Small fix

Makefile

@@ -9,14 +9,14 @@ default:
 	make example-0011
 	make example-0012
 	make example-0013
-	make example-0101
-	make example-0102
-	make example-0111
-	make example-0112
-	make example-0302-u
-	make example-0401
-	make example-0402
-	make example-0404-c
+	make example-0101   #fails!!!!
+	make example-0102   #fails!!!!
+	make example-0111   #fails!!!!
+	make example-0112   #fails!!!!
+	make example-0302-u #fails!!!! needs mesh reader!!!
+	make example-0401   #fails!!!! needs mesh reader!!!
+	make example-0402   #fails!!!! needs mesh reader!!!
+	make example-0404-c #fails!!!!
 	make collect-results
 	make create-figures
 	make latexmk-once

examples/example-0001-u/src/iron/CMakeLists.txt

@@ -1,6 +1,7 @@
-add_executable(${ExampleName} ${ExampleName}.F90 ${IRON_MESH_READER_ROOT}/src/meshReader.F90)
+add_executable(${ExampleName} ${ExampleName}.F90 ~/software/opencmiss/dependencies/meshReader-master/src/meshReader.F90)
 
 target_link_libraries(${ExampleName} opencmisslibs)
-
 install(TARGETS ${ExampleName} DESTINATION ${PROJECT_SOURCE_DIR}/bin)
+configure_file(visualise.cmgui visualise.cmgui)
+
 

examples/example-0001-u/src/iron/example.F90

@@ -272,8 +272,8 @@ PROGRAM LAPLACEEXAMPLE
   CALL cmfe_Basis_CreateFinish(Basis,Err)
 
   ! get user-defined mesh file name
-  WRITE(Filename, "(A26,I1,A1,I1,A1,I1,A2,I1,A1,I1,A1,I1,A2,I1,A3)") &
-    & "src/cheart/meshes/domain_l", &
+  WRITE(Filename, "(A29,I1,A1,I1,A1,I1,A2,I1,A1,I1,A1,I1,A2,I1,A3)") &
+    & "../src/cheart/meshes/domain_l", &
     & INT(WIDTH),"x",INT(HEIGHT),"x",INT(LENGTH), &
     & "_n", &
     & NUMBER_GLOBAL_X_ELEMENTS,"x",NUMBER_GLOBAL_Y_ELEMENTS,"x",NUMBER_GLOBAL_Z_ELEMENTS, &
@@ -384,6 +384,8 @@ PROGRAM LAPLACEEXAMPLE
   END DO
   CALL cmfe_Field_ParameterSetUpdateStart(GeometricField, &
     & CMFE_FIELD_U_VARIABLE_TYPE,CMFE_FIELD_VALUES_SET_TYPE,Err)
+  CALL cmfe_Field_ParameterSetUpdateFinish(GeometricField, &
+    & CMFE_FIELD_U_VARIABLE_TYPE,CMFE_FIELD_VALUES_SET_TYPE,Err)
 
   !Create the Standard Laplace Equations set
   CALL cmfe_EquationsSet_Initialise(EquationsSet,Err)
@@ -502,11 +504,16 @@ PROGRAM LAPLACEEXAMPLE
     & NUMBER_GLOBAL_X_ELEMENTS,"x",NUMBER_GLOBAL_Y_ELEMENTS,"x",NUMBER_GLOBAL_Z_ELEMENTS, &
     & "_i",INTERPOLATION_TYPE,"_s",SOLVER_TYPE,"/Example"
   filename=trim(filename)
-  CALL cmfe_Fields_NodesExport(Fields,filename,"FORTRAN",Err)
-  CALL cmfe_Fields_ElementsExport(Fields,filename,"FORTRAN",Err)
-  CALL cmfe_Fields_Finalise(Fields,Err)
-
-  !Finialise CMISS
+  ! With develop 10.2018: Directory should be created first, this call will cause an error:
+  !CALL cmfe_Fields_NodesExport(Fields,filename,"FORTRAN",Err)
+  !CALL cmfe_Fields_ElementsExport(Fields,filename,"FORTRAN",Err)
+  ! Easy alternative:
+  CALL cmfe_Fields_NodesExport(Fields,"laplace_equation","FORTRAN",Err)
+  CALL cmfe_Fields_ElementsExport(Fields,"laplace_equation","FORTRAN",Err)
+
+  CALL cmfe_Fields_Finalise(Fields,Err)  
+
+  !Finalise CMISS
   ! Deallocate variables that store mesh data as soon as we don't need them anymore
   IF(ALLOCATED(NodesImport))            DEALLOCATE(NodesImport)
   IF(ALLOCATED(ElementsImport))         DEALLOCATE(ElementsImport)

examples/example-0001-u/src/iron/visualise.cmgui

@@ -0,0 +1,22 @@
+$name = "laplace_equation";
+
+gfx read node $name.part0.exnode;
+gfx read elem $name.part0.exelem;
+
+gfx def faces egroup $name;
+
+gfx modify g_element $name general clear circle_discretization 6 default_coordinate Coordinate element_discretization "4*4*4" native_discretization none;
+gfx modify g_element $name lines select_on invisible material default selected_material default_selected;
+gfx modify g_element $name surfaces select_on material default data Phi spectrum default selected_material default_selected render_shaded;
+gfx modify g_element $name node_points glyph sphere general size "0.025*0.025*0.025" centre 0,0,0 font default label cmiss_number select_on material blue selected_material default_selected;
+gfx modify g_element $name cylinders constant_radius 0.005 select_on material gold selected_material default_selected render_shaded;
+
+gfx create window 1 double_buffer;
+gfx modify window 1 image scene default light_model default;
+gfx modify window 1 image add_light default;
+gfx modify window 1 layout simple ortho_axes z -y eye_spacing 0.25 width 567 height 653;
+gfx modify window 1 set current_pane 1;
+gfx modify window 1 background colour 0 0 0 texture none;
+gfx modify window 1 view parallel eye_point -1.32423 -1.97615 2.23909 interest_point 0.5 0.5 0.5 up_vector 0.305326 0.386341 0.870354 view_angle 37.5028 near_clipping_plane 0.0353321 far_clipping_plane 12.6265 relative_viewport ndc_placement -1 1 2 2 viewport_coordinates 0 0 1 1;
+gfx modify window 1 overlay scene none;
+gfx modify window 1 set transform_tool current_pane 1 std_view_angle 40 normal_lines no_antialias depth_of_field 0.0 fast_transparency blend_normal;

examples/example-0001/src/iron/example.F90

@@ -433,8 +433,14 @@ PROGRAM LAPLACEEXAMPLE
     & NUMBER_GLOBAL_X_ELEMENTS,"x",NUMBER_GLOBAL_Y_ELEMENTS,"x",NUMBER_GLOBAL_Z_ELEMENTS, &
     & "_i",INTERPOLATION_TYPE,"_s",SOLVER_TYPE,"/Example"
   filename=trim(filename)
+
+  ! With develop 10.2018: Directory should be created first, this call will cause an error:
   CALL cmfe_Fields_NodesExport(Fields,filename,"FORTRAN",Err)
   CALL cmfe_Fields_ElementsExport(Fields,filename,"FORTRAN",Err)
+  ! Easy alternative:
+  !CALL cmfe_Fields_NodesExport(Fields,"laplace_equation","FORTRAN",Err)
+  !CALL cmfe_Fields_ElementsExport(Fields,"laplace_equation","FORTRAN",Err)
+
   CALL cmfe_Fields_Finalise(Fields,Err)
 
   !Finialise CMISS

examples/example-0201-u/src/iron/CMakeLists.txt

@@ -1,6 +1,8 @@
-add_executable(${ExampleName} ${ExampleName}.F90 ${IRON_MESH_READER_ROOT}/src/meshReader.F90)
+#add_executable(${ExampleName} ${ExampleName}.F90 ${IRON_MESH_READER_ROOT}/src/meshReader.F90)
+add_executable(${ExampleName} ${ExampleName}.F90 ~/software/opencmiss/dependencies/meshReader/src/meshReader.F90)
 
 target_link_libraries(${ExampleName} opencmisslibs)
 
 install(TARGETS ${ExampleName} DESTINATION ${PROJECT_SOURCE_DIR}/bin)
 
+#configure_file(visualise.cmgui visualise.cmgui) #???

examples/example-0201-u/src/iron/example.F90

@@ -252,16 +252,16 @@ PROGRAM FORTRANEXAMPLE
     WIDTH                         = 1.0_CMISSRP
     HEIGHT                        = 0.2_CMISSRP
     LENGTH                        = 0.2_CMISSRP
-    NumberGlobalXElements         = 2
-    NumberGlobalYElements         = 2
-    NumberGlobalZElements         = 2
+    NumberGlobalXElements         = 2!1
+    NumberGlobalYElements         = 2!1
+    NumberGlobalZElements         = 2!1
     SolverIsDirect                = 1 ! direct solver by default
     JACOBIAN_FD                   = 1 ! finite-difference Jacobian by default
     MooneyRivlin1                 = 0.5_CMISSRP*35.7_CMISSRP ! see note above for Neo-Hookean solid
     MooneyRivlin2                 = 0.0_CMISSRP  ! If MooneyRivlin2 == 0 --> Neo-Hookean solid
     useGeneratedMesh              = 1 ! generated mesh by default
     BCDISP_MAX                    = 0.2_CMISSRP
-    bcDirichlet                   = 1 ! Dirichlet BC by default
+    bcDirichlet                   = 2 ! Dirichlet BC by default
   ENDIF
   IF(NumberGlobalZElements >= 1) THEN
     NumberOfDimensions  = 3
@@ -542,7 +542,8 @@ PROGRAM FORTRANEXAMPLE
   CALL cmfe_Equations_Initialise(Equations,Err)
   CALL cmfe_EquationsSet_EquationsCreateStart(EquationsSet,Equations,Err)
   CALL cmfe_Equations_SparsityTypeSet(Equations,CMFE_EQUATIONS_SPARSE_MATRICES,Err)
-  CALL cmfe_Equations_OutputTypeSet(Equations,CMFE_EQUATIONS_NO_OUTPUT,Err)
+!  CALL cmfe_Equations_OutputTypeSet(Equations,CMFE_EQUATIONS_NO_OUTPUT,Err)
+  CALL cmfe_Equations_OutputTypeSet(equations,CMFE_EQUATIONS_MATRIX_OUTPUT,err) 
   CALL cmfe_EquationsSet_EquationsCreateFinish(EquationsSet,Err)
 
   !Initialise dependent field from undeformed geometry and displacement bcs and set hydrostatic pressure
@@ -652,7 +653,7 @@ PROGRAM FORTRANEXAMPLE
       ! corresponding traction value
       NeumannBCvalue = 2.0_CMISSRP * MooneyRivlin1 * (lambda - 1.0_CMISSRP / lambda / lambda) * HEIGHT * LENGTH
       WRITE(*,*) "  getting nodal weights"
-      ! compute consistent nodal weights
+      ! compute consistent nodal weights (mesh_reader function!)
       CALL GeneratedMesh_SurfaceWeightsGet(nodalWeights,CMFE_GENERATED_MESH_REGULAR_RIGHT_SURFACE, &
         & numberGlobalXelements,numberGlobalYelements,numberGlobalZelements,Err)
       WRITE(*,*) "  applying consistent nodal forces"

examples/example-0201-u_mod/.gitignore

@@ -0,0 +1,20 @@
+debug/
+release/
+doc/*.aux
+*-eps-converted-to.pdf
+*.log
+*.out
+*.diag
+*~
+results/results.summary
+results/failed.tests
+CMakeCache.txt
+CMakeFiles/
+Makefile
+cmake_install.cmake
+install_manifest.txt
+src/iron/CMakeFiles
+src/iron/Makefile
+src/iron/cmake_install.cmake
+src/iron/example
+src/iron/*.mod

examples/example-0201-u_mod/CMakeLists.txt

@@ -0,0 +1,12 @@
+set(ExampleName "example")
+
+cmake_minimum_required(VERSION 3.4 FATAL_ERROR)
+
+project(${ExampleName} VERSION 1.0 LANGUAGES C Fortran)
+
+list(APPEND CMAKE_PREFIX_PATH "${OPENCMISS_INSTALL_DIR}")
+
+find_package(OpenCMISSLibs 1.3.0 REQUIRED COMPONENTS Iron CONFIG)
+
+add_subdirectory(src/iron)
+