void
AnalysisDataDisplacementModule::setMSDHistogram(AnalysisDataBinAverageModule *histm)
{
GMX_RELEASE_ASSERT(!_impl->histm, "Can only set MSD histogram once");
_impl->histm = histm;
histm->setIgnoreMissing(true);
addModule(histm);
}
AnalysisDataHandle
TrajectoryAnalysisModuleData::dataHandle(const AnalysisData &data)
{
Impl::HandleContainer::const_iterator i = impl_->handles_.find(&data);
GMX_RELEASE_ASSERT(i != impl_->handles_.end(),
"Data handle requested on unknown dataset");
return i->second;
}
void TopologyManager::initUniformMolecules(int moleculeSize)
{
GMX_RELEASE_ASSERT(mtop_ != nullptr, "Topology not initialized");
GMX_RELEASE_ASSERT(mtop_->molblock.size() == 1, "initUniformMolecules only implemented for a single molblock");
gmx_molblock_t &molblock = mtop_->molblock[0];
t_atoms &atoms = mtop_->moltype[molblock.type].atoms;
GMX_RELEASE_ASSERT(atoms.nr % moleculeSize == 0,
"The number of atoms should be a multiple of moleculeSize");
molblock.nmol = atoms.nr/moleculeSize;
atoms.nr = moleculeSize;
const int nres = atoms.atom[atoms.nr].resind;
GMX_RELEASE_ASSERT(atoms.atom[atoms.nr-1].resind != nres,
"The residues should break at molecule boundaries");
atoms.nres = nres;
mtop_->haveMoleculeIndices = true;
gmx_mtop_finalize(mtop_.get());
}
void
AnalysisDataDisplacementModule::setMSDHistogram(
AnalysisDataBinAverageModulePointer histm)
{
GMX_RELEASE_ASSERT(_impl->histm == NULL, "Can only set MSD histogram once");
_impl->histm = histm.get();
addModule(histm);
}
void OptionsAssigner::finishSection()
{
// Should only be called if we are in a subsection.
GMX_RELEASE_ASSERT(impl_->inSection(), "startSection() not called");
Impl::Section *section = impl_->sectionStack_.back();
section->finish();
impl_->sectionStack_.pop_back();
}
void
AbstractAnalysisArrayData::setColumnCount(int ncols)
{
GMX_RELEASE_ASSERT(!isAllocated(),
"Cannot change column count after data has been allocated");
AbstractAnalysisData::setColumnCount(0, ncols);
pointSetInfo_ = AnalysisDataPointSetInfo(0, ncols, 0, 0);
}
/*! \brief Replace duplicated spaces with a single one in string
*
* Only the first character will be kept for multiple adjacent characters that
* are both identical and where the first one returns true for isspace().
*
* \param str String that will be modified.
*/
static void
removeExtraSpaces(std::string *str)
{
GMX_RELEASE_ASSERT(str != nullptr, "A pointer to an actual string must be provided");
std::string::iterator newEnd =
std::unique( str->begin(), str->end(), [ = ](char a, char b){ return isspace(a) != 0 && (a == b); } );
str->erase(newEnd, str->end());
}
void
AnalysisDataModuleManager::applyModule(AbstractAnalysisData *data,
AnalysisDataModuleInterface *module)
{
impl_->checkModuleProperties(*module);
GMX_RELEASE_ASSERT(impl_->state_ == Impl::eFinished,
"Data module can only be applied to ready data");
impl_->presentData(data, module);
}
void
gmx_omp_nthreads_set(int mod, int nthreads)
{
/* Catch an attempt to set the number of threads on an invalid
* OpenMP module. */
GMX_RELEASE_ASSERT(mod >= 0 && mod < emntNR, "Trying to set nthreads on invalid OpenMP module");
modth.nth[mod] = nthreads;
}
void AbstractOptionStorage::finish()
{
GMX_RELEASE_ASSERT(!bInSet_, "finishSet() not called");
processAll();
if (isRequired() && !(isSet() || hasFlag(efOption_ExplicitDefaultValue)))
{
GMX_THROW(InvalidInputError("Option is required, but not set"));
}
}
void
_gmx_sel_mempool_reserve(gmx_sel_mempool_t *mp, size_t size)
{
GMX_RELEASE_ASSERT(mp->nblocks == 0,
"Cannot reserve memory pool when there is something allocated");
GMX_RELEASE_ASSERT(!mp->buffer, "Cannot reserve memory pool twice");
if (size == 0)
{
size = mp->maxsize;
}
mp->buffer = (char *)malloc(size);
if (!mp->buffer)
{
throw std::bad_alloc();
}
mp->freesize = size;
mp->freeptr = mp->buffer;
}
void dd_collect_state(gmx_domdec_t *dd,
const t_state *state_local, t_state *state)
{
int nh = state_local->nhchainlength;
if (DDMASTER(dd))
{
GMX_RELEASE_ASSERT(state->nhchainlength == nh, "The global and local Nose-Hoover chain lengths should match");
for (int i = 0; i < efptNR; i++)
{
state->lambda[i] = state_local->lambda[i];
}
state->fep_state = state_local->fep_state;
state->veta = state_local->veta;
state->vol0 = state_local->vol0;
copy_mat(state_local->box, state->box);
copy_mat(state_local->boxv, state->boxv);
copy_mat(state_local->svir_prev, state->svir_prev);
copy_mat(state_local->fvir_prev, state->fvir_prev);
copy_mat(state_local->pres_prev, state->pres_prev);
for (int i = 0; i < state_local->ngtc; i++)
{
for (int j = 0; j < nh; j++)
{
state->nosehoover_xi[i*nh+j] = state_local->nosehoover_xi[i*nh+j];
state->nosehoover_vxi[i*nh+j] = state_local->nosehoover_vxi[i*nh+j];
}
state->therm_integral[i] = state_local->therm_integral[i];
}
for (int i = 0; i < state_local->nnhpres; i++)
{
for (int j = 0; j < nh; j++)
{
state->nhpres_xi[i*nh+j] = state_local->nhpres_xi[i*nh+j];
state->nhpres_vxi[i*nh+j] = state_local->nhpres_vxi[i*nh+j];
}
}
state->baros_integral = state_local->baros_integral;
}
if (state_local->flags & (1 << estX))
{
gmx::ArrayRef<gmx::RVec> globalXRef = state ? makeArrayRef(state->x) : gmx::EmptyArrayRef();
dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->x), globalXRef);
}
if (state_local->flags & (1 << estV))
{
gmx::ArrayRef<gmx::RVec> globalVRef = state ? makeArrayRef(state->v) : gmx::EmptyArrayRef();
dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->v), globalVRef);
}
if (state_local->flags & (1 << estCGP))
{
gmx::ArrayRef<gmx::RVec> globalCgpRef = state ? makeArrayRef(state->cg_p) : gmx::EmptyArrayRef();
dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->cg_p), globalCgpRef);
}
}
void TopologyManager::requestFrame()
{
GMX_RELEASE_ASSERT(mtop_ == nullptr,
"Frame must be requested before initializing topology");
if (frame_ == nullptr)
{
snew(frame_, 1);
}
}
void OptionsAssigner::appendValue(const std::string &value)
{
AbstractOptionStorage *option = _impl->_currentOption;
GMX_RELEASE_ASSERT(option != NULL, "startOption() not called");
// Does not count correctly, but the actual count is not really used.
// TODO: Rename the variable to better reflect the usage.
++_impl->_currentValueCount;
option->appendValue(value);
}
/*! \internal
* This method is not const because the dataStarted() methods of the attached
* modules can request storage of the data.
*/
void
AbstractAnalysisData::notifyDataStart()
{
GMX_RELEASE_ASSERT(!impl_->bDataStart_,
"notifyDataStart() called more than once");
GMX_RELEASE_ASSERT(columnCount_ > 0, "Data column count is not set");
impl_->bDataStart_ = impl_->bInData_ = true;
Impl::ModuleList::const_iterator i;
for (i = impl_->modules_.begin(); i != impl_->modules_.end(); ++i)
{
if (columnCount_ > 1 && !((*i)->flags() & AnalysisDataModuleInterface::efAllowMulticolumn))
{
GMX_THROW(APIError("Data module not compatible with data object properties"));
}
(*i)->dataStarted(this);
}
}
void UpdateGroupsCog::addCogs(gmx::ArrayRef<const int> globalAtomIndices,
gmx::ArrayRef<const gmx::RVec> coordinates)
{
const int localAtomBegin = cogIndices_.size();
const size_t cogBegin = cogs_.size();
GMX_RELEASE_ASSERT(globalAtomIndices.size() >= localAtomBegin,
"addCogs should only be called to add COGs to the list that is already present (which could be empty)");
cogIndices_.reserve(globalAtomIndices.size());
int moleculeBlock = 0;
for (int localAtom = localAtomBegin; localAtom < globalAtomIndices.size(); localAtom++)
{
const int globalAtom = globalAtomIndices[localAtom];
int moleculeIndex;
int atomIndexInMolecule;
mtopGetMolblockIndex(&mtop_, globalAtom,
&moleculeBlock, &moleculeIndex, &atomIndexInMolecule);
const auto &indicesForBlock = indicesPerMoleculeblock_[moleculeBlock];
int globalUpdateGroupIndex =
indicesForBlock.groupStart_ +
moleculeIndex*indicesForBlock.numGroupsPerMolecule_ +
indicesForBlock.groupIndex_[atomIndexInMolecule];
if (const int *cogIndexPtr = globalToLocalMap_.find(globalUpdateGroupIndex))
{
GMX_ASSERT(static_cast<size_t>(*cogIndexPtr) >= cogBegin,
"Added atoms should not be part of previously present groups");
cogIndices_.push_back(*cogIndexPtr);
cogs_[*cogIndexPtr] += coordinates[localAtom];
numAtomsPerCog_[*cogIndexPtr]++;
}
else
{
const int cogIndex = cogs_.size();
globalToLocalMap_.insert(globalUpdateGroupIndex, cogIndex);
cogIndices_.push_back(cogIndex);
cogs_.push_back(coordinates[localAtom]);
numAtomsPerCog_.push_back(1);
}
}
/* Divide sum of coordinates for each COG by the number of atoms */
for (size_t i = cogBegin; i < cogs_.size(); i++)
{
const int numAtoms = numAtomsPerCog_[i];
if (numAtoms > 1)
{
cogs_[i] /= numAtoms;
}
}
}
void
AbstractAnalysisArrayData::setRowCount(int rowCount)
{
GMX_RELEASE_ASSERT(rowCount > 0, "Invalid number of rows");
GMX_RELEASE_ASSERT(!isAllocated(),
"Cannot change row count after data has been allocated");
GMX_RELEASE_ASSERT(bUniformX_ || xvalue_.empty()
|| rowCount == static_cast<int>(xvalue_.size()),
"X axis set with setXAxisValue() does not match the row count");
xvalue_.resize(rowCount);
if (bUniformX_ && rowCount > rowCount_)
{
for (int i = rowCount_; i < rowCount; ++i)
{
xvalue_[i] = xvalue_[0] + i * xstep_;
}
}
rowCount_ = rowCount;
}
void
SelectionCollection::setOutputPosType(const char *type)
{
GMX_RELEASE_ASSERT(type != NULL, "Cannot assign NULL position type");
// Check that the type is valid, throw if it is not.
e_poscalc_t dummytype;
int dummyflags;
PositionCalculationCollection::typeFromEnum(type, &dummytype, &dummyflags);
impl_->spost_ = type;
}
bool File::isInteractive() const
{
GMX_RELEASE_ASSERT(impl_->fp_ != NULL,
"Attempted to access a file object that is not open");
#ifdef HAVE_UNISTD_H
return isatty(fileno(impl_->fp_));
#else
return true;
#endif
}
void TopologyManager::requestVelocities()
{
GMX_RELEASE_ASSERT(frame_ != nullptr,
"Velocities requested before requesting a frame");
frame_->bV = TRUE;
if (frame_->natoms > 0)
{
snew(frame_->v, frame_->natoms);
}
}
void TimeUnitBehavior::setTimeUnit(TimeUnit timeUnit)
{
GMX_RELEASE_ASSERT(timeUnit >= 0 && timeUnit <= TimeUnit_s,
"Invalid time unit");
timeUnit_ = timeUnit;
if (timeUnitStore_ != NULL)
{
*timeUnitStore_ = timeUnit;
}
}
void
SelectionCollection::setOutputPosType(const char *type)
{
GMX_RELEASE_ASSERT(type != NULL, "Cannot assign NULL position type");
//! Check that the type is valid.
e_poscalc_t dummytype;
int dummyflags;
gmx_ana_poscalc_type_from_enum(type, &dummytype, &dummyflags);
_impl->_spost = type;
}
void TopologyManager::requestForces()
{
GMX_RELEASE_ASSERT(frame_ != nullptr,
"Forces requested before requesting a frame");
frame_->bF = TRUE;
if (frame_->natoms > 0)
{
snew(frame_->f, frame_->natoms);
}
}
HelpWriterContext::HelpWriterContext(File *file, HelpOutputFormat format,
const HelpLinks *links)
: impl_(new Impl(Impl::StatePointer(new Impl::SharedState(file, format, links))))
{
if (links != NULL)
{
GMX_RELEASE_ASSERT(links->impl_->format_ == format,
"Links must have the same output format as the context");
}
}
bool
AbstractAnalysisData::requestStorage(int nframes)
{
GMX_RELEASE_ASSERT(nframes >= -1, "Invalid number of frames requested");
if (nframes == 0)
{
return true;
}
return requestStorageInternal(nframes);
}
CommandLineModuleManager::Impl::Impl(const char *binaryName,
CommandLineProgramContext *programContext)
: programContext_(*programContext),
binaryName_(binaryName != NULL ? binaryName : ""),
helpModule_(NULL), singleModule_(NULL),
bQuiet_(false)
{
GMX_RELEASE_ASSERT(binaryName_.find('-') == std::string::npos,
"Help export does not currently work with binary names with dashes");
}
void MessageStringCollector::finishContext()
{
GMX_RELEASE_ASSERT(!impl_->contexts_.empty(),
"finishContext() called without context");
impl_->contexts_.pop_back();
if (impl_->prevContext_ > impl_->contexts_.size())
{
impl_->prevContext_ = impl_->contexts_.size();
}
}
/*!
* \param[in,out] pos Position data structure.
*
* Currently, this function can only be called after gmx_ana_pos_reserve()
* has been called at least once with a \p n >= 0.
*/
void
gmx_ana_pos_reserve_forces(gmx_ana_pos_t *pos)
{
GMX_RELEASE_ASSERT(pos->nalloc_x > 0,
"No memory reserved yet for positions");
if (!pos->f)
{
snew(pos->f, pos->nalloc_x);
}
}
void
AnalysisDataProxy::dataStarted(AbstractAnalysisData *data)
{
GMX_RELEASE_ASSERT(data == &source_, "Source data mismatch");
setDataSetCount(data->dataSetCount());
for (int i = 0; i < data->dataSetCount(); ++i)
{
setColumnCount(i, columnSpan_);
}
moduleManager().notifyDataStart(this);
}
static void copy_state_serial(const t_state *src, t_state *dest)
{
if (dest != src)
{
/* Currently the local state is always a pointer to the global
* in serial, so we should never end up here.
* TODO: Implement a (trivial) t_state copy once converted to C++.
*/
GMX_RELEASE_ASSERT(false, "State copying is currently not implemented in replica exchange");
}
}