src/brains/ForceManager.cpp

/*
 * Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
 * 
 * Contact: oopse@oopse.org
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 */
 
 /**
  * @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:	1901
Committed:	Tue Jan 4 22:18:36 2005 UTC (19 years, 6 months ago) by tim
File size:	6728 byte(s)
Log Message:	constraints in progress
#	Content
1	/*
2	* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project
3	*
4	* Contact: oopse@oopse.org
5	*
6	* This program is free software; you can redistribute it and/or
7	* modify it under the terms of the GNU Lesser General Public License
8	* as published by the Free Software Foundation; either version 2.1
9	* of the License, or (at your option) any later version.
10	* All we ask is that proper credit is given for our work, which includes
11	* - but is not limited to - adding the above copyright notice to the beginning
12	* of your source code files, and to any copyright notice that you may distribute
13	* with programs based on this work.
14	*
15	* This program is distributed in the hope that it will be useful,
16	* but WITHOUT ANY WARRANTY; without even the implied warranty of
17	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18	* GNU Lesser General Public License for more details.
19	*
20	* You should have received a copy of the GNU Lesser General Public License
21	* along with this program; if not, write to the Free Software
22	* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
23	*
24	*/
25
26	/**
27	* @file ForceManager.cpp
28	* @author tlin
29	* @date 11/09/2004
30	* @time 10:39am
31	* @version 1.0
32	*/
33
34	#include "brains/ForceManager.hpp"
35	#include "primitives/Molecule.hpp"
36	#include "UseTheForce/doForces_interface.h"
37	#include "utils/simError.h"
38	namespace oopse {
39
40	void ForceManager::calcForces(bool needPotential, bool needStress) {
41
42	if (!info_->isFortranInitialized()) {
43	info_->update();
44	}
45
46	preCalculation();
47
48	calcShortRangeInteraction();
49
50	calcLongRangeInteraction(needPotential, needStress);
51
52	postCalculation();
53
54	}
55
56	void ForceManager::preCalculation() {
57	SimInfo::MoleculeIterator mi;
58	Molecule* mol;
59	Molecule::AtomIterator ai;
60	Atom* atom;
61	Molecule::RigidBodyIterator rbIter;
62	RigidBody* rb;
63
64	// forces are zeroed here, before any are accumulated.
65	// NOTE: do not rezero the forces in Fortran.
66	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
67	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
68	atom->zeroForcesAndTorques();
69	}
70
71	//change the positions of atoms which belong to the rigidbodies
72	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
73	rb->zeroForcesAndTorques();
74	}
75	}
76
77	}
78
79	void ForceManager::calcShortRangeInteraction() {
80	Molecule* mol;
81	RigidBody* rb;
82	Bond* bond;
83	Bend* bend;
84	Torsion* torsion;
85	SimInfo::MoleculeIterator mi;
86	Molecule::RigidBodyIterator rbIter;
87	Molecule::BondIterator bondIter;;
88	Molecule::BendIterator bendIter;
89	Molecule::TorsionIterator torsionIter;
90
91	//calculate short range interactions
92	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
93
94	//change the positions of atoms which belong to the rigidbodies
95	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
96	rb->updateAtoms();
97	}
98
99	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
100	bond->calcForce();
101	}
102
103	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
104	bend->calcForce();
105	}
106
107	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
108	torsion->calcForce();
109	}
110
111	}
112
113	double shortRangePotential = 0.0;
114	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
115	shortRangePotential += mol->getPotential();
116	}
117
118	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
119	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
120	}
121
122	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
123	Snapshot* curSnapshot;
124	DataStorage* config;
125	double* frc;
126	double* pos;
127	double* trq;
128	double* A;
129	double* electroFrame;
130	double* rc;
131
132	//get current snapshot from SimInfo
133	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
134
135	//get array pointers
136	config = &(curSnapshot->atomData);
137	frc = config->getArrayPointer(DataStorage::dslForce);
138	pos = config->getArrayPointer(DataStorage::dslPosition);
139	trq = config->getArrayPointer(DataStorage::dslTorque);
140	A = config->getArrayPointer(DataStorage::dslAmat);
141	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
142
143	//calculate the center of mass of cutoff group
144	SimInfo::MoleculeIterator mi;
145	Molecule* mol;
146	Molecule::CutoffGroupIterator ci;
147	CutoffGroup* cg;
148	Vector3d com;
149	std::vector<Vector3d> rcGroup;
150
151	if(info_->getNCutoffGroups() > 0){
152
153	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
154	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
155	cg->getCOM(com);
156	rcGroup.push_back(com);
157	}
158	}// end for (mol)
159
160	rc = rcGroup[0].getArrayPointer();
161	} else {
162	// center of mass of the group is the same as position of the atom if cutoff group does not exist
163	rc = pos;
164	}
165
166	//initialize data before passing to fortran
167	double longRangePotential = 0.0;
168	Mat3x3d tau;
169	short int passedCalcPot = needPotential;
170	short int passedCalcStress = needStress;
171	int isError = 0;
172
173	doForceLoop( pos,
174	rc,
175	A,
176	electroFrame,
177	frc,
178	trq,
179	tau.getArrayPointer(),
180	&longRangePotential,
181	&passedCalcPot,
182	&passedCalcStress,
183	&isError );
184
185	if( isError ){
186	sprintf( painCave.errMsg,
187	"Error returned from the fortran force calculation.\n" );
188	painCave.isFatal = 1;
189	simError();
190	}
191
192	//store the tau and long range potential
193	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
194	curSnapshot->statData.setTau(tau);
195	}
196
197
198	void ForceManager::postCalculation() {
199	SimInfo::MoleculeIterator mi;
200	Molecule* mol;
201	Molecule::RigidBodyIterator rbIter;
202	RigidBody* rb;
203
204	// collect the atomic forces onto rigid bodies
205	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
206	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
207	rb->calcForcesAndTorques();
208	}
209	}
210
211	}
212
213	} //end namespace oopse