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Implements Refactoring in Player Class and Initial Working Version

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This commit is contained in:
Vitor Hideyoshi
2023-06-02 20:20:38 -03:00
parent b440a0f05d
commit 33612f2d7b
21 changed files with 1193 additions and 983 deletions
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134
diceplayer/shared/interface/dice_interface.py
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@@ -1,7 +1,7 @@
from __future__ import annotations
from diceplayer.shared.config.dice_dto import DiceDTO
from diceplayer.shared.config.step_dto import StepDTO
from diceplayer.shared.config.player_config import PlayerConfig
from diceplayer.shared.environment.system import System
from diceplayer.shared.interface import Interface
from diceplayer import logger
@@ -26,23 +26,14 @@ MAX_SEED: Final[int] = 4294967295
class DiceInterface(Interface):
title = "Diceplayer run"
def __init__(self, data: dict):
self.config: DiceDTO = self.set_config(data)
self.step: StepDTO | None = None
@staticmethod
def set_config(data: dict) -> DiceDTO:
return DiceDTO.from_dict(data)
def configure(self, step: any):
def configure(self, step: PlayerConfig, system: System):
self.step = step
self.system = system
def start(self, cycle: int):
procs = []
sentinels = []
logger.info(f"---------------------- DICE - CYCLE {cycle} --------------------------\n")
for proc in range(1, self.step.nprocs + 1):
p = Process(target=self._simulation_process, args=(cycle, proc))
p.start()
@@ -66,6 +57,7 @@ class DiceInterface(Interface):
def reset(self):
del self.step
del self.system
def _simulation_process(self, cycle: int, proc: int):
setproctitle(f"diceplayer-step{cycle:0d}-p{proc:0d}")
@@ -102,7 +94,7 @@ class DiceInterface(Interface):
# This is logic is used to make the initial configuration file
# for the next cycle using the last.xyz file from the previous cycle.
if self.config.randominit == 'first' and cycle > 1:
if self.step.dice.randominit == 'first' and cycle > 1:
last_xyz = Path(
self.step.simulation_dir,
f"step{(cycle - 1):02d}",
@@ -115,15 +107,15 @@ class DiceInterface(Interface):
with open(last_xyz, 'r') as last_xyz_file:
self._make_init_file(proc_dir, last_xyz_file)
last_xyz_file.seek(0)
self.config.dens = self._new_density(last_xyz_file)
self.step.dice.dens = self._new_density(last_xyz_file)
else:
self._make_nvt_ter(cycle, proc_dir)
if len(self.config.nstep) == 2:
self._make_nvt_eq(proc_dir)
if len(self.step.dice.nstep) == 2:
self._make_nvt_eq(cycle, proc_dir)
elif len(self.config.nstep) == 3:
elif len(self.step.dice.nstep) == 3:
self._make_npt_ter(cycle, proc_dir)
self._make_npt_eq(proc_dir)
@@ -142,13 +134,13 @@ class DiceInterface(Interface):
os.chdir(proc_dir)
if not (self.config.randominit == 'first' and cycle > 1):
if not (self.step.dice.randominit == 'first' and cycle > 1):
self.run_dice_file(cycle, proc, "NVT.ter")
if len(self.config.nstep) == 2:
if len(self.step.dice.nstep) == 2:
self.run_dice_file(cycle, proc, "NVT.eq")
elif len(self.config.nstep) == 3:
elif len(self.step.dice.nstep) == 3:
self.run_dice_file(cycle, proc, "NPT.ter")
self.run_dice_file(cycle, proc, "NPT.eq")
@@ -175,15 +167,15 @@ class DiceInterface(Interface):
xyz_lines = last_xyz_file.readlines()
nsites_mm = 0
for i in range(1, len(self.step.nmol)):
nsites_mm += self.step.nmol[i] * len(self.step.molecule[i].atom)
for i in range(1, len(self.step.dice.nmol)):
