import copy
import logging
import random
from typing import (
List,
)
import numpy as np
from dpgen2.constants import (
calypso_check_opt_file,
calypso_input_file,
calypso_run_opt_file,
)
from .calypso import (
make_calypso_input,
)
from .task import (
ExplorationTask,
)
from .task_group import (
ExplorationTaskGroup,
)
atomic_symbols = (
'X', # placeholder
'H', 'He',
'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne',
'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar',
'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr',
'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I', 'Xe',
'Cs', 'Ba',
'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu',
'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn',
'Fr', 'Ra',
'Ac','Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', 'Md', 'No', 'Lr',
'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt', 'Ds', 'Rg', 'Cn', 'Nh', 'Fl', 'Mc', 'Lv', 'Ts', 'Og',
) # fmt: skip
atomic_number_map = {key: value for value, key in enumerate(atomic_symbols)}
# Covalent radii from:
#
# Covalent radii revisited,
# Beatriz Cordero, Verónica Gómez, Ana E. Platero-Prats, Marc Revés,
# Jorge Echeverría, Eduard Cremades, Flavia Barragán and Santiago Alvarez,
# Dalton Trans., 2008, 2832-2838 DOI:10.1039/B801115J
UNKN = 0.2
covalent_radii = [
# X, placeholder
UNKN,
# H He
0.31, 0.28,
# Li Be B C N O F Ne
1.28, 0.96, 0.84, 0.76, 0.71, 0.66, 0.57, 0.58,
# Na Mg Al Si P S Cl Ar
1.66, 1.41, 1.21, 1.11, 1.07, 1.05, 1.02, 1.06,
# K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
2.03, 1.76, 1.70, 1.60, 1.53, 1.39, 1.39, 1.32, 1.26, 1.24, 1.32, 1.22, 1.22, 1.20, 1.19, 1.20, 1.20, 1.16,
# Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Au Cd In Sn Sb Te I Xe
2.20, 1.95, 1.90, 1.75, 1.64, 1.54, 1.47, 1.46, 1.42, 1.39, 1.45, 1.44, 1.42, 1.39, 1.39, 1.38, 1.39, 1.40,
# Cs Ba
2.44, 2.15,
# La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu
2.07, 2.04, 2.03, 2.01, 1.99, 1.98, 1.98, 1.96, 1.94, 1.92, 1.92, 1.89, 1.90, 1.87, 1.87,
# Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
1.75, 1.70, 1.62, 1.51, 1.44, 1.41, 1.36, 1.36, 1.32, 1.45, 1.46, 1.48, 1.40, 1.50, 1.50,
# Fr Ra
2.60, 2.21,
# Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr
2.15, 2.06, 2.00, 1.96, 1.90, 1.87, 1.80, 1.69, UNKN, UNKN, UNKN, UNKN, UNKN, UNKN, UNKN,
# Rf Db Sg Bh Hs Mt Ds Rg Cn Nh Fl Mc Lv Ts Og
UNKN, UNKN, UNKN, UNKN, UNKN, UNKN, UNKN, UNKN, UNKN, UNKN, UNKN, UNKN, UNKN, UNKN, UNKN,
] # fmt: skip
[docs]
class CalyTaskGroup(ExplorationTaskGroup):
def __init__(self):
super().__init__()
[docs]
def set_params(
self,
numb_of_species,
name_of_atoms,
numb_of_atoms,
distance_of_ions=None,
atomic_number=None,
pop_size: int = 30,
max_step: int = 5,
system_name: str = "CALYPSO",
numb_of_formula: List[int] = [1, 1],
pressure: float = 0.001,
fmax: float = 0.01,
volume: float = 0,
ialgo: int = 2,
pso_ratio: float = 0.6,
icode: int = 15,
numb_of_lbest: int = 4,
numb_of_local_optim: int = 4,
command: str = "sh submit.sh",
max_time: int = 9000,
gen_type: int = 1,
pick_up: bool = False,
pick_step: int = 1,
parallel: bool = False,
split: bool = True,
spec_space_group: List[int] = [2, 230],
vsc: bool = True,
ctrl_range: List[List[int]] = [[1, 10]],
max_numb_atoms: int = 100,
):
"""
Set calypso parameters
"""
self.numb_of_species = numb_of_species
self.numb_of_atoms = numb_of_atoms
if isinstance(name_of_atoms, list) and all(
[isinstance(i, list) for i in name_of_atoms]
):
overlap = set(name_of_atoms[0])
for temp in name_of_atoms[1:]:
overlap = overlap & set(temp)
if any(map(lambda s: (set(s) - overlap) == 0, name_of_atoms)):
raise ValueError(
f"Any sub-list should not equal with intersection, e.g. [[A,B,C], [B,C], [C]] is not allowed."
)
while True:
choice = []
for _atoms in name_of_atoms:
value = random.choice(_atoms)
logging.info(
f"randomly choose {value} from {_atoms}, already choose: {choice}"
)
if value in choice:
break
choice.append(value)
else:
break
self.name_of_atoms = choice
logging.info(f"The final choice is {self.name_of_atoms}")
self.atomic_number = [atomic_symbols.index(i) for i in self.name_of_atoms]
else:
self.name_of_atoms = name_of_atoms
self.atomic_number = atomic_number
if isinstance(distance_of_ions, dict):
updated_table = copy.deepcopy(covalent_radii)
for key, value in distance_of_ions.items():
updated_table[atomic_number_map[key]] = value
temp_distance_mtx = np.zeros((numb_of_species, numb_of_species))
for i in range(numb_of_species):
for j in range(numb_of_species):
temp_distance_mtx[i][j] = round(
updated_table[atomic_number_map[self.name_of_atoms[i]]] * 0.7
+ updated_table[atomic_number_map[self.name_of_atoms[j]]] * 0.7,
2,
)
self.distance_of_ions = temp_distance_mtx
else:
self.distance_of_ions = distance_of_ions
self.pop_size = pop_size
self.max_step = max_step
self.system_name = system_name
self.numb_of_formula = numb_of_formula
self.pressure = pressure
self.fmax = fmax
self.volume = volume
self.ialgo = ialgo
self.pso_ratio = pso_ratio
self.icode = icode
self.numb_of_lbest = numb_of_lbest
self.numb_of_local_optim = numb_of_local_optim
self.command = command
self.max_time = max_time
self.gen_type = gen_type
self.pick_up = pick_up
self.pick_step = pick_step
self.parallel = parallel
self.split = split
self.spec_space_group = spec_space_group
self.vsc = vsc
self.ctrl_range = ctrl_range
self.max_numb_atoms = max_numb_atoms
self.caly_set = True
[docs]
def make_task(self) -> ExplorationTaskGroup:
"""
Make the CALYPSO task group.
Returns
-------
task_grp: ExplorationTaskGroup
Return one calypso task group.
"""
if not self.caly_set:
raise RuntimeError("calypso settings are not set")
# clear all existing tasks
self.clear()
self.add_task(self._make_caly_task())
return self
def _make_caly_task(self) -> ExplorationTask:
input_file_str, run_opt_str, check_opt_str = make_calypso_input(
self.numb_of_species,
self.name_of_atoms,
self.atomic_number,
self.numb_of_atoms,
self.distance_of_ions,
self.pop_size,
self.max_step,
self.system_name,
self.numb_of_formula,
self.pressure,
self.fmax,
self.volume,
self.ialgo,
self.pso_ratio,
self.icode,
self.numb_of_lbest,
self.numb_of_local_optim,
self.command,
self.max_time,
self.gen_type,
self.pick_up,
self.pick_step,
self.parallel,
self.split,
self.spec_space_group,
self.vsc,
self.ctrl_range,
self.max_numb_atoms,
)
task = ExplorationTask()
task.add_file(calypso_input_file, input_file_str)
task.add_file(calypso_run_opt_file, run_opt_str)
task.add_file(calypso_check_opt_file, check_opt_str)
return task