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38 * Implements gmx::analysismodules::Angle.
40 * \author Teemu Murtola <teemu.murtola@gmail.com>
41 * \ingroup module_trajectoryanalysis
52 #include "gromacs/analysisdata/analysisdata.h"
53 #include "gromacs/analysisdata/modules/average.h"
54 #include "gromacs/analysisdata/modules/histogram.h"
55 #include "gromacs/analysisdata/modules/plot.h"
56 #include "gromacs/math/units.h"
57 #include "gromacs/math/vec.h"
58 #include "gromacs/options/basicoptions.h"
59 #include "gromacs/options/filenameoption.h"
60 #include "gromacs/options/ioptionscontainer.h"
61 #include "gromacs/pbcutil/pbc.h"
62 #include "gromacs/selection/selection.h"
63 #include "gromacs/selection/selectionoption.h"
64 #include "gromacs/trajectory/trajectoryframe.h"
65 #include "gromacs/trajectoryanalysis/analysissettings.h"
66 #include "gromacs/utility/arrayref.h"
67 #include "gromacs/utility/enumerationhelpers.h"
68 #include "gromacs/utility/exceptions.h"
69 #include "gromacs/utility/gmxassert.h"
70 #include "gromacs/utility/stringutil.h"
75 namespace analysismodules
81 /********************************************************************
86 * Helper to encapsulate logic for looping over input selections.
88 * This class provides two-dimensional iteration:
89 * - Over _angle groups_, corresponding to an input selection. If the input
90 * selection list contains a single selection, that selection gets used
91 * for all angle groups.
92 * - Within a group, over _values_, each consisting of a fixed number of
93 * selection positions. If there is only a single value within a selection,
94 * that value is returned over and over again.
95 * This transparently provides the semantics of using a single selection/vector
96 * to compute angles against multiple selections/vectors as described in the
99 * This class isn't perferctly self-contained and requires the caller to know
100 * some of the internals to use it properly, but it serves its purpose for this
101 * single analysis tool by simplifying the loops.
102 * Some methods have also been tailored to allow the caller to use it a bit
105 * \ingroup module_trajectoryanalysis
107 class AnglePositionIterator
111 * Creates an iterator to loop over input selection positions.
113 * \param[in] selections List of selections.
114 * \param[in] posCountPerValue Number of selection positions that
115 * constitute a single value for the iteration.
117 * If \p selections is empty, and/or \p posCountPerValue is zero, the
118 * iterator can still be advanced and hasValue()/hasSingleValue()
119 * called, but values cannot be accessed.
121 AnglePositionIterator(const SelectionList& selections, int posCountPerValue) :
122 selections_(selections),
123 posCountPerValue_(posCountPerValue),
124 currentSelection_(0),
129 //! Advances the iterator to the next group of angles.
132 if (selections_.size() > 1)
138 //! Advances the iterator to the next angle in the current group.
141 if (!hasSingleValue())
143 nextPosition_ += posCountPerValue_;
148 * Returns whether this iterator represents any values.
150 * If the return value is `false`, only nextGroup(), nextValue() and
151 * hasSingleValue() are allowed to be called.
153 bool hasValue() const { return !selections_.empty(); }
155 * Returns whether the current selection only contains a single value.
157 * Returns `false` if hasValue() returns false, which allows cutting
158 * some corners in consistency checks.
160 bool hasSingleValue() const
162 return hasValue() && currentSelection().posCount() == posCountPerValue_;
164 //! Returns whether the current selection is dynamic.
165 bool isDynamic() const { return currentSelection().isDynamic(); }
167 * Returns whether positions in the current value are either all
168 * selected or all unselected.
170 bool allValuesConsistentlySelected() const
172 if (posCountPerValue_ <= 1)
176 const bool bSelected = currentPosition(0).selected();
177 for (int i = 1; i < posCountPerValue_; ++i)
179 if (currentPosition(i).selected() != bSelected)
187 * Returns whether positions in the current value are selected.
189 * Only works reliably if allValuesConsistentlySelected() returns
192 bool currentValuesSelected() const
194 return selections_.empty() || currentPosition(0).selected();
197 //! Returns the currently active selection.
