src/integrators/Velocitizer.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/Velocitizer.hpp"
#include "math/SquareMatrix3.hpp"
#include "primitives/Molecule.hpp"
#include "primitives/StuntDouble.hpp"

#ifndef IS_MPI
#include "math/SeqRandNumGen.hpp"
#else
#include "math/ParallelRandNumGen.hpp"
#endif

/* Remove me after testing*/
/*
#include <cstdio>
#include <iostream>
*/
/*End remove me*/

namespace OpenMD {
  
  Velocitizer::Velocitizer(SimInfo* info) : info_(info) {
    
    int seedValue;
    Globals * simParams = info->getSimParams();
    
#ifndef IS_MPI
    if (simParams->haveSeed()) {
      seedValue = simParams->getSeed();
      randNumGen_ = new SeqRandNumGen(seedValue);
    }else {
      randNumGen_ = new SeqRandNumGen();
    }    
#else
    if (simParams->haveSeed()) {
      seedValue = simParams->getSeed();
      randNumGen_ = new ParallelRandNumGen(seedValue);
    }else {
      randNumGen_ = new ParallelRandNumGen();
    }    
#endif 
  }
  
  Velocitizer::~Velocitizer() {
    delete randNumGen_;
  }
  
  void Velocitizer::velocitize(RealType temperature) {
    Vector3d aVel;
    Vector3d aJ;
    Mat3x3d I;
    int l;
    int m;
    int n; 
    Vector3d vdrift;
    RealType vbar;
    /**@todo refactory kb */
    const RealType kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
    RealType av2;
    RealType kebar;
    
    Globals * simParams = info_->getSimParams();
    
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator j;
    Molecule * mol;
    StuntDouble * integrableObject;

    kebar = kb * temperature * info_->getNdfRaw() / (2.0 * info_->getNdf());
    for( mol = info_->beginMolecule(i); mol != NULL;
         mol = info_->nextMolecule(i) ) {
      for( integrableObject = mol->beginIntegrableObject(j);
           integrableObject != NULL;
           integrableObject = mol->nextIntegrableObject(j) ) {
        
        // uses equipartition theory to solve for vbar in angstrom/fs
        
        av2 = 2.0 * kebar / integrableObject->getMass();
        vbar = sqrt(av2);
        
        // picks random velocities from a gaussian distribution
        // centered on vbar
        
        for( int k = 0; k < 3; k++ ) {
          aVel[k] = vbar * randNumGen_->randNorm(0.0, 1.0);
        }
        integrableObject->setVel(aVel);
        
        if (integrableObject->isDirectional()) {
          I = integrableObject->getI();
          
          if (integrableObject->isLinear()) {
            l = integrableObject->linearAxis();
            m = (l + 1) % 3;
            n = (l + 2) % 3;
            
            aJ[l] = 0.0;
            vbar = sqrt(2.0 * kebar * I(m, m));
            aJ[m] = vbar * randNumGen_->randNorm(0.0, 1.0);
            vbar = sqrt(2.0 * kebar * I(n, n));
            aJ[n] = vbar * randNumGen_->randNorm(0.0, 1.0);
          } else {
            for( int k = 0; k < 3; k++ ) {
              vbar = sqrt(2.0 * kebar * I(k, k));
              aJ[k] = vbar *randNumGen_->randNorm(0.0, 1.0);
            }
          } // else isLinear
          
          integrableObject->setJ(aJ);
        }     //isDirectional 
      }
    }             //end for (mol = beginMolecule(i); ...)
    
    
    
    removeComDrift();
    // Remove angular drift if we are not using periodic boundary conditions.
    if(!simParams->getUsePeriodicBoundaryConditions()) removeAngularDrift();
    
  }
  
  
  
  void Velocitizer::removeComDrift() {
    // Get the Center of Mass drift velocity.
    Vector3d vdrift = info_->getComVel();
    
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator j;
    Molecule * mol;
    StuntDouble * integrableObject;
    
    //  Corrects for the center of mass drift.
    // sums all the momentum and divides by total mass.
    for( mol = info_->beginMolecule(i); mol != NULL;
         mol = info_->nextMolecule(i) ) {
      for( integrableObject = mol->beginIntegrableObject(j);
           integrableObject != NULL;
           integrableObject = mol->nextIntegrableObject(j) ) {
        integrableObject->setVel(integrableObject->getVel() - vdrift);
      }
    }
    
  }
  
   
  void Velocitizer::removeAngularDrift() {
    // Get the Center of Mass drift velocity.
      
