52 |
|
selection \ |
53 |
|
restraints \ |
54 |
|
lattice \ |
55 |
< |
|
55 |
> |
openbabel\ |
56 |
> |
antlr\ |
57 |
> |
mdParser |
58 |
|
#packages containing applications |
59 |
|
Applications = \ |
60 |
|
applications/oopse \ |
61 |
|
applications/dump2Xyz \ |
62 |
|
applications/staticProps \ |
63 |
|
applications/dynamicProps \ |
64 |
< |
applications/simpleBuilder\ |
64 |
> |
applications/simpleBuilder \ |
65 |
|
applications/nanoRodBuilder \ |
66 |
+ |
applications/nanoparticleBuilder \ |
67 |
+ |
applications/atom2mdin \ |
68 |
+ |
applications/hydrodynamics |
69 |
|
|
70 |
+ |
|
71 |
|
Samples = \ |
72 |
+ |
samples/alkane \ |
73 |
|
samples/argon \ |
74 |
< |
samples/water/dimer \ |
74 |
> |
samples/cutoff \ |
75 |
> |
samples/dipole \ |
76 |
> |
samples/gbljtest \ |
77 |
> |
samples/lipid \ |
78 |
> |
samples/metals/EAM \ |
79 |
> |
samples/metals/EAM/nanoparticle \ |
80 |
> |
samples/metals/EAM/nanorod \ |
81 |
> |
samples/metals/Sutton-Chen \ |
82 |
> |
samples/minimizer \ |
83 |
> |
samples/shape \ |
84 |
> |
samples/thermoIntegration/liquid \ |
85 |
> |
samples/thermoIntegration/solid \ |
86 |
> |
samples/water/dimer \ |
87 |
|
samples/water/spce \ |
88 |
|
samples/water/ssd \ |
89 |
|
samples/water/ssde \ |
90 |
+ |
samples/water/ssdrf \ |
91 |
+ |
samples/water/ssd-ion \ |
92 |
|
samples/water/tip3p_ice \ |
93 |
|
samples/water/tip4p \ |
94 |
< |
samples/lipid \ |
74 |
< |
samples/alkane \ |
75 |
< |
samples/minimizer \ |
76 |
< |
samples/metals \ |
77 |
< |
samples/zcons \ |
94 |
> |
samples/zcons |
95 |
|
|
96 |
|
IncludeDirs = \ |
97 |
|
@CGAL_INC_DIR@ \ |
102 |
|
@MPI_LIB_DIR@ |
103 |
|
|
104 |
|
Libraries = \ |
105 |
+ |
@LIBS@ \ |
106 |
|
@CGAL_LIBS@ \ |
107 |
|
@MPI_LIB@ \ |
108 |
|
@MPI_F90_LIB@ |
119 |
|
ModuleCase = @F90_MODULE_NAMES@ |
120 |
|
ModSuffix = @MOD@ |
121 |
|
LinkOptions = \ |
122 |
< |
@F90LIBS@ |
122 |
> |
@FCLIBS@ \ |
123 |
> |
@CXXFLAGS@ |
124 |
|
|
125 |
|
ParallelLinkOptions = \ |
126 |
< |
@F90LIBS@ |
126 |
> |
@FCLIBS@ \ |
127 |
> |
@CXXFLAGS@ |
128 |
|
|
129 |
|
|
130 |
|
#--------------------------------------------------------------------------- |
138 |
|
ParallelTargetDir = $(DEV_ROOT)/MPIobj |
139 |
|
LibDir = $(DEV_ROOT)/lib |
140 |
|
MakeDir = $(DEV_ROOT)/make |
141 |
+ |
MainMakefile = $(MakeDir)/Makefile |
142 |
|
BinDir = $(DEV_ROOT)/bin |
143 |
|
DocsDir = $(DEV_ROOT)/docs |
144 |
|
CurrentDir = $(CURDIR) |
346 |
|
CppCompiler = @CXX@ |
347 |
|
Linker = @CXX@ |
348 |
|
MakeDepend = makedepend |
349 |
+ |
LN_S = @LN_S@ |
350 |
|
INSTALL = @INSTALL@ |
351 |
+ |
EGREP = @EGREP@ |
352 |
|
InstallProgram = @INSTALL_PROGRAM@ |
353 |
|
InstallScript = @INSTALL_SCRIPT@ |
354 |
|
InstallData = @INSTALL_DATA@ |
355 |
|
MkDir = @MKINSTALLDIRS@ |
356 |
< |
Delete = rm -fr |
356 |
> |
Delete = rm -f |
357 |
|
StaticArchiver = @AR@ |
358 |
|
DynamicArchiver = @CC@ |
359 |
|
FortranCompiler = @FC@ |
337 |
– |
F90Compiler = @F90@ |
360 |
|
JavaCompiler = $(JAVA_HOME)/bin/javac |
361 |
|
JavaArchiver = $(JAVA_HOME)/bin/jar |
362 |
|
JarSigner = $(JAVA_HOME)/bin/jarsigner |
382 |
|
-sourcepath $(SourceDir) |
383 |
|
COptions = $(FrcDeclare) @CFLAGS@ |
384 |
|
CParallelOptions = $(FrcDeclare) $(ParallelDeclare) @CFLAGS@ |
385 |
< |
CppOptions = $(FrcDeclare) @CXXFLAGS@ @OOPSE_TEMPLATE_FLAGS@ |
386 |
< |
CppParallelOptions = $(FrcDeclare) $(ParallelDeclare) @CXXFLAGS@ @OOPSE_TEMPLATE_FLAGS@ |
387 |
< |
FortranOptions = |
388 |
< |
F90Options = @PREPFLAG@ @F90FLAGS@ @MODDIRFLAG@$(SourceDir) @MODDIRFLAG@$(TargetDir) |
367 |
< |
F90ParallelOptions = @PREPFLAG@ @F90FLAGS@ @MODDIRFLAG@$(SourceDir) @MODDIRFLAG@$(ParallelTargetDir) @PREPDEFFLAG@$(ParallelDeclare) |
385 |
> |
CppOptions = $(FrcDeclare) @CXXFLAGS@ |
386 |
> |
CppParallelOptions = $(FrcDeclare) $(ParallelDeclare) @CXXFLAGS@ |
387 |
> |
FortranOptions = @FCFLAGS@ @MODDIRFLAG@$(SourceDir) @MODDIRFLAG@$(TargetDir) @FCFLAGS_SRCEXT@ |
388 |
> |
FortranParallelOptions = @FCFLAGS@ @MODDIRFLAG@$(SourceDir) @MODDIRFLAG@$(ParallelTargetDir) @PREPDEFFLAG@$(ParallelDeclare) @FCFLAGS_SRCEXT@ |
389 |
|
JavaCompilerOptions = -d $(TargetDir) -classpath $(ClassPath) \ |
390 |
|
-sourcepath $(SourceDir) -deprecation |
391 |
|
JavaRunOptions = -classpath $(ClassPath) |
430 |
|
InstallFiles = $(Executable) |
431 |
|
endif |
432 |
|
InstallCommand = $(InstallProgram) |
433 |
+ |
ifneq "$(words $(LinkTargets))" "0" |
434 |
+ |
MyLinkSource = $(patsubst %, $(MyInstallDir)/%,$(Main)) |
435 |
+ |
MyLinkTargets = $(patsubst %, $(MyInstallDir)/%,$(LinkTargets)) |
436 |
+ |
endif |
437 |
|
endif |
438 |
|
|
439 |
|
ifneq "$(words $(ForcefieldFiles))" "0" |
470 |
|
$(MkDir) $@ |
471 |
|
|
472 |
|
# .c -> .o |
473 |
< |
$(PackageTargetDir)/%.o : %.c |
473 |
> |
$(PackageTargetDir)/%.o : %.c $(MainMakefile) |
474 |
|
$(Print) $@ |
475 |
|
$(CCompiler) $(COptions) -c $(IncludePath) $< -o $@ |
476 |
|
|
477 |
< |
$(PackageParallelTargetDir)/%.o : %.c |
477 |
> |
$(PackageParallelTargetDir)/%.o : %.c $(MainMakefile) |
478 |
|
$(Print) $@ |
479 |
|
$(CCompiler) $(CParallelOptions) -c $(IncludePath) $< -o $@ |
480 |
|
|
481 |
|
ifeq "$(UseMPI)" "yes" |
482 |
< |
%.o : %.c |
482 |
> |
%.o : %.c $(MainMakefile) |
483 |
|
$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@ |
484 |
|
$(MAKE) $(MakeOptions) $(PackageParallelTargetDir)/$@ |
485 |
|
else |
486 |
< |
%.o : %.c |
486 |
> |
%.o : %.c $(MainMakefile) |
487 |
|
$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@ |
488 |
|
endif |
489 |
|
|
490 |
|
# .cpp -> .o |
491 |
< |
$(PackageTargetDir)/%.o : %.cpp |
491 |
> |
$(PackageTargetDir)/%.o : %.cpp $(MainMakefile) |
492 |
|
$(CppCompiler) $(CppOptions) -c $(IncludePath) $< -o $@ |
493 |
|
|
494 |
< |
$(PackageParallelTargetDir)/%.o : %.cpp |
494 |
> |
$(PackageParallelTargetDir)/%.o : %.cpp $(MainMakefile) |
495 |
|
$(CppCompiler) $(CppParallelOptions) -c $(IncludePath) $< -o $@ |
496 |
|
|
497 |
|
ifeq "$(UseMPI)" "yes" |
498 |
< |
%.o : %.cpp |
498 |
> |
%.o : %.cpp $(MainMakefile) |
499 |
|
$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@ |
500 |
|
$(MAKE) $(MakeOptions) $(PackageParallelTargetDir)/$@ |
501 |
|
else |
502 |
< |
%.o : %.cpp |
502 |
> |
%.o : %.cpp $(MainMakefile) |
503 |
|
$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@ |
504 |
|
endif |
505 |
|
|
506 |
|
# .f -> .o |
507 |
< |
$(PackageTargetDir)/%.o : %.f |
507 |
> |
$(PackageTargetDir)/%.o : %.f $(MainMakefile) |
508 |
|
$(FortranCompiler) $(FortranOptions) -c $< -o $@ |
509 |
|
|
510 |
< |
$(PackageParallelTargetDir)/%.o : %.f |
510 |
> |
$(PackageParallelTargetDir)/%.o : %.f $(MainMakefile) |
511 |
|
$(FortranCompiler) $(FortranParallelOptions) -c $< -o $@ |
512 |
|
|
513 |
|
ifeq "$(UseMPI)" "yes" |
514 |
< |
%.o : %.f |
514 |
> |
%.o : %.f $(MainMakefile) |
515 |
|
$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@ |
516 |
|
$(MAKE) $(MakeOptions) $(PackageParallelTargetDir)/$@ |
517 |
|
else |
518 |
< |
%.o : %.f |
518 |
> |
%.o : %.f $(MainMakefile) |
519 |
|
$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@ |
520 |
|
endif |
521 |
|
|
522 |
|
# .F90 -> .o |
523 |
< |
$(PackageTargetDir)/%.o : %.F90 |
524 |
< |
$(F90Compiler) $(F90Options) $(IncludePath) -c $< -o $@ |
523 |
> |
$(PackageTargetDir)/%.o : %.F90 $(MainMakefile) |
524 |
> |
$(FortranCompiler) $(FortranOptions) $(IncludePath) -c $< -o $@ |
525 |
|
if test -n "`ls *.$(ModSuffix)`"; then \ |
526 |
|
$(Move) `ls *.$(ModSuffix)` $(PackageTargetDir);\ |
527 |
|
fi |
528 |
|
|
529 |
< |
$(PackageParallelTargetDir)/%.o : %.F90 |
530 |
< |
$(F90Compiler) $(F90ParallelOptions) $(IncludePath) -c $< -o $@ |
529 |
> |
$(PackageParallelTargetDir)/%.o : %.F90 $(MainMakefile) |
530 |
> |
$(FortranCompiler) $(FortranParallelOptions) $(IncludePath) -c $< -o $@ |
531 |
|
if test -n "`ls *.$(ModSuffix)`"; then \ |
532 |
|
$(Move) "`ls *.$(ModSuffix)`" $(PackageParallelTargetDir);\ |
533 |
|
fi |
534 |
|
|
535 |
|
ifeq "$(UseMPI)" "yes" |
536 |
< |
%.o : %.F90 |
536 |
> |
%.o : %.F90 $(MainMakefile) |
537 |
|
$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@ |
538 |
|
if test -n "`ls *.$(ModSuffix)`"; then\ |
539 |
|
$(Move) "`ls *.$(ModSuffix)`" $(PackageTargetDir);\ |
545 |
|
fi |
546 |
|
|
547 |
|
else |
548 |
< |
%.o : %.F90 |
548 |
> |
%.o : %.F90 $(MainMakefile) |
549 |
|
$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@ |
550 |
|
if test -n "`ls *.$(ModSuffix)`"; then\ |
551 |
|
$(Move) "`ls *.$(ModSuffix)`" $(PackageTargetDir);\ |
652 |
|
$(Doxygen) $(DEV_ROOT)/make/Doxyfile |
653 |
|
|
654 |
|
#GUN make funtions to merge the libraries |
655 |
< |
find_objs = $(shell $(StaticArchiver) -t $(1)) |
655 |
> |
find_objs = $(shell $(StaticArchiver) -t $(1) | $(EGREP) -v "SYMDEF") |
656 |
|
extract_objs = $(shell $(StaticArchiver) -x $(1) $(call find_objs, $(1))) |
657 |
|
create_archive = $(shell $(StaticArchiver) $(StaticArchiverOptions) $(2) $(call find_objs, $(1))) |
658 |
|
remove_objs = $(shell $(Delete) $(call find_objs, $(1))) |
659 |
|
do_create = $(call extract_objs,$(1))$(call create_archive,$(1),$(2))$(call remove_objs,$(1)) |
660 |
+ |
do_link = $(shell $(LN_S) $(1) $(2)) |
661 |
+ |
all_objs = $(foreach thisLib,$(LibNames), $(call find_objs, $(thisLib))) |
662 |
+ |
all_parallel_objs = $(foreach thisLib,$(ParallelLibNames), $(call find_objs, $(thisLib))) |
663 |
+ |
all_lib_objs = $(patsubst %,$(TargetDir)/%,$(call all_objs)) |
664 |
+ |
all_lib_parallel_objs = $(patsubst %,$(ParallelTargetDir)/%,$(call all_parallel_objs)) |
665 |
|
|
666 |
|
$(CombinedStaticLib) : $(LibDir)/.stamp_UP |
667 |
< |
$(Print) create $@ |
668 |
< |
$(foreach thisLib,$(LibNames),$(call do_create,$(thisLib),$@)) |
667 |
> |
$(Print) creating $@ |
668 |
> |
$(StaticArchiver) $(StaticArchiverOptions) $@ $(call all_lib_objs) |
669 |
|
$(Ranlib) $(CombinedStaticLib) |
670 |
|
|
671 |
|
$(CombinedParallelStaticLib) : $(LibDir)/.stamp_MPI |
672 |
< |
$(Print) create $@ |
673 |
< |
$(foreach thisLib,$(ParallelLibNames), $(call do_create, $(thisLib), $@)) |
672 |
> |
$(Print) creating $@ |
673 |
> |
$(StaticArchiver) $(StaticArchiverOptions) $@ $(call all_lib_parallel_objs) |
674 |
|
$(Ranlib) $(CombinedParallelStaticLib) |
675 |
|
|
676 |
|
# Executable |
677 |
< |
$(Executable) : $(CombinedStaticLib) $(ObjectFiles) $(BinDir) |
677 |
> |
$(Executable) : $(CombinedStaticLib) $(ObjectFiles) |
678 |
> |
if test ! -d $(BinDir); then \ |
679 |
> |
$(MkDir) $(BinDir) ;\ |
680 |
> |
fi |
681 |
|
$(Linker) $(ObjectFiles) $(CombinedStaticLib) $(LinkOptions) $(LibDirs) $(Libraries) -o $@ |
682 |
|
|
683 |
< |
$(ParallelExecutable) : $(CombinedParallelStaticLib) $(ParallelObjectFiles) $(BinDir) |
683 |
> |
$(ParallelExecutable) : $(CombinedParallelStaticLib) $(ParallelObjectFiles) |
684 |
> |
if test ! -d $(BinDir); then \ |
685 |
> |
$(MkDir) $(BinDir) ;\ |
686 |
> |
fi |
687 |
|
$(Linker) $(ParallelObjectFiles) $(CombinedParallelStaticLib) $(ParallelLinkOptions) $(LibDirs) $(Libraries) -o $@ |
688 |
|
|
689 |
|
# Anything else is just copied from source to target |
827 |
|
install : $(InstallListLoop) |
828 |
|
$(Print) Done Install |
829 |
|
|
830 |
< |
_installall : _buildall _installdata |
830 |
> |
_installall : _buildall _installdata _installlinks |
831 |
|
|
832 |
|
$(MyInstallDir) : |
833 |
|
$(MkDir) $@ |
838 |
|
$(InstallCommand) $(InstallFiles) $(MyInstallDir) |
839 |
|
endif |
840 |
|
|
841 |
+ |
_installlinks : $(MyInstallDir) |
842 |
+ |
ifneq "$(words $(MyLinkTargets))" "0" |
843 |
+ |
@cd $(MyInstallDir) |
844 |
+ |
$(foreach thisLink,$(MyLinkTargets),$(call do_link,$(MyLinkSource),$(thisLink))) |
845 |
+ |
endif |
846 |
+ |
|
847 |
|
# make statistics |
848 |
|
_statisticsall : |
849 |
|
@$(Print) $(patsubst %,$(CurrentDir)/%,$(SourceFiles)) >> $(DEV_ROOT)/files.tmp |
854 |
|
$(Print) Done statistics. |
855 |
|
|
856 |
|
# make pure |
857 |
< |
$(Executable).pure : |
858 |
< |
$(Purify) $(PurifyOptions) $(CppCompiler) $(LinkOptions) $(LibDirs) \ |
859 |
< |
$(LibList) $(ObjectFiles) -o $@ |
857 |
> |
#$(Executable).pure : |
858 |
> |
# $(Purify) $(PurifyOptions) $(CppCompiler) $(LinkOptions) $(LibDirs) \ |
859 |
> |
# $(LibList) $(ObjectFiles) -o $@ |
860 |
> |
# |
861 |
> |
#pure : $(Executable).pure |
862 |
|
|
819 |
– |
pure : $(Executable).pure |
820 |
– |
|
863 |
|
#make cvslog |
864 |
|
cvslog: |
865 |
|
$(DEV_ROOT)/scripts/cvs2cl |