compute_isotherm.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%aiida\n",
    "import os\n",
    "import sys\n",
    "\n",
    "import ipywidgets as ipw\n",
    "import urllib.parse as urlparse\n",
    "\n",
    "from aiidalab_widgets_base import CodeDropdown, SubmitButtonWidget, OptimadeQueryWidget\n",
    "from aiidalab_widgets_base import StructureBrowserWidget, StructureManagerWidget, StructureUploadWidget\n",
    "\n",
    "IsothermWorkChain = WorkflowFactory('lsmo.isotherm')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def on_submit():\n",
    "    output.value = ''\n",
    "    options = {\n",
    "            \"resources\": {\n",
    "                \"num_machines\": 1,\n",
    "                \"tot_num_mpiprocs\": 1,\n",
    "                \"num_mpiprocs_per_machine\": 1,\n",
    "            },\n",
    "            \"max_wallclock_seconds\": 5 * 60 * 60,\n",
    "            \"withmpi\": False,\n",
    "    }\n",
    "    \n",
    "    builder = IsothermWorkChain.get_builder()\n",
    "    \n",
    "    # Options.\n",
    "    builder.raspa_base.raspa.metadata.options = options\n",
    "    builder.zeopp.metadata.options = options\n",
    "\n",
    "    # Molecule.\n",
    "    if struct_widget.structure is None:\n",
    "        output.value = \"Specify the framework, please.\"\n",
    "        return None\n",
    "    builder.molecule = Str(molecule.value)\n",
    "    \n",
    "    \n",
    "    # Codes.\n",
    "    if zeopp_code_widget.selected_code is None:\n",
    "        output.value = \"Specify Zeo++ code, please.\"\n",
    "        return None\n",
    "    builder.zeopp.code = zeopp_code_widget.selected_code\n",
    "\n",
    "    if raspa_code_widget.selected_code is None:\n",
    "        output.value = \"Specify RASPA code, please.\"\n",
    "        return None\n",
    "    builder.raspa_base.raspa.code = raspa_code_widget.selected_code\n",
    "\n",
    "    # Structure.\n",
    "    builder.structure = struct_widget.structure_node\n",
    "    \n",
    "    # Parameters.\n",
    "    \n",
    "    input_dict = {  #TODO: create IsothermParameters instead of Dict # pylint: disable=fixme\n",
    "        \"ff_framework\": ff_framework.value,  # (str) Forcefield of the structure.\n",
    "        \"ff_separate_interactions\": ff_separate_interactions.value,  # (bool) Use \"separate_interactions\" in the FF builder.\n",
    "        \"ff_mixing_rule\": ff_mixing_rule.value,  # (string) Choose 'Lorentz-Berthelot' or 'Jorgensen'.\n",
    "        \"ff_tail_corrections\": ff_tail_corrections.value,  # (bool) Apply tail corrections.\n",
    "        \"ff_shifted\": ff_shifted.value,  # (bool) Shift or truncate the potential at cutoff.\n",
    "        \"ff_cutoff\": ff_cutoff.value,  # (float) CutOff truncation for the VdW interactions (Angstrom).\n",
    "        \"temperature\": temperature.value,  # (float) Temperature of the simulation.\n",
    "        \"temperature_list\": None,  # (list) To be used by IsothermMultiTempWorkChain.\n",
    "        \"zeopp_volpo_samples\": zeopp_volpo_samples.value,  # (int) Number of samples for VOLPO calculation (per UC volume).\n",
    "        \"zeopp_block_samples\": zeopp_block_samples.value,  # (int) Number of samples for BLOCK calculation (per A^3).\n",
    "        \"raspa_verbosity\": raspa_verbosity.value,  # (int) Print stats every: number of cycles / raspa_verbosity.\n",
    "        \"raspa_widom_cycles\": raspa_widom_cycles.value,  # (int) Number of Widom cycles.\n",
    "    }\n",
    "    if compute_kh_only.value:\n",
    "        input_dict[\"raspa_minKh\"] = 1e100\n",
    "    else:\n",
    "        input_dict[\"raspa_minKh\"] = raspa_minKh.value  # (float) If Henry coefficient < raspa_minKh do not run the isotherm (mol/kg/Pa).\n",
    "        input_dict[\"raspa_gcmc_init_cycles\"] = raspa_gcmc_init_cycles.value  # (int) Number of GCMC initialization cycles.\n",
    "        input_dict[\"raspa_gcmc_prod_cycles\"] = raspa_gcmc_prod_cycles.value  # (int) Number of GCMC production cycles.\n",
    "        input_dict[\"pressure_list\"] = None  # (list) Pressure list for the isotherm (bar): if given it will skip to guess it.\n",
    "        input_dict[\"pressure_precision\"] = pressure_precision.value  # (float) Precision in the sampling of the isotherm: 0.1 ok, 0.05 for high resolution.\n",
    "        input_dict[\"pressure_maxstep\"] = pressure_maxstep.value  # (float) Max distance between pressure points (bar).\n",
    "        input_dict[\"pressure_min\"] = pressure_min.value  # (float) Lower pressure to sample (bar).\n",
    "        input_dict[\"pressure_max\"] = pressure_max.value  # (float) Upper pressure to sample (bar).\n",
    "\n",
    "    \n",
    "    builder.parameters = Dict(dict=input_dict)\n",
    "    return builder\n",
    "\n",
    "btn_submit = SubmitButtonWidget(IsothermWorkChain,input_dictionary_function=on_submit, disable_after_submit=False, append_output=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Framework selection.\n",
    "optimade_widget = OptimadeQueryWidget()\n",
    "optimade_widget.title = \"OPTIMADE\"\n",
    "\n",
    "struct_widget = StructureManagerWidget(\n",
    "    importers=[\n",
    "        StructureUploadWidget(title=\"From computer\"),\n",
    "        StructureBrowserWidget(title=\"AiiDA database\"),\n",
    "        optimade_widget,\n",
    "    ],\n",
    "    storable=False,\n",
    "    node_class='CifData')\n",
    "\n",
    "# Codes selection\n",
    "raspa_code_widget = CodeDropdown(input_plugin='raspa')\n",
    "zeopp_code_widget = CodeDropdown(input_plugin='zeopp.network')\n",
    "\n",
    "# Guest molecule and temperature.\n",
    "temperature = ipw.BoundedIntText(value=400, min=0, max=1e4, description=\"Temperature:\", step=10)\n",
    "molecule = ipw.Dropdown(\n",
    "    options=[\n",
    "        (\"CO2\", \"co2\"),\n",
    "        (\"CH4\", \"ch4\"),\n",
    "        (\"N2\",  \"n2\"),\n",
    "        (\"H2O\", \"h2o\"),\n",
    "        (\"H2\",  \"h2\"),\n",
    "        (\"O2\",  \"o2\"),\n",
    "    ],\n",
    "    description=\"Guest molecule\",\n",
    "    style={'description_width':'initial'},\n",
    ")\n",
    "\n",
    "\n",
    "# Force field related parameters.\n",
    "ff_framework = ipw.Dropdown(\n",
    "    options=[\"UFF\"],\n",
    "    value='UFF',\n",
    "    description='Forcefield of the framework:',\n",
    "    style={'description_width':'initial'},\n",
    "    disabled=False\n",
    ")\n",
    "ff_separate_interactions = ipw.ToggleButtons(\n",
    "    options=[('Yes', True), ('No', False)],\n",
    "    description='Separate interactions:',\n",
    "    #layout={'width':'initial'},\n",
    "    style={'description_width':'initial'},\n",
    "    disabled=False,\n",
    "    button_style='', # 'success', 'info', 'warning', 'danger' or ''\n",
    ")\n",
    "\n",
    "ff_mixing_rule = ipw.ToggleButtons(\n",
    "    options=['Lorentz-Berthelot', 'Jorgensen'],\n",
    "    description='Forcefield mixing rule:',\n",
    "    style={'description_width':'initial'},\n",
    "    disabled=False,\n",
    "    button_style='',\n",
    ")\n",
    "ff_tail_corrections = ipw.ToggleButtons(\n",
    "    options=[('Yes', True), ('No', False)],\n",
    "    description='Apply tail corrections:',\n",
    "    style={'description_width':'initial'},\n",
    "    disabled=False,\n",
    "    button_style='',\n",
    ")\n",
    "ff_shifted = ipw.ToggleButtons(\n",
    "    options=[('Shift', True), ('Truncate', False)],\n",
    "    description='Shift or truncate the potential at cutoff:',\n",
    "    style={'description_width':'initial'},\n",
    "    disabled=False,\n",
    "    button_style='', # 'success', 'info', 'warning', 'danger' or ''\n",
    ")\n",
    "ff_cutoff = ipw.IntText(value=12.0, step=1, description=\"VdW interactions cutoff:\")\n",
    "\n",
    "ff_box = ipw.VBox([ff_framework, ff_separate_interactions, ff_mixing_rule, ff_shifted])\n",
    "\n",
