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Merge pull request #2556 from akohlmey/eam-he-pair-style

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Add eam/he pair style for modeling He bubbles in metals
This commit is contained in:
Axel Kohlmeyer
2021-01-15 12:34:59 -05:00
committed by GitHub
parent 9ff011728c 6d1babfe89
commit 8060a750d4
17 changed files with 12637 additions and 104 deletions
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1
doc/src/Commands_pair.rst
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@ -96,6 +96,7 @@ OPT.
* :doc:`eam/cd <pair_eam>`
* :doc:`eam/cd/old <pair_eam>`
* :doc:`eam/fs (gikot) <pair_eam>`
* :doc:`eam/he <pair_eam>`
* :doc:`edip (o) <pair_edip>`
* :doc:`edip/multi <pair_edip>`
* :doc:`edpd <pair_mesodpd>`

75
doc/src/pair_eam.rst
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@ -18,6 +18,7 @@
.. index:: pair_style eam/fs/kk
.. index:: pair_style eam/fs/omp
.. index:: pair_style eam/fs/opt
.. index:: pair_style eam/he
pair_style eam command
======================
@ -38,6 +39,9 @@ pair_style eam/cd/old command
pair_style eam/fs command
=========================
pair_style eam/he command
=========================
Accelerator Variants: *eam/fs/gpu*, *eam/fs/intel*, *eam/fs/kk*, *eam/fs/omp*, *eam/fs/opt*
Syntax
@ -47,7 +51,7 @@ Syntax
pair_style style
* style = *eam* or *eam/alloy* or *eam/cd* or *eam/cd/old* or *eam/fs*
* style = *eam* or *eam/alloy* or *eam/cd* or *eam/cd/old* or *eam/fs* or *eam/he*
Examples
""""""""
@ -67,6 +71,9 @@ Examples
pair_style eam/fs
pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni
pair_style eam/he
pair_coeff * * PdHHe.eam.he Pd H He
Description
"""""""""""
@ -104,8 +111,8 @@ are parameterized in terms of LAMMPS :doc:`metal units <units>`.
potentials, the same way that DYNAMO does. Alternatively, a single
DYNAMO *setfl* file or Finnis/Sinclair EAM file can be used by LAMMPS
to model alloy systems by invoking the *eam/alloy* or *eam/cd* or
*eam/fs* styles as described below. These files require no mixing
since they specify alloy interactions explicitly.
*eam/fs* or *eam/he* styles as described below. These files require no
mixing since they specify alloy interactions explicitly.
.. note::
@ -143,10 +150,6 @@ DYNAMO single-element *funcfl* format. If the DYNAMO file was created
by a Fortran program, it cannot have "D" values in it for exponents.
C only recognizes "e" or "E" for scientific notation.
Note that unlike for other potentials, cutoffs for EAM potentials are
not set in the pair_style or pair_coeff command; they are specified in
the EAM potential files themselves.
For style *eam* a potential file must be assigned to each I,I pair of
atom types by using one or more pair_coeff commands, each with a
single argument:
@ -336,8 +339,11 @@ distribution have a ".cdeam" suffix.
Style *eam/fs* computes pairwise interactions for metals and metal
alloys using a generalized form of EAM potentials due to Finnis and
Sinclair :ref:`(Finnis) <Finnis1>`. The total energy Ei of an atom I is
given by
Sinclair :ref:`(Finnis) <Finnis1>`. Style *eam/he* is similar to
*eam/fs* except that it allows for negative electron density in
order to capture the behavior of helium in metals :ref:`(Zhou6) <Zhou6>`.
The total energy Ei of an atom I is given by
.. math::
@ -355,36 +361,36 @@ electron density at an atomic site depending on the identity of the
element at that atomic site.
