Commit d0a7e5db authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@785 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent e78440db

src/fix_deform.cpp

+88 −74
Original line number Diff line number Diff line
@@ -205,48 +205,10 @@ FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) 
    else if (set[i].style == VEL) set[i].vel *= map[i];

  }



  // set initial/final values for box size and shape for FINAL,DELTA,SCALE

  // final not possible for VEL,ERATE,TRATE since don't know length of run yet

  // final = initial if no setting



  for (int i = 0; i < 3; i++) {

    set[i].lo_target = set[i].lo_stop = set[i].lo_start = domain->boxlo[i];

    set[i].hi_target = set[i].hi_stop = set[i].hi_start = domain->boxhi[i];



    if (set[i].style == FINAL) {

      set[i].lo_stop = set[i].flo;

      set[i].hi_stop = set[i].fhi;

    } else if (set[i].style == DELTA) {

      set[i].lo_stop = set[i].lo_start + set[i].dlo;

      set[i].hi_stop = set[i].hi_start + set[i].dhi;

    } else if (set[i].style == SCALE) {

      set[i].lo_stop = 0.5*(set[i].lo_start+set[i].hi_start) - 

	0.5*set[i].scale*(set[i].hi_start-set[i].lo_start);

      set[i].hi_stop = 0.5*(set[i].lo_start+set[i].hi_start) + 

	0.5*set[i].scale*(set[i].hi_start-set[i].lo_start);

    }

  }



  for (int i = 3; i < 6; i++) {

    if (i == 5) set[i].tilt_start = domain->xy;

    else if (i == 4) set[i].tilt_start = domain->xz;

    else if (i == 3) set[i].tilt_start = domain->yz;

    set[i].tilt_flip = set[i].tilt_target = 

      set[i].tilt_stop = set[i].tilt_start;



    if (set[i].style == FINAL) {

      set[i].tilt_stop = set[i].ftilt;

    } else if (set[i].style == DELTA) {

      set[i].tilt_stop = set[i].tilt_start + set[i].dtilt;

    }

  }



  // for VOLUME, setup links to other dims

  // fixed, dynamic1,2, vol_start

  // fixed, dynamic1, dynamic2



  for (int i = 0; i < 3; i++) {

    set[i].vol_start = domain->xprd * domain->yprd * domain->zprd;



    if (set[i].style != VOLUME) continue;

    int other1 = (i+1) % 3;

    int other2 = (i+2) % 3;
@@ -282,6 +244,19 @@ FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) 
    }

  }



  // set initial values at time fix deform is issued



  for (int i = 0; i < 3; i++) {

    set[i].lo_initial = domain->boxlo[i];

    set[i].hi_initial = domain->boxhi[i];

  }

  for (int i = 3; i < 6; i++) {

    if (i == 5) set[i].tilt_initial = domain->xy;

    else if (i == 4) set[i].tilt_initial = domain->xz;

    else if (i == 3) set[i].tilt_initial = domain->yz;

    set[i].vol_initial = domain->xprd * domain->yprd * domain->zprd;

  }



  // initial settings

  // reneighboring only forced if flips will occur due to shape changes
@@ -329,15 +304,36 @@ void FixDeform::init() 
  else kspace_flag = 0;



  // elapsed time for entire simulation, including multiple runs if defined

  // cannot be 0.0 since can't deform a finite distance in 0 time



  double delt = (update->endstep - update->beginstep) * update->dt;



  // set final values for box size and shape for VEL,ERATE,TRATE

  // now possible since length of run is known

  // set start/stop values for box size and shape

  // if single run, start is current values

  // if multiple runs enabled via run start/stop settings,

  //   start is value when fix deform was issued

  // if NONE, no need to set



  for (int i = 0; i < 3; i++) {

    if (set[i].style == VEL) {

    if (update->firststep == update->beginstep) {

      set[i].lo_start = domain->boxlo[i];

      set[i].hi_start = domain->boxhi[i];

    } else {

      set[i].lo_start = set[i].lo_initial;

      set[i].hi_start = set[i].hi_initial;

    }



    if (set[i].style == FINAL) {

      set[i].lo_stop = set[i].flo;

      set[i].hi_stop = set[i].fhi;

