void
TrajectoryAnalysisRunnerCommon::Impl::initTopology(bool required)
{
// Return immediately if the topology has already been loaded.
if (topInfo_.hasTopology())
{
return;
}
if (required && topfile_.empty())
{
GMX_THROW(InconsistentInputError("No topology provided, but one is required for analysis"));
}
// Load the topology if requested.
if (!topfile_.empty())
{
snew(topInfo_.top_, 1);
topInfo_.bTop_ = read_tps_conf(topfile_.c_str(), topInfo_.top_, &topInfo_.ePBC_,
&topInfo_.xtop_, NULL, topInfo_.boxtop_, TRUE);
if (hasTrajectory()
&& !settings_.hasFlag(TrajectoryAnalysisSettings::efUseTopX))
{
sfree(topInfo_.xtop_);
topInfo_.xtop_ = NULL;
}
}
}
void
TrajectoryAnalysisRunnerCommon::initTopology(SelectionCollection *selections)
{
// Return immediately if the topology has already been loaded.
if (impl_->topInfo_.hasTopology())
{
return;
}
const TrajectoryAnalysisSettings &settings = impl_->settings_;
const bool bRequireTop
= settings.hasFlag(TrajectoryAnalysisSettings::efRequireTop)
|| selections->requiresTopology();
if (bRequireTop && impl_->topfile_.empty())
{
GMX_THROW(InconsistentInputError("No topology provided, but one is required for analysis"));
}
// Load the topology if requested.
if (!impl_->topfile_.empty())
{
char title[STRLEN];
snew(impl_->topInfo_.top_, 1);
impl_->topInfo_.bTop_ = read_tps_conf(impl_->topfile_.c_str(), title,
impl_->topInfo_.top_, &impl_->topInfo_.ePBC_,
&impl_->topInfo_.xtop_, NULL, impl_->topInfo_.boxtop_, TRUE);
if (hasTrajectory()
&& !settings.hasFlag(TrajectoryAnalysisSettings::efUseTopX))
{
sfree(impl_->topInfo_.xtop_);
impl_->topInfo_.xtop_ = NULL;
}
}
// Read the first frame if we don't know the maximum number of atoms
// otherwise.
int natoms = -1;
if (!impl_->topInfo_.hasTopology())
{
initFirstFrame();
natoms = impl_->fr->natoms;
}
selections->setTopology(impl_->topInfo_.topology(), natoms);
/*
if (impl_->bSelDump)
{
gmx_ana_poscalc_coll_print_tree(stderr, impl_->pcc);
fprintf(stderr, "\n");
}
*/
}
bool
TrajectoryAnalysisRunnerCommon::readNextFrame()
{
bool bContinue = false;
if (hasTrajectory())
{
bContinue = read_next_frame(impl_->oenv_, impl_->status_, impl_->fr);
}
if (!bContinue)
{
impl_->finishTrajectory();
}
return bContinue;
}
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);
}
}