src/integrators/LDForceManager.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 <fstream> 
#include "integrators/LDForceManager.hpp"
#include "math/CholeskyDecomposition.hpp"
#include "utils/OOPSEConstant.hpp"
namespace oopse {

  LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
    Globals* simParams = info->getSimParams();
    std::map<std::string, HydroProp> hydroPropMap;
    if (simParams->haveHydroPropFile()) {
        hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
    } else {
        //error
    }

    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* integrableObject;
    for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) {
      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
              integrableObject = mol->nextIntegrableObject(j)) {
            std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
            if (iter != hydroPropMap.end()) {
                hydroProps_.push_back(iter->second);
            } else {
                //error
            }
            
           }
    }
    variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
  }
  std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
    std::map<std::string, HydroProp> props;
    std::ifstream ifs(filename.c_str());
    if (ifs.is_open()) {

    }

    const unsigned int BufferSize = 65535;
    char buffer[BufferSize];   
    while (ifs.getline(buffer, BufferSize)) {
        StringTokenizer tokenizer(buffer);
        HydroProp currProp;
        if (tokenizer.countTokens() >= 40) {
            std::string atomName = tokenizer.nextToken();
            currProp.cor[0] = tokenizer.nextTokenAsDouble();
            currProp.cor[1] = tokenizer.nextTokenAsDouble();
            currProp.cor[2] = tokenizer.nextTokenAsDouble();
            
            currProp.Xirtt(0,0) = tokenizer.nextTokenAsDouble();
            currProp.Xirtt(0,1) = tokenizer.nextTokenAsDouble();
            currProp.Xirtt(0,2) = tokenizer.nextTokenAsDouble();
            currProp.Xirtt(1,0) = tokenizer.nextTokenAsDouble();
            currProp.Xirtt(1,1) = tokenizer.nextTokenAsDouble();
            currProp.Xirtt(1,2) = tokenizer.nextTokenAsDouble();
            currProp.Xirtt(2,0) = tokenizer.nextTokenAsDouble();
            currProp.Xirtt(2,1) = tokenizer.nextTokenAsDouble();
            currProp.Xirtt(2,2) = tokenizer.nextTokenAsDouble();

            currProp.Xirrt(0,0) = tokenizer.nextTokenAsDouble();
            currProp.Xirrt(0,1) = tokenizer.nextTokenAsDouble();
            currProp.Xirrt(0,2) = tokenizer.nextTokenAsDouble();
            currProp.Xirrt(1,0) = tokenizer.nextTokenAsDouble();
            currProp.Xirrt(1,1) = tokenizer.nextTokenAsDouble();
            currProp.Xirrt(1,2) = tokenizer.nextTokenAsDouble();
            currProp.Xirrt(2,0) = tokenizer.nextTokenAsDouble();
            currProp.Xirrt(2,1) = tokenizer.nextTokenAsDouble();
            currProp.Xirrt(2,2) = tokenizer.nextTokenAsDouble();
         
            currProp.Xirtr(0,0) = tokenizer.nextTokenAsDouble();
            currProp.Xirtr(0,1) = tokenizer.nextTokenAsDouble();
            currProp.Xirtr(0,2) = tokenizer.nextTokenAsDouble();
            currProp.Xirtr(1,0) = tokenizer.nextTokenAsDouble();
            currProp.Xirtr(1,1) = tokenizer.nextTokenAsDouble();
            currProp.Xirtr(1,2) = tokenizer.nextTokenAsDouble();
            currProp.Xirtr(2,0) = tokenizer.nextTokenAsDouble();
            currProp.Xirtr(2,1) = tokenizer.nextTokenAsDouble();
            currProp.Xirtr(2,2) = tokenizer.nextTokenAsDouble();

            currProp.Xirrr(0,0) = tokenizer.nextTokenAsDouble();
            currProp.Xirrr(0,1) = tokenizer.nextTokenAsDouble();
            currProp.Xirrr(0,2) = tokenizer.nextTokenAsDouble();
            currProp.Xirrr(1,0) = tokenizer.nextTokenAsDouble();
            currProp.Xirrr(1,1) = tokenizer.nextTokenAsDouble();
            currProp.Xirrr(1,2) = tokenizer.nextTokenAsDouble();
            currProp.Xirrr(2,0) = tokenizer.nextTokenAsDouble();
            currProp.Xirrr(2,1) = tokenizer.nextTokenAsDouble();
            currProp.Xirrr(2,2) = tokenizer.nextTokenAsDouble(); 

            SquareMatrix<double, 6> Xir;
            Xir.setSubMatrix(0, 0, currProp.Xirtt);
            Xir.setSubMatrix(0, 3, currProp.Xirrt);
            Xir.setSubMatrix(3, 0, currProp.Xirtr);
            Xir.setSubMatrix(3, 3, currProp.Xirrr);
            CholeskyDecomposition(Xir, currProp.S);            

            props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp));
        }
    }

    return props;
  }
  
  void LDForceManager::postCalculation() {
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* integrableObject;
    Vector3d vel;
    Vector3d pos;
    Vector3d frc;
    Mat3x3d A;
    Mat3x3d Atrans;
    Vector3d Tb;
    Vector3d ji;
    double mass;
    unsigned int index = 0;
    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
           integrableObject = mol->nextIntegrableObject(j)) {

          vel =integrableObject->getVel(); 
          if (integrableObject->isDirectional()){
             //calculate angular velocity in lab frame
             Mat3x3d I = integrableObject->getI();
             Vector3d angMom = integrableObject->getJ();
             Vector3d omega;

             if (integrableObject->isLinear()) {
                int linearAxis = integrableObject->linearAxis();
                int l = (linearAxis +1 )%3;
                int m = (linearAxis +2 )%3;
                omega[l] = angMom[l] /I(l, l);
                omega[m] = angMom[m] /I(m, m);
                
             } else {
                 omega[0] = angMom[0] /I(0, 0);
                 omega[1] = angMom[1] /I(1, 1);
                 omega[2] = angMom[2] /I(2, 2);
             }

             //apply friction force and torque at center of resistance
             A = integrableObject->getA();
             Atrans = A.transpose();
             Vector3d rcr = Atrans * hydroProps_[index].cor;  
             Vector3d vcdLab = vel + cross(omega, rcr);
             Vector3d vcdBody = A* vcdLab;
             Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega);
             Vector3d frictionForceLab = Atrans*frictionForceBody;
             integrableObject->addFrc(frictionForceLab);
             Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega);
             Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
             integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));

             //apply random force and torque at center of resistance
             Vector3d randomForceBody;
             Vector3d randomTorqueBody;
             genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
             Vector3d randomForceLab = Atrans*randomForceBody;
             Vector3d randomTorqueLab = Atrans* randomTorqueBody;
             integrableObject->addFrc(randomForceLab);            
             integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));             

          } else {
             //spheric atom
             Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);     
             Vector3d randomForce;
             Vector3d randomTorque;
             genRandomForceAndTorque(randomForce, randomTorque, index, variance_);

             integrableObject->addFrc(frictionForce+randomForce);             
          }

        ++index;
    
      }
    }    

    ForceManager::postCalculation();


  }

void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) {


    Vector<double, 6> Z;
    Vector<double, 6> generalForce;

        
    Z[0] = randNumGen_.randNorm(0, variance);
    Z[1] = randNumGen_.randNorm(0, variance);
    Z[2] = randNumGen_.randNorm(0, variance);
    Z[3] = randNumGen_.randNorm(0, variance);
    Z[4] = randNumGen_.randNorm(0, variance);
    Z[5] = randNumGen_.randNorm(0, variance);
     

    generalForce = hydroProps_[index].S*Z;
    
    force[0] = generalForce[0];
    force[1] = generalForce[1];
    force[2] = generalForce[2];
    torque[0] = generalForce[3];
    torque[1] = generalForce[4];
    torque[2] = generalForce[5];
    
}

}
Revision:	908
Committed:	Mon Mar 20 19:12:14 2006 UTC (19 years, 7 months ago) by tim
File size:	10704 byte(s)
Log Message:	Verify the correctness of Ellipsoid's hydrodynamics properties
#	User	Rev	Content
1	tim	895	/*
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			#include <fstream>
42			#include "integrators/LDForceManager.hpp"
43			#include "math/CholeskyDecomposition.hpp"
44	tim	904	#include "utils/OOPSEConstant.hpp"
45	tim	895	namespace oopse {
46
47			LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
48			Globals* simParams = info->getSimParams();
49			std::map<std::string, HydroProp> hydroPropMap;
50			if (simParams->haveHydroPropFile()) {
51			hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
52			} else {
53			//error
54			}
55
56			SimInfo::MoleculeIterator i;
57			Molecule::IntegrableObjectIterator j;
58			Molecule* mol;
59			StuntDouble* integrableObject;
60			for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) {
61			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
62			integrableObject = mol->nextIntegrableObject(j)) {
63			std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
64			if (iter != hydroPropMap.end()) {
65			hydroProps_.push_back(iter->second);
66			} else {
67			//error
68			}
69
70			}
71			}
72	tim	904	variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
73	tim	895	}
74			std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
75			std::map<std::string, HydroProp> props;
76			std::ifstream ifs(filename.c_str());
77			if (ifs.is_open()) {
78
79			}
80
81			const unsigned int BufferSize = 65535;
82			char buffer[BufferSize];
83			while (ifs.getline(buffer, BufferSize)) {
84			StringTokenizer tokenizer(buffer);
85			HydroProp currProp;
86	tim	906	if (tokenizer.countTokens() >= 40) {
87	tim	895	std::string atomName = tokenizer.nextToken();
88	tim	906	currProp.cor[0] = tokenizer.nextTokenAsDouble();
89			currProp.cor[1] = tokenizer.nextTokenAsDouble();
90			currProp.cor[2] = tokenizer.nextTokenAsDouble();
91	tim	908
92	tim	906	currProp.Xirtt(0,0) = tokenizer.nextTokenAsDouble();
93			currProp.Xirtt(0,1) = tokenizer.nextTokenAsDouble();
94			currProp.Xirtt(0,2) = tokenizer.nextTokenAsDouble();
95			currProp.Xirtt(1,0) = tokenizer.nextTokenAsDouble();
96			currProp.Xirtt(1,1) = tokenizer.nextTokenAsDouble();
97			currProp.Xirtt(1,2) = tokenizer.nextTokenAsDouble();
98			currProp.Xirtt(2,0) = tokenizer.nextTokenAsDouble();
99			currProp.Xirtt(2,1) = tokenizer.nextTokenAsDouble();
100			currProp.Xirtt(2,2) = tokenizer.nextTokenAsDouble();
101	tim	895
102	tim	906	currProp.Xirrt(0,0) = tokenizer.nextTokenAsDouble();
103			currProp.Xirrt(0,1) = tokenizer.nextTokenAsDouble();
104			currProp.Xirrt(0,2) = tokenizer.nextTokenAsDouble();
105			currProp.Xirrt(1,0) = tokenizer.nextTokenAsDouble();
106			currProp.Xirrt(1,1) = tokenizer.nextTokenAsDouble();
107			currProp.Xirrt(1,2) = tokenizer.nextTokenAsDouble();
108			currProp.Xirrt(2,0) = tokenizer.nextTokenAsDouble();
109			currProp.Xirrt(2,1) = tokenizer.nextTokenAsDouble();
110			currProp.Xirrt(2,2) = tokenizer.nextTokenAsDouble();
111
112			currProp.Xirtr(0,0) = tokenizer.nextTokenAsDouble();
113			currProp.Xirtr(0,1) = tokenizer.nextTokenAsDouble();
114			currProp.Xirtr(0,2) = tokenizer.nextTokenAsDouble();
115			currProp.Xirtr(1,0) = tokenizer.nextTokenAsDouble();
116			currProp.Xirtr(1,1) = tokenizer.nextTokenAsDouble();
117			currProp.Xirtr(1,2) = tokenizer.nextTokenAsDouble();
118			currProp.Xirtr(2,0) = tokenizer.nextTokenAsDouble();
119			currProp.Xirtr(2,1) = tokenizer.nextTokenAsDouble();
120			currProp.Xirtr(2,2) = tokenizer.nextTokenAsDouble();
121
122			currProp.Xirrr(0,0) = tokenizer.nextTokenAsDouble();
123			currProp.Xirrr(0,1) = tokenizer.nextTokenAsDouble();
124			currProp.Xirrr(0,2) = tokenizer.nextTokenAsDouble();
125			currProp.Xirrr(1,0) = tokenizer.nextTokenAsDouble();
126			currProp.Xirrr(1,1) = tokenizer.nextTokenAsDouble();
127			currProp.Xirrr(1,2) = tokenizer.nextTokenAsDouble();
128			currProp.Xirrr(2,0) = tokenizer.nextTokenAsDouble();
129			currProp.Xirrr(2,1) = tokenizer.nextTokenAsDouble();
130			currProp.Xirrr(2,2) = tokenizer.nextTokenAsDouble();
131
132			SquareMatrix<double, 6> Xir;
133			Xir.setSubMatrix(0, 0, currProp.Xirtt);
134			Xir.setSubMatrix(0, 3, currProp.Xirrt);
135			Xir.setSubMatrix(3, 0, currProp.Xirtr);
136			Xir.setSubMatrix(3, 3, currProp.Xirrr);
137			CholeskyDecomposition(Xir, currProp.S);
138
139	tim	895	props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp));
140			}
141			}
142
143			return props;
144			}
145
146			void LDForceManager::postCalculation() {
147			SimInfo::MoleculeIterator i;
148			Molecule::IntegrableObjectIterator j;
149			Molecule* mol;
150			StuntDouble* integrableObject;
151			Vector3d vel;
152			Vector3d pos;
153			Vector3d frc;
154			Mat3x3d A;
155	tim	904	Mat3x3d Atrans;
156	tim	895	Vector3d Tb;
157			Vector3d ji;
158			double mass;
159			unsigned int index = 0;
160			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
161			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
162			integrableObject = mol->nextIntegrableObject(j)) {
163
164			vel =integrableObject->getVel();
165			if (integrableObject->isDirectional()){
166			//calculate angular velocity in lab frame
167			Mat3x3d I = integrableObject->getI();
168			Vector3d angMom = integrableObject->getJ();
169			Vector3d omega;
170
171			if (integrableObject->isLinear()) {
172			int linearAxis = integrableObject->linearAxis();
173			int l = (linearAxis +1 )%3;
174			int m = (linearAxis +2 )%3;
175			omega[l] = angMom[l] /I(l, l);
176			omega[m] = angMom[m] /I(m, m);
177
178			} else {
179			omega[0] = angMom[0] /I(0, 0);
180			omega[1] = angMom[1] /I(1, 1);
181			omega[2] = angMom[2] /I(2, 2);
182			}
183
184	tim	906	//apply friction force and torque at center of resistance
185	tim	895	A = integrableObject->getA();
186	tim	904	Atrans = A.transpose();
187	tim	906	Vector3d rcr = Atrans * hydroProps_[index].cor;
188			Vector3d vcdLab = vel + cross(omega, rcr);
189			Vector3d vcdBody = A* vcdLab;
190			Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega);
191			Vector3d frictionForceLab = Atrans*frictionForceBody;
192			integrableObject->addFrc(frictionForceLab);
193			Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega);
194			Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
195			integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
196
197			//apply random force and torque at center of resistance
198			Vector3d randomForceBody;
199			Vector3d randomTorqueBody;
200			genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
201			Vector3d randomForceLab = Atrans*randomForceBody;
202			Vector3d randomTorqueLab = Atrans* randomTorqueBody;
203			integrableObject->addFrc(randomForceLab);
204			integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));
205
206	tim	895	} else {
207			//spheric atom
208	tim	906	Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);
209	tim	895	Vector3d randomForce;
210			Vector3d randomTorque;
211			genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
212	tim	904
213	tim	895	integrableObject->addFrc(frictionForce+randomForce);
214			}
215
216			++index;
217
218			}
219			}
220
221			ForceManager::postCalculation();
222
223
224
225			}
226
227			void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) {
228	tim	904
229	tim	906
230	tim	904	Vector<double, 6> Z;
231			Vector<double, 6> generalForce;
232
233
234	tim	895	Z[0] = randNumGen_.randNorm(0, variance);
235			Z[1] = randNumGen_.randNorm(0, variance);
236			Z[2] = randNumGen_.randNorm(0, variance);
237			Z[3] = randNumGen_.randNorm(0, variance);
238			Z[4] = randNumGen_.randNorm(0, variance);
239			Z[5] = randNumGen_.randNorm(0, variance);
240	tim	904
241
242	tim	906	generalForce = hydroProps_[index].S*Z;
243	tim	904
244	tim	895	force[0] = generalForce[0];
245			force[1] = generalForce[1];
246			force[2] = generalForce[2];
247			torque[0] = generalForce[3];
248			torque[1] = generalForce[4];
249			torque[2] = generalForce[5];
250
251			}
252
253			}