Commit: 15f70245dcfd881d33b65b67342a3f97da46d5f2 - MolDS (git)

Commit MetaInfo

• Revisão: 15f70245dcfd881d33b65b67342a3f97da46d5f2 (tree)
• Hora: 2014-04-29 01:28:16
• Autor: Mikiya Fujii <mikiya.fujii@gmai...>
• Commiter: Mikiya Fujii

Mensagem de Log

F (fluorine) is added. #33721

git-svn-id: https://svn.sourceforge.jp/svnroot/molds/trunk@1667 1136aad2-a195-0410-b898-f5ea1d11b9d8

Mudança Sumário

• modified: doc/README.txt
• modified: doc/refferences.txt
• modified: src/Makefile
• modified: src/Makefile_GNU
• modified: src/am1/Am1.cpp
• modified: src/am1/Am1D.cpp
• modified: src/base/InputParser.cpp
• modified: src/base/atoms/Atom.h
• add: src/base/atoms/Fatom.cpp
• add: src/base/atoms/Fatom.h
• modified: src/base/atoms/Znatom.cpp
• add: src/base/atoms/ghost/GhostFatom.cpp
• add: src/base/atoms/ghost/GhostFatom.h
• modified: src/base/factories/AtomFactory.cpp
• modified: src/cndo/Cndo2.cpp
• modified: src/indo/Indo.cpp
• modified: src/mndo/Mndo.cpp
• modified: src/pm3/Pm3.cpp
• modified: src/pm3/Pm3D.cpp
• add: src/tools/deriveParametersNDDO/data/AM1_Fatom.dat
• add: src/tools/deriveParametersNDDO/data/MNDO_Fatom.dat
• add: src/tools/deriveParametersNDDO/data/PM3_Fatom.dat
• modified: src/tools/deriveParametersNDDO/deriveParametersNDDO.cpp
• modified: src/zindo/ZindoS.cpp
• modified: test/Test_Of_MolDS.rb
• add: test/ch3f_am1.dat
• add: test/ch3f_am1.in
• add: test/ch3f_mndo.dat
• add: test/ch3f_mndo.in
• add: test/ch3f_pm3.dat
• add: test/ch3f_pm3.in

Diff

--- a/doc/README.txt
+++ b/doc/README.txt
@@ -182,15 +182,18 @@ CAPABILITIES:
       i.e., MD(gs) and MD(es) mean Born-Oppenheimer Molecular Dynamics on ground and excited states, respectively. 
 
    -Elements
-    CNDO2    | H, Li, C, N, O, S
-    INDO     | H, Li, C, N, O
-    ZINDO/S  | H,     C, N, O, S
-    MNDO     | H,     C, N, O, S, Zn
-    AM1      | H,     C, N, O, S, Zn
-    AM1-D    | H,     C, N, O, S 
-    PM3      | H,     C, N, O, S, Zn
-    PM3-D    | H,     C, N, O, S 
-    PM3/PDDG | H,     C, N, O, S 
+    CNDO2    | H, Li, C, N, O, F, S
+    INDO     | H, Li, C, N, O, F, 
+    ZINDO/S  | H,     C, N, O, F, S
+    MNDO     | H,     C, N, O, F, S, Zn
+    AM1      | H,     C, N, O, F, S, Zn
+    AM1-D    | H,     C, N, O, F, S       *
+    PM3      | H,     C, N, O, F, S, Zn
+    PM3-D    | H,     C, N, O, F, S       *
+    PM3/PDDG | H,     C, N, O,    S 
+
+    * For fluorine, semiempirical parameters used in the SCF of AM1-D and PM3-D are same with 
+      the original semiempirical parameters used in the SCF of AM1 and PM3, respectively.
 
    -Parallelization
     Open MP parallelization: everywhere in MolDS

--- a/doc/refferences.txt
+++ b/doc/refferences.txt
@@ -38,6 +38,7 @@
 [DZHS_1985] M. J. S. Dewar, E. G. Zoebisch, E. F. Healy, and J. J. P. Stewart, J. Am. Chem. Soc. 107, 3902 (1985)
 [DR_1986] M. J. S. Dewar and C. H. Reynolds, J. Comp. Chem. 7, 140 (1986)
 [AEZ_1986] W. P. Anderson, W. D. Edwards, and M. C. Zerner, Inorg. Chem. 25, 2728 (1986)
+[DZ_1988] M. J. S. Dewar and E. G. Zoebisch, J. Mol. Struc. (Theochem) 180, 1 (1988)
 [S_1989] J. J. P. Stewart, J. Comp. Chem. 10, 209 (1989)
 [S_1989-2] J. J. P. Stewart, J. Comp. Chem. 10, 221 (1989)
 [DL_1990] M. J. S. Dewar and D. A. Liotard, J. Mol. Struc.(Theochem) 206, 123(1990)
@@ -61,5 +62,6 @@
 [S_2007] J. J. P. Stewart, J. Mol. Model. 13, 1173 (2007)
 [MH_2007] J. P. McNamara and I. H. Hillier, Phys. Chem. Chem. Phys. 9, 2362 (2007)
 [MMHBV_2007] C. A. Morgado, J. P. McNamara, I. H. Hillier, N. A. Burton, and M. A. Vincent, J. Chem. Theory Comput. 3, 1656 (2007)
+[MSVHM_2008] J. P. McNamara, R. Sharma, M. A. Vincent, I. H. Hillier, and C. A. Morgado, Phys. Chem. Chem. Phys. 10, 128 (2008)
 [F_2011] M. Fujii, J. Chem. Phys. 135, 114102-1 (2011)
 

--- 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/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/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
-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/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/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
-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/Znatom.o                obj/Ghost.o             obj/GhostHatom.o                   obj/GhostLiatom.o                obj/GhostCatom.o                obj/GhostNatom.o                obj/GhostOatom.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
+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
+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
+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
 
 $(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/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/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
-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/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/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
-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/Znatom.o                obj/Ghost.o                obj/GhostHatom.o                obj/GhostLiatom.o                obj/GhostCatom.o                obj/GhostNatom.o                obj/GhostOatom.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
+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
+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
+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
 
 $(EXENAME): $(DEPFILE) $(ALL_OBJ_FILES)
 	$(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
@@ -40,6 +40,7 @@
 #include"../base/atoms/Catom.h"
 #include"../base/atoms/Natom.h"
 #include"../base/atoms/Oatom.h"
+#include"../base/atoms/Fatom.h"
 #include"../base/atoms/Satom.h"
 #include"../base/Molecule.h"
 #include"../base/ElectronicStructure.h"
@@ -132,6 +133,7 @@ void Am1::SetEnableAtomTypes(){
    this->enableAtomTypes.push_back(C);
    this->enableAtomTypes.push_back(N);
    this->enableAtomTypes.push_back(O);
+   this->enableAtomTypes.push_back(F);
    this->enableAtomTypes.push_back(S);
    this->enableAtomTypes.push_back(Zn);
 }

--- a/src/am1/Am1D.cpp
+++ b/src/am1/Am1D.cpp
@@ -40,6 +40,7 @@
 #include"../base/atoms/Catom.h"
 #include"../base/atoms/Natom.h"
 #include"../base/atoms/Oatom.h"
+#include"../base/atoms/Fatom.h"
 #include"../base/atoms/Satom.h"
 #include"../base/Molecule.h"
 #include"../base/ElectronicStructure.h"
@@ -134,6 +135,7 @@ void Am1D::SetEnableAtomTypes(){
    this->enableAtomTypes.push_back(C);
    this->enableAtomTypes.push_back(N);
    this->enableAtomTypes.push_back(O);
+   this->enableAtomTypes.push_back(F);
    this->enableAtomTypes.push_back(S);
 }
 

--- a/src/base/InputParser.cpp
+++ b/src/base/InputParser.cpp
@@ -490,6 +490,9 @@ int InputParser::ParseMolecularConfiguration(Molecule* molecule, vector<string>*
       else if((*inputTerms)[parseIndex] == "o"){
          atomType = O;
       }
+      else if((*inputTerms)[parseIndex] == "f"){
+         atomType = F;
+      }
       else if((*inputTerms)[parseIndex] == "s"){
          atomType = S;
       }
@@ -526,6 +529,9 @@ int InputParser::ParseGhostsConfiguration(Molecule* molecule, vector<string>* in
       else if((*inputTerms)[parseIndex] == "o"){
          atomType = ghostO;
       }
+      else if((*inputTerms)[parseIndex] == "f"){
+         atomType = ghostF;
+      }
       else if((*inputTerms)[parseIndex] == "s"){
          atomType = ghostS;
       }

