Commit fa7543b7 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14506 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent dca90d44

src/GRANULAR/fix_pour.cpp

+22 −2
Original line number Diff line number Diff line
@@ -156,7 +156,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) : 
  memory->create(coords,natom_max,4,"pour:coords");

  memory->create(imageflags,natom_max,"pour:imageflags");



  // find current max atom and molecule IDs if necessary

  // find max atom and molecule IDs just once



  if (idnext) find_maxid();
@@ -385,7 +385,7 @@ void FixPour::pre_exchange() 
  atom->nghost = 0;

  atom->avec->clear_bonus();



  // find current max atom and molecule IDs if necessary

  // find current max atom and molecule IDs on every insertion step



  if (!idnext) find_maxid();
@@ -737,12 +737,19 @@ void FixPour::find_maxid() 
   return 1 if yes, 0 if no

   for ATOM mode, use delta with maximum size for inserted atoms

   for MOLECULE mode, use delta with max radius of inserted molecules

   if ignore line/tri set, ignore line or tri particles

   account for PBC in overlap decision via outside() and minimum_image()

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



int FixPour::overlap(int i)

{

  double delta;



  if (ignoreflag) {

    if (ignoreline && atom->line[i] >= 0) return 0;

    if (ignoretri && atom->tri[i] >= 0) return 0;

  }



  if (mode == ATOM) delta = atom->radius[i] + radius_max;

  else delta = atom->radius[i] + molradius_max;
@@ -860,6 +867,7 @@ void FixPour::options(int narg, char **arg) 
  shakeflag = 0;

  idshake = NULL;

  idnext = 0;

  ignoreflag = ignoreline = ignoretri = 0;

  dstyle = ONE;

  radius_max = radius_one = 0.5;

  radius_poly = frac_poly = NULL;
@@ -925,6 +933,13 @@ void FixPour::options(int narg, char **arg) 
      else if (strcmp(arg[iarg+1],"next") == 0) idnext = 1;

      else error->all(FLERR,"Illegal fix pour command");

      iarg += 2;



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

      if (atom->line_flag) ignoreline = 1;

      if (atom->tri_flag) ignoretri = 1;

      if (ignoreline || ignoretri) ignoreflag = 1;

      iarg += 1;



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

      if (iarg+2 > narg) error->all(FLERR,"Illegal fix pour command");

      if (strcmp(arg[iarg+1],"one") == 0) {
@@ -938,6 +953,7 @@ void FixPour::options(int narg, char **arg) 
        dstyle = RANGE;

        radius_lo = 0.5 * force->numeric(FLERR,arg[iarg+2]);

        radius_hi = 0.5 * force->numeric(FLERR,arg[iarg+3]);

        if (radius_lo > radius_hi) error->all(FLERR,"Illegal fix pour command");

        radius_max = radius_hi;

        iarg += 4;

      } else if (strcmp(arg[iarg+1],"poly") == 0) {
@@ -968,6 +984,7 @@ void FixPour::options(int narg, char **arg) 
      if (iarg+3 > narg) error->all(FLERR,"Illegal fix pour command");

      density_lo = force->numeric(FLERR,arg[iarg+1]);

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

      if (density_lo > density_hi) error->all(FLERR,"Illegal fix pour command");

      iarg += 3;

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

      if (iarg+3 > narg) error->all(FLERR,"Illegal fix pour command");
@@ -985,6 +1002,8 @@ void FixPour::options(int narg, char **arg) 
        vxhi = force->numeric(FLERR,arg[iarg+2]);

        vylo = force->numeric(FLERR,arg[iarg+3]);

        vyhi = force->numeric(FLERR,arg[iarg+4]);

        if (vxlo > vxhi || vylo > vyhi) 

          error->all(FLERR,"Illegal fix pour command");

        vz = force->numeric(FLERR,arg[iarg+5]);

        iarg += 6;

      } else {
@@ -993,6 +1012,7 @@ void FixPour::options(int narg, char **arg) 
        vxhi = force->numeric(FLERR,arg[iarg+2]);

        vy = force->numeric(FLERR,arg[iarg+3]);

        vz = 0.0;

        if (vxlo > vxhi) error->all(FLERR,"Illegal fix pour command");

        iarg += 4;

      }

    } else error->all(FLERR,"Illegal fix pour command");

src/atom_vec_tri.cpp

+88 −24
Original line number Diff line number Diff line
@@ -41,7 +41,7 @@ AtomVecTri::AtomVecTri(LAMMPS *lmp) : AtomVec(lmp) 
  size_forward = 7;

  size_reverse = 6;

  size_border = 26;

  size_velocity = 6;

  size_velocity = 9;

  size_data_atom = 8;

  size_data_vel = 7;

  size_data_bonus = 10;
@@ -49,7 +49,9 @@ AtomVecTri::AtomVecTri(LAMMPS *lmp) : AtomVec(lmp) 


  atom->tri_flag = 1;

  atom->molecule_flag = atom->rmass_flag = 1;

  atom->radius_flag = atom->angmom_flag = atom->torque_flag = 1;

  atom->radius_flag = atom->omega_flag = atom->angmom_flag = 1;

  atom->torque_flag = 1;

  atom->sphere_flag = 1;



  nlocal_bonus = nghost_bonus = nmax_bonus = 0;

  bonus = NULL;
@@ -100,6 +102,7 @@ void AtomVecTri::grow(int n) 
  molecule = memory->grow(atom->molecule,nmax,"atom:molecule");

  rmass = memory->grow(atom->rmass,nmax,"atom:rmass");

  radius = memory->grow(atom->radius,nmax,"atom:radius");

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

  angmom = memory->grow(atom->angmom,nmax,3,"atom:angmom");

  torque = memory->grow(atom->torque,nmax*comm->nthreads,3,"atom:torque");

  tri = memory->grow(atom->tri,nmax,"atom:tri");
@@ -119,7 +122,8 @@ void AtomVecTri::grow_reset() 
  mask = atom->mask; image = atom->image;

  x = atom->x; v = atom->v; f = atom->f;

  molecule = atom->molecule; rmass = atom->rmass;

  radius = atom->radius; angmom = atom->angmom; torque = atom->torque;

  radius = atom->radius; omega = atom->omega;

  angmom = atom->angmom; torque = atom->torque;

  tri = atom->tri;

}
@@ -158,6 +162,9 @@ void AtomVecTri::copy(int i, int j, int delflag) 
  molecule[j] = molecule[i];

  rmass[j] = rmass[i];

  radius[j] = radius[i];

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

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

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

  angmom[j][0] = angmom[i][0];

  angmom[j][1] = angmom[i][1];

  angmom[j][2] = angmom[i][2];
@@ -343,6 +350,9 @@ int AtomVecTri::pack_comm_vel(int n, int *list, double *buf, 
      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];

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

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

      buf[m++] = angmom[j][2];
@@ -373,6 +383,9 @@ int AtomVecTri::pack_comm_vel(int n, int *list, double *buf, 
        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];

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

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

        buf[m++] = angmom[j][2];
@@ -402,6 +415,9 @@ int AtomVecTri::pack_comm_vel(int n, int *list, double *buf, 
          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];

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

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

        buf[m++] = angmom[j][2];
@@ -479,6 +495,9 @@ void AtomVecTri::unpack_comm_vel(int n, int first, double *buf) 
    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++];

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

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

    angmom[i][2] = buf[m++];
@@ -728,6 +747,9 @@ int AtomVecTri::pack_border_vel(int n, int *list, double *buf, 
      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];

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

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

      buf[m++] = angmom[j][2];
@@ -782,6 +804,9 @@ int AtomVecTri::pack_border_vel(int n, int *list, double *buf, 
        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];

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

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

        buf[m++] = angmom[j][2];
@@ -835,6 +860,9 @@ int AtomVecTri::pack_border_vel(int n, int *list, double *buf, 
          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];

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

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

        buf[m++] = angmom[j][2];
@@ -1002,6 +1030,9 @@ void AtomVecTri::unpack_border_vel(int n, int first, double *buf) 
    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++];

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

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

    angmom[i][2] = buf[m++];
@@ -1082,6 +1113,9 @@ int AtomVecTri::pack_exchange(int i, double *buf) 
  buf[m++] = ubuf(molecule[i]).d;

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

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

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

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

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

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

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

  buf[m++] = angmom[i][2];
@@ -1143,6 +1177,9 @@ int AtomVecTri::unpack_exchange(double *buf) 
  molecule[nlocal] = (tagint) ubuf(buf[m++]).i;

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

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

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

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

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

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

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

  angmom[nlocal][2] = buf[m++];
@@ -1197,8 +1234,8 @@ int AtomVecTri::size_restart() 
  int n = 0;

  int nlocal = atom->nlocal;

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

    if (tri[i] >= 0) n += 34;

    else n += 18;

    if (tri[i] >= 0) n += 37;

    else n += 21;



  if (atom->nextra_restart)

    for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
@@ -1231,6 +1268,9 @@ int AtomVecTri::pack_restart(int i, double *buf) 
  buf[m++] = ubuf(molecule[i]).d;

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

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

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

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

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

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

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

  buf[m++] = angmom[i][2];
@@ -1298,6 +1338,9 @@ int AtomVecTri::unpack_restart(double *buf) 
  molecule[nlocal] = (tagint) ubuf(buf[m++]).i;

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

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

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

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

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

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

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

  angmom[nlocal][2] = buf[m++];
@@ -1366,6 +1409,9 @@ void AtomVecTri::create_atom(int itype, double *coord) 
  molecule[nlocal] = 0;

  radius[nlocal] = 0.5;

  rmass[nlocal] = 4.0*MY_PI/3.0 * radius[nlocal]*radius[nlocal]*radius[nlocal];

  omega[nlocal][0] = 0.0;

  omega[nlocal][1] = 0.0;

  omega[nlocal][2] = 0.0;

  angmom[nlocal][0] = 0.0;

  angmom[nlocal][1] = 0.0;

  angmom[nlocal][2] = 0.0;
@@ -1415,6 +1461,9 @@ void AtomVecTri::data_atom(double *coord, imageint imagetmp, char **values) 
  v[nlocal][0] = 0.0;

  v[nlocal][1] = 0.0;

  v[nlocal][2] = 0.0;

  omega[nlocal][0] = 0.0;

  omega[nlocal][1] = 0.0;

  omega[nlocal][2] = 0.0;

  angmom[nlocal][0] = 0.0;

  angmom[nlocal][1] = 0.0;

  angmom[nlocal][2] = 0.0;
@@ -1591,21 +1640,27 @@ void AtomVecTri::data_vel(int m, char **values) 
  v[m][0] = atof(values[0]);

  v[m][1] = atof(values[1]);

  v[m][2] = atof(values[2]);

  angmom[m][0] = atof(values[3]);

  angmom[m][1] = atof(values[4]);

  angmom[m][2] = atof(values[5]);

  omega[m][0] = atof(values[3]);

  omega[m][1] = atof(values[4]);

  omega[m][2] = atof(values[5]);

  angmom[m][0] = atof(values[6]);

  angmom[m][1] = atof(values[7]);

  angmom[m][2] = atof(values[8]);

}



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

   unpack hybrid quantities from one tri in Velocities section of data file

   unpack hybrid quantities from one line in Velocities section of data file

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



int AtomVecTri::data_vel_hybrid(int m, char **values)

{

  angmom[m][0] = atof(values[0]);

  angmom[m][1] = atof(values[1]);

  angmom[m][2] = atof(values[2]);

  return 3;

  omega[m][0] = atof(values[0]);

  omega[m][1] = atof(values[1]);

  omega[m][2] = atof(values[2]);

  angmom[m][0] = atof(values[3]);

  angmom[m][1] = atof(values[4]);

  angmom[m][2] = atof(values[5]);

  return 6;

}



/* ----------------------------------------------------------------------
@@ -1703,9 +1758,12 @@ void AtomVecTri::pack_vel(double **buf) 
    buf[i][1] = v[i][0];

    buf[i][2] = v[i][1];

    buf[i][3] = v[i][2];

    buf[i][4] = angmom[i][0];

    buf[i][5] = angmom[i][1];

    buf[i][6] = angmom[i][2];

    buf[i][4] = omega[i][0];

    buf[i][5] = omega[i][1];

    buf[i][6] = omega[i][2];

    buf[i][7] = angmom[i][0];

    buf[i][8] = angmom[i][1];

    buf[i][9] = angmom[i][2];

  }

}
@@ -1715,10 +1773,13 @@ void AtomVecTri::pack_vel(double **buf) 


int AtomVecTri::pack_vel_hybrid(int i, double *buf)

{

  buf[0] = angmom[i][0];

  buf[1] = angmom[i][1];

  buf[2] = angmom[i][2];

  return 3;

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

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

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

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

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

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

  return 6;

}



/* ----------------------------------------------------------------------
@@ -1729,9 +1790,10 @@ void AtomVecTri::write_vel(FILE *fp, int n, double **buf) 
{

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

    fprintf(fp,TAGINT_FORMAT

            " %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e\n",

            " %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e "

            "%-1.16e %-1.16e %-1.16e\n",

            (tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],

            buf[i][4],buf[i][5],buf[i][6]);

            buf[i][4],buf[i][5],buf[i][6],buf[i][7],buf[i][8],buf[i][9]);

}



/* ----------------------------------------------------------------------
@@ -1740,8 +1802,9 @@ void AtomVecTri::write_vel(FILE *fp, int n, double **buf) 


int AtomVecTri::write_vel_hybrid(FILE *fp, double *buf)

{

  fprintf(fp," %-1.16e %-1.16e %-1.16e",buf[0],buf[1],buf[2]);

  return 3;

  fprintf(fp," %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e",

          buf[0],buf[1],buf[2],buf[3],buf[4],buf[5]);

  return 6;

}



/* ----------------------------------------------------------------------
@@ -1763,6 +1826,7 @@ bigint AtomVecTri::memory_usage() 
  if (atom->memcheck("molecule")) bytes += memory->usage(molecule,nmax);

  if (atom->memcheck("rmass")) bytes += memory->usage(rmass,nmax);

  if (atom->memcheck("radius")) bytes += memory->usage(radius,nmax);

  if (atom->memcheck("omega")) bytes += memory->usage(omega,nmax,3);

  if (atom->memcheck("angmom")) bytes += memory->usage(angmom,nmax,3);

  if (atom->memcheck("torque")) bytes +=

                                  memory->usage(torque,nmax*comm->nthreads,3);

src/atom_vec_tri.h

+1 −1
Original line number Diff line number Diff line
@@ -92,7 +92,7 @@ class AtomVecTri : public AtomVec { 
  double **x,**v,**f;

  tagint *molecule;

  double *rmass,*radius;

  double **angmom,**torque;

  double **omega,**angmom,**torque;

  int *tri;



  int nlocal_bonus,nghost_bonus,nmax_bonus;

src/displace_atoms.cpp

+9 −5
Original line number Diff line number Diff line
@@ -232,8 +232,16 @@ void DisplaceAtoms::command(int narg, char **arg) 
    runit[2] = axis[2]/len;



    double angle = MY_PI*theta/180.0;

    double sine = sin(angle);

    double cosine = cos(angle);

    double sine = sin(angle);



    double qcosine = cos(0.5*angle);

    double qsine = sin(0.5*angle);

    qrotate[0] = qcosine;

    qrotate[1] = runit[0]*qsine;

    qrotate[2] = runit[1]*qsine;

    qrotate[3] = runit[2]*qsine;



    double ddotr;



    // flags for additional orientation info stored by some atom styles
@@ -304,10 +312,6 @@ void DisplaceAtoms::command(int narg, char **arg) 
          else if (body_flag && body[i] >= 0)

            quat = avec_body->bonus[body[i]].quat;

          if (quat) {

            qrotate[0] = cosine;

            qrotate[1] = runit[0]*sine;

            qrotate[2] = runit[1]*sine;

            qrotate[3] = runit[2]*sine;

            MathExtra::quatquat(qrotate,quat,qnew);

            quat[0] = qnew[0];

            quat[1] = qnew[1];

src/dump_image.cpp

+17 −3
Original line number Diff line number Diff line
@@ -178,11 +178,13 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) : 
      iarg += 3;



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

      if (iarg+2 > narg) error->all(FLERR,"Illegal dump image command");

      if (iarg+4 > narg) error->all(FLERR,"Illegal dump image command");

      triflag = YES;

      if (strcmp(arg[iarg+1],"type") == 0) tcolor = TYPE;

      else error->all(FLERR,"Illegal dump image command");

      iarg += 2;

      tstyle = force->inumeric(FLERR,arg[iarg+2]);

      tdiamvalue = force->numeric(FLERR,arg[iarg+3]);

      iarg += 4;



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

      if (iarg+4 > narg) error->all(FLERR,"Illegal dump image command");
@@ -806,12 +808,19 @@ void DumpImage::create_image() 
  }



  // render atoms that are triangles

  // tstyle = 1 for tri only, 2 for edges only, 3 for both



  if (triflag) {

    int tridraw = 1;

    if (tstyle == 2) tridraw = 0;

    int edgedraw = 1;

    if (tstyle == 1) edgedraw = 0;



    double **x = atom->x;

    int *tri = atom->tri;

    int *type = atom->type;





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

      j = clist[i];

      if (tri[j] < 0) continue;
@@ -828,7 +837,12 @@ void DumpImage::create_image() 
      MathExtra::add3(pt2,x[i],pt2);

      MathExtra::add3(pt3,x[i],pt3);



      image->draw_triangle(pt1,pt2,pt3,color);

      if (tridraw) image->draw_triangle(pt1,pt2,pt3,color);

      if (edgedraw) {

        image->draw_cylinder(pt1,pt2,color,tdiamvalue,3);

        image->draw_cylinder(pt2,pt3,color,tdiamvalue,3);

        image->draw_cylinder(pt3,pt1,color,tdiamvalue,3);

      }

    }

  }

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