src/brains/Thermo.cpp

#include <math.h>
#include <iostream>
using namespace std;

#ifdef IS_MPI
#include <mpi.h>
#endif //is_mpi

#include "brains/Thermo.hpp"
#include "primitives/SRI.hpp"
#include "integrators/Integrator.hpp"
#include "utils/simError.h"
#include "math/MatVec3.h"

#ifdef IS_MPI
#define __C
#include "brains/mpiSimulation.hpp"
#endif // is_mpi

inline double roundMe( double x ){
          return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
}

Thermo::Thermo( SimInfo* the_info ) { 
  info = the_info;
  int baseSeed = the_info->getSeed();
  
  gaussStream = new gaussianSPRNG( baseSeed );
}

Thermo::~Thermo(){
  delete gaussStream;
}

double Thermo::getKinetic(){

  const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
  double kinetic;
  double amass;
  double aVel[3], aJ[3], I[3][3];
  int i, j, k, kl;

  double kinetic_global;
  vector<StuntDouble *> integrableObjects = info->integrableObjects;
  
  kinetic = 0.0;
  kinetic_global = 0.0;

  for (kl=0; kl<integrableObjects.size(); kl++) {
    integrableObjects[kl]->getVel(aVel);
    amass = integrableObjects[kl]->getMass();

   for(j=0; j<3; j++) 
      kinetic += amass*aVel[j]*aVel[j];

   if (integrableObjects[kl]->isDirectional()){
 
      integrableObjects[kl]->getJ( aJ );
      integrableObjects[kl]->getI( I );

      if (integrableObjects[kl]->isLinear()) {
        i = integrableObjects[kl]->linearAxis();
        j = (i+1)%3;
        k = (i+2)%3;
        kinetic += aJ[j]*aJ[j]/I[j][j] + aJ[k]*aJ[k]/I[k][k];
      } else {
        for (j=0; j<3; j++) 
          kinetic += aJ[j]*aJ[j] / I[j][j];
      }
   }
  }
#ifdef IS_MPI
  MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
                MPI_SUM, MPI_COMM_WORLD);
  kinetic = kinetic_global;
#endif //is_mpi
  
  kinetic = kinetic * 0.5 / e_convert;

  return kinetic;
}

double Thermo::getPotential(){
  
  double potential_local;
  double potential;
  int el, nSRI;
  Molecule* molecules;

  molecules = info->molecules;
  nSRI = info->n_SRI;

  potential_local = 0.0;
  potential = 0.0;
  potential_local += info->lrPot;

  for( el=0; el<info->n_mol; el++ ){    
    potential_local += molecules[el].getPotential();
  }

  // Get total potential for entire system from MPI.
#ifdef IS_MPI
  MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE,
                MPI_SUM, MPI_COMM_WORLD);
#else
  potential = potential_local; 
#endif // is_mpi

  return potential;
}

double Thermo::getTotalE(){

  double total;

  total = this->getKinetic() + this->getPotential();
  return total;
}

double Thermo::getTemperature(){

  const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
  double temperature;

  temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
  return temperature;
}

double Thermo::getVolume() {

  return info->boxVol;
}

double Thermo::getPressure() {

  // Relies on the calculation of the full molecular pressure tensor
  
  const double p_convert = 1.63882576e8;
  double press[3][3];
  double pressure;

  this->getPressureTensor(press);

  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;

  return pressure;
}

double Thermo::getPressureX() {

  // Relies on the calculation of the full molecular pressure tensor
  
  const double p_convert = 1.63882576e8;
  double press[3][3];
  double pressureX;

  this->getPressureTensor(press);

  pressureX = p_convert * press[0][0];

  return pressureX;
}

double Thermo::getPressureY() {

  // Relies on the calculation of the full molecular pressure tensor
  
  const double p_convert = 1.63882576e8;
  double press[3][3];
  double pressureY;

  this->getPressureTensor(press);

  pressureY = p_convert * press[1][1];

  return pressureY;
}

double Thermo::getPressureZ() {

  // Relies on the calculation of the full molecular pressure tensor
  
  const double p_convert = 1.63882576e8;
  double press[3][3];
  double pressureZ;

  this->getPressureTensor(press);

  pressureZ = p_convert * press[2][2];

  return pressureZ;
}


void Thermo::getPressureTensor(double press[3][3]){
  // returns pressure tensor in units amu*fs^-2*Ang^-1
  // routine derived via viral theorem description in:
  // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322

  const double e_convert = 4.184e-4;

  double molmass, volume;
  double vcom[3];
  double p_local[9], p_global[9];
  int i, j, k;

  for (i=0; i < 9; i++) {    
    p_local[i] = 0.0;
    p_global[i] = 0.0;
  }

  // use velocities of integrableObjects and their masses:  

  for (i=0; i < info->integrableObjects.size(); i++) {

    molmass = info->integrableObjects[i]->getMass();
    
    info->integrableObjects[i]->getVel(vcom);
    
    p_local[0] += molmass * (vcom[0] * vcom[0]); 
    p_local[1] += molmass * (vcom[0] * vcom[1]); 
    p_local[2] += molmass * (vcom[0] * vcom[2]); 
    p_local[3] += molmass * (vcom[1] * vcom[0]); 
    p_local[4] += molmass * (vcom[1] * vcom[1]); 
    p_local[5] += molmass * (vcom[1] * vcom[2]); 
    p_local[6] += molmass * (vcom[2] * vcom[0]); 
    p_local[7] += molmass * (vcom[2] * vcom[1]); 
    p_local[8] += molmass * (vcom[2] * vcom[2]); 

  }

  // Get total for entire system from MPI.
  
#ifdef IS_MPI
  MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
#else
  for (i=0; i<9; i++) {
    p_global[i] = p_local[i]; 
  }
#endif // is_mpi

  volume = this->getVolume();


  for(i = 0; i < 3; i++) {
    for (j = 0; j < 3; j++) {
      k = 3*i + j;
      press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
    }
  }
}

void Thermo::velocitize() {
  
  double aVel[3], aJ[3], I[3][3];
  int i, j, l, m, n, vr, vd; // velocity randomizer loop counters
  double vdrift[3];
  double vbar;
  const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
  double av2;
  double kebar;
  double temperature;
  int nobj;

  if (!info->have_target_temp) {
    sprintf( painCave.errMsg,
             "You can't resample the velocities without a targetTemp!\n"
             );
    painCave.isFatal = 1;
    painCave.severity = OOPSE_ERROR;
    simError();
    return;
  }

  nobj = info->integrableObjects.size();
  
  temperature   = info->target_temp;
  
  kebar = kb * temperature * (double)info->ndfRaw / 
    ( 2.0 * (double)info->ndf );
  
  for(vr = 0; vr < nobj; vr++){
    
    // uses equipartition theory to solve for vbar in angstrom/fs

    av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass();
    vbar = sqrt( av2 );

    // picks random velocities from a gaussian distribution
    // centered on vbar

    for (j=0; j<3; j++) 
      aVel[j] = vbar * gaussStream->getGaussian();
    
    info->integrableObjects[vr]->setVel( aVel );
    
    if(info->integrableObjects[vr]->isDirectional()){

      info->integrableObjects[vr]->getI( I );

      if (info->integrableObjects[vr]->isLinear()) {

        l= info->integrableObjects[vr]->linearAxis();
        m = (l+1)%3;
        n = (l+2)%3;

        aJ[l] = 0.0;
        vbar = sqrt( 2.0 * kebar * I[m][m] );
        aJ[m] = vbar * gaussStream->getGaussian();
        vbar = sqrt( 2.0 * kebar * I[n][n] );
        aJ[n] = vbar * gaussStream->getGaussian();
        
      } else {
        for (j = 0 ; j < 3; j++) {
          vbar = sqrt( 2.0 * kebar * I[j][j] );
          aJ[j] = vbar * gaussStream->getGaussian();
        }       
      } // else isLinear

      info->integrableObjects[vr]->setJ( aJ ); 
      
    }//isDirectional 

  }

  // Get the Center of Mass drift velocity.

  getCOMVel(vdrift);
  
  //  Corrects for the center of mass drift.
  // sums all the momentum and divides by total mass.

  for(vd = 0; vd < nobj; vd++){
    
    info->integrableObjects[vd]->getVel(aVel);
    
    for (j=0; j < 3; j++) 
      aVel[j] -= vdrift[j];
        
    info->integrableObjects[vd]->setVel( aVel );
  }

}

void Thermo::getCOMVel(double vdrift[3]){

  double mtot, mtot_local;
  double aVel[3], amass;
  double vdrift_local[3];
  int vd, j;
  int nobj;

  nobj   = info->integrableObjects.size();

  mtot_local = 0.0;
  vdrift_local[0] = 0.0;
  vdrift_local[1] = 0.0;
  vdrift_local[2] = 0.0;
  
  for(vd = 0; vd < nobj; vd++){
    
    amass = info->integrableObjects[vd]->getMass();
    info->integrableObjects[vd]->getVel( aVel );

    for(j = 0; j < 3; j++) 
      vdrift_local[j] += aVel[j] * amass;
    
    mtot_local += amass;
  }

#ifdef IS_MPI
  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
  MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
#else
  mtot = mtot_local;
  for(vd = 0; vd < 3; vd++) {
    vdrift[vd] = vdrift_local[vd];
  }
#endif
    
  for (vd = 0; vd < 3; vd++) {
    vdrift[vd] = vdrift[vd] / mtot;
  }
  
}

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

  double mtot, mtot_local;
  double aPos[3], amass;
  double COM_local[3];
  int i, j;
  int nobj;

  mtot_local = 0.0;
  COM_local[0] = 0.0;
  COM_local[1] = 0.0;
  COM_local[2] = 0.0;

  nobj = info->integrableObjects.size();
  for(i = 0; i < nobj; i++){
    
    amass = info->integrableObjects[i]->getMass();
    info->integrableObjects[i]->getPos( aPos );

    for(j = 0; j < 3; j++) 
      COM_local[j] += aPos[j] * amass;
    
    mtot_local += amass;
  }

#ifdef IS_MPI
  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
  MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
#else
  mtot = mtot_local;
  for(i = 0; i < 3; i++) {
    COM[i] = COM_local[i];
  }
#endif
    
  for (i = 0; i < 3; i++) {
    COM[i] = COM[i] / mtot;
  }
}

void Thermo::removeCOMdrift() {
  double vdrift[3], aVel[3];
  int vd, j, nobj;

  nobj = info->integrableObjects.size();

  // Get the Center of Mass drift velocity.

  getCOMVel(vdrift);
  
  //  Corrects for the center of mass drift.
  // sums all the momentum and divides by total mass.

  for(vd = 0; vd < nobj; vd++){
    
    info->integrableObjects[vd]->getVel(aVel);
    
    for (j=0; j < 3; j++) 
      aVel[j] -= vdrift[j];
        