The associated :doc:`pair_coeff <pair_coeff>` command for style *eam/fs*
reads a DYNAMO *setfl* file that has been extended to include
additional rho_alpha_beta arrays of tabulated values. A discussion of
how FS EAM differs from conventional EAM alloy potentials is given in
:ref:`(Ackland1) <Ackland1>`. An example of such a potential is the same
author's Fe-P FS potential :ref:`(Ackland2) <Ackland2>`. Note that while FS
potentials always specify the embedding energy with a square root
or *eam/he* reads a DYNAMO *setfl* file that has been extended to include
additional :math:`\rho_{\alpha\beta}` arrays of tabulated values. A
discussion of how FS EAM differs from conventional EAM alloy potentials is
given in :ref:`(Ackland1) <Ackland1>`. An example of such a potential is the
same author's Fe-P FS potential :ref:`(Ackland2) <Ackland2>`. Note that while
FS potentials always specify the embedding energy with a square root
dependence on the total density, the implementation in LAMMPS does not
require that; the user can tabulate any functional form desired in the
FS potential files.
For style *eam/fs*\ , the form of the pair_coeff command is exactly the
same as for style *eam/alloy*\ , e.g.
For style *eam/fs* and *eam/he* the form of the pair_coeff command is exactly
the same as for style *eam/alloy*\ , e.g.
.. code-block:: LAMMPS
pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al
where there are N additional arguments after the filename, where N is
with N additional arguments after the filename, where N is
the number of LAMMPS atom types. See the :doc:`pair_coeff <pair_coeff>`
doc page for alternate ways to specify the path for the potential
file. The N values determine the mapping of LAMMPS atom types to EAM
elements in the file, as described above for style *eam/alloy*\ . As
with *eam/alloy*\ , if a mapping value is NULL, the mapping is not
performed. This can be used when an *eam/fs* potential is used as
part of the *hybrid* pair style. The NULL values are used as
performed. This can be used when an *eam/fs* or *eam/he* potential is
used as part of a *hybrid* pair style. The NULL values are used as
placeholders for atom types that will be used with other potentials.
FS EAM files include more information than the DYNAMO *setfl* format
files read by *eam/alloy*\ , in that i,j density functionals for all
pairs of elements are included as needed by the Finnis/Sinclair
FS EAM and HE EAM files include more information than the DYNAMO *setfl*
format files read by *eam/alloy*\ , in that i,j density functionals for
all pairs of elements are included as needed by the Finnis/Sinclair
formulation of the EAM.
FS EAM files in the *potentials* directory of the LAMMPS distribution
@ -417,6 +423,25 @@ eV-Angstroms) as in EAM *setfl* files. Note that in Finnis/Sinclair,
the phi(r) arrays are still symmetric, so only phi arrays for i >= j
are listed.
HE EAM files in the *potentials* directory of the LAMMPS distribution
have an ".eam.he" suffix. They are formatted as follows:
* lines 1,2,3 = comments (ignored)
* line 4: Nelements Element1 Element2 ... ElementN
* line 5: Nrho, drho, Nr, dr, cutoff, rhomax
The 5-line header section is identical to an FS EAM file
except that line 5 lists an additional value, rhomax. Unlike in FS EAM
files where embedding energies F(rho) are always defined between rho = 0
and rho = (Nrho -1)drho, F(rho) in HE EAM files are defined between
rho = rhomin and rho = rhomax. Since drho = (rhomax - rhomin)/(Nrho - 1),
rhomin = rhomax - (Nrho - 1)drho. The embedding energies F(rho) are
listed for rho = rhomin, rhomin + drho, rhomin + 2drho, ..., rhomax.
This gives users additional flexibility to define a negative rhomin and
therefore an embedding energy function that works for both positive and
negative electron densities. The format and units of these sections are
identical to the FS EAM files (see above).
----------
.. include:: accel_styles.rst
@ -480,6 +505,10 @@ Daw, Baskes, Phys Rev B, 29, 6443 (1984).
**(Finnis)** Finnis, Sinclair, Philosophical Magazine A, 50, 45 (1984).
.. _Zhou6:
**(Zhou6)** Zhou, Bartelt, Sills, Physical Review B, 103, 014108 (2021).
.. _Stukowski:
**(Stukowski)** Stukowski, Sadigh, Erhart, Caro; Modeling Simulation

1
doc/src/pair_style.rst
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@ -159,6 +159,7 @@ accelerated styles exist.
* :doc:`eam/cd <pair_eam>` - concentration-dependent EAM
* :doc:`eam/cd/old <pair_eam>` - older two-site model for concentration-dependent EAM
* :doc:`eam/fs <pair_eam>` - Finnis-Sinclair EAM
* :doc:`eam/he <pair_eam>` - Finnis-Sinclair EAM modified for Helium in metals
* :doc:`edip <pair_edip>` - three-body EDIP potential
* :doc:`edip/multi <pair_edip>` - multi-element EDIP potential
* :doc:`edpd <pair_mesodpd>` - eDPD particle interactions

3
doc/utils/sphinx-config/false_positives.txt
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@ -200,6 +200,7 @@ barostatted
barostatting
Barostatting
Barrat
Bartelt
Bartels
barycenter
barye
@ -2678,6 +2679,8 @@ rhodo
Rhodo
rhodopsin
rhok
rhomax
rhomin
rhorho
rhosum
ri

12008
potentials/PdHHe.eam.he Normal file
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File diff suppressed because it is too large Load Diff

2
src/MANYBODY/pair_eam.cpp
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@ -63,6 +63,8 @@ PairEAM::PairEAM(LAMMPS *lmp) : Pair(lmp)
z2r = nullptr;
scale = nullptr;
rhomax = rhomin = 0.0;
frho_spline = nullptr;
rhor_spline = nullptr;
z2r_spline = nullptr;

2
src/MANYBODY/pair_eam.h
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@ -42,7 +42,7 @@ class PairEAM : public Pair {
// potentials in spline form used for force computation
double dr,rdr,drho,rdrho,rhomax;
double dr,rdr,drho,rdrho,rhomax,rhomin;
double ***rhor_spline,***frho_spline,***z2r_spline;
PairEAM(class LAMMPS *);

12
src/MANYBODY/pair_eam_fs.cpp
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@ -34,6 +34,7 @@ PairEAMFS::PairEAMFS(LAMMPS *lmp) : PairEAM(lmp)
{
one_coeff = 1;
manybody_flag = 1;
he_flag = 0;
}
/* ----------------------------------------------------------------------
@ -118,7 +119,8 @@ void PairEAMFS::read_file(char *filename)
// read potential file
if (comm->me == 0) {
PotentialFileReader reader(lmp, filename, "eam/fs", unit_convert_flag);
PotentialFileReader reader(lmp, filename, he_flag ? "eam/he" : "eam/fs",
unit_convert_flag);
// transparently convert units for supported conversions
@ -149,12 +151,14 @@ void PairEAMFS::read_file(char *filename)
//
values = reader.next_values(5);
if (he_flag) values = reader.next_values(6);
else values = reader.next_values(5);
file->nrho = values.next_int();
file->drho = values.next_double();
file->nr = values.next_int();
file->dr = values.next_double();
file->cut = values.next_double();
if (he_flag) rhomax = values.next_double();
if ((file->nrho <= 0) || (file->nr <= 0) || (file->dr <= 0.0))
error->one(FLERR,"Invalid EAM potential file");
@ -202,6 +206,7 @@ void PairEAMFS::read_file(char *filename)
MPI_Bcast(&file->nr, 1, MPI_INT, 0, world);
MPI_Bcast(&file->dr, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&file->cut, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&rhomax, 1, MPI_DOUBLE, 0, world);
// allocate memory on other procs
if (comm->me != 0) {
@ -255,7 +260,8 @@ void PairEAMFS::file2array()
nr = fs->nr;
drho = fs->drho;
dr = fs->dr;
rhomax = (nrho-1) * drho;
if (he_flag) rhomin = rhomax - (nrho-1) * drho;
else rhomax = (nrho-1) * drho;
// ------------------------------------------------------------------
// setup frho arrays

1
src/MANYBODY/pair_eam_fs.h
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@ -35,6 +35,7 @@ class PairEAMFS : virtual public PairEAM {
protected:
void read_file(char *);
void file2array();
int he_flag;
};
}

238
src/MANYBODY/pair_eam_he.cpp Normal file
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@ -0,0 +1,238 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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: Xiaowng Zhou (Sandia)
------------------------------------------------------------------------- */
#include "pair_eam_he.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "update.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairEAMHE::PairEAMHE(LAMMPS *lmp) : PairEAMFS(lmp), PairEAM(lmp)
{
he_flag = 1;
}
void PairEAMHE::compute(int eflag, int vflag)
{
int i,j,ii,jj,m,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r,p,rhoip,rhojp,z2,z2p,recip,phip,psip,phi;
double *coeff;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
ev_init(eflag,vflag);
// grow energy and fp arrays if necessary
// need to be atom->nmax in length
if (atom->nmax > nmax) {
memory->destroy(rho);
memory->destroy(fp);
memory->destroy(numforce);
nmax = atom->nmax;
memory->create(rho,nmax,"pair:rho");
memory->create(fp,nmax,"pair:fp");
memory->create(numforce,nmax,"pair:numforce");
}
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// zero out density
if (newton_pair) {
for (i = 0; i < nall; i++) rho[i] = 0.0;
} else for (i = 0; i < nlocal; i++) rho[i] = 0.0;
// rho = density at each atom
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq) {
jtype = type[j];
p = sqrt(rsq)*rdr + 1.0;
m = static_cast<int> (p);
m = MIN(m,nr-1);
p -= m;
p = MIN(p,1.0);
coeff = rhor_spline[type2rhor[jtype][itype]][m];
rho[i] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
if (newton_pair || j < nlocal) {
coeff = rhor_spline[type2rhor[itype][jtype]][m];
rho[j] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
}
}
}
}
// communicate and sum densities
if (newton_pair) comm->reverse_comm_pair(this);
// fp = derivative of embedding energy at each atom
// phi = embedding energy at each atom
// if rho > rhomax or rho < rhomin (i.e., table is exceeded),
// add linear term to conserve energy
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
p = (rho[i]-rhomin)*rdrho + 1.0;
m = static_cast<int> (p);
if (m < 2) {
m = 2;
} else if (m > nrho-1) {
m = nrho-1;
}
p -= m;
if (p < -1.0) {
p = -1.0;
} else if (p > 1.0) {
p = 1.0;
}
coeff = frho_spline[type2frho[type[i]]][m];
fp[i] = (coeff[0]*p + coeff[1])*p + coeff[2];
if (eflag) {
phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
if (rho[i] < rhomin) {
phi += fp[i] * (rho[i]-rhomin);
} else if (rho[i] > rhomax) {
phi += fp[i] * (rho[i]-rhomax);
}
phi *= scale[type[i]][type[i]];
if (eflag_global) eng_vdwl += phi;
if (eflag_atom) eatom[i] += phi;
}
}
// communicate derivative of embedding function
comm->forward_comm_pair(this);
embedstep = update->ntimestep;
// compute forces on each atom
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
numforce[i] = 0;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq) {
++numforce[i];
jtype = type[j];
r = sqrt(rsq);
p = r*rdr + 1.0;
m = static_cast<int> (p);
m = MIN(m,nr-1);
p -= m;
p = MIN(p,1.0);
// rhoip = derivative of (density at atom j due to atom i)
// rhojp = derivative of (density at atom i due to atom j)
// phi = pair potential energy
// phip = phi'
// z2 = phi * r
// z2p = (phi * r)' = (phi' r) + phi
// psip needs both fp[i] and fp[j] terms since r_ij appears in two
// terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
// hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
// scale factor can be applied by thermodynamic integration
coeff = rhor_spline[type2rhor[itype][jtype]][m];
rhoip = (coeff[0]*p + coeff[1])*p + coeff[2];
coeff = rhor_spline[type2rhor[jtype][itype]][m];
rhojp = (coeff[0]*p + coeff[1])*p + coeff[2];
coeff = z2r_spline[type2z2r[itype][jtype]][m];
z2p = (coeff[0]*p + coeff[1])*p + coeff[2];
z2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
recip = 1.0/r;
phi = z2*recip;
phip = z2p*recip - phi*recip;
psip = fp[i]*rhojp + fp[j]*rhoip + phip;
fpair = -scale[itype][jtype]*psip*recip;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) evdwl = scale[itype][jtype]*phi;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}

65
src/MANYBODY/pair_eam_he.h Normal file
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@ -0,0 +1,65 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(eam/he,PairEAMHE)
#else
#ifndef LMP_PAIR_EAM_HE_H
#define LMP_PAIR_EAM_HE_H
#include "pair_eam_fs.h"
namespace LAMMPS_NS {
class PairEAMHE : public PairEAMFS {
public:
PairEAMHE(class LAMMPS *);
virtual ~PairEAMHE() {}
protected:
void compute(int, int);
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: No matching element in EAM potential file
The EAM potential file does not contain elements that match the
requested elements.
E: Cannot open EAM potential file %s
The specified EAM potential file cannot be opened. Check that the
path and name are correct.
E: Incorrect element names in EAM potential file
The element names in the EAM file do not match those requested.
E: Invalid EAM potential file
UNDOCUMENTED
*/

89
unittest/force-styles/tests/atomic-pair-eam_he.yaml Normal file
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@ -0,0 +1,89 @@
---
lammps_version: 24 Dec 2020
date_generated: Wed Jan 13 22:16:02 202
epsilon: 5e-12
prerequisites: ! |
pair eam/he
pre_commands: ! ""
post_commands: ! ""
input_file: in.metal
pair_style: eam/he
pair_coeff: ! |
* * PdHHe.eam.he Pd He
extract: ! ""
natoms: 32
init_vdwl: -15.3146152609365
init_coul: 0
init_stress: ! |2-
1.0127679615895376e+02 9.3559970433415444e+01 9.1432412459889193e+01 4.0035576925472673e+00 -9.7686923241135581e-01 2.8980241224200443e+00
init_forces: ! |2
1 1.2005847856522014e+00 2.2040396377071869e+00 -1.0711805842453261e+00
2 -1.5935390465573379e-01 -8.3057674140080351e-01 3.5885201320339977e-01
3 -8.3922102051696701e-02 4.1053523947712707e+00 3.2379570522514384e-01
4 9.6680271004438867e-01 -6.0272944088190550e-01 1.7088406391974090e-01
5 -1.5118032750014099e-01 4.8152982355843301e+00 -2.3396251503834162e-01
6 6.9769996639420007e-01 2.1986594375389688e+00 3.7782787462812606e-01
7 -1.9293747297385899e+00 2.3965302429887498e+00 5.3526894592078611e-01
8 -5.7898968354416502e-01 -1.7424269600946102e-01 4.6553500563912831e-01
9 -1.9170501143342826e+00 -1.5811474204082574e+00 -1.5153955037081890e+00
10 -1.0389874633978984e+00 -1.0136677465869111e+00 -2.8606245342679020e+00
11 -6.8937210559650852e-01 -4.9861949626741522e+00 1.7468278589450823e+00
12 -1.0247245841335400e+00 -2.9144176183755111e+00 1.0162869145592908e+00
13 8.8392380716960872e-01 -2.1032444766660849e-01 -4.5408294970791102e-01
14 3.9708226038326155e-01 -7.8680161984030961e-01 -1.9977901194159892e-01
15 -7.8687732774064545e-02 -2.1157301146984339e-01 3.4042801915998766e-01
16 4.0325457730206029e+00 -2.3548979291247609e+00 9.2949967143894952e-01
17 7.4997446543261548e-01 2.0845833390037725e+00 1.7238817466288217e+00
18 -2.1412087035667221e-01 -5.6906054172322229e-01 -5.2781467006833294e-01
19 -3.0256742141254084e-01 6.0688322127888294e-01 -9.1127162282408275e-02
20 2.3174481031809935e-01 3.0892939020181726e-01 -3.7137738763066941e-01
21 1.1702211057625094e+00 4.2920154821923315e+00 1.3460541385609648e+00
22 3.8027613826247031e-02 4.3239633632972230e-01 -3.8188409283423194e-02
23 1.4000432801696054e+00 1.0040601640391840e+00 -2.4122350019076917e+00
24 -1.5604155772955447e-01 3.4572668285914510e-01 -2.8556703863036959e-01
25 -2.9449464597969849e-01 -3.4630638648128692e-01 1.1805865362173559e-01
26 -1.8108866036308173e+00 -1.8950909756776353e+00 3.3196635723271326e+00
27 -7.7538420123902196e-01 -1.2937697587184989e+00 -9.6725767253143236e-01
