[ViewVC] Diff of: OpenMD/branches/development/src/brains/SimCreator.cpp

Comparing branches/development/src/brains/SimCreator.cpp (file contents):
Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC vs.
Revision 1715 by gezelter, Tue May 22 21:55:31 2012 UTC

+ * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
+ * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
-<
+ * [4]  Vardeman & Gezelter, in progress (2009).
->
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
->
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
+ */
+/**
+#include "antlr/MismatchedTokenException.hpp"
+#include "antlr/NoViableAltForCharException.hpp"
+#include "antlr/NoViableAltException.hpp"
-+
-+
+#include "types/DirectionalAdapter.hpp"
-+
+#include "types/MultipoleAdapter.hpp"
-+
+#include "types/EAMAdapter.hpp"
-+
+#include "types/SuttonChenAdapter.hpp"
-+
+#include "types/PolarizableAdapter.hpp"
-+
+#include "types/FixedChargeAdapter.hpp"
-+
+#include "types/FluctuatingChargeAdapter.hpp"
+#ifdef IS_MPI
+#include "mpi.h"
+    //create the molecules
+    createMolecules(info);
-+
+    //find the storage layout
-+
-+
+    int storageLayout = computeStorageLayout(info);
-+
+    //allocate memory for DataStorage(circular reference, need to
+    //break it)
-<
+    info->setSnapshotManager(new SimSnapshotManager(info));
->
+    info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
+    //set the global index of atoms, rigidbodies and cutoffgroups
+    //(only need to be set once, the global index will never change
+    } //end for(int i=0)
-+
+  int SimCreator::computeStorageLayout(SimInfo* info) {
-+
-+
+    Globals* simParams = info->getSimParams();
-+
+    int nRigidBodies = info->getNGlobalRigidBodies();
-+
+    set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
-+
+    set<AtomType*>::iterator i;
-+
+    bool hasDirectionalAtoms = false;
-+
+    bool hasFixedCharge = false;
-+
+    bool hasMultipoles = false;
-+
+    bool hasPolarizable = false;
-+
+    bool hasFluctuatingCharge = false;
-+
+    bool hasMetallic = false;
-+
+    int storageLayout = 0;
-+
+    storageLayout |= DataStorage::dslPosition;
-+
+    storageLayout |= DataStorage::dslVelocity;
-+
+    storageLayout |= DataStorage::dslForce;
-+
-+
+    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
-+
-+
+      DirectionalAdapter da = DirectionalAdapter( (*i) );
-+
+      MultipoleAdapter ma = MultipoleAdapter( (*i) );
-+
+      EAMAdapter ea = EAMAdapter( (*i) );
-+
+      SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
-+
+      PolarizableAdapter pa = PolarizableAdapter( (*i) );
-+
+      FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
-+
+      FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
-+
-+
+      if (da.isDirectional()){
-+
+        hasDirectionalAtoms = true;
-+
+      }
-+
+      if (ma.isMultipole()){
-+
+        hasMultipoles = true;
-+
+      }
-+
+      if (ea.isEAM() || sca.isSuttonChen()){
-+
+        hasMetallic = true;
-+
+      }
-+
+      if ( fca.isFixedCharge() ){
-+
+        hasFixedCharge = true;
-+
+      }
-+
+      if ( fqa.isFluctuatingCharge() ){
-+
+        hasFluctuatingCharge = true;
-+
+      }
-+
+      if ( pa.isPolarizable() ){
-+
+        hasPolarizable = true;
-+
+      }
-+
+    }
-+
-+
+    if (nRigidBodies > 0 || hasDirectionalAtoms) {
-+
+      storageLayout |= DataStorage::dslAmat;
-+
+      if(storageLayout & DataStorage::dslVelocity) {
-+
+        storageLayout |= DataStorage::dslAngularMomentum;
-+
+      }
-+
+      if (storageLayout & DataStorage::dslForce) {
-+
+        storageLayout |= DataStorage::dslTorque;
-+
+      }
-+
+    }
-+
+    if (hasMultipoles) {
-+
+      storageLayout |= DataStorage::dslElectroFrame;
-+
+    }
-+
+    if (hasFixedCharge || hasFluctuatingCharge) {
-+
+      storageLayout |= DataStorage::dslSkippedCharge;
-+
+    }
-+
+    if (hasMetallic) {
-+
+      storageLayout |= DataStorage::dslDensity;
-+
+      storageLayout |= DataStorage::dslFunctional;
-+
+      storageLayout |= DataStorage::dslFunctionalDerivative;
-+
+    }
-+
+    if (hasPolarizable) {
-+
+      storageLayout |= DataStorage::dslElectricField;
-+
+    }
-+
+    if (hasFluctuatingCharge){
-+
+      storageLayout |= DataStorage::dslFlucQPosition;
-+
+      if(storageLayout & DataStorage::dslVelocity) {
-+
+        storageLayout |= DataStorage::dslFlucQVelocity;
-+
+      }
-+
+      if (storageLayout & DataStorage::dslForce) {
-+
+        storageLayout |= DataStorage::dslFlucQForce;
-+
+      }
-+
+    }
-+
-+
+    // if the user has asked for them, make sure we've got the memory for the
-+
+    // objects defined.
-+
-+
+    if (simParams->getOutputParticlePotential()) {
-+
+      storageLayout |= DataStorage::dslParticlePot;
-+
+    }
-+
+    if (simParams->getOutputElectricField()) {
-+
+      storageLayout |= DataStorage::dslElectricField;
-+
+    }
-+
+    if (simParams->getOutputFluctuatingCharges()) {
-+
+      storageLayout |= DataStorage::dslFlucQPosition;
-+
+      storageLayout |= DataStorage::dslFlucQVelocity;
-+
+      storageLayout |= DataStorage::dslFlucQForce;
-+
+    }
-+
-+
+    return storageLayout;
-+
+  }
-+
+  void SimCreator::setGlobalIndex(SimInfo *info) {
+    SimInfo::MoleculeIterator mi;
+    Molecule::AtomIterator ai;

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Comparing branches/development/src/brains/SimCreator.cpp (file contents): Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC vs. Revision 1715 by gezelter, Tue May 22 21:55:31 2012 UTC

Diff Legend

Comparing branches/development/src/brains/SimCreator.cpp (file contents):
Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC vs.
Revision 1715 by gezelter, Tue May 22 21:55:31 2012 UTC