This class provides the same command-line option functionality to both CLI and API sessions.
This class should not exist, but is necessary now to introduce support for the CLI and API without duplicating code. It should be eliminated following the TODOs below.
- Todo:
- Modules in mdrun should acquire proper option handling so that all of these declarations and defaults are local to the modules.
- Todo:
- Contextual aspects, such as working directory, MPI environment, and environment variable handling are more properly the role of SimulationContext, and should be moved there
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MdrunOptions | mdrunOptions |
| Ongoing collection of mdrun options.
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DomdecOptions | domdecOptions |
| Options for the domain decomposition.
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gmx_hw_opt_t | hw_opt |
| Parallelism-related user options.
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int | nstlist_cmdline = 0 |
| Command-line override for the duration of a neighbor list with the Verlet scheme.
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ReplicaExchangeParameters | replExParams |
| Parameters for replica-exchange simulations.
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std::vector< t_filenm > | filenames |
| Filename options to fill from command-line argument values.
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real | pforce = -1 |
| Print a warning if any force is larger than this (in kJ/mol nm).
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gmx_output_env_t * | oenv = nullptr |
| Output context for writing text files. More...
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LogFilePtr | logFileGuard = nullptr |
| Handle to file used for logging.
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t_commrec * | cr = nullptr |
| Handle to communication object.
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gmx_multisim_t * | ms = nullptr |
| Multi-simulation object.
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rvec | realddxyz = {0, 0, 0} |
| Command line options, defaults, docs and storage for them to fill.
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const char * | ddrank_opt_choices [static_cast< int >(DdRankOrder::nr)+1] |
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const char * | dddlb_opt_choices [static_cast< int >(DlbOption::nr)+1] |
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const char * | thread_aff_opt_choices [threadaffNR+1] |
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const char * | nbpu_opt_choices [5] |
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const char * | pme_opt_choices [5] |
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const char * | pme_fft_opt_choices [5] |
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const char * | bonded_opt_choices [5] |
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gmx_bool | bTryToAppendFiles = true |
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const char * | gpuIdsAvailable = "" |
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const char * | userGpuTaskAssignment = "" |
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ImdOptions & | imdOptions = mdrunOptions.imdOptions |
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t_pargs | pa [48] |
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