https://github.com/superstar54/xaims

https://github.com/superstar54/xaims

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• Host: GitHub
• URL: https://github.com/superstar54/xaims
• Owner: superstar54
• Created: 2016-05-03T14:30:15.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2016-05-19T14:57:38.000Z (over 8 years ago)
• Last Synced: 2024-10-29T02:41:10.567Z (2 months ago)
• Language: Python
• Size: 45.9 KB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: readme.org

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README

        
=xaims= is an extension module for ase.calculators.aims.  Its primary purpose is smarter restarting capability, and job management/workflow, but it also has some enhanced capability too.

1. xaims automatically changes into the calculation directory to run jobs, and automatically changes back out when it is done.

2. xaims automatically submits jobs to the queue, and supports parallel and multiprocessing jobs.

3. xaims supports a lot more data extraction than ase.calculators.aims.

xaims requires python 2.6+ to work, and the latest svn version of ase.

* Installing xaims

** stable

2. Installation  requirement:

You need to install FHI-aims 

and ASE  

Make sure you can run FHI-aims from the command line, make sure the ase tests pass.

Python modules that xaims depends on:

ase

numpy

matplotlib

Optional:

scipy (for thermodynamics)

3. Installation :

** Configuring xaims

Create an executable script named runaims.py on your executable path.  This script is typically located in $HOME/bin

The script simply needs to run your aims executable in the current directory.

Here is an example file that chooses between serial and parallel executables depending on environment variables that are present in the TORQUE queue system:

#+BEGIN_SRC python

#!/usr/bin/env python

import os

serial_aims = '/home/xingwang/src/aims/bin/aims_serial_intel_mkl'

parallel_aims = '/home/xingwang/src/aims/bin/aims_openmpi_intel_mkl'

if 'PBS_NODEFILE' in os.environ:

    NPROCS = len(open(os.environ['PBS_NODEFILE']).readlines())

    if NPROCS == 1:

        print 'NPROCS = ',NPROCS

        exitcode = os.system(serial_aims)

    else:

        print 'NPROCS = ',NPROCS

        parcmd = 'mpirun -np %i %s' % (NPROCS,parallel_aims)

        exitcode = os.system(parcmd)

else:

    exitcode = os.system(serial_aims)

#end

#+END_SRC

Add  to your $HOME/.bashrc these commands:

#+BEGIN_SRC sh

export AIMS_SCRIPT=/your path to runaims.py/runaims.py  # example $HOME/bin/runaims.py

#+END_SRC

Create $HOME/.xaimsrc file. This hidden file contains the following informtation:

#+BEGIN_EXAMPLE

# xaims configuration file

# adjust these for the your system

aims.executable.serial = /opt/xingwang/aims-5.2.12/build/bin/aims-vtst

aims.executable.parallel = /home/xingwang/src/aims/bin/aims_openmpi_intel_mkl

user.name = xingwang

user.email = [email protected]

mode = queue   # run|queue|None

multiprocessing.cores_per_process = None

# these are only needed if you run in a queue

queue.command = qsub

queue.options = -joe

queue.walltime = 168:00:00

queue.nodes = 1

queue.ppn = 1

queue.mem = 2GB

queue.jobname = None

#+END_EXAMPLE

* Uninstalling xaims

#+BEGIN_SRC sh

pip uninstall xaims

#+END_SRC

* Long-term plans for Xaims

* Files

[[./__init__.py]] - just imports everything from xaims

[[./xaims.py]]

Contains the xaims class and xaims context manager. Code to see if calculation finished ok. Code to see if you are in a aims directory. Is also an executable script that runs xaims

[[./xaimsrc.py]] - configuration for xaims

[[./xaims_extensions.py]] - monkey patches to ase.calculators.aims, hook functions, run and calculate function, pretty print functions. some additional get functions.