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"

namespace oopse {

void ForceManager::calcForces(bool needPotential, bool needStress) {

    if (!info_->isFortranInitialized()) {
        info_->update();
    }

    preCalculation();
    
    calcShortRangeInteraction();

    calcLongRangeInteraction();

    postCalculation()
        
}

void ForceManager::preCalculation() {
    typename SimInfo::MoleculeIterator mi;
    Molecule* mol;
    typename Molecule::AtomIterator ai;
    Atom* atom;

    // 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->zeroForces();
        }
    }
    
}

void ForceManager::calcShortRangeInteraction() {
    Molecule* mol;
    RigidBody* rb;
    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    typename SimInfo::MoleculeIterator mi;
    typename Molecule::RigidBodyIterator rbIter;
    typename Molecule::BondIterator bondIter;;
    typename Molecule::BendIterator  bendIter;
    typename 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->calc_forces();
        }

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

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

    }
    
}

void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
    Snapshot* curSnapshot;
    DataStorage* config;
    double* frc;
    double* pos;
    double* trq;
    double* A;
    double* u_l;
    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);
    u_l = config->getArrayPointer(DataStorage::dslUnitVector);

    //calculate the center of mass of cutoff group
    typename SimInfo::MoleculeIterator mi;
    Molecule* mol;
    typename 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,
            u_l,
            frc,
            trq,
            tau,
            &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::LONGRANGEPOTENTIAL] = longRangePotential;
    curSnapshot->statData[Stats::TAUXX] = tau[0];
    curSnapshot->statData[Stats::TAUXY] = tau[1];
    curSnapshot->statData[Stats::TAUXZ] = tau[2];
    curSnapshot->statData[Stats::TAUYX] = tau[3];
    curSnapshot->statData[Stats::TAUYY] = tau[4];
    curSnapshot->statData[Stats::TAUYZ] = tau[5];
    curSnapshot->statData[Stats::TAUZX] = tau[6];
    curSnapshot->statData[Stats::TAUZY] = tau[7];
    curSnapshot->statData[Stats::TAUZZ] = tau[8];
}


void ForceManager::postCalculation() {
    typename SimInfo::MoleculeIterator mi;
    Molecule* mol;
    typename 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:	1738
Committed:	Sat Nov 13 05:08:12 2004 UTC (19 years, 8 months ago) by tim
File size:	6413 byte(s)
Log Message:	refactory, refactory, refactory
#	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
36	namespace oopse {
37
38	void ForceManager::calcForces(bool needPotential, bool needStress) {
39
40	if (!info_->isFortranInitialized()) {
41	info_->update();
42	}
43
44	preCalculation();
45
46	calcShortRangeInteraction();
47
48	calcLongRangeInteraction();
49
50	postCalculation()
51
52	}
53
54	void ForceManager::preCalculation() {
55	typename SimInfo::MoleculeIterator mi;
56	Molecule* mol;
57	typename Molecule::AtomIterator ai;
58	Atom* atom;
59
60	// forces are zeroed here, before any are accumulated.
61	// NOTE: do not rezero the forces in Fortran.
62	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
63	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
64	atom->zeroForces();
65	}
66	}
67
68	}
69
70	void ForceManager::calcShortRangeInteraction() {
71	Molecule* mol;
72	RigidBody* rb;
73	Bond* bond;
74	Bend* bend;
75	Torsion* torsion;
76	typename SimInfo::MoleculeIterator mi;
77	typename Molecule::RigidBodyIterator rbIter;
78	typename Molecule::BondIterator bondIter;;
79	typename Molecule::BendIterator bendIter;
80	typename Molecule::TorsionIterator torsionIter;
81
82	//calculate short range interactions
83	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
84
85	//change the positions of atoms which belong to the rigidbodies
86	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
87	rb->updateAtoms();
88	}
89
90	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
91	bond->calc_forces();
92	}
93
94	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
95	bend->calc_forces();
96	}
97
98	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
99	torsion->calc_forces();
100	}
101
102	}
103
104	}
105
106	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
107	Snapshot* curSnapshot;
108	DataStorage* config;
109	double* frc;
110	double* pos;
111	double* trq;
112	double* A;
113	double* u_l;
114	double* rc;
115
116	//get current snapshot from SimInfo
117	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot()
118
119	//get array pointers
120	config = &(curSnapshot->atomData);
121	frc = config->getArrayPointer(DataStorage::dslForce);
122	pos = config->getArrayPointer(DataStorage::dslPosition);
123	trq = config->getArrayPointer(DataStorage::dslTorque);
124	A = config->getArrayPointer(DataStorage::dslAmat);
125	u_l = config->getArrayPointer(DataStorage::dslUnitVector);
126
127	//calculate the center of mass of cutoff group
128	typename SimInfo::MoleculeIterator mi;
129	Molecule* mol;
130	typename Molecule::CutoffGroupIterator ci;
131	CutoffGroup* cg;
132	Vector3d com;
133	std::vector<Vector3d> rcGroup;
134
135	if(info_->getNCutoffGroups() > 0){
136
137	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
138	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
139	cg->getCOM(com)
140	rcGroup.push_back(com);
141	}
142	}// end for (mol)
143
144	rc = rcGroup[0]->getArrayPointer();
145	} else {
146	// center of mass of the group is the same as position of the atom if cutoff group does not exist
147	rc = pos;
148	}
149
150	//initialize data before passing to fortran
151	double longRangePotential = 0.0;
152	Mat3x3d tau;
153	short int passedCalcPot = needPotential;
154	short int passedCalcStress = needStress;
155	int isError = 0;
156
157	doForceLoop( pos,
158	rc,
159	A,
160	u_l,
161	frc,
162	trq,
163	tau,
164	&longRangePotential,
165	&passedCalcPot,
166	&passedCalcStress,
167	&isError );
168
169	if( isError ){
170	sprintf( painCave.errMsg,
171	"Error returned from the fortran force calculation.\n" );
172	painCave.isFatal = 1;
173	simError();
174	}
175
176	//store the tau and long range potential
177	curSnapshot->statData[Stats::LONGRANGEPOTENTIAL] = longRangePotential;
178	curSnapshot->statData[Stats::TAUXX] = tau[0];
179	curSnapshot->statData[Stats::TAUXY] = tau[1];
180	curSnapshot->statData[Stats::TAUXZ] = tau[2];
181	curSnapshot->statData[Stats::TAUYX] = tau[3];
182	curSnapshot->statData[Stats::TAUYY] = tau[4];
183	curSnapshot->statData[Stats::TAUYZ] = tau[5];
184	curSnapshot->statData[Stats::TAUZX] = tau[6];
185	curSnapshot->statData[Stats::TAUZY] = tau[7];
186	curSnapshot->statData[Stats::TAUZZ] = tau[8];
187	}
188
189
190	void ForceManager::postCalculation() {
191	typename SimInfo::MoleculeIterator mi;
192	Molecule* mol;
193	typename Molecule::RigidBodyIterator rbIter;
194	RigidBody* rb;
195
196	// collect the atomic forces onto rigid bodies
197	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
198	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
199	rb->calcForcesAndTorques();
200	}
201	}
202
203	}
204
205	} //end namespace oopse