[ViewVC] Diff of: OpenMD/branches/devel_omp/src/brains/ForceManager.cpp

Comparing:
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1571 by gezelter, Fri May 27 16:45:44 2011 UTC vs.
branches/devel_omp/src/brains/ForceManager.cpp (file contents), Revision 1595 by chuckv, Tue Jul 19 18:50:04 2011 UTC

+ * @version 1.0
+ */
-+
+#include "brains/ForceManager.hpp"
+#include "primitives/Molecule.hpp"
+#define __OPENMD_C
+#include "nonbonded/NonBondedInteraction.hpp"
+#include "parallel/ForceMatrixDecomposition.hpp"
-+
+#include <cstdio>
-+
+#include <iostream>
-+
+#include <iomanip>
-+
+using namespace std;
+namespace OpenMD {
+  ForceManager::ForceManager(SimInfo * info) : info_(info) {
-<
-<
+    fDecomp_ = new ForceMatrixDecomposition(info_);
->
+    forceField_ = info_->getForceField();
->
+    interactionMan_ = new InteractionManager();
->
+    fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
-+
-+
+  /**
-+
+   * setupCutoffs
-+
+   *
-+
+   * Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
-+
+   * and cutoffPolicy
-+
+   *
-+
+   * cutoffRadius : realType
-+
+   *  If the cutoffRadius was explicitly set, use that value.
-+
+   *  If the cutoffRadius was not explicitly set:
-+
+   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
-+
+   *      No electrostatic atoms?  Poll the atom types present in the
-+
+   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
-+
+   *      Use the maximum suggested value that was found.
-+
+   *
-+
+   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
-+
+   *                        or SHIFTED_POTENTIAL)
-+
+   *      If cutoffMethod was explicitly set, use that choice.
-+
+   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
-+
+   *
-+
+   * cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
-+
+   *      If cutoffPolicy was explicitly set, use that choice.
-+
+   *      If cutoffPolicy was not explicitly set, use TRADITIONAL
-+
+   *
-+
+   * switchingRadius : realType
-+
+   *  If the cutoffMethod was set to SWITCHED:
-+
+   *      If the switchingRadius was explicitly set, use that value
-+
+   *          (but do a sanity check first).
-+
+   *      If the switchingRadius was not explicitly set: use 0.85 *
-+
+   *      cutoffRadius_
-+
+   *  If the cutoffMethod was not set to SWITCHED:
-+
+   *      Set switchingRadius equal to cutoffRadius for safety.
-+
+   */
-+
+  void ForceManager::setupCutoffs() {
-+
-+
+    Globals* simParams_ = info_->getSimParams();
-+
+    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
-+
-+
+    if (simParams_->haveCutoffRadius()) {
-+
+      rCut_ = simParams_->getCutoffRadius();
-+
+    } else {
-+
+      if (info_->usesElectrostaticAtoms()) {
-+
+        sprintf(painCave.errMsg,
-+
+                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
-+
+                "\tOpenMD will use a default value of 12.0 angstroms"
-+
+                "\tfor the cutoffRadius.\n");
-+
+        painCave.isFatal = 0;
-+
+        painCave.severity = OPENMD_INFO;
-+
+        simError();
-+
+        rCut_ = 12.0;
-+
+      } else {
-+
+        RealType thisCut;
-+
+        set<AtomType*>::iterator i;
-+
+        set<AtomType*> atomTypes;
-+
+        atomTypes = info_->getSimulatedAtomTypes();
-+
+        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
-+
+          thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
-+
+          rCut_ = max(thisCut, rCut_);
-+
+        }
-+
+        sprintf(painCave.errMsg,
-+
+                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
-+
+                "\tOpenMD will use %lf angstroms.\n",
-+
+                rCut_);
-+
+        painCave.isFatal = 0;
-+
+        painCave.severity = OPENMD_INFO;
-+
+        simError();
-+
+      }
-+
+    }
-+
-+
+    fDecomp_->setUserCutoff(rCut_);
-+
+    interactionMan_->setCutoffRadius(rCut_);
-+
-+
+    map<string, CutoffMethod> stringToCutoffMethod;
-+
+    stringToCutoffMethod["HARD"] = HARD;
-+
+    stringToCutoffMethod["SWITCHED"] = SWITCHED;
-+
+    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
-+
+    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
-<
+  void ForceManager::calcForces() {
->
+    if (simParams_->haveCutoffMethod()) {
->
+      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
->
+      map<string, CutoffMethod>::iterator i;
->
+      i = stringToCutoffMethod.find(cutMeth);
->
+      if (i == stringToCutoffMethod.end()) {
->
+        sprintf(painCave.errMsg,
->
+                "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
->
+                "\tShould be one of: "
->
+                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
->
+                cutMeth.c_str());
->
+        painCave.isFatal = 1;
->
+        painCave.severity = OPENMD_ERROR;
->
+        simError();
->
+      } else {
->
+        cutoffMethod_ = i->second;
->
+      }
->
+    } else {
->
+      sprintf(painCave.errMsg,
->
+              "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
->
+              "\tOpenMD will use SHIFTED_FORCE.\n");
->
+      painCave.isFatal = 0;
->
+      painCave.severity = OPENMD_INFO;
->
+      simError();
->
+      cutoffMethod_ = SHIFTED_FORCE;
->
+    }
->
->
+    map<string, CutoffPolicy> stringToCutoffPolicy;
->
+    stringToCutoffPolicy["MIX"] = MIX;
->
+    stringToCutoffPolicy["MAX"] = MAX;
->
+    stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
->
->
+    std::string cutPolicy;
->
+    if (forceFieldOptions_.haveCutoffPolicy()){
->
+      cutPolicy = forceFieldOptions_.getCutoffPolicy();
->
+    }else if (simParams_->haveCutoffPolicy()) {
->
+      cutPolicy = simParams_->getCutoffPolicy();
->
+    }
->
->
+    if (!cutPolicy.empty()){
->
+      toUpper(cutPolicy);
->
+      map<string, CutoffPolicy>::iterator i;
->
+      i = stringToCutoffPolicy.find(cutPolicy);
->
->
+      if (i == stringToCutoffPolicy.end()) {
->
+        sprintf(painCave.errMsg,
->
+                "ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
->
+                "\tShould be one of: "
->
+                "MIX, MAX, or TRADITIONAL\n",
->
+                cutPolicy.c_str());
->
+        painCave.isFatal = 1;
->
+        painCave.severity = OPENMD_ERROR;
->
+        simError();
->
+      } else {
->
+        cutoffPolicy_ = i->second;
->
+      }
->
+    } else {
->
+      sprintf(painCave.errMsg,
->
+              "ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
->
+              "\tOpenMD will use TRADITIONAL.\n");
->
+      painCave.isFatal = 0;
->
+      painCave.severity = OPENMD_INFO;
->
+      simError();
->
+      cutoffPolicy_ = TRADITIONAL;
->
+    }
->
->
+    fDecomp_->setCutoffPolicy(cutoffPolicy_);
->
->
+    // create the switching function object:
->
->
+    switcher_ = new SwitchingFunction();
->
->
+    if (cutoffMethod_ == SWITCHED) {
->
+      if (simParams_->haveSwitchingRadius()) {
->
+        rSwitch_ = simParams_->getSwitchingRadius();
->
+        if (rSwitch_ > rCut_) {
->
+          sprintf(painCave.errMsg,
->
+                  "ForceManager::setupCutoffs: switchingRadius (%f) is larger "
->
+                  "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
->
+          painCave.isFatal = 1;
->
+          painCave.severity = OPENMD_ERROR;
->
+          simError();
->
+        }
->
+      } else {
->
+        rSwitch_ = 0.85 * rCut_;
->
+        sprintf(painCave.errMsg,
->
+                "ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
->
+                "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
->
+                "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
->
+        painCave.isFatal = 0;
->
+        painCave.severity = OPENMD_WARNING;
->
+        simError();
->
+      }
->
+    } else {
->
+      if (simParams_->haveSwitchingRadius()) {
->
+        map<string, CutoffMethod>::const_iterator it;
->
+        string theMeth;
->
+        for (it = stringToCutoffMethod.begin();
->
+             it != stringToCutoffMethod.end(); ++it) {
->
+          if (it->second == cutoffMethod_) {
->
+            theMeth = it->first;
->
+            break;
->
+          }
->
+        }
->
+        sprintf(painCave.errMsg,
->
+                "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
->
+                "\tis not set to SWITCHED, so switchingRadius value\n"
->
+                "\twill be ignored for this simulation\n", theMeth.c_str());
->
+        painCave.isFatal = 0;
->
+        painCave.severity = OPENMD_WARNING;
->
+        simError();
->
+      }
->
->
+      rSwitch_ = rCut_;
->
+    }
-+
+    // Default to cubic switching function.
-+
+    sft_ = cubic;
-+
+    if (simParams_->haveSwitchingFunctionType()) {
-+
+      string funcType = simParams_->getSwitchingFunctionType();
-+
+      toUpper(funcType);
-+
+      if (funcType == "CUBIC") {
-+
+        sft_ = cubic;
-+
+      } else {
-+
+        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
-+
+          sft_ = fifth_order_poly;
-+
+        } else {
-+
+          // throw error
-+
+          sprintf( painCave.errMsg,
-+
+                   "ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
-+
+                   "\tswitchingFunctionType must be one of: "
-+
+                   "\"cubic\" or \"fifth_order_polynomial\".",
-+
+                   funcType.c_str() );
-+
+          painCave.isFatal = 1;
-+
+          painCave.severity = OPENMD_ERROR;
-+
+          simError();
-+
+        }
-+
+      }
-+
+    }
-+
+    switcher_->setSwitchType(sft_);
-+
+    switcher_->setSwitch(rSwitch_, rCut_);
-+
+    interactionMan_->setSwitchingRadius(rSwitch_);
-+
+  }
-+
-+
+  void ForceManager::initialize() {
-+
+    if (!info_->isTopologyDone()) {
-+
+      info_->update();
+      interactionMan_->setSimInfo(info_);
+      interactionMan_->initialize();
-<
+      swfun_ = interactionMan_->getSwitchingFunction();
-<
+      info_->prepareTopology();
-<
+      fDecomp_->distributeInitialData();
->
->
+      // We want to delay the cutoffs until after the interaction
->
+      // manager has set up the atom-atom interactions so that we can
->
+      // query them for suggested cutoff values
->
+      setupCutoffs();
->
->
+      info_->prepareTopology();
-+
-+
+    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
-+
+    // Force fields can set options on how to scale van der Waals and
-+
+    // electrostatic interactions for atoms connected via bonds, bends
-+
+    // and torsions in this case the topological distance between
-+
+    // atoms is:
-+
+    // 0 = topologically unconnected
-+
+    // 1 = bonded together
-+
+    // 2 = connected via a bend
-+
+    // 3 = connected via a torsion
-+
-+
+    vdwScale_.reserve(4);
-+
+    fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
-+
-+
+    electrostaticScale_.reserve(4);
-+
+    fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
-+
-+
+    vdwScale_[0] = 1.0;
-+
+    vdwScale_[1] = fopts.getvdw12scale();
-+
+    vdwScale_[2] = fopts.getvdw13scale();
-+
+    vdwScale_[3] = fopts.getvdw14scale();
-+
-+
+    electrostaticScale_[0] = 1.0;
-+
+    electrostaticScale_[1] = fopts.getelectrostatic12scale();
-+
+    electrostaticScale_[2] = fopts.getelectrostatic13scale();
-+
+    electrostaticScale_[3] = fopts.getelectrostatic14scale();
-+
-+
+    fDecomp_->distributeInitialData();
-+
-+
+    initialized_ = true;
-+
-+
+  }
-+
-+
+  void ForceManager::calcForces() {
-+
-+
+    if (!initialized_) initialize();
-+
+    preCalculation();
+    shortRangeInteractions();
-<
+    longRangeInteractions();
-<
+    postCalculation();
-<
->
+//    longRangeInteractions();
->
+    longRangeInteractionsRapaport();
->
+    postCalculation();
+  void ForceManager::preCalculation() {
+    for (mol = info_->beginMolecule(mi); mol != NULL;
+         mol = info_->nextMolecule(mi)) {
-<
+      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
->
+      for(atom = mol->beginAtom(ai); atom != NULL;
->
+          atom = mol->nextAtom(ai)) {
+        atom->zeroForcesAndTorques();
-<
->
+      //change the positions of atoms which belong to the rigidbodies
+      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
+           rb = mol->nextRigidBody(rbIter)) {
+        rb->zeroForcesAndTorques();
-<
->
+      if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
+        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
+            cg = mol->nextCutoffGroup(ci)) {
-<
->
+    // Zero out the stress tensor
+    tau *= 0.0;
+          dataSet.prev.angle = dataSet.curr.angle = angle;
+          dataSet.prev.potential = dataSet.curr.potential = currBendPot;
+          dataSet.deltaV = 0.0;
-<
+          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
->
+          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
->
+                                                                  dataSet));
+        }else {
+          i->second.prev.angle = i->second.curr.angle;
+          i->second.prev.potential = i->second.curr.potential;
+    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
-<
+  void ForceManager::longRangeInteractions() {
->
+  void ForceManager::longRangeInteractionsRapaport() {
-–
+    // some of this initial stuff will go away:
+    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
+    DataStorage* config = &(curSnapshot->atomData);
+    DataStorage* cgConfig = &(curSnapshot->cgData);
-–
+    RealType* frc = config->getArrayPointer(DataStorage::dslForce);
-–
+    RealType* pos = config->getArrayPointer(DataStorage::dslPosition);
-–
+    RealType* trq = config->getArrayPointer(DataStorage::dslTorque);
-–
+    RealType* A = config->getArrayPointer(DataStorage::dslAmat);
-–
+    RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
-–
+    RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
-–
+    RealType* rc;
-<
+    if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
-<
+      rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
->
+    //calculate the center of mass of cutoff group
->
->
+    SimInfo::MoleculeIterator mi;
->
+    Molecule* mol;
->
+    Molecule::CutoffGroupIterator ci;
->
+    CutoffGroup* cg;
->
->
+    if(info_->getNCutoffGroups() > 0){
->
+      for (mol = info_->beginMolecule(mi); mol != NULL;
->
+           mol = info_->nextMolecule(mi)) {
->
+        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
->
+            cg = mol->nextCutoffGroup(ci)) {
->
+          cerr << "branch1\n";
->
+          cerr << "globind = " << cg->getGlobalIndex() << "\n";
->
+          cg->updateCOM();
->
+        }
->
+      }
+    } else {
-<
+      // center of mass of the group is the same as position of the atom
->
+      // center of mass of the group is the same as position of the atom
+      // if cutoff group does not exist
-<
+      rc = pos;
->
+      cerr << "branch2\n";
->
+      cgConfig->position = config->position;
-–
-–
+    //initialize data before passing to fortran
-–
+    RealType longRangePotential[N_INTERACTION_FAMILIES];
-–
+    RealType lrPot = 0.0;
-–
+    int isError = 0;
-<
+    // dangerous to iterate over enums, but we'll live on the edge:
-<
+    for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
-<
+      longRangePotential[i]=0.0; //Initialize array
->
+    fDecomp_->zeroWorkArrays();
->
+    fDecomp_->distributeData();
->
->
+    int cg1, cg2, atom1, atom2, topoDist;
->
+    Vector3d d_grp, dag, d;
->
+    RealType rgrpsq, rgrp, r2, r;
->
+    RealType electroMult, vdwMult;
->
+    RealType vij;
->
+    Vector3d fij, fg, f1;
->
+    tuple3<RealType, RealType, RealType> cuts;
->
+    RealType rCutSq;
->
+    bool in_switching_region;
->
+    RealType sw, dswdr, swderiv;
->
+    vector<int> atomListColumn, atomListRow, atomListLocal;
->
+    InteractionData idat;
->
+    SelfData sdat;
->
+    RealType mf;
->
+    RealType lrPot;
->
+    RealType vpair;
->
+    potVec longRangePotential(0.0);
->
+    potVec workPot(0.0);
->
->
+    int loopStart, loopEnd;
->
->
+    idat.vdwMult = &vdwMult;
->
+    idat.electroMult = &electroMult;
->
+    idat.pot = &workPot;
->
+    sdat.pot = fDecomp_->getEmbeddingPotential();
->
+    idat.vpair = &vpair;
->
+    idat.f1 = &f1;
->
+    idat.sw = &sw;
->
+    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
->
+    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
->
->
+    loopEnd = PAIR_LOOP;
->
+    if (info_->requiresPrepair() ) {
->
+      loopStart = PREPAIR_LOOP;
->
+    } else {
->
+      loopStart = PAIR_LOOP;
-<
+    // new stuff starts here:
->
+    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
-<
+    fDecomp_->distributeData();
-<
-<
+    int cg1, cg2, atom1, atom2;
-<
+    Vector3d d_grp, dag;
-<
+    RealType rgrpsq, rgrp;
->
+      if (iLoop == loopStart) {
->
+        bool update_nlist = fDecomp_->checkNeighborList();
->
+        if (update_nlist)
->
+                neighborMatW = fDecomp_->buildLayerBasedNeighborList();
->
+      }
->
->
+      int i;
->
+#pragma omp parallel for num_threads(2) private(i)
->
+      for(i = 0; i < neighborMatW.size(); ++i)
->
+          for(vector<int>::iterator j = neighborMatW[i].begin(); j != neighborMatW[i].end(); ++j)
->
+                  {
->
+                         cg1 = i;
->
+                         cg2 = *j;
->
->
+                        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
->
->
+                        d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
->
+                        curSnapshot->wrapVector(d_grp);
->
+                        rgrpsq = d_grp.lengthSquare();
->
->
+                        rCutSq = cuts.second;
->
->
+                        if (rgrpsq < rCutSq) {
->
+                          idat.rcut = &cuts.first;
->
+                          if (iLoop == PAIR_LOOP) {
->
+                                vij = 0.0;
->
+                                fij = V3Zero;
->
+                          }
->
->
+                          in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
->
+                                                                                                                 rgrp);
->
->
+                          atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
->
+                          atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
->
->
+                          for (vector<int>::iterator ia = atomListRow.begin();
->
+                                   ia != atomListRow.end(); ++ia) {
->
+                                atom1 = (*ia);
->
->
+                                for (vector<int>::iterator jb = atomListColumn.begin();
->
+                                         jb != atomListColumn.end(); ++jb) {
->
+                                  atom2 = (*jb);
->
->
+                                  if (!fDecomp_->skipAtomPair(atom1, atom2)) {
->
+                                        vpair = 0.0;
->
+                                        workPot = 0.0;
->
+                                        f1 = V3Zero;
->
->
+                                        fDecomp_->fillInteractionData(idat, atom1, atom2);
->
->
+                                        topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
->
+                                        vdwMult = vdwScale_[topoDist];
->
+                                        electroMult = electrostaticScale_[topoDist];
->
->
+                                        if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
->
+                                          idat.d = &d_grp;
->
+                                          idat.r2 = &rgrpsq;
->
+                                          cerr << "dgrp = " << d_grp << "\n";
->
+                                        } else {
->
+                                          d = fDecomp_->getInteratomicVector(atom1, atom2);
->
+                                          curSnapshot->wrapVector( d );
->
+                                          r2 = d.lengthSquare();
->
+                                          cerr << "datm = " << d<< "\n";
->
+                                          idat.d = &d;
->
+                                          idat.r2 = &r2;
->
+                                        }
->
->
+                                        cerr << "idat.d = " << *(idat.d) << "\n";
->
+                                        r = sqrt( *(idat.r2) );
->
+                                        idat.rij = &r;
->
->
+                                        if (iLoop == PREPAIR_LOOP) {
->
+                                          interactionMan_->doPrePair(idat);
->
+                                        } else {
->
+                                          interactionMan_->doPair(idat);
->
+                                          fDecomp_->unpackInteractionData(idat, atom1, atom2);
->
->
+                                          cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << "\n";
->
+                                          vij += vpair;
->
+                                          fij += f1;
->
+                                          tau -= outProduct( *(idat.d), f1);
->
+                                        }
->
+                                  }
->
+                                }
->
+                          }
->
->
+                          if (iLoop == PAIR_LOOP) {
->
+                                if (in_switching_region) {
->
+                                  swderiv = vij * dswdr / rgrp;
->
+                                  fg = swderiv * d_grp;
->
+                                  fij += fg;
->
->
+                                  if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
->
+                                        tau -= outProduct( *(idat.d), fg);
->
+                                  }
->
->
+                                  for (vector<int>::iterator ia = atomListRow.begin();
->
+                                           ia != atomListRow.end(); ++ia) {
->
+                                        atom1 = (*ia);
->
+                                        mf = fDecomp_->getMassFactorRow(atom1);
->
+                                        // fg is the force on atom ia due to cutoff group's
->
+                                        // presence in switching region
->
+                                        fg = swderiv * d_grp * mf;
->
+                                        fDecomp_->addForceToAtomRow(atom1, fg);
->
->
+                                        if (atomListRow.size() > 1) {
->
+                                          if (info_->usesAtomicVirial()) {
->
+                                                // find the distance between the atom
->
+                                                // and the center of the cutoff group:
->
+                                                dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
->
+                                                tau -= outProduct(dag, fg);
->
+                                          }
->
+                                        }
->
+                                  }
->
+                                  for (vector<int>::iterator jb = atomListColumn.begin();
->
+                                           jb != atomListColumn.end(); ++jb) {
->
+                                        atom2 = (*jb);
->
+                                        mf = fDecomp_->getMassFactorColumn(atom2);
->
+                                        // fg is the force on atom jb due to cutoff group's
->
+                                        // presence in switching region
->
+                                        fg = -swderiv * d_grp * mf;
->
+                                        fDecomp_->addForceToAtomColumn(atom2, fg);
->
->
+                                        if (atomListColumn.size() > 1) {
->
+                                          if (info_->usesAtomicVirial()) {
->
+                                                // find the distance between the atom
->
+                                                // and the center of the cutoff group:
->
+                                                dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
->
+                                                tau -= outProduct(dag, fg);
->
+                                          }
->
+                                        }
->
+                                  }
->
+                                }
->
+                                //if (!SIM_uses_AtomicVirial) {
->
+                                //  tau -= outProduct(d_grp, fij);
->
+                                //}
->
+                          }
->
+                        }
->
+                  }
->
->
+      if (iLoop == PREPAIR_LOOP) {
->
+        if (info_->requiresPrepair()) {
->
->
+          fDecomp_->collectIntermediateData();
->
->
+          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
->
+            fDecomp_->fillSelfData(sdat, atom1);
->
+            interactionMan_->doPreForce(sdat);
->
+          }
->
->
+          fDecomp_->distributeIntermediateData();
->
->
+        }
->
+      }
->
->
+    }
->
->
+    fDecomp_->collectData();
->
->
+    if (info_->requiresSelfCorrection()) {
->
->
+      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
->
+        fDecomp_->fillSelfData(sdat, atom1);
->
+        interactionMan_->doSelfCorrection(sdat);
->
+      }
->
->
+    }
->
->
+    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
->
+      *(fDecomp_->getPairwisePotential());
->
->
+    lrPot = longRangePotential.sum();
->
->
+    //store the tau and long range potential
->
+    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
->
+    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
->
+    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
->
+  }
->
->
+  void ForceManager::longRangeInteractions() {
->
->
+    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
->
+    DataStorage* config = &(curSnapshot->atomData);
->
+    DataStorage* cgConfig = &(curSnapshot->cgData);
->
->
+    //calculate the center of mass of cutoff group
->
->
+    SimInfo::MoleculeIterator mi;
->
+    Molecule* mol;
->
+    Molecule::CutoffGroupIterator ci;
->
+    CutoffGroup* cg;
->
->
+    if(info_->getNCutoffGroups() > 0){
->
+      for (mol = info_->beginMolecule(mi); mol != NULL;
->
+           mol = info_->nextMolecule(mi)) {
->
+        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
->
+            cg = mol->nextCutoffGroup(ci)) {
->
+          cerr << "branch1\n";
->
+          cerr << "globind = " << cg->getGlobalIndex() << "\n";
->
+          cg->updateCOM();
->
+        }
->
+      }
->
+    } else {
->
+      // center of mass of the group is the same as position of the atom
->
+      // if cutoff group does not exist
->
+      cerr << "branch2\n";
->
+      cgConfig->position = config->position;
->
+    }
->
->
+    fDecomp_->zeroWorkArrays();
->
+    fDecomp_->distributeData();
->
->
+    int cg1, cg2, atom1, atom2, topoDist;
->
+    Vector3d d_grp, dag, d;
->
+    RealType rgrpsq, rgrp, r2, r;
->
+    RealType electroMult, vdwMult;
+    RealType vij;
-<
+    Vector3d fij, fg;
-<
+    pair<int, int> gtypes;
->
+    Vector3d fij, fg, f1;
->
+    tuple3<RealType, RealType, RealType> cuts;
+    RealType rCutSq;
+    bool in_switching_region;
+    RealType sw, dswdr, swderiv;
+    InteractionData idat;
+    SelfData sdat;
+    RealType mf;
-+
+    RealType lrPot;
-+
+    RealType vpair;
-+
+    potVec longRangePotential(0.0);
-+
+    potVec workPot(0.0);
+    int loopStart, loopEnd;
-+
+    idat.vdwMult = &vdwMult;
-+
+    idat.electroMult = &electroMult;
-+
+    idat.pot = &workPot;
-+
+    sdat.pot = fDecomp_->getEmbeddingPotential();
-+
+    idat.vpair = &vpair;
-+
+    idat.f1 = &f1;
-+
+    idat.sw = &sw;
-+
+    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
-+
+    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
-+
+    loopEnd = PAIR_LOOP;
+    if (info_->requiresPrepair() ) {
+      loopStart = PREPAIR_LOOP;
+    } else {
+      loopStart = PAIR_LOOP;
-<
-<
+    for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
-<
->
->
+    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
->
+      if (iLoop == loopStart) {
+        bool update_nlist = fDecomp_->checkNeighborList();
-<
+        if (update_nlist)
->
+        if (update_nlist)
+          neighborList = fDecomp_->buildNeighborList();
-–
+      }
-<
+      for (vector<pair<int, int> >::iterator it = neighborList.begin();
-<
+             it != neighborList.end(); ++it) {
->
+      }
-+
+      for (vector<pair<int, int> >::iterator it = neighborList.begin();
-+
+             it != neighborList.end(); ++it)
-+
+      {
+        cg1 = (*it).first;
+        cg2 = (*it).second;
-+
-+
+        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
-–
+        gtypes = fDecomp_->getGroupTypes(cg1, cg2);
+        d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
+        curSnapshot->wrapVector(d_grp);
+        rgrpsq = d_grp.lengthSquare();
-–
+        rCutSq = groupCutoffMap[gtypes].first;
-+
+        rCutSq = cuts.second;
-+
+        if (rgrpsq < rCutSq) {
-<
+          *(idat.rcut) = groupCutoffMap[gtypes].second;
->
+          idat.rcut = &cuts.first;
+          if (iLoop == PAIR_LOOP) {
-<
+            vij *= 0.0;
->
+            vij = 0.0;
+            fij = V3Zero;
-<
+          in_switching_region = swfun_->getSwitch(rgrpsq, *(idat.sw), dswdr,
-<
+                                                  rgrp);
->
+          in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
->
+                                                     rgrp);
->
+          atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
+          atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
+            for (vector<int>::iterator jb = atomListColumn.begin();
+                 jb != atomListColumn.end(); ++jb) {
+              atom2 = (*jb);
-<
->
+              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
-+
+                vpair = 0.0;
-+
+                workPot = 0.0;
-+
+                f1 = V3Zero;
-+
-+
+                fDecomp_->fillInteractionData(idat, atom1, atom2);
-<
+                idat = fDecomp_->fillInteractionData(atom1, atom2);
->
+                topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
->
+                vdwMult = vdwScale_[topoDist];
->
+                electroMult = electrostaticScale_[topoDist];
+                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
-<
+                  *(idat.d) = d_grp;
-<
+                  *(idat.r2) = rgrpsq;
->
+                  idat.d = &d_grp;
->
+                  idat.r2 = &rgrpsq;
->
+                  cerr << "dgrp = " << d_grp << "\n";
+                } else {
-<
+                  *(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2);
-<
+                  curSnapshot->wrapVector( *(idat.d) );
-<
+                  *(idat.r2) = idat.d->lengthSquare();
->
+                  d = fDecomp_->getInteratomicVector(atom1, atom2);
->
+                  curSnapshot->wrapVector( d );
->
+                  r2 = d.lengthSquare();
->
+                  cerr << "datm = " << d<< "\n";
->
+                  idat.d = &d;
->
+                  idat.r2 = &r2;
-<
+                *(idat.rij) = sqrt( *(idat.r2) );
->
+                cerr << "idat.d = " << *(idat.d) << "\n";
->
+                r = sqrt( *(idat.r2) );
->
+                idat.rij = &r;
+                if (iLoop == PREPAIR_LOOP) {
+                  interactionMan_->doPrePair(idat);
+                } else {
+                  interactionMan_->doPair(idat);
-<
+                  vij += *(idat.vpair);
-<
+                  fij += *(idat.f1);
-<
+                  tau -= outProduct( *(idat.d), *(idat.f1));
->
+                  fDecomp_->unpackInteractionData(idat, atom1, atom2);
->
->
+                  cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << "\n";
->
+                  vij += vpair;
->
+                  fij += f1;
->
+                  tau -= outProduct( *(idat.d), f1);
+            if (in_switching_region) {
+              swderiv = vij * dswdr / rgrp;
+              fg = swderiv * d_grp;
-–
+              fij += fg;
+              if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
+      if (iLoop == PREPAIR_LOOP) {
-<
+        if (info_->requiresPrepair()) {
->
+        if (info_->requiresPrepair()) {
->
+          fDecomp_->collectIntermediateData();
+          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
-<
+            sdat = fDecomp_->fillSelfData(atom1);
->
+            fDecomp_->fillSelfData(sdat, atom1);
+            interactionMan_->doPreForce(sdat);
-<
+          fDecomp_->distributeIntermediateData();
->
+          fDecomp_->distributeIntermediateData();
->
+    fDecomp_->collectData();
-–
-–
+    if ( info_->requiresSkipCorrection() ) {
-–
-–
+      for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
-–
-–
+        vector<int> skipList = fDecomp_->getSkipsForRowAtom( atom1 );
-–
+        for (vector<int>::iterator jb = skipList.begin();
-–
+             jb != skipList.end(); ++jb) {
-–
-–
+          atom2 = (*jb);
-–
+          idat = fDecomp_->fillSkipData(atom1, atom2);
-–
+          interactionMan_->doSkipCorrection(idat);
-–
-–
+        }
-–
+      }
-–
+    }
-–
+    if (info_->requiresSelfCorrection()) {
+      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
-<
+        sdat = fDecomp_->fillSelfData(atom1);
->
+        fDecomp_->fillSelfData(sdat, atom1);
+        interactionMan_->doSelfCorrection(sdat);
-<
+    // dangerous to iterate over enums, but we'll live on the edge:
-<
+    for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
-<
+      lrPot += longRangePotential[i]; //Quick hack
-<
+    }
-<
->
+    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
->
+      *(fDecomp_->getPairwisePotential());
->
->
+    lrPot = longRangePotential.sum();
->
+    //store the tau and long range potential
+    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
+    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];

Diff Legend

-–
+Removed lines
-+
+Added lines
-<
+Changed lines
->
+Changed lines

Comparing: branches/development/src/brains/ForceManager.cpp (file contents), Revision 1571 by gezelter, Fri May 27 16:45:44 2011 UTC vs. branches/devel_omp/src/brains/ForceManager.cpp (file contents), Revision 1595 by chuckv, Tue Jul 19 18:50:04 2011 UTC

Diff Legend

Comparing:
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1571 by gezelter, Fri May 27 16:45:44 2011 UTC vs.
branches/devel_omp/src/brains/ForceManager.cpp (file contents), Revision 1595 by chuckv, Tue Jul 19 18:50:04 2011 UTC