Commit fbc435a0 authored by PabloPiaggi's avatar PabloPiaggi
Browse files

Formatted according to Lammps guidelines

parent 108c31e2

src/USER-MISC/compute_pair_entropy_atom.cpp

+42 −45
Original line number Diff line number Diff line
@@ -40,23 +40,30 @@ using namespace MathConst; 


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



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

ComputePairEntropyAtom::

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

  Compute(lmp, narg, arg),

  pair_entropy(NULL), pair_entropy_avg(NULL)

{

  if (narg < 5 || narg > 10)

    error->all(FLERR,"Illegal compute pentropy/atom command");

    error->all(FLERR,"Illegal compute pentropy/atom command; wrong number"

               " of arguments");



  // Arguments are: sigma cutoff avg yes/no cutoff2

  // Arguments are: sigma cutoff avg yes/no cutoff2 local yes/no

  //   sigma is the gaussian width 

  //   cutoff is the cutoff for the calculation of g(r) 

  //   avg is optional and it means averaginf the pair entropy over the neighbors

  //   avg is optional and allows averaging the pair entropy over neighbors

  //   the next argument should be yes or no 

  //   cutoff2 is the cutoff for the averaging

  //   local is optional and allows using the local density to normalize

  //     the g(r)



  sigma = force->numeric(FLERR,arg[3]);

  if (sigma < 0.0) error->all(FLERR,"Illegal compute pentropy/atom"

                              " command; negative sigma");

  cutoff = force->numeric(FLERR,arg[4]);

  if (cutoff < 0.0) error->all(FLERR,"Illegal compute pentropy/atom command; negative cutoff");

  if (cutoff < 0.0) error->all(FLERR,"Illegal compute pentropy/atom"

                               " command; negative cutoff");



  avg_flag = 0;

  local_flag = 0;
@@ -66,20 +73,25 @@ ComputePairEntropyAtom::ComputePairEntropyAtom(LAMMPS *lmp, int narg, char **arg 
  while (iarg < narg) {

    if (strcmp(arg[iarg],"avg") == 0) {

      if (iarg+2 > narg)

        error->all(FLERR,"Illegal compute pentropy/atom missing arguments after avg");

        error->all(FLERR,"Illegal compute pentropy/atom;"

                   " missing arguments after avg");

      if (strcmp(arg[iarg+1],"yes") == 0) avg_flag = 1;

      else if (strcmp(arg[iarg+1],"no") == 0) avg_flag = 0;

      else error->all(FLERR,"Illegal compute pentropy/atom argument after avg should be yes or no");

      else error->all(FLERR,"Illegal compute pentropy/atom;"

                      " argument after avg should be yes or no");

      cutoff2 = force->numeric(FLERR,arg[iarg+2]);

      if (cutoff2 < 0.0) error->all(FLERR,"Illegal compute pentropy/atom command; negative cutoff2");

      if (cutoff2 < 0.0) error->all(FLERR,"Illegal compute pentropy/atom"

                                    " command; negative cutoff2");

      cutsq2 = cutoff2*cutoff2;

      iarg += 3;

    } else if (strcmp(arg[iarg],"local") == 0) {

      if (strcmp(arg[iarg+1],"yes") == 0) local_flag = 1;

      else if (strcmp(arg[iarg+1],"no") == 0) local_flag = 0;

      else error->all(FLERR,"Illegal compute pentropy/atom argument after local should be yes or no");

      else error->all(FLERR,"Illegal compute pentropy/atom;"

                      " argument after local should be yes or no");

      iarg += 2;

    } else error->all(FLERR,"Illegal compute pentropy/atom argument after sigma and cutoff should be avg or local");

    } else error->all(FLERR,"Illegal compute pentropy/atom; argument after"

                      " sigma and cutoff should be avg or local");

  }
@@ -87,7 +99,10 @@ ComputePairEntropyAtom::ComputePairEntropyAtom(LAMMPS *lmp, int narg, char **arg 
  nbin = static_cast<int>(cutoff / sigma) + 1;

  nmax = 0;

  maxneigh = 0;

  deltabin = 2; // 2 seems a good compromise between speed and good mollification

  // Number of bins above and below the central one that will be

  // considered as affected by the gaussian kernel

  // 2 seems a good compromise between speed and good mollification

  deltabin = 2; 

  deltar = sigma; 

  peratom_flag = 1;

  size_peratom_cols = 0;
@@ -106,25 +121,16 @@ ComputePairEntropyAtom::~ComputePairEntropyAtom() 
void ComputePairEntropyAtom::init()

{

  if (force->pair == NULL)

    error->all(FLERR,"Compute centro/atom requires a pair style be defined");



  //double largest_cutsq;

  //largest_cutsq = cutsq;

  //if (cutsq2 > cutsq) largest_cutsq = cutsq2;

    error->all(FLERR,"Compute centro/atom requires a pair style be"

               " defined");



  if ( (cutoff+cutoff2) > (force->pair->cutforce  + neighbor->skin) ) 

    {

	//fprintf(screen, "%f %f %f %f \n", cutoff, cutoff2, (cutoff+cutoff2) , force->pair->cutforce  + neighbor->skin );

    	error->all(FLERR,"Compute pentropy/atom cutoff is longer than pairwise cutoff. Increase the neighbor list skin distance.");

    	error->all(FLERR,"Compute pentropy/atom cutoff is longer than the"

                   " pairwise cutoff. Increase the neighbor list skin"

                   " distance.");

    }



  /*

  if (2.0*sqrt(largest_cutsq) > force->pair->cutforce + neighbor->skin &&

      comm->me == 0)

    error->warning(FLERR,"Compute pentropy/atom cutoff may be too large to find "

                   "ghost atom neighbors");

  */



  int count = 0;

  for (int i = 0; i < modify->ncompute; i++)

    if (strcmp(modify->compute[i]->style,"pentropy/atom") == 0) count++;
@@ -180,15 +186,12 @@ void ComputePairEntropyAtom::compute_peratom() 
      memory->destroy(pair_entropy_avg);

      nmax = atom->nmax;

      memory->create(pair_entropy,nmax,"pentropy/atom:pair_entropy");

      memory->create(pair_entropy_avg,nmax,"pentropy/atom:pair_entropy_avg");

      memory->create(pair_entropy_avg,nmax,

                     "pentropy/atom:pair_entropy_avg");

      vector_atom = pair_entropy_avg;

    }

  }



  // invoke full neighbor list (will copy or build if necessary)



  //neighbor->build_one(list);



  inum = list->inum +  list->gnum;

  ilist = list->ilist;

  numneigh = list->numneigh;
@@ -218,13 +221,16 @@ void ComputePairEntropyAtom::compute_peratom() 
      // If local density is used, calculate it

      if (local_flag) {

        double neigh_cutoff = force->pair->cutforce  + neighbor->skin;

        double volume = (4./3.)*MY_PI*neigh_cutoff*neigh_cutoff*neigh_cutoff;

        double volume = 

               (4./3.)*MY_PI*neigh_cutoff*neigh_cutoff*neigh_cutoff;

        density = jnum / volume;

      }



      // calculate kernel normalization

      double normConstantBase = 4*MY_PI*density; // Normalization of g(r)

      normConstantBase *= sqrt(2.*MY_PI)*sigma; // Normalization of gaussian

      // Normalization of g(r)

      double normConstantBase = 4*MY_PI*density; 

      // Normalization of gaussian

      normConstantBase *= sqrt(2.*MY_PI)*sigma; 

      double invNormConstantBase = 1./normConstantBase;



      // loop over list of all neighbors within force cutoff
@@ -245,8 +251,7 @@ void ComputePairEntropyAtom::compute_peratom() 
          // contribute to gofr

          double r=sqrt(rsq);

          int bin=floor(r/deltar);

          int minbin, maxbin; // These cannot be unsigned

          // Only consider contributions to g(r) of atoms less than n*sigma bins apart from the actual distance

          int minbin, maxbin;

          minbin=bin - deltabin;

          if (minbin < 0) minbin=0;

          if (minbin > (nbin-1)) minbin=nbin-1;
@@ -260,14 +265,6 @@ void ComputePairEntropyAtom::compute_peratom() 
        }

      }



      /*

      if (ii==500) {

        for(int k=0;k<nbin;++k) {

          fprintf(screen,"%f %f \n",rbin[k], gofr[k]);

        }

      }

      */



      // Calculate integrand

      double integrand[nbin];

      for(int k=0;k<nbin;++k){
@@ -305,8 +302,8 @@ void ComputePairEntropyAtom::compute_peratom() 
 

        pair_entropy_avg[i] = pair_entropy[i];

        double counter = 1;

        // loop over list of all neighbors within force cutoff



        // loop over list of all neighbors within force cutoff

        for (jj = 0; jj < jnum; jj++) {

          j = jlist[jj];

          j &= NEIGHMASK;

src/USER-MISC/compute_pair_entropy_atom.h

+1 −13
Original line number Diff line number Diff line
@@ -59,21 +59,9 @@ Self-explanatory. Check the input script syntax and compare to the 
documentation for the command.  You can use -echo screen as a

command-line option when running LAMMPS to see the offending line.



E: Illegal compute pentropy/atom command3



UNDOCUMENTED



E: Illegal compute pentropy/atom command2



UNDOCUMENTED



E: Illegal compute pentropy/atom command1



UNDOCUMENTED



E: Compute pentropy/atom requires a pair style be defined



This is because the computation of the centro-symmetry values

This is because the computation of the pair entropy values

uses a pairwise neighbor list.



W: More than one compute pentropy/atom

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