1 /*____________________________________________________________________________
3 | libxdrf - portable fortran interface to xdr. some xdr routines
4 | are C routines for compressed coordinates
8 | This collection of routines is intended to write and read
9 | data in a portable way to a file, so data written on one type
10 | of machine can be read back on a different type.
12 | all fortran routines use an integer 'xdrid', which is an id to the
13 | current xdr file, and is set by xdrfopen.
14 | most routines have in integer 'ret' which is the return value.
15 | The value of 'ret' is zero on failure, and most of the time one
18 | There are three routines useful for C users:
19 | xdropen(), xdrclose(), xdr3dfcoord().
20 | The first two replace xdrstdio_create and xdr_destroy, and *must* be
21 | used when you plan to use xdr3dfcoord(). (they are also a bit
22 | easier to interface). For writing data other than compressed coordinates
23 | you should use the standard C xdr routines (see xdr man page)
25 | xdrfopen(xdrid, filename, mode, ret)
26 | character *(*) filename
29 | this will open the file with the given filename (string)
30 | and the given mode, it returns an id in xdrid, which is
31 | to be used in all other calls to xdrf routines.
32 | mode is 'w' to create, or update an file, for all other
33 | values of mode the file is opened for reading
35 | you need to call xdrfclose to flush the output and close
37 | Note that you should not use xdrstdio_create, which comes with the
38 | standard xdr library
40 | xdrfclose(xdrid, ret)
41 | flush the data to the file, and closes the file;
42 | You should not use xdr_destroy (which comes standard with
45 | xdrfbool(xdrid, bp, ret)
48 | This filter produces values of either 1 or 0
50 | xdrfchar(xdrid, cp, ret)
53 | filter that translate between characters and their xdr representation
54 | Note that the characters in not compressed and occupies 4 bytes.
56 | xdrfdouble(xdrid, dp, ret)
59 | read/write a double.
61 | xdrffloat(xdrid, fp, ret)
66 | xdrfint(xdrid, ip, ret)
71 | xdrflong(xdrid, lp, ret)
74 | this routine has a possible portablility problem due to 64 bits longs.
76 | xdrfshort(xdrid, sp, ret)
79 | xdrfstring(xdrid, sp, maxsize, ret)
83 | read/write a string, with maximum length given by maxsize
85 | xdrfwrapstring(xdris, sp, ret)
88 | read/write a string (it is the same as xdrfstring accept that it finds
89 | the stringlength itself.
91 | xdrfvector(xdrid, cp, size, xdrfproc, ret)
96 | read/write an array pointed to by cp, with number of elements
97 | defined by 'size'. the routine 'xdrfproc' is the name
98 | of one of the above routines to read/write data (like xdrfdouble)
99 | In contrast with the c-version you don't need to specify the
100 | byte size of an element.
101 | xdrfstring is not allowed here (it is in the c version)
103 | xdrf3dfcoord(xdrid, fp, size, precision, ret)
108 | this is *NOT* a standard xdr routine. I named it this way, because
109 | it invites people to use the other xdr routines.
110 | It is introduced to store specifically 3d coordinates of molecules
111 | (as found in molecular dynamics) and it writes it in a compressed way.
112 | It starts by multiplying all numbers by precision and
113 | rounding the result to integer. effectively converting
114 | all floating point numbers to fixed point.
115 | it uses an algorithm for compression that is optimized for
116 | molecular data, but could be used for other 3d coordinates
117 | as well. There is subtantial overhead involved, so call this
118 | routine only if you have a large number of coordinates to read/write
120 | ________________________________________________________________________
122 | Below are the routines to be used by C programmers. Use the 'normal'
123 | xdr routines to write integers, floats, etc (see man xdr)
125 | int xdropen(XDR *xdrs, const char *filename, const char *type)
126 | This will open the file with the given filename and the
127 | given mode. You should pass it an allocated XDR struct
128 | in xdrs, to be used in all other calls to xdr routines.
129 | Mode is 'w' to create, or update an file, and for all
130 | other values of mode the file is opened for reading.
131 | You need to call xdrclose to flush the output and close
134 | Note that you should not use xdrstdio_create, which
135 | comes with the standard xdr library.
137 | int xdrclose(XDR *xdrs)
138 | Flush the data to the file, and close the file;
139 | You should not use xdr_destroy (which comes standard
140 | with the xdr libraries).
142 | int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
143 | This is \fInot\fR a standard xdr routine. I named it this
144 | way, because it invites people to use the other xdr
147 | (c) 1995 Frans van Hoesel, hoesel@chem.rug.nl
160 int ftocstr(char *, int, char *, int);
161 int ctofstr(char *, int, char *);
164 static FILE *xdrfiles[MAXID];
165 static XDR *xdridptr[MAXID];
166 static char xdrmodes[MAXID];
167 static unsigned int cnt;
169 typedef void (* FUNCTION(xdrfproc)) (int *, void *, int *);
172 FUNCTION(xdrfbool) ARGS(`xdrid, pb, ret')
176 *ret = xdr_bool(xdridptr[*xdrid], (bool_t *) pb);
181 FUNCTION(xdrfchar) ARGS(`xdrid, cp, ret')
185 *ret = xdr_char(xdridptr[*xdrid], cp);
190 FUNCTION(xdrfdouble) ARGS(`xdrid, dp, ret')
194 *ret = xdr_double(xdridptr[*xdrid], dp);
195 cnt += sizeof(double);
199 FUNCTION(xdrffloat) ARGS(`xdrid, fp, ret')
203 *ret = xdr_float(xdridptr[*xdrid], fp);
204 cnt += sizeof(float);
208 FUNCTION(xdrfint) ARGS(`xdrid, ip, ret')
212 *ret = xdr_int(xdridptr[*xdrid], ip);
217 FUNCTION(xdrflong) ARGS(`xdrid, lp, ret')
221 *ret = xdr_long(xdridptr[*xdrid], lp);
226 FUNCTION(xdrfshort) ARGS(`xdrid, sp, ret')
230 *ret = xdr_short(xdridptr[*xdrid], sp);
235 FUNCTION(xdrfuchar) ARGS(`xdrid, ucp, ret')
239 *ret = xdr_u_char(xdridptr[*xdrid], ucp);
244 FUNCTION(xdrfulong) ARGS(`xdrid, ulp, ret')
248 *ret = xdr_u_long(xdridptr[*xdrid], ulp);
249 cnt += sizeof(unsigned long);
253 FUNCTION(xdrfushort) ARGS(`xdrid, usp, ret')
257 *ret = xdr_u_short(xdridptr[*xdrid], usp);
258 cnt += sizeof(unsigned short);
262 FUNCTION(xdrf3dfcoord) ARGS(`xdrid, fp, size, precision, ret')
268 *ret = xdr3dfcoord(xdridptr[*xdrid], fp, size, precision);
272 FUNCTION(xdrfstring) ARGS(`xdrid, STRING_ARG(sp), maxsize, ret')
279 tsp = (char*) malloc(((STRING_LEN(sp)) + 1) * sizeof(char));
284 if (ftocstr(tsp, *maxsize+1, STRING_PTR(sp), STRING_LEN(sp))) {
289 *ret = xdr_string(xdridptr[*xdrid], (char **) &tsp, (u_int) *maxsize);
290 ctofstr( STRING_PTR(sp), STRING_LEN(sp), tsp);
296 FUNCTION(xdrfwrapstring) ARGS(`xdrid, STRING_ARG(sp), ret')
302 maxsize = (STRING_LEN(sp)) + 1;
303 tsp = (char*) malloc(maxsize * sizeof(char));
308 if (ftocstr(tsp, maxsize, STRING_PTR(sp), STRING_LEN(sp))) {
313 *ret = xdr_string(xdridptr[*xdrid], (char **) &tsp, (u_int)maxsize);
314 ctofstr( STRING_PTR(sp), STRING_LEN(sp), tsp);
320 FUNCTION(xdrfopaque) ARGS(`xdrid, cp, ccnt, ret')
325 *ret = xdr_opaque(xdridptr[*xdrid], (caddr_t)*cp, (u_int)*ccnt);
330 FUNCTION(xdrfsetpos) ARGS(`xdrid, pos, ret')
334 *ret = xdr_setpos(xdridptr[*xdrid], (u_int) *pos);
338 FUNCTION(xdrf) ARGS(`xdrid, pos')
341 *pos = xdr_getpos(xdridptr[*xdrid]);
345 FUNCTION(xdrfvector) ARGS(`xdrid, cp, size, elproc, ret')
349 FUNCTION(xdrfproc) elproc;
353 for (lcnt = 0; lcnt < *size; lcnt++) {
354 elproc(xdrid, (cp+cnt) , ret);
360 FUNCTION(xdrfclose) ARGS(`xdrid, ret')
364 *ret = xdrclose(xdridptr[*xdrid]);
369 FUNCTION(xdrfopen) ARGS(`xdrid, STRING_ARG(fp), STRING_ARG(mode), ret')
372 STRING_ARG_DECL(mode);
378 if (ftocstr(fname, sizeof(fname), STRING_PTR(fp), STRING_LEN(fp))) {
381 if (ftocstr(fmode, sizeof(fmode), STRING_PTR(mode),
386 *xdrid = xdropen(NULL, fname, fmode);
393 /*___________________________________________________________________________
395 | what follows are the C routines for opening, closing xdr streams
396 | and the routine to read/write compressed coordinates together
397 | with some routines to assist in this task (those are marked
398 | static and cannot be called from user programs)
400 #define MAXABS INT_MAX-2
403 #define MIN(x,y) ((x) < (y) ? (x):(y))
406 #define MAX(x,y) ((x) > (y) ? (x):(y))
409 #define SQR(x) ((x)*(x))
411 static int magicints[] = {
412 0, 0, 0, 0, 0, 0, 0, 0, 0,
413 8, 10, 12, 16, 20, 25, 32, 40, 50, 64,
414 80, 101, 128, 161, 203, 256, 322, 406, 512, 645,
415 812, 1024, 1290, 1625, 2048, 2580, 3250, 4096, 5060, 6501,
416 8192, 10321, 13003, 16384, 20642, 26007, 32768, 41285, 52015, 65536,
417 82570, 104031, 131072, 165140, 208063, 262144, 330280, 416127, 524287, 660561,
418 832255, 1048576, 1321122, 1664510, 2097152, 2642245, 3329021, 4194304, 5284491, 6658042,
419 8388607, 10568983, 13316085, 16777216 };
422 /* note that magicints[FIRSTIDX-1] == 0 */
423 #define LASTIDX (sizeof(magicints) / sizeof(*magicints))
426 /*__________________________________________________________________________
428 | xdropen - open xdr file
430 | This versions differs from xdrstdio_create, because I need to know
431 | the state of the file (read or write) so I can use xdr3dfcoord
432 | in eigther read or write mode, and the file descriptor
433 | so I can close the file (something xdr_destroy doesn't do).
437 int xdropen(XDR *xdrs, const char *filename, const char *type) {
438 static int init_done = 0;
443 if (init_done == 0) {
444 for (xdrid = 1; xdrid < MAXID; xdrid++) {
445 xdridptr[xdrid] = NULL;
450 while (xdrid < MAXID && xdridptr[xdrid] != NULL) {
453 if (xdrid == MAXID) {
456 if (*type == 'w' || *type == 'W') {
464 xdrfiles[xdrid] = fopen(filename, type1);
465 if (xdrfiles[xdrid] == NULL) {
469 xdrmodes[xdrid] = *type;
470 /* next test isn't usefull in the case of C language
471 * but is used for the Fortran interface
472 * (C users are expected to pass the address of an already allocated
476 xdridptr[xdrid] = (XDR *) malloc(sizeof(XDR));
477 xdrstdio_create(xdridptr[xdrid], xdrfiles[xdrid], lmode);
479 xdridptr[xdrid] = xdrs;
480 xdrstdio_create(xdrs, xdrfiles[xdrid], lmode);
485 /*_________________________________________________________________________
487 | xdrclose - close a xdr file
489 | This will flush the xdr buffers, and destroy the xdr stream.
490 | It also closes the associated file descriptor (this is *not*
491 | done by xdr_destroy).
495 int xdrclose(XDR *xdrs) {
499 fprintf(stderr, "xdrclose: passed a NULL pointer\n");
502 for (xdrid = 1; xdrid < MAXID; xdrid++) {
503 if (xdridptr[xdrid] == xdrs) {
506 fclose(xdrfiles[xdrid]);
507 xdridptr[xdrid] = NULL;
511 fprintf(stderr, "xdrclose: no such open xdr file\n");
516 /*____________________________________________________________________________
518 | sendbits - encode num into buf using the specified number of bits
520 | This routines appends the value of num to the bits already present in
521 | the array buf. You need to give it the number of bits to use and you
522 | better make sure that this number of bits is enough to hold the value
523 | Also num must be positive.
527 static void sendbits(int buf[], int num_of_bits, int num) {
529 unsigned int cnt, lastbyte;
531 unsigned char * cbuf;
533 cbuf = ((unsigned char *)buf) + 3 * sizeof(*buf);
534 cnt = (unsigned int) buf[0];
536 lastbyte =(unsigned int) buf[2];
537 while (num_of_bits >= 8) {
538 lastbyte = (lastbyte << 8) | ((num >> (num_of_bits -8)) /* & 0xff*/);
539 cbuf[cnt++] = lastbyte >> lastbits;
542 if (num_of_bits > 0) {
543 lastbyte = (lastbyte << num_of_bits) | num;
544 lastbits += num_of_bits;
547 cbuf[cnt++] = lastbyte >> lastbits;
554 cbuf[cnt] = lastbyte << (8 - lastbits);
558 /*_________________________________________________________________________
560 | sizeofint - calculate bitsize of an integer
562 | return the number of bits needed to store an integer with given max size
566 static int sizeofint(const int size) {
567 unsigned int num = 1;
570 while (size >= num && num_of_bits < 32) {
577 /*___________________________________________________________________________
579 | sizeofints - calculate 'bitsize' of compressed ints
581 | given the number of small unsigned integers and the maximum value
582 | return the number of bits needed to read or write them with the
583 | routines receiveints and sendints. You need this parameter when
584 | calling these routines. Note that for many calls I can use
585 | the variable 'smallidx' which is exactly the number of bits, and
586 | So I don't need to call 'sizeofints for those calls.
589 static int sizeofints( const int num_of_ints, unsigned int sizes[]) {
591 unsigned int num_of_bytes, num_of_bits, bytes[32], bytecnt, tmp;
595 for (i=0; i < num_of_ints; i++) {
597 for (bytecnt = 0; bytecnt < num_of_bytes; bytecnt++) {
598 tmp = bytes[bytecnt] * sizes[i] + tmp;
599 bytes[bytecnt] = tmp & 0xff;
603 bytes[bytecnt++] = tmp & 0xff;
606 num_of_bytes = bytecnt;
610 while (bytes[num_of_bytes] >= num) {
614 return num_of_bits + num_of_bytes * 8;
618 /*____________________________________________________________________________
620 | sendints - send a small set of small integers in compressed format
622 | this routine is used internally by xdr3dfcoord, to send a set of
623 | small integers to the buffer.
624 | Multiplication with fixed (specified maximum ) sizes is used to get
625 | to one big, multibyte integer. Allthough the routine could be
626 | modified to handle sizes bigger than 16777216, or more than just
627 | a few integers, this is not done, because the gain in compression
628 | isn't worth the effort. Note that overflowing the multiplication
629 | or the byte buffer (32 bytes) is unchecked and causes bad results.
633 static void sendints(int buf[], const int num_of_ints, const int num_of_bits,
634 unsigned int sizes[], unsigned int nums[]) {
637 unsigned int bytes[32], num_of_bytes, bytecnt, tmp;
642 bytes[num_of_bytes++] = tmp & 0xff;
646 for (i = 1; i < num_of_ints; i++) {
647 if (nums[i] >= sizes[i]) {
648 fprintf(stderr,"major breakdown in sendints num %d doesn't "
649 "match size %d\n", nums[i], sizes[i]);
652 /* use one step multiply */
654 for (bytecnt = 0; bytecnt < num_of_bytes; bytecnt++) {
655 tmp = bytes[bytecnt] * sizes[i] + tmp;
656 bytes[bytecnt] = tmp & 0xff;
660 bytes[bytecnt++] = tmp & 0xff;
663 num_of_bytes = bytecnt;
665 if (num_of_bits >= num_of_bytes * 8) {
666 for (i = 0; i < num_of_bytes; i++) {
667 sendbits(buf, 8, bytes[i]);
669 sendbits(buf, num_of_bits - num_of_bytes * 8, 0);
671 for (i = 0; i < num_of_bytes-1; i++) {
672 sendbits(buf, 8, bytes[i]);
674 sendbits(buf, num_of_bits- (num_of_bytes -1) * 8, bytes[i]);
679 /*___________________________________________________________________________
681 | receivebits - decode number from buf using specified number of bits
683 | extract the number of bits from the array buf and construct an integer
684 | from it. Return that value.
688 static int receivebits(int buf[], int num_of_bits) {
691 unsigned int lastbits, lastbyte;
692 unsigned char * cbuf;
693 int mask = (1 << num_of_bits) -1;
695 cbuf = ((unsigned char *)buf) + 3 * sizeof(*buf);
697 lastbits = (unsigned int) buf[1];
698 lastbyte = (unsigned int) buf[2];
701 while (num_of_bits >= 8) {
702 lastbyte = ( lastbyte << 8 ) | cbuf[cnt++];
703 num |= (lastbyte >> lastbits) << (num_of_bits - 8);
706 if (num_of_bits > 0) {
707 if (lastbits < num_of_bits) {
709 lastbyte = (lastbyte << 8) | cbuf[cnt++];
711 lastbits -= num_of_bits;
712 num |= (lastbyte >> lastbits) & ((1 << num_of_bits) -1);
721 /*____________________________________________________________________________
723 | receiveints - decode 'small' integers from the buf array
725 | this routine is the inverse from sendints() and decodes the small integers
726 | written to buf by calculating the remainder and doing divisions with
727 | the given sizes[]. You need to specify the total number of bits to be
728 | used from buf in num_of_bits.
732 static void receiveints(int buf[], const int num_of_ints, int num_of_bits,
733 unsigned int sizes[], int nums[]) {
735 int i, j, num_of_bytes, p, num;
737 bytes[1] = bytes[2] = bytes[3] = 0;
739 while (num_of_bits > 8) {
740 bytes[num_of_bytes++] = receivebits(buf, 8);
743 if (num_of_bits > 0) {
744 bytes[num_of_bytes++] = receivebits(buf, num_of_bits);
746 for (i = num_of_ints-1; i > 0; i--) {
748 for (j = num_of_bytes-1; j >=0; j--) {
749 num = (num << 8) | bytes[j];
752 num = num - p * sizes[i];
756 nums[0] = bytes[0] | (bytes[1] << 8) | (bytes[2] << 16) | (bytes[3] << 24);
759 /*____________________________________________________________________________
761 | xdr3dfcoord - read or write compressed 3d coordinates to xdr file.
763 | this routine reads or writes (depending on how you opened the file with
764 | xdropen() ) a large number of 3d coordinates (stored in *fp).
765 | The number of coordinates triplets to write is given by *size. On
766 | read this number may be zero, in which case it reads as many as were written
767 | or it may specify the number if triplets to read (which should match the
769 | Compression is achieved by first converting all floating numbers to integer
770 | using multiplication by *precision and rounding to the nearest integer.
771 | Then the minimum and maximum value are calculated to determine the range.
772 | The limited range of integers so found, is used to compress the coordinates.
773 | In addition the differences between succesive coordinates is calculated.
774 | If the difference happens to be 'small' then only the difference is saved,
775 | compressing the data even more. The notion of 'small' is changed dynamically
776 | and is enlarged or reduced whenever needed or possible.
777 | Extra compression is achieved in the case of GROMOS and coordinates of
778 | water molecules. GROMOS first writes out the Oxygen position, followed by
779 | the two hydrogens. In order to make the differences smaller (and thereby
780 | compression the data better) the order is changed into first one hydrogen
781 | then the oxygen, followed by the other hydrogen. This is rather special, but
782 | it shouldn't harm in the general case.
