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Working on documenation

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Anthony Scemama 2018-02-23 18:41:30 +01:00
parent d7d018b3ea
commit e1da54cd67
24 changed files with 151 additions and 621 deletions
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11
Basis/Basis.ml
View File

@ -1,11 +1,12 @@
type t = type t =
{ {
size : int; size : int;
contracted_shells : Contracted_shell.t array; contracted_shells : ContractedShell.t array;
} }
module Cs = Contracted_shell module Cs = ContractedShell
module Gb = General_basis module Gb = GeneralBasis
(** Returns an array of the basis set per atom *) (** Returns an array of the basis set per atom *)
let of_nuclei_and_general_basis n b = let of_nuclei_and_general_basis n b =
@ -62,9 +63,11 @@ let to_string b =
) )
^ line ^ line
let of_nuclei_and_basis_filename ~nuclei ~filename = let of_nuclei_and_basis_filename ~nuclei ~filename =
let general_basis = let general_basis =
Gamess_reader.read ~filename GamessReader.read ~filename
in in
of_nuclei_and_general_basis nuclei general_basis of_nuclei_and_general_basis nuclei general_basis

33
Basis/Basis.mli
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@ -1,22 +1,29 @@
(** The atomic basis set is represented as an array of {!ContractedShell.t}. *)
type t = private type t = private
{ {
(** Number of contracted Gaussians *) size : int ; (** Number of contracted Gaussians *)
size : int; contracted_shells :
ContractedShell.t array ; (** Contracted shells *)
(** Array of contracted shells *)
contracted_shells : Contracted_shell.t array;
} }
(** Returns an array of the basis set per atom *)
val of_nuclei_and_general_basis : Nuclei.t -> General_basis.t list -> t
(** Pretty prints the basis set in a string *)
val to_string : t -> string val to_string : t -> string
(** Pretty prints the basis set in a string. *)
val of_nuclei_and_general_basis : Nuclei.t -> GeneralBasis.t list -> t
(** Takes an array of {!Nuclei.t}, and a {!GeneralBasis.t} (such as cc-pVDZ
for instance) and creates the corresponding atomic basis set.
All the {!Element.t}s of the array of {!Nuclei.t} are searched in
the {!GeneralBasis.t}, and the basis is built by creating
{!ContractedShell.t}s centered on the nuclei with the exponents
and contraction coefficients given by the {!GeneralBasis.t}.
*)
(** Create a basis using the coordinates of Nuclei and a the filename of
the general basis set *)
val of_nuclei_and_basis_filename : nuclei:Nuclei.t -> filename:string -> t val of_nuclei_and_basis_filename : nuclei:Nuclei.t -> filename:string -> t
(** Same as {!of_nuclei_and_general_basis}, but taking the {!GeneralBasis.t}
from a file.
*)

33
Basis/Basis_lexer.mll
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@ -1,33 +0,0 @@
{
exception SyntaxError of string
open Gamess_parser
}
let eol = ['\n']
let white = [' ' '\t']+
let element = ['A'-'Z' 'a'-'z']+ white? eol
let ang_mom = ['S' 'P' 'D' 'F' 'G' 'H' 'I' 'J' 'K' 'L' 'M' 'N' 'O'
's' 'p' 'd' 'f' 'g' 'h' 'i' 'j' 'k' 'l' 'm' 'n' 'o' ]
white
let integer = ['0'-'9']+
let real = '-'? integer '.' integer (['e' 'E'] ('+'|'-')? integer)?
rule read_all_rule = parse
| eol { EOL }
| white { SPACE }
| ang_mom as a { ANG_MOM (a.[0]) }
| element as e { ELEMENT (String.trim e) }
| integer as i { INTEGER (int_of_string i) }
| real as f { FLOAT (float_of_string f) }
| eof { EOF }
{
let rec read_all lexbuf =
match read_all_rule lexbuf with
| SPACE -> read_all_rule lexbuf
| x -> x
}

8
Basis/ContractedShellPair.ml
View File

@ -5,8 +5,8 @@ exception Null_contribution
type t = type t =
{ {
shell_a : Contracted_shell.t; shell_a : ContractedShell.t;
shell_b : Contracted_shell.t; shell_b : ContractedShell.t;
shell_pairs : ShellPair.t array; shell_pairs : ShellPair.t array;
coef : float array; coef : float array;
expo_inv : float array; expo_inv : float array;
@ -18,9 +18,9 @@ type t =
} }
module Am = Angular_momentum module Am = AngularMomentum
module Co = Coordinate module Co = Coordinate
module Cs = Contracted_shell module Cs = ContractedShell
module Sp = ShellPair module Sp = ShellPair
(** Creates an contracted shell pair : an array of pairs of primitive shells. (** Creates an contracted shell pair : an array of pairs of primitive shells.

129
Basis/Contracted_shell.ml
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@ -1,129 +0,0 @@
open Util
open Constants
open Coordinate
type shell_contracted = {
expo : float array; (* Gaussian exponents *)
coef : float array; (* Contraction coefficients *)
center : Coordinate.t; (* Center of all the Gaussians *)
totAngMom : Angular_momentum.t; (* Total angular momentum *)
size : int; (* Number of contracted Gaussians *)
norm_coef : float array; (* Normalization coefficient of the class
corresponding to the i-th contraction *)
norm_coef_scale : float array; (* Inside a class, the norm is the norm
of the function with (totAngMom,0,0) *.
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 *)
}
type t = shell_contracted
module Am = Angular_momentum
(** Normalization coefficient of contracted function i, which depends on the
exponent and the angular momentum. Two conventions can be chosen : a single
normalisation factor for all functions of the class, or a coefficient which
depends on the powers of x,y and z.
Returns, for each contracted function, an array of functions taking as
argument the [|x;y;z|] powers.
*)
let compute_norm_coef expo totAngMom =
let atot =
Am.to_int totAngMom
in
let factor int_array =
let dfa = Array.map (fun j ->
( float_of_int (1 lsl j) *. fact j) /. fact (j+j)
) int_array
in
sqrt (dfa.(0) *.dfa.(1) *. dfa.(2))
in
let expo =
if atot mod 2 = 0 then
Array.map (fun alpha ->
let alpha_2 = alpha +. alpha in
(alpha_2 *. pi_inv)**(0.75) *. (pow (alpha_2 +. alpha_2) (atot/2))
) expo
else
Array.map (fun alpha ->
let alpha_2 = alpha +. alpha in
(alpha_2 *. pi_inv)**(0.75) *. sqrt (pow (alpha_2 +. alpha_2) atot)
) expo
in
Array.map (fun x -> let f a = x *. (factor a) in f) expo
let make ~index ~expo ~coef ~center ~totAngMom =
assert (Array.length expo = Array.length coef);
assert (Array.length expo > 0);
let norm_coef_func =
compute_norm_coef expo totAngMom
in
let powers =
Am.zkey_array (Am.Singlet totAngMom)
in
let norm_coef =
Array.map (fun f -> f [| Am.to_int totAngMom ; 0 ; 0 |]) norm_coef_func
in
let norm_coef_scale =
Array.map (fun a ->
(norm_coef_func.(0) (Zkey.to_int_array ~kind:Zkey.Kind_3 a)) /. norm_coef.(0)
) powers
in
{ index ; expo ; coef ; center ; totAngMom ; size=Array.length expo ; norm_coef ;
norm_coef_scale ; powers }
let with_index a i =
{ a with index = i }
let to_string s =
let coord = s.center in
let open Printf in
(match s.totAngMom with
| Am.S -> sprintf "%3d " (s.index+1)
| _ -> sprintf "%3d-%-3d" (s.index+1) (s.index+(Array.length s.powers))
) ^
( sprintf "%1s %8.3f %8.3f %8.3f " (Am.to_string s.totAngMom)
(get X coord) (get Y coord) (get Z coord) ) ^
(Array.map2 (fun e c -> sprintf "%16.8e %16.8e" e c) s.expo s.coef
|> Array.to_list |> String.concat (sprintf "\n%36s" " ") )
(** Normalization coefficient of contracted function i, which depends on the
exponent and the angular momentum. Two conventions can be chosen : a single
normalisation factor for all functions of the class, or a coefficient which
depends on the powers of x,y and z.
Returns, for each contracted function, an array of functions taking as
argument the [|x;y;z|] powers.
*)
let compute_norm_coef expo totAngMom =
let atot =
Am.to_int totAngMom
in
let factor int_array =
let dfa = Array.map (fun j ->
(float_of_int (1 lsl j) *. fact j) /. fact (j+j)
) int_array
in
sqrt (dfa.(0) *.dfa.(1) *. dfa.(2))
in
let expo =
if atot mod 2 = 0 then
Array.map (fun alpha ->
let alpha_2 = alpha +. alpha in
(alpha_2 *. pi_inv)**(0.75) *. (pow (alpha_2 +. alpha_2) (atot/2))
) expo
else
Array.map (fun alpha ->
let alpha_2 = alpha +. alpha in
(alpha_2 *. pi_inv)**(0.75) *. sqrt (pow (alpha_2 +. alpha_2) atot)
) expo
in
Array.map (fun x -> let f a = x *. factor a in f) expo

27
Basis/Contracted_shell.mli
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@ -1,27 +0,0 @@
type shell_contracted = private {
expo : float array;
coef : float array;
center : Coordinate.t;
totAngMom : Angular_momentum.t;
size : int;
norm_coef : float array;
norm_coef_scale : float array;
index : int;
powers : Zkey.t array;
}
type t = shell_contracted
(** Pretty-printing of the contracted shell in a string *)
val to_string : t -> string
(** Creates a contracted shell *)
val make :
index:int ->
expo:float array ->
coef:float array ->
center:Coordinate.t -> totAngMom:Angular_momentum.t -> t
(** Returns a copy of the contracted shell with a modified index *)
val with_index : t -> int -> t

2
Basis/ERI.ml
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@ -7,7 +7,7 @@ open Bigarray
type t = (float, float32_elt, fortran_layout) Bigarray.Genarray.t type t = (float, float32_elt, fortran_layout) Bigarray.Genarray.t
module Bs = Basis module Bs = Basis
module Cs = Contracted_shell module Cs = ContractedShell
module Csp = ContractedShellPair module Csp = ContractedShellPair
(** (00|00)^m : Fundamental electron repulsion integral (** (00|00)^m : Fundamental electron repulsion integral

49
Basis/Gamess_parser.mly
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@ -1,49 +0,0 @@
/* Parses basis sets GAMESS format */
%{
%}
%token <string> ELEMENT
%token <char> ANG_MOM
%token <int> INTEGER
%token <float> FLOAT
%token SPACE
%token EOL
%token EOF
%start input
%type <General_basis.t> input
%% /* Grammar rules and actions follow */
input:
| basis { $1 }
| EOL input { $2 }
basis:
| element shell_array EOL { ($1, $2) }
| element shell_array EOF { ($1, $2) }
element:
| ELEMENT { Element.of_string $1 }
shell_array:
| shell_list { Array.of_list @@ List.rev $1 }
shell_list:
| { [] }
| shell_list shell { $2 :: $1 }
shell:
| ANG_MOM INTEGER EOL primitive_list { (Angular_momentum.of_char $1, Array.of_list @@ List.rev $4 ) }
primitive_list:
| { [] }
| primitive_list primitive { $2 :: $1 }
primitive:
| INTEGER FLOAT FLOAT EOL { General_basis.{exponent=$2 ; coefficient=$3 } }

18
Basis/Gamess_reader.ml
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@ -1,18 +0,0 @@
(** Read a basis set file in GAMESS format and return an association list where the key is an
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
in
let rec aux accu =
try
let key, basis =
Gamess_parser.input Basis_lexer.read_all lexbuf
in
aux ((key, basis)::accu)
with
| Parsing.Parse_error -> List.rev accu
in
aux []

40
Basis/General_basis.ml
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@ -1,40 +0,0 @@
(** General basis set read from a file *)
type primitive = {
exponent: float ;
coefficient: float
}
type general_contracted_shell = Angular_momentum.t * (primitive array)
type t = Element.t * (general_contracted_shell array)
module Am = Angular_momentum
let string_of_primitive ?id prim =
match id with
| None -> (string_of_float prim.exponent)^" "^(string_of_float prim.coefficient)
| Some i -> (string_of_int i)^" "^(string_of_float prim.exponent)^" "^(string_of_float prim.coefficient)
let string_of_contracted_shell (angular_momentum, prim_array) =
let n =
Array.length prim_array
in
Printf.sprintf "%s %d\n%s"
(Am.to_string angular_momentum) n
(Array.init n (fun i -> string_of_primitive ~id:(i+1) prim_array.(i))
|> Array.to_list
|> String.concat "\n")
let string_of_contracted_shell_array a =
Array.map string_of_contracted_shell a
|> Array.to_list
|> String.concat "\n"
let to_string (name, contracted_shell_array) =
Printf.sprintf "%s\n%s" name (string_of_contracted_shell_array contracted_shell_array)

4
Basis/KinInt.ml
View File

@ -2,10 +2,10 @@ open Util
open Constants open Constants
open Lacaml.D open Lacaml.D
module Am = Angular_momentum module Am = AngularMomentum
module Bs = Basis module Bs = Basis
module Co = Coordinate module Co = Coordinate
module Cs = Contracted_shell module Cs = ContractedShell
module Csp = ContractedShellPair module Csp = ContractedShellPair
module Sp = ShellPair module Sp = ShellPair

4
Basis/OneElectronRR.ml
View File

@ -3,9 +3,9 @@ open Constants
exception NullPair exception NullPair
module Am = Angular_momentum module Am = AngularMomentum
module Co = Coordinate module Co = Coordinate
module Cs = Contracted_shell module Cs = ContractedShell
module Csp = ContractedShellPair module Csp = ContractedShellPair
module Po = Powers module Po = Powers
module Sp = ShellPair module Sp = ShellPair

4
Basis/Overlap.ml
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@ -4,10 +4,10 @@ open Lacaml.D
type t = Mat.t type t = Mat.t
module Am = Angular_momentum module Am = AngularMomentum
module Bs = Basis module Bs = Basis
module Co = Coordinate module Co = Coordinate
module Cs = Contracted_shell module Cs = ContractedShell
module Csp = ContractedShellPair module Csp = ContractedShellPair
module Sp = ShellPair module Sp = ShellPair

6
Basis/ShellPair.ml
View File

@ -14,8 +14,8 @@ type t = {
totAngMomInt : int ; totAngMomInt : int ;
i : int; i : int;
j : int; j : int;
shell_a : Contracted_shell.t; shell_a : ContractedShell.t;
shell_b : Contracted_shell.t; shell_b : ContractedShell.t;
monocentric : bool monocentric : bool
} }
@ -27,7 +27,7 @@ let hash a =
let equivalent a b = let equivalent a b =
a = b a = b
(* (*
Hashtbl.hash (a.expo, a.center_a, a.center_ab, a.coef, Contracted_shell.totAngMom a.shell_a, Contracted_shell.totAngMom a.shell_b) Hashtbl.hash (a.expo, a.center_a, a.center_ab, a.coef, ContractedShell.totAngMom a.shell_a, ContractedShell.totAngMom a.shell_b)
*) *)

4
Basis/TwoElectronRR.ml
View File

@ -1,9 +1,9 @@
open Util open Util
open Constants open Constants
module Am = Angular_momentum module Am = AngularMomentum
module Co = Coordinate module Co = Coordinate
module Cs = Contracted_shell module Cs = ContractedShell
module Csp = ContractedShellPair module Csp = ContractedShellPair
module Sp = ShellPair module Sp = ShellPair
module Po = Powers module Po = Powers

