Merge branch 'modernize-testing' into 'development'

Modernize testing

See merge request damask/DAMASK!280

.gitlab-ci.yml

@@ -187,8 +187,6 @@ grid_mech_compile_Intel:
   stage: compilePETSc
   script:
     - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel
-    - cp -r grid_mech_compile grid_mech_compile_Intel
-    - grid_mech_compile_Intel/test.py
     - cd pytest
     - pytest -k 'compile and grid' --basetemp=${TESTROOT}/compile_grid_Intel
   except:
@@ -199,8 +197,6 @@ Compile_FEM_Intel:
   stage: compilePETSc
   script:
     - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel
-    - cp -r FEM_compile FEM_compile_Intel
-    - FEM_compile_Intel/test.py
     - cd pytest
     - pytest -k 'compile and mesh' --basetemp=${TESTROOT}/compile_mesh_Intel
   except:
@@ -211,8 +207,6 @@ grid_mech_compile_GNU:
   stage: compilePETSc
   script:
     - module load $GNUCompiler $MPICH_GNU $PETSc_MPICH_GNU
-    - cp -r grid_mech_compile grid_mech_compile_GNU
-    - grid_mech_compile_GNU/test.py
     - cd pytest
     - pytest -k 'compile and grid' --basetemp=${TESTROOT}/compile_grid_GNU
   except:
@@ -223,8 +217,6 @@ Compile_FEM_GNU:
   stage: compilePETSc
   script:
     - module load $GNUCompiler $MPICH_GNU $PETSc_MPICH_GNU
-    - cp -r FEM_compile FEM_compile_GNU
-    - FEM_compile_GNU/test.py
     - cd pytest
     - pytest -k 'compile and mesh' --basetemp=${TESTROOT}/compile_mesh_GNU
   except:
@@ -274,22 +266,6 @@ Nonlocal_Damage_DetectChanges:
     - master
     - release
 
-grid_all_restart:
-  stage: grid
-  script: grid_all_restart/test.py
-  except:
-    - master
-    - release
-
-grid_all_restartMPI:
-  stage: grid
-  script:
-    - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel
-    - grid_all_restartMPI/test.py
-  except:
-    - master
-    - release
-
 Plasticity_DetectChanges:
   stage: grid
   script: Plasticity_DetectChanges/test.py

PRIVATE

@@ -1 +1 @@
-Subproject commit 281e7eb84f76a2974a50eb54faf35ea25ec89b20
+Subproject commit 2105ed1c6e4800050010ca4d73b1882022f81551

processing/pre/geom_fromMinimalSurface.py

@@ -1,69 +0,0 @@
-#!/usr/bin/env python3
-
-import os
-import sys
-from optparse import OptionParser
-
-import damask
-
-
-scriptName = os.path.splitext(os.path.basename(__file__))[0]
-scriptID   = ' '.join([scriptName,damask.version])
-
-
-minimal_surfaces = list(damask.Geom._minimal_surface.keys())
-
-# --------------------------------------------------------------------
-#                                MAIN
-# --------------------------------------------------------------------
-
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile]', description = """
-Generate a bicontinuous structure of given type.
-
-""", version = scriptID)
-
-
-parser.add_option('-t','--type',
-                  dest = 'type',
-                  choices = minimal_surfaces, metavar = 'string',
-                  help = 'type of minimal surface [primitive] {%s}' %(','.join(minimal_surfaces)))
-parser.add_option('-f','--threshold',
-                  dest = 'threshold',
-                  type = 'float', metavar = 'float',
-                  help = 'threshold value defining minimal surface [%default]')
-parser.add_option('-g', '--grid',
-                  dest = 'grid',
-                  type = 'int', nargs = 3, metavar = 'int int int',
-                  help = 'a,b,c grid of hexahedral box [%default]')
-parser.add_option('-s', '--size',
-                  dest = 'size',
-                  type = 'float', nargs = 3, metavar = 'float float float',
-                  help = 'x,y,z size of hexahedral box [%default]')
-parser.add_option('-p', '--periods',
-                  dest = 'periods',
-                  type = 'int', metavar = 'int',
-                  help = 'number of repetitions of unit cell [%default]')
-parser.add_option('--m',
-                  dest = 'microstructure',
-                  type = 'int', nargs = 2, metavar = 'int int',
-                  help = 'two microstructure indices to be used [%default]')
-
-parser.set_defaults(type = minimal_surfaces[0],
-                    threshold = 0.0,
-                    periods = 1,
-                    grid = (16,16,16),
-                    size = (1.0,1.0,1.0),
-                    microstructure = (1,2),
-                   )
-
-(options,filename) = parser.parse_args()
-
-
-name = None if filename == [] else filename[0]
-damask.util.report(scriptName,name)
-
-geom=damask.Geom.from_minimal_surface(options.grid,options.size,options.type,options.threshold,
-                                      options.periods,options.microstructure)
-damask.util.croak(geom)
-
-geom.save_ASCII(sys.stdout if name is None else name)

python/damask/_environment.py

@@ -3,10 +3,6 @@ from pathlib import Path
 
 class Environment:
 
