コード例 #1
0
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:
コード例 #2
0
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)),
コード例 #3
0
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 ) 
コード例 #4
0
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])
コード例 #5
0
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])