NAMD
Macros | Functions
dcdlib.C File Reference
#include "dcdlib.h"

Go to the source code of this file.

Macros

#define OUTPUT_SINGLE_FILE   1
 
#define NAMD_write   NAMD_write64
 
#define LSEEK   lseek
 
#define READ   read
 
#define LSEEK   NAMD_seek
 
#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)
 

Functions

void NAMD_write (int fd, const char *buf, size_t count)
 
OFF_T NAMD_seek (int file, OFF_T offset, int whence)
 
void pad (char *s, int len)
 
int open_dcd_read (char *filename)
 
int open_dcd_write (const 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_cell (int fd, double *cell)
 
int write_dcdstep_par_XYZUnits (int fd, int N)
 
int update_dcdstep_par_header (int fd)
 
int write_dcdstep_par_slave (int fd, int parL, int parU, int N, float *X, float *Y, float *Z)
 
int write_dcdheader (int fd, const char *filename, int N, int NFILE, int NPRIV, int NSAVC, int NSTEP, double DELTA, int with_unitcell)
 
int get_dcdheader_size ()
 
void close_dcd_read (int fd, int num_fixed, int *indexes)
 
void close_dcd_write (int fd)
 

Macro Definition Documentation

#define CHECK_FEOF (   X,
  msg 
)
Value:
if (X==0) \
{ \
return(DCD_BADEOF); \
}
#define X
Definition: msm_defn.h:29
#define DCD_BADEOF
Definition: dcdlib.h:50

Definition at line 97 of file dcdlib.C.

#define CHECK_FREAD (   X,
  msg 
)
Value:
if (X==-1) \
{ \
return(DCD_BADREAD); \
}
#define X
Definition: msm_defn.h:29
#define DCD_BADREAD
Definition: dcdlib.h:49

Definition at line 80 of file dcdlib.C.

#define LSEEK   lseek
#define LSEEK   NAMD_seek

Definition at line 61 of file dcdlib.C.

#define NAMD_write   NAMD_write64
#define NFILE_POS   ((OFF_T) 8)

Definition at line 628 of file dcdlib.C.

Referenced by update_dcdstep_par_header(), and write_dcdstep().

#define NPRIV_POS   ((OFF_T) 12)

Definition at line 629 of file dcdlib.C.

#define NSAVC_POS   ((OFF_T) 16)

Definition at line 630 of file dcdlib.C.

Referenced by update_dcdstep_par_header(), and write_dcdstep().

#define NSTEP_POS   ((OFF_T) 20)

Definition at line 631 of file dcdlib.C.

Referenced by update_dcdstep_par_header(), and write_dcdstep().

#define O_LARGEFILE   0x0

Definition at line 64 of file dcdlib.C.

Referenced by open_dcd_read(), open_dcd_write(), and open_dcd_write_par_slave().

#define OUTPUT_SINGLE_FILE   1

Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved.

Definition at line 16 of file dcdlib.C.

#define READ   read

Definition at line 46 of file dcdlib.C.

Referenced by update_dcdstep_par_header(), and write_dcdstep().

Function Documentation

void close_dcd_read ( int  fd,
int  num_fixed,
int *  indexes 
)

Definition at line 1033 of file dcdlib.C.

1035 {
1036 #ifdef WIN32
1037  _close(fd);
1038 #else
1039  close(fd);
1040 #endif
1041 
1042  if (num_fixed)
1043  {
1044  delete [] indexes;
1045  }
1046 }
void close_dcd_write ( int  fd)

Definition at line 1063 of file dcdlib.C.

References NAMD_err().

Referenced by Output::recvReplicaDcdInit(), and ComputeQMMgr::~ComputeQMMgr().

1065 {
1066 #ifdef WIN32
1067  if ( _close(fd) )
1068 #else
1069  if ( fsync(fd) || close(fd) )
1070 #endif
1071  {
1072  NAMD_err("Error closing DCD file");
1073  }
1074 }
void NAMD_err(const char *err_msg)
Definition: common.C:102
int get_dcdheader_size ( )

Definition at line 1005 of file dcdlib.C.

1005  {
1006  int headersize = 0;
1007  int totalInt32s = 27; /* 27 writes from out_integer */
1008  int totalChars = 164; /* 3 writes from title_string */
1009  int totalFloats = 1; /* 1 write from out_float */
1010  headersize = sizeof(int32)*totalInt32s+totalChars+sizeof(float)*totalFloats;
1011  return headersize;
1012 }
short int32
Definition: dumpdcd.c:24
OFF_T NAMD_seek ( int  file,
OFF_T  offset,
int  whence 
)

Definition at line 49 of file dcdlib.C.

