Commit: 9b831ac5c4801a84cf241b3696443b774f6c442a - MolDS (git)

Commit MetaInfo

• Révision: 9b831ac5c4801a84cf241b3696443b774f6c442a (tree)
• l'heure: 2014-01-04 19:14:15
• Auteur: Mikiya Fujii <mikiya.fujii@gmai...>
• Commiter: Mikiya Fujii

Message de Log

Bq is renamed to Ghost. #32750

git-svn-id: https://svn.sourceforge.jp/svnroot/molds/trunk@1611 1136aad2-a195-0410-b898-f5ea1d11b9d8

Change Summary

• modified: src/Makefile
• modified: src/Makefile_GNU
• modified: src/base/Enums.h
• modified: src/base/InputParser.cpp
• modified: src/base/Molecule.cpp
• modified: src/base/Molecule.h
• delete: src/base/atoms/bq/BqNatom.h
• delete: src/base/atoms/bq/BqOatom.h
• delete: src/base/atoms/bq/BqSatom.h
• add: src/base/atoms/ghost/GhostLiatom.h
• add: src/base/atoms/ghost/GhostOatom.h
• add: src/base/atoms/ghost/GhostSatom.h
• delete: src/base/atoms/{bq/Bq.cpp => ghost/Ghost.cpp}
• delete: src/base/atoms/{bq/Bq.h => ghost/Ghost.h}
• delete: src/base/atoms/{bq/BqCatom.cpp => ghost/GhostCatom.cpp}
• delete: src/base/atoms/{bq/BqCatom.h => ghost/GhostNatom.h}
• delete: src/base/atoms/{bq/BqHatom.cpp => ghost/GhostHatom.cpp}
• delete: src/base/atoms/{bq/BqHatom.h => ghost/GhostCatom.h}
• delete: src/base/atoms/{bq/BqLiatom.cpp => ghost/GhostLiatom.cpp}
• delete: src/base/atoms/{bq/BqLiatom.h => ghost/GhostHatom.h}
• delete: src/base/atoms/{bq/BqNatom.cpp => ghost/GhostNatom.cpp}
• delete: src/base/atoms/{bq/BqOatom.cpp => ghost/GhostOatom.cpp}
• delete: src/base/atoms/{bq/BqSatom.cpp => ghost/GhostSatom.cpp}
• modified: src/base/factories/AtomFactory.cpp

Modification

--- a/src/Makefile
+++ b/src/Makefile
@@ -38,9 +38,9 @@ DEPFILE = obj/objfile.dep
 LDFLAGS = -Wl,-rpath=$(BOOST_LIB_DIR)
 THIS_MAKEFILE := $(word $(words $(MAKEFILE_LIST)),$(MAKEFILE_LIST))
 
-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/bq/Bq.cpp base/atoms/bq/BqHatom.cpp base/atoms/bq/BqLiatom.cpp base/atoms/bq/BqCatom.cpp base/atoms/bq/BqNatom.cpp base/atoms/bq/BqOatom.cpp base/atoms/bq/BqSatom.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
-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/bq/Bq.h   base/atoms/bq/BqHatom.h   base/atoms/bq/BqLiatom.h   base/atoms/bq/BqCatom.h   base/atoms/bq/BqNatom.h   base/atoms/bq/BqOatom.h   base/atoms/bq/BqSatom.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
-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/Bq.o             obj/BqHatom.o             obj/BqLiatom.o             obj/BqCatom.o             obj/BqNatom.o             obj/BqOatom.o             obj/BqSatom.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
+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/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/GhostSatom.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
+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/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/GhostSatom.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
+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/Ghost.o             obj/GhostHatom.o             obj/GhostLiatom.o             obj/GhostCatom.o             obj/GhostNatom.o             obj/GhostOatom.o             obj/GhostSatom.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
 
 $(EXENAME): $(DEPFILE) $(ALL_OBJ_FILES)
 	$(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
 LDFLAGS = -Wl,-rpath=$(BOOST_LIB_DIR) -Wl,-rpath=$(OPENBLAS_LIB_DIR)
 THIS_MAKEFILE := $(word $(words $(MAKEFILE_LIST)),$(MAKEFILE_LIST))
 
-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/Satom.cpp base/atoms/bq/Bq.cpp base/atoms/bq/BqHatom.cpp base/atoms/bq/BqLiatom.cpp base/atoms/bq/BqCatom.cpp base/atoms/bq/BqNatom.cpp base/atoms/bq/BqOatom.cpp base/atoms/bq/BqSatom.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
-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/Satom.h   base/atoms/bq/Bq.h   base/atoms/bq/BqHatom.h   base/atoms/bq/BqLiatom.h   base/atoms/bq/BqCatom.h   base/atoms/bq/BqNatom.h   base/atoms/bq/BqOatom.h   base/atoms/bq/BqSatom.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
-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/Satom.o             obj/Bq.o             obj/BqHatom.o             obj/BqLiatom.o             obj/BqCatom.o             obj/BqNatom.o             obj/BqOatom.o             obj/BqSatom.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
+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/Satom.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/GhostSatom.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
+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/Satom.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/GhostSatom.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
+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/Satom.o             obj/Ghost.o             obj/GhostHatom.o             obj/GhostLiatom.o             obj/GhostCatom.o             obj/GhostNatom.o             obj/GhostOatom.o             obj/GhostSatom.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
 
 $(EXENAME): $(DEPFILE) $(ALL_OBJ_FILES)
 	$(CC) -o $@ $(LDFLAGS) $(ALL_OBJ_FILES) -L$(BOOST_LIB_DIR) -L$(OPENBLAS_LIB_DIR) $(LIBS)

--- a/src/base/Enums.h
+++ b/src/base/Enums.h
@@ -125,24 +125,24 @@ RENUMSTR_BEGIN( AtomType, AtomTypeStr )
    RENUMSTR( S,    "S" )
    RENUMSTR( Cl,   "Cl" )
    RENUMSTR( Ar,   "Ar" )
-   RENUMSTR( bqH,  "ghost-H" )
-   RENUMSTR( bqHe, "ghost-He" )
-   RENUMSTR( bqLi, "ghost-Li" )
-   RENUMSTR( bqBe, "ghost-Be" )
-   RENUMSTR( bqB,  "ghost-B" )
-   RENUMSTR( bqC,  "ghost-C" )
-   RENUMSTR( bqN,  "ghost-N" )
-   RENUMSTR( bqO,  "ghost-O" )
-   RENUMSTR( bqF,  "ghost-F" )
-   RENUMSTR( bqNe, "ghost-Ne" )
-   RENUMSTR( bqNa, "ghost-Na" )
-   RENUMSTR( bqMg, "ghost-Mg" )
-   RENUMSTR( bqAl, "ghost-Al" )
-   RENUMSTR( bqSi, "ghost-Si" )
-   RENUMSTR( bqP,  "ghost-P" )
-   RENUMSTR( bqS,  "ghost-S" )
-   RENUMSTR( bqCl, "ghost-Cl" )
-   RENUMSTR( bqAr, "ghost-Ar" )
+   RENUMSTR( ghostH,  "ghost-H" )
+   RENUMSTR( ghostHe, "ghost-He" )
+   RENUMSTR( ghostLi, "ghost-Li" )
+   RENUMSTR( ghostBe, "ghost-Be" )
+   RENUMSTR( ghostB,  "ghost-B" )
+   RENUMSTR( ghostC,  "ghost-C" )
+   RENUMSTR( ghostN,  "ghost-N" )
+   RENUMSTR( ghostO,  "ghost-O" )
+   RENUMSTR( ghostF,  "ghost-F" )
+   RENUMSTR( ghostNe, "ghost-Ne" )
+   RENUMSTR( ghostNa, "ghost-Na" )
+   RENUMSTR( ghostMg, "ghost-Mg" )
+   RENUMSTR( ghostAl, "ghost-Al" )
+   RENUMSTR( ghostSi, "ghost-Si" )
+   RENUMSTR( ghostP,  "ghost-P" )
+   RENUMSTR( ghostS,  "ghost-S" )
+   RENUMSTR( ghostCl, "ghost-Cl" )
+   RENUMSTR( ghostAr, "ghost-Ar" )
    RENUMSTR( EPC,  "Environmental Point Charge" )
    RENUMSTR( AtomType_end,  "AtomType_end" )
 RENUMSTR_END()

--- a/src/base/InputParser.cpp
+++ b/src/base/InputParser.cpp
@@ -40,12 +40,6 @@
 #include"Parameters.h"
 #include"RealSphericalHarmonicsIndex.h"
 #include"atoms/Atom.h"
-#include"atoms/Hatom.h"
-#include"atoms/Liatom.h"
-#include"atoms/Catom.h"
-#include"atoms/Natom.h"
-#include"atoms/Oatom.h"
-#include"atoms/Satom.h"
 #include"factories/AtomFactory.h"
 #include"Molecule.h"
 #include"InputParser.h"
@@ -250,7 +244,7 @@ void InputParser::SetMessages(){
    this->stringGeometry    = "geometry";
    this->stringGeometryEnd = "geometry_end";
 
-   // Ghost (bq) atoms
+   // Ghost (ghost) atoms
    this->stringGhost       = "ghost";
    this->stringGhostEnd    = "ghost_end";
 
@@ -491,7 +485,7 @@ int InputParser::ParseMolecularConfiguration(Molecule* molecule, vector<string>*
       else if((*inputTerms)[parseIndex] == "s"){
          atomType = S;
       }
-      int index = molecule->GetRealAtomVect().size() + molecule->GetBqAtomVect().size();
+      int index = molecule->GetRealAtomVect().size() + molecule->GetGhostAtomVect().size();
       Atom* atom = AtomFactory::Create(atomType, index, x, y, z);
       molecule->AddRealAtom(atom);
       parseIndex += 4;
@@ -507,26 +501,26 @@ int InputParser::ParseGhostsConfiguration(Molecule* molecule, vector<string>* in
       double z = atof((*inputTerms)[parseIndex+3].c_str()) * Parameters::GetInstance()->GetAngstrom2AU();
       AtomType atomType = H;
       if((*inputTerms)[parseIndex] == "h"){
-        atomType = bqH;
+        atomType = ghostH;
       }
       else if((*inputTerms)[parseIndex] == "li"){
-         atomType = bqLi;
+         atomType = ghostLi;
       }
       else if((*inputTerms)[parseIndex] == "c"){
-         atomType = bqC;
+         atomType = ghostC;
       }
       else if((*inputTerms)[parseIndex] == "n"){
-         atomType = bqN;
+         atomType = ghostN;
       }
       else if((*inputTerms)[parseIndex] == "o"){
-         atomType = bqO;
+         atomType = ghostO;
       }
       else if((*inputTerms)[parseIndex] == "s"){
-         atomType = bqS;
+         atomType = ghostS;
       }
-      int index = molecule->GetRealAtomVect().size() + molecule->GetBqAtomVect().size();
+      int index = molecule->GetRealAtomVect().size() + molecule->GetGhostAtomVect().size();
       Atom* atom = AtomFactory::Create(atomType, index, x, y, z);
-      molecule->AddBqAtom(atom);
+      molecule->AddGhostAtom(atom);
       parseIndex += 4;
    }
    return parseIndex;
@@ -1233,7 +1227,7 @@ void InputParser::Parse(Molecule* molecule, int argc, char *argv[]) const{
          i = this->ParseMolecularConfiguration(molecule, &inputTerms, i);
       }
 
-      // ghost atom (bq) configuration
+      // ghost atom configuration
       if(inputTerms[i].compare(this->stringGhost) == 0){
          i = this->ParseGhostsConfiguration(molecule, &inputTerms, i);
       }

--- a/src/base/Molecule.cpp
+++ b/src/base/Molecule.cpp
@@ -63,12 +63,12 @@ Molecule& Molecule::operator=(const Molecule& rhs){
    double** oldDistanceAtomsEpcs = this->distanceAtomsEpcs;
    vector<Atom*>* oldAtomVect     = this->atomVect;
    vector<Atom*>* oldRealAtomVect = this->realAtomVect;
-   vector<Atom*>* oldBqAtomVect   = this->bqAtomVect;
+   vector<Atom*>* oldGhostAtomVect= this->ghostAtomVect;
    vector<Atom*>* oldEpcVect      = this->epcVect;
    this->CopyInitialize(rhs);
    this->Finalize(&oldAtomVect, 
                   &oldRealAtomVect, 
-                  &oldBqAtomVect, 
+                  &oldGhostAtomVect, 
                   &oldEpcVect, 
                   &oldXyzCOM, 
                   &oldXyzCOC, 
@@ -81,7 +81,7 @@ Molecule& Molecule::operator=(const Molecule& rhs){
 Molecule::~Molecule(){
    this->Finalize(&this->atomVect, 
                   &this->realAtomVect, 
-                  &this->bqAtomVect, 
+                  &this->ghostAtomVect, 
                   &this->epcVect, 
                   &this->xyzCOM, 
                   &this->xyzCOC, 
@@ -115,11 +115,11 @@ void Molecule::CopyInitialize(const Molecule& rhs){
          (*this->realAtomVect)[i]->SetFirstAOIndex(atom->GetFirstAOIndex());
       }
    }
-   if(rhs.bqAtomVect != NULL){
-      int bqAtomNum = rhs.bqAtomVect->size();
-      for(int i=0; i<bqAtomNum; i++){
-         Atom* atom = (*rhs.bqAtomVect)[i];
-         this->bqAtomVect->push_back(AtomFactory::Create(atom->GetAtomType(),
+   if(rhs.ghostAtomVect != NULL){
+      int ghostAtomNum = rhs.ghostAtomVect->size();
+      for(int i=0; i<ghostAtomNum; i++){
+         Atom* atom = (*rhs.ghostAtomVect)[i];
+         this->ghostAtomVect->push_back(AtomFactory::Create(atom->GetAtomType(),
                                                          atom->GetIndex(),
                                                          atom->GetXyz()[XAxis],
                                                          atom->GetXyz()[YAxis],
@@ -131,7 +131,7 @@ void Molecule::CopyInitialize(const Molecule& rhs){
       }
    }
    if(rhs.atomVect != NULL){
-      this->CopyRealBqAtom2Atom();
+      this->CopyRealGhostAtom2Atom();
       int atomNum = this->atomVect->size();
       MallocerFreer::GetInstance()->Malloc<double>(&this->distanceAtoms, atomNum, atomNum);
       for(int i=0; i<atomNum; i++){
@@ -184,12 +184,12 @@ void Molecule::Initialize(){
    this->distanceAtomsEpcs  = NULL;
    this->atomVect           = NULL;
    this->realAtomVect       = NULL;
-   this->bqAtomVect         = NULL;
+   this->ghostAtomVect         = NULL;
    this->epcVect            = NULL;
    try{
       this->atomVect     = new vector<Atom*>;
       this->realAtomVect = new vector<Atom*>;
-      this->bqAtomVect   = new vector<Atom*>;
+      this->ghostAtomVect= new vector<Atom*>;
       this->epcVect      = new vector<Atom*>;
       MallocerFreer::GetInstance()->Malloc<double>(&this->xyzCOM, CartesianType_end);
       MallocerFreer::GetInstance()->Malloc<double>(&this->xyzCOC, CartesianType_end);
@@ -197,7 +197,7 @@ void Molecule::Initialize(){
    catch(exception ex){
       this->Finalize(&this->atomVect, 
                      &this->realAtomVect, 
-                     &this->bqAtomVect, 
+                     &this->ghostAtomVect, 
                      &this->epcVect, 
                      &this->xyzCOM, 
                      &this->xyzCOC, 
@@ -210,7 +210,7 @@ void Molecule::Initialize(){
 
 void Molecule::Finalize(vector<Atom*>** atomVect, 
                         vector<Atom*>** realAtomVect, 
-                        vector<Atom*>** bqAtomVect, 
+                        vector<Atom*>** ghostAtomVect, 
                         vector<Atom*>** epcVect, 
                         double** xyzCOM, 
                         double** xyzCOC, 
@@ -246,18 +246,18 @@ void Molecule::Finalize(vector<Atom*>** atomVect,
       *realAtomVect = NULL;
       //this->OutputLog("realAtomVect deleted\n");
    }
-   if(*bqAtomVect != NULL){
-      int bqAtomNum = (*bqAtomVect)->size();
-      for(int i=0; i<bqAtomNum; i++){
-         if((**bqAtomVect)[i] != NULL){
-            delete (**bqAtomVect)[i];
-            (**bqAtomVect)[i] = NULL;
+   if(*ghostAtomVect != NULL){
+      int ghostAtomNum = (*ghostAtomVect)->size();
+      for(int i=0; i<ghostAtomNum; i++){
+         if((**ghostAtomVect)[i] != NULL){
+            delete (**ghostAtomVect)[i];
+            (**ghostAtomVect)[i] = NULL;
          }
       }
-      (*bqAtomVect)->clear();
-      delete *bqAtomVect;
-      *bqAtomVect = NULL;
-      //this->OutputLog("bqAtomVect deleted\n");
+      (*ghostAtomVect)->clear();
+      delete *ghostAtomVect;
+      *ghostAtomVect = NULL;
+      //this->OutputLog("ghostAtomVect deleted\n");
    }
    if(*epcVect != NULL){
       epcNum = (*epcVect)->size();
@@ -278,13 +278,13 @@ void Molecule::Finalize(vector<Atom*>** atomVect,
 void Molecule::SetMessages(){
    this->errorMessageGetAtomVectNull  = "Error in base::Molecule::GetAtomVect: atomVect is NULL.\n";
    this->errorMessageGetRealAtomVectNull  = "Error in base::Molecule::GetRealAtomVect: realAtomVect is NULL.\n";
-   this->errorMessageGetBqAtomVectNull  = "Error in base::Molecule::GetBqAtomVect: bqAtomVect is NULL.\n";
+   this->errorMessageGetGhostAtomVectNull  = "Error in base::Molecule::GetGhostAtomVect: ghostAtomVect is NULL.\n";
    this->errorMessageGetEPCVectNull  = "Error in base::Molecule::GetEpcVect: epcVect is NULL.\n";
    this->errorMessageAddAtomNull = "Error in base::Molecule::AddAtom: atomVect is NULL.\n";
    this->errorMessageAddRealAtomNull = "Error in base::Molecule::AddAtom: realAtomVect is NULL.\n";
-   this->errorMessageAddBqAtomNull = "Error in base::Molecule::AddAtom: bqAtomVect is NULL.\n";
+   this->errorMessageAddGhostAtomNull = "Error in base::Molecule::AddAtom: ghostAtomVect is NULL.\n";
    this->errorMessageAddEPCNull  = "Error in base::Molecule::AddEnviromentalPointCharge: epcVect is NULL.\n";
-   this->errorMessageCopyRealBqAtom2AtomNotEmpty = "Error in base::Molecule::CopyRealBqAtom2Atom: atomVect is not empty.\n";
+   this->errorMessageCopyRealGhostAtom2AtomNotEmpty = "Error in base::Molecule::CopyRealGhostAtom2Atom: atomVect is not empty.\n";
    this->errorMessageGetXyzCOMNull = "Error in base::Molecule::GetXyzCOM: xyzCOM is NULL.\n";
    this->errorMessageGetXyzCOCNull = "Error in base::Molecule::GetXyzCOC: xyzCOC is NULL.\n";
    this->errorMessageCalcXyzCOMNull = "Error in base::Molecule::CalcXyzCOM: xyzCOM is NULL.\n";
@@ -339,11 +339,11 @@ void Molecule::AddRealAtom(Atom* atom){
    this->realAtomVect->push_back(atom);
 }
 
-void Molecule::AddBqAtom(Atom* atom){
+void Molecule::AddGhostAtom(Atom* atom){
 #ifdef MOLDS_DBG
-   if(this->bqAtomVect==NULL) throw MolDSException(this->errorMessageAddBqAtomNull);
+   if(this->ghostAtomVect==NULL) throw MolDSException(this->errorMessageAddGhostAtomNull);
 #endif
-   this->bqAtomVect->push_back(atom);
+   this->ghostAtomVect->push_back(atom);
 }
 
 void Molecule::AddEpc(Atom* epc){
@@ -475,7 +475,7 @@ void Molecule::CalcDistanceAtomsEpcs(){
 }
 
 void Molecule::CalcBasics(){
-   this->CopyRealBqAtom2Atom();
+   this->CopyRealGhostAtom2Atom();
    this->CalcTotalNumberAOs();
    this->CalcTotalNumberValenceElectrons();
    this->CalcTotalCoreMass();
@@ -490,23 +490,23 @@ void Molecule::CalcBasicsConfiguration(){
    this->CalcDistanceAtomsEpcs();
 }
 
-void Molecule::CopyRealBqAtom2Atom(){
+void Molecule::CopyRealGhostAtom2Atom(){
    if(!this->atomVect->empty()){
-      throw MolDSException(this->errorMessageCopyRealBqAtom2AtomNotEmpty);
+      throw MolDSException(this->errorMessageCopyRealGhostAtom2AtomNotEmpty);
    }
    int realAtomNum = this->realAtomVect->size();
-   int bqAtomNum   = this->bqAtomVect->size();
+   int ghostAtomNum   = this->ghostAtomVect->size();
    for(int i=0; i<realAtomNum; i++){
       Atom* atom = (*this->realAtomVect)[i];
       this->atomVect->push_back(atom);
    }
-   for(int i=0; i<bqAtomNum; i++){
-      Atom* atom = (*this->bqAtomVect)[i];
+   for(int i=0; i<ghostAtomNum; i++){
+      Atom* atom = (*this->ghostAtomVect)[i];
       this->atomVect->push_back(atom);
    }
-   std::sort(this->realAtomVect->begin(), this->realAtomVect->end(), MolDS_base_atoms::LessAtomIndex());
-   std::sort(this->bqAtomVect->begin(),   this->bqAtomVect->end(),   MolDS_base_atoms::LessAtomIndex());
-   std::sort(this->atomVect->begin(),     this->atomVect->end(),     MolDS_base_atoms::LessAtomIndex());
+   std::sort(this->realAtomVect->begin(),  this->realAtomVect->end(),  MolDS_base_atoms::LessAtomIndex());
+   std::sort(this->ghostAtomVect->begin(), this->ghostAtomVect->end(), MolDS_base_atoms::LessAtomIndex());
+   std::sort(this->atomVect->begin(),      this->atomVect->end(),      MolDS_base_atoms::LessAtomIndex());
 }
 
 void Molecule::CalcTotalNumberAOs(){

--- a/src/base/Molecule.h
+++ b/src/base/Molecule.h
@@ -38,11 +38,11 @@ public:
 #endif
       return *this->realAtomVect;
    }
-   inline const std::vector<MolDS_base_atoms::Atom*>& GetBqAtomVect() const{
+   inline const std::vector<MolDS_base_atoms::Atom*>& GetGhostAtomVect() const{
 #ifdef MOLDS_DBG
-      if(this->bqAtomVect==NULL) throw MolDS_base::MolDSException(this->errorMessageGetBqAtomVectNull);
+      if(this->ghostAtomVect==NULL) throw MolDS_base::MolDSException(this->errorMessageGetGhostAtomVectNull);
 #endif
-      return *this->bqAtomVect;
+      return *this->ghostAtomVect;
    }
    inline const std::vector<MolDS_base_atoms::Atom*>& GetEpcVect() const{
 #ifdef MOLDS_DBG
@@ -52,7 +52,7 @@ public:
    }
    void AddAtom(MolDS_base_atoms::Atom* atom);
    void AddRealAtom(MolDS_base_atoms::Atom* atom);
-   void AddBqAtom(MolDS_base_atoms::Atom* atom);
+   void AddGhostAtom(MolDS_base_atoms::Atom* atom);
    void AddEpc(MolDS_base_atoms::Atom* epc);
    double const* GetXyzCOM() const;
    double const* GetXyzCOC() const;
@@ -88,7 +88,7 @@ public:
 private:
    std::vector<MolDS_base_atoms::Atom*>* atomVect;
    std::vector<MolDS_base_atoms::Atom*>* realAtomVect; // Vector of real (=not ghost) atoms
-   std::vector<MolDS_base_atoms::Atom*>* bqAtomVect;   // Vector of ghost atoms
+   std::vector<MolDS_base_atoms::Atom*>* ghostAtomVect;   // Vector of ghost atoms
    std::vector<MolDS_base_atoms::Atom*>* epcVect;      // Vector of Environmental Point Charges
    double*  xyzCOM; // x, y, z coordinates of Center of Mass;
    double*  xyzCOC; // x, y, z coordinates of Center of Core;
@@ -102,7 +102,7 @@ private:
    void CopyInitialize(const Molecule& rhs);
    void Finalize(std::vector<MolDS_base_atoms::Atom*>** atomVect, 
                  std::vector<MolDS_base_atoms::Atom*>** realAtomVect,
-                 std::vector<MolDS_base_atoms::Atom*>** bqAtomVect,
+                 std::vector<MolDS_base_atoms::Atom*>** ghostAtomVect,
                  std::vector<MolDS_base_atoms::Atom*>** epcVect,
                  double** xyzCOM, 
                  double** xyzCOC, 
@@ -110,7 +110,7 @@ private:
                  double*** distanceEpcs,
                  double*** distanceAtomsEpcs);
    void SetMessages();
-   void CopyRealBqAtom2Atom();
+   void CopyRealGhostAtom2Atom();
    void CalcTotalNumberAOs();
    void CalcTotalNumberValenceElectrons();
    void CalcTotalCoreMass();
@@ -137,13 +137,13 @@ private:
    void OutputTranslatingConditions(double const* translatingDifference) const;
    std::string errorMessageGetAtomVectNull;
    std::string errorMessageGetRealAtomVectNull;
-   std::string errorMessageGetBqAtomVectNull;
+   std::string errorMessageGetGhostAtomVectNull;
    std::string errorMessageGetEPCVectNull;
    std::string errorMessageAddAtomNull;
    std::string errorMessageAddRealAtomNull;
-   std::string errorMessageAddBqAtomNull;
+   std::string errorMessageAddGhostAtomNull;
    std::string errorMessageAddEPCNull;
-   std::string errorMessageCopyRealBqAtom2AtomNotEmpty;
+   std::string errorMessageCopyRealGhostAtom2AtomNotEmpty;
    std::string errorMessageGetXyzCOMNull;
    std::string errorMessageGetXyzCOCNull;
    std::string errorMessageCalcXyzCOMNull;

--- a/src/base/atoms/bq/BqNatom.h
+++ /dev/null
@@ -1,31 +0,0 @@
-//************************************************************************//
-// Copyright (C) 2011-2012 Mikiya Fujii                                   // 
-//                                                                        // 
-// This file is part of MolDS.                                            // 
-//                                                                        // 
-// MolDS is free software: you can redistribute it and/or modify          // 
-// it under the terms of the GNU General Public License as published by   // 
-// the Free Software Foundation, either version 3 of the License, or      // 
-// (at your option) any later version.                                    // 
-//                                                                        // 
-// MolDS is distributed in the hope that it will be useful,               // 
-// but WITHOUT ANY WARRANTY; without even the implied warranty of         // 
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the          // 
-// GNU General Public License for more details.                           // 
-//                                                                        // 
-// You should have received a copy of the GNU General Public License      // 
-// along with MolDS.  If not, see <http://www.gnu.org/licenses/>.         // 
-//************************************************************************//
-#ifndef INCLUDED_BQNATOM
-#define INCLUDED_BQNATOM
-namespace MolDS_base_atoms_bq{
-class BqNatom : public MolDS_base_atoms::Natom, public Bq {
-public:
-   BqNatom(int index);
-protected:
-   void virtual SetAtomicParameters();
-private:
-   BqNatom();
-};
-}
-#endif

--- a/src/base/atoms/bq/BqOatom.h
+++ /dev/null
@@ -1,31 +0,0 @@
-//************************************************************************//
-// Copyright (C) 2011-2012 Mikiya Fujii                                   // 
-//                                                                        // 
-// This file is part of MolDS.                                            // 
-//                                                                        // 
-// MolDS is free software: you can redistribute it and/or modify          // 
-// it under the terms of the GNU General Public License as published by   // 
-// the Free Software Foundation, either version 3 of the License, or      // 
-// (at your option) any later version.                                    // 
-//                                                                        // 
-// MolDS is distributed in the hope that it will be useful,               // 
-// but WITHOUT ANY WARRANTY; without even the implied warranty of         // 
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the          // 
-// GNU General Public License for more details.                           // 
-//                                                                        // 
-// You should have received a copy of the GNU General Public License      // 
-// along with MolDS.  If not, see <http://www.gnu.org/licenses/>.         // 
-//************************************************************************//
-#ifndef INCLUDED_BQOATOM
-#define INCLUDED_BQOATOM
-namespace MolDS_base_atoms_bq{
-class BqOatom : public MolDS_base_atoms::Oatom, public Bq {
-public:
-   BqOatom(int index);
-protected:
-   void virtual SetAtomicParameters();
-private:
-   BqOatom();
-};
-}
-#endif

--- a/src/base/atoms/bq/BqSatom.h
+++ /dev/null
@@ -1,31 +0,0 @@
-//************************************************************************//
-// Copyright (C) 2011-2012 Mikiya Fujii                                   // 
-//                                                                        // 
-// This file is part of MolDS.                                            // 
-//                                                                        // 
-// MolDS is free software: you can redistribute it and/or modify          // 
-// it under the terms of the GNU General Public License as published by   // 
-// the Free Software Foundation, either version 3 of the License, or      // 
-// (at your option) any later version.                                    // 
-//                                                                        // 
-// MolDS is distributed in the hope that it will be useful,               // 
-// but WITHOUT ANY WARRANTY; without even the implied warranty of         // 
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the          // 
-// GNU General Public License for more details.                           // 
-//                                                                        // 
-// You should have received a copy of the GNU General Public License      // 
-// along with MolDS.  If not, see <http://www.gnu.org/licenses/>.         // 
-//************************************************************************//
-#ifndef INCLUDED_BQSATOM
-#define INCLUDED_BQSATOM
-namespace MolDS_base_atoms_bq{
-class BqSatom : public MolDS_base_atoms::Satom, public Bq {
-public:
-   BqSatom(int index);
-protected:
-   void virtual SetAtomicParameters();
-private:
-   BqSatom();
-};
-}
-#endif

