/home/pedro/work/mdcore/src/engine_io.c File Reference

#include <stdlib.h>
#include <stdio.h>
#include <pthread.h>
#include <math.h>
#include <float.h>
#include <string.h>
#include "../config.h"
#include <omp.h>
#include "cycle.h"
#include "errs.h"
#include "fptype.h"
#include "lock.h"
#include "part.h"
#include "cell.h"
#include "fifo.h"
#include "space.h"
#include "potential.h"
#include "runner.h"
#include "bond.h"
#include "rigid.h"
#include "angle.h"
#include "dihedral.h"
#include "exclusion.h"
#include "reader.h"
#include "engine.h"

Defines
#define	error(id)   ( engine_err = errs_register( id , engine_err_msg[-(id)] , __LINE__ , __FUNCTION__ , __FILE__ ) )
Functions
int	engine_read_xplor (struct engine *e, FILE *xplor, double kappa, double tol, int rigidH)
	Read the potentials from a XPLOR parameter file.
int	engine_read_cpf (struct engine *e, FILE *cpf, double kappa, double tol, int rigidH)
	Read the potentials from a CHARMM parameter file.
int	engine_read_psf (struct engine *e, FILE *psf, FILE *pdb)
	Read the simulation setup from a PSF and PDB file pair.
int	engine_dump_PSF (struct engine *e, FILE *psf, FILE *pdb, char *excl[], int nr_excl)
	Dump the contents of the enginge to a PSF and PDB file.

---

Define Documentation

#define error

(

id

)

( engine_err = errs_register( id , engine_err_msg[-(id)] , __LINE__ , __FUNCTION__ , __FILE__ ) )

---

Function Documentation

int engine_dump_PSF	(	struct engine *	e,
		FILE *	psf,
		FILE *	pdb,
		char *	excl[],
		int	nr_excl
	)

Dump the contents of the enginge to a PSF and PDB file.

Parameters:

e	The engine.
psf	A pointer to FILE to which to write the PSF file.
pdb	A pointer to FILE to which to write the PDB file.

If any of psf or pdb are NULL, the respective output will not be generated.

Returns:

engine_err_ok or < 0 on error (see engine_err).

int engine_read_cpf	(	struct engine *	e,
		FILE *	cpf,
		double	kappa,
		double	tol,
		int	rigidH
	)

Read the potentials from a CHARMM parameter file.

Parameters:

e	The engine.
cpf	The open CHARMM parameter file.
kappa	The PME screening width.
tol	The absolute tolerance for interpolation.
rigidH	Convert all bonds over a type starting with 'H' to a rigid constraint.

If kappa is zero, truncated Coulomb electrostatic interactions are assumed. If kappa is less than zero, no electrostatic interactions are computed.

Returns:

engine_err_ok or < 0 on error (see engine_err).

int engine_read_psf	(	struct engine *	e,
		FILE *	psf,
		FILE *	pdb
	)

Read the simulation setup from a PSF and PDB file pair.

Parameters:

e	The engine.
psf	The open PSF file.
pdb	The open PDB file.

Returns:

engine_err_ok or < 0 on error (see engine_err).

int engine_read_xplor	(	struct engine *	e,
		FILE *	xplor,
		double	kappa,
		double	tol,
		int	rigidH
	)

Read the potentials from a XPLOR parameter file.

Parameters:

e	The engine.
xplor	The open XPLOR parameter file.
kappa	The PME screening width.
tol	The absolute tolerance for interpolation.
rigidH	Convert all bonds over a type starting with 'H' to a rigid constraint.

If kappa is zero, truncated Coulomb electrostatic interactions are assumed. If kappa is less than zero, no electrostatic interactions are computed.

Returns:

engine_err_ok or < 0 on error (see engine_err).