src/integrators/NVT.cpp

 /*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
#include "integrators/NVT.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
#include "utils/OOPSEConstant.hpp"

namespace oopse {

NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6) {

    Globals* simParams = info_->getSimParams();

    if (simParams->getUseInitXSstate()) {
        Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
        currSnapshot->setChi(0.0);
        currSnapshot->setIntegralOfChiDt(0.0);
    }
    
    if (!simParams->haveTargetTemp()) {
        sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp_!\n");
        painCave.isFatal = 1;
        painCave.severity = OOPSE_ERROR;
        simError();
    } else {
        targetTemp_ = simParams->getTargetTemp();
    }

    // We must set tauThermostat_.

    if (!simParams->haveTauThermostat()) {
        sprintf(painCave.errMsg, "If you use the constant temperature\n"
                                     "\tintegrator, you must set tauThermostat_.\n");

        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();
    } else {
        tauThermostat_ = simParams->getTauThermostat();
    }

    update();
}

void NVT::doUpdate() {
    oldVel_.resize(info_->getNIntegrableObjects());
    oldJi_.resize(info_->getNIntegrableObjects());    
}
void NVT::moveA() {
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* integrableObject;
    Vector3d Tb;
    Vector3d ji;
    double mass;
    Vector3d vel;
    Vector3d pos;
    Vector3d frc;

    double chi = currentSnapshot_->getChi();
    double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
    
    // We need the temperature at time = t for the chi update below:

    double instTemp = thermo.getTemperature();

    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
               integrableObject = mol->nextIntegrableObject(j)) {

        vel = integrableObject->getVel();
        pos = integrableObject->getPos();
        frc = integrableObject->getFrc();

        mass = integrableObject->getMass();

        // velocity half step  (use chi from previous step here):
        //vel[j] += dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - vel[j]*chi);
        vel += dt2 *OOPSEConstant::energyConvert/mass*frc - dt2*chi*vel;
        
        // position whole step
        //pos[j] += dt * vel[j];
        pos += dt * vel;

        integrableObject->setVel(vel);
        integrableObject->setPos(pos);

        if (integrableObject->isDirectional()) {

            //convert the torque to body frame
            Tb = integrableObject->lab2Body(integrableObject->getTrq());

            // get the angular momentum, and propagate a half step

            ji = integrableObject->getJ();

            //ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi);
            ji += dt2*OOPSEConstant::energyConvert*Tb - dt2*chi *ji;
            rotAlgo->rotate(integrableObject, ji, dt);

            integrableObject->setJ(ji);
        }
    }

    }
    
    rattle->constraintA();

    // Finally, evolve chi a half step (just like a velocity) using
    // temperature at time t, not time t+dt/2

    
    chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
    integralOfChidt += chi * dt2;

    currentSnapshot_->setChi(chi);
    currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
}

void NVT::moveB() {
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* integrableObject;
    
    Vector3d Tb;
    Vector3d ji;    
    Vector3d vel;
    Vector3d frc;
    double mass;
    double instTemp;
    int index;
    // Set things up for the iteration:

    double chi = currentSnapshot_->getChi();
    double oldChi = chi;
    double  prevChi;
    double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();

    index = 0;
    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
               integrableObject = mol->nextIntegrableObject(j)) {
                oldVel_[index] = integrableObject->getVel();
                oldJi_[index] = integrableObject->getJ();                

                ++index;    
        }
           
    }

    // do the iteration:

    for(int k = 0; k < maxIterNum_; k++) {
        index = 0;
        instTemp = thermo.getTemperature();

        // evolve chi another half step using the temperature at t + dt/2

        prevChi = chi;
        chi = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);

        for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
            for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
                   integrableObject = mol->nextIntegrableObject(j)) {

                frc = integrableObject->getFrc();
                vel = integrableObject->getVel();

                mass = integrableObject->getMass();

                // velocity half step
                //for(j = 0; j < 3; j++)
                //    vel[j] = oldVel_[3*i+j] + dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - oldVel_[3*i + j]*chi);
                vel = oldVel_[index] + dt2/mass*OOPSEConstant::energyConvert * frc - dt2*chi*oldVel_[index];
            
                integrableObject->setVel(vel);

                if (integrableObject->isDirectional()) {

                    // get and convert the torque to body frame

                    Tb =  integrableObject->lab2Body(integrableObject->getTrq());

                    //for(j = 0; j < 3; j++)
                    //    ji[j] = oldJi_[3*i + j] + dt2 * (Tb[j] * OOPSEConstant::energyConvert - oldJi_[3*i+j]*chi);
                    ji = oldJi_[index] + dt2*OOPSEConstant::energyConvert*Tb - dt2*chi *oldJi_[index];

                    integrableObject->setJ(ji);
                }


                ++index;
            }
        }
    

        rattle->constraintB();

        if (fabs(prevChi - chi) <= chiTolerance_)
            break;

    }

    integralOfChidt += dt2 * chi;

    currentSnapshot_->setChi(chi);
    currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
}


double NVT::calcConservedQuantity() {

    double chi = currentSnapshot_->getChi();
    double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
    double conservedQuantity;
    double fkBT;
    double Energy;
    double thermostat_kinetic;
    double thermostat_potential;
    
    fkBT = info_->getNdf() *OOPSEConstant::kB *targetTemp_;

    Energy = thermo.getTotalE();

    thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * OOPSEConstant::energyConvert);

    thermostat_potential = fkBT * integralOfChidt / OOPSEConstant::energyConvert;

    conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;

    return conservedQuantity;
}


}//end namespace oopse
Revision:	1927
Committed:	Wed Jan 12 17:14:35 2005 UTC (21 years, 4 months ago) by tim
File size:	9263 byte(s)
Log Message:	change license
#	User	Rev	Content
1	tim	1927	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42	tim	1821	#include "integrators/NVT.hpp"
43			#include "primitives/Molecule.hpp"
44			#include "utils/simError.h"
45			#include "utils/OOPSEConstant.hpp"
46	tim	1837
47	tim	1765	namespace oopse {
48	tim	1762
49	tim	1774	NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6) {
50	tim	1762
51	tim	1841	Globals* simParams = info_->getSimParams();
52	tim	1762
53	tim	1841	if (simParams->getUseInitXSstate()) {
54	tim	1774	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
55			currSnapshot->setChi(0.0);
56			currSnapshot->setIntegralOfChiDt(0.0);
57			}
58
59	tim	1841	if (!simParams->haveTargetTemp()) {
60	tim	1774	sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp_!\n");
61			painCave.isFatal = 1;
62			painCave.severity = OOPSE_ERROR;
63			simError();
64			} else {
65	tim	1841	targetTemp_ = simParams->getTargetTemp();
66	tim	1774	}
67	tim	1762
68	tim	1774	// We must set tauThermostat_.
69	tim	1762
70	tim	1841	if (!simParams->haveTauThermostat()) {
71	tim	1774	sprintf(painCave.errMsg, "If you use the constant temperature\n"
72			"\tintegrator, you must set tauThermostat_.\n");
73	tim	1762
74	tim	1774	painCave.severity = OOPSE_ERROR;
75			painCave.isFatal = 1;
76			simError();
77			} else {
78	tim	1841	tauThermostat_ = simParams->getTauThermostat();
79	tim	1762	}
80
81	tim	1774	update();
82	tim	1762	}
83
84	tim	1867	void NVT::doUpdate() {
85	tim	1774	oldVel_.resize(info_->getNIntegrableObjects());
86			oldJi_.resize(info_->getNIntegrableObjects());
87			}
88	tim	1765	void NVT::moveA() {
89	tim	1821	SimInfo::MoleculeIterator i;
90			Molecule::IntegrableObjectIterator j;
91	tim	1765	Molecule* mol;
92			StuntDouble* integrableObject;
93	tim	1762	Vector3d Tb;
94			Vector3d ji;
95			double mass;
96			Vector3d vel;
97			Vector3d pos;
98			Vector3d frc;
99
100	tim	1867	double chi = currentSnapshot_->getChi();
101			double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
102	tim	1821
103	tim	1762	// We need the temperature at time = t for the chi update below:
104
105	tim	1821	double instTemp = thermo.getTemperature();
106	tim	1762
107	tim	1765	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
108			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
109			integrableObject = mol->nextIntegrableObject(j)) {
110	tim	1762
111	tim	1765	vel = integrableObject->getVel();
112			pos = integrableObject->getPos();
113			frc = integrableObject->getFrc();
114	tim	1762
115	tim	1765	mass = integrableObject->getMass();
116	tim	1762
117	tim	1765	// velocity half step (use chi from previous step here):
118	tim	1821	//vel[j] += dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - vel[j]*chi);
119	tim	1852	vel += dt2 OOPSEConstant::energyConvert/massfrc - dt2chivel;
120	tim	1765
121			// position whole step
122			//pos[j] += dt * vel[j];
123	tim	1774	pos += dt * vel;
124	tim	1762
125	tim	1765	integrableObject->setVel(vel);
126			integrableObject->setPos(pos);
127	tim	1762
128	tim	1765	if (integrableObject->isDirectional()) {
129	tim	1762
130	tim	1871	//convert the torque to body frame
131			Tb = integrableObject->lab2Body(integrableObject->getTrq());
132	tim	1762
133			// get the angular momentum, and propagate a half step
134
135	tim	1765	ji = integrableObject->getJ();
136	tim	1762
137	tim	1821	//ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi);
138			ji += dt2OOPSEConstant::energyConvertTb - dt2chi ji;
