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!")
print " computing convolution with tip by FFT "
Fel_x,Fel_y,Fel_z = fFFT.potential2forces(V, lvec, nDim, rho=rho, sigma = options.sigma, multipole = multipole)
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:
multipole = {options.tip:1.0} if ( options.tip in {'s','px','py','pz','dx2','dy2','dz2','dxy','dxz','dyz'} ) else {PPU.params['tip']:1.0}
print " computing convolution with tip by FFT "
"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)
if options.prolongez[0] > 0.0:
V = np.array(V)
assert options.prolongez[0] < lvec[
3, 2], "prolongez is higher than height of the cell"
print("prolonging_z at height %f by appr. %f" %
(options.prolongez[0], options.prolongez[1]))
#print "Debug: nDim", nDim
nz = int(nDim[0] * options.prolongez[0] / lvec[3, 2])
nn = int(nDim[0] * options.prolongez[1] / lvec[3, 2])
print("this means adding %i new z-voxels in between above z-voxel %i" %
(nn, nz))
