Commit af4e49a5 authored by Dan S. Bolintineanu's avatar Dan S. Bolintineanu
Browse files

Merge branch 'rigid-gravity' of github.com:lammps/lammps into rigid-gravity

parents a6a35427 5859b18d

src/RIGID/fix_rigid.cpp

+52 −10
Original line number Diff line number Diff line
@@ -52,8 +52,8 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) : 
  torque(NULL), quat(NULL), imagebody(NULL), fflag(NULL),

  tflag(NULL), langextra(NULL), sum(NULL), all(NULL),

  remapflag(NULL), xcmimage(NULL), eflags(NULL), orient(NULL),

  dorient(NULL), id_dilate(NULL), random(NULL), avec_ellipsoid(NULL),

  avec_line(NULL), avec_tri(NULL)

  dorient(NULL), id_dilate(NULL), id_gravity(NULL), random(NULL), 

  avec_ellipsoid(NULL), avec_line(NULL), avec_tri(NULL)

{

  int i,ibody;
@@ -124,14 +124,17 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) : 
    if (custom_flag) {

      if (narg < 5) error->all(FLERR,"Illegal fix rigid command");



      // determine whether atom-style variable or atom property is used.

      // determine whether atom-style variable or atom property is used



      if (strstr(arg[4],"i_") == arg[4]) {

        int is_double=0;

        int custom_index = atom->find_custom(arg[4]+2,is_double);

        if (custom_index == -1)

          error->all(FLERR,"Fix rigid custom requires previously defined property/atom");

          error->all(FLERR,"Fix rigid custom requires "

                     "previously defined property/atom");

        else if (is_double)

          error->all(FLERR,"Fix rigid custom requires integer-valued property/atom");

          error->all(FLERR,"Fix rigid custom requires "

                     "integer-valued property/atom");

        int minval = INT_MAX;

        int *value = atom->ivector[custom_index];

        for (i = 0; i < nlocal; i++)
@@ -163,12 +166,15 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) : 
          if (mask[i] & groupbit)

            molecule[i] = (tagint)((tagint)value[i] - minval + 1);

        delete[] value;



      } else error->all(FLERR,"Unsupported fix rigid custom property");



    } else {

      if (atom->molecule_flag == 0)

        error->all(FLERR,"Fix rigid molecule requires atom attribute molecule");

      molecule = atom->molecule;

    }



    iarg = 4 + custom_flag;



    tagint maxmol_tag = -1;
@@ -297,6 +303,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) : 
  }



  // number of linear rigid bodies is counted later



  nlinear = 0;



  // parse optional args
@@ -308,12 +315,14 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) : 
  tstat_flag = 0;

  pstat_flag = 0;

  allremap = 1;

  id_dilate = NULL;

  t_chain = 10;

  t_iter = 1;

  t_order = 3;

  p_chain = 10;



  inpfile = NULL;

  id_gravity = NULL;

  id_dilate = NULL;



  pcouple = NONE;

  pstyle = ANISO;
@@ -543,12 +552,20 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) : 
      iarg += 2;



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

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

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

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

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

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

      iarg += 2;



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

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

      delete [] id_gravity;

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

      id_gravity = new char[n];

      strcpy(id_gravity,arg[iarg+1]);

      iarg += 2;



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

  }
@@ -621,6 +638,9 @@ FixRigid::~FixRigid() 


  delete random;

  delete [] inpfile;

  delete [] id_dilate;

  delete [] id_gravity;



  memory->destroy(mol2body);

  memory->destroy(body2mol);
@@ -687,7 +707,7 @@ void FixRigid::init() 
  avec_tri = (AtomVecTri *) atom->style_match("tri");



  // warn if more than one rigid fix

  // if earlyflag, warn if any post-force fixes come after POEMS fix

  // if earlyflag, warn if any post-force fixes come after a rigid fix



  int count = 0;

  for (i = 0; i < modify->nfix; i++)
@@ -701,7 +721,8 @@ void FixRigid::init() 
      if (rflag && (modify->fmask[i] & POST_FORCE) &&

          !modify->fix[i]->rigid_flag) {

        char str[128];

        snprintf(str,128,"Fix %s alters forces after fix rigid",modify->fix[i]->id);

        snprintf(str,128,"Fix %s alters forces after fix rigid",

                 modify->fix[i]->id);

        error->warning(FLERR,str);

      }

    }
@@ -713,12 +734,24 @@ void FixRigid::init() 
    if (strcmp(modify->fix[i]->style,"npt") == 0) break;

    if (strcmp(modify->fix[i]->style,"nph") == 0) break;

  }



  if (i < modify->nfix) {

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

      if (strcmp(modify->fix[j]->style,"rigid") == 0)

        error->all(FLERR,"Rigid fix must come before NPT/NPH fix");

  }



  // add gravity forces based on gravity vector from fix



  if (id_gravity) {

    int ifix = modify->find_fix(id_gravity);

    if (ifix < 0) error->all(FLERR,"Fix rigid cannot find fix gravity ID");

    if (strcmp(modify->fix[ifix]->style,"gravity") != 0) 

      error->all(FLERR,"Fix rigid gravity fix is invalid");

    int tmp;

    gvec = (double *) modify->fix[ifix]->extract("gvec",tmp);

  }



  // timestep info



  dtv = update->dt;
@@ -1061,8 +1094,17 @@ void FixRigid::compute_forces_and_torques() 
    torque[ibody][1] = all[ibody][4] + langextra[ibody][4];

    torque[ibody][2] = all[ibody][5] + langextra[ibody][5];

  }

}



  // add gravity force to COM of each body



  if (id_gravity) {

    for (ibody = 0; ibody < nbody; ibody++) {

      fcm[ibody][0] += gvec[0]*masstotal[ibody];

      fcm[ibody][1] += gvec[1]*masstotal[ibody];

      fcm[ibody][2] += gvec[2]*masstotal[ibody];

    }

  }

}



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

src/RIGID/fix_rigid.h

+5 −1
Original line number Diff line number Diff line
@@ -67,6 +67,7 @@ class FixRigid : public Fix { 
  int triclinic;



  char *inpfile;            // file to read rigid body attributes from



  int rstyle;               // SINGLE,MOLECULE,GROUP

  int setupflag;            // 1 if body properties are setup, else 0

  int earlyflag;            // 1 if forces/torques computed at post_force()
@@ -131,6 +132,9 @@ class FixRigid : public Fix { 
  int dilate_group_bit;      // mask for dilation group

  char *id_dilate;           // group name to dilate



  char *id_gravity;         // ID of fix gravity command to add gravity forces

  double *gvec;             // ptr to gravity vector inside the fix



  class RanMars *random;

  class AtomVecEllipsoid *avec_ellipsoid;

  class AtomVecLine *avec_line;

src/RIGID/fix_rigid_small.cpp

+37 −3
Original line number Diff line number Diff line
@@ -57,7 +57,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) : 
  xcmimage(NULL), displace(NULL), eflags(NULL), orient(NULL), dorient(NULL),

  avec_ellipsoid(NULL), avec_line(NULL), avec_tri(NULL), counts(NULL),

  itensor(NULL), mass_body(NULL), langextra(NULL), random(NULL),

  id_dilate(NULL), onemols(NULL)

  id_dilate(NULL), id_gravity(NULL), onemols(NULL)

{

  int i;
@@ -107,7 +107,8 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) : 
      bodyID = new tagint[nlocal];

      customflag = 1;



      // determine whether atom-style variable or atom property is used.

      // determine whether atom-style variable or atom property is used



      if (strstr(arg[4],"i_") == arg[4]) {

        int is_double=0;

        int custom_index = atom->find_custom(arg[4]+2,is_double);
@@ -356,6 +357,13 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) : 
      p_chain = force->numeric(FLERR,arg[iarg+1]);

      iarg += 2;



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

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

      delete [] id_gravity;

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

      id_gravity = new char[n];

      strcpy(id_gravity,arg[iarg+1]);

      iarg += 2;



    } else error->all(FLERR,"Illegal fix rigid/small command");

  }
@@ -515,6 +523,8 @@ FixRigidSmall::~FixRigidSmall() 


  delete random;

  delete [] inpfile;

  delete [] id_dilate;

  delete [] id_gravity;



  memory->destroy(langextra);

  memory->destroy(mass_body);
@@ -543,6 +553,7 @@ void FixRigidSmall::init() 
  triclinic = domain->triclinic;



  // warn if more than one rigid fix

  // if earlyflag, warn if any post-force fixes come after a rigid fix



  int count = 0;

  for (i = 0; i < modify->nfix; i++)
@@ -575,6 +586,17 @@ void FixRigidSmall::init() 
        error->all(FLERR,"Rigid fix must come before NPT/NPH fix");

  }



  // add gravity forces based on gravity vector from fix



  if (id_gravity) {

    int ifix = modify->find_fix(id_gravity);

    if (ifix < 0) error->all(FLERR,"Fix rigid/small cannot find fix gravity ID");

    if (strcmp(modify->fix[ifix]->style,"gravity") != 0) 

      error->all(FLERR,"Fix rigid/small gravity fix is invalid");

    int tmp;

    gvec = (double *) modify->fix[ifix]->extract("gvec",tmp);

