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 {
                sprintf( painCave.errMsg,
                       "HydroPropFile keyword must be set if Lagevin Dynamics is used\n");
                painCave.severity = OOPSE_ERROR;
                painCave.isFatal = 1;
                simError();  
    }

    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 {
                sprintf( painCave.errMsg,
                       "Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
                painCave.severity = OOPSE_ERROR;
                painCave.isFatal = 1;
                simError();  
            }
            
           }
    }
    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:	909
Committed:	Tue Mar 21 00:26:55 2006 UTC (19 years, 7 months ago) by tim
File size:	11184 byte(s)
Log Message:	Fix a bug in friction calculation for ellipsoid
#	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	tim	909	sprintf( painCave.errMsg,
54			"HydroPropFile keyword must be set if Lagevin Dynamics is used\n");
55			painCave.severity = OOPSE_ERROR;
56			painCave.isFatal = 1;
57			simError();
58	tim	895	}
59
60			SimInfo::MoleculeIterator i;
61			Molecule::IntegrableObjectIterator j;
62			Molecule* mol;
63			StuntDouble* integrableObject;
64			for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) {
65			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
66			integrableObject = mol->nextIntegrableObject(j)) {
67			std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
68			if (iter != hydroPropMap.end()) {
69			hydroProps_.push_back(iter->second);
70			} else {
71	tim	909	sprintf( painCave.errMsg,
72			"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
73			painCave.severity = OOPSE_ERROR;
74			painCave.isFatal = 1;
75			simError();
76	tim	895	}
77
78			}
79			}
80	tim	904	variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
81	tim	895	}
82			std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
83			std::map<std::string, HydroProp> props;
84			std::ifstream ifs(filename.c_str());
85			if (ifs.is_open()) {
86
87			}
88
89			const unsigned int BufferSize = 65535;
90			char buffer[BufferSize];
91			while (ifs.getline(buffer, BufferSize)) {
92			StringTokenizer tokenizer(buffer);
93			HydroProp currProp;
94	tim	906	if (tokenizer.countTokens() >= 40) {
95	tim	895	std::string atomName = tokenizer.nextToken();
96	tim	906	currProp.cor[0] = tokenizer.nextTokenAsDouble();
97			currProp.cor[1] = tokenizer.nextTokenAsDouble();
98			currProp.cor[2] = tokenizer.nextTokenAsDouble();
99	tim	908
100	tim	906	currProp.Xirtt(0,0) = tokenizer.nextTokenAsDouble();
101			currProp.Xirtt(0,1) = tokenizer.nextTokenAsDouble();
102			currProp.Xirtt(0,2) = tokenizer.nextTokenAsDouble();
103			currProp.Xirtt(1,0) = tokenizer.nextTokenAsDouble();
104			currProp.Xirtt(1,1) = tokenizer.nextTokenAsDouble();
105			currProp.Xirtt(1,2) = tokenizer.nextTokenAsDouble();
106			currProp.Xirtt(2,0) = tokenizer.nextTokenAsDouble();
107			currProp.Xirtt(2,1) = tokenizer.nextTokenAsDouble();
108			currProp.Xirtt(2,2) = tokenizer.nextTokenAsDouble();
109	tim	895
110	tim	906	currProp.Xirrt(0,0) = tokenizer.nextTokenAsDouble();
111			currProp.Xirrt(0,1) = tokenizer.nextTokenAsDouble();
112			currProp.Xirrt(0,2) = tokenizer.nextTokenAsDouble();
113			currProp.Xirrt(1,0) = tokenizer.nextTokenAsDouble();
114			currProp.Xirrt(1,1) = tokenizer.nextTokenAsDouble();
115			currProp.Xirrt(1,2) = tokenizer.nextTokenAsDouble();
116			currProp.Xirrt(2,0) = tokenizer.nextTokenAsDouble();
117			currProp.Xirrt(2,1) = tokenizer.nextTokenAsDouble();
118			currProp.Xirrt(2,2) = tokenizer.nextTokenAsDouble();
119
120			currProp.Xirtr(0,0) = tokenizer.nextTokenAsDouble();
121			currProp.Xirtr(0,1) = tokenizer.nextTokenAsDouble();
122			currProp.Xirtr(0,2) = tokenizer.nextTokenAsDouble();
123			currProp.Xirtr(1,0) = tokenizer.nextTokenAsDouble();
124			currProp.Xirtr(1,1) = tokenizer.nextTokenAsDouble();
125			currProp.Xirtr(1,2) = tokenizer.nextTokenAsDouble();
126			currProp.Xirtr(2,0) = tokenizer.nextTokenAsDouble();
127			currProp.Xirtr(2,1) = tokenizer.nextTokenAsDouble();
128			currProp.Xirtr(2,2) = tokenizer.nextTokenAsDouble();
129
130			currProp.Xirrr(0,0) = tokenizer.nextTokenAsDouble();
131			currProp.Xirrr(0,1) = tokenizer.nextTokenAsDouble();
132			currProp.Xirrr(0,2) = tokenizer.nextTokenAsDouble();
133			currProp.Xirrr(1,0) = tokenizer.nextTokenAsDouble();
134			currProp.Xirrr(1,1) = tokenizer.nextTokenAsDouble();
135			currProp.Xirrr(1,2) = tokenizer.nextTokenAsDouble();
136			currProp.Xirrr(2,0) = tokenizer.nextTokenAsDouble();
137			currProp.Xirrr(2,1) = tokenizer.nextTokenAsDouble();
138			currProp.Xirrr(2,2) = tokenizer.nextTokenAsDouble();
139
140			SquareMatrix<double, 6> Xir;
141			Xir.setSubMatrix(0, 0, currProp.Xirtt);
142			Xir.setSubMatrix(0, 3, currProp.Xirrt);
143			Xir.setSubMatrix(3, 0, currProp.Xirtr);
144			Xir.setSubMatrix(3, 3, currProp.Xirrr);
145			CholeskyDecomposition(Xir, currProp.S);
146
147	tim	895	props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp));
148			}
149			}
150
151			return props;
152			}
153
154			void LDForceManager::postCalculation() {
155			SimInfo::MoleculeIterator i;
156			Molecule::IntegrableObjectIterator j;
157			Molecule* mol;
158			StuntDouble* integrableObject;
159			Vector3d vel;
160			Vector3d pos;
161			Vector3d frc;
162			Mat3x3d A;
163	tim	904	Mat3x3d Atrans;
164	tim	895	Vector3d Tb;
165			Vector3d ji;
166			double mass;
167			unsigned int index = 0;
168			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
169			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
170			integrableObject = mol->nextIntegrableObject(j)) {
171
172			vel =integrableObject->getVel();
173			if (integrableObject->isDirectional()){
174			//calculate angular velocity in lab frame
175			Mat3x3d I = integrableObject->getI();
176			Vector3d angMom = integrableObject->getJ();
177			Vector3d omega;
178
179			if (integrableObject->isLinear()) {
180			int linearAxis = integrableObject->linearAxis();
181			int l = (linearAxis +1 )%3;
182			int m = (linearAxis +2 )%3;
183			omega[l] = angMom[l] /I(l, l);
184			omega[m] = angMom[m] /I(m, m);
185
186			} else {
187			omega[0] = angMom[0] /I(0, 0);
188			omega[1] = angMom[1] /I(1, 1);
189			omega[2] = angMom[2] /I(2, 2);
190			}
191
192	tim	906	//apply friction force and torque at center of resistance
193	tim	895	A = integrableObject->getA();
194	tim	904	Atrans = A.transpose();
195	tim	906	Vector3d rcr = Atrans * hydroProps_[index].cor;
196			Vector3d vcdLab = vel + cross(omega, rcr);
197			Vector3d vcdBody = A* vcdLab;
198			Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega);
199			Vector3d frictionForceLab = Atrans*frictionForceBody;
200			integrableObject->addFrc(frictionForceLab);
201			Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega);
202			Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
203			integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
204
205			//apply random force and torque at center of resistance
206			Vector3d randomForceBody;
207			Vector3d randomTorqueBody;
208			genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
209			Vector3d randomForceLab = Atrans*randomForceBody;
210			Vector3d randomTorqueLab = Atrans* randomTorqueBody;
211			integrableObject->addFrc(randomForceLab);
212			integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));
213
214	tim	895	} else {
215			//spheric atom
216	tim	906	Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);
217	tim	895	Vector3d randomForce;
218			Vector3d randomTorque;
219			genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
220	tim	904
221	tim	895	integrableObject->addFrc(frictionForce+randomForce);
222			}
223
224			++index;
225
226			}
227			}
228
229			ForceManager::postCalculation();
230
231
232
233			}
234
235			void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) {
236	tim	904
237	tim	906
238	tim	904	Vector<double, 6> Z;
239			Vector<double, 6> generalForce;
240
241
242	tim	895	Z[0] = randNumGen_.randNorm(0, variance);
243			Z[1] = randNumGen_.randNorm(0, variance);
244			Z[2] = randNumGen_.randNorm(0, variance);
245			Z[3] = randNumGen_.randNorm(0, variance);
246			Z[4] = randNumGen_.randNorm(0, variance);
247			Z[5] = randNumGen_.randNorm(0, variance);
248	tim	904
249
250	tim	906	generalForce = hydroProps_[index].S*Z;
251	tim	904
252	tim	895	force[0] = generalForce[0];
253			force[1] = generalForce[1];
254			force[2] = generalForce[2];
255			torque[0] = generalForce[3];
256			torque[1] = generalForce[4];
257			torque[2] = generalForce[5];
258
259			}
260
261			}