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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 1723 by gezelter, Thu May 24 20:59:54 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()) {
62	<	i = integrableObjects[kl]->linearAxis();
63	<	j = (i+1)%3;
64	<	k = (i+2)%3;
65	<	kinetic += aJ[j]*aJ[j]/I[j][j] + aJ[k]*aJ[k]/I[k][k];
66	<	} else {
67	<	for (j=0; j<3; j++)
68	<	kinetic += aJ[j]*aJ[j] / I[j][j];
69	<	}
70	<	}
71	<	}
72	<	#ifdef IS_MPI
73	<	MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
74	<	MPI_SUM, MPI_COMM_WORLD);
75	<	kinetic = kinetic_global;
76	<	#endif //is_mpi
77	<
78	<	kinetic = kinetic * 0.5 / e_convert;
128	>	potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
129
130	<	return kinetic;
81	<	}
130	>	#endif // is_mpi
131
132	<	double Thermo::getPotential(){
133	<
85	<	double potential_local;
86	<	double potential;
87	<	int el, nSRI;
88	<	Molecule* molecules;
132	>	return potential;
133	>	}
134
135	<	molecules = info->molecules;
136	<	nSRI = info->n_SRI;
135	>	RealType Thermo::getTotalE() {
136	>	RealType total;
137
138	<	potential_local = 0.0;
139	<	potential = 0.0;
140	<	potential_local += info->lrPot;
138	>	total = this->getKinetic() + this->getPotential();
139	>	return total;
140	>	}
141
142	<	for( el=0; el<info->n_mol; el++ ){
143	<	potential_local += molecules[el].getPotential();
142	>	RealType Thermo::getTemperature() {
143	>
144	>	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
145	>	return temperature;
146		}
147
148	<	// Get total potential for entire system from MPI.
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
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
170
171	<	return potential;
172	<	}
171	>	MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
172	>	MPI_COMM_WORLD);
173	>	kinetic = kinetic_global;
174
175	<	double Thermo::getTotalE(){
175	>	#endif //is_mpi
176
177	<	double total;
177	>	kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
178	>	return ( 2.0 * kinetic) / (info_->getNFluctuatingCharges()* PhysicalConstants::kb );
179	>	}
180
116	–	total = this->getKinetic() + this->getPotential();
117	–	return total;
118	–	}
181
120	–	double Thermo::getTemperature(){
182
122	–	const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
123	–	double temperature;
183
184	<	temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
185	<	return temperature;
186	<	}
184	>	RealType Thermo::getVolume() {
185	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
186	>	return curSnapshot->getVolume();
187	>	}
188
189	<	double Thermo::getVolume() {
189	>	RealType Thermo::getPressure() {
190
191	<	return info->boxVol;
132	<	}
191	>	// Relies on the calculation of the full molecular pressure tensor
192
134	–	double Thermo::getPressure() {
193
194	<	// Relies on the calculation of the full molecular pressure tensor
195	<
138	<	const double p_convert = 1.63882576e8;
139	<	double press[3][3];
140	<	double pressure;
194	>	Mat3x3d tensor;
195	>	RealType pressure;
196
197	<	this->getPressureTensor(press);
197	>	tensor = getPressureTensor();
198
199	<	pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
199	>	pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
200
201	<	return pressure;
202	<	}
201	>	return pressure;
202	>	}
203
204	<	double Thermo::getPressureX() {
204	>	RealType Thermo::getPressure(int direction) {
205
206	<	// 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;
206	>	// Relies on the calculation of the full molecular pressure tensor
207
208	<	this->getPressureTensor(press);
208	>
209	>	Mat3x3d tensor;
210	>	RealType pressure;
211
212	<	pressureX = p_convert * press[0][0];
212	>	tensor = getPressureTensor();
213
214	<	return pressureX;
162	<	}
214	>	pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);
215
216	<	double Thermo::getPressureY() {
216	>	return pressure;
217	>	}
218
219	<	// Relies on the calculation of the full molecular pressure tensor
220	<
221	<	const double p_convert = 1.63882576e8;
222	<	double press[3][3];
223	<	double pressureY;
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	<	this->getPressureTensor(press);
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	<	pressureY = p_convert * press[1][1];
235	>	RealType mass = integrableObject->getMass();
236	>	Vector3d vcom = integrableObject->getVel();
237	>	p_local += mass * outProduct(vcom, vcom);
238	>	}
239	>	}
240	>
241	>	#ifdef IS_MPI
242	>	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
243	>	#else
244	>	p_global = p_local;
245	>	#endif // is_mpi
246
247	<	return pressureY;
248	<	}
247	>	RealType volume = this->getVolume();
248	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
249	>	Mat3x3d stressTensor = curSnapshot->getStressTensor();
250
251	<	double Thermo::getPressureZ() {
251	>	pressureTensor =  (p_global +
252	>	PhysicalConstants::energyConvert * stressTensor)/volume;
253	>
254	>	return pressureTensor;
255	>	}
256
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;
257
258	<	this->getPressureTensor(press);
258	>	void Thermo::saveStat(){
259	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
260	>	Stats& stat = currSnapshot->statData;
261	>
262	>	stat[Stats::KINETIC_ENERGY] = getKinetic();
263	>	stat[Stats::POTENTIAL_ENERGY] = getPotential();
264	>	stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY]  + stat[Stats::POTENTIAL_ENERGY] ;
265	>	stat[Stats::TEMPERATURE] = getTemperature();
266	>	stat[Stats::PRESSURE] = getPressure();
267	>	stat[Stats::VOLUME] = getVolume();
268
269	<	pressureZ = p_convert * press[2][2];
269	>	Mat3x3d tensor =getPressureTensor();
270	>	stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);
271	>	stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);
272	>	stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);
273	>	stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);
274	>	stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);
275	>	stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);
276	>	stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);
277	>	stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);
278	>	stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);
279
280	<	return pressureZ;
281	<	}
280	>	// grab the simulation box dipole moment if specified
281	>	if (info_->getCalcBoxDipole()){
282	>	Vector3d totalDipole = getBoxDipole();
283	>	stat[Stats::BOX_DIPOLE_X] = totalDipole(0);
284	>	stat[Stats::BOX_DIPOLE_Y] = totalDipole(1);
285	>	stat[Stats::BOX_DIPOLE_Z] = totalDipole(2);
286	>	}
287
288	+	Globals* simParams = info_->getSimParams();
289	+	// grab the heat flux if desired
290	+	if (simParams->havePrintHeatFlux()) {
291	+	if (simParams->getPrintHeatFlux()){
292	+	Vector3d heatFlux = getHeatFlux();
293	+	stat[Stats::HEATFLUX_X] = heatFlux(0);
294	+	stat[Stats::HEATFLUX_Y] = heatFlux(1);
295	+	stat[Stats::HEATFLUX_Z] = heatFlux(2);
296	+	}
297	+	}
298
299	<	void Thermo::getPressureTensor(double press[3][3]){
300	<	// returns pressure tensor in units amu*fs^-2*Ang^-1
301	<	// routine derived via viral theorem description in:
302	<	// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
299	>	if (simParams->haveTaggedAtomPair() &&
300	>	simParams->havePrintTaggedPairDistance()) {
301	>	if ( simParams->getPrintTaggedPairDistance()) {
302	>
303	>	std::pair<int, int> tap = simParams->getTaggedAtomPair();
304	>	Vector3d pos1, pos2, rab;
305
306	<	const double e_convert = 4.184e-4;
306	>	#ifdef IS_MPI
307	>	std::cerr << "tap = " << tap.first << "  " << tap.second << std::endl;
308
309	<	double molmass, volume;
310	<	double vcom[3];
311	<	double p_local[9], p_global[9];
205	<	int i, j, k;
309	>	int mol1 = info_->getGlobalMolMembership(tap.first);
310	>	int mol2 = info_->getGlobalMolMembership(tap.second);
311	>	std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
312
313	<	for (i=0; i < 9; i++) {
314	<	p_local[i] = 0.0;
209	<	p_global[i] = 0.0;
210	<	}
313	>	int proc1 = info_->getMolToProc(mol1);
314	>	int proc2 = info_->getMolToProc(mol2);
315
316	<	// use velocities of integrableObjects and their masses:
316	>	std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
317
318	<	for (i=0; i < info->integrableObjects.size(); i++) {
319	<
320	<	molmass = info->integrableObjects[i]->getMass();
321	<
322	<	info->integrableObjects[i]->getVel(vcom);
323	<
324	<	p_local[0] += molmass * (vcom[0] * vcom[0]);
325	<	p_local[1] += molmass * (vcom[0] * vcom[1]);
326	<	p_local[2] += molmass * (vcom[0] * vcom[2]);
327	<	p_local[3] += molmass * (vcom[1] * vcom[0]);
328	<	p_local[4] += molmass * (vcom[1] * vcom[1]);
329	<	p_local[5] += molmass * (vcom[1] * vcom[2]);
330	<	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();
318	>	RealType data[3];
319	>	if (proc1 == worldRank) {
320	>	StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
321	>	std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
322	>	pos1 = sd1->getPos();
323	>	data[0] = pos1.x();
324	>	data[1] = pos1.y();
325	>	data[2] = pos1.z();
326	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
327	>	} else {
328	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
329	>	pos1 = Vector3d(data);
330	>	}
331
332
333	<
334	<	for(i = 0; i < 3; i++) {
335	<	for (j = 0; j < 3; j++) {
336	<	k = 3*i + j;
337	<	press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
333	>	if (proc2 == worldRank) {
334	>	StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
335	>	std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
336	>	pos2 = sd2->getPos();
337	>	data[0] = pos2.x();
338	>	data[1] = pos2.y();
339	>	data[2] = pos2.z();
340	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
341	>	} else {
342	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
343	>	pos2 = Vector3d(data);
344	>	}
345	>	#else
346	>	StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
347	>	StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
348	>	pos1 = at1->getPos();
349	>	pos2 = at2->getPos();
350	>	#endif
351	>	rab = pos2 - pos1;
352	>	currSnapshot->wrapVector(rab);
353	>	stat[Stats::TAGGED_PAIR_DISTANCE] =  rab.length();
354	>	}
355		}
356	+
357	+	/**@todo need refactorying*/
358	+	//Conserved Quantity is set by integrator and time is set by setTime
359	+
360		}
252	–	}
361
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;
362
363	<	if (!info->have_target_temp) {
364	<	sprintf( painCave.errMsg,
365	<	"You can't resample the velocities without a targetTemp!\n"
366	<	);
367	<	painCave.isFatal = 1;
368	<	painCave.severity = OOPSE_ERROR;
369	<	simError();
370	<	return;
371	<	}
363	>	Vector3d Thermo::getBoxDipole() {
364	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
365	>	SimInfo::MoleculeIterator miter;
366	>	std::vector<Atom*>::iterator aiter;
367	>	Molecule* mol;
368	>	Atom* atom;
369	>	RealType charge;
370	>	RealType moment(0.0);
371	>	Vector3d ri(0.0);
372	>	Vector3d dipoleVector(0.0);
373	>	Vector3d nPos(0.0);
374	>	Vector3d pPos(0.0);
375	>	RealType nChg(0.0);
376	>	RealType pChg(0.0);
377	>	int nCount = 0;
378	>	int pCount = 0;
379
380	<	nobj = info->integrableObjects.size();
381	<
382	<	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++){
380	>	RealType chargeToC = 1.60217733e-19;
381	>	RealType angstromToM = 1.0e-10;
382	>	RealType debyeToCm = 3.33564095198e-30;
383
384	<	// uses equipartition theory to solve for vbar in angstrom/fs
384	>	for (mol = info_->beginMolecule(miter); mol != NULL;
385	>	mol = info_->nextMolecule(miter)) {
386
387	<	av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass();
388	<	vbar = sqrt( av2 );
387	>	for (atom = mol->beginAtom(aiter); atom != NULL;
388	>	atom = mol->nextAtom(aiter)) {
389	>
390	>	if (atom->isCharge() ) {
391	>	charge = 0.0;
392	>	GenericData* data = atom->getAtomType()->getPropertyByName("Charge");
393	>	if (data != NULL) {
394
395	<	// picks random velocities from a gaussian distribution
396	<	// centered on vbar
395	>	charge = (dynamic_cast<DoubleGenericData*>(data))->getData();
396	>	charge *= chargeToC;
397
398	<	for (j=0; j<3; j++)
399	<	aVel[j] = vbar * gaussStream->getGaussian();
398	>	ri = atom->getPos();
399	>	currSnapshot->wrapVector(ri);
400	>	ri *= angstromToM;
401	>
402	>	if (charge < 0.0) {
403	>	nPos += ri;
404	>	nChg -= charge;
405	>	nCount++;
406	>	} else if (charge > 0.0) {
407	>	pPos += ri;
408	>	pChg += charge;
409	>	pCount++;
410	>	}
411	>	}
412	>	}
413	>
414	>	MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType());
415	>	if (ma.isDipole() ) {
416	>	Vector3d u_i = atom->getElectroFrame().getColumn(2);
417	>	moment = ma.getDipoleMoment();
418	>	moment *= debyeToCm;
419	>	dipoleVector += u_i * moment;
420	>	}
421	>	}
422	>	}
423
424	<	info->integrableObjects[vr]->setVel( aVel );
425	<
426	<	if(info->integrableObjects[vr]->isDirectional()){
424	>
425	>	#ifdef IS_MPI
426	>	RealType pChg_global, nChg_global;
427	>	int pCount_global, nCount_global;
428	>	Vector3d pPos_global, nPos_global, dipVec_global;
429
430	<	info->integrableObjects[vr]->getI( I );
430	>	MPI_Allreduce(&pChg, &pChg_global, 1, MPI_REALTYPE, MPI_SUM,
431	>	MPI_COMM_WORLD);
432	>	pChg = pChg_global;
433	>	MPI_Allreduce(&nChg, &nChg_global, 1, MPI_REALTYPE, MPI_SUM,
434	>	MPI_COMM_WORLD);
435	>	nChg = nChg_global;
436	>	MPI_Allreduce(&pCount, &pCount_global, 1, MPI_INTEGER, MPI_SUM,
437	>	MPI_COMM_WORLD);
438	>	pCount = pCount_global;
439	>	MPI_Allreduce(&nCount, &nCount_global, 1, MPI_INTEGER, MPI_SUM,
440	>	MPI_COMM_WORLD);
441	>	nCount = nCount_global;
442	>	MPI_Allreduce(pPos.getArrayPointer(), pPos_global.getArrayPointer(), 3,
443	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
444	>	pPos = pPos_global;
445	>	MPI_Allreduce(nPos.getArrayPointer(), nPos_global.getArrayPointer(), 3,
446	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
447	>	nPos = nPos_global;
448	>	MPI_Allreduce(dipoleVector.getArrayPointer(),
449	>	dipVec_global.getArrayPointer(), 3,
450	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
451	>	dipoleVector = dipVec_global;
452	>	#endif //is_mpi
453
454	<	if (info->integrableObjects[vr]->isLinear()) {
454	>	// first load the accumulated dipole moment (if dipoles were present)
455	>	Vector3d boxDipole = dipoleVector;
456	>	// now include the dipole moment due to charges
457	>	// use the lesser of the positive and negative charge totals
458	>	RealType chg_value = nChg <= pChg ? nChg : pChg;
459	>
460	>	// find the average positions
461	>	if (pCount > 0 && nCount > 0 ) {
462	>	pPos /= pCount;
463	>	nPos /= nCount;
464	>	}
465
466	<	l= info->integrableObjects[vr]->linearAxis();
467	<	m = (l+1)%3;
306	<	n = (l+2)%3;
466	>	// dipole is from the negative to the positive (physics notation)
467	>	boxDipole += (pPos - nPos) * chg_value;
468
469	<	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	<
469	>	return boxDipole;
470		}
471
472	<	// Get the Center of Mass drift velocity.
472	>	// Returns the Heat Flux Vector for the system
473	>	Vector3d Thermo::getHeatFlux(){
474	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
475	>	SimInfo::MoleculeIterator miter;
476	>	std::vector<StuntDouble*>::iterator iiter;
477	>	Molecule* mol;
478	>	StuntDouble* integrableObject;
479	>	RigidBody::AtomIterator ai;
480	>	Atom* atom;
481	>	Vector3d vel;
482	>	Vector3d angMom;
483	>	Mat3x3d I;
484	>	int i;
485	>	int j;
486	>	int k;
487	>	RealType mass;
488
489	<	getCOMVel(vdrift);
490	<
491	<	//  Corrects for the center of mass drift.
492	<	// sums all the momentum and divides by total mass.
489	>	Vector3d x_a;
490	>	RealType kinetic;
491	>	RealType potential;
492	>	RealType eatom;
493	>	RealType AvgE_a_ = 0;
494	>	// Convective portion of the heat flux
495	>	Vector3d heatFluxJc = V3Zero;
496
497	<	for(vd = 0; vd < nobj; vd++){
498	<
499	<	info->integrableObjects[vd]->getVel(aVel);
500	<
501	<	for (j=0; j < 3; j++)
502	<	aVel[j] -= vdrift[j];
497	>	/* Calculate convective portion of the heat flux */
498	>	for (mol = info_->beginMolecule(miter); mol != NULL;
499	>	mol = info_->nextMolecule(miter)) {
500	>
501	>	for (integrableObject = mol->beginIntegrableObject(iiter);
502	>	integrableObject != NULL;
503	>	integrableObject = mol->nextIntegrableObject(iiter)) {
504
505	<	info->integrableObjects[vd]->setVel( aVel );
506	<	}
505	>	mass = integrableObject->getMass();
506	>	vel = integrableObject->getVel();
507
508	<	}
508	>	kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
509	>
510	>	if (integrableObject->isDirectional()) {
511	>	angMom = integrableObject->getJ();
512	>	I = integrableObject->getI();
513
514	<	void Thermo::getCOMVel(double vdrift[3]){
514	>	if (integrableObject->isLinear()) {
515	>	i = integrableObject->linearAxis();
516	>	j = (i + 1) % 3;
517	>	k = (i + 2) % 3;
518	>	kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
519	>	} else {
520	>	kinetic += angMom[0]*angMom[0]/I(0, 0) + angMom[1]*angMom[1]/I(1, 1)
521	>	+ angMom[2]*angMom[2]/I(2, 2);
522	>	}
523	>	}
524
525	<	double mtot, mtot_local;
349	<	double aVel[3], amass;
350	<	double vdrift_local[3];
351	<	int vd, j;
352	<	int nobj;
525	>	potential = 0.0;
526
527	<	nobj   = info->integrableObjects.size();
527	>	if (integrableObject->isRigidBody()) {
528	>	RigidBody* rb = dynamic_cast<RigidBody*>(integrableObject);
529	>	for (atom = rb->beginAtom(ai); atom != NULL;
530	>	atom = rb->nextAtom(ai)) {
531	>	potential +=  atom->getParticlePot();
532	>	}
533	>	} else {
534	>	potential = integrableObject->getParticlePot();
535	>	cerr << "ppot = "  << potential << "\n";
536	>	}
537
538	<	mtot_local = 0.0;
539	<	vdrift_local[0] = 0.0;
540	<	vdrift_local[1] = 0.0;
541	<	vdrift_local[2] = 0.0;
542	<
543	<	for(vd = 0; vd < nobj; vd++){
544	<
545	<	amass = info->integrableObjects[vd]->getMass();
364	<	info->integrableObjects[vd]->getVel( aVel );
538	>	potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2
539	>	// The potential may not be a 1/2 factor
540	>	eatom = (kinetic + potential)/2.0;  // amu A^2/fs^2
541	>	heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3
542	>	heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3
543	>	heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3
544	>	}
545	>	}
546
547	<	for(j = 0; j < 3; j++)
367	<	vdrift_local[j] += aVel[j] * amass;
368	<
369	<	mtot_local += amass;
370	<	}
547	>	std::cerr << "Heat flux heatFluxJc is: " << heatFluxJc << std::endl;
548
549	+	/* The J_v vector is reduced in fortan so everyone has the global
550	+	*  Jv. Jc is computed over the local atoms and must be reduced
551	+	*  among all processors.
552	+	*/
553		#ifdef IS_MPI
554	<	MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
555	<	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	<	}
554	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &heatFluxJc[0], 3, MPI::REALTYPE,
555	>	MPI::SUM);
556		#endif
557
558	<	for (vd = 0; vd < 3; vd++) {
383	<	vdrift[vd] = vdrift[vd] / mtot;
384	<	}
385	<
386	<	}
558	>	// (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3
559
560	<	void Thermo::getCOM(double COM[3]){
561	<
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++){
560	>	Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() *
561	>	PhysicalConstants::energyConvert;
562
563	<	amass = info->integrableObjects[i]->getMass();
564	<	info->integrableObjects[i]->getPos( aPos );
406	<
407	<	for(j = 0; j < 3; j++)
408	<	COM_local[j] += aPos[j] * amass;
563	>	std::cerr << "Heat flux Jc is: " << heatFluxJc << std::endl;
564	>	std::cerr << "Heat flux Jv is: " << heatFluxJv << std::endl;
565
566	<	mtot_local += amass;
566	>	// Correct for the fact the flux is 1/V (Jc + Jv)
567	>	return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3
568		}
569	<
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	<	}
569	>	} //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 1723 by gezelter, Thu May 24 20:59:54 2012 UTC

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