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Merge branch 'master' into symbolic-atom-constants

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This commit is contained in:
Axel Kohlmeyer
2020-09-15 14:58:13 -04:00
parent 828ce84df5 2165f6ed38
commit 618b08dcfc
459 changed files with 11521 additions and 10514 deletions
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106
src/library.cpp
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@ -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 \
@ -534,6 +534,72 @@ int lammps_version(void *handle)
/* ---------------------------------------------------------------------- */
/** Get memory usage information
*
\verbatim embed:rst
This function will retrieve memory usage information for the current
LAMMPS instance or process. The *meminfo* buffer will be filled with
3 different numbers (if supported by the operating system). The first
is the tally (in MBytes) of all large memory allocations made by LAMMPS.
This is a lower boundary of how much memory is requested and does not
account for memory allocated on the stack or allocations via ``new``.
The second number is the current memory allocation of the current process
as returned by a memory allocation reporting in the system library. The
third number is the maximum amount of RAM (not swap) used by the process
so far. If any of the two latter parameters is not supported by the operating
system it will be set to zero.
.. versionadded:: 15Sep2020
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance
* \param meminfo buffer with space for at least 3 double to store
* data in. */
void lammps_memory_usage(void *handle, double *meminfo)
{
LAMMPS *lmp = (LAMMPS *) handle;
Info info(lmp);
info.get_memory_info(meminfo);
}
/* ---------------------------------------------------------------------- */
/** Return current LAMMPS world communicator as integer
*
\verbatim embed:rst
This will take the LAMMPS "world" communicator and convert it to an
integer using ``MPI_Comm_c2f()``, so it is equivalent to the
corresponding MPI communicator in Fortran. This way it can be safely
passed around between different programming languages. To convert it
to the C language representation use ``MPI_Comm_f2c()``.
If LAMMPS was compiled with MPI_STUBS, this function returns -1.
.. versionadded:: 15Sep2020
\endverbatim
* \sa lammps_open_fortran
*
* \param handle pointer to a previously created LAMMPS instance
* \return Fortran representation of the LAMMPS world communicator */
int lammps_get_mpi_comm(void *handle)
{
#ifdef MPI_STUBS
return -1;
#else
LAMMPS *lmp = (LAMMPS *) handle;
MPI_Fint f_comm = MPI_Comm_c2f(lmp->world);
return f_comm;
#endif
}
/* ---------------------------------------------------------------------- */
/** Return the total number of atoms in the system.
*
\verbatim embed:rst
@ -560,7 +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;
}
@ -582,7 +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;
@ -773,7 +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;
@ -831,7 +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
@ -1039,7 +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;
@ -1131,7 +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);
@ -3690,7 +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;
}
@ -3730,7 +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';
@ -3754,14 +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;
}
/* ---------------------------------------------------------------------- */
@ -3779,7 +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();
@ -3805,7 +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);
@ -4231,10 +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();