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Merge branch 'develop' of github.com:lammps/lammps into alphataubio-kokkos-fixes

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This commit is contained in:
Stan Moore
2024-10-04 09:30:33 -06:00
parent 13ceebe82c 2ae4062a6b
commit 130548156d
77 changed files with 33326 additions and 10988 deletions
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1
doc/src/Commands_fix.rst
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@ -178,6 +178,7 @@ OPT.
* :doc:`python/move <fix_python_move>`
* :doc:`qbmsst <fix_qbmsst>`
* :doc:`qeq/comb (o) <fix_qeq_comb>`
* :doc:`qeq/ctip <fix_qeq>`
* :doc:`qeq/dynamic <fix_qeq>`
* :doc:`qeq/fire <fix_qeq>`
* :doc:`qeq/point <fix_qeq>`

1
doc/src/Commands_pair.rst
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@ -59,6 +59,7 @@ OPT.
* :doc:`comb (o) <pair_comb>`
* :doc:`comb3 <pair_comb>`
* :doc:`cosine/squared <pair_cosine_squared>`
* :doc:`coul/ctip <pair_coul>`
* :doc:`coul/cut (gko) <pair_coul>`
* :doc:`coul/cut/dielectric <pair_dielectric>`
* :doc:`coul/cut/global (o) <pair_coul>`

2
doc/src/compute_rheo_property_atom.rst
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@ -81,7 +81,7 @@ includes *xx*, *xy*, *yx*, and *yy*. In 3D, this includes *xx*, *xy*, *xz*,
Many properties require their respective fixes, listed below in related
commands, be defined. For instance, the *viscosity* attribute is the
viscosity of a particle calculated by
:doc:`fix rheo/viscous <fix_rheo_viscosity>`. The meaning of less obvious
:doc:`fix rheo/viscosity <fix_rheo_viscosity>`. The meaning of less obvious
properties is described below.
The *phase* property indicates whether the particle is in a fluid state,

1
doc/src/fix.rst
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@ -357,6 +357,7 @@ accelerated styles exist.
* :doc:`python/move <fix_python_move>` - move particles using a Python function during a simulation run
* :doc:`qbmsst <fix_qbmsst>` - quantum bath multi-scale shock technique time integrator
* :doc:`qeq/comb <fix_qeq_comb>` - charge equilibration for COMB potential
* :doc:`qeq/ctip <fix_qeq>` - charge equilibration for CTIP potential
* :doc:`qeq/dynamic <fix_qeq>` - charge equilibration via dynamic method
* :doc:`qeq/fire <fix_qeq>` - charge equilibration via FIRE minimizer
* :doc:`qeq/point <fix_qeq>` - charge equilibration via point method

7
doc/src/fix_nonaffine_displacement.rst
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@ -102,7 +102,6 @@ zeroed. The *update* reference style implies the reference state will be updated
*nstep* timesteps. The *offset* reference will update the reference state *nstep*
timesteps before a multiple of *nevery* timesteps.
----------
Restart, fix_modify, output, run start/stop, minimize info
@ -129,6 +128,12 @@ This compute is part of the EXTRA-FIX package. It is only enabled if
LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` page for more info.
As this fix depends on a run including specific reference timesteps, it
currently does not update peratom values if used in conjunction with the
:doc:`rerun command <rerun>` since it cannot ensure the necessary reference
timesteps are included.
Related commands
""""""""""""""""

16
doc/src/fix_pour.rst
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@ -155,6 +155,22 @@ many timesteps until the desired # of particles has been inserted.
the :doc:`compute_modify dynamic/dof yes <compute_modify>` command
for the temperature compute you are using.
.. admonition:: Implementation Notes
:class: Hint
The exact insertion procedure depends on many factors (e.g. the range of
diameters inserted or whether molecules are being inserted). However, in
the simplest scenario of monodisperse atoms, the procedure works as
follows. First, the number of timesteps between two insertion events is
calculated as the time for a particle to fall through the insertion region,
accounting for gravity and any region motion. Next, the target number of
particles inserted per event (assuming no failed insertions due to overlaps)
is calculated as the product of the volume fraction and the volume of the
insertion region divided by the volume of a particle (or area in 2D).
Events are repeated until all N particles have been inserted, where
the final event is likely interrupted upon reaching N. Estimates of this
process are printed to the log/screen at the start of a run.
----------
All other keywords are optional with defaults as shown below.

60
doc/src/fix_qeq.rst
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@ -1,6 +1,7 @@
.. index:: fix qeq/point
.. index:: fix qeq/shielded
.. index:: fix qeq/slater
.. index:: fix qeq/ctip
.. index:: fix qeq/dynamic
.. index:: fix qeq/fire
@ -13,6 +14,9 @@ fix qeq/shielded command
fix qeq/slater command
======================
fix qeq/ctip command
====================
fix qeq/dynamic command
=======================
@ -27,18 +31,20 @@ Syntax
fix ID group-ID style Nevery cutoff tolerance maxiter qfile keyword ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* style = *qeq/point* or *qeq/shielded* or *qeq/slater* or *qeq/dynamic* or *qeq/fire*
* style = *qeq/point* or *qeq/shielded* or *qeq/slater* or *qeq/ctip* or *qeq/dynamic* or *qeq/fire*
* Nevery = perform charge equilibration every this many steps
* cutoff = global cutoff for charge-charge interactions (distance unit)
* tolerance = precision to which charges will be equilibrated
* maxiter = maximum iterations to perform charge equilibration
* qfile = a filename with QEq parameters or *coul/streitz* or *reaxff*
* qfile = a filename with QEq parameters or *coul/streitz* or *coul/ctip* or *reaxff*
* zero or more keyword/value pairs may be appended
* keyword = *alpha* or *qdamp* or *qstep* or *warn*
* keyword = *alpha* or *cdamp* or *maxrepeat* or *qdamp* or *qstep* or *warn*
.. parsed-literal::
*alpha* value = Slater type orbital exponent (qeq/slater only)
*cdamp* value = damping parameter for Coulomb interactions (qeq/ctip only)
*maxrepeat* value = number of equilibration cycles allowed to ensure no atoms cross charge bounds (qeq/ctip only)
*qdamp* value = damping factor for damped dynamics charge solver (qeq/dynamic and qeq/fire only)
*qstep* value = time step size for damped dynamics charge solver (qeq/dynamic and qeq/fire only)
*warn* value = do (=yes) or do not (=no) print a warning when the maximum number of iterations is reached
@ -51,6 +57,7 @@ Examples
fix 1 all qeq/point 1 10 1.0e-6 200 param.qeq1
fix 1 qeq qeq/shielded 1 8 1.0e-6 100 param.qeq2
fix 1 all qeq/slater 5 10 1.0e-6 100 params alpha 0.2
fix 1 all qeq/ctip 1 12 1.0e-8 100 coul/ctip cdamp 0.30 maxrepeat 10
fix 1 qeq qeq/dynamic 1 12 1.0e-3 100 my_qeq
fix 1 all qeq/fire 1 10 1.0e-3 100 my_qeq qdamp 0.2 qstep 0.1
@ -103,7 +110,7 @@ equalizes the derivative of energy with respect to charge of all the
atoms) by adjusting the partial charge on individual atoms based on
interactions with their neighbors within *cutoff*\ . It requires a few
parameters in the appropriate units for each atom type which are read
from a file specified by *qfile*\ . The file has the following format
from a file specified by *qfile*\ . The file has the following format:
.. parsed-literal::
@ -112,20 +119,32 @@ from a file specified by *qfile*\ . The file has the following format
...
Ntype chi eta gamma zeta qcore
except for fix style *qeq/ctip* where the format is:
.. parsed-literal::
1 chi eta gamma zeta qcore qmin qmax omega
2 chi eta gamma zeta qcore qmin qmax omega
...
Ntype chi eta gamma zeta qcore qmin qmax omega
There have to be parameters given for every atom type. Wildcard entries
are possible using the same type range syntax as for "coeff" commands
(i.e., n\*m, n\*, \*m, \*). Later entries will overwrite previous ones.
Empty lines or any text following the pound sign (#) are ignored.
Each line starts with the atom type followed by five parameters.
Only a subset of the parameters is used by each QEq style as described
