fully working 2D problem with remeshing and extend functionality

growing_domain/full_model/parameters.json

 {
     "morphogen" : false,
-
     "dimension" : 2,
-    "resolution" : 100,
-    "system_size" : 1,
-    "meshfile" : "disk.xml.gz",
-
-    "dirichlet_boundary_rho": false,
-    "zero_rho_boundary":false,
-    "rho0_boundary": false,
-
-    "neumann_boundary_rho": true,
-    "zero_grad_rho_boundary": true,
-
-    "difference_in_density_active_stress": false,
-    "difference_in_morphogen_active_stress": false,
-    "saturating_density_active_stress": true,
-    "saturating_density_and_difference_in_morphogen_active_stress": false,
-    "saturating_density_and_difference_in_density_active_stress":false,
 
-    "morphogen_mediated_turnover_rho": false,
-    "density_dependent_turnover_rho": true,
+    "resolution" : 128,
+    "system_size" : 1,
 
-    "morphogen_mediated_average_rho": false,
+    "bulk_elasticity" : 1,
+    "shear_elasticity": 1,
 
-    "bulk_elasticity" : 1.0,
-    "shear_elasticity": 1.0,
     "shear_viscosity" : 1.0,
-    "bulk_viscosity" : 1.0,
+    "bulk_viscosity" : 3.0,
+
     "friction" : 1.0,
-    "lamda": -1.0,
-    "diffusion_rho" : 1.0,
-    "turnover_rho" : 1.0,
+    "lamda": -1,
+
+    "diffusion_rho" : 0.1,
+    "turnover_rho" : 1,
     "average_rho" : 1.0,
     "saturation_rho" : 1.0,
-    "diffusion_c" : 1.0,
-    "turnover_c" : 1.0,
-    "average_c" : 1.0,
+    "stress_setpoint_rho": 2.0,
+
     "noise_level": 0.0,
 
-    "timestep" : 0.1,
-    "savetime": 0.2,
-    "maxtime" : 100.0
+    "timestep" : 0.01,
+    "savetime": 0.1,
+    "maxtime" : 100.0,
+
+    "q_xx" : 1.0,
+    "q_xy" : 0.0
 
 }
\ No newline at end of file

growing_domain/full_model/run_growing_domain.py

+import json, datetime
+import os
+from growing_domain import Growing_Domain
+from viz_growing_domain import visualize
+import argparse
+import dolfin as df
+import h5py
+import numpy as np
+
+parser = argparse.ArgumentParser()
+parser.add_argument('-j','--jsonfile', help='data file',
+        default='parameters.json')
+parser.add_argument('-t','--time', help='time to run', type=float)
+args = parser.parse_args()
+
+assert os.path.isfile(args.jsonfile), '%s file not found' % args.jsonfile
+with open(args.jsonfile) as jsonFile:
+    parameters = json.load(jsonFile)
+
+if args.jsonfile=='parameters.json':
+    extend = False
+    print('Fresh run...')
+    timestamp = datetime.datetime.now().strftime("%d%m%y-%H%M%S")
+    parameters['timestamp'] = timestamp
+    parametersFile = timestamp + '_parameters.json'
+    initu = None
+    initv = None
+    initrho = None
+    initTime = 0.0
+    mesh = None
+
+else:
+    extend = True
+    print('Extending run %s...' % parameters['timestamp'])
+    parametersFile = args.jsonfile
+
+    savesteps = round(parameters['maxtime']/parameters['savetime'])
+
+    # read geometry and topology at the last timepoint from h5 file
+    var = 'density'
+    h5 = h5py.File( '%s_%s.h5' % (parameters['timestamp'], var,), 'r+')
+    geometry = np.array(h5['%s/%s_%d/mesh/geometry'%(var,var,savesteps)])
+    topology = np.array(h5['%s/%s_%d/mesh/topology'%(var,var,savesteps)])
+
+    # create mesh with this geometry and topology
+    mesh = df.Mesh()
+    editor = df.MeshEditor()
+    editor.open(mesh, 
+                type='triangle' if parameters['dimension']==2 else 'tetrahedron', 
+                tdim=parameters['dimension'], gdim=parameters['dimension'])
+    editor.init_vertices(len(geometry))
+    editor.init_cells(len(topology))
+    for j in range(len(geometry)):
+        editor.add_vertex(j, geometry[j])
+    for j in range(len(topology)):
+        editor.add_cell(j, topology[j])
+
+    editor.close()
+    # Read field values at the last time point
+    SFS = df.FunctionSpace(mesh, 'P', 1)
+    VFS = df.VectorFunctionSpace(mesh, 'P', 1)
+
+    initu, initv, initrho = df.Function(VFS), df.Function(VFS), df.Function(SFS)
+    uFile   = df.XDMFFile('%s_displacement.xdmf' % parameters['timestamp'])
+    vFile   = df.XDMFFile('%s_velocity.xdmf' % parameters['timestamp'])
+    rhoFile = df.XDMFFile('%s_density.xdmf' % parameters['timestamp'])
+    uFile.read_checkpoint(initu, 'displacement', savesteps)
+    vFile.read_checkpoint(initv, 'velocity', savesteps)
+    rhoFile.read_checkpoint(initrho, 'density', savesteps)
+
+    uFile.close()
+    vFile.close()
+    rhoFile.close()
+    initTime = parameters['maxtime']
+    parameters['maxtime'] = args.time
+
+tissue = Growing_Domain(parameters, mesh)
+tissue.solve(initu, initv, initrho, initTime, extend)
+
+if extend:
+    parameters['maxtime'] = initTime + parameters['maxtime']
+
+with open(parametersFile, "w") as jsonFile:
+    json.dump(parameters, jsonFile, indent=4, sort_keys=True)
+
+visualize(parameters, DIR='')