dcd.h File Reference

DCD trajectory file writer. More...

#include "mdio/file.h"
#include "mdapi/mdtypes.h"

Go to the source code of this file.

Classes
struct	mdio_DcdHeader_t
	DCD header information provided by user. More...
struct	mdio_DcdCell_t
	DCD periodic cell information provided by user. More...
struct	mdio_Dcd_t
	DCD trajectory file writer class. More...
Typedefs
typedef mdio_DcdHeader_t	mdio_DcdHeader
	DCD header information provided by user.
typedef mdio_DcdCell_t	mdio_DcdCell
	DCD periodic cell information provided by user.
typedef mdio_Dcd_t	mdio_Dcd
	DCD trajectory file writer class.
Enumerations
enum	{ MDIO_DCD_UNITCELL = 0x001, MDIO_DCD_FIXEDCELL = 0x002 }
Functions
mdio_Dcd *	mdio_createDcd (void)
	Constructor.
void	mdio_destroyDcd (mdio_Dcd *)
	Destructor.
int	mdio_writeBeginDcd (mdio_Dcd *, const char *name)
	Begin writing DCD file.
int	mdio_writeHeaderDcd (mdio_Dcd *, const mdio_DcdHeader *header)
	Write header information to DCD file.
int	mdio_writeFrameDcd (mdio_Dcd *, const MD_Dvec *coord, const mdio_DcdCell *cell, int32 stepnum)
	Write set of coordinates to DCD file.
int	mdio_writeEndDcd (mdio_Dcd *)
	End writing DCD file.
int	mdio_initializeDcd (mdio_Dcd *)
	Alternative constructor.
void	mdio_cleanupDcd (mdio_Dcd *)
	Alternative destructor.

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Detailed Description

DCD trajectory file writer.

Author:

David J. Hardy

Date:

2004-2005

The mdio_Dcd class writes DCD trajectory files equivalent to those produced by NAMD. For now, support is only available for file sizes less than 2 gigabytes.

Writing the DCD file is performed by the following sequence of routines:

• calling mdio_writeBeginDcd() once to open the file
• calling mdio_writeHeaderDcd() once to write the required header information
• calling mdio_writeFrameDcd() multiple times, once for each frame of atomic coordinates
• calling mdio_writeEndDcd() once to close the file

The mdio_Dcd class is derived from mdio_File so that error handling is performed by typecasting (mdio_Bincoord *) to (mdio_File *).

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Typedef Documentation

typedef struct mdio_Dcd_t mdio_Dcd

DCD trajectory file writer class. Members should be treated as private.

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Enumeration Type Documentation

anonymous enum

Set appropriate cellstatus flag to indicate periodic cell. Enumeration values: MDIO_DCD_UNITCELL  Flag for a periodic cell. MDIO_DCD_FIXEDCELL  Flag showing cell dimensions are fixed.

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Function Documentation

void mdio_cleanupDcd (  mdio_Dcd *   )

Alternative destructor. Use to destroy a preallocated mdio_Dcd object (i.e. one constructed using mdio_initializeDcd() ).

mdio_Dcd* mdio_createDcd (  void   )

Constructor. Creates dynamically allocated DCD trajectory file writer object. Returns: Pointer to new object or NULL on failure.

void mdio_destroyDcd (  mdio_Dcd *   )

Destructor. Frees dynamically allocated DCD trajectory file writer object.

int mdio_initializeDcd (  mdio_Dcd *   )

Alternative constructor. Use to construct a preallocated mdio_Dcd object. See mdio_createDcd() for a description of expected arguments.

int mdio_writeBeginDcd (  mdio_Dcd *  , const char *  name )

Begin writing DCD file. Parameters: [in]  name  A nil-terminated string naming the DCD file. Call this once when writing a DCD file. Opens file for writing. Returns: 0 on success, MDIO_ERROR on failure.

int mdio_writeEndDcd (  mdio_Dcd *   )

End writing DCD file. User calls this once at end of DCD file writing. Closes the file. Returns: 0 on success, MDIO_ERROR on failure.

int mdio_writeFrameDcd (  mdio_Dcd *  , const MD_Dvec *  coord, const mdio_DcdCell *  cell, int32  stepnum )

Write set of coordinates to DCD file. Parameters: [in]  coord  Array of coordinates. [in]  cell  Periodic cell information. [in]  stepnum  The number of this timestep. User should call this repeatedly for every frame of coordinates supplied to the DCD file during the simulation. The length of coord array is supplied to the mdio_DcdHeader structure. If system is not periodic, cell should be set to NULL. The value of stepnum is validated against the framestepcnt supplied to mdio_DcdHeader. Returns: 0 on success, MDIO_ERROR on failure.

int mdio_writeHeaderDcd (  mdio_Dcd *  , const mdio_DcdHeader *  header )

Write header information to DCD file. Parameters: [in]  header  Contains header information from user. User must supply appropriate values to mdio_DcdHeader fields. Call this once when writing a DCD file. Returns: 0 on success, MDIO_ERROR on failure.

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