ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge branch 'develop' into netcdf-standard

Browse Source
This commit is contained in:
Axel Kohlmeyer
2021-12-22 22:54:30 -05:00
parent 0576d525ad 09944f5d7a
commit b53cda778c
23 changed files with 930 additions and 172 deletions
Download Patch File Download Diff File Expand all files Collapse all files

1
doc/src/Commands_compute.rst
View File

@ -28,6 +28,7 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`angle <compute_angle>`
* :doc:`angle/local <compute_angle_local>`
* :doc:`angmom/chunk <compute_angmom_chunk>`
* :doc:`ave/sphere/atom (k) <compute_ave_sphere_atom>`
* :doc:`basal/atom <compute_basal_atom>`
* :doc:`body/local <compute_body_local>`
* :doc:`bond <compute_bond>`

3
doc/src/Errors_messages.rst
View File

@ -7772,9 +7772,6 @@ keyword to allow for additional bonds to be formed
The system size must fit in a 32-bit integer to use this dump
style.
*Too many atoms to dump sort*
Cannot sort when running with more than 2\^31 atoms.
*Too many elements extracted from MEAM library.*
Increase 'maxelt' in meam.h and recompile.

38
doc/src/angle_class2.rst
View File

@ -64,34 +64,44 @@ These are the 4 coefficients for the :math:`E_a` formula:
radians internally; hence the various :math:`K` are effectively energy
per radian\^2 or radian\^3 or radian\^4.
For the :math:`E_{bb}` formula, each line in a :doc:`angle_coeff <angle_coeff>`
command in the input script lists 4 coefficients, the first of which
is "bb" to indicate they are BondBond coefficients. In a data file,
these coefficients should be listed under a "BondBond Coeffs" heading
and you must leave out the "bb", i.e. only list 3 coefficients after
the angle type.
For the :math:`E_{bb}` formula, each line in a :doc:`angle_coeff
<angle_coeff>` command in the input script lists 4 coefficients, the
first of which is "bb" to indicate they are BondBond coefficients. In
a data file, these coefficients should be listed under a "BondBond
Coeffs" heading and you must leave out the "bb", i.e. only list 3
coefficients after the angle type.
* bb
* :math:`M` (energy/distance\^2)
* :math:`r_1` (distance)
* :math:`r_2` (distance)
For the :math:`E_{ba}` formula, each line in a :doc:`angle_coeff <angle_coeff>`
command in the input script lists 5 coefficients, the first of which
is "ba" to indicate they are BondAngle coefficients. In a data file,
these coefficients should be listed under a "BondAngle Coeffs" heading
and you must leave out the "ba", i.e. only list 4 coefficients after
the angle type.
For the :math:`E_{ba}` formula, each line in a :doc:`angle_coeff
<angle_coeff>` command in the input script lists 5 coefficients, the
first of which is "ba" to indicate they are BondAngle coefficients.
In a data file, these coefficients should be listed under a "BondAngle
Coeffs" heading and you must leave out the "ba", i.e. only list 4
coefficients after the angle type.
* ba
* :math:`N_1` (energy/distance\^2)
* :math:`N_2` (energy/distance\^2)
* :math:`N_1` (energy/distance)
* :math:`N_2` (energy/distance)
* :math:`r_1` (distance)
* :math:`r_2` (distance)
The :math:`\theta_0` value in the :math:`E_{ba}` formula is not specified,
since it is the same value from the :math:`E_a` formula.
.. note::
It is important that the order of the I,J,K atoms in each angle
listed in the Angles section of the data file read by the
:doc:`read_data <read_data>` command be consistent with the order
of the :math:`r_1` and :math:`r_2` BondBond and BondAngle
coefficients. This is because the terms in the formulas for
:math:`E_{bb}` and :math:`E_{ba}` will use the I,J atoms to compute
:math:`r_{ij}` and the J,K atoms to compute :math:`r_{jk}`.
----------
.. include:: accel_styles.rst

1
doc/src/compute.rst
View File

@ -174,6 +174,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`angle <compute_angle>` - energy of each angle sub-style
* :doc:`angle/local <compute_angle_local>` - theta and energy of each angle
* :doc:`angmom/chunk <compute_angmom_chunk>` - angular momentum for each chunk
* :doc:`ave/sphere/atom <compute_ave_sphere_atom>` - compute local density and temperature around each atom
* :doc:`basal/atom <compute_basal_atom>` - calculates the hexagonal close-packed "c" lattice vector of each atom
* :doc:`body/local <compute_body_local>` - attributes of body sub-particles
* :doc:`bond <compute_bond>` - energy of each bond sub-style

101
doc/src/compute_ave_sphere_atom.rst Normal file
View File

@ -0,0 +1,101 @@
.. index:: compute ave/sphere/atom
.. index:: compute ave/sphere/atom/kk
compute ave/sphere/atom command
================================
Accelerator Variants: *ave/sphere/atom/kk*
Syntax
""""""
.. parsed-literal::
compute ID group-ID ave/sphere/atom keyword values ...
* ID, group-ID are documented in :doc:`compute <compute>` command
* ave/sphere/atom = style name of this compute command
* one or more keyword/value pairs may be appended
.. parsed-literal::
keyword = *cutoff*
*cutoff* value = distance cutoff
Examples
""""""""
.. code-block:: LAMMPS
compute 1 all ave/sphere/atom
compute 1 all ave/sphere/atom cutoff 5.0
comm_modify cutoff 5.0
Description
"""""""""""
Define a computation that calculates the local density and temperature
for each atom and neighbors inside a spherical cutoff.
The optional keyword *cutoff* defines the distance cutoff
used when searching for neighbors. The default value is the cutoff
specified by the pair style. If no pair style is defined, then a cutoff
must be defined using this keyword. If the specified cutoff is larger than
that of the pair_style plus neighbor skin (or no pair style is defined),
the *comm_modify cutoff* option must also be set to match that of the
*cutoff* keyword.
The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently.
.. note::
If you have a bonded system, then the settings of
:doc:`special_bonds <special_bonds>` command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the :doc:`special_bonds <special_bonds>`
command, and means those pairwise interactions do not appear in the
neighbor list. Because this fix uses the neighbor list, it also means
those pairs will not be included in the order parameter. This
difficulty can be circumvented by writing a dump file, and using the
:doc:`rerun <rerun>` command to compute the order parameter for
snapshots in the dump file. The rerun script can use a
:doc:`special_bonds <special_bonds>` command that includes all pairs in
the neighbor list.
----------
.. include:: accel_styles.rst
----------
Output info
"""""""""""
This compute calculates a per-atom array with two columns: density and temperature.
These values can be accessed by any command that uses per-atom values
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
page for an overview of LAMMPS output options.
Restrictions
""""""""""""
This compute is part of the EXTRA-COMPUTE package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`comm_modify <comm_modify>`
Default
"""""""
The option defaults are *cutoff* = pair style cutoff

4
doc/src/dump_modify.rst
View File

@ -561,7 +561,9 @@ The dump *local* style cannot be sorted by atom ID, since there are
typically multiple lines of output per atom. Some dump styles, such
as *dcd* and *xtc*, require sorting by atom ID to format the output
file correctly. If multiple processors are writing the dump file, via
the "%" wildcard in the dump filename, then sorting cannot be
the "%" wildcard in the dump filename and the *nfile* or *fileper*
keywords are set to non-default values (i.e. the number of dump file
pieces is not equal to the number of procs), then sorting cannot be
performed.
.. note::

2
src/.gitignore vendored
View File

@ -429,6 +429,8 @@
/commgrid.h
/compute_ackland_atom.cpp
/compute_ackland_atom.h
/compute_ave_sphere_atom.cpp
/compute_ave_sphere_atom.h
/compute_basal_atom.cpp
/compute_basal_atom.h
/compute_body_local.cpp

5
src/CLASS2/angle_class2.cpp
View File

@ -169,6 +169,8 @@ void AngleClass2::compute(int eflag, int vflag)
// force & energy for bond-angle term
dr1 = r1 - ba_r1[type];
dr2 = r2 - ba_r2[type];
aa1 = s * dr1 * ba_k1[type];
aa2 = s * dr2 * ba_k2[type];
@ -459,6 +461,9 @@ double AngleClass2::single(int type, int i1, int i2, int i3)
double dr2 = r2 - bb_r2[type];
energy += bb_k[type]*dr1*dr2;
dr1 = r1 - ba_r1[type];
dr2 = r2 - ba_r2[type];
energy += ba_k1[type]*dr1*dtheta + ba_k2[type]*dr2*dtheta;
return energy;
}

4
src/Depend.sh
View File

@ -77,6 +77,10 @@ if (test $1 = "DPD-BASIC") then
depend INTEL
fi
if (test $1 = "EXTRA-COMPUTE") then
depend KOKKOS
fi
if (test $1 = "EXTRA-MOLECULE") then
depend GPU
depend OPENMP

278
src/EXTRA-COMPUTE/compute_ave_sphere_atom.cpp Normal file
View File

@ -0,0 +1,278 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, 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.
------------------------------------------------------------------------- */
#include "compute_ave_sphere_atom.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "group.h"
#include "memory.h"
#include "modify.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor.h"
#include "pair.h"
#include "update.h"
#include "math_const.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
/* ---------------------------------------------------------------------- */
ComputeAveSphereAtom::ComputeAveSphereAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
result(nullptr)
{
if (narg < 3 || narg > 5) error->all(FLERR,"Illegal compute ave/sphere/atom command");
// process optional args
cutoff = 0.0;
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"cutoff") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute ave/sphere/atom command");
cutoff = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (cutoff <= 0.0) error->all(FLERR,"Illegal compute ave/sphere/atom command");
iarg += 2;
} else error->all(FLERR,"Illegal compute ave/sphere/atom command");
}
peratom_flag = 1;
size_peratom_cols = 2;
comm_forward = 3;
nmax = 0;
}
/* ---------------------------------------------------------------------- */
ComputeAveSphereAtom::~ComputeAveSphereAtom()
{
if (copymode) return;
memory->destroy(result);
}
/* ---------------------------------------------------------------------- */
void ComputeAveSphereAtom::init()
{
if (!force->pair && cutoff == 0.0)
error->all(FLERR,"Compute ave/sphere/atom requires a cutoff be specified "
"or a pair style be defined");
double skin = neighbor->skin;
if (cutoff != 0.0) {
double cutghost; // as computed by Neighbor and Comm
if (force->pair)
cutghost = MAX(force->pair->cutforce+skin,comm->cutghostuser);
else
cutghost = comm->cutghostuser;
if (cutoff > cutghost)
error->all(FLERR,"Compute ave/sphere/atom cutoff exceeds ghost atom range - "
"use comm_modify cutoff command");
}
int cutflag = 1;
if (force->pair) {
if (cutoff == 0.0) {
cutoff = force->pair->cutforce;
}
if (cutoff <= force->pair->cutforce+skin) cutflag = 0;
}
cutsq = cutoff*cutoff;
sphere_vol = 4.0/3.0*MY_PI*cutsq*cutoff;
// need an occasional full neighbor list
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->occasional = 1;
if (cutflag) {
neighbor->requests[irequest]->cut = 1;
neighbor->requests[irequest]->cutoff = cutoff;
}
}
/* ---------------------------------------------------------------------- */
void ComputeAveSphereAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void ComputeAveSphereAtom::compute_peratom()
{
int i,j,ii,jj,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
int count;
double vsum[3],vavg[3],vnet[3];
invoked_peratom = update->ntimestep;
// grow result array if necessary
if (atom->nmax > nmax) {
memory->destroy(result);
nmax = atom->nmax;
memory->create(result,nmax,2,"ave/sphere/atom:result");
array_atom = result;
}
// need velocities of ghost atoms
comm->forward_comm_compute(this);
// invoke full neighbor list (will copy or build if necessary)
neighbor->build_one(list);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// compute properties for each atom in group
// use full neighbor list to count atoms less than cutoff
double **x = atom->x;
double **v = atom->v;
int *mask = atom->mask;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
// i atom contribution
count = 1;
vsum[0] = v[i][0];
vsum[1] = v[i][1];
vsum[2] = v[i][2];
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 < cutsq) {
count++;
vsum[0] += v[j][0];
vsum[1] += v[j][1];
vsum[2] += v[j][2];
}
}
vavg[0] = vsum[0]/count;
vavg[1] = vsum[1]/count;
vavg[2] = vsum[2]/count;
// i atom contribution
count = 1;
vnet[0] = v[i][0] - vavg[0];
vnet[1] = v[i][1] - vavg[1];
vnet[2] = v[i][2] - vavg[2];
double ke_sum = vnet[0]*vnet[0] + vnet[1]*vnet[1] + vnet[2]*vnet[2];
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 < cutsq) {
count++;
vnet[0] = v[j][0] - vavg[0];
vnet[1] = v[j][1] - vavg[1];
vnet[2] = v[j][2] - vavg[2];
ke_sum += vnet[0]*vnet[0] + vnet[1]*vnet[1] + vnet[2]*vnet[2];
}
}
double density = count/sphere_vol;
double temp = ke_sum/3.0/count;
result[i][0] = density;
result[i][1] = temp;
}
}
}
/* ---------------------------------------------------------------------- */
int ComputeAveSphereAtom::pack_forward_comm(int n, int *list, double *buf,
int /*pbc_flag*/, int * /*pbc*/)
{
double **v = atom->v;
int i,m=0;
for (i = 0; i < n; ++i) {
buf[m++] = v[list[i]][0];
buf[m++] = v[list[i]][1];
buf[m++] = v[list[i]][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
void ComputeAveSphereAtom::unpack_forward_comm(int n, int first, double *buf)
{
double **v = atom->v;
int i,last,m=0;
last = first + n;
for (i = first; i < last; ++i) {
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeAveSphereAtom::memory_usage()
{
double bytes = (double)2*nmax * sizeof(double);
return bytes;
}

67
src/EXTRA-COMPUTE/compute_ave_sphere_atom.h Normal file
View File

@ -0,0 +1,67 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, 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 COMPUTE_CLASS
ComputeStyle(ave/sphere/atom,ComputeAveSphereAtom)
#else
#ifndef LMP_COMPUTE_AVE_SPHERE_ATOM_H
#define LMP_COMPUTE_AVE_SPHERE_ATOM_H
#include "compute.h"
namespace LAMMPS_NS {
class ComputeAveSphereAtom : public Compute {
public:
ComputeAveSphereAtom(class LAMMPS *, int, char **);
virtual ~ComputeAveSphereAtom();
virtual void init();
void init_list(int, class NeighList *);
virtual void compute_peratom();
int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *);
double memory_usage();
protected:
int nmax;
double cutoff,cutsq,sphere_vol;
class NeighList *list;
double **result;
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Compute ave/sphere/atom requires a cutoff be specified or a pair style be defined
Self-explanatory.
E: Compute ave/sphere/atom cutoff exceeds ghost atom range - use comm_modify cutoff command
Self-explanatory.
*/

1
src/H5MD/dump_h5md.cpp
View File

@ -181,6 +181,7 @@ DumpH5MD::DumpH5MD(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
// allocate global array for atom coords
bigint n = group->count(igroup);
if ((bigint) domain->dimension*n > MAXSMALLINT) error->all(FLERR,"Too many atoms for dump h5md");
natoms = static_cast<int> (n);
if (every_position>=0)

5
src/H5MD/dump_h5md.h
View File

@ -90,6 +90,11 @@ E: Dump h5md requires sorting by atom ID
Use the dump_modify sort command to enable this.
E: Too many atoms for dump h5md
The system size must fit in a 32-bit integer to use this dump
style.
E: Cannot use variable every setting for dump xtc
The format of this file requires snapshots at regular intervals.

2
src/KOKKOS/Install.sh
View File

@ -88,6 +88,8 @@ action comm_kokkos.cpp
action comm_kokkos.h
action comm_tiled_kokkos.cpp
action comm_tiled_kokkos.h
action compute_ave_sphere_atom_kokkos.cpp compute_ave_sphere_atom.cpp
action compute_ave_sphere_atom_kokkos.h compute_ave_sphere_atom.h
action compute_coord_atom_kokkos.cpp
action compute_coord_atom_kokkos.h
action compute_orientorder_atom_kokkos.cpp

6
src/KOKKOS/angle_class2_kokkos.cpp
View File

@ -224,8 +224,8 @@ void AngleClass2Kokkos<DeviceType>::operator()(TagAngleClass2Compute<NEWTON_BOND
// force & energy for bond-bond term
const F_FLOAT dr1 = r1 - d_bb_r1[type];
const F_FLOAT dr2 = r2 - d_bb_r2[type];
F_FLOAT dr1 = r1 - d_bb_r1[type];
F_FLOAT dr2 = r2 - d_bb_r2[type];
const F_FLOAT tk1 = d_bb_k[type] * dr1;
const F_FLOAT tk2 = d_bb_k[type] * dr2;
@ -241,6 +241,8 @@ void AngleClass2Kokkos<DeviceType>::operator()(TagAngleClass2Compute<NEWTON_BOND
// force & energy for bond-angle term
dr1 = r1 - d_ba_r1[type];
dr2 = r2 - d_ba_r2[type];
const F_FLOAT aa1 = s * dr1 * d_ba_k1[type];
const F_FLOAT aa2 = s * dr2 * d_ba_k2[type];

209
src/KOKKOS/compute_ave_sphere_atom_kokkos.cpp Normal file
View File

@ -0,0 +1,209 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, 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.
------------------------------------------------------------------------- */
#include "compute_ave_sphere_atom_kokkos.h"
#include "atom_kokkos.h"
#include "atom_masks.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "memory_kokkos.h"
#include "modify.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor_kokkos.h"
#include "pair.h"
#include "update.h"
#include "math_const.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
/* ---------------------------------------------------------------------- */
template<class DeviceType>
ComputeAveSphereAtomKokkos<DeviceType>::ComputeAveSphereAtomKokkos(LAMMPS *lmp, int narg, char **arg) :
ComputeAveSphereAtom(lmp, narg, arg)
{
kokkosable = 1;
atomKK = (AtomKokkos *) atom;
execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
datamask_read = EMPTY_MASK;
datamask_modify = EMPTY_MASK;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
ComputeAveSphereAtomKokkos<DeviceType>::~ComputeAveSphereAtomKokkos()
{
if (copymode) return;
memoryKK->destroy_kokkos(k_result,result);
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void ComputeAveSphereAtomKokkos<DeviceType>::init()
{
ComputeAveSphereAtom::init();
// need an occasional full neighbor list
// irequest = neigh request made by parent class
int irequest = neighbor->nrequest - 1;
neighbor->requests[irequest]->
kokkos_host = std::is_same<DeviceType,LMPHostType>::value &&
!std::is_same<DeviceType,LMPDeviceType>::value;
neighbor->requests[irequest]->
kokkos_device = std::is_same<DeviceType,LMPDeviceType>::value;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void ComputeAveSphereAtomKokkos<DeviceType>::compute_peratom()
{
invoked_peratom = update->ntimestep;
// grow result array if necessary
if (atom->nmax > nmax) {
memoryKK->destroy_kokkos(k_result,result);
nmax = atom->nmax;
memoryKK->create_kokkos(k_result,result,nmax,2,"ave/sphere/atom:result");
d_result = k_result.view<DeviceType>();
array_atom = result;
}
// need velocities of ghost atoms
atomKK->sync(Host,V_MASK);
comm->forward_comm_compute(this);
atomKK->modified(Host,V_MASK);
// invoke full neighbor list (will copy or build if necessary)
neighbor->build_one(list);
int inum = list->inum;
NeighListKokkos<DeviceType>* k_list = static_cast<NeighListKokkos<DeviceType>*>(list);
d_numneigh = k_list->d_numneigh;
d_neighbors = k_list->d_neighbors;
d_ilist = k_list->d_ilist;
// compute properties for each atom in group
// use full neighbor list to count atoms less than cutoff
atomKK->sync(execution_space,X_MASK|V_MASK|TYPE_MASK|MASK_MASK);
x = atomKK->k_x.view<DeviceType>();
v = atomKK->k_v.view<DeviceType>();
mask = atomKK->k_mask.view<DeviceType>();
Kokkos::deep_copy(d_result,0.0);
copymode = 1;
typename Kokkos::RangePolicy<DeviceType, TagComputeAveSphereAtom> policy(0,inum);
Kokkos::parallel_for("ComputeAveSphereAtom",policy,*this);
copymode = 0;
k_result.modify<DeviceType>();
k_result.sync_host();
}
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void ComputeAveSphereAtomKokkos<DeviceType>::operator()(TagComputeAveSphereAtom, const int &ii) const
{
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
const X_FLOAT xtmp = x(i,0);
const X_FLOAT ytmp = x(i,1);
const X_FLOAT ztmp = x(i,2);
const int jnum = d_numneigh[i];
// i atom contribution
int count = 1;
double vsum[3];
vsum[0] = v(i,0);
vsum[1] = v(i,1);
vsum[2] = v(i,2);
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors(i,jj);
j &= NEIGHMASK;
const F_FLOAT delx = x(j,0) - xtmp;
const F_FLOAT dely = x(j,1) - ytmp;
const F_FLOAT delz = x(j,2) - ztmp;
const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutsq) {
count++;
vsum[0] += v(j,0);
vsum[1] += v(j,1);
vsum[2] += v(j,2);
}
}
double vavg[3];
vavg[0] = vsum[0]/count;
vavg[1] = vsum[1]/count;
vavg[2] = vsum[2]/count;
// i atom contribution
count = 1;
double vnet[3];
vnet[0] = v(i,0) - vavg[0];
vnet[1] = v(i,1) - vavg[1];
vnet[2] = v(i,2) - vavg[2];
double ke_sum = vnet[0]*vnet[0] + vnet[1]*vnet[1] + vnet[2]*vnet[2];
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors(i,jj);
j &= NEIGHMASK;
const F_FLOAT delx = x(j,0) - xtmp;
const F_FLOAT dely = x(j,1) - ytmp;
const F_FLOAT delz = x(j,2) - ztmp;
const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutsq) {
count++;
vnet[0] = v(j,0) - vavg[0];
vnet[1] = v(j,1) - vavg[1];
vnet[2] = v(j,2) - vavg[2];
ke_sum += vnet[0]*vnet[0] + vnet[1]*vnet[1] + vnet[2]*vnet[2];
}
}
double density = count/sphere_vol;
double temp = ke_sum/3.0/count;
d_result(i,0) = density;
d_result(i,1) = temp;
}
}
namespace LAMMPS_NS {
template class ComputeAveSphereAtomKokkos<LMPDeviceType>;
#ifdef LMP_KOKKOS_GPU
template class ComputeAveSphereAtomKokkos<LMPHostType>;
#endif
}

66
src/KOKKOS/compute_ave_sphere_atom_kokkos.h Normal file
View File

@ -0,0 +1,66 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, 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 COMPUTE_CLASS
ComputeStyle(ave/sphere/atom/kk,ComputeAveSphereAtomKokkos<LMPDeviceType>)
ComputeStyle(ave/sphere/atom/kk/device,ComputeAveSphereAtomKokkos<LMPDeviceType>)
ComputeStyle(ave/sphere/atom/kk/host,ComputeAveSphereAtomKokkos<LMPHostType>)
#else
#ifndef LMP_COMPUTE_AVE_SPHERE_ATOM_KOKKOS_H
#define LMP_COMPUTE_AVE_SPHERE_ATOM_KOKKOS_H
#include "compute_ave_sphere_atom.h"
#include "kokkos_type.h"
namespace LAMMPS_NS {
struct TagComputeAveSphereAtom{};
template<class DeviceType>
class ComputeAveSphereAtomKokkos : public ComputeAveSphereAtom {
public:
typedef DeviceType device_type;
typedef ArrayTypes<DeviceType> AT;
ComputeAveSphereAtomKokkos(class LAMMPS *, int, char **);
virtual ~ComputeAveSphereAtomKokkos();
void init();
void compute_peratom();
KOKKOS_INLINE_FUNCTION
void operator()(TagComputeAveSphereAtom, const int&) const;
private:
typename AT::t_x_array_randomread x;
typename AT::t_v_array_randomread v;
typename ArrayTypes<DeviceType>::t_int_1d mask;
typename AT::t_neighbors_2d d_neighbors;
typename AT::t_int_1d_randomread d_ilist;
typename AT::t_int_1d_randomread d_numneigh;
DAT::tdual_float_2d k_result;
typename AT::t_float_2d d_result;
};
}
#endif
#endif
/* ERROR/WARNING messages:
*/

5
src/MOFFF/angle_class2_p6.cpp
View File

@ -174,6 +174,8 @@ void AngleClass2P6::compute(int eflag, int vflag)
// force & energy for bond-angle term
dr1 = r1 - ba_r1[type];
dr2 = r2 - ba_r2[type];
aa1 = s * dr1 * ba_k1[type];
aa2 = s * dr2 * ba_k2[type];
@ -479,6 +481,9 @@ double AngleClass2P6::single(int type, int i1, int i2, int i3)
double dr2 = r2 - bb_r2[type];
energy += bb_k[type]*dr1*dr2;
dr1 = r1 - ba_r1[type];
dr2 = r2 - ba_r2[type];
energy += ba_k1[type]*dr1*dtheta + ba_k2[type]*dr2*dtheta;
return energy;
}

2
src/OPENMP/angle_class2_omp.cpp
View File

@ -175,6 +175,8 @@ void AngleClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
// force & energy for bond-angle term
dr1 = r1 - ba_r1[type];
dr2 = r2 - ba_r2[type];
aa1 = s * dr1 * ba_k1[type];
aa2 = s * dr2 * ba_k2[type];

31
src/dump.cpp
View File

@ -228,7 +228,7 @@ void Dump::init()
if (sort_flag) {
if (multiproc > 1)
error->all(FLERR,
"Cannot dump sort when multiple dump files are written");
"Cannot dump sort when 'nfile' or 'fileper' keywords are set to non-default values");
if (sortcol == 0 && atom->tag_enable == 0)
error->all(FLERR,"Cannot dump sort on atom IDs with no atom IDs defined");
if (sortcol && sortcol > size_one)
@ -237,8 +237,6 @@ void Dump::init()
irregular = new Irregular(lmp);
bigint size = group->count(igroup);
if (size > MAXSMALLINT) error->all(FLERR,"Too many atoms to dump sort");
int isize = static_cast<int> (size);
// set reorderflag = 1 if can simply reorder local atoms rather than sort
// criteria: sorting by ID, atom IDs are consecutive from 1 to Natoms
@ -268,7 +266,7 @@ void Dump::init()
MPI_Allreduce(&min,&minall,1,MPI_LMP_TAGINT,MPI_MIN,world);
MPI_Allreduce(&max,&maxall,1,MPI_LMP_TAGINT,MPI_MAX,world);
if (maxall-minall+1 == isize) {
if (maxall-minall+1 == size) {
reorderflag = 1;
double range = maxall-minall + EPSILON;
idlo = static_cast<tagint> (range*me/nprocs + minall);
@ -284,7 +282,7 @@ void Dump::init()
else if (me+1 != hi) idhi++;
nme_reorder = idhi-idlo;
ntotal_reorder = isize;
ntotal_reorder = size;
}
}
}
@ -369,16 +367,6 @@ void Dump::write()
if (multiproc != nprocs) MPI_Allreduce(&nme,&nmax,1,MPI_INT,MPI_MAX,world);
else nmax = nme;
// write timestep header
// for multiproc,
// nheader = # of lines in this file via Allreduce on clustercomm
bigint nheader = ntotal;
if (multiproc)
MPI_Allreduce(&bnme,&nheader,1,MPI_LMP_BIGINT,MPI_SUM,clustercomm);
if (filewriter && write_header_flag) write_header(nheader);
// insure buf is sized for packing and communicating
// use nmax to insure filewriter proc can receive info from others
// limit nmax*size_one to int since used as arg in MPI calls
@ -431,6 +419,19 @@ void Dump::write()
else pack(nullptr);
if (sort_flag) sort();
// write timestep header
// for multiproc,
// nheader = # of lines in this file via Allreduce on clustercomm
// must come after sort, which can change nme
bigint nheader = ntotal;
if (multiproc) {
bnme = nme;
MPI_Allreduce(&bnme,&nheader,1,MPI_LMP_BIGINT,MPI_SUM,clustercomm);
}
if (filewriter && write_header_flag) write_header(nheader);
// if buffering, convert doubles into strings
// insure sbuf is sized for communicating
// cannot buffer if output is to binary file

11
src/dump.h
View File

@ -116,7 +116,7 @@ class Dump : protected Pointers {
bigint ntotal; // total # of per-atom lines in snapshot
int reorderflag; // 1 if OK to reorder instead of sort
int ntotal_reorder; // # of atoms that must be in snapshot
bigint ntotal_reorder; // # of atoms that must be in snapshot
int nme_reorder; // # of atoms I must own in snapshot
tagint idlo; // lowest ID I own when reordering
@ -173,10 +173,9 @@ E: Dump file MPI-IO output not allowed with % in filename
This is because a % signifies one file per processor and MPI-IO
creates one large file for all processors.
E: Cannot dump sort when multiple dump files are written
E: Cannot dump sort when 'nfile' or 'fileper' keywords are set to non-default values
In this mode, each processor dumps its atoms to a file, so
no sorting is allowed.
Can only dump sort when the number of dump file pieces using % in filename equals the number of processors
E: Cannot dump sort on atom IDs with no atom IDs defined
@ -186,10 +185,6 @@ E: Dump sort column is invalid
Self-explanatory.
E: Too many atoms to dump sort
Cannot sort when running with more than 2^31 atoms.
E: Dump could not find refresh compute ID
UNDOCUMENTED

129
unittest/force-styles/tests/angle-class2.yaml
View File

@ -1,7 +1,8 @@
---
lammps_version: 10 Feb 2021
date_generated: Fri Feb 26 23:09:23 2021
lammps_version: 14 Dec 2021
date_generated: Tue Dec 21 11:26:44 2021
epsilon: 1e-12
skip_tests:
prerequisites: ! |
atom full
angle class2
@ -21,73 +22,73 @@ angle_coeff: ! |
1 ba 20.0 0.0 1.5 1.5
3 ba 10.0 10.0 1.5 1.5
4 ba 0.0 20.0 1.5 1.5
equilibrium: 4 1.9216075064457565 1.9373154697137058 2.0943951023931953 1.8936822384138474
equilibrium: 4 1.9216075064457567 1.9373154697137058 2.0943951023931953 1.8936822384138476
extract: ! ""
natoms: 29
init_energy: 45.6315872862689
init_energy: 46.440896837749044
init_stress: ! |2-
1.0380900034455654e+02 -8.5596888576343744e+01 1.0543371457027396e+01 9.3533772092305199e+01 -3.0453078736699425e+01 1.6197471265279837e+00
1.1893382158997322e+02 -8.8291447119046992e+01 -1.8868912456859972e+00 1.1299617626314146e+02 -8.5358891009896780e+00 7.6967639957246794e+00
init_forces: ! |2
1 4.7202113476907201e+01 9.2452097148049379e+00 -2.1894202744712533e+01
2 -1.7062797644104073e+00 -1.3815331678107317e+01 -1.1109216556988997e+01
3 -1.0818552868961547e+01 4.2757153900854306e+01 4.0134050204129267e+01
4 -1.6107291199158311e+01 -2.0450831607561582e+01 1.2394641799374179e+01
5 -4.1997303662023540e+01 -4.1453062742803219e+01 -1.7536792897035419e+01
6 5.6639792403457349e+01 -1.3580769610788053e+01 -3.9712060060785255e+01
7 -1.8054439727078506e+01 1.6983062508083172e+01 1.5587306726806713e+00
8 -1.0525801597483865e+01 -1.5574411954009244e+01 8.4303126221362277e+01
9 -1.4606126670427546e+01 1.7088847325775880e+01 3.5265027966992148e+00
10 -9.2168170333014618e+00 2.5310906045489432e+01 -6.6219876033939016e+01
1 4.9843771864003834e+01 3.0925122596911816e+00 -3.5312722193312226e+01
2 -7.6547115157834666e-01 -6.1978334793953476e+00 -4.9838162348189323e+00
3 -2.0132137208074248e+01 6.1565994561526715e+01 5.8548546756498347e+01
4 -1.1800898073962109e+01 -2.7342191490108263e+01 3.6024091179236257e+00
5 -3.5756372747916700e+01 -5.0661360858658405e+01 -1.9085859271498553e+01
6 5.0734800121225135e+01 -1.5633459340466136e+01 -3.6451541950394720e+01
7 -1.8030285239813821e+01 1.7009172193091111e+01 1.5544411167675971e+00
8 -1.5632958318497042e+01 -2.1571227015465091e+01 7.4636601692831320e+01
9 -1.4606126670427546e+01 1.7088847325775880e+01 3.5265027966992157e+00
10 4.9412614063426892e+00 3.2891848318072718e+01 -5.8999099084298045e+01
11 -2.0537012066379056e+01 -7.0930129287428976e+00 7.5068656204459945e+00
12 -2.8436344574011141e-01 -6.5767250423083183e+00 -7.8126221608778286e+00
13 3.1055904718024561e+00 8.1431271170459514e+00 -1.2597779054058647e+00
14 1.6321646299623836e+01 -6.4737292023940052e+00 -6.0969666237587319e+00
15 1.2014703003264437e+01 -4.7819952969181587e+00 1.5497667618539472e+01
16 9.3845211462413065e+00 9.2380044230210405e+00 6.9332654848904189e+00
17 -8.1437876633224571e-01 1.0335590285580882e+00 -2.1333543461785509e-01
18 4.7908728028679270e-01 1.6800089801308631e+00 -5.5268875505867383e+00
19 -2.0533806941129176e+00 -2.3525964439530416e+00 2.1320670955883561e+00
20 1.5742934138261249e+00 6.7258746382217860e-01 3.3948204549983823e+00
21 3.9487378529081880e+00 4.3175316427012014e+00 -1.1481919601133793e+01
22 -6.5477089696018744e+00 -4.1918690971369452e+00 3.4304260006102911e+00
23 2.5989711166936864e+00 -1.2566254556425660e-01 8.0514936005235018e+00
24 -8.4094048868779181e-01 4.6838060982897600e+00 -2.5056979703433946e+00
25 -1.3589399152326838e+00 -3.2194810517526529e+00 2.1726606908305435e-01
26 2.1998804039204756e+00 -1.4643250465371074e+00 2.2884319012603402e+00
27 -1.3120258950869723e-01 2.3248353742613195e+00 -7.0687277526256109e-01
28 -7.9798149428972343e-01 -1.3623378004463826e+00 -7.5274691791676882e-02
29 9.2918408379842066e-01 -9.6249757381493684e-01 7.8214746705423799e-01
run_energy: 45.4459195202412
12 1.3804183606931298e+01 6.4447653590032914e+00 -2.7232856026007504e+01
13 3.5360349619705711e-01 9.1396982628926138e-01 4.4753951517849107e+00
14 9.6171168365401805e+00 -1.2052302426663841e+01 -3.9493877514992031e+00
15 6.4860723734536965e+00 -7.3468753785680629e+00 2.2291265160011950e+01
16 -2.1230106290243054e+00 1.3874285421512146e+01 6.8398804299585079e+00
17 3.6034624009792791e+00 -4.9831323468942506e+00 3.0333746689077179e+00
