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234 Commits

Author SHA1 Message Date
Oleg Peil
33f9e75857 Changed 'generate_ortho_plos()' to 'generate_plo()' 
Generation and orthogonalization of PLOs should be separated
because some quantities (such as the LDA density matrix) are calculated
using the original raw projectors.
The orthogonalization routine is now called from 'main.py'.
 2015-10-11 13:55:48 +02:00
Oleg Peil
b325028efd Fixed the calculation of 'nelect' 
In the previous commit the calculation of 'nelect' was implemented
incorrectly. The sum over k-points must also contain k-weights
and a spin factor (2.0 for ns = 1).

The calculation of 'nelect' is now implemented as a separate method
of ProjectorGroup.
 2015-10-11 13:55:48 +02:00
Oleg Peil
b78a06d36f Added output of PLO groups 
Output of PLO groups into a text file is added to 'plo_output()'.
The file format is provisional and can change in future versions.

Also, an attribute 'nelect' providing the number of electrons in
the selected energy window is added to ProjectorGroup.
 2015-10-11 13:55:48 +02:00
Oleg Peil
6ab916d2d0 Added (empty) function 'plo_output()' 2015-10-11 13:55:05 +02:00
Oleg Peil
b6250477f2 Fixed 'generate_ortho_plos()' to produce orthogonalized PLOs 2015-10-11 13:55:05 +02:00
Oleg Peil
d0a75edec3 Added a simplest workflow to 'main.py' 
Simplest workflow: read config-file, vasp data, generate PLOs,
and output them to text files.
 2015-10-11 13:55:05 +02:00
Oleg Peil
bec28dbefd Added examples directory with one example 'simple' 
Apart from their direct purpose as a help to users, examples may serve
as integrity tests. Eventually, one can convert them into a test suite.
 2015-10-11 13:55:05 +02:00
Oleg E. Peil
5d8423a30e Added preliminary 'main.py' 2015-10-11 13:55:05 +02:00
Oleg E. Peil
89ab594253 Added test output files forgotten in the previous commit 2015-10-11 13:55:05 +02:00
Oleg E. Peil
4c920b8312 Added some documentation on PLOtools 
The documentation has been slightly rewritten and extended to follow
the recent changes. The modifications include:

- ProjectorSet class is now replaced by ProjectorShell
- the workflow has been refined
- the electronic structure part is represented by class ElectronicStructure
 2015-10-11 13:55:05 +02:00
Oleg E. Peil
3317371762 Added calculation of density matrices for a shell 
A method 'density_matrix()' for evaluating a density matrix of a given shell
has been added to class ProjectorShell. It requires an ElectronicStructure
object as an input an by default produces a site- and spin-diagonal
part of the density matrix using the Fermi-weights obtained directly from VASP.
Ideally, this density matrix should coincide with the one calculated
within VASP itself (inside the LDA+U module).

Corresponding sanity test has been added, which shows only that the
calculation does not crash. Real numerical tests are needed.
 2015-10-11 13:55:05 +02:00
Oleg E. Peil
ad6b3ab708 Added class ElectronicStructure 
Class ElectronicStructure is intended for the internal representation
of the band structure and raw projector data from VASP.
In addition, its purpose is to perform a simple consistency check
of the input VASP data (as they are read from different files).
 2015-10-11 13:55:05 +02:00
Oleg E. Peil
0c4e3ad006 Changed order of indices of 'proj_arr' array 
When a ProjectorShell is created it creates a view of the full
projector array with orbital 'ilm' and band 'ib' indices interchanged.
The reason for this is that this corresponds more naturally to the
definition of the projector P_{m\nu} and also allows for multiplications
of projector matrices without additional transposition.

