| | /*
* $Id$
*
* This source code is part of
*
* G R O M A C S
*
* GROningen MAchine for Chemical Simulations
*
* VERSION 3.2.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team,
* check out http://www.gromacs.org for more information.
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
*
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
*
* For more info, check our website at http://www.gromacs.org
*
* And Hey:
* GROningen Mixture of Alchemy and Childrens' Stories
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <limits.h>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "statutil.h"
#include "xdrf.h"
#ifdef HAVE_FSEEKO
#define gmx_fseek(A,B,C) fseeko(A,B,C)
#define gmx_ftell(A) ftello(A)
#define gmx_off_t off_t
#ifndef _LARGEFILE_SOURCE
#warning Declaring fseeko and ftello explicitly so as to bypass an autoconf 2.61 bug
#warning If you have an incompatible declaration error please comment out the fseeko and ftello declarations just after this warning
int fseeko(FILE *stream, off_t offset, int whence);
off_t ftello(FILE *stream);
#endif
#else
#define gmx_fseek(A,B,C) fseek(A,B,C)
#define gmx_ftell(A) ftell(A)
#define gmx_off_t int
#endif
#define MAXID 256
static FILE *xdrfiles[MAXID];
static XDR *xdridptr[MAXID];
static char xdrmodes[MAXID];
static unsigned int cnt;
#ifdef GMX_FORTRAN
typedef void (* F77_FUNC(xdrfproc,XDRFPROC))(int *, void *, int *);
int ftocstr(char *ds, int dl, char *ss, int sl)
/* dst, src ptrs */
/* dst max len */
/* src len */
{
char *p;
p = ss + sl;
while ( --p >= ss && *p == ' ' );
sl = p - ss + 1;
dl--;
ds[0] = 0;
if (sl > dl)
return 1;
while (sl--)
(*ds++ = *ss++);
*ds = '\0';
return 0;
}
int ctofstr(char *ds, int dl, char *ss)
/* dest space */
/* max dest length */
/* src string (0-term) */
{
while (dl && *ss) {
*ds++ = *ss++;
dl--;
}
while (dl--)
*ds++ = ' ';
return 0;
}
void
F77_FUNC(xdrfbool,XDRFBOOL)(int *xdrid, int *pb, int *ret)
{
*ret = xdr_bool(xdridptr[*xdrid], pb);
cnt += sizeof(int);
}
void
F77_FUNC(xdrfchar,XDRFCHAR)(int *xdrid, char *cp, int *ret)
{
*ret = xdr_char(xdridptr[*xdrid], cp);
cnt += sizeof(char);
}
void
F77_FUNC(xdrfdouble,XDRFDOUBLE)(int *xdrid, double *dp, int *ret)
{
*ret = xdr_double(xdridptr[*xdrid], dp);
cnt += sizeof(double);
}
void
F77_FUNC(xdrffloat,XDRFFLOAT)(int *xdrid, float *fp, int *ret)
{
*ret = xdr_float(xdridptr[*xdrid], fp);
cnt += sizeof(float);
}
void
F77_FUNC(xdrfint,XDRFINT)(int *xdrid, int *ip, int *ret)
{
*ret = xdr_int(xdridptr[*xdrid], ip);
cnt += sizeof(int);
}
F77_FUNC(xdrfshort,XDRFSHORT)(int *xdrid, short *sp, int *ret)
{
*ret = xdr_short(xdridptr[*xdrid], sp);
cnt += sizeof(sp);
}
void
F77_FUNC(xdrfuchar,XDRFUCHAR)(int *xdrid, unsigned char *ucp, int *ret)
{
*ret = xdr_u_char(xdridptr[*xdrid], (u_char *)ucp);
cnt += sizeof(char);
}
void
F77_FUNC(xdrfushort,XDRFUSHORT)(int *xdrid, unsigned short *usp, int *ret)
{
*ret = xdr_u_short(xdridptr[*xdrid], (unsigned short *)usp);
cnt += sizeof(unsigned short);
}
void
F77_FUNC(xdrf3dfcoord,XDRF3DFCOORD)(int *xdrid, float *fp, int *size, float *precision, int *ret)
{
*ret = xdr3dfcoord(xdridptr[*xdrid], fp, size, precision);
}
void
F77_FUNC(xdrfstring,XDRFSTRING)(int *xdrid, char * sp_ptr,
int *maxsize, int *ret, int sp_len)
{
char *tsp;
tsp = (char*) malloc((size_t)(((sp_len) + 1) * sizeof(char)));
if (tsp == NULL) {
*ret = -1;
return;
}
if (ftocstr(tsp, *maxsize+1, sp_ptr, sp_len)) {
*ret = -1;
free(tsp);
return;
}
*ret = xdr_string(xdridptr[*xdrid], (char **) &tsp, (unsigned int) *maxsize);
ctofstr( sp_ptr, sp_len , tsp);
cnt += *maxsize;
free(tsp);
}
void
F77_FUNC(xdrfwrapstring,XDRFWRAPSTRING)(int *xdrid, char *sp_ptr,
int *ret, int sp_len)
{
char *tsp;
int maxsize;
maxsize = (sp_len) + 1;
tsp = (char*) malloc((size_t)(maxsize * sizeof(char)));
if (tsp == NULL) {
*ret = -1;
return;
}
if (ftocstr(tsp, maxsize, sp_ptr, sp_len)) {
*ret = -1;
free(tsp);
return;
}
*ret = xdr_string(xdridptr[*xdrid], (char **) &tsp, (u_int)maxsize);
ctofstr( sp_ptr, sp_len, tsp);
cnt += maxsize;
free(tsp);
}
void
F77_FUNC(xdrfopaque,XDRFOPAQUE)(int *xdrid, caddr_t *cp, int *ccnt, int *ret)
{
*ret = xdr_opaque(xdridptr[*xdrid], (caddr_t)*cp, (u_int)*ccnt);
cnt += *ccnt;
}
void
F77_FUNC(xdrfsetpos,XDRFSETPOS)(int *xdrid, int *pos, int *ret)
{
*ret = xdr_setpos(xdridptr[*xdrid], (u_int) *pos);
}
void
F77_FUNC(xdrf,XDRF)(int *xdrid, int *pos)
{
