source: src/Dynamics/ForceAnnealing.hpp@ 9861d0

AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
Last change on this file since 9861d0 was 9861d0, checked in by Frederik Heber <frederik.heber@…>, 7 years ago

BondVectors now return subset of BondVectors for a given atom.

  • functionality extracted from ForceAnnealing::annealWithBondgraph().
  • also the mapped_t type is now kept up-to-date internally as we need it for returning the subset efficiently over a number of atoms, e.g. all in the given range.
  • also moved a few simple implementations over to _impl module.
  • Property mode set to 100644
File size: 25.0 KB
Line 
1/*
2 * ForceAnnealing.hpp
3 *
4 * Created on: Aug 02, 2014
5 * Author: heber
6 */
7
8#ifndef FORCEANNEALING_HPP_
9#define FORCEANNEALING_HPP_
10
11// include config.h
12#ifdef HAVE_CONFIG_H
13#include <config.h>
14#endif
15
16#include <algorithm>
17#include <functional>
18#include <iterator>
19
20#include <boost/bind.hpp>
21
22#include "Atom/atom.hpp"
23#include "Atom/AtomSet.hpp"
24#include "CodePatterns/Assert.hpp"
25#include "CodePatterns/Info.hpp"
26#include "CodePatterns/Log.hpp"
27#include "CodePatterns/Verbose.hpp"
28#include "Descriptors/AtomIdDescriptor.hpp"
29#include "Dynamics/AtomicForceManipulator.hpp"
30#include "Dynamics/BondVectors.hpp"
31#include "Fragmentation/ForceMatrix.hpp"
32#include "Graph/BoostGraphCreator.hpp"
33#include "Graph/BoostGraphHelpers.hpp"
34#include "Graph/BreadthFirstSearchGatherer.hpp"
35#include "Helpers/helpers.hpp"
36#include "Helpers/defs.hpp"
37#include "LinearAlgebra/LinearSystemOfEquations.hpp"
38#include "LinearAlgebra/MatrixContent.hpp"
39#include "LinearAlgebra/Vector.hpp"
40#include "LinearAlgebra/VectorContent.hpp"
41#include "Thermostats/ThermoStatContainer.hpp"
42#include "Thermostats/Thermostat.hpp"
43#include "World.hpp"
44
45/** This class is the essential build block for performing structural optimization.
46 *
47 * Sadly, we have to use some static instances as so far values cannot be passed
48 * between actions. Hence, we need to store the current step and the adaptive-
49 * step width (we cannot perform a line search, as we have no control over the
50 * calculation of the forces).
51 *
52 * However, we do use the bond graph, i.e. if a single atom needs to be shifted
53 * to the left, then the whole molecule left of it is shifted, too. This is
54 * controlled by the \a max_distance parameter.
55 */
56template <class T>
57class ForceAnnealing : public AtomicForceManipulator<T>
58{
59public:
60 /** Constructor of class ForceAnnealing.
61 *
62 * \note We use a fixed delta t of 1.
63 *
64 * \param _atoms set of atoms to integrate
65 * \param _Deltat time step width in atomic units
66 * \param _IsAngstroem whether length units are in angstroem or bohr radii
67 * \param _maxSteps number of optimization steps to perform
68 * \param _max_distance up to this bond order is bond graph taken into account.
69 */
70 ForceAnnealing(
71 AtomSetMixin<T> &_atoms,
72 const double _Deltat,
73 bool _IsAngstroem,
74 const size_t _maxSteps,
75 const int _max_distance,
76 const double _damping_factor) :
77 AtomicForceManipulator<T>(_atoms, _Deltat, _IsAngstroem),
78 maxSteps(_maxSteps),
79 max_distance(_max_distance),
80 damping_factor(_damping_factor)
81 {}
82
83 /** Destructor of class ForceAnnealing.
84 *
85 */
86 ~ForceAnnealing()
87 {}
88
89 /** Performs Gradient optimization.
90 *
91 * We assume that forces have just been calculated.
92 *
93 *
94 * \param CurrentTimeStep current time step (i.e. \f$ t + \Delta t \f$ in the sense of the velocity verlet)
95 * \param offset offset in matrix file to the first force component
96 * \todo This is not yet checked if it is correctly working with DoConstrainedMD set >0.
97 */
98 void operator()(
99 const int _CurrentTimeStep,
100 const size_t _offset,
101 const bool _UseBondgraph)
102 {
103 // make sum of forces equal zero
104 AtomicForceManipulator<T>::correctForceMatrixForFixedCenterOfMass(
105 _offset,
106 _CurrentTimeStep-1>=0 ? _CurrentTimeStep - 1 : 0);
107
108 // are we in initial step? Then set static entities
109 Vector maxComponents(zeroVec);
110 if (currentStep == 0) {
111 currentDeltat = AtomicForceManipulator<T>::Deltat;
112 currentStep = 1;
113 LOG(2, "DEBUG: Initial step, setting values, current step is #" << currentStep);
114
115 // always use atomic annealing on first step
116 anneal(_CurrentTimeStep, _offset, maxComponents);
117 } else {
118 ++currentStep;
119 LOG(2, "DEBUG: current step is #" << currentStep);
120
121 if (_UseBondgraph)
122 annealWithBondGraph(_CurrentTimeStep, _offset, maxComponents);
123 else
124 anneal(_CurrentTimeStep, _offset, maxComponents);
125 }
126
127
128 LOG(1, "STATUS: Largest remaining force components at step #"
129 << currentStep << " are " << maxComponents);
130
131 // are we in final step? Remember to reset static entities
132 if (currentStep == maxSteps) {
133 LOG(2, "DEBUG: Final step, resetting values");
134 reset();
135 }
136 }
137
138 /** Helper function to calculate the Barzilai-Borwein stepwidth.
139 *
140 * \param _PositionDifference difference in position between current and last step
141 * \param _GradientDifference difference in gradient between current and last step
142 * \return step width according to Barzilai-Borwein
143 */
144 double getBarzilaiBorweinStepwidth(const Vector &_PositionDifference, const Vector &_GradientDifference)
145 {
146 double stepwidth = 0.;
147 if (_GradientDifference.NormSquared() > MYEPSILON)
148 stepwidth = fabs(_PositionDifference.ScalarProduct(_GradientDifference))/
149 _GradientDifference.NormSquared();
150 if (fabs(stepwidth) < 1e-10) {
151 // dont' warn in first step, deltat usage normal
152 if (currentStep != 1)
153 ELOG(1, "INFO: Barzilai-Borwein stepwidth is zero, using deltat " << currentDeltat << " instead.");
154 stepwidth = currentDeltat;
155 }
156 return stepwidth;
157 }
158
159 /** Performs Gradient optimization on the atoms.
160 *
161 * We assume that forces have just been calculated.
