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"
#define __C
#include "UseTheForce/DarkSide/fInteractionMap.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[LR_POT_TYPES];
    double lrPot = 0.0;
    
    Mat3x3d tau;
    short int passedCalcPot = needPotential;
    short int passedCalcStress = needStress;
    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, 
                 &passedCalcPot,
                 &passedCalcStress,
                 &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::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:	2363
Committed:	Wed Oct 12 21:57:16 2005 UTC (18 years, 8 months ago) by chuckv
File size:	7794 byte(s)
Log Message:	Fix to forceManager to pass potential array to fortran.
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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	gezelter	2204	/**
43			* @file ForceManager.cpp
44			* @author tlin
45			* @date 11/09/2004
46			* @time 10:39am
47			* @version 1.0
48			*/
49	gezelter	1930
50			#include "brains/ForceManager.hpp"
51			#include "primitives/Molecule.hpp"
52			#include "UseTheForce/doForces_interface.h"
53	chuckv	2363	#define __C
54			#include "UseTheForce/DarkSide/fInteractionMap.h"
55	gezelter	1930	#include "utils/simError.h"
56			namespace oopse {
57
58	gezelter	2204	void ForceManager::calcForces(bool needPotential, bool needStress) {
59	gezelter	1930
60			if (!info_->isFortranInitialized()) {
61	gezelter	2204	info_->update();
62	gezelter	1930	}
63
64			preCalculation();
65
66			calcShortRangeInteraction();
67
68			calcLongRangeInteraction(needPotential, needStress);
69
70			postCalculation();
71
72	gezelter	2204	}
73	gezelter	1930
74	gezelter	2204	void ForceManager::preCalculation() {
75	gezelter	1930	SimInfo::MoleculeIterator mi;
76			Molecule* mol;
77			Molecule::AtomIterator ai;
78			Atom* atom;
79			Molecule::RigidBodyIterator rbIter;
80			RigidBody* rb;
81
82			// forces are zeroed here, before any are accumulated.
83			// NOTE: do not rezero the forces in Fortran.
84			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
85	gezelter	2204	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
86			atom->zeroForcesAndTorques();
87			}
88	gezelter	1930
89	gezelter	2204	//change the positions of atoms which belong to the rigidbodies
90			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
91			rb->zeroForcesAndTorques();
92			}
93	gezelter	1930	}
94
95	gezelter	2204	}
96	gezelter	1930
97	gezelter	2204	void ForceManager::calcShortRangeInteraction() {
98	gezelter	1930	Molecule* mol;
99			RigidBody* rb;
100			Bond* bond;
101			Bend* bend;
102			Torsion* torsion;
103			SimInfo::MoleculeIterator mi;
104			Molecule::RigidBodyIterator rbIter;
105			Molecule::BondIterator bondIter;;
106			Molecule::BendIterator bendIter;
107			Molecule::TorsionIterator torsionIter;
108
109			//calculate short range interactions
110			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
111
112	gezelter	2204	//change the positions of atoms which belong to the rigidbodies
113			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
114			rb->updateAtoms();
115			}
116	gezelter	1930
117	gezelter	2204	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
118			bond->calcForce();
119			}
120	gezelter	1930
121	gezelter	2204	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
122			bend->calcForce();
123			}
124	gezelter	1930
125	gezelter	2204	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
126			torsion->calcForce();
127			}
128	gezelter	1930
129			}
130
131			double shortRangePotential = 0.0;
132			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
133	gezelter	2204	shortRangePotential += mol->getPotential();
134	gezelter	1930	}
135
136			Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
137			curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
138	gezelter	2204	}
139	gezelter	1930
140	gezelter	2204	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
141	gezelter	1930	Snapshot* curSnapshot;
142			DataStorage* config;
143			double* frc;
144			double* pos;
145			double* trq;
146			double* A;
147			double* electroFrame;
148			double* rc;
149
150			//get current snapshot from SimInfo
151			curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
152
153			//get array pointers
154			config = &(curSnapshot->atomData);
155			frc = config->getArrayPointer(DataStorage::dslForce);
156			pos = config->getArrayPointer(DataStorage::dslPosition);
157			trq = config->getArrayPointer(DataStorage::dslTorque);
158			A = config->getArrayPointer(DataStorage::dslAmat);
159			electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
160
161			//calculate the center of mass of cutoff group
162			SimInfo::MoleculeIterator mi;
163			Molecule* mol;
164			Molecule::CutoffGroupIterator ci;
165			CutoffGroup* cg;
166			Vector3d com;
167			std::vector<Vector3d> rcGroup;
168	chrisfen	2344
169	gezelter	1930	if(info_->getNCutoffGroups() > 0){
170	chrisfen	2344
171	gezelter	2204	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
172	gezelter	1930	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
173	gezelter	2204	cg->getCOM(com);
174			rcGroup.push_back(com);
175	gezelter	1930	}
176	gezelter	2204	}// end for (mol)
177	gezelter	1930
178	gezelter	2204	rc = rcGroup[0].getArrayPointer();
179	gezelter	1930	} else {
180	gezelter	2204	// center of mass of the group is the same as position of the atom if cutoff group does not exist
181			rc = pos;
182	gezelter	1930	}
183
184			//initialize data before passing to fortran
185	chuckv	2363	double longRangePotential[LR_POT_TYPES];
186			double lrPot = 0.0;
187
188	gezelter	1930	Mat3x3d tau;
189			short int passedCalcPot = needPotential;
190			short int passedCalcStress = needStress;
191			int isError = 0;
192
193	chuckv	2363	for (int i=0; i<LR_POT_TYPES;i++){
194			longRangePotential[i]=0.0; //Initialize array
195			}
196
197
198
199	gezelter	1930	doForceLoop( pos,
200	gezelter	2204	rc,
201			A,
202			electroFrame,
203			frc,
204			trq,
205			tau.getArrayPointer(),
206	chuckv	2363	longRangePotential,
207	gezelter	2204	&passedCalcPot,
208			&passedCalcStress,
209			&isError );
210	gezelter	1930
211			if( isError ){
212	gezelter	2204	sprintf( painCave.errMsg,
213			"Error returned from the fortran force calculation.\n" );
214			painCave.isFatal = 1;
215			simError();
216	gezelter	1930	}
217	chuckv	2363	for (int i=0; i<LR_POT_TYPES;i++){
218			lrPot += longRangePotential[i]; //Quick hack
219			}
220	gezelter	1930
221			//store the tau and long range potential
222	chuckv	2363	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
223			// curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
224	gezelter	1930	curSnapshot->statData.setTau(tau);
225	gezelter	2204	}
226	gezelter	1930
227
228	gezelter	2204	void ForceManager::postCalculation() {
229	gezelter	1930	SimInfo::MoleculeIterator mi;
230			Molecule* mol;
231			Molecule::RigidBodyIterator rbIter;
232			RigidBody* rb;
233
234			// collect the atomic forces onto rigid bodies
235			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
236	gezelter	2204	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
237			rb->calcForcesAndTorques();
238			}
239	gezelter	1930	}
240
241	gezelter	2204	}
242	gezelter	1930
243			} //end namespace oopse