206
Basis/TwoElectronRRVectorized.ml
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@ -1,16 +1,19 @@
open Util open Util
open Lacaml.D open Lacaml.D
open Bigarray open Bigarray
open Powers
open Coordinate
open Contracted_shell_type
let cutoff = Constants.cutoff module Am = AngularMomentum
let cutoff2 = cutoff *. cutoff module Co = Coordinate
module Csp = ContractedShellPair
module Sp = ShellPair
module Po = Powers
exception NullQuartet exception NullQuartet
exception Found exception Found
let cutoff = Constants.cutoff
let cutoff2 = cutoff *. cutoff
let at_least_one_valid arr = let at_least_one_valid arr =
try try
Array.iter (fun x -> if (abs_float x > cutoff) then raise Found) arr ; false Array.iter (fun x -> if (abs_float x > cutoff) then raise Found) arr ; false
@ -31,14 +34,14 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
let get_xyz angMom = let get_xyz angMom =
match angMom with match angMom with
| { y=0 ; z=0 ; _ } -> X | { Po.y=0 ; z=0 ; _ } -> Co.X
| { z=0 ; _ } -> Y | { z=0 ; _ } -> Co.Y
| _ -> Z | _ -> Co.Z
in in
(** Vertical recurrence relations *) (** Vertical recurrence relations *)
let rec vrr0_v angMom_a = let rec vrr0_v angMom_a =
match angMom_a.tot with match angMom_a.Po.tot with
| 0 -> zero_m_array | 0 -> zero_m_array
| _ -> | _ ->
let key = Zkey.of_powers_three angMom_a let key = Zkey.of_powers_three angMom_a
@ -48,9 +51,9 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
| Not_found -> | Not_found ->
let result = let result =
let xyz = get_xyz angMom_a in let xyz = get_xyz angMom_a in
let am = Powers.decr xyz angMom_a in let am = Po.decr xyz angMom_a in
let cab = Coordinate.get xyz center_ab in let cab = Co.get xyz center_ab in
let result = Array.init (maxm+1-angMom_a.tot) (fun _ -> Array.make_matrix np nq 0.) in let result = Array.init (maxm+1-angMom_a.Po.tot) (fun _ -> Array.make_matrix np nq 0.) in
let v_am= vrr0_v am in let v_am= vrr0_v am in
begin begin
@ -66,7 +69,7 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
) result_m ) result_m
) result ) result
end; end;
let amxyz = Powers.get xyz am in let amxyz = Po.get xyz am in
if amxyz < 1 then if amxyz < 1 then
Array.iteri (fun l expo_inv_p_l -> Array.iteri (fun l expo_inv_p_l ->
let center_pq_xyz_l = (center_pq xyz).(l) in let center_pq_xyz_l = (center_pq xyz).(l) in
@ -83,7 +86,7 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
) expo_inv_p ) expo_inv_p
else else
begin begin
let amm = Powers.decr xyz am in let amm = Po.decr xyz am in
let amxyz = float_of_int amxyz in let amxyz = float_of_int amxyz in
let v_amm = vrr0_v amm in let v_amm = vrr0_v amm in
Array.iteri (fun l expo_inv_p_l -> Array.iteri (fun l expo_inv_p_l ->
@ -113,7 +116,7 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
and vrr_v m angMom_a angMom_c = and vrr_v m angMom_a angMom_c =
match (angMom_a.tot, angMom_c.tot) with match (angMom_a.Po.tot, angMom_c.Po.tot) with
| (i,0) -> Some (vrr0_v angMom_a).(m) | (i,0) -> Some (vrr0_v angMom_a).(m)
| (_,_) -> | (_,_) ->
@ -124,12 +127,12 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
let result = let result =
begin begin
let xyz = get_xyz angMom_c in let xyz = get_xyz angMom_c in
let cm = Powers.decr xyz angMom_c in let cm = Po.decr xyz angMom_c in
let axyz = Powers.get xyz angMom_a in let axyz = Po.get xyz angMom_a in
let do_compute = ref false in let do_compute = ref false in
let v1 = let v1 =
let f = -. (Coordinate.get xyz center_cd) in let f = -. (Co.get xyz center_cd) in
let f1 = let f1 =
Array.init nq (fun k -> Array.init nq (fun k ->
@ -198,10 +201,10 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
end end
in in
let cxyz = Powers.get xyz angMom_c in let cxyz = Po.get xyz angMom_c in
let p2 = let p2 =
if cxyz < 2 then p1 else if cxyz < 2 then p1 else
let cmm = Powers.decr xyz cm in let cmm = Po.decr xyz cm in
let fcm = (float_of_int (cxyz-1)) *. 0.5 in let fcm = (float_of_int (cxyz-1)) *. 0.5 in
let f1 = let f1 =
Array.init nq (fun k -> Array.init nq (fun k ->
@ -312,7 +315,7 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
end end
in in
if (axyz < 1) || (cxyz < 1) then p2 else if (axyz < 1) || (cxyz < 1) then p2 else
let am = Powers.decr xyz angMom_a in let am = Po.decr xyz angMom_a in
let v = let v =
vrr_v (m+1) am cm vrr_v (m+1) am cm
in in
@ -344,7 +347,7 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
(* (*
and trr_v angMom_a angMom_c = and trr_v angMom_a angMom_c =
match (angMom_a.tot, angMom_c.tot) with match (angMom_a.Po.tot, angMom_c.Po.tot) with
| (i,0) -> Some (vrr0_v angMom_a).(0) | (i,0) -> Some (vrr0_v angMom_a).(0)
| (_,_) -> | (_,_) ->
@ -353,9 +356,9 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
try Zmap.find map_2d.(0) key with try Zmap.find map_2d.(0) key with
| Not_found -> | Not_found ->
let xyz = get_xyz angMom_c in let xyz = get_xyz angMom_c in
let axyz = Powers.get xyz angMom_a in let axyz = Po.get xyz angMom_a in
let cm = Powers.decr xyz angMom_c in let cm = Po.decr xyz angMom_c in
let cmxyz = Powers.get xyz cm in let cmxyz = Po.get xyz cm in
let expo_inv_q_over_p = let expo_inv_q_over_p =
Array.mapi (fun l expo_inv_p_l -> Array.mapi (fun l expo_inv_p_l ->
let expo_p_l = 1./.expo_inv_p_l in let expo_p_l = 1./.expo_inv_p_l in
@ -368,7 +371,7 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
if cmxyz < 1 then result else if cmxyz < 1 then result else
begin begin
let f = 0.5 *. (float_of_int cmxyz) in let f = 0.5 *. (float_of_int cmxyz) in
let cmm = Powers.decr xyz cm in let cmm = Po.decr xyz cm in
match result, trr_v angMom_a cmm with match result, trr_v angMom_a cmm with
| None, None -> None | None, None -> None
| None, Some v3 -> | None, Some v3 ->
@ -420,7 +423,7 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
let result = let result =
if cmxyz < 0 then result else if cmxyz < 0 then result else
begin begin
let ap = Powers.incr xyz angMom_a in let ap = Po.incr xyz angMom_a in
match result, trr_v ap cm with match result, trr_v ap cm with
| Some result, None -> Some result | Some result, None -> Some result
| Some result, Some v4 -> | Some result, Some v4 ->
@ -445,7 +448,7 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
if axyz < 1 then result else if axyz < 1 then result else
begin begin
let f = 0.5 *. (float_of_int axyz) in let f = 0.5 *. (float_of_int axyz) in
let am = Powers.decr xyz angMom_a in let am = Po.decr xyz angMom_a in
match result, trr_v am cm with match result, trr_v am cm with
| Some result, None -> Some result | Some result, None -> Some result
| Some result, Some v2 -> | Some result, Some v2 ->
@ -476,7 +479,7 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
let vrr_v a c = let vrr_v a c =
let v = let v =
(* (*
if c.tot <> 0 then if c.Po.tot <> 0 then
vrr_v 0 a c vrr_v 0 a c
else trr_v a c else trr_v a c
*) *)
@ -491,48 +494,48 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
(** Horizontal recurrence relations *) (** Horizontal recurrence relations *)
let rec hrr0_v angMom_a angMom_b angMom_c = let rec hrr0_v angMom_a angMom_b angMom_c =
match angMom_b.tot with match angMom_b.Po.tot with
| 0 -> | 0 ->
begin begin
match (angMom_a.tot, angMom_c.tot) with match (angMom_a.Po.tot, angMom_c.Po.tot) with
| (0,0) -> sum zero_m_array.(0) | (0,0) -> sum zero_m_array.(0)
| (_,_) -> vrr_v angMom_a angMom_c | (_,_) -> vrr_v angMom_a angMom_c
end end
| 1 -> | 1 ->
let xyz = get_xyz angMom_b in let xyz = get_xyz angMom_b in
let ap = Powers.incr xyz angMom_a in let ap = Po.incr xyz angMom_a in
let f = Coordinate.get xyz center_ab in let f = Co.get xyz center_ab in
let v1 = vrr_v ap angMom_c in let v1 = vrr_v ap angMom_c in
if (abs_float f < cutoff) then v1 else if (abs_float f < cutoff) then v1 else
let v2 = vrr_v angMom_a angMom_c in let v2 = vrr_v angMom_a angMom_c in
v1 +. v2 *. f v1 +. v2 *. f
| _ -> | _ ->
let xyz = get_xyz angMom_b in let xyz = get_xyz angMom_b in
let bxyz = Powers.get xyz angMom_b in let bxyz = Po.get xyz angMom_b in
if (bxyz < 0) then 0. else if (bxyz < 0) then 0. else
let ap = Powers.incr xyz angMom_a in let ap = Po.incr xyz angMom_a in
let bm = Powers.decr xyz angMom_b in let bm = Po.decr xyz angMom_b in
let h1 = hrr0_v ap bm angMom_c in let h1 = hrr0_v ap bm angMom_c in
let f = Coordinate.get xyz center_ab in let f = Co.get xyz center_ab in
if abs_float f < cutoff then h1 else if abs_float f < cutoff then h1 else
let h2 = hrr0_v angMom_a bm angMom_c in let h2 = hrr0_v angMom_a bm angMom_c in
h1 +. h2 *. f h1 +. h2 *. f
and hrr_v angMom_a angMom_b angMom_c angMom_d = and hrr_v angMom_a angMom_b angMom_c angMom_d =
match (angMom_b.tot, angMom_d.tot) with match (angMom_b.Po.tot, angMom_d.Po.tot) with
| (_,0) -> if angMom_b.tot = 0 then | (_,0) -> if angMom_b.Po.tot = 0 then
vrr_v angMom_a angMom_c vrr_v angMom_a angMom_c
else else
hrr0_v angMom_a angMom_b angMom_c hrr0_v angMom_a angMom_b angMom_c
| (_,_) -> | (_,_) ->
let xyz = get_xyz angMom_d in let xyz = get_xyz angMom_d in
let cp = Powers.incr xyz angMom_c in let cp = Po.incr xyz angMom_c in
let dm = Powers.decr xyz angMom_d in let dm = Po.decr xyz angMom_d in
let h1 = let h1 =
hrr_v angMom_a angMom_b cp dm hrr_v angMom_a angMom_b cp dm
in in
let f = Coordinate.get xyz center_cd in let f = Co.get xyz center_cd in
if abs_float f < cutoff then if abs_float f < cutoff then
h1 h1
else else
@ -550,24 +553,23 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
