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, 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), maxIterNum_(4),
                            chiTolerance_(1e-6) {

    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();
          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:	2071
Committed:	Sat Mar 7 21:41:51 2015 UTC (10 years, 4 months ago) by gezelter
File size:	8224 byte(s)
Log Message:	Reducing the number of warnings when using g++ to compile.
#	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, 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), maxIterNum_(4),
51	chiTolerance_(1e-6) {
52
53	Globals* simParams = info_->getSimParams();
54
55	if (!simParams->getUseIntialExtendedSystemState()) {
56	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
57	snap->setThermostat(make_pair(0.0, 0.0));
58	}
59
60	if (!simParams->haveTargetTemp()) {
61	sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp_!\n");
62	painCave.isFatal = 1;
63	painCave.severity = OPENMD_ERROR;
64	simError();
65	} else {
66	targetTemp_ = simParams->getTargetTemp();
67	}
68
69	// We must set tauThermostat.
70
71	if (!simParams->haveTauThermostat()) {
72	sprintf(painCave.errMsg, "If you use the constant temperature\n"
73	"\tintegrator, you must set tauThermostat.\n");
74
75	painCave.severity = OPENMD_ERROR;
76	painCave.isFatal = 1;
77	simError();
78	} else {
79	tauThermostat_ = simParams->getTauThermostat();
80	}
81
82	updateSizes();
83	}
84
85	void NVT::doUpdateSizes() {
86	oldVel_.resize(info_->getNIntegrableObjects());
87	oldJi_.resize(info_->getNIntegrableObjects());
88	}
89
90	void NVT::moveA() {
91	SimInfo::MoleculeIterator i;
92	Molecule::IntegrableObjectIterator j;
93	Molecule* mol;
94	StuntDouble* sd;
95	Vector3d Tb;
96	Vector3d ji;
97	RealType mass;
98	Vector3d vel;
99	Vector3d pos;
100	Vector3d frc;
101
102	pair<RealType, RealType> thermostat = snap->getThermostat();
103
104	// We need the temperature at time = t for the chi update below:
105
106	RealType instTemp = thermo.getTemperature();
107
108	for (mol = info_->beginMolecule(i); mol != NULL;
109	mol = info_->nextMolecule(i)) {
110
111	for (sd = mol->beginIntegrableObject(j); sd != NULL;
112	sd = mol->nextIntegrableObject(j)) {
113
114	vel = sd->getVel();
115	pos = sd->getPos();
116	frc = sd->getFrc();
117
118	mass = sd->getMass();
119
120	// velocity half step (use chi from previous step here):
121	vel += dt2 PhysicalConstants::energyConvert/massfrc
122	- dt2thermostat.firstvel;
123
124	// position whole step
125	pos += dt * vel;
126
127	sd->setVel(vel);
128	sd->setPos(pos);
129
130	if (sd->isDirectional()) {
131
132	//convert the torque to body frame
133	Tb = sd->lab2Body(sd->getTrq());
134
135	// get the angular momentum, and propagate a half step
136
137	ji = sd->getJ();
138
139	ji += dt2PhysicalConstants::energyConvertTb
140	- dt2thermostat.first ji;
141
142	rotAlgo_->rotate(sd, ji, dt);
143
144	sd->setJ(ji);
145	}
146	}
147
148	}
149
150	flucQ_->moveA();
151	rattle_->constraintA();
152
153	// Finally, evolve chi a half step (just like a velocity) using
154	// temperature at time t, not time t+dt/2
155
156	thermostat.first += dt2 * (instTemp / targetTemp_ - 1.0)
157	/ (tauThermostat_ * tauThermostat_);
158	thermostat.second += thermostat.first * dt2;
159
160	snap->setThermostat(thermostat);
161	}
162
163	void NVT::moveB() {
164	SimInfo::MoleculeIterator i;
165	Molecule::IntegrableObjectIterator j;
166	Molecule* mol;
167	StuntDouble* sd;
168
169	Vector3d Tb;
170	Vector3d ji;
171	Vector3d vel;
172	Vector3d frc;
173	RealType mass;
174	RealType instTemp;
175	int index;
176	// Set things up for the iteration:
177
178	pair<RealType, RealType> thermostat = snap->getThermostat();
179	RealType oldChi = thermostat.first;
180	RealType prevChi;
181
182	index = 0;
183	for (mol = info_->beginMolecule(i); mol != NULL;
184	mol = info_->nextMolecule(i)) {
185
186	for (sd = mol->beginIntegrableObject(j); sd != NULL;
187	sd = mol->nextIntegrableObject(j)) {
188
189	oldVel_[index] = sd->getVel();
190
191	if (sd->isDirectional())
192	oldJi_[index] = sd->getJ();
193
194	++index;
195	}
196	}
197
198	// do the iteration:
199
200	for(int k = 0; k < maxIterNum_; k++) {
201	index = 0;
202	instTemp = thermo.getTemperature();
203
204	// evolve chi another half step using the temperature at t + dt/2
205
206	prevChi = thermostat.first;
207	thermostat.first = oldChi + dt2 * (instTemp / targetTemp_ - 1.0)
208	/ (tauThermostat_ * tauThermostat_);
209
210	for (mol = info_->beginMolecule(i); mol != NULL;
211	mol = info_->nextMolecule(i)) {
212
213	for (sd = mol->beginIntegrableObject(j); sd != NULL;
214	sd = mol->nextIntegrableObject(j)) {
215
216	frc = sd->getFrc();
217	mass = sd->getMass();
218
219	// velocity half step
220
221	vel = oldVel_[index]
222	+ dt2/massPhysicalConstants::energyConvert frc
223	- dt2thermostat.firstoldVel_[index];
224
225	sd->setVel(vel);
226
227	if (sd->isDirectional()) {
228
229	// get and convert the torque to body frame
230
231	Tb = sd->lab2Body(sd->getTrq());
232
233	ji = oldJi_[index] + dt2PhysicalConstants::energyConvertTb
234	- dt2thermostat.first oldJi_[index];
235
236	sd->setJ(ji);
237	}
238
239
240	++index;
241	}
242	}
243
244	rattle_->constraintB();
245
246	if (fabs(prevChi - thermostat.first) <= chiTolerance_)
247	break;
248
249	}
250
251	flucQ_->moveB();
252
253	thermostat.second += dt2 * thermostat.first;
254	snap->setThermostat(thermostat);
255	}
256
257	void NVT::resetIntegrator() {
258	snap->setThermostat(make_pair(0.0, 0.0));
259	}
260
261	RealType NVT::calcConservedQuantity() {
262
263	pair<RealType, RealType> thermostat = snap->getThermostat();
264	RealType conservedQuantity;
265	RealType fkBT;
266	RealType Energy;
267	RealType thermostat_kinetic;
268	RealType thermostat_potential;
269
270	fkBT = info_->getNdf() PhysicalConstants::kB targetTemp_;
271
272	Energy = thermo.getTotalEnergy();
273
274	thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * thermostat.first * thermostat.first / (2.0 * PhysicalConstants::energyConvert);
275
276	thermostat_potential = fkBT * thermostat.second / PhysicalConstants::energyConvert;
277
278	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
279
280	return conservedQuantity;
281	}
282
283
284	}//end namespace OpenMD