198 const Selection& currentSelection() const
200 GMX_ASSERT(currentSelection_ < ssize(selections_), "Accessing an invalid selection");
201 return selections_[currentSelection_];
203 //! Returns the `i`th position for the current value.
204 SelectionPosition currentPosition(int i) const
206 return currentSelection().position(nextPosition_ + i);
209 * Extracts all coordinates corresponding to the current value.
211 * \param[out] x Array to which the positions are extracted.
213 * \p x should contain at minimum the number of positions per value
214 * passed to the constructor.
216 void getCurrentPositions(rvec x[]) const
218 GMX_ASSERT(posCountPerValue_ > 0, "Accessing positions for an invalid angle type");
219 GMX_ASSERT(nextPosition_ + posCountPerValue_ <= currentSelection().posCount(),
220 "Accessing an invalid position");
221 for (int i = 0; i < posCountPerValue_; ++i)
223 copy_rvec(currentPosition(i).x(), x[i]);
228 const SelectionList& selections_;
229 const int posCountPerValue_;
230 int currentSelection_;
233 GMX_DISALLOW_COPY_AND_ASSIGN(AnglePositionIterator);
236 /********************************************************************
237 * Actual analysis module
240 //! How to interpret the selections in -group1.
241 enum class Group1Type : int
249 //! How to interpret the selections in -group2.
250 enum class Group2Type : int
260 //! String values corresponding to Group1Type.
261 const EnumerationArray<Group1Type, const char*> c_group1TypeEnumNames = { { "angle", "dihedral",
262 "vector", "plane" } };
263 //! String values corresponding to Group2Type.
264 const EnumerationArray<Group2Type, const char*> c_group2TypeEnumNames = {
265 { "none", "vector", "plane", "t0", "z", "sphnorm" }
268 class Angle : public TrajectoryAnalysisModule
273 void initOptions(IOptionsContainer* options, TrajectoryAnalysisSettings* settings) override;
274 void optionsFinished(TrajectoryAnalysisSettings* settings) override;
275 void initAnalysis(const TrajectoryAnalysisSettings& settings, const TopologyInformation& top) override;
277 void analyzeFrame(int frnr, const t_trxframe& fr, t_pbc* pbc, TrajectoryAnalysisModuleData* pdata) override;
279 void finishAnalysis(int nframes) override;
280 void writeOutput() override;
283 void initFromSelections(const SelectionList& sel1, const SelectionList& sel2);
284 void checkSelections(const SelectionList& sel1, const SelectionList& sel2) const;
288 SelectionOptionInfo* sel1info_;
289 SelectionOptionInfo* sel2info_;
290 std::string fnAverage_;
292 std::string fnHistogram_;
298 AnalysisData angles_;
299 AnalysisDataFrameAverageModulePointer averageModule_;
300 AnalysisDataSimpleHistogramModulePointer histogramModule_;
302 std::vector<int> angleCount_;
305 std::vector<std::vector<RVec>> vt0_;
307 // Copy and assign disallowed by base.
