library.cpp
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Created: Sat, Jul 12, 23:57

library.cpp
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	/* ----------------------------------------------------------------------
	LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
	http://lammps.sandia.gov, Sandia National Laboratories
	Steve Plimpton, sjplimp@sandia.gov

	Copyright (2003) Sandia Corporation. Under the terms of Contract
	DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
	certain rights in this software. This software is distributed under
	the GNU General Public License.

	See the README file in the top-level LAMMPS directory.
	------------------------------------------------------------------------- */

	// C or Fortran style library interface to LAMMPS
	// customize by adding new LAMMPS-specific functions

	#include <mpi.h>
	#include <string.h>
	#include <stdlib.h>
	#include "library.h"
	#include "lmptype.h"
	#include "lammps.h"
	#include "universe.h"
	#include "input.h"
	#include "atom_vec.h"
	#include "atom.h"
	#include "domain.h"
	#include "update.h"
	#include "group.h"
	#include "input.h"
	#include "variable.h"
	#include "modify.h"
	#include "output.h"
	#include "thermo.h"
	#include "compute.h"
	#include "fix.h"
	#include "comm.h"
	#include "memory.h"
	#include "error.h"
	#include "force.h"

	using namespace LAMMPS_NS;

	// ----------------------------------------------------------------------
	// utility macros
	// ----------------------------------------------------------------------

	/* ----------------------------------------------------------------------
	macros for optional code path which captures all exceptions
	and stores the last error message. These assume there is a variable lmp
	which is a pointer to the current LAMMPS instance.

	Usage:

	BEGIN_CAPTURE
	{
	// code paths which might throw exception
	...
	}
	END_CAPTURE
	------------------------------------------------------------------------- */

	#ifdef LAMMPS_EXCEPTIONS
	#define BEGIN_CAPTURE \
	Error * error = lmp->error; \
	try

	#define END_CAPTURE \
	catch(LAMMPSAbortException & ae) { \
	int nprocs = 0; \
	MPI_Comm_size(ae.universe, &nprocs ); \
	\
	if (nprocs > 1) { \
	error->set_last_error(ae.message.c_str(), ERROR_ABORT); \
	} else { \
	error->set_last_error(ae.message.c_str(), ERROR_NORMAL); \
	} \
	} catch(LAMMPSException & e) { \
	error->set_last_error(e.message.c_str(), ERROR_NORMAL); \
	}
	#else
	#define BEGIN_CAPTURE
	#define END_CAPTURE
	#endif

	// ----------------------------------------------------------------------
	// helper functions, not in library API
	// ----------------------------------------------------------------------

	/* ----------------------------------------------------------------------
	concatenate one or more LAMMPS input lines starting at ptr
	removes NULL terminator when last printable char of line = '&'
	by replacing both NULL and '&' with space character
	repeat as many times as needed
	on return, ptr now points to longer line
	------------------------------------------------------------------------- */

	void concatenate_lines(char *ptr)
	{
	int nend = strlen(ptr);
	int n = nend-1;
	while (n && isspace(ptr[n])) n--;
	while (ptr[n] == '&') {
	ptr[nend] = ' ';
	ptr[n] = ' ';
	strtok(ptr,"\n");
	nend = strlen(ptr);
	n = nend-1;
	while (n && isspace(ptr[n])) n--;
	}
	}

	// ----------------------------------------------------------------------
	// library API functions to create/destroy an instance of LAMMPS
	// and communicate commands to it
	// ----------------------------------------------------------------------

	/* ----------------------------------------------------------------------
	create an instance of LAMMPS and return pointer to it
	pass in command-line args and MPI communicator to run on
	------------------------------------------------------------------------- */

	void lammps_open(int argc, char argv, MPI_Comm communicator, void ptr)
	{
	#ifdef LAMMPS_EXCEPTIONS
	try
	{
	LAMMPS *lmp = new LAMMPS(argc,argv,communicator);
	ptr = (void ) lmp;
	}
	catch(LAMMPSException & e) {
	fprintf(stderr, "LAMMPS Exception: %s", e.message.c_str());
	ptr = (void ) NULL;
	}
	#else
	LAMMPS *lmp = new LAMMPS(argc,argv,communicator);
	ptr = (void ) lmp;
	#endif
	}

	/* ----------------------------------------------------------------------
	create an instance of LAMMPS and return pointer to it
	caller doesn't know MPI communicator, so use MPI_COMM_WORLD
	initialize MPI if needed
	------------------------------------------------------------------------- */

	void lammps_open_no_mpi(int argc, char argv, void ptr)
	{
	int flag;
	MPI_Initialized(&flag);

	if (!flag) {
	int argc = 0;
	char **argv = NULL;
	MPI_Init(&argc,&argv);
	}

	MPI_Comm communicator = MPI_COMM_WORLD;

