Top Level Directory Structure

arch - make file architectures
bin - support scripts for compilation
doc - various forms of documentation, such as doxygen and man file
docker - docker files for building FLOOXS on various platforms (how we test on platforms we don't run)
Params - simulation parameter files
src - source code
TclLib - TCL front end support functions, such as models
Test - Test simulation files accumulated over many years

Source Structure

BasePDE
- engine for alagator scripting
- builds and solves partial differential equations
db
- specific sqlite3 version and interface for flooxs
device
- code specific to the device command and FLOODS solutions
diffuse
- All code pertaining specifically to diffusion
- The newton solver is also located here
doalldirs
- script that is used to build the templates in all directories
etch
- Old etching code
- Still contains the OctTree, mask and machine commands
field
- Finite element specific code,
- Contains the field server that controls all mesh properties
- Where all elements, meshes, and data fields are defined
flooxs.cc
- where TCL commands are defined
FLOOXS.models
- Master tcl startup model file
front
- Tcl front end user commands
help.cc
- old help menu command
implant
- contains implant command code
include
- helpful include files for use in the code
LevelSet
- All code that pertains to level set geometry formation and meshing
mater
- material specific code
math
- vector and matrix specific functions
main.cc
- contains program main function
param.tcl
- a file that contains pdbSet commands
plot
- old plot directory, still contains some useful functions used elsewhere
plplot
- new plotting directory, contains plplot bindings
plplot.tcl
- A blank file needed for plplot
pltcltk
- directory for testing plplot
template
- template files for flooxs Seq and List objects
test
- contains simple tests that can be run when building flooxs (make test)