Documentation

Basis/Basis.ml

@@ -67,7 +67,7 @@ let to_string b =
 
 let of_nuclei_and_basis_filename ~nuclei ~filename = 
   let general_basis = 
-    GamessReader.read ~filename
+    GamessReader.read_basis filename
   in
   of_nuclei_and_general_basis nuclei general_basis
 

Basis/ContractedShell.mli

@@ -1,4 +1,4 @@
-(** A contracted shell is the set of functions is given by
+(** Set of contracted Gaussians with a given {!AngularMomentum.t}
 
 {% \\[
 (x-X_A)^{n_x} (y-Y_A)^{n_y} (z-Z_A)^{n_z} \sum_{i=1}^{m} \mathcal{N}_i f_i d_i \exp \left( -\alpha_i |r-R_A|^2 \right)
@@ -15,7 +15,7 @@ where:
 - {% $\mathcal{N}_i$ %} is the normalization coefficient of the i-th primitive:
 
 {% \\[
-\mathcal{N}_i = \sqrt{\iiint \left[ (x-X_A)^{l} \exp (-\alpha_i |r-R_A|^2) \right]^2 \, dx dy dz}
+\mathcal{N}_i = \sqrt{\iiint \left[ (x-X_A)^{l} \exp (-\alpha_i |r-R_A|^2) \right]^2 \, dx\, dy\, dz}
    \\] %}
 
 - {% $f_i$ %} is a scaling factor adjusting the normalization coefficient for the
@@ -23,7 +23,7 @@ where:
 
 {% \\[
 f_i = \frac{1}{\mathcal{N}_i}
-    \sqrt{\iiint \left[ (x-X_A)^{n_x} (y-Y_A)^{n_y} (z-Z_A)^{n_z} \exp (-\alpha_i |r-R_A|^2) \right]^2 \, dx dy dz}
+    \sqrt{\iiint \left[ (x-X_A)^{n_x} (y-Y_A)^{n_y} (z-Z_A)^{n_z} \exp (-\alpha_i |r-R_A|^2) \right]^2 \, dx\, dy\, dz}
    \\] %}
 
 *)

Basis/GamessReader.ml

@@ -1,6 +1,4 @@
-(** Read a basis set file in GAMESS format and return an association list where the key is an
+let read_basis filename =
-    Element.t and the value is the parsed basis set. *)
-let read ~filename =
   let lexbuf =
     let ic = open_in filename in
     Lexing.from_channel ic

INSTALL.md

@@ -21,7 +21,7 @@ This plugin allows to embed equations in the documentation generated by Ocamldoc
 Download the source code [here](https://github.com/scemama/odoc-ltxhtml). 
 
 ```bash
-git clone https://github.com/akabe/odoc-ltxhtml
+git clone https://github.com/scemama/odoc-ltxhtml
 cd odoc-ltxhtml
 make install
 ```

Makefile

@@ -5,8 +5,8 @@ LIBS=
 PKGS=
 OCAMLCFLAGS="-g -warn-error A"
 OCAMLOPTFLAGS="opt -O3 -nodynlink -remove-unused-arguments -rounds 16 -inline 100 -inline-max-unroll 100"
-ODOC_LTXHTML_DIR=qpackage.docdir/ltx
+#ODOC_LTXHTML_DIR=qpackage.docdir/ltx
-ODOCFLAGS=-docflags "-g ltxhtml.cma"
+ODOCFLAGS=-docflags "-g ltxhtml.cma -sort"
 OCAMLBUILD=ocamlbuild -j 0 -cflags $(OCAMLCFLAGS) -lflags $(OCAMLCFLAGS) $(ODOCFLAGS) -Is $(INCLUDE_DIRS) -ocamlopt $(OCAMLOPTFLAGS)
 MLLFILES=$(wildcard */*.mll) $(wildcard *.mll) Utils/math_functions.c
 MLYFILES=$(wildcard */*.mly) $(wildcard *.mly) 

Utils/AngularMomentum.mli

@@ -1,4 +1,4 @@
-(** Azimuthal quantum number, represented as s,p,d,... *)
+(** Azimuthal quantum number, represented as {% $s,p,d,\dots$ %} *)
 
 type t = S | P | D | F | G | H | I | J | K | L | M | N | O
 

Utils/Constants.mli

@@ -3,28 +3,28 @@
 
 
 val epsilon : float
-(** Value below which a float is considered null. Default is 10{^-20}. *)
+(** Value below which a float is considered null. Default is {% $\epsilon$ %} = 10{^-20}. *)
 
 val integrals_cutoff : float
 (** Cutoff value for integrals. Default is 10{^-15}. *)
 
 val pi : float
-(** pi = 3.141_592_653_589_793_12 *)
+(** {% $\pi$ %} = 3.141_592_653_589_793_12 *)
 
 val sq_pi : float
-(** [sqrt pi] *)
+(** {% $\sqrt{\pi}$ %} *)
 
 val sq_pi_over_two : float
-(** [(sqrt pi) /. 2.] *)
+(** {% $\frac{\sqrt{\pi}}{2}$ %} *)
 
 val pi_inv : float
-(** [ 1. /. pi ] *)
+(** {% $\frac{1}{\pi}$ %} *)
 
 val two_over_sq_pi : float
-(** [ 2. /. (sqrt pi) ] *)
+(** {% $\frac{2}{\sqrt{\pi}}$ %} *)
 
 val a0 : float
-(** Bohr radius : a{_0} = 0.529_177_210_671_2 Angstrom *)
+(** Bohr radius : {% $a_0$ %} = 0.529_177_210_671_2 Angstrom *)
 
 val a0_inv : float
-(** [ 1. /. a0 ] *)
+(** {% $\frac{1}{a_0}$ %} *)

Utils/Electrons.mli

@@ -3,7 +3,7 @@
 type t = {
   n_alpha      : int ;  (** Number of alpha electrons *)
   n_beta       : int ;  (** Number of beta  electrons *)
-  multiplicity : int ;  (** Spin multiplicity: 2S+1 *)
+  multiplicity : int ;  (** Spin multiplicity: {% $2S+1$ %} *)
 }
 
 

Utils/Util.mli

@@ -1,6 +1,6 @@
 (** All utilities which should be included in all source files are defined here *)
 
-(** {1 Functions from libm} *)
+(** {2 Functions from libm} *)
 
 external erf_float : float -> float = "erf_float_bytecode" "erf_float"
   [@@unboxed] [@@noalloc]
@@ -16,7 +16,7 @@ external gamma_float : float -> float = "gamma_float_bytecode" "gamma_float"
 
 
 
-(** {1 General functions} *)
+(** {2 General functions} *)
 
 val fact : int -> float
 (** Factorial function.
@@ -33,7 +33,7 @@ val chop : float -> (unit -> float) -> float
 
 
 
-(** {1 Functions related to the Boys function} *)
+(** {2 Functions related to the Boys function} *)
 
 val incomplete_gamma : alpha:float -> float -> float
 (** {{:https://en.wikipedia.org/wiki/Incomplete_gamma_function}
@@ -48,7 +48,7 @@ val boys_function : maxm:int -> float -> float array
   *)
 
 
-(** {1 Extension of the Array module} *)
+(** {2 Extension of the Array module} *)
 
 val array_sum : float array -> float
 (** Returns the sum of all the elements of the array *)
@@ -57,7 +57,7 @@ val array_product : float array -> float
 (** Returns the product of all the elements of the array *)
 
 
-(** {1 Linear algebra } *)
+(** {2 Linear algebra } *)
 
 val diagonalize_symm : Lacaml.D.mat -> Lacaml.D.mat * Lacaml.D.vec
 (** Diagonalize a symmetric matrix. Returns the eigenvectors and the eigenvalues. *)