Adding STL support and changing volume check to relative test

proteus/SpatialTools.py

@@ -1114,6 +1114,37 @@ def __init__(self, domain, filename):
             self.BC[key] = self.BC_class(shape=self, name=key)
             self.BC_list += [self.BC[key]]
         # self.BC = BCContainer(self.BC_dict)
+
+    def reloadBCList(self):
+        """ 
+        Allows for easier addition/modification of shape BC's from the input file directly. 
+        Calls to this function should be made after adding a new entry to boundaryTags dict, 
+        and before assignment of boundary conditions.
+
+        ex:
+        tank.boundaryTags["top"]=2 #<-new BC flag
+        tank.reloadBCList()
+        """
+        self.BC={}
+        self.BC_list=[]
+        for key,value in self.boundaryTags.items():
+            self.BC[key] = self.BC_class(shape=self, name=key)
+            self.BC_list += [self.BC[key]]
+
+    def assignFacetFlagsFromSTL(self,flag,boundary_stl):
+        """
+        Add flags to ShapeSTL facets using a separate STL surface containing only the boundary facets.
+
+        ex:
+        tank.assignFacetFlagsFromSTL(boundaryTags["inflow"],"inflow.stl")
+        """
+
+        boundary_stl_info=getInfoFromSTL(boundary_stl)
+        for i in range(len(self.facets)):
+            if ((self.vertices[self.facets[i][0][0]].tolist() in boundary_stl_info[0].tolist()) and
+                (self.vertices[self.facets[i][0][1]].tolist() in boundary_stl_info[0].tolist()) and
+                (self.vertices[self.facets[i][0][2]].tolist() in boundary_stl_info[0].tolist())):
+                self.facetFlags[i]=flag
 
 def getInfoFromSTL(filename):
     """

proteus/mprans/VOF.py

@@ -7,7 +7,7 @@
 from builtins import range
 from past.utils import old_div
 import numpy as np
-from math import fabs
+from math import fabs, isclose
 import proteus
 from proteus import cfemIntegrals, Quadrature, Norms, Comm
 from proteus.NonlinearSolvers import NonlinearEquation
@@ -1082,9 +1082,7 @@ def getMassMatrix(self):
         self.ML = np.zeros((self.nFreeDOF_global[0],), 'd')
         for i in range(self.nFreeDOF_global[0]):
             self.ML[i] = self.MC_a[self.rowptr[i]:self.rowptr[i + 1]].sum()
-        np.testing.assert_almost_equal(self.ML.sum(),
-                                       self.mesh.volume,
-                                       err_msg="Trace of lumped mass matrix should be the domain volume", verbose=True)
+        assert isclose(self.ML.sum(),self.mesh.volume,rel_tol=1e-7), "Trace of lumped mass matrix should be the domain volume"+": "+str(self.ML.sum())+" =/= "+str(self.mesh.volume)
 
     def initVectors(self):
         if self.coefficients.porosity_dof is None: