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feat: reads potentions from ljc file

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This commit is contained in:
Vitor Hideyoshi
2026-03-16 01:24:01 -03:00
parent 30be88e6b4
commit 0763c4a9e1
19 changed files with 250 additions and 210 deletions
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9
control.example.yml
View File

@@ -3,7 +3,7 @@ diceplayer:
switch_cyc: 3
max_cyc: 5
mem: 24
ncores: 5
ncores: 20
qmprog: 'g16'
lps: no
ghosts: no
@@ -11,14 +11,15 @@ diceplayer:
dice:
nprocs: 4
nmol: [1, 100]
nmol: [1, 1000]
dens: 1.5
nstep: [2000, 3000]
isave: 1000
isave: 0
outname: 'phb'
progname: '~/.local/bin/dice'
ljname: 'phb.ljc'
ljname: 'phb.ljc.example'
randominit: 'always'
seed: 12345
gaussian:
qmprog: 'g16'

11
diceplayer/config/dice_config.py
View File

@@ -1,3 +1,5 @@
from pathlib import Path
from pydantic import BaseModel, ConfigDict, Field
from typing_extensions import Literal
@@ -16,7 +18,7 @@ class DiceConfig(BaseModel):
..., description="Number of processes to use for the DICE simulations"
)
ljname: str = Field(..., description="Name of the Lennard-Jones potential file")
ljname: Path = Field(..., description="Name of the Lennard-Jones potential file")
outname: str = Field(
..., description="Name of the output file for the simulation results"
)
@@ -47,10 +49,13 @@ class DiceConfig(BaseModel):
isave: int = Field(1000, description="Frequency of saving the simulation results")
press: float = Field(1.0, description="Pressure of the system")
temp: float = Field(300.0, description="Temperature of the system")
progname: str = Field(
progname: Path = Field(
"dice", description="Name of the program to run the simulation"
)
randominit: str = Field(
"first", description="Method for initializing the random number generator"
)
seed: int = Field(default_factory=lambda: random.randint(0, 2**32 - 1), description="Seed for the random number generator")
seed: int = Field(
default_factory=lambda: int(1e6 * random.random()),
description="Seed for the random number generator",
)

63
diceplayer/dice/dice_handler.py
View File

@@ -1,10 +1,14 @@
import shutil
from diceplayer.dice.dice_input import NVTTerConfig, NVTEqConfig, NPTEqConfig, NPTTerConfig
from diceplayer.dice.dice_input import (
NPTEqConfig,
NPTTerConfig,
NVTEqConfig,
NVTTerConfig,
)
from diceplayer.dice.dice_wrapper import DiceWrapper
from diceplayer.logger import logger
from diceplayer.state.state_model import StateModel
import shutil
from pathlib import Path
from threading import Thread
@@ -15,7 +19,9 @@ class DiceHandler:
def run(self, state: StateModel, cycle: int) -> StateModel:
if self.dice_directory.exists():
logger.info(f"Found dice directory: {self.dice_directory}, this directory will be purged for a clean state")
logger.info(
f"Found dice directory: {self.dice_directory}, this directory will be purged for a clean state"
)
shutil.rmtree(self.dice_directory)
self.dice_directory.mkdir(parents=True)
@@ -38,7 +44,9 @@ class DiceHandler:
t.join()
if len(results) != state.config.dice.nprocs:
raise RuntimeError(f"Expected {state.config.dice.nprocs} simulation results, but got {len(results)}")
raise RuntimeError(
f"Expected {state.config.dice.nprocs} simulation results, but got {len(results)}"
)
return results
@@ -47,21 +55,23 @@ class DiceHandler:
def commit_simulation_state(self, state: StateModel, result: dict) -> StateModel:
return state
def _simulation_process(self, state: StateModel, cycle: int, proc: int, results: list[dict]) -> None:
def _simulation_process(
self, state: StateModel, cycle: int, proc: int, results: list[dict]
) -> None:
proc_directory = self.dice_directory / f"{proc:02d}"
if proc_directory.exists():
shutil.rmtree(proc_directory)
proc_directory.mkdir(parents=True)
dice = DiceWrapper(
state.config.dice, proc_directory
)
dice = DiceWrapper(state.config.dice, proc_directory)
if state.config.dice.randominit == "first" and cycle == 0:
self._generate_phb_file(state, proc_directory)
if state.config.dice.randominit == "first" and cycle >= 0:
self._generate_last_xyz(state, proc_directory)
else:
nvt_ter_config = NVTTerConfig.from_config(state.config)
dice.run(nvt_ter_config)
else:
self._generate_last_xyz(state, proc_directory)
if len(state.config.dice.nstep) == 2:
nvt_eq_config = NVTEqConfig.from_config(state.config)
@@ -76,5 +86,30 @@ class DiceHandler:
results.append(dice.extract_results())
def _generate_last_xyz(self, state: StateModel, proc_directory: Path) -> None:
...
@staticmethod
def _generate_phb_file(state: StateModel, proc_directory: Path) -> None:
fstr = "{:<3d} {:>3d} {:>10.5f} {:>10.5f} {:>10.5f} {:>10.6f} {:>9.5f} {:>7.4f}\n"
phb_file = proc_directory / state.config.dice.ljname
with open(phb_file, "w") as f:
f.write(f"{state.config.dice.combrule}\n")
f.write(f"{len(state.config.dice.nmol)}\n")
for molecule in state.system.molecule:
f.write(f"{len(molecule.atom)} {molecule.molname}\n")
for atom in molecule.atom:
f.write(
fstr.format(
atom.lbl,
atom.na,
atom.rx,
atom.ry,
atom.rz,
atom.chg,
atom.eps,
atom.sig,
)
)
def _generate_last_xyz(self, state: StateModel, proc_directory: Path) -> None: ...