786 int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision) {
789 static int *ip = NULL;
793 int minint[3], maxint[3], mindiff, *lip, diff;
794 int lint1, lint2, lint3, oldlint1, oldlint2, oldlint3, smallidx;
796 unsigned sizeint[3], sizesmall[3], bitsizeint[3], size3, *luip;
798 int small, smaller, larger, i, is_small, is_smaller, run, prevrun;
800 int tmp, *thiscoord, prevcoord[3];
801 unsigned int tmpcoord[30];
803 int bufsize, xdrid, lsize;
804 unsigned int bitsize;
808 /* find out if xdrs is opened for reading or for writing */
810 while (xdridptr[xdrid] != xdrs) {
812 if (xdrid >= MAXID) {
813 fprintf(stderr, "xdr error. no open xdr stream\n");
817 if (xdrmodes[xdrid] == 'w') {
819 /* xdrs is open for writing */
821 if (xdr_int(xdrs, size) == 0)
824 /* when the number of coordinates is small, don't try to compress; just
825 * write them as floats using xdr_vector
828 return (xdr_vector(xdrs, (char *) fp, size3, sizeof(*fp),
829 (xdrproc_t)xdr_float));
832 xdr_float(xdrs, precision);
834 ip = (int *)malloc(size3 * sizeof(*ip));
836 fprintf(stderr,"malloc failed\n");
839 bufsize = size3 * 1.2;
840 buf = (int *)malloc(bufsize * sizeof(*buf));
842 fprintf(stderr,"malloc failed\n");
846 } else if (*size > oldsize) {
847 ip = (int *)realloc(ip, size3 * sizeof(*ip));
849 fprintf(stderr,"malloc failed\n");
852 bufsize = size3 * 1.2;
853 buf = (int *)realloc(buf, bufsize * sizeof(*buf));
855 fprintf(stderr,"malloc failed\n");
860 /* buf[0-2] are special and do not contain actual data */
861 buf[0] = buf[1] = buf[2] = 0;
862 minint[0] = minint[1] = minint[2] = INT_MAX;
863 maxint[0] = maxint[1] = maxint[2] = INT_MIN;
868 oldlint1 = oldlint2 = oldlint3 = 0;
869 while(lfp < fp + size3 ) {
870 /* find nearest integer */
872 lf = *lfp * *precision + 0.5;
874 lf = *lfp * *precision - 0.5;
875 if (fabs(lf) > MAXABS) {
876 /* scaling would cause overflow */
880 if (lint1 < minint[0]) minint[0] = lint1;
881 if (lint1 > maxint[0]) maxint[0] = lint1;
885 lf = *lfp * *precision + 0.5;
887 lf = *lfp * *precision - 0.5;
888 if (fabs(lf) > MAXABS) {
889 /* scaling would cause overflow */
893 if (lint2 < minint[1]) minint[1] = lint2;
894 if (lint2 > maxint[1]) maxint[1] = lint2;
898 lf = *lfp * *precision + 0.5;
900 lf = *lfp * *precision - 0.5;
901 if (fabs(lf) > MAXABS) {
902 /* scaling would cause overflow */
906 if (lint3 < minint[2]) minint[2] = lint3;
907 if (lint3 > maxint[2]) maxint[2] = lint3;
910 diff = abs(oldlint1-lint1)+abs(oldlint2-lint2)+abs(oldlint3-lint3);
911 if (diff < mindiff && lfp > fp + 3)
917 xdr_int(xdrs, &(minint[0]));
918 xdr_int(xdrs, &(minint[1]));
919 xdr_int(xdrs, &(minint[2]));
921 xdr_int(xdrs, &(maxint[0]));
922 xdr_int(xdrs, &(maxint[1]));
923 xdr_int(xdrs, &(maxint[2]));
925 if ((float)maxint[0] - (float)minint[0] >= MAXABS ||
926 (float)maxint[1] - (float)minint[1] >= MAXABS ||
927 (float)maxint[2] - (float)minint[2] >= MAXABS) {
928 /* turning value in unsigned by subtracting minint
929 * would cause overflow
933 sizeint[0] = maxint[0] - minint[0]+1;
934 sizeint[1] = maxint[1] - minint[1]+1;
935 sizeint[2] = maxint[2] - minint[2]+1;
937 /* check if one of the sizes is to big to be multiplied */
938 if ((sizeint[0] | sizeint[1] | sizeint[2] ) > 0xffffff) {
939 bitsizeint[0] = sizeofint(sizeint[0]);
940 bitsizeint[1] = sizeofint(sizeint[1]);
941 bitsizeint[2] = sizeofint(sizeint[2]);
942 bitsize = 0; /* flag the use of large sizes */
944 bitsize = sizeofints(3, sizeint);
947 luip = (unsigned int *) ip;
949 while (smallidx < LASTIDX && magicints[smallidx] < mindiff) {
952 xdr_int(xdrs, &smallidx);
953 maxidx = MIN(LASTIDX, smallidx + 8) ;
954 minidx = maxidx - 8; /* often this equal smallidx */
955 smaller = magicints[MAX(FIRSTIDX, smallidx-1)] / 2;
956 small = magicints[smallidx] / 2;
957 sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];
958 larger = magicints[maxidx] / 2;
962 thiscoord = (int *)(luip) + i * 3;
963 if (smallidx < maxidx && i >= 1 &&
964 abs(thiscoord[0] - prevcoord[0]) < larger &&
965 abs(thiscoord[1] - prevcoord[1]) < larger &&
966 abs(thiscoord[2] - prevcoord[2]) < larger) {
968 } else if (smallidx > minidx) {
974 if (abs(thiscoord[0] - thiscoord[3]) < small &&
975 abs(thiscoord[1] - thiscoord[4]) < small &&
976 abs(thiscoord[2] - thiscoord[5]) < small) {
977 /* interchange first with second atom for better
978 * compression of water molecules
980 tmp = thiscoord[0]; thiscoord[0] = thiscoord[3];
982 tmp = thiscoord[1]; thiscoord[1] = thiscoord[4];
984 tmp = thiscoord[2]; thiscoord[2] = thiscoord[5];
990 tmpcoord[0] = thiscoord[0] - minint[0];
991 tmpcoord[1] = thiscoord[1] - minint[1];
992 tmpcoord[2] = thiscoord[2] - minint[2];
994 sendbits(buf, bitsizeint[0], tmpcoord[0]);
995 sendbits(buf, bitsizeint[1], tmpcoord[1]);
996 sendbits(buf, bitsizeint[2], tmpcoord[2]);
998 sendints(buf, 3, bitsize, sizeint, tmpcoord);
1000 prevcoord[0] = thiscoord[0];
1001 prevcoord[1] = thiscoord[1];
1002 prevcoord[2] = thiscoord[2];
1003 thiscoord = thiscoord + 3;
1007 if (is_small == 0 && is_smaller == -1)
1009 while (is_small && run < 8*3) {
1010 if (is_smaller == -1 && (
1011 SQR(thiscoord[0] - prevcoord[0]) +
1012 SQR(thiscoord[1] - prevcoord[1]) +
1013 SQR(thiscoord[2] - prevcoord[2]) >= smaller * smaller)) {
1017 tmpcoord[run++] = thiscoord[0] - prevcoord[0] + small;
1018 tmpcoord[run++] = thiscoord[1] - prevcoord[1] + small;
1019 tmpcoord[run++] = thiscoord[2] - prevcoord[2] + small;
1021 prevcoord[0] = thiscoord[0];
1022 prevcoord[1] = thiscoord[1];
1023 prevcoord[2] = thiscoord[2];
1026 thiscoord = thiscoord + 3;
1029 abs(thiscoord[0] - prevcoord[0]) < small &&
1030 abs(thiscoord[1] - prevcoord[1]) < small &&
1031 abs(thiscoord[2] - prevcoord[2]) < small) {
1035 if (run != prevrun || is_smaller != 0) {
1037 sendbits(buf, 1, 1); /* flag the change in run-length */
1038 sendbits(buf, 5, run+is_smaller+1);
1040 sendbits(buf, 1, 0); /* flag the fact that runlength did not change */
1042 for (k=0; k < run; k+=3) {
1043 sendints(buf, 3, smallidx, sizesmall, &tmpcoord[k]);
1045 if (is_smaller != 0) {
1046 smallidx += is_smaller;
1047 if (is_smaller < 0) {
1049 smaller = magicints[smallidx-1] / 2;
1052 small = magicints[smallidx] / 2;
1054 sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];
1057 if (buf[1] != 0) buf[0]++;;
1058 xdr_int(xdrs, &(buf[0])); /* buf[0] holds the length in bytes */
1059 return errval * (xdr_opaque(xdrs, (caddr_t)&(buf[3]), (u_int)buf[0]));
1062 /* xdrs is open for reading */
1064 if (xdr_int(xdrs, &lsize) == 0)
1066 if (*size != 0 && lsize != *size) {
1067 fprintf(stderr, "wrong number of coordinates in xdr3dfcoor; "
1068 "%d arg vs %d in file", *size, lsize);
1073 return (xdr_vector(xdrs, (char *) fp, size3, sizeof(*fp),
1074 (xdrproc_t)xdr_float));
1076 xdr_float(xdrs, precision);
1078 ip = (int *)malloc(size3 * sizeof(*ip));
1080 fprintf(stderr,"malloc failed\n");
