# [ [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)
if opt_dict["charge"]:
print "Electrostatic Field from xyzq file"
FFel, VeL = PPH.computeCoulomb( Rs, Qs, FFel=None, Vpot=options.energy )
print "--- Save ---"
GU.save_vec_field('FFel', FFel, lvec, format=format)
if options.energy :
Vmax = 10.0; Vel[ Vel>Vmax ] = Vmax
GU.save_scal_field( 'Vel.xsf', Vel, lvec, format=format)
GU.save_scal_field('VLJ', VLJ, lvec, data_format=data_format)
if opt_dict["charge"]:
print "Electrostatic Field from xyzq file"
multipole = {
options.tip: 1.0
} if (options.tip in {
's', 'px', 'py', 'pz', 'dx2', 'dy2', 'dz2', 'dxy', 'dxz', 'dyz'
}) else {
PPU.params['tip']: 1.0
}
sigma = options.sigma if (options.sigma > 0.0) else PPU.params['sigma']
print "DEBUG: multipole, sigma", multipole, sigma
Vpot = options.energy if (multipole == {'s': 1.0}) else True
print "DEBUG: Vpot", Vpot
FFel, Vel = PPH.computeCoulomb(Rs, Qs, FFel=None, Vpot=Vpot)
if (multipole != {'s': 1.0}):
print " computing convolution with tip by FFT "
Fel_x, Fel_y, Fel_z = fFFT.potential2forces(Vel,
lvec,
PPU.params['gridN'][::-1],
rho=None,
sigma=sigma,
multipole=multipole)
del multipole
FFel = GU.packVecGrid(Fel_x, Fel_y, Fel_z)
del Fel_x, Fel_y, Fel_z
print "--- Save ---"
GU.save_vec_field('FFel', FFel, lvec, data_format=data_format)
if options.energy:
Vmax = 10.0
# [ [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
GU.save_scal_field( 'VLJ', VLJ, lvec,data_format=data_format)
if opt_dict["charge"]:
print "Electrostatic Field from xyzq file"
FFel, VeL = PPH.computeCoulomb( Rs, Qs, FFel=None, Vpot=options.energy )
print "--- Save ---"
GU.save_vec_field('FFel', FFel, lvec, data_format=data_format)
if options.energy :
Vmax = 10.0; Vel[ Vel>Vmax ] = Vmax
GU.save_scal_field( 'Vel', Vel, lvec, data_format=data_format)
