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Fixes Continue from Last Run and Implements Geoms File

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This commit is contained in:
Vitor Hideyoshi
2023-06-10 23:56:57 -03:00
parent d0be244d3c
commit 8bed68c451
6 changed files with 49 additions and 14 deletions
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11
diceplayer/shared/interface/dice_interface.py
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@@ -166,11 +166,14 @@ class DiceInterface(Interface):
def _make_init_file(self, proc_dir: Path, last_xyz_file: TextIO):
xyz_lines = last_xyz_file.readlines()
nsites_mm = 0
for i in range(1, len(self.step.dice.nmol)):
nsites_mm += self.step.dice.nmol[i] * len(self.system.molecule[i].atom)
HEADER_LENGTH = 2
MAIN_MOLECULE_LENGTH = len(self.system.molecule[0].atom)
xyz_lines = xyz_lines[-nsites_mm:]
SECONDARY_MOLECULES_LENGTH = HEADER_LENGTH + MAIN_MOLECULE_LENGTH
for i in range(1, len(self.step.dice.nmol)):
SECONDARY_MOLECULES_LENGTH += self.step.dice.nmol[i] * len(self.system.molecule[i].atom)
xyz_lines = xyz_lines[HEADER_LENGTH + MAIN_MOLECULE_LENGTH: SECONDARY_MOLECULES_LENGTH]
input_file = Path(proc_dir, self.step.dice.outname + ".xy")
with open(input_file, 'w') as f: