Add JOSS paper (#203)

* added initial joss paper * added GHA * added some basic summary * start parametric tools section * actually commit the paper * mystery paragraph * constraints * added FFD section * constraints * whitespace * format fixes * cst * fix constraints * wording * start examples * started statement of need * added some comments * clarify esp/vsp need * Updated DVGeoCST description * esp/vsp process * expanded FFD a bit * added some short text on parallelism and gradients * added DVGeoMulti description and figure * edited ffd derivatives * comments and edits up to geometry parametrization * added description of children FFDs, to be reviewed * addressed a few marco comments * removed references to module names * esp and vsp pictures, children FFD-> child FFD * clarifying solver independence * added authors * Make global FFD DV figures nicer * Added CST figure * include cst figure, ffd figure works slightly better * trying to fix FFD DV figure * pdfs * started geometry generation section + pic * geometry generation * fix figure * orcid * captions * minor edits * orcids * josh edits (#172) * josh edits * add missed edit * minor updates to Josh edits Co-authored-by: Hannah Hajdik <hajdik@umich.edu> * Sabet JOSS paper edits (#173) * edits through FFD * finished edits and added todos * higher resolution images from papers * addressed some Sabet todos * condense parametric geometry section * talking to Sabet Co-authored-by: Hannah Hajdik <hajdik@umich.edu> * Finished my edits. Please check all my changes to make sure I did not change the meaning or introduce innacuracis. Check and respond to the TODOs. * fixed figure labels * updated multi FFD figure * minor changes * Marco's paper edits (#174) * rephrased abstract - MDO not only aerostructural * edits up to hierarchical FFD * minor fixes up to cst * some details and comments on constraints * more reprasings suggestions and commments * finalize marco edits Co-authored-by: Hannah Hajdik <hajdik@umich.edu> * added Lyu 2014 BWB paper citation * added CST derivatives * Joss paper anil's edits (#175) * anil edits * fixed footnotes * some anil todos * take out geometry generation * constraint figure --------- Co-authored-by: Sabet Seraj <48863473+sseraj@users.noreply.github.com> Co-authored-by: Hannah Hajdik <hajdik@umich.edu> * Ben B edits and additions to the paper * Misc. edits (#184) * josh edits * add missed edit * cleaning up extra detail * cropped figure for triangulated surface constraint * new figures for child ffd & trisurfcon * delete old versions of figures * removed abstracts in bib file * small edits * cleaned up some comments * neil comments * removing old TODOs * saved old sections elsewhere and deleted comments * deleted old comments * sabet todo * clarifying * fixed sabet's todo. with sabet. todone. * anil said it's fine * redid summary & statement of need with sabet --------- Co-authored-by: Josh Anibal <joanibal@umich.edu> Co-authored-by: Neil Wu <neilwu0626@gmail.com> * removed paper pdf * updated bib * move SVD reference * standardize name formats * zenodo metadata * version bump * formatting * isort again * even more sorted * comments? * another one * Finished my edits. * grammar/format * A few more edits. * A few more edits. * sabet comments * zenodo metadata * quim comments * citation and acronym fixes * citation again * remove yml --------- Co-authored-by: Neil Wu <602725+nwu63@users.noreply.github.com> Co-authored-by: eytanadler <eytana@umich.edu> Co-authored-by: Marco Mangano <mmangano@umich.edu> Co-authored-by: Alasdair Gray <alachris@umich.edu> Co-authored-by: Josh Anibal <joanibal@umich.edu> Co-authored-by: Sabet Seraj <48863473+sseraj@users.noreply.github.com> Co-authored-by: Joaquim Martins <jrram@umich.edu> Co-authored-by: Marco Mangano <36549388+marcomangano@users.noreply.github.com> Co-authored-by: Anil Yildirim <42349285+anilyil@users.noreply.github.com> Co-authored-by: Ben Brelje <benjamin.brelje@gmail.com>
mdolab · Jun 9, 2023 · 2827954 · 2827954
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diff --git a/.zenodo.json b/.zenodo.json
@@ -0,0 +1,41 @@
+{
+    "creators": [
+        {
+            "name": "Hannah M. Hajdik"
+        },
+        {
+            "name": "Anil Yildirim"
+        },
+        {
+            "name": "Neil Wu"
+        },
+        {
+            "name": "Benjamin J. Brelje"
+        },
+        {
+            "name": "Sabet Seraj"
+        },
+        {
+            "name": "Marco Mangano"
+        },
+        {
+            "name": "Joshua L. Anibal"
+        },
+        {
+            "name": "Eirikur Jonsson"
+        },
+        {
+            "name": "Eytan J. Adler"
+        },
+        {
+            "name": "Charles A. Mader"
+        },
+        {
+            "name": "Gaetan K. W. Kenway"
+        },
+        {
+            "name": "Joaquim R. R. A. Martins"
+        }
+    ],
+    "title": "pyGeo: A geometry package for multidisciplinary design optimization",
+}
diff --git a/paper/Global-FFD-DV-Demo.py b/paper/Global-FFD-DV-Demo.py
@@ -0,0 +1,59 @@
+# Standard Python modules
+import copy
+
+# External modules
+import numpy as np
+
+# First party modules
+from pygeo import DVGeometry
+
+FFDFile = "ffd.xyz"
+DVGeo = DVGeometry(FFDFile)
+
+nRefAxPts = DVGeo.addRefAxis("wing", xFraction=0.25, alignIndex="k")
+
+
+def dihedral(val, geo):
+    C = geo.extractCoef("wing")
+    for i in range(1, nRefAxPts):
+        C[i, 1] += val[i - 1]
+    geo.restoreCoef(C, "wing")
+
+
+# rst Twist
+def twist(val, geo):
+    for i in range(1, nRefAxPts):
+        geo.rot_z["wing"].coef[i] = val[i - 1]
+
+
+# rst Taper
+def taper(val, geo):
+    s = geo.extractS("wing")
+    slope = (val[1] - val[0]) / (s[-1] - s[0])
+    for i in range(nRefAxPts):
+        geo.scale_x["wing"].coef[i] = slope * (s[i] - s[0]) + val[0]
+
+
+nTwist = nRefAxPts - 1
+DVGeo.addGlobalDV(dvName="dihedral", value=[0] * nTwist, func=dihedral, lower=-10, upper=10, scale=1)
+DVGeo.addGlobalDV(dvName="twist", value=[0] * nTwist, func=twist, lower=-10, upper=10, scale=1)
+DVGeo.addGlobalDV(dvName="taper", value=[1] * 2, func=taper, lower=0.5, upper=1.5, scale=1)
+
+# Comment out one or the other
+DVGeo.addLocalDV("local", lower=-0.5, upper=0.5, axis="y", scale=1)
+
+dvDict = DVGeo.getValues()
+dvDictCopy = copy.deepcopy(dvDict)
+dvDictCopy["twist"] = np.linspace(0, 50, nRefAxPts)[1:]
+DVGeo.setDesignVars(dvDictCopy)
+DVGeo.writePlot3d("ffd_deformed-twist.xyz")
+
+dvDictCopy = copy.deepcopy(dvDict)
+dvDictCopy["dihedral"] = np.linspace(0, 3, nRefAxPts)[1:]
+DVGeo.setDesignVars(dvDictCopy)
+DVGeo.writePlot3d("ffd_deformed-dihedral.xyz")
+
+dvDictCopy = copy.deepcopy(dvDict)
+dvDictCopy["taper"] = np.array([1.2, 0.5])
+DVGeo.setDesignVars(dvDictCopy)
+DVGeo.writePlot3d("ffd_deformed-taper.xyz")
diff --git a/paper/child_ffd.pdf b/paper/child_ffd.pdf
diff --git a/paper/constraints_3d.pdf b/paper/constraints_3d.pdf
diff --git a/paper/cst_example.pdf b/paper/cst_example.pdf
diff --git a/paper/cst_example.py b/paper/cst_example.py
@@ -0,0 +1,51 @@
+# Standard Python modules
+import os
+
+# External modules
+import matplotlib.pyplot as plt
+import numpy as np
+
+# First party modules
+from pygeo.parameterization.DVGeoCST import DVGeometryCST
+
+cur_dir = os.path.dirname(os.path.abspath(__file__))
+out_file = os.path.join(cur_dir, "cst_example.pdf")
+
+# Airfoil shape inputs
+x = np.linspace(0, 1, 10000)
+N1 = 0.5
+N2 = 1.0
+yte = 0.0
+num_cst = 3
+coeff = [
+    {"upper": np.full(num_cst, 0.5), "lower": np.full(num_cst, 0.5)},
+    {"upper": np.array([1.5, 0.5, 0.5]), "lower": np.full(num_cst, 0.5)},
+]
+
+# Line styles
+colors = ["#0CAAEF", "#003268"]
+poly_linewidth = 0.8
+alpha = 0.5
+
+fig, axs = plt.subplots(1, 2, figsize=[5.5, 2])
+
+for i_foil, c in enumerate(coeff):
+    for surf, color in zip(["upper", "lower"], colors):
+        for i in range(num_cst):
+            w = np.zeros(num_cst)
+            w[i] = c[surf][i]
+            y = DVGeometryCST.computeCSTCoordinates(x, N1, N2, w, yte)
+            y = -y if surf == "lower" else y
+            axs[i_foil].plot(x, y, color=color, linewidth=poly_linewidth, alpha=alpha)
+
+        y = DVGeometryCST.computeCSTCoordinates(x, N1, N2, c[surf], yte)
+        y = -y if surf == "lower" else y
+        axs[i_foil].plot(x, y, color=color)
+
+    axs[i_foil].set_aspect("equal")
+    axs[i_foil].axis("off")
+    axs[i_foil].set_ylim([-0.2, 0.45])
+
+plt.subplots_adjust(left=0, right=1, bottom=0, top=1, wspace=0.0)
+
+fig.savefig(out_file)
diff --git a/paper/esp_example.png b/paper/esp_example.png
diff --git a/paper/ffd.xyz b/paper/ffd.xyz
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diff --git a/paper/ffd_dvs.pdf b/paper/ffd_dvs.pdf
diff --git a/paper/ffd_multi.png b/paper/ffd_multi.png