Computer Programs
NEA-1678 BOT3P5.4.
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NEA-1678 BOT3P5.4.

BOT3P5.4, 3D Mesh Generator and Graphical Display of Geometry for Radiation Transport Codes, Display of Results

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1. NAME OR DESIGNATION OF PROGRAM

BOT3P5.4

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2. COMPUTERS
To submit a request, click below on the link of the version you wish to order. Rules for end-users are available here.
Program name Package id Status Status date
BOT3P5.4 NEA-1678/10 Tested 12-DEC-2019

Machines used:

Package ID Orig. computer Test computer
NEA-1678/10 Linux-based PC Linux-based PC
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3. DESCRIPTION OF PROGRAM OR FUNCTION

BOT3P was originally conceived as a set of standard FORTRAN 77 language programs in order to give the users of the DORT and TORT deterministic transport codes some useful diagnostic tools to prepare and check their input data files. Later versions extended the possibility to produce the geometrical, material distribution and fixed neutron source data to other deterministic transport codes such as TWODANT/THREEDANT of the DANTSYS system, PARTISN and, potentially, to any transport code through BOT3P binary output files that can be easily interfaced (see, for example, the Russian two-dimensional (2D) and three-dimensional (3D) discrete ordinates neutron, photon and charged particle transport codes KASKAD-S-2.5 and KATRIN-2.0). As from Version 5.1 BOT3P contained important additions specifically addressed to radiation transport analysis for medical applications.

 

BOT3P-5.4 improves pre-processing features and contains enhanced post-processing capabilities thanks to the revised RVARSCL module.

 

The following programs are included in the BOT3P software package: GGDM, DDM, GGTM, DTM2, DTM3, RVARSCL, COMPARE, MKSRC, CATSM, DTET, and PDTM.

 

GGDM requires in input all the geometrical, material and fixed neutron source information to generate the fine mesh boundary arrays, the material density factor for each fine space mesh array, the material number for each material zone array and the distributed source distribution array for DORT/TWODANT/PARTISN (two-dimensional (2D) transport applications) for both X-Y, R-Z and R-Theta geometries. GGTM is the 'twin' code of GGDM for three-dimensional applications. It requires in input all the geometrical, material and fixed neutron source information to generate the geometrical, material and distributed source distribution arrays for TORT/THREEDANT/PARTISN for both X-Y-Z and R-Theta-Z geometries.

 

The main feature of GGDM and GGTM consists in de-coupling the geometrical model description, which must be prepared once and for all, and the mesh grid refinement options. If users decide to create a more or less refined mesh than the one they have got or to switch from a X-Y/X-Y-Z mesh grid to a R-Theta/R-Theta-Z mesh grid or vice versa, it is sufficient for them to change very few data entries and to run GGDM/GGTM again, without modifying the geometrical description of the model to be analysed. Both GGDM and GGTM can also produce the data entries related to the presence of a fixed volumetric isotropic neutron source as a function of the generated mesh.

 

Users can define model areas/volumes with a more (or less) refined mesh grid with respect to the standard one for all the geometry. Moreover, GGDM and GGTM allow creating 'very small' geometrical zones centred about the key flux positions for edit purposes. That gives users the possibility to get the target quantity values in such locations directly from the transport code outputs as region response averages, without any need to interpolate the cell results.

 

CATSM reads a voxelized geometry and prepares a geometry with smaller size with respect to the original one for TORT and potentially for any other transport code that can manage CATSM output binary files. It can optionally and automatically generate tetrahedron mesh grids starting from the same voxelized geometry, even though the implemented algorithm is still rough and to be improved in future. CATSM is particularly addressed to medical applications.

 

DDM is graphics pre/post processor and it allows users to check the correctness of the entries generated by GGDM by plotting the geometry, the material mixture distribution or the fixed neutron source distribution, if any. DDM can work as a DORT/TWODANT (or other transport codes, through simple interfaces) post-processor also, by displaying any non-negative scalar target quantities of the transport analysis, such as, for example, the scalar neutron flux.

 

DTM2 and DTM3 allow users to check the correctness of the entries generated by GGTM by plotting the geometry, the material mixture distribution or the fixed neutron source distribution, if any, in two dimensional plots and three dimensional plots, respectively. Both DTM2 and DTM3 can work as TORT/THREEDANT (or other transport codes, through simple interfaces) post-processors also, by displaying any non-negative scalar target quantity of the transport analysis, such as, for example, the scalar neutron flux.

 

DTM2 makes 2D cuts of the model normal to one of the 3 co-ordinate directions X-Y-Z/R-Theta-Z and plots the material distribution or any non-negative target quantity on those cuts. As from BOT3P Version 5.1, DTM2 can visualize cuts of a tetrahedron mesh grid. In addition, users can overlap a tetrahedron mesh grid cut and the corresponding voxelized geometry (in input to CATSM to generate the tetrahedrons) to show how well the unstructured mesh grid matches the exact (voxelized) geometry boundaries.

 

DTM3 can make 3D parallel projections of a selected set of model material mixtures in a user defined model volume by reproducing the material distribution or a target quantity distribution on the visible surfaces of the selected model.

 

DTET can make 3D parallel views of a tetrahedron mesh grid (or of a related cut-away) on a selected set of material zones.

 

DDM, DTM2, DTM3 and DTET generate plots by using the RSCORS Graphics System subroutines which are included in (at least up to) the DOORS-3.3 software package together with DORT and TORT.

 

DDM, DTM2 and DTM3 can visualize the geometrical content (fine mesh boundaries and zone map) stored in a binary file. This feature makes it possible to easily interface them with other transport codes in order to use them as pre/post-processors not only of DORT and TORT.

 

RVARSCL can read a VARSCL sequential format file produced by DORT/TORT and the RTFLUX file produced by TWODANT/THREDANT/PARTISN, when the discontinuous space mesh option is not used, and can write a new binary sequential format file according to the input requirements of the post-processors DDM, DTM2, DTM3. RVARSCL gets the spatial distribution of the scalar neutron flux as the result of the sum of a selected number of energy groups. It accepts any user's non-negative weight (response) input function too, depending only on the energy group structure used in the DORT/TORT analysis, to be multiplied by the scalar neutron flux obtained in the DORT/TORT transport calculations.

 

COMPARE makes it possible to calculate the ratio between two positive target quantities in output from transport analyses (for example the neutron flux in output from DORT/TORT and TWODANT/THREEDANT, using the same fine mesh grid), to store it in a binary file in order to be visualized by the plot programs DDM, DTM2 and DTM3.

 

MKSRC makes it possible to produce a source binary file in format 'varsor' for DORT, format 'flxmom' for TORT and format 'fixsrc' for TWODANT and THREEDANT, by reading the region map and the scalar source produced by GGDM/GGTM and the spectra associated to each spatial region (up to now, only one moment different from zero can be input).

 

PDTM reads the matmap and mixmpl binary files generated by GGTM and can reconstruct as many mesh grids defined in partial space domains of the complete original one as the user requires. These mesh grids are at the finer possible refinement between the two refinement levels contained in GGTM output binary files.

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4. METHODS

GGDM and GGTM work similarly from the logical point of view. Since the 3D case is more general, the following description refers to GGTM. All the co-ordinate values that characterise the geometrical scheme at the basis of the 3D transport code geometrical and material model are read, sorted and all stored if different from the neighbouring ones more than an input tolerance established by the user. These co-ordinates are always present in the fine-mesh boundary arrays independently of the mesh grid refinement options, because they describe the user's scheme. According to the mesh grid refinement options, GGTM introduces further co-ordinate values, which complete the input mesh grid. A loop for each cell is performed to determine the zone and the material to be attributed to the cell. The cell is ideally represented by its centre and it is relatively simple to determine which material zone the cell belongs to. Material zones may have very complicated geometrical shapes in space thanks to the combinatorial geometry among volumes existing in GGTM. Moreover, the priority parameter associated to each material zone can easily solve any overlapping situation among zones. Fixed neutron sources, if any, are adapted to the mesh refinement at the same time.

 

As from version 5.0, GGTM can optionally calculate errors in volume values due to the stair-cased approximation in geometry. GGTM considers a 'very' refined uniform sub-grid for those single meshes cutting more than one material zone at zone interfaces and works in same way as previously described in the mesh attribution to zones for each single sub-mesh. This method lets users calculate the exact material zone volume values with great precision, independently of the geometry complexity and lets GGTM automatically update material zone densities to conserve mass.
As for the plot programs DDM, DTM2 and DTM3, they do not make any value interpolations among cell values to have contours, when used as post-processors or to plot any fixed neutron source distribution; they simply attribute the entire single mesh grid cell the colour corresponding to the adopted value scale. This simple and fast method lets users faithfully reproduce transport results and overlap material, zone, body or mesh borders on the same plots without overcrowding them with too many lines.

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5. RESTRICTIONS ON THE COMPLEXITY OF THE PROBLEM

Only a continuous space mesh grid can be generated by GGDM and GGTM and input to DDM, DTM2, DTM3, RVARSCL, COMPARE and MKSRC.

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6. TYPICAL RUNNING TIME

Central processor unit (CPU) time is roughly proportional to the number of cells the 2D/3D models created by GGDM/GGTM consist of and of the number of geometrical objects defined in the combinatorial geometry. For 3D applications, the distributed source distribution array generation may really be time consuming for the R-Theta-Z model if a core simulating neutron source is present.
Just to give an idea of the typical running time of GGTM, it is worth while mentioning that the CPU times required by BOT3P Version 1.0 to produce the ENEA VENUS-3 X-Y-Z and R-Theta-Z models, distributed source distribution array included, were respectively 148 s and 293 s on a DIGITAL UNIX ALPHA 500/333 workstation. Both models were more or less one million cells large.

 

CPU time for CATSM is proportional to the dimension of the input voxelixed geometry. CPU time greatly increases if a tetrahedron mesh grid is required in output also.

 

BOT3P Version 5.4 contains two sets of test cases in the test/ folder: a short set of 6 tests (using the run_6_tests_linux script) and a set of 100 tests (using the run_test script). Running both took ~10 minutes.

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8. RELATED OR AUXILIARY PROGRAMS
  • DOORS-3.2: One-,Two-, and Three-Dimensional, Multigroup, Discrete-Ordinate Transport Code System

  • DANTSYS 3: One-,Two-, and Three-Dimensional, Multigroup, Discrete-Ordinate Transport Code System

  • MCNP - A General Monte Carlo N-Particle Transport Code. Version 4c. LA-1309-M, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.

  • SUSD3D, 1-,2-,3-Dimensional Cross Section Sensitivity and Uncertainty Code, NEA-1628 SUSD3D, OECD/NEA Data Bank, Issy-les-Moulineaux, France.

  • PARTISN: a Code Package for Parallel, Time-dependent SN Transport, Los Alamos National Laboratory, LA-UR-02-5633, Los Alamos, New Mexico, USA.

  • KASKAD-S-2.5 - Two-Dimensional Discrete Ordinates Neutron, Photon and Charged Particle Transport Code, Keldysh Institute of Applied Mathematics, Moscow.

  • KATRIN-2.0 - Three-Dimensional Discrete Ordinates Neutron, Photon and Charged Particle Transport Code, Keldysh Institute of Applied Mathematics, Moscow.

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9. STATUS
Package ID Status date Status
NEA-1678/10 12-DEC-2019 Tested restricted
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10. REFERENCES
  • W.A. Rhoades, R.L. Childs., RSIC Computer Code Collection DOORS-3.1, DORT: A Two-dimensional Discrete Ordinates Transport Code, RSIC Code Package CCC-650, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.

  • W.A. Rhoades, D.B. Simpson, The TORT Three-dimensional Discrete Ordinates Neutron/Photon Transport Code (TORT Version 3), ORNL/TM-13221, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.

  • RSIC COMPUTER CODE COLLECTION DOORS-3.2, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA, distributed by RSICC and OECD/NEA-DATA BANK.

  • S.L. Thompson, The RSCORS Graphics System, Sandia National Laboratories, Albuquerque, New Mexico, U.S.A., 'The RSCORS (Version 3.13) Reference Manual'.

  • R.E. Alcouffe, R.A. Baker, F.W. Brinkley, D.R. Marr, R.D. 'Dell, W.F. Walters, 'DANTSYS 3.0: One-,Two-, and Three-Dimensional, Multigroup, Discrete-Ordinate Transport Code System', LA-12969-M, Los Alamos National Laboratory, Los Alamos, New Mexico, USA (1995).

  • R. E. Alcouffe, R. S. Baker, S. A. Turner, J. A. Dahl,'PARTISN Manual', LA-UR-02-5633, Los Alamos National Laboratory, Los Alamos, NM, USA (2002)

  • 'MCNP TM - A General Monte Carlo N-Particle Transport Code. Version 4c.' LA-1309-M, Los Alamos National Laboratory, Los Alamos, New Mexico, USA (March 2000).

  • Kodeli,'NEA-1628 SUSD3D. SUSD3D, 1-,2-,3-Dimensional Cross Section Sensitivity and Uncertainty Code', OECD/NEA Data Bank, Issy-les-Moulineaux, France, (2000).

  • R.D. 'Dell, 'Standard Interface Files and Procedures for Reactor Physics Codes, Version IV.' LA-6941-MS, Los Alamos National Laboratory, Los Alamos, New Mexico, USA (Sept.1977).

  • R. Orsi,'BOT3P: Bologna Transport Analysis Pre-Post-processors Version 1.', Nuclear Science and Engineering, n.142, pages 349-354, American Nuclear Society, USA, (2002).

  • R. Orsi,'BOT3P: A Mesh Generation Software Package for the Transport Analysis Codes DORT, TORT, TWODANT, THREEDANT and MCNP', International Conference on Supercomputing in Nuclear Applications SNA'2003, Paris, France, (September 22-24, 2003).

  • R. Orsi,'BOT3P: Bologna Transport Analysis Pre-Post-processors Version 3.0', Nuclear Science and Engineering, n.146, pages 248-255, American Nuclear Society, USA, (2004).

  • R. Orsi,'BOT3P: Bologna Radiation Transport Analysis Pre-Post-Processors Version 4.0', Nuclear Science and Engineering, n. 150, pages 368-373. American Nuclear Society, USA, (2005).

  • R.Orsi, 'A General Method to Conserve Mass in Complex Geometry Simulation on Mesh Grids and Its Implementation in BOT3P5.0', Nuclear Science and Engineering, n.154, pages 247-259, American Nuclear Society, USA, (2006).

  • R. Orsi, 'Potential Enhanced Performances in Radiation Transport Analysis on Structured Mesh Grids Made Available by BOT3P', Nuclear Science and Engineering, n. 157, pages 110-116 American Nuclear Society, USA, (2007).

  • Prediction of Neutron Embrittlement in the Reactor Pressure Vessel: VENUS-1 and VENUS-3 Benchmarks, NEA/NSC/DOC(2000)5, OECD/NEA-DATA BANK.

  • M. Pescarini, R. Orsi, M.G. Borgia, T. Martinelli, ENEA Nuclear Data Centre Neutron Transport Analysis of the VENUS-3 Shielding Benchmark Experiment, KT-SCG-00013, ENEA-Bologna, Italy.

  • 'Expert Group on 3-D Radiation Transport Benchmarks. Summary of meeting on C5G7 MOX Benchmark', Hollywood, Florida, USA, June 11, 2002, NEA/NSC/DOC(2002)13.

  • Y. Y. Azmy, J. C. Gehin, R. Orsi,'DORT Solutions to the Two-Dimensional C5G7MOX Benchmark Problem', Progress in Nuclear Energy, Vol. 45, No. 2-4, pp. 215-231, Elsevier, GB (2004).

  • M. Voloschenko, A. V. Shwetsov,'KASKAD-S-2.5- Two-Dimensional Discrete Ordinates Neutron, Photon and Charged Particle Transport Code', KIAM Rep. No. 7-26-2004, Keldysh Institute of Applied Mathematics, Moscow (Dec. 2004).

  • M. Voloschenko, V. P. Kryuchkov,'KATRIN-2.0- Three-Dimensional Discrete Ordinates Neutron, Photon and Charged Particle Transport Code', KIAM Rep. No. 7-27-2004 Keldysh Institute of Applied Mathematics, Moscow (Dec. 2004).

  • E. Botta, R. Orsi, G. Saiu, M. Pescarini,'Westinghouse AP1000 Internals Heating Rate Distribution Calculation Using a 3D Deterministic Transport Method', 13th International Conference on Nuclear Engineering, ICONE 13-50746, Beijing, China, May 16-20, 2005.

  • R. Orsi, 'H.B. Robinson-2 Pressure Vessel Dosimetry Benchmark: Deterministic three-dimensional analysis with the TORT Transport code, Nuclear Engineering and Technology', https://doi.org/10.1016/j.net.2019.07.025.

 

NEA-1678/10, included references:
- R. Orsi:
BOT3P Version 5.4: A Pre/Post-Processor System for Transport Analysis
SICNUC-P9H6-006, ENEA-Bologna, Italy (September 11, 2019)
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11. HARDWARE REQUIREMENTS

The author has run BOT3P Version 5.4 programs on P.C. under openSUSE and Red Hat Linux. But they are very likely to run on all UNIX W.S.

 

BOT3P Version 5.4 was tested at the NEA Data Bank on: Dell Precision M6800 with Intel(R) Core (TM) i7-4800MQ CPU at 2.70 GHz x 8, RAM: 16.0 GB.

 

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12. PROGRAMMING LANGUAGE(S) USED
Package ID Computer language
NEA-1678/10 FORTRAN-77
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13. SOFTWARE REQUIREMENTS

Up to now BOT3P has been successfully tested under the following LINUX systems:

  • Personal computer, openSUSE 10.2 (i586), g77 version 3.3.5-38.

  • personal computer, Red Hat Linux 7.0 and 7.1, g77 version 2.96 20000731 (from FSF-g77 version 0.5.26 20000731);

 

BOT3P up to Version 5.1 was successfully developed and tested on DEC Alpha, OSF1 V4.0F, DIGITAL Fortran, Version 5.2;
BOT3P Version 1.0 was successfully tested on the following UNIX system: IBM RS/6000, AIX 4.3.2, XLF 3.2.5.

 

BOT3P as from Version 5.3 was not tested by the author on these platforms. However, there is no reason to believe that it does not run on both DEC Alpha W.S. and IBM W.S.

 

BOT3P Version 5.4 was tested at the NEA Data Bank on:

  • OPERATING SYSTEM: Ubuntu 18.04

  • COMPILER: gfortran v7.4, g77 v3.4.6

It is recommended to use g77 to compile BOT3P.

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14. OTHER PROGRAMMING OR OPERATING INFORMATION OR RESTRICTIONS

DDM, DTM2, DTM3 and DTET call many RSCORS Graphics System subroutines distributed with DOORS. The compiled library where the graphical primitives are grouped, named librscors.a (see DOORS documentation), must therefore exist before BOT3P installation.  Linux and DEC-Alpha versions of librscors.a are included in the package.

 

It must be remembered that DDM, DTM2 and DTM3, if used in combination with DORT/TORT geometrical and compositional models not coming out from GGDM/GGTM, can read only the FIDO free format with some limitations reported in the user manuals.

 

DTM3 can generate up to ten different frames per run. However for very large geometrical models, users are suggested not to generate more then 2 or 3 frames in the same DTM3 run in order to avoid too big metafiles and postscript files.

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15. NAME AND ESTABLISHMENT OF AUTHORS

Author of programs GGDM, GGTM, DDM, DTM2, DTM3, RVARSCL, MKSRC, CATSM, DTET, PDTM:

Roberto Orsi

ENEA C.R.E. E. Clementel

ENEA FPN-FISNUC

Via Martiri di Monte Sole, 4

I-40129 Bologna, Italy

E.mail: roberto.orsi(at)enea.it

 

 

Author of programs RVARSCL, COMPARE:

Adrien Bidaud

Institut de Physique Nucleaire Orsay

15, rue Georges Clemenceau

F-91406 ORSAY CEDEX, France

 

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16. MATERIAL AVAILABLE
NEA-1678/10
Information file
README          Read-me file with BOT3P Version 5.4 generalities
install_BOT3P   Script file to install BOT3P
run_BOT3P       Script file to run any BOT3P program

\bin\ Directory containing the RSCORS graphics library ready to be linked with
the plot modules of BOT3P for DEC-ALPHA and Linux (g77) platforms and executable
files "poppst" to convert metafiles into PostScript files (DEC-ALPHA and Linux)

\src\  Directory containing the BOT3P source files

\Doc\  SICNUC-P9H6-006_rev0.pdf Report with BOT3P Version 5.4 description and
manuals

\test\ Directory containing all input, output, read-me and script files to
perform BOT3P test cases

\test\README_test: Read-me file with test case information
\test\run_6_tests_linux: Script file to run 6 BOT3P test cases for Linux
platform (probably working on other UNIX platforms)
\test\run_test: Script file to run all the 100 BOT3P test cases (for all
Linux/UNIX platforms)

\test\inp\ Directory containing 113 input files

\test\out\ Directory containing 260 BOT3P output files obtained after running
all test cases on Linux openSUSE 10.2 (g77)

\test\venus1_xy\ Directory containing all the files related to a GIP-DORT run in
order to produce a VARSCL format sequential binary file for BOT3P post-processor
applications in case of installation on UNIX platforms different from the tested
ones, and the VARSCL format binary files directly obtained in the tested ones
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17. CATEGORIES
  • C. Static Design Studies
  • L. Data Preparation

Keywords: mesh generation, three-dimensional, transport theory, two-dimensional.