partial docs also for future pedone/coul/long implementation

doc/src/Commands_pair.rst

@@ -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>`

doc/src/pair_pedone.rst

@@ -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)

doc/src/pair_style.rst

@@ -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:`local/density <pair_local_density>` - Generalized basic local density potential
-* :doc:`lubricate <pair_lubricate>` - hydrodynamic lubrication forces
+* :doc:`lubricate <pair_lubricate>` - Hydrodynamic lubrication forces
-* :doc:`lubricate/poly <pair_lubricate>` - hydrodynamic lubrication forces with polydispersity
+* :doc:`lubricate/poly <pair_lubricate>` - Hydrodynamic lubrication forces with polydispersity
-* :doc:`lubricateU <pair_lubricateU>` - hydrodynamic lubrication forces for Fast Lubrication Dynamics
+* :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:`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 <pair_meam>` - Modified embedded atom method (MEAM)
-* :doc:`meam/ms <pair_meam>` - multi-state modified embedded atom method (MS-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/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:`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 <pair_mesocnt>` - Mesoscopic vdW potential for (carbon) nanotubes
-* :doc:`mesocnt/viscous <pair_mesocnt>` - mesoscopic vdW potential for (carbon) nanotubes with friction
+* :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:`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/harmonic <pair_nb3b>` - Non-bonded 3-body harmonic potential
-* :doc:`nb3b/screened <pair_nb3b>` - non-bonded 3-body screened 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/eps <pair_peri>` - Peridynamic EPS potential
-* :doc:`peri/lps <pair_peri>` - peridynamic LPS potential
+* :doc:`peri/lps <pair_peri>` - Peridynamic LPS potential
-* :doc:`peri/pmb <pair_peri>` - peridynamic PMB potential
+* :doc:`peri/pmb <pair_peri>` - Peridynamic PMB potential
-* :doc:`peri/ves <pair_peri>` - peridynamic VES potential
+* :doc:`peri/ves <pair_peri>` - Peridynamic VES potential
-* :doc:`polymorphic <pair_polymorphic>` - polymorphic 3-body 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:`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:`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>` -