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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 1665 by gezelter, Tue Nov 22 20:38:56 2011 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"
13	<	#include "MatVec3.h"
50	>	#include "brains/Thermo.hpp"
51	>	#include "primitives/Molecule.hpp"
52	>	#include "utils/simError.h"
53	>	#include "utils/PhysicalConstants.hpp"
54
55	<	#ifdef IS_MPI
16	<	#define __C
17	<	#include "mpiSimulation.hpp"
18	<	#endif // is_mpi
55	>	namespace OpenMD {
56
57	<	inline double roundMe( double x ){
58	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
59	<	}
57	>	RealType Thermo::getKinetic() {
58	>	SimInfo::MoleculeIterator miter;
59	>	std::vector<StuntDouble*>::iterator iiter;
60	>	Molecule* mol;
61	>	StuntDouble* integrableObject;
62	>	Vector3d vel;
63	>	Vector3d angMom;
64	>	Mat3x3d I;
65	>	int i;
66	>	int j;
67	>	int k;
68	>	RealType mass;
69	>	RealType kinetic = 0.0;
70	>	RealType kinetic_global = 0.0;
71	>
72	>	for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
73	>	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
74	>	integrableObject = mol->nextIntegrableObject(iiter)) {
75	>
76	>	mass = integrableObject->getMass();
77	>	vel = integrableObject->getVel();
78	>
79	>	kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
80	>
81	>	if (integrableObject->isDirectional()) {
82	>	angMom = integrableObject->getJ();
83	>	I = integrableObject->getI();
84
85	<	Thermo::Thermo( SimInfo* the_info ) {
86	<	info = the_info;
87	<	int baseSeed = the_info->getSeed();
88	<
89	<	gaussStream = new gaussianSPRNG( baseSeed );
90	<	}
85	>	if (integrableObject->isLinear()) {
86	>	i = integrableObject->linearAxis();
87	>	j = (i + 1) % 3;
88	>	k = (i + 2) % 3;
89	>	kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
90	>	} else {
91	>	kinetic += angMom[0]*angMom[0]/I(0, 0) + angMom[1]*angMom[1]/I(1, 1)
92	>	+ angMom[2]*angMom[2]/I(2, 2);
93	>	}
94	>	}
95	>
96	>	}
97	>	}
98	>
99	>	#ifdef IS_MPI
100
101	<	Thermo::~Thermo(){
102	<	delete gaussStream;
103	<	}
101	>	MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
102	>	MPI_COMM_WORLD);
103	>	kinetic = kinetic_global;
104
105	<	double Thermo::getKinetic(){
105	>	#endif //is_mpi
106
107	<	const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
38	<	double kinetic;
39	<	double amass;
40	<	double aVel[3], aJ[3], I[3][3];
41	<	int i, j, k, kl;
107	>	kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
108
109	<	double kinetic_global;
110	<	vector<StuntDouble *> integrableObjects = info->integrableObjects;
45	<
46	<	kinetic = 0.0;
47	<	kinetic_global = 0.0;
109	>	return kinetic;
110	>	}
111
112	<	for (kl=0; kl<integrableObjects.size(); kl++) {
113	<	integrableObjects[kl]->getVel(aVel);
114	<	amass = integrableObjects[kl]->getMass();
112	>	RealType Thermo::getPotential() {
113	>	RealType potential = 0.0;
114	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
115	>	RealType shortRangePot_local =  curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
116
117	<	for(j=0; j<3; j++)
54	<	kinetic += amass*aVel[j]*aVel[j];
117	>	// Get total potential for entire system from MPI.
118
56	–	if (integrableObjects[kl]->isDirectional()){
57	–
58	–	integrableObjects[kl]->getJ( aJ );
59	–	integrableObjects[kl]->getI( I );
60	–
61	–	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	–	}
119		#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;
120
121	<	return kinetic;
122	<	}
121	>	MPI_Allreduce(&shortRangePot_local, &potential, 1, MPI_REALTYPE, MPI_SUM,
122	>	MPI_COMM_WORLD);
123	>	potential += curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
124
125	<	double Thermo::getPotential(){
84	<
85	<	double potential_local;
86	<	double potential;
87	<	int el, nSRI;
88	<	Molecule* molecules;
125	>	#else
126
127	<	molecules = info->molecules;
91	<	nSRI = info->n_SRI;
127	>	potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
128
129	<	potential_local = 0.0;
94	<	potential = 0.0;
95	<	potential_local += info->lrPot;
129	>	#endif // is_mpi
130
131	<	for( el=0; el<info->n_mol; el++ ){
98	<	potential_local += molecules[el].getPotential();
131	>	return potential;
132		}
133
134	<	// Get total potential for entire system from MPI.
135	<	#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
134	>	RealType Thermo::getTotalE() {
135	>	RealType total;
136
137	<	return potential;
138	<	}
137	>	total = this->getKinetic() + this->getPotential();
138	>	return total;
139	>	}
140
141	<	double Thermo::getTotalE(){
141	>	RealType Thermo::getTemperature() {
142	>
143	>	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
144	>	return temperature;
145	>	}
146
147	<	double total;
147	>	RealType Thermo::getVolume() {
148	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
149	>	return curSnapshot->getVolume();
150	>	}
151
152	<	total = this->getKinetic() + this->getPotential();
117	<	return total;
118	<	}
152	>	RealType Thermo::getPressure() {
153
154	<	double Thermo::getTemperature(){
154	>	// Relies on the calculation of the full molecular pressure tensor
155
122	–	const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
123	–	double temperature;
156
157	<	temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
158	<	return temperature;
127	<	}
157	>	Mat3x3d tensor;
158	>	RealType pressure;
159
160	<	double Thermo::getVolume() {
160	>	tensor = getPressureTensor();
161
162	<	return info->boxVol;
132	<	}
162	>	pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
163
164	<	double Thermo::getPressure() {
164	>	return pressure;
165	>	}
166
167	<	// 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;
167	>	RealType Thermo::getPressure(int direction) {
168
169	<	this->getPressureTensor(press);
169	>	// Relies on the calculation of the full molecular pressure tensor
170
171	<	pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
171	>
172	>	Mat3x3d tensor;
173	>	RealType pressure;
174
175	<	return pressure;
147	<	}
175	>	tensor = getPressureTensor();
176
177	<	double Thermo::getPressureX() {
177	>	pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);
178
179	<	// Relies on the calculation of the full molecular pressure tensor
180	<
153	<	const double p_convert = 1.63882576e8;
154	<	double press[3][3];
155	<	double pressureX;
179	>	return pressure;
180	>	}
181
182	<	this->getPressureTensor(press);
182	>	Mat3x3d Thermo::getPressureTensor() {
183	>	// returns pressure tensor in units amu*fs^-2*Ang^-1
184	>	// routine derived via viral theorem description in:
185	>	// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
186	>	Mat3x3d pressureTensor;
187	>	Mat3x3d p_local(0.0);
188	>	Mat3x3d p_global(0.0);
189
190	<	pressureX = p_convert * press[0][0];
190	>	SimInfo::MoleculeIterator i;
191	>	std::vector<StuntDouble*>::iterator j;
192	>	Molecule* mol;
193	>	StuntDouble* integrableObject;
194	>	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
195	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
196	>	integrableObject = mol->nextIntegrableObject(j)) {
197
198	<	return pressureX;
199	<	}
198	>	RealType mass = integrableObject->getMass();
199	>	Vector3d vcom = integrableObject->getVel();
200	>	p_local += mass * outProduct(vcom, vcom);
201	>	}
202	>	}
203	>
204	>	#ifdef IS_MPI
205	>	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
206	>	#else
207	>	p_global = p_local;
208	>	#endif // is_mpi
209
210	<	double Thermo::getPressureY() {
210	>	RealType volume = this->getVolume();
211	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
212	>	Mat3x3d tau = curSnapshot->statData.getTau();
213
214	<	// Relies on the calculation of the full molecular pressure tensor
215	<
216	<	const double p_convert = 1.63882576e8;
217	<	double press[3][3];
170	<	double pressureY;
214	>	pressureTensor =  (p_global + PhysicalConstants::energyConvert* tau)/volume;
215	>
216	>	return pressureTensor;
217	>	}
218
172	–	this->getPressureTensor(press);
219
220	<	pressureY = p_convert * press[1][1];
220	>	void Thermo::saveStat(){
221	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
222	>	Stats& stat = currSnapshot->statData;
223	>
224	>	stat[Stats::KINETIC_ENERGY] = getKinetic();
225	>	stat[Stats::POTENTIAL_ENERGY] = getPotential();
226	>	stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY]  + stat[Stats::POTENTIAL_ENERGY] ;
227	>	stat[Stats::TEMPERATURE] = getTemperature();
228	>	stat[Stats::PRESSURE] = getPressure();
229	>	stat[Stats::VOLUME] = getVolume();
230
231	<	return pressureY;
232	<	}
231	>	Mat3x3d tensor =getPressureTensor();
232	>	stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);
233	>	stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);
234	>	stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);
235	>	stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);
236	>	stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);
237	>	stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);
238	>	stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);
239	>	stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);
240	>	stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);
241
242	<	double Thermo::getPressureZ() {
242	>	// grab the simulation box dipole moment if specified
243	>	if (info_->getCalcBoxDipole()){
244	>	Vector3d totalDipole = getBoxDipole();
245	>	stat[Stats::BOX_DIPOLE_X] = totalDipole(0);
246	>	stat[Stats::BOX_DIPOLE_Y] = totalDipole(1);
247	>	stat[Stats::BOX_DIPOLE_Z] = totalDipole(2);
248	>	}
249
250	<	// 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;
250	>	Globals* simParams = info_->getSimParams();
251
252	<	this->getPressureTensor(press);
252	>	if (simParams->haveTaggedAtomPair() &&
253	>	simParams->havePrintTaggedPairDistance()) {
254	>	if ( simParams->getPrintTaggedPairDistance()) {
255	>
256	>	std::pair<int, int> tap = simParams->getTaggedAtomPair();
257	>	Vector3d pos1, pos2, rab;
258
259	<	pressureZ = p_convert * press[2][2];
259	>	#ifdef IS_MPI
260	>	std::cerr << "tap = " << tap.first << "  " << tap.second << std::endl;
261
262	<	return pressureZ;
263	<	}
262	>	int mol1 = info_->getGlobalMolMembership(tap.first);
263	>	int mol2 = info_->getGlobalMolMembership(tap.second);
264	>	std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
265
266	+	int proc1 = info_->getMolToProc(mol1);
267	+	int proc2 = info_->getMolToProc(mol2);
268
269	<	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
269	>	std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
270
271	<	const double e_convert = 4.184e-4;
271	>	RealType data[3];
272	>	if (proc1 == worldRank) {
273	>	StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
274	>	std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
275	>	pos1 = sd1->getPos();
276	>	data[0] = pos1.x();
277	>	data[1] = pos1.y();
278	>	data[2] = pos1.z();
279	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
280	>	} else {
281	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
282	>	pos1 = Vector3d(data);
283	>	}
284
202	–	double molmass, volume;
203	–	double vcom[3];
204	–	double p_local[9], p_global[9];
205	–	int i, j, k;
285
286	<	for (i=0; i < 9; i++) {
287	<	p_local[i] = 0.0;
288	<	p_global[i] = 0.0;
289	<	}
290	<
291	<	// use velocities of integrableObjects and their masses:
292	<
293	<	for (i=0; i < info->integrableObjects.size(); i++) {
294	<
295	<	molmass = info->integrableObjects[i]->getMass();
296	<
297	<	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);
286	>	if (proc2 == worldRank) {
287	>	StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
288	>	std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
289	>	pos2 = sd2->getPos();
290	>	data[0] = pos2.x();
291	>	data[1] = pos2.y();
292	>	data[2] = pos2.z();
293	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
294	>	} else {
295	>	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
296	>	pos2 = Vector3d(data);
297	>	}
298		#else
299	<	for (i=0; i<9; i++) {
300	<	p_global[i] = p_local[i];
301	<	}
302	<	#endif // is_mpi
303	<
304	<	volume = this->getVolume();
305	<
306	<
307	<
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;
299	>	StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
300	>	StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
301	>	pos1 = at1->getPos();
302	>	pos2 = at2->getPos();
303	>	#endif
304	>	rab = pos2 - pos1;
305	>	currSnapshot->wrapVector(rab);
306	>	stat[Stats::TAGGED_PAIR_DISTANCE] =  rab.length();
307	>	}
308		}
309	+
310	+	/**@todo need refactorying*/
311	+	//Conserved Quantity is set by integrator and time is set by setTime
312	+
313		}
252	–	}
314
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;
315
316	<	if (!info->have_target_temp) {
317	<	sprintf( painCave.errMsg,
318	<	"You can't resample the velocities without a targetTemp!\n"
319	<	);
320	<	painCave.isFatal = 1;
321	<	painCave.severity = OOPSE_ERROR;
322	<	simError();
323	<	return;
324	<	}
316	>	Vector3d Thermo::getBoxDipole() {
317	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
318	>	SimInfo::MoleculeIterator miter;
319	>	std::vector<Atom*>::iterator aiter;
320	>	Molecule* mol;
321	>	Atom* atom;
322	>	RealType charge;
323	>	RealType moment(0.0);
324	>	Vector3d ri(0.0);
325	>	Vector3d dipoleVector(0.0);
326	>	Vector3d nPos(0.0);
327	>	Vector3d pPos(0.0);
328	>	RealType nChg(0.0);
329	>	RealType pChg(0.0);
330	>	int nCount = 0;
331	>	int pCount = 0;
332
333	<	nobj = info->integrableObjects.size();
334	<
335	<	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++){
333	>	RealType chargeToC = 1.60217733e-19;
334	>	RealType angstromToM = 1.0e-10;
335	>	RealType debyeToCm = 3.33564095198e-30;
336
337	<	// uses equipartition theory to solve for vbar in angstrom/fs
337	>	for (mol = info_->beginMolecule(miter); mol != NULL;
338	>	mol = info_->nextMolecule(miter)) {
339
340	<	av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass();
341	<	vbar = sqrt( av2 );
289	<
290	<	// picks random velocities from a gaussian distribution
291	<	// centered on vbar
292	<
293	<	for (j=0; j<3; j++)
294	<	aVel[j] = vbar * gaussStream->getGaussian();
295	<
296	<	info->integrableObjects[vr]->setVel( aVel );
297	<
298	<	if(info->integrableObjects[vr]->isDirectional()){
299	<
300	<	info->integrableObjects[vr]->getI( I );
301	<
302	<	if (info->integrableObjects[vr]->isLinear()) {
303	<
304	<	l= info->integrableObjects[vr]->linearAxis();
305	<	m = (l+1)%3;
306	<	n = (l+2)%3;
307	<
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();
340	>	for (atom = mol->beginAtom(aiter); atom != NULL;
341	>	atom = mol->nextAtom(aiter)) {
342
343	<	} else {
344	<	for (j = 0 ; j < 3; j++) {
345	<	vbar = sqrt( 2.0 * kebar * I[j][j] );
346	<	aJ[j] = vbar * gaussStream->getGaussian();
318	<	}
319	<	} // else isLinear
343	>	if (atom->isCharge() ) {
344	>	charge = 0.0;
345	>	GenericData* data = atom->getAtomType()->getPropertyByName("Charge");
346	>	if (data != NULL) {
347
348	<	info->integrableObjects[vr]->setJ( aJ );
349	<
323	<	}//isDirectional
348	>	charge = (dynamic_cast<DoubleGenericData*>(data))->getData();
349	>	charge *= chargeToC;
350
351	<	}
351	>	ri = atom->getPos();
352	>	currSnapshot->wrapVector(ri);
353	>	ri *= angstromToM;
354
355	<	// Get the Center of Mass drift velocity.
356	<
357	<	getCOMVel(vdrift);
358	<
359	<	//  Corrects for the center of mass drift.
360	<	// sums all the momentum and divides by total mass.
361	<
362	<	for(vd = 0; vd < nobj; vd++){
363	<
364	<	info->integrableObjects[vd]->getVel(aVel);
365	<
338	<	for (j=0; j < 3; j++)
339	<	aVel[j] -= vdrift[j];
355	>	if (charge < 0.0) {
356	>	nPos += ri;
357	>	nChg -= charge;
358	>	nCount++;
359	>	} else if (charge > 0.0) {
360	>	pPos += ri;
361	>	pChg += charge;
362	>	pCount++;
363	>	}
364	>	}
365	>	}
366
367	<	info->integrableObjects[vd]->setVel( aVel );
368	<	}
369	<
370	<	}
371	<
372	<	void Thermo::getCOMVel(double vdrift[3]){
373	<
374	<	double mtot, mtot_local;
375	<	double aVel[3], amass;
376	<	double vdrift_local[3];
377	<	int vd, j;
378	<	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++){
367	>	if (atom->isDipole() ) {
368	>	Vector3d u_i = atom->getElectroFrame().getColumn(2);
369	>	GenericData* data = dynamic_cast<DirectionalAtomType*>(atom->getAtomType())->getPropertyByName("Dipole");
370	>	if (data != NULL) {
371	>	moment = (dynamic_cast<DoubleGenericData*>(data))->getData();
372	>
373	>	moment *= debyeToCm;
374	>	dipoleVector += u_i * moment;
375	>	}
376	>	}
377	>	}
378	>	}
379
380	<	amass = info->integrableObjects[vd]->getMass();
364	<	info->integrableObjects[vd]->getVel( aVel );
365	<
366	<	for(j = 0; j < 3; j++)
367	<	vdrift_local[j] += aVel[j] * amass;
368	<
369	<	mtot_local += amass;
370	<	}
371	<
380	>
381		#ifdef IS_MPI
382	<	MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
383	<	MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
384	<	#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	<	}
382	>	RealType pChg_global, nChg_global;
383	>	int pCount_global, nCount_global;
384	>	Vector3d pPos_global, nPos_global, dipVec_global;
385
386	<	void Thermo::getCOM(double COM[3]){
386	>	MPI_Allreduce(&pChg, &pChg_global, 1, MPI_REALTYPE, MPI_SUM,
387	>	MPI_COMM_WORLD);
388	>	pChg = pChg_global;
389	>	MPI_Allreduce(&nChg, &nChg_global, 1, MPI_REALTYPE, MPI_SUM,
390	>	MPI_COMM_WORLD);
391	>	nChg = nChg_global;
392	>	MPI_Allreduce(&pCount, &pCount_global, 1, MPI_INTEGER, MPI_SUM,
393	>	MPI_COMM_WORLD);
394	>	pCount = pCount_global;
395	>	MPI_Allreduce(&nCount, &nCount_global, 1, MPI_INTEGER, MPI_SUM,
396	>	MPI_COMM_WORLD);
397	>	nCount = nCount_global;
398	>	MPI_Allreduce(pPos.getArrayPointer(), pPos_global.getArrayPointer(), 3,
399	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
400	>	pPos = pPos_global;
401	>	MPI_Allreduce(nPos.getArrayPointer(), nPos_global.getArrayPointer(), 3,
402	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
403	>	nPos = nPos_global;
404	>	MPI_Allreduce(dipoleVector.getArrayPointer(),
405	>	dipVec_global.getArrayPointer(), 3,
406	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
407	>	dipoleVector = dipVec_global;
408	>	#endif //is_mpi
409
410	<	double mtot, mtot_local;
411	<	double aPos[3], amass;
412	<	double COM_local[3];
413	<	int i, j;
414	<	int nobj;
410	>	// first load the accumulated dipole moment (if dipoles were present)
411	>	Vector3d boxDipole = dipoleVector;
412	>	// now include the dipole moment due to charges
413	>	// use the lesser of the positive and negative charge totals
414	>	RealType chg_value = nChg <= pChg ? nChg : pChg;
415	>
416	>	// find the average positions
417	>	if (pCount > 0 && nCount > 0 ) {
418	>	pPos /= pCount;
419	>	nPos /= nCount;
420	>	}
421
422	<	mtot_local = 0.0;
423	<	COM_local[0] = 0.0;
398	<	COM_local[1] = 0.0;
399	<	COM_local[2] = 0.0;
422	>	// dipole is from the negative to the positive (physics notation)
423	>	boxDipole += (pPos - nPos) * chg_value;
424
425	<	nobj = info->integrableObjects.size();
402	<	for(i = 0; i < nobj; i++){
403	<
404	<	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;
425	>	return boxDipole;
426		}
427	<
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	<	}
427	>	} //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 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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