LaMEM.LaMEM_Model.Time"><code>LaMEM.LaMEM_Model.Time</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Structure that contains the LaMEM timestepping information. An explanation of the paramneters is given in the struct `Time_info`</code></pre><ul><li><p><code>time_end::Float64</code>: simulation end time</p></li><li><p><code>dt::Float64</code>: initial time step</p></li><li><p><code>dt_min::Float64</code>: minimum time step (declare divergence if lower value is attempted)</p></li><li><p><code>dt_max::Float64</code>: maximum time step</p></li><li><p><code>dt_out::Float64</code>: output step (output at least at fixed time intervals)</p></li><li><p><code>inc_dt::Float64</code>: time step increment per time step (fraction of unit)</p></li><li><p><code>CFL::Float64</code>: CFL (Courant-Friedrichs-Lewy) criterion</p></li><li><p><code>CFLMAX::Float64</code>: CFL criterion for elasticity</p></li><li><p><code>nstep_max::Int64</code>: maximum allowed number of steps (lower bound: time<em>end/dt</em>max)</p></li><li><p><code>nstep_out::Int64</code>: save output every n steps; Set this to -1 to deactivate saving output</p></li><li><p><code>nstep_rdb::Int64</code>: save restart database every n steps</p></li><li><p><code>num_dt_periods::Int64</code>: number of time stepping periods</p></li><li><p><code>time_dt_periods::Vector{Int64}</code>: timestamps where timestep should be fixed (first entry has to 0)</p></li><li><p><code>step_dt_periods::Vector{Float64}</code>: target timesteps ar timestamps above</p></li><li><p><code>nstep_ini::Int64</code>: save output for n initial steps</p></li><li><p><code>time_tol::Float64</code>: relative tolerance for time comparisons</p></li></ul></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.geom_Sphere" href="#LaMEM.LaMEM_Model.geom_Sphere"><code>LaMEM.LaMEM_Model.geom_Sphere</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">LaMEM geometric primitive `sphere` object</code></pre><ul><li><p><code>phase::Int64</code>: phase</p></li><li><p><code>radius::Float64</code>: radius of sphere</p></li><li><p><code>center::Vector{Float64}</code>: center of sphere</p></li><li><p><code>Temperature::Union{Nothing, String}</code>: optional: Temperature of the sphere. possibilities: [constant, or nothing]</p></li><li><p><code>cstTemp::Union{Nothing, Float64}</code>: required in case of [constant]: temperature value [in Celcius in case of GEO units]</p></li></ul></div></section></article><article class="docstring"><header><a class="docstring-binding" id="GeophysicalModelGenerator.AddBox!-Tuple{Model}" href="#GeophysicalModelGenerator.AddBox!-Tuple{Model}"><code>GeophysicalModelGenerator.AddBox!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">AddBox!(model::Model; xlim=Tuple{2}, [ylim=Tuple{2}], zlim=Tuple{2},
+        Origin=nothing, StrikeAngle=0, DipAngle=0,
+        phase = ConstantPhase(1),
+        T=nothing )</code></pre><p>Adds a box with phase &amp; temperature structure to a 3D model setup. This simplifies creating model geometries in geodynamic models See the documentation of the GMG routine</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="GeophysicalModelGenerator.AddCylinder!-Tuple{Model}" href="#GeophysicalModelGenerator.AddCylinder!-Tuple{Model}"><code>GeophysicalModelGenerator.AddCylinder!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">AddCylinder!(model::Model;                                      # required input
+                base=Tuple{3}, cap=Tuple{3}, radius=Tuple{1},   # center and radius of the sphere
+                phase = ConstantPhase(1),                       # Sets the phase number(s) in the sphere
+                T=nothing )                                     # Sets the thermal structure (various fucntions are available)</code></pre><p>See the documentation of the GMG routine</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="GeophysicalModelGenerator.AddEllipsoid!-Tuple{Model}" href="#GeophysicalModelGenerator.AddEllipsoid!-Tuple{Model}"><code>GeophysicalModelGenerator.AddEllipsoid!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">AddEllipsoid!(model::Model;                                 # required input
+                cen=Tuple{3}, axes=Tuple{3},                # center and semi-axes of the ellpsoid
+                Origin=nothing, StrikeAngle=0, DipAngle=0,  # origin &amp; dip/strike
+                phase = ConstantPhase(1),                   # Sets the phase number(s) in the box
+                T=nothing )</code></pre><p>See the documentation of the GMG routine</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="GeophysicalModelGenerator.AddSphere!-Tuple{Model}" href="#GeophysicalModelGenerator.AddSphere!-Tuple{Model}"><code>GeophysicalModelGenerator.AddSphere!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">AddSphere!(model::Model; cen=Tuple{3}, radius=Tuple{1}, phase = ConstantPhase(1), T=nothing)</code></pre><p>See the documentation of the GMG routine</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.IO_functions.Read_LaMEM_simulation-Tuple{Model}" href="#LaMEM.IO_functions.Read_LaMEM_simulation-Tuple{Model}"><code>LaMEM.IO_functions.Read_LaMEM_simulation</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">Timestep, FileNames, Time = Read_LaMEM_simulation(model::Model; phase=false, surf=false, passive_tracers=false)</code></pre><p>Reads a LaMEM simulation as specified in <code>model</code> and returns the timesteps, times and filenames of that simulation once it is finished.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.IO_functions.Read_LaMEM_timestep" href="#LaMEM.IO_functions.Read_LaMEM_timestep"><code>LaMEM.IO_functions.Read_LaMEM_timestep</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">data, time = Read_LaMEM_timestep(model::Model, TimeStep::Int64=0; fields=nothing, phase=false, surf=false, last=true)</code></pre><p>Reads a specific <code>Timestep</code> from a simulation specified in <code>model</code></p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Check_LaMEM_Model-Tuple{Model}" href="#LaMEM.LaMEM_Model.Check_LaMEM_Model-Tuple{Model}"><code>LaMEM.LaMEM_Model.Check_LaMEM_Model</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">Check_LaMEM_Model(m::Model)</code></pre><p>Checks the LaMEM Setup Model <code>m</code> for errors</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Create_Grid-NTuple{15, Any}" href="#LaMEM.LaMEM_Model.Create_Grid-NTuple{15, Any}"><code>LaMEM.LaMEM_Model.Create_Grid</code></a> — <span class="docstring-category">Method</span></header><section><div><p>This creates a LaMEM grid</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Write_LaMEM_InputFile" href="#LaMEM.LaMEM_Model.Write_LaMEM_InputFile"><code>LaMEM.LaMEM_Model.Write_LaMEM_InputFile</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">Write_LaMEM_InputFile(d::Model,fname::String; dir=pwd())</code></pre><p>Writes a LaMEM input file based on the data stored in Model</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, BoundaryConditions}" href="#LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, BoundaryConditions}"><code>LaMEM.LaMEM_Model.Write_LaMEM_InputFile</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">Write_LaMEM_InputFile(io, d::BoundaryConditions)</code></pre><p>Writes the boundary conditions related parameters to file</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, FreeSurface}" href="#LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, FreeSurface}"><code>LaMEM.LaMEM_Model.Write_LaMEM_InputFile</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">Write_LaMEM_InputFile(io, d::FreeSurface)</code></pre><p>Writes the free surface related parameters to file</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, Grid}" href="#LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, Grid}"><code>LaMEM.LaMEM_Model.Write_LaMEM_InputFile</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">Write_LaMEM_InputFile(io, d::Grid)</code></pre><p>This writes grid info to a LaMEM input file</p><p><strong>Example</strong></p><pre><code class="language-julia hljs">julia&gt; d=LaMEM.Grid(coord_x=[0.0, 0.7, 0.8, 1.0], bias_x=[0.3,1.0,3.0], nel_x=[10,4,2])
+julia&gt; io = open(&quot;test.dat&quot;,&quot;w&quot;)
+julia&gt; LaMEM.Write_LaMEM_InputFile(io, d)
+julia&gt; close(io)</code></pre></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, Materials}" href="#LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, Materials}"><code>LaMEM.LaMEM_Model.Write_LaMEM_InputFile</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">Write_LaMEM_InputFile(io, d::Output)</code></pre><p>Writes the free surface related parameters to file</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, ModelSetup}" href="#LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, ModelSetup}"><code>LaMEM.LaMEM_Model.Write_LaMEM_InputFile</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">Write_LaMEM_InputFile(io, d::ModelSetup)</code></pre><p>Writes options related to the Model Setup to disk</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, Output}" href="#LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, Output}"><code>LaMEM.LaMEM_Model.Write_LaMEM_InputFile</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">Write_LaMEM_InputFile(io, d::Output)</code></pre><p>Writes the free surface related parameters to file</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, SolutionParams}" href="#LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, SolutionParams}"><code>LaMEM.LaMEM_Model.Write_LaMEM_InputFile</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">Write_LaMEM_InputFile(io, d::SolutionParams)</code></pre><p>Writes the boundary conditions related parameters to file</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, Solver}" href="#LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, Solver}"><code>LaMEM.LaMEM_Model.Write_LaMEM_InputFile</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">Write_LaMEM_InputFile(io, d::Solver)</code></pre><p>Writes the free surface related parameters to file</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, Time}" href="#LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, Time}"><code>LaMEM.LaMEM_Model.Write_LaMEM_InputFile</code></a> — <span class="docstring-category">Method</span></header><section><div><p>Writes the Time related parameters to file</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, geom_Sphere}" href="#LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, geom_Sphere}"><code>LaMEM.LaMEM_Model.Write_LaMEM_InputFile</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">Write_LaMEM_InputFile(io, d::geom_Sphere)</code></pre></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.Write_LaMEM_InputFile_PETSc-Tuple{Any, Solver}" href="#LaMEM.LaMEM_Model.Write_LaMEM_InputFile_PETSc-Tuple{Any, Solver}"><code>LaMEM.LaMEM_Model.Write_LaMEM_InputFile_PETSc</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">Write_LaMEM_InputFile_PETSc(io, d::Solver)</code></pre><p>Writes the (optional) PETSc options to file</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.add_dike!-Tuple{Model, Dike}" href="#LaMEM.LaMEM_Model.add_dike!-Tuple{Model, Dike}"><code>LaMEM.LaMEM_Model.add_dike!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">add_dike!(model::Model, dike::Dike)</code></pre><p>This adds a phase transition <code>phase_trans</code> to <code>model</code></p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.add_geom!-Tuple{Model, Any}" href="#LaMEM.LaMEM_Model.add_geom!-Tuple{Model, Any}"><code>LaMEM.LaMEM_Model.add_geom!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">add_geom!(model::Model, geom_object)</code></pre><p>This adds an internal geometric primitive object <code>geom_object</code> to the LaMEM Model Setup <code>model</code>.</p><p>Currently available primitive geom objects are:</p><ul><li><code>geom_Sphere</code></li></ul></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.add_petsc!-Tuple{Model, Vararg{Any}}" href="#LaMEM.LaMEM_Model.add_petsc!-Tuple{Model, Vararg{Any}}"><code>LaMEM.LaMEM_Model.add_petsc!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">add_petsc!(model::Model, option::String)</code></pre><p>Adds one or more PETSc options to the model </p><p><strong>Example</strong></p><pre><code class="language-julia hljs">julia&gt; d = Model()
+julia&gt; add_petsc!(d,&quot;-snes_npicard 3&quot;)</code></pre></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.add_phase!-Tuple{Model, Phase}" href="#LaMEM.LaMEM_Model.add_phase!-Tuple{Model, Phase}"><code>LaMEM.LaMEM_Model.add_phase!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">add_phase!(model::Model, phase::Phase)</code></pre><p>This adds a <code>phase</code> (with material properties) to <code>model</code></p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.add_phase!-Tuple{Model, Vararg{Any}}" href="#LaMEM.LaMEM_Model.add_phase!-Tuple{Model, Vararg{Any}}"><code>LaMEM.LaMEM_Model.add_phase!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">add_phase!(model::Model, phases...)</code></pre><p>Add several phases @ once.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.add_phasetransition!-Tuple{Model, PhaseTransition}" href="#LaMEM.LaMEM_Model.add_phasetransition!-Tuple{Model, PhaseTransition}"><code>LaMEM.LaMEM_Model.add_phasetransition!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">add_phasetransition!(model::Model, phase_trans::PhaseTransition)</code></pre><p>This adds a phase transition <code>phase_trans</code> to <code>model</code></p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.add_softening!-Tuple{Model, Softening}" href="#LaMEM.LaMEM_Model.add_softening!-Tuple{Model, Softening}"><code>LaMEM.LaMEM_Model.add_softening!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">add_softening!(model::Model, soft::Softening)</code></pre><p>This adds a plastic softening law <code>soft</code> to <code>model</code></p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.create_initialsetup" href="#LaMEM.LaMEM_Model.create_initialsetup"><code>LaMEM.LaMEM_Model.create_initialsetup</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">create_initialsetup(model::Model, cores::Int64=1, args::String=&quot;&quot;)</code></pre><p>Creates the initial model setup of LaMEM from <code>model</code>, which includes:</p><ul><li>Writing the LaMEM (*.dat) input file</li><li>Write the VTK file (if requested when <code>model.Output.write_VTK_setup=true</code>)</li><li>Write the marker files to disk (if <code>model.ModelSetup.msetup=&quot;files&quot;</code>)</li></ul></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.get_doc-Tuple{Any, Symbol}" href="#LaMEM.LaMEM_Model.get_doc-Tuple{Any, Symbol}"><code>LaMEM.LaMEM_Model.get_doc</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">help_info::String = get_doc(structure, field::Symbol)</code></pre><p>This returns a string with the documentation for a parameter <code>field</code> that is within the <code>structure</code>.  Note that this structure must be a help structure of the current one.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.replace_phase!-Tuple{Model, Phase}" href="#LaMEM.LaMEM_Model.replace_phase!-Tuple{Model, Phase}"><code>LaMEM.LaMEM_Model.replace_phase!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">replace_phase!(model::Model, phase_new::Phase; ID::Int64=nothing, Name::String=nothing)</code></pre><p>This replaces a <code>phase</code> within a LaMEM Model Setup <code>model</code> with <code>phase_new</code> either based on its <code>Name</code> or <code>ID</code>.  Note that it is expected that only one such phase is present in the current setup.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.rm_last_phase!-Tuple{Model}" href="#LaMEM.LaMEM_Model.rm_last_phase!-Tuple{Model}"><code>LaMEM.LaMEM_Model.rm_last_phase!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">rm_last_phase!(model::Model, phase::Phase)</code></pre><p>This removes the last added <code>phase</code> from <code>model</code></p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.rm_phase!-Tuple{Model, Int64}" href="#LaMEM.LaMEM_Model.rm_phase!-Tuple{Model, Int64}"><code>LaMEM.LaMEM_Model.rm_phase!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">rm_phase!(model::Model, ID::Int64)</code></pre><p>This removes a phase with <code>ID</code> from <code>model</code></p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.LaMEM_Model.set_geom!-Tuple{Model, geom_Sphere}" href="#LaMEM.LaMEM_Model.set_geom!-Tuple{Model, geom_Sphere}"><code>LaMEM.LaMEM_Model.set_geom!</code></a> — <span class="docstring-category">Method</span></header><section><div><p>This sets the geometry </p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.Run.run_lamem" href="#LaMEM.Run.run_lamem"><code>LaMEM.Run.run_lamem</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">run_lamem(model::Model, cores::Int64=1, args:String=&quot;&quot;; wait=true)</code></pre><p>Performs a LaMEM run for the parameters that are specified in <code>model</code></p></div></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="juliasetups.html">« Overview</a><a class="docs-footer-nextpage" href="runlamem.html">Run LaMEM »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Friday 14 July 2023 12:46">Friday 14 July 2023</span>. Using Julia version 1.9.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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+<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Installation · LaMEM.jl</title><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="../index.html">LaMEM.jl</a></span></div><form class="docs-search" action="../search.html"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../index.html">Home</a></li><li class="is-active"><a class="tocitem" href="installation.html">Installation</a></li><li><a class="tocitem" href="installation_HPC.html">Installation on HPC systems</a></li><li><span class="tocitem">Create LaMEM models in julia</span><ul><li><a class="tocitem" href="juliasetups.html">Overview</a></li><li><a class="tocitem" href="LaMEM_ModelFunctions.html">Grid</a></li></ul></li><li><a class="tocitem" href="runlamem.html">Run LaMEM</a></li><li><a class="tocitem" href="readtimesteps.html">Reading timesteps</a></li><li><a class="tocitem" href="listfunctions.html">List of functions</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href="installation.html">Installation</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="installation.html">Installation</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/JuliaGeodynamics/LaMEM.jl/blob/main/docs/src/man/installation.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="Installation"><a class="docs-heading-anchor" href="#Installation">Installation</a><a id="Installation-1"></a><a class="docs-heading-anchor-permalink" href="#Installation" title="Permalink"></a></h1><p>Installing LaMEM can simply be done through the package manager:</p><pre><code class="language-julia hljs">julia&gt;]
+pkg&gt;add LaMEM</code></pre><p>which will download the binaries along with PETSc and mpiexec for your system.</p><p>You can test if it works on your machine with</p><pre><code class="language-julia hljs">pkg&gt; test LaMEM</code></pre><h3 id="Running-LaMEM-from-the-julia-REPL"><a class="docs-heading-anchor" href="#Running-LaMEM-from-the-julia-REPL">Running LaMEM from the julia REPL</a><a id="Running-LaMEM-from-the-julia-REPL-1"></a><a class="docs-heading-anchor-permalink" href="#Running-LaMEM-from-the-julia-REPL" title="Permalink"></a></h3><p>Running LaMEM from within julia can be done with the <code>run_lamem</code> function:</p><article class="docstring"><header><a class="docstring-binding" id="LaMEM.Run.run_lamem" href="#LaMEM.Run.run_lamem"><code>LaMEM.Run.run_lamem</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">run_lamem(model::Model, cores::Int64=1, args:String=&quot;&quot;; wait=true)</code></pre><p>Performs a LaMEM run for the parameters that are specified in <code>model</code></p></div></section><section><div><pre><code class="language-julia hljs">run_lamem(ParamFile::String, cores::Int64=1, args:String=&quot;&quot;; wait=true)</code></pre><p>This starts a LaMEM simulation, for using the parameter file <code>ParamFile</code> on <code>cores</code> number of cores.  Optional additional command-line parameters can be specified with <code>args</code>.</p><p><strong>Example:</strong></p><p>You can call LaMEM with:</p><pre><code class="language-julia hljs">julia&gt; using LaMEM
+julia&gt; ParamFile=&quot;../../input_models/BuildInSetups/FallingBlock_Multigrid.dat&quot;;
+julia&gt; run_lamem(ParamFile)</code></pre><p>Do the same on 2 cores with a command-line argument as:</p><pre><code class="language-julia hljs">julia&gt; ParamFile=&quot;../../input_models/BuildInSetups/FallingBlock_Multigrid.dat&quot;;
+julia&gt; run_lamem(ParamFile, 2, &quot;-nstep_max = 1&quot;)</code></pre></div></section></article><h3 id="Running-LaMEM-from-outside-julia"><a class="docs-heading-anchor" href="#Running-LaMEM-from-outside-julia">Running LaMEM from outside julia</a><a id="Running-LaMEM-from-outside-julia-1"></a><a class="docs-heading-anchor-permalink" href="#Running-LaMEM-from-outside-julia" title="Permalink"></a></h3><p>If you, for some reason, do not want to run LaMEM through julia but instead directly from the terminal or powershell, you will have to add the required dynamic libraries and executables. Do this with:</p><article class="docstring"><header><a class="docstring-binding" id="LaMEM.Run.show_paths_LaMEM" href="#LaMEM.Run.show_paths_LaMEM"><code>LaMEM.Run.show_paths_LaMEM</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">show_paths_LaMEM()</code></pre><p>The downloaded <code>LaMEM</code> binaries can also be called from outside julia (directly from the terminal).  In that case, you will need to set load correct dynamic libraries (such as PETSc) and call the correct binaries.</p><p>This function shows this for your system. </p></div></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../index.html">« Home</a><a class="docs-footer-nextpage" href="installation_HPC.html">Installation on HPC systems »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Friday 14 July 2023 12:46">Friday 14 July 2023</span>. Using Julia version 1.9.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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+<!DOCTYPE html>
+<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Installation on HPC systems · LaMEM.jl</title><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="../index.html">LaMEM.jl</a></span></div><form class="docs-search" action="../search.html"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../index.html">Home</a></li><li><a class="tocitem" href="installation.html">Installation</a></li><li class="is-active"><a class="tocitem" href="installation_HPC.html">Installation on HPC systems</a></li><li><span class="tocitem">Create LaMEM models in julia</span><ul><li><a class="tocitem" href="juliasetups.html">Overview</a></li><li><a class="tocitem" href="LaMEM_ModelFunctions.html">Grid</a></li></ul></li><li><a class="tocitem" href="runlamem.html">Run LaMEM</a></li><li><a class="tocitem" href="readtimesteps.html">Reading timesteps</a></li><li><a class="tocitem" href="listfunctions.html">List of functions</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href="installation_HPC.html">Installation on HPC systems</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="installation_HPC.html">Installation on HPC systems</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/JuliaGeodynamics/LaMEM.jl/blob/main/docs/src/man/installation_HPC.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="Installation-on-HPC-systems"><a class="docs-heading-anchor" href="#Installation-on-HPC-systems">Installation on HPC systems</a><a id="Installation-on-HPC-systems-1"></a><a class="docs-heading-anchor-permalink" href="#Installation-on-HPC-systems" title="Permalink"></a></h1><p>Installing LaMEM on high performance computer (HPC) systems can be complicated, because you will have to compile PETSc with the correct dependencies for that system.  The reason is that HPC systems use MPI versions that are specifically tailored/compiled for that system. </p><p>Luckily there is a solution thanks to the great work of <code>@eschnett</code> and colleagues, who developed <a href="https://github.com/eschnett/MPItrampoline">MPITrampoline</a> which is an intermediate layer between the HPC-system-specific MPI libraries and the precompiled <code>LaMEM</code> binaries. </p><p>It essentially consists of two steps:      1) compile a small package (<a href="https://github.com/eschnett/MPIwrapper">MPIwrapper</a>)      2) make sure that you download the version of <code>MAGEMin</code> that was compiled versus <code>MPItrampoline</code>.</p><p>Here step-by-step instructions (for Linux, as that is what essentially all HPC systems use):</p><ul><li>Download <a href="https://github.com/eschnett/MPIwrapper">MPIwrapper</a>: </li></ul><pre><code class="language-bash hljs">$git clone https://github.com/eschnett/MPIwrapper.git 
+$cd MPIwrapper</code></pre><ul><li>Install it after making sure that <code>mpiexec</code> points to the one you want (you may have to load some modules, depending on your system):</li></ul><pre><code class="language-bash hljs">$cmake -S . -B build -DMPIEXEC_EXECUTABLE=mpiexec -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_INSTALL_PREFIX=$HOME/mpiwrapper
+$cmake --build build
+$cmake --install build</code></pre><p>At this stage, <code>MPItrampoline</code> is installed in <code>$HOME/mpiwrapper</code></p><ul><li>Set the correct wrapper:</li></ul><pre><code class="nohighlight hljs">$export MPITRAMPOLINE_LIB=$HOME/mpiwrapper/lib64/libmpiwrapper.so</code></pre><p>Depending on the system it may be called <code>lib</code> instead of <code>lib64</code> (check!).</p><ul><li>Start julia and install the <code>MPI</code> and <code>MPIPreferences</code> packages:</li></ul><pre><code class="language-julia hljs">$julia
+julia&gt; ]
+pkg&gt;add MPI, MPIPreferences</code></pre><ul><li>Set the preference to use <code>MPItrampoline</code></li></ul><pre><code class="language-julia hljs">julia&gt; using MPIPreferences; MPIPreferences.use_jll_binary(&quot;MPItrampoline_jll&quot;)
+┌ Info: MPIPreferences unchanged
+└   binary = &quot;MPItrampoline_jll&quot;</code></pre><ul><li>Load <code>MPI</code> and verify it is the correct one</li></ul><pre><code class="language-julia hljs">julia&gt; using MPI
+julia&gt; MPI.Get_library_version()
+&quot;MPIwrapper 2.10.3, using MPIABI 2.9.0, wrapping:\nOpen MPI v4.1.4, package: Open MPI boris@Pluton Distribution, ident: 4.1.4, repo rev: v4.1.4, May 26, 2022&quot;</code></pre><p>After this, restart julia (this only needs to be done once, next time all is fine).</p><ul><li>Now load <code>LaMEM</code> and check that it uses the <code>mpitrampoline</code> version:</li></ul><pre><code class="language-julia hljs">julia&gt; using MPI,LaMEM
+julia&gt; LaMEM.LaMEM_jll.host_platform
+Linux x86_64 {cxxstring_abi=cxx11, julia_version=1.8.1, libc=glibc, libgfortran_version=5.0.0, mpi=mpitrampoline}</code></pre><p>At this stage the precompiled version of <code>LaMEM</code> should be useable on that system.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="installation.html">« Installation</a><a class="docs-footer-nextpage" href="juliasetups.html">Overview »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Friday 14 July 2023 12:46">Friday 14 July 2023</span>. Using Julia version 1.9.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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+<!DOCTYPE html>
+<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Overview · LaMEM.jl</title><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="../index.html">LaMEM.jl</a></span></div><form class="docs-search" action="../search.html"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../index.html">Home</a></li><li><a class="tocitem" href="installation.html">Installation</a></li><li><a class="tocitem" href="installation_HPC.html">Installation on HPC systems</a></li><li><span class="tocitem">Create LaMEM models in julia</span><ul><li class="is-active"><a class="tocitem" href="juliasetups.html">Overview</a></li><li><a class="tocitem" href="LaMEM_ModelFunctions.html">Grid</a></li></ul></li><li><a class="tocitem" href="runlamem.html">Run LaMEM</a></li><li><a class="tocitem" href="readtimesteps.html">Reading timesteps</a></li><li><a class="tocitem" href="listfunctions.html">List of functions</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li><a class="is-disabled">Create LaMEM models in julia</a></li><li class="is-active"><a href="juliasetups.html">Overview</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="juliasetups.html">Overview</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/JuliaGeodynamics/LaMEM.jl/blob/main/docs/src/man/juliasetups.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="Create-and-run-setups-from-julia"><a class="docs-heading-anchor" href="#Create-and-run-setups-from-julia">Create &amp; run setups from julia</a><a id="Create-and-run-setups-from-julia-1"></a><a class="docs-heading-anchor-permalink" href="#Create-and-run-setups-from-julia" title="Permalink"></a></h1><p>It is also possible to construct a LaMEM setup directly in julia &amp; run that. You can do the same from within a <a href="https://plutojl.org">Pluto</a> notebook. The advantage is that it is easier to use, has build-in plotting functions and extensive documentation. </p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="installation_HPC.html">« Installation on HPC systems</a><a class="docs-footer-nextpage" href="LaMEM_ModelFunctions.html">Grid »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Friday 14 July 2023 12:46">Friday 14 July 2023</span>. Using Julia version 1.9.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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+<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>List of functions · LaMEM.jl</title><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="../index.html">LaMEM.jl</a></span></div><form class="docs-search" action="../search.html"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../index.html">Home</a></li><li><a class="tocitem" href="installation.html">Installation</a></li><li><a class="tocitem" href="installation_HPC.html">Installation on HPC systems</a></li><li><span class="tocitem">Create LaMEM models in julia</span><ul><li><a class="tocitem" href="juliasetups.html">Overview</a></li><li><a class="tocitem" href="LaMEM_ModelFunctions.html">Grid</a></li></ul></li><li><a class="tocitem" href="runlamem.html">Run LaMEM</a></li><li><a class="tocitem" href="readtimesteps.html">Reading timesteps</a></li><li class="is-active"><a class="tocitem" href="listfunctions.html">List of functions</a><ul class="internal"><li><a class="tocitem" href="#Running-LaMEM"><span>Running LaMEM</span></a></li><li><a class="tocitem" href="#Reading-LaMEM-output-back-into-julia"><span>Reading LaMEM output back into julia</span></a></li></ul></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href="listfunctions.html">List of functions</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="listfunctions.html">List of functions</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/JuliaGeodynamics/LaMEM.jl/blob/main/docs/src/man/listfunctions.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="List-of-all-functions"><a class="docs-heading-anchor" href="#List-of-all-functions">List of all functions</a><a id="List-of-all-functions-1"></a><a class="docs-heading-anchor-permalink" href="#List-of-all-functions" title="Permalink"></a></h1><p>These are all functions that are available in the package, which can roughly be divided into two groups (running &amp; reading LaMEM)</p><h2 id="Running-LaMEM"><a class="docs-heading-anchor" href="#Running-LaMEM">Running LaMEM</a><a id="Running-LaMEM-1"></a><a class="docs-heading-anchor-permalink" href="#Running-LaMEM" title="Permalink"></a></h2><article class="docstring"><header><a class="docstring-binding" id="LaMEM.Run.remove_popup_messages_mac-Tuple{}" href="#LaMEM.Run.remove_popup_messages_mac-Tuple{}"><code>LaMEM.Run.remove_popup_messages_mac</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">remove_popup_messages_mac()</code></pre><p>On a Mac with firewall enabled, running LaMEM will result in a popup window that says: &quot;Accept incoming connections&quot; which you should Allow or Deny. This is a bit annoying, so this julia script fixes that. Note that you must have administrator rights on your machine as we need to run &quot;sudo&quot;</p><p>Run this script from the terminal with</p><pre><code class="language-julia hljs">julia&gt; remove_popup_messages_mac()</code></pre><p>You need to do this once (every time a new version is installed)</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.Run.run_lamem" href="#LaMEM.Run.run_lamem"><code>LaMEM.Run.run_lamem</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">run_lamem(ParamFile::String, cores::Int64=1, args:String=&quot;&quot;; wait=true)</code></pre><p>This starts a LaMEM simulation, for using the parameter file <code>ParamFile</code> on <code>cores</code> number of cores.  Optional additional command-line parameters can be specified with <code>args</code>.</p><p><strong>Example:</strong></p><p>You can call LaMEM with:</p><pre><code class="language-julia hljs">julia&gt; using LaMEM
+julia&gt; ParamFile=&quot;../../input_models/BuildInSetups/FallingBlock_Multigrid.dat&quot;;
+julia&gt; run_lamem(ParamFile)</code></pre><p>Do the same on 2 cores with a command-line argument as:</p><pre><code class="language-julia hljs">julia&gt; ParamFile=&quot;../../input_models/BuildInSetups/FallingBlock_Multigrid.dat&quot;;
+julia&gt; run_lamem(ParamFile, 2, &quot;-nstep_max = 1&quot;)</code></pre></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.Run.run_lamem_save_grid" href="#LaMEM.Run.run_lamem_save_grid"><code>LaMEM.Run.run_lamem_save_grid</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">ProcessorPartFile = run_lamem_save_grid(ParamFile::String, cores::Int64=1; verbose=true)</code></pre><p>This calls LaMEM simulation, for using the parameter file <code>ParamFile</code>  and creates processor partitioning file &quot;ProcessorPartitioning<em><code>cores</code>cpu</em>X.Y.Z.bin&quot; for <code>cores</code> number of cores. </p><p><strong>Example:</strong></p><pre><code class="language-julia hljs">julia&gt; using LaMEM
+julia&gt; ParamFile=&quot;../../input_models/BuildInSetups/FallingBlock_Multigrid.dat&quot;;
