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Avoid crushing when can't trsh scan #763

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merged 2 commits into from
Aug 19, 2024
Merged

Avoid crushing when can't trsh scan #763

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0ff829a
Organised imports in job trsh
alongd Aug 18, 2024
82f6c48
BugFix: Only call conf_xyzs[min_index] if the length makes sense
alongd Aug 18, 2024
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15 changes: 8 additions & 7 deletions arc/job/trsh.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,11 +4,11 @@

import math
import os
import re
from typing import List, Optional, Tuple, Union

import numpy as np
import pandas as pd
import re

from arc.common import (check_torsion_change,
convert_to_hours,
Expand All @@ -18,26 +18,26 @@
get_number_with_ordinal_indicator,
is_same_pivot,
is_same_sequence_sublist,
is_str_float
is_str_float,
)
from arc.exceptions import InputError, SpeciesError, TrshError
from arc.imports import settings
from arc.level import Level
from arc.job.local import execute_command
from arc.job.ssh import SSHClient
from arc.level import Level
from arc.species import ARCSpecies
from arc.species.conformers import determine_smallest_atom_index_in_scan
from arc.species.converter import (displace_xyz, ics_to_scan_constraints)
from arc.species.converter import displace_xyz, ics_to_scan_constraints
from arc.species.species import determine_rotor_symmetry
from arc.species.vectors import calculate_dihedral_angle, calculate_distance

from arc.parser import (parse_1d_scan_coords,
parse_normal_mode_displacement,
parse_scan_args,
parse_scan_conformers,
parse_xyz_from_file,
)


logger = get_logger()


Expand Down Expand Up @@ -1537,8 +1537,9 @@ def scan_quality_check(label: str,
# Find the dihedrals in degrees of the lowest conformer:
min_index = np.argmin(energies)
conf_xyzs = parse_1d_scan_coords(log_file)
actions = {'change conformer': conf_xyzs[min_index]}
return invalidate, invalidation_reason, message, actions
if len(conf_xyzs) > min_index:
actions = {'change conformer': conf_xyzs[min_index]}
return invalidate, invalidation_reason, message, actions

# 1.3 Check consistency
if 0 in changed_ic_dict.keys() and len(changed_ic_dict) == 1:
Expand Down
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