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"

namespace OpenMD {
  
  ForceManager::ForceManager(SimInfo * info) : info_(info), 
                                               NBforcesInitialized_(false) {
  }
 
  void ForceManager::calcForces() {
    
    if (!info_->isFortranInitialized()) {
      info_->update();
    }
    
    preCalculation();
    
    calcShortRangeInteraction();

    calcLongRangeInteraction();

    postCalculation();
    
  }
  
  void ForceManager::preCalculation() {
    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::AtomIterator ai;
    Atom* atom;
    Molecule::RigidBodyIterator rbIter;
    RigidBody* rb;
    
    // 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();
      }        
          
    }
    
    // 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;
    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);

    //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){
      
      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);
        }
      }// 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;
    }
    
    //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
    }
    
    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();
    }
    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:	1503
Committed:	Sat Oct 2 19:54:41 2010 UTC (14 years, 7 months ago) by gezelter
File size:	12336 byte(s)
Log Message:	Changes to remove more of the low level stuff from the fortran side.
#	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	1467
61	gezelter	1390	namespace OpenMD {
62	gezelter	1469
63			ForceManager::ForceManager(SimInfo * info) : info_(info),
64			NBforcesInitialized_(false) {
65			}
66
67	gezelter	1464	void ForceManager::calcForces() {
68	gezelter	1126
69	gezelter	246	if (!info_->isFortranInitialized()) {
70	gezelter	507	info_->update();
71	gezelter	246	}
72	gezelter	1126
73	gezelter	246	preCalculation();
74
75			calcShortRangeInteraction();
76
77	gezelter	1464	calcLongRangeInteraction();
78	gezelter	246
79	gezelter	1464	postCalculation();
80	tim	749
81	gezelter	507	}
82	gezelter	1126
83	gezelter	507	void ForceManager::preCalculation() {
84	gezelter	246	SimInfo::MoleculeIterator mi;
85			Molecule* mol;
86			Molecule::AtomIterator ai;
87			Atom* atom;
88			Molecule::RigidBodyIterator rbIter;
89			RigidBody* rb;
90
91			// forces are zeroed here, before any are accumulated.
92			// NOTE: do not rezero the forces in Fortran.
93	chuckv	1245
94	gezelter	1126	for (mol = info_->beginMolecule(mi); mol != NULL;
95			mol = info_->nextMolecule(mi)) {
96	gezelter	507	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
97			atom->zeroForcesAndTorques();
98			}
99	chuckv	1245
100	gezelter	507	//change the positions of atoms which belong to the rigidbodies
101	gezelter	1126	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
102			rb = mol->nextRigidBody(rbIter)) {
103	gezelter	507	rb->zeroForcesAndTorques();
104			}
105	chuckv	1245
106	gezelter	246	}
107
108	gezelter	1126	// Zero out the stress tensor
109			tau *= 0.0;
110
111	gezelter	507	}
112	gezelter	1126
113	gezelter	507	void ForceManager::calcShortRangeInteraction() {
114	gezelter	246	Molecule* mol;
115			RigidBody* rb;
116			Bond* bond;
117			Bend* bend;
118			Torsion* torsion;
119	cli2	1275	Inversion* inversion;
120	gezelter	246	SimInfo::MoleculeIterator mi;
121			Molecule::RigidBodyIterator rbIter;
122			Molecule::BondIterator bondIter;;
123			Molecule::BendIterator bendIter;
124			Molecule::TorsionIterator torsionIter;
125	cli2	1275	Molecule::InversionIterator inversionIter;
126	tim	963	RealType bondPotential = 0.0;
127			RealType bendPotential = 0.0;
128			RealType torsionPotential = 0.0;
129	cli2	1275	RealType inversionPotential = 0.0;
130	gezelter	246
131			//calculate short range interactions
132	gezelter	1126	for (mol = info_->beginMolecule(mi); mol != NULL;
133			mol = info_->nextMolecule(mi)) {
134	gezelter	246
135	gezelter	507	//change the positions of atoms which belong to the rigidbodies
136	gezelter	1126	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
137			rb = mol->nextRigidBody(rbIter)) {
138			rb->updateAtoms();
139	gezelter	507	}
140	gezelter	246
141	gezelter	1126	for (bond = mol->beginBond(bondIter); bond != NULL;
142			bond = mol->nextBond(bondIter)) {
143	tim	749	bond->calcForce();
144			bondPotential += bond->getPotential();
145	gezelter	507	}
146	gezelter	246
147	gezelter	1126	for (bend = mol->beginBend(bendIter); bend != NULL;
148			bend = mol->nextBend(bendIter)) {
149
150			RealType angle;
151			bend->calcForce(angle);
152			RealType currBendPot = bend->getPotential();
153	gezelter	1448
154	gezelter	1126	bendPotential += bend->getPotential();
155			std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
156			if (i == bendDataSets.end()) {
157			BendDataSet dataSet;
158			dataSet.prev.angle = dataSet.curr.angle = angle;
159			dataSet.prev.potential = dataSet.curr.potential = currBendPot;
160			dataSet.deltaV = 0.0;
161			bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
162			}else {
163			i->second.prev.angle = i->second.curr.angle;
164			i->second.prev.potential = i->second.curr.potential;
165			i->second.curr.angle = angle;
166			i->second.curr.potential = currBendPot;
167			i->second.deltaV = fabs(i->second.curr.potential -
168			i->second.prev.potential);
169			}
170	gezelter	507	}
171	gezelter	1126
172			for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
173			torsion = mol->nextTorsion(torsionIter)) {
174	tim	963	RealType angle;
175	gezelter	1126	torsion->calcForce(angle);
176	tim	963	RealType currTorsionPot = torsion->getPotential();
177	gezelter	1126	torsionPotential += torsion->getPotential();
178			std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
179			if (i == torsionDataSets.end()) {
180			TorsionDataSet dataSet;
181			dataSet.prev.angle = dataSet.curr.angle = angle;
182			dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
183			dataSet.deltaV = 0.0;
184			torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
185			}else {
186			i->second.prev.angle = i->second.curr.angle;
187			i->second.prev.potential = i->second.curr.potential;
188			i->second.curr.angle = angle;
189			i->second.curr.potential = currTorsionPot;
190			i->second.deltaV = fabs(i->second.curr.potential -
191			i->second.prev.potential);
192			}
193			}
194	cli2	1275
195			for (inversion = mol->beginInversion(inversionIter);
196			inversion != NULL;
197			inversion = mol->nextInversion(inversionIter)) {
198			RealType angle;
199			inversion->calcForce(angle);
200			RealType currInversionPot = inversion->getPotential();
201			inversionPotential += inversion->getPotential();
202			std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
203			if (i == inversionDataSets.end()) {
204			InversionDataSet dataSet;
205			dataSet.prev.angle = dataSet.curr.angle = angle;
206			dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
207			dataSet.deltaV = 0.0;
208			inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
209			}else {
210			i->second.prev.angle = i->second.curr.angle;
211			i->second.prev.potential = i->second.curr.potential;
212			i->second.curr.angle = angle;
213			i->second.curr.potential = currInversionPot;
214			i->second.deltaV = fabs(i->second.curr.potential -
215			i->second.prev.potential);
216			}
217			}
218	gezelter	246	}
219
220	gezelter	1126	RealType shortRangePotential = bondPotential + bendPotential +
221	cli2	1275	torsionPotential + inversionPotential;
222	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
223			curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
224	tim	665	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
225			curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
226			curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
227	cli2	1275	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
228	tim	665
229	gezelter	507	}
230	gezelter	1126
231	gezelter	1464	void ForceManager::calcLongRangeInteraction() {
232	gezelter	246	Snapshot* curSnapshot;
233			DataStorage* config;
234	tim	963	RealType* frc;
235			RealType* pos;
236			RealType* trq;
237			RealType* A;
238			RealType* electroFrame;
239			RealType* rc;
240	chuckv	1245	RealType* particlePot;
241	gezelter	246
242			//get current snapshot from SimInfo
243			curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
244	gezelter	1126
245	gezelter	246	//get array pointers
246			config = &(curSnapshot->atomData);
247			frc = config->getArrayPointer(DataStorage::dslForce);
248			pos = config->getArrayPointer(DataStorage::dslPosition);
249			trq = config->getArrayPointer(DataStorage::dslTorque);
250			A = config->getArrayPointer(DataStorage::dslAmat);
251			electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
252	chuckv	1245	particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
253	gezelter	246
254			//calculate the center of mass of cutoff group
255			SimInfo::MoleculeIterator mi;
256			Molecule* mol;
257			Molecule::CutoffGroupIterator ci;
258			CutoffGroup* cg;
259			Vector3d com;
260			std::vector<Vector3d> rcGroup;
261	gezelter	1126
262	gezelter	246	if(info_->getNCutoffGroups() > 0){
263	gezelter	1126
264			for (mol = info_->beginMolecule(mi); mol != NULL;
265			mol = info_->nextMolecule(mi)) {
266			for(cg = mol->beginCutoffGroup(ci); cg != NULL;
267			cg = mol->nextCutoffGroup(ci)) {
268	gezelter	507	cg->getCOM(com);
269			rcGroup.push_back(com);
270	gezelter	246	}
271	gezelter	507	}// end for (mol)
272	gezelter	246
273	gezelter	507	rc = rcGroup[0].getArrayPointer();
274	gezelter	246	} else {
275	gezelter	1126	// center of mass of the group is the same as position of the atom
276			// if cutoff group does not exist
277	gezelter	507	rc = pos;
278	gezelter	246	}
279	gezelter	1126
280	gezelter	246	//initialize data before passing to fortran
281	tim	963	RealType longRangePotential[LR_POT_TYPES];
282			RealType lrPot = 0.0;
283	gezelter	246	int isError = 0;
284
285	chuckv	664	for (int i=0; i<LR_POT_TYPES;i++){
286			longRangePotential[i]=0.0; //Initialize array
287			}
288	gezelter	1126
289	xsun	1215	doForceLoop(pos,
290			rc,
291			A,
292			electroFrame,
293			frc,
294			trq,
295			tau.getArrayPointer(),
296			longRangePotential,
297	chuckv	1245	particlePot,
298	xsun	1215	&isError );
299
300	gezelter	246	if( isError ){
301	gezelter	507	sprintf( painCave.errMsg,
302			"Error returned from the fortran force calculation.\n" );
303			painCave.isFatal = 1;
304			simError();
305	gezelter	246	}
306	chuckv	664	for (int i=0; i<LR_POT_TYPES;i++){
307			lrPot += longRangePotential[i]; //Quick hack
308			}
309	gezelter	1503
310	gezelter	246	//store the tau and long range potential
311	chuckv	664	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
312	chrisfen	691	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
313	tim	681	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
314	gezelter	507	}
315	gezelter	246
316	gezelter	1126
317	gezelter	1464	void ForceManager::postCalculation() {
318	gezelter	246	SimInfo::MoleculeIterator mi;
319			Molecule* mol;
320			Molecule::RigidBodyIterator rbIter;
321			RigidBody* rb;
322	gezelter	1126	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
323	gezelter	246
324			// collect the atomic forces onto rigid bodies
325	gezelter	1126
326			for (mol = info_->beginMolecule(mi); mol != NULL;
327			mol = info_->nextMolecule(mi)) {
328			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
329			rb = mol->nextRigidBody(rbIter)) {
330	gezelter	1464	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
331			tau += rbTau;
332	gezelter	507	}
333	gezelter	1126	}
334	gezelter	1464
335	gezelter	1126	#ifdef IS_MPI
336	gezelter	1464	Mat3x3d tmpTau(tau);
337			MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
338			9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
339	gezelter	1126	#endif
340	gezelter	1464	curSnapshot->statData.setTau(tau);
341	gezelter	507	}
342	gezelter	246
343	gezelter	1390	} //end namespace OpenMD