/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
*
- *
+ *
* This source code is part of
- *
+ *
* G R O M A C S
- *
+ *
* GROningen MAchine for Chemical Simulations
- *
+ *
* VERSION 3.2.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
- *
+ *
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
- *
+ *
* For more info, check our website at http://www.gromacs.org
- *
+ *
* And Hey:
* GROningen Mixture of Alchemy and Childrens' Stories
*/
#include "windows.h"
#endif
-/* we keep a linked list of all files opened through pipes (i.e.
+/* we keep a linked list of all files opened through pipes (i.e.
compressed or .gzipped files. This way we can distinguish between them
- without having to change the semantics of reading from/writing to files)
- */
+ without having to change the semantics of reading from/writing to files)
+ */
typedef struct t_pstack {
- FILE *fp;
+ FILE *fp;
struct t_pstack *prev;
} t_pstack;
-static t_pstack *pstack=NULL;
-static gmx_bool bUnbuffered=FALSE;
+static t_pstack *pstack = NULL;
+static gmx_bool bUnbuffered = FALSE;
#ifdef GMX_THREAD_MPI
/* this linked list is an intrinsically globally shared object, so we have
to protect it with mutexes */
-static tMPI_Thread_mutex_t pstack_mutex=TMPI_THREAD_MUTEX_INITIALIZER;
+static tMPI_Thread_mutex_t pstack_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
#endif
void no_buffers(void)
{
- bUnbuffered=TRUE;
+ bUnbuffered = TRUE;
}
void push_ps(FILE *fp)
tMPI_Thread_mutex_lock(&pstack_mutex);
#endif
- snew(ps,1);
+ snew(ps, 1);
ps->fp = fp;
ps->prev = pstack;
pstack = ps;
#ifndef GMX_FAHCORE
#ifndef HAVE_PIPES
-static FILE *popen(const char *nm,const char *mode)
+static FILE *popen(const char *nm, const char *mode)
{
gmx_impl("Sorry no pipes...");
#ifdef SKIP_FFOPS
return fclose(fp);
#else
- t_pstack *ps,*tmp;
- int ret=0;
+ t_pstack *ps, *tmp;
+ int ret = 0;
#ifdef GMX_THREAD_MPI
tMPI_Thread_mutex_lock(&pstack_mutex);
#endif
- ps=pstack;
- if (ps == NULL) {
- if (fp != NULL)
+ ps = pstack;
+ if (ps == NULL)
+ {
+ if (fp != NULL)
+ {
ret = fclose(fp);
+ }
}
- else if (ps->fp == fp) {
+ else if (ps->fp == fp)
+ {
if (fp != NULL)
+ {
ret = pclose(fp);
- pstack=pstack->prev;
+ }
+ pstack = pstack->prev;
sfree(ps);
}
- else {
+ else
+ {
while ((ps->prev != NULL) && (ps->prev->fp != fp))
- ps=ps->prev;
- if ((ps->prev != NULL) && ps->prev->fp == fp) {
+ {
+ ps = ps->prev;
+ }
+ if ((ps->prev != NULL) && ps->prev->fp == fp)
+ {
if (ps->prev->fp != NULL)
+ {
ret = pclose(ps->prev->fp);
- tmp=ps->prev;
- ps->prev=ps->prev->prev;
+ }
+ tmp = ps->prev;
+ ps->prev = ps->prev->prev;
sfree(tmp);
}
- else {
+ else
+ {
if (fp != NULL)
+ {
ret = fclose(fp);
+ }
}
}
#ifdef GMX_THREAD_MPI
tMPI_Thread_mutex_lock(&pstack_mutex);
#endif
- ps=pstack;
- while (ps != NULL) {
- if (ps->fp == fp) {
- fprintf(stderr,"Cannot rewind compressed file!\n");
+ ps = pstack;
+ while (ps != NULL)
+ {
+ if (ps->fp == fp)
+ {
+ fprintf(stderr, "Cannot rewind compressed file!\n");
#ifdef GMX_THREAD_MPI
tMPI_Thread_mutex_unlock(&pstack_mutex);
#endif
return;
}
- ps=ps->prev;
+ ps = ps->prev;
}
rewind(fp);
#ifdef GMX_THREAD_MPI
#ifdef HAVE_FSEEKO
return ftello(stream);
#else
-#ifdef HAVE__FSEEKI64
+#ifdef HAVE__FSEEKI64
return _ftelli64(stream);
#else
return ftell(stream);
tMPI_Thread_mutex_lock(&pstack_mutex);
#endif
- ps=pstack;
- while (ps != NULL) {
- if (ps->fp == fp) {
+ ps = pstack;
+ while (ps != NULL)
+ {
+ if (ps->fp == fp)
+ {
#ifdef GMX_THREAD_MPI
tMPI_Thread_mutex_unlock(&pstack_mutex);
#endif
return TRUE;
}
- ps=ps->prev;
