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)
xTips, yTips, zTips, lvecScan = PP.prepareScanGrids()
#Ks = [ 0.25, 0.5, 1.0 ]
#Qs = [ -0.2, 0.0, +0.2 ]
#Amps = [ 2.0 ]
for iq, Q in enumerate(Qs):
FF = FFLJ + FFel * Q
PP.setFF_Pointer(FF)
for ik, K in enumerate(Ks):
dirname = "Q%1.2fK%1.2f" % (Q, K)
os.makedirs(dirname)
PP.setTip(kSpring=np.array((K, K, 0.0)) / -PP.eVA_Nm)
#GU.saveVecFieldXsf( 'FFtot', FF, lvec, head )
fzs = PP.relaxedScan3D(xTips, yTips, zTips)
GU.saveXSF(dirname + '/OutFz.xsf', fzs, lvecScan, GU.XSF_HEAD_DEFAULT)
for iA, Amp in enumerate(Amps):
AmpStr = "/Amp%2.2f" % Amp
print("Amp= ", AmpStr)
os.makedirs(dirname + AmpStr)
dz = PP.params['scanStep'][2]
dfs = PP.Fz2df(fzs,
dz=dz,
k0=PP.params['kCantilever'],
f0=PP.params['f0Cantilever'],
n=Amp / dz)
extent = (xTips[0], xTips[-1], yTips[0], yTips[-1])
PPPlot.plotImages(dirname + AmpStr + "/df",
dfs,
slices=list(range(0, len(dfs))),
extent=extent)
#Ks = [ 0.25, 0.5, 1.0 ] #Qs = [ -0.2, 0.0, +0.2 ] #Amps = [ 2.0 ] for iq,Q in enumerate( Qs ): FF = FFLJ + FFel * Q PP.setFF_Pointer( FF ) for ik,K in enumerate( Ks ): dirname = "Q%1.2fK%1.2f" %(Q,K) os.makedirs( dirname ) PP.setTip( kSpring = np.array((K,K,0.0))/-PP.eVA_Nm ) #GU.saveVecFieldXsf( 'FFtot', FF, lvec, head ) fzs = PP.relaxedScan3D( xTips, yTips, zTips ) GU.saveXSF( dirname+'/OutFz.xsf', fzs, lvecScan, GU.XSF_HEAD_DEFAULT ) for iA,Amp in enumerate( Amps ): AmpStr = "/Amp%2.2f" %Amp print "Amp= ",AmpStr os.makedirs( dirname+AmpStr ) dz = PP.params['scanStep'][2] dfs = PP.Fz2df( fzs, dz = dz, k0 = PP.params['kCantilever'], f0=PP.params['f0Cantilever'], n=Amp/dz ) extent=( xTips[0], xTips[-1], yTips[0], yTips[-1] ) PPPlot.plotImages( dirname+AmpStr+"/df", dfs, slices = range( 0, len(dfs) ), extent=extent ) print " ***** ALL DONE ***** " #plt.show()
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)
X, Y, Z = getMGrid(dims, dd)
print '--- Get Probe Density ---'
rho = getProbeDensity(sampleSize, X, Y, Z, sigma, dd)
print '--- Get Forces ---'
Fx, Fy, Fz = getForces( V, rho, sampleSize, dims, dd, X, Y, Z)
print 'Fx.max(), Fx.min() = ', Fx.max(), Fx.min()
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)
#show()
# mask atoms which should not to be included into the expansion
natoms = len(atom_types)
atom_mask = np.array([True] * natoms)
atom_mask[2:] = False
# set basiset for each atom
atom_basis = MP.make_bas_list([len(atom_pos)], basis=[['s', 'px', 'py', 'pz']])
#print "atom_pos: ", atom_pos
#print "atom_Rmin: ", atom_Rmin
#print "atom_Rmax: ", atom_Rmax
#print "atom_mask: ", atom_mask
#print "atom_basis: ", atom_basis
# ============== do the fitting
coefs, basis_assignment = MP.fitMultipolesPotential(atom_pos,
atom_basis,
atom_Rmin,
atom_Rmax,
atom_mask=atom_mask,
show_where=True)
# ============== output results
for i in range(len(coefs)):
print basis_assignment[i], coefs[i]
print "saving LOCPOT_debug.xsf "
GU.saveXSF(WORK_DIR + 'LOCPOT_debug.xsf', V, lvec, head)
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 natoms = len( atom_types ) atom_mask = np.array( [ True ] * natoms ); atom_mask[ 2: ] = False # set basiset for each atom atom_basis = MP.make_bas_list( [ len( atom_pos ) ], basis=[ ['s','px','py','pz'] ] ) #print "atom_pos: ", atom_pos #print "atom_Rmin: ", atom_Rmin #print "atom_Rmax: ", atom_Rmax #print "atom_mask: ", atom_mask #print "atom_basis: ", atom_basis # ============== do the fitting coefs, basis_assignment = MP.fitMultipolesPotential( atom_pos, atom_basis, atom_Rmin, atom_Rmax, atom_mask=atom_mask, show_where=True ); # ============== output results for i in range( len( coefs ) ): print basis_assignment[i], coefs[i] print "saving LOCPOT_debug.xsf " GU.saveXSF( WORK_DIR + 'LOCPOT_debug.xsf', V, lvec, head );
for ix,x in enumerate( xTips ):
print "relax ix:", ix
rTips[:,0] = x
for iy,y in enumerate( yTips ):
rTips[:,1] = y
itrav = PP.relaxTipStroke( rTips, rs, fs ) / float( len(zTips) )
fzs[:,iy,ix] = fs[:,2].copy()
print " # ============ convert Fz -> df "
dfs = PP.Fz2df( fzs, dz = dz, k0 = PP.params['kCantilever'], f0=PP.params['f0Cantilever'], n=int(PP.params['Amplitude']/dz) )
if(options.df == True):
GU.saveXSF('df.xsf', dfs, lvec, head)
print " # ============ Plot Relaxed Scan 3D "
slices = range( 0, len(dfs) )
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=PP.params['imageInterpolation'], vmin=fmin, vmax=fmax, cmap=PP.params['colorscale'], extent=extent )
else:
plt.imshow( dfs[i], origin='image', interpolation=PP.params['imageInterpolation'], cmap=PP.params['colorscale'], extent=extent )
z = zTips[i]
# z = zTips[i] - PP.params['moleculeShift' ][2]
z = zTips[i]
rTips[:, 0] = x
for iy, y in enumerate(yTips):
rTips[:, 1] = y
itrav = PP.relaxTipStroke(rTips, rs, fs) / float(len(zTips))
fzs[:, iy, ix] = fs[:, 2].copy()
print " # ============ convert Fz -> df "
dfs = PP.Fz2df(fzs,
dz=dz,
k0=PP.params['kCantilever'],
f0=PP.params['f0Cantilever'],
n=int(PP.params['Amplitude'] / dz))
if (options.df == True):
GU.saveXSF('df.xsf', dfs, lvec, head)
print " # ============ Plot Relaxed Scan 3D "
slices = range(0, len(dfs))
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=PP.params['imageInterpolation'],
vmin=fmin,
vmax=fmax,
cmap=PP.params['colorscale'],
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()
