material load needs to come before mesh

cylinder/cyl_01.geo

+SetFactory("OpenCASCADE");
+
+Point(1) = {0, 0, 0};
+Point(2) = {0, .5, 0};
+Circle(1) = {0,0,0,0.5,0,2*Pi};
+Extrude {0, 0, 1} {
+  Curve{1}; 
+}
+//+
+Curve Loop(2) = {3};
+//+
+Plane Surface(2) = {2};
+
+Curve Loop(3) = {1};
+Plane Surface(3) = {3};
+
+Physical Surface("bottom") = {3};
+Physical Surface("top") = {2};
+Physical Surface("surface") = {1};

cylinder/cyl_01.ipynb

+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "59a9f2d7-aadb-4d96-9b19-0cfcf7c950dc",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "import akantu as aka"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "c1339e28-e6b1-4155-b25e-f3b848025838",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "material_file = \"\"\"\n",
+    "material elastic [\n",
+    "    name = steel\n",
+    "    rho = 1     # density\n",
+    "    E   = 1   # young's modulus\n",
+    "    nu  = 0.3      # poisson's ratio\n",
+    "]\"\"\"\n",
+    "# writing the material file\n",
+    "open('material.dat', 'w').write(material_file)\n",
+    "#reading the material file\n",
+    "material_file = 'material.dat'\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "30c1bb68-80b2-41ea-9aa6-a08daf741c9b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mesh = aka.Mesh(3)\n",
+    "mesh.read('cyl_02.msh')\n",
+    "\n",
+    "model = aka.SolidMechanicsModel(mesh)\n",
+    "model.initFull(_analysis_method=aka._static)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "23cdc1b2-692e-4457-a454-89d49722e94a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mesh.createBoundaryGroupFromGeometry()\n",
+    "aka.parseInput(material_file)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "a1d797dd-c63c-4b8b-9aaa-5d00947a414a",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "array([[0.00000000e+00, 0.00000000e+00, 0.00000000e+00],\n",
+       "       [0.00000000e+00, 0.00000000e+00, 1.00506689e-05],\n",
+       "       [0.00000000e+00, 0.00000000e+00, 0.00000000e+00],\n",
+       "       ...,\n",
+       "       [0.00000000e+00, 0.00000000e+00, 2.04378535e-03],\n",
+       "       [0.00000000e+00, 0.00000000e+00, 2.01312308e-03],\n",
+       "       [0.00000000e+00, 0.00000000e+00, 2.40760514e-03]])"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "for dir in [aka._x, aka._y, aka._z]:\n",
+    "    model.applyBC(aka.FixedValue(0, dir), \"bottom\")\n",
+    "\n",
+    "# trac = np.eye(3)\n",
+    "trac = [0, 0, 1]\n",
+    "model.applyBC(aka.FromTraction(trac), \"top\")\n",
+    "model.getExternalForce()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "e26678ea-2a60-44fb-8956-6ce84db4174f",
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "Exception",
+     "evalue": "akantu::debug::CriticalError : Error in mumps during solve process, check mumps user guide INFO(1) = -3 [/tmp/app/spack-stage/spack-stage-akantu-master-t5tv2fws2j5an4dr4sqytng27g7b3fyr/spack-src/src/solver/sparse_solver_mumps.cc:445]",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mException\u001b[0m                                 Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-6-68da59902414>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      4\u001b[0m \u001b[0msolver\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mset\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"convergence_type\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0maka\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mSolveConvergenceCriteria\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mresidual\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 6\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msolveStep\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+      "\u001b[0;31mException\u001b[0m: akantu::debug::CriticalError : Error in mumps during solve process, check mumps user guide INFO(1) = -3 [/tmp/app/spack-stage/spack-stage-akantu-master-t5tv2fws2j5an4dr4sqytng27g7b3fyr/spack-src/src/solver/sparse_solver_mumps.cc:445]"
+     ]
+    }
+   ],
+   "source": [
+    "solver = model.getNonLinearSolver()\n",
+    "solver.set(\"max_iterations\", 2)\n",
+    "solver.set(\"threshold\", 1e-10)\n",
+    "solver.set(\"convergence_type\", aka.SolveConvergenceCriteria.residual)\n",
+    "\n",
+    "model.solveStep()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
+%% Cell type:code id:59a9f2d7-aadb-4d96-9b19-0cfcf7c950dc tags:
+
+``` python
+import numpy as np
+import akantu as aka
+```
+
+%% Cell type:code id:c1339e28-e6b1-4155-b25e-f3b848025838 tags:
+
+``` python
+material_file = """
+material elastic [
+    name = steel
+    rho = 1     # density
+    E   = 1   # young's modulus
+    nu  = 0.3      # poisson's ratio
+]"""
+# writing the material file
+open('material.dat', 'w').write(material_file)
+#reading the material file
+material_file = 'material.dat'
+```
+
+%% Cell type:code id:30c1bb68-80b2-41ea-9aa6-a08daf741c9b tags:
+
+``` python
+mesh = aka.Mesh(3)
+mesh.read('cyl_02.msh')
+
+model = aka.SolidMechanicsModel(mesh)
+model.initFull(_analysis_method=aka._static)
+```
+
+%% Cell type:code id:23cdc1b2-692e-4457-a454-89d49722e94a tags:
+
+``` python
+mesh.createBoundaryGroupFromGeometry()
+aka.parseInput(material_file)
+```
+
+%% Cell type:code id:a1d797dd-c63c-4b8b-9aaa-5d00947a414a tags:
+
+``` python
+for dir in [aka._x, aka._y, aka._z]:
+    model.applyBC(aka.FixedValue(0, dir), "bottom")
+
+# trac = np.eye(3)
+trac = [0, 0, 1]
+model.applyBC(aka.FromTraction(trac), "top")
+model.getExternalForce()
+```
+
+%%%% Output: execute_result
+
+    array([[0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
+           [0.00000000e+00, 0.00000000e+00, 1.00506689e-05],
+           [0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
+           ...,
+           [0.00000000e+00, 0.00000000e+00, 2.04378535e-03],
+           [0.00000000e+00, 0.00000000e+00, 2.01312308e-03],
+           [0.00000000e+00, 0.00000000e+00, 2.40760514e-03]])
+
+%% Cell type:code id:e26678ea-2a60-44fb-8956-6ce84db4174f tags:
+
+``` python
+solver = model.getNonLinearSolver()
+solver.set("max_iterations", 2)
+solver.set("threshold", 1e-10)
+solver.set("convergence_type", aka.SolveConvergenceCriteria.residual)
+
+model.solveStep()
+```
+
+%%%% Output: error
+
+    ---------------------------------------------------------------------------
+    Exception                                 Traceback (most recent call last)
+    <ipython-input-6-68da59902414> in <module>
+          4 solver.set("convergence_type", aka.SolveConvergenceCriteria.residual)
+          5
+    ----> 6 model.solveStep()
+
+    Exception: akantu::debug::CriticalError : Error in mumps during solve process, check mumps user guide INFO(1) = -3 [/tmp/app/spack-stage/spack-stage-akantu-master-t5tv2fws2j5an4dr4sqytng27g7b3fyr/spack-src/src/solver/sparse_solver_mumps.cc:445]

