Changeset 9f1fee5
- Timestamp:
- Nov 29, 2017, 11:06:09 PM (7 years ago)
- Branches:
- ForceAnnealing_with_BondGraph_continued_betteresults
- Children:
- 0dd99b
- Parents:
- 08470b8
- git-author:
- Frederik Heber <frederik.heber@…> (08/03/17 09:24:07)
- git-committer:
- Frederik Heber <frederik.heber@…> (11/29/17 23:06:09)
- Files:
-
- 4 edited
-
src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) (1 diff)
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src/Dynamics/ForceAnnealing.hpp (modified) (16 diffs)
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tests/Python/ForceAnnealing/post/five_carbon_test_no-bondgraph.data (modified) (1 diff)
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tests/Python/ForceAnnealing/testsuite-python-forceannealing-ising.at (modified) (4 diffs)
Legend:
- Unmodified
- Added
- Removed
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src/Actions/MoleculeAction/ForceAnnealingAction.cpp
r08470b8 r9f1fee5 120 120 // perform optimization step 121 121 LOG(1, "Structural optimization."); 122 optimizer(CurrentStep -1, 1, params.UseBondGraph.get());122 optimizer(CurrentStep, 1, params.UseBondGraph.get()); 123 123 STATUS("Successfully optimized structure by one step."); 124 124 -
src/Dynamics/ForceAnnealing.hpp
r08470b8 r9f1fee5 92 92 * 93 93 * 94 * \param CurrentTimeStep current time step(i.e. \f$ t + \Delta t \f$ in the sense of the velocity verlet)94 * \param _TimeStep time step to update (i.e. \f$ t + \Delta t \f$ in the sense of the velocity verlet) 95 95 * \param offset offset in matrix file to the first force component 96 96 * \todo This is not yet checked if it is correctly working with DoConstrainedMD set >0. 97 97 */ 98 98 void operator()( 99 const int _ CurrentTimeStep,99 const int _TimeStep, 100 100 const size_t _offset, 101 101 const bool _UseBondgraph) 102 102 { 103 const int CurrentTimeStep = _TimeStep-1; 104 ASSERT( CurrentTimeStep >= 0, 105 "ForceAnnealing::operator() - a new time step (upon which we work) must already have been copied."); 106 103 107 // make sum of forces equal zero 104 108 AtomicForceManipulator<T>::correctForceMatrixForFixedCenterOfMass( 105 109 _offset, 106 _CurrentTimeStep-1>=0 ? _CurrentTimeStep - 1 : 0);110 CurrentTimeStep); 107 111 108 112 // are we in initial step? Then set static entities … … 114 118 115 119 // always use atomic annealing on first step 116 maxComponents = anneal(_ CurrentTimeStep);120 maxComponents = anneal(_TimeStep); 117 121 } else { 118 122 ++currentStep; … … 121 125 // bond graph annealing is always followed by a normal annealing 122 126 if (_UseBondgraph) 123 maxComponents = annealWithBondGraph (_CurrentTimeStep);127 maxComponents = annealWithBondGraph_BarzilaiBorwein(_TimeStep); 124 128 // cannot store RemnantGradient in Atom's Force as it ruins BB stepwidth calculation 125 129 else 126 maxComponents = anneal (_CurrentTimeStep);130 maxComponents = anneal_BarzilaiBorwein(_TimeStep); 127 131 } 128 132 … … 163 167 * We assume that forces have just been calculated. 164 168 * 165 * \param CurrentTimeStep current time step(i.e. \f$ t + \Delta t \f$ in the sense of the velocity verlet)169 * \param _TimeStep time step to update (i.e. \f$ t + \Delta t \f$ in the sense of the velocity verlet) 166 170 * \return to be filled with maximum force component over all atoms 167 171 */ 168 172 Vector anneal( 169 const int CurrentTimeStep)173 const int _TimeStep) 170 174 { 175 const int CurrentTimeStep = _TimeStep-1; 176 ASSERT( CurrentTimeStep >= 0, 177 "ForceAnnealing::anneal() - a new time step (upon which we work) must already have been copied."); 178 179 LOG(1, "STATUS: performing simple anneal with default stepwidth " << currentDeltat << " at step #" << currentStep); 180 171 181 Vector maxComponents; 172 182 bool deltat_decreased = false; … … 174 184 iter != AtomicForceManipulator<T>::atoms.end(); ++iter) { 175 185 // atom's force vector gives steepest descent direction 176 const Vector oldPosition = (*iter)->getPositionAtStep(CurrentTimeStep-1 >= 0 ? CurrentTimeStep - 1 : 0);177 186 const Vector currentPosition = (*iter)->getPositionAtStep(CurrentTimeStep); 178 const Vector oldGradient = (*iter)->getAtomicForceAtStep(CurrentTimeStep-1 >= 0 ? CurrentTimeStep - 1 : 0);179 187 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); 188 LOG(4, "DEBUG: currentPosition for atom #" << (*iter)->getId() << " is " << currentPosition); 189 LOG(4, "DEBUG: currentGradient for atom #" << (*iter)->getId() << " is " << currentGradient); 184 190 // LOG(4, "DEBUG: Force for atom " << **iter << " is " << currentGradient); 185 191 186 192 // we use Barzilai-Borwein update with position reversed to get descent 187 const double stepwidth = getBarzilaiBorweinStepwidth( 188 currentPosition - oldPosition, currentGradient - oldGradient); 193 double stepwidth = currentDeltat; 189 194 Vector PositionUpdate = stepwidth * currentGradient; 190 195 LOG(3, "DEBUG: Update would be " << stepwidth << "*" << currentGradient << " = " << PositionUpdate); … … 197 202 // have different sign: Check whether this is the case and one step with 198 203 // deltat to interrupt this sequence 199 const Vector PositionDifference = currentPosition - oldPosition; 200 if ((currentStep > 1) && (!PositionDifference.IsZero())) 204 if (currentStep > 1) { 205 const int OldTimeStep = CurrentTimeStep-1; 206 ASSERT( OldTimeStep >= 0, 207 "ForceAnnealing::anneal() - if currentStep is "+toString(currentStep) 208 +", then there should be at least three time steps."); 209 const Vector oldPosition = (*iter)->getPositionAtStep(OldTimeStep); 210 const Vector PositionDifference = currentPosition - oldPosition; 211 LOG(4, "DEBUG: oldPosition for atom #" << (*iter)->getId() << " is " << oldPosition); 212 LOG(4, "DEBUG: PositionDifference for atom #" << (*iter)->getId() << " is " << PositionDifference); 201 213 if ((PositionUpdate.ScalarProduct(PositionDifference) < 0) 202 214 && (fabs(PositionUpdate.NormSquared()-PositionDifference.NormSquared()) < 1e-3)) { … … 210 222 << ", using deltat: " << currentDeltat); 211 223 PositionUpdate = currentDeltat * currentGradient; 224 } 212 225 } 213 226 214 227 // finally set new values 215 (*iter)->setPosition(currentPosition + PositionUpdate); 228 (*iter)->setPositionAtStep(_TimeStep, currentPosition + PositionUpdate); 229 } 230 231 return maxComponents; 232 } 233 234 /** Performs Gradient optimization on the atoms using BarzilaiBorwein step width. 235 * 236 * \note this can only be called when there are at least two optimization 237 * time steps present, i.e. this must be preceeded by a simple anneal(). 238 * 239 * We assume that forces have just been calculated. 240 * 241 * \param _TimeStep time step to update (i.e. \f$ t + \Delta t \f$ in the sense of the velocity verlet) 242 * \return to be filled with maximum force component over all atoms 243 */ 244 Vector anneal_BarzilaiBorwein( 245 const int _TimeStep) 246 { 247 const int OldTimeStep = _TimeStep-2; 248 const int CurrentTimeStep = _TimeStep-1; 249 ASSERT( OldTimeStep >= 0, 250 "ForceAnnealing::anneal_BarzilaiBorwein() - we need two present optimization steps to compute stepwidth."); 251 ASSERT(currentStep > 1, 252 "ForceAnnealing::anneal_BarzilaiBorwein() - we need two present optimization steps to compute stepwidth."); 253 254 LOG(1, "STATUS: performing BarzilaiBorwein anneal at step #" << currentStep); 255 256 Vector maxComponents; 257 bool deltat_decreased = false; 258 for(typename AtomSetMixin<T>::iterator iter = AtomicForceManipulator<T>::atoms.begin(); 259 iter != AtomicForceManipulator<T>::atoms.end(); ++iter) { 260 // atom's force vector gives steepest descent direction 261 const Vector oldPosition = (*iter)->getPositionAtStep(OldTimeStep); 262 const Vector currentPosition = (*iter)->getPositionAtStep(CurrentTimeStep); 263 const Vector oldGradient = (*iter)->getAtomicForceAtStep(OldTimeStep); 264 const Vector currentGradient = (*iter)->getAtomicForceAtStep(CurrentTimeStep); 265 LOG(4, "DEBUG: oldPosition for atom #" << (*iter)->getId() << " is " << oldPosition); 266 LOG(4, "DEBUG: currentPosition for atom #" << (*iter)->getId() << " is " << currentPosition); 267 LOG(4, "DEBUG: oldGradient for atom #" << (*iter)->getId() << " is " << oldGradient); 268 LOG(4, "DEBUG: currentGradient for atom #" << (*iter)->getId() << " is " << currentGradient); 269 // LOG(4, "DEBUG: Force for atom #" << (*iter)->getId() << " is " << currentGradient); 270 271 // we use Barzilai-Borwein update with position reversed to get descent 272 const Vector PositionDifference = currentPosition - oldPosition; 273 const Vector GradientDifference = (currentGradient - oldGradient); 274 double stepwidth = getBarzilaiBorweinStepwidth(PositionDifference, GradientDifference); 275 Vector PositionUpdate = stepwidth * currentGradient; 276 LOG(3, "DEBUG: Update would be " << stepwidth << "*" << currentGradient << " = " << PositionUpdate); 277 278 // extract largest components for showing progress of annealing 279 for(size_t i=0;i<NDIM;++i) 280 maxComponents[i] = std::max(maxComponents[i], fabs(currentGradient[i])); 281 282 // // steps may go back and forth again (updates are of same magnitude but 283 // // have different sign: Check whether this is the case and one step with 284 // // deltat to interrupt this sequence 285 // if (!PositionDifference.IsZero()) 286 // if ((PositionUpdate.ScalarProduct(PositionDifference) < 0) 287 // && (fabs(PositionUpdate.NormSquared()-PositionDifference.NormSquared()) < 1e-3)) { 288 // // for convergence we want a null sequence here, too 289 // if (!deltat_decreased) { 290 // deltat_decreased = true; 291 // currentDeltat = .5*currentDeltat; 292 // } 293 // LOG(2, "DEBUG: Upgrade in other direction: " << PositionUpdate 294 // << " > " << PositionDifference 295 // << ", using deltat: " << currentDeltat); 296 // PositionUpdate = currentDeltat * currentGradient; 297 // } 298 299 // finally set new values 300 (*iter)->setPositionAtStep(_TimeStep, currentPosition + PositionUpdate); 216 301 } 217 302 … … 256 341 } 257 342 258 /** Performs Gradient optimization on the bonds. 