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feature_structures.py
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feature_structures.py
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'''
mega-script used for generating defective features from templates. Deals with straining the system and applying
thermal pertubations to the atoms. Incorporates each of the defects listed in the paper/thesis. Will need template
files provided in the same folder and a working lammps-python library for bi-spectrum coefficient generation.
'''
import random
import numpy as np
from lammps import lammps
import pandas as pd
import itertools
import subprocess
from template_generation import template_gen
from ovito_master import *
import time
def get_boxes(scale):
b=['x scale '+str(scale), ' y scale '+str(scale), ' z scale '+str(scale)]
return [b[0],b[1],b[2], b[0]+b[1],b[0]+b[2],b[1]+b[2],b[0]+b[1]+b[2]]
def get_boxesf(scale,f):
b=['x scale '+str(scale*f), ' y scale '+str(scale*f), ' z scale '+str(scale*f)]
return [b[0]+b[1]+b[2]]
# the lammps file templates need to be able to dynamically assign the correct number of vb spots, so the the B can be changed from 8 to W/E.
class Timer(object):
def __init__(self, name=None):
self.name = name
def __enter__(self):
self.tstart = time.time()
def __exit__(self, type, value, traceback):
if self.name:
print '[%s]' % self.name,
print 'Elapsed: %s' % (time.time() - self.tstart)
# we need to nab the bispec components for every defect type, then merge them all into one dataframe, then standardize the coefficients, then perform the PCA
def nab_bispec_train(infile):
df=pd.read_csv(infile,skiprows=8,delim_whitespace=True,low_memory=False)
# get rid of the bogus first columns
cols=df.columns[2::]
df.drop(df.columns[-2::],1,inplace=True)
df.columns=cols
return df
#need one of every surface type and of each structure -- then need to apply the
#prototype to EACH one of the systems
def make_surface_prototypes(se,alld,dic,lt):
DOUT={}
tdict={(se.structs[0],tuple(se.indicies[0][0])):'fcc_111',\
(se.structs[0],tuple(se.indicies[0][1])):'fcc_110',\
(se.structs[0],tuple(se.indicies[0][2])):'fcc_112',\
(se.structs[0],tuple(se.indicies[1][2])):'fcc_100',\
(se.structs[1],tuple(se.indicies[0][0])):'bcc_111',\
(se.structs[1],tuple(se.indicies[0][1])):'bcc_110',\
(se.structs[1],tuple(se.indicies[0][2])):'bcc_112',\
(se.structs[1],tuple(se.indicies[1][2])):'bcc_100'}
counter=0
for stru in se.structs:
for i in se.indicies:
for bound in se.bounds:
if i[dic[bound]]==[0,1,0] or i[dic[bound]]==[0,0,1]:
break
lx=se.lattice*np.sqrt(i[0][0]**2+i[0][1]**2+i[0][2]**2)
ly=se.lattice*np.sqrt(i[1][0]**2+i[1][1]**2+i[1][2]**2)
lz=se.lattice*np.sqrt(i[2][0]**2+i[2][1]**2+i[2][2]**2)
fiz='tempstruct_'+str(counter)
counter+=1
template=lt.adjust_temp_athermal(se.lattice,lx,ly,lz,i[0],i[1],i[2],bound,stru,fiz)
with open('temp.in', 'w') as f:
f.write(template)
f.write('\nrun 0 post no\n')
lmp=lammps()
try:
lmp.file('temp.in')
temp=nab_bispec_train(fiz)
alld=alld.append(temp)
except:
print "\nFAILURE TO RUN LAMMPS."
lmp.close()
#get the CNA parameters from ovito
check=run_ovitos('CNA',fiz,fiz+'CNAOUT')
lil_d={fiz+'CNAOUT':tdict[(stru,tuple(i[dic[bound]]))]}
if stru=='fcc':
lil_cond={fiz+'CNAOUT':['CNA',1]}
elif stru=='bcc':
lil_cond={fiz+'CNAOUT':['CNA',3]}
DOUT[(stru,tuple(i[dic[bound]]))]=initialize_dislocation_descriptors(fiz+'CNAOUT',lil_d,lil_cond)
#reset the index to the atomic IDs for the merge with the bispec data
DOUT[(stru,tuple(i[dic[bound]]))].index=DOUT[(stru,tuple(i[dic[bound]]))]['PID']
#need_proto=False
print "\n\n\n FINISHED SURFACE PROTOTYPES \n\n\n"
return DOUT
def surfaces(se,alld,descriptors,dic,DOUT,lt):
need_proto=False
#DOUT={}
for stru in se.structs:
for i in se.indicies:
for bound in se.bounds:
for s in se.scales:
box=get_boxes(s)
for b in box:
# we only need to check one [100] face!!
if i[dic[bound]]==[0,1,0] or i[dic[bound]]==[0,0,1]:
break
for t in range(se.thermal):
lx=se.lattice*np.sqrt(i[0][0]**2+i[0][1]**2+i[0][2]**2)
ly=se.lattice*np.sqrt(i[1][0]**2+i[1][1]**2+i[1][2]**2)
lz=se.lattice*np.sqrt(i[2][0]**2+i[2][1]**2+i[2][2]**2)
if random.random() < se.sampling_rate:
fiz='example'+'_'+stru+str(random.randint(0,10000))
else:
fiz='temporaryfile'
template=lt.adjust_temp(se.lattice,lx,ly,lz,i[0],i[1],i[2],bound,stru,fiz)
with open('temp.in', 'w') as f:
f.write(template)
f.write('\nchange_box all '+b+' boundary '+bound+' remap units box\n')
f.write('\nrun 0 post no\n')
lmp=lammps()
try:
lmp.file('temp.in')
temp=nab_bispec_train(fiz)
#alld=alld.append(temp)
except:
print "\nFAILURE TO RUN LAMMPS."
lmp.close()
# we need the number of atoms, the bounds (to tell which is periodic), the orientations, and the structure
#descriptors.append([i,s,b,t,bound,len(temp)])
if i == se.indicies[1]:
strang='1 0 0'
else:
strang=str(i[dic[bound]])
print '\n'+strang+' '+stru
temp.index=temp['id']
temp['desc']=DOUT[(stru,tuple(i[dic[bound]]))]['desc']
alld=alld.append(temp)
return alld
def make_vacancy_prototypes(se,alld,dic,lt):
#dictionary of prototype features
DOUT={}
dcheck={se.structs[0]:False,se.structs[1]:False}
tdict={se.structs[0]:'fcc_vacancy',se.structs[1]:'bcc_vacancy'}
counter=0
i = se.indicies[1] #standard cell
for stru in se.structs:
lx=se.lattice*np.sqrt(i[0][0]**2+i[0][1]**2+i[0][2]**2)
ly=se.lattice*np.sqrt(i[1][0]**2+i[1][1]**2+i[1][2]**2)
lz=se.lattice*np.sqrt(i[2][0]**2+i[2][1]**2+i[2][2]**2)
fiz='tempstruct_'+str(counter)
counter+=1
template=lt.adjust_temp_athermal(se.lattice,lx,ly,lz,i[0],i[1],i[2],'p p p',stru,fiz)
with open('temp.in', 'w') as f:
f.write(template)
f.write('\n group g1 id 1')
f.write('\n delete_atoms group g1')
f.write('\nrun 0 post no\n')
lmp=lammps()
try:
lmp.file('temp.in')
temp=nab_bispec_train(fiz)
#alld=alld.append(temp)
except:
print "\nFAILURE TO RUN LAMMPS."
lmp.close()
#make a prototype if needed
#if need_proto==True:
check=run_ovitos('CNA',fiz,fiz+'CNAOUT')
lil_d={fiz+'CNAOUT':tdict[stru]}
if stru=='fcc':
lil_cond={fiz+'CNAOUT':['CNA',1]}
elif stru=='bcc':
lil_cond={fiz+'CNAOUT':['CNA',3]}
DOUT[stru]=initialize_dislocation_descriptors(fiz+'CNAOUT',lil_d,lil_cond)
#reset the index to the atomic IDs for the merge with the bispec data
DOUT[stru].index=DOUT[stru]['PID']
#need_proto=False
print "\n\n\n FINISHED VACANCY PROTOTYPES \n\n\n"
return DOUT
def vacancies(se, alld, descriptors,DOUT,lt):
#loops to create all of the vacancies
for stru in se.structs:
for s in se.scales:
box=get_boxes(s)
for b in box:
for t in range(se.thermal):
lx=se.lattice
ly=se.lattice
lz=se.lattice
if random.random() < se.sampling_rate:
fiz='vacancy_'+stru+str(random.randint(0,10000))
else:
fiz='temporaryfile'
template=lt.adjust_temp(se.lattice,lx,ly,lz,[1,0,0],[0,1,0],[0,0,1],'p p p',stru,fiz)
with open('temp.in', 'w') as f:
f.write(template)
f.write('\n group g1 id 1')
f.write('\n delete_atoms group g1')
f.write('\nchange_box all '+b+' boundary '+'p p p'+' remap units box\n')
f.write('\nrun 0 post no\n')
lmp=lammps()
try:
lmp.file('temp.in')
temp=nab_bispec_train(fiz)
#alld=alld.append(temp)
except:
print "\nFAILURE TO RUN LAMMPS."
