forked from lijiext/lammps
113 lines
4.0 KiB
Plaintext
113 lines
4.0 KiB
Plaintext
<"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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fix bocs command :h3
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[Syntax:]
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fix ID group-ID bocs keyword values ... :pre
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keyword = {temp} or {cgiso} or {analytic} or {linear_spline} or {cubic_spline}
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{temp} values = Tstart Tstop Tdamp
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{cgiso} values = Pstart Pstop Pdamp
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{basis set}
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{analytic} values = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
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{linear_spline} values = input_filename
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{cubic_spline} values = input_filename :pre
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:ule
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[Examples:]
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fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 :pre
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fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline input_Fv.dat :pre
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thermo_modify press 1_press :pre
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[Description:]
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These commands incorporate a pressure correction as described by
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Dunn and Noid in "(Dunn1)"_#bocs-Dunn1 to the standard MTTK
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barostat by Martyna et. al. in "(Martyna)"_#bocs-Martyna .
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The first half of the command mimics a standard fix npt command:
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fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp :pre
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The two differences are replacing {npt} with {bocs}, and replacing
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{iso}/{aniso}/{etc} with {cgiso}.
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The rest of the command details what form you would like to use for
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the pressure correction equation. The choices are: {analytic}, {linear_spline},
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or {cubic_spline}.
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With either spline method, the only argument that needs to follow it
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is the name of a file that contains the desired pressure correction
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as a function of volume. The file must be formatted so each line has:
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Volume_i, PressureCorrection_i :pre
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Note both the COMMA and the SPACE separating the volume's
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value and its corresponding pressure correction. The volumes in the file
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must be uniformly spaced. Both the volumes and the pressure corrections
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should be provided in the proper units, e.g. if you are using {units real},
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the volumes should all be in cubic angstroms, and the pressure corrections
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should all be in atmospheres. Furthermore, the table should start/end at a
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volume considerably smaller/larger than you expect your system to sample
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during the simulation. If the system ever reaches a volume outside of the
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range provided, the simulation will stop.
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With the {analytic} option, the arguments are as follows:
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... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N :pre
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Note that {V_avg} and {Coeff_i} should all be in the proper units, e.g. if you
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are using {units real}, {V_avg} should be in cubic angstroms, and the
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coefficients should all be in atmospheres * cubic angstroms.
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[Restrictions:]
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As this is computing a (modified) pressure, group-ID should be {all}.
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The pressure correction has only been tested for use with an isotropic
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pressure coupling in 3 dimensions.
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By default, LAMMPS will still report the normal value for the pressure
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if the pressure is printed via a {thermo} command, or if the pressures
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are written to a file every so often. In order to have LAMMPS report the
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modified pressure, you must include the {thermo_modify} command given in
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the examples. For the last argument in the command, you should put
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XXXX_press, where XXXX is the ID given to the fix bocs command (in the
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example, the ID of the fix bocs command is 1 ).
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This fix is part of the USER-BOCS package. It is only enabled if
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LAMMPS was built with that package. See the "Build
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package"_Build_package.html doc page for more info.
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[Related:]
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For more details about the pressure correction and the entire BOCS software
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package, visit the "BOCS package on GitHub"_bocsgithub and read the release
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paper by Dunn et. al. "(Dunn2)"_#bocs-Dunn2 .
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:link(bocsgithub,https://github.com/noid-group/BOCS)
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:line
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:link(bocs-Dunn1)
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[(Dunn1)] Dunn and Noid, J Chem Phys, 143, 243148 (2015).
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:link(bocs-Martyna)
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[(Martyna)] Martyna, Tobias, and Klein, J Chem Phys, 101, 4177 (1994).
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:link(bocs-Dunn2)
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[(Dunn2)] Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018).
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