28 -3.5707629120214823e-01 -2.8995606245962768e-01 -1.2007211500278167e-01
29 3.6987879522593697e-01 -4.9287949481541249e-01 5.4972323630766012e-02
30 1.1712105233973889e-01 -6.9110122964840481e-01 9.5437848811806628e-02
31 1.9388288555816860e-01 -2.0146460156127194e-01 -2.0863139798712499e-01
32 -8.8731897202011578e-01 -3.3482718789714783e+00 -1.5659784019873610e+00
run_vdwl: -15.3236335310355
run_coul: 0
run_stress: ! |2-
1.0125543392557182e+02 9.3539230810233988e+01 9.1388997082229878e+01 4.0040941706030253e+00 -9.7826716756924303e-01 2.9018476991088571e+00
run_forces: ! |2
1 1.1949883047712304e+00 2.2060858143622002e+00 -1.0733885545165418e+00
2 -1.5963527935293531e-01 -8.3496477000211577e-01 3.6354718487355586e-01
3 -8.4458087648033864e-02 4.1335068175946956e+00 3.2562083254074076e-01
4 9.7516402928123347e-01 -6.1050193540570252e-01 1.7035859794498676e-01
5 -1.5399721579534215e-01 4.8120569088649683e+00 -2.3294021119313149e-01
6 6.9813149221746262e-01 2.1977391468237610e+00 3.7752101367086355e-01
7 -1.9335938530288574e+00 2.3989898112356141e+00 5.3226592065468015e-01
8 -5.8346129298071359e-01 -1.7815682091755050e-01 4.6582930751668622e-01
9 -1.9172329351091069e+00 -1.5829627245185132e+00 -1.5163042130781048e+00
10 -1.0334176082685609e+00 -1.0148545000176199e+00 -2.8584769425899079e+00
11 -6.8756244404382794e-01 -4.9891360565883884e+00 1.7443920243481270e+00
12 -1.0236334662680082e+00 -2.9150791430800980e+00 1.0158839648906106e+00
13 8.8312645129364897e-01 -2.1071143805836662e-01 -4.5244072317123446e-01
14 3.9927871470591697e-01 -7.8979672016550584e-01 -2.0106817979273284e-01
15 -7.8923521050882781e-02 -2.1032668862489418e-01 3.3903131601122610e-01
16 4.0274555753165444e+00 -2.3555929271854597e+00 9.2684665883544881e-01
17 7.5117151275169469e-01 2.0849083749786277e+00 1.7261549167735377e+00
18 -2.1494836879728668e-01 -5.7509260272248663e-01 -5.3373034744908598e-01
19 -3.0249976756523766e-01 6.0674463278548640e-01 -9.1809428603960672e-02
20 2.3156742504597116e-01 3.0887145855490367e-01 -3.7127049070468199e-01
21 1.1686499084188677e+00 4.2891627780548545e+00 1.3459230037755703e+00
22 3.8179702424449569e-02 4.3243601345801236e-01 -3.8079863481504578e-02
23 1.4067770990537660e+00 1.0070141778822215e+00 -2.4069585948142982e+00
24 -1.5591693014836788e-01 3.4568121542161234e-01 -2.8546260901671355e-01
25 -2.9429104311734711e-01 -3.4618233584978003e-01 1.1804410855998390e-01
26 -1.8072996525588660e+00 -1.8933503719653344e+00 3.3208542120004427e+00
27 -7.7461160804433704e-01 -1.2927908441630280e+00 -9.6864680654489232e-01
28 -3.5780846246953718e-01 -2.8988724628268286e-01 -1.1924240028778682e-01
29 3.6970648233559189e-01 -4.9268726775164107e-01 5.5185028378882096e-02
30 1.1705695741665428e-01 -6.9122064837750197e-01 9.5592509524696681e-02
31 1.9349589373949760e-01 -1.9991899011439837e-01 -2.0661879538790651e-01
32 -8.9145801252527535e-01 -3.3499831182258872e+00 -1.5666124396675569e+00
...

