/* -*- 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.
* Copyright (c) 2001-2004, The GROMACS development team,
* check out http://www.gromacs.org for more information.
-
+
* This program is free software; you can redistribute it and/or
* 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 <sys/sysmp.h>
#endif
-/* The source code in this file should be thread-safe.
+/* The source code in this file should be thread-safe.
Please keep it that way. */
/******************************************************************
gmx_bool bRmod_fd(double a, double b, double c, gmx_bool bDouble)
{
- int iq;
+ int iq;
double tol;
-
+
tol = 2*(bDouble ? GMX_DOUBLE_EPS : GMX_FLOAT_EPS);
-
+
iq = static_cast<int>((a - b + tol*a)/c);
-
+
if (std::fabs(a - b - c*iq) <= tol*std::fabs(a))
+ {
return TRUE;
+ }
else
+ {
return FALSE;
+ }
}
-int check_times2(real t,real t0,real tp, real tpp, gmx_bool bDouble)
+int check_times2(real t, real t0, real tp, real tpp, gmx_bool bDouble)
{
int r;
-
+
#ifndef GMX_DOUBLE
/* since t is float, we can not use double precision for bRmod */
bDouble = FALSE;
#endif
-
- r=-1;
+
+ r = -1;
if ((!bTimeSet(TBEGIN) || (t >= rTimeValue(TBEGIN))) &&
- (!bTimeSet(TEND) || (t <= rTimeValue(TEND)))) {
- if (bTimeSet(TDELTA) && !bRmod_fd(t,t0,rTimeValue(TDELTA),bDouble))
+ (!bTimeSet(TEND) || (t <= rTimeValue(TEND))))
+ {
+ if (bTimeSet(TDELTA) && !bRmod_fd(t, t0, rTimeValue(TDELTA), bDouble))
+ {
r = -1;
+ }
else
+ {
r = 0;
+ }
}
else if (bTimeSet(TEND) && (t >= rTimeValue(TEND)))
+ {
r = 1;
- if (debug)
- fprintf(debug,"t=%g, t0=%g, b=%g, e=%g, dt=%g: r=%d\n",
- t,t0,rTimeValue(TBEGIN),rTimeValue(TEND),rTimeValue(TDELTA),r);
+ }
+ if (debug)
+ {
+ fprintf(debug, "t=%g, t0=%g, b=%g, e=%g, dt=%g: r=%d\n",
+ t, t0, rTimeValue(TBEGIN), rTimeValue(TEND), rTimeValue(TDELTA), r);
+ }
return r;
}
int check_times(real t)
{
- return check_times2(t,t,t,t,FALSE);
+ return check_times2(t, t, t, t, FALSE);
}
static void set_default_time_unit(const char *time_list[], gmx_bool bCanTime)
{
- int i=0;
+ int i = 0;
const char *select = NULL;
if (bCanTime)
if (select != NULL)
{
i = 1;
- while(time_list[i] && strcmp(time_list[i], select) != 0)
+ while (time_list[i] && strcmp(time_list[i], select) != 0)
{
i++;
}
}
}
- if (!bCanTime || select == NULL ||
- time_list[i]==NULL || strcmp(time_list[i], select) != 0)
+ if (!bCanTime || select == NULL ||
+ time_list[i] == NULL || strcmp(time_list[i], select) != 0)
{
/* Set it to the default: ps */
i = 1;
- while(time_list[i] && strcmp(time_list[i], "ps") != 0)
+ while (time_list[i] && strcmp(time_list[i], "ps") != 0)
{
i++;
}
-
+
}
time_list[0] = time_list[i];
}
static void set_default_xvg_format(const char *xvg_list[])
{
- int i;
+ int i;
const char *select;
select = getenv("GMX_VIEW_XVG");
/***** T O P O L O G Y S T U F F ******/
-t_topology *read_top(const char *fn,int *ePBC)
+t_topology *read_top(const char *fn, int *ePBC)
{
- int epbc,natoms;
+ int epbc, natoms;
t_topology *top;
-
- snew(top,1);
- epbc = read_tpx_top(fn,NULL,NULL,&natoms,NULL,NULL,NULL,top);
+
+ snew(top, 1);
