Change style of input files

- Allows for either float or cpp string containing phi, R, tau

src/input.py

@@ -50,34 +50,34 @@ class Input:
                     "type": "dict",
                     "schema": {
                         "theta_w": {
-                            'anyof': [{'type': "string"}, {'type': "float"}],
+                            "anyof": [{"type": "string"}, {"type": "float"}],
                             "required": True,
                         },
                         "v_t": {
-                            'anyof': [{'type': "string"}, {'type': "float"}],
+                            "anyof": [{"type": "string"}, {"type": "float"}],
                             "required": True
                         },
                         "v_n": {
-                            'anyof': [{'type': "string"}, {'type': "float"}],
+                            "anyof": [{"type": "string"}, {"type": "float"}],
                             "required": True
                         },
                         "p_w": {
-                            'anyof': [{'type': "string"}, {'type': "float"}],
+                            "anyof": [{"type": "string"}, {"type": "float"}],
                             "required": True
                         },
                         "gamma": {
-                            'anyof': [{'type': "string"}, {'type': "float"}],
+                            "anyof": [{"type": "string"}, {"type": "float"}],
                             "required": True
                         },
                     }
                 }
             },
             "heat_source": {
-                "type": "string",
+                "anyof": [{"type": "string"}, {"type": "float"}],
                 "required": True,
             },
             "mass_source": {
-                "type": "string",
+                "anyof": [{"type": "string"}, {"type": "float"}],
                 "required": True,
             },
             "convergence_study": {

src/solver.py

@@ -57,6 +57,7 @@ class Solver:
         self.phi = df.Expression("atan2(x[1],x[0])", degree=2)
 
         # Create boundary field expressions
+        # FIXME: Create function to create dolfin expression, also for sources
         self.bcs = copy.deepcopy(self.params["bcs"])
         for edge_id in self.bcs:
             for field in self.bcs[edge_id].keys():
@@ -66,11 +67,11 @@ class Solver:
                 )
 
         self.heat_source = df.Expression(
-            self.params["heat_source"], degree=2,
+            str(self.params["heat_source"]), degree=2,
             tau=self.tau, phi=self.phi, R=self.R
         )
         self.mass_source = df.Expression(
-            self.params["mass_source"], degree=2,
+            str(self.params["mass_source"]), degree=2,
             tau=self.tau, phi=self.phi, R=self.R
         )
 

tests/coupled/inputs/1_coeffs_sources_rot_p1p1p1p1p1_stab.yml

@@ -17,21 +17,21 @@ meshes:
   # - ../mesh/ring6.h5
 
 elements:
-  "theta":
-    "shape": "Lagrange"
-    "degree": 1
-  "s":
-    "shape": "Lagrange"
-    "degree": 1
-  "p":
-    "shape": "Lagrange"
-    "degree": 1
-  "u":
-    "shape": "Lagrange"
-    "degree": 1
-  "sigma":
-    "shape": "Lagrange"
-    "degree": 1
+  theta:
+    shape: Lagrange
+    degree: 1
+  s:
+    shape: Lagrange
+    degree: 1
+  p:
+    shape: Lagrange
+    degree: 1
+  u:
+    shape: Lagrange
+    degree: 1
+  sigma:
+    shape: Lagrange
+    degree: 1
 
 # Stabilization
 # =============
@@ -50,7 +50,7 @@ stabilization:
 nsd: 2
 
 # heat, stress, coupled
-mode: "coupled"
+mode: coupled
 
 # Coefficients as in westerkamp2019 or without as in torrilhon2017
 use_coeffs: True
@@ -77,10 +77,10 @@ bcs:
     gamma: 0
 
 # heat source
-heat_source: "0"
+heat_source: 0
 
 # mass source
-mass_source: "1.0 * (1.0 - (5.0*pow(R,2))/(18.0*pow(tau,2))) * cos(phi)"
+mass_source: 1.0 * (1.0 - (5.0*pow(R,2))/(18.0*pow(tau,2))) * cos(phi)
 
 # Perform convergence study on given set of meshes with exact solution
 convergence_study:

tests/coupled/inputs/1_coeffs_sources_rot_p2p2p2p2p2_stab.yml

@@ -17,21 +17,21 @@ meshes:
   # - ../mesh/ring6.h5
 
 elements:
-  "theta":
-    "shape": "Lagrange"
-    "degree": 2
-  "s":
-    "shape": "Lagrange"
-    "degree": 2
-  "p":
-    "shape": "Lagrange"
-    "degree": 2
-  "u":
-    "shape": "Lagrange"
-    "degree": 2
-  "sigma":
-    "shape": "Lagrange"
-    "degree": 2
+  theta:
+    shape: Lagrange
+    degree: 2
+  s:
+    shape: Lagrange
+    degree: 2
+  p:
+    shape: Lagrange
+    degree: 2
+  u:
+    shape: Lagrange
+    degree: 2
+  sigma:
+    shape: Lagrange
+    degree: 2
 
 # Stabilization
 # =============
@@ -50,7 +50,7 @@ stabilization:
 nsd: 2
 
 # heat, stress, coupled
-mode: "coupled"
+mode: coupled
 
 # Coefficients as in westerkamp2019 or without as in torrilhon2017
 use_coeffs: True
@@ -79,10 +79,10 @@ bcs:
 
 
 # heat source
-heat_source: "0"
+heat_source: 0
 
 # mass source
-mass_source: "1.0 * (1.0 - (5.0*pow(R,2))/(18.0*pow(tau,2))) * cos(phi)"
+mass_source: 1.0 * (1.0 - (5.0*pow(R,2))/(18.0*pow(tau,2))) * cos(phi)
 
 # Perform convergence study on given set of meshes with exact solution
 convergence_study:

tests/coupled/test_coupled_convergence.py

@@ -35,10 +35,10 @@ class TestCoupledConvergence(object):
                 "diff", "-u", "--strip-trailing-cr", errorsfile, ref_errorsfile
             ], cwd=self.working_dir)
         """
-        subprocess.check_call([
+        print(subprocess.check_output([
             "numdiff", "-s", "\"\n\r ,\"", "-a", "1E-10",
             errorsfile, ref_errorsfile
-        ], cwd=self.working_dir)
+        ], cwd=self.working_dir))
 
     # @pytest.fixture(scope="module", autouse=True)
     @pytest.mark.skip(reason="Not needed because meshes are in repo")

tests/full/inputs/1_coeffs_p1p1p1p1p1_stab.yml

@@ -17,21 +17,21 @@ meshes:
   # - ../mesh/ring6.h5
 
 elements:
-  "theta":
-    "shape": "Lagrange"
-    "degree": 1
-  "s":
-    "shape": "Lagrange"
-    "degree": 1
-  "p":
-    "shape": "Lagrange"
-    "degree": 1
-  "u":
-    "shape": "Lagrange"
-    "degree": 1
-  "sigma":
-    "shape": "Lagrange"
-    "degree": 1
+  theta:
+    shape: Lagrange
+    degree: 1
+  s:
+    shape: Lagrange
+    degree: 1
+  p:
+    shape: Lagrange
+    degree: 1
+  u:
+    shape: Lagrange
+    degree: 1
+  sigma:
+    shape: Lagrange
+    degree: 1
 
 # Stabilization
 # =============
@@ -50,7 +50,7 @@ stabilization:
 nsd: 2
 
 # heat, stress, coupled
-mode: "coupled"
+mode: coupled
 
 # Coefficients as in westerkamp2019 or without as in torrilhon2017
 use_coeffs: True
@@ -77,10 +77,10 @@ bcs:
     gamma: pow(10,+3)
 
