fully integrate acks2/reaxff fix into documentation build

doc/src/Commands_fix.rst

@@ -23,6 +23,7 @@ OPT.
    :columns: 5
 
    * :doc:`accelerate/cos <fix_accelerate_cos>`
+   * :doc:`acks2/reaxff (k) <fix_acks2_reaxff>`
    * :doc:`adapt <fix_adapt>`
    * :doc:`adapt/fep <fix_adapt_fep>`
    * :doc:`addforce <fix_addforce>`

doc/src/fix.rst

@@ -166,6 +166,7 @@ page are followed by one or more of (g,i,k,o,t) to indicate which
 accelerated styles exist.
 
 * :doc:`accelerate/cos <fix_accelerate_cos>` - apply cosine-shaped acceleration to atoms
+* :doc:`acks2/reaxff <fix_acks2_reaxff>` - apply ACKS2 charge equilibration
 * :doc:`adapt <fix_adapt>` - change a simulation parameter over time
 * :doc:`adapt/fep <fix_adapt_fep>` - enhanced version of fix adapt
 * :doc:`addforce <fix_addforce>` - add a force to each atom

doc/src/fix_acks2_reaxff.rst

@@ -1,9 +1,8 @@
 .. index:: fix acks2/reaxff
 .. index:: fix acks2/reaxff/kk
 
-
 fix acks2/reaxff command
-====================
+========================
 
 Accelerator Variants: *acks2/reaxff/kk*
 
@@ -35,45 +34,46 @@ Description
 Perform the atom-condensed Kohn-Sham DFT to second order (ACKS2) charge
 equilibration method as described in :ref:`(Verstraelen) <Verstraelen>`.
 ACKS2 impedes unphysical long-range charge transfer sometimes seen with
-QEq (e.g. for dissociation of molecules), at increased computational cost.
+QEq (e.g. for dissociation of molecules), at increased computational
-It is typically used in conjunction with the ReaxFF force field model as
+cost.  It is typically used in conjunction with the ReaxFF force field
-implemented in the :doc:`pair_style reaxff <pair_reaxff>` command, but
+model as implemented in the :doc:`pair_style reaxff <pair_reaxff>`
-it can be used with any potential in LAMMPS, so long as it defines and
+command, but it can be used with any potential in LAMMPS, so long as it
-uses charges on each atom.  For more technical details about the
+defines and uses charges on each atom.  For more technical details about
-charge equilibration performed by fix acks2/reaxff, see the
+the charge equilibration performed by fix acks2/reaxff, see the
 :ref:`(O'Hearn) <O'Hearn>` paper.
 
 The ACKS2 method minimizes the electrostatic energy of the system by
 adjusting the partial charge on individual atoms based on interactions
-with their neighbors. It requires some parameters
+with their neighbors. It requires some parameters for each atom type.
-for each atom type.
 If the *params* setting above is the word "reaxff", then these are
 extracted from the :doc:`pair_style reaxff <pair_reaxff>` command and
 the ReaxFF force field file it reads in.  If a file name is specified
 for *params*\ , then the parameters are taken from the specified file
-and the file must contain one line for each atom type.  The latter
+and the file must contain one line for each atom type.  The latter form
-form must be used when performing QeQ with a non-ReaxFF potential.
+must be used when performing QeQ with a non-ReaxFF potential.  The lines
-The lines should be formatted as follows:
+should be formatted as follows:
 
 .. parsed-literal::
 
    bond_softness
    itype chi eta gamma bcut
 
-where the first line is the global parameter *bond_softness*. The remaining
+where the first line is the global parameter *bond_softness*. The
-1 to Ntypes lines include *itype*, the atom type from 1 to Ntypes, *chi*, the
+remaining 1 to Ntypes lines include *itype*, the atom type from 1 to
-electronegativity in eV, *eta*, the self-Coulomb
+Ntypes, *chi*, the electronegativity in eV, *eta*, the self-Coulomb
-potential in eV, *gamma*, the valence orbital
+potential in eV, *gamma*, the valence orbital exponent, and *bcut*, the
-exponent, and *bcut*, the bond cutoff distance.  Note that these 4 quantities are also in the ReaxFF
+bond cutoff distance.  Note that these 4 quantities are also in the
-potential file, except that eta is defined here as twice the eta value
+ReaxFF potential file, except that eta is defined here as twice the eta
-in the ReaxFF file. Note that unlike the rest of LAMMPS, the units
+value in the ReaxFF file. Note that unlike the rest of LAMMPS, the units
 of this fix are hard-coded to be A, eV, and electronic charge.
 
 **Restart, fix_modify, output, run start/stop, minimize info:**
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  No global scalar or vector or per-atom
+No information about this fix is written to :doc:`binary restart files
-quantities are stored by this fix for access by various :doc:`output commands <Howto_output>`.  No parameter of this fix can be used
+<restart>`.  No global scalar or vector or per-atom quantities are
-with the *start/stop* keywords of the :doc:`run <run>` command.
+stored by this fix for access by various :doc:`output commands
+<Howto_output>`.  No parameter of this fix can be used with the
+*start/stop* keywords of the :doc:`run <run>` command.
 
 This fix is invoked during :doc:`energy minimization <minimize>`.
 
@@ -86,12 +86,13 @@ This fix is invoked during :doc:`energy minimization <minimize>`.
 Restrictions
 """"""""""""
 
-This fix is part of the REAXFF package.  It is only enabled if
+This fix is part of the REAXFF package.  It is only enabled if LAMMPS
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+was built with that package.  See the :doc:`Build package
+<Build_package>` doc page for more info.
 
