コード例 #1
0
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 = 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 )
				plotImages( dirname+AmpStr+"/df", dfs, slices = range( 0, len(dfs) ) )
コード例 #2
0
print " # ============ define Scan and allocate arrays   - do this before simulation, in case it will crash "

dz    = PP.params['scanStep'][2]
zTips = np.arange( PP.params['scanMin'][2], PP.params['scanMax'][2]+0.00001, dz )[::-1];
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 

PP.setTip()

xTips  = np.arange( PP.params['scanMin'][0], PP.params['scanMax'][0]+0.00001, 0.1 )
yTips  = np.arange( PP.params['scanMin'][1], PP.params['scanMax'][1]+0.00001, 0.1 )
extent=( xTips[0], xTips[-1], yTips[0], yTips[-1] )
fzs    = np.zeros(( len(zTips), len(yTips ), len(xTips ) ));

nslice = 10;

atomTypesFile = os.path.dirname(sys.argv[0]) + '/../code/defaults/atomtypes.ini'
FFparams = PP.loadSpecies( atomTypesFile  )
C6,C12   = PP.getAtomsLJ( PP.params['probeType'], iZs, FFparams )

print " # ============ define Grid "

cell =np.array([
コード例 #3
0
print " # ============ define Scan and allocate arrays   - do this before simulation, in case it will crash "

dz = PP.params['scanStep'][2]
zTips = np.arange(PP.params['scanMin'][2], PP.params['scanMax'][2] + 0.00001,
                  dz)[::-1]
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

PP.setTip()

xTips = np.arange(PP.params['scanMin'][0], PP.params['scanMax'][0] + 0.00001,
                  0.1)
yTips = np.arange(PP.params['scanMin'][1], PP.params['scanMax'][1] + 0.00001,
                  0.1)
extent = (xTips[0], xTips[-1], yTips[0], yTips[-1])
fzs = np.zeros((len(zTips), len(yTips), len(xTips)))

nslice = 10

atomTypesFile = os.path.dirname(
    sys.argv[0]) + '/../code/defaults/atomtypes.ini'
FFparams = PP.loadSpecies(atomTypesFile)
C6, C12 = PP.getAtomsLJ(PP.params['probeType'], iZs, FFparams)
コード例 #4
0
ファイル: ppr.new.py プロジェクト: jhv5a/ProbeParticleModel
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 ]

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)
        #GU.saveVecFieldXsf( 'FFtot', FF, lvec, head )
        fzs = PP.relaxedScan3D(xTips, yTips, zTips)
        GU.saveXSF(dirname + '/OutFz.xsf', fzs, lvecScan, GU.XSF_HEAD_DEFAULT)
        for iA, Amp in enumerate(Amps):
            AmpStr = "/Amp%2.2f" % Amp
            print("Amp= ", AmpStr)
            os.makedirs(dirname + AmpStr)
            dz = PP.params['scanStep'][2]
            dfs = PP.Fz2df(fzs,
                           dz=dz,
                           k0=PP.params['kCantilever'],
                           f0=PP.params['f0Cantilever'],
                           n=Amp / dz)
            extent = (xTips[0], xTips[-1], yTips[0], yTips[-1])
            PPPlot.plotImages(dirname + AmpStr + "/df",
コード例 #5
0
xTips,yTips,zTips,lvecScan = PP.prepareScanGrids( )

#Ks   = [ 0.25, 0.5, 1.0 ]
#Qs   = [ -0.2, 0.0, +0.2 ]
#Amps = [ 2.0 ]



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 )
		#GU.saveVecFieldXsf( 'FFtot', FF, lvec, head )
		fzs = PP.relaxedScan3D( xTips, yTips, zTips )
		GU.saveXSF( dirname+'/OutFz.xsf', fzs, lvecScan, GU.XSF_HEAD_DEFAULT )
		for iA,Amp in enumerate( Amps ):
			AmpStr = "/Amp%2.2f" %Amp
			print "Amp= ",AmpStr
			os.makedirs( dirname+AmpStr )
			dz  = PP.params['scanStep'][2]
			dfs = PP.Fz2df( fzs, dz = dz, k0 = PP.params['kCantilever'], f0=PP.params['f0Cantilever'], n=Amp/dz )
			extent=( xTips[0], xTips[-1], yTips[0], yTips[-1] )
			PPPlot.plotImages( dirname+AmpStr+"/df", dfs, slices = range( 0, len(dfs) ), extent=extent )

print " ***** ALL DONE ***** "

#plt.show()