ex_model_driver_P_Morse.c

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/*                                                                            */
/* Copyright (c) 2013--2019, Regents of the University of Minnesota.          */
/* All rights reserved.                                                       */
/*                                                                            */
/* Contributors:                                                              */
/*    Ryan S. Elliott                                                         */
/*    Ellad B. Tadmor                                                         */
/*    Stephen M. Whalen                                                       */
/*                                                                            */

/******************************************************************************/
/*                                                                            */
/* ex_model_driver_P_Morse pair potential KIM Model Driver                    */
/* shifted to have zero energy at the cutoff radius                           */
/*                                                                            */
/* Language: C                                                                */
/*                                                                            */
/******************************************************************************/


#include "KIM_LogMacros.h"
#include "KIM_ModelDriverHeaders.h"
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>

#define TRUE 1
#define FALSE 0

/******************************************************************************/
/* Below are the definitions for some constants                               */
/******************************************************************************/
#define DIM 3 /* dimensionality of space */
#define SPECCODE 1 /* internal species code */
#define SPEC_NAME_LEN 64 /* max length of species name string */
#define SPEC_NAME_FMT "%63s"


/* Define prototype for Model Driver init */
int model_driver_create(KIM_ModelDriverCreate * const modelDriverCreate,
                        KIM_LengthUnit const requestedLengthUnit,
                        KIM_EnergyUnit const requestedEnergyUnit,
                        KIM_ChargeUnit const requestedChargeUnit,
                        KIM_TemperatureUnit const requestedTemperatureUnit,
                        KIM_TimeUnit const requestedTimeUnit);

/* Define prototypes for destroy */
/* defined as static to avoid namespace clashes with other codes */
static int destroy_routine(KIM_ModelDestroy * const modelDestroy);

/* Define prototype for routines */
static int
compute_routine(KIM_ModelCompute const * const modelCompute,
                KIM_ModelComputeArguments const * const modelComputeArguments);
static int compute_arguments_create(
    KIM_ModelCompute const * const modelCompute,
    KIM_ModelComputeArgumentsCreate * const modelComputeArgumentsCreate);
static int compute_arguments_destroy(
    KIM_ModelCompute const * const modelCompute,
    KIM_ModelComputeArgumentsDestroy * const modelComputeArgumentsDestroy);
static int refresh_routine(KIM_ModelRefresh * const modelRefresh);
static int
write_parameterized_model(KIM_ModelWriteParameterizedModel const * const
                              modelWriteParameterizedModel);

/* Define prototypes for pair potential calculations */
static void calc_phi(double const * epsilon,
                     double const * C,
                     double const * Rzero,
                     double const * shift,
                     double const cutoff,
                     double const r,
                     double * phi);

static void calc_phi_dphi(double const * epsilon,
                          double const * C,
                          double const * Rzero,
                          double const * shift,
                          double const cutoff,
                          double const r,
                          double * phi,
                          double * dphi);

/* Define model_buffer structure */
struct model_buffer
{
  double influenceDistance;
  double cutoff;
  double cutsq;
  int modelWillNotRequestNeighborsOfNoncontributingParticles;
  char speciesName[SPEC_NAME_LEN];
  double epsilon;
  double C;
  double Rzero;
  double shift;
};


/* Calculate pair potential phi(r) */
static void calc_phi(double const * epsilon,
                     double const * C,
                     double const * Rzero,
                     double const * shift,
                     double const cutoff,
                     double const r,
                     double * phi)
{
  /* local variables */
  double ep;
  double ep2;

  ep = exp(-(*C) * (r - *Rzero));
  ep2 = ep * ep;

  if (r > cutoff)
  {
    /* Argument exceeds cutoff radius */
    *phi = 0.0;
  }
  else
  {
    *phi = (*epsilon) * (-ep2 + 2.0 * ep) + *shift;
  }

  return;
}

/* Calculate pair potential phi(r) and its derivative dphi(r) */
static void calc_phi_dphi(double const * epsilon,
                          double const * C,
                          double const * Rzero,
                          double const * shift,
                          double const cutoff,
                          double const r,
                          double * phi,
                          double * dphi)
{
  /* local variables */
  double ep;
  double ep2;