*pos = xdr_getpos(xdridptr[*xdrid]);
}
void
F77_FUNC(xdrfvector,XDRFVECTOR)(int *xdrid, char *cp, int *size, F77_FUNC(xdrfproc,XDRFPROC) elproc, int *ret)
{
int lcnt;
cnt = 0;
for (lcnt = 0; lcnt < *size; lcnt++) {
elproc(xdrid, (cp+cnt) , ret);
}
}
void
F77_FUNC(xdrfclose,XDRFCLOSE)(int *xdrid, int *ret)
{
*ret = xdrclose(xdridptr[*xdrid]);
cnt = 0;
}
void
F77_FUNC(xdrfopen,XDRFOPEN)(int *xdrid, char *fp_ptr, char *mode_ptr,
int *ret, int fp_len, int mode_len)
{
char fname[512];
char fmode[3];
if (ftocstr(fname, sizeof(fname), fp_ptr, fp_len)) {
*ret = 0;
}
if (ftocstr(fmode, sizeof(fmode), mode_ptr,
mode_len)) {
*ret = 0;
}
*xdrid = xdropen(NULL, fname, fmode);
if (*xdrid == 0)
*ret = 0;
else
*ret = 1;
}
#endif /* GMX_FORTRAN */
/*___________________________________________________________________________
|
| what follows are the C routines for opening, closing xdr streams
| and the routine to read/write compressed coordinates together
| with some routines to assist in this task (those are marked
| static and cannot be called from user programs)
*/
#define MAXABS INT_MAX-2
#ifndef MIN
#define MIN(x,y) ((x) < (y) ? (x):(y))
#endif
#ifndef MAX
#define MAX(x,y) ((x) > (y) ? (x):(y))
#endif
#ifndef SQR
#define SQR(x) ((x)*(x))
#endif
static int magicints[] = {
0, 0, 0, 0, 0, 0, 0, 0, 0,
8, 10, 12, 16, 20, 25, 32, 40, 50, 64,
80, 101, 128, 161, 203, 256, 322, 406, 512, 645,
812, 1024, 1290, 1625, 2048, 2580, 3250, 4096, 5060, 6501,
8192, 10321, 13003, 16384, 20642, 26007, 32768, 41285, 52015, 65536,
82570, 104031, 131072, 165140, 208063, 262144, 330280, 416127, 524287, 660561,
832255, 1048576, 1321122, 1664510, 2097152, 2642245, 3329021, 4194304, 5284491, 6658042,
8388607, 10568983, 13316085, 16777216 };
#define FIRSTIDX 9
/* note that magicints[FIRSTIDX-1] == 0 */
#define LASTIDX (sizeof(magicints) / sizeof(*magicints))
/*__________________________________________________________________________
|
| xdropen - open xdr file
|
| This versions differs from xdrstdio_create, because I need to know
| the state of the file (read or write) so I can use xdr3dfcoord
| in eigther read or write mode, and the file descriptor
| so I can close the file (something xdr_destroy doesn't do).
|
*/
int xdropen(XDR *xdrs, const char *filename, const char *type) {
static int init_done = 0;
enum xdr_op lmode;
int xdrid;
char newtype[5];
if (init_done == 0) {
for (xdrid = 1; xdrid < MAXID; xdrid++) {
xdridptr[xdrid] = NULL;
}
init_done = 1;
}
xdrid = 1;
while (xdrid < MAXID && xdridptr[xdrid] != NULL) {
xdrid++;
}
if (xdrid == MAXID) {
return 0;
}
if (*type == 'w' || *type == 'W') {
strcpy(newtype,"wb+");
lmode = XDR_ENCODE;
} else if (*type == 'a' || *type == 'A') {
strcpy(newtype,"ab+");
lmode = XDR_ENCODE;
} else {
strcpy(newtype,"rb");
lmode = XDR_DECODE;
}
xdrfiles[xdrid] = fopen(filename, newtype);
if (xdrfiles[xdrid] == NULL) {
xdrs = NULL;
return 0;
}
xdrmodes[xdrid] = *type;
/* next test isn't usefull in the case of C language
* but is used for the Fortran interface
* (C users are expected to pass the address of an already allocated
* XDR staructure)
*/
if (xdrs == NULL) {
xdridptr[xdrid] = (XDR *) malloc((size_t)sizeof(XDR));
xdrstdio_create(xdridptr[xdrid], xdrfiles[xdrid], lmode);
} else {
xdridptr[xdrid] = xdrs;
xdrstdio_create(xdrs, xdrfiles[xdrid], lmode);
}
return xdrid;
}
/*_________________________________________________________________________
|
| xdrclose - close a xdr file
|
| This will flush the xdr buffers, and destroy the xdr stream.
| It also closes the associated file descriptor (this is *not*
| done by xdr_destroy).
|
*/
int xdrclose(XDR *xdrs) {
int xdrid;
if (xdrs == NULL) {
fprintf(stderr, "xdrclose: passed a NULL pointer\n");
exit(1);
}
for (xdrid = 1; xdrid < MAXID; xdrid++) {
if (xdridptr[xdrid] == xdrs) {
xdr_destroy(xdrs);
fclose(xdrfiles[xdrid]);
xdridptr[xdrid] = NULL;
return 1;
}
}
fprintf(stderr, "xdrclose: no such open xdr file\n");
exit(1);
/* to make some compilers happy: */
return 0;
}
/*____________________________________________________________________________
|
| sendbits - encode num into buf using the specified number of bits
|
| This routines appends the value of num to the bits already present in
| the array buf. You need to give it the number of bits to use and you
| better make sure that this number of bits is enough to hold the value
| Also num must be positive.
|
*/
static void sendbits(int buf[], int num_of_bits, int num) {
unsigned int cnt, lastbyte;
int lastbits;
unsigned char * cbuf;
cbuf = ((unsigned char *)buf) + 3 * sizeof(*buf);
cnt = (unsigned int) buf[0];
lastbits = buf[1];
lastbyte =(unsigned int) buf[2];
while (num_of_bits >= 8) {
lastbyte = (lastbyte << 8) | ((num >> (num_of_bits -8)) /* & 0xff*/);
cbuf[cnt++] = lastbyte >> lastbits;
num_of_bits -= 8;
}
if (num_of_bits > 0) {
lastbyte = (lastbyte << num_of_bits) | num;
lastbits += num_of_bits;
if (lastbits >= 8) {
lastbits -= 8;
cbuf[cnt++] = lastbyte >> lastbits;
}
}
buf[0] = cnt;
buf[1] = lastbits;
buf[2] = lastbyte;
if (lastbits>0) {
cbuf[cnt] = lastbyte << (8 - lastbits);
}
}
/*_________________________________________________________________________
|
| sizeofint - calculate bitsize of an integer
|
| return the number of bits needed to store an integer with given max size
|
*/
static int sizeofint(const int size) {
unsigned int num = 1;
int num_of_bits = 0;
while (size >= num && num_of_bits < 32) {
num_of_bits++;
num <<= 1;
}
return num_of_bits;
}
/*___________________________________________________________________________
|
| sizeofints - calculate 'bitsize' of compressed ints
|
| given the number of small unsigned integers and the maximum value
| return the number of bits needed to read or write them with the
| routines receiveints and sendints. You need this parameter when
| calling these routines. Note that for many calls I can use
| the variable 'smallidx' which is exactly the number of bits, and
| So I don't need to call 'sizeofints for those calls.
*/
static int sizeofints( const int num_of_ints, unsigned int sizes[]) {
int i, num;
unsigned int num_of_bytes, num_of_bits, bytes[32], bytecnt, tmp;
num_of_bytes = 1;
bytes[0] = 1;
num_of_bits = 0;
for (i=0; i < num_of_ints; i++) {
tmp = 0;
for (bytecnt = 0; bytecnt < num_of_bytes; bytecnt++) {
tmp = bytes[bytecnt] * sizes[i] + tmp;
bytes[bytecnt] = tmp & 0xff;
tmp >>= 8;
}
while (tmp != 0) {
bytes[bytecnt++] = tmp & 0xff;
tmp >>= 8;
}
num_of_bytes = bytecnt;
}
num = 1;
num_of_bytes--;
while (bytes[num_of_bytes] >= num) {
num_of_bits++;
num *= 2;
}
return num_of_bits + num_of_bytes * 8;
}
/*____________________________________________________________________________
|
| sendints - send a small set of small integers in compressed format
|
| this routine is used internally by xdr3dfcoord, to send a set of
| small integers to the buffer.
| Multiplication with fixed (specified maximum ) sizes is used to get
| to one big, multibyte integer. Allthough the routine could be
| modified to handle sizes bigger than 16777216, or more than just
| a few integers, this is not done, because the gain in compression
| isn't worth the effort. Note that overflowing the multiplication
| or the byte buffer (32 bytes) is unchecked and causes bad results.
|
*/
static void sendints(int buf[], const int num_of_ints, const int num_of_bits,
unsigned int sizes[], unsigned int nums[]) {
int i;
unsigned int bytes[32], num_of_bytes, bytecnt, tmp;
tmp = nums[0];
num_of_bytes = 0;
do {
bytes[num_of_bytes++] = tmp & 0xff;
tmp >>= 8;
} while (tmp != 0);
for (i = 1; i < num_of_ints; i++) {
if (nums[i] >= sizes[i]) {
fprintf(stderr,"major breakdown in sendints num %u doesn't "
"match size %u\n", nums[i], sizes[i]);
exit(1);
}
/* use one step multiply */
tmp = nums[i];
for (bytecnt = 0; bytecnt < num_of_bytes; bytecnt++) {
tmp = bytes[bytecnt] * sizes[i] + tmp;
bytes[bytecnt] = tmp & 0xff;
tmp >>= 8;
}
while (tmp != 0) {
bytes[bytecnt++] = tmp & 0xff;
tmp >>= 8;
}
num_of_bytes = bytecnt;
}
if (num_of_bits >= num_of_bytes * 8) {
for (i = 0; i < num_of_bytes; i++) {
sendbits(buf, 8, bytes[i]);
}
sendbits(buf, num_of_bits - num_of_bytes * 8, 0);
} else {
for (i = 0; i < num_of_bytes-1; i++) {
sendbits(buf, 8, bytes[i]);
}
sendbits(buf, num_of_bits- (num_of_bytes -1) * 8, bytes[i]);
}
}
/*___________________________________________________________________________
|
| receivebits - decode number from buf using specified number of bits
|
| extract the number of bits from the array buf and construct an integer
| from it. Return that value.
|
*/
static int receivebits(int buf[], int num_of_bits) {
int cnt, num;
unsigned int lastbits, lastbyte;
unsigned char * cbuf;
int mask = (1 << num_of_bits) -1;
cbuf = ((unsigned char *)buf) + 3 * sizeof(*buf);
cnt = buf[0];
lastbits = (unsigned int) buf[1];
lastbyte = (unsigned int) buf[2];
num = 0;
while (num_of_bits >= 8) {
lastbyte = ( lastbyte << 8 ) | cbuf[cnt++];
num |= (lastbyte >> lastbits) << (num_of_bits - 8);
num_of_bits -=8;
}
if (num_of_bits > 0) {
if (lastbits < num_of_bits) {
lastbits += 8;
lastbyte = (lastbyte << 8) | cbuf[cnt++];
}
lastbits -= num_of_bits;
num |= (lastbyte >> lastbits) & ((1 << num_of_bits) -1);
}
num &= mask;
buf[0] = cnt;
buf[1] = lastbits;
buf[2] = lastbyte;
return num;
}
/*____________________________________________________________________________
|
| receiveints - decode 'small' integers from the buf array
|
| this routine is the inverse from sendints() and decodes the small integers
| written to buf by calculating the remainder and doing divisions with
| the given sizes[]. You need to specify the total number of bits to be
| used from buf in num_of_bits.
|
*/
static void receiveints(int buf[], const int num_of_ints, int num_of_bits,
unsigned int sizes[], int nums[]) {
int bytes[32];
int i, j, num_of_bytes, p, num;
bytes[1] = bytes[2] = bytes[3] = 0;
num_of_bytes = 0;
while (num_of_bits > 8) {
bytes[num_of_bytes++] = receivebits(buf, 8);
num_of_bits -= 8;
}
if (num_of_bits > 0) {
bytes[num_of_bytes++] = receivebits(buf, num_of_bits);
}
for (i = num_of_ints-1; i > 0; i--) {
num = 0;
for (j = num_of_bytes-1; j >=0; j--) {
num = (num << 8) | bytes[j];
p = num / sizes[i];
bytes[j] = p;
num = num - p * sizes[i];
}
nums[i] = num;
}
nums[0] = bytes[0] | (bytes[1] << 8) | (bytes[2] << 16) | (bytes[3] << 24);
}
/*____________________________________________________________________________
|
| xdr3dfcoord - read or write compressed 3d coordinates to xdr file.
|
| this routine reads or writes (depending on how you opened the file with
| xdropen() ) a large number of 3d coordinates (stored in *fp).
| The number of coordinates triplets to write is given by *size. On
| read this number may be zero, in which case it reads as many as were written
| or it may specify the number if triplets to read (which should match the
| number written).
| Compression is achieved by first converting all floating numbers to integer
| using multiplication by *precision and rounding to the nearest integer.
| Then the minimum and maximum value are calculated to determine the range.
| The limited range of integers so found, is used to compress the coordinates.
| In addition the differences between succesive coordinates is calculated.
| If the difference happens to be 'small' then only the difference is saved,
| compressing the data even more. The notion of 'small' is changed dynamically
| and is enlarged or reduced whenever needed or possible.
| Extra compression is achieved in the case of GROMOS and coordinates of
| water molecules. GROMOS first writes out the Oxygen position, followed by
| the two hydrogens. In order to make the differences smaller (and thereby
| compression the data better) the order is changed into first one hydrogen
| then the oxygen, followed by the other hydrogen. This is rather special, but
| it shouldn't harm in the general case.
|
*/
int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision) {
static int *ip = NULL;
static int oldsize;
static int *buf;
int minint[3], maxint[3], mindiff, *lip, diff;
int lint1, lint2, lint3, oldlint1, oldlint2, oldlint3, smallidx;
int minidx, maxidx;
unsigned sizeint[3], sizesmall[3], bitsizeint[3], size3, *luip;
int flag, k;
int smallnum, smaller, larger, i, is_small, is_smaller, run, prevrun;
float *lfp, lf;
int tmp, *thiscoord, prevcoord[3];
unsigned int tmpcoord[30];
int bufsize, xdrid, lsize;
unsigned int bitsize;
float inv_precision;
int errval = 1;
bitsizeint[0] = bitsizeint[1] = bitsizeint[2] = 0;
prevcoord[0] = prevcoord[1] = prevcoord[2] = 0;
/* find out if xdrs is opened for reading or for writing */
xdrid = 0;
while (xdridptr[xdrid] != xdrs) {
xdrid++;
if (xdrid >= MAXID) {
fprintf(stderr, "xdr error. no open xdr stream\n");
exit (1);
}
}
if ((xdrmodes[xdrid] == 'w') || (xdrmodes[xdrid] == 'a')) {
/* xdrs is open for writing */
if (xdr_int(xdrs, size) == 0)
return 0;
size3 = *size * 3;
/* when the number of coordinates is small, don't try to compress; just
* write them as floats using xdr_vector
*/
if (*size <= 9 ) {
return (xdr_vector(xdrs, (char *) fp, (unsigned int)size3,
(unsigned int)sizeof(*fp), (xdrproc_t)xdr_float));
}
xdr_float(xdrs, precision);
if (ip == NULL) {
ip = (int *)malloc((size_t)(size3 * sizeof(*ip)));
if (ip == NULL) {
fprintf(stderr,"malloc failed\n");
exit(1);
}
bufsize = size3 * 1.2;
buf = (int *)malloc((size_t)(bufsize * sizeof(*buf)));
if (buf == NULL) {
fprintf(stderr,"malloc failed\n");
exit(1);
}
oldsize = *size;
} else if (*size > oldsize) {
ip = (int *)realloc(ip, (size_t)(size3 * sizeof(*ip)));
if (ip == NULL) {
fprintf(stderr,"malloc failed\n");
exit(1);
}
bufsize = size3 * 1.2;
buf = (int *)realloc(buf, (size_t)(bufsize * sizeof(*buf)));
if (buf == NULL) {
fprintf(stderr,"realloc failed\n");
exit(1);
}
oldsize = *size;
}
/* buf[0-2] are special and do not contain actual data */
buf[0] = buf[1] = buf[2] = 0;
minint[0] = minint[1] = minint[2] = INT_MAX;
maxint[0] = maxint[1] = maxint[2] = INT_MIN;
prevrun = -1;
lfp = fp;
lip = ip;
mindiff = INT_MAX;
oldlint1 = oldlint2 = oldlint3 = 0;
while(lfp < fp + size3 ) {
/* find nearest integer */
if (*lfp >= 0.0)
lf = *lfp * *precision + 0.5;
else
lf = *lfp * *precision - 0.5;
if (fabs(lf) > MAXABS) {
/* scaling would cause overflow */
errval = 0;
}
lint1 = lf;
if (lint1 < minint[0]) minint[0] = lint1;
if (lint1 > maxint[0]) maxint[0] = lint1;
*lip++ = lint1;
lfp++;
if (*lfp >= 0.0)
lf = *lfp * *precision + 0.5;
else
lf = *lfp * *precision - 0.5;
if (fabs(lf) > MAXABS) {
/* scaling would cause overflow */
errval = 0;
}
lint2 = lf;
if (lint2 < minint[1]) minint[1] = lint2;
if (lint2 > maxint[1]) maxint[1] = lint2;
*lip++ = lint2;
lfp++;
if (*lfp >= 0.0)
lf = *lfp * *precision + 0.5;
else
lf = *lfp * *precision - 0.5;
if (fabs(lf) > MAXABS) {
/* scaling would cause overflow */
errval = 0;
}
lint3 = lf;
if (lint3 < minint[2]) minint[2] = lint3;
if (lint3 > maxint[2]) maxint[2] = lint3;
*lip++ = lint3;
lfp++;
diff = abs(oldlint1-lint1)+abs(oldlint2-lint2)+abs(oldlint3-lint3);
if (diff < mindiff && lfp > fp + 3)
mindiff = diff;
oldlint1 = lint1;
oldlint2 = lint2;
oldlint3 = lint3;
}
xdr_int(xdrs, &(minint[0]));
xdr_int(xdrs, &(minint[1]));
xdr_int(xdrs, &(minint[2]));
xdr_int(xdrs, &(maxint[0]));
xdr_int(xdrs, &(maxint[1]));
xdr_int(xdrs, &(maxint[2]));
if ((float)maxint[0] - (float)minint[0] >= MAXABS ||
(float)maxint[1] - (float)minint[1] >= MAXABS ||
(float)maxint[2] - (float)minint[2] >= MAXABS) {
/* turning value in unsigned by subtracting minint
* would cause overflow
*/
errval = 0;
}
sizeint[0] = maxint[0] - minint[0]+1;
sizeint[1] = maxint[1] - minint[1]+1;
sizeint[2] = maxint[2] - minint[2]+1;
/* check if one of the sizes is to big to be multiplied */
if ((sizeint[0] | sizeint[1] | sizeint[2] ) > 0xffffff) {
bitsizeint[0] = sizeofint(sizeint[0]);
bitsizeint[1] = sizeofint(sizeint[1]);
bitsizeint[2] = sizeofint(sizeint[2]);
bitsize = 0; /* flag the use of large sizes */
} else {
bitsize = sizeofints(3, sizeint);
}
lip = ip;
luip = (unsigned int *) ip;
smallidx = FIRSTIDX;
while (smallidx < LASTIDX && magicints[smallidx] < mindiff) {
smallidx++;
}
xdr_int(xdrs, &smallidx);
maxidx = MIN(LASTIDX, smallidx + 8) ;
minidx = maxidx - 8; /* often this equal smallidx */
smaller = magicints[MAX(FIRSTIDX, smallidx-1)] / 2;
smallnum = magicints[smallidx] / 2;
sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];
larger = magicints[maxidx] / 2;
i = 0;
while (i < *size) {
is_small = 0;
thiscoord = (int *)(luip) + i * 3;
if (smallidx < maxidx && i >= 1 &&
abs(thiscoord[0] - prevcoord[0]) < larger &&
abs(thiscoord[1] - prevcoord[1]) < larger &&
abs(thiscoord[2] - prevcoord[2]) < larger) {
is_smaller = 1;
} else if (smallidx > minidx) {
is_smaller = -1;
} else {
is_smaller = 0;
}
if (i + 1 < *size) {
if (abs(thiscoord[0] - thiscoord[3]) < smallnum &&
abs(thiscoord[1] - thiscoord[4]) < smallnum &&
abs(thiscoord[2] - thiscoord[5]) < smallnum) {
/* interchange first with second atom for better
* compression of water molecules
*/
tmp = thiscoord[0]; thiscoord[0] = thiscoord[3];
thiscoord[3] = tmp;
tmp = thiscoord[1]; thiscoord[1] = thiscoord[4];
thiscoord[4] = tmp;
tmp = thiscoord[2]; thiscoord[2] = thiscoord[5];
thiscoord[5] = tmp;
is_small = 1;
}
}
tmpcoord[0] = thiscoord[0] - minint[0];
tmpcoord[1] = thiscoord[1] - minint[1];
tmpcoord[2] = thiscoord[2] - minint[2];
if (bitsize == 0) {
sendbits(buf, bitsizeint[0], tmpcoord[0]);
sendbits(buf, bitsizeint[1], tmpcoord[1]);
sendbits(buf, bitsizeint[2], tmpcoord[2]);
} else {
sendints(buf, 3, bitsize, sizeint, tmpcoord);
}
prevcoord[0] = thiscoord[0];
prevcoord[1] = thiscoord[1];
prevcoord[2] = thiscoord[2];
thiscoord = thiscoord + 3;
i++;
run = 0;
if (is_small == 0 && is_smaller == -1)
is_smaller = 0;
while (is_small && run < 8*3) {
if (is_smaller == -1 && (
SQR(thiscoord[0] - prevcoord[0]) +
SQR(thiscoord[1] - prevcoord[1]) +
SQR(thiscoord[2] - prevcoord[2]) >= smaller * smaller)) {
is_smaller = 0;
}
tmpcoord[run++] = thiscoord[0] - prevcoord[0] + smallnum;
tmpcoord[run++] = thiscoord[1] - prevcoord[1] + smallnum;
tmpcoord[run++] = thiscoord[2] - prevcoord[2] + smallnum;
prevcoord[0] = thiscoord[0];
prevcoord[1] = thiscoord[1];
prevcoord[2] = thiscoord[2];
i++;
thiscoord = thiscoord + 3;
is_small = 0;
if (i < *size &&
abs(thiscoord[0] - prevcoord[0]) < smallnum &&
abs(thiscoord[1] - prevcoord[1]) < smallnum &&
abs(thiscoord[2] - prevcoord[2]) < smallnum) {
is_small = 1;
}
}
if (run != prevrun || is_smaller != 0) {
prevrun = run;
sendbits(buf, 1, 1); /* flag the change in run-length */
sendbits(buf, 5, run+is_smaller+1);
} else {
sendbits(buf, 1, 0); /* flag the fact that runlength did not change */
}
for (k=0; k < run; k+=3) {
sendints(buf, 3, smallidx, sizesmall, &tmpcoord[k]);
}
if (is_smaller != 0) {
smallidx += is_smaller;
if (is_smaller < 0) {
smallnum = smaller;
smaller = magicints[smallidx-1] / 2;
} else {
smaller = smallnum;
smallnum = magicints[smallidx] / 2;
}
sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];
}
}
if (buf[1] != 0) buf[0]++;
xdr_int(xdrs, &(buf[0])); /* buf[0] holds the length in bytes */