-    def __init__(self):
-        """Do Nothing."""
-        pass
-
     @property
     def screen_size(self):
         width  = 1024
@@ -43,8 +39,3 @@ class Environment:
     def root_dir(self):
         """Return DAMASK root path."""
         return Path(__file__).parents[2]
-
-
-    # for compatibility
-    def rootDir(self):
-        return str(self.root_dir)

python/damask/_table.py

@@ -31,7 +31,7 @@ class Table:
 
     def __repr__(self):
         """Brief overview."""
-        return util.srepr(self.comments)+'\n'+self.data.__repr__()
+        return '\n'.join(['# '+c for c in self.comments])+'\n'+self.data.__repr__()
 
     def __len__(self):
         """Number of rows."""
@@ -159,7 +159,7 @@ class Table:
         comments = [util.execution_stamp('Table','from_ang')]
         for line in content:
             if line.startswith('#'):
-                comments.append(line.strip())
+                comments.append(line.split('#',1)[1].strip())
             else:
                 break
 
@@ -222,6 +222,7 @@ class Table:
             dup.data[label]       = data.reshape(dup.data[label].shape)
         return dup
 
+
     def add(self,label,data,info=None):
         """
         Add column data.

src/DAMASK_interface.f90

@@ -127,9 +127,9 @@ subroutine DAMASK_interface_init
     if (err /= 0) call quit(1)
     select case(trim(arg))                                                                          ! extract key
       case ('-h','--help')
-        print'(a)',  ' #######################################################################'
+        print'(/,a)',' #######################################################################'
         print'(a)',  ' DAMASK Command Line Interface:'
-        print'(a)',  ' For PETSc-based solvers for the Düsseldorf Advanced Material Simulation Kit'
+        print'(a)',  ' Düsseldorf Advanced Material Simulation Kit with PETSc-based solvers'
         print'(a,/)',' #######################################################################'
         print'(a,/)',' Valid command line switches:'
         print'(a)',  '    --geom         (-g, --geometry)'

src/grid/grid_mech_spectral_polarisation.f90

@@ -498,7 +498,7 @@ subroutine converged(snes_local,PETScIter,devNull1,devNull2,devNull3,reason,dumm
             err_div/divTol,  ' (',err_div, ' / m, tol = ',divTol,')'
   print  '(a,f12.2,a,es8.2,a,es9.2,a)', ' error curl       = ', &
             err_curl/curlTol,' (',err_curl,' -,   tol = ',curlTol,')'
-  print  '(a,f12.2,a,es8.2,a,es9.2,a)', ' error stress BC         = ', &
+  print  '(a,f12.2,a,es8.2,a,es9.2,a)', ' error stress BC  = ', &
             err_BC/BCTol,    ' (',err_BC,  ' Pa,  tol = ',BCTol,')'
   print'(/,a)', ' ==========================================================================='
   flush(IO_STDOUT)

src/mesh/DAMASK_mesh.f90

@@ -20,7 +20,7 @@ program DAMASK_mesh
   use discretization_mesh
   use FEM_Utilities
   use mesh_mech_FEM
-  
+
   implicit none
 
 !--------------------------------------------------------------------------------------------------
@@ -56,7 +56,7 @@ program DAMASK_mesh
     totalIncsCounter = 0, &                                                                         !< total # of increments
     statUnit = 0, &                                                                                 !< file unit for statistics output
     stagIter, &
-    component  
+    component
   class(tNode), pointer :: &
     num_mesh
   character(len=pStringLen), dimension(:), allocatable :: fileContent
@@ -80,7 +80,7 @@ program DAMASK_mesh
   call CPFEM_initAll
   print'(/,a)', ' <<<+-  DAMASK_mesh init  -+>>>'; flush(IO_STDOUT)
 
