OOPSE/libmdtools/Molecule.cpp

#include <stdlib.h>


#include "Molecule.hpp"
#include "simError.h"


Molecule::Molecule( void ){

  myAtoms = NULL;
  myBonds = NULL;
  myBends = NULL;
  myTorsions = NULL;
}

Molecule::~Molecule( void ){
  int i;
  CutoffGroup* cg;
  vector<CutoffGroup*>::iterator iter;
  
  if( myAtoms != NULL ){
    for(i=0; i<nAtoms; i++) if(myAtoms[i] != NULL ) delete myAtoms[i];
    delete[] myAtoms;
  }

  if( myBonds != NULL ){
    for(i=0; i<nBonds; i++) if(myBonds[i] != NULL ) delete myBonds[i];
    delete[] myBonds;
  }

  if( myBends != NULL ){
    for(i=0; i<nBends; i++) if(myBends[i] != NULL ) delete myBends[i];
    delete[] myBends;
  }

  if( myTorsions != NULL ){
    for(i=0; i<nTorsions; i++) if(myTorsions[i] != NULL ) delete myTorsions[i];
    delete[] myTorsions;
  }

  for(cg = beginCutoffGroup(iter);  cg != NULL; cg = nextCutoffGroup(iter))
    delete cg;
  myCutoffGroups.clear();
  
}


void Molecule::initialize( molInit &theInit ){

  CutoffGroup* curCutoffGroup;
  vector<CutoffGroup*>::iterator iterCutoff;
  Atom* cutoffAtom;
  vector<Atom*>::iterator iterAtom;
  int atomIndex;
  
  nAtoms = theInit.nAtoms;
  nMembers = nAtoms;
  nBonds = theInit.nBonds;
  nBends = theInit.nBends;
  nTorsions = theInit.nTorsions;
  nRigidBodies = theInit.nRigidBodies;
  nOriented = theInit.nOriented;

  myAtoms = theInit.myAtoms;
  myBonds = theInit.myBonds;
  myBends = theInit.myBends;
  myTorsions = theInit.myTorsions;
  myRigidBodies = theInit.myRigidBodies;

  myIntegrableObjects = theInit.myIntegrableObjects;

  for (int i = 0; i < myRigidBodies.size(); i++) 
      myRigidBodies[i]->calcRefCoords();

  myCutoffGroups = theInit.myCutoffGroups;
  nCutoffGroups = myCutoffGroups.size();
  
}

void Molecule::calcForces( void ){
  
  int i;
  double com[3];

  for(i=0; i<myRigidBodies.size(); i++) {
    myRigidBodies[i]->updateAtoms();
  }

  //calculate the center of mass of the molecule
  //getCOM(com);  
  //for(int i = 0; i < nAtoms; i ++)
  //  myAtoms[i]->setRc(com);  
  

  for(i=0; i<nBonds; i++){
    myBonds[i]->calc_forces();
  }

  for(i=0; i<nBends; i++){
    myBends[i]->calc_forces();
  }

  for(i=0; i<nTorsions; i++){
    myTorsions[i]->calc_forces();
  }

  // Rigid Body forces and torques are done after the fortran force loop

}


double Molecule::getPotential( void ){
  
  int i;
  double myPot = 0.0;

  for(i=0; i<myRigidBodies.size(); i++) {
    myRigidBodies[i]->updateAtoms();
  }
   
  for(i=0; i<nBonds; i++){
    myPot += myBonds[i]->get_potential();
  }

  for(i=0; i<nBends; i++){
    myPot += myBends[i]->get_potential();
  }

  for(i=0; i<nTorsions; i++){
    myPot += myTorsions[i]->get_potential();
  }

  return myPot;
}

void Molecule::printMe( void ){
  
  int i;

  for(i=0; i<nBonds; i++){
    myBonds[i]->printMe();
  }

  for(i=0; i<nBends; i++){
    myBends[i]->printMe();
  }

  for(i=0; i<nTorsions; i++){
    myTorsions[i]->printMe();
  }

}

void Molecule::moveCOM(double delta[3]){
  double aPos[3];
  int i, j;

