#include "largefiles.h"#include "dcdlib.h"#include "common.h"#include "Vector.h"#include <stdio.h>#include <string.h>#include <malloc.h>#include <unistd.h>#include <fcntl.h>#include <sys/stat.h>#include <sys/types.h>#include <errno.h>#include <pwd.h>#include <time.h>Go to the source code of this file.
Defines | |
| #define | NAMD_write NAMD_write64 |
| #define | O_LARGEFILE 0x0 |
| #define | CHECK_FREAD(X, msg) |
| #define | CHECK_FEOF(X, msg) |
| #define | NFILE_POS (off_t) 8 |
| #define | NPRIV_POS (off_t) 12 |
| #define | NSAVC_POS (off_t) 16 |
| #define | NSTEP_POS (off_t) 20 |
| #define | LSEEK lseek |
| #define | READ read |
| #define | FBUFSIZE 4096 |
| #define | LSEEK lseek |
| #define | READ read |
Functions | |
| void | NAMD_write (int fd, const char *buf, size_t count) |
| void | pad (char *s, int len) |
| int | open_dcd_read (char *filename) |
| int | open_dcd_write (char *dcdname) |
| int | open_dcd_write_par_slave (char *dcdname) |
| int | write_dcdstep (int fd, int N, float *X, float *Y, float *Z, double *cell) |
| int | write_dcdstep_par_units (int fd, int N, float *X, float *Y, float *Z, double *cell, int unitoffset) |
| int | write_dcdstep_par_header (int fd, int N, float *X, float *Y, float *Z, double *cell) |
| int | write_dcdstep (int fd, int N, FloatVector *coor, double *cell) |
| int | write_dcdstep_par_slave (int fd, int N, float *X, float *Y, float *Z, double *cell, int xoffset, int yoffset, int zoffset) |
| int | write_dcdheader (int fd, char *filename, int N, int NFILE, int NPRIV, int NSAVC, int NSTEP, double DELTA, int with_unitcell) |
| void | close_dcd_read (int fd, int num_fixed, int *indexes) |
| void | close_dcd_write (int fd) |
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Value: if (X==0) \ { \ return(DCD_BADEOF); \ } |
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Value: if (X==-1) \ { \ return(DCD_BADREAD); \ } |
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Referenced by write_dcdstep(), write_dcdstep_par_header(), write_dcdstep_par_slave(), and write_dcdstep_par_units(). |
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Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved. |
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Definition at line 55 of file dcdlib.C. Referenced by open_dcd_read(), and open_dcd_write(). |
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Referenced by write_dcdstep(), and write_dcdstep_par_header(). |
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Definition at line 1082 of file dcdlib.C. 01084 {
01085 #ifdef WIN32
01086 _close(fd);
01087 #else
01088 close(fd);
01089 #endif
01090
01091 if (num_fixed)
01092 {
01093 delete [] indexes;
01094 }
01095 }
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Definition at line 1112 of file dcdlib.C. 01114 {
01115 #ifdef WIN32
01116 _close(fd);
01117 #else
01118 close(fd);
01119 #endif
01120 }
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Definition at line 40 of file dcdlib.C. References NAMD_bug(), and NAMD_die(). 00040 {
00041 while ( count ) {
00042 #if defined(WIN32) && !defined(__CYGWIN__)
00043 long retval = _write(fd,buf,count);
00044 #else
00045 ssize_t retval = write(fd,buf,count);
00046 #endif
00047 if ( retval < 0 ) NAMD_die(strerror(errno));
00048 if ( retval > count ) NAMD_bug("extra bytes written in NAMD_write64()");
00049 buf += retval;
00050 count -= retval;
00051 }
00052 }
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Definition at line 136 of file dcdlib.C. References O_LARGEFILE. 00138 {
00139 struct stat stbuf; /* Stat structure to check file */
00140 int dcdfd; /* file descriptor for dcd file */
00141
00142 /* Do a stat just to see if the file really exists */
00143 if (stat(filename, &stbuf) != 0)
00144 {
00145 if (errno == ENOENT)
00146 {
00147 return(DCD_DNE);
00148 }
00149 }
00150
00151 /* Try and open the file */
00152 #ifdef WIN32
00153 dcdfd=_open(filename, O_RDONLY|O_BINARY|O_LARGEFILE);
00154 #else
00155 dcdfd=open(filename, O_RDONLY|O_LARGEFILE);
00156 #endif
00157
00158 if (dcdfd == -1)
00159 {
00160 return(DCD_OPENFAILED);
00161 }
00162
00163 return(dcdfd);
00164 }
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Definition at line 638 of file dcdlib.C. References DCD_OPENFAILED, and O_LARGEFILE. 00640 {
00641 struct stat sbuf;
00642 int dcdfd;
00643 char *newdcdname = 0;
00644
00645 if (stat(dcdname, &sbuf) == 0)
00646 {
00647 newdcdname = new char[strlen(dcdname)+5];
00648 if(newdcdname == (char *) 0)
00649 return DCD_OPENFAILED;
00650 strcpy(newdcdname, dcdname);
00651 strcat(newdcdname, ".BAK");
00652 #if defined(WIN32) && !defined(__CYGWIN__)
00653 remove(newdcdname);
00654 #endif
00655 if(rename(dcdname, newdcdname))
00656 return(DCD_OPENFAILED);
00657 delete [] newdcdname;
00658 }
00659 #ifdef WIN32
00660 if ( (dcdfd = _open(dcdname, O_RDWR|O_CREAT|O_EXCL|O_BINARY|O_LARGEFILE,
00661 _S_IREAD|_S_IWRITE)) < 0)
00662 #else
00663 #ifdef NAMD_NO_O_EXCL
00664 if ( (dcdfd = open(dcdname, O_RDWR|O_CREAT|O_TRUNC|O_LARGEFILE,
00665 #else
00666 if ( (dcdfd = open(dcdname, O_RDWR|O_CREAT|O_EXCL|O_LARGEFILE,
00667 #endif
00668 S_IRUSR|S_IWUSR|S_IRGRP|S_IROTH)) < 0)
00669 #endif
00670 {
00671 return(DCD_OPENFAILED);
00672 }
00673
00674 return(dcdfd);
00675 }
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Definition at line 680 of file dcdlib.C. 00682 {
00683 struct stat sbuf;
00684 int dcdfd;
00685 #ifdef WIN32
00686 if ( (dcdfd = _open(dcdname, O_RDWR|O_BINARY|O_LARGEFILE,
00687 _S_IREAD|_S_IWRITE)) < 0)
00688 #else
00689
00690 if ( (dcdfd = open(dcdname, O_RDWR|O_LARGEFILE,
00691 S_IRUSR|S_IWUSR|S_IRGRP|S_IROTH)) < 0)
00692 #endif
00693 {
00694 return(DCD_OPENFAILED);
00695 }
00696
00697 return(dcdfd);
00698 }
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Definition at line 96 of file dcdlib.C. 00097 {
00098 int curlen;
00099 int i;
00100
00101 curlen=strlen(s);
00102
00103 if (curlen>len)
00104 {
00105 s[len]='\0';
00106 return;
00107 }
00108
00109 for (i=curlen; i<len; i++)
00110 {
00111 s[i]=' ';
00112 }
00113
00114 s[i]='\0';
00115 }
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Definition at line 973 of file dcdlib.C. 00975 {
00976 int32 out_integer;
00977 float out_float;
00978 char title_string[200];
00979 int user_id;
00980 #ifndef WIN32
00981 struct passwd *pwbuf;
00982 #endif
00983 time_t cur_time;
00984 struct tm *tmbuf;
00985 char time_str[11];
00986
00987 out_integer = 84;
00988 NAMD_write(fd, (char *) & out_integer, sizeof(int32));
00989 strcpy(title_string, "CORD");
00990 NAMD_write(fd, title_string, 4);
00991 out_integer = NFILE; /* located at fpos 8 */
00992 out_integer = 0; /* ignore the lies */
00993 NAMD_write(fd, (char *) & out_integer, sizeof(int32));
00994 out_integer = NPRIV; /* located at fpos 12 */
00995 NAMD_write(fd, (char *) & out_integer, sizeof(int32));
00996 out_integer = NSAVC; /* located at fpos 16 */
00997 NAMD_write(fd, (char *) & out_integer, sizeof(int32));
00998 out_integer = NSTEP; /* located at fpos 20 */
00999 out_integer = NPRIV - NSAVC; /* ignore the lies */
01000 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
01001 out_integer=0;
01002 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
01003 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
01004 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
01005 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
01006 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
01007 out_float = DELTA;
01008 NAMD_write(fd, (char *) &out_float, sizeof(float));
01009 out_integer = with_unitcell ? 1 : 0;
01010 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
01011 out_integer = 0;
01012 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
01013 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
01014 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
01015 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
01016 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
01017 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
01018 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
01019 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
01020 out_integer = 24; // PRETEND TO BE CHARMM24 -JCP
01021 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
01022 out_integer = 84;
01023 NAMD_write(fd, (char *) & out_integer, sizeof(int32));
01024
01025 out_integer = 164;
01026 NAMD_write(fd, (char *) & out_integer, sizeof(int32));
01027 out_integer = 2;
01028 NAMD_write(fd, (char *) & out_integer, sizeof(int32));
01029
01030 sprintf(title_string, "REMARKS FILENAME=%s CREATED BY NAMD", filename);
01031 pad(title_string, 80);
01032 NAMD_write(fd, title_string, 80);
01033
01034 char username[100];
01035 #if defined(WIN32) || defined(NO_GETPWUID)
01036 sprintf(username,"Win32");
01037 #else
01038 user_id= (int) getuid();
01039 pwbuf=getpwuid(user_id);
01040 if ( pwbuf ) sprintf(username,"%s",pwbuf->pw_name);
01041 else sprintf(username,"%d",user_id);
01042 #endif
01043 cur_time=time(NULL);
01044 tmbuf=localtime(&cur_time);
01045 strftime(time_str, 10, "%m/%d/%y", tmbuf);
01046
01047 sprintf(title_string, "REMARKS DATE: %s CREATED BY USER: %s",
01048 time_str, username);
01049 pad(title_string, 80);
01050 NAMD_write(fd, title_string, 80);
01051 out_integer = 164;
01052 NAMD_write(fd, (char *) & out_integer, sizeof(int32));
01053 out_integer = 4;
01054 NAMD_write(fd, (char *) & out_integer, sizeof(int32));
01055 out_integer = N;
01056 NAMD_write(fd, (char *) & out_integer, sizeof(int32));
01057 out_integer = 4;
01058 NAMD_write(fd, (char *) & out_integer, sizeof(int32));
01059
01060 return(0);
01061 }
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Definition at line 842 of file dcdlib.C. 00844 {
00845 int32 NSAVC,NSTEP,NFILE;
00846 int32 out_integer;
00847
00848 /* Unit cell */
00849 if (cell) {
00850 out_integer = 48;
00851 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00852 NAMD_write(fd, (char *) cell, out_integer);
00853 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00854 }
00855
00856 /* Coordinates */
00857 #define FBUFSIZE 4096
00858 float fBuf[FBUFSIZE];
00859
00860 int32 remains = N;
00861 int32 coorstart = 0;
00862
00863 out_integer = N*4;
00864 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00865 //writing X-coor in batch mode
00866 while(remains>0){
00867 int32 writesize = FBUFSIZE;
00868 if(remains<FBUFSIZE) writesize=remains;
00869 for(int i=0; i<writesize; i++)
00870 fBuf[i] = coor[i+coorstart].x;
00871 NAMD_write(fd, (char *)fBuf, writesize*4);
00872 coorstart += writesize;
00873 remains -= FBUFSIZE;
00874 }
00875 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00876
00877 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00878 //writing Y-coor in batch mode
00879 remains = N;
00880 coorstart = 0;
00881 while(remains>0){
00882 int32 writesize = FBUFSIZE;
00883 if(remains<FBUFSIZE) writesize=remains;
00884 for(int i=0; i<writesize; i++)
00885 fBuf[i] = coor[i+coorstart].y;
00886 NAMD_write(fd, (char *)fBuf, writesize*4);
00887 coorstart += writesize;
00888 remains -= FBUFSIZE;
00889 }
00890 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00891
00892 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00893 //writing Z-coor in batch mode
00894 remains = N;
00895 coorstart = 0;
00896 while(remains>0){
00897 int32 writesize = FBUFSIZE;
00898 if(remains<FBUFSIZE) writesize=remains;
00899 for(int i=0; i<writesize; i++)
00900 fBuf[i] = coor[i+coorstart].z;
00901 NAMD_write(fd, (char *)fBuf, writesize*4);
00902 coorstart += writesize;
00903 remains -= FBUFSIZE;
00904 }
00905 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00906
00907 #ifdef WIN32
00908 #define LSEEK _lseek
00909 #define READ _read
00910 #else
00911 #define LSEEK lseek
00912 #define READ read
00913 #endif
00914
00915 /* don't update header until after write succeeds */
00916
00917 LSEEK(fd,NSAVC_POS,SEEK_SET);
00918 READ(fd,(void*) &NSAVC,sizeof(int32));
00919 LSEEK(fd,NSTEP_POS,SEEK_SET);
00920 READ(fd,(void*) &NSTEP,sizeof(int32));
00921 LSEEK(fd,NFILE_POS,SEEK_SET);
00922 READ(fd,(void*) &NFILE,sizeof(int32));
00923 NSTEP += NSAVC;
00924 NFILE += 1;
00925 LSEEK(fd,NSTEP_POS,SEEK_SET);
00926 NAMD_write(fd,(char*) &NSTEP,sizeof(int32));
00927 LSEEK(fd,NFILE_POS,SEEK_SET);
00928 NAMD_write(fd,(char*) &NFILE,sizeof(int32));
00929 LSEEK(fd,0,SEEK_END);
00930 return(0);
00931 }
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Definition at line 720 of file dcdlib.C. 00722 {
00723 int32 NSAVC,NSTEP,NFILE;
00724 int32 out_integer;
00725
00726 /* Unit cell */
00727 if (cell) {
00728 out_integer = 48;
00729 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00730 NAMD_write(fd, (char *) cell, out_integer);
00731 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00732 }
00733
00734 /* Coordinates */
00735 out_integer = N*4;
00736 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00737 NAMD_write(fd, (char *) X, out_integer);
00738 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00739 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00740 NAMD_write(fd, (char *) Y, out_integer);
00741 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00742 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00743 NAMD_write(fd, (char *) Z, out_integer);
00744 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00745
00746 #ifdef WIN32
00747 #define LSEEK _lseek
00748 #define READ _read
00749 #else
00750 #define LSEEK lseek
00751 #define READ read
00752 #endif
00753
00754 /* don't update header until after write succeeds */
00755 LSEEK(fd,NSAVC_POS,SEEK_SET);
00756 READ(fd,(void*) &NSAVC,sizeof(int32));
00757 LSEEK(fd,NSTEP_POS,SEEK_SET);
00758 READ(fd,(void*) &NSTEP,sizeof(int32));
00759 LSEEK(fd,NFILE_POS,SEEK_SET);
00760 READ(fd,(void*) &NFILE,sizeof(int32));
00761 NSTEP += NSAVC;
00762 NFILE += 1;
00763 LSEEK(fd,NSTEP_POS,SEEK_SET);
00764 NAMD_write(fd,(char*) &NSTEP,sizeof(int32));
00765 LSEEK(fd,NFILE_POS,SEEK_SET);
00766 NAMD_write(fd,(char*) &NFILE,sizeof(int32));
00767 LSEEK(fd,0,SEEK_END);
00768
00769 return(0);
00770 }
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Definition at line 820 of file dcdlib.C. 00821 {
00822 int32 NSAVC,NSTEP,NFILE;
00823 /* don't update header until after write succeeds */
00824 LSEEK(fd,NSAVC_POS,SEEK_SET);
00825 READ(fd,(void*) &NSAVC,sizeof(int32));
00826 LSEEK(fd,NSTEP_POS,SEEK_SET);
00827 READ(fd,(void*) &NSTEP,sizeof(int32));
00828 LSEEK(fd,NFILE_POS,SEEK_SET);
00829 READ(fd,(void*) &NFILE,sizeof(int32));
00830 NSTEP += NSAVC;
00831 NFILE += 1;
00832 LSEEK(fd,NSTEP_POS,SEEK_SET);
00833 NAMD_write(fd,(char*) &NSTEP,sizeof(int32));
00834 LSEEK(fd,NFILE_POS,SEEK_SET);
00835 NAMD_write(fd,(char*) &NFILE,sizeof(int32));
00836 LSEEK(fd,0,SEEK_END);
00837
00838 return(0);
00839 }
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Definition at line 934 of file dcdlib.C. References LSEEK. 00936 {
00937 int32 out_integer;
00938 /* Coordinates for the N elements handled by this writer */
00939 out_integer = N*4;
00940 LSEEK(fd, xoffset, SEEK_SET);
00941 NAMD_write(fd, (char *) X, out_integer);
00942 LSEEK(fd, yoffset, SEEK_SET);
00943 NAMD_write(fd, (char *) Y, out_integer);
00944 LSEEK(fd, zoffset, SEEK_SET);
00945 NAMD_write(fd, (char *) Z, out_integer);
00946 return(0);
00947 }
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Definition at line 789 of file dcdlib.C. References LSEEK. 00791 {
00792 int32 NSAVC,NSTEP,NFILE;
00793 int32 out_integer;
00794
00795 /* Unit cell */
00796 if (cell) {
00797 LSEEK(fd, unitoffset, SEEK_SET);
00798 out_integer = 48;
00799 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00800 NAMD_write(fd, (char *) cell, out_integer);
00801 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00802 }
00803 // number of elements
00804 out_integer = N*4;
00805 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00806 // seek to the end of each x y z block and write out the count
00807 LSEEK(fd, out_integer, SEEK_SET);
00808 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00809 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00810 LSEEK(fd, out_integer, SEEK_SET);
00811 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00812 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00813 LSEEK(fd, out_integer, SEEK_SET);
00814 NAMD_write(fd, (char *) &out_integer, sizeof(int32));
00815 return(0);
00816 }
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1.3.9.1