src/brains/ForceManager.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [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).                        
 */
 
/**
 * @file ForceManager.cpp
 * @author tlin
 * @date 11/09/2004
 * @time 10:39am
 * @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 "parallel/ForceDecomposition.hpp"
//#include "parallel/SerialDecomposition.hpp"

namespace OpenMD {
  
  ForceManager::ForceManager(SimInfo * info) : info_(info), 
                                               NBforcesInitialized_(false) {
#ifdef IS_MPI
    decomp_ = new ForceDecomposition(info_);
#else
    //  decomp_ = new SerialDecomposition(info);
#endif
  }
 
  void ForceManager::calcForces() {
    

    if (!info_->isFortranInitialized()) {
      info_->update();
      nbiMan_->setSimInfo(info_);
      nbiMan_->initialize();
      decomp_->distributeInitialData();
      info_->setupFortran();
    }
    
    preCalculation();   
    calcShortRangeInteraction();
    calcLongRangeInteraction();
    postCalculation();
    
  }
  
  void ForceManager::preCalculation() {
    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::AtomIterator ai;
    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)) {
        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()){
        std::cerr << "should not see me \n";
        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
    tau *= 0.0;
    
  }
  
  void ForceManager::calcShortRangeInteraction() {
    Molecule* mol;
    RigidBody* rb;
    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    Inversion* inversion;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    Molecule::BondIterator bondIter;;
    Molecule::BendIterator  bendIter;
    Molecule::TorsionIterator  torsionIter;
    Molecule::InversionIterator  inversionIter;
    RealType bondPotential = 0.0;
    RealType bendPotential = 0.0;
    RealType torsionPotential = 0.0;
    RealType inversionPotential = 0.0;

    //calculate short range interactions    
    for (mol = info_->beginMolecule(mi); mol != NULL; 
         mol = info_->nextMolecule(mi)) {

      //change the positions of atoms which belong to the rigidbodies
      for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
           rb = mol->nextRigidBody(rbIter)) {
        rb->updateAtoms();
      }

      for (bond = mol->beginBond(bondIter); bond != NULL; 
           bond = mol->nextBond(bondIter)) {
        bond->calcForce();
        bondPotential += bond->getPotential();
      }

      for (bend = mol->beginBend(bendIter); bend != NULL; 
           bend = mol->nextBend(bendIter)) {
        
        RealType angle;
        bend->calcForce(angle);
        RealType currBendPot = bend->getPotential();          
         
        bendPotential += bend->getPotential();
        std::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));
        }else {
          i->second.prev.angle = i->second.curr.angle;
          i->second.prev.potential = i->second.curr.potential;
          i->second.curr.angle = angle;
          i->second.curr.potential = currBendPot;
          i->second.deltaV =  fabs(i->second.curr.potential -  
                                   i->second.prev.potential);
        }
      }
      
      for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; 
           torsion = mol->nextTorsion(torsionIter)) {
        RealType angle;
        torsion->calcForce(angle);
        RealType currTorsionPot = torsion->getPotential();
        torsionPotential += torsion->getPotential();
        std::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));
        }else {
          i->second.prev.angle = i->second.curr.angle;
          i->second.prev.potential = i->second.curr.potential;
          i->second.curr.angle = angle;
          i->second.curr.potential = currTorsionPot;
          i->second.deltaV =  fabs(i->second.curr.potential -  
                                   i->second.prev.potential);
        }      
      }      

      for (inversion = mol->beginInversion(inversionIter); 
           inversion != NULL; 
           inversion = mol->nextInversion(inversionIter)) {
        RealType angle;
        inversion->calcForce(angle);
        RealType currInversionPot = inversion->getPotential();
        inversionPotential += inversion->getPotential();
        std::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));
        }else {
          i->second.prev.angle = i->second.curr.angle;
          i->second.prev.potential = i->second.curr.potential;
          i->second.curr.angle = angle;
          i->second.curr.potential = currInversionPot;
          i->second.deltaV =  fabs(i->second.curr.potential -  
                                   i->second.prev.potential);
        }      
      }      
    }
    
    RealType  shortRangePotential = bondPotential + bendPotential + 
      torsionPotential +  inversionPotential;    
    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
    
  }
  
  void ForceManager::calcLongRangeInteraction() {
    Snapshot* curSnapshot;
    DataStorage* config;
    DataStorage* cgConfig;
    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);
    cgConfig = &(curSnapshot->cgData);
    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);

    if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
      std::cerr << "should not see me \n";
      rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
    } else {
      // center of mass of the group is the same as position of the atom  
      // if cutoff group does not exist
      rc = pos;
    }
    
    //initialize data before passing to fortran
    RealType longRangePotential[LR_POT_TYPES];
    RealType lrPot = 0.0;
    int isError = 0;

    for (int i=0; i<LR_POT_TYPES;i++){
      longRangePotential[i]=0.0; //Initialize array
    }
    
    decomp_->distributeData();

    int nLoops = 1;
    for (int iLoop = 0; iLoop < nLoops; iLoop++) {
      doForceLoop(pos,
                  rc,
                  A,
                  electroFrame,
                  frc,
                  trq,
                  tau.getArrayPointer(),
                  longRangePotential, 
                  particlePot,
                  &isError );   

      if (nLoops > 1) {
        decomp_->collectIntermediateData();
        decomp_->distributeIntermediateData();
      }
    }
   
    decomp_->collectData();

    if( isError ){
      sprintf( painCave.errMsg,
               "Error returned from the fortran force calculation.\n" );
      painCave.isFatal = 1;
      simError();
    }
    for (int i=0; i<LR_POT_TYPES;i++){
      lrPot += longRangePotential[i]; //Quick hack
    }
        
    //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];
  }

  
  void ForceManager::postCalculation() {
    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::RigidBodyIterator rbIter;
    RigidBody* rb;
    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    
    // collect the atomic forces onto rigid bodies
    
    for (mol = info_->beginMolecule(mi); mol != NULL; 
         mol = info_->nextMolecule(mi)) {
      for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
           rb = mol->nextRigidBody(rbIter)) { 
        Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
        tau += rbTau;
      }
    }
    
#ifdef IS_MPI
    Mat3x3d tmpTau(tau);
    MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(), 
                  9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
#endif
    curSnapshot->statData.setTau(tau);
  }

} //end namespace OpenMD
Revision:	1544
Committed:	Fri Mar 18 19:31:52 2011 UTC (14 years, 1 month ago) by gezelter
File size:	12982 byte(s)
Log Message:	More modifications for paralllel rewrite
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	246	*/
41
42	gezelter	507	/**
43			* @file ForceManager.cpp
44			* @author tlin
45			* @date 11/09/2004
46			* @time 10:39am
47			* @version 1.0
48			*/
49	gezelter	246
50			#include "brains/ForceManager.hpp"
51			#include "primitives/Molecule.hpp"
52			#include "UseTheForce/doForces_interface.h"
53	gezelter	1390	#define __OPENMD_C
54	chuckv	664	#include "UseTheForce/DarkSide/fInteractionMap.h"
55	gezelter	246	#include "utils/simError.h"
56	xsun	1215	#include "primitives/Bond.hpp"
57	tim	749	#include "primitives/Bend.hpp"
58	cli2	1275	#include "primitives/Torsion.hpp"
59			#include "primitives/Inversion.hpp"
60	gezelter	1544	#include "parallel/ForceDecomposition.hpp"
61			//#include "parallel/SerialDecomposition.hpp"
62	gezelter	1467
63	gezelter	1390	namespace OpenMD {
64	gezelter	1469
65			ForceManager::ForceManager(SimInfo * info) : info_(info),
66			NBforcesInitialized_(false) {
67	gezelter	1544	#ifdef IS_MPI
68			decomp_ = new ForceDecomposition(info_);
69			#else
70			// decomp_ = new SerialDecomposition(info);
71			#endif
72	gezelter	1469	}
73
74	gezelter	1464	void ForceManager::calcForces() {
75	gezelter	1126
76	gezelter	1535
77	gezelter	246	if (!info_->isFortranInitialized()) {
78	gezelter	507	info_->update();
79	gezelter	1535	nbiMan_->setSimInfo(info_);
80	gezelter	1544	nbiMan_->initialize();
81			decomp_->distributeInitialData();
82	gezelter	1535	info_->setupFortran();
83	gezelter	246	}
84	gezelter	1126
85	gezelter	1544	preCalculation();
86	gezelter	246	calcShortRangeInteraction();
87	gezelter	1464	calcLongRangeInteraction();
88			postCalculation();
89	tim	749
90	gezelter	507	}
91	gezelter	1126
92	gezelter	507	void ForceManager::preCalculation() {
93	gezelter	246	SimInfo::MoleculeIterator mi;
94			Molecule* mol;
95			Molecule::AtomIterator ai;
96			Atom* atom;
97			Molecule::RigidBodyIterator rbIter;
98			RigidBody* rb;
99	gezelter	1540	Molecule::CutoffGroupIterator ci;
100			CutoffGroup* cg;
101	gezelter	246
102			// forces are zeroed here, before any are accumulated.
103			// NOTE: do not rezero the forces in Fortran.
104	chuckv	1245
105	gezelter	1126	for (mol = info_->beginMolecule(mi); mol != NULL;
106			mol = info_->nextMolecule(mi)) {
107	gezelter	507	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
108			atom->zeroForcesAndTorques();
109			}
110	chuckv	1245
111	gezelter	507	//change the positions of atoms which belong to the rigidbodies
112	gezelter	1126	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
113			rb = mol->nextRigidBody(rbIter)) {
114	gezelter	507	rb->zeroForcesAndTorques();
115			}
116	gezelter	1540
117			if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
118			std::cerr << "should not see me \n";
119			for(cg = mol->beginCutoffGroup(ci); cg != NULL;
120			cg = mol->nextCutoffGroup(ci)) {
121			//calculate the center of mass of cutoff group
122			cg->updateCOM();
123			}
124			}
125	gezelter	246	}
126	gezelter	1540
127	gezelter	1126	// Zero out the stress tensor
128			tau *= 0.0;
129
130	gezelter	507	}
131	gezelter	1126
132	gezelter	507	void ForceManager::calcShortRangeInteraction() {
133	gezelter	246	Molecule* mol;
134			RigidBody* rb;
135			Bond* bond;
136			Bend* bend;
137			Torsion* torsion;
138	cli2	1275	Inversion* inversion;
139	gezelter	246	SimInfo::MoleculeIterator mi;
140			Molecule::RigidBodyIterator rbIter;
141			Molecule::BondIterator bondIter;;
142			Molecule::BendIterator bendIter;
143			Molecule::TorsionIterator torsionIter;
144	cli2	1275	Molecule::InversionIterator inversionIter;
145	tim	963	RealType bondPotential = 0.0;
146			RealType bendPotential = 0.0;
147			RealType torsionPotential = 0.0;
148	cli2	1275	RealType inversionPotential = 0.0;
149	gezelter	246
150			//calculate short range interactions
151	gezelter	1126	for (mol = info_->beginMolecule(mi); mol != NULL;
152			mol = info_->nextMolecule(mi)) {
153	gezelter	246
154	gezelter	507	//change the positions of atoms which belong to the rigidbodies
155	gezelter	1126	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
156			rb = mol->nextRigidBody(rbIter)) {
157			rb->updateAtoms();
158	gezelter	507	}
159	gezelter	246
160	gezelter	1126	for (bond = mol->beginBond(bondIter); bond != NULL;
161			bond = mol->nextBond(bondIter)) {
162	tim	749	bond->calcForce();
163			bondPotential += bond->getPotential();
164	gezelter	507	}
165	gezelter	246
166	gezelter	1126	for (bend = mol->beginBend(bendIter); bend != NULL;
167			bend = mol->nextBend(bendIter)) {
168
169			RealType angle;
170			bend->calcForce(angle);
171			RealType currBendPot = bend->getPotential();
172	gezelter	1448
173	gezelter	1126	bendPotential += bend->getPotential();
174			std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
175			if (i == bendDataSets.end()) {
176			BendDataSet dataSet;
177			dataSet.prev.angle = dataSet.curr.angle = angle;
178			dataSet.prev.potential = dataSet.curr.potential = currBendPot;
179			dataSet.deltaV = 0.0;
180			bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
181			}else {
182			i->second.prev.angle = i->second.curr.angle;
183			i->second.prev.potential = i->second.curr.potential;
184			i->second.curr.angle = angle;
185			i->second.curr.potential = currBendPot;
186			i->second.deltaV = fabs(i->second.curr.potential -
187			i->second.prev.potential);
188			}
189	gezelter	507	}
190	gezelter	1126
191			for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
192			torsion = mol->nextTorsion(torsionIter)) {
193	tim	963	RealType angle;
194	gezelter	1126	torsion->calcForce(angle);
195	tim	963	RealType currTorsionPot = torsion->getPotential();
196	gezelter	1126	torsionPotential += torsion->getPotential();
197			std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
198			if (i == torsionDataSets.end()) {
199			TorsionDataSet dataSet;
