https://github.com/zerothi/sisl

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Revision Author Date Message Commit Date
9643a9d sisl release: 0.9.2 Signed-off-by: Nick Papior <nickpapior@gmail.com> 25 October 2017, 19:35:17 UTC
60dcab7 maint: updated changelog Signed-off-by: Nick Papior <nickpapior@gmail.com> 25 October 2017, 19:33:13 UTC
2f2a3e3 bug: fixed supercell skipping if atoms are not with-in unit-cell This was due to commits around 8327fb54. These plane *can* be re-inserted once we shift the initial supercell position to the minimum XYZ coordinates. Added checks when writing a Hamiltonian in Siesta if one misses the diagonal terms in a tight-binding Hamiltonian (otherwise we cannot ensure S == I) Signed-off-by: Nick Papior <nickpapior@gmail.com> 25 October 2017, 19:29:53 UTC
f70e85b bug: fixed XSF file for vesta, read/write multiple energy points XSF files for VESTA cannot have blank lines, now we insert # for everything. The Hamiltonian will now complain if you will try write a Hamiltonian with 0 non-zero elements. deltanc file could, apparently, not read/write multiple energy-points. I am not to sure why this was the case, but know I have changed it slightly and added more tests for this to assert it works. Signed-off-by: Nick Papior <nickpapior@gmail.com> 25 October 2017, 18:50:10 UTC
dedffd1 bug: fixed wannier90 read of the Hamiltonian Tried this on the Silicon example and could reproduce the system. Signed-off-by: Nick Papior <nickpapior@gmail.com> 24 October 2017, 15:46:53 UTC
78ca408 bug: fixed bug in orbital_current when isc was used Currently isc is not used, so it should not be of quick importance Signed-off-by: Nick Papior <nickpapior@gmail.com> 24 October 2017, 07:28:47 UTC
3ff0565 Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> 23 October 2017, 08:04:45 UTC
7370f9c sisl release: 0.9.1 Signed-off-by: Nick Papior <nickpapior@gmail.com> 23 October 2017, 08:03:33 UTC
b8f248d bug: fixed reading when the tabular has too many delimiters Also added more tests for this. Signed-off-by: Nick Papior <nickpapior@gmail.com> 22 October 2017, 13:00:13 UTC
d601f0e bug: fixed SileError issuing and raise on Table-write Signed-off-by: Nick Papior <nickpapior@gmail.com> 20 October 2017, 12:44:52 UTC
a154742 bug: fixed command-line utility for TBT.nc Now the arguments seem to be parsed in the correct order. One should *only* run_collect_action when it *has* to be forced for all arguments. Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 October 2017, 19:08:05 UTC
27e7712 doc: fixed links in other.rst Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 October 2017, 17:03:51 UTC
6423397 maint: added license badge Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 October 2017, 16:59:21 UTC
94238c4 doc: added other document Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 October 2017, 11:31:28 UTC
dfa6e92 maint: updated changelog Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 October 2017, 09:37:31 UTC
d10d857 bug: fixed position of take keyword in orbital_current And speeded up extraction of sub-columns. Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 October 2017, 08:11:21 UTC
ff354c1 maint: updated defaults for bond-currents etc. orbital_current still returns all, bond_current defaults to only positive. The reasoning is that orbital currents are typically not used in their bare form. They are typically used for post-processing in bond_current_from_orbital or atom_current_from_orbital where the defaults are different. atom_current requires *all* values while bond_currents will it-self default to remove the negative values Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 October 2017, 07:52:42 UTC
ebb4493 enh: fixed un-needed loop and also used _array in atom Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 October 2017, 07:43:16 UTC
a8da40b maint: used Atom() instead of Atom[] and fixed minor things Signed-off-by: Nick Papior <nickpapior@gmail.com> 18 October 2017, 07:30:29 UTC
36e08cc enh: enabled empty start-end in energy range and atom range The strmap and strseq now accepts start and end such that one can specify everything up-to 1 eV e.g. 10 atoms. This however, has the consequence that if one specifies non-allowed atoms they are silently removed. There will only be a warning issued if *all* atoms are outside the region. Signed-off-by: Nick Papior <nickpapior@gmail.com> 17 October 2017, 18:47:58 UTC