cylinder/cyl_02.geo

+
+SetFactory("OpenCASCADE");
+Circle(1) = {0,0,0,0.5,0,Pi}; //Point 1, 2
+Circle(2) = {0, 0, 1, 0.5, 0, Pi}; //Point 3, 4
+Circle(3) = {0,0,0,0.5, Pi, 2*Pi}; //Point 1, 2
+Circle(4) = {0, 0, 1, 0.5, Pi, 2*Pi}; //Point 3, 4
+Line(5) = {1, 3};
+Line(6) = {2, 4};
+Line(7) = {1, 2};
+Line(8) = {3, 4};
+Line Loop(9) = {1, 6, -2, -5};
+Line Loop(10) = {3, 5, -4, -6};
+Curve Loop(11) = {1, 7};
+Curve Loop(12) = {2, 8};
+Curve Loop(13) = {3, 7};
+Curve Loop(14) = {4, 8};
+Curve Loop(15) = {5, 8, -6, -7};
+
+Plane Surface(1) = {11};
+Plane Surface(2) = {12};
+// Plane Surface(100) = {13};
+// Plane Surface(101) = {14};
+Plane Surface(102) = {15};
+
+Surface(3) = {9};
+// Surface(4) = {10};
+// Surface Loop(5) = {4, 101, 102, 100};
+Surface Loop(6) = {3, 1, 102, 2};
+Physical Surface("bottom") = {1};
+Physical Surface("top") = {2};
+
+// Volume(1) = {5};
+Volume(2) = {6};
+Physical Volume("volume") = {2};
+
+
+
+