200			dataSet.prev.angle = dataSet.curr.angle = angle;
201			dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
202			dataSet.deltaV = 0.0;
203			torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
204			}else {
205			i->second.prev.angle = i->second.curr.angle;
206			i->second.prev.potential = i->second.curr.potential;
207			i->second.curr.angle = angle;
208			i->second.curr.potential = currTorsionPot;
209			i->second.deltaV = fabs(i->second.curr.potential -
210			i->second.prev.potential);
211			}
212			}
213	cli2	1275
214			for (inversion = mol->beginInversion(inversionIter);
215			inversion != NULL;
216			inversion = mol->nextInversion(inversionIter)) {
217			RealType angle;
218			inversion->calcForce(angle);
219			RealType currInversionPot = inversion->getPotential();
220			inversionPotential += inversion->getPotential();
221			std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
222			if (i == inversionDataSets.end()) {
223			InversionDataSet dataSet;
224			dataSet.prev.angle = dataSet.curr.angle = angle;
225			dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
226			dataSet.deltaV = 0.0;
227			inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
228			}else {
229			i->second.prev.angle = i->second.curr.angle;
230			i->second.prev.potential = i->second.curr.potential;
231			i->second.curr.angle = angle;
232			i->second.curr.potential = currInversionPot;
233			i->second.deltaV = fabs(i->second.curr.potential -
234			i->second.prev.potential);
235			}
236			}
237	gezelter	246	}
238
239	gezelter	1126	RealType shortRangePotential = bondPotential + bendPotential +
240	cli2	1275	torsionPotential + inversionPotential;
241	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
242			curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
243	tim	665	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
244			curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
245			curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
246	cli2	1275	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
247	tim	665
248	gezelter	507	}
249	gezelter	1126
250	gezelter	1464	void ForceManager::calcLongRangeInteraction() {
251	gezelter	246	Snapshot* curSnapshot;
252			DataStorage* config;
253	gezelter	1540	DataStorage* cgConfig;
254	tim	963	RealType* frc;
255			RealType* pos;
256			RealType* trq;
257			RealType* A;
258			RealType* electroFrame;
259			RealType* rc;
260	chuckv	1245	RealType* particlePot;
261	gezelter	246
262			//get current snapshot from SimInfo
263			curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
264	gezelter	1126
265	gezelter	246	//get array pointers
266			config = &(curSnapshot->atomData);
267	gezelter	1540	cgConfig = &(curSnapshot->cgData);
268	gezelter	246	frc = config->getArrayPointer(DataStorage::dslForce);
269			pos = config->getArrayPointer(DataStorage::dslPosition);
270			trq = config->getArrayPointer(DataStorage::dslTorque);
271			A = config->getArrayPointer(DataStorage::dslAmat);
272			electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
273	chuckv	1245	particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
274	gezelter	246
275	gezelter	1540	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
276			std::cerr << "should not see me \n";
277			rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
278	gezelter	246	} else {
279	gezelter	1126	// center of mass of the group is the same as position of the atom
280			// if cutoff group does not exist
281	gezelter	507	rc = pos;
282	gezelter	246	}
283	gezelter	1126
284	gezelter	246	//initialize data before passing to fortran
285	tim	963	RealType longRangePotential[LR_POT_TYPES];
286			RealType lrPot = 0.0;
287	gezelter	246	int isError = 0;
288
289	chuckv	664	for (int i=0; i<LR_POT_TYPES;i++){
290			longRangePotential[i]=0.0; //Initialize array
291			}
292	gezelter	1126
293	gezelter	1544	decomp_->distributeData();
294
295			int nLoops = 1;
296			for (int iLoop = 0; iLoop < nLoops; iLoop++) {
297			doForceLoop(pos,
298			rc,
299			A,
300			electroFrame,
301			frc,
302			trq,
303			tau.getArrayPointer(),
304			longRangePotential,
305			particlePot,
306			&isError );
307
308			if (nLoops > 1) {
309			decomp_->collectIntermediateData();
310			decomp_->distributeIntermediateData();
311			}
312			}
313
314			decomp_->collectData();
315
316	gezelter	246	if( isError ){
317	gezelter	507	sprintf( painCave.errMsg,
318			"Error returned from the fortran force calculation.\n" );
319			painCave.isFatal = 1;
320			simError();
321	gezelter	246	}
322	chuckv	664	for (int i=0; i<LR_POT_TYPES;i++){
323			lrPot += longRangePotential[i]; //Quick hack
324			}
325	gezelter	1503
326	gezelter	246	//store the tau and long range potential
327	chuckv	664	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
328	chrisfen	691	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
329	tim	681	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
330	gezelter	507	}
331	gezelter	246
332	gezelter	1126
333	gezelter	1464	void ForceManager::postCalculation() {
334	gezelter	246	SimInfo::MoleculeIterator mi;
335			Molecule* mol;
336			Molecule::RigidBodyIterator rbIter;
337			RigidBody* rb;
338	gezelter	1126	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
339	gezelter	246
340			// collect the atomic forces onto rigid bodies
341	gezelter	1126
342			for (mol = info_->beginMolecule(mi); mol != NULL;
343			mol = info_->nextMolecule(mi)) {
344			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
345			rb = mol->nextRigidBody(rbIter)) {
346	gezelter	1464	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
347			tau += rbTau;
348	gezelter	507	}
349	gezelter	1126	}
350	gezelter	1464
351	gezelter	1126	#ifdef IS_MPI
352	gezelter	1464	Mat3x3d tmpTau(tau);
353			MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
354			9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
355	gezelter	1126	#endif
356	gezelter	1464	curSnapshot->statData.setTau(tau);
357	gezelter	507	}
358	gezelter	246
359	gezelter	1390	} //end namespace OpenMD