LennardJones612Implementation.cpp

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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").
//
// You can obtain a copy of the license at
// http://www.opensource.org/licenses/CDDL-1.0.  See the License for the
// specific language governing permissions and limitations under the License.
//
// When distributing Covered Code, include this CDDL HEADER in each file and
// include the License file in a prominent location with the name LICENSE.CDDL.
// If applicable, add the following below this CDDL HEADER, with the fields
// enclosed by brackets "[]" replaced with your own identifying information:
//
// Portions Copyright (c) [yyyy] [name of copyright owner]. All rights reserved.
//
// CDDL HEADER END
//

//
// Copyright (c) 2013--2015, Regents of the University of Minnesota.
// All rights reserved.
//
// Contributors:
//    Ryan S. Elliott
//    Stephen M. Whalen
//    Andrew Akerson
//


#include <cmath>
#include <cstdlib>
#include <cstring>
#include <fstream>
#include <iostream>
#include <map>
#include <sstream>

#include "KIM_ModelDriverHeaders.hpp"
#include "LennardJones612Implementation.hpp"

#define MAXLINE 1024
#define IGNORE_RESULT(fn) \
  if (fn) {}


//==============================================================================
//
// Implementation of LennardJones612Implementation public member functions
//
//==============================================================================

//******************************************************************************
#undef KIM_LOGGER_OBJECT_NAME
#define KIM_LOGGER_OBJECT_NAME modelDriverCreate
//
LennardJones612Implementation::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) :
    numberModelSpecies_(0),
    numberUniqueSpeciesPairs_(0),
    shift_(0),
    cutoffs_(NULL),
    epsilons_(NULL),
    sigmas_(NULL),
    influenceDistance_(0.0),
    cutoffsSq2D_(NULL),
    modelWillNotRequestNeighborsOfNoncontributingParticles_(1),
    fourEpsilonSigma6_2D_(NULL),
    fourEpsilonSigma12_2D_(NULL),
    twentyFourEpsilonSigma6_2D_(NULL),
    fortyEightEpsilonSigma12_2D_(NULL),
    oneSixtyEightEpsilonSigma6_2D_(NULL),
    sixTwentyFourEpsilonSigma12_2D_(NULL),
    shifts2D_(NULL),
    cachedNumberOfParticles_(0)
{
  FILE * parameterFilePointers[MAX_PARAMETER_FILES];
  int numberParameterFiles;
  modelDriverCreate->GetNumberOfParameterFiles(&numberParameterFiles);
  *ier = OpenParameterFiles(
      modelDriverCreate, numberParameterFiles, parameterFilePointers);
  if (*ier) return;

  *ier = ProcessParameterFiles(
      modelDriverCreate, numberParameterFiles, parameterFilePointers);
  CloseParameterFiles(numberParameterFiles, parameterFilePointers);
  if (*ier) return;

  *ier = ConvertUnits(modelDriverCreate,
                      requestedLengthUnit,
                      requestedEnergyUnit,
                      requestedChargeUnit,
                      requestedTemperatureUnit,
                      requestedTimeUnit);
  if (*ier) return;

  *ier = SetRefreshMutableValues(modelDriverCreate);
  if (*ier) return;

  *ier = RegisterKIMModelSettings(modelDriverCreate);
  if (*ier) return;

  *ier = RegisterKIMParameters(modelDriverCreate);
  if (*ier) return;

  *ier = RegisterKIMFunctions(modelDriverCreate);
  if (*ier) return;

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

//******************************************************************************
LennardJones612Implementation::~LennardJones612Implementation()
{  // note: it is ok to delete a null pointer and we have ensured that
  // everything is initialized to null

  delete[] cutoffs_;
  Deallocate2DArray(cutoffsSq2D_);
  delete[] epsilons_;
  delete[] sigmas_;
  Deallocate2DArray(fourEpsilonSigma6_2D_);
  Deallocate2DArray(fourEpsilonSigma12_2D_);
  Deallocate2DArray(twentyFourEpsilonSigma6_2D_);
  Deallocate2DArray(fortyEightEpsilonSigma12_2D_);
  Deallocate2DArray(oneSixtyEightEpsilonSigma6_2D_);
  Deallocate2DArray(sixTwentyFourEpsilonSigma12_2D_);
  Deallocate2DArray(shifts2D_);
}

//******************************************************************************
#undef KIM_LOGGER_OBJECT_NAME
#define KIM_LOGGER_OBJECT_NAME modelRefresh
//
int LennardJones612Implementation::Refresh(
    KIM::ModelRefresh * const modelRefresh)
{
  int ier;

  ier = SetRefreshMutableValues(modelRefresh);
  if (ier) return ier;

  // nothing else to do for this case

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

//******************************************************************************
int LennardJones612Implementation::Compute(
    KIM::ModelCompute const * const modelCompute,
    KIM::ModelComputeArguments const * const modelComputeArguments)
{
  int ier;

  // KIM API Model Input compute flags
  bool isComputeProcess_dEdr = false;
  bool isComputeProcess_d2Edr2 = false;
  //
  // KIM API Model Output compute flags
  bool isComputeEnergy = false;
  bool isComputeForces = false;
  bool isComputeParticleEnergy = false;
  bool isComputeVirial = false;
  bool isComputeParticleVirial = false;
  //
  // KIM API Model Input
  int const * particleSpeciesCodes = NULL;
  int const * particleContributing = NULL;
  VectorOfSizeDIM const * coordinates = NULL;
  //
  // KIM API Model Output
  double * energy = NULL;
  double * particleEnergy = NULL;
  VectorOfSizeDIM * forces = NULL;
  VectorOfSizeSix * virial = NULL;
  VectorOfSizeSix * particleVirial = NULL;
  ier = SetComputeMutableValues(modelComputeArguments,
                                isComputeProcess_dEdr,
                                isComputeProcess_d2Edr2,
                                isComputeEnergy,
                                isComputeForces,
                                isComputeParticleEnergy,
                                isComputeVirial,
                                isComputeParticleVirial,
                                particleSpeciesCodes,
                                particleContributing,
                                coordinates,
                                energy,
                                particleEnergy,
                                forces,
                                virial,
                                particleVirial);
  if (ier) return ier;

  // Skip this check for efficiency
  //
  // ier = CheckParticleSpecies(modelComputeArguments, particleSpeciesCodes);
  // if (ier) return ier;

  bool const isShift = (1 == shift_);

#include "LennardJones612ImplementationComputeDispatch.cpp"
  return ier;
}

//******************************************************************************
int LennardJones612Implementation::ComputeArgumentsCreate(
    KIM::ModelComputeArgumentsCreate * const modelComputeArgumentsCreate) const
{
  int ier;

  ier = RegisterKIMComputeArgumentsSettings(modelComputeArgumentsCreate);
  if (ier) return ier;

  // nothing else to do for this case

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

//******************************************************************************
int LennardJones612Implementation::ComputeArgumentsDestroy(
    KIM::ModelComputeArgumentsDestroy * const modelComputeArgumentsDestroy)
    const
{
  int ier;

  (void) modelComputeArgumentsDestroy;  // avoid unused parameter warning

  // nothing else to do for this case

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

//==============================================================================
//
// Implementation of LennardJones612Implementation private member functions
//
//==============================================================================

//******************************************************************************
void LennardJones612Implementation::AllocatePrivateParameterMemory()
{
  // nothing to do for this case
}

//******************************************************************************
void LennardJones612Implementation::AllocateParameterMemory()
{  // allocate memory for data
  cutoffs_ = new double[numberUniqueSpeciesPairs_];
  AllocateAndInitialize2DArray(
      cutoffsSq2D_, numberModelSpecies_, numberModelSpecies_);

  epsilons_ = new double[numberUniqueSpeciesPairs_];
  sigmas_ = new double[numberUniqueSpeciesPairs_];
  AllocateAndInitialize2DArray(
      fourEpsilonSigma6_2D_, numberModelSpecies_, numberModelSpecies_);
  AllocateAndInitialize2DArray(
      fourEpsilonSigma12_2D_, numberModelSpecies_, numberModelSpecies_);
  AllocateAndInitialize2DArray(
      twentyFourEpsilonSigma6_2D_, numberModelSpecies_, numberModelSpecies_);
  AllocateAndInitialize2DArray(
      fortyEightEpsilonSigma12_2D_, numberModelSpecies_, numberModelSpecies_);
  AllocateAndInitialize2DArray(
      oneSixtyEightEpsilonSigma6_2D_, numberModelSpecies_, numberModelSpecies_);
  AllocateAndInitialize2DArray(sixTwentyFourEpsilonSigma12_2D_,
                               numberModelSpecies_,
                               numberModelSpecies_);

  AllocateAndInitialize2DArray(
      shifts2D_, numberModelSpecies_, numberModelSpecies_);
}