+ epbc = read_tpx_top(fn, NULL, NULL, &natoms, NULL, NULL, NULL, top);
if (ePBC)
+ {
*ePBC = epbc;
-
+ }
+
return top;
}
*
*************************************************************/
-static void usage(const char *type,const char *arg)
+static void usage(const char *type, const char *arg)
{
GMX_ASSERT(arg != NULL, "NULL command-line argument should not occur");
- gmx_fatal(FARGS,"Expected %s argument for option %s\n",type,arg);
+ gmx_fatal(FARGS, "Expected %s argument for option %s\n", type, arg);
}
-int iscan(int argc,char *argv[],int *i)
+int iscan(int argc, char *argv[], int *i)
{
const char *const arg = argv[*i];
if (argc <= (*i)+1)
usage("an integer", arg);
}
const char *const value = argv[++(*i)];
- char *endptr;
- int var = std::strtol(value, &endptr, 10);
+ char *endptr;
+ int var = std::strtol(value, &endptr, 10);
if (*value == '\0' || *endptr != '\0')
{
usage("an integer", arg);
return var;
}
-gmx_large_int_t istepscan(int argc,char *argv[],int *i)
+gmx_large_int_t istepscan(int argc, char *argv[], int *i)
{
const char *const arg = argv[*i];
if (argc <= (*i)+1)
usage("an integer", arg);
}
const char *const value = argv[++(*i)];
- char *endptr;
- gmx_large_int_t var = str_to_large_int_t(value, &endptr);
+ char *endptr;
+ gmx_large_int_t var = str_to_large_int_t(value, &endptr);
if (*value == '\0' || *endptr != '\0')
{
usage("an integer", arg);
return var;
}
-double dscan(int argc,char *argv[],int *i)
+double dscan(int argc, char *argv[], int *i)
{
const char *const arg = argv[*i];
if (argc <= (*i)+1)
usage("a real", arg);
}
const char *const value = argv[++(*i)];
- char *endptr;
- double var = std::strtod(value, &endptr);
+ char *endptr;
+ double var = std::strtod(value, &endptr);
if (*value == '\0' || *endptr != '\0')
{
usage("a real", arg);
return var;
}
-char *sscan(int argc,char *argv[],int *i)
+char *sscan(int argc, char *argv[], int *i)
{
- if (argc > (*i)+1)
+ if (argc > (*i)+1)
{
- if ( (argv[(*i)+1][0]=='-') && (argc > (*i)+2) &&
- (argv[(*i)+2][0]!='-') )
+ if ( (argv[(*i)+1][0] == '-') && (argc > (*i)+2) &&
+ (argv[(*i)+2][0] != '-') )
{
- fprintf(stderr,"Possible missing string argument for option %s\n\n",
+ fprintf(stderr, "Possible missing string argument for option %s\n\n",
argv[*i]);
}
- }
+ }
else
- usage("a string",argv[*i]);
-
+ {
+ usage("a string", argv[*i]);
+ }
+
return argv[++(*i)];
}
int nenum(const char *const enumc[])
{
int i;
-
- i=1;
+
+ i = 1;
/* we *can* compare pointers directly here! */
- while(enumc[i] && enumc[0]!=enumc[i])
+ while (enumc[i] && enumc[0] != enumc[i])
+ {
i++;
-
+ }
+
return i;
}
static void pdesc(char *desc)
{
- char *ptr,*nptr;
-
- ptr=desc;
+ char *ptr, *nptr;
+
+ ptr = desc;
if ((int)strlen(ptr) < 70)
- fprintf(stderr,"\t%s\n",ptr);
- else {
- for(nptr=ptr+70; (nptr != ptr) && (!std::isspace(*nptr)); nptr--)
+ {
+ fprintf(stderr, "\t%s\n", ptr);
+ }
+ else
+ {
+ for (nptr = ptr+70; (nptr != ptr) && (!std::isspace(*nptr)); nptr--)
+ {
;
+ }
if (nptr == ptr)
- fprintf(stderr,"\t%s\n",ptr);
- else {
- *nptr='\0';
+ {
+ fprintf(stderr, "\t%s\n", ptr);
+ }
+ else
+ {
+ *nptr = '\0';
nptr++;
- fprintf(stderr,"\t%s\n",ptr);
+ fprintf(stderr, "\t%s\n", ptr);
pdesc(nptr);
}
}
}
-static FILE *man_file(const output_env_t oenv,const char *mantp)
+static FILE *man_file(const output_env_t oenv, const char *mantp)
{
- FILE *fp;
- char buf[256];
+ FILE *fp;
+ char buf[256];
const char *pr = output_env_get_short_program_name(oenv);
-
- if (strcmp(mantp,"ascii") != 0)
- sprintf(buf,"%s.%s",pr,mantp);
+
+ if (strcmp(mantp, "ascii") != 0)
+ {
+ sprintf(buf, "%s.%s", pr, mantp);
+ }
else
- sprintf(buf,"%s.txt",pr);
- fp = gmx_fio_fopen(buf,"w");
-
+ {
+ sprintf(buf, "%s.txt", pr);
+ }
+ fp = gmx_fio_fopen(buf, "w");
+
return fp;
}
-static int add_parg(int npargs,t_pargs *pa,t_pargs *pa_add)
+static int add_parg(int npargs, t_pargs *pa, t_pargs *pa_add)
{
- memcpy(&(pa[npargs]),pa_add,sizeof(*pa_add));
-
+ memcpy(&(pa[npargs]), pa_add, sizeof(*pa_add));
+
return npargs+1;
}
static char *mk_desc(t_pargs *pa, const char *time_unit_str)
{
- char *newdesc=NULL,*ndesc=NULL,*nptr=NULL;
- const char*ptr=NULL;
- int len,k;
-
+ char *newdesc = NULL, *ndesc = NULL, *nptr = NULL;
+ const char*ptr = NULL;
+ int len, k;
+
/* First compute length for description */
len = strlen(pa->desc)+1;
- if ((ptr = strstr(pa->desc,"HIDDEN")) != NULL)
+ if ((ptr = strstr(pa->desc, "HIDDEN")) != NULL)
+ {
len += 4;
- if (pa->type == etENUM) {
+ }
+ if (pa->type == etENUM)
+ {
len += 10;
- for(k=1; (pa->u.c[k] != NULL); k++) {
+ for (k = 1; (pa->u.c[k] != NULL); k++)
+ {
len += strlen(pa->u.c[k])+12;
}
}
- snew(newdesc,len);
-
+ snew(newdesc, len);
+
/* add label for hidden options */
- if (is_hidden(pa))
- sprintf(newdesc,"[hidden] %s",ptr+6);
+ if (is_hidden(pa))
+ {
+ sprintf(newdesc, "[hidden] %s", ptr+6);
+ }
else
- strcpy(newdesc,pa->desc);
-
+ {
+ strcpy(newdesc, pa->desc);
+ }
+
/* change '%t' into time_unit */
#define TUNITLABEL "%t"
#define NTUNIT strlen(TUNITLABEL)
if (pa->type == etTIME)
- while( (nptr=strstr(newdesc,TUNITLABEL)) != NULL ) {
- nptr[0]='\0';
- nptr+=NTUNIT;
- len+=strlen(time_unit_str)-NTUNIT;
- snew(ndesc,len);
- strcpy(ndesc,newdesc);
- strcat(ndesc,time_unit_str);
- strcat(ndesc,nptr);
+ {
+ while ( (nptr = strstr(newdesc, TUNITLABEL)) != NULL)
+ {
+ nptr[0] = '\0';
+ nptr += NTUNIT;
+ len += strlen(time_unit_str)-NTUNIT;
+ snew(ndesc, len);
+ strcpy(ndesc, newdesc);
+ strcat(ndesc, time_unit_str);
+ strcat(ndesc, nptr);
sfree(newdesc);
- newdesc=ndesc;
- ndesc=NULL;
+ newdesc = ndesc;
+ ndesc = NULL;
}
+ }
#undef TUNITLABEL
#undef NTUNIT
-
+
/* Add extra comment for enumerateds */
- if (pa->type == etENUM) {
- strcat(newdesc,": ");
- for(k=1; (pa->u.c[k] != NULL); k++) {
- strcat(newdesc,"[TT]");
- strcat(newdesc,pa->u.c[k]);
- strcat(newdesc,"[tt]");
+ if (pa->type == etENUM)
+ {
+ strcat(newdesc, ": ");
+ for (k = 1; (pa->u.c[k] != NULL); k++)
+ {
+ strcat(newdesc, "[TT]");
+ strcat(newdesc, pa->u.c[k]);
+ strcat(newdesc, "[tt]");
/* Print a comma everywhere but at the last one */
- if (pa->u.c[k+1] != NULL) {
+ if (pa->u.c[k+1] != NULL)
+ {
