Add more information to several output files#1579
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Write a #-comment header block at the start of msd.out (and any msd_step*.out intermediate files) to make them self-describing. The header records the originating command with its full argument list, format version, atom count, group count, atoms per group, cell matrix, time spacing between rows (in ps), and column names. Column names are generated dynamically: plain names for single-group runs, indexed names (msdx_0, msdx_1, ...) when all_groups is used. The cell matrix is cached in a new cpu_h_[9] member during preprocess since write() has no direct access to Box.
Write a #-comment header block at the start of thermo.out recording the originating command, format version, atom count, time spacing between rows (fs), and column names. The columns line is generated dynamically: classical ensembles label the first two columns T and KE; RPMD/TRPMD/PIMD ensembles (integrate.type >= 31) label them T_target and KE_quantum to reflect that the temperature is the target value and the kinetic energy is the quantum estimator. The cell is omitted from the header because thermo.out already writes the full box matrix in every data row.
Write a #-comment header block at the start of viscosity.out recording the originating command, format version, atom count, initial cell matrix, time spacing between correlation lags (ps), and column names. The 19 fixed columns are: correlation lag time, stress autocorrelation function (SACF) and running viscosity integral for each of the 9 stress tensor components in the order xx yy zz xy xz yz yx zx zy. The header is written in postprocess where box and atom are directly available, so no member variable caching is needed.
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Thanks, I will let some users to know this first, and see if there is any question. |
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Sounds good. |
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This PR adds headers to several output files analogously to #1552, specifically including
thermo.out(dump_thermo)msd.out(compute_msd)viscosity.out(compute_viscosity)sdc.out(compute_sdc)This makes parsing these files simpler and much less error prone since information such as the number of atoms, the cell metric, and the time step or dump frequency are included in the file and do not have to provided externally.
Each header records the originating command and its call signature,
format_version,num_atoms, cell metric (where not already in every data row), the time spacing between output rows, and column names.The headers are compatible with numpy/pandas comment-skipping parsers.