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(double temperature) {
    Vector3d aVel;
    Vector3d aJ;
    Mat3x3d I;
    int l;
    int m;
    int n; 
    Vector3d vdrift;
    double vbar;
    /**@todo refactory kb */
    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
    double av2;
    double 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->getPBC()) 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;

      
      inertiaTensor.inverse();
      
      
      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:	555
Committed:	Mon May 30 14:01:52 2005 UTC (20 years, 5 months ago) by chuckv
File size:	7605 byte(s)
Log Message:	Added method to remove system angular momentum to velocitizer and added method to calculate system angular momentum to siminfo.
#	User	Rev	Content
1	gezelter	507	/*
2	tim	381	* 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	gezelter	507
42	tim	381	#include "integrators/Velocitizer.hpp"
43			#include "math/SquareMatrix3.hpp"
44			#include "primitives/Molecule.hpp"
45			#include "primitives/StuntDouble.hpp"
46	tim	384
47	tim	392	#ifndef IS_MPI
48			#include "math/SeqRandNumGen.hpp"
49			#else
50			#include "math/ParallelRandNumGen.hpp"
51			#endif
52
53	chuckv	555	/* Remove me after testing*/
54			#include <cstdio>
55			#include <iostream>
56			/End remove me/
57
58	tim	381	namespace oopse {
59	gezelter	507
60			Velocitizer::Velocitizer(SimInfo* info) : info_(info) {
61
62	tim	384	int seedValue;
63			Globals * simParams = info->getSimParams();
64	gezelter	507
65	tim	388	#ifndef IS_MPI
66	tim	384	if (simParams->haveSeed()) {
67	gezelter	507	seedValue = simParams->getSeed();
68			randNumGen_ = new SeqRandNumGen(seedValue);
69	tim	384	}else {
70	gezelter	507	randNumGen_ = new SeqRandNumGen();
71	tim	384	}
72	tim	388	#else
73			if (simParams->haveSeed()) {
74	gezelter	507	seedValue = simParams->getSeed();
75			randNumGen_ = new ParallelRandNumGen(seedValue);
76	tim	388	}else {
77	gezelter	507	randNumGen_ = new ParallelRandNumGen();
78	tim	388	}
79			#endif
80	gezelter	507	}
81
82			Velocitizer::~Velocitizer() {
83	tim	384	delete randNumGen_;
84	gezelter	507	}
85
86			void Velocitizer::velocitize(double temperature) {
87	tim	381	Vector3d aVel;
88			Vector3d aJ;
89			Mat3x3d I;
90			int l;
91			int m;
92			int n;
93			Vector3d vdrift;
94			double vbar;
95			/*@todo refactory kb /
96			const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
97			double av2;
98			double kebar;
99	gezelter	507
100	chuckv	555	Globals * simParams = info_->getSimParams();
101
102	tim	381	SimInfo::MoleculeIterator i;
103			Molecule::IntegrableObjectIterator j;
104			Molecule * mol;
105			StuntDouble * integrableObject;
106	gezelter	507
107
108
109	tim	381	kebar = kb * temperature * info_->getNdfRaw() / (2.0 * info_->getNdf());
110	gezelter	507
111	tim	381	for( mol = info_->beginMolecule(i); mol != NULL;
112	gezelter	507	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
129			integrableObject->setVel(aVel);
130
131			if (integrableObject->isDirectional()) {
132			I = integrableObject->getI();
133
134			if (integrableObject->isLinear()) {
135			l = integrableObject->linearAxis();
136			m = (l + 1) % 3;
137			n = (l + 2) % 3;
138
139			aJ[l] = 0.0;
140			vbar = sqrt(2.0 * kebar * I(m, m));
141			aJ[m] = vbar * randNumGen_->randNorm(0.0, 1.0);
142			vbar = sqrt(2.0 * kebar * I(n, n));
143			aJ[n] = vbar * randNumGen_->randNorm(0.0, 1.0);
144			} else {
145			for( int k = 0; k < 3; k++ ) {
146			vbar = sqrt(2.0 * kebar * I(k, k));
147			aJ[k] = vbar *randNumGen_->randNorm(0.0, 1.0);
148			}
149			} // else isLinear
150
151			integrableObject->setJ(aJ);
152			} //isDirectional
153			}
154	tim	381	} //end for (mol = beginMolecule(i); ...)
155	gezelter	507
156
157
158	tim	381	removeComDrift();
159	chuckv	555	// Remove angular drift if we are not using periodic boundary conditions.
160			if(simParams->getPBC()) removeAngularDrift();
161	gezelter	507
162			}
163
164
165
166			void Velocitizer::removeComDrift() {
167	tim	381	// Get the Center of Mass drift velocity.
168			Vector3d vdrift = info_->getComVel();
169
170			SimInfo::MoleculeIterator i;
171			Molecule::IntegrableObjectIterator j;
172			Molecule * mol;
173			StuntDouble * integrableObject;
174
175			// Corrects for the center of mass drift.
176			// sums all the momentum and divides by total mass.
177			for( mol = info_->beginMolecule(i); mol != NULL;
178	gezelter	507	mol = info_->nextMolecule(i) ) {
179			for( integrableObject = mol->beginIntegrableObject(j);
180			integrableObject != NULL;
181			integrableObject = mol->nextIntegrableObject(j) ) {
182			integrableObject->setVel(integrableObject->getVel() - vdrift);
183			}
184	tim	381	}
185	gezelter	507
186			}
187
188	chuckv	555
189			void Velocitizer::removeAngularDrift() {
190			// Get the Center of Mass drift velocity.
191
192			Vector3d vdrift;
193			Vector3d com;
194
195			info_->getComAll(com,vdrift);
196
197			Mat3x3d inertiaTensor;
198			Vector3d angularMomentum;
199			Vector3d omega;
200
201
202
203			info_->getInertiaTensor(inertiaTensor,angularMomentum);
204			// We now need the inverse of the inertia tensor.
205
206			std::cerr << "Angular Momentum before is "
207			<< angularMomentum << std::endl;
208
209
210			inertiaTensor.inverse();
211
212
213			omega = inertiaTensor*angularMomentum;
214
215			SimInfo::MoleculeIterator i;
216			Molecule::IntegrableObjectIterator j;
217			Molecule * mol;
218			StuntDouble * integrableObject;
219			Vector3d tempComPos;
220
221			// Corrects for the center of mass angular drift.
222			// sums all the angular momentum and divides by total mass.
223			for( mol = info_->beginMolecule(i); mol != NULL;
224			mol = info_->nextMolecule(i) ) {
225			for( integrableObject = mol->beginIntegrableObject(j);
226			integrableObject != NULL;
227			integrableObject = mol->nextIntegrableObject(j) ) {
228			tempComPos = integrableObject->getPos()-com;
229			integrableObject->setVel((integrableObject->getVel() - vdrift)-cross(omega,tempComPos));
230			}
231			}
232
233			angularMomentum = info_->getAngularMomentum();
234			std::cerr << "Angular Momentum after is "
235			<< angularMomentum << std::endl;
236
237
238			}
239
240
241
242
243	tim	381	}