OOPSE/libmdtools/Thermo.cpp

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

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

#include "Thermo.hpp"
#include "SRI.hpp"
#include "Integrator.hpp"
#include "simError.h"

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

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 j, 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 );

      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, nMols;
  Molecule* molecules;

  nMols = info->n_mol;
  molecules = info->molecules;
  //tau = info->tau;

  // use velocities of molecular centers of mass and molecular masses:
  for (i=0; i < 9; i++) {    
    p_local[i] = 0.0;
    p_global[i] = 0.0;
  }

  for (i=0; i < nMols; i++) {
    molmass = molecules[i].getCOMvel(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, 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;
  int n_atoms;
  Atom** atoms;
  DirectionalAtom* dAtom;
  double temperature;
  int n_oriented;
  int n_constraints;

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

    av2 = 2.0 * kebar / atoms[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();
    
    atoms[vr]->setVel( aVel );

  }

  // 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 < n_atoms; vd++){
    
    atoms[vd]->getVel(aVel);
    
    for (j=0; j < 3; j++) 
      aVel[j] -= vdrift[j];
        
    atoms[vd]->setVel( aVel );
  }
  if( n_oriented ){
  
    for( i=0; i<n_atoms; i++ ){
      
      if( atoms[i]->isDirectional() ){
        
        dAtom = (DirectionalAtom *)atoms[i];
        dAtom->getI( I );
        
        for (j = 0 ; j < 3; j++) {

          vbar = sqrt( 2.0 * kebar * I[j][j] );
          aJ[j] = vbar * gaussStream->getGaussian();

        }       

        dAtom->setJ( aJ );

      }
    }   
  }
}

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

  double mtot, mtot_local;
  double aVel[3], amass;
  double vdrift_local[3];
  int vd, n_atoms, j;
  Atom** atoms;

  // We are very careless here with the distinction between n_atoms and n_local
  // We should really fix this before someone pokes an eye out.

  n_atoms = info->n_atoms;  
  atoms   = info->atoms;

  mtot_local = 0.0;
  vdrift_local[0] = 0.0;
  vdrift_local[1] = 0.0;
  vdrift_local[2] = 0.0;
  
  for(vd = 0; vd < n_atoms; vd++){
    
    amass = atoms[vd]->getMass();
    atoms[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, n_atoms, j;
  Atom** atoms;

  // We are very careless here with the distinction between n_atoms and n_local
  // We should really fix this before someone pokes an eye out.

  n_atoms = info->n_atoms;  
  atoms   = info->atoms;

  mtot_local = 0.0;
  COM_local[0] = 0.0;
  COM_local[1] = 0.0;
  COM_local[2] = 0.0;
  
  for(i = 0; i < n_atoms; i++){
    
    amass = atoms[i]->getMass();
    atoms[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;
  }
}
Revision:	1113
Committed:	Thu Apr 15 16:18:26 2004 UTC (20 years, 5 months ago) by tim
File size:	8842 byte(s)
Log Message:	fix whole bunch of bugs :-)
#	User	Rev	Content
1	gezelter	829	#include <math.h>
2	mmeineke	377	#include <iostream>
3			using namespace std;
4
5			#ifdef IS_MPI
6			#include <mpi.h>
7			#endif //is_mpi
8
9			#include "Thermo.hpp"
10			#include "SRI.hpp"
11			#include "Integrator.hpp"
12	chuckv	438	#include "simError.h"
13	mmeineke	402
14			#ifdef IS_MPI
15	chuckv	401	#define __C
16	mmeineke	402	#include "mpiSimulation.hpp"
17			#endif // is_mpi
18	mmeineke	377
19	mmeineke	614	Thermo::Thermo( SimInfo* the_info ) {
20			info = the_info;
21	tim	708	int baseSeed = the_info->getSeed();
22	mmeineke	377
23			gaussStream = new gaussianSPRNG( baseSeed );
24			}
25
26			Thermo::~Thermo(){
27			delete gaussStream;
28			}
29
30			double Thermo::getKinetic(){
31
32			const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
33	gezelter	608	double kinetic;
34			double amass;
35			double aVel[3], aJ[3], I[3][3];
36			int j, kl;
37	mmeineke	377
38			double kinetic_global;
39	tim	1113	vector<StuntDouble *> integrableObjects = info->integrableObjects;
40	mmeineke	377
41			kinetic = 0.0;
42			kinetic_global = 0.0;
43
44	tim	1113	for (kl=0; kl<integrableObjects.size(); kl++) {
45			integrableObjects[kl]->getVel(aVel);
46			amass = integrableObjects[kl]->getMass();
47	gezelter	608
48	tim	1113	for(j=0; j<3; j++)
49			kinetic += amassaVel[j]aVel[j];
50
51			if (integrableObjects[kl]->isDirectional()){
52
53			integrableObjects[kl]->getJ( aJ );
54			integrableObjects[kl]->getI( I );
55
56	gezelter	608	for (j=0; j<3; j++)
57			kinetic += aJ[j]*aJ[j] / I[j][j];
58	mmeineke	377
59			}
60			}
61			#ifdef IS_MPI
62	mmeineke	447	MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
63			MPI_SUM, MPI_COMM_WORLD);
64	mmeineke	377	kinetic = kinetic_global;
65			#endif //is_mpi
66
67			kinetic = kinetic * 0.5 / e_convert;
68
69			return kinetic;
70			}
71
72			double Thermo::getPotential(){
73
74	chuckv	401	double potential_local;
75	mmeineke	377	double potential;
76			int el, nSRI;
77	mmeineke	428	Molecule* molecules;
78	mmeineke	377
79	mmeineke	614	molecules = info->molecules;
80			nSRI = info->n_SRI;
81	mmeineke	377
82	chuckv	401	potential_local = 0.0;
83	chuckv	438	potential = 0.0;
84	mmeineke	614	potential_local += info->lrPot;
85	mmeineke	377
86	mmeineke	614	for( el=0; el<info->n_mol; el++ ){
87	mmeineke	428	potential_local += molecules[el].getPotential();
88	mmeineke	377	}
89
90			// Get total potential for entire system from MPI.
91			#ifdef IS_MPI
92	mmeineke	447	MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE,
93			MPI_SUM, MPI_COMM_WORLD);
94	chuckv	401	#else
95			potential = potential_local;
96	mmeineke	377	#endif // is_mpi
97
98			return potential;
99			}
100
101			double Thermo::getTotalE(){
102
103			double total;
104
105			total = this->getKinetic() + this->getPotential();
106			return total;
107			}
108
109	gezelter	454	double Thermo::getTemperature(){
110
111	tim	763	const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
112	gezelter	454	double temperature;
113	tim	1113
114	mmeineke	614	temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
115	mmeineke	377	return temperature;
116			}
117
118	gezelter	484	double Thermo::getVolume() {
119	gezelter	574
120	mmeineke	614	return info->boxVol;
121	gezelter	484	}
122
123	gezelter	483	double Thermo::getPressure() {
124	gezelter	574
125	gezelter	483	// Relies on the calculation of the full molecular pressure tensor
126
127			const double p_convert = 1.63882576e8;
128	gezelter	588	double press[3][3];
129	gezelter	483	double pressure;
130
131			this->getPressureTensor(press);
132
133	gezelter	588	pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
134	gezelter	483
135			return pressure;
136			}
137
138	mmeineke	755	double Thermo::getPressureX() {
139	gezelter	483
140	mmeineke	755	// Relies on the calculation of the full molecular pressure tensor
141
142			const double p_convert = 1.63882576e8;
143			double press[3][3];
144			double pressureX;
145
146			this->getPressureTensor(press);
147
148			pressureX = p_convert * press[0][0];
149
150			return pressureX;
151			}
152
153			double Thermo::getPressureY() {
154
155			// Relies on the calculation of the full molecular pressure tensor
156
157			const double p_convert = 1.63882576e8;
158			double press[3][3];
159			double pressureY;
160
161			this->getPressureTensor(press);
162
163			pressureY = p_convert * press[1][1];
164
165			return pressureY;
166			}
167
168			double Thermo::getPressureZ() {
169
170			// Relies on the calculation of the full molecular pressure tensor
171
172			const double p_convert = 1.63882576e8;
173			double press[3][3];
174			double pressureZ;
175
176			this->getPressureTensor(press);
177
178			pressureZ = p_convert * press[2][2];
179
180			return pressureZ;
181			}
182
183
184	gezelter	588	void Thermo::getPressureTensor(double press[3][3]){
185	gezelter	483	// returns pressure tensor in units amufs^-2Ang^-1
186	gezelter	445	// routine derived via viral theorem description in:
187			// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
188	mmeineke	377
189	gezelter	477	const double e_convert = 4.184e-4;
190	gezelter	483
191			double molmass, volume;
192	gezelter	468	double vcom[3];
193	gezelter	483	double p_local[9], p_global[9];
194	mmeineke	614	int i, j, k, nMols;
195	gezelter	468	Molecule* molecules;
196
197	mmeineke	614	nMols = info->n_mol;
198			molecules = info->molecules;
199			//tau = info->tau;
200	gezelter	468
201			// use velocities of molecular centers of mass and molecular masses:
202	gezelter	483	for (i=0; i < 9; i++) {
203			p_local[i] = 0.0;
204			p_global[i] = 0.0;
205			}
206	gezelter	475
207	gezelter	468	for (i=0; i < nMols; i++) {
208	gezelter	475	molmass = molecules[i].getCOMvel(vcom);
209	gezelter	483
210			p_local[0] += molmass * (vcom[0] * vcom[0]);
211			p_local[1] += molmass * (vcom[0] * vcom[1]);
212			p_local[2] += molmass * (vcom[0] * vcom[2]);
213			p_local[3] += molmass * (vcom[1] * vcom[0]);
214			p_local[4] += molmass * (vcom[1] * vcom[1]);
215			p_local[5] += molmass * (vcom[1] * vcom[2]);
216			p_local[6] += molmass * (vcom[2] * vcom[0]);
217			p_local[7] += molmass * (vcom[2] * vcom[1]);
218			p_local[8] += molmass * (vcom[2] * vcom[2]);
219	gezelter	468	}
220
221			// Get total for entire system from MPI.
222	chuckv	479
223	gezelter	468	#ifdef IS_MPI
224	gezelter	483	MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
225	gezelter	468	#else
226	gezelter	483	for (i=0; i<9; i++) {
227			p_global[i] = p_local[i];
228			}
229	gezelter	468	#endif // is_mpi
230
231	gezelter	611	volume = this->getVolume();
232	gezelter	468
233	gezelter	588	for(i = 0; i < 3; i++) {
234			for (j = 0; j < 3; j++) {
235			k = 3*i + j;
236	mmeineke	614	press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
237
238	gezelter	588	}
239	gezelter	483	}
240	mmeineke	377	}
241
242			void Thermo::velocitize() {
243
244	gezelter	608	double aVel[3], aJ[3], I[3][3];
245			int i, j, vr, vd; // velocity randomizer loop counters
246	chuckv	403	double vdrift[3];
247	mmeineke	377	double vbar;
248			const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
249			double av2;
250			double kebar;
251			int n_atoms;
252			Atom** atoms;
253			DirectionalAtom* dAtom;
254			double temperature;
255			int n_oriented;
256			int n_constraints;
257
258	mmeineke	614	atoms = info->atoms;
259			n_atoms = info->n_atoms;
260			temperature = info->target_temp;
261			n_oriented = info->n_oriented;
262			n_constraints = info->n_constraints;
263	mmeineke	377
264	tim	763	kebar = kb * temperature * (double)info->ndfRaw /
265			( 2.0 * (double)info->ndf );
266	chuckv	403
267	mmeineke	377	for(vr = 0; vr < n_atoms; vr++){
268
269			// uses equipartition theory to solve for vbar in angstrom/fs
270
271			av2 = 2.0 * kebar / atoms[vr]->getMass();
272			vbar = sqrt( av2 );
273	mmeineke	853
274	mmeineke	377	// picks random velocities from a gaussian distribution
275			// centered on vbar
276
277	gezelter	608	for (j=0; j<3; j++)
278			aVel[j] = vbar * gaussStream->getGaussian();
279
280			atoms[vr]->setVel( aVel );
281	mmeineke	377
282			}
283	chuckv	401
284			// Get the Center of Mass drift velocity.
285
286	chuckv	403	getCOMVel(vdrift);
287	mmeineke	377
288			// Corrects for the center of mass drift.
289			// sums all the momentum and divides by total mass.
290
291			for(vd = 0; vd < n_atoms; vd++){
292
293	gezelter	608	atoms[vd]->getVel(aVel);
294
295			for (j=0; j < 3; j++)
296			aVel[j] -= vdrift[j];
297	chuckv	401
298	gezelter	608	atoms[vd]->setVel( aVel );
299	mmeineke	377	}
300			if( n_oriented ){
301
302			for( i=0; i<n_atoms; i++ ){
303
304			if( atoms[i]->isDirectional() ){
305
306			dAtom = (DirectionalAtom *)atoms[i];
307	gezelter	608	dAtom->getI( I );
308
309			for (j = 0 ; j < 3; j++) {
310	mmeineke	377
311	gezelter	608	vbar = sqrt( 2.0 * kebar * I[j][j] );
312			aJ[j] = vbar * gaussStream->getGaussian();
313	mmeineke	377
314	gezelter	608	}
315
316			dAtom->setJ( aJ );
317
318	mmeineke	377	}
319			}
320			}
321			}
322	chuckv	401
323	chuckv	403	void Thermo::getCOMVel(double vdrift[3]){
324	chuckv	401
325			double mtot, mtot_local;
326	gezelter	608	double aVel[3], amass;
327	chuckv	401	double vdrift_local[3];
328	gezelter	608	int vd, n_atoms, j;
329	chuckv	401	Atom** atoms;
330
331			// We are very careless here with the distinction between n_atoms and n_local
332			// We should really fix this before someone pokes an eye out.
333
334	mmeineke	614	n_atoms = info->n_atoms;
335			atoms = info->atoms;
336	chuckv	401
337			mtot_local = 0.0;
338			vdrift_local[0] = 0.0;
339			vdrift_local[1] = 0.0;
340			vdrift_local[2] = 0.0;
341
342			for(vd = 0; vd < n_atoms; vd++){
343
344	gezelter	608	amass = atoms[vd]->getMass();
345			atoms[vd]->getVel( aVel );
346
347			for(j = 0; j < 3; j++)
348			vdrift_local[j] += aVel[j] * amass;
349	chuckv	401
350	gezelter	608	mtot_local += amass;
351	chuckv	401	}
352
353			#ifdef IS_MPI
354	mmeineke	447	MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
355			MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
356	chuckv	401	#else
357			mtot = mtot_local;
358			for(vd = 0; vd < 3; vd++) {
359			vdrift[vd] = vdrift_local[vd];
360			}
361			#endif
362
363			for (vd = 0; vd < 3; vd++) {
364			vdrift[vd] = vdrift[vd] / mtot;
365			}
366
367			}
368
369	tim	763	void Thermo::getCOM(double COM[3]){
370
371			double mtot, mtot_local;
372			double aPos[3], amass;
373			double COM_local[3];
374			int i, n_atoms, j;
375			Atom** atoms;
376
377			// We are very careless here with the distinction between n_atoms and n_local
378			// We should really fix this before someone pokes an eye out.
379
380			n_atoms = info->n_atoms;
381			atoms = info->atoms;
382
383			mtot_local = 0.0;
384			COM_local[0] = 0.0;
385			COM_local[1] = 0.0;
386			COM_local[2] = 0.0;
387
388			for(i = 0; i < n_atoms; i++){
389
390			amass = atoms[i]->getMass();
391			atoms[i]->getPos( aPos );
392
393			for(j = 0; j < 3; j++)
394			COM_local[j] += aPos[j] * amass;
395
396			mtot_local += amass;
397			}
398
399			#ifdef IS_MPI
400			MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
401			MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
402			#else
403			mtot = mtot_local;
404			for(i = 0; i < 3; i++) {
405			COM[i] = COM_local[i];
406			}
407			#endif
408
409			for (i = 0; i < 3; i++) {
410			COM[i] = COM[i] / mtot;
411			}
412			}