--- trunk/src/brains/Stats.cpp 2006/07/03 13:18:43 998 +++ trunk/src/brains/Stats.cpp 2009/11/25 20:02:06 1390 @@ -6,19 +6,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -37,6 +28,15 @@ * arising out of the use of or inability to use software, even if the * University of Notre Dame has been advised of the possibility of * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). + * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). + * [4] Vardeman & Gezelter, in progress (2009). */ /** @@ -49,7 +49,7 @@ #include "brains/Stats.hpp" -namespace oopse { +namespace OpenMD { bool Stats::isInit_ = false; std::string Stats::title_[Stats::ENDINDEX - Stats::BEGININDEX]; @@ -73,6 +73,8 @@ namespace oopse { Stats::title_[TEMPERATURE] = "Temperature"; Stats::title_[PRESSURE] = "Pressure"; Stats::title_[VOLUME] = "Volume"; + Stats::title_[HULLVOLUME] = "Hull Volume"; + Stats::title_[GYRVOLUME] = "Gyrational Volume"; Stats::title_[CONSERVED_QUANTITY] = "Conserved Quantity"; Stats::title_[TRANSLATIONAL_KINETIC] = "Translational Kinetic"; Stats::title_[ROTATIONAL_KINETIC] = "Rotational Kinetic"; @@ -83,16 +85,24 @@ namespace oopse { Stats::title_[BOND_POTENTIAL] = "Bond Potential"; Stats::title_[BEND_POTENTIAL] = "Bend Potential"; Stats::title_[DIHEDRAL_POTENTIAL] = "Dihedral Potential"; - Stats::title_[IMPROPER_POTENTIAL] = "Improper Potential"; + Stats::title_[INVERSION_POTENTIAL] = "Inversion Potential"; Stats::title_[VRAW] = "Raw Potential"; Stats::title_[VHARM] = "Harmonic Potential"; - Stats::title_[PRESSURE_TENSOR_X] = "pressure tensor x"; - Stats::title_[PRESSURE_TENSOR_Y] = "pressure tensor y"; - Stats::title_[PRESSURE_TENSOR_Z] = "pressure tensor z"; + Stats::title_[PRESSURE_TENSOR_XX] = "P_xx"; + Stats::title_[PRESSURE_TENSOR_XY] = "P_xy"; + Stats::title_[PRESSURE_TENSOR_XZ] = "P_xz"; + Stats::title_[PRESSURE_TENSOR_YX] = "P_yx"; + Stats::title_[PRESSURE_TENSOR_YY] = "P_yy"; + Stats::title_[PRESSURE_TENSOR_YZ] = "P_yz"; + Stats::title_[PRESSURE_TENSOR_ZX] = "P_zx"; + Stats::title_[PRESSURE_TENSOR_ZY] = "P_zy"; + Stats::title_[PRESSURE_TENSOR_ZZ] = "P_zz"; Stats::title_[BOX_DIPOLE_X] = "box dipole x"; Stats::title_[BOX_DIPOLE_Y] = "box dipole y"; Stats::title_[BOX_DIPOLE_Z] = "box dipole z"; - + Stats::title_[TAGGED_PAIR_DISTANCE] = "Tagged_Pair_Distance"; + Stats::title_[RNEMD_EXCHANGE_TOTAL] = "RNEMD_exchange_total"; + Stats::units_[TIME] = "fs"; Stats::units_[TOTAL_ENERGY] = "kcal/mol"; Stats::units_[POTENTIAL_ENERGY] = "kcal/mol"; @@ -100,6 +110,8 @@ namespace oopse { Stats::units_[TEMPERATURE] = "K"; Stats::units_[PRESSURE] = "atm"; Stats::units_[VOLUME] = "A^3"; + Stats::units_[HULLVOLUME] = "A^3"; + Stats::units_[GYRVOLUME] = "A^3"; Stats::units_[CONSERVED_QUANTITY] = "kcal/mol"; Stats::units_[TRANSLATIONAL_KINETIC] = "kcal/mol"; Stats::units_[ROTATIONAL_KINETIC] = "kcal/mol"; @@ -110,15 +122,23 @@ namespace oopse { Stats::units_[BOND_POTENTIAL] = "kcal/mol"; Stats::units_[BEND_POTENTIAL] = "kcal/mol"; Stats::units_[DIHEDRAL_POTENTIAL] = "kcal/mol"; - Stats::units_[IMPROPER_POTENTIAL] = "kcal/mol"; + Stats::units_[INVERSION_POTENTIAL] = "kcal/mol"; Stats::units_[VRAW] = "kcal/mol"; Stats::units_[VHARM] = "kcal/mol"; - Stats::units_[PRESSURE_TENSOR_X] = "amu*fs^-2*Ang^-1"; - Stats::units_[PRESSURE_TENSOR_Y] = "amu*fs^-2*Ang^-1"; - Stats::units_[PRESSURE_TENSOR_Z] = "amu*fs^-2*Ang^-1"; + Stats::units_[PRESSURE_TENSOR_XX] = "amu*fs^-2*Ang^-1"; + Stats::units_[PRESSURE_TENSOR_XY] = "amu*fs^-2*Ang^-1"; + Stats::units_[PRESSURE_TENSOR_XZ] = "amu*fs^-2*Ang^-1"; + Stats::units_[PRESSURE_TENSOR_YX] = "amu*fs^-2*Ang^-1"; + Stats::units_[PRESSURE_TENSOR_YY] = "amu*fs^-2*Ang^-1"; + Stats::units_[PRESSURE_TENSOR_YZ] = "amu*fs^-2*Ang^-1"; + Stats::units_[PRESSURE_TENSOR_ZX] = "amu*fs^-2*Ang^-1"; + Stats::units_[PRESSURE_TENSOR_ZY] = "amu*fs^-2*Ang^-1"; + Stats::units_[PRESSURE_TENSOR_ZZ] = "amu*fs^-2*Ang^-1"; Stats::units_[BOX_DIPOLE_X] = "C*m"; Stats::units_[BOX_DIPOLE_Y] = "C*m"; Stats::units_[BOX_DIPOLE_Z] = "C*m"; + Stats::units_[TAGGED_PAIR_DISTANCE] = "Ang"; + Stats::units_[RNEMD_EXCHANGE_TOTAL] = "Variable"; Stats::statsMap.insert(StatsMapType::value_type("TIME", TIME)); Stats::statsMap.insert(StatsMapType::value_type("TOTAL_ENERGY", TOTAL_ENERGY)); @@ -127,6 +147,8 @@ namespace oopse { Stats::statsMap.insert(StatsMapType::value_type("TEMPERATURE", TEMPERATURE)); Stats::statsMap.insert(StatsMapType::value_type("PRESSURE", PRESSURE)); Stats::statsMap.insert(StatsMapType::value_type("VOLUME", VOLUME)); + Stats::statsMap.insert(StatsMapType::value_type("HULLVOLUME", HULLVOLUME)); + Stats::statsMap.insert(StatsMapType::value_type("GYRVOLUME", GYRVOLUME)); Stats::statsMap.insert(StatsMapType::value_type("CONSERVED_QUANTITY", CONSERVED_QUANTITY)); Stats::statsMap.insert(StatsMapType::value_type("TRANSLATIONAL_KINETIC", TRANSLATIONAL_KINETIC)); Stats::statsMap.insert(StatsMapType::value_type("ROTATIONAL_KINETIC", ROTATIONAL_KINETIC)); @@ -137,15 +159,23 @@ namespace oopse { Stats::statsMap.insert(StatsMapType::value_type("BOND_POTENTIAL", BOND_POTENTIAL)); Stats::statsMap.insert(StatsMapType::value_type("BEND_POTENTIAL", BEND_POTENTIAL)); Stats::statsMap.insert(StatsMapType::value_type("DIHEDRAL_POTENTIAL", DIHEDRAL_POTENTIAL)); - Stats::statsMap.insert(StatsMapType::value_type("IMPROPER_POTENTIAL", IMPROPER_POTENTIAL)); + Stats::statsMap.insert(StatsMapType::value_type("INVERSION_POTENTIAL", INVERSION_POTENTIAL)); Stats::statsMap.insert(StatsMapType::value_type("VRAW", VRAW)); Stats::statsMap.insert(StatsMapType::value_type("VHARM", VHARM)); - Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_X", PRESSURE_TENSOR_X)); - Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_Y", PRESSURE_TENSOR_Y)); - Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_Z", PRESSURE_TENSOR_Z)); + Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_XX", PRESSURE_TENSOR_XX)); + Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_XY", PRESSURE_TENSOR_XY)); + Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_XZ", PRESSURE_TENSOR_XZ)); + Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_YX", PRESSURE_TENSOR_YX)); + Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_YY", PRESSURE_TENSOR_YY)); + Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_YZ", PRESSURE_TENSOR_YZ)); + Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_ZX", PRESSURE_TENSOR_ZX)); + Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_ZY", PRESSURE_TENSOR_ZY)); + Stats::statsMap.insert(StatsMapType::value_type("PRESSURE_TENSOR_ZZ", PRESSURE_TENSOR_ZZ)); Stats::statsMap.insert(StatsMapType::value_type("BOX_DIPOLE_X", BOX_DIPOLE_X)); Stats::statsMap.insert(StatsMapType::value_type("BOX_DIPOLE_Y", BOX_DIPOLE_Y)); Stats::statsMap.insert(StatsMapType::value_type("BOX_DIPOLE_Z", BOX_DIPOLE_Z)); + Stats::statsMap.insert(StatsMapType::value_type("TAGGED_PAIR_DISTANCE", TAGGED_PAIR_DISTANCE)); + Stats::statsMap.insert(StatsMapType::value_type("RNEMD_EXCHANGE_TOTAL", RNEMD_EXCHANGE_TOTAL)); } }