#print "atom_colors: ", atom_colors
if opt_dict['bonds']:
bonds = basUtils.findBonds(atoms, iZs, 1.0, FFparams=FFparams)
#print "bonds ", bonds
atomSize = 0.15
cbar_str = ""
if opt_dict['cbar']:
cbar_str = "_cbar"
for iq, Q in enumerate(Qs):
for ik, K in enumerate(Ks):
dirname = "Q%1.2fK%1.2f" % (Q, K)
if opt_dict['pos']:
try:
PPpos, lvec, nDim = GU.load_vec_field(dirname + '/PPpos',
data_format=data_format)
print " plotting PPpos : "
PPPlot.plotDistortions(dirname + "/xy" + atoms_str + cbar_str,
PPpos[:, :, :, 0],
PPpos[:, :, :, 1],
slices=range(0, len(PPpos)),
BG=PPpos[:, :, :, 2],
extent=extent,
atoms=atoms,
bonds=bonds,
atomSize=atomSize,
markersize=2.0,
cbar=opt_dict['cbar'])
del PPpos
except:
print "error: ", sys.exc_info()
if opt_dict['arange'] is not None:
Amps = np.linspace( opt_dict['arange'][0], opt_dict['arange'][1], opt_dict['arange'][2] )
elif opt_dict['a'] is not None:
Amps = [ opt_dict['a'] ]
else:
Amps = [ PPU.params['Amplitude'] ]
for iq,Q in enumerate( Qs ):
for ik,K in enumerate( Ks ):
dirname = "Q%1.2fK%1.2f" %(Q,K)
print "Working in {} directory".format(dirname)
fzs,lvec,nDim=GU.load_scal_field(dirname+'/OutFz',format=format)
dfs = PPU.Fz2df( fzs, dz = dz, k0 = PPU.params['kCantilever'], f0=PPU.params['f0Cantilever'], n=Amp/dz )
# print "TYT", fzs.shape
for p in options.points:
xmin=float(p[0].split('x')[0])
ymin=float(p[0].split('x')[1])
zmin=float(p[0].split('x')[2])
xmax=float(p[1].split('x')[0])
ymax=float(p[1].split('x')[1])
zmax=float(p[1].split('x')[2])
npoints=float(p[2])
print opt_dict['disp']
if opt_dict['disp'] :
print "Displacment {}".format(opt_dict['disp'][0])
import pyProbeParticle.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)
parser.add_option( "--npy" , action="store_true" , help="load and save fields in npy instead of xsf" , default=False)
(options, args) = parser.parse_args()
if options.npy:
format ="npy"
else:
format ="xsf"
dfs,lvec,nDim=GU.load_scal_field('df',format=format)
#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)
action="store",
type="float",
help="Range of plotted frequency shift (df)",
nargs=2)
parser.add_option("--npy",
action="store_true",
help="load and save fields in npy instead of xsf",
default=False)
(options, args) = parser.parse_args()
if options.npy:
data_format = "npy"
else:
data_format = "xsf"
dfs, lvec, nDim = GU.load_scal_field('df', data_format=data_format)
#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],
for i in range(len(Voltages)):
if didv_b:
print("Importing dIdV data for V:", namez[i])
#print("DEBUG:WF:", WorkFunction , "Voltages[i]:", Voltages[i], "WF_decay", WF_decay )
name_file1 = 'didv_' + namez[
i] + "_tip_" + tip_type + "-" + tip_orb1 + "_WF_" + str(
WorkFunction - Voltages[i] * WF_decay
) + "_eta_" + str(
eta
) # WorkFunction gets higher with lower (higher negative) sample bias
name_file2 = 'didv_' + namez[
