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), maxIterNum_(4) {

    Globals* simParams = info_->getSimParams();

    if (!simParams->getUseIntialExtendedSystemState()) {
      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);
  }

  void NVT::resetIntegrator() {
      currentSnapshot_->setChi(0.0);
      currentSnapshot_->setIntegralOfChiDt(0.0);
  }
  
  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:	665
Committed:	Thu Oct 13 22:26:47 2005 UTC (20 years ago) by tim
File size:	8941 byte(s)
Log Message:	rewrite Globals
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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			#include "integrators/NVT.hpp"
43			#include "primitives/Molecule.hpp"
44	tim	3	#include "utils/simError.h"
45	gezelter	246	#include "utils/OOPSEConstant.hpp"
46	gezelter	2
47	gezelter	246	namespace oopse {
48	gezelter	2
49	gezelter	507	NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6), maxIterNum_(4) {
50	gezelter	2
51	gezelter	246	Globals* simParams = info_->getSimParams();
52	gezelter	2
53	tim	665	if (!simParams->getUseIntialExtendedSystemState()) {
54	gezelter	507	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
55			currSnapshot->setChi(0.0);
56			currSnapshot->setIntegralOfChiDt(0.0);
57	gezelter	246	}
58
59			if (!simParams->haveTargetTemp()) {
60	gezelter	507	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	gezelter	246	} else {
65	gezelter	507	targetTemp_ = simParams->getTargetTemp();
66	gezelter	246	}
67	gezelter	2
68	gezelter	246	// We must set tauThermostat_.
69	gezelter	2
70	gezelter	246	if (!simParams->haveTauThermostat()) {
71	gezelter	507	sprintf(painCave.errMsg, "If you use the constant temperature\n"
72			"\tintegrator, you must set tauThermostat_.\n");
73	gezelter	2
74	gezelter	507	painCave.severity = OOPSE_ERROR;
75			painCave.isFatal = 1;
76			simError();
77	gezelter	246	} else {
78	gezelter	507	tauThermostat_ = simParams->getTauThermostat();
79	gezelter	2	}
80
81	gezelter	246	update();
82	gezelter	507	}
83	gezelter	2
84	gezelter	507	void NVT::doUpdate() {
85	gezelter	246	oldVel_.resize(info_->getNIntegrableObjects());
86			oldJi_.resize(info_->getNIntegrableObjects());
87	gezelter	507	}
88			void NVT::moveA() {
89	gezelter	246	SimInfo::MoleculeIterator i;
90			Molecule::IntegrableObjectIterator j;
91			Molecule* mol;
92			StuntDouble* integrableObject;
93			Vector3d Tb;
94			Vector3d ji;
95			double mass;
96			Vector3d vel;
97			Vector3d pos;
98			Vector3d frc;
99	gezelter	2
100	gezelter	246	double chi = currentSnapshot_->getChi();
101			double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
102
103			// We need the temperature at time = t for the chi update below:
104	gezelter	2
105	gezelter	246	double instTemp = thermo.getTemperature();
106	gezelter	2
107	gezelter	246	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
108	gezelter	507	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
109			integrableObject = mol->nextIntegrableObject(j)) {
110	gezelter	2
111	gezelter	246	vel = integrableObject->getVel();
112			pos = integrableObject->getPos();
113			frc = integrableObject->getFrc();
114	gezelter	2
115	gezelter	246	mass = integrableObject->getMass();
116	gezelter	2
117	gezelter	246	// velocity half step (use chi from previous step here):
118			//vel[j] += dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - vel[j]*chi);
119			vel += dt2 OOPSEConstant::energyConvert/massfrc - dt2chivel;
120
121			// position whole step
122			//pos[j] += dt * vel[j];
123			pos += dt * vel;
124	gezelter	2
125	gezelter	246	integrableObject->setVel(vel);
126			integrableObject->setPos(pos);
127	gezelter	2
128	gezelter	246	if (integrableObject->isDirectional()) {
129	gezelter	2
130	gezelter	507	//convert the torque to body frame
131			Tb = integrableObject->lab2Body(integrableObject->getTrq());
132	gezelter	2
133	gezelter	507	// get the angular momentum, and propagate a half step
134	gezelter	2
135	gezelter	507	ji = integrableObject->getJ();
136	gezelter	2
137	gezelter	507	//ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi);
138			ji += dt2OOPSEConstant::energyConvertTb - dt2chi ji;
139			rotAlgo->rotate(integrableObject, ji, dt);
140	gezelter	2
141	gezelter	507	integrableObject->setJ(ji);
142	gezelter	246	}
143	gezelter	507	}
144	gezelter	2
145			}
146	gezelter	246
