scripting

import common libraries

import os
import numpy as np
import matplotlib.pyplot as plt
import elements
import basUtils

load ProbeParticle 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

setup system and simulation parameters

PP.loadParams( 'params.ini' ) # load parametes from ini file

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' ]:
	PP.autoGeom( Rs, shiftXY=True,  fitCell=True,  border=3.0 )

Rs[0] += PP.params['moleculeShift' ][0]          # shift molecule so that we sample reasonable part of potential 
Rs[1] += PP.params['moleculeShift' ][1]          
Rs[2] += PP.params['moleculeShift' ][2]          
Rs     = np.transpose( Rs, (1,0) ).copy() 

Qs = np.array( atoms[4] )

if PP.params['PBC' ]:
	iZs,Rs,Qs = PP.PBCAtoms( iZs, Rs, Qs, avec=PP.params['gridA'], bvec=PP.params['gridB'] )





### Define 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;

FFparams = PP.loadSpecies ( 'atomtypes.ini' ) C6,C12 = PP.getAtomsLJ( PP.params['probeType'], iZs, FFparams )

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

cell =np.array([ PP.params['gridA'], PP.params['gridB'], PP.params['gridC'], ]).copy()

gridN = PP.params['gridN']

FF = np.zeros( (gridN[2],gridN[1],gridN[0],3) )