Python GridUtils.loadXSF Examples

Example #1

File: generateElFF.py Project: ga32xan/ProbeParticleModel

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:

Example #2

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)

Example #3

File: generateElFF.py Project: ProkopHapala/ProbeParticleModel

    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!")    

Example #4

File: generateElFF.py Project: jhv5a/ProbeParticleModel

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)

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])