NAMD: common.h File Reference

00272 {
00273   int rc = -1;
00274 #if !defined(NOCOMPRESSED)
00275   rc = pclose(fout);
00276 #endif
00277   if (rc == -1) // stream not associated with a popen()
00278     {
00279     rc = fclose(fout);
00280     }
00281   return rc;
00282 } /* Fclose() */

00178 {
00179   struct stat buf;
00180   // check if basic filename exists (and not a directory)
00181 
00182 #if defined(NOCOMPRESSED)
00183   if (!stat(filename,&buf))
00184     {
00185       FILE *rval;
00186       while ( ! (rval = fopen(filename,mode)) ) {
00187         if ( errno != EINTR ) break;
00188       }
00189       return(rval);
00190     }
00191 #else
00192   if (!stat(filename,&buf))
00193     {
00194       if (!S_ISDIR(buf.st_mode)) {
00195         FILE *rval;
00196         while ( ! (rval = fopen(filename,mode)) ) {
00197           if ( errno != EINTR ) break;
00198         }
00199         return(rval);
00200       }
00201     }
00202   // check for a compressed file
00203   char *realfilename;
00204   char *command;
00205   FILE *fout;
00206   command = (char *)malloc(strlen(filename)+25);
00207   // check for .Z (unix compress)
00208   sprintf(command,"zcat %s.Z",filename);
00209   realfilename = command+5;
00210   iout << "Command = " << command << "\n" << endi;
00211   iout << "Filename.Z = " << realfilename << "\n" << endi;
00212   if (!stat(realfilename,&buf))
00213         {
00214         if (!S_ISDIR(buf.st_mode))
00215                 {
00216                 fout = popen(command,mode);
00217                 // on HP-UX, the first character(s) out of pipe may be
00218                 // garbage!  (Argh!)
00219                 int C;
00220                 do
00221                   {
00222                   C = fgetc(fout);
00223                   // iout << "C is " << C << "\n" << endi;
00224                   if (isalnum(C) || isspace(C))
00225                         {
00226                         ungetc(C,fout);
00227                         C = -1; // outta loop
00228                         }
00229                   } while(C != -1);
00230                 free(command);
00231                 return(fout);
00232                 }
00233         }
00234   // check for .gz (gzip)
00235   sprintf(command,"gzip -d -c %s.gz",filename);
00236   realfilename = command+11;
00237   iout << "Command = " << command << "\n" << endi;
00238   iout << "Filename.gz = " << realfilename << "\n" << endi;
00239   if (!stat(realfilename,&buf))
00240         {
00241         if (!S_ISDIR(buf.st_mode))
00242                 {
00243                 fout = popen(command,mode);
00244                 // on HP-UX, the first character(s) out of pipe may be
00245                 // garbage!  (Argh!)
00246                 int C;
00247                 do
00248                   {
00249                   C = fgetc(fout);
00250                   // iout << "C is " << C << "\n" << endi;
00251                   if (isalnum(C) || isspace(C))
00252                         {
00253                         ungetc(C,fout);
00254                         C = -1; // outta loop
00255                         }
00256                   } while(C != -1);
00257                 free(command);
00258                 return(fout);
00259                 }
00260         }
00261   free(command);
00262 #endif /* !defined(NOCOMPRESSED) */
00263 
00264   return(NULL);
00265 } /* Fopen() */

00119 {
00120   if (access(filename, F_OK) == 0) {
00121     if ( ! extension ) extension = ".BAK";
00122     char *backup = new char[strlen(filename)+strlen(extension)+1];
00123     strcpy(backup, filename);
00124     strcat(backup, extension);
00125 #if defined(WIN32) && !defined(__CYGWIN__)
00126     if ( remove(backup) ) if ( errno != ENOENT ) {
00127       char *sys_err_msg = strerror(errno);
00128       if ( ! sys_err_msg ) sys_err_msg = "(unknown error)";
00129       iout << iERROR << "Error on removing file "
00130         << backup << ": " << sys_err_msg << "\n" << endi;
00131       fflush(stdout);
00132     }
00133 #endif
00134     if ( rename(filename,backup) )
00135     {
00136       char *sys_err_msg = strerror(errno);
00137       if ( ! sys_err_msg ) sys_err_msg = "(unknown error)";
00138       iout << iERROR << "Error on renaming file " << filename
00139         << " to " << backup << ": " << sys_err_msg << "\n" << endi;
00140       fflush(stdout);
00141       // char errmsg[256];
00142       // sprintf(errmsg, "Error on renaming file %s to %s",filename,backup);
00143       // NAMD_err(errmsg);
00144     }
00145     delete [] backup;
00146   }
00147 }

00106 {
00107    const char *bug_msg = 
00108      "FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html";
00109    char *new_err_msg = new char[strlen(err_msg) + 20 + strlen(bug_msg)];
00110    sprintf(new_err_msg,"FATAL ERROR: %s\n%s\n",err_msg,bug_msg);
00111    CkPrintf(new_err_msg);
00112    fflush(stdout);
00113    CmiAbort(new_err_msg);
00114    delete [] new_err_msg;
00115 }

00078 {
00079    char *new_err_msg = new char[strlen(err_msg) + 20];
00080    sprintf(new_err_msg,"FATAL ERROR: %s\n",err_msg);
00081    CkPrintf(new_err_msg);
00082    fflush(stdout);
00083    CmiAbort(new_err_msg);
00084    delete [] new_err_msg;
00085 }

00091 {
00092    char *sys_err_msg = strerror(errno);
00093    if ( ! sys_err_msg ) sys_err_msg = "(unknown error)";
00094    char *new_err_msg = new char[strlen(err_msg) + 20 + strlen(sys_err_msg)];
00095    sprintf(new_err_msg,"FATAL ERROR: %s: %s\n",err_msg, sys_err_msg);
00096    CkPrintf(new_err_msg);
00097    fflush(stdout);
00098    CmiAbort(new_err_msg);
00099    delete [] new_err_msg;
00100 }

00065 {
00066    char *new_err_msg = new char[strlen(err_msg) + 20];
00067    sprintf(new_err_msg,"EXITING: %s\n",err_msg);
00068    CkPrintf(new_err_msg);
00069    fflush(stdout);
00070    CmiAbort(new_err_msg);
00071    delete [] new_err_msg;
00072 }

00049                                     {
00050   char *rs;
00051 
00052   if(!s)
00053     return NULL;
00054 
00055   rs = new char[strlen(s) + 1];
00056   strcpy(rs,s);
00057 
00058   return rs;
00059 }


Defines
#define	COULOMB 332.0636
#define	BOLTZMANN 0.001987191
#define	TIMEFACTOR 48.88821
#define	PRESSUREFACTOR 6.95E4
#define	PDBVELFACTOR 20.45482706
#define	PDBVELINVFACTOR (1.0/PDBVELFACTOR)
#define	PNPERKCALMOL 69.479
#define	mynearbyint(x) floor((x)+0.5)
#define	PI 3.141592653589793
#define	TWOPI 2.0 * PI
#define	ONE 1.000000000000000
#define	ZERO 0.000000000000000
#define	SMALLRAD 0.0005
#define	SMALLRAD2 SMALLRAD*SMALLRAD
#define	FALSE 0
#define	TRUE 1
#define	NO 0
#define	YES 1
#define	STRINGNULL '\0'
#define	MAX_NEIGHBORS 27
#define	SIMPARAMSTAG 100
#define	STATICPARAMSTAG 101
#define	MOLECULETAG 102
#define	FULLTAG 104
#define	FULLFORCETAG 105
#define	DPMTATAG 106
#define	GRIDFORCEGRIDTAG 107
#define	CYCLE_BARRIER 0
#define	PME_BARRIER 0
#define	STEP_BARRIER 0
#define	USE_BARRIER (CYCLE_BARRIER \|\| PME_BARRIER \|\| STEP_BARRIER)
#define	NAMD_SeparateWaters 0
#define	NAMD_ComputeNonbonded_SortAtoms 1
#define	NAMD_ComputeNonbonded_SortAtoms_LessBranches 1
#define	WAT_TIP3 0
#define	WAT_TIP4 1
#define	WAT_SWM4 2
Typedefs
typedef long long	int64
typedef float	Real
typedef double	BigReal
typedef int	Bool
Functions
void	NAMD_quit (const char *)
void	NAMD_die (const char *)
void	NAMD_err (const char *)
void	NAMD_bug (const char *)
void	NAMD_backup_file (const char filename, const char extension=0)
void	NAMD_write (int fd, const void *buf, size_t count)
char *	NAMD_stringdup (const char *)
FILE *	Fopen (const char filename, const char mode)
int	Fclose (FILE *fout)

common.h File Reference

Defines

Typedefs

Functions

Define Documentation

Typedef Documentation

Function Documentation