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Checks on Zkey

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This commit is contained in:
Anthony Scemama 2018-03-09 00:08:12 +01:00
commit 7d0f8efffa
10 changed files with 87 additions and 32 deletions
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6
Basis/ContractedShell.mli
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@ -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}
\\] %}
*)

16
Basis/GamessReader.ml Normal file
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@ -0,0 +1,16 @@
let read_basis filename =
let lexbuf =
let ic = open_in filename in
Lexing.from_channel ic
in
let rec aux accu =
try
let key, basis =
GamessParser.input BasisLexer.read_all lexbuf
in
aux ((key, basis)::accu)
with
| Parsing.Parse_error -> List.rev accu
in
aux []

2
INSTALL.md
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@ -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
```

4
Makefile
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@ -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
ODOCFLAGS=-docflags "-g ltxhtml.cma"
#ODOC_LTXHTML_DIR=qpackage.docdir/ltx
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)

2
Utils/AngularMomentum.mli
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@ -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

16
Utils/Constants.mli
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@ -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 ] *)
(** {% $\frac{1}{a_0}$ %} *)

2
Utils/Electrons.mli
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@ -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: {% $2S+1$ %} *)
}

10
Utils/Util.mli
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@ -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. *)

31
Utils/Zkey.ml
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@ -35,21 +35,40 @@ type kind =
| Nine of (Powers.t * Powers.t * Powers.t)
| Twelve of (Powers.t * Powers.t * Powers.t * Powers.t)
let of_powers_three { x=a ; y=b ; z=c ; _ } = make 3 a <+ b <+ c
let of_powers_three { x=a ; y=b ; z=c ; _ } =
assert (
let alpha = a lor b lor c in
alpha >= 0 && alpha < (1 lsl 15)
);
make 3 a <+ b <+ c
let of_powers_six { x=a ; y=b ; z=c ; _ } { x=d ; y=e ; z=f ; _ } =
assert (
let alpha = a lor b lor c lor d lor e lor f in
alpha >= 0 && alpha < (1 lsl 10)
);
make 6 a << b << c << d << e << f
let of_powers_twelve { x=a ; y=b ; z=c ; _ } { x=d ; y=e ; z=f ; _ }
{ x=g ; y=h ; z=i ; _ } { x=j ; y=k ; z=l ; _ } =
make 12 a << b << c << d << e << f
<| g << h << i << j << k << l
let of_powers_nine { x=a ; y=b ; z=c ; _ } { x=d ; y=e ; z=f ; _ }
{ x=g ; y=h ; z=i ; _ } =
assert (
let alpha = a lor b lor c lor d lor e lor f lor g lor h lor i in
alpha >= 0 && alpha < (1 lsl 10)
);
make 9 a << b << c << d << e << f
<| g << h << i
let of_powers_twelve { x=a ; y=b ; z=c ; _ } { x=d ; y=e ; z=f ; _ }
{ x=g ; y=h ; z=i ; _ } { x=j ; y=k ; z=l ; _ } =
assert (
let alpha = a lor b lor c lor d lor e lor f
lor g lor h lor i lor j lor k lor l
in
alpha >= 0 && alpha < (1 lsl 10)
);
make 12 a << b << c << d << e << f
<| g << h << i << j << k << l
let of_powers a =
match a with

22
Utils/Zkey.mli
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@ -1,5 +1,25 @@
(** Encodes the powers of x, y, z in a compact form, suitable for being
used in a hash table.
used as keys in a hash table.
Internally, the {Zkey.t} is made of two integers, [left] and [right].
The small integers x, y and z are stored compactly in this 126-bits
space:
{[
Left Right
3 [--------------------------------------------------------------] [------------------|---------------|---------------|---------------]
x y z
6 [--------------------------------------------------------------] [---|----------|----------|----------|----------|----------|---------]
x1 y1 z1 x2 y2 z2
9 [---------------------------------|----------|----------|---------] [---|----------|----------|----------|----------|----------|---------]
x1 y1 z1 x2 y2 z2 x3 y3 z3
12 [---|----------|----------|----------|----------|----------|---------] [---|----------|----------|----------|----------|----------|---------]
x1 y1 z1 x2 y2 z2 x3 y3 z3 x4 y4 z4
]}
*)
type t