src/integrators/myNVT.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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include "integrators/NVT.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
#include "utils/PhysicalConstants.hpp"

namespace OpenMD {

  NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6), maxIterNum_(4) {

    Globals* simParams = info_->getSimParams();

    if (!simParams->getUseIntialExtendedSystemState()) {
      Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
      snap->setThermostat(make_pair(0.0, 0.0));
    }
    
    if (!simParams->haveTargetTemp()) {
      sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp_!\n");
      painCave.isFatal = 1;
      painCave.severity = OPENMD_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 = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    } else {
      tauThermostat_ = simParams->getTauThermostat();
    }

    updateSizes();
  }

  void NVT::doUpdateSizes() {
    oldVel_.resize(info_->getNIntegrableObjects());
    oldJi_.resize(info_->getNIntegrableObjects());
  }

  void NVT:evolveChiA(){
    pair<RealType, RealType> thermostat = snap->getThermostat();
    RealType instTemp = thermo.getTemperature();
    thermostat.first += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
    thermostat.second += thermostat.first * dt2;
    snap->setThermostat(thermostat);
    oldChi_ = thermostat.first;
    oldChiInt_ = thermostat.second;
  }

  void NVT::evolveChiB(){
    pair<RealType, RealType> thermostat = snap->getThermostat();
    RealType instTemp = thermo.getTemperature();
    prevChi_ = thermostat.first;
    thermostat.first = oldChi_ + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
    thermostat.second = oldChiInt_ + dt2 * thermostat.first;
    snap->setThermostat(thermostat);
  }

  void NVT::moveA() {
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* sd;
    Vector3d Tb;
    Vector3d ji;
    RealType mass;
    Vector3d vel;
    Vector3d pos;
    Vector3d frc;

    pair<RealType, RealType> thermostat = snap->getThermostat();

    // We need the temperature at time = t for the chi update below:

    RealType instTemp = thermo.getTemperature();

    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {

      for (sd = mol->beginIntegrableObject(j); sd != NULL;
           sd = mol->nextIntegrableObject(j)) {

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

        mass = sd->getMass();

        // velocity half step (use chi from previous step here):
        vel += dt2 *PhysicalConstants::energyConvert/mass*frc 
          - dt2*thermostat.first*vel;
        
        // position whole step
        pos += dt * vel;

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

        if (sd->isDirectional()) {

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

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

          ji = sd->getJ();

          ji += dt2*PhysicalConstants::energyConvert*Tb 
            - dt2*thermostat.first *ji;

          rotAlgo_->rotate(sd, ji, dt);

          sd->setJ(ji);
        }
      }

    }
    
    flucQ_->moveA();
    rattle_->constraintA();

    // Finally, evolve chi a half step (just like a velocity) using
    // temperature at time t, not time t+dt/2
    this->evolveChiA();
    //thermostat.first += dt2 * (instTemp / targetTemp_ - 1.0) 
    //  / (tauThermostat_ * tauThermostat_);
    //thermostat.second += thermostat.first * dt2;

    //snap->setThermostat(thermostat);
  }

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

    /*
     * oldChi and prevChi are now oldChi_ and prevChi_ and are set in evolveChiB
     */
    //RealType oldChi = thermostat.first;
    //RealType  prevChi;

    index = 0;
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {

      for (sd = mol->beginIntegrableObject(j); sd != NULL;
           sd = mol->nextIntegrableObject(j)) {

        oldVel_[index] = sd->getVel();
        
        if (sd->isDirectional()) 
          oldJi_[index] = sd->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
      
      /*
       * calls this files modified version of evolveChiB();
       */
      this->evolveChiB();
      
      /* 
       * prevChi_ and thermostat.first are set in evolveChiB()
       */
      //prevChi = thermostat.first;
      //thermostat.first = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) 
      //  / (tauThermostat_ * tauThermostat_);

      /*
       * Since it is changed in a different method, need to get the updated version here
       */
      pair<RealType, RealType> thermostat = snap->getThermostat();  

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

          frc = sd->getFrc();
          mass = sd->getMass();

          // velocity half step

          vel = oldVel_[index] 
            + dt2/mass*PhysicalConstants::energyConvert * frc 
            - dt2*thermostat.first*oldVel_[index];
            
          sd->setVel(vel);

          if (sd->isDirectional()) {

            // get and convert the torque to body frame

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

            ji = oldJi_[index] + dt2*PhysicalConstants::energyConvert*Tb 
              - dt2*thermostat.first *oldJi_[index];

            sd->setJ(ji);
          }


          ++index;
        }
      }
    
      rattle_->constraintB();
      
      /* 
       * prevChi_ is defined in evolveChiB now
       */
      //if (fabs(prevChi - thermostat.first) <= chiTolerance_)
      if (fabs(prevChi_ - thermostat.first) <= chiTolerance_)
        break;

    }

    flucQ_->moveB();

    /* 
     * This has already happened in evolveChiB
     */
    //thermostat.second += dt2 * thermostat.first;
    //snap->setThermostat(thermostat);
  }

  void NVT::resetIntegrator() {
    snap->setThermostat(make_pair(0.0, 0.0));
  }
  
  RealType NVT::calcConservedQuantity() {

    pair<RealType, RealType> thermostat = snap->getThermostat();
    RealType conservedQuantity;
    RealType fkBT;
    RealType Energy;
    RealType thermostat_kinetic;
    RealType thermostat_potential;
    
    fkBT = info_->getNdf() *PhysicalConstants::kB *targetTemp_;

    Energy = thermo.getTotalEnergy();

    thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * thermostat.first * thermostat.first / (2.0 * PhysicalConstants::energyConvert);

    thermostat_potential = fkBT * thermostat.second / PhysicalConstants::energyConvert;

    conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;

    return conservedQuantity;
  }


}//end namespace OpenMD
Revision:	1997
Committed:	Thu May 29 21:03:19 2014 UTC (10 years, 11 months ago) by jmichalk
File size:	9652 byte(s)
Log Message:	myNVT.hpp and myNVT.cpp are my (Joe) attempts at separating out the chi evolution into evolveChiA and evolveChiB functions as a precursor to implementing a langevin thermostat
#	User	Rev	Content
1	jmichalk	1997	/*
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. Redistributions of source code must retain the above copyright
10			* notice, this list of conditions and the following disclaimer.
11			*
12			* 2. Redistributions in binary form must reproduce the above copyright
13			* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31			*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39			* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41			*/
42
43			#include "integrators/NVT.hpp"
44			#include "primitives/Molecule.hpp"
45			#include "utils/simError.h"
46			#include "utils/PhysicalConstants.hpp"
47
48			namespace OpenMD {
49
50			NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6), maxIterNum_(4) {
51
52			Globals* simParams = info_->getSimParams();
53
54			if (!simParams->getUseIntialExtendedSystemState()) {
55			Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
56			snap->setThermostat(make_pair(0.0, 0.0));
57			}
58
59			if (!simParams->haveTargetTemp()) {
60			sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp_!\n");
61			painCave.isFatal = 1;
62			painCave.severity = OPENMD_ERROR;
63			simError();
64			} else {
65			targetTemp_ = simParams->getTargetTemp();
66			}
67
68			// We must set tauThermostat.
69
70			if (!simParams->haveTauThermostat()) {
71			sprintf(painCave.errMsg, "If you use the constant temperature\n"
72			"\tintegrator, you must set tauThermostat.\n");
73
74			painCave.severity = OPENMD_ERROR;
75			painCave.isFatal = 1;
76			simError();
77			} else {
78			tauThermostat_ = simParams->getTauThermostat();
79			}
80
81			updateSizes();
82			}
83
84			void NVT::doUpdateSizes() {
85			oldVel_.resize(info_->getNIntegrableObjects());
86			oldJi_.resize(info_->getNIntegrableObjects());
87			}
88
89			void NVT:evolveChiA(){
90			pair<RealType, RealType> thermostat = snap->getThermostat();
91			RealType instTemp = thermo.getTemperature();
92			thermostat.first += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
93			thermostat.second += thermostat.first * dt2;
94			snap->setThermostat(thermostat);
95			oldChi_ = thermostat.first;
96			oldChiInt_ = thermostat.second;
97			}
98
99			void NVT::evolveChiB(){
100			pair<RealType, RealType> thermostat = snap->getThermostat();
101			RealType instTemp = thermo.getTemperature();
102			prevChi_ = thermostat.first;
103			thermostat.first = oldChi_ + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
104			thermostat.second = oldChiInt_ + dt2 * thermostat.first;
105			snap->setThermostat(thermostat);
106			}
107
108			void NVT::moveA() {
109			SimInfo::MoleculeIterator i;
110			Molecule::IntegrableObjectIterator j;
111			Molecule* mol;
112			StuntDouble* sd;
113			Vector3d Tb;
114			Vector3d ji;
115			RealType mass;
116			Vector3d vel;
117			Vector3d pos;
118			Vector3d frc;
119
120			pair<RealType, RealType> thermostat = snap->getThermostat();
121
122			// We need the temperature at time = t for the chi update below:
123
124			RealType instTemp = thermo.getTemperature();
125
126			for (mol = info_->beginMolecule(i); mol != NULL;
127			mol = info_->nextMolecule(i)) {
128
129			for (sd = mol->beginIntegrableObject(j); sd != NULL;
130			sd = mol->nextIntegrableObject(j)) {
131
132			vel = sd->getVel();
133			pos = sd->getPos();
134			frc = sd->getFrc();
135
136			mass = sd->getMass();
137
138			// velocity half step (use chi from previous step here):
139			vel += dt2 PhysicalConstants::energyConvert/massfrc
140			- dt2thermostat.firstvel;
141
142			// position whole step
143			pos += dt * vel;
144
145			sd->setVel(vel);
146			sd->setPos(pos);
147
148			if (sd->isDirectional()) {
149
150			//convert the torque to body frame
151			Tb = sd->lab2Body(sd->getTrq());
152
153			// get the angular momentum, and propagate a half step
154
155			ji = sd->getJ();
156
157			ji += dt2PhysicalConstants::energyConvertTb
158			- dt2thermostat.first ji;
159
160			rotAlgo_->rotate(sd, ji, dt);
161
162			sd->setJ(ji);
163			}
164			}
165
166			}
167
168			flucQ_->moveA();
169			rattle_->constraintA();
170
171			// Finally, evolve chi a half step (just like a velocity) using
172			// temperature at time t, not time t+dt/2
173			this->evolveChiA();
174			//thermostat.first += dt2 * (instTemp / targetTemp_ - 1.0)
175			// / (tauThermostat_ * tauThermostat_);
176			//thermostat.second += thermostat.first * dt2;
177
178			//snap->setThermostat(thermostat);
179			}
180
181			void NVT::moveB() {
182			SimInfo::MoleculeIterator i;
183			Molecule::IntegrableObjectIterator j;
184			Molecule* mol;
185			StuntDouble* sd;
186
187			Vector3d Tb;
188			Vector3d ji;
189			Vector3d vel;
190			Vector3d frc;
191			RealType mass;
192			RealType instTemp;
193			int index;
194			// Set things up for the iteration:
195
196			/*
197			* oldChi and prevChi are now oldChi_ and prevChi_ and are set in evolveChiB
198			*/
199			//RealType oldChi = thermostat.first;
200			//RealType prevChi;
201
202			index = 0;
203			for (mol = info_->beginMolecule(i); mol != NULL;
204			mol = info_->nextMolecule(i)) {
205
206			for (sd = mol->beginIntegrableObject(j); sd != NULL;
207			sd = mol->nextIntegrableObject(j)) {
208
209			oldVel_[index] = sd->getVel();
210
211			if (sd->isDirectional())
212			oldJi_[index] = sd->getJ();
213
214			++index;
215			}
216			}
217
218			// do the iteration:
219
220			for(int k = 0; k < maxIterNum_; k++) {
221			index = 0;
222			instTemp = thermo.getTemperature();
223
224			// evolve chi another half step using the temperature at t + dt/2
225
226			/*
227			* calls this files modified version of evolveChiB();
228			*/
229			this->evolveChiB();
230
231			/*
232			* prevChi_ and thermostat.first are set in evolveChiB()
233			*/
234			//prevChi = thermostat.first;
235			//thermostat.first = oldChi + dt2 * (instTemp / targetTemp_ - 1.0)
236			// / (tauThermostat_ * tauThermostat_);
237
238			/*
239			* Since it is changed in a different method, need to get the updated version here
240			*/
241			pair<RealType, RealType> thermostat = snap->getThermostat();
242
243			for (mol = info_->beginMolecule(i); mol != NULL;
244			mol = info_->nextMolecule(i)) {
245
246			for (sd = mol->beginIntegrableObject(j); sd != NULL;
247			sd = mol->nextIntegrableObject(j)) {
248
249			frc = sd->getFrc();
250			mass = sd->getMass();
251
252			// velocity half step
253
254			vel = oldVel_[index]
255			+ dt2/massPhysicalConstants::energyConvert frc
256			- dt2thermostat.firstoldVel_[index];
257
258			sd->setVel(vel);
259
260			if (sd->isDirectional()) {
261
262			// get and convert the torque to body frame
263
264			Tb = sd->lab2Body(sd->getTrq());
265
266			ji = oldJi_[index] + dt2PhysicalConstants::energyConvertTb
267			- dt2thermostat.first oldJi_[index];
268
269			sd->setJ(ji);
270			}
271
272
273			++index;
274			}
275			}
276
277			rattle_->constraintB();
278
279			/*
280			* prevChi_ is defined in evolveChiB now
281			*/
282			//if (fabs(prevChi - thermostat.first) <= chiTolerance_)
283			if (fabs(prevChi_ - thermostat.first) <= chiTolerance_)
284			break;
285
286			}
287
288			flucQ_->moveB();
289
290			/*
291			* This has already happened in evolveChiB
292			*/
293			//thermostat.second += dt2 * thermostat.first;
294			//snap->setThermostat(thermostat);
295			}
296
297			void NVT::resetIntegrator() {
298			snap->setThermostat(make_pair(0.0, 0.0));
299			}
300
301			RealType NVT::calcConservedQuantity() {
302
303			pair<RealType, RealType> thermostat = snap->getThermostat();
304			RealType conservedQuantity;
305			RealType fkBT;
306			RealType Energy;
307			RealType thermostat_kinetic;
308			RealType thermostat_potential;
309
310			fkBT = info_->getNdf() PhysicalConstants::kB targetTemp_;
311
312			Energy = thermo.getTotalEnergy();
313
314			thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * thermostat.first * thermostat.first / (2.0 * PhysicalConstants::energyConvert);
315
316			thermostat_potential = fkBT * thermostat.second / PhysicalConstants::energyConvert;
317
318			conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
319
320			return conservedQuantity;
321			}
322
323
324			}//end namespace OpenMD