--- a/src/base/atoms/bq/Bq.cpp
+++ b/src/base/atoms/ghost/Ghost.cpp
@@ -34,15 +34,15 @@
 #include"../../Parameters.h"
 #include"../../RealSphericalHarmonicsIndex.h"
 #include"../Atom.h"
-#include"Bq.h"
+#include"Ghost.h"
 using namespace std;
 using namespace MolDS_base;
 using namespace MolDS_base_atoms;
-namespace MolDS_base_atoms_bq{
-Bq::Bq() : Atom(){
+namespace MolDS_base_atoms_ghost{
+Ghost::Ghost() : Atom(){
 }
 
-void Bq::SetAtomicParameters(){
+void Ghost::SetAtomicParameters(){
    this->atomicMass = 0.0;
    this->coreCharge = 0.0;
    this->numberValenceElectrons = 0;

--- a/src/base/atoms/bq/Bq.h
+++ b/src/base/atoms/ghost/Ghost.h
@@ -16,12 +16,12 @@
 // You should have received a copy of the GNU General Public License      // 
 // along with MolDS.  If not, see <http://www.gnu.org/licenses/>.         // 
 //************************************************************************//
-#ifndef INCLUDED_BQ
-#define INCLUDED_BQ
-namespace MolDS_base_atoms_bq{
-class Bq : virtual public MolDS_base_atoms::Atom {
+#ifndef INCLUDED_GHOST
+#define INCLUDED_GHOST
+namespace MolDS_base_atoms_ghost{
+class Ghost : virtual public MolDS_base_atoms::Atom {
 public:
-   Bq();
+   Ghost();
 protected:
    void virtual SetAtomicParameters();
 private:

--- a/src/base/atoms/bq/BqCatom.cpp
+++ b/src/base/atoms/ghost/GhostCatom.cpp
@@ -35,18 +35,18 @@
 #include"../../RealSphericalHarmonicsIndex.h"
 #include"../Atom.h"
 #include"../Catom.h"
-#include"Bq.h"
-#include"BqCatom.h"
+#include"Ghost.h"
+#include"GhostCatom.h"
 using namespace std;
 using namespace MolDS_base;
 using namespace MolDS_base_atoms;
-namespace MolDS_base_atoms_bq{
-BqCatom::BqCatom(int index) : Catom(index),Bq(){
+namespace MolDS_base_atoms_ghost{
+GhostCatom::GhostCatom(int index) : Catom(index),Ghost(){
 }
 
-void BqCatom::SetAtomicParameters(){
+void GhostCatom::SetAtomicParameters(){
    Catom::SetAtomicParameters();
-   Bq::SetAtomicParameters();
-   this->atomType = bqC;
+   Ghost::SetAtomicParameters();
+   this->atomType = ghostC;
 }
 }

--- a/src/base/atoms/bq/BqHatom.h
+++ b/src/base/atoms/ghost/GhostCatom.h
@@ -16,16 +16,16 @@
 // You should have received a copy of the GNU General Public License      // 
 // along with MolDS.  If not, see <http://www.gnu.org/licenses/>.         // 
 //************************************************************************//
-#ifndef INCLUDED_BQHATOM
-#define INCLUDED_BQHATOM
-namespace MolDS_base_atoms_bq{
-class BqHatom : public MolDS_base_atoms::Hatom, public Bq {
+#ifndef INCLUDED_GHOSTCATOM
+#define INCLUDED_GHOSTCATOM
+namespace MolDS_base_atoms_ghost{
+class GhostCatom : public MolDS_base_atoms::Catom, public Ghost {
 public:
-   BqHatom(int index);
+   GhostCatom(int index);
 protected:
    void virtual SetAtomicParameters();
 private:
-   BqHatom();
+   GhostCatom();
 };
 }
 #endif

--- a/src/base/atoms/bq/BqHatom.cpp
+++ b/src/base/atoms/ghost/GhostHatom.cpp
@@ -35,18 +35,18 @@
 #include"../../RealSphericalHarmonicsIndex.h"
 #include"../Atom.h"
 #include"../Hatom.h"
-#include"Bq.h"
-#include"BqHatom.h"
+#include"Ghost.h"
+#include"GhostHatom.h"
 using namespace std;
 using namespace MolDS_base;
 using namespace MolDS_base_atoms;
-namespace MolDS_base_atoms_bq{
-BqHatom::BqHatom(int index) : Hatom(index),Bq(){
+namespace MolDS_base_atoms_ghost{
+GhostHatom::GhostHatom(int index) : Hatom(index),Ghost(){
 }
 
-void BqHatom::SetAtomicParameters(){
+void GhostHatom::SetAtomicParameters(){
    Hatom::SetAtomicParameters();
-   Bq::SetAtomicParameters();
-   this->atomType = bqH;
+   Ghost::SetAtomicParameters();
+   this->atomType = ghostH;
 }
 }

--- a/src/base/atoms/bq/BqLiatom.h
+++ b/src/base/atoms/ghost/GhostHatom.h
@@ -16,16 +16,16 @@
 // You should have received a copy of the GNU General Public License      // 
 // along with MolDS.  If not, see <http://www.gnu.org/licenses/>.         // 
 //************************************************************************//
-#ifndef INCLUDED_BQLIATOM
-#define INCLUDED_BQLIATOM
-namespace MolDS_base_atoms_bq{
-class BqLiatom : public MolDS_base_atoms::Liatom, public Bq {
+#ifndef INCLUDED_GHOSTHATOM
+#define INCLUDED_GHOSTHATOM
+namespace MolDS_base_atoms_ghost{
+class GhostHatom : public MolDS_base_atoms::Hatom, public Ghost {
 public:
-   BqLiatom(int index);
+   GhostHatom(int index);
 protected:
    void virtual SetAtomicParameters();
 private:
-   BqLiatom();
+   GhostHatom();
 };
 }
 #endif