--- a/src/base/atoms/Atom.h
+++ b/src/base/atoms/Atom.h
@@ -65,45 +65,45 @@ public:
                           MolDS_base::TheoryType theory) const;
    inline double GetIndoF2() const{return this->indoF2;}
    inline double GetIndoG1() const{return this->indoG1;}
-   inline double GetZindoF0ss()      const{return this->zindoF0ss;}       // Table 1 in ref. [RZ_1976], Table 1 in [AEZ_1986], or Table 1 in [GD_1972]
+   inline double GetZindoF0ss()      const{return this->zindoF0ss;}       // Table 1 in [RZ_1976], Table 1 in [AEZ_1986], or Table 1 in [GD_1972]
    inline double GetZindoF0sd()      const{return this->zindoF0sd;}       // Table 1 in [AEZ_1986]
    inline double GetZindoF0dd()      const{return this->zindoF0dd;}       // Table 1 in [AEZ_1986]
-   inline double GetZindoG1sp()      const{return this->zindoG1sp;}       // Table 3 in ref. [BZ_1979]
-   inline double GetZindoF2pp()      const{return this->zindoF2pp;}       // Table 3 in ref. [BZ_1979]
-   inline double GetZindoG2sd()      const{return this->zindoG2sd;}       // Table 3 in ref. [BZ_1979]
-   inline double GetZindoG1pd()      const{return this->zindoG1pd;}       // Table 3 in ref. [BZ_1979]
-   inline double GetZindoF2pd()      const{return this->zindoF2pd;}       // Table 3 in ref. [BZ_1979]
-   inline double GetZindoG3pd()      const{return this->zindoG3pd;}       // Table 3 in ref. [BZ_1979]
-   inline double GetZindoF2dd()      const{return this->zindoF2dd;}       // Table 3 in ref. [BZ_1979]
-   inline double GetZindoF4dd()      const{return this->zindoF4dd;}       // Table 3 in ref. [BZ_1979]
-   inline double GetZindoF0ssLower() const{return this->zindoF0ss;}       // Apendix in ref. [BZ_1979] 
-   inline double GetZindoF0sdLower() const{return this->zindoF0sd;}       // Apendix in ref. [BZ_1979]
-   inline double GetZindoF0ddLower() const{return this->zindoF0dd;}       // Apendix in ref. [BZ_1979]
-   inline double GetZindoG1spLower() const{return this->zindoG1sp/3.0;  } // Apendix in ref. [BZ_1979]
-   inline double GetZindoF2ppLower() const{return this->zindoF2pp/25.0; } // Apendix in ref. [BZ_1979]
-   inline double GetZindoG2sdLower() const{return this->zindoG2sd/5.0;  } // Apendix in ref. [BZ_1979]
-   inline double GetZindoG1pdLower() const{return this->zindoG1pd/15.0; } // Apendix in ref. [BZ_1979]
-   inline double GetZindoF2pdLower() const{return this->zindoF2pd/35.0; } // Apendix in ref. [BZ_1979]
-   inline double GetZindoG3pdLower() const{return this->zindoG3pd/245.0;} // Apendix in ref. [BZ_1979]
-   inline double GetZindoF2ddLower() const{return this->zindoF2dd/49.0; } // Apendix in ref. [BZ_1979]
-   inline double GetZindoF4ddLower() const{return this->zindoF4dd/441.0;} // Apendix in ref. [BZ_1979]
+   inline double GetZindoG1sp()      const{return this->zindoG1sp;}       // Table 3 in [BZ_1979]
+   inline double GetZindoF2pp()      const{return this->zindoF2pp;}       // Table 3 in [BZ_1979]
+   inline double GetZindoG2sd()      const{return this->zindoG2sd;}       // Table 3 in [BZ_1979]
+   inline double GetZindoG1pd()      const{return this->zindoG1pd;}       // Table 3 in [BZ_1979]
+   inline double GetZindoF2pd()      const{return this->zindoF2pd;}       // Table 3 in [BZ_1979]
+   inline double GetZindoG3pd()      const{return this->zindoG3pd;}       // Table 3 in [BZ_1979]
+   inline double GetZindoF2dd()      const{return this->zindoF2dd;}       // Table 3 in [BZ_1979]
+   inline double GetZindoF4dd()      const{return this->zindoF4dd;}       // Table 3 in [BZ_1979]
+   inline double GetZindoF0ssLower() const{return this->zindoF0ss;}       // Apendix in [BZ_1979] 
+   inline double GetZindoF0sdLower() const{return this->zindoF0sd;}       // Apendix in [BZ_1979]
+   inline double GetZindoF0ddLower() const{return this->zindoF0dd;}       // Apendix in [BZ_1979]
+   inline double GetZindoG1spLower() const{return this->zindoG1sp/3.0;  } // Apendix in [BZ_1979]
+   inline double GetZindoF2ppLower() const{return this->zindoF2pp/25.0; } // Apendix in [BZ_1979]
+   inline double GetZindoG2sdLower() const{return this->zindoG2sd/5.0;  } // Apendix in [BZ_1979]
+   inline double GetZindoG1pdLower() const{return this->zindoG1pd/15.0; } // Apendix in [BZ_1979]
+   inline double GetZindoF2pdLower() const{return this->zindoF2pd/35.0; } // Apendix in [BZ_1979]
+   inline double GetZindoG3pdLower() const{return this->zindoG3pd/245.0;} // Apendix in [BZ_1979]
+   inline double GetZindoF2ddLower() const{return this->zindoF2dd/49.0; } // Apendix in [BZ_1979]
+   inline double GetZindoF4ddLower() const{return this->zindoF4dd/441.0;} // Apendix in [BZ_1979]
    double GetZindoIonPot(MolDS_base::OrbitalType orbital) const;
-   double GetNddoAlpha(MolDS_base::TheoryType theory) const; // Table III in ref. [DT_1977-2] for H, B, C, N, O, and F. Table I & II in ref. [DMR_1978] and Table I in ref. [DR_1986] for S for MNDO. Table I in ref. [DZHS_1985] for H, C, N, O, and Table I in re. [DY_1990] for S for AM1. [S_1989] for PM3.
+   double GetNddoAlpha(MolDS_base::TheoryType theory) const; // Table III in [DT_1977-2] for H, B, C, N, O, and F. Table I & II in [DMR_1978] and Table I in [DR_1986] for S for MNDO. Table I in [DZHS_1985] for H, C, N, and O. Table I in re. [DY_1990] for S for AM1. [S_1989] for PM3.
    double GetNddoDerivedParameterD(MolDS_base::TheoryType theory, 
-                                   MolDS_base::MultipoleType multipole) const;    // Table III in ref. [DT_1977-2] for H, B, C, N, O, and F. Table I & II in ref. [DMR_1978] and Table I in ref. [DR_1986] for S. Or, calculated in tools/deriveParametersNDDO/deriveParametersNDDO.cpp.
+                                   MolDS_base::MultipoleType multipole) const;    // Table III in [DT_1977-2] for H, B, C, N, O, and F. Table I & II in [DMR_1978] and Table I in [DR_1986] for S. Or, calculated in tools/deriveParametersNDDO/deriveParametersNDDO.cpp.
    double GetNddoDerivedParameterRho(MolDS_base::TheoryType theory, 
-                                     MolDS_base::MultipoleType multipole) const;  // Table III in ref. [DT_1977-2] for H, B, C, N, O, and F. Table I & II in ref. [DMR_1978] and Table I in ref. [DR_1986] for S. Or, calculated in tools/deriveParametersNDDO/deriveParametersNDDO.cpp.
-   double GetMndoElecEnergyAtom() const;        // Table III in ref. [DT_1977-2] for H, B, C, N, O, and F. Table I & II in ref. [DMR_1978] and Table I in ref. [DR_1986] for S.
-   double GetMndoHeatsFormAtom() const;         // Table III in ref. [DT_1977-2] for H, B, C, N, O, and F. Table I & II in ref. [DMR_1978] and Table I in ref. [DR_1986] for S.
+                                     MolDS_base::MultipoleType multipole) const;  // Table III in [DT_1977-2] for H, B, C, N, O, and F. Table I & II in [DMR_1978] and Table I in [DR_1986] for S. Or, calculated in tools/deriveParametersNDDO/deriveParametersNDDO.cpp.
+   double GetMndoElecEnergyAtom() const;        // Table III in [DT_1977-2] for H, B, C, N, O, and F. Table I & II in [DMR_1978] and Table I in [DR_1986] for S.
+   double GetMndoHeatsFormAtom() const;         // Table III in [DT_1977-2] for H, B, C, N, O, and F. Table I & II in [DMR_1978] and Table I in [DR_1986] for S.
    double GetNddoGss(MolDS_base::TheoryType theory) const;
    double GetNddoGpp(MolDS_base::TheoryType theory) const;
    double GetNddoGsp(MolDS_base::TheoryType theory) const;
    double GetNddoGpp2(MolDS_base::TheoryType theory) const;
    double GetNddoHsp(MolDS_base::TheoryType theory) const;
    double GetNddoHpp(MolDS_base::TheoryType theory) const;
-   double GetNddoParameterK(MolDS_base::TheoryType theory, int kIndex) const;//Table I in ref. [DZHS_1985] for H, C, N, O, and Table I in re. [DY_1990] for S for AM1. [S_1989] for PM3.
-   double GetNddoParameterL(MolDS_base::TheoryType theory, int lIndex) const;//Table I in ref. [DZHS_1985] for H, C, N, O, and Table I in re. [DY_1990] for S for AM1. [S_1989] for PM3.
-   double GetNddoParameterM(MolDS_base::TheoryType theory, int mIndex) const;//Table I in ref. [DZHS_1985] for H, C, N, O, and Table I in re. [DY_1990] for S for AM1. [S_1989] for PM3.
+   double GetNddoParameterK(MolDS_base::TheoryType theory, int kIndex) const;//Table I in [DZHS_1985] for H, C, N, and O. Table I in re. [DY_1990] for S for AM1. [S_1989] for PM3.
+   double GetNddoParameterL(MolDS_base::TheoryType theory, int lIndex) const;//Table I in [DZHS_1985] for H, C, N, and O. Table I in re. [DY_1990] for S for AM1. [S_1989] for PM3.
+   double GetNddoParameterM(MolDS_base::TheoryType theory, int mIndex) const;//Table I in [DZHS_1985] for H, C, N, and O. Table I in re. [DY_1990] for S for AM1. [S_1989] for PM3.
    double GetPm3PddgParameterPa(int paIndex) const;
    double GetPm3PddgParameterDa(int daIndex) const;
 protected:
@@ -116,8 +116,8 @@ protected:
    MolDS_base::ShellType valenceShellType;
    int firstAOIndex;
    int numberValenceElectrons;
-   double vdWCoefficient;               // Table 1 in [G_2004] and [G_2006]
-   double vdWRadii;                     // Table 1 in [G_2004] and [G_2006]
+   double vdWCoefficient;               // Table 1 in [G_2004] for H, C, N, O, F, and Ne. And also [G_2006]. Table 1 in [MSVHM_2008] for H, C, N, O, and Cl.
+   double vdWRadii;                     // Table 1 in [G_2004] for H, C, N, O, F, and Ne. And also [G_2006]. Table 1 in [MSVHM_2008] for H, C, N, O, and Cl.
    double imuAmuS;                      // Table 3.4 or 3.5 in J. A. Pople book
    double imuAmuP;                      // Table 3.4 or 3.5 in J. A. Pople book
    double imuAmuD;                      // Table 3.4 or 3.5 in J. A. Pople book
@@ -138,97 +138,97 @@ protected:
    double indoF2CoefficientP;       // (3.93-3.99) in J. A. Pople book
    double zindoBondingParameterS;        // Table 1 in [RZ_1976], table 1 in [HKLWNZ_1982], or table 3 in [AEZ_1986]
    double zindoBondingParameterD;        // Table 1 in [RZ_1976], table 1 in [HKLWNZ_1982], or table 3 in [AEZ_1986]
-   double zindoF0ss;                // Table 1 in ref. [RZ_1976], Table 1 in [AEZ_1986], or Table 1 in [GD_1972]
+   double zindoF0ss;                // Table 1 in [RZ_1976], Table 1 in [AEZ_1986], or Table 1 in [GD_1972]
    double zindoF0sd;        // Table 1 in [AEZ_1986]
    double zindoF0dd;        // Table 1 in [AEZ_1986]
-   double zindoG1sp;       // Table 3 in ref. [BZ_1979] or table 1 in [HKLWNZ_1982]
-   double zindoF2pp;       // Table 3 in ref. [BZ_1979] or table 1 in [HKLWNZ_1982]
-   double zindoG2sd;       // Table 3 in ref. [BZ_1979] or table 1 in [HKLWNZ_1982]
-   double zindoG1pd;       // Table 3 in ref. [BZ_1979] or table 1 in [HKLWNZ_1982]
-   double zindoF2pd;       // Table 3 in ref. [BZ_1979] or table 1 in [HKLWNZ_1982]
-   double zindoG3pd;       // Table 3 in ref. [BZ_1979] or table 1 in [HKLWNZ_1982]
-   double zindoF2dd;       // Table 3 in ref. [BZ_1979] or table 1 in [HKLWNZ_1982]
-   double zindoF4dd;       // Table 3 in ref. [BZ_1979] or table 1 in [HKLWNZ_1982]
+   double zindoG1sp;       // Table 3 in [BZ_1979] or table 1 in [HKLWNZ_1982]
+   double zindoF2pp;       // Table 3 in [BZ_1979] or table 1 in [HKLWNZ_1982]
+   double zindoG2sd;       // Table 3 in [BZ_1979] or table 1 in [HKLWNZ_1982]
+   double zindoG1pd;       // Table 3 in [BZ_1979] or table 1 in [HKLWNZ_1982]
+   double zindoF2pd;       // Table 3 in [BZ_1979] or table 1 in [HKLWNZ_1982]
+   double zindoG3pd;       // Table 3 in [BZ_1979] or table 1 in [HKLWNZ_1982]
+   double zindoF2dd;       // Table 3 in [BZ_1979] or table 1 in [HKLWNZ_1982]
+   double zindoF4dd;       // Table 3 in [BZ_1979] or table 1 in [HKLWNZ_1982]
    int zindoL;              // see l of (13) in [BZ_1979]
    int zindoM;              // see m of (13) in [BZ_1979]
    int zindoN;              // see n (13) in [BZ_1979]
    double zindoIonPotS;   // Ionization potential, Table 4 in [BZ_1979]
    double zindoIonPotP;   // Ionization potential, Table 4 in [BZ_1979]
    double zindoIonPotD;   // Ionization potential, Table 4 in [BZ_1979]
-   double mndoCoreintegralS;         // Table III in ref. [DT_1977-2] for H, B, C, N, O, and F. Table I & II in ref. [DMR_1978] and Table I in ref. [DR_1986] for S.
-   double mndoCoreintegralP;         // Table III in ref. [DT_1977-2] for H, B, C, N, O, and F. Table I & II in ref. [DMR_1978] and Table I in ref. [DR_1986] for S. 
-   double mndoOrbitalExponentS;      // Table III in ref. [DT_1977-2] for H, B, C, N, O, and F. Table I & II in ref. [DMR_1978] and Table I in ref. [DR_1986] for S.
-   double mndoOrbitalExponentP;      // Table III in ref. [DT_1977-2] for H, B, C, N, O, and F. Table I & II in ref. [DMR_1978] and Table I in ref. [DR_1986] for S.
-   double mndoBondingParameterS;     // Table III in ref. [DT_1977-2] for H, B, C, N, O, and F. Table I & II in ref. [DMR_1978] and Table I in ref. [DR_1986] for S.
-   double mndoBondingParameterP;     // Table III in ref. [DT_1977-2] for H, B, C, N, O, and F. Table I & II in ref. [DMR_1978] and Table I in ref. [DR_1986] for S.
-   double mndoAlpha;        // Table III in ref. [DT_1977-2] for H, B, C, N, O, and F. Table I & II in ref. [DMR_1978] and Table I in ref. [DR_1986] for S.
-   double mndoDerivedParameterD[3];    // Table III in ref. [DT_1977-2] for H, B, C, N, O, and F. Table I & II in ref. [DMR_1978] and Table I in ref. [DR_1986] for S. Or, calculated by tools/deriveParametersNDDO/deriveParametersNDDO.cpp.
-   double mndoDerivedParameterRho[3];  // Table III in ref. [DT_1977-2] for H, B, C, N, O, and F. Table I & II in ref. [DMR_1978] and Table I in ref. [DR_1986] for S. Or, calculated by tools/deriveParametersNDDO/deriveParametersNDDO.cpp.
-   double mndoElecEnergyAtom;        // Table III in ref. [DT_1977-2] for H, B, C, N, O, and F. Table I & II in ref. [DMR_1978] and Table I in ref. [DR_1986] for S.
-   double mndoHeatsFormAtom;         // Table III in ref. [DT_1977-2] for H, B, C, N, O, and F. Table I & II in ref. [DMR_1978] and Table I in ref. [DR_1986] for S.
-   double mndoGss;   //Table I in ref. [BDL_1975] for H, B, C, N, O, F, Si, P, S, and Cl.
-   double mndoGpp;   //Table I in ref. [BDL_1975] for H, B, C, N, O, F, Si, P, S, and Cl.
-   double mndoGsp;   //Table I in ref. [BDL_1975] for H, B, C, N, O, F, Si, P, S, and Cl.
-   double mndoGpp2;  //Table I in ref. [BDL_1975] for H, B, C, N, O, F, Si, P, S, and Cl.
-   double mndoHsp;   //Table I in ref. [BDL_1975] for H, B, C, N, O, F, Si, P, S, and Cl.
-   double am1CoreintegralS; // Table I in ref. [DZHS_1985] for H, C, N, O, and Table I in re. [DY_1990] for S.
-   double am1CoreintegralP; // Table I in ref. [DZHS_1985] for H, C, N, O, and Table I in re. [DY_1990] for S.
-   double am1OrbitalExponentS;// Table I in ref. [DZHS_1985] for H, C, N, O, and Table I in re. [DY_1990] for S.
-   double am1OrbitalExponentP;// Table I in ref. [DZHS_1985] for H, C, N, O, and Table I in re. [DY_1990] for S.
-   double am1BondingParameterS; // Table I in ref. [DZHS_1985] for H, C, N, O, and Table I in re. [DY_1990] for S.
-   double am1BondingParameterP; // Table I in ref. [DZHS_1985] for H, C, N, O, and Table I in re. [DY_1990] for S.
-   double am1Alpha;// Table I in ref. [DZHS_1985] for H, C, N, O, and Table I in re. [DY_1990] for S.
-   double am1Gss; // Table I in ref. [DZHS_1985] for H, C, N, O, and Table I in re. [DY_1990] for S.
-   double am1Gpp; // Table I in ref. [DZHS_1985] for H, C, N, O, and Table I in re. [DY_1990] for S.
-   double am1Gsp; // Table I in ref. [DZHS_1985] for H, C, N, O, and Table I in re. [DY_1990] for S.
-   double am1Gpp2; // Table I in ref. [DZHS_1985] for H, C, N, O, and Table I in re. [DY_1990] for S.
-   double am1Hsp; // Table I in ref. [DZHS_1985] for H, C, N, O, and Table I in re. [DY_1990] for S.
+   double mndoCoreintegralS;         // Table III in [DT_1977-2] for H, B, C, N, O, and F. Table I & II in [DMR_1978] and Table I in [DR_1986] for S.
+   double mndoCoreintegralP;         // Table III in [DT_1977-2] for H, B, C, N, O, and F. Table I & II in [DMR_1978] and Table I in [DR_1986] for S. 
+   double mndoOrbitalExponentS;      // Table III in [DT_1977-2] for H, B, C, N, O, and F. Table I & II in [DMR_1978] and Table I in [DR_1986] for S.
+   double mndoOrbitalExponentP;      // Table III in [DT_1977-2] for H, B, C, N, O, and F. Table I & II in [DMR_1978] and Table I in [DR_1986] for S.
+   double mndoBondingParameterS;     // Table III in [DT_1977-2] for H, B, C, N, O, and F. Table I & II in [DMR_1978] and Table I in [DR_1986] for S.
+   double mndoBondingParameterP;     // Table III in [DT_1977-2] for H, B, C, N, O, and F. Table I & II in [DMR_1978] and Table I in [DR_1986] for S.
+   double mndoAlpha;                 // Table III in [DT_1977-2] for H, B, C, N, O, and F. Table I & II in [DMR_1978] and Table I in [DR_1986] for S.
+   double mndoDerivedParameterD[3];  // Table III in [DT_1977-2] for H, B, C, N, O, and F. Table I & II in [DMR_1978] and Table I in [DR_1986] for S. Or, calculated by tools/deriveParametersNDDO/deriveParametersNDDO.cpp.
+   double mndoDerivedParameterRho[3];// Table III in [DT_1977-2] for H, B, C, N, O, and F. Table I & II in [DMR_1978] and Table I in [DR_1986] for S. Or, calculated by tools/deriveParametersNDDO/deriveParametersNDDO.cpp.
+   double mndoElecEnergyAtom;        // Table III in [DT_1977-2] for H, B, C, N, O, and F. Table I & II in [DMR_1978] and Table I in [DR_1986] for S.
+   double mndoHeatsFormAtom;         // Table III in [DT_1977-2] for H, B, C, N, O, and F. Table I & II in [DMR_1978] and Table I in [DR_1986] for S.
+   double mndoGss;   //Table I in [BDL_1975] for H, B, C, N, O, F, Si, P, S, and Cl.
+   double mndoGpp;   //Table I in [BDL_1975] for H, B, C, N, O, F, Si, P, S, and Cl.
+   double mndoGsp;   //Table I in [BDL_1975] for H, B, C, N, O, F, Si, P, S, and Cl.
+   double mndoGpp2;  //Table I in [BDL_1975] for H, B, C, N, O, F, Si, P, S, and Cl.
+   double mndoHsp;   //Table I in [BDL_1975] for H, B, C, N, O, F, Si, P, S, and Cl.
+   double am1CoreintegralS;     // Table I in [DZHS_1985] for H, C, N, and O. Table I in [DZ_1988] for F, Cl, Br, and I. Table I in re. [DY_1990] for S.
+   double am1CoreintegralP;     // Table I in [DZHS_1985] for H, C, N, and O. Table I in [DZ_1988] for F, Cl, Br, and I. Table I in re. [DY_1990] for S.
+   double am1OrbitalExponentS;  // Table I in [DZHS_1985] for H, C, N, and O. Table I in [DZ_1988] for F, Cl, Br, and I. Table I in re. [DY_1990] for S.
+   double am1OrbitalExponentP;  // Table I in [DZHS_1985] for H, C, N, and O. Table I in [DZ_1988] for F, Cl, Br, and I. Table I in re. [DY_1990] for S.
+   double am1BondingParameterS; // Table I in [DZHS_1985] for H, C, N, and O. Table I in [DZ_1988] for F, Cl, Br, and I. Table I in re. [DY_1990] for S.
+   double am1BondingParameterP; // Table I in [DZHS_1985] for H, C, N, and O. Table I in [DZ_1988] for F, Cl, Br, and I. Table I in re. [DY_1990] for S.
+   double am1Alpha;             // Table I in [DZHS_1985] for H, C, N, and O. Table I in [DZ_1988] for F, Cl, Br, and I. Table I in re. [DY_1990] for S.
+   double am1Gss;  // See the section "Parameters" in [DZHS_1985]. Table I in [BDL_1975] for H, B, C, N, O, F, Si, P, S, and Cl. Table I in re. [DY_1990] for S.
+   double am1Gpp;  // See the section "Parameters" in [DZHS_1985]. Table I in [BDL_1975] for H, B, C, N, O, F, Si, P, S, and Cl. Table I in re. [DY_1990] for S.
+   double am1Gsp;  // See the section "Parameters" in [DZHS_1985]. Table I in [BDL_1975] for H, B, C, N, O, F, Si, P, S, and Cl. Table I in re. [DY_1990] for S.
+   double am1Gpp2; // See the section "Parameters" in [DZHS_1985]. Table I in [BDL_1975] for H, B, C, N, O, F, Si, P, S, and Cl. Table I in re. [DY_1990] for S.
+   double am1Hsp;  // See the section "Parameters" in [DZHS_1985]. Table I in [BDL_1975] for H, B, C, N, O, F, Si, P, S, and Cl. Table I in re. [DY_1990] for S.
    double am1DerivedParameterD[3];    // Calculated by tools/deriveParametersNDDO/deriveParametersNDDO.cpp.
    double am1DerivedParameterRho[3];  // Calculated by tools/deriveParametersNDDO/deriveParametersNDDO.cpp.
-   double am1ParameterK[4];// Table I in ref. [DZHS_1985] for H, C, N, O, and Table I in re. [DY_1990] for S.
-   double am1ParameterL[4];// Table I in ref. [DZHS_1985] for H, C, N, O, and Table I in re. [DY_1990] for S.
-   double am1ParameterM[4];// Table I in ref. [DZHS_1985] for H, C, N, O, and Table I in re. [DY_1990] for S.
-   double am1DCoreintegralS; // Table II in ref. [MH_2007] for H, C, N, and O and Table IV in ref. [MMHBV_2007] for S.
-   double am1DCoreintegralP; // Table II in ref. [MH_2007] for H, C, N, and O and Table IV in ref. [MMHBV_2007] for S.
-   double am1DBondingParameterS; // Table II in ref. [MH_2007] for H, C, N, O, and Table IV in re. [MMHBV_2007] for S.
-   double am1DBondingParameterP; // Table II in ref. [MH_2007] for H, C, N, O, and Table IV in re. [MMHBV_2007] for S.
-   double am1DAlpha; // Table II in ref. [MH_2007] for H, C, N, O, and Table IV in re. [MMHBV_2007] for S.
-   double pm3CoreintegralS; // Table II in ref. [S_1989].
-   double pm3CoreintegralP; // Table II in ref. [S_1989].
-   double pm3OrbitalExponentS;// Table II in ref. [S_1989].
-   double pm3OrbitalExponentP;// Table II in ref. [S_1989].
-   double pm3BondingParameterS; // Table II in ref. [S_1989].
-   double pm3BondingParameterP; // Table II in ref. [S_1989].
-   double pm3Alpha;// Table II in ref. [S_1989].
+   double am1ParameterK[4];// Table I in [DZHS_1985] for H, C, N, and O. Table I in [DZ_1988] for F, Cl, Br, and I. Table I in re. [DY_1990] for S.
+   double am1ParameterL[4];// Table I in [DZHS_1985] for H, C, N, and O. Table I in [DZ_1988] for F, Cl, Br, and I. Table I in re. [DY_1990] for S.
+   double am1ParameterM[4];// Table I in [DZHS_1985] for H, C, N, and O. Table I in [DZ_1988] for F, Cl, Br, and I. Table I in re. [DY_1990] for S.
+   double am1DCoreintegralS;     // Table II in [MH_2007] for H, C, N, and O. Table IV in [MMHBV_2007] for S.
+   double am1DCoreintegralP;     // Table II in [MH_2007] for H, C, N, and O. Table IV in [MMHBV_2007] for S.
+   double am1DBondingParameterS; // Table II in [MH_2007] for H, C, N, and O. Table IV in [MMHBV_2007] for S.
+   double am1DBondingParameterP; // Table II in [MH_2007] for H, C, N, and O. Table IV in [MMHBV_2007] for S.
+   double am1DAlpha;             // Table II in [MH_2007] for H, C, N, and O. Table IV in [MMHBV_2007] for S.
+   double pm3CoreintegralS;     // Table II in [S_1989].
+   double pm3CoreintegralP;     // Table II in [S_1989].
+   double pm3OrbitalExponentS;  // Table II in [S_1989].
+   double pm3OrbitalExponentP;  // Table II in [S_1989].
+   double pm3BondingParameterS; // Table II in [S_1989].
+   double pm3BondingParameterP; // Table II in [S_1989].
+   double pm3Alpha;             // Table II in [S_1989].
    double pm3DerivedParameterD[3];    // Calculated by tools/deriveParametersNDDO/deriveParametersNDDO.cpp.
    double pm3DerivedParameterRho[3];  // Calculated by tools/deriveParametersNDDO/deriveParametersNDDO.cpp.
-   double pm3ParameterK[4];// Table II in ref. [S_1989].
-   double pm3ParameterL[4];// Table II in ref. [S_1989].
-   double pm3ParameterM[4];// Table II in ref. [S_1989].
-   double pm3Gss; // Table II in ref. [S_1989].
-   double pm3Gpp; // Table II in ref. [S_1989].
-   double pm3Gsp; // Table II in ref. [S_1989].
-   double pm3Gpp2; // Table II in ref. [S_1989].
-   double pm3Hsp; // Table II in ref. [S_1989].
-   double pm3PddgCoreintegralS; // Table II in ref. [RCJ_2002] for H, C, N, O, and Table II in re. [BGJ_2003] for S.
-   double pm3PddgCoreintegralP; // Table II in ref. [RCJ_2002] for H, C, N, O, and Table II in re. [BGJ_2003] for S.
-   double pm3PddgOrbitalExponentS;// Table II in ref. [RCJ_2002] for H, C, N, O, and Table II in re. [BGJ_2003] for S.
-   double pm3PddgOrbitalExponentP;// Table II in ref. [RCJ_2002] for H, C, N, O, and Table II in re. [BGJ_2003] for S.
-   double pm3PddgBondingParameterS; // Table II in ref. [RCJ_2002] for H, C, N, O, and Table II in re. [BGJ_2003] for S.
-   double pm3PddgBondingParameterP; // Table II in ref. [RCJ_2002] for H, C, N, O, and Table II in re. [BGJ_2003] for S.
-   double pm3PddgAlpha;// Table II in ref. [RCJ_2002] for H, C, N, O, and Table II in re. [BGJ_2003] for S.
-   double pm3PddgDerivedParameterD[3];    // Table II in ref. [RCJ_2002] for H, C, N, O, and Table II in re. [BGJ_2003] for S.
-   double pm3PddgDerivedParameterRho[3];  // Table II in ref. [RCJ_2002] for H, C, N, O, and Table II in re. [BGJ_2003] for S.
-   double pm3PddgParameterK[4];// Table II in ref. [RCJ_2002] for H, C, N, O, and Table II in re. [BGJ_2003] for S.
-   double pm3PddgParameterL[4];// Table II in ref. [RCJ_2002] for H, C, N, O, and Table II in re. [BGJ_2003] for S.
-   double pm3PddgParameterM[4];// Table II in ref. [RCJ_2002] for H, C, N, O, and Table II in re. [BGJ_2003] for S.
-   double pm3PddgParameterPa[2];// Table II in ref. [RCJ_2002] for H, C, N, O, and Table II in re. [BGJ_2003] for S.
-   double pm3PddgParameterDa[2];// Table II in ref. [RCJ_2002] for H, C, N, O, and Table II in re. [BGJ_2003] for S.
-   double pm3DCoreintegralS; // Table II in ref. [MH_2007] for H, C, N, and O and Table IV in ref. [MMHBV_2007] for S.
-   double pm3DCoreintegralP; // Table II in ref. [MH_2007] for H, C, N, and O and Table IV in ref. [MMHBV_2007] for S.
-   double pm3DBondingParameterS; // Table II in ref. [MH_2007] for H, C, N, O, and Table IV in re. [MMHBV_2007] for S.
-   double pm3DBondingParameterP; // Table II in ref. [MH_2007] for H, C, N, O, and Table IV in re. [MMHBV_2007] for S.
-   double pm3DAlpha; // Table II in ref. [MH_2007] for H, C, N, O, and Table IV in re. [MMHBV_2007] for S.
+   double pm3ParameterK[4];// Table II in [S_1989].
+   double pm3ParameterL[4];// Table II in [S_1989].
+   double pm3ParameterM[4];// Table II in [S_1989].
+   double pm3Gss; // Table II in [S_1989].
+   double pm3Gpp; // Table II in [S_1989].
+   double pm3Gsp; // Table II in [S_1989].
+   double pm3Gpp2;// Table II in [S_1989].
+   double pm3Hsp; // Table II in [S_1989].
+   double pm3PddgCoreintegralS;         // Table II in [RCJ_2002] for H, C, N, O, and Table II in re. [BGJ_2003] for S.
+   double pm3PddgCoreintegralP;         // Table II in [RCJ_2002] for H, C, N, O, and Table II in re. [BGJ_2003] for S.
+   double pm3PddgOrbitalExponentS;      // Table II in [RCJ_2002] for H, C, N, O, and Table II in re. [BGJ_2003] for S.
+   double pm3PddgOrbitalExponentP;      // Table II in [RCJ_2002] for H, C, N, O, and Table II in re. [BGJ_2003] for S.
+   double pm3PddgBondingParameterS;     // Table II in [RCJ_2002] for H, C, N, O, and Table II in re. [BGJ_2003] for S.
+   double pm3PddgBondingParameterP;     // Table II in [RCJ_2002] for H, C, N, O, and Table II in re. [BGJ_2003] for S.
+   double pm3PddgAlpha;                 // Table II in [RCJ_2002] for H, C, N, O, and Table II in re. [BGJ_2003] for S.
+   double pm3PddgDerivedParameterD[3];  // Table II in [RCJ_2002] for H, C, N, O, and Table II in re. [BGJ_2003] for S.
+   double pm3PddgDerivedParameterRho[3];// Table II in [RCJ_2002] for H, C, N, O, and Table II in re. [BGJ_2003] for S.
+   double pm3PddgParameterK[4]; // Table II in [RCJ_2002] for H, C, N, and O. Table II in re. [BGJ_2003] for S.
+   double pm3PddgParameterL[4]; // Table II in [RCJ_2002] for H, C, N, and O. Table II in re. [BGJ_2003] for S.
+   double pm3PddgParameterM[4]; // Table II in [RCJ_2002] for H, C, N, and O. Table II in re. [BGJ_2003] for S.
+   double pm3PddgParameterPa[2];// Table II in [RCJ_2002] for H, C, N, and O. Table II in re. [BGJ_2003] for S.
+   double pm3PddgParameterDa[2];// Table II in [RCJ_2002] for H, C, N, and O. Table II in re. [BGJ_2003] for S.
+   double pm3DCoreintegralS;     // Table II in [MH_2007] for H, C, N, and O. Table IV in [MMHBV_2007] for S.
+   double pm3DCoreintegralP;     // Table II in [MH_2007] for H, C, N, and O. Table IV in [MMHBV_2007] for S.
+   double pm3DBondingParameterS; // Table II in [MH_2007] for H, C, N, and O. Table IV in [MMHBV_2007] for S.
+   double pm3DBondingParameterP; // Table II in [MH_2007] for H, C, N, and O. Table IV in [MMHBV_2007] for S.
+   double pm3DAlpha;             // Table II in [MH_2007] for H, C, N, and O. Table IV in [MMHBV_2007] for S.
    virtual void SetAtomicParameters() = 0;
 private:
    Atom();

