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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
 /**
  * @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"
#include "utils/simError.h"
namespace oopse {

void ForceManager::calcForces(bool needPotential, bool needStress) {

    if (!info_->isFortranInitialized()) {
        info_->update();
    }

    preCalculation();
    
    calcShortRangeInteraction();

    calcLongRangeInteraction(needPotential, needStress);

    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();
        }        
    }
    
}

void ForceManager::calcShortRangeInteraction() {
    Molecule* mol;
    RigidBody* rb;
    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    Molecule::BondIterator bondIter;;
    Molecule::BendIterator  bendIter;
    Molecule::TorsionIterator  torsionIter;

    //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();
        }

        for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
            bend->calcForce();
        }

        for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
            torsion->calcForce();
        }

    }
    
    double  shortRangePotential = 0.0;
    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
        shortRangePotential += mol->getPotential();
    }

    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
}

void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
    Snapshot* curSnapshot;
    DataStorage* config;
    double* frc;
    double* pos;
    double* trq;
    double* A;
    double* electroFrame;
    double* rc;
    
    //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);

    //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
    double longRangePotential = 0.0;
    Mat3x3d tau;
    short int passedCalcPot = needPotential;
    short int passedCalcStress = needStress;
    int isError = 0;

    doForceLoop( pos,
            rc,
            A,
            electroFrame,
            frc,
            trq,
            tau.getArrayPointer(),
            &longRangePotential, 
            &passedCalcPot,
            &passedCalcStress,
            &isError );

    if( isError ){
        sprintf( painCave.errMsg,
             "Error returned from the fortran force calculation.\n" );
        painCave.isFatal = 1;
        simError();
    }

    //store the tau and long range potential    
    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
    curSnapshot->statData.setTau(tau);
}


void ForceManager::postCalculation() {
    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::RigidBodyIterator rbIter;
    RigidBody* rb;
    
    // 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)) {
            rb->calcForcesAndTorques();
        }
    }

}

} //end namespace oopse
Revision:	1930
Committed:	Wed Jan 12 22:41:40 2005 UTC (19 years, 5 months ago) by gezelter
File size:	7657 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	User	Rev	Content
1	gezelter	1930	/*
2			* 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			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			/**
43			* @file ForceManager.cpp
44			* @author tlin
45			* @date 11/09/2004
46			* @time 10:39am
47			* @version 1.0
48			*/
49
50			#include "brains/ForceManager.hpp"
51			#include "primitives/Molecule.hpp"
52			#include "UseTheForce/doForces_interface.h"
53			#include "utils/simError.h"
54			namespace oopse {
55
56			void ForceManager::calcForces(bool needPotential, bool needStress) {
57
58			if (!info_->isFortranInitialized()) {
59			info_->update();
60			}
61
62			preCalculation();
63
64			calcShortRangeInteraction();
65
66			calcLongRangeInteraction(needPotential, needStress);
67
68			postCalculation();
69
70			}
71
72			void ForceManager::preCalculation() {
73			SimInfo::MoleculeIterator mi;
74			Molecule* mol;
75			Molecule::AtomIterator ai;
76			Atom* atom;
77			Molecule::RigidBodyIterator rbIter;
78			RigidBody* rb;
79
80			// forces are zeroed here, before any are accumulated.
81			// NOTE: do not rezero the forces in Fortran.
82			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
83			for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
84			atom->zeroForcesAndTorques();
85			}
86
87			//change the positions of atoms which belong to the rigidbodies
88			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
89			rb->zeroForcesAndTorques();
90			}
91			}
92
93			}
94
95			void ForceManager::calcShortRangeInteraction() {
96			Molecule* mol;
97			RigidBody* rb;
98			Bond* bond;
99			Bend* bend;
100			Torsion* torsion;
101			SimInfo::MoleculeIterator mi;
102			Molecule::RigidBodyIterator rbIter;
103			Molecule::BondIterator bondIter;;
104			Molecule::BendIterator bendIter;
105			Molecule::TorsionIterator torsionIter;
106
107			//calculate short range interactions
108			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
109
110			//change the positions of atoms which belong to the rigidbodies
111			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
112			rb->updateAtoms();
113			}
114
115			for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
116			bond->calcForce();
117			}
118
119			for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
120			bend->calcForce();
121			}
122
123			for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
124			torsion->calcForce();
125			}
126
127			}
128
129			double shortRangePotential = 0.0;
130			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
131			shortRangePotential += mol->getPotential();
132			}
133
134			Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
135			curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
136			}
137
138			void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
139			Snapshot* curSnapshot;
140			DataStorage* config;
141			double* frc;
142			double* pos;
143			double* trq;
144			double* A;
145			double* electroFrame;
146			double* rc;
147
148			//get current snapshot from SimInfo
149			curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
150
151			//get array pointers
152			config = &(curSnapshot->atomData);
153			frc = config->getArrayPointer(DataStorage::dslForce);
154			pos = config->getArrayPointer(DataStorage::dslPosition);
155			trq = config->getArrayPointer(DataStorage::dslTorque);
156			A = config->getArrayPointer(DataStorage::dslAmat);
157			electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
158
159			//calculate the center of mass of cutoff group
160			SimInfo::MoleculeIterator mi;
161			Molecule* mol;
162			Molecule::CutoffGroupIterator ci;
163			CutoffGroup* cg;
164			Vector3d com;
165			std::vector<Vector3d> rcGroup;
166
167			if(info_->getNCutoffGroups() > 0){
168
169			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
170			for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
171			cg->getCOM(com);
172			rcGroup.push_back(com);
173			}
174			}// end for (mol)
175
176			rc = rcGroup[0].getArrayPointer();
177			} else {
178			// center of mass of the group is the same as position of the atom if cutoff group does not exist
179			rc = pos;
180			}
181
182			//initialize data before passing to fortran
183			double longRangePotential = 0.0;
184			Mat3x3d tau;
185			short int passedCalcPot = needPotential;
186			short int passedCalcStress = needStress;
187			int isError = 0;
188
189			doForceLoop( pos,
190			rc,
191			A,
192			electroFrame,
193			frc,
194			trq,
195			tau.getArrayPointer(),
196			&longRangePotential,
197			&passedCalcPot,
198			&passedCalcStress,
199			&isError );
200
201			if( isError ){
202			sprintf( painCave.errMsg,
203			"Error returned from the fortran force calculation.\n" );
204			painCave.isFatal = 1;
205			simError();
206			}
207
208			//store the tau and long range potential
209			curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
210			curSnapshot->statData.setTau(tau);
211			}
212
213
214			void ForceManager::postCalculation() {
215			SimInfo::MoleculeIterator mi;
216			Molecule* mol;
217			Molecule::RigidBodyIterator rbIter;
218			RigidBody* rb;
219
220			// collect the atomic forces onto rigid bodies
221			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
222			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
223			rb->calcForcesAndTorques();
224			}
225			}
226
227			}
228
229			} //end namespace oopse