141 lines
4.1 KiB
ReStructuredText
141 lines
4.1 KiB
ReStructuredText
.. index:: fix bocs
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fix bocs command
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================
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID bocs keyword values ...
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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
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Examples
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""""""""
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.. parsed-literal::
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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
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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
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thermo_modify press 1_press
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Description
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"""""""""""
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These commands incorporate a pressure correction as described by
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Dunn and Noid in :ref:`(Dunn1) <bocs-Dunn1>` to the standard MTTK
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barostat by Martyna et. al. in :ref:`(Martyna) <bocs-Martyna>` .
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The first half of the command mimics a standard fix npt command:
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.. parsed-literal::
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fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp
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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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.. parsed-literal::
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Volume_i, PressureCorrection_i
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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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.. parsed-literal::
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... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
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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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""""""""""""
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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 :doc:`Build package <Build_package>` 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. :ref:`(Dunn2) <bocs-Dunn2>` .
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.. _bocsgithub: https://github.com/noid-group/BOCS
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----------
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.. _bocs-Dunn1:
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**(Dunn1)** Dunn and Noid, J Chem Phys, 143, 243148 (2015).
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.. _bocs-Martyna:
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**(Martyna)** Martyna, Tobias, and Klein, J Chem Phys, 101, 4177 (1994).
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.. _bocs-Dunn2:
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**(Dunn2)** Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018).
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Commands_all.html
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