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Merge branch 'master' into consistent-memory-usage

This commit is contained in:
Axel Kohlmeyer 2020-09-15 12:25:16 -04:00
parent bb76215ef0 165444004e
commit 3576464268
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45 changed files with 1287 additions and 501 deletions
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1
.github/CONTRIBUTING.md vendored
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@ -67,6 +67,7 @@ How quickly your contribution will be integrated depends largely on how much eff
Here is a checklist of steps you need to follow to submit a single file or user package for our consideration. Following these steps will save both you and us time. See existing files in packages in the source directory for examples. If you are uncertain, please ask on the lammps-users mailing list.
* C++ source code must be compatible with the C++-11 standard. Packages may require a later standard, if justified.
* All source files you provide must compile with the most current version of LAMMPS with multiple configurations. In particular you need to test compiling LAMMPS from scratch with `-DLAMMPS_BIGBIG` set in addition to the default `-DLAMMPS_SMALLBIG` setting. Your code will need to work correctly in serial and in parallel using MPI.
* For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no trailing whitespace, no lines over 80 characters. I/O is done via the C-style stdio library, style class header files should not import any system headers, STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (<name>.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included (<cstdio> instead of <stdio.h>, or <cstring> instead of <string.h>). This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages.
* Source, style name, and documentation file should follow the following naming convention: style names should be lowercase and words separated by a forward slash; for a new fix style 'foo/bar', the class should be named FixFooBar, the name of the source files should be 'fix_foo_bar.h' and 'fix_foo_bar.cpp' and the corresponding documentation should be in a file 'fix_foo_bar.rst'.

5
doc/Makefile
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@ -41,7 +41,10 @@ HAS_PDFLATEX = YES
endif
SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())') $(shell test -f $(BUILDDIR)/doxygen/xml/run.stamp && printf -- "-E")
#SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())') $(shell test -f $(BUILDDIR)/doxygen/xml/run.stamp && printf -- "-E")
# temporarily disable caching so that the hack for the sphinx-tabs extensions to get proper non-html output works
SPHINXEXTRA = -E -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
# grab list of sources from doxygen config file.
# we only want to use explicitly listed files.

7
doc/github-development-workflow.md
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@ -136,7 +136,8 @@ Here are some items to check:
* string.h -> cstring
* time.h -> ctime
* Do NOT replace (as they are C++-11): `inttypes.h` and `stdint.h`.
* Code should follow the C++-98 standard. C++-11 is only accepted
* Code must follow the C++-11 standard. C++98-only is no longer accepted
* Code should use `nullptr` instead of `NULL` where applicable.
in individual special purpose packages
* indentation is 2 spaces per level
* there should be NO tabs and no trailing whitespace (review the "checkstyle" test on pull requests)
@ -145,6 +146,8 @@ Here are some items to check:
Forward declarations should be used instead when possible.
* iostreams should be avoided. LAMMPS uses stdio from the C-library.
* use of STL in headers and class definitions should be avoided.
exception is <string>, but it won't need to be explicitly included
since pointers.h already includes it. so std::string can be used directly.
* there MUST NOT be any "using namespace XXX;" statements in headers.
* static class members should be avoided at all cost.
* anything storing atom IDs should be using `tagint` and not `int`.
@ -152,6 +155,8 @@ Here are some items to check:
compiling LAMMPS with `-DLAMMPS_BIGBIG`.
* when including both `lmptype.h` (and using defines or macros from it)
and `mpi.h`, `lmptype.h` must be included first.
* see https://github.com/lammps/lammps/blob/master/doc/include-file-conventions.md
for general include file conventions and best practices
* when pair styles are added, check if settings for flags like
`single_enable`, `writedata`, `reinitflag`, `manybody_flag`
and others are correctly set and supported.

6
doc/src/Build_extras.rst
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@ -373,8 +373,8 @@ More information on Kokkos can be found on the
Available Architecture settings
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
These are the possible choices for the Kokkos architecture ID as of
version 3.2 of the Kokkos library. They must be specified in uppercase.
These are the possible choices for the Kokkos architecture ID.
They must be specified in uppercase.
.. list-table::
:header-rows: 0
@ -486,6 +486,8 @@ version 3.2 of the Kokkos library. They must be specified in uppercase.
- GPU
- Intel GPUs Gen9+
This list was last updated for version 3.2 of the Kokkos library.
.. tabs::
.. tab:: Basic CMake build settings:

4
doc/src/Build_settings.rst
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@ -228,9 +228,9 @@ LAMMPS system size restrictions
- :math:`2^{63}` steps (= :math:`9.223 \cdot 10^{18}`)
- :math:`2^{31}` steps (= :math:`2.147 \cdot 10^9`)
* - Atom ID values
- :math:`1 \le i \le 2^{31} (= 2.147 \dot 10^9)`
- :math:`1 \le i \le 2^{31} (= 2.147 \cdot 10^9)`
- :math:`1 \le i \le 2^{63} (= 9.223 \cdot 10^{18})`
- :math:`1 \le i \le 2^{31} (= 2.147 \dot 10^9)`
- :math:`1 \le i \le 2^{31} (= 2.147 \cdot 10^9)`
* - Image flag values
- :math:`-512 \le i \le 511`
- :math:`- 1\,048\,576 \le i \le 1\,048\,575`

2
doc/src/compute_reduce.rst
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@ -53,7 +53,7 @@ Examples
compute 1 all reduce sum c_force
compute 1 all reduce/region subbox sum c_force
compute 2 all reduce min c_press[2] f_ave v_myKE
compute 2 all reduce min c_press[\*] f_ave v_myKE
compute 2 all reduce min c_press[*] f_ave v_myKE
compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
Description

6
doc/src/compute_stress_mop.rst
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@ -28,14 +28,16 @@ Syntax
origin = *lower* or *center* or *upper* or coordinate value (distance units) is the position of the first plane
delta = value (distance units) is the distance between planes
.. code-block:: LAMMPS
compute 1 all stress/mop x lower total
compute 1 liquid stress/mop z 0.0 kin conf
fix 1 all ave/time 10 1000 10000 c_1[\*] file mop.time
fix 1 all ave/time 10 1000 10000 c_1[*] file mop.time
fix 1 all ave/time 10 1000 10000 c_1[2] file mop.time
compute 1 all stress/mop/profile x lower 0.1 total
compute 1 liquid stress/mop/profile z 0.0 0.25 kin conf
fix 1 all ave/time 500 20 10000 c_1[\*] ave running overwrite file mopp.time mode vector
fix 1 all ave/time 500 20 10000 c_1[*] ave running overwrite file mopp.time mode vector
Description
"""""""""""

10
doc/src/dump.rst
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@ -36,8 +36,7 @@ Syntax
* ID = user-assigned name for the dump
* group-ID = ID of the group of atoms to be dumped
* style = *atom* or *atom/gz* or *atom/mpiio* or *cfg* or *cfg/gz* or
*cfg/mpiio* or *custom* or *custom/gz* or *custom/mpiio* or *dcd* or *h5md* or *image* or *local* or *local/gz* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/mpiio*
* style = *atom* or *atom/gz* or *atom/zstd or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *dcd* 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 *xyz/mpiio*
* N = dump every this many timesteps
* file = name of file to write dump info to
* args = list of arguments for a particular style
@ -138,7 +137,7 @@ Examples
dump 2 subgroup atom 50 dump.run.mpiio.bin
dump 4a all custom 100 dump.myforce.* id type x y vx fx
dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
dump 4b flow custom 100 dump.%.myforce id type c_myF[\*] v_ke
dump 4b flow custom 100 dump.%.myforce id type c_myF[*] v_ke
dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]
dump 1 all xtc 1000 file.xtc
@ -204,8 +203,9 @@ of the required filename suffix.
Similarly, the *atom/zstd*\ , *cfg/zstd*\ , *custom/zstd*\ , *local/zstd*,
and *xyz/zstd* styles are identical to the gz styles, but use the Zstd
compression library instead. See the :doc:`dump_modify <dump_modify>` doc
page for details on how to control the compression level in both variants.
compression library instead and require the ".zst" suffix. See the
:doc:`dump_modify <dump_modify>` doc page for details on how to control
the compression level in both variants.
As explained below, the *atom/mpiio*\ , *cfg/mpiio*\ , *custom/mpiio*\ , and
*xyz/mpiio* styles are identical in command syntax and in the format

2
doc/src/fix_nh.rst
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@ -51,7 +51,7 @@ Syntax
*couple* = *none* or *xyz* or *xy* or *yz* or *xz*
*tchain* value = N
N = length of thermostat chain (1 = single thermostat)
*pchain* values = N
*pchain* value = N
N length of thermostat chain on barostat (0 = no thermostat)
*mtk* value = *yes* or *no* = add in MTK adjustment term or not
*tloop* value = M

16
doc/src/fix_qeq_reax.rst
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@ -20,7 +20,14 @@ Syntax
* cutlo,cuthi = lo and hi cutoff for Taper radius
* tolerance = precision to which charges will be equilibrated
* params = reax/c or a filename
* args = *dual* (optional)
* one or more keywords or keyword/value pairs may be appended
.. parsed-literal::
keyword = *dual* or *maxiter*
*dual* = process S and T matrix in parallel (only for qeq/reax/omp)
*maxiter* N = limit the number of iterations to *N*
Examples
""""""""
@ -28,7 +35,7 @@ Examples
.. code-block:: LAMMPS
fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq
fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq maxiter 500
Description
"""""""""""
@ -69,6 +76,9 @@ The optional *dual* keyword allows to perform the optimization
of the S and T matrices in parallel. This is only supported for
the *qeq/reax/omp* style. Otherwise they are processed separately.
The optional *maxiter* keyword allows changing the max number
of iterations in the linear solver. The default value is 200.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@ -102,7 +112,7 @@ Related commands
Default
"""""""
none
maxiter 200
----------

2
doc/src/min_modify.rst
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@ -19,7 +19,7 @@ Syntax
max = maximum distance for line search to move (distance units)
*line* value = *backtrack* or *quadratic* or *forcezero* or *spin_cubic* or *spin_none*
backtrack,quadratic,forcezero,spin_cubic,spin_none = style of linesearch to use
*norm* value = *two* or *max*
*norm* value = *two* or *inf* or *max*
two = Euclidean two-norm (length of 3N vector)
inf = max force component across all 3-vectors
max = max force norm across all 3-vectors

48
doc/src/pg_lib_config.rst
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@ -1,9 +1,51 @@
Retrieving LAMMPS configuration information
===========================================
The following library functions can be used to query the
LAMMPS library about compile time settings and included
packages and styles.
The following library functions can be used to query the LAMMPS library
about compile time settings and included packages and styles. This
enables programs that use the library interface to run LAMMPS
simulations to determine, whether the linked LAMMPS library is compatible
with the requirements of the application without crashing during the
LAMMPS functions (e.g. due to missing pair styles from packages) or to
choose between different options (e.g. whether to use ``lj/cut``,
``lj/cut/opt``, ``lj/cut/omp`` or ``lj/cut/intel``). Most of the
functions can be called directly without first creating a LAMMPS
instance. While crashes within LAMMPS may be recovered from through
enabling :ref:`exceptions <exceptions>`, avoiding them proactively is
a safer approach.
.. code-block:: C
:caption: Example for using configuration settings functions
#include "library.h"
#include <stdio.h>
int main(int argc, char **argv)
{
void *handle;
handle = lammps_open_no_mpi(0, NULL, NULL);
lammps_file(handle, "in.missing");
if (lammps_has_error(handle)) {
char errmsg[256];
int errtype;
errtype = lammps_get_last_error_message(handle, errmsg, 256);
fprintf(stderr, "LAMMPS failed with error: %s\n", errmsg);
return 1;
}
/* write compressed dump file depending on available of options */
if (lammps_has_style(handle, "dump", "atom/zstd")) {
lammps_command(handle, "dump d1 all atom/zstd 100 dump.zst");
} else if (lammps_has_style(handle, "dump", "atom/gz")) {
lammps_command(handle, "dump d1 all atom/gz 100 dump.gz");
} else if (lammps_config_has_gzip_support()) {
lammps_command(handle, "dump d1 all atom 100 dump.gz");
} else {
lammps_command(handle, "dump d1 all atom 100 dump");
}
lammps_close(handle);
return 0;
}
-----------------------

32
doc/src/pg_lib_properties.rst
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@ -2,8 +2,8 @@ Retrieving or setting LAMMPS system properties
==============================================
The library interface allows to extract different kinds of information
about the active simulation instance and also to modify some of them.
This allows to combine MD simulation steps with other processing and
about the active simulation instance and also to modify some of it.
This enables combining MD simulation steps with other processing and
simulation methods computed in the calling code or another code that is
coupled to LAMMPS via the library interface. In some cases the data
returned is direct reference to the original data inside LAMMPS cast
@ -14,6 +14,34 @@ is the per-processor **local** data and indexed accordingly. These arrays
can change sizes and order at every neighbor list rebuild and atom sort
event as atoms are migrating between sub-domains.
.. code-block:: C
#include "library.h"
#include <stdio.h>
int main(int argc, char **argv)
{
void *handle;
int i;
handle = lammps_open_no_mpi(0, NULL, NULL);
lammps_file(handle,"in.sysinit");
printf("running simulation with %g atoms\n",
lammps_get_natoms(handle));
lammps_command(handle,"run 1000 post no");
for (i=0; i < 10; ++i) {
lammps_command(handle,"run 100 pre no post no");
printf("PE = %g\nKE = %g\n",
lammps_get_thermo(handle,"pe"),
lammps_get_thermo(handle,"ke"));
}
lammps_close(handle);
return 0;
}
-----------------------
.. doxygenfunction:: lammps_version

4
doc/utils/sphinx-config/_static/css/lammps.css
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@ -14,3 +14,7 @@
display: block;
margin-bottom: 0.405em;
}
.versionmodified {
font-weight: bold;
}

2
doc/utils/sphinx-config/false_positives.txt
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@ -1003,6 +1003,7 @@ formatarg
formulae
Forschungszentrum
Fortran
fortran
Fosado
fourier
fp
@ -3454,6 +3455,7 @@ zmin
zmq
zN
zs
zst
zsu
zu
zx

31
src/KOKKOS/fix_qeq_reax_kokkos.cpp
View File

@ -112,7 +112,7 @@ void FixQEqReaxKokkos<DeviceType>::init()
("FixQEqReax::params",ntypes+1);
params = k_params.template view<DeviceType>();
for (n = 1; n <= ntypes; n++) {
for (int n = 1; n <= ntypes; n++) {
k_params.h_view(n).chi = chi[n];
k_params.h_view(n).eta = eta[n];
k_params.h_view(n).gamma = gamma[n];
@ -351,34 +351,35 @@ void FixQEqReaxKokkos<DeviceType>::allocate_array()
if (atom->nmax > nmax) {
nmax = atom->nmax;
k_o = DAT::tdual_ffloat_1d("qeq/kk:h_o",nmax);
k_o = DAT::tdual_ffloat_1d("qeq/kk:o",nmax);
d_o = k_o.template view<DeviceType>();
h_o = k_o.h_view;
d_Hdia_inv = typename AT::t_ffloat_1d("qeq/kk:h_Hdia_inv",nmax);
d_Hdia_inv = typename AT::t_ffloat_1d("qeq/kk:Hdia_inv",nmax);
d_b_s = typename AT::t_ffloat_1d("qeq/kk:h_b_s",nmax);
d_b_s = typename AT::t_ffloat_1d("qeq/kk:b_s",nmax);
d_b_t = typename AT::t_ffloat_1d("qeq/kk:h_b_t",nmax);
d_b_t = typename AT::t_ffloat_1d("qeq/kk:b_t",nmax);
k_s = DAT::tdual_ffloat_1d("qeq/kk:h_s",nmax);
k_s = DAT::tdual_ffloat_1d("qeq/kk:s",nmax);
d_s = k_s.template view<DeviceType>();
h_s = k_s.h_view;
k_t = DAT::tdual_ffloat_1d("qeq/kk:h_t",nmax);
k_t = DAT::tdual_ffloat_1d("qeq/kk:t",nmax);
d_t = k_t.template view<DeviceType>();
h_t = k_t.h_view;
d_p = typename AT::t_ffloat_1d("qeq/kk:h_p",nmax);
d_p = typename AT::t_ffloat_1d("qeq/kk:p",nmax);
d_r = typename AT::t_ffloat_1d("qeq/kk:h_r",nmax);
d_r = typename AT::t_ffloat_1d("qeq/kk:r",nmax);
k_d = DAT::tdual_ffloat_1d("qeq/kk:h_d",nmax);
k_d = DAT::tdual_ffloat_1d("qeq/kk:d",nmax);
d_d = k_d.template view<DeviceType>();
h_d = k_d.h_view;
}
// init_storage
FixQEqReaxKokkosZeroFunctor<DeviceType> zero_functor(this);
Kokkos::parallel_for(ignum,zero_functor);
@ -779,8 +780,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve1()
F_FLOAT sig_new = dot_sqr;
int loop;
const int loopmax = 200;
for (loop = 1; (loop < loopmax) && (sqrt(sig_new)/b_norm > tolerance); loop++) {
for (loop = 1; (loop < imax) && (sqrt(sig_new)/b_norm > tolerance); loop++) {
// comm->forward_comm_fix(this); //Dist_vector( d );
pack_flag = 1;
@ -848,7 +848,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve1()
Kokkos::parallel_for(inum,vecsum2_functor);
}
if (loop >= loopmax && comm->me == 0) {
if (loop >= imax && comm->me == 0) {
char str[128];
sprintf(str,"Fix qeq/reax cg_solve1 convergence failed after %d iterations "
"at " BIGINT_FORMAT " step: %f",loop,update->ntimestep,sqrt(sig_new)/b_norm);
@ -918,8 +918,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve2()
F_FLOAT sig_new = dot_sqr;
int loop;
const int loopmax = 200;
for (loop = 1; (loop < loopmax) && (sqrt(sig_new)/b_norm > tolerance); loop++) {
for (loop = 1; (loop < imax) && (sqrt(sig_new)/b_norm > tolerance); loop++) {
// comm->forward_comm_fix(this); //Dist_vector( d );
pack_flag = 1;
@ -987,7 +986,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve2()
Kokkos::parallel_for(inum,vecsum2_functor);
}
if (loop >= loopmax && comm->me == 0) {
if (loop >= imax && comm->me == 0) {
char str[128];
sprintf(str,"Fix qeq/reax cg_solve2 convergence failed after %d iterations "
"at " BIGINT_FORMAT " step: %f",loop,update->ntimestep,sqrt(sig_new)/b_norm);

12
src/KSPACE/msm.cpp
View File

@ -206,9 +206,9 @@ void MSM::init()
if (me == 0) {
std::string mesg = fmt::format(" 3d grid size/proc = {}\n", ngrid_max);
mesg += fmt::format(" estimated absolute RMS force accuracy = {:.8g}\n",
mesg += fmt::format(" estimated absolute RMS force accuracy = {:.8}\n",
estimated_error);
mesg += fmt::format(" estimated relative force accuracy = {:.8g}\n",
mesg += fmt::format(" estimated relative force accuracy = {:.8}\n",
estimated_error/two_charge_force);
mesg += fmt::format(" grid = {} {} {}\n",nx_msm[0],ny_msm[0],nz_msm[0]);
mesg += fmt::format(" order = {}\n",order);
@ -1028,6 +1028,7 @@ void MSM::set_grid_global()
int flag = 0;
int xlevels,ylevels,zlevels;
xlevels = ylevels = zlevels = 1;
while (!factorable(nx_max,flag,xlevels)) {
double k = log(nx_max)/log(2.0);
@ -1077,7 +1078,7 @@ void MSM::set_grid_global()
if (me == 0)
error->warning(FLERR,fmt::format("Adjusting Coulombic cutoff for "
"MSM, new cutoff = {}", cutoff));
"MSM, new cutoff = {:.8}", cutoff));
}
if (triclinic == 0) {
@ -1432,16 +1433,15 @@ void MSM::setup_grid()
return 1 if yes, 0 if no
------------------------------------------------------------------------- */
int MSM::factorable(int n, int &flag, int &levels)
int MSM::factorable(int n, int &flag, int &nlevels)
{
int i;
levels = 1;
while (n > 1) {
for (i = 0; i < nfactors; i++) {
if (n % factors[i] == 0) {
n /= factors[i];
levels++;
nlevels++;
break;
}
}

2
src/KSPACE/msm_cg.cpp
View File

@ -133,7 +133,7 @@ void MSMCG::compute(int eflag, int vflag)
/ static_cast<double>(atom->natoms);
if (me == 0)
utils::logmesg(lmp,fmt::format(" MSM/cg optimization cutoff: {:.8g}\n"
utils::logmesg(lmp,fmt::format(" MSM/cg optimization cutoff: {:.8}\n"
" Total charged atoms: {:.1f}%\n"
" Min/max charged atoms/proc: {:.1f}%"
" {:.1f}%\n",smallq,

76
src/MC/fix_widom.cpp
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@ -62,10 +62,10 @@ FixWidom::FixWidom(LAMMPS *lmp, int narg, char **arg) :
local_gas_list(NULL), molcoords(NULL), molq(NULL), molimage(NULL),
random_equal(NULL)
{
if (narg < 8) error->all(FLERR,"Illegal fix Widom command");
if (narg < 8) error->all(FLERR,"Illegal fix widom command");
if (atom->molecular == 2)
error->all(FLERR,"Fix Widom does not (yet) work with atom_style template");
error->all(FLERR,"Fix widom does not (yet) work with atom_style template");
dynamic_group_allow = 1;
@ -86,11 +86,11 @@ FixWidom::FixWidom(LAMMPS *lmp, int narg, char **arg) :
seed = utils::inumeric(FLERR,arg[6],false,lmp);
insertion_temperature = utils::numeric(FLERR,arg[7],false,lmp);
if (nevery <= 0) error->all(FLERR,"Illegal fix Widom command");
if (ninsertions < 0) error->all(FLERR,"Illegal fix Widom command");
if (seed <= 0) error->all(FLERR,"Illegal fix Widom command");
if (nevery <= 0) error->all(FLERR,"Illegal fix widom command");
if (ninsertions < 0) error->all(FLERR,"Illegal fix widom command");
if (seed <= 0) error->all(FLERR,"Illegal fix widom command");
if (insertion_temperature < 0.0)
error->all(FLERR,"Illegal fix Widom command");
error->all(FLERR,"Illegal fix widom command");
// read options from end of input line
@ -106,9 +106,9 @@ FixWidom::FixWidom(LAMMPS *lmp, int narg, char **arg) :
region_zlo = region_zhi = 0.0;
if (regionflag) {
if (domain->regions[iregion]->bboxflag == 0)
error->all(FLERR,"Fix Widom region does not support a bounding box");
error->all(FLERR,"Fix widom region does not support a bounding box");
if (domain->regions[iregion]->dynamic_check())
error->all(FLERR,"Fix Widom region cannot be dynamic");
error->all(FLERR,"Fix widom region cannot be dynamic");
region_xlo = domain->regions[iregion]->extent_xlo;
region_xhi = domain->regions[iregion]->extent_xhi;
@ -120,7 +120,7 @@ FixWidom::FixWidom(LAMMPS *lmp, int narg, char **arg) :
if (region_xlo < domain->boxlo[0] || region_xhi > domain->boxhi[0] ||
region_ylo < domain->boxlo[1] || region_yhi > domain->boxhi[1] ||
region_zlo < domain->boxlo[2] || region_zhi > domain->boxhi[2])
error->all(FLERR,"Fix Widom region extends outside simulation box");
error->all(FLERR,"Fix widom region extends outside simulation box");
// estimate region volume using MC trials
@ -146,22 +146,22 @@ FixWidom::FixWidom(LAMMPS *lmp, int narg, char **arg) :
if (exchmode == EXCHMOL) {
if (onemols[imol]->xflag == 0)
error->all(FLERR,"Fix Widom molecule must have coordinates");
error->all(FLERR,"Fix widom molecule must have coordinates");
if (onemols[imol]->typeflag == 0)
error->all(FLERR,"Fix Widom molecule must have atom types");
error->all(FLERR,"Fix widom molecule must have atom types");
if (nwidom_type != 0)
error->all(FLERR,"Atom type must be zero in fix Widom mol command");
error->all(FLERR,"Atom type must be zero in fix widom mol command");
if (onemols[imol]->qflag == 1 && atom->q == NULL)
error->all(FLERR,"Fix Widom molecule has charges, but atom style does not");
error->all(FLERR,"Fix widom molecule has charges, but atom style does not");
if (atom->molecular == 2 && onemols != atom->avec->onemols)
error->all(FLERR,"Fix Widom molecule template ID must be same "
error->all(FLERR,"Fix widom molecule template ID must be same "
"as atom_style template ID");
onemols[imol]->check_attributes(0);
}
if (charge_flag && atom->q == NULL)
error->all(FLERR,"Fix Widom atom has charge, but atom style does not");
error->all(FLERR,"Fix widom atom has charge, but atom style does not");
// setup of array of coordinates for molecule insertion
@ -186,7 +186,7 @@ FixWidom::FixWidom(LAMMPS *lmp, int narg, char **arg) :
void FixWidom::options(int narg, char **arg)
{
if (narg < 0) error->all(FLERR,"Illegal fix Widom command");
if (narg < 0) error->all(FLERR,"Illegal fix widom command");
// defaults
@ -208,29 +208,29 @@ void FixWidom::options(int narg, char **arg)
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"mol") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix Widom command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix widom command");
imol = atom->find_molecule(arg[iarg+1]);
if (imol == -1)
error->all(FLERR,"Molecule template ID for fix Widom does not exist");
error->all(FLERR,"Molecule template ID for fix widom does not exist");
if (atom->molecules[imol]->nset > 1 && comm->me == 0)
error->warning(FLERR,"Molecule template for "
"fix Widom has multiple molecules");
"fix widom has multiple molecules");
exchmode = EXCHMOL;
onemols = atom->molecules;
nmol = onemols[imol]->nset;
iarg += 2;
} else if (strcmp(arg[iarg],"region") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix Widom command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix widom command");
iregion = domain->find_region(arg[iarg+1]);
if (iregion == -1)
error->all(FLERR,"Region ID for fix Widom does not exist");
error->all(FLERR,"Region ID for fix widom does not exist");
int n = strlen(arg[iarg+1]) + 1;
idregion = new char[n];
strcpy(idregion,arg[iarg+1]);
regionflag = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"charge") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix Widom command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix widom command");
charge = utils::numeric(FLERR,arg[iarg+1],false,lmp);
charge_flag = true;
iarg += 2;
@ -238,10 +238,10 @@ void FixWidom::options(int narg, char **arg)
full_flag = true;
iarg += 1;
} else if (strcmp(arg[iarg],"intra_energy") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix Widom command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix widom command");
energy_intra = utils::numeric(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else error->all(FLERR,"Illegal fix Widom command");
} else error->all(FLERR,"Illegal fix widom command");
}
}
@ -291,7 +291,7 @@ void FixWidom::init()
) {
full_flag = true;
if (comm->me == 0)
error->warning(FLERR,"Fix Widom using full_energy option");
error->warning(FLERR,"Fix widom using full_energy option");
}
}
@ -299,7 +299,7 @@ void FixWidom::init()
if (exchmode == EXCHATOM) {
if (nwidom_type <= 0 || nwidom_type > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix Widom command");
error->all(FLERR,"Invalid atom type in fix widom command");
}
// if molecules are exchanged or moved, check for unset mol IDs
@ -314,17 +314,17 @@ void FixWidom::init()
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall && comm->me == 0)
error->all(FLERR,
"All mol IDs should be set for fix Widom group atoms");
"All mol IDs should be set for fix widom group atoms");
}
if (exchmode == EXCHMOL)
if (atom->molecule_flag == 0 || !atom->tag_enable || !atom->map_style)
error->all(FLERR,
"Fix Widom molecule command requires that "
"Fix widom molecule command requires that "
"atoms have molecule attributes");
if (domain->dimension == 2)
error->all(FLERR,"Cannot use fix Widom in a 2d simulation");
error->all(FLERR,"Cannot use fix widom in a 2d simulation");
// create a new group for interaction exclusions
// used for attempted atom or molecule deletions
@ -387,7 +387,7 @@ void FixWidom::init()
} else gas_mass = atom->mass[nwidom_type];
if (gas_mass <= 0.0)
error->all(FLERR,"Illegal fix Widom gas mass <= 0");
error->all(FLERR,"Illegal fix widom gas mass <= 0");
// check that no deletable atoms are in atom->firstgroup
// deleting such an atom would not leave firstgroup atoms first
@ -404,7 +404,7 @@ void FixWidom::init()
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall)
error->all(FLERR,"Cannot do Widom on atoms in atom_modify first group");
error->all(FLERR,"Cannot use fix widom on atoms in atom_modify first group");
}
// compute beta
@ -417,7 +417,7 @@ void FixWidom::init()
// full_flag on molecules on more than one processor.
// Print error if this is the current mode
if (full_flag && (exchmode == EXCHMOL) && comm->nprocs > 1)
error->all(FLERR,"fix Widom does currently not support full_energy option with molecules on more than 1 MPI process.");
error->all(FLERR,"fix widom does currently not support full_energy option with molecules on more than 1 MPI process.");
}
@ -535,7 +535,7 @@ void FixWidom::attempt_atomic_insertion()
if (triclinic == 0) {
domain->remap(coord);
if (!domain->inside(coord))
error->one(FLERR,"Fix Widom put atom outside box");
error->one(FLERR,"Fix widom put atom outside box");
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2]) proc_flag = 1;
@ -648,7 +648,7 @@ void FixWidom::attempt_molecule_insertion()
xtmp[2] = molcoords[i][2];
domain->remap(xtmp);
if (!domain->inside(xtmp))
error->one(FLERR,"Fix Widom put atom outside box");
error->one(FLERR,"Fix widom put atom outside box");
procflag[i] = false;
if (triclinic == 0) {
@ -737,7 +737,7 @@ void FixWidom::attempt_atomic_insertion_full()
if (triclinic == 0) {
domain->remap(coord);
if (!domain->inside(coord))
error->one(FLERR,"Fix Widom put atom outside box");
error->one(FLERR,"Fix widom put atom outside box");
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2]) proc_flag = 1;
@ -803,7 +803,7 @@ void FixWidom::attempt_molecule_insertion_full()
MPI_Allreduce(&maxmol,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
maxmol_all++;
if (maxmol_all >= MAXTAGINT)
error->all(FLERR,"Fix Widom ran out of available molecule IDs");
error->all(FLERR,"Fix widom ran out of available molecule IDs");
int insertion_molecule = maxmol_all;
tagint maxtag = 0;
@ -883,7 +883,7 @@ void FixWidom::attempt_molecule_insertion_full()
imageint imagetmp = imagezero;
domain->remap(xtmp,imagetmp);
if (!domain->inside(xtmp))
error->one(FLERR,"Fix Widom put atom outside box");
error->one(FLERR,"Fix widom put atom outside box");
int proc_flag = 0;
if (triclinic == 0) {
@ -904,7 +904,7 @@ void FixWidom::attempt_molecule_insertion_full()
atom->image[m] = imagetmp;
atom->molecule[m] = insertion_molecule;
if (maxtag_all+i+1 >= MAXTAGINT)
error->all(FLERR,"Fix Widom ran out of available atom IDs");
error->all(FLERR,"Fix widom ran out of available atom IDs");
atom->tag[m] = maxtag_all + i + 1;
atom->v[m][0] = 0;
atom->v[m][1] = 0;

2
src/USER-EFF/pair_eff_cut.cpp
View File

@ -869,7 +869,7 @@ void PairEffCut::init_style()
// make sure to use the appropriate timestep when using real units
if (update->whichflag == 1) {
if (force->qqr2e == 332.06371 && update->dt == 1.0)
if (utils::strmatch(update->unit_style,"^real") && update->dt_default)
error->all(FLERR,"Must lower the default real units timestep for pEFF ");
}

144
src/USER-OMP/fix_qeq_reax_omp.cpp
View File

@ -63,8 +63,6 @@ using namespace FixConst;
FixQEqReaxOMP::FixQEqReaxOMP(LAMMPS *lmp, int narg, char **arg) :
FixQEqReax(lmp, narg, arg)
{
if (narg<8 || narg>9) error->all(FLERR,"Illegal fix qeq/reax/omp command");
b_temp = NULL;
// ASPC: Kolafa, J. Comp. Chem., 25(3), 335 (2003)
@ -85,6 +83,11 @@ FixQEqReaxOMP::~FixQEqReaxOMP()
void FixQEqReaxOMP::post_constructor()
{
grow_arrays(atom->nmax);
for (int i = 0; i < atom->nmax; i++)
for (int j = 0; j < nprev; ++j)
s_hist[i][j] = t_hist[i][j] = 0;
pertype_parameters(pertype_option);
}
@ -148,7 +151,6 @@ void FixQEqReaxOMP::init()
void FixQEqReaxOMP::compute_H()
{
int inum, *ilist, *numneigh, **firstneigh;
double SMALL = 0.0001;
int *type = atom->type;
@ -156,17 +158,6 @@ void FixQEqReaxOMP::compute_H()
double **x = atom->x;
int *mask = atom->mask;
if (reaxc) {
inum = reaxc->list->inum;
ilist = reaxc->list->ilist;
numneigh = reaxc->list->numneigh;
firstneigh = reaxc->list->firstneigh;
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
}
int ai, num_nbrs;
// sumscan of the number of neighbors per atom to determine the offsets
@ -175,7 +166,7 @@ void FixQEqReaxOMP::compute_H()
num_nbrs = 0;
for (int itr_i = 0; itr_i < inum; ++itr_i) {
for (int itr_i = 0; itr_i < nn; ++itr_i) {
ai = ilist[itr_i];
H.firstnbr[ai] = num_nbrs;
num_nbrs += numneigh[ai];
@ -197,7 +188,7 @@ void FixQEqReaxOMP::compute_H()
#if defined(_OPENMP)
#pragma omp for schedule(guided)
#endif
for (int ii = 0; ii < inum; ii++) {
for (int ii = 0; ii < nn; ii++) {
int i = ilist[ii];
if (mask[i] & groupbit) {
jlist = firstneigh[i];
@ -214,7 +205,7 @@ void FixQEqReaxOMP::compute_H()
flag = 0;
if (r_sqr <= SQR(swb)) {
if (j < n) flag = 1;
if (j < atom->nlocal) flag = 1;
else if (tag[i] < tag[j]) flag = 1;
else if (tag[i] == tag[j]) {
if (dz > SMALL) flag = 1;
@ -251,11 +242,6 @@ void FixQEqReaxOMP::compute_H()
void FixQEqReaxOMP::init_storage()
{
int NN;
if (reaxc) NN = reaxc->list->inum + reaxc->list->gnum;
else NN = list->inum + list->gnum;
#if defined(_OPENMP)
#pragma omp parallel for schedule(static)
#endif
@ -284,8 +270,21 @@ void FixQEqReaxOMP::pre_force(int /* vflag */)
if (update->ntimestep % nevery) return;
if (comm->me == 0) t_start = MPI_Wtime();
n = atom->nlocal;
N = atom->nlocal + atom->nghost;
int n = atom->nlocal;
if (reaxc) {
nn = reaxc->list->inum;
NN = reaxc->list->inum + reaxc->list->gnum;
ilist = reaxc->list->ilist;
numneigh = reaxc->list->numneigh;
firstneigh = reaxc->list->firstneigh;
} else {
nn = list->inum;
NN = list->inum + list->gnum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
}
// grow arrays if necessary
// need to be atom->nmax in length
@ -365,16 +364,7 @@ void FixQEqReaxOMP::init_matvec()
/* fill-in H matrix */
compute_H();
int nn,i;
int *ilist;
if (reaxc) {
nn = reaxc->list->inum;
ilist = reaxc->list->ilist;
} else {
nn = list->inum;
ilist = list->ilist;
}
int i;
// Should really be more careful with initialization and first (aspc_order+2) MD steps
if (do_aspc) {
@ -450,24 +440,12 @@ void FixQEqReaxOMP::init_matvec()
int FixQEqReaxOMP::CG( double *b, double *x)
{
int i, imax;
int i;
double alpha, beta, b_norm;
double sig_old, sig_new;
double my_buf[2], buf[2];
int nn;
int *ilist;
if (reaxc) {
nn = reaxc->list->inum;
ilist = reaxc->list->ilist;
} else {
nn = list->inum;
ilist = list->ilist;
}
imax = 200;
pack_flag = 1;
sparse_matvec( &H, x, q );
comm->reverse_comm_fix( this); //Coll_Vector( q );
@ -579,8 +557,7 @@ void FixQEqReaxOMP::sparse_matvec( sparse_matrix *A, double *x, double *b)
#endif
{
int i, j, itr_j;
int nn, NN, ii;
int *ilist;
int ii;
int nthreads = comm->nthreads;
#if defined(_OPENMP)
int tid = omp_get_thread_num();
@ -588,16 +565,6 @@ void FixQEqReaxOMP::sparse_matvec( sparse_matrix *A, double *x, double *b)
int tid = 0;
#endif
if (reaxc) {
nn = reaxc->list->inum;
NN = reaxc->list->inum + reaxc->list->gnum;
ilist = reaxc->list->ilist;
} else {
nn = list->inum;
NN = list->inum + list->gnum;
ilist = list->ilist;
}
#if defined(_OPENMP)
#pragma omp for schedule(dynamic,50)
#endif
@ -655,17 +622,6 @@ void FixQEqReaxOMP::calculate_Q()
int i;
double *q = atom->q;
int nn;
int *ilist;
if (reaxc) {
nn = reaxc->list->inum;
ilist = reaxc->list->ilist;
} else {
nn = list->inum;
ilist = list->ilist;
}
double tmp1, tmp2;
tmp1 = tmp2 = 0.0;
#if defined(_OPENMP)
@ -718,10 +674,6 @@ void FixQEqReaxOMP::vector_sum( double* dest, double c, double* v,
double d, double* y, int k)
{
int i;
int *ilist;
if (reaxc) ilist = reaxc->list->ilist;
else ilist = list->ilist;
#if defined(_OPENMP)
#pragma omp parallel for schedule(static) private(i)
@ -737,10 +689,6 @@ void FixQEqReaxOMP::vector_sum( double* dest, double c, double* v,
void FixQEqReaxOMP::vector_add( double* dest, double c, double* v, int k)
{
int i;
int *ilist;
if (reaxc) ilist = reaxc->list->ilist;
else ilist = list->ilist;
#if defined(_OPENMP)
#pragma omp parallel for schedule(static) private(i)
@ -765,24 +713,12 @@ int FixQEqReaxOMP::dual_CG( double *b1, double *b2, double *x1, double *x2)
startTimeBase = MPI_Wtime();
#endif
int i, imax;
int i;
double alpha_s, alpha_t, beta_s, beta_t, b_norm_s, b_norm_t;
double sig_old_s, sig_old_t, sig_new_s, sig_new_t;
double my_buf[4], buf[4];
int nn;
int *ilist;
if (reaxc) {
nn = reaxc->list->inum;
ilist = reaxc->list->ilist;
} else {
nn = list->inum;
ilist = list->ilist;
}
imax = 200;
pack_flag = 5; // forward 2x d and reverse 2x q
dual_sparse_matvec( &H, x1, x2, q );
comm->reverse_comm_fix(this); //Coll_Vector( q );
@ -975,8 +911,7 @@ void FixQEqReaxOMP::dual_sparse_matvec( sparse_matrix *A, double *x1, double *x2
#endif
{
int i, j, itr_j;
int nn, NN, ii;
int *ilist;
int ii;
int indxI, indxJ;
int nthreads = comm->nthreads;
@ -986,16 +921,6 @@ void FixQEqReaxOMP::dual_sparse_matvec( sparse_matrix *A, double *x1, double *x2
int tid = 0;
#endif
if (reaxc) {
nn = reaxc->list->inum;
NN = reaxc->list->inum + reaxc->list->gnum;
ilist = reaxc->list->ilist;
} else {
nn = list->inum;
NN = list->inum + list->gnum;
ilist = list->ilist;
}
#if defined(_OPENMP)
#pragma omp for schedule(dynamic,50)
#endif
@ -1077,8 +1002,7 @@ void FixQEqReaxOMP::dual_sparse_matvec( sparse_matrix *A, double *x, double *b )
#endif
{
int i, j, itr_j;
int nn, NN, ii;
int *ilist;
int ii;
int indxI, indxJ;
int nthreads = comm->nthreads;
@ -1088,16 +1012,6 @@ void FixQEqReaxOMP::dual_sparse_matvec( sparse_matrix *A, double *x, double *b )
int tid = 0;
#endif
if (reaxc) {
nn = reaxc->list->inum;
NN = reaxc->list->inum + reaxc->list->gnum;
ilist = reaxc->list->ilist;
} else {
nn = list->inum;
NN = list->inum + list->gnum;
ilist = list->ilist;
}
#if defined(_OPENMP)
#pragma omp for schedule(dynamic,50)
#endif

2
src/USER-OMP/msm_cg_omp.cpp
View File

@ -137,7 +137,7 @@ void MSMCGOMP::compute(int eflag, int vflag)
/ static_cast<double>(atom->natoms);
if (me == 0)
utils::logmesg(MSM::lmp,fmt::format(" MSM/cg optimization cutoff: {:.8g}\n"
utils::logmesg(MSM::lmp,fmt::format(" MSM/cg optimization cutoff: {:.8}\n"
" Total charged atoms: {:.1f}%\n"
" Min/max charged atoms/proc: {:.1f}%"
" {:.1f}%\n",smallq,

178
src/USER-REAXC/fix_qeq_reax.cpp
View File

@ -62,9 +62,7 @@ static const char cite_fix_qeq_reax[] =
FixQEqReax::FixQEqReax(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), pertype_option(NULL)
{
if (lmp->citeme) lmp->citeme->add(cite_fix_qeq_reax);
if (narg<8 || narg>9) error->all(FLERR,"Illegal fix qeq/reax command");
if (narg<8 || narg>11) error->all(FLERR,"Illegal fix qeq/reax command");
nevery = utils::inumeric(FLERR,arg[3],false,lmp);
if (nevery <= 0) error->all(FLERR,"Illegal fix qeq/reax command");
@ -79,14 +77,23 @@ FixQEqReax::FixQEqReax(LAMMPS *lmp, int narg, char **arg) :
// dual CG support only available for USER-OMP variant
// check for compatibility is in Fix::post_constructor()
dual_enabled = 0;
if (narg == 9) {
if (strcmp(arg[8],"dual") == 0) dual_enabled = 1;
else error->all(FLERR,"Illegal fix qeq/reax command");
imax = 200;
int iarg = 8;
while (iarg < narg) {
if (strcmp(arg[iarg],"dual") == 0) dual_enabled = 1;
else if (strcmp(arg[iarg],"maxiter") == 0) {
if (iarg+1 > narg-1)
error->all(FLERR,"Illegal fix qeq/reax command");
imax = utils::numeric(FLERR,arg[iarg+1],false,lmp);
iarg++;
} else error->all(FLERR,"Illegal fix qeq/reax command");
iarg++;
}
shld = NULL;
n = n_cap = 0;
N = nmax = 0;
nn = n_cap = 0;
NN = nmax = 0;
m_fill = m_cap = 0;
pack_flag = 0;
s = NULL;
@ -123,11 +130,7 @@ FixQEqReax::FixQEqReax(LAMMPS *lmp, int narg, char **arg) :
reaxc = (PairReaxC *) force->pair_match("^reax/c",0);
s_hist = t_hist = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
for (int i = 0; i < atom->nmax; i++)
for (int j = 0; j < nprev; ++j)
s_hist[i][j] = t_hist[i][j] = 0;
}
/* ---------------------------------------------------------------------- */
@ -161,6 +164,13 @@ FixQEqReax::~FixQEqReax()
void FixQEqReax::post_constructor()
{
if (lmp->citeme) lmp->citeme->add(cite_fix_qeq_reax);
grow_arrays(atom->nmax);
for (int i = 0; i < atom->nmax; i++)
for (int j = 0; j < nprev; ++j)
s_hist[i][j] = t_hist[i][j] = 0;
pertype_parameters(pertype_option);
if (dual_enabled)
error->all(FLERR,"Dual keyword only supported with fix qeq/reax/omp");
@ -287,8 +297,7 @@ void FixQEqReax::reallocate_storage()
void FixQEqReax::allocate_matrix()
{
int i,ii,inum,m;
int *ilist, *numneigh;
int i,ii,n,m;
int mincap;
double safezone;
@ -306,18 +315,8 @@ void FixQEqReax::allocate_matrix()
// determine the total space for the H matrix
if (reaxc) {
inum = reaxc->list->inum;
ilist = reaxc->list->ilist;
numneigh = reaxc->list->numneigh;
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
}
m = 0;
for (ii = 0; ii < inum; ii++) {
for (ii = 0; ii < nn; ii++) {
i = ilist[ii];
m += numneigh[i];
}
@ -432,6 +431,20 @@ void FixQEqReax::init_taper()
void FixQEqReax::setup_pre_force(int vflag)
{
if (reaxc) {
nn = reaxc->list->inum;
NN = reaxc->list->inum + reaxc->list->gnum;
ilist = reaxc->list->ilist;
numneigh = reaxc->list->numneigh;
firstneigh = reaxc->list->firstneigh;
} else {
nn = list->inum;
NN = list->inum + list->gnum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
}
deallocate_storage();
allocate_storage();
@ -495,8 +508,21 @@ void FixQEqReax::pre_force(int /*vflag*/)
if (update->ntimestep % nevery) return;
if (comm->me == 0) t_start = MPI_Wtime();
n = atom->nlocal;
N = atom->nlocal + atom->nghost;
int n = atom->nlocal;
if (reaxc) {
nn = reaxc->list->inum;
NN = reaxc->list->inum + reaxc->list->gnum;
ilist = reaxc->list->ilist;
numneigh = reaxc->list->numneigh;
firstneigh = reaxc->list->firstneigh;
} else {
nn = list->inum;
NN = list->inum + list->gnum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
}
// grow arrays if necessary
// need to be atom->nmax in length
@ -540,16 +566,7 @@ void FixQEqReax::init_matvec()
/* fill-in H matrix */
compute_H();
int nn, ii, i;
int *ilist;
if (reaxc) {
nn = reaxc->list->inum;
ilist = reaxc->list->ilist;
} else {
nn = list->inum;
ilist = list->ilist;
}
int ii, i;
for (ii = 0; ii < nn; ++ii) {
i = ilist[ii];
@ -578,7 +595,7 @@ void FixQEqReax::init_matvec()
void FixQEqReax::compute_H()
{
int inum, jnum, *ilist, *jlist, *numneigh, **firstneigh;
int jnum;
int i, j, ii, jj, flag;
double dx, dy, dz, r_sqr;
const double SMALL = 0.0001;
@ -588,22 +605,10 @@ void FixQEqReax::compute_H()
double **x = atom->x;
int *mask = atom->mask;
if (reaxc) {
inum = reaxc->list->inum;
ilist = reaxc->list->ilist;
numneigh = reaxc->list->numneigh;
firstneigh = reaxc->list->firstneigh;
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
}
// fill in the H matrix
m_fill = 0;
r_sqr = 0;
for (ii = 0; ii < inum; ii++) {
for (ii = 0; ii < nn; ii++) {
i = ilist[ii];
if (mask[i] & groupbit) {
jlist = firstneigh[i];
@ -621,7 +626,7 @@ void FixQEqReax::compute_H()
flag = 0;
if (r_sqr <= SQR(swb)) {
if (j < n) flag = 1;
if (j < atom->nlocal) flag = 1;
else if (tag[i] < tag[j]) flag = 1;
else if (tag[i] == tag[j]) {
if (dz > SMALL) flag = 1;
@ -676,21 +681,11 @@ double FixQEqReax::calculate_H( double r, double gamma)
int FixQEqReax::CG( double *b, double *x)
{
int i, j, imax;
int i, j;
double tmp, alpha, beta, b_norm;
double sig_old, sig_new;
int nn, jj;
int *ilist;
if (reaxc) {
nn = reaxc->list->inum;
ilist = reaxc->list->ilist;
} else {
nn = list->inum;
ilist = list->ilist;
}
imax = 200;
int jj;
pack_flag = 1;
sparse_matvec( &H, x, q);
@ -748,18 +743,7 @@ int FixQEqReax::CG( double *b, double *x)
void FixQEqReax::sparse_matvec( sparse_matrix *A, double *x, double *b)
{
int i, j, itr_j;
int nn, NN, ii;
int *ilist;
if (reaxc) {
nn = reaxc->list->inum;
NN = reaxc->list->inum + reaxc->list->gnum;
ilist = reaxc->list->ilist;
} else {
nn = list->inum;
NN = list->inum + list->gnum;
ilist = list->ilist;
}
int ii;
for (ii = 0; ii < nn; ++ii) {
i = ilist[ii];
@ -794,16 +778,7 @@ void FixQEqReax::calculate_Q()
double u, s_sum, t_sum;
double *q = atom->q;
int nn, ii;
int *ilist;
if (reaxc) {
nn = reaxc->list->inum;
ilist = reaxc->list->ilist;
} else {
nn = list->inum;
ilist = list->ilist;
}
int ii;
s_sum = parallel_vector_acc( s, nn);
t_sum = parallel_vector_acc( t, nn);
@ -988,12 +963,6 @@ double FixQEqReax::parallel_norm( double *v, int n)
double my_sum, norm_sqr;
int ii;
int *ilist;
if (reaxc)
ilist = reaxc->list->ilist;
else
ilist = list->ilist;
my_sum = 0.0;
norm_sqr = 0.0;
@ -1016,12 +985,6 @@ double FixQEqReax::parallel_dot( double *v1, double *v2, int n)
double my_dot, res;
int ii;
int *ilist;
if (reaxc)
ilist = reaxc->list->ilist;
else
ilist = list->ilist;
my_dot = 0.0;
res = 0.0;
@ -1044,12 +1007,6 @@ double FixQEqReax::parallel_vector_acc( double *v, int n)
double my_acc, res;
int ii;
int *ilist;
if (reaxc)
ilist = reaxc->list->ilist;
else
ilist = list->ilist;
my_acc = 0.0;
res = 0.0;
@ -1070,12 +1027,6 @@ void FixQEqReax::vector_sum( double* dest, double c, double* v,
double d, double* y, int k)
{
int kk;
int *ilist;
if (reaxc)
ilist = reaxc->list->ilist;
else
ilist = list->ilist;
for (--k; k>=0; --k) {
kk = ilist[k];
@ -1089,12 +1040,6 @@ void FixQEqReax::vector_sum( double* dest, double c, double* v,
void FixQEqReax::vector_add( double* dest, double c, double* v, int k)
{
int kk;
int *ilist;
if (reaxc)
ilist = reaxc->list->ilist;
else
ilist = list->ilist;
for (--k; k>=0; --k) {
kk = ilist[k];
@ -1102,3 +1047,4 @@ void FixQEqReax::vector_add( double* dest, double c, double* v, int k)
dest[kk] += c * v[kk];
}
}

4
src/USER-REAXC/fix_qeq_reax.h
View File

@ -57,12 +57,13 @@ class FixQEqReax : public Fix {
protected:
int nevery,reaxflag;
int n, N, m_fill;
int nn, NN, m_fill;
int n_cap, nmax, m_cap;
int pack_flag;
int nlevels_respa;
class NeighList *list;
class PairReaxC *reaxc;
int *ilist, *jlist, *numneigh, **firstneigh;
double swa, swb; // lower/upper Taper cutoff radius
double Tap[8]; // Taper function
@ -94,6 +95,7 @@ class FixQEqReax : public Fix {
//CG storage
double *p, *q, *r, *d;
int imax;
//GMRES storage
//double *g,*y;

1
src/USER-SMD/fix_smd_adjust_dt.cpp
View File

@ -186,6 +186,7 @@ void FixSMDTlsphDtReset::end_of_step() {
update->dt = dt;
update->dt_default = 0;
if (force->pair)
force->pair->reset_dt();
for (int i = 0; i < modify->nfix; i++)

2
src/atom.cpp
View File

@ -2508,7 +2508,7 @@ length of the data area, and a short description.
Typically the name of the pointer variable returned
* \return pointer to the requested data cast to ``void *`` or NULL */
void *Atom::extract(char *name)
void *Atom::extract(const char *name)
{
// --------------------------------------------------------------------
// 4th customization section: customize by adding new variable name

2
src/atom.h
View File

@ -331,7 +331,7 @@ class Atom : protected Pointers {
virtual void sync_modify(ExecutionSpace, unsigned int, unsigned int) {}
void *extract(char *);
void *extract(const char *);
inline int* get_map_array() {return map_array;};
inline int get_map_size() {return map_tag_max+1;};

6
src/finish.cpp
View File

@ -202,12 +202,12 @@ void Finish::end(int flag)
update->minimize->einitial,
update->minimize->eprevious,
update->minimize->efinal);
mesg += fmt::format(" Force two-norm initial, final = {} {}\n",
mesg += fmt::format(" Force two-norm initial, final = {:.8} {:.8}\n",
update->minimize->fnorm2_init,update->minimize->fnorm2_final);
mesg += fmt::format(" Force max component initial, final = {} {}\n",
mesg += fmt::format(" Force max component initial, final = {:.8} {:.8}\n",
update->minimize->fnorminf_init,
update->minimize->fnorminf_final);
mesg += fmt::format(" Final line search alpha, max atom move = {} {}\n",
mesg += fmt::format(" Final line search alpha, max atom move = {:.8} {:.8}\n",
update->minimize->alpha_final,
update->minimize->alpha_final*
update->minimize->fnorminf_final);

1
src/fix_dt_reset.cpp
View File

@ -190,6 +190,7 @@ void FixDtReset::end_of_step()
update->update_time();
update->dt = dt;
update->dt_default = 0;
if (respaflag) update->integrate->reset_dt();
if (force->pair) force->pair->reset_dt();
for (int i = 0; i < modify->nfix; i++) modify->fix[i]->reset_dt();

1
src/input.cpp
View File

@ -1871,6 +1871,7 @@ void Input::timestep()
{
if (narg != 1) error->all(FLERR,"Illegal timestep command");
update->dt = utils::numeric(FLERR,arg[0],false,lmp);
update->dt_default = 0;
}
/* ---------------------------------------------------------------------- */

40
src/library.cpp
View File

@ -69,7 +69,7 @@ using namespace LAMMPS_NS;
#ifdef LAMMPS_EXCEPTIONS
#define BEGIN_CAPTURE \
Error * error = lmp->error; \
Error *error = lmp->error; \
try
#define END_CAPTURE \
@ -626,7 +626,7 @@ double lammps_get_natoms(void *handle)
{
LAMMPS *lmp = (LAMMPS *) handle;
double natoms = static_cast<double> (lmp->atom->natoms);
double natoms = static_cast<double>(lmp->atom->natoms);
if (natoms > 9.0e15) return 0; // TODO:XXX why not -1?
return natoms;
}
@ -648,7 +648,7 @@ a double, so it can also return information that is computed on-the-fly.
* \param keyword string with the name of the thermo keyword
* \return value of the requested thermo property or 0.0 */
double lammps_get_thermo(void *handle, char *keyword)
double lammps_get_thermo(void *handle, const char *keyword)
{
LAMMPS *lmp = (LAMMPS *) handle;
double dval = 0.0;
@ -839,7 +839,7 @@ recognized, the function returns -1. Please also see :cpp:func:`lammps_extract_
* \param keyword string with the name of the thermo keyword
* \return value of the queried setting or -1 if unknown */
int lammps_extract_setting(void * handle, char *keyword)
int lammps_extract_setting(void *handle, const char *keyword)
{
LAMMPS *lmp = (LAMMPS *) handle;
@ -897,7 +897,8 @@ Please also see :cpp:func:`lammps_extract_setting`,
This table lists the supported names, their data types, length of the
data area, and a short description. The ``bigint`` type may be defined
to be either an ``int`` or an ``int64_t``. This is selected at
:ref:`compile time <size>`.
:ref:`compile time <size>` and can be queried through calling
:cpp:func:`lammps_extract_setting`.
.. list-table::
:header-rows: 1
@ -1105,7 +1106,7 @@ to be either an ``int`` or an ``int64_t``. This is selected at
* \return pointer (cast to ``void *``) to the location of the
requested property. NULL if name is not known. */
void *lammps_extract_global(void *handle, char *name)
void *lammps_extract_global(void *handle, const char *name)
{
LAMMPS *lmp = (LAMMPS *) handle;
@ -1197,7 +1198,7 @@ of the :cpp:func:`Atom::extract() <LAMMPS_NS::Atom::extract>` function.
* \return pointer (cast to ``void *``) to the location of the
* requested data or ``NULL`` if not found. */
void *lammps_extract_atom(void *handle, char *name)
void *lammps_extract_atom(void *handle, const char *name)
{
LAMMPS *lmp = (LAMMPS *) handle;
return lmp->atom->extract(name);
@ -3756,7 +3757,7 @@ specific :doc:`LAMMPS package <Packages>` provided as argument.
* \param name string with the name of the package
* \return 1 if included, 0 if not.
*/
int lammps_config_has_package(char * name) {
int lammps_config_has_package(const char *name) {
return Info::has_package(name) ? 1 : 0;
}
@ -3796,7 +3797,7 @@ the function returns 0 and *buffer* is set to an empty string, otherwise 1;
* \param buf_size size of the provided string buffer
* \return 1 if successful, otherwise 0
*/
int lammps_config_package_name(int idx, char * buffer, int buf_size) {
int lammps_config_package_name(int idx, char *buffer, int buf_size) {
int maxidx = lammps_config_package_count();
if ((idx < 0) || (idx >= maxidx)) {
buffer[0] = '\0';
@ -3820,14 +3821,14 @@ Valid categories are: *atom*\ , *integrate*\ , *minimize*\ ,
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
* \param category category of the style
* \param name name of the style
* \return 1 if included, 0 if not.
* \param category category of the style
* \param name name of the style
* \return 1 if included, 0 if not.
*/
int lammps_has_style(void * handle, char * category, char * name) {
int lammps_has_style(void *handle, const char *category, const char *name) {
LAMMPS *lmp = (LAMMPS *) handle;
Info info(lmp);
return info.has_style(category, name) ? 0 : 1;
return info.has_style(category, name) ? 1 : 0;
}
/* ---------------------------------------------------------------------- */
@ -3845,7 +3846,7 @@ categories.
* \param category category of styles
* \return number of styles in category
*/
int lammps_style_count(void * handle, char * category) {
int lammps_style_count(void *handle, const char *category) {
LAMMPS *lmp = (LAMMPS *) handle;
Info info(lmp);
return info.get_available_styles(category).size();
@ -3871,7 +3872,8 @@ Please see :cpp:func:`lammps_has_style` for a list of valid categories.
* \param buf_size size of the provided string buffer
* \return 1 if successful, otherwise 0
*/
int lammps_style_name(void* handle, char * category, int idx, char * buffer, int buf_size) {
int lammps_style_name(void *handle, const char *category, int idx,
char *buffer, int buf_size) {
LAMMPS *lmp = (LAMMPS *) handle;
Info info(lmp);
auto styles = info.get_available_styles(category);
@ -4297,10 +4299,10 @@ the failing MPI ranks to send messages.
* \param buf_size size of the provided string buffer
* \return 1 when all ranks had the error, 1 on a single rank error.
*/
int lammps_get_last_error_message(void *handle, char * buffer, int buf_size) {
int lammps_get_last_error_message(void *handle, char *buffer, int buf_size) {
#ifdef LAMMPS_EXCEPTIONS
LAMMPS * lmp = (LAMMPS *) handle;
Error * error = lmp->error;
LAMMPS *lmp = (LAMMPS *) handle;
Error *error = lmp->error;
if(!error->get_last_error().empty()) {
int error_type = error->get_last_error_type();

16
src/library.h
View File

@ -101,7 +101,7 @@ int lammps_version(void *handle);
void lammps_memory_usage(void *handle, double *meminfo);
int lammps_get_mpi_comm(void *handle);
double lammps_get_natoms(void *handle);
double lammps_get_thermo(void *handle, char *keyword);
double lammps_get_thermo(void *handle, const char *keyword);
void lammps_extract_box(void *handle, double *boxlo, double *boxhi,
double *xy, double *yz, double *xz,
@ -109,9 +109,9 @@ void lammps_extract_box(void *handle, double *boxlo, double *boxhi,
void lammps_reset_box(void *handle, double *boxlo, double *boxhi,
double xy, double yz, double xz);
int lammps_extract_setting(void *handle, char *keyword);
void *lammps_extract_global(void *handle, char *name);
void *lammps_extract_atom(void *handle, char *name);
int lammps_extract_setting(void *handle, const char *keyword);
void *lammps_extract_global(void *handle, const char *name);
void *lammps_extract_atom(void *handle, const char *name);
#if !defined(LAMMPS_BIGBIG)
int lammps_create_atoms(void *handle, int n, int *id, int *type,
@ -153,7 +153,7 @@ void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *);
* ---------------------------------------------------------------------- */
int lammps_config_has_mpi_support();
int lammps_config_has_package(char *);
int lammps_config_has_package(const char *);
int lammps_config_package_count();
int lammps_config_package_name(int, char *, int);
int lammps_config_has_gzip_support();
@ -162,9 +162,9 @@ int lammps_config_has_jpeg_support();
int lammps_config_has_ffmpeg_support();
int lammps_config_has_exceptions();
int lammps_has_style(void *, char *, char *);
int lammps_style_count(void *, char *);
int lammps_style_name(void *, char *, int, char *, int);
int lammps_has_style(void *, const char *, const char *);
int lammps_style_count(void *, const char *);
int lammps_style_name(void *, const char *, int, char *, int);
/* ----------------------------------------------------------------------
* Library functions for accessing neighbor lists

5
src/read_data.cpp
View File

@ -294,8 +294,11 @@ void ReadData::command(int narg, char **arg)
// error checks
if (domain->dimension == 2 && domain->zperiodic == 0)
if ((domain->dimension == 2) && (domain->zperiodic == 0))
error->all(FLERR,"Cannot run 2d simulation with nonperiodic Z dimension");
if ((domain->nonperiodic == 2) && utils::strmatch(force->kspace_style,"^msm"))
error->all(FLERR,"Reading a data file with shrinkwrap boundaries is "
"not compatible with a MSM KSpace style");
if (domain->box_exist && !addflag)
error->all(FLERR,"Cannot read_data without add keyword "
"after simulation box is defined");

31
src/update.cpp
View File

@ -12,18 +12,22 @@
------------------------------------------------------------------------- */
#include "update.h"
#include <cstring>
#include "integrate.h"
#include "min.h"
#include "style_integrate.h" // IWYU pragma: keep
#include "style_minimize.h" // IWYU pragma: keep
#include "neighbor.h"
#include "force.h"
#include "modify.h"
#include "fix.h"
#include "comm.h"
#include "compute.h"
#include "output.h"
#include "integrate.h"
#include "error.h"
#include "fix.h"
#include "force.h"
#include "min.h"
#include "modify.h"
#include "neighbor.h"
#include "output.h"
#include <cstring>
using namespace LAMMPS_NS;
@ -48,6 +52,7 @@ Update::Update(LAMMPS *lmp) : Pointers(lmp)
eflag_global = vflag_global = -1;
dt_default = 1;
unit_style = NULL;
set_units("lj");
@ -121,6 +126,8 @@ void Update::set_units(const char *style)
// http://physics.nist.gov/cuu/Constants/Table/allascii.txt
// using thermochemical calorie = 4.184 J
double dt_old = dt;
if (strcmp(style,"lj") == 0) {
force->boltz = 1.0;
force->hplanck = 1.0;
@ -295,6 +302,14 @@ void Update::set_units(const char *style)
int n = strlen(style) + 1;
unit_style = new char[n];
strcpy(unit_style,style);
// check if timestep was changed from default value
if (!dt_default && (comm->me == 0)) {
error->warning(FLERR,fmt::format("Changing timestep from {:.6} to {:.6} "
"due to changing units to {}",
dt_old, dt, unit_style));
}
dt_default = 1;
}
/* ---------------------------------------------------------------------- */

1
src/update.h
View File

@ -37,6 +37,7 @@ class Update : protected Pointers {
int setupflag; // set when setup() is computing forces
int post_integrate; // 1 if now at post_integrate() in timestep
int multireplica; // 1 if min across replicas, else 0
int dt_default; // 1 if dt is at default value, else 0
bigint eflag_global,eflag_atom; // timestep global/peratom eng is tallied on
bigint vflag_global,vflag_atom; // ditto for virial

56
unittest/c-library/CMakeLists.txt
View File

@ -1,13 +1,57 @@
add_executable(test_library_open test_library_open.cpp)
target_link_libraries(test_library_open PRIVATE lammps GTest::GTest GTest::GTestMain)
add_executable(test_library_open test_library_open.cpp test_main.cpp)
target_link_libraries(test_library_open PRIVATE lammps GTest::GTest GTest::GMock)
add_test(LibraryOpen test_library_open)
add_executable(test_library_commands test_library_commands.cpp)
target_link_libraries(test_library_commands PRIVATE lammps GTest::GTest GTest::GTestMain)
add_executable(test_library_commands test_library_commands.cpp test_main.cpp)
target_link_libraries(test_library_commands PRIVATE lammps GTest::GTest GTest::GMock)
add_test(LibraryCommands test_library_commands)
add_executable(test_library_properties test_library_properties.cpp)
target_link_libraries(test_library_properties PRIVATE lammps GTest::GTest GTest::GTestMain)
add_executable(test_library_properties test_library_properties.cpp test_main.cpp)
target_link_libraries(test_library_properties PRIVATE lammps GTest::GTest GTest::GMock)
target_compile_definitions(test_library_properties PRIVATE -DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR})
add_test(LibraryProperties test_library_properties)
set(TEST_CONFIG_DEFS "-DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR};-DLAMMPS_${LAMMPS_SIZES}")
set(PKG_COUNT 0)
foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
if(PKG_${PKG})
MATH(EXPR PKG_COUNT "${PKG_COUNT}+1")
endif()
endforeach()
list(APPEND TEST_CONFIG_DEFS -DNUM_LAMMPS_PACKAGES=${PKG_COUNT})
if(PKG_MANYBODY)
set(HAS_MANYBODY 1)
else()
set(HAS_MANYBODY 0)
endif()
list(APPEND TEST_CONFIG_DEFS -DLAMMPS_HAS_MANYBODY=${HAS_MANYBODY})
if(BUILD_MPI)
set(HAS_MPI 1)
else()
set(HAS_MPI 0)
endif()
list(APPEND TEST_CONFIG_DEFS -DLAMMPS_HAS_MPI=${HAS_MPI})
if(LAMMPS_EXCEPTIONS)
set(HAS_EXCEPTIONS 1)
else()
set(HAS_EXCEPTIONS 0)
endif()
list(APPEND TEST_CONFIG_DEFS -DLAMMPS_HAS_EXCEPTIONS=${HAS_EXCEPTIONS})
foreach(WITH "JPEG" "PNG" "GZIP" "FFMPEG")
if(WITH_${WITH})
set(HAS_${WITH} 1)
else()
set(HAS_${WITH} 0)
endif()
list(APPEND TEST_CONFIG_DEFS -DLAMMPS_HAS_${WITH}=${HAS_${WITH}})
endforeach()
add_executable(test_library_config test_library_config.cpp test_main.cpp)
target_link_libraries(test_library_config PRIVATE lammps GTest::GTest GTest::GMock)
target_compile_definitions(test_library_config PRIVATE ${TEST_CONFIG_DEFS})
add_test(LibraryConfig test_library_config)

210
unittest/c-library/data.fourmol Normal file
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@ -0,0 +1,210 @@
LAMMPS data file via write_data, version 5 May 2020, timestep = 0
29 atoms
5 atom types
24 bonds
5 bond types
30 angles
4 angle types
31 dihedrals
5 dihedral types
2 impropers
2 improper types
-6.024572 8.975428 xlo xhi
-7.692866 7.307134 ylo yhi
-8.086924 6.913076 zlo zhi
Masses
1 12.0107
2 4.00794
3 14.0067
4 15.9994
5 15.9994
Pair Coeffs # zero
1
2
3
4
5
Bond Coeffs # zero
1 1.5
2 1.1
3 1.3
4 1.2
5 1
Angle Coeffs # zero
1 110.1
2 111
3 120
4 108.5
Atoms # full
10 2 1 7.0000000000000007e-02 2.0185283555536988e+00 -1.4283966846517357e+00 -9.6733527271133024e-01 0 0 0
11 2 2 8.9999999999999997e-02 1.7929780509347666e+00 -1.9871047540768743e+00 -1.8840626643185674e+00 0 0 0
12 2 1 -2.7000000000000002e-01 3.0030247876861225e+00 -4.8923319967572748e-01 -1.6188658531537248e+00 0 0 0
13 2 2 8.9999999999999997e-02 4.0447273787895934e+00 -9.0131998547446246e-01 -1.6384447268320836e+00 0 0 0
14 2 2 8.9999999999999997e-02 2.6033152817257075e+00 -4.0789761505963579e-01 -2.6554413538823063e+00 0 0 0
2 1 2 3.1000000000000000e-01 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 0 0 0
3 1 1 -2.0000000000000000e-02 -6.9435377880558602e-01 1.2440473127136711e+00 -6.2233801468892025e-01 0 0 0
4 1 2 8.9999999999999997e-02 -1.5771614164685133e+00 1.4915333140468066e+00 -1.2487126845040522e+00 0 0 0
6 1 1 5.1000000000000001e-01 2.9412607937706009e-01 2.2719282656652909e-01 -1.2843094067857870e+00 0 0 0
7 1 4 -5.1000000000000001e-01 3.4019871062879609e-01 -9.1277350075786561e-03 -2.4633113224304561e+00 0 0 0
19 3 2 4.2359999999999998e-01 1.5349125211132961e+00 2.6315969880333707e+00 -4.2472859440220647e+00 0 0 0
15 2 2 8.9999999999999997e-02 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 0 0 0
18 3 4 -8.4719999999999995e-01 2.1384791188033843e+00 3.0177261773770208e+00 -3.5160827596876225e+00 0 0 0
20 3 2 4.2359999999999998e-01 2.7641167828863153e+00 3.6833419064000221e+00 -3.9380850623312638e+00 0 0 0
8 2 3 -4.6999999999999997e-01 1.1641187171852805e+00 -4.8375305955385234e-01 -6.7659823767368688e-01 0 0 0
9 2 2 3.1000000000000000e-01 1.3777459838125838e+00 -2.5366338669522998e-01 2.6877644730326306e-01 0 0 0
16 2 1 5.1000000000000001e-01 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 0 0 0
17 2 4 -5.1000000000000001e-01 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 0 0 0
1 1 3 -4.6999999999999997e-01 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 0 0 0
5 1 2 8.9999999999999997e-02 -8.9501761359359255e-01 9.3568128743071344e-01 4.0227731871484346e-01 0 0 0
21 4 5 -8.4719999999999995e-01 4.9064454390208301e+00 -4.0751205255383196e+00 -3.6215576073601046e+00 0 0 0
22 4 2 4.2359999999999998e-01 4.3687453488627543e+00 -4.2054270536772504e+00 -4.4651491269372565e+00 0 0 0
23 4 2 4.2359999999999998e-01 5.7374928154769504e+00 -3.5763355905184966e+00 -3.8820297194230728e+00 0 0 0
24 5 5 -8.4719999999999995e-01 2.0684115301174013e+00 3.1518221747664397e+00 3.1554242678474576e+00 0 0 0
25 5 2 4.2359999999999998e-01 1.2998381073113014e+00 3.2755513587518097e+00 2.5092990173114837e+00 0 0 0
26 5 2 4.2359999999999998e-01 2.5807438597688113e+00 4.0120175892854135e+00 3.2133398379059099e+00 0 0 0
27 6 5 -8.4719999999999995e-01 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 0 0 0
28 6 2 4.2359999999999998e-01 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 0 0 0
29 6 2 4.2359999999999998e-01 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 0 0 0
Velocities
1 7.7867804888392077e-04 5.8970331623292821e-04 -2.2179517633030531e-04
2 2.7129529964126462e-03 4.6286427111164284e-03 3.5805549693846352e-03
3 -1.2736791029204805e-03 1.6108674226414498e-03 -3.3618185901550799e-04
4 -9.2828595122009308e-04 -1.2537885319521818e-03 -4.1204974953432108e-03
5 -1.1800848061603740e-03 7.5424401975844038e-04 6.9023177964912290e-05
6 -3.0914004879905335e-04 1.2755385764678133e-03 7.9574303350202582e-04
7 -1.1037894966874103e-04 -7.6764845099077425e-04 -7.7217630460203659e-04
8 3.9060281273221989e-04 -8.1444231918053418e-04 1.5134641148324972e-04
9 1.2475530960659720e-03 -2.6608454451432528e-03 1.1117602907112732e-03
10 4.5008983776042893e-04 4.9530197647538077e-04 -2.3336234361093645e-04
11 -3.6977669078869707e-04 -1.5289071951960539e-03 -2.9176389881837113e-03
12 1.0850834530183159e-03 -6.4965897903201833e-04 -1.2971152622619948e-03
13 4.0754559196230639e-03 3.5043502394946119e-03 -7.8324487687854666e-04
14 -1.3837220448746613e-04 -4.0656048637594394e-03 -3.9333461173944500e-03
15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03
16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03
17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04
18 -6.0936815808025862e-04 -9.3774557532468582e-04 -3.3558072507805731e-04
19 -6.9919768291957119e-04 -3.6060777270430031e-03 4.2833405289822791e-03
20 4.7777805013736515e-03 5.1003745845520452e-03 1.8002873923729241e-03
21 -9.5568188553430398e-04 1.6594630943762931e-04 -1.8199788009966615e-04
22 -3.3137518957653462e-03 -2.8683968287936054e-03 3.6384389958326871e-03
23 2.4209481134686401e-04 -4.5457709985051130e-03 2.7663581642115042e-03
24 2.5447450568861086e-04 4.8412447786110117e-04 -4.8021914527341357e-04
25 4.3722771097312743e-03 -4.5184411669545515e-03 2.5200952006556795e-03
26 -1.9250110555001179e-03 -3.0342169883610837e-03 3.5062814567984532e-03
27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04
28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03
29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03
Bonds
1 5 1 2
2 3 1 3
3 2 3 4
4 2 3 5
5 1 3 6
6 3 6 8
7 4 6 7
8 5 8 9
9 3 8 10
10 2 10 11
11 1 10 12
12 1 10 16
13 2 12 13
14 2 12 14
15 2 12 15
16 4 16 17
17 5 18 19
18 5 18 20
19 5 21 22
20 5 21 23
21 5 24 25
22 5 24 26
23 5 27 28
24 5 27 29
Angles
1 4 2 1 3
2 4 1 3 5
3 4 1 3 4
4 4 1 3 6
5 4 4 3 5
6 2 5 3 6
7 2 4 3 6
8 3 3 6 7
9 3 3 6 8
10 3 7 6 8
11 2 6 8 9
12 2 9 8 10
13 3 6 8 10
14 2 8 10 11
15 3 8 10 16
16 2 11 10 12
17 1 12 10 16
18 1 8 10 12
19 2 11 10 16
20 2 10 12 15
21 2 10 12 14
22 2 10 12 13
23 4 13 12 15
24 4 13 12 14
25 4 14 12 15
26 4 10 16 17
27 1 19 18 20
28 1 22 21 23
29 1 25 24 26
30 1 28 27 29
Dihedrals
1 2 2 1 3 6
2 2 2 1 3 4
3 3 2 1 3 5
4 1 1 3 6 8
5 1 1 3 6 7
6 5 4 3 6 8
7 5 4 3 6 7
8 5 5 3 6 8
9 5 5 3 6 7
10 4 3 6 8 9
11 3 3 6 8 10
12 3 7 6 8 9
13 4 7 6 8 10
14 2 6 8 10 12
15 2 6 8 10 16
16 2 6 8 10 11
17 2 9 8 10 12
18 4 9 8 10 16
19 5 9 8 10 11
20 5 8 10 12 13
21 1 8 10 12 14
22 5 8 10 12 15
23 4 8 10 16 17
24 5 11 10 12 13
25 5 11 10 12 14
26 5 11 10 12 15
27 2 11 10 16 17
28 2 12 10 16 17
29 5 16 10 12 13
30 5 16 10 12 14
31 5 16 10 12 15
Impropers
1 1 6 3 8 7
2 2 8 6 10 9

25
unittest/c-library/in.fourmol Normal file
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variable units index real
variable input_dir index .
variable data_file index ${input_dir}/data.fourmol
variable pair_style index 'zero 8.0'
variable bond_style index zero
variable angle_style index zero
variable dihedral_style index zero
variable improper_style index zero
atom_style full
atom_modify map array
neigh_modify delay 2 every 2 check no
timestep 0.1
units ${units}
pair_style ${pair_style}
bond_style ${bond_style}
angle_style ${angle_style}
dihedral_style ${dihedral_style}
improper_style ${improper_style}
read_data ${data_file}
dihedral_coeff *
improper_coeff *

122
unittest/c-library/test_library_commands.cpp
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// unit tests for issuing command to a LAMMPS instance through the library interface
#include "library.h"
#include "lammps.h"
#include "library.h"
#include <string>
#include "gmock/gmock.h"
#include "gtest/gtest.h"
const char *demo_input[] = {
"region box block 0 $x 0 2 0 2",
"create_box 1 box",
"create_atoms 1 single 1.0 1.0 ${zpos}" };
const char *cont_input[] = {
"create_atoms 1 single &",
"0.2 0.1 0.1" };
#include "test_main.h"
class LAMMPS_commands : public ::testing::Test
{
using ::testing::HasSubstr;
using ::testing::StartsWith;
const char *demo_input[] = {"region box block 0 $x 0 2 0 2", "create_box 1 box",
"create_atoms 1 single 1.0 1.0 ${zpos}"};
const char *cont_input[] = {"create_atoms 1 single &", "0.2 0.1 0.1"};
class LibraryCommands : public ::testing::Test {
protected:
void *lmp;
LAMMPS_commands() {};
~LAMMPS_commands() override {};
LibraryCommands(){};
~LibraryCommands() override{};
void SetUp() override
{
const char *args[] = {"LAMMPS_test", "-log", "none", "-echo", "screen", "-nocite",
"-var", "x", "2", "-var", "zpos", "1.5"};
void SetUp() override {
const char *args[] = {"LAMMPS_test",
"-log", "none",
"-echo", "screen",
"-nocite", "-var","x","2",
"-var", "zpos", "1.5"};
char **argv = (char **)args;
int argc = sizeof(args)/sizeof(char *);
int argc = sizeof(args) / sizeof(char *);
::testing::internal::CaptureStdout();
lmp = lammps_open_no_mpi(argc, argv, NULL);
lmp = lammps_open_no_mpi(argc, argv, NULL);
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0,8).c_str(), "LAMMPS (");
if (verbose) std::cout << output;
EXPECT_THAT(output, StartsWith("LAMMPS ("));
}
void TearDown() override {
void TearDown() override
{
::testing::internal::CaptureStdout();
lammps_close(lmp);
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0,16).c_str(), "Total wall time:");
EXPECT_THAT(output, HasSubstr("Total wall time:"));
if (verbose) std::cout << output;
lmp = nullptr;
}
};
TEST_F(LAMMPS_commands, from_file) {
TEST_F(LibraryCommands, from_file)
{
FILE *fp;
const char demo_file[] = "in.test";
const char cont_file[] = "in.cont";
fp = fopen(demo_file,"w");
for (unsigned int i=0; i < sizeof(demo_input)/sizeof(char *); ++i) {
fputs(demo_input[i],fp);
fputc('\n',fp);
fp = fopen(demo_file, "w");
for (unsigned int i = 0; i < sizeof(demo_input) / sizeof(char *); ++i) {
fputs(demo_input[i], fp);
fputc('\n', fp);
}
fclose(fp);
fp = fopen(cont_file,"w");
for (unsigned int i=0; i < sizeof(cont_input)/sizeof(char *); ++i) {
fputs(cont_input[i],fp);
fputc('\n',fp);
fp = fopen(cont_file, "w");
for (unsigned int i = 0; i < sizeof(cont_input) / sizeof(char *); ++i) {
fputs(cont_input[i], fp);
fputc('\n', fp);
}
fclose(fp);
EXPECT_EQ(lammps_get_natoms(lmp),0);
lammps_file(lmp,demo_file);
lammps_file(lmp,cont_file);
EXPECT_EQ(lammps_get_natoms(lmp),2);
EXPECT_EQ(lammps_get_natoms(lmp), 0);
if (!verbose) ::testing::internal::CaptureStdout();
lammps_file(lmp, demo_file);
if (!verbose) ::testing::internal::GetCapturedStdout();
EXPECT_EQ(lammps_get_natoms(lmp), 1);
if (!verbose) ::testing::internal::CaptureStdout();
lammps_file(lmp, cont_file);
if (!verbose) ::testing::internal::GetCapturedStdout();
EXPECT_EQ(lammps_get_natoms(lmp), 2);
unlink(demo_file);
unlink(cont_file);
};
TEST_F(LAMMPS_commands, from_line) {
EXPECT_EQ(lammps_get_natoms(lmp),0);
for (unsigned int i=0; i < sizeof(demo_input)/sizeof(char *); ++i) {
lammps_command(lmp,demo_input[i]);
TEST_F(LibraryCommands, from_line)
{
EXPECT_EQ(lammps_get_natoms(lmp), 0);
if (!verbose) ::testing::internal::CaptureStdout();
for (unsigned int i = 0; i < sizeof(demo_input) / sizeof(char *); ++i) {
lammps_command(lmp, demo_input[i]);
}
EXPECT_EQ(lammps_get_natoms(lmp),1);
if (!verbose) ::testing::internal::GetCapturedStdout();
EXPECT_EQ(lammps_get_natoms(lmp), 1);
};
TEST_F(LAMMPS_commands, from_list) {
EXPECT_EQ(lammps_get_natoms(lmp),0);
lammps_commands_list(lmp,sizeof(demo_input)/sizeof(char *),demo_input);
lammps_commands_list(lmp,sizeof(cont_input)/sizeof(char *),cont_input);
EXPECT_EQ(lammps_get_natoms(lmp),2);
TEST_F(LibraryCommands, from_list)
{
EXPECT_EQ(lammps_get_natoms(lmp), 0);
if (!verbose) ::testing::internal::CaptureStdout();
lammps_commands_list(lmp, sizeof(demo_input) / sizeof(char *), demo_input);
lammps_commands_list(lmp, sizeof(cont_input) / sizeof(char *), cont_input);
if (!verbose) ::testing::internal::GetCapturedStdout();
EXPECT_EQ(lammps_get_natoms(lmp), 2);
};
TEST_F(LAMMPS_commands, from_string) {
TEST_F(LibraryCommands, from_string)
{
std::string cmds("");
for (unsigned int i=0; i < sizeof(demo_input)/sizeof(char *); ++i) {
for (unsigned int i = 0; i < sizeof(demo_input) / sizeof(char *); ++i) {
cmds += demo_input[i];
cmds += "\n";
}
for (unsigned int i=0; i < sizeof(cont_input)/sizeof(char *); ++i) {
for (unsigned int i = 0; i < sizeof(cont_input) / sizeof(char *); ++i) {
cmds += cont_input[i];
cmds += "\n";
}
EXPECT_EQ(lammps_get_natoms(lmp),0);
lammps_commands_string(lmp,cmds.c_str());
EXPECT_EQ(lammps_get_natoms(lmp),2);
EXPECT_EQ(lammps_get_natoms(lmp), 0);
if (!verbose) ::testing::internal::CaptureStdout();
lammps_commands_string(lmp, cmds.c_str());
if (!verbose) ::testing::internal::GetCapturedStdout();
EXPECT_EQ(lammps_get_natoms(lmp), 2);
};