  for(i=0; i<myIntegrableObjects.size(); i++) {
    if(myIntegrableObjects[i] != NULL ) {
      
      myIntegrableObjects[i]->getPos( aPos );
      
      for (j=0; j< 3; j++) 
        aPos[j] += delta[j];

      myIntegrableObjects[i]->setPos( aPos );
    }
  }

  for(i=0; i<myRigidBodies.size(); i++) {

      myRigidBodies[i]->getPos( aPos );

      for (j=0; j< 3; j++) 
        aPos[j] += delta[j];
      
      myRigidBodies[i]->setPos( aPos );
    }
}

void Molecule::atoms2rigidBodies( void ) {
  int i;
  for (i = 0; i < myRigidBodies.size(); i++) {
    myRigidBodies[i]->calcForcesAndTorques();   
  }
}

void Molecule::getCOM( double COM[3] ) {

  double mass, mtot;
  double aPos[3];
  int i, j;

  for (j=0; j<3; j++) 
    COM[j] = 0.0;

  mtot   = 0.0;

  for (i=0; i < myIntegrableObjects.size(); i++) {
    if (myIntegrableObjects[i] != NULL) {

      mass = myIntegrableObjects[i]->getMass();
      mtot   += mass;
      
      myIntegrableObjects[i]->getPos( aPos );

      for( j = 0; j < 3; j++) 
        COM[j] += aPos[j] * mass;

    }
  }

  for (j = 0; j < 3; j++) 
    COM[j] /= mtot; 
}

double Molecule::getCOMvel( double COMvel[3] ) {

  double mass, mtot;
  double aVel[3];
  int i, j;


  for (j=0; j<3; j++) 
    COMvel[j] = 0.0;

  mtot   = 0.0;

  for (i=0; i < myIntegrableObjects.size(); i++) {
    if (myIntegrableObjects[i] != NULL) {

      mass = myIntegrableObjects[i]->getMass();
      mtot   += mass;

      myIntegrableObjects[i]->getVel(aVel);

      for (j=0; j<3; j++) 
        COMvel[j] += aVel[j]*mass;

    }
  }

  for (j=0; j<3; j++) 
    COMvel[j] /= mtot;
 
  return mtot;

}

double Molecule::getTotalMass()
{

  double totalMass;
  
  totalMass = 0;
  for(int i =0; i < myIntegrableObjects.size(); i++){
    totalMass += myIntegrableObjects[i]->getMass();
  }

  return totalMass;
}
Revision:	1167
Committed:	Wed May 12 16:38:45 2004 UTC (20 years, 4 months ago) by tim
File size:	4830 byte(s)
Log Message:	get rid of rc and massratio from simState, creat cutoff group forevery atom which does not belong to cutoff group defined at mdl file
#	User	Rev	Content
1	gezelter	829	#include <stdlib.h>
2	mmeineke	426
3
4			#include "Molecule.hpp"
5	chuckv	438	#include "simError.h"
6	mmeineke	426
7
8
9			Molecule::Molecule( void ){
10
11			myAtoms = NULL;
12			myBonds = NULL;
13			myBends = NULL;
14			myTorsions = NULL;
15			}
16
17			Molecule::~Molecule( void ){
18			int i;
19	tim	1167	CutoffGroup* cg;
20			vector<CutoffGroup*>::iterator iter;
21	mmeineke	426
22			if( myAtoms != NULL ){
23			for(i=0; i<nAtoms; i++) if(myAtoms[i] != NULL ) delete myAtoms[i];
24			delete[] myAtoms;
25			}
26
27			if( myBonds != NULL ){
28			for(i=0; i<nBonds; i++) if(myBonds[i] != NULL ) delete myBonds[i];
29			delete[] myBonds;
30			}
31
32			if( myBends != NULL ){
33			for(i=0; i<nBends; i++) if(myBends[i] != NULL ) delete myBends[i];
34			delete[] myBends;
35			}
36
37			if( myTorsions != NULL ){
38			for(i=0; i<nTorsions; i++) if(myTorsions[i] != NULL ) delete myTorsions[i];
39			delete[] myTorsions;
40			}
41
42	tim	1167	for(cg = beginCutoffGroup(iter); cg != NULL; cg = nextCutoffGroup(iter))
43			delete cg;
44			myCutoffGroups.clear();
45
46	mmeineke	426	}
47
48
49			void Molecule::initialize( molInit &theInit ){
50	tim	1140
51	tim	1157	CutoffGroup* curCutoffGroup;
52			vector<CutoffGroup*>::iterator iterCutoff;
53			Atom* cutoffAtom;
54			vector<Atom*>::iterator iterAtom;
55			int atomIndex;
56
57	mmeineke	426	nAtoms = theInit.nAtoms;
58			nMembers = nAtoms;
59			nBonds = theInit.nBonds;
60			nBends = theInit.nBends;
61			nTorsions = theInit.nTorsions;
62	gezelter	1097	nRigidBodies = theInit.nRigidBodies;
63	mmeineke	426	nOriented = theInit.nOriented;
64
65			myAtoms = theInit.myAtoms;
66			myBonds = theInit.myBonds;
67			myBends = theInit.myBends;
68			myTorsions = theInit.myTorsions;
69	gezelter	1097	myRigidBodies = theInit.myRigidBodies;
70	gezelter	1104
71			myIntegrableObjects = theInit.myIntegrableObjects;
72	tim	1113
73			for (int i = 0; i < myRigidBodies.size(); i++)
74			myRigidBodies[i]->calcRefCoords();
75	tim	1136
76	tim	1157	myCutoffGroups = theInit.myCutoffGroups;
77	tim	1167	nCutoffGroups = myCutoffGroups.size();
78	tim	1157
79	mmeineke	426	}
80
81			void Molecule::calcForces( void ){
82
83			int i;
84	tim	1136	double com[3];
85	mmeineke	426
86	gezelter	1104	for(i=0; i<myRigidBodies.size(); i++) {
87	gezelter	1097	myRigidBodies[i]->updateAtoms();
88			}
89
90	tim	1136	//calculate the center of mass of the molecule
91	tim	1157	//getCOM(com);
92			//for(int i = 0; i < nAtoms; i ++)
93			// myAtoms[i]->setRc(com);
94	tim	1136
95
96	mmeineke	426	for(i=0; i<nBonds; i++){
97			myBonds[i]->calc_forces();
98			}
99
100			for(i=0; i<nBends; i++){
101			myBends[i]->calc_forces();
102			}
103
104			for(i=0; i<nTorsions; i++){
105			myTorsions[i]->calc_forces();
106			}
107	gezelter	1097
108			// Rigid Body forces and torques are done after the fortran force loop
109
110	mmeineke	426	}
111
112
113	mmeineke	428	double Molecule::getPotential( void ){
114	mmeineke	426
115			int i;
116			double myPot = 0.0;
117	gezelter	1109
118			for(i=0; i<myRigidBodies.size(); i++) {
119			myRigidBodies[i]->updateAtoms();
120			}
121	mmeineke	426
122			for(i=0; i<nBonds; i++){
123			myPot += myBonds[i]->get_potential();
124			}
125
126			for(i=0; i<nBends; i++){
127			myPot += myBends[i]->get_potential();
128			}
129
130			for(i=0; i<nTorsions; i++){
131			myPot += myTorsions[i]->get_potential();
132			}
133
134			return myPot;
135			}
136	mmeineke	435
137			void Molecule::printMe( void ){
138
139			int i;
140
141			for(i=0; i<nBonds; i++){
142			myBonds[i]->printMe();
143			}
144
145			for(i=0; i<nBends; i++){
146			myBends[i]->printMe();
147			}
148
149			for(i=0; i<nTorsions; i++){
150			myTorsions[i]->printMe();
151			}
152	gezelter	1097
153	mmeineke	435	}
154	gezelter	446
155	mmeineke	449	void Molecule::moveCOM(double delta[3]){
156	gezelter	610	double aPos[3];
157			int i, j;
158	gezelter	446
159	tim	1113	for(i=0; i<myIntegrableObjects.size(); i++) {
160			if(myIntegrableObjects[i] != NULL ) {
161	gezelter	610
162	tim	1113	myIntegrableObjects[i]->getPos( aPos );
163	gezelter	610
164			for (j=0; j< 3; j++)
165			aPos[j] += delta[j];
166	gezelter	446
167	tim	1113	myIntegrableObjects[i]->setPos( aPos );
168	gezelter	446	}
169			}
170	gezelter	1097
171	gezelter	1104	for(i=0; i<myRigidBodies.size(); i++) {
172	gezelter	1097
173			myRigidBodies[i]->getPos( aPos );
174
175			for (j=0; j< 3; j++)
176			aPos[j] += delta[j];
177
178			myRigidBodies[i]->setPos( aPos );
179			}
180	gezelter	446	}
181
182	gezelter	1097	void Molecule::atoms2rigidBodies( void ) {
183			int i;
184	gezelter	1104	for (i = 0; i < myRigidBodies.size(); i++) {
185			myRigidBodies[i]->calcForcesAndTorques();
186	gezelter	1097	}
187			}
188
189	mmeineke	449	void Molecule::getCOM( double COM[3] ) {
190	gezelter	446
191			double mass, mtot;
192	gezelter	610	double aPos[3];
193			int i, j;
194	gezelter	446
195	gezelter	610	for (j=0; j<3; j++)
196			COM[j] = 0.0;
197
198	gezelter	446	mtot = 0.0;
199
200	tim	1113	for (i=0; i < myIntegrableObjects.size(); i++) {
201			if (myIntegrableObjects[i] != NULL) {
202	gezelter	446
203	tim	1113	mass = myIntegrableObjects[i]->getMass();
204	gezelter	446	mtot += mass;
205	gezelter	610
206	tim	1113	myIntegrableObjects[i]->getPos( aPos );
207	gezelter	446
208	gezelter	610	for( j = 0; j < 3; j++)
209			COM[j] += aPos[j] * mass;
210
211	gezelter	446	}
212			}
213
214	gezelter	610	for (j = 0; j < 3; j++)
215			COM[j] /= mtot;
216	gezelter	446	}
217	gezelter	468
218	gezelter	475	double Molecule::getCOMvel( double COMvel[3] ) {
219	gezelter	468
220	gezelter	475	double mass, mtot;
221	gezelter	607	double aVel[3];
222			int i, j;
223	gezelter	468
224	gezelter	607
225			for (j=0; j<3; j++)
226			COMvel[j] = 0.0;
227
228	gezelter	468	mtot = 0.0;
229
230	tim	1113	for (i=0; i < myIntegrableObjects.size(); i++) {
231			if (myIntegrableObjects[i] != NULL) {
232	mmeineke	489
233	tim	1113	mass = myIntegrableObjects[i]->getMass();
234	gezelter	468	mtot += mass;
235
236	tim	1113	myIntegrableObjects[i]->getVel(aVel);
237	gezelter	607
238			for (j=0; j<3; j++)
239			COMvel[j] += aVel[j]*mass;
240
241	gezelter	468	}
242			}
243
244	gezelter	607	for (j=0; j<3; j++)
245			COMvel[j] /= mtot;
246	gezelter	468
247	gezelter	475	return mtot;
248
249	gezelter	468	}
250	tim	658
251			double Molecule::getTotalMass()
252			{
253	tim	1113
254	tim	658	double totalMass;
255
256			totalMass = 0;
257	tim	1113	for(int i =0; i < myIntegrableObjects.size(); i++){
258			totalMass += myIntegrableObjects[i]->getMass();
259	tim	658	}
260
261			return totalMass;
262			}