update formatting to closer match LAMMPS' programming style

#include "plumed/wrapper/Plumed.h"

/* -------------------------------------------------------------------- */

using namespace LAMMPS_NS;

using namespace FixConst;

FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) :

  Fix(lmp, narg, arg),

  p(NULL),

  nlocal(0),

  gatindex(NULL),

  masses(NULL),

  charges(NULL),

  id_pe(NULL),

  id_press(NULL)

  p(NULL), nlocal(0), gatindex(NULL), masses(NULL), charges(NULL),

  id_pe(NULL), id_press(NULL)

{

// Not sure this is really necessary:

  if (!atom->tag_enable) error->all(FLERR,"fix plumed requires atom tags");

// Initialize plumed:

  if (!atom->tag_enable)

    error->all(FLERR,"Fix plumed requires atom tags");

  if (igroup != 0 && comm->me == 0)

    error->warning(FLERR,"Fix group for fix plumed is not 'all'. "

                   "Group will be ignored.");

  p=new PLMD::Plumed;

  // Check API version

  int api_version; p->cmd("getApiVersion",&api_version);

  if( api_version>6 ) error->all(FLERR,"invalid api version for PLUMED");

// If the -partition option is activated then enable inter-partition communication

  int api_version;

  p->cmd("getApiVersion",&api_version);

  if (api_version > 6)

    error->all(FLERR,"Incompatible API version for PLUMED in fix plumed");

  // If the -partition option is activated then enable

  // inter-partition communication

  if (universe->existflag == 1) {

    int me;

    MPI_Comm inter_comm;

    MPI_Comm_rank(world,&me);

    // Change MPI_COMM_WORLD to universe->uworld which seems more appropriate

    MPI_Comm_split(universe->uworld,me,0,&inter_comm);

    p->cmd("GREX setMPIIntracomm",&world);

    if (me == 0) {

    }

    p->cmd("GREX init",NULL);

  }

  // The general communicator is independent of the existence of partitions,

  // if there are partitions, world is defined within each partition,

  //   whereas if partitions are not defined then world is equal to MPI_COMM_WORLD.

  // whereas if partitions are not defined then world is equal to

  // MPI_COMM_WORLD.

  p->cmd("setMPIComm",&world);

  // Set up units

  // Read fix parameters:

  int next=0;

  for (int i=3;i<narg;++i) {

    if(!strcmp(arg[i],"outfile")) next=1;

    else if(next==1){

    if (!strcmp(arg[i],"outfile")) {

      next=1;

    } else if (next==1) {

      if (universe->existflag == 1) {

        // Each replica writes an independent log file

        //  with suffix equal to the replica id

        p->cmd("setLogFile",arg[i]);

        next=0;

      }

    }

    else if(!strcmp(arg[i],"plumedfile"))next=2;

    else if(next==2){

    } else if (!strcmp(arg[i],"plumedfile")) {

      next=2;

    } else if (next==2) {

      p->cmd("setPlumedDat",arg[i]);

      next=0;

    }

    else error->all(FLERR,"syntax error in fix plumed - use 'fix name plumed plumedfile plumed.dat outfile plumed.out' ");

    } else error->all(FLERR,"Syntax error - use 'fix <fix-ID> plumed "

                      "plumedfile plumed.dat outfile plumed.out' ");

  }

  if (next==1) error->all(FLERR,"missing argument for outfile option");

  if (next==2) error->all(FLERR,"missing argument for plumedfile option");

  scalar_flag = 1;

  // This is the real initialization:

  p->cmd("init");

  // Define compute to calculate potential energy

  id_pe = new char[7];

  id_pe = (char *) "plmd_pe";

  char **newarg = new char*[3];