source: src/Atom/atom_bondedparticle.cpp@ 9d7c6a

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Last change on this file since 9d7c6a was 760c4c, checked in by Frederik Heber <heber@…>, 13 years ago

Cleaned observer structure in atom.

  • Added new channel BondsRemoved and used in bonds removal functions.
  • FIX: Removed PropertyChanged for setNr and alikes, Nr is molecule's responsibility. Made note of this in documentation.
  • Property mode set to 100644
File size: 10.6 KB
RevLine 
[bcf653]1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
[0aa122]4 * Copyright (C) 2010-2012 University of Bonn. All rights reserved.
[bcf653]5 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
6 */
7
[6b919f8]8/*
9 * atom_bondedparticle.cpp
10 *
11 * Created on: Oct 19, 2009
12 * Author: heber
13 */
14
[bf3817]15// include config.h
16#ifdef HAVE_CONFIG_H
17#include <config.h>
18#endif
19
[ad011c]20#include "CodePatterns/MemDebug.hpp"
[112b09]21
[6b919f8]22#include "atom.hpp"
23#include "atom_bondedparticle.hpp"
[129204]24#include "Bond/bond.hpp"
[d557374]25#include "CodePatterns/Assert.hpp"
[ad011c]26#include "CodePatterns/Log.hpp"
27#include "CodePatterns/Verbose.hpp"
[3bdb6d]28#include "Element/element.hpp"
[db7e6d]29#include "WorldTime.hpp"
[6b919f8]30
31/** Constructor of class BondedParticle.
32 */
[70ff32]33BondedParticle::BondedParticle()
34{
[9d83b6]35 ListOfBonds.push_back(BondList());
[70ff32]36};
[6b919f8]37
38/** Destructor of class BondedParticle.
39 */
40BondedParticle::~BondedParticle()
41{
[5e2f80]42 removeAllBonds();
[6b919f8]43};
44
45/** Outputs the current atom::AdaptiveOrder and atom::MaxOrder to \a *file.
46 * \param *file output stream
47 */
[b453f9]48void BondedParticle::OutputOrder(ofstream *file) const
[6b919f8]49{
[735b1c]50 *file << getNr() << "\t" << (int)AdaptiveOrder << "\t" << (int)MaxOrder << endl;
[47d041]51 //LOG(2, "Storing: " << getNr() << "\t" << (int)AdaptiveOrder << "\t" << (int)MaxOrder << ".");
[6b919f8]52};
53
54/** Prints all bonds of this atom with total degree.
55 */
[4b5cf8]56void BondedParticle::OutputBondOfAtom(std::ostream &ost) const
[6b919f8]57{
[9d83b6]58 const BondList& ListOfBonds = getListOfBonds();
[4b5cf8]59 ost << "Atom " << getName() << "/" << getNr() << " with " << ListOfBonds.size() << " bonds: ";
[e138de]60 int TotalDegree = 0;
61 for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); ++Runner) {
[4b5cf8]62 ost << **Runner << "\t";
[e138de]63 TotalDegree += (*Runner)->BondDegree;
64 }
[4b5cf8]65 ost << " -- TotalDegree: " << TotalDegree;
[6b919f8]66};
67
[5309ba]68/** Output of atom::Nr along with all bond partners.
[6b919f8]69 * \param *AdjacencyFile output stream
70 */
[1f1b23]71void BondedParticle::OutputAdjacency(ofstream * const AdjacencyFile) const
[6b919f8]72{
[9d83b6]73 const BondList& ListOfBonds = getListOfBonds();
[52ed5b]74 *AdjacencyFile << getNr() << "\t";
[6b919f8]75 for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); (++Runner))
[52ed5b]76 *AdjacencyFile << (*Runner)->GetOtherAtom(this)->getNr() << "\t";
[6b919f8]77 *AdjacencyFile << endl;
78};
79
[5309ba]80/** Output of atom::Nr along each bond partner per line.
81 * Only bonds are printed where atom::Nr is smaller than the one of the bond partner.
[1f1b23]82 * \param *AdjacencyFile output stream
83 */
84void BondedParticle::OutputBonds(ofstream * const BondFile) const
85{
[9d83b6]86 const BondList& ListOfBonds = getListOfBonds();
[1f1b23]87 for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); (++Runner))
[735b1c]88 if (getNr() < (*Runner)->GetOtherAtom(this)->getNr())
[52ed5b]89 *BondFile << getNr() << "\t" << (*Runner)->GetOtherAtom(this)->getNr() << "\n";
[1f1b23]90};
91
[b8d4a3]92/**
[db7e6d]93 * Adds a bond between this bonded particle and another. Returns present instance if this
[b8d4a3]94 * bond already exists.
95 *
[073a9e4]96 * @param _step time step to access
[db7e6d]97 * @param bonding partner
[05a885]98 * @return const pointer to created bond or to already present bonds
[b8d4a3]99 */
[05a885]100bond * const BondedParticle::addBond(const unsigned int _step, BondedParticle* Partner)
[db7e6d]101{
102 const BondList &bondlist = getListOfBondsAtStep(_step);
103 for (BondList::const_iterator runner = bondlist.begin();
104 runner != bondlist.end();
105 runner++) {
106 if ((*runner)->Contains(Partner))
107 return *runner;
[b8d4a3]108 }
109
[efe516]110 bond* newBond = new bond((atom*) this, (atom*) Partner, 1);
[073a9e4]111 RegisterBond(_step, newBond);
112 Partner->RegisterBond(_step, newBond);
[db7e6d]113
114 return newBond;
115}
116
117/** Removes a bond for this atom.
118 *
119 * @param Binder bond to remove
120 */
121void BondedParticle::removeBond(bond * binder)
122{
123 UnregisterBond(binder);
[b8d4a3]124}
125
[cc9119]126/** Removes all bonds in all timesteps and their instances, too.
[5e2f80]127 *
128 */
129void BondedParticle::removeAllBonds()
130{
131 for (size_t index = 0; index < ListOfBonds.size(); ++index)
[cc9119]132 removeAllBonds(index);
133}
134
135/** Removes all bonds for a given \a _step and their instances, too.
136 *
137 * @param _step time step to access
138 */
139void BondedParticle::removeAllBonds(const unsigned int _step)
140{
141 for (BondList::iterator iter = ListOfBonds[_step].begin();
142 !ListOfBonds[_step].empty();
143 iter = ListOfBonds[_step].begin()) {
144 delete (*iter);
145 // unregister/NOTIFY is done by bond::~bond()
[5e2f80]146 }
147}
148
[6b919f8]149/** Puts a given bond into atom::ListOfBonds.
[073a9e4]150 * @param _step time step to access
[6b919f8]151 * \param *Binder bond to insert
152 */
[05a885]153bool BondedParticle::RegisterBond(const unsigned int _step, bond * const Binder)
[6b919f8]154{
[db7e6d]155 OBSERVE;
[6b919f8]156 bool status = false;
157 if (Binder != NULL) {
158 if (Binder->Contains(this)) {
[d557374]159 //LOG(3,"INFO: Registering bond "<< *Binder << " with atom " << *this << " at step " << _step);
[5e2f80]160 if (ListOfBonds.size() <= _step)
161 ListOfBonds.resize(_step+1);
162 ListOfBonds[_step].push_back(Binder);
[74ec1f]163 if (WorldTime::getTime() == _step)
[2ad1ec]164 NOTIFY(AtomObservable::BondsAdded);
[6b919f8]165 status = true;
166 } else {
[47d041]167 ELOG(1, *Binder << " does not contain " << *this << ".");
[6b919f8]168 }
169 } else {
[47d041]170 ELOG(1, "Binder is " << Binder << ".");
[6b919f8]171 }
172 return status;
173};
174
175/** Removes a given bond from atom::ListOfBonds.
[9d83b6]176 * @param _step time step to access
[6b919f8]177 * \param *Binder bond to remove
178 */
[05a885]179bool BondedParticle::UnregisterBond(bond * const Binder)
[6b919f8]180{
[db7e6d]181 OBSERVE;
[6b919f8]182 bool status = false;
[d557374]183 ASSERT(Binder != NULL, "BondedParticle::UnregisterBond() - Binder is NULL.");
184 const int step = ContainsBondAtStep(Binder);
185 if (step != -1) {
[5e2f80]186 //LOG(0,"INFO: Unregistering bond "<< *Binder << " from list " << &ListOfBonds << " of atom " << *this << " at step " << step);
[d557374]187 ListOfBonds[step].remove(Binder);
[760c4c]188 if (WorldTime::getTime() == step)
189 NOTIFY(AtomObservable::BondsRemoved);
[d557374]190 status = true;
[6b919f8]191 } else {
[47d041]192 ELOG(1, *Binder << " does not contain " << *this << ".");
[6b919f8]193 }
194 return status;
195};
196
197/** Removes all bonds from atom::ListOfBonds.
198 * \note Does not do any memory de-allocation.
199 */
[a2bdbe]200void BondedParticle::UnregisterAllBond(const unsigned int _step)
[6b919f8]201{
[74ec1f]202 OBSERVE;
[760c4c]203 NOTIFY(AtomObservable::BondsRemoved);
[af897f]204 ListOfBonds[_step].clear();
205}
[6b919f8]206
[583081]207/** Removes all bonds of given \a _step with freeing memory.
208 *
209 * @param _step time step whose bonds to free
210 */
211void BondedParticle::ClearBondsAtStep(const unsigned int _step)
212{
[db7e6d]213 OBSERVE;
[760c4c]214 NOTIFY(AtomObservable::BondsRemoved);
[583081]215 //LOG(3,"INFO: Clearing all bonds of " << *this << ": " << ListOfBonds[_step]);
216 for (BondList::iterator iter = (ListOfBonds[_step]).begin();
217 !(ListOfBonds[_step]).empty();
218 iter = (ListOfBonds[_step]).begin()) {
219 //LOG(3,"INFO: Clearing bond (" << *iter << ") " << *(*iter) << " of list " << &ListOfBonds);
220 delete((*iter)); // will also unregister with us and remove from list
221 }
222}
223
[93c6e9]224/** Searches for the time step where the given bond \a *Binder is a bond of this particle.
225 *
226 * @param Binder bond to check
227 * @return >=0 - first time step where bond appears, -1 - bond not present in lists
228 */
[db7e6d]229int BondedParticle::ContainsBondAtStep(bond *Binder) const
[93c6e9]230{
231 int step = -1;
232 int tempstep = 0;
233 for(std::vector<BondList>::const_iterator iter = ListOfBonds.begin();
234 iter != ListOfBonds.end();
235 ++iter,++tempstep) {
236 for (BondList::const_iterator bonditer = iter->begin();
237 bonditer != iter->end();
238 ++bonditer) {
239 if ((*bonditer) == Binder) {
240 step = tempstep;
241 break;
242 }
243 }
244 if (step != -1)
245 break;
246 }
247
248 return step;
249}
250
[6b919f8]251/** Corrects the bond degree by one at most if necessary.
[93c6e9]252 * \return number of corrections done
[6b919f8]253 */
[e138de]254int BondedParticle::CorrectBondDegree()
[6b919f8]255{
[db7e6d]256 OBSERVE;
[74ec1f]257 NOTIFY(AtomObservable::BondDegreeChanged);
[6b919f8]258 int NoBonds = 0;
259 int OtherNoBonds = 0;
260 int FalseBondDegree = 0;
261 atom *OtherWalker = NULL;
262 bond *CandidateBond = NULL;
263
264 NoBonds = CountBonds();
[47d041]265 //LOG(3, "Walker " << *this << ": " << (int)this->type->NoValenceOrbitals << " > " << NoBonds << "?");
[83f176]266 if ((int)(getType()->getNoValenceOrbitals()) > NoBonds) { // we have a mismatch, check all bonding partners for mismatch
[9d83b6]267 const BondList& ListOfBonds = getListOfBonds();
[6b919f8]268 for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); (++Runner)) {
269 OtherWalker = (*Runner)->GetOtherAtom(this);
270 OtherNoBonds = OtherWalker->CountBonds();
[47d041]271 //LOG(3, "OtherWalker " << *OtherWalker << ": " << (int)OtherWalker->type->NoValenceOrbitals << " > " << OtherNoBonds << "?");
[83f176]272 if ((int)(OtherWalker->getType()->getNoValenceOrbitals()) > OtherNoBonds) { // check if possible candidate
[9d83b6]273 const BondList& OtherListOfBonds = OtherWalker->getListOfBonds();
274 if ((CandidateBond == NULL) || (ListOfBonds.size() > OtherListOfBonds.size())) { // pick the one with fewer number of bonds first
[6b919f8]275 CandidateBond = (*Runner);
[47d041]276 //LOG(3, "New candidate is " << *CandidateBond << ".");
[6b919f8]277 }
278 }
279 }
280 if ((CandidateBond != NULL)) {
281 CandidateBond->BondDegree++;
[47d041]282 //LOG(2, "Increased bond degree for bond " << *CandidateBond << ".");
[6b919f8]283 } else {
[47d041]284 ELOG(2, "Could not find correct degree for atom " << *this << ".");
[6b919f8]285 FalseBondDegree++;
286 }
287 }
288 return FalseBondDegree;
289};
290
[5e2f80]291/** Sets the weight of all connected bonds to one.
292 */
293void BondedParticle::resetBondDegree()
294{
295 OBSERVE;
[74ec1f]296 NOTIFY(BondedParticle::BondDegreeChanged);
[5e2f80]297 for (std::vector<BondList>::iterator Runner = ListOfBonds.begin();
298 Runner != ListOfBonds.end();
299 ++Runner)
300 for (BondList::iterator BondRunner = (*Runner).begin();
301 BondRunner != (*Runner).end();
302 ++BondRunner)
303 (*BondRunner)->BondDegree = 1;
304};
305
[c0d9eb]306/** Counts the number of bonds weighted by bond::BondDegree.
307 * @param _step time step to access
308 * \param bonds times bond::BondDegree
309 */
310int BondedParticle::CountBonds() const
311{
312 int NoBonds = 0;
[9d83b6]313 const BondList& ListOfBonds = getListOfBonds();
[c0d9eb]314 for (BondList::const_iterator Runner = ListOfBonds.begin();
315 Runner != ListOfBonds.end();
316 (++Runner))
317 NoBonds += (*Runner)->BondDegree;
318 return NoBonds;
319};
320
[b70721]321/** Checks whether there is a bond between \a this atom and the given \a *BondPartner.
[073a9e4]322 * @param _step time step to access
[b70721]323 * \param *BondPartner atom to check for
324 * \return true - bond exists, false - bond does not exist
325 */
[073a9e4]326bool BondedParticle::IsBondedTo(const unsigned int _step, BondedParticle * const BondPartner) const
[b70721]327{
328 bool status = false;
329
[073a9e4]330 const BondList& ListOfBonds = getListOfBondsAtStep(_step);
331 for (BondList::const_iterator runner = ListOfBonds.begin();
332 runner != ListOfBonds.end();
333 runner++) {
[b70721]334 status = status || ((*runner)->Contains(BondPartner));
335 }
336 return status;
337};
338
[d74077]339std::ostream & BondedParticle::operator << (std::ostream &ost) const
340{
341 ParticleInfo::operator<<(ost);
342 ost << "," << getPosition();
343 return ost;
344}
345
346std::ostream & operator << (std::ostream &ost, const BondedParticle &a)
347{
348 a.ParticleInfo::operator<<(ost);
349 ost << "," << a.getPosition();
350 return ost;
351}
352
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