LCPQ/quantum_package
10
0
Fork 0
mirror of https://github.com/LCPQ/quantum_package synced 2024-11-19 04:22:36 +01:00
Code Issues Releases Wiki Activity

Merge branch 'master' of github.com:scemama/quantum_package

Browse Source
This commit is contained in:
Anthony Scemama 2017-08-18 19:47:04 +02:00
commit 996f46d630
73 changed files with 445 additions and 264 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

7
ocaml/Address.ml
View File

@ -1,4 +1,3 @@
open Core.Std
module Tcp : sig
type t
@ -8,7 +7,7 @@ module Tcp : sig
end = struct
type t = string
let of_string x =
if not (String.is_prefix ~prefix:"tcp://" x) then
if not (String_ext.is_prefix ~prefix:"tcp://" x) then
invalid_arg "Address Invalid"
;
x
@ -26,7 +25,7 @@ module Ipc : sig
end = struct
type t = string
let of_string x =
assert (String.is_prefix ~prefix:"ipc://" x);
assert (String_ext.is_prefix ~prefix:"ipc://" x);
x
let create name =
Printf.sprintf "ipc://%s" name
@ -41,7 +40,7 @@ module Inproc : sig
end = struct
type t = string
let of_string x =
assert (String.is_prefix ~prefix:"inproc://" x);
assert (String_ext.is_prefix ~prefix:"inproc://" x);
x
let create name =
Printf.sprintf "inproc://%s" name

4
ocaml/Atom.ml
View File

@ -1,4 +1,4 @@
open Core.Std
open Core
exception AtomError of string
@ -6,7 +6,7 @@ type t =
{ element : Element.t ;
charge : Charge.t ;
coord : Point3d.t ;
} with sexp
} [@@deriving sexp]
(** Read xyz coordinates of the atom *)
let of_string ~units s =

10
ocaml/Basis.ml
View File

@ -1,7 +1,7 @@
open Core.Std
open Sexplib.Std
open Qptypes
type t = (Gto.t * Nucl_number.t) list with sexp
type t = (Gto.t * Nucl_number.t) list [@@deriving sexp]
(** Read all the basis functions of an element *)
let read in_channel at_number =
@ -16,7 +16,7 @@ let read in_channel at_number =
(** Find an element in the basis set file *)
let find in_channel element =
In_channel.seek in_channel 0L;
seek_in in_channel 0;
let element_read = ref Element.X in
while !element_read <> element
do
@ -56,13 +56,13 @@ let to_string_general ~fmt ~atom_sep ?ele_array b =
do_work ((Gto.to_string ~fmt g)::accu) n tail
in
do_work [new_nucleus 1] 1 b
|> String.concat ~sep:"\n"
|> String.concat "\n"
let to_string_gamess ?ele_array =
to_string_general ?ele_array ~fmt:Gto.Gamess ~atom_sep:""
let to_string_gaussian ?ele_array b =
String.concat ~sep:"\n"
String.concat "\n"
[ to_string_general ?ele_array ~fmt:Gto.Gaussian ~atom_sep:"****" b ; "****" ]
let to_string ?(fmt=Gto.Gamess) =

4
ocaml/Bit.ml
View File

@ -1,4 +1,4 @@
open Core.Std;;
open Core;;
(*
Type for bits
@ -11,7 +11,7 @@ Zero | One
type t =
| One
| Zero
with sexp
[@@deriving sexp]
let to_string = function
| Zero -> "0"

2
ocaml/Bit.mli
View File

@ -1,4 +1,4 @@
type t = One | Zero with sexp
type t = One | Zero [@@deriving sexp]
(** String conversions for printing *)
val to_string : t -> string

2
ocaml/Bitlist.ml
View File

@ -1,5 +1,5 @@
open Qptypes
open Core.Std
open Core
(*
Type for bits strings

4
ocaml/Charge.ml
View File

@ -1,6 +1,6 @@
open Core.Std
open Core
type t = float with sexp
type t = float [@@deriving sexp]
let of_float x = x
let of_int i = Float.of_int i

2
ocaml/Charge.mli
View File

@ -1,4 +1,4 @@
type t = float with sexp
type t = float [@@deriving sexp]
(** Float conversion functions *)
val to_float : t -> float

26
ocaml/Determinant.ml
View File

@ -1,7 +1,7 @@
open Core.Std;;
open Qptypes;;
open Qptypes
open Sexplib.Std
type t = int64 array with sexp
type t = int64 array [@@deriving sexp]
let to_int64_array (x:t) = (x:int64 array)
@ -9,8 +9,8 @@ let to_int64_array (x:t) = (x:int64 array)
let to_alpha_beta x =
let x = to_int64_array x in
let n_int = (Array.length x)/2 in
( Array.init n_int ~f:(fun i -> x.(i)) ,
Array.init n_int ~f:(fun i -> x.(i+n_int)) )
( Array.init n_int (fun i -> x.(i)) ,
Array.init n_int (fun i -> x.(i+n_int)) )
let to_bitlist_couple x =
@ -28,12 +28,14 @@ let bitlist_to_string ~mo_tot_num x =
let len =
MO_number.to_int mo_tot_num
in
List.map x ~f:(function
| Bit.Zero -> "-"
| Bit.One -> "+"
)
|> String.concat
|> String.sub ~pos:0 ~len
let s =
List.map (function
| Bit.Zero -> "-"
| Bit.One -> "+"
) x
|> String.concat ""
in
String.sub s 0 len
@ -77,6 +79,6 @@ let to_string ~mo_tot_num x =
let (xa,xb) = to_bitlist_couple x in
[ " " ; bitlist_to_string ~mo_tot_num xa ; "\n" ;
" " ; bitlist_to_string ~mo_tot_num xb ]
|> String.concat
|> String.concat ""

2
ocaml/Determinant.mli
View File

@ -5,7 +5,7 @@
* where each int64 is a list of 64 MOs. When the bit is set
* to 1, the MO is occupied.
*)
type t = int64 array with sexp
type t = int64 array [@@deriving sexp]
(** Transform to an int64 array *)
val to_int64_array : t -> int64 array

4
ocaml/Element.ml
View File

@ -1,4 +1,4 @@
open Core.Std
open Core
open Qptypes
exception ElementError of string
@ -11,7 +11,7 @@ type t =
|K |Ca|Sc|Ti|V |Cr|Mn|Fe|Co|Ni|Cu|Zn|Ga|Ge|As|Se|Br|Kr
|Rb|Sr|Y |Zr|Nb|Mo|Tc|Ru|Rh|Pd|Ag|Cd|In|Sn|Sb|Te|I |Xe
|Pt
with sexp
[@@deriving sexp]
let of_string x =
match (String.capitalize (String.lowercase x)) with

2
ocaml/Element.mli
View File

@ -8,7 +8,7 @@ type t =
|K |Ca|Sc|Ti|V |Cr|Mn|Fe|Co|Ni|Cu|Zn|Ga|Ge|As|Se|Br|Kr
|Rb|Sr|Y |Zr|Nb|Mo|Tc|Ru|Rh|Pd|Ag|Cd|In|Sn|Sb|Te|I |Xe
|Pt
with sexp
[@@deriving sexp]
(** String conversion functions *)
val of_string : string -> t

18
ocaml/Excitation.ml
View File

@ -1,14 +1,14 @@
open Core.Std;;
open Qptypes;;
open Core
open Qptypes
module Hole = struct
type t = MO_class.t with sexp
type t = MO_class.t [@@deriving sexp]
let of_mo_class x = x
let to_mo_class x = x
end
module Particle = struct
type t = MO_class.t with sexp
type t = MO_class.t [@@deriving sexp]
let of_mo_class x = x
let to_mo_class x = x
end
@ -16,7 +16,7 @@ end
type t =
| Single of Hole.t*Particle.t
| Double of Hole.t*Particle.t*Hole.t*Particle.t
with sexp;;
[@@deriving sexp]
let create_single ~hole ~particle =
MO_class.(
@ -29,7 +29,7 @@ let create_single ~hole ~particle =
| ( _, Inactive _ ) -> failwith "Particles can not be in virtual MOs"
| (h, p) -> Single ( (Hole.of_mo_class h), (Particle.of_mo_class p) )
)
;;
let double_of_singles s1 s2 =
let (h1,p1) = match s1 with
@ -40,14 +40,14 @@ let double_of_singles s1 s2 =
| _ -> assert false
in
Double (h1,p1,h2,p2)
;;
let create_double ~hole1 ~particle1 ~hole2 ~particle2 =
let s1 = create_single ~hole:hole1 ~particle:particle1
and s2 = create_single ~hole:hole2 ~particle:particle2
in
double_of_singles s1 s2
;;
let to_string = function
| Single (h,p) ->
@ -68,5 +68,5 @@ let to_string = function
(MO_class.to_string (Particle.to_mo_class p2));
"]"]
|> String.concat ~sep:" "
;;

2
ocaml/Excitation.mli
View File

@ -18,7 +18,7 @@ module Particle :
type t =
| Single of Hole.t * Particle.t
| Double of Hole.t * Particle.t * Hole.t * Particle.t
with sexp
[@@deriving sexp]
val create_single : hole:MO_class.t -> particle:MO_class.t -> t

4
ocaml/GaussianPrimitive.ml
View File

@ -1,10 +1,10 @@
open Qptypes
open Core.Std
open Core
type t =
{ sym : Symmetry.t ;
expo : AO_expo.t ;
} with sexp
} [@@deriving sexp]
let to_string p =
let { sym = s ; expo = e } = p in

2
ocaml/Generic_input_of_rst.ml
View File

@ -1,4 +1,4 @@
open Core.Std;;
open Core;;
open Qptypes;;

27
ocaml/Gto.ml
View File

@ -1,5 +1,5 @@
open Core.Std
open Qptypes
open Sexplib.Std
exception GTO_Read_Failure of string
exception End_Of_Basis
@ -11,11 +11,11 @@ type fmt =
type t =
{ sym : Symmetry.t ;
lc : ((GaussianPrimitive.t * AO_coef.t) list)
} with sexp
} [@@deriving sexp]
let of_prim_coef_list pc =
let (p,c) = List.hd_exn pc in
let (p,c) = List.hd pc in
let sym = p.GaussianPrimitive.sym in
let rec check = function
| [] -> `OK
@ -37,12 +37,12 @@ let of_prim_coef_list pc =
let read_one in_channel =
(* Fetch number of lines to read on first line *)
let buffer = input_line in_channel in
if ( (String.strip buffer) = "" ) then
if ( (String_ext.strip buffer) = "" ) then
raise End_Of_Basis;
let sym_str = String.sub buffer 0 2 in
let n_str = String.sub buffer 2 ((String.length buffer)-2) in
let sym = Symmetry.of_string (String.strip sym_str) in
let n = Int.of_string (String.strip n_str) in
let sym = Symmetry.of_string (String_ext.strip sym_str) in
let n = int_of_string (String_ext.strip n_str) in
(* Read all the primitives *)
let rec read_lines result = function
| 0 -> result
@ -50,18 +50,19 @@ let read_one in_channel =
begin
let line_buffer = input_line in_channel in
let buffer = line_buffer
|> String.split ~on:' '
|> List.filter ~f:(fun x -> x <> "")
|> String_ext.split ~on:' '
|> List.filter (fun x -> x <> "")
in
match buffer with
| [ j ; expo ; coef ] ->
begin
let coef = String.tr ~target:'D' ~replacement:'e' coef
let coef =
Str.global_replace (Str.regexp "D") "e" coef
in
let p =
GaussianPrimitive.of_sym_expo sym
(AO_expo.of_float (Float.of_string expo) )
and c = AO_coef.of_float (Float.of_string coef) in
(AO_expo.of_float (float_of_string expo) )
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)
@ -89,7 +90,7 @@ let to_string_gamess { sym = sym ; lc = lc } =
do_work (result::accu) (i+1) tail
in
(do_work [result] 1 lc)
|> String.concat ~sep:"\n"
|> String.concat "\n"
(** Write the GTO in Gaussian format *)
@ -109,7 +110,7 @@ let to_string_gaussian { sym = sym ; lc = lc } =
do_work (result::accu) (i+1) tail
in
(do_work [result] 1 lc)
|> String.concat ~sep:"\n"
|> String.concat "\n"
(** Transform the gto to a string *)

2
ocaml/Gto.mli
View File

@ -7,7 +7,7 @@ type fmt =
type t =
{ sym : Symmetry.t ;
lc : (GaussianPrimitive.t * Qptypes.AO_coef.t) list;
} with sexp
} [@@deriving sexp]
(** Create from a list of GaussianPrimitive.t * Qptypes.AO_coef.t *)
val of_prim_coef_list :

2
ocaml/Input.ml
View File

@ -1,6 +1,6 @@
open Qputils;;
open Qptypes;;
open Core.Std;;
open Core;;
include Input_ao_basis;;
include Input_bitmasks;;

6
ocaml/Input_ao_basis.ml
View File

@ -1,6 +1,6 @@
open Qptypes;;
open Qputils;;
open Core.Std;;
open Core;;
module Ao_basis : sig
type t =
@ -13,7 +13,7 @@ module Ao_basis : sig
ao_coef : AO_coef.t array;
ao_expo : AO_expo.t array;
ao_cartesian : bool;
} with sexp
} [@@deriving sexp]
;;
val read : unit -> t option
val to_string : t -> string
@ -32,7 +32,7 @@ end = struct
ao_coef : AO_coef.t array;
ao_expo : AO_expo.t array;
ao_cartesian : bool;
} with sexp
} [@@deriving sexp]
;;
let get_default = Qpackage.get_ezfio_default "ao_basis";;

6
ocaml/Input_bi_integrals.ml
View File

@ -1,6 +1,6 @@
open Qptypes;;
open Qputils;;
open Core.Std;;
open Core;;
module Bielec_integrals : sig
type t =
@ -11,7 +11,7 @@ module Bielec_integrals : sig
threshold_ao : Threshold.t;
threshold_mo : Threshold.t;
direct : bool;
} with sexp
} [@@deriving sexp]
;;
val read : unit -> t option
val write : t -> unit
@ -27,7 +27,7 @@ end = struct
threshold_ao : Threshold.t;
threshold_mo : Threshold.t;
direct : bool;
} with sexp
} [@@deriving sexp]
;;
let get_default = Qpackage.get_ezfio_default "bielec_integrals";;

6
ocaml/Input_bitmasks.ml
View File

@ -1,6 +1,6 @@
open Qptypes;;
open Qputils;;
open Core.Std;;
open Core;;
module Bitmasks : sig
type t =
@ -10,7 +10,7 @@ module Bitmasks : sig
generators : int64 array;
n_mask_cas : Bitmask_number.t;
cas : int64 array;
} with sexp
} [@@deriving sexp]
;;
val read : unit -> t option
val to_string : t -> string
@ -22,7 +22,7 @@ end = struct
generators : int64 array;
n_mask_cas : Bitmask_number.t;
cas : int64 array;
} with sexp
} [@@deriving sexp]
;;
let get_default = Qpackage.get_ezfio_default "bitmasks";;

6
ocaml/Input_determinants_by_hand.ml
View File

@ -1,6 +1,6 @@
open Qptypes;;
open Qputils;;
open Core.Std;;
open Core;;
module Determinants_by_hand : sig
type t =
@ -11,7 +11,7 @@ module Determinants_by_hand : sig
expected_s2 : Positive_float.t;
psi_coef : Det_coef.t array;
psi_det : Determinant.t array;
} with sexp
} [@@deriving sexp]
val read : unit -> t
val read_maybe : unit -> t option
val write : t -> unit
@ -30,7 +30,7 @@ end = struct
expected_s2 : Positive_float.t;
psi_coef : Det_coef.t array;
psi_det : Determinant.t array;
} with sexp
} [@@deriving sexp]
;;
let get_default = Qpackage.get_ezfio_default "determinants";;

6
ocaml/Input_electrons.ml
View File

@ -1,12 +1,12 @@
open Qptypes;;
open Qputils;;
open Core.Std;;
open Core;;
module Electrons : sig
type t =
{ elec_alpha_num : Elec_alpha_number.t;
elec_beta_num : Elec_beta_number.t;
} with sexp
} [@@deriving sexp]
;;
val read : unit -> t option
val write : t -> unit
@ -18,7 +18,7 @@ end = struct
type t =
{ elec_alpha_num : Elec_alpha_number.t;
elec_beta_num : Elec_beta_number.t;
} with sexp
} [@@deriving sexp]
;;
let get_default = Qpackage.get_ezfio_default "electrons";;

4
ocaml/Input_mo_basis.ml
View File

@ -1,6 +1,6 @@
open Qptypes
open Qputils
open Core.Std
open Core
type t_mo =
{ mo_tot_num : MO_number.t ;
@ -9,7 +9,7 @@ type t_mo =
mo_occ : MO_occ.t array;
mo_coef : (MO_coef.t array) array;
ao_md5 : MD5.t;
} with sexp
} [@@deriving sexp]
module Mo_basis : sig
type t = t_mo

6
ocaml/Input_nuclei_by_hand.ml
View File

@ -1,6 +1,6 @@
open Qptypes;;
open Qputils;;
open Core.Std;;
open Core;;
module Nuclei_by_hand : sig
type t =
@ -8,7 +8,7 @@ module Nuclei_by_hand : sig
nucl_label : Element.t array;
nucl_charge : Charge.t array;
nucl_coord : Point3d.t array;
} with sexp
} [@@deriving sexp]
;;
val read : unit -> t option
val write : t -> unit
@ -22,7 +22,7 @@ end = struct
nucl_label : Element.t array;
nucl_charge : Charge.t array;
nucl_coord : Point3d.t array;
} with sexp
} [@@deriving sexp]
;;
let get_default = Qpackage.get_ezfio_default "nuclei";;

24
ocaml/Io_ext.ml Normal file
View File

@ -0,0 +1,24 @@
let input_lines filename =
let in_channel =
open_in filename
in
let rec aux accu =
try
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"

26
ocaml/Long_basis.ml
View File

@ -1,7 +1,7 @@
open Core.Std;;
open Qptypes;;
open Qptypes
open Sexplib.Std
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
@ -10,14 +10,14 @@ let of_basis b =
begin
let new_accu =
Symmetry.Xyz.of_symmetry g.Gto.sym
|> List.rev_map ~f:(fun x-> (x,g,n))
|> List.rev_map (fun x-> (x,g,n))
in
do_work (new_accu@accu) tail
end
in
do_work [] b
|> List.rev
;;
let to_basis b =
let rec do_work accu = function
@ -25,7 +25,7 @@ let to_basis b =
| (s,g,n)::tail ->
let first_sym =
Symmetry.Xyz.of_symmetry g.Gto.sym
|> List.hd_exn
|> List.hd
in
let new_accu =
if ( s = first_sym ) then
@ -36,19 +36,19 @@ let to_basis b =
do_work new_accu tail
in
do_work [] b
;;
let to_string b =
let middle = List.map ~f:(fun (x,y,z) ->
"( "^((Int.to_string (Nucl_number.to_int z)))^", "^
let middle = List.map (fun (x,y,z) ->
"( "^((string_of_int (Nucl_number.to_int z)))^", "^
(Symmetry.Xyz.to_string x)^", "^(Gto.to_string y)
^" )"
) b
|> String.concat ~sep:",\n"
|> String.concat ",\n"
in "("^middle^")"
;;
include To_md5;;
include To_md5
let to_md5 = to_md5 sexp_of_t
;;

2
ocaml/Long_basis.mli
View File

@ -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 :

4
ocaml/MO_class.ml
View File

@ -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 =

2
ocaml/MO_class.mli
View File

@ -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 *)

4
ocaml/MO_label.ml
View File

@ -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

2
ocaml/MO_label.mli
View File

@ -5,7 +5,7 @@ type t =
| Localized
| Orthonormalized
| None
with sexp
[@@deriving sexp]
(** String representation *)
val to_string : t -> string

4
ocaml/Makefile
View File

@ -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

2
ocaml/Message.ml
View File

@ -1,4 +1,4 @@
open Core.Std
open Core
open Qptypes
(** New job : Request to create a new multi-tasked job *)

63
ocaml/Molecule.ml
View File

@ -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'
let lines =
match Io_ext.input_lines filename with
| natoms :: title :: rest ->
begin
try
if (int_of_string @@ String_ext.strip natoms) <= 0 then
raise XYZError
with
| _ -> raise XYZError
end;
String.concat "\n" rest
| _ -> failwith ("Problem in xyz file "^filename)
in
let result =
try
(int_of_string @@ String.strip x) > 0
with
| Failure "int_of_string" -> false
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

2
ocaml/Molecule.mli
View File

@ -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

4
ocaml/Multiplicity.ml
View File

@ -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 ;;

2
ocaml/Multiplicity.mli
View File

@ -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

4
ocaml/Point3d.ml
View File

@ -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
ocaml/Point3d.mli
View File

@ -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

2
ocaml/Primitive.mli
View File

@ -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

18
ocaml/Progress_bar.ml
View File

@ -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.) }

12
ocaml/Pseudo.ml
View File

@ -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;

2
ocaml/Qpackage.ml
View File

@ -1,4 +1,4 @@
open Core.Std;;
open Core;;
open Qptypes;;
open Qputils;;

22
ocaml/Qputils.ml
View File

@ -1,4 +1,4 @@
open Core.Std
open Sexplib
(*
let rec transpose = function
@ -14,12 +14,12 @@ let rec transpose = function
let input_to_sexp s =
let result =
String.split_lines s
|> List.filter ~f:(fun x->
(String.strip x) <> "")
|> List.map ~f:(fun x->
"("^(String.tr '=' ' ' x)^")")
|> String.concat
String_ext.split ~on:'\n' s
|> List.filter (fun x-> (String_ext.strip x) <> "")
|> List.map (fun x-> "("^
(Str.global_replace (Str.regexp "=") " " x)
^")")
|> String.concat ""
in
print_endline ("("^result^")");
"("^result^")"
@ -29,10 +29,10 @@ let rmdir dirname =
let rec remove_one dir =
Sys.chdir dir;
Sys.readdir "."
|> Array.iter ~f:(fun x ->
match (Sys.is_directory x, Sys.is_file x) with
| (`Yes, _) -> remove_one x
| (_, `Yes) -> Sys.remove x
|> Array.iter (fun x ->
match (Sys.is_directory x, Sys.file_exists x) with
| (true, _) -> remove_one x
| (_, true) -> Sys.remove x
| _ -> failwith ("Unable to remove file "^x^".")
);
Sys.chdir "..";

4
ocaml/README_qp_edit.rst
View File

@ -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";;

37
ocaml/Range.ml
View File

@ -1,4 +1,4 @@
open Core.Std;;
open Sexplib.Std
(* A range is a string of the type:
*
@ -12,14 +12,14 @@ 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
match String_ext.lsplit2 ~on:'-' r with
| Some (s, f) ->
begin
let start = Int.of_string s
and finish = Int.of_string f
let start = int_of_string s
and finish = int_of_string f
in
assert (start <= finish) ;
let rec do_work = function
@ -31,9 +31,9 @@ let expand_range r =
begin
match r with
| "" -> []
| _ -> [Int.of_string r]
| _ -> [int_of_string r]
end
;;
let of_string s =
match s.[0] with
@ -43,36 +43,37 @@ let of_string s =
assert (s.[0] = '[') ;
assert (s.[(String.length s)-1] = ']') ;
let s = String.sub s 1 ((String.length s) - 2) in
let l = String.split ~on:',' s in
let l = List.map ~f:expand_range l in
List.concat l |> List.dedup ~compare:Int.compare |> List.sort ~cmp:Int.compare
;;
let l = String_ext.split ~on:',' s in
let l = List.map expand_range l in
List.concat l
|> List.sort_uniq compare
let to_string l =
let rec do_work buf symbol = function
| [] -> buf
| a::([] as t) ->
do_work (buf^symbol^(Int.to_string a)) "" t
do_work (buf^symbol^(string_of_int a)) "" t
| a::(b::q as t) ->
if (b-a = 1) then
do_work buf "-" t
else
do_work (buf^symbol^(Int.to_string a)^","^(Int.to_string b)) "" t
do_work (buf^symbol^(string_of_int a)^","^(string_of_int b)) "" t
in
let result =
match l with
| [] ->
"[]"
| h::t ->
do_work ("["^(Int.to_string h)) "" l in
do_work ("["^(string_of_int h)) "" l in
(String.sub result 0 ((String.length result)))^"]"
;;
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 () ;
;;
List.iter (fun x -> Printf.printf "%d, " x) l ; print_newline () ;
to_string l |> print_string ; print_newline ();

2
ocaml/Range.mli
View File

@ -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 :

142
ocaml/String_ext.ml Normal file
View File

@ -0,0 +1,142 @@
include String
(** Split a string on a given character *)
let split ?(on=' ') str =
split_on_char 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 lsplit2 ?(on=' ') s =
try
Some (lsplit2_exn ~on s)
with
| Not_found -> None
let rsplit2 ?(on=' ') s =
try
Some (rsplit2_exn ~on s)
with
| Not_found -> None
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
let is_prefix ~prefix s =
let len =
String.length prefix
in
if len > String.length s then
false
else
prefix = String.sub s 0 len
let of_char c =
String.make 1 c

13
ocaml/Symmetry.ml
View File

@ -1,7 +1,7 @@
open Qptypes
open Core.Std
open Sexplib.Std
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.
@ -86,7 +86,7 @@ module Xyz = struct
let flush state accu number =
let n =
if (number = "") then 1
else (Int.of_string number)
else (int_of_string number)
in
match state with
| X -> { x= Positive_int.(of_int ( (to_int accu.x) +n));
@ -111,10 +111,9 @@ module Xyz = struct
| '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
| c::rest -> do_work state accu (number^(String_ext.of_char c)) rest
in
String.to_list_rev s
|> List.rev
String_ext.to_list s
|> do_work Null
{ x=Positive_int.of_int 0 ;
y=Positive_int.of_int 0 ;

4
ocaml/Symmetry.mli
View File

@ -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" *)

4
ocaml/TaskServer.ml
View File

@ -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

4
ocaml/To_md5.ml
View File

@ -1,5 +1,5 @@
open Core.Std;;
open Qptypes;;
open Qptypes
open Sexplib
let to_md5 sexp_of_t t =
sexp_of_t t

2
ocaml/_tags
View File

@ -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

2
ocaml/qp_basis_clean.ml
View File

@ -1,4 +1,4 @@
open Core.Std
open Core
let filenames =
let dir_name = Qpackage.root^"/data/basis/"

2
ocaml/qp_create_ezfio_from_xyz.ml
View File

@ -1,6 +1,6 @@
open Qputils
open Qptypes
open Core.Std
open Core
let spec =
let open Command.Spec in

2
ocaml/qp_create_guess.ml
View File

@ -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

2
ocaml/qp_print.ml
View File

@ -1,6 +1,6 @@
open Qputils;;
open Qptypes;;
open Core.Std;;
open Core;;
type input_action =
| Basis

2
ocaml/qp_print_basis.ml
View File

@ -1,4 +1,4 @@
open Core.Std
open Core
open Qptypes
let basis () =

4
ocaml/qp_run.ml
View File

@ -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

2
ocaml/qp_set_mo_class.ml
View File

@ -1,6 +1,6 @@
open Qputils
open Qptypes
open Core.Std
open Core
(*
* Command-line arguments

84
ocaml/qptypes_generator.ml
View File

@ -1,4 +1,10 @@
open Core.Std;;
let global_replace x =
x
|> Str.global_replace (Str.regexp "Float.to_string") "string_of_float"
|> Str.global_replace (Str.regexp "Float.of_string") "float_of_string"
|> Str.global_replace (Str.regexp "Int.to_string") "string_of_int"
|> Str.global_replace (Str.regexp "Int.of_string") "int_of_string"
|> Str.global_replace (Str.regexp "String.\(to\|of\)_string") ""
let input_data = "
* Positive_float : float
@ -118,8 +124,12 @@ let input_data = "
* MD5 : string
assert ((String.length x) = 32);
assert (String.fold x ~init:true ~f:(fun accu x ->
accu && (x < 'g')));
assert (
let a =
Array.init (String.length x) (fun i -> x.[i])
in
Array.fold_left (fun accu x -> accu && (x < 'g')) true a
);
* Rst_string : string
@ -127,7 +137,7 @@ let input_data = "
assert (x <> \"\") ;
"
;;
let input_ezfio = "
* MO_number : int
@ -156,18 +166,18 @@ let input_ezfio = "
More than 10 billion of determinants
"
;;
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 +192,7 @@ 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 +200,7 @@ end = struct
| Read
| Write
| None
with sexp
[@@deriving sexp]
let to_string = function
| Read -> \"Read\"
@ -206,62 +216,63 @@ end = struct
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
end
"
;;
let parse_input input=
print_string "open Core.Std;;\nlet warning = print_string;;\n" ;
print_string "open Sexplib.Std\nlet warning = print_string\n" ;
let rec parse result = function
| [] -> result
| ( "" , "" )::tail -> parse result tail
| ( t , text )::tail ->
let name,typ,params,params_val =
match String.split ~on:':' t with
match String_ext.split ~on:':' t with
| [name;typ] -> (name,typ,"","")
| name::typ::params::params_val -> (name,typ,params,
(String.concat params_val ~sep:":") )
(String.concat ":" params_val) )
| _ -> assert false
in
let typ = String.strip typ
and name = String.strip name in
let typ = String_ext.strip typ
and name = String_ext.strip name in
let typ_cap = String.capitalize typ in
let newstring = Printf.sprintf template name typ typ typ params_val typ typ
typ typ params ( String.strip text ) typ_cap
typ typ params ( String_ext.strip text ) typ_cap
in
List.rev (parse (newstring::result) tail )
in
String.split ~on:'*' input
|> List.map ~f:(String.lsplit2_exn ~on:'\n')
String_ext.split ~on:'*' input
|> List.map (String_ext.lsplit2_exn ~on:'\n')
|> parse []
|> String.concat
|> String.concat ""
|> global_replace
|> print_string
;;
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
@ -287,24 +298,24 @@ end = struct
end
end
"
;;
let parse_input_ezfio input=
let parse s =
match (
String.split s ~on:'\n'
|> List.filter ~f:(fun x -> (String.strip x) <> "")
String_ext.split s ~on:'\n'
|> List.filter (fun x -> (String_ext.strip x) <> "")
) with
| [] -> ""
| a :: b :: c :: d :: [] ->
begin
let (name,typ) = String.lsplit2_exn ~on:':' a
let (name,typ) = String_ext.lsplit2_exn ~on:':' a
and ezfio_func = b
and (min, max) = String.lsplit2_exn ~on:':' c
and (min, max) = String_ext.lsplit2_exn ~on:':' c
and msg = d
in
let (name, typ, ezfio_func, min, max, msg) =
match (List.map [ name ; typ ; ezfio_func ; min ; max ; msg ] ~f:String.strip) with
match List.map String_ext.strip [ name ; typ ; ezfio_func ; min ; max ; msg ] with
| [ name ; typ ; ezfio_func ; min ; max ; msg ] -> (name, typ, ezfio_func, min, max, msg)
| _ -> assert false
in
@ -314,16 +325,17 @@ let parse_input_ezfio input=
end
| _ -> failwith "Error in input_ezfio"
in
String.split ~on:'*' input
|> List.map ~f:parse
|> String.concat
String_ext.split ~on:'*' input
|> List.map parse
|> String.concat ""
|> global_replace
|> print_string
;;
let () =
parse_input input_data ;
parse_input_ezfio input_ezfio;
print_endline untouched;
print_endline untouched

2
ocaml/test_basis.ml
View File

@ -1,4 +1,4 @@
open Core.Std;;
open Core;;
open Qputils;;
open Qptypes;;

2
ocaml/test_gto.ml
View File

@ -1,4 +1,4 @@
open Core.Std
open Core
open Qptypes
let test_prim () =

2
ocaml/test_message.ml
View File

@ -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"

2
ocaml/test_molecule.ml
View File

@ -1,4 +1,4 @@
open Core.Std ;;
open Core ;;
open Qptypes ;;
let test_molecule () =

2
ocaml/test_pseudo.ml
View File

@ -1,4 +1,4 @@
open Core.Std
open Core
open Qputils
open Qptypes

2
ocaml/test_queuing_system.ml
View File

@ -1,4 +1,4 @@
open Core.Std
open Core
let () =

10
ocaml/test_symmetry.ml
View File

@ -1,15 +1,13 @@
open Core.Std
open Qputils
open Qptypes
open Symmetry
let () =
"SPDFGHIJKL"
|> String.to_list_rev
|> List.rev
|> List.map ~f:of_char
|> List.map ~f:Xyz.of_symmetry
|> List.iter ~f:(fun x -> List.iter x ~f:(fun y -> Xyz.to_string y |> print_endline) ;
|> String_ext.to_list
|> List.map of_char
|> List.map Xyz.of_symmetry
|> List.iter (fun x -> List.iter (fun y -> Xyz.to_string y |> print_endline) x ;
print_newline ();)

2
ocaml/test_task_server.ml
View File

@ -1,5 +1,3 @@
open Core
let () =
TaskServer.run 12345

2
scripts/ezfio_interface/ezfio_generate_ocaml.py
View File

@ -170,7 +170,7 @@ class EZFIO_ocaml(object):
else:
l_template += [" {0:<30} : {1};".format(p, t.ocaml)]
l_template += [" } with sexp",
l_template += [" } [@@deriving sexp]",
";;"]
# ~#~#~#~#~#~ #

2
scripts/ezfio_interface/qp_edit_template
View File

@ -4,7 +4,7 @@
open Qputils
open Qptypes
open Core.Std
open Core
(** Interactive editing of the input.