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]  Vardeman & Gezelter, in progress (2009).                        
 */

#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:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 11 months ago) by gezelter
File size:	7576 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	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] Vardeman & Gezelter, in progress (2009).
40	*/
41
42	#include "integrators/Velocitizer.hpp"
43	#include "math/SquareMatrix3.hpp"
44	#include "primitives/Molecule.hpp"
45	#include "primitives/StuntDouble.hpp"
46
47	#ifndef IS_MPI
48	#include "math/SeqRandNumGen.hpp"
49	#else
50	#include "math/ParallelRandNumGen.hpp"
51	#endif
52
53	/* Remove me after testing*/
54	/*
55	#include <cstdio>
56	#include <iostream>
57	*/
58	/End remove me/
59
60	namespace OpenMD {
61
62	Velocitizer::Velocitizer(SimInfo* info) : info_(info) {
63
64	int seedValue;
65	Globals * simParams = info->getSimParams();
66
67	#ifndef IS_MPI
68	if (simParams->haveSeed()) {
69	seedValue = simParams->getSeed();
70	randNumGen_ = new SeqRandNumGen(seedValue);
71	}else {
72	randNumGen_ = new SeqRandNumGen();
73	}
74	#else
75	if (simParams->haveSeed()) {
76	seedValue = simParams->getSeed();
77	randNumGen_ = new ParallelRandNumGen(seedValue);
78	}else {
79	randNumGen_ = new ParallelRandNumGen();
80	}
81	#endif
82	}
83
84	Velocitizer::~Velocitizer() {
85	delete randNumGen_;
86	}
87
88	void Velocitizer::velocitize(RealType temperature) {
89	Vector3d aVel;
90	Vector3d aJ;
91	Mat3x3d I;
92	int l;
93	int m;
94	int n;
95	Vector3d vdrift;
96	RealType vbar;
97	/*@todo refactory kb /
98	const RealType kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
99	RealType av2;
100	RealType kebar;
101
102	Globals * simParams = info_->getSimParams();
103
104	SimInfo::MoleculeIterator i;
105	Molecule::IntegrableObjectIterator j;
106	Molecule * mol;
107	StuntDouble * integrableObject;
108
109	kebar = kb * temperature * info_->getNdfRaw() / (2.0 * info_->getNdf());
110	for( mol = info_->beginMolecule(i); mol != NULL;
111	mol = info_->nextMolecule(i) ) {
112	for( integrableObject = mol->beginIntegrableObject(j);
113	integrableObject != NULL;
114	integrableObject = mol->nextIntegrableObject(j) ) {
115
116	// uses equipartition theory to solve for vbar in angstrom/fs
117
118	av2 = 2.0 * kebar / integrableObject->getMass();
119	vbar = sqrt(av2);
120
121	// picks random velocities from a gaussian distribution
122	// centered on vbar
123
124	for( int k = 0; k < 3; k++ ) {
125	aVel[k] = vbar * randNumGen_->randNorm(0.0, 1.0);
126	}
127	integrableObject->setVel(aVel);
128
129	if (integrableObject->isDirectional()) {
130	I = integrableObject->getI();
131
132	if (integrableObject->isLinear()) {
133	l = integrableObject->linearAxis();
134	m = (l + 1) % 3;
135	n = (l + 2) % 3;
136
137	aJ[l] = 0.0;
138	vbar = sqrt(2.0 * kebar * I(m, m));
139	aJ[m] = vbar * randNumGen_->randNorm(0.0, 1.0);
140	vbar = sqrt(2.0 * kebar * I(n, n));
141	aJ[n] = vbar * randNumGen_->randNorm(0.0, 1.0);
142	} else {
143	for( int k = 0; k < 3; k++ ) {
144	vbar = sqrt(2.0 * kebar * I(k, k));
145	aJ[k] = vbar *randNumGen_->randNorm(0.0, 1.0);
146	}
147	} // else isLinear
148
149	integrableObject->setJ(aJ);
150	} //isDirectional
151	}
152	} //end for (mol = beginMolecule(i); ...)
153
154
155
156	removeComDrift();
157	// Remove angular drift if we are not using periodic boundary conditions.
158	if(!simParams->getUsePeriodicBoundaryConditions()) removeAngularDrift();
159
160	}
161
162
163
164	void Velocitizer::removeComDrift() {
165	// Get the Center of Mass drift velocity.
166	Vector3d vdrift = info_->getComVel();
167
168	SimInfo::MoleculeIterator i;
169	Molecule::IntegrableObjectIterator j;
170	Molecule * mol;
171	StuntDouble * integrableObject;
172
173	// Corrects for the center of mass drift.
174	// sums all the momentum and divides by total mass.
175	for( mol = info_->beginMolecule(i); mol != NULL;
176	mol = info_->nextMolecule(i) ) {
177	for( integrableObject = mol->beginIntegrableObject(j);
178	integrableObject != NULL;
179	integrableObject = mol->nextIntegrableObject(j) ) {
180	integrableObject->setVel(integrableObject->getVel() - vdrift);
181	}
182	}
183
184	}
185
186
187	void Velocitizer::removeAngularDrift() {
188	// Get the Center of Mass drift velocity.
189
190	Vector3d vdrift;
191	Vector3d com;
192
193	info_->getComAll(com,vdrift);
194
195	Mat3x3d inertiaTensor;
196	Vector3d angularMomentum;
197	Vector3d omega;
198
199
200
201	info_->getInertiaTensor(inertiaTensor,angularMomentum);
202	// We now need the inverse of the inertia tensor.
203	/*
204	std::cerr << "Angular Momentum before is "
205	<< angularMomentum << std::endl;
206	std::cerr << "Inertia Tensor before is "
207	<< inertiaTensor << std::endl;
208	*/
209	inertiaTensor =inertiaTensor.inverse();
210	/*
211	std::cerr << "Inertia Tensor after inverse is "
212	<< inertiaTensor << std::endl;
213	*/
214	omega = inertiaTensor*angularMomentum;
215
216	SimInfo::MoleculeIterator i;
217	Molecule::IntegrableObjectIterator j;
218	Molecule * mol;
219	StuntDouble * integrableObject;
220	Vector3d tempComPos;
221
222	// Corrects for the center of mass angular drift.
223	// sums all the angular momentum and divides by total mass.
224	for( mol = info_->beginMolecule(i); mol != NULL;
225	mol = info_->nextMolecule(i) ) {
226	for( integrableObject = mol->beginIntegrableObject(j);
227	integrableObject != NULL;
228	integrableObject = mol->nextIntegrableObject(j) ) {
229	tempComPos = integrableObject->getPos()-com;
230	integrableObject->setVel((integrableObject->getVel() - vdrift)-cross(omega,tempComPos));
231	}
232	}
233
234	angularMomentum = info_->getAngularMomentum();
235	/*
236	std::cerr << "Angular Momentum after is "
237	<< angularMomentum << std::endl;
238	*/
239	}
240
241
242
243
244	}