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Merge branch 'master' of gitlab.com:scemama/QCaml
This commit is contained in:
commit
a7a07bd1d9
@ -5,6 +5,7 @@ type t =
|
||||
{
|
||||
basis : Basis.t ;
|
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overlap : Overlap.t lazy_t;
|
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multipole : Multipole.t lazy_t;
|
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ortho : Orthonormalization.t lazy_t;
|
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eN_ints : NucInt.t lazy_t;
|
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kin_ints : KinInt.t lazy_t;
|
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@ -17,6 +18,7 @@ type t =
|
||||
|
||||
let basis t = t.basis
|
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let overlap t = Lazy.force t.overlap
|
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let multipole t = Lazy.force t.multipole
|
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let ortho t = Lazy.force t.ortho
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let eN_ints t = Lazy.force t.eN_ints
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let kin_ints t = Lazy.force t.kin_ints
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@ -62,7 +64,11 @@ let make ~cartesian ~basis ?f12 nuclei =
|
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ScreenedERI.of_basis basis
|
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) in
|
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|
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{ basis ; overlap ; ortho ; eN_ints ; kin_ints ; ee_ints ;
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let multipole = lazy (
|
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Multipole.of_basis basis
|
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) in
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|
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{ basis ; overlap ; multipole ; ortho ; eN_ints ; kin_ints ; ee_ints ;
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ee_lr_ints ; f12_ints ; f12_over_r12_ints ; cartesian ;
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}
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|
@ -10,6 +10,9 @@ val basis : t -> Basis.t
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val overlap : t -> Overlap.t
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(** Overlap matrix *)
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val multipole : t -> Multipole.t
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(** Multipole matrices *)
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val ortho : t -> Orthonormalization.t
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(** Orthonormalization matrix of the overlap *)
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|
@ -93,6 +93,12 @@ let of_nuclei_and_basis_filename ~nuclei filename =
|
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in
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of_nuclei_and_general_basis nuclei general_basis
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let of_nuclei_and_basis_string ~nuclei str =
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let general_basis =
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GeneralBasis.of_string str
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in
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of_nuclei_and_general_basis nuclei general_basis
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|
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let of_nuclei_and_basis_filenames ~nuclei filenames =
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let general_basis =
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|
@ -18,6 +18,11 @@ val of_nuclei_and_basis_filename : nuclei:Nuclei.t -> string -> t
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from a file.
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*)
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|
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val of_nuclei_and_basis_string : nuclei:Nuclei.t -> string -> t
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(** Same as {!of_nuclei_and_general_basis}, but taking the {!GeneralBasis.t}
|
||||
from a string.
|
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*)
|
||||
|
||||
val of_nuclei_and_basis_filenames : nuclei:Nuclei.t -> string list -> t
|
||||
(** Same as {!of_nuclei_and_general_basis}, but taking the {!GeneralBasis.t}
|
||||
from multiple files.
|
||||
|
@ -17,23 +17,24 @@ exception No_shell
|
||||
exception Malformed_shell of string
|
||||
|
||||
|
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let read_shell ic =
|
||||
let read_shell line_stream =
|
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try
|
||||
|
||||
let shell, n =
|
||||
try
|
||||
let line = input_line ic in
|
||||
let line = Stream.next line_stream in
|
||||
if String.trim line = "$END" then raise End_of_file;
|
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Scanf.sscanf line " %c %d " (fun shell n -> shell, n)
|
||||
with
|
||||
| End_of_file -> raise No_shell
|
||||
| Stream.Failure -> raise No_shell
|
||||
| Scanf.Scan_failure m -> raise (Malformed_shell m)
|
||||
in
|
||||
|
||||
let rec loop = function
|
||||
| 0 -> []
|
||||
| i -> let contraction =
|
||||
let line = (input_line ic) in
|
||||
let line = Stream.next line_stream in
|
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try Scanf.sscanf line " %_d %f %f "
|
||||
(fun exponent coefficient -> { exponent ; coefficient })
|
||||
with _ -> raise (Malformed_shell (Printf.sprintf
|
||||
@ -50,36 +51,46 @@ let read_shell ic =
|
||||
|
||||
|
||||
|
||||
let read_element ic =
|
||||
let read_element line_stream =
|
||||
try
|
||||
|
||||
let line = Stream.next line_stream in
|
||||
let element =
|
||||
Scanf.sscanf (input_line ic) " %s " Element.of_string
|
||||
Scanf.sscanf line " %s " Element.of_string
|
||||
in
|
||||
|
||||
let rec loop () =
|
||||
match read_shell ic with
|
||||
match read_shell line_stream with
|
||||
| Some shell -> shell :: loop ()
|
||||
| None -> []
|
||||
in
|
||||
Some (element, Array.of_list (loop ()) )
|
||||
|
||||
with
|
||||
| End_of_file -> None
|
||||
| Stream.Failure -> None
|
||||
|
||||
|
||||
|
||||
let read filename =
|
||||
let ic = open_in filename in
|
||||
let read_stream line_stream =
|
||||
let rec loop accu =
|
||||
try
|
||||
match read_element ic with
|
||||
match read_element line_stream with
|
||||
| Some e -> loop (e :: accu)
|
||||
| None -> accu
|
||||
with
|
||||
Element.ElementError _ -> loop accu
|
||||
in
|
||||
loop []
|
||||
loop []
|
||||
|
||||
let read filename =
|
||||
let ic = open_in filename in
|
||||
let line_stream =
|
||||
Stream.from (fun _ ->
|
||||
try Some (input_line ic)
|
||||
with End_of_file -> None )
|
||||
in
|
||||
let result = read_stream line_stream in
|
||||
close_in ic;
|
||||
result
|
||||
|
||||
|
||||
let combine basis_list =
|
||||
@ -124,3 +135,8 @@ let to_string (name, contracted_shell_array) =
|
||||
Printf.sprintf "%s\n%s" name (string_of_contracted_shell_array contracted_shell_array)
|
||||
|
||||
|
||||
let of_string input_string =
|
||||
String.split_on_char '\n' input_string
|
||||
|> Stream.of_list
|
||||
|> read_stream
|
||||
|
||||
|
@ -46,7 +46,7 @@ exception Malformed_shell of string
|
||||
|
||||
|
||||
val read : string -> t
|
||||
(** Reads a basis set file and return an association list where
|
||||
(** Reads a basis-set file and return an association list where
|
||||
the key is an {!Element.t} and the value is the parsed basis set.
|
||||
*)
|
||||
|
||||
@ -65,8 +65,10 @@ val read_many : string list -> t
|
||||
|
||||
|
||||
|
||||
val read_element : in_channel -> element_basis option
|
||||
(** Reads an element from the input channel [ic]. For example,
|
||||
val read_element : string Stream.t -> element_basis option
|
||||
(** Reads an element from the input [string Stream]. The [string Stream] is a
|
||||
stream of lines, like a text file split on the end-of-line character.
|
||||
For example,
|
||||
{[
|
||||
HYDROGEN
|
||||
S 3
|
||||
@ -95,8 +97,10 @@ Some
|
||||
*)
|
||||
|
||||
|
||||
val read_shell : in_channel -> general_contracted_shell option
|
||||
(** Reads a shell from the input channel [ic]. For example,
|
||||
val read_shell : string Stream.t -> general_contracted_shell option
|
||||
(** Reads a shell from the input [string Stream]. The [string Stream] is a
|
||||
stream of lines, like a text file split on the end-of-line character.
|
||||
For example,
|
||||
{[
|
||||
S 3
|
||||
1 13.0100000 0.0196850
|
||||
@ -119,4 +123,6 @@ Some
|
||||
val to_string : string * (general_contracted_shell array) -> string
|
||||
(** Pretty-prints the basis set of an {Element.t}. *)
|
||||
|
||||
val of_string : string -> t
|
||||
(** Reads a GAMESS-formatted string. *)
|
||||
|
||||
|
199
Basis/Multipole.ml
Normal file
199
Basis/Multipole.ml
Normal file
@ -0,0 +1,199 @@
|
||||
open Util
|
||||
open Constants
|
||||
open Lacaml.D
|
||||
|
||||
type t = Mat.t array
|
||||
(*
|
||||
[| "x"; "y"; "z"; "x2"; "y2"; "z2" |]
|
||||
*)
|
||||
|
||||
module Am = AngularMomentum
|
||||
module Bs = Basis
|
||||
module Co = Coordinate
|
||||
module Cs = ContractedShell
|
||||
module Csp = ContractedShellPair
|
||||
module Po = Powers
|
||||
module Psp = PrimitiveShellPair
|
||||
|
||||
let multiply a b =
|
||||
let n = Mat.dim1 a in
|
||||
let c = Mat.create n n in
|
||||
Mat.cpab c a b;
|
||||
c
|
||||
|
||||
let x0 t = t.(0)
|
||||
let y0 t = t.(1)
|
||||
let z0 t = t.(2)
|
||||
let x1 t = t.(3)
|
||||
let y1 t = t.(4)
|
||||
let z1 t = t.(5)
|
||||
let x2 t = t.(6)
|
||||
let y2 t = t.(7)
|
||||
let z2 t = t.(8)
|
||||
|
||||
let matrix_x t = multiply (x1 t) @@ multiply (y0 t) (z0 t)
|
||||
let matrix_y t = multiply (x0 t) @@ multiply (y1 t) (z0 t)
|
||||
let matrix_z t = multiply (x0 t) @@ multiply (y0 t) (z1 t)
|
||||
let matrix_x2 t = multiply (x2 t) @@ multiply (y0 t) (z0 t)
|
||||
let matrix_y2 t = multiply (x0 t) @@ multiply (y2 t) (z0 t)
|
||||
let matrix_z2 t = multiply (x0 t) @@ multiply (y0 t) (z2 t)
|
||||
let matrix_xy t = multiply (x1 t) @@ multiply (y1 t) (z0 t)
|
||||
let matrix_yz t = multiply (x0 t) @@ multiply (y1 t) (z1 t)
|
||||
let matrix_zx t = multiply (x1 t) @@ multiply (y0 t) (z1 t)
|
||||
|
||||
let cutoff = integrals_cutoff
|
||||
|
||||
let to_powers x =
|
||||
let open Zkey in
|
||||
match to_powers x with
|
||||
| Six x -> x
|
||||
| _ -> assert false
|
||||
|
||||
(** Computes all the integrals of the contracted shell pair *)
|
||||
let contracted_class shell_a shell_b : float Zmap.t array =
|
||||
|
||||
match Csp.make shell_a shell_b with
|
||||
| None -> Array.init 9 (fun _ -> Zmap.create 0)
|
||||
| Some shell_p ->
|
||||
begin
|
||||
|
||||
(* Pre-computation of integral class indices *)
|
||||
let class_indices = Csp.zkey_array shell_p in
|
||||
|
||||
let contracted_class =
|
||||
Array.init 9 (fun _ -> Array.make (Array.length class_indices) 0.)
|
||||
in
|
||||
|
||||
let a_minus_b =
|
||||
Csp.a_minus_b shell_p
|
||||
in
|
||||
let norm_coef_scales =
|
||||
Csp.norm_scales shell_p
|
||||
in
|
||||
|
||||
(* Compute all integrals in the shell for each pair of significant shell pairs *)
|
||||
|
||||
let xyz_of_int k =
|
||||
match k with
|
||||
| 0 -> Co.X
|
||||
| 1 -> Co.Y
|
||||
| _ -> Co.Z
|
||||
in
|
||||
|
||||
List.iter (fun (coef_prod, psp) ->
|
||||
(** Screening on the product of coefficients *)
|
||||
if (abs_float coef_prod) > 1.e-6*.cutoff then
|
||||
begin
|
||||
let expo_inv = Psp.exponent_inv psp
|
||||
and center_pa = Psp.center_minus_a psp
|
||||
and xa = Co.get Co.X @@ Cs.center shell_a
|
||||
and ya = Co.get Co.Y @@ Cs.center shell_a
|
||||
and za = Co.get Co.Z @@ Cs.center shell_a
|
||||
in
|
||||
|
||||
Array.iteri (fun i key ->
|
||||
let (angMomA, angMomB) = to_powers key in
|
||||
(* 1D Overlap <i|j> *)
|
||||
let f k =
|
||||
let xyz = xyz_of_int k in
|
||||
Overlap_primitives.hvrr (Po.get xyz angMomA, Po.get xyz angMomB)
|
||||
expo_inv
|
||||
(Co.get xyz a_minus_b, Co.get xyz center_pa)
|
||||
in
|
||||
(* 1D <i|x-Xa|j> *)
|
||||
let g k =
|
||||
let xyz = xyz_of_int k in
|
||||
Overlap_primitives.hvrr (Po.get xyz angMomA + 1, Po.get xyz angMomB)
|
||||
expo_inv
|
||||
(Co.get xyz a_minus_b, Co.get xyz center_pa)
|
||||
in
|
||||
(* 1D <i|(x-Xa)^2|j> *)
|
||||
let h k =
|
||||
let xyz = xyz_of_int k in
|
||||
Overlap_primitives.hvrr (Po.get xyz angMomA + 2, Po.get xyz angMomB)
|
||||
expo_inv
|
||||
(Co.get xyz a_minus_b, Co.get xyz center_pa)
|
||||
in
|
||||
let norm = norm_coef_scales.(i) in
|
||||
let f0, f1, f2, g0, g1, g2, h0, h1, h2 =
|
||||
f 0, f 1, f 2, g 0, g 1, g 2, h 0, h 1, h 2
|
||||
in
|
||||
let x = g0 +. f0 *. xa in
|
||||
let y = g1 +. f1 *. ya in
|
||||
let z = g2 +. f2 *. za in
|
||||
let x2 = h0 +. xa *. (2. *. x -. xa *. f0) in
|
||||
let y2 = h1 +. ya *. (2. *. y -. ya *. f1) in
|
||||
let z2 = h2 +. za *. (2. *. z -. za *. f2) in
|
||||
let c = contracted_class in
|
||||
let d = coef_prod *. norm in
|
||||
c.(0).(i) <- c.(0).(i) +. d *. f0 ;
|
||||
c.(1).(i) <- c.(1).(i) +. d *. f1 ;
|
||||
c.(2).(i) <- c.(2).(i) +. d *. f2 ;
|
||||
c.(3).(i) <- c.(3).(i) +. d *. x ;
|
||||
c.(4).(i) <- c.(4).(i) +. d *. y ;
|
||||
c.(5).(i) <- c.(5).(i) +. d *. z ;
|
||||
c.(6).(i) <- c.(6).(i) +. d *. x2 ;
|
||||
c.(7).(i) <- c.(7).(i) +. d *. y2 ;
|
||||
c.(8).(i) <- c.(8).(i) +. d *. z2 ;
|
||||
) class_indices
|
||||
end
|
||||
) (Csp.coefs_and_shell_pairs shell_p);
|
||||
let result =
|
||||
Array.map (fun c -> Zmap.create (Array.length c) ) contracted_class
|
||||
in
|
||||
for j=0 to Array.length result do
|
||||
let rj = result.(j) in
|
||||
let cj = contracted_class.(j) in
|
||||
Array.iteri (fun i key -> Zmap.add rj key cj.(i)) class_indices
|
||||
done;
|
||||
result
|
||||
end
|
||||
|
||||
|
||||
(** Create multipole matrices *)
|
||||
let of_basis basis =
|
||||
let to_powers x =
|
||||
let open Zkey in
|
||||
match to_powers x with
|
||||
| Three x -> x
|
||||
| _ -> assert false
|
||||
in
|
||||
|
||||
let n = Bs.size basis
|
||||
and shell = Bs.contracted_shells basis
|
||||
in
|
||||
|
||||
let result = Array.init 9 (fun _ -> Mat.create n n) in
|
||||
for j=0 to (Array.length shell) - 1 do
|
||||
for i=0 to j do
|
||||
(* Compute all the integrals of the class *)
|
||||
let cls =
|
||||
contracted_class shell.(i) shell.(j)
|
||||
in
|
||||
|
||||
for k=0 to 8 do
|
||||
Array.iteri (fun j_c powers_j ->
|
||||
let j_c = Cs.index shell.(j) + j_c + 1 in
|
||||
let xj = to_powers powers_j in
|
||||
Array.iteri (fun i_c powers_i ->
|
||||
let i_c = Cs.index shell.(i) + i_c + 1 in
|
||||
let xi = to_powers powers_i in
|
||||
let key =
|
||||
Zkey.of_powers_six xi xj
|
||||
in
|
||||
let value =
|
||||
try Zmap.find cls.(k) key
|
||||
with Not_found -> 0.
|
||||
in
|
||||
result.(k).{i_c,j_c} <- value;
|
||||
result.(k).{j_c,i_c} <- value;
|
||||
) (Am.zkey_array (Singlet (Cs.ang_mom shell.(i))))
|
||||
) (Am.zkey_array (Singlet (Cs.ang_mom shell.(j))))
|
||||
done;
|
||||
done;
|
||||
done;
|
||||
for k=0 to 8 do
|
||||
Mat.detri result.(k);
|
||||
done;
|
||||
result
|
||||
|
34
Basis/Multipole.mli
Normal file
34
Basis/Multipole.mli
Normal file
@ -0,0 +1,34 @@
|
||||
(** Multipole atomic integrals:
|
||||
|
||||
{% $$ \langle \chi_i | x | \chi_j \rangle $$ %}
|
||||
{% $$ \langle \chi_i | y | \chi_j \rangle $$ %}
|
||||
{% $$ \langle \chi_i | z | \chi_j \rangle $$ %}
|
||||
{% $$ \langle \chi_i | x^2 | \chi_j \rangle $$ %}
|
||||
{% $$ \langle \chi_i | y^2 | \chi_j \rangle $$ %}
|
||||
{% $$ \langle \chi_i | z^2 | \chi_j \rangle $$ %}
|
||||
|
||||
*)
|
||||
|
||||
open Lacaml.D
|
||||
|
||||
type t
|
||||
|
||||
val matrix_x : t -> Mat.t
|
||||
(** {% $$ \langle \chi_i | x | \chi_j \rangle $$ %} *)
|
||||
|
||||
val matrix_y : t -> Mat.t
|
||||
(** {% $$ \langle \chi_i | y | \chi_j \rangle $$ %} *)
|
||||
|
||||
val matrix_z : t -> Mat.t
|
||||
(** {% $$ \langle \chi_i | z | \chi_j \rangle $$ %} *)
|
||||
|
||||
val matrix_x2 : t -> Mat.t
|
||||
(** {% $$ \langle \chi_i | x^2 | \chi_j \rangle $$ %} *)
|
||||
|
||||
val matrix_y2 : t -> Mat.t
|
||||
(** {% $$ \langle \chi_i | y^2 | \chi_j \rangle $$ %} *)
|
||||
|
||||
val matrix_z2 : t -> Mat.t
|
||||
(** {% $$ \langle \chi_i | z^2 | \chi_j \rangle $$ %} *)
|
||||
|
||||
val of_basis : Basis.t -> t
|
124
Basis/Overlap.ml
124
Basis/Overlap.ml
@ -18,77 +18,77 @@ module Psp = PrimitiveShellPair
|
||||
|
||||
let cutoff = integrals_cutoff
|
||||
|
||||
let to_powers x =
|
||||
let to_powers x =
|
||||
let open Zkey in
|
||||
match to_powers x with
|
||||
| Six x -> x
|
||||
| _ -> assert false
|
||||
|
||||
(** Computes all the overlap integrals of the contracted shell pair *)
|
||||
let contracted_class shell_a shell_b : float Zmap.t =
|
||||
let contracted_class shell_a shell_b : float Zmap.t =
|
||||
|
||||
match Csp.make shell_a shell_b with
|
||||
| Some shell_p ->
|
||||
| None -> Zmap.create 0
|
||||
| Some shell_p ->
|
||||
begin
|
||||
|
||||
(* Pre-computation of integral class indices *)
|
||||
let class_indices = Csp.zkey_array shell_p in
|
||||
(* Pre-computation of integral class indices *)
|
||||
let class_indices = Csp.zkey_array shell_p in
|
||||
|
||||
let contracted_class =
|
||||
Array.make (Array.length class_indices) 0.
|
||||
in
|
||||
let contracted_class =
|
||||
Array.make (Array.length class_indices) 0.
|
||||
in
|
||||
|
||||
let a_minus_b =
|
||||
Csp.a_minus_b shell_p
|
||||
in
|
||||
let norm_coef_scales =
|
||||
Csp.norm_scales shell_p
|
||||
in
|
||||
let a_minus_b =
|
||||
Csp.a_minus_b shell_p
|
||||
in
|
||||
let norm_coef_scales =
|
||||
Csp.norm_scales shell_p
|
||||
in
|
||||
|
||||
(* Compute all integrals in the shell for each pair of significant shell pairs *)
|
||||
(* Compute all integrals in the shell for each pair of significant shell pairs *)
|
||||
|
||||
let xyz_of_int k =
|
||||
match k with
|
||||
| 0 -> Co.X
|
||||
| 1 -> Co.Y
|
||||
| _ -> Co.Z
|
||||
in
|
||||
let xyz_of_int k =
|
||||
match k with
|
||||
| 0 -> Co.X
|
||||
| 1 -> Co.Y
|
||||
| _ -> Co.Z
|
||||
in
|
||||
|
||||
List.iter (fun (coef_prod, psp) ->
|
||||
(** Screening on thr product of coefficients *)
|
||||
if (abs_float coef_prod) > 1.e-3*.cutoff then
|
||||
begin
|
||||
let expo_inv = Psp.exponent_inv psp
|
||||
and center_pa = Psp.center_minus_a psp
|
||||
in
|
||||
|
||||
Array.iteri (fun i key ->
|
||||
let (angMomA,angMomB) = to_powers key in
|
||||
let f k =
|
||||
let xyz = xyz_of_int k in
|
||||
Overlap_primitives.hvrr (Po.get xyz angMomA, Po.get xyz angMomB)
|
||||
expo_inv
|
||||
(Co.get xyz a_minus_b,
|
||||
Co.get xyz center_pa)
|
||||
List.iter (fun (coef_prod, psp) ->
|
||||
(** Screening on the product of coefficients *)
|
||||
if (abs_float coef_prod) > 1.e-6*.cutoff then
|
||||
begin
|
||||
let expo_inv = Psp.exponent_inv psp
|
||||
and center_pa = Psp.center_minus_a psp
|
||||
in
|
||||
let norm = norm_coef_scales.(i) in
|
||||
let integral = chop norm (fun () -> (f 0)*.(f 1)*.(f 2)) in
|
||||
contracted_class.(i) <- contracted_class.(i) +. coef_prod *. integral
|
||||
) class_indices
|
||||
end
|
||||
) (Csp.coefs_and_shell_pairs shell_p);
|
||||
let result =
|
||||
Zmap.create (Array.length contracted_class)
|
||||
in
|
||||
Array.iteri (fun i key -> Zmap.add result key contracted_class.(i)) class_indices;
|
||||
result
|
||||
end
|
||||
| None -> Zmap.create 0
|
||||
|
||||
Array.iteri (fun i key ->
|
||||
let (angMomA,angMomB) = to_powers key in
|
||||
let f k =
|
||||
let xyz = xyz_of_int k in
|
||||
Overlap_primitives.hvrr (Po.get xyz angMomA, Po.get xyz angMomB)
|
||||
expo_inv
|
||||
(Co.get xyz a_minus_b,
|
||||
Co.get xyz center_pa)
|
||||
in
|
||||
let norm = norm_coef_scales.(i) in
|
||||
let integral = chop norm (fun () -> (f 0)*.(f 1)*.(f 2)) in
|
||||
contracted_class.(i) <- contracted_class.(i) +. coef_prod *. integral
|
||||
) class_indices
|
||||
end
|
||||
) (Csp.coefs_and_shell_pairs shell_p);
|
||||
let result =
|
||||
Zmap.create (Array.length contracted_class)
|
||||
in
|
||||
Array.iteri (fun i key -> Zmap.add result key contracted_class.(i)) class_indices;
|
||||
result
|
||||
end
|
||||
|
||||
|
||||
(** Create overlap matrix *)
|
||||
let of_basis basis =
|
||||
let to_powers x =
|
||||
let to_powers x =
|
||||
let open Zkey in
|
||||
match to_powers x with
|
||||
| Three x -> x
|
||||
@ -104,7 +104,7 @@ let of_basis basis =
|
||||
for i=0 to j do
|
||||
(* Compute all the integrals of the class *)
|
||||
let cls =
|
||||
contracted_class shell.(i) shell.(j)
|
||||
contracted_class shell.(i) shell.(j)
|
||||
in
|
||||
|
||||
Array.iteri (fun j_c powers_j ->
|
||||
@ -113,11 +113,11 @@ let of_basis basis =
|
||||
Array.iteri (fun i_c powers_i ->
|
||||
let i_c = Cs.index shell.(i) + i_c + 1 in
|
||||
let xi = to_powers powers_i in
|
||||
let key =
|
||||
let key =
|
||||
Zkey.of_powers_six xi xj
|
||||
in
|
||||
let value =
|
||||
try Zmap.find cls key
|
||||
let value =
|
||||
try Zmap.find cls key
|
||||
with Not_found -> 0.
|
||||
in
|
||||
result.{i_c,j_c} <- value;
|
||||
@ -132,7 +132,7 @@ let of_basis basis =
|
||||
|
||||
(** Create mixed overlap matrix *)
|
||||
let of_basis_pair first_basis second_basis =
|
||||
let to_powers x =
|
||||
let to_powers x =
|
||||
let open Zkey in
|
||||
match to_powers x with
|
||||
| Three x -> x
|
||||
@ -140,7 +140,7 @@ let of_basis_pair first_basis second_basis =
|
||||
in
|
||||
|
||||
let n = Bs.size first_basis
|
||||
and m = Bs.size second_basis
|
||||
and m = Bs.size second_basis
|
||||
and first = Bs.contracted_shells first_basis
|
||||
and second = Bs.contracted_shells second_basis
|
||||
in
|
||||
@ -150,7 +150,7 @@ let of_basis_pair first_basis second_basis =
|
||||
for i=0 to (Array.length first) - 1 do
|
||||
(* Compute all the integrals of the class *)
|
||||
let cls =
|
||||
contracted_class first.(i) second.(j)
|
||||
contracted_class first.(i) second.(j)
|
||||
in
|
||||
|
||||
Array.iteri (fun j_c powers_j ->
|
||||
@ -159,11 +159,11 @@ let of_basis_pair first_basis second_basis =
|
||||
Array.iteri (fun i_c powers_i ->
|
||||
let i_c = Cs.index first.(i) + i_c + 1 in
|
||||
let xi = to_powers powers_i in
|
||||
let key =
|
||||
let key =
|
||||
Zkey.of_powers_six xi xj
|
||||
in
|
||||
let value =
|
||||
try Zmap.find cls key
|
||||
let value =
|
||||
try Zmap.find cls key
|
||||
with Not_found -> 0.
|
||||
in
|
||||
result.{i_c,j_c} <- value;
|
||||
@ -180,7 +180,7 @@ let to_file ~filename overlap =
|
||||
|
||||
let oc = open_out filename in
|
||||
let n =
|
||||
Mat.dim1 overlap
|
||||
Mat.dim1 overlap
|
||||
in
|
||||
|
||||
for j=1 to n do
|
||||
|
@ -1,7 +1,7 @@
|
||||
# Generic installation
|
||||
|
||||
```bash
|
||||
opam install ocamlbuild lacaml mpi getopt alcotest zarith
|
||||
opam install ocamlbuild ocamlfind lacaml mpi getopt alcotest zarith
|
||||
```
|
||||
|
||||
|
||||
|
File diff suppressed because it is too large
Load Diff
@ -3,11 +3,7 @@ open Xyz_ast
|
||||
|
||||
type t = (Element.t * Coordinate.t) array
|
||||
|
||||
let of_xyz_file filename =
|
||||
let lexbuf =
|
||||
let ic = open_in filename in
|
||||
Lexing.from_channel ic
|
||||
in
|
||||
let of_xyz_lexbuf lexbuf =
|
||||
let data =
|
||||
Xyz_parser.input Nuclei_lexer.read_all lexbuf
|
||||
in
|
||||
@ -24,6 +20,30 @@ let of_xyz_file filename =
|
||||
|> Array.of_list
|
||||
|
||||
|
||||
let of_xyz_string buffer =
|
||||
Zmatrix.of_string buffer
|
||||
|> Zmatrix.to_xyz
|
||||
|> Array.map (fun (e,x,y,z) ->
|
||||
(e, Coordinate.(angstrom_to_bohr @@ make_angstrom { x ; y ; z} ))
|
||||
)
|
||||
|
||||
|
||||
let of_xyz_string input_string =
|
||||
Lexing.from_string input_string
|
||||
|> of_xyz_lexbuf
|
||||
|
||||
|
||||
let of_xyz_file filename =
|
||||
let ic = open_in filename in
|
||||
let lexbuf =
|
||||
Lexing.from_channel ic
|
||||
in
|
||||
let result =
|
||||
of_xyz_lexbuf lexbuf
|
||||
in
|
||||
close_in ic;
|
||||
result
|
||||
|
||||
|
||||
let of_zmt_string buffer =
|
||||
Zmatrix.of_string buffer
|
||||
|
@ -5,6 +5,9 @@ of tuples ({!Element.t}, {!Coordinate.t}).
|
||||
type t = (Element.t * Coordinate.t) array
|
||||
|
||||
|
||||
val of_xyz_string : string -> t
|
||||
(** Create from a string, in [xyz] format. *)
|
||||
|
||||
val of_xyz_file : string -> t
|
||||
(** Create from a file, in [xyz] format. *)
|
||||
|
||||
|
@ -1,6 +1,6 @@
|
||||
type t = {
|
||||
charge : Charge.t;
|
||||
electrons : Electrons.t ;
|
||||
electrons : Electrons.t;
|
||||
nuclei : Nuclei.t;
|
||||
basis : Basis.t;
|
||||
ao_basis : AOBasis.t;
|
||||
@ -19,12 +19,12 @@ let mu_erf t = t.mu_erf
|
||||
let f12 t = t.f12
|
||||
|
||||
let make ?cartesian:(cartesian=false)
|
||||
?multiplicity:(multiplicity=1)
|
||||
?charge:(charge=0)
|
||||
?f12
|
||||
?mu_erf
|
||||
~nuclei
|
||||
basis
|
||||
?multiplicity:(multiplicity=1)
|
||||
?charge:(charge=0)
|
||||
?f12
|
||||
?mu_erf
|
||||
~nuclei
|
||||
basis
|
||||
=
|
||||
|
||||
(* Tune Garbage Collector *)
|
||||
@ -39,11 +39,11 @@ let make ?cartesian:(cartesian=false)
|
||||
Charge.(Nuclei.charge nuclei + Electrons.charge electrons)
|
||||
in
|
||||
|
||||
let ao_basis =
|
||||
let ao_basis =
|
||||
AOBasis.make ?f12 ~basis ~cartesian nuclei
|
||||
in
|
||||
|
||||
let nuclear_repulsion =
|
||||
let nuclear_repulsion =
|
||||
Nuclei.repulsion nuclei
|
||||
in
|
||||
|
||||
|
Loading…
Reference in New Issue
Block a user