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. 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, 24107 (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::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

    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:

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

      prevChi = thermostat.first;
      thermostat.first = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) 
        / (tauThermostat_ * tauThermostat_);

      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();
          vel = sd->getVel();

          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();

      if (fabs(prevChi - thermostat.first) <= chiTolerance_)
        break;

    }

    flucQ_->moveB();

    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:	1764
Committed:	Tue Jul 3 18:32:27 2012 UTC (12 years, 10 months ago) by gezelter
File size:	8241 byte(s)
Log Message:	Refactored Snapshot and Stats to use the Accumulator classes. Collected a number of methods into Thermo that belonged there.
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43			#include "integrators/NVT.hpp"
44			#include "primitives/Molecule.hpp"
45	tim	3	#include "utils/simError.h"
46	gezelter	1390	#include "utils/PhysicalConstants.hpp"
47	gezelter	2
48	gezelter	1390	namespace OpenMD {
49	gezelter	2
50	gezelter	507	NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6), maxIterNum_(4) {
51	gezelter	2
52	gezelter	246	Globals* simParams = info_->getSimParams();
53	gezelter	2
54	tim	665	if (!simParams->getUseIntialExtendedSystemState()) {
55	gezelter	1764	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
56			snap->setThermostat(make_pair(0.0, 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	gezelter	1390	painCave.severity = OPENMD_ERROR;
63	gezelter	507	simError();
64	gezelter	246	} else {
65	gezelter	507	targetTemp_ = simParams->getTargetTemp();
66	gezelter	246	}
67	gezelter	2
68	gezelter	1277	// 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	gezelter	1277	"\tintegrator, you must set tauThermostat.\n");
73	gezelter	2
74	gezelter	1390	painCave.severity = OPENMD_ERROR;
75	gezelter	507	painCave.isFatal = 1;
76			simError();
77	gezelter	246	} else {
78	gezelter	507	tauThermostat_ = simParams->getTauThermostat();
79	gezelter	2	}
80
81	gezelter	1715	updateSizes();
82	gezelter	507	}
83	gezelter	2
84	gezelter	1715	void NVT::doUpdateSizes() {
85	gezelter	246	oldVel_.resize(info_->getNIntegrableObjects());
86	gezelter	1715	oldJi_.resize(info_->getNIntegrableObjects());
87	gezelter	507	}
88	gezelter	1764
89	gezelter	507	void NVT::moveA() {
90	gezelter	246	SimInfo::MoleculeIterator i;
91			Molecule::IntegrableObjectIterator j;
92			Molecule* mol;
93	gezelter	1764	StuntDouble* sd;
94	gezelter	246	Vector3d Tb;
95			Vector3d ji;
96	tim	963	RealType mass;
97	gezelter	246	Vector3d vel;
98			Vector3d pos;
99			Vector3d frc;
100	gezelter	2
101	gezelter	1764	pair<RealType, RealType> thermostat = snap->getThermostat();
102
103	gezelter	246	// We need the temperature at time = t for the chi update below:
104	gezelter	2
105	tim	963	RealType instTemp = thermo.getTemperature();
106	gezelter	2
107	gezelter	1764	for (mol = info_->beginMolecule(i); mol != NULL;
108			mol = info_->nextMolecule(i)) {
109	gezelter	2
110	gezelter	1764	for (sd = mol->beginIntegrableObject(j); sd != NULL;
111			sd = mol->nextIntegrableObject(j)) {
112	gezelter	2
113	gezelter	1764	vel = sd->getVel();
114			pos = sd->getPos();
115			frc = sd->getFrc();
116	gezelter	2
117	gezelter	1764	mass = sd->getMass();
118
119			// velocity half step (use chi from previous step here):
120			vel += dt2 PhysicalConstants::energyConvert/massfrc
121			- dt2thermostat.firstvel;
122	gezelter	246
123			// position whole step
124			pos += dt * vel;
125	gezelter	2
126	gezelter	1764	sd->setVel(vel);
127			sd->setPos(pos);
128	gezelter	2
129	gezelter	1764	if (sd->isDirectional()) {
130	gezelter	2
131	gezelter	507	//convert the torque to body frame
132	gezelter	1764	Tb = sd->lab2Body(sd->getTrq());
133	gezelter	2
134	gezelter	507	// get the angular momentum, and propagate a half step
135	gezelter	2
136	gezelter	1764	ji = sd->getJ();
137	gezelter	2
138	gezelter	1764	ji += dt2PhysicalConstants::energyConvertTb
139			- dt2thermostat.first ji;
140	gezelter	2
141	gezelter	1764	rotAlgo_->rotate(sd, ji, dt);
142
143			sd->setJ(ji);
144	gezelter	246	}
145	gezelter	507	}
146	gezelter	2
147			}
148	gezelter	246
149	gezelter	1715	flucQ_->moveA();
150			rattle_->constraintA();
151	gezelter	2
152	gezelter	246	// Finally, evolve chi a half step (just like a velocity) using
153			// temperature at time t, not time t+dt/2
154	gezelter	2
155	gezelter	1764	thermostat.first += dt2 * (instTemp / targetTemp_ - 1.0)
156			/ (tauThermostat_ * tauThermostat_);
157			thermostat.second += thermostat.first * dt2;
158	gezelter	2
159	gezelter	1764	snap->setThermostat(thermostat);
160	gezelter	507	}
161	gezelter	2
162	gezelter	507	void NVT::moveB() {
163	gezelter	246	SimInfo::MoleculeIterator i;
164			Molecule::IntegrableObjectIterator j;
165			Molecule* mol;
166	gezelter	1764	StuntDouble* sd;
167	gezelter	246
168			Vector3d Tb;
169			Vector3d ji;
170			Vector3d vel;
171			Vector3d frc;
172	tim	963	RealType mass;
173			RealType instTemp;
174	gezelter	246	int index;
175			// Set things up for the iteration:
176	gezelter	2
177	gezelter	1764	pair<RealType, RealType> thermostat = snap->getThermostat();
178			RealType oldChi = thermostat.first;
179	tim	963	RealType prevChi;
180	gezelter	2
181	gezelter	246	index = 0;
182	gezelter	1764	for (mol = info_->beginMolecule(i); mol != NULL;
183			mol = info_->nextMolecule(i)) {
184	gezelter	1710
185	gezelter	1764	for (sd = mol->beginIntegrableObject(j); sd != NULL;
186			sd = mol->nextIntegrableObject(j)) {
187
188			oldVel_[index] = sd->getVel();
189	gezelter	1710
190	gezelter	1764	if (sd->isDirectional())
191			oldJi_[index] = sd->getJ();
192	gezelter	1710
193	gezelter	507	++index;
194	gezelter	1710	}
195	gezelter	2	}
196
197	gezelter	246	// do the iteration:
198	gezelter	2
199	gezelter	246	for(int k = 0; k < maxIterNum_; k++) {
200	gezelter	507	index = 0;
201			instTemp = thermo.getTemperature();
202	gezelter	2
203	gezelter	507	// evolve chi another half step using the temperature at t + dt/2
204	gezelter	2
205	gezelter	1764	prevChi = thermostat.first;
206			thermostat.first = oldChi + dt2 * (instTemp / targetTemp_ - 1.0)
207			/ (tauThermostat_ * tauThermostat_);
208	gezelter	2
209	gezelter	1764	for (mol = info_->beginMolecule(i); mol != NULL;
210			mol = info_->nextMolecule(i)) {
211
212			for (sd = mol->beginIntegrableObject(j); sd != NULL;
213			sd = mol->nextIntegrableObject(j)) {
214	gezelter	2
215	gezelter	1764	frc = sd->getFrc();
216			vel = sd->getVel();
217	gezelter	2
218	gezelter	1764	mass = sd->getMass();
219	gezelter	2
220	gezelter	507	// velocity half step
221	gezelter	1764
222			vel = oldVel_[index]
223			+ dt2/massPhysicalConstants::energyConvert frc
224			- dt2thermostat.firstoldVel_[index];
225	gezelter	246
226	gezelter	1764	sd->setVel(vel);
227	gezelter	2
228	gezelter	1764	if (sd->isDirectional()) {
229	gezelter	2
230	gezelter	507	// get and convert the torque to body frame
231	gezelter	2
232	gezelter	1764	Tb = sd->lab2Body(sd->getTrq());
233	gezelter	2
234	gezelter	1764	ji = oldJi_[index] + dt2PhysicalConstants::energyConvertTb
235			- dt2thermostat.first oldJi_[index];
236	gezelter	2
237	gezelter	1764	sd->setJ(ji);
238	gezelter	507	}
239	gezelter	2
240
241	gezelter	507	++index;
242			}
243			}
244	gezelter	2
245	gezelter	1715	rattle_->constraintB();
246	gezelter	2
247	gezelter	1764	if (fabs(prevChi - thermostat.first) <= chiTolerance_)
248	gezelter	507	break;
249	gezelter	2
250	gezelter	246	}
251	gezelter	2
252	gezelter	1715	flucQ_->moveB();
253
254	gezelter	1764	thermostat.second += dt2 * thermostat.first;
255			snap->setThermostat(thermostat);
256	gezelter	507	}
257	gezelter	2
258	tim	546	void NVT::resetIntegrator() {
259	gezelter	1764	snap->setThermostat(make_pair(0.0, 0.0));
260	tim	546	}
261
262	tim	963	RealType NVT::calcConservedQuantity() {
263	gezelter	2
264	gezelter	1764	pair<RealType, RealType> thermostat = snap->getThermostat();
265	tim	963	RealType conservedQuantity;
266			RealType fkBT;
267			RealType Energy;
268			RealType thermostat_kinetic;
269			RealType thermostat_potential;
270	gezelter	246
271	gezelter	1390	fkBT = info_->getNdf() PhysicalConstants::kB targetTemp_;
272	gezelter	2
273	gezelter	1764	Energy = thermo.getTotalEnergy();
274	gezelter	2
275	gezelter	1764	thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * thermostat.first * thermostat.first / (2.0 * PhysicalConstants::energyConvert);
276	gezelter	2
277	gezelter	1764	thermostat_potential = fkBT * thermostat.second / PhysicalConstants::energyConvert;
278	gezelter	2
279	gezelter	246	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
280	gezelter	2
281	gezelter	246	return conservedQuantity;
282	gezelter	507	}
283	gezelter	2
284
285	gezelter	1390	}//end namespace OpenMD