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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
#include "integrators/NVT.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
#include "utils/OOPSEConstant.hpp"

namespace oopse {

  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 = OOPSE_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 = OOPSE_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 ) * OOPSEConstant::energyConvert - vel[j]*chi);
        vel += dt2 *OOPSEConstant::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] * OOPSEConstant::energyConvert - ji[j]*chi);
          ji += dt2*OOPSEConstant::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();
        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 ) * OOPSEConstant::energyConvert - oldVel_[3*i + j]*chi);
          vel = oldVel_[index] + dt2/mass*OOPSEConstant::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] * OOPSEConstant::energyConvert - oldJi_[3*i+j]*chi);
            ji = oldJi_[index] + dt2*OOPSEConstant::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() *OOPSEConstant::kB *targetTemp_;

    Energy = thermo.getTotalE();

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

    thermostat_potential = fkBT * integralOfChidt / OOPSEConstant::energyConvert;

    conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;

    return conservedQuantity;
  }


}//end namespace oopse
Revision:	1277
Committed:	Mon Jul 14 12:35:58 2008 UTC (16 years, 9 months ago) by gezelter
File size:	8975 byte(s)
Log Message:	Changes for implementing Amber force field: Added Inversions and worked on BaseAtomTypes so that they'd function with the fortran side.
#	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. Acknowledgement of the program authors must be made in any
10	* publication of scientific results based in part on use of the
11	* program. An acceptable form of acknowledgement is citation of
12	* the article in which the program was described (Matthew
13	* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	* Parallel Simulation Engine for Molecular Dynamics,"
16	* J. Comput. Chem. 26, pp. 252-271 (2005))
17	*
18	* 2. Redistributions of source code must retain the above copyright
19	* notice, this list of conditions and the following disclaimer.
20	*
21	* 3. Redistributions in binary form must reproduce the above copyright
22	* notice, this list of conditions and the following disclaimer in the
23	* documentation and/or other materials provided with the
24	* distribution.
25	*
26	* This software is provided "AS IS," without a warranty of any
27	* kind. All express or implied conditions, representations and
28	* warranties, including any implied warranty of merchantability,
29	* fitness for a particular purpose or non-infringement, are hereby
30	* excluded. The University of Notre Dame and its licensors shall not
31	* be liable for any damages suffered by licensee as a result of
32	* using, modifying or distributing the software or its
33	* derivatives. In no event will the University of Notre Dame or its
34	* licensors be liable for any lost revenue, profit or data, or for
35	* direct, indirect, special, consequential, incidental or punitive
36	* damages, however caused and regardless of the theory of liability,
37	* arising out of the use of or inability to use software, even if the
38	* University of Notre Dame has been advised of the possibility of
39	* such damages.
40	*/
41
42	#include "integrators/NVT.hpp"
43	#include "primitives/Molecule.hpp"
44	#include "utils/simError.h"
45	#include "utils/OOPSEConstant.hpp"
46
47	namespace oopse {
48
49	NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6), maxIterNum_(4) {
50
51	Globals* simParams = info_->getSimParams();
52
53	if (!simParams->getUseIntialExtendedSystemState()) {
54	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
55	currSnapshot->setChi(0.0);
56	currSnapshot->setIntegralOfChiDt(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 = OOPSE_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 = OOPSE_ERROR;
75	painCave.isFatal = 1;
76	simError();
77	} else {
78	tauThermostat_ = simParams->getTauThermostat();
79	}
80
81	update();
82	}
83
84	void NVT::doUpdate() {
85	oldVel_.resize(info_->getNIntegrableObjects());
86	oldJi_.resize(info_->getNIntegrableObjects());
87	}
88	void NVT::moveA() {
89	SimInfo::MoleculeIterator i;
90	Molecule::IntegrableObjectIterator j;
91	Molecule* mol;
92	StuntDouble* integrableObject;
93	Vector3d Tb;
94	Vector3d ji;
95	RealType mass;
96	Vector3d vel;
97	Vector3d pos;
98	Vector3d frc;
99
100	RealType chi = currentSnapshot_->getChi();
101	RealType integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
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; mol = info_->nextMolecule(i)) {