i] + "_tip_" + tip_type + "-" + tip_orb2 + "_WF_" + str(
WorkFunction - Voltages[i] * WF_decay) + "_eta_" + str(eta)
#print ("DEBUG: name_file1", name_file1)
tmp_dIdV1, lvec1, nDim1 = GU.load_scal_field(files_path + name_file1,
data_format=data_format)
didv1 = np.array([tmp_dIdV1]) if i == 0 else np.append(
didv1, np.array([tmp_dIdV1]), axis=0)
#print "DEBUG: name_file2", name_file2
tmp_dIdV2, lvec2, nDim2 = GU.load_scal_field(files_path + name_file2,
data_format=data_format)
didv2 = np.array([tmp_dIdV2]) if i == 0 else np.append(
didv2, np.array([tmp_dIdV2]), axis=0)
assert np.array(lvec1).all() == np.array(
lvec2).all(), "lvec1 != lvec2 control your input files"
assert np.array(nDim2).all() == np.array(
nDim2).all(), "nDim1 != nDim2 control your input files"
print("dIdV for V:", namez[i], " imported")
#print "DEBUG: didv1.shape", didv1.shape
if STM_b:
print("Importing STM data for V:", namez[i])
# Amps
if opt_dict['arange'] is not None:
Amps = np.linspace(opt_dict['arange'][0], opt_dict['arange'][1],
opt_dict['arange'][2])
elif opt_dict['a'] is not None:
Amps = [opt_dict['a']]
else:
Amps = [PPU.params['Amplitude']]
for iq, Q in enumerate(Qs):
for ik, K in enumerate(Ks):
dirname = "Q%1.2fK%1.2f" % (Q, K)
print "Working in {} directory".format(dirname)
fzs, lvec, nDim = GU.load_scal_field(dirname + '/OutFz',
data_format=data_format)
dfs = PPU.Fz2df(fzs,
dz=dz,
k0=PPU.params['kCantilever'],
f0=PPU.params['f0Cantilever'],
n=Amp / dz)
# print "TYT", fzs.shape
for p in options.points:
xmin = float(p[0].split('x')[0])
ymin = float(p[0].split('x')[1])
zmin = float(p[0].split('x')[2])
xmax = float(p[1].split('x')[0])
ymax = float(p[1].split('x')[1])
zmax = float(p[1].split('x')[2])
npoints = float(p[2])
if opt_dict['arange'] is not None:
Amps = np.linspace( opt_dict['arange'][0], opt_dict['arange'][1], opt_dict['arange'][2] )
elif opt_dict['a'] is not None:
Amps = [ opt_dict['a'] ]
else:
Amps = [ PPU.params['Amplitude'] ]
for iq,Q in enumerate( Qs ):
for ik,K in enumerate( Ks ):
dirname = "Q%1.2fK%1.2f" %(Q,K)
print "Working in {} directory".format(dirname)
fzs,lvec,nDim,head=GU.load_scal_field(dirname+'/OutFz', format=format)
dfs = PPU.Fz2df( fzs, dz = dz, k0 = PPU.params['kCantilever'], f0=PPU.params['f0Cantilever'], n=Amp/dz )
for p in options.points:
x=float(p.split('x')[0])
y=float(p.split('x')[1])
x_pos=int(x/scan_step)
y_pos=int(y/scan_step)
Zplot=np.zeros(fzs.shape[0])
Fplot=np.zeros(fzs.shape[0])
DFplot=np.zeros(fzs.shape[0])
for k in range(0,fzs.shape[0]):
Fplot[k]=fzs[-k-1][y_pos][x_pos]
Zplot[k]=scan_max-scan_step*k
parser.add_option( "--npy" , action="store_true" , help="load and save fields in npy instead of xsf" , default=False)
(options, args) = parser.parse_args()
try:
points = np.genfromtxt( options.p ,dtype='int')
print("plotting in points", points)
except:
print(options.p+" not found => exiting ...")