83
diceplayer/dice/dice_input.py
View File

@@ -9,6 +9,30 @@ from pathlib import Path
from typing import Any, Sequence, TextIO
DICE_KEYWORD_ORDER = [
"title",
"ncores",
"ljname",
"outname",
"nmol",
"dens",
"temp",
"press",
"seed",
"init",
"nstep",
"vstep",
"mstop",
"accum",
"iprint",
"isave",
"irdf",
"upbuf",
]
@dataclass(slots=True)
class BaseConfig(ABC):
ncores: int
@@ -18,13 +42,14 @@ class BaseConfig(ABC):
temp: float
seed: int
isave: int
press: float = 1.0
def write(self, directory: Path, filename: str = "input") -> Path:
input_path = directory / filename
if input_path.exists():
logger.info(f"Dice input file {input_path} already exists and will be overwritten")
logger.info(
f"Dice input file {input_path} already exists and will be overwritten"
)
input_path.unlink()
input_path.parent.mkdir(parents=True, exist_ok=True)
@@ -34,13 +59,18 @@ class BaseConfig(ABC):
return input_path
def write_dice_config(self, io_writer: TextIO) -> None:
for field in fields(self):
key = field.name
value = getattr(self, key)
values = {f.name: getattr(self, f.name) for f in fields(self)}
for key in DICE_KEYWORD_ORDER:
value = values.pop(key, None)
if value is None:
continue
io_writer.write(f"{key} = {self._serialize_value(value)}\n")
# write any remaining fields (future extensions)
for key, value in values.items():
if value is None:
continue
io_writer.write(f"{key} = {self._serialize_value(value)}\n")
io_writer.write("$end\n")
@@ -48,7 +78,7 @@ class BaseConfig(ABC):
@classmethod
def from_config(cls, config: PlayerConfig, **kwargs) -> Self:
base_fields = cls._extract_base_fields(config)
return cls(**base_fields, **kwargs)
return cls(**(base_fields | kwargs))
@staticmethod
def _extract_base_fields(config: PlayerConfig) -> dict[str, Any]:
@@ -60,7 +90,6 @@ class BaseConfig(ABC):
temp=config.dice.temp,
seed=config.dice.seed,
isave=config.dice.isave,
press=config.dice.press,
)
@staticmethod
@@ -91,10 +120,18 @@ class BaseConfig(ABC):
@dataclass(slots=True)
class NVTConfig(BaseConfig):
title: str = "Diceplayer Run - NVT"
dens: float = 0.0
nstep: int = 0
dens: float = ...
nstep: int = ...
vstep: int = 0
@classmethod
def from_config(cls, config: PlayerConfig, **kwargs) -> Self:
return super(NVTConfig, cls).from_config(
config,
dens=config.dice.dens,
nstep=cls._get_nstep(config, 0),
)
# -----------------------------------------------------
# NVT THERMALIZATION
@@ -105,12 +142,12 @@ class NVTConfig(BaseConfig):
class NVTTerConfig(NVTConfig):
title: str = "Diceplayer Run - NVT Thermalization"
upbuf: int = 360
init: str = "yes"
@classmethod
def from_config(cls, config: PlayerConfig, **kwargs) -> Self:
return super(NVTTerConfig, cls).from_config(
config,
dens=config.dice.dens,
nstep=cls._get_nstep(config, 0),
upbuf=config.dice.upbuf,
vstep=0,
@@ -118,9 +155,7 @@ class NVTTerConfig(NVTConfig):
)
def write(self, directory: Path, filename: str = "nvt.ter") -> Path:
return super(NVTTerConfig, self).write(
