mirror of
https://github.com/LCPQ/quantum_package
synced 2024-08-24 21:41:46 +02:00
Modified for ocaml 4.04
This commit is contained in:
parent
6c7d768730
commit
8523096a90
@ -1,4 +1,4 @@
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open Core.Std
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open Core
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module Tcp : sig
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type t
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@ -1,4 +1,4 @@
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open Core.Std
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open Core
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exception AtomError of string
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@ -6,7 +6,7 @@ type t =
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{ element : Element.t ;
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charge : Charge.t ;
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coord : Point3d.t ;
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} with sexp
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} [@@deriving sexp]
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(** Read xyz coordinates of the atom *)
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let of_string ~units s =
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@ -1,7 +1,7 @@
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open Core.Std
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open Core
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open Qptypes
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type t = (Gto.t * Nucl_number.t) list with sexp
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type t = (Gto.t * Nucl_number.t) list [@@deriving sexp]
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(** Read all the basis functions of an element *)
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let read in_channel at_number =
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@ -1,4 +1,4 @@
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open Core.Std;;
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open Core;;
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(*
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Type for bits
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@ -11,7 +11,7 @@ Zero | One
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type t =
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| One
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| Zero
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with sexp
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[@@deriving sexp]
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let to_string = function
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| Zero -> "0"
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@ -1,4 +1,4 @@
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type t = One | Zero with sexp
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type t = One | Zero [@@deriving sexp]
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(** String conversions for printing *)
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val to_string : t -> string
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@ -1,5 +1,5 @@
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open Qptypes
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open Core.Std
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open Core
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(*
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Type for bits strings
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@ -1,6 +1,6 @@
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open Core.Std
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open Core
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type t = float with sexp
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type t = float [@@deriving sexp]
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let of_float x = x
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let of_int i = Float.of_int i
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@ -1,4 +1,4 @@
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type t = float with sexp
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type t = float [@@deriving sexp]
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(** Float conversion functions *)
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val to_float : t -> float
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@ -1,7 +1,7 @@
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open Core.Std;;
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open Core;;
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open Qptypes;;
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type t = int64 array with sexp
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type t = int64 array [@@deriving sexp]
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let to_int64_array (x:t) = (x:int64 array)
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@ -5,7 +5,7 @@
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* where each int64 is a list of 64 MOs. When the bit is set
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* to 1, the MO is occupied.
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*)
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type t = int64 array with sexp
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type t = int64 array [@@deriving sexp]
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(** Transform to an int64 array *)
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val to_int64_array : t -> int64 array
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open Core.Std
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open Core
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open Qptypes
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exception ElementError of string
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@ -11,7 +11,7 @@ type t =
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|K |Ca|Sc|Ti|V |Cr|Mn|Fe|Co|Ni|Cu|Zn|Ga|Ge|As|Se|Br|Kr
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|Rb|Sr|Y |Zr|Nb|Mo|Tc|Ru|Rh|Pd|Ag|Cd|In|Sn|Sb|Te|I |Xe
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|Pt
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with sexp
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[@@deriving sexp]
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let of_string x =
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match (String.capitalize (String.lowercase x)) with
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@ -8,7 +8,7 @@ type t =
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|K |Ca|Sc|Ti|V |Cr|Mn|Fe|Co|Ni|Cu|Zn|Ga|Ge|As|Se|Br|Kr
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|Rb|Sr|Y |Zr|Nb|Mo|Tc|Ru|Rh|Pd|Ag|Cd|In|Sn|Sb|Te|I |Xe
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|Pt
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with sexp
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[@@deriving sexp]
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(** String conversion functions *)
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val of_string : string -> t
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open Core.Std;;
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open Qptypes;;
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open Core
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open Qptypes
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module Hole = struct
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type t = MO_class.t with sexp
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type t = MO_class.t [@@deriving sexp]
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let of_mo_class x = x
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let to_mo_class x = x
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end
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module Particle = struct
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type t = MO_class.t with sexp
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type t = MO_class.t [@@deriving sexp]
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let of_mo_class x = x
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let to_mo_class x = x
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end
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@ -16,7 +16,7 @@ end
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type t =
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| Single of Hole.t*Particle.t
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| Double of Hole.t*Particle.t*Hole.t*Particle.t
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with sexp;;
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[@@deriving sexp]
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let create_single ~hole ~particle =
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MO_class.(
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@ -29,7 +29,7 @@ let create_single ~hole ~particle =
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| ( _, Inactive _ ) -> failwith "Particles can not be in virtual MOs"
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| (h, p) -> Single ( (Hole.of_mo_class h), (Particle.of_mo_class p) )
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)
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;;
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let double_of_singles s1 s2 =
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let (h1,p1) = match s1 with
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@ -40,14 +40,14 @@ let double_of_singles s1 s2 =
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| _ -> assert false
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in
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Double (h1,p1,h2,p2)
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;;
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let create_double ~hole1 ~particle1 ~hole2 ~particle2 =
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let s1 = create_single ~hole:hole1 ~particle:particle1
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and s2 = create_single ~hole:hole2 ~particle:particle2
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in
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double_of_singles s1 s2
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;;
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let to_string = function
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| Single (h,p) ->
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@ -68,5 +68,5 @@ let to_string = function
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(MO_class.to_string (Particle.to_mo_class p2));
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"]"]
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|> String.concat ~sep:" "
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;;
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@ -18,7 +18,7 @@ module Particle :
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type t =
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| Single of Hole.t * Particle.t
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| Double of Hole.t * Particle.t * Hole.t * Particle.t
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with sexp
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[@@deriving sexp]
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val create_single : hole:MO_class.t -> particle:MO_class.t -> t
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open Qptypes
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open Core.Std
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open Core
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type t =
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{ sym : Symmetry.t ;
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expo : AO_expo.t ;
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} with sexp
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} [@@deriving sexp]
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let to_string p =
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let { sym = s ; expo = e } = p in
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open Core.Std;;
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open Core;;
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open Qptypes;;
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open Core.Std
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open Core
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open Qptypes
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exception GTO_Read_Failure of string
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type t =
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{ sym : Symmetry.t ;
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lc : ((GaussianPrimitive.t * AO_coef.t) list)
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} with sexp
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} [@@deriving sexp]
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let of_prim_coef_list pc =
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type t =
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{ sym : Symmetry.t ;
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lc : (GaussianPrimitive.t * Qptypes.AO_coef.t) list;
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} with sexp
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} [@@deriving sexp]
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(** Create from a list of GaussianPrimitive.t * Qptypes.AO_coef.t *)
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val of_prim_coef_list :
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open Qputils;;
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open Qptypes;;
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open Core.Std;;
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open Core;;
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include Input_ao_basis;;
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include Input_bitmasks;;
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open Qptypes;;
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open Qputils;;
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open Core.Std;;
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open Core;;
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module Ao_basis : sig
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type t =
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@ -13,7 +13,7 @@ module Ao_basis : sig
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ao_coef : AO_coef.t array;
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ao_expo : AO_expo.t array;
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ao_cartesian : bool;
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} with sexp
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} [@@deriving sexp]
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;;
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val read : unit -> t option
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val to_string : t -> string
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@ -32,7 +32,7 @@ end = struct
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ao_coef : AO_coef.t array;
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ao_expo : AO_expo.t array;
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ao_cartesian : bool;
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} with sexp
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} [@@deriving sexp]
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;;
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let get_default = Qpackage.get_ezfio_default "ao_basis";;
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open Qptypes;;
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open Qputils;;
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open Core.Std;;
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open Core;;
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module Bielec_integrals : sig
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type t =
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@ -11,7 +11,7 @@ module Bielec_integrals : sig
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threshold_ao : Threshold.t;
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threshold_mo : Threshold.t;
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direct : bool;
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} with sexp
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} [@@deriving sexp]
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;;
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val read : unit -> t option
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val write : t -> unit
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@ -27,7 +27,7 @@ end = struct
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threshold_ao : Threshold.t;
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threshold_mo : Threshold.t;
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direct : bool;
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} with sexp
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} [@@deriving sexp]
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;;
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let get_default = Qpackage.get_ezfio_default "bielec_integrals";;
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open Qptypes;;
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open Qputils;;
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open Core.Std;;
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open Core;;
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module Bitmasks : sig
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type t =
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@ -10,7 +10,7 @@ module Bitmasks : sig
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generators : int64 array;
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n_mask_cas : Bitmask_number.t;
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cas : int64 array;
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} with sexp
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} [@@deriving sexp]
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;;
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val read : unit -> t option
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val to_string : t -> string
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@ -22,7 +22,7 @@ end = struct
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generators : int64 array;
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n_mask_cas : Bitmask_number.t;
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cas : int64 array;
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} with sexp
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} [@@deriving sexp]
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;;
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let get_default = Qpackage.get_ezfio_default "bitmasks";;
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@ -1,6 +1,6 @@
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open Qptypes;;
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open Qputils;;
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open Core.Std;;
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open Core;;
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module Determinants_by_hand : sig
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type t =
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@ -11,7 +11,7 @@ module Determinants_by_hand : sig
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expected_s2 : Positive_float.t;
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psi_coef : Det_coef.t array;
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psi_det : Determinant.t array;
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} with sexp
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} [@@deriving sexp]
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val read : unit -> t
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val read_maybe : unit -> t option
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val write : t -> unit
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@ -30,7 +30,7 @@ end = struct
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expected_s2 : Positive_float.t;
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psi_coef : Det_coef.t array;
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psi_det : Determinant.t array;
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} with sexp
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} [@@deriving sexp]
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;;
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let get_default = Qpackage.get_ezfio_default "determinants";;
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|
@ -1,12 +1,12 @@
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open Qptypes;;
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open Qputils;;
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open Core.Std;;
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open Core;;
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module Electrons : sig
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type t =
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{ elec_alpha_num : Elec_alpha_number.t;
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elec_beta_num : Elec_beta_number.t;
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} with sexp
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} [@@deriving sexp]
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;;
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val read : unit -> t option
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val write : t -> unit
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@ -18,7 +18,7 @@ end = struct
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type t =
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{ elec_alpha_num : Elec_alpha_number.t;
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elec_beta_num : Elec_beta_number.t;
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} with sexp
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} [@@deriving sexp]
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;;
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let get_default = Qpackage.get_ezfio_default "electrons";;
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|
@ -1,6 +1,6 @@
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open Qptypes
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open Qputils
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open Core.Std
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open Core
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type t_mo =
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{ mo_tot_num : MO_number.t ;
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@ -9,7 +9,7 @@ type t_mo =
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mo_occ : MO_occ.t array;
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mo_coef : (MO_coef.t array) array;
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ao_md5 : MD5.t;
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} with sexp
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} [@@deriving sexp]
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module Mo_basis : sig
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type t = t_mo
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|
@ -1,6 +1,6 @@
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open Qptypes;;
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open Qputils;;
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open Core.Std;;
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open Core;;
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module Nuclei_by_hand : sig
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type t =
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@ -8,7 +8,7 @@ module Nuclei_by_hand : sig
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nucl_label : Element.t array;
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nucl_charge : Charge.t array;
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nucl_coord : Point3d.t array;
|
||||
} with sexp
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} [@@deriving sexp]
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||||
;;
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val read : unit -> t option
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val write : t -> unit
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@ -22,7 +22,7 @@ end = struct
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nucl_label : Element.t array;
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nucl_charge : Charge.t array;
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nucl_coord : Point3d.t array;
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} with sexp
|
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} [@@deriving sexp]
|
||||
;;
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||||
|
||||
let get_default = Qpackage.get_ezfio_default "nuclei";;
|
||||
|
24
ocaml/Io_ext.ml
Normal file
24
ocaml/Io_ext.ml
Normal file
@ -0,0 +1,24 @@
|
||||
let input_lines filename =
|
||||
let in_channel =
|
||||
open_in filename
|
||||
in
|
||||
let rec aux accu =
|
||||
try
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||||
let newline =
|
||||
input_line in_channel
|
||||
in
|
||||
aux (newline::accu)
|
||||
with End_of_file -> accu
|
||||
in
|
||||
let result =
|
||||
List.rev (aux [])
|
||||
in
|
||||
close_in in_channel;
|
||||
result
|
||||
|
||||
|
||||
|
||||
let read_all filename =
|
||||
input_lines filename
|
||||
|> String.concat "\n"
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||||
|
@ -1,7 +1,7 @@
|
||||
open Core.Std;;
|
||||
open Core;;
|
||||
open Qptypes;;
|
||||
|
||||
type t = (Symmetry.Xyz.t * Gto.t * Nucl_number.t ) list with sexp
|
||||
type t = (Symmetry.Xyz.t * Gto.t * Nucl_number.t ) list [@@deriving sexp]
|
||||
|
||||
let of_basis b =
|
||||
let rec do_work accu = function
|
||||
|
@ -5,7 +5,7 @@ open Qptypes;;
|
||||
* all the D orbitals are converted to xx, xy, xz, yy, yx
|
||||
* etc
|
||||
*)
|
||||
type t = (Symmetry.Xyz.t * Gto.t * Nucl_number.t) list with sexp
|
||||
type t = (Symmetry.Xyz.t * Gto.t * Nucl_number.t) list [@@deriving sexp]
|
||||
|
||||
(** Transform a basis to a long basis *)
|
||||
val of_basis :
|
||||
|
@ -1,4 +1,4 @@
|
||||
open Core.Std
|
||||
open Core
|
||||
open Qptypes
|
||||
|
||||
type t =
|
||||
@ -7,7 +7,7 @@ type t =
|
||||
| Active of MO_number.t list
|
||||
| Virtual of MO_number.t list
|
||||
| Deleted of MO_number.t list
|
||||
with sexp
|
||||
[@@deriving sexp]
|
||||
|
||||
|
||||
let to_string x =
|
||||
|
@ -4,7 +4,7 @@ type t =
|
||||
| Active of Qptypes.MO_number.t list
|
||||
| Virtual of Qptypes.MO_number.t list
|
||||
| Deleted of Qptypes.MO_number.t list
|
||||
with sexp
|
||||
[@@deriving sexp]
|
||||
|
||||
|
||||
(** Create different excitation classes *)
|
||||
|
@ -1,4 +1,4 @@
|
||||
open Core.Std;;
|
||||
open Core;;
|
||||
|
||||
type t =
|
||||
| Guess
|
||||
@ -7,7 +7,7 @@ type t =
|
||||
| Localized
|
||||
| Orthonormalized
|
||||
| None
|
||||
with sexp
|
||||
[@@deriving sexp]
|
||||
;;
|
||||
|
||||
let to_string = function
|
||||
|
@ -5,7 +5,7 @@ type t =
|
||||
| Localized
|
||||
| Orthonormalized
|
||||
| None
|
||||
with sexp
|
||||
[@@deriving sexp]
|
||||
|
||||
(** String representation *)
|
||||
val to_string : t -> string
|
||||
|
@ -11,8 +11,8 @@ endif
|
||||
|
||||
LIBS=
|
||||
PKGS=
|
||||
OCAMLCFLAGS="-g -warn-error A"
|
||||
OCAMLBUILD=ocamlbuild -j 0 -syntax camlp4o -cflags $(OCAMLCFLAGS) -lflags $(OCAMLCFLAGS)
|
||||
OCAMLCFLAGS="-g"
|
||||
OCAMLBUILD=ocamlbuild -j 0 -cflags $(OCAMLCFLAGS) -lflags $(OCAMLCFLAGS)
|
||||
MLLFILES=$(wildcard *.mll)
|
||||
MLFILES=$(wildcard *.ml) ezfio.ml Qptypes.ml Input_auto_generated.ml qp_edit.ml
|
||||
MLIFILES=$(wildcard *.mli) git
|
||||
|
@ -1,4 +1,4 @@
|
||||
open Core.Std
|
||||
open Core
|
||||
open Qptypes
|
||||
|
||||
(** New job : Request to create a new multi-tasked job *)
|
||||
|
@ -1,14 +1,14 @@
|
||||
open Core.Std ;;
|
||||
open Qptypes ;;
|
||||
open Qptypes
|
||||
open Sexplib.Std
|
||||
|
||||
exception MultiplicityError of string;;
|
||||
exception XYZError ;;
|
||||
exception MultiplicityError of string
|
||||
exception XYZError
|
||||
|
||||
type t = {
|
||||
nuclei : Atom.t list ;
|
||||
elec_alpha : Elec_alpha_number.t ;
|
||||
elec_beta : Elec_beta_number.t ;
|
||||
} with sexp
|
||||
} [@@deriving sexp]
|
||||
|
||||
let get_charge { nuclei ; elec_alpha ; elec_beta } =
|
||||
let result =
|
||||
@ -19,7 +19,7 @@ let get_charge { nuclei ; elec_alpha ; elec_beta } =
|
||||
| a::rest -> (Charge.to_float a.Atom.charge) +. nucl_charge rest
|
||||
| [] -> 0.
|
||||
in
|
||||
Charge.of_float (nucl_charge nuclei -. (Float.of_int result))
|
||||
Charge.of_float (nucl_charge nuclei -. (float_of_int result))
|
||||
|
||||
|
||||
let get_multiplicity m =
|
||||
@ -59,9 +59,10 @@ let name m =
|
||||
| a::rest ->
|
||||
begin
|
||||
let e = a.Atom.element in
|
||||
match (List.Assoc.find accu e) with
|
||||
| None -> build_list (List.Assoc.add accu e 1) rest
|
||||
| Some i -> build_list (List.Assoc.add accu e (i+1)) rest
|
||||
try
|
||||
let i = List.assoc e accu in
|
||||
build_list ( (e,i+1)::(List.remove_assoc e accu) ) rest
|
||||
with Not_found -> build_list ( (e,1)::accu ) rest
|
||||
end
|
||||
| [] -> accu
|
||||
in
|
||||
@ -83,7 +84,7 @@ let name m =
|
||||
let result =
|
||||
build_list [] nuclei |> build_name [c ; ", " ; mult]
|
||||
in
|
||||
String.concat (result)
|
||||
String.concat "" result
|
||||
|
||||
|
||||
let to_string_general ~f m =
|
||||
@ -95,8 +96,8 @@ let to_string_general ~f m =
|
||||
let title =
|
||||
name m
|
||||
in
|
||||
[ Int.to_string n ; title ] @ (List.map ~f nuclei)
|
||||
|> String.concat ~sep:"\n"
|
||||
[ string_of_int n ; title ] @ (List.map f nuclei)
|
||||
|> String.concat "\n"
|
||||
|
||||
let to_string =
|
||||
to_string_general ~f:(fun x -> Atom.to_string Units.Angstrom x)
|
||||
@ -109,9 +110,9 @@ let of_xyz_string
|
||||
?(charge=(Charge.of_int 0)) ?(multiplicity=(Multiplicity.of_int 1))
|
||||
?(units=Units.Angstrom)
|
||||
s =
|
||||
let l = String.split s ~on:'\n'
|
||||
|> List.filter ~f:(fun x -> x <> "")
|
||||
|> List.map ~f:(fun x -> Atom.of_string units x)
|
||||
let l = String_ext.split s ~on:'\n'
|
||||
|> List.filter (fun x -> x <> "")
|
||||
|> List.map (fun x -> Atom.of_string units x)
|
||||
in
|
||||
let ne = ( get_charge {
|
||||
nuclei=l ;
|
||||
@ -145,25 +146,28 @@ let of_xyz_file
|
||||
?(charge=(Charge.of_int 0)) ?(multiplicity=(Multiplicity.of_int 1))
|
||||
?(units=Units.Angstrom)
|
||||
filename =
|
||||
let (x,buffer) = In_channel.read_all filename
|
||||
|> String.lsplit2_exn ~on:'\n'
|
||||
in
|
||||
let result =
|
||||
let lines =
|
||||
match Io_ext.input_lines filename with
|
||||
| natoms :: title :: rest ->
|
||||
begin
|
||||
try
|
||||
(int_of_string @@ String.strip x) > 0
|
||||
if (int_of_string @@ String_ext.strip natoms) <= 0 then
|
||||
raise XYZError
|
||||
with
|
||||
| Failure "int_of_string" -> false
|
||||
| _ -> raise XYZError
|
||||
end;
|
||||
String.concat "\n" rest
|
||||
| _ -> failwith ("Problem in xyz file "^filename)
|
||||
in
|
||||
if not result then raise XYZError;
|
||||
let (_,buffer) = String.lsplit2_exn buffer ~on:'\n' in
|
||||
of_xyz_string ~charge ~multiplicity ~units buffer
|
||||
of_xyz_string ~charge:charge ~multiplicity:multiplicity
|
||||
~units:units lines
|
||||
|
||||
|
||||
let of_zmt_file
|
||||
?(charge=(Charge.of_int 0)) ?(multiplicity=(Multiplicity.of_int 1))
|
||||
?(units=Units.Angstrom)
|
||||
filename =
|
||||
In_channel.read_all filename
|
||||
Io_ext.read_all filename
|
||||
|> Zmatrix.of_string
|
||||
|> Zmatrix.to_xyz_string
|
||||
|> of_xyz_string ~charge ~multiplicity ~units
|
||||
@ -182,14 +186,14 @@ let of_file
|
||||
let distance_matrix molecule =
|
||||
let coord =
|
||||
molecule.nuclei
|
||||
|> List.map ~f:(fun x -> x.Atom.coord)
|
||||
|> List.map (fun x -> x.Atom.coord)
|
||||
|> Array.of_list
|
||||
in
|
||||
let n =
|
||||
Array.length coord
|
||||
in
|
||||
let result =
|
||||
Array.make_matrix ~dimx:n ~dimy:n 0.
|
||||
Array.make_matrix n n 0.
|
||||
in
|
||||
for i = 0 to (n-1)
|
||||
do
|
||||
@ -203,6 +207,7 @@ let distance_matrix molecule =
|
||||
|
||||
|
||||
|
||||
open Core ;;
|
||||
include To_md5
|
||||
let to_md5 = to_md5 sexp_of_t
|
||||
|
||||
|
@ -4,7 +4,7 @@ type t = {
|
||||
nuclei : Atom.t list;
|
||||
elec_alpha : Qptypes.Elec_alpha_number.t;
|
||||
elec_beta : Qptypes.Elec_beta_number.t;
|
||||
} with sexp
|
||||
} [@@deriving sexp]
|
||||
|
||||
(** Returns the charge of the molecule *)
|
||||
val get_charge : t -> Charge.t
|
||||
|
@ -1,7 +1,7 @@
|
||||
open Core.Std;;
|
||||
open Core;;
|
||||
open Qptypes ;;
|
||||
|
||||
type t = Strictly_positive_int.t with sexp
|
||||
type t = Strictly_positive_int.t [@@deriving sexp]
|
||||
|
||||
let of_int = Strictly_positive_int.of_int ;;
|
||||
let to_int = Strictly_positive_int.to_int ;;
|
||||
|
@ -1,4 +1,4 @@
|
||||
type t = Qptypes.Strictly_positive_int.t with sexp
|
||||
type t = Qptypes.Strictly_positive_int.t [@@deriving sexp]
|
||||
|
||||
(** Conversion from int *)
|
||||
val of_int : int -> t
|
||||
|
@ -1,11 +1,11 @@
|
||||
open Core.Std;;
|
||||
open Core;;
|
||||
open Qptypes;;
|
||||
|
||||
type t = {
|
||||
x : float ;
|
||||
y : float ;
|
||||
z : float ;
|
||||
} with sexp
|
||||
} [@@deriving sexp]
|
||||
|
||||
let of_tuple ~units (x,y,z) =
|
||||
let f = match units with
|
||||
|
@ -2,7 +2,7 @@ type t =
|
||||
{ x : float;
|
||||
y : float;
|
||||
z : float;
|
||||
} with sexp
|
||||
} [@@deriving sexp]
|
||||
|
||||
(** Create from a tuple of floats *)
|
||||
val of_tuple : units:Units.units -> float*float*float -> t
|
||||
|
@ -1,7 +1,7 @@
|
||||
type t =
|
||||
{ sym : Symmetry.t;
|
||||
expo : Qptypes.AO_expo.t;
|
||||
} with sexp
|
||||
} [@@deriving sexp]
|
||||
|
||||
(** Conversion to string for printing *)
|
||||
val to_string : t -> string
|
||||
|
@ -1,4 +1,4 @@
|
||||
open Core.Std
|
||||
open Core
|
||||
|
||||
type t =
|
||||
{
|
||||
@ -53,13 +53,13 @@ let display_tty bar =
|
||||
in
|
||||
let stop_time =
|
||||
let x =
|
||||
Time.Span.to_float running_time
|
||||
Time.Span.to_sec running_time
|
||||
in
|
||||
if (percent > 0.) then
|
||||
x *. 100. /. percent -. x
|
||||
|> Time.Span.of_float
|
||||
|> Time.Span.of_sec
|
||||
else
|
||||
Time.Span.of_float 0.
|
||||
Time.Span.of_sec 0.
|
||||
in
|
||||
Printf.eprintf "%s : [%s] %4.1f%% | %10s, ~%10s left\r%!"
|
||||
bar.title
|
||||
@ -67,7 +67,7 @@ let display_tty bar =
|
||||
percent
|
||||
(Time.Span.to_string running_time)
|
||||
(stop_time |> Time.Span.to_string );
|
||||
{ bar with dirty = false ; next = Time.add now (Time.Span.of_float 0.1) }
|
||||
{ bar with dirty = false ; next = Time.add now (Time.Span.of_sec 0.1) }
|
||||
|
||||
|
||||
let display_file bar =
|
||||
@ -80,19 +80,19 @@ let display_file bar =
|
||||
in
|
||||
let stop_time =
|
||||
let x =
|
||||
Time.Span.to_float running_time
|
||||
Time.Span.to_sec running_time
|
||||
in
|
||||
if (percent > 0.) then
|
||||
x *. 100. /. percent -. x
|
||||
|> Time.Span.of_float
|
||||
|> Time.Span.of_sec
|
||||
else
|
||||
Time.Span.of_float 0.
|
||||
Time.Span.of_sec 0.
|
||||
in
|
||||
Printf.eprintf "%5.2f %% in %20s, ~%20s left\n%!"
|
||||
percent
|
||||
(Time.Span.to_string running_time)
|
||||
(Time.Span.to_string stop_time);
|
||||
{ bar with dirty = false ; next = Time.add (Time.now ()) (Time.Span.of_float 2.) }
|
||||
{ bar with dirty = false ; next = Time.add (Time.now ()) (Time.Span.of_sec 2.) }
|
||||
|
||||
|
||||
|
||||
|
@ -1,4 +1,4 @@
|
||||
open Core.Std
|
||||
open Core
|
||||
open Qptypes
|
||||
|
||||
|
||||
@ -7,7 +7,7 @@ module GaussianPrimitive_local : sig
|
||||
type t = {
|
||||
expo : AO_expo.t ;
|
||||
r_power : R_power.t ;
|
||||
} with sexp
|
||||
} [@@deriving sexp]
|
||||
|
||||
val of_expo_r_power : AO_expo.t -> R_power.t -> t
|
||||
val to_string : t -> string
|
||||
@ -17,7 +17,7 @@ end = struct
|
||||
type t = {
|
||||
expo : AO_expo.t ;
|
||||
r_power : R_power.t ;
|
||||
} with sexp
|
||||
} [@@deriving sexp]
|
||||
|
||||
let of_expo_r_power dz n =
|
||||
{ expo = dz ; r_power = n }
|
||||
@ -35,7 +35,7 @@ module GaussianPrimitive_non_local : sig
|
||||
expo : AO_expo.t ;
|
||||
r_power : R_power.t ;
|
||||
proj : Positive_int.t
|
||||
} with sexp
|
||||
} [@@deriving sexp]
|
||||
|
||||
val of_proj_expo_r_power : Positive_int.t -> AO_expo.t -> R_power.t -> t
|
||||
val to_string : t -> string
|
||||
@ -46,7 +46,7 @@ end = struct
|
||||
expo : AO_expo.t ;
|
||||
r_power : R_power.t ;
|
||||
proj : Positive_int.t
|
||||
} with sexp
|
||||
} [@@deriving sexp]
|
||||
|
||||
let of_proj_expo_r_power p dz n =
|
||||
{ expo = dz ; r_power = n ; proj = p }
|
||||
@ -66,7 +66,7 @@ type t = {
|
||||
n_elec : Positive_int.t ;
|
||||
local : (GaussianPrimitive_local.t * AO_coef.t ) list ;
|
||||
non_local : (GaussianPrimitive_non_local.t * AO_coef.t ) list
|
||||
} with sexp
|
||||
} [@@deriving sexp]
|
||||
|
||||
let empty e =
|
||||
{ element = e;
|
||||
|
@ -1,4 +1,4 @@
|
||||
open Core.Std;;
|
||||
open Core;;
|
||||
open Qptypes;;
|
||||
open Qputils;;
|
||||
|
||||
|
@ -1,4 +1,4 @@
|
||||
open Core.Std
|
||||
open Core
|
||||
|
||||
(*
|
||||
let rec transpose = function
|
||||
|
@ -19,7 +19,7 @@ of the block.
|
||||
r_y : Y_type.t
|
||||
...
|
||||
last_r : bool
|
||||
} with sexp
|
||||
} [@@deriving sexp]
|
||||
;;
|
||||
val read : unit -> t
|
||||
val write : t -> unit
|
||||
@ -31,7 +31,7 @@ of the block.
|
||||
r_y : Y_type.t
|
||||
...
|
||||
last_r : bool
|
||||
} with sexp
|
||||
} [@@deriving sexp]
|
||||
;;
|
||||
|
||||
let get_default = Qpackage.get_ezfio_default "new_keyword";;
|
||||
|
@ -1,4 +1,4 @@
|
||||
open Core.Std;;
|
||||
open Core;;
|
||||
|
||||
(* A range is a string of the type:
|
||||
*
|
||||
@ -12,7 +12,7 @@ open Core.Std;;
|
||||
*)
|
||||
|
||||
|
||||
type t = int list with sexp
|
||||
type t = int list [@@deriving sexp]
|
||||
|
||||
let expand_range r =
|
||||
match String.lsplit2 ~on:'-' r with
|
||||
@ -71,8 +71,8 @@ let to_string l =
|
||||
let test_module () =
|
||||
let s = "[72-107,36-53,126-131]" in
|
||||
let l = of_string s in
|
||||
print_string s ; print_newline () ;
|
||||
List.iter ~f:(fun x -> Printf.printf "%d, " x) l ; print_newline () ;
|
||||
to_string l |> print_string ; print_newline () ;
|
||||
print_string s ; Out_channel.newline stdout ;
|
||||
List.iter ~f:(fun x -> Printf.printf "%d, " x) l ; Out_channel.newline stdout ;
|
||||
to_string l |> print_string ; Out_channel.newline stdout
|
||||
;;
|
||||
|
||||
|
@ -1,4 +1,4 @@
|
||||
type t = int list with sexp
|
||||
type t = int list [@@deriving sexp]
|
||||
|
||||
(** A range is a sorted list of ints in an interval.
|
||||
It is created using a string :
|
||||
|
112
ocaml/String_ext.ml
Normal file
112
ocaml/String_ext.ml
Normal file
@ -0,0 +1,112 @@
|
||||
include String
|
||||
|
||||
(** Split a string on a given character *)
|
||||
let split ?(on=' ') str =
|
||||
let rec do_work ?(accu=[]) ?(left="") = function
|
||||
| "" -> List.rev (left::accu)
|
||||
| s ->
|
||||
let new_s =
|
||||
(length s) - 1
|
||||
|> sub s 1
|
||||
in
|
||||
if (s.[0] = on) then
|
||||
let new_accu =
|
||||
left :: accu
|
||||
in
|
||||
do_work ~accu:new_accu new_s
|
||||
else
|
||||
let new_left =
|
||||
concat "" [ left ; make 1 s.[0] ]
|
||||
in
|
||||
do_work ~accu ~left:new_left new_s
|
||||
in
|
||||
do_work str
|
||||
|
||||
|
||||
(** Strip blanks on the left of a string *)
|
||||
let ltrim s =
|
||||
let rec do_work s l =
|
||||
match s.[0] with
|
||||
| '\n'
|
||||
| ' ' -> do_work (sub s 1 (l-1)) (l-1)
|
||||
| _ -> s
|
||||
in
|
||||
let l =
|
||||
length s
|
||||
in
|
||||
if (l > 0) then
|
||||
do_work s l
|
||||
else
|
||||
s
|
||||
|
||||
(** Strip blanks on the right of a string *)
|
||||
let rtrim s =
|
||||
let rec do_work s l =
|
||||
let newl =
|
||||
l-1
|
||||
in
|
||||
match s.[newl] with
|
||||
| '\n'
|
||||
| ' ' -> do_work (sub s 0 (newl)) (newl)
|
||||
| _ -> s
|
||||
in
|
||||
let l =
|
||||
length s
|
||||
in
|
||||
if (l > 0) then
|
||||
do_work s l
|
||||
else
|
||||
s
|
||||
|
||||
|
||||
(** Strip blanks on the right and left of a string *)
|
||||
let strip = String.trim
|
||||
|
||||
|
||||
(** Split a string in two pieces when a character is found the 1st time from the left *)
|
||||
let lsplit2_exn ?(on=' ') s =
|
||||
let length =
|
||||
String.length s
|
||||
in
|
||||
let rec do_work i =
|
||||
if (i = length) then
|
||||
begin
|
||||
raise Not_found
|
||||
end
|
||||
else if (s.[i] = on) then
|
||||
( String.sub s 0 i,
|
||||
String.sub s (i+1) (length-i-1) )
|
||||
else
|
||||
do_work (i+1)
|
||||
in
|
||||
do_work 0
|
||||
|
||||
|
||||
(** Split a string in two pieces when a character is found the 1st time from the right *)
|
||||
let rsplit2_exn ?(on=' ') s =
|
||||
let length =
|
||||
String.length s
|
||||
in
|
||||
let rec do_work i =
|
||||
if (i = -1) then
|
||||
begin
|
||||
raise Not_found
|
||||
end
|
||||
else if (s.[i] = on) then
|
||||
( String.sub s 0 i,
|
||||
String.sub s (i+1) (length-i-1) )
|
||||
else
|
||||
do_work (i-1)
|
||||
in
|
||||
do_work length
|
||||
|
||||
|
||||
let to_list s =
|
||||
Array.init (String.length s) (fun i -> s.[i])
|
||||
|> Array.to_list
|
||||
|
||||
let fold ~init ~f s =
|
||||
to_list s
|
||||
|> List.fold_left f init
|
||||
|
||||
|
@ -1,7 +1,7 @@
|
||||
open Qptypes
|
||||
open Core.Std
|
||||
open Core
|
||||
|
||||
type t = S|P|D|F|G|H|I|J|K|L with sexp
|
||||
type t = S|P|D|F|G|H|I|J|K|L [@@deriving sexp]
|
||||
|
||||
let to_string = function
|
||||
| S -> "S"
|
||||
@ -77,7 +77,7 @@ type st = t
|
||||
module Xyz = struct
|
||||
type t = { x: Positive_int.t ;
|
||||
y: Positive_int.t ;
|
||||
z: Positive_int.t } with sexp
|
||||
z: Positive_int.t } [@@deriving sexp]
|
||||
type state_type = Null | X | Y | Z
|
||||
|
||||
(** Builds an XYZ triplet from a string.
|
||||
|
@ -1,4 +1,4 @@
|
||||
type t = S | P | D | F | G | H | I | J | K | L with sexp
|
||||
type t = S | P | D | F | G | H | I | J | K | L [@@deriving sexp]
|
||||
|
||||
(** Creatio from strings *)
|
||||
val to_string : t -> string
|
||||
@ -16,7 +16,7 @@ module Xyz :
|
||||
x : Qptypes.Positive_int.t;
|
||||
y : Qptypes.Positive_int.t;
|
||||
z : Qptypes.Positive_int.t;
|
||||
} with sexp
|
||||
} [@@deriving sexp]
|
||||
|
||||
(** The string format contains the powers of x,y and z in a
|
||||
format like "x2z3" *)
|
||||
|
@ -1,4 +1,4 @@
|
||||
open Core.Std
|
||||
open Core
|
||||
open Qptypes
|
||||
|
||||
|
||||
@ -63,7 +63,7 @@ let bind_socket ~socket_type ~socket ~port =
|
||||
ZMQ.Socket.bind socket @@ Printf.sprintf "tcp://*:%d" port;
|
||||
loop (-1)
|
||||
with
|
||||
| Unix.Unix_error _ -> (Time.pause @@ Time.Span.of_float 1. ; loop (i-1) )
|
||||
| Unix.Unix_error _ -> (Time.pause @@ Time.Span.of_sec 1. ; loop (i-1) )
|
||||
| other_exception -> raise other_exception
|
||||
in loop 60
|
||||
|
||||
|
@ -1,4 +1,4 @@
|
||||
open Core.Std;;
|
||||
open Core;;
|
||||
open Qptypes;;
|
||||
|
||||
let to_md5 sexp_of_t t =
|
||||
|
@ -1,3 +1,3 @@
|
||||
true: package(core,cryptokit,ZMQ,sexplib.syntax,str)
|
||||
true: package(core,cryptokit,ZMQ,str,ppx_sexp_conv,ppx_deriving)
|
||||
true: thread
|
||||
false: profile
|
||||
|
@ -1,206 +0,0 @@
|
||||
open Qputils
|
||||
open Qptypes
|
||||
open Core.Std
|
||||
|
||||
let spec =
|
||||
let open Command.Spec in
|
||||
empty
|
||||
+> flag "o" (optional string)
|
||||
~doc:"file Name of the new EZFIO file. Default is suffixed by .RI"
|
||||
+> flag "b" (required string)
|
||||
~doc:"string Name of basis set."
|
||||
+> anon (" EZFIO file)" %: file )
|
||||
|
||||
type element =
|
||||
| Element of Element.t
|
||||
| Int_elem of (Nucl_number.t * Element.t)
|
||||
|
||||
|
||||
(** Returns the list of available basis sets *)
|
||||
let list_basis () =
|
||||
let basis_list =
|
||||
Qpackage.root ^ "/install/emsl/EMSL_api.py list_basis | grep \"-RI\" "
|
||||
|> Unix.open_process_in
|
||||
|> In_channel.input_lines
|
||||
|> List.map ~f:(fun x ->
|
||||
match String.split x ~on:'\'' with
|
||||
| [] -> ""
|
||||
| a :: []
|
||||
| _ :: a :: _ -> String.strip a
|
||||
)
|
||||
in
|
||||
List.sort basis_list ~cmp:String.ascending
|
||||
|> String.concat ~sep:"\n"
|
||||
|
||||
|
||||
(** Run the program *)
|
||||
let run ?o b ezfio_file =
|
||||
|
||||
let new_filename =
|
||||
match o with
|
||||
| Some filename -> filename
|
||||
| None -> ezfio_file ^ ".RI"
|
||||
in
|
||||
let () =
|
||||
match Sys.is_directory new_filename with
|
||||
| `Yes -> failwith "Output directory exists"
|
||||
| _ -> ()
|
||||
in
|
||||
let status =
|
||||
Printf.sprintf "cp -r %s %s" ezfio_file new_filename
|
||||
|> Unix.system
|
||||
in
|
||||
ignore status;
|
||||
|
||||
Ezfio.set_file new_filename;
|
||||
|
||||
(**********
|
||||
Basis set
|
||||
**********)
|
||||
|
||||
let basis_table =
|
||||
Hashtbl.Poly.create ()
|
||||
in
|
||||
|
||||
(* Open basis set channels *)
|
||||
let basis_channel element =
|
||||
let key =
|
||||
match element with
|
||||
| Element e -> Element.to_string e
|
||||
| Int_elem (i,e) -> Printf.sprintf "%d,%s" (Nucl_number.to_int i) (Element.to_string e)
|
||||
in
|
||||
match Hashtbl.find basis_table key with
|
||||
| Some in_channel ->
|
||||
in_channel
|
||||
| None -> raise Not_found
|
||||
in
|
||||
|
||||
let temp_filename =
|
||||
Filename.temp_file "qp_create_" ".basis"
|
||||
in
|
||||
let () =
|
||||
Sys.remove temp_filename
|
||||
in
|
||||
|
||||
let fetch_channel basis =
|
||||
let command =
|
||||
Qpackage.root ^ "/scripts/get_basis.sh \"" ^ temp_filename
|
||||
^ "." ^ basis ^ "\" \"" ^ basis ^"\""
|
||||
in
|
||||
let long_basis =
|
||||
Qpackage.root ^ "/data/basis/" ^ basis
|
||||
in
|
||||
match
|
||||
Sys.is_file basis,
|
||||
Sys.is_file long_basis
|
||||
with
|
||||
| `Yes, _ -> In_channel.create basis
|
||||
| `No , `Yes -> In_channel.create long_basis
|
||||
| _ ->
|
||||
begin
|
||||
let filename =
|
||||
Unix.open_process_in command
|
||||
|> In_channel.input_all
|
||||
|> String.strip
|
||||
in
|
||||
let new_channel =
|
||||
In_channel.create filename
|
||||
in
|
||||
Unix.unlink filename;
|
||||
new_channel
|
||||
end
|
||||
in
|
||||
|
||||
let rec build_basis = function
|
||||
| [] -> ()
|
||||
| elem_and_basis_name :: rest ->
|
||||
begin
|
||||
match (String.lsplit2 ~on:':' elem_and_basis_name) with
|
||||
| None -> (* Principal basis *)
|
||||
begin
|
||||
let basis =
|
||||
elem_and_basis_name
|
||||
in
|
||||
let new_channel =
|
||||
fetch_channel basis
|
||||
in
|
||||
List.iter nuclei ~f:(fun elem->
|
||||
let key =
|
||||
Element.to_string elem.Atom.element
|
||||
in
|
||||
match Hashtbl.add basis_table ~key:key ~data:new_channel with
|
||||
| `Ok -> ()
|
||||
| `Duplicate -> ()
|
||||
)
|
||||
end
|
||||
| Some (key, basis) -> (*Aux basis *)
|
||||
begin
|
||||
let elem =
|
||||
try
|
||||
Element (Element.of_string key)
|
||||
with Element.ElementError _ ->
|
||||
let result =
|
||||
match (String.split ~on:',' key) with
|
||||
| i :: k :: [] -> (Nucl_number.of_int @@ int_of_string i, Element.of_string k)
|
||||
| _ -> failwith "Expected format is int,Element:basis"
|
||||
in Int_elem result
|
||||
and basis =
|
||||
String.lowercase basis
|
||||
in
|
||||
let key =
|
||||
match elem with
|
||||
| Element e -> Element.to_string e
|
||||
| Int_elem (i,e) -> Printf.sprintf "%d,%s" (Nucl_number.to_int i) (Element.to_string e)
|
||||
in
|
||||
let new_channel =
|
||||
fetch_channel basis
|
||||
in
|
||||
begin
|
||||
match Hashtbl.add basis_table ~key:key ~data:new_channel with
|
||||
| `Ok -> ()
|
||||
| `Duplicate ->
|
||||
let e =
|
||||
match elem with
|
||||
| Element e -> e
|
||||
| Int_elem (_,e) -> e
|
||||
in
|
||||
failwith ("Duplicate definition of basis for "^(Element.to_long_string e))
|
||||
end
|
||||
end
|
||||
end;
|
||||
build_basis rest
|
||||
in
|
||||
String.split ~on:'|' b
|
||||
|> List.rev_map ~f:String.strip
|
||||
|> build_basis
|
||||
in
|
||||
|
||||
let basis =
|
||||
Input.AO_basis.read ()
|
||||
in
|
||||
()
|
||||
|
||||
|
||||
let command =
|
||||
Command.basic
|
||||
~summary: "Quantum Package command"
|
||||
~readme:(fun () -> "
|
||||
|
||||
=== Available basis sets ===
|
||||
|
||||
" ^ (list_basis ()) ^ "
|
||||
|
||||
============================
|
||||
|
||||
Extents the basis set to add an auxiliary basis set.
|
||||
" )
|
||||
spec
|
||||
(fun o b ezfio_file () -> run ?o b ezfio_file )
|
||||
|
||||
|
||||
let () =
|
||||
Command.run command
|
||||
|
||||
|
||||
|
||||
|
@ -1,4 +1,4 @@
|
||||
open Core.Std
|
||||
open Core
|
||||
|
||||
let filenames =
|
||||
let dir_name = Qpackage.root^"/data/basis/"
|
||||
|
@ -1,6 +1,6 @@
|
||||
open Qputils
|
||||
open Qptypes
|
||||
open Core.Std
|
||||
open Core
|
||||
|
||||
let spec =
|
||||
let open Command.Spec in
|
||||
|
@ -1,6 +1,6 @@
|
||||
open Qputils
|
||||
open Qptypes
|
||||
open Core.Std
|
||||
open Core
|
||||
|
||||
let run ~multiplicity ezfio_file =
|
||||
if (not (Sys.file_exists_exn ezfio_file)) then
|
||||
|
@ -1,6 +1,6 @@
|
||||
open Qputils;;
|
||||
open Qptypes;;
|
||||
open Core.Std;;
|
||||
open Core;;
|
||||
|
||||
type input_action =
|
||||
| Basis
|
||||
|
@ -1,4 +1,4 @@
|
||||
open Core.Std
|
||||
open Core
|
||||
open Qptypes
|
||||
|
||||
let basis () =
|
||||
|
@ -1,4 +1,4 @@
|
||||
open Core.Std
|
||||
open Core
|
||||
open Qputils
|
||||
|
||||
(* Environment variables :
|
||||
@ -132,7 +132,7 @@ let run slave exe ezfio_file =
|
||||
Sys.remove qp_run_address_filename;
|
||||
|
||||
let duration = Time.diff (Time.now()) time_start
|
||||
|> Core.Span.to_string in
|
||||
|> Time.Span.to_string in
|
||||
Printf.printf "Wall time : %s\n\n" duration;
|
||||
if (exit_code <> 0) then
|
||||
exit exit_code
|
||||
|
@ -1,6 +1,6 @@
|
||||
open Qputils
|
||||
open Qptypes
|
||||
open Core.Std
|
||||
open Core
|
||||
|
||||
(*
|
||||
* Command-line arguments
|
||||
|
@ -1,4 +1,4 @@
|
||||
open Core.Std;;
|
||||
open Core;;
|
||||
|
||||
let input_data = "
|
||||
* Positive_float : float
|
||||
@ -160,14 +160,14 @@ let input_ezfio = "
|
||||
|
||||
let untouched = "
|
||||
module MO_guess : sig
|
||||
type t with sexp
|
||||
type t [@@deriving sexp]
|
||||
val to_string : t -> string
|
||||
val of_string : string -> t
|
||||
end = struct
|
||||
type t =
|
||||
| Huckel
|
||||
| HCore
|
||||
with sexp
|
||||
[@@deriving sexp]
|
||||
|
||||
let to_string = function
|
||||
| Huckel -> \"Huckel\"
|
||||
@ -182,7 +182,7 @@ end = struct
|
||||
end
|
||||
|
||||
module Disk_access : sig
|
||||
type t with sexp
|
||||
type t [@@deriving sexp]
|
||||
val to_string : t -> string
|
||||
val of_string : string -> t
|
||||
end = struct
|
||||
@ -190,7 +190,7 @@ end = struct
|
||||
| Read
|
||||
| Write
|
||||
| None
|
||||
with sexp
|
||||
[@@deriving sexp]
|
||||
|
||||
let to_string = function
|
||||
| Read -> \"Read\"
|
||||
@ -210,12 +210,12 @@ end
|
||||
|
||||
let template = format_of_string "
|
||||
module %s : sig
|
||||
type t with sexp
|
||||
type t [@@deriving sexp]
|
||||
val to_%s : t -> %s
|
||||
val of_%s : %s %s -> t
|
||||
val to_string : t -> string
|
||||
end = struct
|
||||
type t = %s with sexp
|
||||
type t = %s [@@deriving sexp]
|
||||
let to_%s x = x
|
||||
let of_%s %s x = ( %s x )
|
||||
let to_string x = %s.to_string x
|
||||
@ -225,7 +225,7 @@ end
|
||||
;;
|
||||
|
||||
let parse_input input=
|
||||
print_string "open Core.Std;;\nlet warning = print_string;;\n" ;
|
||||
print_string "open Core;;\nlet warning = print_string;;\n" ;
|
||||
let rec parse result = function
|
||||
| [] -> result
|
||||
| ( "" , "" )::tail -> parse result tail
|
||||
@ -255,13 +255,13 @@ let parse_input input=
|
||||
|
||||
let ezfio_template = format_of_string "
|
||||
module %s : sig
|
||||
type t with sexp
|
||||
type t [@@deriving sexp]
|
||||
val to_%s : t -> %s
|
||||
val get_max : unit -> %s
|
||||
val of_%s : ?min:%s -> ?max:%s -> %s -> t
|
||||
val to_string : t -> string
|
||||
end = struct
|
||||
type t = %s with sexp
|
||||
type t = %s [@@deriving sexp]
|
||||
let to_string x = %s.to_string x
|
||||
let get_max () =
|
||||
if (Ezfio.has_%s ()) then
|
||||
|
@ -1,4 +1,4 @@
|
||||
open Core.Std;;
|
||||
open Core;;
|
||||
open Qputils;;
|
||||
open Qptypes;;
|
||||
|
||||
|
@ -1,4 +1,4 @@
|
||||
open Core.Std
|
||||
open Core
|
||||
open Qptypes
|
||||
|
||||
let test_prim () =
|
||||
|
@ -1,4 +1,4 @@
|
||||
open Core.Std
|
||||
open Core
|
||||
|
||||
let () =
|
||||
Message.of_string "new_job ao_integrals tcp://127.0.0.1 inproc://ao_ints:12345"
|
||||
|
@ -1,4 +1,4 @@
|
||||
open Core.Std ;;
|
||||
open Core ;;
|
||||
open Qptypes ;;
|
||||
|
||||
let test_molecule () =
|
||||
|
@ -1,4 +1,4 @@
|
||||
open Core.Std
|
||||
open Core
|
||||
open Qputils
|
||||
open Qptypes
|
||||
|
||||
|
@ -1,4 +1,4 @@
|
||||
open Core.Std
|
||||
open Core
|
||||
|
||||
let () =
|
||||
|
||||
|
@ -1,4 +1,4 @@
|
||||
open Core.Std
|
||||
open Core
|
||||
open Qputils
|
||||
open Qptypes
|
||||
open Symmetry
|
||||
|
Loading…
Reference in New Issue
Block a user