  }



  // timestep info



  dtv = update->dt;
@@ -954,8 +976,20 @@ void FixRigidSmall::compute_forces_and_torques() 
      tcm[2] += langextra[ibody][5];

    }

  }

}



  // add gravity force to COM of each body



  if (id_gravity) {

    double mass;

    for (ibody = 0; ibody < nlocal_body; ibody++) {

      mass = body[ibody].mass;

      fcm = body[ibody].fcm;

      fcm[0] += gvec[0]*mass;

      fcm[1] += gvec[1]*mass;

      fcm[2] += gvec[2]*mass;

    }

  }

}



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

src/RIGID/fix_rigid_small.h

+3 −0
Original line number Diff line number Diff line
@@ -164,6 +164,9 @@ class FixRigidSmall : public Fix { 
  int dilate_group_bit;      // mask for dilation group

  char *id_dilate;           // group name to dilate



  char *id_gravity;         // ID of fix gravity command to add gravity forces

  double *gvec;             // ptr to gravity vector inside the fix



  double p_current[3],p_target[3];



  // molecules added on-the-fly as rigid bodies

src/fix_gravity.cpp

+45 −7
Original line number Diff line number Diff line
@@ -37,7 +37,8 @@ enum{CONSTANT,EQUAL}; 


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

  Fix(lmp, narg, arg),

  mstr(NULL), vstr(NULL), pstr(NULL), tstr(NULL), xstr(NULL), ystr(NULL), zstr(NULL)

  mstr(NULL), vstr(NULL), pstr(NULL), tstr(NULL), 

  xstr(NULL), ystr(NULL), zstr(NULL)

{

  if (narg < 5) error->all(FLERR,"Illegal fix gravity command");
@@ -61,8 +62,10 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) : 
    mstyle = CONSTANT;

  }



  int iarg;



  if (strcmp(arg[4],"chute") == 0) {

    if (narg != 6) error->all(FLERR,"Illegal fix gravity command");

    if (narg < 6) error->all(FLERR,"Illegal fix gravity command");

    style = CHUTE;

    if (strstr(arg[5],"v_") == arg[5]) {

      int n = strlen(&arg[5][2]) + 1;
@@ -73,9 +76,10 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) : 
      vert = force->numeric(FLERR,arg[5]);

      vstyle = CONSTANT;

    }

    iarg = 6;



  } else if (strcmp(arg[4],"spherical") == 0) {

    if (narg != 7) error->all(FLERR,"Illegal fix gravity command");

    if (narg < 7) error->all(FLERR,"Illegal fix gravity command");

    style = SPHERICAL;

    if (strstr(arg[5],"v_") == arg[5]) {

      int n = strlen(&arg[5][2]) + 1;
@@ -95,9 +99,10 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) : 
      theta = force->numeric(FLERR,arg[6]);

      tstyle = CONSTANT;

    }

    iarg = 7;



  } else if (strcmp(arg[4],"vector") == 0) {

    if (narg != 8) error->all(FLERR,"Illegal fix gravity command");

    if (narg < 8) error->all(FLERR,"Illegal fix gravity command");

    style = VECTOR;

    if (strstr(arg[5],"v_") == arg[5]) {

      int n = strlen(&arg[5][2]) + 1;
@@ -126,9 +131,23 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) : 
      zdir = force->numeric(FLERR,arg[7]);

      zstyle = CONSTANT;

    }

    iarg = 8;



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



  // optional keywords



  disable = 0;



  while (iarg < narg) {

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

      disable = 1;

      iarg++;

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

  }



  // initializations



  degree2rad = MY_PI/180.0;

  time_origin = update->ntimestep;
@@ -266,6 +285,12 @@ void FixGravity::post_force(int /*vflag*/) 
    set_acceleration();

  }



  // just exit if application of force is disabled



  if (disable) return;



  // apply gravity force to each particle



  double **x = atom->x;

  double **f = atom->f;

  double *rmass = atom->rmass;
@@ -338,9 +363,9 @@ void FixGravity::set_acceleration() 
    }

  }



  xacc = magnitude*xgrav;

  yacc = magnitude*ygrav;

  zacc = magnitude*zgrav;

  gvec[0] = xacc = magnitude*xgrav;

  gvec[1] = yacc = magnitude*ygrav;

  gvec[2] = zacc = magnitude*zgrav;

}



/* ----------------------------------------------------------------------
@@ -357,3 +382,16 @@ double FixGravity::compute_scalar() 
  }

  return egrav_all;

}



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

   extract current gravity direction vector

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



void *FixGravity::extract(const char *name, int &dim)

{

  if (strcmp(name,"gvec") == 0) {

    dim = 1;

    return (void *) gvec;

  }

  return NULL;

}

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