LCPQ
/
QCaml
mirror of https://gitlab.com/scemama/QCaml.git
10
1
Fork 0
Code Releases Activity

Working on input

This commit is contained in:
Anthony Scemama 2018-01-18 00:21:05 +01:00
parent 97e4a09664
commit 0687671098
10 changed files with 120 additions and 57 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

49
Basis/Basis.ml
View File

@ -1,41 +1,20 @@
(** General basis set read from a file *)
type primitive = {
exponent: float ;
coefficient: float
}
type t
type element_name = string
type general_contracted_shell = Angular_momentum.t * (primitive array)
type basis_set = element_name * (general_contracted_shell array)
let of_nuclei_and_general_basis n b =
Array.map (fun (e, center) ->
List.assoc e b
|> Array.map (fun (totAngMom, shell) ->
let expo = Array.map (fun General_basis.{exponent ; coefficient} ->
exponent) shell
and coef = Array.map (fun General_basis.{exponent ; coefficient} ->
coefficient) shell
in
Contracted_shell.create ~expo ~coef ~totAngMom ~center)
) n
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"
(Angular_momentum.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
let to_string b =
Array.map (fun i -> Contracted_shell.to_string i) b
|> 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)

8
Basis/Contracted_shell.ml
View File

@ -17,6 +17,14 @@ let totAngMom a = a.totAngMom
let norm_coef a i = a.norm_coef.(i)
let to_string s =
let open Printf in
[ sprintf "center: %s" (Coordinate.to_string s.center) ;
sprintf "angular momentum: %s" (Angular_momentum.to_string s.totAngMom) ]
@ (Array.map2 (fun e c -> sprintf "expo: %e coeff: %e" e c) s.expo s.coef
|> Array.to_list) @ ["\n"]
|> String.concat "\n"
(** 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

4
Basis/ERI.ml
View File

@ -210,8 +210,8 @@ let erint_contracted_class shell_a shell_b shell_c shell_d : float Zmap.t =
let class_indices =
Angular_momentum.zkey_array
(Angular_momentum.Kind_4
(Contracted_shell.totAngMom shell_a, Contracted_shell.totAngMom shell_b,
Contracted_shell.totAngMom shell_c, Contracted_shell.totAngMom shell_d))
Contracted_shell.(totAngMom shell_a, totAngMom shell_b,
totAngMom shell_c, totAngMom shell_d))
in
let contracted_class =

4
Basis/Gamess_parser.mly
View File

@ -13,7 +13,7 @@
%token EOF
%start input
%type <Basis.basis_set> input
%type <General_basis.t> input
%% /* Grammar rules and actions follow */
@ -43,7 +43,7 @@ primitive_list:
| primitive_list primitive { $2 :: $1 }
primitive:
| INTEGER FLOAT FLOAT EOL { Basis.{exponent=$2 ; coefficient=$3 } }
| INTEGER FLOAT FLOAT EOL { General_basis.{exponent=$2 ; coefficient=$3 } }

40
Basis/General_basis.ml Normal file
View File

@ -0,0 +1,40 @@
(** General basis set read from a file *)
type primitive = {
exponent: float ;
coefficient: float
}
type element_name = string
type general_contracted_shell = Angular_momentum.t * (primitive array)
type t = element_name * (general_contracted_shell array)
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"
(Angular_momentum.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)

16
Basis/Shell_pair.ml
View File

@ -21,15 +21,15 @@ let create_array ?(cutoff=0.) p_a p_b =
else -. (log cutoff)
in
let center_ab =
Coordinate.(Contracted_shell.center p_a |- Contracted_shell.center p_b)
let center_ab = Coordinate.(
Contracted_shell.center p_a |- Contracted_shell.center p_b )
in
let norm_sq =
Coordinate.dot center_ab center_ab
in
Array.init (Contracted_shell.size p_a) (fun i ->
let p_a_expo_center =
Coordinate.(Contracted_shell.expo p_a i |. Contracted_shell.center p_a)
let p_a_expo_center = Coordinate.(
Contracted_shell.expo p_a i |. Contracted_shell.center p_a )
in
let f1 =
Contracted_shell.norm_coef p_a i
@ -50,13 +50,13 @@ let create_array ?(cutoff=0.) p_a p_b =
in
if (norm < cutoff) then
raise Null_contribution;
let p_b_expo_center =
Coordinate.(Contracted_shell.expo p_b j |. Contracted_shell.center p_b)
let p_b_expo_center = Coordinate.(
Contracted_shell.expo p_b j |. Contracted_shell.center p_b )
in
let expo = Contracted_shell.(expo p_a i +. expo p_b j) in
let expo_inv = 1. /. expo in
let center =
Coordinate.( expo_inv |. (p_a_expo_center |+ p_b_expo_center ) )
let center = Coordinate.(
expo_inv |. (p_a_expo_center |+ p_b_expo_center ) )
in
let argexpo =
Contracted_shell.(expo p_a i *. expo p_b j) *. norm_sq *. expo_inv

5
Makefile
View File

@ -9,12 +9,11 @@ MLLFILES=$(wildcard */*.mll) $(wildcard *.mll)
MLYFILES=$(wildcard */*.mly) $(wildcard *.mly)
MLFILES= $(wildcard */*.ml) $(wildcard *.ml)
MLIFILES=$(wildcard */*.mli) $(wildcard *.mli)
ALL_EXE=$(patsubst %.ml,%.native,$(wildcard qp_*.ml))
ALL_EXE=$(patsubst %.ml,%.native,$(wildcard run_*.ml))
.PHONY: default
#default: $(ALL_EXE)
default: test.byte
default: $(ALL_EXE)
tests: $(ALL_TESTS)

4
Nuclei/Nuclei.ml
View File

@ -1,4 +1,4 @@
type coordinates = ( (Element.t * (float array)) array)
type coordinates = ( (Element.t * Coordinate.t) array)
let of_xyz_file ~filename =
let lexbuf =
@ -21,5 +21,5 @@ let of_zmt_file ~filename =
in aux []
|> Zmatrix.of_string
|> Zmatrix.to_xyz
|> Array.map (fun (e,x,y,z) -> (e, [|x;y;z|]))
|> Array.map (fun (e,x,y,z) -> (e, Coordinate.of_3_floats x y z ))

10
Nuclei/Xyz_parser.mly
View File

@ -12,7 +12,7 @@ exception InputError of string
%token EOF
%start input
%type <(Element.t * (float array)) array> input
%type <(Element.t * Coordinate.t) array> input
%% /* Grammar rules and actions follow */
@ -49,10 +49,10 @@ atoms_xyz:
atoms_list:
| { [] }
| atoms_list WORD SPACE FLOAT SPACE FLOAT SPACE FLOAT EOL { (Element.of_string $2, [| $4;$6;$8 |]) :: $1 }
| atoms_list WORD SPACE FLOAT SPACE FLOAT SPACE FLOAT SPACE EOL { (Element.of_string $2, [| $4;$6;$8 |]) :: $1 }
| atoms_list INTEGER SPACE FLOAT SPACE FLOAT SPACE FLOAT EOL { (Element.of_int $2, [| $4;$6;$8 |]) :: $1 }
| atoms_list INTEGER SPACE FLOAT SPACE FLOAT SPACE FLOAT SPACE EOL { (Element.of_int $2, [| $4;$6;$8 |]) :: $1 }
| atoms_list WORD SPACE FLOAT SPACE FLOAT SPACE FLOAT EOL { (Element.of_string $2, Coordinate.of_3_floats $4 $6 $8 ) :: $1 }
| atoms_list WORD SPACE FLOAT SPACE FLOAT SPACE FLOAT SPACE EOL { (Element.of_string $2, Coordinate.of_3_floats $4 $6 $8 ) :: $1 }
| atoms_list INTEGER SPACE FLOAT SPACE FLOAT SPACE FLOAT EOL { (Element.of_int $2, Coordinate.of_3_floats $4 $6 $8 ) :: $1 }
| atoms_list INTEGER SPACE FLOAT SPACE FLOAT SPACE FLOAT SPACE EOL { (Element.of_int $2, Coordinate.of_3_floats $4 $6 $8 ) :: $1 }

37
run_integrals.ml Normal file
View File

@ -0,0 +1,37 @@
let basis_file : string option ref = ref None
let coord_file : string option ref = ref None
let speclist = [
( "-b" , Arg.String (fun x -> basis_file := Some x) ,
"File containing the atomic basis set.") ;
( "-c" , Arg.String (fun x -> coord_file := Some x) ,
"File containing the nuclear coordinates.") ;
]
let run ~coord ~basis =
let coord_file =
match coord with
| None -> raise (Invalid_argument "Coordinate file should be specified")
| Some x -> x
and basis_file =
match basis with
| None -> raise (Invalid_argument "Basis set file should be specified")
| Some x -> x
in
let nuclei =
Nuclei.of_xyz_file ~filename:coord_file
and general_basis =
Gamess_reader.read ~filename:basis_file
in
let basis =
Basis.of_nuclei_and_general_basis nuclei general_basis
in
Array.map Basis.to_string basis
|> Array.iter print_endline
let () =
let usage_msg = "Quantum Chemistry Package. Options available:" in
Arg.parse speclist (fun _ -> ()) usage_msg;
run ~coord:!coord_file ~basis:!basis_file