import os, sys
import ase.io as fio
import ase.db as db
from gocia.interface import Interface
import gocia.utils.report as rp
# $ python plotCPK.py asym-4l.vasp Ga3N3.vasp
# # Timing: 1.4265 s, ~10% faster than BS
subsName = sys.argv[1]
surfName = sys.argv[2]
baseName = surfName.split('/')[-1].split('.')[0]
surf = Interface(
tags=baseName,
subAtoms=fio.read(subsName),
allAtoms=fio.read(surfName),
)
surf.info['eV'] = 0.1
surf.print()
surf.draw('CPK', title='%s, %.3f eV' % (surf.get_formula(), surf.info['eV']))
surf.draw('BS', title='%s, %.3f eV' % (surf.get_formula(), surf.info['eV']))
srtDB = connect(sys.argv[2])
baseName = ''
eneList = []
for r in srtDB.select([('eV2GM', '<', 5.0)]):
a = r.toatoms()
eneList.append(r.eV)
surf = Interface(
allAtoms=a,
subAtoms=substrate,
)
baseName = surf.tags
surf.tags += '-%i' % r.id
surf.draw(
'BS',
title='#%i, E=%.3f eV, mag=%.2f'%\
(r.id, r.eV2GM, r.mag),
)
# myImgList = [f for f in os.listdir() if baseName in f and 'png' in f]
# rp.gen_pdf_test(
# projName='Global Optimization of Restructured %s'%baseName,
# description=\
# '\\begin{itemize}\n'+\
# '\\item From direct BLDA sampling with random rattling of 0.1 Angstrom and Hookean pre-optimization.\n'+\
# '\\item The same-element probability penalty is set to 50\%, and desorbed N$_2$ structures are filtered out.\n'+\
# '\\item Color code: Ga - light brown; N - blue.\n'+\
# '\\item For clarity, the constrained atoms are drawn in white, and the buffer atoms are drawn in shallow color.\n'+\
# '\\end{itemize}',
# imgList=myImgList,
# )
from gocia.interface import Interface
import sys, os
from gocia.ga.crossover import crossover_snsSurf_2d_GC
subs = sys.argv[1]
surf1 = sys.argv[2]
surf2 = sys.argv[3]
#surf0 = Interface(subAtoms=subs, allAtoms=subs)
surf1 = Interface(allAtoms=surf1, subAtoms=subs)
surf2 = Interface(allAtoms=surf2, subAtoms=subs)
surf1.print()
surf1.draw('CPK')
os.system('mv Ga47N51-cpk.png mom.png')
surf2.print()
surf2.draw('CPK')
os.system('mv Ga47N51-cpk.png dad.png')
#print(surf1.get_fixBufPos())
#print(surf1.get_fixBufAtoms())
nova = crossover_snsSurf_2d_GC(surf1, surf2)
nova.print()
nova.write('nova.vasp')
nova.draw('CPK')
os.system('mv Ga47N51-cpk.png kid.png')
tmp = nova.copy()
nova = tmp.copy()