Unverified Commit 52f7f362 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

Merge branch 'master' into programmer-guide

parents 2a365c17 876c53a2

python/lammps.py

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src/.gitignore

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@@ -52,6 +52,13 @@ 
/pair_meamc.cpp

/pair_meamc.h



/compute_mliap.cpp

/compute_mliap.h

/mliap_*.cpp

/mliap_*.h

/pair_mliap.cpp

/pair_mliap.h



/ptm_*.cpp

/ptm_*.h

/compute_ptm.cpp
@@ -308,6 +315,8 @@ 
/bond_oxrna2_fene.h

/bond_quartic.cpp

/bond_quartic.h

/bond_special.cpp

/bond_special.h

/bond_table.cpp

/bond_table.h

/cg_cmm_parms.cpp
@@ -592,6 +601,8 @@ 
/fix_meso_move.h

/fix_meso_stationary.cpp

/fix_meso_stationary.h

/fix_momentum_chunk.cpp

/fix_momentum_chunk.h

/fix_mscg.cpp

/fix_mscg.h

/fix_msst.cpp
@@ -753,6 +764,8 @@ 
/fix_wall_piston.h

/fix_wall_srd.cpp

/fix_wall_srd.h

/fix_widom.cpp

/fix_widom.h

/gpu_extra.h

/gridcomm.cpp

/gridcomm.h

src/library.cpp

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src/library.h

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/* -*- c++ -*- ----------------------------------------------------------

/* -*- c -*- ------------------------------------------------------------

   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator

   http://lammps.sandia.gov, Sandia National Laboratories

   Steve Plimpton, sjplimp@sandia.gov
@@ -14,54 +14,123 @@ 
#ifndef LAMMPS_LIBRARY_H

#define LAMMPS_LIBRARY_H



/*

   C or Fortran style library interface to LAMMPS

   new LAMMPS-specific functions can be added

*/

/* C style library interface to LAMMPS which allows to create and

 * control instances of the LAMMPS C++ class and exchange data with it.

 * The C bindings are the basis for the Python and Fortran modules.

 *

 * If needed, new LAMMPS-specific functions can be added to expose

 * additional LAMMPS functionality to this library interface. */



/*

 * Follow the behavior of regular LAMMPS compilation and assume

 * -DLAMMPS_SMALLBIG when no define is set.

 */

#if !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG) && !defined(LAMMPS_SMALLSMALL)

/* We follow the behavior of regular LAMMPS compilation and assume

 * -DLAMMPS_SMALLBIG when no define is set. */



#if  !defined(LAMMPS_BIGBIG)     \

  && !defined(LAMMPS_SMALLBIG)   \

  && !defined(LAMMPS_SMALLSMALL)

#define LAMMPS_SMALLBIG

#endif



/* To allow including the library interface without MPI */



#if !defined(LAMMPS_LIB_NO_MPI)

#include <mpi.h>

#endif



#if defined(LAMMPS_BIGBIG) || defined(LAMMPS_SMALLBIG)

#include <inttypes.h>  /* for int64_t */

#endif



/* ifdefs allow this file to be included in a C program */

/** Style constants for extracting data from computes and fixes.

 *

 * Must be kept in sync with the equivalent constants in lammps.py */



enum _LMP_STYLE_CONST {

  LMP_STYLE_GLOBAL=0,           /*!< return global data */

  LMP_STYLE_ATOM  =1,           /*!< return per-atom data */

  LMP_STYLE_LOCAL =2            /*!< return local data */

};



/** Type and size constants for extracting data from computes and fixes.

 *

 * Must be kept in sync with the equivalent constants in lammps.py */



enum _LMP_TYPE_CONST {

  LMP_TYPE_SCALAR=0,            /*!< return scalar */

  LMP_TYPE_VECTOR=1,            /*!< return vector */

  LMP_TYPE_ARRAY =2,            /*!< return array */

  LMP_SIZE_VECTOR=3,            /*!< return length of vector */

  LMP_SIZE_ROWS  =4,            /*!< return number of rows */

  LMP_SIZE_COLS  =5             /*!< return number of columns */

};



/* Ifdefs to allow this file to be included in C and C++ programs */



#ifdef __cplusplus

extern "C" {

#endif



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 *);



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 *);



double lammps_get_thermo(void *, char *);

int lammps_get_natoms(void *);

/* ----------------------------------------------------------------------

 * Library functions to create/destroy an instance of LAMMPS

 * ---------------------------------------------------------------------- */



#if !defined(LAMMPS_LIB_NO_MPI)

void *lammps_open(int argc, char **argv, MPI_Comm comm, void **ptr);

#endif

void *lammps_open_no_mpi(int argc, char **argv, void **ptr);

void *lammps_open_fortran(int argc, char **argv, int f_comm, void **ptr);

void  lammps_close(void *handle);

void  lammps_mpi_init();

void  lammps_mpi_finalize();

void  lammps_free(void *ptr);



/* ----------------------------------------------------------------------

 * Library functions to process commands

 * ---------------------------------------------------------------------- */



void  lammps_file(void *handle, const char *file);



char *lammps_command(void *handle, const char *cmd);

void  lammps_commands_list(void *handle, int ncmd, const char **cmds);

void  lammps_commands_string(void *handle, const char *str);



/* -----------------------------------------------------------------------

 * Library functions to extract info from LAMMPS or set data in LAMMPS

 * ----------------------------------------------------------------------- */



int    lammps_version(void *handle);

double lammps_get_natoms(void *handle);

double lammps_get_thermo(void *handle, char *keyword);



void   lammps_extract_box(void *handle, double *boxlo, double *boxhi,

                          double *xy, double *yz, double *xz,

                          int *pflags, int *boxflag);

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);



#if !defined(LAMMPS_BIGBIG)

int    lammps_create_atoms(void *handle, int n, int *id, int *type,

                           double *x, double *v, int *image, int bexpand);

#else

int    lammps_create_atoms(void *handle, int n, int64_t *id, int *type,

                           double *x, double *v, int64_t* image, int bexpand);

#endif



/* ----------------------------------------------------------------------

 * Library functions to access data from computes, fixes, variables in LAMMPS

 * ---------------------------------------------------------------------- */



void *lammps_extract_compute(void *handle, char *id, int, int);

void *lammps_extract_fix(void *handle, char *, int, int, int, int);

void *lammps_extract_variable(void *handle, char *, char *);

int   lammps_set_variable(void *, char *, char *);

void lammps_reset_box(void *, double *, double *, double, double, double);



/* ----------------------------------------------------------------------

 * Library functions for scatter/gather operations of data

 * ---------------------------------------------------------------------- */



void lammps_gather_atoms(void *, char *, int, int, void *);

void lammps_gather_atoms_concat(void *, char *, int, int, void *);
@@ -69,59 +138,68 @@ 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 *);



#if defined(LAMMPS_BIGBIG)

typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **);

void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*);

#elif defined(LAMMPS_SMALLBIG)

typedef void (*FixExternalFnPtr)(void *, int64_t, int, int *, double **, double **);

void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*);

#else

typedef void (*FixExternalFnPtr)(void *, int, int, int *, double **, double **);

void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*);

#endif

/* ----------------------------------------------------------------------

 * Library functions for retrieving configuration information

 * ---------------------------------------------------------------------- */



int lammps_config_has_package(char * package_name);

int lammps_config_has_mpi_support();

int lammps_config_has_package(char *);

int lammps_config_package_count();

int lammps_config_package_name(int index, char * buffer, int max_size);

int lammps_config_package_name(int, char *, int);

int lammps_config_has_gzip_support();

int lammps_config_has_png_support();

int lammps_config_has_jpeg_support();

int lammps_config_has_ffmpeg_support();

int lammps_config_has_exceptions();



int lammps_has_style(void* ptr, char * category, char * name);

int lammps_style_count(void* ptr, char * category);

int lammps_style_name(void*ptr, char * category, int index, char * buffer, int max_size);

int lammps_has_style(void *, char *, char *);

int lammps_style_count(void *, char *);

int lammps_style_name(void *, char *, int, char *, int);



/* ----------------------------------------------------------------------

 * Library functions for accessing neighbor lists

 * ---------------------------------------------------------------------- */



int lammps_find_pair_neighlist(void* ptr, char * style, int exact, int nsub, int request);

int lammps_find_fix_neighlist(void* ptr, char * id, int request);

int lammps_find_compute_neighlist(void* ptr, char * id, int request);

int lammps_neighlist_num_elements(void* ptr, int idx);

void lammps_neighlist_element_neighbors(void * ptr, int idx, int element, int * iatom, int * numneigh, int ** neighbors);

int lammps_find_pair_neighlist(void*, char *, int, int, int);

int lammps_find_fix_neighlist(void*, char *, int);

int lammps_find_compute_neighlist(void*, char *, int);

int lammps_neighlist_num_elements(void*, int);

void lammps_neighlist_element_neighbors(void *, int, int, int *, int *, int ** );



// lammps_create_atoms() takes tagint and imageint as args

// ifdef insures they are compatible with rest of LAMMPS

// caller must match to how LAMMPS library is built

/* ----------------------------------------------------------------------

 * Utility functions

 * ---------------------------------------------------------------------- */



#ifdef LAMMPS_BIGBIG

void lammps_create_atoms(void *, int, int64_t *, int *,

                         double *, double *, int64_t *, int);

#if !defined(LAMMPS_BIGBIG)

int lammps_encode_image_flags(int ix, int iy, int iz);

void lammps_decode_image_flags(int image, int *flags);

#else

void lammps_create_atoms(void *, int, int *, int *,

                         double *, double *, int *, int);

int64_t lammps_encode_image_flags(int ix, int iy, int iz);

void lammps_decode_image_flags(int64_t image, int *flags);

#endif



#ifdef LAMMPS_EXCEPTIONS

int lammps_has_error(void *);

int lammps_get_last_error_message(void *, char *, int);

#if defined(LAMMPS_BIGBIG)

typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **);

void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*);

#elif defined(LAMMPS_SMALLBIG)

typedef void (*FixExternalFnPtr)(void *, int64_t, int, int *, double **, double **);

void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*);

#else

typedef void (*FixExternalFnPtr)(void *, int, int, int *, double **, double **);

void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*);

#endif

void lammps_fix_external_set_energy_global(void *, char *, double);

void lammps_fix_external_set_virial_global(void *, char *, double *);



int lammps_has_error(void *handle);

int lammps_get_last_error_message(void *handle, char *buffer, int buf_size);



#undef LAMMPS

#ifdef __cplusplus

}

#endif



#endif /* LAMMPS_LIBRARY_H */



/* ERROR/WARNING messages:



E: Library error: issuing LAMMPS command during run
@@ -172,3 +250,7 @@ W: Library warning in lammps_create_atoms, invalid total atoms %ld %ld 
UNDOCUMENTED



*/



/* Local Variables:

 * fill-column: 72

 * End: */

unittest/CMakeLists.txt

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@@ -3,6 +3,9 @@ include(GTest) 
add_subdirectory(utils)

add_subdirectory(formats)

add_subdirectory(commands)

add_subdirectory(c-library)

add_subdirectory(cplusplus)

add_subdirectory(python)

add_subdirectory(force-styles)



find_package(ClangFormat 8.0)

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