+ ps = ps->prev;
}
#ifdef GMX_THREAD_MPI
tMPI_Thread_mutex_unlock(&pstack_mutex);
}
-static FILE *uncompress(const char *fn,const char *mode)
+static FILE *uncompress(const char *fn, const char *mode)
{
FILE *fp;
- char buf[256];
+ char buf[256];
- sprintf(buf,"uncompress -c < %s",fn);
- fprintf(stderr,"Going to execute '%s'\n",buf);
- if ((fp=popen(buf,mode)) == NULL)
+ sprintf(buf, "uncompress -c < %s", fn);
+ fprintf(stderr, "Going to execute '%s'\n", buf);
+ if ((fp = popen(buf, mode)) == NULL)
+ {
gmx_open(fn);
+ }
push_ps(fp);
return fp;
}
-static FILE *gunzip(const char *fn,const char *mode)
+static FILE *gunzip(const char *fn, const char *mode)
{
FILE *fp;
- char buf[256];
+ char buf[256];
- sprintf(buf,"gunzip -c < %s",fn);
- fprintf(stderr,"Going to execute '%s'\n",buf);
- if ((fp=popen(buf,mode)) == NULL)
+ sprintf(buf, "gunzip -c < %s", fn);
+ fprintf(stderr, "Going to execute '%s'\n", buf);
+ if ((fp = popen(buf, mode)) == NULL)
+ {
gmx_open(fn);
+ }
push_ps(fp);
return fp;
FILE *test;
if (fname == NULL)
+ {
return FALSE;
- test=fopen(fname,"r");
- if (test == NULL) {
+ }
+ test = fopen(fname, "r");
+ if (test == NULL)
+ {
/*Windows doesn't allow fopen of directory - so we need to check this seperately */
#ifdef GMX_NATIVE_WINDOWS
- DWORD attr = GetFileAttributes(fname);
- return (attr != INVALID_FILE_ATTRIBUTES) && (attr & FILE_ATTRIBUTE_DIRECTORY);
- #else
- return FALSE;
+ DWORD attr = GetFileAttributes(fname);
+ return (attr != INVALID_FILE_ATTRIBUTES) && (attr & FILE_ATTRIBUTE_DIRECTORY);
+ #else
+ return FALSE;
#endif
- } else {
+ }
+ else
+ {
fclose(test);
return TRUE;
}
FILE *test;
if (fname == NULL)
+ {
return FALSE;
- test=fopen(fname,"r");
+ }
+ test = fopen(fname, "r");
if (test == NULL)
{
return FALSE;
/*Windows doesn't allow fopen of directory - so we don't need to check this seperately */
#if (!((defined WIN32 || defined _WIN32 || defined WIN64 || defined _WIN64) && !defined __CYGWIN__ && !defined __CYGWIN32__))
{
- int status;
+ int status;
struct stat st_buf;
status = stat (fname, &st_buf);
if (status != 0 || !S_ISREG(st_buf.st_mode))
gmx_bool gmx_fexist_master(const char *fname, t_commrec *cr)
{
- gmx_bool bExist;
-
- if (SIMMASTER(cr))
- {
- bExist = gmx_fexist(fname);
- }
- if (PAR(cr))
- {
- gmx_bcast(sizeof(bExist),&bExist,cr);
- }
- return bExist;
+ gmx_bool bExist;
+
+ if (SIMMASTER(cr))
+ {
+ bExist = gmx_fexist(fname);
+ }
+ if (PAR(cr))
+ {
+ gmx_bcast(sizeof(bExist), &bExist, cr);
+ }
+ return bExist;
}
gmx_bool gmx_eof(FILE *fp)
{
- char data[4];
+ char data[4];
gmx_bool beof;
if (is_pipe(fp))
+ {
return feof(fp);
- else {
- if ((beof=fread(data,1,1,fp))==1)
- gmx_fseek(fp,-1,SEEK_CUR);
+ }
+ else
+ {
+ if ((beof = fread(data, 1, 1, fp)) == 1)
+ {
+ gmx_fseek(fp, -1, SEEK_CUR);
+ }
return !beof;
}
}
-static char *backup_fn(const char *file,int count_max)
+static char *backup_fn(const char *file, int count_max)
{
/* Use a reasonably low value for countmax; we might
* generate 4-5 files in each round, and we dont
* want to hit directory limits of 1024 or 2048 files.
*/
#define COUNTMAX 99
- int i,count=1;
- char *directory,*fn;
+ int i, count = 1;
+ char *directory, *fn;
char *buf;
if (count_max == -1)
smalloc(buf, GMX_PATH_MAX);
- for(i=strlen(file)-1; ((i > 0) && (file[i] != DIR_SEPARATOR)); i--)
+ for (i = strlen(file)-1; ((i > 0) && (file[i] != DIR_SEPARATOR)); i--)
+ {
;
+ }
/* Must check whether i > 0, i.e. whether there is a directory
* in the file name. In that case we overwrite the / sign with
* a '\0' to end the directory string .
