When developing MOOSE Kernels bugs in the implementation of the On- and Off-Diagonal Jacobian may lead to bad (or no) convergence of problems utilizing the new kernel.
One way of determining if a faulty Jacobian implementation is the problem is to run the simulation with a finite difference preconditioner. Insert
[Preconditioning] [./SMP] type = FDP full = true [../] 
into your input file. If the problem converges well with the (slow) finite difference preconditioner the next step is determining the exact Jacobian terms that are faulty.
MOOSE comes with a Jacobian Debugger script to assist the developers with this task. First remove the FDP preconditioner setting from the input file again. Then simply run the Jacobian Debugger on your input file as follows
This runs the moose application (same autodetection peacock uses) and computes the Jacobian using the user supplied
compute[..]Jacobian() methods and through finite differencing the residuals. If both Jacobian matrices agree the analyzer outputs.
No errors detected. :-)
Otherwise it outputs a human readable diagnosis of the input file, which could look like this:
Kernel for variable 's': (0,0) On-diagonal Jacobian is slightly off (by 0.500073 %) Kernel for variable 't': (1,1) On-diagonal Jacobian is wrong (off by 100.0 %) (1,2) Off-diagonal Jacobian for variable 'u' is questionable (off by 4.5 %) Kernel for variable 'u': (2,2) On-diagonal Jacobian needs to be implemented Kernel for variable 'u2': (3,3) On-diagonal Jacobian should just return zero
Note how the analyzer puts relative discrepancies between the hand coded and finite differenced into natural language.
The Jacobian analyzer is still under development and a major feature that is being worked on is the output of the faulty kernel class names. This is not straightforward as in an input file multiple kernels can be contributing to the residual/Jacobian of any given variable.
To view the available commandline options for the Jacobian Debugger run the script with the
Notable options are
type = GeneratedMeshmesh by setting the
nzvalues to either 1 or the value given by option