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:	2387
Committed:	Wed Oct 19 16:49:59 2005 UTC (18 years, 8 months ago) by tim
File size:	8753 byte(s)
Log Message:	fix an index mismathcing between c and fortran
#	Content
1	/*
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	#define __C
54	#include "UseTheForce/DarkSide/fInteractionMap.h"
55	#include "utils/simError.h"
56	namespace oopse {
57
58	void ForceManager::calcForces(bool needPotential, bool needStress) {
59
60	if (!info_->isFortranInitialized()) {
61	info_->update();
62	}
63
64	preCalculation();
65
66	calcShortRangeInteraction();
67
68	calcLongRangeInteraction(needPotential, needStress);
69
70	postCalculation();
71
72	}
73
74	void ForceManager::preCalculation() {
75	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	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
86	atom->zeroForcesAndTorques();
87	}
88
89	//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	}
94
95	}
96
97	void ForceManager::calcShortRangeInteraction() {
98	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	//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
117	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
118	bond->calcForce();
119	}
120
121	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
122	bend->calcForce();
123	}
124
125	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
126	torsion->calcForce();
127	}
128
129	}
130
131
132	double bondPotential = 0.0;
133	double bendPotential = 0.0;
134	double torsionPotential = 0.0;
135
136	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
137
138	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	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
154	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
155	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
156	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
157	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
158
159	}
160
161	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
162	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
190	if(info_->getNCutoffGroups() > 0){
191
192	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
193	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
194	cg->getCOM(com);
195	rcGroup.push_back(com);
196	}
197	}// end for (mol)
198
199	rc = rcGroup[0].getArrayPointer();
200	} else {
201	// center of mass of the group is the same as position of the atom if cutoff group does not exist
202	rc = pos;
203	}
204
205	//initialize data before passing to fortran
206	double longRangePotential[LR_POT_TYPES];
207	double lrPot = 0.0;
208
209	Mat3x3d tau;
210	short int passedCalcPot = needPotential;
211	short int passedCalcStress = needStress;
212	int isError = 0;
213
214	for (int i=0; i<LR_POT_TYPES;i++){
215	longRangePotential[i]=0.0; //Initialize array
216	}
217
218
219
220	doForceLoop( pos,
221	rc,
222	A,
223	electroFrame,
224	frc,
225	trq,
226	tau.getArrayPointer(),
227	longRangePotential,
228	&passedCalcPot,
229	&passedCalcStress,
230	&isError );
231
232	if( isError ){
233	sprintf( painCave.errMsg,
234	"Error returned from the fortran force calculation.\n" );
235	painCave.isFatal = 1;
236	simError();
237	}
238	for (int i=0; i<LR_POT_TYPES;i++){
239	lrPot += longRangePotential[i]; //Quick hack
240	}
241
242	//store the tau and long range potential
243	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
244	// curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
245	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
246	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
247
248	curSnapshot->statData.setTau(tau);
249	}
250
251
252	void ForceManager::postCalculation() {
253	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	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
261	rb->calcForcesAndTorques();
262	}
263	}
264
265	}
266
267	} //end namespace oopse