147			rattle->constraintA();
148	gezelter	2
149	gezelter	246	// Finally, evolve chi a half step (just like a velocity) using
150			// temperature at time t, not time t+dt/2
151	gezelter	2
152	gezelter	246
153			chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
154			integralOfChidt += chi * dt2;
155	gezelter	2
156	gezelter	246	currentSnapshot_->setChi(chi);
157			currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
158	gezelter	507	}
159	gezelter	2
160	gezelter	507	void NVT::moveB() {
161	gezelter	246	SimInfo::MoleculeIterator i;
162			Molecule::IntegrableObjectIterator j;
163			Molecule* mol;
164			StuntDouble* integrableObject;
165
166			Vector3d Tb;
167			Vector3d ji;
168			Vector3d vel;
169			Vector3d frc;
170			double mass;
171			double instTemp;
172			int index;
173			// Set things up for the iteration:
174	gezelter	2
175	gezelter	246	double chi = currentSnapshot_->getChi();
176			double oldChi = chi;
177			double prevChi;
178			double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
179	gezelter	2
180	gezelter	246	index = 0;
181			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
182	gezelter	507	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
183			integrableObject = mol->nextIntegrableObject(j)) {
184			oldVel_[index] = integrableObject->getVel();
185			oldJi_[index] = integrableObject->getJ();
186	gezelter	2
187	gezelter	507	++index;
188			}
189	gezelter	246
190	gezelter	2	}
191
192	gezelter	246	// do the iteration:
193	gezelter	2
194	gezelter	246	for(int k = 0; k < maxIterNum_; k++) {
195	gezelter	507	index = 0;
196			instTemp = thermo.getTemperature();
197	gezelter	2
198	gezelter	507	// evolve chi another half step using the temperature at t + dt/2
199	gezelter	2
200	gezelter	507	prevChi = chi;
201			chi = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
202	gezelter	2
203	gezelter	507	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	gezelter	2
207	gezelter	507	frc = integrableObject->getFrc();
208			vel = integrableObject->getVel();
209	gezelter	2
210	gezelter	507	mass = integrableObject->getMass();
211	gezelter	2
212	gezelter	507	// velocity half step
213			//for(j = 0; j < 3; j++)
214			// 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	gezelter	246
217	gezelter	507	integrableObject->setVel(vel);
218	gezelter	2
219	gezelter	507	if (integrableObject->isDirectional()) {
220	gezelter	2
221	gezelter	507	// get and convert the torque to body frame
222	gezelter	2
223	gezelter	507	Tb = integrableObject->lab2Body(integrableObject->getTrq());
224	gezelter	2
225	gezelter	507	//for(j = 0; j < 3; j++)
226			// ji[j] = oldJi_[3i + j] + dt2 (Tb[j] * OOPSEConstant::energyConvert - oldJi_[3i+j]chi);
227			ji = oldJi_[index] + dt2OOPSEConstant::energyConvertTb - dt2chi oldJi_[index];
228	gezelter	2
229	gezelter	507	integrableObject->setJ(ji);
230			}
231	gezelter	2
232
233	gezelter	507	++index;
234			}
235			}
236	gezelter	2
237
238	gezelter	507	rattle->constraintB();
239	gezelter	2
240	gezelter	507	if (fabs(prevChi - chi) <= chiTolerance_)
241			break;
242	gezelter	2
243	gezelter	246	}
244	gezelter	2
245	gezelter	246	integralOfChidt += dt2 * chi;
246	gezelter	2
247	gezelter	246	currentSnapshot_->setChi(chi);
248			currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
249	gezelter	507	}
250	gezelter	2
251	tim	546	void NVT::resetIntegrator() {
252			currentSnapshot_->setChi(0.0);
253			currentSnapshot_->setIntegralOfChiDt(0.0);
254			}
255
256	gezelter	507	double NVT::calcConservedQuantity() {
257	gezelter	2
258	gezelter	246	double chi = currentSnapshot_->getChi();
259			double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
260			double conservedQuantity;
261			double fkBT;
262			double Energy;
263			double thermostat_kinetic;
264			double thermostat_potential;
265
266			fkBT = info_->getNdf() OOPSEConstant::kB targetTemp_;
267	gezelter	2
268	gezelter	246	Energy = thermo.getTotalE();
269	gezelter	2
270	gezelter	246	thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * OOPSEConstant::energyConvert);
271	gezelter	2
272	gezelter	246	thermostat_potential = fkBT * integralOfChidt / OOPSEConstant::energyConvert;
273	gezelter	2
274	gezelter	246	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
275	gezelter	2
276	gezelter	246	return conservedQuantity;
277	gezelter	507	}
278	gezelter	2
279
280	gezelter	246	}//end namespace oopse