1083 bufsize = size3 * 1.2;
1084 buf = (int *)malloc(bufsize * sizeof(*buf));
1086 fprintf(stderr,"malloc failed\n");
1090 } else if (*size > oldsize) {
1091 ip = (int *)realloc(ip, size3 * sizeof(*ip));
1093 fprintf(stderr,"malloc failed\n");
1096 bufsize = size3 * 1.2;
1097 buf = (int *)realloc(buf, bufsize * sizeof(*buf));
1099 fprintf(stderr,"malloc failed\n");
1104 buf[0] = buf[1] = buf[2] = 0;
1106 xdr_int(xdrs, &(minint[0]));
1107 xdr_int(xdrs, &(minint[1]));
1108 xdr_int(xdrs, &(minint[2]));
1110 xdr_int(xdrs, &(maxint[0]));
1111 xdr_int(xdrs, &(maxint[1]));
1112 xdr_int(xdrs, &(maxint[2]));
1114 sizeint[0] = maxint[0] - minint[0]+1;
1115 sizeint[1] = maxint[1] - minint[1]+1;
1116 sizeint[2] = maxint[2] - minint[2]+1;
1118 /* check if one of the sizes is to big to be multiplied */
1119 if ((sizeint[0] | sizeint[1] | sizeint[2] ) > 0xffffff) {
1120 bitsizeint[0] = sizeofint(sizeint[0]);
1121 bitsizeint[1] = sizeofint(sizeint[1]);
1122 bitsizeint[2] = sizeofint(sizeint[2]);
1123 bitsize = 0; /* flag the use of large sizes */
1125 bitsize = sizeofints(3, sizeint);
1128 xdr_int(xdrs, &smallidx);
1129 maxidx = MIN(LASTIDX, smallidx + 8) ;
1130 minidx = maxidx - 8; /* often this equal smallidx */
1131 smaller = magicints[MAX(FIRSTIDX, smallidx-1)] / 2;
1132 small = magicints[smallidx] / 2;
1133 sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx] ;
1134 larger = magicints[maxidx];
1136 /* buf[0] holds the length in bytes */
1138 if (xdr_int(xdrs, &(buf[0])) == 0)
1140 if (xdr_opaque(xdrs, (caddr_t)&(buf[3]), (u_int)buf[0]) == 0)
1142 buf[0] = buf[1] = buf[2] = 0;
1145 inv_precision = 1.0 / * precision;
1149 while ( i < lsize ) {
1150 thiscoord = (int *)(lip) + i * 3;
1153 thiscoord[0] = receivebits(buf, bitsizeint[0]);
1154 thiscoord[1] = receivebits(buf, bitsizeint[1]);
1155 thiscoord[2] = receivebits(buf, bitsizeint[2]);
1157 receiveints(buf, 3, bitsize, sizeint, thiscoord);
1161 thiscoord[0] += minint[0];
1162 thiscoord[1] += minint[1];
1163 thiscoord[2] += minint[2];
1165 prevcoord[0] = thiscoord[0];
1166 prevcoord[1] = thiscoord[1];
1167 prevcoord[2] = thiscoord[2];
1170 flag = receivebits(buf, 1);
1173 run = receivebits(buf, 5);
1174 is_smaller = run % 3;
1180 for (k = 0; k < run; k+=3) {
1181 receiveints(buf, 3, smallidx, sizesmall, thiscoord);
1183 thiscoord[0] += prevcoord[0] - small;
1184 thiscoord[1] += prevcoord[1] - small;
1185 thiscoord[2] += prevcoord[2] - small;
1187 /* interchange first with second atom for better
1188 * compression of water molecules
1190 tmp = thiscoord[0]; thiscoord[0] = prevcoord[0];
1192 tmp = thiscoord[1]; thiscoord[1] = prevcoord[1];
1194 tmp = thiscoord[2]; thiscoord[2] = prevcoord[2];
1196 *lfp++ = prevcoord[0] * inv_precision;
1197 *lfp++ = prevcoord[1] * inv_precision;
1198 *lfp++ = prevcoord[2] * inv_precision;
1200 prevcoord[0] = thiscoord[0];
1201 prevcoord[1] = thiscoord[1];
1202 prevcoord[2] = thiscoord[2];
1204 *lfp++ = thiscoord[0] * inv_precision;
1205 *lfp++ = thiscoord[1] * inv_precision;
1206 *lfp++ = thiscoord[2] * inv_precision;
1209 *lfp++ = thiscoord[0] * inv_precision;
1210 *lfp++ = thiscoord[1] * inv_precision;
1211 *lfp++ = thiscoord[2] * inv_precision;
1213 smallidx += is_smaller;
1214 if (is_smaller < 0) {
1216 if (smallidx > FIRSTIDX) {
1217 smaller = magicints[smallidx - 1] /2;
1221 } else if (is_smaller > 0) {
1223 small = magicints[smallidx] / 2;
1225 sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx] ;