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
(options, args) = parser.parse_args()
num = len(sys.argv)
if (num < 2):
sys.exit("Number of arguments = "+str(num-1)+". This script should have at least one argument. I am terminating...")
finput = sys.argv[num-1]
# --- initialization ---
sigma = 1.0 # [ Angstroem ]
print('--- Data Loading ---')
# TODO with time implement reading a hartree potential generated by different software
if(options.input == 'vasp.locpot.xsf'):
V, lvec, nDim, head = GU.loadXSF(finput)
elif(options.input == 'aims.cube'):
V, lvec, nDim, head = GU.loadCUBE(finput)
print('--- Preprocessing ---')
sampleSize = getSampleDimensions(lvec)
dims = (nDim[2], nDim[1], nDim[0])
xsize, dx = getSize('x', dims, sampleSize)
ysize, dy = getSize('y', dims, sampleSize)
zsize, dz = getSize('z', dims, sampleSize)
dd = (dx, dy, dz)
parser = OptionParser()
parser.add_option( "-i", "--input", action="store", type="string", help="format of input file", default='vasp.locpot.xsf')
(options, args) = parser.parse_args()
num = len(sys.argv)
finput = sys.argv[num-1]
# --- initialization ---
sigma = 1.0 # [ Angstroem ]
print '--- Data Loading ---'
# TODO with time implement reading a hartree potential generated by different software
if(options.input == 'vasp.locpot.xsf'):
V, lvec, nDim, head = GU.loadXSF(finput)
elif(options.input == 'aims.cube'):
V, lvec, nDim, head = GU.loadCUBE(finput)
print '--- Preprocessing ---'
sampleSize = getSampleDimensions(lvec)
dims = (nDim[2], nDim[1], nDim[0])
xsize, dx = getSize('x', dims, sampleSize)
ysize, dy = getSize('y', dims, sampleSize)
zsize, dz = getSize('z', dims, sampleSize)
dd = (dx, dy, dz)
# This is a sead of simple plotting script which should get AFM frequency delta 'df.xsf' and generate 2D plots for different 'z'
import os
import sys
import numpy as np
import matplotlib.pyplot as plt
import GridUtils as GU
from optparse import OptionParser
parser = OptionParser()
parser.add_option( "--dfrange", action="store", type="float", help="Range of plotted frequency shift (df)", nargs=2)
(options, args) = parser.parse_args()
dfs,lvec,nDim,head=GU.loadXSF('df.xsf')
#print lvec
#print nDim
print " # ============ Plot Relaxed Scan 3D "
slices = range( 0, len(dfs) )
#print slices
extent=( 0.0, lvec[1][0], 0.0, lvec[2][1])
for ii,i in enumerate(slices):
print " plotting ", i
plt.figure( figsize=( 10,10 ) )
if(options.dfrange != None):
fmin = options.dfrange[0]
fmax = options.dfrange[1]
plt.imshow( dfs[i], origin='image', interpolation='bicubic', vmin=fmin, vmax=fmax, cmap='gray', extent=extent)
makeclean()
import GridUtils as GU
import Multipoles as MP
import ProbeParticle as PP
# ============== Setup
WORK_DIR = '/home/prokop/Desktop/Probe_Particle_Simulations/Multipoles/COCu4/'
# NOTE: Data for COCu4 tip example are on tarkil /auto/praha1/prokop/STHM/vasp/COCu4
# ============== load reference grid
V, lvec, nDim, head = GU.loadXSF(WORK_DIR + 'LOCPOT.xsf')
cell = np.array([lvec[1], lvec[2], lvec[3]])
MP.setGrid(V, cell)
# ============== prepare atoms
atom_types, atom_pos = GU.getFromHead_PRIMCOORD(
head) # load atoms from header of xsf file
# set sample region around atom atom_Rmin, atom_Rmax
spacies = PP.loadSpecies('./defaults/atomtypes.ini')
R_type = spacies[:, 0]
atom_Rmin, atom_Rmax = MP.make_Ratoms(atom_types, R_type)
sys.path = [ LWD ]
print " sys.path = ", sys.path
import basUtils
import elements
import GridUtils as GU
import ProbeParticle as PP
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)
LWD = '/home/prokop/git/ProbeParticleModel/code'
def makeclean():
import os
[os.remove(f) for f in os.listdir(".") if f.endswith(".so")]
[os.remove(f) for f in os.listdir(".") if f.endswith(".o")]
[os.remove(f) for f in os.listdir(".") if f.endswith(".pyc")]
CWD = os.getcwd()
os.chdir(LWD)
print " >> WORKDIR: ", os.getcwd()
makeclean()
sys.path.insert(0, ".")
import GridUtils as gu
os.chdir(CWD)
print " >> WORKDIR: ", os.getcwd()
print " ============= RUN "
Fz, lvec, nDim, head = gu.loadXSF('Fz.xsf')
nslice = min(len(Fz), 10)
for i in range(nslice):
plt.figure()
plt.imshow(Fz[i, :, :], origin='image', interpolation='nearest')
plt.show()
os.chdir(CWD) makeclean( ) import GridUtils as GU import Multipoles as MP import ProbeParticle as PP # ============== Setup WORK_DIR = '/home/prokop/Desktop/Probe_Particle_Simulations/Multipoles/COCu4/' # NOTE: Data for COCu4 tip example are on tarkil /auto/praha1/prokop/STHM/vasp/COCu4 # ============== load reference grid V, lvec, nDim, head = GU.loadXSF( WORK_DIR + 'LOCPOT.xsf' ) cell = np.array( [ lvec[1], lvec[2], lvec[3] ]); MP.setGrid( V, cell ); # ============== prepare atoms atom_types,atom_pos = GU.getFromHead_PRIMCOORD( head ) # load atoms from header of xsf file # set sample region around atom atom_Rmin, atom_Rmax spacies = PP.loadSpecies( './defaults/atomtypes.ini' ) R_type = spacies[:,0] atom_Rmin, atom_Rmax = MP.make_Ratoms( atom_types, R_type ) # mask atoms which should not to be included into the expansion
LWD = '/home/prokop/git/ProbeParticleModel/code'
def makeclean( ):
import os
[ os.remove(f) for f in os.listdir(".") if f.endswith(".so") ]
[ os.remove(f) for f in os.listdir(".") if f.endswith(".o") ]
[ os.remove(f) for f in os.listdir(".") if f.endswith(".pyc") ]
CWD = os.getcwd()
os.chdir(LWD); print " >> WORKDIR: ", os.getcwd()
makeclean( )
sys.path.insert(0, ".")
import GridUtils as gu
os.chdir(CWD); print " >> WORKDIR: ", os.getcwd()
print " ============= RUN "
Fz,lvec,nDim,head=gu.loadXSF('Fz.xsf')
nslice = min( len( Fz ), 10 )
for i in range(nslice):
plt.figure()
plt.imshow( Fz[i,:,:], origin='image', interpolation='nearest' )
plt.show()
exit(1)
parser = OptionParser()
parser.add_option( "--dfrange", action="store", type="float", help="Range of plotted frequency shift (df)", nargs=2)
parser.add_option( "--df", action="store_true", help="Write AFM frequency shift in df.xsf file", default=False)
(options, args) = parser.parse_args()
print "Reading coordinates from the file {}".format(sys.argv[1])
print " >> WARNING!!! OVERWRITING SETTINGS by params.ini "
PP.loadParams( 'params.ini' )
Fx,lvec,nDim,head=GU.loadXSF('FFel_x.xsf')
Fy,lvec,nDim,head=GU.loadXSF('FFel_y.xsf')
Fz,lvec,nDim,head=GU.loadXSF('FFel_z.xsf')
PP.params['gridA'] = lvec[ 1,: ].copy()
PP.params['gridB'] = lvec[ 2,: ].copy()
PP.params['gridC'] = lvec[ 3,: ].copy()
PP.params['gridN'] = nDim.copy()
FF = np.zeros( (nDim[0],nDim[1],nDim[2],3) )
FFLJ = np.zeros( np.shape( FF ) )
FFel = np.zeros( np.shape( FF ) )
FFel[:,:,:,0]=Fx
FFel[:,:,:,1]=Fy
FFel[:,:,:,2]=Fz
type="float",
help="Range of plotted frequency shift (df)",
nargs=2)
parser.add_option("--df",
action="store_true",
help="Write AFM frequency shift in df.xsf file",
default=False)
(options, args) = parser.parse_args()
print "Reading coordinates from the file {}".format(sys.argv[1])
print " >> WARNING!!! OVERWRITING SETTINGS by params.ini "
PP.loadParams('params.ini')
Fx, lvec, nDim, head = GU.loadXSF('FFel_x.xsf')
Fy, lvec, nDim, head = GU.loadXSF('FFel_y.xsf')
Fz, lvec, nDim, head = GU.loadXSF('FFel_z.xsf')
PP.params['gridA'] = lvec[1, :].copy()
PP.params['gridB'] = lvec[2, :].copy()
PP.params['gridC'] = lvec[3, :].copy()
PP.params['gridN'] = nDim.copy()
FF = np.zeros((nDim[0], nDim[1], nDim[2], 3))
FFLJ = np.zeros(np.shape(FF))
FFel = np.zeros(np.shape(FF))
FFel[:, :, :, 0] = Fx
FFel[:, :, :, 1] = Fy
FFel[:, :, :, 2] = Fz
print " # ========== make & load ProbeParticle C++ library "
def makeclean( ):
import os
[ os.remove(f) for f in os.listdir(".") if f.endswith(".so") ]
[ os.remove(f) for f in os.listdir(".") if f.endswith(".o") ]
[ os.remove(f) for f in os.listdir(".") if f.endswith(".pyc") ]
CWD = os.getcwd()
os.chdir(LWD); print " >> WORKDIR: ", os.getcwd()
makeclean( )
sys.path.insert(0, "./")
import GridUtils as GU
import ProbeParticle as PP
os.chdir(CWD); print " >> WORKDIR: ", os.getcwd()
print " ============= RUN "
F,lvec,nDim,head=GU.loadXSF('LOCPOT.xsf')
F4 = 0.25*( F + F[:,:,::-1] + F[:,::-1,:] + F[:,::-1,::-1] )
#GU.saveXSF('LOCPOT_4sym.xsf', GU.XSF_HEAD_DEFAULT, lvec, F4 )
GU.saveXSF('LOCPOT_4sym.xsf', head, lvec, F4 )
plt.show()
