ex_test_Ar_fcc_cluster_cpp.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").
//
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// http://www.opensource.org/licenses/CDDL-1.0.  See the License for the
// specific language governing permissions and limitations under the License.
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// 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.
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//
//
// Copyright (c) 2013--2020, Regents of the University of Minnesota.
// All rights reserved.
//
// Contributors:
//    Ryan S. Elliott
//    Stephen M. Whalen
//
//


#include "KIM_SimulatorHeaders.hpp"
#include "KIM_SupportedExtensions.hpp"
#include <cmath>
#include <iomanip>
#include <iostream>
#include <stdio.h>
#include <stdlib.h>
#include <string>

#define NAMESTRLEN 128

#define FCCSPACING 5.260
#define DIM 3
#define NCELLSPERSIDE 2
#define NCLUSTERPARTS                                  \
  (4 * (NCELLSPERSIDE * NCELLSPERSIDE * NCELLSPERSIDE) \
   + 6 * (NCELLSPERSIDE * NCELLSPERSIDE) + 3 * (NCELLSPERSIDE) + 1)

#define MY_ERROR(message)                                                \
  {                                                                      \
    std::cout << "* Error : \"" << message << "\" : " << __LINE__ << ":" \
              << __FILE__ << std::endl;                                  \
    exit(1);                                                             \
  }

#define MY_WARNING(message)                                                \
  {                                                                        \
    std::cout << "* Warning : \"" << message << "\" : " << __LINE__ << ":" \
              << __FILE__ << std::endl;                                    \
  }


/* Define neighborlist structure */
typedef struct
{
  double cutoff;
  int numberOfParticles;
  int * NNeighbors;
  int * neighborList;
} NeighList;

/* Define prototypes */
void fcc_cluster_neighborlist(int half,
                              int numberOfParticles,
                              double * coords,
                              double cutoff,
                              NeighList * nl);

int get_cluster_neigh(void * const dataObject,
                      int const numberOfNeighborLists,
                      double const * const cutoffs,
                      int const neighborListIndex,
                      int const particleNumber,
                      int * const numberOfNeighbors,
                      int const ** const neighborsOfParticle);

void create_FCC_cluster(double FCCspacing, int nCellsPerSide, double * coords);

void compute_loop(double const MinSpacing,
                  double const MaxSpacing,
                  double const SpacingIncr,
                  int const numberOfParticles_cluster,
                  double * const coords_cluster,
                  double const cutoff,
                  NeighList * nl,
                  KIM::Model const * const kim_cluster_model,
                  KIM::ComputeArguments const * const computeArguments,
                  double * const forces_cluster,
                  double * const energy_cluster_model);


/* Main program */
int main()
{
  /* Local variable declarations */
  double const MinSpacing = 0.8 * FCCSPACING;
  double const MaxSpacing = 1.2 * FCCSPACING;
  double const SpacingIncr = 0.025 * FCCSPACING;
  int i;
  int error;


  /* model inputs */
  int numberOfParticles_cluster = NCLUSTERPARTS;
  int particleSpecies_cluster_model[NCLUSTERPARTS];
  int particleContributing_cluster_model[NCLUSTERPARTS];
  double coords_cluster[NCLUSTERPARTS][DIM];
  NeighList nl_cluster_model;
  /* model outputs */
  double influence_distance_cluster_model;
  int number_of_neighbor_lists;
  double const * cutoff_cluster_model;
  double energy_cluster_model;
  double forces_cluster[NCLUSTERPARTS * DIM];

  std::string modelname;

  /* Get KIM Model names */
  printf("Please enter valid KIM Model name: \n");
  std::cin >> modelname;


  /* initialize the model */
  KIM::Model * kim_cluster_model;
  int requestedUnitsAccepted;
  error = KIM::Model::Create(KIM::NUMBERING::zeroBased,
                             KIM::LENGTH_UNIT::A,
                             KIM::ENERGY_UNIT::eV,
                             KIM::CHARGE_UNIT::e,
                             KIM::TEMPERATURE_UNIT::K,
                             KIM::TIME_UNIT::ps,
                             modelname,
                             &requestedUnitsAccepted,
                             &kim_cluster_model);
  if (error) { MY_ERROR("KIM::Model::Create()"); }

  // Check for compatibility with the model
  if (!requestedUnitsAccepted) { MY_ERROR("Must Adapt to model units"); }

  // Check that we know about all required routines
  int numberOfModelRoutineNames;
  KIM::MODEL_ROUTINE_NAME::GetNumberOfModelRoutineNames(
      &numberOfModelRoutineNames);
  for (int i = 0; i < numberOfModelRoutineNames; ++i)
  {
    KIM::ModelRoutineName modelRoutineName;
    int error
        = KIM::MODEL_ROUTINE_NAME::GetModelRoutineName(i, &modelRoutineName);
    if (error) { MY_ERROR("Unable to get ModelRoutineName."); }
    int present;
    int required;
    error = kim_cluster_model->IsRoutinePresent(
        modelRoutineName, &present, &required);
    if (error) { MY_ERROR("Unable to get routine present/required."); }

    std::cout << "Model routine name \"" << modelRoutineName.ToString()
              << "\" has present = " << present
              << " and required = " << required << "." << std::endl;

    if ((present == true) && (required == true))
    {
      using namespace KIM::MODEL_ROUTINE_NAME;
      if (!((modelRoutineName == Create)
            || (modelRoutineName == ComputeArgumentsCreate)
            || (modelRoutineName == Compute) || (modelRoutineName == Refresh)
            || (modelRoutineName == ComputeArgumentsDestroy)
            || (modelRoutineName == Destroy)))
      {
        MY_ERROR("Unknown Routine \"" + modelRoutineName.ToString()
                 + "\" is required by model.");
      }
    }
  }

  // print model units
  KIM::LengthUnit lengthUnit;
  KIM::EnergyUnit energyUnit;
  KIM::ChargeUnit chargeUnit;
  KIM::TemperatureUnit temperatureUnit;
  KIM::TimeUnit timeUnit;

  kim_cluster_model->GetUnits(
      &lengthUnit, &energyUnit, &chargeUnit, &temperatureUnit, &timeUnit);

  std::cout << "LengthUnit is \"" << lengthUnit.ToString() << "\"" << std::endl
            << "EnergyUnit is \"" << energyUnit.ToString() << "\"" << std::endl
            << "ChargeUnit is \"" << chargeUnit.ToString() << "\"" << std::endl
            << "TemperatureUnit is \"" << temperatureUnit.ToString() << "\""
            << std::endl
            << "TimeUnit is \"" << timeUnit.ToString() << "\"" << std::endl;

  // check species
  int speciesIsSupported;
  int modelArCode;
  error = kim_cluster_model->GetSpeciesSupportAndCode(
      KIM::SPECIES_NAME::Ar, &speciesIsSupported, &modelArCode);
  if ((error) || (!speciesIsSupported))
  {
    MY_ERROR("Species Ar not supported");
  }

  KIM::ComputeArguments * computeArguments;
  error = kim_cluster_model->ComputeArgumentsCreate(&computeArguments);
  if (error) { MY_ERROR("Unable to create a ComputeArguments object."); }

