qmcpack/nexus

====================
==  Nexus Readme  ==
====================

Contents
  1) About Nexus 
  2) Installation instructions
  3) Summary of library files 




1. About Nexus
======================================================================
  
  Nexus was written by Jaron T. Krogel starting in 2012 at UIUC.
  Most of the code was developed at ORNL after Dec. 2012.




2. Installation instructions (Linux only)
======================================================================

 a. Ensure that Python and NumPy are available
 -------------------------------------------------

   The vast majority Linux distributions come with Python pre-installed.
  
   To check for Python, type "python3 --version" at the command line.
   You should see something like "Python 3.6.9".  Nexus is only 
   compatible with Python 3.x (2.x is no longer supported). If Python 3
   is not present on your system, you can install it by following the 
   instructions at:
  
     https://docs.python-guide.org/starting/installation/
  
   With Python present, check for pip3.  Type "pip3 --version" at the
   command line.  You should see something like:

     pip 9.0.1 from /usr/lib/python3/dist-packages (python 3.6)

   For basic (minimum) functioning of Nexus, numpy is required.
   Optional dependencies include scipy, matplotlib, h5py, pydot, 
   spglib, pycifrw, cif2cell and seekpath.  If not already present, 
   these can all be installed via pip3:

     pip3 install --user numpy
     pip3 install --user scipy
     pip3 install --user matplotlib
     pip3 install --user h5py
     pip3 install --user pydot
     pip3 install --user spglib
     pip3 install --user PyCifRW
     pip3 install --user cif2cell
     pip3 install --user seekpath

   Please see the Nexus user guide (PDF) for more information about 
   installing dependencies and how they are used by Nexus.


 b. "Install" Nexus
 -------------------------------------------------
   All that should be needed to get Nexus working on your system
   is to add the path to its library files to the PYTHONPATH 
   environment variable. 
   
   If the path to the directory this README file sits in is:
   
     /your/path/to/nexus/
   
   Then you can add one line to the .bashrc file in your 
   home directory:
   
     export PYTHONPATH=/your/path/to/nexus/lib/:$PYTHONPATH
   
   After adding this line, type "source $HOME/.bashrc".  Now check 
   that Nexus is available by typing "python" then "import nexus".
   You should be able to use Nexus if the the import proceeds 
   without incident (i.e. no messages displayed).

   The executables packaged with Nexus can be used once they are 
   added to the PATH environment variable.  Do this by adding 
   the following line to your .bashrc file:
   
     export PATH=/your/path/to/nexus/bin/:$PATH

   Both of these steps can alternately be performed by the 
   installer packaged with Nexus.  To use it, simply type 
   the following at the command line:

     >/your/path/to/nexus/install

   Check the end of your .bashrc (or equivalent) to make sure the 
   PATH and PYTHONPATH variables have been set properly.

   If you want the binaries to be copied to a location outside 
   the downloaded Nexus distribution, then just provide that as 
   a path to the installer:

     >/your/path/to/nexus/install /some/other/location


3. Summary of important library files
======================================================================

 The information below can assist in navigating the Nexus program.
 See headers of individual Python files for more detail.

 a. Core facilities
 -------------------------------------------------

   abilities.py, generic.py, developer.py 
   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Abstract base classes for all Nexus classes.  Defines abilities 
     such as querying, printing, etc.  Also provides developer 
     interface functions such as error reporting and redirection for 
     unimplemented base class functions.  Void class protects imports 
     and halts execution if items from unavailable modules are 
     encountered.
 
   project_base.py
   ~~~~~~~~~~~~~~~
     Base class for core Nexus classes. Communicates settings 
     information throughout the system.
 
   project.py, nexus.py
   ~~~~~~~~~~~~~~~~~~~~
     Central collection (imports) of all Nexus classes.  Interface 
     to the "settings" function.
 
   structure.py
   ~~~~~~~~~~~~
     Contains the Structure class and structure generator functions.
 
   physical_system.py
   ~~~~~~~~~~~~~~~~~~
     Contains PhysicalSystem class and particle information.
 
   simulation.py
   ~~~~~~~~~~~~~
     Contains Simulation, SimulationInput, and SimulationAnalyzer 
     base classes.  All core functionality of Simulation objects is 
     defined here.  Also contains derived simulation classes (sim, 
     input, analyzer) for generic simulation codes.  Enables driving 
     of virtually any single or multi- input file simulation code by 
     using input file templates.
 
   machine.py
   ~~~~~~~~~~
     Contains Job, Machine, Workstation, and Supercomputer classes.
     Also contains all derived Supercomputer classes (Titan, Edison, 
     Mira, etc.)
 
   project_manager.py
   ~~~~~~~~~~~~~~~~~~
     Contains ProjectManager class.  Code controlling workflow 
     management is generally shared between ProjectManager and 
     Simulation.
 
   bundle.py
   ~~~~~~~~~
     Contains a facility (the "bundle" function) for bundling 
     many simulation jobs into a single, larger batch job.



 b. Derived classes for specific simulation codes
 -------------------------------------------------

   QMCPACK
   ~~~~~~~
     Simulation:         qmcpack.py
     SimulationInput:    qmcpack_input.py 
     SimulationAnalyzer: qmcpack_analyzer.py
   
     Supporting analysis classes: 
       qaobject.py, qmcpack_analyzer_base.py, 
       qmcpack_method_analyzers.py, qmcpack_property_analyzers.py,
       qmcpack_quantity_analyzers.py,qmcpack_result_analyzers.py,
       spacegrid.py
 
     Orbital conversion tools for QMCPACK:
       convert4qmc.py, pw2qmcpack.py, wfconvert.py
 
   PWSCF
   ~~~~~
     Simulation:         pwscf.py
     SimulationInput:    pwscf_input.py    (read/write any input file)
     SimulationAnalyzer: pwscf_analyzer.py (parse log output and data~file.xml)
 
   VASP
   ~~~~~
     Simulation:         vasp.py
     SimulationInput:    vasp_input.py    (read/write any input file)
     SimulationAnalyzer: vasp_analyzer.py (parse OUTCAR and vasprun.xml)
 
   GAMESS
   ~~~~~~
     Simulation:         gamess.py
     SimulationInput:    gamess_input.py    (read/write any input file)
     SimulationAnalyzer: gamess_analyzer.py (parse log output)
 
   SQD
   ~~~
     Simulation:         sqd.py
     SimulationInput:    sqd_input.py    
     SimulationAnalyzer: sqd_analyzer.py 
     
   OPIUM
   ~~~~~
     opium.py contains all three (sim, input, analyzer)



 c. Miscellaneous facilities
 -------------------------------------------------

   debug.py
   ~~~~~~~~
     Adds support for interactive code break points.
 
   periodic_table.py
   ~~~~~~~~~~~~~~~~~
     Access to periodic table data in a structured object format.
 
   numerics.py, extended_numpy.py
   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Statistics and curve fitting support.
 
   unit_converter.py
   ~~~~~~~~~~~~~~~~~
     Unit conversion of scalars and arrays.
 
   xmlreader.py
   ~~~~~~~~~~~~
     Class to convert XML file into structured object format.
 
   hdfreader.py
   ~~~~~~~~~~~~
     Class to convert HDF5 file into structured object containing 
     numpy arrays.
 
   fileio.py
   ~~~~~~~~~
     Interface to XSF files.  Other will go here later.
 
   plotting.py
   ~~~~~~~~~~~
     Access to plotting functions via matplotlib.
 
   pseudopotential.py
   ~~~~~~~~~~~~~~~~~~
     Classes representing pseudopotentials.  Functions supporting 
     pseudopotential conversion.
 
   template_simulation.py
   ~~~~~~~~~~~~~~~~~~~~~~
     Example and explanation for developers interested in 
     implementing new derived Simulation classes for codes 
     not yet supported by Nexus.