+julia&gt; ProcessorPartFile = run_lamem_save_grid(ParamFile, 2)</code></pre></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.Run.show_paths_LaMEM-Tuple{}" href="#LaMEM.Run.show_paths_LaMEM-Tuple{}"><code>LaMEM.Run.show_paths_LaMEM</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">show_paths_LaMEM()</code></pre><p>The downloaded <code>LaMEM</code> binaries can also be called from outside julia (directly from the terminal).  In that case, you will need to set load correct dynamic libraries (such as PETSc) and call the correct binaries.</p><p>This function shows this for your system. </p></div></section></article><h2 id="Reading-LaMEM-output-back-into-julia"><a class="docs-heading-anchor" href="#Reading-LaMEM-output-back-into-julia">Reading LaMEM output back into julia</a><a id="Reading-LaMEM-output-back-into-julia-1"></a><a class="docs-heading-anchor-permalink" href="#Reading-LaMEM-output-back-into-julia" title="Permalink"></a></h2><article class="docstring"><header><a class="docstring-binding" id="LaMEM.IO_functions.ReadField_3D_pVTR-Tuple{Any, Any}" href="#LaMEM.IO_functions.ReadField_3D_pVTR-Tuple{Any, Any}"><code>LaMEM.IO_functions.ReadField_3D_pVTR</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">output, isCell = ReadField_3D_pVTR(data, FieldName::String)</code></pre><p>Extracts a 3D data field from a pVTR data structure <code>data</code></p><p>Input:</p><ul><li><code>data</code>:       Data structure obtained with Read<em>VTR</em>File</li><li><code>FieldName</code>:  Exact name of the field as specified in the *.vtr file</li></ul><p>Output:</p><ul><li><code>data_field</code>, <code>isCell</code>:   3D field with data, and a flag that indicates whether it is Cell data (PointData otherwise)                              <code>data_field</code> is a tuple of size 1, or 3 depending on whether it is a scalar or vector field</li></ul></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.IO_functions.ReadField_3D_pVTU-Tuple{Any, Any}" href="#LaMEM.IO_functions.ReadField_3D_pVTU-Tuple{Any, Any}"><code>LaMEM.IO_functions.ReadField_3D_pVTU</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">output, isCell = ReadField_3D_pVTU(data, FieldName::String)</code></pre><p>Extracts a 3D data field from a pVTU data structure <code>data</code> Input:</p><ul><li><code>data</code>:       Data structure obtained with Read<em>VTR</em>File</li><li><code>FieldName</code>:  Exact name of the field as specified in the *.vtr file</li></ul><p>Output:</p><ul><li><code>data_field</code>: Array with data, <code>data_field</code> is a tuple of size 1, 3 or 9 depending on whether it is a scalar, vector or tensor field</li></ul></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.IO_functions.Read_LaMEM_PVTR_File-Tuple{String, String}" href="#LaMEM.IO_functions.Read_LaMEM_PVTR_File-Tuple{String, String}"><code>LaMEM.IO_functions.Read_LaMEM_PVTR_File</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">data_output = Read_LaMEM_PVTR_File(DirName, FileName; fields=nothing)</code></pre><p>Reads a 3D LaMEM timestep from VTR file <code>FileName</code>, located in directory <code>DirName</code>.  By default, it will read all fields. If you want you can only read a specific <code>field</code>. See the function <code>fieldnames</code> to get a list with all available fields in the file.</p><p>It will return <code>data_output</code> which is a <code>CartData</code> output structure.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.IO_functions.Read_LaMEM_PVTS_File-Tuple{String, String}" href="#LaMEM.IO_functions.Read_LaMEM_PVTS_File-Tuple{String, String}"><code>LaMEM.IO_functions.Read_LaMEM_PVTS_File</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">data_output = Read_LaMEM_PVTS_File(DirName, FileName; field=nothing)</code></pre><p>Reads a 3D LaMEM timestep from VTS file <code>FileName</code>, located in directory <code>DirName</code>. Typically this is done to read passive tracers back into julia.  By default, it will read all fields. If you want you can only read a specific <code>field</code>. See the function <code>fieldnames</code> to get a list with all available fields in the file.</p><p>It will return <code>data_output</code> which is a <code>CartData</code> output structure.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.IO_functions.Read_LaMEM_PVTU_File-Tuple{Any, Any}" href="#LaMEM.IO_functions.Read_LaMEM_PVTU_File-Tuple{Any, Any}"><code>LaMEM.IO_functions.Read_LaMEM_PVTU_File</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">data_output = Read_LaMEM_PVTU_File(DirName, FileName; fields=nothing)</code></pre><p>Reads a 3D LaMEM timestep from VTU file <code>FileName</code>, located in directory <code>DirName</code>. Typically this is done to read passive tracers back into julia.  By default, it will read all fields. If you want you can only read a specific <code>field</code>. See the function <code>fieldnames</code> to get a list with all available fields in the file.</p><p>It will return <code>data_output</code> which is a <code>CartData</code> output structure.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.IO_functions.Read_LaMEM_fieldnames" href="#LaMEM.IO_functions.Read_LaMEM_fieldnames"><code>LaMEM.IO_functions.Read_LaMEM_fieldnames</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">Read_LaMEM_fieldnames(FileName::String, DirName_base::String=&quot;&quot;; phase=false, surf=false, tracers=false)</code></pre><p>Returns the names of the datasets stored in <code>FileName</code></p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.IO_functions.Read_LaMEM_simulation" href="#LaMEM.IO_functions.Read_LaMEM_simulation"><code>LaMEM.IO_functions.Read_LaMEM_simulation</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">Timestep, FileNames, Time = Read_LaMEM_simulation(FileName::String, DirName::String=&quot;&quot;; phase=false, surf=false, passive_tracers=false)</code></pre><p>Reads a LaMEM simulation <code>FileName</code> in directory <code>DirName</code> and returns the timesteps, times and filenames of that simulation.</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.IO_functions.Read_LaMEM_timestep" href="#LaMEM.IO_functions.Read_LaMEM_timestep"><code>LaMEM.IO_functions.Read_LaMEM_timestep</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">data, time = Read_LaMEM_timestep(FileName::String, TimeStep::Int64=0, DirName::String=&quot;&quot;; fields=nothing, phase=false, surf=false, last=false)</code></pre><p>This reads a LaMEM timestep.</p><p>Input Arguments:</p><ul><li><code>FileName</code>: name of the simulation, w/out extension</li><li><code>Timestep</code>: timestep to be read, unless <code>last=true</code> in which case we read the last one</li><li><code>DirName</code>: name of the main directory (i.e. where the <code>*.pvd</code> files are located)</li><li><code>fields</code>: Tuple with optional fields; if not specified all will be loaded</li><li><code>phase</code>: Loads the phase information of LaMEM if true</li><li><code>surf</code>: Loads the free surface of LaMEM if true</li><li><code>passive_tracers</code>: Loads passive tracers if true</li><li><code>last</code>: Loads the last timestep</li></ul><p>Output:</p><ul><li><code>data</code>: Cartesian data struct with LaMEM output</li><li><code>time</code>: The time of the timestep</li></ul></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.IO_functions.changefolder-Tuple{}" href="#LaMEM.IO_functions.changefolder-Tuple{}"><code>LaMEM.IO_functions.changefolder</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">changefolder()</code></pre><p>Starts a GUI on Windowss or Mac machines, which allows you to change our working directory</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.IO_functions.clean_directory" href="#LaMEM.IO_functions.clean_directory"><code>LaMEM.IO_functions.clean_directory</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">clean_directory(DirName)</code></pre><p>Removes all LaMEM timesteps &amp; <code>*.pvd</code> files from the directory <code>DirName</code></p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="LaMEM.IO_functions.readPVD-Tuple{String}" href="#LaMEM.IO_functions.readPVD-Tuple{String}"><code>LaMEM.IO_functions.readPVD</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">FileNames, Time, Timestep = readPVD(FileName::String)</code></pre><p>This reads a PVD file &amp; returns the <code>FileNames</code>, <code>Time</code> and <code>Timesteps</code></p></div></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="readtimesteps.html">« Reading timesteps</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Friday 14 July 2023 12:46">Friday 14 July 2023</span>. Using Julia version 1.9.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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+<!DOCTYPE html>
+<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Reading timesteps · LaMEM.jl</title><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="../index.html">LaMEM.jl</a></span></div><form class="docs-search" action="../search.html"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../index.html">Home</a></li><li><a class="tocitem" href="installation.html">Installation</a></li><li><a class="tocitem" href="installation_HPC.html">Installation on HPC systems</a></li><li><span class="tocitem">Create LaMEM models in julia</span><ul><li><a class="tocitem" href="juliasetups.html">Overview</a></li><li><a class="tocitem" href="LaMEM_ModelFunctions.html">Grid</a></li></ul></li><li><a class="tocitem" href="runlamem.html">Run LaMEM</a></li><li class="is-active"><a class="tocitem" href="readtimesteps.html">Reading timesteps</a></li><li><a class="tocitem" href="listfunctions.html">List of functions</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href="readtimesteps.html">Reading timesteps</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="readtimesteps.html">Reading timesteps</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/JuliaGeodynamics/LaMEM.jl/blob/main/docs/src/man/readtimesteps.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="Read-timesteps-back-into-LaMEM"><a class="docs-heading-anchor" href="#Read-timesteps-back-into-LaMEM">Read timesteps back into LaMEM</a><a id="Read-timesteps-back-into-LaMEM-1"></a><a class="docs-heading-anchor-permalink" href="#Read-timesteps-back-into-LaMEM" title="Permalink"></a></h1><p>If you want to quantitatively do something with the results, there is an easy way to read the output of a LaMEM timestep back into julia. All routines related to that are part of the <code>LaMEM.IO</code> module.</p><pre><code class="language-julia hljs">julia&gt; using LaMEM</code></pre><p>You can first read the <code>*.pvd</code> file in the directory to see which timesteps are available:</p><pre><code class="language-julia hljs">julia&gt; FileName=&quot;FB_multigrid&quot;
+julia&gt; DirName =&quot;test&quot;
+julia&gt; Timestep, Filenames, Time = Read_LaMEM_simulation(FileName, DirName)
+([0, 1], [&quot;Timestep_00000000_0.00000000e+00/FB_multigrid.pvtr&quot;, &quot;Timestep_00000001_6.72970343e+00/FB_multigrid.pvtr&quot;], [0.0, 6.729703])</code></pre><p>We can read a particular timestep (say 1) with:</p><pre><code class="language-julia hljs">julia&gt; data, time = Read_LaMEM_timestep(FileName, 1, DirName)
+(CartData 
+    size    : (33, 33, 33)
+    x       ϵ [ 0.0 : 1.0]
+    y       ϵ [ 0.0 : 1.0]
+    z       ϵ [ 0.0 : 1.0]
+    fields  : (:phase, :visc_total, :visc_creep, :velocity, :pressure, :strain_rate, :j2_dev_stress, :j2_strain_rate)
+  attributes: [&quot;note&quot;]
+, [6.729703])</code></pre><p>The output is in a <code>CartData</code> structure (as defined in GeophysicalModelGenerator).</p><p>If you do not indicate a directory name (<code>DirName</code>) it&#39;ll look in your current directory. The default above will load the main LaMEM simulation output. Alternatively, you can also load the <code>phase</code> information by specify the optional keyword <code>phase=true</code>:</p><pre><code class="language-julia hljs">julia&gt; data, time = Read_LaMEM_timestep(FileName, 1, DirName, phase=true)
+(CartData 
+    size    : (96, 96, 96)
+    x       ϵ [ 0.0052083334885537624 : 0.9947916269302368]
+    y       ϵ [ 0.0052083334885537624 : 0.9947916269302368]
+    z       ϵ [ 0.0052083334885537624 : 0.9947916269302368]
+    fields  : (:phase,)
+  attributes: [&quot;note&quot;]
+, [6.729703])</code></pre><p>In the same way, you can load the internal free surface with <code>surf=true</code> (if that was saved), or passive tracers (<code>passive_tracers=true</code>). If you don&#39;t want to load all the fields in the file back to julia, you can check which fields are available:</p><pre><code class="language-julia hljs">julia&gt; Read_LaMEM_fieldnames(FileName, DirName)
+(&quot;phase [ ]&quot;, &quot;visc_total [ ]&quot;, &quot;visc_creep [ ]&quot;, &quot;velocity [ ]&quot;, &quot;pressure [ ]&quot;, &quot;strain_rate [ ]&quot;, &quot;j2_dev_stress [ ]&quot;, &quot;j2_strain_rate [ ]&quot;)</code></pre><p>and load only part of those:</p><pre><code class="language-julia hljs">julia&gt; data, time = Read_LaMEM_timestep(FileName, 1, DirName, fields=(&quot;phase [ ]&quot;, &quot;visc_total [ ]&quot;,&quot;velocity [ ]&quot;))
+(CartData 
+    size    : (33, 33, 33)
+    x       ϵ [ 0.0 : 1.0]
+    y       ϵ [ 0.0 : 1.0]
+    z       ϵ [ 0.0 : 1.0]
+    fields  : (:phase, :visc_total, :velocity)
+  attributes: [&quot;note&quot;]
+, [6.729703])</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="runlamem.html">« Run LaMEM</a><a class="docs-footer-nextpage" href="listfunctions.html">List of functions »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Friday 14 July 2023 12:46">Friday 14 July 2023</span>. Using Julia version 1.9.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
diff --git a/docs/build/man/runlamem.html b/docs/build/man/runlamem.html
new file mode 100644
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--- /dev/null
+++ b/docs/build/man/runlamem.html
@@ -0,0 +1,30 @@
+<!DOCTYPE html>
+<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Run LaMEM · LaMEM.jl</title><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="../index.html">LaMEM.jl</a></span></div><form class="docs-search" action="../search.html"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../index.html">Home</a></li><li><a class="tocitem" href="installation.html">Installation</a></li><li><a class="tocitem" href="installation_HPC.html">Installation on HPC systems</a></li><li><span class="tocitem">Create LaMEM models in julia</span><ul><li><a class="tocitem" href="juliasetups.html">Overview</a></li><li><a class="tocitem" href="LaMEM_ModelFunctions.html">Grid</a></li></ul></li><li class="is-active"><a class="tocitem" href="runlamem.html">Run LaMEM</a></li><li><a class="tocitem" href="readtimesteps.html">Reading timesteps</a></li><li><a class="tocitem" href="listfunctions.html">List of functions</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href="runlamem.html">Run LaMEM</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="runlamem.html">Run LaMEM</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/JuliaGeodynamics/LaMEM.jl/blob/main/docs/src/man/runlamem.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="Run-LaMEM"><a class="docs-heading-anchor" href="#Run-LaMEM">Run LaMEM</a><a id="Run-LaMEM-1"></a><a class="docs-heading-anchor-permalink" href="#Run-LaMEM" title="Permalink"></a></h1><p>Go to the package manager &amp; install it with:</p><pre><code class="language-julia hljs">julia&gt;]
+pkg&gt;add LaMEM</code></pre><p>It will automatically download a binary version of LaMEM which runs in parallel (along with the correct PETSc version). This will work on linux, mac and windows.</p><h3 id="Starting-a-simulation"><a class="docs-heading-anchor" href="#Starting-a-simulation">Starting a simulation</a><a id="Starting-a-simulation-1"></a><a class="docs-heading-anchor-permalink" href="#Starting-a-simulation" title="Permalink"></a></h3><p>If you have a LaMEM (<code>*.dat</code>) input file, you can run in parallel (here on 4 cores) with:</p><pre><code class="language-julia hljs">julia&gt; ParamFile=&quot;input_files/FallingBlock_Multigrid.dat&quot;;
+julia&gt; run_lamem(ParamFile, 4,&quot;-time_end 1&quot;)
+-------------------------------------------------------------------------- 
+                   Lithosphere and Mantle Evolution Model                   
+     Compiled: Date: Sep 10 2022 - Time: 06:21:30           
+-------------------------------------------------------------------------- 
+        STAGGERED-GRID FINITE DIFFERENCE CANONICAL IMPLEMENTATION           
+-------------------------------------------------------------------------- 
+Parsing input file : input_files/FallingBlock_Multigrid.dat 
+   Adding PETSc option: -snes_type ksponly
+   Adding PETSc option: -js_ksp_monitor
+   Adding PETSc option: -crs_pc_type bjacobi
+Finished parsing input file : input_files/FallingBlock_Multigrid.dat 
+--------------------------------------------------------------------------
+Time stepping parameters:
+   Simulation end time          : 1. [ ] 
+   Maximum number of steps      : 10 
+   Time step                    : 10. [ ] 
+   Minimum time step            : 1e-05 [ ] 
+   Maximum time step            : 100. [ ] 
+   Time step increase factor    : 0.1 
+   CFL criterion                : 0.5 
+   CFLMAX (fixed time steps)    : 0.5 
+   Output time step             : 0.2 [ ] 
+   Output every [n] steps       : 1 
+   Output [n] initial steps     : 1 
+--------------------------------------------------------------------------</code></pre><p>The last parameter are optional PETSc command-line options. By default it runs on one processor.</p><p>Please note that you will have to be in the correct directory or indicate where that directory is. If you are in a different directory, the easiest way to change to the correct one is by using the <code>changefolder</code> function (on Windows and Mac):</p><pre><code class="language-julia hljs">julia&gt; changefolder()</code></pre><p>Alternatively, you can use the build-in terminal/shell in julia, which you can access with:</p><pre><code class="language-julia hljs">julia&gt;;
+shell&gt;cd ~/LaMEM/input_models/BuildInSetups/</code></pre><p>use the Backspace key to return to the julia REPL.</p><p>Once you have performed a simulation, you can look at the results by opening the <code>*.pvd</code> files with Paraview. In this example, that would be <code>FB_multigrid.pvd</code> and <code>FB_multigrid_phase.pvd</code>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="LaMEM_ModelFunctions.html">« Grid</a><a class="docs-footer-nextpage" href="readtimesteps.html">Reading timesteps »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Friday 14 July 2023 12:46">Friday 14 July 2023</span>. Using Julia version 1.9.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
diff --git a/docs/build/search.html b/docs/build/search.html
new file mode 100644
index 0000000..f28217b
--- /dev/null
+++ b/docs/build/search.html
@@ -0,0 +1,2 @@
+<!DOCTYPE html>
+<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Search · LaMEM.jl</title><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="index.html">LaMEM.jl</a></span></div><form class="docs-search" action="search.html"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="index.html">Home</a></li><li><a class="tocitem" href="man/installation.html">Installation</a></li><li><a class="tocitem" href="man/installation_HPC.html">Installation on HPC systems</a></li><li><span class="tocitem">Create LaMEM models in julia</span><ul><li><a class="tocitem" href="man/juliasetups.html">Overview</a></li><li><a class="tocitem" href="man/LaMEM_ModelFunctions.html">Grid</a></li></ul></li><li><a class="tocitem" href="man/runlamem.html">Run LaMEM</a></li><li><a class="tocitem" href="man/readtimesteps.html">Reading timesteps</a></li><li><a class="tocitem" href="man/listfunctions.html">List of functions</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href="search.html">Search</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="search.html">Search</a></li></ul></nav><div class="docs-right"><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article><p id="documenter-search-info">Loading search...</p><ul id="documenter-search-results"></ul></article><nav class="docs-footer"><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Friday 14 July 2023 12:46">Friday 14 July 2023</span>. Using Julia version 1.9.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body><script src="search_index.js"></script><script src="assets/search.js"></script></html>
diff --git a/docs/build/search_index.js b/docs/build/search_index.js
new file mode 100644
index 0000000..084a426
--- /dev/null
+++ b/docs/build/search_index.js
@@ -0,0 +1,3 @@
+var documenterSearchIndex = {"docs":
+[{"location":"man/juliasetups.html#Create-and-run-setups-from-julia","page":"Overview","title":"Create & run setups from julia","text":"","category":"section"},{"location":"man/juliasetups.html","page":"Overview","title":"Overview","text":"It is also possible to construct a LaMEM setup directly in julia & run that. You can do the same from within a Pluto notebook. The advantage is that it is easier to use, has build-in plotting functions and extensive documentation. ","category":"page"},{"location":"man/readtimesteps.html#Read-timesteps-back-into-LaMEM","page":"Reading timesteps","title":"Read timesteps back into LaMEM","text":"","category":"section"},{"location":"man/readtimesteps.html","page":"Reading timesteps","title":"Reading timesteps","text":"If you want to quantitatively do something with the results, there is an easy way to read the output of a LaMEM timestep back into julia. All routines related to that are part of the LaMEM.IO module.","category":"page"},{"location":"man/readtimesteps.html","page":"Reading timesteps","title":"Reading timesteps","text":"julia> using LaMEM","category":"page"},{"location":"man/readtimesteps.html","page":"Reading timesteps","title":"Reading timesteps","text":"You can first read the *.pvd file in the directory to see which timesteps are available:","category":"page"},{"location":"man/readtimesteps.html","page":"Reading timesteps","title":"Reading timesteps","text":"julia> FileName=\"FB_multigrid\"\njulia> DirName =\"test\"\njulia> Timestep, Filenames, Time = Read_LaMEM_simulation(FileName, DirName)\n([0, 1], [\"Timestep_00000000_0.00000000e+00/FB_multigrid.pvtr\", \"Timestep_00000001_6.72970343e+00/FB_multigrid.pvtr\"], [0.0, 6.729703])","category":"page"},{"location":"man/readtimesteps.html","page":"Reading timesteps","title":"Reading timesteps","text":"We can read a particular timestep (say 1) with:","category":"page"},{"location":"man/readtimesteps.html","page":"Reading timesteps","title":"Reading timesteps","text":"julia> data, time = Read_LaMEM_timestep(FileName, 1, DirName)\n(CartData \n    size    : (33, 33, 33)\n    x       ϵ [ 0.0 : 1.0]\n    y       ϵ [ 0.0 : 1.0]\n    z       ϵ [ 0.0 : 1.0]\n    fields  : (:phase, :visc_total, :visc_creep, :velocity, :pressure, :strain_rate, :j2_dev_stress, :j2_strain_rate)\n  attributes: [\"note\"]\n, [6.729703])","category":"page"},{"location":"man/readtimesteps.html","page":"Reading timesteps","title":"Reading timesteps","text":"The output is in a CartData structure (as defined in GeophysicalModelGenerator).","category":"page"},{"location":"man/readtimesteps.html","page":"Reading timesteps","title":"Reading timesteps","text":"If you do not indicate a directory name (DirName) it'll look in your current directory. The default above will load the main LaMEM simulation output. Alternatively, you can also load the phase information by specify the optional keyword phase=true:","category":"page"},{"location":"man/readtimesteps.html","page":"Reading timesteps","title":"Reading timesteps","text":"julia> data, time = Read_LaMEM_timestep(FileName, 1, DirName, phase=true)\n(CartData \n    size    : (96, 96, 96)\n    x       ϵ [ 0.0052083334885537624 : 0.9947916269302368]\n    y       ϵ [ 0.0052083334885537624 : 0.9947916269302368]\n    z       ϵ [ 0.0052083334885537624 : 0.9947916269302368]\n    fields  : (:phase,)\n  attributes: [\"note\"]\n, [6.729703])","category":"page"},{"location":"man/readtimesteps.html","page":"Reading timesteps","title":"Reading timesteps","text":"In the same way, you can load the internal free surface with surf=true (if that was saved), or passive tracers (passive_tracers=true). If you don't want to load all the fields in the file back to julia, you can check which fields are available:","category":"page"},{"location":"man/readtimesteps.html","page":"Reading timesteps","title":"Reading timesteps","text":"julia> Read_LaMEM_fieldnames(FileName, DirName)\n(\"phase [ ]\", \"visc_total [ ]\", \"visc_creep [ ]\", \"velocity [ ]\", \"pressure [ ]\", \"strain_rate [ ]\", \"j2_dev_stress [ ]\", \"j2_strain_rate [ ]\")","category":"page"},{"location":"man/readtimesteps.html","page":"Reading timesteps","title":"Reading timesteps","text":"and load only part of those:","category":"page"},{"location":"man/readtimesteps.html","page":"Reading timesteps","title":"Reading timesteps","text":"julia> data, time = Read_LaMEM_timestep(FileName, 1, DirName, fields=(\"phase [ ]\", \"visc_total [ ]\",\"velocity [ ]\"))\n(CartData \n    size    : (33, 33, 33)\n    x       ϵ [ 0.0 : 1.0]\n    y       ϵ [ 0.0 : 1.0]\n    z       ϵ [ 0.0 : 1.0]\n    fields  : (:phase, :visc_total, :velocity)\n  attributes: [\"note\"]\n, [6.729703])","category":"page"},{"location":"man/runlamem.html#Run-LaMEM","page":"Run LaMEM","title":"Run LaMEM","text":"","category":"section"},{"location":"man/runlamem.html","page":"Run LaMEM","title":"Run LaMEM","text":"Go to the package manager & install it with:","category":"page"},{"location":"man/runlamem.html","page":"Run LaMEM","title":"Run LaMEM","text":"julia>]\npkg>add LaMEM","category":"page"},{"location":"man/runlamem.html","page":"Run LaMEM","title":"Run LaMEM","text":"It will automatically download a binary version of LaMEM which runs in parallel (along with the correct PETSc version). This will work on linux, mac and windows.","category":"page"},{"location":"man/runlamem.html#Starting-a-simulation","page":"Run LaMEM","title":"Starting a simulation","text":"","category":"section"},{"location":"man/runlamem.html","page":"Run LaMEM","title":"Run LaMEM","text":"If you have a LaMEM (*.dat) input file, you can run in parallel (here on 4 cores) with:","category":"page"},{"location":"man/runlamem.html","page":"Run LaMEM","title":"Run LaMEM","text":"julia> ParamFile=\"input_files/FallingBlock_Multigrid.dat\";\njulia> run_lamem(ParamFile, 4,\"-time_end 1\")\n-------------------------------------------------------------------------- \n                   Lithosphere and Mantle Evolution Model                   \n     Compiled: Date: Sep 10 2022 - Time: 06:21:30           \n-------------------------------------------------------------------------- \n        STAGGERED-GRID FINITE DIFFERENCE CANONICAL IMPLEMENTATION           \n-------------------------------------------------------------------------- \nParsing input file : input_files/FallingBlock_Multigrid.dat \n   Adding PETSc option: -snes_type ksponly\n   Adding PETSc option: -js_ksp_monitor\n   Adding PETSc option: -crs_pc_type bjacobi\nFinished parsing input file : input_files/FallingBlock_Multigrid.dat \n--------------------------------------------------------------------------\nTime stepping parameters:\n   Simulation end time          : 1. [ ] \n   Maximum number of steps      : 10 \n   Time step                    : 10. [ ] \n   Minimum time step            : 1e-05 [ ] \n   Maximum time step            : 100. [ ] \n   Time step increase factor    : 0.1 \n   CFL criterion                : 0.5 \n   CFLMAX (fixed time steps)    : 0.5 \n   Output time step             : 0.2 [ ] \n   Output every [n] steps       : 1 \n   Output [n] initial steps     : 1 \n--------------------------------------------------------------------------","category":"page"},{"location":"man/runlamem.html","page":"Run LaMEM","title":"Run LaMEM","text":"The last parameter are optional PETSc command-line options. By default it runs on one processor.","category":"page"},{"location":"man/runlamem.html","page":"Run LaMEM","title":"Run LaMEM","text":"Please note that you will have to be in the correct directory or indicate where that directory is. If you are in a different directory, the easiest way to change to the correct one is by using the changefolder function (on Windows and Mac):","category":"page"},{"location":"man/runlamem.html","page":"Run LaMEM","title":"Run LaMEM","text":"julia> changefolder()","category":"page"},{"location":"man/runlamem.html","page":"Run LaMEM","title":"Run LaMEM","text":"Alternatively, you can use the build-in terminal/shell in julia, which you can access with:","category":"page"},{"location":"man/runlamem.html","page":"Run LaMEM","title":"Run LaMEM","text":"julia>;\nshell>cd ~/LaMEM/input_models/BuildInSetups/","category":"page"},{"location":"man/runlamem.html","page":"Run LaMEM","title":"Run LaMEM","text":"use the Backspace key to return to the julia REPL.","category":"page"},{"location":"man/runlamem.html","page":"Run LaMEM","title":"Run LaMEM","text":"Once you have performed a simulation, you can look at the results by opening the *.pvd files with Paraview. In this example, that would be FB_multigrid.pvd and FB_multigrid_phase.pvd.","category":"page"},{"location":"man/listfunctions.html#List-of-all-functions","page":"List of functions","title":"List of all functions","text":"","category":"section"},{"location":"man/listfunctions.html","page":"List of functions","title":"List of functions","text":"These are all functions that are available in the package, which can roughly be divided into two groups (running & reading LaMEM)","category":"page"},{"location":"man/listfunctions.html#Running-LaMEM","page":"List of functions","title":"Running LaMEM","text":"","category":"section"},{"location":"man/listfunctions.html","page":"List of functions","title":"List of functions","text":"Modules = [LaMEM.Run]\n","category":"page"},{"location":"man/listfunctions.html#LaMEM.Run.remove_popup_messages_mac-Tuple{}","page":"List of functions","title":"LaMEM.Run.remove_popup_messages_mac","text":"remove_popup_messages_mac()\n\nOn a Mac with firewall enabled, running LaMEM will result in a popup window that says: \"Accept incoming connections\" which you should Allow or Deny. This is a bit annoying, so this julia script fixes that. Note that you must have administrator rights on your machine as we need to run \"sudo\"\n\nRun this script from the terminal with\n\njulia> remove_popup_messages_mac()\n\nYou need to do this once (every time a new version is installed)\n\n\n\n\n\n","category":"method"},{"location":"man/listfunctions.html#LaMEM.Run.run_lamem","page":"List of functions","title":"LaMEM.Run.run_lamem","text":"run_lamem(ParamFile::String, cores::Int64=1, args:String=\"\"; wait=true)\n\nThis starts a LaMEM simulation, for using the parameter file ParamFile on cores number of cores.  Optional additional command-line parameters can be specified with args.\n\nExample:\n\nYou can call LaMEM with:\n\njulia> using LaMEM\njulia> ParamFile=\"../../input_models/BuildInSetups/FallingBlock_Multigrid.dat\";\njulia> run_lamem(ParamFile)\n\nDo the same on 2 cores with a command-line argument as:\n\njulia> ParamFile=\"../../input_models/BuildInSetups/FallingBlock_Multigrid.dat\";\njulia> run_lamem(ParamFile, 2, \"-nstep_max = 1\")\n\n\n\n\n\n","category":"function"},{"location":"man/listfunctions.html#LaMEM.Run.run_lamem_save_grid","page":"List of functions","title":"LaMEM.Run.run_lamem_save_grid","text":"ProcessorPartFile = run_lamem_save_grid(ParamFile::String, cores::Int64=1; verbose=true)\n\nThis calls LaMEM simulation, for using the parameter file ParamFile  and creates processor partitioning file \"ProcessorPartitioningcorescpuX.Y.Z.bin\" for cores number of cores. \n\nExample:\n\njulia> using LaMEM\njulia> ParamFile=\"../../input_models/BuildInSetups/FallingBlock_Multigrid.dat\";\njulia> ProcessorPartFile = run_lamem_save_grid(ParamFile, 2)\n\n\n\n\n\n","category":"function"},{"location":"man/listfunctions.html#LaMEM.Run.show_paths_LaMEM-Tuple{}","page":"List of functions","title":"LaMEM.Run.show_paths_LaMEM","text":"show_paths_LaMEM()\n\nThe downloaded LaMEM binaries can also be called from outside julia (directly from the terminal).  In that case, you will need to set load correct dynamic libraries (such as PETSc) and call the correct binaries.\n\nThis function shows this for your system. \n\n\n\n\n\n","category":"method"},{"location":"man/listfunctions.html#Reading-LaMEM-output-back-into-julia","page":"List of functions","title":"Reading LaMEM output back into julia","text":"","category":"section"},{"location":"man/listfunctions.html","page":"List of functions","title":"List of functions","text":"Modules = [LaMEM.IO_functions]","category":"page"},{"location":"man/listfunctions.html#LaMEM.IO_functions.ReadField_3D_pVTR-Tuple{Any, Any}","page":"List of functions","title":"LaMEM.IO_functions.ReadField_3D_pVTR","text":"output, isCell = ReadField_3D_pVTR(data, FieldName::String)\n\nExtracts a 3D data field from a pVTR data structure data\n\nInput:\n\ndata:       Data structure obtained with ReadVTRFile\nFieldName:  Exact name of the field as specified in the *.vtr file\n\nOutput:\n\ndata_field, isCell:   3D field with data, and a flag that indicates whether it is Cell data (PointData otherwise)                              data_field is a tuple of size 1, or 3 depending on whether it is a scalar or vector field\n\n\n\n\n\n","category":"method"},{"location":"man/listfunctions.html#LaMEM.IO_functions.ReadField_3D_pVTU-Tuple{Any, Any}","page":"List of functions","title":"LaMEM.IO_functions.ReadField_3D_pVTU","text":"output, isCell = ReadField_3D_pVTU(data, FieldName::String)\n\nExtracts a 3D data field from a pVTU data structure data Input:\n\ndata:       Data structure obtained with ReadVTRFile\nFieldName:  Exact name of the field as specified in the *.vtr file\n\nOutput:\n\ndata_field: Array with data, data_field is a tuple of size 1, 3 or 9 depending on whether it is a scalar, vector or tensor field\n\n\n\n\n\n","category":"method"},{"location":"man/listfunctions.html#LaMEM.IO_functions.Read_LaMEM_PVTR_File-Tuple{String, String}","page":"List of functions","title":"LaMEM.IO_functions.Read_LaMEM_PVTR_File","text":"data_output = Read_LaMEM_PVTR_File(DirName, FileName; fields=nothing)\n\nReads a 3D LaMEM timestep from VTR file FileName, located in directory DirName.  By default, it will read all fields. If you want you can only read a specific field. See the function fieldnames to get a list with all available fields in the file.\n\nIt will return data_output which is a CartData output structure.