    } else if (set[i].style == DELTA) {

      set[i].lo_stop = set[i].lo_start + set[i].dlo;

      set[i].hi_stop = set[i].hi_start + set[i].dhi;

    } else if (set[i].style == SCALE) {

      set[i].lo_stop = 0.5*(set[i].lo_start+set[i].hi_start) - 

	0.5*set[i].scale*(set[i].hi_start-set[i].lo_start);

      set[i].hi_stop = 0.5*(set[i].lo_start+set[i].hi_start) + 

	0.5*set[i].scale*(set[i].hi_start-set[i].lo_start);

    } else if (set[i].style == VEL) {

      set[i].lo_stop = set[i].lo_start - 0.5*delt*set[i].vel;

      set[i].hi_stop = set[i].hi_start + 0.5*delt*set[i].vel;

    } else if (set[i].style == ERATE) {
@@ -356,7 +352,21 @@ void FixDeform::init() 
  }



  for (int i = 3; i < 6; i++) {

    if (set[i].style == VEL) {

    if (update->firststep == update->beginstep) {

      if (i == 5) set[i].tilt_start = domain->xy;

      else if (i == 4) set[i].tilt_start = domain->xz;

      else if (i == 3) set[i].tilt_start = domain->yz;

      set[i].vol_start = domain->xprd * domain->yprd * domain->zprd;

    } else {

      set[i].tilt_start = set[i].tilt_initial;

      set[i].vol_start = set[i].vol_initial;

    }



    if (set[i].style == FINAL) {

      set[i].tilt_stop = set[i].ftilt;

    } else if (set[i].style == DELTA) {

      set[i].tilt_stop = set[i].tilt_start + set[i].dtilt;

    } else if (set[i].style == VEL) {

      set[i].tilt_stop = set[i].tilt_start + delt*set[i].vel;

    } else if (set[i].style == ERATE) {

      if (i == 3) set[i].tilt_stop = set[i].tilt_start +
@@ -373,10 +383,7 @@ void FixDeform::init() 
  // if using tilt TRATE, then initial tilt must be non-zero



  for (int i = 3; i < 6; i++)

    if (set[i].style == TRATE)

      if ((i == 5 && domain->xy == 0.0) || 

	  (i == 4 && domain->xz == 0.0) || 

	  (i == 3 && domain->yz == 0.0)) 

    if (set[i].style == TRATE && set[i].tilt_start == 0.0)

      error->all("Cannot use fix deform trate on a box with zero tilt");



  // if yz changes and will cause box flip, then xy cannot be changing
@@ -384,16 +391,21 @@ void FixDeform::init() 
  //   in order to keep the edge vectors of the flipped shape matrix

  //   a linear combination of the edge vectors of the unflipped shape matrix



  if (set[3].style && set[5].style)

  if (set[3].style && set[5].style) {

    int flag = 0;

    if (set[3].tilt_stop < -0.5*(set[1].hi_start-set[1].lo_start) ||

	set[3].tilt_stop > 0.5*(set[1].hi_start-set[1].lo_start) ||

	set[3].tilt_stop < -0.5*(set[1].hi_stop-set[1].lo_stop) ||

	set[3].tilt_stop > 0.5*(set[1].hi_stop-set[1].lo_stop))

	set[3].tilt_stop > 0.5*(set[1].hi_start-set[1].lo_start)) flag = 1;

    if (set[1].style) {

      if (set[3].tilt_stop < -0.5*(set[1].hi_stop-set[1].lo_stop) ||

	  set[3].tilt_stop > 0.5*(set[1].hi_stop-set[1].lo_stop)) flag = 1;

    }

    if (flag)

      error->all("Fix deform is changing yz by too much with changing xy");

  }



  // set domain->h_rate values for use by domain and other fixes/computes

  // initialize all rates to 0.0

  // cannot set h_rate now for TRATE,VOLUME styles since not constant

  // cannot set h_rate for TRATE,VOLUME styles since not constant



  h_rate = domain->h_rate;

  h_ratelo = domain->h_ratelo;
@@ -483,11 +495,10 @@ void FixDeform::end_of_step() 


  // set new box size

  // for TRATE, set target directly based on current time and set h_rate

  // for NONE, target is current box size

  // for others except VOLUME, target is linear value between start and stop



  for (i = 0; i < 3; i++) {

    if (set[i].style == NONE) continue;



    if (set[i].style == TRATE) {

      double delt = (update->ntimestep - update->beginstep) * update->dt;

      set[i].lo_target = 0.5*(set[i].lo_start+set[i].hi_start) -
@@ -496,7 +507,9 @@ void FixDeform::end_of_step() 
	0.5*((set[i].hi_start-set[i].lo_start)*pow(1.0+set[i].rate,delt));

      h_rate[i] = set[i].rate * domain->h[i];

      h_ratelo[i] = -0.5*h_rate[i];



    } else if (set[i].style == NONE) {

      set[i].lo_target = domain->boxlo[i];

      set[i].hi_target = domain->boxhi[i];

    } else if (set[i].style != VOLUME) {

      set[i].lo_target = set[i].lo_start + 

	delta*(set[i].lo_stop - set[i].lo_start);
@@ -556,20 +569,23 @@ void FixDeform::end_of_step() 
  }



  // for triclinic, set new box shape

  // for TRATE, set target directly based on current time and set h_rate

  // for TRATE, set target directly based on current time. also set h_rate

  // for NONE, target is current tilt

  // for other styles, target is linear value between start and stop values



  if (triclinic) {

    double *h = domain->h;



    for (i = 3; i < 6; i++) {

      if (set[i].style == NONE) continue;



      if (set[i].style == TRATE) {

	double delt = (update->ntimestep - update->beginstep) * update->dt;

	set[i].tilt_target = set[i].tilt_start * pow(1.0+set[i].rate,delt);

	h_rate[i] = set[i].rate * domain->h[i];

      } else if (set[i].style) {

      } else if (set[i].style == NONE) {

	if (i == 5) set[i].tilt_target = domain->xy;

	else if (i == 4) set[i].tilt_target = domain->xz;

	else if (i == 3) set[i].tilt_target = domain->yz;

      } else {

	set[i].tilt_target = set[i].tilt_start + 

	  delta*(set[i].tilt_stop - set[i].tilt_start);

      }
@@ -627,7 +643,7 @@ void FixDeform::end_of_step() 
    }

  }



  // convert atoms to lamda coords

  // convert atoms and rigid bodies to lamda coords



  if (remapflag == X_REMAP) {

    double **x = atom->x;
@@ -637,6 +653,10 @@ void FixDeform::end_of_step() 
    for (i = 0; i < nlocal; i++)

      if (mask[i] & groupbit)

	domain->x2lamda(x[i],x[i]);



    if (nrigid)

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

	modify->fix[rfix[i]]->deform(0);

  }



  // reset global and local box to new size/shape
@@ -663,7 +683,7 @@ void FixDeform::end_of_step() 
  domain->set_global_box();

  domain->set_local_box();



  // convert atoms back to box coords

  // convert atoms and rigid bodies back to box coords



  if (remapflag == X_REMAP) {

    double **x = atom->x;
@@ -673,17 +693,11 @@ void FixDeform::end_of_step() 
    for (i = 0; i < nlocal; i++)

      if (mask[i] & groupbit)

	domain->lamda2x(x[i],x[i]);

  }



  // remap centers-of-mass of rigid bodies

  // needs to be new call, not dilate

  // check where else fix dilate is called from



  /*

    if (nrigid)

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

      modify->fix[rfix[i]]->dilate(2,oldlo,oldhi,newlo,newhi);

  */

	modify->fix[rfix[i]]->deform(1);

  }



  // redo KSpace coeffs since box has changed

src/fix_deform.h

+4 −5
Original line number Diff line number Diff line
@@ -41,11 +41,10 @@ class FixDeform : public Fix { 
    double flo,fhi,ftilt;

    double dlo,dhi,dtilt;

    double scale,vel,rate;

    double lo_start,hi_start;

    double lo_stop,hi_stop;

    double lo_target,hi_target;

    double tilt_start,tilt_stop,tilt_target;

    double vol_start,tilt_flip;

    double lo_initial,hi_initial;

    double lo_start,hi_start,lo_stop,hi_stop,lo_target,hi_target;

    double tilt_initial,tilt_start,tilt_stop,tilt_target,tilt_flip;

    double vol_initial,vol_start;

    int fixed,dynamic1,dynamic2;

  };

  Set *set;

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