  // check compute arguments
  int numberOfComputeArgumentNames;
  KIM::COMPUTE_ARGUMENT_NAME::GetNumberOfComputeArgumentNames(
      &numberOfComputeArgumentNames);
  for (int i = 0; i < numberOfComputeArgumentNames; ++i)
  {
    KIM::ComputeArgumentName computeArgumentName;
    KIM::SupportStatus supportStatus;
    KIM::COMPUTE_ARGUMENT_NAME::GetComputeArgumentName(i, &computeArgumentName);
    KIM::DataType dataType;
    KIM::COMPUTE_ARGUMENT_NAME::GetComputeArgumentDataType(computeArgumentName,
                                                           &dataType);
    error = computeArguments->GetArgumentSupportStatus(computeArgumentName,
                                                       &supportStatus);
    if (error) MY_ERROR("unable to get ComputeArgument SupportStatus");

    std::cout << "ComputeArgument Name \"" << computeArgumentName.ToString()
              << "\""
              << " is of type \"" << dataType.ToString() << "\""
              << " and has supportStatus \"" << supportStatus.ToString() << "\""
              << std::endl;

    // can only handle energy and force as a required arg
    if (supportStatus == KIM::SUPPORT_STATUS::required)
    {
      if ((computeArgumentName != KIM::COMPUTE_ARGUMENT_NAME::partialEnergy)
          && (computeArgumentName != KIM::COMPUTE_ARGUMENT_NAME::partialForces))
      {
        MY_ERROR("unsupported required ComputeArgument");
      }
    }

    // must have energy and forces
    if ((computeArgumentName == KIM::COMPUTE_ARGUMENT_NAME::partialEnergy)
        || (computeArgumentName == KIM::COMPUTE_ARGUMENT_NAME::partialForces))
    {
      if (!((supportStatus == KIM::SUPPORT_STATUS::required)
            || (supportStatus == KIM::SUPPORT_STATUS::optional)))
      {
        MY_ERROR("energy or forces not available");
      }
    }
  }

  // check compute callbacks
  int numberOfComputeCallbackNames;
  KIM::COMPUTE_CALLBACK_NAME::GetNumberOfComputeCallbackNames(
      &numberOfComputeCallbackNames);
  for (int i = 0; i < numberOfComputeCallbackNames; ++i)
  {
    KIM::ComputeCallbackName computeCallbackName;
    KIM::COMPUTE_CALLBACK_NAME::GetComputeCallbackName(i, &computeCallbackName);
    KIM::SupportStatus supportStatus;
    computeArguments->GetCallbackSupportStatus(computeCallbackName,
                                               &supportStatus);

    std::cout << "ComputeCallback Name \"" << computeCallbackName.ToString()
              << "\""
              << " has supportStatus \"" << supportStatus.ToString() << "\""
              << std::endl;

    // cannot handle any "required" callbacks
    if (supportStatus == KIM::SUPPORT_STATUS::required)
    {
      MY_ERROR("unsupported required ComputeCallback");
    }
  }

  int numberOfParameters;
  kim_cluster_model->GetNumberOfParameters(&numberOfParameters);
  for (int i = 0; i < numberOfParameters; ++i)
  {
    KIM::DataType dataType;
    std::string const * strName;
    std::string const * strDesc;
    int extent;
    kim_cluster_model->GetParameterMetadata(
        i, &dataType, &extent, &strName, &strDesc);
    std::cout << "Parameter No. " << i << " has" << std::endl
              << " data type   : \"" << dataType.ToString() << "\"" << std::endl
              << " extent      : " << extent << std::endl
              << " name        : " << *strName << std::endl
              << " description : " << *strDesc << std::endl;
  }

  // Check supported extensions, if any
  int present;
  error = kim_cluster_model->IsRoutinePresent(
      KIM::MODEL_ROUTINE_NAME::Extension, &present, NULL);
  if (error) { MY_ERROR("Unable to get Extension present/required."); }
  if (present)
  {
    KIM::SupportedExtensions supportedExtensions;
    error = kim_cluster_model->Extension(KIM_SUPPORTED_EXTENSIONS_ID,
                                         &supportedExtensions);
    if (error) { MY_ERROR("Error returned from KIM::Model::Extension()."); }
    std::cout << "Model Supports "
              << supportedExtensions.numberOfSupportedExtensions
              << " Extensions:" << std::endl;
    for (int i = 0; i < supportedExtensions.numberOfSupportedExtensions; ++i)
    {
      std::cout << " spportedExtensionID[" << std::setw(2) << i << "] = \""
                << supportedExtensions.supportedExtensionID[i] << "\" "
                << "which has required = "
                << supportedExtensions.supportedExtensionRequired[i] << "."
                << std::endl;
    }
  }

