Installing and running Serpent

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Compiling the source code

Compiler options

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
-mix  : decompose mixtures in file (see detailed description)

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

Running parallel calculations

Miscellaneous input options

Monte Carlo volume calculation routine

Incorrect material volumes can lead to a number of problems in burnup calculation and the normalization of reaction rates. To deal with these issues 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. Checking the material volumes is also a good means to confirm that the geometry was properly set up.

The Monte Carlo based volume calculation routine is invoked by command line option "-checkvolumes", followed by the number of random points and the name of the input file. The calculation works also in OpenMP parallel mode. The usage is best illustrated by an example:

sss2 -omp 24 -checkvolumes 10000000 bwr

...

Calculating material volumes by Monte Carlo...

Estimated calculation time: 0:00:09
Realized calculation time:  0:00:08

Volumes (2D problem, the values are in cm2) :

Material fuel1         : 5.9038E-01 5.9015E-01 (0.00562) : -0.00038   (100.0 % den.)
Material fuel2         : 2.3615E+00 2.3635E+00 (0.00366) :  0.00084   (100.0 % den.)
Material fuel3         : 3.5423E+00 3.5525E+00 (0.00281) :  0.00288   (100.0 % den.)
Material fuel4         : 1.1808E+00 1.1795E+00 (0.00436) : -0.00108   (100.0 % den.)
Material fuel5         : 1.1808E+01 1.1798E+01 (0.00154) : -0.00081   (100.0 % den.)
Material fuel6         : 2.8338E+01 2.8316E+01 (0.00090) : -0.00078   (100.0 % den.)
Material fuel7         : 5.9038E+00 5.9094E+00 (0.00202) :  0.00096   (100.0 % den.)
Material clad          : 1.6336E+01 1.6340E+01 (0.00111) :  0.00026   (100.0 % den.)
Material box           : 0.0000E+00 1.3505E+01 (0.00128) :      N/A * (100.0 % den.)
Material cool          :        N/A 9.5257E+01 (0.00036) :      N/A * (100.0 % den.)
Material moder         : 0.0000E+00 5.5451E+01 (0.00055) :      N/A * (100.0 % den.)

Volumes written in file "bwr.mvol"

The volumes are printed separately for each material. If automated depletion zone division is used, the volumes are also printed for each sub-zone. The first column of results shows the volume actually used in the calculation and the next column the Monte Carlo estimate together with the associated relative statistical error. The next column gives the difference between the used and estimated volume, accompanied by '*' if the difference is suspiciously large compared to statistical accuracy (note that the results are random variables so it is possible that the estimate is off by chance). The last column shows the relative density compared to the input value in the material card. The value can be below 100% if the multi-physics interface is used. It should also be noted that in 2D geometries the calculated volumes are actually cross-sectional areas in cm2.

The volume calculation routine also prints an output file [input].mvol, which for the previous example is:

% --- Material volumes:

% Produced Fri Sep 16 09:18:39 2016 by MC volume calculation routine by
% sampling 10000000 random points in the geometry.

set mvol

fuel1           0 5.90149E-01 % (0.006)
fuel2           0 2.36348E+00 % (0.004)
fuel3           0 3.55245E+00 % (0.003)
fuel4           0 1.17947E+00 % (0.004)
fuel5           0 1.17979E+01 % (0.002)
fuel6           0 2.83158E+01 % (0.001)
fuel7           0 5.90941E+00 % (0.002)
clad            0 1.63403E+01 % (0.001)
box             0 1.35046E+01 % (0.001)
cool            0 9.52565E+01 % (0.000)
moder           0 5.54508E+01 % (0.001)

The set mvol card is one of the options to define material volumes and the output from the volume checker can be copy-pasted into the input or the entire file linked using the include command. The volume calculation routine can be run automatically using the set mcvol input option.

Checking for holes in STL geometries

Particle disperser routine

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.

Material decomposition

The -mix command line option processes all mixtures defined in the input and decomposes them into standard material compositions. The compositions are written in material input card format in file [input].mix.

For example, coolant can be defined as a mixture of two materials:

% --- Water: 

mat water  -0.76973  moder lwtr 1001
 1001.03c   0.66667
 8016.03c   0.33333

therm lwtr lwe7.10t

% --- Natural boron:

mat boron   1.00000  tmp 550
 5010.03c   0.19900
 5011.03c   0.80100

% --- Coolant:

mix cool
water      -0.99950
boron      -500E-6

Serpent decomposes mixture cool into a conventional material before running the transport simulation. The -mix command line option prints out the decomposed material composition:

% Material cool is a mixture of 2 components:

% -----------------------------------------
% Material             v. frac      m. frac
% -----------------------------------------
% water            9.99979E-01  9.99500E-01
% boron            2.14484E-05  5.00000E-04
% -----------------------------------------

mat cool  7.72309E-02 moder lwtr 1001

  1001.03c  5.14732E-02
  8016.03c  2.57362E-02
  5010.03c  4.26822E-06
  5011.03c  1.71801E-05