Before AK commits

This is a technical release of the code state before major merge with AK branch of siman.

pypi rev2

Most importantly, now all modules are moved to siman package
be careful updating your code

new regime for calc_method in add_loop:
'Monte-Carlo' - Monter Carlo simulation above DFT

sshpass parameter in clusters now can take 'proxy' value. this allows to connect cluster with sshpass using proxy.
TODO: now proxy server and path to password is hardcoded in run_on_server(), push_to_server() and download()

new attibute added to calculation objects: self.cluster - dictionary with all parameters for cluster

read_poscar() moved from classes.py to inout.py as a separate function

new type 'void' with Z = 300 added to system. It is not written in POSCAR. Be carefull, bugs are expected,
since cl.add_potcar() and cl.calculate_nbands() are affected

BUGS:
bug related to the wrong reading of forces with selective dynamics was fixed (st.select was used from init, while in end the order of atoms can change)
now in the end structure is always created as new one. So, no i

but with incorrect writing of magmom in the case of atom reordering for poscar was fixed;
warning! if you provide magmom in set, than you should take care that the provided order is consistent with that in generated POSCAR

further_improvent

cl.fix_atoms() method added

bug fixed in cl.run()

calc_oxidation_states() improved, use silent = 0 to show charges

get_surface_area() added to Structure()

get_dipole() added to Structure()

cl.get_bader_ACF() improved

creating_sets tutorial updated

'jmol' option of show in res() added

calculation name in output changed to db['name']

st.jmol() now uses vasp format

new property st.outfile - path to output file added

mcif argument added to write_xyz() enabling visualization of magnetic structures with jmol=1

cl.add_new_name() method added

cluster_tools/fit_tool.py new paths added for numpy support on cee cluster (local change for skoltech)

now modules are written for SLURM from project_conf.py, please add them as in example below:
CLUSTERS['cee']['modules'] = 'module add prun/1.0; module add intel/16.0.2.181; module add impi/5.1.3.181\n'

New tutorial for calc_barriers subroutine

bug chgcar

1. Bug with copy chgcar on server was eliminated

Bader tutorial

1. New tutorial for Bader charges
2. Small bug fix for Bader calculations

stable master

From this point the master is stabilised.
dimonaks makes updates to simanaks branch
every month all branches are merged into master and new version is released

Improvements

0.7

auto

Further_improvements

v0.6

auto

2017

v0.5

auto

supercell tutorial

v0.4

auto