# print print print dir + '=========================' # mirdir = aflowdir+dir+'/' path = maindir+dir+'/' print path os.chdir(path) # os.system('cp %sKPOINTS .' % maindir) # os.system('cp %sINCAR .' % maindir) # os.system('cp %sPOTCAR .' % maindir) os.system('cp ../../KPOINTS .') #standard files 2 levels up os.system('cp ../../INCAR .') os.system('cp ../../POTCAR .') if vaspexec == 'vasp533mod': km.writekpts_vasp(maindir,dir+'/','KPOINTS',Nkppra) #correct 2 lines nameadd = 'mod' elif vaspexec == 'vasp533': nameadd = 'clean' km.writejobfile(maindir,dir+'/','vaspjob',nameadd,vaspexec) # if len(irrat)>0: # print dir, irrat # print irrat os.system('rm slurm*') # os.system('cp POSCAR.orig POSCAR') #in case aflow setup went too far. km.aflow2poscar(path) #generates POSCAR from aflow.in. A subprocess.call(['rm', 'vasp.out']) subprocess.call(['rm', 'OUTCAR']) subprocess.call(['sbatch', 'vaspjob']) os.chdir(maindir) #km.checkq('bch') #loops for days print 'Done'
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 print dir + '=========================' path = maindir + dir + '/' os.chdir(path) # os.system('rm POSCAR*') os.system('cp ../../KPOINTS .') os.system('cp ../../INCAR .') os.system('cp ../../POTCAR .') totatoms = km.aflow2poscar(path) # os.system('aconvasp --sprim < POSCAR0 > POSCAR') # back = subprocess.check_output(["echo", "Hello World!"]) # back = check_out(["echo", "Hello World!"]) # back = os.system('mink_reduction.py < POSCAR0 ') # back = subprocess.check_output(['mink_reduction.py',' <',' POSCAR0 '], shell=True,) # back = nstrip(subprocess.check_output(['mink_reduction.py < POSCAR0'], shell=True,).split()) # print 'back' # print back N = np.rint(Nkppra / totatoms).astype(int) pfile = open('POSCAR0', 'r') rlines = [i.strip() for i in pfile.readlines()] pos = POSCAR(lines=rlines) oldROD = pos.rod oldbvecs = np.array(pos.bvecs) print "Real lattice orth defect:", pos.orthogonality_defect
print print dir + '=========================' # mirdir = aflowdir+dir+'/' path = maindir + dir + '/' print path os.chdir(path) # os.system('cp %sKPOINTS .' % maindir) # os.system('cp %sINCAR .' % maindir) # os.system('cp %sPOTCAR .' % maindir) os.system('cp ../../KPOINTS .') #standard files 2 levels up os.system('cp ../../INCAR .') os.system('cp ../../POTCAR .') if vaspexec == 'vasp533mod': km.writekpts_vasp(maindir, dir + '/', 'KPOINTS', Nkppra) #correct 2 lines nameadd = 'mod' elif vaspexec == 'vasp533': nameadd = 'clean' km.writejobfile(maindir, dir + '/', 'vaspjob', nameadd, vaspexec) # if len(irrat)>0: # print dir, irrat # print irrat os.system('rm slurm*') # os.system('cp POSCAR.orig POSCAR') #in case aflow setup went too far. km.aflow2poscar(path) #generates POSCAR from aflow.in. A subprocess.call(['rm', 'vasp.out']) subprocess.call(['rm', 'OUTCAR']) subprocess.call(['sbatch', 'vaspjob']) os.chdir(maindir) #km.checkq('bch') #loops for days print 'Done'
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 print dir + '=========================' path = maindir+dir+'/' os.chdir(path) # os.system('rm POSCAR*') os.system('cp ../../KPOINTS .') os.system('cp ../../INCAR .') os.system('cp ../../POTCAR .') totatoms = km.aflow2poscar(path) # os.system('aconvasp --sprim < POSCAR0 > POSCAR') # back = subprocess.check_output(["echo", "Hello World!"]) # back = check_out(["echo", "Hello World!"]) # back = os.system('mink_reduction.py < POSCAR0 ') # back = subprocess.check_output(['mink_reduction.py',' <',' POSCAR0 '], shell=True,) # back = nstrip(subprocess.check_output(['mink_reduction.py < POSCAR0'], shell=True,).split()) # print 'back' # print back N = np.rint(Nkppra/totatoms).astype(int) pfile = open('POSCAR0','r') rlines = [i.strip() for i in pfile.readlines()] pos = POSCAR(lines=rlines) oldROD = pos.rod oldbvecs = np.array(pos.bvecs) print "Real lattice orth defect:",pos.orthogonality_defect