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root/OpenMD/branches/development/src/brains/Thermo.cpp

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trunk/src/brains/Thermo.cpp (file contents), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/brains/Thermo.cpp (file contents), Revision 1715 by gezelter, Tue May 22 21:55:31 2012 UTC

#	Line 1 | Line 1
1	+	/*
2	+	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	+	*
4	+	* The University of Notre Dame grants you ("Licensee") a
5	+	* non-exclusive, royalty free, license to use, modify and
6	+	* redistribute this software in source and binary code form, provided
7	+	* that the following conditions are met:
8	+	*
9	+	* 1. Redistributions of source code must retain the above copyright
10	+	*    notice, this list of conditions and the following disclaimer.
11	+	*
12	+	* 2. Redistributions in binary form must reproduce the above copyright
13	+	*    notice, this list of conditions and the following disclaimer in the
14	+	*    documentation and/or other materials provided with the
15	+	*    distribution.
16	+	*
17	+	* This software is provided "AS IS," without a warranty of any
18	+	* kind. All express or implied conditions, representations and
19	+	* warranties, including any implied warranty of merchantability,
20	+	* fitness for a particular purpose or non-infringement, are hereby
21	+	* excluded.  The University of Notre Dame and its licensors shall not
22	+	* be liable for any damages suffered by licensee as a result of
23	+	* using, modifying or distributing the software or its
24	+	* derivatives. In no event will the University of Notre Dame or its
25	+	* licensors be liable for any lost revenue, profit or data, or for
26	+	* direct, indirect, special, consequential, incidental or punitive
27	+	* damages, however caused and regardless of the theory of liability,
28	+	* arising out of the use of or inability to use software, even if the
29	+	* University of Notre Dame has been advised of the possibility of
30	+	* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	+	*/
42	+
43		#include <math.h>
44		#include <iostream>
3	–	using namespace std;
45
46		#ifdef IS_MPI
47		#include <mpi.h>
48		#endif //is_mpi
49
50		#include "brains/Thermo.hpp"
51	<	#include "primitives/SRI.hpp"
11	<	#include "integrators/Integrator.hpp"
51	>	#include "primitives/Molecule.hpp"
52		#include "utils/simError.h"
53	<	#include "math/MatVec3.h"
53	>	#include "utils/PhysicalConstants.hpp"
54	>	#include "types/MultipoleAdapter.hpp"
55
56	+	namespace OpenMD {
57	+
58	+	RealType Thermo::getKinetic() {
59	+	SimInfo::MoleculeIterator miter;
60	+	std::vector<StuntDouble*>::iterator iiter;
61	+	Molecule* mol;
62	+	StuntDouble* integrableObject;
63	+	Vector3d vel;
64	+	Vector3d angMom;
65	+	Mat3x3d I;
66	+	int i;
67	+	int j;
68	+	int k;
69	+	RealType mass;
70	+	RealType kinetic = 0.0;
71	+	RealType kinetic_global = 0.0;
72	+
73	+	for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
74	+	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
75	+	integrableObject = mol->nextIntegrableObject(iiter)) {
76	+
77	+	mass = integrableObject->getMass();
78	+	vel = integrableObject->getVel();
79	+
80	+	kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
81	+
82	+	if (integrableObject->isDirectional()) {
83	+	angMom = integrableObject->getJ();
84	+	I = integrableObject->getI();
85	+
86	+	if (integrableObject->isLinear()) {
87	+	i = integrableObject->linearAxis();
88	+	j = (i + 1) % 3;
89	+	k = (i + 2) % 3;
90	+	kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
91	+	} else {
92	+	kinetic += angMom[0]*angMom[0]/I(0, 0) + angMom[1]*angMom[1]/I(1, 1)
93	+	+ angMom[2]*angMom[2]/I(2, 2);
94	+	}
95	+	}
96	+
97	+	}
98	+	}
99	+
100		#ifdef IS_MPI
16	–	#define __C
17	–	#include "brains/mpiSimulation.hpp"
18	–	#endif // is_mpi
101
102	<	inline double roundMe( double x ){
103	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
104	<	}
102	>	MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
103	>	MPI_COMM_WORLD);
104	>	kinetic = kinetic_global;
105
106	<	Thermo::Thermo( SimInfo* the_info ) {
25	<	info = the_info;
26	<	int baseSeed = the_info->getSeed();
27	<
28	<	gaussStream = new gaussianSPRNG( baseSeed );
29	<	}
106	>	#endif //is_mpi
107
108	<	Thermo::~Thermo(){
32	<	delete gaussStream;
33	<	}
108	>	kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
109
110	<	double Thermo::getKinetic(){
110	>	return kinetic;
111	>	}
112
113	<	const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
114	<	double kinetic;
115	<	double amass;
116	<	double aVel[3], aJ[3], I[3][3];
41	<	int i, j, k, kl;
113	>	RealType Thermo::getPotential() {
114	>	RealType potential = 0.0;
115	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
116	>	RealType shortRangePot_local =  curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
117
118	<	double kinetic_global;
44	<	vector<StuntDouble *> integrableObjects = info->integrableObjects;
45	<
46	<	kinetic = 0.0;
47	<	kinetic_global = 0.0;
118	>	// Get total potential for entire system from MPI.
119
120	<	for (kl=0; kl<integrableObjects.size(); kl++) {
50	<	integrableObjects[kl]->getVel(aVel);
51	<	amass = integrableObjects[kl]->getMass();
120	>	#ifdef IS_MPI
121
122	<	for(j=0; j<3; j++)
123	<	kinetic += amass*aVel[j]*aVel[j];
122	>	MPI_Allreduce(&shortRangePot_local, &potential, 1, MPI_REALTYPE, MPI_SUM,
123	>	MPI_COMM_WORLD);
124	>	potential += curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
125
126	<	if (integrableObjects[kl]->isDirectional()){
57	<
58	<	integrableObjects[kl]->getJ( aJ );
59	<	integrableObjects[kl]->getI( I );
126	>	#else
127
128	<	if (integrableObjects[kl]->isLinear()) {
129	<	i = integrableObjects[kl]->linearAxis();
130	<	j = (i+1)%3;
131	<	k = (i+2)%3;
132	<	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	<	}
128	>	potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
129	>
130	>	#endif // is_mpi
131	>
132	>	return potential;
133		}
134	+
135	+	RealType Thermo::getTotalE() {
136	+	RealType total;
137	+
138	+	total = this->getKinetic() + this->getPotential();
139	+	return total;
140	+	}
141	+
142	+	RealType Thermo::getTemperature() {
143	+
144	+	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
145	+	return temperature;
146	+	}
147	+
148	+	RealType Thermo::getElectronicTemperature() {
149	+	SimInfo::MoleculeIterator miter;
150	+	std::vector<Atom*>::iterator iiter;
151	+	Molecule* mol;
152	+	Atom* atom;
153	+	RealType cvel;
154	+	RealType cmass;
155	+	RealType kinetic = 0.0;
156	+	RealType kinetic_global = 0.0;
157	+
158	+	for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
159	+	for (atom = mol->beginFluctuatingCharge(iiter); atom != NULL;
160	+	atom = mol->nextFluctuatingCharge(iiter)) {
161	+	cmass = atom->getChargeMass();
162	+	cvel = atom->getFlucQVel();
163	+
164	+	kinetic += cmass * cvel * cvel;
165	+
166	+	}
167	+	}
168	+
169		#ifdef IS_MPI
170	<	MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
171	<	MPI_SUM, MPI_COMM_WORLD);
172	<	kinetic = kinetic_global;
170	>
171	>	MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
172	>	MPI_COMM_WORLD);
173	>	kinetic = kinetic_global;
174	>
175		#endif //is_mpi
77	–
78	–	kinetic = kinetic * 0.5 / e_convert;
176
177	<	return kinetic;
178	<	}
177	>	kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
178	>	return ( 2.0 * kinetic) / (info_->getNFluctuatingCharges()* PhysicalConstants::kb );
179	>	}
180
83	–	double Thermo::getPotential(){
84	–
85	–	double potential_local;
86	–	double potential;
87	–	int el, nSRI;
88	–	Molecule* molecules;
181
90	–	molecules = info->molecules;
91	–	nSRI = info->n_SRI;
182
93	–	potential_local = 0.0;
94	–	potential = 0.0;
95	–	potential_local += info->lrPot;
183
184	<	for( el=0; el<info->n_mol; el++ ){
185	<	potential_local += molecules[el].getPotential();
184	>	RealType Thermo::getVolume() {
185	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
186	>	return curSnapshot->getVolume();
187		}
188
189	<	// 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
189	>	RealType Thermo::getPressure() {
190
191	<	return potential;
110	<	}
191	>	// Relies on the calculation of the full molecular pressure tensor
192
112	–	double Thermo::getTotalE(){
193
194	<	double total;
194	>	Mat3x3d tensor;
195	>	RealType pressure;
196
197	<	total = this->getKinetic() + this->getPotential();
117	<	return total;
118	<	}
197	>	tensor = getPressureTensor();
198
199	<	double Thermo::getTemperature(){
199	>	pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
200
201	<	const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
202	<	double temperature;
201	>	return pressure;
202	>	}
203
204	<	temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
126	<	return temperature;
127	<	}
204	>	RealType Thermo::getPressure(int direction) {
205
206	<	double Thermo::getVolume() {
206	>	// Relies on the calculation of the full molecular pressure tensor
207
208	<	return info->boxVol;
209	<	}
208	>
209	>	Mat3x3d tensor;
210	>	RealType pressure;
211
212	<	double Thermo::getPressure() {
212	>	tensor = getPressureTensor();
213
214	<	// 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;
214	>	pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);
215
216	<	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 amu*fs^-2*Ang^-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;
216	>	return pressure;
217		}
218
219	<	// use velocities of integrableObjects and their masses:
219	>	Mat3x3d Thermo::getPressureTensor() {
220	>	// returns pressure tensor in units amu*fs^-2*Ang^-1
221	>	// routine derived via viral theorem description in:
222	>	// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
223	>	Mat3x3d pressureTensor;
224	>	Mat3x3d p_local(0.0);
225	>	Mat3x3d p_global(0.0);
226
227	<	for (i=0; i < info->integrableObjects.size(); i++) {
227	>	SimInfo::MoleculeIterator i;
228	>	std::vector<StuntDouble*>::iterator j;
229	>	Molecule* mol;
230	>	StuntDouble* integrableObject;
231	>	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
232	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
233	>	integrableObject = mol->nextIntegrableObject(j)) {
234
235	<	molmass = info->integrableObjects[i]->getMass();
235	>	RealType mass = integrableObject->getMass();
236	>	Vector3d vcom = integrableObject->getVel();
237	>	p_local += mass * outProduct(vcom, vcom);
238	>	}
239	>	}
240
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	–
241		#ifdef IS_MPI
242	<	MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
242	>	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
243		#else
244	<	for (i=0; i<9; i++) {
238	<	p_global[i] = p_local[i];
239	<	}
244	>	p_global = p_local;
245		#endif // is_mpi
246
247	<	volume = this->getVolume();
247	>	RealType volume = this->getVolume();
248	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
249	>	Mat3x3d tau = curSnapshot->getTau();
250
251	+	pressureTensor =  (p_global + PhysicalConstants::energyConvert* tau)/volume;
252	+
253	+	return pressureTensor;
254	+	}
255
256
257	<	for(i = 0; i < 3; i++) {
258	<	for (j = 0; j < 3; j++) {
259	<	k = 3*i + j;
260	<	press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
261	<	}
262	<	}
263	<	}
257	>	void Thermo::saveStat(){
258	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
259	>	Stats& stat = currSnapshot->statData;
260	>
261	>	stat[Stats::KINETIC_ENERGY] = getKinetic();
262	>	stat[Stats::POTENTIAL_ENERGY] = getPotential();
263	>	stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY]  + stat[Stats::POTENTIAL_ENERGY] ;
264	>	stat[Stats::TEMPERATURE] = getTemperature();
265	>	stat[Stats::PRESSURE] = getPressure();
266	>	stat[Stats::VOLUME] = getVolume();
267
268	<	void Thermo::velocitize() {
269	<
270	<	double aVel[3], aJ[3], I[3][3];
271	<	int i, j, l, m, n, vr, vd; // velocity randomizer loop counters
272	<	double vdrift[3];
273	<	double vbar;
274	<	const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
275	<	double av2;
276	<	double kebar;
277	<	double temperature;
264	<	int nobj;
268	>	Mat3x3d tensor =getPressureTensor();
269	>	stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);
270	>	stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);
271	>	stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);
272	>	stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);
273	>	stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);
274	>	stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);
275	>	stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);
276	>	stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);
277	>	stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);
278
279	<	if (!info->have_target_temp) {
280	<	sprintf( painCave.errMsg,
281	<	"You can't resample the velocities without a targetTemp!\n"
282	<	);
283	<	painCave.isFatal = 1;
284	<	painCave.severity = OOPSE_ERROR;
285	<	simError();
273	<	return;
274	<	}
279	>	// grab the simulation box dipole moment if specified
280	>	if (info_->getCalcBoxDipole()){
281	>	Vector3d totalDipole = getBoxDipole();
282	>	stat[Stats::BOX_DIPOLE_X] = totalDipole(0);
283	>	stat[Stats::BOX_DIPOLE_Y] = totalDipole(1);
284	>	stat[Stats::BOX_DIPOLE_Z] = totalDipole(2);
285	>	}
286
287	<	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
287	>	Globals* simParams = info_->getSimParams();
288
289	<	av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass();
290	<	vbar = sqrt( av2 );
289	>	if (simParams->haveTaggedAtomPair() &&
290	>	simParams->havePrintTaggedPairDistance()) {
291	>	if ( simParams->getPrintTaggedPairDistance()) {
292	>
293	>	std::pair<int, int> tap = simParams->getTaggedAtomPair();
294	>	Vector3d pos1, pos2, rab;
295
296	<	// picks random velocities from a gaussian distribution
297	<	// centered on vbar
296	>	#ifdef IS_MPI
297	>	std::cerr << "tap = " << tap.first << "  " << tap.second << std::endl;
298
299	<	for (j=0; j<3; j++)
300	<	aVel[j] = vbar * gaussStream->getGaussian();
301	<
296	<	info->integrableObjects[vr]->setVel( aVel );
297	<
298	<	if(info->integrableObjects[vr]->isDirectional()){
299	>	int mol1 = info_->getGlobalMolMembership(tap.first);
300	>	int mol2 = info_->getGlobalMolMembership(tap.second);
301	>	std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
302
303	<	info->integrableObjects[vr]->getI( I );
303	>	int proc1 = info_->getMolToProc(mol1);
304	>	int proc2 = info_->getMolToProc(mol2);
305
306	<	if (info->integrableObjects[vr]->isLinear()) {
306	>	std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
307
308	<	l= info->integrableObjects[vr]->linearAxis();
309	<	m = (l+1)%3;
310	<	n = (l+2)%3;
308	>	RealType data[3];
309	>	if (proc1 == worldRank) {
310	>	StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
311	>	std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
312	>	pos1 = sd1->getPos();
313	>	data[0] = pos1.x();
314	>	data[1] = pos1.y();
315	>	data[2] = pos1.z();
316	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
317	>	} else {
318	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
319	>	pos1 = Vector3d(data);
320	>	}
321
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
322
323	<	info->integrableObjects[vr]->setJ( aJ );
323	>	if (proc2 == worldRank) {
324	>	StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
325	>	std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
326	>	pos2 = sd2->getPos();
327	>	data[0] = pos2.x();
328	>	data[1] = pos2.y();
329	>	data[2] = pos2.z();
330	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
331	>	} else {
332	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
333	>	pos2 = Vector3d(data);
334	>	}
335	>	#else
336	>	StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
337	>	StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
338	>	pos1 = at1->getPos();
339	>	pos2 = at2->getPos();
340	>	#endif
341	>	rab = pos2 - pos1;
342	>	currSnapshot->wrapVector(rab);
343	>	stat[Stats::TAGGED_PAIR_DISTANCE] =  rab.length();
344	>	}
345	>	}
346
347	<	}//isDirectional
348	<
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++){
347	>	/**@todo need refactorying*/
348	>	//Conserved Quantity is set by integrator and time is set by setTime
349
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 );
350		}
351
344	–	}
352
353	<	void Thermo::getCOMVel(double vdrift[3]){
353	>	Vector3d Thermo::getBoxDipole() {
354	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
355	>	SimInfo::MoleculeIterator miter;
356	>	std::vector<Atom*>::iterator aiter;
357	>	Molecule* mol;
358	>	Atom* atom;
359	>	RealType charge;
360	>	RealType moment(0.0);
361	>	Vector3d ri(0.0);
362	>	Vector3d dipoleVector(0.0);
363	>	Vector3d nPos(0.0);
364	>	Vector3d pPos(0.0);
365	>	RealType nChg(0.0);
366	>	RealType pChg(0.0);
367	>	int nCount = 0;
368	>	int pCount = 0;
369
370	<	double mtot, mtot_local;
371	<	double aVel[3], amass;
372	<	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++){
370	>	RealType chargeToC = 1.60217733e-19;
371	>	RealType angstromToM = 1.0e-10;
372	>	RealType debyeToCm = 3.33564095198e-30;
373
374	<	amass = info->integrableObjects[vd]->getMass();
375	<	info->integrableObjects[vd]->getVel( aVel );
374	>	for (mol = info_->beginMolecule(miter); mol != NULL;
375	>	mol = info_->nextMolecule(miter)) {
376
377	<	for(j = 0; j < 3; j++)
378	<	vdrift_local[j] += aVel[j] * amass;
379	<
380	<	mtot_local += amass;
381	<	}
377	>	for (atom = mol->beginAtom(aiter); atom != NULL;
378	>	atom = mol->nextAtom(aiter)) {
379	>
380	>	if (atom->isCharge() ) {
381	>	charge = 0.0;
382	>	GenericData* data = atom->getAtomType()->getPropertyByName("Charge");
383	>	if (data != NULL) {
384
385	<	#ifdef IS_MPI
386	<	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	<	}
385	>	charge = (dynamic_cast<DoubleGenericData*>(data))->getData();
386	>	charge *= chargeToC;
387
388	<	void Thermo::getCOM(double COM[3]){
388	>	ri = atom->getPos();
389	>	currSnapshot->wrapVector(ri);
390	>	ri *= angstromToM;
391
392	<	double mtot, mtot_local;
393	<	double aPos[3], amass;
394	<	double COM_local[3];
395	<	int i, j;
396	<	int nobj;
397	<
398	<	mtot_local = 0.0;
399	<	COM_local[0] = 0.0;
400	<	COM_local[1] = 0.0;
401	<	COM_local[2] = 0.0;
402	<
403	<	nobj = info->integrableObjects.size();
404	<	for(i = 0; i < nobj; i++){
392	>	if (charge < 0.0) {
393	>	nPos += ri;
394	>	nChg -= charge;
395	>	nCount++;
396	>	} else if (charge > 0.0) {
397	>	pPos += ri;
398	>	pChg += charge;
399	>	pCount++;
400	>	}
401	>	}
402	>	}
403	>
404	>	MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType());
405	>	if (ma.isDipole() ) {
406	>	Vector3d u_i = atom->getElectroFrame().getColumn(2);
407	>	moment = ma.getDipoleMoment();
408	>	moment *= debyeToCm;
409	>	dipoleVector += u_i * moment;
410	>	}
411	>	}
412	>	}
413
414	<	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	<
414	>
415		#ifdef IS_MPI
416	<	MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
417	<	MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
418	<	#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	<	}
416	>	RealType pChg_global, nChg_global;
417	>	int pCount_global, nCount_global;
418	>	Vector3d pPos_global, nPos_global, dipVec_global;
419
420	<	void Thermo::removeCOMdrift() {
421	<	double vdrift[3], aVel[3];
422	<	int vd, j, nobj;
420	>	MPI_Allreduce(&pChg, &pChg_global, 1, MPI_REALTYPE, MPI_SUM,
421	>	MPI_COMM_WORLD);
422	>	pChg = pChg_global;
423	>	MPI_Allreduce(&nChg, &nChg_global, 1, MPI_REALTYPE, MPI_SUM,
424	>	MPI_COMM_WORLD);
425	>	nChg = nChg_global;
426	>	MPI_Allreduce(&pCount, &pCount_global, 1, MPI_INTEGER, MPI_SUM,
427	>	MPI_COMM_WORLD);
428	>	pCount = pCount_global;
429	>	MPI_Allreduce(&nCount, &nCount_global, 1, MPI_INTEGER, MPI_SUM,
430	>	MPI_COMM_WORLD);
431	>	nCount = nCount_global;
432	>	MPI_Allreduce(pPos.getArrayPointer(), pPos_global.getArrayPointer(), 3,
433	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
434	>	pPos = pPos_global;
435	>	MPI_Allreduce(nPos.getArrayPointer(), nPos_global.getArrayPointer(), 3,
436	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
437	>	nPos = nPos_global;
438	>	MPI_Allreduce(dipoleVector.getArrayPointer(),
439	>	dipVec_global.getArrayPointer(), 3,
440	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
441	>	dipoleVector = dipVec_global;
442	>	#endif //is_mpi
443
444	<	nobj = info->integrableObjects.size();
444	>	// first load the accumulated dipole moment (if dipoles were present)
445	>	Vector3d boxDipole = dipoleVector;
446	>	// now include the dipole moment due to charges
447	>	// use the lesser of the positive and negative charge totals
448	>	RealType chg_value = nChg <= pChg ? nChg : pChg;
449	>
450	>	// find the average positions
451	>	if (pCount > 0 && nCount > 0 ) {
452	>	pPos /= pCount;
453	>	nPos /= nCount;
454	>	}
455
456	<	// Get the Center of Mass drift velocity.
456	>	// dipole is from the negative to the positive (physics notation)
457	>	boxDipole += (pPos - nPos) * chg_value;
458
459	<	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 );
459	>	return boxDipole;
460		}
461	<	}
461	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/Thermo.cpp (property svn:keywords), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/brains/Thermo.cpp (property svn:keywords), Revision 1715 by gezelter, Tue May 22 21:55:31 2012 UTC

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