    "\n",
    "# Zeo++ settings.\n",
    "zeopp_volpo_samples = ipw.IntText(value=100000, description=\"Zeopp volpo samples:\", style={'description_width':'initial'})\n",
    "zeopp_block_samples = ipw.IntText(value=100, description=\"Number of samples for BLOCK calculation\", style={'description_width':'initial'})\n",
    "\n",
    "zeopp_box = ipw.VBox([zeopp_volpo_samples, zeopp_block_samples])\n",
    "\n",
    "\n",
    "# Raspa settings.\n",
    "raspa_minKh = ipw.FloatText(value=1e-10, description=\"Henry coefficient threshold:\", style={'description_width':'initial'})\n",
    "raspa_verbosity = ipw.IntText(value=10, description=\"Raspa verbosity (smaller the value more often output is printed):\", layout={'width':'500px'}, style={'description_width':'initial'})\n",
    "raspa_widom_cycles = ipw.IntText(value=100000, description=\"Number of Widom cycles:\", style={'description_width':'initial'})\n",
    "raspa_gcmc_init_cycles = ipw.IntText(value=5000, description=\"Number of GCMC initialization cycles:\", style={'description_width':'initial'})\n",
    "raspa_gcmc_prod_cycles = ipw.IntText(value=10000, description=\"Number of GCMC production cycles:\", style={'description_width':'initial'})\n",
    "\n",
    "raspa_box = ipw.VBox([raspa_minKh, raspa_verbosity, raspa_widom_cycles, raspa_gcmc_init_cycles, raspa_gcmc_prod_cycles])\n",
    "\n",
    "\n",
    "# Pressure settings.\n",
    "pressure_precision = ipw.FloatText(value=0.1, description=\"Precision in sampling the isotherm:\", style={'description_width':'initial'})\n",
    "pressure_maxstep = ipw.FloatText(value=5, description=\"Max distance between pressure points (bar):\", style={'description_width':'initial'})\n",
    "pressure_min = ipw.FloatText(value=0.001, description=\"Lower pressure to sample (bar):\", style={'description_width':'initial'})\n",
    "pressure_max = ipw.FloatText(value=10, description=\"Upper pressure to sample (bar):\", style={'description_width':'initial'})\n",
    "\n",
    "pressure_box = ipw.VBox([pressure_precision, pressure_maxstep, pressure_min, pressure_max])\n",
    "\n",
    "\n",
    "# Packing things together.\n",
    "simulation_accordion = ipw.Accordion([ff_box, zeopp_box, raspa_box, pressure_box])\n",
    "simulation_accordion.selected_index = None\n",
    "simulation_accordion.set_title(0, 'Force Field')\n",
    "simulation_accordion.set_title(1, 'Zeo++ Parameters')\n",
    "simulation_accordion.set_title(2, 'Raspa Parameters')\n",
    "simulation_accordion.set_title(3, 'Pressure Settings')\n",
    "\n",
    "output = ipw.HTML(\"\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "url = urlparse.urlsplit(jupyter_notebook_url)\n",
    "parsed_url = urlparse.parse_qs(url.query)\n",
    "if 'structure_uuid' in parsed_url:\n",
    "    struct_widget.input_structure = load_node(parsed_url['structure_uuid'][0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "compute_kh_only = ipw.Checkbox(value=False, description=\"Compute Henry's coefficient only\", style={'description_width':'initial'})\n",
    "def observe_compute_kh_only(_=None):\n",
    "    raspa_minKh.disabled = compute_kh_only.value\n",
    "    raspa_gcmc_init_cycles.disabled = compute_kh_only.value\n",
    "    raspa_gcmc_prod_cycles.disabled = compute_kh_only.value\n",
    "    pressure_precision.disabled = compute_kh_only.value\n",
    "    pressure_maxstep.disabled = compute_kh_only.value\n",
    "    pressure_min.disabled = compute_kh_only.value\n",
    "    pressure_max.disabled = compute_kh_only.value\n",
    "\n",
    "compute_kh_only.observe(observe_compute_kh_only, 'value')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "display(\n",
    "    struct_widget,\n",
    "    ipw.HBox([molecule, temperature]),\n",
    "    compute_kh_only,\n",
    "    simulation_accordion,\n",
    "    ipw.HBox([zeopp_code_widget, raspa_code_widget]),\n",
    "    btn_submit,\n",
    "    output\n",
    ")"
   ]
  }
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