sh

examples/cutout/cinit.F90

@@ -128,67 +128,6 @@ subroutine recenterWalls
 
  end subroutine recenterWalls
 
- recursive subroutine choose_point(pt)
- real(WP) :: pt(3)
-
- type(t_wall), pointer :: wall
- real(WP) :: rad = 3., len, maxN, minN
- real(WP) :: threshold
- integer :: i
-
- wall => walls(1)
- len = RandomNumber(ranseed)*actlen
- threshold = 0.2
- maxN = -1E9
- minN = 1E9
-
- ! figure out the radius based on the location in the tube
- do i = 1, wall%nvert
- if (abs(wall%x(i, 3) - len) .le. threshold) then
- maxN = maxval((/maxN, wall%x(i, 1), wall%x(i, 2)/))
- minN = minval((/minN, wall%x(i, 1), wall%x(i, 2)/))
- end if
- end do
-
- rad = (maxN - minN)/2
- ! rad = 3
-
- pt(2) = RandomNumber(ranseed)*2*PI
- pt(3) = sqrt(RandomNumber(ranseed))*(rad)
- pt(1) = pt(3)*cos(pt(2)) + rad + minN ! x
- pt(2) = pt(3)*sin(pt(2)) + rad + minN ! y
- pt(3) = len
-
- end subroutine choose_point
-
-! generate point inside sphere with center and radius
- subroutine get_point(pt, center, rad)
-
- real(WP) :: pt(3)
- real(WP) :: center(3), rad
- real(WP) :: d = 100., x, y, z, tmp_pt(3)
- do while (d .gt. rad)
- call random_number(x)
- call random_number(y)
- call random_number(z)
- x = (x*rad*2) - rad
- y = (y*rad*2) - rad
- z = (z*rad*2) - rad
- ! if (rootWorld) print *, "tmp_pt: ", tmp_pt
-
- d = sum(tmp_pt*tmp_pt)
- ! if (rootWorld) print *, "d: ", d, "tmp_pt: ", tmp_pt
- end do
- ! if (rootWorld) print *, "tmp_pt after: ", x, y, z
-
- pt = tmp_pt
- ! if (rootWorld) print *, "tmp_pt: ", tmp_pt
- pt(1) = x + center(1)
- pt(2) = y + center(2)
- pt(3) = z + center(3)
- ! if (rootWorld) print *, "pt after: ", pt
- end subroutine get_point
-
 ! find an open spot in the simulation to place a cell
  subroutine place_cell(celltype, num)
 
@@ -235,7 +174,7 @@ subroutine place_cell(celltype, num)
  call rotate_cell(newcell)
 
  ! randomly select a tmp_xc
- ! call choose_point(tmp_xc)
+ ! place first 22 cells in sphere
  if (num .le. 22) then
  sphere_center = (/4.5, 5., 9./)
  sphere_rad = 4.5
@@ -248,6 +187,7 @@ subroutine place_cell(celltype, num)
  end do
  d = 100.
  tmp_xc = tmp_xc + sphere_center
+ ! place rest of the cells in cylinder
  else
  tmp_xc(2) = RandomNumber(ranseed)*2*PI
  tmp_xc(3) = sqrt(RandomNumber(ranseed))*(tuber)
@@ -318,12 +258,12 @@ subroutine rotate_cell(cell)
  zv(3) = 1 - (2*vsq)
 
  !generate rotation matrix
- rotmat = RotateMatrix(zv) !(/ 0., 1., 0./))
+ rotmat = RotateMatrix(zv)
 
  !rotate cell with rotmat
  !each point: x = Rx
  forall (i=1:cell%nlat, j=1:cell%nlon)
- ! reshpe is unnecessary?
+ ! reshape is unnecessary
  cell%x(i, j, :) = matmul(rotmat, cell%x(i, j, :))
  end forall
 

examples/cutout/ctube.F90

@@ -113,27 +113,10 @@ subroutine InitSystem
  rbc%ES = 12.4
  rbc%ED = 200.
  rbc%EB = 6.69D-2
- ! Mechanical properties of leukocytes
- ! Calculated according to section 6 of reference paper with WBC radius of 1.4 sim units
- ! and Es* scaled by 10^2
- ! Reference:
- ! Zhao, H., Isfahani, A. H., Olson, L. N., & Freund, J. B. (2010).
- ! A spectral boundary integral method for flowing blood cells.
- ! Journal of Computational Physics, 229(10), 3726-3744.
  case (2)
  rbc%ES = 887
  rbc%ED = 200.
  rbc%EB = 2.44D-2
-
- ! Mechanical properties for sickle cell roughly determined to be
- ! Es = (20 / 7.1) * Es for a healthy RBC (case(1) cell)
- ! Ed = (49.4 / 15.4) * Ed for healthy RBC (case(1) cell)
- ! Eb = (19.5 / 5.7) * Eb for a healthy RBC (case(1) cell)
- ! Reference:
- ! HeeSu Byun, Timothy R. Hillman, John M. Higgins, Monica Diez-Silva, Zhangli Peng, Ming Dao, Ramachandra R. Dasari, Subra Suresh, YongKeun Park
- ! Optical measurement of biomechanical properties of individual erythrocytes
- ! Acta Biomaterialia, Volume 8, Issue 11, 2012, Pages 4130-4138,
- ! https://doi.org/10.1016/j.actbio.2012.07.011
  case (3)
  rbc%ES = 10.*50
  rbc%ED = 50.