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What input files are required by flowCart?
What output files are produced by flowCart?
How do I Extract "pretty" cutting planes? 
How do I restart a calculation? 
Show me examples of various Cart3D files.. 

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flowCart requires 4 files to get underway.

1. an Input control file (default name <input.cntl>) which controls the behavior of the solver.
2. the Mesh.c3d.Info file produced by cubes when you generated the mesh (see Note 1).
3. a Cart3D wetted surface triangulation <Components.i.tri> which describes the geometry to the solver. This geometry is generally produced by the intersect code (but any *.i.tri file will do). This file is specified in the Input control file, and must be the same as that used by cubes to produce the mesh.
4. a Cart3D mesh file (default name <Mesh.c3d> but most frequently this will be <Mesh.mg.c3d>) which is produced by cubes, reorder, or mgPrep.
5. If you're using the new (Cart3D v1.4)  "$__Force_Moment_Processing" section in input.cntl you will also have to have a GMP-style Config.xml file, but flowCart will automatically produce one of these if the only component you're interested in is "entire".

flowCart produces 3 types of output files.
1. "Restart" or "checkpoint" files: see "How do I restart a calculation?" below for information about the uses of these files
2. Optionally, flowCart can be asked to produce various types of postprocessing files.  These files have filename extensions of "*.triq" or "*.dat".  "*.dat" files may be read directly into Ametc's "Tecplot" program (see Note 2).These files can contain snapshots of the final discrete solution displayed on cutting planes through the mesh <cutPlanes.dat> or mapped to the input wetted surface triangulation <inputSurfFileName.dat>.  The "*.triq" files conform to Cart3D's annotated surface triangulation file format, and can be used directly by the integrated force and moment computation module (clic).  Using clic, you can extract any force, moment, and Cp profiles for any configuration or collections of components within a configuraiton. This table summarizes the flowCart command line arguments and/or input control file flags used to create postprocessing files.  By the way, yes, you can always restart a calculation for 0 (zero) additional iterations to extract postprocessing files.

cmd line option	input.cntl file section heading	file produced
-T	(none)	inputSurfFileName.dat (Tecplottable)
-clic	(none)	inputSurfFileName.triq (clic input file)
(none)	$__PostProcessing:	cutPlanes.dat
-{X,Y,Z}cut	(none)	disjointCutPlanes.dat (ugly see Note 3)
-his	(none)	forces.dat, moments.dat, history.dat
(none)	$__Force_Moment_Processing:	loadsTri.dat, loadsCC.dat (ASCII files with final component loads data)
(none)	$__Force_Moment_Processing:	<GMPCompName>.dat (xy-plot file with loads history for selected component)

3. Convergence monitoring  files: The "-his" command line flag turns on generation of "./history.dat" and "./forces.dat" "./moments.dat" for recording convergence information. These files are directly plottable with the free solftware packages xmgr or xmgrace availible on most X-windows systems. Both of these files begin with a comment region containing meta information including details of the run so that the run can be reproduced at a later time. They also include a copy of the exact command line just incase you forget what you did. One column in each of these files contains the elapsed wall-clock time between iterations, click on history.dat, forces.dator moments.dat to see an example of each.
The Force or Moment  tags in the $__Force_Moment_Processing: section of input.cntl also can be used to trigger convergence monitoring. In this case it will give an iterative history of integrated loads on the requested GMP component.
The pointSensor tag in the $__Convergence_History_reporting: section of input.cntl will monitor the values of the state vector and Cp at the point specifiec by the sensor.

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There are 2 ways of extracting cutting planes from flowCart simulations, In the table above, the Xcut, -Ycut, -Zcut options will do this, however, these will show the solution reconstructed on a cell-by-cell basis, and you'll get different "zones" for each partition in the domain decomposition. These were really only intended for use durring development, and I dont recommend these options Much better way is to use the $__Post_Processing category in the input.cntl file. In this category, you can request specific cutting plane lists to be output at the end of your run using the Xslices, Yslices, or Zslices tags. Here is an example (goes anyplace in your input.cntl file):

$__Post_Processing: # Pretty printed cutting planes 
Xslices -.5  0.1   # X-stations for cutPlane extraction
Zslices 0.001 .297 # Z-stations for cutPlane extraction

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See the page on running flowCart (here).