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xyz to ezfio works

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This commit is contained in:
Anthony Scemama 2014-09-18 17:01:43 +02:00
parent 12c7bcf99d
commit 0fb8c3b7ae
15 changed files with 149 additions and 50 deletions
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7
ocaml/Atom.ml
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@ -26,7 +26,8 @@ type t =
coord : Point3d.t ;
}
let of_string s =
(** Read xyz coordinates of the atom with unit u *)
let of_string u s =
let buffer = s
|> String.split ~on:' '
|> List.filter ~f:(fun x -> x <> "")
@ -35,13 +36,13 @@ let of_string s =
| [ name; charge; x; y; z ] ->
{ element = Element.of_string name ;
charge = Charge.of_string charge ;
coord = Point3d.of_string (String.concat [x; y; z] ~sep:" ")
coord = Point3d.of_string u (String.concat [x; y; z] ~sep:" ")
}
| [ name; x; y; z ] ->
let e = Element.of_string name in
{ element = e ;
charge = Charge.of_int (Element.charge e);
coord = Point3d.of_string (String.concat [x; y; z] ~sep:" ")
coord = Point3d.of_string u (String.concat [x; y; z] ~sep:" ")
}
| _ -> raise (AtomError s)
;;

6
ocaml/Gto.ml
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@ -6,7 +6,7 @@ exception End_Of_Basis
type t =
{ sym : Symmetry.t ;
lc : ((Primitive.t * float) list)
lc : ((Primitive.t * AO_coef.t) list)
}
;;
@ -56,7 +56,7 @@ let read_one in_channel =
Primitive.expo = Positive_float.of_float
(Float.of_string expo)
}
and c = Float.of_string coef in
and c = AO_coef.of_float (Float.of_string coef) in
read_lines ( (p,c)::result) (i-1)
end
| _ -> raise (GTO_Read_Failure line_buffer)
@ -68,7 +68,7 @@ let read_one in_channel =
(** Transform the gto to a string *)
let to_string { sym = sym ; lc = lc } =
let f (p,c) = Printf.sprintf "( %s, %f )" (Primitive.to_string p) c
let f (p,c) = Printf.sprintf "( %s, %f )" (Primitive.to_string p) (AO_coef.to_float c)
in
Printf.sprintf "[ %s : %s ]" (Symmetry.to_string sym)
(String.concat (List.map ~f:f lc) ~sep:", ")

2
ocaml/Makefile
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@ -12,7 +12,7 @@ endif
LIBS=
PKGS=
OCAMLCFLAGS=-g
OCAMLCFLAGS=-g
OCAMLBUILD=ocamlbuild -j 0 -cflags $(OCAMLCFLAGS) -lflags -g
MLFILES=$(wildcard *.ml) ezfio.ml Qptypes.ml
MLIFILES=$(wildcard *.mli)

3
ocaml/Molecule.ml
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@ -76,10 +76,11 @@ let to_string m =
let of_xyz_string
?(charge=0) ?(multiplicity=(Multiplicity.of_int 1))
?(units=Point3d.Angstrom)
s =
let l = String.split s ~on:'\n'
|> List.filter ~f:(fun x -> x <> "")
|> List.map ~f:Atom.of_string
|> List.map ~f:(fun x -> Atom.of_string units x)
in
let ne = ( get_charge {
nuclei=l ;

20
ocaml/Point3d.ml
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@ -1,21 +1,33 @@
open Core.Std;;
type units =
| Bohr
| Angstrom
;;
type t = {
x : float ;
y : float ;
z : float ;
}
let of_string s =
(** Read x y z coordinates in string s with units u *)
let of_string u s =
let f =
begin match u with
| Bohr -> 1.
| Angstrom -> 1. /. 0.52917721092
end
in
let l = s
|> String.split ~on:' '
|> List.filter ~f:(fun x -> x <> "")
|> List.map ~f:Float.of_string
|> Array.of_list
in
{ x = l.(0) ;
y = l.(1) ;
z = l.(2) }
{ x = l.(0) *. f ;
y = l.(1) *. f ;
z = l.(2) *. f }
;;

10
ocaml/Qputils.ml
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@ -1,4 +1,14 @@
let (/) (a:string) (b:string) = a^"/"^b;;
let rec transpose = function
| [] -> []
| []::tail -> transpose tail
| (x::t1)::t2 ->
let new_head = (x::(List.map List.hd t2))
and new_tail = (transpose (t1 :: (List.map List.tl t2) ))
in
new_head @ new_tail
;;

5
ocaml/Symmetry.ml
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@ -58,7 +58,9 @@ type st = t
;;
module Xyz : sig
type t
type t = { x: Positive_int.t ;
y: Positive_int.t ;
z: Positive_int.t }
val of_string : string -> t
val to_string : t -> string
val get_l : t -> Positive_int.t
@ -67,7 +69,6 @@ end = struct
type t = { x: Positive_int.t ;
y: Positive_int.t ;
z: Positive_int.t }
type state_type = Null | X | Y | Z
(** Builds an XYZ triplet from a string.

18
ocaml/Symmetry.mli Normal file
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@ -0,0 +1,18 @@
open Qptypes;;
type t = S | P | D | F | G | H | I | J | K | L
val to_string : t -> string
val of_string : string -> t
val of_char : char -> t
val to_l : t -> Positive_int.t
type st = t
module Xyz :
sig
type t = { x: Positive_int.t ;
y: Positive_int.t ;
z: Positive_int.t }
val of_string : string -> t
val to_string : t -> string
val get_l : t -> Positive_int.t
val of_symmetry : st -> t list
end

58
ocaml/qp_create_ezfio_from_xyz.ml
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@ -98,21 +98,59 @@ File : %s\n" c m b xyz_file;
Ezfio.set_ao_basis_ao_num ao_num;
let ao_prim_num = List.map long_basis ~f:(fun (_,g,_) -> List.length g.Gto.lc)
and ao_nucl = List.map long_basis ~f:(fun (_,_,n) -> Atom_number.to_int n)
and ao_power=
let l = List.map long_basis ~f:(fun (x,_,_) -> x) in
(List.map l ~f:(fun t -> Positive_int.to_int Symmetry.Xyz.(t.x)) )@
(List.map l ~f:(fun t -> Positive_int.to_int Symmetry.Xyz.(t.y)) )@
(List.map l ~f:(fun t -> Positive_int.to_int Symmetry.Xyz.(t.z)) )
in
let ao_prim_num_max = List.fold ~init:0 ~f:(fun s x ->
if x > s then x
else s) ao_prim_num
in
let gtos = List.map long_basis ~f:(fun (_,x,_) -> x) in
let create_expo_coef ec =
let coefs =
begin match ec with
| `Coefs -> List.map gtos ~f:(fun x->
List.map x.Gto.lc ~f:(fun (_,coef) -> AO_coef.to_float coef) )
| `Expos -> List.map gtos ~f:(fun x->
List.map x.Gto.lc ~f:(fun (prim,_) -> Positive_float.to_float
prim.Primitive.expo) )
end
in
let rec get_n n accu = function
| [] -> List.rev accu
| h::tail ->
let y =
begin match List.nth h n with
| Some x -> x
| None -> 0.
end
in
get_n n (y::accu) tail
in
let rec build accu = function
| n when n=ao_prim_num_max -> accu
| n -> build ( accu @ (get_n n [] coefs) ) (n+1)
in
build [] 0
in
let ao_coef = create_expo_coef `Coefs
and ao_expo = create_expo_coef `Expos
in
Ezfio.set_ao_basis_ao_prim_num (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| ao_num |] ~data:ao_prim_num) ;
Ezfio.set_ao_basis_ao_nucl(Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| ao_num |] ~data:ao_nucl) ;
(*
ao_basis
ao_power integer (ao_basis_ao_num,3)
ao_prim_num_max integer = maxval(ao_basis_ao_prim_num)
ao_coef double precision (ao_basis_ao_num,ao_basis_ao_prim_num_max)
ao_expo double precision (ao_basis_ao_num,ao_basis_ao_prim_num_max)
*)
Ezfio.set_ao_basis_ao_power(Ezfio.ezfio_array_of_list
~rank:2 ~dim:[| ao_num ; 3 |] ~data:ao_power) ;
Ezfio.set_ao_basis_ao_coef(Ezfio.ezfio_array_of_list
~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_coef) ;
Ezfio.set_ao_basis_ao_expo(Ezfio.ezfio_array_of_list
~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_expo) ;
;;
let command =

18
ocaml/qptypes_generator.ml
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@ -54,7 +54,7 @@ let input_data = "
if (x > 100) then
warning \"N_int > 100\";
if (Ezfio.has_determinants_n_int ()) then
assert (x == (Ezfio.get_determinants_n_int ()));
assert (x = (Ezfio.get_determinants_n_int ()));
* Det_number : int
assert (x > 0) ;
@ -75,6 +75,10 @@ let input_data = "
| _ -> raise (Failure \"Bit_kind should be (1|2|4|8).\")
end;
* MO_coef : float
* AO_coef : float
"
;;
@ -84,17 +88,19 @@ module %s : sig
type t
val to_%s : t -> %s
val of_%s : %s -> t
val to_string : %s -> string
end = struct
type t = %s
let to_%s x = x
let of_%s x = ( %s x )
let to_string x = %s.to_string x
end
"
;;
let parse_input input=
print_string "let warning = print_string;;\n" ;
print_string "open Core.Std;;\nlet warning = print_string;;\n" ;
let rec parse result = function
| [] -> result
| ( "" , "" )::tail -> parse result tail
@ -102,10 +108,10 @@ let parse_input input=
let name , typ = String.lsplit2_exn ~on:':' t
in
let typ = String.strip typ
and name = String.strip name
in
let newstring = Printf.sprintf template name typ typ typ typ typ typ typ
( String.strip text )
and name = String.strip name in
let typ_cap = String.capitalize typ in
let newstring = Printf.sprintf template name typ typ typ typ typ typ typ typ
( String.strip text ) typ_cap
in
List.rev (parse (newstring::result) tail )
in

2
ocaml/test_atom.ml
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@ -1,5 +1,5 @@
let test_atom =
let line = "C 6.0 1. 2. 3." in
let atom = Atom.of_string line in
let atom = Atom.of_string Point3d.Bohr line in
print_string (Atom.to_string atom)
;;

12
ocaml/test_point3d.ml
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@ -1,13 +1,15 @@
let test_point3d_1 () =
let input = "7.4950000 -0.1499810 0.5085570" in
let p3d = Point3d.of_string input in
print_string (Point3d.to_string p3d)
let p3d = Point3d.of_string Point3d.Angstrom input in
print_endline(Point3d.to_string p3d);
let p3d = Point3d.of_string Point3d.Bohr input in
print_endline (Point3d.to_string p3d)
;;
let test_point3d () =
let p1 = Point3d.of_string "1. 2. 3."
and p2 = Point3d.of_string "-2. 1. 1.5" in
let p1 = Point3d.of_string Point3d.Bohr "1. 2. 3."
and p2 = Point3d.of_string Point3d.Bohr "-2. 1. 1.5" in
Printf.printf "%f\n" (Point3d.distance p1 p2)
;;
test_point3d ();
test_point3d_1 ();

2
robots.txt
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@ -1,2 +0,0 @@
User-agent: *
Allow: /

35
src/MOs/mos.irp.f
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@ -4,7 +4,13 @@ BEGIN_PROVIDER [ integer, mo_tot_num ]
! Total number of molecular orbitals and the size of the keys corresponding
END_DOC
PROVIDE ezfio_filename
call ezfio_get_mo_basis_mo_tot_num(mo_tot_num)
logical :: exists
call ezfio_has_mo_basis_mo_tot_num(exists)
if (exists) then
call ezfio_get_mo_basis_mo_tot_num(mo_tot_num)
else
mo_tot_num = ao_num
endif
ASSERT (mo_tot_num > 0)
END_PROVIDER
@ -42,18 +48,23 @@ END_PROVIDER
endif
! Coefs
allocate(buffer(ao_num,mo_tot_num))
buffer = 0.d0
call ezfio_get_mo_basis_mo_coef(buffer)
do i=1,mo_tot_num
do j=1,ao_num
mo_coef(j,i) = buffer(j,i)
call ezfio_has_mo_basis_mo_coef(exists)
if (exists) then
allocate(buffer(ao_num,mo_tot_num))
buffer = 0.d0
call ezfio_get_mo_basis_mo_coef(buffer)
do i=1,mo_tot_num
do j=1,ao_num
mo_coef(j,i) = buffer(j,i)
enddo
do j=ao_num+1,ao_num_align
mo_coef(j,i) = 0.d0
enddo
enddo
do j=ao_num+1,ao_num_align
mo_coef(j,i) = 0.d0
enddo
enddo
deallocate(buffer)
deallocate(buffer)
else
mo_coef = 0.d0
endif
END_PROVIDER

1
src/MOs/utils.irp.f
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@ -5,6 +5,7 @@ subroutine save_mos
call system('$QPACKAGE_ROOT/scripts/save_current_mos.sh '//trim(ezfio_filename))
call ezfio_set_mo_basis_mo_tot_num(mo_tot_num)
call ezfio_set_mo_basis_mo_label(mo_label)
allocate ( buffer(ao_num,mo_tot_num) )
buffer = 0.d0