Documentation

Basis/ContractedShell.ml

@@ -3,19 +3,15 @@ open Constants
 open Coordinate
 
 type t = {
-  expo      : float array;         (* Gaussian exponents *)
+  expo      : float array;
-  coef      : float array;         (* Contraction coefficients *)
+  coef      : float array;
-  center    : Coordinate.t;        (* Center of all the Gaussians *)
+  center    : Coordinate.t;
-  totAngMom : AngularMomentum.t;  (* Total angular momentum *)
+  totAngMom : AngularMomentum.t;
-  size      : int;                 (* Number of contracted Gaussians *)
+  size      : int;
-  norm_coef : float array;         (* Normalization coefficient of the class
+  norm_coef : float array;
-                                      corresponding to the i-th contraction *)
+  norm_coef_scale : float array;
-  norm_coef_scale : float array;   (* Inside a class, the norm is the norm
+  powers   : Zkey.t array;
-                                      of the function with (totAngMom,0,0) *. 
+  index    : int;
-                                      this scaling factor *)
-  index    : int;                  (* Index in the array of contracted shells *)
-  powers   : Zkey.t array;         (* Array of Zkeys corresponding to the
-                                      powers of (x,y,z) in the class *)
 }
 
 module Am = AngularMomentum

Basis/ContractedShell.mli

@@ -1,13 +1,43 @@
+(** A contracted shell is the set of functions is given by
+
+{% \\[
+(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)
+   \\] %}
+
+where:
+
+- {% $n_x + n_y + n_z = l$ %}, the total angular momentum
+
+- {% $\alpha_i$ %} are the exponents (tabulated)
+
+- {% $d_i$ %} are the contraction coefficients
+
+- {% $\mathcal{N}_i$ %} 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}
+   \\] %}
+
+- {% $f_i$ %} is a scaling factor adjusting the normalization coefficient for the
+  particular powers of {% $x,y,z$ %}:
+
+{% \\[
+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}
+   \\] %}
+
+*)
+
 type t = private {
-  expo      : float array;
+  expo      : float array;       (** Array of exponents {% $\alpha_i$ %} *)
-  coef      : float array;
+  coef      : float array;       (** Array of contraction coefficients {% $d_i$ %} *)
-  center    : Coordinate.t;
+  center    : Coordinate.t;      (** Coordinate of the center {% $\mathbf{A} = (X_A,Y_A,Z_A)$ %} *)
-  totAngMom : AngularMomentum.t;
+  totAngMom : AngularMomentum.t; (** Total angular momentum : {% $l = n_x + n_y + n_z$ %} *)
-  size      : int;
+  size      : int;               (** Number of contracted functions, {% $m$ %} in the formula *)
-  norm_coef : float array;
+  norm_coef : float array;       (** Normalization coefficients of primitive functions {% $\mathcal{N}_i$ %} *)
-  norm_coef_scale : float array;
+  norm_coef_scale : float array; (** Scaling factors {% $f_i$ %}, given in the same order as [powers]. *)
-  index    : int;
+  powers   : Zkey.t array;       (** Triplets {% $(n_x,n_y,n_z)$ %} encoded in a {!Zkey.t}. *)
-  powers   : Zkey.t array;
+  index    : int;                (** Index in the basis set, represented as an array of contracted shells. *)
 }
 
 

INSTALL.md

@@ -0,0 +1,28 @@
+# BLAS/Lapack
+
+Install OpenBLAS from your system package manager, for example:
+
+```bash
+sudo apt-get install libopenblas-dev
+```
+
+# LaCAML
+
+LaCAML is the OCaml binding to the LAPACK library.
+
+```bash
+opam install lacaml
+```
+
+# odoc-ltxhtml
+
+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
+cd odoc-ltxhtml
+make install
+```
+

Makefile

@@ -4,9 +4,10 @@ INCLUDE_DIRS=Nuclei,Utils,Basis,HartreeFock
 LIBS=
 PKGS=
 OCAMLCFLAGS="-g -warn-error A"
-#OCAMLOPTFLAGS="opt -O3 -nodynlink -remove-unused-arguments -rounds 16 -inline 100 -inline-max-unroll 100 -noassert -unsafe"
 OCAMLOPTFLAGS="opt -O3 -nodynlink -remove-unused-arguments -rounds 16 -inline 100 -inline-max-unroll 100"
-OCAMLBUILD=ocamlbuild -j 0 -cflags $(OCAMLCFLAGS) -lflags $(OCAMLCFLAGS) -Is $(INCLUDE_DIRS) -ocamlopt $(OCAMLOPTFLAGS)
+ODOC_LTXHTML_DIR=qpackage.docdir/ltx
+ODOCFLAGS=-docflags "-g ltxhtml.cma"
+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) 
 MLFILES= $(wildcard */*.ml)  $(wildcard *.ml) 
@@ -49,7 +50,7 @@ doc: qpackage.odocl
 	$(OCAMLBUILD) -ocamlc ocamlcp $*.byte -use-ocamlfind $(PKGS)
 
 clean: 
-	rm -rf _build $(ALL_EXE) $(ALL_TESTS) *.native *.byte
+	$(OCAMLBUILD) -clean # rm -rf _build $(ALL_EXE) $(ALL_TESTS) *.native *.byte
 
 debug: run_integrals.native
 	./debug.sh

README.rst

@@ -1,9 +1,9 @@
 Requirements
 ------------
 
-* gmp : GNU Multiple Precision arithmetic library
 * BLAS/LAPACK : Linear algebra
-* Zarith : Arbitrary-precision integers
 * LaCaml : LAPACK OCaml interface
-* SklMl : Parallel skeletons for OCaml
+* Zarith : Arbitrary-precision integers
+* gmp : GNU Multiple Precision arithmetic library
+* odoc-ltxhtml : https://github.com/akabe/odoc-ltxhtml
 

_tags

@@ -1,3 +1,4 @@
 true: package(str,unix,bigarray,zarith,lacaml)
 <*.byte>  : linkdep(Utils/math_functions.o), custom
 <*.native>: linkdep(Utils/math_functions.o)
+<odoc-ltxhtml>: not_hygienic