tx258/lammps-gran-kokkos
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge pull request #4519 from fxcoudert/extxyz2

Browse Source 
Add extended XYZ dump style extxyz
This commit is contained in:
Axel Kohlmeyer
2025-04-02 10:59:18 -04:00
committed by GitHub
parent 8defe0e798 c0321b5f00
commit 9f7653dd37
12 changed files with 427 additions and 34 deletions
Download Patch File Download Diff File Expand all files Collapse all files

1
.github/CODEOWNERS vendored
View File

@ -71,6 +71,7 @@ src/EXTRA-COMMAND/group_ndx.* @akohlmey
src/EXTRA-COMMAND/ndx_group.* @akohlmey
src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
src/EXTRA-DUMP/dump_extxyz.* @fxcoudert
src/EXTRA-FIX/fix_deform_pressure.* @jtclemm
src/EXTRA-PAIR/pair_dispersion_d3.* @soniasolomoni @arthurfl
src/EXTRA-PAIR/d3_parameters.h @soniasolomoni @arthurfl

1
doc/src/Commands_dump.rst
View File

@ -19,6 +19,7 @@ An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
* :doc:`custom/gz <dump>`
* :doc:`custom/zstd <dump>`
* :doc:`dcd <dump>`
* :doc:`extxyz <dump>`
* :doc:`grid <dump>`
* :doc:`grid/vtk <dump>`
* :doc:`h5md <dump_h5md>`

59
doc/src/dump.rst
View File

@ -3,6 +3,7 @@
.. index:: dump cfg
.. index:: dump custom
.. index:: dump dcd
.. index:: dump extxyz
.. index:: dump grid
.. index:: dump grid/vtk
.. index:: dump local
@ -59,7 +60,7 @@ Syntax
* ID = user-assigned name for the dump
* group-ID = ID of the group of atoms to be dumped
* style = *atom* or *atom/adios* or *atom/gz* or *atom/zstd* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/adios* or *dcd* or *grid* or *grid/vtk* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *yaml*
* style = *atom* or *atom/adios* or *atom/gz* or *atom/zstd* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/adios* or *dcd* or *extxyz* or *grid* or *grid/vtk* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *yaml*
* N = dump on timesteps which are multiples of N
* file = name of file to write dump info to
* attribute1,attribute2,... = list of attributes for a particular style
@ -77,6 +78,7 @@ Syntax
*custom*, *custom/gz*, *custom/zstd* attributes = see below
*custom/adios* attributes = same as *custom* attributes, discussed on :doc:`dump custom/adios <dump_adios>` page
*dcd* attributes = none
*extxyz* attributes = none
*h5md* attributes = discussed on :doc:`dump h5md <dump_h5md>` page
*grid* attributes = see below
*grid/vtk* attributes = see below
@ -242,28 +244,29 @@ all the processors or multiple smaller files.
frames consistently to the same atom. This can lead to incorrect
visualizations or results. LAMMPS will print a warning in such cases.
For the *atom*, *custom*, *cfg*, *grid*, and *local* styles, sorting
is off by default. For the *dcd*, *grid/vtk*, *xtc*, *xyz*, and
For the *atom*, *custom*, *cfg*, *grid*, and *local* styles, sorting is
off by default. For the *dcd*, *extxyz*, *grid/vtk*, *xtc*, *xyz*, and
*molfile* styles, sorting by atom ID or grid ID is on by default. See
the :doc:`dump_modify <dump_modify>` page for details.
The *style* keyword determines what kind of data is written to the
dump file(s) and in what format.
Note that *atom*, *custom*, *dcd*, *xtc*, *xyz*, and *yaml* style dump
files can be read directly by `VMD <https://www.ks.uiuc.edu/Research/vmd>`_,
a popular tool for visualizing and analyzing trajectories from atomic
and molecular systems. For reading *netcdf* style dump files, the
netcdf plugin needs to be recompiled from source using a NetCDF version
compatible with the one used by LAMMPS. The bundled plugin binary
uses a very old version of NetCDF that is not compatible with LAMMPS.
Note that *atom*, *custom*, *dcd*, *extxyz*, *xtc*, *xyz*, and *yaml*
style dump files can be read directly by `VMD
<https://www.ks.uiuc.edu/Research/vmd>`_, a popular tool for visualizing
and analyzing trajectories from atomic and molecular systems. For
reading *netcdf* style dump files, the netcdf plugin needs to be
recompiled from source using a NetCDF version compatible with the one
used by LAMMPS. The bundled plugin binary uses a very old version of
NetCDF that is not compatible with LAMMPS.
Likewise the `OVITO visualization package <https://www.ovito.org>`_,
popular for materials modeling, can read the *atom*, *custom*,
popular for materials modeling, can read the *atom*, *custom*, *extxyz*,
*local*, *xtc*, *cfg*, *netcdf*, and *xyz* style atom dump files
directly. With version 3.8 and above, OVITO can also read and
visualize *grid* style dump files with grid cell data, including
iso-surface images of the grid cell values.
directly. With version 3.8 and above, OVITO can also read and visualize
*grid* style dump files with grid cell data, including iso-surface
images of the grid cell values.
Note that settings made via the :doc:`dump_modify <dump_modify>`
command can also alter the format of individual values and content of
@ -475,6 +478,24 @@ label). This option will help many visualization programs to guess bonds
and colors. You can use the :doc:`dump_modify types labels <dump_modify>`
option to replace numeric atom types with :doc:`type labels <Howto_type_labels>`.
.. versionadded:: TBD
The *extxyz* style writes XYZ files compatible with the Extended XYZ (or
ExtXYZ) format as defined as defined in `the libAtoms specification
<https://github.com/libAtoms/extxyz>`_. Specifically, the following
information will be dumped:
* timestep
* time, which can be disabled with :doc:`dump_modify time no <dump_modify>`
* simulation box lattice and pbc conditions
* atomic forces, which can be disabled with :doc:`dump_modify forces no <dump_modify>`
* atomic velocities, which can be disabled with :doc:`dump_modify vel no <dump_modify>`
* atomic masses, if enabled with :doc:`dump_modify mass yes <dump_modify>`
Dump style *extxyz* requires either that a :doc:`type label map for atoms types
<labelmap>` is defined or :doc:`dump_modify element <dump_modify>` is used to
set up an atom type number to atom name mapping.
.. versionadded:: 22Dec2022
The *grid/vtk* style writes VTK files for grid data on a regular
@ -607,8 +628,8 @@ with the processor ID from :math:`0` to :math:`P-1`. For example,
tmp.dump.% becomes tmp.dump.0, tmp.dump.1, ... tmp.dump.:math:`P-1`,
etc. This creates smaller files and can be a fast mode of output on
parallel machines that support parallel I/O for output. This option is
**not** available for the *dcd*, *xtc*, *xyz*, *grid/vtk*, and *yaml*
styles.
**not** available for the *dcd*, *extxyz*, *xtc*, *xyz*, *grid/vtk*, and
*yaml* styles.
By default, :math:`P` is the the number of processors, meaning one file per
processor, but :math:`P` can be set to a smaller value via the *nfile* or
@ -1017,9 +1038,9 @@ the COMPRESS package. They are only enabled if LAMMPS was built with
that package. See the :doc:`Build package <Build_package>` page for
more info.
The *xtc*, *dcd*, and *yaml* styles are part of the EXTRA-DUMP package.
They are only enabled if LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` page for more info.
The *dcd*, *extxyz*, *xtc*, and *yaml* styles are part of the EXTRA-DUMP
package. They are only enabled if LAMMPS was built with that package.
See the :doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""