  ep = exp(-(*C) * (r - *Rzero));
  ep2 = ep * ep;

  if (r > cutoff)
  {
    /* Argument exceeds cutoff radius */
    *phi = 0.0;
    *dphi = 0.0;
  }
  else
  {
    *phi = (*epsilon) * (-ep2 + 2.0 * ep) + *shift;
    *dphi = 2.0 * (*epsilon) * (*C) * (-ep + ep2);
  }

  return;
}

/* compute function */
#undef KIM_LOGGER_FUNCTION_NAME
#define KIM_LOGGER_FUNCTION_NAME KIM_ModelCompute_LogEntry
#undef KIM_LOGGER_OBJECT_NAME
#define KIM_LOGGER_OBJECT_NAME modelCompute
static int
compute_routine(KIM_ModelCompute const * const modelCompute,
                KIM_ModelComputeArguments const * const modelComputeArguments)
{
  /* local variables */
  double R;
  double Rsqij;
  double phi;
  double dphi;
  double dEidr;
  double Rij[DIM];
  int ier;
  int i;
  int j;
  int jj;
  int k;
  int const * neighListOfCurrentPart;
  struct model_buffer * buffer;
  int comp_energy;
  int comp_force;
  int comp_particleEnergy;

  int * nParts;
  int * particleSpeciesCodes;
  int * particleContributing;
  double cutoff;
  double * cutsq;
  double * epsilon;
  double * C;
  double * Rzero;
  double * shift;
  double * coords;
  double * energy;
  double * force;
  double * particleEnergy;
  int numOfPartNeigh;

  /* get buffer from KIM object */
  KIM_ModelCompute_GetModelBufferPointer(modelCompute, (void **) &buffer);

  /* unpack info from the buffer */
  cutoff = buffer->influenceDistance;
  cutsq = &(buffer->cutsq);
  epsilon = &(buffer->epsilon);
  C = &(buffer->C);
  Rzero = &(buffer->Rzero);
  shift = &(buffer->shift);

  ier = KIM_ModelComputeArguments_GetArgumentPointerInteger(
            modelComputeArguments,
            KIM_COMPUTE_ARGUMENT_NAME_numberOfParticles,
            &nParts)
        || KIM_ModelComputeArguments_GetArgumentPointerInteger(
            modelComputeArguments,
            KIM_COMPUTE_ARGUMENT_NAME_particleSpeciesCodes,
            &particleSpeciesCodes)
        || KIM_ModelComputeArguments_GetArgumentPointerInteger(
            modelComputeArguments,
            KIM_COMPUTE_ARGUMENT_NAME_particleContributing,
            &particleContributing)
        || KIM_ModelComputeArguments_GetArgumentPointerDouble(
            modelComputeArguments,
            KIM_COMPUTE_ARGUMENT_NAME_coordinates,
            &coords)
        || KIM_ModelComputeArguments_GetArgumentPointerDouble(
            modelComputeArguments,
            KIM_COMPUTE_ARGUMENT_NAME_partialEnergy,
            &energy)
        || KIM_ModelComputeArguments_GetArgumentPointerDouble(
            modelComputeArguments,
            KIM_COMPUTE_ARGUMENT_NAME_partialForces,
            &force)
        || KIM_ModelComputeArguments_GetArgumentPointerDouble(
            modelComputeArguments,
            KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy,
            &particleEnergy);
  if (ier)
  {
    LOG_ERROR("GetArgumentPointer");
    return ier;
  }

  comp_energy = (energy != NULL);
  comp_force = (force != NULL);
  comp_particleEnergy = (particleEnergy != NULL);

  /* Check to be sure that the species are correct */
  
  ier = TRUE; /* assume an error */
  for (i = 0; i < *nParts; ++i)
  {
    if (SPECCODE != particleSpeciesCodes[i])
    {
      LOG_ERROR("Unexpected species code detected");
      return ier;
    }
  }
  ier = FALSE; /* everything is ok */

  /* initialize potential energies, forces, and virial term */
  if (comp_particleEnergy)
  {
    for (i = 0; i < *nParts; ++i) { particleEnergy[i] = 0.0; }
  }
  if (comp_energy) { *energy = 0.0; }

  if (comp_force)
  {
    for (i = 0; i < *nParts; ++i)
    {
      for (k = 0; k < DIM; ++k) { force[i * DIM + k] = 0.0; }
    }
  }

  /* Compute energy and forces */

  /* loop over particles and compute enregy and forces */
  for (i = 0; i < *nParts; ++i)
  {
    if (particleContributing[i])
    {
      ier = KIM_ModelComputeArguments_GetNeighborList(modelComputeArguments,
                                                      0,
                                                      i,
                                                      &numOfPartNeigh,
                                                      &neighListOfCurrentPart);
      if (ier)
      {
        /* some sort of problem, exit */
        LOG_ERROR("KIM_get_neigh");
        ier = TRUE;
        return ier;
      }

      /* loop over the neighbors of particle i */
      for (jj = 0; jj < numOfPartNeigh; ++jj)
      {
        j = neighListOfCurrentPart[jj]; /* get neighbor ID */

        /* compute relative position vector and squared distance */
        Rsqij = 0.0;
        for (k = 0; k < DIM; ++k)
        {
          Rij[k] = coords[j * DIM + k] - coords[i * DIM + k];
          /* compute squared distance */
          Rsqij += Rij[k] * Rij[k];
        }

        /* compute energy and force */
        if (Rsqij < *cutsq)
        {
          /* particles are interacting ? */
          R = sqrt(Rsqij);
          if (comp_force)
          {
            /* compute pair potential and its derivative */
            calc_phi_dphi(epsilon, C, Rzero, shift, cutoff, R, &phi, &dphi);

            /* compute dEidr */
            dEidr = 0.5 * dphi;
          }
          else
          {
            /* compute just pair potential */
            calc_phi(epsilon, C, Rzero, shift, cutoff, R, &phi);
          }

          /* contribution to energy */
          if (comp_particleEnergy) { particleEnergy[i] += 0.5 * phi; }
          if (comp_energy) { *energy += 0.5 * phi; }

          /* contribution to forces */
          if (comp_force)
          {
            for (k = 0; k < DIM; ++k)
            {
              force[i * DIM + k]
                  += dEidr * Rij[k] / R; /* accumulate force on i */
              force[j * DIM + k]
                  -= dEidr * Rij[k] / R; /* accumulate force on j */
            }
          }
        } /* if Rsqij */
      } /* loop on jj */
    } /* if particleContributing */
  } /* infinite while loop (terminated by break statements above) */

  /* everything is great */
  ier = FALSE;

  return ier;
}

/* Create function */
#undef KIM_LOGGER_FUNCTION_NAME
#define KIM_LOGGER_FUNCTION_NAME KIM_ModelDriverCreate_LogEntry
#undef KIM_LOGGER_OBJECT_NAME
#define KIM_LOGGER_OBJECT_NAME modelDriverCreate
int model_driver_create(KIM_ModelDriverCreate * const modelDriverCreate,
                        KIM_LengthUnit const requestedLengthUnit,
                        KIM_EnergyUnit const requestedEnergyUnit,
                        KIM_ChargeUnit const requestedChargeUnit,
                        KIM_TemperatureUnit const requestedTemperatureUnit,
                        KIM_TimeUnit const requestedTimeUnit)
{
  /* KIM variables */
  int numberOfParameterFiles;
  char const * paramfile1name;

  /* Local variables */
  FILE * fid;
  char speciesNameString[SPEC_NAME_LEN];
  KIM_SpeciesName speciesName;
  double cutoff;
  double epsilon;
  double C;
  double Rzero;
  int ier;
  double dummy;
  struct model_buffer * buffer;

  /* Use function pointer definitions to verify prototypes */
  KIM_ModelDriverCreateFunction * create = model_driver_create;
  KIM_ModelComputeArgumentsCreateFunction * CACreate = compute_arguments_create;
  KIM_ModelComputeFunction * compute = compute_routine;
  KIM_ModelRefreshFunction * refresh = refresh_routine;
  KIM_ModelWriteParameterizedModelFunction * writeModel
      = write_parameterized_model;
  KIM_ModelComputeArgumentsDestroyFunction * CADestroy
      = compute_arguments_destroy;
  KIM_ModelDestroyFunction * destroy = destroy_routine;


