LennardJones612Implementation.hpp

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//
// CDDL HEADER START
//
// The contents of this file are subject to the terms of the Common Development
// and Distribution License Version 1.0 (the "License").
//
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//
// Copyright (c) 2015, Regents of the University of Minnesota.
// All rights reserved.
//
// Contributors:
//    Ryan S. Elliott
//    Andrew Akerson
//


#ifndef LENNARD_JONES_612_IMPLEMENTATION_HPP_
#define LENNARD_JONES_612_IMPLEMENTATION_HPP_

#include "KIM_LogMacros.hpp"
#include "KIM_ModelDriverHeaders.hpp"
#include <cmath>
#include <cstdio>
#include <vector>

#define DIMENSION 3
#define ONE 1.0
#define HALF 0.5

#define MAX_PARAMETER_FILES 1

#define PARAM_SHIFT_INDEX 0
#define PARAM_CUTOFFS_INDEX 1
#define PARAM_EPSILONS_INDEX 2
#define PARAM_SIGMAS_INDEX 3


//==============================================================================
//
// Type definitions, enumerations, and helper function prototypes
//
//==============================================================================

// type declaration for get neighbor functions
typedef int(GetNeighborFunction)(void const * const,
                                 int const,
                                 int * const,
                                 int const ** const);
// type declaration for vector of constant dimension
typedef double VectorOfSizeDIM[DIMENSION];
typedef double VectorOfSizeSix[6];

// helper routine declarations
void AllocateAndInitialize2DArray(double **& arrayPtr,
                                  int const extentZero,
                                  int const extentOne);
void Deallocate2DArray(double **& arrayPtr);

//==============================================================================
//
// Declaration of LennardJones612Implementation class
//
//==============================================================================

//******************************************************************************
class LennardJones612Implementation
{
 public:
  LennardJones612Implementation(
      KIM::ModelDriverCreate * const modelDriverCreate,
      KIM::LengthUnit const requestedLengthUnit,
      KIM::EnergyUnit const requestedEnergyUnit,
      KIM::ChargeUnit const requestedChargeUnit,
      KIM::TemperatureUnit const requestedTemperatureUnit,
      KIM::TimeUnit const requestedTimeUnit,
      int * const ier);
  ~LennardJones612Implementation();  // no explicit Destroy() needed here

  int Refresh(KIM::ModelRefresh * const modelRefresh);
  int Compute(KIM::ModelCompute const * const modelCompute,
              KIM::ModelComputeArguments const * const modelComputeArguments);
  int ComputeArgumentsCreate(KIM::ModelComputeArgumentsCreate * const
                                 modelComputeArgumentsCreate) const;
  int ComputeArgumentsDestroy(KIM::ModelComputeArgumentsDestroy * const
                                  modelComputeArgumentsDestroy) const;


 private:
  // Constant values that never change
  //   Set in constructor (via SetConstantValues)
  //
  //
  // LennardJones612Implementation: constants
  int numberModelSpecies_;
  std::vector<int> modelSpeciesCodeList_;
  int numberUniqueSpeciesPairs_;


  // Constant values that are read from the input files and never change
  //   Set in constructor (via functions listed below)
  //
  //
  // Private Model Parameters
  //   Memory allocated in AllocatePrivateParameterMemory() (from constructor)
  //   Memory deallocated in destructor
  //   Data set in ReadParameterFile routines
  // none
  //
  // KIM API: Model Parameters whose (pointer) values never change
  //   Memory allocated in AllocateParameterMemory() (from constructor)
  //   Memory deallocated in destructor
  //   Data set in ReadParameterFile routines OR by KIM Simulator
  int shift_;
  double * cutoffs_;
  double * epsilons_;
  double * sigmas_;

  // Mutable values that only change when Refresh() executes
  //   Set in Refresh (via SetRefreshMutableValues)
  //
  //
  // KIM API: Model Parameters (can be changed directly by KIM Simulator)
  // none
  //
  // LennardJones612Implementation: values (changed only by Refresh())
  double influenceDistance_;
  double ** cutoffsSq2D_;
  int modelWillNotRequestNeighborsOfNoncontributingParticles_;
  double ** fourEpsilonSigma6_2D_;
  double ** fourEpsilonSigma12_2D_;
  double ** twentyFourEpsilonSigma6_2D_;
  double ** fortyEightEpsilonSigma12_2D_;
  double ** oneSixtyEightEpsilonSigma6_2D_;
  double ** sixTwentyFourEpsilonSigma12_2D_;
  double ** shifts2D_;


  // Mutable values that can change with each call to Refresh() and Compute()
  //   Memory may be reallocated on each call
  //
  //
  // LennardJones612Implementation: values that change
  int cachedNumberOfParticles_;


  // Helper methods
  //
  //
  // Related to constructor
  void AllocatePrivateParameterMemory();
  void AllocateParameterMemory();
  static int
  OpenParameterFiles(KIM::ModelDriverCreate * const modelDriverCreate,
                     int const numberParameterFiles,
                     FILE * parameterFilePointers[MAX_PARAMETER_FILES]);
  int ProcessParameterFiles(
      KIM::ModelDriverCreate * const modelDriverCreate,
      int const numberParameterFiles,
      FILE * const parameterFilePointers[MAX_PARAMETER_FILES]);
  void getNextDataLine(FILE * const filePtr,
                       char * const nextLine,
                       int const maxSize,
                       int * endOfFileFlag);
  static void
  CloseParameterFiles(int const numberParameterFiles,
                      FILE * const parameterFilePointers[MAX_PARAMETER_FILES]);
  int ConvertUnits(KIM::ModelDriverCreate * const modelDriverCreate,
                   KIM::LengthUnit const requestedLengthUnit,
                   KIM::EnergyUnit const requestedEnergyUnit,
                   KIM::ChargeUnit const requestedChargeUnit,
                   KIM::TemperatureUnit const requestedTemperatureUnit,
                   KIM::TimeUnit const requestedTimeUnit);
  int RegisterKIMModelSettings(
      KIM::ModelDriverCreate * const modelDriverCreate) const;
  int RegisterKIMComputeArgumentsSettings(
      KIM::ModelComputeArgumentsCreate * const modelComputeArgumentsCreate)
      const;
  int RegisterKIMParameters(KIM::ModelDriverCreate * const modelDriverCreate);
  int RegisterKIMFunctions(
      KIM::ModelDriverCreate * const modelDriverCreate) const;
  //
  // Related to Refresh()
  template<class ModelObj>
  int SetRefreshMutableValues(ModelObj * const modelObj);

  //
  // Related to Compute()
  int SetComputeMutableValues(
      KIM::ModelComputeArguments const * const modelComputeArguments,
      bool & isComputeProcess_dEdr,
      bool & isComputeProcess_d2Edr2,
      bool & isComputeEnergy,
      bool & isComputeForces,
      bool & isComputeParticleEnergy,
      bool & isComputeVirial,
      bool & isComputeParticleVirial,
      int const *& particleSpeciesCodes,
      int const *& particleContributing,
      VectorOfSizeDIM const *& coordinates,
      double *& energy,
      double *& particleEnergy,
      VectorOfSizeDIM *& forces,
      VectorOfSizeSix *& virial,
      VectorOfSizeSix *& particleViral);
  int CheckParticleSpeciesCodes(KIM::ModelCompute const * const modelCompute,
                                int const * const particleSpeciesCodes) const;
  int GetComputeIndex(const bool & isComputeProcess_dEdr,
                      const bool & isComputeProcess_d2Edr2,
                      const bool & isComputeEnergy,
                      const bool & isComputeForces,
                      const bool & isComputeParticleEnergy,
                      const bool & isComputeVirial,
                      const bool & isComputeParticleVirial,
                      const bool & isShift) const;
  void ProcessVirialTerm(const double & dEidr,
                         const double & rij,
                         const double * const r_ij,
                         const int & i,
                         const int & j,
                         VectorOfSizeSix virial) const;
  void ProcessParticleVirialTerm(const double & dEidr,
                                 const double & rij,
                                 const double * const r_ij,
                                 const int & i,
                                 const int & j,
                                 VectorOfSizeSix * const particleVirial) const;

  // compute functions
  template<bool isComputeProcess_dEdr,
           bool isComputeProcess_d2Edr2,
           bool isComputeEnergy,
           bool isComputeForces,
           bool isComputeParticleEnergy,
           bool isComputeVirial,
           bool isComputeParticleVirial,
           bool isShift>
  int Compute(KIM::ModelCompute const * const modelCompute,
              KIM::ModelComputeArguments const * const modelComputeArguments,
              const int * const particleSpeciesCodes,
              const int * const particleContributing,
              const VectorOfSizeDIM * const coordinates,
              double * const energy,
              VectorOfSizeDIM * const forces,
              double * const particleEnergy,
              VectorOfSizeSix virial,
              VectorOfSizeSix * const particleVirial) const;
};

//==============================================================================
//
// Definition of LennardJones612Implementation::Compute functions
//
// NOTE: Here we rely on the compiler optimizations to prune dead code
//       after the template expansions.  This provides high efficiency
//       and easy maintenance.
//
//==============================================================================

//******************************************************************************
// MACRO to compute Lennard-Jones phi
// (used for efficiency)
//
// exshift - expression to be added to the end of the phi value
#define LENNARD_JONES_PHI(exshift)                         \
  phi = r6iv                                               \
        * (constFourEpsSig12_2D[iSpecies][jSpecies] * r6iv \
           - constFourEpsSig6_2D[iSpecies][jSpecies]) exshift;

//******************************************************************************
#undef KIM_LOGGER_OBJECT_NAME
#define KIM_LOGGER_OBJECT_NAME modelCompute
//
template<bool isComputeProcess_dEdr,
         bool isComputeProcess_d2Edr2,
         bool isComputeEnergy,
         bool isComputeForces,
         bool isComputeParticleEnergy,
         bool isComputeVirial,
         bool isComputeParticleVirial,
         bool isShift>
int LennardJones612Implementation::Compute(
    KIM::ModelCompute const * const modelCompute,
    KIM::ModelComputeArguments const * const modelComputeArguments,
    const int * const particleSpeciesCodes,
    const int * const particleContributing,
    const VectorOfSizeDIM * const coordinates,
    double * const energy,
    VectorOfSizeDIM * const forces,
    double * const particleEnergy,
    VectorOfSizeSix virial,
    VectorOfSizeSix * const particleVirial) const
{
  int ier = false;

  if ((isComputeEnergy == false) && (isComputeParticleEnergy == false)
      && (isComputeForces == false) && (isComputeProcess_dEdr == false)
      && (isComputeProcess_d2Edr2 == false) && (isComputeVirial == false)
      && (isComputeParticleVirial == false))
    return ier;

  // initialize energy and forces
  if (isComputeEnergy == true) { *energy = 0.0; }
  if (isComputeVirial == true)
  {
    for (int i = 0; i < 6; ++i) virial[i] = 0.0;
  }
  if (isComputeParticleEnergy == true)
  {
    int const cachedNumParticles = cachedNumberOfParticles_;
    for (int i = 0; i < cachedNumParticles; ++i) { particleEnergy[i] = 0.0; }
  }
  if (isComputeForces == true)
  {
    int const cachedNumParticles = cachedNumberOfParticles_;
    for (int i = 0; i < cachedNumParticles; ++i)
    {
      for (int j = 0; j < DIMENSION; ++j) forces[i][j] = 0.0;
    }
  }
  if (isComputeParticleVirial == true)
  {
    int const cachedNumParticles = cachedNumberOfParticles_;
    for (int i = 0; i < cachedNumParticles; ++i)
    {
      for (int j = 0; j < 6; ++j) particleVirial[i][j] = 0.0;
    }
  }

  // calculate contribution from pair function
  //
  // Setup loop over contributing particles
  int ii = 0;
  int numnei = 0;
  int const * n1atom = NULL;
  double const * const * const constCutoffsSq2D = cutoffsSq2D_;
  double const * const * const constFourEpsSig6_2D = fourEpsilonSigma6_2D_;
  double const * const * const constFourEpsSig12_2D = fourEpsilonSigma12_2D_;
  double const * const * const constTwentyFourEpsSig6_2D
      = twentyFourEpsilonSigma6_2D_;
  double const * const * const constFortyEightEpsSig12_2D
      = fortyEightEpsilonSigma12_2D_;
  double const * const * const constOneSixtyEightEpsSig6_2D
      = oneSixtyEightEpsilonSigma6_2D_;
  double const * const * const constSixTwentyFourEpsSig12_2D
      = sixTwentyFourEpsilonSigma12_2D_;
  double const * const * const constShifts2D = shifts2D_;
  for (ii = 0; ii < cachedNumberOfParticles_; ++ii)
  {
    if (particleContributing[ii])
    {
      modelComputeArguments->GetNeighborList(0, ii, &numnei, &n1atom);
      int const numNei = numnei;
      int const * const n1Atom = n1atom;
      int const i = ii;
      int const iSpecies = particleSpeciesCodes[i];

      // Setup loop over neighbors of current particle
      for (int jj = 0; jj < numNei; ++jj)
      {
        int const j = n1Atom[jj];
        int const jContrib = particleContributing[j];

        if (!(jContrib && (j < i)))  // effective half-list
        {
          int const jSpecies = particleSpeciesCodes[j];
          double * r_ij;
          double r_ijValue[DIMENSION];
          // Compute r_ij
          r_ij = r_ijValue;
          for (int k = 0; k < DIMENSION; ++k)
            r_ij[k] = coordinates[j][k] - coordinates[i][k];
          double const * const r_ij_const = const_cast<double *>(r_ij);

          // compute distance squared
          double const rij2 = r_ij_const[0] * r_ij_const[0]
                              + r_ij_const[1] * r_ij_const[1]
                              + r_ij_const[2] * r_ij_const[2];

          if (rij2 <= constCutoffsSq2D[iSpecies][jSpecies])
          {  // compute contribution to energy, force, etc.
            double phi = 0.0;
            double dphiByR = 0.0;
            double d2phi = 0.0;
            double dEidrByR = 0.0;
            double d2Eidr2 = 0.0;
            double const r2iv = 1.0 / rij2;
            double const r6iv = r2iv * r2iv * r2iv;
            // Compute pair potential and its derivatives
            if (isComputeProcess_d2Edr2 == true)
            {  // Compute d2phi
              d2phi
                  = r6iv
                    * (constSixTwentyFourEpsSig12_2D[iSpecies][jSpecies] * r6iv
                       - constOneSixtyEightEpsSig6_2D[iSpecies][jSpecies])
                    * r2iv;
              if (jContrib == 1) { d2Eidr2 = d2phi; }
              else
              {
                d2Eidr2 = 0.5 * d2phi;
              }
            }

            if ((isComputeProcess_dEdr == true) || (isComputeForces == true)
                || (isComputeVirial == true)
                || (isComputeParticleVirial == true))
            {  // Compute dphi
              dphiByR
                  = r6iv
                    * (constTwentyFourEpsSig6_2D[iSpecies][jSpecies]
                       - constFortyEightEpsSig12_2D[iSpecies][jSpecies] * r6iv)
                    * r2iv;
              if (jContrib == 1) { dEidrByR = dphiByR; }
              else
              {
                dEidrByR = 0.5 * dphiByR;
              }
            }

            if ((isComputeEnergy == true) || (isComputeParticleEnergy == true))
            {  // Compute phi
              if (isShift == true)
              {
                LENNARD_JONES_PHI(-constShifts2D[iSpecies][jSpecies]);
              }
              else
              {
                LENNARD_JONES_PHI(;);
              }
            }

            // Contribution to energy
            if (isComputeEnergy == true)
            {
              if (jContrib == 1) { *energy += phi; }
              else
              {
                *energy += 0.5 * phi;
              }
            }

            // Contribution to particleEnergy
            if (isComputeParticleEnergy == true)
            {
              double const halfPhi = 0.5 * phi;
              particleEnergy[i] += halfPhi;
              if (jContrib == 1) { particleEnergy[j] += halfPhi; }
            }

            // Contribution to forces
            if (isComputeForces == true)
            {
              for (int k = 0; k < DIMENSION; ++k)
              {
                double const contrib = dEidrByR * r_ij_const[k];
                forces[i][k] += contrib;
                forces[j][k] -= contrib;
              }
            }

            // Call process_dEdr
            if ((isComputeProcess_dEdr == true) || (isComputeVirial == true)
                || (isComputeParticleVirial == true))
            {
              double const rij = sqrt(rij2);
              double const dEidr = dEidrByR * rij;

              if (isComputeProcess_dEdr == true)
              {
                ier = modelComputeArguments->ProcessDEDrTerm(
                    dEidr, rij, r_ij_const, i, j);
                if (ier)
                {
                  LOG_ERROR("process_dEdr");
                  return ier;
                }
              }

              if (isComputeVirial == true)
              {
                ProcessVirialTerm(dEidr, rij, r_ij_const, i, j, virial);
              }

              if (isComputeParticleVirial == true)
              {
                ProcessParticleVirialTerm(
                    dEidr, rij, r_ij_const, i, j, particleVirial);
              }
            }

            // Call process_d2Edr2
            if (isComputeProcess_d2Edr2 == true)
            {
              double const rij = sqrt(rij2);
              double const R_pairs[2] = {rij, rij};
              double const * const pRs = &R_pairs[0];
              double const Rij_pairs[6] = {r_ij_const[0],
                                           r_ij_const[1],
                                           r_ij_const[2],
                                           r_ij_const[0],
                                           r_ij_const[1],
                                           r_ij_const[2]};
              double const * const pRijConsts = &Rij_pairs[0];
              int const i_pairs[2] = {i, i};
              int const j_pairs[2] = {j, j};
              int const * const pis = &i_pairs[0];
              int const * const pjs = &j_pairs[0];

              ier = modelComputeArguments->ProcessD2EDr2Term(
                  d2Eidr2, pRs, pRijConsts, pis, pjs);
              if (ier)
              {
                LOG_ERROR("process_d2Edr2");
                return ier;
              }
            }
          }  // if particleContributing
        }  // if i < j or j non contributing
      }  // if particles i and j interact
    }  // end of first neighbor loop
  }  // end of loop over contributing particles

  // everything is good
  ier = false;
  return ier;
}

#endif  // LENNARD_JONES_612_IMPLEMENTATION_HPP_