Removed old STM script
New STM code along the FD method propagating WFs into the vacuum gap
Fix scale factor for electronic band structure in unit cell
Fix factor for H symmetry point at hexagonal lattices. Electronic band structure still not working.
SupercellPhonons: Skip looking for point group when running an electronic band structure calculation (type TSdir=True)
SupercellPhonons: lasto variable was not correctly identified if the geometry was the primitive cell
Include verbose option on setkpoint function to avoid printing to many data.
Allow for electronic band structure calculation on unit-cells. Include new keyword TSdir on Bandstructures utility.
SetupRuns: Added writing of keyword TS.HS.Save to SetupFCrun [the older TS.SaveHS appears to be deprecated since siesta 4.1 r833]
Script added to k-average IETS spectra calculated at specific k-points
scripts: updated siesta_cleanup and added average-gridfunc
ValueCheck: Fix for absolute path to electrode TSHS files
SiestaIO: Ignore _.- characters when looking up FDF keywords
SiestaIO.WriteXYZFile: Print only skipped number of ghost atoms if any
SiestaIO.WriteXYZFile: Fix if atomnumber is a list (instead of array)
Skip writing ghost atoms to .xyz files (ask for .XYZ instead if you want to keep ghost atoms)
VaspIO: Fixed sign when reading imaginary phonon frequencies
NEGF.py: Speed-up of eigenchannel calculations (thanks to N. Papior for patch)
MakeGeom.rotate(): Fixed RotationCenter.
MakeGeom: Allow rotation of lattice vectors too
geom2zmat fix
Inelastica.py: Added some comments on the LOE expressions
MiscMath.SpectralMatrix: Sign error in the subtraction algorithm fixed. This bug should not have affected any real results as subtraction is apparently not used in the code (apart from in a non-critical LOE-WBA print check of 'aK21-Iasym' in Inelastica.py).
kaverage-TBT: Fix to handle Gamma-only files wh...
Inelastica.py: Changed append->write (a->w) in ...
Replaced deprecated optparse with argparse in E...
Replaced deprecated optparse with argparse in s...
Added script for easy extraction and k-averagin...
Inelastica/SupercellPhonons: Removed import of ...
Phonons: Write netCDF4 directly (skip WriteNetC...
TestCalculations: Fixed some issues with the ex...
Phonons.py: Fixed datatype specifiers (integer ...
Minor stuff, a simple print statement and asser...
Inelastica.py: Removing CurrentHWidx check whic...
Replaced dependency on Scientific.IO.NetCDF wit...
pyTBT: Computing PDOS onto MPSH states
NEGF: enabled transport in x or y (A1 or A2) di...
ValueCheck: Look up TS.Elecs block instead of a...
EigenChannels: Skip bond currents if k!=Gamma (...
EigenChannels: Changed default format to XSF
SetupRuns.SetupFCrun: Copy also .TSDE files to ...
Phonons.py: Changed isotope option, now one spe...
NEGF.py: Print energy and transmission to sdout
Inelastica.py: Simplified anr consistency check
SiestaIO.WriteXYZFile(...): Unknown elements ge...
Introduced a k-point check before calculating b...
SupercellPhonons.py: New functionality to compu...
Added scripts WriteWavefunctions and agr2pdf
SiestaIO: Fix when path-to-file is not provided...
Updated electrode read
SupercellPhonons: More complete info written to...
Symmetry.py: Fixed warning message (variable sh...
MakeGeom.BuildOnlyS(...): Displacement amplitud...
Symmetry.py: Orthorhombic lattice type added.
ValueCheck: New electrode format now takes prec...
ValueCheck: Fixed issue with function call with...
Made electrode value-checks easier
EigenChannels: Write also absolute square of wa...
More appropriate variable names for the semi-in...
ValueCheck: Set path to current directory (if n...
EigenChannels/Inelastica/pyTBT generalized to a...
Phonons: Included a sanity check of .onlyS file...
Phonons: Added option -g to write the real-spac...
Phonons: Unified numpy array types (H,S,dH,...)...
VaspIO: Fix to read POSCAR/CONTCAR in cartesian...
Phonons: Cleanup (removed stuff to modify atomi...
Inelastica.py: Added reference to Bevilacqua et...
EigenChannels: Write all molecular eigenvalues ...
SupercellPhonons.py: Implemented sorting method...
Vasp2Siesta/VaspIO: Improved flexibility
Only to specify on the previous fix: The bug wi...
BUG: Gamma are not real matrices. This should o...
SpectralMatrix: adding numpy + spectral matrix ...
Stupid bug: Assert real diag part of Gamma
Fix: Assert diag(Gamma) is real (not full matrix)
Fix: cast to real for Gamma point Heph calc
VaspIO.py improve read/write of constraints
ValueCheck.py: Avoid raise LookupError(...)
Updated option readings for the latest transies...
ValueCheck.py: Finds electrode TSHS files and r...
Changed all type calls to isinstance which also...
NEGF.py: Minor fix (A.shape not defined for a S...
MiscMath.py: Fixed runtime warning for Spectral...
Inelastica.py: Fixed dagger operator for Spectr...
Inelastica.py: First implementation of inelasti...
Inelastica.py: Renaming and more output from As...
Phonons.py: Fixed EPHfirst=FCfirst and EPHlast=...
Symmetry.py: Fixed high-symmetry points for lat...
Updated new_dist.sh and removed dist/
ComputeDOS script now also handles spin
SupercellPhonons.py: Enabled spin polarized cal...
SupercellPhonons.py: Missed a factor 2pi on gen...
SupercellPhonons.py: Redefined wavevectors acco...
Symmetry.py: Adopted Magnus' recent changes
SupercellPhonons.py: Reduced some data to stdou...
Bandstructures/ComputeDOS: Scripts enabled for ...
SupercellPhonons.py: Output to netcdf only. Ban...
Examples/Phonon_bands: Updated Reference_Results
Phonons.py: Bugfix for eigenvectors multiplied ...