diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index effccd55bf..66b27c8a36 100644 --- a/doc/src/Commands_fix.rst +++ b/doc/src/Commands_fix.rst @@ -23,6 +23,7 @@ OPT. :columns: 5 * :doc:`accelerate/cos ` + * :doc:`acks2/reaxff (k) ` * :doc:`adapt ` * :doc:`adapt/fep ` * :doc:`addforce ` diff --git a/doc/src/fix.rst b/doc/src/fix.rst index c45ae6a801..028f4e3a94 100644 --- a/doc/src/fix.rst +++ b/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 ` - apply cosine-shaped acceleration to atoms +* :doc:`acks2/reaxff ` - apply ACKS2 charge equilibration * :doc:`adapt ` - change a simulation parameter over time * :doc:`adapt/fep ` - enhanced version of fix adapt * :doc:`addforce ` - add a force to each atom diff --git a/doc/src/fix_acks2_reaxff.rst b/doc/src/fix_acks2_reaxff.rst index 8a84ec4a9a..4ba8c36ee6 100644 --- a/doc/src/fix_acks2_reaxff.rst +++ b/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) `. 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 ` 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 ` +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) ` 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 ` 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 `. No global scalar or vector or per-atom -quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used -with the *start/stop* keywords of the :doc:`run ` command. +No information about this fix is written to :doc:`binary restart files +`. No global scalar or vector or per-atom quantities are +stored by this fix for access by various :doc:`output commands +`. No parameter of this fix can be used with the +*start/stop* keywords of the :doc:`run ` command. This fix is invoked during :doc:`energy minimization `. @@ -86,12 +86,13 @@ This fix is invoked during :doc:`energy minimization `. 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 ` 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 +` 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: diff --git a/doc/src/pair_reaxff.rst b/doc/src/pair_reaxff.rst index be49f565c2..a2aa0f356d 100644 --- a/doc/src/pair_reaxff.rst +++ b/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 ` or the -:doc:`fix qeq/shielded ` or :doc:`fix acks2/reaxff ` +:doc:`fix qeq/shielded ` or :doc:`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 ` or -:doc:`fix qeq/shielded ` or :doc:`fix acks2/reaxff ` +:doc:`fix qeq/shielded ` or :doc:`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 `, :doc:`fix qeq/reaxff `, -:doc:`fix acks2/reax `, :doc:`fix reaxff/bonds `, +:doc:`fix acks2/reaxff `, :doc:`fix reaxff/bonds `, :doc:`fix reaxff/species ` Default diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py index 6c1fd6dd35..2ad75aeeda 100755 --- a/doc/utils/check-styles.py +++ b/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"]) diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index fff23a01b0..fbb5d3ce6b 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/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