Merge branches 'master' and 'master' of https://github.com/KVSlab/tur…

…tleFSI

docs/examples/example.config

@@ -1,5 +1,5 @@
 # Configuration file for turtleFSI
-
+[Parameter for turtleFSI] # Section is required by configargparse but is not used anywhere in turtleFSI
 ################################################################################
 # Define solver, numerics, and problem file
 ################################################################################
@@ -22,21 +22,21 @@ theta=0.501
 ################################################################################
 
 # Turn on/off solving of the fluid problem ('fluid', 'no_fluid')
-fluid="fluid"
+fluid=fluid
 
 # Turn on/off solving of the solid problem ('solid', 'no_solid')
-solid="solid"
+solid=solid
 
 # Use Robin boundary conditions for solid
 robin_bc=False
 
 # Set approach for extrapolating the deformation into the fluid domain
 # ('laplace', 'elastic', 'biharmonic', 'no_extrapolation')
-extrapolation="laplace"
+extrapolation=laplace
 
 # Set the sub type of the extrapolation method ('constant'," 'small_constant',
 # 'volume', 'volume_change', 'constrained_disp', 'constrained_disp_vel')
-extrapolation-sub-type="constant"
+extrapolation-sub-type=constant
 
 # List of boundary ids for the weak formulation of the biharmonic mesh lifting
 # operator with 'constrained_disp_vel'
@@ -95,7 +95,7 @@ dx-s-id=2
 
 # Selected linear solver for each Newton iteration, to see a complete list
 # run list_linear_solvers()
-linear-solver="mumps"
+linear-solver=mumps
 
 # Absolute error tolerance for the Newton iterations
 atol=1e-7
@@ -140,7 +140,7 @@ save-deg=1
 checkpoint-step=500
 
 # Path to store the results. You can store multiple simulations in one folder
-folder="results"
+folder=results
 
 # Over write the standard 1, 2, 3 name of the sub folders
 #sub-folder=None

docs/examples/example.yaml

@@ -1,13 +1,13 @@
 # Configuration file for turtleFSI
-
+[Parameter for turtleFSI] # Section is required by configargparse but is not used anywhere in turtleFSI
 ################################################################################
 # Define solver, numerics, and problem file
 ################################################################################
 
 # Name of problem file to solve. Could either be located in the turtleFSI
 # repository (TF_cfd, TF_csm, TF_fsi, turtle_demo) or it could be a problem
 # file you have created locally.
-problem: "turtle_demo"
+problem: turtle_demo
 
 # Setting temporal integration.
 # (theta=0 : first order explicit forward Euler scheme)
@@ -22,21 +22,21 @@ theta: 0.501
 ################################################################################
 
 # Turn on/off solving of the fluid problem ('fluid', 'no_fluid')
-fluid: "fluid"
+fluid: fluid
 
 # Turn on/off solving of the solid problem ('solid', 'no_solid')
-solid: "solid"
+solid: solid
 
 # Use Robin boundary conditions for solid
 robin_bc: False
 
 # Set approach for extrapolating the deformation into the fluid domain
 # ('laplace', 'elastic', 'biharmonic', 'no_extrapolation')
-extrapolation: "laplace"
+extrapolation: laplace
 
 # Set the sub type of the extrapolation method ('constant'," 'small_constant',
 # 'volume', 'volume_change', 'constrained_disp', 'constrained_disp_vel')
-extrapolation-sub-type: "constant"
+extrapolation-sub-type: constant
 
 # List of boundary ids for the weak formulation of the biharmonic mesh lifting
 # operator with 'constrained_disp_vel'
@@ -95,7 +95,7 @@ dx-s-id: 2
 
 # Selected linear solver for each Newton iteration, to see a complete list
 # run list_linear_solvers()
-linear-solver: "mumps"
+linear-solver: mumps
 
 # Absolute error tolerance for the Newton iterations
 atol: 1e-7
@@ -140,7 +140,7 @@ save-deg: 1
 checkpoint-step: 500
 
 # Path to store the results. You can store multiple simulations in one folder
-folder: "results"
+folder: results
 
 # Over write the standard 1, 2, 3 name of the sub folders
 #sub-folder: None

environment.yml

@@ -10,5 +10,6 @@ dependencies:
   - scipy
   - configargparse
   - numpy
+  - pyyaml
   - pip:
     - cppimport

setup.py

@@ -4,7 +4,7 @@
     long_description = fh.read()
 
 DEPENDENCIES = ['configargparse', "fenics-dolfin",
-                "scipy", "cppimport", "numpy"]
+                "scipy", "cppimport", "numpy", "pyyaml"]
 TEST_DEPENDENCIES = ['pytest']
 
