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Révision4e2573bfb36b7d08b4f137459803e8eaa83ca0f0 (tree)
l'heure2014-04-29 10:19:14
AuteurMikiya Fujii <mikiya.fujii@gmai...>
CommiterMikiya Fujii

Message de Log

Add Cl (chlorine) #33722

git-svn-id: https://svn.sourceforge.jp/svnroot/molds/trunk@1668 1136aad2-a195-0410-b898-f5ea1d11b9d8

Change Summary

Modification

--- a/doc/README.txt
+++ b/doc/README.txt
@@ -182,18 +182,18 @@ CAPABILITIES:
182182 i.e., MD(gs) and MD(es) mean Born-Oppenheimer Molecular Dynamics on ground and excited states, respectively.
183183
184184 -Elements
185- CNDO2 | H, Li, C, N, O, F, S
185+ CNDO2 | H, Li, C, N, O, F, S, Cl
186186 INDO | H, Li, C, N, O, F,
187- ZINDO/S | H, C, N, O, F, S
188- MNDO | H, C, N, O, F, S, Zn
189- AM1 | H, C, N, O, F, S, Zn
190- AM1-D | H, C, N, O, F, S *
191- PM3 | H, C, N, O, F, S, Zn
192- PM3-D | H, C, N, O, F, S *
187+ ZINDO/S | H, C, N, O, F, S, Cl
188+ MNDO | H, C, N, O, F, S, Cl, Zn
189+ AM1 | H, C, N, O, F, S, Cl, Zn
190+ AM1-D | H, C, N, O, F, S, Cl *
191+ PM3 | H, C, N, O, F, S, Cl, Zn
192+ PM3-D | H, C, N, O, F, S, Cl *
193193 PM3/PDDG | H, C, N, O, S
194194
195- * For fluorine, semiempirical parameters used in the SCF of AM1-D and PM3-D are same with
196- the original semiempirical parameters used in the SCF of AM1 and PM3, respectively.
195+ * For fluorine(F) and chlorine(Cl), semiempirical parameters used in SCF of AM1-D and PM3-D are same with
196+ the original semiempirical parameters used in SCF of AM1 and PM3, respectively.
197197
198198 -Parallelization
199199 Open MP parallelization: everywhere in MolDS
--- a/src/Makefile
+++ b/src/Makefile
@@ -38,9 +38,9 @@ DEPFILE = obj/objfile.dep
3838 LDFLAGS = -Wl,-rpath=$(BOOST_LIB_DIR)
3939 THIS_MAKEFILE := $(word $(words $(MAKEFILE_LIST)),$(MAKEFILE_LIST))
4040
41-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/Fatom.cpp base/atoms/Satom.cpp base/atoms/Znatom.cpp base/atoms/ghost/Ghost.cpp base/atoms/ghost/GhostHatom.cpp base/atoms/ghost/GhostLiatom.cpp base/atoms/ghost/GhostCatom.cpp base/atoms/ghost/GhostNatom.cpp base/atoms/ghost/GhostOatom.cpp base/atoms/ghost/GhostFatom.cpp base/atoms/ghost/GhostSatom.cpp base/atoms/ghost/GhostZnatom.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
42-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/Fatom.h base/atoms/Satom.h base/atoms/Znatom.h base/atoms/ghost/Ghost.h base/atoms/ghost/GhostHatom.h base/atoms/ghost/GhostLiatom.h base/atoms/ghost/GhostCatom.h base/atoms/ghost/GhostNatom.h base/atoms/ghost/GhostOatom.h base/atoms/ghost/GhostFatom.h base/atoms/ghost/GhostSatom.h base/atoms/ghost/GhostZnatom.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
43-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/Fatom.o obj/Satom.o obj/Znatom.o obj/Ghost.o obj/GhostHatom.o obj/GhostLiatom.o obj/GhostCatom.o obj/GhostNatom.o obj/GhostOatom.o obj/GhostFatom.o obj/GhostSatom.o obj/GhostZnatom.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
41+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/Fatom.cpp base/atoms/Satom.cpp base/atoms/Clatom.cpp base/atoms/Znatom.cpp base/atoms/ghost/Ghost.cpp base/atoms/ghost/GhostHatom.cpp base/atoms/ghost/GhostLiatom.cpp base/atoms/ghost/GhostCatom.cpp base/atoms/ghost/GhostNatom.cpp base/atoms/ghost/GhostOatom.cpp base/atoms/ghost/GhostFatom.cpp base/atoms/ghost/GhostSatom.cpp base/atoms/ghost/GhostClatom.cpp base/atoms/ghost/GhostZnatom.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
42+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/Fatom.h base/atoms/Satom.h base/atoms/Clatom.h base/atoms/Znatom.h base/atoms/ghost/Ghost.h base/atoms/ghost/GhostHatom.h base/atoms/ghost/GhostLiatom.h base/atoms/ghost/GhostCatom.h base/atoms/ghost/GhostNatom.h base/atoms/ghost/GhostOatom.h base/atoms/ghost/GhostFatom.h base/atoms/ghost/GhostSatom.h base/atoms/ghost/GhostClatom.h base/atoms/ghost/GhostZnatom.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
43+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/Fatom.o obj/Satom.o obj/Clatom.o obj/Znatom.o obj/Ghost.o obj/GhostHatom.o obj/GhostLiatom.o obj/GhostCatom.o obj/GhostNatom.o obj/GhostOatom.o obj/GhostFatom.o obj/GhostSatom.o obj/GhostClatom.o obj/GhostZnatom.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
4444
4545 $(EXENAME): $(DEPFILE) $(ALL_OBJ_FILES)
4646 $(CC) -o $@ $(LDFLAGS) -L$(BOOST_LIB_DIR) $(ALL_OBJ_FILES) $(LIBS)
--- a/src/Makefile_GNU
+++ b/src/Makefile_GNU
@@ -35,9 +35,9 @@ DEPFILE = obj/objfile.dep
3535 LDFLAGS = -Wl,-rpath=$(BOOST_LIB_DIR) -Wl,-rpath=$(OPENBLAS_LIB_DIR)
3636 THIS_MAKEFILE := $(word $(words $(MAKEFILE_LIST)),$(MAKEFILE_LIST))
3737
38-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/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/Fatom.cpp base/atoms/Satom.cpp base/atoms/Znatom.cpp base/atoms/ghost/Ghost.cpp base/atoms/ghost/GhostHatom.cpp base/atoms/ghost/GhostLiatom.cpp base/atoms/ghost/GhostCatom.cpp base/atoms/ghost/GhostNatom.cpp base/atoms/ghost/GhostOatom.cpp base/atoms/ghost/GhostFatom.cpp base/atoms/ghost/GhostSatom.cpp base/atoms/ghost/GhostZnatom.cpp base/atoms/mm/EnvironmentalPointCharge.cpp base/factories/AtomFactory.cpp base/Molecule.cpp base/InputParser.cpp base/GTOExpansionSTO.cpp base/RealSphericalHarmonicsIndex.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
39-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/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/Fatom.h base/atoms/Satom.h base/atoms/Znatom.h base/atoms/ghost/Ghost.h base/atoms/ghost/GhostHatom.h base/atoms/ghost/GhostLiatom.h base/atoms/ghost/GhostCatom.h base/atoms/ghost/GhostNatom.h base/atoms/ghost/GhostOatom.h base/atoms/ghost/GhostFatom.h base/atoms/ghost/GhostSatom.h base/atoms/ghost/GhostZnatom.h base/atoms/mm/EnvironmentalPointCharge.h base/factories/AtomFactory.h base/Molecule.h base/InputParser.h base/GTOExpansionSTO.h base/RealSphericalHarmonicsIndex.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
40-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/Atom.o obj/Hatom.o obj/Liatom.o obj/Catom.o obj/Natom.o obj/Oatom.o obj/Fatom.o obj/Satom.o obj/Znatom.o obj/Ghost.o obj/GhostHatom.o obj/GhostLiatom.o obj/GhostCatom.o obj/GhostNatom.o obj/GhostOatom.o obj/GhostFatom.o obj/GhostSatom.o obj/GhostZnatom.o obj/EnvironmentalPointCharge.o obj/AtomFactory.o obj/Molecule.o obj/InputParser.o obj/GTOExpansionSTO.o obj/RealSphericalHarmonicsIndex.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
38+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/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/Fatom.cpp base/atoms/Satom.cpp base/atoms/Clatom.cpp base/atoms/Znatom.cpp base/atoms/ghost/Ghost.cpp base/atoms/ghost/GhostHatom.cpp base/atoms/ghost/GhostLiatom.cpp base/atoms/ghost/GhostCatom.cpp base/atoms/ghost/GhostNatom.cpp base/atoms/ghost/GhostOatom.cpp base/atoms/ghost/GhostFatom.cpp base/atoms/ghost/GhostSatom.cpp base/atoms/ghost/GhostClatom.cpp base/atoms/ghost/GhostZnatom.cpp base/atoms/mm/EnvironmentalPointCharge.cpp base/factories/AtomFactory.cpp base/Molecule.cpp base/InputParser.cpp base/GTOExpansionSTO.cpp base/RealSphericalHarmonicsIndex.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
39+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/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/Fatom.h base/atoms/Satom.h base/atoms/Clatom.h base/atoms/Znatom.h base/atoms/ghost/Ghost.h base/atoms/ghost/GhostHatom.h base/atoms/ghost/GhostLiatom.h base/atoms/ghost/GhostCatom.h base/atoms/ghost/GhostNatom.h base/atoms/ghost/GhostOatom.h base/atoms/ghost/GhostFatom.h base/atoms/ghost/GhostSatom.h base/atoms/ghost/GhostClatom.h base/atoms/ghost/GhostZnatom.h base/atoms/mm/EnvironmentalPointCharge.h base/factories/AtomFactory.h base/Molecule.h base/InputParser.h base/GTOExpansionSTO.h base/RealSphericalHarmonicsIndex.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
40+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/Atom.o obj/Hatom.o obj/Liatom.o obj/Catom.o obj/Natom.o obj/Oatom.o obj/Fatom.o obj/Satom.o obj/Clatom.o obj/Znatom.o obj/Ghost.o obj/GhostHatom.o obj/GhostLiatom.o obj/GhostCatom.o obj/GhostNatom.o obj/GhostOatom.o obj/GhostFatom.o obj/GhostSatom.o obj/GhostClatom.o obj/GhostZnatom.o obj/EnvironmentalPointCharge.o obj/AtomFactory.o obj/Molecule.o obj/InputParser.o obj/GTOExpansionSTO.o obj/RealSphericalHarmonicsIndex.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
4141
4242 $(EXENAME): $(DEPFILE) $(ALL_OBJ_FILES)
4343 $(CC) -o $@ $(LDFLAGS) $(ALL_OBJ_FILES) -L$(BOOST_LIB_DIR) -L$(OPENBLAS_LIB_DIR) $(LIBS)
--- a/src/am1/Am1.cpp
+++ b/src/am1/Am1.cpp
@@ -42,6 +42,7 @@
4242 #include"../base/atoms/Oatom.h"
4343 #include"../base/atoms/Fatom.h"
4444 #include"../base/atoms/Satom.h"
45+#include"../base/atoms/Clatom.h"
4546 #include"../base/Molecule.h"
4647 #include"../base/ElectronicStructure.h"
4748 #include"../cndo/Cndo2.h"
@@ -135,6 +136,7 @@ void Am1::SetEnableAtomTypes(){
135136 this->enableAtomTypes.push_back(O);
136137 this->enableAtomTypes.push_back(F);
137138 this->enableAtomTypes.push_back(S);
139+ this->enableAtomTypes.push_back(Cl);
138140 this->enableAtomTypes.push_back(Zn);
139141 }
140142
--- a/src/am1/Am1D.cpp
+++ b/src/am1/Am1D.cpp
@@ -42,6 +42,7 @@
4242 #include"../base/atoms/Oatom.h"
4343 #include"../base/atoms/Fatom.h"
4444 #include"../base/atoms/Satom.h"
45+#include"../base/atoms/Clatom.h"
4546 #include"../base/Molecule.h"
4647 #include"../base/ElectronicStructure.h"
4748 #include"../cndo/Cndo2.h"
@@ -137,6 +138,7 @@ void Am1D::SetEnableAtomTypes(){
137138 this->enableAtomTypes.push_back(O);
138139 this->enableAtomTypes.push_back(F);
139140 this->enableAtomTypes.push_back(S);
141+ this->enableAtomTypes.push_back(Cl);
140142 }
141143
142144
--- a/src/base/InputParser.cpp
+++ b/src/base/InputParser.cpp
@@ -496,6 +496,9 @@ int InputParser::ParseMolecularConfiguration(Molecule* molecule, vector<string>*
496496 else if((*inputTerms)[parseIndex] == "s"){
497497 atomType = S;
498498 }
499+ else if((*inputTerms)[parseIndex] == "cl"){
500+ atomType = Cl;
501+ }
499502 else if((*inputTerms)[parseIndex] == "zn"){
500503 atomType = Zn;
501504 }
@@ -535,6 +538,9 @@ int InputParser::ParseGhostsConfiguration(Molecule* molecule, vector<string>* in
535538 else if((*inputTerms)[parseIndex] == "s"){
536539 atomType = ghostS;
537540 }
541+ else if((*inputTerms)[parseIndex] == "cl"){
542+ atomType = ghostCl;
543+ }
538544 else if((*inputTerms)[parseIndex] == "zn"){
539545 atomType = ghostZn;
540546 }
--- /dev/null
+++ b/src/base/atoms/Clatom.cpp
@@ -0,0 +1,237 @@
1+//************************************************************************//
2+// Copyright (C) 2011-2014 Mikiya Fujii //
3+// //
4+// This file is part of MolDS. //
5+// //
6+// MolDS is free software: you can redistribute it and/or modify //
7+// it under the terms of the GNU General Public License as published by //
8+// the Free Software Foundation, either version 3 of the License, or //
9+// (at your option) any later version. //
10+// //
11+// MolDS is distributed in the hope that it will be useful, //
12+// but WITHOUT ANY WARRANTY; without even the implied warranty of //
13+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the //
14+// GNU General Public License for more details. //
15+// //
16+// You should have received a copy of the GNU General Public License //
17+// along with MolDS. If not, see <http://www.gnu.org/licenses/>. //
18+//************************************************************************//
19+#include<stdio.h>
20+#include<stdlib.h>
21+#include<iostream>
22+#include<sstream>
23+#include<math.h>
24+#include<vector>
25+#include<boost/format.hpp>
26+#include"../Enums.h"
27+#include"../Uncopyable.h"
28+#include"../PrintController.h"
29+#include"../MolDSException.h"
30+#include"../MallocerFreer.h"
31+#include"../../mpi/MpiInt.h"
32+#include"../../mpi/MpiProcess.h"
33+#include"../EularAngle.h"
34+#include"../Parameters.h"
35+#include"../RealSphericalHarmonicsIndex.h"
36+#include"Atom.h"
37+#include"Clatom.h"
38+using namespace std;
39+using namespace MolDS_base;
40+namespace MolDS_base_atoms{
41+Clatom::Clatom(int index) : Atom(index){
42+ this->SetAtomicParameters();
43+}
44+
45+Clatom::~Clatom(){}
46+
47+void Clatom::SetAtomicParameters(){
48+ this->atomType = Cl;
49+ this->atomicMass = 35.453*Parameters::GetInstance()->GetGMolin2AU();
50+ this->coreCharge = 7.0;
51+ this->numberValenceElectrons = 7;
52+ this->valenceShellType = mShell;
53+ this->valence.push_back(s);
54+ this->valence.push_back(py);
55+ this->valence.push_back(pz);
56+ this->valence.push_back(px);
57+ if(Parameters::GetInstance()->GetCurrentTheory() == CNDO2){
58+ this->valence.push_back(dxy);
59+ this->valence.push_back(dyz);
60+ this->valence.push_back(dzz);
61+ this->valence.push_back(dzx);
62+ this->valence.push_back(dxxyy);
63+ }
64+ for(int i=0; i<this->valence.size();i++){
65+ this->realSphericalHarmonicsIndeces.push_back(new RealSphericalHarmonicsIndex(this->valence[i]));
66+ }
67+ this->vdWCoefficient = 8.00*Parameters::GetInstance()->GetJ2AU()
68+ *pow(Parameters::GetInstance()->GetNm2AU(),6.0)
69+ /Parameters::GetInstance()->GetAvogadro();
70+ this->vdWRadii = 1.820*Parameters::GetInstance()->GetAngstrom2AU();
71+ this->bondingParameter = -22.330*Parameters::GetInstance()->GetEV2AU();
72+ this->imuAmuS = 21.591*Parameters::GetInstance()->GetEV2AU();
73+ this->imuAmuP = 8.708*Parameters::GetInstance()->GetEV2AU();
74+ this->imuAmuD = 0.977*Parameters::GetInstance()->GetEV2AU();
75+ this->effectiveNuclearChargeK = 16.70;
76+ this->effectiveNuclearChargeL = 12.85;
77+ if(Parameters::GetInstance()->GetCurrentTheory() == ZINDOS){
78+ this->effectiveNuclearChargeMsp = 2.130*3.0; // from orca 3.0.1
79+ this->effectiveNuclearChargeMd = 0.0; // not used
80+ }
81+ else{
82+ this->effectiveNuclearChargeMsp = 6.10;
83+ this->effectiveNuclearChargeMd = 6.10;
84+ }
85+ //this->indoG1 = 0.0;
86+ //this->indoF2 = 0.0;
87+ //this->indoF0CoefficientS = 0.0;
88+ //this->indoF0CoefficientP = 0.0;
89+ //this->indoG1CoefficientS = 0.0;
90+ //this->indoG1CoefficientP = 0.0;
91+ //this->indoF2CoefficientS = 0.0;
92+ //this->indoF2CoefficientP = 0.0;
93+
94+ // ORCA parameter 3.0.1 set
95+ // see "ORCA 2.8"( http://www.thch.uni-bonn.de/tc/orca/ ).
96+ this->zindoBondingParameterS = -11.0*Parameters::GetInstance()->GetEV2AU();
97+ this->zindoBondingParameterD = 0.0*Parameters::GetInstance()->GetEV2AU();
98+ this->zindoF0ss = 11.25 * Parameters::GetInstance()->GetEV2AU();
99+ this->zindoF0sd = 0.0;
100+ this->zindoF0dd = 0.0;
101+ this->zindoG1sp = 8.8027 * Parameters::GetInstance()->GetEV2AU();
102+ this->zindoF2pp = 6.4470 * Parameters::GetInstance()->GetEV2AU();
103+ this->zindoG2sd = 0.0;
104+ this->zindoG1pd = 0.0;
105+ this->zindoF2pd = 0.0;
106+ this->zindoG3pd = 0.0;
107+ this->zindoF2dd = 0.0;
108+ this->zindoF4dd = 0.0;
109+ // end (ORCA 2.8 parameter set)
110+
111+ this->zindoL = 2;
112+ this->zindoM = 5;
113+ this->zindoN = 0;
114+ this->zindoIonPotS = 25.23 * Parameters::GetInstance()->GetEV2AU();
115+ this->zindoIonPotP = 15.03 * Parameters::GetInstance()->GetEV2AU();
116+ this->zindoIonPotD = 6.00 * Parameters::GetInstance()->GetEV2AU();
117+ this->mndoCoreintegralS = -100.227166 * Parameters::GetInstance()->GetEV2AU();
118+ this->mndoCoreintegralP = -77.378667 * Parameters::GetInstance()->GetEV2AU();
119+ this->mndoOrbitalExponentS = 3.784645;
120+ this->mndoOrbitalExponentP = 2.036263;
121+ this->mndoBondingParameterS = -14.262320 * Parameters::GetInstance()->GetEV2AU();
122+ this->mndoBondingParameterP = -14.26320 * Parameters::GetInstance()->GetEV2AU();
123+ this->mndoAlpha = 2.542201 / Parameters::GetInstance()->GetAngstrom2AU();
124+ this->mndoElecEnergyAtom = -353.137667 * Parameters::GetInstance()->GetEV2AU();
125+ this->mndoHeatsFormAtom = 28.99 * Parameters::GetInstance()->GetKcalMolin2AU();
126+ this->mndoGss = 15.03 * Parameters::GetInstance()->GetEV2AU();
127+ this->mndoGpp = 11.30 * Parameters::GetInstance()->GetEV2AU();
128+ this->mndoGsp = 13.16 * Parameters::GetInstance()->GetEV2AU();
129+ this->mndoGpp2 = 9.97 * Parameters::GetInstance()->GetEV2AU();
130+ this->mndoHsp = 2.42 * Parameters::GetInstance()->GetEV2AU();
131+ this->mndoDerivedParameterD[0] = 0.0;
132+ this->mndoDerivedParameterD[1] = 0.4986870220;
133+ this->mndoDerivedParameterD[2] = 0.8217602800;
134+ this->mndoDerivedParameterRho[0] = 0.5/0.5523379209;
135+ this->mndoDerivedParameterRho[1] = 0.5/0.8061021276;
136+ this->mndoDerivedParameterRho[2] = 0.5/0.6053315152;
137+ this->am1CoreintegralS = -111.613948 * Parameters::GetInstance()->GetEV2AU();
138+ this->am1CoreintegralP = -76.640107 * Parameters::GetInstance()->GetEV2AU();
139+ this->am1OrbitalExponentS = 3.631376;
140+ this->am1OrbitalExponentP = 2.076799;
141+ this->am1BondingParameterS = -24.594670 * Parameters::GetInstance()->GetEV2AU();
142+ this->am1BondingParameterP = -14.637216 * Parameters::GetInstance()->GetEV2AU();
143+ this->am1Alpha = 2.919368 / Parameters::GetInstance()->GetAngstrom2AU();
144+ this->am1Gss = this->mndoGss;
145+ this->am1Gpp = this->mndoGpp;
146+ this->am1Gsp = this->mndoGsp;
147+ this->am1Gpp2 = this->mndoGpp2;
148+ this->am1Hsp = this->mndoHsp;
149+ this->am1DerivedParameterD[0] = 0.0;
150+ this->am1DerivedParameterD[1] = 0.5406286370;
151+ this->am1DerivedParameterD[2] = 0.8057207525;
152+ this->am1DerivedParameterRho[0] = 0.5/0.5523379209;
153+ this->am1DerivedParameterRho[1] = 0.5/0.7693007940;
154+ this->am1DerivedParameterRho[2] = 0.5/0.6133247965;
155+ this->am1ParameterK[0] = 0.094243 * Parameters::GetInstance()->GetEV2AU();
156+ this->am1ParameterK[1] = 0.027168 * Parameters::GetInstance()->GetEV2AU();
157+ this->am1ParameterK[2] = 0.00 * Parameters::GetInstance()->GetEV2AU();
158+ this->am1ParameterK[3] = 0.00 * Parameters::GetInstance()->GetEV2AU();
159+ this->am1ParameterL[0] = 4.00 / pow(Parameters::GetInstance()->GetAngstrom2AU(),2.0);
160+ this->am1ParameterL[1] = 4.00 / pow(Parameters::GetInstance()->GetAngstrom2AU(),2.0);
161+ this->am1ParameterL[2] = 0.00 / pow(Parameters::GetInstance()->GetAngstrom2AU(),2.0);
162+ this->am1ParameterL[3] = 0.00 / pow(Parameters::GetInstance()->GetAngstrom2AU(),2.0);
163+ this->am1ParameterM[0] = 1.30 * Parameters::GetInstance()->GetAngstrom2AU();
164+ this->am1ParameterM[1] = 2.10 * Parameters::GetInstance()->GetAngstrom2AU();
165+ this->am1ParameterM[2] = 0.00 * Parameters::GetInstance()->GetAngstrom2AU();
166+ this->am1ParameterM[3] = 0.00 * Parameters::GetInstance()->GetAngstrom2AU();
167+ this->am1DCoreintegralS = this->am1CoreintegralS;
168+ this->am1DCoreintegralP = this->am1CoreintegralP;
169+ this->am1DBondingParameterS = this->am1BondingParameterS;
170+ this->am1DBondingParameterP = this->am1BondingParameterP;
171+ this->am1DAlpha = this->am1DAlpha;
172+ this->pm3CoreintegralS = -100.626747 * Parameters::GetInstance()->GetEV2AU();
173+ this->pm3CoreintegralP = -53.614396 * Parameters::GetInstance()->GetEV2AU();
174+ this->pm3OrbitalExponentS = 2.246210;
175+ this->pm3OrbitalExponentP = 2.151010;
176+ this->pm3BondingParameterS = -27.528560 * Parameters::GetInstance()->GetEV2AU();
177+ this->pm3BondingParameterP = -11.593922 * Parameters::GetInstance()->GetEV2AU();
178+ this->pm3Alpha = 2.517296 / Parameters::GetInstance()->GetAngstrom2AU();
179+ this->pm3DerivedParameterD[0] = 0.0;
180+ this->pm3DerivedParameterD[1] = 0.9175855709;
181+ this->pm3DerivedParameterD[2] = 0.7779229539;
182+ this->pm3DerivedParameterRho[0] = 0.5/0.5884843036;
183+ this->pm3DerivedParameterRho[1] = 0.5/0.6814322305;
184+ this->pm3DerivedParameterRho[2] = 0.5/0.2074800643;
185+ this->pm3ParameterK[0] = -0.171591 * Parameters::GetInstance()->GetEV2AU();
186+ this->pm3ParameterK[1] = -0.013458 * Parameters::GetInstance()->GetEV2AU();
187+ this->pm3ParameterK[2] = 0.0;
188+ this->pm3ParameterK[3] = 0.0;
189+ this->pm3ParameterL[0] = 6.000802 / pow(Parameters::GetInstance()->GetAngstrom2AU(),2.0);
190+ this->pm3ParameterL[1] = 1.966618 / pow(Parameters::GetInstance()->GetAngstrom2AU(),2.0);
191+ this->pm3ParameterL[2] = 0.00;
192+ this->pm3ParameterL[3] = 0.00;
193+ this->pm3ParameterM[0] = 1.087502 * Parameters::GetInstance()->GetAngstrom2AU();
194+ this->pm3ParameterM[1] = 2.292891 * Parameters::GetInstance()->GetAngstrom2AU();
195+ this->pm3ParameterM[2] = 0.00;
196+ this->pm3ParameterM[3] = 0.00;
197+ this->pm3Gss = 16.013601 * Parameters::GetInstance()->GetEV2AU();
198+ this->pm3Gpp = 7.522215 * Parameters::GetInstance()->GetEV2AU();
199+ this->pm3Gsp = 8.048115 * Parameters::GetInstance()->GetEV2AU();
200+ this->pm3Gpp2 = 7.504154 * Parameters::GetInstance()->GetEV2AU();
201+ this->pm3Hsp = 3.481153 * Parameters::GetInstance()->GetEV2AU();
202+ //this->pm3PddgCoreintegralS = -43.906366 * Parameters::GetInstance()->GetEV2AU();
203+ //this->pm3PddgCoreintegralP = -43.461348 * Parameters::GetInstance()->GetEV2AU();
204+ //this->pm3PddgOrbitalExponentS = 1.012002;
205+ //this->pm3PddgOrbitalExponentP = 1.876999;
206+ //this->pm3PddgBondingParameterS = -2.953912 * Parameters::GetInstance()->GetEV2AU();
207+ //this->pm3PddgBondingParameterP = -8.507779 * Parameters::GetInstance()->GetEV2AU();
208+ //this->pm3PddgAlpha = 2.539751 / Parameters::GetInstance()->GetAngstrom2AU();
209+ //this->pm3PddgDerivedParameterD[0] = 0.0;
210+ //this->pm3PddgDerivedParameterD[1] = 1.006989;
211+ //this->pm3PddgDerivedParameterD[2] = 0.891487;
212+ //this->pm3PddgDerivedParameterRho[0] = 1.517625;
213+ //this->pm3PddgDerivedParameterRho[1] = 0.711672;
214+ //this->pm3PddgDerivedParameterRho[2] = 0.754336;
215+ //this->pm3PddgParameterK[0] =-0.330692 * Parameters::GetInstance()->GetEV2AU();
216+ //this->pm3PddgParameterK[1] = 0.024171 * Parameters::GetInstance()->GetEV2AU();
217+ //this->pm3PddgParameterK[2] = 0.0;
218+ //this->pm3PddgParameterK[3] = 0.0;
219+ //this->pm3PddgParameterL[0] = 6.000000 / pow(Parameters::GetInstance()->GetAngstrom2AU(),2.0);
220+ //this->pm3PddgParameterL[1] = 6.000000 / pow(Parameters::GetInstance()->GetAngstrom2AU(),2.0);
221+ //this->pm3PddgParameterL[2] = 0.00;
222+ //this->pm3PddgParameterL[3] = 0.00;
223+ //this->pm3PddgParameterM[0] = 0.823837 * Parameters::GetInstance()->GetAngstrom2AU();
224+ //this->pm3PddgParameterM[1] = 2.017756 * Parameters::GetInstance()->GetAngstrom2AU();
225+ //this->pm3PddgParameterM[2] = 0.00;
226+ //this->pm3PddgParameterM[3] = 0.00;
227+ //this->pm3PddgParameterPa[0] = 0.120434 * Parameters::GetInstance()->GetEV2AU();
228+ //this->pm3PddgParameterPa[1] =-0.002663 * Parameters::GetInstance()->GetEV2AU();
229+ //this->pm3PddgParameterDa[0] = 0.672870 * Parameters::GetInstance()->GetAngstrom2AU();
230+ //this->pm3PddgParameterDa[1] = 2.032340 * Parameters::GetInstance()->GetAngstrom2AU();
231+ this->pm3DCoreintegralS = this->pm3CoreintegralS;
232+ this->pm3DCoreintegralP = this->pm3CoreintegralP;
233+ this->pm3DBondingParameterS = this->pm3BondingParameterS;
234+ this->pm3DBondingParameterP = this->pm3BondingParameterP;
235+ this->pm3DAlpha = this->pm3Alpha;
236+}
237+}
--- /dev/null
+++ b/src/base/atoms/Clatom.h
@@ -0,0 +1,32 @@
1+//************************************************************************//
2+// Copyright (C) 2011-2014 Mikiya Fujii //
3+// //
4+// This file is part of MolDS. //
5+// //
6+// MolDS is free software: you can redistribute it and/or modify //
7+// it under the terms of the GNU General Public License as published by //
8+// the Free Software Foundation, either version 3 of the License, or //
9+// (at your option) any later version. //
10+// //
11+// MolDS is distributed in the hope that it will be useful, //
12+// but WITHOUT ANY WARRANTY; without even the implied warranty of //
13+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the //
14+// GNU General Public License for more details. //
15+// //
16+// You should have received a copy of the GNU General Public License //
17+// along with MolDS. If not, see <http://www.gnu.org/licenses/>. //
18+//************************************************************************//
19+#ifndef INCLUDED_CLATOM
20+#define INCLUDED_CLATOM
21+namespace MolDS_base_atoms{
22+class Clatom : virtual public Atom {
23+public:
24+ Clatom(int index);
25+ virtual ~Clatom();
26+protected:
27+ void virtual SetAtomicParameters();
28+private:
29+ Clatom();
30+};
31+}
32+#endif
--- /dev/null
+++ b/src/base/atoms/ghost/GhostClatom.cpp
@@ -0,0 +1,53 @@
1+//************************************************************************//
2+// Copyright (C) 2011-2014 Mikiya Fujii //
3+// //
4+// This file is part of MolDS. //
5+// //
6+// MolDS is free software: you can redistribute it and/or modify //
7+// it under the terms of the GNU General Public License as published by //
8+// the Free Software Foundation, either version 3 of the License, or //
9+// (at your option) any later version. //
10+// //
11+// MolDS is distributed in the hope that it will be useful, //
12+// but WITHOUT ANY WARRANTY; without even the implied warranty of //
13+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the //
14+// GNU General Public License for more details. //
15+// //
16+// You should have received a copy of the GNU General Public License //
17+// along with MolDS. If not, see <http://www.gnu.org/licenses/>. //
18+//************************************************************************//
19+#include<stdio.h>
20+#include<stdlib.h>
21+#include<iostream>
22+#include<sstream>
23+#include<math.h>
24+#include<vector>
25+#include<boost/format.hpp>
26+#include"../../Enums.h"
27+#include"../../Uncopyable.h"
28+#include"../../PrintController.h"
29+#include"../../MolDSException.h"
30+#include"../../MallocerFreer.h"
31+#include"../../../mpi/MpiInt.h"
32+#include"../../../mpi/MpiProcess.h"
33+#include"../../EularAngle.h"
34+#include"../../Parameters.h"
35+#include"../../RealSphericalHarmonicsIndex.h"
36+#include"../Atom.h"
37+#include"../Clatom.h"
38+#include"Ghost.h"
39+#include"GhostClatom.h"
40+using namespace std;
41+using namespace MolDS_base;
42+using namespace MolDS_base_atoms;
43+namespace MolDS_base_atoms_ghost{
44+GhostClatom::GhostClatom(int index) : Atom(index),Clatom(index),Ghost(index){
45+ this->SetAtomicParameters();
46+}
47+
48+GhostClatom::~GhostClatom(){}
49+
50+void GhostClatom::SetAtomicParameters(){
51+ this->atomType = ghostCl;
52+}
53+}
--- /dev/null
+++ b/src/base/atoms/ghost/GhostClatom.h
@@ -0,0 +1,32 @@
1+//************************************************************************//
2+// Copyright (C) 2011-2014 Mikiya Fujii //
3+// //
4+// This file is part of MolDS. //
5+// //
6+// MolDS is free software: you can redistribute it and/or modify //
7+// it under the terms of the GNU General Public License as published by //
8+// the Free Software Foundation, either version 3 of the License, or //
9+// (at your option) any later version. //
10+// //
11+// MolDS is distributed in the hope that it will be useful, //
12+// but WITHOUT ANY WARRANTY; without even the implied warranty of //
13+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the //
14+// GNU General Public License for more details. //
15+// //
16+// You should have received a copy of the GNU General Public License //
17+// along with MolDS. If not, see <http://www.gnu.org/licenses/>. //
18+//************************************************************************//
19+#ifndef INCLUDED_GHOSTCLATOM
20+#define INCLUDED_GHOSTCLATOM
21+namespace MolDS_base_atoms_ghost{
22+class GhostClatom : public MolDS_base_atoms::Clatom, public Ghost {
23+public:
24+ GhostClatom(int index);
25+ ~GhostClatom();
26+protected:
27+ void virtual SetAtomicParameters();
28+private:
29+ GhostClatom();
30+};
31+}
32+#endif
--- a/src/base/factories/AtomFactory.cpp
+++ b/src/base/factories/AtomFactory.cpp
@@ -39,6 +39,7 @@
3939 #include"../atoms/Oatom.h"
4040 #include"../atoms/Fatom.h"
4141 #include"../atoms/Satom.h"
42+#include"../atoms/Clatom.h"
4243 #include"../atoms/Znatom.h"
4344 #include"../atoms/ghost/Ghost.h"
4445 #include"../atoms/ghost/GhostHatom.h"
@@ -48,6 +49,7 @@
4849 #include"../atoms/ghost/GhostOatom.h"
4950 #include"../atoms/ghost/GhostFatom.h"
5051 #include"../atoms/ghost/GhostSatom.h"
52+#include"../atoms/ghost/GhostClatom.h"
5153 #include"../atoms/ghost/GhostZnatom.h"
5254 #include"../atoms/mm/EnvironmentalPointCharge.h"
5355 #include"AtomFactory.h"
@@ -85,6 +87,9 @@ Atom* AtomFactory::Create(AtomType atomType, int index, double x, double y, doub
8587 else if(atomType == S){
8688 atom = new Satom(index);
8789 }
90+ else if(atomType == Cl){
91+ atom = new Clatom(index);
92+ }
8893 else if(atomType == Zn){
8994 atom = new Znatom(index);
9095 }
@@ -109,6 +114,9 @@ Atom* AtomFactory::Create(AtomType atomType, int index, double x, double y, doub
109114 else if(atomType == ghostS){
110115 atom = new GhostSatom(index);
111116 }
117+ else if(atomType == ghostCl){
118+ atom = new GhostClatom(index);
119+ }
112120 else if(atomType == ghostZn){
113121 atom = new GhostZnatom(index);
114122 }
--- a/src/cndo/Cndo2.cpp
+++ b/src/cndo/Cndo2.cpp
@@ -54,6 +54,7 @@
5454 #include"../base/atoms/Oatom.h"
5555 #include"../base/atoms/Fatom.h"
5656 #include"../base/atoms/Satom.h"
57+#include"../base/atoms/Clatom.h"
5758 #include"../base/Molecule.h"
5859 #include"../base/GTOExpansionSTO.h"
5960 #include"../base/loggers/MOLogger.h"
@@ -277,7 +278,7 @@ void Cndo2::SetEnableAtomTypes(){
277278 //this->enableAtomTypes.push_back(Si);
278279 //this->enableAtomTypes.push_back(P);
279280 this->enableAtomTypes.push_back(S);
280- //this->enableAtomTypes.push_back(Cl);
281+ this->enableAtomTypes.push_back(Cl);
281282 }
282283
283284 TheoryType Cndo2::GetTheoryType() const{
--- a/src/mndo/Mndo.cpp
+++ b/src/mndo/Mndo.cpp
@@ -50,6 +50,7 @@
5050 #include"../base/atoms/Oatom.h"
5151 #include"../base/atoms/Fatom.h"
5252 #include"../base/atoms/Satom.h"
53+#include"../base/atoms/Clatom.h"
5354 #include"../base/atoms/mm/EnvironmentalPointCharge.h"
5455 #include"../base/Molecule.h"
5556 #include"../base/ElectronicStructure.h"
@@ -218,6 +219,7 @@ void Mndo::SetEnableAtomTypes(){
218219 this->enableAtomTypes.push_back(O);
219220 this->enableAtomTypes.push_back(F);
220221 this->enableAtomTypes.push_back(S);
222+ this->enableAtomTypes.push_back(Cl);
221223 this->enableAtomTypes.push_back(Zn);
222224 }
223225
--- a/src/pm3/Pm3.cpp
+++ b/src/pm3/Pm3.cpp
@@ -42,6 +42,7 @@
4242 #include"../base/atoms/Oatom.h"
4343 #include"../base/atoms/Fatom.h"
4444 #include"../base/atoms/Satom.h"
45+#include"../base/atoms/Clatom.h"
4546 #include"../base/Molecule.h"
4647 #include"../base/ElectronicStructure.h"
4748 #include"../cndo/Cndo2.h"
@@ -137,6 +138,7 @@ void Pm3::SetEnableAtomTypes(){
137138 this->enableAtomTypes.push_back(O);
138139 this->enableAtomTypes.push_back(F);
139140 this->enableAtomTypes.push_back(S);
141+ this->enableAtomTypes.push_back(Cl);
140142 this->enableAtomTypes.push_back(Zn);
141143 }
142144
--- a/src/pm3/Pm3D.cpp
+++ b/src/pm3/Pm3D.cpp
@@ -42,6 +42,7 @@
4242 #include"../base/atoms/Oatom.h"
4343 #include"../base/atoms/Fatom.h"
4444 #include"../base/atoms/Satom.h"
45+#include"../base/atoms/Clatom.h"
4546 #include"../base/Molecule.h"
4647 #include"../base/ElectronicStructure.h"
4748 #include"../cndo/Cndo2.h"
@@ -138,6 +139,7 @@ void Pm3D::SetEnableAtomTypes(){
138139 this->enableAtomTypes.push_back(O);
139140 this->enableAtomTypes.push_back(F);
140141 this->enableAtomTypes.push_back(S);
142+ this->enableAtomTypes.push_back(Cl);
141143 }
142144
143145
--- /dev/null
+++ b/src/tools/deriveParametersNDDO/data/AM1_Clatom.dat
@@ -0,0 +1,57 @@
1+===== NDDO parameters =====
2+orbital exponent S in [a.u.] = 3.6313760000
3+orbital exponent P in [a.u.] = 2.0767990000
4+Gss in [a.u.] = 0.5523379209
5+Gpp in [a.u.] = 0.4152640390
6+Gsp in [a.u.] = 0.4836172348
7+Gpp2 in [a.u.] = 0.3663878291
8+Hsp in [a.u.] = 0.0889326526
9+Hpp = 0.5*(Gpp - Gpp2)
10+
11+
12+===== NDDO derived parameters =====
13+D1 in [a.u.] = 0.5406286370
14+D2 in [a.u.] = 0.8057207525
15+AM in [a.u.] = 0.5523379209
16+
17+iter=0 AD in [a.u.] = 0.7563751022
18+iter=1 AD in [a.u.] = 0.7702430755
19+iter=2 AD in [a.u.] = 0.7692925963
20+iter=3 AD in [a.u.] = 0.7693007889
21+iter=4 AD in [a.u.] = 0.7693007940
22+iter=5 AD in [a.u.] = 0.7693007940
23+iter=6 AD in [a.u.] = 0.7693007940
24+iter=7 AD in [a.u.] = 0.7693007940
25+iter=8 AD in [a.u.] = 0.7693007940
26+iter=9 AD in [a.u.] = 0.7693007940
27+iter=10 AD in [a.u.] = nan
28+iter=11 AD in [a.u.] = nan
29+iter=12 AD in [a.u.] = nan
30+iter=13 AD in [a.u.] = nan
31+iter=14 AD in [a.u.] = nan
32+iter=15 AD in [a.u.] = nan
33+iter=16 AD in [a.u.] = nan
34+iter=17 AD in [a.u.] = nan
35+iter=18 AD in [a.u.] = nan
36+iter=19 AD in [a.u.] = nan
37+
38+iter=0 AQ in [a.u.] = 0.5455551299
39+iter=1 AQ in [a.u.] = 0.6389388701
40+iter=2 AQ in [a.u.] = 0.6111695696
41+iter=3 AQ in [a.u.] = 0.6132635377
42+iter=4 AQ in [a.u.] = 0.6133249494
43+iter=5 AQ in [a.u.] = 0.6133247965
44+iter=6 AQ in [a.u.] = 0.6133247965
45+iter=7 AQ in [a.u.] = 0.6133247965
46+iter=8 AQ in [a.u.] = 0.6133247965
47+iter=9 AQ in [a.u.] = 0.6133247965
48+iter=10 AQ in [a.u.] = nan
49+iter=11 AQ in [a.u.] = nan
50+iter=12 AQ in [a.u.] = nan
51+iter=13 AQ in [a.u.] = nan
52+iter=14 AQ in [a.u.] = nan
53+iter=15 AQ in [a.u.] = nan
54+iter=16 AQ in [a.u.] = nan
55+iter=17 AQ in [a.u.] = nan
56+iter=18 AQ in [a.u.] = nan
57+iter=19 AQ in [a.u.] = nan
--- /dev/null
+++ b/src/tools/deriveParametersNDDO/data/MNDO_Clatom.dat
@@ -0,0 +1,57 @@
1+===== NDDO parameters =====
2+orbital exponent S in [a.u.] = 3.7846450000
3+orbital exponent P in [a.u.] = 2.0362630000
4+Gss in [a.u.] = 0.5523379209
5+Gpp in [a.u.] = 0.4152640390
6+Gsp in [a.u.] = 0.4836172348
7+Gpp2 in [a.u.] = 0.3663878291
8+Hsp in [a.u.] = 0.0889326526
9+Hpp = 0.5*(Gpp - Gpp2)
10+
11+
12+===== NDDO derived parameters =====
13+D1 in [a.u.] = 0.4986870220
14+D2 in [a.u.] = 0.8217602800
15+AM in [a.u.] = 0.5523379209
16+
17+iter=0 AD in [a.u.] = 0.7949584121
18+iter=1 AD in [a.u.] = 0.8068944037
19+iter=2 AD in [a.u.] = 0.8060962659
20+iter=3 AD in [a.u.] = 0.8061021245
21+iter=4 AD in [a.u.] = 0.8061021276
22+iter=5 AD in [a.u.] = 0.8061021276
23+iter=6 AD in [a.u.] = 0.8061021276
24+iter=7 AD in [a.u.] = 0.8061021276
25+iter=8 AD in [a.u.] = 0.8061021276
26+iter=9 AD in [a.u.] = nan
27+iter=10 AD in [a.u.] = nan
28+iter=11 AD in [a.u.] = nan
29+iter=12 AD in [a.u.] = nan
30+iter=13 AD in [a.u.] = nan
31+iter=14 AD in [a.u.] = nan
32+iter=15 AD in [a.u.] = nan
33+iter=16 AD in [a.u.] = nan
34+iter=17 AD in [a.u.] = nan
35+iter=18 AD in [a.u.] = nan
36+iter=19 AD in [a.u.] = nan
37+
38+iter=0 AQ in [a.u.] = 0.5388047404
39+iter=1 AQ in [a.u.] = 0.6298387670
40+iter=2 AQ in [a.u.] = 0.6032977712
41+iter=3 AQ in [a.u.] = 0.6052759324
42+iter=4 AQ in [a.u.] = 0.6053316466
43+iter=5 AQ in [a.u.] = 0.6053315152
44+iter=6 AQ in [a.u.] = 0.6053315152
45+iter=7 AQ in [a.u.] = 0.6053315152
46+iter=8 AQ in [a.u.] = 0.6053315152
47+iter=9 AQ in [a.u.] = 0.6053315152
48+iter=10 AQ in [a.u.] = 0.6053315152
49+iter=11 AQ in [a.u.] = 0.6053315152
50+iter=12 AQ in [a.u.] = nan
51+iter=13 AQ in [a.u.] = nan
52+iter=14 AQ in [a.u.] = nan
53+iter=15 AQ in [a.u.] = nan
54+iter=16 AQ in [a.u.] = nan
55+iter=17 AQ in [a.u.] = nan
56+iter=18 AQ in [a.u.] = nan
57+iter=19 AQ in [a.u.] = nan
--- /dev/null
+++ b/src/tools/deriveParametersNDDO/data/PM3_Clatom.dat
@@ -0,0 +1,57 @@
1+===== NDDO parameters =====
2+orbital exponent S in [a.u.] = 2.2462100000
3+orbital exponent P in [a.u.] = 2.1510100000
4+Gss in [a.u.] = 0.5884843036
5+Gpp in [a.u.] = 0.2764341047
6+Gsp in [a.u.] = 0.2957604196
7+Gpp2 in [a.u.] = 0.2757703805
8+Hsp in [a.u.] = 0.1279289960
9+Hpp = 0.5*(Gpp - Gpp2)
10+
11+
12+===== NDDO derived parameters =====
13+D1 in [a.u.] = 0.9175855709
14+D2 in [a.u.] = 0.7779229539
15+AM in [a.u.] = 0.5884843036
16+
17+iter=0 AD in [a.u.] = 0.6643695054
18+iter=1 AD in [a.u.] = 0.6828387966
19+iter=2 AD in [a.u.] = 0.6814216153
20+iter=3 AD in [a.u.] = 0.6814322241
21+iter=4 AD in [a.u.] = 0.6814322305
22+iter=5 AD in [a.u.] = 0.6814322305
23+iter=6 AD in [a.u.] = 0.6814322305
24+iter=7 AD in [a.u.] = 0.6814322305
25+iter=8 AD in [a.u.] = 0.6814322305
26+iter=9 AD in [a.u.] = nan
27+iter=10 AD in [a.u.] = nan
28+iter=11 AD in [a.u.] = nan
29+iter=12 AD in [a.u.] = nan
30+iter=13 AD in [a.u.] = nan
31+iter=14 AD in [a.u.] = nan
32+iter=15 AD in [a.u.] = nan
33+iter=16 AD in [a.u.] = nan
34+iter=17 AD in [a.u.] = nan
35+iter=18 AD in [a.u.] = nan
36+iter=19 AD in [a.u.] = nan
37+
38+iter=0 AQ in [a.u.] = 0.1804397695
39+iter=1 AQ in [a.u.] = 0.2159885336
40+iter=2 AQ in [a.u.] = 0.2054423597
41+iter=3 AQ in [a.u.] = 0.2073431403
42+iter=4 AQ in [a.u.] = 0.2074823624
43+iter=5 AQ in [a.u.] = 0.2074800617
44+iter=6 AQ in [a.u.] = 0.2074800643
45+iter=7 AQ in [a.u.] = 0.2074800643
46+iter=8 AQ in [a.u.] = 0.2074800643
47+iter=9 AQ in [a.u.] = 0.2074800643
48+iter=10 AQ in [a.u.] = 0.2074800643
49+iter=11 AQ in [a.u.] = 0.2074800643
50+iter=12 AQ in [a.u.] = 0.2074800643
51+iter=13 AQ in [a.u.] = 0.2074800643
52+iter=14 AQ in [a.u.] = nan
53+iter=15 AQ in [a.u.] = nan
54+iter=16 AQ in [a.u.] = nan
55+iter=17 AQ in [a.u.] = nan
56+iter=18 AQ in [a.u.] = nan
57+iter=19 AQ in [a.u.] = nan
--- a/src/tools/deriveParametersNDDO/deriveParametersNDDO.cpp
+++ b/src/tools/deriveParametersNDDO/deriveParametersNDDO.cpp
@@ -66,18 +66,18 @@ int main(){
6666
6767 // following variables should be set as input
6868 double eV2AU = 0.03674903;
69- long double orbitalExponentS=4.708555;
70- long double orbitalExponentP=2.491178;
71- long double Gss = 10.496667 * eV2AU;
72- long double Gpp = 14.817256 * eV2AU;
73- long double Gsp = 16.073689 * eV2AU;
74- long double Gpp2= 14.418393 * eV2AU;
75- long double Hsp = 0.727763 * eV2AU;
69+ long double orbitalExponentS=2.246210;
70+ long double orbitalExponentP=2.151010;
71+ long double Gss = 16.013601 * eV2AU;
72+ long double Gpp = 7.522215 * eV2AU;
73+ long double Gsp = 8.048115 * eV2AU;
74+ long double Gpp2= 7.504154 * eV2AU;
75+ long double Hsp = 3.481153 * eV2AU;
7676 long double Hpp = 0.5*(Gpp - Gpp2);
7777 // n=2 for l-shell (C, N, O and etc.)
