Changeset e77580 for src/Dynamics

Timestamp:

Apr 10, 2018, 6:43:29 AM (7 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

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

Children:

355915

Parents:

d3e1d5

git-author:

Frederik Heber <frederik.heber@…> (05/30/17 20:31:38)

git-committer:

Frederik Heber <frederik.heber@…> (04/10/18 06:43:29)

Message:

ForceAnnealing converts atomic forces to bond forces and optimize these.

• the initial idea was using the bond graph (i.e. pushing also the adjacent atoms in order not to ruin the distance to them). However, this falls short when bonds need to be shortened - we update each bond partner twice.
• Therefore, we convert the atomic force to a force per bond via an SVD and shift then both bond partners (and adjacent neighbors) at the same time.

File:

• src/Dynamics/ForceAnnealing.hpp (modified) (2 diffs)

src/Dynamics/ForceAnnealing.hpp

@@ -28 +28 @@
 #include "Helpers/helpers.hpp"
 #include "Helpers/defs.hpp"
+#include "LinearAlgebra/LinearSystemOfEquations.hpp"
+#include "LinearAlgebra/MatrixContent.hpp"
 #include "LinearAlgebra/Vector.hpp"
+#include "LinearAlgebra/VectorContent.hpp"
 #include "Thermostats/ThermoStatContainer.hpp"
 #include "Thermostats/Thermostat.hpp"
@@ -232 +235 @@
     BreadthFirstSearchGatherer NodeGatherer(BGcreator);
 
-    std::map<atomId_t, Vector> GatheredUpdates; //!< gathers all updates which are applied at the end
+    /// We assume that a force is local, i.e. a bond is too short yet and hence
+    /// the atom needs to be moved. However, all the adjacent (bound) atoms might
+    /// already be at the perfect distance. If we just move the atom alone, we ruin
+    /// all the other bonds. Hence, it would be sensible to move every atom found
+    /// through the bond graph in the direction of the force as well by the same
+    /// PositionUpdate. This is almost what we are going to do.
+
+    /// One more issue is: If we need to shorten bond, then we use the PositionUpdate
+    /// also on the the other bond partner already. This is because it is in the
+    /// direction of the bond. Therefore, the update is actually performed twice on
+    /// each bond partner, i.e. the step size is twice as large as it should be.
+    /// This problem only occurs when bonds need to be shortened, not when they
+    /// need to be made longer (then the force vector is facing the other
+    /// direction than the bond vector).
+    /// As a remedy we need to know the forces "per bond" and not per atom.
+    /// In effect, the gradient is the error per atom. However, we need an
+    /// error per bond. To this end, we set up a matrix A that translate the
+    /// vector of bond energies into a vector of atomic force component and
+    /// then we simply solve the linear system (inverse problem) via an SVD
+    /// and use the bond gradients to get the PositionUpdate for both bond
+    /// partners at the same time when we go through all bonds.
+
+    // gather/enumerate all bonds
+    std::set<bond::ptr> allbonds;
+    std::vector<atomId_t> allatomids;
     for(typename AtomSetMixin<T>::iterator iter = AtomicForceManipulator<T>::atoms.begin();
         iter != AtomicForceManipulator<T>::atoms.end(); ++iter) {
-      // atom's force vector gives steepest descent direction
-      const Vector oldPosition = (*iter)->getPositionAtStep(CurrentTimeStep-1 >= 0 ? CurrentTimeStep - 1 : 0);
-      const Vector currentPosition = (*iter)->getPositionAtStep(CurrentTimeStep);
-      const Vector oldGradient = (*iter)->getAtomicForceAtStep(CurrentTimeStep-1 >= 0 ? CurrentTimeStep - 1 : 0);
-      const Vector currentGradient = (*iter)->getAtomicForceAtStep(CurrentTimeStep);
-      LOG(4, "DEBUG: Force for atom " << **iter << " is " << currentGradient);
-
-      // we use Barzilai-Borwein update with position reversed to get descent
-      const double stepwidth = getBarzilaiBorweinStepwidth(
