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[submit_gmx_analyses_lintf2_ether.py]: Change Default of --every
Change the default value of the `--every` option from 0 to 1. The value of the `--every` option is passed to the `-dt` option of the submitted Gromacs tools that support this option. The default value was set to 0 in PR #74 (#74), because `gmx trjconv` did not process all frames when `-dt` was set to 1 and the spacing between trajectory frames was less than 1 ps. However, it now turned out that the other Gromacs tools only process the first frame when `-dt` is set to 0. Therefore, we reset the default value for `--every` (i.e. `-dt`) to 1. In a following commit, we will replace the `-dt` option for `gmx trjconv` with `-skip`, which should be more robust (see https://www.mail-archive.com/gmx-users@gromacs.org/msg35903.html and https://www.mail-archive.com/gmx-users@gromacs.org/msg06868.html).
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analysis/lintf2_ether/gmx/submit_gmx_analyses_lintf2_ether.py

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@@ -57,8 +57,12 @@
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:file:`${settings}_out_${system}.log`. Reading from |log_file|\s
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compressed with gzip, bzip2, XZ or LZMA is supported.
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--every
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Only use frame if t MOD every == first time (in ps). Default:
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``0``.
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Read every n-th frame from the trajectory. The value given here is
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passed to the -skip option of the submitted Gromacs tools that
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support this option. If the -skip option is not supported, the
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value of \--every is passed to the -dt option. For Gromacs tools
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that do not support either of the two options, \--every has no
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effect. Default: ``1``.
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Options for MSD Calculation
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^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -455,12 +459,11 @@ def _submit(sbatch_opts, job_script):
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)
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parser_trj_reading.add_argument(
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"--every",
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type=float,
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type=int,
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required=False,
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default=0,
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default=1,
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help=(
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"Only use frame if t MOD every == first time (in ps). Default:"
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" %(default)s."
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"Read every n-th frame from the trajectory. Default: %(default)s."
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),
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)
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parser_msd = parser.add_argument_group(title="Options for MSD Calculation")

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