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36 /*! \internal \file
37 * \brief
38 * Implements classes in analysismodule.h.
39 *
40 * \author Teemu Murtola <teemu.murtola@gmail.com>
41 * \ingroup module_trajectoryanalysis
42 */
43 #include "gmxpre.h"
44
45 #include "analysismodule.h"
46
47 #include <map>
48 #include <utility>
49
50 #include "gromacs/analysisdata/analysisdata.h"
51 #include "gromacs/selection/selection.h"
52 #include "gromacs/utility/exceptions.h"
53 #include "gromacs/utility/gmxassert.h"
54
55 namespace gmx
56 {
57
58 /********************************************************************
59 * TrajectoryAnalysisModule::Impl
60 */
61
62 /*! \internal \brief
63 * Private implementation class for TrajectoryAnalysisModule.
64 *
65 * \ingroup module_trajectoryanalysis
66 */
67 class TrajectoryAnalysisModule::Impl
68 {
69 public:
70 //! Container that associates a data set with its name.
71 typedef std::map<std::string, AbstractAnalysisData*> DatasetContainer;
72 //! Container that associates a AnalysisData object with its name.
73 typedef std::map<std::string, AnalysisData*> AnalysisDatasetContainer;
74
75 //! List of registered data set names.
76 std::vector<std::string> datasetNames_;
77 /*! \brief
78 * Keeps all registered data sets.
79 *
80 * This container also includes datasets from \a analysisDatasets_.
81 */
82 DatasetContainer datasets_;
83 //! Keeps registered AnalysisData objects.
84 AnalysisDatasetContainer analysisDatasets_;
85 };
86
87 /********************************************************************
88 * TrajectoryAnalysisModuleData::Impl
89 */
90
91 /*! \internal \brief
92 * Private implementation class for TrajectoryAnalysisModuleData.
93 *
94 * \ingroup module_trajectoryanalysis
95 */
96 class TrajectoryAnalysisModuleData::Impl
97 {
98 public:
99 //! Container that associates a data handle to its AnalysisData object.
100 typedef std::map<const AnalysisData*, AnalysisDataHandle> HandleContainer;
101
102 //! \copydoc TrajectoryAnalysisModuleData::TrajectoryAnalysisModuleData()
103 Impl(TrajectoryAnalysisModule* module,
104 const AnalysisDataParallelOptions& opt,
105 const SelectionCollection& selections);
106
107 //! Checks whether the given AnalysisData has been initialized.
108 static bool isInitialized(const AnalysisData& data);
109
110 //! Keeps a data handle for each AnalysisData object.
111 HandleContainer handles_;
112 //! Stores thread-local selections.
113 const SelectionCollection& selections_;
114 };
115
Impl(TrajectoryAnalysisModule * module,const AnalysisDataParallelOptions & opt,const SelectionCollection & selections)116 TrajectoryAnalysisModuleData::Impl::Impl(TrajectoryAnalysisModule* module,
117 const AnalysisDataParallelOptions& opt,
118 const SelectionCollection& selections) :
119 selections_(selections)
120 {
121 TrajectoryAnalysisModule::Impl::AnalysisDatasetContainer::const_iterator i;
122 for (i = module->impl_->analysisDatasets_.begin(); i != module->impl_->analysisDatasets_.end(); ++i)
123 {
124 AnalysisDataHandle handle;
125 if (isInitialized(*i->second))
126 {
127 handle = i->second->startData(opt);
128 }
129 handles_.insert(std::make_pair(i->second, handle));
130 }
131 }
132
isInitialized(const AnalysisData & data)133 bool TrajectoryAnalysisModuleData::Impl::isInitialized(const AnalysisData& data)
134 {
135 for (int i = 0; i < data.dataSetCount(); ++i)
136 {
137 if (data.columnCount(i) > 0)
138 {
139 // If not all of the column counts are set, startData() in the
140 // constructor asserts, so that does not need to be checked here.
141 return true;
142 }
143 }
144 return false;
145 }
146
147
148 /********************************************************************
149 * TrajectoryAnalysisModuleData
150 */
151
TrajectoryAnalysisModuleData(TrajectoryAnalysisModule * module,const AnalysisDataParallelOptions & opt,const SelectionCollection & selections)152 TrajectoryAnalysisModuleData::TrajectoryAnalysisModuleData(TrajectoryAnalysisModule* module,
153 const AnalysisDataParallelOptions& opt,
154 const SelectionCollection& selections) :
155 impl_(new Impl(module, opt, selections))
156 {
157 }
158
159
~TrajectoryAnalysisModuleData()160 TrajectoryAnalysisModuleData::~TrajectoryAnalysisModuleData() {}
161
162
finishDataHandles()163 void TrajectoryAnalysisModuleData::finishDataHandles()
164 {
165 // FIXME: Call finishData() for all handles even if one throws
166 Impl::HandleContainer::iterator i;
167 for (i = impl_->handles_.begin(); i != impl_->handles_.end(); ++i)
168 {
169 if (i->second.isValid())
170 {
171 i->second.finishData();
172 }
173 }
174 impl_->handles_.clear();
175 }
176
177
dataHandle(const AnalysisData & data)178 AnalysisDataHandle TrajectoryAnalysisModuleData::dataHandle(const AnalysisData& data)
179 {
180 Impl::HandleContainer::const_iterator i = impl_->handles_.find(&data);
181 GMX_RELEASE_ASSERT(i != impl_->handles_.end(), "Data handle requested on unknown dataset");
182 return i->second;
183 }
184
185
parallelSelection(const Selection & selection)186 Selection TrajectoryAnalysisModuleData::parallelSelection(const Selection& selection)
187 {
188 // TODO: Implement properly.
189 return selection;
190 }
191
192
parallelSelections(const SelectionList & selections)193 SelectionList TrajectoryAnalysisModuleData::parallelSelections(const SelectionList& selections)
194 {
195 // TODO: Consider an implementation that does not allocate memory every time.
196 SelectionList newSelections;
197 newSelections.reserve(selections.size());
198 SelectionList::const_iterator i = selections.begin();
199 for (; i != selections.end(); ++i)
200 {
201 newSelections.push_back(parallelSelection(*i));
202 }
203 return newSelections;
204 }
205
206
207 /********************************************************************
208 * TrajectoryAnalysisModuleDataBasic
209 */
210
211 namespace
212 {
213
214 /*! \brief
215 * Basic thread-local trajectory analysis data storage class.
216 *
217 * Most simple tools should only require data handles and selections to be
218 * thread-local, so this class implements just that.
219 *
220 * \ingroup module_trajectoryanalysis
221 */
222 class TrajectoryAnalysisModuleDataBasic : public TrajectoryAnalysisModuleData
223 {
224 public:
225 /*! \brief
226 * Initializes thread-local storage for data handles and selections.
227 *
228 * \param[in] module Analysis module to use for data objects.
229 * \param[in] opt Data parallelization options.
230 * \param[in] selections Thread-local selection collection.
231 */
232 TrajectoryAnalysisModuleDataBasic(TrajectoryAnalysisModule* module,
233 const AnalysisDataParallelOptions& opt,
234 const SelectionCollection& selections);
235
236 void finish() override;
237 };
238
TrajectoryAnalysisModuleDataBasic(TrajectoryAnalysisModule * module,const AnalysisDataParallelOptions & opt,const SelectionCollection & selections)239 TrajectoryAnalysisModuleDataBasic::TrajectoryAnalysisModuleDataBasic(TrajectoryAnalysisModule* module,
240 const AnalysisDataParallelOptions& opt,
241 const SelectionCollection& selections) :
242 TrajectoryAnalysisModuleData(module, opt, selections)
243 {
244 }
245
246
finish()247 void TrajectoryAnalysisModuleDataBasic::finish()
248 {
249 finishDataHandles();
250 }
251
252 } // namespace
253
254
255 /********************************************************************
256 * TrajectoryAnalysisModule
257 */
258
TrajectoryAnalysisModule()259 TrajectoryAnalysisModule::TrajectoryAnalysisModule() : impl_(new Impl()) {}
260
261
~TrajectoryAnalysisModule()262 TrajectoryAnalysisModule::~TrajectoryAnalysisModule() {}
263
264
optionsFinished(TrajectoryAnalysisSettings *)265 void TrajectoryAnalysisModule::optionsFinished(TrajectoryAnalysisSettings* /*settings*/) {}
266
267
initAfterFirstFrame(const TrajectoryAnalysisSettings &,const t_trxframe &)268 void TrajectoryAnalysisModule::initAfterFirstFrame(const TrajectoryAnalysisSettings& /*settings*/,
269 const t_trxframe& /*fr*/)
270 {
271 }
272
273
startFrames(const AnalysisDataParallelOptions & opt,const SelectionCollection & selections)274 TrajectoryAnalysisModuleDataPointer TrajectoryAnalysisModule::startFrames(const AnalysisDataParallelOptions& opt,
275 const SelectionCollection& selections)
276 {
277 return TrajectoryAnalysisModuleDataPointer(new TrajectoryAnalysisModuleDataBasic(this, opt, selections));
278 }
279
280
finishFrames(TrajectoryAnalysisModuleData *)281 void TrajectoryAnalysisModule::finishFrames(TrajectoryAnalysisModuleData* /*pdata*/) {}
282
283
datasetCount() const284 int TrajectoryAnalysisModule::datasetCount() const
285 {
286 return impl_->datasetNames_.size();
287 }
288
289
datasetNames() const290 const std::vector<std::string>& TrajectoryAnalysisModule::datasetNames() const
291 {
292 return impl_->datasetNames_;
293 }
294
295
datasetFromIndex(int index) const296 AbstractAnalysisData& TrajectoryAnalysisModule::datasetFromIndex(int index) const
297 {
298 if (index < 0 || index >= datasetCount())
299 {
300 GMX_THROW(APIError("Out of range data set index"));
301 }
302 Impl::DatasetContainer::const_iterator item = impl_->datasets_.find(impl_->datasetNames_[index]);
303 GMX_RELEASE_ASSERT(item != impl_->datasets_.end(), "Inconsistent data set names");
304 return *item->second;
305 }
306
307
datasetFromName(const char * name) const308 AbstractAnalysisData& TrajectoryAnalysisModule::datasetFromName(const char* name) const
309 {
310 Impl::DatasetContainer::const_iterator item = impl_->datasets_.find(name);
311 if (item == impl_->datasets_.end())
312 {
313 GMX_THROW(APIError("Unknown data set name"));
314 }
315 return *item->second;
316 }
317
318
registerBasicDataset(AbstractAnalysisData * data,const char * name)319 void TrajectoryAnalysisModule::registerBasicDataset(AbstractAnalysisData* data, const char* name)
320 {
321 GMX_RELEASE_ASSERT(data != nullptr, "Attempting to register NULL data");
322 // TODO: Strong exception safety should be possible to implement.
323 GMX_RELEASE_ASSERT(impl_->datasets_.find(name) == impl_->datasets_.end(),
324 "Duplicate data set name registered");
325 impl_->datasets_[name] = data;
326 impl_->datasetNames_.emplace_back(name);
327 }
328
329
registerAnalysisDataset(AnalysisData * data,const char * name)330 void TrajectoryAnalysisModule::registerAnalysisDataset(AnalysisData* data, const char* name)
331 {
332 // TODO: Strong exception safety should be possible to implement.
333 registerBasicDataset(data, name);
334 impl_->analysisDatasets_[name] = data;
335 }
336
337
finishFrameSerial(int frameIndex)338 void TrajectoryAnalysisModule::finishFrameSerial(int frameIndex)
339 {
340 Impl::AnalysisDatasetContainer::const_iterator data;
341 for (data = impl_->analysisDatasets_.begin(); data != impl_->analysisDatasets_.end(); ++data)
342 {
343 data->second->finishFrameSerial(frameIndex);
344 }
345 }
346
347 } // namespace gmx
348