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  • #1060
Closed
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Issue created Sep 15, 2022 by Joseph Rudzinski@jrudzDeveloper

Error in gromacs parser pruning thermo data

Error in gromacs parser:

"root":{ "errors":string"parser failed with exception" "event":string"process failed" "proc":string"Entry" "process":string"process_entry" "process_worker_id":string"4cfR3BQpTM-UcL8bWaoyXQ" "parser":string"parsers/gromacs" "error":string"list index out of range" "step":string"parsers/gromacs" "logger":string"nomad.processing" "exception":string"Traceback (most recent call last): File "/home/jfrudzinski/work/soft/nomad/nomad/processing/data.py", line 1089, in parsing parser.parse(self.mainfile_file.os_path, self._parser_results, logger=logger, **kwargs) File "/home/jfrudzinski/work/soft/nomad/nomad/parsing/parser.py", line 350, in parse self.mainfile_parser.parse(mainfile, archive, logger) File "/home/jfrudzinski/work/soft/nomad/dependencies/parsers/atomistic/atomisticparsers/gromacs/parser.py", line 1159, in parse self.parse_thermodynamic_data() File "/home/jfrudzinski/work/soft/nomad/dependencies/parsers/atomistic/atomisticparsers/gromacs/parser.py", line 623, in parse_thermodynamic_data sec_scc.system_ref = sec_run.system[n] IndexError: list index out of range" "timestamp":string"2022-09-15 13:34.21" "level":string"ERROR" }

SOLUTION:

need to change line 623: sec_scc.system_ref = sec_run.system[n // self.frame_rate]

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