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, 234107 (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) : 
    FluctuatingChargePropagator(info), maxIterNum_(4), chiTolerance_ (1e-6), 
    snap(info->getSnapshotManager()->getCurrentSnapshot()), thermo(info) {  
  }

  void FluctuatingChargeNVT::initialize() {
    FluctuatingChargePropagator::initialize();  
    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()) {
        snap->setElectronicThermostat(make_pair(0.0, 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::moveA() {

    if (!hasFlucQ_) return;

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

    pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
    RealType chi = thermostat.first;
    RealType integralOfChidt = thermostat.second;
    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();       

        // velocity half step
        cvel += dt2_ * cfrc / cmass - dt2_*chi*cvel;                    
        // position whole step
        cpos += dt_ * cvel;
        
        atom->setFlucQVel(cvel);
        atom->setFlucQPos(cpos);
      }
    }
    
    chi += dt2_ * (instTemp / targetTemp_ - 1.0) / 
      (tauThermostat_ * tauThermostat_);

    integralOfChidt += chi * dt2_;
    snap->setElectronicThermostat(make_pair(chi, integralOfChidt));
  }

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

  void FluctuatingChargeNVT::moveB() {
    if (!hasFlucQ_) return;
    SimInfo::MoleculeIterator i;
    Molecule::FluctuatingChargeIterator  j;
    Molecule* mol;
    Atom* atom;
    RealType instTemp;
    pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
    RealType chi = thermostat.first;
    RealType oldChi = chi;
    RealType prevChi;
    RealType integralOfChidt = thermostat.second;
    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();
      // 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();
          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;
    snap->setElectronicThermostat(make_pair(chi, integralOfChidt));
  }
  
  void FluctuatingChargeNVT::resetPropagator() {
    if (!hasFlucQ_) return;
    snap->setElectronicThermostat(make_pair(0.0, 0.0));
  }
  
