Updates to CrystalOutputPlugin

populate final with energy and primitive_cell:

• if optimisation, energy taken from last optimisation step
• if scf only, energy and primitive_cell taken from initial

Also fixed and changed initial/calculation/hamiltonian to initial/calculation/functional

Finalise charge/spin density parsing

• corrected array transpose
• removed na, nb, nc as superfluous
• added more tests (QE and Crystal)
• added validation schema
• added validation of numpy arrays
• added reading and conversion of QE plotnum to density type

Use Feedback Updates

• added gaussian cube parser and standardised QE/Crystal density
• added gcube.ejdict_to_gcube, to output back to gaussian cube format
• changed program type Crystal14 to CRYSTAL
• replaced DOSSPlugin with CrystalDOSPlugin
• added testing fro Crystal17
• added band gap extraction from Crystal17 outputs
• added extraction of meta/elapsed_time for crystal and quantum espresso
• added QEdosPlugin
• added case where no optimisation steps required (crystal)
• updated pymatgen outputs (which has added charges to structure)

Improved/corrected gaussian cube charge/spin density parsing


Changes:

• Crystal: computation of cell vectors from (voxel) delta vectors
• QEspresso: coords are ccords/alat, rather than fcoords

added QELowdinPlugin

v0.4.5

added QELowdinPlugin

Updated QEspresso main plugin

• final scf iteration run if zero absolute magnetization found in lsda
  relaxation
• magnetic moments per atom printed every 100 scf iterations

added QEChargeDensityPlugin

v0.4.3

added QEChargeDensityPlugin

Crystal: attempt to read complete sections on error

v0.4.2

Crystal: attempt to read complete sections on error

Crystal: added total_corrected energy and CrystalSCFLogPlugin

also added pymatgen and ase encoder/decoder plugins

improved error message

v0.3.1

added init