--- /dev/null
+++ b/src/base/atoms/Fatom.cpp
@@ -0,0 +1,219 @@
+//************************************************************************//
+// Copyright (C) 2011-2014 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/>.         // 
+//************************************************************************//
+#include<stdio.h>
+#include<stdlib.h>
+#include<iostream>
+#include<sstream>
+#include<math.h>
+#include<vector>
+#include<boost/format.hpp>
+#include"../Enums.h"
+#include"../Uncopyable.h"
+#include"../PrintController.h"
+#include"../MolDSException.h"
+#include"../MallocerFreer.h"
+#include"../../mpi/MpiInt.h"
+#include"../../mpi/MpiProcess.h"
+#include"../EularAngle.h"
+#include"../Parameters.h"
+#include"../RealSphericalHarmonicsIndex.h"
+#include"Atom.h"
+#include"Fatom.h"
+using namespace std;
+using namespace MolDS_base;
+namespace MolDS_base_atoms{
+Fatom::Fatom(int index) : Atom(index){
+   this->SetAtomicParameters();
+}
+
+Fatom::~Fatom(){}
+
+void Fatom::SetAtomicParameters(){
+   this->atomType = F;
+   this->atomicMass = 18.9984032*Parameters::GetInstance()->GetGMolin2AU();
+   this->coreCharge = 7.0;
+   this->numberValenceElectrons = 7;
+   this->valenceShellType = lShell;
+   this->valence.push_back(s);
+   this->valence.push_back(py);
+   this->valence.push_back(pz);
+   this->valence.push_back(px);
+   for(int i=0; i<this->valence.size();i++){
+      this->realSphericalHarmonicsIndeces.push_back(new RealSphericalHarmonicsIndex(this->valence[i]));
+   }
+   this->vdWCoefficient = 0.57*Parameters::GetInstance()->GetJ2AU()
+                              *pow(Parameters::GetInstance()->GetNm2AU(),6.0)
+                              /Parameters::GetInstance()->GetAvogadro();
+   this->vdWRadii = 1.430*Parameters::GetInstance()->GetAngstrom2AU();
+   this->bondingParameter = -39.0*Parameters::GetInstance()->GetEV2AU();
+   this->imuAmuS = 32.272*Parameters::GetInstance()->GetEV2AU();
+   this->imuAmuP = 11.080*Parameters::GetInstance()->GetEV2AU();
+   this->imuAmuD = 0.0;
+   this->effectiveNuclearChargeK = 8.7;
+   this->effectiveNuclearChargeL = 5.20;
+   this->effectiveNuclearChargeMsp = 0.0;
+   this->effectiveNuclearChargeMd = 0.0;
+   this->indoG1 = 0.532305;
+   this->indoF2 = 0.31580;
+   this->indoF0CoefficientS = (this->coreCharge - 0.5);
+   this->indoF0CoefficientP = (this->coreCharge - 0.5);
+   this->indoG1CoefficientS = -1.0*(this->coreCharge - 1.5)/6.0;
+   this->indoG1CoefficientP = -1.0/3.0;
+   this->indoF2CoefficientS = 0.0;
+   this->indoF2CoefficientP = -2.0*(this->coreCharge - 2.5)/25.0;
+   this->zindoBondingParameterS = -44.0*Parameters::GetInstance()->GetEV2AU(); //from orca3.0.1
+   this->zindoBondingParameterD = 0.0;
+   this->zindoF0ss = 14.00 * Parameters::GetInstance()->GetEV2AU(); // from orca3.0.1
+   this->zindoF0sd = 0.0;                   
+   this->zindoF0dd = 0.0;                  
+   this->zindoG1sp = 116828*Parameters::GetInstance()->GetKayser2AU();                 
+   this->zindoF2pp =  69310*Parameters::GetInstance()->GetKayser2AU();                 
+   this->zindoG2sd = 0.0;                 
+   this->zindoG1pd = 0.0;                 
+   this->zindoF2pd = 0.0;                 
+   this->zindoG3pd = 0.0;                 
+   this->zindoF2dd = 0.0;                 
+   this->zindoF4dd = 0.0;                 
+   this->zindoL = 2;
+   this->zindoM = 5;
+   this->zindoN = 0;
+   this->zindoIonPotS = 39.39 * Parameters::GetInstance()->GetEV2AU();
+   this->zindoIonPotP = 20.86 * Parameters::GetInstance()->GetEV2AU();
+   this->zindoIonPotD = 0.0 * Parameters::GetInstance()->GetEV2AU();
+   this->mndoCoreintegralS = -131.071548 * Parameters::GetInstance()->GetEV2AU();         
+   this->mndoCoreintegralP = -105.782137 * Parameters::GetInstance()->GetEV2AU();         
+   this->mndoOrbitalExponentS = 2.848487;      
+   this->mndoOrbitalExponentP = 2.848487;      
+   this->mndoBondingParameterS = -48.290460 * Parameters::GetInstance()->GetEV2AU();     
+   this->mndoBondingParameterP = -36.508540 * Parameters::GetInstance()->GetEV2AU();     
+   this->mndoAlpha =  3.419661 / Parameters::GetInstance()->GetAngstrom2AU();        
+   this->mndoElecEnergyAtom = -476.683781 * Parameters::GetInstance()->GetEV2AU();        
+   this->mndoHeatsFormAtom = 18.86 * Parameters::GetInstance()->GetKcalMolin2AU();
+   this->mndoGss =  16.92 * Parameters::GetInstance()->GetEV2AU();   
+   this->mndoGpp =  16.71 * Parameters::GetInstance()->GetEV2AU();   
+   this->mndoGsp =  17.25 * Parameters::GetInstance()->GetEV2AU();   
+   this->mndoGpp2 = 14.91 * Parameters::GetInstance()->GetEV2AU();  
+   this->mndoHsp =   4.83 * Parameters::GetInstance()->GetEV2AU();   
+   this->mndoDerivedParameterD[0] =   0.0;
+   this->mndoDerivedParameterD[1] =   0.5067166088;
+   this->mndoDerivedParameterD[2] =   0.4299633003;    
+   this->mndoDerivedParameterRho[0] = 0.5/0.6217935876;  
+   this->mndoDerivedParameterRho[1] = 0.5/1.0850000098;  
+   this->mndoDerivedParameterRho[2] = 0.5/1.0343451703;  
+   this->am1CoreintegralS = -136.105579 * Parameters::GetInstance()->GetEV2AU();         
+   this->am1CoreintegralP = -104.889885 * Parameters::GetInstance()->GetEV2AU();         
+   this->am1OrbitalExponentS = 3.770082;      
+   this->am1OrbitalExponentP = 2.494670;      
+   this->am1BondingParameterS = -69.590277 * Parameters::GetInstance()->GetEV2AU();     
+   this->am1BondingParameterP = -27.922360 * Parameters::GetInstance()->GetEV2AU();     
+   this->am1Alpha = 5.517800/ Parameters::GetInstance()->GetAngstrom2AU();        
+   this->am1Gss = this->mndoGss;
+   this->am1Gpp = this->mndoGpp;
+   this->am1Gsp = this->mndoGsp;
+   this->am1Gpp2 = this->mndoGpp2;
+   this->am1Hsp = this->mndoHsp;
+   this->am1DerivedParameterD[0] = 0.0;    
+   this->am1DerivedParameterD[1] = 0.4145203025;    
+   this->am1DerivedParameterD[2] = 0.4909446425;    
+   this->am1DerivedParameterRho[0] = 0.5/0.6217935876;
+   this->am1DerivedParameterRho[1] = 0.5/1.2088469198;  
+   this->am1DerivedParameterRho[2] = 0.5/0.9449175360;  
+   this->am1ParameterK[0] = 0.242079 * Parameters::GetInstance()->GetEV2AU();
+   this->am1ParameterK[1] = 0.003607 * Parameters::GetInstance()->GetEV2AU();
+   this->am1ParameterK[2] = 0.0 * Parameters::GetInstance()->GetEV2AU();
+   this->am1ParameterK[3] = 0.0 * Parameters::GetInstance()->GetEV2AU();
+   this->am1ParameterL[0] = 4.80 / pow(Parameters::GetInstance()->GetAngstrom2AU(),2.0);
+   this->am1ParameterL[1] = 4.60 / pow(Parameters::GetInstance()->GetAngstrom2AU(),2.0);
+   this->am1ParameterL[2] = 0.00 / pow(Parameters::GetInstance()->GetAngstrom2AU(),2.0);
+   this->am1ParameterL[3] = 0.00 / pow(Parameters::GetInstance()->GetAngstrom2AU(),2.0);
+   this->am1ParameterM[0] = 0.930 * Parameters::GetInstance()->GetAngstrom2AU();
+   this->am1ParameterM[1] = 1.660 * Parameters::GetInstance()->GetAngstrom2AU();
+   this->am1ParameterM[2] = 0.00 * Parameters::GetInstance()->GetAngstrom2AU();
+   this->am1ParameterM[3] = 0.00 * Parameters::GetInstance()->GetAngstrom2AU();
+   this->am1DCoreintegralS = this->am1CoreintegralS;
+   this->am1DCoreintegralP = this->am1CoreintegralP;
+   this->am1DBondingParameterS = this->am1BondingParameterS;
+   this->am1DBondingParameterP = this->am1BondingParameterP;
+   this->am1DAlpha = this->am1DAlpha;
+   this->pm3CoreintegralS = -110.435303 * Parameters::GetInstance()->GetEV2AU();         
+   this->pm3CoreintegralP = -105.685047 * Parameters::GetInstance()->GetEV2AU();         
+   this->pm3OrbitalExponentS = 4.708555;      
+   this->pm3OrbitalExponentP = 2.491178;      
+   this->pm3BondingParameterS = -48.405939 * Parameters::GetInstance()->GetEV2AU();     
+   this->pm3BondingParameterP = -27.744660 * Parameters::GetInstance()->GetEV2AU();     
+   this->pm3Alpha = 3.358921 / Parameters::GetInstance()->GetAngstrom2AU();        
+   this->pm3DerivedParameterD[0] = 0.0;    
+   this->pm3DerivedParameterD[1] = 0.3125302275;    
+   this->pm3DerivedParameterD[2] = 0.4916328225;    
+   this->pm3DerivedParameterRho[0] = 0.5/0.3857423305;
+   this->pm3DerivedParameterRho[1] = 0.5/0.6768359077;  
+   this->pm3DerivedParameterRho[2] = 0.5/0.6119953427;  
+   this->pm3ParameterK[0] = -0.012166 * Parameters::GetInstance()->GetEV2AU();
+   this->pm3ParameterK[1] = -0.002852 * Parameters::GetInstance()->GetEV2AU();
+   this->pm3ParameterK[2] = 0.0;
+   this->pm3ParameterK[3] = 0.0;
+   this->pm3ParameterL[0] = 6.023574 / pow(Parameters::GetInstance()->GetAngstrom2AU(),2.0);
+   this->pm3ParameterL[1] = 6.003717 / pow(Parameters::GetInstance()->GetAngstrom2AU(),2.0);
+   this->pm3ParameterL[2] = 0.00;
+   this->pm3ParameterL[3] = 0.00;
+   this->pm3ParameterM[0] = 1.856859 * Parameters::GetInstance()->GetAngstrom2AU();
+   this->pm3ParameterM[1] = 2.636158 * Parameters::GetInstance()->GetAngstrom2AU();
+   this->pm3ParameterM[2] = 0.00;
+   this->pm3ParameterM[3] = 0.00;
+   this->pm3Gss = 10.496667 * Parameters::GetInstance()->GetEV2AU();   
+   this->pm3Gpp = 14.817256 * Parameters::GetInstance()->GetEV2AU();   
+   this->pm3Gsp = 16.073689 * Parameters::GetInstance()->GetEV2AU();   
+   this->pm3Gpp2= 14.418393 * Parameters::GetInstance()->GetEV2AU();   
+   this->pm3Hsp =  0.727763 * Parameters::GetInstance()->GetEV2AU();   
+   //this->pm3PddgCoreintegralS = -48.241241 * Parameters::GetInstance()->GetEV2AU();         
+   //this->pm3PddgCoreintegralP = -36.461256 * Parameters::GetInstance()->GetEV2AU();
+   //this->pm3PddgOrbitalExponentS = 1.567864;      
+   //this->pm3PddgOrbitalExponentP = 1.846659;      
+   //this->pm3PddgBondingParameterS = -11.952818 * Parameters::GetInstance()->GetEV2AU();     
+   //this->pm3PddgBondingParameterP =  -9.922411 * Parameters::GetInstance()->GetEV2AU();
+   //this->pm3PddgAlpha = 2.725772 / Parameters::GetInstance()->GetAngstrom2AU();        
+   //this->pm3PddgDerivedParameterD[0] = 0.0;    
+   //this->pm3PddgDerivedParameterD[1] = 0.831413;    
+   //this->pm3PddgDerivedParameterD[2] = 0.663222;    
+   //this->pm3PddgDerivedParameterRho[0] = 1.214657;
+   //this->pm3PddgDerivedParameterRho[1] = 0.848467;  
+   //this->pm3PddgDerivedParameterRho[2] = 0.652785;  
+   //this->pm3PddgParameterK[0] = 0.048906 * Parameters::GetInstance()->GetEV2AU();
+   //this->pm3PddgParameterK[1] = 0.047697 * Parameters::GetInstance()->GetEV2AU();
+   //this->pm3PddgParameterK[2] = 0.0;
+   //this->pm3PddgParameterK[3] = 0.0;
+   //this->pm3PddgParameterL[0] = 5.765340 / pow(Parameters::GetInstance()->GetAngstrom2AU(),2.0);
+   //this->pm3PddgParameterL[1] = 5.973721 / pow(Parameters::GetInstance()->GetAngstrom2AU(),2.0);
+   //this->pm3PddgParameterL[2] = 0.00;
+   //this->pm3PddgParameterL[3] = 0.00;
+   //this->pm3PddgParameterM[0] = 1.682232 * Parameters::GetInstance()->GetAngstrom2AU();
+   //this->pm3PddgParameterM[1] = 0.894406 * Parameters::GetInstance()->GetAngstrom2AU();
+   //this->pm3PddgParameterM[2] = 0.00;
+   //this->pm3PddgParameterM[3] = 0.00;
+   //this->pm3PddgParameterPa[0] =-0.000743 * Parameters::GetInstance()->GetEV2AU();
+   //this->pm3PddgParameterPa[1] = 0.000985 * Parameters::GetInstance()->GetEV2AU();
+   //this->pm3PddgParameterDa[0] = 0.836915 * Parameters::GetInstance()->GetAngstrom2AU();
+   //this->pm3PddgParameterDa[1] = 1.585236 * Parameters::GetInstance()->GetAngstrom2AU();
+   this->pm3DCoreintegralS = this->pm3CoreintegralS;
+   this->pm3DCoreintegralP = this->pm3CoreintegralP;
+   this->pm3DBondingParameterS = this->pm3BondingParameterS;
+   this->pm3DBondingParameterP = this->pm3BondingParameterP;
+   this->pm3DAlpha = this->pm3Alpha;
+}
+}

