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 (13 years, 3 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.
#	Content
1	/*
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, 24107 (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::moveA() {
90	SimInfo::MoleculeIterator i;
91	Molecule::IntegrableObjectIterator j;
92	Molecule* mol;
93	StuntDouble* sd;
94	Vector3d Tb;
95	Vector3d ji;
96	RealType mass;
97	Vector3d vel;
98	Vector3d pos;
99	Vector3d frc;
100
101	pair<RealType, RealType> thermostat = snap->getThermostat();
102
103	// We need the temperature at time = t for the chi update below:
104
105	RealType instTemp = thermo.getTemperature();
106
107	for (mol = info_->beginMolecule(i); mol != NULL;
108	mol = info_->nextMolecule(i)) {
109
110	for (sd = mol->beginIntegrableObject(j); sd != NULL;
111	sd = mol->nextIntegrableObject(j)) {
112
113	vel = sd->getVel();
114	pos = sd->getPos();
115	frc = sd->getFrc();
116
117	mass = sd->getMass();
118
119	// velocity half step (use chi from previous step here):
120	vel += dt2 PhysicalConstants::energyConvert/massfrc
121	- dt2thermostat.firstvel;
122
123	// position whole step
124	pos += dt * vel;
125
126	sd->setVel(vel);
127	sd->setPos(pos);
128
129	if (sd->isDirectional()) {
130
131	//convert the torque to body frame
132	Tb = sd->lab2Body(sd->getTrq());
133
134	// get the angular momentum, and propagate a half step
135
136	ji = sd->getJ();
137
138	ji += dt2PhysicalConstants::energyConvertTb
139	- dt2thermostat.first ji;
140
141	rotAlgo_->rotate(sd, ji, dt);
142
143	sd->setJ(ji);
144	}
145	}
146
147	}
148
149	flucQ_->moveA();
150	rattle_->constraintA();
151
152	// Finally, evolve chi a half step (just like a velocity) using
153	// temperature at time t, not time t+dt/2
154
155	thermostat.first += dt2 * (instTemp / targetTemp_ - 1.0)
156	/ (tauThermostat_ * tauThermostat_);
157	thermostat.second += thermostat.first * dt2;
158
159	snap->setThermostat(thermostat);
160	}
161
162	void NVT::moveB() {
163	SimInfo::MoleculeIterator i;
164	Molecule::IntegrableObjectIterator j;
165	Molecule* mol;
166	StuntDouble* sd;
167
168	Vector3d Tb;
169	Vector3d ji;
170	Vector3d vel;
171	Vector3d frc;
172	RealType mass;
173	RealType instTemp;
174	int index;
175	// Set things up for the iteration:
176
177	pair<RealType, RealType> thermostat = snap->getThermostat();
178	RealType oldChi = thermostat.first;
179	RealType prevChi;
180
181	index = 0;
182	for (mol = info_->beginMolecule(i); mol != NULL;
183	mol = info_->nextMolecule(i)) {
184
185	for (sd = mol->beginIntegrableObject(j); sd != NULL;
186	sd = mol->nextIntegrableObject(j)) {
187
188	oldVel_[index] = sd->getVel();
189
190	if (sd->isDirectional())
191	oldJi_[index] = sd->getJ();
192
193	++index;
194	}
195	}
196
197	// do the iteration:
198
199	for(int k = 0; k < maxIterNum_; k++) {
200	index = 0;
201	instTemp = thermo.getTemperature();
202
203	// evolve chi another half step using the temperature at t + dt/2
204
205	prevChi = thermostat.first;
206	thermostat.first = oldChi + dt2 * (instTemp / targetTemp_ - 1.0)
207	/ (tauThermostat_ * tauThermostat_);
208
209	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
215	frc = sd->getFrc();
216	vel = sd->getVel();
217
218	mass = sd->getMass();
219
220	// velocity half step
221
222	vel = oldVel_[index]
223	+ dt2/massPhysicalConstants::energyConvert frc
224	- dt2thermostat.firstoldVel_[index];
225
226	sd->setVel(vel);
227
228	if (sd->isDirectional()) {
229
230	// get and convert the torque to body frame
231
232	Tb = sd->lab2Body(sd->getTrq());
233
234	ji = oldJi_[index] + dt2PhysicalConstants::energyConvertTb
235	- dt2thermostat.first oldJi_[index];
236
237	sd->setJ(ji);
238	}
239
240
241	++index;
242	}
243	}
244
245	rattle_->constraintB();
246
247	if (fabs(prevChi - thermostat.first) <= chiTolerance_)
248	break;
249
250	}
251
252	flucQ_->moveB();
253
254	thermostat.second += dt2 * thermostat.first;
255	snap->setThermostat(thermostat);
256	}
257
258	void NVT::resetIntegrator() {
259	snap->setThermostat(make_pair(0.0, 0.0));
260	}
261
262	RealType NVT::calcConservedQuantity() {
263
264	pair<RealType, RealType> thermostat = snap->getThermostat();
265	RealType conservedQuantity;
266	RealType fkBT;
267	RealType Energy;
268	RealType thermostat_kinetic;
269	RealType thermostat_potential;
270
271	fkBT = info_->getNdf() PhysicalConstants::kB targetTemp_;
272
273	Energy = thermo.getTotalEnergy();
274
275	thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * thermostat.first * thermostat.first / (2.0 * PhysicalConstants::energyConvert);
276
277	thermostat_potential = fkBT * thermostat.second / PhysicalConstants::energyConvert;
278
279	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
280
281	return conservedQuantity;
282	}
283
284
285	}//end namespace OpenMD