18 8.4504245756073892e-01 5.5042293626682808e+00 -2.1046811461460457e+01
19 -6.5342341140829419e+00 -7.9348302620004993e+00 8.7785874834232587e+00
20 5.6891916565222029e+00 2.4306008993322186e+00 1.2268223978037199e+01
21 7.8687847056106097e+00 9.2247825951126554e+00 -2.6147407661059020e+01
22 -1.3528173582118603e+01 -8.9511461518324538e+00 8.6148798736605858e+00
23 5.6593888765079932e+00 -2.7363644328020120e-01 1.7532527787398436e+01
24 -4.3228091413199312e+00 1.8218035887352222e+01 -1.0563459250035294e+01
25 -4.1518972409293955e+00 -1.2576945219214169e+01 1.7476216234117312e+00
26 8.4747063822493267e+00 -5.6410906681380535e+00 8.8158376266235621e+00
27 -1.9941459534406549e+00 1.7618141002760062e+01 -5.9162802776486032e+00
28 -4.8714180504657234e+00 -1.0506429973856317e+01 1.3714179563487131e-01
29 6.8655640039063783e+00 -7.1117110289037466e+00 5.7791384820137317e+00
run_energy: 46.04254213414856
run_stress: ! |2-
1.0224296939567702e+02 -8.5149951148281033e+01 1.1077450496851872e+01 9.2245165502849829e+01 -3.1084418227269154e+01 5.2366663320491313e-01
1.1725321346181148e+02 -8.7851127936553254e+01 -1.2820805825603960e+00 1.1164348489319656e+02 -9.3238396977559397e+00 6.5868867241338807e+00
run_forces: ! |2
1 4.6696948163060675e+01 9.5469544165543052e+00 -2.1330948302985508e+01
2 -1.7341210851964273e+00 -1.4128897827282087e+01 -1.1408863992275160e+01
3 -1.0105551089272240e+01 4.2277702428791336e+01 3.9657670069675063e+01
4 -1.6122111935066883e+01 -2.0098532812588481e+01 1.2653235408843411e+01
5 -4.2111565648427224e+01 -4.1283493356078523e+01 -1.7589964848850386e+01
6 5.6633343610296642e+01 -1.3630420678353568e+01 -3.9740642386699271e+01
7 -1.8067962126721181e+01 1.7005582120491120e+01 1.5568169485445109e+00
8 -1.0459403976386902e+01 -1.5611162457913967e+01 8.4226500676174069e+01
9 -1.4631300686651667e+01 1.7116506905325277e+01 3.5366459989463483e+00
10 -9.1067423535925318e+00 2.5083637022662394e+01 -6.6120603070314331e+01
11 -2.0531188000382802e+01 -7.0572039110412836e+00 7.4976926119744087e+00
12 -4.5804053460484440e-01 -6.7408368318088137e+00 -7.3612432437675679e+00
13 3.0256565331949181e+00 7.9773964875310250e+00 -1.1599249084139895e+00
14 1.6325797226942768e+01 -6.0364594808671850e+00 -6.0596304628457736e+00
15 1.2032950547216590e+01 -4.6547008559207024e+00 1.4984306358892226e+01
16 9.4390365741788855e+00 9.1831264349550388e+00 6.8856125869099509e+00
17 -8.2574521858778427e-01 1.0508023955441044e+00 -2.2665944380799952e-01
18 4.1662989783566795e-01 1.4355996853101134e+00 -4.6916036738076876e+00
19 -1.7454972366844239e+00 -2.0016596312326365e+00 1.8125096846165301e+00
20 1.3288673388487560e+00 5.6605994592252307e-01 2.8790939891911576e+00
21 3.7257661846966093e+00 4.0481711597815977e+00 -1.0827752619904448e+01
22 -6.1593135050903065e+00 -3.9305106214838132e+00 3.2463364124342222e+00
23 2.4335473203936973e+00 -1.1766053829778456e-01 7.5814162074702249e+00
24 -7.6007405188534261e-01 4.2086623877720974e+00 -2.2508903613389659e+00
25 -1.2107922910240914e+00 -2.8924997143595577e+00 1.9797185345341334e-01
26 1.9708663429094340e+00 -1.3161626734125400e+00 2.0529185078855527e+00
27 -1.2690270648686752e-01 2.1785298399231308e+00 -6.5914069723159696e-01
28 -7.4337188418354749e-01 -1.2769741286441925e+00 -7.1075298614674390e-02
29 8.7027459067041502e-01 -9.0155571127893830e-01 7.3021599584627139e-01
1 4.9310488854556048e+01 3.4204699131043999e+00 -3.4719646460390109e+01
2 -8.0299294685685085e-01 -6.5454065929116556e+00 -5.2863994125400326e+00
3 -1.9344188743451483e+01 6.1008236345827427e+01 5.7990450617574737e+01
4 -1.1820915021801847e+01 -2.6960419197209372e+01 3.9252515610422387e+00
5 -3.5905034771726200e+01 -5.0435101635947014e+01 -1.9146824911182328e+01
6 5.0729278972279332e+01 -1.5703691297521928e+01 -3.6490325001299325e+01
7 -1.8043757960499846e+01 1.7038616039733434e+01 1.5516900804512148e+00
8 -1.5552591757457865e+01 -2.1589081417070179e+01 7.4580844287823936e+01
9 -1.4632487393832747e+01 1.7116771489893083e+01 3.5369114786793467e+00
10 5.0177324966376649e+00 3.2655409113932286e+01 -5.8914010758009439e+01
11 -2.0526018243356614e+01 -7.0603095274350611e+00 7.4991583014498691e+00
12 1.3523522841409502e+01 6.2514718031216852e+00 -2.6685798485651077e+01
13 3.0043046271322960e-01 7.8431109074530148e-01 4.5328635576848786e+00
14 9.6740453376714228e+00 -1.1603919453433887e+01 -3.9205080570168040e+00
15 6.5345442098934683e+00 -7.2391735244141353e+00 2.1740136588792641e+01
16 -2.0494434617404407e+00 1.3825958913895089e+01 6.7881976680816249e+00
17 3.5873871255632257e+00 -4.9641420643094554e+00 3.0180089445086313e+00
18 7.9531230378610207e-01 5.2629626454507630e+00 -2.0172279025467247e+01
19 -6.1997999385006839e+00 -7.5645533008417640e+00 8.4605118212170112e+00
20 5.4044876347145818e+00 2.3015906553910015e+00 1.1711767204250236e+01
21 7.6462499201271452e+00 8.9238366526271982e+00 -2.5489460284469285e+01
22 -1.3116044133706563e+01 -8.6583255717724796e+00 8.4434021193141291e+00
23 5.4697942135794175e+00 -2.6551108085471875e-01 1.7046058165155156e+01
24 -4.2497082139356905e+00 1.7742951256065766e+01 -1.0303002556901220e+01
25 -3.9777181755411437e+00 -1.2246864111150519e+01 1.7323644652289971e+00
26 8.2274263894768342e+00 -5.4960871449152453e+00 8.5706380916722225e+00
27 -2.0048516565658536e+00 1.7446299537442144e+01 -5.8315780788096188e+00
28 -4.7894277572886974e+00 -1.0406054769833135e+01 1.3027326655161572e-01
29 6.7942794138545510e+00 -7.0402447676090096e+00 5.7013048122580035e+00
...

131
unittest/force-styles/tests/angle-class2_p6.yaml
View File

@ -1,7 +1,8 @@
---
lammps_version: 10 Feb 2021
date_generated: Fri Feb 26 23:09:23 2021
lammps_version: 14 Dec 2021
date_generated: Tue Dec 21 11:26:44 2021
epsilon: 5e-13
skip_tests:
prerequisites: ! |
atom full
angle class2/p6
@ -21,73 +22,73 @@ angle_coeff: ! |
1 ba 20.0 0.0 1.5 1.5
3 ba 10.0 10.0 1.5 1.5
4 ba 0.0 20.0 1.5 1.5
equilibrium: 4 1.9216075064457565 1.9373154697137058 2.0943951023931953 1.8936822384138474
equilibrium: 4 1.9216075064457567 1.9373154697137058 2.0943951023931953 1.8936822384138476
extract: ! ""
natoms: 29
init_energy: 45.6314933281677
init_energy: 46.440802879647805
init_stress: ! |2-
1.0380655176146676e+02 -8.5598294304263064e+01 1.0547225768036466e+01 9.3533997442530364e+01 -3.0452940351933286e+01 1.6213985364060581e+00
1.1893137300688346e+02 -8.8292852846966269e+01 -1.8830369346769591e+00 1.1299640161336661e+02 -8.5357507162235464e+00 7.6984154056027378e+00
init_forces: ! |2
1 4.7202230480286389e+01 9.2446782757168187e+00 -2.1892853730746999e+01
2 -1.7062799943363052e+00 -1.3815333539761312e+01 -1.1109218053986531e+01
3 -1.0819442137600213e+01 4.2755643579721394e+01 4.0131978148937094e+01
4 -1.6107331786015202e+01 -2.0450833016170897e+01 1.2394698445624217e+01
5 -4.1996775288710346e+01 -4.1451276926607676e+01 -1.7536151963373857e+01
6 5.6640330905804802e+01 -1.3581373316126099e+01 -3.9714075413905050e+01
7 -1.8054191673295325e+01 1.6982840171711775e+01 1.5587849314106879e+00
8 -1.0524752828621686e+01 -1.5572494690475857e+01 8.4307006012653105e+01
9 -1.4606116746275049e+01 1.7088845087132931e+01 3.5265010989798085e+00
10 -9.2183983294618113e+00 2.5308833813269253e+01 -6.6220570658369525e+01
11 -2.0536178089795950e+01 -7.0922505905966178e+00 7.5061958159305595e+00
12 -2.8507497680544613e-01 -6.5761946491161254e+00 -7.8131884119322397e+00
13 3.1055913097859387e+00 8.1431291943766304e+00 -1.2597770427903630e+00
14 1.6321556949530429e+01 -6.4737931388148002e+00 -6.0969371866598330e+00
15 1.2014697273266693e+01 -4.7819939276460772e+00 1.5497663357748195e+01
16 9.3845137052789855e+00 9.2380146356987876e+00 6.9332800900251534e+00
17 -8.1437877303591466e-01 1.0335590376878656e+00 -2.1333543954444023e-01
18 4.7908727278798890e-01 1.6800089017685975e+00 -5.5268872325673071e+00
19 -2.0533806022955563e+00 -2.3525963295672470e+00 2.1320669593942201e+00
20 1.5742933295075674e+00 6.7258742779864933e-01 3.3948202731730870e+00
21 3.9487365123920992e+00 4.3175299645965515e+00 -1.1481914586060395e+01
22 -6.5477065825321601e+00 -4.1918674696340856e+00 3.4304242277121375e+00
23 2.5989700701400609e+00 -1.2566249496246562e-01 8.0514903583482571e+00
24 -8.4094044796366130e-01 4.6838059399926504e+00 -2.5056978760993669e+00
25 -1.3589398825660985e+00 -3.2194809423072277e+00 2.1726605118393005e-01
26 2.1998803305297598e+00 -1.4643249976854225e+00 2.2884318249154370e+00
27 -1.3120258888530634e-01 2.3248353691437700e+00 -7.0687277351935407e-01
28 -7.9798149292664289e-01 -1.3623377973865247e+00 -7.5274691862757134e-02
29 9.2918408181194923e-01 -9.6249757175724537e-01 7.8214746538211122e-01
run_energy: 45.4458285940593
1 4.9843888867383036e+01 3.0919808206030721e+00 -3.5311373179346681e+01
2 -7.6547138150424543e-01 -6.1978353410493483e+00 -4.9838177318164663e+00
3 -2.0133026476712903e+01 6.1564484240393824e+01 5.8546474701306153e+01
4 -1.1800938660819003e+01 -2.7342192898717585e+01 3.6024657641736728e+00
5 -3.5755844374603512e+01 -5.0659575042462862e+01 -1.9085218337836995e+01
6 5.0735338623572588e+01 -1.5634063045804186e+01 -3.6453557303514501e+01
7 -1.8030037186030640e+01 1.7008949856719713e+01 1.5544953754976136e+00
8 -1.5631909549634866e+01 -2.1569309751931716e+01 7.4640481484122148e+01
9 -1.4606116746275049e+01 1.7088845087132935e+01 3.5265010989798080e+00
10 4.9396801101823433e+00 3.2889776085852560e+01 -5.8999793708728561e+01
11 -2.0536178089795950e+01 -7.0922505905966178e+00 7.5061958159305604e+00
12 1.3803472075865960e+01 6.4452957521954772e+00 -2.7233422277061912e+01
13 3.5360433418053783e-01 9.1397190361994329e-01 4.4753960144004115e+00
14 9.6170274864467693e+00 -1.2052366363084635e+01 -3.9493583144003042e+00
15 6.4860666434559526e+00 -7.3468740092959814e+00 2.2291260899220667e+01
16 -2.1230180699866263e+00 1.3874295634189895e+01 6.8398950350932433e+00
17 3.6034623942756108e+00 -4.9831323377644736e+00 3.0333746639811334e+00
18 8.4504245006193557e-01 5.5042292843060157e+00 -2.1046811143441026e+01
19 -6.5342340222655810e+00 -7.9348301476147052e+00 8.7785873472291236e+00
20 5.6891915722036455e+00 2.4306008633086891e+00 1.2268223796211903e+01
21 7.8687833650945196e+00 9.2247809170080028e+00 -2.6147402645985622e+01
22 -1.3528171195048888e+01 -8.9511445243295924e+00 8.6148781007624322e+00
23 5.6593878299543681e+00 -2.7363639267841045e-01 1.7532524545223190e+01
24 -4.3228091005958014e+00 1.8218035729055110e+01 -1.0563459155791266e+01