The tests have been modified accordingly.
 2015-10-11 13:55:04 +02:00
Oleg E. Peil
a0e9d1a18e Added a test suite for ProjectorGroup class 
A preliminary test suite for class 'ProjectorGroup' was added.
Currently, only a simplest test is performed testing that
after the input is processed the resulting projectors selected
within a given energy window are corret.
 2015-10-11 13:55:04 +02:00
Oleg E. Peil
9bbd71afb9 Fixed a bug in 'inpconf.py' 
The problem was that when one shell was specified without an explicit
group the created automatic group was lacking the default values for
parameters 'normalize' and 'normion'. The current design, however,
assumes that they must always be set.
 2015-10-11 13:55:04 +02:00
Oleg E. Peil
5c3b3d0b8d Added several tests 
Tests for 'select_bands()' and class 'ProjectorShell' have been added.
The function and class methods have been fixed accordingly to pass
the tests.
 2015-10-11 13:55:04 +02:00
Oleg E. Peil
90c93c4693 Fixed a bug in 'inpconf.py', added a corresponding test 2015-10-11 13:55:04 +02:00
Oleg E. Peil
b05d176f39 Fixed 'vaspio.py' to pass the tests' 2015-10-11 13:55:04 +02:00
Oleg E. Peil
82cc06d41e Added a test suite for module 'vaspio' 2015-10-11 13:55:04 +02:00
Oleg E. Peil
36aadf6ff4 Removed redundant index reassignments in 'c_plocar_io.c' 2015-10-11 13:55:04 +02:00
Oleg E. Peil
46474c0b3e Modified 'c_plocar_io.c' to conform Numpy 1.7 API 2015-10-11 13:55:04 +02:00
Oleg E. Peil
7e894d98f6 Added a small test suite for 'c_plocar_io' module 2015-10-11 13:55:04 +02:00
Oleg E. Peil
19a30034f5 * Replaced direct compilation in Makefile by 'setup.py' from 'distutils' 
* NO_DEPRECATED_API flag was added and now 'c_plocar_io.c' does not compile
 2015-10-11 13:55:04 +02:00
Oleg E. Peil
f0ae1c9927 Added untested 'ProjectorGroup' class (including orthogonalization routine) 2015-10-11 13:55:04 +02:00
Oleg E. Peil
ba015d4b62 Added untested version of 'ProjectorShell' class 2015-10-11 13:55:04 +02:00
Oleg E. Peil
74ef3ca93e Added defulats to optional group parameters 2015-10-11 13:55:04 +02:00
Oleg E. Peil
9d4fb22572 Rearranged test cases for 'inpconf.py'. 
A single-file test suite for 'inpconf.py' is split into several files,
each containing a separate TestCase class. In addition, all test cases
are derived from class ArrayTestCase (in turn derived from TestCase)
which contains a numpy-array equality method.
 2015-10-11 13:55:04 +02:00
Oleg E. Peil
a58ec59c9c Added Scenario 5 to 'test_parse_input()' and fixed 'inpconf.py' to pass it 2015-10-11 13:55:04 +02:00
Oleg E. Peil
74a1ad280d Added Scenario 4 to 'test_parse_input()' (test10.cfg) 2015-10-11 13:55:04 +02:00
Oleg E. Peil
bcc20a0399 * Added Scenario 3 to 'test_parse_input()' (test9.cfg) 
* Fixed 'parse_input()' to pass the test
 2015-10-11 13:55:04 +02:00
Oleg E. Peil
8928fa3118 * Added Scenario 2 to 'test_input()' (test8.cfg) 
* Removed group parameter 'shells' from a dict of required parameters
   for a single [Shell] section
 2015-10-11 13:55:04 +02:00
Oleg E. Peil
8b60a91e49 Completed 'test_parse_groups()' 2015-10-11 13:55:04 +02:00
Oleg E. Peil
3516ebd285 * Replaced 'test_groups_shells_consistency()' with 'test_parse_input()' 
* Fixed Scenario 1 of 'test_parse_input()'
  * Fixed Scenario 1 of 'test_parse_groups()'
 2015-10-11 13:55:04 +02:00
Oleg E. Peil
d2fe6d50e8 * Fixed tests for the modified version of 'parse_shells()' 
* Removed redundant prints in 'parse_shells()'
 2015-10-11 13:55:04 +02:00
Oleg Peil
76d0b4a6bb Small syntax fix in inpconf.py 2015-10-11 13:55:04 +02:00
Oleg Peil
0816d45d59 * Added (empty) function 'parse_general()' * Completed 'parse_input()' 2015-10-11 13:55:03 +02:00
Oleg Peil
9ab6116b28 * Completed group parser 
* Added a consistency check for groups and shells
 * Added scenario descriptions to the test suite
 2015-10-11 13:55:03 +02:00
Oleg Peil
0d1ef0ac97 Small fixes in config.rst 2015-10-11 13:55:03 +02:00
Oleg Peil
f393168d16 * Added a test 'parse_groups()' 
* Added to docs for config-file a description of all features that
    are implemented or under active development
 2015-10-11 13:55:03 +02:00
Oleg Peil
bd6198d264 * Restructured the directory structure * Added some half-day long development including tests 2015-10-11 13:55:03 +02:00
Oleg Peil
e85d3b4f2b Initial commit 2015-10-11 13:55:03 +02:00
Manuel Zingl
929b459681 Removes work around for issue #41 2015-08-10 16:14:51 +02:00
Manuel Zingl
6ecbf6720d Fix converter bug occuring in sp case. 
max(n_orbitals) changed to numpy.max(n_orbitals)
 2015-07-16 12:27:01 +02:00
Priyanka Seth
335dee2042 Fixes a bug when reading case.oubwin 
Code does not crash anymore if number of k-points differ
