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full integration into documentation build system

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This commit is contained in:
Axel Kohlmeyer
2021-04-12 09:59:02 -04:00
parent e95cbf618b
commit bc25fa8268
3 changed files with 12 additions and 4 deletions
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1
doc/src/Commands_fix.rst
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@ -46,6 +46,7 @@ OPT.
* :doc:`bond/react <fix_bond_react>` * :doc:`bond/react <fix_bond_react>`
* :doc:`bond/swap <fix_bond_swap>` * :doc:`bond/swap <fix_bond_swap>`
* :doc:`box/relax <fix_box_relax>` * :doc:`box/relax <fix_box_relax>`
* :doc:`charge/regulation <fix_charge_regulation>`
* :doc:`client/md <fix_client_md>` * :doc:`client/md <fix_client_md>`
* :doc:`cmap <fix_cmap>` * :doc:`cmap <fix_cmap>`
* :doc:`colvars <fix_colvars>` * :doc:`colvars <fix_colvars>`

1
doc/src/fix.rst
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@ -189,6 +189,7 @@ accelerated styles exist.
* :doc:`bond/react <fix_bond_react>` - apply topology changes to model reactions * :doc:`bond/react <fix_bond_react>` - apply topology changes to model reactions
* :doc:`bond/swap <fix_bond_swap>` - Monte Carlo bond swapping * :doc:`bond/swap <fix_bond_swap>` - Monte Carlo bond swapping
* :doc:`box/relax <fix_box_relax>` - relax box size during energy minimization * :doc:`box/relax <fix_box_relax>` - relax box size during energy minimization
* :doc:`charge/regulation <fix_charge_regulation>` - Monte Carlo sampling of charge regulation
* :doc:`client/md <fix_client_md>` - MD client for client/server simulations * :doc:`client/md <fix_client_md>` - MD client for client/server simulations
* :doc:`cmap <fix_cmap>` - enables CMAP cross-terms of the CHARMM force field * :doc:`cmap <fix_cmap>` - enables CMAP cross-terms of the CHARMM force field
* :doc:`colvars <fix_colvars>` - interface to the collective variables "Colvars" library * :doc:`colvars <fix_colvars>` - interface to the collective variables "Colvars" library

14
doc/src/fix_charge_regulation.rst
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@ -225,7 +225,7 @@ quantities:
Restrictions Restrictions
"""""""""""" """"""""""""
This fix is part of the USER-MISC package. It is only enabled if LAMMPS This fix is part of the MC package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info. <Build_package>` doc page for more info.
@ -243,7 +243,9 @@ the LJ potential must be shifted so that it vanishes at the cutoff. This
can be easily achieved using the :doc:`pair_modify <pair_modify>` can be easily achieved using the :doc:`pair_modify <pair_modify>`
command, i.e., by using: *pair_modify shift yes*. command, i.e., by using: *pair_modify shift yes*.
Note: Region restrictions are not yet implemented. .. note::
Region restrictions are not yet implemented.
Related commands Related commands
"""""""""""""""" """"""""""""""""
@ -253,7 +255,11 @@ Related commands
Default Default
""""""" """""""
pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs = 14.0; acid_type = -1; base_type = -1; lunit_nm = 0.71; temp = 1.0; nevery = 100; nmc = 100; xrd = 0; seed = 0; tag = no; onlysalt = no, pmcmoves = [1/3, 1/3, 1/3], group-ID = all
pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs = 14.0;
acid_type = -1; base_type = -1; lunit_nm = 0.71; temp = 1.0; nevery =
100; nmc = 100; xrd = 0; seed = 0; tag = no; onlysalt = no, pmcmoves =
[1/3, 1/3, 1/3], group-ID = all
---------- ----------
@ -267,4 +273,4 @@ pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs = 14.0; acid_type
.. _Landsgesell: .. _Landsgesell:
**(Landsgesell)** J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, "Grand-reaction method for simulations of ionization equilibria coupled to ion partitioning", Macromolecules 53, 3007–3020 (2020). **(Landsgesell)** J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, "Grand-reaction method for simulations of ionization equilibria coupled to ion partitioning", Macromolecules 53, 3007-3020 (2020).