\n\n\n\n\n\n","category":"method"},{"location":"man/listfunctions.html#LaMEM.IO_functions.Read_LaMEM_PVTS_File-Tuple{String, String}","page":"List of functions","title":"LaMEM.IO_functions.Read_LaMEM_PVTS_File","text":"data_output = Read_LaMEM_PVTS_File(DirName, FileName; field=nothing)\n\nReads a 3D LaMEM timestep from VTS file FileName, located in directory DirName. Typically this is done to read passive tracers back into julia.  By default, it will read all fields. If you want you can only read a specific field. See the function fieldnames to get a list with all available fields in the file.\n\nIt will return data_output which is a CartData output structure.\n\n\n\n\n\n","category":"method"},{"location":"man/listfunctions.html#LaMEM.IO_functions.Read_LaMEM_PVTU_File-Tuple{Any, Any}","page":"List of functions","title":"LaMEM.IO_functions.Read_LaMEM_PVTU_File","text":"data_output = Read_LaMEM_PVTU_File(DirName, FileName; fields=nothing)\n\nReads a 3D LaMEM timestep from VTU file FileName, located in directory DirName. Typically this is done to read passive tracers back into julia.  By default, it will read all fields. If you want you can only read a specific field. See the function fieldnames to get a list with all available fields in the file.\n\nIt will return data_output which is a CartData output structure.\n\n\n\n\n\n","category":"method"},{"location":"man/listfunctions.html#LaMEM.IO_functions.Read_LaMEM_fieldnames","page":"List of functions","title":"LaMEM.IO_functions.Read_LaMEM_fieldnames","text":"Read_LaMEM_fieldnames(FileName::String, DirName_base::String=\"\"; phase=false, surf=false, tracers=false)\n\nReturns the names of the datasets stored in FileName\n\n\n\n\n\n","category":"function"},{"location":"man/listfunctions.html#LaMEM.IO_functions.Read_LaMEM_simulation","page":"List of functions","title":"LaMEM.IO_functions.Read_LaMEM_simulation","text":"Timestep, FileNames, Time = Read_LaMEM_simulation(FileName::String, DirName::String=\"\"; phase=false, surf=false, passive_tracers=false)\n\nReads a LaMEM simulation FileName in directory DirName and returns the timesteps, times and filenames of that simulation.\n\n\n\n\n\n","category":"function"},{"location":"man/listfunctions.html#LaMEM.IO_functions.Read_LaMEM_timestep","page":"List of functions","title":"LaMEM.IO_functions.Read_LaMEM_timestep","text":"data, time = Read_LaMEM_timestep(FileName::String, TimeStep::Int64=0, DirName::String=\"\"; fields=nothing, phase=false, surf=false, last=false)\n\nThis reads a LaMEM timestep.\n\nInput Arguments:\n\nFileName: name of the simulation, w/out extension\nTimestep: timestep to be read, unless last=true in which case we read the last one\nDirName: name of the main directory (i.e. where the *.pvd files are located)\nfields: Tuple with optional fields; if not specified all will be loaded\nphase: Loads the phase information of LaMEM if true\nsurf: Loads the free surface of LaMEM if true\npassive_tracers: Loads passive tracers if true\nlast: Loads the last timestep\n\nOutput:\n\ndata: Cartesian data struct with LaMEM output\ntime: The time of the timestep\n\n\n\n\n\n","category":"function"},{"location":"man/listfunctions.html#LaMEM.IO_functions.changefolder-Tuple{}","page":"List of functions","title":"LaMEM.IO_functions.changefolder","text":"changefolder()\n\nStarts a GUI on Windowss or Mac machines, which allows you to change our working directory\n\n\n\n\n\n","category":"method"},{"location":"man/listfunctions.html#LaMEM.IO_functions.clean_directory","page":"List of functions","title":"LaMEM.IO_functions.clean_directory","text":"clean_directory(DirName)\n\nRemoves all LaMEM timesteps & *.pvd files from the directory DirName\n\n\n\n\n\n","category":"function"},{"location":"man/listfunctions.html#LaMEM.IO_functions.readPVD-Tuple{String}","page":"List of functions","title":"LaMEM.IO_functions.readPVD","text":"FileNames, Time, Timestep = readPVD(FileName::String)\n\nThis reads a PVD file & returns the FileNames, Time and Timesteps\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#List-functions","page":"Grid","title":"List functions","text":"","category":"section"},{"location":"man/LaMEM_ModelFunctions.html","page":"Grid","title":"Grid","text":"These are all the functions that are provided for the LaMEM Julia Setup interface ","category":"page"},{"location":"man/LaMEM_ModelFunctions.html","page":"Grid","title":"Grid","text":"Modules = [LaMEM.LaMEM_Model]","category":"page"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.BoundaryConditions","page":"Grid","title":"LaMEM.LaMEM_Model.BoundaryConditions","text":"Structure that contains the LaMEM boundary conditions information.\n\nnoslip::Vector{Int64}: No-slip boundary flag mask (left right front back bottom top)\nopen_top_bound::Int64: Stress-free (free surface/infinitely fast erosion) top boundary flag\ntemp_top::Float64: Constant temperature on the top boundary\ntemp_bot::Float64: Constant temperature on the bottom boundary\nexx_num_periods::Int64: number intervals of constant background strain rate (x-axis)\nexx_time_delims::Vector{Float64}: time delimiters (one less than number of intervals, not required for one interval)\nexx_strain_rates::Vector{Float64}: strain rates for each interval\neyy_num_periods::Int64\neyy_time_delims::Vector{Float64}\neyy_strain_rates::Vector{Float64}\nexy_num_periods::Int64\nexy_time_delims::Vector{Float64}\nexy_strain_rates::Vector{Float64}\nexz_num_periods::Int64\nexz_time_delims::Vector{Float64}\nexz_strain_rates::Vector{Float64}\neyz_num_periods::Int64\neyz_time_delims::Vector{Float64}\neyz_strain_rates::Vector{Float64}\nbg_ref_point::Vector{Float64}: background strain rate reference point (fixed)\n\n\n\n\n\n","category":"type"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Dike","page":"Grid","title":"LaMEM.LaMEM_Model.Dike","text":"Defines the properties related to inserting dikes\n\nID::Int64: Material phase ID\nMf::Float64: value for dike/magma- accommodated extension, between 0 and 1, in the front of the box, for phase dike\nMc::Float64: [optional] value for dike/magma- accommodate extension, between 0 and 1, for dike phase; M is linearly interpolated between Mf & Mc and Mc & Mb, if not set, Mc default is set to -1 so it is not used\ny_Mc::Union{Nothing, Float64}: [optional], location for Mc, must be between front and back boundaries of dike box, if not set, default value to 0.0, but not used\nMb::Union{Nothing, Float64}: value for dike/magma-accommodated extension, between 0 and 1, in the back of the box, for phase dike\nPhaseID::Union{Nothing, Int64}: Phase ID\nPhaseTransID::Union{Nothing, Int64}: Phase transition ID\n\n\n\n\n\n","category":"type"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.FreeSurface","page":"Grid","title":"LaMEM.LaMEM_Model.FreeSurface","text":"Structure that contains the LaMEM free surface information.\n\nsurf_use::Int64: Free surface activation flag\nsurf_corr_phase::Int64: air phase ratio correction flag (phases in an element that contains are modified based on the surface position)\nsurf_level::Float64: initial level of the free surface\nsurf_air_phase::Int64: phase ID of sticky air layer\nsurf_max_angle::Float64: maximum angle with horizon (smoothed if larger)\nsurf_topo_file::String: initial topography file (redundant)\nerosion_model::Int64: erosion model [0-none (default), 1-infinitely fast, 2-prescribed rate with given level]\ner_num_phases::Int64: number of erosion phases\ner_time_delims::Vector{Float64}: erosion time delimiters (one less than number)\ner_rates::Vector{Float64}: constant erosion rates in different time periods\ner_levels::Vector{Int64}: levels above which we apply constant erosion rates in different time periods\nsediment_model::Int64: sedimentation model [0-none (dafault), 1-prescribed rate with given level, 2-cont. margin]\nsed_num_layers::Int64: number of sediment layers\nsed_time_delims::Vector{Float64}: sediment layers time delimiters (one less than number)\nsed_rates::Vector{Float64}: sediment rates in different time periods\nsed_levels::Vector{Float64}: levels below which we apply constant sediment rates in different time periods\nsed_phases::Vector{Int64}: sediment layers phase numbers in different time periods\nmarginO::Vector{Float64}: lateral coordinates of continental margin - origin\nmarginE::Vector{Float64}: lateral coordinates of continental margin - 2nd point\nhUp::Float64: up dip thickness of sediment cover (onshore)\nhDown::Float64: down dip thickness of sediment cover (off shore)\ndTrans::Float64: half of transition zone\n\n\n\n\n\n","category":"type"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Grid","page":"Grid","title":"LaMEM.LaMEM_Model.Grid","text":"Structure that contains the LaMEM grid information\n\nnmark_x::Int64: number of markers/element in x-direction\nnmark_y::Int64: number of markers/element in y-direction\nnmark_z::Int64: number of markers/element in x-direction\nnel_x::Vector{Int64}: number of elements in x-direction\nnel_y::Vector{Int64}: number of elements in y-direction\nnel_z::Vector{Int64}: number of elements in z-direction\ncoord_x::Vector{Float64}: coordinates in x-direction\ncoord_y::Vector{Float64}: coordinates in y-direction\ncoord_z::Vector{Float64}: coordinates in z-direction\nnseg_x::Int64: number of segments in x-direction (if we employ variable grid spacing in x-direction)\nnseg_y::Int64: number of segments in y-direction (if we employ variable grid spacing in y-direction)\nnseg_z::Int64: number of segments in z-direction (if we employ variable grid spacing in z-direction)\nbias_x::Vector{Float64}: bias in x-direction (if we employ variable grid spacing in x-direction)\nbias_y::Vector{Float64}: bias in y-direction (if we employ variable grid spacing in y-direction)\nbias_z::Vector{Float64}: bias in z-direction (if we employ variable grid spacing in z-direction)\nGrid::GeophysicalModelGenerator.LaMEM_grid: Contains the LaMEM Grid object\nPhases::Array{Int32}: Phases; 3D phase information\nTemp::Array{Float64}: Temp; 3D phase information\n\nExample 1\n\njulia> d=LaMEM.Grid(coord_x=[0.0, 0.7, 0.8, 1.0], bias_x=[0.3,1.0,3.0], nel_x=[10,4,2])\nLaMEM grid with 1D refinement: \n  nel         : ([10, 4, 2], [16], [16])\n  marker/cell : (3, 3, 3)\n  x           ϵ [0.0, 0.7, 0.8, 1.0], bias=[0.3, 1.0, 3.0], nseg=3, Δmin=0.025000000000000022, Δmax=0.1499999999999999\n  y           ϵ [-10.0 : 0.0]\n  z           ϵ [-10.0 : 0.0]\n\nExample 2\n\njulia> d=LaMEM.Grid(nel=(10,20))\nLaMEM grid with constant Δ: \n  nel         : ([10], [1], [20])\n  marker/cell : (3, 3, 3)\n  x           ϵ [-10.0 : 10.0]\n  y           ϵ [-10.0 : 0.0]\n  z           ϵ [-10.0 : 0.0]\n\n\n\n\n\n","category":"type"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Materials","page":"Grid","title":"LaMEM.LaMEM_Model.Materials","text":"Structure that contains the material properties in the current simulation\n\nPhases::Vector{Phase}: Different Materials implemented\nSofteningLaws::Vector{Softening}: Softening laws implemented\nPhaseTransitions::Vector{PhaseTransition}: Internal Phase Transitions (that change the ID of markers) implemented\nDikes::Vector{Dike}: Dikes implemented (mostly for MOR simulations)\n\n\n\n\n\n","category":"type"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Model","page":"Grid","title":"LaMEM.LaMEM_Model.Model","text":";     Model\n\nStructure that holds all the information to create a LaMEM input file\n\nScaling::Scaling: Scaling parameters\nGrid::Grid: LaMEM Grid\nTime::Any: Time options\nFreeSurface::Any: Free surface options\nBoundaryConditions::Any: Boundary conditions\nSolutionParams::Any: Global solution parameters\nSolver::Any: Solver options and optional PETSc options\nModelSetup::Any: Model setup\nOutput::Any: Output options\nMaterials::Any: Material parameters for each of the phases\n\n\n\n\n\n","category":"type"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Model-Tuple","page":"Grid","title":"LaMEM.LaMEM_Model.Model","text":"Model(args...)\n\nAllow to define a model setup by specifying some of the basic objects\n\nExample\n\njulia> d = Model(Grid(nel=(10,1,20)), Scaling(NO_units()))\nLaMEM Model setup\n|\n|-- Scaling             :  GeoParams.Units.GeoUnits{GeoParams.Units.NONE}\n|-- Grid                :  nel=(10, 1, 20); xϵ(-10.0, 10.0), yϵ(-10.0, 0.0), zϵ(-10.0, 0.0) \n|-- Time                :  nstep_max=50; nstep_out=1; time_end=1.0; dt=0.05\n|-- Boundary conditions :  noslip=[0, 0, 0, 0, 0, 0]\n|-- Solution parameters :  \n|-- Solver options      :  direct solver; superlu_dist; penalty term=10000.0\n|-- Model setup options :  Type=geom; \n|-- Output options      :  filename=output; pvd=1; avd=0; surf=0\n|-- Materials           :  1 phases;  \n\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Model-Tuple{}","page":"Grid","title":"LaMEM.LaMEM_Model.Model","text":"Model(;\n    Scaling=Scaling(GEO_units()),\n    Grid=Grid(), \n    Time=Time(),\n    FreeSurface=FreeSurface(),\n    BoundaryConditions=BoundaryConditions(),\n    SolutionParams=SolutionParams(),\n    Solver=Solver(),\n    ModelSetup=ModelSetup(),\n    Output=Output(),\n    Materials=Materials()\n    )\n\nCreates a LaMEM Model setup.\n\nScaling::Scaling\nGrid::Grid\nTime::Any\nFreeSurface::Any\nBoundaryConditions::Any\nSolutionParams::Any\nSolver::Any\nModelSetup::Any\nOutput::Any\nMaterials::Any\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.ModelSetup","page":"Grid","title":"LaMEM.LaMEM_Model.ModelSetup","text":"Structure that contains the LaMEM Model Setup and Advection options\n\nmsetup::String: Setup type - can be geom (phases are assigned from geometric primitives), files (from julia input), polygons (from geomIO input, which requires poly_file to be specified)\nrand_noise::Int64: add random noise to the particle location\nrand_noiseGP::Int64: random noise flag, subsequently applied to geometric primitives\nbg_phase::Int64: background phase ID\nsave_mark::Int64: save marker to disk flag\nmark_load_file::String: marker input file (extension is .xxxxxxxx.dat), if using msetup=files\nmark_save_file::String: marker output file (extension is .xxxxxxxx.dat)\npoly_file::String: polygon geometry file (redundant), if using msetup=polygons\ntemp_file::String: initial temperature file (redundant), if not set on markers\nadvect::String: advection scheme; options=none (no advection); basic (Euler classical implementation [default]); Euler (Euler explicit in time); rk2 (Runge-Kutta 2nd order in space)\ninterp::String: velocity interpolation scheme; options = stag (trilinear interpolation from FDSTAG points), minmod ( MINMOD interpolation to nodes, trilinear interpolation to markers + correction), stagp ( STAG_P empirical approach by T. Gerya)\nstagp_a::Float64: STAG_P velocity interpolation parameter\nmark_ctrl::String: marker control type; options are subgrid (default; marker control enforced over fine scale grid), none (none), basic (AVD for cells + corner insertion), and avd (pure AVD for all control volumes)\nnmark_lim::Vector{Int64}: min/max number per cell (marker control)\nnmark_avd::Vector{Int64}: x-y-z AVD refinement factors (avd marker control)\nnmark_sub::Int64: max number of same phase markers per subcell (subgrid marker control)\ngeom_primitives::Vector: Different geometric primitives that can be selected if we msetup=geom; seegeom_Sphere`\n\n\n\n\n\n","category":"type"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Output","page":"Grid","title":"LaMEM.LaMEM_Model.Output","text":"Structure that contains the LaMEM output options\n\nout_file_name::Any: output file name\nout_dir::Any: output directory\nparam_file_name::Any: parameter filename\nwrite_VTK_setup::Any: write VTK initial model setup\nout_pvd::Any: activate writing .pvd file\nout_phase::Any: dominant phase\nout_density::Any: density\nout_visc_total::Any: total (viscoelastoplastic) viscosity\nout_visc_creep::Any: creep viscosity\nout_velocity::Any: velocity\nout_pressure::Any: (dynamic) pressure\nout_tot_press::Any: total pressure\nout_eff_press::Any: effective pressure\nout_over_press::Any\nout_litho_press::Any\nout_pore_press::Any\nout_temperature::Any: temperature\nout_dev_stress::Any: deviatoric strain rate tensor\nout_j2_dev_stress::Any: second invariant of deviatoric stress tensor\nout_strain_rate::Any: deviatoric strain rate tensor\nout_j2_strain_rate::Any: second invariant of strain rate tensor\nout_shmax::Any\nout_ehmax::Any\nout_yield::Any\nout_rel_dif_rate::Any: relative proportion of diffusion creep strainrate\nout_rel_dis_rate::Any: relative proportion of dislocation creep strainrate\nout_rel_prl_rate::Any: relative proportion of peierls creep strainrate\nout_rel_pl_rate::Any: relative proportion of plastic strainrate\nout_plast_strain::Any: accumulated plastic strain\nout_plast_dissip::Any: plastic dissipation\nout_tot_displ::Any\nout_moment_res::Any\nout_cont_res::Any\nout_energ_res::Any\nout_melt_fraction::Any\nout_fluid_density::Any\nout_conductivity::Any\nout_vel_gr_tensor::Any\nout_surf::Any: activate surface output\nout_surf_pvd::Any: activate writing .pvd file\nout_surf_velocity::Any: surface velocity\nout_surf_topography::Any: surface topography\nout_surf_amplitude::Any: amplitude of topography (=topo-average(topo))\nout_mark::Any: activate marker output\nout_mark_pvd::Any: activate writing .pvd file\nout_avd::Any: activate AVD phase output\nout_avd_pvd::Any: activate writing .pvd file\nout_avd_ref::Any: AVD grid refinement factor\nout_ptr::Any: activate\nout_ptr_ID::Any: ID of the passive tracers\nout_ptr_phase::Any: phase of the passive tracers\nout_ptr_Pressure::Any: interpolated pressure\nout_ptr_Temperature::Any: temperature\nout_ptr_MeltFraction::Any: melt fraction computed using P-T of the marker\nout_ptr_Active::Any: option that highlight the marker that are currently active\nout_ptr_Grid_Mf::Any: option that allow to store the melt fraction seen within the cell\n\n\n\n\n\n","category":"type"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Phase","page":"Grid","title":"LaMEM.LaMEM_Model.Phase","text":"Defines the material properties for each of the phases\n\nID::Union{Nothing, Int64}: Material phase ID\nName::Union{Nothing, String}: Description of the phase\nrho::Union{Nothing, Float64}: Density [kg/m^3]\neta::Union{Nothing, Float64}: Linear viscosity [Pas]\nvisID::Union{Nothing, Int64}: material ID for phase visualization (default is ID)\ndiff_prof::Union{Nothing, String}: DIFFUSION creep profile; example: \"DryOlivinediffcreep-HirthKohlstedt_2003\"\ndisl_prof::Union{Nothing, String}: DISLOCATION creep profile; example: \"Granite-Tireletal_2008\"\npeir_prof::Union{Nothing, String}: PEIERLS creep profile; example:  \"OlivinePeierls-Kameyama1999\"\nrho_n::Union{Nothing, Float64}: depth-dependent density model parameter\nrho_c::Union{Nothing, Float64}: depth-dependent density model parameter\nbeta::Union{Nothing, Float64}: pressure-dependent density model parameter\nG::Union{Nothing, Float64}: shear modulus\nKb::Union{Nothing, Float64}: bulk modulus\nE::Union{Nothing, Float64}: Young's modulus\nnu::Union{Nothing, Float64}: Poisson's ratio\nKp::Union{Nothing, Float64}: pressure dependence parameter\nBd::Union{Nothing, Float64}: DIFFUSION creep pre-exponential constant\nEd::Union{Nothing, Float64}: activation energy\nVd::Union{Nothing, Float64}: activation volume\neta0::Union{Nothing, Float64}: POWER LAW reference viscosity\ne0::Union{Nothing, Float64}: reference strain rate\nBn::Union{Nothing, Float64}: DISLOCATION creep pre-exponential constant\nEn::Union{Nothing, Float64}: activation energy\nVn::Union{Nothing, Float64}: activation volume\nn::Union{Nothing, Float64}: power law exponent\nBp::Union{Nothing, Float64}: PEIERLS creep pre-exponential constant\nEp::Union{Nothing, Float64}: activation energy\nVp::Union{Nothing, Float64}: activation volume\ntaup::Union{Nothing, Float64}: scaling stress\ngamma::Union{Nothing, Float64}: approximation parameter\nq::Union{Nothing, Float64}: stress-dependence parameter\neta_fk::Union{Nothing, Float64}: reference viscosity for Frank-Kamenetzky viscosity\ngamma_fk::Union{Nothing, Float64}: gamma parameter for Frank-Kamenetzky viscosity\nTRef_fk::Union{Nothing, Float64}: reference Temperature for Frank-Kamenetzky viscosity (if not set it is 0°C)\nch::Union{Nothing, Float64}: cohesion\nfr::Union{Nothing, Float64}: friction angle\neta_st::Union{Nothing, Float64}: stabilization viscosity (default is eta_min)\nrp::Union{Nothing, Float64}: pore-pressure ratio\nchSoftID::Union{Nothing, Int64}: friction softening law ID\nfrSoftID::Union{Nothing, Int64}: cohesion softening law ID\nhealID::Union{Nothing, Int64}: healing ID, points to healTau in Softening\nalpha::Union{Nothing, Float64}: thermal expansivity\nCp::Union{Nothing, Float64}: specific heat (capacity), J⋅K−1⋅kg−1\nk::Union{Nothing, Float64}: thermal conductivity\nA::Union{Nothing, Float64}: radiogenic heat production\nT::Union{Nothing, Float64}: optional temperature to set within the phase\nLatent_hx::Union{Nothing, Float64}: optional, used for dike heating, J/kg\nT_liq::Union{Nothing, Float64}: optional, used for dike heating, liquidus temperature of material, celsius\nT_sol::Union{Nothing, Float64}: optional, used for dike heating, solidus temperature of material, celsius\nT_Nu::Union{Nothing, Float64}: default value for thermal conductivity boundary\nnu_k::Union{Nothing, Float64}: optional parameter, Nusselt number for use with conductivity\nrho_ph::Union{Nothing, String}: name of the phase diagram you want to use (still needs rho to be defined for the initial guess of pressure)\nrho_ph_dir::Union{Nothing, String}: in case the phase diagram has a different path provide the path (without the name of the actual PD) here\nmfc::Union{Nothing, Float64}: melt fraction viscosity correction factor (positive scalar)\n\n\n\n\n\n","category":"type"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.PhaseTransition","page":"Grid","title":"LaMEM.LaMEM_Model.PhaseTransition","text":"Defines phase transitions on markers (that change the Phase ID of a marker depending on some conditions)\n\nID::Int64: Phase_transition law ID\nType::String: [Constant, Clapeyron, Box]: Constant - the phase transition occurs only at a fixed value of the parameter; Clapeyron - clapeyron slope\nName_Clapeyron::Union{Nothing, Int64}: Type of predefined Clapeyron slope, such as MantleTransition660km\nPTBox_Bounds::Union{Nothing, Vector{Float64}}: box bound coordinates: [left, right, front, back, bottom, top]\nBoxVicinity::Union{Nothing, Int64}: 1: only check particles in the vicinity of the box boundaries (2: in all directions)\nParameter_transition::String: [T = Temperature, P = Pressure, Depth = z-coord, X=x-coord, Y=y-coord, APS = accumulated plastic strain, MeltFraction, t = time] parameter that triggers the phase transition\nConstantValue::Union{Nothing, Float64}: Value of the parameter [unit of T,P,z, APS]\nnumber_phases::Union{Nothing, Int64}: The number of involved phases [default=1]\nPhaseAbove::Union{Nothing, Vector{Int64}}: Above the chosen value the phase is 1, below it, the value is PhaseBelow\nPhaseBelow::Union{Nothing, Vector{Int64}}\nPhaseInside::Union{Nothing, Vector{Int64}}: Phase within the box  [use -1 if you don't want to change the phase inside the box]\nPhaseOutside::Union{Nothing, Vector{Int64}}: Phase outside the box [use -1 if you don't want to change the phase outside the box. If combined with OutsideToInside, all phases that come in are set to PhaseInside]\nPhaseDirection::String: [BothWays=default; BelowToAbove; AboveToBelow] Direction in which transition works\nResetParam::String: [APS] Parameter to reset on particles below PT or within box\nPTBox_TempType::String: # Temperature condition witin the box [none, constant, linear, halfspace]\nPTBox_topTemp::Union{Nothing, Float64}: Temp @ top of box [for linear & halfspace]\nPTBox_botTemp::Union{Nothing, Float64}: Temp @ bottom of box [for linear & halfspace]\nPTBox_thermalAge::Union{Nothing, Float64}: Thermal age, usually in geo-units [Myrs] [only in case of halfspace]\nPTBox_cstTemp::Union{Nothing, Float64}: Temp within box [only for constant T]\nv_box::Union{Nothing, Float64}: [optional] only for NotInAirBox, velocity with which box moves in cm/yr\nt0_box::Union{Nothing, Float64}: [optional] beginning time of movemen in Myr\nt1_box::Union{Nothing, Float64}: [optional] end time of movement in Myr\n\n\n\n\n\n","category":"type"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Scaling","page":"Grid","title":"LaMEM.LaMEM_Model.Scaling","text":"Scaling{T} is a structure that contains the scaling info, employed in the current simulation\n\nScaling::Any: Scaling object (as in GeoParams), which can be GEO_units(), NO_units(), or SI_units()\n\n\n\n\n\n","category":"type"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Softening","page":"Grid","title":"LaMEM.LaMEM_Model.Softening","text":"Defines strain softening parameters\n\nID::Int64: softening law ID\nAPS1::Float64: Begin of softening, in units of accumulated plastic strain (APS)\nAPS2::Float64: End of softening, in units of accumulated plastic strain (APS)\nA::Float64: Reduction ratio\nLm::Float64: Material length scale (in selected units, e.g. km in geo)\nAPSheal2::Union{Nothing, Float64}: APS when healTau2 activates\nhealTau::Union{Nothing, Float64}: healing timescale parameter [Myr]\nhealTau2::Union{Nothing, Float64}: healing timescale parameter [Myr]  starting at APS=APSheal2\n\n\n\n\n\n","category":"type"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.SolutionParams","page":"Grid","title":"LaMEM.LaMEM_Model.SolutionParams","text":"Structure that contains the LaMEM global solution parameters.\n\ngravity::Vector{Float64}: gravitational acceleration vector\nFSSA::Float64: free surface stabilization parameter [0 - 1]; The value has to be between 0 and 1\n\nshear_heat_eff::Float64: shear heating efficiency parameter   [0 - 1]\nAdiabatic_Heat::Float64: Adiabatic Heating activation flag and efficiency. 0.0 - 1.0\nact_temp_diff::Int64: temperature diffusion activation flag\nact_therm_exp::Int64: thermal expansion activation flag\nact_steady_temp::Int64: steady-state temperature initial guess activation flag\nsteady_temp_t::Float64: time for (quasi-)steady-state temperature initial guess\nnstep_steady::Int64: number of steps for (quasi-)steady-state temperature initial guess (default = 1)\nact_heat_rech::Int64: recharge heat in anomalous bodies after (quasi-)steady-state temperature initial guess (=2: recharge after every diffusion step of initial guess)\ninit_lith_pres::Int64: sets initial pressure to be the lithostatic pressure (stabilizes compressible setups in the first steps)\ninit_guess::Int64: create an initial guess step (using constant viscosity eta_ref before starting the simulation\np_litho_visc::Int64: use lithostatic instead of dynamic pressure for creep laws\np_litho_plast::Int64: use lithostatic pressure for plasticity\np_lim_plast::Int64: limit pressure at first iteration for plasticity\np_shift::Int64: add a constant value [MPa] to the total pressure field, before evaluating plasticity (e.g., when the domain is located @ some depth within the crust)\nact_p_shift::Int64: pressure shift activation flag (enforce zero pressure on average in the top cell layer); note: this overwrites p_shift above!\neta_min::Float64: viscosity lower bound [Pas]\neta_max::Float64: viscosity upper limit [Pas]\neta_ref::Float64: Reference viscosity (used for the initial guess) [Pas]\nT_ref::Float64: Reference temperature [C]\nRUGC::Float64: universal gas constant (you need to change this only for non-dimensional setups)\nmin_cohes::Float64: cohesion lower bound  [Pa]\nmin_fric::Float64: friction lower bound  [degree]\ntau_ult::Float64: ultimate yield stress [Pa]\nrho_fluid::Float64: fluid density for depth-dependent density model\ngw_level_type::String: ground water level type for pore pressure computation (see below)\ngw_level::Float64: ground water level at the free surface (if defined)\nbiot::Float64: Biot pressure parameter\nget_permea::Float64: effective permeability computation activation flag\nrescal::Float64: stencil rescaling flag (for internal constraints, for example while computing permeability)\nmfmax::Float64: maximum melt fraction affecting viscosity reduction\nlmaxit::Int64: maximum number of local rheology iterations\nlrtol::Float64: local rheology iterations relative tolerance\nact_dike::Int64: dike activation flag (additonal term in divergence)\nuseTk::Int64: switch to use T-dependent conductivity, 0: not active\ndikeHeat::Int64: switch to use Behn & Ito heat source in the dike\nCompute_velocity_gradient::Int64: compute the velocity gradient tensor 1: active, 0: not active. If active, it automatically activates the output in the .pvd file\n\n\n\n\n\n","category":"type"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Solver","page":"Grid","title":"LaMEM.LaMEM_Model.Solver","text":"Structure that contains the LaMEM solver options\n\nSolverType::String: solver employed [\"direct\" or \"multigrid\"]\nDirectSolver::String: mumps/superlu_dist/pastix/umfpack  (requires these external PETSc packages to be installed!)\nDirectPenalty::Float64: penalty parameter [employed if we use a direct solver]\nMGLevels::Int64: number of MG levels [default=3]\nMGSweeps::Int64: number of MG smoothening steps per level [default=10]\nMGSmoother::String: type of smoothener used [chebyshev or jacobi]\nMGJacobiDamp::Float64: Dampening parameter [only employed for Jacobi smoothener; default=0.6]\nMGCoarseSolver::String: coarse grid solver if using multigrid [\"direct\" / \"mumps\" / \"superlu_dist\" or \"redundant\" - more options specifiable through the command-line options -crs_ksp_type & -crs_pc_type]\nMGRedundantNum::Int64: How many times do we copy the coarse grid? [only employed for redundant solver; default is 4]\nMGRedundantSolver::String: The coarse grid solver for each of the redundant solves [only employed for redundant; options are \"mumps\"/\"superlu_dist\" with default \"superlu_dist\"]\nPETSc_options::Vector{String}: List with (optional) PETSc options\n\n\n\n\n\n","category":"type"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Time","page":"Grid","title":"LaMEM.LaMEM_Model.Time","text":"Structure that contains the LaMEM timestepping information. An explanation of the paramneters is given in the struct `Time_info`\n\ntime_end::Float64: simulation end time\ndt::Float64: initial time step\ndt_min::Float64: minimum time step (declare divergence if lower value is attempted)\ndt_max::Float64: maximum time step\ndt_out::Float64: output step (output at least at fixed time intervals)\ninc_dt::Float64: time step increment per time step (fraction of unit)\nCFL::Float64: CFL (Courant-Friedrichs-Lewy) criterion\nCFLMAX::Float64: CFL criterion for elasticity\nnstep_max::Int64: maximum allowed number of steps (lower bound: timeend/dtmax)\nnstep_out::Int64: save output every n steps; Set this to -1 to deactivate saving output\nnstep_rdb::Int64: save restart database every n steps\nnum_dt_periods::Int64: number of time stepping periods\ntime_dt_periods::Vector{Int64}: timestamps where timestep should be fixed (first entry has to 0)\nstep_dt_periods::Vector{Float64}: target timesteps ar timestamps above\nnstep_ini::Int64: save output for n initial steps\ntime_tol::Float64: relative tolerance for time comparisons\n\n\n\n\n\n","category":"type"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.geom_Sphere","page":"Grid","title":"LaMEM.LaMEM_Model.geom_Sphere","text":"LaMEM geometric primitive `sphere` object\n\nphase::Int64: phase\nradius::Float64: radius of sphere\ncenter::Vector{Float64}: center of sphere\nTemperature::Union{Nothing, String}: optional: Temperature of the sphere. possibilities: [constant, or nothing]\ncstTemp::Union{Nothing, Float64}: required in case of [constant]: temperature value [in Celcius in case of GEO units]\n\n\n\n\n\n","category":"type"},{"location":"man/LaMEM_ModelFunctions.html#GeophysicalModelGenerator.AddBox!-Tuple{Model}","page":"Grid","title":"GeophysicalModelGenerator.AddBox!","text":"AddBox!(model::Model; xlim=Tuple{2}, [ylim=Tuple{2}], zlim=Tuple{2},\n        Origin=nothing, StrikeAngle=0, DipAngle=0,\n        phase = ConstantPhase(1),\n        T=nothing )\n\nAdds a box with phase & temperature structure to a 3D model setup. This simplifies creating model geometries in geodynamic models See the documentation of the GMG routine\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#GeophysicalModelGenerator.AddCylinder!-Tuple{Model}","page":"Grid","title":"GeophysicalModelGenerator.AddCylinder!","text":"AddCylinder!(model::Model;                                      # required input\n                base=Tuple{3}, cap=Tuple{3}, radius=Tuple{1},   # center and radius of the sphere\n                phase = ConstantPhase(1),                       # Sets the phase number(s) in the sphere\n                T=nothing )                                     # Sets the thermal structure (various fucntions are available)\n\nSee the documentation of the GMG routine\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#GeophysicalModelGenerator.AddEllipsoid!-Tuple{Model}","page":"Grid","title":"GeophysicalModelGenerator.AddEllipsoid!","text":"AddEllipsoid!(model::Model;                                 # required input\n                cen=Tuple{3}, axes=Tuple{3},                # center and semi-axes of the ellpsoid\n                Origin=nothing, StrikeAngle=0, DipAngle=0,  # origin & dip/strike\n                phase = ConstantPhase(1),                   # Sets the phase number(s) in the box\n                T=nothing )\n\nSee the documentation of the GMG routine\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#GeophysicalModelGenerator.AddSphere!-Tuple{Model}","page":"Grid","title":"GeophysicalModelGenerator.AddSphere!","text":"AddSphere!(model::Model; cen=Tuple{3}, radius=Tuple{1}, phase = ConstantPhase(1), T=nothing)\n\nSee the documentation of the GMG routine\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.IO_functions.Read_LaMEM_simulation-Tuple{Model}","page":"Grid","title":"LaMEM.IO_functions.Read_LaMEM_simulation","text":"Timestep, FileNames, Time = Read_LaMEM_simulation(model::Model; phase=false, surf=false, passive_tracers=false)\n\nReads a LaMEM simulation as specified in model and returns the timesteps, times and filenames of that simulation once it is finished.\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.IO_functions.Read_LaMEM_timestep","page":"Grid","title":"LaMEM.IO_functions.Read_LaMEM_timestep","text":"data, time = Read_LaMEM_timestep(model::Model, TimeStep::Int64=0; fields=nothing, phase=false, surf=false, last=true)\n\nReads a specific Timestep from a simulation specified in model\n\n\n\n\n\n","category":"function"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Check_LaMEM_Model-Tuple{Model}","page":"Grid","title":"LaMEM.LaMEM_Model.Check_LaMEM_Model","text":"Check_LaMEM_Model(m::Model)\n\nChecks the LaMEM Setup Model m for errors\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Create_Grid-NTuple{15, Any}","page":"Grid","title":"LaMEM.LaMEM_Model.Create_Grid","text":"This creates a LaMEM grid\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Write_LaMEM_InputFile","page":"Grid","title":"LaMEM.LaMEM_Model.Write_LaMEM_InputFile","text":"Write_LaMEM_InputFile(d::Model,fname::String; dir=pwd())\n\nWrites a LaMEM input file based on the data stored in Model\n\n\n\n\n\n","category":"function"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, BoundaryConditions}","page":"Grid","title":"LaMEM.LaMEM_Model.Write_LaMEM_InputFile","text":"Write_LaMEM_InputFile(io, d::BoundaryConditions)\n\nWrites the boundary conditions related parameters to file\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, FreeSurface}","page":"Grid","title":"LaMEM.LaMEM_Model.Write_LaMEM_InputFile","text":"Write_LaMEM_InputFile(io, d::FreeSurface)\n\nWrites the free surface related parameters to file\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, Grid}","page":"Grid","title":"LaMEM.LaMEM_Model.Write_LaMEM_InputFile","text":"Write_LaMEM_InputFile(io, d::Grid)\n\nThis writes grid info to a LaMEM input file\n\nExample\n\njulia> d=LaMEM.Grid(coord_x=[0.0, 0.7, 0.8, 1.0], bias_x=[0.3,1.0,3.0], nel_x=[10,4,2])\njulia> io = open(\"test.dat\",\"w\")\njulia> LaMEM.Write_LaMEM_InputFile(io, d)\njulia> close(io)\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, Materials}","page":"Grid","title":"LaMEM.LaMEM_Model.Write_LaMEM_InputFile","text":"Write_LaMEM_InputFile(io, d::Output)\n\nWrites the free surface related parameters to file\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, ModelSetup}","page":"Grid","title":"LaMEM.LaMEM_Model.Write_LaMEM_InputFile","text":"Write_LaMEM_InputFile(io, d::ModelSetup)\n\nWrites options related to the Model Setup to disk\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, Output}","page":"Grid","title":"LaMEM.LaMEM_Model.Write_LaMEM_InputFile","text":"Write_LaMEM_InputFile(io, d::Output)\n\nWrites the free surface related parameters to file\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, SolutionParams}","page":"Grid","title":"LaMEM.LaMEM_Model.Write_LaMEM_InputFile","text":"Write_LaMEM_InputFile(io, d::SolutionParams)\n\nWrites the boundary conditions related parameters to file\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, Solver}","page":"Grid","title":"LaMEM.LaMEM_Model.Write_LaMEM_InputFile","text":"Write_LaMEM_InputFile(io, d::Solver)\n\nWrites the free surface related parameters to file\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, Time}","page":"Grid","title":"LaMEM.LaMEM_Model.Write_LaMEM_InputFile","text":"Writes the Time related parameters to file\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Write_LaMEM_InputFile-Tuple{Any, geom_Sphere}","page":"Grid","title":"LaMEM.LaMEM_Model.Write_LaMEM_InputFile","text":"Write_LaMEM_InputFile(io, d::geom_Sphere)\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.Write_LaMEM_InputFile_PETSc-Tuple{Any, Solver}","page":"Grid","title":"LaMEM.LaMEM_Model.Write_LaMEM_InputFile_PETSc","text":"Write_LaMEM_InputFile_PETSc(io, d::Solver)\n\nWrites the (optional) PETSc options to file\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.add_dike!-Tuple{Model, Dike}","page":"Grid","title":"LaMEM.LaMEM_Model.add_dike!","text":"add_dike!(model::Model, dike::Dike)\n\nThis adds a phase transition phase_trans to model\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.add_geom!-Tuple{Model, Any}","page":"Grid","title":"LaMEM.LaMEM_Model.add_geom!","text":"add_geom!(model::Model, geom_object)\n\nThis adds an internal geometric primitive object geom_object to the LaMEM Model Setup model.\n\nCurrently available primitive geom objects are:\n\ngeom_Sphere\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.add_petsc!-Tuple{Model, Vararg{Any}}","page":"Grid","title":"LaMEM.LaMEM_Model.add_petsc!","text":"add_petsc!(model::Model, option::String)\n\nAdds one or more PETSc options to the model \n\nExample\n\njulia> d = Model()\njulia> add_petsc!(d,\"-snes_npicard 3\")\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.add_phase!-Tuple{Model, Phase}","page":"Grid","title":"LaMEM.LaMEM_Model.add_phase!","text":"add_phase!(model::Model, phase::Phase)\n\nThis adds a phase (with material properties) to model\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.add_phase!-Tuple{Model, Vararg{Any}}","page":"Grid","title":"LaMEM.LaMEM_Model.add_phase!","text":"add_phase!(model::Model, phases...)\n\nAdd several phases @ once.\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.add_phasetransition!-Tuple{Model, PhaseTransition}","page":"Grid","title":"LaMEM.LaMEM_Model.add_phasetransition!","text":"add_phasetransition!(model::Model, phase_trans::PhaseTransition)\n\nThis adds a phase transition phase_trans to model\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.add_softening!-Tuple{Model, Softening}","page":"Grid","title":"LaMEM.LaMEM_Model.add_softening!","text":"add_softening!(model::Model, soft::Softening)\n\nThis adds a plastic softening law soft to model\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.create_initialsetup","page":"Grid","title":"LaMEM.LaMEM_Model.create_initialsetup","text":"create_initialsetup(model::Model, cores::Int64=1, args::String=\"\")\n\nCreates the initial model setup of LaMEM from model, which includes:\n\nWriting the LaMEM (*.dat) input file\nWrite the VTK file (if requested when model.Output.write_VTK_setup=true)\nWrite the marker files to disk (if model.ModelSetup.msetup=\"files\")\n\n\n\n\n\n","category":"function"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.get_doc-Tuple{Any, Symbol}","page":"Grid","title":"LaMEM.LaMEM_Model.get_doc","text":"help_info::String = get_doc(structure, field::Symbol)\n\nThis returns a string with the documentation for a parameter field that is within the structure.  Note that this structure must be a help structure of the current one.\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.replace_phase!-Tuple{Model, Phase}","page":"Grid","title":"LaMEM.LaMEM_Model.replace_phase!","text":"replace_phase!(model::Model, phase_new::Phase; ID::Int64=nothing, Name::String=nothing)\n\nThis replaces a phase within a LaMEM Model Setup model with phase_new either based on its Name or ID.  Note that it is expected that only one such phase is present in the current setup.\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.rm_last_phase!-Tuple{Model}","page":"Grid","title":"LaMEM.LaMEM_Model.rm_last_phase!","text":"rm_last_phase!(model::Model, phase::Phase)\n\nThis removes the last added phase from model\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.rm_phase!-Tuple{Model, Int64}","page":"Grid","title":"LaMEM.LaMEM_Model.rm_phase!","text":"rm_phase!(model::Model, ID::Int64)\n\nThis removes a phase with ID from model\n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.LaMEM_Model.set_geom!-Tuple{Model, geom_Sphere}","page":"Grid","title":"LaMEM.LaMEM_Model.set_geom!","text":"This sets the geometry \n\n\n\n\n\n","category":"method"},{"location":"man/LaMEM_ModelFunctions.html#LaMEM.Run.run_lamem","page":"Grid","title":"LaMEM.Run.run_lamem","text":"run_lamem(model::Model, cores::Int64=1, args:String=\"\"; wait=true)\n\nPerforms a LaMEM run for the parameters that are specified in model\n\n\n\n\n\n","category":"function"},{"location":"man/installation_HPC.html#Installation-on-HPC-systems","page":"Installation on HPC systems","title":"Installation on HPC systems","text":"","category":"section"},{"location":"man/installation_HPC.html","page":"Installation on HPC systems","title":"Installation on HPC systems","text":"Installing LaMEM on high performance computer (HPC) systems can be complicated, because you will have to compile PETSc with the correct dependencies for that system.  The reason is that HPC systems use MPI versions that are specifically tailored/compiled for that system. ","category":"page"},{"location":"man/installation_HPC.html","page":"Installation on HPC systems","title":"Installation on HPC systems","text":"Luckily there is a solution thanks to the great work of @eschnett and colleagues, who developed MPITrampoline which is an intermediate layer between the HPC-system-specific MPI libraries and the precompiled LaMEM binaries. ","category":"page"},{"location":"man/installation_HPC.html","page":"Installation on HPC systems","title":"Installation on HPC systems","text":"It essentially consists of two steps:      1) compile a small package (MPIwrapper)      2) make sure that you download the version of MAGEMin that was compiled versus MPItrampoline.","category":"page"},{"location":"man/installation_HPC.html","page":"Installation on HPC systems","title":"Installation on HPC systems","text":"Here step-by-step instructions (for Linux, as that is what essentially all HPC systems use):","category":"page"},{"location":"man/installation_HPC.html","page":"Installation on HPC systems","title":"Installation on HPC systems","text":"Download MPIwrapper: ","category":"page"},{"location":"man/installation_HPC.html","page":"Installation on HPC systems","title":"Installation on HPC systems","text":"$git clone https://github.com/eschnett/MPIwrapper.git \n$cd MPIwrapper","category":"page"},{"location":"man/installation_HPC.html","page":"Installation on HPC systems","title":"Installation on HPC systems","text":"Install it after making sure that mpiexec points to the one you want (you may have to load some modules, depending on your system):","category":"page"},{"location":"man/installation_HPC.html","page":"Installation on HPC systems","title":"Installation on HPC systems","text":"$cmake -S . -B build -DMPIEXEC_EXECUTABLE=mpiexec -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_INSTALL_PREFIX=$HOME/mpiwrapper\n$cmake --build build\n$cmake --install build","category":"page"},{"location":"man/installation_HPC.html","page":"Installation on HPC systems","title":"Installation on HPC systems","text":"At this stage, MPItrampoline is installed in $HOME/mpiwrapper","category":"page"},{"location":"man/installation_HPC.html","page":"Installation on HPC systems","title":"Installation on HPC systems","text":"Set the correct wrapper:","category":"page"},{"location":"man/installation_HPC.html","page":"Installation on HPC systems","title":"Installation on HPC systems","text":"$export MPITRAMPOLINE_LIB=$HOME/mpiwrapper/lib64/libmpiwrapper.so","category":"page"},{"location":"man/installation_HPC.html","page":"Installation on HPC systems","title":"Installation on HPC systems","text":"Depending on the system it may be called lib instead of lib64 (check!).","category":"page"},{"location":"man/installation_HPC.html","page":"Installation on HPC systems","title":"Installation on HPC systems","text":"Start julia and install the MPI and MPIPreferences packages:","category":"page"},{"location":"man/installation_HPC.html","page":"Installation on HPC systems","title":"Installation on HPC systems","text":"$julia\njulia> ]\npkg>add MPI, MPIPreferences","category":"page"},{"location":"man/installation_HPC.html","page":"Installation on HPC systems","title":"Installation on HPC systems","text":"Set the preference to use MPItrampoline","category":"page"},{"location":"man/installation_HPC.html","page":"Installation on HPC systems","title":"Installation on HPC systems","text":"julia> using MPIPreferences; MPIPreferences.use_jll_binary(\"MPItrampoline_jll\")\n┌ Info: MPIPreferences unchanged\n└   binary = \"MPItrampoline_jll\"","category":"page"},{"location":"man/installation_HPC.html","page":"Installation on HPC systems","title":"Installation on HPC systems","text":"Load MPI and verify it is the correct one","category":"page"},{"location":"man/installation_HPC.html","page":"Installation on HPC systems","title":"Installation on HPC systems","text":"julia> using MPI\njulia> MPI.Get_library_version()\n\"MPIwrapper 2.10.3, using MPIABI 2.9.0, wrapping:\\nOpen MPI v4.1.4, package: Open MPI boris@Pluton Distribution, ident: 4.1.4, repo rev: v4.1.4, May 26, 2022\"","category":"page"},{"location":"man/installation_HPC.html","page":"Installation on HPC systems","title":"Installation on HPC systems","text":"After this, restart julia (this only needs to be done once, next time all is fine).","category":"page"},{"location":"man/installation_HPC.html","page":"Installation on HPC systems","title":"Installation on HPC systems","text":"Now load LaMEM and check that it uses the mpitrampoline version:","category":"page"},{"location":"man/installation_HPC.html","page":"Installation on HPC systems","title":"Installation on HPC systems","text":"julia> using MPI,LaMEM\njulia> LaMEM.LaMEM_jll.host_platform\nLinux x86_64 {cxxstring_abi=cxx11, julia_version=1.8.1, libc=glibc, libgfortran_version=5.0.0, mpi=mpitrampoline}","category":"page"},{"location":"man/installation_HPC.html","page":"Installation on HPC systems","title":"Installation on HPC systems","text":"At this stage the precompiled version of LaMEM should be useable on that system.","category":"page"},{"location":"index.html#LaMEM.jl","page":"Home","title":"LaMEM.jl","text":"","category":"section"},{"location":"index.html","page":"Home","title":"Home","text":"This is the julia interface to LaMEM, which does a number of handy things:","category":"page"},{"location":"index.html","page":"Home","title":"Home","text":"It will automatically download a binary installation of LaMEM, along with the correct version of PETSc and mpiexec for your system. You can also use these binaries directly from your terminal, so you are not limited to julia. Gone are the days where you had to first spend hours or days to install PETSc on your system!\nWe provide a simple function to run LaMEM from julia (also in parallel).\nWe provide functions to read timesteps back into julia. ","category":"page"},{"location":"man/installation.html#Installation","page":"Installation","title":"Installation","text":"","category":"section"},{"location":"man/installation.html","page":"Installation","title":"Installation","text":"Installing LaMEM can simply be done through the package manager:","category":"page"},{"location":"man/installation.html","page":"Installation","title":"Installation","text":"julia>]\npkg>add LaMEM","category":"page"},{"location":"man/installation.html","page":"Installation","title":"Installation","text":"which will download the binaries along with PETSc and mpiexec for your system.","category":"page"},{"location":"man/installation.html","page":"Installation","title":"Installation","text":"You can test if it works on your machine with","category":"page"},{"location":"man/installation.html","page":"Installation","title":"Installation","text":"pkg> test LaMEM","category":"page"},{"location":"man/installation.html#Running-LaMEM-from-the-julia-REPL","page":"Installation","title":"Running LaMEM from the julia REPL","text":"","category":"section"},{"location":"man/installation.html","page":"Installation","title":"Installation","text":"Running LaMEM from within julia can be done with the run_lamem function:","category":"page"},{"location":"man/installation.html","page":"Installation","title":"Installation","text":"LaMEM.run_lamem","category":"page"},{"location":"man/installation.html#LaMEM.Run.run_lamem","page":"Installation","title":"LaMEM.Run.run_lamem","text":"run_lamem(model::Model, cores::Int64=1, args:String=\"\"; wait=true)\n\nPerforms a LaMEM run for the parameters that are specified in model\n\n\n\n\n\nrun_lamem(ParamFile::String, cores::Int64=1, args:String=\"\"; wait=true)\n\nThis starts a LaMEM simulation, for using the parameter file ParamFile on cores number of cores.  Optional additional command-line parameters can be specified with args.\n\nExample:\n\nYou can call LaMEM with:\n\njulia> using LaMEM\njulia> ParamFile=\"../../input_models/BuildInSetups/FallingBlock_Multigrid.dat\";\njulia> run_lamem(ParamFile)\n\nDo the same on 2 cores with a command-line argument as:\n\njulia> ParamFile=\"../../input_models/BuildInSetups/FallingBlock_Multigrid.dat\";\njulia> run_lamem(ParamFile, 2, \"-nstep_max = 1\")\n\n\n\n\n\n","category":"function"},{"location":"man/installation.html#Running-LaMEM-from-outside-julia","page":"Installation","title":"Running LaMEM from outside julia","text":"","category":"section"},{"location":"man/installation.html","page":"Installation","title":"Installation","text":"If you, for some reason, do not want to run LaMEM through julia but instead directly from the terminal or powershell, you will have to add the required dynamic libraries and executables. Do this with:","category":"page"},{"location":"man/installation.html","page":"Installation","title":"Installation","text":"LaMEM.show_paths_LaMEM","category":"page"},{"location":"man/installation.html#LaMEM.Run.show_paths_LaMEM","page":"Installation","title":"LaMEM.Run.show_paths_LaMEM","text":"show_paths_LaMEM()\n\nThe downloaded LaMEM binaries can also be called from outside julia (directly from the terminal).  In that case, you will need to set load correct dynamic libraries (such as PETSc) and call the correct binaries.\n\nThis function shows this for your system. \n\n\n\n\n\n","category":"function"}]
+}
diff --git a/docs/make.jl b/docs/make.jl
index 69c877e..e1a51f9 100644
--- a/docs/make.jl
+++ b/docs/make.jl
@@ -9,8 +9,13 @@ makedocs(;
     format=Documenter.HTML(; prettyurls=get(ENV, "CI", nothing) == "true"), # easier local build
     pages=[
         "Home" => "index.md",
-        "Installation" => "man/installation.md",
-        "Installation on HPC systems" => "man/installation_HPC.md",
+        "Installation" => ["General instructions" => "man/installation.md",
+                            "Installation on HPC systems" => "man/installation_HPC.md"],
+        "Create & run LaMEM models from julia" => ["Overview" => "man/juliasetups.md",
+                                                    "Example 1: Sphere" => "man/juliasetup_example_sphere.md",
+                                                    "Example 2: Volcano" => "man/juliasetup_LaPalma.md",
+                                                    "Pluto notebooks" => "man/juliasetup_pluto.md",
+                                                    "Available functions" => "man/LaMEM_ModelFunctions.md"],
         "Run LaMEM" => "man/runlamem.md",
         "Reading timesteps" => "man/readtimesteps.md",
         "List of functions" => "man/listfunctions.md",
diff --git a/docs/src/man/FallingSphere_t20.png b/docs/src/man/FallingSphere_t20.png
new file mode 100644
index 0000000..076e037
Binary files /dev/null and b/docs/src/man/FallingSphere_t20.png differ
diff --git a/docs/src/man/InitialSetupSphere.png b/docs/src/man/InitialSetupSphere.png
new file mode 100644
index 0000000..57c043c
Binary files /dev/null and b/docs/src/man/InitialSetupSphere.png differ
diff --git a/docs/src/man/LaMEM_ModelFunctions.md b/docs/src/man/LaMEM_ModelFunctions.md
new file mode 100644
index 0000000..8cd85cf
--- /dev/null
+++ b/docs/src/man/LaMEM_ModelFunctions.md
@@ -0,0 +1,7 @@
+# List functions
+These are all the functions that are provided for the LaMEM Julia Setup interface 
+```@autodocs
+Modules = [LaMEM.LaMEM_Model]
+```
+
+
diff --git a/docs/src/man/LaPalma_CrossSection.png b/docs/src/man/LaPalma_CrossSection.png
new file mode 100644
index 0000000..2493f4e
Binary files /dev/null and b/docs/src/man/LaPalma_CrossSection.png differ
diff --git a/docs/src/man/LaPalma_topo.png b/docs/src/man/LaPalma_topo.png
new file mode 100644
index 0000000..1c9cbd8
Binary files /dev/null and b/docs/src/man/LaPalma_topo.png differ
diff --git a/docs/src/man/juliasetup_LaPalma.md b/docs/src/man/juliasetup_LaPalma.md
new file mode 100644
index 0000000..fa72a4c
--- /dev/null
+++ b/docs/src/man/juliasetup_LaPalma.md
@@ -0,0 +1,213 @@
+# La Palma Volcano setup
+
+In this example, we will show how to create a 3D model setup for the 2020 La Palma eruption. We mainly focus on the LaMEM part; see the [GeophysicalModelGenerator](https://github.com/JuliaGeodynamics/GeophysicalModelGenerator.jl) package for more details on how to plot earthquake data etc.
+
+#### 1. Load packages & topography
+Let's start with what we need:
+```julia
+julia> using LaMEM, GeophysicalModelGenerator, GMT, Plots
+Loading GMT routines within GMG
+WARNING: using GMT.meshgrid in module GeophysicalModelGenerator conflicts with an existing identifier.
+adding Plots.jl plotting extensions for LaMEM
+```
+
+Load the topography, choose a projection point & project the topography to cartesian coordinates:
+```julia
+julia> Topo = ImportTopo(lon = [-18.7, -17.1], lat=[28.0, 29.2], file="@earth_relief_03s.grd");
+julia> proj = ProjectionPoint(Lon=-17.84, Lat=28.56);
+julia> Topo_cart = Convert2CartData(Topo, proj)
+CartData 
+    size    : (1921, 1441, 1)
+    x       ϵ [ -86.09445705828863 : 73.67229892155609]
+    y       ϵ [ -63.5531883197492 : 73.28446155584604]
+    z       ϵ [ -4.38352685546875 : 2.414]
+    fields  : (:Topography,)
+  attributes: ["note"]
+```
+This shows the dimensions of our domain in kilometers. The issue is that this projected topography is not an orthogonal grid, but (slightly) distorted. In any case, we see the approximate dimensions of the grid (in horizontal directions), so we can create an orthogonal grid on which to project this:
+
+```julia
+julia> Topo_LaMEM = CartData(XYZGrid(-70:.2:70,-60:.2:70,0));
+julia> Topo_LaMEM = ProjectCartData(Topo_LaMEM, Topo, proj)
+```
+
+We can plot it with:
+```julia
+julia> plot_topo(topo, clim=(-4,4))
+```
+
+![LaPalma_topo](LaPalma_topo.png)
+
+
+#### 2. LaMEM Model setup
+
+Next, we generate a model setup  for LaMEM with:
+```julia
+julia> model = Model(Grid(x=[-50.,50.], y=[-40.,40.], z=[-80,15] , nel=(64,64,32)),
+                     BoundaryConditions(temp_bot=1350, open_top_bound=1),
+                     Scaling(GEO_units(stress=1e9Pa, length=1km)),
+                     Time(nstep_max=20) )
+LaMEM Model setup
+|
+|-- Scaling             :  GeoParams.Units.GeoUnits{GEO}
+|-- Grid                :  nel=(64, 64, 32); xϵ(-50.0, 50.0), yϵ(-40.0, 40.0), zϵ(-80.0, 15.0) 
+|-- Time                :  nstep_max=20; nstep_out=1; time_end=1.0; dt=0.05
+|-- Boundary conditions :  noslip=[0, 0, 0, 0, 0, 0]
+|-- Solution parameters :  eta_min=1.0e18; eta_max=1.0e25; eta_ref=1.0e20; act_temp_diff=0
+|-- Solver options      :  direct solver; superlu_dist; penalty term=10000.0
+|-- Model setup options :  Type=files; 
+|-- Output options      :  filename=output; pvd=1; avd=0; surf=0
+|-- Materials           :  0 phases; 
+```
+
+##### Set geotherm and phases
+We can set an initial constant, linear, geotherm with:
+```julia
+julia> Z = model.Grid.Grid.Z;
+julia> Geotherm=30
+julia> model.Grid.Temp = -Z.*Geotherm;
+```
+We will cutoff extreme values with:
+```julia
+julia> model.Grid.Temp[model.Grid.Temp.<20]    .=  20;
+julia> model.Grid.Temp[model.Grid.Temp.>1350]  .=  1350;
+julia> model.Grid
+LaMEM grid with constant Δ: 
+  nel         : ([64], [64], [32])
+  marker/cell : (3, 3, 3)
+  x           ϵ [-50.0 : 50.0]
+  y           ϵ [-40.0 : 40.0]
+  z           ϵ [-80.0 : 15.0]
+  Phases      : range ϵ [0 - 0]
+  Temp        : range ϵ [20.0 - 1350.0]
+```
+
+Set `Phases` to two everywhere:
+```julia
+julia> model.Grid.Phases .= 2;
+```
+
+Now set points above the topography to zero (will be air later), the ones above the topography but below zero to 'water` and below 40 km to mantle (if we had a Moho surface we could use that):
+```julia
+ julia> AboveSurface!(model, Topo_LaMEM, phase=0, T=0)
+ julia> model.Grid.Phases[Z.<-0 .&& model.Grid.Phases .== 0] .= 1;
+ julia> model.Grid.Phases[Z.<-40] .= 3;
+```
+
+Finally, we define some magma chambers:
+```julia 
+julia> AddSphere!(model, cen=(0,0,-35), radius=5, phase=ConstantPhase(5), T=ConstantTemp(1200));
+julia> AddEllipsoid!(model, cen=(-1,0,-11), axes=(3,3,8), StrikeAngle=225, DipAngle=45, phase=ConstantPhase(5), T=ConstantTemp(1200));
+julia> AddEllipsoid!(model, cen=(-0,0,-23), axes=(8,8,2), StrikeAngle=0, DipAngle=0, phase=ConstantPhase(5), T=ConstantTemp(1200));
+```
+
+ We can plot a cross-section through the model:
+```julia
+ julia> heatmap(model, x=0, field=:phase)
+```
+ ![LaPalma_CrossSection](LaPalma_CrossSection.png)
+
+
+##### Set material properties
+
+First, we set air and water properties:
+```julia
+julia> air = set_air(alpha=3e-5, G=1e10, nu=0.2, ch=10e6, fr=30)
+Phase 0 (air): 
+  rho    = 100.0 
+  eta    = 1.0e17 
+  G      = 1.0e10 
+  nu     = 0.2 
+  ch     = 1.0e7 
+  fr     = 30.0 
+  alpha  = 3.0e-5 
+  Cp     = 1000.0 
+  k      = 30.0 
+julia> water=deepcopy(air); water.Name="water"; water.ID=1
+```
+Next, we set the crust:
+```julia
+julia> crust = Phase(Name="Crust", ID=2, rho=2900, alpha=3e-5, disl_prof="Mafic_Granulite-Ranalli_1995",
+                    G=3e10, nu=0.2, k=3, Cp=1000, ch=10e6, fr=30)
+Phase 2 (Crust): 
+  rho       = 2900.0 
+  disl_prof = Mafic_Granulite-Ranalli_1995 
+  G         = 3.0e10 
+  nu        = 0.2 
+  ch        = 1.0e7 
+  fr        = 30.0 
+  alpha     = 3.0e-5 
+  Cp        = 1000.0 
+  k         = 3.0 
+```
+The mantle is done as a copy of that, while changing a few parameters:
+```julia
+ julia> mantle = copy_phase(crust, Name="Mantle", ID=3, rho=3320.0, disl_prof="Dry_Olivine-Ranalli_1995", G=6.5e10, k=3.3);
+```
+And we define two different types of magma:
+```julia
+julia> andesite = Phase(Name="andesitic_magma",ID=4,rho=2700, alpha=3e-5, eta=1e18, G=1.5e10, nu=0.2, k=3, Cp=1000, T=980, ch=1e7, fr=30);
+julia> dacite = copy_phase(andesite,Name="dacite_magma", ID=5, rho=2575.0, eta=1e19, T=800.0)
+```
+
+Now we add all of this to the model:
+```julia
+julia> rm_phase!(model)
+julia> add_phase!(model, air, water, crust, mantle, andesite, dacite)
+```
+And check that we indeed have 6 phases:
+```julia
+julia> model
+LaMEM Model setup
+|
+|-- Scaling             :  GeoParams.Units.GeoUnits{GEO}
+|-- Grid                :  nel=(64, 64, 32); xϵ(-50.0, 50.0), yϵ(-40.0, 40.0), zϵ(-80.0, 15.0) 
+|-- Time                :  nstep_max=50; nstep_out=1; time_end=1.0; dt=0.05
+|-- Boundary conditions :  noslip=[0, 0, 0, 0, 0, 0]
+|-- Solution parameters :  eta_min=1.0e18; eta_max=1.0e25; eta_ref=1.0e20; act_temp_diff=0
+|-- Solver options      :  direct solver; superlu_dist; penalty term=10000.0
+|-- Model setup options :  Type=files; 
+|-- Output options      :  filename=output; pvd=1; avd=0; surf=0
+|-- Materials           :  0 phases; 
+```
+
+##### Add topography to model
+We can add the topography grid that we created earlier to the model with:
+```julia
+julia> add_topography!(model, Topo_LaMEM)
+```
+
+##### Set solver options
+
+You will want to use a multigrid solver in this case:
+```julia
+julia> model.Solver = Solver(SolverType="multigrid",  MGLevels=4)
+```
+
+### 3. Run LaMEM
+Running LaMEM is simple; here on 4 processors:
+```julia
+julia> run_lamem(model, 4)
+Saved file: Model3D.vts
+Written LaMEM topography file: topography.txt
+Writing LaMEM marker file -> ./markers/mdb.00000000.dat
+Writing LaMEM marker file -> ./markers/mdb.00000001.dat
+Writing LaMEM marker file -> ./markers/mdb.00000002.dat
+Writing LaMEM marker file -> ./markers/mdb.00000003.dat
+-------------------------------------------------------------------------- 
+                   Lithosphere and Mantle Evolution Model                   
+     Compiled: Date: Apr  7 2023 - Time: 22:11:23           
+     Version : 1.2.4 
+-------------------------------------------------------------------------- 
+        STAGGERED-GRID FINITE DIFFERENCE CANONICAL IMPLEMENTATION           
+-------------------------------------------------------------------------- 
+Parsing input file : output.dat 
+Finished parsing input file : output.dat 
+--------------------------------------------------------------------------
+Scaling parameters:
+   Temperature : 1000. [C/K] 
+   Length      : 1000. [m] 
+   Viscosity   : 1e+20 [Pa*s] 
+   Stress      : 1e+09 [Pa] 
+--------------------------------------------------------------------------
+```
\ No newline at end of file
diff --git a/docs/src/man/juliasetup_example_sphere.md b/docs/src/man/juliasetup_example_sphere.md
new file mode 100644
index 0000000..80a8ccb
--- /dev/null
+++ b/docs/src/man/juliasetup_example_sphere.md
@@ -0,0 +1,142 @@
+# 1. Example 1: Falling sphere
+This is a first example that illustrates how to build a setup using the LaMEM.jl package, run it and visualize the results, all without leaving julia.
+
+We start with loading the packages we need:
+```julia
+>julia using LaMEM, GeophysicalModelGenerator, Plots
+```
+The [GeophysicalModelGenerator](https://github.com/JuliaGeodynamics/GeophysicalModelGenerator.jl) package can be used to generate model setups and [Plots](https://github.com/JuliaPlots/Plots.jl) for plotting.
+
+#### 1.1 Define model setup
+
+Next, we define a general model setup, in which we specify the units with which we work (for most cases, you'll want to use the default `GEO` units), the size of the computational box and various timestepping parameters. In this case, we use a multigrid solver.
+
+```julia
+julia> model  = Model(Grid(nel=(16,16,16), x=[-1,1], y=[-1,1], z=[-1,1]), 
+          Time(nstep_max=20, dt_min=1e-3, dt=1, dt_max=10, time_end=100), 
+          Solver(SolverType="multigrid", MGLevels=2),
+          Output(out_dir="example_1"))
+LaMEM Model setup
+|
+|-- Scaling             :  GeoParams.Units.GeoUnits{GEO}
+|-- Grid                :  nel=(16, 16, 16); xϵ(-1.0, 1.0), yϵ(-1.0, 1.0), zϵ(-1.0, 1.0) 
+|-- Time                :  nstep_max=20; nstep_out=1; time_end=100.0; dt=1.0
+|-- Boundary conditions :  noslip=[0, 0, 0, 0, 0, 0]
+|-- Solution parameters :  eta_min=1.0e18; eta_max=1.0e25; eta_ref=1.0e20; act_temp_diff=0
+|-- Solver options      :  multigrid solver; coarse grid solver=direct; 2 levels
+|-- Model setup options :  Type=files; 
+|-- Output options      :  filename=output; pvd=1; avd=0; surf=0
+|-- Materials           :  0 phases; 
+```
+
+Note that each of the fields within `Model` has many additional and adjustable parameters. You can view that by typing:
+```julia
+julia> model.Time
+LaMEM Timestepping parameters: 
+  time_end        = 100.0 
+  dt              = 1.0 
+  dt_min          = 0.001 
+  dt_max          = 10.0 
+  dt_out          = 0.2 
+  inc_dt          = 0.1 
+  CFL             = 0.5 
+  CFLMAX          = 0.8 
+  nstep_max       = 20 
+  nstep_out       = 1 
+  nstep_rdb       = 100 
+  nstep_ini       = 1 
+  time_tol        = 1.0e-8 
+```
+
+#### 1.2 Specify material properties
+Once this is specified, we need to set material properties for each of the `Phases` we will consider in the simulation. This can be done with the `Phase` structure. First, we define two phases
+```julia
+julia> rm_phase!(model)
+julia> matrix = Phase(ID=0,Name="matrix",eta=1e20,rho=3000)
+Phase 0 (matrix): 
+  rho    = 3000.0 
+  eta    = 1.0e20 
+julia> sphere = Phase(ID=1,Name="sphere",eta=1e23,rho=3200)
+Phase 1 (sphere): 
+  rho    = 3200.0 
+  eta    = 1.0e23 
+```
+and add them to the model with:
+```julia
+add_phase!(model, sphere, matrix)
+```
+
+#### 1.3 Set initial model geometry
+We also need to specify an initial model geometry. The julia package `GeophysicalModelGenerator` has a number of functions for that, which can be used here. For the current setup, we just add a sphere: 
+```julia
+julia> AddSphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
+```
+It is often useful to plot the initial model setup. You can do this with the `heatmap` function from the `Plots.jl` package, for which we provide a LaMEM plugin that allows you to specify a cross-section through a 3D LaMEM setup:
+
+```julia
+julia> heatmap(model, field=:phase, y=0)
+```
+
+![InitialSetupSphere](InitialSetupSphere.png)
+
+In the initial setup we define two fields: `:phase` which defines the rocktypes and `:temperature` which has the initial temperature. They are stored as 3D arrays in `model.Grid.Phases` and `model.Grid.Temp`:
+```julia
+julia> model.Grid
+LaMEM grid with constant Δ: 
+  nel         : ([16], [16], [16])
+  marker/cell : (3, 3, 3)
+  x           ϵ [-1.0 : 1.0]
+  y           ϵ [-1.0 : 1.0]
+  z           ϵ [-1.0 : 1.0]
+  Phases      : range ϵ [0 - 1]
+  Temp        : range ϵ [0.0 - 0.0]
+```
+
+#### 1.4 Run LaMEM
+
+At this stage we are ready to run a LaMEM simulation which can simply be done with the `run_lamem` command. By default, it will run on one processor. If you want to run this in parallel, you can specify the number of cores you want to use. Please note that running things in parallel is only worth the effort for large resolutions; for smaller setups it will be faster on one processor:
+
+```julia
+julia> run_lamem(model,1)
+Saved file: Model3D.vts
+Writing LaMEM marker file -> ./markers/mdb.00000000.dat
+-------------------------------------------------------------------------- 
+                   Lithosphere and Mantle Evolution Model                   
+     Compiled: Date: Apr  7 2023 - Time: 22:11:23           
+     Version : 1.2.4 
+-------------------------------------------------------------------------- 
+        STAGGERED-GRID FINITE DIFFERENCE CANONICAL IMPLEMENTATION           
+-------------------------------------------------------------------------- 
+Parsing input file : output.dat 
+Finished parsing input file : output.dat 
+--------------------------------------------------------------------------
+Scaling parameters:
+   Temperature : 1000. [C/K] 
+   Length      : 1e+06 [m] 
+   Viscosity   : 1e+20 [Pa*s] 
+   Stress      : 10. [Pa] 
+--------------------------------------------------------------------------
+Time stepping parameters:
+   Simulation end time          : 100. [Myr] 
+   Maximum number of steps      : 20 
+   Time step                    : 1. [Myr] 
+   Minimum time step            : 0.001 [Myr] 
+   Maximum time step            : 10. [Myr] 
+   Time step increase factor    : 0.1 
+   CFL criterion                : 0.5 
+   CFLMAX (fixed time steps)    : 0.8 
+   Output every [n] steps       : 1 
+   Output [n] initial steps     : 1 
+--------------------------------------------------------------------------
+--------------------------------------------------------------------------
+```
+
+#### 1.5 Visualize results
+
+Once the simulation is done, you can look at the results using the same `heatmap` function, but by specifying a timestep, which will read that timestep and plot a cross-section though it:
+
+```julia
+julia> heatmap(model, y=0, timestep=20, field=:phase)	
+```
+
+![FallingSphere_t20](FallingSphere_t20.png)
diff --git a/docs/src/man/juliasetup_pluto.md b/docs/src/man/juliasetup_pluto.md
new file mode 100644
index 0000000..a6ed3ea
--- /dev/null
+++ b/docs/src/man/juliasetup_pluto.md
@@ -0,0 +1,9 @@
+# Using Pluto notebooks
+
+You can also run LaMEM directly using Pluto notebooks:
+```julia
+julia> using Pluto
+julia> Pluto.run()
+```
+we have provided examples in the `notebooks` directory of the `LaMEM.jl` package.
+
diff --git a/docs/src/man/juliasetups.md b/docs/src/man/juliasetups.md
new file mode 100644
index 0000000..2e477d3
--- /dev/null
+++ b/docs/src/man/juliasetups.md
@@ -0,0 +1,146 @@
+# Create & run setups from julia
+
+It is also possible to construct a LaMEM setup directly in julia & run that. You can do the same from within a [Pluto](https://plutojl.org) notebook. The advantage is that it is easier to use, has build-in plotting functions and extensive documentation. 
+
+The main routine to do this is: 
+
+```julia
+julia> using LaMEM
+julia> model  = Model()
+LaMEM Model setup
+|
+|-- Scaling             :  GeoParams.Units.GeoUnits{GEO}
+|-- Grid                :  nel=(16, 16, 16); xϵ(-10.0, 10.0), yϵ(-10.0, 0.0), zϵ(-10.0, 0.0) 
+|-- Time                :  nstep_max=50; nstep_out=1; time_end=1.0; dt=0.05
+|-- Boundary conditions :  noslip=[0, 0, 0, 0, 0, 0]
+|-- Solution parameters :  eta_min=1.0e18; eta_max=1.0e25; eta_ref=1.0e20; act_temp_diff=0
+|-- Solver options      :  direct solver; superlu_dist; penalty term=10000.0
+|-- Model setup options :  Type=files; 
+|-- Output options      :  filename=output; pvd=1; avd=0; surf=0
+|-- Materials           :  0 phases; 
+```
+
+`Model` is a structure that contains all the information about the LaMEM simulation and consists of the following sub-structures that can all be adjusted.
+```
+BoundaryConditions  FreeSurface         Grid                
+Materials           ModelSetup          Output              
+Scaling             SolutionParams      Solver              
+Time
+```
+
+You can, for example, look at the current `Grid`:
+```julia
+julia> model.Grid
+LaMEM grid with constant Δ: 
+  nel         : ([16], [16], [16])
+  marker/cell : (3, 3, 3)
+  x           ϵ [-10.0 : 10.0]
+  y           ϵ [-10.0 : 0.0]
+  z           ϵ [-10.0 : 0.0]
+  Phases      : range ϵ [0 - 0]
+  Temp        : range ϵ [0.0 - 0.0]
+```
+and change the dimensions and number of grid-cells with:
+```julia
+julia> model.Grid = Grid(nel=[32,32,32], x=[-20,20])
+LaMEM grid with constant Δ: 
+  nel         : ([32], [32], [32])
+  marker/cell : (3, 3, 3)
+  x           ϵ [-20.0 : 20.0]
+  y           ϵ [-10.0 : 0.0]
+  z           ϵ [-10.0 : 0.0]
+  Phases      : range ϵ [0 - 0]
+  Temp        : range ϵ [0.0 - 0.0]
+```
+or do it by directly accessing the respectyive data field:
+```julia
+julia> model.Grid.nel_x = [32]
+1-element Vector{Int64}:
+ 32
+ ```
+
+Every LaMEM model setup needs to specify material properties for the different materials. By default it has nothing:
+```
+julia> model.Materials
+LaMEM Material Properties: 
+  Softening       = 
+  PhaseTransition = 
+ ```
+
+yet, we can specify different materials using the `Phase` structure:
+```julia
+julia> sphere = Phase(Name="Sphere", ID=1, eta=1e20, rho=2800)
+Phase 1 (Sphere): 
+  rho    = 2800.0 
+  eta    = 1.0e20 
+ ```
+and add that to the model with:
+```julia
+julia> add_phase!(model, sphere)
+julia> model
+LaMEM Model setup
+|
+|-- Scaling             :  GeoParams.Units.GeoUnits{GEO}
+|-- Grid                :  nel=(32, 32, 32); xϵ(-20.0, 20.0), yϵ(-10.0, 0.0), zϵ(-10.0, 0.0) 
+|-- Time                :  nstep_max=50; nstep_out=1; time_end=1.0; dt=0.05
+|-- Boundary conditions :  noslip=[0, 0, 0, 0, 0, 0]
+|-- Solution parameters :  eta_min=1.0e18; eta_max=1.0e25; eta_ref=1.0e20; act_temp_diff=0
+|-- Solver options      :  direct solver; superlu_dist; penalty term=10000.0
+|-- Model setup options :  Type=files; 
+|-- Output options      :  filename=output; pvd=1; avd=0; surf=0
+|-- Materials           :  1 phases; 
+ ```
+Note that the model now has 1 phase.
+
+In order to run a simulation, we need to define at least 1 phase and heterogeneities in either the initial temperature field (`model.Grid.Temp`) or the Phases field (`model.Grid.Phases`).
+The easiest way to do that is to use routines from the `GeophyicalModelGenerator` package, for which we created simple interfaces to many of the relevant routines:
+```julia
+julia> using GeophysicalModelGenerator
+julia> AddSphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
+ ```
+
+For the sake of this example, lets add another phase:
+```julia
+julia> matrix = Phase(ID=0,Name="matrix",eta=1e20,rho=3000)
+Phase 0 (matrix): 
+  rho    = 3000.0 
+  eta    = 1.0e20 
+julia> add_phase!(model, matrix)
+```
+
+At this stage you have a model setup with 2 phases and heterogeneities in the `Phases` field, which you can check with:
+```julia 
+julia> model
+LaMEM Model setup
+|
+|-- Scaling             :  GeoParams.Units.GeoUnits{GEO}
+|-- Grid                :  nel=(32, 32, 32); xϵ(-20.0, 20.0), yϵ(-10.0, 0.0), zϵ(-10.0, 0.0) 
+|-- Time                :  nstep_max=50; nstep_out=1; time_end=1.0; dt=0.05
+|-- Boundary conditions :  noslip=[0, 0, 0, 0, 0, 0]
+|-- Solution parameters :  eta_min=1.0e18; eta_max=1.0e25; eta_ref=1.0e20; act_temp_diff=0
+|-- Solver options      :  direct solver; superlu_dist; penalty term=10000.0
+|-- Model setup options :  Type=files; 
+|-- Output options      :  filename=output; pvd=1; avd=0; surf=0
+|-- Materials           :  2 phases; 
+
+
+julia> model.Grid
+LaMEM grid with constant Δ: 
+  nel         : ([32], [32], [32])
+  marker/cell : (3, 3, 3)
+  x           ϵ [-20.0 : 20.0]
+  y           ϵ [-10.0 : 0.0]
+  z           ϵ [-10.0 : 0.0]
+  Phases      : range ϵ [0 - 1]
+  Temp        : range ϵ [0.0 - 0.0]
+   ```
+
+Running a model is very simple:
+```julia
+julia> run_lamem(model,1)
+```
+
+
+
+### More examples
+More examples can be found on the left hand side menu.
\ No newline at end of file
diff --git a/docs/src/man/listfunctions.md b/docs/src/man/listfunctions.md
index 6e3af1d..fbb2bfd 100644
--- a/docs/src/man/listfunctions.md
+++ b/docs/src/man/listfunctions.md
@@ -1,6 +1,6 @@
 # List of all functions
 
-These are all functions that are available in the package, which can roughly be divided inton two groups (running & reading LaMEM)
+These are all functions that are available in the package, which can roughly be divided into two groups (running & reading LaMEM)
 
 ## Running LaMEM
 ```@autodocs
@@ -9,5 +9,5 @@ Modules = [LaMEM.Run]
 ```
 ## Reading LaMEM output back into julia
 ```@autodocs
-Modules = [LaMEM.IO_functions] 
-``` 
+Modules = [LaMEM.IO_functions]
+
diff --git a/docs/src/man/runlamem.md b/docs/src/man/runlamem.md
index 40cc117..e982159 100644
--- a/docs/src/man/runlamem.md
+++ b/docs/src/man/runlamem.md
@@ -7,7 +7,7 @@ pkg>add LaMEM
 It will automatically download a binary version of LaMEM which runs in parallel (along with the correct PETSc version). This will work on linux, mac and windows.
 
 ### Starting a simulation
-As usual, you need a LaMEM (`*.dat`) input file, which you can run in parallel (here on 4 cores) with:
+If you have a LaMEM (`*.dat`) input file, you can run in parallel (here on 4 cores) with:
 ```julia
 julia> ParamFile="input_files/FallingBlock_Multigrid.dat";
 julia> run_lamem(ParamFile, 4,"-time_end 1")
diff --git a/notebooks/FallingSphere_1.jl b/notebooks/FallingSphere_1.jl
new file mode 100644
index 0000000..6656f6d
--- /dev/null
+++ b/notebooks/FallingSphere_1.jl
@@ -0,0 +1,217 @@
+### A Pluto.jl notebook ###
+# v0.19.26
+
+using Markdown
+using InteractiveUtils
+
+# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
+macro bind(def, element)
+    quote
+        local iv = try Base.loaded_modules[Base.PkgId(Base.UUID("6e696c72-6542-2067-7265-42206c756150"), "AbstractPlutoDingetjes")].Bonds.initial_value catch; b -> missing; end
+        local el = $(esc(element))
+        global $(esc(def)) = Core.applicable(Base.get, el) ? Base.get(el) : iv(el)
+        el
+    end
+end
+
+# ╔═╡ f744857e-20e6-11ee-1720-311279133704
+begin
+    import Pkg
+    Pkg.activate(mktempdir())
+    Pkg.add(Pkg.PackageSpec(name="LaMEM", rev="bk-julia-model-setup"))
+    using LaMEM, GeophysicalModelGenerator, Plots, PlutoUI, GMT
+end
+
+# ╔═╡ 78136b07-5d33-407a-afcf-e0a656181043
+md"""
+# Falling Sphere example using LaMEM
+
+This is a first example that illustrates how to build a setup using the LaMEM.jl package, run it and visualize the results, all within a Pluto Notebook.
+
+### Load packages
+We start with loading a few packages.
+"""
+
+# ╔═╡ 4cd42d73-d63d-4149-9062-037a82f54255
+Topo = ImportTopo(lon = [-18.7, -17.1], lat=[28.0, 29.2], file="@earth_relief_03s.grd");
+
+# ╔═╡ 03abfcd4-b3bb-44eb-ba97-c03d64126195
+md"""
+### Define model setup
+
+Next, we define a general model setup, in which we specify the units with which we work (for most cases, you'll want to use the default `GEO` units), the size of the computational box and various timestepping parameters. In this case, we use a multigrid solver.
+"""
+
+# ╔═╡ 4a533c45-2ad6-4970-963b-abbbc798275b
+  model  = Model(Grid(nel=(32,16,16), x=[-1,1], y=[-1,1], z=[-1,1]), 
+  				 Time(nstep_max=20, dt_min=1e-3, dt=1, dt_max=10, time_end=100), 
+                 Solver(SolverType="multigrid", MGLevels=2),
+  				 Output(out_dir="example_1"))
+
+# ╔═╡ b192e665-20f2-4f65-ace9-fe7fffd7b7c7
+md"""
+Note that each of the fields within `Model` has many additional and adjustable parameters. You can view that by typing `Model.Time`: 
+"""
+
+# ╔═╡ 965f3210-d4da-4a0b-8db5-cce85779fd58
+model.Time
+
+# ╔═╡ e85b89ee-7452-45dc-8484-1e2497cf3f7a
+md"""
+### Specify materials
+Once this is specified, we need to set material properties for each of the `Phases` we will consider in the simulation. This can be done with the `Phase` structure. If you want to know which options are available, you can use the `Live Docs` within Pluto (right hand collumn) to get more info about `Phase`.
+"""
+
+# ╔═╡ bd63ef7e-af77-44d8-8127-456f7f6d38a6
+md""" 
+In this simulation, we will consider two materials, the matrix and a sphere with higher density. Since pluto is reactive (implying that all cells are updated once one changes), we start with removing any previously defined phases from the setup:
+"""
+
+# ╔═╡ be5335db-5535-49c6-95d2-49e53d644523
+rm_phase!(model)
+
+# ╔═╡ 6b59fe59-0d0f-4984-8464-c76c18bc8f19
+md"""
+Next, specify the matrix:
+"""
+
+# ╔═╡ 87dbe840-1d59-4608-a73b-d4dee2bd2c7a
+matrix = Phase(ID=0,Name="matrix",eta=1e20,rho=3000)
+
+# ╔═╡ 0c1c92d8-9846-4e31-9112-6c2b57e7a069
+sphere = Phase(ID=1,Name="sphere",eta=1e23,rho=3200)
+
+# ╔═╡ 78c4db3c-3f5d-4a91-9ab9-bd00ce0810af
+md"""
+And add them to the model:
+"""
+
+# ╔═╡ 2e88e435-288e-4d08-b482-e3d2398563f1
+add_phase!(model, sphere, matrix)
+
+# ╔═╡ 773314ed-bc12-4097-88a7-bad62b5b1b66
+model
+
+# ╔═╡ 5681b716-2959-4ff4-bd14-4c94641310a4
+md"""
+### Set initial model geometry
+
+We also need to specify an initial model geometry. The julia package `GeophysicalModelGenerator` has a number of functions for that, which can be used here. For the current setup, we just add a sphere: 
+"""
+
+# ╔═╡ a3afc50b-2fcd-4067-895d-fde7fb7f8742
+AddSphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
+
+# ╔═╡ e0411cc1-60ae-43cf-9500-93a246e62e1b
+md"""
+It is often useful to plot the initial model setup. You can do this with the `heatmap` function from the `Plots.jl` package, for which we provide a LaMEM plugin that allows you to specify a cross-section through a 3D LaMEM setup:
+"""
+
+# ╔═╡ fb23a0a3-1485-4726-8b6e-1a810e50ce7a
+heatmap(model, field=:phase, y=0.1)
+
+# ╔═╡ 4e5cb7d3-f6c0-4dd9-b508-643e38335297
+md"""
+In the initial serup we define two fields: `:phase` which defines the rocktypes and `:temperature` which has the initial temperature. They are stored as 3D arrays in `model.Grid.Phases` and `model.Grid.Temp`.
+"""
+
+# ╔═╡ 0993d48a-e07a-4b28-bd0c-89b2a8f08af3
+md"""
+### Run LaMEM
+
+At this stage we are ready to run a LaMEM simulation which can simply be done with the `run_lamem` command. By default, it will run on one processor. If you want to run this in parallel, you can specify the number of cores you want to use. Please note that running things in parallel is only worth the effort for large resolutions; for smaller setups it will be faster on one processor:
+"""
+
+# ╔═╡ 0873aa40-111d-421b-a72c-9ed8240a8782
+run_lamem(model,1)
+
+# ╔═╡ 319aa787-f641-42ab-bdfa-76b04e6e478a
+md"""
+### Visualize results
+
+Once the simulation is done, you can look at the results using the same `heatmap` function, but by specifying a timestep, which will read that timestep and plot a cross-section though it:
+"""
+
+# ╔═╡ eaa307f7-5655-4cf3-8638-47faa28a6a4b
+md"""
+We can read all timesteps of the simulation with:
+"""
+
+# ╔═╡ 3040c159-7281-4971-80ad-8104abb3a6d9
+timesteps,_,_ = Read_LaMEM_simulation(model)
+
+# ╔═╡ b7ca7625-4910-4faf-919c-4b785438c574
+md"""
+Lets add a slider to move through the timesteps:
+"""
+
+# ╔═╡ b99498a4-ba99-4d60-ac9e-fc70b227f91e
+md"""Timestep $(@bind t Slider(timesteps, show_value=true, default=0))"""
+
+# ╔═╡ 651f376e-e686-4288-b070-4fc14b66fb80
+md"""
+And use that to slice through time
+"""
+
+# ╔═╡ 66d66323-71a4-455a-9a7b-bd1ec3d5ae1c
+heatmap(model, y=0.2, timestep=t, field=:phase, dim=3)	
+
+# ╔═╡ 2cb9ffa5-48da-4d48-8381-51c5d8f65da5
+md"""
+If you want to know which fields have been saved, you can read a timestep back into julia:
+"""
+
+# ╔═╡ c72ffd0d-dbf7-4b88-af5e-de4f76d5ec33
+data_cart, time = Read_LaMEM_timestep(model,1)
+
+# ╔═╡ e73a3f02-c1f4-46d8-a0c2-c6f6058e1ca1
+md"""
+The results are saved to disk and you can also visualize the results with paraview.
+"""
+
+# ╔═╡ f7147dc1-17d6-47af-8d92-2f780d471e91
+md"""
+### Changing parameters
+
+Since we are using Pluto, changing values in one cell will update the full notebook. You can therefore change, for example, the maximum number of timesteps of the simulation at the top of this notebook (`nstep_max`) and it'll redo the simulation but for longer. Try it out!
+"""
+
+# ╔═╡ 778d540b-5e56-463f-87a3-d14f17e452ba
+
+
+# ╔═╡ Cell order:
+# ╟─78136b07-5d33-407a-afcf-e0a656181043
+# ╠═f744857e-20e6-11ee-1720-311279133704
+# ╠═4cd42d73-d63d-4149-9062-037a82f54255
+# ╟─03abfcd4-b3bb-44eb-ba97-c03d64126195
+# ╠═4a533c45-2ad6-4970-963b-abbbc798275b
+# ╟─b192e665-20f2-4f65-ace9-fe7fffd7b7c7
+# ╠═965f3210-d4da-4a0b-8db5-cce85779fd58
+# ╟─e85b89ee-7452-45dc-8484-1e2497cf3f7a
+# ╟─bd63ef7e-af77-44d8-8127-456f7f6d38a6
+# ╠═be5335db-5535-49c6-95d2-49e53d644523
+# ╟─6b59fe59-0d0f-4984-8464-c76c18bc8f19
+# ╠═87dbe840-1d59-4608-a73b-d4dee2bd2c7a
+# ╠═0c1c92d8-9846-4e31-9112-6c2b57e7a069
+# ╟─78c4db3c-3f5d-4a91-9ab9-bd00ce0810af
+# ╠═2e88e435-288e-4d08-b482-e3d2398563f1
+# ╠═773314ed-bc12-4097-88a7-bad62b5b1b66
+# ╟─5681b716-2959-4ff4-bd14-4c94641310a4
+# ╠═a3afc50b-2fcd-4067-895d-fde7fb7f8742
+# ╟─e0411cc1-60ae-43cf-9500-93a246e62e1b
+# ╠═fb23a0a3-1485-4726-8b6e-1a810e50ce7a
+# ╟─4e5cb7d3-f6c0-4dd9-b508-643e38335297
+# ╟─0993d48a-e07a-4b28-bd0c-89b2a8f08af3
+# ╠═0873aa40-111d-421b-a72c-9ed8240a8782
+# ╟─319aa787-f641-42ab-bdfa-76b04e6e478a
+# ╟─eaa307f7-5655-4cf3-8638-47faa28a6a4b
+# ╠═3040c159-7281-4971-80ad-8104abb3a6d9
+# ╟─b7ca7625-4910-4faf-919c-4b785438c574
+# ╟─b99498a4-ba99-4d60-ac9e-fc70b227f91e
+# ╟─651f376e-e686-4288-b070-4fc14b66fb80
+# ╠═66d66323-71a4-455a-9a7b-bd1ec3d5ae1c
+# ╟─2cb9ffa5-48da-4d48-8381-51c5d8f65da5
+# ╠═c72ffd0d-dbf7-4b88-af5e-de4f76d5ec33
+# ╟─e73a3f02-c1f4-46d8-a0c2-c6f6058e1ca1
+# ╟─f7147dc1-17d6-47af-8d92-2f780d471e91
+# ╠═778d540b-5e56-463f-87a3-d14f17e452ba
diff --git a/src/DocUtils.jl b/src/DocUtils.jl
new file mode 100644
index 0000000..50fcf04
--- /dev/null
+++ b/src/DocUtils.jl
@@ -0,0 +1,26 @@
+# Auto-generate comments from the documentation
+
+using DocStringExtensions
+export get_doc
+"""
+    help_info::String = get_doc(structure, field::Symbol) 
+This returns a string with the documentation for a parameter `field` that is within the `structure`. 
+Note that this structure must be a help structure of the current one.
+"""
+function get_doc(structure, field::Symbol) 
+    alldocs       =   Docs.meta(LaMEM.LaMEM_Model);
+    
+    var           =   eval(Meta.parse("Docs.@var($structure)"))
+    fields_local  =   alldocs[var].docs[Union{}].data[:fields]
+    str = fields_local[field]
+
+    # Add comment to next line (if required)
+    str = replace(str, "\n" => "\n #")
+
+    # remove the # at the end of the string
+    if str[end]=='#'
+        str = str[1:end-1]
+    end
+
+    return str
+end
\ No newline at end of file
diff --git a/src/LaMEM.jl b/src/LaMEM.jl
index 860480f..77f38b3 100644
--- a/src/LaMEM.jl
+++ b/src/LaMEM.jl
@@ -1,5 +1,11 @@
 module LaMEM
 
+using GeoParams
+using .GeoParams
+using Requires
+export NO_units, GEO_units, SI_units, km, m, Pa, Pas, kg, cm, yr
+#export GeoParams
+
 # Functions to read LaMEM output
 include("IO_functions.jl")
 using .IO_functions
@@ -13,13 +19,31 @@ using .Run
 export run_lamem, run_lamem_save_grid, mpiexec
 export remove_popup_messages_mac, show_paths_LaMEM
 
-include("LaMEM_ModelGeneration/LaMEM_ModelGeneration.jl")
+include("DocUtils.jl")
+
+# Functions that help running LaMEM directly from julia
+include("LaMEM_ModelGeneration/LaMEM_Model.jl")
 using .LaMEM_Model
-export Model, Grid
+export  LaMEM_Model, Model, Write_LaMEM_InputFile, create_initialsetup,
+        Scaling, Grid, Time, FreeSurface, BoundaryConditions, SolutionParams,
+        Solver, ModelSetup, 
+        geom_Sphere,
+        Output,
+        Materials, Phase, Softening, PhaseTransition, Dike, 
+        add_phase!, rm_phase!, rm_last_phase!, replace_phase!, add_petsc!, add_softening!,
+        add_phasetransition!, add_dike!, add_geom!, set_air, copy_phase,
+        add_topography!, AboveSurface!, BelowSurface!    
+
 
 using .Run.LaMEM_jll
 export LaMEM_jll        # export LaMEM_jll as well & directories
 
+function __init__()
+    #@require GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a" begin 
+    @require Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" begin
+        @eval include("PlotsExt.jl")
+    end
+end
 
 
 end # module
diff --git a/src/LaMEM_ModelGeneration/BoundaryConditions.jl b/src/LaMEM_ModelGeneration/BoundaryConditions.jl
new file mode 100644
index 0000000..d8d46e9
--- /dev/null
+++ b/src/LaMEM_ModelGeneration/BoundaryConditions.jl
@@ -0,0 +1,105 @@
+#Specify Boundary Conditions
+#
+# WARNING: incomplete, more parameters to be added 
+
+export BoundaryConditions, Write_LaMEM_InputFile
+
+"""
+    Structure that contains the LaMEM boundary conditions information. 
+    
+    $(TYPEDFIELDS)
+
+"""
+Base.@kwdef mutable struct BoundaryConditions
+    
+    "No-slip boundary flag mask (left right front back bottom top)"
+    noslip::Vector{Int64} = [0, 0, 0, 0, 0, 0]  
+
+    "Stress-free (free surface/infinitely fast erosion) top boundary flag"
+    open_top_bound::Int64 = 0                   
+    
+    "Constant temperature on the top boundary"
+    temp_top::Float64   =   0.0            
+    
+    "Constant temperature on the bottom boundary  "                 
+    temp_bot::Float64   =   1300.0              
+
+    "number intervals of constant background strain rate (x-axis)"
+    exx_num_periods::Int64  = 3                            
+    
+    "time delimiters (one less than number of intervals, not required for one interval) "    
+    exx_time_delims::Vector{Float64}  = [0.1, 5.0]    
+    
+    "strain rates for each interval          "
+    exx_strain_rates::Vector{Float64} = [1e-15, 2e-15, 1e-15]   
+
+    eyy_num_periods::Int64  = 2               
+    eyy_time_delims::Vector{Float64}  = [1.0]
+    eyy_strain_rates::Vector{Float64} = [1e-15, 2e-15]
+
+    exy_num_periods::Int64  = 2                 # same for simple shear components in x/y direction
+    exy_time_delims::Vector{Float64}  = [1.0]
+    exy_strain_rates::Vector{Float64} = [1e-15, 2e-15]
+
+    exz_num_periods::Int64  = 2                 # same for simple shear components in x/z direction
+    exz_time_delims::Vector{Float64}  = [1.0]
+    exz_strain_rates::Vector{Float64} = [1e-15, 2e-15]
+
+    eyz_num_periods::Int64  = 2                 # same for simple shear components in y/z direction
+    eyz_time_delims::Vector{Float64}  = [1.0]
+    eyz_strain_rates::Vector{Float64} = [1e-15, 2e-15]
+
+    "background strain rate reference point (fixed)"
+    bg_ref_point::Vector{Float64}     = [0.0, 0.0, 0.0]      
+
+end
+
+# Print info about the structure
+function show(io::IO, d::BoundaryConditions)
+    Reference = BoundaryConditions();    # reference values
+    println(io, "LaMEM Boundary conditions : ")
+    fields    = fieldnames(typeof(d))
+
+    # print fields
+    for f in fields
+        col = gettext_color(d,Reference, f)
+        printstyled(io,"  $(rpad(String(f),17)) = $(getfield(d,f)) \n", color=col)        
+    end
+    
+    return nothing
+end
+
+function show_short(io::IO, d::BoundaryConditions)
+    println(io,"|-- Boundary conditions :  noslip=$(d.noslip)")
+    
+    return nothing
+end
+
+
+
+"""
+    Write_LaMEM_InputFile(io, d::BoundaryConditions)
+Writes the boundary conditions related parameters to file
+"""
+function Write_LaMEM_InputFile(io, d::BoundaryConditions)
+    Reference = BoundaryConditions();    # reference values
+    fields    = fieldnames(typeof(d))
+    
+    println(io, "#===============================================================================")
+    println(io, "# Boundary conditions")
+    println(io, "#===============================================================================")
+    println(io,"")
+
+    for f in fields
+        if getfield(d,f) != getfield(Reference,f) 
+            # only print if value differs from reference value
+            name = rpad(String(f),15)
+            comment = get_doc(BoundaryConditions, f)
+            data = getfield(d,f) 
+            println(io,"    $name  = $(write_vec(data))     # $(comment)")
+        end
+    end
+
+    println(io,"")
+    return nothing
+end
\ No newline at end of file
diff --git a/src/LaMEM_ModelGeneration/ErrorChecking.jl b/src/LaMEM_ModelGeneration/ErrorChecking.jl
new file mode 100644
index 0000000..968dd7a
--- /dev/null
+++ b/src/LaMEM_ModelGeneration/ErrorChecking.jl
@@ -0,0 +1,65 @@
+# This checks the LaMEM Model setup for errors and catches them before you run a model
+export Check_LaMEM_Model
+
+
+"""
+    Check_LaMEM_Model(m::Model)
+
+Checks the LaMEM Setup Model `m` for errors
+"""
+function Check_LaMEM_Model(m::Model)
+    
+    if length(m.Materials.Phases)==0
+        error("You need to specify properties for the phases, with add_phase!(mode, Phase(ID=1,...))")
+    end
+
+    if (m.ModelSetup.msetup=="geom") && length(m.ModelSetup.geom_primitives) == 0
+        error("If you use internal geometries to set phases, you need to at least specify one internal geometry object. 
+               Example: add_geom!(model, geom_Sphere())")
+    end
+
+    if (m.ModelSetup.msetup=="files") && diff([extrema(m.Grid.Phases)...])[1]==0 && diff([extrema(m.Grid.Temp)...])[1]==0
+        error("Your initial `Temp` grid is constant, as is your initial `Phases` grid. 
+        You do need to set some variability to see action, for example with the GMG function `AddSphere!(model,cen=(0.0,0.0,0.0), radius=(0.15, ))` ")
+    end
+
+    if (m.Solver.SolverType!="direct") &&  (m.Solver.SolverType!="multigrid")
+        error("Unknown SolverType; choose either \"direct\" or \"multigrid\"!")
+    end
+
+    
+    return nothing
+end
+
+"""
+    is_rectilinear(topography::CartData)
+
+Checks whether `topography` is rectilinear
+"""
+function is_rectilinear(topography::CartData)
+    dx = extrema(diff(ustrip.(topography.x.val[:,:,1]), dims=1))
+    dy = extrema(diff(ustrip.(topography.y.val[:,:,1]), dims=2))
+    
+    return (dx[2] ≈ dx[1]) .& (dy[2] ≈ dy[1])
+end
+
+"""
+    within_bounds(model::Model, topography::CartData)
+
+Verifies that the bounds of the topography grid are larger than that of the model
+"""
+function within_bounds(model::Model, topography::CartData)
+    x_topo = extrema(topography.x.val)
+    y_topo = extrema(topography.y.val)
+    x =extrema(model.Grid.Grid.X)
+    y =extrema(model.Grid.Grid.Y)
+
+    if (x_topo[1]>x[1]) ||  (x_topo[2]<x[2]) ||
+       (y_topo[1]>y[1]) ||  (y_topo[2]<y[2])
+        within = false
+    else
+        within = true
+    end
+    return within
+end
+
diff --git a/src/LaMEM_ModelGeneration/FreeSurface.jl b/src/LaMEM_ModelGeneration/FreeSurface.jl
new file mode 100644
index 0000000..fb2ebbf
--- /dev/null
+++ b/src/LaMEM_ModelGeneration/FreeSurface.jl
@@ -0,0 +1,144 @@
+# Parameters related to the free surface
+
+# related to timestepping
+
+export FreeSurface, Write_LaMEM_InputFile
+
+"""
+    Structure that contains the LaMEM free surface information.
+
+    $(TYPEDFIELDS)
+"""
+Base.@kwdef mutable struct FreeSurface
+    "Free surface activation flag"
+    surf_use::Int64             = 0                 
+
+    "air phase ratio correction flag (phases in an element that contains are modified based on the surface position)"
+    surf_corr_phase::Int64      = 1                 
+
+    "initial level of the free surface"
+    surf_level::Union{Float64,Nothing}  = nothing               
+
+    "phase ID of sticky air layer"
+    surf_air_phase::Union{Int64,Nothing}       = nothing                 
+
+    "maximum angle with horizon (smoothed if larger)"
+    surf_max_angle::Float64     = 45.0              
+
+    "initial topography file (redundant)"
+    surf_topo_file::String      = ""                
+
+    "erosion model [0-none (default), 1-infinitely fast, 2-prescribed rate with given level]"
+    erosion_model::Int64        = 2                 
+
+    "number of erosion phases"
+    er_num_phases::Int64        = 3                 
+
+    "erosion time delimiters (one less than number)"
+    er_time_delims::Vector{Float64} = [0.5,   2.5]  
+
+    "constant erosion rates in different time periods"
+    er_rates::Vector{Float64}   = [0.2, 0.1, 0.2]   
+
+    "levels above which we apply constant erosion rates in different time periods"
+    er_levels::Vector{Int64}    = [1,   2,   1]     
+
+    "sedimentation model [0-none (dafault), 1-prescribed rate with given level, 2-cont. margin]"
+    sediment_model::Int64       = 1                 
+
+    "number of sediment layers"
+    sed_num_layers::Int64       = 3                 
+
+    "sediment layers time delimiters (one less than number)"
+    sed_time_delims::Vector{Float64} = [0.5,   2.5] 
+
+    "sediment rates in different time periods"
+    sed_rates::Vector{Float64}  = [0.3, 0.2, 0.3]   
+
+    "levels below which we apply constant sediment rates in different time periods"
+    sed_levels::Vector{Float64} = [-5,  -2,  -2]    
+
+    "sediment layers phase numbers in different time periods"
+    sed_phases::Vector{Int64}   = [1,   2,   3]     
+
+    "lateral coordinates of continental margin - origin"
+    marginO::Vector{Float64}    = [0.0, 0.0]        
+
+    "lateral coordinates of continental margin - 2nd point"
+    marginE::Vector{Float64}    = [10.0, 10.0]      
+
+    "up dip thickness of sediment cover (onshore)"
+    hUp::Float64                = 1.5               
+
+    "down dip thickness of sediment cover (off shore)"
+    hDown::Float64              = 0.1               
+
+    "half of transition zone"
+    dTrans::Float64             = 1.0    
+    
+    "Topography grid"
+    Topography::Union{CartData, Nothing} =   nothing
+end
+
+# Print info about the structure
+function show(io::IO, d::FreeSurface)
+    Reference = FreeSurface();
+    println(io, "LaMEM Free Surface parameters: ")
+    fields    = fieldnames(typeof(d))
+
+    # Do we have multiple timestepping periods? 
+    surf_use = d.surf_use
+    if surf_use==1
+        
+        # print fields
+        for f in fields
+            col = gettext_color(d,Reference, f)
+            printstyled(io,"  $(rpad(String(f),15)) = $(getfield(d,f)) \n", color=col)        
+        end
+    else
+        println(io,"  Free surface inactive")        
+    end
+  
+    return nothing
+end
+
+function show_short(io::IO, d::FreeSurface)
+    surf_use = d.surf_use
+    if surf_use==1
+        println(io,"|-- Free Surface        :  surf_level=$(d.surf_level); topo_file=$(d.surf_topo_file)")
+    end
+    
+    return nothing
+end
+
+
+
+"""
+    Write_LaMEM_InputFile(io, d::FreeSurface)
+Writes the free surface related parameters to file
+"""
+function Write_LaMEM_InputFile(io, d::FreeSurface)
+    Reference = FreeSurface();    # reference values
+    fields    = fieldnames(typeof(d))
+    surf_use  = d.surf_use
+
+    println(io, "#===============================================================================")
+    println(io, "# Free surface")
+    println(io, "#===============================================================================")
+    println(io,"")
+
+    if surf_use==1
+        for f in fields
+            if getfield(d,f) != getfield(Reference,f) && (f != :Topography)
+                # only print if value differs from reference value
+                name = rpad(String(f),15)
+                comment = get_doc(FreeSurface, f)
+                data = getfield(d,f) 
+                println(io,"    $name  = $(write_vec(data))     # $(comment)")
+            end
+        end
+    end
+
+    println(io,"")
+    return nothing
+end
\ No newline at end of file
diff --git a/src/LaMEM_ModelGeneration/GMG_interface.jl b/src/LaMEM_ModelGeneration/GMG_interface.jl
new file mode 100644
index 0000000..215a9bb
--- /dev/null
+++ b/src/LaMEM_ModelGeneration/GMG_interface.jl
@@ -0,0 +1,108 @@
+#GMG_interface
+#
+# Some wrappers around GMG routines
+
+import GeophysicalModelGenerator: AddBox!, AddSphere!, AddEllipsoid!, AddCylinder!, AboveSurface, BelowSurface
+export AboveSurface!, BelowSurface!
+
+"""
+    AddBox!(model::Model; xlim=Tuple{2}, [ylim=Tuple{2}], zlim=Tuple{2},
+            Origin=nothing, StrikeAngle=0, DipAngle=0,
+            phase = ConstantPhase(1),
+            T=nothing )
+
+Adds a box with phase & temperature structure to a 3D model setup. This simplifies creating model geometries in geodynamic models
+See the documentation of the GMG routine
+
+"""
+AddBox!(model::Model; kwargs...) = AddBox!(model.Grid.Phases, model.Grid.Temp, model.Grid.Grid; kwargs...) 
+
+
+"""
+    AddSphere!(model::Model; cen=Tuple{3}, radius=Tuple{1}, phase = ConstantPhase(1), T=nothing)
+
+See the documentation of the GMG routine
+
+"""
+AddSphere!(model::Model; kwargs...) = AddSphere!(model.Grid.Phases, model.Grid.Temp, model.Grid.Grid; kwargs...) 
+
+"""
+    AddCylinder!(model::Model;                                      # required input
+                    base=Tuple{3}, cap=Tuple{3}, radius=Tuple{1},   # center and radius of the sphere
+                    phase = ConstantPhase(1),                       # Sets the phase number(s) in the sphere
+                    T=nothing )                                     # Sets the thermal structure (various fucntions are available)
+
+
+See the documentation of the GMG routine
+
+"""
+AddCylinder!(model::Model; kwargs...) = AddCylinder!(model.Grid.Phases, model.Grid.Temp, model.Grid.Grid; kwargs...) 
+
+
+"""
+    AddEllipsoid!(model::Model;                                 # required input
+                    cen=Tuple{3}, axes=Tuple{3},                # center and semi-axes of the ellpsoid
+                    Origin=nothing, StrikeAngle=0, DipAngle=0,  # origin & dip/strike
+                    phase = ConstantPhase(1),                   # Sets the phase number(s) in the box
+                    T=nothing ) 
+
+See the documentation of the GMG routine
+
+"""
+AddEllipsoid!(model::Model; kwargs...) = AddEllipsoid!(model.Grid.Phases, model.Grid.Temp, model.Grid.Grid; kwargs...) 
+
+
+"""
+    AboveSurface(model::Model, DataSurface_Cart::CartData)
+
+Returns a boolean grid that is `true` if the `Phases/Temp` grid are above the surface
+"""
+AboveSurface(model::Model, DataSurface_Cart::CartData) = AboveSurface(model.Grid.Grid, DataSurface_Cart)
+
+
+"""
+    AboveSurface!(model::Model, DataSurface_Cart::CartData; phase::Int64=nothing, T::Number=nothing) 
+    
+Sets the `Temp` or `Phases` above the surface `DataSurface_Cart` to a constant value.
+"""
+function AboveSurface!(model::Model, DataSurface_Cart::CartData; phase::Union{Int64,Nothing}=nothing, T::Union{Number,Nothing}=nothing) 
+    
+    id = AboveSurface(model, DataSurface_Cart)
+    if !isnothing(phase)
+        model.Grid.Phases[id] .= phase
+    end
+    if !isnothing(T)
+        model.Grid.Temp[id] .= T
+    end
+
+    return nothing
+end
+
+
+
+
+"""
+    BelowSurface(model::Model, DataSurface_Cart::CartData)
+
+Returns a boolean grid that is `true` if the `Phases/Temp` grid are below the surface
+"""
+BelowSurface(model::Model, DataSurface_Cart::CartData) = BelowSurface(model.Grid.Grid, DataSurface_Cart)
+
+
+"""
+    BelowSurface!(model::Model, DataSurface_Cart::CartData; phase::Union{Int64,Nothing}=nothing, T::Union{Number,Nothing}=nothing) 
+    
+Sets the `Temp` or `Phases` below the surface `DataSurface_Cart` to a constant value.
+"""
+function BelowSurface!(model::Model, DataSurface_Cart::CartData; phase::Union{Int64,Nothing}=nothing, T::Union{Number,Nothing}=nothing) 
+    
+    id = BelowSurface(model, DataSurface_Cart)
+    if !isnothing(phase)
+        model.Grid.Phases[id] .= phase
+    end
+    if !isnothing(T)
+        model.Grid.Temp[id] .= T
+    end
+
+    return nothing
+end
\ No newline at end of file
diff --git a/src/LaMEM_ModelGeneration/Grid.jl b/src/LaMEM_ModelGeneration/Grid.jl
index 0b5802e..5d8ecf9 100644
--- a/src/LaMEM_ModelGeneration/Grid.jl
+++ b/src/LaMEM_ModelGeneration/Grid.jl
@@ -1,10 +1,10 @@
 # This is the data that stores LaMEM grid-related info
-
 export Grid, Write_LaMEM_InputFile, show_short
 
 """
     Structure that contains the LaMEM grid information
 
+    $(TYPEDFIELDS)
 
 Example 1
 ====
@@ -31,28 +31,66 @@ LaMEM grid with constant Δ:
 ```
 """
 mutable struct Grid
+    "number of markers/element in x-direction"
     nmark_x :: Int64
+    
+    "number of markers/element in y-direction"
     nmark_y :: Int64 
+    
+    "number of markers/element in x-direction"
     nmark_z :: Int64
+
+    "number of elements in x-direction"
     nel_x   :: Vector{Int64}
+
+    "number of elements in y-direction"
     nel_y   :: Vector{Int64}
+
+    "number of elements in z-direction"
     nel_z   :: Vector{Int64}
+
+    "coordinates in x-direction"
     coord_x :: Vector{Float64} 
+
+    "coordinates in y-direction"
     coord_y :: Vector{Float64} 
+
+    "coordinates in z-direction"
     coord_z :: Vector{Float64} 
+
+    "number of segments in x-direction (if we employ variable grid spacing in x-direction)"
     nseg_x  :: Int64
+
+    "number of segments in y-direction (if we employ variable grid spacing in y-direction)"
     nseg_y  :: Int64
+
+    "number of segments in z-direction (if we employ variable grid spacing in z-direction)"
     nseg_z  :: Int64
+
+    "bias in x-direction (if we employ variable grid spacing in x-direction)"
     bias_x  :: Vector{Float64} 
+
+    "bias in y-direction (if we employ variable grid spacing in y-direction)"
     bias_y  :: Vector{Float64} 
+
+    "bias in z-direction (if we employ variable grid spacing in z-direction)"
     bias_z  :: Vector{Float64} 
-    Grid:: GeophysicalModelGenerator.LaMEM_grid
+
+    "Contains the LaMEM Grid object"
+    Grid    :: GeophysicalModelGenerator.LaMEM_grid
+
+    "Phases; 3D phase information"
+    Phases  ::  Array{Int32} 
+
+    "Temp; 3D phase information"
+    Temp    ::  Array{Float64} 
 
     # set default parameters
     function Grid(;
         nmark_x=3, nmark_y=3, nmark_z=3,
         nel_x=[16], nel_y=16, nel_z=16,
         coord_x=[-10.0, 10.0], coord_y=[-10.0,0.0], coord_z=[-10.0,0.0],
+        x=nothing, y=nothing, z=nothing,
         bias_x=1.0, bias_y=1.0, bias_z=0.0,
         nel=nothing, nmark=nothing
     )   
@@ -65,6 +103,11 @@ mutable struct Grid
             end
         end
 
+        # alternative (shorter) way to define coordinates
+        if !isnothing(x);   coord_x = x;    end
+        if !isnothing(y);   coord_y = y;    end
+        if !isnothing(z);   coord_z = z;    end
+
         # Define number of markers/cell with a shortcut
         if !isnothing(nmark)
             nmark_x,nmark_y,nmark_z = nmark[1], 1, nmark[end];
@@ -75,22 +118,24 @@ mutable struct Grid
         nseg_x = length(nel_x)
         nseg_y = length(nel_y)
         nseg_z = length(nel_z)
-        
 
         # Create a LaMEM grid
         Grid_LaMEM = Create_Grid(nmark_x, nmark_y, nmark_z, nel_x, nel_y, nel_z, coord_x, coord_y, coord_z, 
-        nseg_x, nseg_y, nseg_z, bias_x, bias_y, bias_z)
+                                 nseg_x, nseg_y, nseg_z, bias_x, bias_y, bias_z)
+
+        # Define Phase and Temp structs                                 
+        Phases  = zeros(Int32,size(Grid_LaMEM.X));
+        Temp    = zeros(Float64,size(Grid_LaMEM.X));
 
         # Create struct
         return new(nmark_x, nmark_y, nmark_z, [nel_x...], [nel_y...], [nel_z...], [coord_x...], [coord_y...], [coord_z...], 
-            nseg_x, nseg_y, nseg_z, [bias_x...], [bias_y...], [bias_z...], Grid_LaMEM)
+            nseg_x, nseg_y, nseg_z, [bias_x...], [bias_y...], [bias_z...], Grid_LaMEM, Phases, Temp)
     end
 
 end
 
 
 """
-
 This creates a LaMEM grid
 """
 function  Create_Grid(nmark_x, nmark_y, nmark_z, nel_x, nel_y, nel_z, coord_x, coord_y, coord_z, 
@@ -149,6 +194,9 @@ function show(io::IO, d::Grid)
     print_coord(io, "x", d.coord_x, d.bias_x, d.nseg_x, d.Grid.xn_vec)
     print_coord(io, "y", d.coord_y, d.bias_y, d.nseg_y, d.Grid.yn_vec)
     print_coord(io, "z", d.coord_z, d.bias_z, d.nseg_z, d.Grid.zn_vec)
+    println(io,"  Phases      : range ϵ [$(minimum(d.Phases)) - $(maximum(d.Phases))]")
+    println(io,"  Temp        : range ϵ [$(minimum(d.Temp)) - $(maximum(d.Temp))]")
+
 
     return nothing
 end
@@ -156,8 +204,8 @@ end
 function show_short(io::IO, d::Grid)
     nel   = (sum(d.nel_x), sum(d.nel_y), sum(d.nel_z)) 
     x,y,z = extrema(d.coord_x), extrema(d.coord_y), extrema(d.coord_z)
-    println(io,"|-- Grid     :  nel=$(nel); xϵ$x, yϵ$y, zϵ$z ")
-
+    println(io,"|-- Grid                :  nel=$(nel); xϵ$x, yϵ$y, zϵ$z ")
+    
     return nothing
 end
 
@@ -172,13 +220,6 @@ function print_coord(io, direction, coord, bias, nseg, coord_vec)
     end
 end
 
-function write_vec(data)
-    str = ""
-    for d in data
-        str = str*" $d"
-    end
-    return str
-end
 
 """
     Write_LaMEM_InputFile(io, d::Grid)
@@ -196,8 +237,6 @@ julia> close(io)
 
 """
 function Write_LaMEM_InputFile(io, d::Grid)
-    
-    io = open("test.dat","w")
 
     println(io, "#===============================================================================")
     println(io, "# Grid & discretization parameters")
@@ -236,7 +275,6 @@ function Write_LaMEM_InputFile(io, d::Grid)
     println(io,"    nmark_z =  $(d.nmark_z)")
     
     println(io,"")
-    close(io)
 
     return nothing
 end
diff --git a/src/LaMEM_ModelGeneration/LaMEM_Model.jl b/src/LaMEM_ModelGeneration/LaMEM_Model.jl
new file mode 100644
index 0000000..dc31065
--- /dev/null
+++ b/src/LaMEM_ModelGeneration/LaMEM_Model.jl
@@ -0,0 +1,110 @@
+# These are routines that allow us to fully create a LaMEM model in julia & run it
+# In the background, it will create a lamem *.dat model setup and run that
+
+module LaMEM_Model
+
+using GeophysicalModelGenerator
+using GeophysicalModelGenerator.GeoParams
+using DocStringExtensions
+import Base: show
+import LaMEM: get_doc
+
+# Few utils that are being used
+filter_fields(fields, filter_out) = (setdiff(fields, filter_out)...,)
+gettext_color(d,Reference, field) = getfield(d,field) != getfield(Reference,field) ? :blue : :default
+
+function write_vec(data)
+    if !isa(data,String)
+        str = ""; for d in data; str = str*" $d" end
+    else
+        str = data
+    end
+
+    return str
+end
+
+
+include("Scaling.jl")   # Scaling
+export Scaling 
+
+include("Grid.jl")      # LaMEM grid 
+export Grid
+
+include("Time.jl")      # Timestepping
+export Time
+
+include("FreeSurface.jl")           # Free surface
+export FreeSurface
+
+include("BoundaryConditions.jl")    # Boundary Conditions
+export BoundaryConditions
+
+include("SolutionParams.jl")        # Solution parameters 
+export SolutionParams
+
+include("Solver.jl")                # solver options
+export Solver
+
+include("ModelSetup.jl")            # model setup options
+export ModelSetup, geom_Sphere, set_geom!
+
+include("Output.jl")                # output options
+export Output
+
+include("Materials.jl")             # main LaMEM_Model
+export Materials, Phase, Softening, PhaseTransition, Dike
+
+include("Model.jl")                 # main LaMEM_Model
+export Model
+
+include("GMG_interface.jl")
+export AboveSurface!, BelowSurface!
+
+include("Utils.jl")
+export  add_phase!, rm_phase!, rm_last_phase!, add_petsc!, add_softening!,
+        add_phasetransition!, add_dike!, add_geom!, cross_section, add_topography!
+
+
+include("ErrorChecking.jl")
+export Check_LaMEM_Model
+
+# optional dependency
+#if !isdefined(Base, :get_extension)
+#    include("MakieExt.jl")
+#end
+
+
+end
+
+
+
+
+
+
+#=
+
+# this simplifies the process to create the correct structures from the LaMEM input *.dat file
+function transfer_data()
+    io = open("test_in.dat","r")
+    io_w = open("test_out.dat","w")
+
+    while !eof(io)
+        line = readline(io)
+        line_new    = split(line,"#")
+        if length(line_new)==2
+            line_new = line_new[2:-1:1]
+            line_new[1] = "    \""*strip(line_new[1])*"\""
+        end
+        for i=1:length(line_new)
+            println(io_w,line_new[i])
+        end
+        println(io_w,"")
+
+    end
+
+    close(io)
+    close(io_w)
+end
+
+
+=#
diff --git a/src/LaMEM_ModelGeneration/LaMEM_ModelGeneration.jl b/src/LaMEM_ModelGeneration/LaMEM_ModelGeneration.jl
deleted file mode 100644
index 31e2dc4..0000000
--- a/src/LaMEM_ModelGeneration/LaMEM_ModelGeneration.jl
+++ /dev/null
@@ -1,15 +0,0 @@
-# These are routines that allow us to fully create a LaMEM model in julia & run it
-# In the background, it will create a lamem *.dat model setup and run that
-
-module LaMEM_Model
-
-using GeophysicalModelGenerator
-import Base: show
-
-include("Grid.jl")  # LaMEM grid 
-export Grid, Write_LaMEM_InputFile
-
-include("Model.jl") # main LaMEM_Model
-export Model
-
-end
\ No newline at end of file
diff --git a/src/LaMEM_ModelGeneration/Materials.jl b/src/LaMEM_ModelGeneration/Materials.jl
new file mode 100644
index 0000000..af6e3bd
--- /dev/null
+++ b/src/LaMEM_ModelGeneration/Materials.jl
@@ -0,0 +1,629 @@
+# Specify Material properties
+export Materials, Phase, Softening, PhaseTransition, Dike, Write_LaMEM_InputFile
+
+
+
+"""
+    Defines the material properties for each of the phases
+
+    $(TYPEDFIELDS)
+"""
+Base.@kwdef mutable struct Phase
+    "Material phase ID"
+    ID::Union{Nothing,Int64}    = nothing     
+
+    "Description of the phase" 
+    Name::Union{Nothing,String} = nothing   
+
+    "Density [kg/m^3]"
+    rho::Union{Nothing,Float64} = nothing
+
+    "Linear viscosity [Pas]"
+    eta::Union{Nothing,Float64} = nothing
+
+    "material ID for phase visualization (default is ID)"
+    visID::Union{Nothing,Int64}      = nothing     
+
+    "DIFFUSION creep profile; example: \"Dry_Olivine_diff_creep-Hirth_Kohlstedt_2003\""
+    diff_prof::Union{Nothing,String}  = nothing
+
+    "DISLOCATION creep profile; example: \"Granite-Tirel_et_al_2008\""
+    disl_prof::Union{Nothing,String}  = nothing                    
+
+    "PEIERLS creep profile; example:  \"Olivine_Peierls-Kameyama_1999\""
+    peir_prof::Union{Nothing,String}  = nothing               
+
+    "depth-dependent density model parameter"
+    rho_n::Union{Nothing,Float64}       = nothing   
+
+    "depth-dependent density model parameter"
+    rho_c::Union{Nothing,Float64}       = nothing   
+
+    "pressure-dependent density model parameter"
+    beta::Union{Nothing,Float64}       = nothing   
+
+    "shear modulus"
+    G::Union{Nothing,Float64}       = nothing   
+
+    "bulk modulus"
+    Kb::Union{Nothing,Float64}       = nothing   
+
+    "Young's modulus"
+    E::Union{Nothing,Float64}       = nothing   
+
+    "Poisson's ratio"
+    nu::Union{Nothing,Float64}       = nothing   
+
+    "pressure dependence parameter"
+    Kp::Union{Nothing,Float64}       = nothing   
+
+    "DIFFUSION creep pre-exponential constant"
+    Bd::Union{Nothing,Float64}       = nothing   
+
+    "activation energy"
+    Ed::Union{Nothing,Float64}       = nothing   
+
+    "activation volume"
+    Vd::Union{Nothing,Float64}       = nothing   
+
+    "POWER LAW reference viscosity"
+    eta0::Union{Nothing,Float64}       = nothing   
+
+    "reference strain rate"
+    e0 ::Union{Nothing,Float64}       = nothing   
+
+    "DISLOCATION creep pre-exponential constant"
+    Bn::Union{Nothing,Float64}       = nothing   
+
+    "activation energy"
+    En::Union{Nothing,Float64}       = nothing   
+
+    "activation volume"
+    Vn::Union{Nothing,Float64}       = nothing   
+
+    "power law exponent"
+    n::Union{Nothing,Float64}       = nothing   
+
+    "PEIERLS creep pre-exponential constant"
+    Bp::Union{Nothing,Float64}       = nothing   
+
+    "activation energy"
+    Ep::Union{Nothing,Float64}       = nothing   
+
+    "activation volume"
+    Vp::Union{Nothing,Float64}       = nothing   
+
+    "scaling stress"
+    taup::Union{Nothing,Float64}       = nothing   
+
+    "approximation parameter"
+    gamma::Union{Nothing,Float64}       = nothing   
+
+    "stress-dependence parameter"
+    q ::Union{Nothing,Float64}       = nothing   
+
+    "reference viscosity for Frank-Kamenetzky viscosity"
+    eta_fk::Union{Nothing,Float64}       = nothing   
+
+    "gamma parameter for Frank-Kamenetzky viscosity"
+    gamma_fk::Union{Nothing,Float64}       = nothing   
+
+    "reference Temperature for Frank-Kamenetzky viscosity (if not set it is 0°C)"
+    TRef_fk::Union{Nothing,Float64}       = nothing   
+
+    "cohesion"
+    ch::Union{Nothing,Float64}       = nothing   
+
+    "friction angle"
+    fr::Union{Nothing,Float64}       = nothing   
+
+    "stabilization viscosity (default is eta_min)"
+    eta_st::Union{Nothing,Float64}       = nothing   
+
+    "pore-pressure ratio"
+    rp::Union{Nothing,Float64}       = nothing   
+
+    "friction softening law ID"
+    chSoftID::Union{Nothing,Int64}       = nothing   
+
+    "cohesion softening law ID"
+    frSoftID::Union{Nothing,Int64}       = nothing  
+
+    "healing ID, points to healTau in Softening"
+    healID::Union{Nothing,Int64}       = nothing  
+
+    "thermal expansivity"
+    alpha::Union{Nothing,Float64}       = nothing 
+
+    "specific heat (capacity), J⋅K−1⋅kg−1"
+    Cp::Union{Nothing,Float64}       = nothing 
+
+    "thermal conductivity"
+    k::Union{Nothing,Float64}       = nothing 
+
+    "radiogenic heat production"
+    A::Union{Nothing,Float64}       = nothing 
+
+    "optional temperature to set within the phase"
+    T::Union{Nothing,Float64}       = nothing 
+
+    "optional, used for dike heating, J/kg"
+    Latent_hx::Union{Nothing,Float64}       = nothing 
+
+    "optional, used for dike heating, liquidus temperature of material, celsius"
+    T_liq::Union{Nothing,Float64}       = nothing 
+
+    "optional, used for dike heating, solidus temperature of material, celsius"
+    T_sol::Union{Nothing,Float64}       = nothing 
+
+    "default value for thermal conductivity boundary"
+    T_Nu::Union{Nothing,Float64}       = nothing 
+
+    "optional parameter, Nusselt number for use with conductivity"
+    nu_k::Union{Nothing,Float64}       = nothing 
+
+    "name of the phase diagram you want to use (still needs rho to be defined for the initial guess of pressure)"
+    rho_ph::Union{Nothing,String}     = nothing
+
+    "in case the phase diagram has a different path provide the path (without the name of the actual PD) here"
+    rho_ph_dir::Union{Nothing,String}     = nothing
+
+    "melt fraction viscosity correction factor (positive scalar)"
+    mfc::Union{Nothing,Float64}       = nothing 
+end
+
+function show(io::IO, d::Phase)
+    println(io, "Phase $(d.ID) ($(d.Name)): ")
+    fields    = fieldnames(typeof(d))
+
+    # print fields
+    for f in fields
+        if !isnothing(getfield(d,f)) & (f != :ID) & (f != :Name)
+            printstyled(io,"  $(rpad(String(f),9)) = $(getfield(d,f)) \n")        
+        end
+    end
+
+    return nothing
+end
+
+function show_short(d::Phase)
+    fields    = fieldnames(typeof(d))
+    str = "Phase("
+    for (i,f) in enumerate(fields)
+        if !isnothing(getfield(d,f))
+            str=str*"$(String(f))=$(getfield(d,f))"        
+            if i<length(fields)
+                str=str*","
+            end
+        end
+    end
+    str=str*")"
+    return str
+end
+
+
+"""
+    Defines strain softening parameters
+
+    $(TYPEDFIELDS)
+"""
+Base.@kwdef mutable struct Softening
+    "softening law ID"
+    ID::Int64          =   0    
+
+    "Begin of softening, in units of accumulated plastic strain (APS)"
+    APS1::Float64        =   0.1    
+
+    "End of softening, in units of accumulated plastic strain (APS)"
+    APS2::Float64        =   1.0     
+    
+    "Reduction ratio"
+    A::Float64           =   0.7     
+    
+    "Material length scale (in selected units, e.g. km in geo)"
+    Lm::Float64          =   0.2    
+    
+    # healing parameters
+    "APS when healTau2 activates"
+    APSheal2::Union{Float64,Nothing}      =   nothing 
+
+    "healing timescale parameter [Myr]  "
+    healTau::Union{Float64,Nothing}       =   nothing  
+
+    "healing timescale parameter [Myr]  starting at APS=APSheal2"
+    healTau2::Union{Float64,Nothing}      =   nothing    
+end
+
+function show(io::IO, d::Softening)
+    println(io, "Softening Law $(d.ID): ")
+    fields    = fieldnames(typeof(d))
+
+    # print fields
+    for f in fields
+        if !isnothing(getfield(d,f)) & (f != :ID) & (f != :Name)
+            printstyled(io,"  $(rpad(String(f),6)) = $(getfield(d,f)) \n")        
+        end
+    end
+
+    return nothing
+end
+
+function show_short(d::Softening)
+    fields    = fieldnames(typeof(d))
+    str = "Softening("
+    for (i,f) in enumerate(fields)
+        if !isnothing(getfield(d,f))
+            str=str*"$(String(f))=$(getfield(d,f))"        
+            if i<length(fields)
+                str=str*","
+            end
+        end
+    end
+    if str[end]==','; str = str[1:end-1] end
+    str=str*")"
+    return str
+end
+
+
+
+"""
+    Defines phase transitions on markers (that change the Phase ID of a marker depending on some conditions)
+
+    $(TYPEDFIELDS)
+"""
+Base.@kwdef mutable struct PhaseTransition
+    "Phase_transition law ID"
+    ID::Int64                      =   0           
+
+    "[Constant, Clapeyron, Box]: Constant - the phase transition occurs only at a fixed value of the parameter; Clapeyron - clapeyron slope"
+    Type::String                    =   "Constant"      
+    
+    "Type of predefined Clapeyron slope, such as Mantle_Transition_660km"
+    Name_Clapeyron::Union{Int64, Nothing}          =  nothing
+
+    "box bound coordinates: [left, right, front, back, bottom, top]"
+    PTBox_Bounds::Union{Vector{Float64}, Nothing} =   nothing   
+    
+    "1: only check particles in the vicinity of the box boundaries (2: in all directions)"
+    BoxVicinity::Union{Int64, Nothing} 	        =	1								
+
+    "[T = Temperature, P = Pressure, Depth = z-coord, X=x-coord, Y=y-coord, APS = accumulated plastic strain, MeltFraction, t = time] parameter that triggers the phase transition"
+    Parameter_transition::String                =   "T"     
+
+    "Value of the parameter [unit of T,P,z, APS] "        
+    ConstantValue::Union{Float64, Nothing}      =   1200          
+
+    "The number of involved phases [default=1]"
+    number_phases::Union{Int64, Nothing}        =   1              
+
+    "Above the chosen value the phase is 1, below it, the value is PhaseBelow"
+    PhaseAbove::Union{Vector{Int64}, Nothing}   =   nothing              
+    PhaseBelow::Union{Vector{Int64}, Nothing}   =   nothing               
+    
+    "Phase within the box  [use -1 if you don't want to change the phase inside the box]"
+    PhaseInside::Union{Vector{Int64}, Nothing}  =   nothing
+
+    "Phase outside the box [use -1 if you don't want to change the phase outside the box. If combined with OutsideToInside, all phases that come in are set to PhaseInside]"
+    PhaseOutside::Union{Vector{Int64}, Nothing} =   nothing       
+
+    "[BothWays=default; BelowToAbove; AboveToBelow] Direction in which transition works"
+    PhaseDirection::String                      =   "BothWays"      
+
+    "[APS] Parameter to reset on particles below PT or within box"
+    ResetParam::String                          =   "APS"        
+    
+    "# Temperature condition witin the box [none, constant, linear, halfspace]"
+    PTBox_TempType::String                      =   "linear"          
+    
+    "Temp @ top of box [for linear & halfspace] "               
+    PTBox_topTemp::Union{Float64, Nothing}      =   nothing                        
+
+    "Temp @ bottom of box [for linear & halfspace] "     
+    PTBox_botTemp::Union{Float64, Nothing}      =   nothing                            
+    
+    "Thermal age, usually in geo-units [Myrs] [only in case of halfspace]"
+    PTBox_thermalAge::Union{Float64, Nothing}   =   nothing        
+
+    "Temp within box [only for constant T]"                     
+    PTBox_cstTemp::Union{Float64, Nothing}      =   nothing                            
+
+    "[optional] only for NotInAirBox, velocity with which box moves in cm/yr  "
+    v_box::Union{Float64, Nothing}   =   nothing  
+
+    "[optional] beginning time of movemen in Myr"
+    t0_box::Union{Float64, Nothing}   =   nothing                    
+
+    "[optional] end time of movement in Myr"
+    t1_box::Union{Float64, Nothing}   =   nothing                         
+end
+
+function show(io::IO, d::PhaseTransition)
+    println(io, "Phase Transition Law $(d.ID): ")
+    fields    = fieldnames(typeof(d))
+
+    # print fields
+    for f in fields
+        if !isnothing(getfield(d,f)) & (f != :ID) & (f != :Name)
+            printstyled(io,"     $(rpad(String(f),20)) = $(getfield(d,f)) \n")        
+        end
+    end
+
+    return nothing
+end
+
+function show_short(d::PhaseTransition)
+    fields    = fieldnames(typeof(d))
+    str = "PhaseTransition("
+    for (i,f) in enumerate(fields)
+        if !isnothing(getfield(d,f))
+            str=str*"$(String(f))=$(getfield(d,f))"        
+            if i<length(fields)
+                str=str*","
+            end
+        end
+    end
+    if str[end]==','; str = str[1:end-1] end
+    str=str*")"
+    return str
+end
+
+
+"""
+    Defines the properties related to inserting dikes
+
+    $(TYPEDFIELDS)
+"""
+Base.@kwdef mutable struct Dike
+    "Material phase ID"
+    ID::Int64   = 0     
+
+    "value for dike/magma- accommodated extension, between 0 and 1, in the front of the box, for phase dike" 
+    Mf::Float64 = 0.5	
+
+    "[optional] value for dike/magma- accommodate extension, between 0 and 1, for dike phase; M is linearly interpolated between Mf & Mc and Mc & Mb, if not set, Mc default is set to -1 so it is not used"
+    Mc::Float64 = 0.5	   # 
+	
+    "[optional], location for Mc, must be between front and back boundaries of dike box, if not set, default value to 0.0, but not used"
+    y_Mc::Union{Nothing,Float64} = 0.5 	   # 
+
+    "value for dike/magma-accommodated extension, between 0 and 1, in the back of the box, for phase dike"    
+    Mb::Union{Nothing,Float64} = 0.5           # 
+        
+    "Phase ID "
+    PhaseID::Union{Nothing,Int64} = 0
+	    
+    "Phase transition ID "
+    PhaseTransID::Union{Nothing,Int64} = 0
+end
+
+function show(io::IO, d::Dike)
+    println(io, "Dike $(d.ID): ")
+    fields    = fieldnames(typeof(d))
+
+    # print fields
+    for f in fields
+        if !isnothing(getfield(d,f)) & (f != :ID) & (f != :Name)
+            printstyled(io,"     $(rpad(String(f),12)) = $(getfield(d,f)) \n")        
+        end
+    end
+
+    return nothing
+end
+
+function show_short(d::Dike)
+    fields    = fieldnames(typeof(d))
+    str = "Dike("
+    for (i,f) in enumerate(fields)
+        if !isnothing(getfield(d,f))
+            str=str*"$(String(f))=$(getfield(d,f))"        
+            if i<length(fields)
+                str=str*","
+            end
+        end
+    end
+    str=str*")"
+    return str
+end
+
+
+"""
+    Structure that contains the material properties in the current simulation
+    
+    $(TYPEDFIELDS)
+"""
+Base.@kwdef mutable struct Materials
+    "Different Materials implemented"
+    Phases::Vector{Phase}               =	[]
+
+    "Softening laws implemented"
+    SofteningLaws::Vector{Softening}    =	[]
+
+    "Internal Phase Transitions (that change the ID of markers) implemented"
+    PhaseTransitions::Vector{PhaseTransition}    =	[]
+
+    "Dikes implemented (mostly for MOR simulations)"
+    Dikes::Vector{Dike}             =	[]
+
+end
+
+# Print info about the structure
+function show(io::IO, d::Materials)
+    Reference = Materials();
+    println(io, "LaMEM Material Properties: ")
+
+    
+    # print phases fields
+    phases = d.Phases;
+    col = gettext_color(d,Reference, :Phases)
+    for (i,phase) in enumerate(phases)
+        str = show_short(phase)
+        if i==1
+            printstyled(io,"  $(rpad("Phases",15)) = $(str) \n", color=col)        
+        else
+            printstyled(io,"  $(rpad(" ",15)) = $(str) \n", color=col)        
+        end
+    end
+
+    # print softening laws fields
+    softening = d.SofteningLaws;
+    col = gettext_color(d,Reference, :SofteningLaws)
+    for (i,soft) in enumerate(softening)
+        str = show_short(soft)
+        if i==1
+            printstyled(io,"  $(rpad("Softening",15)) = $(str) \n", color=col)        
+        else
+            printstyled(io,"  $(rpad(" ",15)) = $(str) \n", color=col)        
+        end
+    end
+    if length(softening)==0
+        printstyled(io,"  $(rpad("Softening",15)) = \n", color=:default)        
+    end
+
+    # print Phase Transitions laws fields
+    phasetransitions = d.PhaseTransitions;
+    col = gettext_color(d,Reference, :PhaseTransitions)
+    for (i,phasetrans) in enumerate(phasetransitions)
+        str = show_short(phasetrans)
+        if i==1
+            printstyled(io,"  $(rpad("PhaseTransition",15)) = $(str) \n", color=col)        
+        else
+            printstyled(io,"     $(rpad(" ",15)) = $(str) \n", color=col)        
+        end
+    end
+    if length(phasetransitions)==0
+        printstyled(io,"  $(rpad("PhaseTransition",15)) = \n", color=:default)        
+    end
+
+    # print Phase Transitions laws fields
+    dikes = d.Dikes;
+    col = gettext_color(d,Reference, :Dikes)
+    for (i,dike) in enumerate(dikes)
+        str = show_short(dike)
+        if i==1
+            printstyled(io,"  $(rpad("Dikes",15)) = $(str) \n", color=col)        
+        else
+            printstyled(io,"  $(rpad(" ",15)) = $(str) \n", color=col)        
+        end
+    end
+    #if length(dikes)==0
+    #    printstyled(io,"  $(rpad("Dikes",15)) = \n", color=:default)        
+    #end
+
+    return nothing
+end
+
+function show_short(io::IO, d::Materials)
+    str = "|-- Materials           :  $(length(d.Phases)) phases; "
+    if length(d.SofteningLaws)>0
+        str = str*"$(length(d.SofteningLaws)) softening laws; "
+    end
+    if length(d.PhaseTransitions)>0
+        str = str*"$(length(d.PhaseTransitions)) phase transitions; "
+    end
+    if length(d.Dikes)>0
+        str = str*"$(length(d.Dikes)) dikes; "
+    end
+    println(io,str)
+
+    return nothing
+end
+
+
+"""
+    Write_LaMEM_InputFile(io, d::Output)
+Writes the free surface related parameters to file
+"""
+function Write_LaMEM_InputFile(io, d::Materials)
+
+    println(io, "#===============================================================================")
+    println(io, "# Material phase parameters")
+    println(io, "#===============================================================================")
+    println(io,"")
+
+    # Define softening laws
+    println(io, "   # Define softening laws (maximum 10)")
+    for Soft in d.SofteningLaws
+      
+        println(io, "   <SofteningStart>")
+        
+        soft_fields    = fieldnames(typeof(Soft))
+        for soft in soft_fields
+            if !isnothing(getfield(Soft,soft))
+                name = rpad(String(soft),15)
+                comment = get_doc(Softening, soft)
+                data = getfield(Soft,soft) 
+                println(io,"        $name  = $(write_vec(data))     # $(comment)")
+            end
+        end
+
+        println(io,"   <SofteningEnd>")
+        println(io,"")
+    end
+    
+    # Define PhaseTransitions laws
+    println(io, "   # Define Phase Transition laws (maximum 10)")
+    for PT in d.PhaseTransitions
+      
+        println(io, "   <PhaseTransitionStart>")
+        
+        pt_fields    = fieldnames(typeof(PT))
+        for pt in pt_fields
+            if !isnothing(getfield(PT,pt))
+                name = rpad(String(pt),15)
+                comment = get_doc(PhaseTransition, pt)
+                data = getfield(PT,pt) 
+                println(io,"        $name  = $(write_vec(data))     # $(comment)")
+            end
+        end
+
+        println(io,"   <PhaseTransitionEnd>")
+        println(io,"")
+    end
+    
+    # Define Dikes parameters
+    if length(d.Dikes)>0
+        println(io, "   # Define properties for the dike (additional source term/RHS in the continuity equation):   ")
+        println(io, "   # Define the associated phase, the amount of magma-accommodated extension on the front (Mf) and on the back (Mb) of the box and set its ID")
+    end
+    for dike in d.Dikes
+        println(io, "   <DikeStart>")
+        
+        dike_fields    = fieldnames(typeof(dike))
+        for pt in dike_fields
+            if !isnothing(getfield(dike, pt))
+                name = rpad(String(pt),15)
+                comment = get_doc(Dike, pt)
+                data = getfield(dike,pt) 
+                println(io,"        $name  = $(write_vec(data))     # $(comment)")
+            end
+        end
+
+        println(io,"   <DikeEnd>")
+        println(io,"")
+    end
+
+    # Define materials 
+    println(io, "   # Define material properties for all phases (maximum 32)")
+    println(io, "   # By default all rheological mechanisms are deactivated")
+    println(io, "   # List only active parameters in the material data block")
+    println(io,"")
+
+    # Write material properties for the different phases
+    for phase in d.Phases
+        println(io, "   <MaterialStart>")
+        phase_fields    = fieldnames(typeof(phase))
+        for p in phase_fields
+            if !isnothing(getfield(phase,p))
+                name = rpad(String(p),15)
+                comment = get_doc(Phase, p)
+                data = getfield(phase,p) 
+                println(io,"        $name  = $(write_vec(data))     # $(comment)")
+            end
+        end
+        println(io,"   <MaterialEnd>")
+        println(io,"")
+    end
+    println(io,"")
+
+    return nothing
+end
\ No newline at end of file
diff --git a/src/LaMEM_ModelGeneration/Model.jl b/src/LaMEM_ModelGeneration/Model.jl
index ebdb77f..a366829 100644
--- a/src/LaMEM_ModelGeneration/Model.jl
+++ b/src/LaMEM_ModelGeneration/Model.jl
@@ -1,26 +1,233 @@
 # This is the main LaMEM Model struct
+using GeophysicalModelGenerator.GeoParams
+import LaMEM.Run: run_lamem, run_lamem_save_grid
+using LaMEM.Run.LaMEM_jll
 
-export Model
+export Model, Write_LaMEM_InputFile, create_initialsetup, run_lamem
 
+""";
+    Model
+
+Structure that holds all the information to create a LaMEM input file
+
+    $(TYPEDFIELDS)
+"""
 mutable struct Model
+    "Scaling parameters"
+    Scaling::Scaling
+    
+    "LaMEM Grid"
     Grid::Grid
-    output_Dir::String
+    
+    "Time options"
+    Time
 
-    function Model(;
-        LaMEM_Grid=Grid(), 
-        output_Dir="output"
-        )
+    "Free surface options"
+    FreeSurface
+
+    "Boundary conditions"
+    BoundaryConditions
+
+    "Global solution parameters"
+    SolutionParams
+
+    "Solver options and optional PETSc options"
+    Solver
+
+    "Model setup"
+    ModelSetup
+
+    "Output options"
+    Output
+
+    "Material parameters for each of the phases"
+    Materials
 
-        return new(LaMEM_Grid, output_Dir)
-    end
     
 end
 
-# Show brief overview 
+"""
+    Model(;
+        Scaling=Scaling(GEO_units()),
+        Grid=Grid(), 
+        Time=Time(),
+        FreeSurface=FreeSurface(),
+        BoundaryConditions=BoundaryConditions(),
+        SolutionParams=SolutionParams(),
+        Solver=Solver(),
+        ModelSetup=ModelSetup(),
+        Output=Output(),
+        Materials=Materials()
+        )
+
+Creates a LaMEM Model setup.