12
doc/src/dump_modify.rst
View File

@ -92,6 +92,15 @@ Syntax
see the :doc:`dump image <dump_image>` doc page for details
* these keywords apply only to the extxyz dump style
* keyword = *forces* or *mass* or *vel*
.. parsed-literal::
*forces* arg = *yes* or *no*
*mass* arg = *yes* or *no*
*vel* arg = *yes* or *no*
* these keywords apply only to the */gz* and */zstd* dump styles
* keyword = *compression_level*
@ -972,9 +981,11 @@ The option defaults are
* fileper = # of processors
* first = no
* flush = yes
* forces = yes
* format = %d and %g for each integer or floating point value
* image = no
* label = ENTRIES
* mass = no
* maxfiles = -1
* nfile = 1
* pad = 0
@ -990,6 +1001,7 @@ The option defaults are
* types = numeric
* units = no
* unwrap = no
* vel = yes
* compression_level = 9 (gz variants)
* compression_level = 0 (zstd variants)

2
src/.gitignore vendored
View File

@ -419,6 +419,8 @@
/compute_hexorder_atom.h
/dump_dcd.cpp
/dump_dcd.h
/dump_extxyz.cpp
/dump_extxyz.h
/fix_controller.cpp
/fix_controller.h
/fix_drag.cpp