 # heat source
-heat_source: "0"
+heat_source: 0
 
 # mass source
-mass_source: "0"
+mass_source: 0
 
 # Perform convergence study on given set of meshes with exact solution
 convergence_study:

tests/heat/inputs/01_coeffs_p1p1_stab.yml

@@ -16,21 +16,21 @@ meshes:
   # - ../mesh/ring7.h5 # fails at 8GB with P1P1
 
 elements:
-  "theta":
-    "shape": "Lagrange"
-    "degree": 1
-  "s":
-    "shape": "Lagrange"
-    "degree": 1
-  "p":
-    "shape": "Lagrange"
-    "degree": 1
-  "u":
-    "shape": "Lagrange"
-    "degree": 1
-  "sigma":
-    "shape": "Lagrange"
-    "degree": 1
+  theta:
+    shape: Lagrange
+    degree: 1
+  s:
+    shape: Lagrange
+    degree: 1
+  p:
+    shape: Lagrange
+    degree: 1
+  u:
+    shape: Lagrange
+    degree: 1
+  sigma:
+    shape: Lagrange
+    degree: 1
 
 # Stabilization
 # =============
@@ -49,7 +49,7 @@ stabilization:
 nsd: 2
 
 # heat, stress, coupled
-mode: "heat"
+mode: heat
 
 # Coefficients as in westerkamp2019 or without as in torrilhon2017
 use_coeffs: True
@@ -75,10 +75,10 @@ bcs:
     gamma: 0
 
 # heat source
-heat_source: "2.0 - 1.0 * pow(sqrt(pow(x[0],2)+pow(x[1],2)),2)"
+heat_source: 2.0 - 1.0 * pow(sqrt(pow(x[0],2)+pow(x[1],2)),2)
 
 # mass source
-mass_source: "2.0/5.0 * (1.0 - (5.0*std::pow(sqrt(pow(x[0],2)+pow(x[1],2)),2))/(18.0*pow(tau,2))) * std::cos(phi)"
+mass_source: 2.0/5.0 * (1.0 - (5.0*std::pow(sqrt(pow(x[0],2)+pow(x[1],2)),2))/(18.0*pow(tau,2))) * std::cos(phi)
 
 # Perform convergence study on given set of meshes with exact solution
 convergence_study:

tests/heat/inputs/01_coeffs_p1p2_nostab.yml

@@ -16,21 +16,21 @@ meshes:
   # - ../mesh/ring7.h5 # fails at 8GB with P1P1
 
 elements:
-  "theta":
-    "shape": "Lagrange"
-    "degree": 1
-  "s":
-    "shape": "Lagrange"
-    "degree": 2
-  "p":
-    "shape": "Lagrange"
-    "degree": 1
-  "u":
-    "shape": "Lagrange"
-    "degree": 1
-  "sigma":
-    "shape": "Lagrange"
-    "degree": 1
+  theta:
+    shape: Lagrange
+    degree: 1
+  s:
+    shape: Lagrange
+    degree: 2
+  p:
+    shape: Lagrange
+    degree: 1
+  u:
+    shape: Lagrange
+    degree: 1
+  sigma:
+    shape: Lagrange
+    degree: 1
 
 # Stabilization
 # =============
@@ -49,7 +49,7 @@ stabilization:
 nsd: 2
 
 # heat, stress, coupled
-mode: "heat"
+mode: heat
 
 # Coefficients as in westerkamp2019 or without as in torrilhon2017
 use_coeffs: True
@@ -75,10 +75,10 @@ bcs:
     gamma: 0
 
 # heat source
-heat_source: "2.0 - 1.0 * pow(sqrt(pow(x[0],2)+pow(x[1],2)),2)"
+heat_source: 2.0 - 1.0 * pow(sqrt(pow(x[0],2)+pow(x[1],2)),2)
 
 # mass source
-mass_source: "2.0/5.0 * (1.0 - (5.0*std::pow(sqrt(pow(x[0],2)+pow(x[1],2)),2))/(18.0*pow(tau,2))) * std::cos(phi)"
+mass_source: 2.0/5.0 * (1.0 - (5.0*std::pow(sqrt(pow(x[0],2)+pow(x[1],2)),2))/(18.0*pow(tau,2))) * std::cos(phi)
 
 # Perform convergence study on given set of meshes with exact solution
 convergence_study:

tests/heat/inputs/01_coeffs_p2p2_stab.yml

@@ -18,21 +18,21 @@ meshes:
   # - ../mesh/ring9.h5
 
 elements:
-  "theta":
-    "shape": "Lagrange"
-    "degree": 2
-  "s":
-    "shape": "Lagrange"
-    "degree": 2
-  "p":
-    "shape": "Lagrange"
-    "degree": 1
-  "u":
-    "shape": "Lagrange"
-    "degree": 1
-  "sigma":
-    "shape": "Lagrange"
-    "degree": 1
+  theta:
+    shape: Lagrange
+    degree: 2
+  s:
+    shape: Lagrange
+    degree: 2
+  p:
+    shape: Lagrange
+    degree: 1
+  u:
+    shape: Lagrange
+    degree: 1
+  sigma:
+    shape: Lagrange
+    degree: 1
 
 # Stabilization
 # =============
@@ -51,7 +51,7 @@ stabilization:
 nsd: 2
 
 # heat, stress, coupled
-mode: "heat"
+mode: heat
 
 # Coefficients as in westerkamp2019 or without as in torrilhon2017
 use_coeffs: True
@@ -77,10 +77,10 @@ bcs:
     gamma: 0
 
 # heat source
-heat_source: "2.0 - 1.0 * pow(sqrt(pow(x[0],2)+pow(x[1],2)),2)"
+heat_source: 2.0 - 1.0 * pow(sqrt(pow(x[0],2)+pow(x[1],2)),2)
 
 # mass source
-mass_source: "2.0/5.0 * (1.0 - (5.0*std::pow(sqrt(pow(x[0],2)+pow(x[1],2)),2))/(18.0*pow(tau,2))) * std::cos(phi)"
+mass_source: 2.0/5.0 * (1.0 - (5.0*std::pow(sqrt(pow(x[0],2)+pow(x[1],2)),2))/(18.0*pow(tau,2))) * std::cos(phi)
 
 # Perform convergence study on given set of meshes with exact solution
 convergence_study:

tests/heat/inputs/01_nocoeffs_p1p2_nostab.yml

@@ -16,21 +16,21 @@ meshes:
   # - ../mesh/ring7.h5 # fails at 8GB with P1P1
 
 elements:
-  "theta":
-    "shape": "Lagrange"
-    "degree": 1
-  "s":
-    "shape": "Lagrange"
-    "degree": 2
-  "p":
-    "shape": "Lagrange"
-    "degree": 1
-  "u":
-    "shape": "Lagrange"
-    "degree": 1
-  "sigma":
-    "shape": "Lagrange"
-    "degree": 1
+  theta:
+    shape: Lagrange
+    degree: 1
+  s:
+    shape: Lagrange
+    degree: 2
+  p:
+    shape: Lagrange
+    degree: 1
+  u:
+    shape: Lagrange
+    degree: 1
+  sigma:
+    shape: Lagrange
+    degree: 1
 
 # Stabilization
 # =============
@@ -49,7 +49,7 @@ stabilization:
 nsd: 2
 
 # heat, stress, coupled
-mode: "heat"
+mode: heat
 
 # Coefficients as in westerkamp2019 or without as in torrilhon2017
 use_coeffs: False
@@ -75,10 +75,10 @@ bcs:
     gamma: 0
 
 # heat source
-heat_source: "2.0 - 1.0 * pow(sqrt(pow(x[0],2)+pow(x[1],2)),2)"
+heat_source: 2.0 - 1.0 * pow(sqrt(pow(x[0],2)+pow(x[1],2)),2)
 
 # mass source
-mass_source: "2.0/5.0 * (1.0 - (5.0*std::pow(sqrt(pow(x[0],2)+pow(x[1],2)),2))/(18.0*pow(tau,2))) * std::cos(phi)"
+mass_source: 2.0/5.0 * (1.0 - (5.0*std::pow(sqrt(pow(x[0],2)+pow(x[1],2)),2))/(18.0*pow(tau,2))) * std::cos(phi)
 
