xTips,yTips,zTips,lvecScan = PPU.prepareScanGrids( ) 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:
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)
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)),
xTips,yTips,zTips,lvecScan = PPU.prepareScanGrids( ) 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 ) 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 ), lvecScan, data_format=data_format ) if which > 0: GU.save_vec_field( dirname+'/eigvecK1', evecs[0].reshape( rTips.shape ), lvecScan, data_format=data_format ) if which > 1: GU.save_vec_field( dirname+'/eigvecK2', evecs[1].reshape( rTips.shape ), lvecScan, data_format=data_format ) if which > 2: GU.save_vec_field( dirname+'/eigvecK3', evecs[2].reshape( rTips.shape ), lvecScan, data_format=data_format ) #print "SHAPE", PPpos.shape, xTips.shape, yTips.shape, zTips.shape if opt_dict['disp']: GU.save_vec_field( dirname+'/PPdisp', rPPs-rTips+PPU.params['r0Probe'][0], lvecScan, data_format=data_format ) if ( opt_dict['pos'] or opt_dict['stm']): GU.save_vec_field( dirname+'/PPpos', rPPs, lvecScan, data_format=data_format )
sys.path.append('../')
#import pyProbeParticle as PPU
import pyProbeParticle.core as PPC
S = np.genfromtxt('TipRSpline.ini')
print "TipRSpline.ini overrides harmonic tip"
xs = S[:, 0].copy()
print "xs: ", xs
ydys = S[:, 1:].copy()
print "ydys: ", ydys
plt.plot(xs, ydys[:, 0], 'o')
plt.plot(xs, ydys[:, 0] + ydys[:, 1], '.')
PPC.setTipSpline(xs, ydys)
PPC.setTip()
fs = np.zeros((60, 3))
r0 = np.array([0.0, 0.0, 0.5])
dr = np.array([0.0, 0.0, 0.1])
R = np.array([0.0, 0.0, 0.0])
xs = np.array(range(len(fs))) * dr[2] + r0[2]
#print "xs=",xs
print ">>> PPC.test_force( 1, r0, dr, R, fs )"
PPC.test_force(1, r0, dr, R, fs)
plt.plot(xs, fs[:, 2])
print ">>> PPC.test_force( 2, r0, dr, R, fs )"
PPC.test_force(2, r0, dr, R, fs)
plt.plot(xs, fs[:, 2])
sys.path.append("../")
# import pyProbeParticle as PPU
import pyProbeParticle.core as PPC
S = np.genfromtxt("TipRSpline.ini")
print "TipRSpline.ini overrides harmonic tip"
xs = S[:, 0].copy()
print "xs: ", xs
ydys = S[:, 1:].copy()
print "ydys: ", ydys
plt.plot(xs, ydys[:, 0], "o")
plt.plot(xs, ydys[:, 0] + ydys[:, 1], ".")
PPC.setTipSpline(xs, ydys)
PPC.setTip()
fs = np.zeros((60, 3))
r0 = np.array([0.0, 0.0, 0.5])
dr = np.array([0.0, 0.0, 0.1])
R = np.array([0.0, 0.0, 0.0])
xs = np.array(range(len(fs))) * dr[2] + r0[2]
# print "xs=",xs
print ">>> PPC.test_force( 1, r0, dr, R, fs )"
PPC.test_force(1, r0, dr, R, fs)
plt.plot(xs, fs[:, 2])
print ">>> PPC.test_force( 2, r0, dr, R, fs )"
PPC.test_force(2, r0, dr, R, fs)
plt.plot(xs, fs[:, 2])