directory, filename
)
return super(NVTTerConfig, self).write(directory, filename)
# -----------------------------------------------------
@@ -132,12 +167,12 @@ class NVTTerConfig(NVTConfig):
class NVTEqConfig(NVTConfig):
title: str = "Diceplayer Run - NVT Production"
irdf: int = 0
init: str = "yesreadxyz"
@classmethod
def from_config(cls, config: PlayerConfig, **kwargs) -> Self:
return super(NVTEqConfig, cls).from_config(
config,
dens=config.dice.dens,
nstep=cls._get_nstep(config, 1),
irdf=config.dice.irdf,
vstep=0,
@@ -145,9 +180,7 @@ class NVTEqConfig(NVTConfig):
)
def write(self, directory: Path, filename: str = "nvt.eq") -> Path:
return super(NVTEqConfig, self).write(
directory, filename
)
return super(NVTEqConfig, self).write(directory, filename)
# -----------------------------------------------------
@@ -160,6 +193,14 @@ class NPTConfig(BaseConfig):
title: str = "Diceplayer Run - NPT"
nstep: int = 0
vstep: int = 5000
press: float = 1.0
@classmethod
def from_config(cls, config: PlayerConfig, **kwargs) -> Self:
return super(NPTConfig, cls).from_config(
config,
press=config.dice.press,
)
# -----------------------------------------------------
@@ -183,9 +224,7 @@ class NPTTerConfig(NPTConfig):
)
def write(self, directory: Path, filename: str = "npt.ter") -> Path:
return super(NPTTerConfig, self).write(
directory, filename
)
return super(NPTTerConfig, self).write(directory, filename)
# -----------------------------------------------------
@@ -209,6 +248,4 @@ class NPTEqConfig(NPTConfig):
)
def write(self, directory: Path, filename: str = "npt.eq") -> Path:
return super(NPTEqConfig, self).write(
directory, filename
)
return super(NPTEqConfig, self).write(directory, filename)

14
diceplayer/dice/dice_wrapper.py
View File

@@ -1,12 +1,10 @@
import subprocess
from typing import Final
import diceplayer.dice.dice_input as dice_input
from pathlib import Path
from diceplayer.config import DiceConfig
import subprocess
from pathlib import Path
from typing import Final
DICE_FLAG_LINE: Final[int] = -2
DICE_END_FLAG: Final[str] = "End of simulation"
@@ -22,8 +20,9 @@ class DiceWrapper:
output_path = input_path.parent / (input_path.name + ".out")
with open(output_path, "w") as outfile, open(input_path, "r") as infile:
bin_path = self.dice_config.progname.expanduser()
exit_status = subprocess.call(
self.dice_config.progname, stdin=infile, stdout=outfile
bin_path, stdin=infile, stdout=outfile, cwd=self.working_directory
)
if exit_status != 0:
@@ -38,4 +37,3 @@ class DiceWrapper:
def extract_results(self) -> dict:
return {}

4
diceplayer/environment/atom.py
View File

@@ -1,9 +1,9 @@
from diceplayer.utils.ptable import AtomInfo, PTable
from dataclasses import dataclass
from pydantic.dataclasses import dataclass
@dataclass
@dataclass(slots=True)
class Atom:
"""
Atom class declaration. This class is used throughout the DicePlayer program to represent atoms.

