PTEROSOR/QuantumPackage
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Merge branch 'dev' into dev-lct

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This commit is contained in:
Emmanuel Giner 2019-03-21 00:14:17 +01:00
commit 24acfa6938
47 changed files with 661 additions and 906 deletions
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2
INSTALL.rst
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@ -291,7 +291,7 @@ OCaml
.. code:: bash
opam install ocamlbuild cryptokit zmq core sexplib ppx_sexp_conv ppx_deriving getopt
opam install ocamlbuild cryptokit zmq sexplib ppx_sexp_conv ppx_deriving getopt
EZFIO

2
configure vendored
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@ -60,7 +60,7 @@ function execute () {
}
PACKAGES=""
OCAML_PACKAGES="ocamlbuild cryptokit zmq core.v0.11.3 sexplib ppx_sexp_conv ppx_deriving getopt"
OCAML_PACKAGES="ocamlbuild cryptokit zmq sexplib ppx_sexp_conv ppx_deriving getopt"
while true ; do
case "$1" in

43
ocaml/.gitignore vendored
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@ -1,43 +0,0 @@
_build
element_create_db
element_create_db.byte
ezfio.ml
.gitignore
Git.ml
Input_ao_one_e_ints.ml
Input_ao_two_e_erf_ints.ml
Input_ao_two_e_ints.ml
Input_auto_generated.ml
Input_becke_numerical_grid.ml
Input_davidson.ml
Input_density_for_dft.ml
Input_determinants.ml
Input_dft_keywords.ml
Input_dft_mu_of_r.ml
Input_dressing.ml
Input_firth_order_der.ml
Input_ijkl_ints_in_r3.ml
Input_mo_one_e_ints.ml
Input_mo_two_e_erf_ints.ml
Input_mo_two_e_ints.ml
Input_mu_of_r_ints.ml
Input_mu_of_r.ml
Input_nuclei.ml
Input_perturbation.ml
Input_pseudo.ml
Input_rsdft_ecmd.ml
Input_scf_utils.ml
Input_two_body_dm.ml
qp_create_ezfio
qp_create_ezfio.native
qp_edit
qp_edit.ml
qp_edit.native
qp_print_basis
qp_print_basis.native
qp_run
qp_run.native
qp_set_mo_class
qp_set_mo_class.native
qptypes_generator.byte
Qptypes.ml

12
ocaml/Atom.ml
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@ -1,4 +1,4 @@
open Core
open Sexplib.Std
exception AtomError of string
@ -11,20 +11,20 @@ type t =
(** Read xyz coordinates of the atom *)
let of_string ~units s =
let buffer = s
|> String.split ~on:' '
|> List.filter ~f:(fun x -> x <> "")
|> String_ext.split ~on:' '
|> List.filter (fun x -> x <> "")
in
match buffer with
| [ name; charge; x; y; z ] ->
{ element = Element.of_string name ;
charge = Charge.of_string charge ;
coord = Point3d.of_string ~units (String.concat [x; y; z] ~sep:" ")
coord = Point3d.of_string ~units (String.concat " " [x; y; z] )
}
| [ name; x; y; z ] ->
let e = Element.of_string name in
{ element = e ;
charge = Element.to_charge e;
coord = Point3d.of_string ~units (String.concat [x; y; z] ~sep:" ")
coord = Point3d.of_string ~units (String.concat " " [x; y; z])
}
| _ -> raise (AtomError s)
@ -33,7 +33,7 @@ let to_string ~units a =
[ Element.to_string a.element ;
Charge.to_string a.charge ;
Point3d.to_string ~units a.coord ]
|> String.concat ~sep:" "
|> String.concat " "
let to_xyz a =

12
ocaml/Bit.ml
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@ -1,4 +1,4 @@
open Core;;
open Sexplib.Std
(*
Type for bits
@ -16,31 +16,31 @@ type t =
let to_string = function
| Zero -> "0"
| One -> "1"
;;
let and_operator a b =
match a, b with
| Zero, _ -> Zero
| _, Zero -> Zero
| _, _ -> One
;;
let or_operator a b =
match a, b with
| One, _ -> One
| _, One -> One
| _, _ -> Zero
;;
let xor_operator a b =
match a, b with
| One, Zero -> One
| Zero, One -> One
| _, _ -> Zero
;;
let not_operator = function
| One -> Zero
| Zero -> One
;;

27
ocaml/Bitlist.ml
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@ -1,5 +1,4 @@
open Qptypes
open Core
(*
Type for bits strings
@ -22,15 +21,15 @@ let to_string b =
let of_string ?(zero='0') ?(one='1') s =
String.to_list s
|> List.rev_map ~f:( fun c ->
List.init (String.length s) (String.get s)
|> List.rev_map ( fun c ->
if (c = zero) then Bit.Zero
else if (c = one) then Bit.One
else (failwith ("Error in bitstring ") ) )
let of_string_mp s =
String.to_list s
|> List.rev_map ~f:(function
List.init (String.length s) (String.get s)
|> List.rev_map (function
| '-' -> Bit.Zero
| '+' -> Bit.One
| _ -> failwith ("Error in bitstring ") )
@ -44,7 +43,7 @@ let of_int64 i =
| 1L -> Bit.One :: accu |> List.rev
| i ->
let b =
match (Int64.bit_and i 1L ) with
match (Int64.logand i 1L ) with
| 0L -> Bit.Zero
| 1L -> Bit.One
| _ -> raise (Failure "i land 1 not in (0,1)")
@ -70,18 +69,18 @@ let to_int64 l =
let rec do_work accu = function
| [] -> accu
| Bit.Zero::tail -> do_work Int64.(shift_left accu 1) tail
| Bit.One::tail -> do_work Int64.(bit_or one (shift_left accu 1)) tail
| Bit.One::tail -> do_work Int64.(logor one (shift_left accu 1)) tail
in do_work Int64.zero (List.rev l)
(* Create a bit list from a list of int64 *)
let of_int64_list l =
List.map ~f:of_int64 l
List.map of_int64 l
|> List.concat
(* Create a bit list from an array of int64 *)
let of_int64_array l =
Array.map ~f:of_int64 l
Array.map of_int64 l
|> Array.to_list
|> List.concat
@ -116,7 +115,7 @@ let to_int64_list l =
in
let l = do_work [] [] 1 l
in
List.rev_map ~f:to_int64 l
List.rev_map to_int64 l
(* Create an array of int64 from a bit list *)
let to_int64_array l =
@ -127,8 +126,8 @@ let to_int64_array l =
let of_mo_number_list n_int l =
let n_int = N_int_number.to_int n_int in
let length = n_int*64 in
let a = Array.create length (Bit.Zero) in
List.iter ~f:(fun i-> a.((MO_number.to_int i)-1) <- Bit.One) l;
let a = Array.make length (Bit.Zero) in
List.iter (fun i-> a.((MO_number.to_int i)-1) <- Bit.One) l;
Array.to_list a
@ -183,10 +182,10 @@ let not_operator b = logical_operator1 Bit.not_operator b
let popcnt b =
List.fold_left b ~init:0 ~f:(fun accu -> function
List.fold_left (fun accu -> function
| Bit.One -> accu+1
| Bit.Zero -> accu
)
) 0 b

8
ocaml/Charge.ml
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@ -1,14 +1,14 @@
open Core
open Sexplib.Std
type t = float [@@deriving sexp]
let of_float x = x
let of_int i = Float.of_int i
let of_string s = Float.of_string s
let of_int i = float_of_int i
let of_string s = float_of_string s
let to_float x = x
let to_int x = Float.to_int x
let to_int x = int_of_float x
let to_string x =
if x >= 0. then
Printf.sprintf "+%f" x

4
ocaml/Element.ml
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@ -1,4 +1,4 @@
open Core
open Sexplib.Std
open Qptypes
exception ElementError of string
@ -14,7 +14,7 @@ type t =
[@@deriving sexp]
let of_string x =
match (String.capitalize (String.lowercase x)) with
match (String.capitalize_ascii (String.lowercase_ascii x)) with
| "X" | "Dummy" -> X
| "H" | "Hydrogen" -> H
| "He" | "Helium" -> He

5
ocaml/Excitation.ml
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@ -1,4 +1,3 @@
open Core
open Qptypes
module Hole = struct
@ -56,7 +55,7 @@ let to_string = function
"," ;
(MO_class.to_string (Particle.to_mo_class p));
"]"]
|> String.concat ~sep:" "
|> String.concat " "
| Double (h1,p1,h2,p2) ->
[ "Double Exc. : [" ;
(MO_class.to_string (Hole.to_mo_class h1));
@ -67,6 +66,6 @@ let to_string = function
"," ;
(MO_class.to_string (Particle.to_mo_class p2));
"]"]
|> String.concat ~sep:" "
|> String.concat " "

9
ocaml/Gamess.ml
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@ -1,5 +1,6 @@
(** CONTRL *)
type scftyp_t = RHF | ROHF | MCSCF | NONE
let string_of_scftyp = function
| RHF -> "RHF"
| ROHF -> "ROHF"
@ -79,14 +80,14 @@ let read_until_found f tries =
begin
try
Some (read_mos x f)
with Caml.Not_found ->
with Not_found ->
None
end
) None tries
in
match result with
| Some mos -> mos
| None -> raise Caml.Not_found
| None -> raise Not_found
let read_natural_mos f =
let tries = [
@ -116,7 +117,7 @@ type guess_t =
| Natural of (int*string)
let guess_of_string s =
match String.lowercase s with
match String.lowercase_ascii s with
| "huckel" -> Huckel
| "hcore" -> Hcore
| _ -> raise (Invalid_argument "Bad MO guess")
@ -430,7 +431,7 @@ let create_cas_input ?(vecfile="") ~guess ~nstate s n_e n_a =
in
try
string_of_guess (Natural (norb, vecfile))
with Caml.Not_found ->
with Not_found ->
string_of_guess (Canonical (norb, vecfile))
end
;

6
ocaml/GaussianPrimitive.ml
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@ -1,10 +1,10 @@
open Qptypes
open Core
open Sexplib.Std
type t =
{ sym : Symmetry.t ;
{ sym : Symmetry.t ;
expo : AO_expo.t ;
} [@@deriving sexp]
} [@@deriving sexp]
let to_string p =
let { sym = s ; expo = e } = p in

44
ocaml/Generic_input_of_rst.ml
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@ -1,5 +1,6 @@
open Core;;
open Qptypes;;
open Sexplib
open Sexplib.Std
open Qptypes
let fail_msg str (ex,range) =
@ -15,25 +16,25 @@ let fail_msg str (ex,range) =
let start_pos = range.start_pos.offset
and end_pos = range.end_pos.offset
in
let pre = String.sub ~pos:0 ~len:start_pos str
and mid = String.sub ~pos:start_pos ~len:(end_pos-start_pos) str
and post = String.sub ~pos:(end_pos)
~len:((String.length str)-(end_pos)) str
let pre = String.sub str 0 start_pos
and mid = String.sub str start_pos (end_pos-start_pos)
and post = String.sub str (end_pos)
((String.length str)-(end_pos))
in
let str = Printf.sprintf "%s ## %s ## %s" pre mid post
in
let str = String.tr str ~target:'(' ~replacement:' '
|> String.split ~on:')'
|> List.map ~f:String.strip
|> List.filter ~f:(fun x ->
match String.substr_index x ~pos:0 ~pattern:"##" with
let str = String_ext.tr str ~target:'(' ~replacement:' '
|> String_ext.split ~on:')'
|> List.map String_ext.strip
|> List.filter (fun x ->
match String_ext.substr_index ~pos:0 ~pattern:"##" x with
| None -> false
| Some _ -> true
)
|> String.concat ~sep:"\n"
|> String.concat "\n"
in
Printf.eprintf "Error: (%s)\n\n %s\n\n" msg str;
;;
Printf.eprintf "Error: (%s)\n\n %s\n\n" msg str
let evaluate_sexp t_of_sexp s =
@ -41,20 +42,19 @@ let evaluate_sexp t_of_sexp s =
match ( Sexp.of_string_conv sexp t_of_sexp ) with
| `Result r -> Some r
| `Error ex -> ( fail_msg sexp ex; None)
;;
let of_rst t_of_sexp s =
Rst_string.to_string s
|> String.split ~on:'\n'
|> List.filter ~f:(fun line ->
String.contains line '=')
|> List.map ~f:(fun line ->
|> String_ext.split ~on:'\n'
|> List.filter (fun line -> String.contains line '=')
|> List.map (fun line ->
"("^(
String.tr line ~target:'=' ~replacement:' '
String_ext.tr ~target:'=' ~replacement:' ' line
)^")" )
|> String.concat
|> String.concat ""
|> evaluate_sexp t_of_sexp
;;

1
ocaml/Input.ml
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@ -1,6 +1,5 @@
open Qputils;;
open Qptypes;;
open Core;;
include Input_ao_basis;;
include Input_bitmasks;;

132
ocaml/Input_ao_basis.ml
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@ -1,6 +1,6 @@
open Qptypes;;
open Qputils;;
open Core;;
open Sexplib.Std;;
module Ao_basis : sig
type t =
@ -52,13 +52,13 @@ end = struct
let read_ao_prim_num () =
Ezfio.get_ao_basis_ao_prim_num ()
|> Ezfio.flattened_ezfio
|> Array.map ~f:AO_prim_number.of_int
|> Array.map AO_prim_number.of_int
;;
let read_ao_prim_num_max () =
Ezfio.get_ao_basis_ao_prim_num ()
|> Ezfio.flattened_ezfio
|> Array.fold ~f:(fun x y -> if x>y then x else y) ~init:0
|> Array.fold_left (fun x y -> if x>y then x else y) 0
|> AO_prim_number.of_int
;;
@ -66,42 +66,42 @@ end = struct
let nmax = Nucl_number.get_max () in
Ezfio.get_ao_basis_ao_nucl ()
|> Ezfio.flattened_ezfio
|> Array.map ~f:(fun x-> Nucl_number.of_int ~max:nmax x)
|> Array.map (fun x-> Nucl_number.of_int ~max:nmax x)
;;
let read_ao_power () =
let x = Ezfio.get_ao_basis_ao_power () in
let dim = x.Ezfio.dim.(0) in
let data = Ezfio.flattened_ezfio x in
let result = Array.init dim ~f:(fun x -> "") in
let result = Array.init dim (fun x -> "") in
for i=1 to dim
do
if (data.(i-1) > 0) then
result.(i-1) <- result.(i-1)^"x"^(Int.to_string data.(i-1));
result.(i-1) <- result.(i-1)^"x"^(string_of_int data.(i-1));
if (data.(dim+i-1) > 0) then
result.(i-1) <- result.(i-1)^"y"^(Int.to_string data.(dim+i-1));
result.(i-1) <- result.(i-1)^"y"^(string_of_int data.(dim+i-1));
if (data.(2*dim+i-1) > 0) then
result.(i-1) <- result.(i-1)^"z"^(Int.to_string data.(2*dim+i-1));
result.(i-1) <- result.(i-1)^"z"^(string_of_int data.(2*dim+i-1));
done;
Array.map ~f:Symmetry.Xyz.of_string result
Array.map Symmetry.Xyz.of_string result
;;
let read_ao_coef () =
Ezfio.get_ao_basis_ao_coef ()
|> Ezfio.flattened_ezfio
|> Array.map ~f:AO_coef.of_float
|> Array.map AO_coef.of_float
;;
let read_ao_expo () =
Ezfio.get_ao_basis_ao_expo ()
|> Ezfio.flattened_ezfio
|> Array.map ~f:AO_expo.of_float
|> Array.map AO_expo.of_float
;;
let read_ao_cartesian () =
if not (Ezfio.has_ao_basis_ao_cartesian ()) then
get_default "ao_cartesian"
|> Bool.of_string
|> bool_of_string
|> Ezfio.set_ao_basis_ao_cartesian
;
Ezfio.get_ao_basis_ao_cartesian ()
@ -110,10 +110,10 @@ end = struct
let to_long_basis b =
let ao_num = AO_number.to_int b.ao_num in
let gto_array = Array.init (AO_number.to_int b.ao_num)
~f:(fun i ->
(fun i ->
let s = Symmetry.Xyz.to_symmetry b.ao_power.(i) in
let ao_prim_num = AO_prim_number.to_int b.ao_prim_num.(i) in
let prims = List.init ao_prim_num ~f:(fun j ->
let prims = List.init ao_prim_num (fun j ->
let prim = { GaussianPrimitive.sym = s ;
GaussianPrimitive.expo = b.ao_expo.(ao_num*j+i)
}
@ -178,14 +178,14 @@ end = struct
in
let ao_prim_num =
Array.to_list ao_prim_num
|> List.map ~f:AO_prim_number.to_int
|> List.map AO_prim_number.to_int
in
Ezfio.set_ao_basis_ao_prim_num (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| ao_num |] ~data:ao_prim_num) ;
let ao_nucl =
Array.to_list ao_nucl
|> List.map ~f:Nucl_number.to_int
|> List.map Nucl_number.to_int
in
Ezfio.set_ao_basis_ao_nucl(Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| ao_num |] ~data:ao_nucl) ;
@ -193,9 +193,9 @@ end = struct
let ao_power =
let l = Array.to_list ao_power in
List.concat [
(List.map ~f:(fun a -> Positive_int.to_int a.Symmetry.Xyz.x) l) ;
(List.map ~f:(fun a -> Positive_int.to_int a.Symmetry.Xyz.y) l) ;
(List.map ~f:(fun a -> Positive_int.to_int a.Symmetry.Xyz.z) l) ]
(List.map (fun a -> Positive_int.to_int a.Symmetry.Xyz.x) l) ;
(List.map (fun a -> Positive_int.to_int a.Symmetry.Xyz.y) l) ;
(List.map (fun a -> Positive_int.to_int a.Symmetry.Xyz.z) l) ]
in
Ezfio.set_ao_basis_ao_power(Ezfio.ezfio_array_of_list
~rank:2 ~dim:[| ao_num ; 3 |] ~data:ao_power) ;
@ -204,14 +204,14 @@ end = struct
let ao_coef =
Array.to_list ao_coef
|> List.map ~f:AO_coef.to_float
|> List.map AO_coef.to_float
in
Ezfio.set_ao_basis_ao_coef(Ezfio.ezfio_array_of_list
~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_coef) ;
let ao_expo =
Array.to_list ao_expo
|> List.map ~f:AO_expo.to_float
|> List.map AO_expo.to_float
in
Ezfio.set_ao_basis_ao_expo(Ezfio.ezfio_array_of_list
~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_expo) ;
@ -271,58 +271,56 @@ end = struct
| Some (s', g', n') ->
if s <> s' || n <> n' then find2 (s,g,n) a (i+1)
else
let lc = List.map ~f:(fun (prim, _) -> prim) g.Gto.lc
and lc' = List.map ~f:(fun (prim, _) -> prim) g'.Gto.lc
let lc = List.map (fun (prim, _) -> prim) g.Gto.lc
and lc' = List.map (fun (prim, _) -> prim) g'.Gto.lc
in
if lc <> lc' then find2 (s,g,n) a (i+1) else (a.(i) <- None ; i)
in
find x a 0
in
let search_array = Array.map ~f:(fun i -> Some i) unordered_basis in
Array.map ~f:(fun x -> find x search_array) ordered_basis
let search_array = Array.map (fun i -> Some i) unordered_basis in
Array.map (fun x -> find x search_array) ordered_basis
;;
let of_long_basis long_basis name ao_cartesian =
let ao_num = List.length long_basis |> AO_number.of_int in
let ao_prim_num =
List.map long_basis ~f:(fun (_,g,_) -> List.length g.Gto.lc
|> AO_prim_number.of_int )
List.map (fun (_,g,_) -> List.length g.Gto.lc
|> AO_prim_number.of_int ) long_basis
|> Array.of_list
and ao_nucl =
List.map long_basis ~f:(fun (_,_,n) -> n)
List.map (fun (_,_,n) -> n) long_basis
|> Array.of_list
and ao_power =
List.map ~f:(fun (x,_,_) -> x) long_basis
List.map (fun (x,_,_) -> x) long_basis
|> Array.of_list
in
let ao_prim_num_max = Array.fold ~init:0 ~f:(fun s x ->
if AO_prim_number.to_int x > s then AO_prim_number.to_int x else s)
let ao_prim_num_max = Array.fold_left (fun s x ->
if AO_prim_number.to_int x > s then AO_prim_number.to_int x else s) 0
ao_prim_num
|> AO_prim_number.of_int
in
let gtos =
List.map long_basis ~f:(fun (_,x,_) -> x)
List.map (fun (_,x,_) -> x) long_basis
in
let create_expo_coef ec =
let coefs =
begin match ec with
| `Coefs -> List.map gtos ~f:(fun x->
List.map x.Gto.lc ~f:(fun (_,coef) -> AO_coef.to_float coef) )
| `Expos -> List.map gtos ~f:(fun x->
List.map x.Gto.lc ~f:(fun (prim,_) -> AO_expo.to_float
prim.GaussianPrimitive.expo) )
| `Coefs -> List.map (fun x->
List.map (fun (_,coef) -> AO_coef.to_float coef) x.Gto.lc ) gtos
| `Expos -> List.map (fun x->
List.map (fun (prim,_) -> AO_expo.to_float
prim.GaussianPrimitive.expo) x.Gto.lc ) gtos
end
in
let rec get_n n accu = function
| [] -> List.rev accu
| h::tail ->
let y =
begin match List.nth h n with
| Some x -> x
| None -> 0.
end
try List.nth h n
with _ -> 0.
in
get_n n (y::accu) tail
in
@ -335,10 +333,10 @@ end = struct
let ao_coef = create_expo_coef `Coefs
|> Array.of_list
|> Array.map ~f:AO_coef.of_float
|> Array.map AO_coef.of_float
and ao_expo = create_expo_coef `Expos
|> Array.of_list
|> Array.map ~f:AO_expo.of_float
|> Array.map AO_expo.of_float
in
{ ao_basis = name ;
ao_num ; ao_prim_num ; ao_prim_num_max ; ao_nucl ;
@ -347,17 +345,17 @@ end = struct
let reorder b =
let order = ordering b in
let f a = Array.init (Array.length a) ~f:(fun i -> a.(order.(i))) in
let f a = Array.init (Array.length a) (fun i -> a.(order.(i))) in
let ao_prim_num_max = AO_prim_number.to_int b.ao_prim_num_max
and ao_num = AO_number.to_int b.ao_num in
let ao_coef =
Array.init ao_prim_num_max ~f:(fun i ->
f @@ Array.init ao_num ~f:(fun j -> b.ao_coef.(i*ao_num + j) )
Array.init ao_prim_num_max (fun i ->
f @@ Array.init ao_num (fun j -> b.ao_coef.(i*ao_num + j) )
) |> Array.to_list |> Array.concat
in
let ao_expo =
Array.init ao_prim_num_max ~f:(fun i ->
f @@ Array.init ao_num ~f:(fun j -> b.ao_expo.(i*ao_num + j) )
Array.init ao_prim_num_max (fun i ->
f @@ Array.init ao_num (fun j -> b.ao_expo.(i*ao_num + j) )
) |> Array.to_list |> Array.concat
in
{ b with
@ -373,7 +371,7 @@ end = struct
let to_rst b =
let print_sym =
let l = List.init (Array.length b.ao_power) ~f:(
let l = List.init (Array.length b.ao_power) (
fun i -> ( (i+1),b.ao_nucl.(i),b.ao_power.(i) ) )
in
let rec do_work = function
@ -383,7 +381,7 @@ end = struct
(Symmetry.Xyz.to_string x)
)::(do_work tail)
in do_work l
|> String.concat
|> String.concat ""
in
let short_basis = to_basis b in
@ -408,11 +406,11 @@ Basis set (read-only) ::
======= ========= ===========
" (AO_basis_name.to_string b.ao_basis)
(Bool.to_string b.ao_cartesian)
(string_of_bool b.ao_cartesian)
(Basis.to_string short_basis
|> String.split ~on:'\n'
|> List.map ~f:(fun x-> " "^x)
|> String.concat ~sep:"\n"
|> String_ext.split ~on:'\n'
|> List.map (fun x-> " "^x)
|> String.concat "\n"
) print_sym
|> Rst_string.of_string
@ -420,14 +418,14 @@ Basis set (read-only) ::
let read_rst s =
let s = Rst_string.to_string s
|> String.split ~on:'\n'
|> String_ext.split ~on:'\n'
in
let rec extract_basis = function
| [] -> failwith "Error in basis set"
| line :: tail ->
let line = String.strip line in
let line = String.trim line in
if line = "Basis set (read-only) ::" then
String.concat tail ~sep:"\n"
String.concat "\n" tail
else
extract_basis tail
in
@ -450,17 +448,17 @@ md5 = %s
(AO_basis_name.to_string b.ao_basis)
(AO_number.to_string b.ao_num)
(b.ao_prim_num |> Array.to_list |> List.map
~f:(AO_prim_number.to_string) |> String.concat ~sep:", " )
(AO_prim_number.to_string) |> String.concat ", " )
(AO_prim_number.to_string b.ao_prim_num_max)
(b.ao_nucl |> Array.to_list |> List.map ~f:Nucl_number.to_string |>
String.concat ~sep:", ")
(b.ao_power |> Array.to_list |> List.map ~f:(fun x->
"("^(Symmetry.Xyz.to_string x)^")" )|> String.concat ~sep:", ")
(b.ao_coef |> Array.to_list |> List.map ~f:AO_coef.to_string
|> String.concat ~sep:", ")
(b.ao_expo |> Array.to_list |> List.map ~f:AO_expo.to_string
|> String.concat ~sep:", ")
(b.ao_cartesian |> Bool.to_string)
(b.ao_nucl |> Array.to_list |> List.map Nucl_number.to_string |>
String.concat ", ")
(b.ao_power |> Array.to_list |> List.map (fun x->
"("^(Symmetry.Xyz.to_string x)^")" )|> String.concat ", ")
(b.ao_coef |> Array.to_list |> List.map AO_coef.to_string
|> String.concat ", ")
(b.ao_expo |> Array.to_list |> List.map AO_expo.to_string
|> String.concat ", ")
(b.ao_cartesian |> string_of_bool)
(to_md5 b |> MD5.to_string )
;;

228
ocaml/Input_bi_integrals.ml
View File

@ -1,228 +0,0 @@
open Qptypes;;
open Qputils;;
open Core;;
module Bielec_integrals : sig
type t =
{ read_ao_integrals : bool;
read_mo_integrals : bool;
write_ao_integrals : bool;
write_mo_integrals : bool;
threshold_ao : Threshold.t;
threshold_mo : Threshold.t;
direct : bool;
} [@@deriving sexp]
;;
val read : unit -> t option
val write : t -> unit
val to_string : t -> string
val to_rst : t -> Rst_string.t
val of_rst : Rst_string.t -> t option
end = struct
type t =
{ read_ao_integrals : bool;
read_mo_integrals : bool;
write_ao_integrals : bool;
write_mo_integrals : bool;
threshold_ao : Threshold.t;
threshold_mo : Threshold.t;
direct : bool;
} [@@deriving sexp]
;;
let get_default = Qpackage.get_ezfio_default "bielec_integrals";;
let read_read_ao_integrals () =
if not (Ezfio.has_bielec_integrals_read_ao_integrals ()) then
get_default "read_ao_integrals"
|> Bool.of_string
|> Ezfio.set_bielec_integrals_read_ao_integrals
;
Ezfio.get_bielec_integrals_read_ao_integrals ()
;;
let write_read_ao_integrals =
Ezfio.set_bielec_integrals_read_ao_integrals
;;
let read_read_mo_integrals () =
if not (Ezfio.has_bielec_integrals_read_mo_integrals ()) then
get_default "read_mo_integrals"
|> Bool.of_string
|> Ezfio.set_bielec_integrals_read_mo_integrals
;
Ezfio.get_bielec_integrals_read_mo_integrals ()
;;
let write_read_mo_integrals =
Ezfio.set_bielec_integrals_read_mo_integrals
;;
let read_write_ao_integrals () =
if not (Ezfio.has_bielec_integrals_write_ao_integrals ()) then
get_default "write_ao_integrals"
|> Bool.of_string
|> Ezfio.set_bielec_integrals_write_ao_integrals
;
Ezfio.get_bielec_integrals_write_ao_integrals ()
;;
let write_write_ao_integrals =
Ezfio.set_bielec_integrals_write_ao_integrals
;;
let read_write_mo_integrals () =
if not (Ezfio.has_bielec_integrals_write_mo_integrals ()) then
get_default "write_mo_integrals"
|> Bool.of_string
|> Ezfio.set_bielec_integrals_write_mo_integrals
;
Ezfio.get_bielec_integrals_write_mo_integrals ()
;;
let write_write_mo_integrals =
Ezfio.set_bielec_integrals_write_mo_integrals
;;
let read_direct () =
if not (Ezfio.has_bielec_integrals_direct ()) then
get_default "direct"
|> Bool.of_string
|> Ezfio.set_bielec_integrals_direct
;
Ezfio.get_bielec_integrals_direct ()
;;
let write_direct =
Ezfio.set_bielec_integrals_direct
;;
let read_threshold_ao () =
if not (Ezfio.has_bielec_integrals_threshold_ao ()) then
get_default "threshold_ao"
|> Float.of_string
|> Ezfio.set_bielec_integrals_threshold_ao
;
Ezfio.get_bielec_integrals_threshold_ao ()
|> Threshold.of_float
;;
let write_threshold_ao t =
Threshold.to_float t
|> Ezfio.set_bielec_integrals_threshold_ao
;;
let read_threshold_mo () =
if not (Ezfio.has_bielec_integrals_threshold_mo ()) then
get_default "threshold_mo"
|> Float.of_string
|> Ezfio.set_bielec_integrals_threshold_mo
;
Ezfio.get_bielec_integrals_threshold_mo ()
|> Threshold.of_float
;;
let write_threshold_mo t =
Threshold.to_float t
|> Ezfio.set_bielec_integrals_threshold_mo
;;
let read ()=
let result =
{ read_ao_integrals = read_read_ao_integrals();
read_mo_integrals = read_read_mo_integrals () ;
write_ao_integrals = read_write_ao_integrals ();
write_mo_integrals = read_write_mo_integrals ();
threshold_ao = read_threshold_ao ();
threshold_mo = read_threshold_mo ();
direct = read_direct () ;
} in
if (result.read_ao_integrals &&
result.write_ao_integrals) then
failwith "Read and Write AO integrals are both true.";
if (result.read_mo_integrals &&
result.write_mo_integrals) then
failwith "Read and Write MO integrals are both true.";
Some result
;;
let write b =
if (b.read_ao_integrals &&
b.write_ao_integrals) then
failwith "Read and Write AO integrals are both true.";
if (b.read_mo_integrals &&
b.write_mo_integrals) then
failwith "Read and Write MO integrals are both true.";
write_read_ao_integrals b.read_ao_integrals;
write_read_mo_integrals b.read_mo_integrals;
write_write_ao_integrals b.write_ao_integrals ;
write_write_mo_integrals b.write_mo_integrals ;
write_threshold_ao b.threshold_ao;
write_threshold_mo b.threshold_mo;
write_direct b.direct;
;;
let to_string b =
Printf.sprintf "
read_ao_integrals = %s
read_mo_integrals = %s
write_ao_integrals = %s
write_mo_integrals = %s
threshold_ao = %s
threshold_mo = %s
direct = %s
"
(Bool.to_string b.read_ao_integrals)
(Bool.to_string b.read_mo_integrals)
(Bool.to_string b.write_ao_integrals)
(Bool.to_string b.write_mo_integrals)
(Threshold.to_string b.threshold_ao)
(Threshold.to_string b.threshold_mo)
(Bool.to_string b.direct)
;;
let to_rst b =
Printf.sprintf "
Read AO/MO integrals from disk ::
read_ao_integrals = %s
read_mo_integrals = %s
Write AO/MO integrals to disk ::
write_ao_integrals = %s
write_mo_integrals = %s
Thresholds on integrals ::
threshold_ao = %s
threshold_mo = %s
Direct calculation of integrals ::
direct = %s
"
(Bool.to_string b.read_ao_integrals)
(Bool.to_string b.read_mo_integrals)
(Bool.to_string b.write_ao_integrals)
(Bool.to_string b.write_mo_integrals)
(Threshold.to_string b.threshold_ao)
(Threshold.to_string b.threshold_mo)
(Bool.to_string b.direct)
|> Rst_string.of_string
;;
include Generic_input_of_rst;;
let of_rst = of_rst t_of_sexp;;
end

20
ocaml/Input_bitmasks.ml
View File

@ -1,6 +1,6 @@
open Qptypes;;
open Qputils;;
open Core;;
open Qptypes
open Qputils
open Sexplib.Std
module Bitmasks : sig
type t =
@ -59,7 +59,7 @@ end = struct
let full_mask n_int =
let range = "[1-"^
(Int.to_string (Ezfio.get_mo_basis_mo_num ()))^"]"
(string_of_int (Ezfio.get_mo_basis_mo_num ()))^"]"
in
MO_class.create_active range
|> MO_class.to_bitlist n_int
@ -75,7 +75,7 @@ end = struct
full_mask n_int
in
let result = [ act ; act ; act ; act ; act ; act ]
|> List.map ~f:(fun x ->
|> List.map (fun x ->
let y = Bitlist.to_int64_list x in y@y )
|> List.concat
in
@ -107,7 +107,7 @@ end = struct
full_mask n_int
in
let result = [ act ; act ]
|> List.map ~f:(fun x ->
|> List.map (fun x ->
let y = Bitlist.to_int64_list x in y@y )
|> List.concat
in
@ -147,12 +147,12 @@ cas = %s
(Bit_kind.to_string b.bit_kind)
(Bitmask_number.to_string b.n_mask_gen)
(Array.to_list b.generators
|> List.map ~f:(fun x-> Int64.to_string x)
|> String.concat ~sep:", ")
|> List.map (fun x-> Int64.to_string x)
|> String.concat ", ")
(Bitmask_number.to_string b.n_mask_cas)
(Array.to_list b.cas
|> List.map ~f:(fun x-> Int64.to_string x)
|> String.concat ~sep:", ")
|> List.map (fun x-> Int64.to_string x)
|> String.concat ", ")
end

103
ocaml/Input_determinants_by_hand.ml
View File

@ -1,6 +1,6 @@
open Qptypes;;
open Qputils;;
open Core;;
open Sexplib.Std;;
module Determinants_by_hand : sig
type t =
@ -112,7 +112,7 @@ end = struct
begin
Ezfio.set_determinants_n_states n_states;
let data =
Array.create n_states 1.
Array.make n_states 1.
|> Array.to_list
in
Ezfio.ezfio_array_of_list ~rank:1 ~dim:[| n_states |] ~data
@ -126,7 +126,7 @@ end = struct
|> States_number.to_int
in
let data =
Array.map ~f:Positive_float.to_float data
Array.map Positive_float.to_float data
|> Array.to_list
in
Ezfio.ezfio_array_of_list ~rank:1 ~dim:[| n_states |] ~data
@ -142,21 +142,21 @@ end = struct
begin
let data =
Array.init n_states (fun _ -> 1./.(float_of_int n_states))
|> Array.map ~f:Positive_float.of_float
|> Array.map Positive_float.of_float
in
write_state_average_weight data
end;
let result =
Ezfio.get_determinants_state_average_weight ()
|> Ezfio.flattened_ezfio
|> Array.map ~f:Positive_float.of_float
|> Array.map Positive_float.of_float
in
if Array.length result = n_states then
result
else
let data =
Array.init n_states (fun _ -> 1./.(float_of_int n_states))
|> Array.map ~f:Positive_float.of_float
|> Array.map Positive_float.of_float
in
(write_state_average_weight data; data)
;;
@ -189,18 +189,18 @@ end = struct
|> States_number.to_int
in
Ezfio.ezfio_array_of_list ~rank:2 ~dim:[| 1 ; n_states |]
~data:(List.init n_states ~f:(fun i -> if (i=0) then 1. else 0. ))
~data:(List.init n_states (fun i -> if (i=0) then 1. else 0. ))
|> Ezfio.set_determinants_psi_coef
end;
Ezfio.get_determinants_psi_coef ()
|> Ezfio.flattened_ezfio
|> Array.map ~f:Det_coef.of_float
|> Array.map Det_coef.of_float
;;
let write_psi_coef ~n_det ~n_states c =
let n_det = Det_number.to_int n_det
and c = Array.to_list c
|> List.map ~f:Det_coef.to_float
|> List.map Det_coef.to_float
and n_states =
States_number.to_int n_states
in
@ -242,9 +242,9 @@ end = struct
assert (n_int = dim.(0));
assert (dim.(1) = 2);
assert (dim.(2) = (Det_number.to_int (read_n_det ())));
List.init dim.(2) ~f:(fun i ->
Array.sub ~pos:(2*n_int*i) ~len:(2*n_int) data)
|> List.map ~f:(Determinant.of_int64_array
List.init dim.(2) (fun i ->
Array.sub data (2*n_int*i) (2*n_int) )
|> List.map (Determinant.of_int64_array
~n_int:(N_int_number.of_int n_int)
~alpha:n_alpha ~beta:n_beta )
|> Array.of_list
@ -332,18 +332,19 @@ end = struct
else
"0."
)
|> String.concat_array ~sep:"\t"
|> Array.to_list |> String.concat "\t"
in
Array.init ndet ~f:(fun i ->
Array.init ndet (fun i ->
Printf.sprintf " %s\n%s\n"
(coefs_string i)
(Determinant.to_string ~mo_num:mo_num b.psi_det.(i)
|> String.split ~on:'\n'
|> List.map ~f:(fun x -> " "^x)
|> String.concat ~sep:"\n"
|> String_ext.split ~on:'\n'
|> List.map (fun x -> " "^x)
|> String.concat "\n"
)
)
|> String.concat_array ~sep:"\n"
|> Array.to_list
|> String.concat "\n"
in
Printf.sprintf "
Force the selected wave function to be an eigenfunction of S^2.
@ -365,7 +366,7 @@ Determinants ::
"
(b.expected_s2 |> Positive_float.to_string)
(b.n_det |> Det_number.to_string)
(b.state_average_weight |> Array.to_list |> List.map ~f:Positive_float.to_string |> String.concat ~sep:"\t")
(b.state_average_weight |> Array.to_list |> List.map Positive_float.to_string |> String.concat "\t")
det_text
|> Rst_string.of_string
;;
@ -388,11 +389,11 @@ psi_det = %s
(b.n_det |> Det_number.to_string)
(b.n_states |> States_number.to_string)
(b.expected_s2 |> Positive_float.to_string)
(b.state_average_weight |> Array.to_list |> List.map ~f:Positive_float.to_string |> String.concat ~sep:",")
(b.psi_coef |> Array.to_list |> List.map ~f:Det_coef.to_string
|> String.concat ~sep:", ")
(b.psi_det |> Array.to_list |> List.map ~f:(Determinant.to_string
~mo_num) |> String.concat ~sep:"\n\n")
(b.state_average_weight |> Array.to_list |> List.map Positive_float.to_string |> String.concat ",")
(b.psi_coef |> Array.to_list |> List.map Det_coef.to_string
|> String.concat ", ")
(b.psi_det |> Array.to_list |> List.map (Determinant.to_string
~mo_num) |> String.concat "\n\n")
;;
let of_rst r =
@ -400,33 +401,36 @@ psi_det = %s
in
(* Split into header and determinants data *)
let idx = String.substr_index_exn r ~pos:0 ~pattern:"\nDeterminants"
let idx =
match String_ext.substr_index r ~pos:0 ~pattern:"\nDeterminants" with
| Some x -> x
| None -> assert false
in
let (header, dets) =
(String.prefix r idx, String.suffix r ((String.length r)-idx) )
(String.sub r 0 idx, String.sub r idx (String.length r - idx) )
in
(* Handle header *)
let header = r
|> String.split ~on:'\n'
|> List.filter ~f:(fun line ->
|> String_ext.split ~on:'\n'
|> List.filter (fun line ->
if (line = "") then
false
else
( (String.contains line '=') && (line.[0] = ' ') )
)
|> List.map ~f:(fun line ->
|> List.map (fun line ->
"("^(
String.tr line ~target:'=' ~replacement:' '
|> String.strip
String_ext.tr line ~target:'=' ~replacement:' '
|> String.trim
)^")" )
|> String.concat
|> String.concat ""
in
(* Handle determinant coefs *)
let dets = match ( dets
|> String.split ~on:'\n'
|> List.map ~f:(String.strip)
|> String_ext.split ~on:'\n'
|> List.map String.trim
) with
| _::lines -> lines
| _ -> failwith "Error in determinants"
@ -438,8 +442,8 @@ psi_det = %s
| ""::""::tail -> read_coefs accu tail
| ""::c::tail ->
let c =
String.split ~on:'\t' c
|> List.map ~f:(fun x -> Det_coef.of_float (Float.of_string x))
String_ext.split ~on:'\t' c
|> List.map (fun x -> Det_coef.of_float (Float.of_string x))
|> Array.of_list
in
read_coefs (c::accu) tail
@ -450,15 +454,15 @@ psi_det = %s
read_coefs [] dets
in
let nstates =
List.hd_exn buffer
List.hd buffer
|> Array.length
in
let extract_state i =
let i =
i-1
in
List.map ~f:(fun x -> Det_coef.to_string x.(i)) buffer
|> String.concat ~sep:" "
List.map (fun x -> Det_coef.to_string x.(i)) buffer
|> String.concat " "
in
let rec build_result = function
| 1 -> extract_state 1
@ -492,21 +496,12 @@ psi_det = %s
| _::tail -> read_dets accu tail
in
let dets =
List.map ~f:String.rev dets
List.map String_ext.rev dets
in
let sze =
List.fold ~init:0 ~f:(fun accu x -> accu + (String.length x)) dets
in
let control =
Gc.get ()
in
Gc.tune ~minor_heap_size:(sze) ~space_overhead:(sze/10)
~max_overhead:100000 ~major_heap_increment:(sze/10) ();
let a =
read_dets [] dets
|> String.concat
|> String.concat ""
in
Gc.set control;
"(psi_det ("^a^"))"
in
@ -520,7 +515,7 @@ psi_det = %s
Printf.sprintf "(n_states %d)" (States_number.to_int @@ read_n_states ())
in
let s =
String.concat [ header ; bitkind ; n_int ; n_states ; psi_coef ; psi_det]
String.concat "" [ header ; bitkind ; n_int ; n_states ; psi_coef ; psi_det]
in
@ -603,16 +598,16 @@ psi_det = %s
States_number.to_int det.n_states
in
Range.to_int_list range
|> List.iter ~f:(fun istate ->
|> List.iter (fun istate ->
if istate > n_states then
failwith "State to extract should not be greater than n_states")
;
let sorted_list =
Range.to_int_list range
|> List.sort ~compare
|> List.sort compare
in
let state_shift = ref 0 in
List.iter ~f:(fun istate ->
List.iter (fun istate ->
let j =
istate - 1
in

6
ocaml/Input_electrons.ml
View File

@ -1,6 +1,6 @@
open Qptypes;;
open Qputils;;
open Core;;
open Qptypes
open Qputils
open Sexplib.Std
module Electrons : sig
type t =

55
ocaml/Input_mo_basis.ml
View File

@ -1,6 +1,6 @@
open Qptypes
open Qputils
open Core
open Sexplib.Std
module Mo_basis : sig
@ -38,9 +38,10 @@ end = struct
let reorder b ordering =
{ b with mo_coef =
Array.map ~f:(fun mo ->
Array.init ~f:(fun i -> mo.(ordering.(i))) (Array.length mo) )
b.mo_coef
Array.map (fun mo ->
Array.init (Array.length mo)
(fun i -> mo.(ordering.(i)))
) b.mo_coef
}
let read_ao_md5 () =
@ -73,7 +74,7 @@ end = struct
begin
let mo_num = MO_number.to_int (read_mo_num ()) in
let data =
Array.init mo_num ~f:(fun _ -> MO_class.(to_string (Active [])))
Array.init mo_num (fun _ -> MO_class.(to_string (Active [])))
|> Array.to_list
in
Ezfio.ezfio_array_of_list ~rank:1
@ -81,7 +82,7 @@ end = struct
|> Ezfio.set_mo_basis_mo_class
end;
Ezfio.flattened_ezfio (Ezfio.get_mo_basis_mo_class () )
|> Array.map ~f:MO_class.of_string
|> Array.map MO_class.of_string
let read_mo_occ () =
@ -90,7 +91,7 @@ end = struct
let elec_alpha_num = Ezfio.get_electrons_elec_alpha_num ()
and elec_beta_num = Ezfio.get_electrons_elec_beta_num ()
and mo_num = MO_number.to_int (read_mo_num ()) in
let data = Array.init mo_num ~f:(fun i ->
let data = Array.init mo_num (fun i ->
if (i<elec_beta_num) then 2.
else if (i < elec_alpha_num) then 1.
else 0.) |> Array.to_list in
@ -99,18 +100,18 @@ end = struct
|> Ezfio.set_mo_basis_mo_occ
end;
Ezfio.flattened_ezfio (Ezfio.get_mo_basis_mo_occ () )
|> Array.map ~f:MO_occ.of_float
|> Array.map MO_occ.of_float
let read_mo_coef () =
let a = Ezfio.get_mo_basis_mo_coef ()
|> Ezfio.flattened_ezfio
|> Array.map ~f:MO_coef.of_float
|> Array.map MO_coef.of_float
in
let mo_num = read_mo_num () |> MO_number.to_int in
let ao_num = (Array.length a)/mo_num in
Array.init mo_num ~f:(fun j ->
Array.sub ~pos:(j*ao_num) ~len:(ao_num) a
Array.init mo_num (fun j ->
Array.sub a (j*ao_num) (ao_num)
)
@ -136,14 +137,14 @@ end = struct
| 1 ->
let header = [ Printf.sprintf " #%15d" (imin+1) ; ] in
let new_lines =
List.init ao_num ~f:(fun i ->
List.init ao_num (fun i ->
Printf.sprintf " %3d %15.10f " (i+1)
(MO_coef.to_float mo_coef.(imin ).(i)) )
in header @ new_lines
| 2 ->
let header = [ Printf.sprintf " #%15d %15d" (imin+1) (imin+2) ; ] in
let new_lines =
List.init ao_num ~f:(fun i ->
List.init ao_num (fun i ->
Printf.sprintf " %3d %15.10f %15.10f" (i+1)
(MO_coef.to_float mo_coef.(imin ).(i))
(MO_coef.to_float mo_coef.(imin+1).(i)) )
@ -152,7 +153,7 @@ end = struct
let header = [ Printf.sprintf " #%15d %15d %15d"
(imin+1) (imin+2) (imin+3); ] in
let new_lines =
List.init ao_num ~f:(fun i ->
List.init ao_num (fun i ->
Printf.sprintf " %3d %15.10f %15.10f %15.10f" (i+1)
(MO_coef.to_float mo_coef.(imin ).(i))
(MO_coef.to_float mo_coef.(imin+1).(i))
@ -162,7 +163,7 @@ end = struct
let header = [ Printf.sprintf " #%15d %15d %15d %15d"
(imin+1) (imin+2) (imin+3) (imin+4) ; ] in
let new_lines =
List.init ao_num ~f:(fun i ->
List.init ao_num (fun i ->
Printf.sprintf " %3d %15.10f %15.10f %15.10f %15.10f" (i+1)
(MO_coef.to_float mo_coef.(imin ).(i))
(MO_coef.to_float mo_coef.(imin+1).(i))
@ -173,7 +174,7 @@ end = struct
let header = [ Printf.sprintf " #%15d %15d %15d %15d %15d"
(imin+1) (imin+2) (imin+3) (imin+4) (imin+5) ; ] in
let new_lines =
List.init ao_num ~f:(fun i ->
List.init ao_num (fun i ->
Printf.sprintf " %3d %15.10f %15.10f %15.10f %15.10f %15.10f" (i+1)
(MO_coef.to_float mo_coef.(imin ).(i))
(MO_coef.to_float mo_coef.(imin+1).(i))
@ -185,11 +186,11 @@ end = struct
in
let rec create_list accu i =
if (i+4 < mo_num) then
create_list ( (print_five i (i+3) |> String.concat ~sep:"\n")::accu ) (i+4)
create_list ( (print_five i (i+3) |> String.concat "\n")::accu ) (i+4)
else
(print_five i (mo_num-1) |> String.concat ~sep:"\n")::accu |> List.rev
(print_five i (mo_num-1) |> String.concat "\n")::accu |> List.rev
in
create_list [] 0 |> String.concat ~sep:"\n\n"
create_list [] 0 |> String.concat "\n\n"
let to_rst b =
@ -224,13 +225,13 @@ mo_coef = %s
(MO_label.to_string b.mo_label)
(MO_number.to_string b.mo_num)
(b.mo_class |> Array.to_list |> List.map
~f:(MO_class.to_string) |> String.concat ~sep:", " )
(MO_class.to_string) |> String.concat ", " )
(b.mo_occ |> Array.to_list |> List.map
~f:(MO_occ.to_string) |> String.concat ~sep:", " )
(MO_occ.to_string) |> String.concat ", " )
(b.mo_coef |> Array.map
~f:(fun x-> Array.map ~f:MO_coef.to_string x |> String.concat_array
~sep:"," ) |>
String.concat_array ~sep:"\n" )
(fun x-> Array.map MO_coef.to_string x |>
Array.to_list |> String.concat "," ) |>
Array.to_list |> String.concat "\n" )
let write_mo_num n =
@ -245,7 +246,7 @@ mo_coef = %s
let write_mo_class a =
let mo_num = Array.length a in
let data = Array.map ~f:MO_class.to_string a
let data = Array.map MO_class.to_string a
|> Array.to_list
in Ezfio.ezfio_array_of_list ~rank:1 ~dim:[| mo_num |] ~data
|> Ezfio.set_mo_basis_mo_class
@ -253,7 +254,7 @@ mo_coef = %s
let write_mo_occ a =
let mo_num = Array.length a in
let data = Array.map ~f:MO_occ.to_float a
let data = Array.map MO_occ.to_float a
|> Array.to_list
in Ezfio.ezfio_array_of_list ~rank:1 ~dim:[| mo_num |] ~data
|> Ezfio.set_mo_basis_mo_occ
@ -268,7 +269,7 @@ mo_coef = %s
let mo_num = Array.length a in
let ao_num = Array.length a.(0) in
let data =
Array.map ~f:(fun mo -> Array.map ~f:MO_coef.to_float mo
Array.map (fun mo -> Array.map MO_coef.to_float mo
|> Array.to_list) a
|> Array.to_list
|> List.concat

55
ocaml/Input_nuclei_by_hand.ml
View File

@ -1,6 +1,6 @@
open Qptypes;;
open Qputils;;
open Core;;
open Sexplib.Std;;
module Nuclei_by_hand : sig
type t =
@ -41,7 +41,7 @@ end = struct
let read_nucl_label () =
Ezfio.get_nuclei_nucl_label ()
|> Ezfio.flattened_ezfio
|> Array.map ~f:Element.of_string
|> Array.map Element.of_string
;;
let write_nucl_label ~nucl_num labels =
@ -50,7 +50,7 @@ end = struct
in
let labels =
Array.to_list labels
|> List.map ~f:Element.to_string
|> List.map Element.to_string
in
Ezfio.ezfio_array_of_list ~rank:1
~dim:[| nucl_num |] ~data:labels
@ -61,7 +61,7 @@ end = struct
let read_nucl_charge () =
Ezfio.get_nuclei_nucl_charge ()
|> Ezfio.flattened_ezfio
|> Array.map ~f:Charge.of_float
|> Array.map Charge.of_float
;;
let write_nucl_charge ~nucl_num charges =
@ -70,7 +70,7 @@ end = struct
in
let charges =
Array.to_list charges
|> List.map ~f:Charge.to_float
|> List.map Charge.to_float
in
Ezfio.ezfio_array_of_list ~rank:1
~dim:[| nucl_num |] ~data:charges
@ -85,7 +85,7 @@ end = struct
|> Ezfio.flattened_ezfio
in
let zero = Point3d.of_string Units.Bohr "0. 0. 0." in
let result = Array.create nucl_num zero in
let result = Array.make nucl_num zero in
for i=0 to (nucl_num-1)
do
result.(i) <- Point3d.({ x=raw_data.(i);
@ -101,9 +101,9 @@ end = struct
in
let coord = Array.to_list coord in
let coord =
(List.map ~f:(fun x-> x.Point3d.x) coord) @
(List.map ~f:(fun x-> x.Point3d.y) coord) @
(List.map ~f:(fun x-> x.Point3d.z) coord)
(List.map (fun x-> x.Point3d.x) coord) @
(List.map (fun x-> x.Point3d.y) coord) @
(List.map (fun x-> x.Point3d.z) coord)
in
Ezfio.ezfio_array_of_list ~rank:2
~dim:[| nucl_num ; 3 |] ~data:coord
@ -160,11 +160,11 @@ nucl_coord = %s
"
(Nucl_number.to_string b.nucl_num)
(b.nucl_label |> Array.to_list |> List.map
~f:(Element.to_string) |> String.concat ~sep:", " )
(Element.to_string) |> String.concat ", " )
(b.nucl_charge |> Array.to_list |> List.map
~f:(Charge.to_string) |> String.concat ~sep:", " )
(Charge.to_string) |> String.concat ", " )
(b.nucl_coord |> Array.to_list |> List.map
~f:(Point3d.to_string ~units:Units.Bohr) |> String.concat ~sep:"\n" )
(Point3d.to_string ~units:Units.Bohr) |> String.concat "\n" )
;;
@ -174,12 +174,12 @@ nucl_coord = %s
( Printf.sprintf " %d\n "
nucl_num
) :: (
List.init nucl_num ~f:(fun i->
List.init nucl_num (fun i->
Printf.sprintf " %-3s %d %s"
(b.nucl_label.(i) |> Element.to_string)
(b.nucl_charge.(i) |> Charge.to_int )
(b.nucl_coord.(i) |> Point3d.to_string ~units:Units.Angstrom) )
) |> String.concat ~sep:"\n"
) |> String.concat "\n"
in
Printf.sprintf "
Nuclear coordinates in xyz format (Angstroms) ::
@ -192,16 +192,15 @@ Nuclear coordinates in xyz format (Angstroms) ::
let of_rst s =
let l = Rst_string.to_string s
|> String.split ~on:'\n'
|> String_ext.split ~on:'\n'
in
(* Find lines containing the xyz data *)
let rec extract_begin = function
| [] -> raise Caml.Not_found
| [] -> raise Not_found
| line::tail ->
let line = String.strip line in
let line = String.trim line in
if (String.length line > 3) &&
(String.sub line ~pos:((String.length line)-2)
~len:2 = "::") then
(String.sub line ((String.length line)-2) 2 = "::") then
tail
else
extract_begin tail
@ -213,12 +212,12 @@ Nuclear coordinates in xyz format (Angstroms) ::
| _ :: nucl_num :: title :: lines ->
begin
let nucl_num = nucl_num
|> String.strip
|> Int.of_string
|> String.trim
|> int_of_string
|> Nucl_number.of_int ~max:nmax
and lines = Array.of_list lines
in
List.init (Nucl_number.to_int nucl_num) ~f:(fun i ->
List.init (Nucl_number.to_int nucl_num) (fun i ->
Atom.of_string Units.Angstrom lines.(i))
end
| _ -> failwith "Error in xyz format"
@ -227,12 +226,12 @@ Nuclear coordinates in xyz format (Angstroms) ::
let result =
{ nucl_num = List.length atom_list
|> Nucl_number.of_int ~max:nmax;
nucl_label = List.map atom_list ~f:(fun x ->
x.Atom.element) |> Array.of_list ;
nucl_charge = List.map atom_list ~f:(fun x ->
x.Atom.charge ) |> Array.of_list ;
nucl_coord = List.map atom_list ~f:(fun x ->
x.Atom.coord ) |> Array.of_list ;
nucl_label = List.map (fun x ->
x.Atom.element) atom_list |> Array.of_list ;
nucl_charge = List.map (fun x ->
x.Atom.charge ) atom_list |> Array.of_list ;
nucl_coord = List.map (fun x ->
x.Atom.coord ) atom_list |> Array.of_list ;
}
in Some result
;;

11
ocaml/MO_class.ml
View File

@ -1,5 +1,6 @@
open Core
open Qptypes
open Sexplib.Std
type t =
| Core of MO_number.t list
@ -12,8 +13,8 @@ type t =
let to_string x =
let print_list l =
let s = List.map ~f:(fun x-> MO_number.to_int x |> string_of_int )l
|> (String.concat ~sep:", ")
let s = List.map (fun x-> MO_number.to_int x |> string_of_int ) l
|> (String.concat ", ")
in
"("^s^")"
in
@ -32,7 +33,7 @@ let to_string x =
let of_string s =
match (String.lowercase s) with
match (String.lowercase_ascii s) with
| "core" -> Core []
| "inactive" -> Inactive []
| "active" -> Active []
@ -42,7 +43,7 @@ let of_string s =
let _mo_number_list_of_range range =
Range.of_string range |> List.map ~f:MO_number.of_int
Range.of_string range |> List.map MO_number.of_int
let create_core range = Core (_mo_number_list_of_range range)

6
ocaml/MO_label.ml
View File

@ -1,4 +1,4 @@
open Core;;
open Sexplib.Std
type t =
| Guess
@ -8,7 +8,7 @@ type t =
| Orthonormalized
| None
[@@deriving sexp]
;;
let to_string = function
| Guess -> "Guess"
@ -20,7 +20,7 @@ let to_string = function
;;
let of_string s =
match String.lowercase (String.strip s) with
match String.lowercase_ascii (String.trim s) with
| "guess" -> Guess
| "canonical" -> Canonical
| "natural" -> Natural