    Vector3d vdrift;
    Vector3d com; 
      
    info_->getComAll(com,vdrift);
         
    Mat3x3d inertiaTensor;
    Vector3d angularMomentum;
    Vector3d omega;
      
      
      
    info_->getInertiaTensor(inertiaTensor,angularMomentum);
    // We now need the inverse of the inertia tensor.
    /*
    std::cerr << "Angular Momentum before is "
              << angularMomentum <<  std::endl;
    std::cerr << "Inertia Tensor before is "
              << inertiaTensor <<  std::endl;
    */
    inertiaTensor =inertiaTensor.inverse();
    /*
    std::cerr << "Inertia Tensor after inverse is "
              << inertiaTensor <<  std::endl;
    */
    omega = inertiaTensor*angularMomentum;
      
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator j;
    Molecule * mol;
    StuntDouble * integrableObject;
    Vector3d tempComPos;
      
    //  Corrects for the center of mass angular drift.
    // sums all the angular momentum and divides by total mass.
    for( mol = info_->beginMolecule(i); mol != NULL;
         mol = info_->nextMolecule(i) ) {
      for( integrableObject = mol->beginIntegrableObject(j);
           integrableObject != NULL;
           integrableObject = mol->nextIntegrableObject(j) ) {
        tempComPos = integrableObject->getPos()-com;
        integrableObject->setVel((integrableObject->getVel() - vdrift)-cross(omega,tempComPos));
      }
    }
      
    angularMomentum = info_->getAngularMomentum();
    /*
    std::cerr << "Angular Momentum after is "
              << angularMomentum <<  std::endl;
    */ 
  }
   
   
   
