def chgcarBondAnalysis(chgcarfile,
bondLengths,
normalize=False,
verbose=False):
BLs = bondLengths
nBLs = len(BLs)
#Parse CHGCAR
chgcar = open(chgcarfile, "r").readlines()
(v1, v2, v3, atypes, axs, ays, azs,
header), gridSize, chg = chgcarIO.read(chgcar)
basis = asarray([v1, v2, v3])
lengths = array([v1[0], v2[1], v3[2]])
atoms = array(zip(axs, ays, azs))
#Grid properties
nGridPoints = reduce(operator.mul, gridSize)
#Neighbors
halfNeighbors = voronoiNeighbors(atoms, basis, atypes, style='half')
a = chg.shape
AvgChg = sum([sum([sum(line) for line in plane])
for plane in chg]) / a[0] / a[1] / a[2]
if verbose:
print "Average CHG value:", AvgChg
#Evaluate the CHG between each nieghbor pair
avgchgline, xchglines, ychglines, halfNeighbors = fieldNeighbors1D(
atoms, atypes, basis, chg, gridSize, halfNeighbors)
#Cutoff neighbors that fall below the thresh-hold
Ninterp = len(avgchgline)
avgIBL = zeros([nBLs, Ninterp]) #avg line inside the bond length
avgOBL = zeros([nBLs, Ninterp]) #avg line outside the bond length
nibl = zeros(nBLs)
nobl = zeros(nBLs)
cnt = 0
for a, jNeighbors in enumerate(halfNeighbors):
atoma = atoms[a]
for b, jNeighb in enumerate(jNeighbors):
atomb = atoms[jNeighb]
d = dist_periodic(atoma, atomb, lengths)
vals = ychglines[a][b]
xx = xchglines[a][b]
for j, bl in enumerate(BLs):
if normalize:
avals = array(vals) / AvgChg
else:
avals = array(vals)
if d < bl:
nibl[j] += 2
avgIBL[j] += avals
avgIBL[j] += avals[::-1]
else:
cnt += 1
nobl[j] += 2
avgOBL[j] += avals
avgOBL[j] += avals[::-1]
for i in range(nBLs):
if nibl[i] == 0:
nibl[i] = 1
if nobl[i] == 0:
nobl[i] = 1
avgOBL = [avgOBL[i] / nobl[i] for i in range(nBLs)]
avgIBL = [avgIBL[i] / nibl[i] for i in range(nBLs)]
return avgOBL, nobl, avgIBL, nibl
ay=atoms[:,1]
az=atoms[:,2]
types=[0]*atypes[0]
fig=mlab.figure(bgcolor=(1.0,1.0,1.0))
rlen=list()
soft=list()
s2=list()
mxSoft=0
mnSoft=10
mxLen=0
mnLen=10
for i in range(nIon):
s2.append(list())
for j in neighbs[i]:
r=dist_periodic(atoms[i],atoms[j],lengths)
#g(E,atomi)
ga=occGrid[i][uBounds]
gb=occGrid[j][uBounds]
#soft.append(sum(ga*gb)/d/delU*2)
soft.append(sum(ga+gb)/delU)
s2[-1].append(sum(ga+gb)/delU)
mxSoft=max(mxSoft,soft[-1])
mnSoft=min(mnSoft,soft[-1])
rlen.append(r)
if r<3.2:
mxLen=max(mxLen,rlen[-1])
mnLen=min(mnLen,rlen[-1])
mnSoft,mxSoft=0.15,4.0
mnLen,mxLen = 2.40,2.9
def chgcarBondAnalysis(chgcarfile,bondLengths,normalize=False,verbose=False):
BLs=bondLengths
nBLs=len(BLs)
#Parse CHGCAR
chgcar=open(chgcarfile,"r").readlines()
(v1,v2,v3,atypes,axs,ays,azs,header),gridSize,chg = chgcarIO.read(chgcar)
basis=asarray([v1,v2,v3])
lengths=array([v1[0],v2[1],v3[2]])
atoms=array(zip(axs,ays,azs))
#Grid properties
nGridPoints=reduce(operator.mul,gridSize)
#Neighbors
halfNeighbors=voronoiNeighbors(atoms,basis,atypes,style='half')
a=chg.shape
AvgChg=sum([sum([sum(line) for line in plane]) for plane in chg])/a[0]/a[1]/a[2]
if verbose:
print "Average CHG value:",AvgChg
#Evaluate the CHG between each nieghbor pair
avgchgline,xchglines,ychglines,halfNeighbors=fieldNeighbors1D(atoms,atypes,basis,chg,gridSize,halfNeighbors)
#Cutoff neighbors that fall below the thresh-hold
Ninterp=len(avgchgline)
avgIBL=zeros([nBLs,Ninterp]) #avg line inside the bond length
avgOBL=zeros([nBLs,Ninterp]) #avg line outside the bond length
nibl=zeros(nBLs)
nobl=zeros(nBLs)
cnt=0
for a,jNeighbors in enumerate(halfNeighbors):
atoma=atoms[a]
for b,jNeighb in enumerate(jNeighbors):
atomb=atoms[jNeighb]
d=dist_periodic(atoma,atomb,lengths)
vals=ychglines[a][b]
xx=xchglines[a][b]
for j,bl in enumerate(BLs):
if normalize:
avals=array(vals)/AvgChg
else:
avals=array(vals)
if d<bl:
nibl[j]+=2
avgIBL[j]+=avals
avgIBL[j]+=avals[::-1]
else:
cnt+=1
nobl[j]+=2
avgOBL[j]+=avals
avgOBL[j]+=avals[::-1]
for i in range(nBLs):
if nibl[i]==0:
nibl[i]=1
if nobl[i]==0:
nobl[i]=1
avgOBL=[avgOBL[i]/nobl[i] for i in range(nBLs)]
avgIBL=[avgIBL[i]/nibl[i] for i in range(nBLs)]
return avgOBL,nobl,avgIBL,nibl
ay = atoms[:, 1]
az = atoms[:, 2]
types = [0] * atypes[0]
fig = mlab.figure(bgcolor=(1.0, 1.0, 1.0))
rlen = list()
soft = list()
s2 = list()
mxSoft = 0
mnSoft = 10
mxLen = 0
mnLen = 10
for i in range(nIon):
s2.append(list())
for j in neighbs[i]:
r = dist_periodic(atoms[i], atoms[j], lengths)
#g(E,atomi)
ga = occGrid[i][uBounds]
gb = occGrid[j][uBounds]
#soft.append(sum(ga*gb)/d/delU*2)
soft.append(sum(ga + gb) / delU)
s2[-1].append(sum(ga + gb) / delU)
mxSoft = max(mxSoft, soft[-1])
mnSoft = min(mnSoft, soft[-1])
rlen.append(r)
if r < 3.2:
mxLen = max(mxLen, rlen[-1])
mnLen = min(mnLen, rlen[-1])
mnSoft, mxSoft = 0.15, 4.0
mnLen, mxLen = 2.40, 2.9
def fieldNeighbors1D(atoms,atypes,basis,field,halfNeighbors=None,Ninterp=50):
[v1,v2,v3]=basis
latoms=array(atoms)
#Ensure simulation box is orthorhombic
if sum(map(fabs,v1))-fabs(v1[0]) > 1e-10 or \
sum(map(fabs,v2))-fabs(v2[1]) > 1e-10 or \
sum(map(fabs,v3))-fabs(v3[2]) > 1e-10:
print "Error: simulation axes are not sufficiently orthogonal. Use script poscarRectify.py and regenerate doscar"
exit(0)
bounds=[[0.,v1[0]],[0.,v2[1]],[0.,v3[2]]]
simSize=asarray([v1[0],v2[1],v3[2]])
if halfNeighbors==None:
halfNeighbors=voronoiNeighbors(atoms=latoms,basis=basis,atypes=atypes,style='half')
#Interpolation and summation properties
xlines=list()
ylines=list()
avgyline=zeros(Ninterp)
nlines=float(sum(map(len,halfNeighbors)))
#Local Grid size
fieldSize=elf.size
delGrids=simSize/fieldSize
lGridSize=fieldSize
nlGridPoints=reduce(operator.mul,lGridSize)
for iNeighb,jNeighbors in enumerate(halfNeighbors):
xlines.append(list())
ylines.append(list())
if len(jNeighbors)==0:
continue
atomi=latoms[iNeighb]
for i,ai in enumerate(atomi):
if ai < 0.0:
atomi[i]+=simSize[i]
if ai > simSize[i]:
atomi[i]-=simSize[i]
lGridCenter = map(int,atomi/simSize*fieldSize)
lGridBounds = [[lGridCenter[i]-lGridSize[i]/2,lGridCenter[i]+lGridSize[i]/2] for i in range(3)]