20
ocaml/Message.ml
View File

@ -1,4 +1,4 @@
open Core
open Sexplib.Std
open Qptypes
(** New job : Request to create a new multi-tasked job *)
@ -161,7 +161,7 @@ end = struct
}
let create ~state ~tasks = { state = State.of_string state ; tasks }
let to_string x =
Printf.sprintf "add_task %s %s" (State.to_string x.state) (String.concat ~sep:"|" x.tasks)
Printf.sprintf "add_task %s %s" (State.to_string x.state) (String.concat "|" x.tasks)
end
@ -193,12 +193,12 @@ end = struct
}
let create ~state ~task_ids =
{ state = State.of_string state ;
task_ids = List.map ~f:Id.Task.of_int task_ids
task_ids = List.map Id.Task.of_int task_ids
}
let to_string x =
Printf.sprintf "del_task %s %s"
(State.to_string x.state)
(String.concat ~sep:"|" @@ List.map ~f:Id.Task.to_string x.task_ids)
(String.concat "|" @@ List.map Id.Task.to_string x.task_ids)
end
@ -219,7 +219,7 @@ end = struct
else "done"
in
Printf.sprintf "del_task_reply %s %s"
more (String.concat ~sep:"|" @@ List.map ~f:Id.Task.to_string x.task_ids)
more (String.concat "|" @@ List.map Id.Task.to_string x.task_ids)
end
@ -303,11 +303,11 @@ end = struct
"get_tasks_reply ok"
let to_string_list x =
"get_tasks_reply ok" :: (
List.map x ~f:(fun (task_id, task) ->
List.map (fun (task_id, task) ->
match task_id with
| Some task_id -> Printf.sprintf "%d %s" (Id.Task.to_int task_id) task
| None -> Printf.sprintf "0 terminate"
) )
) x )
end
@ -408,14 +408,14 @@ end = struct
let create ~state ~client_id ~task_ids =
{ client_id = Id.Client.of_int client_id ;
state = State.of_string state ;
task_ids = List.map ~f:Id.Task.of_int task_ids;
task_ids = List.map Id.Task.of_int task_ids;
}
let to_string x =
Printf.sprintf "task_done %s %d %s"
(State.to_string x.state)
(Id.Client.to_int x.client_id)
(String.concat ~sep:"|" @@ List.map ~f:Id.Task.to_string x.task_ids)
(String.concat "|" @@ List.map Id.Task.to_string x.task_ids)
end
(** Terminate *)
@ -460,7 +460,7 @@ end = struct
type t = string
let create x = x
let to_string x =
String.concat ~sep:" " [ "error" ; x ]
String.concat " " [ "error" ; x ]
end

4
ocaml/Molecule.ml
View File

@ -62,7 +62,7 @@ let name m =
try
let i = List.assoc e accu in
build_list ( (e,i+1)::(List.remove_assoc e accu) ) rest
with Caml.Not_found -> build_list ( (e,1)::accu ) rest
with Not_found -> build_list ( (e,1)::accu ) rest
end
| [] -> accu
in
@ -207,7 +207,7 @@ let distance_matrix molecule =
open Core ;;
include To_md5
let to_md5 = to_md5 sexp_of_t

15
ocaml/Multiplicity.ml
View File

@ -1,10 +1,11 @@
open Core;;
open Qptypes ;;
open Qptypes
open Sexplib.Std
type t = Strictly_positive_int.t [@@deriving sexp]
let of_int = Strictly_positive_int.of_int ;;
let to_int = Strictly_positive_int.to_int ;;
let of_int = Strictly_positive_int.of_int
let to_int = Strictly_positive_int.to_int
let to_string m =
match (to_int m) with
@ -18,7 +19,7 @@ let to_string m =
| 8 -> "Octet"
| 9 -> "Nonet"
| i -> Printf.sprintf "%d-et" i
;;
let of_alpha_beta a b =
let a = Elec_alpha_number.to_int a
@ -26,11 +27,11 @@ let of_alpha_beta a b =
in
assert (a >= b);
of_int (1 + a - b)
;;
let to_alpha_beta ne m =
let ne = Elec_number.to_int ne in
let nb = (ne-(to_int m)+1)/2 in
let na = ne - nb in
(Elec_alpha_number.of_int na, Elec_beta_number.of_int nb)
;;

10
ocaml/Point3d.ml
View File

@ -1,5 +1,5 @@
open Core;;
open Qptypes;;
open Qptypes
open Sexplib.Std
type t = {
x : float ;
@ -21,9 +21,9 @@ let of_string ~units s =
| Units.Angstrom -> Units.angstrom_to_bohr
in
let l = s
|> String.split ~on:' '
|> List.filter ~f:(fun x -> x <> "")
|> List.map ~f:Float.of_string
|> String_ext.split ~on:' '
|> List.filter (fun x -> x <> "")
|> List.map float_of_string
|> Array.of_list
in
{ x = l.(0) *. f ;

30
ocaml/Progress_bar.ml
View File

@ -1,5 +1,3 @@
open Core
type t =
{
title: string;
@ -7,14 +5,14 @@ type t =
cur_value : float;
end_value : float;
bar_length : int;
init_time : Time.t;
init_time : float;
dirty : bool;
next : Time.t;
next : float;
}
let init ?(bar_length=20) ?(start_value=0.) ?(end_value=1.) ~title =
{ title ; start_value ; end_value ; bar_length ; cur_value=start_value ;
init_time= Time.now () ; dirty = false ; next = Time.now () }
init_time= Unix.time () ; dirty = false ; next = Unix.time () }
let update ~cur_value bar =
{ bar with cur_value ; dirty=true }
@ -40,23 +38,23 @@ let display_tty bar =
|> Float.to_int
in
let hashes =
String.init bar.bar_length ~f:(fun i ->
String.init bar.bar_length (fun i ->
if (i < n_hashes) then '#'
else ' '
)
in
let now =
Time.now ()
Unix.time ()
in
let running_time =
Time.abs_diff now bar.init_time
now -. bar.init_time
in
Printf.eprintf "%s : [%s] %4.1f%% | %10s\r%!"
Printf.eprintf "%s : [%s] %4.1f%% | %8.0f s\r%!"
bar.title
hashes
percent
(Time.Span.to_string running_time);
{ bar with dirty = false ; next = Time.add now (Time.Span.of_sec 0.1) }
running_time;
{ bar with dirty = false ; next = now +. 0.1 }
let display_file bar =
@ -65,19 +63,19 @@ let display_file bar =
(bar.end_value -. bar.start_value)
in
let running_time =
Time.abs_diff (Time.now ()) bar.init_time
(Unix.time ()) -. bar.init_time
in
Printf.eprintf "%5.2f %% in %20s \n%!"
Printf.eprintf "%5.2f %% in %20.0f seconds \n%!"
percent
(Time.Span.to_string running_time);
{ bar with dirty = false ; next = Time.add (Time.now ()) (Time.Span.of_sec 10.) }
running_time;
{ bar with dirty = false ; next = (Unix.time ()) +. 10. }
let display bar =
if (not bar.dirty) then
bar
else if (Time.now () < bar.next) then
else if (Unix.time () < bar.next) then
bar
else
begin

69
ocaml/Pseudo.ml
View File

@ -1,4 +1,4 @@
open Core
open Sexplib.Std
open Qptypes
@ -81,12 +81,12 @@ let to_string_local = function
| t ->
"Local component:" ::
( Printf.sprintf "%20s %8s %20s" "Coeff." "r^n" "Exp." ) ::
( List.map t ~f:(fun (l,c) -> Printf.sprintf "%20f %8d %20f"
( List.map (fun (l,c) -> Printf.sprintf "%20f %8d %20f"
(AO_coef.to_float c)
(R_power.to_int l.GaussianPrimitive_local.r_power)
(AO_expo.to_float l.GaussianPrimitive_local.expo)
) )
|> String.concat ~sep:"\n"
) t )
|> String.concat "\n"
(** Transform the non-local component of the pseudopotential to a string *)
@ -95,7 +95,7 @@ let to_string_non_local = function
| t ->
"Non-local component:" ::
( Printf.sprintf "%20s %8s %20s %8s" "Coeff." "r^n" "Exp." "Proj") ::
( List.map t ~f:(fun (l,c) ->
( List.map (fun (l,c) ->
let p =
Positive_int.to_int l.GaussianPrimitive_non_local.proj
in
@ -104,8 +104,8 @@ let to_string_non_local = function
(R_power.to_int l.GaussianPrimitive_non_local.r_power)
(AO_expo.to_float l.GaussianPrimitive_non_local.expo)
p p
) )
|> String.concat ~sep:"\n"
) t )
|> String.concat "\n"
(** Transform the Pseudopotential to a string *)
let to_string t =
@ -116,29 +116,30 @@ let to_string t =
:: to_string_local t.local
:: to_string_non_local t.non_local
:: []
|> List.filter ~f:(fun x -> x <> "")
|> String.concat ~sep:"\n"
|> List.filter (fun x -> x <> "")
|> String.concat "\n"
(** Find an element in the file *)
let find in_channel element =
In_channel.seek in_channel 0L;
seek_in in_channel 0;
let loop, element_read, old_pos =
ref true,
ref None,
ref (In_channel.pos in_channel)
ref (pos_in in_channel)
in
while !loop
do
try
let buffer =
old_pos := In_channel.pos in_channel;
match In_channel.input_line in_channel with
| Some line -> String.split ~on:' ' line
|> List.hd_exn
| None -> raise End_of_file
old_pos := pos_in in_channel;
try
input_line in_channel
|> String_ext.split ~on:' '
|> List.hd
with _ -> raise End_of_file
in
element_read := Some (Element.of_string buffer);
loop := !element_read <> (Some element)
@ -146,7 +147,7 @@ let find in_channel element =
| Element.ElementError _ -> ()
| End_of_file -> loop := false
done ;
In_channel.seek in_channel !old_pos;
seek_in in_channel !old_pos;
!element_read
@ -156,13 +157,13 @@ let read_element in_channel element =
| Some e when e = element ->
begin
let rec read result =
match In_channel.input_line in_channel with
| None -> result
| Some line ->
if (String.strip line = "") then
try
let line = input_line in_channel in
if (String.trim line = "") then
result
else
read (line::result)
with _ -> result
in
let data =
@ -171,20 +172,20 @@ let read_element in_channel element =
in
let debug_data =
String.concat ~sep:"\n" data
String.concat "\n" data
in
let decode_first_line = function
| first_line :: rest ->
begin
let first_line_split =
String.split first_line ~on:' '
|> List.filter ~f:(fun x -> (String.strip x) <> "")
String_ext.split first_line ~on:' '
|> List.filter (fun x -> (String.trim x) <> "")
in
match first_line_split with
| e :: "GEN" :: n :: p ->
{ element = Element.of_string e ;
n_elec = Int.of_string n |> Positive_int.of_int ;
n_elec = int_of_string n |> Positive_int.of_int ;
local = [] ;
non_local = []
}, rest
@ -200,18 +201,18 @@ let read_element in_channel element =
| (n,line::rest) ->
begin
match
String.split line ~on:' '
|> List.filter ~f:(fun x -> String.strip x <> "")
String_ext.split line ~on:' '
|> List.filter (fun x -> String.trim x <> "")
with
| c :: i :: e :: [] ->
let i =
Int.of_string i
int_of_string i
in
let elem =
( create_primitive
(Float.of_string e |> AO_expo.of_float)
(float_of_string e |> AO_expo.of_float)
(i-2 |> R_power.of_int),
Float.of_string c |> AO_coef.of_float
float_of_string c |> AO_coef.of_float
)
in
loop create_primitive (elem::accu) (n-1, rest)
@ -230,8 +231,8 @@ let read_element in_channel element =
match data with
| n :: rest ->
let n =
String.strip n
|> Int.of_string
String.trim n
|> int_of_string
|> Positive_int.of_int
in
decode_local_n n rest
@ -250,8 +251,8 @@ let read_element in_channel element =
match data with
| n :: rest ->
let n =
String.strip n
|> Int.of_string
String.trim n
|> int_of_string
|> Positive_int.of_int
in
let result =

94
ocaml/Qpackage.ml
View File

@ -1,45 +1,45 @@
open Core;;
open Qptypes;;
open Qputils;;
open Qptypes
open Qputils
(** Variables related to the quantum package installation *)
let root =
match (Sys.getenv "QP_ROOT") with
match (Sys.getenv_opt "QP_ROOT") with
| None -> failwith "QP_ROOT environment variable is not set.
Please source the quantum_package.rc file."
| Some x -> x
;;
let bit_kind_size = lazy (
let filename = root^"/src/bitmask/bitmasks_module.f90" in
if not (Sys.file_exists_exn filename) then
if not (Sys.file_exists filename) then
raise (Failure ("File "^filename^" not found"));
let in_channel = In_channel.create filename in
let lines = In_channel.input_lines in_channel in
In_channel.close in_channel;
let in_channel = open_in filename in
let lines = input_lines in_channel in
close_in in_channel;
let rec get_data = function
| [] -> raise (Failure ("bit_kind_size not found in "^filename))
| line::tail ->
let line =
begin match String.split ~on:'!' line |> List.hd with
| Some x -> x
| None -> ""
end in
begin match (String.rsplit2 ~on:':' line) with
try
String_ext.split ~on:'!' line
|> List.hd
with _ -> line
in
begin match (String_ext.rsplit2 ~on:':' line) with
| Some (_ ,buffer) ->
begin match (String.split ~on:'=' buffer |> List.map ~f:String.strip) with
begin match (String_ext.split ~on:'=' buffer |> List.map String.trim) with
| ["bit_kind_size"; x] ->
Int.of_string x |> Bit_kind_size.of_int
int_of_string x |> Bit_kind_size.of_int
| _ -> get_data tail
end
| _ -> get_data tail
end
in
get_data lines )
;;
let bit_kind = lazy (
Lazy.force bit_kind_size
@ -47,23 +47,26 @@ let bit_kind = lazy (
|> fun x -> x / 8
|> Bit_kind.of_int
)
;;
let executables = lazy (
let filename = root^"/data/executables"
and func in_channel =
In_channel.input_lines in_channel
|> List.map ~f:(fun x ->
let e = String.split ~on:' ' x
|> List.filter ~f:(fun x -> x <> "")
let filename = root^"/data/executables" in
let lines =
let in_channel = open_in filename in
let result = input_lines in_channel in
close_in in_channel;
result
in
lines
|> List.map (fun x ->
let e = String_ext.split ~on:' ' x
|> List.filter (fun x -> x <> "")
in
match e with
| [a;b] -> (a,String.substr_replace_all ~pattern:"$QP_ROOT" ~with_:root b)
| [a;b] -> (a,String_ext.substr_replace_all ~pattern:"$QP_ROOT" ~with_:root b)
| _ -> ("","")
)
in
In_channel.with_file filename ~f:func
|> List.sort ~compare:(fun (x,_) (y,_) ->
|> List.sort (fun (x,_) (y,_) ->
if x < y then -1
else if x > y then 1
else 0)
@ -72,33 +75,37 @@ let executables = lazy (
let get_ezfio_default_in_file ~directory ~data ~filename =
let lines = In_channel.with_file filename ~f:(fun in_channel ->
In_channel.input_lines in_channel) in
let lines =
let in_channel = open_in filename in
let result = input_lines in_channel in
close_in in_channel;
result
in
let rec find_dir = function
| line :: rest ->
if ((String.strip line) = directory) then
if ((String.trim line) = directory) then
rest
else
find_dir rest
| [] -> raise Caml.Not_found
| [] -> raise Not_found
in
let rec find_data = function
| line :: rest ->
if (line = "") then
raise Caml.Not_found
raise Not_found
else if (line.[0] <> ' ') then
raise Caml.Not_found
raise Not_found
else
begin
match (String.lsplit2 ~on:' ' (String.strip line)) with
match (String_ext.lsplit2 ~on:' ' (String.trim line)) with
| Some (l,r) ->
if (l = data) then
String.strip r
String.trim r
else
find_data rest
| None -> raise Caml.Not_found
| None -> raise Not_found
end
| [] -> raise Caml.Not_found
| [] -> raise Not_found
in
find_dir lines
|> find_data ;
@ -111,7 +118,7 @@ let get_ezfio_default directory data =
| [] ->
begin
Printf.printf "%s/%s not found\n%!" directory data;
raise Caml.Not_found
raise Not_found
end
| filename :: tail ->
let filename =
@ -120,7 +127,7 @@ let get_ezfio_default directory data =
try
get_ezfio_default_in_file ~directory ~data ~filename
with
| Caml.Not_found -> aux tail
| Not_found -> aux tail
in
Sys.readdir dirname
|> Array.to_list
@ -131,10 +138,7 @@ let ezfio_work ezfio_file =
let result =
Filename.concat ezfio_file "work"
in
begin
match Sys.is_directory result with
| `Yes -> ()
| _ -> ( Ezfio.set_file ezfio_file ; Ezfio.set_work_empty false)
end;
if not (Sys.file_exists result) then
( Ezfio.set_file ezfio_file ; Ezfio.set_work_empty false);
result
;;

11
ocaml/Qputils.ml
View File

@ -42,3 +42,14 @@ let rmdir dirname =
let input_lines ic =
let n = in_channel_length ic in
let s = Bytes.create n in
really_input ic s 0 n;
close_in ic;
Bytes.to_string s
|> String_ext.split ~on:'\n'
let string_of_string s = s

4
ocaml/Queuing_system.ml
View File

@ -83,7 +83,7 @@ let pop_task ~client_id q =
}
and found =
try Some (TasksMap.find task_id q.tasks)
with Caml.Not_found -> None
with Not_found -> None
in new_q, Some task_id, found
| [] -> q, None, None
@ -104,7 +104,7 @@ let end_task ~task_id ~client_id q =
let () =
let client_id_check =
try RunningMap.find task_id running with
Caml.Not_found -> failwith "Task already finished"
Not_found -> failwith "Task already finished"
in
assert (client_id_check = client_id)
in

52
ocaml/String_ext.ml
View File

@ -3,27 +3,6 @@ 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 *)
@ -101,7 +80,7 @@ let rsplit2_exn ?(on=' ') s =
else
do_work (i-1)
in
do_work length
do_work (length-1)
let lsplit2 ?(on=' ') s =
@ -123,6 +102,15 @@ let to_list s =
|> Array.to_list
let of_list l =
let a = Array.of_list l in
String.init (Array.length a) (fun i -> a.(i))
let rev s =
to_list s
|> List.rev
|> of_list
let fold ~init ~f s =
to_list s
|> List.fold_left f init
@ -140,3 +128,23 @@ let is_prefix ~prefix s =
let of_char c =
String.make 1 c
let tr ~target ~replacement s =
String.map (fun c -> if c = target then replacement else c) s
let substr_index ?(pos=0) ~pattern s =
try
let regexp =
Str.regexp pattern
in
Some (Str.search_forward regexp s pos)
with Not_found -> None
let substr_replace_all ~pattern ~with_ s =
let regexp =
Str.regexp pattern
in
Str.global_replace regexp with_ s

2
ocaml/TaskServer.ml
View File

@ -33,7 +33,7 @@ type t =
let debug_env =
try
Sys.getenv "QP_TASK_DEBUG"; true
Sys.getenv "QP_TASK_DEBUG" = "1"
with Not_found -> false

2
ocaml/_tags
View File

@ -1,4 +1,4 @@
true: package(core,cryptokit,zmq,str,ppx_sexp_conv,ppx_deriving,getopt)
true: package(cryptokit,zmq,str,sexplib,ppx_sexp_conv,ppx_deriving,getopt)
true: thread
false: profile
<*byte> : linkdep(c_bindings.o), custom

7
ocaml/create_git_sha1.sh
View File

@ -4,9 +4,8 @@ SHA1=$(git log -1 | head -1 | cut -d ' ' -f 2)
DATE=$(git log -1 | grep Date | cut -d ':' -f 2-)
MESSAGE=$(git log -1 | tail -1 | sed 's/"/\\"/g')
cat << EOF > Git.ml
open Core
let sha1 = "$SHA1" |> String_ext.strip
let date = "$DATE" |> String_ext.strip
let message = "$MESSAGE" |> String_ext.strip
let sha1 = "$SHA1" |> String.trim
let date = "$DATE" |> String.trim
let message = "$MESSAGE" |> String.trim
EOF

13
ocaml/element_create_db.ml
View File

@ -1,4 +1,3 @@
open Core
open Qptypes
open Element
@ -6,9 +5,10 @@ let () =
let indices =
Array.init 78 (fun i -> i)
in
Out_channel.with_file (Qpackage.root ^ "/data/list_element.txt")
~f:(fun out_channel ->
Array.init 110 ~f:(fun i ->
let out_channel =
open_out (Qpackage.root ^ "/data/list_element.txt")
in
Array.init 110 (fun i ->
let element =
try
Some (of_charge (Charge.of_int i))
@ -21,7 +21,6 @@ let () =
i (to_string x) (to_long_string x) (Positive_float.to_float @@ mass x )
)
|> Array.to_list
|> String.concat ~sep:""
|> Out_channel.output_string out_channel
)
|> String.concat ""
|> Printf.fprintf out_channel "%s"