+
+    $(TYPEDFIELDS)
+
+"""
+function Model(;
+    Scaling=Scaling(GEO_units()),
+    Grid=Grid(), 
+    Time=Time(),
+    FreeSurface=FreeSurface(),
+    BoundaryConditions=BoundaryConditions(),
+    SolutionParams=SolutionParams(),
+    Solver=Solver(),
+    ModelSetup=ModelSetup(),
+    Output=Output(),
+    Materials=Materials()
+    )
+
+    return Model(Scaling, Grid, Time, FreeSurface, BoundaryConditions, 
+                SolutionParams, Solver, ModelSetup, Output, Materials)
+end
+
+"""
+    Model(args...)
+
+Allow to define a model setup by specifying some of the basic objects
+
+Example
+===
+```julia
+julia> d = Model(Grid(nel=(10,1,20)), Scaling(NO_units()))
+LaMEM Model setup
+|
+|-- Scaling             :  GeoParams.Units.GeoUnits{GeoParams.Units.NONE}
+|-- Grid                :  nel=(10, 1, 20); xϵ(-10.0, 10.0), yϵ(-10.0, 0.0), zϵ(-10.0, 0.0) 
+|-- Time                :  nstep_max=50; nstep_out=1; time_end=1.0; dt=0.05
+|-- Boundary conditions :  noslip=[0, 0, 0, 0, 0, 0]
+|-- Solution parameters :  
+|-- Solver options      :  direct solver; superlu_dist; penalty term=10000.0
+|-- Model setup options :  Type=geom; 
+|-- Output options      :  filename=output; pvd=1; avd=0; surf=0
+|-- Materials           :  1 phases;  
+
+```
+
+"""
+function Model(args...)
+    names_str = typeof.(args);  # this may have { } in them
+    names_strip = ();
+    for name in names_str
+        name_str = split("$name","{")[1]
+        name_str = split("$name_str",".")[end]
+        
+        names_strip = (names_strip..., name_str)
+    end 
+    args_tuple = NamedTuple{Symbol.(names_strip)}(args)
+
+    return Model(; args_tuple...)
+end
+
+# Show brief overview of Model
 function show(io::IO, d::Model)
     println(io,"LaMEM Model setup")
     println(io,"|")
-    println(io,"|-- Scaling  : ")
-    show_short(io, d.Grid)  # grid
+    show_short(io, d.Scaling)   
+    show_short(io, d.Grid)     
+    show_short(io, d.Time)      
+    show_short(io, d.FreeSurface)   
+    show_short(io, d.BoundaryConditions)   
+    show_short(io, d.SolutionParams)   
+    show_short(io, d.Solver)   
+    show_short(io, d.ModelSetup)   
+    show_short(io, d.Output)   
+    show_short(io, d.Materials)
+end
+
+"""
+    Write_LaMEM_InputFile(d::Model,fname::String; dir=pwd())
+
+Writes a LaMEM input file based on the data stored in Model
+"""
+function Write_LaMEM_InputFile(d::Model, fname::String="input.dat"; dir=pwd())
+    Check_LaMEM_Model(d)    # check for mistakes in input
+
+    if d.Output.write_VTK_setup
+        # If we want to write an input file 
+        Write_Paraview(CartData(d.Grid.Grid, (Phases=d.Grid.Phases,Temp=d.Grid.Temp)),"Model3D")
+    end
+
+        
+    io = open(fname,"w")
+
+    Write_LaMEM_InputFile(io, d.Scaling)
+    Write_LaMEM_InputFile(io, d.Grid)
+    Write_LaMEM_InputFile(io, d.Time)
+    Write_LaMEM_InputFile(io, d.FreeSurface)
+    Write_LaMEM_InputFile(io, d.BoundaryConditions)
+    Write_LaMEM_InputFile(io, d.SolutionParams)
+    Write_LaMEM_InputFile(io, d.Solver)
+    Write_LaMEM_InputFile(io, d.ModelSetup)
+    Write_LaMEM_InputFile(io, d.Output)
+    Write_LaMEM_InputFile(io, d.Materials)
+    
+    Write_LaMEM_InputFile_PETSc(io, d.Solver)   # add PETSc options last
+
+    close(io)
+end
+
+
+"""
+    run_lamem(model::Model, cores::Int64=1, args:String=""; wait=true)
+
+Performs a LaMEM run for the parameters that are specified in `model`
+"""
+function run_lamem(model::Model, cores::Int64=1, args::String=""; wait=true)
+
+    create_initialsetup(model, cores, args);    
+    
+    cur_dir = pwd(); 
+    if !isempty(model.Output.out_dir)
+        cd(model.Output.out_dir)
+    end
+    
+    run_lamem(model.Output.param_file_name, cores, args; wait=wait)
+    
+    cd(cur_dir)
+
+    return nothing
+end
+
+"""
+    create_initialsetup(model::Model, cores::Int64=1, args::String="")
+
+Creates the initial model setup of LaMEM from `model`, which includes:
+- Writing the LaMEM (*.dat) input file
+- Write the VTK file (if requested when `model.Output.write_VTK_setup=true`)
+- Write the marker files to disk (if `model.ModelSetup.msetup="files"`)
+
+"""
+function create_initialsetup(model::Model, cores::Int64=1, args::String="")
+    
+    # Move to the working directory
+    cur_dir = pwd()
+    if !isempty(model.Output.out_dir)
+        if !isdir(model.Output.out_dir);  mkdir(model.Output.out_dir); end # create directory if needed
+        cd(model.Output.out_dir)
+    end
+
+    Write_LaMEM_InputFile(model, model.Output.param_file_name)
+    
+    if !isnothing(model.FreeSurface.Topography)
+        Save_LaMEMTopography(model.FreeSurface.Topography, model.FreeSurface.surf_topo_file)
+    end
+
+    if model.ModelSetup.msetup=="files"
+        # write marker files to disk before running LaMEM
+        Model3D = CartData(model.Grid.Grid, (Phases=model.Grid.Phases,Temp=model.Grid.Temp));
+
+        if cores>1
+            PartFile = run_lamem_save_grid(model.Output.param_file_name, cores)
+
+            Save_LaMEMMarkersParallel(Model3D, PartitioningFile=PartFile)
+        else
+            Save_LaMEMMarkersParallel(Model3D)
+        end
+    end
+
+    cd(cur_dir)
+    return nothing
+end
 
-end
\ No newline at end of file
diff --git a/src/LaMEM_ModelGeneration/ModelSetup.jl b/src/LaMEM_ModelGeneration/ModelSetup.jl
new file mode 100644
index 0000000..f9ed4bf
--- /dev/null
+++ b/src/LaMEM_ModelGeneration/ModelSetup.jl
@@ -0,0 +1,193 @@
+# Model Setup
+
+export ModelSetup, Write_LaMEM_InputFile, geom_Sphere, set_geom!
+
+"""
+    Structure that contains the LaMEM Model Setup and Advection options
+    
+    $(TYPEDFIELDS)
+"""
+Base.@kwdef mutable struct ModelSetup
+    "Setup type - can be `geom` (phases are assigned from geometric primitives), `files` (from julia input), `polygons` (from geomIO input, which requires `poly_file` to be specified) "
+    msetup::String          = "files"              
+     
+    "add random noise to the particle location"
+    rand_noise::Int64      = 1                 
+
+    "random noise flag, subsequently applied to geometric primitives"
+    rand_noiseGP::Int64    = 1                 
+
+    "background phase ID"
+    bg_phase::Int64        = 0                 
+
+    "save marker to disk flag"
+    save_mark::Int64       = 1                 
+
+    "marker input file (extension is .xxxxxxxx.dat), if using `msetup`=`files`"
+    mark_load_file::String  = "./markers/mdb"     
+
+    "marker output file (extension is .xxxxxxxx.dat)"
+    mark_save_file::String  = "./markers/mdb"     
+
+    "polygon geometry file (redundant), if using `msetup`=`polygons`"
+    poly_file::String       = "./input/poly.dat"
+
+    "initial temperature file (redundant), if not set on markers"
+    temp_file::String   = "./input/temp.dat"  
+
+    "advection scheme; options=`none` (no advection); `basic` (Euler classical implementation [default]); `Euler` (Euler explicit in time); `rk2` (Runge-Kutta 2nd order in space)"
+    advect::String      = "basic"             
+
+    "velocity interpolation scheme; options = `stag` (trilinear interpolation from FDSTAG points), `minmod` ( MINMOD interpolation to nodes, trilinear interpolation to markers + correction), `stagp` ( STAG_P empirical approach by T. Gerya) "
+    interp::String      = "stag"              
+
+    "STAG_P velocity interpolation parameter"
+    stagp_a::Float64      = 0.7               
+
+    "marker control type; options are `subgrid` (default; marker control enforced over fine scale grid), `none` (none), `basic` (AVD for cells + corner insertion), and `avd` (pure AVD for all control volumes)"
+    mark_ctrl::String           = "subgrid"              
+
+    "min/max number per cell (marker control)"
+    nmark_lim::Vector{Int64}        = [10, 100]            
+
+    "x-y-z AVD refinement factors (avd marker control)"
+    nmark_avd::Vector{Int64}        = [3, 3, 3]             
+
+    "max number of same phase markers per subcell (subgrid marker control)"
+    nmark_sub::Int64                = 1        
+
+    "Different geometric primitives that can be selected if we `msetup``=`geom`; see `geom_Sphere`"
+    geom_primitives::Vector    = []
+end
+
+# Print info about the structure
+function show(io::IO, d::ModelSetup)
+    Reference = ModelSetup();
+    println(io, "LaMEM Model Setup options: ")
+    fields    = fieldnames(typeof(d))
+
+    # print fields
+    for f in fields
+        if (f!=:geom_primitives)
+            col = gettext_color(d,Reference, f)
+            printstyled(io,"  $(rpad(String(f),17)) = $(getfield(d,f)) \n", color=col)      
+        else
+            col = gettext_color(d,Reference, f)
+            geom_objects = getfield(d,:geom_primitives)
+            if length(geom_objects)>0
+                printstyled(io,"  $(rpad(String(f),17)) = $(geom_objects[1])", color=col)   
+                for i = 2:length(geom_objects)
+                    printstyled(io,"                      $(geom_objects[i])", color=col)   
+                end
+            else
+                printstyled(io,"  $(rpad(String(f),17)) = ", color=col)   
+            end
+        end
+    end
+
+  
+    return nothing
+end
+
+
+function show_short(io::IO, d::ModelSetup)
+    println(io,"|-- Model setup options :  Type=$(d.msetup); ")
+
+    return nothing
+end
+
+
+# Geometric primitives======
+"""
+    LaMEM geometric primitive `sphere` object 
+    
+    $(TYPEDFIELDS)
+"""
+Base.@kwdef struct geom_Sphere
+    "phase"
+    phase::Int64          = 1          
+     
+    "radius of sphere"
+    radius::Float64      = 1.5
+      
+    "center of sphere"
+    center::Vector{Float64} = [1.0, 2.0, 3.0]
+        
+    "optional: Temperature of the sphere. possibilities: [constant, or nothing]"
+    Temperature::Union{String,Nothing} = nothing
+        
+    "required in case of [constant]: temperature value [in Celcius in case of GEO units]"
+    cstTemp::Union{Float64,Nothing}     = nothing   
+end
+
+
+function show(io::IO, d::geom_Sphere)
+    println(io, "Sphere(ph=$(d.phase), r=$(d.radius), cen=$(d.center), T=$(d.Temperature)=$(d.cstTemp))")
+    return nothing
+end
+
+"""
+    Write_LaMEM_InputFile(io, d::geom_Sphere)
+
+"""
+function Write_LaMEM_InputFile(io, d::geom_Sphere)
+    fields    = fieldnames(typeof(d))
+    println(io, "    <SphereStart>")
+    for f in fields
+        if !isnothing(getfield(d,f))
+            name = rpad(String(f),15)
+            comment = get_doc(geom_Sphere, f)
+            data = getfield(d,f) 
+            println(io,"        $name  = $(write_vec(data))     # $(comment)")
+        end
+    end
+    println(io, "    <SphereEnd>")
+    return nothing
+end
+# ==========================
+
+
+
+"""
+    Write_LaMEM_InputFile(io, d::ModelSetup)
+Writes options related to the Model Setup to disk
+"""
+function Write_LaMEM_InputFile(io, d::ModelSetup)
+    Reference = ModelSetup();    # reference values
+    fields    = fieldnames(typeof(d))
+
+    println(io, "#===============================================================================")
+    println(io, "# Model setup & advection")
+    println(io, "#===============================================================================")
+    println(io,"")
+
+    for f in fields
+        if getfield(d,f) != getfield(Reference,f)  ||
+            (f == :bg_phase) ||
+            (f == :msetup)
+
+            if (f != :geom_primitives)
+                # only print if value differs from reference value
+                name = rpad(String(f),15)
+                comment = get_doc(ModelSetup, f)
+                data = getfield(d,f) 
+                println(io,"    $name  = $(write_vec(data))     # $(comment)")
+            end
+        end
+    end
+
+    # Write geometric primitives in a separate block
+    if length(d.geom_primitives)>0
+        println(io, "")
+        println(io, "# Geometric primitives: \n")
+        for object in d.geom_primitives
+            Write_LaMEM_InputFile(io, object)
+        end
+
+        println("WARNING! Still need to implement geometric primitives!!")
+    end
+
+
+    println(io,"")
+    return nothing
+end
\ No newline at end of file
diff --git a/src/LaMEM_ModelGeneration/Output.jl b/src/LaMEM_ModelGeneration/Output.jl
new file mode 100644
index 0000000..e3a8532
--- /dev/null
+++ b/src/LaMEM_ModelGeneration/Output.jl
@@ -0,0 +1,214 @@
+# Output options
+
+
+export Output, Write_LaMEM_InputFile
+
+"""
+    Structure that contains the LaMEM output options
+    
+    $(TYPEDFIELDS)
+"""
+Base.@kwdef mutable struct Output
+    "output file name"
+    out_file_name       = "output"
+
+    "output directory"
+    out_dir             = ""
+
+    "parameter filename"
+    param_file_name     =   "output.dat"
+
+    "write VTK initial model setup"
+    write_VTK_setup     = true
+
+    "activate writing .pvd file"
+    out_pvd             = 1     
+
+    "dominant phase"
+    out_phase           = 1     
+
+    "density"
+    out_density         = 1     
+
+    "total (viscoelastoplastic) viscosity"
+    out_visc_total      = 1     
+
+    "creep viscosity"
+    out_visc_creep      = 1     
+
+    "velocity"
+    out_velocity        = 1     
+
+    "(dynamic) pressure"
+    out_pressure        = 0     
+
+    "total pressure"
+    out_tot_press       = 0     
+
+    "effective pressure"
+    out_eff_press       = 0     
+
+    out_over_press      = 0
+
+    out_litho_press     = 0
+
+    out_pore_press      = 0
+
+    "temperature"
+    out_temperature     = 0     
+
+    "deviatoric strain rate tensor"
+    out_dev_stress      = 0     
+
+    "second invariant of deviatoric stress tensor"
+    out_j2_dev_stress   = 0     
+
+    "deviatoric strain rate tensor"
+    out_strain_rate     = 0     
+
+    "second invariant of strain rate tensor"
+    out_j2_strain_rate  = 0     
+
+    out_shmax           = 0
+
+    out_ehmax           = 0
+
+    out_yield           = 0
+
+    "relative proportion of diffusion creep strainrate"
+    out_rel_dif_rate    = 0     
+
+    "relative proportion of dislocation creep strainrate"
+    out_rel_dis_rate    = 0     
+
+    "relative proportion of peierls creep strainrate"
+    out_rel_prl_rate    = 0     
+
+    "relative proportion of plastic strainrate"
+    out_rel_pl_rate     = 0     
+
+    "accumulated plastic strain"
+    out_plast_strain    = 0     
+
+    "plastic dissipation"
+    out_plast_dissip    = 0     
+
+    out_tot_displ       = 0
+
+    out_moment_res      = 0
+
+    out_cont_res        = 0
+
+    out_energ_res       = 0
+
+    out_melt_fraction   = 0
+
+    out_fluid_density   = 0
+
+    out_conductivity    = 0
+
+    out_vel_gr_tensor   = 0 
+
+    "activate surface output"
+    out_surf            = 0 
+
+    "activate writing .pvd file"
+    out_surf_pvd        = 0 
+    
+    "surface velocity"
+    out_surf_velocity   = 0
+
+    "surface topography "
+    out_surf_topography = 0
+
+    "amplitude of topography (=topo-average(topo))"
+    out_surf_amplitude  = 0
+
+    "activate marker output"
+    out_mark     = 0 
+
+    "activate writing .pvd file"
+    out_mark_pvd = 0 
+
+    "activate AVD phase output"
+    out_avd     = 0 
+
+    "activate writing .pvd file"
+    out_avd_pvd = 0 
+
+    "AVD grid refinement factor"
+    out_avd_ref = 0 
+
+    "activate"
+    out_ptr              = 0    
+
+    "ID of the passive tracers"
+    out_ptr_ID           = 0    
+
+    "phase of the passive tracers"
+    out_ptr_phase        = 0    
+
+    "interpolated pressure"
+    out_ptr_Pressure     = 0    
+
+    "temperature"
+    out_ptr_Temperature  = 0    
+
+    "melt fraction computed using P-T of the marker"
+    out_ptr_MeltFraction = 0    
+
+    "option that highlight the marker that are currently active"
+    out_ptr_Active       = 0    
+
+    "option that allow to store the melt fraction seen within the cell"
+    out_ptr_Grid_Mf      = 0    
+end
+
+# Print info about the structure
+function show(io::IO, d::Output)
+    Reference = Output();
+    println(io, "LaMEM Output options: ")
+    fields    = fieldnames(typeof(d))
+
+    # print fields
+    for f in fields
+        col = gettext_color(d,Reference, f)
+        printstyled(io,"  $(rpad(String(f),20)) = $(getfield(d,f)) \n", color=col)        
+    end
+
+  
+    return nothing
+end
+
+function show_short(io::IO, d::Output)
+    println(io,"|-- Output options      :  filename=$(d.out_file_name); pvd=$(d.out_pvd); avd=$(d.out_avd); surf=$(d.out_surf)")
+
+    return nothing
+end
+
+"""
+    Write_LaMEM_InputFile(io, d::Output)
+Writes the free surface related parameters to file
+"""
+function Write_LaMEM_InputFile(io, d::Output)
+    fields    = fieldnames(typeof(d))
+
+    println(io, "#===============================================================================")
+    println(io, "# Output options")
+    println(io, "#===============================================================================")
+    println(io,"")
+
+    # Write all fields that are active
+    for f in fields
+        if getfield(d,f) == 1
+            # only print if value differs from reference value
+            name = rpad(String(f),15)
+            comment = get_doc(Output, f)
+            data = getfield(d,f) 
+            println(io,"    $name  = $(write_vec(data))     # $(comment)")
+        end
+    end
+
+    println(io,"")
+    return nothing
+end
\ No newline at end of file
diff --git a/src/LaMEM_ModelGeneration/Scaling.jl b/src/LaMEM_ModelGeneration/Scaling.jl
new file mode 100644
index 0000000..32ddeb4
--- /dev/null
+++ b/src/LaMEM_ModelGeneration/Scaling.jl
@@ -0,0 +1,59 @@
+export Scaling, Write_LaMEM_InputFile 
+
+"""
+    Scaling{T} is a structure that contains the scaling info, employed in the current simulation
+    
+    $(TYPEDFIELDS)
+
+"""
+mutable struct Scaling{T}
+
+    "Scaling object (as in GeoParams), which can be `GEO_units()`, `NO_units()`, or `SI_units()`"
+    Scaling::T
+    
+    function Scaling(
+        Scaling=GEO_units()
+        )
+        return new{typeof(Scaling)}(Scaling)
+    end
+    
+end
+
+# Show brief overview 
+function show(io::IO, d::Scaling{T}) where T
+    println(io,"$(d.Scaling)")
+end
+
+function show_short(io::IO, d::Scaling{T}) where T
+    println(io,"|-- Scaling             :  $T")
+end
+
+
+function Write_LaMEM_InputFile(io, d::Scaling) 
+    println(io, "#===============================================================================")
+    println(io, "# Scaling")
+    println(io, "#===============================================================================")
+    println(io,"")
+    if isa(d,Scaling{GeoUnits{GEO}}) || isa(d,Scaling{GeoUnits{SI}})
+        if isa(d,Scaling{GeoUnits{GEO}})
+            println(io,"    units = geo")
+        elseif isa(d,Scaling{GeoUnits{SI}})
+            println(io,"    units = si")
+        end
+        char_T = ustrip(d.Scaling.temperature)
+        char_L = uconvert(u"m",d.Scaling.length);
+        char_η = uconvert(u"Pa*s",d.Scaling.viscosity);
+        char_τ = uconvert(u"Pa",d.Scaling.stress);
+        println(io,"    unit_temperature = $char_T")
+        println(io,"    unit_length      = $char_L")
+        println(io,"    unit_viscosity   = $char_η")
+        println(io,"    unit_stress      = $char_τ")
+
+    elseif isa(d,Scaling{GeoUnits{NONE}}) 
+        println(io,"    units = none")
+    else
+        error("unknown scaling")
+    end
+    println(io,"")
+
+end
diff --git a/src/LaMEM_ModelGeneration/SolutionParams.jl b/src/LaMEM_ModelGeneration/SolutionParams.jl
new file mode 100644
index 0000000..4c91974
--- /dev/null
+++ b/src/LaMEM_ModelGeneration/SolutionParams.jl
@@ -0,0 +1,183 @@
+#Solution Parameters
+
+# Capture meta-data with:
+# Docs.meta(LaMEM.LaMEM_Model)[Docs.@var(LaMEM.LaMEM_Model.SolutionParams)].docs[Union{}].data
+
+export SolutionParams, Write_LaMEM_InputFile
+
+"""
+    Structure that contains the LaMEM global solution parameters. 
+
+    $(TYPEDFIELDS)
+
+"""
+Base.@kwdef mutable struct SolutionParams
+    "gravitational acceleration vector"
+    gravity::Vector{Float64} = [0.0, 0.0, -9.81] 
+
+    """
+    free surface stabilization parameter [0 - 1]; The value has to be between 0 and 1
+    """
+    FSSA::Float64            = 1.0         
+
+    "shear heating efficiency parameter   [0 - 1]"   
+    shear_heat_eff::Float64  = 1.0             
+    
+    "Adiabatic Heating activation flag and efficiency. [0.0 - 1.0] (e.g. 0.5 means that only 50% of the potential adiabatic heating affects the energy equation)"
+    Adiabatic_Heat::Float64  = 0.0    
+    
+    "temperature diffusion activation flag"
+    act_temp_diff::Int64   = 0        
+
+    "thermal expansion activation flag"
+    act_therm_exp::Int64   = 1              
+    
+    "steady-state temperature initial guess activation flag"
+    act_steady_temp::Int64 = 1        
+    
+    "time for (quasi-)steady-state temperature initial guess"
+    steady_temp_t::Float64   = 0.0           
+
+    "number of steps for (quasi-)steady-state temperature initial guess (default = 1)"
+    nstep_steady::Int64    = 1               
+    
+    "recharge heat in anomalous bodies after (quasi-)steady-state temperature initial guess (=2: recharge after every diffusion step of initial guess)"
+    act_heat_rech::Int64   = 1               
+
+    "sets initial pressure to be the lithostatic pressure (stabilizes compressible setups in the first steps)"
+    init_lith_pres::Int64  = 1       
+    
+    "create an initial guess step (using constant viscosity `eta_ref` before starting the simulation"
+    init_guess::Int64      = 1              
+
+    "use lithostatic instead of dynamic pressure for creep laws"
+    p_litho_visc::Int64    = 1              
+    
+    "use lithostatic pressure for plasticity"
+    p_litho_plast::Int64   = 1         
+
+    "limit pressure at first iteration for plasticity"      
+    p_lim_plast::Int64     = 1              
+    
+    "add a constant value [MPa] to the total pressure field, before evaluating plasticity (e.g., when the domain is located @ some depth within the crust)  	"
+    p_shift::Int64 		    = 0
+
+    "pressure shift activation flag (enforce zero pressure on average in the top cell layer); note: this overwrites p_shift above!"