 # Perform convergence study on given set of meshes with exact solution
 convergence_study:

tests/heat/inputs/10_coeffs_p2p2_stab.yml

@@ -16,21 +16,21 @@ meshes:
   # - ../mesh/ring7.h5 # fails at 8GB with P1P1
 
 elements:
-  "theta":
-    "shape": "Lagrange"
-    "degree": 1
-  "s":
-    "shape": "Lagrange"
-    "degree": 1
-  "p":
-    "shape": "Lagrange"
-    "degree": 1
-  "u":
-    "shape": "Lagrange"
-    "degree": 1
-  "sigma":
-    "shape": "Lagrange"
-    "degree": 1
+  theta:
+    shape: Lagrange
+    degree: 1
+  s:
+    shape: Lagrange
+    degree: 1
+  p:
+    shape: Lagrange
+    degree: 1
+  u:
+    shape: Lagrange
+    degree: 1
+  sigma:
+    shape: Lagrange
+    degree: 1
 
 # Stabilization
 # =============
@@ -49,7 +49,7 @@ stabilization:
 nsd: 2
 
 # heat, stress, coupled
-mode: "heat"
+mode: heat
 
 # Coefficients as in westerkamp2019 or without as in torrilhon2017
 use_coeffs: True
@@ -75,10 +75,10 @@ bcs:
     gamma: 0
 
 # heat source
-heat_source: "2.0 - 1.0 * pow(sqrt(pow(x[0],2)+pow(x[1],2)),2)"
+heat_source: 2.0 - 1.0 * pow(sqrt(pow(x[0],2)+pow(x[1],2)),2)
 
 # mass source
-mass_source: "2.0/5.0 * (1.0 - (5.0*std::pow(sqrt(pow(x[0],2)+pow(x[1],2)),2))/(18.0*pow(tau,2))) * std::cos(phi)"
+mass_source: 2.0/5.0 * (1.0 - (5.0*std::pow(sqrt(pow(x[0],2)+pow(x[1],2)),2))/(18.0*pow(tau,2))) * std::cos(phi)
 
 # Perform convergence study on given set of meshes with exact solution
 convergence_study:

tests/heat/test_heat_convergence.py

@@ -35,10 +35,10 @@ class TestHeatConvergence(object):
                 "diff", "-u", "--strip-trailing-cr", errorsfile, ref_errorsfile
             ], cwd=self.working_dir)
         """
-        subprocess.check_call([
+        print(subprocess.check_output([
             "numdiff", "-s", "\"\n\r ,\"", "-a", "1E-10",
             errorsfile, ref_errorsfile
-        ], cwd=self.working_dir)
+        ], cwd=self.working_dir))
 
     # @pytest.fixture(scope="module", autouse=True)
     @pytest.mark.skip(reason="Not needed because meshes are in repo")

tests/stress/inputs/01_nosource_rot_p1p1p1_stab.yml

@@ -17,21 +17,21 @@ meshes:
   # - ../mesh/ring6.h5
 
 elements:
-  "theta":
-    "shape": "Lagrange"
-    "degree": 1
-  "s":
-    "shape": "Lagrange"
-    "degree": 1
-  "p":
-    "shape": "Lagrange"
-    "degree": 1
-  "u":
-    "shape": "Lagrange"
-    "degree": 1
-  "sigma":
-    "shape": "Lagrange"
-    "degree": 1
+  theta:
+    shape: Lagrange
+    degree: 1
+  s:
+    shape: Lagrange
+    degree: 1
+  p:
+    shape: Lagrange
+    degree: 1
+  u:
+    shape: Lagrange
+    degree: 1
+  sigma:
+    shape: Lagrange
+    degree: 1
 
 # Stabilization
 # =============
@@ -50,7 +50,7 @@ stabilization:
 nsd: 2