def __init__(
self,
substrate=None,
gadb=None,
popSize=20,
zLim=None,
compParam=None,
matingMethod=None,
convergeCrit=None,
):
if gadb is not None:
self.gadb = connect(gadb)
if type(substrate) is str:
self.substrate = read(substrate)
else:
self.substrate = substrate
if zLim is not None:
self.zLim = zLim
if zLim is None:
self.zLim = Interface(self.substrate, self.substrate).zLim
self.popSize = popSize
if convergeCrit is None:
self.convergeCrit = 5 * self.popSize
else:
self.convergeCrit = convergeCrit
if chemPotDict is not None:
self.chemPotDict = chemPotDict
self.iniSize = len(self)
def gen_offspring_box(self, mutRate=0.3, xyzLims=[], bondRejList = None, constrainTop=False, rattleOn=True, growOn=True, leachOn=True, permuteOn = True, transOn = True, transVec=[[-2,2],[-2,2]]):
kid, parent = None, None
mater, pater = 0, 0
while kid is None:
mater, pater = self.choose_parents()
a1 = self.gadb.get(id=mater).toatoms()
a2 = self.gadb.get(id=pater).toatoms()
surf1 = Interface(a1, self.substrate, zLim=self.zLim)
surf2 = Interface(a2, self.substrate, zLim=self.zLim)
kid = crossover_snsSurf_2d_GC(surf1, surf2, tolerance=0.75)
parent = surf1.copy()
print('PARENTS: %i and %i'%(mater, pater))
myMutate = ''
if srtDist_similar_zz(a1, a2)\
or srtDist_similar_zz(a1, kid.get_allAtoms())\
or srtDist_similar_zz(a2, kid.get_allAtoms()):
print(' |- TOO SIMILAR!')
mutRate = 1
if np.random.rand() < mutRate:
mutType = np.random.choice([0,1,2,3,4], size=1)[0]
if mutType == 0 and rattleOn:
myMutate = 'rattle'
kid.rattleMut()
if mutType == 1 and growOn:
myMutate = 'grow'
kid.growMut_box([l for l in self.chemPotDict], xyzLims=xyzLims, bondRejList=bondRejList, constrainTop=constrainTop)
if mutType == 2 and leachOn:
myMutate = 'leach'
kid.leachMut([l for l in self.chemPotDict])
if mutType == 3 and permuteOn:
myMutate = 'permute'
kid.permuteMut()
if mutType == 4 and transOn:
myMutate = 'translate'
kid.transMut(transVec=transVec)
if len(kid.get_adsList()) <= 1:
myMutate = 'init'
print(' |- Bare substrate, BAD!')
kid = parent.copy()
kid.rattleMut()
kid.growMut([l for l in self.chemPotDict])
open('label', 'w').write('%i %i %s'%(mater, pater, myMutate))
self.gadb.update(mater, mated=self.gadb.get(id=mater).mated+1)
self.gadb.update(pater, mated=self.gadb.get(id=pater).mated+1)
return kid
def calc_grandPot(self, atoms, dftene):
# myRow = self.gadb.get(id=myID)
# myPot = myRow['eV']
myPot = dftene - self.subsPot
adsSymbol = Interface(atoms, self.substrate).\
get_adsAtoms().get_chemical_symbols()
for s in adsSymbol:
if s in self.chemPotDict:
myPot -= self.chemPotDict[s]
return myPot
def gen_offspring(self, mutRate=0.4):
kid = None
mater, pater = 0, 0
while kid is None:
mater, pater = self.choose_parents()
a1 = self.gadb.get(id=mater).toatoms()
a2 = self.gadb.get(id=pater).toatoms()
surf1 = Interface(a1, self.substrate, zLim=self.zLim)
surf2 = Interface(a2, self.substrate, zLim=self.zLim)
kid = crossover_snsSurf_2d(surf1, surf2, tolerance=0.75)
print('PARENTS: %i and %i' % (mater, pater))
if srtDist_similar_zz(a1, a2)\
or srtDist_similar_zz(a1, kid.get_allAtoms())\
or srtDist_similar_zz(a2, kid.get_allAtoms()):
print(' |- TOO SIMILAR!')
