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keep cluster #6

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keep cluster #6

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7f17604
keep cluster atoms (if unique) constant during crossover
WinstonGee Feb 17, 2023
9a4b03f
keep cluster (if unique element)
WinstonGee Feb 17, 2023
b4207f2
keep cluster
WinstonGee Feb 18, 2023
08ce8f0
keep cluster
WinstonGee Feb 18, 2023
eaa102b
keep cluster
WinstonGee Feb 18, 2023
e54573a
keep cluster
WinstonGee Feb 18, 2023
6c49e26
sample OH and C3H8
WinstonGee Feb 25, 2023
129176b
Merge branch 'zishengz:master' into master
WinstonGee Apr 21, 2023
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9 changes: 7 additions & 2 deletions gocia/ga/crossover.py
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Original file line number Diff line number Diff line change
Expand Up @@ -100,7 +100,7 @@ def splice_2d_GC(surf1, badPos, goodPos, center, direction):
tmpSurf.set_allPos(childPos)
return tmpSurf

def crossover_snsSurf_2d_GC(surf1, surf2, tolerance=0.5):
def crossover_snsSurf_2d_GC(surf1, surf2, tolerance=0.5, keepCluster=''):
matPos, patPos = surf1.get_fixBufPos(), surf2.get_fixBufPos() # positions of fixed and buffer atoms in substrate
matAds, patAds = surf1.get_adsAtoms(), surf2.get_adsAtoms() # adsorbate atoms
goodPos, badPos = [], []
Expand Down Expand Up @@ -164,6 +164,8 @@ def crossover_snsSurf_2d_GC(surf1, surf2, tolerance=0.5):
newSurf.set_adsAtoms(Atoms(newAdsElem, newAdsPos))
newSurf.wrap()
isBADSTRUCTURE = newSurf.has_badContact(tolerance=tolerance)
if newSurf.get_chemical_symbols().count(keepCluster) != surf1.get_chemical_symbols().count(keepCluster) or newSurf.get_chemical_symbols().count(keepCluster) != surf2.get_chemical_symbols().count(keepCluster):
isBADSTRUCTURE = True
if n_trial > 1000:
isBADSTRUCTURE = False
newSurf = None
Expand All @@ -172,7 +174,7 @@ def crossover_snsSurf_2d_GC(surf1, surf2, tolerance=0.5):
(n_trial, tolerance))
return newSurf

def crossover_snsSurf_2d_GC_poly(surf1, surf2, tolerance=0.5):
def crossover_snsSurf_2d_GC_poly(surf1, surf2, tolerance=0.5, keepCluster=''):
# Get relevant positions from mother and father surfaces
matFixBufPos, patFixBufPos = surf1.get_fixBufPos(), surf2.get_fixBufPos() # positions of fixed and buffer atoms, or equivalently, substrate atoms with get_subPos()
matBridPos, patBridPos = surf1.get_bridPos(), surf2.get_bridPos() # positions of bridle atoms
Expand Down Expand Up @@ -280,10 +282,13 @@ def crossover_snsSurf_2d_GC_poly(surf1, surf2, tolerance=0.5):

# Evaluate quality of kid structure
isBADSTRUCTURE = childSurf.has_badContact(tolerance=tolerance)
if childSurf.get_chemical_symbols().count(keepCluster) != surf1.get_chemical_symbols().count(keepCluster) or childSurf.get_chemical_symbols().count(keepCluster) != surf2.get_chemical_symbols().count(keepCluster):
isBADSTRUCTURE = True
if n_trial > 1000:
isBADSTRUCTURE = False
childSurf = None
if childSurf is not None:
print('\nOffspring is created at attempt #%i\t|Tolerance = %.3f'%\
(n_trial, tolerance))
return childSurf

8 changes: 4 additions & 4 deletions gocia/ga/popGrandCanon.py
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Original file line number Diff line number Diff line change
Expand Up @@ -220,7 +220,7 @@ def is_uniqueInAll_geom(self, atoms):
break
return isUnique

def gen_offspring(self, mutRate=0.3, rattleOn=True, growOn=True, leachOn=True, permuteOn=True, transOn=True, transVec=[[-2, 2], [-2, 2]]):
def gen_offspring(self, mutRate=0.3, rattleOn=True, growOn=True, leachOn=True, permuteOn=True, transOn=True, transVec=[[-2, 2], [-2, 2]], keepCluster=''):
kid, parent = None, None
mater, pater = 0, 0
while kid is None:
Expand All @@ -229,7 +229,7 @@ def gen_offspring(self, mutRate=0.3, rattleOn=True, growOn=True, leachOn=True, p
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)
kid = crossover_snsSurf_2d_GC(surf1, surf2, tolerance=0.75, keepCluster=keepCluster)
parent = surf1.copy()
print('PARENTS: %i and %i' % (mater, pater))
myMutate = ''
Expand Down Expand Up @@ -268,7 +268,7 @@ def gen_offspring(self, mutRate=0.3, rattleOn=True, growOn=True, leachOn=True, p
self.gadb.update(pater, mated=self.gadb.get(id=pater).mated+1)
return kid

