Merge pull request #23 from kousuke-nakano/update.design

Redesign manual landing pages and theming

Author: kousuke-nakano

source/_sources/01turborvb_manual/00index.rst

@@ -3,94 +3,73 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-TurboRVB manual
+TurboRVB Manual
 ======================================================
 
 .. figure:: /_static/07logo/logo.png
     :width: 600px
 
+TurboRVB is the core QMC engine for electronic systems, from molecules to extended materials.
+Use this manual when you work directly with executables, input files, wave functions, and low-level workflow details.
 
-**TurboRVB** is software for ab initio quantum Monte Carlo (QMC) simulations of electronic systems, from molecules to extended materials. It is built around many-body trial wave functions and implements, in particular, variational Monte Carlo (VMC) and diffusion Monte Carlo in its lattice-regularized form. 
-
-This manual emphasizes how to run the code—installation, input, and typical workflows. For theoretical background, detailed numerical methods, validation, and literature context, please refer to the article:
+For theoretical background, numerical methods, and validation, please refer to:
 
 | `TurboRVB: A many-body toolkit for ab initio electronic simulations by quantum Monte Carlo <https://doi.org/10.1063/5.0005037>`__
 | K. Nakano, C. Attaccalite, M. Barborini, L. Capriotti, M. Casula, E. Coccia, M. Dagrada, Y. Luo, G. Mazzola, A. Zen, and S. Sorella,
 | *J. Chem. Phys.* **152**, 204121 (2020).
 
-	    
+.. container:: manual-section-intro
+
+   **Choose Where to Start**
+
+.. container:: manual-card-grid
+
+   .. container:: manual-card
+
+      **Getting Started**
+
+      Learn the basic concepts, installation steps, and workflow overview before working with input files.
+
+      - :doc:`Open Getting Started <./getting_started/index>`
+
+   .. container:: manual-card
+
+      **Tutorials**
+
+      Follow end-to-end examples for representative molecular and condensed-matter calculations.
+
+      - :doc:`Open Tutorials <./tutorials/00index>`
+
+   .. container:: manual-card
+
+      **Reference Guide**
+
+      Look up input formats, commands, and technical reference material.
+
+      - :doc:`Open the Reference Guide <./reference/index>`
+
+   .. container:: manual-card
+
+      **Code Structure**
+
+      Use this section when you want executable-level documentation for DFT, conversion, optimization, and related code structure.
+
+      - :doc:`Open Code Structure <./structure/00index>`
+
+   .. container:: manual-card
+
+      **Appendix**
+
+      Check supporting notes and supplementary material that complement the main manual.
+
+      - :doc:`Open the Appendix <./appendix/00index>`
+
 .. toctree::
+   :hidden:
    :maxdepth: 1
 
    ./getting_started/index.rst
    ./structure/00index.rst
    ./tutorials/00index.rst
    ./reference/index.rst
    ./appendix/00index.rst
-
-
-.. todo:: 
-        
-    02_01Li-dimer (open,  all-electron)
-        - Calc_type:VMCopt, VMC and LRDMC
-        - Ansatz:JSD, JsAGPs
-        - AS basis_set:uncontracted XXX, hybrid
-        - Jastrow basis_set: XXX
-
-    02_02Li-dimer (open,  pseudo potential)
-        - Calc_type:VMCopt, VMC
-        - Ansatz:JSD
-        - AS basis_set:uncontracted XXX, hybrid
-        - Jastrow basis_set: XXX
-        
-    03_01Diamond (PBC, pseudo-potential)
-        - Calc_type:VMCopt, VMC, VMC-Force, Phonon
-        - Ansatz:JSD
-        - Twist:(pi pi pi) and 2*2*2 <- twist average
-        - AS basis_set: XXX
-        - Jastrow basis_set: XXX
-
-    03_02Diamond (PBC, all-electron)
-        - Calc_type:VMCopt, VMC
-        - Ansatz:JSD
-        - Twist:(pi pi pi)
-        - AS basis_set: XXX  <- crystal19 basis set
-        - Jastrow basis_set: XXX
-        
-    04_01Hydrogen-chain (PBC, all-electron)
-        - Calc_type:VMCopt, VMC.
-        - Ansatz:JsAGPs
-        - Twist:gamma
-        - AS basis_set: XXX
-        - Jastrow basis_set: XXX
-        
-    05_01Graphene (PBC, pseudo-potential)
-        - Calc_type:VMCopt, VMC
-        - Ansatz:JsAGPs
-        - Twist:3*3*1 <- twist average (phase attached, adiabatic expansion).
-        - AS basis_set: XXX
-        - Jastrow basis_set: XXX
-    
-    06_01H2O molecule (Open, all-electron)
-        - Calc_type:VMC LRDMC + electron density + spin density (S^2, Sz)
-        - Ansatz:JSD, JsAGPs, JAGPu, JPf
-        - AS basis_set:uncontraced XXX, hybrid
-        - Jastrow basis_set:XXX
-        
-    07_01H2O molecule (Open, all-electron)
-        - Calc_type:VMC-Structural optimization (idyn=5)
-        - Ansatz:JsAGPs
-        - AS basis_set:XXX
-        - Jastrow basis_set:XXX
-        
-    08_01H2-liquid (PBC, all-electron)
-        - Calc_type:FOLD (First-order Langevin Dynamics), SOLD (Second-order Langevin Dynamics),
-        - Ansatz:JSD
-        - AS basis_set:XXX
-        - Jastrow basis_set:XXX
-
-    09_01zundel cation (PBC, all-electron)
-        - Calc_type:PIOUD
-        - Ansatz:JsAGPs
-        - AS basis_set:XXX
-        - Jastrow basis_set:XXX

source/_sources/01turborvb_manual/appendix/00index.rst

@@ -4,7 +4,10 @@ Appendix
 .. figure:: /_static/07logo/logo.png
     :width: 700px
 
+Use this section for supporting notes and practical tips that complement the main manual.
+
 .. toctree::
+   :hidden:
    :maxdepth: 3
 
    ./tips/tutorial.rst

source/_sources/01turborvb_manual/getting_started/index.rst

@@ -1,10 +1,45 @@
-Getting started
+Getting Started
 ===========================================
 
 .. figure:: /_static/07logo/logo.png
     :width: 700px
 
+Start here if you are new to TurboRVB. Read the nutshell first for a compact conceptual overview, then install the code, and finally review the basic workflow before moving to tutorials or reference material.
+
+Use this section when you want the minimum background needed before editing input files or running the full tutorials.
+
+.. container:: manual-section-intro
+
+   **Recommended Order**
+
+.. container:: manual-card-grid
+
+   .. container:: manual-card
+
+      **Step 1: Nutshell**
+
+      Get a compact overview of what TurboRVB is and how the main calculation stages fit together.
+
+      - :doc:`Open Nutshell <./01nutshell>`
+
+   .. container:: manual-card
+
+      **Step 2: Installation**
+
+      Install the package and required runtime dependencies.
+
+      - :doc:`Open Installation <./02installation>`
+
+   .. container:: manual-card
+
+      **Step 3: Workflow Overview**
+
+      See the typical order of operations before running the full tutorials.
+
+      - :doc:`Open Basic Workflow <./03basic_workflow>`
+
 .. toctree::
+   :hidden:
    :maxdepth: 2
 
    ./01nutshell.rst

source/_sources/01turborvb_manual/reference/index.rst

@@ -1,12 +1,36 @@
-Reference guide
+Reference Guide
 ======================================================
 
 .. figure:: /_static/07logo/logo.png
     :width: 600px
 
-Here are references for formats of input file, executions, and scripts with TurboRVB.
+Use this section when you need file-format details, command behavior, or lower-level execution reference.
+Start from the wave function format if you are inspecting inputs, or from the command reference if you are looking for executable behavior.
+
+.. container:: manual-section-intro
+
+   **Reference Overview**
+
+.. container:: manual-card-grid
+
+   .. container:: manual-card
+
+      **Wave Function Format**
+
+      Read this section for the structure and meaning of TurboRVB wave function files.
+
+      - :doc:`Open wave function reference <./01wavefunction>`
+
+   .. container:: manual-card
+
+      **Command Reference**
+
+      Look up available executables, scripts, and their roles in the workflow.
+
+      - :doc:`Open command reference <./02command>`
 
 .. toctree::
+   :hidden:
    :maxdepth: 2
 
    ./01wavefunction.rst

source/_sources/01turborvb_manual/structure/00index.rst

@@ -4,10 +4,22 @@ Structure of TurboRVB
 .. figure:: /_static/07logo/logo.png
     :width: 700px
 
+Use this section to understand how the TurboRVB executables and workflow components are organized.
+For the detailed format of ``fort.10`` and related wave function files, use the Reference Guide instead.
+
+.. container:: manual-card-grid
+
+   .. container:: manual-card
+
+      **Wave Function Format**
+
+      Read the file-format reference when you need the structure and meaning of the wave function input.
+
+      - :doc:`Open wave function reference <../reference/01wavefunction>`
+
 .. toctree::
    :maxdepth: 1
 
-   ../reference/01wavefunction.rst
    ./07makefort10.rst
 
 .. toctree::

source/_sources/01turborvb_manual/tutorials/00index.rst

@@ -3,87 +3,49 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-TurboRVB tutorials
+TurboRVB Tutorials
 ======================================================
 
 .. figure:: /_static/07logo/logo.png
     :width: 600px
 
-Here are examples of various calculations with TurboRVB.
-
-.. todo:: 
-        
-    02_01Li-dimer (open,  all-electron)
-        - Calc_type:VMCopt, VMC and LRDMC
-        - Ansatz:JSD, JsAGPs
-        - AS basis_set:uncontracted XXX, hybrid
-        - Jastrow basis_set: XXX
-
-    02_02Li-dimer (open,  pseudo potential)
-        - Calc_type:VMCopt, VMC
-        - Ansatz:JSD
-        - AS basis_set:uncontracted XXX, hybrid
-        - Jastrow basis_set: XXX
-        
-    03_01Diamond (PBC, pseudo-potential)
-        - Calc_type:VMCopt, VMC, VMC-Force, Phonon
-        - Ansatz:JSD
-        - Twist:(pi pi pi) and 2*2*2 <- twist average
-        - AS basis_set: XXX
-        - Jastrow basis_set: XXX
-
-    03_02Diamond (PBC, all-electron)
-        - Calc_type:VMCopt, VMC
-        - Ansatz:JSD
-        - Twist:(pi pi pi)
-        - AS basis_set: XXX  <- crystal19 basis set
-        - Jastrow basis_set: XXX
-        
-    04_01Hydrogen-chain (PBC, all-electron)
-        - Calc_type:VMCopt, VMC.
-        - Ansatz:JsAGPs
-        - Twist:gamma
-        - AS basis_set: XXX
-        - Jastrow basis_set: XXX
-        
-    05_01Graphene (PBC, pseudo-potential)
-        - Calc_type:VMCopt, VMC
-        - Ansatz:JsAGPs
-        - Twist:3*3*1 <- twist average (phase attached, adiabatic expansion).
-        - AS basis_set: XXX
-        - Jastrow basis_set: XXX
-    
-    06_01H2O molecule (Open, all-electron)
-        - Calc_type:VMC LRDMC + electron density + spin density (S^2, Sz)
-        - Ansatz:JSD, JsAGPs, JAGPu, JPf
-        - AS basis_set:uncontraced XXX, hybrid
-        - Jastrow basis_set:XXX
-        
-    07_01H2O molecule (Open, all-electron)
-        - Calc_type:VMC-Structural optimization (idyn=5)
-        - Ansatz:JsAGPs
-        - AS basis_set:XXX
-        - Jastrow basis_set:XXX
-        
-    08_01H2-liquid (PBC, all-electron)
-        - Calc_type:FOLD (First-order Langevin Dynamics), SOLD (Second-order Langevin Dynamics),
-        - Ansatz:JSD
-        - AS basis_set:XXX
-        - Jastrow basis_set:XXX
-
-    09_01zundel cation (PBC, all-electron)
-        - Calc_type:PIOUD
-        - Ansatz:JsAGPs
-        - AS basis_set:XXX
-        - Jastrow basis_set:XXX
+Choose a tutorial based on the system and workflow you want to reproduce. Start from the hydrogen dimer examples before moving to more involved cases.
+
+.. container:: manual-section-intro
+
+   **Available Tutorials**
+
+.. container:: manual-card-grid
+
+   .. container:: manual-card
+
+      **Hydrogen Dimer: Standard Workflow**
+
+      Introductory example for a compact molecular workflow in TurboRVB.
+
+      - :doc:`Open tutorial <./01_01Hydrogen_dimer/tutorial>`
+
+   .. container:: manual-card
+
+      **Hydrogen Dimer: Alternative Setup**
+
+      A second hydrogen-dimer example with a different setup path.
+
+      - :doc:`Open tutorial <./01_02Hydrogen_dimer/tutorial>`
+
+   .. container:: manual-card
+
+      **Lithium Dimer**
+
+      Tutorial for a larger molecular example with optimization and production calculations.
+
+      - :doc:`Open tutorial <./02_01Li-dimer/tutorial>`
 
 
 .. toctree::
+   :hidden:
    :maxdepth: 3
 
    ./01_01Hydrogen_dimer/tutorial.rst
    ./01_02Hydrogen_dimer/tutorial.rst
    ./02_01Li-dimer/tutorial.rst
-
-..
-   ./98_wf_optimization/tutorial.rst