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, 3 months ago) by gezelter
File size:	8224 byte(s)
Log Message:	Reducing the number of warnings when using g++ to compile.
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [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	2071	NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), maxIterNum_(4),
51			chiTolerance_(1e-6) {
52	gezelter	2
53	gezelter	246	Globals* simParams = info_->getSimParams();
54	gezelter	2
55	tim	665	if (!simParams->getUseIntialExtendedSystemState()) {
56	gezelter	1782	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
57			snap->setThermostat(make_pair(0.0, 0.0));
58	gezelter	246	}
59
60			if (!simParams->haveTargetTemp()) {
61	gezelter	507	sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp_!\n");
62			painCave.isFatal = 1;
63	gezelter	1390	painCave.severity = OPENMD_ERROR;
64	gezelter	507	simError();
65	gezelter	246	} else {
66	gezelter	507	targetTemp_ = simParams->getTargetTemp();
67	gezelter	246	}
68	gezelter	2
69	gezelter	1277	// We must set tauThermostat.
70	gezelter	2
71	gezelter	246	if (!simParams->haveTauThermostat()) {
72	gezelter	507	sprintf(painCave.errMsg, "If you use the constant temperature\n"
73	gezelter	1277	"\tintegrator, you must set tauThermostat.\n");
74	gezelter	2
75	gezelter	1390	painCave.severity = OPENMD_ERROR;
76	gezelter	507	painCave.isFatal = 1;
77			simError();
78	gezelter	246	} else {
79	gezelter	507	tauThermostat_ = simParams->getTauThermostat();
80	gezelter	2	}
81
82	gezelter	1782	updateSizes();
83	gezelter	507	}
84	gezelter	2
85	gezelter	1782	void NVT::doUpdateSizes() {
86	gezelter	246	oldVel_.resize(info_->getNIntegrableObjects());
87	gezelter	1782	oldJi_.resize(info_->getNIntegrableObjects());
88	gezelter	507	}
89	gezelter	1782
90	gezelter	507	void NVT::moveA() {
91	gezelter	246	SimInfo::MoleculeIterator i;
92			Molecule::IntegrableObjectIterator j;
93			Molecule* mol;
94	gezelter	1782	StuntDouble* sd;
95	gezelter	246	Vector3d Tb;
96			Vector3d ji;
97	tim	963	RealType mass;
98	gezelter	246	Vector3d vel;
99			Vector3d pos;
100			Vector3d frc;
101	gezelter	2
102	gezelter	1782	pair<RealType, RealType> thermostat = snap->getThermostat();
103
104	gezelter	246	// We need the temperature at time = t for the chi update below:
105	gezelter	2
106	tim	963	RealType instTemp = thermo.getTemperature();
107	gezelter	2
108	gezelter	1782	for (mol = info_->beginMolecule(i); mol != NULL;
109			mol = info_->nextMolecule(i)) {
110	gezelter	2
111	gezelter	1782	for (sd = mol->beginIntegrableObject(j); sd != NULL;
112			sd = mol->nextIntegrableObject(j)) {
113	gezelter	2
114	gezelter	1782	vel = sd->getVel();
115			pos = sd->getPos();
116			frc = sd->getFrc();
117	gezelter	2
118	gezelter	1782	mass = sd->getMass();
119
120			// velocity half step (use chi from previous step here):
121			vel += dt2 PhysicalConstants::energyConvert/massfrc
122			- dt2thermostat.firstvel;
123	gezelter	246
124			// position whole step
125			pos += dt * vel;
126	gezelter	2
127	gezelter	1782	sd->setVel(vel);
128			sd->setPos(pos);
129	gezelter	2
130	gezelter	1782	if (sd->isDirectional()) {
131	gezelter	2
132	gezelter	507	//convert the torque to body frame
133	gezelter	1782	Tb = sd->lab2Body(sd->getTrq());
134	gezelter	2
135	gezelter	507	// get the angular momentum, and propagate a half step
136	gezelter	2
137	gezelter	1782	ji = sd->getJ();
138	gezelter	2
139	gezelter	1782	ji += dt2PhysicalConstants::energyConvertTb
140			- dt2thermostat.first ji;
141	gezelter	2
142	gezelter	1782	rotAlgo_->rotate(sd, ji, dt);
143
144			sd->setJ(ji);
145	gezelter	246	}
146	gezelter	507	}
147	gezelter	2
148			}
149	gezelter	246
150	gezelter	1782	flucQ_->moveA();
151			rattle_->constraintA();
152	gezelter	2
153	gezelter	246	// Finally, evolve chi a half step (just like a velocity) using
154			// temperature at time t, not time t+dt/2
155	gezelter	2
156	gezelter	1782	thermostat.first += dt2 * (instTemp / targetTemp_ - 1.0)
