SimpleSimulationEngine/python/test_RigidMol.py at master · ProkopHapala/SimpleSimulationEngine · GitHub

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#!/usr/bin/python

import sys
import os
import numpy as np
import pyMolecular.RigidMol as rmol

os.chdir("/u/25/prokoph1/unix/git/SimpleSimulationEngine/cpp/Build/apps/MolecularEditor2")

# ========= Molecules

rmol.initParams( "common_resources/AtomTypes.dat", "common_resources/BondTypes.dat" )
water = rmol.loadMolType( "inputs/water_T5_ax.xyz" );
Na    = rmol.loadMolType( "inputs/NaIon.xyz" );
Cl    = rmol.loadMolType( "inputs/ClIon.xyz" );

rot = np.array([[1.0,0.0,0.0],[0.0,1.0,0.0],[0.0,0.0,1.0]])

print rmol.insertMolecule( water, np.array([0.0,0.0,4.0]), rot, True );
print rmol.insertMolecule( water, np.array([4.0,0.0,4.0]), rot, True );

print rmol.insertMolecule( Na, np.array([4.0,6.0,5.0]), rot, True );
print rmol.insertMolecule( Na, np.array([4.0,4.0,2.0]), rot, True );
print rmol.insertMolecule( Na, np.array([4.0,8.0,2.0]), rot, True );

print rmol.insertMolecule( Cl, np.array([2.0,6.0,2.0]), rot, True );
print rmol.insertMolecule( Cl, np.array([6.0,6.0,2.0]), rot, True );
rmol.save2xyz( "world_debug_00.xyz" )

# ========= RigidSurface

'''
print "pyDEBUG 1"

print "pyDEBUG 2"
rmol.initRigidSubstrate( "inputs/NaCl_wo4.xyz", np.array([60,60,100],dtype=np.int32), np.array([0.0,0.0,4.5]), np.array([[12.0173,0.0,0.0],[0.0,12.0173,0.0],[0.0,0.0,20.0]]) )
#rmol.initRigidSubstrate( "inputs/NaCl_wo4.xyz", np.array([60,60,100],dtype=np.int32), np.array([0.0,0.0,0.0]), np.array([[12.0173,0.0,0.0],[0.0,12.0173,0.0],[0.0,0.0,20.0]]) )
print "pyDEBUG 3"

if os.path.isfile("data/FFPauli.bin"):
    print "gridFF found on disk => loading "
    rmol.loadGridFF()
else:
    print "gridFF not found on disk => recalc "
    rmol.recalcGridFF( np.array([1,1,1],dtype=np.int32) )
    rmol.saveGridFF()

rmol.debugSaveGridFF( "FFtot_z_Na.xsf", np.array([1.3,0.0447214,0.0]) )
'''

# ========= Relaxation

rmol.bakeMMFF()

rmol.prepareOpt()

fout = rmol.openf( "movie.xyz", -1, "w" )

for i in range(50):
    print ">>> i ", i
    rmol.relaxNsteps( 1, 0.0 )
    rmol.write2xyz( fout )
    #rmol.save2xyz( "world_debug_%03i.xyz" %i )