if (pa->u.c[k+2] == NULL)
- strcat(newdesc," or ");
+ {
+ strcat(newdesc, " or ");
+ }
else
- strcat(newdesc,", ");
+ {
+ strcat(newdesc, ", ");
+ }
}
}
}
}
-void parse_common_args(int *argc,char *argv[],unsigned long Flags,
- int nfile,t_filenm fnm[],int npargs,t_pargs *pa,
- int ndesc,const char **desc,
- int nbugs,const char **bugs,
+void parse_common_args(int *argc, char *argv[], unsigned long Flags,
+ int nfile, t_filenm fnm[], int npargs, t_pargs *pa,
+ int ndesc, const char **desc,
+ int nbugs, const char **bugs,
output_env_t *oenv)
{
- gmx_bool bHelp=FALSE,bHidden=FALSE,bQuiet=FALSE,bVersion=FALSE;
- const char *manstr[] = { NULL, "no", "html", "tex", "nroff", "ascii",
- "completion", "py", "xml", "wiki", NULL };
+ gmx_bool bHelp = FALSE, bHidden = FALSE, bQuiet = FALSE, bVersion = FALSE;
+ const char *manstr[] = {
+ NULL, "no", "html", "tex", "nroff", "ascii",
+ "completion", "py", "xml", "wiki", NULL
+ };
/* This array should match the order of the enum in oenv.h */
const char *xvg_format[] = { NULL, "xmgrace", "xmgr", "none", NULL };
/* This array should match the order of the enum in oenv.h */
- const char *time_units[] = { NULL, "fs", "ps", "ns", "us", "ms", "s",
- NULL };
- int nicelevel=0,debug_level=0,verbose_level=0;
- char *deffnm=NULL;
- real tbegin=0,tend=0,tdelta=0;
- gmx_bool bView=FALSE;
-
- t_pargs *all_pa=NULL;
-
+ const char *time_units[] = {
+ NULL, "fs", "ps", "ns", "us", "ms", "s",
+ NULL
+ };
+ int nicelevel = 0, debug_level = 0, verbose_level = 0;
+ char *deffnm = NULL;
+ real tbegin = 0, tend = 0, tdelta = 0;
+ gmx_bool bView = FALSE;
+
+ t_pargs *all_pa = NULL;
+
#ifdef __sgi
- int npri=0;
- t_pargs npri_pa = { "-npri", FALSE, etINT, {&npri},
- "HIDDEN Set non blocking priority (try 128)" };
+ int npri = 0;
+ t_pargs npri_pa = {
+ "-npri", FALSE, etINT, {&npri},
+ "HIDDEN Set non blocking priority (try 128)"
+ };
#endif
- t_pargs nice_pa = { "-nice", FALSE, etINT, {&nicelevel},
- "Set the nicelevel" };
- t_pargs deffnm_pa = { "-deffnm", FALSE, etSTR, {&deffnm},
- "Set the default filename for all file options" };
- t_pargs begin_pa = { "-b", FALSE, etTIME, {&tbegin},
- "First frame (%t) to read from trajectory" };
- t_pargs end_pa = { "-e", FALSE, etTIME, {&tend},
- "Last frame (%t) to read from trajectory" };
- t_pargs dt_pa = { "-dt", FALSE, etTIME, {&tdelta},
- "Only use frame when t MOD dt = first time (%t)" };
- t_pargs view_pa = { "-w", FALSE, etBOOL, {&bView},
- "View output [TT].xvg[tt], [TT].xpm[tt], [TT].eps[tt] and [TT].pdb[tt] files" };
- t_pargs xvg_pa = { "-xvg", FALSE, etENUM, {xvg_format},
- "xvg plot formatting" };
- t_pargs time_pa = { "-tu", FALSE, etENUM, {time_units},
- "Time unit" };
+ t_pargs nice_pa = {
+ "-nice", FALSE, etINT, {&nicelevel},
+ "Set the nicelevel"
+ };
+ t_pargs deffnm_pa = {
+ "-deffnm", FALSE, etSTR, {&deffnm},
+ "Set the default filename for all file options"
+ };
+ t_pargs begin_pa = {
+ "-b", FALSE, etTIME, {&tbegin},
+ "First frame (%t) to read from trajectory"
+ };
+ t_pargs end_pa = {
+ "-e", FALSE, etTIME, {&tend},
+ "Last frame (%t) to read from trajectory"
+ };
+ t_pargs dt_pa = {
+ "-dt", FALSE, etTIME, {&tdelta},
+ "Only use frame when t MOD dt = first time (%t)"
+ };
+ t_pargs view_pa = {
+ "-w", FALSE, etBOOL, {&bView},
+ "View output [TT].xvg[tt], [TT].xpm[tt], [TT].eps[tt] and [TT].pdb[tt] files"
+ };
+ t_pargs xvg_pa = {
+ "-xvg", FALSE, etENUM, {xvg_format},
+ "xvg plot formatting"
+ };
+ t_pargs time_pa = {
+ "-tu", FALSE, etENUM, {time_units},
+ "Time unit"
+ };
/* Maximum number of extra arguments */
#define EXTRA_PA 16
-
- t_pargs pca_pa[] = {
- { "-h", FALSE, etBOOL, {&bHelp},
- "Print help info and quit" },
- { "-version", FALSE, etBOOL, {&bVersion},
- "Print version info and quit" },
- { "-verb", FALSE, etINT, {&verbose_level},
- "HIDDENLevel of verbosity for this program" },
- { "-hidden", FALSE, etBOOL, {&bHidden},
- "HIDDENPrint hidden options" },
- { "-quiet",FALSE, etBOOL, {&bQuiet},
- "HIDDENDo not print help info" },
- { "-man", FALSE, etENUM, {manstr},
- "HIDDENWrite manual and quit" },
- { "-debug",FALSE, etINT, {&debug_level},
- "HIDDENWrite file with debug information, 1: short, 2: also x and f" },
+
+ t_pargs pca_pa[] = {
+ { "-h", FALSE, etBOOL, {&bHelp},
+ "Print help info and quit" },
+ { "-version", FALSE, etBOOL, {&bVersion},
+ "Print version info and quit" },
+ { "-verb", FALSE, etINT, {&verbose_level},
+ "HIDDENLevel of verbosity for this program" },
+ { "-hidden", FALSE, etBOOL, {&bHidden},
+ "HIDDENPrint hidden options" },
+ { "-quiet", FALSE, etBOOL, {&bQuiet},
+ "HIDDENDo not print help info" },
+ { "-man", FALSE, etENUM, {manstr},
+ "HIDDENWrite manual and quit" },
+ { "-debug", FALSE, etINT, {&debug_level},
+ "HIDDENWrite file with debug information, 1: short, 2: also x and f" },
};
#define NPCA_PA asize(pca_pa)
- FILE *fp;
- gmx_bool bPrint,bExit,bXvgr;
- int i,j,k,npall,max_pa;
-
-#define FF(arg) ((Flags & arg)==arg)
+ FILE *fp;
+ gmx_bool bPrint, bExit, bXvgr;
+ int i, j, k, npall, max_pa;
+
+#define FF(arg) ((Flags & arg) == arg)
/* Check for double arguments */
- for (i=1; (i<*argc); i++)
+ for (i = 1; (i < *argc); i++)
{
if (argv[i] && (strlen(argv[i]) > 1) && (!std::isdigit(argv[i][1])))
{
- for (j=i+1; (j<*argc); j++)
+ for (j = i+1; (j < *argc); j++)
{
- if ( (argv[i][0]=='-') && (argv[j][0]=='-') &&
- (strcmp(argv[i],argv[j])==0) )
+ if ( (argv[i][0] == '-') && (argv[j][0] == '-') &&
+ (strcmp(argv[i], argv[j]) == 0) )
{
if (FF(PCA_NOEXIT_ON_ARGS))
- fprintf(stderr,"Double command line argument %s\n",
+ {
+ fprintf(stderr, "Double command line argument %s\n",
argv[i]);
+ }
else
- gmx_fatal(FARGS,"Double command line argument %s\n",
+ {
+ gmx_fatal(FARGS, "Double command line argument %s\n",
argv[i]);
+ }
}
}
}
}
debug_gmx();
gmx::ProgramInfo::init(*argc, argv);
-
- /* Handle the flags argument, which is a bit field
+
+ /* Handle the flags argument, which is a bit field
* The FF macro returns whether or not the bit is set
*/
bPrint = !FF(PCA_SILENT);
-
+
/* Check ALL the flags ... */
max_pa = NPCA_PA + EXTRA_PA + npargs+1;
- snew(all_pa,max_pa);
-
- for(i=npall=0; (i<static_cast<int>(NPCA_PA)); i++)
- npall = add_parg(npall,all_pa,&(pca_pa[i]));
-
+ snew(all_pa, max_pa);
+
+ for (i = npall = 0; (i < static_cast<int>(NPCA_PA)); i++)
+ {
+ npall = add_parg(npall, all_pa, &(pca_pa[i]));
+ }
+
#ifdef __sgi
const char *envstr = getenv("GMXNPRIALL");
if (envstr)
- npri=strtol(envstr,NULL,10);
- if (FF(PCA_BE_NICE)) {
+ {
+ npri = strtol(envstr, NULL, 10);
+ }
+ if (FF(PCA_BE_NICE))
+ {
envstr = getenv("GMXNPRI");
if (envstr)
- npri=strtol(envstr,NULL,10);
+ {
+ npri = strtol(envstr, NULL, 10);
+ }
}
- npall = add_parg(npall,all_pa,&npri_pa);
+ npall = add_parg(npall, all_pa, &npri_pa);
#endif
-
- if (FF(PCA_BE_NICE))
- nicelevel=19;
- npall = add_parg(npall,all_pa,&nice_pa);
-
- if (FF(PCA_CAN_SET_DEFFNM))
- npall = add_parg(npall,all_pa,&deffnm_pa);
- if (FF(PCA_CAN_BEGIN))
- npall = add_parg(npall,all_pa,&begin_pa);
+
+ if (FF(PCA_BE_NICE))
+ {
+ nicelevel = 19;
+ }
+ npall = add_parg(npall, all_pa, &nice_pa);
+
+ if (FF(PCA_CAN_SET_DEFFNM))
+ {
+ npall = add_parg(npall, all_pa, &deffnm_pa);
+ }
+ if (FF(PCA_CAN_BEGIN))
+ {
+ npall = add_parg(npall, all_pa, &begin_pa);
+ }
if (FF(PCA_CAN_END))
- npall = add_parg(npall,all_pa,&end_pa);
+ {
+ npall = add_parg(npall, all_pa, &end_pa);
+ }
if (FF(PCA_CAN_DT))
{
- npall = add_parg(npall,all_pa,&dt_pa);
+ npall = add_parg(npall, all_pa, &dt_pa);
}
- if (FF(PCA_TIME_UNIT)) {
- npall = add_parg(npall,all_pa,&time_pa);
- }
- if (FF(PCA_CAN_VIEW))
- npall = add_parg(npall,all_pa,&view_pa);
-
+ if (FF(PCA_TIME_UNIT))
+ {
+ npall = add_parg(npall, all_pa, &time_pa);
+ }
+ if (FF(PCA_CAN_VIEW))
+ {
+ npall = add_parg(npall, all_pa, &view_pa);
+ }
+
bXvgr = FALSE;
- for(i=0; (i<nfile); i++)
+ for (i = 0; (i < nfile); i++)
{
bXvgr = bXvgr || (fnm[i].ftp == efXVG);
}
if (bXvgr)
{
- npall = add_parg(npall,all_pa,&xvg_pa);
+ npall = add_parg(npall, all_pa, &xvg_pa);
}
-
+
/* Now append the program specific arguments */
- for(i=0; (i<npargs); i++)
- npall = add_parg(npall,all_pa,&(pa[i]));
-
+ for (i = 0; (i < npargs); i++)
+ {
+ npall = add_parg(npall, all_pa, &(pa[i]));
+ }
+
/* set etENUM options to default */
- for(i=0; (i<npall); i++)
+ for (i = 0; (i < npall); i++)
{
- if (all_pa[i].type==etENUM)
+ if (all_pa[i].type == etENUM)
{
- all_pa[i].u.c[0]=all_pa[i].u.c[1];
+ all_pa[i].u.c[0] = all_pa[i].u.c[1];
}
}
- set_default_time_unit(time_units,FF(PCA_TIME_UNIT));
+ set_default_time_unit(time_units, FF(PCA_TIME_UNIT));
set_default_xvg_format(xvg_format);
-
+
/* Now parse all the command-line options */
- get_pargs(argc,argv,npall,all_pa,FF(PCA_KEEP_ARGS));
+ get_pargs(argc, argv, npall, all_pa, FF(PCA_KEEP_ARGS));
/* set program name, command line, and default values for output options */
output_env_init(oenv, *argc, argv, (time_unit_t)nenum(time_units), bView,
(xvg_format_t)nenum(xvg_format), verbose_level, debug_level);
-
- if (bVersion) {
- printf("Program: %s\n",output_env_get_program_name(*oenv));
- gmx_print_version_info(stdout);
- exit(0);
- }
-
- if (FF(PCA_CAN_SET_DEFFNM) && (deffnm!=NULL))
+
+ if (bVersion)
+ {
+ printf("Program: %s\n", output_env_get_program_name(*oenv));
+ gmx_print_version_info(stdout);
+ exit(0);
+ }
+
+ if (FF(PCA_CAN_SET_DEFFNM) && (deffnm != NULL))
+ {
set_default_file_name(deffnm);
-
+ }
+
/* Parse the file args */
- parse_file_args(argc,argv,nfile,fnm,FF(PCA_KEEP_ARGS),!FF(PCA_NOT_READ_NODE));
-
+ parse_file_args(argc, argv, nfile, fnm, FF(PCA_KEEP_ARGS), !FF(PCA_NOT_READ_NODE));
+
/* Open the debug file */
- if (debug_level > 0) {
+ if (debug_level > 0)
+ {
char buf[256];
-
+
if (gmx_mpi_initialized())
- sprintf(buf,"%s%d.debug",output_env_get_short_program_name(*oenv),
+ {
+ sprintf(buf, "%s%d.debug", output_env_get_short_program_name(*oenv),
gmx_node_rank());
+ }
else
- sprintf(buf,"%s.debug",output_env_get_short_program_name(*oenv));
-
- init_debug(debug_level,buf);
- fprintf(stderr,"Opening debug file %s (src code file %s, line %d)\n",
- buf,__FILE__,__LINE__);
+ {
+ sprintf(buf, "%s.debug", output_env_get_short_program_name(*oenv));
+ }
+
+ init_debug(debug_level, buf);
+ fprintf(stderr, "Opening debug file %s (src code file %s, line %d)\n",
+ buf, __FILE__, __LINE__);
}
-
+
/* Now copy the results back... */
- for(i=0,k=npall-npargs; (i<npargs); i++,k++)
- memcpy(&(pa[i]),&(all_pa[k]),(size_t)sizeof(pa[i]));
+ for (i = 0, k = npall-npargs; (i < npargs); i++, k++)
+ {
+ memcpy(&(pa[i]), &(all_pa[k]), (size_t)sizeof(pa[i]));
+ }
- for(i=0; (i<npall); i++)
+ for (i = 0; (i < npall); i++)
+ {
all_pa[i].desc = mk_desc(&(all_pa[i]), output_env_get_time_unit(*oenv));
-
- bExit = bHelp || (strcmp(manstr[0],"no") != 0);
-
+ }
+
+ bExit = bHelp || (strcmp(manstr[0], "no") != 0);
+
#if (defined __sgi && USE_SGI_FPE)
doexceptions();
#endif
-
+
/* Set the nice level */
#ifdef __sgi
- if (npri != 0 && !bExit) {
- schedctl(MPTS_RTPRI,0,npri);
+ if (npri != 0 && !bExit)
+ {
+ schedctl(MPTS_RTPRI, 0, npri);
}
-#endif
-
+#endif
+
#ifdef HAVE_UNISTD_H
#ifndef GMX_NO_NICE
/* The some system, e.g. the catamount kernel on cray xt3 do not have nice(2). */
if (nicelevel != 0 && !bExit)
{
- static gmx_bool nice_set=FALSE; /* only set it once */
+ static gmx_bool nice_set = FALSE; /* only set it once */
static tMPI_Thread_mutex_t init_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
tMPI_Thread_mutex_lock(&init_mutex);
if (!nice_set)
{
/* Do nothing, but use the return value to avoid warnings. */
}
- nice_set=TRUE;
+ nice_set = TRUE;
}
tMPI_Thread_mutex_unlock(&init_mutex);
}
#endif
#endif
-
- if (!(FF(PCA_QUIET) || bQuiet )) {
+
+ if (!(FF(PCA_QUIET) || bQuiet ))
+ {
if (bHelp)
- write_man(stderr,"help",output_env_get_program_name(*oenv),
- ndesc,desc,nfile, fnm,npall,all_pa, nbugs,bugs,bHidden);
- else if (bPrint) {
- pr_fns(stderr,nfile,fnm);
- print_pargs(stderr,npall,all_pa,FALSE);
+ {
+ write_man(stderr, "help", output_env_get_program_name(*oenv),
+ ndesc, desc, nfile, fnm, npall, all_pa, nbugs, bugs, bHidden);
+ }
+ else if (bPrint)
+ {
+ pr_fns(stderr, nfile, fnm);
+ print_pargs(stderr, npall, all_pa, FALSE);
}
}
-
- if (strcmp(manstr[0],"no") != 0) {
- if(!strcmp(manstr[0],"completion")) {
+
+ if (strcmp(manstr[0], "no") != 0)
+ {
+ if (!strcmp(manstr[0], "completion"))
+ {
/* one file each for csh, bash and zsh if we do completions */
- fp=man_file(*oenv,"completion-zsh");
-
- write_man(fp,"completion-zsh",output_env_get_program_name(*oenv),
- ndesc,desc,nfile, fnm, npall,all_pa,nbugs,bugs,bHidden);
+ fp = man_file(*oenv, "completion-zsh");
+
+ write_man(fp, "completion-zsh", output_env_get_program_name(*oenv),
+ ndesc, desc, nfile, fnm, npall, all_pa, nbugs, bugs, bHidden);
gmx_fio_fclose(fp);
- fp=man_file(*oenv,"completion-bash");
- write_man(fp,"completion-bash",output_env_get_program_name(*oenv),
- ndesc,desc,nfile, fnm, npall,all_pa,nbugs,bugs,bHidden);
+ fp = man_file(*oenv, "completion-bash");
+ write_man(fp, "completion-bash", output_env_get_program_name(*oenv),
+ ndesc, desc, nfile, fnm, npall, all_pa, nbugs, bugs, bHidden);
gmx_fio_fclose(fp);
- fp=man_file(*oenv,"completion-csh");
- write_man(fp,"completion-csh",output_env_get_program_name(*oenv),
- ndesc,desc,nfile, fnm, npall,all_pa,nbugs,bugs,bHidden);
+ fp = man_file(*oenv, "completion-csh");
+ write_man(fp, "completion-csh", output_env_get_program_name(*oenv),
+ ndesc, desc, nfile, fnm, npall, all_pa, nbugs, bugs, bHidden);
gmx_fio_fclose(fp);
- } else {
- fp=man_file(*oenv,manstr[0]);
- write_man(fp,manstr[0],output_env_get_program_name(*oenv),
- ndesc,desc,nfile,fnm, npall, all_pa,nbugs,bugs,bHidden);
+ }
+ else
+ {
+ fp = man_file(*oenv, manstr[0]);
+ write_man(fp, manstr[0], output_env_get_program_name(*oenv),
+ ndesc, desc, nfile, fnm, npall, all_pa, nbugs, bugs, bHidden);
gmx_fio_fclose(fp);
}
}
-
+
/* convert time options, must be done after printing! */
-
- for(i=0; i<npall; i++) {
- if ((all_pa[i].type == etTIME) && (*all_pa[i].u.r >= 0)) {
+
+ for (i = 0; i < npall; i++)
+ {
+ if ((all_pa[i].type == etTIME) && (*all_pa[i].u.r >= 0))
+ {
*all_pa[i].u.r *= output_env_get_time_invfactor(*oenv);
}
}
-
+
/* Extract Time info from arguments */
- if (FF(PCA_CAN_BEGIN) && opt2parg_bSet("-b",npall,all_pa))
- setTimeValue(TBEGIN,opt2parg_real("-b",npall,all_pa));
-
- if (FF(PCA_CAN_END) && opt2parg_bSet("-e",npall,all_pa))
- setTimeValue(TEND,opt2parg_real("-e",npall,all_pa));
-
- if (FF(PCA_CAN_DT) && opt2parg_bSet("-dt",npall,all_pa))
- setTimeValue(TDELTA,opt2parg_real("-dt",npall,all_pa));
-
+ if (FF(PCA_CAN_BEGIN) && opt2parg_bSet("-b", npall, all_pa))
+ {
+ setTimeValue(TBEGIN, opt2parg_real("-b", npall, all_pa));
+ }
+
+ if (FF(PCA_CAN_END) && opt2parg_bSet("-e", npall, all_pa))
+ {
+ setTimeValue(TEND, opt2parg_real("-e", npall, all_pa));
+ }
+
+ if (FF(PCA_CAN_DT) && opt2parg_bSet("-dt", npall, all_pa))
+ {
+ setTimeValue(TDELTA, opt2parg_real("-dt", npall, all_pa));
+ }
+
/* clear memory */
for (i = 0; i < npall; ++i)
+ {
sfree((void *)all_pa[i].desc);
+ }
sfree(all_pa);
-
- if (!FF(PCA_NOEXIT_ON_ARGS)) {
- if (*argc > 1) {
+
+ if (!FF(PCA_NOEXIT_ON_ARGS))
+ {
+ if (*argc > 1)
+ {
gmx_cmd(argv[1]);
}
- }
+ }
if (bExit)
{
gmx_finalize_par();
}
#undef FF
}
-
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff