def relaxMeshSym(self, B, targetNmesh, path):
#1. nCoarse random points in the cell parallelpiped.
# nCoarseMax = 200
self.B = B
print 'B', B
[self.symops, self.nops] = getGroup(self.B)
self.nTarget = targetNmesh
self.path = path
print 'Number of desired points:', targetNmesh
print 'Symmetry operations:', self.nops
vol = abs(det(B))
self.ravg = (vol / targetNmesh)**(1 / 3.0)
self.edgeFactor = 3.0
self.rmin = 0.8 * self.ravg #
self.rmax = self.edgeFactor * self.ravg #cutoff for forces, neighbors in other cells.
print 'Typical spacing:', self.ravg
self.initPoints()
self.initTets()
self.movetoVoronoi()
self.addBorders()
self.delauPoints()
self.fillTets()
self.relax()
self.plotPoints(self.points, self.npoints, 'pos')
sys.exit('stop')
return meshvecs, Nmesh, lattype, pfB, pf, status
def relaxMeshSym(self,B,targetNmesh,path):
#1. nCoarse random points in the cell parallelpiped.
# nCoarseMax = 200
self.B = B
print 'B',B
[self.symops,self.nops] = getGroup(self.B)
self.nTarget = targetNmesh
self.path = path
print 'Number of desired points:', targetNmesh
print 'Symmetry operations:', self.nops
vol = abs(det(B))
self.ravg = (vol/targetNmesh)**(1/3.0)
self.edgeFactor = 3.0
self.rmin = 0.8*self.ravg #
self.rmax = self.edgeFactor*self.ravg #cutoff for forces, neighbors in other cells.
print 'Typical spacing:', self.ravg
self.initPoints()
self.initTets()
self.movetoVoronoi()
self.addBorders()
self.delauPoints()
self.fillTets()
self.relax()
self.plotPoints(self.points,self.npoints,'pos')
sys.exit('stop')
return meshvecs, Nmesh, lattype, pfB, pf, status
def orthsuper(B):
'''For lattice with orthogonal nonprimitive lattice vectors (cubic, tetragonal, orthorhombic),
finds the simple orthorhombic superlattice with minimum s/v.'''
# Find a set of three shortest lattice vectors that are perpendicular
A = lattice()
A.vecs = trimSmall(inv(transpose(B.vecs)))
# print 'A'; print A.vecs
# print 'det a', det(A.vecs)
[A.symops, A.nops] = getGroup(A.vecs)
A.lattype = latticeType(A.nops)
# printops_eigs(A)
# print 'transp A'; print transpose(A)
S = zeros((3, 3), dtype=float)
M = zeros((3, 3), dtype=int)
K = zeros((3, 3), dtype=float)
# S_orth = three_perp(A.vecs,B.lattype)
print
S_orth = three_perp_eigs(A)
# sys.exit('stop')
M = rint(transpose(dot(inv(A.vecs), S_orth))).astype(int)
print 'M by finding 3 shortest perpendicular vectors'
print M
print 'det M', det(M)
#starting mesh Q with 3 free directions.
Q = dot(B.vecs, inv(M))
print 'mesh numbers'
[n0, n1, n2] = svmesh(B.Nmesh / abs(det(M)), Q)[0]
print[n0, n1, n2]
K[:, 0] = Q[:, 0] / n0
K[:, 1] = Q[:, 1] / n1
K[:, 2] = Q[:, 2] / n2
# print K
Nmesh = B.det / abs(det(K))
if checksymmetry(K, B):
pf = packingFraction(K)
print 'Packing fraction (orthmesh)', pf, 'vs original B', packingFraction(
B.vecs)
print 'Nmesh', Nmesh, 'vs target', B.Nmesh
else:
sys.exit('Symmetry failed in orthsuper')
return [K, pf, True]
def orthsuper(B):
'''For lattice with orthogonal nonprimitive lattice vectors (cubic, tetragonal, orthorhombic),
finds the simple orthorhombic superlattice with minimum s/v.'''
# Find a set of three shortest lattice vectors that are perpendicular
A = lattice()
A.vecs = trimSmall(inv(transpose(B.vecs)))
# print 'A'; print A.vecs
# print 'det a', det(A.vecs)
[A.symops,A.nops] = getGroup(A.vecs)
A.lattype = latticeType(A.nops)
# printops_eigs(A)
# print 'transp A'; print transpose(A)
S = zeros((3,3),dtype = float)
M = zeros((3,3),dtype = int)
K = zeros((3,3),dtype = float)
# S_orth = three_perp(A.vecs,B.lattype)
print; S_orth = three_perp_eigs(A)
# sys.exit('stop')
M = rint(transpose(dot(inv(A.vecs),S_orth))).astype(int)
print 'M by finding 3 shortest perpendicular vectors';print M
print 'det M', det(M)
#starting mesh Q with 3 free directions.
Q = dot(B.vecs,inv(M))
print 'mesh numbers';
[n0,n1,n2] = svmesh(B.Nmesh/abs(det(M)),Q)[0]
print [n0,n1,n2]
K[:,0] = Q[:,0]/n0; K[:,1] = Q[:,1]/n1; K[:,2] = Q[:,2]/n2
# print K
Nmesh = B.det/abs(det(K))
if checksymmetry(K,B):
pf = packingFraction(K)
print 'Packing fraction (orthmesh)', pf, 'vs original B', packingFraction(B.vecs)
print 'Nmesh', Nmesh, 'vs target', B.Nmesh
else:
sys.exit('Symmetry failed in orthsuper')
return [K,pf,True]
def bestmeshIter_vary_pf(Blatt, Nmesh, path):
'''The kmesh can be related to the reciprocal lattice B by B = KM, where M is an integer 3x3 matrix
So K = B Inv(M). Change M one element at a time to minimize the errors in symmetry and the cost in S/V and Nmesh '''
##############################################################
########################## Script ############################
# print path.split('/')
npathsegs = len(path.split('/'))
# print npathsegs
vaspinputdir = '/'.join(
path.split('/')[0:npathsegs - 3]
) + '/vaspinput/' #up two levels, 2 are for spaces at beg and end
# print vaspinputdir
M = zeros((3, 3), dtype=int)
S = zeros((3, 3), dtype=fprec)
B = lattice()
A = lattice()
K = lattice()
status = ''
pf_minsv = 0
pf_sv2fcc = 0
pf_maxpf = 0
pf_pf2fcc = 0
#kvecs_pf2fcc = identity(3)
sym_maxpf = False
sym_sv2fcc = False
sym_minsv = False
sym_pf2fcc = False
print 'Target mesh number', Nmesh
B.vecs = Blatt / 2 / pi #Don't use 2pi constants in reciprocal lattice here
# B.pftarget = 0.7405 #default best packing fraction
#############End BCT lattice
eps = 1.0e-6
B.Nmesh = Nmesh
print 'B vectors (differ by 2pi from traditional)'
print B.vecs #
#print 'B transpose'; print transpose(B.vecs)
B.det = det(B.vecs)
print 'Det of B', B.det
print 'Orth Defect of B', orthdef(B.vecs)
print 'Surf/vol of B', surfvol(B.vecs)
pfB = packingFraction(B.vecs)
print 'Packing fraction of B:', pfB
[B.symops, B.nops] = getGroup(B.vecs)
B.msymops = intsymops(B) #integer sym operations in B basis
# print'Symmetry operators in basis of B'
# for i in range:
# print B.msymops[:,:,i];print
# printops_eigs(B)
B.lattype = latticeType(B.nops)
print 'Lattice type:', B.lattype
A = lattice()
A.vecs = trimSmall(inv(transpose(B.vecs)))
[A.symops, A.nops] = getGroup(A.vecs)
A.msymops = intsymops(A)
print 'Real space lattice A'
print A.vecs
print 'Det A', det(A.vecs)
pfA = packingFraction(A.vecs)
print 'Packing fraction of A:', pfA
# print 'current dir for meshesfile', os.getcwd()
meshesfile = open('meshesfile', 'w')
# meshesfile = open('meshesfile2','w')
meshesfile.write('N target %i\n' % B.Nmesh)
meshesfile.write('Format: pf then Nmesh then kmesh\n\n')
pflist = []
# for pftry in frange(pfB/2,0.75,0.005):
for pftry in frange(pfB / 2, 0.75, 0.01):
# for pftry in frange(.3,0.505,0.005):
print '\nPacking fraction target', pftry
B.pftarget = pftry
pf_orth = 0
pf_orth2fcc = 0
sym_orth = False
sym_orth2fcc = False
#'--------------------------------------------------------------------------------------------------------'
#'--------------------------------------------------------------------------------------------------------'
M = zeros((3, 3), dtype=int)
ctest = []
type = 'maxpfsym'
print type
ctrials = [3]
