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dcdplugin_s.c
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/***************************************************************************
*cr
*cr (C) Copyright 1995-2009 The Board of Trustees of the
*cr University of Illinois
*cr All Rights Reserved
*cr
***************************************************************************/
/***************************************************************************
* RCS INFORMATION:
*
* $RCSfile: dcdplugin.c,v $
* $Author: johns $ $Locker: $ $State: Exp $
* $Revision: 1.75 $ $Date: 2010/10/19 16:22:12 $
*
***************************************************************************
* DESCRIPTION:
* Code for reading and writing CHARMM, NAMD, and X-PLOR format
* molecular dynamic trajectory files.
*
* TODO:
* Integrate improvements from the NAMD source tree
* - NAMD's writer code has better type-correctness for the sizes
* of "int". NAMD uses "int32" explicitly, which is required on
* machines like the T3E. VMD's version of the code doesn't do that
* presently.
*
* Try various alternative I/O API options:
* - use mmap(), with read-once flags
* - use O_DIRECT open mode on new revs of Linux kernel
* - use directio() call on a file descriptor to enable on Solaris
* - use aio_open()/read()/write()
* - use readv/writev() etc.
*
* Standalone test binary compilation flags:
* cc -fast -xarch=v9a -I../../include -DTEST_DCDPLUGIN dcdplugin.c \
* -o ~/bin/readdcd -lm
*
* Profiling flags:
* cc -xpg -fast -xarch=v9a -g -I../../include -DTEST_DCDPLUGIN dcdplugin.c \
* -o ~/bin/readdcd -lm
*
***************************************************************************/
#include "largefiles.h" /* platform dependent 64-bit file I/O defines */
#include <stdio.h>
#include <sys/stat.h>
#include <sys/types.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <time.h>
#include "endianswap.h"
#include "fastio.h"
#include "molfile_plugin.h"
#ifndef M_PI_2
#define M_PI_2 1.57079632679489661922
#endif
#define RECSCALE32BIT 1
#define RECSCALE64BIT 2
#define RECSCALEMAX 2
typedef struct {
fio_fd fd;
int natoms;
int nsets;
int setsread;
int istart;
int nsavc;
double delta;
int nfixed;
float *x, *y, *z;
int *freeind;
float *fixedcoords;
int reverse;
int charmm;
int first;
int with_unitcell;
} dcdhandle;
/* Define error codes that may be returned by the DCD routines */
#define DCD_SUCCESS 0 /* No problems */
#define DCD_EOF -1 /* Normal EOF */
#define DCD_DNE -2 /* DCD file does not exist */
#define DCD_OPENFAILED -3 /* Open of DCD file failed */
#define DCD_BADREAD -4 /* read call on DCD file failed */
#define DCD_BADEOF -5 /* premature EOF found in DCD file */
#define DCD_BADFORMAT -6 /* format of DCD file is wrong */
#define DCD_FILEEXISTS -7 /* output file already exists */
#define DCD_BADMALLOC -8 /* malloc failed */
#define DCD_BADWRITE -9 /* write call on DCD file failed */
/* Define feature flags for this DCD file */
#define DCD_IS_XPLOR 0x00
#define DCD_IS_CHARMM 0x01
#define DCD_HAS_4DIMS 0x02
#define DCD_HAS_EXTRA_BLOCK 0x04
#define DCD_HAS_64BIT_REC 0x08
/* defines used by write_dcdstep */
#define NFILE_POS 8L
#define NSTEP_POS 20L
/* READ Macro to make porting easier */
#define READ(fd, buf, size) fio_fread(((void *) buf), (size), 1, (fd))
/* WRITE Macro to make porting easier */
#define WRITE(fd, buf, size) fio_fwrite(((void *) buf), (size), 1, (fd))
/* XXX This is broken - fread never returns -1 */
#define CHECK_FREAD(X, msg) if (X==-1) { return(DCD_BADREAD); }
#define CHECK_FEOF(X, msg) if (X==0) { return(DCD_BADEOF); }
/* print DCD error in a human readable way */
/*static*/ void print_dcderror(const char *func, int errcode) {
const char *errstr;
switch (errcode) {
case DCD_EOF: errstr = "end of file"; break;
case DCD_DNE: errstr = "file not found"; break;
case DCD_OPENFAILED: errstr = "file open failed"; break;
case DCD_BADREAD: errstr = "error during read"; break;
case DCD_BADEOF: errstr = "premature end of file"; break;
case DCD_BADFORMAT: errstr = "corruption or unrecognized file structure"; break;
case DCD_FILEEXISTS: errstr = "output file already exists"; break;
case DCD_BADMALLOC: errstr = "memory allocation failed"; break;
case DCD_BADWRITE: errstr = "error during write"; break;
case DCD_SUCCESS:
default:
errstr = "no error";
break;
}
printf("dcdplugin) %s: %s\n", func, errstr);
}
/*
* Read the header information from a dcd file.
* Input: fd - a file struct opened for binary reading.
