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rename pair style and fully integrate into build and manual

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This commit is contained in:
Axel Kohlmeyer
2024-12-11 15:32:25 -05:00
parent 335069f1ca
commit 3aeb64de89
9 changed files with 297 additions and 282 deletions
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1
doc/src/Commands_pair.rst
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@ -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>`

84
doc/src/pair_d3.rst → doc/src/pair_dispersion_d3.rst
View File

@ -1,21 +1,17 @@
.. index:: pair_style d3
..
.. index:: pair_style d3/kk
.. index:: pair_style dispersion/d3
pair_style d3 command
=====================
..
Accelerator Variants: *d3/kk*
pair_style dispersion/d3 command
================================
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
method of Grimme :ref:`(Grimme1) <Grimme1>`.
.. versionadded:: TBD
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:
@ -46,14 +47,17 @@ 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
dispersion contributions, according for example to the Axilrod-Teller-Muto model.
.. note::
Available damping functions are the original "zero-damping" :ref:`(Grimme1) <Grimme1>`,
Becke-Johnson damping :ref:`(Grimme2) <Grimme2>`, and their revised forms :ref:`(Sherrill) <Sherrill>`.
It is currently *not* possible to calculate three-body dispersion
contributions, according for example to the Axilrod-Teller-Muto model.
Available XC functional scaling factors are listed in the table below, and depend on
the selected damping function.
Available damping functions are the original "zero-damping"
: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
interatomic potential trained on a DFT dataset (the selected XC functional
should be chosen accordingly) via the *pair_style hybrid* command.
This style is primarly supposed to be used combined with a
machine-learned interatomic potential trained on a DFT dataset (the
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.
The only information to provide are the chemical symbols of the atoms.
The number of chemical symbols given must be equal to the number of atom types
used and should match their ordering.
All the required coefficients are already stored internally, in the
d3_paramerters.h file. The only information to provide are the chemical
symbols of the atoms. The number of chemical symbols given must be
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
was built with that package.
See the :doc:`Build package <Build_package>` page for more info.
Style *dispersion/d3* is part of the EXTRA-PAIR package. It is only
enabled if LAMMPS was built with that package. See the :doc:`Build
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,
J. Chem. Phys. 132, 154104 (2010).
.
**(Grimme1)** S. Grimme, J. Antony, S. Ehrlich, and H. Krieg, J. Chem. Phys. 132, 154104 (2010).
.. _Grimme2:
**(Grimme2)** S. Grimme, S. Ehrlich and L. Goerigk,
J. Comput. Chem. 32, 1456 (2011); DOI:10.1002/jcc.21759.
**(Grimme2)** S. Grimme, S. Ehrlich and L. Goerigk, 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,
J. Phys. Chem. Lett., 7, 2197, (2016); DOI: 10.1021/acs.jpclett.6b00780.
**(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.

1
doc/src/pair_style.rst
View File

@ -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

3
src/.gitignore vendored
View File

@ -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

23
src/EXTRA-PAIR/pair_d3_pars.h → src/EXTRA-PAIR/d3_parameters.h
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@ -1,3 +1,25 @@
/* -*- 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}, \
@ -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

79
src/EXTRA-PAIR/pair_d3.cpp → src/EXTRA-PAIR/pair_dispersion_d3.cpp
View File

@ -20,14 +20,8 @@
^2: SCAI, Sorbonne Universite, Paris, France
------------------------------------------------------------------------- */
#include "pair_d3.h"
#include "pair_d3_pars.h"
#include <cmath>
#include <iostream>
#include <string>
#include <algorithm>
#include <unordered_map>
#include "pair_dispersion_d3.h"
#include "d3_parameters.h"
#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) {
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"
);
}
if (narg != 4) error->all(FLERR, "Pair_style dispersion/d3 needs 4 arguments");
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) {
@ -204,10 +193,10 @@ 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;
@ -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;
@ -460,10 +449,10 @@ 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;
@ -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}
@ -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}
@ -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;
@ -1086,7 +1075,7 @@ int PairD3::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, i
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;

19
src/EXTRA-PAIR/pair_d3.h → src/EXTRA-PAIR/pair_dispersion_d3.h
View File

@ -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
#define LMP_PAIR_D3_H
#ifndef LMP_PAIR_DISPERSION_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 *);
~PairD3() override;
PairDispersionD3(class LAMMPS *);
~PairDispersionD3() override;
void compute(int, int) override;

155
unittest/force-styles/tests/manybody-pair-d3.yaml
View File

@ -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
36 6.3043838063683473e-03 2.2728472759162045e-02 -5.6021644135329923e-03
37 2.6212204686130034e-02 -1.3029975561842381e-02 3.1750286301194183e-02
38 2.0139944495106622e-02 4.3293211982739187e-03 -6.1649221929395912e-03
39 -7.8960492061368320e-02 -3.6406243903921401e-02 1.2184492984680016e-01
40 -3.9632145335340999e-02 1.3535049462025148e-02 -1.1321798674348533e-02
41 -2.4388307314468449e-02 2.3366329744906832e-02 3.8928089365769816e-02
42 1.1996964454673913e-01 6.9851097788973082e-02 -6.7069886963212297e-02
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
...

154
unittest/force-styles/tests/manybody-pair-dispersion_d3.yaml Normal file
View File

@ -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
22 3.3256958035759267e-02 -3.5876634662328263e-03 -5.5658445807261810e-03
23 -9.4983041888941230e-02 -1.6190744700903256e-01 6.5979264480813399e-02
24 -3.9837469539795965e-02 2.5364084079376788e-02 -2.8343465953968475e-02
25 -7.3424056398832139e-03 -1.1672660207324508e-02 -4.2413533423389452e-03
26 7.1482435767536698e-02 7.9794866672039319e-02 -1.2051822893472583e-01
27 -1.2443813900029382e-02 -4.4129788887813590e-03 -4.9977235842165457e-03
28 -5.0454676878239251e-03 -4.8367643826771898e-03 -9.7359590852317181e-03
29 5.0973790709941257e-02 -3.5296812997722318e-02 -1.5607922729704526e-02
30 6.9152527680774289e-02 -1.5810831557831798e-03 3.8412598766233222e-02
31 2.4462930027397904e-02 -3.5045454052408158e-02 -1.9154039485981871e-02
32 2.9037764598216036e-02 -6.8595457693026449e-03 -3.2736895722578810e-03
33 -2.3571014326886783e-02 7.4043101437256172e-03 -2.8705289218120600e-02
34 -1.4606618211317998e-02 -9.1068965341847558e-04 -8.5624377570787912e-03
35 -3.2510043401035402e-02 -2.8006234725365901e-02 -4.6845303279608771e-02
36 6.2991561249353990e-03 2.3238393607814253e-02 -5.8116057369683007e-03
37 2.6891579366883651e-02 -1.3896976671852732e-02 3.1371675512071220e-02
38 2.0868635140715318e-02 5.0357172404813764e-03 -5.3296214134632008e-03
39 -8.0127916540111269e-02 -3.7084303697709070e-02 1.2218320413943409e-01
40 -3.9584086191698675e-02 1.4186027994256518e-02 -1.1786983662869569e-02
41 -2.4078556290238202e-02 2.3979806392354495e-02 3.9808779679712705e-02
42 1.2092253594807115e-01 7.0237820528219294e-02 -6.7634093701619297e-02
43 -4.7905857363210326e-02 1.7234517679973846e-01 6.1081728342102619e-02
44 -8.9268222669576444e-02 1.0935256558697629e-01 4.9391188655423857e-02
45 -1.0932468625449131e-02 -1.1437973186082834e-02 2.2070666035756106e-02
46 -3.6031863627779687e-02 2.6734739238025461e-02 -3.3611450612771009e-02
47 1.4499510792417522e-03 -1.4213296744594713e-02 -2.3112799817407201e-04
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