-          currentPosition - oldPosition, currentGradient - oldGradient);
-      const Vector PositionUpdate = stepwidth * currentGradient;
-      LOG(3, "DEBUG: Update would be " << stepwidth << "*" << currentGradient << " = " << PositionUpdate);
-
-//      // add update to central atom
-//      const atomId_t atomid = (*iter)->getId();
-//      if (GatheredUpdates.count(atomid)) {
-//        GatheredUpdates[atomid] += PositionUpdate;
-//      } else
-//        GatheredUpdates.insert( std::make_pair(atomid, PositionUpdate) );
-
-      // We assume that a force is local, i.e. a bond is too short yet and hence
-      // the atom needs to be moved. However, all the adjacent (bound) atoms might
-      // already be at the perfect distance. If we just move the atom alone, we ruin
-      // all the other bonds. Hence, it would be sensible to move every atom found
-      // through the bond graph in the direction of the force as well by the same
-      // PositionUpdate. This is just what we are going to do.
-
-      /// get all nodes from bonds in the direction of the current force
-
-      // remove edges facing in the wrong direction
-      std::vector<bond::ptr> removed_bonds;
-      const BondList& ListOfBonds = (*iter)->getListOfBonds();
+      const atom &walker = *(*iter);
+      allatomids.push_back(walker.getId());
+      const BondList& ListOfBonds = walker.getListOfBonds();
       for(BondList::const_iterator bonditer = ListOfBonds.begin();
           bonditer != ListOfBonds.end(); ++bonditer) {
-        const bond &current_bond = *(*bonditer);
-        LOG(2, "DEBUG: Looking at bond " << current_bond);
-        Vector BondVector = (*iter)->getPositionAtStep(CurrentTimeStep);
-        BondVector -= ((*iter)->getId() == current_bond.rightatom->getId())
-            ? current_bond.rightatom->getPositionAtStep(CurrentTimeStep) : current_bond.leftatom->getPositionAtStep(CurrentTimeStep);
-        BondVector.Normalize();
-        if (BondVector.ScalarProduct(currentGradient) < 0) {
-          removed_bonds.push_back(*bonditer);
-#ifndef NDEBUG
-          const bool status =
-#endif
-              BGcreator.removeEdge(current_bond.leftatom->getId(), current_bond.rightatom->getId());
-          ASSERT( status, "ForceAnnealing() - edge to found bond is not present?");
-        }
-      }
-      BoostGraphHelpers::Nodeset_t bondside_set = NodeGatherer((*iter)->getId(), max_distance);
-      const BreadthFirstSearchGatherer::distance_map_t &distance_map = NodeGatherer.getDistances();
-      std::sort(bondside_set.begin(), bondside_set.end());
-      // re-add those edges
-      for (std::vector<bond::ptr>::const_iterator bonditer = removed_bonds.begin();
-          bonditer != removed_bonds.end(); ++bonditer)
-        BGcreator.addEdge((*bonditer)->leftatom->getId(), (*bonditer)->rightatom->getId());
-
-      // apply PositionUpdate to all nodes in the bondside_set
-      for (BoostGraphHelpers::Nodeset_t::const_iterator setiter = bondside_set.begin();
-          setiter != bondside_set.end(); ++setiter) {
-        const BreadthFirstSearchGatherer::distance_map_t::const_iterator diter
-          = distance_map.find(*setiter);
-        ASSERT( diter != distance_map.end(),
-            "ForceAnnealing() - could not find distance to an atom.");
-        const double factor = pow(damping_factor, diter->second);
-        LOG(3, "DEBUG: Update for atom #" << *setiter << " will be "
-            << factor << "*" << PositionUpdate);
-        if (GatheredUpdates.count((*setiter))) {
-          GatheredUpdates[(*setiter)] += factor*PositionUpdate;
-        } else {
-          GatheredUpdates.insert(
-              std::make_pair(
-                  (*setiter),
-                  factor*PositionUpdate) );
-        }
+        const bond::ptr &current_bond = *bonditer;
+        allbonds.insert(current_bond);
       }
 