25 -4.1518972082628096e+00 -1.2576945109768744e+01 1.7476216055126070e+00
26 8.4747063088586110e+00 -5.6410906192863681e+00 8.8158375502786583e+00
27 -1.9941459528172638e+00 1.7618140997642513e+01 -5.9162802759053958e+00
28 -4.8714180491026431e+00 -1.0506429970796459e+01 1.3714179556379100e-01
29 6.8655640019199069e+00 -7.1117110268460557e+00 5.7791384803416053e+00
run_energy: 46.04245232805462
run_stress: ! |2-
1.0224054425179162e+02 -8.5151354715203126e+01 1.1081280882090672e+01 9.2245389115064398e+01 -3.1084294543117402e+01 5.2530572051471558e-01
1.1725078883087194e+02 -8.7852531332776422e+01 -1.2782508811995987e+00 1.1164371026778049e+02 -9.3237176305934248e+00 6.5885234111489295e+00
run_forces: ! |2
1 4.6697063144899758e+01 9.5464292184313084e+00 -2.1329615486413495e+01
2 -1.7341213469343071e+00 -1.4128899311205867e+01 -1.1408865229626386e+01
3 -1.0106423829890657e+01 4.2276216760085092e+01 3.9655618981253937e+01
4 -1.6122153804166530e+01 -2.0098535935851185e+01 1.2653292967815302e+01
5 -4.2111045474433908e+01 -4.1281732299841927e+01 -1.7589329659171515e+01
6 5.6633872451307042e+01 -1.3631017853516695e+01 -3.9742648484553712e+01
7 -1.8067710814224181e+01 1.7005356519278848e+01 1.5568722867815019e+00
8 -1.0458368774535296e+01 -1.5609267760781632e+01 8.4230369919214809e+01
9 -1.4631291097137083e+01 1.7116505329041448e+01 3.5366441447941890e+00
10 -9.1083165882262076e+00 2.5081593622661249e+01 -6.6121298210985884e+01
11 -2.0530357257878578e+01 -7.0564447871249403e+00 7.4970247183653580e+00
12 -4.5873997835014801e-01 -6.7403152848189372e+00 -7.3618095936615644e+00
13 3.0256572433426814e+00 7.9773984059331964e+00 -1.1599242567025270e+00
14 1.6325706512702343e+01 -6.0365250687180749e+00 -6.0596004500231722e+00
15 1.2032945183866531e+01 -4.6546995895395877e+00 1.4984301967909428e+01
16 9.4390297519529085e+00 9.1831355042234861e+00 6.8856259318712949e+00
17 -8.2574532229437936e-01 1.0508025317442151e+00 -2.2665954686757872e-01
18 4.1662989358421232e-01 1.4355996421935044e+00 -4.6916034993533247e+00
19 -1.7454971864999060e+00 -2.0016595685522596e+00 1.8125096096904596e+00
20 1.3288672929156937e+00 5.6605992635875502e-01 2.8790938896628648e+00
21 3.7257651397379274e+00 4.0481698601097618e+00 -1.0827748711362894e+01
22 -6.1593116505043302e+00 -3.9305093611054267e+00 3.2463350269770475e+00
23 2.4335465107664027e+00 -1.1766049900433539e-01 7.5814136843858462e+00
24 -7.6007402633523591e-01 4.2086622887143186e+00 -2.2508903023980524e+00
25 -1.2107922707762828e+00 -2.8924996458903025e+00 1.9797184221876996e-01
26 1.9708662971115187e+00 -1.3161626428240165e+00 2.0529184601792827e+00
27 -1.2690270602781828e-01 2.1785298361926788e+00 -6.5914069596767511e-01
28 -7.4337188319492098e-01 -1.2769741264135199e+00 -7.1075298663885261e-02
29 8.7027458922273926e-01 -9.0155570977915866e-01 7.3021599463156039e-01
1 4.9310604335655682e+01 3.4199456337672487e+00 -3.4718316191911107e+01
2 -8.0299317271452264e-01 -6.5454081333117653e+00 -5.2864006747626604e+00
3 -1.9345060126536442e+01 6.1006753750400470e+01 5.7988403049659411e+01
4 -1.1820957153105841e+01 -2.6960422682106536e+01 3.9253092142830135e+00
5 -3.5904516097808205e+01 -5.0433344031821314e+01 -1.9146190690682918e+01
6 5.0729808044888514e+01 -1.5704289267936588e+01 -3.6492333161602460e+01
7 -1.8043506480508537e+01 1.7038390298430201e+01 1.5517454554100727e+00
8 -1.5551557230614444e+01 -2.1587186230569777e+01 7.4584717878493251e+01
9 -1.4632477702925939e+01 1.7116769814092336e+01 3.5369096257061594e+00
10 5.0161578855418893e+00 3.2653366582115979e+01 -5.8914707964769292e+01
11 -2.0525187366514267e+01 -7.0595502886286221e+00 7.4984902661515953e+00
12 1.3522823846822945e+01 6.2519930281569955e+00 -2.6686365074578834e+01
13 3.0043118312382699e-01 7.8431307047186760e-01 4.5328641811452499e+00
14 9.6739544192178748e+00 -1.1603985265483198e+01 -3.9204779603734119e+00
15 6.5345389143893406e+00 -7.2391722622226151e+00 2.1740132205563690e+01
16 -2.0494503520587521e+00 1.3825967887607892e+01 6.7882109957643362e+00
17 3.5873870531468781e+00 -4.9641419029625879e+00 3.0180088465038910e+00
18 7.9531229968056927e-01 5.2629626038099762e+00 -2.0172278856982508e+01
19 -6.1997998900621667e+00 -7.5645532403308380e+00 8.4605117488474431e+00
20 5.4044875903815974e+00 2.3015906365208618e+00 1.1711767108135064e+01
21 7.6462488915955822e+00 8.9238353733854954e+00 -2.5489456437353834e+01
22 -1.3116042308945529e+01 -8.6583243315139509e+00 8.4434007553408890e+00
23 5.4697934173499467e+00 -2.6551104187154384e-01 1.7046055682012945e+01
24 -4.2497081893768893e+00 1.7742951160854016e+01 -1.0303002500248269e+01
25 -3.9777181560986339e+00 -1.2246864045350220e+01 1.7323644544198329e+00
26 8.2274263454755232e+00 -5.4960871155037951e+00 8.5706380458284350e+00
27 -2.0048516561480048e+00 1.7446299534047586e+01 -5.8315780776594286e+00
28 -4.7894277563898591e+00 -1.0406054767803472e+01 1.3027326650644638e-01
29 6.7942794125378638e+00 -7.0402447662441157e+00 5.7013048111529825e+00
...