| 49 |
|
*/ |
| 50 |
|
|
| 51 |
|
#include "brains/Stats.hpp" |
| 52 |
+ |
#include "brains/Thermo.hpp" |
| 53 |
|
|
| 54 |
|
namespace OpenMD { |
| 55 |
|
|
| 56 |
< |
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() { |
| 56 |
> |
Stats::Stats(SimInfo* info) : isInit_(false), info_(info) { |
| 57 |
|
|
| 58 |
|
if (!isInit_) { |
| 59 |
|
init(); |
| 60 |
|
isInit_ = true; |
| 61 |
|
} |
| 65 |
– |
|
| 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_[SHADOWH] = "Shadow Hamiltonian"; |
| 91 |
< |
Stats::title_[PRESSURE_TENSOR_XX] = "P_xx"; |
| 92 |
< |
Stats::title_[PRESSURE_TENSOR_XY] = "P_xy"; |
| 93 |
< |
Stats::title_[PRESSURE_TENSOR_XZ] = "P_xz"; |
| 94 |
< |
Stats::title_[PRESSURE_TENSOR_YX] = "P_yx"; |
| 95 |
< |
Stats::title_[PRESSURE_TENSOR_YY] = "P_yy"; |
| 96 |
< |
Stats::title_[PRESSURE_TENSOR_YZ] = "P_yz"; |
| 97 |
< |
Stats::title_[PRESSURE_TENSOR_ZX] = "P_zx"; |
| 98 |
< |
Stats::title_[PRESSURE_TENSOR_ZY] = "P_zy"; |
| 99 |
< |
Stats::title_[PRESSURE_TENSOR_ZZ] = "P_zz"; |
| 100 |
< |
Stats::title_[BOX_DIPOLE_X] = "box dipole x"; |
| 101 |
< |
Stats::title_[BOX_DIPOLE_Y] = "box dipole y"; |
| 102 |
< |
Stats::title_[BOX_DIPOLE_Z] = "box dipole z"; |
| 103 |
< |
Stats::title_[TAGGED_PAIR_DISTANCE] = "Tagged_Pair_Distance"; |
| 104 |
< |
Stats::title_[RNEMD_EXCHANGE_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 = "Metallic 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"; |
| 115 |
< |
Stats::units_[HULLVOLUME] = "A^3"; |
| 116 |
< |
Stats::units_[GYRVOLUME] = "A^3"; |
| 117 |
< |
Stats::units_[CONSERVED_QUANTITY] = "kcal/mol"; |
| 118 |
< |
Stats::units_[TRANSLATIONAL_KINETIC] = "kcal/mol"; |
| 119 |
< |
Stats::units_[ROTATIONAL_KINETIC] = "kcal/mol"; |
| 120 |
< |
Stats::units_[LONG_RANGE_POTENTIAL] = "kcal/mol"; |
| 121 |
< |
Stats::units_[SHORT_RANGE_POTENTIAL] = "kcal/mol"; |
| 122 |
< |
Stats::units_[VANDERWAALS_POTENTIAL] = "kcal/mol"; |
| 123 |
< |
Stats::units_[ELECTROSTATIC_POTENTIAL] = "kcal/mol"; |
| 124 |
< |
Stats::units_[BOND_POTENTIAL] = "kcal/mol"; |
| 125 |
< |
Stats::units_[BEND_POTENTIAL] = "kcal/mol"; |
| 126 |
< |
Stats::units_[DIHEDRAL_POTENTIAL] = "kcal/mol"; |
| 127 |
< |
Stats::units_[INVERSION_POTENTIAL] = "kcal/mol"; |
| 128 |
< |
Stats::units_[VRAW] = "kcal/mol"; |
| 129 |
< |
Stats::units_[VHARM] = "kcal/mol"; |
| 130 |
< |
Stats::units_[SHADOWH] = "kcal/mol"; |
| 131 |
< |
Stats::units_[PRESSURE_TENSOR_XX] = "amu*fs^-2*Ang^-1"; |
| 132 |
< |
Stats::units_[PRESSURE_TENSOR_XY] = "amu*fs^-2*Ang^-1"; |
| 133 |
< |
Stats::units_[PRESSURE_TENSOR_XZ] = "amu*fs^-2*Ang^-1"; |
| 134 |
< |
Stats::units_[PRESSURE_TENSOR_YX] = "amu*fs^-2*Ang^-1"; |
| 135 |
< |
Stats::units_[PRESSURE_TENSOR_YY] = "amu*fs^-2*Ang^-1"; |
| 136 |
< |
Stats::units_[PRESSURE_TENSOR_YZ] = "amu*fs^-2*Ang^-1"; |
| 137 |
< |
Stats::units_[PRESSURE_TENSOR_ZX] = "amu*fs^-2*Ang^-1"; |
| 138 |
< |
Stats::units_[PRESSURE_TENSOR_ZY] = "amu*fs^-2*Ang^-1"; |
| 139 |
< |
Stats::units_[PRESSURE_TENSOR_ZZ] = "amu*fs^-2*Ang^-1"; |
| 140 |
< |
Stats::units_[BOX_DIPOLE_X] = "C*m"; |
| 141 |
< |
Stats::units_[BOX_DIPOLE_Y] = "C*m"; |
| 142 |
< |
Stats::units_[BOX_DIPOLE_Z] = "C*m"; |
| 143 |
< |
Stats::units_[TAGGED_PAIR_DISTANCE] = "Ang"; |
| 144 |
< |
Stats::units_[RNEMD_EXCHANGE_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_EXCHANGE_TOTAL", RNEMD_EXCHANGE_TOTAL)); |
| 272 |
< |
Stats::statsMap.insert(StatsMapType::value_type("SHADOWH", SHADOWH)); |
| 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 |
+ |
data_[i].accumulator->add(snap->getTime()); |
| 408 |
+ |
break; |
| 409 |
+ |
case KINETIC_ENERGY: |
| 410 |
+ |
data_[i].accumulator->add(thermo.getKinetic()); |
| 411 |
+ |
break; |
| 412 |
+ |
case POTENTIAL_ENERGY: |
| 413 |
+ |
data_[i].accumulator->add(thermo.getPotential()); |
| 414 |
+ |
break; |
| 415 |
+ |
case TOTAL_ENERGY: |
| 416 |
+ |
data_[i].accumulator->add(thermo.getTotalEnergy()); |
| 417 |
+ |
break; |
| 418 |
+ |
case TEMPERATURE: |
| 419 |
+ |
data_[i].accumulator->add(thermo.getTemperature()); |
| 420 |
+ |
break; |
| 421 |
+ |
case PRESSURE: |
| 422 |
+ |
data_[i].accumulator->add(thermo.getPressure()); |
| 423 |
+ |
break; |
| 424 |
+ |
case VOLUME: |
| 425 |
+ |
data_[i].accumulator->add(thermo.getVolume()); |
| 426 |
+ |
break; |
| 427 |
+ |
case CONSERVED_QUANTITY: |
| 428 |
+ |
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 |
+ |
data_[i].accumulator->add(thermo.getHullVolume()); |
| 441 |
+ |
break; |
| 442 |
+ |
case GYRVOLUME: |
| 443 |
+ |
data_[i].accumulator->add(thermo.getGyrationalVolume()); |
| 444 |
+ |
break; |
| 445 |
+ |
case TRANSLATIONAL_KINETIC: |
| 446 |
+ |
data_[i].accumulator->add(thermo.getTranslationalKinetic()); |
| 447 |
+ |
break; |
| 448 |
+ |
case ROTATIONAL_KINETIC: |
| 449 |
+ |
data_[i].accumulator->add(thermo.getRotationalKinetic()); |
| 450 |
+ |
break; |
| 451 |
+ |
case LONG_RANGE_POTENTIAL: |
| 452 |
+ |
data_[i].accumulator->add(snap->getLongRangePotential()); |
| 453 |
+ |
break; |
| 454 |
+ |
case VANDERWAALS_POTENTIAL: |
| 455 |
+ |
data_[i].accumulator->add(snap->getLongRangePotentials()[VANDERWAALS_FAMILY]); |
| 456 |
+ |
break; |
| 457 |
+ |
case ELECTROSTATIC_POTENTIAL: |
| 458 |
+ |
data_[i].accumulator->add(snap->getLongRangePotentials()[ELECTROSTATIC_FAMILY]); |
| 459 |
+ |
break; |
| 460 |
+ |
case METALLIC_POTENTIAL: |
| 461 |
+ |
data_[i].accumulator->add(snap->getLongRangePotentials()[METALLIC_FAMILY]); |
| 462 |
+ |
break; |
| 463 |
+ |
case HYDROGENBONDING_POTENTIAL: |
| 464 |
+ |
data_[i].accumulator->add(snap->getLongRangePotentials()[HYDROGENBONDING_FAMILY]); |
| 465 |
+ |
break; |
| 466 |
+ |
case SHORT_RANGE_POTENTIAL: |
| 467 |
+ |
data_[i].accumulator->add(snap->getShortRangePotential()); |
| 468 |
+ |
break; |
| 469 |
+ |
case BOND_POTENTIAL: |
| 470 |
+ |
data_[i].accumulator->add(snap->getBondPotential()); |
| 471 |
+ |
break; |
| 472 |
+ |
case BEND_POTENTIAL: |
| 473 |
+ |
data_[i].accumulator->add(snap->getBendPotential()); |
| 474 |
+ |
break; |
| 475 |
+ |
case DIHEDRAL_POTENTIAL: |
| 476 |
+ |
data_[i].accumulator->add(snap->getTorsionPotential()); |
| 477 |
+ |
break; |
| 478 |
+ |
case INVERSION_POTENTIAL: |
| 479 |
+ |
data_[i].accumulator->add(snap->getInversionPotential()); |
| 480 |
+ |
break; |
| 481 |
+ |
case RAW_POTENTIAL: |
| 482 |
+ |
data_[i].accumulator->add(snap->getRawPotential()); |
| 483 |
+ |
break; |
| 484 |
+ |
case RESTRAINT_POTENTIAL: |
| 485 |
+ |
data_[i].accumulator->add(snap->getRestraintPotential()); |
| 486 |
+ |
break; |
| 487 |
+ |
case TAGGED_PAIR_DISTANCE: |
| 488 |
+ |
data_[i].accumulator->add(thermo.getTaggedAtomPairDistance()); |
| 489 |
+ |
break; |
| 490 |
+ |
/* |
| 491 |
+ |
case SHADOWH: |
| 492 |
+ |
data_[i].accumulator->add(thermo.getShadowHamiltionian()); |
| 493 |
+ |
break; |
| 494 |
+ |
case HELFANDMOMENT: |
| 495 |
+ |
data_[i].accumulator->add(thermo.getHelfandMoment()); |
| 496 |
+ |
break; |
| 497 |
+ |
*/ |
| 498 |
+ |
case ELECTRONIC_TEMPERATURE: |
| 499 |
+ |
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 |
+ |
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 |
+ |
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 |
|
} |
