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, 9 months ago) by gezelter
File size:	7642 byte(s)
Log Message:	updated copyright notices
#	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 "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	/*
56	#include <cstdio>
57	#include <iostream>
58	*/
59	/End remove me/
60
61	namespace OpenMD {
62
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
110	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	*/
210	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	*/
240	}
241
242
243
244
245	}