src/utils/MoLocator.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 <iostream>

#include <cstdlib>
#include <cmath>

#include "utils/simError.h"
#include "utils/MoLocator.hpp"
#include "types/AtomType.hpp"

namespace oopse {
  MoLocator::MoLocator( MoleculeStamp* theStamp, ForceField* theFF){
    
    myStamp = theStamp;
    myFF = theFF;
    nIntegrableObjects = myStamp->getNIntegrable();
    calcRef();
  }
  
  void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol){
    Vector3d newCoor;
    Vector3d curRefCoor;  
    RotMat3x3d rotMat = latVec2RotMat(ort);
    
    if(mol->getNIntegrableObjects() != nIntegrableObjects){
      sprintf( painCave.errMsg,
               "MoLocator error.\n"
               "  The number of integrable objects of MoleculeStamp is not the same as  that of Molecule\n");
      painCave.isFatal = 1;
      simError();
    }
    
    Molecule::IntegrableObjectIterator ii;
    StuntDouble* integrableObject;
    int i;
    for (integrableObject = mol->beginIntegrableObject(ii), i = 0; integrableObject != NULL; 
         integrableObject = mol->nextIntegrableObject(ii), ++i) { 
      
      newCoor = rotMat * refCoords[i];
      newCoor += offset;
      
      integrableObject->setPos( newCoor);
      integrableObject->setVel(V3Zero);
      
      if(integrableObject->isDirectional()){
        integrableObject->setA(rotMat * integrableObject->getA());
        integrableObject->setJ(V3Zero);  
      }        
    }
  }
  
  void MoLocator::calcRef( void ){
    AtomStamp* currAtomStamp;
    RigidBodyStamp* rbStamp;
    int nAtoms; 
    int nRigidBodies;
    std::vector<double> mass;
    Vector3d coor;
    Vector3d refMolCom;  
    int nAtomsInRb;
    double totMassInRb;
    double currAtomMass;
    double molMass;
    
    nAtoms= myStamp->getNAtoms();
    nRigidBodies = myStamp->getNRigidBodies();
    
    for(size_t i=0; i<nAtoms; i++){
      
      currAtomStamp = myStamp->getAtom(i);
      
      if( !currAtomStamp->havePosition() ){
        sprintf( painCave.errMsg,
                 "MoLocator error.\n"
                 "  Component %s, atom %s does not have a position specified.\n"
                 "  This means MoLocator cannot initalize it's position.\n",
                 myStamp->getID(),
                 currAtomStamp->getType() );
        
        painCave.isFatal = 1;
        simError();
      }
      
      //if atom belongs to rigidbody, just skip it
      if(myStamp->isAtomInRigidBody(i))
        continue;
      //get mass and the reference coordinate 
      else{
        currAtomMass = getAtomMass(currAtomStamp->getType(), myFF);   
        mass.push_back(currAtomMass);
        coor.x() = currAtomStamp->getPosX();
        coor.y() = currAtomStamp->getPosY();
        coor.z() = currAtomStamp->getPosZ();
        refCoords.push_back(coor);
        
      }
    }
    
    for(int i = 0; i < nRigidBodies; i++){
      
      rbStamp = myStamp->getRigidBody(i);
      nAtomsInRb = rbStamp->getNMembers();
      
      coor.x() = 0.0;
      coor.y() = 0.0;
      coor.z() = 0.0;
      totMassInRb = 0.0;
      
      for(int j = 0; j < nAtomsInRb; j++){
        
        currAtomStamp = myStamp->getAtom(rbStamp->getMember(j));
        currAtomMass = getAtomMass(currAtomStamp->getType(), myFF);
        totMassInRb +=  currAtomMass;
        
        coor.x() += currAtomStamp->getPosX() * currAtomMass;
        coor.y() += currAtomStamp->getPosY() * currAtomMass;
        coor.z() += currAtomStamp->getPosZ() * currAtomMass;
      }
      
      mass.push_back(totMassInRb);
      coor /= totMassInRb;
      refCoords.push_back(coor);
    }
    
    
    //calculate the reference center of mass
    molMass = 0;
    refMolCom.x() = 0;
    refMolCom.y() = 0;
    refMolCom.z() = 0;
    
    for(int i = 0; i < nIntegrableObjects; i++){
      refMolCom += refCoords[i] * mass[i];
      molMass += mass[i];
    }
    
    refMolCom /= molMass;
    
    //move the reference center of mass to (0,0,0) and adjust the reference coordinate 
    //of the integrabel objects
  for(int i = 0; i < nIntegrableObjects; i++)
    refCoords[i] -= refMolCom;
  }
  
  double getAtomMass(const std::string& at, ForceField* myFF) {
    double mass;
    AtomType* atomType= myFF->getAtomType(at);
    if (atomType != NULL) {
      mass =     atomType->getMass();
    } else {
      mass = 0.0;
      std::cerr << "Can not find AtomType: " << at << std::endl;
    }
    return mass;
  }
  
  double getMolMass(MoleculeStamp *molStamp, ForceField *myFF) {
    int nAtoms;
    double totMass = 0;
    nAtoms = molStamp->getNAtoms();
    
    for(size_t i = 0; i < nAtoms; i++) {
      AtomStamp *currAtomStamp = molStamp->getAtom(i);
      totMass += getAtomMass(currAtomStamp->getType(), myFF);         
    }
    return totMass;
  }
  RotMat3x3d latVec2RotMat(const Vector3d& lv){
    
    double theta =acos(lv[2]);
    double phi = atan2(lv[1], lv[0]);
    double psi = 0;
    
    return RotMat3x3d(phi, theta, psi);
    
  }
}

Revision:	2198
Committed:	Thu Apr 14 21:20:36 2005 UTC (19 years, 2 months ago) by gezelter
File size:	7042 byte(s)
Log Message:	Fixed a bug in RigidBodyStamp section of MoLocator
#	User	Rev	Content
1	gezelter	2180	/*
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 <iostream>
43
44			#include <cstdlib>
45			#include <cmath>
46
47			#include "utils/simError.h"
48			#include "utils/MoLocator.hpp"
49			#include "types/AtomType.hpp"
50	gezelter	2198
51	gezelter	2180	namespace oopse {
52	gezelter	2198	MoLocator::MoLocator( MoleculeStamp* theStamp, ForceField* theFF){
53
54			myStamp = theStamp;
55			myFF = theFF;
56			nIntegrableObjects = myStamp->getNIntegrable();
57			calcRef();
58			}
59
60			void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol){
61	gezelter	2180	Vector3d newCoor;
62			Vector3d curRefCoor;
63			RotMat3x3d rotMat = latVec2RotMat(ort);
64	gezelter	2198
65	gezelter	2180	if(mol->getNIntegrableObjects() != nIntegrableObjects){
66	gezelter	2198	sprintf( painCave.errMsg,
67			"MoLocator error.\n"
68			" The number of integrable objects of MoleculeStamp is not the same as that of Molecule\n");
69			painCave.isFatal = 1;
70			simError();
71	gezelter	2180	}
72	gezelter	2198
73	gezelter	2180	Molecule::IntegrableObjectIterator ii;
74			StuntDouble* integrableObject;
75			int i;
76			for (integrableObject = mol->beginIntegrableObject(ii), i = 0; integrableObject != NULL;
77	gezelter	2198	integrableObject = mol->nextIntegrableObject(ii), ++i) {
78
79			newCoor = rotMat * refCoords[i];
80			newCoor += offset;
81
82			integrableObject->setPos( newCoor);
83			integrableObject->setVel(V3Zero);
84
85			if(integrableObject->isDirectional()){
86			integrableObject->setA(rotMat * integrableObject->getA());
87			integrableObject->setJ(V3Zero);
88			}
89	gezelter	2180	}
90	gezelter	2198	}
91	gezelter	2180
92	gezelter	2198	void MoLocator::calcRef( void ){
93			AtomStamp* currAtomStamp;
94			RigidBodyStamp* rbStamp;
95			int nAtoms;
96			int nRigidBodies;
97			std::vector<double> mass;
98			Vector3d coor;
99			Vector3d refMolCom;
100			int nAtomsInRb;
101			double totMassInRb;
102			double currAtomMass;
103			double molMass;
104
105			nAtoms= myStamp->getNAtoms();
106			nRigidBodies = myStamp->getNRigidBodies();
107
108			for(size_t i=0; i<nAtoms; i++){