//******************************************************************************
#undef KIM_LOGGER_OBJECT_NAME
#define KIM_LOGGER_OBJECT_NAME modelDriverCreate
//
int LennardJones612Implementation::OpenParameterFiles(
    KIM::ModelDriverCreate * const modelDriverCreate,
    int const numberParameterFiles,
    FILE * parameterFilePointers[MAX_PARAMETER_FILES])
{
  int ier;

  if (numberParameterFiles > MAX_PARAMETER_FILES)
  {
    ier = true;
    LOG_ERROR("LennardJones612 given too many parameter files");
    return ier;
  }

  for (int i = 0; i < numberParameterFiles; ++i)
  {
    std::string const * paramFileName;
    ier = modelDriverCreate->GetParameterFileName(i, &paramFileName);
    if (ier)
    {
      LOG_ERROR("Unable to get parameter file name");
      return ier;
    }
    parameterFilePointers[i] = fopen(paramFileName->c_str(), "r");
    if (parameterFilePointers[i] == 0)
    {
      char message[MAXLINE];
      sprintf(message,
              "LennardJones612 parameter file number %d cannot be opened",
              i);
      ier = true;
      LOG_ERROR(message);
      for (int j = i - 1; i <= 0; --i) { fclose(parameterFilePointers[j]); }
      return ier;
    }
  }

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

//******************************************************************************
#undef KIM_LOGGER_OBJECT_NAME
#define KIM_LOGGER_OBJECT_NAME modelDriverCreate
//
int LennardJones612Implementation::ProcessParameterFiles(
    KIM::ModelDriverCreate * const modelDriverCreate,
    int const numberParameterFiles,
    FILE * const parameterFilePointers[MAX_PARAMETER_FILES])
{
  int N, ier;
  int endOfFileFlag = 0;
  char spec1[MAXLINE], spec2[MAXLINE], nextLine[MAXLINE];
  char * nextLinePtr;
  int iIndex, jIndex, indx, iiIndex, jjIndex;
  double nextCutoff, nextEpsilon, nextSigma;

  (void) numberParameterFiles;  // avoid unused parameter warning

  nextLinePtr = nextLine;

  getNextDataLine(
      parameterFilePointers[0], nextLinePtr, MAXLINE, &endOfFileFlag);
  ier = sscanf(nextLine, "%d %d", &N, &shift_);
  if (ier != 2)
  {
    sprintf(nextLine, "unable to read first line of the parameter file");
    ier = true;
    LOG_ERROR(nextLine);
    fclose(parameterFilePointers[0]);
    return ier;
  }
  numberModelSpecies_ = N;
  numberUniqueSpeciesPairs_
      = ((numberModelSpecies_ + 1) * numberModelSpecies_) / 2;
  AllocateParameterMemory();

  // set all values in the arrays to -1 for mixing later
  for (int i = 0; i < ((N + 1) * N / 2); i++)
  {
    cutoffs_[i] = -1;
    epsilons_[i] = -1;
    sigmas_[i] = -1;
  }


  // keep track of known species
  std::map<KIM::SpeciesName const, int, KIM::SPECIES_NAME::Comparator>
      modelSpeciesMap;
  std::vector<KIM::SpeciesName> speciesNameVector;
  int index = 0;

  // Read and process data lines
  getNextDataLine(
      parameterFilePointers[0], nextLinePtr, MAXLINE, &endOfFileFlag);
  while (endOfFileFlag == 0)
  {
    ier = sscanf(nextLine,
                 "%s  %s %lg %lg %lg",
                 spec1,
                 spec2,
                 &nextCutoff,
                 &nextEpsilon,
                 &nextSigma);
    if (ier != 5)
    {
      sprintf(nextLine, "error reading lines of the parameter file");
      LOG_ERROR(nextLine);
      return true;
    }

    // convert species strings to proper type instances
    KIM::SpeciesName const specName1(spec1);
    KIM::SpeciesName const specName2(spec2);

    // check for new species
    std::map<KIM::SpeciesName const, int, KIM::SPECIES_NAME::Comparator>::
        const_iterator iIter
        = modelSpeciesMap.find(specName1);
    if (iIter == modelSpeciesMap.end())
    {
      modelSpeciesMap[specName1] = index;
      modelSpeciesCodeList_.push_back(index);
      speciesNameVector.push_back(specName1);

      ier = modelDriverCreate->SetSpeciesCode(specName1, index);
      if (ier) return ier;
      iIndex = index;
      index++;
    }
    else
    {
      iIndex = modelSpeciesMap[specName1];
    }
    std::map<KIM::SpeciesName const, int, KIM::SPECIES_NAME::Comparator>::
        const_iterator jIter
        = modelSpeciesMap.find(specName2);
    if (jIter == modelSpeciesMap.end())
    {
      modelSpeciesMap[specName2] = index;
      modelSpeciesCodeList_.push_back(index);
      speciesNameVector.push_back(specName2);

      ier = modelDriverCreate->SetSpeciesCode(specName2, index);
      if (ier) return ier;
      jIndex = index;
      index++;
    }
    else
    {
      jIndex = modelSpeciesMap[specName2];
    }

    if (iIndex >= jIndex)
    { indx = jIndex * N + iIndex - (jIndex * jIndex + jIndex) / 2; }
    else
    {
      indx = iIndex * N + jIndex - (iIndex * iIndex + iIndex) / 2;
    }
    cutoffs_[indx] = nextCutoff;
    epsilons_[indx] = nextEpsilon;
    sigmas_[indx] = nextSigma;

    getNextDataLine(
        parameterFilePointers[0], nextLinePtr, MAXLINE, &endOfFileFlag);
  }

  // check that we got all like - like pairs
  sprintf(nextLine, "There are not values for like-like pairs of:");
  for (int i = 0; i < N; i++)
  {
    if (cutoffs_[(i * N + i - (i * i + i) / 2)] == -1)
    {
      strcat(nextLine, "  ");
      strcat(nextLine, (speciesNameVector[i].ToString()).c_str());
      ier = -1;
    }
  }
  if (ier == -1)
  {
    LOG_ERROR(nextLine);
    return true;
  }

  // Perform Mixing if nessisary
  for (int jIndex = 0; jIndex < N; jIndex++)
  {
    jjIndex = (jIndex * N + jIndex - (jIndex * jIndex + jIndex) / 2);
    for (int iIndex = (jIndex + 1); iIndex < N; iIndex++)
    {
      indx = jIndex * N + iIndex - (jIndex * jIndex + jIndex) / 2;
      if (cutoffs_[indx] == -1)
      {
        iiIndex = (iIndex * N + iIndex - (iIndex * iIndex + iIndex) / 2);
        epsilons_[indx] = sqrt(epsilons_[iiIndex] * epsilons_[jjIndex]);
        sigmas_[indx] = (sigmas_[iiIndex] + sigmas_[jjIndex]) / 2.0;
        cutoffs_[indx] = (cutoffs_[iiIndex] + cutoffs_[jjIndex]) / 2.0;
      }
    }
  }

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

//******************************************************************************
void LennardJones612Implementation::getNextDataLine(FILE * const filePtr,
                                                    char * nextLinePtr,
                                                    int const maxSize,
                                                    int * endOfFileFlag)
{
  do
  {
    if (fgets(nextLinePtr, maxSize, filePtr) == NULL)
    {
      *endOfFileFlag = 1;
      break;
    }
    while ((nextLinePtr[0] == ' ' || nextLinePtr[0] == '\t')
           || (nextLinePtr[0] == '\n' || nextLinePtr[0] == '\r'))
    { nextLinePtr = (nextLinePtr + 1); }
  } while ((strncmp("#", nextLinePtr, 1) == 0) || (strlen(nextLinePtr) == 0));
}

//******************************************************************************
void LennardJones612Implementation::CloseParameterFiles(
    int const numberParameterFiles,
    FILE * const parameterFilePointers[MAX_PARAMETER_FILES])
{
  for (int i = 0; i < numberParameterFiles; ++i)
    fclose(parameterFilePointers[i]);
}

//******************************************************************************
#undef KIM_LOGGER_OBJECT_NAME
#define KIM_LOGGER_OBJECT_NAME modelDriverCreate
//
int LennardJones612Implementation::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 ier;

  // define default base units
  KIM::LengthUnit fromLength = KIM::LENGTH_UNIT::A;
  KIM::EnergyUnit fromEnergy = KIM::ENERGY_UNIT::eV;
  KIM::ChargeUnit fromCharge = KIM::CHARGE_UNIT::e;
  KIM::TemperatureUnit fromTemperature = KIM::TEMPERATURE_UNIT::K;
  KIM::TimeUnit fromTime = KIM::TIME_UNIT::ps;

  // changing units of cutoffs and sigmas
  double convertLength = 1.0;
  ier = KIM::ModelDriverCreate::ConvertUnit(fromLength,
                                            fromEnergy,
                                            fromCharge,
                                            fromTemperature,
                                            fromTime,
                                            requestedLengthUnit,
                                            requestedEnergyUnit,
                                            requestedChargeUnit,
                                            requestedTemperatureUnit,
                                            requestedTimeUnit,
                                            1.0,
                                            0.0,
                                            0.0,
                                            0.0,
                                            0.0,
                                            &convertLength);
  if (ier)
  {
    LOG_ERROR("Unable to convert length unit");
    return ier;
  }
  if (convertLength != ONE)
  {
    for (int i = 0; i < numberUniqueSpeciesPairs_; ++i)
    {
      cutoffs_[i] *= convertLength;  // convert to active units
      sigmas_[i] *= convertLength;  // convert to active units
    }
  }
  // changing units of epsilons
  double convertEnergy = 1.0;
  ier = KIM::ModelDriverCreate::ConvertUnit(fromLength,
                                            fromEnergy,
                                            fromCharge,
                                            fromTemperature,
                                            fromTime,
                                            requestedLengthUnit,
                                            requestedEnergyUnit,
                                            requestedChargeUnit,
                                            requestedTemperatureUnit,
                                            requestedTimeUnit,
                                            0.0,
                                            1.0,
                                            0.0,
                                            0.0,
                                            0.0,
                                            &convertEnergy);
  if (ier)
  {
    LOG_ERROR("Unable to convert energy unit");
    return ier;
  }
  if (convertEnergy != ONE)
  {
    for (int i = 0; i < numberUniqueSpeciesPairs_; ++i)
    {
      epsilons_[i] *= convertEnergy;  // convert to active units
    }
  }

