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

+%% 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

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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

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