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Merge branch 'library-progguide' into symbolic-atom-constants

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This commit is contained in:
Axel Kohlmeyer
2020-09-15 19:50:18 -04:00
parent 0f6a34775c 4b25eb1a34
commit cf7d2109a3
5 changed files with 56 additions and 29 deletions
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2
src/atom.cpp
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@ -2506,7 +2506,7 @@ length of the data area, and a short description.
*
* \param name string with the keyword of the desired property.
Typically the name of the pointer variable returned
* \return pointer to the requested data cast to ``void *`` or nullptr */
* \return pointer to the requested data cast to ``void *`` or ``nullptr`` */
void *Atom::extract(const char *name)
{

46
src/library.cpp
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@ -105,7 +105,7 @@ LAMMPS executable, and an MPI communicator for LAMMPS to run under.
Since the list of arguments is **exactly** as when called from the
command line, the first argument would be the name of the executable and
thus is otherwise ignored. However ``argc`` may be set to 0 and then
``argv`` may be ``nullptr``. If MPI is not yet initialized, ``MPI_Init()``
``argv`` may be ``NULL``. If MPI is not yet initialized, ``MPI_Init()``
will be called during creation of the LAMMPS class instance.
If for some reason the creation or initialization of the LAMMPS instance
@ -117,7 +117,7 @@ fails a null pointer is returned.
instance as return value. For backward compatibility it is still
possible to provide the address of a pointer variable as final
argument *ptr*\ . This use is deprecated and may be removed in
the future. The *ptr* argument may be ``nullptr`` and is then ignored.
the future. The *ptr* argument may be ``NULL`` and is then ignored.
.. note::
@ -133,7 +133,7 @@ fails a null pointer is returned.
* \param argv list of command line argument strings
* \param comm MPI communicator for this LAMMPS instance
* \param ptr pointer to a void pointer variable which serves
* as a handle; may be ``nullptr``
* as a handle; may be ``NULL``
* \return pointer to new LAMMPS instance cast to ``void *`` */
void *lammps_open(int argc, char **argv, MPI_Comm comm, void **ptr)
@ -183,14 +183,14 @@ fails a null pointer is returned.
instance as return value. For backward compatibility it is still
possible to provide the address of a pointer variable as final
argument *ptr*\ . This use is deprecated and may be removed in
the future. The *ptr* argument may be ``nullptr`` and is then ignored.
the future. The *ptr* argument may be ``NULL`` and is then ignored.
\endverbatim
*
* \param argc number of command line arguments
* \param argv list of command line argument strings
* \param ptr pointer to a void pointer variable
* which serves as a handle; may be ``nullptr``
* which serves as a handle; may be ``NULL``
* \return pointer to new LAMMPS instance cast to ``void *`` */
void *lammps_open_no_mpi(int argc, char **argv, void **ptr)
@ -375,14 +375,14 @@ string, however, will be treated as part of the command and will **not**
start a second command. The function :cpp:func:`lammps_commands_string`
processes a string with multiple command lines.
The function returns the name of the command on success or ``nullptr`` when
The function returns the name of the command on success or ``NULL`` when
passing a string without a command.
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance
* \param cmd string with a single LAMMPS command
* \return string with parsed command name or ``nullptr`` */
* \return string with parsed command name or ``NULL`` */
char *lammps_command(void *handle, const char *cmd)
{
@ -671,7 +671,7 @@ double lammps_get_thermo(void *handle, const char *keyword)
This function (re-)initializes the simulation box and boundary
information and then assign the designated data to the locations in the
pointers passed as arguments. Any argument (except the first) may be
a nullptr pointer and then will not be assigned.
a NULL pointer and then will not be assigned.
\endverbatim
*
@ -1104,7 +1104,7 @@ to be either an ``int`` or an ``int64_t``. This is selected at
* \param handle pointer to a previously created LAMMPS instance
* \param name string with the name of the extracted property
* \return pointer (cast to ``void *``) to the location of the
requested property. nullptr if name is not known. */
requested property. NULL if name is not known. */
void *lammps_extract_global(void *handle, const char *name)
{
@ -1196,7 +1196,7 @@ of the :cpp:func:`Atom::extract() <LAMMPS_NS::Atom::extract>` function.
* \param handle pointer to a previously created LAMMPS instance
* \param name string with the name of the extracted property
* \return pointer (cast to ``void *``) to the location of the
* requested data or ``nullptr`` if not found. */
* requested data or ``NULL`` if not found. */
void *lammps_extract_atom(void *handle, const char *name)
{
@ -1246,13 +1246,13 @@ X(1),Y(1),Z(1),X(2),Y(2),Z(2),...,X(N),Y(N),Z(N).
*
* \param handle pointer to a previously created LAMMPS instance
* \param n number of atoms, N, to be added to the system
* \param id pointer to N atom IDs; ``nullptr`` will generate IDs
* \param id pointer to N atom IDs; ``NULL`` will generate IDs
* \param type pointer to N atom types (required)
* \param x pointer to 3N doubles with x-,y-,z- positions
of the new atoms (required)
* \param v pointer to 3N doubles with x-,y-,z- velocities
of the new atoms (set to 0.0 if ``nullptr``)
* \param image pointer to N imageint sets of image flags, or ``nullptr``
of the new atoms (set to 0.0 if ``NULL``)
* \param image pointer to N imageint sets of image flags, or ``NULL``
* \param bexpand if 1, atoms outside of shrink-wrap boundaries will
still be created and not dropped and the box extended
* \return number of atoms created on success;
@ -1365,7 +1365,7 @@ dimensions of the respective data. Since computes may provide multiple
kinds of data, it is required to set style and type flags representing
what specific data is desired. This also determines to what kind of
pointer the returned pointer needs to be cast to access the data
correctly. The function returns ``nullptr`` if the compute ID is not found
correctly. The function returns ``NULL`` if the compute ID is not found
or the requested data is not available or current. The following table
lists the available options.
@ -1453,7 +1453,7 @@ be used after other LAMMPS commands have been issued.
* \param type constant indicating type of data (scalar, vector,
or array) or size of rows or columns
* \return pointer (cast to ``void *``) to the location of the
* requested data or ``nullptr`` if not found. */
* requested data or ``NULL`` if not found. */
void *lammps_extract_compute(void *handle, char *id, int style, int type)
{
@ -1533,7 +1533,7 @@ Since individual fixes may provide multiple kinds of data, it is
required to set style and type flags representing what specific data is
desired. This also determines to what kind of pointer the returned
pointer needs to be cast to access the data correctly. The function
returns ``nullptr`` if the fix ID is not found or the requested data is not
returns ``NULL`` if the fix ID is not found or the requested data is not
available.
.. note::
@ -1637,7 +1637,7 @@ been issued.
* \param nrow row index (only used for global vectors and arrays)
* \param ncol column index (only used for global arrays)
* \return pointer (cast to ``void *``) to the location of the
* requested data or ``nullptr`` if not found. */
* requested data or ``NULL`` if not found. */
void *lammps_extract_fix(void *handle, char *id, int style, int type,
int nrow, int ncol)
@ -1714,9 +1714,9 @@ identified by its name. The variable must be either an *equal*\ -style
compatible or an *atom*\ -style variable. Variables of style *internal*
are compatible with *equal*\ -style variables and so are *python*\
-style variables, if they return a numeric value. The function returns
``nullptr`` when a variable of the provided *name* is not found or of an
``NULL`` when a variable of the provided *name* is not found or of an
incompatible style. The *group* argument is only used for *atom*\
-style variables and ignored otherwise. If set to ``nullptr`` when
-style variables and ignored otherwise. If set to ``NULL`` when
extracting data from and *atom*\ -style variable, the group is assumed
to be "all".
@ -1730,7 +1730,7 @@ to be "all".
.. code-block:: c
double *dptr = (double *) lammps_extract_variable(handle,name,nullptr);
double *dptr = (double *) lammps_extract_variable(handle,name,NULL);
double value = *dptr;
lammps_free((void *)dptr);
@ -1753,9 +1753,9 @@ values will not be updated, in case the variable is re-evaluated.
*
* \param handle pointer to a previously created LAMMPS instance
* \param name name of the variable
* \param group group-ID for atom style variable or ``nullptr``
* \param group group-ID for atom style variable or ``NULL``
* \return pointer (cast to ``void *``) to the location of the
* requested data or ``nullptr`` if not found. */
* requested data or ``NULL`` if not found. */
void *lammps_extract_variable(void *handle, char *name, char *group)
{
@ -4142,7 +4142,7 @@ int lammps_neighlist_num_elements(void * handle, int idx) {
invalid idx or element value
* \param[out] numneigh number of neighbors of atom iatom or 0
* \param[out] neighbors pointer to array of neighbor atom local indices or
* nullptr
* NULL
*/
void lammps_neighlist_element_neighbors(void * handle, int idx, int element, int * iatom, int * numneigh, int ** neighbors) {
LAMMPS * lmp = (LAMMPS *) handle;

8
src/utils.h
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@ -354,8 +354,8 @@ namespace LAMMPS_NS {
* If the potential file has a ``UNITS`` tag in the first line, the
* tag's value is compared to the current unit style setting.
* The behavior of the function then depends on the value of the
* *auto_convert* parameter. If it is ``nullptr``, then the unit values
* must match or else the open will fail with an error. Otherwise
* *auto_convert* parameter. If it is a null pointer, then the unit
* values must match or else the open will fail with an error. Otherwise
* the bitmask that *auto_convert* points to is used check for
* compatibility with possible automatic conversions by the calling
* function. If compatible, the bitmask is set to the required
@ -363,8 +363,8 @@ namespace LAMMPS_NS {
*
* \param name file- or pathname of the potential file
* \param lmp pointer to top-level LAMMPS class instance
* \param auto_convert pointer to unit conversion bitmask or nullptr
* \return FILE pointer of the opened potential file or nullptr*/
* \param auto_convert pointer to unit conversion bitmask or ``nullptr``
* \return FILE pointer of the opened potential file or ``nullptr`` */
FILE *open_potential(const std::string &name, LAMMPS *lmp, int *auto_convert);

2
unittest/c-library/in.fourmol
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@ -10,8 +10,8 @@ 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}
timestep 0.1
pair_style ${pair_style}
bond_style ${bond_style}

27
unittest/c-library/test_library_properties.cpp
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@ -2,6 +2,7 @@
#include "lammps.h"
#include "library.h"
#include "lmptype.h"
#include <string>
#include "gmock/gmock.h"
@ -14,6 +15,7 @@
using ::testing::HasSubstr;
using ::testing::StartsWith;
using ::testing::StrEq;
class LibraryProperties : public ::testing::Test {
protected:
@ -171,6 +173,7 @@ TEST_F(LibraryProperties, box)
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)
@ -225,3 +228,27 @@ TEST_F(LibraryProperties, setting)
EXPECT_EQ(lammps_extract_setting(lmp, "rmass_flag"), 1);
}
};
TEST_F(LibraryProperties, global)
{
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();
LAMMPS_NS::bigint *b_ptr;
char *c_ptr;
double *d_ptr;
int *i_ptr;
EXPECT_EQ(lammps_extract_global(lmp, "UNKNOWN"), nullptr);
c_ptr = (char *)lammps_extract_global(lmp, "units");
EXPECT_THAT(c_ptr, StrEq("real"));
b_ptr = (LAMMPS_NS::bigint *)lammps_extract_global(lmp, "ntimestep");
EXPECT_EQ((*b_ptr), 2);
d_ptr = (double *)lammps_extract_global(lmp, "dt");
EXPECT_DOUBLE_EQ((*d_ptr), 0.1);
};