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]
print "New real lattice"
reallatt = 2 * np.pi**np.linalg.inv(np.transpose(reciplatt))
print reallatt
pos.write_poscar('POSCAR')
# [descriptor, scale, latticevecs, reciplatt, natoms, postype, positions] = km.readposcar('POSCAR0',path) #
# print 'lattice from aconvasp --sprim < POSCAR0 > POSCAR'
## print 'lattice from aconvasp --sprim < POSCAR0 > POSCAR'
# print latticevecs
# print
# print 'reciprocal lattice vectors'
# print reciplatt
# print
# reciplatt = np.array((pos.bvecs[0],pos.bvecs[1],pos.bvecs[2]))
# print reciplatt
## print 'bvecs'
## print pos.bvecs
## print pos.bvecs[1,:]
# [mesh_ns, irrat] = km.svmesh(N,pos.bvecs)
[mesh_ns, irrat] = km.svmesh(N, reciplatt)
km.writekpts_vasp(maindir, dir, 'KPOINTS', mesh_ns) #correct kmesh
print mesh_ns, 's/v method'
# if len(irrat)>0:
# print dir, irrat
print irrat
os.system('rm slurm*')
subprocess.call(['rm', 'vasp.out'])
subprocess.call(['rm', 'OUTCAR'])
# subprocess.call(['sbatch', 'vaspjob'])
os.chdir(maindir)
print 'Done'
print "New real lattice"
reallatt = 2*np.pi**np.linalg.inv(np.transpose(reciplatt))
print reallatt
pos.write_poscar('POSCAR')
# [descriptor, scale, latticevecs, reciplatt, natoms, postype, positions] = km.readposcar('POSCAR0',path) #
# print 'lattice from aconvasp --sprim < POSCAR0 > POSCAR'
## print 'lattice from aconvasp --sprim < POSCAR0 > POSCAR'
# print latticevecs
# print
# print 'reciprocal lattice vectors'
# print reciplatt
# print
# reciplatt = np.array((pos.bvecs[0],pos.bvecs[1],pos.bvecs[2]))
# print reciplatt
## print 'bvecs'
## print pos.bvecs
## print pos.bvecs[1,:]
# [mesh_ns, irrat] = km.svmesh(N,pos.bvecs)
[mesh_ns, irrat] = km.svmesh(N,reciplatt)
km.writekpts_vasp(maindir,dir,'KPOINTS',mesh_ns) #correct kmesh
print mesh_ns, 's/v method'
# if len(irrat)>0:
# print dir, irrat
print irrat
os.system('rm slurm*')
subprocess.call(['rm', 'vasp.out'])
subprocess.call(['rm', 'OUTCAR'])
# subprocess.call(['sbatch', 'vaspjob'])
os.chdir(maindir)
print 'Done'
os.chdir(currdir)
print currdir
file1 = open(testfile,'r')
vaspout = file1.readlines()
file1.close()
for i in [4,5,6,7]:
print vaspout[i].replace('\n','')
kmesh = km.getkpts_vasp(currdir)
print kmesh, kmesh[0]*kmesh[1]*kmesh[2]
[descriptor, scale, reallatt, natoms, type_pos, positions] [natoms,reallatt,reciplatt] = km.readposcar('POSCAR',currdir)
Nkppra = 10000
N = np.rint(Nkppra/natoms).astype(int)
print 'natoms', natoms
print 'reciplatt'
print reciplatt
print 'mesh', km.svmesh(N,reciplatt)
# os.system('grep -i "bad news" slurm*')
# os.system('grep -i kpts slurm*')
# os.system('grep -i exceed slurm*')
# os.system('grep -i sgrcon slurm*')
# os.system('grep -i bad vasp.out')
# print subprocess.call(['grep','-i','bad','vasp.out'])
# slurm = os.system('find slurm*')
slurms = [f for f in os.listdir(os.getcwd()) if 'slurm' in f]
for slurm in slurms:
km.regpy_nocase('bad',currdir+slurm)
# print subprocess.check_output(['grep','-i','bad','vasp.out'])
# print slurm
# km.regpy_nocase('bad',currdir+ slurm)
km.regpy_nocase('bad',currdir+'vasp.out')
# subprocess.call(['grep','-i','bad','vasp.out'])
for dir in dirs:
if testfile in os.listdir(dir):
print
print dir
file1 = open(maindir + dir + '/' + testfile, 'r')
poscar = file1.readlines()
file1.close()
if len(poscar) > 0:
scale = np.sum(np.array(float(poscar[1])))
# print 'natoms', np.array(poscar[5].split(),dtype=np.int16)
N = np.rint(
Nkppra /
np.sum(np.array(poscar[5].split(), dtype=np.int16))).astype(
int) # number of kpts desired
reallatt[0, :] = np.array(poscar[2].split())
reallatt[1, :] = np.array(poscar[3].split())
reallatt[2, :] = np.array(poscar[4].split())
reallatt = scale * reallatt.astype(np.float)
# print reallatt
reciplatt = 2 * np.pi * np.transpose(np.linalg.inv(reallatt))
# print reciplatt
mesh_ns = km.svmesh(N, reciplatt)
print mesh_ns, 's/v method'
if 'KPOINTS.relax1' in os.listdir(dir):
os.chdir(dir)
os.system('cp KPOINTS.relax1 KPOINTS')
os.chdir(maindir)
print km.getkpts_vasp(dir), 'Aflow'
# writekpts_vasp(dir, mesh_ns)
#
print 'Done'
file1 = open(testfile, 'r')
vaspout = file1.readlines()
file1.close()
for i in [4, 5, 6, 7]:
print vaspout[i].replace('\n', '')
kmesh = km.getkpts_vasp(currdir)
print kmesh, kmesh[0] * kmesh[1] * kmesh[2]
[descriptor, scale, reallatt, natoms, type_pos,
positions][natoms, reallatt,
reciplatt] = km.readposcar('POSCAR', currdir)
Nkppra = 10000
N = np.rint(Nkppra / natoms).astype(int)
print 'natoms', natoms
print 'reciplatt'
print reciplatt
print 'mesh', km.svmesh(N, reciplatt)
# os.system('grep -i "bad news" slurm*')
# os.system('grep -i kpts slurm*')
# os.system('grep -i exceed slurm*')
# os.system('grep -i sgrcon slurm*')
# os.system('grep -i bad vasp.out')
# print subprocess.call(['grep','-i','bad','vasp.out'])
# slurm = os.system('find slurm*')
slurms = [f for f in os.listdir(os.getcwd()) if 'slurm' in f]
for slurm in slurms:
km.regpy_nocase('bad', currdir + slurm)
# print subprocess.check_output(['grep','-i','bad','vasp.out'])
# print slurm
# km.regpy_nocase('bad',currdir+ slurm)
km.regpy_nocase('bad', currdir + 'vasp.out')
# subprocess.call(['grep','-i','bad','vasp.out'])
reallatt = np.zeros((3,3))
os.chdir(maindir)
dirs= sorted([d for d in os.listdir(os.getcwd()) if os.path.isdir(d)])
for dir in dirs:
if testfile in os.listdir(dir):
print
print dir
file1 = open(maindir+dir+'/'+testfile,'r')
poscar = file1.readlines()
file1.close()
if len(poscar) >0:
scale = np.sum(np.array(float(poscar[1])))
# print 'natoms', np.array(poscar[5].split(),dtype=np.int16)
N = np.rint(Nkppra/np.sum(np.array(poscar[5].split(),dtype=np.int16))).astype(int) # number of kpts desired
reallatt[0,:] = np.array(poscar[2].split())
reallatt[1,:] = np.array(poscar[3].split())
reallatt[2,:] = np.array(poscar[4].split())
reallatt = scale*reallatt.astype(np.float)
# print reallatt
reciplatt = 2*np.pi*np.transpose(np.linalg.inv(reallatt))
# print reciplatt
mesh_ns = km.svmesh(N,reciplatt)
print mesh_ns, 's/v method'
if 'KPOINTS.relax1' in os.listdir(dir):
os.chdir(dir)
os.system('cp KPOINTS.relax1 KPOINTS')
os.chdir(maindir)
print km.getkpts_vasp(dir), 'Aflow'
# writekpts_vasp(dir, mesh_ns)
#
print 'Done'