3
diceplayer/environment/molecule.py
View File

@@ -10,10 +10,11 @@ import numpy as np
import numpy.linalg as linalg
import numpy.typing as npt
from typing_extensions import List, Self, Tuple
from pydantic.dataclasses import dataclass
import math
from copy import deepcopy
from dataclasses import dataclass, field
from dataclasses import field
from functools import cached_property

2
diceplayer/optimization/optimization_handler.py
View File

@@ -16,4 +16,4 @@ class OptimizationHandler:
if current_cycle < state.config.switch_cyc:
return RoutineType.CHARGE
return RoutineType.GEOMETRY
return RoutineType.GEOMETRY

9
diceplayer/player.py
View File

@@ -1,12 +1,13 @@
from diceplayer.config.player_config import PlayerConfig
from diceplayer.dice.dice_handler import DiceHandler
from diceplayer.logger import logger
from diceplayer.optimization.optimization_handler import OptimizationHandler
from diceplayer.state.state_handler import StateHandler
from diceplayer.state.state_model import StateModel
from typing_extensions import TypedDict, Unpack
from diceplayer.utils.potential import read_system_from_phb
class PlayerFlags(TypedDict):
continuation: bool
@@ -30,9 +31,11 @@ class Player:
self._state_handler.delete()
state = None
if state is None:
state = StateModel.from_config(self.config)
system = read_system_from_phb(self.config)
state = StateModel(
config=self.config, system=system
)
else:
logger.info("Resuming from existing state.")

2
diceplayer/state/state_model.py
View File

@@ -8,7 +8,7 @@ from typing_extensions import Self
class StateModel(BaseModel):
config: PlayerConfig
system: System
current_cycle: int
current_cycle: int = 0
@classmethod
def from_config(cls, config: PlayerConfig) -> Self:

62
diceplayer/utils/potential.py Normal file
View File

@@ -0,0 +1,62 @@
from diceplayer.config import PlayerConfig
from diceplayer.environment import System, Molecule, Atom
from pathlib import Path
from diceplayer.logger import logger
from diceplayer.state.state_model import StateModel
def read_system_from_phb(config: PlayerConfig) -> System:
phb_file = Path(config.dice.ljname)
if not phb_file.exists():
raise FileNotFoundError
ljc_data = phb_file.read_text(encoding="utf-8").splitlines()
combrule = ljc_data.pop(0).strip()
if combrule != config.dice.combrule:
raise ValueError(
f"Invalid combrule defined in {phb_file}. Expected the same value configured in the config file"
)
ntypes = ljc_data.pop(0).strip()
if not ntypes.isdigit():
raise ValueError(f"Invalid ntypes defined in {phb_file}")
nmol = int(ntypes)
if nmol != len(config.dice.nmol):
raise ValueError(f"Invalid nmol defined in {phb_file}")
sys = System()
for i in range(nmol):
nsites, molname = ljc_data.pop(0).split()
if not nsites.isdigit():
raise ValueError(f"Invalid nsites defined in {phb_file}")
nsites = int(nsites)
mol = Molecule(molname)
for j in range(nsites):
_fields = ljc_data.pop(0).split()
mol.add_atom(
Atom(*_fields)
)
sys.add_type(mol)
return sys
# def write_phb(phb_file: Path, state: StateModel) -> None:
# if phb_file.exists():
# raise RuntimeError(f"File {phb_file} already exists")
#
# with open(phb_file, "w") as f:
# f.write(f"{state.config.dice.combrule}\n")
# f.write(f"{len(state.system.nmols)}\n")
# f.write(f"{state.config.dice.nmol}\n")

