def read_data(address, struct_num):
xlist = []
ylist = []
counter = 0
for dir in os.listdir(address):
counter += 1
if counter % 10 == 0:
print("number of structures read: %d" % counter, end="\n")
if counter > struct_num and struct_num > 0:
break
# print("Structure ", counter, " is ", dir)
poscar = address / dir / "POSCAR"
oszicar = address / dir / "OSZICAR"
atoms, cell = utils.read_poscar(poscar)
atoms = utils.CN(atoms, cell)
nis_num = len(atoms)/2
code = utils.struc_code(atoms)
xlist.append(code)
eng = utils.read_oszicar(oszicar)
eng_bar = eng - eng_NiS * nis_num
ylist.append(eng_bar)
xsum = np.sum(code)
y_temp = np.divide(eng_bar, xsum)
x = np.array(xlist).T
y = np.array(ylist)
return x, y
print("reading vasp files to build the training set ...")
counter = 0
xlist = []
ylist = []
for dir_path in os.listdir(address):
counter += 1
print("Structure %s" % dir_path, end="\n")
# first read the unrelaxed structure
oszicar = address / dir_path / "OSZICAR"
if os.path.isfile(oszicar):
eng = utils.read_oszicar(
oszicar
) # red energy from oszicar. eng = 0.0 if simulation is not finished
if eng != 0.0: # deal with the simulation onle if it is finished
poscar = address / dir_path / "POSCAR"
atoms, cell = utils.read_poscar(poscar)
atom_num = len(atoms)
atoms = utils.CN(atoms, cell)
atoms = utils.steinhardt(atoms, cell, 2.55, [4, 6, 8, 10])
x, y = sinle_example(atoms, eng)
xlist.append(x)
ylist.append(y)
x = np.array(xlist)
y = np.array(ylist)
print(x.shape)
print(y.shape)
print(np.max(x))
h5f = h5py.File('old_datasets/surface_2D.h5', 'w')
h5f.create_dataset('x', data=x)
f.write('write_data %s/rlx.lmp\n' % (str(address)))
command = 'source /opt/LAMMPS/lammps-intel.sh; lmp_intel < ' + str(
address) + '/in.temp > ' + str(address) + '/out.lmp'
os.system(command)
# os.system('lmp_intel < in.temp')
for dir in os.listdir(address):
print(dir)
#
poscar = address / dir / "POSCAR"
# potcar = address / dir / "POTCAR"
# incar = address / dir / "INCAR"
# kpoints = address / dir / "KPOINTS"
# # read atoms from the original POSCAR file
atoms, cell = utils.read_poscar(poscar)
atoms = utils.CN(atoms, cell)
#
# # Make GEOM_OPT directory to geometry optimize the structure with lammps
geom_opt_dir = address / dir / "GEOM_OPT"
# if os.path.isdir(geom_opt_dir):
# command = 'rm -rf ' + str(geom_opt_dir)
# os.system(command)
#
# os.mkdir(geom_opt_dir)
# # copy VASP files to the GEOM_OPT directory
# cp_command = 'cp ' + str(incar) + ' ' + str(geom_opt_dir)
# os.system(cp_command)
# cp_command = 'cp ' + str(poscar) + ' ' + str(geom_opt_dir)
# os.system(cp_command)
# cp_command = 'cp ' + str(potcar) + ' ' + str(geom_opt_dir)