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

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
#!/usr/bin/python

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

#import pyMolecular.RigidMol


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

#Cu          = np.genfromtxt  ( "inputs/Campher.xyz",      dtype= None, skip_header=2 )
#atoms       = np.genfromtxt  ( "inputs/Cu111_6x6_2L.xyz", dtype= None, skip_header=2 )
#print "atoms", atoms

Campher = au.loadAtoms( "inputs/Campher.xyz" );      #print Campher
Surf    = au.loadAtoms( "inputs/Cu111_6x6_2L.xyz" ); #print Surf

nAtomCampher = len(Campher[0])
es   = Campher[0] + Surf[0]
xyzs = np.hstack( [np.array( Campher[1:4] ), np.array( Surf [1:4] )] ).transpose().copy()

'''
print "============================="
print "xyzs.shape", xyzs.shape
print "xyzs", xyzs
print es
au.saveXYZ( es, xyzs, "test_Cu+Campher.xyz" )
'''

#exit()

# ========= Molecules

rmol.initParams( "common_resources/AtomTypes.dat", "common_resources/BondTypes.dat" )
water = rmol.loadMolType( "inputs/Campher.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([ 5.78, 6.7, 12.24 ]), rot, True );

rmol.save2xyz( "world_debug_00.xyz" )

# ========= RigidSurface


rmol.initRigidSubstrate ( "inputs/Cu111_6x6_2L.xyz", np.array([60,60,100],dtype=np.int32), np.array([0.0,0.0,0.0]), np.array([[15.31593,0.0,0.0],[0.0,13.26399,0.0],[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]]) )

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()

rmol.setOptFIRE( dt_max=0.2, dt_min=0.01, damp_max=0.1, minLastNeg=5, finc=1.1, fdec=0.5, falpha=0.98, kickStart=1.0 )

poses = rmol.getPoses();    #print "rmol.getPoses() ", poses_
apos  = rmol.getAtomPos();  #print "rmol.getAtomPos() ", apos

#fout = rmol.openf( "movie.xyz", -1, "w" )
fout = open( "movie.xyz",'w')
for i in range(200):
    print ">>> i ", i
    F2 = rmol.relaxNsteps( 1, 0.0 );
    print "|F| ", np.sqrt(F2)
    xyzs[:nAtomCampher,:] = apos[:,:]
    au.writeToXYZ( fout, es, xyzs )
    #rmol.write2xyz( fout )
    #rmol.save2xyz( "world_debug_%03i.xyz" %i )
fout.close()