* Output: 0 on success, negative error code on failure.
* Side effects: *natoms set to number of atoms per frame
* *nsets set to number of frames in dcd file
* *istart set to starting timestep of dcd file
* *nsavc set to timesteps between dcd saves
* *delta set to value of trajectory timestep
* *nfixed set to number of fixed atoms
* *freeind may be set to heap-allocated space
* *reverse set to one if reverse-endian, zero if not.
* *charmm set to internal code for handling charmm data.
*/
/*static*/ int read_dcdheader(fio_fd fd, int *N, int *NSET, int *ISTART,
int *NSAVC, double *DELTA, int *NAMNF,
int **FREEINDEXES, float **fixedcoords, int *reverseEndian,
int *charmm)
{
unsigned int input_integer[2]; /* buffer space */
int i, ret_val, rec_scale;
char hdrbuf[84]; /* char buffer used to store header */
int NTITLE;
int dcdcordmagic;
char *corp = (char *) &dcdcordmagic;
/* coordinate dcd file magic string 'CORD' */
corp[0] = 'C';
corp[1] = 'O';
corp[2] = 'R';
corp[3] = 'D';
/* First thing in the file should be an 84.
* some 64-bit compiles have a 64-bit record length indicator,
* so we have to read two ints and check in a more complicated
* way. :-( */
ret_val = READ(fd, input_integer, 2*sizeof(unsigned int));
CHECK_FREAD(ret_val, "reading first int from dcd file");
CHECK_FEOF(ret_val, "reading first int from dcd file");
/* Check magic number in file header and determine byte order*/
if ((input_integer[0]+input_integer[1]) == 84) {
*reverseEndian=0;
rec_scale=RECSCALE64BIT;
printf("dcdplugin) detected CHARMM -i8 64-bit DCD file of native endianness\n");
} else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) {
*reverseEndian=0;
rec_scale=RECSCALE32BIT;
printf("dcdplugin) detected standard 32-bit DCD file of native endianness\n");
} else {
/* now try reverse endian */
swap4_aligned(input_integer, 2); /* will have to unswap magic if 32-bit */
if ((input_integer[0]+input_integer[1]) == 84) {
*reverseEndian=1;
rec_scale=RECSCALE64BIT;
printf("dcdplugin) detected CHARMM -i8 64-bit DCD file of opposite endianness\n");
} else {
swap4_aligned(&input_integer[1], 1); /* unswap magic (see above) */
if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) {
*reverseEndian=1;
rec_scale=RECSCALE32BIT;
printf("dcdplugin) detected standard 32-bit DCD file of opposite endianness\n");
} else {
/* not simply reversed endianism or -i8, something rather more evil */
printf("dcdplugin) unrecognized DCD header:\n");
printf("dcdplugin) [0]: %10d [1]: %10d\n", input_integer[0], input_integer[1]);
printf("dcdplugin) [0]: 0x%08x [1]: 0x%08x\n", input_integer[0], input_integer[1]);
return DCD_BADFORMAT;
}
}
}
/* check for magic string, in case of long record markers */
if (rec_scale == RECSCALE64BIT) {
ret_val = READ(fd, input_integer, sizeof(unsigned int));
if (input_integer[0] != dcdcordmagic) {
printf("dcdplugin) failed to find CORD magic in CHARMM -i8 64-bit DCD file\n");
return DCD_BADFORMAT;
}
}
/* Buffer the entire header for random access */
ret_val = READ(fd, hdrbuf, 80);
CHECK_FREAD(ret_val, "buffering header");
CHECK_FEOF(ret_val, "buffering header");
/* CHARMm-genereate DCD files set the last integer in the */
/* header, which is unused by X-PLOR, to its version number. */
/* Checking if this is nonzero tells us this is a CHARMm file */
/* and to look for other CHARMm flags. */
if (*((int *) (hdrbuf + 76)) != 0) {
(*charmm) = DCD_IS_CHARMM;
if (*((int *) (hdrbuf + 40)) != 0)
(*charmm) |= DCD_HAS_EXTRA_BLOCK;
if (*((int *) (hdrbuf + 44)) == 1)
(*charmm) |= DCD_HAS_4DIMS;
if (rec_scale == RECSCALE64BIT)
(*charmm) |= DCD_HAS_64BIT_REC;
} else {
(*charmm) = DCD_IS_XPLOR; /* must be an X-PLOR format DCD file */
}
if (*charmm & DCD_IS_CHARMM) {
/* CHARMM and NAMD versions 2.1b1 and later */
printf("dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)\n");
} else {
/* CHARMM and NAMD versions prior to 2.1b1 */
printf("dcdplugin) X-PLOR format DCD file (also NAMD 2.0 and earlier)\n");
}
/* Store the number of sets of coordinates (NSET) */
(*NSET) = *((int *) (hdrbuf));
if (*reverseEndian) swap4_unaligned(NSET, 1);
/* Store ISTART, the starting timestep */
(*ISTART) = *((int *) (hdrbuf + 4));
if (*reverseEndian) swap4_unaligned(ISTART, 1);
/* Store NSAVC, the number of timesteps between dcd saves */
(*NSAVC) = *((int *) (hdrbuf + 8));
if (*reverseEndian) swap4_unaligned(NSAVC, 1);
/* Store NAMNF, the number of fixed atoms */
(*NAMNF) = *((int *) (hdrbuf + 32));
if (*reverseEndian) swap4_unaligned(NAMNF, 1);
/* Read in the timestep, DELTA */
/* Note: DELTA is stored as a double with X-PLOR but as a float with CHARMm */
if ((*charmm) & DCD_IS_CHARMM) {
float ftmp;
ftmp = *((float *)(hdrbuf+36)); /* is this safe on Alpha? */
if (*reverseEndian)
swap4_aligned(&ftmp, 1);
*DELTA = (double)ftmp;
} else {
(*DELTA) = *((double *)(hdrbuf + 36));
if (*reverseEndian) swap8_unaligned(DELTA, 1);
}
/* Get the end size of the first block */
ret_val = READ(fd, input_integer, rec_scale*sizeof(int));
CHECK_FREAD(ret_val, "reading second 84 from dcd file");
CHECK_FEOF(ret_val, "reading second 84 from dcd file");
if (*reverseEndian) swap4_aligned(input_integer, rec_scale);
if (rec_scale == RECSCALE64BIT) {
if ((input_integer[0]+input_integer[1]) != 84) {
return DCD_BADFORMAT;
}
} else {
if (input_integer[0] != 84) {
return DCD_BADFORMAT;
}
}
/* Read in the size of the next block */
input_integer[1] = 0;
ret_val = READ(fd, input_integer, rec_scale*sizeof(int));
CHECK_FREAD(ret_val, "reading size of title block");
CHECK_FEOF(ret_val, "reading size of title block");
if (*reverseEndian) swap4_aligned(input_integer, rec_scale);
if ((((input_integer[0]+input_integer[1])-4) % 80) == 0) {
/* Read NTITLE, the number of 80 character title strings there are */
ret_val = READ(fd, &NTITLE, sizeof(int));
CHECK_FREAD(ret_val, "reading NTITLE");
CHECK_FEOF(ret_val, "reading NTITLE");
if (*reverseEndian) swap4_aligned(&NTITLE, 1);
if (NTITLE < 0) {
printf("dcdplugin) WARNING: Bogus NTITLE value: %d (hex: %08x)\n",
NTITLE, NTITLE);
return DCD_BADFORMAT;
}
if (NTITLE > 1000) {
printf("dcdplugin) WARNING: Bogus NTITLE value: %d (hex: %08x)\n",
NTITLE, NTITLE);
if (NTITLE == 1095062083) {
printf("dcdplugin) WARNING: Broken Vega ZZ 2.4.0 DCD file detected\n");
printf("dcdplugin) Assuming 2 title lines, good luck...\n");
NTITLE = 2;
} else {
printf("dcdplugin) Assuming zero title lines, good luck...\n");
NTITLE = 0;
}
}
for (i=0; i<NTITLE; i++) {
fio_fseek(fd, 80, FIO_SEEK_CUR);
CHECK_FEOF(ret_val, "reading TITLE");
}
/* Get the ending size for this block */
ret_val = READ(fd, input_integer, rec_scale*sizeof(int));
CHECK_FREAD(ret_val, "reading size of title block");
CHECK_FEOF(ret_val, "reading size of title block");
} else {
return DCD_BADFORMAT;
}
/* Read in an integer '4' */
input_integer[1] = 0;
ret_val = READ(fd, input_integer, rec_scale*sizeof(int));
CHECK_FREAD(ret_val, "reading a '4'");
CHECK_FEOF(ret_val, "reading a '4'");
if (*reverseEndian) swap4_aligned(input_integer, rec_scale);
if ((input_integer[0]+input_integer[1]) != 4) {
return DCD_BADFORMAT;
}
/* Read in the number of atoms */
ret_val = READ(fd, N, sizeof(int));
CHECK_FREAD(ret_val, "reading number of atoms");
CHECK_FEOF(ret_val, "reading number of atoms");
if (*reverseEndian) swap4_aligned(N, 1);
/* Read in an integer '4' */
input_integer[1] = 0;
ret_val = READ(fd, input_integer, rec_scale*sizeof(int));
CHECK_FREAD(ret_val, "reading a '4'");
CHECK_FEOF(ret_val, "reading a '4'");
if (*reverseEndian) swap4_aligned(input_integer, rec_scale);
if ((input_integer[0]+input_integer[1]) != 4) {
return DCD_BADFORMAT;
}
*FREEINDEXES = NULL;
*fixedcoords = NULL;
if (*NAMNF != 0) {
(*FREEINDEXES) = (int *) calloc(((*N)-(*NAMNF)), sizeof(int));
if (*FREEINDEXES == NULL)
return DCD_BADMALLOC;
*fixedcoords = (float *) calloc((*N)*4 - (*NAMNF), sizeof(float));
if (*fixedcoords == NULL)
return DCD_BADMALLOC;
/* Read in index array size */
input_integer[1]=0;
ret_val = READ(fd, input_integer, rec_scale*sizeof(int));
CHECK_FREAD(ret_val, "reading size of index array");
CHECK_FEOF(ret_val, "reading size of index array");
if (*reverseEndian) swap4_aligned(input_integer, rec_scale);
if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) {
return DCD_BADFORMAT;
}
ret_val = READ(fd, (*FREEINDEXES), ((*N)-(*NAMNF))*sizeof(int));
CHECK_FREAD(ret_val, "reading size of index array");
CHECK_FEOF(ret_val, "reading size of index array");
if (*reverseEndian)
swap4_aligned((*FREEINDEXES), ((*N)-(*NAMNF)));
input_integer[1]=0;
ret_val = READ(fd, input_integer, rec_scale*sizeof(int));
CHECK_FREAD(ret_val, "reading size of index array");
CHECK_FEOF(ret_val, "reading size of index array");
if (*reverseEndian) swap4_aligned(input_integer, rec_scale);
if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) {
return DCD_BADFORMAT;
}
}
return DCD_SUCCESS;
}
/*static*/ int read_charmm_extrablock(fio_fd fd, int charmm, int reverseEndian,
float *unitcell) {
int i, input_integer[2], rec_scale;
if (charmm & DCD_HAS_64BIT_REC) {
rec_scale = RECSCALE64BIT;
} else {
rec_scale = RECSCALE32BIT;
}
if ((charmm & DCD_IS_CHARMM) && (charmm & DCD_HAS_EXTRA_BLOCK)) {
/* Leading integer must be 48 */
input_integer[1] = 0;
if (fio_fread(input_integer, sizeof(int), rec_scale, fd) != rec_scale)
return DCD_BADREAD;
if (reverseEndian) swap4_aligned(input_integer, rec_scale);
if ((input_integer[0]+input_integer[1]) == 48) {
double tmp[6];
if (fio_fread(tmp, 48, 1, fd) != 1) return DCD_BADREAD;
if (reverseEndian)
swap8_aligned(tmp, 6);
for (i=0; i<6; i++) unitcell[i] = (float)tmp[i];
} else {
/* unrecognized block, just skip it */
if (fio_fseek(fd, (input_integer[0]+input_integer[1]), FIO_SEEK_CUR)) return DCD_BADREAD;
}
if (fio_fread(input_integer, sizeof(int), rec_scale, fd) != rec_scale) return DCD_BADREAD;
}
return DCD_SUCCESS;
}
/*static*/ int read_fixed_atoms(fio_fd fd, int N, int num_free, const int *indexes,
int reverseEndian, const float *fixedcoords,
float *freeatoms, float *pos, int charmm) {
int i, input_integer[2], rec_scale;
if(charmm & DCD_HAS_64BIT_REC) {
rec_scale=RECSCALE64BIT;
} else {
rec_scale=RECSCALE32BIT;
}
/* Read leading integer */
input_integer[1]=0;
if (fio_fread(input_integer, sizeof(int), rec_scale, fd) != rec_scale) return DCD_BADREAD;
if (reverseEndian) swap4_aligned(input_integer, rec_scale);
if ((input_integer[0]+input_integer[1]) != 4*num_free) return DCD_BADFORMAT;
/* Read free atom coordinates */
if (fio_fread(freeatoms, 4*num_free, 1, fd) != 1) return DCD_BADREAD;
if (reverseEndian)
swap4_aligned(freeatoms, num_free);
/* Copy fixed and free atom coordinates into position buffer */
memcpy(pos, fixedcoords, 4*N);
for (i=0; i<num_free; i++)
pos[indexes[i]-1] = freeatoms[i];
/* Read trailing integer */
input_integer[1]=0;
if (fio_fread(input_integer, sizeof(int), rec_scale, fd) != rec_scale) return DCD_BADREAD;
if (reverseEndian) swap4_aligned(input_integer, rec_scale);
if ((input_integer[0]+input_integer[1]) != 4*num_free) return DCD_BADFORMAT;
return DCD_SUCCESS;
}
/*static*/ int read_charmm_4dim(fio_fd fd, int charmm, int reverseEndian) {
int input_integer[2],rec_scale;
if (charmm & DCD_HAS_64BIT_REC) {
rec_scale=RECSCALE64BIT;
} else {
rec_scale=RECSCALE32BIT;
}
/* If this is a CHARMm file and contains a 4th dimension block, */
/* we must skip past it to avoid problems */
if ((charmm & DCD_IS_CHARMM) && (charmm & DCD_HAS_4DIMS)) {
input_integer[1]=0;
if (fio_fread(input_integer, sizeof(int), rec_scale, fd) != rec_scale) return DCD_BADREAD;
if (reverseEndian) swap4_aligned(input_integer, rec_scale);
if (fio_fseek(fd, (input_integer[0]+input_integer[1]), FIO_SEEK_CUR)) return DCD_BADREAD;
if (fio_fread(input_integer, sizeof(int), rec_scale, fd) != rec_scale) return DCD_BADREAD;
}
return DCD_SUCCESS;
}
/*
* Read a dcd timestep from a dcd file
* Input: fd - a file struct opened for binary reading, from which the
* header information has already been read.
* natoms, nfixed, first, *freeind, reverse, charmm - the corresponding
* items as set by read_dcdheader
* first - true if this is the first frame we are reading.
* x, y, z: space for natoms each of floats.
* unitcell - space for six floats to hold the unit cell data.
* Not set if no unit cell data is present.
* Output: 0 on success, negative error code on failure.
* Side effects: x, y, z contain the coordinates for the timestep read.
* unitcell holds unit cell data if present.
*/
/*static*/ int read_dcdstep(fio_fd fd, int N, float *X, float *Y, float *Z,
float *unitcell, int num_fixed,
int first, int *indexes, float *fixedcoords,
int reverseEndian, int charmm) {
int ret_val, rec_scale; /* Return value from read */
if (charmm & DCD_HAS_64BIT_REC) {
rec_scale=RECSCALE64BIT;
} else {
rec_scale=RECSCALE32BIT;
}
if ((num_fixed==0) || first) {
/* temp storage for reading formatting info */
/* note: has to be max size we'll ever use */
int tmpbuf[6*RECSCALEMAX];
fio_iovec iov[7]; /* I/O vector for fio_readv() call */
fio_size_t readlen; /* number of bytes actually read */
int i;
/* if there are no fixed atoms or this is the first timestep read */
/* then we read all coordinates normally. */
/* read the charmm periodic cell information */
/* XXX this too should be read together with the other items in a */
/* single fio_readv() call in order to prevent lots of extra */
/* kernel/user context switches. */
ret_val = read_charmm_extrablock(fd, charmm, reverseEndian, unitcell);
if (ret_val) return ret_val;
/* setup the I/O vector for the call to fio_readv() */
iov[0].iov_base = (fio_caddr_t) &tmpbuf[0]; /* read format integer */
iov[0].iov_len = rec_scale*sizeof(int);
iov[1].iov_base = (fio_caddr_t) X; /* read X coordinates */
iov[1].iov_len = sizeof(float)*N;
iov[2].iov_base = (fio_caddr_t) &tmpbuf[1*rec_scale]; /* read 2 format integers */
iov[2].iov_len = rec_scale*sizeof(int) * 2;
iov[3].iov_base = (fio_caddr_t) Y; /* read Y coordinates */
iov[3].iov_len = sizeof(float)*N;
iov[4].iov_base = (fio_caddr_t) &tmpbuf[3*rec_scale]; /* read 2 format integers */
iov[4].iov_len = rec_scale*sizeof(int) * 2;
iov[5].iov_base = (fio_caddr_t) Z; /* read Y coordinates */
iov[5].iov_len = sizeof(float)*N;
iov[6].iov_base = (fio_caddr_t) &tmpbuf[5*rec_scale]; /* read format integer */
iov[6].iov_len = rec_scale*sizeof(int);
readlen = fio_readv(fd, &iov[0], 7);
if (readlen != (rec_scale*6*sizeof(int) + 3*N*sizeof(float)))
return DCD_BADREAD;
/* convert endianism if necessary */
if (reverseEndian) {
swap4_aligned(&tmpbuf[0], rec_scale*6);
swap4_aligned(X, N);
swap4_aligned(Y, N);
swap4_aligned(Z, N);
}
/* double-check the fortran format size values for safety */
if(rec_scale == 1) {
for (i=0; i<6; i++) {
if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT;
}
} else {
for (i=0; i<6; i++) {
if ((tmpbuf[2*i]+tmpbuf[2*i+1]) != sizeof(float)*N) return DCD_BADFORMAT;
}
}
/* copy fixed atom coordinates into fixedcoords array if this was the */
/* first timestep, to be used from now on. We just copy all atoms. */
if (num_fixed && first) {
memcpy(fixedcoords, X, N*sizeof(float));
memcpy(fixedcoords+N, Y, N*sizeof(float));
memcpy(fixedcoords+2*N, Z, N*sizeof(float));
}
/* read in the optional charmm 4th array */
/* XXX this too should be read together with the other items in a */
/* single fio_readv() call in order to prevent lots of extra */
/* kernel/user context switches. */
ret_val = read_charmm_4dim(fd, charmm, reverseEndian);
if (ret_val) return ret_val;
} else {
/* if there are fixed atoms, and this isn't the first frame, then we */
/* only read in the non-fixed atoms for all subsequent timesteps. */
ret_val = read_charmm_extrablock(fd, charmm, reverseEndian, unitcell);
if (ret_val) return ret_val;
ret_val = read_fixed_atoms(fd, N, N-num_fixed, indexes, reverseEndian,
fixedcoords, fixedcoords+3*N, X, charmm);
if (ret_val) return ret_val;
ret_val = read_fixed_atoms(fd, N, N-num_fixed, indexes, reverseEndian,
fixedcoords+N, fixedcoords+3*N, Y, charmm);
if (ret_val) return ret_val;
ret_val = read_fixed_atoms(fd, N, N-num_fixed, indexes, reverseEndian,
fixedcoords+2*N, fixedcoords+3*N, Z, charmm);
if (ret_val) return ret_val;
ret_val = read_charmm_4dim(fd, charmm, reverseEndian);
if (ret_val) return ret_val;
}
return DCD_SUCCESS;
}
/*
* Skip past a timestep. If there are fixed atoms, this cannot be used with
* the first timestep.
* Input: fd - a file struct from which the header has already been read
* natoms - number of atoms per timestep
* nfixed - number of fixed atoms
* charmm - charmm flags as returned by read_dcdheader
* Output: 0 on success, negative error code on failure.
* Side effects: One timestep will be skipped; fd will be positioned at the
* next timestep.
*/
/*static*/ int skip_dcdstep(fio_fd fd, int natoms, int nfixed, int charmm) {
int seekoffset = 0;
int rec_scale;
if (charmm & DCD_HAS_64BIT_REC) {
rec_scale=RECSCALE64BIT;
} else {
rec_scale=RECSCALE32BIT;
}
/* Skip charmm extra block */
if ((charmm & DCD_IS_CHARMM) && (charmm & DCD_HAS_EXTRA_BLOCK)) {
seekoffset += 4*rec_scale + 48 + 4*rec_scale;
}
/* For each atom set, seek past an int, the free atoms, and another int. */
seekoffset += 3 * (2*rec_scale + natoms - nfixed) * 4;
/* Assume that charmm 4th dim is the same size as the other three. */
if ((charmm & DCD_IS_CHARMM) && (charmm & DCD_HAS_4DIMS)) {
seekoffset += (2*rec_scale + natoms - nfixed) * 4;
}
if (fio_fseek(fd, seekoffset, FIO_SEEK_CUR)) return DCD_BADEOF;
return DCD_SUCCESS;
}
/*
* Write a timestep to a dcd file
* Input: fd - a file struct for which a dcd header has already been written
* curframe: Count of frames written to this file, starting with 1.
* curstep: Count of timesteps elapsed = istart + curframe * nsavc.
* natoms - number of elements in x, y, z arrays
* x, y, z: pointers to atom coordinates
* Output: 0 on success, negative error code on failure.
* Side effects: coordinates are written to the dcd file.
*/
/*static*/ int write_dcdstep(fio_fd fd, int curframe, int curstep, int N,
const float *X, const float *Y, const float *Z,
const double *unitcell, int charmm) {
int out_integer;
if (charmm) {
/* write out optional unit cell */
if (unitcell != NULL) {
out_integer = 48; /* 48 bytes (6 floats) */
fio_write_int32(fd, out_integer);
WRITE(fd, unitcell, out_integer);
fio_write_int32(fd, out_integer);
}
}
/* write out coordinates */
out_integer = N*4; /* N*4 bytes per X/Y/Z array (N floats per array) */
fio_write_int32(fd, out_integer);
if (fio_fwrite((void *) X, out_integer, 1, fd) != 1) return DCD_BADWRITE;
fio_write_int32(fd, out_integer);
fio_write_int32(fd, out_integer);
if (fio_fwrite((void *) Y, out_integer, 1, fd) != 1) return DCD_BADWRITE;
fio_write_int32(fd, out_integer);
fio_write_int32(fd, out_integer);
if (fio_fwrite((void *) Z, out_integer, 1, fd) != 1) return DCD_BADWRITE;
fio_write_int32(fd, out_integer);
/* update the DCD header information */
fio_fseek(fd, NFILE_POS, FIO_SEEK_SET);
fio_write_int32(fd, curframe);
fio_fseek(fd, NSTEP_POS, FIO_SEEK_SET);
fio_write_int32(fd, curstep);
fio_fseek(fd, 0, FIO_SEEK_END);
return DCD_SUCCESS;
}
/*
* Write a header for a new dcd file
* Input: fd - file struct opened for binary writing
* remarks - string to be put in the remarks section of the header.
* The string will be truncated to 70 characters.
* natoms, istart, nsavc, delta - see comments in read_dcdheader
* Output: 0 on success, negative error code on failure.
* Side effects: Header information is written to the dcd file.
*/
/*static*/ int write_dcdheader(fio_fd fd, const char *remarks, int N,
int ISTART, int NSAVC, double DELTA, int with_unitcell,
int charmm) {
int out_integer;
float out_float;
char title_string[200];
time_t cur_time;
struct tm *tmbuf;
char time_str[81];
out_integer = 84;
WRITE(fd, (char *) & out_integer, sizeof(int));
strcpy(title_string, "CORD");
WRITE(fd, title_string, 4);
fio_write_int32(fd, 0); /* Number of frames in file, none written yet */
fio_write_int32(fd, ISTART); /* Starting timestep */
fio_write_int32(fd, NSAVC); /* Timesteps between frames written to the file */
fio_write_int32(fd, 0); /* Number of timesteps in simulation */
fio_write_int32(fd, 0); /* NAMD writes NSTEP or ISTART - NSAVC here? */
fio_write_int32(fd, 0);
fio_write_int32(fd, 0);
fio_write_int32(fd, 0);
fio_write_int32(fd, 0);
if (charmm) {
out_float = DELTA;
WRITE(fd, (char *) &out_float, sizeof(float));
if (with_unitcell) {
fio_write_int32(fd, 1);
} else {
fio_write_int32(fd, 0);
}
} else {
WRITE(fd, (char *) &DELTA, sizeof(double));
}
fio_write_int32(fd, 0);
fio_write_int32(fd, 0);
fio_write_int32(fd, 0);
fio_write_int32(fd, 0);
fio_write_int32(fd, 0);
fio_write_int32(fd, 0);
fio_write_int32(fd, 0);
fio_write_int32(fd, 0);
if (charmm) {
fio_write_int32(fd, 24); /* Pretend to be CHARMM version 24 */
} else {
fio_write_int32(fd, 0);
}
fio_write_int32(fd, 84);
fio_write_int32(fd, 164);
fio_write_int32(fd, 2);
strncpy(title_string, remarks, 80);
title_string[79] = '\0';
WRITE(fd, title_string, 80);
cur_time=time(NULL);
tmbuf=localtime(&cur_time);
strftime(time_str, 80, "REMARKS Created %d %B, %Y at %R", tmbuf);
WRITE(fd, time_str, 80);
fio_write_int32(fd, 164);
fio_write_int32(fd, 4);
fio_write_int32(fd, N);
fio_write_int32(fd, 4);
return DCD_SUCCESS;
}
/*
* clean up dcd data
* Input: nfixed, freeind - elements as returned by read_dcdheader
* Output: None
* Side effects: Space pointed to by freeind is freed if necessary.
*/
/*static*/ void close_dcd_read(int *indexes, float *fixedcoords) {
free(indexes);
free(fixedcoords);
}
/*static*/ void *open_dcd_read(const char *path, const char *filetype,
int *natoms) {
dcdhandle *dcd;
fio_fd fd;
int rc;
struct stat stbuf;
if (!path) return NULL;
/* See if the file exists, and get its size */
memset(&stbuf, 0, sizeof(struct stat));
if (stat(path, &stbuf)) {
printf("dcdplugin) Could not access file '%s'.\n", path);
return NULL;
}
if (fio_open(path, FIO_READ, &fd) < 0) {
printf("dcdplugin) Could not open file '%s' for reading.\n", path);
return NULL;
}
dcd = (dcdhandle *)malloc(sizeof(dcdhandle));
memset(dcd, 0, sizeof(dcdhandle));
dcd->fd = fd;
if ((rc = read_dcdheader(dcd->fd, &dcd->natoms, &dcd->nsets, &dcd->istart,
&dcd->nsavc, &dcd->delta, &dcd->nfixed, &dcd->freeind,
&dcd->fixedcoords, &dcd->reverse, &dcd->charmm))) {
print_dcderror("read_dcdheader", rc);
fio_fclose(dcd->fd);
free(dcd);
return NULL;
}
/*
* Check that the file is big enough to really hold the number of sets
* it claims to have. Then we'll use nsets to keep track of where EOF
* should be.
*/
{
fio_size_t ndims, firstframesize, framesize, extrablocksize;
fio_size_t trjsize, filesize, curpos;
int newnsets;
extrablocksize = dcd->charmm & DCD_HAS_EXTRA_BLOCK ? 48 + 8 : 0;
ndims = dcd->charmm & DCD_HAS_4DIMS ? 4 : 3;
firstframesize = (dcd->natoms+2) * ndims * sizeof(float) + extrablocksize;
framesize = (dcd->natoms-dcd->nfixed+2) * ndims * sizeof(float)
+ extrablocksize;
/*
* It's safe to use ftell, even though ftell returns a long, because the
* header size is < 4GB.
*/
curpos = fio_ftell(dcd->fd); /* save current offset (end of header) */
#if defined(_MSC_VER) && defined(FASTIO_NATIVEWIN32)
/* the stat() call is not 64-bit savvy on Windows */
/* so we have to use the fastio fseek/ftell routines for this */
/* until we add a portable filesize routine for this purpose */
fio_fseek(dcd->fd, 0, FIO_SEEK_END); /* seek to end of file */
filesize = fio_ftell(dcd->fd);
fio_fseek(dcd->fd, curpos, FIO_SEEK_SET); /* return to end of header */
#else
filesize = stbuf.st_size; /* this works ok on Unix machines */
#endif
trjsize = filesize - curpos - firstframesize;
if (trjsize < 0) {
printf("dcdplugin) file '%s' appears to contain no timesteps.\n", path);
fio_fclose(dcd->fd);
free(dcd);
return NULL;
}
newnsets = trjsize / framesize + 1;
if (dcd->nsets > 0 && newnsets != dcd->nsets) {
printf("dcdplugin) Warning: DCD header claims %d frames, file size indicates there are actually %d frames\n", dcd->nsets, newnsets);
}
dcd->nsets = newnsets;
dcd->setsread = 0;
}
dcd->first = 1;
dcd->x = (float *)malloc(dcd->natoms * sizeof(float));
dcd->y = (float *)malloc(dcd->natoms * sizeof(float));
dcd->z = (float *)malloc(dcd->natoms * sizeof(float));
if (!dcd->x || !dcd->y || !dcd->z) {
printf("dcdplugin) Unable to allocate space for %d atoms.\n", dcd->natoms);
if (dcd->x)
free(dcd->x);
if (dcd->y)
free(dcd->y);
if (dcd->z)
free(dcd->z);
fio_fclose(dcd->fd);
free(dcd);
return NULL;
}
*natoms = dcd->natoms;
return dcd;
}
/*static*/ int read_next_timestep(void *v, int natoms, molfile_timestep_t *ts) {
dcdhandle *dcd;
int i, j, rc;
float unitcell[6];
unitcell[0] = unitcell[2] = unitcell[5] = 1.0f;
unitcell[1] = unitcell[3] = unitcell[4] = 90.0f;
dcd = (dcdhandle *)v;
/* Check for EOF here; that way all EOF's encountered later must be errors */
if (dcd->setsread == dcd->nsets) return MOLFILE_EOF;
dcd->setsread++;
if (!ts) {
if (dcd->first && dcd->nfixed) {
/* We can't just skip it because we need the fixed atom coordinates */
rc = read_dcdstep(dcd->fd, dcd->natoms, dcd->x, dcd->y, dcd->z,
unitcell, dcd->nfixed, dcd->first, dcd->freeind, dcd->fixedcoords,
dcd->reverse, dcd->charmm);
dcd->first = 0;
return rc; /* XXX this needs to be updated */
}
dcd->first = 0;
/* XXX this needs to be changed */
return skip_dcdstep(dcd->fd, dcd->natoms, dcd->nfixed, dcd->charmm);
}
rc = read_dcdstep(dcd->fd, dcd->natoms, dcd->x, dcd->y, dcd->z, unitcell,
dcd->nfixed, dcd->first, dcd->freeind, dcd->fixedcoords,
dcd->reverse, dcd->charmm);
dcd->first = 0;
if (rc < 0) {
print_dcderror("read_dcdstep", rc);
return MOLFILE_ERROR;
}
/* copy timestep data from plugin-local buffers to VMD's buffer */
/* XXX
* This code is still the root of all evil. Just doing this extra copy
* cuts the I/O rate of the DCD reader from 728 MB/sec down to
* 394 MB/sec when reading from a ram filesystem.
* For a physical disk filesystem, the I/O rate goes from
* 187 MB/sec down to 122 MB/sec. Clearly this extra copy has to go.
*/
{
int natoms = dcd->natoms;
float *nts = ts->coords;
const float *bufx = dcd->x;
const float *bufy = dcd->y;
const float *bufz = dcd->z;
for (i=0, j=0; i<natoms; i++, j+=3) {
nts[j ] = bufx[i];
nts[j + 1] = bufy[i];
nts[j + 2] = bufz[i];
}
}
ts->A = unitcell[0];
ts->B = unitcell[2];
ts->C = unitcell[5];
if (unitcell[1] >= -1.0 && unitcell[1] <= 1.0 &&
unitcell[3] >= -1.0 && unitcell[3] <= 1.0 &&
unitcell[4] >= -1.0 && unitcell[4] <= 1.0) {
/* This file was generated by CHARMM, or by NAMD > 2.5, with the angle */
/* cosines of the periodic cell angles written to the DCD file. */
/* This formulation improves rounding behavior for orthogonal cells */
/* so that the angles end up at precisely 90 degrees, unlike acos(). */
ts->alpha = 90.0 - asin(unitcell[4]) * 90.0 / M_PI_2; /* cosBC */
ts->beta = 90.0 - asin(unitcell[3]) * 90.0 / M_PI_2; /* cosAC */
ts->gamma = 90.0 - asin(unitcell[1]) * 90.0 / M_PI_2; /* cosAB */
} else {
/* This file was likely generated by NAMD 2.5 and the periodic cell */
/* angles are specified in degrees rather than angle cosines. */
ts->alpha = unitcell[4]; /* angle between B and C */
ts->beta = unitcell[3]; /* angle between A and C */
ts->gamma = unitcell[1]; /* angle between A and B */
}
return MOLFILE_SUCCESS;