    info->integrableObjects[vd]->setVel( aVel );
  }
}
Revision:	1492
Committed:	Fri Sep 24 16:27:58 2004 UTC (21 years, 1 month ago) by tim
File size:	9957 byte(s)
Log Message:	change the #include in source files
#	User	Rev	Content
1	gezelter	1490	#include <math.h>
2			#include <iostream>
3			using namespace std;
4
5			#ifdef IS_MPI
6			#include <mpi.h>
7			#endif //is_mpi
8
9	tim	1492	#include "brains/Thermo.hpp"
10			#include "primitives/SRI.hpp"
11			#include "integrators/Integrator.hpp"
12			#include "utils/simError.h"
13			#include "math/MatVec3.h"
14	gezelter	1490
15			#ifdef IS_MPI
16			#define __C
17	tim	1492	#include "brains/mpiSimulation.hpp"
18	gezelter	1490	#endif // is_mpi
19
20			inline double roundMe( double x ){
21			return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
22			}
23
24			Thermo::Thermo( SimInfo* the_info ) {
25			info = the_info;
26			int baseSeed = the_info->getSeed();
27
28			gaussStream = new gaussianSPRNG( baseSeed );
29			}
30
31			Thermo::~Thermo(){
32			delete gaussStream;
33			}
34
35			double Thermo::getKinetic(){
36
37			const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
38			double kinetic;
39			double amass;
40			double aVel[3], aJ[3], I[3][3];
41			int i, j, k, kl;
42
43			double kinetic_global;
44			vector<StuntDouble *> integrableObjects = info->integrableObjects;
45
46			kinetic = 0.0;
47			kinetic_global = 0.0;
48
49			for (kl=0; kl<integrableObjects.size(); kl++) {
50			integrableObjects[kl]->getVel(aVel);
51			amass = integrableObjects[kl]->getMass();
52
53			for(j=0; j<3; j++)
54			kinetic += amassaVel[j]aVel[j];
55
56			if (integrableObjects[kl]->isDirectional()){
57
58			integrableObjects[kl]->getJ( aJ );
59			integrableObjects[kl]->getI( I );
60
61			if (integrableObjects[kl]->isLinear()) {
62			i = integrableObjects[kl]->linearAxis();
63			j = (i+1)%3;
64			k = (i+2)%3;
65			kinetic += aJ[j]aJ[j]/I[j][j] + aJ[k]aJ[k]/I[k][k];
66			} else {
67			for (j=0; j<3; j++)
68			kinetic += aJ[j]*aJ[j] / I[j][j];
69			}
70			}
71			}
72			#ifdef IS_MPI
73			MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
74			MPI_SUM, MPI_COMM_WORLD);
75			kinetic = kinetic_global;
76			#endif //is_mpi
77
78			kinetic = kinetic * 0.5 / e_convert;
79
80			return kinetic;
81			}
82
83			double Thermo::getPotential(){
84
85			double potential_local;
86			double potential;
87			int el, nSRI;
88			Molecule* molecules;
89
90			molecules = info->molecules;
91			nSRI = info->n_SRI;
92
93			potential_local = 0.0;
94			potential = 0.0;
95			potential_local += info->lrPot;
96
97			for( el=0; el<info->n_mol; el++ ){
98			potential_local += molecules[el].getPotential();
99			}
100
101			// Get total potential for entire system from MPI.
102			#ifdef IS_MPI
103			MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE,
104			MPI_SUM, MPI_COMM_WORLD);
105			#else
106			potential = potential_local;
107			#endif // is_mpi
108
109			return potential;
110			}
111
112			double Thermo::getTotalE(){
113
114			double total;
115
116			total = this->getKinetic() + this->getPotential();
117			return total;
118			}
119
120			double Thermo::getTemperature(){
121
122			const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
123			double temperature;
124
125			temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
126			return temperature;
127			}
128
129			double Thermo::getVolume() {
130
131			return info->boxVol;
132			}
133
134			double Thermo::getPressure() {
135
136			// Relies on the calculation of the full molecular pressure tensor
137
138			const double p_convert = 1.63882576e8;
139			double press[3][3];
140			double pressure;
141
142			this->getPressureTensor(press);
143
144			pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
145
146			return pressure;
147			}
148
149			double Thermo::getPressureX() {
150
151			// Relies on the calculation of the full molecular pressure tensor
152
153			const double p_convert = 1.63882576e8;
154			double press[3][3];
155			double pressureX;
156
157			this->getPressureTensor(press);
158
159			pressureX = p_convert * press[0][0];
160
161			return pressureX;
162			}
163
164			double Thermo::getPressureY() {
165
166			// Relies on the calculation of the full molecular pressure tensor
167
168			const double p_convert = 1.63882576e8;
169			double press[3][3];
170			double pressureY;
171
172			this->getPressureTensor(press);
173
174			pressureY = p_convert * press[1][1];
175
176			return pressureY;
177			}
178
179			double Thermo::getPressureZ() {
180
181			// Relies on the calculation of the full molecular pressure tensor
182
183			const double p_convert = 1.63882576e8;
184			double press[3][3];
185			double pressureZ;
186
187			this->getPressureTensor(press);
188
189			pressureZ = p_convert * press[2][2];
190
191			return pressureZ;
192			}
193
194
195			void Thermo::getPressureTensor(double press[3][3]){
196			// returns pressure tensor in units amufs^-2Ang^-1
197			// routine derived via viral theorem description in:
198			// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
199
200			const double e_convert = 4.184e-4;
201
202			double molmass, volume;
203			double vcom[3];
204			double p_local[9], p_global[9];
205			int i, j, k;
206
207			for (i=0; i < 9; i++) {
208			p_local[i] = 0.0;
209			p_global[i] = 0.0;
210			}
211
212			// use velocities of integrableObjects and their masses:
213
214			for (i=0; i < info->integrableObjects.size(); i++) {
215
216			molmass = info->integrableObjects[i]->getMass();
217
218			info->integrableObjects[i]->getVel(vcom);
219
220			p_local[0] += molmass * (vcom[0] * vcom[0]);
221			p_local[1] += molmass * (vcom[0] * vcom[1]);
222			p_local[2] += molmass * (vcom[0] * vcom[2]);
223			p_local[3] += molmass * (vcom[1] * vcom[0]);
224			p_local[4] += molmass * (vcom[1] * vcom[1]);
225			p_local[5] += molmass * (vcom[1] * vcom[2]);
226			p_local[6] += molmass * (vcom[2] * vcom[0]);
227			p_local[7] += molmass * (vcom[2] * vcom[1]);
228			p_local[8] += molmass * (vcom[2] * vcom[2]);
229
230			}
231
232			// Get total for entire system from MPI.
233
234			#ifdef IS_MPI
235			MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
236			#else
237			for (i=0; i<9; i++) {
238			p_global[i] = p_local[i];
239			}
240			#endif // is_mpi
241
242			volume = this->getVolume();
243
244
245
246			for(i = 0; i < 3; i++) {
247			for (j = 0; j < 3; j++) {
248			k = 3*i + j;
249			press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
250			}
251			}
252			}
253
254			void Thermo::velocitize() {
255
256			double aVel[3], aJ[3], I[3][3];
257			int i, j, l, m, n, vr, vd; // velocity randomizer loop counters
258			double vdrift[3];
259			double vbar;
260			const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
261			double av2;
262			double kebar;
263			double temperature;
264			int nobj;
265
266			if (!info->have_target_temp) {
267			sprintf( painCave.errMsg,
268			"You can't resample the velocities without a targetTemp!\n"
269			);
270			painCave.isFatal = 1;
271			painCave.severity = OOPSE_ERROR;
272			simError();
273			return;
274			}
275
276			nobj = info->integrableObjects.size();
277
278			temperature = info->target_temp;
279
280			kebar = kb * temperature * (double)info->ndfRaw /
281			( 2.0 * (double)info->ndf );
282
283			for(vr = 0; vr < nobj; vr++){
284
285			// uses equipartition theory to solve for vbar in angstrom/fs
286
287			av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass();
288			vbar = sqrt( av2 );
289
290			// picks random velocities from a gaussian distribution
291			// centered on vbar
292
293			for (j=0; j<3; j++)
294			aVel[j] = vbar * gaussStream->getGaussian();
295
296			info->integrableObjects[vr]->setVel( aVel );
297
298			if(info->integrableObjects[vr]->isDirectional()){
299
300			info->integrableObjects[vr]->getI( I );
301
302			if (info->integrableObjects[vr]->isLinear()) {
303
304			l= info->integrableObjects[vr]->linearAxis();
305			m = (l+1)%3;
306			n = (l+2)%3;
307
308			aJ[l] = 0.0;
309			vbar = sqrt( 2.0 * kebar * I[m][m] );
310			aJ[m] = vbar * gaussStream->getGaussian();
311			vbar = sqrt( 2.0 * kebar * I[n][n] );
312			aJ[n] = vbar * gaussStream->getGaussian();
313
314			} else {
315			for (j = 0 ; j < 3; j++) {
316			vbar = sqrt( 2.0 * kebar * I[j][j] );
317			aJ[j] = vbar * gaussStream->getGaussian();
318			}
319			} // else isLinear
320
321			info->integrableObjects[vr]->setJ( aJ );
322
323			}//isDirectional
324
325			}
326
327			// Get the Center of Mass drift velocity.
328
329			getCOMVel(vdrift);
330
331			// Corrects for the center of mass drift.
332			// sums all the momentum and divides by total mass.
333
334			for(vd = 0; vd < nobj; vd++){
335
336			info->integrableObjects[vd]->getVel(aVel);
337
338			for (j=0; j < 3; j++)
339			aVel[j] -= vdrift[j];
340
341			info->integrableObjects[vd]->setVel( aVel );
342			}
343
344			}
345
346			void Thermo::getCOMVel(double vdrift[3]){
347
348			double mtot, mtot_local;
349			double aVel[3], amass;
350			double vdrift_local[3];
351			int vd, j;
352			int nobj;
353
354			nobj = info->integrableObjects.size();
355
356			mtot_local = 0.0;
357			vdrift_local[0] = 0.0;
358			vdrift_local[1] = 0.0;
359			vdrift_local[2] = 0.0;
360
361			for(vd = 0; vd < nobj; vd++){
362
363			amass = info->integrableObjects[vd]->getMass();
364			info->integrableObjects[vd]->getVel( aVel );
365
366			for(j = 0; j < 3; j++)
367			vdrift_local[j] += aVel[j] * amass;
368
369			mtot_local += amass;
370			}
371
372			#ifdef IS_MPI
373			MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
374			MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
375			#else
376			mtot = mtot_local;
377			for(vd = 0; vd < 3; vd++) {
378			vdrift[vd] = vdrift_local[vd];
379			}
380			#endif
381
382			for (vd = 0; vd < 3; vd++) {
383			vdrift[vd] = vdrift[vd] / mtot;
384			}
385
386			}
387
388			void Thermo::getCOM(double COM[3]){
389
390			double mtot, mtot_local;
391			double aPos[3], amass;
392			double COM_local[3];
393			int i, j;
394			int nobj;
395
396			mtot_local = 0.0;
397			COM_local[0] = 0.0;
398			COM_local[1] = 0.0;
399			COM_local[2] = 0.0;
400
401			nobj = info->integrableObjects.size();
402			for(i = 0; i < nobj; i++){
403
404			amass = info->integrableObjects[i]->getMass();
405			info->integrableObjects[i]->getPos( aPos );
406
407			for(j = 0; j < 3; j++)
408			COM_local[j] += aPos[j] * amass;
409
410			mtot_local += amass;
411			}
412
413			#ifdef IS_MPI
414			MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
415			MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
416			#else
417			mtot = mtot_local;
418			for(i = 0; i < 3; i++) {
419			COM[i] = COM_local[i];
420			}
421			#endif
422
423			for (i = 0; i < 3; i++) {
424			COM[i] = COM[i] / mtot;
425			}
426			}
427
428			void Thermo::removeCOMdrift() {
429			double vdrift[3], aVel[3];
430			int vd, j, nobj;
431
432			nobj = info->integrableObjects.size();
433
434			// Get the Center of Mass drift velocity.
435
436			getCOMVel(vdrift);
437
438			// Corrects for the center of mass drift.
439			// sums all the momentum and divides by total mass.
440
441			for(vd = 0; vd < nobj; vd++){
442
443			info->integrableObjects[vd]->getVel(aVel);
444
445			for (j=0; j < 3; j++)
446			aVel[j] -= vdrift[j];
447
448			info->integrableObjects[vd]->setVel( aVel );
449			}
450			}