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

Comparing:
trunk/src/brains/Thermo.cpp (file contents), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/brains/Thermo.cpp (file contents), Revision 1710 by gezelter, Fri May 18 21:44:02 2012 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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>
#	Line 49 | Line 50
50		#include "brains/Thermo.hpp"
51		#include "primitives/Molecule.hpp"
52		#include "utils/simError.h"
53	<	#include "utils/OOPSEConstant.hpp"
53	>	#include "utils/PhysicalConstants.hpp"
54	>	#include "types/MultipoleAdapter.hpp"
55
56	<	namespace oopse {
56	>	namespace OpenMD {
57
58	<	double Thermo::getKinetic() {
58	>	RealType Thermo::getKinetic() {
59		SimInfo::MoleculeIterator miter;
60		std::vector<StuntDouble*>::iterator iiter;
61		Molecule* mol;
#	Line 64 | Line 66 | namespace oopse {
66		int i;
67		int j;
68		int k;
69	<	double kinetic = 0.0;
70	<	double kinetic_global = 0.0;
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	<	double mass = integrableObject->getMass();
78	<	Vector3d vel = integrableObject->getVel();
79	<
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	<
81	>
82		if (integrableObject->isDirectional()) {
83		angMom = integrableObject->getJ();
84		I = integrableObject->getI();
#	Line 96 | Line 99 | namespace oopse {
99
100		#ifdef IS_MPI
101
102	<	MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_DOUBLE, MPI_SUM,
102	>	MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
103		MPI_COMM_WORLD);
104		kinetic = kinetic_global;
105
106		#endif //is_mpi
107
108	<	kinetic = kinetic * 0.5 / OOPSEConstant::energyConvert;
108	>	kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
109
110		return kinetic;
111		}
112
113	<	double Thermo::getPotential() {
114	<	double potential = 0.0;
113	>	RealType Thermo::getPotential() {
114	>	RealType potential = 0.0;
115		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
116	<	double potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] +
114	<	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
116	>	RealType shortRangePot_local =  curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
117
118		// Get total potential for entire system from MPI.
119
120		#ifdef IS_MPI
121
122	<	MPI_Allreduce(&potential_local, &potential, 1, MPI_DOUBLE, MPI_SUM,
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		#else
127
128	<	potential = potential_local;
128	>	potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
129
130		#endif // is_mpi
131
132		return potential;
133		}
134
135	<	double Thermo::getTotalE() {
136	<	double total;
135	>	RealType Thermo::getTotalE() {
136	>	RealType total;
137
138		total = this->getKinetic() + this->getPotential();
139		return total;
140		}
141
142	<	double Thermo::getTemperature() {
142	>	RealType Thermo::getTemperature() {
143
144	<	double temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb );
144	>	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
145		return temperature;
146		}
147
148	<	double Thermo::getVolume() {
148	>	RealType Thermo::getVolume() {
149		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
150		return curSnapshot->getVolume();
151		}
152
153	<	double Thermo::getPressure() {
153	>	RealType Thermo::getPressure() {
154
155		// Relies on the calculation of the full molecular pressure tensor
156
157
158		Mat3x3d tensor;
159	<	double pressure;
159	>	RealType pressure;
160
161		tensor = getPressureTensor();
162
163	<	pressure = OOPSEConstant::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
163	>	pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
164
165		return pressure;
166		}
167
168	+	RealType Thermo::getPressure(int direction) {
169	+
170	+	// Relies on the calculation of the full molecular pressure tensor
171	+
172	+
173	+	Mat3x3d tensor;
174	+	RealType pressure;
175	+
176	+	tensor = getPressureTensor();
177	+
178	+	pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);
179	+
180	+	return pressure;
181	+	}
182	+
183		Mat3x3d Thermo::getPressureTensor() {
184		// returns pressure tensor in units amu*fs^-2*Ang^-1
185		// routine derived via viral theorem description in:
#	Line 178 | Line 196 | namespace oopse {
196		for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
197		integrableObject = mol->nextIntegrableObject(j)) {
198
199	<	double mass = integrableObject->getMass();
199	>	RealType mass = integrableObject->getMass();
200		Vector3d vcom = integrableObject->getVel();
201		p_local += mass * outProduct(vcom, vcom);
202		}
203		}
204
205		#ifdef IS_MPI
206	<	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
206	>	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
207		#else
208		p_global = p_local;
209		#endif // is_mpi
210
211	<	double volume = this->getVolume();
211	>	RealType volume = this->getVolume();
212		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
213	<	Mat3x3d tau = curSnapshot->statData.getTau();
213	>	Mat3x3d tau = curSnapshot->getTau();
214
215	<	pressureTensor =  (p_global + OOPSEConstant::energyConvert* tau)/volume;
216	<
215	>	pressureTensor =  (p_global + PhysicalConstants::energyConvert* tau)/volume;
216	>
217		return pressureTensor;
218		}
219
220	+
221		void Thermo::saveStat(){
222		Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
223		Stats& stat = currSnapshot->statData;
#	Line 210 | Line 229 | namespace oopse {
229		stat[Stats::PRESSURE] = getPressure();
230		stat[Stats::VOLUME] = getVolume();
231
232	+	Mat3x3d tensor =getPressureTensor();
233	+	stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);
234	+	stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);
235	+	stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);
236	+	stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);
237	+	stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);
238	+	stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);
239	+	stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);
240	+	stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);
241	+	stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);
242	+
243	+	// grab the simulation box dipole moment if specified
244	+	if (info_->getCalcBoxDipole()){
245	+	Vector3d totalDipole = getBoxDipole();
246	+	stat[Stats::BOX_DIPOLE_X] = totalDipole(0);
247	+	stat[Stats::BOX_DIPOLE_Y] = totalDipole(1);
248	+	stat[Stats::BOX_DIPOLE_Z] = totalDipole(2);
249	+	}
250	+
251	+	Globals* simParams = info_->getSimParams();
252	+
253	+	if (simParams->haveTaggedAtomPair() &&
254	+	simParams->havePrintTaggedPairDistance()) {
255	+	if ( simParams->getPrintTaggedPairDistance()) {
256	+
257	+	std::pair<int, int> tap = simParams->getTaggedAtomPair();
258	+	Vector3d pos1, pos2, rab;
259	+
260	+	#ifdef IS_MPI
261	+	std::cerr << "tap = " << tap.first << "  " << tap.second << std::endl;
262	+
263	+	int mol1 = info_->getGlobalMolMembership(tap.first);
264	+	int mol2 = info_->getGlobalMolMembership(tap.second);
265	+	std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
266	+
267	+	int proc1 = info_->getMolToProc(mol1);
268	+	int proc2 = info_->getMolToProc(mol2);
269	+
270	+	std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
271	+
272	+	RealType data[3];
273	+	if (proc1 == worldRank) {
274	+	StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
275	+	std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
276	+	pos1 = sd1->getPos();
277	+	data[0] = pos1.x();
278	+	data[1] = pos1.y();
279	+	data[2] = pos1.z();
280	+	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
281	+	} else {
282	+	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
283	+	pos1 = Vector3d(data);
284	+	}
285	+
286	+
287	+	if (proc2 == worldRank) {
288	+	StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
289	+	std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
290	+	pos2 = sd2->getPos();
291	+	data[0] = pos2.x();
292	+	data[1] = pos2.y();
293	+	data[2] = pos2.z();
294	+	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
295	+	} else {
296	+	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
297	+	pos2 = Vector3d(data);
298	+	}
299	+	#else
300	+	StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
301	+	StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
302	+	pos1 = at1->getPos();
303	+	pos2 = at2->getPos();
304	+	#endif
305	+	rab = pos2 - pos1;
306	+	currSnapshot->wrapVector(rab);
307	+	stat[Stats::TAGGED_PAIR_DISTANCE] =  rab.length();
308	+	}
309	+	}
310	+
311		/**@todo need refactorying*/
312		//Conserved Quantity is set by integrator and time is set by setTime
313
314		}
315
316	<	} //end namespace oopse
316	>
317	>	Vector3d Thermo::getBoxDipole() {
318	>	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
319	>	SimInfo::MoleculeIterator miter;
320	>	std::vector<Atom*>::iterator aiter;
321	>	Molecule* mol;
322	>	Atom* atom;
323	>	RealType charge;
324	>	RealType moment(0.0);
325	>	Vector3d ri(0.0);
326	>	Vector3d dipoleVector(0.0);
327	>	Vector3d nPos(0.0);
328	>	Vector3d pPos(0.0);
329	>	RealType nChg(0.0);
330	>	RealType pChg(0.0);
331	>	int nCount = 0;
332	>	int pCount = 0;
333	>
334	>	RealType chargeToC = 1.60217733e-19;
335	>	RealType angstromToM = 1.0e-10;
336	>	RealType debyeToCm = 3.33564095198e-30;
337	>
338	>	for (mol = info_->beginMolecule(miter); mol != NULL;
339	>	mol = info_->nextMolecule(miter)) {
340	>
341	>	for (atom = mol->beginAtom(aiter); atom != NULL;
342	>	atom = mol->nextAtom(aiter)) {
343	>
344	>	if (atom->isCharge() ) {
345	>	charge = 0.0;
346	>	GenericData* data = atom->getAtomType()->getPropertyByName("Charge");
347	>	if (data != NULL) {
348	>
349	>	charge = (dynamic_cast<DoubleGenericData*>(data))->getData();
350	>	charge *= chargeToC;
351	>
352	>	ri = atom->getPos();
353	>	currSnapshot->wrapVector(ri);
354	>	ri *= angstromToM;
355	>
356	>	if (charge < 0.0) {
357	>	nPos += ri;
358	>	nChg -= charge;
359	>	nCount++;
360	>	} else if (charge > 0.0) {
361	>	pPos += ri;
362	>	pChg += charge;
363	>	pCount++;
364	>	}
365	>	}
366	>	}
367	>
368	>	MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType());
369	>	if (ma.isDipole() ) {
370	>	Vector3d u_i = atom->getElectroFrame().getColumn(2);
371	>	moment = ma.getDipoleMoment();
372	>	moment *= debyeToCm;
373	>	dipoleVector += u_i * moment;
374	>	}
375	>	}
376	>	}
377	>
378	>
379	>	#ifdef IS_MPI
380	>	RealType pChg_global, nChg_global;
381	>	int pCount_global, nCount_global;
382	>	Vector3d pPos_global, nPos_global, dipVec_global;
383	>
384	>	MPI_Allreduce(&pChg, &pChg_global, 1, MPI_REALTYPE, MPI_SUM,
385	>	MPI_COMM_WORLD);
386	>	pChg = pChg_global;
387	>	MPI_Allreduce(&nChg, &nChg_global, 1, MPI_REALTYPE, MPI_SUM,
388	>	MPI_COMM_WORLD);
389	>	nChg = nChg_global;
390	>	MPI_Allreduce(&pCount, &pCount_global, 1, MPI_INTEGER, MPI_SUM,
391	>	MPI_COMM_WORLD);
392	>	pCount = pCount_global;
393	>	MPI_Allreduce(&nCount, &nCount_global, 1, MPI_INTEGER, MPI_SUM,
394	>	MPI_COMM_WORLD);
395	>	nCount = nCount_global;
396	>	MPI_Allreduce(pPos.getArrayPointer(), pPos_global.getArrayPointer(), 3,
397	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
398	>	pPos = pPos_global;
399	>	MPI_Allreduce(nPos.getArrayPointer(), nPos_global.getArrayPointer(), 3,
400	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
401	>	nPos = nPos_global;
402	>	MPI_Allreduce(dipoleVector.getArrayPointer(),
403	>	dipVec_global.getArrayPointer(), 3,
404	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
405	>	dipoleVector = dipVec_global;
406	>	#endif //is_mpi
407	>
408	>	// first load the accumulated dipole moment (if dipoles were present)
409	>	Vector3d boxDipole = dipoleVector;
410	>	// now include the dipole moment due to charges
411	>	// use the lesser of the positive and negative charge totals
412	>	RealType chg_value = nChg <= pChg ? nChg : pChg;
413	>
414	>	// find the average positions
415	>	if (pCount > 0 && nCount > 0 ) {
416	>	pPos /= pCount;
417	>	nPos /= nCount;
418	>	}
419	>
420	>	// dipole is from the negative to the positive (physics notation)
421	>	boxDipole += (pPos - nPos) * chg_value;
422	>
423	>	return boxDipole;
424	>	}
425	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/Thermo.cpp (property svn:keywords), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/brains/Thermo.cpp (property svn:keywords), Revision 1710 by gezelter, Fri May 18 21:44:02 2012 UTC

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