    in case.oubwin and case.klist. Added a warning.
 2015-07-07 15:26:04 +02:00
Manuel Zingl
60c6466ace Some changes wien2k_converter 
convert_bands_input and convert_parproj_input can now be called
    without calling convert_dft_input directly before.
 2015-07-07 15:08:53 +02:00
Manuel Zingl
aef5072cad Fixes a little bug in wien2k_converter.py 2015-04-30 19:05:24 +02:00
Priyanka Seth
79b4b426a8 Modify HDFArchive calls to 'r' where possible to handle corrupt files 2015-04-27 13:12:28 +02:00
Priyanka Seth
8dc42b08ae [doc] New documentation 
* restructuring
* added user reference
* started working on user guide
* added schematic to structure
 2015-04-21 14:31:15 +02:00
Priyanka Seth
335fd6cbc6 [converter] fix bug in misc_converter 2015-03-22 18:15:05 +01:00
Priyanka Seth
9585f6f482 [converter] removed n_k consistency check 2015-03-18 10:30:01 +01:00
Priyanka Seth
cff9015362 [converter] rm debug statement 2015-03-11 17:52:41 +01:00
Manuel Zingl
1fbdf8bf38 Fix for issue #32 2015-03-03 18:43:50 +01:00
Manuel Zingl
a24c7869b1 Corrects a bug in convert_misc_input 2015-02-24 18:14:05 +01:00
Manuel Zingl
8db46b16b5 Reading misc_input files only if present 2015-02-20 15:15:17 +01:00
Manuel Zingl
373764f680 Fix error in transport code, some modifications 2015-02-18 00:27:00 +01:00
Priyanka Seth
674059506f Minor clean up. 2015-02-10 16:35:12 +01:00
Priyanka Seth
54de186ebb Move oubwin, struct and outputs info into dft_misc_input 2015-02-10 11:55:44 +01:00
Manuel Zingl
e0509ab741 Fix for minor bug, changes in transport test 2015-01-27 20:32:50 +01:00
Priyanka Seth
fc742ffa3d Fixed bug in convert_bands_input 2015-01-22 14:15:29 +01:00
Priyanka Seth
c1ac9c85c8 Unify notation in sumk_dft_tools. 
You *may* need to run
"pytriqs update_archive.py filename.h5 v1.2"
to update the archive if you have dft_parproj_input is present.
 2015-01-22 10:47:53 +01:00
Manuel Zingl
4249d7d9d3 Correction of a minor bug in transport code. 2014-12-23 13:03:01 +01:00
Manuel Zingl
b3b199bf40 Restore everything which was lost in rebase. 2014-12-19 11:53:06 +01:00
Priyanka Seth
f24913b8a7 [transport] more minor changes 2014-12-18 18:23:00 +01:00
Priyanka Seth
6f1ffdfb86 [transport] Preliminary tidiying up of transport converter 2014-12-09 17:01:14 +01:00
Manuel Zingl
e1b8c4757b [transport] API changes 2014-12-09 17:00:49 +01:00
Manuel Zingl
9283702fc1 [transport] Change names, correct some issues in merge 
Simplify writing/reading from h5
 2014-12-09 17:00:46 +01:00
Manuel Zingl
2ee744854e [transport] Divide transport into appropriate files 
Put functions of the initial transport files to the appropriate places in
wien2k_converter and sumk_dft_tools
 2014-12-09 17:00:29 +01:00
Priyanka Seth
3c6b3e3093 Fix typo in routine name convert_dmft_input 2014-12-09 12:26:00 +01:00
Priyanka Seth
ff6dd7ce73 [API] Changed form of shells and corr_shells to list of dicts. 2014-11-26 17:37:57 +01:00
Manuel Zingl
acfd19fa87 Add mpi import in converter_tools (related to issue #23) 2014-11-20 14:25:07 +01:00
Priyanka Seth
376d9b3693 Fix #23 : repack error, add path to hdf5 2014-11-19 18:50:53 +01:00
Priyanka Seth
84bd1ed655 Allow for hdf filename that differs from dft data basename 2014-11-19 16:38:52 +01:00
Priyanka Seth
88f4105e5b Renamed everything from 'lda' to 'dft' 2014-11-18 11:44:14 +01:00
Priyanka Seth
518cbccd8c Write shell equivalency information directly into h5 at conversion 
* changed shellmap and invshellmap to corr_to_inequiv and inequiv_to_corr
* update_archive now calculates and stores these quantities for old archives
 2014-11-16 18:03:53 +01:00
Priyanka Seth
b672839f83 Tidy up of symmetry 
*changed map -> orb_map in symmetry to avoid using python keyword
 2014-11-16 18:03:53 +01:00
Priyanka Seth
a7f2a5096f Move repeated converter functions in converter_tools.py 2014-11-14 09:41:03 +01:00
Priyanka Seth
8bbbe81c7d Converters clean up, new subgroup names 
* Provided script update_archive.py to convert old h5 archives.
* Fixed all tests
 2014-11-05 15:56:40 +01:00
Priyanka Seth
9793daf86b Change execs to setattr, getattr, etc 2014-11-05 15:56:33 +01:00
Priyanka Seth
906398894a Changes to old interface files to comply with new gf_struct 
Minor tidy-up too.
 2014-09-22 19:27:27 +02:00
aichhorn
4fb1f67645 bugfixes in hk_converter 2014-04-03 14:34:36 +02:00
aichhorn
3f5ce764a7 Added more flexible H(k) reading 2014-04-02 18:36:48 +02:00
aichhorn
e10c48e106 Added first draft of general converter to handle general H(k) 
Added also routine to rotate basis sets
 2014-04-02 17:54:31 +02:00
Michel Ferrero
cd650884d3 Clean CMakeLists.txt 2013-08-07 16:30:09 +02:00
Olivier Parcollet
0e585ad9b4 First import. triqs 1.0 alpha1 2013-07-23 20:55:29 +02:00