IBIS internal file formats:

IBIS creates files that are used internally and files that are used for postprocessing. The internal files are stored in a directory called ibisdat. This directory has reserved filenames. Do not createyour own files with any of the following names. If you do, IBIS will not execute properly.

cplot.dat      link.dat     rsdata.13    rspart.dat
ibpts.dat      lplot.dat    rsfluid.dat  visual.dat
ibpts.error    preview.dat  rsibpts.dat  vmax.dat
init.dat       rs.data      rslink.dat

It is possible to edit these files, and this section of the manual contains detailed information on the contents of these files. If the internal data files are corrupted or improperly edited, IBIS will not work properly.

These files contain the following information

$$\begin{tabular} {\vert cllc\vert} \hline & & & \ & & & \... ...ernal communication data & \ & & & \ \hline\end{tabular}$$

In the following pages, the file structures of the internal files are may be important to the user are described. A number of files in the previous list are ommitted. These files serve only for communication between programs and are not otherwise useful. They are mentioned above only for completeness. The files rsfluid.dat, rsibpts.dat and rspart.dat are documented as fluid.dat, ibpts.dat and part.dat, respectively.

ibpts.dat

This is a shortened ibpts.dat file example.

0 1 1 0
poly
  1398      1     -2      0      0     0.000e+00 0.000e+00
 1 1.500e+00 8.750e-01 1.500e+00 8.750e-01 5.025e-03 1.000e+06 6.288e-07 1.000e+02 1.000e+08
 1 1.505e+00 8.750e-01 1.505e+00 8.750e-01 5.025e-03 1.000e+06 0.000e+00 1.000e+02 1.000e+08
 1 1.510e+00 8.750e-01 1.510e+00 8.750e-01 5.025e-03 1.000e+06 0.000e+00 1.000e+02 1.000e+08
 1 1.515e+00 8.750e-01 1.515e+00 8.750e-01 5.025e-03 1.000e+06 0.000e+00 1.000e+02 1.000e+08
        ....
     1398 (1395 more) lines of points and link data
        ....
circ
    21      1      1      0      0     1.900e+00 5.700e-01
 1 1.950e+00 5.700e-01 1.950e+00 5.700e-01 1.562e-02 1.000e+03 -7.359e-06 1.000e+03 0.000e+00
 1 1.947e+00 5.854e-01 1.947e+00 5.858e-01 1.562e-02 1.000e+03 -7.359e-06 1.000e+03 0.000e+00
 1 1.940e+00 5.993e-01 1.940e+00 5.993e-01 1.562e-02 1.000e+03 -7.359e-06 1.000e+03 0.000e+00
 1 1.929e+00 6.104e-01 1.929e+00 6.108e-01 1.562e-02 1.000e+03 -7.359e-06 1.000e+03 0.000e+00
        ....
     21 (17 more) lines of points and link data
        ....

Generally the file format has the following form and meaning. This file can be edited.

number_filaments number_polygons number_circles number_linked_entities
type
  number closure category active name x-center-mass y-center-mass 
  continue xibpt yibpt xtether ytether link-rest link-stf theta-rest theta-stf tether-stf

The commands have the following significance. The FORTRAN codes read this file with free formats, therefore, the formatting is not important.

• type variable is included only for convenience. It abbreviates the IBIS command (with 4 characters) used to write the data.
• number integer specifying the number of immersed boundary points in the entity.
• closure = 1 if the entity is closed and the interior is to be plotted with a different color than the boundary. = 0 if the entity is not closed.
• category entity category - see the overview of the FORTRAN code for more information.
• active = 1 if the entity is active. = 0 if the entity is not active.
• name = integer $\geq 0$ if the entity has been assigned a name in the IBIS program.
• x-center-mass = x coordinate of the center of mass - used in graphics
• y-center-mass = y coordinate of the center of mass - used in graphics
• continue = 1 if more immersed boundary points in the current entity. = 0 if the current point is the last point in the entity. Allows for users to add immersed boundary points without changing number.
• xibpt = x coordinate of an immersed boundary point.
• yibpt = y coordinate of an immersed boundary point.
• xtether = x tether coordinate of the immersed boundary point (xibpt,yibpt).
• ytether = x tether coordinate of the immersed boundary point (xibpt,yibpt).
• link-rest = rest length of the link between the current point and the next point.
• link-stf = stiffness of the link between the current point and the next point.
• theta-rest = rest angle between the current point and the next and previous point.
• theta-stf = angle stiffness between the current point and the next and previous point.
• tether-stf = tether stiffness between the current point and (xibpt,yibpt).

init.dat

This file is a namelist used by the FORTRAN program to get data defined in the ibis program from the preprocessor. The data in this file should not be edited by hand.

 $IBPTS
  cfile      = 'binary/ball',      <- color graphics file path, base names
  lfile      = 'line/ball',        <- line graphics file path, base names
  ffile      = 'null',             <- fluid velocity input file
  xmin       = 0.000000e+00,       <- minimum value of x in physical domain
  xmax       = 4.000000e+00,       <- maximum value of x in physical domain
  ymin       = 0.000000e+00,       <- minimum value of y in physical domain
  ymax       = 2.000000e+00,       <- maximum value of y in physical domain
  dlt        = 3.120000e-05,       <- time step
  h          = 1.562500e-02,       <- space grid step
  mu         = 1.600000e+00,       <- viscosity of the fluid
  ro         = 1.000000e+00,       <- density of the fluid  
  umax       = 0.000000e+00,       <- max tube flow velocity
  fbpx       = 0.000000e+00,       <- background force in x direction
  fbpy       = 0.000000e+00,       <- background force in y direction
  ntstart    = 0,                  <- start time step count
  ntmax      = 100000,             <- maximum number of time steps
  vit        = 500,                <- output frequency for color graphics files
  nfreq      = 1000,               <- output frequency for line graphics files
  ivdens     = 2,                  <- output density of velocity (force) vectors
  usave      = 1,                  <- save velocity vectors if 1
  fsave      = 0,                  <- save force vectors if 1
  jfil       = 0,                  <- number of periodic lines in input file
  jplat      = 0,                  <- number of circles in the input file
  jpoly      = 1,                  <- number of polygons in the input file
  ipbx       = 0,                  <- periodic markers in x if 0, nuemann if 1
  ipby       = 0,                  <- periodic markers in y if 0, nuemann if 1
  nlinke     = 0,                  <- number of linked entities
  ibtube     = 0,                  <- coordinate of the bottom tube
  ittube     = 128,                <- coordinate of the top tube
  btubil     = 0,                  <- coordinate of the bottom tube injury (left)
  btubir     = 0,                  <- coordinate of the bottom tube injury (right)
  ttubil     = 0,                  <- coordinate of the top tube injury (left)
  ttubir     = 0,                  <- coordinate of the top tube injury (right)
  iplat      = 0,                  <- platelet flag
  maxlink    = 0,                  <- remainder are platelet only variables
  pltdif     = 0.000000e+00,
  pdens      = 0.000000e+00,
  scoh       = 0.000000e+00,
  scgap      = 0.000000e+00,
  sadh       = 0.000000e+00,
  sagap      = 0.000000e+00,
  sbreaka    = 0.000000e+00,
  sbreakc    = 0.000000e+00,
  stiffa     = 0.000000e+00,
  stiffc     = 0.000000e+00,
  rlinkc     = 0.000000e+00,
  rlinka     = 0.000000e+00,
 $END

link.dat

This file is an example link.dat file.

1 7 1 5.000000e-01 4.000000e+07 8.000000e+00 
2 7 1 5.000000e-01 4.000000e+07 8.000000e+00 
3 7 3 5.000000e-01 4.000000e+07 8.000000e+00

The file format has the following form and meaning. This file can be edited.

entity-name entity-name number rest stiff break

The commands have the following significance. The FORTRAN codes read this file with free formats, therefore, the formatting is not important.

• entity-name name of one of the entities to be linked.
• number number of links created between specified entities.
• rest rest length of the link is rest*h/2.
• stiff link stiffness.
• break length when the link break break*h/2.

parm.inc

An example of parm.inc for balloon.ibis. This parameter file consists of FORTRAN source code that is included in every routine of the FORTRAN programs.

c  global parameters 
c
      implicit none
c
c  fluid grid parameters
c
      integer l2nx,l2ny
      parameter(l2nx=5,l2ny=6)
      integer nx,ny
      parameter(nx=32,ny=64)
c
      integer nxp1,nyp1,nxp2,nyp2,nyv4
      parameter(nxp1=nx+1,nyp1=ny+1)
      parameter(nxp2=nx+2,nyp2=ny+2)
      parameter(nyv4=ny/4)
c
c  graphics parameters
c
      integer nxx, nyy, np, npd
      parameter(nxx=256,nyy=512)
      parameter(npd=8,np=2048)
c
c  immersed boundary point parameters
c
      integer ment, nfil, nring
      parameter(ment=50,nfil=0,nring=20)
      integer mpts, mcoor, mlink, mlkpt, mwhere
      parameter(mpts=237+(ment*nring)+np+ment)
      parameter(mcoor=2*mpts)
      parameter(mlink=9*ment,mlkpt=6*ment)
      parameter(mwhere=(ment*(ment-1))/2)
c
c  immersed boundary point input file parameters
c
      integer idat1, idat2
      parameter(idat1=100,idat2=100)
c
c  number of active elements
c
      integer nact
      parameter (nact=1000)
c

None of the variables in this file should be edited by hand. If preibis is used to parse an ibis program, this file is copied directly to the Fcode subdirectory.

visual.dat

An example of visual.dat for balloon.ibis. Each line of the file, except the first consists of a variable name and the variable.

balloon.ibis                <-  program name
path binary                 <-  color graphics output directory
base ball                   <-  color graphics base filename
height 256                  <-  height of color graphics files
width 512                   <-  width of color graphics files
color cmap                  <-  name of colormap file
zoom 1                      <-  default output zoom
increment 1                 <-  default movie increment
first 0                     <-  first output frame
last 0                      <-  last output frame (updated)
lpth line                   <-  line graphics output directory
lbse ball                   <-  line graphics base filename
llst 0                      <-  last line plot created (updated)
vmax 0.0                    <-  global maximum velocity
xmin 0.000000e+00           <-  physical domain x_min
ymin 0.000000e+00           <-  physical domain y_min
xlength 4.000000e+00        <-  x length of the physical domain
ylength 2.000000e+00        <-  y length of the physical domain
nfvector 1                  <-  number of field vectors
fvector1 velocity           <-  name of first field vector
fvmax1 3.013256e+05         <-  max of first field vector
fvmin1 0.0                  <-  min of first field vector
fvector2 force              <-  name of second field vector
fvmax2 2.039035e+04         <-  max of second field vector
fvmin2 0.0                  <-  min of second field vector
npvector 1                  <-  number of point vectors
pvector1 velocity           <-  name of the first point vector
pvmax1 3.013256e+05         <-  max of the first point vector
pvmin1 0.0                  <-  min of the first point vector
npscalar 0                  <-  number of point scalars
nfscalar 0                  <-  number of field scalars

The following variables may be safely edited by hand; color, zoom increment, first, last, llst. All other variables are intrinsic to the computation, and changing will result in unpredictable results.

To change the remaining variables, edit parameters in the ibis program and rerun the preprocessor and the simulation.

The pattern for the point and field variables is repeated to match their respective numbers.