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Merge pull request #4383 from akohlmey/collected-small-changes

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Collected small changes and fixes
This commit is contained in:
Axel Kohlmeyer
2024-11-17 22:15:36 -05:00
committed by GitHub
parent 5928389c5e 18329ac86a
commit 48c27365ee
23 changed files with 537 additions and 64 deletions
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3
.github/CODEOWNERS vendored
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@ -101,7 +101,8 @@ src/group.* @sjplimp
src/improper.* @sjplimp
src/info.* @akohlmey
src/kspace.* @sjplimp
src/lmptyp.h @sjplimp
src/lmptype.h @sjplimp
src/label_map.* @jrgissing @akohlmey
src/library.* @sjplimp @akohlmey
src/main.cpp @sjplimp
src/min_*.* @sjplimp

9
doc/documentation_conventions.md
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@ -10,7 +10,7 @@ Last change: 2022-12-30
In fall 2019, the LAMMPS documentation file format has changed from a
home grown markup designed to generate HTML format files only, to
[reStructuredText](https://docutils.sourceforge.io/rst.html>. For a
[reStructuredText](https://docutils.sourceforge.io/rst.html>). For a
transition period all files in the old .txt format were transparently
converted to .rst and then processed. The `txt2rst tool` is still
included in the distribution to obtain an initial .rst file for legacy
@ -45,8 +45,7 @@ what kind of information and sections are needed.
## Formatting conventions
For headlines we try to follow the conventions posted here:
https://documentation-style-guide-sphinx.readthedocs.io/en/latest/style-guide.html#headings
For headlines we try to follow the conventions posted [here](https://documentation-style-guide-sphinx.readthedocs.io/en/latest/style-guide.html#headings).
It seems to be sufficient to have this consistent only within
any single file and it is not (yet) enforced strictly, but making
this globally consistent makes it easier to move sections around.
@ -64,7 +63,7 @@ Groups of shell commands or LAMMPS input script or C/C++/Python source
code should be typeset into a `.. code-block::` section. A syntax
highlighting extension for LAMMPS input scripts is provided, so `LAMMPS`
can be used to indicate the language in the code block in addition to
`bash`, `c`, `c++`, `console`, `csh`, `diff', `fortran`, `json`, `make`,
`bash`, `c`, `c++`, `console`, `csh`, `diff`, `fortran`, `json`, `make`,
`perl`, `powershell`, `python`, `sh`, or `tcl`, `text`, or `yaml`. When
no syntax style is indicated, no syntax highlighting is performed. When
typesetting commands executed on the shell, please do not prefix
@ -84,7 +83,7 @@ block can be used, followed by multiple `.. tab::` blocks, one
for each alternative. This is only used for HTML output. For other
outputs, the `.. tabs::` directive is transparently removed and
the individual `.. tab::` blocks will be replaced with an
`.. admonition::`` block. Thus in PDF and ePUB output those will
`.. admonition::` block. Thus in PDF and ePUB output those will
be realized as sequential and plain notes.
Special remarks can be highlighted with a `.. note::` block and

15
doc/github-development-workflow.md
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@ -6,7 +6,9 @@ choices the LAMMPS developers have agreed on. Git and GitHub provide the
tools, but do not set policies, so it is up to the developers to come to
an agreement as to how to define and interpret policies. This document
is likely to change as our experiences and needs change, and we try to
adapt it accordingly. Last change 2023-02-10.
adapt it accordingly.
Last change: 2023-02-10
## Table of Contents
@ -72,7 +74,7 @@ be assigned to signal urgency to merge this pull request quickly.
People can be assigned to review a pull request in two ways:
* They can be assigned manually to review a pull request
by the submitter or a LAMMPS developer
by the submitter or a LAMMPS developer.
* They can be automatically assigned, because a developer's GitHub
handle matches a file pattern in the `.github/CODEOWNERS` file,
which associates developers with the code they contributed and
@ -86,9 +88,9 @@ required before merging, in addition to passing all automated
compilation and unit tests. Merging counts as implicit approval, so
does submission of a pull request (by a LAMMPS developer). So the person
doing the merge may not also submit an approving review. The GitHub
feature, that reviews from code owners are "hard" reviews (i.e. they
must all approve before merging is allowed), is currently disabled.
It is in the discretion of the merge maintainer to assess when a
feature that reviews from code owners are "hard" reviews (i.e. they
must all approve before merging is allowed) is currently disabled.
It is at the discretion of the merge maintainer to assess when a
sufficient degree of approval has been reached, especially from external
collaborators. Reviews may be (automatically) dismissed, when the
reviewed code has been changed. Review may be requested a second time.
@ -147,7 +149,8 @@ only contain bug fixes, feature additions to peripheral functionality,
and documentation updates. In between stable releases, bug fixes and
infrastructure updates are back-ported from the "develop" branch to the
"maintenance" branch and occasionally merged into "stable" and published
as update releases.
as update releases. Further explanation of LAMMPS versions can be found
[in the documentation](https://docs.lammps.org/Manual_version.html).
## Project Management

8
doc/src/fix_adapt.rst
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@ -119,6 +119,14 @@ style supports it. Note that the :doc:`pair_style <pair_style>` and
to specify these parameters initially; the fix adapt command simply
overrides the parameters.
.. note::
Pair_coeff settings must be made **explicitly** in order for fix
adapt to be able to change them. Settings inferred from mixing
are not suitable. If necessary all mixed settings can be output
to a file using the :doc:`write_coeff command <write_coeff>` and
then the desired mixed pair_coeff settings copied from that file.
The *pstyle* argument is the name of the pair style. If
:doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is used,
*pstyle* should be a sub-style name. If there are multiple

22
doc/src/fix_adapt_fep.rst
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@ -116,12 +116,22 @@ style supports it. Note that the :doc:`pair_style <pair_style>` and
to specify these parameters initially; the fix adapt command simply
overrides the parameters.
The *pstyle* argument is the name of the pair style. If :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is used, *pstyle* should be
a sub-style name. For example, *pstyle* could be specified as "soft"
or "lubricate". The *pparam* argument is the name of the parameter to
change. This is the current list of pair styles and parameters that
can be varied by this fix. See the doc pages for individual pair
styles and their energy formulas for the meaning of these parameters:
.. note::
Pair_coeff settings must be made **explicitly** in order for fix
adapt/fep to be able to change them. Settings inferred from mixing
are not suitable. If necessary all mixed settings can be output
to a file using the :doc:`write_coeff command <write_coeff>` and
then the desired mixed pair_coeff settings copied from that file.
The *pstyle* argument is the name of the pair style. If
:doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is used,
*pstyle* should be a sub-style name. For example, *pstyle* could be
specified as "soft" or "lubricate". The *pparam* argument is the name
of the parameter to change. This is the current list of pair styles and
parameters that can be varied by this fix. See the doc pages for
individual pair styles and their energy formulas for the meaning of
these parameters:
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`born <pair_born>` | a,b,c | type pairs |

13
doc/src/fix_colvars.rst
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@ -1,8 +1,11 @@
.. index:: fix colvars
.. index:: fix colvars/kk
fix colvars command
===================
Accelerator Variants: *colvars/kk*
Syntax
""""""
@ -118,6 +121,16 @@ thermostat target temperature.
The *seed* keyword contains the seed for the random number generator
that will be used in the colvars module.
----------
.. note::
Fix colvars/kk is not really ported to KOKKOS, since the colvars
library has not been ported to KOKKOS. It merely has some
optimizations to reduce the data transfers between host and device
for KOKKOS with GPUs.
----------
Restarting
""""""""""

23
doc/src/fix_spring_self.rst
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@ -13,7 +13,7 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command
* spring/self = style name of this fix command
* K = spring constant (force/distance units)
* K = spring constant (force/distance units), can be a variable (see below)
* dir = xyz, xy, xz, yz, x, y, or z (optional, default: xyz)
Examples
@ -22,6 +22,7 @@ Examples
.. code-block:: LAMMPS
fix tether boundary-atoms spring/self 10.0
fix var all spring/self v_kvar
fix zrest move spring/self 10.0 z
Description
@ -42,6 +43,22 @@ directions, but it can be limited to the xy-, xz-, yz-plane and the
x-, y-, or z-direction, thus restraining the atoms to a line or a
plane, respectively.
The force constant *k* can be specified as an equal-style or atom-style
:doc:`variable <variable>`. If the value is a variable, it should be specified
as v_name, where name is the variable name. In this case, the variable
will be evaluated each time step, and its value(s) will be used as
force constant for the spring force.
Equal-style variables can specify formulas with various mathematical
functions and include :doc:`thermo_style <thermo_style>` command
keywords for the simulation box parameters, time step, and elapsed time.
Thus, it is easy to specify a time-dependent force field.
Atom-style variables can specify the same formulas as equal-style
variables but can also include per-atom values, such as atom
coordinates. Thus, it is easy to specify a spatially-dependent force
field with optional time-dependence as well.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@ -89,7 +106,9 @@ invoked by the :doc:`minimize <minimize>` command.
Restrictions
""""""""""""
none
The KOKKOS version, *fix spring/self/kk* may only be used with a constant
value of K, not a variable.
Related commands
""""""""""""""""

9
doc/utils/check-styles.py
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@ -73,8 +73,6 @@ omp = re.compile("(.+)/omp\\s*$")
opt = re.compile("(.+)/opt\\s*$")
removed = re.compile("(.*)Deprecated$")
accel_pattern = re.compile(r"^.. include::\s+accel_styles.rst$")
def require_accel_include(path):
found = False
needs = False
@ -94,6 +92,7 @@ def require_accel_include(path):
if kokkos.match(line): needs = True
if intel.match(line): needs = True
if opt.match(line): needs = True
if path == "src/fix_colvars.rst": needs = False
m = cmd_pattern.match(line)
if m:
if gpu.match(line): needs = True
@ -167,7 +166,9 @@ def check_style(filename, dirname, pattern, styles, name, suffix=False, skip=set
# known undocumented aliases we need to skip
if c in skip: continue
s = c
if suffix: s = add_suffix(styles, c)
if suffix:
s = add_suffix(styles, c)
if s == 'colvars (k)' : continue
if not s in matches:
if not styles[c]['removed']:
print(f"{name} style entry {s} is missing or incomplete in {filename}")
@ -300,7 +301,7 @@ for command_type, entries in index.items():
print("Total number of style index entries:", total_index)
skip_angle = ('sdk')
skip_fix = ('python', 'NEIGH_HISTORY/omp','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species', 'pimd')
skip_fix = ('python', 'NEIGH_HISTORY/omp','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species', 'pimd', 'colvars/kk')
skip_pair = ('meam/c','lj/sf','reax/c','lj/sdk','lj/sdk/coul/long','lj/sdk/coul/msm')
skip_compute = ('pressure/cylinder')

3
src/KOKKOS/fix_spring_self_kokkos.cpp
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@ -79,6 +79,9 @@ void FixSpringSelfKokkos<DeviceType>::init()
{
FixSpringSelf::init();
if (kstyle != CONSTANT)
error->all(FLERR, "Fix spring/self/kk does not support variable spring constants (yet)");
if (utils::strmatch(update->integrate_style,"^respa"))
error->all(FLERR,"Cannot (yet) use respa with Kokkos");
}

10
src/MANYBODY/pair_sw_angle_table.cpp
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@ -402,14 +402,18 @@ void PairSWAngleTable::threebody_table(Param *paramij, Param *paramik, ParamTabl
rinv12 = 1.0/(r1*r2);
cs = (delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2]) * rinv12;
var = acos(cs);
cs = MAX(-1.0,MIN(cs,1.0));
// look up energy (f(theta), ftheta) and force (df(theta)/dtheta, fprimetheta) at
// angle theta (var) in angle table belonging to parameter set paramijk
var = acos(cs);
uf_lookup(table_paramijk, var, ftheta, fprimetheta);
acosprime = 1.0 / (sqrt(1 - cs*cs ) );
if ((cs*cs - 1.0) != 0.0)
acosprime = 1.0 / (sqrt(1 - cs*cs ) );
else
acosprime = 0.0;
facradtable = facexp*ftheta;
frad1table = facradtable*gsrainvsq1;

4
src/OPENMP/pair_reaxff_omp.cpp
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@ -106,7 +106,9 @@ void PairReaxFFOMP::init_style()
auto acks2_fixes = modify->get_fix_by_style("^acks2/reax");
int have_qeq = modify->get_fix_by_style("^qeq/reax").size()
+ modify->get_fix_by_style("^qeq/shielded").size() + acks2_fixes.size();
+ modify->get_fix_by_style("^qeq/shielded").size() + acks2_fixes.size()
+ modify->get_fix_by_style("^qtpie/reax").size();
if (qeqflag && (have_qeq != 1))
error->all(FLERR,"Pair style reaxff/omp requires use of exactly one of the "

2
src/REAXFF/fix_qeq_reaxff.cpp
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@ -344,7 +344,7 @@ void FixQEqReaxFF::allocate_matrix()
int mincap;
double safezone;
if (reaxflag) {
if (reaxflag && reaxff) {
mincap = reaxff->api->system->mincap;
safezone = reaxff->api->system->safezone;
} else {

6
src/REAXFF/fix_qtpie_reaxff.cpp
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@ -199,7 +199,9 @@ void FixQtpieReaxFF::pertype_parameters(char *arg)
if (comm->me == 0) {
gauss_exp[0] = 0.0;
try {
TextFileReader reader(gauss_file,"qtpie/reaxff gaussian exponents");
FILE *fp = utils::open_potential(gauss_file, lmp, nullptr);
if (!fp) throw TokenizerException("Fix qtpie/reaxff: could not open gauss file", gauss_file);
TextFileReader reader(fp,"qtpie/reaxff gaussian exponents");
reader.ignore_comments = true;
for (int i = 1; i <= ntypes; i++) {
const char *line = reader.next_line();
@ -370,7 +372,7 @@ void FixQtpieReaxFF::allocate_matrix()
int mincap;
double safezone;
if (reaxflag) {
if (reaxflag && reaxff) {
mincap = reaxff->api->system->mincap;
safezone = reaxff->api->system->safezone;
} else {

8
src/REAXFF/fix_qtpie_reaxff.h
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@ -81,16 +81,16 @@ class FixQtpieReaxFF : public Fix {
double *Hdia_inv;
double *b_s, *b_t;
double *b_prc, *b_prm;
double *chi_eff; // array of effective electronegativities
double *chi_eff; // array of effective electronegativities
//CG storage
double *p, *q, *r, *d;
int imax, maxwarn;
char *pertype_option; // argument to determine how per-type info is obtained
char *gauss_file; // input file for gaussian orbital exponents
double *gauss_exp; // array of gaussian orbital exponents for each atom type
double dist_cutoff; // separation distance beyond which to neglect overlap integrals
char *gauss_file; // input file for gaussian orbital exponents
double *gauss_exp; // array of gaussian orbital exponents for each atom type
double dist_cutoff; // separation distance beyond which to neglect overlap integrals
void pertype_parameters(char *);
void init_shielding();

10
src/REAXFF/fix_reaxff_species.cpp
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@ -143,9 +143,10 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
x0 = nullptr;
clusterID = nullptr;
int ntmp = 1;
int ntmp = atom->nmax;
memory->create(x0, ntmp, "reaxff/species:x0");
memory->create(clusterID, ntmp, "reaxff/species:clusterID");
memset(clusterID, 0, sizeof(double) * ntmp);
vector_atom = clusterID;
nmax = 0;
@ -193,8 +194,7 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
if (iarg + ntypes + 1 > narg)
utils::missing_cmd_args(FLERR, "fix reaxff/species element", error);
for (int i = 0; i < ntypes; i++)
eletype[i] = arg[iarg + 1 + i];
for (int i = 0; i < ntypes; i++) eletype[i] = arg[iarg + 1 + i];
GetUniqueElements();
iarg += ntypes + 1;
@ -348,8 +348,7 @@ void FixReaxFFSpecies::setup(int /*vflag*/)
ntotal = static_cast<int>(atom->natoms);
if (!eleflag) {
for (int i = 0; i < ntypes; i++)
eletype[i] = reaxff->eletype[i+1];
for (int i = 0; i < ntypes; i++) eletype[i] = reaxff->eletype[i + 1];
GetUniqueElements();
}
memory->destroy(Name);
@ -441,6 +440,7 @@ void FixReaxFFSpecies::Output_ReaxFF_Bonds(bigint ntimestep, FILE * /*fp*/)
memory->destroy(clusterID);
memory->create(x0, nmax, "reaxff/species:x0");
memory->create(clusterID, nmax, "reaxff/species:clusterID");
memset(clusterID, 0, sizeof(double) * nmax);
vector_atom = clusterID;
}

2
src/command.h
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@ -20,7 +20,7 @@ namespace LAMMPS_NS {
class Command : protected Pointers {
public:
Command(class LAMMPS *lmp) : Pointers(lmp) {};
Command(class LAMMPS *lmp) : Pointers(lmp), copymode(0) {};
virtual void command(int, char **) = 0;
protected:

105
src/fix_spring_self.cpp
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@ -21,9 +21,11 @@
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "input.h"
#include "memory.h"
#include "respa.h"
#include "update.h"
#include "variable.h"
#include <cstring>
@ -33,8 +35,7 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixSpringSelf::FixSpringSelf(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
xoriginal(nullptr)
Fix(lmp, narg, arg), xoriginal(nullptr), kstr(nullptr), kval(nullptr)
{
if ((narg < 4) || (narg > 5))
error->all(FLERR,"Illegal fix spring/self command");
@ -45,9 +46,17 @@ FixSpringSelf::FixSpringSelf(LAMMPS *lmp, int narg, char **arg) :
extscalar = 1;
energy_global_flag = 1;
respa_level_support = 1;
maxatom = 0;
kvar = -1;
k = utils::numeric(FLERR,arg[3],false,lmp);
if (k <= 0.0) error->all(FLERR,"Illegal fix spring/self command");
if (utils::strmatch(arg[3], "^v_")) {
kstr = utils::strdup(arg[3] + 2);
kstyle = NONE;
} else {
k = utils::numeric(FLERR,arg[3],false,lmp);
kstyle = CONSTANT;
if (k <= 0.0) error->all(FLERR,"Illegal force constant for fix spring/self command");
}
xflag = yflag = zflag = 1;
@ -103,8 +112,10 @@ FixSpringSelf::~FixSpringSelf()
atom->delete_callback(id,Atom::GROW);
atom->delete_callback(id,Atom::RESTART);
// delete locally stored array
// delete locally stored arrays
delete[] kstr;
memory->destroy(kval);
memory->destroy(xoriginal);
}
@ -123,6 +134,25 @@ int FixSpringSelf::setmask()
void FixSpringSelf::init()
{
// check variable
if (kstr) {
kvar = input->variable->find(kstr);
if (kvar < 0) error->all(FLERR, "Variable {} for fix spring/self does not exist", kstr);
if (input->variable->equalstyle(kvar))
kstyle = EQUAL;
else if (input->variable->atomstyle(kvar))
kstyle = ATOM;
else
error->all(FLERR, "Variable {} for fix spring/self is invalid style", kstr);
}
if ((kstyle == ATOM) && (atom->nmax > maxatom)) {
maxatom = atom->nmax;
memory->destroy(kval);
memory->create(kval, maxatom, "sprint/self:kval");
}
if (utils::strmatch(update->integrate_style,"^respa")) {
ilevel_respa = (dynamic_cast<Respa *>(update->integrate))->nlevels-1;
if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa);
@ -162,24 +192,58 @@ void FixSpringSelf::post_force(int /*vflag*/)
double dx,dy,dz;
double unwrap[3];
// reallocate kval array if necessary
if ((kstyle == ATOM) && (atom->nmax > maxatom)) {
maxatom = atom->nmax;
memory->destroy(kval);
memory->create(kval, maxatom, "sprint/self:kval");
}
espring = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - xoriginal[i][0];
dy = unwrap[1] - xoriginal[i][1];
dz = unwrap[2] - xoriginal[i][2];
if (!xflag) dx = 0.0;
if (!yflag) dy = 0.0;
if (!zflag) dz = 0.0;
f[i][0] -= k*dx;
f[i][1] -= k*dy;
f[i][2] -= k*dz;
espring += k * (dx*dx + dy*dy + dz*dz);
if ((kstyle == CONSTANT) || (kstyle == EQUAL)) {
// update k if equal style variable
if (kstyle == EQUAL) {
k = input->variable->compute_equal(kvar);
if (k < 0.0)
error->all(FLERR,"Evaluation of {} gave bad value {} for fix spring/self", kstr, k);
}
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - xoriginal[i][0];
dy = unwrap[1] - xoriginal[i][1];
dz = unwrap[2] - xoriginal[i][2];
if (!xflag) dx = 0.0;
if (!yflag) dy = 0.0;
if (!zflag) dz = 0.0;
f[i][0] -= k*dx;
f[i][1] -= k*dy;
f[i][2] -= k*dz;
espring += k * (dx*dx + dy*dy + dz*dz);
}
espring *= 0.5;
} else {
// update kval for kstyle == ATOM
input->variable->compute_atom(kvar, igroup, kval, 1, 0);
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - xoriginal[i][0];
dy = unwrap[1] - xoriginal[i][1];
dz = unwrap[2] - xoriginal[i][2];
if (!xflag) dx = 0.0;
if (!yflag) dy = 0.0;
if (!zflag) dz = 0.0;
f[i][0] -= kval[i]*dx;
f[i][1] -= kval[i]*dy;
f[i][2] -= kval[i]*dz;
espring += kval[i] * (dx*dx + dy*dy + dz*dz);
}
espring *= 0.5;
espring *= 0.5;
}
}
/* ---------------------------------------------------------------------- */
@ -213,7 +277,8 @@ double FixSpringSelf::compute_scalar()
double FixSpringSelf::memory_usage()
{
double bytes = (double)atom->nmax*3 * sizeof(double);
double bytes = (double)atom->nmax*4 * sizeof(double);
if (kstyle == ATOM) bytes += (double)atom->nmax * sizeof(double);
return bytes;
}

6
src/fix_spring_self.h
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@ -26,6 +26,7 @@ namespace LAMMPS_NS {
class FixSpringSelf : public Fix {
public:
enum { NONE, CONSTANT, EQUAL, ATOM };
FixSpringSelf(class LAMMPS *, int, char **);
~FixSpringSelf() override;
int setmask() override;
@ -50,8 +51,11 @@ class FixSpringSelf : public Fix {
protected:
double k, espring;
double **xoriginal; // original coords of atoms
char *kstr; // name of variable for K
double *kval; // per-atom variable values for K
int kvar, kstyle;
int xflag, yflag, zflag;
int ilevel_respa;
int ilevel_respa, maxatom;
};
} // namespace LAMMPS_NS

6
src/label_map.cpp
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@ -43,8 +43,6 @@ LabelMap::LabelMap(LAMMPS *_lmp, int _natomtypes, int _nbondtypes, int _nanglety
Pointers(_lmp), natomtypes(_natomtypes), nbondtypes(_nbondtypes), nangletypes(_nangletypes),
ndihedraltypes(_ndihedraltypes), nimpropertypes(_nimpropertypes)
{
if (lmp->citeme) lmp->citeme->add(cite_type_label_framework);
lmap2lmap.atom = lmap2lmap.bond = lmap2lmap.angle = lmap2lmap.dihedral = lmap2lmap.improper =
nullptr;
reset_type_labels();
@ -112,6 +110,8 @@ void LabelMap::modify_lmap(int narg, char **arg)
if ((narg < 1) || ((narg > 2) && ((narg % 2) == 0)))
error->all(FLERR, "Incorrect number of arguments for labelmap command");
if (lmp->citeme) lmp->citeme->add(cite_type_label_framework);
int ntypes;
std::vector<std::string> *labels;
std::unordered_map<std::string, int> *labels_map;
@ -238,6 +238,8 @@ int LabelMap::find_or_create(const std::string &mylabel, std::vector<std::string
auto search = labels_map.find(mylabel);
if (search != labels_map.end()) return search->second;
if (lmp->citeme) lmp->citeme->add(cite_type_label_framework);
// if no match found, create new label at next available index
// label map assumed to be intialized with numeric index
// user labels are assumed to be alphanumeric (not a number)

177
unittest/force-styles/tests/atomic-pair-reaxff-qtpie.yaml Normal file
View File

@ -0,0 +1,177 @@
---
lammps_version: 29 Aug 2024
tags: slow, unstable
date_generated: Fri Nov 15 13:22:57 2024
epsilon: 2e-10
skip_tests: kokkos_omp
prerequisites: ! |
pair reaxff
fix qtpie/reaxff
pre_commands: ! |
echo screen
variable newton_pair delete
variable newton_pair index on
atom_modify map array
units real
atom_style charge
lattice diamond 3.77
region box block 0 2 0 2 0 2
create_box 3 box
create_atoms 1 box
displace_atoms all random 0.1 0.1 0.1 623426
mass 1 1.0
mass 2 12.0
mass 3 16.0
set type 1 type/fraction 2 0.5 998877
set type 2 type/fraction 3 0.5 887766
set type 1 charge 0.00
set type 2 charge 0.01
set type 3 charge -0.01
velocity all create 100 4534624 loop geom
post_commands: ! |
fix qeq all qtpie/reaxff 1 0.0 8.0 1.0e-20 reaxff ${input_dir}/gauss_exp.txt
input_file: in.empty
pair_style: reaxff NULL checkqeq yes
pair_coeff: ! |
* * ffield.reax.mattsson H C O
extract: ! ""
natoms: 64
init_vdwl: -3296.3503506624793
init_coul: -268.63677950571287
init_stress: ! |-
-1.0115766891336298e+03 -1.2088131753999489e+03 -8.2791874767348656e+02 -2.3899453277851464e+02 1.9901049958702231e+02 -6.5090424115686358e+02
init_forces: ! |2
1 -8.6436073169042203e+01 -2.4400814471028966e+01 1.0905778351740135e+02
2 -1.0912360851161381e+02 -1.7785390915789219e+02 -2.2174396944101937e+02
3 -1.7205686042941795e+02 1.8323463801374010e+02 1.3330073949860362e+01
4 3.5074883698050790e+01 -5.4658573523678996e+01 8.8946983653047340e+01
5 1.8037666038924445e+02 1.5258130212658664e+01 -8.1473951707266664e+01
6 1.3687016587487102e+02 -2.9993359047535205e+02 3.1610843762057812e+01
7 -5.3040478511967407e+01 -1.2906564054460426e+02 -1.6364626011721845e+02
8 -1.5098093043741406e+02 4.1651970160590970e+01 1.5340103366817354e+02
9 1.7340129928959293e+01 8.8054766076132950e+01 2.4310262794648661e+01
10 8.3732473664111822e+01 1.4163802420547773e+02 1.2086953212785974e+02
11 -4.2433035390388874e+01 6.5812517236648006e+01 1.3461956725415703e+02
12 -9.6266601388748128e+01 -2.5379001755851835e+01 7.7659919394842500e+00
13 -6.5393078499150931e+01 -4.9454699468880946e+01 -3.8254305288102898e+01
14 8.2607951316806449e+01 -6.8984439086417567e+01 -9.2468559306204710e+01
15 -6.6187434150450684e+01 2.1289685674401704e+02 7.8580288164394176e+01
16 1.8897543273751987e+02 5.3397684583320228e+01 6.3460608305143431e+01
17 1.4554759813765031e+02 -3.9370375612854211e+01 -9.7056561289015221e+01
18 -4.5104710861585204e+01 -1.8896520586433442e+02 1.1164278206176432e+02
19 2.6896526778434691e+02 3.6948523216182610e+02 -3.3986956263391414e+02
20 -7.5462858727084978e+01 -8.6024949892680127e+01 -4.6529428267542672e-01
21 -7.3095936427312608e+01 -5.7463824581552551e+01 -1.1787940398446622e+02
22 1.5517223233172072e+02 -1.2975611741340879e+02 8.0541352960578152e+01
23 7.9113780255105098e+01 -1.3159747874504722e+01 -2.5876270623789040e+01
24 -2.0721357932150298e+02 2.1426998940883044e+02 -1.2404916276617425e+02
25 -1.1375172605965993e+02 1.9145650691697844e+02 -8.3221527665980318e+01
26 2.8613004810395404e+02 -2.1814761019305757e+02 2.3221022419460809e+02
27 -6.4957092731555079e+01 6.8730894090822545e+01 1.7879679090575814e+02
28 -3.5591147454501368e+00 3.8919120211497962e+01 3.2899891202019738e+01
29 -7.1006654872719238e+01 3.4395396834237154e+01 2.5490290273424105e+01
30 -1.7028325267142560e+02 -1.9865767607180553e+02 -1.1525322636144483e+02
31 -1.4030343203666592e+02 1.6505252880438636e+02 -1.2536824728321348e+02
32 2.8083940532792852e+01 -5.9613080258602423e+01 -1.7589243121123940e+02
33 -6.0786787938223988e+01 -6.2914083425882403e+01 6.1724187337270543e+01
34 -2.2381506031982109e+01 1.0258481649700494e+02 -7.2581426601092289e+01
35 2.6826897000164860e+02 -2.1830766483611634e+02 1.2929910897210587e+02
36 1.0617788606545010e+02 1.8844480945948908e+02 -1.9952637621677195e+02
37 -1.8500771626166176e+02 1.2691494490100189e+02 -6.1799194093629900e+01
38 -2.9568079732966703e+02 1.0466330586524869e+02 1.5539102098367138e+02
39 9.0313772894092821e+01 -5.7763893527493209e+01 2.4405485803219346e+01
40 2.0368385039374967e+01 -1.0212243725288241e+02 5.8977256992383225e+01
41 -5.4472403223120203e+01 1.3664060494004097e+01 -7.0498722233072925e+01
42 -1.0110613172512772e+02 3.7733470557342038e+01 -7.1384152705391784e+01
43 2.2496360806160274e+02 9.5374846176895645e+01 1.2314600313131321e+02
44 8.9930414141415653e+01 -9.8548000406723986e+01 -8.6016793720029909e+01
45 1.8042451487789609e+01 1.2291681595021672e+02 4.8750513798444771e+01
46 1.4360528923605511e+01 -2.8393705665522205e+01 2.5000665776800748e+01
47 3.3430180733495789e+01 -1.9134003719608592e+02 -6.9378872162649785e+01
48 6.5977481507414737e+01 -2.0569144157798024e+02 -2.3305633430859448e+01
49 -3.6805309882726834e+02 -2.5080697208449138e+01 1.0725330582435194e+02
50 3.3568380074196661e+01 -7.2887959381521910e+01 8.4247363622347109e+01
51 1.3937571489940009e+02 -1.0241922204671263e+02 1.5837793886668237e+02
52 -1.1015736921987484e+02 1.2143381508599626e+02 -1.3301954780997897e+02
53 -5.5053511032747757e+01 3.3318719859853354e+02 -5.4695756604566270e-02
54 -9.3809048702850468e+00 6.3003589530582012e+01 1.8485428176102951e+02
55 1.1268442794862931e+02 -1.7912573126673601e+02 7.6216834182693233e+01
56 -4.5797371929680743e+01 -1.3685285921363297e+02 4.1670118112644616e+01
57 9.5486141883804535e+01 7.3675172824019725e+01 -6.4017779318177091e+01
58 -2.6940387352055815e+01 -9.1882719416077734e+00 -1.6496876672222488e+01
59 -6.1110604213739784e+01 1.0339564891274583e+02 8.0387279300896552e+01
60 -1.3438307290047304e+01 6.2821560489016619e+01 -1.4960910695536089e+02
61 -3.7436807177941901e+01 -1.0060440409572418e+02 -7.2129567761936670e+01
62 1.5913069360497735e+01 -7.4587444709681003e+00 2.7411930168532034e+01
63 1.3132402121938716e+02 -1.2633666867998599e+02 -5.9237822651056007e+01
64 1.0528416436964088e+02 1.1185676743727093e+02 7.6927706681792429e+01
run_vdwl: -3296.3468820327244
run_coul: -268.63661874354375
run_stress: ! |-
-1.0114879837664473e+03 -1.2087430287015966e+03 -8.2783958944769802e+02 -2.3908224870200783e+02 1.9895929948999779e+02 -6.5093393277361292e+02
run_forces: ! |2
1 -8.6437645087040067e+01 -2.4400562180957351e+01 1.0906066254553539e+02
2 -1.0912275665241053e+02 -1.7786252590616218e+02 -2.2173930761917526e+02
3 -1.7205763157578019e+02 1.8323288100722453e+02 1.3329429976402201e+01
4 3.5076762638460409e+01 -5.4659870228622246e+01 8.8949923949362500e+01
5 1.8037851727311079e+02 1.5258819157296621e+01 -8.1471824505046186e+01
6 1.3693758232722558e+02 -2.9996076554788232e+02 3.1544103577304767e+01
7 -5.3040940882157734e+01 -1.2906590024224255e+02 -1.6365072194268137e+02
8 -1.5098199162393547e+02 4.1652246872814757e+01 1.5340185354669362e+02
9 1.7338937131206805e+01 8.8052623671376480e+01 2.4311464733168261e+01
10 8.3731216255426517e+01 1.4163544349001512e+02 1.2086773194932107e+02
11 -4.2431645167783358e+01 6.5809284879610303e+01 1.3461058585127651e+02
12 -9.6268502974108401e+01 -2.5380508031933715e+01 7.7613919613213387e+00
13 -6.5394480799184038e+01 -4.9454690134569510e+01 -3.8251921533789378e+01
14 8.2607648143581144e+01 -6.8981518310093449e+01 -9.2465919648906919e+01
15 -6.6184911564685194e+01 2.1289827790699042e+02 7.8579764996083128e+01
16 1.8897212100631526e+02 5.3401557991805042e+01 6.3454265397142500e+01
17 1.4554879673647156e+02 -3.9369818695332363e+01 -9.7059433050641857e+01
18 -4.5104364652465691e+01 -1.8896630466961875e+02 1.1164283921546559e+02
19 2.6896544439509694e+02 3.6948380976016932e+02 -3.3986849873937234e+02
20 -7.5474652635907873e+01 -8.6015213272245504e+01 -4.8259676480768809e-01
21 -7.3095940937548960e+01 -5.7464788467137694e+01 -1.1787855066724634e+02
22 1.5517351794732136e+02 -1.2975689546114967e+02 8.0540859481818742e+01
23 7.9115865455975012e+01 -1.3150472802357561e+01 -2.5876503956346053e+01
24 -2.0722276003223385e+02 2.1428270990874043e+02 -1.2405357611708547e+02
25 -1.1375429959489580e+02 1.9146061264686494e+02 -8.3222256641294663e+01
26 2.8613970510624404e+02 -2.1815485596507278e+02 2.3221441960858138e+02
27 -6.4953545994003377e+01 6.8732504333245046e+01 1.7879777515705371e+02
28 -3.5609706858523174e+00 3.8914845051174211e+01 3.2895014258375397e+01
29 -7.1006962970615220e+01 3.4395946962585107e+01 2.5490302918559674e+01
30 -1.7028397298399719e+02 -1.9865780309887722e+02 -1.1525330878428163e+02
31 -1.4030595583104076e+02 1.6505149109610096e+02 -1.2536961295119134e+02
32 2.8084746879715730e+01 -5.9606705649399501e+01 -1.7588207877218977e+02
33 -6.0786242960574022e+01 -6.2913885176828828e+01 6.1724433850103161e+01
34 -2.2381168039316268e+01 1.0258398798459802e+02 -7.2580420302975753e+01
35 2.6830990081622787e+02 -2.1835204404249015e+02 1.2931018843147504e+02
36 1.0617963217845744e+02 1.8843796909876622e+02 -1.9952176446060335e+02
37 -1.8503402227685811e+02 1.2695504061699209e+02 -6.1823411355500355e+01
38 -2.9568399770704622e+02 1.0466662636959578e+02 1.5539009610875451e+02
39 9.0314570392701199e+01 -5.7764115394488343e+01 2.4405095735494033e+01
40 2.0369156227530599e+01 -1.0212187254286960e+02 5.8977622919450276e+01
41 -5.4470510869266015e+01 1.3662227244573693e+01 -7.0490380604491506e+01
42 -1.0110530047858049e+02 3.7731202989968210e+01 -7.1386374496910719e+01
43 2.2495960799582232e+02 9.5372714343303912e+01 1.2314241456430595e+02
44 8.9934882887196963e+01 -9.8543527246862695e+01 -8.6022172212180365e+01
45 1.8033520031139599e+01 1.2290938260195539e+02 4.8756688104804162e+01
46 1.4361839506594013e+01 -2.8393917262125949e+01 2.5000422631182474e+01
47 3.3429877782459641e+01 -1.9133540583883391e+02 -6.9377262749149708e+01
48 6.5990004078562464e+01 -2.0569338794984392e+02 -2.3314637198125183e+01
49 -3.6809322631363733e+02 -2.5025981981696823e+01 1.0734144239898833e+02
50 3.3569219922950602e+01 -7.2886698417202680e+01 8.4245785013977056e+01
51 1.3937840161131851e+02 -1.0242257034381630e+02 1.5838167570232804e+02
52 -1.1015632519571759e+02 1.2143397586854937e+02 -1.3302347496060023e+02
53 -5.5089426238213143e+01 3.3316281975316286e+02 -7.4271240172002706e-02
54 -9.3687742955109137e+00 6.2990741970756417e+01 1.8487238090605700e+02
55 1.1268678311310606e+02 -1.7912913164827566e+02 7.6217416717889748e+01
56 -4.5806154616486943e+01 -1.3684453580988600e+02 4.1676759373489766e+01
57 9.5485704227965911e+01 7.3672454441368231e+01 -6.4019152364471736e+01
58 -2.6940596532815384e+01 -9.1863734979434319e+00 -1.6497051289566816e+01
59 -6.1118963218972965e+01 1.0340128135495597e+02 8.0392569432165885e+01
60 -1.3439582130914836e+01 6.2820376074347955e+01 -1.4960914576393716e+02
61 -3.7435810911347573e+01 -1.0060262070691427e+02 -7.2129466739698870e+01
62 1.5913491338811767e+01 -7.4593609075659995e+00 2.7412825126279046e+01
63 1.3132146995609114e+02 -1.2633718643910591e+02 -5.9233334916534574e+01
64 1.0528511106781713e+02 1.1185795842149707e+02 7.6928226208764087e+01
...

77
unittest/force-styles/tests/fix-timestep-spring_self_atom.yaml Normal file
View File

@ -0,0 +1,77 @@
---
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:01 2022
epsilon: 5e-14
skip_tests: kokkos_omp
prerequisites: ! |
atom full
fix spring/self
pre_commands: ! |
variable kvar atom 10.0
post_commands: ! |
fix move all nve
fix test solute spring/self v_kvar xyz
input_file: in.fourmol
natoms: 29
global_scalar: 0.12623705370750438
run_pos: ! |2
1 -2.7045669792379945e-01 2.4912140072031601e+00 -1.6695897908630153e-01
2 3.1003572362014503e-01 2.9612290242130319e+00 -8.5466689099875615e-01
3 -7.0398410505917419e-01 1.2305522448803927e+00 -6.2777452858703953e-01
4 -1.5818137373512378e+00 1.4837442978868092e+00 -1.2538665277734968e+00
5 -9.0719266809604937e-01 9.2652365891304722e-01 3.9954299416556610e-01
6 2.4832271436421161e-01 2.8312320769893828e-01 -1.2314303818391423e+00
7 3.4143518373063453e-01 -2.2645187306940717e-02 -2.5292229406165907e+00
8 1.1743540824610306e+00 -4.8863162985819381e-01 -6.3783828665914544e-01
9 1.3800508883119953e+00 -2.5274565574966718e-01 2.8353436538531862e-01
10 2.0510726036138696e+00 -1.4604027090169940e+00 -9.8323554549077119e-01
11 1.7878052123899795e+00 -1.9921835931655048e+00 -1.8890566136917575e+00
12 3.0063000763288268e+00 -4.9013323763786637e-01 -1.6231890083142151e+00
13 4.0515352007695906e+00 -8.9202569828585798e-01 -1.6399995011867139e+00
14 2.6066952690925067e+00 -4.1788633645045253e-01 -2.6633949696742012e+00
15 2.9695337662435719e+00 5.5423141568538492e-01 -1.2342076641871542e+00
16 2.6747001492056977e+00 -2.4124097322472577e+00 -2.3429048072365732e-02
17 2.2153591049025310e+00 -2.0897997214660862e+00 1.1963106355359285e+00
18 2.1369701704115056e+00 3.0158507413628213e+00 -3.5179348337213843e+00
19 1.5355837136087338e+00 2.6255292355375399e+00 -4.2353987779878857e+00
20 2.7727573005678758e+00 3.6923910449610102e+00 -3.9330842459133470e+00
21 4.9040128073205524e+00 -4.0752348172959030e+00 -3.6210314709893159e+00
22 4.3582355554440877e+00 -4.2126119427287101e+00 -4.4612844196314150e+00
23 5.7439382849307670e+00 -3.5821957939275060e+00 -3.8766361295935892e+00
24 2.0689243582422914e+00 3.1513346907271247e+00 3.1550389754829422e+00
25 1.3045351331492516e+00 3.2665125705842941e+00 2.5111855257434352e+00
26 2.5809237402711318e+00 4.0117602605482858e+00 3.2212060529089945e+00
27 -1.9611343130357277e+00 -4.3563411931359841e+00 2.1098293115523528e+00
28 -2.7473562684513411e+00 -4.0200819932379330e+00 1.5830052163433952e+00
29 -1.3126000191359812e+00 -3.5962518039482934e+00 2.2746342468737817e+00
run_vel: ! |2
1 8.1685220941861477e-03 1.6512578512542727e-02 4.7892799147935001e-03
2 5.4427456394786321e-03 5.1693257879352533e-03 -1.4414043022813649e-03
3 -8.2272458036248362e-03 -1.2923813188884230e-02 -4.0970749471144546e-03
4 -3.7660861920462349e-03 -6.5659911420830365e-03 -1.1120922532834726e-03
5 -1.1012635909013241e-02 -9.8847866026321157e-03 -2.8391869073674538e-03
6 -3.9665990411620729e-02 4.6803722380071487e-02 3.7135522426802389e-02
7 9.1016763589152859e-04 -1.0126055720737583e-02 -5.1556610019025714e-02
8 7.9043585267658430e-03 -3.3496064544244345e-03 3.4549326598010660e-02
9 1.5620907286754389e-03 3.7378245105921431e-03 1.5036774253075934e-02
10 2.9193799040059056e-02 -2.9242248165535563e-02 -1.5014281912567770e-02
11 -4.7797459644718264e-03 -3.7436196398511232e-03 -2.3410499103477603e-03
12 2.2686069875175316e-03 -3.4732729502899497e-04 -3.0627334265471650e-03
13 2.7456854188010020e-03 5.8081889921879817e-03 -7.9308949311655092e-04
14 3.5223319737918667e-03 -5.7842699330258648e-03 -3.9396805101296825e-03
15 -1.8475459117759364e-03 -5.8469790281561471e-03 6.2849983323582511e-03
16 1.8676069228413028e-02 -1.3258381729410438e-02 -4.5625616778429308e-02
17 -1.2893668780819389e-02 9.7505325833410258e-03 3.7288200735675299e-02
18 -8.0065794869105819e-04 -8.6270473288011819e-04 -1.4483040693746142e-03
19 1.2452390836051499e-03 -2.5061097119616180e-03 7.2998631010316650e-03
20 3.5930060229538143e-03 3.6938860309035470e-03 3.2322732687958995e-03
21 -1.4689220366910704e-03 -2.7352129796142532e-04 7.0581624168175334e-04
22 -7.0694199254520765e-03 -4.2577148925037030e-03 2.8079117611209205e-04
23 6.0446963117617505e-03 -1.4000131614895336e-03 2.5819754846773601e-03
24 3.1926367911308686e-04 -9.9445664741642462e-04 1.4999996978363057e-04
25 1.3789754526895179e-04 -4.4335894884219599e-03 -8.1808136698604454e-04
26 2.0485904035342870e-03 2.7813358633902757e-03 4.3245727149365584e-03
27 4.5604120291626942e-04 -1.0305523027244966e-03 2.1188058375789067e-04
28 -6.2544520861839200e-03 1.4127711176141612e-03 -1.8429821884806304e-03
29 6.4110631535703737e-04 3.1273432719578029e-03 3.7253671105604122e-03
...

77
unittest/force-styles/tests/fix-timestep-spring_self_equal.yaml Normal file
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---
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:01 2022
epsilon: 5e-14
skip_tests: kokkos_omp
prerequisites: ! |
atom full
fix spring/self
pre_commands: ! |
variable kvar equal 10.0
post_commands: ! |
fix move all nve
fix test solute spring/self v_kvar xyz
input_file: in.fourmol
natoms: 29
global_scalar: 0.12623705370750438
run_pos: ! |2
1 -2.7045669792379945e-01 2.4912140072031601e+00 -1.6695897908630153e-01
2 3.1003572362014503e-01 2.9612290242130319e+00 -8.5466689099875615e-01
3 -7.0398410505917419e-01 1.2305522448803927e+00 -6.2777452858703953e-01
4 -1.5818137373512378e+00 1.4837442978868092e+00 -1.2538665277734968e+00
5 -9.0719266809604937e-01 9.2652365891304722e-01 3.9954299416556610e-01
6 2.4832271436421161e-01 2.8312320769893828e-01 -1.2314303818391423e+00
7 3.4143518373063453e-01 -2.2645187306940717e-02 -2.5292229406165907e+00
8 1.1743540824610306e+00 -4.8863162985819381e-01 -6.3783828665914544e-01
9 1.3800508883119953e+00 -2.5274565574966718e-01 2.8353436538531862e-01
10 2.0510726036138696e+00 -1.4604027090169940e+00 -9.8323554549077119e-01
11 1.7878052123899795e+00 -1.9921835931655048e+00 -1.8890566136917575e+00
12 3.0063000763288268e+00 -4.9013323763786637e-01 -1.6231890083142151e+00
13 4.0515352007695906e+00 -8.9202569828585798e-01 -1.6399995011867139e+00
14 2.6066952690925067e+00 -4.1788633645045253e-01 -2.6633949696742012e+00
15 2.9695337662435719e+00 5.5423141568538492e-01 -1.2342076641871542e+00
16 2.6747001492056977e+00 -2.4124097322472577e+00 -2.3429048072365732e-02
17 2.2153591049025310e+00 -2.0897997214660862e+00 1.1963106355359285e+00
18 2.1369701704115056e+00 3.0158507413628213e+00 -3.5179348337213843e+00
19 1.5355837136087338e+00 2.6255292355375399e+00 -4.2353987779878857e+00
20 2.7727573005678758e+00 3.6923910449610102e+00 -3.9330842459133470e+00
21 4.9040128073205524e+00 -4.0752348172959030e+00 -3.6210314709893159e+00
22 4.3582355554440877e+00 -4.2126119427287101e+00 -4.4612844196314150e+00
23 5.7439382849307670e+00 -3.5821957939275060e+00 -3.8766361295935892e+00
24 2.0689243582422914e+00 3.1513346907271247e+00 3.1550389754829422e+00
25 1.3045351331492516e+00 3.2665125705842941e+00 2.5111855257434352e+00
26 2.5809237402711318e+00 4.0117602605482858e+00 3.2212060529089945e+00
27 -1.9611343130357277e+00 -4.3563411931359841e+00 2.1098293115523528e+00
28 -2.7473562684513411e+00 -4.0200819932379330e+00 1.5830052163433952e+00
29 -1.3126000191359812e+00 -3.5962518039482934e+00 2.2746342468737817e+00
run_vel: ! |2
1 8.1685220941861477e-03 1.6512578512542727e-02 4.7892799147935001e-03
2 5.4427456394786321e-03 5.1693257879352533e-03 -1.4414043022813649e-03
3 -8.2272458036248362e-03 -1.2923813188884230e-02 -4.0970749471144546e-03
4 -3.7660861920462349e-03 -6.5659911420830365e-03 -1.1120922532834726e-03
5 -1.1012635909013241e-02 -9.8847866026321157e-03 -2.8391869073674538e-03
6 -3.9665990411620729e-02 4.6803722380071487e-02 3.7135522426802389e-02
7 9.1016763589152859e-04 -1.0126055720737583e-02 -5.1556610019025714e-02
8 7.9043585267658430e-03 -3.3496064544244345e-03 3.4549326598010660e-02
9 1.5620907286754389e-03 3.7378245105921431e-03 1.5036774253075934e-02
10 2.9193799040059056e-02 -2.9242248165535563e-02 -1.5014281912567770e-02
11 -4.7797459644718264e-03 -3.7436196398511232e-03 -2.3410499103477603e-03
12 2.2686069875175316e-03 -3.4732729502899497e-04 -3.0627334265471650e-03
13 2.7456854188010020e-03 5.8081889921879817e-03 -7.9308949311655092e-04
14 3.5223319737918667e-03 -5.7842699330258648e-03 -3.9396805101296825e-03
15 -1.8475459117759364e-03 -5.8469790281561471e-03 6.2849983323582511e-03
16 1.8676069228413028e-02 -1.3258381729410438e-02 -4.5625616778429308e-02
17 -1.2893668780819389e-02 9.7505325833410258e-03 3.7288200735675299e-02
18 -8.0065794869105819e-04 -8.6270473288011819e-04 -1.4483040693746142e-03
19 1.2452390836051499e-03 -2.5061097119616180e-03 7.2998631010316650e-03
20 3.5930060229538143e-03 3.6938860309035470e-03 3.2322732687958995e-03
21 -1.4689220366910704e-03 -2.7352129796142532e-04 7.0581624168175334e-04
22 -7.0694199254520765e-03 -4.2577148925037030e-03 2.8079117611209205e-04
23 6.0446963117617505e-03 -1.4000131614895336e-03 2.5819754846773601e-03
24 3.1926367911308686e-04 -9.9445664741642462e-04 1.4999996978363057e-04
25 1.3789754526895179e-04 -4.4335894884219599e-03 -8.1808136698604454e-04
26 2.0485904035342870e-03 2.7813358633902757e-03 4.3245727149365584e-03
27 4.5604120291626942e-04 -1.0305523027244966e-03 2.1188058375789067e-04
28 -6.2544520861839200e-03 1.4127711176141612e-03 -1.8429821884806304e-03
29 6.4110631535703737e-04 3.1273432719578029e-03 3.7253671105604122e-03
...

6
unittest/force-styles/tests/gauss_exp.txt Normal file
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# Gaussian orbital exponents (required for fix qtpie/reaxff) taken from Table 2.2
# of Chen, J. (2009). Theory and applications of fluctuating-charge models.
# The units of the exponents are 1 / (Bohr radius)^2 .
1 0.5434 # H
2 0.2069 # C
3 0.2240 # O