polishing compile_CoreModule, bug fix for Makefile

code/Makefile

@@ -46,7 +46,7 @@ COMPILERNAME ?= $(F90)
 INCLUDE_DIRS :=-I../lib
 LIBRARIES :=-lfftw3
 LIB_DIRS  :=-L$(FFTW_ROOT)/lib
-RUN_PATH  :=-Wl,-rpath,$(FFTW_ROOT)/lib
+RUN_PATH  :=-Wl,-rpath=$(FFTW_ROOT)/lib
 
 ifeq "$(FASTBUILD)" "YES"
 OPENMP := OFF
@@ -95,18 +95,18 @@ endif
 
 ifneq  "x$(IMKL_ROOT)" "x"
 LIB_DIRS  :=-L$(IMKL_ROOT)/lib/intel64
-RUN_PATH  +=$(RUNPATH) -Wl,-rpath,$(IMKL_ROOT)/lib/intel64
+RUN_PATH  +=$(RUNPATH) -Wl,-rpath=$(IMKL_ROOT)/lib/intel64
 INCLUDE_DIRS +=-I$(IMKL_ROOT)/include
-LIBRARIES +=-lmkl_intel_lp64 -lmkl_core -lmkl$(ACML_ARCH) -lm -lpthread -liomp5
+LIBRARIES +=-lmkl_intel_lp64 -lmkl_core -lmkl$(IMKL_ARCH) -lm -lpthread -liomp5
 else
 ifneq  "x$(ACML_ROOT)" "x"
 LIB_DIRS  +=-L$(ACML_ROOT)/$(F90)64$(ACML_ARCH)/lib
-RUN_PATH  +=$(RUNPATH) -Wl,-rpath,$(ACML_ROOT)/$(F90)64$(ACML_ARCH)/lib
+RUN_PATH  +=$(RUNPATH) -Wl,-rpath=$(ACML_ROOT)/$(F90)64$(ACML_ARCH)/lib
 LIBRARIES +=-lacml$(ACML_ARCH)
 else
 ifneq  "x$(LAPACK_ROOT)" "x"
 LIB_DIRS  +=-L$(LAPACK_ROOT)/lib64 -L$(LAPACK_ROOT)/lib
-RUN_PATH  +=$(RUN_PATH) -Wl,-rpath,$(LAPACK_ROOT)/lib64 -Wl,-rpath,$(LAPACK_ROOT)/lib
+RUN_PATH  +=$(RUN_PATH) -Wl,-rpath=$(LAPACK_ROOT)/lib64 -Wl,-rpath=$(LAPACK_ROOT)/lib
 LIBRARIES +=-llapack
 endif
 endif
@@ -116,7 +116,7 @@ endif
 ifeq "$(HDF5)" "ON"
 LIBRARIES +=-lhdf5hl_fortran -lhdf5_hl -lhdf5_fortran -lhdf5
 LIB_DIRS  +=-L$(HDF5_ROOT)/lib
-RUN_PATH  +=$(RUNPATH) -Wl,-rpath,$(HDF5_ROOT)/lib
+RUN_PATH  +=$(RUNPATH) -Wl,-rpath=$(HDF5_ROOT)/lib
 INCLUDE_DIRS +=-I$(HDF5_ROOT)/include -DHDF
 endif
 
@@ -142,7 +142,7 @@ OPTIMIZATION_OFF_ifort           :=-O0 -no-ip
 OPTIMIZATION_OFF_gfortran        :=-O0
 OPTIMIZATION_DEFENSIVE_ifort     :=-O2
 OPTIMIZATION_DEFENSIVE_gfortran  :=-O2
-OPTIMIZATION_AGGRESSIVE_ifort    :=-O3 $(PORTABLE_SWITCH) -no-prec-div -fp-model fast=2 -ipo #-static causes trouble at the moment
+OPTIMIZATION_AGGRESSIVE_ifort    :=-O3 $(PORTABLE_SWITCH) -no-prec-div -fp-model fast=2 -ipo
 OPTIMIZATION_AGGRESSIVE_gfortran :=-O3 $(PORTABLE_SWITCH) -ffast-math -funroll-loops -ftree-vectorize 
 
 

installation/compile_CoreModule.py

@@ -1,18 +1,20 @@
 #!/usr/bin/env python
-
+# -*- coding: UTF-8 no BOM -*-
-# compiles fortran code for Python
 
 import os,sys,glob,string,subprocess,shlex
 from damask import Environment
 
+# compiles fortran code for Python
+scriptID = '$Id$'
+
 damaskEnv = Environment()
 baseDir = damaskEnv.relPath('installation/')
 codeDir = damaskEnv.relPath('code/')
 
-options={}
 keywords=['IMKL_ROOT','ACML_ROOT','LAPACK_ROOT','FFTW_ROOT','F90']
+options={}
 
-# getting options from damask.conf or, if not present, from envinronment
+#--- getting options from damask.conf or, if not present, from envinronment -----------------------
 for option in keywords:
   try:
     value = damaskEnv.options[option]
@@ -21,12 +23,13 @@ for option in keywords:
     if value is None: value = ''           # env not set
   options[option]=value
 