+    act_p_shift::Int64       = 1 
+
+    "viscosity lower bound [Pas]"
+    eta_min::Float64         = 1e18        
+    
+    "viscosity upper limit [Pas]   "
+    eta_max::Float64         = 1e25         
+    
+    "Reference viscosity (used for the initial guess) [Pas]"
+    eta_ref::Float64         = 1e20      
+     
+    "Reference temperature [C]"
+    T_ref::Float64           = 20.0          
+    
+    "universal gas constant (you need to change this only for non-dimensional setups)"
+    RUGC::Float64            = 8.31  
+    
+    "cohesion lower bound  [Pa]"
+    min_cohes::Float64       = 2e7           
+    
+    "friction lower bound  [degree]"
+    min_fric::Float64        = 5.0      
+     
+    "ultimate yield stress [Pa]     "
+    tau_ult::Float64         = 1e9        
+    
+    "fluid density for depth-dependent density model"
+    rho_fluid::Float64       = 1e3      
+    
+    "ground water level type for pore pressure computation (see below)"
+    gw_level_type::String    = "top"          
+    
+    "ground water level at the free surface (if defined)"
+    gw_level::Float64        = 1e100
+    
+    "Biot pressure parameter"
+    biot::Float64            = 1.0           
+    
+    "effective permeability computation activation flag"
+    get_permea::Float64      = 1             
+    
+    "stencil rescaling flag (for internal constraints, for example while computing permeability)"
+    rescal::Float64          = 1             
+    
+    "maximum melt fraction affecting viscosity reduction"
+    mfmax::Float64           = 0.15            
+    
+    "maximum number of local rheology iterations "
+    lmaxit::Int64          = 25              
+    
+    "local rheology iterations relative tolerance"
+    lrtol::Float64          = 1e-6         
+    
+    "dike activation flag (additonal term in divergence)  "
+    act_dike::Int64         = 1               
+    
+    "switch to use T-dependent conductivity, 0: not active"
+    useTk::Int64            = 1              
+    
+    "switch to use Behn & Ito heat source in the dike "
+    dikeHeat::Int64         = 1		        
+
+    "compute the velocity gradient tensor 1: active, 0: not active. If active, it automatically activates the output in the .pvd file"
+    Compute_velocity_gradient::Int64 = 1     
+    
+end
+
+# Print info about the structure
+function show(io::IO, d::SolutionParams)
+    Reference = SolutionParams();    # reference values
+    println(io, "LaMEM Solution parameters : ")
+    fields    = fieldnames(typeof(d))
+
+    # print fields
+    for f in fields
+        col = gettext_color(d,Reference, f)
+        printstyled(io,"  $(rpad(String(f),15)) = $(getfield(d,f)) \n", color=col)        
+    end
+    
+    return nothing
+end
+
+function show_short(io::IO, d::SolutionParams)
+    println(io,"|-- Solution parameters :  eta_min=$(d.eta_min); eta_max=$(d.eta_max); eta_ref=$(d.eta_ref); act_temp_diff=$(d.act_temp_diff)")
+    return nothing
+end
+
+
+
+"""
+    Write_LaMEM_InputFile(io, d::SolutionParams)
+Writes the boundary conditions related parameters to file
+"""
+function Write_LaMEM_InputFile(io, d::SolutionParams)
+    Reference = SolutionParams();    # reference values
+    fields    = fieldnames(typeof(d))
+    
+    println(io, "#===============================================================================")
+    println(io, "# Solution parameters & controls")
+    println(io, "#===============================================================================")
+    println(io,"")
+
+    for f in fields
+        if getfield(d,f) != getfield(Reference,f) ||
+            (f == :eta_ref) ||
+            (f == :gravity)
+
+            # only print if value differs from reference value
+            name = rpad(String(f),15)
+            data = getfield(d,f) 
+            help_string  = get_doc(SolutionParams, f)
+            println(io,"    $name  = $(write_vec(data))     # $(help_string)")
+        end
+    end
+
+    println(io,"")
+    return nothing
+end
diff --git a/src/LaMEM_ModelGeneration/Solver.jl b/src/LaMEM_ModelGeneration/Solver.jl
new file mode 100644
index 0000000..08a135a
--- /dev/null
+++ b/src/LaMEM_ModelGeneration/Solver.jl
@@ -0,0 +1,131 @@
+# Solver options
+
+export Solver, Write_LaMEM_InputFile
+
+"""
+    Structure that contains the LaMEM solver options
+    
+    $(TYPEDFIELDS)
+"""
+Base.@kwdef mutable struct Solver
+    "solver employed [`\"direct\"` or `\"multigrid\"`]"
+    SolverType::String      =	"direct"
+
+    "mumps/superlu_dist/pastix/umfpack  (requires these external PETSc packages to be installed!)"
+    DirectSolver::String    =	"superlu_dist"		
+
+    "penalty parameter [employed if we use a direct solver]"
+    DirectPenalty::Float64  =	1e4			
+
+    "number of MG levels [default=3]"
+    MGLevels::Int64 	    =	3			
+
+    "number of MG smoothening steps per level [default=10]"
+    MGSweeps::Int64 	    =	10			
+
+    "type of smoothener used [chebyshev or jacobi]"
+    MGSmoother::String      =	"chebyshev" 	
+
+    "Dampening parameter [only employed for Jacobi smoothener; default=0.6]"
+    MGJacobiDamp::Float64   =	0.5			
+
+    "coarse grid solver if using multigrid [`\"direct\"` / `\"mumps\"` / `\"superlu_dist\"` or `\"redundant\"` - more options specifiable through the command-line options `-crs_ksp_type` & `-crs_pc_type`]"
+    MGCoarseSolver::String  =	"direct" 		
+
+    "How many times do we copy the coarse grid? [only employed for redundant solver; default is 4]"
+    MGRedundantNum::Int64   =	4			
+
+    "The coarse grid solver for each of the redundant solves [only employed for redundant; options are `\"mumps\"`/`\"superlu_dist\"` with default `\"superlu_dist\"`]"
+    MGRedundantSolver::String   = 	"superlu_dist"		
+
+    "List with (optional) PETSc options"
+    PETSc_options::Vector{String} = []
+end
+
+# Print info about the structure
+function show(io::IO, d::Solver)
+    Reference = Solver();
+    println(io, "LaMEM Solver options: ")
+    fields    = fieldnames(typeof(d))
+
+    # print fields
+    for f in fields
+        col = gettext_color(d,Reference, f)
+        printstyled(io,"  $(rpad(String(f),17)) = $(getfield(d,f)) \n", color=col)        
+    end
+
+  
+    return nothing
+end
+
+function show_short(io::IO, d::Solver)
+    if d.SolverType=="direct"
+        println(io,"|-- Solver options      :  $(d.SolverType) solver; $(d.DirectSolver); penalty term=$(d.DirectPenalty)")
+    else
+        println(io,"|-- Solver options      :  $(d.SolverType) solver; coarse grid solver=$(d.MGCoarseSolver); $(d.MGLevels) levels")
+    end
+
+    return nothing
+end
+
+
+
+"""
+    Write_LaMEM_InputFile(io, d::Solver)
+Writes the free surface related parameters to file
+"""
+function Write_LaMEM_InputFile(io, d::Solver)
+    Reference = Solver();    # reference values
+    fields    = fieldnames(typeof(d))
+
+    println(io, "#===============================================================================")
+    println(io, "# Solver options")
+    println(io, "#===============================================================================")
+    println(io,"")
+
+    for f in fields
+        # Note that some keywords should always be specified
+        if (getfield(d,f) != getfield(Reference,f)) || 
+            (f == :SolverType)  ||
+            (f == :DirectPenalty)
+
+
+            if (f != :PETSc_options)
+                # only print if value differs from reference value
+                name = rpad(String(f),15)
+                comment = get_doc(Solver, f)
+                data = getfield(d,f) 
+                println(io,"    $name  = $(write_vec(data))     # $(comment)")
+            end
+
+        end
+    end
+
+    println(io,"")
+    return nothing
+end
+
+
+"""
+    Write_LaMEM_InputFile_PETSc(io, d::Solver)
+Writes the (optional) PETSc options to file
+"""
+function Write_LaMEM_InputFile_PETSc(io, d::Solver)
+    PETSc_options = d.PETSc_options
+
+    println(io, "#===============================================================================")
+    println(io, "# PETSc options")
+    println(io, "#===============================================================================")
+    println(io,"")
+
+    if length(PETSc_options)>0
+        println(io, "<PetscOptionsStart>")
+        for opt in PETSc_options
+            println(io,"    $opt")
+        end
+
+        println(io, "<PetscOptionsEnd>")
+    end
+    println(io,"")
+    return nothing
+end
\ No newline at end of file
diff --git a/src/LaMEM_ModelGeneration/Time.jl b/src/LaMEM_ModelGeneration/Time.jl
new file mode 100644
index 0000000..71c3694
--- /dev/null
+++ b/src/LaMEM_ModelGeneration/Time.jl
@@ -0,0 +1,118 @@
+# related to timestepping
+
+export Time, Write_LaMEM_InputFile
+
+"""
+    Structure that contains the LaMEM timestepping information. An explanation of the paramneters is given in the struct `Time_info`
+
+    $(TYPEDFIELDS)
+"""
+Base.@kwdef mutable struct Time
+    "simulation end time"
+    time_end::Float64  = 1.0      
+
+    "initial time step"
+    dt::Float64        = 0.05     
+
+    "minimum time step (declare divergence if lower value is attempted)"
+    dt_min:: Float64   = 0.01     
+
+    "maximum time step"
+    dt_max::Float64    = 0.2      
+
+    "output step (output at least at fixed time intervals)"
+	dt_out::Float64    = 0.2      
+
+    "time step increment per time step (fraction of unit)"
+	inc_dt::Float64    = 0.1      
+
+    "CFL (Courant-Friedrichs-Lewy) criterion"
+	CFL::Float64       = 0.5      
+
+    "CFL criterion for elasticity"
+	CFLMAX::Float64    = 0.8      
+
+    "maximum allowed number of steps (lower bound: time_end/dt_max)"
+	nstep_max::Int64   = 50       
+
+    "save output every n steps; Set this to -1 to deactivate saving output"
+	nstep_out::Int64   = 1        
+
+    "save restart database every n steps"
+	nstep_rdb::Int64   = 100      
+
+    "number of time stepping periods"
+    num_dt_periods::Int64 = 0     
+
+    "timestamps where timestep should be fixed (first entry has to 0)"
+    time_dt_periods::Vector{Int64} = []     
+
+    "target timesteps ar timestamps above"
+    step_dt_periods::Vector{Float64} = []   
+
+    "save output for n initial steps"
+    nstep_ini::Int64   = 1            
+
+    "relative tolerance for time comparisons"
+    time_tol::Float64  = 1e-8        
+end
+
+# Print info about the structure
+function show(io::IO, d::Time)
+    Reference = Time();    # reference values
+    println(io, "LaMEM Timestepping parameters: ")
+    fields         = fieldnames(typeof(d))
+
+    # Do we have multiple timestepping periods? 
+    num_dt_periods = d.num_dt_periods   
+    if num_dt_periods==0
+        fields = filter_fields(fields, (:num_dt_periods, :time_dt_periods, :step_dt_periods))
+    end
+
+    # print fields
+    for f in fields
+        col = gettext_color(d,Reference, f)
+        printstyled(io,"  $(rpad(String(f),15)) = $(getfield(d,f)) \n", color=col)        
+    end
+  
+    return nothing
+end
+
+function show_short(io::IO, d::Time)
+    println(io,"|-- Time                :  nstep_max=$(d.nstep_max); nstep_out=$(d.nstep_out); time_end=$(d.time_end); dt=$(d.dt)")
+    return nothing
+end
+
+
+
+"""
+Writes the Time related parameters to file
+"""
+function Write_LaMEM_InputFile(io, d::Time)
+    Reference = Time();    # reference values
+    fields    = fieldnames(typeof(d))
+
+    println(io, "#===============================================================================")
+    println(io, "# Time stepping parameters")
+    println(io, "#===============================================================================")
+    println(io,"")
+
+    for f in fields
+        if getfield(d,f) != getfield(Reference,f) ||
+            (f == :dt_max)  ||  
+            (f == :time_end) ||
+            (f == :nstep_max)
+            
+
+            # only print if value differs from reference value
+            name = rpad(String(f),15)
+            comment = get_doc(Time, f)
+            data = getfield(d,f) 
+            
+            println(io,"    $name  = $(write_vec(data))     # $(comment)")
+        end
+    end
+
+    println(io,"")
+    return nothing
+end
\ No newline at end of file
diff --git a/src/LaMEM_ModelGeneration/Utils.jl b/src/LaMEM_ModelGeneration/Utils.jl
new file mode 100644
index 0000000..d167d2e
--- /dev/null
+++ b/src/LaMEM_ModelGeneration/Utils.jl
@@ -0,0 +1,323 @@
+# Contains a number of useful functions
+import LaMEM.IO_functions: Read_LaMEM_simulation, Read_LaMEM_timestep
+
+export  add_phase!, rm_phase!, rm_last_phase!, replace_phase!,
+        add_softening!, add_phasetransition!, 
+        add_dike!, add_geom! , cross_section,
+        set_air, copy_phase
+
+
+"""
+    add_phase!(model::Model, phase::Phase)
+This adds a `phase` (with material properties) to `model`
+"""
+function add_phase!(model::Model, phase::Phase) 
+    push!(model.Materials.Phases, phase);
+    return nothing
+end
+
+"""
+    add_phase!(model::Model, phases...) 
+Add several phases @ once.
+"""
+function add_phase!(model::Model, phases...) 
+    for phase in phases
+        push!(model.Materials.Phases, phase);
+    end
+end
+
+
+"""
+    rm_last_phase!(model::Model, phase::Phase)
+This removes the last added `phase` from `model`
+"""
+function rm_last_phase!(model::Model) 
+    if length(model.Materials.Phases)>0
+        model.Materials.Phases= model.Materials.Phases[1:end-1]
+    end
+    return nothing
+end
+
+"""
+    rm_phase!(model::Model, ID::Int64)
+This removes a phase with `ID` from `model`
+"""
+function rm_phase!(model::Model, ID::Int64) 
+    id_vec = [phase.ID for phase in model.Materials.Phases]
+    id = findall(id_vec .== ID)
+    deleteat!(model.Materials.Phases,id)
+    return nothing
+end
+
+"""
+    rm_phase!(model::Model)
+This removes all existing phases from `model`
+"""
+function rm_phase!(model::Model) 
+    model.Materials.Phases = []
+    return nothing
+end
+
+"""
+    replace_phase!(model::Model, phase_new::Phase; ID::Int64=nothing, Name::String=nothing)
+
+This replaces a `phase` within a LaMEM Model Setup `model` with `phase_new` either based on its `Name` or `ID`. 
+Note that it is expected that only one such phase is present in the current setup.
+"""
+function replace_phase!(model::Model, phase_new::Phase; ID::Union{Nothing,Int64}=nothing, Name::Union{Nothing,String}=nothing) 
+    id_vec   = [phase.ID for phase in model.Materials.Phases]
+    name_vec = [phase.Name for phase in model.Materials.Phases]
+    if !isnothing(ID)
+        id = findfirst(id_vec .== ID)
+    elseif !isnothing(Name)
+        id = findfirst(name_vec .== Name)
+    end
+    model.Materials.Phases[id] = phase_new
+
+    return nothing
+end
+
+
+"""
+    add_petsc!(model::Model, option::String) 
+
+Adds one or more PETSc options to the model 
+
+Example
+===
+```julia
+julia> d = Model()
+julia> add_petsc!(d,"-snes_npicard 3")
+```
+
+"""
+function add_petsc!(model::Model, args...) 
+    for arg in args
+        push!(model.Solver.PETSc_options , arg);
+    end
+    return nothing
+end
+
+
+function add_softening!(model::Model, args...) 
+    for arg in args
+        push!(model.Solver.PETSc_options , arg);
+    end
+    return nothing
+end
+
+"""
+    add_softening!(model::Model, soft::Softening)
+This adds a plastic softening law `soft` to `model`
+"""
+function add_softening!(model::Model, soft::Softening) 
+    push!(model.Materials.SofteningLaws, soft);
+    return nothing
+end
+
+"""
+    add_phasetransition!(model::Model, phase_trans::PhaseTransition)
+This adds a phase transition `phase_trans` to `model`
+"""
+function add_phasetransition!(model::Model, phase_trans::PhaseTransition) 
+    push!(model.Materials.PhaseTransitions, phase_trans);
+    return nothing
+end
+
+"""
+    add_dike!(model::Model, dike::Dike)
+This adds a phase transition `phase_trans` to `model`
+"""
+function add_dike!(model::Model, dike::Dike)
+    push!(model.Materials.Dikes, dike);
+    return nothing
+end
+
+
+"""
+    add_geom!(model::Model, geom_object)
+This adds an internal geometric primitive object `geom_object` to the LaMEM Model Setup `model`.
+
+Currently available primitive geom objects are:
+- `geom_Sphere`
+"""
+function add_geom!(model::Model, geom_object)
+    push!(model.ModelSetup.geom_primitives, geom_object);
+    set_geom!(model, geom_object)
+    return nothing
+end
+
+
+"""
+
+This sets the geometry 
+"""
+function set_geom!(model::Model, d::geom_Sphere)
+   
+    cen = (d.center...,)
+    radius = d.radius
+    phase  =  ConstantPhase(d.phase)
+    T = d.Temperature
+    if !isnothing(T)
+        T=ConstantTemp(T)
+    end
+
+    # call a GMG routine
+    AddSphere!(model.Grid.Phases,model.Grid.Temp,model.Grid.Grid, cen=cen, radius=radius, phase=phase, T=T)
+
+    return nothing
+end
+
+
+"""
+    Timestep, FileNames, Time = Read_LaMEM_simulation(model::Model; phase=false, surf=false, passive_tracers=false)
+
+Reads a LaMEM simulation as specified in `model` and returns the timesteps, times and filenames of that simulation once it is finished.
+"""
+Read_LaMEM_simulation(model::Model; kwargs...) = Read_LaMEM_simulation(model.Output.out_file_name,model.Output.out_dir; kwargs...)
+
+"""
+    data, time = Read_LaMEM_timestep(model::Model, TimeStep::Int64=0; fields=nothing, phase=false, surf=false, last=true)
+
+Reads a specific `Timestep` from a simulation specified in `model`
+"""
+function Read_LaMEM_timestep(model::Model, TimeStep::Int64=0; kwargs...) 
+    FileName    = model.Output.out_file_name
+
+    cur_dir = pwd(); 
+    if !isempty(model.Output.out_dir)
+        cd(model.Output.out_dir)
+    end
+
+    data, time = Read_LaMEM_timestep(FileName,TimeStep; kwargs...)
+    
+    cd(cur_dir)
+
+    return data, time
+end
+
+
+
+"""
+    data_tuple, axes_str = cross_section(model::LaMEM.Model, field=:phases; x=nothing, y=nothing, z=nothing)
+
+This creates a cross-section through the initial model setup & returns a 2D array
+"""
+function cross_section(model::Model, field::Symbol=:phase; x=nothing, y=nothing, z=nothing)
+    Model3D = CartData(model.Grid.Grid, (phase=model.Grid.Phases,temperature=model.Grid.Temp));
+    
+    data_tuple, axes_str = cross_section(Model3D, field; x=x, y=y, z=z)
+    
+    return data_tuple, axes_str
+end
+
+"""
+    Cross = cross_section(cart::CartData, field::Symbol =:phase; x=nothing, y=nothing, z=nothing)
+
+Creates a cross-section through the data and returns `x,z` coordinates
+"""
+function cross_section(cart::CartData, field::Symbol=:phase; x=nothing, y=nothing, z=nothing)
+    
+    if !isnothing(z); Depth_level = z*km; else Depth_level=nothing; end
+    if !isnothing(x); Lon_level = x; else Lon_level=nothing; end
+    if !isnothing(y); Lat_level = y; else Lat_level=nothing; end
+    
+    Cross = CrossSectionVolume(cart, Depth_level=Depth_level, Lat_level=Lat_level, Lon_level=Lon_level)
+
+    data_tuple, axes_str = flatten(Cross, field,x,y,z)
+    return data_tuple, axes_str
+end
+
+"""
+Creates a 2D array out of a cross-section and a specified data field
+"""
+function flatten(cross::CartData, field::Symbol,x,y,z)
+    dim     =   findall(size(cross.x.val) .== 1)[1]
+    X       =   dropdims(cross.x.val, dims=dim)
+    Y       =   dropdims(cross.y.val, dims=dim)
+    Z       =   dropdims(cross.z.val, dims=dim)
+    data_or =   getfield(cross.fields,field)
+
+    # flatten data array
+    if isa(data_or, Array)
+        data = dropdims(data_or, dims=dim)
+    elseif isa(data_or,Tuple)
+        # vectors or tensors
+        data = ()
+        for d in data_or
+            data = (data..., dropdims(d, dims=dim) )
+        end
+    end
+
+    if  dim==1
+        title_str = "x = $x"
+        x_str,z_str = "y","z"
+        x, z = Y[:,1],  Z[1,:]
+    elseif  dim==2
+        title_str = "y = $y"
+        x_str,z_str = "x","z"
+        x, z = X[:,1],  Z[1,:]
+    elseif dim==3
+        title_str = "z = $z"
+        x_str,z_str = "x","y"
+        x, z = X[:,1],  Y[1,:]
+    end
+    axes_str = (x_str=x_str, z_str=z_str, title_str=title_str)
+    data_tuple = (x=x,z=z,data=data)
+    return data_tuple, axes_str
+end
+
+    
+"""
+    set_air(; Name="air", ID=0, rho=1, alpha=nothing, eta=1e17, G=nothing, nu=nothing, fr=nothing, ch=nothing, k=30,Cp=1000)
+Sets an air phase, with high conductivity 
+"""
+function set_air(; Name="air", ID=0, rho=1, alpha=nothing, eta=1e17, G=nothing, nu=nothing, fr=nothing, ch=nothing,
+                k=30,Cp=1000)
+    return Phase(Name=Name, ID=ID, rho=100, alpha=alpha, eta=eta, G=G, nu=nu, k=k, Cp=Cp, fr=fr, ch=ch)
+end
+
+
+"""
+    copy_phase(phase::Phase; kwargs...)
+
+This copies a phase with material properties, while allowing to change some parameters
+"""
+function copy_phase(phase::Phase; kwargs...)
+    phase_new = deepcopy(phase)
+    # update fields
+    for ph in keys(kwargs)
+        setfield!(phase_new,ph, kwargs[ph])
+    end
+
+    return phase_new
+end
+
+
+"""
+    add_topography!(model::Model, topography::CartData; surf_air_phase=0, surf_topo_file="topography.txt", open_top_bound=1,  surf_level=0.0)
+
+Adds the topography surface to the model
+"""
+function add_topography!(model::Model, topography::CartData; surf_air_phase=0, surf_topo_file="topography.txt", 
+            open_top_bound=1, surf_level=0.0)
+    if !is_rectilinear(topography)
+        error("topography grid must be rectilinear")
+    end
+    if !within_bounds(model, topography)
+        error("topography grid must be larger than the model")
+    end
+
+    model.FreeSurface.Topography = topography # add topo
+    model.FreeSurface.surf_use = 1
+    model.FreeSurface.surf_air_phase = surf_air_phase
+    model.FreeSurface.surf_level = surf_level
+    if isempty(model.FreeSurface.surf_topo_file)
+        model.FreeSurface.surf_topo_file = surf_topo_file
+    end
+
+    # usually we want an open top boundary when we have a free surface:
+    model.BoundaryConditions.open_top_bound=open_top_bound
+
+    return nothing
+end
\ No newline at end of file
diff --git a/src/PlotsExt.jl b/src/PlotsExt.jl
new file mode 100644
index 0000000..b46ed62
--- /dev/null
+++ b/src/PlotsExt.jl
@@ -0,0 +1,70 @@
+# Plotting extensions, that are only loaded when GLMakie is available
+println("Adding Plots.jl plotting extensions for LaMEM")
+
+using LaMEM, GeophysicalModelGenerator
+using .Plots
+import .Plots: heatmap
+export plot_topo
+ 
+"""
+    Plots.heatmap(model::Union{Model,CartData}, args...; field::Symbol=:phase,  dim=1, x=nothing, y=nothing, z=nothing, aspect_ratio::Union{Real, Symbol}=:equal)
+   
+This plots a `Plots` heatmap of a cross-section through the LaMEM `model`, of the field  `field`. If that is a vector or tensor field, specify `dim` to indicate which of the fields you want to see.
+If the keyword `timestep` is specified, it will load a timestep 
+"""
+function Plots.heatmap(model::Union{Model,CartData}, args...; field::Symbol=:phase, timestep=nothing, dim=1, x=nothing, y=nothing, z=nothing, aspect_ratio::Union{Real, Symbol}=:equal)
+    
+    if !isnothing(timestep)
+        # load a particular timestep
+        data_cart, time = Read_LaMEM_timestep(model,timestep)
+        model = data_cart
+    end
+
+    if isnothing(x) && isnothing(y) && isnothing(z)
+        x = mean(extrema(model.Grid.Grid.X))
+    end
+    
+    data_tuple, axes_str = cross_section(model, field; x=x, y=y, z=z)
+    
+    if isa(data_tuple.data, Array)
+        data_field = data_tuple.data
+        cb_str = String(field)
+    elseif isa(data_tuple.data, Tuple)
+        data_field = data_tuple.data[dim]
+        cb_str = String(field)*"[$dim]"
+    end
+
+    title_str = axes_str.title_str
+    if !isnothing(timestep)
+        title_str=title_str*"; time=$(time[1])"
+    end
+
+    hm = heatmap(data_tuple.x, data_tuple.z, data_field', 
+                aspect_ratio=aspect_ratio, 
+                xlabel=axes_str.x_str,
+                ylabel=axes_str.z_str,
+                title=title_str,
+                colorbar_title=cb_str,
+                args...)
+                
+    return hm
+end
+
+
+"""
+    plot_topo(topo::CartData, args...)
+
+Simple function to plot the topography 
+"""
+function plot_topo(topo::CartData; kwargs...)
+   
+    hm = heatmap(topo.x.val[:,1,1], topo.y.val[1,:,1], topo.fields.Topography[:,:,1]'; 
+                aspect_ratio=:equal, 
+                xlabel="x",
+                ylabel="y",
+                title="topography [km]",
+                colormap=:oleron,
+                kwargs...)
+                
+    return hm
+end
\ No newline at end of file
diff --git a/src/read_timestep.jl b/src/read_timestep.jl
index a895c69..346a092 100644
--- a/src/read_timestep.jl
+++ b/src/read_timestep.jl
@@ -25,7 +25,7 @@ Output:
 """
 function ReadField_3D_pVTR(pvtk, FieldName)
     isCell          =   false;
-    
+
     # first try to get point data 
     data_f = get_point_data(pvtk)
     # if empty then load cell data
@@ -36,10 +36,17 @@ function ReadField_3D_pVTR(pvtk, FieldName)
         if typeof(data_Field[1])==UInt8
             data_Field = Int64.(data_Field)
         end
+
+        data_Field  = ArrayToTuple(data_Field);
+        
         data_Tuple  = (data_Field,)
         isCell      =   true;
     else
-        data_Tuple  = (get_data_reshaped(data_f[FieldName]),)
+        data_Field = get_data_reshaped(data_f[FieldName]);
+        
+        data_Field = ArrayToTuple(data_Field);
+
+        data_Tuple = (data_Field,)
     end
 
     name = filter(x -> !isspace(x), FieldName)  # remove white spaces
@@ -53,6 +60,24 @@ function ReadField_3D_pVTR(pvtk, FieldName)
     return data_out, isCell
 end
 
+"""
+    data_Field = ArrayToTuple(data_Field)
+Transfers a n by 3D array (n>1) to 
+"""
+function ArrayToTuple(data_Field)
+    if length(size(data_Field))>3
+        # this a vector or tensor field. For compatibility with GMG, we need to make a tuple out of this
+        n = size(data_Field)[1]
+        data_t=();
+        for i=1:n
+            data_t = (data_t..., data_Field[i,:,:,:])
+        end
+        data_t
+    else
+        data_t = data_Field
+    end
+    return data_t
+end
 
 function ReadField_3D_pVTS(pvts, FieldName)
     isCell          =   false;
diff --git a/test/CreateMarkers_Subduction_Linear_FreeSlip_parallel.jl b/test/CreateMarkers_Subduction_Linear_FreeSlip_parallel.jl
index 62d4afd..1c3e124 100644
--- a/test/CreateMarkers_Subduction_Linear_FreeSlip_parallel.jl
+++ b/test/CreateMarkers_Subduction_Linear_FreeSlip_parallel.jl
@@ -5,7 +5,7 @@ using GeophysicalModelGenerator
 
 # Load LaMEM particles grid
 ParamFile_2 =   "input_files/Subduction2D_FreeSlip_Particles_Linear_DirectSolver.dat"
-Grid        =   ReadLaMEM_InputFile(ParamFile_2)
+Grid_LaMEM  =   ReadLaMEM_InputFile(ParamFile_2)
 
 # Specify slab parameters
 Trench_x_location   = -500;     # trench location
@@ -21,17 +21,17 @@ T_surface           =   0;
 
 ThicknessSlab = ThicknessCrust+ThicknessML
 
-Phases      =   zeros(Int64, size(Grid.X));             # Rock numbers
-Temp        =   ones(Float64,size(Grid.X))*T_mantle;    # Temperature in C    
+Phases      =   zeros(Int64, size(Grid_LaMEM.X));             # Rock numbers
+Temp        =   ones(Float64,size(Grid_LaMEM.X))*T_mantle;    # Temperature in C    
 
 # Create horizontal part of slab with crust & mantle lithosphere
-AddBox!(Phases,Temp,Grid,
+AddBox!(Phases,Temp,Grid_LaMEM,
         xlim=(Trench_x_location, Trench_x_location+Length_Horiz_Slab), 
         zlim=(-ThicknessSlab   , 0.0),
         phase=LithosphericPhases(Layers=[ThicknessCrust ThicknessML], Phases=[1 2 0]) );               
 
 # Add inclined part of slab                            
-AddBox!(Phases,Temp,Grid,
+AddBox!(Phases,Temp,Grid_LaMEM,
         xlim=(Trench_x_location-Length_Subduct_Slab, Trench_x_location), 
         zlim=(-ThicknessSlab   , 0.0),
         DipAngle=-SubductionAngle,
@@ -39,7 +39,7 @@ AddBox!(Phases,Temp,Grid,
         phase=LithosphericPhases(Layers=[ThicknessCrust ThicknessML], Phases=[1 2 0]) );               
 
 # Save julia setup 
-Model3D     =   CartData(Grid, (Phases=Phases,Temp=Temp))   # Create LaMEM model:
+Model3D     =   CartData(Grid_LaMEM, (Phases=Phases,Temp=Temp))   # Create LaMEM model:
 Write_Paraview(Model3D,"LaMEM_ModelSetup")                  # Save model to paraview   (load with opening LaMEM_ModelSetup.vts in paraview)  
 
 # Save LaMEM markers
diff --git a/test/read_timestep.jl b/test/read_timestep.jl
index b36806a..9e2a872 100644
--- a/test/read_timestep.jl
+++ b/test/read_timestep.jl
@@ -1,5 +1,4 @@
 using Test
-using LaMEM
 
 @testset "read LaMEM output" begin
 
@@ -7,8 +6,8 @@ using LaMEM
     FileName="FB_multigrid"
     Timestep = 1
     data, time = Read_LaMEM_timestep(FileName,Timestep)
-    @test  sum(data.fields.phase) ≈ 736.36414f0
-    @test  sum(data.fields.strain_rate[1,:,:,:]) ≈ -0.019376338f0
+    @test  data.fields.phase[1000] ≈ 0.0f0
+    @test  data.fields.strain_rate[1][1] ≈ -0.0010996389f0
 
     fields = Read_LaMEM_fieldnames(FileName)
     
@@ -18,11 +17,11 @@ using LaMEM
     Timestep = 1
     data, time = Read_LaMEM_timestep(FileName,Timestep, phase=true)
     
-    @test sum(data.fields.phase) == 19822
+    @test data.fields.phase[1000] == 0
 
     # read subduction setup
     data, time = Read_LaMEM_timestep("Subduction2D_FreeSlip_direct",1)
-    @test sum(data.fields.density) ≈ 1.60555f8
+    @test data.fields.density[10000] ≈ 3200.0f0
 
     # Read PVD file 
     Timestep, FileNames, Time  = Read_LaMEM_simulation("Subduction2D_FreeSlip_direct")
diff --git a/test/runLaMEM.jl b/test/runLaMEM.jl
index f541ca5..8777ea7 100644
--- a/test/runLaMEM.jl
+++ b/test/runLaMEM.jl
@@ -1,5 +1,4 @@
 using Test
-using LaMEM
 
 @testset "run LaMEM" begin
  
diff --git a/test/run_lamem_save_grid_test.jl b/test/run_lamem_save_grid_test.jl
index b8b83a3..c91f209 100644
--- a/test/run_lamem_save_grid_test.jl
+++ b/test/run_lamem_save_grid_test.jl
@@ -1,5 +1,4 @@
 using Test
-using LaMEM
 
 @testset "run lamem mode save grid test" begin
 
diff --git a/test/runtests.jl b/test/runtests.jl
index f2f95a2..be5b35f 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -1,6 +1,7 @@
 using Test
 using LaMEM
 
+include("test_julia_setups.jl")
 include("runLaMEM.jl")
 include("read_timestep.jl")
 include("run_lamem_save_grid_test.jl")
diff --git a/test/test_julia_setups.jl b/test/test_julia_setups.jl
new file mode 100644
index 0000000..9faa7a0
--- /dev/null
+++ b/test/test_julia_setups.jl
@@ -0,0 +1,39 @@
+# This tests running the full code from julia
+
+using Test
+using GeophysicalModelGenerator
+
+@testset "Julia setup" begin
+
+    # ===============================
+    # Simple linear viscous setup with falling sphere
+
+    # Main model setup
+    model  = Model(Grid(nel=(16,16,16), x=[-2,2], coord_y=[-1,1], coord_z=[-1,1]),
+                   Time(nstep_max=2, dt=1, dt_max=10), 
+                   Solver(SolverType="multigrid", MGLevels=2),
+                   Output(out_dir="example_1"))
+    
+    # Specify material properties
+    matrix = Phase(ID=0,Name="matrix",eta=1e20,rho=3000)
+    sphere = Phase(ID=1,Name="sphere",eta=1e23,rho=3200)
+    add_phase!(model, sphere, matrix)
+
+    # Add an initial geometry (using GeophysicalModelGenerator routines)
+    AddSphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
+
+    # run the simulation on 1 core
+    run_lamem(model, 1);
+
+    # read last timestep
+    data,time = Read_LaMEM_timestep(model,last=true);
+
+    @test  sum(data.fields.velocity[3][:,:,:]) ≈ 0.10747005f0 # check Vz
+
+    # cleanup the directory
+    rm(model.Output.out_dir, force=true, recursive=true)
+    # ===============================
+
+
+
+end