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:	2031
Committed:	Fri Oct 31 18:40:40 2014 UTC (11 years ago) by jmichalk
File size:	9654 byte(s)
Log Message:	Added a surface diffusion analyser to staticProps
#	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), 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