add support for building rigid bodies from custom atom properties or atom style variables

#include "comm.h"

#include "random_mars.h"

#include "force.h"

#include "input.h"

#include "variable.h"

#include "output.h"

#include "math_const.h"

#include "memory.h"

  // nbody = # of non-zero ncount values

  // use nall as incremented ptr to set body[] values for each atom

  } else if (strcmp(arg[3],"molecule") == 0) {

  } else if (strcmp(arg[3],"molecule") == 0 || strcmp(arg[3],"custom") == 0) {

    rstyle = MOLECULE;

    iarg = 4;

    if (atom->molecule_flag == 0)

      error->all(FLERR,"Fix rigid molecule requires atom attribute molecule");

    tagint *molecule;

    int *mask = atom->mask;

    tagint *molecule = atom->molecule;

    int nlocal = atom->nlocal;

    int custom_flag = strcmp(arg[3],"custom") == 0;

    if (custom_flag) {

      if (narg < 5) error->all(FLERR,"Illegal fix rigid command");

      // determine whether atom-style variable or atom property is used.

      if (strstr(arg[4],"i_") == arg[4]) {

        int is_double;

        int custom_index = atom->find_custom(arg[4]+2,is_double);

        if (custom_index == -1)

          error->all(FLERR,"Fix rigid custom requires previously defined property/atom");

        else if (is_double)

          error->all(FLERR,"Fix rigid custom requires integer-valued property/atom");

        int minval = INT_MAX;

        int *value = atom->ivector[custom_index];

        for (i = 0; i < nlocal; i++)

          if (mask[i] & groupbit) minval = MIN(minval,value[i]);

        int vmin = minval;

        MPI_Allreduce(&vmin,&minval,1,MPI_INT,MPI_MIN,world);

        molecule = new tagint[nlocal];

        for (i = 0; i < nlocal; i++)

          if (mask[i] & groupbit) molecule[i] = (tagint)(value[i] - minval + 1);

      } else if (strstr(arg[4],"v_") == arg[4]) {

        int ivariable = input->variable->find(arg[4]+2);

        if (ivariable < 0)

          error->all(FLERR,"Variable name for fix rigid custom does not exist");

        if (input->variable->atomstyle(ivariable) == 0)

          error->all(FLERR,"Fix rigid custom variable is not atom-style variable");

        double *value = new double[nlocal];

        input->variable->compute_atom(ivariable,0,value,1,0);

        int minval = INT_MAX;

        for (i = 0; i < nlocal; i++)

          if (mask[i] & groupbit) minval = MIN(minval,(int)value[i]);

        int vmin = minval;

        MPI_Allreduce(&vmin,&minval,1,MPI_INT,MPI_MIN,world);

        molecule = new tagint[nlocal];

        for (i = 0; i < nlocal; i++)

          if (mask[i] & groupbit) molecule[i] = (tagint)((int)value[i] - minval + 1);

        delete[] value;

      } else error->all(FLERR,"Unsupported fix rigid custom property");

    } else {

      if (atom->molecule_flag == 0)

        error->all(FLERR,"Fix rigid molecule requires atom attribute molecule");

      molecule = atom->molecule;

    }

    iarg = 4 + custom_flag;

    tagint maxmol_tag = -1;

    for (i = 0; i < nlocal; i++)

    }

    memory->destroy(ncount);

    if (custom_flag) delete [] molecule;

  // each listed group is a rigid body

  // check if all listed groups exist