Adds Formatter to Project

This commit is contained in:
2023-06-11 16:04:25 -03:00
parent 82f3092f3e
commit c4dae5e8d1
29 changed files with 1151 additions and 721 deletions

View File

@@ -1,4 +1,4 @@
from typing import runtime_checkable, Protocol
from typing import Protocol, runtime_checkable
@runtime_checkable

View File

@@ -1,12 +1,11 @@
from pathlib import Path
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."
assert logger._was_set, "Logger is not set. Please call set_logger() first."
return func(*args, **kwargs)
@@ -24,7 +23,7 @@ class Logger:
if self._logger is None:
self._logger = logging.getLogger(logger_name)
def set_logger(self, outfile='run.log', level=logging.INFO, stream=None):
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)
@@ -57,14 +56,14 @@ class Logger:
def _create_handlers(self, outfile_path: Path, stream):
handlers = []
if outfile_path is not None:
handlers.append(logging.FileHandler(outfile_path, mode='a+'))
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'))
handler.setFormatter(logging.Formatter("%(message)s"))
self._logger.addHandler(handler)
def close(self):

View File

@@ -14,6 +14,7 @@ ANG2BOHR: Final[float] = 1 / BOHR2ANG
####################################### functions ######################################
def weekday_date_time():
return time.strftime("%A, %d %b %Y at %H:%M:%S")
@@ -31,8 +32,8 @@ def compress_files_1mb(path):
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:
with open(file, "rb") as f_in:
with gzip.open(filegz, "wb") as f_out:
shutil.copyfileobj(f_in, f_out)
except:
sys.exit("Error: cannot compress file {}".format(file))

View File

@@ -2,34 +2,222 @@
dice_ghost_label = "Xx"
#### Tuple of atom symbols
atomsymb = ( "00",
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,
)
"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 )
#### 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
ghost_number = len(atomsymb) - 1