*/
- if (i > 0) {
+ if (i > 0)
+ {
directory = gmx_strdup(file);
directory[i] = '\0';
fn = gmx_strdup(file+i+1);
}
- else {
+ else
+ {
directory = gmx_strdup(".");
fn = gmx_strdup(file);
}
- do {
- sprintf(buf,"%s/#%s.%d#",directory,fn,count);
+ do
+ {
+ sprintf(buf, "%s/#%s.%d#", directory, fn, count);
count++;
- } while ((count <= count_max) && gmx_fexist(buf));
+ }
+ while ((count <= count_max) && gmx_fexist(buf));
/* Arbitrarily bail out */
- if (count > count_max)
- gmx_fatal(FARGS,"Won't make more than %d backups of %s for you.\n"
+ if (count > count_max)
+ {
+ gmx_fatal(FARGS, "Won't make more than %d backups of %s for you.\n"
"The env.var. GMX_MAXBACKUP controls this maximum, -1 disables backups.",
- count_max,fn);
+ count_max, fn);
+ }
sfree(directory);
sfree(fn);
gmx_bool make_backup(const char * name)
{
char * env;
- int count_max;
+ int count_max;
char * backup;
#ifdef GMX_FAHCORE
if (env != NULL)
{
count_max = 0;
- sscanf(env,"%d",&count_max);
+ sscanf(env, "%d", &count_max);
if (count_max == -1)
{
/* Do not make backups and possibly overwrite old files */
/* Use the default maximum */
count_max = -1;
}
- backup = backup_fn(name,count_max);
- if(rename(name, backup) == 0) {
+ backup = backup_fn(name, count_max);
+ if (rename(name, backup) == 0)
+ {
fprintf(stderr, "\nBack Off! I just backed up %s to %s\n",
name, backup);
- } else {
+ }
+ else
+ {
fprintf(stderr, "Sorry couldn't backup %s to %s\n", name, backup);
return FALSE;
}
#endif
}
-FILE *ffopen(const char *file,const char *mode)
+FILE *ffopen(const char *file, const char *mode)
{
#ifdef SKIP_FFOPS
- return fopen(file,mode);
+ return fopen(file, mode);
#else
- FILE *ff=NULL;
- char buf[256],*bf,*bufsize=0,*ptr;
+ FILE *ff = NULL;
+ char buf[256], *bf, *bufsize = 0, *ptr;
gmx_bool bRead;
- int bs;
+ int bs;
- if (file == NULL)
+ if (file == NULL)
{
return NULL;
}
- if (mode[0]=='w') {
+ if (mode[0] == 'w')
+ {
make_backup(file);
}
where();
- bRead= (mode[0]=='r'&&mode[1]!='+');
- strcpy(buf,file);
- if (!bRead || gmx_fexist(buf)) {
- if ((ff=fopen(buf,mode))==NULL)
+ bRead = (mode[0] == 'r' && mode[1] != '+');
+ strcpy(buf, file);
+ if (!bRead || gmx_fexist(buf))
+ {
+ if ((ff = fopen(buf, mode)) == NULL)
+ {
gmx_file(buf);
+ }
where();
/* Check whether we should be using buffering (default) or not
* (for debugging)
*/
- if (bUnbuffered || ((bufsize=getenv("LOG_BUFS")) != NULL)) {
+ if (bUnbuffered || ((bufsize = getenv("LOG_BUFS")) != NULL))
+ {
/* Check whether to use completely unbuffered */
if (bUnbuffered)
+ {
bs = 0;
+ }
else
- bs=strtol(bufsize, NULL, 10);
+ {
+ bs = strtol(bufsize, NULL, 10);
+ }
if (bs <= 0)
- setbuf(ff,NULL);
- else {
- snew(ptr,bs+8);
- if (setvbuf(ff,ptr,_IOFBF,bs) != 0)
+ {
+ setbuf(ff, NULL);
+ }
+ else
+ {
+ snew(ptr, bs+8);
+ if (setvbuf(ff, ptr, _IOFBF, bs) != 0)
+ {
gmx_file("Buffering File");
+ }
}
}
where();
}
- else {
- sprintf(buf,"%s.Z",file);
- if (gmx_fexist(buf)) {
- ff=uncompress(buf,mode);
+ else
+ {
+ sprintf(buf, "%s.Z", file);
+ if (gmx_fexist(buf))
+ {
+ ff = uncompress(buf, mode);
}
- else {
- sprintf(buf,"%s.gz",file);
- if (gmx_fexist(buf)) {
- ff=gunzip(buf,mode);
+ else
+ {
+ sprintf(buf, "%s.gz", file);
+ if (gmx_fexist(buf))
+ {
+ ff = gunzip(buf, mode);
}
- else
+ else
+ {
gmx_file(file);
+ }
}
}
return ff;
struct _finddata_t finddata;
int first;
#else
- int dummy;
+ int dummy;
#endif
};
int
-gmx_directory_open(gmx_directory_t *p_gmxdir,const char *dirname)
+gmx_directory_open(gmx_directory_t *p_gmxdir, const char *dirname)
{
struct gmx_directory * gmxdir;
int rc;
-
- snew(gmxdir,1);
-
+
+ snew(gmxdir, 1);
+
*p_gmxdir = gmxdir;
-
+
#ifdef HAVE_DIRENT_H
- if( (gmxdir->dirent_handle = opendir(dirname)) != NULL)
+ if ( (gmxdir->dirent_handle = opendir(dirname)) != NULL)
{
rc = 0;
}
- else
+ else
{
sfree(gmxdir);
*p_gmxdir = NULL;
rc = EINVAL;
}
#elif (defined GMX_NATIVE_WINDOWS)
-
- if(dirname!=NULL && strlen(dirname)>0)
+
+ if (dirname != NULL && strlen(dirname) > 0)
{
char * tmpname;
size_t namelength;
int len;
-
+
len = strlen(dirname);
- snew(tmpname,len+3);
-