mutRate = 1
if np.random.rand() < mutRate:
print(' |- MUTATION!')
kid.transMut()
kid.rattleMut()
self.gadb.update(mater, mated=self.gadb.get(id=mater).mated + 1)
self.gadb.update(pater, mated=self.gadb.get(id=pater).mated + 1)
return kid
from ase.db import connect
from ase.io import read
from gocia.interface import Interface
import gocia.utils.report as rp
from gocia.utils.visualize import histogram
substrate = read(sys.argv[1])
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'+\
from gocia.interface import Interface
from ase.io import read, write
from gocia.utils import conv_formula2list
import sys
import numpy as np
from ase.db import connect
import random
fn_substrate = sys.argv[1]
nsamples = int(sys.argv[2])
s = read(fn_substrate)
mycell = np.array(s.get_cell(complete=True))
myLim = np.array([[0, mycell[0][0]], [0, mycell[0][0]], [7.0, 11.0]])
surf = Interface(s, s, zLim=myLim[2])
surf.print()
with connect('%s-rand.db' % (fn_substrate.split('.')[0]), append=False) as db:
for i in range(nsamples):
nB = random.randint(2, 8)
nO = random.randint(int(nB / 2), nB)
nH = random.randint(1, int(nO / 2) + 1)
adatoms = ['B'] * nB + ['O'] * nO + ['H'] * nH
print('%i\t%s' % (i, ''.join(adatoms)), end='\t')
genAds = boxSample_adatom(surf,
adatoms,
myLim,
toler_BLmin=-0.2,
toler_BLmax=0.2,
toler_CNmin=1,
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']))
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()
def get_extended_atoms(atoms):
tmpAtoms = atoms.copy()
# tmpAtoms.set_positions(tmpAtoms.get_positions()\
# -atoms.get_cell()[0]/2-atoms.get_cell()[1]/2)
tmpAtoms = atoms * [3, 3, 1]
tmpAtoms.set_positions(tmpAtoms.get_positions()\
-atoms.get_cell()[0]/1-atoms.get_cell()[1]/1)
return tmpAtoms
# TODO DUPLICATE CHECK
# TODO ADD ATOP
# TODO ADD HOLLOW
# TODO ADD BRIDGE
surf = Interface(allAtoms='calcSlab.vasp', subAtoms='sub-calcSlab.vasp')
surf.print()
surf = read('out-Cu111.vasp')
#surf = read('WBsurf2.vasp')
#print(get_surf_byZ(surf, [9.5, 10.5]))
#print(get_surf_grid(surf, 20))
surfList = get_surf_byZ(surf, [16, 18])
#surfList = get_surf_grid(surf, 20)
print(surfList)
del surf[[i for i in range(len(surf)) if i not in surfList]]
surf_ext = get_extended_atoms(surf)
#surf_ext = surf
import os, sys
import ase.io as ai
from ase.db import connect
from gocia.interface import Interface
from gocia.geom import build
from gocia.utils import conv_formula2list
# $ python directSample.py GaN_4-l_vac-1.vasp 'N N N' 10
# # Timing: 0.7767 s/structure
surfName = sys.argv[1]
adsInp = conv_formula2list(sys.argv[2])
nSample = int(sys.argv[3])
surf = Interface(tags=surfName.split('.')[0] + ' + ' + sys.argv[2],
allAtoms=ai.read(surfName),
subAtoms=ai.read(surfName),
zLim=None)
surf.print()
myDB = connect('tmp.db', append=False)
for i in range(nSample):
print('Structure %i' % i, end='\t')
newsurf = build.grow_adatom(surf,
adsInp,
toler=0.25,
doShuffle=True,
cnCount=True,
sameElemPenalty=0,
rattle=True,
rattleStdev=0.1,
rattleZEnhance=True,
import sys
sys.path.append('/home/zisheng/windir/github')
from ase.io import read, write
import numpy as np
from gocia.geom import cart2frac, frac2cart
from gocia.interface import Interface
surf = Interface('test.vasp', 'substrate.vasp')
surf.print()
surf.permuteMut()
surf.print()
surf.write('permute.vasp')