lmp.close()
# we need the number of atoms, the structure, flag that it's a vacancy
print '\n'+'vacancy '+stru
temp.index=temp['id']
temp['desc']=DOUT[stru]['desc']
alld=alld.append(temp)
return alld
def make_interstitial_prototypes(se,alld,dic,lt):
#dictionary of prototype features
DOUT={}
ot={0:'tetrahedral',1:'octahedral'}
tdict={(se.structs[0],ot[0]):'fcc_tet_interstitial',\
(se.structs[0],ot[1]):'fcc_oct_interstitial',\
(se.structs[1],ot[0]):'bcc_tet_interstitial',\
(se.structs[1],ot[1]):'bcc_oct_interstitial'}
counter=0
i = se.indicies[1] #standard cell
for stru in se.structs:
c=0
for inter in se.interstitial[stru]:
lx=se.lattice*np.sqrt(i[0][0]**2+i[0][1]**2+i[0][2]**2)
ly=se.lattice*np.sqrt(i[1][0]**2+i[1][1]**2+i[1][2]**2)
lz=se.lattice*np.sqrt(i[2][0]**2+i[2][1]**2+i[2][2]**2)
fiz='tempstruct_'+str(counter)
counter+=1
template=lt.adjust_temp_athermal(se.lattice,lx,ly,lz,i[0],i[1],i[2],'p p p',stru,fiz)
with open('temp.in', 'w') as f:
f.write(template)
f.write('\ncreate_atoms 1 single '+str(inter[0])+' '+str(inter[1])+' '+str(inter[2]))
f.write('\nrun 0 post no\n')
lmp=lammps()
try:
lmp.file('temp.in')
temp=nab_bispec_train(fiz)
except:
print "\nFAILURE TO RUN LAMMPS."
lmp.close()
#make a prototype if needed
check=run_ovitos('CNA',fiz,fiz+'CNAOUT')
lil_d={fiz+'CNAOUT':tdict[(stru,ot[c])]}
if stru=='fcc':
lil_cond={fiz+'CNAOUT':['CNA',1]}
elif stru=='bcc':
lil_cond={fiz+'CNAOUT':['CNA',3]}
DOUT[(stru,ot[c])]=initialize_dislocation_descriptors(fiz+'CNAOUT',lil_d,lil_cond)
#reset the index to the atomic IDs for the merge with the bispec data
DOUT[(stru,ot[c])].index=DOUT[(stru,ot[c])]['PID']
c+=1
#need_proto=False
print "\n\n\n FINISHED INTERSTITIAL PROTOTYPES \n\n\n"
return DOUT
def interstitials(se,alld,descriptors,DOUT,lt):
ot={0:'tetrahedral',1:'octahedral'}
for stru in se.structs:
c=0
for inter in se.interstitial[stru]:
for s in se.scales:
box=get_boxes(s)
for b in box:
for t in range(se.thermal):
lx=se.lattice
ly=se.lattice
lz=se.lattice
if random.random() < se.sampling_rate:
fiz='keep_'+ot[c]+'interstitial_'+stru+str(random.randint(0,10000))
else:
fiz='temporaryfile'
template=lt.adjust_temp(se.lattice,lx,ly,lz,[1,0,0],[0,1,0],[0,0,1],'p p p',stru,fiz)
with open('temp.in', 'w') as f:
f.write(template)
f.write('\ncreate_atoms 1 single '+str(inter[0])+' '+str(inter[1])+' '+str(inter[2]))
f.write('\nchange_box all '+b+' boundary '+'p p p'+' remap units box\n')
f.write('\nrun 0 post no\n')
lmp=lammps()
try:
lmp.file('temp.in')
temp=nab_bispec_train(fiz)
#alld=alld.append(temp)
except:
print "\nFAILURE TO RUN LAMMPS."