  // We're compatible with the model. Let's do it.

  error
      = computeArguments->SetArgumentPointer(
            KIM::COMPUTE_ARGUMENT_NAME::numberOfParticles,
            (int *) &numberOfParticles_cluster)
        || computeArguments->SetArgumentPointer(
            KIM::COMPUTE_ARGUMENT_NAME::particleSpeciesCodes,
            particleSpecies_cluster_model)
        || computeArguments->SetArgumentPointer(
            KIM::COMPUTE_ARGUMENT_NAME::particleContributing,
            particleContributing_cluster_model)
        || computeArguments->SetArgumentPointer(
            KIM::COMPUTE_ARGUMENT_NAME::coordinates, (double *) coords_cluster)
        || computeArguments->SetArgumentPointer(
            KIM::COMPUTE_ARGUMENT_NAME::partialEnergy, &energy_cluster_model)
        || computeArguments->SetArgumentPointer(
            KIM::COMPUTE_ARGUMENT_NAME::partialForces,
            (double *) forces_cluster);
  if (error) MY_ERROR("KIM_API_set_data");
  error = computeArguments->SetCallbackPointer(
      KIM::COMPUTE_CALLBACK_NAME::GetNeighborList,
      KIM::LANGUAGE_NAME::cpp,
      (KIM::Function *) &get_cluster_neigh,
      &nl_cluster_model);
  if (error) MY_ERROR("set_call_back");

  kim_cluster_model->GetInfluenceDistance(&influence_distance_cluster_model);
  int const * modelWillNotRequestNeighborsOfNoncontributingParticles;
  kim_cluster_model->GetNeighborListPointers(
      &number_of_neighbor_lists,
      &cutoff_cluster_model,
      &modelWillNotRequestNeighborsOfNoncontributingParticles);
  std::cout << "Model has influence distance of : "
            << influence_distance_cluster_model << std::endl;
  std::cout << "Model has numberOfNeighborLists : " << number_of_neighbor_lists
            << std::endl;
  for (int i = 0; i < number_of_neighbor_lists; ++i)
  {
    std::cout << "\t"
              << "Neighbor list " << i << " has cutoff "
              << cutoff_cluster_model[i]
              << " with "
                 "modelWillNotRequestNeighborsOfNoncontributingParticles "
              << modelWillNotRequestNeighborsOfNoncontributingParticles[i]
              << std::endl;
  }
  // ignoring hints from here on...
  if (number_of_neighbor_lists != 1) MY_ERROR("too many neighbor lists");

  /* setup particleSpecies */
  int isSpeciesSupported;
  error = kim_cluster_model->GetSpeciesSupportAndCode(
      KIM::SPECIES_NAME::Ar,
      &isSpeciesSupported,
      &(particleSpecies_cluster_model[0]));
  if (error) MY_ERROR("get_species_code");
  for (i = 1; i < NCLUSTERPARTS; ++i)
    particleSpecies_cluster_model[i] = particleSpecies_cluster_model[0];
  /* setup particleContributing */
  for (i = 0; i < NCLUSTERPARTS; ++i)
    particleContributing_cluster_model[i] = 1; /* every particle contributes */

  /* setup neighbor lists */
  /* allocate memory for list */
  nl_cluster_model.numberOfParticles = NCLUSTERPARTS;
  nl_cluster_model.NNeighbors = new int[NCLUSTERPARTS];
  if (NULL == nl_cluster_model.NNeighbors) MY_ERROR("new unsuccessful");

  nl_cluster_model.neighborList = new int[NCLUSTERPARTS * NCLUSTERPARTS];
  if (NULL == nl_cluster_model.neighborList) MY_ERROR("new unsuccessful");

  /* ready to compute */
  std::ios oldState(NULL);
  oldState.copyfmt(std::cout);
  std::cout << std::setiosflags(std::ios::scientific) << std::setprecision(10);
  std::cout << "This is Test : ex_test_Ar_fcc_cluster_cpp\n";
  std::cout << "---------------------------------------------------------------"
               "-----------------\n";
  std::cout << "Results for KIM Model : " << modelname << std::endl;

  compute_loop(MinSpacing,
               MaxSpacing,
               SpacingIncr,
               numberOfParticles_cluster,
               &(coords_cluster[0][0]),
               *cutoff_cluster_model,
               &nl_cluster_model,
               kim_cluster_model,
               computeArguments,
               forces_cluster,
               &energy_cluster_model);

  if (numberOfParameters > 0)
  {
    int index = numberOfParameters / 2;
    KIM::DataType dataType;
    std::string const * name;
    double value;
    error = kim_cluster_model->GetParameterMetadata(
        index, &dataType, NULL, &name, NULL);
    if (error) { MY_ERROR("Cannot get parameter metadata."); }
    if (dataType != KIM::DATA_TYPE::Double)
    {
      MY_WARNING("Can't change an integer.");
    }
    else
    {
      error = kim_cluster_model->GetParameter(index, 0, &value);
      if (error) { MY_ERROR("Cannot get parameter value."); }
      value *= 1.5;
      error = kim_cluster_model->SetParameter(index, 0, value);
      if (error) { MY_ERROR("Cannot set parameter value."); }
      error = kim_cluster_model->ClearThenRefresh();
      if (error) { MY_ERROR("Model ClearThenRefresh returned error."); }

      std::cout << std::endl
                << "Updated parameter \"" << *name << "\" to value " << value
                << "." << std::endl;

      kim_cluster_model->GetInfluenceDistance(
          &influence_distance_cluster_model);
      kim_cluster_model->GetNeighborListPointers(
          &number_of_neighbor_lists,
          &cutoff_cluster_model,
          &modelWillNotRequestNeighborsOfNoncontributingParticles);

      compute_loop(MinSpacing,
                   MaxSpacing,
                   SpacingIncr,
                   numberOfParticles_cluster,
                   &(coords_cluster[0][0]),
                   *cutoff_cluster_model,
                   &nl_cluster_model,
                   kim_cluster_model,
                   computeArguments,
                   forces_cluster,
                   &energy_cluster_model);
    }

    int present;
    kim_cluster_model->IsRoutinePresent(
        KIM::MODEL_ROUTINE_NAME::WriteParameterizedModel, &present, NULL);
    if (present == true)
    {
      error = kim_cluster_model->WriteParameterizedModel(
          ".", "This_IsTheNewModelName");
      if (error) { MY_ERROR("WriteParameterizedModel returned an error."); }
    }
  }

  /* call compute arguments destroy */
  error = kim_cluster_model->ComputeArgumentsDestroy(&computeArguments);
  if (error) { MY_ERROR("Unable to destroy compute arguments"); }

  /* call model destroy */
  KIM::Model::Destroy(&kim_cluster_model);

  /* free memory of neighbor lists */
  delete[] nl_cluster_model.NNeighbors;
  delete[] nl_cluster_model.neighborList;

  /* everything is great */
  std::cout.copyfmt(oldState);
  return 0;
}

void compute_loop(double const MinSpacing,
                  double const MaxSpacing,
                  double const SpacingIncr,
                  int const numberOfParticles_cluster,
                  double * const coords_cluster,
                  double const cutoff,
                  NeighList * nl,
                  KIM::Model const * const kim_cluster_model,
                  KIM::ComputeArguments const * const computeArguments,
                  double * const forces_cluster,
                  double * const energy_cluster_model)
{
  double const cutpad = 0.75; /* Angstroms */

  std::cout << std::setw(20) << "Energy" << std::setw(20) << "Force Norm"
            << std::setw(20) << "Lattice Spacing" << std::endl;
  for (double CurrentSpacing = MinSpacing; CurrentSpacing < MaxSpacing;
       CurrentSpacing += SpacingIncr)
  {
    /* update coordinates for cluster */
    create_FCC_cluster(CurrentSpacing, NCELLSPERSIDE, coords_cluster);
    /* compute neighbor lists */
    fcc_cluster_neighborlist(
        0, NCLUSTERPARTS, coords_cluster, (cutoff + cutpad), nl);

    /* call compute functions */
    int error = kim_cluster_model->Compute(computeArguments);
    if (error) MY_ERROR("compute");

    /* compute force norm */
    double force_norm = 0.0;
    for (int i = 0; i < DIM * numberOfParticles_cluster; ++i)
    {
      force_norm += forces_cluster[i] * forces_cluster[i];
    }
    force_norm = sqrt(force_norm);

    /* print the results */
    std::cout << std::setw(20) << *energy_cluster_model << std::setw(20)
              << force_norm << std::setw(20) << CurrentSpacing << std::endl;
  }
}

void create_FCC_cluster(double FCCspacing, int nCellsPerSide, double * coords)
{
  /* local variables */
  double FCCshifts[4][DIM];
  double latVec[DIM];
  int a;
  int i;
  int j;
  int k;
  int m;
  int n;

  /* create a cubic FCC cluster of parts */
  FCCshifts[0][0] = 0.0;
  FCCshifts[0][1] = 0.0;
  FCCshifts[0][2] = 0.0;
  FCCshifts[1][0] = 0.5 * FCCspacing;
  FCCshifts[1][1] = 0.5 * FCCspacing;
  FCCshifts[1][2] = 0.0;
  FCCshifts[2][0] = 0.5 * FCCspacing;
  FCCshifts[2][1] = 0.0;
  FCCshifts[2][2] = 0.5 * FCCspacing;
  FCCshifts[3][0] = 0.0;
  FCCshifts[3][1] = 0.5 * FCCspacing;
  FCCshifts[3][2] = 0.5 * FCCspacing;

  a = 0;
  for (i = 0; i < nCellsPerSide; ++i)
  {
    latVec[0] = ((double) i) * FCCspacing;
    for (j = 0; j < nCellsPerSide; ++j)
    {
      latVec[1] = ((double) j) * FCCspacing;
      for (k = 0; k < nCellsPerSide; ++k)
      {
        latVec[2] = ((double) k) * FCCspacing;
        for (m = 0; m < 4; ++m)
        {
          for (n = 0; n < DIM; ++n)
          {
            coords[a * DIM + n] = latVec[n] + FCCshifts[m][n];
          }
          a++;
        }
      }
      /* add in the remaining three faces */
      /* pos-x face */
      latVec[0] = NCELLSPERSIDE * FCCspacing;
      latVec[1] = ((double) i) * FCCspacing;
      latVec[2] = ((double) j) * FCCspacing;
      for (n = 0; n < DIM; ++n) { coords[a * DIM + n] = latVec[n]; }
      a++;
      for (n = 0; n < DIM; ++n)
      {
        coords[a * DIM + n] = latVec[n] + FCCshifts[3][n];
      }
      a++;
      /* pos-y face */
      latVec[0] = ((double) i) * FCCspacing;
      latVec[1] = NCELLSPERSIDE * FCCspacing;
      latVec[2] = ((double) j) * FCCspacing;
      for (n = 0; n < DIM; ++n) { coords[a * DIM + n] = latVec[n]; }
      a++;
      for (n = 0; n < DIM; ++n)
      {
        coords[a * DIM + n] = latVec[n] + FCCshifts[2][n];
      }
      a++;
      /* pos-z face */
      latVec[0] = ((double) i) * FCCspacing;
      latVec[1] = ((double) j) * FCCspacing;
      latVec[2] = NCELLSPERSIDE * FCCspacing;
      for (n = 0; n < DIM; ++n) { coords[a * DIM + n] = latVec[n]; }
      a++;
      for (n = 0; n < DIM; ++n)
      {
        coords[a * DIM + n] = latVec[n] + FCCshifts[1][n];
      }
      a++;
    }
    /* add in the remaining three edges */
    latVec[0] = ((double) i) * FCCspacing;
    latVec[1] = NCELLSPERSIDE * FCCspacing;
    latVec[2] = NCELLSPERSIDE * FCCspacing;
    for (n = 0; n < DIM; ++n) { coords[a * DIM + n] = latVec[n]; }
    a++;
    latVec[0] = NCELLSPERSIDE * FCCspacing;
    latVec[1] = ((double) i) * FCCspacing;
    latVec[2] = NCELLSPERSIDE * FCCspacing;
    for (n = 0; n < DIM; ++n) { coords[a * DIM + n] = latVec[n]; }
    a++;
    latVec[0] = NCELLSPERSIDE * FCCspacing;
    latVec[1] = NCELLSPERSIDE * FCCspacing;
    latVec[2] = ((double) i) * FCCspacing;
    for (n = 0; n < DIM; ++n) { coords[a * DIM + n] = latVec[n]; }
    a++;
  }
  /* add in the remaining corner */
  for (n = 0; n < DIM; ++n)
  {
    coords[a * DIM + n] = NCELLSPERSIDE * FCCspacing;
  }
  a++;

  return;
}


void fcc_cluster_neighborlist(int half,
                              int numberOfParticles,
                              double * coords,
                              double cutoff,
                              NeighList * nl)
{
  /* local variables */
  int i;
  int j;
  int k;
  int a;

  double dx[DIM];
  double r2;
  double cutoff2;

  nl->cutoff = cutoff;

  cutoff2 = cutoff * cutoff;

  for (i = 0; i < numberOfParticles; ++i)
  {
    a = 0;
    for (j = 0; j < numberOfParticles; ++j)
    {
      r2 = 0.0;
      for (k = 0; k < DIM; ++k)
      {
        dx[k] = coords[j * DIM + k] - coords[i * DIM + k];
        r2 += dx[k] * dx[k];
      }

      if (r2 < cutoff2)
      {
        if ((half && i < j) || (!half && i != j))
        {
          /* part j is a neighbor of part i */
          (*nl).neighborList[i * NCLUSTERPARTS + a] = j;
          a++;
        }
      }
    }
    /* part i has `a' neighbors */
    (*nl).NNeighbors[i] = a;
  }

  return;
}

int get_cluster_neigh(void * const dataObject,
                      int const numberOfNeighborLists,
                      double const * const cutoffs,
                      int const neighborListIndex,
                      int const particleNumber,
                      int * const numberOfNeighbors,
                      int const ** const neighborsOfParticle)
{
  /* local variables */
  int error = true;
  NeighList * nl = (NeighList *) dataObject;
  int numberOfParticles = nl->numberOfParticles;

  if ((numberOfNeighborLists != 1) || (cutoffs[0] > nl->cutoff)) return error;

  if (neighborListIndex != 0) return error;

  /* initialize numNeigh */
  *numberOfNeighbors = 0;

  if ((particleNumber >= numberOfParticles)
      || (particleNumber < 0)) /* invalid id */
  {
    MY_WARNING("Invalid part ID in get_cluster_neigh");
    return true;
  }

  /* set the returned number of neighbors for the returned part */
  *numberOfNeighbors = (*nl).NNeighbors[particleNumber];

  /* set the location for the returned neighbor list */
  *neighborsOfParticle
      = &((*nl).neighborList[(particleNumber) *numberOfParticles]);

  return false;
}