return errval * (xdr_opaque(xdrs, (char *)&(buf[3]), (unsigned int)buf[0]));
} else {
/* xdrs is open for reading */
if (xdr_int(xdrs, &lsize) == 0)
return 0;
if (*size != 0 && lsize != *size) {
fprintf(stderr, "wrong number of coordinates in xdr3dfcoord; "
"%d arg vs %d in file", *size, lsize);
}
*size = lsize;
size3 = *size * 3;
if (*size <= 9) {
*precision = -1;
return (xdr_vector(xdrs, (char *) fp, (unsigned int)size3,
(unsigned int)sizeof(*fp), (xdrproc_t)xdr_float));
}
xdr_float(xdrs, precision);
if (ip == NULL) {
ip = (int *)malloc((size_t)(size3 * sizeof(*ip)));
if (ip == NULL) {
fprintf(stderr,"malloc failed\n");
exit(1);
}
bufsize = size3 * 1.2;
buf = (int *)malloc((size_t)(bufsize * sizeof(*buf)));
if (buf == NULL) {
fprintf(stderr,"malloc failed\n");
exit(1);
}
oldsize = *size;
} else if (*size > oldsize) {
ip = (int *)realloc(ip, (size_t)(size3 * sizeof(*ip)));
if (ip == NULL) {
fprintf(stderr,"malloc failed\n");
exit(1);
}
bufsize = size3 * 1.2;
buf = (int *)realloc(buf, (size_t)(bufsize * sizeof(*buf)));
if (buf == NULL) {
fprintf(stderr,"malloc failed\n");
exit(1);
}
oldsize = *size;
}
buf[0] = buf[1] = buf[2] = 0;
xdr_int(xdrs, &(minint[0]));
xdr_int(xdrs, &(minint[1]));
xdr_int(xdrs, &(minint[2]));
xdr_int(xdrs, &(maxint[0]));
xdr_int(xdrs, &(maxint[1]));
xdr_int(xdrs, &(maxint[2]));
sizeint[0] = maxint[0] - minint[0]+1;
sizeint[1] = maxint[1] - minint[1]+1;
sizeint[2] = maxint[2] - minint[2]+1;
/* check if one of the sizes is to big to be multiplied */
if ((sizeint[0] | sizeint[1] | sizeint[2] ) > 0xffffff) {
bitsizeint[0] = sizeofint(sizeint[0]);
bitsizeint[1] = sizeofint(sizeint[1]);
bitsizeint[2] = sizeofint(sizeint[2]);
bitsize = 0; /* flag the use of large sizes */
} else {
bitsize = sizeofints(3, sizeint);
}
if (xdr_int(xdrs, &smallidx) == 0)
return 0;
maxidx = MIN(LASTIDX, smallidx + 8) ;
minidx = maxidx - 8; /* often this equal smallidx */
smaller = magicints[MAX(FIRSTIDX, smallidx-1)] / 2;
smallnum = magicints[smallidx] / 2;
sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx] ;
larger = magicints[maxidx];
/* buf[0] holds the length in bytes */
if (xdr_int(xdrs, &(buf[0])) == 0)
return 0;
if (xdr_opaque(xdrs, (char *)&(buf[3]), (unsigned int)buf[0]) == 0)
return 0;
buf[0] = buf[1] = buf[2] = 0;
lfp = fp;
inv_precision = 1.0 / * precision;
run = 0;
i = 0;
lip = ip;
while ( i < lsize ) {
thiscoord = (int *)(lip) + i * 3;
if (bitsize == 0) {
thiscoord[0] = receivebits(buf, bitsizeint[0]);
thiscoord[1] = receivebits(buf, bitsizeint[1]);
thiscoord[2] = receivebits(buf, bitsizeint[2]);
} else {
receiveints(buf, 3, bitsize, sizeint, thiscoord);
}
i++;
thiscoord[0] += minint[0];
thiscoord[1] += minint[1];
thiscoord[2] += minint[2];
prevcoord[0] = thiscoord[0];
prevcoord[1] = thiscoord[1];
prevcoord[2] = thiscoord[2];
flag = receivebits(buf, 1);
is_smaller = 0;
if (flag == 1) {
run = receivebits(buf, 5);
is_smaller = run % 3;
run -= is_smaller;
is_smaller--;
}
if (run > 0) {
thiscoord += 3;
for (k = 0; k < run; k+=3) {
receiveints(buf, 3, smallidx, sizesmall, thiscoord);
i++;
thiscoord[0] += prevcoord[0] - smallnum;
thiscoord[1] += prevcoord[1] - smallnum;
thiscoord[2] += prevcoord[2] - smallnum;
if (k == 0) {
/* interchange first with second atom for better
* compression of water molecules
*/
tmp = thiscoord[0]; thiscoord[0] = prevcoord[0];
prevcoord[0] = tmp;
tmp = thiscoord[1]; thiscoord[1] = prevcoord[1];
prevcoord[1] = tmp;
tmp = thiscoord[2]; thiscoord[2] = prevcoord[2];
prevcoord[2] = tmp;
*lfp++ = prevcoord[0] * inv_precision;
*lfp++ = prevcoord[1] * inv_precision;
*lfp++ = prevcoord[2] * inv_precision;
} else {
prevcoord[0] = thiscoord[0];
prevcoord[1] = thiscoord[1];
prevcoord[2] = thiscoord[2];
}
*lfp++ = thiscoord[0] * inv_precision;
*lfp++ = thiscoord[1] * inv_precision;
*lfp++ = thiscoord[2] * inv_precision;
}
} else {
*lfp++ = thiscoord[0] * inv_precision;
*lfp++ = thiscoord[1] * inv_precision;
*lfp++ = thiscoord[2] * inv_precision;
}
smallidx += is_smaller;
if (is_smaller < 0) {
smallnum = smaller;
if (smallidx > FIRSTIDX) {
smaller = magicints[smallidx - 1] /2;
} else {
smaller = 0;
}
} else if (is_smaller > 0) {
smaller = smallnum;
smallnum = magicints[smallidx] / 2;
}
sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx] ;
}
}
return 1;
}
/******************************************************************
XTC files have a relatively simple structure.
They have a header of 16 bytes and the rest are
the compressed coordinates of the files. Due to the
compression 00 is not present in the coordinates.
The first 4 bytes of the header are the magic number
1995 (0x000007CB). If we find this number we are guaranteed
to be in the header, due to the presence of so many zeros.
The second 4 bytes are the number of atoms in the frame, and is
assumed to be constant. The third 4 bytes are the frame number.
The last 4 bytes are a floating point representation of the time.
********************************************************************/
/* Must match definition in xtcio.c */
#ifndef XTC_MAGIC
#define XTC_MAGIC 1995
#endif
static const int header_size = 16;
/* Check if we are at the header start.
At the same time it will also read 1 int */
static int xtc_at_header_start(int fp, int natoms, int * timestep, float * time){
int i_inp[3];
float f_inp[10];
int i;
gmx_off_t off;
if((off = gmx_ftell(xdrfiles[fp+1])) < 0){
return -1;
}
/* read magic natoms and timestep */
for(i = 0;i<3;i++){
if(!xdr_int(xdridptr[fp+1], &(i_inp[i]))){
gmx_fseek(xdrfiles[fp+1],off+sizeof(int),SEEK_SET);
return -1;
}
}
/* quick return */
if(i_inp[0] != XTC_MAGIC){
if(gmx_fseek(xdrfiles[fp+1],off+sizeof(int),SEEK_SET)){
return -1;
}
return 0;
}
/* read time and box */
for(i = 0;i<10;i++){
if(!xdr_float(xdridptr[fp+1], &(f_inp[i]))){
gmx_fseek(xdrfiles[fp+1],off+sizeof(int),SEEK_SET);
return -1;
}
}
/* Make a rigourous check to see if we are in the beggining of a header
Hopefully there are no ambiguous cases */
/* This check makes use of the fact that the box matrix has 3 zeroes on the upper
right triangle and that the first element must be nonzero unless the entire matrix is zero
*/
if(i_inp[1] == natoms &&
((f_inp[1] != 0 && f_inp[6] == 0) ||
(f_inp[1] == 0 && f_inp[5] == 0 && f_inp[9] == 0))){
if(gmx_fseek(xdrfiles[fp+1],off+sizeof(int),SEEK_SET)){
return -1;
}
*time = f_inp[0];
*timestep = i_inp[2];
return 1;
}
if(gmx_fseek(xdrfiles[fp+1],off+sizeof(int),SEEK_SET)){
return -1;
}
return 0;
}
static int
xtc_get_next_frame_number(int fp,int natoms)
{
gmx_off_t off;
int step;
float time;
int ret;
if((off = gmx_ftell(xdrfiles[fp+1])) < 0){
return -1;
}
/* read one int just to make sure we dont read this frame but the next */
xdr_int(xdridptr[fp+1],&step);
while(1){
ret = xtc_at_header_start(fp,natoms,&step,&time);
if(ret == 1){
if(gmx_fseek(xdrfiles[fp+1],off,SEEK_SET)){
return -1;
}
return step;
}else if(ret == -1){
if(gmx_fseek(xdrfiles[fp+1],off,SEEK_SET)){
return -1;
}
}
}
return -1;
}
static float
xtc_get_next_frame_time(int fp,int natoms, bool * bOK)
{
gmx_off_t off;
float time;
int step;
int ret;
*bOK = 0;
if((off = gmx_ftell(xdrfiles[fp+1])) < 0){
return -1;
}
/* read one int just to make sure we dont read this frame but the next */
xdr_int(xdridptr[fp+1],&step);
while(1){
ret = xtc_at_header_start(fp,natoms,&step,&time);
if(ret == 1){
*bOK = 1;
if(gmx_fseek(xdrfiles[fp+1],off,SEEK_SET)){
*bOK = 0;
return -1;
}
return time;
}else if(ret == -1){
if(gmx_fseek(xdrfiles[fp+1],off,SEEK_SET)){
return -1;
}
return -1;
}
}
return -1;
}
static float
xtc_get_current_frame_time(int fp,int natoms, bool * bOK)
{
gmx_off_t off;
int step;
float time;
int ret;
*bOK = 0;
if((off = gmx_ftell(xdrfiles[fp+1])) < 0){
return -1;
}
while(1){
ret = xtc_at_header_start(fp,natoms,&step,&time);
if(ret == 1){
*bOK = 1;
if(gmx_fseek(xdrfiles[fp+1],off,SEEK_SET)){
*bOK = 0;
return -1;
}
return time;
}else if(ret == -1){
if(gmx_fseek(xdrfiles[fp+1],off,SEEK_SET)){
return -1;
}
return -1;
}else if(ret == 0){
/*Go back.*/
if(gmx_fseek(xdrfiles[fp+1],-8,SEEK_CUR)){
return -1;
}
}
}
return -1;
}
/* Currently not used, just for completeness */
static int
xtc_get_current_frame_number(int fp,int natoms, bool * bOK)
{
gmx_off_t off;
int ret;
int step;
float time;
*bOK = 0;
if((off = gmx_ftell(xdrfiles[fp+1])) < 0){
return -1;
}
while(1){
ret = xtc_at_header_start(fp,natoms,&step,&time);
if(ret == 1){
*bOK = 1;
if(gmx_fseek(xdrfiles[fp+1],off,SEEK_SET)){
return -1;
}
return step;
}else if(ret == -1){
if(gmx_fseek(xdrfiles[fp+1],off,SEEK_SET)){
return -1;
}
return -1;
}
}
return -1;
}
static gmx_off_t xtc_get_next_frame_start(int fp, int natoms)
{
int inp;
gmx_off_t res;
int ret;
int step;
float time;
/* read one int just to make sure we dont read this frame but the next */
xdr_int(xdridptr[fp+1],&step);
while(1)
{
ret = xtc_at_header_start(fp,natoms,&step,&time);
if(ret == 1){
if((res = gmx_ftell(xdrfiles[fp+1])) >= 0){
return res - sizeof(int);
}else{
return res;
}
}else if(ret == -1){
return -1;
}
}
return -1;
}
static float
xtc_estimate_dt(int fp, int natoms, bool * bOK)
{
float res;
float tinit;
gmx_off_t off;
if((off = gmx_ftell(xdrfiles[fp+1])) < 0){
return -1;
}
tinit = xtc_get_current_frame_time(fp,natoms,bOK);
*bOK = 1;
if(!bOK)
{
return -1;
}
res = xtc_get_next_frame_time(fp,natoms,bOK);
if(!bOK)
{
return -1;
}
res -= tinit;
if(gmx_fseek(xdrfiles[fp+1],off,SEEK_SET)){
*bOK = 0;
return -1;
}
return res;
}
int
xtc_seek_frame(int frame, int fp, int natoms)
{
gmx_off_t low = 0;
gmx_off_t high,pos;
/* round to 4 bytes */
int fr;
gmx_off_t offset;
if(gmx_fseek(xdrfiles[fp+1],0,SEEK_END)){
return -1;
}
if((high = gmx_ftell(xdrfiles[fp+1])) < 0){
return -1;
}
/* round to 4 bytes */
high /= sizeof(int);
high *= sizeof(int);
offset = ((high/2)/sizeof(int))*sizeof(int);
if(gmx_fseek(xdrfiles[fp+1],offset,SEEK_SET)){
return -1;
}
while(1)
{
fr = xtc_get_next_frame_number(fp,natoms);
if(fr < 0)
{
return -1;
}
if(fr != frame && abs(low-high) > header_size)
{
if(fr < frame)
{
low = offset;
}
else
{
high = offset;
}
/* round to 4 bytes */
offset = (((high+low)/2)/4)*4;
if(gmx_fseek(xdrfiles[fp+1],offset,SEEK_SET)){
return -1;
}
}
else
{
break;
}
}
if(offset <= header_size)
{
offset = low;
}
if(gmx_fseek(xdrfiles[fp+1],offset,SEEK_SET)){
return -1;
}
if((pos = xtc_get_next_frame_start(fp,natoms))< 0){
/* we probably hit an end of file */
return -1;
}
if(gmx_fseek(xdrfiles[fp+1],pos,SEEK_SET)){
return -1;
}
return 0;
}
int
xtc_seek_time(real time, int fp, int natoms)
{
float t;
float dt;
bool bOK;
gmx_off_t low = 0;
gmx_off_t high,offset,pos;
int res;
int dt_sign = 0;
if(gmx_fseek(xdrfiles[fp+1],0,SEEK_END)){
return -1;
}
if((high = gmx_ftell(xdrfiles[fp+1])) < 0){
return -1;
}
/* round to int */
high /= sizeof(int);
high *= sizeof(int);
offset = ((high/2)/sizeof(int))*sizeof(int);
if(gmx_fseek(xdrfiles[fp+1],offset,SEEK_SET)){
return -1;
}
dt = xtc_estimate_dt(fp,natoms,&bOK);
if(!bOK)
{
return -1;
}
while(1)
{
dt = xtc_estimate_dt(fp,natoms,&bOK);
if(!bOK)
{
return -1;
}else{
if(dt > 0){
if(dt_sign == -1){
/* Found a place in the trajectory that has positive time step while
other has negative time step */
return -2;
}
dt_sign = 1;
}else if(dt < 0){
if(dt_sign == 1){
/* Found a place in the trajectory that has positive time step while
other has negative time step */
return -2;
}
dt_sign = -1;
}
}
t = xtc_get_next_frame_time(fp,natoms,&bOK);
if(!bOK)
{
return -1;
}
/* If we are before the target time and the time step is positive or 0, or we have
after the target time and the time step is negative, or the difference between
the current time and the target time is bigger than dt and above all the distance between high
and low is bigger than 1 frame, then do another step of binary search. Otherwise stop and check
if we reached the solution */
if((((t < time && dt_sign >= 0) || (t > time && dt_sign == -1)) || ((t-time) >= dt && dt_sign >= 0) || ((time-t) >= -dt && dt_sign < 0)) && (abs(low-high) > header_size))
{
if(dt >= 0 && dt_sign != -1)
{
if(t < time)
{
low = offset;
}
else
{
high = offset;
}
}
else if(dt <= 0 && dt_sign == -1)
{
if(t >= time)
{
low = offset;
}
else
{
high = offset;
}
}else{
/* We should never reach here */
return -1;
}
/* round to 4 bytes and subtract header*/
offset = (((high+low)/2)/sizeof(int))*sizeof(int);
if(gmx_fseek(xdrfiles[fp+1],offset,SEEK_SET)){
return -1;
}
}
else
{
if(abs(low-high) <= header_size)
{
break;
}
/* reestimate dt */
if(xtc_estimate_dt(fp,natoms,&bOK) != dt)
{
if(bOK)
{
dt = xtc_estimate_dt(fp,natoms,&bOK);
}
}
if(t >= time && t-time < dt)
{
break;
}
}
}
if(offset <= header_size)
{
offset = low;
}
gmx_fseek(xdrfiles[fp+1],offset,SEEK_SET);
if((pos = xtc_get_next_frame_start(fp,natoms)) < 0){
return -1;
}
if(gmx_fseek(xdrfiles[fp+1],pos,SEEK_SET)){
return -1;
}
return 0;
}
float
xtc_get_last_frame_time(int fp, int natoms, bool * bOK)
{
float time;
gmx_off_t off;
int res;
*bOK = 1;
off = gmx_ftell(xdrfiles[fp+1]);
if(off < 0){
*bOK = 0;
return -1;
}
if( (res = gmx_fseek(xdrfiles[fp+1],-4,SEEK_END)) != 0){
*bOK = 0;
return -1;
}
time = xtc_get_current_frame_time(fp, natoms, bOK);
if(!(*bOK)){
return -1;
}
if( (res = gmx_fseek(xdrfiles[fp+1],off,SEEK_SET)) != 0){
*bOK = 0;
return -1;
}
return time;
}
int
xtc_get_last_frame_number(int fp, int natoms, bool * bOK)
{
int frame;
gmx_off_t off;
int res;
*bOK = 1;
if((off = gmx_ftell(xdrfiles[fp+1])) < 0){
*bOK = 0;
return -1;
}
if(gmx_fseek(xdrfiles[fp+1],-4,SEEK_END)){
*bOK = 0;
return -1;
}
frame = xtc_get_current_frame_number(fp, natoms, bOK);
if(!bOK){
return -1;
}
if(gmx_fseek(xdrfiles[fp+1],off,SEEK_SET)){
*bOK = 0;
return -1;
}
return frame;
}
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