   
}
Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	7642 byte(s)
Log Message:	updated copyright notices
#	User	Rev	Content
1	gezelter	1079	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	1079	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	1079	* 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	gezelter	1390	*
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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	1079	*/
42
43			#include "integrators/Velocitizer.hpp"
44			#include "math/SquareMatrix3.hpp"
45			#include "primitives/Molecule.hpp"
46			#include "primitives/StuntDouble.hpp"
47
48			#ifndef IS_MPI
49			#include "math/SeqRandNumGen.hpp"
50			#else
51			#include "math/ParallelRandNumGen.hpp"
52			#endif
53
54			/* Remove me after testing*/
55	gezelter	1313	/*
56	gezelter	1079	#include <cstdio>
57			#include <iostream>
58	gezelter	1313	*/
59	gezelter	1079	/End remove me/
60
61	gezelter	1390	namespace OpenMD {
62	gezelter	1079
63			Velocitizer::Velocitizer(SimInfo* info) : info_(info) {
64
65			int seedValue;
66			Globals * simParams = info->getSimParams();
67
68			#ifndef IS_MPI
69			if (simParams->haveSeed()) {
70			seedValue = simParams->getSeed();
71			randNumGen_ = new SeqRandNumGen(seedValue);
72			}else {
73			randNumGen_ = new SeqRandNumGen();
74			}
75			#else
76			if (simParams->haveSeed()) {
77			seedValue = simParams->getSeed();
78			randNumGen_ = new ParallelRandNumGen(seedValue);
79			}else {
80			randNumGen_ = new ParallelRandNumGen();
81			}
82			#endif
83			}
84
85			Velocitizer::~Velocitizer() {
86			delete randNumGen_;
87			}
88
89			void Velocitizer::velocitize(RealType temperature) {
90			Vector3d aVel;
91			Vector3d aJ;
92			Mat3x3d I;
93			int l;
94			int m;
95			int n;
96			Vector3d vdrift;
97			RealType vbar;
98			/*@todo refactory kb /
99			const RealType kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
100			RealType av2;
101			RealType kebar;
102
103			Globals * simParams = info_->getSimParams();
104
105			SimInfo::MoleculeIterator i;
106			Molecule::IntegrableObjectIterator j;
107			Molecule * mol;
108			StuntDouble * integrableObject;
109	gezelter	1313
110	gezelter	1079	kebar = kb * temperature * info_->getNdfRaw() / (2.0 * info_->getNdf());
111			for( mol = info_->beginMolecule(i); mol != NULL;
112			mol = info_->nextMolecule(i) ) {
113			for( integrableObject = mol->beginIntegrableObject(j);
114			integrableObject != NULL;
115			integrableObject = mol->nextIntegrableObject(j) ) {
116
117			// uses equipartition theory to solve for vbar in angstrom/fs
118
119			av2 = 2.0 * kebar / integrableObject->getMass();
120			vbar = sqrt(av2);
121
122			// picks random velocities from a gaussian distribution
123			// centered on vbar
124
125			for( int k = 0; k < 3; k++ ) {
126			aVel[k] = vbar * randNumGen_->randNorm(0.0, 1.0);
127			}
128			integrableObject->setVel(aVel);
129
130			if (integrableObject->isDirectional()) {
131			I = integrableObject->getI();
132
133			if (integrableObject->isLinear()) {
134			l = integrableObject->linearAxis();
135			m = (l + 1) % 3;
136			n = (l + 2) % 3;
137
138			aJ[l] = 0.0;
139			vbar = sqrt(2.0 * kebar * I(m, m));
140			aJ[m] = vbar * randNumGen_->randNorm(0.0, 1.0);
141			vbar = sqrt(2.0 * kebar * I(n, n));
142			aJ[n] = vbar * randNumGen_->randNorm(0.0, 1.0);
143			} else {
144			for( int k = 0; k < 3; k++ ) {
145			vbar = sqrt(2.0 * kebar * I(k, k));
146			aJ[k] = vbar *randNumGen_->randNorm(0.0, 1.0);
147			}
148			} // else isLinear
149
150			integrableObject->setJ(aJ);
151			} //isDirectional
152			}
153			} //end for (mol = beginMolecule(i); ...)
154
155
156
157			removeComDrift();
158			// Remove angular drift if we are not using periodic boundary conditions.
159			if(!simParams->getUsePeriodicBoundaryConditions()) removeAngularDrift();
160
161			}
162
163
164
165			void Velocitizer::removeComDrift() {
166			// Get the Center of Mass drift velocity.
167			Vector3d vdrift = info_->getComVel();
168
169			SimInfo::MoleculeIterator i;
170			Molecule::IntegrableObjectIterator j;
171			Molecule * mol;
172			StuntDouble * integrableObject;
173
174			// Corrects for the center of mass drift.
175			// sums all the momentum and divides by total mass.
176			for( mol = info_->beginMolecule(i); mol != NULL;
177			mol = info_->nextMolecule(i) ) {
178			for( integrableObject = mol->beginIntegrableObject(j);
179			integrableObject != NULL;
180			integrableObject = mol->nextIntegrableObject(j) ) {
181			integrableObject->setVel(integrableObject->getVel() - vdrift);
182			}
183			}
184
185			}
186
187
188			void Velocitizer::removeAngularDrift() {
189			// Get the Center of Mass drift velocity.
190
191			Vector3d vdrift;
192			Vector3d com;
193
194			info_->getComAll(com,vdrift);
195
196			Mat3x3d inertiaTensor;
197			Vector3d angularMomentum;
198			Vector3d omega;
199
200
201
202			info_->getInertiaTensor(inertiaTensor,angularMomentum);
203			// We now need the inverse of the inertia tensor.
204			/*
205			std::cerr << "Angular Momentum before is "
206			<< angularMomentum << std::endl;
207			std::cerr << "Inertia Tensor before is "
208			<< inertiaTensor << std::endl;
209	gezelter	1313	*/
210	gezelter	1079	inertiaTensor =inertiaTensor.inverse();
211			/*
212			std::cerr << "Inertia Tensor after inverse is "
213			<< inertiaTensor << std::endl;
214			*/
215			omega = inertiaTensor*angularMomentum;
216
217			SimInfo::MoleculeIterator i;
218			Molecule::IntegrableObjectIterator j;
219			Molecule * mol;
220			StuntDouble * integrableObject;
221			Vector3d tempComPos;
222
223			// Corrects for the center of mass angular drift.
224			// sums all the angular momentum and divides by total mass.
225			for( mol = info_->beginMolecule(i); mol != NULL;
226			mol = info_->nextMolecule(i) ) {
227			for( integrableObject = mol->beginIntegrableObject(j);
228			integrableObject != NULL;
229			integrableObject = mol->nextIntegrableObject(j) ) {
230			tempComPos = integrableObject->getPos()-com;
231			integrableObject->setVel((integrableObject->getVel() - vdrift)-cross(omega,tempComPos));
232			}
233			}
234
235			angularMomentum = info_->getAngularMomentum();
236			/*
237			std::cerr << "Angular Momentum after is "
238			<< angularMomentum << std::endl;
239	gezelter	1313	*/
240	gezelter	1079	}
241
242
243
244
245			}