a = rint(Nmesh**(1 / 3.0))
# f = int(Nmesh/a/a)
randnums = zeros(9)
print 'M scale a', a
for c in ctrials:
# ri = [randint(5) for i in range(9)]
# M = array([[-a+ri[0], a/c +ri[1] , a/c+ri[2]],[a/c+ri[3],-a+ri[4],a/c+ri[5]],\
# [a/c+ri[6],a/c+ri[7],-a+ri[8]]]) #bcc like best avg pf on 50: 0.66
#HNF::::::
M = array([[a, 0 , 0],
[a/c,a,0],\
[a/c,a/c,a]]) #bcc like best avg pf on 50: 0.66
#
# M = array([[-a+1, a/c , a/c],[a/c,-a,a/c],[a/c,a/c,-a-1]]) #bcc like best avg pf on 50: 0.66
# M = array([[a, 0,0],[0,a,0],[0,0,a+3]])
# M = array([[-16 , 1 , 5 ],
# [6 , -10 , 5],
# [-6 , -1 , 6 ]])
# M = array([[5, a/c , a/c],[a/c,0,a/c],[a/c,a/c,-5]]) #fcc like best avg pf on 50: 0.59
M = rint(M * (B.Nmesh / abs(det(M)))**(1 / 3.0))
print 'Start mesh trial'
print M
# [M,K] = findmin(M,B,type)
# print 'Test trial M'; print M
ctest.append(cost(M, B, type))
# print'Trial costs',ctest
cbest = ctrials[argmin(ctest)]
# print'Best c', cbest
iternpf = 0
itermaxnpf = 10
itermaxsym = 5
# bestpf = 100
# NPFcost = 100;delNPFcost = -1 #initial values
type = 'maxpfsym'
print type
delcost = -1
lowcost = 1000 #initialize
#### while iternpf<itermaxnpf and delNPFcost <0 and abs(delNPFcost)>0.1 :
while iternpf < itermaxnpf and delcost < -0.1:
oldcost = cost(M, B, type)
# NPFcost = cost(M,B,'maxpf')
# delNPFcost = (NPFcost-oldNPFcost)/NPFcost :
'''Here we let M vary in the search, but record pf and kvecs when we find min cost'''
# print 'cost(N,PF):', cost(M,B,type)
# while not symm and and iternpf<itermax:
M = rint(M * (B.Nmesh / abs(det(M)))**(1 / 3.0))
print 'Scaled M'
print M
iternpf += 1
print 'Iteration', type, iternpf, '**********'
[M, K] = findmin(M, B, type)
M = rint(M)
itersym = 0
symm = False
while not symm and itersym < itermaxsym:
itersym += 1
print 'Symmetry iteration', itersym, '-------'
# print 'Nmesh', abs(det(M)), 'packing', packingFraction(dot(B.vecs,inv(M)))
# M = rint(minkM(M,B))#; print'Mink reduced M'; print M
for iop in range(B.nops):
M = rint(findmin_i(M, B, iop))
# M = rint(minkM(M,B))#; print'Mink reduced M'; print M
if abs(det(M) - B.Nmesh
) / B.Nmesh > 0.15: #how far off from target N
M = rint(M * (B.Nmesh / abs(det(M)))**(1 / 3.0))
print 'Scaled M'
print M
K = lattice()
K.vecs = trimSmall(dot(B.vecs, inv(M)))
K.det = abs(det(K.vecs))
K.Nmesh = B.det / K.det
symm = checksymmetry(K.vecs, B)
print 'Symmetry check', symm
if symm:
newcost = cost(M, B, type)
if newcost - lowcost < 0:
lowcost = newcost
print 'New lowcost', newcost
pf_maxpf = packingFraction(K.vecs)
sym_maxpf = True
kvecs_maxpf = K.vecs
# if pf_maxpf<bestpf: bestpf = pf_maxpf; bestM = M
print 'Packing fraction', pf_maxpf, 'vs original B', pfB
print 'Nmesh', K.Nmesh, 'vs target', B.Nmesh
delcost = cost(M, B, type) - oldcost
#write to files
# meshesfile.write('Packing fraction target %f\n' % pftry)
if symm and pf_maxpf not in pflist:
pflist.append(pf_maxpf)
# meshesfile.write('Packing fraction achieved %f\n' % pf_maxpf)
meshesfile.write('%12.8f %8.3f \n' % (pf_maxpf, K.Nmesh))
# meshesfile.write('M\n')
# for i in range(3):
# for j in range(3):
# meshesfile.write('%i6' %M[i,j])
# meshesfile.write('\n')
## meshesfile.write('\n')
# meshesfile.write('k mesh\n')
M = rint(dot(inv(K.vecs), B.vecs))
for i in range(3):
for j in range(3):
meshesfile.write('%i ' % int(rint(M[i, j])))
meshesfile.write('\n')
meshesfile.write('\n')
meshesfile.flush()
M = rint(dot(inv(K.vecs), B.vecs)
) #We assign K only when M is ideal, so remake the best M
print 'Check M'
print M
print 'Check K'
print K.vecs
print 'Check B'
print B.vecs
print 'Check pf'
print packingFraction(K.vecs)
#create a dir and prepare for vasp run
newdir = str(round(pf_maxpf, 4))
newpath = path + newdir + '/'
if not os.path.isdir(newpath):
os.system('mkdir %s' % newpath)
os.chdir(newpath)
os.system('cp %s* %s' % (vaspinputdir, newpath))
os.system('cp %sPOSCAR %s' % (path, newpath))
print 'SKIPPING writekpts_vasp_M AND submission'
# writekpts_vasp_M(newpath,B,M,K)
# writekpts_vasp_pf(newpath,K.vecs,pf_maxpf,K.Nmesh)
writejobfile(newpath)
# subprocess.call(['sbatch', 'vaspjob']) #!!!!!!! Submit jobs
os.chdir(path)
else:
'do nothing'
# meshesfile.write('Failed symmetry\n\n')
meshesfile.close()
# Summary
pfs = [pfB]
pftypes = ['B_latt']
ks = [B.vecs / a] #one solutions is to simply divide B by an integer
if not (sym_minsv or sym_sv2fcc or sym_maxpf or pf_pf2fcc or sym_orth
or sym_orth2fcc):
meshtype = 'B_latt_revert'
#status += 'MHPrevert;'
K.vecs = B.vecs / a
K.det = abs(det(K.vecs))
K.Nmesh = abs(B.det / K.det)
pfmax = packingFraction(K.vecs)
else:
if sym_orth:
pfs.append(pf_orth)
pftypes.append('orth')
ks.append(kvecs_orth)
if sym_orth2fcc:
pfs.append(pf_orth2fcc)
pftypes.append('orth2fcc')
ks.append(kvecs_orth2fcc)
if sym_maxpf:
pfs.append(pf_maxpf)
pftypes.append('maxpf')
ks.append(kvecs_maxpf)
if sym_pf2fcc:
pfs.append(pf_pf2fcc)
pftypes.append('pf2fcc')
ks.append(kvecs_pf2fcc)
pfmax = max(pfs)
meshtype = pftypes[argmax(pfs)]
K.vecs = ks[argmax(pfs)]
K.det = abs(det(K.vecs))
K.Nmesh = B.det / K.det
# return [K.vecs, K.Nmesh, B.Nmesh, B.lattype, pfB, pf_orth, pf_orth2fcc, pf_maxpf, pf_minsv, pf_sv2fcc, pfmax, meshtype, fcctype(B),status]
return [
K.vecs, K.Nmesh, B.Nmesh, B.lattype, pfB, pf_orth, pf_orth2fcc,
pf_maxpf, pf_pf2fcc, pfmax, meshtype,
fcctype(B), cbest, status
]
#multlist = [3,5]
#multlist = [2,4,6]
#multlist = [7,8]
#labeledstructs = [structchar + struct for struct in structs]
for struct in structs: #these are simply the numbers with no prefix
for m in multlist:
dir = structchar + struct + '_%i/' % m
print
print dir
if not os.path.isdir(finalDir + dir):
os.system('mkdir %s' % finalDir + dir)
os.chdir(finalDir + dir)
makestr2poscar(struct)
if m == multlist[0]: #things to do only once per structure
A = readlatt('POSCAR')
[symops, nops] = getGroup(A)
lattype = latticeType(nops)
B = transpose(inv(A))
[Bsymops, Bnops] = getGroup(A)
L = getL(platt) #L is integer matrix for this lattice
print 'Integer L matrix for lattice'
print L
dL = abs(det(L))
print 'det(L)', dL
print 'detL*inv(L))'
print dL * inv(L)
print 'Cubic mesh compatibility:'
print 'detL*inv(L)*inv(platt)'
print dL * dot(inv(L), transpose(inv(platt)))
print 'Fcc mesh compatibility for fcc lattice):'
print 'detL*bccsq*trans(inv(L))'
def bestmeshEigen(Blatt,Nmesh):
'''The kmesh can be related to the reciprocal lattice B by B = KM, where M is an integer 3x3 matrix
So K = B Inv(M) . Work in the inverse space of this problem, where we can work with M instead of Inv(M).
T(InvK) = T(InvB)T(M).
Define S = T(InvK), and the real lattice A = T(InvB). So S = A T(M) is a superlattice on the real lattice.
Minimization scheme'''
##############################################################
########################## Script ############################
M = zeros((3,3),dtype = int)
S = zeros((3,3),dtype = fprec)
B = lattice()
A = lattice()
K = lattice()
B.vecs = Blatt/2/pi #Don't use 2pi constants in RL here.