313 g1type_(Group1Type::Angle),
314 g2type_(Group2Type::None),
319 averageModule_ = std::make_unique<AnalysisDataFrameAverageModule>();
320 angles_.addModule(averageModule_);
321 histogramModule_ = std::make_unique<AnalysisDataSimpleHistogramModule>();
322 angles_.addModule(histogramModule_);
324 registerAnalysisDataset(&angles_, "angle");
325 registerBasicDataset(averageModule_.get(), "average");
326 registerBasicDataset(&histogramModule_->averager(), "histogram");
330 void Angle::initOptions(IOptionsContainer* options, TrajectoryAnalysisSettings* settings)
332 static const char* const desc[] = {
333 "[THISMODULE] computes different types of angles between vectors.",
334 "It supports both vectors defined by two positions and normals of",
335 "planes defined by three positions.",
336 "The z axis or the local normal of a sphere can also be used as",
337 "one of the vectors.",
338 "There are also convenience options 'angle' and 'dihedral' for",
339 "calculating bond angles and dihedrals defined by three/four",
341 "The type of the angle is specified with [TT]-g1[tt] and [TT]-g2[tt].",
342 "If [TT]-g1[tt] is [TT]angle[tt] or [TT]dihedral[tt], [TT]-g2[tt]",
343 "should not be specified.",
344 "In this case, [TT]-group1[tt] should specify one or more selections,",
345 "and each should contain triplets or quartets of positions that define",
346 "the angles to be calculated.[PAR]",
347 "If [TT]-g1[tt] is [TT]vector[tt] or [TT]plane[tt], [TT]-group1[tt]",
348 "should specify selections that contain either pairs ([TT]vector[tt])",
349 "or triplets ([TT]plane[tt]) of positions. For vectors, the positions",
350 "set the endpoints of the vector, and for planes, the three positions",
351 "are used to calculate the normal of the plane. In both cases,",
352 "[TT]-g2[tt] specifies the other vector to use (see below).[PAR]",
353 "With [TT]-g2 vector[tt] or [TT]-g2 plane[tt], [TT]-group2[tt] should",
354 "specify another set of vectors. [TT]-group1[tt] and [TT]-group2[tt]",
355 "should specify the same number of selections. It is also allowed to",
356 "only have a single selection for one of the options, in which case",
357 "the same selection is used with each selection in the other group.",
358 "Similarly, for each selection in [TT]-group1[tt], the corresponding",
359 "selection in [TT]-group2[tt] should specify the same number of",
360 "vectors or a single vector. In the latter case, the angle is",
361 "calculated between that single vector and each vector from the other",
363 "With [TT]-g2 sphnorm[tt], each selection in [TT]-group2[tt] should",
364 "specify a single position that is the center of the sphere.",
365 "The second vector is calculated as the vector from the center to the",
366 "midpoint of the positions specified by [TT]-group1[tt].[PAR]",
367 "With [TT]-g2 z[tt], [TT]-group2[tt] is not necessary, and angles",
368 "between the first vectors and the positive Z axis are calculated.[PAR]",
369 "With [TT]-g2 t0[tt], [TT]-group2[tt] is not necessary, and angles",
370 "are calculated from the vectors as they are in the first frame.[PAR]",
371 "There are three options for output:",
372 "[TT]-oav[tt] writes an xvg file with the time and the average angle",
374 "[TT]-oall[tt] writes all the individual angles.",
375 "[TT]-oh[tt] writes a histogram of the angles. The bin width can be",
376 "set with [TT]-binw[tt].",
377 "For [TT]-oav[tt] and [TT]-oh[tt], separate average/histogram is",
378 "computed for each selection in [TT]-group1[tt]."
381 settings->setHelpText(desc);
383 options->addOption(FileNameOption("oav")
387 .defaultBasename("angaver")
388 .description("Average angles as a function of time"));
389 options->addOption(FileNameOption("oall")
393 .defaultBasename("angles")
394 .description("All angles as a function of time"));
395 options->addOption(FileNameOption("oh")
398 .store(&fnHistogram_)
399 .defaultBasename("anghist")
400 .description("Histogram of the angles"));
402 options->addOption(EnumOption<Group1Type>("g1")
403 .enumValue(c_group1TypeEnumNames)
405 .description("Type of analysis/first vector group"));
407 EnumOption<Group2Type>("g2").enumValue(c_group2TypeEnumNames).store(&g2type_).description("Type of second vector group"));
409 DoubleOption("binw").store(&binWidth_).description("Binwidth for -oh in degrees"));
411 sel1info_ = options->addOption(
412 SelectionOption("group1").required().dynamicMask().storeVector(&sel1_).multiValue().description(
413 "First analysis/vector selection"));
414 sel2info_ = options->addOption(
415 SelectionOption("group2").dynamicMask().storeVector(&sel2_).multiValue().description(
416 "Second analysis/vector selection"));
420 void Angle::optionsFinished(TrajectoryAnalysisSettings* /* settings */)
422 const bool bSingle = (g1type_ == Group1Type::Angle || g1type_ == Group1Type::Dihedral);
424 if (bSingle && g2type_ != Group2Type::None)
427 InconsistentInputError("Cannot use a second group (-g2) with "
428 "-g1 angle or dihedral"));
430 if (bSingle && sel2info_->isSet())
433 InconsistentInputError("Cannot provide a second selection "
434 "(-group2) with -g1 angle or dihedral"));
436 if (!bSingle && g2type_ == Group2Type::None)
439 InconsistentInputError("Should specify a second group (-g2) "
440 "if the first group is not an angle or a dihedral"));
443 // Set up the number of positions per angle.
446 case Group1Type::Angle: natoms1_ = 3; break;
447 case Group1Type::Dihedral: natoms1_ = 4; break;
448 case Group1Type::Vector: natoms1_ = 2; break;
449 case Group1Type::Plane: natoms1_ = 3; break;
450 default: GMX_THROW(InternalError("invalid -g1 value"));
454 case Group2Type::None: natoms2_ = 0; break;
455 case Group2Type::Vector: natoms2_ = 2; break;
456 case Group2Type::Plane: natoms2_ = 3; break;
457 case Group2Type::TimeZero: // Intended to fall through
458 case Group2Type::Z: natoms2_ = 0; break;
459 case Group2Type::SphereNormal: natoms2_ = 1; break;
460 default: GMX_THROW(InternalError("invalid -g2 value"));
462 if (natoms2_ == 0 && sel2info_->isSet())
464 GMX_THROW(InconsistentInputError(
465 "Cannot provide a second selection (-group2) with -g2 t0 or z"));
467 // TODO: If bSingle is not set, the second selection option should be
472 void Angle::initFromSelections(const SelectionList& sel1, const SelectionList& sel2)
474 const int angleGroups = std::max(sel1.size(), sel2.size());
475 const bool bHasSecondSelection = natoms2_ > 0;
477 if (bHasSecondSelection && sel1.size() != sel2.size() && std::min(sel1.size(), sel2.size()) != 1)
479 GMX_THROW(InconsistentInputError(
480 "-group1 and -group2 should specify the same number of selections"));
483 AnglePositionIterator iter1(sel1, natoms1_);
484 AnglePositionIterator iter2(sel2, natoms2_);
485 for (int g = 0; g < angleGroups; ++g, iter1.nextGroup(), iter2.nextGroup())
487 const int posCount1 = iter1.currentSelection().posCount();
488 if (natoms1_ > 1 && posCount1 % natoms1_ != 0)
490 GMX_THROW(InconsistentInputError(formatString(
491 "Number of positions in selection %d in the first group not divisible by %d",
492 static_cast<int>(g + 1), natoms1_)));
494 const int angleCount1 = posCount1 / natoms1_;
495 int angleCount = angleCount1;
497 if (bHasSecondSelection)
499 const int posCount2 = iter2.currentSelection().posCount();
500 if (natoms2_ > 1 && posCount2 % natoms2_ != 0)
502 GMX_THROW(InconsistentInputError(
503 formatString("Number of positions in selection %d in the second group not "
505 static_cast<int>(g + 1), natoms2_)));
507 if (g2type_ == Group2Type::SphereNormal && posCount2 != 1)
509 GMX_THROW(InconsistentInputError(
510 "The second group should contain a single position with -g2 sphnorm"));
513 const int angleCount2 = posCount2 / natoms2_;
514 angleCount = std::max(angleCount1, angleCount2);
515 if (angleCount1 != angleCount2 && std::min(angleCount1, angleCount2) != 1)
517 GMX_THROW(InconsistentInputError(
518 "Number of vectors defined by the two groups are not the same"));
521 angleCount_.push_back(angleCount);
526 void Angle::checkSelections(const SelectionList& sel1, const SelectionList& sel2) const
528 AnglePositionIterator iter1(sel1, natoms1_);
529 AnglePositionIterator iter2(sel2, natoms2_);
530 for (size_t g = 0; g < angleCount_.size(); ++g, iter1.nextGroup(), iter2.nextGroup())
532 if (iter1.isDynamic() || (iter2.hasValue() && iter2.isDynamic()))
534 for (int n = 0; n < angleCount_[g]; ++n, iter1.nextValue(), iter2.nextValue())
537 if (!iter1.allValuesConsistentlySelected())
541 if (!iter2.allValuesConsistentlySelected())
545 if (angleCount_[g] > 1)
547 if (iter1.hasSingleValue() && !iter1.currentValuesSelected())
551 if (iter2.hasSingleValue() && !iter2.currentValuesSelected())
557 && (angleCount_[g] == 1 || (!iter1.hasSingleValue() && !iter2.hasSingleValue()))
558 && iter1.currentValuesSelected() != iter2.currentValuesSelected())
564 std::string message = formatString(
565 "Dynamic selection %d does not select "
566 "a consistent set of angles over the frames",
567 static_cast<int>(g + 1));
568 GMX_THROW(InconsistentInputError(message));
576 void Angle::initAnalysis(const TrajectoryAnalysisSettings& settings, const TopologyInformation& /* top */)
578 initFromSelections(sel1_, sel2_);
580 // checkSelections() ensures that both selection lists have the same size.
581 angles_.setDataSetCount(angleCount_.size());
582 for (size_t i = 0; i < angleCount_.size(); ++i)
584 angles_.setColumnCount(i, angleCount_[i]);
586 double histogramMin = (g1type_ == Group1Type::Dihedral ? -180.0 : 0);
587 histogramModule_->init(histogramFromRange(histogramMin, 180.0).binWidth(binWidth_).includeAll());
589 if (g2type_ == Group2Type::TimeZero)
591 vt0_.resize(sel1_.size());
592 for (size_t g = 0; g < sel1_.size(); ++g)
594 vt0_[g].resize(sel1_[g].posCount() / natoms1_);
598 if (!fnAverage_.empty())
600 AnalysisDataPlotModulePointer plotm(new AnalysisDataPlotModule(settings.plotSettings()));
601 plotm->setFileName(fnAverage_);
602 plotm->setTitle("Average angle");
603 plotm->setXAxisIsTime();
604 plotm->setYLabel("Angle (degrees)");
605 // TODO: Consider adding information about the second selection,
606 // and/or a subtitle describing what kind of angle this is.
607 for (size_t g = 0; g < sel1_.size(); ++g)
609 plotm->appendLegend(sel1_[g].name());
611 averageModule_->addModule(plotm);
616 AnalysisDataPlotModulePointer plotm(new AnalysisDataPlotModule(settings.plotSettings()));
617 plotm->setFileName(fnAll_);
618 plotm->setTitle("Angle");
619 plotm->setXAxisIsTime();
620 plotm->setYLabel("Angle (degrees)");
621 // TODO: Add legends? (there can be a massive amount of columns)
622 angles_.addModule(plotm);
625 if (!fnHistogram_.empty())
627 AnalysisDataPlotModulePointer plotm(new AnalysisDataPlotModule(settings.plotSettings()));
628 plotm->setFileName(fnHistogram_);
629 plotm->setTitle("Angle histogram");
630 plotm->setXLabel("Angle (degrees)");
631 plotm->setYLabel("Probability");
632 // TODO: Consider adding information about the second selection,
633 // and/or a subtitle describing what kind of angle this is.
634 for (size_t g = 0; g < sel1_.size(); ++g)
636 plotm->appendLegend(sel1_[g].name());
638 histogramModule_->averager().addModule(plotm);
643 //! Helper method to calculate a vector from two or three positions.
644 void calc_vec(int natoms, rvec x[], t_pbc* pbc, rvec xout, rvec cout)
651 pbc_dx(pbc, x[1], x[0], xout);
655 rvec_sub(x[1], x[0], xout);
657 svmul(0.5, xout, cout);
658 rvec_add(x[0], cout, cout);
665 pbc_dx(pbc, x[1], x[0], v1);
666 pbc_dx(pbc, x[2], x[0], v2);
670 rvec_sub(x[1], x[0], v1);
671 rvec_sub(x[2], x[0], v2);
674 rvec_add(x[0], x[1], cout);
675 rvec_add(cout, x[2], cout);
676 svmul(1.0 / 3.0, cout, cout);
679 default: GMX_RELEASE_ASSERT(false, "Incorrectly initialized number of atoms");
684 void Angle::analyzeFrame(int frnr, const t_trxframe& fr, t_pbc* pbc, TrajectoryAnalysisModuleData* pdata)
686 AnalysisDataHandle dh = pdata->dataHandle(angles_);
687 const SelectionList& sel1 = TrajectoryAnalysisModuleData::parallelSelections(sel1_);
688 const SelectionList& sel2 = TrajectoryAnalysisModuleData::parallelSelections(sel2_);
690 checkSelections(sel1, sel2);
692 dh.startFrame(frnr, fr.time);
694 AnglePositionIterator iter1(sel1, natoms1_);
695 AnglePositionIterator iter2(sel2, natoms2_);
696 for (size_t g = 0; g < angleCount_.size(); ++g, iter1.nextGroup(), iter2.nextGroup())
701 // v2 & c2 are conditionally set in the switch statement below, and conditionally
702 // used in a different switch statement later. Apparently the clang static analyzer
703 // thinks there are cases where they can be used uninitialzed (which I cannot find),
704 // but to avoid trouble if we ever change just one of the switch statements it
705 // makes sense to clear them outside the first switch.
712 case Group2Type::Z: v2[ZZ] = 1.0; break;
713 case Group2Type::SphereNormal: copy_rvec(sel2_[g].position(0).x(), c2); break;
720 for (int n = 0; n < angleCount_[g]; ++n, iter1.nextValue(), iter2.nextValue())
723 // x[] will be assigned below based on the number of atoms used to initialize iter1,
724 // which in turn should correspond perfectly to g1type_ (which determines how many we
725 // read), but unsurprisingly the static analyzer chokes a bit on that.
729 // checkSelections() ensures that this reflects all the involved
731 const bool bPresent = iter1.currentValuesSelected() && iter2.currentValuesSelected();
732 iter1.getCurrentPositions(x);
735 case Group1Type::Angle:
738 pbc_dx(pbc, x[0], x[1], v1);
739 pbc_dx(pbc, x[2], x[1], v2);
743 rvec_sub(x[0], x[1], v1);
744 rvec_sub(x[2], x[1], v2);
746 angle = gmx_angle(v1, v2);
748 case Group1Type::Dihedral:
753 pbc_dx(pbc, x[0], x[1], dx[0]);
754 pbc_dx(pbc, x[2], x[1], dx[1]);
755 pbc_dx(pbc, x[2], x[3], dx[2]);
759 rvec_sub(x[0], x[1], dx[0]);
760 rvec_sub(x[2], x[1], dx[1]);
761 rvec_sub(x[2], x[3], dx[2]);
763 cprod(dx[0], dx[1], v1);
764 cprod(dx[1], dx[2], v2);
765 angle = gmx_angle(v1, v2);
766 real ipr = iprod(dx[0], v2);
773 case Group1Type::Vector:
774 case Group1Type::Plane:
775 calc_vec(natoms1_, x, pbc, v1, c1);
778 case Group2Type::Vector:
779 case Group2Type::Plane:
780 iter2.getCurrentPositions(x);
781 calc_vec(natoms2_, x, pbc, v2, c2);
783 case Group2Type::TimeZero:
784 // FIXME: This is not parallelizable.
787 copy_rvec(v1, vt0_[g][n]);
789 copy_rvec(vt0_[g][n], v2);
791 case Group2Type::Z: c1[XX] = c1[YY] = 0.0; break;
792 case Group2Type::SphereNormal:
795 pbc_dx(pbc, c1, c2, v2);
799 rvec_sub(c1, c2, v2);
802 default: GMX_THROW(InternalError("invalid -g2 value"));
804 angle = gmx_angle(v1, v2);
806 default: GMX_THROW(InternalError("invalid -g1 value"));
808 dh.setPoint(n, angle * RAD2DEG, bPresent);
815 void Angle::finishAnalysis(int /*nframes*/)
817 AbstractAverageHistogram& averageHistogram = histogramModule_->averager();
818 averageHistogram.normalizeProbability();
819 averageHistogram.done();
823 void Angle::writeOutput() {}
827 const char AngleInfo::name[] = "gangle";
828 const char AngleInfo::shortDescription[] = "Calculate angles";
830 TrajectoryAnalysisModulePointer AngleInfo::create()
832 return TrajectoryAnalysisModulePointer(new Angle);
835 } // namespace analysismodules