From 77fb2ee311f2b51c7d7c3500d4a84c80d6ec8e0d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 30 Sep 2020 21:16:48 -0400 Subject: [PATCH] add list of documented functions at the top of the C-Library doc pages --- doc/src/Library_config.rst | 17 +++++++++++++++ doc/src/Library_create.rst | 12 +++++++++++ doc/src/Library_execute.rst | 9 ++++++++ doc/src/Library_neighbor.rst | 8 ++++++- doc/src/Library_objects.rst | 7 ++++++- doc/src/Library_properties.rst | 18 ++++++++++++++++ doc/src/Library_scatter.rst | 38 ++++++++++++++++++++++++++++++++++ doc/src/Library_utility.rst | 20 +++++++++++++++++- 8 files changed, 126 insertions(+), 3 deletions(-) diff --git a/doc/src/Library_config.rst b/doc/src/Library_config.rst index d33afe3b5b..0c07896ff6 100644 --- a/doc/src/Library_config.rst +++ b/doc/src/Library_config.rst @@ -1,6 +1,23 @@ Retrieving LAMMPS configuration information =========================================== +This section documents the following functions: + +- :cpp:func:`lammps_config_has_mpi_support` +- :cpp:func:`lammps_config_has_gzip_support` +- :cpp:func:`lammps_config_has_png_support` +- :cpp:func:`lammps_config_has_jpeg_support` +- :cpp:func:`lammps_config_has_ffmpeg_support` +- :cpp:func:`lammps_config_has_exceptions` +- :cpp:func:`lammps_config_has_package` +- :cpp:func:`lammps_config_package_count` +- :cpp:func:`lammps_config_package_name` +- :cpp:func:`lammps_has_style` +- :cpp:func:`lammps_style_count` +- :cpp:func:`lammps_style_name` + +-------------------- + 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 diff --git a/doc/src/Library_create.rst b/doc/src/Library_create.rst index 3c3b9da22f..7303c499d1 100644 --- a/doc/src/Library_create.rst +++ b/doc/src/Library_create.rst @@ -1,6 +1,18 @@ Creating or deleting a LAMMPS object ==================================== +This section documents the following functions: + +- :cpp:func:`lammps_open` +- :cpp:func:`lammps_open_no_mpi` +- :cpp:func:`lammps_open_fortran` +- :cpp:func:`lammps_close` +- :cpp:func:`lammps_mpi_init` +- :cpp:func:`lammps_mpi_finalize` +- :cpp:func:`lammps_free` + +-------------------- + The :cpp:func:`lammps_open` and :cpp:func:`lammps_open_no_mpi` functions are used to create and initialize a :cpp:func:`LAMMPS` instance. They return a reference to this instance as a ``void *`` pointer to be used diff --git a/doc/src/Library_execute.rst b/doc/src/Library_execute.rst index 77e7c13f70..b6bcab2ead 100644 --- a/doc/src/Library_execute.rst +++ b/doc/src/Library_execute.rst @@ -1,6 +1,15 @@ Executing LAMMPS commands ========================= +This section documents the following functions: + +- :cpp:func:`lammps_file` +- :cpp:func:`lammps_command` +- :cpp:func:`lammps_commands_list` +- :cpp:func:`lammps_commands_string` + +-------------------- + Once a LAMMPS instance is created, there are multiple ways to "drive" a simulation. In most cases it is easiest to process single or multiple LAMMPS commands like in an input file. This can be done through reading diff --git a/doc/src/Library_neighbor.rst b/doc/src/Library_neighbor.rst index b004e85d0e..3179b669f1 100644 --- a/doc/src/Library_neighbor.rst +++ b/doc/src/Library_neighbor.rst @@ -2,7 +2,13 @@ Accessing LAMMPS Neighbor lists =============================== The following functions allow to access neighbor lists -generated by LAMMPS or query their properties. +generated by LAMMPS or query their properties: + +- :cpp:func:`lammps_find_compute_neighlist` +- :cpp:func:`lammps_find_fix_neighlist` +- :cpp:func:`lammps_find_pair_neighlist` +- :cpp:func:`lammps_neighlist_num_elements` +- :cpp:func:`lammps_neighlist_element_neighbors` ----------------------- diff --git a/doc/src/Library_objects.rst b/doc/src/Library_objects.rst index 301511b848..3b87842169 100644 --- a/doc/src/Library_objects.rst +++ b/doc/src/Library_objects.rst @@ -2,7 +2,12 @@ Retrieving or setting properties of LAMMPS objects ================================================== This section documents accessing or modifying data from objects like -computes, fixes, or variables in LAMMPS. +computes, fixes, or variables in LAMMPS using following functions: + +- :cpp:func:`lammps_extract_compute` +- :cpp:func:`lammps_extract_fix` +- :cpp:func:`lammps_extract_variable` +- :cpp:func:`lammps_set_variable` ----------------------- diff --git a/doc/src/Library_properties.rst b/doc/src/Library_properties.rst index 3e43a80600..e53a3caa0d 100644 --- a/doc/src/Library_properties.rst +++ b/doc/src/Library_properties.rst @@ -1,6 +1,24 @@ Retrieving or setting LAMMPS system properties ============================================== +This section documents the following functions: + +- :cpp:func:`lammps_version` +- :cpp:func:`lammps_memory_usage` +- :cpp:func:`lammps_get_mpi_comm` +- :cpp:func:`lammps_get_natoms` +- :cpp:func:`lammps_get_thermo` +- :cpp:func:`lammps_extract_box` +- :cpp:func:`lammps_reset_box` +- :cpp:func:`lammps_extract_setting` +- :cpp:func:`lammps_extract_global_datatype` +- :cpp:func:`lammps_extract_global` +- :cpp:func:`lammps_extract_atom_datatype` +- :cpp:func:`lammps_extract_atom` +- :cpp:func:`lammps_create_atoms` + +-------------------- + The library interface allows extraction of different kinds of information about the active simulation instance and also modifications to it. This enables combining of a LAMMPS simulation diff --git a/doc/src/Library_scatter.rst b/doc/src/Library_scatter.rst index 5865d22349..e3ca34e999 100644 --- a/doc/src/Library_scatter.rst +++ b/doc/src/Library_scatter.rst @@ -1,6 +1,19 @@ Library functions for scatter/gather operations ================================================ +This section documents the following functions: + +- :cpp:func:`lammps_gather_atoms` +- :cpp:func:`lammps_gather_atoms_concat` +- :cpp:func:`lammps_gather_atoms_subset` +- :cpp:func:`lammps_scatter_atoms` +- :cpp:func:`lammps_scatter_atoms_subset` +- :cpp:func:`lammps_gather` +- :cpp:func:`lammps_gather_concat` +- :cpp:func:`lammps_gather_subset` +- :cpp:func:`lammps_scatter` +- :cpp:func:`lammps_scatter_subset` + .. TODO add description ----------------------- @@ -27,3 +40,28 @@ Library functions for scatter/gather operations .. doxygenfunction:: lammps_scatter_atoms_subset :project: progguide + +----------------------- + +.. doxygenfunction:: lammps_gather + :project: progguide + +----------------------- + +.. doxygenfunction:: lammps_gather_concat + :project: progguide + +----------------------- + +.. doxygenfunction:: lammps_gather_subset + :project: progguide + +----------------------- + +.. doxygenfunction:: lammps_scatter + :project: progguide + +----------------------- + +.. doxygenfunction:: lammps_scatter_subset + :project: progguide diff --git a/doc/src/Library_utility.rst b/doc/src/Library_utility.rst index 8eda4e4988..3d2fae53d3 100644 --- a/doc/src/Library_utility.rst +++ b/doc/src/Library_utility.rst @@ -2,7 +2,15 @@ Library interface utility functions =================================== To simplify some of the tasks, the library interface contains -some utility functions that are not directly calling LAMMPS. +some utility functions that are not directly calling LAMMPS: + +- :cpp:func:`lammps_encode_image_flags` +- :cpp:func:`lammps_decode_image_flags` +- :cpp:func:`lammps_set_fix_external_callback` +- :cpp:func:`lammps_fix_external_set_energy_global` +- :cpp:func:`lammps_fix_external_set_virial_global` +- :cpp:func:`lammps_has_error` +- :cpp:func:`lammps_get_last_error_message` ----------------------- @@ -21,6 +29,16 @@ some utility functions that are not directly calling LAMMPS. ----------------------- +.. doxygenfunction:: lammps_fix_external_set_energy_global + :project: progguide + +----------------------- + +.. doxygenfunction:: lammps_fix_external_set_virial_global + :project: progguide + +----------------------- + .. doxygenfunction:: lammps_has_error :project: progguide