  // register units
  ier = modelDriverCreate->SetUnits(requestedLengthUnit,
                                    requestedEnergyUnit,
                                    KIM::CHARGE_UNIT::unused,
                                    KIM::TEMPERATURE_UNIT::unused,
                                    KIM::TIME_UNIT::unused);
  if (ier)
  {
    LOG_ERROR("Unable to set units to requested values");
    return ier;
  }

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

//******************************************************************************
int LennardJones612Implementation::RegisterKIMModelSettings(
    KIM::ModelDriverCreate * const modelDriverCreate) const
{
  // register numbering
  int error = modelDriverCreate->SetModelNumbering(KIM::NUMBERING::zeroBased);

  return error;
}

//******************************************************************************
#undef KIM_LOGGER_OBJECT_NAME
#define KIM_LOGGER_OBJECT_NAME modelComputeArgumentsCreate
//
int LennardJones612Implementation::RegisterKIMComputeArgumentsSettings(
    KIM::ModelComputeArgumentsCreate * const modelComputeArgumentsCreate) const
{
  // register arguments
  LOG_INFORMATION("Register argument supportStatus");
  int error = modelComputeArgumentsCreate->SetArgumentSupportStatus(
                  KIM::COMPUTE_ARGUMENT_NAME::partialEnergy,
                  KIM::SUPPORT_STATUS::optional)
              || modelComputeArgumentsCreate->SetArgumentSupportStatus(
                  KIM::COMPUTE_ARGUMENT_NAME::partialForces,
                  KIM::SUPPORT_STATUS::optional)
              || modelComputeArgumentsCreate->SetArgumentSupportStatus(
                  KIM::COMPUTE_ARGUMENT_NAME::partialParticleEnergy,
                  KIM::SUPPORT_STATUS::optional)
              || modelComputeArgumentsCreate->SetArgumentSupportStatus(
                  KIM::COMPUTE_ARGUMENT_NAME::partialVirial,
                  KIM::SUPPORT_STATUS::optional)
              || modelComputeArgumentsCreate->SetArgumentSupportStatus(
                  KIM::COMPUTE_ARGUMENT_NAME::partialParticleVirial,
                  KIM::SUPPORT_STATUS::optional);


  // register callbacks
  LOG_INFORMATION("Register callback supportStatus");
  error = error
          || modelComputeArgumentsCreate->SetCallbackSupportStatus(
              KIM::COMPUTE_CALLBACK_NAME::ProcessDEDrTerm,
              KIM::SUPPORT_STATUS::optional)
          || modelComputeArgumentsCreate->SetCallbackSupportStatus(
              KIM::COMPUTE_CALLBACK_NAME::ProcessD2EDr2Term,
              KIM::SUPPORT_STATUS::optional);

  return error;
}

//******************************************************************************
// helper macro
#define SNUM(x) \
  static_cast<std::ostringstream &>(std::ostringstream() << std::dec << x).str()
//******************************************************************************
#undef KIM_LOGGER_OBJECT_NAME
#define KIM_LOGGER_OBJECT_NAME modelDriverCreate
//
int LennardJones612Implementation::RegisterKIMParameters(
    KIM::ModelDriverCreate * const modelDriverCreate)
{
  int ier = false;

  // publish parameters (order is important)
  ier = modelDriverCreate->SetParameterPointer(
      1,
      &shift_,
      "shift",
      "If (shift == 1), all LJ potentials are shifted to zero energy "
      "at their respective cutoff distance.  Otherwise, no shifting is "
      "performed.");
  if (ier)
  {
    LOG_ERROR("set_parameter shift");
    return ier;
  }

  ier = modelDriverCreate->SetParameterPointer(
      numberUniqueSpeciesPairs_,
      cutoffs_,
      "cutoffs",
      "Lower-triangular matrix (of size N=" + SNUM(numberModelSpecies_)
          + ") "
            "in row-major storage.  Ordering is according to SpeciesCode "
            "values.  "
            "For example, to find the parameter related to SpeciesCode 'i' and "
            "SpeciesCode 'j' (i >= j), use (zero-based) "
            "index = (j*N + i - (j*j + j)/2).");
  if (ier)
  {
    LOG_ERROR("set_parameter cutoffs");
    return ier;
  }
  ier = modelDriverCreate->SetParameterPointer(
      numberUniqueSpeciesPairs_,
      epsilons_,
      "epsilons",
      "Lower-triangular matrix (of size N=" + SNUM(numberModelSpecies_)
          + ") "
            "in row-major storage.  Ordering is according to SpeciesCode "
            "values.  "
            "For example, to find the parameter related to SpeciesCode 'i' and "
            "SpeciesCode 'j' (i >= j), use (zero-based) "
            "index = (j*N + i - (j*j + j)/2).");
  if (ier)
  {
    LOG_ERROR("set_parameter epsilons");
    return ier;
  }
  ier = modelDriverCreate->SetParameterPointer(
      numberUniqueSpeciesPairs_,
      sigmas_,
      "sigmas",
      "Lower-triangular matrix (of size N=" + SNUM(numberModelSpecies_)
          + ") "
            "in row-major storage.  Ordering is according to SpeciesCode "
            "values.  "
            "For example, to find the parameter related to SpeciesCode 'i' and "
            "SpeciesCode 'j' (i >= j), use (zero-based) "
            "index = (j*N + i - (j*j + j)/2).");
  if (ier)
  {
    LOG_ERROR("set_parameter sigmas");
    return ier;
  }

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

//******************************************************************************
int LennardJones612Implementation::RegisterKIMFunctions(
    KIM::ModelDriverCreate * const modelDriverCreate) const
{
  int error;

  // Use function pointer definitions to verify correct prototypes
  KIM::ModelDestroyFunction * destroy = LennardJones612::Destroy;
  KIM::ModelRefreshFunction * refresh = LennardJones612::Refresh;
  KIM::ModelComputeFunction * compute = LennardJones612::Compute;
  KIM::ModelComputeArgumentsCreateFunction * CACreate
      = LennardJones612::ComputeArgumentsCreate;
  KIM::ModelComputeArgumentsDestroyFunction * CADestroy
      = LennardJones612::ComputeArgumentsDestroy;

  // register the destroy() and reinit() functions
  error = modelDriverCreate->SetRoutinePointer(
              KIM::MODEL_ROUTINE_NAME::Destroy,
              KIM::LANGUAGE_NAME::cpp,
              true,
              reinterpret_cast<KIM::Function *>(destroy))
          || modelDriverCreate->SetRoutinePointer(
              KIM::MODEL_ROUTINE_NAME::Refresh,
              KIM::LANGUAGE_NAME::cpp,
              true,
              reinterpret_cast<KIM::Function *>(refresh))
          || modelDriverCreate->SetRoutinePointer(
              KIM::MODEL_ROUTINE_NAME::Compute,
              KIM::LANGUAGE_NAME::cpp,
              true,
              reinterpret_cast<KIM::Function *>(compute))
          || modelDriverCreate->SetRoutinePointer(
              KIM::MODEL_ROUTINE_NAME::ComputeArgumentsCreate,
              KIM::LANGUAGE_NAME::cpp,
              true,
              reinterpret_cast<KIM::Function *>(CACreate))
          || modelDriverCreate->SetRoutinePointer(
              KIM::MODEL_ROUTINE_NAME::ComputeArgumentsDestroy,
              KIM::LANGUAGE_NAME::cpp,
              true,
              reinterpret_cast<KIM::Function *>(CADestroy));
  return error;
}

//******************************************************************************
template<class ModelObj>
int LennardJones612Implementation::SetRefreshMutableValues(
    ModelObj * const modelObj)
{  // use (possibly) new values of parameters to compute other quantities
  // NOTE: This function is templated because it's called with both a
  //       modelDriverCreate object during initialization and with a
  //       modelRefresh object when the Model's parameters have been altered
  int ier;

  // update cutoffsSq, epsilons, and sigmas
  for (int i = 0; i < numberModelSpecies_; ++i)
  {
    for (int j = 0; j <= i; ++j)
    {
      int const index = j * numberModelSpecies_ + i - (j * j + j) / 2;
      cutoffsSq2D_[i][j] = cutoffsSq2D_[j][i]
          = (cutoffs_[index] * cutoffs_[index]);
      fourEpsilonSigma6_2D_[i][j] = fourEpsilonSigma6_2D_[j][i]
          = 4.0 * epsilons_[index] * pow(sigmas_[index], 6.0);
      fourEpsilonSigma12_2D_[i][j] = fourEpsilonSigma12_2D_[j][i]
          = 4.0 * epsilons_[index] * pow(sigmas_[index], 12.0);
      twentyFourEpsilonSigma6_2D_[i][j] = twentyFourEpsilonSigma6_2D_[j][i]
          = 6.0 * fourEpsilonSigma6_2D_[i][j];
      fortyEightEpsilonSigma12_2D_[i][j] = fortyEightEpsilonSigma12_2D_[j][i]
          = 12.0 * fourEpsilonSigma12_2D_[i][j];
      oneSixtyEightEpsilonSigma6_2D_[i][j]
          = oneSixtyEightEpsilonSigma6_2D_[j][i]
          = 7.0 * twentyFourEpsilonSigma6_2D_[i][j];
      sixTwentyFourEpsilonSigma12_2D_[i][j]
          = sixTwentyFourEpsilonSigma12_2D_[j][i]
          = 13.0 * fortyEightEpsilonSigma12_2D_[i][j];
    }
  }

  // update cutoff value in KIM API object
  influenceDistance_ = 0.0;

  for (int i = 0; i < numberModelSpecies_; i++)
  {
    int indexI = modelSpeciesCodeList_[i];

    for (int j = 0; j < numberModelSpecies_; j++)
    {
      int indexJ = modelSpeciesCodeList_[j];

      if (influenceDistance_ < cutoffsSq2D_[indexI][indexJ])
      { influenceDistance_ = cutoffsSq2D_[indexI][indexJ]; }
    }
  }

  influenceDistance_ = sqrt(influenceDistance_);
  modelObj->SetInfluenceDistancePointer(&influenceDistance_);
  modelObj->SetNeighborListPointers(
      1,
      &influenceDistance_,
      &modelWillNotRequestNeighborsOfNoncontributingParticles_);

  // update shifts
  // compute and set shifts2D_ check if minus sign
  double const * const * const constFourEpsSig6_2D = fourEpsilonSigma6_2D_;
  double const * const * const constFourEpsSig12_2D = fourEpsilonSigma12_2D_;
  if (1 == shift_)
  {
    double phi;
    for (int iSpecies = 0; iSpecies < numberModelSpecies_; iSpecies++)
    {
      for (int jSpecies = 0; jSpecies <= iSpecies; jSpecies++)
      {
        int const index = jSpecies * numberModelSpecies_ + iSpecies
                          - (jSpecies * jSpecies + jSpecies) / 2;
        double const rij2 = cutoffs_[index] * cutoffs_[index];
        double const r2iv = 1.0 / rij2;
        double const r6iv = r2iv * r2iv * r2iv;
        LENNARD_JONES_PHI(;);
        shifts2D_[iSpecies][jSpecies] = shifts2D_[jSpecies][iSpecies] = phi;
      }
    }
  }

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

//******************************************************************************
#undef KIM_LOGGER_OBJECT_NAME
#define KIM_LOGGER_OBJECT_NAME modelComputeArguments
//
int LennardJones612Implementation::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 *& particleVirial)
{
  int ier = true;

  // get compute flags
  int compProcess_dEdr;
  int compProcess_d2Edr2;

  modelComputeArguments->IsCallbackPresent(
      KIM::COMPUTE_CALLBACK_NAME::ProcessDEDrTerm, &compProcess_dEdr);
  modelComputeArguments->IsCallbackPresent(
      KIM::COMPUTE_CALLBACK_NAME::ProcessD2EDr2Term, &compProcess_d2Edr2);

  isComputeProcess_dEdr = compProcess_dEdr;
  isComputeProcess_d2Edr2 = compProcess_d2Edr2;

  int const * numberOfParticles;
  ier = modelComputeArguments->GetArgumentPointer(
            KIM::COMPUTE_ARGUMENT_NAME::numberOfParticles, &numberOfParticles)
        || modelComputeArguments->GetArgumentPointer(
            KIM::COMPUTE_ARGUMENT_NAME::particleSpeciesCodes,
            &particleSpeciesCodes)
        || modelComputeArguments->GetArgumentPointer(
            KIM::COMPUTE_ARGUMENT_NAME::particleContributing,
            &particleContributing)
        || modelComputeArguments->GetArgumentPointer(
            KIM::COMPUTE_ARGUMENT_NAME::coordinates,
            (double const **) &coordinates)
        || modelComputeArguments->GetArgumentPointer(
            KIM::COMPUTE_ARGUMENT_NAME::partialEnergy, &energy)
        || modelComputeArguments->GetArgumentPointer(
            KIM::COMPUTE_ARGUMENT_NAME::partialParticleEnergy, &particleEnergy)
        || modelComputeArguments->GetArgumentPointer(
            KIM::COMPUTE_ARGUMENT_NAME::partialForces,
            (double const **) &forces)
        || modelComputeArguments->GetArgumentPointer(
            KIM::COMPUTE_ARGUMENT_NAME::partialVirial,
            (double const **) &virial)
        || modelComputeArguments->GetArgumentPointer(
            KIM::COMPUTE_ARGUMENT_NAME::partialParticleVirial,
            (double const **) &particleVirial);
  if (ier)
  {
    LOG_ERROR("GetArgumentPointer");
    return ier;
  }

  isComputeEnergy = (energy != NULL);
  isComputeParticleEnergy = (particleEnergy != NULL);
  isComputeForces = (forces != NULL);
  isComputeVirial = (virial != NULL);
  isComputeParticleVirial = (particleVirial != NULL);

  // update values
  cachedNumberOfParticles_ = *numberOfParticles;

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

//******************************************************************************
#undef KIM_LOGGER_OBJECT_NAME
#define KIM_LOGGER_OBJECT_NAME modelCompute
int LennardJones612Implementation::CheckParticleSpeciesCodes(
    KIM::ModelCompute const * const modelCompute,
    int const * const particleSpeciesCodes) const
{
  int ier;
  for (int i = 0; i < cachedNumberOfParticles_; ++i)
  {
    if ((particleSpeciesCodes[i] < 0)
        || (particleSpeciesCodes[i] >= numberModelSpecies_))
    {
      ier = true;
      LOG_ERROR("unsupported particle species codes detected");
      return ier;
    }
  }

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

//******************************************************************************
int LennardJones612Implementation::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
{
  // const int processdE = 2;
  const int processd2E = 2;
  const int energy = 2;
  const int force = 2;
  const int particleEnergy = 2;
  const int virial = 2;
  const int particleVirial = 2;
  const int shift = 2;


  int index = 0;

  // processdE
  index += (int(isComputeProcess_dEdr)) * processd2E * energy * force
           * particleEnergy * virial * particleVirial * shift;

  // processd2E
  index += (int(isComputeProcess_d2Edr2)) * energy * force * particleEnergy
           * virial * particleVirial * shift;

  // energy
  index += (int(isComputeEnergy)) * force * particleEnergy * virial
           * particleVirial * shift;

  // force
  index += (int(isComputeForces)) * particleEnergy * virial * particleVirial
           * shift;

  // particleEnergy
  index += (int(isComputeParticleEnergy)) * virial * particleVirial * shift;

  // virial
  index += (int(isComputeVirial)) * particleVirial * shift;

  // particleVirial
  index += (int(isComputeParticleVirial)) * shift;

  // shift
  index += (int(isShift));

  return index;
}

//******************************************************************************
void LennardJones612Implementation::ProcessVirialTerm(
    const double & dEidr,
    const double & rij,
    const double * const r_ij,
    const int & i,
    const int & j,
    VectorOfSizeSix virial) const
{
  (void) i;  // avoid unused parameter warning
  (void) j;

  double const v = dEidr / rij;

  virial[0] += v * r_ij[0] * r_ij[0];
  virial[1] += v * r_ij[1] * r_ij[1];
  virial[2] += v * r_ij[2] * r_ij[2];
  virial[3] += v * r_ij[1] * r_ij[2];
  virial[4] += v * r_ij[0] * r_ij[2];
  virial[5] += v * r_ij[0] * r_ij[1];
}

//******************************************************************************
void LennardJones612Implementation::ProcessParticleVirialTerm(
    const double & dEidr,
    const double & rij,
    const double * const r_ij,
    const int & i,
    const int & j,
    VectorOfSizeSix * const particleVirial) const
{
  double const v = dEidr / rij;
  VectorOfSizeSix vir;

  vir[0] = 0.5 * v * r_ij[0] * r_ij[0];
  vir[1] = 0.5 * v * r_ij[1] * r_ij[1];
  vir[2] = 0.5 * v * r_ij[2] * r_ij[2];
  vir[3] = 0.5 * v * r_ij[1] * r_ij[2];
  vir[4] = 0.5 * v * r_ij[0] * r_ij[2];
  vir[5] = 0.5 * v * r_ij[0] * r_ij[1];

  for (int k = 0; k < 6; ++k)
  {
    particleVirial[i][k] += vir[k];
    particleVirial[j][k] += vir[k];
  }
}

//==============================================================================
//
// Implementation of helper functions
//
//==============================================================================

//******************************************************************************
void AllocateAndInitialize2DArray(double **& arrayPtr,
                                  int const extentZero,
                                  int const extentOne)
{  // allocate memory and set pointers
  arrayPtr = new double *[extentZero];
  arrayPtr[0] = new double[extentZero * extentOne];
  for (int i = 1; i < extentZero; ++i)
  { arrayPtr[i] = arrayPtr[i - 1] + extentOne; }

  // initialize
  for (int i = 0; i < extentZero; ++i)
  {
    for (int j = 0; j < extentOne; ++j) { arrayPtr[i][j] = 0.0; }
  }
}

//******************************************************************************
void Deallocate2DArray(double **& arrayPtr)
{  // deallocate memory
  if (arrayPtr != NULL) delete[] arrayPtr[0];
  delete[] arrayPtr;

  // nullify pointer
  arrayPtr = NULL;
}