below, thus the others can be set to 0.0 if desired, but all five
entries per line are required.
Empty lines or any text following the pound sign (#) are ignored. Each
line starts with the atom type followed by eight parameters. Only a
subset of the parameters is used by each QEq style as described below,
thus the others can be set to 0.0 if desired, but all eight entries per
line are required.
* *chi* = electronegativity in energy units
* *eta* = self-Coulomb potential in energy units
* *gamma* = shielded Coulomb constant defined by :ref:`ReaxFF force field <vanDuin>` in distance units
* *zeta* = Slater type orbital exponent defined by the :ref:`Streitz-Mintmire <Streitz1>` potential in reverse distance units
* *qcore* = charge of the nucleus defined by the :ref:`Streitz-Mintmire potential <Streitz1>` potential in charge units
* *qmin* = lower bound on the allowed charge defined by the :ref:`CTIP <CTIP1>` potential in charge units
* *qmax* = upper bound on the allowed charge defined by the :ref:`CTIP <CTIP1>` potential in charge units
* *omega* = penalty parameter used to enforce charge bounds defined by the :ref:`CTIP <CTIP1>` potential in energy units
The fix qeq styles will print a warning if the charges are not
equilibrated within *tolerance* by *maxiter* steps, unless the
@ -171,6 +190,22 @@ on atoms via the matrix inversion method. A tolerance of 1.0e-6 is
usually a good number. Keyword *alpha* can be used to change the Slater
type orbital exponent.
.. versionadded:: TBD
The *qeq/ctip* style describes partial charges on atoms in the same way
as style *qeq/shielded* but also enables the definition of charge
bounds. Only the *chi*, *eta*, *gamma*, *qmin*, *qmax*, and *omega*
parameters from the *qfile* file are used. When using the string
*coul/ctip* as filename, these parameters are extracted directly from an
active *coul/ctip* pair style. This style solves partial charges on
atoms via the matrix inversion method. Keyword *cdamp* can be used to
change the damping parameter used to calculate Coulomb interactions.
Keyword *maxrepeat* can be used to adjust the number of equilibration
cycles allowed to ensure no atoms have crossed the charge bounds. A
value of 10 is usually a good choice. A tolerance between 1.0e-6 and
1.0e-8 is usually a good choice but should be checked in conjunction
with the timestep for adequate energy conservation during dynamic runs.
The *qeq/dynamic* style describes partial charges on atoms as point
charges that interact through 1/r, but the extended Lagrangian method is
used to solve partial charges on atoms. Only the *chi* and *eta*
@ -186,7 +221,7 @@ minimization algorithm to solve for equilibrium charges. Keyword
*qdamp* can be used to change the damping factor, while keyword *qstep*
can be used to change the time step size.
Note that *qeq/point*, *qeq/shielded*, and *qeq/slater* describe
Note that *qeq/point*, *qeq/shielded*, *qeq/slater*, and *qeq/ctip* describe
different charge models, whereas the matrix inversion method and the
extended Lagrangian method (\ *qeq/dynamic* and *qeq/fire*\ ) are
different solvers.
@ -266,6 +301,11 @@ Chemistry, 95, 3358-3363 (1991).
**(Streitz-Mintmire)** F. H. Streitz, J. W. Mintmire, Physical Review B, 50,
16, 11996 (1994)
.. _CTIP1:
**(CTIP)** G. Plummer, J. P. Tavenner, M. I. Mendelev, Z. Wu, J. W. Lawson,
in preparation
.. _vanDuin:
**(ReaxFF)** A. C. T. van Duin, S. Dasgupta, F. Lorant, W. A. Goddard III, J

3
doc/src/fix_rheo.rst
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@ -16,8 +16,7 @@ Syntax
* kstyle = *quintic* or *RK0* or *RK1* or *RK2*
* zmin = minimal number of neighbors for reproducing kernels
* zero or more keyword/value pairs may be appended to args
* keyword = *thermal* or *interface/reconstruct* or *surface/detection* or
*shift* or *rho/sum* or *density* or *self/mass* or *speed/sound*
* keyword = *thermal* or *interface/reconstruct* or *surface/detection* or *shift* or *rho/sum* or *density* or *self/mass* or *speed/sound*
.. parsed-literal::

55
doc/src/pair_coul.rst
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@ -4,6 +4,7 @@
.. index:: pair_style coul/cut/omp
.. index:: pair_style coul/cut/global
.. index:: pair_style coul/cut/global/omp
.. index:: pair_style coul/ctip
.. index:: pair_style coul/debye
.. index:: pair_style coul/debye/gpu
.. index:: pair_style coul/debye/kk
@ -38,6 +39,9 @@ pair_style coul/cut/global command
Accelerator Variants: *coul/cut/omp*
pair_style coul/ctip command
============================
pair_style coul/debye command
=============================
@ -79,7 +83,6 @@ pair_style tip4p/long command
Accelerator Variants: *tip4p/long/omp*
Syntax
""""""
@ -87,6 +90,7 @@ Syntax
pair_style coul/cut cutoff
pair_style coul/cut/global cutoff
pair_style coul/ctip alpha cutoff
pair_style coul/debye kappa cutoff
pair_style coul/dsf alpha cutoff
pair_style coul/exclude cutoff
@ -116,6 +120,9 @@ Examples
pair_coeff * *
pair_coeff 2 2 3.5
pair_style coul/ctip 0.30 12.0
pair_coeff * * NiO.ctip Ni O
pair_style coul/debye 1.4 3.0
pair_coeff * *
pair_coeff 2 2 3.5
@ -173,6 +180,33 @@ coulomb styles in :doc:`hybrid pair styles <pair_hybrid>`.
----------
.. versionadded:: TBD
Style *coul/ctip* computes the Coulomb interactions as described in
:ref:`Plummer <Plummer1>`. It uses the the damped shifted model as in
style *coul/dsf* but is further extended to the second derivative of the
potential and incorporates empirical charge shielding meant to
approximate the more expensive Coulomb integrals used in style
*coul/streitz*. More details can be found in the referenced paper. Like
the style *coul/streitz*, style *coul/ctip* is a variable charge
potential and must be hybridized with a short-range potential via the
:doc:`pair_style hybrid/overlay <pair_hybrid>` command. Charge
equilibration must be performed with the :doc:`fix qeq/ctip <fix_qeq>`
command. For example:
.. code-block:: LAMMPS
pair_style hybrid/overlay eam/fs coul/ctip 0.30 12.0
pair_coeff * * eam/fs NiO.eam.fs Ni O
pair_coeff * * coul/ctip NiO.ctip Ni O
fix 1 all qeq/ctip 1 12.0 1.0e-8 100 coul/ctip cdamp 0.30 maxrepeat 10
See the examples/ctip directory for an example input script using the
CTIP potential. An Ni-O CTIP and EAM/FS parameterization are included
for use with the example.
----------
Style *coul/debye* adds an additional exp() damping factor to the
Coulombic term, given by
@ -399,16 +433,18 @@ Restrictions
""""""""""""
The *coul/long*, *coul/msm*, *coul/streitz*, and *tip4p/long* styles are
part of the KSPACE package. The *coul/cut/global*, *coul/exclude* styles are
part of the EXTRA-PAIR package. The *tip4p/cut* style is part of the MOLECULE
package. A pair style is only enabled if LAMMPS was built with its
corresponding package. See the :doc:`Build package <Build_package>`
doc page for more info.
part of the KSPACE package. The *coul/cut/global*, *coul/exclude*, and
*coul/ctip* styles are part of the EXTRA-PAIR package. The *tip4p/cut*
style is part of the MOLECULE package. A pair style is only enabled if
LAMMPS was built with its corresponding package. See the
:doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style, hybrid/overlay <pair_hybrid>`, :doc:`kspace_style <kspace_style>`
:doc:`pair_coeff <pair_coeff>`,
:doc:`pair_style hybrid/overlay <pair_hybrid>`,
:doc:`kspace_style <kspace_style>`
Default
"""""""
@ -432,6 +468,11 @@ Phys, 110, 8254 (1999).
**(Streitz)** F. H. Streitz, J. W. Mintmire, Phys Rev B, 50, 11996-12003
(1994).
.. _Plummer1:
**(Plummer)** G. Plummer, J. P. Tavenner, M. I. Mendelev, Z. Wu, J. W. Lawson,
in preparation
.. _Jorgensen3:
**(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem

1
doc/src/pair_style.rst
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@ -151,6 +151,7 @@ accelerated styles exist.
* :doc:`comb <pair_comb>` - charge-optimized many-body (COMB) potential
* :doc:`comb3 <pair_comb>` - charge-optimized many-body (COMB3) potential
* :doc:`cosine/squared <pair_cosine_squared>` - Cooke-Kremer-Deserno membrane model potential
* :doc:`coul/ctip <pair_coul>` - Charge Transfer Interatomic (Coulomb) Potential
* :doc:`coul/cut <pair_coul>` - cutoff Coulomb potential
* :doc:`coul/cut/dielectric <pair_dielectric>` -
* :doc:`coul/cut/global <pair_coul>` - cutoff Coulomb potential