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)
GU.saveVecFieldXsf( 'FFLJ', FFLJ, lvec, head)
print " saving electrostatic forcefiled "
GU.saveXSF('FFel_x.xsf', Fel_x, lvec, head)
GU.saveXSF('FFel_y.xsf', Fel_y, lvec, head)
GU.saveXSF('FFel_z.xsf', Fel_z, lvec, head)
del Fel_x, Fel_y, Fel_z, V
print " ========= get lenard jones potential "
PPU.params['gridA'] = lvec[1, :].copy()
PPU.params['gridB'] = lvec[2, :].copy()
PPU.params['gridC'] = lvec[3, :].copy()
PPU.params['gridN'] = nDim.copy()
print "--- Compute Lennard-Jones Force-filed ---"
atoms = basUtils.loadAtoms('input.xyz', elements.ELEMENT_DICT)
iZs, Rs, Qs = PPU.parseAtoms(atoms, autogeom=False, PBC=True)
FFLJ = PPU.computeLJ(Rs, iZs, FFLJ=None, FFparams=None)
# TODO: remove to large values
'''
FRLJ = np.sqrt( FFLJ[:,:,:,0]**2 + FFLJ[:,:,:,1]**2 + FFLJ[:,:,:,2]**2 )
mask = ( FRLJ > 1000.0 )
FFLJ[:][mask] = 1000.0
FFLJ[][mask] = 1000.0
FFLJ[][mask] = 1000.0
'''
print "--- Save ---"
GU.saveVecFieldXsf('FFLJ', FFLJ, lvec, head)
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)
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] )
print "save FFLJ to .xsf "
GU.saveVecFieldXsf( 'FFLJ', FFLJ4, lvec, head )
print " ***** ALL DONE ***** "
#plt.show()
