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molds: Commit


Commit MetaInfo

Revision1598 (tree)
Time2013-12-25 17:05:47
Authormikiya_fujii

Log Message

branch/0.3.x.r1593 is 'manually' merged to trunk 'again'. This merge is related to #32650 and #32655. #32676

Change Summary

Incremental Difference

--- trunk/test/Test_Of_MolDS.rb (revision 1597)
+++ trunk/test/Test_Of_MolDS.rb (revision 1598)
@@ -45,8 +45,8 @@
4545 @@command = "command: "
4646 @@mpiCommand = "mpirun -np "
4747 @@mpiProcesses = "2"
48- @@deleteDiff = " | gawk '{if(($2!=\"SCF\")&&($3!=\"iter\")){print $0}}' | gawk '{if(($4!=\"time:\")){print $0}}' | gawk '{if(($3!=\"Elapsed\")){print $0}}' | gawk '{if(($2!=\"Elapsed\")){print $0}}' | gawk '{if(($3!=\"Welcome\")){print $0}}' | gawk '{if(($7!=\"residual\")){print $0}}' | gawk '{if(($3!=\"mode(nmw):\") ){print $0}}' | gawk '{if( !(($3==\"mode(mw):\")&&($4<6)) ){print $0}}'"
49- @@printed_section = []
48+ @@deleteDiff = " | gawk '{if(($2!=\"SCF\")&&($3!=\"iter\")){print $0}}' | gawk '{if(($4!=\"time:\")){print $0}}' | gawk '{if(($3!=\"Elapsed\")){print $0}}' | gawk '{if(($2!=\"Elapsed\")){print $0}}' | gawk '{if(($3!=\"Welcome\")){print $0}}' | gawk '{if(($7!=\"residual\")){print $0}}' | gawk '{if(($3!=\"mode(nmw):\") ){print $0}}' | gawk '{if( !(($3==\"mode(mw):\")&&($4<6)) ){print $0}}' | gawk '{if(($3!=\"Heap:\")){print $0}}'"
49+ @@printed_section = []
5050 def doesTestOmp(mklNumThreads, ompNumThreads)
5151 return unless should_run?
5252 ENV["MKL_NUM_THREADS"] = mklNumThreads
--- trunk/doc/README.txt (revision 1597)
+++ trunk/doc/README.txt (revision 1598)
@@ -23,8 +23,9 @@
2323
2424
2525 MolDS ("Mol"ecular "D"ynamics "S"imulation package) ver. 0.4.0 (Under developement)
26- developed by Mikiya Fujii, Ph.D., Katsuhiko Nishimra, and Michihiro Okuyama, Ph.D..
27- For Questions and bug reports: molds-dev@lists.sourceforge.jp
26+ Developers: Mikiya Fujii, Ph.D.(project lead), Katsuhiko Nishimra, and Michihiro Okuyama, Ph.D..
27+ Other contributors: Michael Banck
28+ Questions and bug reports: molds-dev@lists.sourceforge.jp
2829
2930
3031 ==============================================================================
--- trunk/src/Makefile (revision 1597)
+++ trunk/src/Makefile (revision 1598)
@@ -36,12 +36,13 @@
3636 EXENAME = molds
3737 DEPFILE = obj/objfile.dep
3838 LDFLAGS = -Wl,-rpath=$(BOOST_LIB_DIR)
39+THIS_MAKEFILE := $(word $(words $(MAKEFILE_LIST)),$(MAKEFILE_LIST))
3940
4041 ALL_CPP_FILES = base/Enums.cpp base/PrintController.cpp base/MolDSException.cpp base/MallocerFreer.cpp mpi/MpiProcess.cpp mpi/AsyncCommunicator.cpp wrappers/Blas.cpp wrappers/Lapack.cpp base/Utilities.cpp base/MathUtilities.cpp base/EularAngle.cpp base/Parameters.cpp base/RealSphericalHarmonicsIndex.cpp base/atoms/Atom.cpp base/atoms/Hatom.cpp base/atoms/Liatom.cpp base/atoms/Catom.cpp base/atoms/Natom.cpp base/atoms/Oatom.cpp base/atoms/Satom.cpp base/atoms/mm/EnvironmentalPointCharge.cpp base/factories/AtomFactory.cpp base/Molecule.cpp base/InputParser.cpp base/GTOExpansionSTO.cpp base/loggers/MOLogger.cpp base/loggers/DensityLogger.cpp base/loggers/HoleDensityLogger.cpp base/loggers/ParticleDensityLogger.cpp cndo/Cndo2.cpp indo/Indo.cpp zindo/ZindoS.cpp mndo/Mndo.cpp am1/Am1.cpp am1/Am1D.cpp pm3/Pm3.cpp pm3/Pm3D.cpp pm3/Pm3Pddg.cpp base/factories/ElectronicStructureFactory.cpp md/MD.cpp mc/MC.cpp rpmd/RPMD.cpp nasco/NASCO.cpp optimization/Optimizer.cpp optimization/ConjugateGradient.cpp optimization/SteepestDescent.cpp optimization/BFGS.cpp optimization/GEDIIS.cpp base/factories/OptimizerFactory.cpp base/MolDS.cpp Main.cpp
4142 ALL_HEAD_FILES = config.h base/Enums.h base/Uncopyable.h base/PrintController.h base/MolDSException.h base/containers/ThreadSafeQueue.h base/MallocerFreer.h mpi/MpiInt.h mpi/MpiProcess.h mpi/AsyncCommunicator.h wrappers/Blas.h wrappers/Lapack.h base/Utilities.h base/MathUtilities.h base/EularAngle.h base/Parameters.h base/RealSphericalHarmonicsIndex.h base/atoms/Atom.h base/atoms/Hatom.h base/atoms/Liatom.h base/atoms/Catom.h base/atoms/Natom.h base/atoms/Oatom.h base/atoms/Satom.h base/atoms/mm/EnvironmentalPointCharge.h base/factories/AtomFactory.h base/Molecule.h base/InputParser.h base/GTOExpansionSTO.h base/loggers/MOLogger.h base/loggers/DensityLogger.h base/loggers/HoleDensityLogger.h base/loggers/ParticleDensityLogger.h base/ElectronicStructure.h cndo/Cndo2.h cndo/ReducedOverlapAOsParameters.h indo/Indo.h zindo/ZindoS.h mndo/Mndo.h am1/Am1.h am1/Am1D.h pm3/Pm3.h pm3/Pm3D.h pm3/Pm3Pddg.h base/factories/ElectronicStructureFactory.h md/MD.h mc/MC.h rpmd/RPMD.h nasco/NASCO.h optimization/Optimizer.h optimization/ConjugateGradient.h optimization/SteepestDescent.h optimization/BFGS.h optimization/GEDIIS.h base/factories/OptimizerFactory.h base/MolDS.h
4243 ALL_OBJ_FILES = obj/Enums.o obj/PrintController.o obj/MolDSException.o obj/MallocerFreer.o obj/MpiProcess.o obj/AsyncCommunicator.o obj/Blas.o obj/Lapack.o obj/Utilities.o obj/MathUtilities.o obj/EularAngle.o obj/Parameters.o obj/RealSphericalHarmonicsIndex.o obj/Atom.o obj/Hatom.o obj/Liatom.o obj/Catom.o obj/Natom.o obj/Oatom.o obj/Satom.o obj/EnvironmentalPointCharge.o obj/AtomFactory.o obj/Molecule.o obj/InputParser.o obj/GTOExpansionSTO.o obj/MOLogger.o obj/DensityLogger.o obj/HoleDensityLogger.o obj/ParticleDensityLogger.o obj/Cndo2.o obj/Indo.o obj/ZindoS.o obj/Mndo.o obj/Am1.o obj/Am1D.o obj/Pm3.o obj/Pm3D.o obj/Pm3Pddg.o obj/ElectronicStructureFactory.o obj/MD.o obj/MC.o obj/RPMD.o obj/NASCO.o obj/Optimizer.o obj/ConjugateGradient.o obj/SteepestDescent.o obj/BFGS.o obj/GEDIIS.o obj/OptimizerFactory.o obj/MolDS.o obj/Main.o
4344
44-$(EXENAME): $(ALL_OBJ_FILES)
45+$(EXENAME): $(DEPFILE) $(ALL_OBJ_FILES)
4546 $(CC) -o $@ $(LDFLAGS) -L$(BOOST_LIB_DIR) $(ALL_OBJ_FILES) $(LIBS)
4647
4748 -include $(DEPFILE)
@@ -48,10 +49,10 @@
4849
4950 .PHONY: depend
5051 depend:
51- rm $(DEPFILE)
52- +make $(DEPFILE)
52+ -rm -f $(DEPFILE)
53+ +make -f $(THIS_MAKEFILE) $(DEPFILE)
5354
54-$(DEPFILE): Makefile
55+$(DEPFILE): $(THIS_MAKEFILE) $(ALL_CPP_FILES) $(ALL_HEAD_FILES)
5556 $(CC) -MM $(ALL_CPP_FILES) -I$(BOOST_INC_DIR) | sed 's/^\([^ ]\)/obj\/\1/g' | sed 's/\($$*\)\.o[ :]*/\1.o : /g' > $(DEPFILE)
5657
5758 $(ALL_OBJ_FILES):
@@ -59,6 +60,6 @@
5960
6061 .PHONY: clean
6162 clean:
62- rm -f $(ALL_OBJ_FILES) $(EXENAME) $(DEPFILE)
63+ -rm -f $(ALL_OBJ_FILES) $(EXENAME) $(DEPFILE)
6364
64-all: clean $(EXENAME)
65+all: clean depend $(EXENAME)
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