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;
  }

}


void Molecule::initialize( molInit &theInit ){

  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();
    
}

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

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

  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:	1113
Committed:	Thu Apr 15 16:18:26 2004 UTC (20 years, 2 months ago) by tim
File size:	4260 byte(s)
Log Message:	fix whole bunch of bugs :-)
#	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			Molecule::~Molecule( void ){
19			int i;
20
21			if( myAtoms != NULL ){
22			for(i=0; i<nAtoms; i++) if(myAtoms[i] != NULL ) delete myAtoms[i];
23			delete[] myAtoms;
24			}
25
26			if( myBonds != NULL ){
27			for(i=0; i<nBonds; i++) if(myBonds[i] != NULL ) delete myBonds[i];
28			delete[] myBonds;
29			}
30
31			if( myBends != NULL ){
32			for(i=0; i<nBends; i++) if(myBends[i] != NULL ) delete myBends[i];
33			delete[] myBends;
34			}
35
36			if( myTorsions != NULL ){
37			for(i=0; i<nTorsions; i++) if(myTorsions[i] != NULL ) delete myTorsions[i];
38			delete[] myTorsions;
39			}
40
41			}
42
43
44			void Molecule::initialize( molInit &theInit ){
45
46			nAtoms = theInit.nAtoms;
47			nMembers = nAtoms;
48			nBonds = theInit.nBonds;
49			nBends = theInit.nBends;
50			nTorsions = theInit.nTorsions;
51	gezelter	1097	nRigidBodies = theInit.nRigidBodies;
52	mmeineke	426	nOriented = theInit.nOriented;
53
54			myAtoms = theInit.myAtoms;
55			myBonds = theInit.myBonds;
56			myBends = theInit.myBends;
57			myTorsions = theInit.myTorsions;
58	gezelter	1097	myRigidBodies = theInit.myRigidBodies;
59	gezelter	1104
60			myIntegrableObjects = theInit.myIntegrableObjects;
61	tim	1113
62			for (int i = 0; i < myRigidBodies.size(); i++)
63			myRigidBodies[i]->calcRefCoords();
64	mmeineke	426
65			}
66
67			void Molecule::calcForces( void ){
68
69			int i;
70
71	gezelter	1104	for(i=0; i<myRigidBodies.size(); i++) {
72	gezelter	1097	myRigidBodies[i]->updateAtoms();
73			}
74
75	mmeineke	426	for(i=0; i<nBonds; i++){
76			myBonds[i]->calc_forces();
77			}
78
79			for(i=0; i<nBends; i++){
80			myBends[i]->calc_forces();
81			}
82
83			for(i=0; i<nTorsions; i++){
84			myTorsions[i]->calc_forces();
85			}
86	gezelter	1097
87			// Rigid Body forces and torques are done after the fortran force loop
88
89	mmeineke	426	}
90
91
92	mmeineke	428	double Molecule::getPotential( void ){
93	mmeineke	426
94			int i;
95			double myPot = 0.0;
96	gezelter	1109
97			for(i=0; i<myRigidBodies.size(); i++) {
98			myRigidBodies[i]->updateAtoms();
99			}
100	mmeineke	426
101			for(i=0; i<nBonds; i++){
102			myPot += myBonds[i]->get_potential();
103			}
104
105			for(i=0; i<nBends; i++){
106			myPot += myBends[i]->get_potential();
107			}
108
109			for(i=0; i<nTorsions; i++){
110			myPot += myTorsions[i]->get_potential();
111			}
112
113			return myPot;
114			}
115	mmeineke	435
116			void Molecule::printMe( void ){
117
118			int i;
119
120			for(i=0; i<nBonds; i++){
121			myBonds[i]->printMe();
122			}
123
124			for(i=0; i<nBends; i++){
125			myBends[i]->printMe();
126			}
127
128			for(i=0; i<nTorsions; i++){
129			myTorsions[i]->printMe();
130			}
131	gezelter	1097
132	mmeineke	435	}
133	gezelter	446
134	mmeineke	449	void Molecule::moveCOM(double delta[3]){
135	gezelter	610	double aPos[3];
136			int i, j;
137	gezelter	446
138	tim	1113	for(i=0; i<myIntegrableObjects.size(); i++) {
139			if(myIntegrableObjects[i] != NULL ) {
140	gezelter	610
141	tim	1113	myIntegrableObjects[i]->getPos( aPos );
142	gezelter	610
143			for (j=0; j< 3; j++)
144			aPos[j] += delta[j];
145	gezelter	446
146	tim	1113	myIntegrableObjects[i]->setPos( aPos );
147	gezelter	446	}
148			}
149	gezelter	1097
150	gezelter	1104	for(i=0; i<myRigidBodies.size(); i++) {
151	gezelter	1097
152			myRigidBodies[i]->getPos( aPos );
153
154			for (j=0; j< 3; j++)
155			aPos[j] += delta[j];
156
157			myRigidBodies[i]->setPos( aPos );
158			}
159	gezelter	446	}
160
161	gezelter	1097	void Molecule::atoms2rigidBodies( void ) {
162			int i;
163	gezelter	1104	for (i = 0; i < myRigidBodies.size(); i++) {
164			myRigidBodies[i]->calcForcesAndTorques();
165	gezelter	1097	}
166			}
167
168	mmeineke	449	void Molecule::getCOM( double COM[3] ) {
169	gezelter	446
170			double mass, mtot;
171	gezelter	610	double aPos[3];
172			int i, j;
173	gezelter	446
174	gezelter	610	for (j=0; j<3; j++)
175			COM[j] = 0.0;
176
177	gezelter	446	mtot = 0.0;
178
179	tim	1113	for (i=0; i < myIntegrableObjects.size(); i++) {
180			if (myIntegrableObjects[i] != NULL) {
181	gezelter	446
182	tim	1113	mass = myIntegrableObjects[i]->getMass();
183	gezelter	446	mtot += mass;
184	gezelter	610
185	tim	1113	myIntegrableObjects[i]->getPos( aPos );
186	gezelter	446
187	gezelter	610	for( j = 0; j < 3; j++)
188			COM[j] += aPos[j] * mass;
189
190	gezelter	446	}
191			}
192
193	gezelter	610	for (j = 0; j < 3; j++)
194			COM[j] /= mtot;
195	gezelter	446	}
196	gezelter	468
197	gezelter	475	double Molecule::getCOMvel( double COMvel[3] ) {
198	gezelter	468
199	gezelter	475	double mass, mtot;
200	gezelter	607	double aVel[3];
201			int i, j;
202	gezelter	468
203	gezelter	607
204			for (j=0; j<3; j++)
205			COMvel[j] = 0.0;
206
207	gezelter	468	mtot = 0.0;
208
209	tim	1113	for (i=0; i < myIntegrableObjects.size(); i++) {
210			if (myIntegrableObjects[i] != NULL) {
211	mmeineke	489
212	tim	1113	mass = myIntegrableObjects[i]->getMass();
213	gezelter	468	mtot += mass;
214
215	tim	1113	myIntegrableObjects[i]->getVel(aVel);
216	gezelter	607
217			for (j=0; j<3; j++)
218			COMvel[j] += aVel[j]*mass;
219
220	gezelter	468	}
221			}
222
223	gezelter	607	for (j=0; j<3; j++)
224			COMvel[j] /= mtot;
225	gezelter	468
226	gezelter	475	return mtot;
227
228	gezelter	468	}
229	tim	658
230			double Molecule::getTotalMass()
231			{
232	tim	1113
233	tim	658	double totalMass;
234
235			totalMass = 0;
236	tim	1113	for(int i =0; i < myIntegrableObjects.size(); i++){
237			totalMass += myIntegrableObjects[i]->getMass();
238	tim	658	}
239
240			return totalMass;
241			}