cylinder/cyl_02_groups_bnd.pos

+View " "{
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+SL(0.4,1.04095e-16,0,0.5,6.12323e-17,0){1,1};
+SL(-0.5,-6.12323e-17,0,-0.4,-4.28626e-17,0){2,2};
+SL(0.5,6.12323e-17,1,0.490393,-0.0975452,1){3,3};
+SL(-0.490393,-0.0975452,1,-0.5,-6.12323e-17,1){4,4};
+SL(0.490393,-0.0975452,1,0.46194,-0.191342,1){5,5};
+SL(0.46194,-0.191342,1,0.415735,-0.277785,1){6,6};
+SL(0.415735,-0.277785,1,0.353553,-0.353553,1){7,7};
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+SL(-0.3,-2.44929e-17,0,-0.2,-6.12323e-18,0){20,20};
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+SL(0.1,4.89859e-17,0,0.2,6.73556e-17,0){24,24};
+SL(0.2,6.73556e-17,0,0.3,8.57253e-17,0){25,25};
+SL(0.3,8.57253e-17,0,0.4,1.04095e-16,0){26,26};
+SL(-0.5,-6.12323e-17,1,-0.4,-4.28626e-17,1){27,27};
+SL(-0.4,-4.28626e-17,1,-0.3,-2.44929e-17,1){28,28};
+SL(-0.3,-2.44929e-17,1,-0.2,-6.12323e-18,1){29,29};
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+SL(-0.1,1.22465e-17,1,0,3.06162e-17,1){31,31};
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+SL(0.2,6.73556e-17,1,0.3,8.57253e-17,1){34,34};
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+SL(0.5,1.22465e-16,0.7,0.5,1.22465e-16,0.8){67,67};
+SL(0.5,1.22465e-16,0.9,0.5,6.12323e-17,1){68,68};
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+SL(0.5,1.22465e-16,0.8,0.5,1.22465e-16,0.9){71,71};
+};

cylinder/cyl_03.geo

+//+
+SetFactory("OpenCASCADE");
+//+
+Cylinder(1) = {0, 0, 0, 0, 0, 1, 0.5, 2*Pi};
+//+
+Surface Loop(2) = {1, 2, 3};
+//+
+Volume(2) = {2};
+
+Physical Surface("bottom") = {3};
+Physical Surface("top") = {2};
+Physical Volume("mass") = {2};

cylinder/cyl_03_mohit.geo

+//+
+SetFactory("OpenCASCADE");
+//+
+Cylinder(1) = {0, 0, 0, 0, 0, 1, 0.5, 2*Pi};
+//+
+//Surface Loop(2) = {1, 2, 3};
+//+
+//Volume(2) = {2};
+
+Physical Surface("bottom") = {3};
+Physical Surface("top") = {2};
+Physical Volume("some") = {1};
\ No newline at end of file

cylinder/cylinder.geo

+Merge "cylinder.stp";
+SetFactory("Built-in");
+//+
+Recombine Surface {4, 1};
+//+
+Recombine Surface {2, 1, 4, 3};
+//+
+Recombine Surface {2, 1, 4, 3};
+//+
+Recombine Surface {2, 1, 4, 3};
+//+
+MeshSize {3, 1, 4, 2} = 0.1;
+//+
+MeshSize {3, 1, 4, 2} = 0.05;
+//+
+MeshSize {3, 1, 4, 2} = 2;
+//+
+MeshSize {3, 1, 4, 2} = 0.001;
+//+
+Curve Loop(7) = {4};
+//+
+Plane Surface(5) = {7};
+//+
+Physical Surface("Inside") = {4};
+//+
+MeshSize {1, 3, 2, 4} = 0.1;
+//+
+MeshSize {1, 3, 2, 4} = 1;
+//+
+MeshSize {1, 3, 2, 4} = 10;
+//+
+MeshSize {1, 3, 2, 4} = 1000;
+//+
+MeshSize {1, 3, 2, 4} = 500;
+//+
+MeshSize {1, 3, 2, 4} = 500;
+//+
+MeshSize {1, 3, 2, 4} = 200;
+//+
+MeshSize {1, 3, 2, 4} = 50;
+//+
+MeshSize {1, 3, 4, 2} = 20;
+//+
+MeshSize {1, 3, 2, 4} = 500;

cylinder/cylinder.msh

+$MeshFormat
+4.1 0 8
+$EndMeshFormat
+$Entities
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