- strncpy(tmpname,dirname,len+1);
-
+ snew(tmpname, len+3);
+
+ strncpy(tmpname, dirname, len+1);
+
/* Remove possible trailing directory separator */
- if(tmpname[len]=='/' || tmpname[len]=='\\')
+ if (tmpname[len] == '/' || tmpname[len] == '\\')
{
- tmpname[len]='\0';
+ tmpname[len] = '\0';
}
-
+
/* Add wildcard */
- strcat(tmpname,"/*");
-
+ strcat(tmpname, "/*");
+
gmxdir->first = 1;
- if( (gmxdir->windows_handle=_findfirst(tmpname,&gmxdir->finddata))>0L)
+ if ( (gmxdir->windows_handle = _findfirst(tmpname, &gmxdir->finddata)) > 0L)
{
rc = 0;
}
else
{
- if(errno==EINVAL)
+ if (errno == EINVAL)
{
sfree(gmxdir);
*p_gmxdir = NULL;
- rc = EINVAL;
+ rc = EINVAL;
}
else
{
int
-gmx_directory_nextfile(gmx_directory_t gmxdir,char *name,int maxlength_name)
+gmx_directory_nextfile(gmx_directory_t gmxdir, char *name, int maxlength_name)
{
int rc;
-
+
#ifdef HAVE_DIRENT_H
-
+
struct dirent * direntp_large;
struct dirent * p;
-
-
- if(gmxdir!=NULL && gmxdir->dirent_handle!=NULL)
+
+
+ if (gmxdir != NULL && gmxdir->dirent_handle != NULL)
{
/* On some platforms no space is present for d_name in dirent.
* Since d_name is guaranteed to be the last entry, allocating
* GMX_MAX_PATH should always be >= the max possible d_name.
*/
smalloc(direntp_large, sizeof(*direntp_large) + GMX_PATH_MAX);
- rc = readdir_r(gmxdir->dirent_handle,direntp_large,&p);
+ rc = readdir_r(gmxdir->dirent_handle, direntp_large, &p);
- if(p!=NULL && rc==0)
+ if (p != NULL && rc == 0)
{
- strncpy(name,direntp_large->d_name,maxlength_name);
+ strncpy(name, direntp_large->d_name, maxlength_name);
}
else
{
}
sfree(direntp_large);
}
- else
+ else
{
name[0] = '\0';
rc = EINVAL;
}
-
+
#elif (defined GMX_NATIVE_WINDOWS)
-
- if(gmxdir!=NULL)
+
+ if (gmxdir != NULL)
{
- if(gmxdir->windows_handle<=0)
+ if (gmxdir->windows_handle <= 0)
{
-
+
name[0] = '\0';
rc = ENOENT;
}
- else if(gmxdir->first==1)
+ else if (gmxdir->first == 1)
{
- strncpy(name,gmxdir->finddata.name,maxlength_name);
+ strncpy(name, gmxdir->finddata.name, maxlength_name);
rc = 0;
gmxdir->first = 0;
}
else
{
- if(_findnext(gmxdir->windows_handle,&gmxdir->finddata)==0)
+ if (_findnext(gmxdir->windows_handle, &gmxdir->finddata) == 0)
{
- strncpy(name,gmxdir->finddata.name,maxlength_name);
+ strncpy(name, gmxdir->finddata.name, maxlength_name);
rc = 0;
}
else
}
}
}
-
+
#else
gmx_fatal(FARGS,
"Source compiled without POSIX dirent or windows support - cannot scan directories.\n");
}
-int
+int
gmx_directory_close(gmx_directory_t gmxdir)
{
int rc;
"Source compiled without POSIX dirent or windows support - cannot scan directories.\n");
rc = -1;
#endif
-
+
sfree(gmxdir);
return rc;
}
static gmx_bool search_subdirs(const char *parent, char *libdir)
{
- char *ptr;
+ char *ptr;
gmx_bool found;
/* Search a few common subdirectory names for the gromacs library dir */
- sprintf(libdir,"%s%cshare%ctop%cgurgle.dat",parent,
- DIR_SEPARATOR,DIR_SEPARATOR,DIR_SEPARATOR);
- found=gmx_fexist(libdir);
- if(!found) {
- sprintf(libdir,"%s%cshare%cgromacs%ctop%cgurgle.dat",parent,
- DIR_SEPARATOR,DIR_SEPARATOR,
- DIR_SEPARATOR,DIR_SEPARATOR);
- found=gmx_fexist(libdir);
- }
- if(!found) {
- sprintf(libdir,"%s%cshare%cgromacs-%s%ctop%cgurgle.dat",parent,
- DIR_SEPARATOR,DIR_SEPARATOR,VERSION,
- DIR_SEPARATOR,DIR_SEPARATOR);
- found=gmx_fexist(libdir);
- }
- if(!found) {
- sprintf(libdir,"%s%cshare%cgromacs%cgromacs-%s%ctop%cgurgle.dat",parent,
- DIR_SEPARATOR,DIR_SEPARATOR,DIR_SEPARATOR,
- VERSION,DIR_SEPARATOR,DIR_SEPARATOR);
- found=gmx_fexist(libdir);
- }
+ sprintf(libdir, "%s%cshare%ctop%cgurgle.dat", parent,
+ DIR_SEPARATOR, DIR_SEPARATOR, DIR_SEPARATOR);
+ found = gmx_fexist(libdir);
+ if (!found)
+ {
+ sprintf(libdir, "%s%cshare%cgromacs%ctop%cgurgle.dat", parent,
+ DIR_SEPARATOR, DIR_SEPARATOR,
+ DIR_SEPARATOR, DIR_SEPARATOR);
+ found = gmx_fexist(libdir);
+ }
+ if (!found)
+ {
+ sprintf(libdir, "%s%cshare%cgromacs-%s%ctop%cgurgle.dat", parent,
+ DIR_SEPARATOR, DIR_SEPARATOR, VERSION,
+ DIR_SEPARATOR, DIR_SEPARATOR);
+ found = gmx_fexist(libdir);
+ }
+ if (!found)
+ {
+ sprintf(libdir, "%s%cshare%cgromacs%cgromacs-%s%ctop%cgurgle.dat", parent,
+ DIR_SEPARATOR, DIR_SEPARATOR, DIR_SEPARATOR,
+ VERSION, DIR_SEPARATOR, DIR_SEPARATOR);
+ found = gmx_fexist(libdir);
+ }
/* Remove the gurgle.dat part from libdir if we found something */
- if(found) {
- ptr=strrchr(libdir,DIR_SEPARATOR); /* slash or backslash always present, no check necessary */
- *ptr='\0';
+ if (found)
+ {
+ ptr = strrchr(libdir, DIR_SEPARATOR); /* slash or backslash always present, no check necessary */
+ *ptr = '\0';
}
return found;
}
static gmx_bool filename_is_absolute(char *name)
{
#ifdef GMX_NATIVE_WINDOWS
- return ((name[0] == DIR_SEPARATOR) || ((strlen(name)>3) && strncmp(name+1,":\\",2)) == 0);
+ return ((name[0] == DIR_SEPARATOR) || ((strlen(name) > 3) && strncmp(name+1, ":\\", 2)) == 0);
#else
return (name[0] == DIR_SEPARATOR);
#endif
gmx_bool get_libdir(char *libdir)
{
#define GMX_BINNAME_MAX 512
- char bin_name[GMX_BINNAME_MAX];
- char buf[GMX_BINNAME_MAX];
- char full_path[GMX_PATH_MAX+GMX_BINNAME_MAX];
- char system_path[GMX_PATH_MAX];
- char *dir,*ptr,*s,*pdum;
- gmx_bool found=FALSE;
- int i;
+ char bin_name[GMX_BINNAME_MAX];
+ char buf[GMX_BINNAME_MAX];
+ char full_path[GMX_PATH_MAX+GMX_BINNAME_MAX];
+ char system_path[GMX_PATH_MAX];
+ char *dir, *ptr, *s, *pdum;
+ gmx_bool found = FALSE;
+ int i;
if (Program() != NULL)
{
- /* First - detect binary name */
- if (strlen(Program()) >= GMX_BINNAME_MAX)
- {
- gmx_fatal(FARGS,"The name of the binary is longer than the allowed buffer size (%d):\n'%s'",GMX_BINNAME_MAX,Program());
- }
- strncpy(bin_name,Program(),GMX_BINNAME_MAX-1);
+ /* First - detect binary name */
+ if (strlen(Program()) >= GMX_BINNAME_MAX)
+ {
+ gmx_fatal(FARGS, "The name of the binary is longer than the allowed buffer size (%d):\n'%s'", GMX_BINNAME_MAX, Program());
+ }
+ strncpy(bin_name, Program(), GMX_BINNAME_MAX-1);
- /* On windows & cygwin we need to add the .exe extension
- * too, or we wont be able to detect that the file exists
- */
+ /* On windows & cygwin we need to add the .exe extension
+ * too, or we wont be able to detect that the file exists
+ */
#if (defined GMX_NATIVE_WINDOWS || defined GMX_CYGWIN)
- if(strlen(bin_name)<3 || gmx_strncasecmp(bin_name+strlen(bin_name)-4,".exe",4))
- strcat(bin_name,".exe");
+ if (strlen(bin_name) < 3 || gmx_strncasecmp(bin_name+strlen(bin_name)-4, ".exe", 4))
+ {
+ strcat(bin_name, ".exe");
+ }
#endif
- /* Only do the smart search part if we got a real name */
- if (NULL!=bin_name && strncmp(bin_name,"GROMACS",GMX_BINNAME_MAX)) {
+ /* Only do the smart search part if we got a real name */
+ if (NULL != bin_name && strncmp(bin_name, "GROMACS", GMX_BINNAME_MAX))
+ {
- if (!strchr(bin_name,DIR_SEPARATOR)) {
- /* No slash or backslash in name means it must be in the path - search it! */
- /* Add the local dir since it is not in the path on windows */
- gmx_getcwd(system_path, sizeof(system_path));
- sprintf(full_path,"%s%c%s",system_path,DIR_SEPARATOR,bin_name);
- found = gmx_is_file(full_path);
- if (!found && (s=getenv("PATH")) != NULL)
+ if (!strchr(bin_name, DIR_SEPARATOR))
{
- char *dupped;
-
- dupped=gmx_strdup(s);
- s=dupped;
- while(!found && (dir=gmx_strsep(&s, PATH_SEPARATOR)) != NULL)
+ /* No slash or backslash in name means it must be in the path - search it! */
+ /* Add the local dir since it is not in the path on windows */
+ gmx_getcwd(system_path, sizeof(system_path));
+ sprintf(full_path, "%s%c%s", system_path, DIR_SEPARATOR, bin_name);
+ found = gmx_is_file(full_path);
+ if (!found && (s = getenv("PATH")) != NULL)
+ {
+ char *dupped;
+
+ dupped = gmx_strdup(s);
+ s = dupped;
+ while (!found && (dir = gmx_strsep(&s, PATH_SEPARATOR)) != NULL)
+ {
+ sprintf(full_path, "%s%c%s", dir, DIR_SEPARATOR, bin_name);
+ found = gmx_is_file(full_path);
+ }
+ sfree(dupped);
+ }
+ if (!found)
{
- sprintf(full_path,"%s%c%s",dir,DIR_SEPARATOR,bin_name);
- found = gmx_is_file(full_path);
+ return FALSE;
}
- sfree(dupped);
}
- if (!found)
+ else if (!filename_is_absolute(bin_name))
{
- return FALSE;
+ /* name contains directory separators, but
+ * it does not start at the root, i.e.
