def main(): 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 ) fzs = PP.relaxedScan3D( xTips, yTips, zTips ) PP.saveXSF( dirname+'/OutFz.xsf', headScan, lvecScan, fzs ) for iA,Amp in enumerate( Amps ): AmpStr = "/Amp%2.2f" %Amp print "Amp= ",AmpStr os.makedirs( dirname+AmpStr ) dfs = PP.Fz2df( fzs, dz = dz, k0 = PP.params['kCantilever'], f0=PP.params['f0Cantilever'], n=Amp/dz ) PP.plotImages( dirname+AmpStr+"/df", dfs, slices = range( 0, len(dfs) ) )
def main():
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)
fzs = PP.relaxedScan3D(xTips, yTips, zTips)
PP.saveXSF(dirname + '/OutFz.xsf', headScan, lvecScan, fzs)
for iA, Amp in enumerate(Amps):
AmpStr = "/Amp%2.2f" % Amp
print("Amp= ", AmpStr)
os.makedirs(dirname + AmpStr)
dfs = PP.Fz2df(fzs,
dz=dz,
k0=PP.params['kCantilever'],
f0=PP.params['f0Cantilever'],
n=Amp / dz)
PP.plotImages(dirname + AmpStr + "/df",
dfs,
slices=list(range(0, len(dfs))))
def relaxedScan3D( xTips, yTips, zTips ): ntips = len(zTips); print " zTips : ",zTips rTips = np.zeros((ntips,3)) rs = np.zeros((ntips,3)) fs = np.zeros((ntips,3)) rTips[:,0] = 1.0 rTips[:,1] = 1.0 rTips[:,2] = zTips fzs = np.zeros(( len(zTips), len(yTips ), len(xTips ) )); 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() return fzs
def relaxedScan3D(xTips, yTips, zTips):
ntips = len(zTips)
print(" zTips : ", zTips)
rTips = np.zeros((ntips, 3))
rs = np.zeros((ntips, 3))
fs = np.zeros((ntips, 3))
rTips[:, 0] = 1.0
rTips[:, 1] = 1.0
rTips[:, 2] = zTips
fzs = np.zeros((len(zTips), len(yTips), len(xTips)))
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()
return fzs
X, Y, Z = getMGrid(dims, dd)
print '--- Get Probe Density ---'
rho = getProbeDensity(sampleSize, X, Y, Z, sigma, dd, {'dz2':1.0})
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', elements.ELEMENT_DICT )
iZs,Rs,Qs = PP.parseAtoms( atoms, autogeom = False, PBC = True )
FFLJ = PP.computeLJ( Rs, iZs, FFLJ=None, FFparams=None)
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)
default=0.0)
parser.add_option("--arange",
action="store",
type="float",
help="amplitude range",
nargs=3)
(options, args) = parser.parse_args()
Ks = [0.3, 0.5, 0.7]
Qs = [-0.2, -0.1, 0.0, 0.1, 0.2]
Amps = [1.0]
print(" ============= RUN ")
print(" >> WARNING!!! OVEWRITING SETTINGS by params.ini ")
PP.loadParams('params.ini')
PPPlot.params = PP.params
print(" load Electrostatic Force-field ")
FFel, lvec, nDim, head = GU.loadVecFieldXsf("FFel")
print(" load Lenard-Jones Force-field ")
FFLJ, lvec, nDim, head = GU.loadVecFieldXsf("FFLJ")
PP.lvec2params(lvec)
PP.setFF(FFel)
xTips, yTips, zTips, lvecScan = PP.prepareScanGrids()
#Ks = [ 0.25, 0.5, 1.0 ]
#Qs = [ -0.2, 0.0, +0.2 ]
#Amps = [ 2.0 ]
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") ]
makeclean( ) # force to recompile
import ProbeParticle as PP
print " >> WARNING!!! OVEWRITING SETTINGS by params.ini "
PP.loadParams( 'params_watter.ini' )
#Fx,lvec,nDim,head=XSFutils.loadXSF('Fx.xsf')
#Fy,lvec,nDim,head=XSFutils.loadXSF('Fy.xsf')
#Fz,lvec,nDim,head=XSFutils.loadXSF('Fz.xsf')
Fx,lvec,nDim,head=PP.loadXSF('Fx.xsf')
Fy,lvec,nDim,head=PP.loadXSF('Fy.xsf')
Fz,lvec,nDim,head=PP.loadXSF('Fz.xsf')
PP.params['gridA'] = lvec[ 1,: ].copy()
PP.params['gridB'] = lvec[ 2,: ].copy()
PP.params['gridC'] = lvec[ 3,: ].copy()
PP.params['gridN'] = nDim.copy()
FFLJ = np.zeros( (nDim[0],nDim[1],nDim[2],3) )
try:
sys.argv[1]
except IndexError:
print "Please specify a file with coordinates"
exit(1)
parser = OptionParser()
parser.add_option( "--dfrange", action="store", type="float", help="Range of plotted frequency shift (df)", nargs=2)
parser.add_option( "--df", action="store_true", help="Write AFM frequency shift in df.xsf file", default=False)
(options, args) = parser.parse_args()
print "Reading coordinates from the file {}".format(sys.argv[1])
print " >> WARNING!!! OVERWRITING SETTINGS by params.ini "
PP.loadParams( 'params.ini' )
Fx,lvec,nDim,head=GU.loadXSF('FFel_x.xsf')
Fy,lvec,nDim,head=GU.loadXSF('FFel_y.xsf')
Fz,lvec,nDim,head=GU.loadXSF('FFel_z.xsf')
PP.params['gridA'] = lvec[ 1,: ].copy()
PP.params['gridB'] = lvec[ 2,: ].copy()
PP.params['gridC'] = lvec[ 3,: ].copy()
PP.params['gridN'] = nDim.copy()
FF = np.zeros( (nDim[0],nDim[1],nDim[2],3) )
FFLJ = np.zeros( np.shape( FF ) )
FFel = np.zeros( np.shape( FF ) )
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)
parser = OptionParser()
parser.add_option( "-i", "--input", action="store", type="string", help="format of input file", default='vasp.locpot.xsf')
(options, args) = parser.parse_args()
num = len(sys.argv)
if (num < 2):
sys.exit("Number of arguments = "+str(num-1)+". This script shoudl have at least one argument. I am terminating...")
finput = sys.argv[num-1]
# --- initialization ---
sigma = 1.0 # [ Angstroem ]
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 == 'vasp.locpot.xsf'):
V, lvec, nDim, head = GU.loadXSF(finput)
elif(options.input == 'aims.cube'):
V, lvec, nDim, head = GU.loadCUBE(finput)
print " computing convolution with tip by FFT "
Fel_x,Fel_y,Fel_z = LFF. potential2forces( V, lvec, nDim, sigma = 1.0 )
print(" # ========== make & load ProbeParticle C++ library ")
LWD = '/home/prokop/git/ProbeParticleModel/code'
sys.path = [LWD]
import basUtils
import elements
import GridUtils as GU
import ProbeParticle as PP
print(" ============= RUN ")
print(" >> WARNING!!! OVEWRITING SETTINGS by params.ini ")
PP.loadParams('params.ini')
print(" load Electrostatic Force-field ")
FFel, lvec, nDim, head = loadVecFieldXsf("FFel")
print(" load Lenard-Jones Force-field ")
FFLJ, lvec, nDim, head = loadVecFieldXsf("FFLJ")
PP.params['gridA'] = lvec[1, :].copy()
PP.params['gridB'] = lvec[2, :].copy()
PP.params['gridC'] = lvec[3, :].copy()
PP.params['gridN'] = nDim.copy()
xTips, yTips, zTips, lvecScan = prepareGrids()
#Ks = [ 0.25, 0.5, 1.0 ]
#Qs = [ -0.2, 0.0, +0.2 ]
#Amps = [ 2.0 ]
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")]
makeclean() # force to recompile
import ProbeParticle as PP
print(" >> WARNING!!! OVEWRITING SETTINGS by params.ini ")
PP.loadParams('params_watter.ini')
#Fx,lvec,nDim,head=XSFutils.loadXSF('Fx.xsf')
#Fy,lvec,nDim,head=XSFutils.loadXSF('Fy.xsf')
#Fz,lvec,nDim,head=XSFutils.loadXSF('Fz.xsf')
Fx, lvec, nDim, head = PP.loadXSF('Fx.xsf')
Fy, lvec, nDim, head = PP.loadXSF('Fy.xsf')
Fz, lvec, nDim, head = PP.loadXSF('Fz.xsf')
PP.params['gridA'] = lvec[1, :].copy()
PP.params['gridB'] = lvec[2, :].copy()
PP.params['gridC'] = lvec[3, :].copy()
PP.params['gridN'] = nDim.copy()
FFLJ = np.zeros((nDim[0], nDim[1], nDim[2], 3))
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")]
#makeclean( ) # force to recompile
import ProbeParticle as PP
print " # ========== server interface file I/O "
PP.loadParams('params.ini')
print " # ============ define atoms "
#bas = basUtils.loadBas('surf.bas')[0]
#bas = basUtils.loadBas('PTCDA_Ruslan_1x1.bas')[0]
#bas = basUtils.loadBas('GrN6x6.bas')[0]
#atoms = basUtils.loadAtoms('GrN6x6.bas', elements.ELEMENT_DICT )
#atoms = basUtils.loadAtoms('GrN6x6.xyz', elements.ELEMENT_DICT )
atoms = basUtils.loadAtoms('input.xyz', elements.ELEMENT_DICT)
Rs = np.array([atoms[1], atoms[2], atoms[3]])
iZs = np.array(atoms[0])
if not PP.params['PBC']:
default='vasp.locpot.xsf')
(options, args) = parser.parse_args()
num = len(sys.argv)
if (num < 2):
sys.exit(
"Number of arguments = " + str(num - 1) +
". This script shoudl have at least one argument. I am terminating...")
finput = sys.argv[num - 1]
# --- initialization ---
sigma = 1.0 # [ Angstroem ]
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 == 'vasp.locpot.xsf'):
V, lvec, nDim, head = GU.loadXSF(finput)
elif (options.input == 'aims.cube'):
V, lvec, nDim, head = GU.loadCUBE(finput)
print " computing convolution with tip by FFT "
Fel_x, Fel_y, Fel_z = LFF.potential2forces(V, lvec, nDim, sigma=1.0)
print " saving electrostatic forcefiled "
GU.saveXSF('FFel_x.xsf', Fel_x, lvec, head)
print "Please specify a file with coordinates"
exit(1)
filename = sys.argv[1]
if not os.path.exists(filename):
print "File {} with coordinates doesn't exist!!! Exiting".format(filename)
exit(1)
ProjName = filename[:-4]
# Working with parameters file
ParamFilename = ProjName + ".ini"
if os.path.exists(ParamFilename):
PP.loadParams(ParamFilename)
else:
print "File {} with parameters doesn't exist!!! Using defaults".format(
ParamFilename)
cell = np.array([
PP.params['gridA'],
PP.params['gridB'],
PP.params['gridC'],
]).copy()
lvec = PP.params2lvec()
atoms = basUtils.loadAtoms(filename, elements.ELEMENT_DICT)
iZs, Rs, Qs = PP.parseAtoms(atoms, autogeom=False, PBC=True)
# Lennard Jonnes contribution to the force field
print " load Electrostatic Force-field "
FFel_x,lvec,nDim,head=GU.loadXSF('FFel_x.xsf')
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('geom.bas')
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 = parseAtoms( atoms, autogeom = False, PBC = True, FFparams=FFparams )
FFLJ = PP.computeLJ( iZs, Rs, FFLJ=None, cell=None, autogeom = False, PBC =
True, FFparams=FFparams)
print "impose 4fold symmetry on FFLJ "
FFLJ4 = np.zeros(np.shape( FFLJ ))
FFLJ4[:,:,:,0] = 0.25*( FFLJ[:,:,:,0] - FFLJ[:,:,::-1,0] + FFLJ[:,::-1,:,0] - FFLJ[:,::-1,::-1,0] )
FFLJ4[:,:,:,1] = 0.25*( FFLJ[:,:,:,1] + FFLJ[:,:,::-1,1] - FFLJ[:,::-1,:,1] - FFLJ[:,::-1,::-1,1] )
FFLJ4[:,:,:,2] = 0.25*( FFLJ[:,:,:,2] + FFLJ[:,:,::-1,2] + FFLJ[:,::-1,:,2] + FFLJ[:,::-1,::-1,2] )
print "save FFLJ to .xsf "
GU.saveVecFieldXsf( 'FFLJ', FFLJ4, lvec, head )
print " ***** ALL DONE ***** "
#plt.show()
# NOTE: Data for COCu4 tip example are on tarkil /auto/praha1/prokop/STHM/vasp/COCu4 # ============== load reference grid V, lvec, nDim, head = GU.loadXSF( WORK_DIR + 'LOCPOT.xsf' ) cell = np.array( [ lvec[1], lvec[2], lvec[3] ]); MP.setGrid( V, cell ); # ============== prepare atoms atom_types,atom_pos = GU.getFromHead_PRIMCOORD( head ) # load atoms from header of xsf file # set sample region around atom atom_Rmin, atom_Rmax spacies = PP.loadSpecies( './defaults/atomtypes.ini' ) 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 " # ========== make & load ProbeParticle C++ library " LWD = '/home/prokop/git/ProbeParticleModel/code' sys.path = [ LWD ] import basUtils import elements import GridUtils as GU import ProbeParticle as PP print " ============= RUN " print " >> WARNING!!! OVEWRITING SETTINGS by params.ini " PP.loadParams( 'params.ini' ) print " load Electrostatic Force-field " FFel, lvec, nDim, head = loadVecFieldXsf( "FFel" ) print " load Lenard-Jones Force-field " FFLJ, lvec, nDim, head = loadVecFieldXsf( "FFLJ" ) PP.params['gridA'] = lvec[ 1,: ].copy() PP.params['gridB'] = lvec[ 2,: ].copy() PP.params['gridC'] = lvec[ 3,: ].copy() PP.params['gridN'] = nDim.copy() xTips,yTips,zTips,lvecScan = prepareGrids( ) #Ks = [ 0.25, 0.5, 1.0 ] #Qs = [ -0.2, 0.0, +0.2 ] #Amps = [ 2.0 ]
# ============== load reference grid
V, lvec, nDim, head = GU.loadXSF(WORK_DIR + 'LOCPOT.xsf')
cell = np.array([lvec[1], lvec[2], lvec[3]])
MP.setGrid(V, cell)
# ============== prepare atoms
atom_types, atom_pos = GU.getFromHead_PRIMCOORD(
head) # load atoms from header of xsf file
# set sample region around atom atom_Rmin, atom_Rmax
spacies = PP.loadSpecies('./defaults/atomtypes.ini')
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
parser.add_option( "--krange", action="store", type="float", help="k parameter range", nargs=3) parser.add_option( "-q", action="store", type="float", help="charge", default=0.0) parser.add_option( "--qrange", action="store", type="float", help="charge range", nargs=3) parser.add_option( "-a", action="store", type="float", help="amplitude", default=0.0) parser.add_option( "--arange", action="store", type="float", help="amplitude range", nargs=3) (options, args) = parser.parse_args() Ks = [ 0.3 ] Qs = [ 0.0] Amps = [ 1.0 ] print " ============= RUN " print " >> WARNING!!! OVEWRITING SETTINGS by params.ini " PP.loadParams( 'params.ini' ) PPPlot.params = PP.params print " load Electrostatic Force-field " FFel, lvec, nDim, head = GU.loadVecFieldXsf( "FFel" ) print " load Lenard-Jones Force-field " FFLJ, lvec, nDim, head = GU.loadVecFieldXsf( "FFLJ" ) PP.lvec2params( lvec ) PP.setFF( FFel ) xTips,yTips,zTips,lvecScan = PP.prepareScanGrids( ) #Ks = [ 0.25, 0.5, 1.0 ] #Qs = [ -0.2, 0.0, +0.2 ] #Amps = [ 2.0 ]
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") ]
#makeclean( ) # force to recompile
import ProbeParticle as PP
print " # ========== server interface file I/O "
PP.loadParams( 'params.ini' )
print " # ============ define atoms "
#bas = basUtils.loadBas('surf.bas')[0]
#bas = basUtils.loadBas('PTCDA_Ruslan_1x1.bas')[0]
#bas = basUtils.loadBas('GrN6x6.bas')[0]
atoms = basUtils.loadAtoms('input.xyz')
Rs = np.array([atoms[1],atoms[2],atoms[3]]);
iZs = np.array( atoms[0])
if not PP.params['PBC' ]:
print " NO PBC => autoGeom "
PP.autoGeom( Rs, shiftXY=True, fitCell=True, border=3.0 )
print " NO PBC => params[ 'gridA' ] ", PP.params[ 'gridA' ]
filename = sys.argv[1]
if not os.path.exists(filename):
print "File {} with coordinates doesn't exist!!! Exiting".format(filename)
exit(1)
ProjName = filename[:-4]
# Working with parameters file
ParamFilename = ProjName + ".ini"
if os.path.exists(ParamFilename):
PP.loadParams(ParamFilename)
else:
print "File {} with parameters doesn't exist!!! Using defaults".format(ParamFilename)
cell = np.array([PP.params["gridA"], PP.params["gridB"], PP.params["gridC"]]).copy()
lvec = PP.params2lvec()
atoms = basUtils.loadAtoms(filename, elements.ELEMENT_DICT)
iZs, Rs, Qs = PP.parseAtoms(atoms, autogeom=False, PBC=True)
# Lennard Jonnes contribution to the force field
if PP.params["useLJ"]:
# checking if files exist: