Add docs/postw90/postw90params.md file

docs/docs/user_guide/introduction.md

@@ -18,7 +18,7 @@ about the `wannier90` code, check the official repository of
 about its functionalities.
 
 Finally, many frequently asked questions are answered in
-Appendix [2](#chap:faq){reference-type="ref" reference="chap:faq"}. An
+Appendix [FAQs](../appendices/faq/). An
 expanded FAQ session may be found on the Wiki page of the GitHub
 repository at
 <https://github.com/wannier-developers/wannier90/wiki/FAQ>.

docs/docs/user_guide/postw90/berry.md

@@ -38,7 +38,7 @@ generalization of the Berry connection,
 
 $$
 \begin{equation}
-\label{eq_berry-connection-matrix}
+\label{eq:berry-connection-matrix}
 {\bf A}_{nm}({\bf k})=\langle u_{n{\bf k}}\vert i\bm{\nabla}_{\bf k}\vert
 u_{m{\bf k}}\rangle={\bf A}_{mn}^*({\bf k}),
 \end{equation}

docs/docs/user_guide/postw90/boltzwann.md

@@ -10,20 +10,16 @@ $\mathrm{\bm{S}}$ and the coefficient $\mathrm{\bm{K}}$ (defined below;
 it is the main ingredient of the thermal conductivity).
 
 The list of parameters of the `BoltzWann` module are summarized in
-<!-- TODO: link the table in sec:wannier -->
-Table [\[parameter_keywords_bw\]](#parameter_keywords_bw){reference-type="ref"
-reference="parameter_keywords_bw"}. 
+Table [ `BoltzWann` Parameters](../postw90params/#boltzwann-parameters). 
 An example of a Boltzmann transport
 calculation can be found in the `wannier90` Tutorial.
 
-!!!Note
+!!! note
     By default, the code assumes to be working with a 3D bulk
     material, with periodicity along all three spatial directions. If you
     are interested in studying 2D systems, set the correct value for the
     `boltz_2d_dir` variable 
-    <!-- TODO: linke with sec in wannier -->
-    (see Sec. [\[sec:boltz2ddir\]](#sec:boltz2ddir){reference-type="ref"
-    reference="sec:boltz2ddir"} for the documentation). 
+    (see Sec. [boltz_2d_dir](../postw90params/#sec:boltz2ddir) for the documentation). 
     This is important
     for the evaluation of the Seebeck coefficient.
 

docs/docs/user_guide/postw90/geninterp.md

@@ -7,9 +7,7 @@ points provided by the user.
 
 The list of parameters of the Generic Band Interpolation module are
 summarized in
-<!-- TODO: link the table in sec wannier -->
-Table [\[parameter_keywords_geninterp\]](#parameter_keywords_geninterp){reference-type="ref"
-reference="parameter_keywords_geninterp"}. 
+Table [ `geninterp` Parameters](../postw90params/#geninterp-parameters). 
 The list of input $k$ points
 for which the band have to be calculated is read from the file named
 `seedname_geninterp.kpt`. The format of this file is described below.

docs/docs/user_guide/postw90/gyrotropic.md

@@ -142,7 +142,7 @@ $$
 The summations over $n$ and $l$ span the occupied ($o$)
 and empty ($e$) bands respectively, $\omega_{ln}=(E_l-E_n)/\hbar$, and
 ${\bm A}_{ln}({\bm k})$ is given by
-[Berry Eq. (3)](../berry/#mjx-eqn:eq:berry-connection-matrix)
+[Berry Eq. \[Berry connection matrix\]](../berry/#mjx-eqn:eq:berry-connection-matrix).
 <!-- Eq. $\eqref{eq:berry-connection-matrix}$.  -->
 Finally, the matrix
 $B_{nl}^{ac}$ has both orbital and spin contributions given by

docs/docs/user_guide/wannier90/files.md

@@ -5,7 +5,7 @@
 INPUT. The master input file; contains the specification of the system
 and any parameters for the run. For a description of input parameters,
 see Chapter [Parameters](../parameters); for examples, see
-Section [`seedname.win`](#seedname.win) and
+Section [`seedname.win`](../sample_inputs/#master-input-file-seednamewin) and
 the `wannier90` Tutorial.
 
 ### Units
@@ -195,7 +195,7 @@ plotting.
 
 This part of the output files provides information on the
 $\mathrm{b}$-vectors and weights chosen to satisfy the condition of
-Eq. [B1](../parameters/mjx-eqn:eq:B1).
+Eq. [B1](../parameters/#mjx-eqn:eq:B1).
 
      *---------------------------------- K-MESH ----------------------------------*
      +----------------------------------------------------------------------------+
@@ -351,8 +351,7 @@ gradient of $\Omega$ with respect to variations in the unitary matrices
 $\mathbf{U}^{(\mathbf{k})}$, and the last is the time taken (in
 seconds). Depending on the input parameters used, the procedure either
 runs for `num_iter` iterations, or a convergence criterion is applied on
-$\Omega$. See Section [2.8](#sec:wann_params){reference-type="ref"
-reference="sec:wann_params"} for details.
+$\Omega$. See Section [Wannierise Parameters](../parameters/#wannierise-parameters) for details.
 
 Similarly, the command
 
@@ -983,7 +982,7 @@ right lead which is in contact with the conductor region. Note that
         0.000000    0.000000    0.000000    0.000000    0.000000    0.000000
         0.000000    0.000000    0.000000
 
-## `seedname.unkg` {#sec:files_unkg}
+## `seedname.unkg`
 
 INPUT. Read if `transport_mode = lcr` and
 `tran_read_ht = .FALSE.`. The first line is the number of

docs/docs/user_guide/wannier90/parameters.md

@@ -197,7 +197,7 @@ window.
 |        dist_cutoff         |  P   | Cut-off for the distance between WF                          |
 |      dist_cutoff_mode      |  S   | Dimension in which the distance between WF is calculated     |
 |  translation_centre_frac   |  R   | Centre of the unit cell to which final WF are translated     |
-| use_ws_distance |  L   | Improve interpolation using minimum distance between WFs, see [Chap. 9](../notes_interpolations)|
+| use_ws_distance |  L   | Improve interpolation using minimum distance between WFs, see Chap. [Some notes on the interpolation](../notes_interpolations)|
 | ws_distance_tol                            |  R   | Absolute tolerance for the distance to equivalent positions. |
 | ws_search_size                           |  I   | Maximum extension in each direction of the super-cell of the Born-von Karmann cell to search for points inside the Wigner-Seitz cell |
 | write_u_matrices                           |  L   | Write $U^{(\bm{k})}$ and $U^{dis(\bm{k})}$ matrices to files |
@@ -369,9 +369,10 @@ end kpoints
 
 There is no default.
 
-**Note**: There is an utility provided with `wannier90`, called
-`kmesh.pl`, which helps to generate the explicit list of $k$ points
-required by `wannier90`. See Sec. [`kmesh.pl`](../../appendices/utilities#kmeshpl).
+!!! note
+    There is an utility provided with `wannier90`, called
+    `kmesh.pl`, which helps to generate the explicit list of $k$ points
+    required by `wannier90`. See Sec. [`kmesh.pl`](../../appendices/utilities#kmeshpl).
 
 ### `logical :: gamma_only`
 
@@ -572,9 +573,10 @@ $A_{mn}^{(\mathbf{k})}$.
 For additional information on the behavior and on the added block, see
 Sec. [`auto_projections` block](../postproc#auto_projections-block).
 
-**Note:** the interface code (e.g. `pw2wannier90.x`) must have at least
-one implementation of a method to automatically generate initial
-projections in order for this option to be usable.
+!!! note
+    the interface code (e.g. `pw2wannier90.x`) must have at least
+    one implementation of a method to automatically generate initial
+    projections in order for this option to be usable.
 
 The default value of this parameter is `false`.
 
@@ -693,10 +695,11 @@ To activate projectability disentanglement procedure, which selectively
 discard/disentangle/freeze state $\vert n \mathbf{k}\rangle$ based on
 its projectability onto some localized atomic orbitals.
 
-Note: this requires the `amn` file is properly normalized, i.e.,
-projectability computed from $A A^\dagger$ must be smaller than or equal
-to 1. The pseudo-atomic projection satisfies such requirement, see
-[Projections via pseudo-atomic orbitals in pw2wannier90](../projections#projections-via-pseudo-atomic-orbitals-in-pw2wannier90).
+!!! note 
+    this requires the `amn` file is properly normalized, i.e.,
+    projectability computed from $A A^\dagger$ must be smaller than or equal
+    to 1. The pseudo-atomic projection satisfies such requirement, see
+    [Projections via pseudo-atomic orbitals in pw2wannier90](../projections#projections-via-pseudo-atomic-orbitals-in-pw2wannier90).
 
 Additionally, one can combine projectability disentanglement with energy
 disentanglement, i.e., enable both `dis_proj_min/max` and
@@ -1197,11 +1200,12 @@ quatity plotted is
 -   `down`. $|\psi|\times sign(Re\{\psi\})$ if
     `wannier_plot_spinor_phase = true`, otherwise $|\psi|$
 
-Note: making a visual representation of a spinor WF is not as
-straightforward as for a scalar WF. While a scalar WF is typically a
-real valued function, a spinor WF is a complex, two component spinor.
-`wannier90` is able to plot several different quantities derived from a
-spinor WF which should give you a good idea of the nature of the WF.
+!!! note 
+    making a visual representation of a spinor WF is not as
+    straightforward as for a scalar WF. While a scalar WF is typically a
+    real valued function, a spinor WF is a complex, two component spinor.
+    `wannier90` is able to plot several different quantities derived from a
+    spinor WF which should give you a good idea of the nature of the WF.
 
 ### `logical :: wannier_plot_spinor_phase`
 
@@ -1258,8 +1262,9 @@ options for this parameter are:
 
 -   `xmgrace`
 
-Note: it is possible to request output in both formats eg
-`bands_format = gnuplot xmgrace`
+!!! note
+    it is possible to request output in both formats eg
+    `bands_format = gnuplot xmgrace`
 
 ### `integer :: bands_plot_project(:)`
 

docs/docs/user_guide/wannier90/postproc.md

@@ -101,7 +101,7 @@ crystallographic co-ordinates relative to the direct lattice vectors.
 `l  mr  r`: three integers; $l$ and $m_\mathrm{r}$ specify the angular
 part $\Theta_{lm_{\mathrm{r}}}(\theta,\varphi)$, and $\mathrm{r}$
 specifies the radial part $R_{\mathrm{r}}(r)$ of the projection function
-(see Tables [Angular functions](../projections/#angular-functions), [Hybrids](../projections#hybrids) and [Radial functions](../projections/#radial-functions).
+(see Tables [Angular functions](../projections/#angular-functions), [Hybrids](../projections#hybrids) and [Radial functions](../projections/#radial-functions)).
 
 `z-axis`: three real numbers; default is `0.0 0.0 1.0`; defines the axis
 from which the polar angle $\theta$ in spherical polar coordinates is

docs/docs/user_guide/wannier90/projections.md

@@ -31,8 +31,8 @@ equation but rather the *real* (in the sense of non-imaginary) states
 $\Theta_{lm_{\mathrm{r}}}$, obtained by a unitary transformation. For
 example, the canonical eigenstates associated with $l=1$, $m=\{-1,0,1\}$
 are not the real p$_{x}$, p$_{y}$ and p$_{z}$ that we want. See
-Section [3.4](#sec:orbital-defs){reference-type="ref"
-reference="sec:orbital-defs"} for our mathematical conventions regarding
+Section [Orbital Definitions](../projections/#orbital-definitions) 
+for our mathematical conventions regarding
 projection orbitals for different $n$, $l$ and $m_{\mathrm{r}}$.
 
 We use the following format to specify projections in `<seedname>.win`:

docs/docs/user_guide/wannier90/transport.md

@@ -17,7 +17,7 @@ calculated using the Hamiltonian in the Wannier function basis of the
 system found by `wannier90`. Setting `tran_read_ht = TRUE`
 allows the user to provide an external Hamiltonian matrix file
 `seedname_htB.dat`, from which the properties are found. See
-Section [sec:post-p parameters](../parameters)
+Section [Post-Processing](../parameters#post-processing)
 for more details of the keywords required for such calculations.
 
 ### `transport_mode = lcr`
@@ -46,7 +46,7 @@ transport properties of an lcr system from a single
 external files provide in the `tran_read_ht = TRUE` case are
 instead built from the Wannier function basis directly. As such, strict
 rules apply to the system geometry, which is shown in
-Figure [7.1](#fig:2c2). These
+Figure [below](#fig:lcr-2c2). These
 rules are as follows:
 
 -   Left and right leads must be identical and periodic.
@@ -121,7 +121,7 @@ $\tilde{u}_{m\mathbf{k}}(\mathbf{G})$ are required. These are found in
 an additional file (`seedname.unkg`) that should be provided by the
 interface between the DFT code and `wannier90` . A detailed description
 of this file may be found in
-Section [`seedname.unkg`](../files/#seedname.unkg).
+Section [`seedname.unkg`](../files/#seednameunkg).
 
 Additionally, the following keywords are also required in the input
 file:

docs/mkdocs.yml

@@ -27,6 +27,7 @@ nav:
         - "Notes on interpolations": "user_guide/wannier90/notes_interpolations.md"
         - "Sample inputs": "user_guide/wannier90/sample_inputs.md"
       - 'postw90.x':
+        - "Parameters": "user_guide/postw90/postw90params.md"
         - "Berry": "user_guide/postw90/berry.md"
         - "Gyrotropic": "user_guide/postw90/gyrotropic.md"
         - "BoltzWann": "user_guide/postw90/boltzwann.md"