163 lines
6.1 KiB
ReStructuredText
163 lines
6.1 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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.. code-block:: LAMMPS
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fix ID group-ID bocs keyword values ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* bocs = style name of this fix command
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* two or more keyword/value pairs may be appended
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* keyword = *temp* or *cgiso* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop*
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.. parsed-literal::
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*temp* values = Tstart Tstop Tdamp
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*cgiso* values = Pstart Pstop Pdamp basis_set args
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basis_set = *analytic* or *linear_spline* or *cubic_spline*
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*analytic* args = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
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*linear_spline* args = input_filename
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*cubic_spline* args = input_filename
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*tchain* value = N = length of thermostat chain (1 = single thermostat)
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*pchain* value = N = length of thermostat on barostat (0 = no thermostat)
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*mtk* value = *yes* or *no* = add MTK adjustment term or not
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*tloop* value = M = number of sub-cycles to perform on thermostat
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*ploop* value = M = number of sub-cycles to perform on barostat
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Examples
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""""""""
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.. code-block:: LAMMPS
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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 :ref:`(Dunn1) <bocs-Dunn1>` to the standard MTK
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barostat by Martyna et al. :ref:`(Martyna) <bocs-Martyna>`.
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The first half of the command mimics a standard :doc:`fix npt <fix_nh>`
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command:
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.. code-block:: LAMMPS
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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 :math:`\mathrm{\mathring{A}}^3` and the pressure
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corrections should all be in atm). 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 :math:`\mathrm{\mathring{A}^3}`
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and the coefficients should all be in
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:math:`\mathrm{atm}\cdot\mathrm{\mathring{A}^3}`\ ).
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----------
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Restart, fix_modify, output, run start/stop, minimize info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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This fix writes the cumulative global energy change to :doc:`binary
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restart files <restart>`. See the :doc:`read_restart <read_restart>`
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command for info on how to re-specify a fix in an input script that
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reads a restart file, so that the fix continues in an uninterrupted
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fashion.
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The :doc:`fix_modify <fix_modify>` *temp* option is supported by this
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fix. You can use it to assign a temperature :doc:`compute <compute>`
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you have defined to this fix which will be used in its thermostatting
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procedure, as described above. For consistency, the group used by
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this fix and by the compute should be the same.
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The cumulative energy change in the system imposed by this fix is
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included in the :doc:`thermodynamic output <thermo_style>` keywords
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*ecouple* and *econserve*. See the :doc:`thermo_style <thermo_style>`
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doc page for details.
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This fix computes a global scalar which can be accessed by various
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:doc:`output commands <Howto_output>`. The scalar is the same
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cumulative energy change due to this fix described in the previous
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paragraph. The scalar value calculated by this fix is "extensive".
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This fix can ramp its target temperature over multiple runs, using the
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*start* and *stop* keywords of the :doc:`run <run>` command. See the
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:doc:`run <run>` command for details of how to do this.
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This fix is not invoked during :doc:`energy minimization <minimize>`.
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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 BOCS package. It is only enabled if
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LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
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Further information
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"""""""""""""""""""
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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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