Implemented ability to specify full-shape xdmf with displacements to …

gel/gel.py

@@ -237,6 +237,7 @@ def __init__(self,
             tola=1e-10,
             tolr=1e-9,
             traction=None,
+            u_init=None,
             formulation_kwargs=dict(),
             **kwargs
         ):
@@ -267,10 +268,12 @@ def __init__(self,
         be in 1st order Lagrange space, will ignore DoFs outside of
         surface. "zero" will automatically contruct a 0 traction
         function
+        * `u_init`: str path to full-shape .xdmf file with initial
+        displacements
         * `formulation_kwargs`: dict of additional kwargs to the
         material model formulation (if applicable) implemented in
         `gel.mechanics`
-        * `kwargs`: dict of kwargs to the the geometry, for instance
+        * `kwargs`: dict of kwargs to the geometry, for instance
         the arguments to `gel.geometry.Geometry`
         """
         # Validate, get geometry
@@ -285,10 +288,14 @@ def __init__(self,
         """Corresponding object of type `gel.geometry.Geometry`"""
 
         # Initialize displacements, kinematic quantities
-        self.kinematics = Kinematics(self.geo)
+        self.kinematics = None
         """Object of type `gel.kinematics.Kinematics` with displacement
         information
         """
+        if u_init is None:
+            self.kinematics = Kinematics(self.geo)
+        else:
+            self.kinematics = kinematics_from_file(self.geo, u_init)
 
         # Prepare modulus control variable
         self.ctl = create_mod_repr(self.geo, mod_repr_init)

gel/helper.py

@@ -49,6 +49,7 @@ def get_common_parser(*args, **kwargs):
     -p PRECONDITIONER
     --bci CELL_SURF_MESH
     --bco OUTER_SURF_MESH
+    --u-init U_INIT
     ```
     """
     if "formatter_class" not in kwargs:
@@ -111,6 +112,13 @@ def get_common_parser(*args, **kwargs):
         default=None,
         help="filename of meshio-compatible mesh with outer nodes and u"
     )
+    parser.add_argument(
+        "--u-init",
+        type=str,
+        metavar="U_INIT",
+        default=None,
+        help="filename of full-shape .xdmf file with initial displacements"
+    )
 
     return parser
 

gel/scripts/forward.py

@@ -39,6 +39,7 @@
     "upper_bound",
     "Inner Mesh",
     "Outer Mesh",
+    "u_init",
     "time"
 ]
 """Names of columns in `table.csv`"""
@@ -77,7 +78,8 @@ def run_experiments(args):
         args.b[0],
         args.b[1],
         args.bci,
-        args.bco
+        args.bco,
+        args.u_init
     )
 
     logger.info(f"Beginning experiment with arguments {exp_info}.")
@@ -109,7 +111,8 @@ def output_single_forward_result(
         lower_bound,
         upper_bound,
         bci,
-        bco
+        bco,
+        u_init
     ):
     r"""Runs a single forward model experiment, writes subdirectory and
     logs progress.
@@ -137,6 +140,8 @@ def output_single_forward_result(
     `gel.geometry.Geometry` for details
     * `bco`: str path to .vtk file with outer BC info, see
     `gel.geometry.Geometry` for details
+    * `u_init`: str path to full-shape .xdmf file with initial
+    displacements
 
     Side-effects: writes many files in new subdirectory to
     `results_dir`, see intro to `gel.scripts.forward`
@@ -163,7 +168,8 @@ def output_single_forward_result(
         lower_bound,
         upper_bound,
         bci,
-        bco
+        bco,
+        u_init
     )
 
     # Setup logging
@@ -183,6 +189,7 @@ def output_single_forward_result(
     logger.info(f"Using load steps: {load_steps}")
     logger.info(f"Override inner BC: {bci}")
     logger.info(f"Override outer BC: {bco}")
+    logger.info(f"Initial displacements: {u_init}")
 
     # Timer start
     timer = ExperimentTimer()
@@ -208,6 +215,7 @@ def output_single_forward_result(
         tola=tola,
         tolr=tolr,
         traction=traction,
+        u_init=u_init,
         formulation_kwargs=formulation_kwargs,
         **addn_args
     )

gel/scripts/inverse.py

@@ -96,6 +96,7 @@ def _expand_obj_info(exp_info):
     "bci",
     "bco",
     "mu_ff",
+    "u_init",
     "outcome",
     "pure_obj",
     "reg",
@@ -143,7 +144,8 @@ def main(args):
         args.opt_backend,
         args.bci,
         args.bco,
-        args.mu
+        args.mu,
+        args.u_init
     )
 
     logger.info(f"Beginning experiment with arguments {exp_info}.")
@@ -208,7 +210,8 @@ def gel_inverse(
         optimizer_backend="scipy",
         bci=None,
         bco=None,
-        mu=108.0
+        mu=108.0,
+        u_init=None
     ):
     r"""Runs the inverse model, writes subdirectory and logs progress.
 
@@ -248,6 +251,8 @@ def gel_inverse(
     * `bco`: str path to .vtk file with outer BC info, see
     `gel.geometry.Geometry` for details
     * `mu`: float far-field shear modulus from rheometry
+    * `u_init`: str path to full-shape .xdmf file with initial
+    displacements
 
     Side-effects: writes many files in new subdirectory to
     `results_dir`, see intro to `gel.scripts.inverse`
@@ -318,6 +323,7 @@ def gel_inverse(
     logger.info(f"Override inner BC: {bci}")
     logger.info(f"Override outer BC: {bco}")
     logger.info(f"Far field modulus: {mu}")
+    logger.info(f"Initial displacements: {u_init}")
     objective_info.log_info(logger)
 
     # RESET TAPE
@@ -351,6 +357,7 @@ def gel_inverse(
         data_directory=cell_data_dir,
         restrict_ctl_dofs_to_veh=restrict_ctl_dofs_to_veh,
         pc=preconditioner,
+        u_init=u_init,
         formulation_kwargs=formulation_kwargs,
         **addn_args
     )