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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include <iostream>

#include <cstdlib>
#include <cmath>

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

namespace OpenMD {
  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::placeMol error.\n"
               "\tThe number of integrable objects of MoleculeStamp is not\n"
               "\tthe same as that of Molecule\n");
      painCave.isFatal = 1;
      simError();
    }
    
    Molecule::IntegrableObjectIterator ii;
    StuntDouble* sd;
    int i;
    for (sd = mol->beginIntegrableObject(ii), i = 0; sd != NULL; 
         sd = mol->nextIntegrableObject(ii), ++i) { 
      
      newCoor = rotMat * refCoords[i];
      newCoor += offset;
     
      sd->setPos(newCoor);
      sd->setVel(V3Zero);
      
      if(sd->isDirectional()){
        sd->setA(rotMat * sd->getA());
        sd->setJ(V3Zero);  
      }        
    }
  }
  
  void MoLocator::calcRef( void ){
    AtomStamp* currAtomStamp;
    RigidBodyStamp* rbStamp;
    unsigned int nAtoms; 
    int nRigidBodies;
    std::vector<RealType> mass;
    Vector3d coor;
    Vector3d refMolCom;  
    int nAtomsInRb;
    RealType totMassInRb;
    RealType currAtomMass;
    RealType molMass;
    
    nAtoms= myStamp->getNAtoms();
    nRigidBodies = myStamp->getNRigidBodies();
    
    for(unsigned int i = 0; i < nAtoms; i++){
      
      currAtomStamp = myStamp->getAtomStamp(i);
      
      if( !currAtomStamp->havePosition() ){
        sprintf( painCave.errMsg,
                 "MoLocator::calcRef error.\n"
                 "\tComponent %s, atom %s does not have a position specified.\n"
                 "\tThis means MoLocator cannot initalize it's position.\n",
                 myStamp->getName().c_str(),
                 currAtomStamp->getType().c_str());
        
        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->getRigidBodyStamp(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->getAtomStamp(rbStamp->getMemberAt(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;
  }
  
  RealType MoLocator::getAtomMass(const std::string& at, ForceField* myFF) {
    RealType 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;
  }
  
  RealType MoLocator::getMolMass(MoleculeStamp *molStamp, ForceField *myFF) {
    unsigned int nAtoms;
    RealType totMass = 0;
    nAtoms = molStamp->getNAtoms();
    
    for(unsigned int i = 0; i < nAtoms; i++) {
      AtomStamp *currAtomStamp = molStamp->getAtomStamp(i);
      totMass += getAtomMass(currAtomStamp->getType(), myFF);         
    }
    return totMass;
  }

  RotMat3x3d MoLocator::latVec2RotMat(const Vector3d& lv){
    
    RealType theta =acos(lv[2]);
    RealType phi = atan2(lv[1], lv[0]);
    RealType psi = 0;
    
    return RotMat3x3d(phi, theta, psi);    
  }
}

Revision:	1808
Committed:	Mon Oct 22 20:42:10 2012 UTC (13 years ago) by gezelter
File size:	7208 byte(s)
Log Message:	A bug fix in the electric field for the new electrostatic code. Also comment fixes for Doxygen
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	483	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	483	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	483	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	483	*/
42
43			#include <iostream>
44
45			#include <cstdlib>
46			#include <cmath>
47
48			#include "utils/simError.h"
49			#include "utils/MoLocator.hpp"
50			#include "types/AtomType.hpp"
51	gezelter	501
52	gezelter	1390	namespace OpenMD {
53	gezelter	501	MoLocator::MoLocator( MoleculeStamp* theStamp, ForceField* theFF){
54
55			myStamp = theStamp;
56			myFF = theFF;
57			nIntegrableObjects = myStamp->getNIntegrable();
58			calcRef();
59			}
60
61	gezelter	1808	void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort,
62			Molecule* mol) {
63	gezelter	1062
64	gezelter	483	Vector3d newCoor;
65			Vector3d curRefCoor;
66			RotMat3x3d rotMat = latVec2RotMat(ort);
67	gezelter	501
68	gezelter	483	if(mol->getNIntegrableObjects() != nIntegrableObjects){
69	gezelter	501	sprintf( painCave.errMsg,
70	gezelter	1808	"MoLocator::placeMol error.\n"
71			"\tThe number of integrable objects of MoleculeStamp is not\n"
72			"\tthe same as that of Molecule\n");
73	gezelter	501	painCave.isFatal = 1;
74			simError();
75	gezelter	483	}
76	gezelter	501
77	gezelter	483	Molecule::IntegrableObjectIterator ii;
78	gezelter	1769	StuntDouble* sd;
79	gezelter	483	int i;
80	gezelter	1769	for (sd = mol->beginIntegrableObject(ii), i = 0; sd != NULL;
81			sd = mol->nextIntegrableObject(ii), ++i) {
82	gezelter	501
83			newCoor = rotMat * refCoords[i];
84			newCoor += offset;
85	gezelter	1062
86	gezelter	1769	sd->setPos(newCoor);
87			sd->setVel(V3Zero);
88	gezelter	501
89	gezelter	1769	if(sd->isDirectional()){
90			sd->setA(rotMat * sd->getA());
91			sd->setJ(V3Zero);
92	gezelter	501	}
93	gezelter	483	}
94	gezelter	501	}
95	gezelter	483
96	gezelter	501	void MoLocator::calcRef( void ){
97			AtomStamp* currAtomStamp;
98			RigidBodyStamp* rbStamp;
99	gezelter	1767	unsigned int nAtoms;
100	gezelter	501	int nRigidBodies;
101	tim	963	std::vector<RealType> mass;
102	gezelter	501	Vector3d coor;
103			Vector3d refMolCom;
104			int nAtomsInRb;
105	tim	963	RealType totMassInRb;
106			RealType currAtomMass;
107			RealType molMass;
108	gezelter	501
109			nAtoms= myStamp->getNAtoms();
110			nRigidBodies = myStamp->getNRigidBodies();
111
112	gezelter	1767	for(unsigned int i = 0; i < nAtoms; i++){
113	gezelter	501
114	tim	770	currAtomStamp = myStamp->getAtomStamp(i);
115	gezelter	501
116			if( !currAtomStamp->havePosition() ){
117			sprintf( painCave.errMsg,
118	gezelter	1808	"MoLocator::calcRef error.\n"
119			"\tComponent %s, atom %s does not have a position specified.\n"
120			"\tThis means MoLocator cannot initalize it's position.\n",
121	tim	770	myStamp->getName().c_str(),
122			currAtomStamp->getType().c_str());
123	gezelter	501
124			painCave.isFatal = 1;
125			simError();
126			}
127
128			//if atom belongs to rigidbody, just skip it
129			if(myStamp->isAtomInRigidBody(i))
130			continue;
131			//get mass and the reference coordinate
132			else{
133			currAtomMass = getAtomMass(currAtomStamp->getType(), myFF);
134			mass.push_back(currAtomMass);
135			coor.x() = currAtomStamp->getPosX();
136			coor.y() = currAtomStamp->getPosY();
137			coor.z() = currAtomStamp->getPosZ();
138			refCoords.push_back(coor);
139
140			}
141	gezelter	483	}
142	gezelter	501
143			for(int i = 0; i < nRigidBodies; i++){
144
145	tim	770	rbStamp = myStamp->getRigidBodyStamp(i);
146	gezelter	501	nAtomsInRb = rbStamp->getNMembers();
147
148			coor.x() = 0.0;
149			coor.y() = 0.0;
150			coor.z() = 0.0;
151			totMassInRb = 0.0;
152
153			for(int j = 0; j < nAtomsInRb; j++){
154
155	tim	770	currAtomStamp = myStamp->getAtomStamp(rbStamp->getMemberAt(j));
156	gezelter	501	currAtomMass = getAtomMass(currAtomStamp->getType(), myFF);
157			totMassInRb += currAtomMass;
158
159			coor.x() += currAtomStamp->getPosX() * currAtomMass;
160			coor.y() += currAtomStamp->getPosY() * currAtomMass;
161			coor.z() += currAtomStamp->getPosZ() * currAtomMass;
162			}
163
164			mass.push_back(totMassInRb);
165			coor /= totMassInRb;
166	gezelter	483	refCoords.push_back(coor);
167			}
168	gezelter	501
169
170			//calculate the reference center of mass
171			molMass = 0;
172			refMolCom.x() = 0;
173			refMolCom.y() = 0;
174			refMolCom.z() = 0;
175
176			for(int i = 0; i < nIntegrableObjects; i++){
177			refMolCom += refCoords[i] * mass[i];
178			molMass += mass[i];
179	gezelter	483	}
180	gezelter	501
181			refMolCom /= molMass;
182
183	gezelter	1808	//move the reference center of mass to (0,0,0) and adjust the
184			//reference coordinate of the integrabel objects
185	gezelter	507	for(int i = 0; i < nIntegrableObjects; i++)
186			refCoords[i] -= refMolCom;
187	gezelter	483	}
188
189	gezelter	1808	RealType MoLocator::getAtomMass(const std::string& at, ForceField* myFF) {
190	tim	963	RealType mass;
191	gezelter	483	AtomType* atomType= myFF->getAtomType(at);
192			if (atomType != NULL) {
193	gezelter	501	mass = atomType->getMass();
194	gezelter	483	} else {
195	gezelter	501	mass = 0.0;
196			std::cerr << "Can not find AtomType: " << at << std::endl;
197	gezelter	483	}
198			return mass;
199	gezelter	501	}
200
201	gezelter	1808	RealType MoLocator::getMolMass(MoleculeStamp molStamp, ForceField myFF) {
202	gezelter	1767	unsigned int nAtoms;
203	tim	963	RealType totMass = 0;
204	gezelter	483	nAtoms = molStamp->getNAtoms();
205	gezelter	501
206	gezelter	1767	for(unsigned int i = 0; i < nAtoms; i++) {
207	tim	770	AtomStamp *currAtomStamp = molStamp->getAtomStamp(i);
208	gezelter	501	totMass += getAtomMass(currAtomStamp->getType(), myFF);
209	gezelter	483	}
210			return totMass;
211	gezelter	501	}
212	gezelter	1808
213			RotMat3x3d MoLocator::latVec2RotMat(const Vector3d& lv){
214	gezelter	501
215	tim	963	RealType theta =acos(lv[2]);
216			RealType phi = atan2(lv[1], lv[0]);
217			RealType psi = 0;
218	gezelter	501
219	gezelter	1808	return RotMat3x3d(phi, theta, psi);
220	gezelter	501	}
221	gezelter	483	}
222