  (void) create; /* avoid unused parameter warnings */
  (void) requestedLengthUnit;
  (void) requestedEnergyUnit;
  (void) requestedChargeUnit;
  (void) requestedTemperatureUnit;
  (void) requestedTimeUnit;


  /* using fixed units */
  ier = KIM_ModelDriverCreate_SetUnits(modelDriverCreate,
                                       KIM_LENGTH_UNIT_A,
                                       KIM_ENERGY_UNIT_eV,
                                       KIM_CHARGE_UNIT_unused,
                                       KIM_TEMPERATURE_UNIT_unused,
                                       KIM_TIME_UNIT_unused);
  if (ier == TRUE)
  {
    LOG_ERROR("Problem setting units");
    return ier;
  }

  ier = KIM_ModelDriverCreate_SetModelNumbering(modelDriverCreate,
                                                KIM_NUMBERING_zeroBased);
  if (ier == TRUE)
  {
    LOG_ERROR("Unable to set numbering");
    return ier;
  }

  /* store pointer to functions in KIM object */
  ier = KIM_ModelDriverCreate_SetRoutinePointer(
            modelDriverCreate,
            KIM_MODEL_ROUTINE_NAME_ComputeArgumentsCreate,
            KIM_LANGUAGE_NAME_c,
            TRUE,
            (KIM_Function *) CACreate)
        || KIM_ModelDriverCreate_SetRoutinePointer(
            modelDriverCreate,
            KIM_MODEL_ROUTINE_NAME_Compute,
            KIM_LANGUAGE_NAME_c,
            TRUE,
            (KIM_Function *) compute)
        || KIM_ModelDriverCreate_SetRoutinePointer(
            modelDriverCreate,
            KIM_MODEL_ROUTINE_NAME_Refresh,
            KIM_LANGUAGE_NAME_c,
            TRUE,
            (KIM_Function *) refresh)
        || KIM_ModelDriverCreate_SetRoutinePointer(
            modelDriverCreate,
            KIM_MODEL_ROUTINE_NAME_WriteParameterizedModel,
            KIM_LANGUAGE_NAME_c,
            FALSE,
            (KIM_Function *) writeModel)
        || KIM_ModelDriverCreate_SetRoutinePointer(
            modelDriverCreate,
            KIM_MODEL_ROUTINE_NAME_ComputeArgumentsDestroy,
            KIM_LANGUAGE_NAME_c,
            TRUE,
            (KIM_Function *) CADestroy)
        || KIM_ModelDriverCreate_SetRoutinePointer(
            modelDriverCreate,
            KIM_MODEL_ROUTINE_NAME_Destroy,
            KIM_LANGUAGE_NAME_c,
            TRUE,
            (KIM_Function *) destroy);

  /* get number of parameter files */
  KIM_ModelDriverCreate_GetNumberOfParameterFiles(modelDriverCreate,
                                                  &numberOfParameterFiles);
  /* set paramfile1name */
  if (numberOfParameterFiles != 1)
  {
    ier = TRUE;
    LOG_ERROR("Incorrect number of parameter files.");
    return ier;
  }
  ier = KIM_ModelDriverCreate_GetParameterFileName(
      modelDriverCreate, 0, &paramfile1name);
  if (ier == TRUE)
  {
    LOG_ERROR("Unable to get parameter file name.");
    return ier;
  }

  /* Read in model parameters from parameter file */
  fid = fopen(paramfile1name, "r");
  if (fid == NULL)
  {
    ier = TRUE;
    LOG_ERROR("Unable to open parameter file for Morse parameters");
    return ier;
  }

  ier = fscanf(fid,
               SPEC_NAME_FMT " \n%lf \n%lf \n%lf \n%lf",
               speciesNameString, /* element symbol */
               &cutoff, /* cutoff distance in angstroms */
               &epsilon, /* Morse epsilon in eV */
               &C, /* Morse C in 1/Angstroms */
               &Rzero /* Morse Rzero in Angstroms */
  );
  fclose(fid);

  /* check that we read the right number of parameters */
  if (5 != ier)
  {
    ier = TRUE;
    LOG_ERROR("Unable to read all parameters");
    return ier;
  }

  /* register species */
  speciesName = KIM_SpeciesName_FromString(speciesNameString);
  ier = KIM_ModelDriverCreate_SetSpeciesCode(
      modelDriverCreate, speciesName, SPECCODE);
  if (ier == TRUE)
  {
    LOG_ERROR("Unable to set species code for Ar.");
    return ier;
  }


  /* allocate buffer */
  buffer = (struct model_buffer *) malloc(sizeof(struct model_buffer));
  if (NULL == buffer)
  {
    ier = TRUE;
    LOG_ERROR("malloc");
    return ier;
  }

  /* setup buffer */
  /* set value of parameters */
  buffer->influenceDistance = cutoff;
  buffer->cutoff = cutoff;
  buffer->cutsq = (cutoff) * (cutoff);
  buffer->modelWillNotRequestNeighborsOfNoncontributingParticles = 1;
  sprintf(buffer->speciesName, "%s", speciesNameString);
  buffer->epsilon = epsilon;
  buffer->C = C;
  buffer->Rzero = Rzero;
  /* set value of parameter shift */
  dummy = 0.0;
  /* call calc_phi with r=cutoff and shift=0.0 */
  calc_phi(&(buffer->epsilon),
           &(buffer->C),
           &(buffer->Rzero),
           &dummy,
           cutoff,
           cutoff,
           &(buffer->shift));
  /* set shift to -shift */
  buffer->shift = -buffer->shift;

  /* end setup buffer */

  /* store in model buffer */
  KIM_ModelDriverCreate_SetModelBufferPointer(modelDriverCreate,
                                              (void *) buffer);

  /* publish model parameters */
  ier = KIM_ModelDriverCreate_SetParameterPointerDouble(modelDriverCreate,
                                                        1,
                                                        &(buffer->cutoff),
                                                        "cutoff",
                                                        "pair cutoff distance")
        || KIM_ModelDriverCreate_SetParameterPointerDouble(modelDriverCreate,
                                                           1,
                                                           &(buffer->epsilon),
                                                           "epsilon",
                                                           "Morse epsilon")
        || KIM_ModelDriverCreate_SetParameterPointerDouble(
            modelDriverCreate, 1, &(buffer->C), "C", "Morse C")
        || KIM_ModelDriverCreate_SetParameterPointerDouble(
            modelDriverCreate, 1, &(buffer->Rzero), "Rzero", "Morse Rzero");
  if (ier == TRUE)
  {
    LOG_ERROR("Unable to set parameter pointer(s).");
    return TRUE;
  }

  /* store model cutoff in KIM object */
  KIM_ModelDriverCreate_SetInfluenceDistancePointer(
      modelDriverCreate, &(buffer->influenceDistance));
  KIM_ModelDriverCreate_SetNeighborListPointers(
      modelDriverCreate,
      1,
      &(buffer->cutoff),
      &(buffer->modelWillNotRequestNeighborsOfNoncontributingParticles));

  return FALSE;
}

/* Refresh function */
#undef KIM_LOGGER_FUNCTION_NAME
#define KIM_LOGGER_FUNCTION_NAME KIM_ModelRefresh_LogEntry
#undef KIM_LOGGER_OBJECT_NAME
#define KIM_LOGGER_OBJECT_NAME modelRefresh
int refresh_routine(KIM_ModelRefresh * const modelRefresh)
{
  double dummy;
  struct model_buffer * buffer;

  /* get model buffer from KIM object */
  KIM_ModelRefresh_GetModelBufferPointer(modelRefresh, (void **) &buffer);

  /* set value of parameter shift */
  dummy = 0.0;
  /* call calc_phi with r=cutoff and shift=0.0 */
  calc_phi(&(buffer->epsilon),
           &(buffer->C),
           &(buffer->Rzero),
           &dummy,
           buffer->cutoff,
           buffer->cutoff,
           &(buffer->shift));
  /* set shift to -shift */
  buffer->shift = -buffer->shift;


  /* store model cutoff in KIM object */
  KIM_ModelRefresh_SetInfluenceDistancePointer(modelRefresh,
                                               &(buffer->influenceDistance));
  KIM_ModelRefresh_SetNeighborListPointers(
      modelRefresh,
      1,
      &(buffer->cutoff),
      &(buffer->modelWillNotRequestNeighborsOfNoncontributingParticles));

  return FALSE;
}


/* destroy function */
static int destroy_routine(KIM_ModelDestroy * const modelDestroy)
{
  /* Local variables */
  struct model_buffer * buffer;
  int ier;

  /* get model buffer from KIM object */
  KIM_ModelDestroy_GetModelBufferPointer(modelDestroy, (void **) &buffer);

  /* free the buffer */
  free(buffer);

  ier = FALSE;
  return ier;
}

/* compute arguments create routine */
#undef KIM_LOGGER_FUNCTION_NAME
#define KIM_LOGGER_FUNCTION_NAME KIM_ModelComputeArgumentsCreate_LogEntry
#undef KIM_LOGGER_OBJECT_NAME
#define KIM_LOGGER_OBJECT_NAME modelComputeArgumentsCreate
static int compute_arguments_create(
    KIM_ModelCompute const * const modelCompute,
    KIM_ModelComputeArgumentsCreate * const modelComputeArgumentsCreate)
{
  int ier;

  (void) modelCompute; /* avoid unused parameter warning */

  /* register arguments */
  ier = KIM_ModelComputeArgumentsCreate_SetArgumentSupportStatus(
            modelComputeArgumentsCreate,
            KIM_COMPUTE_ARGUMENT_NAME_partialEnergy,
            KIM_SUPPORT_STATUS_optional)
        || KIM_ModelComputeArgumentsCreate_SetArgumentSupportStatus(
            modelComputeArgumentsCreate,
            KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy,
            KIM_SUPPORT_STATUS_optional)
        || KIM_ModelComputeArgumentsCreate_SetArgumentSupportStatus(
            modelComputeArgumentsCreate,
            KIM_COMPUTE_ARGUMENT_NAME_partialForces,
            KIM_SUPPORT_STATUS_optional);
  if (ier == TRUE)
  {
    LOG_ERROR("Unable to set argument supportStatus.");
    return TRUE;
  }
  else
  {
    return FALSE;
  }
}

/* compute arguments destroy routine */
static int compute_arguments_destroy(
    KIM_ModelCompute const * const modelCompute,
    KIM_ModelComputeArgumentsDestroy * const modelComputeArgumentsDestroy)
{
  (void) modelCompute; /* avoid unused parameter warning */
  (void) modelComputeArgumentsDestroy;

  /* Nothing further to do */

  return FALSE;
}

/* write parameterized model routine */
#undef KIM_LOGGER_FUNCTION_NAME
#define KIM_LOGGER_FUNCTION_NAME KIM_ModelWriteParameterizedModel_LogEntry
#undef KIM_LOGGER_OBJECT_NAME
#define KIM_LOGGER_OBJECT_NAME modelWriteParameterizedModel
static int write_parameterized_model(
    KIM_ModelWriteParameterizedModel const * const modelWriteParameterizedModel)
{
  FILE * fp;
  char stringBuffer[2048];
  struct model_buffer const * buffer;
  char const * path;
  char const * modelName;

  /* get buffer from KIM object */
  KIM_ModelWriteParameterizedModel_GetModelBufferPointer(
      modelWriteParameterizedModel, (void **) &buffer);

  KIM_ModelWriteParameterizedModel_GetPath(modelWriteParameterizedModel, &path);
  KIM_ModelWriteParameterizedModel_GetModelName(modelWriteParameterizedModel,
                                                &modelName);

  sprintf(stringBuffer, "%s.params", modelName);
  KIM_ModelWriteParameterizedModel_SetParameterFileName(
      modelWriteParameterizedModel, stringBuffer);
  sprintf(stringBuffer, "%s/%s.params", path, modelName);
  fp = fopen(stringBuffer, "w");
  if (NULL == fp)
  {
    LOG_ERROR("Unable to open parameter file for writing.");
    return TRUE;
  }

  fprintf(fp, "%s\n", buffer->speciesName);
  fprintf(fp, "%20.10f\n", buffer->cutoff);
  fprintf(fp, "%20.10f\n", buffer->epsilon);
  fprintf(fp, "%20.10f\n", buffer->C);
  fprintf(fp, "%20.10f\n", buffer->Rzero);
  fclose(fp);

  return FALSE;
}