let contracted_class_shell_pairs ~zero_m ?schwartz_p ?schwartz_q shell_p shell_q : float Zmap.t = let contracted_class_shell_pairs ~zero_m ?schwartz_p ?schwartz_q shell_p shell_q : float Zmap.t =
let shell_a = shell_p.ContractedShellPair.shell_a let shell_a = shell_p.Csp.shell_a
and shell_b = shell_p.ContractedShellPair.shell_b and shell_b = shell_p.Csp.shell_b
and shell_c = shell_q.ContractedShellPair.shell_a and shell_c = shell_q.Csp.shell_a
and shell_d = shell_q.ContractedShellPair.shell_b and shell_d = shell_q.Csp.shell_b
and sp = shell_p.ContractedShellPair.shell_pairs and sp = shell_p.Csp.shell_pairs
and sq = shell_q.ContractedShellPair.shell_pairs and sq = shell_q.Csp.shell_pairs
in in
let maxm = let maxm =
shell_p.ContractedShellPair.totAngMomInt + shell_p.Csp.totAngMomInt +
shell_q.ContractedShellPair.totAngMomInt shell_q.Csp.totAngMomInt
in in
(* Pre-computation of integral class indices *) (* Pre-computation of integral class indices *)
let class_indices = let class_indices =
Angular_momentum.zkey_array Am.zkey_array (Am.Quartet
(Angular_momentum.Quartet (shell_a.totAngMom, shell_b.totAngMom,
(shell_a.totAngMom, shell_b.totAngMom, shell_c.totAngMom, shell_d.totAngMom))
shell_c.totAngMom, shell_d.totAngMom))
in in
let contracted_class = let contracted_class =
@ -575,21 +577,21 @@ let contracted_class_shell_pairs ~zero_m ?schwartz_p ?schwartz_q shell_p shell_q
in in
let monocentric = let monocentric =
shell_p.ContractedShellPair.monocentric && shell_p.Csp.monocentric &&
shell_q.ContractedShellPair.monocentric && shell_q.Csp.monocentric &&
shell_p.ContractedShellPair.shell_a.center = shell_p.Csp.shell_a.center =
shell_q.ContractedShellPair.shell_a.center shell_q.Csp.shell_a.center
in in
(** Screening on the product of coefficients *) (** Screening on the product of coefficients *)
let coef_max_p = let coef_max_p =
Array.fold_left (fun accu x -> Array.fold_left (fun accu x ->
if (abs_float x) > accu then (abs_float x) else accu) if (abs_float x) > accu then (abs_float x) else accu)
0. shell_p.ContractedShellPair.coef 0. shell_p.Csp.coef
and coef_max_q = and coef_max_q =
Array.fold_left (fun accu x -> Array.fold_left (fun accu x ->
if (abs_float x) > accu then (abs_float x) else accu) if (abs_float x) > accu then (abs_float x) else accu)
0. shell_q.ContractedShellPair.coef 0. shell_q.Csp.coef
in in
let rec build_list cutoff vec accu = function let rec build_list cutoff vec accu = function
@ -599,10 +601,10 @@ let contracted_class_shell_pairs ~zero_m ?schwartz_p ?schwartz_q shell_p shell_q
else accu ) (k-1) else accu ) (k-1)
in in
let p_list = let p_list =
let vec = shell_p.ContractedShellPair.coef in let vec = shell_p.Csp.coef in
build_list (cutoff /. coef_max_q) vec [] (Array.length vec - 1) build_list (cutoff /. coef_max_q) vec [] (Array.length vec - 1)
and q_list = and q_list =
let vec = shell_q.ContractedShellPair.coef in let vec = shell_q.Csp.coef in
build_list (cutoff /. coef_max_p) vec [] (Array.length vec - 1) build_list (cutoff /. coef_max_p) vec [] (Array.length vec - 1)
in in
@ -623,21 +625,21 @@ let contracted_class_shell_pairs ~zero_m ?schwartz_p ?schwartz_q shell_p shell_q
begin begin
match (shell_a.totAngMom, shell_b.totAngMom, match (shell_a.totAngMom, shell_b.totAngMom,
shell_c.totAngMom, shell_d.totAngMom) with shell_c.totAngMom, shell_d.totAngMom) with
| Angular_momentum.(S,S,S,S) -> | Am.(S,S,S,S) ->
contracted_class.(0) <- contracted_class.(0) <-
begin begin
try try
let expo_inv_p = let expo_inv_p =
Vec.init np (fun ab -> sp.(ab-1).ShellPair.expo_inv) Vec.init np (fun ab -> sp.(ab-1).Sp.expo_inv)
and expo_inv_q = and expo_inv_q =
Vec.init nq (fun cd -> sq.(cd-1).ShellPair.expo_inv) Vec.init nq (fun cd -> sq.(cd-1).Sp.expo_inv)
in in
let coef = let coef =
let result = Mat.make0 nq np in let result = Mat.make0 nq np in
Lacaml.D.ger Lacaml.D.ger
(Vec.of_array @@ filter_q shell_q.ContractedShellPair.coef) (Vec.of_array @@ filter_q shell_q.Csp.coef)
(Vec.of_array @@ filter_p shell_p.ContractedShellPair.coef) (Vec.of_array @@ filter_p shell_p.Csp.coef)
result; result;
result result
in in
@ -651,10 +653,10 @@ let contracted_class_shell_pairs ~zero_m ?schwartz_p ?schwartz_q shell_p shell_q
in in
let center_pq = let center_pq =
sp.(i-1).ShellPair.center |- sq.(j-1).ShellPair.center Co.(sp.(i-1).Sp.center |- sq.(j-1).Sp.center)
in in
let norm_pq_sq = let norm_pq_sq =
Coordinate.dot center_pq center_pq Co.dot center_pq center_pq
in in
let zero_m_array = let zero_m_array =
@ -669,24 +671,24 @@ let contracted_class_shell_pairs ~zero_m ?schwartz_p ?schwartz_q shell_p shell_q
| _ -> | _ ->
let coef = let coef =
let cp = filter_p shell_p.ContractedShellPair.coef let cp = filter_p shell_p.Csp.coef
and cq = filter_q shell_q.ContractedShellPair.coef and cq = filter_q shell_q.Csp.coef
in in
Array.init np (fun l -> Array.init nq (fun k -> cq.(k) *. cp.(l)) ) Array.init np (fun l -> Array.init nq (fun k -> cq.(k) *. cp.(l)) )
in in
let expo_inv_p = let expo_inv_p =
Array.map (fun shell_ab -> shell_ab.ShellPair.expo_inv) sp Array.map (fun shell_ab -> shell_ab.Sp.expo_inv) sp
and expo_inv_q = and expo_inv_q =
Array.map (fun shell_cd -> shell_cd.ShellPair.expo_inv) sq Array.map (fun shell_cd -> shell_cd.Sp.expo_inv) sq
in in
let expo_b = let expo_b =
Array.map (fun shell_ab -> shell_b.expo.(shell_ab.ShellPair.j)) sp Array.map (fun shell_ab -> shell_b.expo.(shell_ab.Sp.j)) sp
and expo_d = and expo_d =
Array.map (fun shell_cd -> shell_d.expo.(shell_cd.ShellPair.j)) sq Array.map (fun shell_cd -> shell_d.expo.(shell_cd.Sp.j)) sq
in in
let norm_coef_scale_p = shell_p.ContractedShellPair.norm_coef_scale in let norm_coef_scale_p = shell_p.Csp.norm_coef_scale in
let center_pq = let center_pq =
let result = let result =
@ -697,19 +699,19 @@ let contracted_class_shell_pairs ~zero_m ?schwartz_p ?schwartz_q shell_p shell_q
let shell_cd = sq.(cd) let shell_cd = sq.(cd)
in in
let cpq = let cpq =
shell_ab.ShellPair.center |- shell_cd.ShellPair.center Co.(shell_ab.Sp.center |- shell_cd.Sp.center)
in in
match xyz with match xyz with
| 0 -> Coordinate.get X cpq; | 0 -> Co.get X cpq;
| 1 -> Coordinate.get Y cpq; | 1 -> Co.get Y cpq;
| _ -> Coordinate.get Z cpq; | _ -> Co.get Z cpq;
) )
) )
) )
in function in function
| X -> result.(0) | Co.X -> result.(0)
| Y -> result.(1) | Co.Y -> result.(1)
| Z -> result.(2) | Co.Z -> result.(2)
in in
let center_pa = let center_pa =
let result = let result =
@ -717,18 +719,18 @@ let contracted_class_shell_pairs ~zero_m ?schwartz_p ?schwartz_q shell_p shell_q
Array.init np (fun ab -> Array.init np (fun ab ->
let shell_ab = sp.(ab) in let shell_ab = sp.(ab) in
let cpa = let cpa =
shell_ab.ShellPair.center |- shell_a.center Co.(shell_ab.Sp.center |- shell_a.center)
in in
match xyz with match xyz with
| 0 -> Coordinate.get X cpa; | 0 -> Co.(get X cpa);
| 1 -> Coordinate.get Y cpa; | 1 -> Co.(get Y cpa);
| _ -> Coordinate.get Z cpa; | _ -> Co.(get Z cpa);
) )
) )
in function in function
| X -> result.(0) | Co.X -> result.(0)
| Y -> result.(1) | Co.Y -> result.(1)
| Z -> result.(2) | Co.Z -> result.(2)
in in
let center_qc = let center_qc =
let result = let result =
@ -736,18 +738,18 @@ let contracted_class_shell_pairs ~zero_m ?schwartz_p ?schwartz_q shell_p shell_q
Array.init nq (fun cd -> Array.init nq (fun cd ->
let shell_cd = sq.(cd) in let shell_cd = sq.(cd) in
let cqc = let cqc =
shell_cd.ShellPair.center |- shell_c.center Co.(shell_cd.Sp.center |- shell_c.center)
in in
match xyz with match xyz with
| 0 -> Coordinate.get X cqc; | 0 -> Co.(get X cqc);
| 1 -> Coordinate.get Y cqc; | 1 -> Co.(get Y cqc);
| _ -> Coordinate.get Z cqc; | _ -> Co.(get Z cqc);
) )
) )
in function in function
| X -> result.(0) | Co.X -> result.(0)
| Y -> result.(1) | Co.Y -> result.(1)
| Z -> result.(2) | Co.Z -> result.(2)
in in
let zero_m_array = let zero_m_array =
let result = let result =
@ -787,7 +789,7 @@ let contracted_class_shell_pairs ~zero_m ?schwartz_p ?schwartz_q shell_p shell_q
let norm = let norm =
let norm_coef_scale_q = let norm_coef_scale_q =
shell_q.ContractedShellPair.norm_coef_scale shell_q.Csp.norm_coef_scale
in in
Array.to_list norm_coef_scale_p Array.to_list norm_coef_scale_p
|> List.map (fun v1 -> |> List.map (fun v1 ->
@ -843,8 +845,8 @@ let contracted_class_shell_pairs ~zero_m ?schwartz_p ?schwartz_q shell_p shell_q
zero_m_array zero_m_array
(expo_b, expo_d) (expo_b, expo_d)
(expo_inv_p, expo_inv_q) (expo_inv_p, expo_inv_q)
(shell_p.ContractedShellPair.center_ab, (shell_p.Csp.center_ab,
shell_q.ContractedShellPair.center_ab, center_pq) shell_q.Csp.center_ab, center_pq)
(center_pa, center_qc) (center_pa, center_qc)
map_1d map_2d np nq map_1d map_2d np nq
in in
@ -865,8 +867,8 @@ let contracted_class_shell_pairs ~zero_m ?schwartz_p ?schwartz_q shell_p shell_q
(** Computes all the two-electron integrals of the contracted shell quartet *) (** Computes all the two-electron integrals of the contracted shell quartet *)
let contracted_class ~zero_m shell_a shell_b shell_c shell_d : float Zmap.t = let contracted_class ~zero_m shell_a shell_b shell_c shell_d : float Zmap.t =
let shell_p = ContractedShellPair.create ~cutoff shell_a shell_b let shell_p = Csp.create ~cutoff shell_a shell_b
and shell_q = ContractedShellPair.create ~cutoff shell_c shell_d and shell_q = Csp.create ~cutoff shell_c shell_d
in in
contracted_class_shell_pairs ~zero_m shell_p shell_q contracted_class_shell_pairs ~zero_m shell_p shell_q

4
Nuclei/Element.ml
View File

@ -140,7 +140,7 @@ let covalent_radius x =
| Cd -> 1.44 | In -> 1.42 | Sn -> 1.39 | Sb -> 1.39 | Cd -> 1.44 | In -> 1.42 | Sn -> 1.39 | Sb -> 1.39
| Te -> 1.38 | I -> 1.39 | Xe -> 1.40 | Pt -> 1.30 | Te -> 1.38 | I -> 1.39 | Xe -> 1.40 | Pt -> 1.30
in in
Units.angstrom_to_bohr *. (result x) Constants.a0 *. (result x)
|> Radius.of_float |> Radius.of_float
@ -161,7 +161,7 @@ let vdw_radius x =
| Cd -> 1.58 | In -> 1.93 | Sn -> 2.17 | Sb -> 2.06 | Cd -> 1.58 | In -> 1.93 | Sn -> 2.17 | Sb -> 2.06
| Te -> 2.06 | I -> 1.98 | Xe -> 2.16 | Pt -> 1.75 | Te -> 2.06 | I -> 1.98 | Xe -> 2.16 | Pt -> 1.75
in in
Units.angstrom_to_bohr *. (result x) Constants.a0 *. (result x)
|> Radius.of_float |> Radius.of_float

2
Nuclei/Mass.ml
View File

@ -1 +1 @@
include Positive_float include PositiveFloat

134
Utils/Angular_momentum.ml
View File

@ -1,134 +0,0 @@
open Powers
exception AngularMomentumError of string
type t =
| S | P | D | F | G | H | I | J | K | L | M | N | O
let of_char = function
| 's' | 'S' -> S | 'p' | 'P' -> P
| 'd' | 'D' -> D | 'f' | 'F' -> F
| 'g' | 'G' -> G | 'h' | 'H' -> H
| 'i' | 'I' -> I | 'j' | 'J' -> J
| 'k' | 'K' -> K | 'l' | 'L' -> L
| 'm' | 'M' -> M | 'n' | 'N' -> N
| 'o' | 'O' -> O
| c -> raise (AngularMomentumError (String.make 1 c))
let to_string = function
| S -> "S" | P -> "P"
| D -> "D" | F -> "F"
| G -> "G" | H -> "H"
| I -> "I" | J -> "J"
| K -> "K" | L -> "L"
| M -> "M" | N -> "N"
| O -> "O"
let to_char = function
| S -> 'S' | P -> 'P'
| D -> 'D' | F -> 'F'
| G -> 'G' | H -> 'H'
| I -> 'I' | J -> 'J'
| K -> 'K' | L -> 'L'
| M -> 'M' | N -> 'N'
| O -> 'O'
let to_int = function
| S -> 0 | P -> 1
| D -> 2 | F -> 3
| G -> 4 | H -> 5
| I -> 6 | J -> 7
| K -> 8 | L -> 9
| M -> 10 | N -> 11
| O -> 12
let of_int = function
| 0 -> S | 1 -> P
| 2 -> D | 3 -> F
| 4 -> G | 5 -> H
| 6 -> I | 7 -> J
| 8 -> K | 9 -> L
| 10 -> M | 11 -> N
| 12 -> O
| c -> raise (AngularMomentumError (string_of_int c))
type kind =
| Singlet of t
| Doublet of (t*t)
| Triplet of (t*t*t)
| Quartet of (t*t*t*t)
let n_functions a =
let a =
to_int a
in
(a*a + 3*a + 2)/2
(** Returns an array of Zkeys corresponding to all possible angular momenta *)
let zkey_array a =
let keys_1d l =
let create_z { x ; y ; _ } =
Powers.of_int_tuple (x,y,l-(x+y))
in
let rec create_y accu xyz =
let { x ; y ; z } = xyz in
match y with
| 0 -> (create_z xyz)::accu
| i -> let ynew = y-1 in
create_y ( (create_z xyz)::accu) (Powers.of_int_tuple (x,ynew,z))
in
let rec create_x accu xyz =
let { x ; y ; z } = xyz in
match x with
| 0 -> (create_y [] xyz)@accu
| i -> let xnew = x-1 in
let ynew = l-xnew in
create_x ((create_y [] xyz)@accu) (Powers.of_int_tuple (xnew, ynew, z))
in
create_x [] (Powers.of_int_tuple (l,0,0))
|> List.rev
in
begin
match a with
| Singlet l1 ->
List.map (fun x -> Zkey.of_powers (Zkey.Three x)) (keys_1d @@ to_int l1)
| Doublet (l1, l2) ->
List.map (fun a ->
List.map (fun b ->
Zkey.of_powers (Zkey.Six (a,b))) (keys_1d @@ to_int l2)
) (keys_1d @@ to_int l1)
|> List.concat
| Triplet (l1, l2, l3) ->
List.map (fun a ->
List.map (fun b ->
List.map (fun c ->
Zkey.of_powers (Zkey.Nine (a,b,c))) (keys_1d @@ to_int l3)
) (keys_1d @@ to_int l2)
|> List.concat
) (keys_1d @@ to_int l1)
|> List.concat
| Quartet (l1, l2, l3, l4) ->
List.map (fun a ->
List.map (fun b ->
List.map (fun c ->
List.map (fun d ->
Zkey.of_powers (Zkey.Twelve (a,b,c,d))) (keys_1d @@ to_int l4)
) (keys_1d @@ to_int l3)
|> List.concat
) (keys_1d @@ to_int l2)
|> List.concat
) (keys_1d @@ to_int l1)
|> List.concat
end
|> Array.of_list

14
Utils/Positive_float.ml
View File

@ -1,14 +0,0 @@
type t = float
let of_float x =
assert ( x >= 0. );
x
external to_float : t -> float = "%identity"
let to_string x =
let f = to_float x in string_of_float f
let of_string x =
let f = float_of_string x in of_float f

5
Utils/Positive_float.mli
View File

@ -1,5 +0,0 @@
type t = private float
val of_float : float -> t
val to_float : t -> float
val to_string : t -> string
val of_string : string -> t

2
Utils/Radius.ml
View File

@ -1 +1 @@
include Positive_float include PositiveFloat

25
Utils/Units.ml
View File

@ -1,25 +0,0 @@
type units =
| Bohr
| Angstrom
type angle_units =
| Degree
| Radian
let pi = acos (-1.)
let to_degree x =
assert (x <= 2.*.pi);
assert (x >= -2.*.pi);
x *. 180. /. pi
let to_radian x =
assert (x <= 360.);
assert (x >= -360.);
x *. pi /. 180.
let angstrom_to_bohr = 1. /. 0.52917721092
let bohr_to_angstrom = 0.52917721092
;;

8
Utils/Units.mli
View File

@ -1,8 +0,0 @@
type units = Bohr | Angstrom
type angle_units = Degree | Radian
val to_radian : float -> float
val to_degree : float -> float
val angstrom_to_bohr : float
val bohr_to_angstrom : float