149
unittest/c-library/test_library_config.cpp Normal file
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// unit tests for checking LAMMPS configuration settings through the library interface
#include "lammps.h"
#include "library.h"
#include <string>
#include "gmock/gmock.h"
#include "gtest/gtest.h"
#include "test_main.h"
#define STRINGIFY(val) XSTR(val)
#define XSTR(val) #val
using ::testing::HasSubstr;
using ::testing::StartsWith;
using ::testing::StrEq;
class LibraryConfig : public ::testing::Test {
protected:
void *lmp;
std::string INPUT_DIR = STRINGIFY(TEST_INPUT_FOLDER);
LibraryConfig(){};
~LibraryConfig() override{};
void SetUp() override
{
const char *args[] = {"LAMMPS_test", "-log", "none",
"-echo", "screen", "-nocite",
"-var", "input_dir", STRINGIFY(TEST_INPUT_FOLDER)};
char **argv = (char **)args;
int argc = sizeof(args) / sizeof(char *);
::testing::internal::CaptureStdout();
lmp = lammps_open_no_mpi(argc, argv, NULL);
std::string output = ::testing::internal::GetCapturedStdout();
if (verbose) std::cout << output;
EXPECT_THAT(output, StartsWith("LAMMPS ("));
}
void TearDown() override
{
::testing::internal::CaptureStdout();
lammps_close(lmp);
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_THAT(output, HasSubstr("Total wall time:"));
if (verbose) std::cout << output;
lmp = nullptr;
}
};
TEST(LAMMPSConfig, package_count)
{
EXPECT_EQ(lammps_config_package_count(), NUM_LAMMPS_PACKAGES);
};
TEST(LAMMPSConfig, has_package)
{
EXPECT_EQ(lammps_config_has_package("MANYBODY"), LAMMPS_HAS_MANYBODY);
};
TEST(LAMMPSConfig, package_name)
{
char buf[128];
int numpkgs = lammps_config_package_count();
if (numpkgs > 0) {
EXPECT_EQ(lammps_config_package_name(0, buf, 128), 1);
EXPECT_EQ(lammps_config_package_name(numpkgs + 10, buf, 128), 0);
EXPECT_THAT(buf, StrEq(""));
} else {
EXPECT_EQ(lammps_config_package_name(0, buf, 128), 1);
EXPECT_THAT(buf, StrEq(""));
}
};
TEST_F(LibraryConfig, has_style)
{
EXPECT_EQ(lammps_has_style(lmp, "atom", "atomic"), 1);
EXPECT_EQ(lammps_has_style(lmp, "compute", "temp"), 1);
EXPECT_EQ(lammps_has_style(lmp, "fix", "nve"), 1);
EXPECT_EQ(lammps_has_style(lmp, "pair", "lj/cut"), 1);
EXPECT_EQ(lammps_has_style(lmp, "bond", "zero"), 1);
EXPECT_EQ(lammps_has_style(lmp, "dump", "custom"), 1);
EXPECT_EQ(lammps_has_style(lmp, "region", "sphere"), 1);
EXPECT_EQ(lammps_has_style(lmp, "xxxxx", "lj/cut"), 0);
EXPECT_EQ(lammps_has_style(lmp, "pair", "xxxxxx"), 0);
#if LAMMPS_HAS_MANYBODY
EXPECT_EQ(lammps_has_style(lmp, "pair", "sw"), 1);
#else
EXPECT_EQ(lammps_has_style(lmp, "pair", "sw"), 0);
#endif
};
TEST_F(LibraryConfig, style_count)
{
EXPECT_GT(lammps_style_count(lmp, "atom"), 1);
EXPECT_GT(lammps_style_count(lmp, "bond"), 1);
EXPECT_GT(lammps_style_count(lmp, "angle"), 1);
EXPECT_GT(lammps_style_count(lmp, "dihedral"), 1);
EXPECT_GT(lammps_style_count(lmp, "improper"), 1);
EXPECT_GT(lammps_style_count(lmp, "pair"), 1);
EXPECT_GT(lammps_style_count(lmp, "kspace"), 1);
EXPECT_GT(lammps_style_count(lmp, "compute"), 1);
EXPECT_GT(lammps_style_count(lmp, "fix"), 1);
EXPECT_GT(lammps_style_count(lmp, "region"), 1);
EXPECT_GT(lammps_style_count(lmp, "dump"), 1);
EXPECT_GT(lammps_style_count(lmp, "integrate"), 1);
EXPECT_GT(lammps_style_count(lmp, "minimize"), 1);
};
TEST_F(LibraryConfig, style_name)
{
char buf[128];
int numstyles = lammps_style_count(lmp, "atom");
EXPECT_EQ(lammps_style_name(lmp, "atom", 0, buf, 128), 1);
EXPECT_EQ(lammps_style_name(lmp, "atom", numstyles + 10, buf, 128), 0);
EXPECT_THAT(buf, StrEq(""));
};
TEST(LAMMPSConfig, exceptions)
{
EXPECT_EQ(lammps_config_has_exceptions(), LAMMPS_HAS_EXCEPTIONS);
};
TEST(LAMMPSConfig, mpi_support)
{
EXPECT_EQ(lammps_config_has_mpi_support(), LAMMPS_HAS_MPI);
};
TEST(LAMMPSConfig, png_support)
{
EXPECT_EQ(lammps_config_has_png_support(), LAMMPS_HAS_PNG);
};
TEST(LAMMPSConfig, jpeg_support)
{
EXPECT_EQ(lammps_config_has_jpeg_support(), LAMMPS_HAS_JPEG);
};
TEST(LAMMPSConfig, gzip_support)
{
EXPECT_EQ(lammps_config_has_gzip_support(), LAMMPS_HAS_GZIP);
};
TEST(LAMMPSConfig, ffmpeg_support)
{
EXPECT_EQ(lammps_config_has_ffmpeg_support(), LAMMPS_HAS_FFMPEG);
};

123
unittest/c-library/test_library_open.cpp
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// unit tests for the LAMMPS base class
// unit tests creating LAMMPS instances via the library interface
#include "library.h"
#include "lammps.h"
#include "library.h"
#include <cstdio> // for stdin, stdout
#include <mpi.h>
#include <cstdio> // for stdin, stdout
#include <string>
#include "gmock/gmock.h"
#include "gtest/gtest.h"
TEST(lammps_open, null_args) {
#include "test_main.h"
using ::testing::HasSubstr;
using ::testing::StartsWith;
TEST(lammps_open, null_args)
{
::testing::internal::CaptureStdout();
void *handle = lammps_open(0,NULL, MPI_COMM_WORLD, NULL);
void *handle = lammps_open(0, NULL, MPI_COMM_WORLD, NULL);
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0,6).c_str(),"LAMMPS");
int mpi_init=0;
EXPECT_THAT(output, StartsWith("LAMMPS ("));
if (verbose) std::cout << output;
int mpi_init = 0;
MPI_Initialized(&mpi_init);
EXPECT_GT(mpi_init,0);
EXPECT_GT(mpi_init, 0);
LAMMPS_NS::LAMMPS *lmp = (LAMMPS_NS::LAMMPS *)handle;
EXPECT_EQ(lmp->world, MPI_COMM_WORLD);
EXPECT_EQ(lmp->infile, stdin);
@ -24,25 +32,26 @@ TEST(lammps_open, null_args) {
::testing::internal::CaptureStdout();
lammps_close(handle);
output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0,16).c_str(), "Total wall time:");
EXPECT_THAT(output, HasSubstr("Total wall time:"));
if (verbose) std::cout << output;
}
TEST(lammps_open, with_args) {
const char *args[] = {"liblammps",
"-log", "none",
"-nocite"};
char **argv = (char **)args;
int argc = sizeof(args)/sizeof(char *);
TEST(lammps_open, with_args)
{
const char *args[] = {"liblammps", "-log", "none", "-nocite"};
char **argv = (char **)args;
int argc = sizeof(args) / sizeof(char *);
// MPI is already initialized
MPI_Comm mycomm;
MPI_Comm_split(MPI_COMM_WORLD, 0, 1, &mycomm);
::testing::internal::CaptureStdout();
void *alt_ptr;
void *handle = lammps_open(argc, argv, mycomm, &alt_ptr);
void *handle = lammps_open(argc, argv, mycomm, &alt_ptr);
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0,6).c_str(),"LAMMPS");
EXPECT_EQ(handle,alt_ptr);
EXPECT_THAT(output, StartsWith("LAMMPS ("));
if (verbose) std::cout << output;
EXPECT_EQ(handle, alt_ptr);
LAMMPS_NS::LAMMPS *lmp = (LAMMPS_NS::LAMMPS *)handle;
// MPI STUBS uses no real communicators
@ -60,24 +69,24 @@ TEST(lammps_open, with_args) {
::testing::internal::CaptureStdout();
lammps_close(handle);
output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0,16).c_str(), "Total wall time:");
EXPECT_THAT(output, HasSubstr("Total wall time:"));
if (verbose) std::cout << output;
}
TEST(lammps_open, with_kokkos) {
TEST(lammps_open, with_kokkos)
{
if (!LAMMPS_NS::LAMMPS::is_installed_pkg("KOKKOS")) GTEST_SKIP();
const char *args[] = {"liblammps",
"-k", "on", "t", "2",
"-sf", "kk",
"-log", "none" };
char **argv = (char **)args;
int argc = sizeof(args)/sizeof(char *);
const char *args[] = {"liblammps", "-k", "on", "t", "2", "-sf", "kk", "-log", "none"};
char **argv = (char **)args;
int argc = sizeof(args) / sizeof(char *);
::testing::internal::CaptureStdout();
void *alt_ptr;
void *handle = lammps_open(argc, argv, MPI_COMM_WORLD, &alt_ptr);
void *handle = lammps_open(argc, argv, MPI_COMM_WORLD, &alt_ptr);
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0,6).c_str(),"LAMMPS");
EXPECT_EQ(handle,alt_ptr);
EXPECT_THAT(output, StartsWith("LAMMPS ("));
if (verbose) std::cout << output;
EXPECT_EQ(handle, alt_ptr);
LAMMPS_NS::LAMMPS *lmp = (LAMMPS_NS::LAMMPS *)handle;
EXPECT_EQ(lmp->world, MPI_COMM_WORLD);
@ -91,23 +100,22 @@ TEST(lammps_open, with_kokkos) {
::testing::internal::CaptureStdout();
lammps_close(handle);
output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0,16).c_str(), "Total wall time:");
EXPECT_THAT(output, HasSubstr("Total wall time:"));
if (verbose) std::cout << output;
}
TEST(lammps_open_no_mpi, no_screen) {
const char *args[] = {"liblammps",
"-log", "none",
"-screen", "none",
"-nocite"};
char **argv = (char **)args;
int argc = sizeof(args)/sizeof(char *);
TEST(lammps_open_no_mpi, no_screen)
{
const char *args[] = {"liblammps", "-log", "none", "-screen", "none", "-nocite"};
char **argv = (char **)args;
int argc = sizeof(args) / sizeof(char *);
::testing::internal::CaptureStdout();
void *alt_ptr;
void *handle = lammps_open_no_mpi(argc, argv, &alt_ptr);
void *handle = lammps_open_no_mpi(argc, argv, &alt_ptr);
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.c_str(),"");
EXPECT_EQ(handle,alt_ptr);
EXPECT_STREQ(output.c_str(), "");
EXPECT_EQ(handle, alt_ptr);
LAMMPS_NS::LAMMPS *lmp = (LAMMPS_NS::LAMMPS *)handle;
EXPECT_EQ(lmp->world, MPI_COMM_WORLD);
@ -125,22 +133,21 @@ TEST(lammps_open_no_mpi, no_screen) {
EXPECT_STREQ(output.c_str(), "");
}
TEST(lammps_open_no_mpi, with_omp) {
TEST(lammps_open_no_mpi, with_omp)
{
if (!LAMMPS_NS::LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP();
const char *args[] = {"liblammps",
"-pk", "omp", "2", "neigh", "no",
"-sf", "omp",
"-log", "none",
"-nocite"};
char **argv = (char **)args;
int argc = sizeof(args)/sizeof(char *);
const char *args[] = {"liblammps", "-pk", "omp", "2", "neigh", "no",
"-sf", "omp", "-log", "none", "-nocite"};
char **argv = (char **)args;
int argc = sizeof(args) / sizeof(char *);
::testing::internal::CaptureStdout();
void *alt_ptr;
void *handle = lammps_open_no_mpi(argc, argv, &alt_ptr);
void *handle = lammps_open_no_mpi(argc, argv, &alt_ptr);
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0,6).c_str(),"LAMMPS");
EXPECT_EQ(handle,alt_ptr);
EXPECT_THAT(output, StartsWith("LAMMPS ("));
if (verbose) std::cout << output;
EXPECT_EQ(handle, alt_ptr);
LAMMPS_NS::LAMMPS *lmp = (LAMMPS_NS::LAMMPS *)handle;
EXPECT_EQ(lmp->world, MPI_COMM_WORLD);
@ -155,18 +162,21 @@ TEST(lammps_open_no_mpi, with_omp) {
::testing::internal::CaptureStdout();
lammps_close(handle);
output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0,16).c_str(), "Total wall time:");
EXPECT_THAT(output, HasSubstr("Total wall time:"));
if (verbose) std::cout << output;
}
TEST(lammps_open_fortran, no_args) {
TEST(lammps_open_fortran, no_args)
{
// MPI is already initialized
MPI_Comm mycomm;
MPI_Comm_split(MPI_COMM_WORLD, 0, 1, &mycomm);
int fcomm = MPI_Comm_c2f(mycomm);
::testing::internal::CaptureStdout();
void *handle = lammps_open_fortran(0, NULL, fcomm);
void *handle = lammps_open_fortran(0, NULL, fcomm);
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0,6).c_str(),"LAMMPS");
EXPECT_THAT(output, StartsWith("LAMMPS ("));
if (verbose) std::cout << output;
LAMMPS_NS::LAMMPS *lmp = (LAMMPS_NS::LAMMPS *)handle;
// MPI STUBS uses no real communicators
@ -182,5 +192,6 @@ TEST(lammps_open_fortran, no_args) {
::testing::internal::CaptureStdout();
lammps_close(handle);
output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0,16).c_str(), "Total wall time:");
EXPECT_THAT(output, HasSubstr("Total wall time:"));
if (verbose) std::cout << output;
}

