src/integrators/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) : 
    FluctuatingChargePropagator(info), chiTolerance_ (1e-6), maxIterNum_(4),
    thermo(info), 
    currentSnapshot_(info->getSnapshotManager()->getCurrentSnapshot()) {

    if (info_->usesFluctuatingCharges()) {
      if (info_->getNFluctuatingCharges() > 0) {

        hasFlucQ_ = true;
        Globals* simParams = info_->getSimParams();

        if (simParams->haveDt()) {
          dt_ = simParams->getDt();
          dt2_ = dt_ * 0.5;
        } else {
          sprintf(painCave.errMsg,
                  "FluctuatingChargeNVT Error: dt is not set\n");
          painCave.isFatal = 1;
          simError();
        }
        
        if (!simParams->getUseIntialExtendedSystemState()) {
          currentSnapshot_->setChiElectronic(0.0);
          currentSnapshot_->setIntegralOfChiElectronicDt(0.0);
        }
        
        if (!simParams->haveFlucQTargetTemp()) {
          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_ = simParams->getFlucQTargetTemp();
        }
        
        // We must set tauThermostat.
        
        if (!simParams->haveFlucQtauThermostat()) {
          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_ = simParams->getFlucQtauThermostat();
        }
        updateSizes();
      }
    }       
  }

  void FluctuatingChargeNVT::initialize() {

    if (!hasFlucQ_) return;

    SimInfo::MoleculeIterator i;
    Molecule::FluctuatingChargeIterator  j;
    Molecule* mol;
    Atom* atom;
    
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {
      for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
           atom = mol->nextFluctuatingCharge(j)) {
        atom->setFlucQPos(0.0);
        atom->setFlucQVel(0.0);
      }
    }
    
    cerr << "Yeah, you should probably implement this\n";
  }

  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();

    cerr << "why are we here?\n";

    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_ *PhysicalConstants::energyConvert/cmass*cfrc - 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_;
    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();

      // 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_/cmass*PhysicalConstants::energyConvert * cfrc - 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:	1716
Committed:	Wed May 23 01:26:15 2012 UTC (12 years, 11 months ago) by gezelter
File size:	8881 byte(s)
Log Message:	Adding the propagators for FlucQ
#	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 "FluctuatingChargeNVT.hpp"
44	#include "primitives/Molecule.hpp"
45	#include "utils/simError.h"
46	#include "utils/PhysicalConstants.hpp"
47
48	namespace OpenMD {
49
50	FluctuatingChargeNVT::FluctuatingChargeNVT(SimInfo* info) :
51	FluctuatingChargePropagator(info), chiTolerance_ (1e-6), maxIterNum_(4),
52	thermo(info),
53	currentSnapshot_(info->getSnapshotManager()->getCurrentSnapshot()) {
54
55	if (info_->usesFluctuatingCharges()) {
56	if (info_->getNFluctuatingCharges() > 0) {
57
58	hasFlucQ_ = true;
59	Globals* simParams = info_->getSimParams();
60
61	if (simParams->haveDt()) {
62	dt_ = simParams->getDt();
63	dt2_ = dt_ * 0.5;
64	} else {
65	sprintf(painCave.errMsg,
66	"FluctuatingChargeNVT Error: dt is not set\n");
67	painCave.isFatal = 1;
68	simError();
69	}
70
71	if (!simParams->getUseIntialExtendedSystemState()) {
72	currentSnapshot_->setChiElectronic(0.0);
73	currentSnapshot_->setIntegralOfChiElectronicDt(0.0);
74	}
75
76	if (!simParams->haveFlucQTargetTemp()) {
77	sprintf(painCave.errMsg, "You can't use the FluctuatingChargeNVT "
78	"propagator without a flucQ.targetTemp!\n");
79	painCave.isFatal = 1;
80	painCave.severity = OPENMD_ERROR;
81	simError();
82	} else {
83	targetTemp_ = simParams->getFlucQTargetTemp();
84	}
85
86	// We must set tauThermostat.
87
88	if (!simParams->haveFlucQtauThermostat()) {
89	sprintf(painCave.errMsg, "If you use the FluctuatingChargeNVT\n"
90	"\tpropagator, you must set flucQ.tauThermostat .\n");
91
92	painCave.severity = OPENMD_ERROR;
93	painCave.isFatal = 1;
94	simError();
95	} else {
96	tauThermostat_ = simParams->getFlucQtauThermostat();
97	}
98	updateSizes();
99	}
100	}
101	}
102
103	void FluctuatingChargeNVT::initialize() {
104
105	if (!hasFlucQ_) return;
106
107	SimInfo::MoleculeIterator i;
108	Molecule::FluctuatingChargeIterator j;
109	Molecule* mol;
110	Atom* atom;
111
112	for (mol = info_->beginMolecule(i); mol != NULL;
113	mol = info_->nextMolecule(i)) {
114	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
115	atom = mol->nextFluctuatingCharge(j)) {
116	atom->setFlucQPos(0.0);
117	atom->setFlucQVel(0.0);
118	}
119	}
120
121	cerr << "Yeah, you should probably implement this\n";
122	}
123
124	void FluctuatingChargeNVT::moveA() {
125
126	if (!hasFlucQ_) return;
127
128	SimInfo::MoleculeIterator i;
129	Molecule::FluctuatingChargeIterator j;
130	Molecule* mol;
131	Atom* atom;
132	RealType cvel, cpos, cfrc, cmass;
133
134	RealType chi = currentSnapshot_->getChiElectronic();
135	RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
136	RealType instTemp = thermo.getElectronicTemperature();
137
138	cerr << "why are we here?\n";
139
140	for (mol = info_->beginMolecule(i); mol != NULL;
141	mol = info_->nextMolecule(i)) {
142	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
143	atom = mol->nextFluctuatingCharge(j)) {
144
145	cvel = atom->getFlucQVel();
146	cpos = atom->getFlucQPos();
147	cfrc = atom->getFlucQFrc();
148	cmass = atom->getChargeMass();
149
150	// velocity half step
151	cvel += dt2_ PhysicalConstants::energyConvert/cmasscfrc - dt2_chicvel;
152	// position whole step
153	cpos += dt_ * cvel;
154
155	atom->setFlucQVel(cvel);
156	atom->setFlucQPos(cpos);
157	}
158	}
159
160	chi += dt2_ * (instTemp / targetTemp_ - 1.0) /
161	(tauThermostat_ * tauThermostat_);
162
163	integralOfChidt += chi * dt2_;
164	currentSnapshot_->setChiElectronic(chi);
165	currentSnapshot_->setIntegralOfChiElectronicDt(integralOfChidt);
166
167	}
168
169	void FluctuatingChargeNVT::updateSizes() {
170	if (!hasFlucQ_) return;
171	oldVel_.resize(info_->getNFluctuatingCharges());
172	}
173
174	void FluctuatingChargeNVT::moveB() {
175	if (!hasFlucQ_) return;
176	SimInfo::MoleculeIterator i;
177	Molecule::FluctuatingChargeIterator j;
178	Molecule* mol;
179	Atom* atom;
180	RealType instTemp;
181	RealType chi = currentSnapshot_->getChiElectronic();
182	RealType oldChi = chi;
183	RealType prevChi;
184	RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
185	int index;
186	RealType cfrc, cvel, cmass;
187
188	index = 0;
189	for (mol = info_->beginMolecule(i); mol != NULL;
190	mol = info_->nextMolecule(i)) {
191	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
192	atom = mol->nextFluctuatingCharge(j)) {
193
194	oldVel_[index] = atom->getFlucQVel();
195	++index;
196	}
197	}
198
199	// do the iteration:
200
201	for(int k = 0; k < maxIterNum_; k++) {
202	index = 0;
203	instTemp = thermo.getElectronicTemperature();
204
205	// evolve chi another half step using the temperature at t + dt/2
206	prevChi = chi;
207	chi = oldChi + dt2_ * (instTemp / targetTemp_ - 1.0) /
208	(tauThermostat_ * tauThermostat_);
209
210	for (mol = info_->beginMolecule(i); mol != NULL;
211	mol = info_->nextMolecule(i)) {
212	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
213	atom = mol->nextFluctuatingCharge(j)) {
214
215	cfrc = atom->getFlucQFrc();
216	cvel =atom->getFlucQVel();
217	cmass = atom->getChargeMass();
218
219	// velocity half step
220	cvel = oldVel_[index] + dt2_/cmassPhysicalConstants::energyConvert cfrc - dt2_chioldVel_[index];
221
222	atom->setFlucQVel(cvel);
223	++index;
224	}
225	}
226	if (fabs(prevChi - chi) <= chiTolerance_)
227	break;
228	}
229	integralOfChidt += dt2_ * chi;
230	currentSnapshot_->setChiElectronic(chi);
231	currentSnapshot_->setIntegralOfChiElectronicDt(integralOfChidt);
232	}
233
234	void FluctuatingChargeNVT::resetPropagator() {
235	if (!hasFlucQ_) return;
236	currentSnapshot_->setChiElectronic(0.0);
237	currentSnapshot_->setIntegralOfChiElectronicDt(0.0);
238	}
239
240	RealType FluctuatingChargeNVT::calcConservedQuantity() {
241	if (!hasFlucQ_) return 0.0;
242	RealType chi = currentSnapshot_->getChiElectronic();
243	RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
244	RealType fkBT = info_->getNFluctuatingCharges() *
245	PhysicalConstants::kB *targetTemp_;
246
247	RealType thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ *
248	chi * chi / (2.0 * PhysicalConstants::energyConvert);
249
250	RealType thermostat_potential = fkBT * integralOfChidt /
251	PhysicalConstants::energyConvert;
252
253	return thermostat_kinetic + thermostat_potential;
254	}
255	}