partial docs also for future pedone/coul/long implementation
This commit is contained in:
Axel Kohlmeyer
@ -245,6 +245,7 @@ OPT.
|
||||
* :doc:`oxrna2/coaxstk <pair_oxrna2>`
|
||||
* :doc:`pace (k) <pair_pace>`
|
||||
* :doc:`pace/extrapolation (k) <pair_pace>`
|
||||
* :doc:`pedone (o) <pair_pedone>`
|
||||
* :doc:`pod <pair_pod>`
|
||||
* :doc:`peri/eps <pair_peri>`
|
||||
* :doc:`peri/lps (o) <pair_peri>`
|
||||
|
||||
142
doc/src/pair_pedone.rst
Normal file
142
doc/src/pair_pedone.rst
Normal file
@ -0,0 +1,142 @@
|
||||
.. index:: pair_style pedone
|
||||
.. index:: pair_style pedone/omp
|
||||
.. index:: pair_style pedone/coul/long
|
||||
.. index:: pair_style pedone/coul/long/omp
|
||||
|
||||
pair_style pedone command
|
||||
=========================
|
||||
|
||||
Accelerator Variants: *pedone/omp*
|
||||
|
||||
pair_style pedone/coul/long command
|
||||
===================================
|
||||
|
||||
Accelerator Variants: *pedone/coul/long*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style style args
|
||||
|
||||
* style = pedone* or *pedone/coul/long*
|
||||
* args = list of arguments for a particular style
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*pedone* args = cutoff
|
||||
cutoff = global cutoff for Pedone interactions (distance units)
|
||||
*pedone/coul/long* args = cutoff (cutoff2)
|
||||
cutoff = global cutoff for Pedone (and Coulombic if only one arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style morse 2.5
|
||||
pair_style morse/smooth/linear 2.5
|
||||
pair_coeff * * 100.0 2.0 1.5
|
||||
pair_coeff 1 1 100.0 2.0 1.5 3.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Pair style *pedone* computes the non-Coulomb interactions of the Pedone
|
||||
(or PMMCS) potential :ref:`Pedone <Pedone>` which combines Coulomb
|
||||
interactions, a Morse potential, and a repulsive :math:`r^{-12}`
|
||||
Lennard-Jones term (see below). The plain *pedone* pair style is meant
|
||||
to be used in addition to a :doc:`Coulomb pair style <pair_coul>` via
|
||||
pair style :doc:`hybrid/overlay <pair_hybrid>` and thus allows to be
|
||||
combined with different Coulomb variants available in LAMMPS.
|
||||
|
||||
Pair style *pedone/coul/long* includes the Coulomb part with a damping
|
||||
function applied so it can be used in conjunction with the
|
||||
:doc:`kspace_style <kspace_style>` command and its *ewald* or *pppm*
|
||||
option. The Coulombic cutoff specified for this style means that
|
||||
pairwise interactions within this distance are computed directly;
|
||||
interactions outside that distance are computed in reciprocal space.
|
||||
This combination is the preferred way to compute the Pedone potential
|
||||
and should be simpler to use and faster than adding :doc:`pair style
|
||||
coul/long <pair_coul>` to pair style *pedone* via :doc:`pair style
|
||||
hybrid/overlay <pair_hybrid>`.
|
||||
|
||||
.. math::
|
||||
|
||||
E = \frac{C q_i q_j}{\epsilon r}
|
||||
+ D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right]
|
||||
+ \frac{B_0}{r^{12}} \qquad r < r_c
|
||||
|
||||
:math:`r_c` is the cutoff and :math:`C` is a conversion factor so that
|
||||
the entire Coulomb term is in energy units.
|
||||
|
||||
The following coefficients must be defined for each pair of atoms
|
||||
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
|
||||
above, or in the data file or restart files read by the
|
||||
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
|
||||
commands:
|
||||
|
||||
* :math:`D_0` (energy units)
|
||||
* :math:`\alpha` (1/distance units)
|
||||
* :math:`r_0` (distance units)
|
||||
* :math:`C_0` (energy units)
|
||||
* cutoff (distance units)
|
||||
|
||||
The last coefficient is optional. If not specified, the global *pedone*
|
||||
cutoff is used.
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
Mixing, shift, table, tail correction, restart, rRESPA info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
None of these pair styles support mixing. Thus, coefficients for all
|
||||
I,J pairs must be specified explicitly.
|
||||
|
||||
All of these pair styles support the :doc:`pair_modify <pair_modify>`
|
||||
shift option for the energy of the pair interaction.
|
||||
|
||||
The :doc:`pair_modify <pair_modify>` table options are only relevant for
|
||||
pair style *pedone*
|
||||
|
||||
None of these pair styles support the :doc:`pair_modify <pair_modify>`
|
||||
tail option for adding long-range tail corrections to energy and
|
||||
pressure.
|
||||
|
||||
All of these pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do not need
|
||||
to be specified in an input script that reads a restart file.
|
||||
|
||||
These pair styles can only be used via the *pair* keyword of the
|
||||
:doc:`run_style respa <run_style>` command. They do not support the
|
||||
*inner*, *middle*, *outer* keywords.
|
||||
|
||||
----------
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
The *morse/smooth/linear* pair style is only enabled if LAMMPS was
|
||||
built with the EXTRA-PAIR package.
|
||||
See the :doc:`Build package <Build_package>` page for more info.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style */soft <pair_fep_soft>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
-------------
|
||||
|
||||
.. _Pedone:
|
||||
|
||||
**(Pedone)** A. Pedone, G. Malavasi, M. C. Menziani, A. N. Cormack, and U. Segre, J. Phys. Chem. B, 110, 11780 (2006)
|
||||
@ -275,30 +275,30 @@ accelerated styles exist.
|
||||
* :doc:`lj/smooth/linear <pair_lj_smooth_linear>` - linear smoothed LJ potential
|
||||
* :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>` - smoothed LJ vdW potential with Gaussian electrostatics
|
||||
* :doc:`lj96/cut <pair_lj96>` - Lennard-Jones 9/6 potential
|
||||
* :doc:`local/density <pair_local_density>` - generalized basic local density potential
|
||||
* :doc:`lubricate <pair_lubricate>` - hydrodynamic lubrication forces
|
||||
* :doc:`lubricate/poly <pair_lubricate>` - hydrodynamic lubrication forces with polydispersity
|
||||
* :doc:`lubricateU <pair_lubricateU>` - hydrodynamic lubrication forces for Fast Lubrication Dynamics
|
||||
* :doc:`lubricateU/poly <pair_lubricateU>` - hydrodynamic lubrication forces for Fast Lubrication with polydispersity
|
||||
* :doc:`local/density <pair_local_density>` - Generalized basic local density potential
|
||||
* :doc:`lubricate <pair_lubricate>` - Hydrodynamic lubrication forces
|
||||
* :doc:`lubricate/poly <pair_lubricate>` - Hydrodynamic lubrication forces with polydispersity
|
||||
* :doc:`lubricateU <pair_lubricateU>` - Hydrodynamic lubrication forces for Fast Lubrication Dynamics
|
||||
* :doc:`lubricateU/poly <pair_lubricateU>` - Hydrodynamic lubrication forces for Fast Lubrication with polydispersity
|
||||
* :doc:`mdpd <pair_mesodpd>` - mDPD particle interactions
|
||||
* :doc:`mdpd/rhosum <pair_mesodpd>` - mDPD particle interactions for mass density
|
||||
* :doc:`meam <pair_meam>` - modified embedded atom method (MEAM)
|
||||
* :doc:`meam/ms <pair_meam>` - multi-state modified embedded atom method (MS-MEAM)
|
||||
* :doc:`meam/spline <pair_meam_spline>` - splined version of MEAM
|
||||
* :doc:`meam/sw/spline <pair_meam_sw_spline>` - splined version of MEAM with a Stillinger-Weber term
|
||||
* :doc:`mesocnt <pair_mesocnt>` - mesoscopic vdW potential for (carbon) nanotubes
|
||||
* :doc:`mesocnt/viscous <pair_mesocnt>` - mesoscopic vdW potential for (carbon) nanotubes with friction
|
||||
* :doc:`mgpt <pair_mgpt>` - simplified model generalized pseudopotential theory (MGPT) potential
|
||||
* :doc:`meam <pair_meam>` - Modified embedded atom method (MEAM)
|
||||
* :doc:`meam/ms <pair_meam>` - Multi-state modified embedded atom method (MS-MEAM)
|
||||
* :doc:`meam/spline <pair_meam_spline>` - Splined version of MEAM
|
||||
* :doc:`meam/sw/spline <pair_meam_sw_spline>` - Splined version of MEAM with a Stillinger-Weber term
|
||||
* :doc:`mesocnt <pair_mesocnt>` - Mesoscopic vdW potential for (carbon) nanotubes
|
||||
* :doc:`mesocnt/viscous <pair_mesocnt>` - Mesoscopic vdW potential for (carbon) nanotubes with friction
|
||||
* :doc:`mgpt <pair_mgpt>` - Simplified model generalized pseudopotential theory (MGPT) potential
|
||||
* :doc:`mie/cut <pair_mie>` - Mie potential
|
||||
* :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>` - smoothed MM3 vdW potential with Gaussian electrostatics
|
||||
* :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>` - Smoothed MM3 vdW potential with Gaussian electrostatics
|
||||
* :doc:`momb <pair_momb>` - Many-Body Metal-Organic (MOMB) force field
|
||||
* :doc:`morse <pair_morse>` - Morse potential
|
||||
* :doc:`morse/smooth/linear <pair_morse>` - linear smoothed Morse potential
|
||||
* :doc:`morse/smooth/linear <pair_morse>` - Linear smoothed Morse potential
|
||||
* :doc:`morse/soft <pair_morse>` - Morse potential with a soft core
|
||||
* :doc:`multi/lucy <pair_multi_lucy>` - DPD potential with density-dependent force
|
||||
* :doc:`multi/lucy/rx <pair_multi_lucy_rx>` - reactive DPD potential with density-dependent force
|
||||
* :doc:`nb3b/harmonic <pair_nb3b>` - non-bonded 3-body harmonic potential
|
||||
* :doc:`nb3b/screened <pair_nb3b>` - non-bonded 3-body screened harmonic potential
|
||||
* :doc:`nb3b/harmonic <pair_nb3b>` - Non-bonded 3-body harmonic potential
|
||||
* :doc:`nb3b/screened <pair_nb3b>` - Non-bonded 3-body screened harmonic potential
|
||||
* :doc:`nm/cut <pair_nm>` - N-M potential
|
||||
* :doc:`nm/cut/coul/cut <pair_nm>` - N-M potential with cutoff Coulomb
|
||||
* :doc:`nm/cut/coul/long <pair_nm>` - N-M potential with long-range Coulomb
|
||||
@ -322,21 +322,22 @@ accelerated styles exist.
|
||||
* :doc:`oxrna2/xstk <pair_oxrna2>` -
|
||||
* :doc:`pace <pair_pace>` - Atomic Cluster Expansion (ACE) machine-learning potential
|
||||
* :doc:`pace/extrapolation <pair_pace>` - Atomic Cluster Expansion (ACE) machine-learning potential with extrapolation grades
|
||||
* :doc:`pedone <pair_pedone>` - Pedone (PMMCS) potential
|
||||
* :doc:`pod <pair_pod>` - Proper orthogonal decomposition (POD) machine-learning potential
|
||||
* :doc:`peri/eps <pair_peri>` - peridynamic EPS potential
|
||||
* :doc:`peri/lps <pair_peri>` - peridynamic LPS potential
|
||||
* :doc:`peri/pmb <pair_peri>` - peridynamic PMB potential
|
||||
* :doc:`peri/ves <pair_peri>` - peridynamic VES potential
|
||||
* :doc:`polymorphic <pair_polymorphic>` - polymorphic 3-body potential
|
||||
* :doc:`peri/eps <pair_peri>` - Peridynamic EPS potential
|
||||
* :doc:`peri/lps <pair_peri>` - Peridynamic LPS potential
|
||||
* :doc:`peri/pmb <pair_peri>` - Peridynamic PMB potential
|
||||
* :doc:`peri/ves <pair_peri>` - Peridynamic VES potential
|
||||
* :doc:`polymorphic <pair_polymorphic>` - Polymorphic 3-body potential
|
||||
* :doc:`python <pair_python>` -
|
||||
* :doc:`quip <pair_quip>` -
|
||||
* :doc:`rann <pair_rann>` -
|
||||
* :doc:`reaxff <pair_reaxff>` - ReaxFF potential
|
||||
* :doc:`rebo <pair_airebo>` - second generation REBO potential of Brenner
|
||||
* :doc:`rebo <pair_airebo>` - Second generation REBO potential of Brenner
|
||||
* :doc:`rebomos <pair_rebomos>` - REBOMoS potential for MoS2
|
||||
* :doc:`resquared <pair_resquared>` - Everaers RE-Squared ellipsoidal potential
|
||||
* :doc:`saip/metal <pair_saip_metal>` - interlayer potential for hetero-junctions formed with hexagonal 2D materials and metal surfaces
|
||||
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - smoothed dissipative particle dynamics for water at isothermal conditions
|
||||
* :doc:`saip/metal <pair_saip_metal>` - Interlayer potential for hetero-junctions formed with hexagonal 2D materials and metal surfaces
|
||||
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - Smoothed dissipative particle dynamics for water at isothermal conditions
|
||||
* :doc:`smatb <pair_smatb>` - Second Moment Approximation to the Tight Binding
|
||||
* :doc:`smatb/single <pair_smatb>` - Second Moment Approximation to the Tight Binding for single-element systems
|
||||
* :doc:`smd/hertz <pair_smd_hertz>` -
|
||||
|
||||
Reference in New Issue
Block a user