217
unittest/c-library/test_library_properties.cpp
View File

@ -1,53 +1,216 @@
// unit tests for checking and changing simulation properties through the library interface
#include "library.h"
#include "lammps.h"
#include "library.h"
#include <string>
#include "gmock/gmock.h"
#include "gtest/gtest.h"
const char *demo_input[] = {
"region box block 0 $x 0 2 0 2",
"create_box 1 box",
"create_atoms 1 single 1.0 1.0 ${zpos}" };
const char *cont_input[] = {
"create_atoms 1 single &",
"0.2 0.1 0.1" };
#include "test_main.h"
class LAMMPS_properties : public ::testing::Test
{
#define STRINGIFY(val) XSTR(val)
#define XSTR(val) #val
using ::testing::HasSubstr;
using ::testing::StartsWith;
class LibraryProperties : public ::testing::Test {
protected:
void *lmp;
LAMMPS_properties() {};
~LAMMPS_properties() override {};
std::string INPUT_DIR = STRINGIFY(TEST_INPUT_FOLDER);
LibraryProperties(){};
~LibraryProperties() override{};
void SetUp() override
{
const char *args[] = {"LAMMPS_test", "-log", "none",
"-echo", "screen", "-nocite",
"-var", "input_dir", STRINGIFY(TEST_INPUT_FOLDER)};
void SetUp() override {
const char *args[] = {"LAMMPS_test", "-log", "none",
"-echo", "screen", "-nocite" };
char **argv = (char **)args;
int argc = sizeof(args)/sizeof(char *);
int argc = sizeof(args) / sizeof(char *);
::testing::internal::CaptureStdout();
lmp = lammps_open_no_mpi(argc, argv, NULL);
lmp = lammps_open_no_mpi(argc, argv, NULL);
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0,8).c_str(), "LAMMPS (");
if (verbose) std::cout << output;
EXPECT_THAT(output, StartsWith("LAMMPS ("));
}
void TearDown() override {
void TearDown() override
{
::testing::internal::CaptureStdout();
lammps_close(lmp);
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0,16).c_str(), "Total wall time:");
EXPECT_THAT(output, HasSubstr("Total wall time:"));
if (verbose) std::cout << output;
lmp = nullptr;
}
};
TEST_F(LAMMPS_properties, get_mpi_comm) {
int f_comm = lammps_get_mpi_comm(lmp);
if (lammps_config_has_mpi_support())
EXPECT_GE(f_comm,0);
else
EXPECT_EQ(f_comm,-1);
TEST_F(LibraryProperties, version)
{
EXPECT_GE(20200824, lammps_version(lmp));
};
TEST_F(LAMMPS_properties, box) {
TEST_F(LibraryProperties, get_mpi_comm)
{
int f_comm = lammps_get_mpi_comm(lmp);
if (lammps_config_has_mpi_support())
EXPECT_GE(f_comm, 0);
else
EXPECT_EQ(f_comm, -1);
};
TEST_F(LibraryProperties, natoms)
{
if (!lammps_has_style(lmp, "atom", "full")) GTEST_SKIP();
std::string input = INPUT_DIR + PATH_SEP + "in.fourmol";
if (!verbose) ::testing::internal::CaptureStdout();
lammps_file(lmp, input.c_str());
if (!verbose) ::testing::internal::GetCapturedStdout();
EXPECT_EQ(lammps_get_natoms(lmp), 29);
};
TEST_F(LibraryProperties, thermo)
{
if (!lammps_has_style(lmp, "atom", "full")) GTEST_SKIP();
std::string input = INPUT_DIR + PATH_SEP + "in.fourmol";
if (!verbose) ::testing::internal::CaptureStdout();
lammps_file(lmp, input.c_str());
lammps_command(lmp, "run 2 post no");
if (!verbose) ::testing::internal::GetCapturedStdout();
EXPECT_EQ(lammps_get_thermo(lmp, "step"), 2);
EXPECT_EQ(lammps_get_thermo(lmp, "atoms"), 29);
EXPECT_DOUBLE_EQ(lammps_get_thermo(lmp, "vol"), 3375.0);
EXPECT_DOUBLE_EQ(lammps_get_thermo(lmp, "density"), 0.12211250945013695);
EXPECT_DOUBLE_EQ(lammps_get_thermo(lmp, "cellalpha"), 90.0);
};
TEST_F(LibraryProperties, box)
{
if (!lammps_has_style(lmp, "atom", "full")) GTEST_SKIP();
std::string input = INPUT_DIR + PATH_SEP + "in.fourmol";
if (!verbose) ::testing::internal::CaptureStdout();
lammps_file(lmp, input.c_str());
lammps_command(lmp, "run 2 post no");
if (!verbose) ::testing::internal::GetCapturedStdout();
double boxlo[3], boxhi[3], xy, yz, xz;
int pflags[3], boxflag;
lammps_extract_box(lmp, boxlo, boxhi, &xy, &yz, &xz, pflags, &boxflag);
EXPECT_DOUBLE_EQ(boxlo[0], -6.024572);
EXPECT_DOUBLE_EQ(boxlo[1], -7.692866);
EXPECT_DOUBLE_EQ(boxlo[2], -8.086924);
EXPECT_DOUBLE_EQ(boxhi[0], 8.975428);
EXPECT_DOUBLE_EQ(boxhi[1], 7.307134);
EXPECT_DOUBLE_EQ(boxhi[2], 6.913076);
EXPECT_DOUBLE_EQ(xy, 0.0);
EXPECT_DOUBLE_EQ(yz, 0.0);
EXPECT_DOUBLE_EQ(xz, 0.0);
EXPECT_EQ(pflags[0], 1);
EXPECT_EQ(pflags[1], 1);
EXPECT_EQ(pflags[2], 1);
EXPECT_EQ(boxflag, 0);
EXPECT_DOUBLE_EQ(lammps_get_thermo(lmp, "vol"), 3375.0);
EXPECT_DOUBLE_EQ(lammps_get_thermo(lmp, "density"), 0.12211250945013695);
EXPECT_DOUBLE_EQ(lammps_get_thermo(lmp, "cellalpha"), 90.0);
if (!verbose) ::testing::internal::CaptureStdout();
lammps_command(lmp, "change_box all boundary p p f triclinic xy final 0.5");
lammps_command(lmp, "fix box all box/relax x 0.0 y 0.0");
if (!verbose) ::testing::internal::GetCapturedStdout();
lammps_extract_box(lmp, boxlo, boxhi, &xy, &yz, &xz, pflags, &boxflag);
EXPECT_DOUBLE_EQ(boxlo[0], -6.024572);
EXPECT_DOUBLE_EQ(boxlo[1], -7.692866);
EXPECT_DOUBLE_EQ(boxlo[2], -8.086924);
EXPECT_DOUBLE_EQ(boxhi[0], 8.975428);
EXPECT_DOUBLE_EQ(boxhi[1], 7.307134);
EXPECT_DOUBLE_EQ(boxhi[2], 6.913076);
EXPECT_DOUBLE_EQ(xy, 0.5);
EXPECT_DOUBLE_EQ(yz, 0.0);
EXPECT_DOUBLE_EQ(xz, 0.0);
EXPECT_EQ(pflags[0], 1);
EXPECT_EQ(pflags[1], 1);
EXPECT_EQ(pflags[2], 0);
EXPECT_EQ(boxflag, 1);
EXPECT_DOUBLE_EQ(lammps_get_thermo(lmp, "vol"), 3375.0);
EXPECT_DOUBLE_EQ(lammps_get_thermo(lmp, "density"), 0.12211250945013695);
EXPECT_DOUBLE_EQ(lammps_get_thermo(lmp, "cellalpha"), 90.0);
EXPECT_DOUBLE_EQ(lammps_get_thermo(lmp, "cellbeta"), 90.0);
EXPECT_DOUBLE_EQ(lammps_get_thermo(lmp, "cellgamma"), 88.090847567003621);
boxlo[0] = -6.1;
boxhi[1] = 7.3;
xy = 0.1;
lammps_reset_box(lmp, boxlo, boxhi, xy, yz, xz);
lammps_extract_box(lmp, boxlo, boxhi, &xy, &yz, &xz, pflags, &boxflag);
EXPECT_DOUBLE_EQ(boxlo[0], -6.1);
EXPECT_DOUBLE_EQ(boxlo[1], -7.692866);
EXPECT_DOUBLE_EQ(boxlo[2], -8.086924);
EXPECT_DOUBLE_EQ(boxhi[0], 8.975428);
EXPECT_DOUBLE_EQ(boxhi[1], 7.3);
EXPECT_DOUBLE_EQ(boxhi[2], 6.913076);
EXPECT_DOUBLE_EQ(xy, 0.1);
EXPECT_DOUBLE_EQ(yz, 0.0);
EXPECT_DOUBLE_EQ(xz, 0.0);
EXPECT_EQ(pflags[0], 1);
EXPECT_EQ(pflags[1], 1);
EXPECT_EQ(pflags[2], 0);
EXPECT_EQ(boxflag, 1);
EXPECT_DOUBLE_EQ(lammps_get_thermo(lmp, "vol"), 3390.3580784497199);
EXPECT_DOUBLE_EQ(lammps_get_thermo(lmp, "cellgamma"), 89.61785205109274);
};
TEST_F(LibraryProperties, setting)
{
#if defined(LAMMPS_SMALLSMALL)
EXPECT_EQ(lammps_extract_setting(lmp, "bigint"), 4);
#else
EXPECT_EQ(lammps_extract_setting(lmp, "bigint"), 8);
#endif
#if defined(LAMMPS_BIGBIG)
EXPECT_EQ(lammps_extract_setting(lmp, "tagint"), 8);
EXPECT_EQ(lammps_extract_setting(lmp, "imageint"), 8);
#else
EXPECT_EQ(lammps_extract_setting(lmp, "tagint"), 4);
EXPECT_EQ(lammps_extract_setting(lmp, "imageint"), 4);
#endif
EXPECT_EQ(lammps_extract_setting(lmp, "box_exist"), 0);
if (!verbose) ::testing::internal::CaptureStdout();
lammps_command(lmp, "dimension 2");
if (!verbose) ::testing::internal::GetCapturedStdout();
EXPECT_EQ(lammps_extract_setting(lmp, "dimension"), 2);
if (!verbose) ::testing::internal::CaptureStdout();
lammps_command(lmp, "dimension 3");
if (!verbose) ::testing::internal::GetCapturedStdout();
EXPECT_EQ(lammps_extract_setting(lmp, "molecule_flag"), 0);
EXPECT_EQ(lammps_extract_setting(lmp, "q_flag"), 0);
EXPECT_EQ(lammps_extract_setting(lmp, "mu_flag"), 0);
EXPECT_EQ(lammps_extract_setting(lmp, "rmass_flag"), 0);
EXPECT_EQ(lammps_extract_setting(lmp, "UNKNOWN"), -1);
if (lammps_has_style(lmp, "atom", "full")) {
std::string input = INPUT_DIR + PATH_SEP + "in.fourmol";
if (!verbose) ::testing::internal::CaptureStdout();
lammps_file(lmp, input.c_str());
lammps_command(lmp, "run 2 post no");
if (!verbose) ::testing::internal::GetCapturedStdout();
EXPECT_EQ(lammps_extract_setting(lmp, "triclinic"), 0);
EXPECT_EQ(lammps_extract_setting(lmp, "box_exist"), 1);
EXPECT_EQ(lammps_extract_setting(lmp, "dimension"), 3);
EXPECT_EQ(lammps_extract_setting(lmp, "nlocal"), 29);
EXPECT_EQ(lammps_extract_setting(lmp, "nghost"), 518);
EXPECT_EQ(lammps_extract_setting(lmp, "nall"), 547);
EXPECT_EQ(lammps_extract_setting(lmp, "nmax"), 16384);
EXPECT_EQ(lammps_extract_setting(lmp, "molecule_flag"), 1);
EXPECT_EQ(lammps_extract_setting(lmp, "q_flag"), 1);
EXPECT_EQ(lammps_extract_setting(lmp, "mu_flag"), 0);
EXPECT_EQ(lammps_extract_setting(lmp, "rmass_flag"), 0);
if (!verbose) ::testing::internal::CaptureStdout();
lammps_command(lmp, "change_box all triclinic");
lammps_command(lmp, "fix rmass all property/atom rmass ghost yes");
if (!verbose) ::testing::internal::GetCapturedStdout();
EXPECT_EQ(lammps_extract_setting(lmp, "triclinic"), 1);
EXPECT_EQ(lammps_extract_setting(lmp, "rmass_flag"), 1);
}
};

59
unittest/c-library/test_main.cpp Normal file
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@ -0,0 +1,59 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "test_main.h"
#include "utils.h"
#include "gmock/gmock.h"
#include "gtest/gtest.h"
#include <iostream>
#include <mpi.h>
// whether to print verbose output (i.e. not capturing LAMMPS screen output).
bool verbose = false;
int main(int argc, char **argv)
{
MPI_Init(&argc, &argv);
::testing::InitGoogleMock(&argc, argv);
if (argc < 1) {
return 1;
}
// handle arguments passed via environment variable
if (const char *var = getenv("TEST_ARGS")) {
std::vector<std::string> env = LAMMPS_NS::utils::split_words(var);
for (auto arg : env) {
if (arg == "-v") {
verbose = true;
}
}
}
int iarg = 1;
while (iarg < argc) {
if (strcmp(argv[iarg], "-v") == 0) {
verbose = true;
++iarg;
} else {
std::cerr << "unknown option: " << argv[iarg] << "\n\n";
MPI_Finalize();
return 1;
}
}
int rv = RUN_ALL_TESTS();
MPI_Finalize();
return rv;
}

33
unittest/c-library/test_main.h Normal file
View File

@ -0,0 +1,33 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef TEST_MAIN_H
#define TEST_MAIN_H
extern bool verbose;
#define EXPECT_FP_LE_WITH_EPS(val1, val2, eps) \
do { \
const double diff = fabs(val1 - val2); \
const double div = std::min(fabs(val1), fabs(val2)); \
const double err = (div == 0.0) ? diff : diff / div; \
EXPECT_PRED_FORMAT2(::testing::DoubleLE, err, eps); \
} while (0);
#endif
#if defined _WIN32
static const char PATH_SEP = '\\';
#else
static const char PATH_SEP = '/';
#endif

90
unittest/force-styles/tests/kspace-msm_nopbc.yaml Normal file
View File

@ -0,0 +1,90 @@
---
lammps_version: 24 Aug 2020
date_generated: Sat Sep 12 10:33:36 202
epsilon: 5e-11
prerequisites: ! |
atom full
pair coul/msm
kspace msm
pre_commands: ! |
boundary f f f
post_commands: ! |
pair_modify compute no
kspace_style msm 1.0e-4
kspace_modify cutoff/adjust no
kspace_modify pressure/scalar no # required for USER-OMP with msm
input_file: in.fourmol
pair_style: coul/msm 12.0
pair_coeff: ! |
* *
extract: ! ""
natoms: 29
init_vdwl: 0
init_coul: 0
init_stress: ! |2-
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
init_forces: ! |2
1 -1.0766173668302007e-01 3.3042340827626349e-01 -2.9550761278746868e-01
2 1.4576263044966863e-02 -2.2187776206184587e-01 2.1317727080129803e-01
3 -6.2277085668426338e-03 1.1652138650558974e-02 -1.3297461972937180e-02
4 2.8786238443846923e-02 -4.5768542246633188e-02 4.9349101662676420e-02
5 4.2979655856763686e-02 -5.4082950850616152e-02 5.4543059350179231e-02
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