src/flucq/FluctuatingChargeNVT.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 "FluctuatingChargeNVT.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
#include "utils/PhysicalConstants.hpp"

namespace OpenMD {

  FluctuatingChargeNVT::FluctuatingChargeNVT(SimInfo* info, ForceManager* fm) : 
    FluctuatingChargePropagator(info, fm), chiTolerance_ (1e-6), 
    maxIterNum_(4), thermo(info), 
    currentSnapshot_(info->getSnapshotManager()->getCurrentSnapshot()) {
    
    if (hasFlucQ_) {     
      if (info_->getSimParams()->haveDt()) {
        dt_ = info_->getSimParams()->getDt();
        dt2_ = dt_ * 0.5;
      } else {
        sprintf(painCave.errMsg,
                "FluctuatingChargeNVT Error: dt is not set\n");
        painCave.isFatal = 1;
        simError();
      }
      
      if (!info_->getSimParams()->getUseIntialExtendedSystemState()) {
        currentSnapshot_->setChiElectronic(0.0);
        currentSnapshot_->setIntegralOfChiElectronicDt(0.0);
      }
      
      if (!fqParams_->haveTargetTemp()) {
        sprintf(painCave.errMsg, "You can't use the FluctuatingChargeNVT "
                "propagator without a flucQ.targetTemp!\n");
        painCave.isFatal = 1;
        painCave.severity = OPENMD_ERROR;
        simError();
      } else {
        targetTemp_ = fqParams_->getTargetTemp();
      }
      
      // We must set tauThermostat.
      
      if (!fqParams_->haveTauThermostat()) {
        sprintf(painCave.errMsg, "If you use the FluctuatingChargeNVT\n"
                "\tpropagator, you must set flucQ.tauThermostat .\n");
        
        painCave.severity = OPENMD_ERROR;
        painCave.isFatal = 1;
        simError();
      } else {
        tauThermostat_ = fqParams_->getTauThermostat();
      }
      updateSizes();
    }
  }

  void FluctuatingChargeNVT::initialize() {
    FluctuatingChargePropagator::initialize();
  }


  void FluctuatingChargeNVT::moveA() {

    if (!hasFlucQ_) return;

    SimInfo::MoleculeIterator i;
    Molecule::FluctuatingChargeIterator  j;
    Molecule* mol;
    Atom* atom;
    RealType cvel, cpos, cfrc, cmass;

    RealType chi = currentSnapshot_->getChiElectronic();
    RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
    RealType instTemp = thermo.getElectronicTemperature();


    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {
      for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
           atom = mol->nextFluctuatingCharge(j)) {
        
        cvel = atom->getFlucQVel();
        cpos = atom->getFlucQPos();
        cfrc = atom->getFlucQFrc();
        cmass = atom->getChargeMass();
        
        cerr << atom->getType() << "\n";
        cerr << "Before\n";
        cerr << "cvel: " << cvel << "\tcpos: " << cpos << "\tcfrc: " << cfrc << "\tcmass: " << cmass << "\n";
        
        // velocity half step
        cvel += dt2_ * cfrc / cmass - dt2_*chi*cvel;                    
        // position whole step
        cpos += dt_ * cvel;
        
        cerr << "After\n";
        cerr << "cvel: " << cvel << "\tcpos: " << cpos << "\n\n";        

        atom->setFlucQVel(cvel);
        atom->setFlucQPos(cpos);
      }
    }
    
    chi += dt2_ * (instTemp / targetTemp_ - 1.0) / 
      (tauThermostat_ * tauThermostat_);

    integralOfChidt += chi * dt2_;
    cerr << "Move A instTemp: " << instTemp << "\n";
    currentSnapshot_->setChiElectronic(chi);
    currentSnapshot_->setIntegralOfChiElectronicDt(integralOfChidt);
       
  }

  void FluctuatingChargeNVT::updateSizes() {
    if (!hasFlucQ_) return;
    oldVel_.resize(info_->getNFluctuatingCharges());
  }

  void FluctuatingChargeNVT::moveB() {
    if (!hasFlucQ_) return;
    SimInfo::MoleculeIterator i;
    Molecule::FluctuatingChargeIterator  j;
    Molecule* mol;
    Atom* atom;
    RealType instTemp;
    RealType chi = currentSnapshot_->getChiElectronic();
    RealType oldChi = chi;
    RealType prevChi;
    RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
    int index;
    RealType cfrc, cvel, cmass;

    index = 0;
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {
      for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
           atom = mol->nextFluctuatingCharge(j)) {
        
        oldVel_[index] = atom->getFlucQVel();
        ++index;
      }
    }
        
    // do the iteration:
    
    for(int k = 0; k < maxIterNum_; k++) {
      index = 0;
      instTemp = thermo.getElectronicTemperature();
      cerr << "MoveB instTemp: " << instTemp << "\n";
      // 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 (atom = mol->beginFluctuatingCharge(j);  atom != NULL;
             atom = mol->nextFluctuatingCharge(j)) {

          cfrc = atom->getFlucQFrc();
          cvel =atom->getFlucQVel();
          cmass = atom->getChargeMass();
          
          // velocity half step
          cvel = oldVel_[index] + dt2_ * cfrc / cmass - dt2_*chi*oldVel_[index];
          
          atom->setFlucQVel(cvel);      
          ++index;          
        }
      }
      if (fabs(prevChi - chi) <= chiTolerance_)
        break;
    }
    integralOfChidt += dt2_ * chi;
    currentSnapshot_->setChiElectronic(chi);
    currentSnapshot_->setIntegralOfChiElectronicDt(integralOfChidt);
  }
  
  void FluctuatingChargeNVT::resetPropagator() {
    if (!hasFlucQ_) return;
    currentSnapshot_->setChiElectronic(0.0);
    currentSnapshot_->setIntegralOfChiElectronicDt(0.0);
  }
  
  RealType FluctuatingChargeNVT::calcConservedQuantity() {
    if (!hasFlucQ_) return 0.0;
    RealType chi = currentSnapshot_->getChiElectronic();
    RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
    RealType fkBT = info_->getNFluctuatingCharges() * 
      PhysicalConstants::kB *targetTemp_;

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

    RealType thermostat_potential = fkBT * integralOfChidt / 
      PhysicalConstants::energyConvert;

    return thermostat_kinetic + thermostat_potential;
  }
}
Revision:	1739
Committed:	Tue Jun 5 17:58:55 2012 UTC (12 years, 11 months ago) by gezelter
File size:	8489 byte(s)
Log Message:	Moved the propagators for flucq
#	User	Rev	Content
1	gezelter	1716	/*
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 "FluctuatingChargeNVT.hpp"
44			#include "primitives/Molecule.hpp"
45			#include "utils/simError.h"
46			#include "utils/PhysicalConstants.hpp"
47
48			namespace OpenMD {
49
50	gezelter	1739	FluctuatingChargeNVT::FluctuatingChargeNVT(SimInfo* info, ForceManager* fm) :
51			FluctuatingChargePropagator(info, fm), chiTolerance_ (1e-6),
52			maxIterNum_(4), thermo(info),
53	gezelter	1716	currentSnapshot_(info->getSnapshotManager()->getCurrentSnapshot()) {
54	gezelter	1739
55			if (hasFlucQ_) {
56			if (info_->getSimParams()->haveDt()) {
57			dt_ = info_->getSimParams()->getDt();
58			dt2_ = dt_ * 0.5;
59			} else {
60			sprintf(painCave.errMsg,
61			"FluctuatingChargeNVT Error: dt is not set\n");
62			painCave.isFatal = 1;
63			simError();
64			}
65
66			if (!info_->getSimParams()->getUseIntialExtendedSystemState()) {
67			currentSnapshot_->setChiElectronic(0.0);
68			currentSnapshot_->setIntegralOfChiElectronicDt(0.0);
69			}
70
71			if (!fqParams_->haveTargetTemp()) {
72			sprintf(painCave.errMsg, "You can't use the FluctuatingChargeNVT "
73			"propagator without a flucQ.targetTemp!\n");
74			painCave.isFatal = 1;
75			painCave.severity = OPENMD_ERROR;
76			simError();
77			} else {
78			targetTemp_ = fqParams_->getTargetTemp();
79			}
80
81			// We must set tauThermostat.
82
83			if (!fqParams_->haveTauThermostat()) {
84			sprintf(painCave.errMsg, "If you use the FluctuatingChargeNVT\n"
85			"\tpropagator, you must set flucQ.tauThermostat .\n");
86	gezelter	1716
87	gezelter	1739	painCave.severity = OPENMD_ERROR;
88			painCave.isFatal = 1;
89			simError();
90			} else {
91			tauThermostat_ = fqParams_->getTauThermostat();
92	gezelter	1716	}
93	gezelter	1739	updateSizes();
94			}
95	gezelter	1716	}
96
97			void FluctuatingChargeNVT::initialize() {
98	gezelter	1739	FluctuatingChargePropagator::initialize();
99			}
100	gezelter	1716
101
102			void FluctuatingChargeNVT::moveA() {
103
104			if (!hasFlucQ_) return;
105
106			SimInfo::MoleculeIterator i;
107			Molecule::FluctuatingChargeIterator j;
108			Molecule* mol;
109			Atom* atom;
110			RealType cvel, cpos, cfrc, cmass;
111
112			RealType chi = currentSnapshot_->getChiElectronic();
113			RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
114			RealType instTemp = thermo.getElectronicTemperature();
115
116
117			for (mol = info_->beginMolecule(i); mol != NULL;
118			mol = info_->nextMolecule(i)) {
119			for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
120			atom = mol->nextFluctuatingCharge(j)) {
121
122			cvel = atom->getFlucQVel();
123			cpos = atom->getFlucQPos();
124			cfrc = atom->getFlucQFrc();
125			cmass = atom->getChargeMass();
126
127	jmichalk	1735	cerr << atom->getType() << "\n";
128			cerr << "Before\n";
129			cerr << "cvel: " << cvel << "\tcpos: " << cpos << "\tcfrc: " << cfrc << "\tcmass: " << cmass << "\n";
130
131			// velocity half step
132			cvel += dt2_ * cfrc / cmass - dt2_chicvel;
133	gezelter	1716	// position whole step
134			cpos += dt_ * cvel;
135	jmichalk	1735
136			cerr << "After\n";
137			cerr << "cvel: " << cvel << "\tcpos: " << cpos << "\n\n";
138
139	gezelter	1716	atom->setFlucQVel(cvel);
140			atom->setFlucQPos(cpos);
141			}
142			}
143
144			chi += dt2_ * (instTemp / targetTemp_ - 1.0) /
145			(tauThermostat_ * tauThermostat_);
146
147			integralOfChidt += chi * dt2_;
148	jmichalk	1735	cerr << "Move A instTemp: " << instTemp << "\n";
149	gezelter	1716	currentSnapshot_->setChiElectronic(chi);
150			currentSnapshot_->setIntegralOfChiElectronicDt(integralOfChidt);
151
152			}
153
154			void FluctuatingChargeNVT::updateSizes() {
155			if (!hasFlucQ_) return;
156			oldVel_.resize(info_->getNFluctuatingCharges());
157			}
158
159			void FluctuatingChargeNVT::moveB() {
160			if (!hasFlucQ_) return;
161			SimInfo::MoleculeIterator i;
162			Molecule::FluctuatingChargeIterator j;
163			Molecule* mol;
164			Atom* atom;
165			RealType instTemp;
166			RealType chi = currentSnapshot_->getChiElectronic();
167			RealType oldChi = chi;
168			RealType prevChi;
169			RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
170			int index;
171			RealType cfrc, cvel, cmass;
172
173			index = 0;
174			for (mol = info_->beginMolecule(i); mol != NULL;
175			mol = info_->nextMolecule(i)) {
176			for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
177			atom = mol->nextFluctuatingCharge(j)) {
178
179			oldVel_[index] = atom->getFlucQVel();
180			++index;
181			}
182			}
183
184			// do the iteration:
185
186			for(int k = 0; k < maxIterNum_; k++) {
187			index = 0;
188			instTemp = thermo.getElectronicTemperature();
189	jmichalk	1735	cerr << "MoveB instTemp: " << instTemp << "\n";
190	gezelter	1716	// evolve chi another half step using the temperature at t + dt/2
191			prevChi = chi;
192			chi = oldChi + dt2_ * (instTemp / targetTemp_ - 1.0) /
193			(tauThermostat_ * tauThermostat_);
194
195			for (mol = info_->beginMolecule(i); mol != NULL;
196			mol = info_->nextMolecule(i)) {
197			for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
198			atom = mol->nextFluctuatingCharge(j)) {
199
200			cfrc = atom->getFlucQFrc();
201			cvel =atom->getFlucQVel();
202			cmass = atom->getChargeMass();
203
204			// velocity half step
205	jmichalk	1735	cvel = oldVel_[index] + dt2_ * cfrc / cmass - dt2_chioldVel_[index];
206	gezelter	1716
207			atom->setFlucQVel(cvel);
208			++index;
209			}
210			}
211			if (fabs(prevChi - chi) <= chiTolerance_)
212			break;
213			}
214			integralOfChidt += dt2_ * chi;
215			currentSnapshot_->setChiElectronic(chi);
216			currentSnapshot_->setIntegralOfChiElectronicDt(integralOfChidt);
217			}
218
219			void FluctuatingChargeNVT::resetPropagator() {
220			if (!hasFlucQ_) return;
221			currentSnapshot_->setChiElectronic(0.0);
222			currentSnapshot_->setIntegralOfChiElectronicDt(0.0);
223			}
224
225			RealType FluctuatingChargeNVT::calcConservedQuantity() {
226			if (!hasFlucQ_) return 0.0;
227			RealType chi = currentSnapshot_->getChiElectronic();
228			RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
229			RealType fkBT = info_->getNFluctuatingCharges() *
230			PhysicalConstants::kB *targetTemp_;
231
232			RealType thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ *
233			chi * chi / (2.0 * PhysicalConstants::energyConvert);
234
235			RealType thermostat_potential = fkBT * integralOfChidt /
236			PhysicalConstants::energyConvert;
237
238			return thermostat_kinetic + thermostat_potential;
239			}
240			}