nsites_mm += self.step.dice.nmol[i] * len(self.system.molecule[i].atom)
xyz_lines = xyz_lines[-nsites_mm:]
input_file = Path(proc_dir, self.config.outname + ".xy")
input_file = Path(proc_dir, self.step.dice.outname + ".xy")
with open(input_file, 'w') as f:
for atom in self.step.molecule[0].atom:
for atom in self.system.molecule[0].atom:
f.write(
f"{atom.rx:>10.6f} {atom.ry:>10.6f} {atom.rz:>10.6f}\n"
)
@@ -204,8 +196,8 @@ class DiceInterface(Interface):
volume = float(box[-3]) * float(box[-2]) * float(box[-1])
total_mass = 0
for i in range(len(self.step.molecule)):
total_mass += self.step.molecule[i].total_mass * self.step.nmol[i]
for i in range(len(self.system.molecule)):
total_mass += self.system.molecule[i].total_mass * self.step.dice.nmol[i]
density = (total_mass / volume) * UMAANG3_TO_GCM3
@@ -216,21 +208,21 @@ class DiceInterface(Interface):
with open(file, 'w') as f:
f.write(f"title = {self.title} - NVT Thermalization\n")
f.write(f"ncores = {self.step.ncores}\n")
f.write(f"ljname = {self.config.ljname}\n")
f.write(f"outname = {self.config.outname}\n")
f.write(f"ljname = {self.step.dice.ljname}\n")
f.write(f"outname = {self.step.dice.outname}\n")
mol_string = " ".join(str(x) for x in self.config.nmol)
mol_string = " ".join(str(x) for x in self.step.dice.nmol)
f.write(f"nmol = {mol_string}\n")
f.write(f"dens = {self.config.dens}\n")
f.write(f"temp = {self.config.temp}\n")
f.write(f"dens = {self.step.dice.dens}\n")
f.write(f"temp = {self.step.dice.temp}\n")
if self.config.randominit == "first" and cycle > 1:
if self.step.dice.randominit == "first" and cycle > 1:
f.write(f"init = yesreadxyz\n")
f.write(f"nstep = {self.step.altsteps}\n")
else:
f.write(f"init = yes\n")
f.write(f"nstep = {self.config.nstep[0]}\n")
f.write(f"nstep = {self.step.dice.nstep[0]}\n")
f.write("vstep = 0\n")
f.write("mstop = 1\n")
@@ -241,30 +233,36 @@ class DiceInterface(Interface):
seed = int(1e6 * random.random())
f.write(f"seed = {seed}\n")
f.write(f"upbuf = {self.config.upbuf}")
f.write(f"upbuf = {self.step.dice.upbuf}")
def _make_nvt_eq(self, proc_dir):
def _make_nvt_eq(self, cycle, proc_dir):
file = Path(proc_dir, "NVT.eq")
with open(file, 'w') as f:
f.write(f"title = {self.title} - NVT Production\n")
f.write(f"ncores = {self.step.ncores}\n")
f.write(f"ljname = {self.config.ljname}\n")
f.write(f"outname = {self.config.outname}\n")
f.write(f"ljname = {self.step.dice.ljname}\n")
f.write(f"outname = {self.step.dice.outname}\n")
mol_string = " ".join(str(x) for x in self.config.nmol)
mol_string = " ".join(str(x) for x in self.step.dice.nmol)
f.write(f"nmol = {mol_string}\n")
f.write(f"dens = {self.config.dens}\n")
f.write(f"temp = {self.config.temp}\n")
f.write("init = no\n")
f.write(f"nstep = {self.config.nstep[1]}\n")
f.write(f"dens = {self.step.dice.dens}\n")
f.write(f"temp = {self.step.dice.temp}\n")
if self.step.dice.randominit == "first" and cycle > 1:
f.write("init = yesreadxyz\n")
else:
f.write("init = no\n")
f.write(f"nstep = {self.step.dice.nstep[1]}\n")
f.write("vstep = 0\n")
f.write("mstop = 1\n")
f.write("accum = no\n")
f.write("iprint = 1\n")
f.write(f"isave = {self.config.isave}\n")
f.write(f"isave = {self.step.dice.isave}\n")
f.write(f"irdf = {10 * self.step.nprocs}\n")
seed = int(1e6 * random.random())
@@ -276,22 +274,22 @@ class DiceInterface(Interface):
with open(file, 'w') as f:
f.write(f"title = {self.title} - NPT Thermalization\n")
f.write(f"ncores = {self.step.ncores}\n")