#############End BCT lattice
eps = 1.0e-6
B.det = det(B.vecs)
B.Nmesh = Nmesh
print 'B vectors';print B.vecs #
#print 'B transpose'; print transpose(B.vecs)
print 'Det of B', B.det
print 'Orth Defect of B', orthdef(B.vecs)
print 'Surf/vol of B', surfvol(B.vecs)
[B.symops,B.nops] = getGroup(B.vecs)
print 'Number of symmetry operations', B.nops
eigendirs = zeros([3,3,B.nops],dtype = int)
#print 'symmetry operations of B\n'
#for j in range(nopsB):
# print j
# op = array(symopsB[:,:,j])
# print op
#find real lattice
A.vecs = transpose(inv(B.vecs))
A.det = det(A.vecs)
A.Nmesh = Nmesh
print;print 'A vectors';print A.vecs
print 'Det of A', A.det
print 'Orth Defect of A', orthdef(A.vecs)
print 'Surf/vol of A', surfvol(A.vecs)
[A.symops,A.nops] = getGroup(A.vecs)
if A.nops != B.nops:
sys.exit('Number of operations different for A and B; stop')
testvecs = [];testindices = []
# print 'symmetry operations R of A\n'
for k in range(A.nops):
print
print k
op = array(A.symops[:,:,k])
print'symop R of A'; print trimSmall(op)
m = trimSmall(dot(dot(inv(A.vecs), A.symops[:,:,k]),A.vecs))
print'symop m'; print m
# print 'det(m)', det(m)
'Take eigenvectors in cartesian space'
[vals,vecs]=eig(op)
print 'eigen of m',vals
print 'eigenvecs are calculated in cartesian space'; print vecs
#transform to m space
for i in range(3): vecs[:,i] = dot(inv(A.vecs),vecs[:,i])
print 'eigenvecs in m space'; print vecs
print 'scaled to integers'
for i in range(3): vecs[:,i] = vecs[:,i]/abs(vecs[:,i])[nonzero(vecs[:,i])].min()
vecs = rint(vecs)
print vecs
eigendirs[:,:,k]= vecs
#find operations with nondegenerate real eigenvalues
print 'nonDegen', nonDegen(vals)
for i in nonDegen(vals):
if not matchDirection(transpose(vecs[:,i]),testvecs): #keep only unique directions
testvecs.append(vecs[:,i].real/abs(vecs[:,i])[nonzero(vecs[:,i])].min())
testindices.append([k,i])
#print; print oplist;
print 'testvecs'; print testvecs
#print testindices
MT = zeros((3,3),dtype = fprec)
if len(testvecs) == 0:
print 'No eigen directions'
[M,K.vecs] = unconstrainedSVsearch(B)
if det(K.vecs)==0:
sys.exit('Det(K) is zero after unconstrained search! Stop')
if not checksymmetry(K.vecs,B):
sys.exit('Symmetry missing in mesh! Stop')
# MT = unconstrainedmin(B.vecs)
if len(testvecs) == 1:
print 'Only 1 eigen direction'
#Choose this one and the other two in the plane perpendicular to this.
MT[:,0] = testvecs[0]
# print 'testindices',testindices
kop = testindices[0][0] #useful operator
ieigen = testindices[0][1] #index of the only eigendirection
op = array(A.symops[:,:,kop])
# print trimSmall(op)
# find one other direction in the plane perp to the eigendireation; either degenerate eigenvalue will do.
otherindices = nonzero(array([0,1,2])-ieigen)
print eigendirs[:,:,otherindices[0][0]]
MT[:,1] = eigendirs[:,:,kop][:,otherindices[0][0]]
#Make 3rd vector perp as possible to the other two
ur0 = dot(A.vecs,MT[:,0])/norm(dot(A.vecs,MT[:,0])) #unit vectors in real space
ur1 = dot(A.vecs,MT[:,1])/norm(dot(A.vecs,MT[:,1]))
ur2 = cross(ur0,ur1)
print ur0
print ur1
print ur2
print 'ur2 transformed to m space'; print dot(inv(A.vecs),ur2)
mvec = dot(inv(A.vecs),ur2) #transformed to M space, but real
mvec = rint(mvec/abs(mvec[nonzero(mvec)]).min()) #Scale so smallest comp is 1
MT[:,2] = mvec
print 'MT from single operator';print MT
print 'starting superlattice'; print dot(A.vecs,MT)
# Q2 = MT2mesh_three_ns(MT,B)
Q2 = MT2mesh(MT,B,A)
if checksymmetry(Q2,B):
SV = surfvol(Q2)
# print round(surfvol(Q2),4),round(orthdef(Q2),4),'SV of Q2,','OD'
K.vecs = Q2
else:
print'Q from single operator fails symmetry'
if len(testvecs) == 2:
print 'Only 2 eigen directions'
MT[:,0] = testvecs[0]
MT[:,1] = testvecs[1]
#Make 3rd vector perp as possible to the other two
ur0 = dot(A.vecs,MT[:,0])/norm(dot(A.vecs,MT[:,0])) #unit vector in real space
ur1 = dot(A.vecs,MT[:,1])/norm(dot(A.vecs,MT[:,1]))
ur2 = cross(ur0,ur1)
MT[:,2] = rint(dot(inv(A.vecs),ur2))
print 'MT from two eigen directions';print MT
# Q2 = MT2mesh_three_ns(MT,B)
Q2 = MT2mesh(MT,B)
if checksymmetry(Q2,B):
SV = surfvol(Q2)
print round(surfvol(Q2),4),round(orthdef(Q2),4),'SV of Q2,','OD'
K.vecs = Q2
else:
print'Q fails symmetry'
if len(testvecs) >= 3:
print 'MT from three eigen directions'
testvecstrials = [list(x) for x in combinations(testvecs,3)]
print testvecstrials
bestindex = -1
bestcost = 1000
for i,vecs in enumerate(testvecstrials):
print; print 'trial',i
print vecs
MT[:,0] = vecs[0]
MT[:,1] = vecs[1]
MT[:,2] = vecs[2]
print 'MT'; print MT
print 'det MT', det(MT)
if not areEqual(det(MT),0):
Q2 = MT2mesh(MT,B)
if checksymmetry(Q2,B):
Nscale =1*.8; Ncost = Nscale * abs((B.det/det(Q2))-B.Nmesh)/B.Nmesh
cost = surfvol(Q2)*(1+Ncost)
print cost
if cost<bestcost:
bestcost = cost;
bestindex = i;
K.vecs = Q2
print round(surfvol(Q2),4),round(orthdef(Q2),4),'SV of Q2,','OD'
else:
print'Q from trial %i fails symmetry' % i
print '___________ Best mesh ___________'
print 'trial', bestindex
if checksymmetry(K.vecs,B):
print K.vecs
K.det = abs(det(K.vecs))
print 'N of mesh', B.det/K.det
SV = surfvol(K.vecs)
print round(surfvol(K.vecs),4),round(orthdef(K.vecs),4),'SV of Q2,','OD'
else:
print'K mesh fails symmetry'
structs = readstructs(structfile)
#multlist = [3,5]
#multlist = [2,4,6]
#multlist = [7,8]
#labeledstructs = [structchar + struct for struct in structs]
for struct in structs: #these are simply the numbers with no prefix
for m in multlist:
dir = structchar + struct + '_%i/' % m
print;print dir
if not os.path.isdir(finalDir+dir): os.system('mkdir %s' % finalDir+dir)
os.chdir(finalDir+dir)
makestr2poscar(struct)
if m == multlist[0] : #things to do only once per structure
A = readlatt('POSCAR')
[symops,nops] = getGroup(A)
lattype = latticeType(nops)
B = transpose(inv(A))
[Bsymops,Bnops] = getGroup(A)
L = getL(platt) #L is integer matrix for this lattice
print 'Integer L matrix for lattice'; print L
dL = abs(det(L))
print 'det(L)', dL
print 'detL*inv(L))'; print dL*inv(L)
print 'Cubic mesh compatibility:'
print 'detL*inv(L)*inv(platt)'; print dL*dot(inv(L),transpose(inv(platt)))
print 'Fcc mesh compatibility for fcc lattice):'
print 'detL*bccsq*trans(inv(L))'; print dL*dot(bccsq,transpose(inv(L)))
scaleposcar(scale) #inserts length scale into appropriate spot.
writefile([str(dL)],finalDir+dir+'detL')
def bestmeshIter(Blatt, Nmesh):
'''The kmesh can be related to the reciprocal lattice B by B = KM, where M is an integer 3x3 matrix
So K = B Inv(M). Change M one element at a time to minimize the errors in symmetry and the cost in S/V and Nmesh '''
##############################################################
########################## Script ############################
M = zeros((3, 3), dtype=int)
S = zeros((3, 3), dtype=fprec)
B = lattice()
A = lattice()
K = lattice()
status = ''
pf_minsv = 0
pf_sv2fcc = 0
pf_maxpf = 0
pf_pf2fcc = 0
#kvecs_pf2fcc = identity(3)
sym_maxpf = False
sym_sv2fcc = False
sym_minsv = False
sym_pf2fcc = False
a = rint(Nmesh**(1 / 3.0))
f = int(Nmesh / a / a)
print 'Target mesh number', Nmesh
B.vecs = Blatt / 2 / pi #Don't use 2pi constants in reciprocal lattice here
# B.pftarget = 0.7405 #default best packing fraction
B.pftarget = 0.35
#############End BCT lattice
eps = 1.0e-6
B.Nmesh = Nmesh
print 'B vectors (differ by 2pi from traditional)'
print B.vecs #
#print 'B transpose'; print transpose(B.vecs)
B.det = det(B.vecs)
print 'Det of B', B.det
print 'Orth Defect of B', orthdef(B.vecs)
print 'Surf/vol of B', surfvol(B.vecs)
pfB = packingFraction(B.vecs)
print 'Packing fraction of B:', pfB
[B.symops, B.nops] = getGroup(B.vecs)
B.msymops = intsymops(B) #integer sym operations in B basis
# printops_eigs(B)
B.lattype = latticeType(B.nops)
print 'Lattice type:', B.lattype
A = lattice()
A.vecs = trimSmall(inv(transpose(B.vecs)))
[A.symops, A.nops] = getGroup(A.vecs)
A.msymops = intsymops(A)
print 'Real space lattice A'
print A.vecs
print 'Det A', det(A.vecs)
pfA = packingFraction(A.vecs)
print 'Packing fraction of A:', pfA
pf_orth = 0
pf_orth2fcc = 0
sym_orth = False
sym_orth2fcc = False
if B.lattype in ['Orthorhombic', 'Tetragonal', 'Cubic']:
cbest = '' #need for passing other structures' results to main program
[kvecs_orth, pf_orth, sym_orth] = orthsuper(B)
M = rint(dot(inv(kvecs_orth), B.vecs)).astype(int)
print
print 'Try orth2FCC substitution.',
kmesh2 = zeros((3, 3), dtype=float)
scale = 2 / 4**(1 / 3.0)
kmesh2[:, 0] = kvecs_orth[:, 1] / scale + kvecs_orth[:, 2] / scale
kmesh2[:, 1] = kvecs_orth[:, 2] / scale + kvecs_orth[:, 0] / scale
kmesh2[:, 2] = kvecs_orth[:, 0] / scale + kvecs_orth[:, 1] / scale
sym_orth2fcc = checksymmetry(kmesh2, B)
if sym_orth2fcc:
pf = packingFraction(kmesh2)
print
print 'Packing fraction', pf, 'vs original B', pfB
if pf > pf_orth:
M = rint(dot(inv(kmesh2), B.vecs)).astype(int)
print 'M'
print M
else:
' Packing fraction too small'
kvecs_orth2fcc = kmesh2
pf_orth2fcc = pf
else:
print ' It fails symmetry test'
# sys.exit('stop')
else:
#'--------------------------------------------------------------------------------------------------------'
#'--------------------------------------------------------------------------------------------------------'
M = zeros((3, 3), dtype=int)
ctest = []
type = 'maxpfsym'
print type
ctrials = [3]
for c in ctrials:
M = array([[-a + 2, a / c, a / c], [a / c, -a, a / c],
[a / c, a / c,
-a - 2]]) #bcc like best avg pf on 50: 0.66
# M = array([[2, a/c , a/c],[a/c,0,a/c],[a/c,a/c,-2]]) #fcc like best avg pf on 50: 0.59
M = rint(M * (B.Nmesh / abs(det(M)))**(1 / 3.0))
print 'Start mesh trial'
print M
[M, K] = findmin(M, B, type)
print 'Test trial M'
print M
ctest.append(cost(M, B, type))
# print'Trial costs',ctest
cbest = ctrials[argmin(ctest)]
# print'Best c', cbest
iternpf = 0
itermaxnpf = 10
itermaxsym = 5
# bestpf = 100
# NPFcost = 100;delNPFcost = -1 #initial values
type = 'maxpfsym'
print type
delcost = -1
lowcost = 1000 #initialize
#### while iternpf<itermaxnpf and delNPFcost <0 and abs(delNPFcost)>0.1 :
while iternpf < itermaxnpf and delcost < -0.1:
oldcost = cost(M, B, type)
# NPFcost = cost(M,B,'maxpf')
# delNPFcost = (NPFcost-oldNPFcost)/NPFcost :
'''Here we let M vary in the search, but record pf and kvecs when we find min cost'''
# print 'cost(N,PF):', cost(M,B,type)
# while not symm and and iternpf<itermax:
M = rint(M * (B.Nmesh / abs(det(M)))**(1 / 3.0))
print 'Scaled M'
print M
iternpf += 1
print 'Iteration', type, iternpf, '**********'
[M, K] = findmin(M, B, type)
print M
itersym = 0
symm = False
while not symm and itersym < itermaxsym:
itersym += 1
print 'Symmetry iteration', itersym, '-------'
# print 'Nmesh', abs(det(M)), 'packing', packingFraction(dot(B.vecs,inv(M)))
M = minkM(M, B) #; print'Mink reduced M'; print M
for iop in range(B.nops):
M = findmin_i(M, B, iop)
if abs(det(M) - B.Nmesh
) / B.Nmesh > 0.15: #how far off from target N
M = rint(M * (B.Nmesh / abs(det(M)))**(1 / 3.0))
print 'Scaled M'
print M
K = lattice()
K.vecs = trimSmall(dot(B.vecs, inv(M)))
K.det = abs(det(K.vecs))
K.Nmesh = B.det / K.det
symm = checksymmetry(K.vecs, B)
print 'Symmetry check', symm
if symm:
newcost = cost(M, B, type)
if newcost - lowcost < 0:
lowcost = newcost
print 'New lowcost', newcost
pf_maxpf = packingFraction(K.vecs)
sym_maxpf = True
kvecs_maxpf = K.vecs
# if pf_maxpf<bestpf: bestpf = pf_maxpf; bestM = M
print 'Packing fraction', pf_maxpf, 'vs original B', pfB
print 'Nmesh', K.Nmesh, 'vs target', B.Nmesh
print
print 'Try FCC-like substitution.'
kmesh2 = zeros((3, 3), dtype=float)
scale = 2 / 4**(1 / 3.0)
kmesh2[:, 0] = K.vecs[:, 1] / scale + K.vecs[:, 2] / scale
kmesh2[:, 1] = K.vecs[:, 2] / scale + K.vecs[:, 0] / scale
kmesh2[:, 2] = K.vecs[:, 0] / scale + K.vecs[:, 1] / scale
# M = rint(dot(inv(kmesh2),B.vecs)).astype(int) #set this for maxpf run
if checksymmetry(kmesh2, B):
sym_pf2fcc = True
kvecs_pf2fcc = kmesh2
pf_pf2fcc = packingFraction(kmesh2)
Mtemp = rint(dot(inv(kmesh2), B.vecs)).astype(int)
if cost(Mtemp, B, type) < lowcost:
lowcost = cost(M, B, type)
print 'New lowcost', lowcost
M = Mtemp
print 'M'
print Mtemp
print 'Packing fraction', pf_pf2fcc, 'vs original B', pfB
print
else:
print ' Packing fraction too small'
else:
print ' Fails to improve mesh'
delcost = cost(M, B, type) - oldcost
# Summary
pfs = [pfB]
pftypes = ['B_latt']
ks = [B.vecs / a]
if not (sym_minsv or sym_sv2fcc or sym_maxpf or pf_pf2fcc or sym_orth
or sym_orth2fcc):
meshtype = 'B_latt_revert'
#status += 'MHPrevert;'
K.vecs = B.vecs / a
K.det = abs(det(K.vecs))
K.Nmesh = abs(B.det / K.det)
pfmax = packingFraction(K.vecs)
else:
if sym_orth:
pfs.append(pf_orth)
pftypes.append('orth')
ks.append(kvecs_orth)
if sym_orth2fcc:
pfs.append(pf_orth2fcc)
pftypes.append('orth2fcc')
ks.append(kvecs_orth2fcc)
if sym_maxpf:
pfs.append(pf_maxpf)
pftypes.append('maxpf')
ks.append(kvecs_maxpf)
if sym_pf2fcc:
pfs.append(pf_pf2fcc)
pftypes.append('pf2fcc')
ks.append(kvecs_pf2fcc)
pfmax = max(pfs)
meshtype = pftypes[argmax(pfs)]
K.vecs = ks[argmax(pfs)]
K.det = abs(det(K.vecs))
K.Nmesh = B.det / K.det
# return [K.vecs, K.Nmesh, B.Nmesh, B.lattype, pfB, pf_orth, pf_orth2fcc, pf_maxpf, pf_minsv, pf_sv2fcc, pfmax, meshtype, fcctype(B),status]
return [
K.vecs, K.Nmesh, B.Nmesh, B.lattype, pfB, pf_orth, pf_orth2fcc,
pf_maxpf, pf_pf2fcc, pfmax, meshtype,
fcctype(B), cbest, status
]
def bestmeshEigen(Blatt, Nmesh):
'''The kmesh can be related to the reciprocal lattice B by B = KM, where M is an integer 3x3 matrix
So K = B Inv(M) . Work in the inverse space of this problem, where we can work with M instead of Inv(M).
T(InvK) = T(InvB)T(M).
Define S = T(InvK), and the real lattice A = T(InvB). So S = A T(M) is a superlattice on the real lattice.
Minimization scheme
Nothing calls this routine'''
##############################################################
########################## Script ############################
M = zeros((3, 3), dtype=int)
S = zeros((3, 3), dtype=fprec)
B = lattice()
A = lattice()
K = lattice()
B.vecs = Blatt / 2 / pi #Don't use 2pi constants in RL here.
#############End BCT lattice
eps = 1.0e-6
B.det = det(B.vecs)
B.Nmesh = Nmesh
print 'B vectors'
print B.vecs #
#print 'B transpose'; print transpose(B.vecs)
print 'Det of B', B.det
print 'Orth Defect of B', orthdef(B.vecs)
print 'Surf/vol of B', surfvol(B.vecs)
[B.symops, B.nops] = getGroup(B.vecs)
print 'Number of symmetry operations', B.nops
eigendirs = zeros([3, 3, B.nops], dtype=int)
#print 'symmetry operations of B\n'
#for j in range(nopsB):
# print j
# op = array(symopsB[:,:,j])
# print op
#find real lattice
A.vecs = transpose(inv(B.vecs))
A.det = det(A.vecs)
A.Nmesh = Nmesh
print
print 'A vectors'
print A.vecs
print 'Det of A', A.det
print 'Orth Defect of A', orthdef(A.vecs)
print 'Surf/vol of A', surfvol(A.vecs)
[A.symops, A.nops] = getGroup(A.vecs)
if A.nops != B.nops:
sys.exit('Number of operations different for A and B; stop')
testvecs = []
testindices = []
# print 'symmetry operations R of A\n'
for k in range(A.nops):
print
print k
op = array(A.symops[:, :, k])
print 'symop R of A'
print trimSmall(op)
m = trimSmall(dot(dot(inv(A.vecs), A.symops[:, :, k]), A.vecs))
print 'symop m'
print m
# print 'det(m)', det(m)
'Take eigenvectors in cartesian space'
[vals, vecs] = eig(op)
print 'eigen of m', vals
print 'eigenvecs are calculated in cartesian space'
print vecs
#transform to m space
for i in range(3):
vecs[:, i] = dot(inv(A.vecs), vecs[:, i])
print 'eigenvecs in m space'
print vecs
print 'scaled to integers'
for i in range(3):
vecs[:,
i] = vecs[:, i] / abs(vecs[:, i])[nonzero(vecs[:, i])].min()
vecs = rint(vecs)
print vecs
eigendirs[:, :, k] = vecs
#find operations with nondegenerate real eigenvalues
print 'nonDegen', nonDegen(vals)
for i in nonDegen(vals):
if not matchDirection(transpose(vecs[:, i]),
testvecs): #keep only unique directions
testvecs.append(vecs[:, i].real /
abs(vecs[:, i])[nonzero(vecs[:, i])].min())
testindices.append([k, i])
#print; print oplist;
print 'testvecs'
print testvecs
#print testindices
MT = zeros((3, 3), dtype=fprec)
if len(testvecs) == 0:
print 'No eigen directions'
[M, K.vecs] = unconstrainedSVsearch(B)
if det(K.vecs) == 0:
sys.exit('Det(K) is zero after unconstrained search! Stop')
if not checksymmetry(K.vecs, B):
sys.exit('Symmetry missing in mesh! Stop')
# MT = unconstrainedmin(B.vecs)
if len(testvecs) == 1:
print 'Only 1 eigen direction'
#Choose this one and the other two in the plane perpendicular to this.
MT[:, 0] = testvecs[0]
# print 'testindices',testindices
kop = testindices[0][0] #useful operator
ieigen = testindices[0][1] #index of the only eigendirection
op = array(A.symops[:, :, kop])
# print trimSmall(op)
# find one other direction in the plane perp to the eigendireation; either degenerate eigenvalue will do.
otherindices = nonzero(array([0, 1, 2]) - ieigen)
print eigendirs[:, :, otherindices[0][0]]
MT[:, 1] = eigendirs[:, :, kop][:, otherindices[0][0]]
#Make 3rd vector perp as possible to the other two
ur0 = dot(A.vecs, MT[:, 0]) / norm(dot(
A.vecs, MT[:, 0])) #unit vectors in real space
ur1 = dot(A.vecs, MT[:, 1]) / norm(dot(A.vecs, MT[:, 1]))
ur2 = cross(ur0, ur1)
print ur0
print ur1
print ur2
print 'ur2 transformed to m space'
print dot(inv(A.vecs), ur2)
mvec = dot(inv(A.vecs), ur2) #transformed to M space, but real
mvec = rint(
mvec /
abs(mvec[nonzero(mvec)]).min()) #Scale so smallest comp is 1
MT[:, 2] = mvec
print 'MT from single operator'
print MT
print 'starting superlattice'
print dot(A.vecs, MT)
# Q2 = MT2mesh_three_ns(MT,B)
Q2 = MT2mesh(MT, B, A)
if checksymmetry(Q2, B):
SV = surfvol(Q2)
# print round(surfvol(Q2),4),round(orthdef(Q2),4),'SV of Q2,','OD'
K.vecs = Q2
else:
print 'Q from single operator fails symmetry'
if len(testvecs) == 2:
print 'Only 2 eigen directions'
MT[:, 0] = testvecs[0]
MT[:, 1] = testvecs[1]
#Make 3rd vector perp as possible to the other two
ur0 = dot(A.vecs, MT[:, 0]) / norm(dot(
A.vecs, MT[:, 0])) #unit vector in real space
ur1 = dot(A.vecs, MT[:, 1]) / norm(dot(A.vecs, MT[:, 1]))
ur2 = cross(ur0, ur1)
MT[:, 2] = rint(dot(inv(A.vecs), ur2))
print 'MT from two eigen directions'
print MT
# Q2 = MT2mesh_three_ns(MT,B)
Q2 = MT2mesh(MT, B)
if checksymmetry(Q2, B):
SV = surfvol(Q2)
print round(surfvol(Q2), 4), round(orthdef(Q2),
4), 'SV of Q2,', 'OD'
K.vecs = Q2
else:
print 'Q fails symmetry'
if len(testvecs) >= 3:
print 'MT from three eigen directions'
testvecstrials = [list(x) for x in combinations(testvecs, 3)]
print testvecstrials
bestindex = -1
bestcost = 1000
for i, vecs in enumerate(testvecstrials):
print
print 'trial', i
print vecs
MT[:, 0] = vecs[0]
MT[:, 1] = vecs[1]
MT[:, 2] = vecs[2]
print 'MT'
print MT
print 'det MT', det(MT)
if not areEqual(det(MT), 0):
Q2 = MT2mesh(MT, B)
if checksymmetry(Q2, B):
Nscale = 1 * .8
Ncost = Nscale * abs((B.det / det(Q2)) - B.Nmesh) / B.Nmesh
cost = surfvol(Q2) * (1 + Ncost)
print cost
if cost < bestcost:
bestcost = cost
bestindex = i
K.vecs = Q2
print round(surfvol(Q2), 4), round(orthdef(Q2),
4), 'SV of Q2,', 'OD'
else:
print 'Q from trial %i fails symmetry' % i
print '___________ Best mesh ___________'
print 'trial', bestindex
if checksymmetry(K.vecs, B):
print K.vecs
K.det = abs(det(K.vecs))
print 'N of mesh', B.det / K.det
SV = surfvol(K.vecs)
print round(surfvol(K.vecs), 4), round(orthdef(K.vecs),
4), 'SV of Q2,', 'OD'
else:
print 'K mesh fails symmetry'
def bestmeshIter(Blatt,Nmesh):
'''The kmesh can be related to the reciprocal lattice B by B = KM, where M is an integer 3x3 matrix
So K = B Inv(M). Change M one element at a time to minimize the errors in symmetry and the cost in S/V and Nmesh '''
##############################################################
########################## Script ############################
M = zeros((3,3),dtype = int)
S = zeros((3,3),dtype = fprec)
B = lattice()
A = lattice()
K = lattice()
status = ''
pf_minsv = 0; pf_sv2fcc = 0; pf_maxpf = 0; pf_pf2fcc = 0; #kvecs_pf2fcc = identity(3)
sym_maxpf = False; sym_sv2fcc = False; sym_minsv = False; sym_pf2fcc = False
a = rint(Nmesh**(1/3.0)); f = int(Nmesh/a/a)
print 'Target mesh number', Nmesh
B.vecs = Blatt/2/pi #Don't use 2pi constants in reciprocal lattice here
# B.pftarget = 0.7405 #default best packing fraction
B.pftarget = 0.35
#############End BCT lattice
eps = 1.0e-6
B.Nmesh = Nmesh
print 'B vectors (differ by 2pi from traditional)';print B.vecs #
#print 'B transpose'; print transpose(B.vecs)
B.det = det(B.vecs)
print 'Det of B', B.det
print 'Orth Defect of B', orthdef(B.vecs)
print 'Surf/vol of B', surfvol(B.vecs)
pfB = packingFraction(B.vecs)
print 'Packing fraction of B:', pfB
[B.symops,B.nops] = getGroup(B.vecs)
B.msymops = intsymops(B) #integer sym operations in B basis
# printops_eigs(B)
B.lattype = latticeType(B.nops)
print 'Lattice type:', B.lattype
A = lattice()
A.vecs = trimSmall(inv(transpose(B.vecs)))
[A.symops,A.nops] = getGroup(A.vecs)
A.msymops = intsymops(A)