7878 // n=3 for m-shell (S and etc.)
7979 // n=4 for n-shell (Zn and etc.)
80- double n=2;
80+ double n=3;
8181
8282 // following variables are output
8383 long double D1=0.0;
--- a/src/zindo/ZindoS.cpp
+++ b/src/zindo/ZindoS.cpp
@@ -52,6 +52,7 @@
5252 #include"../base/atoms/Oatom.h"
5353 #include"../base/atoms/Fatom.h"
5454 #include"../base/atoms/Satom.h"
55+#include"../base/atoms/Clatom.h"
5556 #include"../base/Molecule.h"
5657 #include"../base/ElectronicStructure.h"
5758 #include"../base/loggers/DensityLogger.h"
@@ -217,6 +218,7 @@ void ZindoS::SetEnableAtomTypes(){
217218 this->enableAtomTypes.push_back(O);
218219 this->enableAtomTypes.push_back(F);
219220 this->enableAtomTypes.push_back(S);
221+ this->enableAtomTypes.push_back(Cl);
220222 }
221223
222224 double ZindoS::GetFockDiagElement(const Atom& atomA,
--- a/test/Test_Of_MolDS.rb
+++ b/test/Test_Of_MolDS.rb
@@ -446,6 +446,20 @@ mklNumThreads = "4"
446446 ompNumThreads = "2"
447447 tester.doesTestMpi(mklNumThreads,ompNumThreads)
448448
449+prefix = "ch3cl_mndo"
450+tester = Tester.new(prefix, <<"TITLE")
451+\t\t\t>>> CH3F <<<
452+TITLE
453+mklNumThreads = "1"
454+ompNumThreads = "1"
455+tester.doesTestOmp(mklNumThreads,ompNumThreads)
456+mklNumThreads = "2"
457+ompNumThreads = "2"
458+tester.doesTestOmp(mklNumThreads,ompNumThreads)
459+mklNumThreads = "4"
460+ompNumThreads = "2"
461+tester.doesTestMpi(mklNumThreads,ompNumThreads)
462+
449463 prefix = "ch4_mndo_directCIS_singlet"
450464 tester = Tester.new(prefix, <<"SECTION", <<"TITLE")
451465 ---------------------------------------------------
@@ -614,6 +628,20 @@ mklNumThreads = "4"
614628 ompNumThreads = "2"
615629 tester.doesTestMpi(mklNumThreads,ompNumThreads)
616630
631+prefix = "ch3cl_am1"
632+tester = Tester.new(prefix, <<"TITLE")
633+\t\t\t>>> CH3F <<<
634+TITLE
635+mklNumThreads = "1"
636+ompNumThreads = "1"
637+tester.doesTestOmp(mklNumThreads,ompNumThreads)
638+mklNumThreads = "2"
639+ompNumThreads = "2"
640+tester.doesTestOmp(mklNumThreads,ompNumThreads)
641+mklNumThreads = "4"
642+ompNumThreads = "2"
643+tester.doesTestMpi(mklNumThreads,ompNumThreads)
644+
617645 prefix = "ch4_am1_directCIS_singlet"
618646 tester = Tester.new(prefix, <<"SECTION", <<"TITLE")
619647 ---------------------------------------------------
@@ -782,6 +810,20 @@ mklNumThreads = "4"
782810 ompNumThreads = "2"
783811 tester.doesTestMpi(mklNumThreads,ompNumThreads)
784812
813+prefix = "ch3cl_pm3"
814+tester = Tester.new(prefix, <<"TITLE")
815+\t\t\t>>> CH3F <<<
816+TITLE
817+mklNumThreads = "1"
818+ompNumThreads = "1"
819+tester.doesTestOmp(mklNumThreads,ompNumThreads)
820+mklNumThreads = "2"
821+ompNumThreads = "2"
822+tester.doesTestOmp(mklNumThreads,ompNumThreads)
823+mklNumThreads = "4"
824+ompNumThreads = "2"
825+tester.doesTestMpi(mklNumThreads,ompNumThreads)
826+
785827 prefix = "ch4_pm3_directCIS_singlet"
786828 tester = Tester.new(prefix, <<"SECTION", <<"TITLE")
787829 ---------------------------------------------------
--- /dev/null
+++ b/test/ch3cl_am1.dat
@@ -0,0 +1,119 @@
1+
2+
3+ >>>>> Welcome to the MolDS world at 2014/4/29(Thu.) 9:29:1 <<<<<
4+
5+
6+********** START: Parse input **********
7+ Total number of atoms: 5
8+ Total number of valence AOs: 11
9+ Total number of valence electrons: 14
10+
11+ | i-th | atom type | x[a.u.] | y[a.u.] | z[a.u.] | | x[angst.] | y[angst.] | z[angst.] |
12+ Atom coordinates: 0 C -4.533892e-01 1.142541e+00 0.000000e+00 -2.399232e-01 6.046065e-01 0.000000e+00
13+ Atom coordinates: 1 H 2.205900e-01 -7.638339e-01 0.000000e+00 1.167312e-01 -4.042035e-01 0.000000e+00
14+ Atom coordinates: 2 H 2.206248e-01 2.095715e+00 -1.650962e+00 1.167496e-01 1.109005e+00 -8.736515e-01
15+ Atom coordinates: 3 H -2.475396e+00 1.142566e+00 0.000000e+00 -1.309923e+00 6.046197e-01 0.000000e+00
16+ Atom coordinates: 4 Cl 3.970023e-01 2.345144e+00 2.082990e+00 2.100846e-01 1.240997e+00 1.102271e+00
17+
18+ | x[a.u.] | y[a.u.] | z[a.u.] | | x[angst.] | y[angst.] | z[angst.] |
19+ Center of Mass: 1.303108e-01 1.967995e+00 1.429743e+00 6.895750e-02 1.041418e+00 7.565872e-01
20+
21+ | x[a.u.] | y[a.u.] | z[a.u.] | | x[angst.] | y[angst.] | z[angst.] |
22+ Center of Core: 1.303422e-01 1.968040e+00 1.429820e+00 6.897414e-02 1.041442e+00 7.566279e-01
23+
24+ SCF conditions:
25+ Max iterations: 500
26+ RMS density: 1.000000e-08
27+ Damping threshold: 1.000000e+00
28+ Damping weight: 0.000000e+00
29+ DIIS number of error vectors: 5
30+ DIIS starting error: 1.000000e-01
31+ DIIS ending error: 0.000000e+00
32+ van der Waals (vdW) correction: no
33+
34+ Memory conditions:
35+ Heap limit: 2.560000e+02[MB]
36+
37+Input terms:
38+theory | am1 | theory_end | scf | max_iter | 500 | rms_density | 1e-8 | damping_thresh | 1.0 |
39+damping_weight | 0.0 | diis_num_error_vect | 5 | diis_start_error | 0.1 | diis_end_error | 0.0 | scf_end | geometry |
40+c | -0.23992322 | 0.60460652 | 0.00000000 | h | 0.11673121 | -0.40420349 | 0.00000000 | h | 0.11674962 |
41+1.10900471 | -0.87365150 | h | -1.30992322 | 0.60461970 | 0.00000000 | cl | 0.21008457 | 1.24099676 | 1.10227059 |
42+geometry_end |
43+
44+********** DONE: Parse input ***********
45+
46+
47+********** START: AM1-SCF **********
48+ | RMS density | DIIS error | DIIS on/off | damping on/off |
49+ SCF iter 0 4.810457e-01 0.000000e+00
50+ SCF iter 1 1.738242e-01 0.000000e+00
51+ SCF iter 2 7.872072e-02 4.744752e-01
52+ SCF iter 3 3.885610e-02 2.490089e-01
53+ SCF iter 4 1.957337e-02 1.355952e-01
54+ SCF iter 5 9.953942e-03 7.092756e-02
55+ SCF iter 6 1.479844e-04 3.691403e-02 on
56+ SCF iter 7 3.888207e-05 4.382503e-04 on
57+ SCF iter 8 6.032490e-06 1.167645e-04 on
58+ SCF iter 9 1.010718e-06 1.456430e-05 on
59+ SCF iter 10 1.435113e-07 3.124439e-06 on
60+ SCF iter 11 2.857086e-08 4.838021e-07 on
61+ SCF iter 12 1.986746e-09 9.056273e-08 on
62+
63+
64+
65+ AM1-SCF met convergence criterion(^^b
66+
67+
68+ | i-th | occ/unocc | e[a.u.] | e[eV] |
69+ Energy of MO: 0 occ -1.537874e+00 -4.184803e+01
70+ Energy of MO: 1 occ -1.094956e+00 -2.979551e+01
71+ Energy of MO: 2 occ -6.357437e-01 -1.729960e+01
72+ Energy of MO: 3 occ -6.357436e-01 -1.729960e+01
73+ Energy of MO: 4 occ -5.802733e-01 -1.579017e+01
74+ Energy of MO: 5 occ -3.850098e-01 -1.047673e+01
75+ Energy of MO: 6 occ -3.850098e-01 -1.047673e+01
76+ Energy of MO: 7 unocc 9.359416e-02 2.546847e+00
77+ Energy of MO: 8 unocc 1.435648e-01 3.906628e+00
78+ Energy of MO: 9 unocc 1.435648e-01 3.906629e+00
79+ Energy of MO: 10 unocc 1.757418e-01 4.782215e+00
80+
81+ | [a.u.] | [eV] |
82+ Electronic energy(SCF): -1.982201e+01 -5.393887e+02
83+ Note that this electronic energy includes core-repulsions.