343 /** Performs Gradient optimization on the bonds with BarzilaiBorwein stepwdith. 344 * 345 * \note this can only be called when there are at least two optimization 346 * time steps present, i.e. this must be preceeded by a simple anneal(). 259 347 * 260 348 * We assume that forces have just been calculated. These forces are projected … … 263 351 * 264 352 * 265 * \param CurrentTimeStep current time step(i.e. \f$ t + \Delta t \f$ in the sense of the velocity verlet)353 * \param _TimeStep time step to update (i.e. \f$ t + \Delta t \f$ in the sense of the velocity verlet) 266 354 * \param maxComponents to be filled with maximum force component over all atoms 267 355 */ 268 Vector annealWithBondGraph (269 const int CurrentTimeStep)356 Vector annealWithBondGraph_BarzilaiBorwein( 357 const int _TimeStep) 270 358 { 359 const int OldTimeStep = _TimeStep-2; 360 const int CurrentTimeStep = _TimeStep-1; 361 ASSERT(OldTimeStep >= 0, 362 "annealWithBondGraph_BarzilaiBorwein() - we need two present optimization steps to compute stepwidth, and the new one to update on already present."); 363 ASSERT(currentStep > 1, 364 "annealWithBondGraph_BarzilaiBorwein() - we need two present optimization steps to compute stepwidth."); 365 366 LOG(1, "STATUS: performing BarzilaiBorwein anneal on bonds at step #" << currentStep); 367 271 368 Vector maxComponents; 272 369 … … 309 406 AtomicForceManipulator<T>::atoms.begin(), 310 407 AtomicForceManipulator<T>::atoms.end(), 311 CurrentTimeStep);408 _TimeStep); // use time step to update here as this is the current set of bonds 312 409 const BondVectors::container_t &sorted_bonds = bv.getSorted(); 313 410 … … 328 425 RemnantGradient_per_atom_t RemnantGradient_per_atom; 329 426 for (size_t timestep = 0; timestep <= 1; ++timestep) { 330 const size_t CurrentStep = CurrentTimeStep-timestep-1 >= 0 ? CurrentTimeStep-timestep-1 : 0;331 LOG(2, "DEBUG: CurrentTimeStep is " << CurrentTimeStep427 const size_t ReferenceTimeStep = CurrentTimeStep-timestep; 428 LOG(2, "DEBUG: given time step is " << _TimeStep 332 429 << ", timestep is " << timestep 333 << ", and CurrentStep is " << CurrentStep);430 << ", and ReferenceTimeStep is " << ReferenceTimeStep); 334 431 335 432 for(typename AtomSetMixin<T>::const_iterator iter = AtomicForceManipulator<T>::atoms.begin(); 336 433 iter != AtomicForceManipulator<T>::atoms.end(); ++iter) { 337 434 const atom &walker = *(*iter); 338 const Vector &walkerGradient = walker.getAtomicForceAtStep( CurrentStep);435 const Vector &walkerGradient = walker.getAtomicForceAtStep(ReferenceTimeStep); 339 436 LOG(3, "DEBUG: Gradient of atom #" << walker.getId() << ", namely " 340 437 << walker << " is " << walkerGradient << " with magnitude of " … … 346 443 // gather subset of BondVectors for the current atom 347 444 const std::vector<Vector> BondVectors = 348 bv.getAtomsBondVectorsAtStep(walker, CurrentStep);445 bv.getAtomsBondVectorsAtStep(walker, ReferenceTimeStep); 349 446 350 447 // go through all its bonds and calculate what magnitude is represented … … 353 450 weights_per_atom[timestep].insert( 354 451 std::make_pair(walker.getId(), 355 bv.getWeightsForAtomAtStep(walker, BondVectors, CurrentStep)) );452 bv.getWeightsForAtomAtStep(walker, BondVectors, ReferenceTimeStep)) ); 356 453 ASSERT( inserter.second, 357 454 "ForceAnnealing::operator() - weight map for atom "+toString(walker) … … 441 538 LOG(4, "DEBUG: current projected gradient for " 442 539 << (side == leftside ? "left" : "right") << " side of bond is " << currentGradient); 443 const Vector &oldPosition = bondatom[side]->getPositionAtStep( CurrentTimeStep-2 >= 0 ? CurrentTimeStep - 2 : 0);444 const Vector ¤tPosition = bondatom[side]->getPositionAtStep(CurrentTimeStep -1>=0 ? CurrentTimeStep - 1 : 0);540 const Vector &oldPosition = bondatom[side]->getPositionAtStep(OldTimeStep); 541 const Vector ¤tPosition = bondatom[side]->getPositionAtStep(CurrentTimeStep); 445 542 const Vector PositionDifference = currentPosition - oldPosition; 446 543 LOG(4, "DEBUG: old position is " << oldPosition); … … 491 588 atom &walker = *(*iter); 492 589 // extract largest components for showing progress of annealing 493 const Vector currentGradient = walker.getAtomicForceAtStep(CurrentTimeStep -1>=0 ? CurrentTimeStep-1 : 0);590 const Vector currentGradient = walker.getAtomicForceAtStep(CurrentTimeStep); 494 591 for(size_t i=0;i<NDIM;++i) 495 592 maxComponents[i] = std::max(maxComponents[i], fabs(currentGradient[i])); 496 497 // reset force vector for next step except on final one498 if (currentStep != maxSteps)499 walker.setAtomicForce(zeroVec);500 593 } 501 594 … … 521 614 LOG(3, "DEBUG: Applying update " << update << " to atom #" << atomid 522 615 << ", namely " << *walker); 523 walker->setPosition (524 walker->getPositionAtStep(CurrentTimeStep -1>=0 ? CurrentTimeStep - 1 : 0)616 walker->setPositionAtStep(_TimeStep, 617 walker->getPositionAtStep(CurrentTimeStep) 525 618 + update - CommonTranslation); 526 walker->setAtomicVelocity(update);527 619 // walker->setAtomicForce( RemnantGradient_per_atom[walker->getId()] ); 528 620 } -
tests/Python/ForceAnnealing/post/five_carbon_test_no-bondgraph.data
r08470b8 r9f1fee5 31 31 C 5 12.3868 10 10 0 0 0 0.0975274 0 0 4 0 0 0 32 32 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 33 C 1 5.99 167 10 10 0 0 0 -0.03029010 0 2 0 0 034 C 2 7.53443 10 10 0 0 0 0.062 1625 0 0 1 3 0 033 C 1 5.99318 10 10 0 0 0 -0.0310892 0 0 2 0 0 0 34 C 2 7.53443 10 10 0 0 0 0.0629615 0 0 1 3 0 0 35 35 C 3 9.19466 10 10 0 0 0 -0.0637606 0 0 2 4 0 0 36 C 4 10.7344 10 10 0 0 0 0.06 221010 0 3 5 0 037 C 5 12.39 17 10 10 0 0 0 -0.03032190 0 4 0 0 036 C 4 10.7344 10 10 0 0 0 0.0630038 0 0 3 5 0 0 37 C 5 12.3932 10 10 0 0 0 -0.0311156 0 0 4 0 0 0 38 38 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 39 C 1 5.99 092 10 10 0 0 0 -0.003032190 0 2 0 0 040 C 2 7.585 19 10 10 0 0 0 0.0008202250 0 1 3 0 041 C 3 9.18101 10 10 0 0 0 0.004 429210 0 2 4 0 042 C 4 10.785 2 10 10 0 0 0 0.0007990580 0 3 5 0 043 C 5 12.39 09 10 10 0 0 0 -0.003016310 0 4 0 0 039 C 1 5.99164 10 10 0 0 0 -0.00314331 0 0 2 0 0 0 40 C 2 7.5857 10 10 0 0 0 0.000661472 0 0 1 3 0 0 41 C 3 9.18101 10 10 0 0 0 0.00496368 0 0 2 4 0 0 42 C 4 10.7857 10 10 0 0 0 0.000640304 0 0 3 5 0 0 43 C 5 12.3916 