Commit d15f2ee3 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@479 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent c501cef9

src/GRANULAR/atom_vec_granular.cpp

+107 −106
Original line number Diff line number Diff line
@@ -73,12 +73,12 @@ void AtomVecGranular::grow(int n) 
  rmass = atom->rmass = (double *)

    memory->srealloc(atom->rmass,nmax*sizeof(double),"atom:rmass");



  phix = atom->phix = 

    memory->grow_2d_double_array(atom->phix,nmax,3,"atom:phix");

  phiv = atom->phiv = 

    memory->grow_2d_double_array(atom->phiv,nmax,3,"atom:phiv");

  phia = atom->phia =

    memory->grow_2d_double_array(atom->phia,nmax,3,"atom:phia");

  xphi = atom->xphi = 

    memory->grow_2d_double_array(atom->xphi,nmax,3,"atom:xphi");

  omega = atom->omega = 

    memory->grow_2d_double_array(atom->omega,nmax,3,"atom:omega");

  torque = atom->torque =

    memory->grow_2d_double_array(atom->torque,nmax,3,"atom:torque");



  if (atom->nextra_grow)

    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
@@ -100,9 +100,9 @@ void AtomVecGranular::reset_ptrs() 
  radius = atom->radius;

  density = atom->density;

  rmass = atom->rmass;

  phix = atom->phix;

  phiv = atom->phiv;

  phia = atom->phia;

  xphi = atom->xphi;

  omega = atom->omega;

  torque = atom->torque;

}



/* ----------------------------------------------------------------------
@@ -115,12 +115,12 @@ void AtomVecGranular::zero_owned(int i) 
  radius[i] = 0.0;

  density[i] = 0.0;

  rmass[i] = 0.0;

  phix[i][0] = 0.0;

  phix[i][1] = 0.0;

  phix[i][2] = 0.0;

  phiv[i][0] = 0.0;

  phiv[i][1] = 0.0;

  phiv[i][2] = 0.0;

  xphi[i][0] = 0.0;

  xphi[i][1] = 0.0;

  xphi[i][2] = 0.0;

  omega[i][0] = 0.0;

  omega[i][1] = 0.0;

  omega[i][2] = 0.0;

}



/* ----------------------------------------------------------------------
@@ -139,9 +139,9 @@ void AtomVecGranular::zero_ghost(int n, int first) 
    v[i][2] = 0.0;

    radius[i] = 0.0;

    rmass[i] = 0.0;

    phiv[i][0] = 0.0;

    phiv[i][1] = 0.0;

    phiv[i][2] = 0.0;

    omega[i][0] = 0.0;

    omega[i][1] = 0.0;

    omega[i][2] = 0.0;

  }

}
@@ -163,12 +163,12 @@ void AtomVecGranular::copy(int i, int j) 
  radius[j] = radius[i];

  density[j] = density[i];

  rmass[j] = rmass[i];

  phix[j][0] = phix[i][0];

  phix[j][1] = phix[i][1];

  phix[j][2] = phix[i][2];

  phiv[j][0] = phiv[i][0];

  phiv[j][1] = phiv[i][1];

  phiv[j][2] = phiv[i][2];

  xphi[j][0] = xphi[i][0];

  xphi[j][1] = xphi[i][1];

  xphi[j][2] = xphi[i][2];

  omega[j][0] = omega[i][0];

  omega[j][1] = omega[i][1];

  omega[j][2] = omega[i][2];



  if (atom->nextra_grow)

    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
@@ -193,9 +193,9 @@ int AtomVecGranular::pack_comm(int n, int *list, double *buf, 
      buf[m++] = v[j][0];

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

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

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

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

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

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

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

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

    }

  } else {

    if (domain->triclinic == 0) {
@@ -215,9 +215,9 @@ int AtomVecGranular::pack_comm(int n, int *list, double *buf, 
      buf[m++] = v[j][0];

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

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

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

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

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

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

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

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

    }

  }

  return m;
@@ -230,9 +230,9 @@ int AtomVecGranular::pack_comm_one(int i, double *buf) 
  buf[0] = v[i][0];

