NAMD: common.h File Reference

00256 {
00257   int rc = -1;
00258 #if !defined(NOCOMPRESSED)
00259   rc = pclose(fout);
00260 #endif
00261   if (rc == -1) // stream not associated with a popen()
00262     {
00263     rc = fclose(fout);
00264     }
00265   return rc;
00266 } /* Fclose() */

00171 {
00172   struct stat buf;
00173   // check if basic filename exists (and not a directory)
00174 
00175 #if defined(NOCOMPRESSED)
00176   if (!stat(filename,&buf))
00177     {
00178       return(fopen(filename,mode));
00179     }
00180 #else
00181   if (!stat(filename,&buf))
00182     {
00183       if (!S_ISDIR(buf.st_mode))
00184         return(fopen(filename,mode));
00185     }
00186   // check for a compressed file
00187   char *realfilename;
00188   char *command;
00189   FILE *fout;
00190   command = (char *)malloc(strlen(filename)+25);
00191   // check for .Z (unix compress)
00192   sprintf(command,"zcat %s.Z",filename);
00193   realfilename = command+5;
00194   iout << "Command = " << command << "\n" << endi;
00195   iout << "Filename.Z = " << realfilename << "\n" << endi;
00196   if (!stat(realfilename,&buf))
00197         {
00198         if (!S_ISDIR(buf.st_mode))
00199                 {
00200                 fout = popen(command,mode);
00201                 // on HP-UX, the first character(s) out of pipe may be
00202                 // garbage!  (Argh!)
00203                 int C;
00204                 do
00205                   {
00206                   C = fgetc(fout);
00207                   // iout << "C is " << C << "\n" << endi;
00208                   if (isalnum(C) || isspace(C))
00209                         {
00210                         ungetc(C,fout);
00211                         C = -1; // outta loop
00212                         }
00213                   } while(C != -1);
00214                 free(command);
00215                 return(fout);
00216                 }
00217         }
00218   // check for .gz (gzip)
00219   sprintf(command,"gzip -d -c %s.gz",filename);
00220   realfilename = command+11;
00221   iout << "Command = " << command << "\n" << endi;
00222   iout << "Filename.gz = " << realfilename << "\n" << endi;
00223   if (!stat(realfilename,&buf))
00224         {
00225         if (!S_ISDIR(buf.st_mode))
00226                 {
00227                 fout = popen(command,mode);
00228                 // on HP-UX, the first character(s) out of pipe may be
00229                 // garbage!  (Argh!)
00230                 int C;
00231                 do
00232                   {
00233                   C = fgetc(fout);
00234                   // iout << "C is " << C << "\n" << endi;
00235                   if (isalnum(C) || isspace(C))
00236                         {
00237                         ungetc(C,fout);
00238                         C = -1; // outta loop
00239                         }
00240                   } while(C != -1);
00241                 free(command);
00242                 return(fout);
00243                 }
00244         }
00245   free(command);
00246 #endif /* !defined(NOCOMPRESSED) */
00247 
00248   return(NULL);
00249 } /* Fopen() */

00118 {
00119   struct stat sbuf;
00120   if (stat(filename, &sbuf) == 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     remove(backup);
00127 #endif
00128     if ( rename(filename,backup) )
00129     {
00130       char *sys_err_msg = strerror(errno);
00131       if ( ! sys_err_msg ) sys_err_msg = "(unknown error)";
00132       iout << iERROR << "Error on renaming file " << filename
00133         << " to " << backup << ": " << sys_err_msg << "\n" << endi;
00134       fflush(stdout);
00135       // char errmsg[256];
00136       // sprintf(errmsg, "Error on renaming file %s to %s",filename,backup);
00137       // NAMD_err(errmsg);
00138     }
00139     delete [] backup;
00140   }
00141 }

00105 {
00106    const char *bug_msg = 
00107      "FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html";
00108    char *new_err_msg = new char[strlen(err_msg) + 20 + strlen(bug_msg)];
00109    sprintf(new_err_msg,"FATAL ERROR: %s\n%s\n",err_msg,bug_msg);
00110    CkPrintf(new_err_msg);
00111    fflush(stdout);
00112    CmiAbort(new_err_msg);
00113    delete [] new_err_msg;
00114 }

00077 {
00078    char *new_err_msg = new char[strlen(err_msg) + 20];
00079    sprintf(new_err_msg,"FATAL ERROR: %s\n",err_msg);
00080    CkPrintf(new_err_msg);
00081    fflush(stdout);
00082    CmiAbort(new_err_msg);
00083    delete [] new_err_msg;
00084 }

00090 {
00091    char *sys_err_msg = strerror(errno);
00092    if ( ! sys_err_msg ) sys_err_msg = "(unknown error)";
00093    char *new_err_msg = new char[strlen(err_msg) + 20 + strlen(sys_err_msg)];
00094    sprintf(new_err_msg,"FATAL ERROR: %s: %s\n",err_msg, sys_err_msg);
00095    CkPrintf(new_err_msg);
00096    fflush(stdout);
00097    CmiAbort(new_err_msg);
00098    delete [] new_err_msg;
00099 }

00064 {
00065    char *new_err_msg = new char[strlen(err_msg) + 20];
00066    sprintf(new_err_msg,"EXITING: %s\n",err_msg);
00067    CkPrintf(new_err_msg);
00068    fflush(stdout);
00069    CmiAbort(new_err_msg);
00070    delete [] new_err_msg;
00071 }

00048                                     {
00049   char *rs;
00050 
00051   if(!s)
00052     return NULL;
00053 
00054   rs = new char[strlen(s) + 1];
00055   strcpy(rs,s);
00056 
00057   return rs;
00058 }


Defines
#define	COLOUMB 332.0636
#define	BOLTZMAN 0.001987191
#define	TIMEFACTOR 48.88821
#define	PRESSUREFACTOR 6.95E4
#define	PDBVELFACTOR 20.45482706
#define	PDBVELINVFACTOR (1.0/PDBVELFACTOR)
#define	PNPERKCALMOL 69.479
#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	CYCLE_BARRIER 0
#define	PME_BARRIER 0
#define	USE_BARRIER (CYCLE_BARRIER \|\| PME_BARRIER)
#define	NAMD_SeparateWaters 0
#define	NAMD_ComputeNonbonded_SortAtoms 0
#define	NAMD_ComputeNonbonded_SortAtoms_LessBranches 1
#define	WAT_TIP3 0
#define	WAT_TIP4 1
#define	CmiMemcpy(D, S, N) memcpy(D,S,N)
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