109
110			currAtomStamp = myStamp->getAtom(i);
111
112			if( !currAtomStamp->havePosition() ){
113			sprintf( painCave.errMsg,
114			"MoLocator error.\n"
115			" Component %s, atom %s does not have a position specified.\n"
116			" This means MoLocator cannot initalize it's position.\n",
117			myStamp->getID(),
118			currAtomStamp->getType() );
119
120			painCave.isFatal = 1;
121			simError();
122			}
123
124			//if atom belongs to rigidbody, just skip it
125			if(myStamp->isAtomInRigidBody(i))
126			continue;
127			//get mass and the reference coordinate
128			else{
129			currAtomMass = getAtomMass(currAtomStamp->getType(), myFF);
130			mass.push_back(currAtomMass);
131			coor.x() = currAtomStamp->getPosX();
132			coor.y() = currAtomStamp->getPosY();
133			coor.z() = currAtomStamp->getPosZ();
134			refCoords.push_back(coor);
135
136			}
137	gezelter	2180	}
138	gezelter	2198
139			for(int i = 0; i < nRigidBodies; i++){
140
141			rbStamp = myStamp->getRigidBody(i);
142			nAtomsInRb = rbStamp->getNMembers();
143
144			coor.x() = 0.0;
145			coor.y() = 0.0;
146			coor.z() = 0.0;
147			totMassInRb = 0.0;
148
149			for(int j = 0; j < nAtomsInRb; j++){
150
151			currAtomStamp = myStamp->getAtom(rbStamp->getMember(j));
152			currAtomMass = getAtomMass(currAtomStamp->getType(), myFF);
153			totMassInRb += currAtomMass;
154
155			coor.x() += currAtomStamp->getPosX() * currAtomMass;
156			coor.y() += currAtomStamp->getPosY() * currAtomMass;
157			coor.z() += currAtomStamp->getPosZ() * currAtomMass;
158			}
159
160			mass.push_back(totMassInRb);
161			coor /= totMassInRb;
162	gezelter	2180	refCoords.push_back(coor);
163			}
164	gezelter	2198
165
166			//calculate the reference center of mass
167			molMass = 0;
168			refMolCom.x() = 0;
169			refMolCom.y() = 0;
170			refMolCom.z() = 0;
171
172			for(int i = 0; i < nIntegrableObjects; i++){
173			refMolCom += refCoords[i] * mass[i];
174			molMass += mass[i];
175	gezelter	2180	}
176	gezelter	2198
177			refMolCom /= molMass;
178
179			//move the reference center of mass to (0,0,0) and adjust the reference coordinate
180			//of the integrabel objects
181			for(int i = 0; i < nIntegrableObjects; i++)
182			refCoords[i] -= refMolCom;
183	gezelter	2180	}
184
185	gezelter	2198	double getAtomMass(const std::string& at, ForceField* myFF) {
186	gezelter	2180	double mass;
187			AtomType* atomType= myFF->getAtomType(at);
188			if (atomType != NULL) {
189	gezelter	2198	mass = atomType->getMass();
190	gezelter	2180	} else {
191	gezelter	2198	mass = 0.0;
192			std::cerr << "Can not find AtomType: " << at << std::endl;
193	gezelter	2180	}
194			return mass;
195	gezelter	2198	}
196
197			double getMolMass(MoleculeStamp molStamp, ForceField myFF) {
198	gezelter	2180	int nAtoms;
199			double totMass = 0;
200			nAtoms = molStamp->getNAtoms();
201	gezelter	2198
202	gezelter	2180	for(size_t i = 0; i < nAtoms; i++) {
203	gezelter	2198	AtomStamp *currAtomStamp = molStamp->getAtom(i);
204			totMass += getAtomMass(currAtomStamp->getType(), myFF);
205	gezelter	2180	}
206			return totMass;
207	gezelter	2198	}
208			RotMat3x3d latVec2RotMat(const Vector3d& lv){
209
210	gezelter	2180	double theta =acos(lv[2]);
211			double phi = atan2(lv[1], lv[0]);
212			double psi = 0;
213	gezelter	2198
214	gezelter	2180	return RotMat3x3d(phi, theta, psi);
215	gezelter	2198
216			}
217	gezelter	2180	}
218