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Implements the Use of a Simple DTO for Communication Between Classes

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This commit is contained in:
Vitor Hideyoshi
2022-05-31 09:55:19 -03:00
parent 0d78c83e91
commit 44cb4268ef
6 changed files with 137 additions and 180 deletions
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144
diceplayer/DPpack/External/Dice.py vendored
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@@ -1,24 +1,16 @@
from dataclasses import dataclass
from diceplayer.DPpack.Utils.PTable import *
from diceplayer.DPpack.Utils.Misc import *
from diceplayer.DPpack.Environment.Molecule import Molecule
from diceplayer.DPpack.Environment.Atom import Atom
from typing import IO, Final, Tuple, List, TextIO, Union
from numpy.core.numeric import partition
from numpy import random
from multiprocessing import Process, connection
import subprocess
import setproctitle
import os
import sys
import shutil
import subprocess
import sys
from multiprocessing import Process, connection
from typing import Final, List, TextIO
import setproctitle
from diceplayer.DPpack.Utils.Misc import *
from diceplayer.DPpack.Utils.PTable import *
from diceplayer.DPpack.Utils.StepDTO import StepDTO
from diceplayer.DPpack.Utils.Validations import NotNull
from numpy import random
DICE_END_FLAG: Final[str] = "End of simulation"
DICE_FLAG_LINE: Final[int] = -2
@@ -26,18 +18,17 @@ UMAANG3_TO_GCM3: Final[float] = 1.6605
MAX_SEED: Final[int] = 4294967295
class Dice:
title = "Diceplayer run"
progname = "dice"
path = None
nprocs: int = None
randominit = "first"
combrule = "*"
ncores = 1
temp = 300.0
press = 1.0
isave = 1000
@@ -53,14 +44,7 @@ class Dice:
self.infile = infile
self.outfile = outfile
@NotNull(requiredArgs = [
"ncores",
"nmol",
"dens",
"nstep",
"ljname",
"outname"
])
@NotNull(requiredArgs=["ncores", "nmol", "dens", "nstep", "ljname", "outname"])
def updateKeywords(self, **data):
self.__dict__.update(data)
@@ -86,9 +70,9 @@ class Dice:
volume = float(box[-3]) * float(box[-2]) * float(box[-1])
total_mass = 0
for i in range(len(self.molecule)):
for i in range(len(self.step.molecule)):
total_mass += self.molecule[i].total_mass * self.nmol[i]
total_mass += self.step.molecule[i].total_mass * self.step.nmol[i]
density = (total_mass / volume) * UMAANG3_TO_GCM3
@@ -109,9 +93,9 @@ class Dice:
except:
sys.exit("Error: cannot open file {}".format(file))
nsites = len(self.molecule[0].atom) * self.nmol[0]
for i in range(1, len(self.nmol)):
nsites += self.nmol[i] * len(self.molecule[i].atom)
nsites = len(self.step.molecule[0].atom) * self.step.nmol[0]
for i in range(1, len(self.step.nmol)):
nsites += self.step.nmol[i] * len(self.step.molecule[i].atom)
nsites += 2
@@ -132,11 +116,11 @@ class Dice:
num = time.time()
num = (num - int(num)) * 1e6
num = int((num - int(num)) * 1e6)
random.seed((os.getpid() * num) % (MAX_SEED + 1))
if self.randominit == "first" and cycle > self.initcyc:
if self.randominit == "first" and cycle > self.step.initcyc:
last_step_dir = "step{:02d}".format(cycle - 1)
last_path = sim_dir + os.sep + last_step_dir + os.sep + proc_dir
xyzfile = last_path + os.sep + "last.xyz"
@@ -149,7 +133,7 @@ class Dice:
elif len(self.nstep) == 3:
if self.randominit == "first" and cycle > self.initcyc:
if self.randominit == "first" and cycle > self.step.initcyc:
self.dens = self.__new_density(cycle, proc)
else:
self.__make_nvt_ter(cycle, path)
@@ -175,15 +159,15 @@ class Dice:
fh.write("ljname = {}\n".format(self.ljname))
fh.write("outname = {}\n".format(self.outname))
string = " ".join(str(x) for x in self.nmol)
string = " ".join(str(x) for x in self.step.nmol)
fh.write("nmol = {}\n".format(string))
fh.write("dens = {}\n".format(self.dens))
fh.write("temp = {}\n".format(self.temp))
if self.randominit == "first" and cycle > self.initcyc:
if self.randominit == "first" and cycle > self.step.initcyc:
fh.write("init = yesreadxyz\n")
fh.write("nstep = {}\n".format(self.altsteps))
fh.write("nstep = {}\n".format(self.step.altsteps))
else:
fh.write("init = yes\n")
fh.write("nstep = {}\n".format(self.nstep[0]))
@@ -214,7 +198,7 @@ class Dice:
fh.write("ljname = {}\n".format(self.ljname))
fh.write("outname = {}\n".format(self.outname))
string = " ".join(str(x) for x in self.nmol)
string = " ".join(str(x) for x in self.step.nmol)
fh.write("nmol = {}\n".format(string))
fh.write("dens = {}\n".format(self.dens))
@@ -226,7 +210,7 @@ class Dice:
fh.write("accum = no\n")
fh.write("iprint = 1\n")
fh.write("isave = {}\n".format(self.isave))
fh.write("irdf = {}\n".format(10 * self.nprocs))
fh.write("irdf = {}\n".format(10 * self.step.nprocs))
seed = int(1e6 * random.random())
fh.write("seed = {}\n".format(seed))
@@ -246,16 +230,16 @@ class Dice:
fh.write("ljname = {}\n".format(self.ljname))
fh.write("outname = {}\n".format(self.outname))
string = " ".join(str(x) for x in self.nmol)
string = " ".join(str(x) for x in self.step.nmol)
fh.write("nmol = {}\n".format(string))
fh.write("press = {}\n".format(self.press))
fh.write("temp = {}\n".format(self.temp))
if self.randominit == "first" and cycle > self.initcyc:
if self.randominit == "first" and cycle > self.step.initcyc:
fh.write("init = yesreadxyz\n")
fh.write("dens = {:<8.4f}\n".format(self.dens))
fh.write("vstep = {}\n".format(int(self.altsteps / 5)))
fh.write("vstep = {}\n".format(int(self.step.altsteps / 5)))
else:
fh.write("init = no\n")
fh.write("vstep = {}\n".format(int(self.nstep[1] / 5)))
@@ -285,7 +269,7 @@ class Dice:
fh.write("ljname = {}\n".format(self.ljname))
fh.write("outname = {}\n".format(self.outname))
string = " ".join(str(x) for x in self.nmol)
string = " ".join(str(x) for x in self.step.nmol)
fh.write("nmol = {}\n".format(string))
fh.write("press = {}\n".format(self.press))
@@ -299,7 +283,7 @@ class Dice:
fh.write("accum = no\n")
fh.write("iprint = 1\n")
fh.write("isave = {}\n".format(self.isave))
fh.write("irdf = {}\n".format(10 * self.nprocs))
fh.write("irdf = {}\n".format(10 * self.step.nprocs))
seed = int(1e6 * random.random())
fh.write("seed = {}\n".format(seed))
@@ -319,11 +303,11 @@ class Dice:
sys.exit("Error: cannot open file {}".format(file))
nsites_mm = 0
for i in range(1, len(self.nmol)):
nsites_mm += self.nmol[i] * len(self.molecule[i].atom)
for i in range(1, len(self.step.nmol)):
nsites_mm += self.step.nmol[i] * len(self.step.molecule[i].atom)
nsites_mm *= -1
xyzfile = xyzfile[nsites_mm:]
file = path + os.sep + self.outname + ".xy"
@@ -333,7 +317,7 @@ class Dice:
except:
sys.exit("Error: cannot open file {}".format(file))
for atom in self.molecule[0].atom:
for atom in self.step.molecule[0].atom:
fh.write(
"{:>10.6f} {:>10.6f} {:>10.6f}\n".format(atom.rx, atom.ry, atom.rz)
)
@@ -360,16 +344,16 @@ class Dice:
sys.exit("Error: cannot open file {}".format(file))
fh.write("{}\n".format(self.combrule))
fh.write("{}\n".format(len(self.nmol)))
fh.write("{}\n".format(len(self.step.nmol)))
nsites_qm = (
len(self.molecule[0].atom)
+ len(self.molecule[0].ghost_atoms)
+ len(self.molecule[0].lp_atoms)
len(self.step.molecule[0].atom)
+ len(self.step.molecule[0].ghost_atoms)
+ len(self.step.molecule[0].lp_atoms)
)
fh.write("{} {}\n".format(nsites_qm, self.molecule[0].molname))
for atom in self.molecule[0].atom:
fh.write("{} {}\n".format(nsites_qm, self.step.molecule[0].molname))
for atom in self.step.molecule[0].atom:
fh.write(
fstr.format(
atom.lbl,
@@ -383,23 +367,23 @@ class Dice:
)
)
ghost_label = self.molecule[0].atom[-1].lbl + 1
for i in self.molecule[0].ghost_atoms:
ghost_label = self.step.molecule[0].atom[-1].lbl + 1
for i in self.step.molecule[0].ghost_atoms:
fh.write(
fstr.format(
ghost_label,
ghost_number,
self.molecule[0].atom[i].rx,
self.molecule[0].atom[i].ry,
self.molecule[0].atom[i].rz,
self.molecule[0].atom[i].chg,
self.step.molecule[0].atom[i].rx,
self.step.molecule[0].atom[i].ry,
self.step.molecule[0].atom[i].rz,
self.step.molecule[0].atom[i].chg,
0,
0,
)
)
ghost_label += 1
for lp in self.molecule[0].lp_atoms:
for lp in self.step.molecule[0].lp_atoms:
fh.write(
fstr.format(
ghost_label,
@@ -413,7 +397,7 @@ class Dice:
)
)
for mol in self.molecule[1:]:
for mol in self.step.molecule[1:]:
fh.write("{} {}\n".format(len(mol.atom), mol.molname))
for atom in mol.atom:
fh.write(
@@ -462,7 +446,7 @@ class Dice:
if len(self.nstep) == 2:
if self.randominit == "first" and cycle > self.initcyc:
if self.randominit == "first" and cycle > self.step.initcyc:
string_tmp = "previous"
else:
string_tmp = "random"
@@ -620,7 +604,7 @@ class Dice:
)
if not self.randominit == "always" or (
(self.randominit == "first" and cycle > self.initcyc)
(self.randominit == "first" and cycle > self.step.initcyc)
):
string = " (from previous configuration) "
else:
@@ -735,28 +719,15 @@ class Dice:
except Exception as err:
sys.exit(err)
def configure(
self,
initcyc: int,
nprocs: int,
altsteps: int,
nmol: List[int],
molecule: List[Molecule],
):
self.initcyc = initcyc
self.nprocs = nprocs
self.altsteps = altsteps
self.nmol = nmol
self.molecule = molecule
def configure(self, step: StepDTO):
self.step = step
def start(self, cycle: int) -> None:
procs = []
sentinels = []
for proc in range(1, self.nprocs + 1):
for proc in range(1, self.step.nprocs + 1):
p = Process(target=self.__simulation_process, args=(cycle, proc))
p.start()
@@ -776,11 +747,8 @@ class Dice:
p.terminate()
sys.exit(status)
for proc in range(1, self.nprocs + 1):
for proc in range(1, self.step.nprocs + 1):
self.__print_last_config(cycle, proc)
def reset(self):
del self.nprocs
del self.altsteps
del self.molecule
del self.step