From 475635cf6c699bbac72269fb2a9d007c159db3ee Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 4 Jan 2021 23:52:36 +0100 Subject: [PATCH] Better doc --- ao/basis_gaussian.org | 4 +- docs/ao.html | 96 +++++++++++++++++++++---------------------- docs/index.html | 51 +++++++++++------------ docs/index.org | 50 ++++++++++++++++++---- docs/top.html | 6 +-- 5 files changed, 121 insertions(+), 86 deletions(-) diff --git a/ao/basis_gaussian.org b/ao/basis_gaussian.org index 0d23ed0..745536a 100644 --- a/ao/basis_gaussian.org +++ b/ao/basis_gaussian.org @@ -17,10 +17,10 @@ Data structure for Gaussian Atomic Orbitals: $$ - \chi(r) = P(X_A,Y_A,Z_A) \sum_k a_k \exp\left( -\alpha_k (\mathbf{r-R_A})^2 \right) + \chi_i(\mathbf{r}) = P_i(\mathbf{r}) \sum_k c_k \exp\left( -\alpha_k (\mathbf{r-R_A})^2 \right) $$ - where the polynomial $P$ and the Gaussian part are both centered on + where the polynomial $P_Ai and the Gaussian part are both centered on nucleus $A$. ** Type diff --git a/docs/ao.html b/docs/ao.html index e84c631..afa195d 100644 --- a/docs/ao.html +++ b/docs/ao.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + Atomic Orbitals @@ -251,36 +251,36 @@

Table of Contents

-
"Atomic basis set"
+
"Atomic basis set"
-
-

1 Gaussian basis

+
+

1 Gaussian basis

Data structure for Gaussian Atomic Orbitals: @@ -288,21 +288,21 @@ Data structure for Gaussian Atomic Orbitals:

\[ - \chi(r) = P(X_A,Y_A,Z_A) \sum_k a_k \exp\left( -\alpha_k (\mathbf{r-R_A})^2 \right) + \chi_i(\mathbf{r}) = P_i(\mathbf{r}) \sum_k c_k \exp\left( -\alpha_k (\mathbf{r-R_A})^2 \right) \]

-where the polynomial \(P\) and the Gaussian part are both centered on +where the polynomial $PAi and the Gaussian part are both centered on nucleus \(A\).

-
-

1.1 Type

+
+

1.1 Type

-
open Common
+
open Common
 open Particles
 open Linear_algebra
 open Gaussian_integrals
@@ -314,8 +314,8 @@ nucleus \(A\).
-
-

1.2 Access

+
+

1.2 Access

val basis             : t -> Gaussian.Basis.t
@@ -406,8 +406,8 @@ nucleus \(A\).
-
-

1.3 Computation

+
+

1.3 Computation

val values : t -> Coordinate.t -> Gaussian.Basis.t Vector.t
@@ -432,8 +432,8 @@ nucleus \(A\).
-
-

1.4 Creation

+
+

1.4 Creation

val make : basis:Gaussian.Basis.t ->
@@ -456,15 +456,15 @@ Defaults:
 
  • cartesian : false
    • 
 
 
-
    +
     let b = Ao.Basis_gaussian.make ~basis nuclei ;;
 val b : Ao.Basis_gaussian.t = Gaussian Basis, spherical, 15 AOs
    -
    -

    1.5 Printers

    +
    +

    1.5 Printers

    val pp : Format.formatter -> t -> unit
@@ -474,23 +474,23 @@ val b : Ao.Basis_gaussian.t = Gaussian Basis, spherical, 15 AOs
    -
    -

    2 Basis

    +
    +

    2 Basis

    Data structure for Atomic Orbitals.

    -
    -

    2.1 Dimensions   noexports

    +
    +

    2.1 Dimensions   noexports

    -
    -

    2.2 Polymorphic types

    +
    +

    2.2 Polymorphic types

    -
    type t =
+
    type t =
   | Unknown
   | Gaussian of Basis_gaussian.t
 
    
@@ -498,8 +498,8 @@ Data structure for Atomic Orbitals.
    -
    -

    2.3 Types

    +
    +

    2.3 Types

    type t
@@ -514,8 +514,8 @@ Data structure for Atomic Orbitals.
    -
    -

    2.4 Conversions

    +
    +

    2.4 Conversions

    val of_nuclei_and_basis_filename :
@@ -549,15 +549,15 @@ Defaults:
 
  • cartesian : false
    • 
 
 
-
    +
     let b = Ao.Basis.of_nuclei_and_basis_filename ~nuclei filename;;
 val b : Ao.Basis.t = Gaussian Basis, spherical, 15 AOs
    -
    -

    2.5 Access

    +
    +

    2.5 Access

    val size              : t -> int
@@ -655,8 +655,8 @@ val b : Ao.Basis.t = Gaussian Basis, spherical, 15 AOs
    -
    -

    2.6 Printers

    +
    +

    2.6 Printers

    val pp : Format.formatter -> t -> unit
@@ -668,7 +668,7 @@ val b : Ao.Basis.t = Gaussian Basis, spherical, 15 AOs

    Author: Anthony Scemama

    -

    Created: 2021-01-04 Mon 23:37

    +

    Created: 2021-01-04 Mon 23:51

    Validate

    diff --git a/docs/index.html b/docs/index.html index a0e3014..6735000 100644 --- a/docs/index.html +++ b/docs/index.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + QCaml documentation @@ -229,21 +229,21 @@

    Table of Contents

    + +
    +

    chamo_bg.png +

    +
    +

    QCaml is an OCaml library for writing quantum chemistry codes. It is written using literate programming with org-mode.

    - -
    -

    chamo_bg.png -

    -
    -

    To use it interactively in the top level or in a Jupyter or org-mode notebook, use @@ -259,30 +259,29 @@ This loads all the sub-libraries provided with QCaml, and installs the pretty printers.

    -
    -

    1 Documentation of Modules

    +

    Author: Anthony Scemama

    -

    Created: 2021-01-04 Mon 23:32

    +

    Created: 2021-01-04 Mon 23:47

    Validate

    diff --git a/docs/index.org b/docs/index.org index 5895cf2..78cb746 100644 --- a/docs/index.org +++ b/docs/index.org @@ -1,12 +1,11 @@ #+TITLE: QCaml documentation #+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup - + [[./chamo_bg.png]] + QCaml is an OCaml library for writing quantum chemistry codes. It is written using literate programming with org-mode. - [[./chamo_bg.png]] - To use it interactively in the top level or in a Jupyter or org-mode notebook, use @@ -19,13 +18,50 @@ * Documentation of Modules - #+NAME: list - #+begin_src sh :exports results :results org + #+NAME: modules + #+begin_src sh :exports none ls ../*/README.org \ - | cut -d '/' -f 2 \ - | sed 's/[^.]*/- \[\[.\/&\.html\]\[\u&\]\]/g' + | cut -d '/' -f 2 #+end_src + #+RESULTS: modules + | ao | + | common | + | gaussian_integrals | + | gaussian | + | linear_algebra | + | mo | + | operators | + | particles | + | perturbation | + | qcaml | + | simulation | + | top | + + #+NAME: list + #+begin_src python :var modules=modules :exports results :results output drawer +for m in modules: + m = m[0] + m2 = m.replace("_"," ").capitalize() + print(f"- [[./{m}.html][{m2}]]") + #+end_src + + #+RESULTS: list + :results: + - [[./ao.html][Ao]] + - [[./common.html][Common]] + - [[./gaussian_integrals.html][Gaussian integrals]] + - [[./gaussian.html][Gaussian]] + - [[./linear_algebra.html][Linear algebra]] + - [[./mo.html][Mo]] + - [[./operators.html][Operators]] + - [[./particles.html][Particles]] + - [[./perturbation.html][Perturbation]] + - [[./qcaml.html][Qcaml]] + - [[./simulation.html][Simulation]] + - [[./top.html][Top]] + :end: + diff --git a/docs/top.html b/docs/top.html index e9102a5..51adb28 100644 --- a/docs/top.html +++ b/docs/top.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + Top-level @@ -226,13 +226,13 @@

    Top-level

    -
    "Installs pretty printers for top-level."
+
    "Installs pretty printers for top-level."

    Author: Anthony Scemama

    -

    Created: 2021-01-04 Mon 23:37

    +

    Created: 2021-01-04 Mon 23:51

    Validate