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;

    // 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;
    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();
        }

    }
    
}

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:	1813
Committed:	Wed Dec 1 17:38:32 2004 UTC (19 years, 7 months ago) by tim
File size:	6079 byte(s)
Log Message:	refactory AtomType
#	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
62	// forces are zeroed here, before any are accumulated.
63	// NOTE: do not rezero the forces in Fortran.
64	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
65	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
66	atom->zeroForces();
67	}
68	}
69
70	}
71
72	void ForceManager::calcShortRangeInteraction() {
73	Molecule* mol;
74	RigidBody* rb;
75	Bond* bond;
76	Bend* bend;
77	Torsion* torsion;
78	SimInfo::MoleculeIterator mi;
79	Molecule::RigidBodyIterator rbIter;
80	Molecule::BondIterator bondIter;;
81	Molecule::BendIterator bendIter;
82	Molecule::TorsionIterator torsionIter;
83
84	//calculate short range interactions
85	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
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->updateAtoms();
90	}
91
92	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
93	bond->calcForce();
94	}
95
96	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
97	bend->calcForce();
98	}
99
100	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
101	torsion->calcForce();
102	}
103
104	}
105
106	}
107
108	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
109	Snapshot* curSnapshot;
110	DataStorage* config;
111	double* frc;
112	double* pos;
113	double* trq;
114	double* A;
115	double* electroFrame;
116	double* rc;
117
118	//get current snapshot from SimInfo
119	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
120
121	//get array pointers
122	config = &(curSnapshot->atomData);
123	frc = config->getArrayPointer(DataStorage::dslForce);
124	pos = config->getArrayPointer(DataStorage::dslPosition);
125	trq = config->getArrayPointer(DataStorage::dslTorque);
126	A = config->getArrayPointer(DataStorage::dslAmat);
127	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
128
129	//calculate the center of mass of cutoff group
130	SimInfo::MoleculeIterator mi;
131	Molecule* mol;
132	Molecule::CutoffGroupIterator ci;
133	CutoffGroup* cg;
134	Vector3d com;
135	std::vector<Vector3d> rcGroup;
136
137	if(info_->getNCutoffGroups() > 0){
138
139	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
140	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
141	cg->getCOM(com);
142	rcGroup.push_back(com);
143	}
144	}// end for (mol)
145
146	rc = rcGroup[0].getArrayPointer();
147	} else {
148	// center of mass of the group is the same as position of the atom if cutoff group does not exist
149	rc = pos;
150	}
151
152	//initialize data before passing to fortran
153	double longRangePotential = 0.0;
154	Mat3x3d tau;
155	short int passedCalcPot = needPotential;
156	short int passedCalcStress = needStress;
157	int isError = 0;
158
159	doForceLoop( pos,
160	rc,
161	A,
162	electroFrame,
163	frc,
164	trq,
165	tau.getArrayPointer(),
166	&longRangePotential,
167	&passedCalcPot,
168	&passedCalcStress,
169	&isError );
170
171	if( isError ){
172	sprintf( painCave.errMsg,
173	"Error returned from the fortran force calculation.\n" );
174	painCave.isFatal = 1;
175	simError();
176	}
177
178	//store the tau and long range potential
179	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
180	curSnapshot->statData.setTau(tau);
181	}
182
183
184	void ForceManager::postCalculation() {
185	SimInfo::MoleculeIterator mi;
186	Molecule* mol;
187	Molecule::RigidBodyIterator rbIter;
188	RigidBody* rb;
189
190	// collect the atomic forces onto rigid bodies
191	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
192	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
193	rb->calcForcesAndTorques();
194	}
195	}
196
197	}
198
199	} //end namespace oopse