lmp.close()
# we need the number of atoms, the structure, flag for the type of intersitial
print '\n'+ot[c]+'interstitial '+stru
temp.index=temp['id']
temp['desc']=DOUT[(stru,ot[c])]['desc']
alld=alld.append(temp)
c+=1
return alld
def make_dislocations_prototypes(se):
#OK what types of defects, FCC full, partial, BCC full... strain and thermalize
DOUT={}
tdict={se.defect_names[0]:'fcc_full_disloc',\
se.defect_names[1]:'fcc_partial_disloc',\
se.defect_names[2]:'bcc_full_disloc'}
for d in se.defect_names:
lil_d={se.flocs[d]:tdict[d]}
if tdict[d].find('fcc')!=-1:
if tdict[d].find('full')!=-1:
lil_cond={se.flocs[d]:['CSP_surf',0.25]}
else:
lil_cond={se.flocs[d]:['CNA',1]}
elif tdict[d].find('bcc')!=-1:
lil_cond={se.flocs[d]:['CNA_surf',3]}
DOUT[d]=initialize_dislocation_descriptors(se.flocs[d],lil_d,lil_cond)
DOUT[d].index=DOUT[d]['PID']
print "\n\n\n FINISHED DISLOCATION PROTOTYPES \n\n\n"
return DOUT
# make system calls to atomsk -- easy way to generate the inital dislocation stuctures, then strain and thermalize them such that they are still identified.
def dislocations(se,alld,descriptors,DOUT,lt):
#OK what types of defects, FCC full, partial, BCC full... strain and thermalize
for d in se.defect_names:
for s in se.scales:
box=get_boxes(s)
for b in box:
for t in range(se.thermal):
lx=se.lattice
ly=se.lattice
lz=se.lattice
if random.random() < se.sampling_rate:
fiz='dislocation'+d+str(random.randint(0,10000))
else:
fiz='temporaryfile'
template=lt.adjust_temp_read(se.lattice,fiz,d)
with open('temp.in', 'w') as f:
f.write(template)
f.write('\nchange_box all '+b+' boundary '+'p p p'+' remap units box\n')
f.write('\nrun 0 post no\n')
lmp=lammps()
try:
lmp.file('temp.in')
temp=nab_bispec_train(fiz)
#alld=alld.append(temp)
except:
print "\nFAILURE TO RUN LAMMPS."
lmp.close()
# we need the number of atoms, the structure, flag for the type of intersitial
print '\n'+d+'dislocation '
temp.index=temp['id']
temp['desc']=DOUT[d]['desc']
alld=alld.append(temp)
return alld
def tensile_prototype(se,lt):
DOUT={}
# we have 3 tensile tests right now
for x in range(1,4):
template=lt.adjust_temp_read(se.lattice,'tensile_'+str(x)+'.struct','tensile_'+str(x)+'.out',athermal=True)
with open('temp.in', 'w') as f:
f.write(template)
f.write('\nrun 0 post no\n')
lmp=lammps()
lmp.file('temp.in')
lmp.close()
check=run_ovitos('CNA','tensile_'+str(x)+'.struct','tensile_'+str(x)+'CNAOUT')
lil_d={'tensile_'+str(x)+'CNAOUT':'fcc_partial_disloc'}
lil_cond={'tensile_'+str(x)+'CNAOUT':['CNAonly',2]}
DOUT[x]=initialize_dislocation_descriptors('tensile_'+str(x)+'CNAOUT',lil_d,lil_cond)
DOUT[x].index=DOUT[x]['PID']
print "\n\n\n FINISHED TENSILE PROTOTYPES \n\n\n"
return DOUT
def add_tensile_dislocations(se,alld,DOUT,lt):
for x in range(1,4):
#for t in range(se.thermal):
template=lt.adjust_temp_read(se.lattice,'temporary.out','tensile_'+str(x)+'.out',athermal=True)
with open('temp.in', 'w') as f:
f.write(template)
f.write('\nrun 0 post no\n')
lmp=lammps()
lmp.file('temp.in')
temp=nab_bispec_train('temporary.out')
lmp.close()
# we need the number of atoms, the structure, flag for the type of intersitial
print '\n tensile dislocation run '+str(x)
temp.index=temp['id']
temp['desc']=DOUT[x]['desc']
alld=alld.append(temp)
return alld
def make_grain_prototypes(se,lt):
#OK what types of defects, FCC full, partial, BCC full... strain and thermalize
DOUT={}
tdict={se.grain_names[0]:'fcc_GB',\
se.grain_names[1]:'bcc_GB'}
for gn in se.grain_names:
template=lt.adjust_temp_read(se.lattice,gn+'.struct',gn,athermal=True)
with open('temp.in', 'w') as f:
f.write(template)
f.write('\nrun 0 post no\n')
lmp=lammps()
lmp.file('temp.in')
lmp.close()
check=run_ovitos('CNA',gn+'.struct',gn+'CNAOUT')
lil_d={gn+'CNAOUT':tdict[gn]}
if tdict[gn].find('fcc')!=-1:
lil_cond={gn+'CNAOUT':['CNA',1]}
elif tdict[gn].find('bcc')!=-1:
lil_cond={gn+'CNAOUT':['CNA',3]}
DOUT[gn]=initialize_dislocation_descriptors(gn+'CNAOUT',lil_d,lil_cond)
DOUT[gn].index=DOUT[gn]['PID']
print "\n\n\n FINISHED GRAIN BOUNDARY PROTOTYPES \n\n\n"
return DOUT
def grain_boundaries(se,alld,DOUT,lt):
for gn in se.grain_names:
template=lt.adjust_temp_read(se.lattice,'temporary.out',gn)
with open('temp.in', 'w') as f:
f.write(template)
f.write('\nrun 0 post no\n')
lmp=lammps()
lmp.file('temp.in')
temp=nab_bispec_train('temporary.out')
lmp.close()
# we need the number of atoms, the structure, flag for the type of intersitial
print '\n'+gn
temp.index=temp['id']
temp['desc']=DOUT[gn]['desc']
alld=alld.append(temp)
return alld
#assign the descriptors for each of the dislocation structures (no Kmeans necessary)
def initialize_dislocation_descriptors(f,tdict,condit):
#f has the each of the files to consider, tdict relates the file name to the defect name
#condit contains the conditions for each simulation, surf or no surf, CNA or CSP [0] spot
# is the description and the [1] spot is the value needed
tdf=pd.read_csv(f,delim_whitespace=True)
tdf['desc']='Please Drop' #all of the spares go to please drop!
if condit[f][0].find('surf')!=-1:#if it needs to trim the surfaces
#filter out the surface atoms
t1=tdf[tdf['X']<tdf['X'].max()-3.]
t1=t1[t1['X']>t1['X'].min()+3.]
t1=t1[t1['Y']<t1['Y'].max()-3.]
t1=t1[t1['Y']>t1['Y'].min()+3.]
