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;
  
  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;
  }

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


void Molecule::initialize( molInit &theInit ){

  nAtoms = theInit.nAtoms;
  nMembers = nAtoms;
  nBonds = theInit.nBonds;
  nBends = theInit.nBends;
  nTorsions = theInit.nTorsions;
  nExcludes = theInit.nExcludes;
  nOriented = theInit.nOriented;

  myAtoms = theInit.myAtoms;
  myBonds = theInit.myBonds;
  myBends = theInit.myBends;
  myTorsions = theInit.myTorsions;
  myExcludes = theInit.myExcludes;
    
}

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

  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();
  }
}


double Molecule::getPotential( void ){
  
  int i;
  double myPot = 0.0;
   
  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<nAtoms; i++) {
    if(myAtoms[i] != NULL ) {
      
      myAtoms[i]->getPos( aPos );
      
      for (j=0; j< 3; j++) 
        aPos[j] += delta[j];

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

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 < nAtoms; i++) {
    if (myAtoms[i] != NULL) {

      mass = myAtoms[i]->getMass();
      mtot   += mass;
      
      myAtoms[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 < nAtoms; i++) {
    if (myAtoms[i] != NULL) {

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

      myAtoms[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()
{
  int natoms;
  Atom** atoms;
  double totalMass;
  
  natoms = getNAtoms();
  atoms = getMyAtoms();
  totalMass = 0;
  for(int i =0; i < natoms; i++){
    totalMass += atoms[i]->getMass();
  }

  return totalMass;
}
Revision:	829
Committed:	Tue Oct 28 16:03:37 2003 UTC (20 years, 8 months ago) by gezelter
File size:	3522 byte(s)
Log Message:	replace c++ header stuff with more portable c header stuff Also, mod file fixes and portability changes Some fortran changes will need to be reversed.
#	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
18
19
20			Molecule::~Molecule( void ){
21			int i;
22
23			if( myAtoms != NULL ){
24			for(i=0; i<nAtoms; i++) if(myAtoms[i] != NULL ) delete myAtoms[i];
25			delete[] myAtoms;
26			}
27
28			if( myBonds != NULL ){
29			for(i=0; i<nBonds; i++) if(myBonds[i] != NULL ) delete myBonds[i];
30			delete[] myBonds;
31			}
32
33			if( myBends != NULL ){
34			for(i=0; i<nBends; i++) if(myBends[i] != NULL ) delete myBends[i];
35			delete[] myBends;
36			}
37
38			if( myTorsions != NULL ){
39			for(i=0; i<nTorsions; i++) if(myTorsions[i] != NULL ) delete myTorsions[i];
40			delete[] myTorsions;
41			}
42
43			if( myExcludes != NULL ){
44			for(i=0; i<nExcludes; i++) if(myExcludes[i] != NULL ) delete myExcludes[i];
45			delete[] myExcludes;
46			}
47			}
48
49
50			void Molecule::initialize( molInit &theInit ){
51
52			nAtoms = theInit.nAtoms;
53			nMembers = nAtoms;
54			nBonds = theInit.nBonds;
55			nBends = theInit.nBends;
56			nTorsions = theInit.nTorsions;
57			nExcludes = theInit.nExcludes;
58			nOriented = theInit.nOriented;
59
60			myAtoms = theInit.myAtoms;
61			myBonds = theInit.myBonds;
62			myBends = theInit.myBends;
63			myTorsions = theInit.myTorsions;
64	mmeineke	428	myExcludes = theInit.myExcludes;
65	mmeineke	426
66			}
67
68			void Molecule::calcForces( void ){
69
70			int i;
71
72			for(i=0; i<nBonds; i++){
73			myBonds[i]->calc_forces();
74			}
75
76			for(i=0; i<nBends; i++){
77			myBends[i]->calc_forces();
78			}
79
80			for(i=0; i<nTorsions; i++){
81			myTorsions[i]->calc_forces();
82			}
83			}
84
85
86	mmeineke	428	double Molecule::getPotential( void ){
87	mmeineke	426
88			int i;
89			double myPot = 0.0;
90
91			for(i=0; i<nBonds; i++){
92			myPot += myBonds[i]->get_potential();
93			}
94
95			for(i=0; i<nBends; i++){
96			myPot += myBends[i]->get_potential();
97			}
98
99			for(i=0; i<nTorsions; i++){
100			myPot += myTorsions[i]->get_potential();
101			}
102
103			return myPot;
104			}
105	mmeineke	435
106			void Molecule::printMe( void ){
107
108			int i;
109
110			for(i=0; i<nBonds; i++){
111			myBonds[i]->printMe();
112			}
113
114			for(i=0; i<nBends; i++){
115			myBends[i]->printMe();
116			}
117
118			for(i=0; i<nTorsions; i++){
119			myTorsions[i]->printMe();
120			}
121			}
122	gezelter	446
123	mmeineke	449	void Molecule::moveCOM(double delta[3]){
124	gezelter	610	double aPos[3];
125			int i, j;
126	gezelter	446
127			for(i=0; i<nAtoms; i++) {
128			if(myAtoms[i] != NULL ) {
129	gezelter	610
130			myAtoms[i]->getPos( aPos );
131
132			for (j=0; j< 3; j++)
133			aPos[j] += delta[j];
134	gezelter	446
135	gezelter	610	myAtoms[i]->setPos( aPos );
136	gezelter	446	}
137			}
138			}
139
140	mmeineke	449	void Molecule::getCOM( double COM[3] ) {
141	gezelter	446
142			double mass, mtot;
143	gezelter	610	double aPos[3];
144			int i, j;
145	gezelter	446
146	gezelter	610	for (j=0; j<3; j++)
147			COM[j] = 0.0;
148
149	gezelter	446	mtot = 0.0;
150
151			for (i=0; i < nAtoms; i++) {
152			if (myAtoms[i] != NULL) {
153
154			mass = myAtoms[i]->getMass();
155			mtot += mass;
156	gezelter	610
157			myAtoms[i]->getPos( aPos );
158	gezelter	446
159	gezelter	610	for( j = 0; j < 3; j++)
160			COM[j] += aPos[j] * mass;
161
162	gezelter	446	}
163			}
164
165	gezelter	610	for (j = 0; j < 3; j++)
166			COM[j] /= mtot;
167	gezelter	446	}
168	gezelter	468
169	gezelter	475	double Molecule::getCOMvel( double COMvel[3] ) {
170	gezelter	468
171	gezelter	475	double mass, mtot;
172	gezelter	607	double aVel[3];
173			int i, j;
174	gezelter	468
175	gezelter	607
176			for (j=0; j<3; j++)
177			COMvel[j] = 0.0;
178
179	gezelter	468	mtot = 0.0;
180
181			for (i=0; i < nAtoms; i++) {
182			if (myAtoms[i] != NULL) {
183	mmeineke	489
184	gezelter	468	mass = myAtoms[i]->getMass();
185			mtot += mass;
186
187	gezelter	607	myAtoms[i]->getVel(aVel);
188
189			for (j=0; j<3; j++)
190			COMvel[j] += aVel[j]*mass;
191
192	gezelter	468	}
193			}
194
195	gezelter	607	for (j=0; j<3; j++)
196			COMvel[j] /= mtot;
197	gezelter	468
198	gezelter	475	return mtot;
199
200	gezelter	468	}
201	tim	658
202			double Molecule::getTotalMass()
203			{
204			int natoms;
205			Atom** atoms;
206			double totalMass;
207
208			natoms = getNAtoms();
209			atoms = getMyAtoms();
210			totalMass = 0;
211			for(int i =0; i < natoms; i++){
212			totalMass += atoms[i]->getMass();
213			}
214
215			return totalMass;
216			}