162 *
163 * \param CurrentTimeStep current time step (i.e. \f$ t + \Delta t \f$ in the sense of the velocity verlet)
164 * \param offset offset in matrix file to the first force component
165 * \param maxComponents to be filled with maximum force component over all atoms
166 */
167 void anneal(
168 const int CurrentTimeStep,
169 const size_t offset,
170 Vector &maxComponents)
171 {
172 bool deltat_decreased = false;
173 for(typename AtomSetMixin<T>::iterator iter = AtomicForceManipulator<T>::atoms.begin();
174 iter != AtomicForceManipulator<T>::atoms.end(); ++iter) {
175 // atom's force vector gives steepest descent direction
176 const Vector oldPosition = (*iter)->getPositionAtStep(CurrentTimeStep-1 >= 0 ? CurrentTimeStep - 1 : 0);
177 const Vector currentPosition = (*iter)->getPositionAtStep(CurrentTimeStep);
178 const Vector oldGradient = (*iter)->getAtomicForceAtStep(CurrentTimeStep-1 >= 0 ? CurrentTimeStep - 1 : 0);
179 const Vector currentGradient = (*iter)->getAtomicForceAtStep(CurrentTimeStep);
180 LOG(4, "DEBUG: oldPosition for atom " << **iter << " is " << oldPosition);
181 LOG(4, "DEBUG: currentPosition for atom " << **iter << " is " << currentPosition);
182 LOG(4, "DEBUG: oldGradient for atom " << **iter << " is " << oldGradient);
183 LOG(4, "DEBUG: currentGradient for atom " << **iter << " is " << currentGradient);
184// LOG(4, "DEBUG: Force for atom " << **iter << " is " << currentGradient);
185
186 // we use Barzilai-Borwein update with position reversed to get descent
187 const double stepwidth = getBarzilaiBorweinStepwidth(
188 currentPosition - oldPosition, currentGradient - oldGradient);
189 Vector PositionUpdate = stepwidth * currentGradient;
190 LOG(3, "DEBUG: Update would be " << stepwidth << "*" << currentGradient << " = " << PositionUpdate);
191
192 // extract largest components for showing progress of annealing
193 for(size_t i=0;i<NDIM;++i)
194 maxComponents[i] = std::max(maxComponents[i], fabs(currentGradient[i]));
195
196 // steps may go back and forth again (updates are of same magnitude but
197 // have different sign: Check whether this is the case and one step with
198 // deltat to interrupt this sequence
199 const Vector PositionDifference = currentPosition - oldPosition;
200 if ((currentStep > 1) && (!PositionDifference.IsZero()))
201 if ((PositionUpdate.ScalarProduct(PositionDifference) < 0)
202 && (fabs(PositionUpdate.NormSquared()-PositionDifference.NormSquared()) < 1e-3)) {
203 // for convergence we want a null sequence here, too
204 if (!deltat_decreased) {
205 deltat_decreased = true;
206 currentDeltat = .5*currentDeltat;
207 }
208 LOG(2, "DEBUG: Upgrade in other direction: " << PositionUpdate
209 << " > " << PositionDifference
210 << ", using deltat: " << currentDeltat);
211 PositionUpdate = currentDeltat * currentGradient;
212 }
213
214 // finally set new values
215 (*iter)->setPosition(currentPosition + PositionUpdate);
216 }
217 }
218
219 /** Performs Gradient optimization on the bonds.
220 *
221 * We assume that forces have just been calculated. These forces are projected
222 * onto the bonds and these are annealed subsequently by moving atoms in the
223 * bond neighborhood on either side conjunctively.
224 *
225 *
226 * \param CurrentTimeStep current time step (i.e. \f$ t + \Delta t \f$ in the sense of the velocity verlet)
227 * \param offset offset in matrix file to the first force component
228 * \param maxComponents to be filled with maximum force component over all atoms
229 */
230 void annealWithBondGraph(
231 const int CurrentTimeStep,
232 const size_t offset,
233 Vector &maxComponents)
234 {
235 // get nodes on either side of selected bond via BFS discovery
236 BoostGraphCreator BGcreator;
237 BGcreator.createFromRange(
238 AtomicForceManipulator<T>::atoms.begin(),
239 AtomicForceManipulator<T>::atoms.end(),
240 AtomicForceManipulator<T>::atoms.size(),
241 BreadthFirstSearchGatherer::AlwaysTruePredicate);
242 BreadthFirstSearchGatherer NodeGatherer(BGcreator);
243
244 /// We assume that a force is local, i.e. a bond is too short yet and hence
245 /// the atom needs to be moved. However, all the adjacent (bound) atoms might
246 /// already be at the perfect distance. If we just move the atom alone, we ruin
247 /// all the other bonds. Hence, it would be sensible to move every atom found
248 /// through the bond graph in the direction of the force as well by the same
249 /// PositionUpdate. This is almost what we are going to do.
250
251 /// One issue is: If we need to shorten bond, then we use the PositionUpdate
252 /// also on the the other bond partner already. This is because it is in the
253 /// direction of the bond. Therefore, the update is actually performed twice on
254 /// each bond partner, i.e. the step size is twice as large as it should be.
