Python loadAtoms Exemples

Exemple #1

Fichier : HighLevel.py Projet : ga32xan/ProbeParticleModel

def importGeometries(fname):
    if (fname.lower().endswith(".xyz") or fname.lower().endswith(".bas")):
        atoms, nDim, lvec = bU.loadAtoms(fname)
    elif fname.lower().endswith(".xsf"):
        atoms, nDim, lvec = bU.loadXSFGeom(fname)
    elif fname.lower().endswith(".cube"):
        atoms, nDim, lvec = bU.loadAtomsCUBE(fname)
    elif fname.lower().endswith(".in"):
        atoms, nDim, lvec = bU.loadGeometryIN(fname)
    else:
        sys.exit("ERROR!!! Unknown format of geometry system. Supported "
                 "formats are: .xyz, .bas., .xsf, .cube, .in \n\n")
    if (nDim != []):
        PPU.params['gridN'] = nDim
    if (lvec != []):
        PPU.params['gridA'] = lvec[1]
        PPU.params['gridB'] = lvec[2]
        PPU.params['gridC'] = lvec[3]
    else:
        lvec = np.zeros((4, 3))
        lvec[1, :] = PPU.params['gridA'].copy()
        lvec[2, :] = PPU.params['gridB'].copy()
        lvec[3, :] = PPU.params['gridC'].copy()
    return atoms, lvec

Exemple #2

Fichier : test_hartree_watter_QKscan.py Projet : jhv5a/ProbeParticleModel

del Fz

cell = np.array([
    PP.params['gridA'],
    PP.params['gridB'],
    PP.params['gridC'],
]).copy()
gridN = PP.params['gridN']

print("cell", cell)

PP.setFF(FFLJ, cell)

print(" # ============ define atoms ")

atoms = basUtils.loadAtoms('watter4NaCl-2.xyz')
Rs = np.array([atoms[1], atoms[2], atoms[3]])
iZs = np.array(atoms[0])

if not PP.params['PBC']:
    print(" NO PBC => autoGeom ")
    PP.autoGeom(Rs, shiftXY=True, fitCell=True, border=3.0)
    print(" NO PBC => params[ 'gridA'   ] ", PP.params['gridA'])
    print(" NO PBC => params[ 'gridB'   ] ", PP.params['gridB'])
    print(" NO PBC => params[ 'gridC'   ] ", PP.params['gridC'])
    print(" NO PBC => params[ 'scanMin' ] ", PP.params['scanMin'])
    print(" NO PBC => params[ 'scanMax' ] ", PP.params['scanMax'])

Rs = np.transpose(Rs, (1, 0)).copy()
Qs = np.array(atoms[4])

Exemple #3

Fichier : test_hartree_watter_QKscan.py Projet : ProkopHapala/ProbeParticleModel

cell =np.array([
PP.params['gridA'],
PP.params['gridB'],
PP.params['gridC'],
]).copy() 
gridN = PP.params['gridN']

print "cell", cell

PP.setFF( FFLJ, cell  )

print " # ============ define atoms "

atoms    = basUtils.loadAtoms('watter4NaCl-2.xyz')
Rs       = np.array([atoms[1],atoms[2],atoms[3]]);  
iZs      = np.array( atoms[0])

if not PP.params['PBC' ]:
	print " NO PBC => autoGeom "
	PP.autoGeom( Rs, shiftXY=True,  fitCell=True,  border=3.0 )
	print " NO PBC => params[ 'gridA'   ] ", PP.params[ 'gridA' ] 
	print " NO PBC => params[ 'gridB'   ] ", PP.params[ 'gridB'   ]
	print " NO PBC => params[ 'gridC'   ] ", PP.params[ 'gridC'   ]
	print " NO PBC => params[ 'scanMin' ] ", PP.params[ 'scanMin' ]
	print " NO PBC => params[ 'scanMax' ] ", PP.params[ 'scanMax' ]

Rs = np.transpose( Rs, (1,0) ).copy() 
Qs = np.array( atoms[4] )

Exemple #4

Fichier : hartree2FFs.py Projet : ProkopHapala/ProbeParticleModel

X, Y, Z = getMGrid(dims, dd)

print '--- Get Probe Density ---'

rho = getProbeDensity(sampleSize, X, Y, Z, sigma, dd, {'dz2':1.0})

print '--- Get Forces ---'
Fx, Fy, Fz = getForces( V, rho, sampleSize, dims, dd, X, Y, Z)
print 'Fx.max(), Fx.min() = ', Fx.max(), Fx.min()


PP.params['gridA'] = lvec[ 1,:  ].copy()
PP.params['gridB'] = lvec[ 2,:  ].copy()
PP.params['gridC'] = lvec[ 3,:  ].copy()
PP.params['gridN'] = nDim.copy()

print "--- Compute Lennard-Jones Force-filed ---"
atoms     = basUtils.loadAtoms('input.xyz', elements.ELEMENT_DICT )
iZs,Rs,Qs = PP.parseAtoms( atoms, autogeom = False, PBC = True )
FFLJ      = PP.computeLJ( Rs, iZs, FFLJ=None, FFparams=None)

print "--- Saving ---"

GU.saveXSF('FFel_x.xsf', Fx, lvec, head)
GU.saveXSF('FFel_y.xsf' , Fy, lvec, head)
GU.saveXSF('FFel_z.xsf' , Fz, lvec, head)

GU.saveVecFieldXsf( 'FFLJ', FFLJ, lvec, head)

Exemple #5

Fichier : hartree2FFs.py Projet : jhv5a/ProbeParticleModel

print('--- Get Probe Density ---')

rho = getProbeDensity(sampleSize, X, Y, Z, sigma, dd, {'dz2':1.0})

print('--- Get Forces ---')
Fx, Fy, Fz = getForces( V, rho, sampleSize, dims, dd, X, Y, Z)
print('Fx.max(), Fx.min() = ', Fx.max(), Fx.min())


PP.params['gridA'] = lvec[ 1,:  ].copy()
PP.params['gridB'] = lvec[ 2,:  ].copy()
PP.params['gridC'] = lvec[ 3,:  ].copy()
PP.params['gridN'] = nDim.copy()

print("--- Compute Lennard-Jones Force-filed ---")
atoms     = basUtils.loadAtoms('input.xyz')
if os.path.isfile( 'atomtypes.ini' ):
    print(">> LOADING LOCAL atomtypes.ini")  
    FFparams=PPU.loadSpecies( 'atomtypes.ini' ) 
else:
    FFparams = PPU.loadSpecies( cpp_utils.PACKAGE_PATH+'/defaults/atomtypes.ini' )

iZs,Rs,Qs = PP.parseAtoms(atoms, autogeom = False, PBC = True,
                          FFparams=FFparams)
FFLJ      = PP.computeLJ( Rs, iZs, FFLJ=None, FFparams=FFparams)

print("--- Saving ---")

GU.saveXSF('FFel_x.xsf', Fx, lvec, head)
GU.saveXSF('FFel_y.xsf' , Fy, lvec, head)
GU.saveXSF('FFel_z.xsf' , Fz, lvec, head)

Exemple #6

Fichier : afm.py Projet : ProkopHapala/ProbeParticleModel

# Working with parameters file
ParamFilename = ProjName + ".ini"

if os.path.exists(ParamFilename):
    PP.loadParams(ParamFilename)
else:
    print "File {} with parameters doesn't exist!!! Using defaults".format(ParamFilename)


cell = np.array([PP.params["gridA"], PP.params["gridB"], PP.params["gridC"]]).copy()


lvec = PP.params2lvec()
atoms = basUtils.loadAtoms(filename, elements.ELEMENT_DICT)
iZs, Rs, Qs = PP.parseAtoms(atoms, autogeom=False, PBC=True)


# Lennard Jonnes contribution to the force field
if PP.params["useLJ"]:
    # checking if files exist:
    exists = True
    for lj_file in ["x", "y", "z"]:
        lj_file = ProjName + "_LJ_F_" + lj_file + ".xsf"
        if not os.path.exists(lj_file):
            exists = False

    if exists:
        if query_yes_no(
            "I have found files containing LJ forcefield. Should I use them (yes) or do you want me to recompute them from scratch (n) ?"

Exemple #7

ParamFilename = ProjName + ".ini"

if os.path.exists(ParamFilename):
    PP.loadParams(ParamFilename)
else:
    print "File {} with parameters doesn't exist!!! Using defaults".format(
        ParamFilename)

cell = np.array([
    PP.params['gridA'],
    PP.params['gridB'],
    PP.params['gridC'],
]).copy()

lvec = PP.params2lvec()
atoms = basUtils.loadAtoms(filename, elements.ELEMENT_DICT)
iZs, Rs, Qs = PP.parseAtoms(atoms, autogeom=False, PBC=True)

# Lennard Jonnes contribution to the force field
if PP.params['useLJ']:
    #checking if files exist:
    exists = True
    for lj_file in ["x", "y", "z"]:
        lj_file = ProjName + "_LJ_F_" + lj_file + ".xsf"
        if not os.path.exists(lj_file):
            exists = False

    if exists:
        if query_yes_no(
                "I have found files containing LJ forcefield. Should I use them (yes) or do you want me to recompute them from scratch (n) ?"
        ):

Exemple #8

Fichier : test_hartree_watter_QKscan.py Projet : ltalirz/ProbeParticleModel

del Fz

cell = np.array([
    PP.params['gridA'],
    PP.params['gridB'],
    PP.params['gridC'],
]).copy()
gridN = PP.params['gridN']

print "cell", cell

PP.setFF(FFLJ, cell)

print " # ============ define atoms "

atoms = basUtils.loadAtoms('watter4NaCl-2.xyz', elements.ELEMENT_DICT)
Rs = np.array([atoms[1], atoms[2], atoms[3]])
iZs = np.array(atoms[0])

if not PP.params['PBC']:
    print " NO PBC => autoGeom "
    PP.autoGeom(Rs, shiftXY=True, fitCell=True, border=3.0)
    print " NO PBC => params[ 'gridA'   ] ", PP.params['gridA']
    print " NO PBC => params[ 'gridB'   ] ", PP.params['gridB']
    print " NO PBC => params[ 'gridC'   ] ", PP.params['gridC']
    print " NO PBC => params[ 'scanMin' ] ", PP.params['scanMin']
    print " NO PBC => params[ 'scanMax' ] ", PP.params['scanMax']

Rs = np.transpose(Rs, (1, 0)).copy()
Qs = np.array(atoms[4])

Exemple #9

Fichier : LJ_4fold.py Projet : ga32xan/ProbeParticleModel

print " ============= RUN  "

print " >> WARNING!!! OVEWRITING SETTINGS by params.ini  "

#PP.loadParams( 'params_carbox.ini' )

print " load Electrostatic Force-field "
FFel_x,lvec,nDim,head=GU.loadXSF('FFel_x.xsf')
PP.params['gridA'] = lvec[ 1,:  ].copy()
PP.params['gridB'] = lvec[ 2,:  ].copy()
PP.params['gridC'] = lvec[ 3,:  ].copy()
PP.params['gridN'] = nDim.copy()

print " compute Lennard-Jones Force-filed "
atoms     = basUtils.loadAtoms('geom.bas')
if os.path.isfile( 'atomtypes.ini' ):
	print ">> LOADING LOCAL atomtypes.ini"  
	FFparams=PPU.loadSpecies( 'atomtypes.ini' ) 
else:
	FFparams = PPU.loadSpecies( cpp_utils.PACKAGE_PATH+'/defaults/atomtypes.ini' )
iZs,Rs,Qs = parseAtoms( atoms, autogeom = False, PBC = True, FFparams=FFparams )
FFLJ      = PP.computeLJ( iZs, Rs, FFLJ=None, cell=None, autogeom = False, PBC =
                         True, FFparams=FFparams)

print "impose 4fold symmetry on FFLJ "
FFLJ4 = np.zeros(np.shape( FFLJ ))
FFLJ4[:,:,:,0] = 0.25*( FFLJ[:,:,:,0] - FFLJ[:,:,::-1,0] + FFLJ[:,::-1,:,0] - FFLJ[:,::-1,::-1,0] )
FFLJ4[:,:,:,1] = 0.25*( FFLJ[:,:,:,1] + FFLJ[:,:,::-1,1] - FFLJ[:,::-1,:,1] - FFLJ[:,::-1,::-1,1] )
FFLJ4[:,:,:,2] = 0.25*( FFLJ[:,:,:,2] + FFLJ[:,:,::-1,2] + FFLJ[:,::-1,:,2] + FFLJ[:,::-1,::-1,2] )

Exemple #10

Fichier : LJ_4fold.py Projet : ProkopHapala/ProbeParticleModel

print " ============= RUN  "

print " >> WARNING!!! OVEWRITING SETTINGS by params.ini  "

#PP.loadParams( 'params_carbox.ini' )

print " load Electrostatic Force-field "
FFel_x,lvec,nDim,head=GU.loadXSF('FFel_x.xsf')
PP.params['gridA'] = lvec[ 1,:  ].copy()
PP.params['gridB'] = lvec[ 2,:  ].copy()
PP.params['gridC'] = lvec[ 3,:  ].copy()
PP.params['gridN'] = nDim.copy()

print " compute Lennard-Jones Force-filed "
atoms     = basUtils.loadAtoms('geom.bas', elements.ELEMENT_DICT )
iZs,Rs,Qs = parseAtoms( atoms, autogeom = False, PBC = True )
FFLJ      = PP.computeLJ( iZs, Rs, FFLJ=None, cell=None, autogeom = False, PBC = True )

print "impose 4fold symmetry on FFLJ "
FFLJ4 = np.zeros(np.shape( FFLJ ))
FFLJ4[:,:,:,0] = 0.25*( FFLJ[:,:,:,0] - FFLJ[:,:,::-1,0] + FFLJ[:,::-1,:,0] - FFLJ[:,::-1,::-1,0] )
FFLJ4[:,:,:,1] = 0.25*( FFLJ[:,:,:,1] + FFLJ[:,:,::-1,1] - FFLJ[:,::-1,:,1] - FFLJ[:,::-1,::-1,1] )
FFLJ4[:,:,:,2] = 0.25*( FFLJ[:,:,:,2] + FFLJ[:,:,::-1,2] + FFLJ[:,::-1,:,2] + FFLJ[:,::-1,::-1,2] )

print "save FFLJ to .xsf "
GU.saveVecFieldXsf( 'FFLJ', FFLJ4, lvec, head )


print " ***** ALL DONE ***** "

Exemple #11

Fichier : test_hartree_watter_QKscan.py Projet : ProkopHapala/ProbeParticleModel

cell =np.array([
PP.params['gridA'],
PP.params['gridB'],
PP.params['gridC'],
]).copy() 
gridN = PP.params['gridN']

print "cell", cell

PP.setFF( FFLJ, cell  )

print " # ============ define atoms "

atoms    = basUtils.loadAtoms('watter4NaCl-2.xyz', elements.ELEMENT_DICT )
Rs       = np.array([atoms[1],atoms[2],atoms[3]]);  
iZs      = np.array( atoms[0])

if not PP.params['PBC' ]:
	print " NO PBC => autoGeom "
	PP.autoGeom( Rs, shiftXY=True,  fitCell=True,  border=3.0 )
	print " NO PBC => params[ 'gridA'   ] ", PP.params[ 'gridA' ] 
	print " NO PBC => params[ 'gridB'   ] ", PP.params[ 'gridB'   ]
	print " NO PBC => params[ 'gridC'   ] ", PP.params[ 'gridC'   ]
	print " NO PBC => params[ 'scanMin' ] ", PP.params[ 'scanMin' ]
	print " NO PBC => params[ 'scanMax' ] ", PP.params[ 'scanMax' ]

Rs = np.transpose( Rs, (1,0) ).copy() 
Qs = np.array( atoms[4] )

Exemple #12

Fichier : ppr.py Projet : ProkopHapala/ProbeParticleModel

FFel[:,:,:,2]=Fz

cell =np.array([
PP.params['gridA'],
PP.params['gridB'],
PP.params['gridC'],
]).copy() 
gridN = PP.params['gridN']




print " # ============ define atoms "


atoms    = basUtils.loadAtoms(sys.argv[1], elements.ELEMENT_DICT )
Rs       = np.array([atoms[1],atoms[2],atoms[3]]);  
iZs      = np.array( atoms[0])

"""
if not PP.params['PBC' ]:
	print " NO PBC => autoGeom "
	PP.autoGeom( Rs, shiftXY=True,  fitCell=True,  border=3.0 )
	print " NO PBC => params[ 'gridA'   ] ", PP.params[ 'gridA' ] 
	print " NO PBC => params[ 'gridB'   ] ", PP.params[ 'gridB'   ]
	print " NO PBC => params[ 'gridC'   ] ", PP.params[ 'gridC'   ]
	print " NO PBC => params[ 'scanMin' ] ", PP.params[ 'scanMin' ]
	print " NO PBC => params[ 'scanMax' ] ", PP.params[ 'scanMax' ]
"""
Rs = np.transpose( Rs, (1,0) ).copy() 
Qs = np.array( atoms[4] )

Exemple #13

Fichier : ppr.py Projet : ltalirz/ProbeParticleModel

FFel = np.zeros(np.shape(FF))

FFel[:, :, :, 0] = Fx
FFel[:, :, :, 1] = Fy
FFel[:, :, :, 2] = Fz

cell = np.array([
    PP.params['gridA'],
    PP.params['gridB'],
    PP.params['gridC'],
]).copy()
gridN = PP.params['gridN']

print " # ============ define atoms "

atoms = basUtils.loadAtoms(sys.argv[1], elements.ELEMENT_DICT)
Rs = np.array([atoms[1], atoms[2], atoms[3]])
iZs = np.array(atoms[0])
"""
if not PP.params['PBC' ]:
	print " NO PBC => autoGeom "
	PP.autoGeom( Rs, shiftXY=True,  fitCell=True,  border=3.0 )
	print " NO PBC => params[ 'gridA'   ] ", PP.params[ 'gridA' ] 
	print " NO PBC => params[ 'gridB'   ] ", PP.params[ 'gridB'   ]
	print " NO PBC => params[ 'gridC'   ] ", PP.params[ 'gridC'   ]
	print " NO PBC => params[ 'scanMin' ] ", PP.params[ 'scanMin' ]
	print " NO PBC => params[ 'scanMax' ] ", PP.params[ 'scanMax' ]
"""
Rs = np.transpose(Rs, (1, 0)).copy()
Qs = np.array(atoms[4])

Exemple #14

print " ============= RUN  "

print " >> WARNING!!! OVEWRITING SETTINGS by params.ini  "

#PP.loadParams( 'params_carbox.ini' )

print " load Electrostatic Force-field "
FFel_x, lvec, nDim, head = GU.loadXSF('FFel_x.xsf')
PP.params['gridA'] = lvec[1, :].copy()
PP.params['gridB'] = lvec[2, :].copy()
PP.params['gridC'] = lvec[3, :].copy()
PP.params['gridN'] = nDim.copy()

print " compute Lennard-Jones Force-filed "
atoms = basUtils.loadAtoms('geom.bas', elements.ELEMENT_DICT)
iZs, Rs, Qs = parseAtoms(atoms, autogeom=False, PBC=True)
FFLJ = PP.computeLJ(iZs, Rs, FFLJ=None, cell=None, autogeom=False, PBC=True)

print "impose 4fold symmetry on FFLJ "
FFLJ4 = np.zeros(np.shape(FFLJ))
FFLJ4[:, :, :, 0] = 0.25 * (FFLJ[:, :, :, 0] - FFLJ[:, :, ::-1, 0] +
                            FFLJ[:, ::-1, :, 0] - FFLJ[:, ::-1, ::-1, 0])
FFLJ4[:, :, :, 1] = 0.25 * (FFLJ[:, :, :, 1] + FFLJ[:, :, ::-1, 1] -
                            FFLJ[:, ::-1, :, 1] - FFLJ[:, ::-1, ::-1, 1])
FFLJ4[:, :, :, 2] = 0.25 * (FFLJ[:, :, :, 2] + FFLJ[:, :, ::-1, 2] +
                            FFLJ[:, ::-1, :, 2] + FFLJ[:, ::-1, ::-1, 2])

print "save FFLJ to .xsf "
GU.saveVecFieldXsf('FFLJ', FFLJ4, lvec, head)

Exemple #15

import ProbeParticle as PP

print " # ==========  server interface file I/O "

PP.loadParams('params.ini')

print " # ============ define atoms "

#bas      = basUtils.loadBas('surf.bas')[0]
#bas      = basUtils.loadBas('PTCDA_Ruslan_1x1.bas')[0]
#bas      = basUtils.loadBas('GrN6x6.bas')[0]

#atoms      = basUtils.loadAtoms('GrN6x6.bas', elements.ELEMENT_DICT )
#atoms      = basUtils.loadAtoms('GrN6x6.xyz', elements.ELEMENT_DICT )

atoms = basUtils.loadAtoms('input.xyz', elements.ELEMENT_DICT)
Rs = np.array([atoms[1], atoms[2], atoms[3]])
iZs = np.array(atoms[0])

if not PP.params['PBC']:
    print " NO PBC => autoGeom "
    PP.autoGeom(Rs, shiftXY=True, fitCell=True, border=3.0)
    print " NO PBC => params[ 'gridA'   ] ", PP.params['gridA']
    print " NO PBC => params[ 'gridB'   ] ", PP.params['gridB']
    print " NO PBC => params[ 'gridC'   ] ", PP.params['gridC']
    print " NO PBC => params[ 'scanMin' ] ", PP.params['scanMin']
    print " NO PBC => params[ 'scanMax' ] ", PP.params['scanMax']

