Changes in / [a6c11a:3e334e]
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- 9 edited
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doc/userguide/userguide.xml (modified) (1 diff)
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src/Dynamics/ForceAnnealing.hpp (modified) (10 diffs)
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tests/Python/ForceAnnealing/post/five_carbon_test_bondgraph.data (modified) (1 diff)
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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) (2 diffs)
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tests/integration/StructureOptimization/testsuite-integration-structureoptimization-ethane.at (modified) (1 diff)
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tests/integration/StructureOptimization/testsuite-integration-structureoptimization-methane.at (modified) (2 diffs)
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tests/integration/StructureOptimization/testsuite-integration-structureoptimization-water.at (modified) (2 diffs)
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tests/integration/testsuite-integration.at (modified) (1 diff)
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doc/userguide/userguide.xml
ra6c11a r3e334e 2464 2464 stepwidth we do not need any 'deltat' parameters. If the computed 2465 2465 step width is zero, we use a default step width of 1.</para> 2466 2467 <section xml:id="dynamics.optimize-structure.bondgraph"> 2468 <title xml:id="dynamics.optimize-structure.bondgraph.title">... using the bond graph</title> 2469 <para>A more efficient optimization, especially for larger molecules 2470 is obtained, if the bond graph is taken into account. To this end, 2471 the structure optimization can be called as follows:</para> 2472 <programlisting>... --optimize-structure \ 2473 --keep-bondgraph 1 \ 2474 --output-every-step 1 \ 2475 --steps 100 \ 2476 --order 3 \ 2477 --distance 3. \ 2478 --deltat 0.5 \ 2479 --keep-fixed-CenterOfMass 1 \ 2480 --fragment-executable mpqc \ 2481 --use-bondgraph 1 \ 2482 --damping-factor 0.5 \ 2483 --max-distance 8 2484 </programlisting> 2485 <para>Note that two additional arguments <emphasis role="bold">use-bondgraph</emphasis>, 2486 <emphasis role="bold">damping-factor</emphasis>and 2487 <emphasis role="bold">max-distance</emphasis>. The first will 2488 switch on using the bond graph while the latter two are parameters 2489 controlling its behavior.</para> 2490 <para>Let us briefly sketch the central idea of using the bond graph: 2491 If a specific atom has a non-zero gradient, then this gradient will 2492 cause the atom to be shifted into its negative direction. The 2493 gradient however is a sum of forces acting on this atom from all 2494 other atoms. The gradient therefore states the net effect on the 2495 toal energy if the atom (and only the atom) would be moved according 2496 to its negative direction. In other words, the force on one side of 2497 the atom are stronger than those on the other side, where the 2498 sides are defined by the plane with the gradient as its normal 2499 vector.</para> 2500 <para>The idea now is to not only move the atom itself but also 2501 all atoms in the direction of the negative gradient by a fraction 2502 as well. The underlying notion is that if there is a misplacement 2503 of the said atom under consideration, then this misplacement 2504 will faster spread out to the edges of the molecule and dissipate 2505 there. If we move only the atom, this will cause a lot of 2506 oscillations that will take a while to settle. One might think of 2507 it like the smoothing step of a multigrid solver. 2508 Essentially, we consider the gradient as a local error that is 2509 smoothed out by powers of <emphasis role="bold">damping-factor</emphasis> 2510 the further out we go in the bond graph from the respective 2511 atom till <emphasis role="bold">max-distance</emphasis>. Note that 2512 the distance is here to be understood in the sense of a graph, i.e. 2513 stepping from one atom to a bond neighbor in the bond graph 2514 is a distance of 1.</para> 2515 <note>The truncated power series of the <emphasis role="bold">max-distance</emphasis> 2516 should sum to 1, i.e. values between 0.5 and 1 work well.</note> 2517 <note>Hydrogens due to their typically much ligher mass compared 2518 to other nuclei are excluded from this procedure. They feel the 2519 dampened gradients of others but their gradient acts only on 2520 themselves</note> 2521 <note>Barzilai-Borwein step width sometimes tends to overshoot 2522 as it is a approximation to the secant and assumes linearity. To 2523 counter this, we cap the step width at 0.2 angstroem.</note> 2524 </section> 2466 2525 </section> 2467 2526 <section xml:id="dynamics.step-world-time"> -
src/Dynamics/ForceAnnealing.hpp
ra6c11a r3e334e 17 17 #include <functional> 18 18 #include <iterator> 19 #include <math.h> 19 20 20 21 #include <boost/bind.hpp> … … 167 168 { 168 169 double stepwidth = 0.; 169 if (_GradientDifference.Norm Squared() > MYEPSILON)170 if (_GradientDifference.Norm() > MYEPSILON) 170 171 stepwidth = fabs(_PositionDifference.ScalarProduct(_GradientDifference))/ 171 172 _GradientDifference.NormSquared(); … … 176 177 stepwidth = currentDeltat; 177 178 } 178 return st epwidth;179 return std::min(1., stepwidth); 179 180 } 180 181 … … 200 201 iter != AtomicForceManipulator<T>::atoms.end(); ++iter) { 201 202 // atom's force vector gives steepest descent direction 202 const Vector currentPosition = (*iter)->getPositionAtStep(CurrentTimeStep);203 const Vector currentGradient = (*iter)->getAtomicForceAtStep(CurrentTimeStep);203 const Vector ¤tPosition = (*iter)->getPositionAtStep(CurrentTimeStep); 204 const Vector ¤tGradient = (*iter)->getAtomicForceAtStep(CurrentTimeStep); 204 205 LOG(4, "DEBUG: currentPosition for atom #" << (*iter)->getId() << " is " << currentPosition); 205 206 LOG(4, "DEBUG: currentGradient for atom #" << (*iter)->getId() << " is " << currentGradient); … … 248 249 } 249 250 251 /** Performs Gradient optimization on a single atom using BarzilaiBorwein step width. 252 * 253 * \param _atom atom to anneal 254 * \param OldTimeStep old time step 255 * \param CurrentTimeStep current time step whose gradient we've just calculated 256 * \param TimeStepToSet time step to update (i.e. \f$ t + \Delta t \f$ in the sense of the velocity verlet) 257 */ 258 void annealAtom_BarzilaiBorwein( 259 atom * const _atom, 260 const int &OldTimeStep, 261 const int &CurrentTimeStep, 262 const int &TimeStepToSet 263 ) 264 { 265 // atom's force vector gives steepest descent direction 266 const Vector &oldPosition = _atom->getPositionAtStep(OldTimeStep); 267 const Vector ¤tPosition = _atom->getPositionAtStep(CurrentTimeStep); 268 const Vector &oldGradient = _atom->getAtomicForceAtStep(OldTimeStep); 269 const Vector ¤tGradient = _atom->getAtomicForceAtStep(CurrentTimeStep); 270 LOG(4, "DEBUG: oldPosition for atom #" << _atom->getId() << " is " << oldPosition); 271 LOG(4, "DEBUG: currentPosition for atom #" << _atom->getId() << " is " << currentPosition); 272 LOG(4, "DEBUG: oldGradient for atom #" << _atom->getId() << " is " << oldGradient); 273 LOG(4, "DEBUG: currentGradient for atom #" << _atom->getId() << " is " << currentGradient); 274 // LOG(4, "DEBUG: Force for atom #" << _atom->getId() << " is " << currentGradient); 275 276 // we use Barzilai-Borwein update with position reversed to get descent 277 const Vector PositionDifference = currentPosition - oldPosition; 278 const Vector GradientDifference = (currentGradient - oldGradient); 279 double stepwidth = getBarzilaiBorweinStepwidth(PositionDifference, GradientDifference); 280 Vector PositionUpdate = stepwidth * currentGradient; 281 LOG(3, "DEBUG: Update would be " << stepwidth << "*" << currentGradient << " = " << PositionUpdate); 282 283 // finally set new values 284 _atom->setPositionAtStep(TimeStepToSet, currentPosition + PositionUpdate); 285 } 286 250 287 /** Performs Gradient optimization on the atoms using BarzilaiBorwein step width. 251 288 * 252 289 * \note this can only be called when there are at least two optimization 253 * time steps present, i.e. this must be prece eded by a simple anneal().290 * time steps present, i.e. this must be preceded by a simple anneal(). 254 291 * 255 292 * We assume that forces have just been calculated. … … 271 308 272 309 Vector maxComponents; 273 bool deltat_decreased = false;274 310 for(typename AtomSetMixin<T>::iterator iter = AtomicForceManipulator<T>::atoms.begin(); 275 311 iter != AtomicForceManipulator<T>::atoms.end(); ++iter) { 276 // atom's force vector gives steepest descent direction 277 const Vector &oldPosition = (*iter)->getPositionAtStep(OldTimeStep);278 const Vector ¤tPosition = (*iter)->getPositionAtStep(CurrentTimeStep); 279 const Vector &oldGradient = (*iter)->getAtomicForceAtStep(OldTimeStep);312 313 annealAtom_BarzilaiBorwein(*iter, OldTimeStep, CurrentTimeStep, _TimeStep); 314 315 // extract largest components for showing progress of annealing 280 316 const Vector ¤tGradient = (*iter)->getAtomicForceAtStep(CurrentTimeStep); 281 LOG(4, "DEBUG: oldPosition for atom #" << (*iter)->getId() << " is " << oldPosition);282 LOG(4, "DEBUG: currentPosition for atom #" << (*iter)->getId() << " is " << currentPosition);283 LOG(4, "DEBUG: oldGradient for atom #" << (*iter)->getId() << " is " << oldGradient);284 LOG(4, "DEBUG: currentGradient for atom #" << (*iter)->getId() << " is " << currentGradient);285 // LOG(4, "DEBUG: Force for atom #" << (*iter)->getId() << " is " << currentGradient);286 287 // we use Barzilai-Borwein update with position reversed to get descent288 const Vector PositionDifference = currentPosition - oldPosition;289 const Vector GradientDifference = (currentGradient - oldGradient);290 double stepwidth = getBarzilaiBorweinStepwidth(PositionDifference, GradientDifference);291 Vector PositionUpdate = stepwidth * currentGradient;292 LOG(3, "DEBUG: Update would be " << stepwidth << "*" << currentGradient << " = " << PositionUpdate);293 294 // extract largest components for showing progress of annealing295 317 for(size_t i=0;i<NDIM;++i) 296 318 maxComponents[i] = std::max(maxComponents[i], fabs(currentGradient[i])); 297 298 // // steps may go back and forth again (updates are of same magnitude but299 // // have different sign: Check whether this is the case and one step with300 // // deltat to interrupt this sequence301 // if (!PositionDifference.IsZero())302 // if ((PositionUpdate.ScalarProduct(PositionDifference) < 0)303 // && (fabs(PositionUpdate.NormSquared()-PositionDifference.NormSquared()) < 1e-3)) {304 // // for convergence we want a null sequence here, too305 // if (!deltat_decreased) {306 // deltat_decreased = true;307 // currentDeltat = .5*currentDeltat;308 // }309 // LOG(2, "DEBUG: Upgrade in other direction: " << PositionUpdate310 // << " > " << PositionDifference311 // << ", using deltat: " << currentDeltat);312 // PositionUpdate = currentDeltat * currentGradient;313 // }314 315 // finally set new values316 (*iter)->setPositionAtStep(_TimeStep, currentPosition + PositionUpdate);317 319 } 318 320 319 321 return maxComponents; 320 322 } 323 324 /** Helper function to insert \a PositionUpdate into a map for every atom. 325 * 326 * \param _GatheredUpdates map of updates per atom 327 * \param _LargestUpdate_per_Atom map with the largest update per atom for checking 328 * \param _atomno key for map 329 * \param _PositionUpdate update to add 330 * \param _factor optional dampening factor 331 */ 332 void updateInserter( 333 std::map<atomId_t, Vector> &_GatheredUpdates, 334 std::map<atomId_t, double> &_LargestUpdate_per_Atom, 335 const atomId_t _atomno, 336 const Vector &_PositionUpdate, 337 const double _factor = 1. 338 ) 339 { 340 if (_GatheredUpdates.count(_atomno)) { 341 _GatheredUpdates[_atomno] += _factor*_PositionUpdate; 342 _LargestUpdate_per_Atom[_atomno] = 343 std::max(_LargestUpdate_per_Atom[_atomno], _factor*_PositionUpdate.Norm()); 344 } else { 345 _GatheredUpdates.insert( 346 std::make_pair( 347 _atomno, 348 _factor*_PositionUpdate) ); 349 _LargestUpdate_per_Atom.insert( 350 std::make_pair( 351 _atomno, 352 _PositionUpdate.Norm()) ); 353 } 354 } 321 355 322 356 /** Performs Gradient optimization on the bonds with BarzilaiBorwein stepwdith. … … 416 450 417 451 std::map<atomId_t, Vector> GatheredUpdates; //!< gathers all updates which are applied at the end 452 std::map<atomId_t, double> LargestUpdate_per_Atom; //!< check whether updates cancelled each other 418 453 for(typename AtomSetMixin<T>::iterator iter = AtomicForceManipulator<T>::atoms.begin(); 419 454 iter != AtomicForceManipulator<T>::atoms.end(); ++iter) { … … 434 469 const Vector PositionDifference = currentPosition - oldPosition; 435 470 const Vector GradientDifference = (currentGradient - oldGradient); 436 double stepwidth = 0.; 437 if (GradientDifference.Norm() > MYEPSILON) 438 stepwidth = fabs(PositionDifference.ScalarProduct(GradientDifference))/ 439 GradientDifference.NormSquared(); 440 if (fabs(stepwidth) < 1e-10) { 441 // dont' warn in first step, deltat usage normal 442 if (currentStep != 1) 443 ELOG(1, "INFO: Barzilai-Borwein stepwidth is zero, using deltat " << currentDeltat << " instead."); 444 stepwidth = currentDeltat; 445 } 471 double stepwidth = getBarzilaiBorweinStepwidth(PositionDifference, GradientDifference); 446 472 Vector PositionUpdate = stepwidth * currentGradient; 473 // cap updates (if non-zero) at 0.2 angstroem. BB tends to overshoot. 474 for (size_t i=0;i<NDIM;++i) 475 if (fabs(PositionUpdate[i]) > MYEPSILON) 476 PositionUpdate[i] = std::min(0.2, fabs(PositionUpdate[i]))*PositionUpdate[i]/fabs(PositionUpdate[i]); 447 477 LOG(3, "DEBUG: Update would be " << stepwidth << "*" << currentGradient << " = " << PositionUpdate); 448 478 449 /** for each atom, we imagine a plane at the position of the atom with 450 * its atomic gradient as the normal vector. We go through all its bonds 451 * and check on which side of the plane the bond is. This defines whether 452 * the bond is contracting (+) or expanding (-) with respect to this atom. 453 * 454 * A bond has two atoms, however. Hence, we do this for either atom and 455 * look at the combination: Is it in sum contracting or expanding given 456 * both projected_forces? 