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 (12 years, 6 months 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
#	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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
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
52	namespace OpenMD {
53	MoLocator::MoLocator( MoleculeStamp* theStamp, ForceField* theFF){
54
55	myStamp = theStamp;
56	myFF = theFF;
57	nIntegrableObjects = myStamp->getNIntegrable();
58	calcRef();
59	}
60
61	void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort,
62	Molecule* mol) {
63
64	Vector3d newCoor;
65	Vector3d curRefCoor;
66	RotMat3x3d rotMat = latVec2RotMat(ort);
67
68	if(mol->getNIntegrableObjects() != nIntegrableObjects){
69	sprintf( painCave.errMsg,
70	"MoLocator::placeMol error.\n"
71	"\tThe number of integrable objects of MoleculeStamp is not\n"
72	"\tthe same as that of Molecule\n");
73	painCave.isFatal = 1;
74	simError();
75	}
76
77	Molecule::IntegrableObjectIterator ii;
78	StuntDouble* sd;
79	int i;
80	for (sd = mol->beginIntegrableObject(ii), i = 0; sd != NULL;
81	sd = mol->nextIntegrableObject(ii), ++i) {
82
83	newCoor = rotMat * refCoords[i];
84	newCoor += offset;
85
86	sd->setPos(newCoor);
87	sd->setVel(V3Zero);
88
89	if(sd->isDirectional()){
90	sd->setA(rotMat * sd->getA());
91	sd->setJ(V3Zero);
92	}
93	}
94	}
95
96	void MoLocator::calcRef( void ){
97	AtomStamp* currAtomStamp;
98	RigidBodyStamp* rbStamp;
99	unsigned int nAtoms;
100	int nRigidBodies;
101	std::vector<RealType> mass;
102	Vector3d coor;
103	Vector3d refMolCom;
104	int nAtomsInRb;
105	RealType totMassInRb;
106	RealType currAtomMass;
107	RealType molMass;
108
109	nAtoms= myStamp->getNAtoms();
110	nRigidBodies = myStamp->getNRigidBodies();
111
112	for(unsigned int i = 0; i < nAtoms; i++){
113
114	currAtomStamp = myStamp->getAtomStamp(i);
115
116	if( !currAtomStamp->havePosition() ){
117	sprintf( painCave.errMsg,
118	"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	myStamp->getName().c_str(),
122	currAtomStamp->getType().c_str());
123
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	}
142
143	for(int i = 0; i < nRigidBodies; i++){
144
145	rbStamp = myStamp->getRigidBodyStamp(i);
146	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	currAtomStamp = myStamp->getAtomStamp(rbStamp->getMemberAt(j));
156	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	refCoords.push_back(coor);
167	}
168
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	}
180
181	refMolCom /= molMass;
182
183	//move the reference center of mass to (0,0,0) and adjust the
184	//reference coordinate of the integrabel objects
185	for(int i = 0; i < nIntegrableObjects; i++)
186	refCoords[i] -= refMolCom;
187	}
188
189	RealType MoLocator::getAtomMass(const std::string& at, ForceField* myFF) {
190	RealType mass;
191	AtomType* atomType= myFF->getAtomType(at);
192	if (atomType != NULL) {
193	mass = atomType->getMass();
194	} else {
195	mass = 0.0;
196	std::cerr << "Can not find AtomType: " << at << std::endl;
197	}
198	return mass;
199	}
200
201	RealType MoLocator::getMolMass(MoleculeStamp molStamp, ForceField myFF) {
202	unsigned int nAtoms;
203	RealType totMass = 0;
204	nAtoms = molStamp->getNAtoms();
205
206	for(unsigned int i = 0; i < nAtoms; i++) {
207	AtomStamp *currAtomStamp = molStamp->getAtomStamp(i);
208	totMass += getAtomMass(currAtomStamp->getType(), myFF);
209	}
210	return totMass;
211	}
212
213	RotMat3x3d MoLocator::latVec2RotMat(const Vector3d& lv){
214
215	RealType theta =acos(lv[2]);
216	RealType phi = atan2(lv[1], lv[0]);
217	RealType psi = 0;
218
219	return RotMat3x3d(phi, theta, psi);
220	}
221	}
222