	#ifdef LAMMPS_EXCEPTIONS
	try
	{
	LAMMPS *lmp = new LAMMPS(argc,argv,communicator);
	ptr = (void ) lmp;
	}
	catch(LAMMPSException & e) {
	fprintf(stderr, "LAMMPS Exception: %s", e.message.c_str());
	ptr = (void) NULL;
	}
	#else
	LAMMPS *lmp = new LAMMPS(argc,argv,communicator);
	ptr = (void ) lmp;
	#endif
	}

	/* ----------------------------------------------------------------------
	destruct an instance of LAMMPS
	------------------------------------------------------------------------- */

	void lammps_close(void *ptr)
	{
	LAMMPS lmp = (LAMMPS ) ptr;
	delete lmp;
	}

	/* ----------------------------------------------------------------------
	get the numerical representation of the current LAMMPS version
	------------------------------------------------------------------------- */

	int lammps_version(void *ptr)
	{
	LAMMPS lmp = (LAMMPS ) ptr;
	return atoi(lmp->universe->num_ver);
	}

	/* ----------------------------------------------------------------------
	process an input script in filename str
	------------------------------------------------------------------------- */

	void lammps_file(void ptr, char str)
	{
	LAMMPS lmp = (LAMMPS ) ptr;

	BEGIN_CAPTURE
	{
	lmp->input->file(str);
	}
	END_CAPTURE
	}

	/* ----------------------------------------------------------------------
	process a single input command in str
	does not matter if str ends in newline
	return command name to caller
	------------------------------------------------------------------------- */

	char lammps_command(void ptr, char *str)
	{
	LAMMPS lmp = (LAMMPS ) ptr;
	char *result = NULL;

	BEGIN_CAPTURE
	{
	result = lmp->input->one(str);
	}
	END_CAPTURE

	return result;
	}

	/* ----------------------------------------------------------------------
	process multiple input commands in cmds = list of strings
	does not matter if each string ends in newline
	create long contatentated string for processing by commands_string()
	insert newlines in concatenated string as needed
	------------------------------------------------------------------------- */

	void lammps_commands_list(void ptr, int ncmd, char *cmds)
	{
	LAMMPS lmp = (LAMMPS ) ptr;

	int n = ncmd+1;
	for (int i = 0; i < ncmd; i++) n += strlen(cmds[i]);

	char str = (char ) lmp->memory->smalloc(n,"lib/commands/list:str");
	str[0] = '\0';
	n = 0;

	for (int i = 0; i < ncmd; i++) {
	strcpy(&str[n],cmds[i]);
	n += strlen(cmds[i]);
	if (str[n-1] != '\n') {
	str[n] = '\n';
	str[n+1] = '\0';
	n++;
	}
	}

	lammps_commands_string(ptr,str);
	lmp->memory->sfree(str);
	}

	/* ----------------------------------------------------------------------
	process multiple input commands in single long str, separated by newlines
	single command can span multiple lines via continuation characters
	multi-line commands enabled by triple quotes will not work
	------------------------------------------------------------------------- */

	void lammps_commands_string(void ptr, char str)
	{
	LAMMPS lmp = (LAMMPS ) ptr;

	// make copy of str so can strtok() it

	int n = strlen(str) + 1;
	char *copy = new char[n];
	strcpy(copy,str);

	BEGIN_CAPTURE
	{
	char *ptr = copy;
	for (int i=0; i < n-1; ++i) {

	// handle continuation character as last character in line or string
	if ((copy[i] == '&') && (copy[i+1] == '\n'))
	copy[i+1] = copy[i] = ' ';
	else if ((copy[i] == '&') && (copy[i+1] == '\0'))
	copy[i] = ' ';

	if (copy[i] == '\n') {
	copy[i] = '\0';
	lmp->input->one(ptr);
	ptr = copy + i+1;
	} else if (copy[i+1] == '\0')
	lmp->input->one(ptr);
	}
	}
	END_CAPTURE

	delete [] copy;
	}

	/* ----------------------------------------------------------------------
	clean-up function to free memory allocated by lib and returned to caller
	------------------------------------------------------------------------- */

	void lammps_free(void *ptr)
	{
	free(ptr);
	}

	// ----------------------------------------------------------------------
	// library API functions to extract info from LAMMPS or set info in LAMMPS
	// ----------------------------------------------------------------------

	/* ----------------------------------------------------------------------
	add LAMMPS-specific library functions
	all must receive LAMMPS pointer as argument
	customize by adding a function here and in library.h header file
	------------------------------------------------------------------------- */