--- a/src/base/atoms/bq/BqLiatom.cpp
+++ b/src/base/atoms/ghost/GhostLiatom.cpp
@@ -35,18 +35,18 @@
 #include"../../RealSphericalHarmonicsIndex.h"
 #include"../Atom.h"
 #include"../Liatom.h"
-#include"Bq.h"
-#include"BqLiatom.h"
+#include"Ghost.h"
+#include"GhostLiatom.h"
 using namespace std;
 using namespace MolDS_base;
 using namespace MolDS_base_atoms;
-namespace MolDS_base_atoms_bq{
-BqLiatom::BqLiatom(int index) : Liatom(index),Bq(){
+namespace MolDS_base_atoms_ghost{
+GhostLiatom::GhostLiatom(int index) : Liatom(index),Ghost(){
 }
 
-void BqLiatom::SetAtomicParameters(){
+void GhostLiatom::SetAtomicParameters(){
    Liatom::SetAtomicParameters();
-   Bq::SetAtomicParameters();
-   this->atomType = bqLi;
+   Ghost::SetAtomicParameters();
+   this->atomType = ghostLi;
 }
 }

--- /dev/null
+++ b/src/base/atoms/ghost/GhostLiatom.h
@@ -0,0 +1,31 @@
+//************************************************************************//
+// Copyright (C) 2011-2012 Mikiya Fujii                                   // 
+//                                                                        // 
+// This file is part of MolDS.                                            // 
+//                                                                        // 
+// MolDS is free software: you can redistribute it and/or modify          // 
+// it under the terms of the GNU General Public License as published by   // 
+// the Free Software Foundation, either version 3 of the License, or      // 
+// (at your option) any later version.                                    // 
+//                                                                        // 
+// MolDS is distributed in the hope that it will be useful,               // 
+// but WITHOUT ANY WARRANTY; without even the implied warranty of         // 
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the          // 
+// GNU General Public License for more details.                           // 
+//                                                                        // 
+// You should have received a copy of the GNU General Public License      // 
+// along with MolDS.  If not, see <http://www.gnu.org/licenses/>.         // 
+//************************************************************************//
+#ifndef INCLUDED_GHOSTLIATOM
+#define INCLUDED_GHOSTLIATOM
+namespace MolDS_base_atoms_ghost{
+class GhostLiatom : public MolDS_base_atoms::Liatom, public Ghost {
+public:
+   GhostLiatom(int index);
+protected:
+   void virtual SetAtomicParameters();
+private:
+   GhostLiatom();
+};
+}
+#endif

--- a/src/base/atoms/bq/BqNatom.cpp
+++ b/src/base/atoms/ghost/GhostNatom.cpp
@@ -35,18 +35,18 @@
 #include"../../RealSphericalHarmonicsIndex.h"
 #include"../Atom.h"
 #include"../Natom.h"
-#include"Bq.h"
-#include"BqNatom.h"
+#include"Ghost.h"
+#include"GhostNatom.h"
 using namespace std;
 using namespace MolDS_base;
 using namespace MolDS_base_atoms;
-namespace MolDS_base_atoms_bq{
-BqNatom::BqNatom(int index) : Natom(index),Bq(){
+namespace MolDS_base_atoms_ghost{
+GhostNatom::GhostNatom(int index) : Natom(index),Ghost(){
 }
 
-void BqNatom::SetAtomicParameters(){
+void GhostNatom::SetAtomicParameters(){
    Natom::SetAtomicParameters();
-   Bq::SetAtomicParameters();
-   this->atomType = bqN;
+   Ghost::SetAtomicParameters();
+   this->atomType = ghostN;
 }
 }

--- a/src/base/atoms/bq/BqCatom.h
+++ b/src/base/atoms/ghost/GhostNatom.h
@@ -16,16 +16,16 @@
 // You should have received a copy of the GNU General Public License      // 
 // along with MolDS.  If not, see <http://www.gnu.org/licenses/>.         // 
 //************************************************************************//
-#ifndef INCLUDED_BQCATOM
-#define INCLUDED_BQCATOM
-namespace MolDS_base_atoms_bq{
-class BqCatom : public MolDS_base_atoms::Catom, public Bq {
+#ifndef INCLUDED_GHOSTNATOM
+#define INCLUDED_GHOSTNATOM
+namespace MolDS_base_atoms_ghost{
+class GhostNatom : public MolDS_base_atoms::Natom, public Ghost {
 public:
-   BqCatom(int index);
+   GhostNatom(int index);
 protected:
    void virtual SetAtomicParameters();
 private:
-   BqCatom();
+   GhostNatom();
 };
 }
 #endif

--- a/src/base/atoms/bq/BqOatom.cpp
+++ b/src/base/atoms/ghost/GhostOatom.cpp
@@ -35,18 +35,18 @@
 #include"../../RealSphericalHarmonicsIndex.h"
 #include"../Atom.h"
 #include"../Oatom.h"
-#include"Bq.h"
-#include"BqOatom.h"
+#include"Ghost.h"
+#include"GhostOatom.h"
 using namespace std;
 using namespace MolDS_base;
 using namespace MolDS_base_atoms;
-namespace MolDS_base_atoms_bq{
-BqOatom::BqOatom(int index) : Oatom(index),Bq(){
+namespace MolDS_base_atoms_ghost{
+GhostOatom::GhostOatom(int index) : Oatom(index),Ghost(){
 }
 
-void BqOatom::SetAtomicParameters(){
+void GhostOatom::SetAtomicParameters(){
    Oatom::SetAtomicParameters();
-   Bq::SetAtomicParameters();
-   this->atomType = bqO;
+   Ghost::SetAtomicParameters();
+   this->atomType = ghostO;
 }
 }

