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 bondPotential = 0.0;
    double bendPotential = 0.0;
    double torsionPotential = 0.0;

    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {

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

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

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

    }    

    double  shortRangePotential = bondPotential + bendPotential + torsionPotential;    
    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;
    
  }

  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[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT]; 
    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];

    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:	688
Committed:	Wed Oct 19 16:49:59 2005 UTC (20 years ago) by tim
File size:	8753 byte(s)
Log Message:	fix an index mismathcing between c and fortran
#	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			* 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	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	chuckv	664	#define __C
54			#include "UseTheForce/DarkSide/fInteractionMap.h"
55	gezelter	246	#include "utils/simError.h"
56			namespace oopse {
57
58	gezelter	507	void ForceManager::calcForces(bool needPotential, bool needStress) {
59	gezelter	246
60			if (!info_->isFortranInitialized()) {
61	gezelter	507	info_->update();
62	gezelter	246	}
63
64			preCalculation();
65
66			calcShortRangeInteraction();
67
68			calcLongRangeInteraction(needPotential, needStress);
69
70			postCalculation();
71
72	gezelter	507	}
73	gezelter	246
74	gezelter	507	void ForceManager::preCalculation() {
75	gezelter	246	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	507	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
86			atom->zeroForcesAndTorques();
87			}
88	gezelter	246
89	gezelter	507	//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	246	}
94
95	gezelter	507	}
96	gezelter	246
97	gezelter	507	void ForceManager::calcShortRangeInteraction() {
98	gezelter	246	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	507	//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	246
117	gezelter	507	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
118			bond->calcForce();
119			}
120	gezelter	246
121	gezelter	507	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
122			bend->calcForce();
123			}
124	gezelter	246
125	gezelter	507	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
126			torsion->calcForce();
127			}
128	gezelter	246
129			}
130
131	tim	665
132			double bondPotential = 0.0;
133			double bendPotential = 0.0;
134			double torsionPotential = 0.0;
135
136	gezelter	246	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
137
138	tim	665	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
139			bondPotential += bond->getPotential();
140			}
141
142			for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
143			bendPotential += bend->getPotential();
144			}
145
146			for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
147			torsionPotential += torsion->getPotential();
148			}
149
150			}
151
152			double shortRangePotential = bondPotential + bendPotential + torsionPotential;
153	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
154			curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
155	tim	665	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
156			curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
157			curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
158
159	gezelter	507	}
160	gezelter	246
161	gezelter	507	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
162	gezelter	246	Snapshot* curSnapshot;
163			DataStorage* config;
164			double* frc;
165			double* pos;
166			double* trq;
167			double* A;
168			double* electroFrame;
169			double* rc;
170
171			//get current snapshot from SimInfo
172			curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
173
174			//get array pointers
175			config = &(curSnapshot->atomData);
176			frc = config->getArrayPointer(DataStorage::dslForce);
177			pos = config->getArrayPointer(DataStorage::dslPosition);
178			trq = config->getArrayPointer(DataStorage::dslTorque);
179			A = config->getArrayPointer(DataStorage::dslAmat);
180			electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
181
182			//calculate the center of mass of cutoff group
183			SimInfo::MoleculeIterator mi;
184			Molecule* mol;
185			Molecule::CutoffGroupIterator ci;
186			CutoffGroup* cg;
187			Vector3d com;
188			std::vector<Vector3d> rcGroup;
189	chrisfen	645
190	gezelter	246	if(info_->getNCutoffGroups() > 0){
191	chrisfen	645
192	gezelter	507	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
193	gezelter	246	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
194	gezelter	507	cg->getCOM(com);
195			rcGroup.push_back(com);
196	gezelter	246	}
197	gezelter	507	}// end for (mol)
198	gezelter	246
199	gezelter	507	rc = rcGroup[0].getArrayPointer();
200	gezelter	246	} else {
201	gezelter	507	// center of mass of the group is the same as position of the atom if cutoff group does not exist
202			rc = pos;
203	gezelter	246	}
204
205			//initialize data before passing to fortran
206	chuckv	664	double longRangePotential[LR_POT_TYPES];
207			double lrPot = 0.0;
208
209	gezelter	246	Mat3x3d tau;
210			short int passedCalcPot = needPotential;
211			short int passedCalcStress = needStress;
212			int isError = 0;
213
214	chuckv	664	for (int i=0; i<LR_POT_TYPES;i++){
215			longRangePotential[i]=0.0; //Initialize array
216			}
217
218
219
220	gezelter	246	doForceLoop( pos,
221	gezelter	507	rc,
222			A,
223			electroFrame,
224			frc,
225			trq,
226			tau.getArrayPointer(),
227	chuckv	664	longRangePotential,
228	gezelter	507	&passedCalcPot,
229			&passedCalcStress,
230			&isError );
231	gezelter	246
232			if( isError ){
233	gezelter	507	sprintf( painCave.errMsg,
234			"Error returned from the fortran force calculation.\n" );
235			painCave.isFatal = 1;
236			simError();
237	gezelter	246	}
238	chuckv	664	for (int i=0; i<LR_POT_TYPES;i++){
239			lrPot += longRangePotential[i]; //Quick hack
240			}
241	gezelter	246
242			//store the tau and long range potential
243	chuckv	664	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
244			// curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
245	tim	688	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
246	tim	681	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
247
248	gezelter	246	curSnapshot->statData.setTau(tau);
249	gezelter	507	}
250	gezelter	246
251
252	gezelter	507	void ForceManager::postCalculation() {
253	gezelter	246	SimInfo::MoleculeIterator mi;
254			Molecule* mol;
255			Molecule::RigidBodyIterator rbIter;
256			RigidBody* rb;
257
258			// collect the atomic forces onto rigid bodies
259			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
260	gezelter	507	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
261			rb->calcForcesAndTorques();
262			}
263	gezelter	246	}
264
265	gezelter	507	}
266	gezelter	246
267			} //end namespace oopse