139			rotAlgo->rotate(integrableObject, ji, dt);
140	tim	1762
141	tim	1765	integrableObject->setJ(ji);
142	tim	1762	}
143			}
144
145	tim	1765	}
146
147	tim	1901	rattle->constraintA();
148	tim	1762
149			// Finally, evolve chi a half step (just like a velocity) using
150			// temperature at time t, not time t+dt/2
151
152	tim	1765
153	tim	1774	chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
154			integralOfChidt += chi * dt2;
155	tim	1762
156	tim	1867	currentSnapshot_->setChi(chi);
157			currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
158	tim	1762	}
159
160	tim	1765	void NVT::moveB() {
161	tim	1821	SimInfo::MoleculeIterator i;
162			Molecule::IntegrableObjectIterator j;
163	tim	1765	Molecule* mol;
164			StuntDouble* integrableObject;
165
166			Vector3d Tb;
167			Vector3d ji;
168			Vector3d vel;
169			Vector3d frc;
170	tim	1762	double mass;
171			double instTemp;
172	tim	1765	int index;
173	tim	1762	// Set things up for the iteration:
174
175	tim	1867	double chi = currentSnapshot_->getChi();
176	tim	1821	double oldChi = chi;
177			double prevChi;
178	tim	1867	double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
179	tim	1762
180	tim	1765	index = 0;
181			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
182			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
183			integrableObject = mol->nextIntegrableObject(j)) {
184			oldVel_[index] = integrableObject->getVel();
185			oldJi_[index] = integrableObject->getJ();
186	tim	1868
187			++index;
188	tim	1762	}
189	tim	1868
190	tim	1762	}
191
192			// do the iteration:
193
194	tim	1765	for(int k = 0; k < maxIterNum_; k++) {
195			index = 0;
196	tim	1821	instTemp = thermo.getTemperature();
197	tim	1762
198			// evolve chi another half step using the temperature at t + dt/2
199
200			prevChi = chi;
201	tim	1774	chi = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
202	tim	1762
203	tim	1765	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
204			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
205			integrableObject = mol->nextIntegrableObject(j)) {
206	tim	1762
207	tim	1765	frc = integrableObject->getFrc();
208			vel = integrableObject->getVel();
209	tim	1762
210	tim	1765	mass = integrableObject->getMass();
211	tim	1762
212	tim	1765	// velocity half step
213			//for(j = 0; j < 3; j++)
214	tim	1821	// vel[j] = oldVel_[3i+j] + dt2 ((frc[j] / mass ) * OOPSEConstant::energyConvert - oldVel_[3i + j]chi);
215			vel = oldVel_[index] + dt2/massOOPSEConstant::energyConvert frc - dt2chioldVel_[index];
216	tim	1765
217			integrableObject->setVel(vel);
218	tim	1762
219	tim	1765	if (integrableObject->isDirectional()) {
220	tim	1762
221	tim	1765	// get and convert the torque to body frame
222	tim	1762
223	tim	1871	Tb = integrableObject->lab2Body(integrableObject->getTrq());
224	tim	1762
225	tim	1765	//for(j = 0; j < 3; j++)
226	tim	1821	// ji[j] = oldJi_[3i + j] + dt2 (Tb[j] * OOPSEConstant::energyConvert - oldJi_[3i+j]chi);
227	tim	1868	ji = oldJi_[index] + dt2OOPSEConstant::energyConvertTb - dt2chi oldJi_[index];
228	tim	1762
229	tim	1765	integrableObject->setJ(ji);
230			}
231	tim	1852
232
233			++index;
234	tim	1762	}
235			}
236	tim	1765
237	tim	1762
238	tim	1901	rattle->constraintB();
239	tim	1762
240	tim	1821	if (fabs(prevChi - chi) <= chiTolerance_)
241	tim	1762	break;
242	tim	1765
243	tim	1762	}
244
245	tim	1774	integralOfChidt += dt2 * chi;
246	tim	1762
247	tim	1867	currentSnapshot_->setChi(chi);
248			currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
249	tim	1762	}
250
251
252	tim	1774	double NVT::calcConservedQuantity() {
253	tim	1867
254			double chi = currentSnapshot_->getChi();
255			double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
256	tim	1762	double conservedQuantity;
257			double fkBT;
258			double Energy;
259			double thermostat_kinetic;
260			double thermostat_potential;
261	tim	1821
262			fkBT = info_->getNdf() OOPSEConstant::kB targetTemp_;
263	tim	1762
264	tim	1821	Energy = thermo.getTotalE();
265	tim	1762
266	tim	1821	thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * OOPSEConstant::energyConvert);
267	tim	1762
268	tim	1821	thermostat_potential = fkBT * integralOfChidt / OOPSEConstant::energyConvert;
269	tim	1762
270			conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
271
272			return conservedQuantity;
273			}
274
275
276	tim	1765	}//end namespace oopse