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37 * Implements classes in selection.h.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_selection
44 #include "selection.h"
46 #include "gromacs/topology/topology.h"
59 /********************************************************************
63 SelectionData::SelectionData(SelectionTreeElement *elem,
65 : name_(elem->name()), selectionText_(selstr),
66 rootElement_(*elem), coveredFractionType_(CFRAC_NONE),
67 coveredFraction_(1.0), averageCoveredFraction_(1.0),
68 bDynamic_(false), bDynamicCoveredFraction_(false)
70 if (elem->child->type == SEL_CONST)
72 // TODO: This is not exception-safe if any called function throws.
73 gmx_ana_pos_copy(&rawPositions_, elem->child->v.u.p, true);
77 SelectionTreeElementPointer child = elem->child;
78 child->flags &= ~SEL_ALLOCVAL;
79 _gmx_selvalue_setstore(&child->v, &rawPositions_);
80 /* We should also skip any modifiers to determine the dynamic
82 while (child->type == SEL_MODIFIER)
85 if (child->type == SEL_SUBEXPRREF)
88 /* Because most subexpression elements are created
89 * during compilation, we need to check for them
92 if (child->type == SEL_SUBEXPR)
98 /* For variable references, we should skip the
99 * SEL_SUBEXPRREF and SEL_SUBEXPR elements. */
100 if (child->type == SEL_SUBEXPRREF)
102 child = child->child->child;
104 bDynamic_ = (child->child->flags & SEL_DYNAMIC);
106 initCoveredFraction(CFRAC_NONE);
110 SelectionData::~SelectionData()
116 SelectionData::initCoveredFraction(e_coverfrac_t type)
118 coveredFractionType_ = type;
119 if (type == CFRAC_NONE)
121 bDynamicCoveredFraction_ = false;
123 else if (!_gmx_selelem_can_estimate_cover(rootElement()))
125 coveredFractionType_ = CFRAC_NONE;
126 bDynamicCoveredFraction_ = false;
130 bDynamicCoveredFraction_ = true;
132 coveredFraction_ = bDynamicCoveredFraction_ ? 0.0 : 1.0;
133 averageCoveredFraction_ = coveredFraction_;
134 return type == CFRAC_NONE || coveredFractionType_ != CFRAC_NONE;
141 * Helper function to compute total masses and charges for positions.
143 * \param[in] top Topology to take atom masses from.
144 * \param[in] pos Positions to compute masses and charges for.
145 * \param[out] masses Output masses.
146 * \param[out] charges Output charges.
148 * Does not throw if enough space has been reserved for the output vectors.
150 void computeMassesAndCharges(const t_topology *top, const gmx_ana_pos_t &pos,
151 std::vector<real> *masses,
152 std::vector<real> *charges)
154 GMX_ASSERT(top != NULL, "Should not have been called with NULL topology");
157 for (int b = 0; b < pos.count(); ++b)
161 for (int i = pos.m.mapb.index[b]; i < pos.m.mapb.index[b+1]; ++i)
163 const int index = pos.m.mapb.a[i];
164 mass += top->atoms.atom[index].m;
165 charge += top->atoms.atom[index].q;
167 masses->push_back(mass);
168 charges->push_back(charge);
175 SelectionData::refreshName()
177 rootElement_.fillNameIfMissing(selectionText_.c_str());
178 name_ = rootElement_.name();
182 SelectionData::initializeMassesAndCharges(const t_topology *top)
184 GMX_ASSERT(posMass_.empty() && posCharge_.empty(),
185 "Should not be called more than once");
186 posMass_.reserve(posCount());
187 posCharge_.reserve(posCount());
190 posMass_.resize(posCount(), 1.0);
191 posCharge_.resize(posCount(), 0.0);
195 computeMassesAndCharges(top, rawPositions_, &posMass_, &posCharge_);
201 SelectionData::refreshMassesAndCharges(const t_topology *top)
203 if (top != NULL && isDynamic() && !hasFlag(efSelection_DynamicMask))
205 computeMassesAndCharges(top, rawPositions_, &posMass_, &posCharge_);
211 SelectionData::updateCoveredFractionForFrame()
213 if (isCoveredFractionDynamic())
215 real cfrac = _gmx_selelem_estimate_coverfrac(rootElement());
216 coveredFraction_ = cfrac;
217 averageCoveredFraction_ += cfrac;
223 SelectionData::computeAverageCoveredFraction(int nframes)
225 if (isCoveredFractionDynamic() && nframes > 0)
227 averageCoveredFraction_ /= nframes;
233 SelectionData::restoreOriginalPositions(const t_topology *top)
237 gmx_ana_pos_t &p = rawPositions_;
238 gmx_ana_indexmap_update(&p.m, rootElement().v.u.g,
239 hasFlag(gmx::efSelection_DynamicMask));
240 refreshMassesAndCharges(top);
244 } // namespace internal
246 /********************************************************************
250 Selection::operator AnalysisNeighborhoodPositions() const
252 AnalysisNeighborhoodPositions pos(data().rawPositions_.x,
253 data().rawPositions_.count());
256 pos.exclusionIds(atomIndices());
263 Selection::printInfo(FILE *fp) const
265 fprintf(fp, "\"%s\" (%d position%s, %d atom%s%s)", name(),
266 posCount(), posCount() == 1 ? "" : "s",
267 atomCount(), atomCount() == 1 ? "" : "s",
268 isDynamic() ? ", dynamic" : "");
274 Selection::printDebugInfo(FILE *fp, int nmaxind) const
276 const gmx_ana_pos_t &p = data().rawPositions_;
280 fprintf(fp, " Group ");
282 gmx_ana_index_set(&g, p.m.mapb.nra, p.m.mapb.a, 0);
283 gmx_ana_index_dump(fp, &g, nmaxind);
285 fprintf(fp, " Block (size=%d):", p.m.mapb.nr);
288 fprintf(fp, " (null)");
293 if (nmaxind >= 0 && n > nmaxind)
297 for (int i = 0; i <= n; ++i)
299 fprintf(fp, " %d", p.m.mapb.index[i]);
309 if (nmaxind >= 0 && n > nmaxind)
313 fprintf(fp, " RefId:");
316 fprintf(fp, " (null)");
320 for (int i = 0; i < n; ++i)
322 fprintf(fp, " %d", p.m.refid[i]);
331 fprintf(fp, " MapId:");
334 fprintf(fp, " (null)");
338 for (int i = 0; i < n; ++i)
340 fprintf(fp, " %d", p.m.mapid[i]);
351 /********************************************************************
355 SelectionPosition::operator AnalysisNeighborhoodPositions() const
357 AnalysisNeighborhoodPositions pos(sel_->rawPositions_.x,
358 sel_->rawPositions_.count());
359 if (sel_->hasOnlyAtoms())
361 // TODO: Move atomIndices() such that it can be reused here as well.
362 pos.exclusionIds(constArrayRefFromArray<int>(sel_->rawPositions_.m.mapb.a,
363 sel_->rawPositions_.m.mapb.nra));
365 return pos.selectSingleFromArray(i_);