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/* |
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* Copyright (c) 2005, 2009 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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/** |
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* @file Stats.cpp |
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* @author tlin |
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* @date 11/04/2004 |
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* @version 1.0 |
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*/ |
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|
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#include "brains/Stats.hpp" |
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#include "brains/Thermo.hpp" |
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|
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namespace OpenMD { |
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|
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Stats::Stats(SimInfo* info) : isInit_(false), info_(info) { |
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|
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if (!isInit_) { |
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init(); |
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isInit_ = true; |
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} |
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} |
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|
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void Stats::init() { |
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|
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data_.resize(Stats::ENDINDEX); |
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|
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StatsData time; |
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time.units = "fs"; |
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time.title = "Time"; |
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time.dataType = "RealType"; |
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time.accumulator = new Accumulator(); |
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data_[TIME] = time; |
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statsMap_["TIME"] = TIME; |
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|
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StatsData total_energy; |
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total_energy.units = "kcal/mol"; |
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total_energy.title = "Total Energy"; |
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total_energy.dataType = "RealType"; |
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total_energy.accumulator = new Accumulator(); |
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data_[TOTAL_ENERGY] = total_energy; |
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statsMap_["TOTAL_ENERGY"] = TOTAL_ENERGY; |
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|
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StatsData potential_energy; |
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potential_energy.units = "kcal/mol"; |
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potential_energy.title = "Potential Energy"; |
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potential_energy.dataType = "RealType"; |
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potential_energy.accumulator = new Accumulator(); |
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data_[POTENTIAL_ENERGY] = potential_energy; |
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statsMap_["POTENTIAL_ENERGY"] = POTENTIAL_ENERGY; |
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|
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StatsData kinetic_energy; |
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kinetic_energy.units = "kcal/mol"; |
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kinetic_energy.title = "Kinetic Energy"; |
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kinetic_energy.dataType = "RealType"; |
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kinetic_energy.accumulator = new Accumulator(); |
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data_[KINETIC_ENERGY] = kinetic_energy; |
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statsMap_["KINETIC_ENERGY"] = KINETIC_ENERGY; |
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|
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StatsData temperature; |
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temperature.units = "K"; |
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temperature.title = "Temperature"; |
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temperature.dataType = "RealType"; |
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temperature.accumulator = new Accumulator(); |
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data_[TEMPERATURE] = temperature; |
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statsMap_["TEMPERATURE"] = TEMPERATURE; |
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|
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StatsData pressure; |
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pressure.units = "atm"; |
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pressure.title = "Pressure"; |
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pressure.dataType = "RealType"; |
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pressure.accumulator = new Accumulator(); |
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data_[PRESSURE] = pressure; |
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statsMap_["PRESSURE"] = PRESSURE; |
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|
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StatsData volume; |
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volume.units = "A^3"; |
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volume.title = "Volume"; |
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volume.dataType = "RealType"; |
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volume.accumulator = new Accumulator(); |
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data_[VOLUME] = volume; |
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statsMap_["VOLUME"] = VOLUME; |
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|
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StatsData hullvolume; |
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hullvolume.units = "A^3"; |
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hullvolume.title = "Hull Volume"; |
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hullvolume.dataType = "RealType"; |
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hullvolume.accumulator = new Accumulator(); |
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data_[HULLVOLUME] = hullvolume; |
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statsMap_["HULLVOLUME"] = HULLVOLUME; |
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|
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StatsData gyrvolume; |
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gyrvolume.units = "A^3"; |
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gyrvolume.title = "Gyrational Volume"; |
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gyrvolume.dataType = "RealType"; |
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gyrvolume.accumulator = new Accumulator(); |
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data_[GYRVOLUME] = gyrvolume; |
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statsMap_["GYRVOLUME"] = GYRVOLUME; |
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|
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StatsData conserved_quantity; |
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conserved_quantity.units = "kcal/mol"; |
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conserved_quantity.title = "Conserved Quantity"; |
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conserved_quantity.dataType = "RealType"; |
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conserved_quantity.accumulator = new Accumulator(); |
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data_[CONSERVED_QUANTITY] = conserved_quantity; |
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statsMap_["CONSERVED_QUANTITY"] = CONSERVED_QUANTITY; |
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|
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StatsData translational_kinetic; |
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translational_kinetic.units = "kcal/mol"; |
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translational_kinetic.title = "Translational Kinetic"; |
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translational_kinetic.dataType = "RealType"; |
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translational_kinetic.accumulator = new Accumulator(); |
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data_[TRANSLATIONAL_KINETIC] = translational_kinetic; |
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statsMap_["TRANSLATIONAL_KINETIC"] = TRANSLATIONAL_KINETIC; |
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|
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StatsData rotational_kinetic; |
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rotational_kinetic.units = "kcal/mol"; |
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rotational_kinetic.title = "Rotational Kinetic"; |
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rotational_kinetic.dataType = "RealType"; |
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rotational_kinetic.accumulator = new Accumulator(); |
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data_[ROTATIONAL_KINETIC] = rotational_kinetic; |
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statsMap_["ROTATIONAL_KINETIC"] = ROTATIONAL_KINETIC; |
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|
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StatsData long_range_potential; |
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long_range_potential.units = "kcal/mol"; |
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long_range_potential.title = "Long Range Potential"; |
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long_range_potential.dataType = "RealType"; |
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long_range_potential.accumulator = new Accumulator(); |
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data_[LONG_RANGE_POTENTIAL] = long_range_potential; |
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statsMap_["LONG_RANGE_POTENTIAL"] = LONG_RANGE_POTENTIAL; |
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|
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StatsData vanderwaals_potential; |
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vanderwaals_potential.units = "kcal/mol"; |
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vanderwaals_potential.title = "van der waals Potential"; |
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vanderwaals_potential.dataType = "RealType"; |
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vanderwaals_potential.accumulator = new Accumulator(); |
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data_[VANDERWAALS_POTENTIAL] = vanderwaals_potential; |
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statsMap_["VANDERWAALS_POTENTIAL"] = VANDERWAALS_POTENTIAL; |
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|
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StatsData electrostatic_potential; |
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electrostatic_potential.units = "kcal/mol"; |
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electrostatic_potential.title = "Electrostatic Potential"; |
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electrostatic_potential.dataType = "RealType"; |
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electrostatic_potential.accumulator = new Accumulator(); |
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data_[ELECTROSTATIC_POTENTIAL] = electrostatic_potential; |
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statsMap_["ELECTROSTATIC_POTENTIAL"] = ELECTROSTATIC_POTENTIAL; |
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|
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StatsData metallic_potential; |
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metallic_potential.units = "kcal/mol"; |
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metallic_potential.title = "Metallic Potential"; |
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metallic_potential.dataType = "RealType"; |
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metallic_potential.accumulator = new Accumulator(); |
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data_[METALLIC_POTENTIAL] = metallic_potential; |
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statsMap_["METALLIC_POTENTIAL"] = METALLIC_POTENTIAL; |
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|
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StatsData hydrogenbonding_potential; |
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hydrogenbonding_potential.units = "kcal/mol"; |
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hydrogenbonding_potential.title = "Metallic Potential"; |
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hydrogenbonding_potential.dataType = "RealType"; |
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hydrogenbonding_potential.accumulator = new Accumulator(); |
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data_[HYDROGENBONDING_POTENTIAL] = hydrogenbonding_potential; |
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statsMap_["HYDROGENBONDING_POTENTIAL"] = HYDROGENBONDING_POTENTIAL; |
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|
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StatsData short_range_potential; |
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short_range_potential.units = "kcal/mol"; |
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short_range_potential.title = "Short Range Potential"; |