7
tests/config/test_dice_config.py
View File

@@ -6,6 +6,7 @@ import pytest
class TestDiceConfig:
def test_class_instantiation(self):
dice_dto = DiceConfig(
nprocs=1,
ljname="test",
outname="test",
dens=1.0,
@@ -18,6 +19,7 @@ class TestDiceConfig:
def test_validate_jname(self):
with pytest.raises(ValueError) as ex:
DiceConfig(
nprocs=1,
ljname=None,
outname="test",
dens=1.0,
@@ -30,6 +32,7 @@ class TestDiceConfig:
def test_validate_outname(self):
with pytest.raises(ValueError) as ex:
DiceConfig(
nprocs=1,
ljname="test",
outname=None,
dens=1.0,
@@ -42,6 +45,7 @@ class TestDiceConfig:
def test_validate_dens(self):
with pytest.raises(ValueError) as ex:
DiceConfig(
nprocs=1,
ljname="test",
outname="test",
dens=None,
@@ -54,6 +58,7 @@ class TestDiceConfig:
def test_validate_nmol(self):
with pytest.raises(ValueError) as ex:
DiceConfig(
nprocs=1,
ljname="test",
outname="test",
dens=1.0,
@@ -66,6 +71,7 @@ class TestDiceConfig:
def test_validate_nstep(self):
with pytest.raises(ValueError) as ex:
DiceConfig(
nprocs=1,
ljname="test",
outname="test",
dens=1.0,
@@ -78,6 +84,7 @@ class TestDiceConfig:
def test_from_dict(self):
dice_dto = DiceConfig.model_validate(
{
"nprocs": 1,
"ljname": "test",
"outname": "test",
"dens": 1.0,

4
tests/config/test_player_config.py
View File

@@ -11,6 +11,7 @@ class TestPlayerConfig:
@pytest.fixture
def dice_payload(self) -> dict[str, Any]:
return {
"nprocs": 4,
"ljname": "test",
"outname": "test",
"dens": 1.0,
@@ -35,7 +36,6 @@ class TestPlayerConfig:
"mem": 12,
"max_cyc": 100,
"switch_cyc": 50,
"nprocs": 4,
"ncores": 4,
"dice": dice_payload,
"gaussian": gaussian_payload,
@@ -57,7 +57,6 @@ class TestPlayerConfig:
mem=12,
max_cyc=100,
switch_cyc=50,
nprocs=4,
ncores=4,
dice=dice_config,
gaussian=gaussian_config,
@@ -75,7 +74,6 @@ class TestPlayerConfig:
mem=12,
max_cyc=100,
switch_cyc=50,
nprocs=4,
ncores=4,
altsteps=0,
dice=dice_config,

2
tests/dice/test_dice_input.py
View File

@@ -20,9 +20,9 @@ class TestDiceInput:
"mem": 12,
"max_cyc": 100,
"switch_cyc": 50,
"nprocs": 4,
"ncores": 4,
"dice": {
"nprocs": 4,
"ljname": "test",
"outname": "test",
"dens": 1.0,

