gmx_bool 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)
{
/* 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;
char *deffnm = NULL;
real tbegin = 0, tend = 0, tdelta = 0;
gmx_bool bView = FALSE;
t_pargs *all_pa = NULL;
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[] = {
{ "-debug", FALSE, etINT, {&debug_level},
"HIDDENWrite file with debug information, 1: short, 2: also x and f" },
};
#define NPCA_PA asize(pca_pa)
gmx_bool bXvgr;
int i, j, k, npall, max_pa;
// Handle the flags argument, which is a bit field
// The FF macro returns whether or not the bit is set
#define FF(arg) ((Flags & arg) == arg)
/* Check for double arguments */
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++)
{
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",
argv[i]);
}
else
{
gmx_fatal(FARGS, "Double command line argument %s\n",
argv[i]);
}
}
}
}
}
debug_gmx();
/* 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]));
}
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);
}
if (FF(PCA_CAN_DT))
{
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);
}
bXvgr = FALSE;
for (i = 0; (i < nfile); i++)
{
bXvgr = bXvgr || (fnm[i].ftp == efXVG);
}
if (bXvgr)
{
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]));
}
/* set etENUM options to default */
for (i = 0; (i < npall); i++)
{
if (all_pa[i].type == etENUM)
{
all_pa[i].u.c[0] = all_pa[i].u.c[1];
}
}
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);
/* set program name, command line, and default values for output options */
output_env_init(oenv, gmx::getProgramContext(), (time_unit_t)nenum(time_units), bView,
(xvg_format_t)nenum(xvg_format), 0, debug_level);
/* Parse the file args */
parse_file_args(argc, argv, nfile, fnm, deffnm, !FF(PCA_NOT_READ_NODE));
/* Open the debug file */
if (debug_level > 0)
{
char buf[256];
if (gmx_mpi_initialized())
{
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__);
}
/* 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]));
}
bool bExit = false;
try
{
const gmx::CommandLineHelpContext *context =
gmx::GlobalCommandLineHelpContext::get();
bExit = (context != NULL);
if (context != NULL && !(FF(PCA_QUIET)))
{
gmx::Options options(NULL, NULL);
options.setDescription(gmx::constArrayRefFromArray(desc, ndesc));
for (i = 0; i < nfile; i++)
{
gmx::filenmToOptions(&options, &fnm[i]);
}
for (i = 0; i < npall; i++)
{
gmx::pargsToOptions(&options, &all_pa[i]);
}
gmx::CommandLineHelpWriter(options)
.setShowDescriptions(true)
.setTimeUnitString(output_env_get_time_unit(*oenv))
.setKnownIssues(gmx::constArrayRefFromArray(bugs, nbugs))
.writeHelp(*context);
}
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
/* Set the nice level */
#if defined(HAVE_UNISTD_H) && !defined(__MINGW32__)
#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 tMPI_Thread_mutex_t init_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
tMPI_Thread_mutex_lock(&init_mutex);
if (!nice_set)
{
if (nice(nicelevel) == -1)
{
/* Do nothing, but use the return value to avoid warnings. */
}
nice_set = TRUE;
}
tMPI_Thread_mutex_unlock(&init_mutex);
}
#endif
#endif
/* convert time options, must be done after printing! */
for (i = 0; i < npall; i++)
{
if (all_pa[i].type == etTIME && all_pa[i].bSet)
{
*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));
}
/* clear memory */
sfree(all_pa);
if (!FF(PCA_NOEXIT_ON_ARGS))
{
if (*argc > 1)
{
gmx_cmd(argv[1]);
}
}
return !bExit;
#undef FF
}
static void edit_files(char **fnms, int nfiles, real *readtime, real *timestep,
real *settime, int *cont_type, gmx_bool bSetTime,
gmx_bool bSort, const output_env_t oenv)
{
int i;
gmx_bool ok;
char inputstring[STRLEN], *chptr;
if (bSetTime)
{
fprintf(stderr, "\n\nEnter the new start time (%s) for each file.\n"
"There are two special options, both disable sorting:\n\n"
"c (continue) - The start time is taken from the end\n"
"of the previous file. Use it when your continuation run\n"
"restarts with t=0.\n\n"
"l (last) - The time in this file will be changed the\n"
"same amount as in the previous. Use it when the time in the\n"
"new run continues from the end of the previous one,\n"
"since this takes possible overlap into account.\n\n",
output_env_get_time_unit(oenv));
fprintf(
stderr,
" File Current start (%s) New start (%s)\n"
"---------------------------------------------------------\n",
output_env_get_time_unit(oenv), output_env_get_time_unit(oenv));
for (i = 0; i < nfiles; i++)
{
fprintf(stderr, "%25s %10.3f %s ", fnms[i],
output_env_conv_time(oenv, readtime[i]), output_env_get_time_unit(oenv));
ok = FALSE;
do
{
if (NULL == fgets(inputstring, STRLEN - 1, stdin))
{
gmx_fatal(FARGS, "Error reading user input" );
}
inputstring[strlen(inputstring)-1] = 0;
if (inputstring[0] == 'c' || inputstring[0] == 'C')
{
cont_type[i] = TIME_CONTINUE;
bSort = FALSE;
ok = TRUE;
settime[i] = FLT_MAX;
}
else if (inputstring[0] == 'l' ||
inputstring[0] == 'L')
{
cont_type[i] = TIME_LAST;
bSort = FALSE;
ok = TRUE;
settime[i] = FLT_MAX;
}
else
{
settime[i] = strtod(inputstring, &chptr)*