157			/ (tauThermostat_ * tauThermostat_);
158			thermostat.second += thermostat.first * dt2;
159	gezelter	2
160	gezelter	1782	snap->setThermostat(thermostat);
161	gezelter	507	}
162	gezelter	2
163	gezelter	507	void NVT::moveB() {
164	gezelter	246	SimInfo::MoleculeIterator i;
165			Molecule::IntegrableObjectIterator j;
166			Molecule* mol;
167	gezelter	1782	StuntDouble* sd;
168	gezelter	246
169			Vector3d Tb;
170			Vector3d ji;
171			Vector3d vel;
172			Vector3d frc;
173	tim	963	RealType mass;
174			RealType instTemp;
175	gezelter	246	int index;
176			// Set things up for the iteration:
177	gezelter	2
178	gezelter	1782	pair<RealType, RealType> thermostat = snap->getThermostat();
179			RealType oldChi = thermostat.first;
180	tim	963	RealType prevChi;
181	gezelter	2
182	gezelter	246	index = 0;
183	gezelter	1782	for (mol = info_->beginMolecule(i); mol != NULL;
184			mol = info_->nextMolecule(i)) {
185	gezelter	2
186	gezelter	1782	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	gezelter	507	++index;
195	gezelter	1782	}
196	gezelter	2	}
197
198	gezelter	246	// do the iteration:
199	gezelter	2
200	gezelter	246	for(int k = 0; k < maxIterNum_; k++) {
201	gezelter	507	index = 0;
202			instTemp = thermo.getTemperature();
203	gezelter	2
204	gezelter	507	// evolve chi another half step using the temperature at t + dt/2
205	gezelter	2
206	gezelter	1782	prevChi = thermostat.first;
207			thermostat.first = oldChi + dt2 * (instTemp / targetTemp_ - 1.0)
208			/ (tauThermostat_ * tauThermostat_);
209	gezelter	2
210	gezelter	1782	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	gezelter	2
216	gezelter	1782	frc = sd->getFrc();
217			mass = sd->getMass();
218	gezelter	2
219	gezelter	507	// velocity half step
220	gezelter	1782
221			vel = oldVel_[index]
222			+ dt2/massPhysicalConstants::energyConvert frc
223			- dt2thermostat.firstoldVel_[index];
224	gezelter	246
225	gezelter	1782	sd->setVel(vel);
226	gezelter	2
227	gezelter	1782	if (sd->isDirectional()) {
228	gezelter	2
229	gezelter	507	// get and convert the torque to body frame
230	gezelter	2
231	gezelter	1782	Tb = sd->lab2Body(sd->getTrq());
232	gezelter	2
233	gezelter	1782	ji = oldJi_[index] + dt2PhysicalConstants::energyConvertTb
234			- dt2thermostat.first oldJi_[index];
235	gezelter	2
236	gezelter	1782	sd->setJ(ji);
237	gezelter	507	}
238	gezelter	2
239
240	gezelter	507	++index;
241			}
242			}
243	gezelter	2
244	gezelter	1782	rattle_->constraintB();
245	gezelter	2
246	gezelter	1782	if (fabs(prevChi - thermostat.first) <= chiTolerance_)
247	gezelter	507	break;
248	gezelter	2
249	gezelter	246	}
250	gezelter	2
251	gezelter	1782	flucQ_->moveB();
252	gezelter	2
253	gezelter	1782	thermostat.second += dt2 * thermostat.first;
254			snap->setThermostat(thermostat);
255	gezelter	507	}
256	gezelter	2
257	tim	546	void NVT::resetIntegrator() {
258	gezelter	1782	snap->setThermostat(make_pair(0.0, 0.0));
259	tim	546	}
260
261	tim	963	RealType NVT::calcConservedQuantity() {
262	gezelter	2
263	gezelter	1782	pair<RealType, RealType> thermostat = snap->getThermostat();
264	tim	963	RealType conservedQuantity;
265			RealType fkBT;
266			RealType Energy;
267			RealType thermostat_kinetic;
268			RealType thermostat_potential;
269	gezelter	246
270	gezelter	1390	fkBT = info_->getNdf() PhysicalConstants::kB targetTemp_;
271	gezelter	2
272	gezelter	1782	Energy = thermo.getTotalEnergy();
273	gezelter	2
274	gezelter	1782	thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * thermostat.first * thermostat.first / (2.0 * PhysicalConstants::energyConvert);
275	gezelter	2
276	gezelter	1782	thermostat_potential = fkBT * thermostat.second / PhysicalConstants::energyConvert;
277	gezelter	2
278	gezelter	246	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
279	gezelter	2
280	gezelter	246	return conservedQuantity;
281	gezelter	507	}
282	gezelter	2
283
284	gezelter	1390	}//end namespace OpenMD