Installing and running Serpent

Running Serpent

Serpent is run from the Linux command line interface. The general syntax is:

sss2 INPUT [ options ]

Where INPUT is the input file name and the available options are:

-version	: print version information and exit
-replay	: run simulation using random number seed from a previous run
-his	: run only burnup history in coefficient calculation
-coe	: run only restarts in coefficient calculation
-plot	: stop after geometry plot
-checkvolumes N	: calculate Monte Carlo estimates for material volumes by sampling N random points in the geometry (see detailed description)
-checkstl N M	: check for holes and errors in STL geometries by sampling M directions in N points (see detailed description)
-mpi N	: run simulation in MPI mode using N parallel tasks
-omp N	: run simulation in OpenMP mode using N parallel threads
-disperse	: generate random particle or pebble distribution files for HTGR calculations (see detailed description)
-rdep	: read binary depletion file from previous calculation and print new output according to inventory list
-tracks N	: draw N particle tracks in the geometry plots or invoke track plot animation
-comp MAT [ ID ]	: print pre-defined composition of material MAT that can be copy-pasted into the inputfile (see detailed description)
-elem SYM DENS [ ID ]	: decomposes natural element identified by symbol SYM at density DENS into its constituent isotopes (see detailed description)
-qp	: quick plot mode (ignore overlaps)
-nofatal	: ignore fatal errors

Most of the input options are self-explanatory, the rest are described below.

Miscellaneous input options

Monte Carlo volume calculation routine

Incorrect material volumes can lead to a number of problems in burnup calculation and normalization of reaction rates. Serpent provides a Monte Carlo based routine for checking and calculating the volumes of complicated material zones. The volumes are evaluated by sampling a large number of random points in the geometry, and the estimate represents the exact volumes seen by the particles during the transport simulation.

Standard compositions

Serpent has a built-in list of more than 350 pre-defined material compositions. These materials cannot be used directly in the input, but the compositions can be printed and copy-pasted into the input file. The materials are numbered and the full list is printed with option "-comp list":

sss2 -comp list

List of available material compositions:

  1  "A-150 Tissue-Equivalent Plastic (A150TEP)"
  2  "Acetone"
  3  "Acetylene"
  4  "Air (Dry, Near Sea Level)"
  5  "Alanine"
  6  "Aluminum"
  7  "Aluminum Oxide"
  8  "Aluminum, Alloy 2024-O"
...

The output is printed in Serpent material card format with the mass density included. The usage is illustrated by an example:

sss2 -comp 4

% --- "Air (Dry, Near Sea Level)" [PNNL-15870, Rev. 1]

mat m4 -1.20500E-03

 6000  -1.24000E-04
 7000  -7.55268E-01
 8000  -2.31781E-01
18000  -1.28270E-02

 6012  -1.22564E-04
 6013  -1.43645E-06
 7014  -7.52324E-01
 7015  -2.94416E-03
 8016  -2.31153E-01
 8017  -9.35803E-05
 8018  -5.34540E-04
18036  -3.88624E-05
18038  -7.70386E-06
18040  -1.27804E-02

The output includes both elemental compositions for photon transport and isotopic compositions for neutron transport calculations. Optional second parameter is the library ID, which is printed after each nuclide ZA:

sss2 -comp 269 06c

% --- "Steel, Boron Stainless" [PNNL-15870, Rev. 1]

mat m269 -7.87000E+00

 5000.06c  -1.00000E-02
 6000.06c  -3.96000E-04
14000.06c  -4.95000E-03
15000.06c  -2.28000E-04
16000.06c  -1.49000E-04
24000.06c  -1.88100E-01
25000.06c  -9.90000E-03
26000.06c  -6.94713E-01
28000.06c  -9.15750E-02

 5010.06c  -1.84309E-03
 5011.06c  -8.15691E-03
 6012.06c  -3.91413E-04
 6013.06c  -4.58738E-06
14028.06c  -4.54739E-03
14029.06c  -2.39265E-04
14030.06c  -1.63344E-04
15031.06c  -2.28000E-04
16032.06c  -1.41126E-04
16033.06c  -1.14910E-06
16034.06c  -6.70834E-06
16036.06c  -1.67133E-08
24050.06c  -7.85070E-03
24052.06c  -1.57439E-01
24053.06c  -1.81960E-02
24054.06c  -4.61478E-03
25055.06c  -9.90000E-03
26054.06c  -3.92204E-02
26056.06c  -6.38452E-01
26057.06c  -1.50084E-02
26058.06c  -2.03234E-03
28058.06c  -6.15363E-02
28060.06c  -2.45201E-02
28061.06c  -1.08366E-03
28062.06c  -3.51174E-03
28064.06c  -9.23214E-04

Note that data for all nuclides may not be found in the Serpent cross section libraries. The complete list of pre-defined material compositions is available here.

Elemental decomposition

This command line option can be used to decompose natural elements in material cards into individual isotopes. The parameters include the element symbol and density or fraction (positive values for atomic and negative values for mass densities / fractions). Optional third parameter is the library ID, which is printed after each nuclide ZA. The usage is illustrated below with examples.

Decomposing natural zirconium with 97.5% mass fraction:

sss2 -elem Zr -0.975 06c

Isotopic composition for natural zirconium:

 40090.06c  -4.94385E-01
 40091.06c  -1.09014E-01
 40092.06c  -1.68461E-01
 40094.06c  -1.74438E-01
 40096.06c  -2.87019E-02

The isotopic fractions sum up to -0.975. Note that data for all nuclides may not be found in the Serpent cross section libraries. Similarly, decomposition of natural boron into atomic fractions:

sss2 -elem B 1.0 

Isotopic composition for natural boron:

  5010  1.99000E-01
  5011  8.01000E-01

The library ID is omitted.