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[submit_gmx_analyses_lintf2_ether.py]: Set Default of --every to 0
Change default of the --every option from 1 to 0. The value of the --every option is parsed to the -dt option of the submitted Gromacs tools. In the Gromacs documentation (https://manual.gromacs.org/documentation/2018-current/onlinehelp/gmx-trjconv.html) it says about the -dt option: > Only write/use frame when t MOD dt = first time (ps) However, when -dt is set to 1 and the spacing between frames is less than 1 ps, not every frame is processed, although t MOD 1 should be 0 for all (integer) values of t. When setting -dt 0, every frame is processed (although t MOD 0 should not be defined. However, 0 is the default value for -dt according to the docs).
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analysis/lintf2_ether/gmx/submit_gmx_analyses_lintf2_ether.py

Lines changed: 4 additions & 3 deletions
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@@ -57,7 +57,8 @@
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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 dt == first time (in ps). Default: ``1``.
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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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Options for MSD Calculation
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^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -454,9 +455,9 @@ def _submit(sbatch_opts, job_script):
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"--every",
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type=float,
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required=False,
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default=1,
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default=0,
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help=(
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"Only use frame if t MOD dt == first time (in ps). Default:"
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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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),
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)

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