8.2.5. Library interface to LAMMPS
All of these methodologies use a C-style interface to LAMMPS that is provided in the files src/library.cpp and src/library.h. The functions therein have a C-style argument list, but contain C++ code you could write yourself in a C++ application that was invoking LAMMPS directly. The C++ code in the functions illustrates how to invoke internal LAMMPS operations. Note that LAMMPS classes are defined within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++ application.
The examples/COUPLE and python/examples directories have example C++ and C and Python codes which show how a driver code can link to LAMMPS as a library, run LAMMPS on a subset of processors, grab data from LAMMPS, change it, and put it back into LAMMPS.
LAMMPS has not initially been conceived as a thread-safe program, but over the years changes have been applied to replace operations that collide with creating multiple LAMMPS instances from multiple-threads of the same process with thread-safe alternatives. This primarily applies to the core LAMMPS code and less so on add-on packages, especially when those packages require additional code in the lib folder, interface LAMMPS to Fortran libraries, or the code uses static variables (like the USER-COLVARS package.
Another major issue to deal with is to correctly handle MPI. Creating a LAMMPS instance requires passing an MPI communicator, or it assumes the MPI_COMM_WORLD communicator, which spans all MPI processor ranks. When creating multiple LAMMPS object instances from different threads, this communicator has to be different for each thread or else collisions can happen, or it has to be guaranteed, that only one thread at a time is active. MPI communicators, however, are not a problem, if LAMMPS is compiled with the MPI STUBS library, which implies that there is no MPI communication and only 1 MPI rank.
The file src/library.cpp contains the following functions for creating and destroying an instance of LAMMPS and sending it commands to execute. See the documentation in the src/library.cpp file for details.
You can write code for additional functions as needed to define how your code talks to LAMMPS and add them to src/library.cpp and src/library.h, as well as to the Python interface. The added functions can access or change any internal LAMMPS data you wish.
void lammps_open(int, char **, MPI_Comm, void **) void lammps_open_no_mpi(int, char **, void **) void lammps_close(void *) int lammps_version(void *) void lammps_file(void *, char *) char *lammps_command(void *, char *) void lammps_commands_list(void *, int, char **) void lammps_commands_string(void *, char *) void lammps_free(void *)
The lammps_open() function is used to initialize LAMMPS, passing in a list of strings as if they were command-line arguments when LAMMPS is run in stand-alone mode from the command line, and a MPI communicator for LAMMPS to run under. It returns a ptr to the LAMMPS object that is created, and which is used in subsequent library calls. The lammps_open() function can be called multiple times, to create multiple instances of LAMMPS.
LAMMPS will run on the set of processors in the communicator. This means the calling code can run LAMMPS on all or a subset of processors. For example, a wrapper script might decide to alternate between LAMMPS and another code, allowing them both to run on all the processors. Or it might allocate half the processors to LAMMPS and half to the other code and run both codes simultaneously before syncing them up periodically. Or it might instantiate multiple instances of LAMMPS to perform different calculations.
The lammps_open_no_mpi() function is similar except that no MPI communicator is passed from the caller. Instead, MPI_COMM_WORLD is used to instantiate LAMMPS, and MPI is initialized if necessary.
The lammps_close() function is used to shut down an instance of LAMMPS and free all its memory.
The lammps_version() function can be used to determined the specific version of the underlying LAMMPS code. This is particularly useful when loading LAMMPS as a shared library via dlopen(). The code using the library interface can than use this information to adapt to changes to the LAMMPS command syntax between versions. The returned LAMMPS version code is an integer (e.g. 2 Sep 2015 results in 20150902) that grows with every new LAMMPS version.
The lammps_file(), lammps_command(), lammps_commands_list(), and lammps_commands_string() functions are used to pass one or more commands to LAMMPS to execute, the same as if they were coming from an input script.
Via these functions, the calling code can read or generate a series of LAMMPS commands one or multiple at a time and pass it through the library interface to setup a problem and then run it in stages. The caller can interleave the command function calls with operations it performs, calls to extract information from or set information within LAMMPS, or calls to another code’s library.
The lammps_file() function passes the filename of an input script. The lammps_command() function passes a single command as a string. The lammps_commands_list() function passes multiple commands in a char** list. In both lammps_command() and lammps_commands_list(), individual commands may or may not have a trailing newline. The lammps_commands_string() function passes multiple commands concatenated into one long string, separated by newline characters. In both lammps_commands_list() and lammps_commands_string(), a single command can be spread across multiple lines, if the last printable character of all but the last line is “&”, the same as if the lines appeared in an input script.
The lammps_free() function is a clean-up function to free memory that the library allocated previously via other function calls. See comments in src/library.cpp file for which other functions need this clean-up.
The file src/library.cpp also contains these functions for extracting information from LAMMPS and setting value within LAMMPS. Again, see the documentation in the src/library.cpp file for details, including which quantities can be queried by name:
int lammps_extract_setting(void *, char *) void *lammps_extract_global(void *, char *) void lammps_extract_box(void *, double *, double *, double *, double *, double *, int *, int *) void *lammps_extract_atom(void *, char *) void *lammps_extract_compute(void *, char *, int, int) void *lammps_extract_fix(void *, char *, int, int, int, int) void *lammps_extract_variable(void *, char *, char *)
The extract_setting() function returns info on the size of data types (e.g. 32-bit or 64-bit atom IDs) used by the LAMMPS executable (a compile-time choice).
The other extract functions return a pointer to various global or per-atom quantities stored in LAMMPS or to values calculated by a compute, fix, or variable. The pointer returned by the extract_global() function can be used as a permanent reference to a value which may change. For the extract_atom() method, see the extract() method in the src/atom.cpp file for a list of valid per-atom properties. New names could easily be added if the property you want is not listed. For the other extract functions, the underlying storage may be reallocated as LAMMPS runs, so you need to re-call the function to assure a current pointer or returned value(s).
double lammps_get_thermo(void *, char *) int lammps_get_natoms(void *) int lammps_set_variable(void *, char *, char *) void lammps_reset_box(void *, double *, double *, double, double, double)
The lammps_get_thermo() function returns the current value of a thermo keyword as a double precision value.
The lammps_get_natoms() function returns the total number of atoms in the system and can be used by the caller to allocate memory for the lammps_gather_atoms() and lammps_scatter_atoms() functions.
The lammps_set_variable() function can set an existing string-style variable to a new string value, so that subsequent LAMMPS commands can access the variable.
The lammps_reset_box() function resets the size and shape of the simulation box, e.g. as part of restoring a previously extracted and saved state of a simulation.
void lammps_gather_atoms(void *, char *, int, int, void *) void lammps_gather_atoms_concat(void *, char *, int, int, void *) void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *) void lammps_scatter_atoms(void *, char *, int, int, void *) void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *)
The gather functions collect peratom info of the requested type (atom coords, atom types, forces, etc) from all processors, and returns the same vector of values to each calling processor. The scatter functions do the inverse. They distribute a vector of peratom values, passed by all calling processors, to individual atoms, which may be owned by different processors.
These functions are not compatible with the -DLAMMPS_BIGBIG setting when compiling LAMMPS. Dummy functions that result in an error message and abort will be substituted instead of resulting in random crashes and memory corruption.
The lammps_gather_atoms() function does this for all N atoms in the system, ordered by atom ID, from 1 to N. The lammps_gather_atoms_concat() function does it for all N atoms, but simply concatenates the subset of atoms owned by each processor. The resulting vector is not ordered by atom ID. Atom IDs can be requested by the same function if the caller needs to know the ordering. The lammps_gather_subset() function allows the caller to request values for only a subset of atoms (identified by ID). For all 3 gather function, per-atom image flags can be retrieved in 2 ways. If the count is specified as 1, they are returned in a packed format with all three image flags stored in a single integer. If the count is specified as 3, the values are unpacked into xyz flags by the library before returning them.
The lammps_scatter_atoms() function takes a list of values for all N atoms in the system, ordered by atom ID, from 1 to N, and assigns those values to each atom in the system. The lammps_scatter_atoms_subset() function takes a subset of IDs as an argument and only scatters those values to the owning atoms.
void lammps_create_atoms(void *, int, tagint *, int *, double *, double *, imageint *, int)
The lammps_create_atoms() function takes a list of N atoms as input with atom types and coords (required), an optionally atom IDs and velocities and image flags. It uses the coords of each atom to assign it as a new atom to the processor that owns it. This function is useful to add atoms to a simulation or (in tandem with lammps_reset_box()) to restore a previously extracted and saved state of a simulation. Additional properties for the new atoms can then be assigned via the lammps_scatter_atoms() or lammps_extract_atom() functions.