OOPSE/libmdtools/Thermo.cpp

#include <cmath>
#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;

  DirectionalAtom *dAtom;

  int n_atoms;
  double kinetic_global;
  Atom** atoms;

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

  kinetic = 0.0;
  kinetic_global = 0.0;
  for( kl=0; kl < n_atoms; kl++ ){
    
    atoms[kl]->getVel(aVel);
    amass = atoms[kl]->getMass();
    
    for (j=0; j < 3; j++) 
      kinetic += amass * aVel[j] * aVel[j];

    if( atoms[kl]->isDirectional() ){
            
      dAtom = (DirectionalAtom *)atoms[kl];

      dAtom->getJ( aJ );
      dAtom->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

#ifdef IS_MPI
  /*
  std::cerr << "node " << worldRank << ": after pot = " << potential << "\n";
  */
#endif

  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 );
 
//     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
    
    // 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:	799
Committed:	Fri Oct 3 22:11:53 2003 UTC (20 years, 9 months ago) by mmeineke
File size:	9068 byte(s)
Log Message:	removed entahlpy from the statwriter and thermo.
#	User	Rev	Content
1	mmeineke	377	#include <cmath>
2			#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			DirectionalAtom *dAtom;
39
40			int n_atoms;
41			double kinetic_global;
42			Atom** atoms;
43
44
45	mmeineke	614	n_atoms = info->n_atoms;
46			atoms = info->atoms;
47	mmeineke	377
48			kinetic = 0.0;
49			kinetic_global = 0.0;
50			for( kl=0; kl < n_atoms; kl++ ){
51	gezelter	608
52			atoms[kl]->getVel(aVel);
53			amass = atoms[kl]->getMass();
54
55			for (j=0; j < 3; j++)
56			kinetic += amass * aVel[j] * aVel[j];
57	mmeineke	377
58			if( atoms[kl]->isDirectional() ){
59
60			dAtom = (DirectionalAtom *)atoms[kl];
61	gezelter	608
62			dAtom->getJ( aJ );
63			dAtom->getI( I );
64	mmeineke	377
65	gezelter	608	for (j=0; j<3; j++)
66			kinetic += aJ[j]*aJ[j] / I[j][j];
67	mmeineke	377
68			}
69			}
70			#ifdef IS_MPI
71	mmeineke	447	MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
72			MPI_SUM, MPI_COMM_WORLD);
73	mmeineke	377	kinetic = kinetic_global;
74			#endif //is_mpi
75
76			kinetic = kinetic * 0.5 / e_convert;
77
78			return kinetic;
79			}
80
81			double Thermo::getPotential(){
82
83	chuckv	401	double potential_local;
84	mmeineke	377	double potential;
85			int el, nSRI;
86	mmeineke	428	Molecule* molecules;
87	mmeineke	377
88	mmeineke	614	molecules = info->molecules;
89			nSRI = info->n_SRI;
90	mmeineke	377
91	chuckv	401	potential_local = 0.0;
92	chuckv	438	potential = 0.0;
93	mmeineke	614	potential_local += info->lrPot;
94	mmeineke	377
95	mmeineke	614	for( el=0; el<info->n_mol; el++ ){
96	mmeineke	428	potential_local += molecules[el].getPotential();
97	mmeineke	377	}
98
99			// Get total potential for entire system from MPI.
100			#ifdef IS_MPI
101	mmeineke	447	MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE,
102			MPI_SUM, MPI_COMM_WORLD);
103	chuckv	401	#else
104			potential = potential_local;
105	mmeineke	377	#endif // is_mpi
106
107	chuckv	438	#ifdef IS_MPI
108			/*
109			std::cerr << "node " << worldRank << ": after pot = " << potential << "\n";
110			*/
111			#endif
112
113	mmeineke	377	return potential;
114			}
115
116			double Thermo::getTotalE(){
117
118			double total;
119
120			total = this->getKinetic() + this->getPotential();
121			return total;
122			}
123
124	gezelter	454	double Thermo::getTemperature(){
125
126	tim	763	const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
127	gezelter	454	double temperature;
128
129	mmeineke	614	temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
130	mmeineke	377	return temperature;
131			}
132
133	gezelter	484	double Thermo::getVolume() {
134	gezelter	574
135	mmeineke	614	return info->boxVol;
136	gezelter	484	}
137
138	gezelter	483	double Thermo::getPressure() {
139	gezelter	574
140	gezelter	483	// Relies on the calculation of the full molecular pressure tensor
141
142			const double p_convert = 1.63882576e8;
143	gezelter	588	double press[3][3];
144	gezelter	483	double pressure;
145
146			this->getPressureTensor(press);
147
148	gezelter	588	pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
149	gezelter	483
150			return pressure;
151			}
152
153	mmeineke	755	double Thermo::getPressureX() {
154	gezelter	483
155	mmeineke	755	// 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 pressureX;
160
161			this->getPressureTensor(press);
162
163			pressureX = p_convert * press[0][0];
164
165			return pressureX;
166			}
167
168			double Thermo::getPressureY() {
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 pressureY;
175
176			this->getPressureTensor(press);
177
178			pressureY = p_convert * press[1][1];
179
180			return pressureY;
181			}
182
183			double Thermo::getPressureZ() {
184
185			// Relies on the calculation of the full molecular pressure tensor
186
187			const double p_convert = 1.63882576e8;
188			double press[3][3];
189			double pressureZ;
190
191			this->getPressureTensor(press);
192
193			pressureZ = p_convert * press[2][2];
194
195			return pressureZ;
196			}
197
198
199	gezelter	588	void Thermo::getPressureTensor(double press[3][3]){
200	gezelter	483	// returns pressure tensor in units amufs^-2Ang^-1
201	gezelter	445	// routine derived via viral theorem description in:
202			// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
203	mmeineke	377
204	gezelter	477	const double e_convert = 4.184e-4;
205	gezelter	483
206			double molmass, volume;
207	gezelter	468	double vcom[3];
208	gezelter	483	double p_local[9], p_global[9];
209	mmeineke	614	int i, j, k, nMols;
210	gezelter	468	Molecule* molecules;
211
212	mmeineke	614	nMols = info->n_mol;
213			molecules = info->molecules;
214			//tau = info->tau;
215	gezelter	468
216			// use velocities of molecular centers of mass and molecular masses:
217	gezelter	483	for (i=0; i < 9; i++) {
218			p_local[i] = 0.0;
219			p_global[i] = 0.0;
220			}
221	gezelter	475
222	gezelter	468	for (i=0; i < nMols; i++) {
223	gezelter	475	molmass = molecules[i].getCOMvel(vcom);
224	gezelter	483
225			p_local[0] += molmass * (vcom[0] * vcom[0]);
226			p_local[1] += molmass * (vcom[0] * vcom[1]);
227			p_local[2] += molmass * (vcom[0] * vcom[2]);
228			p_local[3] += molmass * (vcom[1] * vcom[0]);
229			p_local[4] += molmass * (vcom[1] * vcom[1]);
230			p_local[5] += molmass * (vcom[1] * vcom[2]);
231			p_local[6] += molmass * (vcom[2] * vcom[0]);
232			p_local[7] += molmass * (vcom[2] * vcom[1]);
233			p_local[8] += molmass * (vcom[2] * vcom[2]);
234	gezelter	468	}
235
236			// Get total for entire system from MPI.
237	chuckv	479
238	gezelter	468	#ifdef IS_MPI
239	gezelter	483	MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
240	gezelter	468	#else
241	gezelter	483	for (i=0; i<9; i++) {
242			p_global[i] = p_local[i];
243			}
244	gezelter	468	#endif // is_mpi
245
246	gezelter	611	volume = this->getVolume();
247	gezelter	468
248	gezelter	588	for(i = 0; i < 3; i++) {
249			for (j = 0; j < 3; j++) {
250			k = 3*i + j;
251	mmeineke	614	press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
252
253	gezelter	588	}
254	gezelter	483	}
255	mmeineke	377	}
256
257			void Thermo::velocitize() {
258
259	gezelter	608	double aVel[3], aJ[3], I[3][3];
260			int i, j, vr, vd; // velocity randomizer loop counters
261	chuckv	403	double vdrift[3];
262	mmeineke	377	double vbar;
263			const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
264			double av2;
265			double kebar;
266			int n_atoms;
267			Atom** atoms;
268			DirectionalAtom* dAtom;
269			double temperature;
270			int n_oriented;
271			int n_constraints;
272
273	mmeineke	614	atoms = info->atoms;
274			n_atoms = info->n_atoms;
275			temperature = info->target_temp;
276			n_oriented = info->n_oriented;
277			n_constraints = info->n_constraints;
278	mmeineke	377
279	tim	763	kebar = kb * temperature * (double)info->ndfRaw /
280			( 2.0 * (double)info->ndf );
281	chuckv	403
282	mmeineke	377	for(vr = 0; vr < n_atoms; vr++){
283
284			// uses equipartition theory to solve for vbar in angstrom/fs
285
286			av2 = 2.0 * kebar / atoms[vr]->getMass();
287			vbar = sqrt( av2 );
288	gezelter	444
289	mmeineke	377	// vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
290
291			// picks random velocities from a gaussian distribution
292			// centered on vbar
293
294	gezelter	608	for (j=0; j<3; j++)
295			aVel[j] = vbar * gaussStream->getGaussian();
296
297			atoms[vr]->setVel( aVel );
298	mmeineke	377
299			}
300	chuckv	401
301			// Get the Center of Mass drift velocity.
302
303	chuckv	403	getCOMVel(vdrift);
304	mmeineke	377
305			// Corrects for the center of mass drift.
306			// sums all the momentum and divides by total mass.
307
308			for(vd = 0; vd < n_atoms; vd++){
309
310	gezelter	608	atoms[vd]->getVel(aVel);
311
312			for (j=0; j < 3; j++)
313			aVel[j] -= vdrift[j];
314	chuckv	401
315	gezelter	608	atoms[vd]->setVel( aVel );
316	mmeineke	377	}
317			if( n_oriented ){
318
319			for( i=0; i<n_atoms; i++ ){
320
321			if( atoms[i]->isDirectional() ){
322
323			dAtom = (DirectionalAtom *)atoms[i];
324	gezelter	608	dAtom->getI( I );
325
326			for (j = 0 ; j < 3; j++) {
327	mmeineke	377
328	gezelter	608	vbar = sqrt( 2.0 * kebar * I[j][j] );
329			aJ[j] = vbar * gaussStream->getGaussian();
330	mmeineke	377
331	gezelter	608	}
332
333			dAtom->setJ( aJ );
334
335	mmeineke	377	}
336			}
337			}
338			}
339	chuckv	401
340	chuckv	403	void Thermo::getCOMVel(double vdrift[3]){
341	chuckv	401
342			double mtot, mtot_local;
343	gezelter	608	double aVel[3], amass;
344	chuckv	401	double vdrift_local[3];
345	gezelter	608	int vd, n_atoms, j;
346	chuckv	401	Atom** atoms;
347
348			// We are very careless here with the distinction between n_atoms and n_local
349			// We should really fix this before someone pokes an eye out.
350
351	mmeineke	614	n_atoms = info->n_atoms;
352			atoms = info->atoms;
353	chuckv	401
354			mtot_local = 0.0;
355			vdrift_local[0] = 0.0;
356			vdrift_local[1] = 0.0;
357			vdrift_local[2] = 0.0;
358
359			for(vd = 0; vd < n_atoms; vd++){
360
361	gezelter	608	amass = atoms[vd]->getMass();
362			atoms[vd]->getVel( aVel );
363
364			for(j = 0; j < 3; j++)
365			vdrift_local[j] += aVel[j] * amass;
366	chuckv	401
367	gezelter	608	mtot_local += amass;
368	chuckv	401	}
369
370			#ifdef IS_MPI
371	mmeineke	447	MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
372			MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
373	chuckv	401	#else
374			mtot = mtot_local;
375			for(vd = 0; vd < 3; vd++) {
376			vdrift[vd] = vdrift_local[vd];
377			}
378			#endif
379
380			for (vd = 0; vd < 3; vd++) {
381			vdrift[vd] = vdrift[vd] / mtot;
382			}
383
384			}
385
386	tim	763	void Thermo::getCOM(double COM[3]){
387
388			double mtot, mtot_local;
389			double aPos[3], amass;
390			double COM_local[3];
391			int i, n_atoms, j;
392			Atom** atoms;
393
394			// We are very careless here with the distinction between n_atoms and n_local
395			// We should really fix this before someone pokes an eye out.
396
397			n_atoms = info->n_atoms;
398			atoms = info->atoms;
399
400			mtot_local = 0.0;
401			COM_local[0] = 0.0;
402			COM_local[1] = 0.0;
403			COM_local[2] = 0.0;
404
405			for(i = 0; i < n_atoms; i++){
406
407			amass = atoms[i]->getMass();
408			atoms[i]->getPos( aPos );
409
410			for(j = 0; j < 3; j++)
411			COM_local[j] += aPos[j] * amass;
412
413			mtot_local += amass;
414			}
415
416			#ifdef IS_MPI
417			MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
418			MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
419			#else
420			mtot = mtot_local;
421			for(i = 0; i < 3; i++) {
422			COM[i] = COM_local[i];
423			}
424			#endif
425
426			for (i = 0; i < 3; i++) {
427			COM[i] = COM[i] / mtot;
428			}
429			}