84+
85+ | [a.u.] | [eV] |
86+ Core repulsion energy: 1.940577e+01 5.280620e+02
87+
88+ | x[a.u.] | y[a.u.] | z[a.u.] | magnitude[a.u.] | | x[debye] | y[debye] | z[debye] | magnitude[debye] |
89+ Total Dipole moment(SCF): 3.137621e+00 4.437065e+00 7.685388e+00 9.412619e+00 7.975040e+00 1.127790e+01 1.953431e+01 2.392450e+01
90+
91+ | x[a.u.] | y[a.u.] | z[a.u.] | magnitude[a.u.] | | x[debye] | y[debye] | z[debye] | magnitude[debye] |
92+ Electronic Dipole moment(SCF): 6.031135e+00 8.529003e+00 1.477290e+01 1.809301e+01 1.532962e+01 2.167857e+01 3.754897e+01 4.598785e+01
93+
94+ | x[a.u.] | y[a.u.] | z[a.u.] | magnitude[a.u.] | | x[debye] | y[debye] | z[debye] | magnitude[debye] |
95+ Core Dipole moment: -2.893513e+00 -4.091938e+00 -7.087510e+00 8.680390e+00 -7.354578e+00 -1.040067e+01 -1.801466e+01 2.206335e+01
96+
97+ | k-th eigenstate | i-th atom | atom type | core charge[a.u.] | Mulliken charge[a.u.]|
98+ Mulliken charge(SCF): 0 0 C 4.000000e+00 -2.610085e-01
99+ Mulliken charge(SCF): 0 1 H 1.000000e+00 6.087615e-02
100+ Mulliken charge(SCF): 0 2 H 1.000000e+00 6.087618e-02
101+ Mulliken charge(SCF): 0 3 H 1.000000e+00 6.087618e-02
102+ Mulliken charge(SCF): 0 4 Cl 7.000000e+00 7.838003e-02
103+
104+ Elapsed time(omp) for the SCF = 0.010509[s].
105+********** DONE: AM1-SCF **********
106+
107+
108+ Summary for memory usage:
109+ Max Heap: 0.121728[MB].
110+ Current Heap(Leaked): 0.000000[MB].
111+
112+
113+ >>>>> The MolDS finished normally! <<<<<
114+ >>>>> CPU time: 0.013024[s]. <<<<<
115+ >>>>> Elapsed time: 0[s]. <<<<<
116+ >>>>> Elapsed time(OMP): 0.011549[s]. <<<<<
117+ >>>>> See you. <<<<<
118+
119+
--- /dev/null
+++ b/test/ch3cl_am1.in
@@ -0,0 +1,22 @@
1+THEORY
2+ am1
3+THEORY_END
4+
5+SCF
6+ max_iter 500
7+ rms_density 1e-8
8+ damping_thresh 1.0
9+ damping_weight 0.0
10+ diis_num_error_vect 5
11+ diis_start_error 0.1
12+ diis_end_error 0.0
13+SCF_END
14+
15+GEOMETRY
16+ C -0.23992322 0.60460652 0.00000000
17+ H 0.11673121 -0.40420349 0.00000000
18+ H 0.11674962 1.10900471 -0.87365150
19+ H -1.30992322 0.60461970 0.00000000
20+ Cl 0.21008457 1.24099676 1.10227059
21+GEOMETRY_END
22+
--- /dev/null
+++ b/test/ch3cl_mndo.dat
@@ -0,0 +1,122 @@
1+
2+
3+ >>>>> Welcome to the MolDS world at 2014/4/29(Thu.) 9:26:2 <<<<<
4+
5+
6+********** START: Parse input **********
7+ Total number of atoms: 5
8+ Total number of valence AOs: 11
9+ Total number of valence electrons: 14
10+
11+ | i-th | atom type | x[a.u.] | y[a.u.] | z[a.u.] | | x[angst.] | y[angst.] | z[angst.] |
12+ Atom coordinates: 0 C -4.533892e-01 1.142541e+00 0.000000e+00 -2.399232e-01 6.046065e-01 0.000000e+00
13+ Atom coordinates: 1 H 2.205900e-01 -7.638339e-01 0.000000e+00 1.167312e-01 -4.042035e-01 0.000000e+00
14+ Atom coordinates: 2 H 2.206248e-01 2.095715e+00 -1.650962e+00 1.167496e-01 1.109005e+00 -8.736515e-01
15+ Atom coordinates: 3 H -2.475396e+00 1.142566e+00 0.000000e+00 -1.309923e+00 6.046197e-01 0.000000e+00
16+ Atom coordinates: 4 Cl 3.970023e-01 2.345144e+00 2.082990e+00 2.100846e-01 1.240997e+00 1.102271e+00
17+
18+ | x[a.u.] | y[a.u.] | z[a.u.] | | x[angst.] | y[angst.] | z[angst.] |
19+ Center of Mass: 1.303108e-01 1.967995e+00 1.429743e+00 6.895750e-02 1.041418e+00 7.565872e-01
20+
21+ | x[a.u.] | y[a.u.] | z[a.u.] | | x[angst.] | y[angst.] | z[angst.] |
22+ Center of Core: 1.303422e-01 1.968040e+00 1.429820e+00 6.897414e-02 1.041442e+00 7.566279e-01
23+
24+ SCF conditions:
25+ Max iterations: 500
26+ RMS density: 1.000000e-08
27+ Damping threshold: 1.000000e+00
28+ Damping weight: 0.000000e+00
29+ DIIS number of error vectors: 5
30+ DIIS starting error: 1.000000e-01
31+ DIIS ending error: 0.000000e+00
32+ van der Waals (vdW) correction: no
33+
34+ Memory conditions:
35+ Heap limit: 2.560000e+02[MB]
36+
37+Input terms:
38+theory | mndo | theory_end | scf | max_iter | 500 | rms_density | 1e-8 | damping_thresh | 1.0 |
39+damping_weight | 0.0 | diis_num_error_vect | 5 | diis_start_error | 0.1 | diis_end_error | 0.0 | scf_end | geometry |
40+c | -0.23992322 | 0.60460652 | 0.00000000 | h | 0.11673121 | -0.40420349 | 0.00000000 | h | 0.11674962 |
41+1.10900471 | -0.87365150 | h | -1.30992322 | 0.60461970 | 0.00000000 | cl | 0.21008457 | 1.24099676 | 1.10227059 |
42+geometry_end |
43+
44+********** DONE: Parse input ***********
45+
46+
47+********** START: MNDO-SCF **********
48+ | RMS density | DIIS error | DIIS on/off | damping on/off |
49+ SCF iter 0 4.810457e-01 0.000000e+00
50+ SCF iter 1 1.825801e-01 0.000000e+00
51+ SCF iter 2 7.938076e-02 4.875171e-01
52+ SCF iter 3 3.734192e-02 2.671957e-01
53+ SCF iter 4 1.812267e-02 1.364507e-01
54+ SCF iter 5 8.958158e-03 6.804228e-02
55+ SCF iter 6 1.366246e-04 3.416201e-02 on
56+ SCF iter 7 3.896990e-05 3.471523e-04 on
57+ SCF iter 8 5.270005e-06 1.021873e-04 on
58+ SCF iter 9 6.214582e-07 1.375857e-05 on
59+ SCF iter 10 2.065808e-07 2.331120e-06 on
60+ SCF iter 11 7.084945e-08 8.615367e-07 on
61+ SCF iter 12 3.357867e-09 3.250586e-07 on
62+
63+
64+
65+ MNDO-SCF met convergence criterion(^^b
66+
67+
68+ | i-th | occ/unocc | e[a.u.] | e[eV] |
69+ Energy of MO: 0 occ -1.340759e+00 -3.648421e+01
70+ Energy of MO: 1 occ -9.391719e-01 -2.555637e+01
71+ Energy of MO: 2 occ -6.517757e-01 -1.773586e+01
72+ Energy of MO: 3 occ -6.517756e-01 -1.773586e+01
73+ Energy of MO: 4 occ -5.912163e-01 -1.608794e+01
74+ Energy of MO: 5 occ -4.204756e-01 -1.144182e+01
75+ Energy of MO: 6 occ -4.204756e-01 -1.144182e+01
76+ Energy of MO: 7 unocc 7.595672e-02 2.066904e+00
77+ Energy of MO: 8 unocc 1.332216e-01 3.625173e+00
78+ Energy of MO: 9 unocc 1.332216e-01 3.625174e+00
79+ Energy of MO: 10 unocc 2.032488e-01 5.530727e+00
80+
81+ | [a.u.] | [eV] |
82+ Electronic energy(SCF): -1.909377e+01 -5.195720e+02
83+ Note that this electronic energy includes core-repulsions.
84+
85+ | [a.u.] | [eV] |
86+ Core repulsion energy: 1.954998e+01 5.319864e+02
87+
88+ | x[a.u.] | y[a.u.] | z[a.u.] | magnitude[a.u.] | | x[debye] | y[debye] | z[debye] | magnitude[debye] |
89+ Total Dipole moment(SCF): 2.982128e+00 4.217151e+00 7.304503e+00 8.946128e+00 7.579814e+00 1.071893e+01 1.856620e+01 2.273879e+01
90+
91+ | x[a.u.] | y[a.u.] | z[a.u.] | magnitude[a.u.] | | x[debye] | y[debye] | z[debye] | magnitude[debye] |
92+ Electronic Dipole moment(SCF): 5.875641e+00 8.309089e+00 1.439201e+01 1.762652e+01 1.493439e+01 2.111960e+01 3.658085e+01 4.480215e+01
93+
94+ | x[a.u.] | y[a.u.] | z[a.u.] | magnitude[a.u.] | | x[debye] | y[debye] | z[debye] | magnitude[debye] |
95+ Core Dipole moment: -2.893513e+00 -4.091938e+00 -7.087510e+00 8.680390e+00 -7.354578e+00 -1.040067e+01 -1.801466e+01 2.206335e+01
96+
97+ | k-th eigenstate | i-th atom | atom type | core charge[a.u.] | Mulliken charge[a.u.]|
98+ Mulliken charge(SCF): 0 0 C 4.000000e+00 -6.733750e-03
99+ Mulliken charge(SCF): 0 1 H 1.000000e+00 -1.043201e-02
100+ Mulliken charge(SCF): 0 2 H 1.000000e+00 -1.043197e-02
101+ Mulliken charge(SCF): 0 3 H 1.000000e+00 -1.043197e-02
102+ Mulliken charge(SCF): 0 4 Cl 7.000000e+00 3.802969e-02
103+
104+ | [a.u.] | [Kcal/mol] |
105+ Heats of formation: 1.922293e-01 1.206257e+02
106+
107+ Elapsed time(omp) for the SCF = 0.010490[s].
108+********** DONE: MNDO-SCF **********
109+
110+
111+ Summary for memory usage:
112+ Max Heap: 0.121728[MB].
113+ Current Heap(Leaked): 0.000000[MB].
114+
115+
116+ >>>>> The MolDS finished normally! <<<<<
117+ >>>>> CPU time: 0.012911[s]. <<<<<
118+ >>>>> Elapsed time: 0[s]. <<<<<
119+ >>>>> Elapsed time(OMP): 0.0115039[s]. <<<<<
120+ >>>>> See you. <<<<<
121+
122+
--- /dev/null
+++ b/test/ch3cl_mndo.in
@@ -0,0 +1,22 @@
1+THEORY
2+ mndo
3+THEORY_END
4+
5+SCF
6+ max_iter 500
7+ rms_density 1e-8
8+ damping_thresh 1.0
9+ damping_weight 0.0
10+ diis_num_error_vect 5
11+ diis_start_error 0.1
12+ diis_end_error 0.0
13+SCF_END
14+
15+GEOMETRY
16+ C -0.23992322 0.60460652 0.00000000
17+ H 0.11673121 -0.40420349 0.00000000
18+ H 0.11674962 1.10900471 -0.87365150
19+ H -1.30992322 0.60461970 0.00000000
20+ Cl 0.21008457 1.24099676 1.10227059
21+GEOMETRY_END
22+
--- /dev/null
+++ b/test/ch3cl_pm3.dat
@@ -0,0 +1,119 @@
1+
2+
3+ >>>>> Welcome to the MolDS world at 2014/4/29(Thu.) 9:30:58 <<<<<
4+
5+
6+********** START: Parse input **********
7+ Total number of atoms: 5
8+ Total number of valence AOs: 11
9+ Total number of valence electrons: 14
10+
11+ | i-th | atom type | x[a.u.] | y[a.u.] | z[a.u.] | | x[angst.] | y[angst.] | z[angst.] |
12+ Atom coordinates: 0 C -4.533892e-01 1.142541e+00 0.000000e+00 -2.399232e-01 6.046065e-01 0.000000e+00
13+ Atom coordinates: 1 H 2.205900e-01 -7.638339e-01 0.000000e+00 1.167312e-01 -4.042035e-01 0.000000e+00
14+ Atom coordinates: 2 H 2.206248e-01 2.095715e+00 -1.650962e+00 1.167496e-01 1.109005e+00 -8.736515e-01
15+ Atom coordinates: 3 H -2.475396e+00 1.142566e+00 0.000000e+00 -1.309923e+00 6.046197e-01 0.000000e+00
16+ Atom coordinates: 4 Cl 3.970023e-01 2.345144e+00 2.082990e+00 2.100846e-01 1.240997e+00 1.102271e+00
17+
18+ | x[a.u.] | y[a.u.] | z[a.u.] | | x[angst.] | y[angst.] | z[angst.] |
19+ Center of Mass: 1.303108e-01 1.967995e+00 1.429743e+00 6.895750e-02 1.041418e+00 7.565872e-01
20+
21+ | x[a.u.] | y[a.u.] | z[a.u.] | | x[angst.] | y[angst.] | z[angst.] |
22+ Center of Core: 1.303422e-01 1.968040e+00 1.429820e+00 6.897414e-02 1.041442e+00 7.566279e-01
23+
24+ SCF conditions:
25+ Max iterations: 500
26+ RMS density: 1.000000e-08
27+ Damping threshold: 1.000000e+00
28+ Damping weight: 0.000000e+00
29+ DIIS number of error vectors: 5
30+ DIIS starting error: 1.000000e-01
31+ DIIS ending error: 0.000000e+00
32+ van der Waals (vdW) correction: no
33+
34+ Memory conditions:
35+ Heap limit: 2.560000e+02[MB]
36+
37+Input terms:
38+theory | pm3 | theory_end | scf | max_iter | 500 | rms_density | 1e-8 | damping_thresh | 1.0 |
39+damping_weight | 0.0 | diis_num_error_vect | 5 | diis_start_error | 0.1 | diis_end_error | 0.0 | scf_end | geometry |
40+c | -0.23992322 | 0.60460652 | 0.00000000 | h | 0.11673121 | -0.40420349 | 0.00000000 | h | 0.11674962 |
41+1.10900471 | -0.87365150 | h | -1.30992322 | 0.60461970 | 0.00000000 | cl | 0.21008457 | 1.24099676 | 1.10227059 |
42+geometry_end |
43+
44+********** DONE: Parse input ***********
45+
46+
47+********** START: PM3-SCF **********
48+ | RMS density | DIIS error | DIIS on/off | damping on/off |
49+ SCF iter 0 4.810457e-01 0.000000e+00
50+ SCF iter 1 1.468445e-01 0.000000e+00
51+ SCF iter 2 7.503743e-02 4.413842e-01
52+ SCF iter 3 4.120484e-02 2.487902e-01
53+ SCF iter 4 2.322768e-02 1.514025e-01
54+ SCF iter 5 1.328984e-02 8.816348e-02
55+ SCF iter 6 3.448365e-04 5.094567e-02 on
56+ SCF iter 7 1.123647e-04 1.569942e-03 on
57+ SCF iter 8 2.553334e-05 5.406476e-04 on
58+ SCF iter 9 4.991694e-06 8.201483e-05 on
59+ SCF iter 10 7.718991e-07 1.442922e-05 on
60+ SCF iter 11 2.274014e-07 2.998766e-06 on
61+ SCF iter 12 6.387016e-09 7.548579e-07 on
62+
63+
64+
65+ PM3-SCF met convergence criterion(^^b
66+
67+
68+ | i-th | occ/unocc | e[a.u.] | e[eV] |
69+ Energy of MO: 0 occ -2.193818e+00 -5.969730e+01
70+ Energy of MO: 1 occ -9.950472e-01 -2.707683e+01
71+ Energy of MO: 2 occ -5.978260e-01 -1.626780e+01
72+ Energy of MO: 3 occ -5.978260e-01 -1.626780e+01
73+ Energy of MO: 4 occ -5.493675e-01 -1.494917e+01
74+ Energy of MO: 5 occ -3.675673e-01 -1.000210e+01
75+ Energy of MO: 6 occ -3.675673e-01 -1.000209e+01
76+ Energy of MO: 7 unocc 1.147239e-01 3.121821e+00
77+ Energy of MO: 8 unocc 1.374315e-01 3.739731e+00
78+ Energy of MO: 9 unocc 1.374315e-01 3.739731e+00
79+ Energy of MO: 10 unocc 1.590000e-01 4.326644e+00
80+
81+ | [a.u.] | [eV] |
82+ Electronic energy(SCF): -1.756638e+01 -4.780093e+02
83+ Note that this electronic energy includes core-repulsions.
84+
85+ | [a.u.] | [eV] |
86+ Core repulsion energy: 1.939545e+01 5.277812e+02
87+
88+ | x[a.u.] | y[a.u.] | z[a.u.] | magnitude[a.u.] | | x[debye] | y[debye] | z[debye] | magnitude[debye] |
89+ Total Dipole moment(SCF): 3.011728e+00 4.259132e+00 7.377081e+00 9.035045e+00 7.655050e+00 1.082564e+01 1.875067e+01 2.296480e+01
90+
91+ | x[a.u.] | y[a.u.] | z[a.u.] | magnitude[a.u.] | | x[debye] | y[debye] | z[debye] | magnitude[debye] |
92+ Electronic Dipole moment(SCF): 5.905241e+00 8.351070e+00 1.446459e+01 1.771543e+01 1.500963e+01 2.122631e+01 3.676533e+01 4.502815e+01
93+
94+ | x[a.u.] | y[a.u.] | z[a.u.] | magnitude[a.u.] | | x[debye] | y[debye] | z[debye] | magnitude[debye] |
95+ Core Dipole moment: -2.893513e+00 -4.091938e+00 -7.087510e+00 8.680390e+00 -7.354578e+00 -1.040067e+01 -1.801466e+01 2.206335e+01
96+
97+ | k-th eigenstate | i-th atom | atom type | core charge[a.u.] | Mulliken charge[a.u.]|
98+ Mulliken charge(SCF): 0 0 C 4.000000e+00 4.531892e-02
99+ Mulliken charge(SCF): 0 1 H 1.000000e+00 -9.692291e-03
100+ Mulliken charge(SCF): 0 2 H 1.000000e+00 -9.692245e-03
101+ Mulliken charge(SCF): 0 3 H 1.000000e+00 -9.692244e-03
102+ Mulliken charge(SCF): 0 4 Cl 7.000000e+00 -1.624214e-02
103+
104+ Elapsed time(omp) for the SCF = 0.010730[s].
105+********** DONE: PM3-SCF **********
106+
107+
108+ Summary for memory usage:
109+ Max Heap: 0.121728[MB].
110+ Current Heap(Leaked): 0.000000[MB].
111+
112+
113+ >>>>> The MolDS finished normally! <<<<<
114+ >>>>> CPU time: 0.013263[s]. <<<<<
115+ >>>>> Elapsed time: 0[s]. <<<<<
116+ >>>>> Elapsed time(OMP): 0.011847[s]. <<<<<
117+ >>>>> See you. <<<<<
118+
119+
--- /dev/null
+++ b/test/ch3cl_pm3.in
@@ -0,0 +1,22 @@
1+THEORY
2+ pm3
3+THEORY_END
4+
5+SCF
6+ max_iter 500
7+ rms_density 1e-8
8+ damping_thresh 1.0
9+ damping_weight 0.0
10+ diis_num_error_vect 5
11+ diis_start_error 0.1
12+ diis_end_error 0.0
13+SCF_END
14+
15+GEOMETRY
16+ C -0.23992322 0.60460652 0.00000000
17+ H 0.11673121 -0.40420349 0.00000000
18+ H 0.11674962 1.10900471 -0.87365150
19+ H -1.30992322 0.60461970 0.00000000
20+ Cl 0.21008457 1.24099676 1.10227059
21+GEOMETRY_END
22+