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

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

  buf[3] = phiv[i][0];

  buf[4] = phiv[i][1];

  buf[5] = phiv[i][2];

  buf[3] = omega[i][0];

  buf[4] = omega[i][1];

  buf[5] = omega[i][2];

  return 6;

}
@@ -251,9 +251,9 @@ void AtomVecGranular::unpack_comm(int n, int first, double *buf) 
    v[i][0] = buf[m++];

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

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

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

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

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

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

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

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

  }

}
@@ -264,9 +264,9 @@ int AtomVecGranular::unpack_comm_one(int i, double *buf) 
  v[i][0] = buf[0];

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

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

  phiv[i][0] = buf[3];

  phiv[i][1] = buf[4];

  phiv[i][2] = buf[5];

  omega[i][0] = buf[3];

  omega[i][1] = buf[4];

  omega[i][2] = buf[5];

  return 6;

}
@@ -282,9 +282,9 @@ int AtomVecGranular::pack_reverse(int n, int first, double *buf) 
    buf[m++] = f[i][0];

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

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

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

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

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

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

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

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

  }

  return m;

}
@@ -293,9 +293,9 @@ int AtomVecGranular::pack_reverse(int n, int first, double *buf) 


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

{

  buf[0] = phia[i][0];

  buf[1] = phia[i][1];

  buf[2] = phia[i][2];

  buf[0] = torque[i][0];

  buf[1] = torque[i][1];

  buf[2] = torque[i][2];

  return 3;

}
@@ -311,9 +311,9 @@ void AtomVecGranular::unpack_reverse(int n, int *list, double *buf) 
    f[j][0] += buf[m++];

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

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

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

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

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

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

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

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

  }

}
@@ -321,9 +321,9 @@ void AtomVecGranular::unpack_reverse(int n, int *list, double *buf) 


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

{

  phia[i][0] = buf[0];

  phia[i][1] = buf[1];

  phia[i][2] = buf[2];

  torque[i][0] = buf[0];

  torque[i][1] = buf[1];

  torque[i][2] = buf[2];

  return 3;

}
@@ -350,9 +350,9 @@ int AtomVecGranular::pack_border(int n, int *list, double *buf, 
      buf[m++] = v[j][2];

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

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

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

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

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

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

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

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

    }

  } else {

    if (domain->triclinic == 0) {
@@ -377,9 +377,9 @@ int AtomVecGranular::pack_border(int n, int *list, double *buf, 
      buf[m++] = v[j][2];

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

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

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

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

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

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

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

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

    }

  }

  return m;
@@ -394,9 +394,9 @@ int AtomVecGranular::pack_border_one(int i, double *buf) 
  buf[2] = v[i][2];

  buf[3] = radius[i];

  buf[4] = rmass[i];

  buf[5] = phiv[i][0];

  buf[6] = phiv[i][1];

  buf[7] = phiv[i][2];

  buf[5] = omega[i][0];

  buf[6] = omega[i][1];

  buf[7] = omega[i][2];

  return 8;

}
@@ -421,9 +421,9 @@ void AtomVecGranular::unpack_border(int n, int first, double *buf) 
    v[i][2] = buf[m++];

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

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

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

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

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

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

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

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

  }

}
@@ -436,9 +436,9 @@ int AtomVecGranular::unpack_border_one(int i, double *buf) 
  v[i][2] = buf[2];

  radius[i] = buf[3];

  rmass[i] = buf[4];

  phiv[i][0] = buf[5];

  phiv[i][1] = buf[6];

  phiv[i][2] = buf[7];

  omega[i][0] = buf[5];

  omega[i][1] = buf[6];

  omega[i][2] = buf[7];

  return 8;

}
@@ -464,12 +464,12 @@ int AtomVecGranular::pack_exchange(int i, double *buf) 
  buf[m++] = radius[i];

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

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

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

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

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

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

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

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

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

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

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

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

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

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



  if (atom->nextra_grow)

    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
@@ -501,12 +501,12 @@ int AtomVecGranular::unpack_exchange(double *buf) 
  radius[nlocal] = buf[m++];

  density[nlocal] = buf[m++];

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

  phix[nlocal][0] = buf[m++];

  phix[nlocal][1] = buf[m++];

  phix[nlocal][2] = buf[m++];

  phiv[nlocal][0] = buf[m++];

  phiv[nlocal][1] = buf[m++];

  phiv[nlocal][2] = buf[m++];

  xphi[nlocal][0] = buf[m++];

  xphi[nlocal][1] = buf[m++];

  xphi[nlocal][2] = buf[m++];

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

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

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



  if (atom->nextra_grow)

    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
@@ -569,12 +569,12 @@ int AtomVecGranular::pack_restart(int i, double *buf) 


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

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

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

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

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

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

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

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

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

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

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

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

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

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



  if (atom->nextra_restart)

    for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
@@ -619,12 +619,12 @@ int AtomVecGranular::unpack_restart(double *buf) 
  else

    rmass[nlocal] = PI * radius[nlocal]*radius[nlocal] * density[nlocal];



  phix[nlocal][0] = buf[m++];

  phix[nlocal][1] = buf[m++];

  phix[nlocal][2] = buf[m++];

  phiv[nlocal][0] = buf[m++];

  phiv[nlocal][1] = buf[m++];

  phiv[nlocal][2] = buf[m++];

  xphi[nlocal][0] = buf[m++];

  xphi[nlocal][1] = buf[m++];

  xphi[nlocal][2] = buf[m++];

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

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

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



  double **extra = atom->extra;

  if (atom->nextra_store) {
@@ -664,12 +664,12 @@ void AtomVecGranular::create_atom(int itype, double *coord, int ihybrid) 
      radius[nlocal]*radius[nlocal]*radius[nlocal] * density[nlocal];

  else

    rmass[nlocal] = PI * radius[nlocal]*radius[nlocal] * density[nlocal];

  phix[nlocal][0] = 0.0;

  phix[nlocal][1] = 0.0;

  phix[nlocal][2] = 0.0;

  phiv[nlocal][0] = 0.0;

  phiv[nlocal][1] = 0.0;

  phiv[nlocal][2] = 0.0;

  xphi[nlocal][0] = 0.0;

  xphi[nlocal][1] = 0.0;

  xphi[nlocal][2] = 0.0;

  omega[nlocal][0] = 0.0;

  omega[nlocal][1] = 0.0;

  omega[nlocal][2] = 0.0;



  atom->nlocal++;

}
@@ -711,12 +711,12 @@ void AtomVecGranular::data_atom(double *coord, int imagetmp, char **values, 
  v[nlocal][0] = 0.0;

  v[nlocal][1] = 0.0;

  v[nlocal][2] = 0.0;

  phix[nlocal][0] = 0.0;

  phix[nlocal][1] = 0.0;

  phix[nlocal][2] = 0.0;

  phiv[nlocal][0] = 0.0;

  phiv[nlocal][1] = 0.0;

  phiv[nlocal][2] = 0.0;

  xphi[nlocal][0] = 0.0;

  xphi[nlocal][1] = 0.0;

  xphi[nlocal][2] = 0.0;

  omega[nlocal][0] = 0.0;

  omega[nlocal][1] = 0.0;

  omega[nlocal][2] = 0.0;



  atom->nlocal++;

}
@@ -729,7 +729,8 @@ void AtomVecGranular::data_vel(int m, char *line, int ihybrid) 
{

  int tmp;

  sscanf(line,"%d %lg %lg %lg %lg %lg %lg",

	 &tmp,&v[m][0],&v[m][1],&v[m][2],&phiv[m][0],&phiv[m][1],&phiv[m][2]);

	 &tmp,&v[m][0],&v[m][1],&v[m][2],

	 &omega[m][0],&omega[m][1],&omega[m][2]);

}



/* ----------------------------------------------------------------------
@@ -751,9 +752,9 @@ int AtomVecGranular::memory_usage() 
  if (atom->memcheck("radius")) bytes += nmax * sizeof(double);

  if (atom->memcheck("density")) bytes += nmax * sizeof(double);

  if (atom->memcheck("rmass")) bytes += nmax * sizeof(double);

  if (atom->memcheck("phix")) bytes += nmax*3 * sizeof(double);

  if (atom->memcheck("phiv")) bytes += nmax*3 * sizeof(double);

  if (atom->memcheck("phia")) bytes += nmax*3 * sizeof(double);

  if (atom->memcheck("xphi")) bytes += nmax*3 * sizeof(double);

  if (atom->memcheck("omega")) bytes += nmax*3 * sizeof(double);

  if (atom->memcheck("torque")) bytes += nmax*3 * sizeof(double);



  return bytes;

}

src/GRANULAR/atom_vec_granular.h

+1 −1
Original line number Diff line number Diff line
@@ -55,7 +55,7 @@ class AtomVecGranular : public AtomVec { 
  int *tag,*type,*mask,*image;

  double **x,**v,**f;

  double *radius,*density,*rmass;

  double **phix,**phiv,**phia;

  double **xphi,**omega,**torque;

};



}

src/GRANULAR/fix_freeze.cpp

+5 −4
Original line number Diff line number Diff line
@@ -45,6 +45,7 @@ int FixFreeze::setmask() 
void FixFreeze::init()

{

  // error if more than one freeze fix

  // because accessed by pair style granular and fix gran/diag



  int count = 0;

  for (int i = 0; i < modify->nfix; i++)
@@ -64,7 +65,7 @@ void FixFreeze::setup() 
void FixFreeze::post_force(int vflag)

{

  double **f = atom->f;

  double **phia = atom->phia;

  double **torque = atom->torque;

  int *mask = atom->mask;

  int nlocal = atom->nlocal;
@@ -73,8 +74,8 @@ void FixFreeze::post_force(int vflag) 
      f[i][0] = 0.0;

      f[i][1] = 0.0;

      f[i][2] = 0.0;

      phia[i][0] = 0.0;

      phia[i][1] = 0.0;

      phia[i][2] = 0.0;

      torque[i][0] = 0.0;

      torque[i][1] = 0.0;

      torque[i][2] = 0.0;

    }

}

src/GRANULAR/fix_gran_diag.cpp

+12 −12
Original line number Diff line number Diff line
@@ -467,7 +467,7 @@ void FixGranDiag::stress_no_history() 


  double **x = atom->x;

  double **v = atom->v;

  double **phiv = atom->phiv;

  double **omega = atom->omega;

  double *radius = atom->radius;

  double *rmass = atom->rmass;

  int *mask = atom->mask;
@@ -528,9 +528,9 @@ void FixGranDiag::stress_no_history() 


	//  relative rotational velocity



	wr1 = radi*phiv[i][0] + radj*phiv[j][0];

	wr2 = radi*phiv[i][1] + radj*phiv[j][1];

	wr3 = radi*phiv[i][2] + radj*phiv[j][2];

	wr1 = radi*omega[i][0] + radj*omega[j][0];

	wr2 = radi*omega[i][1] + radj*omega[j][1];

	wr3 = radi*omega[i][2] + radj*omega[j][2];



	wr1 *= dt/r;

	wr2 *= dt/r;
@@ -620,7 +620,7 @@ void FixGranDiag::stress_history() 


  double **x = atom->x;

  double **v = atom->v;

  double **phiv = atom->phiv;

  double **omega = atom->omega;

  double *radius = atom->radius;

  double *rmass = atom->rmass;

  int *mask = atom->mask;
@@ -682,9 +682,9 @@ void FixGranDiag::stress_history() 


	//  relative rotational velocity



	wr1 = radi*phiv[i][0] + radj*phiv[j][0];

	wr2 = radi*phiv[i][1] + radj*phiv[j][1];

	wr3 = radi*phiv[i][2] + radj*phiv[j][2];

	wr1 = radi*omega[i][0] + radj*omega[j][0];

	wr2 = radi*omega[i][1] + radj*omega[j][1];

	wr3 = radi*omega[i][2] + radj*omega[j][2];



	wr1 *= dt/r;

	wr2 *= dt/r;
@@ -803,7 +803,7 @@ void FixGranDiag::stress_hertzian() 


  double **x = atom->x;

  double **v = atom->v;

  double **phiv = atom->phiv;

  double **omega = atom->omega;

  double *radius = atom->radius;

  double *rmass = atom->rmass;

  int *mask = atom->mask;
@@ -865,9 +865,9 @@ void FixGranDiag::stress_hertzian() 


	//  relative rotational velocity



	wr1 = radi*phiv[i][0] + radj*phiv[j][0];

	wr2 = radi*phiv[i][1] + radj*phiv[j][1];

	wr3 = radi*phiv[i][2] + radj*phiv[j][2];

	wr1 = radi*omega[i][0] + radj*omega[j][0];

	wr2 = radi*omega[i][1] + radj*omega[j][1];

	wr3 = radi*omega[i][2] + radj*omega[j][2];



	wr1 *= dt/r;

	wr2 *= dt/r;

src/GRANULAR/fix_nve_gran.cpp

+16 −18
Original line number Diff line number Diff line
@@ -53,10 +53,8 @@ void FixNVEGran::init() 
{

  dtv = update->dt;

  dtf = 0.5 * update->dt * force->ftm2v;

  if (force->dimension == 3)

    dtfphi = 0.5 * update->dt * force->ftm2v / INERTIA3D;

  else

    dtfphi = 0.5 * update->dt * force->ftm2v / INERTIA2D;

  if (force->dimension == 3) dtfphi = dtf / INERTIA3D;

  else dtfphi = dtf / INERTIA2D;

}



/* ---------------------------------------------------------------------- */
@@ -68,9 +66,9 @@ void FixNVEGran::initial_integrate() 
  double **x = atom->x;

  double **v = atom->v;

  double **f = atom->f;

  double **phix = atom->phix;

  double **phiv = atom->phiv;

  double **phia = atom->phia;

  double **xphi = atom->xphi;

  double **omega = atom->omega;

  double **torque = atom->torque;

  double *rmass = atom->rmass;

  double *radius = atom->radius;

  int *mask = atom->mask;
@@ -86,12 +84,12 @@ void FixNVEGran::initial_integrate() 
      x[i][1] += dtv * v[i][1];

      x[i][2] += dtv * v[i][2];

      dtfm = dtfphi / (radius[i]*radius[i]*rmass[i]);

      phiv[i][0] += dtfm * phia[i][0];

      phiv[i][1] += dtfm * phia[i][1];

      phiv[i][2] += dtfm * phia[i][2];

      phix[i][0] += dtv * phiv[i][0];

      phix[i][1] += dtv * phiv[i][1];

      phix[i][2] += dtv * phiv[i][2];

      omega[i][0] += dtfm * torque[i][0];

      omega[i][1] += dtfm * torque[i][1];

      omega[i][2] += dtfm * torque[i][2];

      xphi[i][0] += dtv * omega[i][0];

      xphi[i][1] += dtv * omega[i][1];

      xphi[i][2] += dtv * omega[i][2];

    }

  }

}
@@ -104,8 +102,8 @@ void FixNVEGran::final_integrate() 


  double **v = atom->v;

  double **f = atom->f;

  double **phiv = atom->phiv;

  double **phia = atom->phia;

  double **omega = atom->omega;

  double **torque = atom->torque;

  double *rmass = atom->rmass;

  double *radius = atom->radius;

  int *mask = atom->mask;
@@ -118,9 +116,9 @@ void FixNVEGran::final_integrate() 
      v[i][1] += dtfm * f[i][1];

      v[i][2] += dtfm * f[i][2];

      dtfm = dtfphi / (radius[i]*radius[i]*rmass[i]);

      phiv[i][0] += dtfm * phia[i][0];

      phiv[i][1] += dtfm * phia[i][1];

      phiv[i][2] += dtfm * phia[i][2];

      omega[i][0] += dtfm * torque[i][0];

      omega[i][1] += dtfm * torque[i][1];

      omega[i][2] += dtfm * torque[i][2];

    }

  }

}

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