HideyoshiNakazone/CrystalPol
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Implements Better Tests and Logging

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This commit is contained in:
Vitor Hideyoshi
2023-03-01 02:49:28 -03:00
parent 32ca95086a
commit aea34bf214
17 changed files with 1147 additions and 72 deletions
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11
crystalpol/gaussian.py
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@@ -81,9 +81,6 @@ class Gaussian:
with open(file, 'w+') as fh:
chk_path = file.with_suffix('.chk')
fh.write(f"%Chk={chk_path}\n")
fh.write(f"%Mem={self.config.mem}Gb\n")
fh.write(f"%Nprocs={self.config.n_procs}\n")
@@ -120,13 +117,13 @@ class Gaussian:
fh.seek(0)
return fh.read()
def make_gaussian_charges(self, fh: TextIO, crystal: Crystal) -> None:
@staticmethod
def make_gaussian_charges(fh: TextIO, crystal: Crystal) -> None:
for index_cell, cell in enumerate(crystal):
for index_mol, molecule in enumerate(cell):
if (index_cell == 0 and index_mol != 0) or (index_cell != 0):
for atom in molecule:
symbol = atom_symbol[atom.na]
fh.write(
f"{float(atom.rx):>10.5f} "
f"{float(atom.ry):>10.5f} "
@@ -134,8 +131,6 @@ class Gaussian:
f"{float(atom.chg):>10.5f}\n"
)
fh.write("\n")
def read_charges_from_gaussian_output(self, cycle, number_of_charges: int) -> List[float]:
step_dir = Path(
self.config.simulation_dir,
@@ -156,4 +151,4 @@ class Gaussian:
lines = lines[3:] # Consume 3 more lines
return list(map(lambda x: float(x.split()[2]), lines[:number_of_charges]))
return list(map(lambda x: float(x.split()[2]), lines[:number_of_charges]))