PUMI related additions to PyMFEM

Makefile

@@ -17,7 +17,7 @@ WHOLE_ARCHIVE = --whole_archive
 NO_WHOLE_ARCHIVE = --no-whole-archive
 
 SWIG=$(shell which swig)
-SWIGFLAG = -Wall -c++ -python
+SWIGFLAG = -Wall -c++ -python -fastproxy -olddefs -keyword
 
 #
 # MFEM path:

README

@@ -1,11 +1,11 @@
 '''''
 PyMFEM
-built on mfem 4.0 (commit SHA=4d900b0c5fd6352c92173e74678bcbeeb11c8691)
+built on mfem 4.1 (commit SHA=60b2b7d4238fb72d018ee6f9f7a54bbfc7817e96)
 '''''
 
 PyMFEM is a python wrapper for MFEM, ligith-weight FEM (finite element
 method) library developed by LLNL (http://mfem.org).
-PyMFEM is tested with python = 2.7, 3.7
+PyMFEM is tested with python = 3.6, 3.7
 
 This wrapper is meant for a rapid-prototyping of FEM program, and
 is built using SWIG 3.0.12
@@ -102,6 +102,13 @@ to find more detail of the MFEM libirary.
        Therefore, if one overwrite Eval method, SWIG reroute the
        call to the Python side.
 
+       V/M ConstantCoefficeint supports natrual python object as input
+          MatrixConstantCoefficient([[1,2], [2,3]])
+          VecotrConstantCoefficient([1,2,3])
+
+          Note: thie argument is first tested if it can be converted using
+	        np.array(x,  dtype=float)
+
   4-3) mfem::GridFunction
        GetNodalValues(i) will perform GetNodalValue(Vector(), i) and
        return numpy array of Vector()
@@ -187,6 +194,15 @@ to find more detail of the MFEM libirary.
             virtual void PrintInfo(std::ostream &out = mfem::out)
 
 
+         FindPoints receive only one argument (points to look for) and returns
+	 count, element_id, integration_points. Note points are row order. For example,
+
+         >>> count, elem_ids, int_pts = mesh.FindPoint([1,2,3], [3,4,5], [4,5,6], [7,8,9]],
+ 	                                               warn=True, int_trans=None)
+         will look for 4 points.
+
+
+
   4-5) sparsemat
          RAP has two different implementations. One accept three references.
 	 The other accept a pointer as a third argument, instead.