255 /// This problem only occurs when bonds need to be shortened, not when they
256 /// need to be made longer (then the force vector is facing the other
257 /// direction than the bond vector).
258 /// As a remedy we need to average the force on either end of the bond and
259 /// check whether each gradient points inwards out or outwards with respect
260 /// to the bond and then shift accordingly.
261
262 /// One more issue is that the projection onto the bond directions does not
263 /// recover the gradient but may be larger as the bond directions are a
264 /// generating system and not a basis (e.g. 3 bonds on a plane where 2 would
265 /// suffice to span the plane). To this end, we need to account for the
266 /// overestimation and obtain a weighting for each bond.
267
268 // initialize helper class for bond vectors using bonds from range of atoms
269 BondVectors bv;
270 bv.setFromAtomRange< T >(
271 AtomicForceManipulator<T>::atoms.begin(),
272 AtomicForceManipulator<T>::atoms.end(),
273 CurrentTimeStep);
274 const BondVectors::container_t &sorted_bonds = bv.getSorted();
275
276 // knowing the number of bonds in total, we can setup the storage for the
277 // projected forces
278 enum whichatom_t {
279 leftside=0,
280 rightside=1,
281 MAX_sides
282 };
283 std::vector< // time step
284 std::vector< // which bond side
285 std::vector<double> > // over all bonds
286 > projected_forces(2); // one for leftatoms, one for rightatoms (and for both time steps)
287 for (size_t i=0;i<2;++i) {
288 projected_forces[i].resize(MAX_sides);
289 for (size_t j=0;j<MAX_sides;++j)
290 projected_forces[i][j].resize(sorted_bonds.size(), 0.);
291 }
292
293 // for each atom we need to gather weights and then project the gradient
294 typedef std::deque<double> weights_t;
295 typedef std::map<atomId_t, weights_t > weights_per_atom_t;
296 std::vector<weights_per_atom_t> weights_per_atom(2);
297 for (size_t timestep = 0; timestep <= 1; ++timestep) {
298 const size_t CurrentStep = CurrentTimeStep-timestep-1 >= 0 ? CurrentTimeStep-timestep-1 : 0;
299 LOG(2, "DEBUG: CurrentTimeStep is " << CurrentTimeStep
300 << ", timestep is " << timestep
301 << ", and CurrentStep is " << CurrentStep);
302
303 for(typename AtomSetMixin<T>::const_iterator iter = AtomicForceManipulator<T>::atoms.begin();
304 iter != AtomicForceManipulator<T>::atoms.end(); ++iter) {
305 const atom &walker = *(*iter);
306 const Vector &walkerGradient = walker.getAtomicForceAtStep(CurrentStep);
307 LOG(3, "DEBUG: Gradient of atom #" << walker.getId() << ", namely "
308 << walker << " is " << walkerGradient << " with magnitude of "
309 << walkerGradient.Norm());
310
311 const BondList& ListOfBonds = walker.getListOfBonds();
312 if (walkerGradient.Norm() > MYEPSILON) {
313
314 // gather subset of BondVectors for the current atom
315 std::vector<Vector> BondVectors = bv.getAtomsBondVectorsAtStep(walker, CurrentStep);
316
317 // go through all its bonds and calculate what magnitude is represented
318 // by the others i.e. sum of scalar products against other bonds
319 std::pair<weights_per_atom_t::iterator, bool> inserter =
320 weights_per_atom[timestep].insert(
321 std::make_pair(walker.getId(), weights_t()) );
322 ASSERT( inserter.second,
323 "ForceAnnealing::operator() - weight map for atom "+toString(walker)
324 +" and time step "+toString(timestep)+" already filled?");
325 weights_t &weights = inserter.first->second;
326 for (std::vector<Vector>::const_iterator iter = BondVectors.begin();
327 iter != BondVectors.end(); ++iter) {
328 std::vector<double> scps;
329 scps.reserve(BondVectors.size());
330 std::transform(
331 BondVectors.begin(), BondVectors.end(),
332 std::back_inserter(scps),
333 boost::bind(static_cast< double (*)(double) >(&fabs),
334 boost::bind(&Vector::ScalarProduct, boost::cref(*iter), _1))
335 );
336 const double scp_sum = std::accumulate(scps.begin(), scps.end(), 0.);
337 ASSERT( (scp_sum-1.) > -MYEPSILON,
338 "ForceAnnealing() - sum of weights must be equal or larger one but is "
339 +toString(scp_sum));
340 weights.push_back( 1./scp_sum );
341 }
342 LOG(4, "DEBUG: Weights for atom #" << walker.getId() << ": " << weights);
343
344 // for testing we check whether all weighted scalar products now come out as 1.
345#ifndef NDEBUG
346 for (std::vector<Vector>::const_iterator iter = BondVectors.begin();
347 iter != BondVectors.end(); ++iter) {
348 std::vector<double> scps;
349 scps.reserve(BondVectors.size());
350 std::transform(
351 BondVectors.begin(), BondVectors.end(),
352 weights.begin(),
353 std::back_inserter(scps),
354 boost::bind(static_cast< double (*)(double) >(&fabs),
355 boost::bind(std::multiplies<double>(),
356 boost::bind(&Vector::ScalarProduct, boost::cref(*iter), _1),
357 _2))
358 );
359 const double scp_sum = std::accumulate(scps.begin(), scps.end(), 0.);
360 ASSERT( fabs(scp_sum - 1.) < MYEPSILON,
361 "ForceAnnealing::operator() - for BondVector "+toString(*iter)
362 +" we have weighted scalar product of "+toString(scp_sum)+" != 1.");
363 }
364#endif
365
366 // projected gradient over all bonds and place in one of projected_forces
367 // using the obtained weights
368 {
369 weights_t::const_iterator weightiter = weights.begin();
370 std::vector<Vector>::const_iterator vectoriter = BondVectors.begin();
371 Vector forcesum_check;
372 for(BondList::const_iterator bonditer = ListOfBonds.begin();
373 bonditer != ListOfBonds.end(); ++bonditer, ++weightiter, ++vectoriter) {
374 const bond::ptr &current_bond = *bonditer;
375 const Vector &BondVector = *vectoriter;
376
377 std::vector<double> &forcelist = (&walker == current_bond->leftatom) ?
378 projected_forces[timestep][leftside] : projected_forces[timestep][rightside];
379 const size_t index = bv.getIndexForBond(current_bond);
380 ASSERT( index != (size_t)-1,
381 "ForceAnnealing() - could not find bond "+toString(*current_bond)
382 +" in bondvectors");
383 forcelist[index] = (*weightiter)*walkerGradient.ScalarProduct(BondVector);
384 LOG(4, "DEBUG: BondVector " << BondVector << " receives projected force of "
385 << forcelist[index]);
386 forcesum_check += forcelist[index] * BondVector;
387 }
388 ASSERT( weightiter == weights.end(),
389 "ForceAnnealing - weightiter is not at end when it should be.");
390 ASSERT( vectoriter == BondVectors.end(),
391 "ForceAnnealing - vectoriter is not at end when it should be.");
392 LOG(3, "DEBUG: sum of projected forces is " << forcesum_check);
393 }
394
395 } else {
396 LOG(2, "DEBUG: Gradient is " << walkerGradient << " less than "
397 << MYEPSILON << " for atom " << walker);
398 // note that projected_forces is initialized to full length and filled
399 // with zeros. Hence, nothing to do here
400 }
401 }
402 }
403
404 // step through each bond and shift the atoms
405 std::map<atomId_t, Vector> GatheredUpdates; //!< gathers all updates which are applied at the end
406
407 LOG(3, "DEBUG: current step is " << currentStep << ", given time step is " << CurrentTimeStep);
408 const BondVectors::mapped_t bondvectors = bv.getBondVectorsAtStep(CurrentTimeStep);
409
410 for (BondVectors::container_t::const_iterator bondsiter = sorted_bonds.begin();
411 bondsiter != sorted_bonds.end(); ++bondsiter) {
412 const bond::ptr &current_bond = *bondsiter;
413 const size_t index = bv.getIndexForBond(current_bond);
414 const atom* bondatom[MAX_sides] = {
415 current_bond->leftatom,
416 current_bond->rightatom
417 };
418
419 // remove the edge
420#ifndef NDEBUG
421 const bool status =
422#endif
423 BGcreator.removeEdge(bondatom[leftside]->getId(), bondatom[rightside]->getId());
424 ASSERT( status, "ForceAnnealing() - edge to found bond is not present?");
425
426 // gather nodes for either atom
427 BoostGraphHelpers::Nodeset_t bondside_set[MAX_sides];
428 BreadthFirstSearchGatherer::distance_map_t distance_map[MAX_sides];
429 for (size_t side=leftside;side<MAX_sides;++side) {
430 bondside_set[side] = NodeGatherer(bondatom[side]->getId(), max_distance);
431 distance_map[side] = NodeGatherer.getDistances();
432 std::sort(bondside_set[side].begin(), bondside_set[side].end());
433 }
434
435 // re-add edge
436 BGcreator.addEdge(bondatom[leftside]->getId(), bondatom[rightside]->getId());
437
438 // do for both leftatom and rightatom of bond
439 for (size_t side = leftside; side < MAX_sides; ++side) {
440 const double &bondforce = projected_forces[0][side][index];
441 const double &oldbondforce = projected_forces[1][side][index];
442 const double bondforcedifference = fabs(bondforce - oldbondforce);
443 LOG(4, "DEBUG: bondforce for " << (side == leftside ? "left" : "right")
444 << " side of bond is " << bondforce);
445 LOG(4, "DEBUG: oldbondforce for " << (side == leftside ? "left" : "right")
446 << " side of bond is " << oldbondforce);
447 // if difference or bondforce itself is zero, do nothing
448 if ((fabs(bondforce) < MYEPSILON) || (fabs(bondforcedifference) < MYEPSILON))
449 continue;
450
451 // get BondVector to bond
452 const BondVectors::mapped_t::const_iterator bviter =
453 bondvectors.find(current_bond);
454 ASSERT( bviter != bondvectors.end(),
455 "ForceAnnealing() - cannot find current_bond ?");
456 ASSERT( fabs(bviter->second.Norm() -1.) < MYEPSILON,
457 "ForceAnnealing() - norm of BondVector is not one");
458 const Vector &BondVector = bviter->second;
459
460 // calculate gradient and position differences for stepwidth
461 const Vector currentGradient = bondforce * BondVector;
462 LOG(4, "DEBUG: current projected gradient for "
463 << (side == leftside ? "left" : "right") << " side of bond is " << currentGradient);
464 const Vector &oldPosition = bondatom[side]->getPositionAtStep(CurrentTimeStep-2 >= 0 ? CurrentTimeStep - 2 : 0);
465 const Vector &currentPosition = bondatom[side]->getPositionAtStep(CurrentTimeStep-1>=0 ? CurrentTimeStep - 1 : 0);
466 const Vector PositionDifference = currentPosition - oldPosition;
467 LOG(4, "DEBUG: old position is " << oldPosition);
468 LOG(4, "DEBUG: current position is " << currentPosition);
469 LOG(4, "DEBUG: difference in position is " << PositionDifference);
470 LOG(4, "DEBUG: bondvector is " << BondVector);
471 const double projected_PositionDifference = PositionDifference.ScalarProduct(BondVector);
472 LOG(4, "DEBUG: difference in position projected onto bondvector is "
473 << projected_PositionDifference);
474 LOG(4, "DEBUG: abs. difference in forces is " << bondforcedifference);
475
476 // calculate step width
477 double stepwidth =
478 fabs(projected_PositionDifference)/bondforcedifference;
479 if (fabs(stepwidth) < 1e-10) {
480 // dont' warn in first step, deltat usage normal
481 if (currentStep != 1)
482 ELOG(1, "INFO: Barzilai-Borwein stepwidth is zero, using deltat " << currentDeltat << " instead.");
483 stepwidth = currentDeltat;
484 }
485 Vector PositionUpdate = stepwidth * currentGradient;
486 LOG(3, "DEBUG: Update would be " << stepwidth << "*" << currentGradient << " = " << PositionUpdate);
487
488 // add PositionUpdate for all nodes in the bondside_set
489 for (BoostGraphHelpers::Nodeset_t::const_iterator setiter = bondside_set[side].begin();
490 setiter != bondside_set[side].end(); ++setiter) {
491 const BreadthFirstSearchGatherer::distance_map_t::const_iterator diter
492 = distance_map[side].find(*setiter);
493 ASSERT( diter != distance_map[side].end(),
494 "ForceAnnealing() - could not find distance to an atom.");
495 const double factor = pow(damping_factor, diter->second+1);
496 LOG(3, "DEBUG: Update for atom #" << *setiter << " will be "
497 << factor << "*" << PositionUpdate);
498 if (GatheredUpdates.count((*setiter))) {
499 GatheredUpdates[(*setiter)] += factor*PositionUpdate;
500 } else {
501 GatheredUpdates.insert(
502 std::make_pair(
503 (*setiter),
504 factor*PositionUpdate) );
505 }
506 }
507 }
508 }
509
510 for(typename AtomSetMixin<T>::iterator iter = AtomicForceManipulator<T>::atoms.begin();
511 iter != AtomicForceManipulator<T>::atoms.end(); ++iter) {
512 atom &walker = *(*iter);
513 // extract largest components for showing progress of annealing
514 const Vector currentGradient = walker.getAtomicForceAtStep(CurrentTimeStep-1>=0 ? CurrentTimeStep-1 : 0);
515 for(size_t i=0;i<NDIM;++i)
516 maxComponents[i] = std::max(maxComponents[i], fabs(currentGradient[i]));
517
518 // reset force vector for next step except on final one
519 if (currentStep != maxSteps)
520 walker.setAtomicForce(zeroVec);
521 }
522
523 // apply the gathered updates
524 for (std::map<atomId_t, Vector>::const_iterator iter = GatheredUpdates.begin();
525 iter != GatheredUpdates.end(); ++iter) {
526 const atomId_t &atomid = iter->first;
527 const Vector &update = iter->second;
528 atom* const walker = World::getInstance().getAtom(AtomById(atomid));
529 ASSERT( walker != NULL,
530 "ForceAnnealing() - walker with id "+toString(atomid)+" has suddenly disappeared.");
531 LOG(3, "DEBUG: Applying update " << update << " to atom #" << atomid
532 << ", namely " << *walker);
533 walker->setPosition(
534 walker->getPositionAtStep(CurrentTimeStep-1>=0 ? CurrentTimeStep - 1 : 0)
535 + update);
536 walker->setAtomicVelocity(update);
537// walker->setAtomicForce( RemnantGradient_per_atom[walker->getId()] );
538 }
539 }
540
541 /** Reset function to unset static entities and artificial velocities.
542 *
543 */
544 void reset()
545 {
546 currentDeltat = 0.;
547 currentStep = 0;
548 }
549
550private:
551 //!> contains the current step in relation to maxsteps
552 static size_t currentStep;
553 //!> contains the maximum number of steps, determines initial and final step with currentStep
554 size_t maxSteps;
555 static double currentDeltat;
556 //!> minimum deltat for internal while loop (adaptive step width)
557 static double MinimumDeltat;
558 //!> contains the maximum bond graph distance up to which shifts of a single atom are spread
559 const int max_distance;
560 //!> the shifted is dampened by this factor with the power of the bond graph distance to the shift causing atom
561 const double damping_factor;
562};
563
564template <class T>
565double ForceAnnealing<T>::currentDeltat = 0.;
566template <class T>
567size_t ForceAnnealing<T>::currentStep = 0;
568template <class T>
569double ForceAnnealing<T>::MinimumDeltat = 1e-8;
570
571#endif /* FORCEANNEALING_HPP_ */
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