f.write(f"ljname = {self.config.ljname}\n")
f.write(f"outname = {self.config.outname}\n")
f.write(f"ljname = {self.step.dice.ljname}\n")
f.write(f"outname = {self.step.dice.outname}\n")
mol_string = " ".join(str(x) for x in self.config.nmol)
mol_string = " ".join(str(x) for x in self.step.dice.nmol)
f.write(f"nmol = {mol_string}\n")
f.write(f"press = {self.config.press}\n")
f.write(f"temp = {self.config.temp}\n")
f.write(f"press = {self.step.dice.press}\n")
f.write(f"temp = {self.step.dice.temp}\n")
if self.config.randominit == "first" and cycle > 1:
if self.step.dice.randominit == "first" and cycle > 1:
f.write("init = yesreadxyz\n")
f.write(f"dens = {self.config.dens:<8.4f}\n")
f.write(f"dens = {self.step.dice.dens:<8.4f}\n")
f.write(f"vstep = {int(self.step.altsteps / 5)}\n")
else:
f.write("init = no\n")
f.write(f"vstep = {int(self.config.nstep[1] / 5)}\n")
f.write(f"vstep = {int(self.step.dice.nstep[1] / 5)}\n")
f.write("nstep = 5\n")
f.write("mstop = 1\n")
@@ -308,23 +306,23 @@ class DiceInterface(Interface):
with open(file, 'w') as f:
f.write(f"title = {self.title} - NPT Production\n")
f.write(f"ncores = {self.step.ncores}\n")
f.write(f"ljname = {self.config.ljname}\n")
f.write(f"outname = {self.config.outname}\n")
f.write(f"ljname = {self.step.dice.ljname}\n")
f.write(f"outname = {self.step.dice.outname}\n")
mol_string = " ".join(str(x) for x in self.config.nmol)
mol_string = " ".join(str(x) for x in self.step.dice.nmol)
f.write(f"nmol = {mol_string}\n")
f.write(f"press = {self.config.press}\n")
f.write(f"temp = {self.config.temp}\n")
f.write(f"press = {self.step.dice.press}\n")
f.write(f"temp = {self.step.dice.temp}\n")
f.write(f"nstep = 5\n")
f.write(f"vstep = {int(self.config.nstep[2] / 5)}\n")
f.write(f"vstep = {int(self.step.dice.nstep[2] / 5)}\n")
f.write("init = no\n")
f.write("mstop = 1\n")
f.write("accum = no\n")
f.write("iprint = 1\n")
f.write(f"isave = {self.config.isave}\n")
f.write(f"isave = {self.step.dice.isave}\n")
f.write(f"irdf = {10 * self.step.nprocs}\n")
seed = int(1e6 * random.random())
@@ -333,15 +331,15 @@ class DiceInterface(Interface):
def _make_potentials(self, proc_dir):
fstr = "{:<3d} {:>3d} {:>10.5f} {:>10.5f} {:>10.5f} {:>10.6f} {:>9.5f} {:>7.4f}\n"
file = Path(proc_dir, self.config.ljname)
file = Path(proc_dir, self.step.dice.ljname)
with open(file, 'w') as f:
f.write(f"{self.config.combrule}\n")
f.write(f"{len(self.step.nmol)}\n")
f.write(f"{self.step.dice.combrule}\n")
f.write(f"{len(self.step.dice.nmol)}\n")
nsites_qm = len(self.step.molecule[0].atom)
f.write(f"{nsites_qm} {self.step.molecule[0].molname}\n")
nsites_qm = len(self.system.molecule[0].atom)
f.write(f"{nsites_qm} {self.system.molecule[0].molname}\n")
for atom in self.step.molecule[0].atom:
for atom in self.system.molecule[0].atom:
f.write(
fstr.format(
atom.lbl,
@@ -355,7 +353,7 @@ class DiceInterface(Interface):
)
)
for mol in self.step.molecule[1:]:
for mol in self.system.molecule[1:]:
f.write(f"{len(mol.atom)} {mol.molname}\n")
for atom in mol.atom:
f.write(
@@ -378,12 +376,12 @@ class DiceInterface(Interface):
[
"bash",
"-c",
f"exec -a dice-step{cycle}-p{proc} {self.config.progname} < {infile.name} > {outfile.name}",
f"exec -a dice-step{cycle}-p{proc} {self.step.dice.progname} < {infile.name} > {outfile.name}",
]
)
else:
exit_status = subprocess.call(
self.config.progname, stdin=infile, stdout=outfile
self.step.dice.progname, stdin=infile, stdout=outfile
)
if exit_status != 0: