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();
        }

    }
    
}

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:	1881
Committed:	Fri Dec 10 16:14:53 2004 UTC (19 years, 9 months ago) by tim
File size:	6385 byte(s)
Log Message:	forget to zero out the torque. Sticky and Dipole is working now
#	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	}
114
115	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
116	Snapshot* curSnapshot;
117	DataStorage* config;
118	double* frc;
119	double* pos;
120	double* trq;
121	double* A;
122	double* electroFrame;
123	double* rc;
124
125	//get current snapshot from SimInfo
126	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
127
128	//get array pointers
129	config = &(curSnapshot->atomData);
130	frc = config->getArrayPointer(DataStorage::dslForce);
131	pos = config->getArrayPointer(DataStorage::dslPosition);
132	trq = config->getArrayPointer(DataStorage::dslTorque);
133	A = config->getArrayPointer(DataStorage::dslAmat);
134	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
135
136	//calculate the center of mass of cutoff group
137	SimInfo::MoleculeIterator mi;
138	Molecule* mol;
139	Molecule::CutoffGroupIterator ci;
140	CutoffGroup* cg;
141	Vector3d com;
142	std::vector<Vector3d> rcGroup;
143
144	if(info_->getNCutoffGroups() > 0){
145
146	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
147	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
148	cg->getCOM(com);
149	rcGroup.push_back(com);
150	}
151	}// end for (mol)
152
153	rc = rcGroup[0].getArrayPointer();
154	} else {
155	// center of mass of the group is the same as position of the atom if cutoff group does not exist
156	rc = pos;
157	}
158
159	//initialize data before passing to fortran
160	double longRangePotential = 0.0;
161	Mat3x3d tau;
162	short int passedCalcPot = needPotential;
163	short int passedCalcStress = needStress;
164	int isError = 0;
165
166	doForceLoop( pos,
167	rc,
168	A,
169	electroFrame,
170	frc,
171	trq,
172	tau.getArrayPointer(),
173	&longRangePotential,
174	&passedCalcPot,
175	&passedCalcStress,
176	&isError );
177
178	if( isError ){
179	sprintf( painCave.errMsg,
180	"Error returned from the fortran force calculation.\n" );
181	painCave.isFatal = 1;
182	simError();
183	}
184
185	//store the tau and long range potential
186	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
187	curSnapshot->statData.setTau(tau);
188	}
189
190
191	void ForceManager::postCalculation() {
192	SimInfo::MoleculeIterator mi;
193	Molecule* mol;
194	Molecule::RigidBodyIterator rbIter;
195	RigidBody* rb;
196
197	// collect the atomic forces onto rigid bodies
198	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
199	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
200	rb->calcForcesAndTorques();
201	}
202	}
203
204	}
205
206	} //end namespace oopse