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37 * Implements classes in selection.h.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_selection
42 #include "selection.h"
44 #include "gromacs/topology/topology.h"
57 /********************************************************************
61 SelectionData::SelectionData(SelectionTreeElement *elem,
63 : name_(elem->name()), selectionText_(selstr),
64 rootElement_(*elem), coveredFractionType_(CFRAC_NONE),
65 coveredFraction_(1.0), averageCoveredFraction_(1.0),
66 bDynamic_(false), bDynamicCoveredFraction_(false)
68 if (elem->child->type == SEL_CONST)
70 // TODO: This is not exception-safe if any called function throws.
71 gmx_ana_pos_copy(&rawPositions_, elem->child->v.u.p, true);
75 SelectionTreeElementPointer child = elem->child;
76 child->flags &= ~SEL_ALLOCVAL;
77 _gmx_selvalue_setstore(&child->v, &rawPositions_);
78 /* We should also skip any modifiers to determine the dynamic
80 while (child->type == SEL_MODIFIER)
83 if (child->type == SEL_SUBEXPRREF)
86 /* Because most subexpression elements are created
87 * during compilation, we need to check for them
90 if (child->type == SEL_SUBEXPR)
96 /* For variable references, we should skip the
97 * SEL_SUBEXPRREF and SEL_SUBEXPR elements. */
98 if (child->type == SEL_SUBEXPRREF)
100 child = child->child->child;
102 bDynamic_ = (child->child->flags & SEL_DYNAMIC);
104 initCoveredFraction(CFRAC_NONE);
108 SelectionData::~SelectionData()
114 SelectionData::initCoveredFraction(e_coverfrac_t type)
116 coveredFractionType_ = type;
117 if (type == CFRAC_NONE)
119 bDynamicCoveredFraction_ = false;
121 else if (!_gmx_selelem_can_estimate_cover(rootElement()))
123 coveredFractionType_ = CFRAC_NONE;
124 bDynamicCoveredFraction_ = false;
128 bDynamicCoveredFraction_ = true;
130 coveredFraction_ = bDynamicCoveredFraction_ ? 0.0 : 1.0;
131 averageCoveredFraction_ = coveredFraction_;
132 return type == CFRAC_NONE || coveredFractionType_ != CFRAC_NONE;
139 * Helper function to compute total masses and charges for positions.
141 * \param[in] top Topology to take atom masses from.
142 * \param[in] pos Positions to compute masses and charges for.
143 * \param[out] masses Output masses.
144 * \param[out] charges Output charges.
146 * Does not throw if enough space has been reserved for the output vectors.
148 void computeMassesAndCharges(const t_topology *top, const gmx_ana_pos_t &pos,
149 std::vector<real> *masses,
150 std::vector<real> *charges)
152 GMX_ASSERT(top != NULL, "Should not have been called with NULL topology");
155 for (int b = 0; b < pos.count(); ++b)
159 for (int i = pos.m.mapb.index[b]; i < pos.m.mapb.index[b+1]; ++i)
161 const int index = pos.m.mapb.a[i];
162 mass += top->atoms.atom[index].m;
163 charge += top->atoms.atom[index].q;
165 masses->push_back(mass);
166 charges->push_back(charge);
173 SelectionData::refreshName()
175 rootElement_.fillNameIfMissing(selectionText_.c_str());
176 name_ = rootElement_.name();
180 SelectionData::initializeMassesAndCharges(const t_topology *top)
182 GMX_ASSERT(posMass_.empty() && posCharge_.empty(),
183 "Should not be called more than once");
184 posMass_.reserve(posCount());
185 posCharge_.reserve(posCount());
188 posMass_.resize(posCount(), 1.0);
189 posCharge_.resize(posCount(), 0.0);
193 computeMassesAndCharges(top, rawPositions_, &posMass_, &posCharge_);
199 SelectionData::refreshMassesAndCharges(const t_topology *top)
201 if (top != NULL && isDynamic() && !hasFlag(efSelection_DynamicMask))
203 computeMassesAndCharges(top, rawPositions_, &posMass_, &posCharge_);
209 SelectionData::updateCoveredFractionForFrame()
211 if (isCoveredFractionDynamic())
213 real cfrac = _gmx_selelem_estimate_coverfrac(rootElement());
214 coveredFraction_ = cfrac;
215 averageCoveredFraction_ += cfrac;
221 SelectionData::computeAverageCoveredFraction(int nframes)
223 if (isCoveredFractionDynamic() && nframes > 0)
225 averageCoveredFraction_ /= nframes;
231 SelectionData::restoreOriginalPositions(const t_topology *top)
235 gmx_ana_pos_t &p = rawPositions_;
236 gmx_ana_indexmap_update(&p.m, rootElement().v.u.g,
237 hasFlag(gmx::efSelection_DynamicMask));
238 refreshMassesAndCharges(top);
242 } // namespace internal
244 /********************************************************************
248 Selection::operator AnalysisNeighborhoodPositions() const
250 return AnalysisNeighborhoodPositions(data().rawPositions_.x,
251 data().rawPositions_.count());
256 Selection::printInfo(FILE *fp) const
258 fprintf(fp, "\"%s\" (%d position%s, %d atom%s%s)", name(),
259 posCount(), posCount() == 1 ? "" : "s",
260 atomCount(), atomCount() == 1 ? "" : "s",
261 isDynamic() ? ", dynamic" : "");
267 Selection::printDebugInfo(FILE *fp, int nmaxind) const
269 const gmx_ana_pos_t &p = data().rawPositions_;
273 fprintf(fp, " Group ");
275 gmx_ana_index_set(&g, p.m.mapb.nra, p.m.mapb.a, 0);
276 gmx_ana_index_dump(fp, &g, nmaxind);
278 fprintf(fp, " Block (size=%d):", p.m.mapb.nr);
281 fprintf(fp, " (null)");
286 if (nmaxind >= 0 && n > nmaxind)
290 for (int i = 0; i <= n; ++i)
292 fprintf(fp, " %d", p.m.mapb.index[i]);
302 if (nmaxind >= 0 && n > nmaxind)
306 fprintf(fp, " RefId:");
309 fprintf(fp, " (null)");
313 for (int i = 0; i < n; ++i)
315 fprintf(fp, " %d", p.m.refid[i]);
324 fprintf(fp, " MapId:");
327 fprintf(fp, " (null)");
331 for (int i = 0; i < n; ++i)
333 fprintf(fp, " %d", p.m.mapid[i]);
344 /********************************************************************
348 SelectionPosition::operator AnalysisNeighborhoodPositions() const
350 return AnalysisNeighborhoodPositions(sel_->rawPositions_.x,
351 sel_->rawPositions_.count())
352 .selectSingleFromArray(i_);