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, 8 months ago) by tim
File size:	6728 byte(s)
Log Message:	constraints in progress
#	User	Rev	Content
1	tim	1722	/*
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	tim	1804	#include "primitives/Molecule.hpp"
36			#include "UseTheForce/doForces_interface.h"
37			#include "utils/simError.h"
38	tim	1722	namespace oopse {
39
40			void ForceManager::calcForces(bool needPotential, bool needStress) {
41
42	tim	1738	if (!info_->isFortranInitialized()) {
43			info_->update();
44			}
45	tim	1722
46	tim	1738	preCalculation();
47
48			calcShortRangeInteraction();
49
50	tim	1804	calcLongRangeInteraction(needPotential, needStress);
51	tim	1738
52	tim	1804	postCalculation();
53	tim	1738
54			}
55
56			void ForceManager::preCalculation() {
57	tim	1804	SimInfo::MoleculeIterator mi;
58	tim	1722	Molecule* mol;
59	tim	1804	Molecule::AtomIterator ai;
60	tim	1722	Atom* atom;
61	tim	1881	Molecule::RigidBodyIterator rbIter;
62			RigidBody* rb;
63
64	tim	1722	// 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	tim	1881	atom->zeroForcesAndTorques();
69	tim	1722	}
70	tim	1881
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	tim	1738	}
76
77			}
78	tim	1722
79	tim	1738	void ForceManager::calcShortRangeInteraction() {
80			Molecule* mol;
81			RigidBody* rb;
82			Bond* bond;
83			Bend* bend;
84			Torsion* torsion;
85	tim	1804	SimInfo::MoleculeIterator mi;
86			Molecule::RigidBodyIterator rbIter;
87			Molecule::BondIterator bondIter;;
88			Molecule::BendIterator bendIter;
89			Molecule::TorsionIterator torsionIter;
90	tim	1738
91	tim	1722	//calculate short range interactions
92			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
93
94	tim	1738	//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	tim	1722
99	tim	1738	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
100	tim	1804	bond->calcForce();
101	tim	1738	}
102
103			for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
104	tim	1804	bend->calcForce();
105	tim	1738	}
106
107			for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
108	tim	1804	torsion->calcForce();
109	tim	1738	}
110
111			}
112
113	tim	1901	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	tim	1738	}
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	tim	1813	double* electroFrame;
130	tim	1738	double* rc;
131
132	tim	1722	//get current snapshot from SimInfo
133	tim	1804	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
134	tim	1722
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	tim	1813	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
142	tim	1722
143			//calculate the center of mass of cutoff group
144	tim	1804	SimInfo::MoleculeIterator mi;
145	tim	1738	Molecule* mol;
146	tim	1804	Molecule::CutoffGroupIterator ci;
147	tim	1738	CutoffGroup* cg;
148			Vector3d com;
149			std::vector<Vector3d> rcGroup;
150
151	tim	1722	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	tim	1804	cg->getCOM(com);
156	tim	1722	rcGroup.push_back(com);
157			}
158			}// end for (mol)
159
160	tim	1804	rc = rcGroup[0].getArrayPointer();
161	tim	1738	} else {
162	tim	1722	// 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	tim	1738	double longRangePotential = 0.0;
168			Mat3x3d tau;
169			short int passedCalcPot = needPotential;
170			short int passedCalcStress = needStress;
171			int isError = 0;
172	tim	1722
173			doForceLoop( pos,
174			rc,
175			A,
176	tim	1813	electroFrame,
177	tim	1722	frc,
178			trq,
179	tim	1804	tau.getArrayPointer(),
180	tim	1722	&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	tim	1804	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
194	tim	1805	curSnapshot->statData.setTau(tau);
195	tim	1738	}
196	tim	1722
197	tim	1738
198			void ForceManager::postCalculation() {
199	tim	1804	SimInfo::MoleculeIterator mi;
200	tim	1738	Molecule* mol;
201	tim	1804	Molecule::RigidBodyIterator rbIter;
202	tim	1738	RigidBody* rb;
203
204	tim	1722	// collect the atomic forces onto rigid bodies
205			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
206	tim	1738	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
207			rb->calcForcesAndTorques();
208			}
209	tim	1722	}
210
211			}
212
213			} //end namespace oopse