def getVCmesh(dir,method,targetNmesh,meshtype):
lastDir = os.getcwd()
meshc = dynamicPacking6.dynamicPack() #instance
[descriptor, scale, latticevecs, reciplatt, natoms, postype, positions] = readposcar('POSCAR',dir)
# create_poscar('POSCAR',descriptor, scale, latticevecs, natoms, postype, positions, path) #just to remove the scale problem
os.chdir(dir)
totatoms = sum(natoms)
atype = 1
aTypes = []
for natom in natoms:
for i in range(natom):
aTypes.append(atype)
atype += 1
aTypes = array(aTypes)
statusOK,nops = meshc.pack(latticevecs,reciplatt,totatoms,aTypes,postype,transpose(positions),targetNmesh,meshtype,dir,method)
os.chdir(lastDir)
return statusOK,nops
def getVCmesh(dir,targetNmesh,meshtype,params) :
lastDir = os.getcwd()
meshc = dynamicPacking7.dynamicPack() #instance
[descriptor, scale, latticevecs, reciplatt, natoms, postype, positions] = readposcar('POSCAR',dir)
# create_poscar('POSCAR',descriptor, scale, latticevecs, natoms, postype, positions, path) #just to remove the scale problem
os.chdir(dir)
totatoms = sum(natoms)
atype = 1
aTypes = []
for natom in natoms:
for i in range(natom):
aTypes.append(atype)
atype += 1
aTypes = array(aTypes)
statusOK,nops = meshc.pack(latticevecs,reciplatt,totatoms,aTypes,postype,transpose(positions),targetNmesh,meshtype,dir,params)
os.chdir(lastDir)
return statusOK,nops
if os.path.exists('meshsummary.csv'):
file1 = open('meshsummary.csv','a')
else:
file1 = open('meshsummary.csv','w')
file1.write('Structure,Lattice,amax/amin,pfB,pf_orth,pf_orth2fcc,pf_maxpf, pf_pf2fcc, pfmax, meshtype' + ',' \
+ 'Improvement,fcc compatibility,Nmesh,TargetNmesh,Nmesh/Target,cbest' + '\n')
#for i,dir in enumerate(dirs):
for dir in dirs:
path = maindir+'/'+dir
if testfile in os.listdir(path):
print
print dir + '=========================================================='
os.chdir(path)
# print readposcar('POSCAR',path)
[descriptor, scale, latticevecs, reciplatt, natoms, postype, positions] = readposcar('POSCAR',path) #
create_poscar('POSCAR',descriptor, scale, latticevecs, natoms, postype, positions, path) #just to remove the scale problem
os.chdir(maindir)
# print 'reciprocal lattice vectors (rows)';print reciplatt
totatoms = sum(natoms)
targetNmesh = Nkppra/totatoms
atype = 1
aTypes = []
for natom in natoms:
for i in range(natom):
aTypes.append(atype)
atype += 1
aTypes = array(aTypes)
meshc.pack(latticevecs,reciplatt,totatoms,aTypes,postype,transpose(positions),targetNmesh,meshtype,path,method)
sys.exit('stop')
file1 = open('meshsummary.csv', 'a')
file1.write('Structure,Lattice,amax/amin,pfB,pf_orth,pf_orth2fcc,pf_maxpf, pf_pf2fcc, pfmax, meshtype' + ',' \
+ 'Improvement,fcc compatibility,Nmesh,TargetNmesh,Nmesh/Target,cbest' + '\n')
#for i,directory in enumerate(dirs):
for directory in dirs:
path = maindir + directory + '/'
if testfile in os.listdir(path):
print
print directory + '=========================================================='
os.chdir(path)
# print readposcar('POSCAR',path)
[
descriptor, scale, latticevecs, reciplatt, natoms, postype,
positions
] = readposcar('POSCAR', path) #
create_poscar('POSCAR', descriptor, scale, latticevecs, natoms,
postype, positions,
path) #just to remove the scale problem
os.chdir(maindir)
# print 'reciprocal lattice vectors (rows)';print reciplatt
totatoms = sum(natoms)
Nmesh = Nkppra / totatoms
#RESTORE THIS [meshvecs, Nmesh, targetNmesh, lattype, pfB, pf_orth, pf_orth2fcc, pf_maxpf, pf_pf2fcc, pfmax, meshtype, fcctype,cbest, status] = bestmeshIter(reciplatt,Nmesh)
# for trials where we want to vary pf for testing
meshesfile = open('meshesfile', 'w')
meshesfile.write(directory + ' ============\n')
[
meshvecs, Nmesh, targetNmesh, lattype, pfB, pf_orth, pf_orth2fcc,
pf_maxpf, pf_pf2fcc, pfmax, meshtype, fcctype, cbest, status
print
print '(* {} *)'.format(struct),
#get bounds from local data
bounds = [[], []]
blines = readfile('{}/{}/bounds'.format(paths[0], struct))
for line in blines:
bounds[0].append(
array([float(str) for str in line.split()[:3]]))
bounds[1].append(float(line.split()[3]))
#read sym operators
#get first run folder
dir1 = os.listdir(os.getcwd())[0]
[
descriptor, scale, latticevecs, reciplatt, natoms,
postype, positions
] = readposcar('POSCAR', dir1)
totatoms = sum(natoms)
atype = 1
aTypes = []
for natom in natoms:
for i in range(natom):
aTypes.append(atype)
atype += 1
aTypes = array(aTypes)
[symopsList,
fracsList] = get_spaceGroup(transpose(latticevecs),
aTypes, positions, 1e-3,
postype.lower()[0] == 'd')
# get_spaceGroup(transpose(A),aTypes,transpose(aPos),1e-3,postype.lower()[0] == 'd')
nops = len(symopsList)
symops = zeros((3, 3, nops), dtype=float)
#sys.stdout = open('testvasp.dat', 'w')
for dir in dirs:
print
print dir +' ***************'
if testfile in os.listdir(dir):
currdir = maindir + dir +'/'
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:
print
print dir + ' ***************'
if testfile in os.listdir(dir):
currdir = maindir + dir + '/'
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:
