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Name Modified Size InfoDownloads / Week
Parent folder
wrappers 2015-06-02
0
force_field 2015-06-02
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useful.py 2015-06-02 36.9 kB
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constants.py 2015-06-02 654 Bytes
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make_clean 2015-06-02 43 Bytes
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setup_cyth.py 2015-06-02 518 Bytes
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to_normal_mode_cyth.c 2015-06-02 15.5 MB
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to_normal_mode_cyth.pyx 2015-06-02 491.1 kB
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transform.c 2015-06-02 1.7 MB
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transform.pyx 2015-06-02 66.2 kB
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coords_transform.py 2015-06-02 596.8 kB
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normal_mode.py 2015-06-02 15.7 kB
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pes_derivs.py 2015-06-02 23.1 kB
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pypes_lib.py 2015-06-02 11.5 kB
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read_input.py 2015-06-02 38.1 kB
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state.py 2015-06-02 15.8 kB
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Totals: 16 Items   18.5 MB 0 
#=================================================================================#
#                                                                                 #
#          PyPES - Python Analytical Potential Energy Surface Library             #
#                             Written by Marat Sibaev                             #
#             University of Canterbury, Department of Chemistry, 2015             #
#                                                                                 #
#=================================================================================#

#=================================================================================#
#                             Contents Summary                                    #
#=================================================================================#
The full distribution is provided in the .tgz file:
   PyPES_Library.tgz
To extract the contents:
   tar xvfz PyPES_Library.tgz
This package contains:
-> code: python and cython source code, with subdirectories;
   -> force_field: force field parser code and force field data file/s
   -> wrappers: a set of code fragments to read and parse derivative data
                generated by PyPES 
-> docs: LaTeX source and compiled manual, with benchmark frequency data
-> tutes: examples of how to use PyPES, each in a separate subdirectory;
   -> tute_1: minimal working examples, will all keywords except those pertaining
              to force field definition (MOLECULE AND PESN) set by default 
   -> tute_2: geometry specification in Cartesian and internal coordinates, 
              geometry optimization with respect to energy, mass specification
              and normal mode analysis 
   -> tute_3: transformation between internal coordinates, saving force field in
              new set of internal coordinates or normal mode coordinates
   -> tute_4: working with force fields saved in normal mode coordinates
   -> tute_5a/5b: using PyPES to generate Cartesian derivative data, analogous
              to output from ab initio program packages. Wrapper scripts in a 
              range of languages that call PyPES and read in derivative data
   -> tute 6: structure of force-field modules, some comments on implementing
              new force fields, designed for force field developers

#=================================================================================#
#                           Installation Instructions                             #
#=================================================================================#
Change into the code directory:
   cd PyPES_Library/code
Remove any old compiled module files (*.so), if existing:
   ./make_clean
Compile new module files from C source (requires Cython + C compiler):
   python setup_cyth.py build_ext --inplace
Add this directory to your path

#=================================================================================#
#                               Usage Instructions                                #
#=================================================================================#
Syntax:
   pypes.py input_file (output_file - optional, see manual)

#=================================================================================#
#                                   Licensing                                     #
#=================================================================================#
All code contained herein released under the MIT license, 
see MIT_license.txt in docs subdirectory for terms and conditions
Source: README, updated 2016-02-29