--- /dev/null
+++ b/src/base/atoms/Fatom.h
@@ -0,0 +1,32 @@
+//************************************************************************//
+// Copyright (C) 2011-2014 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_FATOM
+#define INCLUDED_FATOM
+namespace MolDS_base_atoms{
+class Fatom : virtual public Atom {
+public:
+   Fatom(int index);
+   virtual ~Fatom();
+protected:
+   void virtual SetAtomicParameters();
+private:
+   Fatom();
+};
+}
+#endif

--- a/src/base/atoms/Znatom.cpp
+++ b/src/base/atoms/Znatom.cpp
@@ -93,19 +93,19 @@ void Znatom::SetAtomicParameters(){
    this->indoF2CoefficientS = 0.0;
    this->indoF2CoefficientP = -2.0*(this->coreCharge - 2.5)/25.0;
    */
-   this->zindoBondingParameterS = -10.0*Parameters::GetInstance()->GetEV2AU(); // orca 3.1
-   this->zindoBondingParameterD = -34.0*Parameters::GetInstance()->GetEV2AU(); // orca 3.1
+   this->zindoBondingParameterS = -10.0*Parameters::GetInstance()->GetEV2AU(); // orca 3.0.1
+   this->zindoBondingParameterD = -34.0*Parameters::GetInstance()->GetEV2AU(); // orca 3.0.1
    this->zindoF0ss = 7.98  * Parameters::GetInstance()->GetEV2AU();   // ZHKW_1980
    this->zindoF0sd = 9.39  * Parameters::GetInstance()->GetEV2AU();   // ZHKW_1980
    this->zindoF0dd = 14.55 * Parameters::GetInstance()->GetEV2AU();   // ZHKW_1980
    this->zindoG1sp = 20400 * Parameters::GetInstance()->GetKayser2AU(); // BZ_1979
    this->zindoF2pp =  9500 * Parameters::GetInstance()->GetKayser2AU(); // BZ_1979
-   this->zindoG2sd = 0.6199 * Parameters::GetInstance()->GetEV2AU();   // orca 3.1
-   this->zindoG1pd = 0.8679 * Parameters::GetInstance()->GetEV2AU();   // orca 3.1
-   this->zindoF2pd = 1.4878 * Parameters::GetInstance()->GetEV2AU();   // orca 3.1
-   this->zindoG3pd = 0.9919 * Parameters::GetInstance()->GetEV2AU();   // orca 3.1
-   this->zindoF2dd =11.4063 * Parameters::GetInstance()->GetEV2AU();   // orca 3.1
-   this->zindoF4dd = 7.6249 * Parameters::GetInstance()->GetEV2AU();   // orca 3.1
+   this->zindoG2sd = 0.6199 * Parameters::GetInstance()->GetEV2AU();   // orca 3.0.1
+   this->zindoG1pd = 0.8679 * Parameters::GetInstance()->GetEV2AU();   // orca 3.0.1
+   this->zindoF2pd = 1.4878 * Parameters::GetInstance()->GetEV2AU();   // orca 3.0.1
+   this->zindoG3pd = 0.9919 * Parameters::GetInstance()->GetEV2AU();   // orca 3.0.1
+   this->zindoF2dd =11.4063 * Parameters::GetInstance()->GetEV2AU();   // orca 3.0.1
+   this->zindoF4dd = 7.6249 * Parameters::GetInstance()->GetEV2AU();   // orca 3.0.1
    this->zindoL =  2;
    this->zindoM =  0;
    this->zindoN = 10;

--- /dev/null
+++ b/src/base/atoms/ghost/GhostFatom.cpp
@@ -0,0 +1,53 @@
+//************************************************************************//
+// Copyright (C) 2011-2014 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/>.         // 
+//************************************************************************//
+#include<stdio.h>
+#include<stdlib.h>
+#include<iostream>
+#include<sstream>
+#include<math.h>
+#include<vector>
+#include<boost/format.hpp>
+#include"../../Enums.h"
+#include"../../Uncopyable.h"
+#include"../../PrintController.h"
+#include"../../MolDSException.h"
+#include"../../MallocerFreer.h"
+#include"../../../mpi/MpiInt.h"
+#include"../../../mpi/MpiProcess.h"
+#include"../../EularAngle.h"
+#include"../../Parameters.h"
+#include"../../RealSphericalHarmonicsIndex.h"
+#include"../Atom.h"
+#include"../Fatom.h"
+#include"Ghost.h"
+#include"GhostFatom.h"
+using namespace std;
+using namespace MolDS_base;
+using namespace MolDS_base_atoms;
+namespace MolDS_base_atoms_ghost{
+GhostFatom::GhostFatom(int index) : Atom(index),Fatom(index),Ghost(index){
+   this->SetAtomicParameters();
+}
+
+GhostFatom::~GhostFatom(){}
+
+void GhostFatom::SetAtomicParameters(){
+   this->atomType = ghostF;
+}
+}

--- /dev/null
+++ b/src/base/atoms/ghost/GhostFatom.h
@@ -0,0 +1,32 @@
+//************************************************************************//
+// Copyright (C) 2011-2014 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_GHOSTFATOM
+#define INCLUDED_GHOSTFATOM
+namespace MolDS_base_atoms_ghost{
+class GhostFatom : public MolDS_base_atoms::Fatom, public Ghost {
+public:
+   GhostFatom(int index);
+   ~GhostFatom();
+protected:
+   void virtual SetAtomicParameters();
+private:
+   GhostFatom();
+};
+}
+#endif

--- a/src/base/factories/AtomFactory.cpp
+++ b/src/base/factories/AtomFactory.cpp
@@ -37,6 +37,7 @@
 #include"../atoms/Catom.h"
 #include"../atoms/Natom.h"
 #include"../atoms/Oatom.h"
+#include"../atoms/Fatom.h"
 #include"../atoms/Satom.h"
 #include"../atoms/Znatom.h"
 #include"../atoms/ghost/Ghost.h"
@@ -45,6 +46,7 @@
 #include"../atoms/ghost/GhostCatom.h"
 #include"../atoms/ghost/GhostNatom.h"
 #include"../atoms/ghost/GhostOatom.h"
+#include"../atoms/ghost/GhostFatom.h"
 #include"../atoms/ghost/GhostSatom.h"
 #include"../atoms/ghost/GhostZnatom.h"
 #include"../atoms/mm/EnvironmentalPointCharge.h"
@@ -77,6 +79,9 @@ Atom* AtomFactory::Create(AtomType atomType, int index, double x, double y, doub
    else if(atomType == O){
       atom = new Oatom(index);
    }
+   else if(atomType == F){
+      atom = new Fatom(index);
+   }
    else if(atomType == S){
       atom = new Satom(index);
    }
@@ -98,6 +103,9 @@ Atom* AtomFactory::Create(AtomType atomType, int index, double x, double y, doub
    else if(atomType == ghostO){
       atom = new GhostOatom(index);
    }
+   else if(atomType == ghostF){
+      atom = new GhostFatom(index);
+   }
    else if(atomType == ghostS){
       atom = new GhostSatom(index);
    }

--- a/src/cndo/Cndo2.cpp
+++ b/src/cndo/Cndo2.cpp
@@ -52,6 +52,7 @@
 #include"../base/atoms/Catom.h"
 #include"../base/atoms/Natom.h"
 #include"../base/atoms/Oatom.h"
+#include"../base/atoms/Fatom.h"
 #include"../base/atoms/Satom.h"
 #include"../base/Molecule.h"
 #include"../base/GTOExpansionSTO.h"
@@ -269,7 +270,7 @@ void Cndo2::SetEnableAtomTypes(){
    this->enableAtomTypes.push_back(C);
    this->enableAtomTypes.push_back(N);
    this->enableAtomTypes.push_back(O);
-   //this->enableAtomTypes.push_back(F);
+   this->enableAtomTypes.push_back(F);
    //this->enableAtomTypes.push_back(Na);
    //this->enableAtomTypes.push_back(Mg);
    //this->enableAtomTypes.push_back(Al);

--- a/src/indo/Indo.cpp
+++ b/src/indo/Indo.cpp
@@ -41,6 +41,7 @@
 #include"../base/atoms/Catom.h"
 #include"../base/atoms/Natom.h"
 #include"../base/atoms/Oatom.h"
+#include"../base/atoms/Fatom.h"
 #include"../base/atoms/Satom.h"
 #include"../base/Molecule.h"
 #include"../base/ElectronicStructure.h"
@@ -103,7 +104,7 @@ void Indo::SetEnableAtomTypes(){
    this->enableAtomTypes.push_back(C);
    this->enableAtomTypes.push_back(N);
    this->enableAtomTypes.push_back(O);
-   //this->enableAtomTypes.push_back(F);
+   this->enableAtomTypes.push_back(F);
 }
 
 double Indo::GetFockDiagElement(const Atom& atomA, 

--- a/src/mndo/Mndo.cpp
+++ b/src/mndo/Mndo.cpp
@@ -48,6 +48,7 @@
 #include"../base/atoms/Catom.h"
 #include"../base/atoms/Natom.h"
 #include"../base/atoms/Oatom.h"
+#include"../base/atoms/Fatom.h"
 #include"../base/atoms/Satom.h"
 #include"../base/atoms/mm/EnvironmentalPointCharge.h"
 #include"../base/Molecule.h"
@@ -215,6 +216,7 @@ void Mndo::SetEnableAtomTypes(){
    this->enableAtomTypes.push_back(C);
    this->enableAtomTypes.push_back(N);
    this->enableAtomTypes.push_back(O);
+   this->enableAtomTypes.push_back(F);
    this->enableAtomTypes.push_back(S);
    this->enableAtomTypes.push_back(Zn);
 }

