void
AbstractPlotModule::dataStarted(AbstractAnalysisData * /* data */)
{
if (!impl_->filename_.empty())
{
if (impl_->bPlain_)
{
impl_->fp_ = gmx_fio_fopen(impl_->filename_.c_str(), "w");
}
else
{
time_unit_t time_unit
= static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1);
xvg_format_t xvg_format
= (impl_->settings_.plotFormat() > 0
? static_cast<xvg_format_t>(impl_->settings_.plotFormat())
: exvgNONE);
output_env_t oenv;
output_env_init(&oenv, getProgramContext(), time_unit, FALSE, xvg_format, 0);
boost::shared_ptr<output_env> oenvGuard(oenv, &output_env_done);
impl_->fp_ = xvgropen(impl_->filename_.c_str(), impl_->title_.c_str(),
impl_->xlabel_.c_str(), impl_->ylabel_.c_str(),
oenv);
const SelectionCollection *selections
= impl_->settings_.selectionCollection();
if (selections != NULL)
{
selections->printXvgrInfo(impl_->fp_, oenv);
}
if (!impl_->subtitle_.empty())
{
xvgr_subtitle(impl_->fp_, impl_->subtitle_.c_str(), oenv);
}
if (output_env_get_print_xvgr_codes(oenv)
&& !impl_->legend_.empty())
{
std::vector<const char *> legend;
legend.reserve(impl_->legend_.size());
for (size_t i = 0; i < impl_->legend_.size(); ++i)
{
legend.push_back(impl_->legend_[i].c_str());
}
xvgr_legend(impl_->fp_, legend.size(), &legend[0], oenv);
}
}
}
}
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,
gmx_output_env_t **oenv)
{
/* This array should match the order of the enum in oenv.h */
const char *const xvg_formats[] = { "xmgrace", "xmgr", "none" };
// 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)
try
{
double tbegin = 0.0, tend = 0.0, tdelta = 0.0;
bool bBeginTimeSet = false, bEndTimeSet = false, bDtSet = false;
bool bView = false;
int xvgFormat = 0;
gmx::OptionsAdapter adapter(*argc, argv);
gmx::Options options(NULL, NULL);
gmx::OptionsBehaviorCollection behaviors(&options);
gmx::FileNameOptionManager fileOptManager;
fileOptManager.disableInputOptionChecking(
FF(PCA_NOT_READ_NODE) || FF(PCA_DISABLE_INPUT_FILE_CHECKING));
options.addManager(&fileOptManager);
if (FF(PCA_CAN_SET_DEFFNM))
{
fileOptManager.addDefaultFileNameOption(&options, "deffnm");
}
if (FF(PCA_CAN_BEGIN))
{
options.addOption(
gmx::DoubleOption("b")
.store(&tbegin).storeIsSet(&bBeginTimeSet).timeValue()
.description("First frame (%t) to read from trajectory"));
}
if (FF(PCA_CAN_END))
{
options.addOption(
gmx::DoubleOption("e")
.store(&tend).storeIsSet(&bEndTimeSet).timeValue()
.description("Last frame (%t) to read from trajectory"));
}
if (FF(PCA_CAN_DT))
{
options.addOption(
gmx::DoubleOption("dt")
.store(&tdelta).storeIsSet(&bDtSet).timeValue()
.description("Only use frame when t MOD dt = first time (%t)"));
}
gmx::TimeUnit timeUnit = gmx::TimeUnit_Default;
if (FF(PCA_TIME_UNIT))
{
std::shared_ptr<gmx::TimeUnitBehavior> timeUnitBehavior(
new gmx::TimeUnitBehavior());
timeUnitBehavior->setTimeUnitStore(&timeUnit);
timeUnitBehavior->setTimeUnitFromEnvironment();
timeUnitBehavior->addTimeUnitOption(&options, "tu");
behaviors.addBehavior(timeUnitBehavior);
}
if (FF(PCA_CAN_VIEW))
{
options.addOption(
gmx::BooleanOption("w").store(&bView)
.description("View output [REF].xvg[ref], [REF].xpm[ref], "
"[REF].eps[ref] and [REF].pdb[ref] files"));
}
bool bXvgr = false;
for (int i = 0; i < nfile; i++)
{
bXvgr = bXvgr || (fnm[i].ftp == efXVG);
}
xvgFormat = gmx::getDefaultXvgFormat(xvg_formats);
if (bXvgr)
{
options.addOption(
gmx::EnumIntOption("xvg").enumValue(xvg_formats)
.store(&xvgFormat)
.description("xvg plot formatting"));
}
/* Now append the program specific arguments */
for (int i = 0; i < nfile; i++)
{
adapter.filenmToOptions(&options, &fnm[i]);
}
for (int i = 0; i < npargs; i++)
{
adapter.pargsToOptions(&options, &pa[i]);
}
const gmx::CommandLineHelpContext *context =
gmx::GlobalCommandLineHelpContext::get();
if (context != NULL)
{
GMX_RELEASE_ASSERT(gmx_node_rank() == 0,
"Help output should be handled higher up and "
"only get called only on the master rank");
gmx::CommandLineHelpWriter(options)
.setHelpText(gmx::constArrayRefFromArray<const char *>(desc, ndesc))
.setKnownIssues(gmx::constArrayRefFromArray(bugs, nbugs))
.writeHelp(*context);
return FALSE;
}
/* Now parse all the command-line options */
gmx::CommandLineParser(&options).skipUnknown(FF(PCA_NOEXIT_ON_ARGS))
.parse(argc, argv);
behaviors.optionsFinishing();
options.finish();
/* set program name, command line, and default values for output options */
output_env_init(oenv, gmx::getProgramContext(),
(time_unit_t)(timeUnit + 1), bView,
(xvg_format_t)(xvgFormat + 1), 0);
/* Extract Time info from arguments */
if (bBeginTimeSet)
{
setTimeValue(TBEGIN, tbegin);
}
if (bEndTimeSet)
{
setTimeValue(TEND, tend);
}
if (bDtSet)
{
setTimeValue(TDELTA, tdelta);
}
adapter.copyValues(!FF(PCA_NOT_READ_NODE));
return TRUE;
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
#undef FF
}
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
}
void
TrajectoryAnalysisRunnerCommon::initFirstFrame()
{
// Return if we have already initialized the trajectory.
if (impl_->fr)
{
return;
}
time_unit_t time_unit
= static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1);
output_env_init(&impl_->oenv_, 0, NULL, time_unit, FALSE, exvgNONE, 0, 0);
int frflags = impl_->settings_.frflags();
frflags |= TRX_NEED_X;
snew(impl_->fr, 1);
const TopologyInformation &top = impl_->topInfo_;
if (hasTrajectory())
{
if (!read_first_frame(impl_->oenv_, &impl_->status_,
impl_->trjfile_.c_str(), impl_->fr, frflags))
{
GMX_THROW(FileIOError("Could not read coordinates from trajectory"));
}
impl_->bTrajOpen_ = true;
if (top.hasTopology() && impl_->fr->natoms > top.topology()->atoms.nr)
{
GMX_THROW(InconsistentInputError(formatString(
"Trajectory (%d atoms) does not match topology (%d atoms)",
impl_->fr->natoms, top.topology()->atoms.nr)));
}
// Check index groups if they have been initialized based on the topology.
/*
if (top)
{
for (int i = 0; i < impl_->sel->nr(); ++i)
{
gmx_ana_index_check(impl_->sel->sel(i)->indexGroup(),
impl_->fr->natoms);
}
}
*/
}
else
{
// Prepare a frame from topology information.
// TODO: Initialize more of the fields.
if (frflags & (TRX_NEED_V))
{
GMX_THROW(NotImplementedError("Velocity reading from a topology not implemented"));
}
if (frflags & (TRX_NEED_F))
{
GMX_THROW(InvalidInputError("Forces cannot be read from a topology"));
}
impl_->fr->flags = frflags;
impl_->fr->natoms = top.topology()->atoms.nr;
impl_->fr->bX = TRUE;
snew(impl_->fr->x, impl_->fr->natoms);
memcpy(impl_->fr->x, top.xtop_,
sizeof(*impl_->fr->x) * impl_->fr->natoms);
impl_->fr->bBox = TRUE;
copy_mat(const_cast<rvec *>(top.boxtop_), impl_->fr->box);
}
set_trxframe_ePBC(impl_->fr, top.ePBC());
if (top.hasTopology() && impl_->settings_.hasRmPBC())
{
impl_->gpbc_ = gmx_rmpbc_init(&top.topology()->idef, top.ePBC(),
impl_->fr->natoms, impl_->fr->box);
}
}
void
TrajectoryAnalysisRunnerCommon::Impl::initFirstFrame()
{
// Return if we have already initialized the trajectory.
if (fr != NULL)
{
return;
}
time_unit_t time_unit
= static_cast<time_unit_t>(settings_.timeUnit() + 1);
output_env_init(&oenv_, getProgramContext(), time_unit, FALSE, exvgNONE, 0);
int frflags = settings_.frflags();
frflags |= TRX_NEED_X;
snew(fr, 1);
if (hasTrajectory())
{
if (!read_first_frame(oenv_, &status_, trjfile_.c_str(), fr, frflags))
{
GMX_THROW(FileIOError("Could not read coordinates from trajectory"));
}
bTrajOpen_ = true;
if (topInfo_.hasTopology())
{
const int topologyAtomCount = topInfo_.topology()->atoms.nr;
if (fr->natoms > topologyAtomCount)
{
const std::string message
= formatString("Trajectory (%d atoms) does not match topology (%d atoms)",
fr->natoms, topologyAtomCount);
GMX_THROW(InconsistentInputError(message));
}
}
}
else
{
// Prepare a frame from topology information.
// TODO: Initialize more of the fields.
if (frflags & (TRX_NEED_V))
{
GMX_THROW(NotImplementedError("Velocity reading from a topology not implemented"));
}
if (frflags & (TRX_NEED_F))
{
GMX_THROW(InvalidInputError("Forces cannot be read from a topology"));
}
fr->natoms = topInfo_.topology()->atoms.nr;
fr->bX = TRUE;
snew(fr->x, fr->natoms);
memcpy(fr->x, topInfo_.xtop_,
sizeof(*fr->x) * fr->natoms);
fr->bBox = TRUE;
copy_mat(topInfo_.boxtop_, fr->box);
}
set_trxframe_ePBC(fr, topInfo_.ePBC());
if (topInfo_.hasTopology() && settings_.hasRmPBC())
{
gpbc_ = gmx_rmpbc_init(&topInfo_.topology()->idef, topInfo_.ePBC(),
fr->natoms);
}
}
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
}
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 *const xvg_formats[] = { "xmgrace", "xmgr", "none" };
// 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)
try
{
int nicelevel = 0, debug_level = 0;
double tbegin = 0.0, tend = 0.0, tdelta = 0.0;
bool bView = false;
int xvgFormat = 0;
gmx::TimeUnitManager timeUnitManager;
gmx::OptionsAdapter adapter(*argc, argv);
gmx::Options options(NULL, NULL);
gmx::FileNameOptionManager fileOptManager;
options.addManager(&fileOptManager);
options.setDescription(gmx::ConstArrayRef<const char *>(desc, ndesc));
options.addOption(
gmx::IntegerOption("debug").store(&debug_level).hidden()
.description("Write file with debug information, "
"1: short, 2: also x and f"));
options.addOption(
gmx::IntegerOption("nice").store(&nicelevel)
.defaultValue(FF(PCA_BE_NICE) ? 19 : 0)
.description("Set the nicelevel"));
if (FF(PCA_CAN_SET_DEFFNM))
{
fileOptManager.addDefaultFileNameOption(&options, "deffnm");
}
if (FF(PCA_CAN_BEGIN))
{
options.addOption(
gmx::DoubleOption("b").store(&tbegin).timeValue()
.description("First frame (%t) to read from trajectory"));
}
if (FF(PCA_CAN_END))
{
options.addOption(
gmx::DoubleOption("e").store(&tend).timeValue()
.description("Last frame (%t) to read from trajectory"));
}
if (FF(PCA_CAN_DT))
{
options.addOption(
gmx::DoubleOption("dt").store(&tdelta).timeValue()
.description("Only use frame when t MOD dt = first time (%t)"));
}
if (FF(PCA_TIME_UNIT))
{
timeUnitManager.setTimeUnitFromEnvironment();
timeUnitManager.addTimeUnitOption(&options, "tu");
}
if (FF(PCA_CAN_VIEW))
{
options.addOption(
gmx::BooleanOption("w").store(&bView)
.description("View output [TT].xvg[tt], [TT].xpm[tt], "
"[TT].eps[tt] and [TT].pdb[tt] files"));
}
bool bXvgr = false;
for (int i = 0; i < nfile; i++)
{
bXvgr = bXvgr || (fnm[i].ftp == efXVG);
}
xvgFormat = gmx::getDefaultXvgFormat(xvg_formats);
if (bXvgr)
{
options.addOption(
gmx::StringOption("xvg").enumValue(xvg_formats)
.storeEnumIndex(&xvgFormat)
.description("xvg plot formatting"));
}
/* Now append the program specific arguments */
for (int i = 0; i < nfile; i++)
{
adapter.filenmToOptions(&options, &fnm[i]);
}
for (int i = 0; i < npargs; i++)
{
adapter.pargsToOptions(&options, &pa[i]);
}
const gmx::CommandLineHelpContext *context =
gmx::GlobalCommandLineHelpContext::get();
if (context != NULL)
{
if (!(FF(PCA_QUIET)))
{
gmx::CommandLineHelpWriter(options)
.setShowDescriptions(true)
.setTimeUnitString(timeUnitManager.timeUnitAsString())
.setKnownIssues(gmx::ConstArrayRef<const char *>(bugs, nbugs))
.writeHelp(*context);
}
return FALSE;
}
/* Now parse all the command-line options */
gmx::CommandLineParser(&options).skipUnknown(FF(PCA_NOEXIT_ON_ARGS))
.parse(argc, argv);
options.finish();
/* set program name, command line, and default values for output options */
output_env_init(oenv, gmx::getProgramContext(),
(time_unit_t)(timeUnitManager.timeUnit() + 1), bView,
(xvg_format_t)(xvgFormat + 1), 0, debug_level);
/* 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__);
}
/* Set the nice level */
#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)
{
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
timeUnitManager.scaleTimeOptions(&options);
/* Extract Time info from arguments */
// TODO: Use OptionInfo objects instead of string constants
if (FF(PCA_CAN_BEGIN) && options.isSet("b"))
{
setTimeValue(TBEGIN, tbegin);
}
if (FF(PCA_CAN_END) && options.isSet("e"))
{
setTimeValue(TEND, tend);
}
if (FF(PCA_CAN_DT) && options.isSet("dt"))
{
setTimeValue(TDELTA, tdelta);
}
adapter.copyValues(!FF(PCA_NOT_READ_NODE));
return TRUE;
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
#undef FF
}