ebef481 enh: made vector-current easier to compare between the different settings The default for vector_current(..., sum='+') in which case one *only* probes the outgoing transmission. This makes more sense as the other atoms shows where their electrons are moving, respectively. I have amended the documentation regarding this to clarify the intent. Also made a comment about halving the vector_current in case sum='all'. This is because one can then compare agains the incoming/outgoing vector currents. Signed-off-by: Nick Papior <nickpapior@gmail.com> 17 October 2017, 13:57:00 UTC
fd13d13 bug: fixed bond-current scaling It should not have had the factor 1/2. Now the transmission and bond-transmission can be exactly reproduced and tested for: - bond_current - orbital_current - atom_current - transmission are all the same with a proper setup system (even with k-points). I think this completes the tests for the bond-currents and asserts Kirchoff laws. Signed-off-by: Nick Papior <nickpapior@gmail.com> 17 October 2017, 11:25:36 UTC
eedf509 maint: fixed description Signed-off-by: Nick Papior <nickpapior@gmail.com> 17 October 2017, 08:19:11 UTC
4df3e21 maint: trying to list dependencies in json file Signed-off-by: Nick Papior <nickpapior@gmail.com> 17 October 2017, 07:07:29 UTC
7d7e8ab maint: moved NEWS to CHANGELOG and added a package.json Currently, I can not figure out how to list Python dependencies in the json file, perhaps npm figures this out. Signed-off-by: Nick Papior <nickpapior@gmail.com> 17 October 2017, 07:00:17 UTC
b53fabb Merge branch 'master' of github.com:zerothi/sisl 16 October 2017, 08:12:39 UTC
f7fa715 maint: prepared next release version in NEWS Signed-off-by: Nick Papior <nickpapior@gmail.com> 16 October 2017, 08:12:25 UTC
a0e100f Reverting internal release Signed-off-by: Nick Papior <nickpapior@gmail.com> 16 October 2017, 08:00:56 UTC
be62516 sisl release: 0.9.0 Signed-off-by: Nick Papior <nickpapior@gmail.com> 16 October 2017, 07:59:33 UTC
7de485a bug: fixed TableSile and write-out for numerous things Now it correctly read and writes tables of varying lengths. Since we can now read data, it is also much easier to handle data. Also fixed T-eig extractions etc. Signed-off-by: Nick Papior <nickpapior@gmail.com> 15 October 2017, 12:50:52 UTC
b5492b0 maint: removed landscape.yaml Signed-off-by: Nick Papior <nickpapior@gmail.com> 15 October 2017, 07:32:06 UTC
f1f3e6d maint: added author and copyright to the __init__ file Signed-off-by: Nick Papior <nickpapior@gmail.com> 13 October 2017, 20:00:17 UTC
1481484 maint: add landscape Signed-off-by: Nick Papior <nickpapior@gmail.com> 13 October 2017, 12:19:23 UTC
5d115e2 enh: fixed a_dev We have to assert that tbtrans stores a sorted a_dev Signed-off-by: Nick Papior <nickpapior@gmail.com> 13 October 2017, 11:36:21 UTC
9304198 enh: added geometry to tbt files Signed-off-by: Nick Papior <nickpapior@gmail.com> 13 October 2017, 09:32:52 UTC
158fd88 bug: fixed CDF sile reads by introducing with in get-siles Probably we need to rework the _open keyword so it really is only opened when needed. Signed-off-by: Nick Papior <nickpapior@gmail.com> 12 October 2017, 10:07:07 UTC
4e2134b bug: added close to SileCDF to enable correct closing NetCDF files Also fixed repr of SparseCSR. Signed-off-by: Nick Papior <nickpapior@gmail.com> 12 October 2017, 08:36:32 UTC
9243b21 travis: fixing build (5) Signed-off-by: Nick Papior <nickpapior@gmail.com> 12 October 2017, 07:21:24 UTC
e68537d travis: fixing build (4) Signed-off-by: Nick Papior <nickpapior@gmail.com> 12 October 2017, 07:13:24 UTC
5523022 travis: fixing build (3) Signed-off-by: Nick Papior <nickpapior@gmail.com> 12 October 2017, 07:05:05 UTC
3e5e065 travis: fixing build (2) Signed-off-by: Nick Papior <nickpapior@gmail.com> 12 October 2017, 06:51:11 UTC
b1079ab travis: fixing build (1) Signed-off-by: Nick Papior <nickpapior@gmail.com> 12 October 2017, 06:40:04 UTC
2ac2169 maint: added __bibtex__ to enable easier citations Also added a cite() function which returns __bibtex__. Signed-off-by: Nick Papior <nickpapior@gmail.com> 12 October 2017, 06:31:26 UTC
467de11 maint: moved plot.py to _plot.py Signed-off-by: Nick Papior <nickpapior@gmail.com> 11 October 2017, 20:56:39 UTC
54a5d00 travis: fixed tests Re-inserted the distance maxima in Geometry.distance. Signed-off-by: Nick Papior <nickpapior@gmail.com> 11 October 2017, 20:10:34 UTC
6906e40 travis: trying to fix doctests Signed-off-by: Nick Papior <nickpapior@gmail.com> 11 October 2017, 19:52:11 UTC
dbed267 test: added doctests to ensure we have the documentation up to date Signed-off-by: Nick Papior <nickpapior@gmail.com> 11 October 2017, 19:47:38 UTC
4959e40 doc: removed specific linalg routines from the linalg module Signed-off-by: Nick Papior <nickpapior@gmail.com> 11 October 2017, 13:02:14 UTC
4db8cf1 maint: updated NEWS and trying to remove linalg routines from toc Signed-off-by: Nick Papior <nickpapior@gmail.com> 11 October 2017, 12:42:44 UTC
b464a04 maint: changed which to what in center Signed-off-by: Nick Papior <nickpapior@gmail.com> 11 October 2017, 12:36:21 UTC
04676ba enh: added sum to the sparse matrix, implemented this for rij Added Rij routines to return vectors between the sparse elements. Also added orij and oRij to the geometry. Bugfixes in tbt.py after converting the _array module. Also removed the dH files such that they truly are deprecated. Now dH and dSE are delta files. Added a sum routine to the SparseCSR class. This currently implements row sums and last dimension sums. Simplified the rij routines to not work for what='orbital' if it is a SparseAtom. Perhaps this may be re-enabled later. Added more tests for the above and the new sum routine. Signed-off-by: Nick Papior <nickpapior@gmail.com> 11 October 2017, 09:31:20 UTC
e9b1cb6 doc: added doc to long_description for pypi Signed-off-by: Nick Papior <nickpapior@gmail.com> 08 October 2017, 10:10:35 UTC
ddf5cc1 test: updated quaternion tests Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 October 2017, 20:05:53 UTC
bd1e72e test: finished tests for siesta unit Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 October 2017, 13:09:40 UTC
e611172 test: added all tests for unit Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 October 2017, 12:43:58 UTC
02264bb test: added more cmd tests Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 October 2017, 12:16:33 UTC
675fdc5 maint: updated decorator names for easier usage Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 October 2017, 12:06:13 UTC
187bc82 enh: changed default of iR to 20 Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 October 2017, 10:09:19 UTC
2b6ade5 enh: simplified for nsc == 1 cases Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 October 2017, 09:42:31 UTC
8327fb5 enh: speeded up plane-checks in close Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 October 2017, 09:18:27 UTC
9627dc0 doc: added examples to the plane calulations Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 October 2017, 08:58:45 UTC
38810b3 enh: added plane for supercell and speeded up close Now SuperCell class implements a plane method to retrieve a normal vector and point on the plane (the normal vector ALWAYS points outwards). These utilites are now used in the close() method to reduce computations of unnecessary supercell indices. This has proven to be twice as fast for bigger systems. Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 October 2017, 08:38:55 UTC
67f6c85 maint: added optimization notebook Signed-off-by: Nick Papior <nickpapior@gmail.com> 06 October 2017, 05:48:23 UTC
f40c7ba enh: removed unnecessary check in iR Signed-off-by: Nick Papior <nickpapior@gmail.com> 05 October 2017, 20:10:18 UTC
62b8d6f enh: added info to tbtnc Signed-off-by: Nick Papior <nickpapior@gmail.com> 05 October 2017, 17:29:07 UTC
c9c3f28 enh: added normalization to BDOS Signed-off-by: Nick Papior <nickpapior@gmail.com> 05 October 2017, 13:56:42 UTC
7959e57 maint: codacy warning updates Signed-off-by: Nick Papior <nickpapior@gmail.com> 05 October 2017, 13:41:49 UTC
9dbef1b travis: fixed build script Signed-off-by: Nick Papior <nickpapior@gmail.com> 05 October 2017, 13:19:55 UTC
2659666 travis: again Signed-off-by: Nick Papior <nickpapior@gmail.com> 05 October 2017, 13:16:48 UTC
3f744cd travis: added codacy coverage report Signed-off-by: Nick Papior <nickpapior@gmail.com> 05 October 2017, 13:11:06 UTC
4168bce maint: codacy warning updates Signed-off-by: Nick Papior <nickpapior@gmail.com> 05 October 2017, 12:52:34 UTC
ed2f3b4 maint: codacy warning updates Signed-off-by: Nick Papior <nickpapior@gmail.com> 05 October 2017, 12:47:11 UTC
bf343e4 maint: changed list2range to list2str Signed-off-by: Nick Papior <nickpapior@gmail.com> 05 October 2017, 12:37:58 UTC
2a2c300 test: added even more tests Signed-off-by: Nick Papior <nickpapior@gmail.com> 05 October 2017, 09:38:33 UTC
0e373ab cov: ignore test directories Signed-off-by: Nick Papior <nickpapior@gmail.com> 05 October 2017, 05:34:49 UTC
21336ef bug: fixed spin implementation Now it has a specific kind parameter which fixes the type, independent on the data-type and size used. Also fixed tests. Signed-off-by: Nick Papior <nickpapior@gmail.com> 05 October 2017, 05:22:55 UTC
96269d6 maint: codacy warning updates Signed-off-by: Nick Papior <nickpapior@gmail.com> 05 October 2017, 04:08:55 UTC
8d72da6 enh: split _numpy_scipy to _array and linalg This accommodates two things: 1) It separates the _array manipulation routines from the linear algebra 2) it allows the LA routines to be imported and used more easily. Once scipy 1.X is released we will get access to all eigenvalue solvers. Also added tests for some of the linear algebra routines, to assert they return equivalent as scipy.linalg. Signed-off-by: Nick Papior <nickpapior@gmail.com> 04 October 2017, 19:47:58 UTC
61f9329 enh: split _numpy_scipy to _array and linalg This accommodates two things: 1) It separates the _array manipulation routines from the linear algebra 2) it allows the LA routines to be imported and used more easily. Once scipy 1.X is released we will get access to all eigenvalue solvers. Signed-off-by: Nick Papior <nickpapior@gmail.com> 04 October 2017, 18:23:49 UTC
6dfc229 bug: fixed all check for shape comparison Signed-off-by: Nick Papior <nickpapior@gmail.com> 04 October 2017, 14:58:56 UTC
434ef34 bug: fixed several bugs in the sgrid command utility Also added more tests for the sgrid. Still more to cover, and more elaborate tests. Signed-off-by: Nick Papior <nickpapior@gmail.com> 04 October 2017, 14:56:46 UTC
33cc516 doc: removed skipped members which are only for devs Signed-off-by: Nick Papior <nickpapior@gmail.com> 04 October 2017, 11:14:37 UTC
b514105 enh: changed savetxt and loadtxt to internal read/writes This will accommodate more easy handling of output/input as there were compatibility problems with python 3. Signed-off-by: Nick Papior <nickpapior@gmail.com> 04 October 2017, 08:10:52 UTC
fdfde79 enh: removed buffer, not needed Signed-off-by: Nick Papior <nickpapior@gmail.com> 03 October 2017, 20:48:17 UTC
76887f8 bug: final fix for removal of savetxt Signed-off-by: Nick Papior <nickpapior@gmail.com> 03 October 2017, 20:36:21 UTC
fb5310d bug: again, trying to fix savetxt Signed-off-by: Nick Papior <nickpapior@gmail.com> 03 October 2017, 20:26:53 UTC
2306b7f bug: again, trying to fix savetxt Signed-off-by: Nick Papior <nickpapior@gmail.com> 03 October 2017, 19:53:16 UTC
c7587ab bug: trying to work-around the python 3 savetxt w/wb Signed-off-by: Nick Papior <nickpapior@gmail.com> 03 October 2017, 19:41:56 UTC
e7aaa85 test: added grid tests Signed-off-by: Nick Papior <nickpapior@gmail.com> 03 October 2017, 18:29:29 UTC
9772a88 enh: added write out of the grid.nc files Added write_grid to grid.nc files. Also updated documentation with respect to citations. Signed-off-by: Nick Papior <nickpapior@gmail.com> 03 October 2017, 18:03:08 UTC
0a8a9c7 doc: fixed citation Signed-off-by: Nick Papior <nickpapior@gmail.com> 03 October 2017, 13:13:24 UTC
7c69f80 doc: added citation documentation Signed-off-by: Nick Papior <nickpapior@gmail.com> 03 October 2017, 13:01:36 UTC
0702119 maint: moved units to unit module, shorter and still precise Signed-off-by: Nick Papior <nickpapior@gmail.com> 28 September 2017, 14:58:36 UTC
688e3ec maint: removed conda update to assert used version Signed-off-by: Nick Papior <nickpapior@gmail.com> 28 September 2017, 07:29:24 UTC
8556fef maint: updated representation of geometry Signed-off-by: Nick Papior <nickpapior@gmail.com> 27 September 2017, 20:05:00 UTC
ac955d7 maint: trying to add gcc to apt-get Signed-off-by: Nick Papior <nickpapior@gmail.com> 27 September 2017, 18:38:33 UTC
afcb306 maint: trying to fix rtd build by only building html Signed-off-by: Nick Papior <nickpapior@gmail.com> 27 September 2017, 18:26:43 UTC
419446d doc: updated readme with new io module Signed-off-by: Nick Papior <nickpapior@gmail.com> 26 September 2017, 13:20:18 UTC
0fcb966 bug: fixed angle calculation for supercells Also changed all radians keywords to rad, this is less verbose, yet very clear. Signed-off-by: Nick Papior <nickpapior@gmail.com> 26 September 2017, 11:48:01 UTC
720a889 doc: cleaned docs and removed tons of warnings Signed-off-by: Nick Papior <nickpapior@gmail.com> 26 September 2017, 10:52:54 UTC
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