--- a/src/pm3/Pm3.cpp
+++ b/src/pm3/Pm3.cpp
@@ -40,6 +40,7 @@
 #include"../base/atoms/Catom.h"
 #include"../base/atoms/Natom.h"
 #include"../base/atoms/Oatom.h"
+#include"../base/atoms/Fatom.h"
 #include"../base/atoms/Satom.h"
 #include"../base/Molecule.h"
 #include"../base/ElectronicStructure.h"
@@ -134,6 +135,7 @@ void Pm3::SetEnableAtomTypes(){
    this->enableAtomTypes.push_back(C);
    this->enableAtomTypes.push_back(N);
    this->enableAtomTypes.push_back(O);
+   this->enableAtomTypes.push_back(F);
    this->enableAtomTypes.push_back(S);
    this->enableAtomTypes.push_back(Zn);
 }

--- a/src/pm3/Pm3D.cpp
+++ b/src/pm3/Pm3D.cpp
@@ -40,6 +40,7 @@
 #include"../base/atoms/Catom.h"
 #include"../base/atoms/Natom.h"
 #include"../base/atoms/Oatom.h"
+#include"../base/atoms/Fatom.h"
 #include"../base/atoms/Satom.h"
 #include"../base/Molecule.h"
 #include"../base/ElectronicStructure.h"
@@ -135,6 +136,7 @@ void Pm3D::SetEnableAtomTypes(){
    this->enableAtomTypes.push_back(C);
    this->enableAtomTypes.push_back(N);
    this->enableAtomTypes.push_back(O);
+   this->enableAtomTypes.push_back(F);
    this->enableAtomTypes.push_back(S);
 }
 

--- /dev/null
+++ b/src/tools/deriveParametersNDDO/data/AM1_Fatom.dat
@@ -0,0 +1,57 @@
+=====  NDDO parameters =====
+orbital exponent S in [a.u.] = 3.7700820000
+orbital exponent P in [a.u.] = 2.4946700000
+Gss in [a.u.] = 0.6217935876
+Gpp in [a.u.] = 0.6140762913
+Gsp in [a.u.] = 0.6339207675
+Gpp2 in [a.u.] = 0.5479280373
+Hsp in [a.u.] = 0.1774978149
+Hpp = 0.5*(Gpp - Gpp2)
+
+
+=====  NDDO derived parameters =====
+D1 in [a.u.] = 0.4145203025
+D2 in [a.u.] = 0.4909446425
+AM in [a.u.] = 0.6217935876
+
+iter=0	AD in [a.u.] = 1.2283236244
+iter=1	AD in [a.u.] = 1.2073444405
+iter=2	AD in [a.u.] = 1.2088371512
+iter=3	AD in [a.u.] = 1.2088469248
+iter=4	AD in [a.u.] = 1.2088469198
+iter=5	AD in [a.u.] = 1.2088469198
+iter=6	AD in [a.u.] = 1.2088469198
+iter=7	AD in [a.u.] = 1.2088469198
+iter=8	AD in [a.u.] = 1.2088469198
+iter=9	AD in [a.u.] = nan
+iter=10	AD in [a.u.] = nan
+iter=11	AD in [a.u.] = nan
+iter=12	AD in [a.u.] = nan
+iter=13	AD in [a.u.] = nan
+iter=14	AD in [a.u.] = nan
+iter=15	AD in [a.u.] = nan
+iter=16	AD in [a.u.] = nan
+iter=17	AD in [a.u.] = nan
+iter=18	AD in [a.u.] = nan
+iter=19	AD in [a.u.] = nan
+
+iter=0	AQ in [a.u.] = 0.9174540993
+iter=1	AQ in [a.u.] = 0.9603487201
+iter=2	AQ in [a.u.] = 0.9445669865
+iter=3	AQ in [a.u.] = 0.9449131918
+iter=4	AQ in [a.u.] = 0.9449175372
+iter=5	AQ in [a.u.] = 0.9449175360
+iter=6	AQ in [a.u.] = 0.9449175360
+iter=7	AQ in [a.u.] = 0.9449175360
+iter=8	AQ in [a.u.] = 0.9449175360
+iter=9	AQ in [a.u.] = 0.9449175360
+iter=10	AQ in [a.u.] = 0.9449175360
+iter=11	AQ in [a.u.] = 0.9449175360
+iter=12	AQ in [a.u.] = 0.9449175360
+iter=13	AQ in [a.u.] = nan
+iter=14	AQ in [a.u.] = nan
+iter=15	AQ in [a.u.] = nan
+iter=16	AQ in [a.u.] = nan
+iter=17	AQ in [a.u.] = nan
+iter=18	AQ in [a.u.] = nan
+iter=19	AQ in [a.u.] = nan

--- /dev/null
+++ b/src/tools/deriveParametersNDDO/data/MNDO_Fatom.dat
@@ -0,0 +1,57 @@
+=====  NDDO parameters =====
+orbital exponent S in [a.u.] = 2.8484870000
+orbital exponent P in [a.u.] = 2.8484870000
+Gss in [a.u.] = 0.6217935876
+Gpp in [a.u.] = 0.6140762913
+Gsp in [a.u.] = 0.6339207675
+Gpp2 in [a.u.] = 0.5479280373
+Hsp in [a.u.] = 0.1774978149
+Hpp = 0.5*(Gpp - Gpp2)
+
+
+=====  NDDO derived parameters =====
+D1 in [a.u.] = 0.5067166088
+D2 in [a.u.] = 0.4299633003
+AM in [a.u.] = 0.6217935876
+
+iter=0	AD in [a.u.] = 1.0923581507
+iter=1	AD in [a.u.] = 1.0844153173
+iter=2	AD in [a.u.] = 1.0849985924
+iter=3	AD in [a.u.] = 1.0850000101
+iter=4	AD in [a.u.] = 1.0850000098
+iter=5	AD in [a.u.] = 1.0850000098
+iter=6	AD in [a.u.] = 1.0850000098
+iter=7	AD in [a.u.] = 1.0850000098
+iter=8	AD in [a.u.] = nan
+iter=9	AD in [a.u.] = nan
+iter=10	AD in [a.u.] = nan
+iter=11	AD in [a.u.] = nan
+iter=12	AD in [a.u.] = nan
+iter=13	AD in [a.u.] = nan
+iter=14	AD in [a.u.] = nan
+iter=15	AD in [a.u.] = nan
+iter=16	AD in [a.u.] = nan
+iter=17	AD in [a.u.] = nan
+iter=18	AD in [a.u.] = nan
+iter=19	AD in [a.u.] = nan
+
+iter=0	AQ in [a.u.] = 1.0563037502
+iter=1	AQ in [a.u.] = 1.0213602694
+iter=2	AQ in [a.u.] = 1.0341225934
+iter=3	AQ in [a.u.] = 1.0343474767
+iter=4	AQ in [a.u.] = 1.0343451699
+iter=5	AQ in [a.u.] = 1.0343451703
+iter=6	AQ in [a.u.] = 1.0343451703
+iter=7	AQ in [a.u.] = 1.0343451703
+iter=8	AQ in [a.u.] = 1.0343451703
+iter=9	AQ in [a.u.] = 1.0343451703
+iter=10	AQ in [a.u.] = 1.0343451703
+iter=11	AQ in [a.u.] = nan
+iter=12	AQ in [a.u.] = nan
+iter=13	AQ in [a.u.] = nan
+iter=14	AQ in [a.u.] = nan
+iter=15	AQ in [a.u.] = nan
+iter=16	AQ in [a.u.] = nan
+iter=17	AQ in [a.u.] = nan
+iter=18	AQ in [a.u.] = nan
+iter=19	AQ in [a.u.] = nan

--- /dev/null
+++ b/src/tools/deriveParametersNDDO/data/PM3_Fatom.dat
@@ -0,0 +1,57 @@
+=====  NDDO parameters =====
+orbital exponent S in [a.u.] = 4.7085550000
+orbital exponent P in [a.u.] = 2.4911780000
+Gss in [a.u.] = 0.3857423305
+Gpp in [a.u.] = 0.5445197853
+Gsp in [a.u.] = 0.5906924793
+Gpp2 in [a.u.] = 0.5298619569
+Hsp in [a.u.] = 0.0267445843
+Hpp = 0.5*(Gpp - Gpp2)
+
+
+=====  NDDO derived parameters =====
+D1 in [a.u.] = 0.3125302275
+D2 in [a.u.] = 0.4916328225
+AM in [a.u.] = 0.3857423305
+
+iter=0	AD in [a.u.] = 0.6688994415
+iter=1	AD in [a.u.] = 0.6771081714
+iter=2	AD in [a.u.] = 0.6768332910
+iter=3	AD in [a.u.] = 0.6768359068
+iter=4	AD in [a.u.] = 0.6768359077
+iter=5	AD in [a.u.] = 0.6768359077
+iter=6	AD in [a.u.] = 0.6768359077
+iter=7	AD in [a.u.] = 0.6768359077
+iter=8	AD in [a.u.] = 0.6768359077
+iter=9	AD in [a.u.] = 0.6768359077
+iter=10	AD in [a.u.] = 0.6768359077
+iter=11	AD in [a.u.] = 0.6768359077
+iter=12	AD in [a.u.] = 0.6768359077
+iter=13	AD in [a.u.] = 0.6768359077
+iter=14	AD in [a.u.] = nan
+iter=15	AD in [a.u.] = nan
+iter=16	AD in [a.u.] = nan
+iter=17	AD in [a.u.] = nan
+iter=18	AD in [a.u.] = nan
+iter=19	AD in [a.u.] = nan
+
+iter=0	AQ in [a.u.] = 0.4945714241
+iter=1	AQ in [a.u.] = 0.7079622968
+iter=2	AQ in [a.u.] = 0.5891692549
+iter=3	AQ in [a.u.] = 0.6081313939
+iter=4	AQ in [a.u.] = 0.6121786715
+iter=5	AQ in [a.u.] = 0.6119939256
+iter=6	AQ in [a.u.] = 0.6119953422
+iter=7	AQ in [a.u.] = 0.6119953427
+iter=8	AQ in [a.u.] = 0.6119953427
+iter=9	AQ in [a.u.] = 0.6119953427
+iter=10	AQ in [a.u.] = 0.6119953427
+iter=11	AQ in [a.u.] = 0.6119953427
+iter=12	AQ in [a.u.] = 0.6119953427
+iter=13	AQ in [a.u.] = 0.6119953427
+iter=14	AQ in [a.u.] = 0.6119953427
+iter=15	AQ in [a.u.] = 0.6119953427
+iter=16	AQ in [a.u.] = 0.6119953427
+iter=17	AQ in [a.u.] = 0.6119953427
+iter=18	AQ in [a.u.] = 0.6119953427
+iter=19	AQ in [a.u.] = 0.6119953427

--- a/src/tools/deriveParametersNDDO/deriveParametersNDDO.cpp
+++ b/src/tools/deriveParametersNDDO/deriveParametersNDDO.cpp
@@ -66,18 +66,18 @@ int main(){
 
    // following variables should be set as input
    double eV2AU = 0.03674903;
-   long double orbitalExponentS=2.0473590;
-   long double orbitalExponentP=1.4609460;
-   long double Gss = 11.800000* eV2AU;
-   long double Gpp = 13.300000* eV2AU;
-   long double Gsp = 11.182018* eV2AU;
-   long double Gpp2= 12.930520* eV2AU;
-   long double Hsp =  0.484606* eV2AU;
+   long double orbitalExponentS=4.708555;
+   long double orbitalExponentP=2.491178;
+   long double Gss = 10.496667 * eV2AU;
+   long double Gpp = 14.817256 * eV2AU;
+   long double Gsp = 16.073689 * eV2AU;
+   long double Gpp2= 14.418393 * eV2AU;
+   long double Hsp =  0.727763 * eV2AU;
    long double Hpp = 0.5*(Gpp - Gpp2);
    // n=2 for l-shell (C, N, O and etc.)
    // n=3 for m-shell (S and etc.)
    // n=4 for n-shell (Zn and etc.)
-   double n=4;
+   double n=2;
 
    // following variables are output
    long double D1=0.0;

--- a/src/zindo/ZindoS.cpp
+++ b/src/zindo/ZindoS.cpp
@@ -50,6 +50,7 @@
 #include"../base/atoms/Catom.h"
 #include"../base/atoms/Natom.h"
 #include"../base/atoms/Oatom.h"
+#include"../base/atoms/Fatom.h"
 #include"../base/atoms/Satom.h"
 #include"../base/Molecule.h"
 #include"../base/ElectronicStructure.h"
@@ -214,6 +215,7 @@ void ZindoS::SetEnableAtomTypes(){
    this->enableAtomTypes.push_back(C);
    this->enableAtomTypes.push_back(N);
    this->enableAtomTypes.push_back(O);
+   this->enableAtomTypes.push_back(F);
    this->enableAtomTypes.push_back(S);
 }
 

--- a/test/Test_Of_MolDS.rb
+++ b/test/Test_Of_MolDS.rb
@@ -432,6 +432,20 @@ mklNumThreads = "4"
 ompNumThreads = "2"
 tester.doesTestMpi(mklNumThreads,ompNumThreads)
 
+prefix = "ch3f_mndo"
+tester = Tester.new(prefix, <<"TITLE")
+\t\t\t>>> CH3F <<<
+TITLE
+mklNumThreads = "1"
+ompNumThreads = "1"
+tester.doesTestOmp(mklNumThreads,ompNumThreads)
+mklNumThreads = "2"
+ompNumThreads = "2"
+tester.doesTestOmp(mklNumThreads,ompNumThreads)
+mklNumThreads = "4"
+ompNumThreads = "2"
+tester.doesTestMpi(mklNumThreads,ompNumThreads)
+
 prefix = "ch4_mndo_directCIS_singlet"
 tester = Tester.new(prefix, <<"SECTION", <<"TITLE")
 ---------------------------------------------------
@@ -586,6 +600,20 @@ mklNumThreads = "4"
 ompNumThreads = "2"
 tester.doesTestMpi(mklNumThreads,ompNumThreads)
 
+prefix = "ch3f_am1"
+tester = Tester.new(prefix, <<"TITLE")
+\t\t\t>>> CH3F <<<
+TITLE
+mklNumThreads = "1"
+ompNumThreads = "1"
+tester.doesTestOmp(mklNumThreads,ompNumThreads)
+mklNumThreads = "2"
+ompNumThreads = "2"
+tester.doesTestOmp(mklNumThreads,ompNumThreads)
+mklNumThreads = "4"
+ompNumThreads = "2"
+tester.doesTestMpi(mklNumThreads,ompNumThreads)
+
 prefix = "ch4_am1_directCIS_singlet"
 tester = Tester.new(prefix, <<"SECTION", <<"TITLE")
 ---------------------------------------------------
@@ -740,6 +768,20 @@ mklNumThreads = "4"
 ompNumThreads = "2"
 tester.doesTestMpi(mklNumThreads,ompNumThreads)
 
+prefix = "ch3f_pm3"
+tester = Tester.new(prefix, <<"TITLE")
+\t\t\t>>> CH3F <<<
+TITLE
+mklNumThreads = "1"
+ompNumThreads = "1"
+tester.doesTestOmp(mklNumThreads,ompNumThreads)
+mklNumThreads = "2"
+ompNumThreads = "2"
+tester.doesTestOmp(mklNumThreads,ompNumThreads)
+mklNumThreads = "4"
+ompNumThreads = "2"
+tester.doesTestMpi(mklNumThreads,ompNumThreads)
+
 prefix = "ch4_pm3_directCIS_singlet"
 tester = Tester.new(prefix, <<"SECTION", <<"TITLE")
 ---------------------------------------------------

--- /dev/null
+++ b/test/ch3f_am1.dat
@@ -0,0 +1,119 @@
+
+
+     >>>>>  Welcome to the MolDS world at 2014/4/29(Thu.) 0:48:18  <<<<<
+
+
+**********  START: Parse input  **********
+	Total number of atoms: 5
+	Total number of valence AOs: 11
+	Total number of valence electrons: 14
+
+				| i-th | atom type |   x[a.u.]   |   y[a.u.]   |   z[a.u.]   |		|  x[angst.]  |  y[angst.]  |  z[angst.]  |
+	Atom coordinates:	0	C	-4.533892e-01	1.142541e+00	0.000000e+00		-2.399232e-01	6.046065e-01	0.000000e+00
+	Atom coordinates:	1	H	2.205900e-01	-7.638339e-01	0.000000e+00		1.167312e-01	-4.042035e-01	0.000000e+00
+	Atom coordinates:	2	H	2.206248e-01	2.095715e+00	-1.650962e+00		1.167496e-01	1.109005e+00	-8.736515e-01
+	Atom coordinates:	3	H	-2.475396e+00	1.142566e+00	0.000000e+00		-1.309923e+00	6.046197e-01	0.000000e+00
+	Atom coordinates:	4	F	3.970023e-01	2.345144e+00	2.082990e+00		2.100846e-01	1.240997e+00	1.102271e+00
+
+			|   x[a.u.]   |   y[a.u.]   |   z[a.u.]   |		|  x[angst.]  |  y[angst.]  |  z[angst.]  |
+	Center of Mass:	1.367960e-03	1.785647e+00	1.113904e+00		7.238933e-04	9.449239e-01	5.894525e-01
+
+			|   x[a.u.]   |   y[a.u.]   |   z[a.u.]   |		|  x[angst.]  |  y[angst.]  |  z[angst.]  |
+	Center of Core:	1.385500e-03	1.785672e+00	1.113947e+00		7.331749e-04	9.449370e-01	5.894753e-01
+
+	SCF conditions:
+		Max iterations: 500
+		RMS density: 1.000000e-08
+		Damping threshold: 1.000000e+00
+		Damping weight: 0.000000e+00
+		DIIS number of error vectors: 5
+		DIIS starting error: 1.000000e-01
+		DIIS ending error: 0.000000e+00
+		van der Waals (vdW) correction: no
+
+	Memory conditions:
+		Heap limit: 2.560000e+02[MB]
+
+Input terms:
+theory | am1 | theory_end | scf | max_iter | 500 | rms_density | 1e-8 | damping_thresh | 1.0 | 
+damping_weight | 0.0 | diis_num_error_vect | 5 | diis_start_error | 0.1 | diis_end_error | 0.0 | scf_end | geometry | 
+c | -0.23992322 | 0.60460652 | 0.00000000 | h | 0.11673121 | -0.40420349 | 0.00000000 | h | 0.11674962 | 
+1.10900471 | -0.87365150 | h | -1.30992322 | 0.60461970 | 0.00000000 | f | 0.21008457 | 1.24099676 | 1.10227059 | 
+geometry_end | 
+
+**********  DONE: Parse input  ***********
+
+
+**********  START: AM1-SCF  **********
+			|  RMS density  | DIIS error | DIIS on/off | damping on/off |
+	SCF iter 0	4.810457e-01	0.000000e+00			
+	SCF iter 1	1.813094e-01	0.000000e+00			
+	SCF iter 2	7.213805e-02	4.688753e-01			
+	SCF iter 3	3.219608e-02	2.545192e-01			
+	SCF iter 4	1.498908e-02	1.265996e-01			
+	SCF iter 5	7.162861e-03	6.338147e-02			
+	SCF iter 6	1.124795e-04	3.133790e-02	on		
+	SCF iter 7	2.684330e-05	3.452097e-04	on		
+	SCF iter 8	4.101758e-06	8.013624e-05	on		
+	SCF iter 9	2.948782e-07	1.063658e-05	on		
+	SCF iter 10	7.151809e-08	7.402140e-07	on		
+	SCF iter 11	1.141598e-08	1.901341e-07	on		
+	SCF iter 12	3.270105e-09	4.867728e-08	on		
+
+
+
+		AM1-SCF met convergence criterion(^^b
+
+
+			| i-th | occ/unocc |  e[a.u.]  |  e[eV]  | 
+	Energy of MO:	0	occ	-1.818706e+00	-4.948991e+01
+	Energy of MO:	1	occ	-1.047475e+00	-2.850348e+01
+	Energy of MO:	2	occ	-6.243858e-01	-1.699054e+01
+	Energy of MO:	3	occ	-6.243858e-01	-1.699054e+01
+	Energy of MO:	4	occ	-6.101224e-01	-1.660241e+01
+	Energy of MO:	5	occ	-4.468290e-01	-1.215893e+01
+	Energy of MO:	6	occ	-4.468290e-01	-1.215893e+01
+	Energy of MO:	7	unocc	1.469798e-01	3.999556e+00
+	Energy of MO:	8	unocc	1.469798e-01	3.999556e+00
+	Energy of MO:	9	unocc	1.560625e-01	4.246711e+00
+	Energy of MO:	10	unocc	1.814507e-01	4.937564e+00
+
+				|   [a.u.]   |   [eV]   |
+	Electronic energy(SCF):	-2.406211e+01	-6.547686e+02
+	Note that this electronic energy includes core-repulsions.
+
+				|   [a.u.]   |   [eV]   |
+	Core repulsion energy:	1.944773e+01	5.292038e+02
+
+					|   x[a.u.]   |   y[a.u.]   |   z[a.u.]   |  magnitude[a.u.]  |		|  x[debye]  |  y[debye]  |  z[debye]  |  magnitude[debye]  |
+	Total Dipole moment(SCF):	2.153315e+00	3.045095e+00	5.274389e+00	6.459764e+00		5.473183e+00	7.739862e+00	1.340616e+01	1.641909e+01
+
+					|  x[a.u.]  |  y[a.u.]  |  z[a.u.]  |  magnitude[a.u.]  |		|  x[debye]  |  y[debye]  |  z[debye]  |  magnitude[debye]  |
+	Electronic Dipole moment(SCF):	3.241434e+00	4.583888e+00	7.939680e+00	9.724065e+00		8.238906e+00	1.165108e+01	2.018066e+01	2.471611e+01
+
+					|  x[a.u.]  |  y[a.u.]  |  z[a.u.]  |  magnitude[a.u.]  |		|  x[debye]  |  y[debye]  |  z[debye]  |  magnitude[debye]  |
+	Core Dipole moment:		-1.088119e+00	-1.538792e+00	-2.665291e+00	3.264301e+00		-2.765723e+00	-3.911221e+00	-6.774495e+00	8.297027e+00
+
+				| k-th eigenstate | i-th atom | atom type | core charge[a.u.] | Mulliken charge[a.u.]| 
+	Mulliken charge(SCF):	0	0	C	4.000000e+00	-1.819333e-02
+	Mulliken charge(SCF):	0	1	H	1.000000e+00	6.494912e-02
+	Mulliken charge(SCF):	0	2	H	1.000000e+00	6.494916e-02
+	Mulliken charge(SCF):	0	3	H	1.000000e+00	6.494917e-02
+	Mulliken charge(SCF):	0	4	F	7.000000e+00	-1.766541e-01
+
+	Elapsed time(omp) for the SCF = 0.010500[s].
+**********  DONE: AM1-SCF  **********
+
+
+	Summary for memory usage:
+		Max Heap: 0.121728[MB].
+		Current Heap(Leaked): 0.000000[MB].
+
+
+     >>>>>  The MolDS finished normally!  <<<<<
+     >>>>>  CPU time: 0.012938[s].  <<<<<
+     >>>>>  Elapsed time: 0[s].  <<<<<
+     >>>>>  Elapsed time(OMP): 0.0125909[s].  <<<<<
+     >>>>>  See you.  <<<<<
+
+

--- /dev/null
+++ b/test/ch3f_am1.in
@@ -0,0 +1,22 @@
+THEORY
+   am1
+THEORY_END
+
+SCF
+   max_iter 500
+   rms_density 1e-8
+   damping_thresh 1.0 
+   damping_weight 0.0
+   diis_num_error_vect 5
+   diis_start_error 0.1
+   diis_end_error 0.0
+SCF_END
+
+GEOMETRY
+ C                 -0.23992322    0.60460652    0.00000000
+ H                  0.11673121   -0.40420349    0.00000000
+ H                  0.11674962    1.10900471   -0.87365150
+ H                 -1.30992322    0.60461970    0.00000000
+ F                  0.21008457    1.24099676    1.10227059
+GEOMETRY_END
+

--- /dev/null
+++ b/test/ch3f_mndo.dat
@@ -0,0 +1,121 @@
+
+
+     >>>>>  Welcome to the MolDS world at 2014/4/29(Thu.) 0:49:40  <<<<<
+
+
+**********  START: Parse input  **********
+	Total number of atoms: 5
+	Total number of valence AOs: 11
+	Total number of valence electrons: 14
+
+				| i-th | atom type |   x[a.u.]   |   y[a.u.]   |   z[a.u.]   |		|  x[angst.]  |  y[angst.]  |  z[angst.]  |
+	Atom coordinates:	0	C	-4.533892e-01	1.142541e+00	0.000000e+00		-2.399232e-01	6.046065e-01	0.000000e+00
+	Atom coordinates:	1	H	2.205900e-01	-7.638339e-01	0.000000e+00		1.167312e-01	-4.042035e-01	0.000000e+00
+	Atom coordinates:	2	H	2.206248e-01	2.095715e+00	-1.650962e+00		1.167496e-01	1.109005e+00	-8.736515e-01
+	Atom coordinates:	3	H	-2.475396e+00	1.142566e+00	0.000000e+00		-1.309923e+00	6.046197e-01	0.000000e+00
+	Atom coordinates:	4	F	3.970023e-01	2.345144e+00	2.082990e+00		2.100846e-01	1.240997e+00	1.102271e+00
+
+			|   x[a.u.]   |   y[a.u.]   |   z[a.u.]   |		|  x[angst.]  |  y[angst.]  |  z[angst.]  |
+	Center of Mass:	1.367960e-03	1.785647e+00	1.113904e+00		7.238933e-04	9.449239e-01	5.894525e-01
+
+			|   x[a.u.]   |   y[a.u.]   |   z[a.u.]   |		|  x[angst.]  |  y[angst.]  |  z[angst.]  |
+	Center of Core:	1.385500e-03	1.785672e+00	1.113947e+00		7.331749e-04	9.449370e-01	5.894753e-01
+
+	SCF conditions:
+		Max iterations: 500
+		RMS density: 1.000000e-08
+		Damping threshold: 1.000000e+00
+		Damping weight: 0.000000e+00
+		DIIS number of error vectors: 5
+		DIIS starting error: 1.000000e-01
+		DIIS ending error: 0.000000e+00
+		van der Waals (vdW) correction: no
+
+	Memory conditions:
+		Heap limit: 2.560000e+02[MB]
+
+Input terms:
+theory | mndo | theory_end | scf | max_iter | 500 | rms_density | 1e-8 | damping_thresh | 1.0 | 
+damping_weight | 0.0 | diis_num_error_vect | 5 | diis_start_error | 0.1 | diis_end_error | 0.0 | scf_end | geometry | 
+c | -0.23992322 | 0.60460652 | 0.00000000 | h | 0.11673121 | -0.40420349 | 0.00000000 | h | 0.11674962 | 
+1.10900471 | -0.87365150 | h | -1.30992322 | 0.60461970 | 0.00000000 | f | 0.21008457 | 1.24099676 | 1.10227059 | 
+geometry_end | 
+
+**********  DONE: Parse input  ***********
+
+
+**********  START: MNDO-SCF  **********
+			|  RMS density  | DIIS error | DIIS on/off | damping on/off |
+	SCF iter 0	4.810457e-01	0.000000e+00			
+	SCF iter 1	1.871189e-01	0.000000e+00			
+	SCF iter 2	7.178292e-02	4.945442e-01			
+	SCF iter 3	3.117400e-02	2.689719e-01			
+	SCF iter 4	1.435152e-02	1.327763e-01			
+	SCF iter 5	6.810611e-03	6.433879e-02			
+	SCF iter 6	9.009495e-05	3.110174e-02	on		
+	SCF iter 7	1.844529e-05	2.778082e-04	on		
+	SCF iter 8	4.231855e-06	5.901048e-05	on		
+	SCF iter 9	3.240228e-07	1.081522e-05	on		
+	SCF iter 10	4.527847e-08	7.584081e-07	on		
+	SCF iter 11	4.828388e-09	1.288712e-07	on		
+
+
+
+		MNDO-SCF met convergence criterion(^^b
+
+
+			| i-th | occ/unocc |  e[a.u.]  |  e[eV]  | 
+	Energy of MO:	0	occ	-1.702786e+00	-4.633555e+01
+	Energy of MO:	1	occ	-1.033510e+00	-2.812347e+01
+	Energy of MO:	2	occ	-6.385986e-01	-1.737729e+01
+	Energy of MO:	3	occ	-6.355261e-01	-1.729368e+01
+	Energy of MO:	4	occ	-6.355261e-01	-1.729368e+01
+	Energy of MO:	5	occ	-4.851277e-01	-1.320110e+01
+	Energy of MO:	6	occ	-4.851277e-01	-1.320110e+01
+	Energy of MO:	7	unocc	1.357296e-01	3.693421e+00
+	Energy of MO:	8	unocc	1.357297e-01	3.693421e+00
+	Energy of MO:	9	unocc	1.797346e-01	4.890867e+00
+	Energy of MO:	10	unocc	1.885824e-01	5.131629e+00
+
+				|   [a.u.]   |   [eV]   |
+	Electronic energy(SCF):	-2.390179e+01	-6.504060e+02
+	Note that this electronic energy includes core-repulsions.
+
+				|   [a.u.]   |   [eV]   |
+	Core repulsion energy:	1.955890e+01	5.322291e+02
+
+					|   x[a.u.]   |   y[a.u.]   |   z[a.u.]   |  magnitude[a.u.]  |		|  x[debye]  |  y[debye]  |  z[debye]  |  magnitude[debye]  |
+	Total Dipole moment(SCF):	1.960721e+00	2.772694e+00	4.802614e+00	5.881952e+00		4.983657e+00	7.047486e+00	1.220703e+01	1.495043e+01
+
+					|  x[a.u.]  |  y[a.u.]  |  z[a.u.]  |  magnitude[a.u.]  |		|  x[debye]  |  y[debye]  |  z[debye]  |  magnitude[debye]  |
+	Electronic Dipole moment(SCF):	3.048840e+00	4.311486e+00	7.467905e+00	9.146253e+00		7.749380e+00	1.095871e+01	1.898153e+01	2.324746e+01
+
+					|  x[a.u.]  |  y[a.u.]  |  z[a.u.]  |  magnitude[a.u.]  |		|  x[debye]  |  y[debye]  |  z[debye]  |  magnitude[debye]  |
+	Core Dipole moment:		-1.088119e+00	-1.538792e+00	-2.665291e+00	3.264301e+00		-2.765723e+00	-3.911221e+00	-6.774495e+00	8.297027e+00
+
+				| k-th eigenstate | i-th atom | atom type | core charge[a.u.] | Mulliken charge[a.u.]| 
+	Mulliken charge(SCF):	0	0	C	4.000000e+00	2.761804e-01
+	Mulliken charge(SCF):	0	1	H	1.000000e+00	-7.596358e-03
+	Mulliken charge(SCF):	0	2	H	1.000000e+00	-7.596306e-03
+	Mulliken charge(SCF):	0	3	H	1.000000e+00	-7.596308e-03
+	Mulliken charge(SCF):	0	4	F	7.000000e+00	-2.533914e-01
+
+				|  [a.u.]  |  [Kcal/mol]  | 
+	Heats of formation:	-9.173557e-02	-5.756493e+01
+
+	Elapsed time(omp) for the SCF = 0.009764[s].
+**********  DONE: MNDO-SCF  **********
+
+
+	Summary for memory usage:
+		Max Heap: 0.121728[MB].
+		Current Heap(Leaked): 0.000000[MB].
+
+
+     >>>>>  The MolDS finished normally!  <<<<<
+     >>>>>  CPU time: 0.012207[s].  <<<<<
+     >>>>>  Elapsed time: 0[s].  <<<<<
+     >>>>>  Elapsed time(OMP): 0.010814[s].  <<<<<
+     >>>>>  See you.  <<<<<
+
+

--- /dev/null
+++ b/test/ch3f_mndo.in
@@ -0,0 +1,22 @@
+THEORY
+   mndo
+THEORY_END
+
+SCF
+   max_iter 500
+   rms_density 1e-8
+   damping_thresh 1.0 
+   damping_weight 0.0
+   diis_num_error_vect 5
+   diis_start_error 0.1
+   diis_end_error 0.0
+SCF_END
+
+GEOMETRY
+ C                 -0.23992322    0.60460652    0.00000000
+ H                  0.11673121   -0.40420349    0.00000000
+ H                  0.11674962    1.10900471   -0.87365150
+ H                 -1.30992322    0.60461970    0.00000000
+ F                  0.21008457    1.24099676    1.10227059
+GEOMETRY_END
+

--- /dev/null
+++ b/test/ch3f_pm3.dat
@@ -0,0 +1,120 @@
+
+
+     >>>>>  Welcome to the MolDS world at 2014/4/29(Thu.) 0:44:48  <<<<<
+
+
+**********  START: Parse input  **********
+	Total number of atoms: 5
+	Total number of valence AOs: 11
+	Total number of valence electrons: 14
+
+				| i-th | atom type |   x[a.u.]   |   y[a.u.]   |   z[a.u.]   |		|  x[angst.]  |  y[angst.]  |  z[angst.]  |
+	Atom coordinates:	0	C	-4.533892e-01	1.142541e+00	0.000000e+00		-2.399232e-01	6.046065e-01	0.000000e+00
+	Atom coordinates:	1	H	2.205900e-01	-7.638339e-01	0.000000e+00		1.167312e-01	-4.042035e-01	0.000000e+00
+	Atom coordinates:	2	H	2.206248e-01	2.095715e+00	-1.650962e+00		1.167496e-01	1.109005e+00	-8.736515e-01
+	Atom coordinates:	3	H	-2.475396e+00	1.142566e+00	0.000000e+00		-1.309923e+00	6.046197e-01	0.000000e+00
+	Atom coordinates:	4	F	3.970023e-01	2.345144e+00	2.082990e+00		2.100846e-01	1.240997e+00	1.102271e+00
+
+			|   x[a.u.]   |   y[a.u.]   |   z[a.u.]   |		|  x[angst.]  |  y[angst.]  |  z[angst.]  |
+	Center of Mass:	1.367960e-03	1.785647e+00	1.113904e+00		7.238933e-04	9.449239e-01	5.894525e-01
+
+			|   x[a.u.]   |   y[a.u.]   |   z[a.u.]   |		|  x[angst.]  |  y[angst.]  |  z[angst.]  |
+	Center of Core:	1.385500e-03	1.785672e+00	1.113947e+00		7.331749e-04	9.449370e-01	5.894753e-01
+
+	SCF conditions:
+		Max iterations: 500
+		RMS density: 1.000000e-08
+		Damping threshold: 1.000000e+00
+		Damping weight: 0.000000e+00
+		DIIS number of error vectors: 5
+		DIIS starting error: 1.000000e-01
+		DIIS ending error: 0.000000e+00
+		van der Waals (vdW) correction: no
+
+	Memory conditions:
+		Heap limit: 2.560000e+02[MB]
+
+Input terms:
+theory | pm3 | theory_end | scf | max_iter | 500 | rms_density | 1e-8 | damping_thresh | 1.0 | 
+damping_weight | 0.0 | diis_num_error_vect | 5 | diis_start_error | 0.1 | diis_end_error | 0.0 | scf_end | geometry | 
+c | -0.23992322 | 0.60460652 | 0.00000000 | h | 0.11673121 | -0.40420349 | 0.00000000 | h | 0.11674962 | 
+1.10900471 | -0.87365150 | h | -1.30992322 | 0.60461970 | 0.00000000 | f | 0.21008457 | 1.24099676 | 1.10227059 | 
+geometry_end | 
+
+**********  DONE: Parse input  ***********
+
+
+**********  START: PM3-SCF  **********
+			|  RMS density  | DIIS error | DIIS on/off | damping on/off |
+	SCF iter 0	4.810457e-01	0.000000e+00			
+	SCF iter 1	1.867170e-01	0.000000e+00			
+	SCF iter 2	6.730937e-02	4.641583e-01			
+	SCF iter 3	3.389793e-02	2.377993e-01			
+	SCF iter 4	1.857022e-02	1.407733e-01			
+	SCF iter 5	1.039733e-02	8.234052e-02			
+	SCF iter 6	7.581158e-05	4.696825e-02	on		
+	SCF iter 7	1.723006e-05	1.718827e-04	on		
+	SCF iter 8	6.769747e-06	6.121626e-05	on		
+	SCF iter 9	3.123328e-06	2.309953e-05	on		
+	SCF iter 10	6.924853e-07	1.126421e-05	on		
+	SCF iter 11	8.205988e-08	2.477657e-06	on		
+	SCF iter 12	2.568285e-08	2.749173e-07	on		
+	SCF iter 13	5.739182e-09	1.126507e-07	on		
+
+
+
+		PM3-SCF met convergence criterion(^^b
+
+
+			| i-th | occ/unocc |  e[a.u.]  |  e[eV]  | 
+	Energy of MO:	0	occ	-1.173782e+00	-3.194049e+01
+	Energy of MO:	1	occ	-7.481778e-01	-2.035912e+01
+	Energy of MO:	2	occ	-6.584337e-01	-1.791704e+01
+	Energy of MO:	3	occ	-6.584336e-01	-1.791703e+01
+	Energy of MO:	4	occ	-6.368305e-01	-1.732918e+01
+	Energy of MO:	5	occ	-4.768455e-01	-1.297573e+01
+	Energy of MO:	6	occ	-4.768455e-01	-1.297573e+01
+	Energy of MO:	7	unocc	1.094050e-01	2.977086e+00
+	Energy of MO:	8	unocc	1.428529e-01	3.887258e+00
+	Energy of MO:	9	unocc	1.428530e-01	3.887258e+00
+	Energy of MO:	10	unocc	1.558753e-01	4.241617e+00
+
+				|   [a.u.]   |   [eV]   |
+	Electronic energy(SCF):	-2.224335e+01	-6.052773e+02
+	Note that this electronic energy includes core-repulsions.
+
+				|   [a.u.]   |   [eV]   |
+	Core repulsion energy:	1.828033e+01	4.974371e+02
+
+					|   x[a.u.]   |   y[a.u.]   |   z[a.u.]   |  magnitude[a.u.]  |		|  x[debye]  |  y[debye]  |  z[debye]  |  magnitude[debye]  |
+	Total Dipole moment(SCF):	2.146407e+00	3.035505e+00	5.257579e+00	6.439215e+00		5.455624e+00	7.715485e+00	1.336344e+01	1.636686e+01
+
+					|  x[a.u.]  |  y[a.u.]  |  z[a.u.]  |  magnitude[a.u.]  |		|  x[debye]  |  y[debye]  |  z[debye]  |  magnitude[debye]  |
+	Electronic Dipole moment(SCF):	3.234526e+00	4.574297e+00	7.922870e+00	9.703516e+00		8.221347e+00	1.162671e+01	2.013793e+01	2.466388e+01
+
+					|  x[a.u.]  |  y[a.u.]  |  z[a.u.]  |  magnitude[a.u.]  |		|  x[debye]  |  y[debye]  |  z[debye]  |  magnitude[debye]  |
+	Core Dipole moment:		-1.088119e+00	-1.538792e+00	-2.665291e+00	3.264301e+00		-2.765723e+00	-3.911221e+00	-6.774495e+00	8.297027e+00
+
+				| k-th eigenstate | i-th atom | atom type | core charge[a.u.] | Mulliken charge[a.u.]| 
+	Mulliken charge(SCF):	0	0	C	4.000000e+00	6.107371e-02
+	Mulliken charge(SCF):	0	1	H	1.000000e+00	2.909550e-02
+	Mulliken charge(SCF):	0	2	H	1.000000e+00	2.909555e-02
+	Mulliken charge(SCF):	0	3	H	1.000000e+00	2.909555e-02
+	Mulliken charge(SCF):	0	4	F	7.000000e+00	-1.483603e-01
+
+	Elapsed time(omp) for the SCF = 0.078902[s].
+**********  DONE: PM3-SCF  **********
+
+
+	Summary for memory usage:
+		Max Heap: 0.121728[MB].
+		Current Heap(Leaked): 0.000000[MB].
+
+
+     >>>>>  The MolDS finished normally!  <<<<<
+     >>>>>  CPU time: 0.025291[s].  <<<<<
+     >>>>>  Elapsed time: 0[s].  <<<<<
+     >>>>>  Elapsed time(OMP): 0.079946[s].  <<<<<
+     >>>>>  See you.  <<<<<
+
+

--- /dev/null
+++ b/test/ch3f_pm3.in
@@ -0,0 +1,22 @@
+THEORY
+   pm3
+THEORY_END
+
+SCF
+   max_iter 500
+   rms_density 1e-8
+   damping_thresh 1.0 
+   damping_weight 0.0
+   diis_num_error_vect 5
+   diis_start_error 0.1
+   diis_end_error 0.0
+SCF_END
+
+GEOMETRY
+ C                 -0.23992322    0.60460652    0.00000000
+ H                  0.11673121   -0.40420349    0.00000000
+ H                  0.11674962    1.10900471   -0.87365150
+ H                 -1.30992322    0.60461970    0.00000000
+ F                  0.21008457    1.24099676    1.10227059
+GEOMETRY_END
+