 VERSION = "1.5"

turtleFSI/modules/domain.py

@@ -22,15 +22,18 @@ def assign_domain_properties(dx, dx_f_id, rho_f, mu_f, fluid_properties, dx_s_id
 
     # 1. Create differential for each fluid region, and organize into fluid_properties list of dicts
     dx_f = {}
-    if isinstance(dx_f_id, list): # If dx_f_id is a list (i.e, if there are multiple fluid regions):
-        for fluid_region in range(len(dx_f_id)):
-            dx_f[fluid_region] = dx(dx_f_id[fluid_region], subdomain_data=domains) # Create dx_f for each fluid region
-            fluid_properties.append({"dx_f_id":dx_f_id[fluid_region],"rho_f":rho_f[fluid_region],"mu_f":mu_f[fluid_region]})
-        dx_f_id_list=dx_f_id
-    else:
-        dx_f[0] = dx(dx_f_id, subdomain_data=domains)
-        dx_f_id_list=[dx_f_id]
-        fluid_properties.append({"dx_f_id":dx_f_id,"rho_f":rho_f,"mu_f":mu_f})
+    if len(fluid_properties) == 0:
+        if isinstance(dx_f_id, list): # If dx_f_id is a list (i.e, if there are multiple fluid regions):
+            for fluid_region in range(len(dx_f_id)):
+                dx_f[fluid_region] = dx(dx_f_id[fluid_region], subdomain_data=domains) # Create dx_f for each fluid region
+                fluid_properties.append({"dx_f_id":dx_f_id[fluid_region],"rho_f":rho_f[fluid_region],"mu_f":mu_f[fluid_region]})
+            dx_f_id_list=dx_f_id
+        else:
+            dx_f[0] = dx(dx_f_id, subdomain_data=domains)
+            dx_f_id_list=[dx_f_id]
+            fluid_properties.append({"dx_f_id":dx_f_id,"rho_f":rho_f,"mu_f":mu_f})
+    elif isinstance(fluid_properties, dict):
+        fluid_properties = [fluid_properties]
 
     # Create solid region differentials
     dx_s = {}

turtleFSI/utils/argpar.py

@@ -18,7 +18,7 @@
 import configargparse
 import string
 import ast
-
+import yaml
 
 class StoreDictKeyPair(configargparse.Action):
     def __init__(self, option_strings, dest, nargs=None, **kwargs):
@@ -120,13 +120,13 @@ def restricted_float(x):
 
 def parse():
 
-    parser = configargparse.ArgumentParser(description=(
-        "turtleFSI is an open source Fluid-Structure Interaction (FSI) solver written in Python "
-        + "and built upon the FEniCS finite element library. The purpose of turtleFSI is to "
-        + "provide a user friendly and numerically robust monolithic FSI solver able to handle "
-        + "problems characterized by large deformation. turtleFSI benefites from the state-of-the-art "
-        + "parrallel computing features available from the FEniCS library and can be executed with "
-        + "MPI on large computing resources."))
+    parser = configargparse.ArgParser(config_file_parser_class=configargparse.ConfigparserConfigFileParser, 
+            description=("turtleFSI is an open source Fluid-Structure Interaction (FSI) solver written in Python "
+                        + "and built upon the FEniCS finite element library. The purpose of turtleFSI is to "
+                        + "provide a user friendly and numerically robust monolithic FSI solver able to handle "
+                        + "problems characterized by large deformation. turtleFSI benefites from the state-of-the-art "
+                        + "parrallel computing features available from the FEniCS library and can be executed with "
+                        + "MPI on large computing resources."))
 
     # Configuration file
     parser.add_argument('-c', '--config', is_config_file=True,
@@ -186,6 +186,12 @@ def parse():
                         help="1st Lame Coef. for the solid")
     parser.add_argument("--gravity", type=float, default=None,
                         help="Gravitational force on the solid")
+
+    parser.add_argument("--solid_properties", type=yaml.safe_load, default=None, 
+                        help="Solid properties as a dictionary")
+
+    parser.add_argument("--fluid_properties", type=yaml.safe_load, default=None,
+                        help="Fluid properties as a dictionary")
 
     # Domain settings
     parser.add_argument("--dx-f-id", type=int, default=None,
@@ -266,6 +272,15 @@ def parse():
 
     # Parse arguments
     args, unknownargs = parser.parse_known_args()
+
+    if args.__dict__["solid_properties"]:
+        for k, v in args.__dict__["solid_properties"].items():
+            if k != "material_model":
+                args.__dict__["solid_properties"][k] = float(v)
+
+    if args.__dict__["fluid_properties"]:
+        for k, v in args.__dict__["fluid_properties"].items():
+            args.__dict__["fluid_properties"][k] = float(v)
 
     # Add dt and T as parameters for time-step and end-time respectively
     d = {'dt': args.__dict__['time_step'],