Add write_vec option and lid_two_region example

examples/channel_flow_force/input.yml

@@ -125,9 +125,11 @@ convergence_study:
 # Postprocessing
 # ==============
 # - write_pdfs: Write all solution fields as PDF plot
+# - write_vecs: Write all solution fields as vectors
 # - massflow: List of BC IDs to compute massflow J=int_bc dot(u,n) ds
 postprocessing:
   write_pdfs: True
+  write_vecs: False
   massflow: [3002]
 
 # Parameter Study

examples/channel_flow_pressure/input.yml

@@ -125,9 +125,11 @@ convergence_study:
 # Postprocessing
 # ==============
 # - write_pdfs: Write all solution fields as PDF plot
+# - write_vecs: Write all solution fields as vectors
 # - massflow: List of BC IDs to compute massflow J=int_bc dot(u,n) ds
 postprocessing:
   write_pdfs: True
+  write_vecs: False
   massflow: [3002]
 
 # Parameter Study

examples/knudsen_pump/input.yml

@@ -154,9 +154,11 @@ convergence_study:
 # Postprocessing
 # ==============
 # - write_pdfs: Write all solution fields as PDF plot
+# - write_vecs: Write all solution fields as vectors
 # - massflow: List of BC IDs to compute massflow J=int_bc dot(u,n) ds
 postprocessing:
   write_pdfs: True
+  write_vecs: False
   massflow: []
 
 # Parameter Study

examples/lid_driven_cavity/input.yml

@@ -111,9 +111,11 @@ convergence_study:
 # Postprocessing
 # ==============
 # - write_pdfs: Write all solution fields as PDF plot
+# - write_vecs: Write all solution fields as vectors
 # - massflow: List of BC IDs to compute massflow J=int_bc dot(u,n) ds
 postprocessing:
   write_pdfs: True
+  write_vecs: False
   massflow: []
 
 # Parameter Study

examples/lid_two_regions/input.yml

 # General
 # =======
 # - output_folder: Used as output folder
-output_folder: results_lid_driven_cavity
+output_folder: results_lid_two_regions
 
 # Meshes
 # ======
@@ -64,9 +64,9 @@ body_force: [0,0]
 #     - kn: Knudsen number
 regs:
   4000: # top
-    kn: 0.08
+    kn: 0.1
   4100: # bot
-    kn: 0.08
+    kn: 1.0
 
 # Boundary Conditions
 # ===================
@@ -113,9 +113,11 @@ convergence_study:
 # Postprocessing
 # ==============
 # - write_pdfs: Write all solution fields as PDF plot
+# - write_vecs: Write all solution fields as vectors
 # - massflow: List of BC IDs to compute massflow J=int_bc dot(u,n) ds
 postprocessing:
   write_pdfs: True
+  write_vecs: False
   massflow: []
 
 # Parameter Study

examples/test_examples.py

@@ -45,6 +45,14 @@ class TestExamples(object):
         self.create_meshes(working_dir)
         self.run_solver("input.yml", working_dir)
 
+    def test_lid_two_regions(self):
+        r"""
+        Test the lid case with two region.
+        """
+        working_dir = "examples/lid_two_regions"
+        self.create_meshes(working_dir)
+        self.run_solver("input.yml", working_dir)
+
     @pytest.mark.skip(reason="Skip, needs too much time")
     def test_channel_flow_pressure(self):
         r"""

fenicsR13/input.py

@@ -140,9 +140,12 @@ class Input:
         # Postprocessing
         # ==============
         # - write_pdfs: Write all solution fields as PDF plot
+        # - write_vecs: Write all solution fields as vectors
         # - massflow: List of BC IDs to compute massflow J=int_bc dot(u,n) ds
         postprocessing:
         write_pdfs: True
+        write_vecs: True
+        massflow: []
 
 
         # Parameter Study
@@ -272,6 +275,10 @@ class Input:
                         "type": "boolean",
                         "required": True
                     },
+                    "write_vecs": {
+                        "type": "boolean",
+                        "required": True
+                    },
                     "massflow": {
                         "type": "list",
                         "required": True,

fenicsR13/solver.py

@@ -75,6 +75,7 @@ class Solver:
         self.delta_p = self.params["stabilization"]["cip"]["delta_p"]
 
         self.write_pdfs = self.params["postprocessing"]["write_pdfs"]
+        self.write_vecs = self.params["postprocessing"]["write_vecs"]
         self.massflow = self.params["postprocessing"]["massflow"]
 
