autogeom=False,
PBC=options.noPBC,
FFparams=FFparams)
# This function returns the following information:
# iZs - 1D array, containing the numbers of the elements, which corresponds to
# their position in the atomtypes.ini file (Number of line - 1)
# Rs - 2D array, containing the coordinates of the atoms:
# [ [x1,y1,z1],
# [x2,y2,z2],
# ...
# [xn,yn,zn]]
# Qs - 1D array, containing the atomic charges
FFLJ, VLJ = PPH.computeLJ(Rs,
iZs,
FFLJ=None,
FFparams=FFparams,
Vpot=options.energy)
# This function computes the LJ forces experienced by the ProbeParticle
# FFparams either read from the local "atomtypes.ini" file, or will be read from
# the default one inside the computeLJ function
GU.limit_vec_field(
FFLJ, Fmax=10.0
) # remove too large valuesl; keeps the same direction; good for visualization
print "--- Save ---"
GU.save_vec_field('FFLJ', FFLJ, lvec, data_format=data_format)
if options.energy:
Vmax = 10.0
VLJ[VLJ > Vmax] = Vmax
FFparams = PPU.loadSpecies( cpp_utils.PACKAGE_PATH+'/defaults/atomtypes.ini' )
iZs,Rs,Qs=PPH.parseAtoms(atoms, autogeom = False, PBC = options.noPBC,
FFparams=FFparams )
# This function returns the following information:
# iZs - 1D array, containing the numbers of the elements, which corresponds to
# their position in the atomtypes.ini file (Number of line - 1)
# Rs - 2D array, containing the coordinates of the atoms:
# [ [x1,y1,z1],
# [x2,y2,z2],
# ...
# [xn,yn,zn]]
# Qs - 1D array, containing the atomic charges
FFLJ, VLJ=PPH.computeLJ( Rs, iZs, FFLJ=None, FFparams=FFparams, Vpot=options.energy )
# This function computes the LJ forces experienced by the ProbeParticle
# FFparams either read from the local "atomtypes.ini" file, or will be read from
# the default one inside the computeLJ function
GU.limit_vec_field( FFLJ, Fmax=10.0 ) # remove too large valuesl; keeps the same direction; good for visualization
print "--- Save ---"
GU.save_vec_field( 'FFLJ', FFLJ, lvec,format=format)
if options.energy :
Vmax = 10.0; VLJ[ VLJ>Vmax ] = Vmax
GU.save_scal_field( 'VLJ', VLJ, lvec,format=format)