output_env_get_time_invfactor(oenv);
if (chptr == inputstring)
{
fprintf(stderr, "'%s' not recognized as a floating point number, 'c' or 'l'. "
"Try again: ", inputstring);
}
else
{
cont_type[i] = TIME_EXPLICIT;
ok = TRUE;
}
}
}
while (!ok);
}
if (cont_type[0] != TIME_EXPLICIT)
{
cont_type[0] = TIME_EXPLICIT;
settime[0] = 0;
}
}
else
{
for (i = 0; i < nfiles; i++)
{
settime[i] = readtime[i];
}
}
if (!bSort)
{
fprintf(stderr, "Sorting disabled.\n");
}
else
{
sort_files(fnms, settime, nfiles);
}
/* Write out the new order and start times */
fprintf(stderr, "\nSummary of files and start times used:\n\n"
" File Start time Time step\n"
"---------------------------------------------------------\n");
for (i = 0; i < nfiles; i++)
{
switch (cont_type[i])
{
case TIME_EXPLICIT:
fprintf(stderr, "%25s %10.3f %s %10.3f %s",
fnms[i],
output_env_conv_time(oenv, settime[i]), output_env_get_time_unit(oenv),
output_env_conv_time(oenv, timestep[i]), output_env_get_time_unit(oenv));
if (i > 0 &&
cont_type[i-1] == TIME_EXPLICIT && settime[i] == settime[i-1])
{
fprintf(stderr, " WARNING: same Start time as previous");
}
fprintf(stderr, "\n");
break;
case TIME_CONTINUE:
fprintf(stderr, "%25s Continue from last file\n", fnms[i]);
break;
case TIME_LAST:
fprintf(stderr, "%25s Change by same amount as last file\n",
fnms[i]);
break;
}
}
fprintf(stderr, "\n");
settime[nfiles] = FLT_MAX;
cont_type[nfiles] = TIME_EXPLICIT;
readtime[nfiles] = FLT_MAX;
}
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 };
/* 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,mantp=0,npri=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;
t_pargs npri_pa = { "-npri", FALSE, etINT, {&npri},
"HIDDEN Set non blocking priority (try 128)" };
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 xvg, xpm, eps and pdb 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" },
};
#define NPCA_PA asize(pca_pa)
FILE *fp;
gmx_bool bPrint,bExit,bXvgr;
int i,j,k,npall,max_pa,cmdlength;
char *ptr,*newdesc;
const char *envstr;
#define FF(arg) ((Flags & arg)==arg)
snew(*oenv, 1);
cmdlength = strlen(argv[0]);
/* Check for double arguments */
for (i=1; (i<*argc); i++)
{
cmdlength += strlen(argv[i]);
if (argv[i] && (strlen(argv[i]) > 1) && (!isdigit(argv[i][1])))
{
for (j=i+1; (j<*argc); j++)
{
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",
argv[i]);
else
gmx_fatal(FARGS,"Double command line argument %s\n",
argv[i]);
}
}
}
}
debug_gmx();
set_program_name(argv[0]);
set_command_line(*argc, argv);
/* 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<NPCA_PA); i++)
npall = add_parg(npall,all_pa,&(pca_pa[i]));
#ifdef __sgi
envstr = getenv("GMXNPRIALL");
if (envstr)
npri=strtol(envstr,NULL,10);
if (FF(PCA_BE_NICE)) {
envstr = getenv("GMXNPRI");
if (envstr)
npri=strtol(envstr,NULL,10);
}
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_CAN_END))
npall = add_parg(npall,all_pa,&end_pa);
if (FF(PCA_CAN_DT))
{
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);
bXvgr = FALSE;
for(i=0; (i<nfile); i++)
{
bXvgr = bXvgr || (fnm[i].ftp == efXVG);
}
if (bXvgr)
{
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]));
/* set etENUM options to default */
for(i=0; (i<npall); i++)
{
if (all_pa[i].type==etENUM)
{
all_pa[i].u.c[0]=all_pa[i].u.c[1];
}
}
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));
/* 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))
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));
/* Open the debug file */
if (debug_level > 0) {
char buf[256];
if (gmx_mpi_initialized())
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__);
}
/* 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; (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);
#if (defined __sgi && USE_SGI_FPE)
doexceptions();
#endif
/* Set the nice level */
#ifdef __sgi
if (npri != 0 && !bExit) {
schedctl(MPTS_RTPRI,0,npri);
}
#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)
{
#ifdef GMX_THREADS
static gmx_bool nice_set=FALSE; /* only set it once */
tMPI_Thread_mutex_lock(&init_mutex);
if (!nice_set)
{
#endif
i=nice(nicelevel); /* assign ret value to avoid warnings */
#ifdef GMX_THREADS
nice_set=TRUE;
}
tMPI_Thread_mutex_unlock(&init_mutex);
#endif
}
#endif
#endif
/* Update oenv for parsed command line options settings. */
(*oenv)->xvg_format = (xvg_format_t)nenum(xvg_format);
(*oenv)->time_unit = (time_unit_t)nenum(time_units);
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);
}
}
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);
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);
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);
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);
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)) {
*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));
/* 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) {
gmx_cmd(argv[1]);
}
}
if (bExit) {
if (gmx_parallel_env_initialized())
/*gmx_abort(gmx_node_rank(),gmx_node_num(),0);*/
gmx_finalize();
exit(0);
}
#undef FF
}