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short_range_potential.dataType = "RealType"; |
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short_range_potential.accumulator = new Accumulator(); |
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data_[SHORT_RANGE_POTENTIAL] = short_range_potential; |
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statsMap_["SHORT_RANGE_POTENTIAL"] = SHORT_RANGE_POTENTIAL; |
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|
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StatsData bond_potential; |
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bond_potential.units = "kcal/mol"; |
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bond_potential.title = "Bond Potential"; |
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bond_potential.dataType = "RealType"; |
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bond_potential.accumulator = new Accumulator(); |
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data_[BOND_POTENTIAL] = bond_potential; |
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statsMap_["BOND_POTENTIAL"] = BOND_POTENTIAL; |
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|
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StatsData bend_potential; |
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bend_potential.units = "kcal/mol"; |
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bend_potential.title = "Bend Potential"; |
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bend_potential.dataType = "RealType"; |
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bend_potential.accumulator = new Accumulator(); |
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data_[BEND_POTENTIAL] = bend_potential; |
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statsMap_["BEND_POTENTIAL"] = BEND_POTENTIAL; |
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|
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StatsData dihedral_potential; |
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dihedral_potential.units = "kcal/mol"; |
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dihedral_potential.title = "Dihedral Potential"; |
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dihedral_potential.dataType = "RealType"; |
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dihedral_potential.accumulator = new Accumulator(); |
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data_[DIHEDRAL_POTENTIAL] = dihedral_potential; |
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statsMap_["DIHEDRAL_POTENTIAL"] = DIHEDRAL_POTENTIAL; |
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|
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StatsData inversion_potential; |
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inversion_potential.units = "kcal/mol"; |
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inversion_potential.title = "Inversion Potential"; |
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inversion_potential.dataType = "RealType"; |
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inversion_potential.accumulator = new Accumulator(); |
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data_[INVERSION_POTENTIAL] = inversion_potential; |
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statsMap_["INVERSION_POTENTIAL"] = INVERSION_POTENTIAL; |
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|
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StatsData vraw; |
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vraw.units = "kcal/mol"; |
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vraw.title = "Raw Potential"; |
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vraw.dataType = "RealType"; |
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vraw.accumulator = new Accumulator(); |
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data_[RAW_POTENTIAL] = vraw; |
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statsMap_["RAW_POTENTIAL"] = RAW_POTENTIAL; |
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|
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StatsData vrestraint; |
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vrestraint.units = "kcal/mol"; |
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vrestraint.title = "Restraint Potential"; |
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vrestraint.dataType = "RealType"; |
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vrestraint.accumulator = new Accumulator(); |
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data_[RESTRAINT_POTENTIAL] = vrestraint; |
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statsMap_["RESTRAINT_POTENTIAL"] = RESTRAINT_POTENTIAL; |
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|
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StatsData pressure_tensor; |
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pressure_tensor.units = "amu*fs^-2*Ang^-1"; |
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pressure_tensor.title = "Ptensor"; |
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pressure_tensor.dataType = "Mat3x3d"; |
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pressure_tensor.accumulator = new MatrixAccumulator(); |
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data_[PRESSURE_TENSOR] = pressure_tensor; |
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statsMap_["PRESSURE_TENSOR"] = PRESSURE_TENSOR; |
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|
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StatsData system_dipole; |
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system_dipole.units = "C*m"; |
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system_dipole.title = "System Dipole"; |
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system_dipole.dataType = "Vector3d"; |
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system_dipole.accumulator = new VectorAccumulator(); |
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data_[SYSTEM_DIPOLE] = system_dipole; |
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statsMap_["SYSTEM_DIPOLE"] = SYSTEM_DIPOLE; |
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|
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StatsData tagged_pair_distance; |
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tagged_pair_distance.units = "Ang"; |
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tagged_pair_distance.title = "Tagged_Pair_Distance"; |
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tagged_pair_distance.dataType = "RealType"; |
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tagged_pair_distance.accumulator = new Accumulator(); |
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data_[TAGGED_PAIR_DISTANCE] = tagged_pair_distance; |
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statsMap_["TAGGED_PAIR_DISTANCE"] = TAGGED_PAIR_DISTANCE; |
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|
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StatsData shadowh; |
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shadowh.units = "kcal/mol"; |
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shadowh.title = "Shadow Hamiltonian"; |
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shadowh.dataType = "RealType"; |
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shadowh.accumulator = new Accumulator(); |
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data_[SHADOWH] = shadowh; |
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statsMap_["SHADOWH"] = SHADOWH; |
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|
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StatsData helfandmoment; |
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helfandmoment.units = "Ang*kcal/mol"; |
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helfandmoment.title = "Thermal Helfand Moment"; |
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helfandmoment.dataType = "Vector3d"; |
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helfandmoment.accumulator = new VectorAccumulator(); |
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data_[HELFANDMOMENT] = helfandmoment; |
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statsMap_["HELFANDMOMENT"] = HELFANDMOMENT; |
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|
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StatsData heatflux; |
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heatflux.units = "amu/fs^3"; |
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heatflux.title = "Heat Flux"; |
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heatflux.dataType = "Vector3d"; |
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heatflux.accumulator = new VectorAccumulator(); |
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data_[HEATFLUX] = heatflux; |
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statsMap_["HEATFLUX"] = HEATFLUX; |
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|
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StatsData electronic_temperature; |
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electronic_temperature.units = "K"; |
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electronic_temperature.title = "Electronic Temperature"; |
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electronic_temperature.dataType = "RealType"; |
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electronic_temperature.accumulator = new Accumulator(); |
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data_[ELECTRONIC_TEMPERATURE] = electronic_temperature; |
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statsMap_["ELECTRONIC_TEMPERATURE"] = ELECTRONIC_TEMPERATURE; |
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|
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// Now, set some defaults in the mask: |
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|
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Globals* simParams = info_->getSimParams(); |
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std::string statFileFormatString = simParams->getStatFileFormat(); |
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parseStatFileFormat(statFileFormatString); |
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|
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// if we're doing a thermodynamic integration, we'll want the raw |
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// potential as well as the full potential: |
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|
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if (simParams->getUseThermodynamicIntegration()) |
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statsMask_.set(RAW_POTENTIAL); |
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|
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// if we've got restraints turned on, we'll also want a report of the |
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// total harmonic restraints |
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if (simParams->getUseRestraints()){ |
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statsMask_.set(RESTRAINT_POTENTIAL); |
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} |
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|
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if (simParams->havePrintPressureTensor() && |
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simParams->getPrintPressureTensor()){ |
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statsMask_.set(PRESSURE_TENSOR); |
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} |
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|
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// Why do we have both of these? |
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if (simParams->getAccumulateBoxDipole()) { |
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statsMask_.set(SYSTEM_DIPOLE); |
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} |
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if (info_->getCalcBoxDipole()){ |
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statsMask_.set(SYSTEM_DIPOLE); |
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} |
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|
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if (simParams->havePrintHeatFlux()) { |
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if (simParams->getPrintHeatFlux()){ |
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statsMask_.set(HEATFLUX); |
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} |
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} |
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|
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|
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if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) { |
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if (simParams->getPrintTaggedPairDistance()) { |
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statsMask_.set(TAGGED_PAIR_DISTANCE); |
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} |
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} |
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|
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} |
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|
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void Stats::parseStatFileFormat(const std::string& format) { |
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StringTokenizer tokenizer(format, " ,;|\t\n\r"); |
| 363 |
|
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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 |
} |
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} |
| 379 |
} |
| 380 |
|
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|
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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) { |
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assert(index >=0 && index < ENDINDEX); |
| 389 |
return data_[index].units; |
| 390 |
} |
| 391 |
|
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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 |
} |
