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:	1313
Committed:	Wed Oct 22 20:01:49 2008 UTC (16 years, 6 months ago) by gezelter
Original Path:	*trunk/src/integrators/Velocitizer.cpp*
File size:	7534 byte(s)
Log Message:	General bug-fixes and other changes to make particle pots work with the Helfand Energy correlation function
#	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			* 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	gezelter	1313	/*
55	gezelter	1079	#include <cstdio>
56			#include <iostream>
57	gezelter	1313	*/
58	gezelter	1079	/End remove me/
59
60			namespace oopse {
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	gezelter	1313
109	gezelter	1079	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	gezelter	1313	*/
209	gezelter	1079	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	gezelter	1313	*/
239	gezelter	1079	}
240
241
242
243
244			}