print options
data_format = "npy" if options.npy else "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 "--- Compute Lennard-Jones Force-filed ---"
atoms, lvec = PPH.importGeometries(options.input)
FFparams = None
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')
PBC = False if not options.noPBC else PPU.params['PBC']
iZs, Rs, Qs = PPH.parseAtoms(atoms,
autogeom=False,
PBC=options.noPBC,
FFparams=FFparams)
atoms_str = ""
atoms = None
bonds = None
if opt_dict['atoms'] or opt_dict['bonds']:
atoms_str = "_atoms"
atoms, tmp1, tmp2 = basUtils.loadAtoms('input_plot.xyz')
del tmp1, tmp2
# print "atoms ", atoms
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, Qstmp = PPH.parseAtoms(atoms,
autogeom=False,
PBC=False,
FFparams=FFparams)
atom_colors = basUtils.getAtomColors(iZs, FFparams=FFparams)
Rs = Rs.transpose().copy()
atoms = [iZs, Rs[0], Rs[1], Rs[2], atom_colors]
#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 iq,Q in enumerate( Qs ): if ( charged_system == True): FF = FFLJ + FFel * Q else: FF = FFLJ if options.boltzmann : FF += FFboltz PPC.setFF_Fpointer( FF ) for ik,K in enumerate( Ks ): dirname = "Q%1.2fK%1.2f" %(Q,K) print " relaxed_scan for ", dirname if not os.path.exists( dirname ): os.makedirs( dirname ) PPC.setTip( kSpring = np.array((K,K,0.0))/-PPU.eVA_Nm ) fzs,PPpos = PPH.relaxedScan3D( xTips, yTips, zTips ) GU.save_scal_field( dirname+'/OutFz', fzs, lvecScan, format=format ) #print "SHAPE", PPpos.shape, xTips.shape, yTips.shape, zTips.shape if opt_dict['disp']: PPdisp=PPpos.copy() nx=PPdisp.shape[2] ny=PPdisp.shape[1] nz=PPdisp.shape[0] test=np.meshgrid(xTips,yTips,zTips) #print "TEST SHAPE", np.array(test).shape #print nx,ny,nz i=0 while i<nx: j=0 while j<ny: k=0
FF = FFLJ
if options.boltzmann:
FF += FFboltz
PPC.setFF_Fpointer(FF)
for ik, K in enumerate(Ks):
dirname = "Q%1.2fK%1.2f" % (Q, K)
print(" relaxed_scan for ", dirname)
if not os.path.exists(dirname):
os.makedirs(dirname)
if Bds:
PPC.setTip(kSpring=np.array((PPU.params['stiffness'][0],
PPU.params['stiffness'][1], 0.0)) /
-PPU.eVA_Nm)
else:
PPC.setTip(kSpring=np.array((K, K, 0.0)) / -PPU.eVA_Nm)
Fs, rPPs, rTips = PPH.relaxedScan3D(xTips, yTips, zTips)
GU.save_scal_field(dirname + '/OutFz',
Fs[:, :, :, 2],
lvecScan,
data_format=data_format)
if opt_dict['vib'] >= 0:
which = opt_dict['vib']
print(
" === computing eigenvectors of dynamical matix which=%i ddisp=%f"
% (which, PPU.params['ddisp']))
evals, evecs = PPC.stiffnessMatrix(rTips.reshape((-1, 3)),
rPPs.reshape((-1, 3)),
which=which,
ddisp=PPU.params['ddisp'])
GU.save_vec_field(dirname + '/eigvalKs',
evals.reshape(rTips.shape),
else:
sys.exit("ERROR!!! Unknown format of geometry system. Supported "
"formats are: .xyz, .cube, .xsf \n\n")
FFparams=None
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=PPH.parseAtoms(atoms, autogeom = False, PBC = options.noPBC,
FFparams=FFparams )
# This function returns the following information:
# 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
xTips,yTips,zTips,lvecScan = PPU.prepareScanGrids( )
extent = ( xTips[0], xTips[-1], yTips[0], yTips[-1] )
atoms_str=""
atoms = None
bonds = None
if opt_dict['atoms'] or opt_dict['bonds']:
atoms_str="_atoms"
atoms = basUtils.loadAtoms( 'input_plot.xyz' )
# print "atoms ", atoms
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,Qstmp=PPH.parseAtoms(atoms, autogeom = False,PBC = options.noPBC,
FFparams=FFparams)
atom_colors = basUtils.getAtomColors(iZs,FFparams=FFparams)
Rs=Rs.transpose().copy()
atoms= [iZs,Rs[0],Rs[1],Rs[2],atom_colors]
#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 ):
