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Comparing trunk/src/brains/Stats.cpp (file contents):
Revision 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC vs.
Revision 1925 by gezelter, Wed Aug 7 15:24:16 2013 UTC

#	Line 1 | Line 1
1		/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
2	>	* Copyright (c) 2005, 2009 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. 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, 234107 (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		/**
#	Line 48 | Line 49
49		*/
50
51		#include "brains/Stats.hpp"
52	+	#include "brains/Thermo.hpp"
53
54	<	namespace oopse {
54	>	namespace OpenMD {
55
56	<	bool Stats::isInit_ = false;
55	<	std::string Stats::title_[Stats::ENDINDEX - Stats::BEGININDEX];
56	<	std::string Stats::units_[Stats::ENDINDEX - Stats::BEGININDEX];
57	<	Stats::StatsMapType Stats::statsMap;
58	<	Stats::Stats() {
56	>	Stats::Stats(SimInfo* info) : isInit_(false), info_(info) {
57
58		if (!isInit_) {
59		init();
60		isInit_ = true;
61		}
64	–
62		}
63
64		void Stats::init() {
65	+
66	+	data_.resize(Stats::ENDINDEX);
67
68	<	Stats::title_[TIME] = "Time";
69	<	Stats::title_[TOTAL_ENERGY] = "Total Energy";
70	<	Stats::title_[POTENTIAL_ENERGY] = "Potential Energy";
71	<	Stats::title_[KINETIC_ENERGY] = "Kinetic Energy";
72	<	Stats::title_[TEMPERATURE] = "Temperature";
73	<	Stats::title_[PRESSURE] = "Pressure";
74	<	Stats::title_[VOLUME] = "Volume";
76	<	Stats::title_[CONSERVED_QUANTITY] = "Conserved Quantity";
77	<	Stats::title_[TRANSLATIONAL_KINETIC] = "Translational Kinetic";
78	<	Stats::title_[ROTATIONAL_KINETIC] = "Rotational Kinetic";
79	<	Stats::title_[LONG_RANGE_POTENTIAL] = "Long Range Potential";
80	<	Stats::title_[SHORT_RANGE_POTENTIAL] = "Short Range Potential";
81	<	Stats::title_[VANDERWAALS_POTENTIAL] = "van der waals Potential";
82	<	Stats::title_[ELECTROSTATIC_POTENTIAL] = "Electrostatic Potential";
83	<	Stats::title_[BOND_POTENTIAL] = "Bond Potential";
84	<	Stats::title_[BEND_POTENTIAL] = "Bend Potential";
85	<	Stats::title_[DIHEDRAL_POTENTIAL] = "Dihedral Potential";
86	<	Stats::title_[IMPROPER_POTENTIAL] = "Improper Potential";
87	<	Stats::title_[VRAW] = "Raw Potential";
88	<	Stats::title_[VHARM] = "Harmonic Potential";
89	<	Stats::title_[PRESSURE_TENSOR_X] = "pressure tensor x";
90	<	Stats::title_[PRESSURE_TENSOR_Y] = "pressure tensor y";
91	<	Stats::title_[PRESSURE_TENSOR_Z] = "pressure tensor z";
92	<	Stats::title_[BOX_DIPOLE_X] = "box dipole x";
93	<	Stats::title_[BOX_DIPOLE_Y] = "box dipole y";
94	<	Stats::title_[BOX_DIPOLE_Z] = "box dipole z";
68	>	StatsData time;
69	>	time.units =  "fs";
70	>	time.title =  "Time";
71	>	time.dataType = "RealType";
72	>	time.accumulator = new Accumulator();
73	>	data_[TIME] = time;
74	>	statsMap_["TIME"] = TIME;
75
76	<	Stats::units_[TIME] = "fs";
77	<	Stats::units_[TOTAL_ENERGY] = "kcal/mol";
78	<	Stats::units_[POTENTIAL_ENERGY] = "kcal/mol";
79	<	Stats::units_[KINETIC_ENERGY] = "kcal/mol";
80	<	Stats::units_[TEMPERATURE] = "K";
81	<	Stats::units_[PRESSURE] = "atm";
82	<	Stats::units_[VOLUME] = "A^3";
83	<	Stats::units_[CONSERVED_QUANTITY] = "kcal/mol";
84	<	Stats::units_[TRANSLATIONAL_KINETIC] = "kcal/mol";
85	<	Stats::units_[ROTATIONAL_KINETIC] = "kcal/mol";
86	<	Stats::units_[LONG_RANGE_POTENTIAL] = "kcal/mol";
87	<	Stats::units_[SHORT_RANGE_POTENTIAL] = "kcal/mol";
88	<	Stats::units_[VANDERWAALS_POTENTIAL] = "kcal/mol";
89	<	Stats::units_[ELECTROSTATIC_POTENTIAL] = "kcal/mol";
90	<	Stats::units_[BOND_POTENTIAL] = "kcal/mol";
111	<	Stats::units_[BEND_POTENTIAL] = "kcal/mol";
112	<	Stats::units_[DIHEDRAL_POTENTIAL] = "kcal/mol";
113	<	Stats::units_[IMPROPER_POTENTIAL] = "kcal/mol";
114	<	Stats::units_[VRAW] = "kcal/mol";
115	<	Stats::units_[VHARM] = "kcal/mol";
116	<	Stats::units_[PRESSURE_TENSOR_X] = "amu*fs^-2*Ang^-1";
117	<	Stats::units_[PRESSURE_TENSOR_Y] = "amu*fs^-2*Ang^-1";
118	<	Stats::units_[PRESSURE_TENSOR_Z] = "amu*fs^-2*Ang^-1";
119	<	Stats::units_[BOX_DIPOLE_X] = "C*m";
120	<	Stats::units_[BOX_DIPOLE_Y] = "C*m";
121	<	Stats::units_[BOX_DIPOLE_Z] = "C*m";
76	>	StatsData total_energy;
77	>	total_energy.units =  "kcal/mol";
78	>	total_energy.title =  "Total Energy";
79	>	total_energy.dataType = "RealType";
80	>	total_energy.accumulator = new Accumulator();
81	>	data_[TOTAL_ENERGY] = total_energy;
82	>	statsMap_["TOTAL_ENERGY"] =  TOTAL_ENERGY;
83	>
84	>	StatsData potential_energy;
85	>	potential_energy.units =  "kcal/mol";
86	>	potential_energy.title =  "Potential Energy";
87	>	potential_energy.dataType = "RealType";
88	>	potential_energy.accumulator = new Accumulator();
89	>	data_[POTENTIAL_ENERGY] = potential_energy;
90	>	statsMap_["POTENTIAL_ENERGY"] =  POTENTIAL_ENERGY;
91
92	<	Stats::statsMap.insert(StatsMapType::value_type("TIME", TIME));
93	<	Stats::statsMap.insert(StatsMapType::value_type("TOTAL_ENERGY", TOTAL_ENERGY));
94	<	Stats::statsMap.insert(StatsMapType::value_type("POTENTIAL_ENERGY", POTENTIAL_ENERGY));
95	<	Stats::statsMap.insert(StatsMapType::value_type("KINETIC_ENERGY", KINETIC_ENERGY));
96	<	Stats::statsMap.insert(StatsMapType::value_type("TEMPERATURE", TEMPERATURE));
97	<	Stats::statsMap.insert(StatsMapType::value_type("PRESSURE", PRESSURE));
98	<	Stats::statsMap.insert(StatsMapType::value_type("VOLUME", VOLUME));
99	<	Stats::statsMap.insert(StatsMapType::value_type("CONSERVED_QUANTITY", CONSERVED_QUANTITY));
100	<	Stats::statsMap.insert(StatsMapType::value_type("TRANSLATIONAL_KINETIC", TRANSLATIONAL_KINETIC));
101	<	Stats::statsMap.insert(StatsMapType::value_type("ROTATIONAL_KINETIC", ROTATIONAL_KINETIC));
102	<	Stats::statsMap.insert(StatsMapType::value_type("LONG_RANGE_POTENTIAL", LONG_RANGE_POTENTIAL));
103	<	Stats::statsMap.insert(StatsMapType::value_type("SHORT_RANGE_POTENTIAL", SHORT_RANGE_POTENTIAL));
104	<	Stats::statsMap.insert(StatsMapType::value_type("VANDERWAALS_POTENTIAL", VANDERWAALS_POTENTIAL));
105	<	Stats::statsMap.insert(StatsMapType::value_type("ELECTROSTATIC_POTENTIAL", ELECTROSTATIC_POTENTIAL));
106	<	Stats::statsMap.insert(StatsMapType::value_type("BOND_POTENTIAL", BOND_POTENTIAL));
107	<	Stats::statsMap.insert(StatsMapType::value_type("BEND_POTENTIAL", BEND_POTENTIAL));
108	<	Stats::statsMap.insert(StatsMapType::value_type("DIHEDRAL_POTENTIAL", DIHEDRAL_POTENTIAL));
109	<	Stats::statsMap.insert(StatsMapType::value_type("IMPROPER_POTENTIAL", IMPROPER_POTENTIAL));
110	<	Stats::statsMap.insert(StatsMapType::value_type("VRAW", VRAW));
111	<	Stats::statsMap.insert(StatsMapType::value_type("VHARM", VHARM));
112	<	Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_X", PRESSURE_TENSOR_X));
113	<	Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_Y", PRESSURE_TENSOR_Y));
114	<	Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_Z", PRESSURE_TENSOR_Z));
115	<	Stats::statsMap.insert(StatsMapType::value_type("BOX_DIPOLE_X", BOX_DIPOLE_X));
116	<	Stats::statsMap.insert(StatsMapType::value_type("BOX_DIPOLE_Y", BOX_DIPOLE_Y));
117	<	Stats::statsMap.insert(StatsMapType::value_type("BOX_DIPOLE_Z", BOX_DIPOLE_Z));
92	>	StatsData kinetic_energy;
93	>	kinetic_energy.units =  "kcal/mol";
94	>	kinetic_energy.title =  "Kinetic Energy";
95	>	kinetic_energy.dataType = "RealType";
96	>	kinetic_energy.accumulator = new Accumulator();
97	>	data_[KINETIC_ENERGY] = kinetic_energy;
98	>	statsMap_["KINETIC_ENERGY"] =  KINETIC_ENERGY;
99	>
100	>	StatsData temperature;
101	>	temperature.units =  "K";
102	>	temperature.title =  "Temperature";
103	>	temperature.dataType = "RealType";
104	>	temperature.accumulator = new Accumulator();
105	>	data_[TEMPERATURE] = temperature;
106	>	statsMap_["TEMPERATURE"] =  TEMPERATURE;
107	>
108	>	StatsData pressure;
109	>	pressure.units =  "atm";
110	>	pressure.title =  "Pressure";
111	>	pressure.dataType = "RealType";
112	>	pressure.accumulator = new Accumulator();
113	>	data_[PRESSURE] = pressure;
114	>	statsMap_["PRESSURE"] =  PRESSURE;
115	>
116	>	StatsData volume;
117	>	volume.units =  "A^3";
118	>	volume.title =  "Volume";
119	>	volume.dataType = "RealType";
120	>	volume.accumulator = new Accumulator();
121	>	data_[VOLUME] = volume;
122	>	statsMap_["VOLUME"] =  VOLUME;
123	>
124	>	StatsData hullvolume;
125	>	hullvolume.units =  "A^3";
126	>	hullvolume.title =  "Hull Volume";
127	>	hullvolume.dataType = "RealType";
128	>	hullvolume.accumulator = new Accumulator();
129	>	data_[HULLVOLUME] = hullvolume;
130	>	statsMap_["HULLVOLUME"] =  HULLVOLUME;
131	>
132	>	StatsData gyrvolume;
133	>	gyrvolume.units =  "A^3";
134	>	gyrvolume.title =  "Gyrational Volume";
135	>	gyrvolume.dataType = "RealType";
136	>	gyrvolume.accumulator = new Accumulator();
137	>	data_[GYRVOLUME] = gyrvolume;
138	>	statsMap_["GYRVOLUME"] =  GYRVOLUME;
139	>
140	>	StatsData conserved_quantity;
141	>	conserved_quantity.units =  "kcal/mol";
142	>	conserved_quantity.title =  "Conserved Quantity";
143	>	conserved_quantity.dataType = "RealType";
144	>	conserved_quantity.accumulator = new Accumulator();
145	>	data_[CONSERVED_QUANTITY] = conserved_quantity;
146	>	statsMap_["CONSERVED_QUANTITY"] =  CONSERVED_QUANTITY;
147	>
148	>	StatsData translational_kinetic;
149	>	translational_kinetic.units =  "kcal/mol";
150	>	translational_kinetic.title =  "Translational Kinetic";
151	>	translational_kinetic.dataType = "RealType";
152	>	translational_kinetic.accumulator = new Accumulator();
153	>	data_[TRANSLATIONAL_KINETIC] = translational_kinetic;
154	>	statsMap_["TRANSLATIONAL_KINETIC"] =  TRANSLATIONAL_KINETIC;
155	>
156	>	StatsData rotational_kinetic;
157	>	rotational_kinetic.units =  "kcal/mol";
158	>	rotational_kinetic.title =  "Rotational Kinetic";
159	>	rotational_kinetic.dataType = "RealType";
160	>	rotational_kinetic.accumulator = new Accumulator();
161	>	data_[ROTATIONAL_KINETIC] = rotational_kinetic;
162	>	statsMap_["ROTATIONAL_KINETIC"] =  ROTATIONAL_KINETIC;
163	>
164	>	StatsData long_range_potential;
165	>	long_range_potential.units =  "kcal/mol";
166	>	long_range_potential.title =  "Long Range Potential";
167	>	long_range_potential.dataType = "RealType";
168	>	long_range_potential.accumulator = new Accumulator();
169	>	data_[LONG_RANGE_POTENTIAL] = long_range_potential;
170	>	statsMap_["LONG_RANGE_POTENTIAL"] =  LONG_RANGE_POTENTIAL;
171	>
172	>	StatsData vanderwaals_potential;
173	>	vanderwaals_potential.units =  "kcal/mol";
174	>	vanderwaals_potential.title =  "van der waals Potential";
175	>	vanderwaals_potential.dataType = "RealType";
176	>	vanderwaals_potential.accumulator = new Accumulator();
177	>	data_[VANDERWAALS_POTENTIAL] = vanderwaals_potential;
178	>	statsMap_["VANDERWAALS_POTENTIAL"] =  VANDERWAALS_POTENTIAL;
179	>
180	>	StatsData electrostatic_potential;
181	>	electrostatic_potential.units =  "kcal/mol";
182	>	electrostatic_potential.title =  "Electrostatic Potential";
183	>	electrostatic_potential.dataType = "RealType";
184	>	electrostatic_potential.accumulator = new Accumulator();
185	>	data_[ELECTROSTATIC_POTENTIAL] = electrostatic_potential;
186	>	statsMap_["ELECTROSTATIC_POTENTIAL"] =  ELECTROSTATIC_POTENTIAL;
187	>
188	>	StatsData metallic_potential;
189	>	metallic_potential.units =  "kcal/mol";
190	>	metallic_potential.title =  "Metallic Potential";
191	>	metallic_potential.dataType = "RealType";
192	>	metallic_potential.accumulator = new Accumulator();
193	>	data_[METALLIC_POTENTIAL] = metallic_potential;
194	>	statsMap_["METALLIC_POTENTIAL"] =  METALLIC_POTENTIAL;
195	>
196	>	StatsData hydrogenbonding_potential;
197	>	hydrogenbonding_potential.units =  "kcal/mol";
198	>	hydrogenbonding_potential.title =  "Hydrogen Bonding Potential";
199	>	hydrogenbonding_potential.dataType = "RealType";
200	>	hydrogenbonding_potential.accumulator = new Accumulator();
201	>	data_[HYDROGENBONDING_POTENTIAL] = hydrogenbonding_potential;
202	>	statsMap_["HYDROGENBONDING_POTENTIAL"] =  HYDROGENBONDING_POTENTIAL;
203	>
204	>	StatsData reciprocal_potential;
205	>	reciprocal_potential.units =  "kcal/mol";
206	>	reciprocal_potential.title =  "Reciprocal Space Potential";
207	>	reciprocal_potential.dataType = "RealType";
208	>	reciprocal_potential.accumulator = new Accumulator();
209	>	data_[RECIPROCAL_POTENTIAL] = reciprocal_potential;
210	>	statsMap_["RECIPROCAL_POTENTIAL"] =  RECIPROCAL_POTENTIAL;
211	>
212	>	StatsData short_range_potential;
213	>	short_range_potential.units =  "kcal/mol";
214	>	short_range_potential.title =  "Short Range Potential";
215	>	short_range_potential.dataType = "RealType";
216	>	short_range_potential.accumulator = new Accumulator();
217	>	data_[SHORT_RANGE_POTENTIAL] = short_range_potential;
218	>	statsMap_["SHORT_RANGE_POTENTIAL"] =  SHORT_RANGE_POTENTIAL;
219	>
220	>	StatsData bond_potential;
221	>	bond_potential.units =  "kcal/mol";
222	>	bond_potential.title =  "Bond Potential";
223	>	bond_potential.dataType = "RealType";
224	>	bond_potential.accumulator = new Accumulator();
225	>	data_[BOND_POTENTIAL] = bond_potential;
226	>	statsMap_["BOND_POTENTIAL"] =  BOND_POTENTIAL;
227	>
228	>	StatsData bend_potential;
229	>	bend_potential.units =  "kcal/mol";
230	>	bend_potential.title =  "Bend Potential";
231	>	bend_potential.dataType = "RealType";
232	>	bend_potential.accumulator = new Accumulator();
233	>	data_[BEND_POTENTIAL] = bend_potential;
234	>	statsMap_["BEND_POTENTIAL"] =  BEND_POTENTIAL;
235	>
236	>	StatsData dihedral_potential;
237	>	dihedral_potential.units =  "kcal/mol";
238	>	dihedral_potential.title =  "Dihedral Potential";
239	>	dihedral_potential.dataType = "RealType";
240	>	dihedral_potential.accumulator = new Accumulator();
241	>	data_[DIHEDRAL_POTENTIAL] = dihedral_potential;
242	>	statsMap_["DIHEDRAL_POTENTIAL"] =  DIHEDRAL_POTENTIAL;
243	>
244	>	StatsData inversion_potential;
245	>	inversion_potential.units =  "kcal/mol";
246	>	inversion_potential.title =  "Inversion Potential";
247	>	inversion_potential.dataType = "RealType";
248	>	inversion_potential.accumulator = new Accumulator();
249	>	data_[INVERSION_POTENTIAL] = inversion_potential;
250	>	statsMap_["INVERSION_POTENTIAL"] =  INVERSION_POTENTIAL;
251	>
252	>	StatsData vraw;
253	>	vraw.units =  "kcal/mol";
254	>	vraw.title =  "Raw Potential";
255	>	vraw.dataType = "RealType";
256	>	vraw.accumulator = new Accumulator();
257	>	data_[RAW_POTENTIAL] = vraw;
258	>	statsMap_["RAW_POTENTIAL"] =  RAW_POTENTIAL;
259	>
260	>	StatsData vrestraint;
261	>	vrestraint.units =  "kcal/mol";
262	>	vrestraint.title =  "Restraint Potential";
263	>	vrestraint.dataType = "RealType";
264	>	vrestraint.accumulator = new Accumulator();
265	>	data_[RESTRAINT_POTENTIAL] = vrestraint;
266	>	statsMap_["RESTRAINT_POTENTIAL"] =  RESTRAINT_POTENTIAL;
267	>
268	>	StatsData pressure_tensor;
269	>	pressure_tensor.units =  "amu*fs^-2*Ang^-1";
270	>	pressure_tensor.title =  "Ptensor";
271	>	pressure_tensor.dataType = "Mat3x3d";
272	>	pressure_tensor.accumulator = new MatrixAccumulator();
273	>	data_[PRESSURE_TENSOR] = pressure_tensor;
274	>	statsMap_["PRESSURE_TENSOR"] =  PRESSURE_TENSOR;
275	>
276	>	StatsData system_dipole;
277	>	system_dipole.units =  "C*m";
278	>	system_dipole.title =  "System Dipole";
279	>	system_dipole.dataType = "Vector3d";
280	>	system_dipole.accumulator = new VectorAccumulator();
281	>	data_[SYSTEM_DIPOLE] = system_dipole;
282	>	statsMap_["SYSTEM_DIPOLE"] =  SYSTEM_DIPOLE;
283	>
284	>	StatsData tagged_pair_distance;
285	>	tagged_pair_distance.units =  "Ang";
286	>	tagged_pair_distance.title =  "Tagged_Pair_Distance";
287	>	tagged_pair_distance.dataType = "RealType";
288	>	tagged_pair_distance.accumulator = new Accumulator();
289	>	data_[TAGGED_PAIR_DISTANCE] = tagged_pair_distance;
290	>	statsMap_["TAGGED_PAIR_DISTANCE"] =  TAGGED_PAIR_DISTANCE;
291	>
292	>	StatsData shadowh;
293	>	shadowh.units =  "kcal/mol";
294	>	shadowh.title =  "Shadow Hamiltonian";
295	>	shadowh.dataType = "RealType";
296	>	shadowh.accumulator = new Accumulator();
297	>	data_[SHADOWH] = shadowh;
298	>	statsMap_["SHADOWH"] =  SHADOWH;
299	>
300	>	StatsData helfandmoment;
301	>	helfandmoment.units =  "Ang*kcal/mol";
302	>	helfandmoment.title =  "Thermal Helfand Moment";
303	>	helfandmoment.dataType = "Vector3d";
304	>	helfandmoment.accumulator = new VectorAccumulator();
305	>	data_[HELFANDMOMENT] = helfandmoment;
306	>	statsMap_["HELFANDMOMENT"] = HELFANDMOMENT;
307	>
308	>	StatsData heatflux;
309	>	heatflux.units = "amu/fs^3";
310	>	heatflux.title =  "Heat Flux";
311	>	heatflux.dataType = "Vector3d";
312	>	heatflux.accumulator = new VectorAccumulator();
313	>	data_[HEATFLUX] = heatflux;
314	>	statsMap_["HEATFLUX"] = HEATFLUX;
315	>
316	>	StatsData electronic_temperature;
317	>	electronic_temperature.units = "K";
318	>	electronic_temperature.title =  "Electronic Temperature";
319	>	electronic_temperature.dataType = "RealType";
320	>	electronic_temperature.accumulator = new Accumulator();
321	>	data_[ELECTRONIC_TEMPERATURE] = electronic_temperature;
322	>	statsMap_["ELECTRONIC_TEMPERATURE"] = ELECTRONIC_TEMPERATURE;
323	>
324	>	StatsData com;
325	>	com.units =  "A";
326	>	com.title =  "Center of Mass";
327	>	com.dataType = "Vector3d";
328	>	com.accumulator = new VectorAccumulator();
329	>	data_[COM] = com;
330	>	statsMap_["COM"] =  COM;
331	>
332	>	StatsData comVel;
333	>	comVel.units =  "A/fs";
334	>	comVel.title =  "Center of Mass Velocity";
335	>	comVel.dataType = "Vector3d";
336	>	comVel.accumulator = new VectorAccumulator();
337	>	data_[COM_VELOCITY] = comVel;
338	>	statsMap_["COM_VELOCITY"] =  COM_VELOCITY;
339	>
340	>	StatsData angMom;
341	>	angMom.units =  "amu A^2/fs";
342	>	angMom.title =  "Angular Momentum";
343	>	angMom.dataType = "Vector3d";
344	>	angMom.accumulator = new VectorAccumulator();
345	>	data_[ANGULAR_MOMENTUM] = angMom;
346	>	statsMap_["ANGULAR_MOMENTUM"] =  ANGULAR_MOMENTUM;
347	>
348	>	// Now, set some defaults in the mask:
349	>
350	>	Globals* simParams = info_->getSimParams();
351	>	std::string statFileFormatString = simParams->getStatFileFormat();
352	>	parseStatFileFormat(statFileFormatString);
353	>
354	>	// if we're doing a thermodynamic integration, we'll want the raw
355	>	// potential as well as the full potential:
356	>
357	>	if (simParams->getUseThermodynamicIntegration())
358	>	statsMask_.set(RAW_POTENTIAL);
359	>
360	>	// if we've got restraints turned on, we'll also want a report of the
361	>	// total harmonic restraints
362	>	if (simParams->getUseRestraints()){
363	>	statsMask_.set(RESTRAINT_POTENTIAL);
364	>	}
365	>
366	>	if (simParams->havePrintPressureTensor() &&
367	>	simParams->getPrintPressureTensor()){
368	>	statsMask_.set(PRESSURE_TENSOR);
369	>	}
370	>
371	>	// Why do we have both of these?
372	>	if (simParams->getAccumulateBoxDipole()) {
373	>	statsMask_.set(SYSTEM_DIPOLE);
374	>	}
375	>	if (info_->getCalcBoxDipole()){
376	>	statsMask_.set(SYSTEM_DIPOLE);
377	>	}
378	>
379	>	if (simParams->havePrintHeatFlux()) {
380	>	if (simParams->getPrintHeatFlux()){
381	>	statsMask_.set(HEATFLUX);
382	>	}
383	>	}
384	>
385	>
386	>	if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) {
387	>	if (simParams->getPrintTaggedPairDistance()) {
388	>	statsMask_.set(TAGGED_PAIR_DISTANCE);
389	>	}
390	>	}
391	>
392		}
393
394	+	void Stats::parseStatFileFormat(const std::string& format) {
395	+	StringTokenizer tokenizer(format, " ,;|\t\n\r");
396	+
397	+	while(tokenizer.hasMoreTokens()) {
398	+	std::string token(tokenizer.nextToken());
399	+	toUpper(token);
400	+	StatsMapType::iterator i = statsMap_.find(token);
401	+	if (i != statsMap_.end()) {
402	+	statsMask_.set(i->second);
403	+	} else {
404	+	sprintf( painCave.errMsg,
405	+	"Stats::parseStatFileFormat: %s is not a recognized\n"
406	+	"\tstatFileFormat keyword.\n", token.c_str() );
407	+	painCave.isFatal = 0;
408	+	painCave.severity = OPENMD_ERROR;
409	+	simError();
410	+	}
411	+	}
412	+	}
413	+
414	+	Stats::~Stats() {
415	+	data_.clear();
416	+	statsMap_.clear();
417	+	}
418	+
419	+	std::string Stats::getTitle(int index) {
420	+	assert(index >=0 && index < ENDINDEX);
421	+	return data_[index].title;
422	+	}
423	+
424	+	std::string Stats::getUnits(int index) {
425	+	assert(index >=0 && index < ENDINDEX);
426	+	return data_[index].units;
427	+	}
428	+
429	+	std::string Stats::getDataType(int index) {
430	+	assert(index >=0 && index < ENDINDEX);
431	+	return data_[index].dataType;
432	+	}
433	+
434	+	void Stats::collectStats(){
435	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
436	+	Thermo thermo(info_);
437	+
438	+	for (unsigned int i = 0; i < statsMask_.size(); ++i) {
439	+	if (statsMask_[i]) {
440	+	switch (i) {
441	+	case TIME:
442	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getTime());
443	+	break;
444	+	case KINETIC_ENERGY:
445	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getKinetic());
446	+	break;
447	+	case POTENTIAL_ENERGY:
448	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getPotential());
449	+	break;
450	+	case TOTAL_ENERGY:
451	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTotalEnergy());
452	+	break;
453	+	case TEMPERATURE:
454	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTemperature());
455	+	break;
456	+	case PRESSURE:
457	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getPressure());
458	+	break;
459	+	case VOLUME:
460	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getVolume());
461	+	break;
462	+	case CONSERVED_QUANTITY:
463	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getConservedQuantity());
464	+	break;
465	+	case PRESSURE_TENSOR:
466	+	dynamic_cast<MatrixAccumulator *>(data_[i].accumulator)->add(thermo.getPressureTensor());
467	+	break;
468	+	case SYSTEM_DIPOLE:
469	+	dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getSystemDipole());
470	+	break;
471	+	case HEATFLUX:
472	+	dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getHeatFlux());
473	+	break;
474	+	case HULLVOLUME:
475	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getHullVolume());
476	+	break;
477	+	case GYRVOLUME:
478	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getGyrationalVolume());
479	+	break;
480	+	case TRANSLATIONAL_KINETIC:
481	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTranslationalKinetic());
482	+	break;
483	+	case ROTATIONAL_KINETIC:
484	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getRotationalKinetic());
485	+	break;
486	+	case LONG_RANGE_POTENTIAL:
487	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotential());
488	+	break;
489	+	case VANDERWAALS_POTENTIAL:
490	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[VANDERWAALS_FAMILY]);
491	+	break;
492	+	case ELECTROSTATIC_POTENTIAL:
493	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[ELECTROSTATIC_FAMILY]);
494	+	break;
495	+	case METALLIC_POTENTIAL:
496	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[METALLIC_FAMILY]);
497	+	break;
498	+	case HYDROGENBONDING_POTENTIAL:
499	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[HYDROGENBONDING_FAMILY]);
500	+	break;
501	+	case RECIPROCAL_POTENTIAL:
502	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getReciprocalPotential());
503	+	break;
504	+	case SHORT_RANGE_POTENTIAL:
505	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getShortRangePotential());
506	+	break;
507	+	case BOND_POTENTIAL:
508	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getBondPotential());
509	+	break;
510	+	case BEND_POTENTIAL:
511	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getBendPotential());
512	+	break;
513	+	case DIHEDRAL_POTENTIAL:
514	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getTorsionPotential());
515	+	break;
516	+	case INVERSION_POTENTIAL:
517	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getInversionPotential());
518	+	break;
519	+	case RAW_POTENTIAL:
520	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getRawPotential());
521	+	break;
522	+	case RESTRAINT_POTENTIAL:
523	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getRestraintPotential());
524	+	break;
525	+	case TAGGED_PAIR_DISTANCE:
526	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTaggedAtomPairDistance());
527	+	break;
528	+	case ELECTRONIC_TEMPERATURE:
529	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getElectronicTemperature());
530	+	break;
531	+	case COM:
532	+	dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getCom());
533	+	break;
534	+	case COM_VELOCITY:
535	+	dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getComVel());
536	+	break;
537	+	case ANGULAR_MOMENTUM:
538	+	dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getAngularMomentum());
539	+	break;
540	+	/*
541	+	case SHADOWH:
542	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getShadowHamiltionian());
543	+	break;
544	+	case HELFANDMOMENT:
545	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getHelfandMoment());
546	+	break;
547	+	*/
548	+	}
549	+	}
550	+	}
551	+	}
552	+
553	+	int Stats::getIntData(int index) {
554	+	assert(index >=0 && index < ENDINDEX);
555	+	RealType value;
556	+	dynamic_cast<Accumulator *>(data_[index].accumulator)->getLastValue(value);
557	+	return (int) value;
558	+	}
559	+	RealType Stats::getRealData(int index) {
560	+	assert(index >=0 && index < ENDINDEX);
561	+	RealType value(0.0);
562	+	dynamic_cast<Accumulator *>(data_[index].accumulator)->getLastValue(value);
563	+	return value;
564	+	}
565	+	Vector3d Stats::getVectorData(int index) {
566	+	assert(index >=0 && index < ENDINDEX);
567	+	Vector3d value;
568	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator)->getLastValue(value);
569	+	return value;
570	+	}
571	+	Mat3x3d Stats::getMatrixData(int index) {
572	+	assert(index >=0 && index < ENDINDEX);
573	+	Mat3x3d value;
574	+	dynamic_cast<MatrixAccumulator*>(data_[index].accumulator)->getLastValue(value);
575	+	return value;
576	+	}
577	+
578	+	Stats::StatsBitSet Stats::getStatsMask() {
579	+	return statsMask_;
580	+	}
581	+	Stats::StatsMapType Stats::getStatsMap() {
582	+	return statsMap_;
583	+	}
584	+	void Stats::setStatsMask(Stats::StatsBitSet mask) {
585	+	statsMask_ = mask;
586	+	}
587	+
588		}

Comparing trunk/src/brains/Stats.cpp (property svn:keywords):
Revision 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC vs.
Revision 1925 by gezelter, Wed Aug 7 15:24:16 2013 UTC

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