sys.exit()
if options.npy:
data_format ="npy"
else:
data_format ="xsf"
fzs,lvec,nDim=GU.load_scal_field(options.i,data_format=data_format)
#xs = lvec[3,2]/*np.array( range(nDim[0]) )
xs = np.linspace( 0, lvec[3,2], nDim[0] )
#print nDim
print(xs)
plt.imshow( fzs[options.iz], origin='imgage', cmap='gray' )
for point in points:
plt.plot(point[0],point[1],'o')
plt.xlim(0,nDim[2])
plt.ylim(0,nDim[1])
plt.savefig( options.i+'_zcurves_legend.png', bbox_inches='tight')
plt.figure()
curves = np.zeros((len(points)+1,len(xs)))
def WriteOutput(Potential, Lattice):
lat_mat = np.array([[0, 0, eval_height[0]], Lattice[0], Lattice[1],
[0, 0, eval_height[1] - eval_height[0]]])
GU.saveXSF('dipole_potential.xsf', Potential, lat_mat)
# iZs - 1D array, containing the numbers of the elements, which corresponds to
# their position in the atomtypes.ini file (Number of line - 1)
# Rs - 2D array, containing the coordinates of the atoms:
# [ [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 :
beta = 1/(kBoltz*T) # [eV]
print "T= ", T, " [K] => beta ", beta/1000.0, "[meV] "
#E_cutoff = 32.0 * beta
E_cutoff = 18.0 * beta
wGauss = 2.0
Egauss = -0.01
# =============== main
if options.noProbab :
print " ==== calculating probabilties ===="
# --- tip
V_tip, lvec, nDim = GU.load_scal_field('tip/VLJ',format=format)
#cell = np.array( [ lvec[1],lvec[2],lvec[3] ] ); print "nDim ", nDim, "\ncell ", cell
#X,Y,Z = getXYZ( nDim, cell )
#V_tip = V_tip*0 + Egauss * getProbeDensity( (cell[0,0]/2.+cell[1,0]/2.,cell[1,1]/2,cell[2,2]/2.-3.8), X, Y, Z, wGauss ) # works for tip (the last flexible tip apex atom) in the middle of the cell
limitE( V_tip, E_cutoff )
W_tip = np.exp( -beta * V_tip )
#W_tip = W_cut(W_tip,nz=95,side='down',sm=5)
del V_tip;
GU.save_scal_field ( 'W_tip', W_tip, lvec, format=format)
# --- sample
V_surf, lvec, nDim = GU.load_scal_field('sample/VLJ',format=format)
limitE( V_surf, E_cutoff )
W_surf = np.exp( -beta * V_surf )
#W_surf=W_cut(W_surf,nz=50,side='up',sm=1)
del V_surf;
import pyProbeParticle as PPU from pyProbeParticle import basUtils import pyProbeParticle.GridUtils as GU #import pyProbeParticle.fieldFFT as fFFT #import pyProbeParticle.PPPlot as PPP center = np.array([10.0, 10.0, 10.0]) data1 = 'ddensity-Si232-H.xsf' data2 = 'ddensity-Si232-CH3.xsf' data3 = 'ddensity-Si232-C6.xsf' data4 = 'ddensity-Si232-OH.xsf' data5 = 'ddensity-Si232-CHO.xsf' data6 = 'ddensity-Si232-CH3.xsf' data, lvec, nDim, head = GU.loadXSF(str(data5)) ntot = nDim[0] * nDim[1] * nDim[2] dV = lvec[1][0] * lvec[2][1] * lvec[3][2] / ntot GU.setGridN(np.array(data.shape).astype(np.int32)) GU.setGridCell(np.array((lvec[1], lvec[2], lvec[3])).copy()) center, Hsum = GU.cog(data) #print center, Hsum rs, Hs, Ws = GU.sphericalHist(data, center, 0.1, 400) plt.subplot(2, 1, 1) plt.plot(rs, Hs * (len(Hs) / float(ntot)), label="raw") plt.plot(rs, Hs / Ws, label="weighted") sumHs = np.cumsum(Hs * dV) plt.subplot(2, 1, 2)
#print "atom_colors: ", atom_colors if opt_dict['bonds']: bonds = basUtils.findBonds(atoms,iZs,1.0,FFparams=FFparams) #print "bonds ", bonds atomSize = 0.15 cbar_str ="" if opt_dict['cbar']: cbar_str="_cbar" for iq,Q in enumerate( Qs ): for ik,K in enumerate( Ks ): dirname = "Q%1.2fK%1.2f" %(Q,K) if opt_dict['pos']: try: PPpos, lvec, nDim = GU.load_vec_field( dirname+'/PPpos' ,format=format) print " plotting PPpos : " PPPlot.plotDistortions( dirname+"/xy"+atoms_str+cbar_str, PPpos[:,:,:,0], PPpos[:,:,:,1], slices = range( 0, len(PPpos) ), BG=PPpos[:,:,:,2], extent=extent, atoms=atoms, bonds=bonds, atomSize=atomSize, markersize=2.0, cbar=opt_dict['cbar'] ) del PPpos except: print "error: ", sys.exc_info() print "cannot load : " + ( dirname+'/PPpos_?.' + format ) if ( ( opt_dict['df'] or opt_dict['save_df'] or opt_dict['WSxM'] ) ): try : fzs, lvec, nDim = GU.load_scal_field( dirname+'/OutFz' , format=format) for iA,Amp in enumerate( Amps ): AmpStr = "/Amp%2.2f" %Amp print "Amp= ",AmpStr dirNameAmp = dirname+AmpStr if not os.path.exists( dirNameAmp ): os.makedirs( dirNameAmp )
# --- downloading and examples of downloading of the eigen-energies, the LCAO coefficients and geometry (this time for spin-unpolarized calculations):
#eigEn, coefs, Ratin = RS.read_FIREBALL_all(name = path+'phik_example_', geom=path+'crazy_mol.xyz', fermi=fermi, orbs = orbs, pbc=pbc,
# cut_min=cut_min, cut_max=cut_max,cut_at=cut_at, lower_atoms=lower_atoms, lower_coefs=lower_coefs);
#eigEn, coefs, Ratin = RS.read_AIMS_all(name = 'KS_exx_1_spin_up.out', geom='geometry.in',fermi=fermi, orbs = orbs, pbc=pbc,
# imaginary = False, cut_min=cut_min, cut_max=cut_max, cut_at=cut_at,
# lower_atoms=lower_atoms, lower_coefs=lower_coefs)
eigEn, coefs, Ratin = RS.read_CP2K_all(name = 'TOAT', fermi=fermi, orbs = orbs, pbc=pbc,
cut_min=cut_min, cut_max=cut_max, cut_at=cut_at, lower_atoms=lower_atoms, lower_coefs=lower_coefs);
#eigEn, coefs, Ratin = RS.read_GPAW_all(name = 'out_LCAO_LDA.gpw', fermi=fermi, orbs = orbs, pbc=pbc,
# cut_min=cut_min, cut_max=cut_max, cut_at=cut_at, lower_atoms=lower_atoms, lower_coefs=lower_coefs);
# --- the grid on which the STM signal is calculated; no tip_r1 - PP distored by the relaxation in the PPAFM code; only tip_r2 - uniform grid:
tip_r1, lvec, nDim = GU.load_vec_field( path_pos+'PPpos' ,data_format=data_format)
dz=0.1
dx=dy =0.1
xl = lvec[1,0]
yl = lvec[2,1]
zl = lvec[3,2]
extent = (lvec[0,0],lvec[0,0]+xl,lvec[0,1],lvec[0,1]+yl)
tip_r2 = RS.mkSpaceGrid(lvec[0,0],lvec[0,0]+xl,dx,lvec[0,1],lvec[0,1]+yl,dy,lvec[0,2],lvec[0,2]+zl,dz)
# --- specification on which voltages the STM (dI/dV ...) calculations are performed - two methods - direct specification or sequence of voltages
Voltages=[-0.338, -0.09406976, 0., 2.422684]
namez=['H**O-3-2','H**O-1','H**O','LUMO++1']
sys.exit()
tip_base = options.tip_base
if not tip_base:
tip_base = True if ((PPU.params["tip_base"][0] != 'None') and
(PPU.params["tip_base"][0] != None)) else False
print("Ks =", Ks)
print("Qs =", Qs)
print("tip_base =", tip_base)
print(" ============= RUN ")
if (charged_system == True):
print(" load Electrostatic Force-field ")
FFel, lvec, nDim = GU.load_vec_field("FFel", data_format=data_format)
if (options.boltzmann or options.bI):
print(" load Boltzmann Force-field ")
FFboltz, lvec, nDim = GU.load_vec_field("FFboltz", data_format=data_format)
print(" load Lenard-Jones Force-field ")
FFLJ, lvec, nDim = GU.load_vec_field("FFLJ", data_format=data_format)
PPU.lvec2params(lvec)
PPC.setFF(FFLJ)
xTips, yTips, zTips, lvecScan = PPU.prepareScanGrids()
for iq, Q in enumerate(Qs):
if (charged_system == True):
FF = FFLJ + FFel * Q
#print "atom_colors: ", atom_colors
if opt_dict['bonds']:
bonds = basUtils.findBonds(atoms, iZs, 1.0, FFparams=FFparams)
#print "bonds ", bonds
atomSize = 0.15
cbar_str = ""
if opt_dict['cbar']:
cbar_str = "_cbar"
for iq, Q in enumerate(Qs):
for ik, K in enumerate(Ks):
dirname = "Q%1.2fK%1.2f" % (Q, K)
if opt_dict['pos']:
try:
PPpos, lvec, nDim = GU.load_vec_field(dirname + '/PPpos',
data_format=data_format)
print(" plotting PPpos : ")
PPPlot.plotDistortions(dirname + "/xy" + atoms_str + cbar_str,
PPpos[:, :, :, 0],
PPpos[:, :, :, 1],
slices=list(range(0, len(PPpos))),
BG=PPpos[:, :, :, 2],
extent=extent,
atoms=atoms,
bonds=bonds,
atomSize=atomSize,
markersize=2.0,
cbar=opt_dict['cbar'])
del PPpos
except:
print("error: ", sys.exc_info())
format ="xsf"
if options.input==None:
sys.exit("ERROR!!! Please, specify the input file with the '-i' option \n\n"+HELP_MSG)
print " >> OVEWRITING SETTINGS by params.ini "
PPU.loadParams( 'params.ini' )
print " ========= get electrostatic forcefiled from hartree "
# TODO with time implement reading a hartree potential generated by different software
print " loading Hartree potential from disk "
if(options.input.lower().endswith(".xsf") ):
print "Use loadXSF"
V, lvec, nDim, head = GU.loadXSF(options.input)
elif(options.input.lower().endswith(".cube") ):
print "Use loadCUBE"
V, lvec, nDim, head = GU.loadCUBE(options.input)
V*=27.211396132
else:
sys.exit("ERROR!!! Unknown format of the input file\n\n"+HELP_MSG)
rho = None
multipole = None
if options.tip in {'s','px','py','pz','dx2','dy2','dz2','dxy','dxz','dyz'}:
rho = None
multipole={options.tip:1.0}
elif options.tip.endswith(".xsf"):
rho, lvec_tip, nDim_tip, tiphead = GU.loadXSF(options.tip)
if any(nDim_tip != nDim):
sys.exit("Error: Input file for tip charge density has been specified, but the dimensions are incompatible with the Hartree potential file!")
else:
data_format ="xsf"
if options.input==None:
sys.exit("ERROR!!! Please, specify the input file with the '-i' option \n\n"+HELP_MSG)
print " >> OVEWRITING SETTINGS by params.ini "
PPU.loadParams( 'params.ini' )
print " ========= get electrostatic forcefiled from hartree "
# TODO with time implement reading a hartree potential generated by different software
print " loading Hartree potential from disk "
if(options.input.lower().endswith(".xsf") ):
print "Use loadXSF"
V, lvec, nDim, head = GU.loadXSF(options.input)
elif(options.input.lower().endswith(".cube") ):
print "Use loadCUBE"
V, lvec, nDim, head = GU.loadCUBE(options.input)
V*=27.211396132
else:
sys.exit("ERROR!!! Unknown format of the input file\n\n"+HELP_MSG)
rho = None
sigma = options.sigma if ( options.sigma > 0.0) else PPU.params['sigma']
multipole = None
if (options.tip.endswith(".xsf") or options.tip.endswith(".cube") ) :
rho, lvec_tip, nDim_tip, tiphead = GU.loadXSF(options.tip) if (options.tip.endswith(".xsf")) else GU.loadCUBE(options.tip)
if (nDim_tip != nDim):
sys.exit("Error: Input file for tip charge density has been specified, but the dimensions are incompatible with the Hartree potential file!")
else:
if opt_dict['arange'] is not None:
Amps = np.linspace( opt_dict['arange'][0], opt_dict['arange'][1], int(opt_dict['arange'][2] ) )
elif opt_dict['a'] is not None:
Amps = [ opt_dict['a'] ]
else:
Amps = [ PPU.params['Amplitude'] ]
for iq,Q in enumerate( Qs ):
for ik,K in enumerate( Ks ):
dirname = "Q%1.2fK%1.2f" %(Q,K)
print("Working in {} directory".format(dirname))
fzs,lvec,nDim,head=GU.load_scal_field(dirname+'/OutFz', data_format=data_format)
dfs = PPU.Fz2df( fzs, dz = dz, k0 = PPU.params['kCantilever'], f0=PPU.params['f0Cantilever'], n= int(Amp/dz) )
for p in options.points:
x=float(p.split('x')[0])
y=float(p.split('x')[1])
x_pos=int(x/scan_step)
y_pos=int(y/scan_step)
Zplot=np.zeros(fzs.shape[0])
Fplot=np.zeros(fzs.shape[0])
DFplot=np.zeros(fzs.shape[0])
for k in range(0,fzs.shape[0]):
Fplot[k]=fzs[-k-1][y_pos][x_pos]
Zplot[k]=scan_max-scan_step*k
# [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"
multipole = {
options.tip: 1.0
} if (options.tip in {
's', 'px', 'py', 'pz', 'dx2', 'dy2', 'dz2', 'dxy', 'dxz', 'dyz'
# Amps = np.linspace( opt_dict['arange'][0], opt_dict['arange'][1], opt_dict['arange'][2] )
#elif opt_dict['a'] is not None:
# Amps = [ opt_dict['a'] ]
#else:
# Amps = [ PPU.params['Amplitude'] ]
print "Ks =", Ks
print "Qs =", Qs
#print "Amps =", Amps
print " ============= RUN "
#PPPlot.params = PPU.params # now we dont use PPPlot here
if ( charged_system == True):
print " load Electrostatic Force-field "
FFel, lvec, nDim = GU.load_vec_field( "FFel" ,format=format)
if (options.boltzmann or options.bI) :
print " load Boltzmann Force-field "
FFboltz, lvec, nDim = GU.load_vec_field( "FFboltz", format=format)
print " load Lenard-Jones Force-field "
FFLJ, lvec, nDim = GU.load_vec_field( "FFLJ" , format=format)
PPU.lvec2params( lvec )
PPC.setFF( FFLJ )
xTips,yTips,zTips,lvecScan = PPU.prepareScanGrids( )
for iq,Q in enumerate( Qs ):
if ( charged_system == True):
if (plot_atoms):
geom_plot, tmp1, tmp2 = Bu.loadAtoms('input_plot.xyz')
del tmp1, tmp2
#print "DEBUG: geom_plot", geom_plot
else:
geom_plot = None
# --- the grid on which the STM signal is calculated --- #
if ((tip_type == 'relaxed') or (tip_type == 'r')):
print(
"Importing positions of PP from the PP-AFM calculations. Path for the data:"
)
path_pos = "Q%1.2fK%1.2f/" % (Q, K)
print(path_pos)
tip_r, lvec, nDim = GU.load_vec_field(path_pos + 'PPpos',
data_format=data_format)
extent = (lvec[0, 0], lvec[0, 0] + lvec[1, 0], lvec[0, 1],
lvec[0, 1] + lvec[2, 1])
#print "DEBUG: extent", extent
print("PP postions imported")
dx = lvec[1, 0] / (nDim[2] - 1)
dy = lvec[2, 1] / (nDim[1] - 1)
dz = lvec[3, 2] / (nDim[0] - 1)
tip_r0 = RS.mkSpaceGrid(lvec[0, 0], lvec[0, 0] + lvec[1, 0], dx,
lvec[0, 1], lvec[0, 1] + lvec[2, 1], dy,
lvec[0, 2], lvec[0, 2] + lvec[3, 2], dz)
#print "DEBUG: dx, dy, dz", dx, dy, dz
#print "DEBUG: tip_r.shape, tip_r0.shape", tip_r.shape, tip_r0.shape
else:
print("Priparing the scan grid for fixed scan")
extent = (x[0], x[1], y[0], y[1])
beta = 1/(kBoltz*T) # [eV]
print("T= ", T, " [K] => beta ", beta/1000.0, "[meV] ")
#E_cutoff = 32.0 * beta
E_cutoff = 18.0 * beta
wGauss = 2.0
Egauss = -0.01
# =============== main
if options.noProbab :
print(" ==== calculating probabilties ====")
# --- tip
V_tip, lvec, nDim = GU.load_scal_field('tip/VLJ',data_format=data_format)
#cell = np.array( [ lvec[1],lvec[2],lvec[3] ] ); print "nDim ", nDim, "\ncell ", cell
#X,Y,Z = getXYZ( nDim, cell )
#V_tip = V_tip*0 + Egauss * getProbeDensity( (cell[0,0]/2.+cell[1,0]/2.,cell[1,1]/2,cell[2,2]/2.-3.8), X, Y, Z, wGauss ) # works for tip (the last flexible tip apex atom) in the middle of the cell
limitE( V_tip, E_cutoff )
W_tip = np.exp( -beta * V_tip )
#W_tip = W_cut(W_tip,nz=95,side='down',sm=5)
del V_tip;
GU.save_scal_field ( 'W_tip', W_tip, lvec, data_format=data_format)
# --- sample
V_surf, lvec, nDim = GU.load_scal_field('sample/VLJ',data_format=data_format)
limitE( V_surf, E_cutoff )
W_surf = np.exp( -beta * V_surf )
#W_surf=W_cut(W_surf,nz=50,side='up',sm=1)
del V_surf;
(0.0, 0.0, 6.0)])
rTips = ocl.getPos_f4(lvec)
# ======= Run
t1 = time.clock()
kargs = ocl.initArgs(atoms, CAOs, spectral, rTips)
Gout = ocl.run(kargs, rTips.shape[:3])
t1 = time.clock() - t1
print(" Run time %g [s] " % t1)
# =====================
# ===================== Plotting
# =====================
Ftmp = np.zeros(rTips.shape[:3])
Ftmp[:, :, :] = Gout[:, :, :]
#Ftmp[:,:,:] = rTips[:,:,:,0]
GU.saveXSF(path + "G_s_sp_ocl.xsf", Ftmp, lvec)
'''
import matplotlib
# matplotlib.use('Agg') # Force matplotlib to not use any Xwindows backend. ## !!! important for working on clusters !!!!
import matplotlib.pyplot as plt
extent = (lvec[0,0],lvec[0,0]+lvec[1,0],lvec[0,1],lvec[0,1]+lvec[2,1])
'''
print("===== ALL DONE ==== ")
parser.add_option( "--npy" , action="store_true" , help="load and save fields in npy instead of xsf" , default=False)
(options, args) = parser.parse_args()
try:
points = np.genfromtxt( options.p )
print "plotting in points", points
except:
print options.p+" not found => exiting ..."
sys.exit()
if options.npy:
format ="npy"
else:
format ="xsf"
fzs,lvec,nDim=GU.load_scal_field(options.i,format=format)
#xs = lvec[3,2]/*np.array( range(nDim[0]) )
xs = np.linspace( 0, lvec[3,2], nDim[0] )
#print nDim
print xs
plt.imshow( fzs[options.iz], origin='imgage', cmap='gray' )
for point in points:
plt.plot(point[0],point[1],'o')
plt.xlim(0,nDim[2])
plt.ylim(0,nDim[1])
plt.savefig( options.i+'_zcurves_legend.png', bbox_inches='tight')
plt.figure()
curves = np.zeros((len(points)+1,len(xs)))