Advanced options for the Conley-Morse Database code are available and most of them are accessible within the makefile file.
Makefile Options: the Conley-Morse Database code operates in three stages. First it computes Morse Graphs and clutching information for all parameter regions and adjacent parameter regions. Next, it computes continuation classes. Finally, it computes conley indices. Each of these three steps can be regarded as their own program; the first stage creates a "database.raw" file, the second stage accepts the ".raw" file and creates a "database.mdb" file with the continuation information, and the third stage accepts the ".mdb" file and appends the Conley index data, resulting in a "database.cmdb" file. We can build Conley_Morse_Database to turn off some of these stages by setting some of the preferences at the top of the makefile to "no". This is useful in a case where there seems to be some kind of problem in the computation and we would like to proceed to the next step anyway using the checkpointed output as the input.
COMPUTE_MORSE_SETS := yes
COMPUTE_CONTINUATION := yes
COMPUTE_CONLEY_INDEX := yes
Parameter Space and Phase Space: In "Model.h" file we have a choice of Phase space and Parameter space data structures. See the "examples/Leslie2D/Model.h" example. Usually one will want to choose UniformGrid for the Parameter Space and PointerGrid for the Phase space grid. Alternatively, we could choose SuccinctGrid for the Phase space grid. The difference is that SuccinctGrid is slower, but uses far less space -- there is a space-time tradeoff.