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
def fieldNeighbors3D(atoms,atypes,basis,field,fieldSize,halfNeighbors=None,Ninterps=[7,7,15],cutoffs=None,loc=None):
#loc=["center","bond","half"]
[v1,v2,v3]=basis
latoms=array(atoms)
if loc==None:
loc="bond"
#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)
cutFlag=True
if cutoffs==None:
cutFlag=False
else: #ensure cutoffs is a list and not just a float
cutoffs=list(cutoffs)
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
grids=list()
if cutFlag:
avgGrids=[zeros(Ninterps) for i in range(len(cutoffs))]
bondcnts=zeros(len(cutoffs))
else:
avgGrid=zeros(Ninterps)
bondcnt=0
nlines=float(sum(map(len,halfNeighbors)))
delx=2.0/Ninterps[0]
dely=2.0/Ninterps[1]
#Local Grid size
delGrids=simSize/fieldSize
lGridSize=fieldSize
nlGridPoints=reduce(operator.mul,lGridSize)
for iNeighb,jNeighbors in enumerate(halfNeighbors):
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]
#Make the local grid about the central atom
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) ] )
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
#Now make the field
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:
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]
d=dist(atomj,atomi)
#If this bond is longer than all the cutoffs than don't bother with it
if cutFlag and len([1 for i in cutoffs if d<=i])==0:
continue
#Change the location as requested
if loc=="bond":
delz=mag(atomj-atomi)/Ninterps[2]
Tran=(atomj-atomi)/2.+atomi
if loc=="half":
delz=mag(atomj-atomi)/(Ninterps[2]*2.)
Tran=(atomj-atomi)/4.+atomi
if loc=="center":
delz=dely
Tran=atomi
#Change of coordinate systems into atomj-atomi basis.
Rota=rotmatx(array([0.,0.,1.]),atomj-atomi)
xps=array([(i-Ninterps[0]/2)*delx for i in range(Ninterps[0])]*Ninterps[1]*Ninterps[2]).ravel()
yps=array([[(i-Ninterps[1]/2)*dely]*Ninterps[0] for i in range(Ninterps[1])]*Ninterps[2]).ravel()
zps=array([[(i-Ninterps[2]/2)*delz]*Ninterps[0]*Ninterps[1] for i in range(Ninterps[2])]).ravel()
ipnts=array([dot(Rota,array(pnt))+Tran for pnt in zip(xps,yps,zps)])
#Do the interpolation
if cutFlag:
for j,cut in enumerate(cutoffs):
if d <= cut:
bondcnts[j]+=1
if Ninterps[0]!=1:
grid=array([interp3d(ipnts[i],lGridBoundPoints,lGridPoints,lfield) for i in range(len(ipnts))]).reshape(Ninterps)
else:
grid=array([interp3d(ipnts[i],lGridBoundPoints,lGridPoints,lfield) for i in range(len(ipnts))]).reshape(Ninterps[1:])
grids.append(grid)
avgGrids[j]+=grid
else:
grid=array([interp3d(ipnts[i],lGridBoundPoints,lGridPoints,lfield) for i in range(len(ipnts))]).reshape(Ninterps)
grids.append(grid)
avgGrid+=grid
bondcnt+=1
if cutFlag:
for i,v in enumerate(bondcnts):
if v==0:
bondcnts[i]=1
return [avgGrid/bc for bc,avgGrid in zip(bondcnts,avgGrids)],grids,bondcnts
return avgGrid/bondcnt,grids,bondcnt
