#!/usr/bin/python
import sys
import numpy as np
import pyMolecular.atomicUtils as au
# === read input
fname = sys.argv[1]
celname = sys.argv[2]
nabc = np.array((int(sys.argv[3]), int(sys.argv[4]), int(sys.argv[5])))
# === main
lvec = np.genfromtxt(celname)
xyzs, Zs, enames = au.loadAtoms(fname)
enames_ = []
Zs_ = []
xyzs_ = []
for ia in range(nabc[0]):
for ib in range(nabc[1]):
for ic in range(nabc[2]):
xyzs_.append(xyzs + (lvec[0] * ia + lvec[1] * ib +
lvec[0] * ic)[np.newaxis, :])
enames_ += enames
Zs_.append(Zs)
Zs_ = np.concatenate(Zs_)
xyzs_ = np.concatenate(xyzs_)
au.saveXyz(fname + '_%ix%ix%i.xyz' % (nabc[0], nabc[1], nabc[2]), enames_,
dtype=[('symbol', '|S4'), ('i1', np.int32),
('i2', np.int32), ('i3', np.int32),
('i4', np.int32), ('R', np.float64),
('eps', np.float64),
('alpha', np.int32)],
usecols=(0, 1, 2, 3, 4, 5, 6))
print "atomTypes_dat ", atomTypes_dat
#for a in atomTypes_dat:
# print a
# print a[0]
# print a[1]
atomTypes_dct = {a[0]: (a[5], a[6]) for a in atomTypes_dat}
print "atomTypes_dct ", atomTypes_dct
water = au.loadAtoms("inputs/water_T5_ax.xyz")
#print Campher
campher = au.loadAtoms("inputs/Campher.xyz")
#print Campher
surf = au.loadAtoms("inputs/Cu111_6x6_2L.xyz")
#print Surf
#print water
#exit()
cell = [[15.31593, 0.0, 0.0], [0.0, 13.26399, 0.0], [0.0, 0.0, 20.0]]
'''
#rots = sphereTangentSpace(n=100)
rots = randomRotations(n=10000)
rots = pruneRots(rots, dcut=0.3, ipiv=2)
#rots = getSimilarRotations( rots, rots[0], dcut=0.1, ipiv=2)
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" )
'''