print 'Real space lattice A'; print A.vecs
print 'Det A', det(A.vecs)
pfA = packingFraction(A.vecs)
print 'Packing fraction of A:', pfA
pf_orth=0; pf_orth2fcc=0; sym_orth = False; sym_orth2fcc = False
if B.lattype in ['Orthorhombic', 'Tetragonal','Cubic']:
cbest = '' #need for passing other structures' results to main program
[kvecs_orth,pf_orth,sym_orth] = orthsuper(B)
M = rint(dot(inv(kvecs_orth),B.vecs)).astype(int)
print; print 'Try orth2FCC substitution.',
kmesh2 = zeros((3,3),dtype = float)
scale = 2/4**(1/3.0)
kmesh2[:,0] = kvecs_orth[:,1]/scale + kvecs_orth[:,2]/scale
kmesh2[:,1] = kvecs_orth[:,2]/scale + kvecs_orth[:,0]/scale
kmesh2[:,2] = kvecs_orth[:,0]/scale + kvecs_orth[:,1]/scale
sym_orth2fcc = checksymmetry(kmesh2,B)
if sym_orth2fcc:
pf = packingFraction(kmesh2)
print; print 'Packing fraction', pf, 'vs original B', pfB
if pf>pf_orth:
M = rint(dot(inv(kmesh2),B.vecs)).astype(int)
print 'M';print M
else:
' Packing fraction too small'
kvecs_orth2fcc = kmesh2
pf_orth2fcc = pf
else:
print' It fails symmetry test'
# sys.exit('stop')
else:
#'--------------------------------------------------------------------------------------------------------'
#'--------------------------------------------------------------------------------------------------------'
M = zeros((3,3),dtype=int)
ctest = []
type = 'maxpfsym'; print type
ctrials = [3]
for c in ctrials:
M = array([[-a+2, a/c , a/c],[a/c,-a,a/c],[a/c,a/c,-a-2]]) #bcc like best avg pf on 50: 0.66
# M = array([[2, a/c , a/c],[a/c,0,a/c],[a/c,a/c,-2]]) #fcc like best avg pf on 50: 0.59
M = rint(M * (B.Nmesh/abs(det(M)))**(1/3.0))
print 'Start mesh trial'; print M
[M,K] = findmin(M,B,type)
print 'Test trial M'; print M
ctest.append(cost(M,B,type))
# print'Trial costs',ctest
cbest = ctrials[argmin(ctest)]
# print'Best c', cbest
iternpf = 0
itermaxnpf = 10
itermaxsym = 5
# bestpf = 100
# NPFcost = 100;delNPFcost = -1 #initial values
type = 'maxpfsym'; print type
delcost = -1; lowcost = 1000 #initialize
#### while iternpf<itermaxnpf and delNPFcost <0 and abs(delNPFcost)>0.1 :
while iternpf<itermaxnpf and delcost < -0.1:
oldcost = cost(M,B,type)
# NPFcost = cost(M,B,'maxpf')
# delNPFcost = (NPFcost-oldNPFcost)/NPFcost :
'''Here we let M vary in the search, but record pf and kvecs when we find min cost'''
# print 'cost(N,PF):', cost(M,B,type)
# while not symm and and iternpf<itermax:
M = rint(M * (B.Nmesh/abs(det(M)))**(1/3.0))
print 'Scaled M';print M
iternpf += 1
print 'Iteration',type,iternpf, '**********'
[M,K] = findmin(M,B,type)
print M
itersym = 0
symm = False
while not symm and itersym <itermaxsym:
itersym += 1
print 'Symmetry iteration', itersym, '-------'
# print 'Nmesh', abs(det(M)), 'packing', packingFraction(dot(B.vecs,inv(M)))
M = minkM(M,B)#; print'Mink reduced M'; print M
for iop in range(B.nops):
M = findmin_i(M,B,iop)
if abs(det(M)-B.Nmesh)/B.Nmesh > 0.15: #how far off from target N
M = rint(M * (B.Nmesh/abs(det(M)))**(1/3.0))
print 'Scaled M';print M
K = lattice();K.vecs = trimSmall(dot(B.vecs,inv(M)));K.det = abs(det(K.vecs)); K.Nmesh = B.det/K.det
symm = checksymmetry(K.vecs,B)
print 'Symmetry check', symm
if symm:
newcost = cost(M,B,type)
if newcost - lowcost < 0:
lowcost = newcost;
print'New lowcost',newcost
pf_maxpf = packingFraction(K.vecs)
sym_maxpf = True
kvecs_maxpf = K.vecs
# if pf_maxpf<bestpf: bestpf = pf_maxpf; bestM = M
print 'Packing fraction', pf_maxpf, 'vs original B', pfB
print 'Nmesh', K.Nmesh, 'vs target', B.Nmesh
print; print 'Try FCC-like substitution.'
kmesh2 = zeros((3,3),dtype = float)
scale = 2/4**(1/3.0)
kmesh2[:,0] = K.vecs[:,1]/scale + K.vecs[:,2]/scale
kmesh2[:,1] = K.vecs[:,2]/scale + K.vecs[:,0]/scale
kmesh2[:,2] = K.vecs[:,0]/scale + K.vecs[:,1]/scale
# M = rint(dot(inv(kmesh2),B.vecs)).astype(int) #set this for maxpf run
if checksymmetry(kmesh2,B):
sym_pf2fcc = True
kvecs_pf2fcc = kmesh2
pf_pf2fcc = packingFraction(kmesh2)
Mtemp = rint(dot(inv(kmesh2),B.vecs)).astype(int)
if cost(Mtemp,B,type) < lowcost:
lowcost = cost(M,B,type);print'New lowcost',lowcost
M = Mtemp
print 'M';print Mtemp
print 'Packing fraction', pf_pf2fcc, 'vs original B', pfB
print;
else:
print ' Packing fraction too small'
else:
print ' Fails to improve mesh'
delcost = cost(M,B,type) - oldcost
# Summary
pfs = [pfB]
pftypes = ['B_latt']
ks = [B.vecs/a]
if not (sym_minsv or sym_sv2fcc or sym_maxpf or pf_pf2fcc or sym_orth or sym_orth2fcc):
meshtype = 'B_latt_revert' ; #status += 'MHPrevert;'
K.vecs = B.vecs/a; K.det = abs(det(K.vecs)); K.Nmesh = abs(B.det/K.det)
pfmax = packingFraction(K.vecs)
else:
if sym_orth:
pfs.append(pf_orth)
pftypes.append('orth')
ks.append(kvecs_orth)
if sym_orth2fcc:
pfs.append(pf_orth2fcc)
pftypes.append('orth2fcc')
ks.append(kvecs_orth2fcc)
if sym_maxpf:
pfs.append(pf_maxpf)
pftypes.append('maxpf')
ks.append(kvecs_maxpf)
if sym_pf2fcc:
pfs.append(pf_pf2fcc)
pftypes.append('pf2fcc')
ks.append(kvecs_pf2fcc)
pfmax = max(pfs)
meshtype = pftypes[argmax(pfs)]
K.vecs = ks[argmax(pfs)]; K.det = abs(det(K.vecs)); K.Nmesh = B.det/K.det
# return [K.vecs, K.Nmesh, B.Nmesh, B.lattype, pfB, pf_orth, pf_orth2fcc, pf_maxpf, pf_minsv, pf_sv2fcc, pfmax, meshtype, fcctype(B),status]
return [K.vecs, K.Nmesh, B.Nmesh, B.lattype, pfB, pf_orth, pf_orth2fcc, pf_maxpf, pf_pf2fcc, pfmax, meshtype, fcctype(B),cbest,status]
#crystal = [1,1,sqrt(2),90,90,120] # [a,b,c,alpha,beta,gamma] #crystal = [2,3*sqrt(3),11*sqrt(2),90,90,20] # [a,b,c,alpha,beta,gamma] #crystal = [2,2,2,80,80,80] # [a,b,c,alpha,beta,gamma] #B.vecs = transpose(lattice_vecs(crystal)) #############End BCT lattice eps = 1.0e-6 B.det = det(B.vecs) B.Nmesh = Nmesh print 'B vectors';print B.vecs #print 'B transpose'; print transpose(B.vecs) print 'Det of B', B.det print 'Orth Defect of B', orthdef(B.vecs) print 'Surf/vol of B', surfvol(B.vecs) [B.symops,B.nops] = getGroup(B.vecs) print 'Number of symmetry operations', B.nops #print 'symmetry operations of B\n' #for j in range(nopsB): # print j # op = array(symopsB[:,:,j]) # print op #find real lattice A.vecs = trimSmall(transpose(inv(B.vecs))) A.det = det(A.vecs) A.Nmesh = Nmesh print;print 'A vectors';print A.vecs print 'Det of A', A.det print 'Orth Defect of A', orthdef(A.vecs) print 'Surf/vol of A', surfvol(A.vecs)
def bestmeshIter_vary_N(Blatt, Nmesh, path):
'''The kmesh can be related to the reciprocal lattice B by B = KM, where M is an integer 3x3 matrix
So K = B Inv(M). Change M one element at a time to minimize the errors in symmetry and the cost in S/V and Nmesh '''
##############################################################
########################## Script ############################
vaspinputdir = '/fslhome/bch/cluster_expansion/alir/AFLOWDATAf1_50e/vaspinput/'
M = zeros((3, 3), dtype=int)
S = zeros((3, 3), dtype=fprec)
B = lattice()
A = lattice()
K = lattice()
status = ''
pf_minsv = 0
pf_sv2fcc = 0
pf_maxpf = 0
pf_pf2fcc = 0
#kvecs_pf2fcc = identity(3)
sym_maxpf = False
sym_sv2fcc = False
sym_minsv = False
sym_pf2fcc = False
a = rint(Nmesh**(1 / 3.0))
f = int(Nmesh / a / a)
print 'Target mesh number', Nmesh
B.vecs = Blatt / 2 / pi #Don't use 2pi constants in reciprocal lattice here
# B.pftarget = 0.7405 #default best packing fraction
#############End BCT lattice
eps = 1.0e-6
B.Nmesh = Nmesh
print 'B vectors (differ by 2pi from traditional)'
print B.vecs #
#print 'B transpose'; print transpose(B.vecs)
B.det = det(B.vecs)
print 'Det of B', B.det
print 'Orth Defect of B', orthdef(B.vecs)
print 'Surf/vol of B', surfvol(B.vecs)
pfB = packingFraction(B.vecs)
print 'Packing fraction of B:', pfB
[B.symops, B.nops] = getGroup(B.vecs)
B.msymops = intsymops(B) #integer sym operations in B basis
# print'Symmetry operators in basis of B'
# for i in range:
# print B.msymops[:,:,i];print
# printops_eigs(B)
B.lattype = latticeType(B.nops)
print 'Lattice type:', B.lattype
A = lattice()
A.vecs = trimSmall(inv(transpose(B.vecs)))
[A.symops, A.nops] = getGroup(A.vecs)
A.msymops = intsymops(A)
print 'Real space lattice A'
print A.vecs
print 'Det A', det(A.vecs)
pfA = packingFraction(A.vecs)
print 'Packing fraction of A:', pfA
meshesfile = open('meshesfile', 'a')
meshesfile.write('N target %i\n' % B.Nmesh)
meshesfile.write('Format: pf then Nmesh then kmesh\n\n')
pflist = []
# M0 = array([[2, 2, 2,],
# [2, 2, -2],
# [-2, 2, -2]])
#
# 0.74050000 64.000
#-5 1 -3
#6 2 2
#3 1 -3
M0 = array([[
-5,
1,
-3,
], [6, 2, 2], [3, 1, -3]])
# for div in [256,128,64,32,16,8,4,2,1]:
# print '\nDivisor',div
# nMP = rint((Nmesh/div)**(1/3.0))
# M = array([[nMP,0,0],[0,nMP,0],[0,0,nMP]]);
for fac in [1, 2, 3, 4, 5, 6, 7, 8]:
print '\nMultiplier', fac
M = fac * M0
# M = array([[4,12,-4],
# [-11,4,-26],
# [-26,-4,-11]]);
K = lattice()
K.vecs = trimSmall(dot(B.vecs, inv(M)))
K.det = abs(det(K.vecs))
K.Nmesh = B.det / K.det
print 'Number of points', det(M)
print 'Check M'
print M
print 'Check K'
print K.vecs
print 'Check B'
print B.vecs
print 'Check pf'
print packingFraction(K.vecs)
#create a dir and prepare for vasp run
newdir = str(K.Nmesh)
newpath = path + newdir + '/'
if not os.path.isdir(newpath):
os.system('mkdir %s' % newpath)
os.chdir(newpath)
os.system('cp %s* %s' % (vaspinputdir, newpath))
os.system('cp %sPOSCAR %s' % (path, newpath))
writekpts_vasp_M(newpath, B, M, K)
# writekpts_vasp_pf(newpath,K.vecs,pf_maxpf,K.Nmesh)
writejobfile(newpath)
# print 'submitting job'
subprocess.call(['sbatch', 'vaspjob']) #!!!!!!! Submit jobs
os.chdir(path)
def bestmeshIter_vary_pf(Blatt,Nmesh,path):
'''The kmesh can be related to the reciprocal lattice B by B = KM, where M is an integer 3x3 matrix
So K = B Inv(M). Change M one element at a time to minimize the errors in symmetry and the cost in S/V and Nmesh '''
##############################################################
########################## Script ############################
# print path.split('/')
npathsegs = len(path.split('/'))
# print npathsegs
vaspinputdir = '/'.join(path.split('/')[0:npathsegs-3])+'/vaspinput/' #up two levels, 2 are for spaces at beg and end
# print vaspinputdir
M = zeros((3,3),dtype = int)
S = zeros((3,3),dtype = fprec)
B = lattice()
A = lattice()
K = lattice()
status = ''
pf_minsv = 0; pf_sv2fcc = 0; pf_maxpf = 0; pf_pf2fcc = 0; #kvecs_pf2fcc = identity(3)
sym_maxpf = False; sym_sv2fcc = False; sym_minsv = False; sym_pf2fcc = False
print 'Target mesh number', Nmesh
B.vecs = Blatt/2/pi #Don't use 2pi constants in reciprocal lattice here
# B.pftarget = 0.7405 #default best packing fraction
#############End BCT lattice
eps = 1.0e-6
B.Nmesh = Nmesh
print 'B vectors (differ by 2pi from traditional)';print B.vecs #
#print 'B transpose'; print transpose(B.vecs)
B.det = det(B.vecs)
print 'Det of B', B.det
print 'Orth Defect of B', orthdef(B.vecs)
print 'Surf/vol of B', surfvol(B.vecs)
pfB = packingFraction(B.vecs)
print 'Packing fraction of B:', pfB
[B.symops,B.nops] = getGroup(B.vecs)
B.msymops = intsymops(B) #integer sym operations in B basis
# print'Symmetry operators in basis of B'
# for i in range:
# print B.msymops[:,:,i];print
# printops_eigs(B)
B.lattype = latticeType(B.nops)
print 'Lattice type:', B.lattype
A = lattice()
A.vecs = trimSmall(inv(transpose(B.vecs)))
[A.symops,A.nops] = getGroup(A.vecs)
A.msymops = intsymops(A)
print 'Real space lattice A'; print A.vecs
print 'Det A', det(A.vecs)
pfA = packingFraction(A.vecs)
print 'Packing fraction of A:', pfA
# print 'current dir for meshesfile', os.getcwd()
meshesfile = open('meshesfile','w')
# meshesfile = open('meshesfile2','w')
meshesfile.write('N target %i\n' % B.Nmesh)
meshesfile.write('Format: pf then Nmesh then kmesh\n\n')
pflist = []
# for pftry in frange(pfB/2,0.75,0.005):
for pftry in frange(pfB/2,0.75,0.01):
# for pftry in frange(.3,0.505,0.005):
print '\nPacking fraction target',pftry
B.pftarget = pftry
pf_orth=0; pf_orth2fcc=0; sym_orth = False; sym_orth2fcc = False
#'--------------------------------------------------------------------------------------------------------'
#'--------------------------------------------------------------------------------------------------------'
M = zeros((3,3),dtype=int)
ctest = []
type = 'maxpfsym'; print type
ctrials = [3]
a = rint(Nmesh**(1/3.0));# f = int(Nmesh/a/a)
randnums = zeros(9)
print 'M scale a',a
for c in ctrials:
# ri = [randint(5) for i in range(9)]
# M = array([[-a+ri[0], a/c +ri[1] , a/c+ri[2]],[a/c+ri[3],-a+ri[4],a/c+ri[5]],\
# [a/c+ri[6],a/c+ri[7],-a+ri[8]]]) #bcc like best avg pf on 50: 0.66
#HNF::::::
M = array([[a, 0 , 0],
[a/c,a,0],\
[a/c,a/c,a]]) #bcc like best avg pf on 50: 0.66
#
# M = array([[-a+1, a/c , a/c],[a/c,-a,a/c],[a/c,a/c,-a-1]]) #bcc like best avg pf on 50: 0.66
# M = array([[a, 0,0],[0,a,0],[0,0,a+3]])
# M = array([[-16 , 1 , 5 ],
# [6 , -10 , 5],
# [-6 , -1 , 6 ]])
# M = array([[5, a/c , a/c],[a/c,0,a/c],[a/c,a/c,-5]]) #fcc like best avg pf on 50: 0.59
M = rint(M * (B.Nmesh/abs(det(M)))**(1/3.0))
print 'Start mesh trial'; print M
# [M,K] = findmin(M,B,type)
# print 'Test trial M'; print M
ctest.append(cost(M,B,type))
# print'Trial costs',ctest
cbest = ctrials[argmin(ctest)]
# print'Best c', cbest
iternpf = 0
itermaxnpf = 10
itermaxsym = 5
# bestpf = 100
# NPFcost = 100;delNPFcost = -1 #initial values
type = 'maxpfsym'; print type
delcost = -1; lowcost = 1000 #initialize
#### while iternpf<itermaxnpf and delNPFcost <0 and abs(delNPFcost)>0.1 :
while iternpf<itermaxnpf and delcost < -0.1:
oldcost = cost(M,B,type)
# NPFcost = cost(M,B,'maxpf')
# delNPFcost = (NPFcost-oldNPFcost)/NPFcost :
'''Here we let M vary in the search, but record pf and kvecs when we find min cost'''
# print 'cost(N,PF):', cost(M,B,type)
# while not symm and and iternpf<itermax:
M = rint(M * (B.Nmesh/abs(det(M)))**(1/3.0))
print 'Scaled M';print M
iternpf += 1
print 'Iteration',type,iternpf, '**********'
[M,K] = findmin(M,B,type)
M = rint(M)
itersym = 0
symm = False
while not symm and itersym <itermaxsym:
itersym += 1
print 'Symmetry iteration', itersym, '-------'
# print 'Nmesh', abs(det(M)), 'packing', packingFraction(dot(B.vecs,inv(M)))
# M = rint(minkM(M,B))#; print'Mink reduced M'; print M
for iop in range(B.nops):
M = rint(findmin_i(M,B,iop))
# M = rint(minkM(M,B))#; print'Mink reduced M'; print M
if abs(det(M)-B.Nmesh)/B.Nmesh > 0.15: #how far off from target N
M = rint(M * (B.Nmesh/abs(det(M)))**(1/3.0))
print 'Scaled M';print M
K = lattice();K.vecs = trimSmall(dot(B.vecs,inv(M)));K.det = abs(det(K.vecs)); K.Nmesh = B.det/K.det
symm = checksymmetry(K.vecs,B)
print 'Symmetry check', symm
if symm:
newcost = cost(M,B,type)
if newcost - lowcost < 0:
lowcost = newcost;
print'New lowcost',newcost
pf_maxpf = packingFraction(K.vecs)
sym_maxpf = True
kvecs_maxpf = K.vecs
# if pf_maxpf<bestpf: bestpf = pf_maxpf; bestM = M
print 'Packing fraction', pf_maxpf, 'vs original B', pfB
print 'Nmesh', K.Nmesh, 'vs target', B.Nmesh
delcost = cost(M,B,type) - oldcost
#write to files
# meshesfile.write('Packing fraction target %f\n' % pftry)
if symm and pf_maxpf not in pflist:
pflist.append(pf_maxpf)
# meshesfile.write('Packing fraction achieved %f\n' % pf_maxpf)
meshesfile.write('%12.8f %8.3f \n' % (pf_maxpf,K.Nmesh))
# meshesfile.write('M\n')
# for i in range(3):
# for j in range(3):
# meshesfile.write('%i6' %M[i,j])
# meshesfile.write('\n')
## meshesfile.write('\n')
# meshesfile.write('k mesh\n')
M = rint(dot(inv(K.vecs),B.vecs))
for i in range(3):
for j in range(3):
meshesfile.write('%i ' % int(rint(M[i,j])))
meshesfile.write('\n')
meshesfile.write('\n')
meshesfile.flush()
M = rint(dot(inv(K.vecs),B.vecs)) #We assign K only when M is ideal, so remake the best M
print 'Check M'
print M
print 'Check K'
print K.vecs
print 'Check B'
print B.vecs
print 'Check pf'
print packingFraction(K.vecs)
#create a dir and prepare for vasp run
newdir = str(round(pf_maxpf,4))
newpath = path + newdir + '/'
if not os.path.isdir(newpath):
os.system('mkdir %s' % newpath)
os.chdir(newpath)
os.system ('cp %s* %s' % (vaspinputdir,newpath))
os.system ('cp %sPOSCAR %s' % (path,newpath))
print 'SKIPPING writekpts_vasp_M AND submission'
# writekpts_vasp_M(newpath,B,M,K)
# writekpts_vasp_pf(newpath,K.vecs,pf_maxpf,K.Nmesh)
writejobfile(newpath)
# subprocess.call(['sbatch', 'vaspjob']) #!!!!!!! Submit jobs
os.chdir(path)
else:
'do nothing'
# meshesfile.write('Failed symmetry\n\n')
meshesfile.close()
# Summary
pfs = [pfB]
pftypes = ['B_latt']
ks = [B.vecs/a] #one solutions is to simply divide B by an integer
if not (sym_minsv or sym_sv2fcc or sym_maxpf or pf_pf2fcc or sym_orth or sym_orth2fcc):
meshtype = 'B_latt_revert' ; #status += 'MHPrevert;'
K.vecs = B.vecs/a; K.det = abs(det(K.vecs)); K.Nmesh = abs(B.det/K.det)
pfmax = packingFraction(K.vecs)
else:
if sym_orth:
pfs.append(pf_orth)
pftypes.append('orth')
ks.append(kvecs_orth)
if sym_orth2fcc:
pfs.append(pf_orth2fcc)
pftypes.append('orth2fcc')
ks.append(kvecs_orth2fcc)
if sym_maxpf:
pfs.append(pf_maxpf)
pftypes.append('maxpf')
ks.append(kvecs_maxpf)
if sym_pf2fcc:
pfs.append(pf_pf2fcc)
pftypes.append('pf2fcc')
ks.append(kvecs_pf2fcc)
pfmax = max(pfs)
meshtype = pftypes[argmax(pfs)]
K.vecs = ks[argmax(pfs)]; K.det = abs(det(K.vecs)); K.Nmesh = B.det/K.det
# return [K.vecs, K.Nmesh, B.Nmesh, B.lattype, pfB, pf_orth, pf_orth2fcc, pf_maxpf, pf_minsv, pf_sv2fcc, pfmax, meshtype, fcctype(B),status]
return [K.vecs, K.Nmesh, B.Nmesh, B.lattype, pfB, pf_orth, pf_orth2fcc, pf_maxpf, pf_pf2fcc, pfmax, meshtype, fcctype(B),cbest,status]
def bestmeshIter_vary_N(Blatt,Nmesh,path):
'''The kmesh can be related to the reciprocal lattice B by B = KM, where M is an integer 3x3 matrix
So K = B Inv(M). Change M one element at a time to minimize the errors in symmetry and the cost in S/V and Nmesh '''
##############################################################
########################## Script ############################
vaspinputdir = '/fslhome/bch/cluster_expansion/alir/AFLOWDATAf1_50e/vaspinput/'
M = zeros((3,3),dtype = int)
S = zeros((3,3),dtype = fprec)
B = lattice()
A = lattice()
K = lattice()
status = ''
pf_minsv = 0; pf_sv2fcc = 0; pf_maxpf = 0; pf_pf2fcc = 0; #kvecs_pf2fcc = identity(3)
sym_maxpf = False; sym_sv2fcc = False; sym_minsv = False; sym_pf2fcc = False
a = rint(Nmesh**(1/3.0)); f = int(Nmesh/a/a)
print 'Target mesh number', Nmesh
B.vecs = Blatt/2/pi #Don't use 2pi constants in reciprocal lattice here
# B.pftarget = 0.7405 #default best packing fraction
#############End BCT lattice
eps = 1.0e-6
B.Nmesh = Nmesh
print 'B vectors (differ by 2pi from traditional)';print B.vecs #
#print 'B transpose'; print transpose(B.vecs)
B.det = det(B.vecs)
print 'Det of B', B.det
print 'Orth Defect of B', orthdef(B.vecs)
print 'Surf/vol of B', surfvol(B.vecs)
pfB = packingFraction(B.vecs)
print 'Packing fraction of B:', pfB
[B.symops,B.nops] = getGroup(B.vecs)
B.msymops = intsymops(B) #integer sym operations in B basis
# print'Symmetry operators in basis of B'
# for i in range:
# print B.msymops[:,:,i];print
# printops_eigs(B)
B.lattype = latticeType(B.nops)
print 'Lattice type:', B.lattype
A = lattice()
A.vecs = trimSmall(inv(transpose(B.vecs)))
[A.symops,A.nops] = getGroup(A.vecs)
A.msymops = intsymops(A)
print 'Real space lattice A'; print A.vecs
print 'Det A', det(A.vecs)
pfA = packingFraction(A.vecs)
print 'Packing fraction of A:', pfA
meshesfile = open('meshesfile','a')
meshesfile.write('N target %i\n' % B.Nmesh)
meshesfile.write('Format: pf then Nmesh then kmesh\n\n')
pflist = []
# M0 = array([[2, 2, 2,],
# [2, 2, -2],
# [-2, 2, -2]])
#
# 0.74050000 64.000
#-5 1 -3
#6 2 2
#3 1 -3
M0 = array([[-5, 1, -3,],
[6, 2, 2],
[3, 1, -3]])
# for div in [256,128,64,32,16,8,4,2,1]:
# print '\nDivisor',div
# nMP = rint((Nmesh/div)**(1/3.0))
# M = array([[nMP,0,0],[0,nMP,0],[0,0,nMP]]);
for fac in [1,2,3,4,5,6,7,8]:
print '\nMultiplier',fac
M = fac*M0
# M = array([[4,12,-4],
# [-11,4,-26],
# [-26,-4,-11]]);
K = lattice();K.vecs = trimSmall(dot(B.vecs,inv(M)));K.det = abs(det(K.vecs)); K.Nmesh = B.det/K.det
print 'Number of points',det(M)
print 'Check M'
print M
print 'Check K'
print K.vecs
print 'Check B'
print B.vecs
print 'Check pf'
print packingFraction(K.vecs)
#create a dir and prepare for vasp run
newdir = str(K.Nmesh)
newpath = path + newdir + '/'
if not os.path.isdir(newpath):
os.system('mkdir %s' % newpath)
os.chdir(newpath)
os.system ('cp %s* %s' % (vaspinputdir,newpath))
os.system ('cp %sPOSCAR %s' % (path,newpath))
writekpts_vasp_M(newpath,B,M,K)
# writekpts_vasp_pf(newpath,K.vecs,pf_maxpf,K.Nmesh)
writejobfile(newpath)
# print 'submitting job'
subprocess.call(['sbatch', 'vaspjob']) #!!!!!!! Submit jobs
os.chdir(path)