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Parameter File
A config file format can be used (for now) in which individual items take the form:
vizHandler=dummy
Items expecting lists use spaces as separators:
process=reaction sink
netParam=1000 0 0 1000 1000
# can be used in the parameter text file to comment a line.
The following are a few key points about the JSON file format (see the "benchmarks" directory for examples).
You must begin and end the file with braces:
{
/*...*/
}Items take the form (strings in quotes):
"dimensions": 0,
"vizHandler": "dummy",Items expecting lists may use space separated string lists or JSON lists:
"process": "reaction sink",
"netParam": "1000 0 0 1000 1000", "process": ["reaction", "sink"],
"netParam": [1000, 0, 0, 1000, 1000],Xolotl's JSON reader supports shell (#) and C++ (// and /* ... */) style comments.
This page provides a description of the different key words/lines used in the input parameter file that can be generated by the Preprocessor or taken from the Benchmark Problems.
logLevel: Logging output threshold. (default = info; available debug,extra,info,warning,error).
dimensions: The number of dimensions for the simulation. Can be 0 (no dimension), 1, 2, 3. Note: 0 dimension cannot be run in parallel.
gridType: Grid type to use along X. (default = uniform; available uniform,nonuniform,geometric,cheby,read).
gridParam: At most six parameters for the grid. Alternatives: uniform -> nX hX; nonuniform -> nX; geometric -> nX ratio; cheby -> nX width. The four additional parameters are for a uniform grid in Y and Z -> nY hY nZ hZ.
gridFile: A grid spacing is given by the specified file. NOTE: you need gridParam here only if in 2D/3D.
boundary: This option allows the user to choose the boundary conditions. The first one correspond to the left side (surface) and second one to the right (bulk), then two for Y and two for Z. 0 means mirror or periodic, 1 means free surface.
xBCType: The boundary conditions to use in the X direction, mirror (default), periodic, or robin (for temperature).
interfaceLoc: The value (in nm) of the interface location between two materials (-1000.0 nm by default).
netParam: This option allows the user to define the boundaries of the network. To do so, simply write the values in order maxHe/Xe/Basal maxD maxT maxV maxI.
networkFile: The HDF5 file to use for restart.
process: List of all the processes to use in the simulation (reaction, diff, advec, modifiedTM, movingSurface, bursting, attenuation, resolution, heterogeneous, sink, constant, noSolve).
burstingDepth: The depth (in nm) after which there is an exponential decrease in the probability of bursting (10.0 nm if nothing is specified).
burstingFactor: This option allows the user to set the factor used in computing the likelihood of a bursting event.
material: The material options are as follows: {W100, W110, W111, W211, Pulsed, Fuel, Fe, 800H, AlphaZr}.
grouping: The grouping parameters: the first integer is the size at which the grouping starts (HeV clusters in the PSI case, Xe in the NE case), the second is the first width of the groups (He for PSI, Xe for NE), and the third one in the second width of the groups (V for PSI).
tempHandler: Temperature handler to use. (default = constant; available constant,gradient,heat,profile.
tempParam: At most two parameters for temperature handler. Alternatives: constant -> temp; gradient -> surfaceTemp bulkTemp; heat -> heatFlux bulkTemp.
tempGridPower: The value of the power to use to create the temperature grid spacing, only used if heat temperature handler is used. (default = 2.5).
tempFile: A temperature profile is given by the specified file, then linear interpolation is used to fit the data. NOTE: no need for tempParam here.
heatLossPortion: The portion of heat lost in the bulk (-1.0 by default).
flux: The value of the incoming flux in #/nm2/s. If the Fuel case is used it actually corresponds to the fission rate in #/nm3/s.
fluxFile: A time profile for the flux is given by the specified file, then linear interpolation is used to fit the data. (NOTE: If a flux profile file is given, a constant helium flux should NOT be given).
fluxDepthProfileFilePath: The path to the custom flux profile file; the default is an empty string that will use the default material associated flux handler.
initialConc: The name, size, and value of the initial concentration in the material (in #/nm3).
sputtering: The sputtering yield (in atoms/ion) that will be used.
grain: This option allows the user to add GB in the X, Y, or Z directions. To do so, simply write the direction followed by the distance in nm, for instance: X 3.0 Z 2.5 Z 10.0 .
zeta: The value of the electronic stopping power in the material (0.73 by default).
density: Sets a density in nm-3 for the number of xenon per volume in a bubble for the NE case (default is 10.162795276841 nm-3 as before).
radiusSize: This option allows the user to set a minimum size for the computation for the average radii, in the same order as the netParam option (default is 0).
perfHandler: Which set of performance handlers to use. (default = os, available dummy,os,papi).
perfOutputYAML: Should we write the performance report to a YAML file?
vizHandler: Which set of handlers to use for the visualization. (default = dummy, available std,dummy).
petscArgs: All the arguments that will be given to PETSc. See PETSc Options.
rng: Allows user to specify seed used to initialize random number generator (default = determined from current time) and whether each process should print the seed value it uses (default = don't print).
pulse: The total length of the pulse (in s) if the Pulsed material is used, and the proportion of it that is ON.
lattice: The length of the lattice side in nm.
impurityRadius: The radius of the main impurity (He or Xe) in nm.
biasFactor: This option allows the user to set the bias factor reflecting the fact that interstitial clusters have a larger surrounding strain field.
hydrogenFactor: The factor between the size of He and H.
xenonDiffusivity: The diffusion coefficient for xenon in nm2 s-1.
fissionYield: The number of xenon created for each fission (default is 0.25).
heVRatio: The number of He atoms allowed per V in a bubble.
migrationThreshold: Set a limit on the migration energy above which the diffusion will be ignored.
basalPortion: The value of the basal portion generated for each V (0.1 by default).
transitionSize: The value for the transition within a type of cluster, for instance basal (325 by default).
cascadeDose: The value of the dose at which the cascade overlap effect takes effect, if negative there won't be an effect (-1.0 by default).
cascadeEfficiency: The value of the remaining efficiency once the overlap effect started (0.0 by default).
reactionFilePath: The file path/name for the text file containing the kinetics for NE extended networks.
useSubnetworks: Should we distribute network across subnetworks? (This triggers multi-instance mode.)
couplingTimeStepParams: This option allows the user to define the parameters that control the multi-instance time-stepping. To do so, provide the following values in a list for this parameter:
- initialDt
- maxDt
- growthFactor
- startTime
- endTime
- maxSteps
When a non-uniform grid is used, here is how the spacing is defined in the depth direction:
- above the surface: 0.1 nm
- d < 2.5 nm: 0.1 nm
- 2.5 nm < d < 5.0 nm: 0.25 nm
- 5.0 nm < d < 7.5 nm: 0.5 nm
- 7.5 nm < d < 50.5 nm: 1.0 nm
- 50.5 nm < d < 100.5 nm: 2.0 nm
- 100.5 nm < d < 150.5 nm: 5.0 nm
- 150.5 nm < d < 300.5 nm: 10.0 nm
- 300.5 nm < d < 500.5 nm: 20.0 nm
- 500.5 nm < d < 1000.5 nm: 50.0 nm
- 1000.5 nm < d < 5000.5 nm: 100.0 nm
- 5000.5 nm < d < 10000.5 nm: 200.0 nm
- 10000.5 nm < d < 20000.5 nm: 500.0 nm
- 20000.5 nm < d < 30000.5 nm: 1.0 um
- 30000.5 nm < d < 50000.5 nm: 2.0 um
- 50000.5 nm < d < 100000.5 nm: 5.0 um
- 100000.5 nm < d < 200000.5 nm: 10.0 um
- 200000.5 nm < d < 500000.5 nm: 20.0 um
- 500000.5 nm < d < 1000000.5 nm: 50 um
- 1 mm < d < 2 mm: 100.0 um
- 2 mm < d < 5 mm: 200.0 um
- 5 mm < d < 10 mm: 500.0 um
- 10 mm < d: 1 mm
Except in the case where "Fuel" material is used (use 145 grid points to have a 100 um thick grid):
- d < 200 nm: 10 nm
- 200 nm < d < 1000 nm: 100 nm
- 1000 nm < d < 5000 nm: 1000 nm
- 5000 nm < d < 45000 nm: 5000 nm
- 45000 nm < d < 49000 nm: 1000 nm
- 49000 nm < d < 49800 nm: 100 nm
- 49800 nm < d < 50200 nm: 10 nm
- 50200 nm < d < 51000 nm: 100 nm
- 51000 nm < d < 55000 nm: 1000 nm
- 55000 nm < d < 95000 nm: 5000 nm
- 95000 nm < d < 99000 nm: 1000 nm
- 99000 nm < d < 99800 nm: 100 nm
- 99800 nm < d : 10 nm