lp:~albertog/siesta/4.1-yaml

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Merged into lp:siesta/4.1 at revision 921

Yann Pouillon (community): Approve on 2018-05-29

Diff: 1791 lines (+1671/-5)

16 files modified

Docs/YAML.README (+13/-0)
Docs/yaml_tests/Makefile (+216/-0)
Docs/yaml_tests/README (+5/-0)
Docs/yaml_tests/analysis.rst (+137/-0)
Docs/yaml_tests/conf.py (+290/-0)
Docs/yaml_tests/implementation.rst (+65/-0)
Docs/yaml_tests/index.rst (+22/-0)
Src/Makefile (+5/-4)
Src/m_io_yaml.F90 (+215/-0)
Src/siesta.F (+3/-0)
Tests/Scripts/yaml_compare.py (+303/-0)
Tests/YAML_Refs/benzene.yml (+45/-0)
Tests/YAML_Refs/h2o.yml (+45/-0)
Tests/YAML_Refs/mno_ldau.yml (+45/-0)
Tests/siesta-testsuite.yml (+258/-0)
version.info (+4/-1)

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923. By Alberto Garcia on 2018-05-30

Remove Transiesta pre-processed items

922. By Alberto Garcia on 2018-05-29

Remove _build/html files in Docs/yaml_tests

921. By Alberto Garcia on 2018-05-29

YAML infrastructure for output testing

(By Yann Pouillon)

The implementation consists of:

* A simple hook in siesta.F to call the siesta_write_yaml routine
in module Src/m_io_yaml.F90.

* A YAML reference directory: Tests/YAML_Refs/
  (currently populated by just three token examples)

* A post-processing script: Tests/Scripts/yaml_compare.py

* A configuration file Tests/siesta-testsuite.yml

See Docs/yaml_tests/README for more information.

Notes

- Only energies are processed in this initial implementation.
- The post-processing script depends on ruamel.yaml (pip install [--local] ruamel.yaml)
- SIESTA does not require LibYAML to emit YAML files

920. By Nick Papior on 2018-05-25

Fixed transiesta-tbtrans tests

Some tests did not force the TSHS creation for electrodes.

919. By Alberto Garcia on 2018-05-19

Put an io_close call in the right block

An out-of-block io_close in basis_io might inadvertently close unit 0.

918. By Alberto Garcia on 2018-05-15

Consolidate treatment of KB and LDAU projectors in hsparse/atom_graph

Avoid extra work when both KB and LDAU projectors are present, and
clarify the code.

917. By Alberto Garcia on 2018-05-15

Remove obsolete options related to auxiliary supercell

The options 'FixAuxiliaryCell' and 'NaiveAuxiliaryCell' have
been removed, as they are inconsistent with the more stringent tests
on the adequacy of the auxiliary supercell.

916. By Alberto Garcia on 2018-05-15

Merged 4.0-576: diagnostics and clarifications on folding

915. By Nick Papior on 2018-05-14

Fixed worksize for the self-energy expansion for very small device regions

There was a bug when having a too small device region. In those cases
the calculated work-size was too small. It should be fixed now.

914. By Nick Papior on 2018-05-14

Updated manual for the k-point sampling of electrodes