if condit[f][0].find('CSP')!=-1:
t1.ix[t1[t1['TYPE']>condit[f][1]].index,'desc']=tdict[f]
if tdict[f].find('fcc')!=-1:
t1.ix[t1[t1['TYPE']<=condit[f][1]].index,'desc']='bulk fcc'
else:
t1.ix[t1[t1['TYPE']<=condit[f][1]].index,'desc']='bulk bcc'
elif condit[f][0].find('CNA')!=-1:
t1.ix[t1[t1['TYPE']!=condit[f][1]].index,'desc']=tdict[f]
if tdict[f].find('fcc')!=-1:
t1.ix[t1[t1['TYPE']==condit[f][1]].index,'desc']='bulk fcc'
else:
t1.ix[t1[t1['TYPE']==condit[f][1]].index,'desc']='bulk bcc'
tdf.ix[t1.index,'desc']=t1['desc']
else:
if condit[f][0].find('CNA')!=-1:
if condit[f][0].find('only')!=-1: # say we only want the atoms with a particular CNA
tdf.ix[tdf[tdf['TYPE']==condit[f][1]].index,'desc']=tdict[f]
else: # takes both bulk and non bulkies here
tdf.ix[tdf[tdf['TYPE']!=condit[f][1]].index,'desc']=tdict[f]
if tdict[f].find('fcc')!=-1:
tdf.ix[tdf[tdf['TYPE']==condit[f][1]].index,'desc']='bulk fcc'
else:
tdf.ix[tdf[tdf['TYPE']==condit[f][1]].index,'desc']='bulk bcc'
elif condit[f][0].find('CSP')!=-1:
tdf.ix[tdf[tdf['TYPE']>condit[f][1]].index,'desc']=tdict[f]
if tdict[f].find('fcc')!=-1:
tdf.ix[tdf[tdf['TYPE']<=condit[f][1]].index,'desc']='bulk fcc'
else:
tdf.ix[tdf[tdf['TYPE']<=condit[f][1]].index,'desc']='bulk bcc'
return tdf
def make_all_structures(se,thermal_diff,num_bispec):
lmp_templates=template_gen(thermal_diff,num_bispec)
alld=pd.DataFrame()
dic={se.bounds[0]:2,se.bounds[1]:1,se.bounds[2]:0} #convert the different boundaries to an index
descriptors=[]
#Bi spectrum gathering pipeline
DOUT=make_surface_prototypes(se,alld,dic,lmp_templates)
alld=surfaces(se,alld,descriptors,dic,DOUT,lmp_templates)
DOUT=make_vacancy_prototypes(se,alld,dic,lmp_templates)
alld=vacancies(se,alld,descriptors,DOUT,lmp_templates)
DOUT=make_interstitial_prototypes(se,alld,dic,lmp_templates)
alld=interstitials(se,alld,descriptors,DOUT,lmp_templates)
DOUT=make_dislocations_prototypes(se)
alld=dislocations(se,alld,descriptors,DOUT,lmp_templates)
DOUT=make_grain_prototypes(se,lmp_templates)
alld=grain_boundaries(se,alld,DOUT,lmp_templates)
DOUT=tensile_prototype(se,lmp_templates)
alld=add_tensile_dislocations(se,alld,DOUT,lmp_templates)
alld.index = range(len(alld))
#alld=alld.dropna()
alld=alld[alld['desc']!='Please Drop']
get_timed_performance(se,thermal_diff,num_bispec)
return alld,descriptors,DOUT
def get_timed_performance(se,thermal_diff,num_bispec):
lmp_templates=template_gen(thermal_diff,num_bispec)
with Timer('Grain Generations:'):
DOUT=make_grain_prototypes(se,lmp_templates)
pass
if __name__=="__main__":
class simulation_env:
def __init__(self):
self.sampling_rate = 0.000001#how often we select for keeps
self.num_comp = 5#number of PCA components that the bi components are reduced to
self.sample_size=100000#size of samples when machine learning
self.thermal=10 #number of thermal perturbations for each config.
self.lattice=3.597 #lattice size
self.indicies=[[[1,1,1],[-1,1,0],[-1,-1,2]], [[0,1,0],[0,0,1],[1,0,0]]]#crystal orientations
self.interstitial={'fcc':[[0.25,0.25,0.25],[0.5,0.0,0.0]],'bcc':[[0.5,0.25,0.0],[0.5,0.5,0.0]]}# interstitial sites for fcc, bcc (tet then oct)
self.structs=['fcc','bcc'] #structures considered
self.bounds=['p p s', 'p s p', 's p p'] #boundaries
self.scales=[1+x for x in np.arange(0.01,0.11,0.05)] #scales for straining the simulation cell
self.defect_names=['fccfull.lmp','fccpartial.lmp','bcc_disloc.lmp']
self.flocs={self.defect_names[0]:'fccfull_temp.structures',self.defect_names[2]:'BCC_temp.structures',self.defect_names[1]:'temp.structures'} #dislocation prototype file structural analysis files
self.grain_names=['fcc_polycrystal.lmp','bcc_polycrystal.lmp']
#f has the each of the files to consider, tdict relates the file name to the defect name
#condit contains the conditions for each simulation, surf or no surf, CNA or CSP [0] spot
# is the description and the [1] spot is the value needed
se=simulation_env()
alld,descriptors,DOUT=make_all_structures(se,0.01,2)