#Rs[0] += PP.params['moleculeShift' ][0]          # shift molecule so that we sample reasonable part of potential
#Rs[1] += PP.params['moleculeShift' ][1]
#Rs[2] += PP.params['moleculeShift' ][2]

Exemple #16

Fichier : afm.py Projet : ga32xan/ProbeParticleModel

ParamFilename = ProjName + ".ini"

if os.path.exists(ParamFilename):
    PP.loadParams(ParamFilename)
else:
    print "File {} with parameters doesn't exist!!! Using defaults".format(
        ParamFilename)

cell = np.array([
    PP.params['gridA'],
    PP.params['gridB'],
    PP.params['gridC'],
]).copy()

lvec = PP.params2lvec()
atoms = basUtils.loadAtoms(filename)

FFparams = None
if os.path.isfile('atomtypes.ini'):
    print ">> LOADING LOCAL atomtypes.ini"
    FFparams = PPU.loadSpecies('atomtypes.ini')
else:
    FFparams = PPU.loadSpecies(cpp_utils.PACKAGE_PATH +
                               '/defaults/atomtypes.ini')

iZs, Rs, Qs = PP.parseAtoms(atoms, autogeom=False, PBC=True, FFparams=FFparams)

# Lennard Jonnes contribution to the force field
if PP.params['useLJ']:
    #checking if files exist:
    exists = True

Exemple #17

Fichier : testServer2.py Projet : ProkopHapala/ProbeParticleModel

#makeclean( )  # force to recompile 

import  ProbeParticle as PP

print " # ==========  server interface file I/O "

PP.loadParams( 'params.ini' )

print " # ============ define atoms "

#bas      = basUtils.loadBas('surf.bas')[0]
#bas      = basUtils.loadBas('PTCDA_Ruslan_1x1.bas')[0]
#bas      = basUtils.loadBas('GrN6x6.bas')[0]

atoms    = basUtils.loadAtoms('input.xyz')
Rs       = np.array([atoms[1],atoms[2],atoms[3]]);  
iZs      = np.array( atoms[0])

if not PP.params['PBC' ]:
	print " NO PBC => autoGeom "
	PP.autoGeom( Rs, shiftXY=True,  fitCell=True,  border=3.0 )
	print " NO PBC => params[ 'gridA'   ] ", PP.params[ 'gridA' ] 
	print " NO PBC => params[ 'gridB'   ] ", PP.params[ 'gridB'   ]
	print " NO PBC => params[ 'gridC'   ] ", PP.params[ 'gridC'   ]
	print " NO PBC => params[ 'scanMin' ] ", PP.params[ 'scanMin' ]
	print " NO PBC => params[ 'scanMax' ] ", PP.params[ 'scanMax' ]


#Rs[0] += PP.params['moleculeShift' ][0]          # shift molecule so that we sample reasonable part of potential 
#Rs[1] += PP.params['moleculeShift' ][1]          

Exemple #18

Fichier : afm.py Projet : ProkopHapala/ProbeParticleModel

    PP.loadParams(ParamFilename) 
else:
    print "File {} with parameters doesn't exist!!! Using defaults".format(ParamFilename)


cell =np.array([
PP.params['gridA'],
PP.params['gridB'],
PP.params['gridC'],
]).copy()




lvec = PP.params2lvec()
atoms    = basUtils.loadAtoms(filename )

FFparams=None
if os.path.isfile( 'atomtypes.ini' ):
	print ">> LOADING LOCAL atomtypes.ini"  
	FFparams=PPU.loadSpecies( 'atomtypes.ini' ) 
else:
	FFparams = PPU.loadSpecies( cpp_utils.PACKAGE_PATH+'/defaults/atomtypes.ini' )

iZs,Rs,Qs = PP.parseAtoms( atoms, autogeom = False, PBC = True,FFparams=FFparams )



# Lennard Jonnes contribution to the force field
if PP.params['useLJ']:
#checking if files exist: