def __init__(self, name="Siesta Job", label="siesta"):
self.xyz = base_xyz()
self.name = name
self.label = label
self.incharge = [
"PAO.FixSplitTable",
]
self.params = {}
def __init__(self):
self.params = {}
self.coordinates = coordinates()
self.species = species()
self.velocities = velocities()
self.xyz = base_xyz()
#self.pseudo = qe_pseudo()
self.ifstatic = True # used to determine how to put atomic coordinates to input file
def __init__(self):
self.xyz = base_xyz()
self.pseudo = qe_pseudo()
self.cell_params = {
"cell_dynamics": None,
"press": None,
"wmass": None,
"cell_factor": None,
"press_conv_thr": None,
"cell_dofree": None,
}
self.kpoints_option = "automatic"
self.kpoints_mp = [1, 1, 1, 0, 0, 0]
self.ifstatic = True # used to determine how to put atomic coordinates to input file
self.atomic_forces_status = False # default is no force acting on system
def __init__(self):
#super().__init__()
self.xyz = base_xyz()
self.params = {
"SEED": None,
}
self.status = False
self.cell = cp2k_subsys_cell()
self.colvar = cp2k_subsys_colvar()
self.coord = cp2k_subsys_coord()
self.core_coord = cp2k_subsys_core_coord()
self.core_velocity = cp2k_subsys_core_velocity()
self.kind = cp2k_subsys_kind()
self.multipoles = cp2k_subsys_multipoles()
self.printout = cp2k_subsys_print()
self.rng_init = cp2k_subsys_rng_init()
self.shell_coord = cp2k_subsys_shell_coord()
self.shell_velocity = cp2k_subsys_shell_velocity()
self.topology = cp2k_subsys_topology()
self.velocity = cp2k_subsys_velocity()
# basic_setting
self.kind.status = True
self.cell.status = True
self.topology.status = True
def __init__(self):
self.xyz = base_xyz()
self.status = True
#
self.coordtype = "cartesian" # can be cartesian or reduced
def get_xyz(self, filepath):
self.xyz = base_xyz()
self.xyz.get_xyz(filepath)
help="vasp pot databse directory")
parser.add_argument("--siesta-pot-dir", type=str,
default=os.path.join(os.path.expanduser("~"), ".pot-siesta"),
help="vasp pot databse directory")
args = parser.parse_args()
print("=================================================================\n")
print(" pot-from-xyz-modified.py\n")
print("-----------------------------------------------------------------\n")
print("generate PseudoPotential file from information on the xyz file.\n")
print("\n")
xyz = base_xyz()
xyz.get_xyz(args.xyz)
# --------------------------------------------------------------------------
# deal with program --------> Quantum ESPRESSO
# --------------------------------------------------------------------------
if args.program.lower() == "qe":
if args.qe_type.lower() == "paw_pbe":
pass
elif args.qe_type.lower() == "sssp_efficiency":
# use SSSP
# https://www.materialscloud.org/discover/sssp/table/efficiency
all_pseudos = os.listdir(os.path.join(args.qe_pot_dir, "SSSP_efficiency_pseudos"))
cmd = "cp "
for element in xyz.specie_labels:
for pseudo in all_pseudos:
def get_scf_params_and_run_info(self):
"""
self.run_info[]
start_time: the task start time
stop_time: the task stop time
scf_energies: all the energies during the scf procedure
#fermi_energy: fermi energy of the system (if output)
"""
self.run_info["scf_energies"] = []
for i in range(len(self.lines)):
# if it is an empty line continue to next line
if len(self.lines[i].split()) == 0:
continue
if self.lines[i].split()[0] == "Program" and self.lines[i].split()[1] == "PWSCF" and self.lines[i].split()[3] == "starts":
self.run_info["start_time"] = self.lines[i].split("\n")[0]
elif self.lines[i].split()[0] == "This" and self.lines[i].split()[1] == "run" and self.lines[i].split()[3] == "terminated":
self.run_info["stop_time"] = self.lines[i].split("\n")[0]
elif self.lines[i].split()[0] == "Parallel" and self.lines[i].split()[-1] == "processors":
self.run_info["processors"] = int(self.lines[i].split()[-2])
elif self.lines[i].split()[0] == "MPI" and self.lines[i].split()[-1] == "nodes":
self.run_info["nodes"] = int(self.lines[i].split()[-2])
elif self.lines[i].split()[0] == "bravais-lattice" and self.lines[i].split()[1] == "index":
self.scf_params["alat_au"] = float(self.lines[i+1].split()[4])
self.scf_params["nat"] = int(self.lines[i+3].split()[4])
self.scf_params["nelectron"] = float(self.lines[i+5].split()[4])
self.scf_params["n_ks_state"] = int(self.lines[i+6].split("=")[1])
self.scf_params["ecutwfc"] = int(float(self.lines[i+7].split()[3]))
self.scf_params["ecutrho"] = int(float(self.lines[i+8].split()[4]))
self.scf_params["conv_thr"] = float(self.lines[i+9].split()[3])
self.scf_params["mixing_beta"] = float(self.lines[i+10].split()[3])
elif self.lines[i].split()[0] == "crystal" and self.lines[i].split()[1] == "axes:" and self.lines[i].split()[-1] =="alat)":
self.scf_params["cell_a_alat"] = []
self.scf_params["cell_a_alat"].append([float(self.lines[i+1].split()[3]), float(self.lines[i+1].split()[4]), float(self.lines[i+1].split()[5])])
self.scf_params["cell_a_alat"].append([float(self.lines[i+2].split()[3]), float(self.lines[i+2].split()[4]), float(self.lines[i+2].split()[5])])
self.scf_params["cell_a_alat"].append([float(self.lines[i+3].split()[3]), float(self.lines[i+3].split()[4]), float(self.lines[i+3].split()[5])])
elif self.lines[i].split()[0] == "reciprocal" and self.lines[i].split()[1] == "axes:" and self.lines[i].split()[-1] == "pi/alat)": # actually '2 pi/alat'
self.scf_params["cell_b_2pi_alat"] = []
self.scf_params["cell_b_2pi_alat"].append([float(self.lines[i+1].split()[3]), float(self.lines[i+1].split()[4]), float(self.lines[i+1].split()[5])])
self.scf_params["cell_b_2pi_alat"].append([float(self.lines[i+2].split()[3]), float(self.lines[i+2].split()[4]), float(self.lines[i+2].split()[5])])
self.scf_params["cell_b_2pi_alat"].append([float(self.lines[i+3].split()[3]), float(self.lines[i+3].split()[4]), float(self.lines[i+3].split()[5])])
elif self.lines[i].split()[0] == "site" and self.lines[i].split()[-1] == "units)" and self.lines[i].split()[-2] == "(alat":
self.run_info["site_line_number"] = i
elif self.lines[i].split()[0] == "number" and self.lines[i].split()[2] == 'k':
if self.lines[i].split()[5] == "(tetrahedron":
self.scf_params["degauss"] = "tetrahedron method: degauss not needed"
else:
self.scf_params["degauss"] = float(self.lines[i].split()[9])
self.run_info["number-of-k-points"] = int(self.lines[i].split()[4])
elif self.lines[i].split()[0] == "Estimated" and self.lines[i].split()[1] == "max":
self.run_info["ram_per_process"] = self.lines[i].split()[7] + " " + self.lines[i].split()[8]
self.run_info["total_ram"] = self.lines[i+2].split()[5] + " " + self.lines[i+2].split()[6]
elif self.lines[i].split()[0] == "total" and self.lines[i].split()[1] == "energy":
# the total energy of the last iteration is not print like the previous scf iteration
# it begin with a ! total energy
self.run_info["scf_energies"].append(float(self.lines[i].split()[3]))
elif self.lines[i].split()[0] == "!" and self.lines[i].split()[5] == "Ry":
self.run_info["scf_final_energy"] = float(self.lines[i].split()[4])
elif self.lines[i].split()[0] == "convergence" and self.lines[i].split()[3] == "achieved":
self.run_info["scf_iterations"] = int(self.lines[i].split()[5])
elif self.lines[i].split()[0] == "the" and self.lines[i].split()[1] == "Fermi":
self.run_info["fermi_energy"] = float(self.lines[i].split()[4])
elif self.lines[i].split()[0] == "Total" and self.lines[i].split()[1] == "force":
self.run_info["total_force"] = float(self.lines[i].split()[3])
elif self.lines[i].split()[0] == "Computing" and self.lines[i].split()[-1] == "pressure":
self.run_info["total_stress_ry_bohr_3"] = []
self.run_info["total_stress_kbar"] = []
self.run_info["pressure"] = float(self.lines[i+2].split()[-1])
self.run_info["total_stress_ry_bohr_3"].append([float(self.lines[i+3].split()[0]), float(self.lines[i+3].split()[1]), float(self.lines[i+3].split()[2])])
self.run_info["total_stress_ry_bohr_3"].append([float(self.lines[i+4].split()[0]), float(self.lines[i+4].split()[1]), float(self.lines[i+4].split()[2])])
self.run_info["total_stress_ry_bohr_3"].append([float(self.lines[i+5].split()[0]), float(self.lines[i+5].split()[1]), float(self.lines[i+5].split()[2])])
self.run_info["total_stress_kbar"].append([float(self.lines[i+3].split()[3]), float(self.lines[i+3].split()[4]), float(self.lines[i+3].split()[5])])
self.run_info["total_stress_kbar"].append([float(self.lines[i+4].split()[3]), float(self.lines[i+4].split()[4]), float(self.lines[i+4].split()[5])])
self.run_info["total_stress_kbar"].append([float(self.lines[i+5].split()[3]), float(self.lines[i+5].split()[4]), float(self.lines[i+5].split()[5])])
# note: at present len(self.run_info["scf_energies"]) = len(self.run_info["scf_iterations"]) - 1
# because the total energy of the last step is not printed in format like the previous scf step,
# and it is printed as the '! total energy = ' where there is a "!" in the beginning
# now we append the final scf step energy to self.run_info["scf_energies"]
self.run_info["scf_energies"].append(self.run_info["scf_final_energy"])
# ----------------------------------------------------------------------
# get the xyz structure from information extracted above:
self.xyz = base_xyz()
self.xyz.natom = self.scf_params["nat"]
begin = self.run_info["site_line_number"] + 1
# Warning:
# there are numeric erros when obtaining atom coordinated from qe output
# in unit of alat and multiplied by alat and bohr. namely the acquired
# atomic coordinates have numeric errors compared to the input xyz
# so be cautious when use it.
bohr = 0.529177208 # 1 Bohr = 0.529177208 Angstrom
for i in range(self.xyz.natom):
self.xyz.atoms.append(Atom(
self.lines[begin+i].split()[1],
self.scf_params["alat_au"] * bohr * float(self.lines[begin+i].split()[6]),
self.scf_params["alat_au"] * bohr * float(self.lines[begin+i].split()[7]),
self.scf_params["alat_au"] * bohr * float(self.lines[begin+i].split()[8])))
self.xyz.cell = self.scf_params["cell_a_alat"] # now in unit of alat
for i in range(3):
for j in range(3):
self.xyz.cell[i][j] = self.scf_params["cell_a_alat"][i][i] * self.scf_params["alat_au"] * bohr
def __init__(self):
self.xyz = base_xyz()
def get_opt_params_and_run_info(self):
"""
self.run_info[]
start_time: the task start time
stop_time: the task stop time
#scf_energies: all the energies during the scf procedure
#fermi_energy: fermi energy of the system (if output)
"""
#self.run_info["scf_energies"] = []
for i in range(len(self.lines)):
# if it is an empty line continue to next line
if len(self.lines[i].split()) == 0:
continue
if self.lines[i].split()[0] == "Program" and self.lines[i].split(
)[1] == "PWSCF" and self.lines[i].split()[3] == "starts":
self.run_info["start_time"] = self.lines[i].split("\n")[0]
elif self.lines[i].split()[0] == "This" and self.lines[i].split(
)[1] == "run" and self.lines[i].split()[3] == "terminated":
self.run_info["stop_time"] = self.lines[i].split("\n")[0]
elif self.lines[i].split(
)[0] == "Parallel" and self.lines[i].split()[-1] == "processors":
self.run_info["processors"] = int(self.lines[i].split()[-2])
elif self.lines[i].split()[0] == "MPI" and self.lines[i].split(
)[-1] == "nodes":
self.run_info["nodes"] = int(self.lines[i].split()[-2])
elif self.lines[i].split(
)[0] == "bravais-lattice" and self.lines[i].split()[1] == "index":
self.opt_params["alat_au"] = float(self.lines[i +
1].split()[4])
self.opt_params["nat"] = int(self.lines[i + 3].split()[4])
self.opt_params["nelectron"] = float(self.lines[i +
5].split()[4])
self.opt_params["n_ks_state"] = int(
self.lines[i + 6].split("=")[1])
self.opt_params["ecutwfc"] = int(
float(self.lines[i + 7].split()[3]))
self.opt_params["ecutrho"] = int(
float(self.lines[i + 8].split()[4]))
self.opt_params["conv_thr"] = float(self.lines[i +
9].split()[3])
self.opt_params["mixing_beta"] = float(
self.lines[i + 10].split()[3])
if "nstep" in self.opt_params and self.opt_params[
"nstep"] != None:
pass
else:
self.opt_params["nstep"] = int(self.lines[i +
13].split()[2])
elif self.lines[i].split()[0] == "crystal" and self.lines[i].split(
)[1] == "axes:" and self.lines[i].split()[-1] == "alat)":
self.opt_params["cell_a_alat"] = []
self.opt_params["cell_a_alat"].append([
float(self.lines[i + 1].split()[3]),
float(self.lines[i + 1].split()[4]),
float(self.lines[i + 1].split()[5])
])
self.opt_params["cell_a_alat"].append([
float(self.lines[i + 2].split()[3]),
float(self.lines[i + 2].split()[4]),
float(self.lines[i + 2].split()[5])
])
self.opt_params["cell_a_alat"].append([
float(self.lines[i + 3].split()[3]),
float(self.lines[i + 3].split()[4]),
float(self.lines[i + 3].split()[5])
])
elif self.lines[i].split()[0] == "reciprocal" and self.lines[
i].split()[1] == "axes:" and self.lines[i].split(
)[-1] == "pi/alat)": # actually '2 pi/alat'
self.opt_params["cell_b_2pi_alat"] = []
self.opt_params["cell_b_2pi_alat"].append([
float(self.lines[i + 1].split()[3]),
float(self.lines[i + 1].split()[4]),
float(self.lines[i + 1].split()[5])
])
self.opt_params["cell_b_2pi_alat"].append([
float(self.lines[i + 2].split()[3]),
float(self.lines[i + 2].split()[4]),
float(self.lines[i + 2].split()[5])
])
self.opt_params["cell_b_2pi_alat"].append([
float(self.lines[i + 3].split()[3]),
float(self.lines[i + 3].split()[4]),
float(self.lines[i + 3].split()[5])
])
elif self.lines[i].split()[0] == "site" and self.lines[i].split(
)[-1] == "units)" and self.lines[i].split()[-2] == "(alat":
self.run_info["site_line_number"] = i
elif self.lines[i].split()[0] == "number" and self.lines[i].split(
)[2] == 'k':
if self.lines[i].split()[5] == "(tetrahedron":
self.opt_params[
"degauss"] = "tetrahedron method: degauss not needed"
else:
self.opt_params["degauss"] = float(
self.lines[i].split()[9])
self.run_info["number-of-k-points"] = int(
self.lines[i].split()[4])
elif self.lines[i].split(
)[0] == "Estimated" and self.lines[i].split()[1] == "max":
self.run_info["ram_per_process"] = self.lines[i].split(
)[7] + " " + self.lines[i].split()[8]
self.run_info["total_ram"] = self.lines[
i + 2].split()[5] + " " + self.lines[i + 2].split()[6]
# ----------------------------------------------------------------------
# get the input xyz structure from information extracted above:
self.xyz = base_xyz()
self.xyz.natom = self.opt_params["nat"]
begin = self.run_info["site_line_number"] + 1
# Warning:
# there are numeric erros when obtaining atom coordinated from qe output
# in unit of alat and multiplied by alat and bohr. namely the acquired
# atomic coordinates have numeric errors compared to the input xyz
# so be cautious when use it.
bohr = 0.529177208 # 1 Bohr = 0.529177208 Angstrom
for i in range(self.xyz.natom):
self.xyz.atoms.append(
Atom(
self.lines[begin + i].split()[1],
self.opt_params["alat_au"] * bohr *
float(self.lines[begin + i].split()[6]),
self.opt_params["alat_au"] * bohr *
float(self.lines[begin + i].split()[7]),
self.opt_params["alat_au"] * bohr *
float(self.lines[begin + i].split()[8])))
self.xyz.cell = self.opt_params["cell_a_alat"] # now in unit of alat
for i in range(3):
for j in range(3):
self.xyz.cell[i][j] = self.opt_params["cell_a_alat"][i][
j] * self.opt_params["alat_au"] * bohr
# now self.xyz.cell are in unit of Angstrom
# ----------------------------------------------------------------------
# get information output each ion step
self._get_info_for_each_ions_step()