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root/OpenMD/trunk/src/brains/Stats.cpp

Comparing trunk/src/brains/Stats.cpp (file contents):
Revision 1341 by skuang, Fri May 8 19:47:05 2009 UTC vs.
Revision 1834 by gezelter, Tue Jan 15 16:28:42 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, 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		/**
#	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";
75	<	Stats::title_[HULLVOLUME] = "Hull Volume";
76	<	Stats::title_[GYRVOLUME] = "Gyrational Volume";
77	<	Stats::title_[CONSERVED_QUANTITY] = "Conserved Quantity";
78	<	Stats::title_[TRANSLATIONAL_KINETIC] = "Translational Kinetic";
79	<	Stats::title_[ROTATIONAL_KINETIC] = "Rotational Kinetic";
80	<	Stats::title_[LONG_RANGE_POTENTIAL] = "Long Range Potential";
81	<	Stats::title_[SHORT_RANGE_POTENTIAL] = "Short Range Potential";
82	<	Stats::title_[VANDERWAALS_POTENTIAL] = "van der waals Potential";
83	<	Stats::title_[ELECTROSTATIC_POTENTIAL] = "Electrostatic Potential";
84	<	Stats::title_[BOND_POTENTIAL] = "Bond Potential";
85	<	Stats::title_[BEND_POTENTIAL] = "Bend Potential";
86	<	Stats::title_[DIHEDRAL_POTENTIAL] = "Dihedral Potential";
87	<	Stats::title_[INVERSION_POTENTIAL] = "Inversion Potential";
88	<	Stats::title_[VRAW] = "Raw Potential";
89	<	Stats::title_[VHARM] = "Harmonic Potential";
90	<	Stats::title_[PRESSURE_TENSOR_XX] = "P_xx";
91	<	Stats::title_[PRESSURE_TENSOR_XY] = "P_xy";
92	<	Stats::title_[PRESSURE_TENSOR_XZ] = "P_xz";
93	<	Stats::title_[PRESSURE_TENSOR_YX] = "P_yx";
94	<	Stats::title_[PRESSURE_TENSOR_YY] = "P_yy";
95	<	Stats::title_[PRESSURE_TENSOR_YZ] = "P_yz";
96	<	Stats::title_[PRESSURE_TENSOR_ZX] = "P_zx";
97	<	Stats::title_[PRESSURE_TENSOR_ZY] = "P_zy";
98	<	Stats::title_[PRESSURE_TENSOR_ZZ] = "P_zz";
99	<	Stats::title_[BOX_DIPOLE_X] = "box dipole x";
100	<	Stats::title_[BOX_DIPOLE_Y] = "box dipole y";
101	<	Stats::title_[BOX_DIPOLE_Z] = "box dipole z";
102	<	Stats::title_[TAGGED_PAIR_DISTANCE] = "Tagged_Pair_Distance";
103	<	Stats::title_[RNEMD_SWAP_TOTAL] = "RNEMD_exchange_total";
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	>	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	>	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 short_range_potential;
205	>	short_range_potential.units =  "kcal/mol";
206	>	short_range_potential.title =  "Short Range Potential";
207	>	short_range_potential.dataType = "RealType";
208	>	short_range_potential.accumulator = new Accumulator();
209	>	data_[SHORT_RANGE_POTENTIAL] = short_range_potential;
210	>	statsMap_["SHORT_RANGE_POTENTIAL"] =  SHORT_RANGE_POTENTIAL;
211	>
212	>	StatsData bond_potential;
213	>	bond_potential.units =  "kcal/mol";
214	>	bond_potential.title =  "Bond Potential";
215	>	bond_potential.dataType = "RealType";
216	>	bond_potential.accumulator = new Accumulator();
217	>	data_[BOND_POTENTIAL] = bond_potential;
218	>	statsMap_["BOND_POTENTIAL"] =  BOND_POTENTIAL;
219	>
220	>	StatsData bend_potential;
221	>	bend_potential.units =  "kcal/mol";
222	>	bend_potential.title =  "Bend Potential";
223	>	bend_potential.dataType = "RealType";
224	>	bend_potential.accumulator = new Accumulator();
225	>	data_[BEND_POTENTIAL] = bend_potential;
226	>	statsMap_["BEND_POTENTIAL"] =  BEND_POTENTIAL;
227
228	<	Stats::units_[TIME] = "fs";
229	<	Stats::units_[TOTAL_ENERGY] = "kcal/mol";
230	<	Stats::units_[POTENTIAL_ENERGY] = "kcal/mol";
231	<	Stats::units_[KINETIC_ENERGY] = "kcal/mol";
232	<	Stats::units_[TEMPERATURE] = "K";
233	<	Stats::units_[PRESSURE] = "atm";
234	<	Stats::units_[VOLUME] = "A^3";
113	<	Stats::units_[HULLVOLUME] = "A^3";
114	<	Stats::units_[GYRVOLUME] = "A^3";
115	<	Stats::units_[CONSERVED_QUANTITY] = "kcal/mol";
116	<	Stats::units_[TRANSLATIONAL_KINETIC] = "kcal/mol";
117	<	Stats::units_[ROTATIONAL_KINETIC] = "kcal/mol";
118	<	Stats::units_[LONG_RANGE_POTENTIAL] = "kcal/mol";
119	<	Stats::units_[SHORT_RANGE_POTENTIAL] = "kcal/mol";
120	<	Stats::units_[VANDERWAALS_POTENTIAL] = "kcal/mol";
121	<	Stats::units_[ELECTROSTATIC_POTENTIAL] = "kcal/mol";
122	<	Stats::units_[BOND_POTENTIAL] = "kcal/mol";
123	<	Stats::units_[BEND_POTENTIAL] = "kcal/mol";
124	<	Stats::units_[DIHEDRAL_POTENTIAL] = "kcal/mol";
125	<	Stats::units_[INVERSION_POTENTIAL] = "kcal/mol";
126	<	Stats::units_[VRAW] = "kcal/mol";
127	<	Stats::units_[VHARM] = "kcal/mol";
128	<	Stats::units_[PRESSURE_TENSOR_XX] = "amu*fs^-2*Ang^-1";
129	<	Stats::units_[PRESSURE_TENSOR_XY] = "amu*fs^-2*Ang^-1";
130	<	Stats::units_[PRESSURE_TENSOR_XZ] = "amu*fs^-2*Ang^-1";
131	<	Stats::units_[PRESSURE_TENSOR_YX] = "amu*fs^-2*Ang^-1";
132	<	Stats::units_[PRESSURE_TENSOR_YY] = "amu*fs^-2*Ang^-1";
133	<	Stats::units_[PRESSURE_TENSOR_YZ] = "amu*fs^-2*Ang^-1";
134	<	Stats::units_[PRESSURE_TENSOR_ZX] = "amu*fs^-2*Ang^-1";
135	<	Stats::units_[PRESSURE_TENSOR_ZY] = "amu*fs^-2*Ang^-1";
136	<	Stats::units_[PRESSURE_TENSOR_ZZ] = "amu*fs^-2*Ang^-1";
137	<	Stats::units_[BOX_DIPOLE_X] = "C*m";
138	<	Stats::units_[BOX_DIPOLE_Y] = "C*m";
139	<	Stats::units_[BOX_DIPOLE_Z] = "C*m";
140	<	Stats::units_[TAGGED_PAIR_DISTANCE] = "Ang";
141	<	Stats::units_[RNEMD_SWAP_TOTAL] = "Variable";
228	>	StatsData dihedral_potential;
229	>	dihedral_potential.units =  "kcal/mol";
230	>	dihedral_potential.title =  "Dihedral Potential";
231	>	dihedral_potential.dataType = "RealType";
232	>	dihedral_potential.accumulator = new Accumulator();
233	>	data_[DIHEDRAL_POTENTIAL] = dihedral_potential;
234	>	statsMap_["DIHEDRAL_POTENTIAL"] =  DIHEDRAL_POTENTIAL;
235
236	<	Stats::statsMap.insert(StatsMapType::value_type("TIME", TIME));
237	<	Stats::statsMap.insert(StatsMapType::value_type("TOTAL_ENERGY", TOTAL_ENERGY));
238	<	Stats::statsMap.insert(StatsMapType::value_type("POTENTIAL_ENERGY", POTENTIAL_ENERGY));
239	<	Stats::statsMap.insert(StatsMapType::value_type("KINETIC_ENERGY", KINETIC_ENERGY));
240	<	Stats::statsMap.insert(StatsMapType::value_type("TEMPERATURE", TEMPERATURE));
241	<	Stats::statsMap.insert(StatsMapType::value_type("PRESSURE", PRESSURE));
242	<	Stats::statsMap.insert(StatsMapType::value_type("VOLUME", VOLUME));
243	<	Stats::statsMap.insert(StatsMapType::value_type("HULLVOLUME", HULLVOLUME));
244	<	Stats::statsMap.insert(StatsMapType::value_type("GYRVOLUME", GYRVOLUME));
245	<	Stats::statsMap.insert(StatsMapType::value_type("CONSERVED_QUANTITY", CONSERVED_QUANTITY));
246	<	Stats::statsMap.insert(StatsMapType::value_type("TRANSLATIONAL_KINETIC", TRANSLATIONAL_KINETIC));
247	<	Stats::statsMap.insert(StatsMapType::value_type("ROTATIONAL_KINETIC", ROTATIONAL_KINETIC));
248	<	Stats::statsMap.insert(StatsMapType::value_type("LONG_RANGE_POTENTIAL", LONG_RANGE_POTENTIAL));
249	<	Stats::statsMap.insert(StatsMapType::value_type("SHORT_RANGE_POTENTIAL", SHORT_RANGE_POTENTIAL));
250	<	Stats::statsMap.insert(StatsMapType::value_type("VANDERWAALS_POTENTIAL", VANDERWAALS_POTENTIAL));
251	<	Stats::statsMap.insert(StatsMapType::value_type("ELECTROSTATIC_POTENTIAL", ELECTROSTATIC_POTENTIAL));
252	<	Stats::statsMap.insert(StatsMapType::value_type("BOND_POTENTIAL", BOND_POTENTIAL));
253	<	Stats::statsMap.insert(StatsMapType::value_type("BEND_POTENTIAL", BEND_POTENTIAL));
254	<	Stats::statsMap.insert(StatsMapType::value_type("DIHEDRAL_POTENTIAL", DIHEDRAL_POTENTIAL));
255	<	Stats::statsMap.insert(StatsMapType::value_type("INVERSION_POTENTIAL", INVERSION_POTENTIAL));
256	<	Stats::statsMap.insert(StatsMapType::value_type("VRAW", VRAW));
257	<	Stats::statsMap.insert(StatsMapType::value_type("VHARM", VHARM));
258	<	Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_XX", PRESSURE_TENSOR_XX));
259	<	Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_XY", PRESSURE_TENSOR_XY));
260	<	Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_XZ", PRESSURE_TENSOR_XZ));
261	<	Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_YX", PRESSURE_TENSOR_YX));
262	<	Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_YY", PRESSURE_TENSOR_YY));
263	<	Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_YZ", PRESSURE_TENSOR_YZ));
264	<	Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_ZX", PRESSURE_TENSOR_ZX));
265	<	Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_ZY", PRESSURE_TENSOR_ZY));
266	<	Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_ZZ", PRESSURE_TENSOR_ZZ));
267	<	Stats::statsMap.insert(StatsMapType::value_type("BOX_DIPOLE_X", BOX_DIPOLE_X));
268	<	Stats::statsMap.insert(StatsMapType::value_type("BOX_DIPOLE_Y", BOX_DIPOLE_Y));
269	<	Stats::statsMap.insert(StatsMapType::value_type("BOX_DIPOLE_Z", BOX_DIPOLE_Z));
270	<	Stats::statsMap.insert(StatsMapType::value_type("TAGGED_PAIR_DISTANCE", TAGGED_PAIR_DISTANCE));
271	<	Stats::statsMap.insert(StatsMapType::value_type("RNEMD_SWAP_TOTAL", RNEMD_SWAP_TOTAL));
236	>	StatsData inversion_potential;
237	>	inversion_potential.units =  "kcal/mol";
238	>	inversion_potential.title =  "Inversion Potential";
239	>	inversion_potential.dataType = "RealType";
240	>	inversion_potential.accumulator = new Accumulator();
241	>	data_[INVERSION_POTENTIAL] = inversion_potential;
242	>	statsMap_["INVERSION_POTENTIAL"] =  INVERSION_POTENTIAL;
243	>
244	>	StatsData vraw;
245	>	vraw.units =  "kcal/mol";
246	>	vraw.title =  "Raw Potential";
247	>	vraw.dataType = "RealType";
248	>	vraw.accumulator = new Accumulator();
249	>	data_[RAW_POTENTIAL] = vraw;
250	>	statsMap_["RAW_POTENTIAL"] =  RAW_POTENTIAL;
251	>
252	>	StatsData vrestraint;
253	>	vrestraint.units =  "kcal/mol";
254	>	vrestraint.title =  "Restraint Potential";
255	>	vrestraint.dataType = "RealType";
256	>	vrestraint.accumulator = new Accumulator();
257	>	data_[RESTRAINT_POTENTIAL] = vrestraint;
258	>	statsMap_["RESTRAINT_POTENTIAL"] =  RESTRAINT_POTENTIAL;
259	>
260	>	StatsData pressure_tensor;
261	>	pressure_tensor.units =  "amu*fs^-2*Ang^-1";
262	>	pressure_tensor.title =  "Ptensor";
263	>	pressure_tensor.dataType = "Mat3x3d";
264	>	pressure_tensor.accumulator = new MatrixAccumulator();
265	>	data_[PRESSURE_TENSOR] = pressure_tensor;
266	>	statsMap_["PRESSURE_TENSOR"] =  PRESSURE_TENSOR;
267	>
268	>	StatsData system_dipole;
269	>	system_dipole.units =  "C*m";
270	>	system_dipole.title =  "System Dipole";
271	>	system_dipole.dataType = "Vector3d";
272	>	system_dipole.accumulator = new VectorAccumulator();
273	>	data_[SYSTEM_DIPOLE] = system_dipole;
274	>	statsMap_["SYSTEM_DIPOLE"] =  SYSTEM_DIPOLE;
275	>
276	>	StatsData tagged_pair_distance;
277	>	tagged_pair_distance.units =  "Ang";
278	>	tagged_pair_distance.title =  "Tagged_Pair_Distance";
279	>	tagged_pair_distance.dataType = "RealType";
280	>	tagged_pair_distance.accumulator = new Accumulator();
281	>	data_[TAGGED_PAIR_DISTANCE] = tagged_pair_distance;
282	>	statsMap_["TAGGED_PAIR_DISTANCE"] =  TAGGED_PAIR_DISTANCE;
283	>
284	>	StatsData shadowh;
285	>	shadowh.units =  "kcal/mol";
286	>	shadowh.title =  "Shadow Hamiltonian";
287	>	shadowh.dataType = "RealType";
288	>	shadowh.accumulator = new Accumulator();
289	>	data_[SHADOWH] = shadowh;
290	>	statsMap_["SHADOWH"] =  SHADOWH;
291	>
292	>	StatsData helfandmoment;
293	>	helfandmoment.units =  "Ang*kcal/mol";
294	>	helfandmoment.title =  "Thermal Helfand Moment";
295	>	helfandmoment.dataType = "Vector3d";
296	>	helfandmoment.accumulator = new VectorAccumulator();
297	>	data_[HELFANDMOMENT] = helfandmoment;
298	>	statsMap_["HELFANDMOMENT"] = HELFANDMOMENT;
299	>
300	>	StatsData heatflux;
301	>	heatflux.units = "amu/fs^3";
302	>	heatflux.title =  "Heat Flux";
303	>	heatflux.dataType = "Vector3d";
304	>	heatflux.accumulator = new VectorAccumulator();
305	>	data_[HEATFLUX] = heatflux;
306	>	statsMap_["HEATFLUX"] = HEATFLUX;
307	>
308	>	StatsData electronic_temperature;
309	>	electronic_temperature.units = "K";
310	>	electronic_temperature.title =  "Electronic Temperature";
311	>	electronic_temperature.dataType = "RealType";
312	>	electronic_temperature.accumulator = new Accumulator();
313	>	data_[ELECTRONIC_TEMPERATURE] = electronic_temperature;
314	>	statsMap_["ELECTRONIC_TEMPERATURE"] = ELECTRONIC_TEMPERATURE;
315	>
316	>	// Now, set some defaults in the mask:
317	>
318	>	Globals* simParams = info_->getSimParams();
319	>	std::string statFileFormatString = simParams->getStatFileFormat();
320	>	parseStatFileFormat(statFileFormatString);
321	>
322	>	// if we're doing a thermodynamic integration, we'll want the raw
323	>	// potential as well as the full potential:
324	>
325	>	if (simParams->getUseThermodynamicIntegration())
326	>	statsMask_.set(RAW_POTENTIAL);
327	>
328	>	// if we've got restraints turned on, we'll also want a report of the
329	>	// total harmonic restraints
330	>	if (simParams->getUseRestraints()){
331	>	statsMask_.set(RESTRAINT_POTENTIAL);
332	>	}
333	>
334	>	if (simParams->havePrintPressureTensor() &&
335	>	simParams->getPrintPressureTensor()){
336	>	statsMask_.set(PRESSURE_TENSOR);
337	>	}
338	>
339	>	// Why do we have both of these?
340	>	if (simParams->getAccumulateBoxDipole()) {
341	>	statsMask_.set(SYSTEM_DIPOLE);
342	>	}
343	>	if (info_->getCalcBoxDipole()){
344	>	statsMask_.set(SYSTEM_DIPOLE);
345	>	}
346	>
347	>	if (simParams->havePrintHeatFlux()) {
348	>	if (simParams->getPrintHeatFlux()){
349	>	statsMask_.set(HEATFLUX);
350	>	}
351	>	}
352	>
353	>
354	>	if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) {
355	>	if (simParams->getPrintTaggedPairDistance()) {
356	>	statsMask_.set(TAGGED_PAIR_DISTANCE);
357	>	}
358	>	}
359	>
360		}
361
362	+	void Stats::parseStatFileFormat(const std::string& format) {
363	+	StringTokenizer tokenizer(format, " ,;|\t\n\r");
364	+
365	+	while(tokenizer.hasMoreTokens()) {
366	+	std::string token(tokenizer.nextToken());
367	+	toUpper(token);
368	+	StatsMapType::iterator i = statsMap_.find(token);
369	+	if (i != statsMap_.end()) {
370	+	statsMask_.set(i->second);
371	+	} else {
372	+	sprintf( painCave.errMsg,
373	+	"Stats::parseStatFileFormat: %s is not a recognized\n"
374	+	"\tstatFileFormat keyword.\n", token.c_str() );
375	+	painCave.isFatal = 0;
376	+	painCave.severity = OPENMD_ERROR;
377	+	simError();
378	+	}
379	+	}
380	+	}
381	+
382	+
383	+	std::string Stats::getTitle(int index) {
384	+	assert(index >=0 && index < ENDINDEX);
385	+	return data_[index].title;
386	+	}
387	+
388	+	std::string Stats::getUnits(int index) {
389	+	assert(index >=0 && index < ENDINDEX);
390	+	return data_[index].units;
391	+	}
392	+
393	+	std::string Stats::getDataType(int index) {
394	+	assert(index >=0 && index < ENDINDEX);
395	+	return data_[index].dataType;
396	+	}
397	+
398	+	void Stats::collectStats(){
399	+	Globals* simParams = info_->getSimParams();
400	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
401	+	Thermo thermo(info_);
402	+
403	+	for (unsigned int i = 0; i < statsMask_.size(); ++i) {
404	+	if (statsMask_[i]) {
405	+	switch (i) {
406	+	case TIME:
407	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getTime());
408	+	break;
409	+	case KINETIC_ENERGY:
410	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getKinetic());
411	+	break;
412	+	case POTENTIAL_ENERGY:
413	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getPotential());
414	+	break;
415	+	case TOTAL_ENERGY:
416	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTotalEnergy());
417	+	break;
418	+	case TEMPERATURE:
419	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTemperature());
420	+	break;
421	+	case PRESSURE:
422	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getPressure());
423	+	break;
424	+	case VOLUME:
425	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getVolume());
426	+	break;
427	+	case CONSERVED_QUANTITY:
428	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getConservedQuantity());
429	+	break;
430	+	case PRESSURE_TENSOR:
431	+	dynamic_cast<MatrixAccumulator *>(data_[i].accumulator)->add(thermo.getPressureTensor());
432	+	break;
433	+	case SYSTEM_DIPOLE:
434	+	dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getSystemDipole());
435	+	break;
436	+	case HEATFLUX:
437	+	dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getHeatFlux());
438	+	break;
439	+	case HULLVOLUME:
440	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getHullVolume());
441	+	break;
442	+	case GYRVOLUME:
443	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getGyrationalVolume());
444	+	break;
445	+	case TRANSLATIONAL_KINETIC:
446	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTranslationalKinetic());
447	+	break;
448	+	case ROTATIONAL_KINETIC:
449	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getRotationalKinetic());
450	+	break;
451	+	case LONG_RANGE_POTENTIAL:
452	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotential());
453	+	break;
454	+	case VANDERWAALS_POTENTIAL:
455	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[VANDERWAALS_FAMILY]);
456	+	break;
457	+	case ELECTROSTATIC_POTENTIAL:
458	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[ELECTROSTATIC_FAMILY]);
459	+	break;
460	+	case METALLIC_POTENTIAL:
461	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[METALLIC_FAMILY]);
462	+	break;
463	+	case HYDROGENBONDING_POTENTIAL:
464	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[HYDROGENBONDING_FAMILY]);
465	+	break;
466	+	case SHORT_RANGE_POTENTIAL:
467	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getShortRangePotential());
468	+	break;
469	+	case BOND_POTENTIAL:
470	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getBondPotential());
471	+	break;
472	+	case BEND_POTENTIAL:
473	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getBendPotential());
474	+	break;
475	+	case DIHEDRAL_POTENTIAL:
476	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getTorsionPotential());
477	+	break;
478	+	case INVERSION_POTENTIAL:
479	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getInversionPotential());
480	+	break;
481	+	case RAW_POTENTIAL:
482	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getRawPotential());
483	+	break;
484	+	case RESTRAINT_POTENTIAL:
485	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getRestraintPotential());
486	+	break;
487	+	case TAGGED_PAIR_DISTANCE:
488	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTaggedAtomPairDistance());
489	+	break;
490	+	/*
491	+	case SHADOWH:
492	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getShadowHamiltionian());
493	+	break;
494	+	case HELFANDMOMENT:
495	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getHelfandMoment());
496	+	break;
497	+	*/
498	+	case ELECTRONIC_TEMPERATURE:
499	+	dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getElectronicTemperature());
500	+	break;
501	+	}
502	+	}
503	+	}
504	+	}
505	+
506	+	int Stats::getIntData(int index) {
507	+	assert(index >=0 && index < ENDINDEX);
508	+	RealType value;
509	+	dynamic_cast<Accumulator *>(data_[index].accumulator)->getLastValue(value);
510	+	return (int) value;
511	+	}
512	+	RealType Stats::getRealData(int index) {
513	+	assert(index >=0 && index < ENDINDEX);
514	+	RealType value(0.0);
515	+	dynamic_cast<Accumulator *>(data_[index].accumulator)->getLastValue(value);
516	+	return value;
517	+	}
518	+	Vector3d Stats::getVectorData(int index) {
519	+	assert(index >=0 && index < ENDINDEX);
520	+	Vector3d value;
521	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator)->getLastValue(value);
522	+	return value;
523	+	}
524	+	Mat3x3d Stats::getMatrixData(int index) {
525	+	assert(index >=0 && index < ENDINDEX);
526	+	Mat3x3d value;
527	+	dynamic_cast<MatrixAccumulator*>(data_[index].accumulator)->getLastValue(value);
528	+	return value;
529	+	}
530	+
531	+	Stats::StatsBitSet Stats::getStatsMask() {
532	+	return statsMask_;
533	+	}
534	+	Stats::StatsMapType Stats::getStatsMap() {
535	+	return statsMap_;
536	+	}
537	+	void Stats::setStatsMask(Stats::StatsBitSet mask) {
538	+	statsMask_ = mask;
539	+	}
540	+
541		}

Comparing trunk/src/brains/Stats.cpp (property svn:keywords):
Revision 1341 by skuang, Fri May 8 19:47:05 2009 UTC vs.
Revision 1834 by gezelter, Tue Jan 15 16:28:42 2013 UTC

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