def prepareForceFields( store = True, storeXsf = False, autogeom = False, FFparams=None ):
newEl = False
newLJ = False
head = None
# --- try to load FFel or compute it from LOCPOT.xsf
if ( os.path.isfile('FFel_x.xsf') ):
print " FFel_x.xsf found "
FFel, lvecEl, nDim, head = GU.loadVecField('FFel', FFel)
lvec2params( lvecEl )
else:
print "FFel_x.xsf not found "
if ( xsfLJ and os.path.isfile('LOCPOT.xsf') ):
print " LOCPOT.xsf found "
V, lvecEl, nDim, head = GU.loadXSF('LOCPOT.xsf')
lvec2params( lvecEl )
FFel_x,FFel_y,FFel_z = libFFTfin.potential2forces( V, lvecEl, nDim, sigma = 1.0 )
FFel = GU.packVecGrid( FFel_x,FFel_y,FFel_z )
del FFel_x,FFel_y,FFel_z
GU.saveVecFieldXsf( 'FFel', FF, lvecEl, head = head )
else:
print " LOCPOT.xsf not found "
newEl = True
# --- try to load FFLJ
if ( os.path.isfile('FFLJ_x.xsf') ):
print " FFLJ_x.xsf found "
FFLJ, lvecLJ, nDim, head = GU.loadVecFieldXsf( 'FFLJ' )
lvec2params( lvecLJ )
else:
newLJ = True
# --- compute Forcefield by atom-wise interactions
if ( newEl or newEl ):
atoms = basUtils.loadAtoms('geom.bas', elements.ELEMENT_DICT )
iZs,Rs,Qs = parseAtoms( atoms, autogeom = autogeom, PBC = params['PBC'] )
lvec = params2lvec( )
if head is None:
head = GU.XSF_HEAD_DEFAULT
if newLJ:
FFLJ = computeLJ ( Rs, iZs, FFparams=FFparams )
GU.saveVecFieldXsf( 'FFLJ', FF, lvecEl, head = head )
if newEl:
FFel = computeCoulomb( Rs, Qs, FFel )
GU.saveVecFieldXsf( 'FFel', FF, lvecEl, head = head )
return FFLJ, FFel
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)
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)
if query_yes_no(
"I have found files containing electrostatic forcefield. Should I use them (yes) or do you want me to recompute them from scratch (n) ?"
):
todoEL = 'read'
else:
todoEL = 'compute'
else:
print "I haven't found files containing electrostatic forcefields. Therefore I will recompute them from scratch"
todoEL = 'compute'
#print iZs
if todoLJ == 'compute':
FFLJ = PP.computeLJ(Rs, iZs, FFLJ=None, FFparams=None)
GU.saveVecFieldXsf(ProjName + "_LJ_F",
FFLJ,
lvec=[[0.0, 0.0, 0.0], PP.params['gridA'],
PP.params['gridB'], PP.params['gridC']])
elif todoLJ == 'read':
FFLJ, lvec, nDim, head = GU.loadVecFieldXsf(ProjName + "_LJ_F")
PP.lvec2params(lvec)
xTips, yTips, zTips, lvecScan = PP.prepareScanGrids()
print xTips, yTips, zTips
if todoEL == 'read':
FFEL, lvec, nDim, head = GU.loadVecFieldXsf(ProjName + "_EL_F")
Q = PP.params['charge']
K = 0.3
PP.setTip(kSpring=np.array((K, K, 0.0)) / -PP.eVA_Nm)
):
todoEL = "read"
else:
todoEL = "compute"
else:
print "I haven't found files containing electrostatic forcefields. Therefore I will recompute them from scratch"
todoEL = "compute"
# print iZs
if todoLJ == "compute":
FFLJ = PP.computeLJ(Rs, iZs, FFLJ=None, FFparams=None)
GU.saveVecFieldXsf(
ProjName + "_LJ_F", FFLJ, lvec=[[0.0, 0.0, 0.0], PP.params["gridA"], PP.params["gridB"], PP.params["gridC"]]
)
elif todoLJ == "read":
FFLJ, lvec, nDim, head = GU.loadVecFieldXsf(ProjName + "_LJ_F")
PP.lvec2params(lvec)
xTips, yTips, zTips, lvecScan = PP.prepareScanGrids()
print xTips, yTips, zTips
if todoEL == "read":
FFEL, lvec, nDim, head = GU.loadVecFieldXsf(ProjName + "_EL_F")
Q = PP.params["charge"]
else:
print "I haven't found files containing electrostatic forcefields. Therefore I will recompute them from scratch"
todoEL='compute'
#print iZs
if todoLJ == 'compute':
FFLJ = PP.computeLJ( Rs, iZs, FFLJ=None, FFparams=None)
GU.saveVecFieldXsf(ProjName+"_LJ_F",FFLJ, lvec=[[0.0,0.0,0.0],PP.params['gridA'], PP.params['gridB'],PP.params['gridC']] )
elif todoLJ == 'read':
FFLJ, lvec, nDim, head = GU.loadVecFieldXsf( ProjName+"_LJ_F" )
PP.lvec2params( lvec )
xTips,yTips,zTips,lvecScan = PP.prepareScanGrids( )
print xTips,yTips,zTips
if todoEL == 'read':
FFEL, lvec, nDim, head = GU.loadVecFieldXsf( ProjName+"_EL_F" )
Q=PP.params['charge']
K=0.3