10 10 0 0 0 -0.00312215 0 0 4 0 0 0 44 44 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 45 C 1 5.99 083 10 10 0 0 0 -0.00263001 0 0 2 0 0 046 C 2 7.58 586 10 10 0 0 0 8.99601e-050 0 1 3 0 047 C 3 9.181 06 10 10 0 0 0 0.005101270 0 2 4 0 048 C 4 10.78 59 10 10 0 0 0 3.17506e-050 0 3 5 0 049 C 5 12.39 08 10 10 0 0 0 -0.002592970 0 4 0 0 045 C 1 5.99146 10 10 0 0 0 -0.00276231 0 0 2 0 0 0 46 C 2 7.58624 10 10 0 0 0 0.000513302 0 0 1 3 0 0 47 C 3 9.18199 10 10 0 0 0 0.00447684 0 0 2 4 0 0 48 C 4 10.7862 10 10 0 0 0 0.000576803 0 0 3 5 0 0 49 C 5 12.3915 10 10 0 0 0 -0.00280464 0 0 4 0 0 0 50 50 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 51 C 1 5.9902 8 10 10 0 0 0 -0.002291340 0 2 0 0 052 C 2 7.58 595 10 10 0 0 0 -7.40848e-050 0 1 3 0 053 C 3 9.1 8148 10 10 0 0 0 0.004704390 0 2 4 0 054 C 4 10.7 859 10 10 0 0 0 -1.05835e-050 0 3 5 0 055 C 5 12.39 03 10 10 0 0 0 -0.002328380 0 4 0 0 051 C 1 5.99021 10 10 0 0 0 -0.00110069 0 0 2 0 0 0 52 C 2 7.58813 10 10 0 0 0 0.00265118 0 0 1 3 0 0 53 C 3 9.19106 10 10 0 0 0 -0.00158224 0 0 2 4 0 0 54 C 4 10.791 10 10 0 0 0 -0.000497427 0 0 3 5 0 0 55 C 5 12.39 10 10 0 0 0 0.000529177 0 0 4 0 0 0 56 56 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 57 C 1 5.98 655 10 10 0 0 0 -0.0003175060 0 2 0 0 058 C 2 7.5 8595 10 10 0 0 0 0.0005873870 0 1 3 0 059 C 3 9.18 646 10 10 0 0 0 -0.000566220 0 2 4 0 060 C 4 10.78 59 10 10 0 0 0 0.0002434220 0 3 5 0 061 C 5 12.3 858 10 10 0 0 0 5.29177e-050 0 4 0 0 057 C 1 5.98937 10 10 0 0 0 0.000582095 0 0 2 0 0 0 58 C 2 7.59047 10 10 0 0 0 -0.00152403 0 0 1 3 0 0 59 C 3 9.18869 10 10 0 0 0 0.00100015 0 0 2 4 0 0 60 C 4 10.7888 10 10 0 0 0 0.000682639 0 0 3 5 0 0 61 C 5 12.3902 10 10 0 0 0 -0.000740848 0 0 4 0 0 0 62 62 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 63 C 1 5.98 596 10 10 0 0 0 -5.29177e-060 0 2 0 0 064 C 2 7.58 595 10 10 0 0 0 0.0002751720 0 1 3 0 065 C 3 9.18 646 10 10 0 0 0 -0.000566220 0 2 4 0 066 C 4 10.7 859 10 10 0 0 0 0.0002434220 0 3 5 0 067 C 5 12.3 858 10 10 0 0 0 5.29177e-050 0 4 0 0 063 C 1 5.98966 10 10 0 0 0 -2.64589e-05 0 0 2 0 0 0 64 C 2 7.58961 10 10 0 0 0 2.64589e-05 0 0 1 3 0 0 65 C 3 9.18961 10 10 0 0 0 0.000259297 0 0 2 4 0 0 66 C 4 10.7901 10 10 0 0 0 -0.000259297 0 0 3 5 0 0 67 C 5 12.3901 10 10 0 0 0 0 0 0 4 0 0 0 68 68 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 69 C 1 5.98 595 10 10 0 0 0 -9.48677e-210 0 2 0 0 070 C 2 7.58 595 10 10 0 0 0 0.000269880 0 1 3 0 071 C 3 9.18 646 10 10 0 0 0 -0.000566220 0 2 4 0 072 C 4 10.78 59 10 10 0 0 0 0.000243422 0 0 3 5 0 073 C 5 12.3 858 10 10 0 0 0 5.29177e-050 0 4 0 0 069 C 1 5.98965 10 10 0 0 0 -1.05835e-05 0 0 2 0 0 0 70 C 2 7.58963 10 10 0 0 0 0.000169337 0 0 1 3 0 0 71 C 3 9.18993 10 10 0 0 0 -0.000280464 0 0 2 4 0 0 72 C 4 10.7897 10 10 0 0 0 0.000333382 0 0 3 5 0 0 73 C 5 12.3901 10 10 0 0 0 -0.000211671 0 0 4 0 0 0 74 74 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 75 C 1 5.98 595 10 10 0 0 0 4.23342e-050 0 2 0 0 076 C 2 7.58 603 10 10 0 0 0 0.0001852120 0 1 3 0 077 C 3 9.18 646 10 10 0 0 0 -0.000523885 0 0 2 4 0 078 C 4 10.78 59 10 10 0 0 0 0.0002434220 0 3 5 0 079 C 5 12.3 858 10 10 0 0 05.29177e-05 0 0 4 0 0 075 C 1 5.98964 10 10 0 0 0 1.35525e-21 0 0 2 0 0 0 76 C 2 7.58964 10 10 0 0 0 6.35013e-05 0 0 1 3 0 0 77 C 3 9.18976 10 10 0 0 0 1.05835e-05 0 0 2 4 0 0 78 C 4 10.7899 10 10 0 0 0 -2.11671e-05 0 0 3 5 0 0 79 C 5 12.39 10 10 0 0 0 -5.29177e-05 0 0 4 0 0 0 80 80 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 81 C 1 5.98 595 10 10 0 0 0 0.000137586 0 0 2 0 0 082 C 2 7.58 621 10 10 0 0 0 -1.58753e-05 0 0 1 3 0 083 C 3 9.18 644 10 10 0 0 0 -0.000407466 0 0 2 4 0 084 C 4 10.78 59 10 10 0 0 0 0.0002328380 0 3 5 0 085 C 5 12.3 858 10 10 0 0 05.29177e-05 0 0 4 0 0 081 C 1 5.98964 10 10 0 0 0 5.29177e-06 0 0 2 0 0 0 82 C 2 7.58965 10 10 0 0 0 5.82095e-05 0 0 1 3 0 0 83 C 3 9.18977 10 10 0 0 0 5.29177e-06 0 0 2 4 0 0 84 C 4 10.7899 10 10 0 0 0 -1.58753e-05 0 0 3 5 0 0 85 C 5 12.39 10 10 0 0 0 -5.29177e-05 0 0 4 0 0 0 86 86 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 87 C 1 5.98 595 10 10 0 0 0 0.0001375860 0 2 0 0 088 C 2 7.58 621 10 10 0 0 0 -5.82095e-05 0 0 1 3 0 089 C 3 9.18 636 10 10 0 0 0 -0.0003227980 0 2 4 0 090 C 4 10.78 59 10 10 0 0 0 0.0001905040 0 3 5 0 091 C 5 12.3 858 10 10 0 0 05.29177e-05 0 0 4 0 0 087 C 1 5.98964 10 10 0 0 0 6.8793e-05 0 0 2 0 0 0 88 C 2 7.58977 10 10 0 0 0 -6.8793e-05 0 0 1 3 0 0 89 C 3 9.18977 10 10 0 0 0 6.8793e-05 0 0 2 4 0 0 90 C 4 10.7899 10 10 0 0 0 -1.58753e-05 0 0 3 5 0 0 91 C 5 12.39 10 10 0 0 0 -5.29177e-05 0 0 4 0 0 0 92 92 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 93 C 1 5.98 59510 10 0 0 0 0 0 0 2 0 0 094 C 2 7.58 621 10 10 0 0 0 0 0 0 1 3 0 095 C 3 9.18 60710 10 0 0 0 0 0 0 2 4 0 096 C 4 10.78 610 10 0 0 0 0 0 0 3 5 0 097 C 5 12.3 85810 10 0 0 0 0 0 0 4 0 0 093 C 1 5.98964 10 10 0 0 0 0 0 0 2 0 0 0 94 C 2 7.58971 10 10 0 0 0 0 0 0 1 3 0 0 95 C 3 9.18978 10 10 0 0 0 0 0 0 2 4 0 0 96 C 4 10.7899 10 10 0 0 0 0 0 0 3 5 0 0 97 C 5 12.39 10 10 0 0 0 0 0 0 4 0 0 0 -
tests/Python/ForceAnnealing/testsuite-python-forceannealing-ising.at
r08470b8 r9f1fee5 32 32 AT_SETUP([Python externalization - Force Annealing without bondgraph on 5-body Ising model]) 33 33 AT_KEYWORDS([python force-annealing ising]) 34 AT_XFAIL_IF([/bin/true])35 34 36 35 # we use forces from a simple Ising model with 5 "carbon" atoms in a row along the x axis … … 38 37 file=five_carbon_test.data 39 38 AT_CHECK([../../run ${abs_top_srcdir}/tests/Python/ForceAnnealing/pre/ising_model_chain.py ./$file ./ 15 5 "0"], 0, [stdout], [ignore]) 40 AT_CHECK([grep "Largest remaining force components.* 0.0001" stdout], 0, [ignore], [ignore])39 AT_CHECK([grep "Largest remaining force components.*e-05" stdout], 0, [ignore], [ignore]) 41 40 AT_CHECK([diff $file ${abs_top_srcdir}/tests/Python/ForceAnnealing/post/five_carbon_test_no-bondgraph.data], 0, [ignore], [ignore]) 42 41 … … 45 44 AT_SETUP([Python externalization - Force Annealing with bondgraph on 2-body Ising model]) 46 45 AT_KEYWORDS([python force-annealing ising bondgraph]) 47 AT_XFAIL_IF([/bin/true])48 46 49 47 # we use forces from a simple Ising model with 2 "carbon" atoms in a row along the x axis … … 58 56 AT_SETUP([Python externalization - Force Annealing with bondgraph on 5-body Ising model]) 59 57 AT_KEYWORDS([python force-annealing ising bondgraph]) 60 AT_XFAIL_IF([/bin/true])61 58 62 59 # we use forces from a simple Ising model with 5 "carbon" atoms in a row along the x axis
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