  RealType FluctuatingChargeNVT::calcConservedQuantity() {
    if (!hasFlucQ_) return 0.0;
    pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
    RealType chi = thermostat.first;
    RealType integralOfChidt = thermostat.second;
    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:	2071
Committed:	Sat Mar 7 21:41:51 2015 UTC (10 years, 2 months ago) by gezelter
File size:	7883 byte(s)
Log Message:	Reducing the number of warnings when using g++ to compile.
#	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 "FluctuatingChargeNVT.hpp"
44	#include "primitives/Molecule.hpp"
45	#include "utils/simError.h"
46	#include "utils/PhysicalConstants.hpp"
47
48
49	namespace OpenMD {
50
51	FluctuatingChargeNVT::FluctuatingChargeNVT(SimInfo* info) :
52	FluctuatingChargePropagator(info), maxIterNum_(4), chiTolerance_ (1e-6),
53	snap(info->getSnapshotManager()->getCurrentSnapshot()), thermo(info) {
54	}
55
56	void FluctuatingChargeNVT::initialize() {
57	FluctuatingChargePropagator::initialize();
58	if (hasFlucQ_) {
59	if (info_->getSimParams()->haveDt()) {
60	dt_ = info_->getSimParams()->getDt();
61	dt2_ = dt_ * 0.5;
62	} else {
63	sprintf(painCave.errMsg,
64	"FluctuatingChargeNVT Error: dt is not set\n");
65	painCave.isFatal = 1;
66	simError();
67	}
68
69	if (!info_->getSimParams()->getUseIntialExtendedSystemState()) {
70	snap->setElectronicThermostat(make_pair(0.0, 0.0));
71	}
72
73	if (!fqParams_->haveTargetTemp()) {
74	sprintf(painCave.errMsg, "You can't use the FluctuatingChargeNVT "
75	"propagator without a flucQ.targetTemp!\n");
76	painCave.isFatal = 1;
77	painCave.severity = OPENMD_ERROR;
78	simError();
79	} else {
80	targetTemp_ = fqParams_->getTargetTemp();
81	}
82
83	// We must set tauThermostat.
84
85	if (!fqParams_->haveTauThermostat()) {
86	sprintf(painCave.errMsg, "If you use the FluctuatingChargeNVT\n"
87	"\tpropagator, you must set flucQ.tauThermostat .\n");
88
89	painCave.severity = OPENMD_ERROR;
90	painCave.isFatal = 1;
91	simError();
92	} else {
93	tauThermostat_ = fqParams_->getTauThermostat();
94	}
95	updateSizes();
96	}
97	}
98
99
100	void FluctuatingChargeNVT::moveA() {
101
102	if (!hasFlucQ_) return;
103
104	SimInfo::MoleculeIterator i;
105	Molecule::FluctuatingChargeIterator j;
106	Molecule* mol;
107	Atom* atom;
108	RealType cvel, cpos, cfrc, cmass;
109
110	pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
111	RealType chi = thermostat.first;
112	RealType integralOfChidt = thermostat.second;
113	RealType instTemp = thermo.getElectronicTemperature();
114
115	for (mol = info_->beginMolecule(i); mol != NULL;
116	mol = info_->nextMolecule(i)) {
117	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
118	atom = mol->nextFluctuatingCharge(j)) {
119
120	cvel = atom->getFlucQVel();
121	cpos = atom->getFlucQPos();
122	cfrc = atom->getFlucQFrc();
123	cmass = atom->getChargeMass();
124
125	// velocity half step
126	cvel += dt2_ * cfrc / cmass - dt2_chicvel;
127	// position whole step
128	cpos += dt_ * cvel;
129
130	atom->setFlucQVel(cvel);
131	atom->setFlucQPos(cpos);
132	}
133	}
134
135	chi += dt2_ * (instTemp / targetTemp_ - 1.0) /
136	(tauThermostat_ * tauThermostat_);
137
138	integralOfChidt += chi * dt2_;
139	snap->setElectronicThermostat(make_pair(chi, integralOfChidt));
140	}
141
142	void FluctuatingChargeNVT::updateSizes() {
143	oldVel_.resize(info_->getNFluctuatingCharges());
144	}
145
146	void FluctuatingChargeNVT::moveB() {
147	if (!hasFlucQ_) return;
148	SimInfo::MoleculeIterator i;
149	Molecule::FluctuatingChargeIterator j;
150	Molecule* mol;
151	Atom* atom;
152	RealType instTemp;
153	pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
154	RealType chi = thermostat.first;
155	RealType oldChi = chi;
156	RealType prevChi;
157	RealType integralOfChidt = thermostat.second;
158	int index;
159	RealType cfrc, cvel, cmass;
160
161	index = 0;
162	for (mol = info_->beginMolecule(i); mol != NULL;
163	mol = info_->nextMolecule(i)) {
164	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
165	atom = mol->nextFluctuatingCharge(j)) {
166
167	oldVel_[index] = atom->getFlucQVel();
168	++index;
169	}
170	}
171
172	// do the iteration:
173
174	for(int k = 0; k < maxIterNum_; k++) {
175	index = 0;
176	instTemp = thermo.getElectronicTemperature();
177	// evolve chi another half step using the temperature at t + dt/2
178	prevChi = chi;
179	chi = oldChi + dt2_ * (instTemp / targetTemp_ - 1.0) /
180	(tauThermostat_ * tauThermostat_);
181
182	for (mol = info_->beginMolecule(i); mol != NULL;
183	mol = info_->nextMolecule(i)) {
184	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
185	atom = mol->nextFluctuatingCharge(j)) {
186
187	cfrc = atom->getFlucQFrc();
188	cmass = atom->getChargeMass();
189
190	// velocity half step
191	cvel = oldVel_[index] + dt2_ * cfrc / cmass - dt2_chioldVel_[index];
192	atom->setFlucQVel(cvel);
193	++index;
194	}
195	}
196	if (fabs(prevChi - chi) <= chiTolerance_)
197	break;
198	}
199	integralOfChidt += dt2_ * chi;
200	snap->setElectronicThermostat(make_pair(chi, integralOfChidt));
201	}
202
203	void FluctuatingChargeNVT::resetPropagator() {
204	if (!hasFlucQ_) return;
205	snap->setElectronicThermostat(make_pair(0.0, 0.0));
206	}
207
208	RealType FluctuatingChargeNVT::calcConservedQuantity() {
209	if (!hasFlucQ_) return 0.0;
210	pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
211	RealType chi = thermostat.first;
212	RealType integralOfChidt = thermostat.second;
213	RealType fkBT = info_->getNFluctuatingCharges() *
214	PhysicalConstants::kB *targetTemp_;
215
216	RealType thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ *
217	chi * chi / (2.0 * PhysicalConstants::energyConvert);
218
219	RealType thermostat_potential = fkBT * integralOfChidt /
220	PhysicalConstants::energyConvert;
221
222	return thermostat_kinetic + thermostat_potential;
223	}
224	}