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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */

#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 oopse {
  
  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:	3055
Committed:	Thu Oct 19 15:57:07 2006 UTC (17 years, 8 months ago) by gezelter
File size:	7544 byte(s)
Log Message:	Added velocitizer utility program, added samples of its use to the builder samples.
#	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. Acknowledgement of the program authors must be made in any
10	* publication of scientific results based in part on use of the
11	* program. An acceptable form of acknowledgement is citation of
12	* the article in which the program was described (Matthew
13	* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	* Parallel Simulation Engine for Molecular Dynamics,"
16	* J. Comput. Chem. 26, pp. 252-271 (2005))
17	*
18	* 2. Redistributions of source code must retain the above copyright
19	* notice, this list of conditions and the following disclaimer.
20	*
21	* 3. Redistributions in binary form must reproduce the above copyright
22	* notice, this list of conditions and the following disclaimer in the
23	* documentation and/or other materials provided with the
24	* distribution.
25	*
26	* This software is provided "AS IS," without a warranty of any
27	* kind. All express or implied conditions, representations and
28	* warranties, including any implied warranty of merchantability,
29	* fitness for a particular purpose or non-infringement, are hereby
30	* excluded. The University of Notre Dame and its licensors shall not
31	* be liable for any damages suffered by licensee as a result of
32	* using, modifying or distributing the software or its
33	* derivatives. In no event will the University of Notre Dame or its
34	* licensors be liable for any lost revenue, profit or data, or for
35	* direct, indirect, special, consequential, incidental or punitive
36	* damages, however caused and regardless of the theory of liability,
37	* arising out of the use of or inability to use software, even if the
38	* University of Notre Dame has been advised of the possibility of
39	* such damages.
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	#include <cstdio>
55	#include <iostream>
56	/End remove me/
57
58	namespace oopse {
59
60	Velocitizer::Velocitizer(SimInfo* info) : info_(info) {
61
62	int seedValue;
63	Globals * simParams = info->getSimParams();
64
65	#ifndef IS_MPI
66	if (simParams->haveSeed()) {
67	seedValue = simParams->getSeed();
68	randNumGen_ = new SeqRandNumGen(seedValue);
69	}else {
70	randNumGen_ = new SeqRandNumGen();
71	}
72	#else
73	if (simParams->haveSeed()) {
74	seedValue = simParams->getSeed();
75	randNumGen_ = new ParallelRandNumGen(seedValue);
76	}else {
77	randNumGen_ = new ParallelRandNumGen();
78	}
79	#endif
80	}
81
82	Velocitizer::~Velocitizer() {
83	delete randNumGen_;
84	}
85
86	void Velocitizer::velocitize(RealType temperature) {
87	Vector3d aVel;
88	Vector3d aJ;
89	Mat3x3d I;
90	int l;
91	int m;
92	int n;
93	Vector3d vdrift;
94	RealType vbar;
95	/*@todo refactory kb /
96	const RealType kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
97	RealType av2;
98	RealType kebar;
99
100	Globals * simParams = info_->getSimParams();
101
102	SimInfo::MoleculeIterator i;
103	Molecule::IntegrableObjectIterator j;
104	Molecule * mol;
105	StuntDouble * integrableObject;
106
107	kebar = kb * temperature * info_->getNdfRaw() / (2.0 * info_->getNdf());
108	for( mol = info_->beginMolecule(i); mol != NULL;
109	mol = info_->nextMolecule(i) ) {
110	for( integrableObject = mol->beginIntegrableObject(j);
111	integrableObject != NULL;
112	integrableObject = mol->nextIntegrableObject(j) ) {
113
114	// uses equipartition theory to solve for vbar in angstrom/fs
115
116	av2 = 2.0 * kebar / integrableObject->getMass();
117	vbar = sqrt(av2);
118
119	// picks random velocities from a gaussian distribution
120	// centered on vbar
121
122	for( int k = 0; k < 3; k++ ) {
123	aVel[k] = vbar * randNumGen_->randNorm(0.0, 1.0);
124	}
125	integrableObject->setVel(aVel);
126
127	if (integrableObject->isDirectional()) {
128	I = integrableObject->getI();
129
130	if (integrableObject->isLinear()) {
131	l = integrableObject->linearAxis();
132	m = (l + 1) % 3;
133	n = (l + 2) % 3;
134
135	aJ[l] = 0.0;
136	vbar = sqrt(2.0 * kebar * I(m, m));
137	aJ[m] = vbar * randNumGen_->randNorm(0.0, 1.0);
138	vbar = sqrt(2.0 * kebar * I(n, n));
139	aJ[n] = vbar * randNumGen_->randNorm(0.0, 1.0);
140	} else {
141	for( int k = 0; k < 3; k++ ) {
142	vbar = sqrt(2.0 * kebar * I(k, k));
143	aJ[k] = vbar *randNumGen_->randNorm(0.0, 1.0);
144	}
145	} // else isLinear
146
147	integrableObject->setJ(aJ);
148	} //isDirectional
149	}
150	} //end for (mol = beginMolecule(i); ...)
151
152
153
154	removeComDrift();
155	// Remove angular drift if we are not using periodic boundary conditions.
156	if(!simParams->getUsePeriodicBoundaryConditions()) removeAngularDrift();
157
158	}
159
160
161
162	void Velocitizer::removeComDrift() {
163	// Get the Center of Mass drift velocity.
164	Vector3d vdrift = info_->getComVel();
165
166	SimInfo::MoleculeIterator i;
167	Molecule::IntegrableObjectIterator j;
168	Molecule * mol;
169	StuntDouble * integrableObject;
170
171	// Corrects for the center of mass drift.
172	// sums all the momentum and divides by total mass.
173	for( mol = info_->beginMolecule(i); mol != NULL;
174	mol = info_->nextMolecule(i) ) {
175	for( integrableObject = mol->beginIntegrableObject(j);
176	integrableObject != NULL;
177	integrableObject = mol->nextIntegrableObject(j) ) {
178	integrableObject->setVel(integrableObject->getVel() - vdrift);
179	}
180	}
181
182	}
183
184
185	void Velocitizer::removeAngularDrift() {
186	// Get the Center of Mass drift velocity.
187
188	Vector3d vdrift;
189	Vector3d com;
190
191	info_->getComAll(com,vdrift);
192
193	Mat3x3d inertiaTensor;
194	Vector3d angularMomentum;
195	Vector3d omega;
196
197
198
199	info_->getInertiaTensor(inertiaTensor,angularMomentum);
200	// We now need the inverse of the inertia tensor.
201	/*
202	std::cerr << "Angular Momentum before is "
203	<< angularMomentum << std::endl;
204	std::cerr << "Inertia Tensor before is "
205	<< inertiaTensor << std::endl;
206	*/
207	inertiaTensor =inertiaTensor.inverse();
208	/*
209	std::cerr << "Inertia Tensor after inverse is "
210	<< inertiaTensor << std::endl;
211	*/
212	omega = inertiaTensor*angularMomentum;
213
214	SimInfo::MoleculeIterator i;
215	Molecule::IntegrableObjectIterator j;
216	Molecule * mol;
217	StuntDouble * integrableObject;
218	Vector3d tempComPos;
219
220	// Corrects for the center of mass angular drift.
221	// sums all the angular momentum and divides by total mass.
222	for( mol = info_->beginMolecule(i); mol != NULL;
223	mol = info_->nextMolecule(i) ) {
224	for( integrableObject = mol->beginIntegrableObject(j);
225	integrableObject != NULL;
226	integrableObject = mol->nextIntegrableObject(j) ) {
227	tempComPos = integrableObject->getPos()-com;
228	integrableObject->setVel((integrableObject->getVel() - vdrift)-cross(omega,tempComPos));
229	}
230	}
231
232	angularMomentum = info_->getAngularMomentum();
233	/*
234	std::cerr << "Angular Momentum after is "
235	<< angularMomentum << std::endl;
236	*/
237
238	}
239
240
241
242
243	}