-This fix does not correctly handle interactions
+This fix does not correctly handle interactions involving multiple
-involving multiple periodic images of the same atom. Hence, it should not
+periodic images of the same atom. Hence, it should not be used for
-be used for periodic cell dimensions less than 10 angstroms.
+periodic cell dimensions less than 10 angstroms.
 
 Related commands
 """"""""""""""""
@@ -104,7 +105,7 @@ Related commands
 
 .. _O'Hearn:
 
-**(O'Hearn)** O'Hearn, Alperen, Aktulga, SIAM J. Sci. Comput., 42(1), C1–C22 (2020).
+**(O'Hearn)** O'Hearn, Alperen, Aktulga, SIAM J. Sci. Comput., 42(1), C1-C22 (2020).
 
 .. _Verstraelen:
 

doc/src/pair_reaxff.rst

@@ -20,7 +20,7 @@ Syntax
   .. parsed-literal::
 
      keyword = *checkqeq* or *lgvdw* or *safezone* or *mincap* or *minhbonds*
-       *checkqeq* value = *yes* or *no* = whether or not to require qeq/reaxff or acks2/reax fix
+       *checkqeq* value = *yes* or *no* = whether or not to require qeq/reaxff or acks2/reaxff fix
        *enobonds* value = *yes* or *no* = whether or not to tally energy of atoms with no bonds
        *lgvdw* value = *yes* or *no* = whether or not to use a low gradient vdW correction
        *safezone* = factor used for array allocation
@@ -119,7 +119,7 @@ The ReaxFF parameter files provided were created using a charge
 equilibration (QEq) model for handling the electrostatic interactions.
 Therefore, by default, LAMMPS requires that either the
 :doc:`fix qeq/reaxff <fix_qeq_reaxff>` or the
-:doc:`fix qeq/shielded <fix_qeq>` or :doc:`fix acks2/reaxff <fix_acks2>`
+:doc:`fix qeq/shielded <fix_qeq>` or :doc:`fix acks2/reaxff <fix_acks2_reaxff>`
 command be used with
 *pair_style reaxff* when simulating a ReaxFF model, to equilibrate
 the charges each timestep.
@@ -129,7 +129,7 @@ for the QEq fixes, allowing a simulation to be run without charge
 equilibration. In this case, the static charges you assign to each
 atom will be used for computing the electrostatic interactions in
 the system. See the :doc:`fix qeq/reaxff <fix_qeq_reaxff>` or
-:doc:`fix qeq/shielded <fix_qeq>` or :doc:`fix acks2/reaxff <fix_acks2>`
+:doc:`fix qeq/shielded <fix_qeq>` or :doc:`fix acks2/reaxff <fix_acks2_reaxff>`
 command documentation for more details.
 
 Using the optional keyword *lgvdw* with the value *yes* turns on the
@@ -354,7 +354,7 @@ Related commands
 """"""""""""""""
 
 :doc:`pair_coeff <pair_coeff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`,
-:doc:`fix acks2/reax <fix_acks2_reax>`, :doc:`fix reaxff/bonds <fix_reaxff_bonds>`,
+:doc:`fix acks2/reaxff <fix_acks2_reaxff>`, :doc:`fix reaxff/bonds <fix_reaxff_bonds>`,
 :doc:`fix reaxff/species <fix_reaxff_species>`
 
 Default

doc/utils/check-styles.py

@@ -254,7 +254,7 @@ for command_type, entries in index.items():
 
 print("Total number of style index entries:", total_index)
 
-skip_fix = ('python', 'NEIGH_HISTORY/omp','qeq/reax','reax/c/bonds','reax/c/species')
+skip_fix = ('python', 'NEIGH_HISTORY/omp','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species')
 skip_pair = ('meam/c','lj/sf','reax/c')
 
 counter = 0
@@ -282,7 +282,7 @@ if counter:
 counter = 0
 
 counter += check_style_index("compute", compute, index["compute"])
-counter += check_style_index("fix", fix, index["fix"], skip=['python','qeq/reax','reax/c/bonds','reax/c/species'])
+counter += check_style_index("fix", fix, index["fix"], skip=['python','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species'])
 counter += check_style_index("angle_style", angle, index["angle_style"])
 counter += check_style_index("bond_style", bond, index["bond_style"])
 counter += check_style_index("dihedral_style", dihedral, index["dihedral_style"])

doc/utils/sphinx-config/false_positives.txt

@@ -19,6 +19,7 @@ accuracies
 ach
 ackland
 Ackland
+acks
 acolor
 acos
 Acta
@@ -77,6 +78,7 @@ allocators
 allosws
 AlO
 Alonso
+Alperen
 alphak
 alphashrink
 amap
@@ -1252,6 +1254,7 @@ hbond
 hcp
 hdnnp
 HDNNP
+Hearn
 heatconduction
 Hebbeker
 Hebenstreit
@@ -3074,6 +3077,7 @@ Spearot
 specular
 spellcheck
 Spellmeyer
+Speybroeck
 sph
 SPH
 Spickermann
@@ -3486,6 +3490,7 @@ Verlag
 verlet
 Verlet
 versa
+Verstraelen
 ves
 vflag
 vhi
@@ -3552,6 +3557,7 @@ vzcm
 vzi
 Waals
 Wadley
+Waroquier
 wallstyle
 walltime
 Waltham