         # Create region field expressions
@@ -1145,6 +1146,8 @@ class Solver:
         print("Write fields..")
 
         self.__write_solutions()
+        if self.write_vecs:
+            self.__write_vecs()
         self.__write_parameters()
         if self.write_systemmatrix:
             self.__write_discrete_system()
@@ -1156,6 +1159,13 @@ class Solver:
             if sols[field] is not None:
                 self.__write_xdmf(field, sols[field], self.write_pdfs)
 
+    def __write_vecs(self):
+        """Write all solutions to vectors."""
+        sols = self.sol
+        for field in sols:
+            if sols[field] is not None:
+                self.__write_vec(field, sols[field], self.write_pdfs)
+
     def __write_parameters(self):
         """
         Write parameter functions for debug reasons.
@@ -1356,3 +1366,44 @@ class Solver:
                     print("Write {}".format(fname_pdf))
                     plt.savefig(fname_pdf, dpi=150)
                     plt.close()
+
+    def __write_vec(self, name, field, write_pdf):
+        """
+        Write a given field to a vector.
+        """
+
+        dimension = len(field.value_shape())
+        if dimension == 0:
+            # scalar
+            fname_mat = (
+                self.output_folder + name + "_" + str(self.time)
+                + ".mat"
+            )
+            np.savetxt(
+                self.output_folder + name + "_" + str(self.time) + ".mat",
+                field.compute_vertex_values()
+            )
+            print("Write {}".format(fname_mat))
+        else:
+            # vector or tensor
+            components = len(field.split())
+            indexMap = {
+                1: {
+                    1: "x",
+                    2: "y"
+                },
+                2: {
+                    1: "xx",
+                    2: "xy",
+                    3: "yx",
+                    4: "yy",
+                }
+            }
+            for i in range(components):
+                fieldname = name + "_" + str(indexMap[dimension][i + 1])
+                fname_mat = (
+                    self.output_folder + fieldname + "_" + str(self.time)
+                    + ".mat"
+                )
+                np.savetxt(fname_mat, field.split()[i].compute_vertex_values())
+                print("Write {}".format(fname_mat))

tests/heat/inputs/heat_01_coeffs_p1p1_stab.yml

@@ -118,9 +118,11 @@ convergence_study:
 # Postprocessing
 # ==============
 # - write_pdfs: Write all solution fields as PDF plot
+# - write_vecs: Write all solution fields as vectors
 # - massflow: List of BC IDs to compute massflow J=int_bc dot(u,n) ds
 postprocessing:
   write_pdfs: False
+  write_vecs: False
   massflow: []
 
 # Parameter Study

tests/heat/inputs/heat_01_coeffs_p1p2_nostab.yml

@@ -118,9 +118,11 @@ convergence_study:
 # Postprocessing
 # ==============
 # - write_pdfs: Write all solution fields as PDF plot
+# - write_vecs: Write all solution fields as vectors
 # - massflow: List of BC IDs to compute massflow J=int_bc dot(u,n) ds
 postprocessing:
   write_pdfs: False
+  write_vecs: False
   massflow: []
 
 # Parameter Study

tests/heat/inputs/heat_01_coeffs_p2p2_stab.yml

@@ -118,9 +118,11 @@ convergence_study:
 # Postprocessing
 # ==============
 # - write_pdfs: Write all solution fields as PDF plot
+# - write_vecs: Write all solution fields as vectors
 # - massflow: List of BC IDs to compute massflow J=int_bc dot(u,n) ds
 postprocessing:
   write_pdfs: False
+  write_vecs: False
   massflow: []
 
 # Parameter Study

tests/heat/inputs/heat_10_coeffs_p2p2_stab.yml

@@ -119,9 +119,11 @@ convergence_study:
 # Postprocessing
 # ==============
 # - write_pdfs: Write all solution fields as PDF plot
+# - write_vecs: Write all solution fields as vectors
 # - massflow: List of BC IDs to compute massflow J=int_bc dot(u,n) ds
 postprocessing:
   write_pdfs: False
+  write_vecs: False
   massflow: []
 
