Changeset 866dec
- Timestamp:
- Apr 10, 2018, 6:43:11 AM (7 years ago)
- Branches:
- AutomationFragmentation_failures, Candidate_v1.6.1, ChemicalSpaceEvaluator, Enhanced_StructuralOptimization_continued, Exclude_Hydrogens_annealWithBondGraph, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_contraction-expansion, Gui_displays_atomic_force_velocity, PythonUI_with_named_parameters, StoppableMakroAction, TremoloParser_IncreasedPrecision
- Children:
- 2bb3be
- Parents:
- 216840
- git-author:
- Frederik Heber <frederik.heber@…> (06/27/17 21:10:02)
- git-committer:
- Frederik Heber <frederik.heber@…> (04/10/18 06:43:11)
- Files:
-
- 4 edited
-
src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) (4 diffs)
-
src/Dynamics/ForceAnnealing.hpp (modified) (4 diffs)
-
tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/alkane-3.data (modified) (1 diff)
-
tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/alkane-3.data (modified) (1 diff)
Legend:
- Unmodified
- Added
- Removed
-
src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp
r216840 r866dec 585 585 } 586 586 587 static void AddForces(587 static void SetForces( 588 588 const IndexedVectors::indexedvectors_t &_forces, 589 589 const bool _IsAngstroem) … … 603 603 atom *_atom = World::getInstance().getAtom(AtomById(index)); 604 604 if(_atom != NULL) 605 _atom->setAtomicForce( _atom->getAtomicForce() +ForceVector);605 _atom->setAtomicForce(ForceVector); 606 606 else 607 607 ELOG(2, "Could not find atom to id " << index << "."); … … 687 687 shortrangeresults.Result_Force_fused.back() 688 688 ).getVectors(); 689 AddForces(shortrange_forces,IsAngstroem);689 SetForces(shortrange_forces,IsAngstroem); 690 690 } else { 691 691 LOG(1, "INFO: Full molecule not loaded, hence will not add forces to atoms."); … … 760 760 longrangeresults.Result_ForcesLongRangeIntegrated_fused.back() 761 761 ).getVectors(); 762 AddForces(longrange_forces,IsAngstroem);762 SetForces(longrange_forces,IsAngstroem); 763 763 } else { 764 764 LOG(1, "INFO: Full molecule not loaded, hence will not add forces to atoms."); -
src/Dynamics/ForceAnnealing.hpp
r216840 r866dec 187 187 //std::cout << "Id of atom is " << (*iter)->getId() << std::endl; 188 188 // (*iter)->VelocityVerletUpdateU((*iter)->getId(), CurrentTimeStep-1, Deltat, IsAngstroem); 189 190 // reset force vector for next step except on final one191 if (currentStep != maxSteps)192 (*iter)->setAtomicForce(zeroVec);193 }194 195 LOG(1, "STATUS: Largest remaining force components at step #"196 << currentStep << " are " << maxComponents);197 198 // are we in final step? Remember to reset static entities199 if (currentStep == maxSteps) {200 LOG(2, "DEBUG: Final step, resetting values");201 reset();202 189 } 203 190 } … … 327 314 if (currentGradient[i] > maxComponents[i]) 328 315 maxComponents[i] = currentGradient[i]; 329 330 // reset force vector for next step except on final one331 if (currentStep != maxSteps)332 (*iter)->setAtomicForce(zeroVec);333 316 } 334 317 // apply the gathered updates … … 340 323 ASSERT( walker != NULL, 341 324 "ForceAnnealing() - walker with id "+toString(atomid)+" has suddenly disappeared."); 325 LOG(3, "DEBUG: Applying update " << update << " to atom #" << atomid 326 << ", namely " << *walker); 342 327 walker->setPosition( walker->getPosition() + update ); 343 walker->setAtomicVelocity(update);344 LOG(3, "DEBUG: Applying update " << update << " to atom " << *walker);345 328 } 346 329 } … … 353 336 currentDeltat = 0.; 354 337 currentStep = 0; 355 356 // reset (artifical) velocities357 for(typename AtomSetMixin<T>::iterator iter = AtomicForceManipulator<T>::atoms.begin();358 iter != AtomicForceManipulator<T>::atoms.end(); ++iter)359 (*iter)->setAtomicVelocity(zeroVec);360 338 } 361 339 -
tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/alkane-3.data
r216840 r866dec 1 1 # ATOMDATA Id type x=3 u=3 F=3 2 2 # Box 20 0 0 0 20 0 0 0 20 3 1 C 5.89 6.513 5.89 0 0 0 -0.00161434 -0.00490854 -1.10363e-134 2 C 7.139 5.63 5.89 0 0 0 -0.00299896 0.00787442 -1.50393e-135 3 H 5.89 7.142 5 0 0 0 - 0.00213528 -0.000289904 0.002510646 4 H 5.89 7.142 6.78 0 0 0 - 0.00213528 -0.000289904 -0.002510647 5 H 7.139 5 5 0 0 0 0.000254991 -0.000726836 0.002798168 6 H 7.139 5 6.78 0 0 0 0.000254991 -0.000726836 -0.002798169 7 C 8.388 6.513 5.89 0 0 0 - 0.000234367 -0.0118817 -1.63896e-1310 8 C 9.638 5.63 5.89 0 0 0 0.000234232 0.0115391 -1.55075e-1311 9 H 8.388 7.142 5 0 0 0 - 5.97387e-05 0.000821868 0.0024264312 10 H 8.388 7.142 6.78 0 0 0 -5.97387e-05 0.000821868 -0.0024264313 11 H 9.638 5 5 0 0 0 5.95858e-05 -0.000650729 0.0025466814 12 H 9.638 5 6.78 0 0 0 5.95858e-05 -0.000650729 -0.0025466815 13 C 10.887 6.513 5.89 0 0 0 0.00299486 -0.00822198 -1.35513e-1316 14 C 12.136 5.63 5.89 0 0 0 0.0016146 0.00459057 -1.39521e-1317 15 H 10.887 7.142 5 0 0 0 -0.00025431 0.000898036 0.0026778718 16 H 10.887 7.142 6.78 0 0 0 -0.00025431 0.000898036 -0.0026778719 17 H 12.136 5 5 0 0 0 0.00213567 0.000462277 0.0026326720 18 H 12.136 5 6.78 0 0 0 0.00213567 0.000462277 -0.0026326721 19 H 5 5.884 5.89 0 0 0 - 0.000456201 0.00402573 -9.8489e-1622 20 H 13.026 6.259 5.89 0 0 0 0.00045834 -0.00404705 -5.79475e-163 1 C 5.89 6.513 5.89 0 0 0 6.79302e-17 4.11253e-16 4.40629e-17 4 2 C 7.139 5.63 5.89 0 0 0 2.3133e-16 5.5813e-16 7.0776e-16 5 3 H 5.89 7.142 5 0 0 0 -1.19566e-16 2.93752e-16 -7.34381e-18 6 4 H 5.89 7.142 6.78 0 0 0 -1.11626e-15 9.69383e-16 4.70004e-16 7 5 H 7.139 5 5 0 0 0 5.14067e-16 1.29251e-15 -3.0844e-16 8 6 H 7.139 5 6.78 0 0 0 7.01334e-16 5.28754e-16 1.20438e-15 9 7 C 8.388 6.513 5.89 0 0 0 -1.17501e-15 6.46255e-16 4.84691e-16 10 8 C 9.638 5.63 5.89 0 0 0 7.96803e-16 4.99379e-16 4.70004e-16 11 9 H 8.388 7.142 5 0 0 0 -1.37329e-15 -3.52503e-16 1.58626e-15 12 10 H 8.388 7.142 6.78 0 0 0 4.05745e-16 5.5813e-16 1.08688e-15 13 11 H 9.638 5 5 0 0 0 7.27037e-16 -0 2.35002e-16 14 12 H 9.638 5 6.78 0 0 0 -4.70004e-16 -2.35002e-16 5.80161e-16 15 13 C 10.887 6.513 5.89 0 0 0 1.29251e-15 -2.23252e-15 1.17501e-16 16 14 C 12.136 5.63 5.89 0 0 0 -7.34381e-16 1.17501e-16 2.20314e-17 17 15 H 10.887 7.142 5 0 0 0 1.21907e-15 1.17501e-16 2.35002e-16 18 16 H 10.887 7.142 6.78 0 0 0 5.43442e-16 -5.5813e-16 1.17501e-16 19 17 H 12.136 5 5 0 0 0 -4.84691e-16 2.35002e-16 7.05006e-16 20 18 H 12.136 5 6.78 0 0 0 6.60943e-17 9.98758e-16 -2.93752e-16 21 19 H 5 5.884 5.89 0 0 0 -2.05627e-16 1.70376e-15 5.5813e-16 22 20 H 13.026 6.259 5.89 0 0 0 -2.93752e-16 -4.77348e-16 5.14067e-17 -
tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/alkane-3.data
r216840 r866dec 1 1 # ATOMDATA Id type x=3 u=3 F=3 2 2 # Box 20 0 0 0 20 0 0 0 20 3 1 C 5.89 6.513 5.89 0 0 0 -0.00161434 -0.00490854 -1.10584e-134 2 C 7.139 5.63 5.89 0 0 0 - 0.00299896 0.00787442 -1.51277e-135 3 H 5.89 7.142 5 0 0 0 -0.00213528 -0.000289904 0.002510646 4 H 5.89 7.142 6.78 0 0 0 - 0.00213528 -0.000289904 -0.002510647 5 H 7.139 5 5 0 0 0 0.000254991 -0.000726836 0.002798168 6 H 7.139 5 6.78 0 0 0 0.000254991 -0.000726836 -0.002798169 7 C 8.388 6.513 5.89 0 0 0 - 0.000234367 -0.0118817 -1.64909e-1310 8 C 9.638 5.63 5.89 0 0 0 0.000234232 0.0115391 -1.55457e-1311 9 H 8.388 7.142 5 0 0 0 - 5.97387e-05 0.000821868 0.0024264312 10 H 8.388 7.142 6.78 0 0 0 - 5.97387e-05 0.000821868 -0.0024264313 11 H 9.638 5 5 0 0 0 5.95858e-05 -0.000650729 0.0025466814 12 H 9.638 5 6.78 0 0 0 5.95858e-05 -0.000650729 -0.0025466815 13 C 10.887 6.513 5.89 0 0 0 0.00299486 -0.00822198 -1.35631e-1316 14 C 12.136 5.63 5.89 0 0 0 0.0016146 0.00459057 -1.39484e-1317 15 H 10.887 7.142 5 0 0 0 -0.00025431 0.000898036 0.0026778718 16 H 10.887 7.142 6.78 0 0 0 -0.00025431 0.000898036 -0.0026778719 17 H 12.136 5 5 0 0 0 0.00213567 0.000462277 0.0026326720 18 H 12.136 5 6.78 0 0 0 0.00213567 0.000462277 -0.0026326721 19 H 5 5.884 5.89 0 0 0 -0.000456201 0.00402573 -1.63115e-1522 20 H 13.026 6.259 5.89 0 0 0 0.00045834 -0.00404705 -4.39943e-163 1 C 5.89 6.513 5.89 0 0 0 6.46255e-16 1.76251e-16 -1.76251e-16 4 2 C 7.139 5.63 5.89 0 0 0 -2.93752e-16 -1.46876e-16 -1.76251e-16 5 3 H 5.89 7.142 5 0 0 0 8.81257e-16 -5.87505e-17 1.17501e-16 6 4 H 5.89 7.142 6.78 0 0 0 -6.31568e-16 3.37815e-16 2.05627e-16 7 5 H 7.139 5 5 0 0 0 1.17501e-16 1.76251e-16 -4.11253e-16 8 6 H 7.139 5 6.78 0 0 0 -3.23128e-16 -0 3.23128e-16 9 7 C 8.388 6.513 5.89 0 0 0 -2.24721e-15 -1.17501e-16 -5.28754e-16 10 8 C 9.638 5.63 5.89 0 0 0 1.90939e-16 1.46876e-17 8.81257e-17 11 9 H 8.388 7.142 5 0 0 0 -1.99752e-15 -5.87505e-16 -1.76251e-16 12 10 H 8.388 7.142 6.78 0 0 0 -1.32189e-16 7.78444e-16 1.11626e-15 13 11 H 9.638 5 5 0 0 0 2.35002e-16 -2.35002e-16 -1.76251e-16 14 12 H 9.638 5 6.78 0 0 0 -4.40629e-17 -2.93752e-17 -8.81257e-17 15 13 C 10.887 6.513 5.89 0 0 0 1.17501e-15 -2.93752e-17 -0 16 14 C 12.136 5.63 5.89 0 0 0 1.76251e-16 -3.52503e-16 5.87505e-17 17 15 H 10.887 7.142 5 0 0 0 1.27782e-15 3.52503e-16 -2.93752e-16 18 16 H 10.887 7.142 6.78 0 0 0 8.6657e-16 2.93752e-16 2.35002e-16 19 17 H 12.136 5 5 0 0 0 2.93752e-17 -1.17501e-16 -0 20 18 H 12.136 5 6.78 0 0 0 -0 -1.46876e-16 -0 21 19 H 5 5.884 5.89 0 0 0 1.11626e-15 2.05627e-16 -8.81257e-17 22 20 H 13.026 6.259 5.89 0 0 0 8.81257e-17 -1.46876e-16 1.90939e-16
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