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:	645
Committed:	Tue Oct 4 19:34:03 2005 UTC (20 years, 1 month ago) by chrisfen
File size:	7432 byte(s)
Log Message:	fixed an annoying mass ratio bug that results in simulation failure with massless particles
#	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	#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