RNEMDParameters.cpp

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 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the following paper when you publish your work:
 *
 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
 *
 * Good starting points for code and simulation methodology are:
 *
 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
 */
 
#include "rnemd/RNEMDParameters.hpp"
 
#include <cstdlib>
#include <cstring>
#include <iostream>
 
namespace OpenMD::RNEMD {
 
  RNEMDParameters::RNEMDParameters() {
    DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
    DefineOptionalParameterWithDefaultValue(ObjectSelection, "objectSelection",
                                            "select all");
 
    DefineOptionalParameterWithDefaultValue(Method, "method", "VSS");
    DefineOptionalParameter(FluxType, "fluxType");
 
    DefineOptionalParameterWithDefaultValue(ExchangeTime, "exchangeTime",
                                            100.0);
    DefineOptionalParameter(KineticFlux, "kineticFlux");
    DefineOptionalParameter(ParticleFlux, "particleFlux");
    DefineOptionalParameter(CurrentDensity, "currentDensity");
    DefineOptionalParameter(MomentumFlux, "momentumFlux");
    DefineOptionalParameter(MomentumFluxVector, "momentumFluxVector");
    DefineOptionalParameter(AngularMomentumFlux, "angularMomentumFlux");
    DefineOptionalParameter(AngularMomentumFluxVector,
                            "angularMomentumFluxVector");
    DefineOptionalParameter(SlabWidth, "slabWidth");
    DefineOptionalParameter(SlabACenter, "slabAcenter");
    DefineOptionalParameter(SlabBCenter, "slabBcenter");
    DefineOptionalParameter(SphereARadius, "sphereAradius");
    DefineOptionalParameter(SphereBRadius, "sphereBradius");
    DefineOptionalParameter(SelectionA, "selectionA");
    DefineOptionalParameter(SelectionB, "selectionB");
    DefineOptionalParameter(CoordinateOrigin, "coordinateOrigin");
    DefineOptionalParameter(OutputFileName, "outputFileName");
    DefineOptionalParameterWithDefaultValue(OutputBins, "outputBins", 20);
    DefineOptionalParameterWithDefaultValue(OutputBinWidth, "outputBinWidth",
                                            2.0);
    DefineOptionalParameter(OutputSelection, "outputSelection");
    DefineOptionalParameter(OutputFields, "outputFields");
    DefineOptionalParameter(DividingArea, "dividingArea");
    DefineOptionalParameterWithDefaultValue(PrivilegedAxis, "privilegedAxis",
                                            "z");
    DefineOptionalParameterWithDefaultValue(SPFScalingPower, "spfScalingPower",
                                            3);
    DefineOptionalParameterWithDefaultValue(SPFUniformKineticScaling,
                                            "spfUniformKineticScaling", false);
  }
 
  void RNEMDParameters::validate() {
    CheckParameter(ExchangeTime, isPositive());
    CheckParameter(OutputBins, isPositive());
    CheckParameter(OutputBinWidth, isPositive());
    CheckParameter(Method,
                   isEqualIgnoreCase("Swap") || isEqualIgnoreCase("NIVS") ||
                       isEqualIgnoreCase("VSS") || isEqualIgnoreCase("SPF"));
    CheckParameter(
        FluxType,
        isEqualIgnoreCase("KE") || isEqualIgnoreCase("Px") ||
            isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") ||
            isEqualIgnoreCase("Lx") || isEqualIgnoreCase("Ly") ||
            isEqualIgnoreCase("Lz") || isEqualIgnoreCase("Pvector") ||
            isEqualIgnoreCase("Lvector") || isEqualIgnoreCase("KE+Px") ||
            isEqualIgnoreCase("KE+Py") || isEqualIgnoreCase("KE+Lx") ||
            isEqualIgnoreCase("KE+Ly") || isEqualIgnoreCase("KE+Lz") ||
            isEqualIgnoreCase("KE+Pvector") ||
            isEqualIgnoreCase("KE+Lvector") || isEqualIgnoreCase("Particle") ||
            isEqualIgnoreCase("Particle+KE") ||
            isEqualIgnoreCase("CurrentDensity"));
    CheckParameter(PrivilegedAxis, isEqualIgnoreCase("x") ||
                                       isEqualIgnoreCase("y") ||
                                       isEqualIgnoreCase("z"));
  }
 
  bool RNEMDParameters::requiresElectricField() {
    static bool wasParsed {false};
 
    if (!wasParsed) {
      StringTokenizer tokenizer(getOutputFields(), " ,;|\t\n\r");
 
      while (tokenizer.hasMoreTokens()) {
        std::string token(tokenizer.nextToken());
        toUpper(token);
 
        if (token == "ELECTRICFIELD" || token == "ELECTROSTATICPOTENTIAL") {
          calculateElectricField_ = true;
          break;
        }
      }
 
      wasParsed = true;
    }
 
    return calculateElectricField_;
  }
}  // namespace OpenMD::RNEMD