113
tests/mocks/mock_inputs.py
View File

@@ -1,113 +0,0 @@
from unittest import mock
def get_config_example():
return """
diceplayer:
opt: no
mem: 12
maxcyc: 3
ncores: 4
nprocs: 4
qmprog: 'g16'
lps: no
ghosts: no
altsteps: 20000
dice:
nmol: [1, 50]
dens: 0.75
nstep: [2000, 3000, 4000]
isave: 1000
outname: 'phb'
progname: '~/.local/bin/dice'
ljname: 'phb.ljc'
randominit: 'first'
gaussian:
qmprog: 'g16'
level: 'MP2/aug-cc-pVDZ'
keywords: 'freq'
"""
def get_potentials_exemple():
return """\
*
2
1 TEST
1 1 0.000000 0.000000 0.000000 0.000000 0.0000 0.0000
1 PLACEHOLDER
1 1 0.000000 0.000000 0.000000 0.000000 0.0000 0.0000
"""
def get_potentials_error_combrule():
return """\
.
2
1 TEST
1 1 0.000000 0.000000 0.000000 0.000000 0.0000 0.0000
1 PLACEHOLDER
1 1 0.000000 0.000000 0.000000 0.000000 0.0000 0.0000
"""
def get_potentials_error_ntypes():
return """\
*
a
1 TEST
1 1 0.000000 0.000000 0.000000 0.000000 0.0000 0.0000
1 PLACEHOLDER
1 1 0.000000 0.000000 0.000000 0.000000 0.0000 0.0000
"""
def get_potentials_error_ntypes_config():
return """\
*
3
1 TEST
1 1 0.000000 0.000000 0.000000 0.000000 0.0000 0.0000
1 PLACEHOLDER
1 1 0.000000 0.000000 0.000000 0.000000 0.0000 0.0000
"""
def get_potentials_error_nsites():
return """\
*
2
. TEST
1 1 0.000000 0.000000 0.000000 0.000000 0.0000 0.0000
1 PLACEHOLDER
1 1 0.000000 0.000000 0.000000 0.000000 0.0000 0.0000
"""
def get_potentials_error_molname():
return """\
*
2
1
1 1 0.000000 0.000000 0.000000 0.000000 0.0000 0.0000
1 PLACEHOLDER
1 1 0.000000 0.000000 0.000000 0.000000 0.0000 0.0000
"""
def mock_open(file, *args, **kwargs):
values = {
"control.test.yml": get_config_example(),
"phb.ljc": get_potentials_exemple(),
"phb.error.combrule.ljc": get_potentials_error_combrule(),
"phb.error.ntypes.ljc": get_potentials_error_ntypes(),
"phb.error.ntypes.config.ljc": get_potentials_error_ntypes_config(),
"phb.error.nsites.ljc": get_potentials_error_nsites(),
"phb.error.molname.ljc": get_potentials_error_molname(),
}
if file in values:
return mock.mock_open(read_data=values[file])()
return mock.mock_open(read_data="")()

32
tests/mocks/mock_proc.py
View File

@@ -1,32 +0,0 @@
from typing_extensions import List
import itertools
class MockProc:
pid_counter = itertools.count()
def __init__(self, *args, **kwargs):
self.pid = next(MockProc.pid_counter)
if "exitcode" in kwargs:
self.exitcode = kwargs["exitcode"]
else:
self.exitcode = 0
self.sentinel = self.pid
def __call__(self, *args, **kwargs):
return self
def start(self):
pass
def terminate(self):
pass
class MockConnection:
@staticmethod
def wait(sentinels: List[int]):
return sentinels

2
tests/state/test_state_handler.py
View File

@@ -16,9 +16,9 @@ class TestStateHandler:
mem=12,
max_cyc=100,
switch_cyc=50,
nprocs=4,
ncores=4,
dice=DiceConfig(
nprocs=4,
ljname="test",
outname="test",
dens=1.0,

0
tests/mocks/__init__.py → tests/utils/__init__.py
View File

38
tests/utils/test_potential.py Normal file
View File

@@ -0,0 +1,38 @@
from pathlib import Path
from typing import Any
import pytest
from diceplayer.config import PlayerConfig
from diceplayer.environment import System
from diceplayer.utils.potential import read_system_from_phb
class TestPotential:
@pytest.fixture
def player_config(self) -> PlayerConfig:
return PlayerConfig.model_validate({
"type": "both",
"mem": 12,
"max_cyc": 100,
"switch_cyc": 50,
"ncores": 4,
"dice": {
"nprocs": 4,
"ljname": "phb.ljc.example",
"outname": "test",
"dens": 1.0,
"nmol": [12, 16],
"nstep": [1, 1],
},
"gaussian": {
"level": "test",
"qmprog": "g16",
"keywords": "test",
},
})
def test_read_phb(self, player_config: PlayerConfig):
system = read_system_from_phb(player_config)
assert isinstance(system, System)