lGridBoundPoints = array([[lGridBounds[i][0]*delGrids[i],lGridBounds[i][1]*delGrids[i]] for i in range(3)])
lGridPoints = array([map(lambda x: x*delGrids[i],range(lGridCenter[i]-lGridSize[i]/2,lGridCenter[i]+lGridSize[i]/2)) for i in range(3)])
#Stitch together field in local field (lfield) to enforce periodicity, use bounds to simplify
bnds=list()
lbnds=list()
bnds.append(list(lGridBounds))
lbnds.append(map(list,zip([0,0,0],lGridSize)))
while outOfBounds(bnds,fieldSize):
a=whichBounds(bnds,fieldSize)
bnds.append(map(list,bnds[a]))
lbnds.append(map(list,lbnds[a]))
for i in range(3):
if bnds[-1][i][1] > fieldSize[i]:
lbnds[a][i][1] = lGridSize[i]-(bnds[-1][i][1]-fieldSize[i])
lbnds[-1][i][0] = lGridSize[i]-(bnds[-1][i][1]-fieldSize[i])
lbnds[-1][i][1] = lbnds[-1][i][0]+(bnds[-1][i][1]-fieldSize[i])
bnds[-1][i][0] = 0
bnds[-1][i][1] -= fieldSize[i]
bnds[a][i][1] = fieldSize[i]
break
elif bnds[-1][i][0] < 0:
lbnds[-1][i][0] = 0
lbnds[-1][i][1] = -bnds[-1][i][0]
lbnds[a][i][0] = -bnds[-1][i][0]
bnds[-1][i][1] = fieldSize[i]
bnds[-1][i][0] += fieldSize[i]
bnds[a][i][0] = 0
break
lfield=zeros(lGridSize)
for lbnd,bnd in zip(lbnds,bnds):
[[lxa,lxb],[lya,lyb],[lza,lzb]]=lbnd
[[xa,xb],[ya,yb],[za,zb]]=bnd
lfield[lxa:lxb, lya:lyb, lza:lzb]=field[xa:xb, ya:yb, za:zb]
#Loop over Neighboring atoms within the local grid
for jNeighb in jNeighbors:
xlines[-1].append(zeros([Ninterp]))
ylines[-1].append(zeros([Ninterp]))
atomj=latoms[jNeighb]
for i,aj in enumerate(atomj):
if aj < lGridPoints[i][0]:
atomj[i]+=simSize[i]
if aj > lGridPoints[i][-1]:
atomj[i]-=simSize[i]
#Error detection
if atomj[0]>lGridPoints[0][-1] or atomj[1]>lGridPoints[1][-1] or atomj[2]>lGridPoints[2][-1] or \
atomj[0]<lGridPoints[0][0] or atomj[1]<lGridPoints[1][0] or atomj[2]<lGridPoints[2][0]:
d=dist_periodic(atomi,atomj,array(zip([0,0,0],simSize)))
if d>7.5: continue
print "="*50
print "Start Error Report:"
print "AtomI(%d):"%iNeighb,atomi
print "AtomJ(%d):"%jNeighb,atomj
print "Distance:",dist_periodic(atomi,atomj,array(zip([0,0,0],simSize)))
print "GridX Min,Max:","% 5.5f % 5.5f"%(min(lGridPoints[0]),max(lGridPoints[0]))
print "GridY Min,Max:","% 5.5f % 5.5f"%(min(lGridPoints[1]),max(lGridPoints[1]))
print "GridZ Min,Max:","% 5.5f % 5.5f"%(min(lGridPoints[2]),max(lGridPoints[2]))
print "Error: AtomJ seems to be lying outside the local grid, which should not be possible."
exit(0)
#This is where the magic happens, finally do some computing...
#Interpolate on local FIELD grid between these two atoms 75% of time spent here
pnts2interp=linePoints(atomi,atomj,Ninterp)
yys=array([interp3d(i,lGridBoundPoints,lGridPoints,lfield) for i in pnts2interp])
xwid=dist(pnts2interp[0],pnts2interp[-1])
xdel=xwid/Ninterp
xxs=[xdel*x-xwid/2 for x in range(Ninterp)]
xlines[-1][-1]=xxs
ylines[-1][-1]=yys
avgyline+=yys
avgyline/=nlines
return avgyline,xlines,ylines,halfNeighbors