-!--------------------------------------------------------------------- 
+!---------------------------------------------------------------------
 ! reading field information from numerics file and do sanity checks
   num_mesh => config_numerics%get('mesh', defaultVal=emptyDict)
   stagItMax  = num_mesh%get_asInt('maxStaggeredIter',defaultVal=10)
@@ -100,7 +100,7 @@ program DAMASK_mesh
   do l = 1, size(fileContent)
     line = fileContent(l)
     if (IO_isBlank(line)) cycle                                                                     ! skip empty lines
- 
+
     chunkPos = IO_stringPos(line)
     do i = 1, chunkPos(1)                                                                           ! reading compulsory parameters for loadcase
       select case (IO_lc(IO_stringValue(line,chunkPos,i)))
@@ -109,15 +109,16 @@ program DAMASK_mesh
       end select
     enddo                                                                                           ! count all identifiers to allocate memory and do sanity check
   enddo
- 
+
-  allocate (loadCases(N_def))         
+  if(N_def < 1) call IO_error(error_ID = 837)
- 
+  allocate(loadCases(N_def))
+
   do i = 1, size(loadCases)
     allocate(loadCases(i)%fieldBC(nActiveFields))
     field = 1
     loadCases(i)%fieldBC(field)%ID = FIELD_MECH_ID
   enddo
- 
+
   do i = 1, size(loadCases)
     do field = 1, nActiveFields
       select case (loadCases(i)%fieldBC(field)%ID)
@@ -133,21 +134,21 @@ program DAMASK_mesh
               case (3)
                 loadCases(i)%fieldBC(field)%componentBC(component)%ID = COMPONENT_MECH_Z_ID
             end select
-          enddo  
+          enddo
       end select
       do component = 1, loadCases(i)%fieldBC(field)%nComponents
         allocate(loadCases(i)%fieldBC(field)%componentBC(component)%Value(mesh_Nboundaries), source = 0.0_pReal)
         allocate(loadCases(i)%fieldBC(field)%componentBC(component)%Mask (mesh_Nboundaries), source = .false.)
       enddo
-    enddo       
+    enddo
-  enddo   
+  enddo
 
 !--------------------------------------------------------------------------------------------------
 ! reading the load case and assign values to the allocated data structure
   do l = 1, size(fileContent)
     line = fileContent(l)
     if (IO_isBlank(line)) cycle                                                                     ! skip empty lines
- 
+
     chunkPos = IO_stringPos(line)
     do i = 1, chunkPos(1)
       select case (IO_lc(IO_stringValue(line,chunkPos,i)))
@@ -161,7 +162,7 @@ program DAMASK_mesh
           do faceSet = 1, mesh_Nboundaries
             if (mesh_boundaries(faceSet) == currentFace) currentFaceSet = faceSet
           enddo
-          if (currentFaceSet < 0) call IO_error(error_ID = errorID, ext_msg = 'invalid BC')  
+          if (currentFaceSet < 0) call IO_error(error_ID = 837, ext_msg = 'invalid BC')
         case('t','time','delta')                                                                    ! increment time
           loadCases(currentLoadCase)%time = IO_floatValue(line,chunkPos,i+1)
         case('n','incs','increments','steps')                                                       ! number of increments
@@ -170,7 +171,7 @@ program DAMASK_mesh
           loadCases(currentLoadCase)%incs = IO_intValue(line,chunkPos,i+1)
           loadCases(currentLoadCase)%logscale = 1
         case('freq','frequency','outputfreq')                                                       ! frequency of result writings
-          loadCases(currentLoadCase)%outputfrequency = IO_intValue(line,chunkPos,i+1)                
+          loadCases(currentLoadCase)%outputfrequency = IO_intValue(line,chunkPos,i+1)
         case('guessreset','dropguessing')
           loadCases(currentLoadCase)%followFormerTrajectory = .false.                                ! do not continue to predict deformation along former trajectory
 
@@ -185,7 +186,7 @@ program DAMASK_mesh
             case('z')
               ID = COMPONENT_MECH_Z_ID
            end select
-          
+
            do field = 1, nActiveFields
              if (loadCases(currentLoadCase)%fieldBC(field)%ID == FIELD_MECH_ID) then
                do component = 1, loadcases(currentLoadCase)%fieldBC(field)%nComponents
@@ -197,11 +198,11 @@ program DAMASK_mesh
                  endif
                enddo
              endif
-           enddo  
+           enddo
       end select
     enddo
   enddo
- 
+
 !--------------------------------------------------------------------------------------------------
 ! consistency checks and output of load case
   loadCases(1)%followFormerTrajectory = .false.                                                      ! cannot guess along trajectory for first inc of first currentLoadCase
@@ -215,17 +216,17 @@ program DAMASK_mesh
       select case (loadCases(currentLoadCase)%fieldBC(field)%ID)
         case(FIELD_MECH_ID)
           print'(a)', '  Field '//trim(FIELD_MECH_label)
-      
+
       end select
       do faceSet = 1, mesh_Nboundaries
          do component = 1, loadCases(currentLoadCase)%fieldBC(field)%nComponents
            if (loadCases(currentLoadCase)%fieldBC(field)%componentBC(component)%Mask(faceSet)) &
              print'(a,i2,a,i2,a,f12.7)', '    Face  ', mesh_boundaries(faceSet), &
-                                               ' Component ', component, & 
+                                               ' Component ', component, &
                                                ' Value ', loadCases(currentLoadCase)%fieldBC(field)% &
                                                             componentBC(component)%Value(faceSet)
          enddo
-       enddo       
+       enddo
     enddo
     print'(a,f12.6)', '  time:       ', loadCases(currentLoadCase)%time
     if (loadCases(currentLoadCase)%incs < 1)             errorID = 835                            ! non-positive incs count
@@ -244,7 +245,7 @@ program DAMASK_mesh
       case(FIELD_MECH_ID)
         call FEM_mech_init(loadCases(1)%fieldBC(field))
     end select
-  enddo   
+  enddo
 
