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' ]
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']:
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))
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) )
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
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: