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Added xyz types in symmetry (ocaml)

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This commit is contained in:
Anthony Scemama 2014-08-27 16:38:13 +02:00
parent 19fbdd88c6
commit 563a8bea4d
16 changed files with 284 additions and 90 deletions
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0
data/basis/cc-pVDZ → data/basis/cc-pvdz
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2
ocaml/atom.ml
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@ -5,6 +5,7 @@ exception AtomError of string
module Charge : sig
type t
val to_float : t -> float
val to_int : t -> int
val to_string: t -> string
val of_float : float -> t
val of_int : int -> t
@ -12,6 +13,7 @@ module Charge : sig
end = struct
type t = float
let to_float x = x
let to_int x = Float.to_int x
let to_string x = Float.to_string (to_float x)
let of_float x = x
let of_int i = Float.of_int i

34
ocaml/basis.ml Normal file
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@ -0,0 +1,34 @@
open Core.Std;;
type t = Gto.t list;;
(** Read all the basis functions of an element *)
let read in_channel =
let rec read result =
try
let gto = Gto.read_one in_channel in
read (gto::result)
with
| Gto.End_Of_Basis -> List.rev result
in read []
;;
(** Find an element in the basis set file *)
let find in_channel element =
let element_read = ref Element.X in
while !element_read <> element
do
let buffer = input_line in_channel in
try
element_read := Element.of_string buffer
with
| Element.ElementError _ -> ()
done ;
!element_read
;;
let read_element in_channel element =
ignore (find in_channel element) ;
read in_channel ;
;;

0
ocaml/bit.ml Executable file → Normal file
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0
ocaml/bitlist.ml Executable file → Normal file
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93
ocaml/create_ezfio_from_xyz.ml Normal file
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@ -0,0 +1,93 @@
open Qputils;;
open Qptypes;;
open Core.Std;;
let spec =
let open Command.Spec in
empty
+> flag "o" (optional string)
~doc:"file Name of the created EZFIO file"
+> flag "b" (required string)
~doc:"name Basis set."
+> flag "c" (optional_with_default 0 int)
~doc:"int Total charge of the molecule. Default is 0."
+> flag "m" (optional_with_default 1 int)
~doc:"int Spin multiplicity (2S+1) of the molecule. Default is 1"
+> anon ("xyz_file" %: string)
;;
let run ?o b c m xyz_file =
(* Open basis set channel *)
let basis_channel =
In_channel.create
(Qpackage.root / "data/basis" / (String.lowercase b))
in
(* Read molecule *)
let molecule =
Molecule.of_xyz_file xyz_file
in
(* Build EZFIO File name *)
let ezfio_file =
match o with
| Some x -> x
| None ->
begin
match String.rsplit2 ~on:'.' xyz_file with
| Some (x,"xyz") -> x^".ezfio"
| _ -> xyz_file^".ezfio"
end
in
if Sys.file_exists_exn ezfio_file then
failwith (ezfio_file^" already exists");
(* Create EZFIO *)
Ezfio.set_file ezfio_file;
(* Write Electrons *)
Ezfio.set_electrons_elec_alpha_num ( Positive_int.to_int
molecule.Molecule.elec_alpha ) ;
Ezfio.set_electrons_elec_beta_num ( Positive_int.to_int
molecule.Molecule.elec_beta ) ;
(* Write Nuclei *)
let nuclei = molecule.Molecule.nuclei in
let labels =
List.map ~f:(fun x->Element.to_string x.Atom.element) nuclei
and charges =
List.map ~f:(fun x-> Atom.(Charge.to_float x.charge)) nuclei
and coords =
(List.map ~f:(fun x-> x.Atom.coord.Point3d.x) nuclei) @
(List.map ~f:(fun x-> x.Atom.coord.Point3d.y) nuclei) @
(List.map ~f:(fun x-> x.Atom.coord.Point3d.z) nuclei) in
let nucl_num = (List.length labels) in
Ezfio.set_nuclei_nucl_num nucl_num ;
Ezfio.set_nuclei_nucl_label (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| nucl_num |] ~data:labels);
Ezfio.set_nuclei_nucl_charge (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| nucl_num |] ~data:charges);
Ezfio.set_nuclei_nucl_coord (Ezfio.ezfio_array_of_list
~rank:2 ~dim:[| nucl_num ; 3 |] ~data:coords);
(* Write Basis set *)
;;
let command =
Command.basic
~summary: "Quantum Package command"
~readme:(fun () ->
"Creates an EZFIO directory from a standard xyz file
")
spec
(fun o b c m xyz_file () ->
run ?o b c m xyz_file )
;;
let () =
Command.run command
;;

29
ocaml/gto.ml
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@ -65,35 +65,6 @@ let read_one in_channel =
|> of_prim_coef_list
;;
(** Read all the basis functions of an element *)
let read_basis in_channel =
let rec read result =
try
let gto = read_one in_channel in
read (gto::result)
with
| End_Of_Basis -> List.rev result
in read []
;;
(** Find an element in the basis set file *)
let find in_channel element =
let element_read = ref Element.X in
while !element_read <> element
do
let buffer = input_line in_channel in
try
element_read := Element.of_string buffer
with
| Element.ElementError _ -> ()
done ;
!element_read
;;
let read_basis_of_element in_channel element =
ignore (find in_channel element) ;
read_basis in_channel ;
;;
(** Transform the gto to a string *)
let to_string { sym = sym ; lc = lc } =

4
ocaml/molecule.ml
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@ -22,6 +22,10 @@ let get_multiplicity m =
Multiplicity.of_alpha_beta m.elec_alpha m.elec_beta
;;
let get_nucl_num m =
Strictly_positive_int.of_int (List.length m.nuclei)
;;
let name m =
let cm = Float.to_int (get_charge m) in
let c =

11
ocaml/qpackage.ml Normal file
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@ -0,0 +1,11 @@
open Core.Std;;
(** Variables related to the quantum package installation *)
let root =
match (Sys.getenv "QPACKAGE_ROOT") with
| None -> failwith "QPACKAGE_ROOT environment variable is not set.
Please source the quantum_package.rc file."
| Some x -> x
;;

2
ocaml/qputils.ml
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@ -1 +1,3 @@
let (/) (a:string) (b:string) = a^"/"^b;;

0
ocaml/set_mo_class.ml Executable file → Normal file
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124
ocaml/symmetry.ml
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@ -1,3 +1,6 @@
open Qptypes;;
open Core.Std;;
type t = S|P|D|F|G|H|I|J|K|L
let to_string = function
@ -38,3 +41,124 @@ let of_char = function
| 'K' -> K
| 'L' -> L
| x -> raise (Failure ("Symmetry should be S|P|D|F|G|H|I|J|K|L"))
let to_l = function
| S -> Positive_int.of_int 0
| P -> Positive_int.of_int 1
| D -> Positive_int.of_int 2
| F -> Positive_int.of_int 3
| G -> Positive_int.of_int 4
| H -> Positive_int.of_int 5
| I -> Positive_int.of_int 6
| J -> Positive_int.of_int 7
| K -> Positive_int.of_int 8
| L -> Positive_int.of_int 9
module Xyz : sig
type t
val of_string : string -> t
val to_string : t -> string
val get_l : t -> Positive_int.t
end = struct
type t = { x: Positive_int.t ;
y: Positive_int.t ;
z: Positive_int.t }
type state_type = Null | X | Y | Z
(* Input string is like "x2z3" *)
let of_string s =
let flush state accu number =
let n =
if (number = "") then 0
else (Int.of_string number)
in
match state with
| X -> { x= Positive_int.(of_int ( (to_int accu.x) +n));
y= accu.y ;
z= accu.z }
| Y -> { x= accu.x ;
y= Positive_int.(of_int ( (to_int accu.y) +n));
z= accu.z }
| Z -> { x= accu.x ;
y= accu.y ;
z= Positive_int.(of_int ( (to_int accu.z) +n))}
| Null -> accu
in
let rec do_work state accu number = function
| [] -> flush state accu number
| 'X'::rest | 'x'::rest ->
let new_accu = flush state accu number in
do_work X new_accu "" rest
| 'Y'::rest | 'y'::rest ->
let new_accu = flush state accu number in
do_work Y new_accu "" rest
| 'Z'::rest | 'z'::rest ->
let new_accu = flush state accu number in
do_work Z new_accu "" rest
| c::rest -> do_work state accu (number^(String.of_char c)) rest
in
String.to_list_rev s
|> List.rev
|> do_work Null
{ x=Positive_int.of_int 0 ;
y=Positive_int.of_int 0 ;
z=Positive_int.of_int 0 } ""
;;
let to_string t =
let x = match (Positive_int.to_int t.x) with
| 0 -> ""
| 1 -> "x"
| i -> Printf.sprintf "x%d" i
and y = match (Positive_int.to_int t.y) with
| 0 -> ""
| 1 -> "y"
| i -> Printf.sprintf "y%d" i
and z = match (Positive_int.to_int t.z) with
| 0 -> ""
| 1 -> "z"
| i -> Printf.sprintf "z%d" i
in
x^y^z
;;
let get_l t =
let x = Positive_int.to_int t.x
and y = Positive_int.to_int t.y
and z = Positive_int.to_int t.z
in Positive_int.of_int (x+y+z)
;;
let of_symmetry sym =
let l = Positive_int.to_int (to_l sym) in
let create_z xyz =
{ x=xyz.x ;
y=xyz.y ;
z=Positive_int.(of_int (l-((to_int xyz.x)+(to_int xyz.y))))
}
in
let rec create_y accu xyz =
let {x ; y ; z} = xyz in
match (Positive_int.to_int y) with
| 0 -> (create_z xyz)::accu
| i ->
let ynew = Positive_int.( (to_int y)-1 |> of_int) in
create_y ( (create_z xyz)::accu) { x ; y=ynew ; z}
in
let rec create_x accu xyz =
let {x ; y ; z} = xyz in
match (Positive_int.to_int x) with
| 0 -> (create_y [] xyz)@accu
| i ->
let xnew = Positive_int.( (to_int x)-1 |> of_int) in
let ynew = Positive_int.(l-(to_int xnew) |> of_int)
in
create_x ((create_y [] xyz)@accu) { x=xnew ; y=ynew ; z}
in
create_x [] { x=(to_l sym) ; y=Positive_int.of_int 0 ;
z=Positive_int.of_int 0 }
;;
end

10
ocaml/test_gto.ml
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@ -10,7 +10,7 @@ let test_prim () =
;;
let test_gto_1 () =
let in_channel = open_in "/home/scemama/quantum_package/data/basis/cc-pVDZ" in
let in_channel = open_in "/home/scemama/quantum_package/data/basis/cc-pvdz" in
ignore (input_line in_channel);
let gto = Gto.read_one in_channel in
print_string (Gto.to_string gto);
@ -21,15 +21,15 @@ let test_gto_1 () =
;;
let test_gto_2 () =
let in_channel = open_in "/home/scemama/quantum_package/data/basis/cc-pVDZ" in
let in_channel = open_in "/home/scemama/quantum_package/data/basis/cc-pvdz" in
ignore (input_line in_channel);
let basis = Gto.read_basis in_channel in
let basis = Basis.read in_channel in
List.iter basis ~f:(fun x-> Printf.printf "%s\n" (Gto.to_string x))
;;
let test_gto () =
let in_channel = open_in "/home/scemama/quantum_package/data/basis/cc-pVDZ" in
let basis = Gto.read_basis_of_element in_channel Element.C in
let in_channel = open_in "/home/scemama/quantum_package/data/basis/cc-pvdz" in
let basis = Basis.read_element in_channel Element.C in
List.iter basis ~f:(fun x-> Printf.printf "%s\n" (Gto.to_string x))
;;

1
src/NEEDED_MODULES
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@ -0,0 +1 @@
Utils

8
src/README.rst
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@ -116,3 +116,11 @@ Documentation
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_

56
src/Utils/README.rst
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@ -10,62 +10,6 @@ Documentation
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
`apply_rotation <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L168>`_
Apply the rotation found by find_rotation
`find_rotation <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L149>`_
Find A.C = B
`get_pseudo_inverse <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L95>`_
Find C = A^-1
`lapack_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L247>`_
Diagonalize matrix H
.br
H is untouched between input and ouptut
.br
eigevalues(i) = ith lowest eigenvalue of the H matrix
.br
eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
.br
`lapack_diagd <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L180>`_
Diagonalize matrix H
.br
H is untouched between input and ouptut
.br
eigevalues(i) = ith lowest eigenvalue of the H matrix
.br
eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
.br
`lapack_partial_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L310>`_
Diagonalize matrix H
.br
H is untouched between input and ouptut
.br
eigevalues(i) = ith lowest eigenvalue of the H matrix
.br
eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
.br
`ortho_lowdin <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L1>`_
Compute C_new=C_old.S^-1/2 canonical orthogonalization.
.br
overlap : overlap matrix
.br
LDA : leftmost dimension of overlap array
.br
N : Overlap matrix is NxN (array is (LDA,N) )
.br
C : Coefficients of the vectors to orthogonalize. On exit,
orthogonal vectors
.br
LDC : leftmost dimension of C
.br
m : Coefficients matrix is MxN, ( array is (LDC,N) )
.br
`abort_all <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L1>`_
If True, all the calculation is aborted