-# overwrite default options with keyword=value pair from argument list to mimic make behavior
+#--- overwrite default options with keyword=value pair from argument list to mimic make behavior --
 for i, arg in enumerate(sys.argv):
   for option in keywords:
     if arg.startswith(option):
       options[option] = sys.argv[i][len(option)+1:]
 
+#--- check for valid compiler and set options -----------------------------------------------------
 compilers = ['ifort','gfortran']
 if options['F90'] not in compilers:
   sys.exit('compiler "F90" (in installation/options or as Shell variable) has to be one out of: %s'%(', '.join(compilers)))
@@ -38,11 +41,11 @@ compiler = {
                         ' -real-size 64 -integer-size 32"',
             }[options['F90']]
 
-# option not depending on compiler
+#--- option not depending on compiler -------------------------------------------------------------
 compileOptions =' -DSpectral -DFLOAT=8 -DINT=4 -I%s/lib'%damaskEnv.rootDir()
 
-# this saves the path of libraries during runtime
+#--- this saves the path of libraries to core.so, hence it is known during runtime ----------------
-LDFLAGS ='-shared -Wl,-rpath=/lib -Wl,-rpath=/usr/lib -Wl,-rpath=%s/lib'%(options['FFTW_ROOT'])
+LDFLAGS ='-shared -Wl,-rpath=%s/lib'%(options['FFTW_ROOT'])
 
 # see http://cens.ioc.ee/pipermail/f2py-users/2003-December/000621.html
 if   options['IMKL_ROOT'] != '' and options['F90'] != 'gfortran':
@@ -55,15 +58,16 @@ elif options['LAPACK_ROOT'] != '':
   lib_lapack = '-L%s/lib -L%s/lib64  -llapack'%(options['LAPACK_ROOT'],options['LAPACK_ROOT'])
   LDFLAGS +=' -Wl,-rpath=%s/lib -Wl,-rpath=%s/lib64'%(options['LAPACK_ROOT'],options['LAPACK_ROOT'])
 
+#--------------------------------------------------------------------------------------------------
 # f2py does not (yet) support setting of special flags for the linker, hence they must be set via 
-# environment variable
+# environment variable ----------------------------------------------------------------------------
 my_env = os.environ
 my_env["LDFLAGS"] = LDFLAGS                                    
 
-os.chdir(codeDir)                                                                           # needed for compilation with gfortran and f2py
+#--- delete old file ------------------------------------------------------------------------------
 try:
   os.remove(os.path.join(damaskEnv.relPath('lib/damask'),'core.so'))
-except OSError, e:                                                                          ## if failed, report it back to the user ##
+except OSError, e:
   print ("Error when deleting: %s - %s." % (e.filename,e.strerror))
 
 
@@ -76,6 +80,7 @@ except OSError, e:
 #'f2py -h damask.core.pyf' +\
 #' --overwrite-signature --no-lower prec.f90 DAMASK_spectral_interface.f90 math.f90 mesh.f90,...'
  ###########################################################################
+os.chdir(codeDir)
 cmd = 'f2py damask.core.pyf' +\
       ' -c --no-lower %s'%(compiler) +\
       compileOptions+\
@@ -111,7 +116,7 @@ for module in modules:
   print 'removing', module
   os.remove(module)
 
-#check if compilation of core module was successful
+#--- check if compilation of core module was successful -------------------------------------------
 try:
   with open(damaskEnv.relPath('lib/damask/core.so')) as f: pass
 except IOError as e:

processing/post/3Dvisualize.py

@@ -544,6 +544,8 @@ for filename in args:
              'quadruple': 4,\
             }
 
+  structure = vtk.vtkIntArray()
+  structure.SetName('Microstructures')
   for datatype in fields.keys():
     print '\n%s:'%datatype,
     fields[datatype]['_order_'] = []

processing/post/addCauchyX.py

@@ -68,15 +68,15 @@ for myFile in files:
 # ------------------------------------------ loop over increments -------------------------------------
   for inc in myFile['file']['increments'].keys():
     print("Current Increment: "+inc)
-    for instance in myFile['file']['increments/'+inc].keys():
+    for instance in myFile['file']['increments/'+inc+'/'+options.output].keys():
-      dsets = myFile['file']['increments/'+inc].keys()
+      dsets = myFile['file']['increments/'+inc+'/'+options.output+'/'+instance].keys()
       if (options.defgrad in dsets and options.stress in dsets):
-        defgrad = myFile['file']['increments/'+inc+'/'+options.defgrad]
+        defgrad = myFile['file']['increments/'+inc+'/'+options.output+'/'+instance+'/'+options.defgrad]
-        stress = myFile['file']['increments/'+inc+'/'+options.stress]
+        stress = myFile['file']['increments/'+inc+'/'+options.output+'/'+instance+'/'+options.stress]
         cauchy=np.zeros(np.shape(stress),'f')
         for p in range(stress.shape[0]):
           cauchy[p,...] = 1.0/np.linalg.det(defgrad[p,...])*np.dot(stress[p,...],defgrad[p,...].T)  # [Cauchy] = (1/det(F)) * [P].[F_transpose]
-        cauchyFile = myFile['file']['increments/'+inc].create_dataset('cauchy', data=cauchy)
+        cauchyFile = myFile['file']['increments/'+inc+'/'+options.output+'/'+instance].create_dataset('cauchy', data=cauchy)
         cauchyFile.attrs['units'] = 'Pa'