chore: better project structure

diceplayer/utils/__init__.py

@@ -0,0 +1,22 @@
+from .logger import Logger, valid_logger
+from .misc import (
+    compress_files_1mb,
+    date_time,
+    make_qm_dir,
+    make_step_dir,
+    weekday_date_time,
+)
+from .ptable import atommass, atomsymb
+
+
+__all__ = [
+    "Logger",
+    "valid_logger",
+    "atomsymb",
+    "atommass",
+    "weekday_date_time",
+    "date_time",
+    "compress_files_1mb",
+    "make_step_dir",
+    "make_qm_dir",
+]

diceplayer/utils/dataclass_protocol.py

@@ -0,0 +1,6 @@
+from typing_extensions import Protocol, runtime_checkable
+
+
+@runtime_checkable
+class Dataclass(Protocol):
+    __dataclass_fields__: dict

diceplayer/utils/logger.py

@@ -0,0 +1,72 @@
+import logging
+from pathlib import Path
+
+
+def valid_logger(func):
+    def wrapper(*args, **kwargs):
+        logger = args[0]
+        assert logger._was_set, "Logger is not set. Please call set_logger() first."
+
+        return func(*args, **kwargs)
+
+    return wrapper
+
+
+class Logger:
+    outfile = None
+
+    _logger = None
+
+    _was_set = False
+
+    def __init__(self, logger_name):
+        if self._logger is None:
+            self._logger = logging.getLogger(logger_name)
+
+    def set_logger(self, outfile="run.log", level=logging.INFO, stream=None):
+        outfile_path = None
+        if outfile is not None and stream is None:
+            outfile_path = Path(outfile)
+            if outfile_path.exists():
+                outfile_path.rename(str(outfile_path) + ".backup")
+
+        if level is not None:
+            self._logger.setLevel(level)
+
+        self._create_handlers(outfile_path, stream)
+
+        self._was_set = True
+
+    @valid_logger
+    def info(self, message):
+        self._logger.info(message)
+
+    @valid_logger
+    def debug(self, message):
+        self._logger.debug(message)
+
+    @valid_logger
+    def warning(self, message):
+        self._logger.warning(message)
+
+    @valid_logger
+    def error(self, message):
+        self._logger.error(message)
+
+    def _create_handlers(self, outfile_path: Path, stream):
+        handlers = []
+        if outfile_path is not None:
+            handlers.append(logging.FileHandler(outfile_path, mode="a+"))
+        elif stream is not None:
+            handlers.append(logging.StreamHandler(stream))
+        else:
+            handlers.append(logging.StreamHandler())
+
+        for handler in handlers:
+            handler.setFormatter(logging.Formatter("%(message)s"))
+            self._logger.addHandler(handler)
+
+    def close(self):
+        for handler in self._logger.handlers:
+            handler.close()
+            self._logger.removeHandler(handler)

diceplayer/utils/misc.py

@@ -0,0 +1,67 @@
+from typing_extensions import Final
+
+import gzip
+import os
+import shutil
+import sys
+import time
+
+
+#######################################  constants  ######################################
+
+
+BOHR2ANG: Final[float] = 0.52917721092
+ANG2BOHR: Final[float] = 1 / BOHR2ANG
+
+
+#######################################  functions  ######################################
+
+
+def weekday_date_time():
+    return time.strftime("%A, %d %b %Y at %H:%M:%S")
+
+
+def date_time():
+    return time.strftime("%d %b %Y at %H:%M:%S")
+
+
+def compress_files_1mb(path):
+    working_dir = os.getcwd()
+    os.chdir(path)
+
+    files = filter(os.path.isfile, os.listdir(os.curdir))
+    for file in files:
+        if os.path.getsize(file) > 1024 * 1024:  ## If bigger than 1MB
+            filegz = file + ".gz"
+            try:
+                with open(file, "rb") as f_in:
+                    with gzip.open(filegz, "wb") as f_out:
+                        shutil.copyfileobj(f_in, f_out)
+            except Exception as _:
+                sys.exit("Error: cannot compress file {}".format(file))
+
+    os.chdir(working_dir)
+
+    return
+
+
+def make_step_dir(cycle):
+    sim_dir = "simfiles"
+    step_dir = "step{:02d}".format(cycle)
+    path = sim_dir + os.sep + step_dir
+    if os.path.exists(path):
+        sys.exit("Error: a file or directory {} already exists".format(step_dir))
+    try:
+        os.makedirs(path)
+    except Exception as _:
+        sys.exit("Error: cannot make directory {}".format(step_dir))
+
+
+def make_qm_dir(cycle):
+    sim_dir = "simfiles"
+    step_dir = "step{:02d}".format(cycle)
+    path = sim_dir + os.sep + step_dir + os.sep + "qm"
+    try:
+        os.makedirs(path)
+    except Exception as _:
+        sys.exit("Error: cannot make directory {}".format(path))

diceplayer/utils/ptable.py

@@ -0,0 +1,223 @@
+####  Label used in Dice for a ghost atom
+dice_ghost_label = "Xx"
+
+####  Tuple of atom symbols
+atomsymb = (
+    "00",
+    "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",
+    "Ti",
+    "Pb",
+    "Bi",
+    "Po",
+    "At",
+    "Rn",
+    "Fr",
+    "Ra",
+    "Ac",
+    "Th",
+    "Pa",
+    "U ",
+    "Np",
+    "Pu",
+    "Am",
+    "Cm",
+    "Bk",
+    "Cf",
+    "Es",
+    "Fm",
+    "Md",
+    "No",
+    "Lr",
+    dice_ghost_label,
+)
+
+####  Tuple of atom masses
+atommass = (
+    0.0,
+    1.0079,
+    4.0026,
+    6.9410,
+    9.0122,
+    10.811,
+    12.011,
+    14.007,
+    15.999,
+    18.998,
+    20.180,
+    22.990,
+    24.305,
+    26.982,
+    28.086,
+    30.974,
+    32.065,
+    35.453,
+    39.948,
+    39.098,
+    40.078,
+    44.956,
+    47.867,
+    50.942,
+    51.996,
+    54.938,
+    55.845,
+    58.933,
+    58.693,
+    63.546,
+    65.409,
+    69.723,
+    72.640,
+    74.922,
+    78.960,
+    79.904,
+    83.798,
+    85.468,
+    87.620,
+    88.906,
+    91.224,
+    92.906,
+    95.940,
+    98.000,
+    101.07,
+    102.91,
+    106.42,
+    107.87,
+    112.41,
+    114.82,
+    118.71,
+    121.76,
+    127.60,
+    126.90,
+    131.29,
+    132.91,
+    137.33,
+    138.91,
+    140.12,
+    140.91,
+    144.24,
+    145.00,
+    150.36,
+    151.96,
+    157.25,
+    158.93,
+    162.50,
+    164.93,
+    167.26,
+    168.93,
+    173.04,
+    174.97,
+    178.49,
+    180.95,
+    183.84,
+    186.21,
+    190.23,
+    192.22,
+    195.08,
+    196.97,
+    200.59,
+    204.38,
+    207.20,
+    208.98,
+    209.00,
+    210.00,
+    222.00,
+    223.00,
+    226.00,
+    227.00,
+    232.04,
+    231.04,
+    238.03,
+    237.00,
+    244.00,
+    243.00,
+    247.00,
+    247.00,
+    251.00,
+    252.00,
+    257.00,
+    258.00,
+    259.00,
+    262.00,
+    0.000,
+)
+
+####  Number of the ghost atom
+ghost_number = len(atomsymb) - 1