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]]):
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]], keepCluster=''):
kid, parent = None, None
mater, pater = 0, 0
while kid is None:
Expand All @@ -277,7 +277,7 @@ def gen_offspring_box(self, mutRate=0.3, xyzLims=[], bondRejList=None, constrain
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)
kid = crossover_snsSurf_2d_GC(surf1, surf2, tolerance=0.75,keepCluster=keepCluster)
parent = surf1.copy()
print('PARENTS: %i and %i' % (mater, pater))
mutType = ''
Expand Down
9 changes: 5 additions & 4 deletions gocia/ga/popGrandCanonPoly.py
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Original file line number Diff line number Diff line change
Expand Up @@ -60,6 +60,7 @@ def __init__(
self.simParam1 = simParam1
self.simParam2 = simParam2


def __len__(self):
return len(self.gadb)

Expand Down Expand Up @@ -239,7 +240,7 @@ def convertFragListToInfo(self, fragList):
info['adsorbate_fragments'] = []
return info

def gen_offspring(self, mutRate=0.3, rattleOn=True, growOn=True, leachOn=True, moveOn=True, permuteOn=True, transOn=True, transVec=[[-2, 2], [-2, 2]]):
def gen_offspring(self, mutRate=0.3, rattleOn=True, growOn=True, leachOn=True, moveOn=True, permuteOn=True, transOn=True, transVec=[[-2, 2], [-2, 2]], keepCluster=''):
kid, parent = None, None
mater, pater = 0, 0
while kid is None:
Expand All @@ -252,7 +253,7 @@ def gen_offspring(self, mutRate=0.3, rattleOn=True, growOn=True, leachOn=True, m
patInfo = self.convertFragStrToInfo(patFragStr)
surf1 = Interface(matAtms, self.substrate, zLim=self.zLim, info=matInfo)
surf2 = Interface(patAtms, self.substrate, zLim=self.zLim, info=patInfo)
kid = crossover_snsSurf_2d_GC_poly(surf1, surf2, tolerance=0.75)
kid = crossover_snsSurf_2d_GC_poly(surf1, surf2, tolerance=0.75, keepCore=keepCluster)
parent = surf1.copy()
print('PARENTS: %i and %i' % (mater, pater))
myMutate = ''
Expand Down Expand Up @@ -294,7 +295,7 @@ def gen_offspring(self, mutRate=0.3, rattleOn=True, growOn=True, leachOn=True, m
open('fragments', 'w').write('%s' % kid.get_fragList() )
return kid

def gen_offspring_box(self, mutRate=0.3, xyzLims=[], bondRejList=None, constrainTop=False, rattleOn=True, growOn=True, leachOn=True, moveOn=True, permuteOn=True, transOn=True, transVec=[[-2, 2], [-2, 2]]):
def gen_offspring_box(self, mutRate=0.3, xyzLims=[], bondRejList=None, constrainTop=False, rattleOn=True, growOn=True, leachOn=True, moveOn=True, permuteOn=True, transOn=True, transVec=[[-2, 2], [-2, 2]], keepCluster=''):
kid, parent = None, None
mater, pater = 0, 0
while kid is None:
Expand All @@ -307,7 +308,7 @@ def gen_offspring_box(self, mutRate=0.3, xyzLims=[], bondRejList=None, constrain
patInfo = self.convertFragStrToInfo(patFragStr)
surf1 = Interface(matAtms, self.substrate, zLim=self.zLim, info=matInfo)
surf2 = Interface(patAtms, self.substrate, zLim=self.zLim, info=patInfo)
kid = crossover_snsSurf_2d_GC_poly(surf1, surf2, tolerance=0.5)
kid = crossover_snsSurf_2d_GC_poly(surf1, surf2, tolerance=0.5, keepCluster=keepCluster)
parent = random.choice([surf1, surf2]).copy()
print('PARENTS: %i and %i' % (mater, pater))
print(matInfo['adsorbate_fragments'], [matAtms[l].get_chemical_formula() for l in matInfo['adsorbate_fragments']])
Expand Down
16 changes: 16 additions & 0 deletions gocia/geom/build.py
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Original file line number Diff line number Diff line change
Expand Up @@ -115,8 +115,16 @@ def grow_frag(
frags_to_add.append(Atoms('CO',[(0, 0, 0),(0, 0, 1.15034)]))
elif fragName == 'H':
frags_to_add.append(Atoms('H',[(0,0,0)]))
elif fragName == 'O':
frags_to_add.append(Atoms('O',[(0,0,0)]))
elif fragName =='OH':
frags_to_add.append(Atoms('OH',[(0,0,0),(0,0,0.97)]))
elif fragName =='H2O':
frags_to_add.append(Atoms('OH2',[(0,0,0),(0.758602,0,0.504284),(-0.758602,0,0.504284)]))
#elif fragName =='C3H8':
#frags_to_add.append(Atoms('C3H8',[(0.000000,0.000000,0.000000),(0.000000,1.266857,0.847902),(0.000000,2.533714,0.000000),(-0.876898,1.266857,1.504899),(0.876898,1.266857,1.504899),(0.000000,3.433007,0.622252),(0.000000,-0.899293,0.622252),(0.883619,2.571091,-0.644219),(-0.883619,2.571091,-0.644219),(-0.883619,-0.037377,-0.644219),(0.883619,-0.037377,-0.644219)]))
elif fragName =='C3H8':
frags_to_add.append(Atoms('C3H8',[(0.00000000,0.00000000,0.00000000),(0.00000000,1.26685700,0.84790200),(0.00000000,-1.26685700,0.84790200),(-0.87689800,0.00000000,-0.65699700),(0.87689800,0.00000000,-0.65699700),(0.00000000,2.16615000,0.22565000),(0.00000000,-2.16615000,0.22565000),(0.88361900,1.30423400,1.49212100),(-0.88361900,1.30423400,1.49212100),(-0.88361900,-1.30423400,1.49212100),(0.88361900,-1.30423400,1.49212100)]))
else:
print('Unknown fragment: must add option to grow {} in grow_adFrag() in build.py'.format(fragName))

Expand Down Expand Up @@ -321,8 +329,16 @@ def boxSample_frag(
frags_to_add.append(Atoms('CO',[(0, 0, 0),(0, 0, 1.15034)]))
elif fragName == 'H':
frags_to_add.append(Atoms('H',[(0,0,0)]))
elif fragName == 'O':
frags_to_add.append(Atoms('O',[(0,0,0)]))
elif fragName =='OH':
frags_to_add.append(Atoms('OH',[(0,0,0),(0,0,0.97)]))
elif fragName =='H2O':
frags_to_add.append(Atoms('OH2',[(0,0,0),(0.758602,0,0.504284),(-0.758602,0,0.504284)]))
#elif fragName =='C3H8':
#frags_to_add.append(Atoms('C3H8',[(0.000000,0.000000,0.000000),(0.000000,1.266857,0.847902),(0.000000,2.533714,0.000000),(-0.876898,1.266857,1.504899),(0.876898,1.266857,1.504899),(0.000000,3.433007,0.622252),(0.000000,-0.899293,0.622252),(0.883619,2.571091,-0.644219),(-0.883619,2.571091,-0.644219),(-0.883619,-0.037377,-0.644219),(0.883619,-0.037377,-0.644219)]))
elif fragName =='C3H8':
frags_to_add.append(Atoms('C3H8',[(0.00000000,0.00000000,0.00000000),(0.00000000,1.26685700,0.84790200),(0.00000000,-1.26685700,0.84790200),(-0.87689800,0.00000000,-0.65699700),(0.87689800,0.00000000,-0.65699700),(0.00000000,2.16615000,0.22565000),(0.00000000,-2.16615000,0.22565000),(0.88361900,1.30423400,1.49212100),(-0.88361900,1.30423400,1.49212100),(-0.88361900,-1.30423400,1.49212100),(0.88361900,-1.30423400,1.49212100)]))
else:
print('Unknown fragment: must add option to grow {} in grow_adFrag() in build.py'.format(fragName))

Expand Down
3 changes: 2 additions & 1 deletion gocia/interface.py
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Original file line number Diff line number Diff line change
Expand Up @@ -825,7 +825,7 @@ def moveMut_frag(self, fragPool):
tmpInterfc.growMut_frag([myFrag])
self.set_allAtoms(tmpInterfc.get_allAtoms())

def growMut_box(self, elemList, xyzLims, bondRejList = None, constrainTop=False):
def growMut_box(self, elemList, xyzLims, bondRejList = None, bondMustList = None, constrainTop=False):
print(' |- Growth mutation:', end = '\t')
from gocia.geom.build import boxSample_adatom
tmpInterfc = self.copy()
Expand All @@ -836,6 +836,7 @@ def growMut_box(self, elemList, xyzLims, bondRejList = None, constrainTop=False)
myElem,
xyzLims=xyzLims,
bondRejList=bondRejList,
bondMustList=bondMustList,
constrainTop=constrainTop
)
if tmpInterfc is not None:
Expand Down