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:
