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Migrate user guide/examples to mkdocs #470

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13ff0ae
Convert latex user guide to markdown
qiaojunfeng Feb 13, 2024
d8f5395
Update
qiaojunfeng Feb 13, 2024
047f32a
Switch to mathjax
qiaojunfeng Feb 13, 2024
7e95ef8
Add macro for `bm`
qiaojunfeng Feb 13, 2024
7390d5c
Use gfm flavor tables
qiaojunfeng Feb 13, 2024
b7d0585
Fix projections
qiaojunfeng Feb 13, 2024
4e17398
Fix projections
qiaojunfeng Feb 13, 2024
82e8910
Fix lib mode
qiaojunfeng Feb 13, 2024
f6accf4
Add overview.webp
qiaojunfeng Feb 13, 2024
2968dc2
Fix markdown files for postw90 and appendices (#1)
jiang-yuha0 Feb 13, 2024
df40bb0
Fix markdown file (#2)
jiang-yuha0 Feb 13, 2024
797f9f4
Fix transport
qiaojunfeng Feb 13, 2024
136057e
Fix files
qiaojunfeng Feb 13, 2024
027125d
Firt five tutorials for online version
Feb 14, 2024
7a7b89b
Fix markdown file for parameters chapter (#3)
npaulish Feb 14, 2024
3fbd067
17 tutorials for online version
Feb 14, 2024
aaba067
Add Section postw90/parameters
jiang-yuha0 Feb 14, 2024
7eb04b2
Fix tables in postw90/parameters.md file
npaulish Feb 14, 2024
8ebeb89
Update some links
jiang-yuha0 Feb 14, 2024
01987ae
24 tutorials for online version
Feb 14, 2024
f257c50
Added tutorial.md
Feb 14, 2024
74de353
Check the format of markdown files.
jiang-yuha0 Feb 14, 2024
3078e54
29 tutorials for online version
Feb 14, 2024
5f71b15
Fixing rendering of equations in t18 e t27
Feb 14, 2024
b8883a4
Remove absolute number in cross-file equation ref
jiang-yuha0 Feb 15, 2024
5cf2ccf
Add Section postw90/parameters
jiang-yuha0 Feb 14, 2024
dfd1daa
Fix tables in postw90/parameters.md file
npaulish Feb 14, 2024
836d7f4
Update some links
jiang-yuha0 Feb 14, 2024
77a4977
Check the format of markdown files.
jiang-yuha0 Feb 14, 2024
b6c7c44
Remove absolute number in cross-file equation ref
jiang-yuha0 Feb 15, 2024
abaf991
Merge branch 'mkdocs' of github.com:qiaojunfeng/wannier90 into mkdocs
jiang-yuha0 Feb 15, 2024
b7ca9cf
Up to tutorial 30 with all figures
Feb 15, 2024
f68d31e
Remove more absolute numbers
jiang-yuha0 Feb 15, 2024
23d3b85
Fix the figure label
jiang-yuha0 Feb 15, 2024
77ba15e
Up to tutorial 31 with all figures and bugfix
Feb 15, 2024
270cb92
solving conflicts in mkdocs.yml
Feb 15, 2024
b6eaf80
solving conflicts in mkdocs.yml
Feb 15, 2024
2dc33ca
Fix tutorials 32 and 33
npaulish Feb 15, 2024
ea4dbf2
Fix figures in Tutorials 32 and 33
npaulish Feb 15, 2024
721dad2
Fix figure captions in Tutorials 32 and 33
npaulish Feb 15, 2024
2dea9c3
Minor fixes in Tutorials 32 and 33
npaulish Feb 15, 2024
522da11
Add custom css
qiaojunfeng Feb 15, 2024
4d4f220
Merge tutorials
qiaojunfeng Feb 15, 2024
bc3be71
Firt five tutorials for online version
Feb 14, 2024
360af64
17 tutorials for online version
Feb 14, 2024
ca844ed
24 tutorials for online version
Feb 14, 2024
0ff1863
Added tutorial.md
Feb 14, 2024
772753a
29 tutorials for online version
Feb 14, 2024
084ab06
Fixing rendering of equations in t18 e t27
Feb 14, 2024
e263258
Up to tutorial 30 with all figures
Feb 15, 2024
ed12ac0
Up to tutorial 31 with all figures and bugfix
Feb 15, 2024
2418c8b
solving conflicts in mkdocs.yml
Feb 15, 2024
0cd4017
Fix tutorials 32 and 33
npaulish Feb 15, 2024
c83296b
Fix figures in Tutorials 32 and 33
npaulish Feb 15, 2024
261f917
Fix figure captions in Tutorials 32 and 33
npaulish Feb 15, 2024
41bf59b
Minor fixes in Tutorials 32 and 33
npaulish Feb 15, 2024
fffb333
Add custom css
qiaojunfeng Feb 15, 2024
e26720b
Merge tutorials
qiaojunfeng Feb 15, 2024
de77048
Fix the figure label
jiang-yuha0 Feb 15, 2024
3a5fa2c
Add link from user_guide to tutorial
jiang-yuha0 Feb 15, 2024
7b28553
Fix link
jiang-yuha0 Feb 15, 2024
f88ef6a
Fixing corss-references in the tutorials
Feb 15, 2024
a625afe
Fix caption in Tutorial 8
jiang-yuha0 Feb 15, 2024
2130831
Fixing corss-references in the tutorials
Feb 15, 2024
22e3919
Merge branch 'mkdocs_merge' into mkdocs_merge
qiaojunfeng Feb 15, 2024
c2468f2
Merge pull request #6 from VVitale/mkdocs_merge
qiaojunfeng Feb 15, 2024
0723cd4
Fix figcaption latex
qiaojunfeng Feb 15, 2024
ee9acd2
Changing all examples into tutorials, creating a markedown README and…
Feb 15, 2024
b02af31
Fix links
jiang-yuha0 Feb 15, 2024
27452fc
Fixing typos in Tutorial 17 and Tutorial 8
Feb 15, 2024
4af6254
Added logos folder into the docs
Feb 15, 2024
0a4717f
Set logo
qiaojunfeng Feb 15, 2024
ac55316
Minor fixes in the docs
npaulish Feb 15, 2024
d0f8b00
Merge remote-tracking branch 'upstream/develop' into mkdocs
qiaojunfeng Feb 15, 2024
48b76b4
Cleanup mkdocs yaml
qiaojunfeng Feb 15, 2024
7cf33db
Fix precommit hook for mkdocs.yml
qiaojunfeng Feb 16, 2024
dfdb98c
Add github workflow for mkdocs
qiaojunfeng Feb 16, 2024
743c0d4
Add CI for docs test
qiaojunfeng Feb 16, 2024
d451940
Removing old latex and PDF
giovannipizzi Feb 16, 2024
aa220a3
Fix md links
qiaojunfeng Feb 16, 2024
2bf895b
Enable strict mode of mkdocs
qiaojunfeng Feb 16, 2024
1566bdf
Update docs home
qiaojunfeng Feb 16, 2024
669a346
fixing link to equation in tutorial 29
Feb 16, 2024
4a5902a
Fixing paths to the correct tutorial folder on the github repo in the…
Feb 16, 2024
2767a46
Change docs color
qiaojunfeng Feb 16, 2024
97fc484
Use GITHUB_TOKEN
qiaojunfeng Feb 16, 2024
89a9a7c
Merge remote-tracking branch 'upstream/develop' into mkdocs
qiaojunfeng Feb 16, 2024
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Add link from user_guide to tutorial
Rename the example to tutorial in user_guide and add link from
user_guide to tutorial
jiang-yuha0 committed Feb 15, 2024

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commit 3a5fa2c1cc83e45168a3348e9617614d187e0da6
3 changes: 2 additions & 1 deletion docs/docs/user_guide/postw90/berry.md
Original file line number Diff line number Diff line change
@@ -397,7 +397,8 @@ Same as the case of optical conductivity, the parameter $\eta$ contained
in the
Eq. $\eqref{eq:kubo_shc_berry}$ can be chosen using the keyword
`[kubo_]smr_fixed_en_width`. Also, adaptive smearing can be employed by
the keyword `[kubo_]adpt_smr` (see Examples 29 and 30 in the Tutorial).
the keyword `[kubo_]adpt_smr` (see Tutorials [29](../../tutorials/tutorial_29.md)
and [30](../../tutorials/tutorial_30.md) in the Tutorial).

Please cite the following paper [@qiao-prb2018] or  [@ryoo-prb2019] when
publishing SHC results obtained using this method:
2 changes: 1 addition & 1 deletion docs/docs/user_guide/postw90/boltzwann.md
Original file line number Diff line number Diff line change
@@ -11,7 +11,7 @@ it is the main ingredient of the thermal conductivity).

The list of parameters of the `BoltzWann` module are summarized in
Table [ `BoltzWann` Parameters](../postw90params/#boltzwann-parameters).
An example of a Boltzmann transport
A [tutorial of a Boltzmann transport](../../tutorials/tutorial_16.md)
calculation can be found in the `wannier90` Tutorial.

!!! note
23 changes: 16 additions & 7 deletions docs/docs/user_guide/postw90/postw90params.md
Original file line number Diff line number Diff line change
@@ -82,30 +82,39 @@ The currently available modules in `postw90.x` are:

- `kpath`: Calculation of $k$-space quantities such as energy bands,
Berry curvature and Berry curvature-like term of spin Hall
conductivity along a piecewise linear path in the BZ (see examples
17, 18 and 29 of the tutorial).
conductivity along a piecewise linear path in the BZ (see tutorials
[17](../../tutorials/tutorial_17.md),
[18](../../tutorials/tutorial_18.md)
and [29](../../tutorials/tutorial_29.md) of the tutorial).

- `kslice`: Calculation of $k$-space quantities on a planar slice of
the BZ (see examples 17, 18 and 29 of the tutorial).
the BZ (see tutorials [17](../../tutorials/tutorial_17.md),
[18](../../tutorials/tutorial_18.md)
and [29](../../tutorials/tutorial_29.md) of the tutorial).

- `berry`: Calculation of properties related to the BZ integral of the
Berry curvature, Berry connection and Berry curvature-like term of
spin Hall conductivity, including anomalous Hall conductivity,
orbital magnetisation, optical conductivity, nonlinear shift current
and spin Hall conductivity (see
Chap. [Berry](../berry) and examples 18, 19, 25, 29 and 30 of the
Chap. [Berry](../berry) and tutorials
[18](../../tutorials/tutorial_18.md),
[19](../../tutorials/tutorial_19.md),
[25](../../tutorials/tutorial_25.md),
[29](../../tutorials/tutorial_29.md)
and [30](../../tutorials/tutorial_30.md) of the
tutorial). It also includes an option to compute $k\cdot p$
expansion coefficients (see
Sec. [kdotp](../berry/#sec:kdotp) and example 33 of the tutorial).
Sec. [kdotp](../berry/#sec:kdotp) and tutorial [33](../../tutorials/tutorial_33.md) of the tutorial).

- `gyrotropic`: Calculation of gyrotropic properties, including
natural and current0induced optical rotation, and the
current-induced magnetization (see
Chap. [Gyrotropic](../gyrotropic) and examples of the tutorial).
Chap. [Gyrotropic](../gyrotropic) and tutorial [24](../../tutorials/tutorial_24.md) of the tutorial).

- `BoltzWann`: Calculation of electronic transport properties for bulk
materials using the semiclassical Boltzmann transport equation (see
Chap. [BoltzWann](../boltzwann) and example 16 of the tutorial).
Chap. [BoltzWann](../boltzwann) and tutorial [16](../../tutorials/tutorial_16.md) of the tutorial).

- `geninterp` (Generic Band Interpolation): Calculation band energies
(and band derivatives) on a generic list of $k$ points (see
2 changes: 1 addition & 1 deletion docs/docs/user_guide/wannier90/parameters.md
Original file line number Diff line number Diff line change
@@ -825,7 +825,7 @@ part of the spread functional.

Total number of iterations in the minimisation procedure. Set
`num_iter=0` if you wish to generate projected WFs rather than
maximally-localized WFs (see Example 8 in the Tutorial).
maximally-localized WFs (see Tutorial [8](../../tutorials/tutorial_8.md) in the Tutorial).

The default value is 100

8 changes: 4 additions & 4 deletions docs/docs/user_guide/wannier90/postproc.md
Original file line number Diff line number Diff line change
@@ -207,15 +207,15 @@ method [@LinLin-ArXiv2017] is one way of generating the initial
$A_{mn}^{(\mathbf{k})}$ in an automatic way. This has been implemented
in the `pw2wannier90` interface code (you need v6.3 with the files
provided in the `pwscf` folder of Wannier90, or v6.4), see for instance
Example 27 in the `wannier90` tutorial that shows how to use it.
Tutorial [27](../../tutorials/tutorial_27.md) in the `wannier90` tutorial that shows how to use it.

Moreover, also the automatic generation of initial projections with
spinor WFs is implemented in the `pw2wannier90` interface. See Example
31 in the `wannier90` tutorial that shows how to use it.
spinor WFs is implemented in the `pw2wannier90` interface. See Tutorial
[31](../../tutorials/tutorial_31.md) in the `wannier90` tutorial that shows how to use it.

Another automatic projection method is projectability-disentangled
Wannier function (PDWF) [@Qiao2023-pdwf], which uses pseudo-atomic
orbitals inside pseudopotentials as initial guesses. See Example 34 and
orbitals inside pseudopotentials as initial guesses. See Tutorial [34](../../tutorials/tutorial_34.md) and
35.

#### An example of projections
4 changes: 3 additions & 1 deletion docs/docs/user_guide/wannier90/projections.md
Original file line number Diff line number Diff line change
@@ -440,4 +440,6 @@ format of the file is:
see the script `utility/write_pdwf_projectors.py`.

For an actual example of a `Si.dat` file for silicon, see the file
`examples/example35/ext_proj/Si.dat`.
[`tutorials/tutorial35/ext_proj/Si.dat`]
(https://github.com/wannier-developers/wannier90/tree/develop/tutorials/tutorial35/ext_proj/Si.dat).
<!-- The tutorial35 do not exist now, I just give the link -->
2 changes: 1 addition & 1 deletion docs/docs/user_guide/wannier90/transport.md
Original file line number Diff line number Diff line change
@@ -135,5 +135,5 @@ file:
A further parameter related to these calculations is
`tran_group_threshold`.

Examples of how 2c2 calculations are preformed can be found in the
Tutorial of [how 2c2 calculations are preformed](../../tutorials/tutorial_14.md) can be found in the
`wannier90` Tutorial.