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, 234107 (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

namespace OpenMD {
  
  Velocitizer::Velocitizer(SimInfo* info) : info_(info), thermo(info) {
    

    Globals * simParams = info->getSimParams();
    
#ifndef IS_MPI
    if (simParams->haveSeed()) {
      int seedValue = simParams->getSeed();
      randNumGen_ = new SeqRandNumGen(seedValue);
    }else {
      randNumGen_ = new SeqRandNumGen();
    }    
#else
    if (simParams->haveSeed()) {
      int 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, m, n;
    Vector3d vdrift;
    RealType vbar;
    /**@todo refactor 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 * sd;

    kebar = kb * temperature * info_->getNdfRaw() / (2.0 * info_->getNdf());

    for( mol = info_->beginMolecule(i); mol != NULL;
         mol = info_->nextMolecule(i) ) {

      for( sd = mol->beginIntegrableObject(j); sd != NULL;
           sd = mol->nextIntegrableObject(j) ) {
        
        // uses equipartition theory to solve for vbar in angstrom/fs
        
        av2 = 2.0 * kebar / sd->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);
        }
        sd->setVel(aVel);
        
        if (sd->isDirectional()) {
          I = sd->getI();
          
          if (sd->isLinear()) {
            l = sd->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);
            }
          }
          
          sd->setJ(aJ);
        }
      }
    }
        
    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 = thermo.getComVel();
    
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator j;
    Molecule * mol;
    StuntDouble * sd;
    
    //  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( sd = mol->beginIntegrableObject(j); sd != NULL;
           sd = mol->nextIntegrableObject(j) ) {

        sd->setVel(sd->getVel() - vdrift);

      }
    }    
  }
    
  void Velocitizer::removeAngularDrift() {
    // Get the Center of Mass drift velocity.
      
    Vector3d vdrift;
    Vector3d com; 
      
    thermo.getComAll(com, vdrift);
         
    Mat3x3d inertiaTensor;
    Vector3d angularMomentum;
    Vector3d omega;
               
    thermo.getInertiaTensor(inertiaTensor, angularMomentum);

    // We now need the inverse of the inertia tensor.
    inertiaTensor = inertiaTensor.inverse();
    omega = inertiaTensor * angularMomentum;
    
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator j;
    Molecule* mol;
    StuntDouble* sd;
    Vector3d tempComPos;
    
    // Corrects for the center of mass angular drift by summing all
    // the angular momentum and dividing by the total mass.

    for( mol = info_->beginMolecule(i); mol != NULL;
         mol = info_->nextMolecule(i) ) {

      for( sd = mol->beginIntegrableObject(j); sd != NULL;
           sd = mol->nextIntegrableObject(j) ) {

        tempComPos = sd->getPos() - com;
        sd->setVel((sd->getVel() - vdrift) - cross(omega, tempComPos));
        
      }
    }   
  }   
}
Revision:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (12 years, 4 months ago) by gezelter
File size:	6631 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [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	gezelter	1390	namespace OpenMD {
55	gezelter	1079
56	gezelter	1782	Velocitizer::Velocitizer(SimInfo* info) : info_(info), thermo(info) {
57	gezelter	1079
58	gezelter	1879
59	gezelter	1079	Globals * simParams = info->getSimParams();
60
61			#ifndef IS_MPI
62			if (simParams->haveSeed()) {
63	gezelter	1879	int seedValue = simParams->getSeed();
64	gezelter	1079	randNumGen_ = new SeqRandNumGen(seedValue);
65			}else {
66			randNumGen_ = new SeqRandNumGen();
67			}
68			#else
69			if (simParams->haveSeed()) {
70	gezelter	1879	int seedValue = simParams->getSeed();
71	gezelter	1079	randNumGen_ = new ParallelRandNumGen(seedValue);
72			}else {
73			randNumGen_ = new ParallelRandNumGen();
74			}
75			#endif
76			}
77
78			Velocitizer::~Velocitizer() {
79			delete randNumGen_;
80			}
81
82			void Velocitizer::velocitize(RealType temperature) {
83			Vector3d aVel;
84			Vector3d aJ;
85			Mat3x3d I;
86	gezelter	1782	int l, m, n;
87	gezelter	1079	Vector3d vdrift;
88			RealType vbar;
89	gezelter	1782	/*@todo refactor kb /
90	gezelter	1079	const RealType kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
91			RealType av2;
92			RealType kebar;
93
94			Globals * simParams = info_->getSimParams();
95
96			SimInfo::MoleculeIterator i;
97			Molecule::IntegrableObjectIterator j;
98			Molecule * mol;
99	gezelter	1782	StuntDouble * sd;
100	gezelter	1313
101	gezelter	1079	kebar = kb * temperature * info_->getNdfRaw() / (2.0 * info_->getNdf());
102	gezelter	1782
103	gezelter	1079	for( mol = info_->beginMolecule(i); mol != NULL;
104			mol = info_->nextMolecule(i) ) {
105	gezelter	1782
106			for( sd = mol->beginIntegrableObject(j); sd != NULL;
107			sd = mol->nextIntegrableObject(j) ) {
108	gezelter	1079
109			// uses equipartition theory to solve for vbar in angstrom/fs
110
111	gezelter	1782	av2 = 2.0 * kebar / sd->getMass();
112	gezelter	1079	vbar = sqrt(av2);
113
114			// picks random velocities from a gaussian distribution
115			// centered on vbar
116
117			for( int k = 0; k < 3; k++ ) {
118			aVel[k] = vbar * randNumGen_->randNorm(0.0, 1.0);
119			}
120	gezelter	1782	sd->setVel(aVel);
121	gezelter	1079
122	gezelter	1782	if (sd->isDirectional()) {
123			I = sd->getI();
124	gezelter	1079
125	gezelter	1782	if (sd->isLinear()) {
126			l = sd->linearAxis();
127	gezelter	1079	m = (l + 1) % 3;
128			n = (l + 2) % 3;
129
130			aJ[l] = 0.0;
131			vbar = sqrt(2.0 * kebar * I(m, m));
132			aJ[m] = vbar * randNumGen_->randNorm(0.0, 1.0);
133			vbar = sqrt(2.0 * kebar * I(n, n));
134			aJ[n] = vbar * randNumGen_->randNorm(0.0, 1.0);
135			} else {
136			for( int k = 0; k < 3; k++ ) {
137			vbar = sqrt(2.0 * kebar * I(k, k));
138			aJ[k] = vbar *randNumGen_->randNorm(0.0, 1.0);
139			}
140	gezelter	1782	}
141	gezelter	1079
142	gezelter	1782	sd->setJ(aJ);
143			}
144	gezelter	1079	}
145	gezelter	1782	}
146
147	gezelter	1079	removeComDrift();
148	gezelter	1782
149			// Remove angular drift if we are not using periodic boundary
150			// conditions:
151
152			if(!simParams->getUsePeriodicBoundaryConditions()) removeAngularDrift();
153			}
154	gezelter	1079
155			void Velocitizer::removeComDrift() {
156			// Get the Center of Mass drift velocity.
157	gezelter	1782	Vector3d vdrift = thermo.getComVel();
158	gezelter	1079
159			SimInfo::MoleculeIterator i;
160			Molecule::IntegrableObjectIterator j;
161			Molecule * mol;
162	gezelter	1782	StuntDouble * sd;
163	gezelter	1079
164			// Corrects for the center of mass drift.
165			// sums all the momentum and divides by total mass.
166			for( mol = info_->beginMolecule(i); mol != NULL;
167	gezelter	1782	mol = info_->nextMolecule(i) ) {
168
169			for( sd = mol->beginIntegrableObject(j); sd != NULL;
170			sd = mol->nextIntegrableObject(j) ) {
171
172			sd->setVel(sd->getVel() - vdrift);
173
174	gezelter	1079	}
175	gezelter	1782	}
176			}
177	gezelter	1079
178			void Velocitizer::removeAngularDrift() {
179			// Get the Center of Mass drift velocity.
180
181			Vector3d vdrift;
182			Vector3d com;
183
184	gezelter	1782	thermo.getComAll(com, vdrift);
185	gezelter	1079
186			Mat3x3d inertiaTensor;
187			Vector3d angularMomentum;
188			Vector3d omega;
189	gezelter	1782
190			thermo.getInertiaTensor(inertiaTensor, angularMomentum);
191
192	gezelter	1079	// We now need the inverse of the inertia tensor.
193	gezelter	1782	inertiaTensor = inertiaTensor.inverse();
194			omega = inertiaTensor * angularMomentum;
195
196	gezelter	1079	SimInfo::MoleculeIterator i;
197			Molecule::IntegrableObjectIterator j;
198	gezelter	1782	Molecule* mol;
199			StuntDouble* sd;
200	gezelter	1079	Vector3d tempComPos;
201	gezelter	1782
202			// Corrects for the center of mass angular drift by summing all
203			// the angular momentum and dividing by the total mass.
204
205	gezelter	1079	for( mol = info_->beginMolecule(i); mol != NULL;
206			mol = info_->nextMolecule(i) ) {
207	gezelter	1782
208			for( sd = mol->beginIntegrableObject(j); sd != NULL;
209			sd = mol->nextIntegrableObject(j) ) {
210
211			tempComPos = sd->getPos() - com;
212			sd->setVel((sd->getVel() - vdrift) - cross(omega, tempComPos));
213
214	gezelter	1079	}
215	gezelter	1782	}
216			}
217	gezelter	1079	}