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

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trunk/src/brains/Thermo.cpp (file contents), Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
branches/development/src/brains/Thermo.cpp (file contents), Revision 1760 by gezelter, Thu Jun 21 19:26:46 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 "Thermo.hpp"
51	<	#include "SRI.hpp"
52	<	#include "Integrator.hpp"
53	<	#include "simError.h"
54	<	#include "MatVec3.h"
50	>	#include "brains/Thermo.hpp"
51	>	#include "primitives/Molecule.hpp"
52	>	#include "utils/simError.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 "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;
39	<	double amass;
40	<	double aVel[3], aJ[3], I[3][3];
41	<	int i, j, k, kl;
113	>	RealType Thermo::getPotential() {
114	>	RealType potential = 0.0;
115
116	<	double kinetic_global;
117	<	vector<StuntDouble *> integrableObjects = info->integrableObjects;
118	<
119	<	kinetic = 0.0;
47	<	kinetic_global = 0.0;
116	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
117	>	potential = curSnapshot->getShortRangePotential() + curSnapshot->getLongRangePotential();
118	>	return potential;
119	>	}
120
121	<	for (kl=0; kl<integrableObjects.size(); kl++) {
122	<	integrableObjects[kl]->getVel(aVel);
51	<	amass = integrableObjects[kl]->getMass();
121	>	RealType Thermo::getTotalE() {
122	>	RealType total;
123
124	<	for(j=0; j<3; j++)
125	<	kinetic += amass*aVel[j]*aVel[j];
124	>	total = this->getKinetic() + this->getPotential();
125	>	return total;
126	>	}
127
128	<	if (integrableObjects[kl]->isDirectional()){
129	<
130	<	integrableObjects[kl]->getJ( aJ );
131	<	integrableObjects[kl]->getI( I );
128	>	RealType Thermo::getTemperature() {
129	>
130	>	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
131	>	return temperature;
132	>	}
133
134	<	if (integrableObjects[kl]->isLinear()) {
135	<	i = integrableObjects[kl]->linearAxis();
136	<	j = (i+1)%3;
137	<	k = (i+2)%3;
138	<	kinetic += aJ[j]*aJ[j]/I[j][j] + aJ[k]*aJ[k]/I[k][k];
139	<	} else {
140	<	for (j=0; j<3; j++)
141	<	kinetic += aJ[j]*aJ[j] / I[j][j];
134	>	RealType Thermo::getElectronicTemperature() {
135	>	SimInfo::MoleculeIterator miter;
136	>	std::vector<Atom*>::iterator iiter;
137	>	Molecule* mol;
138	>	Atom* atom;
139	>	RealType cvel;
140	>	RealType cmass;
141	>	RealType kinetic = 0.0;
142	>	RealType kinetic_global = 0.0;
143	>
144	>	for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
145	>	for (atom = mol->beginFluctuatingCharge(iiter); atom != NULL;
146	>	atom = mol->nextFluctuatingCharge(iiter)) {
147	>	cmass = atom->getChargeMass();
148	>	cvel = atom->getFlucQVel();
149	>
150	>	kinetic += cmass * cvel * cvel;
151	>
152		}
153	<	}
154	<	}
153	>	}
154	>
155		#ifdef IS_MPI
156	<	MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
157	<	MPI_SUM, MPI_COMM_WORLD);
158	<	kinetic = kinetic_global;
156	>
157	>	MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
158	>	MPI_COMM_WORLD);
159	>	kinetic = kinetic_global;
160	>
161		#endif //is_mpi
77	–
78	–	kinetic = kinetic * 0.5 / e_convert;
162
163	<	return kinetic;
164	<	}
163	>	kinetic = kinetic * 0.5;
164	>	return ( 2.0 * kinetic) / (info_->getNFluctuatingCharges()* PhysicalConstants::kb );
165	>	}
166
83	–	double Thermo::getPotential(){
84	–
85	–	double potential_local;
86	–	double potential;
87	–	int el, nSRI;
88	–	Molecule* molecules;
167
90	–	molecules = info->molecules;
91	–	nSRI = info->n_SRI;
168
93	–	potential_local = 0.0;
94	–	potential = 0.0;
95	–	potential_local += info->lrPot;
169
170	<	for( el=0; el<info->n_mol; el++ ){
171	<	potential_local += molecules[el].getPotential();
170	>	RealType Thermo::getVolume() {
171	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
172	>	return curSnapshot->getVolume();
173		}
174
175	<	// 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
175	>	RealType Thermo::getPressure() {
176
177	<	return potential;
110	<	}
177	>	// Relies on the calculation of the full molecular pressure tensor
178
112	–	double Thermo::getTotalE(){
179
180	<	double total;
180	>	Mat3x3d tensor;
181	>	RealType pressure;
182
183	<	total = this->getKinetic() + this->getPotential();
117	<	return total;
118	<	}
183	>	tensor = getPressureTensor();
184
185	<	double Thermo::getTemperature(){
185	>	pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
186
187	<	const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
188	<	double temperature;
187	>	return pressure;
188	>	}
189
190	<	temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
126	<	return temperature;
127	<	}
190	>	RealType Thermo::getPressure(int direction) {
191
192	<	double Thermo::getVolume() {
192	>	// Relies on the calculation of the full molecular pressure tensor
193
194	<	return info->boxVol;
195	<	}
194	>
195	>	Mat3x3d tensor;
196	>	RealType pressure;
197
198	<	double Thermo::getPressure() {
198	>	tensor = getPressureTensor();
199
200	<	// 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;
200	>	pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);
201
202	<	this->getPressureTensor(press);
202	>	return pressure;
203	>	}
204
205	<	pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
205	>	Mat3x3d Thermo::getPressureTensor() {
206	>	// returns pressure tensor in units amu*fs^-2*Ang^-1
207	>	// routine derived via viral theorem description in:
208	>	// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
209	>	Mat3x3d pressureTensor;
210	>	Mat3x3d p_local(0.0);
211	>	Mat3x3d p_global(0.0);
212
213	<	return pressure;
214	<	}
213	>	SimInfo::MoleculeIterator i;
214	>	std::vector<StuntDouble*>::iterator j;
215	>	Molecule* mol;
216	>	StuntDouble* integrableObject;
217	>	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
218	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
219	>	integrableObject = mol->nextIntegrableObject(j)) {
220
221	<	double Thermo::getPressureX() {
221	>	RealType mass = integrableObject->getMass();
222	>	Vector3d vcom = integrableObject->getVel();
223	>	p_local += mass * outProduct(vcom, vcom);
224	>	}
225	>	}
226	>
227	>	#ifdef IS_MPI
228	>	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
229	>	#else
230	>	p_global = p_local;
231	>	#endif // is_mpi
232
233	<	// Relies on the calculation of the full molecular pressure tensor
234	<
235	<	const double p_convert = 1.63882576e8;
154	<	double press[3][3];
155	<	double pressureX;
233	>	RealType volume = this->getVolume();
234	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
235	>	Mat3x3d stressTensor = curSnapshot->getStressTensor();
236
237	<	this->getPressureTensor(press);
237	>	pressureTensor =  (p_global +
238	>	PhysicalConstants::energyConvert * stressTensor)/volume;
239	>
240	>	return pressureTensor;
241	>	}
242
159	–	pressureX = p_convert * press[0][0];
243
244	<	return pressureX;
245	<	}
244	>	void Thermo::saveStat(){
245	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
246	>	Stats& stat = currSnapshot->statData;
247	>
248	>	stat[Stats::KINETIC_ENERGY] = getKinetic();
249	>	stat[Stats::POTENTIAL_ENERGY] = getPotential();
250	>	stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY]  + stat[Stats::POTENTIAL_ENERGY] ;
251	>	stat[Stats::TEMPERATURE] = getTemperature();
252	>	stat[Stats::PRESSURE] = getPressure();
253	>	stat[Stats::VOLUME] = getVolume();
254
255	<	double Thermo::getPressureY() {
255	>	Mat3x3d tensor =getPressureTensor();
256	>	stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);
257	>	stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);
258	>	stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);
259	>	stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);
260	>	stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);
261	>	stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);
262	>	stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);
263	>	stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);
264	>	stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);
265
266	<	// Relies on the calculation of the full molecular pressure tensor
267	<
268	<	const double p_convert = 1.63882576e8;
269	<	double press[3][3];
270	<	double pressureY;
266	>	// grab the simulation box dipole moment if specified
267	>	if (info_->getCalcBoxDipole()){
268	>	Vector3d totalDipole = getBoxDipole();
269	>	stat[Stats::BOX_DIPOLE_X] = totalDipole(0);
270	>	stat[Stats::BOX_DIPOLE_Y] = totalDipole(1);
271	>	stat[Stats::BOX_DIPOLE_Z] = totalDipole(2);
272	>	}
273
274	<	this->getPressureTensor(press);
274	>	Globals* simParams = info_->getSimParams();
275	>	// grab the heat flux if desired
276	>	if (simParams->havePrintHeatFlux()) {
277	>	if (simParams->getPrintHeatFlux()){
278	>	Vector3d heatFlux = getHeatFlux();
279	>	stat[Stats::HEATFLUX_X] = heatFlux(0);
280	>	stat[Stats::HEATFLUX_Y] = heatFlux(1);
281	>	stat[Stats::HEATFLUX_Z] = heatFlux(2);
282	>	}
283	>	}
284
285	<	pressureY = p_convert * press[1][1];
285	>	if (simParams->haveTaggedAtomPair() &&
286	>	simParams->havePrintTaggedPairDistance()) {
287	>	if ( simParams->getPrintTaggedPairDistance()) {
288	>
289	>	std::pair<int, int> tap = simParams->getTaggedAtomPair();
290	>	Vector3d pos1, pos2, rab;
291
292	<	return pressureY;
293	<	}
292	>	#ifdef IS_MPI
293	>	std::cerr << "tap = " << tap.first << "  " << tap.second << std::endl;
294
295	<	double Thermo::getPressureZ() {
295	>	int mol1 = info_->getGlobalMolMembership(tap.first);
296	>	int mol2 = info_->getGlobalMolMembership(tap.second);
297	>	std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
298
299	<	// Relies on the calculation of the full molecular pressure tensor
300	<
183	<	const double p_convert = 1.63882576e8;
184	<	double press[3][3];
185	<	double pressureZ;
299	>	int proc1 = info_->getMolToProc(mol1);
300	>	int proc2 = info_->getMolToProc(mol2);
301
302	<	this->getPressureTensor(press);
302	>	std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
303
304	<	pressureZ = p_convert * press[2][2];
304	>	RealType data[3];
305	>	if (proc1 == worldRank) {
306	>	StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
307	>	std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
308	>	pos1 = sd1->getPos();
309	>	data[0] = pos1.x();
310	>	data[1] = pos1.y();
311	>	data[2] = pos1.z();
312	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
313	>	} else {
314	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
315	>	pos1 = Vector3d(data);
316	>	}
317
191	–	return pressureZ;
192	–	}
318
319	<
320	<	void Thermo::getPressureTensor(double press[3][3]){
321	<	// returns pressure tensor in units amu*fs^-2*Ang^-1
322	<	// routine derived via viral theorem description in:
323	<	// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
324	<
325	<	const double e_convert = 4.184e-4;
326	<
327	<	double molmass, volume;
328	<	double vcom[3];
329	<	double p_local[9], p_global[9];
330	<	int i, j, k;
331	<
332	<	for (i=0; i < 9; i++) {
333	<	p_local[i] = 0.0;
334	<	p_global[i] = 0.0;
335	<	}
336	<
337	<	// use velocities of integrableObjects and their masses:
338	<
339	<	for (i=0; i < info->integrableObjects.size(); i++) {
340	<
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;
319	>	if (proc2 == worldRank) {
320	>	StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
321	>	std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
322	>	pos2 = sd2->getPos();
323	>	data[0] = pos2.x();
324	>	data[1] = pos2.y();
325	>	data[2] = pos2.z();
326	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
327	>	} else {
328	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
329	>	pos2 = Vector3d(data);
330	>	}
331	>	#else
332	>	StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
333	>	StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
334	>	pos1 = at1->getPos();
335	>	pos2 = at2->getPos();
336	>	#endif
337	>	rab = pos2 - pos1;
338	>	currSnapshot->wrapVector(rab);
339	>	stat[Stats::TAGGED_PAIR_DISTANCE] =  rab.length();
340	>	}
341		}
342	+
343	+	/**@todo need refactorying*/
344	+	//Conserved Quantity is set by integrator and time is set by setTime
345	+
346		}
252	–	}
347
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;
348
349	<	if (!info->have_target_temp) {
350	<	sprintf( painCave.errMsg,
351	<	"You can't resample the velocities without a targetTemp!\n"
352	<	);
353	<	painCave.isFatal = 1;
354	<	painCave.severity = OOPSE_ERROR;
355	<	simError();
356	<	return;
357	<	}
349	>	Vector3d Thermo::getBoxDipole() {
350	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
351	>	SimInfo::MoleculeIterator miter;
352	>	std::vector<Atom*>::iterator aiter;
353	>	Molecule* mol;
354	>	Atom* atom;
355	>	RealType charge;
356	>	RealType moment(0.0);
357	>	Vector3d ri(0.0);
358	>	Vector3d dipoleVector(0.0);
359	>	Vector3d nPos(0.0);
360	>	Vector3d pPos(0.0);
361	>	RealType nChg(0.0);
362	>	RealType pChg(0.0);
363	>	int nCount = 0;
364	>	int pCount = 0;
365
366	<	nobj = info->integrableObjects.size();
367	<
368	<	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++){
366	>	RealType chargeToC = 1.60217733e-19;
367	>	RealType angstromToM = 1.0e-10;
368	>	RealType debyeToCm = 3.33564095198e-30;
369
370	<	// uses equipartition theory to solve for vbar in angstrom/fs
370	>	for (mol = info_->beginMolecule(miter); mol != NULL;
371	>	mol = info_->nextMolecule(miter)) {
372
373	<	av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass();
374	<	vbar = sqrt( av2 );
373	>	for (atom = mol->beginAtom(aiter); atom != NULL;
374	>	atom = mol->nextAtom(aiter)) {
375	>
376	>	if (atom->isCharge() ) {
377	>	charge = 0.0;
378	>	GenericData* data = atom->getAtomType()->getPropertyByName("Charge");
379	>	if (data != NULL) {
380
381	<	// picks random velocities from a gaussian distribution
382	<	// centered on vbar
381	>	charge = (dynamic_cast<DoubleGenericData*>(data))->getData();
382	>	charge *= chargeToC;
383
384	<	for (j=0; j<3; j++)
385	<	aVel[j] = vbar * gaussStream->getGaussian();
384	>	ri = atom->getPos();
385	>	currSnapshot->wrapVector(ri);
386	>	ri *= angstromToM;
387	>
388	>	if (charge < 0.0) {
389	>	nPos += ri;
390	>	nChg -= charge;
391	>	nCount++;
392	>	} else if (charge > 0.0) {
393	>	pPos += ri;
394	>	pChg += charge;
395	>	pCount++;
396	>	}
397	>	}
398	>	}
399	>
400	>	MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType());
401	>	if (ma.isDipole() ) {
402	>	Vector3d u_i = atom->getElectroFrame().getColumn(2);
403	>	moment = ma.getDipoleMoment();
404	>	moment *= debyeToCm;
405	>	dipoleVector += u_i * moment;
406	>	}
407	>	}
408	>	}
409
410	<	info->integrableObjects[vr]->setVel( aVel );
411	<
412	<	if(info->integrableObjects[vr]->isDirectional()){
410	>
411	>	#ifdef IS_MPI
412	>	RealType pChg_global, nChg_global;
413	>	int pCount_global, nCount_global;
414	>	Vector3d pPos_global, nPos_global, dipVec_global;
415
416	<	info->integrableObjects[vr]->getI( I );
416	>	MPI_Allreduce(&pChg, &pChg_global, 1, MPI_REALTYPE, MPI_SUM,
417	>	MPI_COMM_WORLD);
418	>	pChg = pChg_global;
419	>	MPI_Allreduce(&nChg, &nChg_global, 1, MPI_REALTYPE, MPI_SUM,
420	>	MPI_COMM_WORLD);
421	>	nChg = nChg_global;
422	>	MPI_Allreduce(&pCount, &pCount_global, 1, MPI_INTEGER, MPI_SUM,
423	>	MPI_COMM_WORLD);
424	>	pCount = pCount_global;
425	>	MPI_Allreduce(&nCount, &nCount_global, 1, MPI_INTEGER, MPI_SUM,
426	>	MPI_COMM_WORLD);
427	>	nCount = nCount_global;
428	>	MPI_Allreduce(pPos.getArrayPointer(), pPos_global.getArrayPointer(), 3,
429	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
430	>	pPos = pPos_global;
431	>	MPI_Allreduce(nPos.getArrayPointer(), nPos_global.getArrayPointer(), 3,
432	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
433	>	nPos = nPos_global;
434	>	MPI_Allreduce(dipoleVector.getArrayPointer(),
435	>	dipVec_global.getArrayPointer(), 3,
436	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
437	>	dipoleVector = dipVec_global;
438	>	#endif //is_mpi
439
440	<	if (info->integrableObjects[vr]->isLinear()) {
440	>	// first load the accumulated dipole moment (if dipoles were present)
441	>	Vector3d boxDipole = dipoleVector;
442	>	// now include the dipole moment due to charges
443	>	// use the lesser of the positive and negative charge totals
444	>	RealType chg_value = nChg <= pChg ? nChg : pChg;
445	>
446	>	// find the average positions
447	>	if (pCount > 0 && nCount > 0 ) {
448	>	pPos /= pCount;
449	>	nPos /= nCount;
450	>	}
451
452	<	l= info->integrableObjects[vr]->linearAxis();
453	<	m = (l+1)%3;
306	<	n = (l+2)%3;
452	>	// dipole is from the negative to the positive (physics notation)
453	>	boxDipole += (pPos - nPos) * chg_value;
454
455	<	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	<
455	>	return boxDipole;
456		}
457
458	<	// Get the Center of Mass drift velocity.
458	>	// Returns the Heat Flux Vector for the system
459	>	Vector3d Thermo::getHeatFlux(){
460	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
461	>	SimInfo::MoleculeIterator miter;
462	>	std::vector<StuntDouble*>::iterator iiter;
463	>	Molecule* mol;
464	>	StuntDouble* integrableObject;
465	>	RigidBody::AtomIterator ai;
466	>	Atom* atom;
467	>	Vector3d vel;
468	>	Vector3d angMom;
469	>	Mat3x3d I;
470	>	int i;
471	>	int j;
472	>	int k;
473	>	RealType mass;
474
475	<	getCOMVel(vdrift);
476	<
477	<	//  Corrects for the center of mass drift.
478	<	// sums all the momentum and divides by total mass.
475	>	Vector3d x_a;
476	>	RealType kinetic;
477	>	RealType potential;
478	>	RealType eatom;
479	>	RealType AvgE_a_ = 0;
480	>	// Convective portion of the heat flux
481	>	Vector3d heatFluxJc = V3Zero;
482
483	<	for(vd = 0; vd < nobj; vd++){
484	<
485	<	info->integrableObjects[vd]->getVel(aVel);
486	<
487	<	for (j=0; j < 3; j++)
488	<	aVel[j] -= vdrift[j];
483	>	/* Calculate convective portion of the heat flux */
484	>	for (mol = info_->beginMolecule(miter); mol != NULL;
485	>	mol = info_->nextMolecule(miter)) {
486	>
487	>	for (integrableObject = mol->beginIntegrableObject(iiter);
488	>	integrableObject != NULL;
489	>	integrableObject = mol->nextIntegrableObject(iiter)) {
490
491	<	info->integrableObjects[vd]->setVel( aVel );
492	<	}
491	>	mass = integrableObject->getMass();
492	>	vel = integrableObject->getVel();
493
494	<	}
494	>	kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
495	>
496	>	if (integrableObject->isDirectional()) {
497	>	angMom = integrableObject->getJ();
498	>	I = integrableObject->getI();
499
500	<	void Thermo::getCOMVel(double vdrift[3]){
500	>	if (integrableObject->isLinear()) {
501	>	i = integrableObject->linearAxis();
502	>	j = (i + 1) % 3;
503	>	k = (i + 2) % 3;
504	>	kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
505	>	} else {
506	>	kinetic += angMom[0]*angMom[0]/I(0, 0) + angMom[1]*angMom[1]/I(1, 1)
507	>	+ angMom[2]*angMom[2]/I(2, 2);
508	>	}
509	>	}
510
511	<	double mtot, mtot_local;
349	<	double aVel[3], amass;
350	<	double vdrift_local[3];
351	<	int vd, j;
352	<	int nobj;
511	>	potential = 0.0;
512
513	<	nobj   = info->integrableObjects.size();
513	>	if (integrableObject->isRigidBody()) {
514	>	RigidBody* rb = dynamic_cast<RigidBody*>(integrableObject);
515	>	for (atom = rb->beginAtom(ai); atom != NULL;
516	>	atom = rb->nextAtom(ai)) {
517	>	potential +=  atom->getParticlePot();
518	>	}
519	>	} else {
520	>	potential = integrableObject->getParticlePot();
521	>	cerr << "ppot = "  << potential << "\n";
522	>	}
523
524	<	mtot_local = 0.0;
525	<	vdrift_local[0] = 0.0;
526	<	vdrift_local[1] = 0.0;
527	<	vdrift_local[2] = 0.0;
528	<
529	<	for(vd = 0; vd < nobj; vd++){
530	<
531	<	amass = info->integrableObjects[vd]->getMass();
364	<	info->integrableObjects[vd]->getVel( aVel );
524	>	potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2
525	>	// The potential may not be a 1/2 factor
526	>	eatom = (kinetic + potential)/2.0;  // amu A^2/fs^2
527	>	heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3
528	>	heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3
529	>	heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3
530	>	}
531	>	}
532
533	<	for(j = 0; j < 3; j++)
367	<	vdrift_local[j] += aVel[j] * amass;
368	<
369	<	mtot_local += amass;
370	<	}
533	>	std::cerr << "Heat flux heatFluxJc is: " << heatFluxJc << std::endl;
534
535	+	/* The J_v vector is reduced in fortan so everyone has the global
536	+	*  Jv. Jc is computed over the local atoms and must be reduced
537	+	*  among all processors.
538	+	*/
539		#ifdef IS_MPI
540	<	MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
541	<	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	<	}
540	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &heatFluxJc[0], 3, MPI::REALTYPE,
541	>	MPI::SUM);
542		#endif
543
544	<	for (vd = 0; vd < 3; vd++) {
383	<	vdrift[vd] = vdrift[vd] / mtot;
384	<	}
385	<
386	<	}
544	>	// (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3
545
546	<	void Thermo::getCOM(double COM[3]){
547	<
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++){
546	>	Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() *
547	>	PhysicalConstants::energyConvert;
548
549	<	amass = info->integrableObjects[i]->getMass();
550	<	info->integrableObjects[i]->getPos( aPos );
406	<
407	<	for(j = 0; j < 3; j++)
408	<	COM_local[j] += aPos[j] * amass;
549	>	std::cerr << "Heat flux Jc is: " << heatFluxJc << std::endl;
550	>	std::cerr << "Heat flux Jv is: " << heatFluxJv << std::endl;
551
552	<	mtot_local += amass;
552	>	// Correct for the fact the flux is 1/V (Jc + Jv)
553	>	return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3
554		}
555	<
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	<	}
555	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/Thermo.cpp (property svn:keywords), Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
branches/development/src/brains/Thermo.cpp (property svn:keywords), Revision 1760 by gezelter, Thu Jun 21 19:26:46 2012 UTC

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