gel.scripts.full_shape_to_nodal

  1r"""Implementation of `get_kinematics_mesh` command for $J$ postpro.
  2"""
  3import argparse
  4import os
  5os.environ["SUPPRESS_ADJOINT"] = "1"
  6from gel import *
  7
  8
  9def main(cell_data, input_full_shape, output_nodal, bci=None, bco=None):
 10    r"""Writes .xdmf with element-wise kinematics information.
 11
 12    * `cell_data`: str path to directory with files needed by
 13    `gel.geometry.Geometry`
 14    * `input_full_shape`: str path to full-shape .xdmf file with
 15    displacements "u"
 16    * `output_nodal`: str path to .xdmf file (ending in that extension)
 17    that will be created
 18    * `bci`: str or None. Override path to the inner cell-surface BC .vtk;
 19    when None, `gel.geometry.Geometry` defaults to `cell_data/bci.vtk`
 20    * `bco`: str or None. Override path to the outer boundary BC .vtk
 21
 22    Side-effects: writes `output_nodal` .xdmf and .h5 versions with
 23    kinematic information:
 24    * "u": $\mathbf{u}$
 25    * "J": $J$
 26    * "CC": $\mathbf{C}:\mathbf{C}$
 27    * "w2": $\mathbf{C}:\mathbf{C}-2\text{tr}\mathbf{C}+3$
 28    * "w3": $3\mathbf{C}:\mathbf{C}-\left(\text{tr}\mathbf{C}\right)^2$
 29    """
 30    geo = Geometry(cell_data, bci_data=bci, bco_data=bco)
 31    kinematics = kinematics_from_file(geo, input_full_shape)
 32
 33    simulation_output_file = XDMFFile(output_nodal)
 34    simulation_output_file.parameters["flush_output"] = True
 35    simulation_output_file.parameters["functions_share_mesh"] = True
 36
 37    kinematics.u.rename("u","displacement")
 38
 39    DG_0 = FunctionSpace(geo.mesh, "DG", 0)
 40    J = project(kinematics.Ju, DG_0)
 41    J.rename("J","Jacobian")
 42    
 43    C_norm_sq = inner(kinematics.C, kinematics.C)
 44    C_ns_vec = project(C_norm_sq, DG_0)
 45    C_ns_vec.rename("CC","CNormSquared")
 46
 47    w22 = C_norm_sq - (2*kinematics.Ic) + 3
 48    w2 = sqrt(conditional(gt(w22,0),w22,0))
 49    w2_vec = project(w2, DG_0)
 50    w2_vec.rename("w2","Weight2")
 51
 52    w33 = (3*C_norm_sq) - (kinematics.Ic*kinematics.Ic)
 53    w3 = sqrt(conditional(gt(w33,0),w33,0))
 54    w3_vec = project(w3, DG_0)
 55    w3_vec.rename("w3","Weight3")
 56
 57    # Writes out the variables
 58    simulation_output_file.write(kinematics.u,0)
 59    simulation_output_file.write(J,0)
 60    simulation_output_file.write(C_ns_vec,0)
 61    simulation_output_file.write(w2_vec,0)
 62    simulation_output_file.write(w3_vec,0)
 63
 64
 65def get_kinematics_mesh():
 66    """The function invoked by the command. Parses arguments and passes
 67    to `main`.
 68    """
 69    parser = argparse.ArgumentParser(
 70        description="Convert a full-shape .xdmf file with displacements"
 71        " to a nodal .xdmf file for both visualization and computing J"
 72    )
 73    parser.add_argument(
 74        "-c",
 75        type=str,
 76        metavar="CELL_DATA",
 77        help="directory containing gel geometry"
 78    )
 79    parser.add_argument(
 80        "-i",
 81        type=str,
 82        metavar="INPUT_FULL_SHAPE",
 83        help="full-shape 1st order Lagrange .xdmf with displacements 'u'"
 84    )
 85    parser.add_argument(
 86        "-o",
 87        type=str,
 88        metavar="OUTPUT_NODAL",
 89        help="output .xdmf file with kinematic quantities like J"
 90    )
 91    parser.add_argument(
 92        "--bci",
 93        type=str,
 94        metavar="CELL_SURF_MESH",
 95        default=None,
 96        help="override path to inner cell-surface BC .vtk (default: -c dir's "
 97        "bci.vtk)"
 98    )
 99    parser.add_argument(
100        "--bco",
101        type=str,
102        metavar="OUTER_SURF_MESH",
103        default=None,
104        help="override path to outer boundary BC .vtk (default: -c dir's "
105        "bco.vtk)"
106    )
107    args = parser.parse_args()
108
109    main(args.c, args.i, args.o, args.bci, args.bco)
110
111
112if __name__=="__main__":
113    get_kinematics_mesh()