 # Parameter Study

tests/r13/inputs/r13_1_coeffs_nosources_norot_inflow_p1p1p1p1p1_stab.yml

@@ -118,9 +118,11 @@ convergence_study:
 # Postprocessing
 # ==============
 # - write_pdfs: Write all solution fields as PDF plot
+# - write_vecs: Write all solution fields as vectors
 # - massflow: List of BC IDs to compute massflow J=int_bc dot(u,n) ds
 postprocessing:
   write_pdfs: False
+  write_vecs: False
   massflow: []
 
 # Parameter Study

tests/r13/inputs/r13_1_coeffs_nosources_norot_inflow_p1p2p1p1p2_nostab.yml

@@ -117,9 +117,11 @@ convergence_study:
 # Postprocessing
 # ==============
 # - write_pdfs: Write all solution fields as PDF plot
+# - write_vecs: Write all solution fields as vectors
 # - massflow: List of BC IDs to compute massflow J=int_bc dot(u,n) ds
 postprocessing:
   write_pdfs: False
+  write_vecs: False
   massflow: []
 
 # Parameter Study

tests/r13/inputs/r13_1_coeffs_nosources_norot_inflow_p2p2p2p2p2_stab.yml

@@ -116,9 +116,11 @@ convergence_study:
 # Postprocessing
 # ==============
 # - write_pdfs: Write all solution fields as PDF plot
+# - write_vecs: Write all solution fields as vectors
 # - massflow: List of BC IDs to compute massflow J=int_bc dot(u,n) ds
 postprocessing:
   write_pdfs: False
+  write_vecs: False
   massflow: []
 
 # Parameter Study

tests/r13/inputs/r13_1_coeffs_sources_rot_noinflow_p1p1p1p1p1_stab.yml

@@ -118,9 +118,11 @@ convergence_study:
 # Postprocessing
 # ==============
 # - write_pdfs: Write all solution fields as PDF plot
+# - write_vecs: Write all solution fields as vectors
 # - massflow: List of BC IDs to compute massflow J=int_bc dot(u,n) ds
 postprocessing:
   write_pdfs: False
+  write_vecs: False
   massflow: []
 
 # Parameter Study

tests/r13/inputs/r13_1_coeffs_sources_rot_noinflow_p2p2p2p2p2_stab.yml

@@ -116,9 +116,11 @@ convergence_study:
 # Postprocessing
 # ==============
 # - write_pdfs: Write all solution fields as PDF plot
+# - write_vecs: Write all solution fields as vectors
 # - massflow: List of BC IDs to compute massflow J=int_bc dot(u,n) ds
 postprocessing:
   write_pdfs: False
+  write_vecs: False
   massflow: []
 
 # Parameter Study

tests/stress/inputs/stress_01_nosource_rot_p1p1p1_stab.yml

@@ -118,9 +118,11 @@ convergence_study:
 # Postprocessing
 # ==============
 # - write_pdfs: Write all solution fields as PDF plot
+# - write_vecs: Write all solution fields as vectors
 # - massflow: List of BC IDs to compute massflow J=int_bc dot(u,n) ds
 postprocessing:
   write_pdfs: False
+  write_vecs: False
   massflow: []
 
 # Parameter Study

tests/stress/inputs/stress_01_source_norot_p1p1p1_stab.yml

@@ -119,9 +119,11 @@ convergence_study:
 # Postprocessing
 # ==============
 # - write_pdfs: Write all solution fields as PDF plot
+# - write_vecs: Write all solution fields as vectors
 # - massflow: List of BC IDs to compute massflow J=int_bc dot(u,n) ds
 postprocessing:
   write_pdfs: False
+  write_vecs: False
   massflow: []
 
 # Parameter Study

tests/stress/inputs/stress_01_source_rot_p1p1p1_stab.yml

@@ -118,9 +118,11 @@ convergence_study:
 # Postprocessing
 # ==============
 # - write_pdfs: Write all solution fields as PDF plot
+# - write_vecs: Write all solution fields as vectors
 # - massflow: List of BC IDs to compute massflow J=int_bc dot(u,n) ds
 postprocessing:
   write_pdfs: False
+  write_vecs: False
   massflow: []
 
 # Parameter Study