457 */ 458 459 /** go through all bonds and check projected_forces and side of plane 460 * the idea is that if all bonds on one side are contracting ones or expanding, 461 * respectively, then we may shift not only the atom with respect to its 462 * gradient but also its neighbors (towards contraction or towards 463 * expansion depending on direction of gradient). 464 * if they are mixed on both sides of the plane, then we simply shift 465 * only the atom itself. 466 * if they are not mixed on either side, then we also only shift the 467 * atom, namely away from expanding and towards contracting bonds. 468 * 469 * We may get this information right away by looking at the projected_forces. 470 * They give the atomic gradient of either atom projected onto the BondVector 471 * with an additional weight in [0,1]. 472 */ 473 474 // sign encodes side of plane and also encodes contracting(-) or expanding(+) 475 typedef std::vector<int> sides_t; 476 typedef std::vector<int> types_t; 477 sides_t sides; 478 types_t types; 479 const BondList& ListOfBonds = walker.getListOfBonds(); 480 for(BondList::const_iterator bonditer = ListOfBonds.begin(); 481 bonditer != ListOfBonds.end(); ++bonditer) { 482 const bond::ptr ¤t_bond = *bonditer; 483 484 // BondVector goes from bond::rightatom to bond::leftatom 485 const size_t index = bv.getIndexForBond(current_bond); 486 std::vector<double> &forcelist = (&walker == current_bond->leftatom) ? 487 projected_forces[BondVectors::leftside] : projected_forces[BondVectors::rightside]; 488 // note that projected_forces has sign such as to indicate whether 489 // atomic gradient wants bond to contract (-) or expand (+). 490 // This goes into sides: Minus side points away from gradient, plus side point 491 // towards gradient. 492 // 493 // the sum of both bond sides goes into types, depending on which is 494 // stronger if either wants a different thing 495 const double &temp = forcelist[index]; 496 sides.push_back( -1.*temp/fabs(temp) ); // BondVectors has exactly opposite sign for sides decision 497 const double sum = 498 projected_forces[BondVectors::leftside][index]+projected_forces[BondVectors::rightside][index]; 499 types.push_back( sum/fabs(sum) ); 500 LOG(4, "DEBUG: Bond " << *current_bond << " is on side " << sides.back() 501 << " and has type " << types.back()); 502 } 503 // /// check whether both conditions are compatible: 504 // // i.e. either we have ++/-- for all entries in sides and types 505 // // or we have +-/-+ for all entries 506 // // hence, multiplying and taking the sum and its absolute value 507 // // should be equal to the maximum number of entries 508 // sides_t results; 509 // std::transform( 510 // sides.begin(), sides.end(), 511 // types.begin(), 512 // std::back_inserter(results), 513 // std::multiplies<int>); 514 // int result = abs(std::accumulate(results.begin(), results.end(), 0, std::plus<int>)); 515 516 std::vector<size_t> first_per_side(2, (size_t)-1); //!< mark down one representative from either side 517 std::vector< std::vector<int> > types_per_side(2); //!< gather all types on each side 518 types_t::const_iterator typesiter = types.begin(); 519 for (sides_t::const_iterator sidesiter = sides.begin(); 520 sidesiter != sides.end(); ++sidesiter, ++typesiter) { 521 const size_t index = (*sidesiter+1)/2; 522 types_per_side[index].push_back(*typesiter); 523 if (first_per_side[index] == (size_t)-1) 524 first_per_side[index] = std::distance(const_cast<const sides_t &>(sides).begin(), sidesiter); 525 } 526 LOG(4, "DEBUG: First on side minus is " << first_per_side[0] << ", and first on side plus is " 527 << first_per_side[1]); 528 //!> enumerate types per side with a little witching with the numbers to allow easy setting from types 529 enum whichtypes_t { 530 contracting=0, 531 unset=1, 532 expanding=2, 533 mixed 534 }; 535 std::vector<int> typeside(2, unset); 536 for(size_t i=0;i<2;++i) { 537 for (std::vector<int>::const_iterator tpsiter = types_per_side[i].begin(); 538 tpsiter != types_per_side[i].end(); ++tpsiter) { 539 if (typeside[i] == unset) { 540 typeside[i] = *tpsiter+1; //contracting(0) or expanding(2) 541 } else { 542 if (typeside[i] != (*tpsiter+1)) // no longer he same type 543 typeside[i] = mixed; 479 if (walker.getElementNo() != 1) { 480 /** for each atom, we imagine a plane at the position of the atom with 481 * its atomic gradient as the normal vector. We go through all its bonds 482 * and check on which side of the plane the bond is. This defines whether 483 * the bond is contracting (+) or expanding (-) with respect to this atom. 484 * 485 * A bond has two atoms, however. Hence, we do this for either atom and 486 * look at the combination: Is it in sum contracting or expanding given 487 * both projected_forces? 488 */ 489 490 /** go through all bonds and check projected_forces and side of plane 491 * the idea is that if all bonds on one side are contracting ones or expanding, 492 * respectively, then we may shift not only the atom with respect to its 493 * gradient but also its neighbors (towards contraction or towards 494 * expansion depending on direction of gradient). 495 * if they are mixed on both sides of the plane, then we simply shift 496 * only the atom itself. 497 * if they are not mixed on either side, then we also only shift the 498 * atom, namely away from expanding and towards contracting bonds. 499 * 500 * We may get this information right away by looking at the projected_forces. 501 * They give the atomic gradient of either atom projected onto the BondVector 502 * with an additional weight in [0,1]. 503 */ 504 505 // sign encodes side of plane and also encodes contracting(-) or expanding(+) 506 typedef std::vector<int> sides_t; 507 typedef std::vector<int> types_t; 508 sides_t sides; 509 types_t types; 510 const BondList& ListOfBonds = walker.getListOfBonds(); 511 for(BondList::const_iterator bonditer = ListOfBonds.begin(); 512 bonditer != ListOfBonds.end(); ++bonditer) { 513 const bond::ptr ¤t_bond = *bonditer; 514 515 // BondVector goes from bond::rightatom to bond::leftatom 516 const size_t index = bv.getIndexForBond(current_bond); 517 std::vector<double> &forcelist = (&walker == current_bond->leftatom) ? 518 projected_forces[BondVectors::leftside] : projected_forces[BondVectors::rightside]; 519 // note that projected_forces has sign such as to indicate whether 520 // atomic gradient wants bond to contract (-) or expand (+). 521 // This goes into sides: Minus side points away from gradient, plus side point 522 // towards gradient. 523 // 524 // the sum of both bond sides goes into types, depending on which is 525 // stronger if either wants a different thing 526 const double &temp = forcelist[index]; 527 if (fabs(temp) < MYEPSILON) 528 sides.push_back(1); 529 else 530 sides.push_back( -1.*temp/fabs(temp) ); // BondVectors has exactly opposite sign for sides decision 531 ASSERT( (sides.back() == 1) || (sides.back() == -1), 532 "ForceAnnealing() - sides is not in {-1,1}."); 533 const double sum = 534 projected_forces[BondVectors::leftside][index]+projected_forces[BondVectors::rightside][index]; 535 types.push_back( sum/fabs(sum) ); 536 LOG(4, "DEBUG: Bond " << *current_bond << " is on side " << sides.back() 537 << " and has type " << types.back()); 538 } 539 // /// check whether both conditions are compatible: 540 // // i.e. either we have ++/-- for all entries in sides and types 541 // // or we have +-/-+ for all entries 542 // // hence, multiplying and taking the sum and its absolute value 543 // // should be equal to the maximum number of entries 544 // sides_t results; 545 // std::transform( 546 // sides.begin(), sides.end(), 547 // types.begin(), 548 // std::back_inserter(results), 549 // std::multiplies<int>); 550 // int result = abs(std::accumulate(results.begin(), results.end(), 0, std::plus<int>)); 551 552 std::vector<size_t> first_per_side(2, (size_t)-1); //!< mark down one representative from either side 553 std::vector< std::vector<int> > types_per_side(2); //!< gather all types on each side 554 types_t::const_iterator typesiter = types.begin(); 555 for (sides_t::const_iterator sidesiter = sides.begin(); 556 sidesiter != sides.end(); ++sidesiter, ++typesiter) { 557 const size_t index = (*sidesiter+1)/2; 558 types_per_side[index].push_back(*typesiter); 559 if (first_per_side[index] == (size_t)-1) 560 first_per_side[index] = std::distance(const_cast<const sides_t &>(sides).begin(), sidesiter); 561 } 562 LOG(4, "DEBUG: First on side minus is " << first_per_side[0] << ", and first on side plus is " 563 << first_per_side[1]); 564 //!> enumerate types per side with a little witching with the numbers to allow easy setting from types 565 enum whichtypes_t { 566 contracting=0, 567 unset=1, 568 expanding=2, 569 mixed 570 }; 571 std::vector<int> typeside(2, unset); 572 for(size_t i=0;i<2;++i) { 573 for (std::vector<int>::const_iterator tpsiter = types_per_side[i].begin(); 574 tpsiter != types_per_side[i].end(); ++tpsiter) { 575 if (typeside[i] == unset) { 576 typeside[i] = *tpsiter+1; //contracting(0) or expanding(2) 577 } else { 578 if (typeside[i] != (*tpsiter+1)) // no longer he same type 579 typeside[i] = mixed; 580 } 544 581 } 545 582 } 546 } 547 LOG(4, "DEBUG: Minus side is " << typeside[0] << " and plus side is " << typeside[1]); 548 549 typedef std::vector< std::pair<atomId_t, atomId_t> > RemovedEdges_t; 550 if ((typeside[0] != mixed) || (typeside[1] != mixed)) { 551 const size_t sideno = ((typeside[0] != mixed) && (typeside[0] != unset)) ? 0 : 1; 552 LOG(4, "DEBUG: Chosen side is " << sideno << " with type " << typeside[sideno]); 553 ASSERT( (typeside[sideno] == contracting) || (typeside[sideno] == expanding), 554 "annealWithBondGraph_BB() - chosen side is neither expanding nor contracting."); 555 // one side is not mixed, all bonds on one side are of same type 556 // hence, find out which bonds to exclude 557 const BondList& ListOfBonds = walker.getListOfBonds(); 558 559 // sideno is away (0) or in direction (1) of gradient 560 // tpyes[first_per_side[sideno]] is either contracting (-1) or expanding (+1) 561 // : side (i), where (i) means which bonds we keep for the BFS, bonds 562 // on side (-i) are removed 563 // If all bonds on side away (0) want expansion (+1), move towards side with atom: side 1 564 // if all bonds side towards (1) want contraction (-1), move away side with atom : side -1 565 566 // unsure whether this or do nothing in the remaining cases: 567 // If all bonds on side toward (1) want expansion (+1), move away side with atom : side -1 568 // (the reasoning is that the bond's other atom must have a stronger 569 // gradient in the same direction and they push along atoms in 570 // gradient direction: we don't want to interface with those. 571 // Hence, move atoms along on away side 572 // if all bonds side away (0) want contraction (-1), move towards side with atom: side 1 573 // (the reasoning is the same, don't interfere with update from 574 // stronger gradient) 575 // hence, the decision is only based on sides once we have picked a side 576 // depending on all bonds associated with have same good type. 577 const double sign = sides[first_per_side[sideno]]; 578 LOG(4, "DEBUG: Removing edges from side with sign " << sign); 579 BondList::const_iterator bonditer = ListOfBonds.begin(); 580 RemovedEdges_t RemovedEdges; 581 for (sides_t::const_iterator sidesiter = sides.begin(); 582 sidesiter != sides.end(); ++sidesiter, ++bonditer) { 583 if (*sidesiter == sign) { 584 // remove the edge 585 const bond::ptr ¤t_bond = *bonditer; 586 LOG(5, "DEBUG: Removing edge " << *current_bond); 587 RemovedEdges.push_back( std::make_pair( 588 current_bond->leftatom->getId(), 589 current_bond->rightatom->getId()) 590 ); 591 #ifndef NDEBUG 592 const bool status = 593 #endif 594 BGcreator.removeEdge(RemovedEdges.back()); 595 ASSERT( status, "ForceAnnealing() - edge to found bond is not present?"); 583 LOG(4, "DEBUG: Minus side is " << typeside[0] << " and plus side is " << typeside[1]); 584 585 typedef std::vector< std::pair<atomId_t, atomId_t> > RemovedEdges_t; 586 if ((typeside[0] != mixed) || (typeside[1] != mixed)) { 587 const size_t sideno = ((typeside[0] != mixed) && (typeside[0] != unset)) ? 0 : 1; 588 LOG(4, "DEBUG: Chosen side is " << sideno << " with type " << typeside[sideno]); 589 ASSERT( (typeside[sideno] == contracting) || (typeside[sideno] == expanding), 590 "annealWithBondGraph_BB() - chosen side is neither expanding nor contracting."); 591 // one side is not mixed, all bonds on one side are of same type 592 // hence, find out which bonds to exclude 593 const BondList& ListOfBonds = walker.getListOfBonds(); 594 595 // sideno is away (0) or in direction (1) of gradient 596 // tpyes[first_per_side[sideno]] is either contracting (-1) or expanding (+1) 597 // : side (i), where (i) means which bonds we keep for the BFS, bonds 598 // on side (-i) are removed 599 // If all bonds on side away (0) want expansion (+1), move towards side with atom: side 1 600 // if all bonds side towards (1) want contraction (-1), move away side with atom : side -1 601 602 // unsure whether this or do nothing in the remaining cases: 603 // If all bonds on side toward (1) want expansion (+1), move away side with atom : side -1 604 // (the reasoning is that the bond's other atom must have a stronger 605 // gradient in the same direction and they push along atoms in 606 // gradient direction: we don't want to interface with those. 607 // Hence, move atoms along on away side 608 // if all bonds side away (0) want contraction (-1), move towards side with atom: side 1 609 // (the reasoning is the same, don't interfere with update from 610 // stronger gradient) 611 // hence, the decision is only based on sides once we have picked a side 612 // depending on all bonds associated with have same good type. 613 614 // away from gradient (minus) and contracting 615 // or towards gradient (plus) and expanding 616 // gather all on same side and remove 617 const double sign = 618 (sides[first_per_side[sideno]] == types[first_per_side[sideno]]) 619 ? sides[first_per_side[sideno]] : -1.