References LSEEK, NAMD_die(), NAMD_err(), and OFF_T.

49  {
50  OFF_T retval = LSEEK(file, offset, whence);
51  if ( retval < 0 ) NAMD_err("seek failed while writing DCD file");
52  if ( whence == SEEK_SET && retval != offset ) {
53  char buf[256];
54  sprintf(buf, "seek failed while writing DCD file: SEEK_SET %lld returned %lld\n", offset, retval);
55  NAMD_die(buf);
56  }
57  return retval;
58 }
#define OFF_T
Definition: dcdlib.h:42
void NAMD_err(const char *err_msg)
Definition: common.C:102
void NAMD_die(const char *err_msg)
Definition: common.C:83
#define LSEEK
Definition: dcdlib.C:61
void NAMD_write ( int  fd,
const char *  buf,
size_t  count 
)

Definition at line 26 of file dcdlib.C.

References NAMD_bug(), and NAMD_die().

26  {
27  while ( count ) {
28 #if defined(WIN32) && !defined(__CYGWIN__)
29  long retval = _write(fd,buf,count);
30 #else
31  ssize_t retval = write(fd,buf,count);
32 #endif
33  if ( retval < 0 && errno == EINTR ) retval = 0;
34  if ( retval < 0 ) NAMD_die(strerror(errno));
35  if ( retval > count ) NAMD_bug("extra bytes written in NAMD_write64()");
36  buf += retval;
37  count -= retval;
38  }
39 }
void NAMD_bug(const char *err_msg)
Definition: common.C:123
void NAMD_die(const char *err_msg)
Definition: common.C:83
int open_dcd_read ( char *  filename)

Definition at line 145 of file dcdlib.C.

References DCD_DNE, DCD_OPENFAILED, and O_LARGEFILE.

147 {
148  int dcdfd; /* file descriptor for dcd file */
149 
150  /* Do a stat just to see if the file really exists */
151  if (access(filename, F_OK) != 0)
152  {
153  if (errno == ENOENT)
154  {
155  return(DCD_DNE);
156  }
157  }
158 
159  /* Try and open the file */
160 #ifdef WIN32
161  dcdfd=_open(filename, O_RDONLY|O_BINARY|O_LARGEFILE);
162 #else
163  dcdfd=open(filename, O_RDONLY|O_LARGEFILE);
164 #endif
165 
166  if (dcdfd == -1)
167  {
168  return(DCD_OPENFAILED);
169  }
170 
171  return(dcdfd);
172 }
#define O_LARGEFILE
Definition: dcdlib.C:64
#define DCD_DNE
Definition: dcdlib.h:47
#define DCD_OPENFAILED
Definition: dcdlib.h:48
int open_dcd_write ( const char *  dcdname)

Definition at line 662 of file dcdlib.C.

References DCD_OPENFAILED, NAMD_backup_file(), and O_LARGEFILE.

Referenced by open_dcd_write_par_slave(), ComputeQMMgr::recvPartQM(), and Output::recvReplicaDcdData().

664 {
665  int dcdfd;
666  NAMD_backup_file(dcdname,".BAK");
667 
668 #ifdef WIN32
669  while ( (dcdfd = _open(dcdname, O_RDWR|O_CREAT|O_EXCL|O_BINARY|O_LARGEFILE,
670  _S_IREAD|_S_IWRITE)) < 0)
671 #else
672 #ifdef NAMD_NO_O_EXCL
673  while ( (dcdfd = open(dcdname, O_RDWR|O_CREAT|O_TRUNC|O_LARGEFILE,
674 #else
675  while ( (dcdfd = open(dcdname, O_RDWR|O_CREAT|O_EXCL|O_LARGEFILE,
676 #endif
677  S_IRUSR|S_IWUSR|S_IRGRP|S_IROTH)) < 0)
678 #endif
679  {
680  if ( errno != EINTR ) return(DCD_OPENFAILED);
681  }
682 
683  return(dcdfd);
684 }
#define O_LARGEFILE
Definition: dcdlib.C:64
void NAMD_backup_file(const char *filename, const char *extension)
Definition: common.C:159
#define DCD_OPENFAILED
Definition: dcdlib.h:48
int open_dcd_write_par_slave ( char *  dcdname)

Definition at line 689 of file dcdlib.C.

References DCD_OPENFAILED, O_LARGEFILE, and open_dcd_write().

691 {
692 #if OUTPUT_SINGLE_FILE
693  //In the case of single file, the dcd output by slaves has been created
694  //by the master, so the dcd file doesn't need to be created again and
695  //backed up. --Chao Mei
696  int dcdfd;
697 #ifdef WIN32
698  while ( (dcdfd = _open(dcdname, O_WRONLY|O_BINARY|O_LARGEFILE,
699  _S_IREAD|_S_IWRITE)) < 0)
700 #else
701  while ( (dcdfd = open(dcdname, O_WRONLY|O_LARGEFILE,
702  S_IRUSR|S_IWUSR|S_IRGRP|S_IROTH)) < 0)
703 #endif
704  {
705  if ( errno != EINTR ) return(DCD_OPENFAILED);
706  }
707 
708  return(dcdfd);
709 #else
710  //In the case of multiple output files, each slave has its own output file and
711  //it needs to be created. --Chao Mei
712  return open_dcd_write(dcdname);
713 #endif
714 }
#define O_LARGEFILE
Definition: dcdlib.C:64
int open_dcd_write(const char *dcdname)
Definition: dcdlib.C:662
#define DCD_OPENFAILED
Definition: dcdlib.h:48
void pad ( char *  s,
int  len 
)

Definition at line 105 of file dcdlib.C.

Referenced by write_dcdheader().

106 {
107  int curlen;
108  int i;
109 
110  curlen=strlen(s);
111 
112  if (curlen>len)
113  {
114  s[len]='\0';
115  return;
116  }
117 
118  for (i=curlen; i<len; i++)
119  {
120  s[i]=' ';
121  }
122 
123  s[i]='\0';
124 }
int update_dcdstep_par_header ( int  fd)

Definition at line 839 of file dcdlib.C.

References LSEEK, NAMD_write, NFILE_POS, NSAVC_POS, NSTEP_POS, OFF_T, and READ.

840 {
841  int32 NSAVC,NSTEP,NFILE;
842  /* don't update header until after write succeeds */
843  OFF_T end = LSEEK(fd,0,SEEK_CUR);
844  LSEEK(fd,NSAVC_POS,SEEK_SET);
845  READ(fd,(void*) &NSAVC,sizeof(int32));
846  LSEEK(fd,NSTEP_POS,SEEK_SET);
847  READ(fd,(void*) &NSTEP,sizeof(int32));
848  LSEEK(fd,NFILE_POS,SEEK_SET);
849  READ(fd,(void*) &NFILE,sizeof(int32));
850  NSTEP += NSAVC;
851  NFILE += 1;
852  LSEEK(fd,NSTEP_POS,SEEK_SET);
853  NAMD_write(fd,(char*) &NSTEP,sizeof(int32));
854  LSEEK(fd,NFILE_POS,SEEK_SET);
855  NAMD_write(fd,(char*) &NFILE,sizeof(int32));
856  LSEEK(fd,end,SEEK_SET);
857 
858  return(0);
859 }
#define OFF_T
Definition: dcdlib.h:42
#define NSAVC_POS
Definition: dcdlib.C:630
short int32
Definition: dumpdcd.c:24
#define NAMD_write
Definition: dcdlib.C:24
#define READ
Definition: dcdlib.C:46
#define NFILE_POS
Definition: dcdlib.C:628
#define NSTEP_POS
Definition: dcdlib.C:631
#define LSEEK
Definition: dcdlib.C:61
int write_dcdheader ( int  fd,
const char *  filename,
int  N,
int  NFILE,
int  NPRIV,
int  NSAVC,
int  NSTEP,
double  DELTA,
int  with_unitcell 
)

Definition at line 915 of file dcdlib.C.

References NAMD_write, and pad().

Referenced by ComputeQMMgr::recvPartQM(), and Output::recvReplicaDcdData().

917 {
918  int32 out_integer;
919  float out_float;
920  char title_string[200];
921  int user_id;
922 #ifndef WIN32
923  struct passwd *pwbuf;
924 #endif
925  time_t cur_time;
926  struct tm *tmbuf;
927  char time_str[11];
928 
929  out_integer = 84;
930  NAMD_write(fd, (char *) & out_integer, sizeof(int32));
931  strcpy(title_string, "CORD");
932  NAMD_write(fd, title_string, 4);
933  out_integer = NFILE; /* located at fpos 8 */
934  out_integer = 0; /* ignore the lies */
935  NAMD_write(fd, (char *) & out_integer, sizeof(int32));
936  out_integer = NPRIV; /* located at fpos 12 */
937  NAMD_write(fd, (char *) & out_integer, sizeof(int32));
938  out_integer = NSAVC; /* located at fpos 16 */
939  NAMD_write(fd, (char *) & out_integer, sizeof(int32));
940  out_integer = NSTEP; /* located at fpos 20 */
941  out_integer = NPRIV - NSAVC; /* ignore the lies */
942  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
943  out_integer=0;
944  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
945  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
946  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
947  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
948  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
949  out_float = DELTA;
950  NAMD_write(fd, (char *) &out_float, sizeof(float));
951  out_integer = with_unitcell ? 1 : 0;
952  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
953  out_integer = 0;
954  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
955  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
956  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
957  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
958  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
959  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
960  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
961  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
962  out_integer = 24; // PRETEND TO BE CHARMM24 -JCP
963  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
964  out_integer = 84;
965  NAMD_write(fd, (char *) & out_integer, sizeof(int32));
966 
967  out_integer = 164;
968  NAMD_write(fd, (char *) & out_integer, sizeof(int32));
969  out_integer = 2;
970  NAMD_write(fd, (char *) & out_integer, sizeof(int32));
971 
972  sprintf(title_string, "REMARKS FILENAME=%s CREATED BY NAMD", filename);
973  pad(title_string, 80);
974  NAMD_write(fd, title_string, 80);
975 
976  char username[100];
977 #if defined(WIN32) || defined(NO_GETPWUID)
978  sprintf(username,"Win32");
979 #else
980  user_id= (int) getuid();
981  pwbuf=getpwuid(user_id);
982  if ( pwbuf ) sprintf(username,"%s",pwbuf->pw_name);
983  else sprintf(username,"%d",user_id);
984 #endif
985  cur_time=time(NULL);
986  tmbuf=localtime(&cur_time);
987  strftime(time_str, 10, "%m/%d/%y", tmbuf);
988 
989  sprintf(title_string, "REMARKS DATE: %s CREATED BY USER: %s",
990  time_str, username);
991  pad(title_string, 80);
992  NAMD_write(fd, title_string, 80);
993  out_integer = 164;
994  NAMD_write(fd, (char *) & out_integer, sizeof(int32));
995  out_integer = 4;
996  NAMD_write(fd, (char *) & out_integer, sizeof(int32));
997  out_integer = N;
998  NAMD_write(fd, (char *) & out_integer, sizeof(int32));
999  out_integer = 4;
1000  NAMD_write(fd, (char *) & out_integer, sizeof(int32));
1001 
1002  return(0);
1003 }
short int32
Definition: dumpdcd.c:24
#define NAMD_write
Definition: dcdlib.C:24
void pad(char *s, int len)
Definition: dcdlib.C:105
int write_dcdstep ( int  fd,
int  N,
float *  X,
float *  Y,
float *  Z,
double *  cell 
)

Definition at line 736 of file dcdlib.C.

References LSEEK, NAMD_write, NFILE_POS, NSAVC_POS, NSTEP_POS, OFF_T, and READ.

Referenced by ComputeQMMgr::procQMRes(), and Output::recvReplicaDcdData().

738 {
739  int32 NSAVC,NSTEP,NFILE;
740  int32 out_integer;
741 
742  /* Unit cell */
743  if (cell) {
744  out_integer = 48;
745  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
746  NAMD_write(fd, (char *) cell, out_integer);
747  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
748  }
749 
750  /* Coordinates */
751  // Note: the value of out_integer wraps for N >= 2^30.
752  out_integer = N*4;
753  // Use a separate byte count stored without overflow.
754  size_t nbytes = ((size_t) N) * 4;
755 
756  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
757  NAMD_write(fd, (char *) X, nbytes);
758  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
759  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
760  NAMD_write(fd, (char *) Y, nbytes);
761  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
762  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
763  NAMD_write(fd, (char *) Z, nbytes);
764  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
765 
766  /* don't update header until after write succeeds */
767  OFF_T end = LSEEK(fd,0,SEEK_CUR);
768  LSEEK(fd,NSAVC_POS,SEEK_SET);
769  READ(fd,(void*) &NSAVC,sizeof(int32));
770  LSEEK(fd,NSTEP_POS,SEEK_SET);
771  READ(fd,(void*) &NSTEP,sizeof(int32));
772  LSEEK(fd,NFILE_POS,SEEK_SET);
773  READ(fd,(void*) &NFILE,sizeof(int32));
774  NSTEP += NSAVC;
775  NFILE += 1;
776  LSEEK(fd,NSTEP_POS,SEEK_SET);
777  NAMD_write(fd,(char*) &NSTEP,sizeof(int32));
778  LSEEK(fd,NFILE_POS,SEEK_SET);
779  NAMD_write(fd,(char*) &NFILE,sizeof(int32));
780  LSEEK(fd,end,SEEK_SET);
781 
782  return(0);
783 }
#define OFF_T
Definition: dcdlib.h:42
#define NSAVC_POS
Definition: dcdlib.C:630
short int32
Definition: dumpdcd.c:24
#define X
Definition: msm_defn.h:29
#define NAMD_write
Definition: dcdlib.C:24
#define Z
Definition: msm_defn.h:33
#define READ
Definition: dcdlib.C:46
#define NFILE_POS
Definition: dcdlib.C:628
#define NSTEP_POS
Definition: dcdlib.C:631
#define Y
Definition: msm_defn.h:31
#define LSEEK
Definition: dcdlib.C:61
int write_dcdstep_par_cell ( int  fd,
double *  cell 
)

Definition at line 785 of file dcdlib.C.

References NAMD_write.

785  {
786  if (cell) {
787  int32 out_integer = 48;
788  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
789  NAMD_write(fd, (char *) cell, out_integer);
790  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
791  }
792  return 0;
793 }
short int32
Definition: dumpdcd.c:24
#define NAMD_write
Definition: dcdlib.C:24
int write_dcdstep_par_slave ( int  fd,
int  parL,
int  parU,
int  N,
float *  X,
float *  Y,
float *  Z 
)

Definition at line 864 of file dcdlib.C.

References LSEEK, NAMD_write, and OFF_T.

864  {
865 
866  /* Coordinates for the N elements handled by this writer */
867  int parN = parU-parL+1;
868  size_t nbytes = ((size_t)parN) * 4;
869 
870  /* x's 1st number of Xs */
871  /* skip field for the bytes in X, and the first parL atoms in X*/
872  OFF_T xoffset = sizeof(int)+sizeof(float)*((OFF_T)parL);
873  LSEEK(fd, xoffset, SEEK_CUR);
874  NAMD_write(fd, (char *) X, nbytes);
875 
876  /* skip field for the bytes in X and Y; */
877  /* skip the remaining atoms in X at number of (N-1)-(parU+1)+1
878  * where N-1 is the last atom id, paru+1 is the next atom id. */
879  /* skip the first parL atoms in Y; */
880  OFF_T yoffset = 2*sizeof(int)+sizeof(float)*((OFF_T)(N-parU+parL-1));
881  LSEEK(fd, yoffset, SEEK_CUR);
882  NAMD_write(fd, (char *) Y, nbytes);
883 
884  OFF_T zoffset = yoffset;
885  LSEEK(fd, zoffset, SEEK_CUR);
886  NAMD_write(fd, (char *) Z, nbytes);
887  return(0);
888 }
#define OFF_T
Definition: dcdlib.h:42
#define X
Definition: msm_defn.h:29
#define NAMD_write
Definition: dcdlib.C:24
#define Z
Definition: msm_defn.h:33
#define Y
Definition: msm_defn.h:31
#define LSEEK
Definition: dcdlib.C:61
int write_dcdstep_par_XYZUnits ( int  fd,
int  N 
)

Definition at line 810 of file dcdlib.C.

References LSEEK, NAMD_write, and OFF_T.

811 {
812  int32 out_integer;
813 
814  // number of elements
815  // Note: the value of out_integer wraps for N >= 2^30.
816  out_integer = N*sizeof(float);
817 
818  // For byte seeking, use a properly sized variable.
819  OFF_T nbytes = ((OFF_T) N) * sizeof(float);
820 
821  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
822  // seek to the end of each x y z block and write out the count
823  LSEEK(fd, nbytes, SEEK_CUR);
824  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
825 
826  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
827  LSEEK(fd, nbytes, SEEK_CUR);
828  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
829 
830  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
831  LSEEK(fd, nbytes, SEEK_CUR);
832  NAMD_write(fd, (char *) &out_integer, sizeof(int32));
833 
834  return(0);
835 }
#define OFF_T
Definition: dcdlib.h:42
short int32
Definition: dumpdcd.c:24
#define NAMD_write
Definition: dcdlib.C:24
#define LSEEK
Definition: dcdlib.C:61