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PyVCI_VPT2_manual.tex 2016-06-20 19.7 kB
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PyVCI_VPT2_manual.toc 2016-06-20 226 Bytes
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PyVCI_VPT2_manual.pdf 2016-06-20 198.3 kB
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PyVCI_VPT2_manual.blg 2016-06-20 882 Bytes
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PyVCI_VPT2_manual.log 2016-06-20 25.8 kB
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PyVCI_VPT2_manual.aux 2016-06-20 830 Bytes
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PyVCI_VPT2_manual.bbl 2016-06-20 275 Bytes
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example_3.pdf 2016-06-20 15.9 kB
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PyVCI_VPT2_manual_bib.bib 2016-06-20 1.2 kB
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example_1.pdf 2016-06-20 16.8 kB
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example_2.pdf 2016-06-20 14.7 kB
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Totals: 11 Items   294.6 kB 0 
#=================================================================================#
#                                                                                 #
#               PyVCI+VPT2 - Python VCI screened and corrected by VPT2            #
#                   Written by Marat Sibaev and Deborah Crittenden                #
#              University of Canterbury, Department of Chemistry, 2016            #
#                                                                                 #
#=================================================================================#

#=================================================================================#
#                             Contents Summary                                    #
#=================================================================================#
This package contains:
-> code: python and cython source code, with subdirectories;
   -> force_field: force field parser code and force field data file/s
   -> change_endianness: cython code to alter format of binary data files
   -> change_mat_format: cython code to convert binary data files from old
                         format in PyVCI to the new one
   -> C_code_Py27: cython code converted to C using Cython and Python2.7 
   -> C_code_Py34: cython code converted to C using Cython and Python3.4 
-> docs: LaTeX source and compiled manual, with pdf copies of tutorial input files
-> tutes: examples of how to use PyVCI, each in a separate subdirectory;
   -> tute_1: performing a VCI calculation with normal mode derivatives from file
   -> tute_2: loading derivatives from a force field module, and then
              - performing a serial VCI calculation
              - performing a parallel VCI calculation
   -> tute_3: performing a VCI+VPT2 calculation

#=================================================================================#
#                           Installation Instructions                             #
#=================================================================================#
Change into the code directory:
   cd code
Remove any old compiled module files (*.so), if existing:
   ./make_clean
Compile new module files (requires Cython + C compiler):
   python setup_cyth.py build_ext --inplace
Add this directory to your path (example for Mac OSX given)
   echo 'export PATH="$PATH:'$(pwd)'"' >> ~/.bash_profile
Restart your terminal/X-windows session

#=================================================================================#
#                               Usage Instructions                                #
#=================================================================================#
Change into a separate directory containing your/an example input file.
Invoke PyVCI_VPT2 using the following syntax:
   pyvci_vpt2.py input_file output_file

#=================================================================================#
#                                  Running Tests                                  #
#=================================================================================#
Mandatory tests, from this directory:
   cd tutes/tute_1
   pyvci.py example_1.in example_1.out
   cd ../tute_2
   pyvci.py example_2.in example_2.out
   cd ../tute_3
   pyvci.py example_3.in example_3.out
Source: README, updated 2016-06-20