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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"
55 /********************************************************************
59 SelectionData::SelectionData(SelectionTreeElement *elem,
61 : name_(elem->name()), selectionText_(selstr),
62 rootElement_(*elem), coveredFractionType_(CFRAC_NONE),
63 coveredFraction_(1.0), averageCoveredFraction_(1.0),
64 bDynamic_(false), bDynamicCoveredFraction_(false)
66 if (elem->child->type == SEL_CONST)
68 // TODO: This is not exception-safe if any called function throws.
69 gmx_ana_pos_copy(&rawPositions_, elem->child->v.u.p, true);
73 SelectionTreeElementPointer child = elem->child;
74 child->flags &= ~SEL_ALLOCVAL;
75 _gmx_selvalue_setstore(&child->v, &rawPositions_);
76 /* We should also skip any modifiers to determine the dynamic
78 while (child->type == SEL_MODIFIER)
81 if (child->type == SEL_SUBEXPRREF)
84 /* Because most subexpression elements are created
85 * during compilation, we need to check for them
88 if (child->type == SEL_SUBEXPR)
94 /* For variable references, we should skip the
95 * SEL_SUBEXPRREF and SEL_SUBEXPR elements. */
96 if (child->type == SEL_SUBEXPRREF)
98 child = child->child->child;
100 bDynamic_ = (child->child->flags & SEL_DYNAMIC);
102 initCoveredFraction(CFRAC_NONE);
106 SelectionData::~SelectionData()
112 SelectionData::initCoveredFraction(e_coverfrac_t type)
114 coveredFractionType_ = type;
115 if (type == CFRAC_NONE)
117 bDynamicCoveredFraction_ = false;
119 else if (!_gmx_selelem_can_estimate_cover(rootElement()))
121 coveredFractionType_ = CFRAC_NONE;
122 bDynamicCoveredFraction_ = false;
126 bDynamicCoveredFraction_ = true;
128 coveredFraction_ = bDynamicCoveredFraction_ ? 0.0 : 1.0;
129 averageCoveredFraction_ = coveredFraction_;
130 return type == CFRAC_NONE || coveredFractionType_ != CFRAC_NONE;
137 * Helper function to compute total masses and charges for positions.
139 * \param[in] top Topology to take atom masses from.
140 * \param[in] pos Positions to compute masses and charges for.
141 * \param[out] masses Output masses.
142 * \param[out] charges Output charges.
144 * Does not throw if enough space has been reserved for the output vectors.
146 void computeMassesAndCharges(const t_topology *top, const gmx_ana_pos_t &pos,
147 std::vector<real> *masses,
148 std::vector<real> *charges)
150 GMX_ASSERT(top != NULL, "Should not have been called with NULL topology");
153 for (int b = 0; b < pos.count(); ++b)
157 for (int i = pos.m.mapb.index[b]; i < pos.m.mapb.index[b+1]; ++i)
159 const int index = pos.m.mapb.a[i];
160 mass += top->atoms.atom[index].m;
161 charge += top->atoms.atom[index].q;
163 masses->push_back(mass);
164 charges->push_back(charge);
171 SelectionData::refreshName()
173 rootElement_.fillNameIfMissing(selectionText_.c_str());
174 name_ = rootElement_.name();
178 SelectionData::initializeMassesAndCharges(const t_topology *top)
180 GMX_ASSERT(posMass_.empty() && posCharge_.empty(),
181 "Should not be called more than once");
182 posMass_.reserve(posCount());
183 posCharge_.reserve(posCount());
186 posMass_.resize(posCount(), 1.0);
187 posCharge_.resize(posCount(), 0.0);
191 computeMassesAndCharges(top, rawPositions_, &posMass_, &posCharge_);
197 SelectionData::refreshMassesAndCharges(const t_topology *top)
199 if (top != NULL && isDynamic() && !hasFlag(efSelection_DynamicMask))
201 computeMassesAndCharges(top, rawPositions_, &posMass_, &posCharge_);
207 SelectionData::updateCoveredFractionForFrame()
209 if (isCoveredFractionDynamic())
211 real cfrac = _gmx_selelem_estimate_coverfrac(rootElement());
212 coveredFraction_ = cfrac;
213 averageCoveredFraction_ += cfrac;
219 SelectionData::computeAverageCoveredFraction(int nframes)
221 if (isCoveredFractionDynamic() && nframes > 0)
223 averageCoveredFraction_ /= nframes;
229 SelectionData::restoreOriginalPositions(const t_topology *top)
233 gmx_ana_pos_t &p = rawPositions_;
234 gmx_ana_indexmap_update(&p.m, rootElement().v.u.g,
235 hasFlag(gmx::efSelection_DynamicMask));
236 refreshMassesAndCharges(top);
240 } // namespace internal
242 /********************************************************************
246 Selection::operator AnalysisNeighborhoodPositions() const
248 return AnalysisNeighborhoodPositions(data().rawPositions_.x,
249 data().rawPositions_.count());
254 Selection::printInfo(FILE *fp) const
256 fprintf(fp, "\"%s\" (%d position%s, %d atom%s%s)", name(),
257 posCount(), posCount() == 1 ? "" : "s",
258 atomCount(), atomCount() == 1 ? "" : "s",
259 isDynamic() ? ", dynamic" : "");
265 Selection::printDebugInfo(FILE *fp, int nmaxind) const
267 const gmx_ana_pos_t &p = data().rawPositions_;
271 fprintf(fp, " Group ");
273 gmx_ana_index_set(&g, p.m.mapb.nra, p.m.mapb.a, 0);
274 gmx_ana_index_dump(fp, &g, nmaxind);
276 fprintf(fp, " Block (size=%d):", p.m.mapb.nr);
279 fprintf(fp, " (null)");
284 if (nmaxind >= 0 && n > nmaxind)
288 for (int i = 0; i <= n; ++i)
290 fprintf(fp, " %d", p.m.mapb.index[i]);
300 if (nmaxind >= 0 && n > nmaxind)
304 fprintf(fp, " RefId:");
307 fprintf(fp, " (null)");
311 for (int i = 0; i < n; ++i)
313 fprintf(fp, " %d", p.m.refid[i]);
322 fprintf(fp, " MapId:");
325 fprintf(fp, " (null)");
329 for (int i = 0; i < n; ++i)
331 fprintf(fp, " %d", p.m.mapid[i]);
342 /********************************************************************
346 SelectionPosition::operator AnalysisNeighborhoodPositions() const
348 return AnalysisNeighborhoodPositions(sel_->rawPositions_.x,
349 sel_->rawPositions_.count())
350 .selectSingleFromArray(i_);