296
src/EXTRA-DUMP/dump_extxyz.cpp Normal file
View File

@ -0,0 +1,296 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "dump_extxyz.h"
#include "atom.h"
#include "compute.h"
#include "domain.h"
#include "error.h"
#include "label_map.h"
#include "memory.h"
#include "modify.h"
#include "output.h"
#include "thermo.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
static constexpr int ONELINE = 512;
static constexpr int DELTA = 1048576;
/* ---------------------------------------------------------------------- */
DumpExtXYZ::DumpExtXYZ(LAMMPS *lmp, int narg, char **arg) :
DumpXYZ(lmp, narg, arg), properties_string(nullptr)
{
// style specific customizable settings
with_vel = 1;
with_forces = 1;
with_mass = 0;
with_pe = 1;
with_temp = 1;
with_press = 0;
update_properties();
// We want simulation time by default
time_flag = 1;
// dump may invoke computes
clearstep = 1;
// use type labels by default if present
if (atom->labelmapflag) {
typenames = new char *[ntypes + 1];
for (int itype = 1; itype <= ntypes; itype++) {
typenames[itype] = utils::strdup(atom->lmap->typelabel[itype - 1]);
}
}
}
/* ---------------------------------------------------------------------- */
void DumpExtXYZ::update_properties()
{
// How many per-atom elements we buffer
size_one = 5 + (with_vel ? 3 : 0) + (with_forces ? 3 : 0) + (with_mass ? 1 : 0);
// The properties string
delete[] properties_string;
properties_string = utils::strdup(
fmt::format("species:S:1:pos:R:3{}{}{}", (with_vel ? ":vel:R:3" : ""),
(with_forces ? ":forces:R:3" : ""), (with_mass ? ":mass:R:1" : "")));
// The output printf-style format
delete[] format;
if (format_line_user)
format = utils::strdup(fmt::format("{}\n", format_line_user));
else {
format = utils::strdup(fmt::format("%s %g %g %g{}{}{}\n", (with_vel ? " %g %g %g" : ""),
(with_forces ? " %g %g %g" : ""), (with_mass ? " %g" : "")));
}
}
/* ---------------------------------------------------------------------- */
void DumpExtXYZ::init_style()
{
if (!typenames)
error->all(FLERR, Error::NOLASTLINE,
"Must use either type lables or dump_modify element with dump style extxyz");
DumpXYZ::init_style();
update_properties();
}
/* ---------------------------------------------------------------------- */
int DumpExtXYZ::modify_param(int narg, char **arg)
{
int rv = DumpXYZ::modify_param(narg, arg);
if (rv > 0) return rv;
if (strcmp(arg[0], "vel") == 0) {
if (narg < 2) error->all(FLERR, "Illegal dump_modify command");
with_vel = utils::logical(FLERR, arg[1], false, lmp);
update_properties();
return 2;
}
if (strcmp(arg[0], "forces") == 0) {
if (narg < 2) error->all(FLERR, "Illegal dump_modify command");
with_forces = utils::logical(FLERR, arg[1], false, lmp);
update_properties();
return 2;
}
if (strcmp(arg[0], "mass") == 0) {
if (narg < 2) error->all(FLERR, "Illegal dump_modify command");
with_mass = utils::logical(FLERR, arg[1], false, lmp);
update_properties();
return 2;
}
return 0;
}
/* ---------------------------------------------------------------------- */
void DumpExtXYZ::write_header(bigint n)
{
if (me == 0) {
if (!fp)
error->one(FLERR, Error::NOLASTLINE, "Must not use 'run pre no' after creating a new dump");
std::string header = fmt::format("{}\nTimestep={}", n, update->ntimestep);
if (time_flag) header += fmt::format(" Time={:.6f}", compute_time());
header += fmt::format(" pbc=\"{} {} {}\"", domain->xperiodic ? "T" : "F",
domain->yperiodic ? "T" : "F", domain->zperiodic ? "T" : "F");
header +=
fmt::format(" Lattice=\"{:g} {:g} {:g} {:g} {:g} {:g} {:g} {:g} {:g}\"", domain->xprd, 0.,
0., domain->xy, domain->yprd, 0., domain->xz, domain->yz, domain->zprd);
if (output && output->thermo) {
auto *pe = output->thermo->pe;
if (pe) header += fmt::format(" Potential_energy={}", pe->compute_scalar());
auto *temp = output->thermo->temperature;
if (temp) header += fmt::format(" Temperature={}", temp->compute_scalar());
auto *press = output->thermo->pressure;
if (press) {
press->compute_vector();
header +=
fmt::format(" Stress=\"{} {} {} {} {} {} {} {} {}\"", press->vector[0],
press->vector[3], press->vector[4], press->vector[3], press->vector[1],
press->vector[5], press->vector[4], press->vector[5], press->vector[2]);
}
}
header += fmt::format(" Properties={}", properties_string);
utils::print(fp, header + "\n");
}
}
/* ---------------------------------------------------------------------- */
void DumpExtXYZ::pack(tagint *ids)
{
int m, n;
tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
m = n = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
if (with_vel) {
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
}
if (with_forces) {
buf[m++] = f[i][0];
buf[m++] = f[i][1];
buf[m++] = f[i][2];
}
if (with_mass) {
if (rmass) {
buf[m++] = rmass[i];
} else {
buf[m++] = mass[type[i]];
}
}
if (ids) ids[n++] = tag[i];
}
}
/* ----------------------------------------------------------------------
convert mybuf of doubles to one big formatted string in sbuf
return -1 if strlen exceeds an int, since used as arg in MPI calls in Dump
------------------------------------------------------------------------- */
int DumpExtXYZ::convert_string(int n, double *mybuf)
{
int offset = 0;
int m = 0;
for (int i = 0; i < n; i++) {
if (offset + ONELINE > maxsbuf) {
if ((bigint) maxsbuf + DELTA > MAXSMALLINT) return -1;
maxsbuf += DELTA;
memory->grow(sbuf, maxsbuf, "dump:sbuf");
}
if (size_one == 5) {
offset += snprintf(&sbuf[offset], maxsbuf - offset, format,
typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3],
mybuf[m + 4]);
} else if (size_one == 6) {
offset += snprintf(&sbuf[offset], maxsbuf - offset, format,
typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3],
mybuf[m + 4], mybuf[m + 5]);
} else if (size_one == 8) {
offset += snprintf(&sbuf[offset], maxsbuf - offset, format,
typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3],
mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7]);
} else if (size_one == 9) {
offset += snprintf(&sbuf[offset], maxsbuf - offset, format,
typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3],
mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7], mybuf[m + 8]);
} else if (size_one == 11) {
offset += snprintf(&sbuf[offset], maxsbuf - offset, format,
typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3],
mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7], mybuf[m + 8],
mybuf[m + 9], mybuf[m + 10]);
} else if (size_one == 12) {
offset += snprintf(&sbuf[offset], maxsbuf - offset, format,
typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3],
mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7], mybuf[m + 8],
mybuf[m + 9], mybuf[m + 10], mybuf[m + 11]);
} else {
error->all(FLERR, "Invalid value of size_one for dump extxyz format.");
}
m += size_one;
}
return offset;
}
/* ---------------------------------------------------------------------- */
void DumpExtXYZ::write_lines(int n, double *mybuf)
{
int m = 0;
for (int i = 0; i < n; i++) {
if (size_one == 5) {
fprintf(fp, format, typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3],
mybuf[m + 4]);
} else if (size_one == 6) {
fprintf(fp, format, typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3],
mybuf[m + 4], mybuf[m + 5]);
} else if (size_one == 8) {
fprintf(fp, format, typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3],
mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7]);
} else if (size_one == 9) {
fprintf(fp, format, typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3],
mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7], mybuf[m + 8]);
} else if (size_one == 11) {
fprintf(fp, format, typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3],
mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7], mybuf[m + 8], mybuf[m + 9],
mybuf[m + 10]);
} else if (size_one == 12) {
fprintf(fp, format, typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3],
mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7], mybuf[m + 8], mybuf[m + 9],
mybuf[m + 10], mybuf[m + 11]);
} else {
error->all(FLERR, "Invalid value of size_one for dump extxyz format.");
}
m += size_one;
}
}

50
src/EXTRA-DUMP/dump_extxyz.h Normal file
View File

@ -0,0 +1,50 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef DUMP_CLASS
// clang-format off
DumpStyle(extxyz,DumpExtXYZ);
// clang-format on
#else
#ifndef LMP_DUMP_EXTXYZ_H
#define LMP_DUMP_EXTXYZ_H
#include "dump_xyz.h"
namespace LAMMPS_NS {
class DumpExtXYZ : public DumpXYZ {
public:
DumpExtXYZ(class LAMMPS *, int, char **);
protected:
int with_vel;
int with_forces;
int with_mass;
int with_pe;
int with_temp;
int with_press;
char *properties_string;
void update_properties();
void init_style() override;
void write_header(bigint) override;
void pack(tagint *) override;
int convert_string(int, double *) override;
int modify_param(int, char **) override;
void write_lines(int, double *) override;
};
} // namespace LAMMPS_NS
#endif
#endif

25
src/dump_xyz.cpp
View File

@ -16,6 +16,7 @@
#include "atom.h"
#include "error.h"
#include "input.h"
#include "label_map.h"
#include "memory.h"
#include "update.h"
@ -32,8 +33,8 @@ static constexpr int DELTA = 1048576;
DumpXYZ::DumpXYZ(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg),
typenames(nullptr)
{
if (narg != 5) error->all(FLERR,"Illegal dump xyz command");
if (binary || multiproc) error->all(FLERR,"Invalid dump xyz filename");
if (narg != 5) error->all(FLERR, Error::NOPOINTER, "Illegal dump {} command", style);
if (binary || multiproc) error->all(FLERR, 4, "Invalid dump {} filename", style);
size_one = 5;
@ -43,7 +44,6 @@ DumpXYZ::DumpXYZ(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg),
sortcol = 0;
delete[] format_default;
format_default = utils::strdup("%s %g %g %g");
ntypes = atom->ntypes;
@ -103,9 +103,16 @@ void DumpXYZ::init_style()
int DumpXYZ::modify_param(int narg, char **arg)
{
// determine argument offset, if possible
int ioffset = 0;
if (input->arg) {
for (int i = 0; i < input->narg; ++i)
if (input->arg[i] == arg[0]) ioffset = i;
}
if (strcmp(arg[0],"element") == 0) {
if (narg < ntypes+1)
error->all(FLERR, "Dump modify element names do not match atom types");
error->all(FLERR, ioffset, "Dump modify element names do not match number of atom types");
if (typenames) {
for (int i = 1; i <= ntypes; i++)
@ -120,11 +127,11 @@ int DumpXYZ::modify_param(int narg, char **arg)
typenames[itype] = utils::strdup(arg[itype]);
}
return ntypes+1;
return ntypes + 1;
}
if (strcmp(arg[0],"types") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
if (narg < 2) utils::missing_cmd_args(FLERR,"dump_modify types", error);
if (typenames) {
for (int i = 1; i <= ntypes; i++)
@ -138,8 +145,8 @@ int DumpXYZ::modify_param(int narg, char **arg)
return 2;
} else if (strcmp(arg[1],"labels") == 0) {
if (!atom->labelmapflag)
error->all(FLERR, "Label map must be defined when using 'types labels'");
} else error->all(FLERR, "Illegal option for dump_modify 'types' keyword");
error->all(FLERR, ioffset + 1, "Label map must be defined when using 'types labels'");
} else error->all(FLERR, ioffset + 1, "Unknown option {} for dump_modify 'types' keyword", arg[1]);
typenames = new char*[ntypes+1];
for (int itype = 1; itype <= ntypes; itype++) {
@ -157,7 +164,7 @@ int DumpXYZ::modify_param(int narg, char **arg)
void DumpXYZ::write_header(bigint n)
{
if (me == 0) {
if (!fp) error->one(FLERR, "Must not use 'run pre no' after creating a new dump");
if (!fp) error->one(FLERR, Error::NOLASTLINE, "Must not use 'run pre no' after creating a new dump");
auto header = fmt::format("{}\n Atoms. Timestep: {}", n, update->ntimestep);
if (time_flag) header += fmt::format(" Time: {:.6f}", compute_time());

2
src/dump_xyz.h
View File

@ -43,7 +43,7 @@ class DumpXYZ : public Dump {
typedef void (DumpXYZ::*FnPtrWrite)(int, double *);
FnPtrWrite write_choice; // ptr to write data functions
void write_string(int, double *);
void write_lines(int, double *);
virtual void write_lines(int, double *);
};
} // namespace LAMMPS_NS

1
src/label_map.h
View File

@ -23,6 +23,7 @@ namespace LAMMPS_NS {
class LabelMap : protected Pointers {
friend class AtomVec;
friend class DumpCustom;
friend class DumpExtXYZ;
friend class DumpXYZ;
friend class ReadData;

4
src/thermo.cpp
View File

@ -101,8 +101,8 @@ static char fmtbuf[512];
/* ---------------------------------------------------------------------- */
Thermo::Thermo(LAMMPS *_lmp, int narg, char **arg) :
Pointers(_lmp), style(nullptr), vtype(nullptr), cache_mutex(nullptr), field2index(nullptr),
argindex1(nullptr), argindex2(nullptr), temperature(nullptr), pressure(nullptr), pe(nullptr)
Pointers(_lmp), style(nullptr), temperature(nullptr), pressure(nullptr), pe(nullptr),
vtype(nullptr), cache_mutex(nullptr), field2index(nullptr), argindex1(nullptr), argindex2(nullptr)
{
style = utils::strdup(arg[0]);

8
src/thermo.h
View File

@ -21,8 +21,8 @@
namespace LAMMPS_NS {
class Thermo : protected Pointers {
friend class MinCG; // accesses compute_pe
friend class MinCG; // accesses compute_pe
friend class DumpExtXYZ; // accesses compute_temp, compute_press, compute_pe
public:
char *style;
int normflag; // 0 if do not normalize by atoms, 1 if normalize
@ -57,6 +57,9 @@ class Thermo : protected Pointers {
void set_line(int _nline) { nline = _nline; }
void set_image_fname(const std::string &fname) { image_fname = fname; }
protected:
class Compute *temperature, *pressure, *pe;
private:
int nfield, nfield_initial;
int *vtype;
@ -104,7 +107,6 @@ class Thermo : protected Pointers {
// Compute * = ptrs to the Compute objects
int index_temp, index_press_scalar, index_press_vector, index_pe;
class Compute *temperature, *pressure, *pe;
double press_tensor[3][3];
int ncompute; // # of Compute objects called by thermo