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* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
      currSnapshot->setChi(0.0);
      currSnapshot->setIntegralOfChiDt(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();
    }

    update();
  }

  void NVT::doUpdate() {
    oldVel_.resize(info_->getNIntegrableObjects());
    oldJi_.resize(info_->getNIntegrableObjects());    
  }
  void NVT::moveA() {
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* integrableObject;
    Vector3d Tb;
    Vector3d ji;
    RealType mass;
    Vector3d vel;
    Vector3d pos;
    Vector3d frc;

    RealType chi = currentSnapshot_->getChi();
    RealType integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
    
    // 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 (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
           integrableObject = mol->nextIntegrableObject(j)) {

        vel = integrableObject->getVel();
        pos = integrableObject->getPos();
        frc = integrableObject->getFrc();

        mass = integrableObject->getMass();

        // velocity half step  (use chi from previous step here):
        //vel[j] += dt2 * ((frc[j] / mass ) * PhysicalConstants::energyConvert - vel[j]*chi);
        vel += dt2 *PhysicalConstants::energyConvert/mass*frc - dt2*chi*vel;
        
        // position whole step
        //pos[j] += dt * vel[j];
        pos += dt * vel;

        integrableObject->setVel(vel);
        integrableObject->setPos(pos);

        if (integrableObject->isDirectional()) {

          //convert the torque to body frame
          Tb = integrableObject->lab2Body(integrableObject->getTrq());

          // get the angular momentum, and propagate a half step

          ji = integrableObject->getJ();

          //ji[j] += dt2 * (Tb[j] * PhysicalConstants::energyConvert - ji[j]*chi);
          ji += dt2*PhysicalConstants::energyConvert*Tb - dt2*chi *ji;
          rotAlgo->rotate(integrableObject, ji, dt);

          integrableObject->setJ(ji);
        }
      }

    }
    
    rattle->constraintA();

    // Finally, evolve chi a half step (just like a velocity) using
    // temperature at time t, not time t+dt/2

    
    chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
    integralOfChidt += chi * dt2;

    currentSnapshot_->setChi(chi);
    currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
  }

  void NVT::moveB() {
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* integrableObject;
    
    Vector3d Tb;
    Vector3d ji;    
    Vector3d vel;
    Vector3d frc;
    RealType mass;
    RealType instTemp;
    int index;
    // Set things up for the iteration:

    RealType chi = currentSnapshot_->getChi();
    RealType oldChi = chi;
    RealType  prevChi;
    RealType integralOfChidt = currentSnapshot_->getIntegralOfChiDt();

    index = 0;
    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
           integrableObject = mol->nextIntegrableObject(j)) {

        oldVel_[index] = integrableObject->getVel();
        
        if (integrableObject->isDirectional()) 
          oldJi_[index] = integrableObject->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 = chi;
      chi = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);

      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
             integrableObject = mol->nextIntegrableObject(j)) {

          frc = integrableObject->getFrc();
          vel = integrableObject->getVel();

          mass = integrableObject->getMass();

          // velocity half step
          //for(j = 0; j < 3; j++)
          //    vel[j] = oldVel_[3*i+j] + dt2 * ((frc[j] / mass ) * PhysicalConstants::energyConvert - oldVel_[3*i + j]*chi);
          vel = oldVel_[index] + dt2/mass*PhysicalConstants::energyConvert * frc - dt2*chi*oldVel_[index];
            
          integrableObject->setVel(vel);

          if (integrableObject->isDirectional()) {

            // get and convert the torque to body frame

            Tb =  integrableObject->lab2Body(integrableObject->getTrq());

            //for(j = 0; j < 3; j++)
            //    ji[j] = oldJi_[3*i + j] + dt2 * (Tb[j] * PhysicalConstants::energyConvert - oldJi_[3*i+j]*chi);
            ji = oldJi_[index] + dt2*PhysicalConstants::energyConvert*Tb - dt2*chi *oldJi_[index];

            integrableObject->setJ(ji);
          }


          ++index;
        }
      }
    

      rattle->constraintB();

      if (fabs(prevChi - chi) <= chiTolerance_)
        break;

    }

    integralOfChidt += dt2 * chi;

    currentSnapshot_->setChi(chi);
    currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
  }

  void NVT::resetIntegrator() {
      currentSnapshot_->setChi(0.0);
      currentSnapshot_->setIntegralOfChiDt(0.0);
  }
  
  RealType NVT::calcConservedQuantity() {

    RealType chi = currentSnapshot_->getChi();
    RealType integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
    RealType conservedQuantity;
    RealType fkBT;
    RealType Energy;
    RealType thermostat_kinetic;
    RealType thermostat_potential;
    
    fkBT = info_->getNdf() *PhysicalConstants::kB *targetTemp_;

    Energy = thermo.getTotalE();

    thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * PhysicalConstants::energyConvert);

    thermostat_potential = fkBT * integralOfChidt / PhysicalConstants::energyConvert;

    conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;

    return conservedQuantity;
  }


}//end namespace OpenMD
Revision:	1710
Committed:	Fri May 18 21:44:02 2012 UTC (12 years, 11 months ago) by gezelter
File size:	9208 byte(s)
Log Message:	Added an adapter layer between the AtomType and the rest of the code to handle the bolt-on capabilities of new types. Fixed a long-standing bug in how storageLayout was being set to the maximum possible value. Started to add infrastructure for Polarizable and fluc-Q calculations.
#	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* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
56	currSnapshot->setChi(0.0);
57	currSnapshot->setIntegralOfChiDt(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	update();
83	}
84
85	void NVT::doUpdate() {
86	oldVel_.resize(info_->getNIntegrableObjects());
87	oldJi_.resize(info_->getNIntegrableObjects());
88	}
89	void NVT::moveA() {
90	SimInfo::MoleculeIterator i;
91	Molecule::IntegrableObjectIterator j;
92	Molecule* mol;
93	StuntDouble* integrableObject;
94	Vector3d Tb;
95	Vector3d ji;
96	RealType mass;
97	Vector3d vel;
98	Vector3d pos;
99	Vector3d frc;
100
101	RealType chi = currentSnapshot_->getChi();
102	RealType integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
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; mol = info_->nextMolecule(i)) {
109	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
110	integrableObject = mol->nextIntegrableObject(j)) {
111
112	vel = integrableObject->getVel();
113	pos = integrableObject->getPos();
114	frc = integrableObject->getFrc();
115
116	mass = integrableObject->getMass();
117
118	// velocity half step (use chi from previous step here):
119	//vel[j] += dt2 * ((frc[j] / mass ) * PhysicalConstants::energyConvert - vel[j]*chi);
120	vel += dt2 PhysicalConstants::energyConvert/massfrc - dt2chivel;
121
122	// position whole step
123	//pos[j] += dt * vel[j];
124	pos += dt * vel;
125
126	integrableObject->setVel(vel);
127	integrableObject->setPos(pos);
128
129	if (integrableObject->isDirectional()) {
130
131	//convert the torque to body frame
132	Tb = integrableObject->lab2Body(integrableObject->getTrq());
133
134	// get the angular momentum, and propagate a half step
135
136	ji = integrableObject->getJ();
137
138	//ji[j] += dt2 * (Tb[j] * PhysicalConstants::energyConvert - ji[j]*chi);
139	ji += dt2PhysicalConstants::energyConvertTb - dt2chi ji;
140	rotAlgo->rotate(integrableObject, ji, dt);
141
142	integrableObject->setJ(ji);
143	}
144	}
145
146	}
147
148	rattle->constraintA();
149
150	// Finally, evolve chi a half step (just like a velocity) using
151	// temperature at time t, not time t+dt/2
152
153
154	chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
155	integralOfChidt += chi * dt2;
156
157	currentSnapshot_->setChi(chi);
158	currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
159	}
160
161	void NVT::moveB() {
162	SimInfo::MoleculeIterator i;
163	Molecule::IntegrableObjectIterator j;
164	Molecule* mol;
165	StuntDouble* integrableObject;
166
167	Vector3d Tb;
168	Vector3d ji;
169	Vector3d vel;
170	Vector3d frc;
171	RealType mass;
172	RealType instTemp;
173	int index;
174	// Set things up for the iteration:
175
176	RealType chi = currentSnapshot_->getChi();
177	RealType oldChi = chi;
178	RealType prevChi;
179	RealType integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
180
181	index = 0;
182	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
183	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
184	integrableObject = mol->nextIntegrableObject(j)) {
185
186	oldVel_[index] = integrableObject->getVel();
187
188	if (integrableObject->isDirectional())
189	oldJi_[index] = integrableObject->getJ();
190
191	++index;
192	}
193	}
194
195	// do the iteration:
196
197	for(int k = 0; k < maxIterNum_; k++) {
198	index = 0;
199	instTemp = thermo.getTemperature();
200
201	// evolve chi another half step using the temperature at t + dt/2
202
203	prevChi = chi;
204	chi = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
205
206	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
207	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
208	integrableObject = mol->nextIntegrableObject(j)) {
209
210	frc = integrableObject->getFrc();
211	vel = integrableObject->getVel();
212
213	mass = integrableObject->getMass();
214
215	// velocity half step
216	//for(j = 0; j < 3; j++)
217	// vel[j] = oldVel_[3i+j] + dt2 ((frc[j] / mass ) * PhysicalConstants::energyConvert - oldVel_[3i + j]chi);
218	vel = oldVel_[index] + dt2/massPhysicalConstants::energyConvert frc - dt2chioldVel_[index];
219
220	integrableObject->setVel(vel);
221
222	if (integrableObject->isDirectional()) {
223
224	// get and convert the torque to body frame
225
226	Tb = integrableObject->lab2Body(integrableObject->getTrq());
227
228	//for(j = 0; j < 3; j++)
229	// ji[j] = oldJi_[3i + j] + dt2 (Tb[j] * PhysicalConstants::energyConvert - oldJi_[3i+j]chi);
230	ji = oldJi_[index] + dt2PhysicalConstants::energyConvertTb - dt2chi oldJi_[index];
231
232	integrableObject->setJ(ji);
233	}
234
235
236	++index;
237	}
238	}
239
240
241	rattle->constraintB();
242
243	if (fabs(prevChi - chi) <= chiTolerance_)
244	break;
245
246	}
247
248	integralOfChidt += dt2 * chi;
249
250	currentSnapshot_->setChi(chi);
251	currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
252	}
253
254	void NVT::resetIntegrator() {
255	currentSnapshot_->setChi(0.0);
256	currentSnapshot_->setIntegralOfChiDt(0.0);
257	}
258
259	RealType NVT::calcConservedQuantity() {
260
261	RealType chi = currentSnapshot_->getChi();
262	RealType integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
263	RealType conservedQuantity;
264	RealType fkBT;
265	RealType Energy;
266	RealType thermostat_kinetic;
267	RealType thermostat_potential;
268
269	fkBT = info_->getNdf() PhysicalConstants::kB targetTemp_;
270
271	Energy = thermo.getTotalE();
272
273	thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * PhysicalConstants::energyConvert);
274
275	thermostat_potential = fkBT * integralOfChidt / PhysicalConstants::energyConvert;
276
277	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
278
279	return conservedQuantity;
280	}
281
282
283	}//end namespace OpenMD