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feat: expose create_plumed_input (#483)
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* feat: make stride variable
* feat: expose plumed input creation in cli
* doc: update changes
* make indexgroup interactive and fix file handling
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KRiedmiller authored Sep 11, 2024
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4 changes: 2 additions & 2 deletions _freeze/guide/references/cmd_ref/execute-results/html.json
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"markdown": "---\nexecute:\n echo: true\ntitle: CLI Arguments\n---\n\n\n\n\n\nThe prefered method of starting a KIMMDY run is via the command line, though [Python entry points](../../_reference/cmd.qmd) are supported as well.\n\n## KIMMDY\n\n\n::: {#f025a1ca .cell execution_count=1}\n``` {.python .cell-code}\n!kimmdy --help\n```\n\n::: {.cell-output .cell-output-stdout}\n```\nusage: kimmdy [-h] [--input INPUT] [--checkpoint CHECKPOINT]\r\n [--loglevel LOGLEVEL] [--logfile LOGFILE] [--show-plugins]\r\n [--generate-jobscript] [--version] [--debug] [--callgraph]\r\n\r\nWelcome to KIMMDY. `kimmdy` runs KIMMDY, further tools are available as\r\n`kimmdy-...` commands. These are `-analysis`, `-modify-top` and `-build-\r\nexamples`. Access their help with `kimmdy-... -h.`\r\n\r\noptions:\r\n -h, --help show this help message and exit\r\n --input INPUT, -i INPUT\r\n Kimmdy input file. Default `kimmdy.yml`\r\n --checkpoint CHECKPOINT, -c CHECKPOINT\r\n File path of a kimmdy.cpt file to restart KIMMDY from\r\n a checkpoint. If a directory is given, the file\r\n kimmdy.cpt in that directory is used.\r\n --loglevel LOGLEVEL, -l LOGLEVEL\r\n logging level (CRITICAL, ERROR, WARNING, INFO, DEBUG)\r\n --logfile LOGFILE, -f LOGFILE\r\n logfile\r\n --show-plugins List available plugins\r\n --generate-jobscript Instead of running KIMMDY directly, generate at\r\n jobscript.sh for slurm HPC clusters.You can then run\r\n this jobscript with sbatch jobscript.sh\r\n --version show program's version number and exit\r\n --debug on error, drop into debugger\r\n --callgraph Generate visualization of function calls. Mostly\r\n useful for debugging and documentation.\r\n```\n:::\n:::\n\n\n## Analysis\n\n::: {#ae57bf41 .cell execution_count=2}\n``` {.python .cell-code}\n!kimmdy-analysis --help\n```\n\n::: {.cell-output .cell-output-stdout}\n```\nusage: kimmdy-analysis [-h] module ...\r\n\r\nWelcome to the KIMMDY analysis module. Use this module to analyse existing\r\nKIMMDY runs.\r\n\r\npositional arguments:\r\n module\r\n trjcat Concatenate trajectories of a KIMMDY run\r\n energy Plot GROMACS energy for a KIMMDY run\r\n radical_population\r\n Plot population of radicals for one or multiple KIMMDY\r\n run(s)\r\n rates Plot rates of all possible reactions after a MD run.\r\n Rates must have been saved!\r\n runtime Plot runtime of the tasks of a kimmdy run.\r\n\r\noptions:\r\n -h, --help show this help message and exit\r\n```\n:::\n:::\n\n\n## Remove Hydrogen\n\nThis module builds or restores the example directory in the package.\n\n::: {#d354a57c .cell execution_count=3}\n``` {.python .cell-code}\n!kimmdy-modify-top --help\n```\n\n::: {.cell-output .cell-output-stdout}\n```\nusage: kimmdy-modify-top [-h] [-p] [-r REMOVEH [REMOVEH ...]] [-c GROFILE]\r\n [-t RESIDUETYPES] [-x RADICALS]\r\n top out\r\n\r\nWelcome to the KIMMDY modify top module\r\n\r\npositional arguments:\r\n top GROMACS top file\r\n out Output top file name\r\n\r\noptions:\r\n -h, --help show this help message and exit\r\n -p, --parameterize Parameterize topology with grappa. (default: False)\r\n -r REMOVEH [REMOVEH ...], --removeH REMOVEH [REMOVEH ...]\r\n Remove one or more hydrogens by atom nrs in the top\r\n file. (default: None)\r\n -c GROFILE, --grofile GROFILE\r\n If necessary, also apply actions on gro file to create\r\n a compatible gro/top file pair. (default: None)\r\n -t RESIDUETYPES, --residuetypes RESIDUETYPES\r\n GROMACS style residuetypes file. Necessary for\r\n parameterization with non-amber atom types. (default:\r\n None)\r\n -x RADICALS, --radicals RADICALS\r\n Radicals in the system PRIOR to removing hydrogens\r\n with the removeH option. (default: )\r\n```\n:::\n:::\n\n\n## Examples\n\nThis module builds or restores the example directory in the package.\n\n::: {#8f4df5b5 .cell execution_count=4}\n``` {.python .cell-code}\n!kimmdy-build-examples --help\n```\n\n::: {.cell-output .cell-output-stdout}\n```\nusage: kimmdy-build-examples [-h] [-r [RESTORE]]\r\n\r\nBuild examples for KIMMDY.\r\n\r\noptions:\r\n -h, --help show this help message and exit\r\n -r [RESTORE], --restore [RESTORE]\r\n Overwrite input files in existing example directories,\r\n use keyword 'hard' to also delete output files.\r\n```\n:::\n:::\n\n\n",
"markdown": "---\nexecute:\n echo: true\ntitle: Analysis\n---\n\n\n\n\n\n\n# CLI Arguments\n\nThe prefered method of starting a KIMMDY run is via the command line, though [Python entry points](../../_reference/cmd.qmd) are supported as well.\n\n## KIMMDY\n\n\n::: {#3b93130d .cell execution_count=1}\n``` {.python .cell-code}\n!kimmdy --help\n```\n\n::: {.cell-output .cell-output-stdout}\n```\nusage: kimmdy [-h] [--input INPUT] [--loglevel LOGLEVEL] [--logfile LOGFILE]\r\n [--show-plugins] [--generate-jobscript] [--version] [--debug]\r\n [--callgraph]\r\n\r\nWelcome to KIMMDY. `kimmdy` runs KIMMDY, further tools are available as\r\n`kimmdy-...` commands. These are `-analysis`, `-modify-top` and `-build-\r\nexamples`. Access their help with `kimmdy-... -h.`\r\n\r\noptions:\r\n -h, --help show this help message and exit\r\n --input INPUT, -i INPUT\r\n Kimmdy input file. Default `kimmdy.yml`\r\n --loglevel LOGLEVEL, -l LOGLEVEL\r\n logging level (CRITICAL, ERROR, WARNING, INFO, DEBUG)\r\n --logfile LOGFILE, -f LOGFILE\r\n logfile\r\n --show-plugins List available plugins\r\n --generate-jobscript Instead of running KIMMDY directly, generate at\r\n jobscript.sh for slurm HPC clusters.You can then run\r\n this jobscript with sbatch jobscript.sh\r\n --version show program's version number and exit\r\n --debug on error, drop into debugger\r\n --callgraph Generate visualization of function calls. Mostly\r\n useful for debugging and documentation.\r\n```\n:::\n:::\n\n\n\n\n::: {#da853220 .cell execution_count=2}\n``` {.python .cell-code}\n!kimmdy-analysis --help\n```\n\n::: {.cell-output .cell-output-stdout}\n```\nusage: kimmdy-analysis [-h] module ...\r\n\r\nWelcome to the KIMMDY analysis module. Use this module to analyse existing\r\nKIMMDY runs.\r\n\r\npositional arguments:\r\n module\r\n trjcat Concatenate trajectories of a KIMMDY run\r\n energy Plot GROMACS energy for a KIMMDY run\r\n radical_population Plot population of radicals for one or multiple KIMMDY\r\n run(s)\r\n radical_migration Create a json of radical migration events for further\r\n analysis.\r\n rates Plot rates of all possible reactions after a MD run.\r\n Rates must have been saved!\r\n runtime Plot runtime of the tasks of a kimmdy run.\r\n reaction_participation\r\n Plot counts of reaction participation per atom id\r\n\r\noptions:\r\n -h, --help show this help message and exit\r\n```\n:::\n:::\n\n\n## Create plumed input\n\nThis module creates input files for plumed based on a topology and index file.\n\n::: {#62f32141 .cell execution_count=3}\n``` {.python .cell-code}\n!kimmdy-create-plumed --help\n```\n\n::: {.cell-output .cell-output-stdout}\n```\nusage: kimmdy-create-plumed [-h] [--entries-to-remove [ENTRIES_TO_REMOVE ...]]\r\n [--stride STRIDE] -p TOP -i INDEX --indexgroup\r\n INDEXGROUP\r\n\r\nBuild plumed input file. Requires a topology file and a gromacs index file.\r\n\r\noptions:\r\n -h, --help show this help message and exit\r\n --entries-to-remove [ENTRIES_TO_REMOVE ...]\r\n Either atomnames or bonds, i.e. atomnames separated by\r\n a hyphen that should not be written to the plumed\r\n configuration file. Default: C-N H* O*\r\n --stride STRIDE Frequency of plumed output as multiple of the md\r\n timestep. Default: 100\r\n -p TOP, --top TOP Gromacs topology file path.\r\n -i INDEX, --index INDEX\r\n Gromacs index file path.\r\n --indexgroup INDEXGROUP\r\n Index group name out of which bonds will be written to\r\n the plumed configuration file.\r\n```\n:::\n:::\n\n\n## Remove Hydrogen\n\nThis module builds or restores the example directory in the package.\n\n::: {#5f68f86b .cell execution_count=4}\n``` {.python .cell-code}\n!kimmdy-modify-top --help\n```\n\n::: {.cell-output .cell-output-stdout}\n``````````````````````````\nusage: kimmdy-modify-top [-h] [-p] [--grappa_tag GRAPPA_TAG]\r\n [--grappa_charge_model GRAPPA_CHARGE_MODEL]\r\n [-r REMOVEH [REMOVEH ...]] [-c GRO] [-a]\r\n [-t RESIDUETYPES] [-x RADICALS [RADICALS ...]]\r\n [-w INCLUDE] [-b EXCLUDE]\r\n top out\r\n\r\nWelcome to the KIMMDY modify top module\r\n\r\npositional arguments:\r\n top GROMACS top file\r\n out Output top file name. Stem reused for gro if\r\n applicabel.\r\n\r\noptions:\r\n -h, --help show this help message and exit\r\n -p, --parameterize Parameterize topology with grappa. (default: False)\r\n --grappa_tag GRAPPA_TAG\r\n Set grappa model tag for parameterization. (default:\r\n latest)\r\n --grappa_charge_model GRAPPA_CHARGE_MODEL\r\n Set grappa charge model for parameterization.\r\n (default: amber99)\r\n -r REMOVEH [REMOVEH ...], --removeH REMOVEH [REMOVEH ...]\r\n Remove one or more hydrogens by atom nrs in the top\r\n file. (default: None)\r\n -c GRO, --gro GRO If necessary, also apply actions on gro file to create\r\n a compatible gro/top file pair. Output analog to top.\r\n (default: None)\r\n -a, --search_amber_rad\r\n Automatic radical search only implemented for amber.\r\n If you douse another ff, set this to false, and\r\n provide a list of radicalsmanually, if necessary.\r\n (default: False)\r\n -t RESIDUETYPES, --residuetypes RESIDUETYPES\r\n GROMACS style residuetypes file. Necessary for\r\n parameterization with non-amber atom types. (default:\r\n None)\r\n -x RADICALS [RADICALS ...], --radicals RADICALS [RADICALS ...]\r\n Radicals in the system PRIOR to removing hydrogens\r\n with the removeH option. (default: None)\r\n -w INCLUDE, --include INCLUDE\r\n Include certain GROMACS topology molecules in\r\n `Reactive` molecule. Reads molecule names from a csv\r\n file. (default: None)\r\n -b EXCLUDE, --exclude EXCLUDE\r\n Exclude certain GROMACS topology molecules in\r\n `Reactive` molecule. Reads molecule names from a csv\r\n file. (default: None)\r\n``````````````````````````\n:::\n:::\n\n\n## Examples\n\nThis module builds or restores the example directory in the package.\n\n::: {#ab9478d8 .cell execution_count=5}\n``` {.python .cell-code}\n!kimmdy-build-examples --help\n```\n\n::: {.cell-output .cell-output-stdout}\n```\nusage: kimmdy-build-examples [-h] [-r [RESTORE]]\r\n\r\nBuild examples for KIMMDY.\r\n\r\noptions:\r\n -h, --help show this help message and exit\r\n -r [RESTORE], --restore [RESTORE]\r\n Overwrite input files in existing example directories,\r\n use keyword 'hard' to also delete output files.\r\n```\n:::\n:::\n\n\n",
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