*sides[first_per_side[sideno]]; 620 621 LOG(4, "DEBUG: Removing edges from side with sign " << sign); 622 BondList::const_iterator bonditer = ListOfBonds.begin(); 623 RemovedEdges_t RemovedEdges; 624 for (sides_t::const_iterator sidesiter = sides.begin(); 625 sidesiter != sides.end(); ++sidesiter, ++bonditer) { 626 if (*sidesiter == sign) { 627 // remove the edge 628 const bond::ptr ¤t_bond = *bonditer; 629 LOG(5, "DEBUG: Removing edge " << *current_bond); 630 RemovedEdges.push_back( std::make_pair( 631 current_bond->leftatom->getId(), 632 current_bond->rightatom->getId()) 633 ); 634 #ifndef NDEBUG 635 const bool status = 636 #endif 637 BGcreator.removeEdge(RemovedEdges.back()); 638 ASSERT( status, "ForceAnnealing() - edge to found bond is not present?"); 639 } 596 640 } 597 } 598 // perform limited-horizon BFS 599 BoostGraphHelpers::Nodeset_t bondside_set; 600 BreadthFirstSearchGatherer::distance_map_t distance_map; 601 bondside_set = NodeGatherer(walker.getId(), max_distance); 602 distance_map = NodeGatherer.getDistances(); 603 std::sort(bondside_set.begin(), bondside_set.end()); 604 605 // re-add edge 606 for (RemovedEdges_t::const_iterator edgeiter = RemovedEdges.begin(); 607 edgeiter != RemovedEdges.end(); ++edgeiter) 608 BGcreator.addEdge(edgeiter->first, edgeiter->second); 609 610 // update position with dampening factor on the discovered bonds 611 for (BoostGraphHelpers::Nodeset_t::const_iterator setiter = bondside_set.begin(); 612 setiter != bondside_set.end(); ++setiter) { 613 const BreadthFirstSearchGatherer::distance_map_t::const_iterator diter 614 = distance_map.find(*setiter); 615 ASSERT( diter != distance_map.end(), 616 "ForceAnnealing() - could not find distance to an atom."); 617 const double factor = pow(damping_factor, diter->second+1); 618 LOG(3, "DEBUG: Update for atom #" << *setiter << " will be " 619 << factor << "*" << PositionUpdate); 620 if (GatheredUpdates.count((*setiter))) { 621 GatheredUpdates[(*setiter)] += factor*PositionUpdate; 622 } else { 623 GatheredUpdates.insert( 624 std::make_pair( 625 (*setiter), 626 factor*PositionUpdate) ); 641 // perform limited-horizon BFS 642 BoostGraphHelpers::Nodeset_t bondside_set; 643 BreadthFirstSearchGatherer::distance_map_t distance_map; 644 bondside_set = NodeGatherer(walker.getId(), max_distance); 645 distance_map = NodeGatherer.getDistances(); 646 std::sort(bondside_set.begin(), bondside_set.end()); 647 648 // re-add edge 649 for (RemovedEdges_t::const_iterator edgeiter = RemovedEdges.begin(); 650 edgeiter != RemovedEdges.end(); ++edgeiter) 651 BGcreator.addEdge(edgeiter->first, edgeiter->second); 652 653 // update position with dampening factor on the discovered bonds 654 for (BoostGraphHelpers::Nodeset_t::const_iterator setiter = bondside_set.begin(); 655 setiter != bondside_set.end(); ++setiter) { 656 const BreadthFirstSearchGatherer::distance_map_t::const_iterator diter 657 = distance_map.find(*setiter); 658 ASSERT( diter != distance_map.end(), 659 "ForceAnnealing() - could not find distance to an atom."); 660 const double factor = pow(damping_factor, diter->second+1); 661 LOG(3, "DEBUG: Update for atom #" << *setiter << " will be " 662 << factor << "*" << PositionUpdate); 663 updateInserter(GatheredUpdates, LargestUpdate_per_Atom, *setiter, PositionUpdate, factor); 627 664 } 665 } else { 666 // simple atomic annealing, i.e. damping factor of 1 667 updateInserter(GatheredUpdates, LargestUpdate_per_Atom, walker.getId(), PositionUpdate); 628 668 } 629 669 } else { 630 // simple atomic annealing, i.e. damping factor of 1 631 LOG(3, "DEBUG: Update for atom #" << walker.getId() << " will be " << PositionUpdate); 632 GatheredUpdates.insert( 633 std::make_pair( 634 walker.getId(), 635 PositionUpdate) ); 670 // hydrogens (are light-weighted and therefore) are always updated normally 671 LOG(3, "DEBUG: Update for hydrogen #" << walker.getId() << " will be " << PositionUpdate); 672 updateInserter(GatheredUpdates, LargestUpdate_per_Atom, walker.getId(), PositionUpdate); 636 673 } 637 674 } … … 641 678 atom &walker = *(*iter); 642 679 // extract largest components for showing progress of annealing 643 const Vector currentGradient = walker.getAtomicForceAtStep(CurrentTimeStep);680 const Vector ¤tGradient = walker.getAtomicForceAtStep(CurrentTimeStep); 644 681 for(size_t i=0;i<NDIM;++i) 645 682 maxComponents[i] = std::max(maxComponents[i], fabs(currentGradient[i])); … … 670 707 for (size_t i=0;i<NDIM;++i) 671 708 LargestUpdate[i] = std::max(LargestUpdate[i], fabs(update[i])); 672 walker->setPositionAtStep(_TimeStep, 673 walker->getPositionAtStep(CurrentTimeStep) + update); // - CommonTranslation); 709 710 std::map<atomId_t, double>::const_iterator largestiter = LargestUpdate_per_Atom.find(atomid); 711 ASSERT( largestiter != LargestUpdate_per_Atom.end(), 712 "ForceAnnealing() - walker with id "+toString(atomid)+" not in LargestUpdates."); 713 // if we had large updates but their sum is very small 714 if (update.Norm()/largestiter->second > MYEPSILON) { 715 walker->setPositionAtStep(_TimeStep, 716 walker->getPositionAtStep(CurrentTimeStep) + update); // - CommonTranslation); 717 } else { 718 // then recalc update with simple anneal 719 LOG(2, "WARNING: Updates on atom " << *iter << " cancel themselves, performing simple anneal step."); 720 annealAtom_BarzilaiBorwein(walker, OldTimeStep, CurrentTimeStep, _TimeStep); 721 } 674 722 } 675 723 LOG(1, "STATUS: Largest absolute update components are " << LargestUpdate); -
tests/Python/ForceAnnealing/post/five_carbon_test_bondgraph.data
ra6c11a r3e334e 13 13 C 5 12.4 10 10 0 0 0 -0.0140232 0 0 4 0 0 0 14 14 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 15 C 1 5.97149 10 10 0 0 0 -0.03797380 0 2 0 0 016 C 2 7. 49973 10 10 0 0 0 -0.03730170 0 1 3 0 017 C 3 8. 95748 10 10 0 0 0 0.1505880 0 2 4 0 018 C 4 10. 6998 10 10 0 0 0 -0.03737050 0 3 5 0 019 C 5 12.3 715 10 10 0 0 0 -0.037942 0 0 4 0 0 015 C 1 6.0272 10 10 0 0 0 -0.0269616 0 0 2 0 0 0 16 C 2 7.57625 10 10 0 0 0 -0.156181 0 0 1 3 0 0 17 C 3 8.83016 10 10 0 0 0 0.33054 0 0 2 4 0 0 18 C 4 10.7087 10 10 0 0 0 -0.117287 0 0 3 5 0 0 19 C 5 12.3656 10 10 0 0 0 -0.0301102 0 0 4 0 0 0 20 20 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 21 C 1 5.93924 10 10 0 0 0 -0.02551690 0 2 0 0 022 C 2 7. 49102 10 10 0 0 0 -0.001793910 0 1 3 0 023 C 3 9.03941 10 10 0 0 0 0.0546640 0 2 4 0 024 C 4 10.6 911 10 10 0 0 0 -0.001899750 0 3 5 0 025 C 5 12.3 392 10 10 0 0 0 -0.02545340 0 4 0 0 021 C 1 6.04114 10 10 0 0 0 -0.00806995 0 0 2 0 0 0 22 C 2 7.62589 10 10 0 0 0 -0.147588 0 0 1 3 0 0 23 C 3 8.93174 10 10 0 0 0 0.225858 0 0 2 4 0 0 24 C 4 10.6644 10 10 0 0 0 -0.0370742 0 0 3 5 0 0 25 C 5 12.327 10 10 0 0 0 -0.0331265 0 0 4 0 0 0 26 26 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 27 C 1 5.90802 10 10 0 0 0 -0.00437630 0 2 0 0 028 C 2 7. 49975 10 10 0 0 0 -0.003810080 0 1 3 0 029 C 3 9.08428 10 10 0 0 0 0.01639920 0 2 4 0 030 C 4 10.6 998 10 10 0 0 0 -0.003767740 0 3 5 0 031 C 5 12. 3082 10 10 0 0 0 -0.004445090 0 4 0 0 027 C 1 6.06597 10 10 0 0 0 -0.0332429 0 0 2 0 0 0 28 C 2 7.60315 10 10 0 0 0 -0.0764926 0 0 1 3 0 0 29 C 3 8.99578 10 10 0 0 0 0.129484 0 0 2 4 0 0 30 C 4 10.6331 10 10 0 0 0 0.0122663 0 0 3 5 0 0 31 C 5 12.2936 10 10 0 0 0 -0.0320152 0 0 4 0 0 0 32 32 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 33 C 1 5.90803 10 10 0 0 0 -0.008609710 0 2 0 0 034 C 2 7. 49176 10 10 0 0 0 0.0137480 0 1 3 0 035 C 3 9. 10147 10 10 0 0 0 -0.01078460 0 2 4 0 036 C 4 10.6 908 10 10 0 0 0 0.0146953 0 0 3 5 0 037 C 5 12. 3079 10 10 0 0 0 -0.009048930 0 4 0 0 033 C 1 6.05977 10 10 0 0 0 -0.0256492 0 0 2 0 0 0 34 C 2 7.6113 10 10 0 0 0 -0.0706293 0 0 1 3 0 0 35 C 3 9.02936 10 10 0 0 0 0.0940242 0 0 2 4 0 0 36 C 4 10.6251 10 10 0 0 0 0.0298773 0 0 3 5 0 0 37 C 5 12.2773 10 10 0 0 0 -0.0276231 0 0 4 0 0 0 38 38 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 39 C 1 5.90707 10 10 0 0 0 -0.006276040 0 2 0 0 040 C 2 7. 49521 10 10 0 0 0 0.006582960 0 1 3 0 041 C 3 9.0 9579 10 10 0 0 0 -0.000672055 0 0 2 4 0 042 C 4 10.6 951 10 10 0 0 0 0.00660942 0 0 3 5 0 043 C 5 12. 3069 10 10 0 0 0 -0.006244290 0 4 0 0 039 C 1 6.06029 10 10 0 0 0 -0.0336927 0 0 2 0 0 0 40 C 2 7.59662 10 10 0 0 0 -0.0424771 0 0 1 3 0 0 41 C 3 9.05268 10 10 0 0 0 0.0561775 0 0 2 4 0 0 42 C 4 10.6149 10 10 0 0 0 0.044652 0 0 3 5 0 0 43 C 5 12.2615 10 10 0 0 0 -0.0246597 0 0 4 0 0 0 44 44 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 45 C 1 5.90506 10 10 0 0 0 -0.00418050 0 2 0 0 046 C 2 7. 49716 10 10 0 0 0 0.003286190 0 1 3 0 047 C 3 9.0 9547 10 10 0 0 0 0.00186270 0 2 4 0 048 C 4 10.6 973 10 10 0 0 0 0.003106270 0 3 5 0 049 C 5 12. 305 10 10 0 0 0 -0.004074660 0 4 0 0 045 C 1 6.06307 10 10 0 0 0 -0.0372594 0 0 2 0 0 0 46 C 2 7.59266 10 10 0 0 0 -0.0322851 0 0 1 3 0 0 47 C 3 9.06124 10 10 0 0 0 0.0483562 0 0 2 4 0 0 48 C 4 10.6212 10 10 0 0 0 0.039339 0 0 3 5 0 0 49 C 5 12.2555 10 10 0 0 0 -0.0181508 0 0 4 0 0 0 50 50 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 51 C 1 5.90296 10 10 0 0 0 -0.002201380 0 2 0 0 052 C 2 7. 4988 10 10 0 0 0 0.000746140 0 1 3 0 053 C 3 9.0 9605 10 10 0 0 0 0.002963390 0 2 4 0 054 C 4 10.6 989 10 10 0 0 0 0.0008202250 0 3 5 0 055 C 5 12. 3033 10 10 0 0 0 -0.00232838 0 0 4 0 0 051 C 1 6.05413 10 10 0 0 0 -0.0338621 0 0 2 0 0 0 52 C 2 7.59014 10 10 0 0 0 -0.0262525 0 0 1 3 0 0 53 C 3 9.07654 10 10 0 0 0 0.03718 0 0 2 4 0 0 54 C 4 10.6332 10 10 0 0 0 0.0346294 0 0 3 5 0 0 55 C 5 12.2553 10 10 0 0 0 -0.0116948 0 0 4 0 0 0 56 56 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 57 C 1 5.90167 10 10 0 0 0 -0.001238270 0 2 0 0 058 C 2 7. 49933 10 10 0 0 0 0.00026988 0 0 1 3 0 059 C 3 9.0 975 10 10 0 0 0 0.002079670 0 2 4 0 060 C 4 10.6 996 10 10 0 0 0 0.0001587530 0 3 5 0 061 C 5 12. 302 10 10 0 0 0 -0.001270030 0 4 0 0 057 C 1 6.04174 10 10 0 0 0 -0.0298615 0 0 2 0 0 0 58 C 2 7.58531 10 10 0 0 0 -0.0215798 0 0 1 3 0 0 59 C 3 9.0881 10 10 0 0 0 0.0297451 0 0 2 4 0 0 60 C 4 10.6471 10 10 0 0 0 0.0297927 0 0 3 5 0 0 61 C 5 12.2624 10 10 0 0 0 -0.00809641 0 0 4 0 0 0 62 62 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 63 C 1 5.90028 10 10 0 0 0 -0.000418050 0 2 0 0 064 C 2 7. 49949 10 10 0 0 0 0.0007196810 0 1 3 0 065 C 3 9.100 06 10 10 0 0 0 -0.0005450530 0 2 4 0 066 C 4 10.6 996 10 10 0 0 0 0.0007725990 0 3 5 0 067 C 5 12. 3006 10 10 0 0 0 -0.0005291770 0 4 0 0 063 C 1 6.03225 10 10 0 0 0 -0.0288878 0 0 2 0 0 0 64 C 2 7.57766 10 10 0 0 0 -0.0119753 0 0 1 3 0 0 65 C 3 9.10044 10 10 0 0 0 0.0169231 0 0 2 4 0 0 66 C 4 10.6552 10 10 0 0 0 0.0240987 0 0 3 5 0 0 67 C 5 12.2555 10 10 0 0 0 -0.000158753 0 0 4 0 0 0 68 68 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 69 C 1 5.90018 10 10 0 0 0 -0.000158753 0 0 2 0 0 070 C 2 7. 49988 10 10 0 0 0 0.000148170 0 1 3 0 071 C 3 9. 09986 10 10 0 0 0 -2.11671e-050 0 2 4 0 072 C 4 10.6 998 10 10 0 0 0 0.0002963390 0 3 5 0 073 C 5 12. 3003 10 10 0 0 0 -0.0002645890 0 4 0 0 069 C 1 6.02128 10 10 0 0 0 -0.0257233 0 0 2 0 0 0 70 C 2 7.57267 10 10 0 0 0 -0.00809641 0 0 1 3 0 0 71 C 3 9.10876 10 10 0 0 0 0.0102396 0 0 2 4 0 0 72 C 4 10.6642 10 10 0 0 0 0.0180238 0 0 3 5 0 0 73 C 5 12.2537 10 10 0 0 0 0.00555636 0 0 4 0 0 0 74 74 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 75 C 1 5.90014 10 10 0 0 0 -9.52519e-050 0 2 0 0 076 C 2 7. 49996 10 10 0 0 0 4.7626e-050 0 1 3 0 077 C 3 9. 09987 10 10 0 0 0 6.35013e-05 0 0 2 4 0 078 C 4 10.6 999 10 10 0 0 0 0.0001428780 0 3 5 0 079 C 5 12. 3002 10 10 0 0 0 -0.0001587530 0 4 0 0 075 C 1 6.01067 10 10 0 0 0 -0.0232044 0 0 2 0 0 0 76 C 2 7.56682 10 10 0 0 0 -0.00519652 0 0 1 3 0 0 77 C 3 9.11315 10 10 0 0 0 0.00588445 0 0 2 4 0 0 78 C 4 10.6706 10 10 0 0 0 0.013203 0 0 3 5 0 0 79 C 5 12.253 10 10 0 0 0 0.00931352 0 0 4 0 0 0 80 80 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 81 C 1 5.90011 10 10 0 0 0 -5.82095e-050 0 2 0 0 082 C 2 7.5 10 10 0 0 0 00 0 1 3 0 083 C 3 9. 09989 10 10 0 0 0 0.0001164190 0 2 4 0 084 C 4 10. 7 10 10 0 0 0 -5.29177e-060 0 3 5 0 085 C 5 12. 3001 10 10 0 0 0 -5.29177e-050 0 4 0 0 081 C 1 6.00041 10 10 0 0 0 -0.0206961 0 0 2 0 0 0 82 C 2 7.5613 10 10 0 0 0 -0.00374128 0 0 1 3 0 0 83 C 3 9.11512 10 10 0 0 0 0.00320681 0 0 2 4 0 0 84 C 4 10.675 10 10 0 0 0 0.00937702 0 0 3 5 0 0 85 C 5 12.2526 10 10 0 0 0 0.0118536 0 0 4 0 0 0 86 86 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 87 C 1 5.9 0008 10 10 0 0 0 -4.23342e-050 0 2 0 0 088 C 2 7.5 10 10 0 0 0 5.29177e-06 0 0 1 3 0 089 C 3 9. 09993 10 10 0 0 0 7.40848e-050 0 2 4 0 090 C 4 10. 7 10 10 0 0 0 -3.70424e-050 0 3 5 0 091 C 5 12. 3 10 10 0 0 0 1.35525e-210 0 4 0 0 087 C 1 5.99076 10 10 0 0 0 -0.0184524 0 0 2 0 0 0 88 C 2 7.55589 10 10 0 0 0 -0.00304806 0 0 1 3 0 0 89 C 3 9.11526 10 10 0 0 0 0.00204792 0 0 2 4 0 0 90 C 4 10.6785 10 10 0 0 0 0.00574686 0 0 3 5 0 0 91 C 5 12.2526 10 10 0 0 0 0.0137057 0 0 4 0 0 0 92 92 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 93 C 1 5.90004 10 10 0 0 0 0 0 0 2 0 0 0 94 C 2 7.50001 10 10 0 0 0 0 0 0 1 3 0 0 95 C 3 9.09999 10 10 0 0 0 0 0 0 2 4 0 0 96 C 4 10.6999 10 10 0 0 0 0 0 0 3 5 0 0 97 C 5 12.3 10 10 0 0 0 0 0 0 4 0 0 0 93 C 1 5.98163 10 10 0 0 0 -0.0166426 0 0 2 0 0 0 94 C 2 7.55018 10 10 0 0 0 -0.00277289 0 0 1 3 0 0 95 C 3 9.11349 10 10 0 0 0 0.0014817 0 0 2 4 0 0 96 C 4 10.6796 10 10 0 0 0 0.00327561 0 0 3 5 0 0 97 C 5 12.2519 10 10 0 0 0 0.0146582 0 0 4 0 0 0 98 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 99 C 1 5.97375 10 10 0 0 0 -0.0148328 0 0 2 0 0 0 100 C 2 7.54572 10 10 0 0 0 -0.00236542 0 0 1 3 0 0 101 C 3 9.11322 10 10 0 0 0 0.000624429 0 0 2 4 0 0 102 C 4 10.6819 10 10 0 0 0 0.00345024 0 0 3 5 0 0 103 C 5 12.2571 10 10 0 0 0 0.0131236 0 0 4 0 0 0 104 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 105 C 1 5.96682 10 10 0 0 0 -0.0131448 0 0 2 0 0 0 106 C 2 7.54198 10 10 0 0 0 -0.001995 0 0 1 3 0 0 107 C 3 9.11337 10 10 0 0 0 0.000550344 0 0 2 4 0 0 108 C 4 10.6858 10 10 0 0 0 0.00263001 0 0 3 5 0 0 109 C 5 12.2632 10 10 0 0 0 0.0119594 0 0 4 0 0 0 110 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 111 C 1 5.96072 10 10 0 0 0 -0.0116049 0 0 2 0 0 0 112 C 2 7.53879 10 10 0 0 0 -0.00168808 0 0 1 3 0 0 113 C 3 9.11367 10 10 0 0 0 0.000343965 0 0 2 4 0 0 114 C 4 10.6892 10 10 0 0 0 0.00210083 0 0 3 5 0 0 115 C 5 12.2687 10 10 0 0 0 0.0108481 0 0 4 0 0 0 116 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 117 C 1 5.95531 10 10 0 0 0 -0.0102343 0 0 2 0 0 0 118 C 2 7.53597 10 10 0 0 0 -0.00147111 0 0 1 3 0 0 119 C 3 9.11385 10 10 0 0 0 0.000195796 0 0 2 4 0 0 120 C 4 10.6921 10 10 0 0 0 0.00182566 0 0 3 5 0 0 121 C 5 12.2738 10 10 0 0 0 0.00968394 0 0 4 0 0 0 122 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 123 C 1 5.95052 10 10 0 0 0 -0.00902776 0 0 2 0 0 0 124 C 2 