   if (worldrank == 0) then
     open(newunit=statUnit,file=trim(getSolverJobName())//'.sta',form='FORMATTED',status='REPLACE')
@@ -254,9 +255,9 @@ program DAMASK_mesh
   loadCaseLooping: do currentLoadCase = 1, size(loadCases)
     time0 = time                                                                                    ! load case start time
     guess = loadCases(currentLoadCase)%followFormerTrajectory                                       ! change of load case? homogeneous guess for the first inc
- 
+
     incLooping: do inc = 1, loadCases(currentLoadCase)%incs
-      totalIncsCounter = totalIncsCounter + 1                                                 
+      totalIncsCounter = totalIncsCounter + 1
 
 !--------------------------------------------------------------------------------------------------
 ! forwarding time
@@ -266,7 +267,7 @@ program DAMASK_mesh
       else
         if (currentLoadCase == 1) then                                                              ! 1st load case of logarithmic scale
           if (inc == 1) then                                                                        ! 1st inc of 1st load case of logarithmic scale
-            timeinc = loadCases(1)%time*(2.0_pReal**real(    1-loadCases(1)%incs ,pReal))           ! assume 1st inc is equal to 2nd 
+            timeinc = loadCases(1)%time*(2.0_pReal**real(    1-loadCases(1)%incs ,pReal))           ! assume 1st inc is equal to 2nd
           else                                                                                      ! not-1st inc of 1st load case of logarithmic scale
             timeinc = loadCases(1)%time*(2.0_pReal**real(inc-1-loadCases(1)%incs ,pReal))
           endif
@@ -287,7 +288,7 @@ program DAMASK_mesh
         remainingLoadCaseTime = loadCases(currentLoadCase)%time+time0 - time
         time = time + timeinc                                                                     ! forward target time
         stepFraction = stepFraction + 1                                                           ! count step
-         
+
 !--------------------------------------------------------------------------------------------------
 ! report begin of new step
         print'(/,a)', ' ###########################################################################'
@@ -310,8 +311,8 @@ program DAMASK_mesh
                   guess,timeinc,timeIncOld,loadCases(currentLoadCase)%fieldBC(field))
 
          end select
-        enddo       
+        enddo
-         
+
 !--------------------------------------------------------------------------------------------------
 ! solve fields
         stagIter = 0
@@ -332,10 +333,10 @@ program DAMASK_mesh
           stagIterate =            stagIter < stagItMax &
                        .and.       all(solres(:)%converged) &
                        .and. .not. all(solres(:)%stagConverged)                                     ! stationary with respect to staggered iteration
-        enddo     
+        enddo
-         
+
-! check solution 
+! check solution
-        cutBack = .False.                                                                   
+        cutBack = .False.
         if(.not. all(solres(:)%converged .and. solres(:)%stagConverged)) then                       ! no solution found
           if (cutBackLevel < maxCutBack) then                                                       ! do cut back
             print'(/,a)', ' cut back detected'
@@ -344,7 +345,7 @@ program DAMASK_mesh
             cutBackLevel = cutBackLevel + 1
             time    = time - timeinc                                                                ! rewind time
             timeinc = timeinc/2.0_pReal
-          else                                                                                      ! default behavior, exit if spectral solver does not converge                                
+          else                                                                                      ! default behavior, exit if spectral solver does not converge
             call IO_warning(850)
             call quit(1)                                                                            ! quit
           endif
@@ -374,8 +375,8 @@ program DAMASK_mesh
     enddo incLooping
 
   enddo loadCaseLooping
- 
+
- 
+
 !--------------------------------------------------------------------------------------------------
 ! report summary of whole calculation
   print'(/,a)', ' ###########################################################################'

src/mesh/discretization_mesh.f90

@@ -17,6 +17,7 @@ module discretization_mesh
   use IO
   use config
   use discretization
+  use results
   use FEsolving
   use FEM_quadrature
   use YAML_types
@@ -182,6 +183,10 @@ subroutine discretization_mesh_init(restart)
                            reshape(mesh_ipCoordinates,[3,mesh_maxNips*mesh_NcpElems]), &
                            mesh_node0)
 
+  call results_openJobFile
+  call results_closeGroup(results_addGroup('geometry'))
+  call results_closeJobFile
+
 end subroutine discretization_mesh_init