90
unittest/force-styles/tests/atomic-pair-eam_he_real.yaml Normal file
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@ -0,0 +1,90 @@
---
lammps_version: 24 Dec 2020
date_generated: Wed Jan 13 22:16:02 202
epsilon: 7.5e-12
prerequisites: ! |
pair eam/he
pre_commands: ! |
variable units index real
post_commands: ! ""
input_file: in.metal
pair_style: eam/he
pair_coeff: ! |
* * PdHHe.eam.he Pd He
extract: ! ""
natoms: 32
init_vdwl: -353.163435640974
init_coul: 0
init_stress: ! |2-
2.3354985203865667e+03 2.1575442826183294e+03 2.1084816277194832e+03 9.2324238343315059e+01 -2.2527140800613445e+01 6.6830027278251166e+01
init_forces: ! |2
1 2.7686144278186653e+01 5.0826364063289034e+01 -2.4702012350837244e+01
2 -3.6747885266547895e+00 -1.9153555643332677e+01 8.2753244342250110e+00
3 -1.9352897465461538e+00 9.4671680061884146e+01 7.4669067263334208e+00
4 2.2295001268309708e+01 -1.3899271805198000e+01 3.9406803293404700e+00
5 -3.4863013501526918e+00 1.1104342091130563e+02 -5.3953040422049119e+00
6 1.6089344262331657e+01 5.0702293693679884e+01 8.7129182164280419e+00
7 -4.4492440494497494e+01 5.5265303098423985e+01 1.2343595755584241e+01
8 -1.3351819967863772e+01 -4.0181322292175965e+00 1.0735492808756252e+01
9 -4.4208228097061294e+01 -3.6462127564548197e+01 -3.4945852267642280e+01
10 -2.3959621310073842e+01 -2.3375734739886113e+01 -6.5967572243087659e+01
11 -1.5897299220341502e+01 -1.1498439326030027e+02 4.0282809435768357e+01
12 -2.3630711483916183e+01 -6.7208070295011467e+01 2.3436134191253181e+01
13 2.0383768267501306e+01 -4.8501972313137021e+00 -1.0471402111803629e+01
14 9.1569349225997474e+00 -1.8144077307608963e+01 -4.6070136940518891e+00
15 -1.8145823173352931e+00 -4.8789897980772752e+00 7.8504570168111005e+00
16 9.2992719393484805e+01 -5.4305239084580101e+01 2.1434772718702309e+01
17 1.7294822908857860e+01 4.8071636233680366e+01 3.9753659488339430e+01
18 -4.9377448227825411e+00 -1.3122848506373817e+01 -1.2171696062028875e+01
19 -6.9773708472871210e+00 1.3995060261579386e+01 -2.1014423910442734e+00
20 5.3441625538361990e+00 7.1240813402889511e+00 -8.5641664449490893e+00
21 2.6985941150269763e+01 9.8976233335854843e+01 3.1040747418937880e+01
22 8.7693765199327156e-01 9.9712969013523196e+00 -8.8064568351232408e-01
23 3.2285766664472092e+01 2.3154178611774061e+01 -5.5627463461007146e+01
24 -3.5984039880587519e+00 7.9726471106807173e+00 -6.5853326871205784e+00
25 -6.7912082138528707e+00 -7.9860153944650030e+00 2.7224973667181924e+00
26 -4.1760039256471202e+01 -4.3701838304071202e+01 7.6553264473163750e+01
27 -1.7880785366498504e+01 -2.9835040915646299e+01 -2.2305492953037302e+01
28 -8.2343753100058397e+00 -6.6865459861976770e+00 -2.7689288915546530e+00
29 8.5296080813687887e+00 -1.1366071741285882e+01 1.2676919627309815e+00
30 2.7008757664122220e+00 -1.5937173770267322e+01 2.2008491889792485e+00
31 4.4710457826753673e+00 -4.6458843160683996e+00 -4.8111545762194012e+00
32 -2.0462062632899592e+01 -7.7212987730343386e+01 -3.6112321671970648e+01
run_vdwl: -353.230598025017
run_coul: 0
run_stress: ! |2-
2.3352018947327042e+03 2.1575803047701361e+03 2.1079997407908877e+03 9.2286943467903825e+01 -2.2591362673321409e+01 6.6981941401935686e+01
run_forces: ! |2
1 2.7570840184953529e+01 5.0878936563954468e+01 -2.4745193716885819e+01
2 -3.6751057733124783e+00 -1.9167341173087838e+01 8.2931871358142466e+00
3 -1.9458273195805660e+00 9.4745013001500453e+01 7.4613246126708113e+00
4 2.2322999682742939e+01 -1.3910836126089546e+01 3.9444558071725182e+00
5 -3.5611755339443869e+00 1.1098583048019351e+02 -5.3589546434886657e+00
6 1.6098529359830774e+01 5.0681471667414634e+01 8.7065695410635300e+00
7 -4.4532333454110486e+01 5.5329574524982760e+01 1.2275125678150991e+01
8 -1.3365798458276837e+01 -4.0311665119688325e+00 1.0738893622536514e+01
9 -4.4219909611484340e+01 -3.6506027825529728e+01 -3.4970646977778003e+01
10 -2.3838805073020580e+01 -2.3388505371089686e+01 -6.5920271795280030e+01
11 -1.5863107119046816e+01 -1.1501474143750076e+02 4.0236861649778703e+01
12 -2.3597639915238879e+01 -6.7219256881236532e+01 2.3428611972869568e+01
13 2.0372282061050672e+01 -4.8599967847476790e+00 -1.0435173423332810e+01
14 9.1868968538149876e+00 -1.8180822851027013e+01 -4.6226879613716969e+00
15 -1.8187982708833512e+00 -4.8633248636475823e+00 7.8331412550634454e+00
16 9.2883964220226872e+01 -5.4312212635591663e+01 2.1376066838247318e+01
17 1.7335571325471630e+01 4.8086629272887443e+01 3.9799611586568851e+01
18 -4.9380025631152833e+00 -1.3140883981374724e+01 -1.2192856535881621e+01
19 -6.9765790243039625e+00 1.3993117559236460e+01 -2.1082447485751517e+00
20 5.3413030155749288e+00 7.1244381338347607e+00 -8.5630059362592803e+00
21 2.6939069851048053e+01 9.8929039552947501e+01 3.1025635765431552e+01
22 8.7771899094057326e-01 9.9759331856305540e+00 -8.7675403015085085e-01
23 3.2451609933852048e+01 2.3224549699639688e+01 -5.5509981817200973e+01
24 -3.5964621834607793e+00 7.9732311561843838e+00 -6.5839559665478173e+00
25 -6.7879787318782503e+00 -7.9847098239766732e+00 2.7230073490545976e+00
26 -4.1688921616984544e+01 -4.3653314583134815e+01 7.6583618010794297e+01
27 -1.7863754347437737e+01 -2.9811723761490370e+01 -2.2339924855988965e+01
28 -8.2430574229283415e+00 -6.6852368720976481e+00 -2.7583576098041354e+00
29 8.5269603298722565e+00 -1.1364005508745327e+01 1.2731276160949609e+00
30 2.6994843727982003e+00 -1.5940803816308822e+01 2.2046514286792602e+00
31 4.4654048480426765e+00 -4.6271939008948024e+00 -4.7862215560852475e+00
32 -2.0559378611212470e+01 -7.7265660088866639e+01 -3.6131658295360147e+01
...