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fully integrate acks2/reaxff fix into documentation build

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This commit is contained in:
Axel Kohlmeyer
2021-09-14 15:31:36 -04:00
parent 51cfbaa2ef
commit dfe0e313d5
6 changed files with 44 additions and 35 deletions
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1
doc/src/Commands_fix.rst
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@ -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>`

1
doc/src/fix.rst
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@ -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

59
doc/src/fix_acks2_reaxff.rst
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@ -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.
It is typically used in conjunction with the ReaxFF force field model as
implemented in the :doc:`pair_style reaxff <pair_reaxff>` command, but
it can be used with any potential in LAMMPS, so long as it defines and
uses charges on each atom. For more technical details about the
charge equilibration performed by fix acks2/reaxff, see the
QEq (e.g. for dissociation of molecules), at increased computational
cost. It is typically used in conjunction with the ReaxFF force field
model as implemented in the :doc:`pair_style reaxff <pair_reaxff>`
command, but it can be used with any potential in LAMMPS, so long as it
defines and uses charges on each atom. For more technical details about
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
for each atom type.
with their neighbors. It requires some parameters 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
form must be used when performing QeQ with a non-ReaxFF potential.
The lines should be formatted as follows:
and the file must contain one line for each atom type. The latter form
must be used when performing QeQ with a non-ReaxFF potential. The lines
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
1 to Ntypes lines include *itype*, the atom type from 1 to Ntypes, *chi*, the
electronegativity in eV, *eta*, the self-Coulomb
potential in eV, *gamma*, the valence orbital
exponent, and *bcut*, the bond cutoff distance. Note that these 4 quantities are also in the ReaxFF
potential file, except that eta is defined here as twice the eta value
in the ReaxFF file. Note that unlike the rest of LAMMPS, the units
where the first line is the global parameter *bond_softness*. The
remaining 1 to Ntypes lines include *itype*, the atom type from 1 to
Ntypes, *chi*, the electronegativity in eV, *eta*, the self-Coulomb
potential in eV, *gamma*, the valence orbital exponent, and *bcut*, the
bond cutoff distance. Note that these 4 quantities are also in the
ReaxFF potential file, except that eta is defined here as twice the eta
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
quantities are 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.
No information about this fix is written to :doc:`binary restart files
<restart>`. No global scalar or vector or per-atom quantities are
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
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
This fix is part of the REAXFF package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
This fix does not correctly handle interactions
involving multiple periodic images of the same atom. Hence, it should not
be used for periodic cell dimensions less than 10 angstroms.
This fix does not correctly handle interactions involving multiple
periodic images of the same atom. Hence, it should not be used for
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:

8
doc/src/pair_reaxff.rst
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@ -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

4
doc/utils/check-styles.py
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@ -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"])

6
doc/utils/sphinx-config/false_positives.txt
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@ -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