       // extract largest components for showing progress of annealing
+      const Vector currentGradient = (*iter)->getAtomicForce();
       for(size_t i=0;i<NDIM;++i)
         maxComponents[i] = std::max(maxComponents[i], fabs(currentGradient[i]));
-    }
+
+      // reset force vector for next step except on final one
+      if (currentStep != maxSteps)
+        (*iter)->setAtomicForce(zeroVec);
+    }
+    std::sort(allatomids.begin(), allatomids.end());
+    // converting set back to vector is fastest when requiring sorted and unique,
+    // see https://stackoverflow.com/questions/1041620/whats-the-most-efficient-way-to-erase-duplicates-and-sort-a-vector
+    typedef std::vector<bond::ptr> bondvector_t;
+    bondvector_t bondvector( allbonds.begin(), allbonds.end() );
+
+    // setup matrix A given the enumerated bonds
+    LinearSystemOfEquations lseq(AtomicForceManipulator<T>::atoms.size(), bondvector.size());
+    for (size_t i = 0;i<bondvector.size();++i) {
+      const atom* bondatom[2] = {
+           bondvector[i]->leftatom,
+           bondvector[i]->rightatom
+      };
+      size_t index[2];
+      for (size_t n=0;n<2;++n) {
+        const std::pair<std::vector<atomId_t>::iterator, std::vector<atomId_t>::iterator> atomiditer =
+            std::equal_range(allatomids.begin(), allatomids.end(), bondatom[n]->getId());
+        index[n] = std::distance(allatomids.begin(), atomiditer.first);
+        (*lseq.A).at(index[0],index[1]) = 1.;
+        (*lseq.A).at(index[1],index[0]) = 1.;
+      }
+    }
+    lseq.SetSymmetric(true);
+
+    // for each component and for current and last time step
+    // solve Ax=y with given A and y being the vectorized atomic force
+    double *tmpforces = new double[bondvector.size()];
+    double *bondforces = new double[bondvector.size()];
+    double *oldbondforces = new double[bondvector.size()];
+    double *bondforceref[2] = {
+        bondforces,
+        oldbondforces
+    };
+    for (size_t n=0;n<bondvector.size();++n) {
+      bondforces[n] = 0.;
+      oldbondforces[n] = 0.;
+    }
+    for (size_t timestep = 0; timestep <= 1; ++timestep) {
+      for (size_t component = 0; component < NDIM; ++component) {
+        for(typename AtomSetMixin<T>::iterator iter = AtomicForceManipulator<T>::atoms.begin();
+            iter != AtomicForceManipulator<T>::atoms.end(); ++iter) {
+          const atom &walker = *(*iter);
+          const std::pair<std::vector<atomId_t>::iterator, std::vector<atomId_t>::iterator> atomiditer =
+              std::equal_range(allatomids.begin(), allatomids.end(), walker.getId());
+          const size_t i = std::distance(allatomids.begin(), atomiditer.first);
+        (*lseq.b).at(i) = timestep == 0 ?
+            walker.getAtomicForce()[component] :
+            walker.getAtomicForceAtStep(CurrentTimeStep-2 >= 0 ? CurrentTimeStep - 2 : 0)[component];
+      }
+      lseq.GetSolutionAsArray(tmpforces);
+      for (size_t i = 0;i<bondvector.size();++i)
+        bondforceref[timestep][i] += tmpforces[i];
+      }
+    }
+
+    // step through each bond and shift the atoms
+    std::map<atomId_t, Vector> GatheredUpdates; //!< gathers all updates which are applied at the end
+    for (size_t i = 0;i<bondvector.size();++i) {
+      const atom* bondatom[2] = {
+           bondvector[i]->leftatom,
+           bondvector[i]->rightatom};
+      const double &bondforce = bondforces[i];
+      const double &oldbondforce = oldbondforces[i];
+      const double bondforcedifference = (bondforce - oldbondforce);
+      Vector BondVector = (bondatom[0]->getPosition() - bondatom[1]->getPosition());
+      BondVector.Normalize();
+      double stepwidth = 0.;
+      for (size_t n=0;n<2;++n) {
+        const Vector oldPosition = bondatom[n]->getPositionAtStep(CurrentTimeStep-2 >= 0 ? CurrentTimeStep - 2 : 0);
+        const Vector currentPosition = bondatom[n]->getPosition();
+        stepwidth += fabs((currentPosition - oldPosition).ScalarProduct(BondVector))/bondforcedifference;
+      }
+      stepwidth = stepwidth/2;
+      Vector PositionUpdate = stepwidth * BondVector;
+      if (fabs(stepwidth) < 1e-10) {
+        // dont' warn in first step, deltat usage normal
+        if (currentStep != 1)
+          ELOG(1, "INFO: Barzilai-Borwein stepwidth is zero, using deltat " << currentDeltat << " instead.");
+        PositionUpdate = currentDeltat * BondVector;
+      }
+      LOG(3, "DEBUG: Update would be " << PositionUpdate);
+
+      // remove the edge
+#ifndef NDEBUG
+      const bool status =
+#endif
+          BGcreator.removeEdge(bondatom[0]->getId(), bondatom[1]->getId());
+      ASSERT( status, "ForceAnnealing() - edge to found bond is not present?");
+
+      // gather nodes for either atom
+      BoostGraphHelpers::Nodeset_t bondside_set[2];
+      BreadthFirstSearchGatherer::distance_map_t distance_map[2];
+      for (size_t n=0;n<2;++n) {
+        bondside_set[n] = NodeGatherer(bondatom[n]->getId(), max_distance);
+        distance_map[n] = NodeGatherer.getDistances();
+        std::sort(bondside_set[n].begin(), bondside_set[n].end());
+      }
+
+      // re-add edge
+      BGcreator.addEdge(bondatom[0]->getId(), bondatom[1]->getId());
+
+      // add PositionUpdate for all nodes in the bondside_set
+      for (size_t n=0;n<2;++n) {
+        for (BoostGraphHelpers::Nodeset_t::const_iterator setiter = bondside_set[n].begin();
+            setiter != bondside_set[n].end(); ++setiter) {
+          const BreadthFirstSearchGatherer::distance_map_t::const_iterator diter
+            = distance_map[n].find(*setiter);
+          ASSERT( diter != distance_map[n].end(),
+              "ForceAnnealing() - could not find distance to an atom.");
+          const double factor = pow(damping_factor, diter->second);
+          LOG(3, "DEBUG: Update for atom #" << *setiter << " will be "
+              << factor << "*" << PositionUpdate);
+          if (GatheredUpdates.count((*setiter))) {
+            GatheredUpdates[(*setiter)] += factor*PositionUpdate;
+          } else {
+            GatheredUpdates.insert(
+                std::make_pair(
+                    (*setiter),
+                    factor*PositionUpdate) );
+          }
+        }
+        // invert for other atom
+        PositionUpdate *= -1;
+      }
+    }
+
     // apply the gathered updates
     for (std::map<atomId_t, Vector>::const_iterator iter = GatheredUpdates.begin();