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:	2646
Committed:	Tue Mar 21 00:26:55 2006 UTC (18 years, 4 months ago) by tim
File size:	11184 byte(s)
Log Message:	Fix a bug in friction calculation for ellipsoid
#	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	#include <fstream>
42	#include "integrators/LDForceManager.hpp"
43	#include "math/CholeskyDecomposition.hpp"
44	#include "utils/OOPSEConstant.hpp"
45	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	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	}
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	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	}
77
78	}
79	}
80	variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
81	}
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	if (tokenizer.countTokens() >= 40) {
95	std::string atomName = tokenizer.nextToken();
96	currProp.cor[0] = tokenizer.nextTokenAsDouble();
97	currProp.cor[1] = tokenizer.nextTokenAsDouble();
98	currProp.cor[2] = tokenizer.nextTokenAsDouble();
99
100	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
110	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	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	Mat3x3d Atrans;
164	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	//apply friction force and torque at center of resistance
193	A = integrableObject->getA();
194	Atrans = A.transpose();
195	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	} else {
215	//spheric atom
216	Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);
217	Vector3d randomForce;
218	Vector3d randomTorque;
219	genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
220
221	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
237
238	Vector<double, 6> Z;
239	Vector<double, 6> generalForce;
240
241
242	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
249
250	generalForce = hydroProps_[index].S*Z;
251
252	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	}