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Comparing branches/development/src/brains/Stats.cpp (file contents):
Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC vs.
Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

# Line 44 | Line 44
44   * @file Stats.cpp
45   * @author tlin
46   * @date 11/04/2004
47 – * @time 14:26am
47   * @version 1.0
48   */
49  
50   #include "brains/Stats.hpp"
51 + #include "brains/Thermo.hpp"
52  
53   namespace OpenMD {
54  
55 <  bool Stats::isInit_ = false;
56 <  std::string Stats::title_[Stats::ENDINDEX - Stats::BEGININDEX];
57 <  std::string Stats::units_[Stats::ENDINDEX - Stats::BEGININDEX];
58 <  Stats::StatsMapType Stats::statsMap;
59 <  Stats::Stats() {
55 >  Stats::Stats(SimInfo* info) : isInit_(false), info_(info) {  
56  
57      if (!isInit_) {
58        init();
59        isInit_ = true;
60      }
65 –
61    }
62  
63    void Stats::init() {
64 +  
65 +    data_.resize(Stats::ENDINDEX);
66  
67 <    Stats::title_[TIME] = "Time";
68 <    Stats::title_[TOTAL_ENERGY] = "Total Energy";
69 <    Stats::title_[POTENTIAL_ENERGY] = "Potential Energy";
70 <    Stats::title_[KINETIC_ENERGY] = "Kinetic Energy";
71 <    Stats::title_[TEMPERATURE] = "Temperature";
72 <    Stats::title_[PRESSURE] = "Pressure";
73 <    Stats::title_[VOLUME] = "Volume";
77 <    Stats::title_[HULLVOLUME] = "Hull Volume";
78 <    Stats::title_[GYRVOLUME] = "Gyrational Volume";
79 <    Stats::title_[CONSERVED_QUANTITY] = "Conserved Quantity";            
80 <    Stats::title_[TRANSLATIONAL_KINETIC] = "Translational Kinetic";
81 <    Stats::title_[ROTATIONAL_KINETIC] = "Rotational Kinetic";
82 <    Stats::title_[LONG_RANGE_POTENTIAL] = "Long Range Potential";
83 <    Stats::title_[SHORT_RANGE_POTENTIAL] = "Short Range Potential";
84 <    Stats::title_[VANDERWAALS_POTENTIAL] = "van der waals Potential";
85 <    Stats::title_[ELECTROSTATIC_POTENTIAL] = "Electrostatic Potential";    
86 <    Stats::title_[BOND_POTENTIAL] = "Bond Potential";
87 <    Stats::title_[BEND_POTENTIAL] = "Bend Potential";
88 <    Stats::title_[DIHEDRAL_POTENTIAL] = "Dihedral Potential";
89 <    Stats::title_[INVERSION_POTENTIAL] = "Inversion Potential";
90 <    Stats::title_[VRAW] = "Raw Potential";
91 <    Stats::title_[VHARM] = "Harmonic Potential";
92 <    Stats::title_[SHADOWH] = "Shadow Hamiltonian";
93 <    Stats::title_[PRESSURE_TENSOR_XX] = "P_xx";
94 <    Stats::title_[PRESSURE_TENSOR_XY] = "P_xy";
95 <    Stats::title_[PRESSURE_TENSOR_XZ] = "P_xz";
96 <    Stats::title_[PRESSURE_TENSOR_YX] = "P_yx";
97 <    Stats::title_[PRESSURE_TENSOR_YY] = "P_yy";
98 <    Stats::title_[PRESSURE_TENSOR_YZ] = "P_yz";
99 <    Stats::title_[PRESSURE_TENSOR_ZX] = "P_zx";
100 <    Stats::title_[PRESSURE_TENSOR_ZY] = "P_zy";
101 <    Stats::title_[PRESSURE_TENSOR_ZZ] = "P_zz";
102 <    Stats::title_[BOX_DIPOLE_X] = "box dipole x";
103 <    Stats::title_[BOX_DIPOLE_Y] = "box dipole y";
104 <    Stats::title_[BOX_DIPOLE_Z] = "box dipole z";
105 <    Stats::title_[TAGGED_PAIR_DISTANCE] = "Tagged_Pair_Distance";
106 <    Stats::title_[RNEMD_EXCHANGE_TOTAL] = "RNEMD_exchange_total";
107 <    Stats::title_[THERMAL_HELFANDMOMENT_X] = "Thermal Helfand Moment x";
108 <    Stats::title_[THERMAL_HELFANDMOMENT_Y] = "Thermal Helfand Moment y";
109 <    Stats::title_[THERMAL_HELFANDMOMENT_Z] = "Thermal Helfand Moment z";
110 <    Stats::title_[HEATFLUX_X]= "Heat Flux x component";  
111 <    Stats::title_[HEATFLUX_Y]= "Heat Flux y component";  
112 <    Stats::title_[HEATFLUX_Z]= "Heat Flux z component";  
67 >    StatsData time;
68 >    time.units =  "fs";
69 >    time.title =  "Time";
70 >    time.dataType = "RealType";
71 >    time.accumulator = new Accumulator();
72 >    data_[TIME] = time;
73 >    statsMap_["TIME"] = TIME;
74  
75 <    Stats::units_[TIME] = "fs";
76 <    Stats::units_[TOTAL_ENERGY] = "kcal/mol";
77 <    Stats::units_[POTENTIAL_ENERGY] = "kcal/mol";
78 <    Stats::units_[KINETIC_ENERGY] = "kcal/mol";
79 <    Stats::units_[TEMPERATURE] = "K";
80 <    Stats::units_[PRESSURE] = "atm";
81 <    Stats::units_[VOLUME] = "A^3";
82 <    Stats::units_[HULLVOLUME] = "A^3";
83 <    Stats::units_[GYRVOLUME] = "A^3";
84 <    Stats::units_[CONSERVED_QUANTITY] = "kcal/mol";            
85 <    Stats::units_[TRANSLATIONAL_KINETIC] = "kcal/mol";
86 <    Stats::units_[ROTATIONAL_KINETIC] = "kcal/mol";
87 <    Stats::units_[LONG_RANGE_POTENTIAL] = "kcal/mol";
88 <    Stats::units_[SHORT_RANGE_POTENTIAL] = "kcal/mol";
89 <    Stats::units_[VANDERWAALS_POTENTIAL] = "kcal/mol";
129 <    Stats::units_[ELECTROSTATIC_POTENTIAL] = "kcal/mol";
130 <    Stats::units_[BOND_POTENTIAL] = "kcal/mol";
131 <    Stats::units_[BEND_POTENTIAL] = "kcal/mol";
132 <    Stats::units_[DIHEDRAL_POTENTIAL] = "kcal/mol";
133 <    Stats::units_[INVERSION_POTENTIAL] = "kcal/mol";
134 <    Stats::units_[VRAW] = "kcal/mol";
135 <    Stats::units_[VHARM] = "kcal/mol";
136 <    Stats::units_[SHADOWH] = "kcal/mol";
137 <    Stats::units_[PRESSURE_TENSOR_XX] = "amu*fs^-2*Ang^-1";
138 <    Stats::units_[PRESSURE_TENSOR_XY] = "amu*fs^-2*Ang^-1";
139 <    Stats::units_[PRESSURE_TENSOR_XZ] = "amu*fs^-2*Ang^-1";
140 <    Stats::units_[PRESSURE_TENSOR_YX] = "amu*fs^-2*Ang^-1";
141 <    Stats::units_[PRESSURE_TENSOR_YY] = "amu*fs^-2*Ang^-1";
142 <    Stats::units_[PRESSURE_TENSOR_YZ] = "amu*fs^-2*Ang^-1";
143 <    Stats::units_[PRESSURE_TENSOR_ZX] = "amu*fs^-2*Ang^-1";
144 <    Stats::units_[PRESSURE_TENSOR_ZY] = "amu*fs^-2*Ang^-1";
145 <    Stats::units_[PRESSURE_TENSOR_ZZ] = "amu*fs^-2*Ang^-1";
146 <    Stats::units_[BOX_DIPOLE_X] = "C*m";
147 <    Stats::units_[BOX_DIPOLE_Y] = "C*m";
148 <    Stats::units_[BOX_DIPOLE_Z] = "C*m";
149 <    Stats::units_[TAGGED_PAIR_DISTANCE] = "Ang";
150 <    Stats::units_[RNEMD_EXCHANGE_TOTAL] = "Variable";
151 <    Stats::units_[THERMAL_HELFANDMOMENT_X] = "Ang*kcal/mol";
152 <    Stats::units_[THERMAL_HELFANDMOMENT_Y] = "Ang*kcal/mol";
153 <    Stats::units_[THERMAL_HELFANDMOMENT_Z] = "Ang*kcal/mol";
154 <    Stats::units_[HEATFLUX_X]="amu/fs^3";
155 <    Stats::units_[HEATFLUX_Y]="amu/fs^3";      
156 <    Stats::units_[HEATFLUX_Z]="amu/fs^3";      
75 >    StatsData total_energy;
76 >    total_energy.units =  "kcal/mol";
77 >    total_energy.title =  "Total Energy";
78 >    total_energy.dataType = "RealType";
79 >    total_energy.accumulator = new Accumulator();
80 >    data_[TOTAL_ENERGY] = total_energy;
81 >    statsMap_["TOTAL_ENERGY"] =  TOTAL_ENERGY;
82 >  
83 >    StatsData potential_energy;
84 >    potential_energy.units =  "kcal/mol";
85 >    potential_energy.title =  "Potential Energy";
86 >    potential_energy.dataType = "RealType";
87 >    potential_energy.accumulator = new Accumulator();
88 >    data_[POTENTIAL_ENERGY] = potential_energy;
89 >    statsMap_["POTENTIAL_ENERGY"] =  POTENTIAL_ENERGY;
90  
91 <    Stats::statsMap.insert(StatsMapType::value_type("TIME", TIME));
92 <    Stats::statsMap.insert(StatsMapType::value_type("TOTAL_ENERGY", TOTAL_ENERGY));
93 <    Stats::statsMap.insert(StatsMapType::value_type("POTENTIAL_ENERGY", POTENTIAL_ENERGY));
94 <    Stats::statsMap.insert(StatsMapType::value_type("KINETIC_ENERGY", KINETIC_ENERGY));
95 <    Stats::statsMap.insert(StatsMapType::value_type("TEMPERATURE", TEMPERATURE));
96 <    Stats::statsMap.insert(StatsMapType::value_type("PRESSURE", PRESSURE));
97 <    Stats::statsMap.insert(StatsMapType::value_type("VOLUME", VOLUME));
98 <    Stats::statsMap.insert(StatsMapType::value_type("HULLVOLUME", HULLVOLUME));
99 <    Stats::statsMap.insert(StatsMapType::value_type("GYRVOLUME", GYRVOLUME));
100 <    Stats::statsMap.insert(StatsMapType::value_type("CONSERVED_QUANTITY", CONSERVED_QUANTITY));
101 <    Stats::statsMap.insert(StatsMapType::value_type("TRANSLATIONAL_KINETIC", TRANSLATIONAL_KINETIC));
102 <    Stats::statsMap.insert(StatsMapType::value_type("ROTATIONAL_KINETIC", ROTATIONAL_KINETIC));
103 <    Stats::statsMap.insert(StatsMapType::value_type("LONG_RANGE_POTENTIAL", LONG_RANGE_POTENTIAL));
104 <    Stats::statsMap.insert(StatsMapType::value_type("SHORT_RANGE_POTENTIAL", SHORT_RANGE_POTENTIAL));
105 <    Stats::statsMap.insert(StatsMapType::value_type("VANDERWAALS_POTENTIAL", VANDERWAALS_POTENTIAL));
106 <    Stats::statsMap.insert(StatsMapType::value_type("ELECTROSTATIC_POTENTIAL", ELECTROSTATIC_POTENTIAL));
107 <    Stats::statsMap.insert(StatsMapType::value_type("BOND_POTENTIAL", BOND_POTENTIAL));
108 <    Stats::statsMap.insert(StatsMapType::value_type("BEND_POTENTIAL", BEND_POTENTIAL));
109 <    Stats::statsMap.insert(StatsMapType::value_type("DIHEDRAL_POTENTIAL", DIHEDRAL_POTENTIAL));
110 <    Stats::statsMap.insert(StatsMapType::value_type("INVERSION_POTENTIAL", INVERSION_POTENTIAL));
111 <    Stats::statsMap.insert(StatsMapType::value_type("VRAW", VRAW));    
112 <    Stats::statsMap.insert(StatsMapType::value_type("VHARM", VHARM));    
113 <    Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_XX", PRESSURE_TENSOR_XX));    
114 <    Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_XY", PRESSURE_TENSOR_XY));    
115 <    Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_XZ", PRESSURE_TENSOR_XZ));    
116 <    Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_YX", PRESSURE_TENSOR_YX));    
117 <    Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_YY", PRESSURE_TENSOR_YY));    
118 <    Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_YZ", PRESSURE_TENSOR_YZ));    
119 <    Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_ZX", PRESSURE_TENSOR_ZX));    
120 <    Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_ZY", PRESSURE_TENSOR_ZY));    
121 <    Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_ZZ", PRESSURE_TENSOR_ZZ));    
122 <    Stats::statsMap.insert(StatsMapType::value_type("BOX_DIPOLE_X", BOX_DIPOLE_X));    
123 <    Stats::statsMap.insert(StatsMapType::value_type("BOX_DIPOLE_Y", BOX_DIPOLE_Y));    
124 <    Stats::statsMap.insert(StatsMapType::value_type("BOX_DIPOLE_Z", BOX_DIPOLE_Z));    
125 <    Stats::statsMap.insert(StatsMapType::value_type("TAGGED_PAIR_DISTANCE", TAGGED_PAIR_DISTANCE));    
126 <    Stats::statsMap.insert(StatsMapType::value_type("RNEMD_EXCHANGE_TOTAL", RNEMD_EXCHANGE_TOTAL));    
127 <    Stats::statsMap.insert(StatsMapType::value_type("SHADOWH", SHADOWH));
128 <    Stats::statsMap.insert(StatsMapType::value_type("THERMAL_HELFANDMOMENT_X",THERMAL_HELFANDMOMENT_X));
129 <    Stats::statsMap.insert(StatsMapType::value_type("THERMAL_HELFANDMOMENT_Y",THERMAL_HELFANDMOMENT_Y));
130 <    Stats::statsMap.insert(StatsMapType::value_type("THERMAL_HELFANDMOMENT_Z",THERMAL_HELFANDMOMENT_Z));
131 <    Stats::statsMap.insert(StatsMapType::value_type("HEATFLUX_X",HEATFLUX_X));
132 <    Stats::statsMap.insert(StatsMapType::value_type("HEATFLUX_Y",HEATFLUX_Y));
133 <    Stats::statsMap.insert(StatsMapType::value_type("HEATFLUX_Z",HEATFLUX_Z));
91 >    StatsData kinetic_energy;
92 >    kinetic_energy.units =  "kcal/mol";
93 >    kinetic_energy.title =  "Kinetic Energy";
94 >    kinetic_energy.dataType = "RealType";
95 >    kinetic_energy.accumulator = new Accumulator();
96 >    data_[KINETIC_ENERGY] = kinetic_energy;
97 >    statsMap_["KINETIC_ENERGY"] =  KINETIC_ENERGY;
98 >
99 >    StatsData temperature;
100 >    temperature.units =  "K";
101 >    temperature.title =  "Temperature";
102 >    temperature.dataType = "RealType";
103 >    temperature.accumulator = new Accumulator();
104 >    data_[TEMPERATURE] = temperature;
105 >    statsMap_["TEMPERATURE"] =  TEMPERATURE;
106 >
107 >    StatsData pressure;
108 >    pressure.units =  "atm";
109 >    pressure.title =  "Pressure";
110 >    pressure.dataType = "RealType";
111 >    pressure.accumulator = new Accumulator();
112 >    data_[PRESSURE] = pressure;
113 >    statsMap_["PRESSURE"] =  PRESSURE;
114 >
115 >    StatsData volume;
116 >    volume.units =  "A^3";
117 >    volume.title =  "Volume";
118 >    volume.dataType = "RealType";
119 >    volume.accumulator = new Accumulator();
120 >    data_[VOLUME] = volume;
121 >    statsMap_["VOLUME"] =  VOLUME;
122 >
123 >    StatsData hullvolume;
124 >    hullvolume.units =  "A^3";
125 >    hullvolume.title =  "Hull Volume";
126 >    hullvolume.dataType = "RealType";
127 >    hullvolume.accumulator = new Accumulator();
128 >    data_[HULLVOLUME] = hullvolume;
129 >    statsMap_["HULLVOLUME"] =  HULLVOLUME;
130 >
131 >    StatsData gyrvolume;
132 >    gyrvolume.units =  "A^3";
133 >    gyrvolume.title =  "Gyrational Volume";
134 >    gyrvolume.dataType = "RealType";
135 >    gyrvolume.accumulator = new Accumulator();
136 >    data_[GYRVOLUME] = gyrvolume;
137 >    statsMap_["GYRVOLUME"] =  GYRVOLUME;
138 >
139 >    StatsData conserved_quantity;
140 >    conserved_quantity.units =  "kcal/mol";            
141 >    conserved_quantity.title =  "Conserved Quantity";            
142 >    conserved_quantity.dataType = "RealType";
143 >    conserved_quantity.accumulator = new Accumulator();
144 >    data_[CONSERVED_QUANTITY] = conserved_quantity;
145 >    statsMap_["CONSERVED_QUANTITY"] =  CONSERVED_QUANTITY;
146 >
147 >    StatsData translational_kinetic;
148 >    translational_kinetic.units =  "kcal/mol";
149 >    translational_kinetic.title =  "Translational Kinetic";
150 >    translational_kinetic.dataType = "RealType";
151 >    translational_kinetic.accumulator = new Accumulator();
152 >    data_[TRANSLATIONAL_KINETIC] = translational_kinetic;
153 >    statsMap_["TRANSLATIONAL_KINETIC"] =  TRANSLATIONAL_KINETIC;
154 >
155 >    StatsData rotational_kinetic;
156 >    rotational_kinetic.units =  "kcal/mol";
157 >    rotational_kinetic.title =  "Rotational Kinetic";
158 >    rotational_kinetic.dataType = "RealType";
159 >    rotational_kinetic.accumulator = new Accumulator();
160 >    data_[ROTATIONAL_KINETIC] = rotational_kinetic;
161 >    statsMap_["ROTATIONAL_KINETIC"] =  ROTATIONAL_KINETIC;
162 >
163 >    StatsData long_range_potential;
164 >    long_range_potential.units =  "kcal/mol";
165 >    long_range_potential.title =  "Long Range Potential";
166 >    long_range_potential.dataType = "RealType";
167 >    long_range_potential.accumulator = new Accumulator();
168 >    data_[LONG_RANGE_POTENTIAL] = long_range_potential;
169 >    statsMap_["LONG_RANGE_POTENTIAL"] =  LONG_RANGE_POTENTIAL;
170 >
171 >    StatsData vanderwaals_potential;
172 >    vanderwaals_potential.units =  "kcal/mol";
173 >    vanderwaals_potential.title =  "van der waals Potential";
174 >    vanderwaals_potential.dataType = "RealType";
175 >    vanderwaals_potential.accumulator = new Accumulator();
176 >    data_[VANDERWAALS_POTENTIAL] = vanderwaals_potential;
177 >    statsMap_["VANDERWAALS_POTENTIAL"] =  VANDERWAALS_POTENTIAL;
178 >
179 >    StatsData electrostatic_potential;
180 >    electrostatic_potential.units =  "kcal/mol";
181 >    electrostatic_potential.title =  "Electrostatic Potential";    
182 >    electrostatic_potential.dataType = "RealType";
183 >    electrostatic_potential.accumulator = new Accumulator();
184 >    data_[ELECTROSTATIC_POTENTIAL] = electrostatic_potential;
185 >    statsMap_["ELECTROSTATIC_POTENTIAL"] =  ELECTROSTATIC_POTENTIAL;
186 >
187 >    StatsData metallic_potential;
188 >    metallic_potential.units =  "kcal/mol";
189 >    metallic_potential.title =  "Metallic Potential";    
190 >    metallic_potential.dataType = "RealType";
191 >    metallic_potential.accumulator = new Accumulator();
192 >    data_[METALLIC_POTENTIAL] = metallic_potential;
193 >    statsMap_["METALLIC_POTENTIAL"] =  METALLIC_POTENTIAL;
194 >
195 >    StatsData hydrogenbonding_potential;
196 >    hydrogenbonding_potential.units =  "kcal/mol";
197 >    hydrogenbonding_potential.title =  "Metallic Potential";    
198 >    hydrogenbonding_potential.dataType = "RealType";
199 >    hydrogenbonding_potential.accumulator = new Accumulator();
200 >    data_[HYDROGENBONDING_POTENTIAL] = hydrogenbonding_potential;
201 >    statsMap_["HYDROGENBONDING_POTENTIAL"] =  HYDROGENBONDING_POTENTIAL;
202 >
203 >    StatsData short_range_potential;
204 >    short_range_potential.units =  "kcal/mol";
205 >    short_range_potential.title =  "Short Range Potential";
206 >    short_range_potential.dataType = "RealType";
207 >    short_range_potential.accumulator = new Accumulator();
208 >    data_[SHORT_RANGE_POTENTIAL] = short_range_potential;
209 >    statsMap_["SHORT_RANGE_POTENTIAL"] =  SHORT_RANGE_POTENTIAL;
210 >
211 >    StatsData bond_potential;
212 >    bond_potential.units =  "kcal/mol";
213 >    bond_potential.title =  "Bond Potential";
214 >    bond_potential.dataType = "RealType";
215 >    bond_potential.accumulator = new Accumulator();
216 >    data_[BOND_POTENTIAL] = bond_potential;
217 >    statsMap_["BOND_POTENTIAL"] =  BOND_POTENTIAL;
218 >
219 >    StatsData bend_potential;
220 >    bend_potential.units =  "kcal/mol";
221 >    bend_potential.title =  "Bend Potential";
222 >    bend_potential.dataType = "RealType";
223 >    bend_potential.accumulator = new Accumulator();
224 >    data_[BEND_POTENTIAL] = bend_potential;
225 >    statsMap_["BEND_POTENTIAL"] =  BEND_POTENTIAL;
226 >    
227 >    StatsData dihedral_potential;
228 >    dihedral_potential.units =  "kcal/mol";
229 >    dihedral_potential.title =  "Dihedral Potential";
230 >    dihedral_potential.dataType = "RealType";
231 >    dihedral_potential.accumulator = new Accumulator();
232 >    data_[DIHEDRAL_POTENTIAL] = dihedral_potential;
233 >    statsMap_["DIHEDRAL_POTENTIAL"] =  DIHEDRAL_POTENTIAL;
234 >
235 >    StatsData inversion_potential;
236 >    inversion_potential.units =  "kcal/mol";
237 >    inversion_potential.title =  "Inversion Potential";
238 >    inversion_potential.dataType = "RealType";
239 >    inversion_potential.accumulator = new Accumulator();
240 >    data_[INVERSION_POTENTIAL] = inversion_potential;
241 >    statsMap_["INVERSION_POTENTIAL"] =  INVERSION_POTENTIAL;
242 >
243 >    StatsData vraw;
244 >    vraw.units =  "kcal/mol";
245 >    vraw.title =  "Raw Potential";
246 >    vraw.dataType = "RealType";
247 >    vraw.accumulator = new Accumulator();
248 >    data_[RAW_POTENTIAL] = vraw;
249 >    statsMap_["RAW_POTENTIAL"] =  RAW_POTENTIAL;
250 >
251 >    StatsData vrestraint;
252 >    vrestraint.units =  "kcal/mol";
253 >    vrestraint.title =  "Restraint Potential";
254 >    vrestraint.dataType = "RealType";
255 >    vrestraint.accumulator = new Accumulator();
256 >    data_[RESTRAINT_POTENTIAL] = vrestraint;
257 >    statsMap_["RESTRAINT_POTENTIAL"] =  RESTRAINT_POTENTIAL;
258 >
259 >    StatsData pressure_tensor;
260 >    pressure_tensor.units =  "amu*fs^-2*Ang^-1";
261 >    pressure_tensor.title =  "Ptensor";
262 >    pressure_tensor.dataType = "Mat3x3d";
263 >    pressure_tensor.accumulator = new MatrixAccumulator();
264 >    data_[PRESSURE_TENSOR] = pressure_tensor;
265 >    statsMap_["PRESSURE_TENSOR"] =  PRESSURE_TENSOR;
266 >
267 >    StatsData system_dipole;
268 >    system_dipole.units =  "C*m";
269 >    system_dipole.title =  "System Dipole";
270 >    system_dipole.dataType = "Vector3d";
271 >    system_dipole.accumulator = new VectorAccumulator();
272 >    data_[SYSTEM_DIPOLE] = system_dipole;
273 >    statsMap_["SYSTEM_DIPOLE"] =  SYSTEM_DIPOLE;
274 >
275 >    StatsData tagged_pair_distance;
276 >    tagged_pair_distance.units =  "Ang";
277 >    tagged_pair_distance.title =  "Tagged_Pair_Distance";
278 >    tagged_pair_distance.dataType = "RealType";
279 >    tagged_pair_distance.accumulator = new Accumulator();
280 >    data_[TAGGED_PAIR_DISTANCE] = tagged_pair_distance;
281 >    statsMap_["TAGGED_PAIR_DISTANCE"] =  TAGGED_PAIR_DISTANCE;
282 >
283 >    StatsData shadowh;
284 >    shadowh.units =  "kcal/mol";
285 >    shadowh.title =  "Shadow Hamiltonian";
286 >    shadowh.dataType = "RealType";
287 >    shadowh.accumulator = new Accumulator();
288 >    data_[SHADOWH] = shadowh;
289 >    statsMap_["SHADOWH"] =  SHADOWH;
290 >
291 >    StatsData helfandmoment;
292 >    helfandmoment.units =  "Ang*kcal/mol";
293 >    helfandmoment.title =  "Thermal Helfand Moment";
294 >    helfandmoment.dataType = "Vector3d";
295 >    helfandmoment.accumulator = new VectorAccumulator();
296 >    data_[HELFANDMOMENT] = helfandmoment;
297 >    statsMap_["HELFANDMOMENT"] = HELFANDMOMENT;
298 >
299 >    StatsData heatflux;
300 >    heatflux.units = "amu/fs^3";
301 >    heatflux.title =  "Heat Flux";  
302 >    heatflux.dataType = "Vector3d";
303 >    heatflux.accumulator = new VectorAccumulator();
304 >    data_[HEATFLUX] = heatflux;
305 >    statsMap_["HEATFLUX"] = HEATFLUX;
306 >
307 >    StatsData electronic_temperature;
308 >    electronic_temperature.units = "K";
309 >    electronic_temperature.title =  "Electronic Temperature";  
310 >    electronic_temperature.dataType = "RealType";
311 >    electronic_temperature.accumulator = new Accumulator();
312 >    data_[ELECTRONIC_TEMPERATURE] = electronic_temperature;
313 >    statsMap_["ELECTRONIC_TEMPERATURE"] = ELECTRONIC_TEMPERATURE;
314 >
315 >    // Now, set some defaults in the mask:
316 >
317 >    Globals* simParams = info_->getSimParams();
318 >    std::string statFileFormatString = simParams->getStatFileFormat();
319 >    parseStatFileFormat(statFileFormatString);
320 >
321 >    // if we're doing a thermodynamic integration, we'll want the raw
322 >    // potential as well as the full potential:
323 >    
324 >    if (simParams->getUseThermodynamicIntegration())
325 >      statsMask_.set(RAW_POTENTIAL);
326 >    
327 >    // if we've got restraints turned on, we'll also want a report of the
328 >    // total harmonic restraints
329 >    if (simParams->getUseRestraints()){
330 >      statsMask_.set(RESTRAINT_POTENTIAL);
331 >    }
332 >    
333 >    if (simParams->havePrintPressureTensor() &&
334 >        simParams->getPrintPressureTensor()){
335 >      statsMask_.set(PRESSURE_TENSOR);
336 >    }
337 >
338 >    // Why do we have both of these?
339 >    if (simParams->getAccumulateBoxDipole()) {
340 >      statsMask_.set(SYSTEM_DIPOLE);
341 >    }
342 >    if (info_->getCalcBoxDipole()){
343 >      statsMask_.set(SYSTEM_DIPOLE);
344 >    }
345 >
346 >    if (simParams->havePrintHeatFlux()) {
347 >      if (simParams->getPrintHeatFlux()){
348 >        statsMask_.set(HEATFLUX);
349 >      }
350 >    }    
351 >    
352 >    
353 >    if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) {
354 >      if (simParams->getPrintTaggedPairDistance()) {
355 >        statsMask_.set(TAGGED_PAIR_DISTANCE);
356 >      }
357 >    }
358 >    
359    }
360  
361 +  void Stats::parseStatFileFormat(const std::string& format) {
362 +    StringTokenizer tokenizer(format, " ,;|\t\n\r");
363 +
364 +    while(tokenizer.hasMoreTokens()) {
365 +      std::string token(tokenizer.nextToken());
366 +      toUpper(token);
367 +      StatsMapType::iterator i = statsMap_.find(token);
368 +      if (i != statsMap_.end()) {
369 +        statsMask_.set(i->second);
370 +      } else {
371 +        sprintf( painCave.errMsg,
372 +                 "Stats::parseStatFileFormat: %s is not a recognized\n"
373 +                 "\tstatFileFormat keyword.\n", token.c_str() );
374 +        painCave.isFatal = 0;
375 +        painCave.severity = OPENMD_ERROR;
376 +        simError();            
377 +      }
378 +    }  
379 +  }
380 +
381 +
382 +  std::string Stats::getTitle(int index) {
383 +    assert(index >=0 && index < ENDINDEX);
384 +    return data_[index].title;
385 +  }
386 +
387 +  std::string Stats::getUnits(int index) {
388 +    assert(index >=0 && index < ENDINDEX);
389 +    return data_[index].units;
390 +  }
391 +
392 +  std::string Stats::getDataType(int index) {
393 +    assert(index >=0 && index < ENDINDEX);
394 +    return data_[index].dataType;
395 +  }
396 +
397 +  void Stats::collectStats(){
398 +    Globals* simParams = info_->getSimParams();
399 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
400 +    Thermo thermo(info_);
401 +  
402 +    for (unsigned int i = 0; i < statsMask_.size(); ++i) {
403 +      if (statsMask_[i]) {
404 +        switch (i) {
405 +        case TIME:
406 +          data_[i].accumulator->add(snap->getTime());
407 +          break;
408 +        case KINETIC_ENERGY:
409 +          data_[i].accumulator->add(thermo.getKinetic());
410 +          break;
411 +        case POTENTIAL_ENERGY:
412 +          data_[i].accumulator->add(thermo.getPotential());
413 +          break;
414 +        case TOTAL_ENERGY:
415 +          data_[i].accumulator->add(thermo.getTotalEnergy());
416 +          break;
417 +        case TEMPERATURE:
418 +          data_[i].accumulator->add(thermo.getTemperature());
419 +          break;
420 +        case PRESSURE:
421 +          data_[i].accumulator->add(thermo.getPressure());
422 +          break;
423 +        case VOLUME:
424 +          data_[i].accumulator->add(thermo.getVolume());
425 +          break;
426 +        case CONSERVED_QUANTITY:
427 +          data_[i].accumulator->add(snap->getConservedQuantity());
428 +          break;
429 +        case PRESSURE_TENSOR:
430 +          dynamic_cast<MatrixAccumulator *>(data_[i].accumulator)->add(thermo.getPressureTensor());
431 +          break;
432 +        case SYSTEM_DIPOLE:
433 +          dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getSystemDipole());
434 +          break;
435 +        case HEATFLUX:
436 +          dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getHeatFlux());
437 +          break;
438 +        case HULLVOLUME:
439 +          data_[i].accumulator->add(thermo.getHullVolume());
440 +          break;
441 +        case GYRVOLUME:
442 +          data_[i].accumulator->add(thermo.getGyrationalVolume());
443 +          break;
444 +        case TRANSLATIONAL_KINETIC:
445 +          data_[i].accumulator->add(thermo.getTranslationalKinetic());
446 +          break;
447 +        case ROTATIONAL_KINETIC:
448 +          data_[i].accumulator->add(thermo.getRotationalKinetic());
449 +          break;
450 +        case LONG_RANGE_POTENTIAL:
451 +          data_[i].accumulator->add(snap->getLongRangePotential());
452 +          break;
453 +        case VANDERWAALS_POTENTIAL:
454 +          data_[i].accumulator->add(snap->getLongRangePotentials()[VANDERWAALS_FAMILY]);
455 +          break;
456 +        case ELECTROSTATIC_POTENTIAL:
457 +          data_[i].accumulator->add(snap->getLongRangePotentials()[ELECTROSTATIC_FAMILY]);
458 +          break;
459 +        case METALLIC_POTENTIAL:
460 +          data_[i].accumulator->add(snap->getLongRangePotentials()[METALLIC_FAMILY]);
461 +          break;
462 +        case HYDROGENBONDING_POTENTIAL:
463 +          data_[i].accumulator->add(snap->getLongRangePotentials()[HYDROGENBONDING_FAMILY]);
464 +          break;
465 +        case SHORT_RANGE_POTENTIAL:
466 +          data_[i].accumulator->add(snap->getShortRangePotential());
467 +          break;
468 +        case BOND_POTENTIAL:
469 +          data_[i].accumulator->add(snap->getBondPotential());
470 +          break;
471 +        case BEND_POTENTIAL:
472 +          data_[i].accumulator->add(snap->getBendPotential());
473 +          break;
474 +        case DIHEDRAL_POTENTIAL:
475 +          data_[i].accumulator->add(snap->getTorsionPotential());
476 +          break;
477 +        case INVERSION_POTENTIAL:
478 +          data_[i].accumulator->add(snap->getInversionPotential());
479 +          break;
480 +        case RAW_POTENTIAL:
481 +          data_[i].accumulator->add(snap->getRawPotential());
482 +          break;
483 +        case RESTRAINT_POTENTIAL:
484 +          data_[i].accumulator->add(snap->getRestraintPotential());
485 +          break;
486 +        case TAGGED_PAIR_DISTANCE:
487 +          data_[i].accumulator->add(thermo.getTaggedAtomPairDistance());
488 +          break;
489 +          /*
490 +        case SHADOWH:
491 +          data_[i].accumulator->add(thermo.getShadowHamiltionian());
492 +          break;
493 +        case HELFANDMOMENT:
494 +          data_[i].accumulator->add(thermo.getHelfandMoment());
495 +          break;
496 +          */
497 +        case ELECTRONIC_TEMPERATURE:
498 +          data_[i].accumulator->add(thermo.getElectronicTemperature());
499 +          break;
500 +        }
501 +      }
502 +    }
503 +  }
504 +
505 +  int Stats::getIntData(int index) {
506 +    assert(index >=0 && index < ENDINDEX);
507 +    RealType value;
508 +    data_[index].accumulator->getLastValue(value);
509 +    return (int) value;
510 +  }
511 +  RealType Stats::getRealData(int index) {
512 +    assert(index >=0 && index < ENDINDEX);
513 +    RealType value(0.0);
514 +    data_[index].accumulator->getLastValue(value);
515 +    return value;
516 +  }
517 +  Vector3d Stats::getVectorData(int index) {
518 +    assert(index >=0 && index < ENDINDEX);
519 +    Vector3d value;
520 +    dynamic_cast<VectorAccumulator*>(data_[index].accumulator)->getLastValue(value);
521 +    return value;
522 +  }
523 +  Mat3x3d Stats::getMatrixData(int index) {
524 +    assert(index >=0 && index < ENDINDEX);
525 +    Mat3x3d value;
526 +    dynamic_cast<MatrixAccumulator*>(data_[index].accumulator)->getLastValue(value);
527 +    return value;
528 +  }
529 +
530 +  Stats::StatsBitSet Stats::getStatsMask() {
531 +    return statsMask_;
532 +  }
533 +  Stats::StatsMapType Stats::getStatsMap() {
534 +    return statsMap_;
535 +  }
536 +  void Stats::setStatsMask(Stats::StatsBitSet mask) {
537 +    statsMask_ = mask;
538 +  }
539 +
540   }

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