examples/pumi/ex2.py

@@ -0,0 +1,204 @@
+'''
+   MFEM example 2
+
+   See c++ version in the MFEM library for more detail 
+'''
+import sys, getopt
+import pyCore
+
+
+# from mfem import path
+import mfem.par as mfem
+from mfem.par import intArray
+from mfem.par import named_ifgzstream
+from mfem.par import Vector
+# from os.path import expanduser, join
+# import numpy as np
+from mfem._par.pumi import PumiMesh
+
+
+def main(argv):
+  model_file = ''
+  mesh_file  = ''
+  boundary_file  = ''
+  try:
+    opts, args = getopt.getopt(argv,"hg:m:b:",["model=","mesh=", "boundary="])
+    print opts
+    print args
+  except getopt.GetoptError:
+    print 'ex2.py -g <model> -m <mesh> -b <boundary>'
+    sys.exit(3)
+  for opt, arg in opts:
+    print opt
+    print arg
+    if opt == '-h':
+	print 'ex2.py -g <model> -m <mesh> -b <boundary'
+	sys.exit()
+    elif opt in ("-g", "--model"):
+	model_file = arg
+    elif opt in ("-m", "--mesh"):
+	mesh_file = arg
+    elif opt in ("-b", "--boundary"):
+        boundary_file = arg
+  print 'Model     file is "', model_file
+  print 'Mesh      file is "', mesh_file
+  print 'Boundary  file is "', boundary_file
+
+  # LIONPRINT verbosity level to 1 for debugging
+  pyCore.lion_set_verbosity(1)
+
+  # PCU initialization
+  pyCore.PCU_Comm_Init()
+
+  # SIMX initialization
+  pyCore.start_sim('simlog.txt')
+
+  # gmi initialization
+  pyCore.gmi_register_mesh()
+
+  # gmi_sim start
+  pyCore.gmi_sim_start()
+  pyCore.gmi_register_sim()
+
+  # load the pumi mesh and model and write the initial mesh to vtk
+  pumi_mesh = pyCore.loadMdsMesh(model_file, mesh_file)
+  pyCore.printStats(pumi_mesh)
+  pumi_mesh.verify()
+  pyCore.writeASCIIVtkFiles('before', pumi_mesh);
+
+  # read boundary
+  # for now set them manually.
+  # TODO: figure out how to read the boundary file in python
+  dirichlet = intArray()
+  dirichlet.SetSize(2)
+  dirichlet[0] = 1
+  dirichlet[1] = 11
+  dirichlet.Print()
+
+  load = intArray()
+  load.SetSize(1)
+  load[0] = 5
+  load.Print()
+
+
+
+  # create a mfem mesh object form pumi mesh
+  mfem_mesh = PumiMesh(pumi_mesh, 1, 1)
+  dim = mfem_mesh.Dimension()
+
+  print("HERE 02")
+  it = pumi_mesh.begin(dim-1)
+  bdr_cnt = 0
+  while True:
+    e = pumi_mesh.iterate(it)
+    if not e: break
+    model_type = pumi_mesh.getModelType(pumi_mesh.toModel(e))
+    model_tag  = pumi_mesh.getModelTag(pumi_mesh.toModel(e))
+    if model_type == (dim-1):
+      mfem_mesh.GetBdrElement(bdr_cnt).SetAttribute(3)
+      if dirichlet.Find(model_tag) != -1:
+	mfem_mesh.GetBdrElement(bdr_cnt).SetAttribute(1)
+      elif load.Find(model_tag) != -1:
+	mfem_mesh.GetBdrElement(bdr_cnt).SetAttribute(2)
+    bdr_cnt += 1
+  pumi_mesh.end(it)
+
+  for el in range(0, mfem_mesh.GetNE()):
+    geom = mfem.Geometry()
+    Tr = mfem_mesh.GetElementTransformation(el)
+    ctr = Tr.Transform(geom.GetCenter(mfem_mesh.GetElementBaseGeometry(el)))
+    if ctr[0] <= -0.05:
+      mfem_mesh.SetAttribute(el, 1)
+    elif ctr[0] >= 0.05:
+      mfem_mesh.SetAttribute(el, 2)
+    else:
+      mfem_mesh.SetAttribute(el, 3)
+
+
+  mfem_mesh.SetAttributes()
+  if mfem_mesh.attributes.Max() < 2 or mfem_mesh.bdr_attributes.Max() < 2:
+    sys.exit("Input mesh should have at leaset two materials and two boundary attributes!")
+
+  print("HERE HERE")
+
+  order = 1
+
+  fec = mfem.H1_FECollection(order, dim)
+  fespace = mfem.FiniteElementSpace(mfem_mesh, fec, dim)
+
+  ess_tdof_list = intArray()
+  ess_bdr = intArray([1]+[0]*(mfem_mesh.bdr_attributes.Max()-1))
+  fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list)
+
+  f = mfem.VectorArrayCoefficient(dim)
+  for i in range(dim-1): f.Set(i, mfem.ConstantCoefficient(0.0));
+
+  pull_force = mfem.Vector([0]*mfem_mesh.bdr_attributes.Max())
+  pull_force[1] = -1.0e-2
+  f.Set(dim-1, mfem.PWConstCoefficient(pull_force))
+  f.Set(dim-2, mfem.PWConstCoefficient(pull_force))
+
+  b = mfem.LinearForm(fespace)
+  b.AddBoundaryIntegrator(mfem.VectorBoundaryLFIntegrator(f))
+  b.Assemble()
+
+  x = mfem.GridFunction(fespace)
+  x.Assign(0.0)
+
+  lamb = mfem.Vector(mfem_mesh.attributes.Max())
+  lamb.Assign(1.0)
+  lamb[0] = lamb[1]*10;
+  lamb[1] = lamb[1]*100;
+  lambda_func = mfem.PWConstCoefficient(lamb)
+
+  mu = mfem.Vector(mfem_mesh.attributes.Max())
+  mu.Assign(1.0);
+  mu[0] = mu[1]*10;
+  mu[1] = mu[1]*100;
+  mu_func = mfem.PWConstCoefficient(mu)
+
+  a = mfem.BilinearForm(fespace)
+  a.AddDomainIntegrator(mfem.ElasticityIntegrator(lambda_func,mu_func))
+
+  print('matrix...')
+  static_cond = False
+  if (static_cond): a.EnableStaticCondensation()
+  a.Assemble()
+
+  A = mfem.SparseMatrix()
+  B = mfem.Vector()
+  X = mfem.Vector()
+  a.FormLinearSystem(ess_tdof_list, x, b, A, X, B);
+  print('...done')## Here, original version calls hegith, which is not
+  ## defined in the header...!?
+  print("Size of linear system: " + str(A.Size()))
+
+  M = mfem.GSSmoother(A)
+  mfem.PCG(A, M, B, X, 1, 500, 1e-8, 0.0);
+
+  a.RecoverFEMSolution(X, b, x);
+
+  print("HERE --- ")
+
+  if not mfem_mesh.NURBSext:
+    mfem_mesh.SetNodalFESpace(fespace)
+
+  nodes = mfem_mesh.GetNodes()
+  nodes += x
+  x *= -1
+  mfem_mesh.PrintToFile('displaced.mesh', 8)
+  x.SaveToFile('sol.gf', 8)
+
+
+  # gmi_sim stop
+  pyCore.gmi_sim_stop()
+
+  # SIMX finalization
+  pyCore.stop_sim()
+
+  # gmi finalization
+  pyCore.PCU_Comm_Free()
+
+
+if __name__ == "__main__":
+     main(sys.argv[1:])