Commit 66178b66 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4766 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent edf05df9

src/GRANULAR/atom_vec_granular.cpp

+222 −70
Original line number Diff line number Diff line
@@ -13,12 +13,14 @@ 


#include "math.h"

#include "stdlib.h"

#include "string.h"

#include "atom_vec_granular.h"

#include "atom.h"

#include "domain.h"

#include "modify.h"

#include "force.h"

#include "fix.h"

#include "fix_adapt.h"

#include "memory.h"

#include "error.h"
@@ -46,9 +48,27 @@ AtomVecGranular::AtomVecGranular(LAMMPS *lmp, int narg, char **arg) : 
  atom->radius_flag = atom->density_flag = atom->rmass_flag = 1;

  atom->omega_flag = atom->torque_flag = 1;



  radvary = 0;



  PI = 4.0*atan(1.0);

}



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



void AtomVecGranular::init()

{

  // set radvary if particle diameters are time-varying due to fix adapt



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

    if (strcmp(modify->fix[i]->style,"adapt") == 0) {

      FixAdapt *fix = (FixAdapt *) modify->fix[i];

      if (fix->diamflag) {

	radvary = 1;

	size_forward = 5;

      }

    }

}



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

   grow atom arrays

   n = 0 grows arrays by DELTA
@@ -138,6 +158,7 @@ int AtomVecGranular::pack_comm(int n, int *list, double *buf, 
  int i,j,m;

  double dx,dy,dz;



  if (radvary == 0) {

    m = 0;

    if (pbc_flag == 0) {

      for (i = 0; i < n; i++) {
@@ -163,6 +184,39 @@ int AtomVecGranular::pack_comm(int n, int *list, double *buf, 
	buf[m++] = x[j][2] + dz;

      }

    }



  } else {

    m = 0;

    if (pbc_flag == 0) {

      for (i = 0; i < n; i++) {

	j = list[i];

	buf[m++] = x[j][0];

	buf[m++] = x[j][1];

	buf[m++] = x[j][2];

	buf[m++] = radius[i];

	buf[m++] = rmass[i];

      }

    } else {

      if (domain->triclinic == 0) {

	dx = pbc[0]*domain->xprd;

	dy = pbc[1]*domain->yprd;

	dz = pbc[2]*domain->zprd;

      } else {

	dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;

	dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;

	dz = pbc[2]*domain->zprd;

      }

      for (i = 0; i < n; i++) {

	j = list[i];

	buf[m++] = x[j][0] + dx;

	buf[m++] = x[j][1] + dy;

	buf[m++] = x[j][2] + dz;

	buf[m++] = radius[i];

	buf[m++] = rmass[i];

      }

    }

  }



  return m;

}
@@ -174,6 +228,7 @@ int AtomVecGranular::pack_comm_vel(int n, int *list, double *buf, 
  int i,j,m;

  double dx,dy,dz;



  if (radvary == 0) {

    m = 0;

    if (pbc_flag == 0) {

      for (i = 0; i < n; i++) {
@@ -211,21 +266,89 @@ int AtomVecGranular::pack_comm_vel(int n, int *list, double *buf, 
	buf[m++] = omega[j][2];

      }

    }



  } else {

    m = 0;

    if (pbc_flag == 0) {

      for (i = 0; i < n; i++) {

	j = list[i];

	buf[m++] = x[j][0];

	buf[m++] = x[j][1];

	buf[m++] = x[j][2];

	buf[m++] = radius[i];

	buf[m++] = rmass[i];

	buf[m++] = v[j][0];

	buf[m++] = v[j][1];

	buf[m++] = v[j][2];

	buf[m++] = omega[j][0];

	buf[m++] = omega[j][1];

	buf[m++] = omega[j][2];

      }

    } else {

      if (domain->triclinic == 0) {

	dx = pbc[0]*domain->xprd;

	dy = pbc[1]*domain->yprd;

	dz = pbc[2]*domain->zprd;

      } else {

	dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;

	dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;

	dz = pbc[2]*domain->zprd;

      }

      for (i = 0; i < n; i++) {

	j = list[i];

	buf[m++] = x[j][0] + dx;

	buf[m++] = x[j][1] + dy;

	buf[m++] = x[j][2] + dz;

	buf[m++] = radius[i];

	buf[m++] = rmass[i];

	buf[m++] = v[j][0];

	buf[m++] = v[j][1];

	buf[m++] = v[j][2];

	buf[m++] = omega[j][0];

	buf[m++] = omega[j][1];

	buf[m++] = omega[j][2];

      }

    }

  }



  return m;

}



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



int AtomVecGranular::pack_comm_one(int i, double *buf)

{

  if (radvary == 0) return 0;



  buf[0] = radius[i];

  buf[1] = rmass[i];

  return 2;

}



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



void AtomVecGranular::unpack_comm(int n, int first, double *buf)

{

  int i,m,last;



  if (radvary == 0) {

    m = 0;

    last = first + n;

    for (i = first; i < last; i++) {

      x[i][0] = buf[m++];

      x[i][1] = buf[m++];

      x[i][2] = buf[m++];

    }

  } else {

    m = 0;

    last = first + n;

    for (i = first; i < last; i++) {

      x[i][0] = buf[m++];

      x[i][1] = buf[m++];

      x[i][2] = buf[m++];

      radius[i] = buf[m++];

      rmass[i] = buf[m++];

    }

  }

}
@@ -235,6 +358,7 @@ void AtomVecGranular::unpack_comm_vel(int n, int first, double *buf) 
{

  int i,m,last;



  if (radvary == 0) {

    m = 0;

    last = first + n;

    for (i = first; i < last; i++) {
@@ -248,6 +372,34 @@ void AtomVecGranular::unpack_comm_vel(int n, int first, double *buf) 
      omega[i][1] = buf[m++];

      omega[i][2] = buf[m++];

    }

  } else {

    m = 0;

    last = first + n;

    for (i = first; i < last; i++) {

      x[i][0] = buf[m++];

      x[i][1] = buf[m++];

      x[i][2] = buf[m++];

      radius[i] = buf[m++];

      rmass[i] = buf[m++];

      v[i][0] = buf[m++];

      v[i][1] = buf[m++];

      v[i][2] = buf[m++];

      omega[i][0] = buf[m++];

      omega[i][1] = buf[m++];

      omega[i][2] = buf[m++];

    }

  }

}



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



int AtomVecGranular::unpack_comm_one(int i, double *buf)

{

  if (radvary == 0) return 0;



  radius[i] = buf[0];

  rmass[i] = buf[1];

  return 2;

}



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

src/GRANULAR/atom_vec_granular.h

+4 −0
Original line number Diff line number Diff line
@@ -28,13 +28,16 @@ class AtomVecGranular : public AtomVec { 
 public:

  AtomVecGranular(class LAMMPS *, int, char **);

  ~AtomVecGranular() {}

  void init();

  void grow(int);

  void grow_reset();

  void copy(int, int);

  int pack_comm(int, int *, double *, int, int *);

  int pack_comm_vel(int, int *, double *, int, int *);

  int pack_comm_one(int, double *);

  void unpack_comm(int, int, double *);

  void unpack_comm_vel(int, int, double *);

  int unpack_comm_one(int, double *);

  int pack_reverse(int, int, double *);

  int pack_reverse_one(int, double *);

  void unpack_reverse(int, int *, double *);
@@ -63,6 +66,7 @@ class AtomVecGranular : public AtomVec { 
  double **x,**v,**f;

  double *radius,*density,*rmass;

  double **omega,**torque;

  int radvary;

};



}

src/fix_adapt.cpp

+5 −2
Original line number Diff line number Diff line
@@ -71,6 +71,7 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) 


  // parse keywords



  diamflag = 0;

  nadapt = 0;



  iarg = 4;
@@ -99,6 +100,7 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) 
      int n = strlen(arg[iarg+1]) + 1;

      param[nadapt] = new char[n];

      strcpy(param[nadapt],arg[iarg+1]);

      if (strcmp(param[nadapt],"diameter") == 0) diamflag = 1;

      if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {

	n = strlen(&arg[iarg+2][2]) + 1;

	var[nadapt] = new char[n];
@@ -201,7 +203,7 @@ void FixAdapt::pre_force(int vflag) 
    else if (which[m] == ATOM) {



      // set radius from diameter

      // set rmass if both rmass and density are defined

      // also set rmass if both rmass and density are defined



      if (awhich[m] == DIAMETER) {

	int mflag = 0;
@@ -217,7 +219,8 @@ void FixAdapt::pre_force(int vflag) 
	for (int i = 0; i < nlocal; i++)

	  if (mask[i] & groupbit) {

	    radius[i] = 0.5*value;

	    rmass[i] = 4.0*PI/3.0 * radius[i]*radius[i]*radius[i] * density[i];

	    if (mflag) rmass[i] = 4.0*PI/3.0 * 

			 radius[i]*radius[i]*radius[i] * density[i];

	  }

      }

    }

src/fix_adapt.h

+2 −0
Original line number Diff line number Diff line
@@ -26,6 +26,8 @@ namespace LAMMPS_NS { 


class FixAdapt : public Fix {

 public:

  int diamflag;



  FixAdapt(class LAMMPS *, int, char **);

  ~FixAdapt();

  int setmask();

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