7.53346 10 10 0 0 0 -0.0012859 0 0 1 3 0 0 125 C 3 9.11397 10 10 0 0 0 0.000116419 0 0 2 4 0 0 126 C 4 10.6947 10 10 0 0 0 0.00151874 0 0 3 5 0 0 127 C 5 12.2783 10 10 0 0 0 0.00867851 0 0 4 0 0 0 128 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 129 C 1 5.94629 10 10 0 0 0 -0.00796941 0 0 2 0 0 0 130 C 2 7.53123 10 10 0 0 0 -0.00112715 0 0 1 3 0 0 131 C 3 9.11404 10 10 0 0 0 7.93766e-05 0 0 2 4 0 0 132 C 4 10.697 10 10 0 0 0 0.00129119 0 0 3 5 0 0 133 C 5 12.2824 10 10 0 0 0 0.00772599 0 0 4 0 0 0 134 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 135 C 1 5.94255 10 10 0 0 0 -0.00703277 0 0 2 0 0 0 136 C 2 7.52926 10 10 0 0 0 -0.000989561 0 0 1 3 0 0 137 C 3 9.1141 10 10 0 0 0 3.17506e-05 0 0 2 4 0 0 138 C 4 10.699 10 10 0 0 0 0.00111127 0 0 3 5 0 0 139 C 5 12.286 10 10 0 0 0 0.0068793 0 0 4 0 0 0 140 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 141 C 1 5.93925 10 10 0 0 0 -0.00620725 0 0 2 0 0 0 142 C 2 7.52752 10 10 0 0 0 -0.000883726 0 0 1 3 0 0 143 C 3 9.11412 10 10 0 0 0 4.23342e-05 0 0 2 4 0 0 144 C 4 10.7008 10 10 0 0 0 0.000963103 0 0 3 5 0 0 145 C 5 12.2893 10 10 0 0 0 0.00608554 0 0 4 0 0 0 146 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 147 C 1 5.93633 10 10 0 0 0 -0.00547698 0 0 2 0 0 0 148 C 2 7.52598 10 10 0 0 0 -0.000783182 0 0 1 3 0 0 149 C 3 9.11415 10 10 0 0 0 4.23342e-05 0 0 2 4 0 0 150 C 4 10.7024 10 10 0 0 0 0.000767307 0 0 3 5 0 0 151 C 5 12.2921 10 10 0 0 0 0.00545053 0 0 4 0 0 0 152 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 153 C 1 5.93375 10 10 0 0 0 -0.00484197 0 0 2 0 0 0 154 C 2 7.5246 10 10 0 0 0 -0.000693222 0 0 1 3 0 0 155 C 3 9.11414 10 10 0 0 0 1.05835e-05 0 0 2 4 0 0 156 C 4 10.7037 10 10 0 0 0 0.000762015 0 0 3 5 0 0 157 C 5 12.2947 10 10 0 0 0 0.0047626 0 0 4 0 0 0 158 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 159 C 1 5.93147 10 10 0 0 0 -0.00427575 0 0 2 0 0 0 160 C 2 7.52339 10 10 0 0 0 -0.000613846 0 0 1 3 0 0 161 C 3 9.11415 10 10 0 0 0 -5.29177e-06 0 0 2 4 0 0 162 C 4 10.7049 10 10 0 0 0 0.000661472 0 0 3 5 0 0 163 C 5 12.2969 10 10 0 0 0 0.00423342 0 0 4 0 0 0 164 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 165 C 1 5.92946 10 10 0 0 0 -0.00377833 0 0 2 0 0 0 166 C 2 7.52232 10 10 0 0 0 -0.000539761 0 0 1 3 0 0 167 C 3 9.11416 10 10 0 0 0 -8.67362e-20 0 0 2 4 0 0 168 C 4 10.706 10 10 0 0 0 0.000560928 0 0 3 5 0 0 169 C 5 12.2989 10 10 0 0 0 0.00375716 0 0 4 0 0 0 170 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 171 C 1 5.92768 10 10 0 0 0 -0.00333911 0 0 2 0 0 0 172 C 2 7.52137 10 10 0 0 0 -0.00047626 0 0 1 3 0 0 173 C 3 9.11416 10 10 0 0 0 2.64589e-05 0 0 2 4 0 0 174 C 4 10.707 10 10 0 0 0 0.000455092 0 0 3 5 0 0 175 C 5 12.3007 10 10 0 0 0 0.00333382 0 0 4 0 0 0 176 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 177 C 1 5.92611 10 10 0 0 0 -0.00295281 0 0 2 0 0 0 178 C 2 7.52053 10 10 0 0 0 -0.00041805 0 0 1 3 0 0 179 C 3 9.11416 10 10 0 0 0 5.29177e-06 0 0 2 4 0 0 180 C 4 10.7078 10 10 0 0 0 0.000455092 0 0 3 5 0 0 181 C 5 12.3023 10 10 0 0 0 0.00291047 0 0 4 0 0 0 182 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 183 C 1 5.92469 10 10 0 0 0 0 0 0 2 0 0 0 184 C 2 7.51974 10 10 0 0 0 0 0 0 1 3 0 0 185 C 3 9.11405 10 10 0 0 0 0 0 0 2 4 0 0 186 C 4 10.7083 10 10 0 0 0 0 0 0 3 5 0 0 187 C 5 12.3036 10 10 0 0 0 0 0 0 4 0 0 0 -
tests/Python/ForceAnnealing/post/five_carbon_test_no-bondgraph.data
ra6c11a r3e334e 25 25 C 5 12.3968 10 10 0 0 0 -0.0554578 0 0 4 0 0 0 26 26 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 27 C 1 5.98683 10 10 0 0 0 0.09686060 0 2 0 0 028 C 2 7. 76987 10 10 0 0 0 -0.2261760 0 1 3 0 029 C 3 9. 1255 10 10 0 0 0 0.2592810 0 2 4 0 030 C 4 10. 9711 10 10 0 0 0 -0.2274930 0 3 5 0 031 C 5 12.3868 10 10 0 0 0 0.09752740 0 4 0 0 027 C 1 5.98683 10 10 0 0 0 -0.0286179 0 0 2 0 0 0 28 C 2 7.53275 10 10 0 0 0 0.00789532 0 0 1 3 0 0 29 C 3 9.09359 10 10 0 0 0 0.0414187 0 0 2 4 0 0 30 C 4 10.7327 10 10 0 0 0 0.00793237 0 0 3 5 0 0 31 C 5 12.3868 10 10 0 0 0 -0.0286285 0 0 4 0 0 0 32 32 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 33 C 1 5.9 9318 10 10 0 0 0 -0.03108920 0 2 0 0 034 C 2 7.5 3443 10 10 0 0 0 0.06296150 0 1 3 0 035 C 3 9.1 9466 10 10 0 0 0 -0.06376060 0 2 4 0 036 C 4 10.7 344 10 10 0 0 0 0.06300380 0 3 5 0 037 C 5 12.3 932 10 10 0 0 0 -0.03111560 0 4 0 0 033 C 1 5.9762 10 10 0 0 0 -0.0188123 0 0 2 0 0 0 34 C 2 7.54065 10 10 0 0 0 0.0158277 0 0 1 3 0 0 35 C 3 9.13501 10 10 0 0 0 0.00599558 0 0 2 4 0 0 36 C 4 10.7407 10 10 0 0 0 0.0157219 0 0 3 5 0 0 37 C 5 12.3761 10 10 0 0 0 -0.0187329 0 0 4 0 0 0 38 38 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 39 C 1 5.9 9164 10 10 0 0 0 -0.003143310 0 2 0 0 040 C 2 7.5 857 10 10 0 0 0 0.0006614720 0 1 3 0 041 C 3 9.1 8101 10 10 0 0 0 0.004963680 0 2 4 0 042 C 4 10.7 857 10 10 0 0 0 0.0006403040 0 3 5 0 043 C 5 12.3 916 10 10 0 0 0 -0.003122150 0 4 0 0 039 C 1 5.95739 10 10 0 0 0 -0.000523885 0 0 2 0 0 0 40 C 2 7.5564 10 10 0 0 0 -0.00762015 0 0 1 3 0 0 41 C 3 9.14101 10 10 0 0 0 0.0162881 0 0 2 4 0 0 42 C 4 10.7564 10 10 0 0 0 -0.00761486 0 0 3 5 0 0 43 C 5 12.3574 10 10 0 0 0 -0.000529177 0 0 4 0 0 0 44 44 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 45 C 1 5.9 9146 10 10 0 0 0 -0.00276231 0 0 2 0 0 046 C 2 7.5 8624 10 10 0 0 0 0.0005133020 0 1 3 0 047 C 3 9.1 8199 10 10 0 0 0 0.00447684 0 0 2 4 0 048 C 4 10.7 862 10 10 0 0 0 0.0005768030 0 3 5 0 049 C 5 12.3 915 10 10 0 0 0 -0.002804640 0 4 0 0 045 C 1 5.95686 10 10 0 0 0 -0.00295281 0 0 2 0 0 0 46 C 2 7.55128 10 10 0 0 0 0.00253476 0 0 1 3 0 0 47 C 3 9.15049 10 10 0 0 0 0.000846684 0 0 2 4 0 0 48 C 4 10.7513 10 10 0 0 0 0.00253476 0 0 3 5 0 0 49 C 5 12.3569 10 10 0 0 0 -0.00296339 0 0 4 0 0 0 50 50 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 51 C 1 5.9 9021 10 10 0 0 0 -0.001100690 0 2 0 0 052 C 2 7.5 8813 10 10 0 0 0 0.002651180 0 1 3 0 053 C 3 9.1 9106 10 10 0 0 0 -0.001582240 0 2 4 0 054 C 4 10.7 91 10 10 0 0 0 -0.0004974270 0 3 5 0 055 C 5 12.3 9 10 10 0 0 0 0.0005291770 0 4 0 0 051 C 1 5.95623 10 10 0 0 0 -0.00194208 0 0 2 0 0 0 52 C 2 7.55256 10 10 0 0 0 0.00112186 0 0 1 3 0 0 53 C 3 9.15101 10 10 0 0 0 0.0016087 0 0 2 4 0 0 54 C 4 10.7525 10 10 0 0 0 0.00116948 0 0 3 5 0 0 55 C 5 12.3562 10 10 0 0 0 -0.00195796 0 0 4 0 0 0 56 56 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 57 C 1 5.9 8937 10 10 0 0 0 0.0005820950 0 2 0 0 058 C 2 7.5 9047 10 10 0 0 0 -0.001524030 0 1 3 0 059 C 3 9.1 8869 10 10 0 0 0 0.001000150 0 2 4 0 060 C 4 10.7 888 10 10 0 0 0 0.0006826390 0 3 5 0 061 C 5 12.3 90210 10 0 0 0 -0.000740848 0 0 4 0 0 057 C 1 5.955 10 10 0 0 0 -0.000751432 0 0 2 0 0 0 58 C 2 7.55358 10 10 0 0 0 -2.64589e-05 0 0 1 3 0 0 59 C 3 9.15211 10 10 0 0 0 0.00156636 0 0 2 4 0 0 60 C 4 10.7536 10 10 0 0 0 -4.7626e-05 0 0 3 5 0 0 61 C 5 12.355 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 5.9 8966 10 10 0 0 0 -2.64589e-050 0 2 0 0 064 C 2 7.5 8961 10 10 0 0 0 2.64589e-050 0 1 3 0 065 C 3 9.1 8961 10 10 0 0 0 0.000259297 0 0 2 4 0 066 C 4 10.7 901 10 10 0 0 0 -0.0002592970 0 3 5 0 067 C 5 12.3 901 10 10 0 0 0 00 0 4 0 0 063 C 1 5.95425 10 10 0 0 0 -0.000370424 0 0 2 0 0 0 64 C 2 7.55355 10 10 0 0 0 0.000439217 0 0 1 3 0 0 65 C 3 9.15368 10 10 0 0 0 -0.000111127 0 0 2 4 0 0 66 C 4 10.7536 10 10 0 0 0 0.000359841 0 0 3 5 0 0 67 C 5 12.3542 10 10 0 0 0 -0.000317506 0 0 4 0 0 0 68 68 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 69 C 1 5.9 8965 10 10 0 0 0 -1.05835e-05 0 0 2 0 0 070 C 2 7.5 896310 10 0 0 0 0.000169337 0 0 1 3 0 071 C 3 9.1 8993 10 10 0 0 0 -0.0002804640 0 2 4 0 072 C 4 10.7 897 10 10 0 0 0 0.0003333820 0 3 5 0 073 C 5 12.3 901 10 10 0 0 0 -0.0002116710 0 4 0 0 069 C 1 5.95388 10 10 0 0 0 -0.000164045 0 0 2 0 0 0 70 C 2 7.55357 10 10 0 0 0 0.000169337 0 0 1 3 0 0 71 C 3 9.15358 10 10 0 0 0 5.29177e-06 0 0 2 4 0 0 72 C 4 10.7536 10 10 0 0 0 0.00014817 0 0 3 5 0 0 73 C 5 12.3539 10 10 0 0 0 -0.000158753 0 0 4 0 0 0 74 74 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 75 C 1 5.9 8964 10 10 0 0 0 1.35525e-210 0 2 0 0 076 C 2 7.5 896410 10 0 0 0 6.35013e-05 0 0 1 3 0 077 C 3 9.1 8976 10 10 0 0 0 1.05835e-05 0 0 2 4 0 078 C 4 10.7 899 10 10 0 0 0 -2.11671e-05 0 0 3 5 0 079 C 5 12.3 910 10 0 0 0 -5.29177e-05 0 0 4 0 0 075 C 1 5.95372 10 10 0 0 0 -6.8793e-05 0 0 2 0 0 0 76 C 2 7.55359 10 10 0 0 0 6.35013e-05 0 0 1 3 0 0 77 C 3 9.15358 10 10 0 0 0 6.8793e-05 0 0 2 4 0 0 78 C 4 10.7537 10 10 0 0 0 -1.05835e-05 0 0 3 5 0 0 79 C 5 12.3538 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 5.9 8964 10 10 0 0 0 5.29177e-060 0 2 0 0 082 C 2 7.5 8965 10 10 0 0 0 5.82095e-05 0 0 1 3 0 083 C 3 9.1 8977 10 10 0 0 0 5.29177e-060 0 2 4 0 084 C 4 10.7 899 10 10 0 0 0 -1.58753e-05 0 0 3 5 0 085 C 5 12.3 9 10 10 0 0 0 -5.29177e-050 0 4 0 0 081 C 1 5.95365 10 10 0 0 0 -2.64589e-05 0 0 2 0 0 0 82 C 2 7.5536 10 10 0 0 0 2.11671e-05 0 0 1 3 0 0 83 C 3 9.15359 10 10 0 0 0 6.35013e-05 0 0 2 4 0 0 84 C 4 10.7537 10 10 0 0 0 -5.82095e-05 0 0 3 5 0 0 85 C 5 12.3537 10 10 0 0 0 1.35525e-21 0 0 4 0 0 0 86 86 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 87 C 1 5.9 8964 10 10 0 0 0 6.8793e-05 0 0 2 0 0 088 C 2 7.5 8977 10 10 0 0 0 -6.8793e-05 0 0 1 3 0 089 C 3 9.1 8977 10 10 0 0 0 6.8793e-050 0 2 4 0 090 C 4 10.7 899 10 10 0 0 0 -1.58753e-05 0 0 3 5 0 091 C 5 12.3 9 10 10 0 0 0 -5.29177e-050 0 4 0 0 087 C 1 5.95362 10 10 0 0 0 -1.05835e-05 0 0 2 0 0 0 88 C 2 7.5536 10 10 0 0 0 3.70424e-05 0 0 1 3 0 0 89 C 3 9.15365 10 10 0 0 0 2.03288e-21 0 0 2 4 0 0 90 C 4 10.7537 10 10 0 0 0 -2.64589e-05 0 0 3 5 0 0 91 C 5 12.3537 10 10 0 0 0 2.03288e-21 0 0 4 0 0 0 92 92 # ATOMDATA type Id x=3 u=3 F=3 neighbors=4 93 C 1 5.9 896410 10 0 0 0 0 0 0 2 0 0 094 C 2 7.5 8971 10 10 0 0 0 0 0 0 1 3 0 095 C 3 9.1 897810 10 0 0 0 0 0 0 2 4 0 096 C 4 10.7 89910 10 0 0 0 0 0 0 3 5 0 097 C 5 12.3 910 10 0 0 0 0 0 0 4 0 0 093 C 1 5.95361 10 10 0 0 0 0 0 0 2 0 0 0 94 C 2 7.55361 10 10 0 0 0 0 0 0 1 3 0 0 95 C 3 9.15365 10 10 0 0 0 0 0 0 2 4 0 0 96 C 4 10.7536 10 10 0 0 0 0 0 0 3 5 0 0 97 C 5 12.3537 10 10 0 0 0 0 0 0 4 0 0 0 -
tests/Python/ForceAnnealing/testsuite-python-forceannealing-ising.at
ra6c11a r3e334e 44 44 AT_SETUP([Python externalization - Force Annealing with bondgraph on 2-body Ising model]) 45 45 AT_KEYWORDS([python force-annealing ising bondgraph]) 46 AT_SKIP_IF([/bin/true]) 47 #AT_SKIP_IF([../../run ${abs_top_srcdir}/tests/Python/numpy_check.py]) 46 AT_SKIP_IF([../../run ${abs_top_srcdir}/tests/Python/numpy_check.py]) 48 47 49 48 # we use forces from a simple Ising model with 2 "carbon" atoms in a row along the x axis … … 58 57 AT_SETUP([Python externalization - Force Annealing with bondgraph on 5-body Ising model]) 59 58 AT_KEYWORDS([python force-annealing ising bondgraph]) 60 AT_SKIP_IF([/bin/true]) 61 #AT_SKIP_IF([../../run ${abs_top_srcdir}/tests/Python/numpy_check.py]) 59 AT_SKIP_IF([../../run ${abs_top_srcdir}/tests/Python/numpy_check.py]) 62 60 63 61 # we use forces from a simple Ising model with 5 "carbon" atoms in a row along the x axis 64 62 65 63 file=five_carbon_test.data 66 AT_CHECK([../../run ${abs_top_srcdir}/tests/Python/ForceAnnealing/pre/ising_model_chain.py ./$file ./ 155 "1"], 0, [stdout], [ignore])67 AT_CHECK([grep "Largest remaining force components.* e-05" stdout], 0, [ignore], [ignore])64 AT_CHECK([../../run ${abs_top_srcdir}/tests/Python/ForceAnnealing/pre/ising_model_chain.py ./$file ./ 30 5 "1"], 0, [stdout], [ignore]) 65 AT_CHECK([grep "Largest remaining force components.*0.00" stdout], 0, [ignore], [ignore]) 68 66 AT_CHECK([diff $file ${abs_top_srcdir}/tests/Python/ForceAnnealing/post/five_carbon_test_bondgraph.data], 0, [ignore], [ignore]) 69 67 -
tests/integration/StructureOptimization/testsuite-integration-structureoptimization-ethane.at
ra6c11a r3e334e 21 21 AT_SETUP([Structure Optimization - ethane]) 22 22 AT_KEYWORDS([optimize-structure ethane]) 23 AT_SKIP_IF([/bin/true])24 23 25 24 # check that ports are unique over all tests such that they may run in parallel -
tests/integration/StructureOptimization/testsuite-integration-structureoptimization-methane.at
ra6c11a r3e334e 21 21 AT_SETUP([Structure Optimization - methane]) 22 22 AT_KEYWORDS([optimize-structure methane]) 23 AT_SKIP_IF([/bin/true])24 23 25 24 # check that ports are unique over all tests such that they may run in parallel … … 73 72 components=`grep "at step #30 are (.*,.*,.*)" stdout | sed -e "s#.*(\(.*\),\(.*\),\(.*\)).*#\1\t\2\t\3#"` 74 73 echo "remaining components are ($components)" 75 threshold=" 1.2e-3"76 AT_CHECK([echo "$components" | awk -v threshold="$threshold" -F"\t" '{ for (i=0;i<3;++i) { if (( $i > threshold) || ($i < -threshold)) exit 5} }'], 0, [ignore], [ignore], [kill $server_pid $worker_pid])74 threshold="2e-4" 75 AT_CHECK([echo "$components" | awk -v threshold="$threshold" -F"\t" '{ for (i=0;i<3;++i) { if ((($i+0.) > (threshold+0.)) || (($i+0.) < (-threshold+0.))) exit 5} }'], 0, [ignore], [ignore], [kill $server_pid $worker_pid]) 77 76 78 77 # send removeall to server such that all workers shutdown -
tests/integration/StructureOptimization/testsuite-integration-structureoptimization-water.at
ra6c11a r3e334e 21 21 AT_SETUP([Structure Optimization - water]) 22 22 AT_KEYWORDS([optimize-structure water]) 23 AT_SKIP_IF([/bin/true])24 23 25 24 # check that ports are unique over all tests such that they may run in parallel … … 73 72 components=`grep "at step #30 are (.*,.*,.*)" stdout | sed -e "s#.*(\(.*\),\(.*\),\(.*\)).*#\1\t\2\t\3#"` 74 73 echo "remaining components are ($components)" 75 threshold=" 6e-4"76 AT_CHECK([echo "$components" | awk -v threshold="$threshold" -F"\t" '{ for (i=0;i<3;++i) { if (( $i > threshold) || ($i < -threshold)) exit 5} }'], 0, [ignore], [ignore], [kill $server_pid $worker_pid])74 threshold="3e-5" 75 AT_CHECK([echo "$components" | awk -v threshold="$threshold" -F"\t" '{ for (i=0;i<3;++i) { if ((($i+0.) > (threshold+0.)) || (($i+0.) < (-threshold+0.))) exit 5} }'], 0, [ignore], [ignore], [kill $server_pid $worker_pid]) 77 76 78 77 # send removeall to server such that all workers shutdown -
tests/integration/testsuite-integration.at
ra6c11a r3e334e 25 25 26 26 # check integration of structure optimization 27 #m4_include([StructureOptimization/testsuite-integration-structureoptimization.at])27 m4_include([StructureOptimization/testsuite-integration-structureoptimization.at]) 28 28 29 29 # check integration of potential fitting
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