+ * name is relative to the current dir
+ */
+ gmx_getcwd(buf, sizeof(buf));
+ sprintf(full_path, "%s%c%s", buf, DIR_SEPARATOR, bin_name);
+ }
+ else
+ {
+ strncpy(full_path, bin_name, GMX_PATH_MAX);
}
- } else if (!filename_is_absolute(bin_name)) {
- /* name contains directory separators, but
- * it does not start at the root, i.e.
- * name is relative to the current dir
- */
- gmx_getcwd(buf, sizeof(buf));
- sprintf(full_path,"%s%c%s",buf,DIR_SEPARATOR,bin_name);
- } else {
- strncpy(full_path,bin_name,GMX_PATH_MAX);
- }
- /* Now we should have a full path and name in full_path,
- * but on unix it might be a link, or a link to a link to a link..
- */
+ /* Now we should have a full path and name in full_path,
+ * but on unix it might be a link, or a link to a link to a link..
+ */
#ifndef GMX_NATIVE_WINDOWS
- while( (i=readlink(full_path,buf,sizeof(buf)-1)) > 0 ) {
- buf[i]='\0';
- /* If it doesn't start with "/" it is relative */
- if (buf[0]!=DIR_SEPARATOR) {
- strncpy(strrchr(full_path,DIR_SEPARATOR)+1,buf,GMX_PATH_MAX);
- } else
- strncpy(full_path,buf,GMX_PATH_MAX);
- }
+ while ( (i = readlink(full_path, buf, sizeof(buf)-1)) > 0)
+ {
+ buf[i] = '\0';
+ /* If it doesn't start with "/" it is relative */
+ if (buf[0] != DIR_SEPARATOR)
+ {
+ strncpy(strrchr(full_path, DIR_SEPARATOR)+1, buf, GMX_PATH_MAX);
+ }
+ else
+ {
+ strncpy(full_path, buf, GMX_PATH_MAX);
+ }
+ }
#endif
- /* If running directly from the build tree, try to use the source
- * directory.
- */
+ /* If running directly from the build tree, try to use the source
+ * directory.
+ */
#if (defined CMAKE_SOURCE_DIR && defined CMAKE_BINARY_DIR)
- if (strncmp(full_path, CMAKE_BINARY_DIR, strlen(CMAKE_BINARY_DIR)) == 0)
- {
- if (search_subdirs(CMAKE_SOURCE_DIR, libdir))
+ if (strncmp(full_path, CMAKE_BINARY_DIR, strlen(CMAKE_BINARY_DIR)) == 0)
{
- return TRUE;
+ if (search_subdirs(CMAKE_SOURCE_DIR, libdir))
+ {
+ return TRUE;
+ }
}
- }
#endif
- /* Remove the executable name - it always contains at least one slash */
- *(strrchr(full_path,DIR_SEPARATOR)+1)='\0';
- /* Now we have the full path to the gromacs executable.
- * Use it to find the library dir.
- */
- found=FALSE;
- while(!found && ( (ptr=strrchr(full_path,DIR_SEPARATOR)) != NULL ) ) {
- *ptr='\0';
- found=search_subdirs(full_path,libdir);
+ /* Remove the executable name - it always contains at least one slash */
+ *(strrchr(full_path, DIR_SEPARATOR)+1) = '\0';
+ /* Now we have the full path to the gromacs executable.
+ * Use it to find the library dir.
+ */
+ found = FALSE;
+ while (!found && ( (ptr = strrchr(full_path, DIR_SEPARATOR)) != NULL ) )
+ {
+ *ptr = '\0';
+ found = search_subdirs(full_path, libdir);
+ }
}
}
- }
/* End of smart searching. If we didn't find it in our parent tree,
- * or if the program name wasn't set, at least try some standard
- * locations before giving up, in case we are running from e.g.
+ * or if the program name wasn't set, at least try some standard
+ * locations before giving up, in case we are running from e.g.
* a users home directory. This only works on unix or cygwin...
*/
#ifndef GMX_NATIVE_WINDOWS
- if(!found)
- found=search_subdirs("/usr/local",libdir);
- if(!found)
- found=search_subdirs("/usr",libdir);
- if(!found)
- found=search_subdirs("/opt",libdir);
+ if (!found)
+ {
+ found = search_subdirs("/usr/local", libdir);
+ }
+ if (!found)
+ {
+ found = search_subdirs("/usr", libdir);
+ }
+ if (!found)
+ {
+ found = search_subdirs("/opt", libdir);
+ }
#endif
return found;
}
char *low_gmxlibfn(const char *file, gmx_bool bAddCWD, gmx_bool bFatal)
{
- char *ret;
- char *lib,*dir;
- char buf[1024];
- char libpath[GMX_PATH_MAX];
- gmx_bool env_is_set=FALSE;
- char *s,tmppath[GMX_PATH_MAX];
+ char *ret;
+ char *lib, *dir;
+ char buf[1024];
+ char libpath[GMX_PATH_MAX];
+ gmx_bool env_is_set = FALSE;
+ char *s, tmppath[GMX_PATH_MAX];
/* GMXLIB can be a path now */
- lib=getenv("GMXLIB");
+ lib = getenv("GMXLIB");
if (lib != NULL)
{
- env_is_set=TRUE;
- strncpy(libpath,lib,GMX_PATH_MAX);
- }
+ env_is_set = TRUE;
+ strncpy(libpath, lib, GMX_PATH_MAX);
+ }
else if (!get_libdir(libpath))
{
- strncpy(libpath,GMXLIBDIR,GMX_PATH_MAX);
+ strncpy(libpath, GMXLIBDIR, GMX_PATH_MAX);
}
ret = NULL;
{
ret = gmx_strdup(file);
}
- else
+ else
{
- strncpy(tmppath,libpath,GMX_PATH_MAX);
- s=tmppath;
- while(ret == NULL && (dir=gmx_strsep(&s, PATH_SEPARATOR)) != NULL )
+ strncpy(tmppath, libpath, GMX_PATH_MAX);
+ s = tmppath;
+ while (ret == NULL && (dir = gmx_strsep(&s, PATH_SEPARATOR)) != NULL)
{
- sprintf(buf,"%s%c%s",dir,DIR_SEPARATOR,file);
+ sprintf(buf, "%s%c%s", dir, DIR_SEPARATOR, file);
if (gmx_fexist(buf))
{
ret = gmx_strdup(buf);
}
}
- if (ret == NULL && bFatal)
+ if (ret == NULL && bFatal)
{
- if (env_is_set)
+ if (env_is_set)
{
gmx_fatal(FARGS,
"Library file %s not found %sin your GMXLIB path.",
{
gmx_fatal(FARGS,
"Library file %s not found %sin default directories.\n"
- "(You can set the directories to search with the GMXLIB path variable)",
+ "(You can set the directories to search with the GMXLIB path variable)",
file, bAddCWD ? "in current dir nor " : "");
}
}
-FILE *low_libopen(const char *file,gmx_bool bFatal)
+FILE *low_libopen(const char *file, gmx_bool bFatal)
{
FILE *ff;
char *fn;
- fn=low_gmxlibfn(file,TRUE,bFatal);
+ fn = low_gmxlibfn(file, TRUE, bFatal);
- if (fn==NULL) {
- ff=NULL;
- } else {
- if (debug)
- fprintf(debug,"Opening library file %s\n",fn);
- ff=fopen(fn,"r");
+ if (fn == NULL)
+ {
+ ff = NULL;
+ }
+ else
+ {
+ if (debug)
+ {
+ fprintf(debug, "Opening library file %s\n", fn);
+ }
+ ff = fopen(fn, "r");
}
sfree(fn);
char *gmxlibfn(const char *file)
{
- return low_gmxlibfn(file,TRUE,TRUE);
+ return low_gmxlibfn(file, TRUE, TRUE);
}
FILE *libopen(const char *file)
{
- return low_libopen(file,TRUE);
+ return low_libopen(file, TRUE);
}
void gmx_tmpnam(char *buf)
{
- int i,len,fd;
+ int i, len, fd;
if ((len = strlen(buf)) < 7)
- gmx_fatal(FARGS,"Buf passed to gmx_tmpnam must be at least 7 bytes long");
- for(i=len-6; (i<len); i++) {
+ {
+ gmx_fatal(FARGS, "Buf passed to gmx_tmpnam must be at least 7 bytes long");
+ }
+ for (i = len-6; (i < len); i++)
+ {
buf[i] = 'X';
}
- /* mktemp is dangerous and we should use mkstemp instead, but
+ /* mktemp is dangerous and we should use mkstemp instead, but
* since windows doesnt support it we have to separate the cases.
* 20090307: mktemp deprecated, use iso c++ _mktemp instead.
*/
#else
fd = mkstemp(buf);
- switch (fd) {
+ switch (fd)
+ {
case EINVAL:
- gmx_fatal(FARGS,"Invalid template %s for mkstemp",buf);
+ gmx_fatal(FARGS, "Invalid template %s for mkstemp", buf);
break;
case EEXIST:
- gmx_fatal(FARGS,"mkstemp created existing file",buf);
+ gmx_fatal(FARGS, "mkstemp created existing file", buf);
break;
- case EACCES:
- gmx_fatal(FARGS,"Permission denied for opening %s",buf);
+ case EACCES:
+ gmx_fatal(FARGS, "Permission denied for opening %s", buf);
break;
default:
break;
- }
+ }
close(fd);
#endif
/* name in Buf should now be OK */
{
#ifdef _MSC_VER
/* Microsoft visual studio does not have "truncate" */
- HANDLE fh;
+ HANDLE fh;
LARGE_INTEGER win_length;
win_length.QuadPart = length;
- fh = CreateFile(path,GENERIC_READ | GENERIC_WRITE,0,NULL,
- OPEN_EXISTING,0,NULL);
- SetFilePointerEx(fh,win_length,NULL,FILE_BEGIN);
+ fh = CreateFile(path, GENERIC_READ | GENERIC_WRITE, 0, NULL,
+ OPEN_EXISTING, 0, NULL);
+ SetFilePointerEx(fh, win_length, NULL, FILE_BEGIN);
SetEndOfFile(fh);
CloseHandle(fh);
return 0;
#else
- return truncate(path,length);
+ return truncate(path, length);
#endif
}
/* under unix, rename() is atomic (at least, it should be). */
return rename(oldname, newname);
#else
- if (MoveFileEx(oldname, newname,
+ if (MoveFileEx(oldname, newname,
MOVEFILE_REPLACE_EXISTING|MOVEFILE_WRITE_THROUGH))
+ {
return 0;
+ }
else
+ {
return 1;
+ }
#endif
}
{
/* the full copy buffer size: */
#define FILECOPY_BUFSIZE (1<<16)
- FILE *in=NULL;
- FILE *out=NULL;
+ FILE *in = NULL;
+ FILE *out = NULL;
char *buf;
- snew(buf, FILECOPY_BUFSIZE);
+ snew(buf, FILECOPY_BUFSIZE);
- in=fopen(oldname, "rb");
+ in = fopen(oldname, "rb");
if (!in)
+ {
goto error;
+ }
/* If we don't copy when empty, we postpone opening the file
until we're actually ready to write. */
if (copy_if_empty)
{
- out=fopen(newname, "wb");
+ out = fopen(newname, "wb");
if (!out)
+ {
goto error;
+ }
}
- while(!feof(in))
+ while (!feof(in))
{
size_t nread;
-
- nread=fread(buf, sizeof(char), FILECOPY_BUFSIZE, in);
- if (nread>0)
+
+ nread = fread(buf, sizeof(char), FILECOPY_BUFSIZE, in);
+ if (nread > 0)
{
size_t ret;
if (!out)
{
/* so this is where we open when copy_if_empty is false:
here we know we read something. */
- out=fopen(newname, "wb");
+ out = fopen(newname, "wb");
if (!out)
+ {
goto error;
+ }
}
- ret=fwrite(buf, sizeof(char), nread, out);
- if (ret!=nread)
+ ret = fwrite(buf, sizeof(char), nread, out);
+ if (ret != nread)
{
goto error;
}
}
if (ferror(in))
+ {
goto error;
+ }
}
sfree(buf);
fclose(in);
error:
sfree(buf);
if (in)
+ {
fclose(in);
+ }
if (out)
+ {
fclose(out);
+ }
return 1;
#undef FILECOPY_BUFSIZE
}
int gmx_fsync(FILE *fp)
{
- int rc=0;
+ int rc = 0;
#ifdef GMX_FAHCORE
/* the fahcore defines its own os-independent fsync */
- rc=fah_fsync(fp);
+ rc = fah_fsync(fp);
#else /* GMX_FAHCORE */
{
- int fn=-1;
+ int fn = -1;
/* get the file number */
#if defined(HAVE_FILENO)
- fn= fileno(fp);
+ fn = fileno(fp);
#elif defined(HAVE__FILENO)
- fn= _fileno(fp);
+ fn = _fileno(fp);
#endif
/* do the actual fsync */
if (fn >= 0)
{
#if (defined(HAVE_FSYNC))
- rc=fsync(fn);
-#elif (defined(HAVE__COMMIT))
- rc=_commit(fn);
+ rc = fsync(fn);
+#elif (defined(HAVE__COMMIT))
+ rc = _commit(fn);
#endif
}
}
#ifdef EINTR
/* we don't want to report an error just because fsync() caught a signal.
For our purposes, we can just ignore this. */
- if (rc && errno==EINTR)
- rc=0;
+ if (rc && errno == EINTR)
+ {
+ rc = 0;
+ }
#endif
#ifdef EINVAL
- /* we don't want to report an error just because we tried to fsync()
+ /* we don't want to report an error just because we tried to fsync()
stdout, a socket or a pipe. */
- if (rc && errno==EINVAL)
- rc=0;
+ if (rc && errno == EINVAL)
+ {
+ rc = 0;
+ }
#endif
return rc;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff