First round of fixes towards PA v0.3

.gitignore

@@ -2,6 +2,8 @@
 #*.msh
 *.vtu
 *.pvd
+*.pvtu
+*.bson
 *.jl.*.cov
 *.jl.cov
 *.jl.mem

src/ExtraFunctions.jl

@@ -1,61 +1,54 @@
 ##Functions for mesh manipulation
 
 function strechMHD(coord;domain=(0.0,1.0,0.0,1.0,0.0,1.0),factor=(1.0,1.0,1.0),dirs=(1,2,3))~
-##Mesh streching according to Smolentsev formula
-ncoord = collect(coord.data)
-for (i,dir) in enumerate(dirs)
-  ξ0 = domain[i*2-1]
-  ξ1 = domain[i*2]
-  l =  ξ1 - ξ0
-  c = (factor[i] + 1)/(factor[i] - 1)
+  ##Mesh streching according to Smolentsev formula
+  ncoord = collect(coord.data)
+  for (i,dir) in enumerate(dirs)
+    ξ0 = domain[i*2-1]
+    ξ1 = domain[i*2]
+    l =  ξ1 - ξ0
+    c = (factor[i] + 1)/(factor[i] - 1)
 
-  if l > 0
-        if ξ0 <= coord[dir] <= ξ1
-           ξx = (coord[dir] - ξ0)/l                     #ξx from 0 to 1 uniformly distributed
-           ξx_streched = factor[i]*(c^ξx-1)/(1+c^ξx)    #ξx streched from 0 to 1 towards 1
-           ncoord[dir] =  ξx_streched*l + ξ0            #coords streched towards ξ1
-        end
-  else
-        if ξ1 <= coord[dir] <= ξ0
-           ξx = (coord[dir] - ξ0)/l                        #ξx from 0 to 1 uniformly distributed
-           ξx_streched = factor[i]*(c^ξx-1)/(1+c^ξx)       #ξx streched from 0 to 1 towards 1
-           ncoord[dir] =  ξx_streched*l + ξ0               #coords streched towards ξ1
-
-        end
+    if l > 0
+      if ξ0 <= coord[dir] <= ξ1
+        ξx = (coord[dir] - ξ0)/l                     # ξx from 0 to 1 uniformly distributed
+        ξx_streched = factor[i]*(c^ξx-1)/(1+c^ξx)    # ξx streched from 0 to 1 towards 1
+        ncoord[dir] =  ξx_streched*l + ξ0            # coords streched towards ξ1
+      end
+    else
+      if ξ1 <= coord[dir] <= ξ0
+        ξx = (coord[dir] - ξ0)/l                     # ξx from 0 to 1 uniformly distributed
+        ξx_streched = factor[i]*(c^ξx-1)/(1+c^ξx)    # ξx streched from 0 to 1 towards 1
+        ncoord[dir] =  ξx_streched*l + ξ0            # coords streched towards ξ1
+      end
+    end
   end
-end
-VectorValue(ncoord)
+  return VectorValue(ncoord)
 end
 
 function ChangeDensity(coord;domain=(0.0,1.0,0.0,1.0,0.0,1.0),subDomain=(0.0,1.0,0.0,1.0,0.0,1.0), 
 			     nodesTot=(1.0,1.0,1.0), nodesSub=(1.0,1.0,1.0), dirs=(1,2,3))
-ncoord = collect(coord.data)
-for (i,dir) in enumerate(dirs)
-  ξ0 = domain[i*2-1]
-  ξ1 = domain[i*2]
-  Ltot =  ξ1 - ξ0
-  Lsub = subDomain[i*2] - subDomain[i*2-1]
-
-  alpha = (Lsub/Ltot)*(nodesTot[i]/nodesSub[i])
-  betta = ((Ltot-Lsub)/Ltot)*(nodesTot[i]/(nodesTot[i]-nodesSub[i]))
-
-  if Ltot != Lsub
+  ncoord = collect(coord.data)
+  for (i,dir) in enumerate(dirs)
+    ξ0 = domain[i*2-1]
+    ξ1 = domain[i*2]
+    Ltot =  ξ1 - ξ0
+    Lsub = subDomain[i*2] - subDomain[i*2-1]
+
+    alpha = (Lsub/Ltot)*(nodesTot[i]/nodesSub[i])
+    betta = ((Ltot-Lsub)/Ltot)*(nodesTot[i]/(nodesTot[i]-nodesSub[i]))
 
-     if ξ0 <= coord[dir] <= ξ1
-       
+    if Ltot != Lsub
+      if ξ0 <= coord[dir] <= ξ1
         if coord[dir] <= (Lsub/alpha + ξ0)
-
-           ncoord[dir] = alpha*coord[dir] + ξ0*(1-alpha)
-
-	else
-
-   	   ncoord[dir] = betta*coord[dir] + ξ0*(1-betta) + Lsub*(1-betta/alpha)
-
+          ncoord[dir] = alpha*coord[dir] + ξ0*(1-alpha)
+        else
+          ncoord[dir] = betta*coord[dir] + ξ0*(1-betta) + Lsub*(1-betta/alpha)
         end
-     end
+      end
+    end
   end
-end
-VectorValue(ncoord)
+  return VectorValue(ncoord)
 end
 
 ##Functions for geometry generation
@@ -77,7 +70,7 @@ function cuboid(;dx=1,dy=1,dz=1,x0=Point(0,0,0),name="cuboid",
   geo34 = intersect(plane3,plane4)
   geo56 = intersect(plane5,plane6)
 
-  intersect(intersect(geo12,geo34),geo56,name=name)
+  return intersect(intersect(geo12,geo34),geo56,name=name)
 end
 
 # Function that given a filter set a name to those elements that satisfy the