Activity for Thomas Frederiksen
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Thomas Frederiksen committed [r455]
SupercellPhonons: Skip looking for point group when running an electronic band structure calculation (type TSdir=True)
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SupercellPhonons: lasto variable was not correctly identified if the geometry was the primitive cell
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SetupRuns: Added writing of keyword TS.HS.Save to SetupFCrun [the older TS.SaveHS appears to be deprecated since siesta 4.1 r833]
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Script added to k-average IETS spectra calculated at specific k-points
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scripts: updated siesta_cleanup and added average-gridfunc
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ValueCheck: Fix for absolute path to electrode TSHS files
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SiestaIO: Ignore _.- characters when looking up FDF keywords
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SiestaIO.WriteXYZFile: Print only skipped number of ghost atoms if any
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SiestaIO.WriteXYZFile: Fix if atomnumber is a list (instead of array)
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Skip writing ghost atoms to .xyz files (ask for .XYZ instead if you want to keep ghost atoms)
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VaspIO: Fixed sign when reading imaginary phonon frequencies
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NEGF.py: Speed-up of eigenchannel calculations (thanks to N. Papior for patch)
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MakeGeom.rotate(): Fixed RotationCenter.
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MakeGeom: Allow rotation of lattice vectors too
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geom2zmat fix
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Inelastica.py: Added some comments on the LOE expressions
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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).
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kaverage-TBT: Fix to handle Gamma-only files wh...
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Inelastica.py: Changed append->write (a->w) in ...
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Replaced deprecated optparse with argparse in E...
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Replaced deprecated optparse with argparse in s...
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Added script for easy extraction and k-averagin...
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Inelastica/SupercellPhonons: Removed import of ...
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Phonons: Write netCDF4 directly (skip WriteNetC...
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TestCalculations: Fixed some issues with the ex...
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Phonons.py: Fixed datatype specifiers (integer ...
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Minor stuff, a simple print statement and asser...
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Inelastica.py: Removing CurrentHWidx check whic...
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Replaced dependency on Scientific.IO.NetCDF wit...
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pyTBT: Computing PDOS onto MPSH states
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NEGF: enabled transport in x or y (A1 or A2) di...
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ValueCheck: Look up TS.Elecs block instead of a...
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EigenChannels: Skip bond currents if k!=Gamma (...
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EigenChannels: Changed default format to XSF
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SetupRuns.SetupFCrun: Copy also .TSDE files to ...
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Phonons.py: Changed isotope option, now one spe...
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NEGF.py: Print energy and transmission to sdout
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Inelastica.py: Simplified anr consistency check
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SiestaIO.WriteXYZFile(...): Unknown elements ge...
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Introduced a k-point check before calculating b...
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SupercellPhonons.py: New functionality to compu...
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Added scripts WriteWavefunctions and agr2pdf
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SiestaIO: Fix when path-to-file is not provided...
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SupercellPhonons: More complete info written to...
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Symmetry.py: Fixed warning message (variable sh...
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MakeGeom.BuildOnlyS(...): Displacement amplitud...
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Symmetry.py: Orthorhombic lattice type added.
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ValueCheck: New electrode format now takes prec...
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ValueCheck: Fixed issue with function call with...
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EigenChannels: Write also absolute square of wa...
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More appropriate variable names for the semi-in...
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ValueCheck: Set path to current directory (if n...
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EigenChannels/Inelastica/pyTBT generalized to a...
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Phonons: Included a sanity check of .onlyS file...
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Phonons: Added option -g to write the real-spac...
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Phonons: Unified numpy array types (H,S,dH,...)...
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VaspIO: Fix to read POSCAR/CONTCAR in cartesian...
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Phonons: Cleanup (removed stuff to modify atomi...
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Inelastica.py: Added reference to Bevilacqua et...
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EigenChannels: Write all molecular eigenvalues ...
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SupercellPhonons.py: Implemented sorting method...
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Vasp2Siesta/VaspIO: Improved flexibility
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Only to specify on the previous fix: The bug wi...
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VaspIO.py improve read/write of constraints
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ValueCheck.py: Avoid raise LookupError(...)
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ValueCheck.py: Finds electrode TSHS files and r...
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NEGF.py: Minor fix (A.shape not defined for a S...
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MiscMath.py: Fixed runtime warning for Spectral...
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Inelastica.py: Fixed dagger operator for Spectr...
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Inelastica.py: First implementation of inelasti...
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Inelastica.py: Renaming and more output from As...
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Phonons.py: Fixed EPHfirst=FCfirst and EPHlast=...
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Symmetry.py: Fixed high-symmetry points for lat...
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ComputeDOS script now also handles spin
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SupercellPhonons.py: Enabled spin polarized cal...
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SupercellPhonons.py: Missed a factor 2pi on gen...
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SupercellPhonons.py: Redefined wavevectors acco...
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Symmetry.py: Adopted Magnus' recent changes
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SupercellPhonons.py: Reduced some data to stdou...
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Bandstructures/ComputeDOS: Scripts enabled for ...
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SupercellPhonons.py: Output to netcdf only. Ban...
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Examples/Phonon_bands: Updated Reference_Results
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Phonons.py: Bugfix for eigenvectors multiplied ...
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SupercellPhonons.py: Bugfix, self.basisatom now...
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SupercellPhonons.py: Default is now only to wri...
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The writing of k-path file moved from Symmetry....
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Examples/Phonon_bands: Cleanup, adopted usual F...
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Symmetry.py: Rewrote high-symmetry points and p...
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Examples/Phonon_bands updated (Au_FCC, Na_BCC, ...
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Symmetry/SupercellPhonons: Recovered automatic ...
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Added setupOSrun/setupFCrun scripts; added chec...
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Fixed AuH2 example
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Inelastica.py: digamma function for asymmetric ...
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SupercellPhonons: Fixed description of reciproc...
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SupercellPhonons.py: Separate input files for e...
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Phonons.py: Fixed issue for nonpositive mode fr...
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SupercellPhonons.py: Write band structure in xm...
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Symmetry.py: Cleanup (fix of bug introduced in ...
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Bugfix: Symmetry operations were not applied to...
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The script Bandstructures automatically assumes...
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