	/* ----------------------------------------------------------------------
	extract a LAMMPS setting as an integer
	only use for settings that require return of an int
	customize by adding names
	------------------------------------------------------------------------- */

	int lammps_extract_setting(void ptr, char name)
	{
	if (strcmp(name,"bigint") == 0) return sizeof(bigint);
	if (strcmp(name,"tagint") == 0) return sizeof(tagint);
	if (strcmp(name,"imageint") == 0) return sizeof(imageint);

	return -1;
	}

	/* ----------------------------------------------------------------------
	extract a pointer to an internal LAMMPS global entity
	name = desired quantity, e.g. dt or boxyhi or natoms
	returns a void pointer to the entity
	which the caller can cast to the proper data type
	returns a NULL if name not listed below
	this function need only be invoked once
	the returned pointer is a permanent valid reference to the quantity
	customize by adding names
	------------------------------------------------------------------------- */

	void lammps_extract_global(void ptr, char *name)
	{
	LAMMPS lmp = (LAMMPS ) ptr;

	if (strcmp(name,"dt") == 0) return (void *) &lmp->update->dt;
	if (strcmp(name,"boxlo") == 0) return (void *) lmp->domain->boxlo;
	if (strcmp(name,"boxhi") == 0) return (void *) lmp->domain->boxhi;
	if (strcmp(name,"boxxlo") == 0) return (void *) &lmp->domain->boxlo[0];
	if (strcmp(name,"boxxhi") == 0) return (void *) &lmp->domain->boxhi[0];
	if (strcmp(name,"boxylo") == 0) return (void *) &lmp->domain->boxlo[1];
	if (strcmp(name,"boxyhi") == 0) return (void *) &lmp->domain->boxhi[1];
	if (strcmp(name,"boxzlo") == 0) return (void *) &lmp->domain->boxlo[2];
	if (strcmp(name,"boxzhi") == 0) return (void *) &lmp->domain->boxhi[2];
	if (strcmp(name,"periodicity") == 0) return (void *) lmp->domain->periodicity;

	if (strcmp(name,"xy") == 0) return (void *) &lmp->domain->xy;
	if (strcmp(name,"xz") == 0) return (void *) &lmp->domain->xz;
	if (strcmp(name,"yz") == 0) return (void *) &lmp->domain->yz;
	if (strcmp(name,"natoms") == 0) return (void *) &lmp->atom->natoms;
	if (strcmp(name,"nbonds") == 0) return (void *) &lmp->atom->nbonds;
	if (strcmp(name,"nangles") == 0) return (void *) &lmp->atom->nangles;
	if (strcmp(name,"ndihedrals") == 0) return (void *) &lmp->atom->ndihedrals;
	if (strcmp(name,"nimpropers") == 0) return (void *) &lmp->atom->nimpropers;
	if (strcmp(name,"nlocal") == 0) return (void *) &lmp->atom->nlocal;
	if (strcmp(name,"nghost") == 0) return (void *) &lmp->atom->nghost;
	if (strcmp(name,"nmax") == 0) return (void *) &lmp->atom->nmax;
	if (strcmp(name,"ntypes") == 0) return (void *) &lmp->atom->ntypes;
	if (strcmp(name,"ntimestep") == 0) return (void *) &lmp->update->ntimestep;

	if (strcmp(name,"units") == 0) return (void *) lmp->update->unit_style;
	if (strcmp(name,"triclinic") == 0) return (void *) &lmp->domain->triclinic;

	if (strcmp(name,"q_flag") == 0) return (void *) &lmp->atom->q_flag;

	// update->atime can be referenced as a pointer
	// thermo "timer" data cannot be, since it is computed on request
	// lammps_get_thermo() can access all thermo keywords by value

	if (strcmp(name,"atime") == 0) return (void *) &lmp->update->atime;
	if (strcmp(name,"atimestep") == 0) return (void *) &lmp->update->atimestep;

	// global constants defined by units

	if (strcmp(name,"boltz") == 0) return (void *) &lmp->force->boltz;
	if (strcmp(name,"hplanck") == 0) return (void *) &lmp->force->hplanck;
	if (strcmp(name,"mvv2e") == 0) return (void *) &lmp->force->mvv2e;
	if (strcmp(name,"ftm2v") == 0) return (void *) &lmp->force->ftm2v;
	if (strcmp(name,"mv2d") == 0) return (void *) &lmp->force->mv2d;
	if (strcmp(name,"nktv2p") == 0) return (void *) &lmp->force->nktv2p;
	if (strcmp(name,"qqr2e") == 0) return (void *) &lmp->force->qqr2e;
	if (strcmp(name,"qe2f") == 0) return (void *) &lmp->force->qe2f;
	if (strcmp(name,"vxmu2f") == 0) return (void *) &lmp->force->vxmu2f;
	if (strcmp(name,"xxt2kmu") == 0) return (void *) &lmp->force->xxt2kmu;
	if (strcmp(name,"dielectric") == 0) return (void *) &lmp->force->dielectric;
	if (strcmp(name,"qqrd2e") == 0) return (void *) &lmp->force->qqrd2e;
	if (strcmp(name,"e_mass") == 0) return (void *) &lmp->force->e_mass;
	if (strcmp(name,"hhmrr2e") == 0) return (void *) &lmp->force->hhmrr2e;
	if (strcmp(name,"mvh2r") == 0) return (void *) &lmp->force->mvh2r;

	if (strcmp(name,"angstrom") == 0) return (void *) &lmp->force->angstrom;
	if (strcmp(name,"femtosecond") == 0) return (void *) &lmp->force->femtosecond;
	if (strcmp(name,"qelectron") == 0) return (void *) &lmp->force->qelectron;

	return NULL;
	}

	/* ----------------------------------------------------------------------
	extract simulation box parameters
	see domain.h for definition of these arguments
	domain->init() call needed to set box_change
	------------------------------------------------------------------------- */

	void lammps_extract_box(void ptr, double boxlo, double *boxhi,
	double xy, double yz, double *xz,
	int periodicity, int box_change)
	{
	LAMMPS lmp = (LAMMPS ) ptr;
	Domain *domain = lmp->domain;
	domain->init();

	boxlo[0] = domain->boxlo[0];
	boxlo[1] = domain->boxlo[1];
	boxlo[2] = domain->boxlo[2];
	boxhi[0] = domain->boxhi[0];
	boxhi[1] = domain->boxhi[1];
	boxhi[2] = domain->boxhi[2];

	*xy = domain->xy;
	*yz = domain->yz;
	*xz = domain->xz;

	periodicity[0] = domain->periodicity[0];
	periodicity[1] = domain->periodicity[1];
	periodicity[2] = domain->periodicity[2];

	*box_change = domain->box_change;
	}

	/* ----------------------------------------------------------------------
	extract a pointer to an internal LAMMPS atom-based entity
	name = desired quantity, e.g. x or mass
	returns a void pointer to the entity
	which the caller can cast to the proper data type
	returns a NULL if Atom::extract() does not recognize the name
	the returned pointer is not a permanent valid reference to the
	per-atom quantity, since LAMMPS may reallocate per-atom data
	customize by adding names to Atom::extract()
	------------------------------------------------------------------------- */

	void lammps_extract_atom(void ptr, char *name)
	{
	LAMMPS lmp = (LAMMPS ) ptr;
	return lmp->atom->extract(name);
	}

	/* ----------------------------------------------------------------------
	extract a pointer to an internal LAMMPS compute-based entity
	the compute is invoked if its value(s) is not current
	id = compute ID
	style = 0 for global data, 1 for per-atom data, 2 for local data
	type = 0 for scalar, 1 for vector, 2 for array
	for global data, returns a pointer to the
	compute's internal data structure for the entity
	caller should cast it to (double *) for a scalar or vector
	caller should cast it to (double **) for an array
	for per-atom or local data, returns a pointer to the
	compute's internal data structure for the entity
	caller should cast it to (double *) for a vector
	caller should cast it to (double **) for an array
	returns a void pointer to the compute's internal data structure
	for the entity which the caller can cast to the proper data type
	returns a NULL if id is not recognized or style/type not supported
	the returned pointer is not a permanent valid reference to the
	compute data, this function should be re-invoked
	IMPORTANT: if the compute is not current it will be invoked
	LAMMPS cannot easily check here if it is valid to invoke the compute,
	so caller must insure that it is OK
	------------------------------------------------------------------------- */

	void lammps_extract_compute(void ptr, char *id, int style, int type)
	{
	LAMMPS lmp = (LAMMPS ) ptr;

	BEGIN_CAPTURE
	{
	int icompute = lmp->modify->find_compute(id);
	if (icompute < 0) return NULL;
	Compute *compute = lmp->modify->compute[icompute];

	if (style == 0) {
	if (type == 0) {
	if (!compute->scalar_flag) return NULL;
	if (compute->invoked_scalar != lmp->update->ntimestep)
	compute->compute_scalar();
	return (void *) &compute->scalar;
	}
	if (type == 1) {
	if (!compute->vector_flag) return NULL;
	if (compute->invoked_vector != lmp->update->ntimestep)
	compute->compute_vector();
	return (void *) compute->vector;
	}
	if (type == 2) {
	if (!compute->array_flag) return NULL;
	if (compute->invoked_array != lmp->update->ntimestep)
	compute->compute_array();
	return (void *) compute->array;
	}
	}

	if (style == 1) {
	if (!compute->peratom_flag) return NULL;
	if (type == 1) {
	if (compute->invoked_peratom != lmp->update->ntimestep)
	compute->compute_peratom();
	return (void *) compute->vector_atom;
	}
	if (type == 2) {
	if (compute->invoked_peratom != lmp->update->ntimestep)
	compute->compute_peratom();
	return (void *) compute->array_atom;
	}
	}