108	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
109	integrableObject = mol->nextIntegrableObject(j)) {
110
111	vel = integrableObject->getVel();
112	pos = integrableObject->getPos();
113	frc = integrableObject->getFrc();
114
115	mass = integrableObject->getMass();
116
117	// velocity half step (use chi from previous step here):
118	//vel[j] += dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - vel[j]*chi);
119	vel += dt2 OOPSEConstant::energyConvert/massfrc - dt2chivel;
120
121	// position whole step
122	//pos[j] += dt * vel[j];
123	pos += dt * vel;
124
125	integrableObject->setVel(vel);
126	integrableObject->setPos(pos);
127
128	if (integrableObject->isDirectional()) {
129
130	//convert the torque to body frame
131	Tb = integrableObject->lab2Body(integrableObject->getTrq());
132
133	// get the angular momentum, and propagate a half step
134
135	ji = integrableObject->getJ();
136
137	//ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi);
138	ji += dt2OOPSEConstant::energyConvertTb - dt2chi ji;
139	rotAlgo->rotate(integrableObject, ji, dt);
140
141	integrableObject->setJ(ji);
142	}
143	}
144
145	}
146
147	rattle->constraintA();
148
149	// Finally, evolve chi a half step (just like a velocity) using
150	// temperature at time t, not time t+dt/2
151
152
153	chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
154	integralOfChidt += chi * dt2;
155
156	currentSnapshot_->setChi(chi);
157	currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
158	}
159
160	void NVT::moveB() {
161	SimInfo::MoleculeIterator i;
162	Molecule::IntegrableObjectIterator j;
163	Molecule* mol;
164	StuntDouble* integrableObject;
165
166	Vector3d Tb;
167	Vector3d ji;
168	Vector3d vel;
169	Vector3d frc;
170	RealType mass;
171	RealType instTemp;
172	int index;
173	// Set things up for the iteration:
174
175	RealType chi = currentSnapshot_->getChi();
176	RealType oldChi = chi;
177	RealType prevChi;
178	RealType integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
179
180	index = 0;
181	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
182	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
183	integrableObject = mol->nextIntegrableObject(j)) {
184	oldVel_[index] = integrableObject->getVel();
185	oldJi_[index] = integrableObject->getJ();
186
187	++index;
188	}
189
190	}
191
192	// do the iteration:
193
194	for(int k = 0; k < maxIterNum_; k++) {
195	index = 0;
196	instTemp = thermo.getTemperature();
197
198	// evolve chi another half step using the temperature at t + dt/2
199
200	prevChi = chi;
201	chi = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
202
203	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
204	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
205	integrableObject = mol->nextIntegrableObject(j)) {
206
207	frc = integrableObject->getFrc();
208	vel = integrableObject->getVel();
209
210	mass = integrableObject->getMass();
211
212	// velocity half step
213	//for(j = 0; j < 3; j++)
214	// vel[j] = oldVel_[3i+j] + dt2 ((frc[j] / mass ) * OOPSEConstant::energyConvert - oldVel_[3i + j]chi);
215	vel = oldVel_[index] + dt2/massOOPSEConstant::energyConvert frc - dt2chioldVel_[index];
216
217	integrableObject->setVel(vel);
218
219	if (integrableObject->isDirectional()) {
220
221	// get and convert the torque to body frame
222
223	Tb = integrableObject->lab2Body(integrableObject->getTrq());
224
225	//for(j = 0; j < 3; j++)
226	// ji[j] = oldJi_[3i + j] + dt2 (Tb[j] * OOPSEConstant::energyConvert - oldJi_[3i+j]chi);
227	ji = oldJi_[index] + dt2OOPSEConstant::energyConvertTb - dt2chi oldJi_[index];
228
229	integrableObject->setJ(ji);
230	}
231
232
233	++index;
234	}
235	}
236
237
238	rattle->constraintB();
239
240	if (fabs(prevChi - chi) <= chiTolerance_)
241	break;
242
243	}
244
245	integralOfChidt += dt2 * chi;
246
247	currentSnapshot_->setChi(chi);
248	currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
249	}
250
251	void NVT::resetIntegrator() {
252	currentSnapshot_->setChi(0.0);
253	currentSnapshot_->setIntegralOfChiDt(0.0);
254	}
255
256	RealType NVT::calcConservedQuantity() {
257
258	RealType chi = currentSnapshot_->getChi();
259	RealType integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
260	RealType conservedQuantity;
261	RealType fkBT;
262	RealType Energy;
263	RealType thermostat_kinetic;
264	RealType thermostat_potential;
265
266	fkBT = info_->getNdf() OOPSEConstant::kB targetTemp_;
267
268	Energy = thermo.getTotalE();
269
270	thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * OOPSEConstant::energyConvert);
271
272	thermostat_potential = fkBT * integralOfChidt / OOPSEConstant::energyConvert;
273
274	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
275
276	return conservedQuantity;
277	}
278
279
280	}//end namespace oopse