Updated docs for fix bocs to match source code and include math

doc/src/fix_bocs.rst

@@ -6,17 +6,28 @@ fix bocs command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
-   fix  ID group-ID bocs keyword values ...
+   fix ID group-ID bocs keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* bocs = style name of this fix command
+* two or more keyword/value pairs may be appended
+* keyword = *temp* or *cgiso* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop*
+
+  .. parsed-literal::
 
-   keyword = *temp* or *cgiso* or *analytic* or *linear_spline* or *cubic_spline*
      *temp* values = Tstart Tstop Tdamp
-     *cgiso* values = Pstart Pstop Pdamp
-     *basis set*
-       *analytic* values = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
-       *linear_spline* values = input_filename
-       *cubic_spline* values = input_filename
+     *cgiso* values = Pstart Pstop Pdamp basis_set args
+       basis_set = *analytic* or *linear_spline* or *cubic_spline*
+         *analytic* args = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
+         *linear_spline* args = input_filename
+         *cubic_spline* args = input_filename
+     *tchain* value = N = length of thermostat chain (1 = single thermostat)
+     *pchain* value = N = length of thermostat on barostat (0 = no thermostat)
+     *mtk* value = *yes* or *no* = add MTK adjustment term or not
+     *tloop* value = M = number of sub-cycles to perform on thermostat
+     *ploop* value = M = number of sub-cycles to perform on barostat
 
 Examples
 """"""""
@@ -24,25 +35,24 @@ Examples
 .. code-block:: LAMMPS
 
    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
-
    fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline input_Fv.dat
-
    thermo_modify press 1_press
 
 Description
 """""""""""
 
 These commands incorporate a pressure correction as described by
-Dunn and Noid in :ref:`(Dunn1) <bocs-Dunn1>` to the standard MTTK
-barostat by Martyna et. al. in :ref:`(Martyna) <bocs-Martyna>` .
-The first half of the command mimics a standard fix npt command:
+Dunn and Noid :ref:`(Dunn1) <bocs-Dunn1>` to the standard MTK
+barostat by Martyna et al. :ref:`(Martyna) <bocs-Martyna>` .
+The first half of the command mimics a standard :doc:`fix npt <fix_nh>`
+command:
 
 .. code-block:: LAMMPS
 
    fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp
 
 The two differences are replacing *npt* with *bocs*, and replacing
-*iso*\ /\ *aniso*\ /\ *etc* with *cgiso*\ .
+*iso*\ /\ *aniso*\ /\ etc. with *cgiso*\ .
 The rest of the command details what form you would like to use for
 the pressure correction equation. The choices are: *analytic*, *linear_spline*,
 or *cubic_spline*.
@@ -58,9 +68,9 @@ as a function of volume. The file must be formatted so each line has:
 Note both the COMMA and the SPACE separating the volume's
 value and its corresponding pressure correction. The volumes in the file
 must be uniformly spaced. Both the volumes and the pressure corrections
-should be provided in the proper units, e.g. if you are using *units real*,
-the volumes should all be in cubic Angstroms, and the pressure corrections
-should all be in atmospheres. Furthermore, the table should start/end at a
+should be provided in the proper units (e.g., if you are using *units real*,
+the volumes should all be in :math:`\mathrm{\mathring{A}}^3` and the pressure
+corrections should all be in atm). Furthermore, the table should start/end at a
 volume considerably smaller/larger than you expect your system to sample
 during the simulation. If the system ever reaches a volume outside of the
 range provided, the simulation will stop.
@@ -71,9 +81,10 @@ With the *analytic* option, the arguments are as follows:
 
    ... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
 
-Note that *V_avg* and *Coeff_i* should all be in the proper units, e.g. if you
-are using *units real*, *V_avg* should be in cubic Angstroms, and the
-coefficients should all be in atmospheres \* cubic Angstroms.
+Note that *V_avg* and *Coeff_i* should all be in the proper units (e.g., if you
+are using *units real*, *V_avg* should be in :math:`\mathrm{\mathring{A}^3}`
+and the coefficients should all be in
+:math:`\mathrm{atm}\cdot\mathrm{\mathring{A}^3}`\ ).
 
 ----------
 
@@ -122,7 +133,7 @@ are written to a file every so often. In order to have LAMMPS report the
 modified pressure, you must include the *thermo_modify* command given in
 the examples. For the last argument in the command, you should put
 XXXX_press, where XXXX is the ID given to the fix bocs command (in the
-example, the ID of the fix bocs command is 1 ).
+example, the ID of the fix bocs command is 1).
 
 This fix is part of the BOCS package.  It is only enabled if
 LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
@@ -132,7 +143,7 @@ Further information
 
 For more details about the pressure correction and the entire BOCS software
 package, visit the `BOCS package on GitHub <bocsgithub_>`_ and read the release
-paper by Dunn et. al. :ref:`(Dunn2) <bocs-Dunn2>` .
+paper by Dunn et al. :ref:`(Dunn2) <bocs-Dunn2>` .
 
 .. _bocsgithub: https://github.com/noid-group/BOCS