	if (style == 2) {
	if (!compute->local_flag) return NULL;
	if (type == 1) {
	if (compute->invoked_local != lmp->update->ntimestep)
	compute->compute_local();
	return (void *) compute->vector_local;
	}
	if (type == 2) {
	if (compute->invoked_local != lmp->update->ntimestep)
	compute->compute_local();
	return (void *) compute->array_local;
	}
	}
	}
	END_CAPTURE

	return NULL;
	}

	/* ----------------------------------------------------------------------
	extract a pointer to an internal LAMMPS fix-based entity
	id = fix ID
	style = 0 for global data, 1 for per-atom data, 2 for local data
	type = 0 for scalar, 1 for vector, 2 for array
	i,j = indices needed only to specify which global vector or array value
	for global data, returns a pointer to a memory location
	which is allocated by this function
	which the caller can cast to a (double *) which points to the value
	for per-atom or local data, returns a pointer to the
	fix's internal data structure for the entity
	caller should cast it to (double *) for a vector
	caller should cast it to (double **) for an array
	returns a NULL if id is not recognized or style/type not supported
	IMPORTANT: for global data,
	this function allocates a double to store the value in,
	so the caller must free this memory to avoid a leak, e.g.
	double dptr = (double ) lammps_extract_fix();
	double value = *dptr;
	lammps_free(dptr);
	IMPORTANT: LAMMPS cannot easily check here when info extracted from
	the fix is valid, so caller must insure that it is OK
	------------------------------------------------------------------------- */

	void lammps_extract_fix(void ptr, char *id, int style, int type,
	int i, int j)
	{
	LAMMPS lmp = (LAMMPS ) ptr;

	BEGIN_CAPTURE
	{
	int ifix = lmp->modify->find_fix(id);
	if (ifix < 0) return NULL;
	Fix *fix = lmp->modify->fix[ifix];

	if (style == 0) {
	double dptr = (double ) malloc(sizeof(double));
	if (type == 0) {
	if (!fix->scalar_flag) return NULL;
	*dptr = fix->compute_scalar();
	return (void *) dptr;
	}
	if (type == 1) {
	if (!fix->vector_flag) return NULL;
	*dptr = fix->compute_vector(i);
	return (void *) dptr;
	}
	if (type == 2) {
	if (!fix->array_flag) return NULL;
	*dptr = fix->compute_array(i,j);
	return (void *) dptr;
	}
	}

	if (style == 1) {
	if (!fix->peratom_flag) return NULL;
	if (type == 1) return (void *) fix->vector_atom;
	if (type == 2) return (void *) fix->array_atom;
	}

	if (style == 2) {
	if (!fix->local_flag) return NULL;
	if (type == 1) return (void *) fix->vector_local;
	if (type == 2) return (void *) fix->array_local;
	}
	}
	END_CAPTURE

	return NULL;
	}

	/* ----------------------------------------------------------------------
	extract a pointer to an internal LAMMPS evaluated variable
	name = variable name, must be equal-style or atom-style variable
	group = group ID for evaluating an atom-style variable, else NULL
	for equal-style variable, returns a pointer to a memory location
	which is allocated by this function
	which the caller can cast to a (double *) which points to the value
	for atom-style variable, returns a pointer to the
	vector of per-atom values on each processor,
	which the caller can cast to a (double *) which points to the values
	returns a NULL if name is not recognized or not equal-style or atom-style
	IMPORTANT: for both equal-style and atom-style variables,
	this function allocates memory to store the variable data in
	so the caller must free this memory to avoid a leak
	e.g. for equal-style variables
	double dptr = (double ) lammps_extract_variable();
	double value = *dptr;
	lammps_free(dptr);
	e.g. for atom-style variables
	double vector = (double ) lammps_extract_variable();
	use the vector values
	lammps_free(vector);
	IMPORTANT: LAMMPS cannot easily check here when it is valid to evaluate
	the variable or any fixes or computes or thermodynamic info it references,
	so caller must insure that it is OK
	------------------------------------------------------------------------- */

	void lammps_extract_variable(void ptr, char name, char group)
	{
	LAMMPS lmp = (LAMMPS ) ptr;

	BEGIN_CAPTURE
	{
	int ivar = lmp->input->variable->find(name);
	if (ivar < 0) return NULL;

	if (lmp->input->variable->equalstyle(ivar)) {
	double dptr = (double ) malloc(sizeof(double));
	*dptr = lmp->input->variable->compute_equal(ivar);
	return (void *) dptr;
	}

	if (lmp->input->variable->atomstyle(ivar)) {
	int igroup = lmp->group->find(group);
	if (igroup < 0) return NULL;
	int nlocal = lmp->atom->nlocal;
	double vector = (double ) malloc(nlocal*sizeof(double));
	lmp->input->variable->compute_atom(ivar,igroup,vector,1,0);
	return (void *) vector;
	}
	}
	END_CAPTURE

	return NULL;
	}


	/* ----------------------------------------------------------------------
	reset simulation box parameters
	see domain.h for definition of these arguments
	assumes domain->set_initial_box() has been invoked previously
	------------------------------------------------------------------------- */

	void lammps_reset_box(void ptr, double boxlo, double *boxhi,
	double xy, double yz, double xz)
	{
	LAMMPS lmp = (LAMMPS ) ptr;
	Domain *domain = lmp->domain;

	domain->boxlo[0] = boxlo[0];
	domain->boxlo[1] = boxlo[1];
	domain->boxlo[2] = boxlo[2];
	domain->boxhi[0] = boxhi[0];
	domain->boxhi[1] = boxhi[1];
	domain->boxhi[2] = boxhi[2];

	domain->xy = xy;
	domain->yz = yz;
	domain->xz = xz;

	domain->set_global_box();
	lmp->comm->set_proc_grid();
	domain->set_local_box();
	}

	/* ----------------------------------------------------------------------
	set the value of a STRING variable to str
	return -1 if variable doesn't exist or not a STRING variable
	return 0 for success
	------------------------------------------------------------------------- */

	int lammps_set_variable(void ptr, char name, char *str)
	{
	LAMMPS lmp = (LAMMPS ) ptr;
	int err = -1;

	BEGIN_CAPTURE
	{
	err = lmp->input->variable->set_string(name,str);
	}
	END_CAPTURE

	return err;
	}

	/* ----------------------------------------------------------------------
	return the current value of a thermo keyword as a double
	unlike lammps_extract_global() this does not give access to the
	storage of the data in question
	instead it triggers the Thermo class to compute the current value
	and returns it
	------------------------------------------------------------------------- */

	double lammps_get_thermo(void ptr, char name)
	{
	LAMMPS lmp = (LAMMPS ) ptr;
	double dval = 0.0;

	BEGIN_CAPTURE
	{
	lmp->output->thermo->evaluate_keyword(name,&dval);
	}
	END_CAPTURE

	return dval;
	}

	/* ----------------------------------------------------------------------
	return the total number of atoms in the system
	useful before call to lammps_get_atoms() so can pre-allocate vector
	------------------------------------------------------------------------- */

	int lammps_get_natoms(void *ptr)
	{
	LAMMPS lmp = (LAMMPS ) ptr;

	if (lmp->atom->natoms > MAXSMALLINT) return 0;
	int natoms = static_cast<int> (lmp->atom->natoms);
	return natoms;
	}

	/* ----------------------------------------------------------------------
	gather the named atom-based entity across all processors
	atom IDs must be consecutive from 1 to N
	name = desired quantity, e.g. x or charge
	type = 0 for integer values, 1 for double values
	count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f
	return atom-based values in 1d data, ordered by count, then by atom ID
	e.g. x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...
	data must be pre-allocated by caller to correct length
	------------------------------------------------------------------------- */

	void lammps_gather_atoms(void ptr, char name,
	int type, int count, void *data)
	{
	LAMMPS lmp = (LAMMPS ) ptr;

	BEGIN_CAPTURE
	{
	// error if tags are not defined or not consecutive

	int flag = 0;
	if (lmp->atom->tag_enable == 0 \|\| lmp->atom->tag_consecutive() == 0)
	flag = 1;
	if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
	if (flag) {
	if (lmp->comm->me == 0)
	lmp->error->warning(FLERR,"Library error in lammps_gather_atoms");
	return;
	}

	int natoms = static_cast<int> (lmp->atom->natoms);

	int i,j,offset;
	void *vptr = lmp->atom->extract(name);
	if(vptr == NULL) {
	lmp->error->warning(FLERR,"lammps_gather_atoms: unknown property name");
	return;
	}

	// copy = Natom length vector of per-atom values
	// use atom ID to insert each atom's values into copy
	// MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID

	if (type == 0) {
	int *vector = NULL;
	int **array = NULL;
	const int imgunpack = (count == 3) && (strcmp(name,"image") == 0);

	if ((count == 1) \|\| imgunpack) vector = (int *) vptr;
	else array = (int **) vptr;

	int *copy;
	lmp->memory->create(copy,count*natoms,"lib/gather:copy");
	for (i = 0; i < count*natoms; i++) copy[i] = 0;

	tagint *tag = lmp->atom->tag;
	int nlocal = lmp->atom->nlocal;

	if (count == 1)
	for (i = 0; i < nlocal; i++)
	copy[tag[i]-1] = vector[i];
	else if (imgunpack) {
	for (i = 0; i < nlocal; i++) {
	offset = count*(tag[i]-1);
	const int image = vector[i];
	copy[offset++] = (image & IMGMASK) - IMGMAX;
	copy[offset++] = ((image >> IMGBITS) & IMGMASK) - IMGMAX;
	copy[offset++] = ((image >> IMG2BITS) & IMGMASK) - IMGMAX;
	}
	} else
	for (i = 0; i < nlocal; i++) {
	offset = count*(tag[i]-1);
	for (j = 0; j < count; j++)
	copy[offset++] = array[i][j];
	}

	MPI_Allreduce(copy,data,count*natoms,MPI_INT,MPI_SUM,lmp->world);
	lmp->memory->destroy(copy);

	} else {
	double *vector = NULL;
	double **array = NULL;
	if (count == 1) vector = (double *) vptr;
	else array = (double **) vptr;

	double *copy;
	lmp->memory->create(copy,count*natoms,"lib/gather:copy");
	for (i = 0; i < count*natoms; i++) copy[i] = 0.0;

	tagint *tag = lmp->atom->tag;
	int nlocal = lmp->atom->nlocal;

	if (count == 1) {
	for (i = 0; i < nlocal; i++)
	copy[tag[i]-1] = vector[i];
	} else {
	for (i = 0; i < nlocal; i++) {
	offset = count*(tag[i]-1);
	for (j = 0; j < count; j++)
	copy[offset++] = array[i][j];
	}
	}

	MPI_Allreduce(copy,data,count*natoms,MPI_DOUBLE,MPI_SUM,lmp->world);
	lmp->memory->destroy(copy);
	}
	}
	END_CAPTURE
	}

	/* ----------------------------------------------------------------------
	scatter the named atom-based entity across all processors
	atom IDs must be consecutive from 1 to N
	name = desired quantity, e.g. x or charge
	type = 0 for integer values, 1 for double values
	count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f
	data = atom-based values in 1d data, ordered by count, then by atom ID
	e.g. x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...
	------------------------------------------------------------------------- */

	void lammps_scatter_atoms(void ptr, char name,
	int type, int count, void *data)
	{
	LAMMPS lmp = (LAMMPS ) ptr;

	BEGIN_CAPTURE
	{
	// error if tags are not defined or not consecutive or no atom map

	int flag = 0;
	if (lmp->atom->tag_enable == 0 \|\| lmp->atom->tag_consecutive() == 0)
	flag = 1;
	if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
	if (lmp->atom->map_style == 0) flag = 1;
	if (flag) {
	if (lmp->comm->me == 0)
	lmp->error->warning(FLERR,"Library error in lammps_scatter_atoms");
	return;
	}

	int natoms = static_cast<int> (lmp->atom->natoms);

	int i,j,m,offset;
	void *vptr = lmp->atom->extract(name);
	if(vptr == NULL) {
	lmp->error->warning(FLERR,
	"lammps_scatter_atoms: unknown property name");
	return;
	}

	// copy = Natom length vector of per-atom values
	// use atom ID to insert each atom's values into copy
	// MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID

	if (type == 0) {
	int *vector = NULL;
	int **array = NULL;
	const int imgpack = (count == 3) && (strcmp(name,"image") == 0);

	if ((count == 1) \|\| imgpack) vector = (int *) vptr;
	else array = (int **) vptr;
	int dptr = (int ) data;

	if (count == 1) {
	for (i = 0; i < natoms; i++)
	if ((m = lmp->atom->map(i+1)) >= 0)
	vector[m] = dptr[i];
	} else if (imgpack) {
	for (i = 0; i < natoms; i++)
	if ((m = lmp->atom->map(i+1)) >= 0) {
	offset = count*i;
	int image = dptr[offset++] + IMGMAX;
	image += (dptr[offset++] + IMGMAX) << IMGBITS;
	image += (dptr[offset++] + IMGMAX) << IMG2BITS;
	vector[m] = image;
	}
	} else {
	for (i = 0; i < natoms; i++)
	if ((m = lmp->atom->map(i+1)) >= 0) {
	offset = count*i;
	for (j = 0; j < count; j++)
	array[m][j] = dptr[offset++];
	}
	}
	} else {
	double *vector = NULL;
	double **array = NULL;
	if (count == 1) vector = (double *) vptr;
	else array = (double **) vptr;
	double dptr = (double ) data;

	if (count == 1) {
	for (i = 0; i < natoms; i++)
	if ((m = lmp->atom->map(i+1)) >= 0)
	vector[m] = dptr[i];
	} else {
	for (i = 0; i < natoms; i++) {
	if ((m = lmp->atom->map(i+1)) >= 0) {
	offset = count*i;
	for (j = 0; j < count; j++)
	array[m][j] = dptr[offset++];
	}
	}
	}
	}
	}
	END_CAPTURE
	}

	/* ----------------------------------------------------------------------
	create N atoms and assign them to procs based on coords
	id = atom IDs (optional, NULL will generate 1 to N)
	type = N-length vector of atom types (required)
	x = 3N-length 1d vector of atom coords (required)
	v = 3N-length 1d vector of atom velocities (optional, NULL if just 0.0)
	image flags can be treated in two ways:
	(a) image = vector of current image flags
	each atom will be remapped into periodic box by domain->ownatom()
	image flag will be incremented accordingly and stored with atom
	(b) image = NULL
	each atom will be remapped into periodic box by domain->ownatom()
	image flag will be set to 0 by atom->avec->create_atom()
	shrinkexceed = 1 allows atoms to be outside a shrinkwrapped boundary
	passed to ownatom() which will assign them to boundary proc
	important if atoms may be (slightly) outside non-periodic dim
	e.g. due to restoring a snapshot from a previous run and previous box
	id and image must be 32-bit integers
	x,v = ordered by xyz, then by atom
	e.g. x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...
	------------------------------------------------------------------------- */

	void lammps_create_atoms(void ptr, int n, tagint id, int *type,
	double x, double v, imageint *image,
	int shrinkexceed)
	{
	LAMMPS lmp = (LAMMPS ) ptr;

	BEGIN_CAPTURE
	{
	// error if box does not exist or tags not defined

	int flag = 0;
	if (lmp->domain->box_exist == 0) flag = 1;
	if (lmp->atom->tag_enable == 0) flag = 1;
	if (flag) {
	if (lmp->comm->me == 0)
	lmp->error->warning(FLERR,"Library error in lammps_create_atoms");
	return;
	}

	// loop over N atoms of entire system
	// if this proc owns it based on coords, invoke create_atom()
	// optionally set atom tags and velocities

	Atom *atom = lmp->atom;
	Domain *domain = lmp->domain;
	int nlocal = atom->nlocal;

	bigint natoms_prev = atom->natoms;
	int nlocal_prev = nlocal;
	double xdata[3];

	for (int i = 0; i < n; i++) {
	xdata[0] = x[3*i];
	xdata[1] = x[3*i+1];
	xdata[2] = x[3*i+2];
	imageint * img = image ? &image[i] : NULL;
	tagint tag = id ? id[i] : -1;
	if (!domain->ownatom(tag, xdata, img, shrinkexceed)) continue;

	atom->avec->create_atom(type[i],xdata);
	if (id) atom->tag[nlocal] = id[i];
	else atom->tag[nlocal] = i+1;
	if (v) {
	atom->v[nlocal][0] = v[3*i];
	atom->v[nlocal][1] = v[3*i+1];
	atom->v[nlocal][2] = v[3*i+2];
	}
	if (image) atom->image[nlocal] = image[i];
	nlocal++;
	}

	// need to reset atom->natoms inside LAMMPS

	bigint ncurrent = nlocal;
	MPI_Allreduce(&ncurrent,&lmp->atom->natoms,1,MPI_LMP_BIGINT,
	MPI_SUM,lmp->world);

	// init per-atom fix/compute/variable values for created atoms

	atom->data_fix_compute_variable(nlocal_prev,nlocal);

	// if global map exists, reset it
	// invoke map_init() b/c atom count has grown

	if (lmp->atom->map_style) {
	lmp->atom->map_init();
	lmp->atom->map_set();
	}

	// warn if new natoms is not correct

	if (lmp->atom->natoms != natoms_prev + n) {
	char str[128];
	sprintf(str,"Library warning in lammps_create_atoms, "
	"invalid total atoms %ld %ld",lmp->atom->natoms,natoms_prev+n);
	if (lmp->comm->me == 0)
	lmp->error->warning(FLERR,str);
	}
	}
	END_CAPTURE
	}

	// ----------------------------------------------------------------------
	// library API functions for error handling
	// ----------------------------------------------------------------------

	#ifdef LAMMPS_EXCEPTIONS

	/* ----------------------------------------------------------------------
	check if a new error message
	------------------------------------------------------------------------- */

	int lammps_has_error(void *ptr) {
	LAMMPS * lmp = (LAMMPS *) ptr;
	Error * error = lmp->error;
	return error->get_last_error() ? 1 : 0;
	}

	/* ----------------------------------------------------------------------
	copy the last error message of LAMMPS into a character buffer
	return value encodes which type of error:
	1 = normal error (recoverable)
	2 = abort error (non-recoverable)
	------------------------------------------------------------------------- */

	int lammps_get_last_error_message(void ptr, char buffer, int buffer_size) {
	LAMMPS * lmp = (LAMMPS *) ptr;
	Error * error = lmp->error;

	if(error->get_last_error()) {
	int error_type = error->get_last_error_type();
	strncpy(buffer, error->get_last_error(), buffer_size-1);
	error->set_last_error(NULL, ERROR_NONE);
	return error_type;
	}
	return 0;
	}

	#endif

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