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

Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1467 by gezelter, Sat Jul 17 15:33:03 2010 UTC vs.
Revision 1616 by gezelter, Tue Aug 30 15:45:35 2011 UTC

+ * @version 1.0
+ */
-+
+#include "brains/ForceManager.hpp"
+#include "primitives/Molecule.hpp"
-–
+#include "UseTheForce/doForces_interface.h"
+#define __OPENMD_C
-–
+#include "UseTheForce/DarkSide/fInteractionMap.h"
+#include "utils/simError.h"
+#include "primitives/Bond.hpp"
+#include "primitives/Bend.hpp"
+#include "primitives/Torsion.hpp"
+#include "primitives/Inversion.hpp"
-<
+#include "nonbonded/LJ.hpp"
->
+#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) {
-+
+    forceField_ = info_->getForceField();
-+
+    interactionMan_ = new InteractionManager();
-+
+    fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
-+
+  }
-<
+  void ForceManager::calcForces() {
->
+  /**
->
+   * 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() {
-<
+    if (!info_->isFortranInitialized()) {
-<
+      info_->update();
->
+    Globals* simParams_ = info_->getSimParams();
->
+    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
->
+    int mdFileVersion;
->
->
+    if (simParams_->haveMDfileVersion())
->
+      mdFileVersion = simParams_->getMDfileVersion();
->
+    else
->
+      mdFileVersion = 0;
->
->
+    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;
-+
-+
+    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 {
-+
+      if (mdFileVersion > 1) {
-+
+        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;
-+
+      } else {
-+
+        // handle the case where the old file version was in play
-+
+        // (there should be no cutoffMethod, so we have to deduce it
-+
+        // from other data).
-+
-+
+        sprintf(painCave.errMsg,
-+
+                "ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
-+
+                "\tOpenMD found a file which does not set a cutoffMethod.\n"
-+
+                "\tOpenMD will attempt to deduce a cutoffMethod using the\n"
-+
+                "\tbehavior of the older (version 1) code.  To remove this\n"
-+
+                "\twarning, add an explicit cutoffMethod and change the top\n"
-+
+                "\tof the file so that it begins with <OpenMD version=2>\n");
-+
+        painCave.isFatal = 0;
-+
+        painCave.severity = OPENMD_WARNING;
-+
+        simError();
-+
-+
+        // The old file version tethered the shifting behavior to the
-+
+        // electrostaticSummationMethod keyword.
-+
-+
+        if (simParams_->haveElectrostaticSummationMethod()) {
-+
+          std::string myMethod = simParams_->getElectrostaticSummationMethod();
-+
+          toUpper(myMethod);
-+
-+
+          if (myMethod == "SHIFTED_POTENTIAL") {
-+
+            cutoffMethod_ = SHIFTED_POTENTIAL;
-+
+          } else if (myMethod == "SHIFTED_FORCE") {
-+
+            cutoffMethod_ = SHIFTED_FORCE;
-+
+          }
-+
-+
+          if (simParams_->haveSwitchingRadius())
-+
+            rSwitch_ = simParams_->getSwitchingRadius();
-+
-+
+          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
-+
+            if (simParams_->haveSwitchingRadius()){
-+
+              sprintf(painCave.errMsg,
-+
+                      "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
-+
+                      "\tA value was set for the switchingRadius\n"
-+
+                      "\teven though the electrostaticSummationMethod was\n"
-+
+                      "\tset to %s\n", myMethod.c_str());
-+
+              painCave.severity = OPENMD_WARNING;
-+
+              painCave.isFatal = 1;
-+
+              simError();
-+
+            }
-+
+          }
-+
+          if (abs(rCut_ - rSwitch_) < 0.0001) {
-+
+            if (cutoffMethod_ == SHIFTED_FORCE) {
-+
+              sprintf(painCave.errMsg,
-+
+                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
-+
+                      "\tcutoffRadius and switchingRadius are set to the\n"
-+
+                      "\tsame value.  OpenMD will use shifted force\n"
-+
+                      "\tpotentials instead of switching functions.\n");
-+
+              painCave.isFatal = 0;
-+
+              painCave.severity = OPENMD_WARNING;
-+
+              simError();
-+
+            } else {
-+
+              cutoffMethod_ = SHIFTED_POTENTIAL;
-+
+              sprintf(painCave.errMsg,
-+
+                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
-+
+                      "\tcutoffRadius and switchingRadius are set to the\n"
-+
+                      "\tsame value.  OpenMD will use shifted potentials\n"
-+
+                      "\tinstead of switching functions.\n");
-+
+              painCave.isFatal = 0;
-+
+              painCave.severity = OPENMD_WARNING;
-+
+              simError();
-+
+            }
-+
+          }
-+
+        }
-+
+      }
-+
+    }
-+
-+
+    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_;
-+
+    }
-<
+    if (!NBforcesInitialized_) {
-<
+      LJ* lj = new LJ(info_->getForceField());
-<
+      lj->initialize();
->
+    // 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_);
-+
+  }
-<
+    preCalculation();
->
->
->
->
+  void ForceManager::initialize() {
->
->
+    if (!info_->isTopologyDone()) {
->
->
+      info_->update();
->
+      interactionMan_->setSimInfo(info_);
->
+      interactionMan_->initialize();
->
->
+      // 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();
-<
+    calcShortRangeInteraction();
->
+    // 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);
-<
+    calcLongRangeInteraction();
->
+    electrostaticScale_.reserve(4);
->
+    fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
-<
+    postCalculation();
->
+    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();
-+
+  }
+  void ForceManager::preCalculation() {
+    SimInfo::MoleculeIterator mi;
+    Atom* atom;
+    Molecule::RigidBodyIterator rbIter;
+    RigidBody* rb;
-+
+    Molecule::CutoffGroupIterator ci;
-+
+    CutoffGroup* cg;
+    // forces are zeroed here, before any are accumulated.
-–
+    // NOTE: do not rezero the forces in Fortran.
+    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)) {
->
+          //calculate the center of mass of cutoff group
->
+          cg->updateCOM();
->
+        }
->
+      }
+    // Zero out the stress tensor
-<
+  void ForceManager::calcShortRangeInteraction() {
->
+  void ForceManager::shortRangeInteractions() {
+    Molecule* mol;
+    RigidBody* rb;
+    Bond* bond;
+        RealType currBendPot = bend->getPotential();
+        bendPotential += bend->getPotential();
-<
+        std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
->
+        map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
+        if (i == bendDataSets.end()) {
+          BendDataSet dataSet;
+          dataSet.prev.angle = dataSet.curr.angle = angle;
+          dataSet.prev.potential = dataSet.curr.potential = currBendPot;
+          dataSet.deltaV = 0.0;
-<
+          bendDataSets.insert(std::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;
+        torsion->calcForce(angle);
+        RealType currTorsionPot = torsion->getPotential();
+        torsionPotential += torsion->getPotential();
-<
+        std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
->
+        map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
+        if (i == torsionDataSets.end()) {
+          TorsionDataSet dataSet;
+          dataSet.prev.angle = dataSet.curr.angle = angle;
+          dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
+          dataSet.deltaV = 0.0;
-<
+          torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
->
+          torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
+        }else {
+          i->second.prev.angle = i->second.curr.angle;
+          i->second.prev.potential = i->second.curr.potential;
+                                   i->second.prev.potential);
-<
->
+      for (inversion = mol->beginInversion(inversionIter);
+           inversion != NULL;
+           inversion = mol->nextInversion(inversionIter)) {
+        inversion->calcForce(angle);
+        RealType currInversionPot = inversion->getPotential();
+        inversionPotential += inversion->getPotential();
-<
+        std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
->
+        map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
+        if (i == inversionDataSets.end()) {
+          InversionDataSet dataSet;
+          dataSet.prev.angle = dataSet.curr.angle = angle;
+          dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
+          dataSet.deltaV = 0.0;
-<
+          inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
->
+          inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
+        }else {
+          i->second.prev.angle = i->second.curr.angle;
+          i->second.prev.potential = i->second.curr.potential;
+    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
+    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
+    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
-<
+    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
-<
->
+    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
-<
+  void ForceManager::calcLongRangeInteraction() {
-<
+    Snapshot* curSnapshot;
-<
+    DataStorage* config;
-<
+    RealType* frc;
-<
+    RealType* pos;
-<
+    RealType* trq;
-<
+    RealType* A;
-<
+    RealType* electroFrame;
-<
+    RealType* rc;
-<
+    RealType* particlePot;
-<
-<
+    //get current snapshot from SimInfo
-<
+    curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
-<
-<
+    //get array pointers
-<
+    config = &(curSnapshot->atomData);
-<
+    frc = config->getArrayPointer(DataStorage::dslForce);
-<
+    pos = config->getArrayPointer(DataStorage::dslPosition);
-<
+    trq = config->getArrayPointer(DataStorage::dslTorque);
-<
+    A   = config->getArrayPointer(DataStorage::dslAmat);
-<
+    electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
-<
+    particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
->
+  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;
-<
+    Vector3d com;
-<
+    std::vector<Vector3d> rcGroup;
-<
-<
+    if(info_->getNCutoffGroups() > 0){
-<
->
->
+    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)) {
-<
+          cg->getCOM(com);
-<
+          rcGroup.push_back(com);
->
+          cg->updateCOM();
-<
+      }// end for (mol)
-<
-<
+      rc = rcGroup[0].getArrayPointer();
->
+      }
+    } else {
+      // center of mass of the group is the same as position of the atom
+      // if cutoff group does not exist
-<
+      rc = pos;
->
+      cgConfig->position = config->position;
-+
-+
+    fDecomp_->zeroWorkArrays();
-+
+    fDecomp_->distributeData();
-<
+    //initialize data before passing to fortran
-<
+    RealType longRangePotential[LR_POT_TYPES];
-<
+    RealType lrPot = 0.0;
-<
+    Vector3d totalDipole;
-<
+    int isError = 0;
->
+    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);
-<
+    for (int i=0; i<LR_POT_TYPES;i++){
-<
+      longRangePotential[i]=0.0; //Initialize array
-<
+    }
->
+    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;
-<
+    doForceLoop(pos,
-<
+                rc,
-<
+                A,
-<
+                electroFrame,
-<
+                frc,
-<
+                trq,
-<
+                tau.getArrayPointer(),
-<
+                longRangePotential,
-<
+                particlePot,
-<
+                &isError );
-<
-<
+    if( isError ){
-<
+      sprintf( painCave.errMsg,
-<
+               "Error returned from the fortran force calculation.\n" );
-<
+      painCave.isFatal = 1;
-<
+      simError();
->
+    loopEnd = PAIR_LOOP;
->
+    if (info_->requiresPrepair() ) {
->
+      loopStart = PREPAIR_LOOP;
->
+    } else {
->
+      loopStart = PAIR_LOOP;
-<
+    for (int i=0; i<LR_POT_TYPES;i++){
-<
+      lrPot += longRangePotential[i]; //Quick hack
-<
+    }
-<
-<
+    // grab the simulation box dipole moment if specified
-<
+    if (info_->getCalcBoxDipole()){
-<
+      getAccumulatedBoxDipole(totalDipole.getArrayPointer());
-<
-<
+      curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
-<
+      curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
-<
+      curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
->
->
+    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
->
->
+      if (iLoop == loopStart) {
->
+        bool update_nlist = fDecomp_->checkNeighborList();
->
+        if (update_nlist)
->
+          neighborList = fDecomp_->buildNeighborList();
->
+      }
->
->
+      for (vector<pair<int, int> >::iterator it = neighborList.begin();
->
+             it != neighborList.end(); ++it) {
->
->
+        cg1 = (*it).first;
->
+        cg2 = (*it).second;
->
->
+        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;
->
+                } else {
->
+                  d = fDecomp_->getInteratomicVector(atom1, atom2);
->
+                  curSnapshot->wrapVector( d );
->
+                  r2 = d.lengthSquare();
->
+                  idat.d = &d;
->
+                  idat.r2 = &r2;
->
+                }
->
->
+                r = sqrt( *(idat.r2) );
->
+                idat.rij = &r;
->
->
+                if (iLoop == PREPAIR_LOOP) {
->
+                  interactionMan_->doPrePair(idat);
->
+                } else {
->
+                  interactionMan_->doPair(idat);
->
+                  fDecomp_->unpackInteractionData(idat, atom1, atom2);
->
+                  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 (!info_->usesAtomicVirial()) {
->
+            //  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[VDW_POT];
-<
+    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
->
+    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
->
+    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];

Diff Legend

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

Comparing branches/development/src/brains/ForceManager.cpp (file contents): Revision 1467 by gezelter, Sat Jul 17 15:33:03 2010 UTC vs. Revision 1616 by gezelter, Tue Aug 30 15:45:35 2011 UTC

Diff Legend

Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1467 by gezelter, Sat Jul 17 15:33:03 2010 UTC vs.
Revision 1616 by gezelter, Tue Aug 30 15:45:35 2011 UTC