rename pair style and fully integrate into build and manual

doc/src/Commands_pair.rst

@@ -80,6 +80,7 @@ OPT.
    * :doc:`coul/tt <pair_coul_tt>`
    * :doc:`coul/wolf (ko) <pair_coul>`
    * :doc:`coul/wolf/cs <pair_cs>`
+   * :doc:`dispersion/d3 <pair_dispersion_d3>`
    * :doc:`dpd (giko) <pair_dpd>`
    * :doc:`dpd/coul/slater/long (g) <pair_dpd_coul_slater_long>`
    * :doc:`dpd/ext (ko) <pair_dpd_ext>`

doc/src/pair_dispersion_d3.rst

@@ -1,21 +1,17 @@
-.. index:: pair_style d3
+.. index:: pair_style dispersion/d3
-..    
-    .. index:: pair_style d3/kk
 
-pair_style d3 command
+pair_style dispersion/d3 command
-=====================
+================================
-..
-    Accelerator Variants: *d3/kk*
 
 Syntax
 """"""
 
 .. code-block:: LAMMPS
 
-   pair_style d3 damping functional cutoff cn_cutoff
+   pair_style dispersion/d3 damping functional cutoff cn_cutoff
 
 * damping = damping function: *zero*, *zerom*, *bj*, or *bjm*
-* functional = XC functional form: *pbe*, *pbe0*, etc.
+* functional = XC functional form: *pbe*, *pbe0*, ... (see list below)
 * cutoff = global cutoff (distance units)
 * cn_cutoff = coordination number cutoff (distance units)
 
@@ -24,14 +20,19 @@ Examples
 
 .. code-block:: LAMMPS
 
-   pair_style d3 zero pbe 30.0 20.0
+   pair_style dispersion/d3 zero pbe 30.0 20.0
    pair_coeff * * C
 
 Description
 """""""""""
 
-Style *d3* computes the dispersion energy-correction used in the DFT-D3
+.. versionadded:: TBD
-method of Grimme :ref:`(Grimme1) <Grimme1>`. 
+
+Style *dispersion/d3* computes the dispersion energy-correction used in
+the DFT-D3 method of Grimme :ref:`(Grimme1) <Grimme1>`.  It would
+typically be used with a machine learning potential that was trained
+with results from plain DFT calculations without the dispersion
+correction through pair_style hybrid/overlay.
 
 The energy contribution :math:`E_i` for an atom :math:`i` is given by:
 
@@ -41,19 +42,22 @@ The energy contribution :math:`E_i` for an atom :math:`i` is given by:
                 s_6 \frac{C_{6,ij}}{r^6_{ij}} f_6^{damp}(r_{ij}) +
                 s_8 \frac{C_{8,ij}}{r^8_{ij}} f_8^{damp}(r_{ij}) \big)
 
-where :math:`C_n` is the averaged, geometry-dependent nth-order dispersion 
+where :math:`C_n` is the averaged, geometry-dependent nth-order dispersion
-coefficient for atom pair :math:`ij`, :math:`r_{ij}` their internuclear distance, 
+coefficient for atom pair :math:`ij`, :math:`r_{ij}` their internuclear distance,
 :math:`s_n` are XC functional-dependent scaling factor, and :math:`f_n^{damp}` are
 damping functions.
 
-N.B.: in the current version of the code, it is *not* possible to calculate three-body
+.. note::
-dispersion contributions, according for example to the Axilrod-Teller-Muto model.
 
-Available damping functions are the original "zero-damping" :ref:`(Grimme1) <Grimme1>`, 
+   It is currently *not* possible to calculate three-body dispersion
-Becke-Johnson damping :ref:`(Grimme2) <Grimme2>`, and their revised forms :ref:`(Sherrill) <Sherrill>`.
+   contributions, according for example to the Axilrod-Teller-Muto model.
 
-Available XC functional scaling factors are listed in the table  below, and depend on 
+Available damping functions are the original "zero-damping"
-the selected damping function. 
+:ref:`(Grimme1) <Grimme1>`, Becke-Johnson damping :ref:`(Grimme2)
+<Grimme2>`, and their revised forms :ref:`(Sherrill) <Sherrill>`.
+
+Available XC functional scaling factors are listed in the table below,
+and depend on the selected damping function.
 
 +------------------+--------------------------------------------------------------------------------+
 | Damping function | XC functional                                                                  |
@@ -77,39 +81,45 @@ the selected damping function.
 +------------------+--------------------------------------------------------------------------------+
 
 
-This style is primarly supposed to be used combined with a machine-learned
+This style is primarly supposed to be used combined with a
-interatomic potential trained on a DFT dataset (the selected XC functional 
+machine-learned interatomic potential trained on a DFT dataset (the
-should be chosen accordingly) via the *pair_style hybrid* command.
+selected XC functional should be chosen accordingly) via the *pair_style
+hybrid* command.
 
 Coefficients
 """"""""""""
 
-All the required coefficients are already stored internally, in the pair_d3_pars.h file. 
+All the required coefficients are already stored internally, in the
-The only information to provide are the chemical symbols of the atoms.
+d3_paramerters.h file.  The only information to provide are the chemical
-The number of chemical symbols given must be equal to the number of atom types
+symbols of the atoms.  The number of chemical symbols given must be
-used and should match their ordering.
+equal to the number of atom types used and should match their ordering.
 
 
 Mixing, shift, table, tail correction, restart, rRESPA info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This pair style does not support mixing since all parameters are explicit for each pair.
+This pair style does not support mixing since all parameters are
+explicit for each pair of atom types.
 
-This pair style does not support the :doc:`pair_modify` shift, table, and tail options.
+This pair style does not support the :doc:`pair_modify` shift, table,
+and tail options.
 
-This pair style does not write its information to :doc:`binary restart files <restart>`.
+This pair style does not write its information to :doc:`binary restart
+files <restart>`.
 
 This pair style can only be used via the *pair* keyword of the
 :doc:`run_style respa <run_style>` command.  It does not support the
 *inner*, *middle*, *outer* keywords.
 
-
 Restrictions
 """"""""""""
 
-Style *d3* is part of the EXTRA-PAIR package. It is only enabled if LAMMPS
+Style *dispersion/d3* is part of the EXTRA-PAIR package. It is only
-was built with that package. 
+enabled if LAMMPS was built with that package.  See the :doc:`Build
-See the :doc:`Build package <Build_package>` page for more info.
+package <Build_package>` page for more info.
+
+It is currently *not* possible to calculate three-body dispersion
+contributions, ccording for example to the Axilrod-Teller-Muto model.
 
 Related commands
 """"""""""""""""
@@ -125,16 +135,12 @@ none
 
 .. _Grimme1:
 
-**(Grimme1)** S. Grimme, J. Antony, S. Ehrlich, and H. Krieg, 
+**(Grimme1)** S. Grimme, J. Antony, S. Ehrlich, and H. Krieg, J. Chem. Phys. 132, 154104 (2010).
-J. Chem. Phys. 132, 154104 (2010).
-.
 
 .. _Grimme2:
 
-**(Grimme2)** S. Grimme, S. Ehrlich and L. Goerigk,  
+**(Grimme2)** S. Grimme, S. Ehrlich and L. Goerigk,  J. Comput. Chem. 32, 1456 (2011); DOI:10.1002/jcc.21759.
-J. Comput. Chem. 32, 1456 (2011); DOI:10.1002/jcc.21759.
 
 .. _Sherrill:
 
-**(Sherrill)** D. G. A. Smith, L. A. Burns, K. Patkowski, and C. D. Sherrill,
+**(Sherrill)** D. G. A. Smith, L. A. Burns, K. Patkowski, and C. D. Sherrill, J. Phys. Chem. Lett., 7, 2197, (2016); DOI: 10.1021/acs.jpclett.6b00780.
-J. Phys. Chem. Lett., 7, 2197, (2016); DOI: 10.1021/acs.jpclett.6b00780.

doc/src/pair_style.rst

@@ -172,6 +172,7 @@ accelerated styles exist.
 * :doc:`coul/tt <pair_coul_tt>` - damped charge-dipole Coulomb for Drude dipoles
 * :doc:`coul/wolf <pair_coul>` - Coulomb via Wolf potential
 * :doc:`coul/wolf/cs <pair_cs>` - Coulomb via Wolf potential with core/shell adjustments
+* :doc:`dispersion/d3 <pair_dispersion_d3>` - Dispersion correction for potentials derived from DFT functionals
 * :doc:`dpd <pair_dpd>` - dissipative particle dynamics (DPD)
 * :doc:`dpd/coul/slater/long <pair_dpd_coul_slater_long>` - dissipative particle dynamics (DPD) with electrostatic interactions
 * :doc:`dpd/ext <pair_dpd_ext>` - generalized force field for DPD

src/.gitignore

@@ -1217,6 +1217,9 @@
 /pair_dipole_cut.h
 /pair_dipole_sf.cpp
 /pair_dipole_sf.h
+/d3_parameters.h
+/pair_dispersion_d3.h
+/pair_dispersion_d3.cpp
 /pair_dsmc.cpp
 /pair_dsmc.h
 /pair_e3b.cpp

src/EXTRA-PAIR/d3_parameters.h

@@ -1,4 +1,26 @@
-#define R0AB_TABLE { \
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+  -------------------------------------------------------------------------
+   Contributing authors:
+      Sonia Salomoni^1,^2
+      Arthur France-Lanord^1
+
+      ^1: IMPMC, CNRS, Sorbonne Universite, Paris, France
+      ^2: SCAI, Sorbonne Universite, Paris, France
+------------------------------------------------------------------------- */
+#ifndef LMP_D3_PARAMETERS_H
+#define LMP_D3_PARAMETERS_H
+
+#define R0AB_TABLE {                                                    \
     {2.18230000E+00, 1.85470000E+00, 2.90860000E+00, 2.35500000E+00, 2.51410000E+00, 2.44920000E+00, 2.36670000E+00, 2.17680000E+00, 2.06460000E+00, 1.98920000E+00, 2.98980000E+00, 2.51290000E+00, 2.87660000E+00, 2.88840000E+00, 2.83040000E+00, 2.61900000E+00, 2.47570000E+00, 2.37250000E+00, 3.21470000E+00, 2.75970000E+00, 2.73610000E+00, 2.68320000E+00, 2.63790000E+00, 2.92300000E+00, 2.54900000E+00, 2.49260000E+00, 2.46670000E+00, 2.45150000E+00, 2.44130000E+00, 2.43180000E+00, 2.85020000E+00, 2.92260000E+00, 2.91400000E+00, 2.73000000E+00, 2.60260000E+00, 2.50870000E+00, 3.28930000E+00, 2.87860000E+00, 2.89970000E+00, 2.85350000E+00, 3.09050000E+00, 3.03010000E+00, 2.91890000E+00, 2.85780000E+00, 2.82400000E+00, 2.80040000E+00, 2.78460000E+00, 2.54240000E+00, 2.97430000E+00, 3.07750000E+00, 3.08930000E+00, 2.90910000E+00, 2.78060000E+00, 2.68480000E+00, 3.39680000E+00, 3.06300000E+00, 3.06320000E+00, 2.94550000E+00, 2.92440000E+00, 2.90460000E+00, 2.88780000E+00, 2.87090000E+00, 2.85680000E+00, 2.67980000E+00, 2.51890000E+00, 3.04810000E+00, 2.81360000E+00, 2.80320000E+00, 2.79670000E+00, 2.78970000E+00, 2.83950000E+00, 2.90070000E+00, 2.85590000E+00, 2.81100000E+00, 2.76760000E+00, 2.69120000E+00, 2.78950000E+00, 2.75220000E+00, 2.72020000E+00, 2.53150000E+00, 2.98520000E+00, 3.11600000E+00, 3.14160000E+00, 2.96640000E+00, 2.83880000E+00, 2.74120000E+00, 3.41550000E+00, 3.05480000E+00, 3.38500000E+00, 3.09420000E+00, 3.01870000E+00, 2.98750000E+00, 2.96590000E+00, 2.87630000E+00}, \
     {1.85470000E+00, 1.73470000E+00, 2.57320000E+00, 2.50950000E+00, 2.39170000E+00, 2.25270000E+00, 2.13280000E+00, 2.06250000E+00, 1.98910000E+00, 1.92510000E+00, 2.63970000E+00, 2.73210000E+00, 2.74270000E+00, 2.66050000E+00, 2.55380000E+00, 2.47970000E+00, 2.40190000E+00, 2.32890000E+00, 2.83150000E+00, 3.05880000E+00, 2.97650000E+00, 2.90600000E+00, 2.84940000E+00, 2.62230000E+00, 2.76230000E+00, 2.71360000E+00, 2.67090000E+00, 2.63380000E+00, 2.60060000E+00, 2.57290000E+00, 2.69340000E+00, 2.68380000E+00, 2.62710000E+00, 2.58700000E+00, 2.53550000E+00, 2.48140000E+00, 2.89910000E+00, 3.16580000E+00, 3.09530000E+00, 3.01670000E+00, 2.79980000E+00, 2.73120000E+00, 2.67770000E+00, 2.63340000E+00, 2.59600000E+00, 2.56210000E+00, 2.53240000E+00, 2.66010000E+00, 2.80580000E+00, 2.82750000E+00, 2.79170000E+00, 2.76380000E+00, 2.72090000E+00, 2.67400000E+00, 3.01220000E+00, 3.32710000E+00, 3.26620000E+00, 3.24700000E+00, 3.22410000E+00, 3.20440000E+00, 3.18900000E+00, 3.17370000E+00, 3.16080000E+00, 3.01510000E+00, 2.97030000E+00, 2.95840000E+00, 3.09510000E+00, 3.08050000E+00, 3.06890000E+00, 3.06360000E+00, 3.00810000E+00, 2.96740000E+00, 2.90500000E+00, 2.85200000E+00, 2.80780000E+00, 2.76040000E+00, 2.58490000E+00, 2.55240000E+00, 2.51830000E+00, 2.61040000E+00, 2.78810000E+00, 2.84820000E+00, 2.83250000E+00, 2.82090000E+00, 2.78900000E+00, 2.74890000E+00, 3.05220000E+00, 3.32060000E+00, 3.42080000E+00, 3.20750000E+00, 3.19180000E+00, 3.16740000E+00, 3.14420000E+00, 3.12940000E+00}, \
     {2.90860000E+00, 2.57320000E+00, 3.49560000E+00, 2.98020000E+00, 2.99770000E+00, 3.19330000E+00, 2.87840000E+00, 2.63950000E+00, 2.50860000E+00, 2.41900000E+00, 3.60310000E+00, 3.10520000E+00, 3.27760000E+00, 3.75130000E+00, 3.39320000E+00, 3.13310000E+00, 2.97890000E+00, 2.87600000E+00, 3.87240000E+00, 3.34740000E+00, 3.24750000E+00, 3.26130000E+00, 3.18400000E+00, 3.41610000E+00, 3.09910000E+00, 3.06930000E+00, 3.05750000E+00, 3.05110000E+00, 3.05400000E+00, 3.04160000E+00, 3.24670000E+00, 3.78670000E+00, 3.47710000E+00, 3.24710000E+00, 3.11290000E+00, 3.02390000E+00, 4.03880000E+00, 3.58230000E+00, 3.45240000E+00, 3.39780000E+00, 3.64480000E+00, 3.58210000E+00, 3.49250000E+00, 3.46730000E+00, 3.46350000E+00, 3.46170000E+00, 3.46520000E+00, 3.25550000E+00, 3.48300000E+00, 4.01810000E+00, 3.72620000E+00, 3.50660000E+00, 3.38120000E+00, 3.29250000E+00, 4.22410000E+00, 4.04320000E+00, 3.64320000E+00, 3.61080000E+00, 3.58480000E+00, 3.56210000E+00, 3.54120000E+00, 3.51990000E+00, 3.50500000E+00, 3.25860000E+00, 3.30630000E+00, 3.69190000E+00, 3.46350000E+00, 3.45190000E+00, 3.44450000E+00, 3.43440000E+00, 3.31710000E+00, 3.81740000E+00, 3.83250000E+00, 3.74800000E+00, 3.67250000E+00, 3.60370000E+00, 3.64840000E+00, 3.57420000E+00, 3.49470000E+00, 3.27340000E+00, 3.52840000E+00, 4.07390000E+00, 3.77350000E+00, 3.55470000E+00, 3.43290000E+00, 3.33740000E+00, 4.25410000E+00, 3.81320000E+00, 3.70040000E+00, 3.51520000E+00, 3.51270000E+00, 3.49710000E+00, 3.47950000E+00, 3.55980000E+00}, \
@@ -32481,3 +32503,4 @@
     {3.91125000E+02, 4.82000000E+02, 4.50000000E+02, 3.90980000E+00, 3.91230000E+00}, \
     {4.55285400E+02, 4.82000000E+02, 4.82000000E+02, 3.90980000E+00, 3.90980000E+00} \
 }
+#endif

src/EXTRA-PAIR/pair_dispersion_d3.cpp

@@ -12,7 +12,7 @@
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
-   Contributing authors: 
+   Contributing authors:
       Sonia Salomoni^1,^2
       Arthur France-Lanord^1
 
@@ -20,14 +20,8 @@
       ^2: SCAI, Sorbonne Universite, Paris, France
 ------------------------------------------------------------------------- */
 
-#include "pair_d3.h"
+#include "pair_dispersion_d3.h"
-#include "pair_d3_pars.h"
+#include "d3_parameters.h"
-
-#include <cmath>
-#include <iostream>
-#include <string>
-#include <algorithm>
-#include <unordered_map>
 
 #include "atom.h"
 #include "comm.h"
@@ -37,11 +31,14 @@
 #include "neigh_list.h"
 #include "neighbor.h"
 
+#include <cmath>
+#include <algorithm>
+#include <unordered_map>
+
 using namespace LAMMPS_NS;
 
 // global ad hoc parameters
 static constexpr double K1 = 16.0;
-static constexpr double K2 = 4.0/3.0;
 static constexpr double K3 = -4.0;
 
 /*  reasonable choices for k3 are between 3 and 5 :
@@ -56,7 +53,6 @@ static constexpr double K3 = -4.0;
 static constexpr int NUM_ELEMENTS = 94;         // maximum element number
 static constexpr int N_PARS_COLS = 5;           // number of columns in C6 table
 static constexpr int N_PARS_ROWS = 32385;       // number of rows in C6 table
-static constexpr int MAX_CN_ELEM = 5;           // maximun coordination number for each element
 
 static constexpr double autoang = 0.52917725 ;  // atomic units (Bohr) to Angstrom
 static constexpr double autoev = 27.21140795 ;  // atomic units (Hartree) to eV
@@ -65,7 +61,7 @@ static constexpr double autoev = 27.21140795 ;  // atomic units (Hartree) to eV
    Constructor (Required)
 ------------------------------------------------------------------------- */
 
-PairD3::PairD3(LAMMPS *lmp) : Pair(lmp)
+PairDispersionD3::PairDispersionD3(LAMMPS *lmp) : Pair(lmp)
 {
   nmax = 0;
   comm_forward = 2;
@@ -74,13 +70,14 @@ PairD3::PairD3(LAMMPS *lmp) : Pair(lmp)
   restartinfo = 0;
   manybody_flag = 1;
   one_coeff = 1;
+  single_enable = 0;
 }
 
 /* ----------------------------------------------------------------------
    Destructor (Required)
 ------------------------------------------------------------------------- */
 
-PairD3::~PairD3()
+PairDispersionD3::~PairDispersionD3()
 {
   if (allocated) {
     memory->destroy(setflag);
@@ -103,7 +100,7 @@ PairD3::~PairD3()
    Allocate all arrays (Required)
 ------------------------------------------------------------------------- */
 
-void PairD3::allocate()
+void PairDispersionD3::allocate()
 {
   allocated = 1;
   int n = atom->ntypes;
@@ -128,17 +125,9 @@ void PairD3::allocate()
              pair_style   d3 rthr cn_thr damping_type
 ------------------------------------------------------------------------- */
 
-void PairD3::settings(int narg, char **arg) {
+void PairDispersionD3::settings(int narg, char **arg) {
 
-  if (narg != 4) {
+  if (narg != 4) error->all(FLERR, "Pair_style dispersion/d3 needs 4 arguments");
-      error->all(FLERR,
-              "Pair_style d3 needs 4 arguments:\n"
-              "\t damping_type : type of the damping\n"
-              "\t functional_name : name of the functional\n"
-              "\t rthr : threshold for dispersion interaction\n"
-              "\t cn_thr : threshold for coordination number calculation\n"
-              );
-  }
 
   damping_type = arg[0];
   std::string functional_name = arg[1];
@@ -154,10 +143,10 @@ void PairD3::settings(int narg, char **arg) {
 }
 
 /* ----------------------------------------------------------------------
-   finds atomic number (used in PairD3::coeff)
+   finds atomic number (used in PairDispersionD3::coeff)
 ------------------------------------------------------------------------- */
 
-int PairD3::find_atomic_number(std::string& key) {
+int PairDispersionD3::find_atomic_number(std::string& key) {
 
     std::transform(key.begin(), key.end(), key.begin(), ::tolower);
     if (key.length() == 1) { key += " "; }
@@ -189,10 +178,10 @@ int PairD3::find_atomic_number(std::string& key) {
 }
 
 /* ----------------------------------------------------------------------
-   Check whether an integer value in an integer array (used in PairD3::coeff)
+   Check whether an integer value in an integer array (used in PairDispersionD3::coeff)
 ------------------------------------------------------------------------- */
 
-std::vector<int> PairD3::is_int_in_array(int array[], int size, int value) {
+std::vector<int> PairDispersionD3::is_int_in_array(int array[], int size, int value) {
     std::vector<int> indices;
     for (int i = 0; i < size; ++i) {
         if (array[i] == value) {
@@ -204,11 +193,11 @@ std::vector<int> PairD3::is_int_in_array(int array[], int size, int value) {
 
 
 /* ----------------------------------------------------------------------
-   Read r0ab values from r0ab.csv (used in PairD3::coeff)
+   Read r0ab values from r0ab.csv (used in PairDispersionD3::coeff)
 ------------------------------------------------------------------------- */
 
-void PairD3::read_r0ab(int* atomic_numbers, int ntypes) {
+void PairDispersionD3::read_r0ab(int* atomic_numbers, int ntypes) {
-  
+
   const double r0ab_table[NUM_ELEMENTS][NUM_ELEMENTS] = R0AB_TABLE;
 
   for (int i = 1; i <= ntypes; i++) {
@@ -219,10 +208,10 @@ void PairD3::read_r0ab(int* atomic_numbers, int ntypes) {
 }
 
 /* ----------------------------------------------------------------------
-   Get atom pair indices and grid indices (used in PairD3::read_c6ab)
+   Get atom pair indices and grid indices (used in PairDispersionD3::read_c6ab)
 ------------------------------------------------------------------------- */
 
-void PairD3::set_limit_in_pars_array(int& idx_atom_1, int& idx_atom_2, int& idx_i, int& idx_j) {
+void PairDispersionD3::set_limit_in_pars_array(int& idx_atom_1, int& idx_atom_2, int& idx_i, int& idx_j) {
 
   idx_i = 0;
   idx_j = 0;
@@ -240,10 +229,10 @@ void PairD3::set_limit_in_pars_array(int& idx_atom_1, int& idx_atom_2, int& idx_
 }
 
 /* ----------------------------------------------------------------------
-   Read c6ab values from c6ab.csv (used in PairD3::coeff)
+   Read c6ab values from c6ab.csv (used in PairDispersionD3::coeff)
 ------------------------------------------------------------------------- */
 
-void PairD3::read_c6ab(int* atomic_numbers, int ntypes) {
+void PairDispersionD3::read_c6ab(int* atomic_numbers, int ntypes) {
 
   for (int i = 0; i <= ntypes; i++) { mxci[i] = 0; }
   int grid_i = 0, grid_j = 0;
@@ -292,7 +281,7 @@ void PairD3::read_c6ab(int* atomic_numbers, int ntypes) {
           pair_coeff * * path_r0ab.csv path_c6ab.csv functional element1 element2 ...
 ------------------------------------------------------------------------- */
 
-void PairD3::coeff(int narg, char **arg) {
+void PairDispersionD3::coeff(int narg, char **arg) {
 
     int ntypes = atom->ntypes;
     if (narg != ntypes + 2) { error->all(FLERR, "Pair_coeff * * needs: element1 element2 ..."); }
@@ -391,7 +380,7 @@ void PairD3::coeff(int narg, char **arg) {
    Calculate coordination number of atoms
 ------------------------------------------------------------------------- */
 
-void PairD3::calc_coordination_number() {
+void PairDispersionD3::calc_coordination_number() {
 
   double **x = atom->x;
   int *type  = atom->type;
@@ -433,14 +422,14 @@ void PairD3::calc_coordination_number() {
       delrj[0] = x[i][0] - x[j][0];
       delrj[1] = x[i][1] - x[j][1];
       delrj[2] = x[i][2] - x[j][2];
-        
+
       double rsq = delrj[0]*delrj[0] + delrj[1]*delrj[1] + delrj[2]*delrj[2];
 
       // if the atoms are too far away don't consider the contribution
       if (rsq > cn_thr) continue;
 
       double rr = sqrt(rsq);
-      double rcov_ij = (rcov[itype] + rcov[jtype]) * autoang;    
+      double rcov_ij = (rcov[itype] + rcov[jtype]) * autoang;
       double cn_ij = 1.0f / (1.0f + expf(-K1*((rcov_ij/rr)-1.0f)));
 
       // update coordination number
@@ -460,18 +449,18 @@ void PairD3::calc_coordination_number() {
    Get derivative of C6
 ------------------------------------------------------------------------- */
 
-double* PairD3::get_dC6(int iat, int jat, double cni, double cnj){
+double* PairDispersionD3::get_dC6(int iat, int jat, double cni, double cnj){
 
   static double c6_res[3] = {};
-  double c6_ref, itype, jtype, cni_ref, cnj_ref;
+  double c6_ref, cni_ref, cnj_ref;
   double c6mem, r_save, r;
   double expterm, term;
   double num, den, d_num_i, d_num_j, d_den_i, d_den_j;
 
   c6mem = -1.0e20f, r_save = 1.0e20f;
-  num = 0 ; den = 0 ; d_num_i = 0 ; d_num_j = 0; d_den_i = 0; d_den_j = 0; 
+  num = 0 ; den = 0 ; d_num_i = 0 ; d_num_j = 0; d_den_i = 0; d_den_j = 0;
 
-  for (int ci = 0; ci <= mxci[iat]; ci++){ 
+  for (int ci = 0; ci <= mxci[iat]; ci++){
     for (int cj = 0; cj <= mxci[jat]; cj++){
 
     c6_ref = c6ab[iat][jat][ci][cj][0];
@@ -489,7 +478,7 @@ double* PairD3::get_dC6(int iat, int jat, double cni, double cnj){
       }
 
       expterm = exp(static_cast<double>(K3) * static_cast<double>(r));
- 
+
       num += c6_ref*expterm;
       den += expterm;
 
@@ -512,7 +501,7 @@ double* PairD3::get_dC6(int iat, int jat, double cni, double cnj){
     c6_res[2] = ((d_num_j*den)-(d_den_j*num)) / (den*den);
   } else {
     c6_res[0] = c6mem; c6_res[1] = 0; c6_res[2] = 0;
-  }  
+  }
   return c6_res;
 }
 
@@ -520,7 +509,7 @@ double* PairD3::get_dC6(int iat, int jat, double cni, double cnj){
    Compute : energy, force, and stress (Required)
 ------------------------------------------------------------------------- */
 
-void PairD3::compute(int eflag, int vflag) {
+void PairDispersionD3::compute(int eflag, int vflag) {
 
   std::unordered_map<std::string, int> dampingMap = {
     {"zero", 1},  {"zerom", 2},  {"bj", 3}, {"bjm", 4}
@@ -537,10 +526,10 @@ void PairD3::compute(int eflag, int vflag) {
   int *type  = atom->type;
   int nlocal = atom->nlocal;
 
-  double *special_lj = force->special_lj;   
+  double *special_lj = force->special_lj;
   int newton_pair = force->newton_pair;
 
-  int   inum       = list->inum;  
+  int   inum       = list->inum;
   int*  ilist      = list->ilist;
   int*  numneigh   = list->numneigh;
   int** firstneigh = list->firstneigh;
@@ -556,7 +545,7 @@ void PairD3::compute(int eflag, int vflag) {
 
     int  jnum = numneigh[i];
     int* jlist = firstneigh[i];
-  
+
     // fprintf(stderr, "> i, type[i], CN[i], C6[i,i] :  %d, %d, %f, %f\n", atom->tag[i], type[i], cn[i], get_dC6(type[i],type[i],cn[i],cn[i])[0]/(autoev*pow(autoang,6)));
 
     for (int jj = 0; jj < jnum; jj++) {
@@ -570,7 +559,7 @@ void PairD3::compute(int eflag, int vflag) {
       double delz = ztmp - x[j][2];
 
       double rsq = delx*delx + dely*dely + delz*delz;
-    
+
       if (rsq < cutsq[type[i]][type[j]]) {
 
         double r = sqrt(rsq);
@@ -650,7 +639,7 @@ void PairD3::compute(int eflag, int vflag) {
             t6 = r6+pow((a1*r0+a2),6);
             t8 = r8+pow((a1*r0+a2),8);
 
-            e6 = C6/t6; 
+            e6 = C6/t6;
             e8 = C8/t8;
 
             tmp6 = 6.0*s6*C6*r4/(t6*t6);
@@ -658,7 +647,7 @@ void PairD3::compute(int eflag, int vflag) {
 
             fpair = -(tmp6+tmp8) ;
             fpair *= factor_lj;
-          }       
+          }
           break;
           case 4:{ // bjm
 
@@ -671,7 +660,7 @@ void PairD3::compute(int eflag, int vflag) {
             t6 = r6+pow((a1*r0+a2),6);
             t8 = r8+pow((a1*r0+a2),8);
 
-            e6 = C6/t6; 
+            e6 = C6/t6;
             e8 = C8/t8;
 
             tmp6 = 6.0*s6*C6*r4/(t6*t6);
@@ -701,7 +690,7 @@ void PairD3::compute(int eflag, int vflag) {
           f[j][2] -= delz*fpair;
         }
 
-        if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);  
+        if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
       }
     }
   }
@@ -712,7 +701,7 @@ void PairD3::compute(int eflag, int vflag) {
   comm->forward_comm(this);
 
   // After calculating all derivatives dE/dr_ij w.r.t. distances,
-  // the grad w.r.t. the coordinates is calculated dE/dr_ij * dr_ij/dxyz_i  
+  // the grad w.r.t. the coordinates is calculated dE/dr_ij * dr_ij/dxyz_i
   for (int ii = 0; ii < inum; ii++) {
 
     int i = ilist[ii];
@@ -720,10 +709,10 @@ void PairD3::compute(int eflag, int vflag) {
     double xtmp = x[i][0];
     double ytmp = x[i][1];
     double ztmp = x[i][2];
-  
+
     int  jnum = numneigh[i];
     int* jlist = firstneigh[i];
-  
+
     for (int jj = 0; jj < jnum; jj++) {
 
       int j = jlist[jj];
@@ -735,7 +724,7 @@ void PairD3::compute(int eflag, int vflag) {
       double delz = ztmp - x[j][2];
 
       double rsq = delx*delx + dely*dely + delz*delz;
-      
+
       if (rsq < cutsq[type[i]][type[j]]) {
 
         double r = sqrt(rsq);
@@ -762,7 +751,7 @@ void PairD3::compute(int eflag, int vflag) {
           f[j][1] -= dely*fpair;
           f[j][2] -= delz*fpair;
         }
-        if (evflag) ev_tally(i,j,nlocal,newton_pair,0.0,0.0,fpair,delx,dely,delz);  
+        if (evflag) ev_tally(i,j,nlocal,newton_pair,0.0,0.0,fpair,delx,dely,delz);
       }
     }
   }
@@ -770,7 +759,7 @@ void PairD3::compute(int eflag, int vflag) {
 }
 
 
-void PairD3::set_funcpar(std::string& functional_name) {
+void PairDispersionD3::set_funcpar(std::string& functional_name) {
 
   std::unordered_map<std::string, int> dampingMap = {
     {"zero", 1},  {"zerom", 2},  {"bj", 3}, {"bjm", 4}
@@ -882,7 +871,7 @@ void PairD3::set_funcpar(std::string& functional_name) {
         case 3: rs6 = 1.151808; s8 = 1.020078; rs8 = 0.035964; break;
         case 4: rs6 = 1.279637; s8 = 1.841686; rs8 = 0.014370; break;
         case 5: rs6 = 1.233460; s8 = 1.945174; rs8 = 0.000000; break;
-        case 6: rs6 = 2.340218; s8 = 0.000000; rs8 = 0.129434; break;      
+        case 6: rs6 = 2.340218; s8 = 0.000000; rs8 = 0.129434; break;
         case 7: rs6 = 2.077949; s8 = 0.000081; rs8 = 0.116755; break;
         case 8: rs6 = 1.366361; s8 = 1.280619; rs8 = 0.003160; break;
         default:
@@ -993,7 +982,7 @@ void PairD3::set_funcpar(std::string& functional_name) {
       //fprintf(stderr,"alpha : %f\n", alpha);
 
       a2 = a2*autoang;
-    } 
+    }
     break;
 
     case 4:{ // bjm
@@ -1041,7 +1030,7 @@ void PairD3::set_funcpar(std::string& functional_name) {
    init for one type pair i,j and corresponding j,i
 ------------------------------------------------------------------------- */
 
-double PairD3::init_one(int i, int j) {
+double PairDispersionD3::init_one(int i, int j) {
 
   if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set");
 
@@ -1050,7 +1039,7 @@ double PairD3::init_one(int i, int j) {
   return std::sqrt(rthr);
 }
 
-void PairD3::init_style()
+void PairDispersionD3::init_style()
 {
   if (atom->tag_enable == 0)
     error->all(FLERR,"Pair style D3 requires atom IDs");
@@ -1065,7 +1054,7 @@ void PairD3::init_style()
    Communication
 ------------------------------------------------------------------------- */
 
-int PairD3::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
+int PairDispersionD3::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
 {
   int i,j,m;
 
@@ -1079,14 +1068,14 @@ int PairD3::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, i
   if (communicationStage == 2) {
     for (i = 0; i < n; i ++) {
       j = list[i];
-      buf[m++] = dc6[j]; 
+      buf[m++] = dc6[j];
     }
   }
 
   return m;
 }
 
-void PairD3::unpack_forward_comm(int n, int first, double *buf)
+void PairDispersionD3::unpack_forward_comm(int n, int first, double *buf)
 {
   int i,m,last;
 
@@ -1104,7 +1093,7 @@ void PairD3::unpack_forward_comm(int n, int first, double *buf)
   }
 }
 
-int PairD3::pack_reverse_comm(int n, int first, double *buf)
+int PairDispersionD3::pack_reverse_comm(int n, int first, double *buf)
 {
   int i,m,last;
 
@@ -1123,7 +1112,7 @@ int PairD3::pack_reverse_comm(int n, int first, double *buf)
   return m;
 }
 
-void PairD3::unpack_reverse_comm(int n, int *list, double *buf)
+void PairDispersionD3::unpack_reverse_comm(int n, int *list, double *buf)
 {
   int i,j,m;
 
@@ -1139,5 +1128,5 @@ void PairD3::unpack_reverse_comm(int n, int *list, double *buf)
       j = list[i];
       dc6[j] += buf[m++];
     }
-  }  
+  }
 }

src/EXTRA-PAIR/pair_dispersion_d3.h

@@ -9,34 +9,27 @@
    the GNU General Public License.
 
    See the README file in the top-level LAMMPS directory.
-  -------------------------------------------------------------------------
-   Contributing authors: 
-      Sonia Salomoni^1,^2
-      Arthur France-Lanord^1
-
-      ^1: IMPMC, CNRS, Sorbonne Universite, Paris, France
-      ^2: SCAI, Sorbonne Universite, Paris, France
 ------------------------------------------------------------------------- */
 
 #ifdef PAIR_CLASS
 // clang-format off
-PairStyle(d3,PairD3);
+PairStyle(dispersion/d3,PairDispersionD3);
 // clang-format on
 #else
 
-#ifndef LMP_PAIR_D3_H
+#ifndef LMP_PAIR_DISPERSION_D3_H
-#define LMP_PAIR_D3_H
+#define LMP_PAIR_DISPERSION_D3_H
 
 #include "pair.h"
 
 namespace LAMMPS_NS {
 
-class PairD3 : public Pair {
+class PairDispersionD3 : public Pair {
 
  public:
 
-  PairD3(class LAMMPS *);
+  PairDispersionD3(class LAMMPS *);
-  ~PairD3() override;
+  ~PairDispersionD3() override;
 
   void compute(int, int) override;
 
@@ -74,7 +67,7 @@ class PairD3 : public Pair {
   double* dc6 = nullptr;                // dC6i(iat) saves dE_dsp/dCN(iat)
 
   int communicationStage;               // communication stage
-  
+
   void allocate();
   virtual void set_funcpar(std::string&);
 
@@ -82,7 +75,7 @@ class PairD3 : public Pair {
 
   int find_atomic_number(std::string&);
   std::vector<int> is_int_in_array(int*, int, int);
-  
+
   void read_r0ab(int*, int);
   void set_limit_in_pars_array(int&, int&, int&, int&);
   void read_c6ab(int*, int);

unittest/force-styles/tests/manybody-pair-d3.yaml

@@ -1,155 +0,0 @@
----
-lammps_version: 17 Apr 2024
-tags: generated
-date_generated: Mon Dec  9 17:36:37 2024
-epsilon: 1e-11
-skip_tests: single
-prerequisites: ! |
-  pair d3
-pre_commands: ! ""
-post_commands: ! ""
-input_file: in.manybody
-pair_style: d3 zero pbe 12.0 12.0
-pair_coeff: ! |
-  * * Si Si Si Si Si Si Si Si
-extract: ! ""
-natoms: 64
-init_vdwl: -9.262365243925203
-init_coul: 0
-init_stress: ! |-
-  -1.8070680187151131e+00 -1.8151671933941584e+00 -1.9214651828014326e+00 -4.1552461934576006e-02 -7.1708481007728198e-01 -1.3638435806044302e-01
-init_forces: ! |2
-    1  4.5901745485403295e-04 -5.8645004074280530e-03 -2.6408414312694140e-03
-    2  4.1982212100084848e-02  7.7916988681057701e-03  4.1558505657116980e-03
-    3 -1.0599537920220059e-03 -1.5284351930588387e-03  1.3250226337933743e-03
-    4  1.2952849248662775e-02 -1.2730397233111836e-02  6.4718612422628536e-03
-    5  1.9307066713768282e-03  3.1031437418921910e-03  3.5451961493820740e-03
-    6  6.0636534459212882e-03 -3.4538157278896163e-02 -1.5549038115507513e-02
-    7 -5.5478612765789935e-03  9.7600792853363150e-03 -2.1450928858953930e-02
-    8  1.7128888892908867e-05 -1.3865910341446424e-04  8.9170060388590313e-04
-    9 -5.8527207667384923e-02  8.5011601448529789e-02  7.9837310968768324e-02
-   10 -9.9174557740649288e-03  1.3163286903593812e-02  1.2367199081011528e-02
-   11 -2.0922976094767239e-02  1.7815876096389776e-02 -3.2459912597209782e-02
-   12  9.4039240797152590e-02  3.7466484050302624e-02 -9.4966824527940915e-03
-   13 -4.3611820849020655e-02 -7.5650463282748284e-02  4.1545920231526583e-02
-   14  1.3914348002543740e-02 -9.8186445921730793e-03 -1.5039026972733623e-02
-   15  9.8798529625617471e-02 -9.6939234781371439e-02 -3.5897115913423899e-02
-   16 -1.8828449808052237e-02  1.0084992428372604e-02 -1.6621409829588641e-02
-   17  1.8867454991507823e-02 -3.3410341394944157e-02  5.8649656809196309e-02
-   18 -5.7757244225337357e-03  3.7525864843647697e-03 -1.7465564584510023e-02
-   19  7.3146350316925512e-03 -5.0979152014509572e-03 -5.7918363022845080e-03
-   20  1.2526948567372337e-01  3.4964179752050586e-02 -4.0345565596353550e-02
-   21 -7.9108983380917194e-02 -7.4234491595904575e-02  7.8298798238034567e-02
-   22  3.3256958028948028e-02 -3.5876634770494304e-03 -5.5658445829460078e-03
-   23 -9.4983041889442843e-02 -1.6190744701130849e-01  6.5979264487847342e-02
-   24 -3.9837469553195448e-02  2.5364084068168865e-02 -2.8343465970054268e-02
-   25 -7.3424056488810893e-03 -1.1672660197222877e-02 -4.2413533422096137e-03
-   26  7.1482435753173978e-02  7.9794866671089565e-02 -1.2051822894855302e-01
-   27 -1.2443813759872715e-02 -4.4129787717125659e-03 -4.9977234669242657e-03
-   28 -5.0454676860651063e-03 -4.8367643809983244e-03 -9.7359590837120241e-03
-   29  5.0973790723890279e-02 -3.5296812999801377e-02 -1.5607922719867863e-02
-   30  6.9152527688984819e-02 -1.5810831588146963e-03  3.8412598769159367e-02
-   31  2.4462929866513206e-02 -3.5045453885110815e-02 -1.9154039469347770e-02
-   32  2.9037764603397378e-02 -6.8595457740301298e-03 -3.2736895683665988e-03
-   33 -2.3571014332676696e-02  7.4043101417658073e-03 -2.8705289221235150e-02
-   34 -1.4606618276415169e-02 -9.1068958189810610e-04 -8.5624378212242527e-03
-   35 -3.2510043399847137e-02 -2.8006234735108673e-02 -4.6845303267092589e-02
-   36  6.2991561292220326e-03  2.3238393611931946e-02 -5.8116057373416774e-03
-   37  2.6891579367550652e-02 -1.3896976667148994e-02  3.1371675516263159e-02
-   38  2.0868635137082342e-02  5.0357172401113842e-03 -5.3296214166774630e-03
-   39 -8.0127916540051650e-02 -3.7084303700723187e-02  1.2218320413894672e-01
-   40 -3.9584086175377592e-02  1.4186027995495971e-02 -1.1786983668096024e-02
-   41 -2.4078556291313152e-02  2.3979806393375630e-02  3.9808779679609198e-02
-   42  1.2092253594061965e-01  7.0237820535165529e-02 -6.7634093707697934e-02
-   43 -4.7905857362083089e-02  1.7234517679588787e-01  6.1081728343859443e-02
-   44 -8.9268222626455868e-02  1.0935256562868768e-01  4.9391188697389531e-02
-   45 -1.0932468616629654e-02 -1.1437973175510943e-02  2.2070666035021818e-02
-   46 -3.6031863619124846e-02  2.6734739237702171e-02 -3.3611450622333013e-02
-   47  1.4499510937770043e-03 -1.4213296755659972e-02 -2.3112798778515177e-04
-   48 -1.3767091667320651e-02 -3.0136222295009791e-03  1.3113656018437793e-02
-   49 -9.7091853089158325e-03  3.6127847100198028e-02  1.4509648101942035e-02
-   50  8.4557962872537848e-02 -1.0736631874106438e-01  9.9597088995020677e-02
-   51 -1.0386138512337374e-02 -2.0257306344291497e-02 -3.3076970021155658e-02
-   52 -4.6611247598267555e-02  6.5689772896870391e-02  1.9370639128294540e-02
-   53 -5.5610674299579610e-03 -1.4027210047753987e-02  8.7210863654412565e-03
-   54 -4.3167807436909698e-02  5.3419018642258016e-02 -1.5968205469941175e-02
-   55  2.1005445039043447e-03  1.5540888556331189e-02  3.0653660866053294e-02
-   56 -2.0590128155749919e-04 -4.1762635052692443e-03  1.7714423658216408e-02
-   57  1.0284475500160662e-02  4.9815307652019795e-03  1.2436353037813486e-02
-   58 -1.0342665677846569e-01 -1.9280058549113892e-02 -7.4866501787840767e-02
-   59 -2.3544588144277776e-03  3.6121601436188973e-03 -4.6871795309287806e-03
-   60 -5.4150709547244186e-03  5.8612714168733107e-02  1.4839344483422201e-02
-   61  2.7954413595536829e-03 -5.0942788273584158e-02  7.2754423090722080e-03
-   62  1.1252409113821953e-01 -8.8720719845166385e-02  5.4683231088491491e-02
-   63 -3.1773161310039773e-02  3.6061405688573842e-02 -3.8399113603086052e-02
-   64 -1.4722975703867254e-02 -2.6147363467761031e-02 -2.1059016257482918e-01
-run_vdwl: -9.262826276442015
-run_coul: 0
-run_stress: ! |-
-  -1.8014717164118095e+00 -1.8087390491573838e+00 -1.9142638713109481e+00 -3.9974176680151442e-02 -7.1417886608373016e-01 -1.3759726037342584e-01
-run_forces: ! |2
-    1  4.7667962897357161e-04 -5.8467702637711484e-03 -2.6991867527471512e-03
-    2  4.1869408756652363e-02  8.4979875395407335e-03  3.4984717622547718e-03
-    3 -9.9160928359434165e-04 -1.4869879159063026e-03  1.2223462368831279e-03
-    4  1.3147106330966834e-02 -1.2926544725178195e-02  6.7789603915220410e-03
-    5  1.9770775494690725e-03  3.1765296745866244e-03  3.5629842560420720e-03
-    6  5.7506960289548086e-03 -3.4699407410875724e-02 -1.5506043491316254e-02
-    7 -5.3406567968898640e-03  9.4551314879620617e-03 -2.0752905865024943e-02
-    8  8.7145147977422260e-05 -2.8842759092264801e-05  8.0207322297105345e-04
-    9 -5.8415508752186096e-02  8.4979266053546693e-02  7.9622715915771303e-02
-   10 -9.9578406937796439e-03  1.3145690562643045e-02  1.2350278010619288e-02
-   11 -2.0970548283965822e-02  1.7641558318643526e-02 -3.3050100269831226e-02
-   12  9.5891788552647905e-02  3.8024542707268488e-02 -9.8061835208236598e-03
-   13 -4.4952222762057452e-02 -7.6842596097771221e-02  4.2613909344784678e-02
-   14  1.4295961616915508e-02 -1.0328974978549363e-02 -1.5428512523395358e-02
-   15  9.9943438549559324e-02 -9.7907452663447983e-02 -3.6257259204324190e-02
-   16 -1.8390119036231254e-02  9.7159754167479712e-03 -1.6211888958432827e-02
-   17  1.8981263201349942e-02 -3.3819017834167138e-02  5.9290153984855036e-02
-   18 -5.6513870203370861e-03  3.7641108670888137e-03 -1.7558647302694921e-02
-   19  7.4901241602777988e-03 -4.9270563652220887e-03 -5.9132694166840003e-03
-   20  1.2404887106132249e-01  3.4634285209304783e-02 -4.0135253432049663e-02
-   21 -7.8277898322380690e-02 -7.3279299053891203e-02  7.8010388044320325e-02
-   22  3.3238064217446656e-02 -3.5092881124568851e-03 -5.5130499474961214e-03
-   23 -9.5777464813086854e-02 -1.6270801791195924e-01  6.6577987309083805e-02
-   24 -4.0548984396490580e-02  2.6001318437117903e-02 -2.8710977732994785e-02
-   25 -7.2079783094212008e-03 -1.1551923848041689e-02 -3.9390884716931050e-03
-   26  7.2339414718789685e-02  7.9165643726239313e-02 -1.2169899192698079e-01
-   27 -1.2311213314223447e-02 -4.3068558469614186e-03 -4.9048891096525275e-03
-   28 -5.1134183165409582e-03 -4.9743298117876514e-03 -9.7660849582700982e-03
-   29  5.0646655326840248e-02 -3.5366362317264768e-02 -1.5821692477208313e-02
-   30  6.8872718304629946e-02 -2.6404120131308211e-04  3.9973810776214556e-02
-   31  2.4365821184347394e-02 -3.5211120753030921e-02 -1.9277907381945410e-02
-   32  2.9047476663902016e-02 -6.6602395044956511e-03 -3.0527687948843541e-03
-   33 -2.3100260653032955e-02  7.7806328406423821e-03 -2.8840665483715618e-02
-   34 -1.4082353101335789e-02 -1.2664441844283637e-03 -8.7897343649273926e-03
-   35 -3.2837748483424821e-02 -2.8259033655048716e-02 -4.7109045095735221e-02
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-   43 -4.8078980460622062e-02  1.7214309659743252e-01  6.1467794063077237e-02
-   44 -9.0284549182458221e-02  1.1015441455438249e-01  5.0331470972200497e-02
-   45 -1.0780088805510608e-02 -1.1270483123892882e-02  2.2080179359507665e-02
-   46 -3.6837588908592935e-02  2.7230340588058007e-02 -3.4349458876726219e-02
-   47  1.9027883758890351e-03 -1.3952420712156162e-02 -8.4498460315278066e-04
-   48 -1.3553909305246262e-02 -3.5297267660297201e-03  1.3635814385290735e-02
-   49 -9.5576836166616046e-03  3.6186064165354859e-02  1.4320944961491736e-02
-   50  8.5217870424105446e-02 -1.0799325877459537e-01  1.0051859972453785e-01
-   51 -1.0113063819708310e-02 -2.0226413845647481e-02 -3.3234528125131467e-02
-   52 -4.6943693419275380e-02  6.5649633276221267e-02  1.9270389824586502e-02
-   53 -5.4874429234138388e-03 -1.4030397181841880e-02  8.5032803277714855e-03
-   54 -4.2513762110625415e-02  5.3134910653632295e-02 -1.5583625457217259e-02
-   55  2.2355622337947943e-03  1.5758808063886333e-02  3.0512038080609420e-02
-   56  2.6470325853502827e-04 -3.6590608029393578e-03  1.7588493434887068e-02
-   57  1.0304091828004703e-02  5.7001837787072690e-03  1.2617318639445109e-02
-   58 -1.0367740873897520e-01 -1.9270956096739674e-02 -7.4383753859322305e-02
-   59 -2.4598814289387631e-03  3.6232140002483829e-03 -4.7141806923593913e-03
-   60 -5.0750993143057026e-03  5.8880547695610790e-02  1.4800121802056596e-02
-   61  2.7189101908894160e-03 -5.1306885575781225e-02  7.3310325603516196e-03
-   62  1.1256471950631124e-01 -8.8211823459006702e-02  5.4263270936498222e-02
-   63 -3.2228752476757563e-02  3.6691295193583467e-02 -3.8707049961821866e-02
-   64 -1.5804472791648257e-02 -2.5887199342735968e-02 -2.1134763353880526e-01
-...

unittest/force-styles/tests/manybody-pair-dispersion_d3.yaml

@@ -0,0 +1,154 @@
+---
+lammps_version: 19 Nov 2024
+date_generated: Wed Dec 11 15:29:39 2024
+epsilon: 1e-10
+skip_tests:
+prerequisites: ! |
+  pair dispersion/d3
+pre_commands: ! ""
+post_commands: ! ""
+input_file: in.manybody
+pair_style: dispersion/d3 zero pbe 12.0 12.0
+pair_coeff: ! |
+  * * Si Si Si Si Si Si Si Si
+extract: ! ""
+natoms: 64
+init_vdwl: -9.262365244070887
+init_coul: 0
+init_stress: ! |-
+  -1.8070680161672350e+00 -1.8151671910236220e+00 -1.9214651805560712e+00 -4.1552461721989307e-02 -7.1708481048125128e-01 -1.3638435843456306e-01
+init_forces: ! |2
+    1  4.5901744149339814e-04 -5.8645004258887296e-03 -2.6408414442435817e-03
+    2  4.1982212100397494e-02  7.7916988680959785e-03  4.1558505642265483e-03
+    3 -1.0599537919974110e-03 -1.5284351857714875e-03  1.3250226437598804e-03
+    4  1.2952849248980391e-02 -1.2730397232186651e-02  6.4718612421368858e-03
+    5  1.9307066949767124e-03  3.1031437654175332e-03  3.5451961708816851e-03
+    6  6.0636534612296018e-03 -3.4538157294514024e-02 -1.5549038123319472e-02
+    7 -5.5478612773693318e-03  9.7600792842619001e-03 -2.1450928859339292e-02
+    8  1.7128887807534021e-05 -1.3865910298862735e-04  8.9170060304616253e-04
+    9 -5.8527207660040638e-02  8.5011601463707259e-02  7.9837310973084497e-02
+   10 -9.9174557760647319e-03  1.3163286906290764e-02  1.2367199083459195e-02
+   11 -2.0922976098149738e-02  1.7815876096333588e-02 -3.2459912594439561e-02
+   12  9.4039240797013243e-02  3.7466484052249387e-02 -9.4966824523796730e-03
+   13 -4.3611820846840114e-02 -7.5650463287387754e-02  4.1545920229193796e-02
+   14  1.3914347992697577e-02 -9.8186446053987742e-03 -1.5039026985332828e-02
+   15  9.8798529628413748e-02 -9.6939234786348333e-02 -3.5897115916559530e-02
+   16 -1.8828449808127548e-02  1.0084992417269656e-02 -1.6621409840469250e-02
+   17  1.8867454988099414e-02 -3.3410341395584034e-02  5.8649656805337354e-02
+   18 -5.7757243295743490e-03  3.7525865932555918e-03 -1.7465564682291646e-02
+   19  7.3146350339646261e-03 -5.0979152089016683e-03 -5.7918362966919833e-03
+   20  1.2526948607359642e-01  3.4964179836823706e-02 -4.0345565678621194e-02
+   21 -7.9108983611317768e-02 -7.4234491850519224e-02  7.8298798433197120e-02
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+   42  1.2092253594807115e-01  7.0237820528219294e-02 -6.7634093701619297e-02
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+   44 -8.9268222669576444e-02  1.0935256558697629e-01  4.9391188655423857e-02
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+   47  1.4499510792417522e-03 -1.4213296744594713e-02 -2.3112799817407201e-04
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+   51 -1.0386138512718579e-02 -2.0257306348498042e-02 -3.3076970024004795e-02
+   52 -4.6611247598798901e-02  6.5689772901113247e-02  1.9370639130365311e-02
+   53 -5.5610674070546090e-03 -1.4027210037762585e-02  8.7210863818644770e-03
+   54 -4.3167807623476724e-02  5.3419018792160038e-02 -1.5968205606008208e-02
+   55  2.1005445106472131e-03  1.5540888545067990e-02  3.0653660856435228e-02
+   56 -2.0590128088026315e-04 -4.1762635041913861e-03  1.7714423656329605e-02
+   57  1.0284475505097292e-02  4.9815307763691908e-03  1.2436353033202291e-02
+   58 -1.0342665676627626e-01 -1.9280058551284476e-02 -7.4866501808988087e-02
+   59 -2.3544588605186314e-03  3.6121601861319316e-03 -4.6871794758065605e-03
+   60 -5.4150711425366791e-03  5.8612714396504555e-02  1.4839344681837788e-02
+   61  2.7954413433097583e-03 -5.0942788256137531e-02  7.2754423172912289e-03
+   62  1.1252409114510897e-01 -8.8720719849435095e-02  5.4683231090040328e-02
+   63 -3.1773161308752101e-02  3.6061405691521872e-02 -3.8399113596128895e-02
+   64 -1.4722975703463983e-02 -2.6147363460941667e-02 -2.1059016257148011e-01
+run_vdwl: -9.262826276539041
+run_coul: 0
+run_stress: ! |-
+  -1.8014717148220629e+00 -1.8087390477796537e+00 -1.9142638698777830e+00 -3.9974176411585433e-02 -7.1417886625446692e-01 -1.3759726065342742e-01
+run_forces: ! |2
+    1  4.7667962871302064e-04 -5.8467702639815730e-03 -2.6991867530137183e-03
+    2  4.1869408756196061e-02  8.4979875396755736e-03  3.4984717617200642e-03
+    3 -9.9160928389676294e-04 -1.4869879157543243e-03  1.2223462368121266e-03
+    4  1.3147106326425097e-02 -1.2926544726456277e-02  6.7789603977131685e-03
+    5  1.9770775501047611e-03  3.1765296749256397e-03  3.5629842559820419e-03
+    6  5.7506960260337615e-03 -3.4699407409212034e-02 -1.5506043496333955e-02
+    7 -5.3406567846472110e-03  9.4551314732373871e-03 -2.0752905880674206e-02
+    8  8.7145147942647994e-05 -2.8842758704853994e-05  8.0207322231987555e-04
+    9 -5.8415508752920696e-02  8.4979266050254798e-02  7.9622715923589979e-02
+   10 -9.9578406934257829e-03  1.3145690562371913e-02  1.2350278008781093e-02
+   11 -2.0970548283900613e-02  1.7641558319062160e-02 -3.3050100269910745e-02
+   12  9.5891788559756261e-02  3.8024542707650773e-02 -9.8061835139289615e-03
+   13 -4.4952222762277574e-02 -7.6842596098760999e-02  4.2613909344851382e-02
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+   15  9.9943438550046268e-02 -9.7907452664271769e-02 -3.6257259204378979e-02
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