--- /dev/null
+++ b/src/base/atoms/ghost/GhostOatom.h
@@ -0,0 +1,31 @@
+//************************************************************************//
+// Copyright (C) 2011-2012 Mikiya Fujii                                   // 
+//                                                                        // 
+// This file is part of MolDS.                                            // 
+//                                                                        // 
+// MolDS is free software: you can redistribute it and/or modify          // 
+// it under the terms of the GNU General Public License as published by   // 
+// the Free Software Foundation, either version 3 of the License, or      // 
+// (at your option) any later version.                                    // 
+//                                                                        // 
+// MolDS is distributed in the hope that it will be useful,               // 
+// but WITHOUT ANY WARRANTY; without even the implied warranty of         // 
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the          // 
+// GNU General Public License for more details.                           // 
+//                                                                        // 
+// You should have received a copy of the GNU General Public License      // 
+// along with MolDS.  If not, see <http://www.gnu.org/licenses/>.         // 
+//************************************************************************//
+#ifndef INCLUDED_GHOSTOATOM
+#define INCLUDED_GHOSTOATOM
+namespace MolDS_base_atoms_ghost{
+class GhostOatom : public MolDS_base_atoms::Oatom, public Ghost {
+public:
+   GhostOatom(int index);
+protected:
+   void virtual SetAtomicParameters();
+private:
+   GhostOatom();
+};
+}
+#endif

--- a/src/base/atoms/bq/BqSatom.cpp
+++ b/src/base/atoms/ghost/GhostSatom.cpp
@@ -35,18 +35,18 @@
 #include"../../RealSphericalHarmonicsIndex.h"
 #include"../Atom.h"
 #include"../Satom.h"
-#include"Bq.h"
-#include"BqSatom.h"
+#include"Ghost.h"
+#include"GhostSatom.h"
 using namespace std;
 using namespace MolDS_base;
 using namespace MolDS_base_atoms;
-namespace MolDS_base_atoms_bq{
-BqSatom::BqSatom(int index) : Satom(index),Bq(){
+namespace MolDS_base_atoms_ghost{
+GhostSatom::GhostSatom(int index) : Satom(index),Ghost(){
 }
 
-void BqSatom::SetAtomicParameters(){
+void GhostSatom::SetAtomicParameters(){
    Satom::SetAtomicParameters();
-   Bq::SetAtomicParameters();
-   this->atomType = bqS;
+   Ghost::SetAtomicParameters();
+   this->atomType = ghostS;
 }
 }

--- /dev/null
+++ b/src/base/atoms/ghost/GhostSatom.h
@@ -0,0 +1,31 @@
+//************************************************************************//
+// Copyright (C) 2011-2012 Mikiya Fujii                                   // 
+//                                                                        // 
+// This file is part of MolDS.                                            // 
+//                                                                        // 
+// MolDS is free software: you can redistribute it and/or modify          // 
+// it under the terms of the GNU General Public License as published by   // 
+// the Free Software Foundation, either version 3 of the License, or      // 
+// (at your option) any later version.                                    // 
+//                                                                        // 
+// MolDS is distributed in the hope that it will be useful,               // 
+// but WITHOUT ANY WARRANTY; without even the implied warranty of         // 
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the          // 
+// GNU General Public License for more details.                           // 
+//                                                                        // 
+// You should have received a copy of the GNU General Public License      // 
+// along with MolDS.  If not, see <http://www.gnu.org/licenses/>.         // 
+//************************************************************************//
+#ifndef INCLUDED_GHOSTSATOM
+#define INCLUDED_GHOSTSATOM
+namespace MolDS_base_atoms_ghost{
+class GhostSatom : public MolDS_base_atoms::Satom, public Ghost {
+public:
+   GhostSatom(int index);
+protected:
+   void virtual SetAtomicParameters();
+private:
+   GhostSatom();
+};
+}
+#endif

--- a/src/base/factories/AtomFactory.cpp
+++ b/src/base/factories/AtomFactory.cpp
@@ -38,19 +38,19 @@
 #include"../atoms/Natom.h"
 #include"../atoms/Oatom.h"
 #include"../atoms/Satom.h"
-#include"../atoms/bq/Bq.h"
-#include"../atoms/bq/BqHatom.h"
-#include"../atoms/bq/BqLiatom.h"
-#include"../atoms/bq/BqCatom.h"
-#include"../atoms/bq/BqNatom.h"
-#include"../atoms/bq/BqOatom.h"
-#include"../atoms/bq/BqSatom.h"
+#include"../atoms/ghost/Ghost.h"
+#include"../atoms/ghost/GhostHatom.h"
+#include"../atoms/ghost/GhostLiatom.h"
+#include"../atoms/ghost/GhostCatom.h"
+#include"../atoms/ghost/GhostNatom.h"
+#include"../atoms/ghost/GhostOatom.h"
+#include"../atoms/ghost/GhostSatom.h"
 #include"../atoms/mm/EnvironmentalPointCharge.h"
 #include"AtomFactory.h"
 using namespace std;
 using namespace MolDS_base;
 using namespace MolDS_base_atoms;
-using namespace MolDS_base_atoms_bq;
+using namespace MolDS_base_atoms_ghost;
 using namespace MolDS_base_atoms_mm;
 namespace MolDS_base_factories{
 
@@ -78,23 +78,23 @@ Atom* AtomFactory::Create(AtomType atomType, int index, double x, double y, doub
    else if(atomType == S){
       atom = new Satom(index);
    }
-   else if(atomType == bqH){
-      atom = new BqHatom(index);
+   else if(atomType == ghostH){
+      atom = new GhostHatom(index);
    }
-   else if(atomType == bqLi){
-      atom = new BqLiatom(index);
+   else if(atomType == ghostLi){
+      atom = new GhostLiatom(index);
    }
-   else if(atomType == bqC){
-      atom = new BqCatom(index);
+   else if(atomType == ghostC){
+      atom = new GhostCatom(index);
    }
-   else if(atomType == bqN){
-      atom = new BqNatom(index);
+   else if(atomType == ghostN){
+      atom = new GhostNatom(index);
    }
-   else if(atomType == bqO){
-      atom = new BqOatom(index);
+   else if(atomType == ghostO){
+      atom = new GhostOatom(index);
    }
-   else if(atomType == bqS){
-      atom = new BqSatom(index);
+   else if(atomType == ghostS){
+      atom = new GhostSatom(index);
    }
    else{
       stringstream ss;