KUCRS-Building
(c) 2002–2017 by A. Miyoshi
All rights reserved.
KUCRS
– Knowledge-basing Utilities for Complex Reaction Systems –

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Building KUCRS

  Here is an instruction to build and execute KUCRS on UNIX.  See Getting Started to use the pre-build binaries on Windows.  Below may also be helpful to rebuild KUCRS on Windows.

1. Building

  In the following instruction, KUCRS is assumed to be extracted in the user's home directory, ~/, though actual location can be anywhere.  If you have extracted KUCRS in the another location, assume ~/KUCRS to be the directory where you actually extracted it. 

Decompress

  Decompress the downloaded zip archive, 'KUCRS-xxxxxxxx.zip', as follows.
[usr@machine ~]$ unzip KUCRS-xxxxxxxx.zip

Compile

Change directory to ~/KUCRS/sources.  The following makefiles are provided.  Select appropriate one and edit if necessary.
makeGnu.makeGNU compiler (UNIX/BSD/Linux)
makeIntelLinux.makeIntel compiler (Linux)
makeIntelWin.makeIntel compiler (Windows)
Execute make (nmake on Windows).
[usr@machine sources]$ make -f selected_make.make
After confirming that the compilation has been successfully completed, execute the 'install' target.  Executable files will be moved to ~/KUCRS/bin.
[usr@machine sources]$ make -f selected_make.make install
Execute the 'clean' target to remove temporary files.
[usr@machine sources]$ make -f selected_make.make clean
Change directory to ~/KUCRS and execute the cshell script ~/KUCRS/prep_envKUCRS.
[usr@machine ~/KUCRS]$ csh prep_envKUCRS
This sets execution permission to cshell script files in ~/KUCRS/bin and generates a file ~/KUCRS/work/envKUCRS.csh.

2. Execution of samples

Setting environment

If you are using a shell other than csh or tcsh, invoke csh or tcsh.  Then source ~/KUCRS/work/envKUCRS.csh.  Note that this must be done every time you log-in.  Set the content of ~/KUCRS/work/envKUCRS.csh in .cshrc if necessary.
[usr@machine work]$ source envKUCRS.csh

Running autogeneration program

Change directory to ~/KUCRS/work/sample and type:
[usr@machine sample]$ run_comb i-butane
to run autogeneration program with the sample input i-butane.inp.
  If properly executed, this will give seven new files named
i-butane.log
i-butane_chg.log
i-butane_chm.inp
i-butane_mol.dat
i-butane_mol.log
i-butane_snk.inp
i-butane_trn.dat
  i-butane_mol.log contains information on the chemical structures etc. of the chemical species.   It contains SMILES representations of the chemical structures.   If you need a simple list of the names and SMILES of the chemical species, convert the KUCRS internal format data in i-butane_mol.dat to SMILES representations by the mol2smiles tool.   For this, type,
[usr@machine sample]$ mol2smiles i-butane_mol.dat i-butane_sml.inp
The files i-butane_mol.dat and i-butane_mol.log contain the information only on the automatically generated chemical species.  The C2 species or smaller are registered in the base mechanism and the information on these base species are written in the corresponding files, ~/KUCRS/libdat/\mol_main.dat and ~/KUCRS/libdata/ref/mol_main.log.
- The shell script run_com provides the simplest way of running the autogeneration program.  For simplicity, it deletes intermediate outputs which are not necessary to run CHEMKIN.  To keep all the intermediate outputs, use run_comb_nodel.
- Use 'run_comb_htnox' script to append the high-temperature NOx production mechanism.
  Some more sample inputs other than i-butane.inp can be found in ~/KUCRS/work/advanced_examples.
alcohols.inp
alkanes.inp
alkenes.inp
diesel-prf.inp
gasoline-prf.inp

Running tools for chemical species data generation

In ~/KUCRS/work/sample, type:
[usr@machine sample]$ proc_smiles spcex
to generate following files containing the thermodynamic and transport data from the list of species names and SMILES structure representations provided in spcex.inp
spcex_thg.dat
spcex_thg.lst
spcex_trn.dat
  The file spcex_thg.dat contains thermodynamic data in NASA polynomial format used by CHEMKIN, spcex_thg.lst contins thermodynamic data in list format of THERM, and, spcex_trn.dat contains the transport data used by CHEMKIN.  The details of the KUCRS components invoked by proc_smiles can be found in the User's
Guide
.