252
ocaml/qp_create_ezfio.ml
View File

@ -1,6 +1,6 @@
open Qputils
open Qptypes
open Core
open Sexplib.Std
type element =
| Element of Element.t
@ -38,7 +38,7 @@ let dummy_centers ~threshold ~molecule ~nuclei =
| _ -> assert false
in
aux [] (n-1,n-1)
|> List.map ~f:(fun (i,x,j,y,r) ->
|> List.map (fun (i,x,j,y,r) ->
let f =
x /. (x +. y)
in
@ -58,22 +58,22 @@ let dummy_centers ~threshold ~molecule ~nuclei =
(** Returns the list of available basis sets *)
let list_basis () =
let basis_list =
let ic = Pervasives.open_in (Qpackage.root ^ "/data/basis/00_README.rst") in
let n = Pervasives.in_channel_length ic in
let ic = open_in (Qpackage.root ^ "/data/basis/00_README.rst") in
let n = in_channel_length ic in
let s = Bytes.create n in
Pervasives.really_input ic s 0 n;
Pervasives.close_in ic;
really_input ic s 0 n;
close_in ic;
Bytes.to_string s
|> String.split ~on:'\n'
|> List.filter ~f:(fun line -> String.length line > 1 && line.[0] <> '#')
|> List.map ~f:(fun line ->
match String.split ~on:'\'' line with
|> String_ext.split ~on:'\n'
|> List.filter (fun line -> String.length line > 1 && line.[0] <> '#')
|> List.map (fun line ->
match String_ext.split ~on:'\'' line with
| file :: name :: descr :: _ ->
Printf.sprintf "%s\n %s\n %s\n\n" file name (String.strip descr)
Printf.sprintf "%s\n %s\n %s\n\n" file name (String.trim descr)
| _ -> assert false
)
in
List.sort basis_list ~compare:String.ascending
List.sort compare basis_list
(** Run the program *)
@ -101,7 +101,7 @@ let run ?o b au c d m p cart xyz_file =
**********)
let basis_table =
Hashtbl.Poly.create ()
Hashtbl.create 63
in
(* Open basis set channels *)
@ -111,10 +111,7 @@ let run ?o b au c d m p cart xyz_file =
| 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 Caml.Not_found
Hashtbl.find basis_table key
in
let temp_filename =
@ -129,11 +126,11 @@ let run ?o b au c d m p cart xyz_file =
Qpackage.root ^ "/data/basis/" ^ basis
in
match
Sys.is_file basis,
Sys.is_file long_basis
Sys.file_exists basis,
Sys.file_exists long_basis
with
| `Yes, _ -> In_channel.create basis
| `No , `Yes -> In_channel.create long_basis
| true , _ -> open_in basis
| false, true -> open_in long_basis
| _ -> failwith ("Basis "^basis^" not found")
in
@ -141,7 +138,7 @@ let run ?o b au c d m p cart xyz_file =
| [] -> ()
| elem_and_basis_name :: rest ->
begin
match (String.lsplit2 ~on:':' elem_and_basis_name) with
match (String_ext.lsplit2 ~on:':' elem_and_basis_name) with
| None -> (* Principal basis *)
begin
let basis =
@ -150,14 +147,12 @@ let run ?o b au c d m p cart xyz_file =
let new_channel =
fetch_channel basis
in
List.iter nuclei ~f:(fun elem->
List.iter (fun elem->
let key =
Element.to_string elem.Atom.element
in
match Hashtbl.add basis_table ~key:key ~data:new_channel with
| `Ok -> ()
| `Duplicate -> ()
)
Hashtbl.add basis_table key new_channel
) nuclei
end
| Some (key, basis) -> (*Aux basis *)
begin
@ -166,12 +161,12 @@ let run ?o b au c d m p cart xyz_file =
Element (Element.of_string key)
with Element.ElementError _ ->
let result =
match (String.split ~on:',' key) with
match (String_ext.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
String.lowercase_ascii basis
in
let key =
match elem with
@ -181,23 +176,13 @@ let run ?o b au c d m p cart xyz_file =
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
Hashtbl.add basis_table key new_channel
end
end;
build_basis rest
in
String.split ~on:'|' b
|> List.rev_map ~f:String.strip
String_ext.split ~on:'|' b
|> List.rev_map String.trim
|> build_basis;
@ -207,7 +192,7 @@ let run ?o b au c d m p cart xyz_file =
***************)
let pseudo_table =
Hashtbl.Poly.create ()
Hashtbl.create 63
in
(* Open pseudo channels *)
@ -215,7 +200,7 @@ let run ?o b au c d m p cart xyz_file =
let key =
Element.to_string element
in
Hashtbl.find pseudo_table key
Hashtbl.find_opt pseudo_table key
in
let temp_filename =
Filename.temp_file "qp_create_" ".pseudo"
@ -229,11 +214,11 @@ let run ?o b au c d m p cart xyz_file =
Qpackage.root ^ "/data/pseudo/" ^ pseudo
in
match
Sys.is_file pseudo,
Sys.is_file long_pseudo
Sys.file_exists pseudo,
Sys.file_exists long_pseudo
with
| `Yes, _ -> In_channel.create pseudo
| `No , `Yes -> In_channel.create long_pseudo
| true , _ -> open_in pseudo
| false, true-> open_in long_pseudo
| _ -> failwith ("Pseudo file "^pseudo^" not found.")
in
@ -241,7 +226,7 @@ let run ?o b au c d m p cart xyz_file =
| [] -> ()
| elem_and_pseudo_name :: rest ->
begin
match (String.lsplit2 ~on:':' elem_and_pseudo_name) with
match (String_ext.lsplit2 ~on:':' elem_and_pseudo_name) with
| None -> (* Principal pseudo *)
begin
let pseudo =
@ -250,21 +235,19 @@ let run ?o b au c d m p cart xyz_file =
let new_channel =
fetch_channel pseudo
in
List.iter nuclei ~f:(fun elem->
List.iter (fun elem->
let key =
Element.to_string elem.Atom.element
in
match Hashtbl.add pseudo_table ~key:key ~data:new_channel with
| `Ok -> ()
| `Duplicate -> ()
)
Hashtbl.add pseudo_table key new_channel
) nuclei
end
| Some (key, pseudo) -> (*Aux pseudo *)
begin
let elem =
Element.of_string key
and pseudo =
String.lowercase pseudo
String.lowercase_ascii pseudo
in
let key =
Element.to_string elem
@ -272,11 +255,7 @@ let run ?o b au c d m p cart xyz_file =
let new_channel =
fetch_channel pseudo
in
begin
match Hashtbl.add pseudo_table ~key:key ~data:new_channel with
| `Ok -> ()
| `Duplicate -> failwith ("Duplicate definition of pseudo for "^(Element.to_long_string elem))
end
Hashtbl.add pseudo_table key new_channel
end
end;
build_pseudo rest
@ -285,8 +264,8 @@ let run ?o b au c d m p cart xyz_file =
match p with
| None -> ()
| Some p ->
String.split ~on:'|' p
|> List.rev_map ~f:String.strip
String_ext.split ~on:'|' p
|> List.rev_map String.trim
|> build_pseudo
in
@ -296,13 +275,13 @@ let run ?o b au c d m p cart xyz_file =
| Some x -> x
| None ->
begin
match String.rsplit2 ~on:'.' xyz_file with
match String_ext.rsplit2 ~on:'.' xyz_file with
| Some (x,"xyz")
| Some (x,"zmt") -> x^".ezfio"
| _ -> xyz_file^".ezfio"
end
in
if Sys.file_exists_exn ezfio_file then
if Sys.file_exists ezfio_file then
failwith (ezfio_file^" already exists");
let write_file () =
@ -311,17 +290,17 @@ let run ?o b au c d m p cart xyz_file =
(* Write Pseudo *)
let pseudo =
List.map nuclei ~f:(fun x ->
List.map (fun x ->
match pseudo_channel x.Atom.element with
| Some channel -> Pseudo.read_element channel x.Atom.element
| None -> Pseudo.empty x.Atom.element
)
) nuclei
in
let molecule =
let n_elec_to_remove =
List.fold pseudo ~init:0 ~f:(fun accu x ->
accu + (Positive_int.to_int x.Pseudo.n_elec))
List.fold_left (fun accu x ->
accu + (Positive_int.to_int x.Pseudo.n_elec)) 0 pseudo
in
{ Molecule.elec_alpha =
(Elec_alpha_number.to_int molecule.Molecule.elec_alpha)
@ -333,14 +312,14 @@ let run ?o b au c d m p cart xyz_file =
|> Elec_beta_number.of_int;
Molecule.nuclei =
let charges =
List.map pseudo ~f:(fun x -> Positive_int.to_int x.Pseudo.n_elec
|> Float.of_int)
List.map (fun x -> Positive_int.to_int x.Pseudo.n_elec
|> Float.of_int) pseudo
|> Array.of_list
in
List.mapi molecule.Molecule.nuclei ~f:(fun i x ->
List.mapi (fun i x ->
{ x with Atom.charge = (Charge.to_float x.Atom.charge) -. charges.(i)
|> Charge.of_float }
)
) molecule.Molecule.nuclei
}
in
let nuclei =
@ -356,13 +335,13 @@ let run ?o b au c d m p cart xyz_file =
(* Write Nuclei *)
let labels =
List.map ~f:(fun x->Element.to_string x.Atom.element) nuclei
List.map (fun x->Element.to_string x.Atom.element) nuclei
and charges =
List.map ~f:(fun x-> Atom.(Charge.to_float x.charge)) nuclei
List.map (fun x-> Atom.(Charge.to_float x.charge)) nuclei
and coords =
(List.map ~f:(fun x-> x.Atom.coord.Point3d.x) nuclei) @
(List.map ~f:(fun x-> x.Atom.coord.Point3d.y) nuclei) @
(List.map ~f:(fun x-> x.Atom.coord.Point3d.z) nuclei) in
(List.map (fun x-> x.Atom.coord.Point3d.x) nuclei) @
(List.map (fun x-> x.Atom.coord.Point3d.y) nuclei) @
(List.map (fun x-> x.Atom.coord.Point3d.z) nuclei) in
let nucl_num = (List.length labels) in
Ezfio.set_nuclei_nucl_num nucl_num ;
Ezfio.set_nuclei_nucl_label (Ezfio.ezfio_array_of_list
@ -381,40 +360,41 @@ let run ?o b au c d m p cart xyz_file =
in
let klocmax =
List.fold pseudo ~init:0 ~f:(fun accu x ->
List.fold_left (fun accu x ->
let x =
List.length x.Pseudo.local
in
if (x > accu) then x
else accu
)
) 0 pseudo
and lmax =
List.fold pseudo ~init:0 ~f:(fun accu x ->
List.fold_left (fun accu x ->
let x =
List.fold x.Pseudo.non_local ~init:0 ~f:(fun accu (x,_) ->
List.fold_left (fun accu (x,_) ->
let x =
Positive_int.to_int x.Pseudo.GaussianPrimitive_non_local.proj
in
if (x > accu) then x
else accu
)
) 0 x.Pseudo.non_local
in
if (x > accu) then x
else accu
)
) 0 pseudo
in
let kmax =
Array.init (lmax+1) ~f:(fun i->
List.map pseudo ~f:(fun x ->
List.filter x.Pseudo.non_local ~f:(fun (y,_) ->
Array.init (lmax+1) (fun i->
List.map (fun x ->
List.filter (fun (y,_) ->
(Positive_int.to_int y.Pseudo.GaussianPrimitive_non_local.proj) = i)
|> List.length )
|> List.fold ~init:0 ~f:(fun accu x ->
if accu > x then accu else x)
x.Pseudo.non_local
|> List.length ) pseudo
|> List.fold_left (fun accu x ->
if accu > x then accu else x) 0
)
|> Array.fold ~init:0 ~f:(fun accu i ->
if i > accu then i else accu)
|> Array.fold_left (fun accu i ->
if i > accu then i else accu) 0
in
@ -423,12 +403,12 @@ let run ?o b au c d m p cart xyz_file =
Ezfio.set_pseudo_pseudo_kmax kmax;
Ezfio.set_pseudo_pseudo_lmax lmax;
let tmp_array_v_k, tmp_array_dz_k, tmp_array_n_k =
Array.make_matrix ~dimx:klocmax ~dimy:nucl_num 0. ,
Array.make_matrix ~dimx:klocmax ~dimy:nucl_num 0. ,
Array.make_matrix ~dimx:klocmax ~dimy:nucl_num 0
Array.make_matrix klocmax nucl_num 0. ,
Array.make_matrix klocmax nucl_num 0. ,
Array.make_matrix klocmax nucl_num 0
in
List.iteri pseudo ~f:(fun j x ->
List.iteri x.Pseudo.local ~f:(fun i (y,c) ->
List.iteri (fun j x ->
List.iteri (fun i (y,c) ->
tmp_array_v_k.(i).(j) <- AO_coef.to_float c;
let y, z =
AO_expo.to_float y.Pseudo.GaussianPrimitive_local.expo,
@ -436,11 +416,11 @@ let run ?o b au c d m p cart xyz_file =
in
tmp_array_dz_k.(i).(j) <- y;
tmp_array_n_k.(i).(j) <- z;
)
);
) x.Pseudo.local
) pseudo ;
let concat_2d tmp_array =
let data =
Array.map tmp_array ~f:Array.to_list
Array.map Array.to_list tmp_array
|> Array.to_list
|> List.concat
in
@ -454,18 +434,18 @@ let run ?o b au c d m p cart xyz_file =
|> Ezfio.set_pseudo_pseudo_n_k;
let tmp_array_v_kl, tmp_array_dz_kl, tmp_array_n_kl =
Array.init (lmax+1) ~f:(fun _ ->
(Array.make_matrix ~dimx:kmax ~dimy:nucl_num 0. )),
Array.init (lmax+1) ~f:(fun _ ->
(Array.make_matrix ~dimx:kmax ~dimy:nucl_num 0. )),
Array.init (lmax+1) ~f:(fun _ ->
(Array.make_matrix ~dimx:kmax ~dimy:nucl_num 0 ))
Array.init (lmax+1) (fun _ ->
(Array.make_matrix kmax nucl_num 0. )),
Array.init (lmax+1) (fun _ ->
(Array.make_matrix kmax nucl_num 0. )),
Array.init (lmax+1) (fun _ ->
(Array.make_matrix kmax nucl_num 0 ))
in
List.iteri pseudo ~f:(fun j x ->
List.iteri (fun j x ->
let last_idx =
Array.create ~len:(lmax+1) 0
Array.make (lmax+1) 0
in
List.iter x.Pseudo.non_local ~f:(fun (y,c) ->
List.iter (fun (y,c) ->
let k, y, z =
Positive_int.to_int y.Pseudo.GaussianPrimitive_non_local.proj,
AO_expo.to_float y.Pseudo.GaussianPrimitive_non_local.expo,
@ -478,14 +458,14 @@ let run ?o b au c d m p cart xyz_file =
tmp_array_dz_kl.(k).(i).(j) <- y;
tmp_array_n_kl.(k).(i).(j) <- z;
last_idx.(k) <- i+1;
)
);
) x.Pseudo.non_local
) pseudo ;
let concat_3d tmp_array =
let data =
Array.map tmp_array ~f:(fun x ->
Array.map x ~f:Array.to_list
Array.map (fun x ->
Array.map Array.to_list x
|> Array.to_list
|> List.concat)
|> List.concat) tmp_array
|> Array.to_list
|> List.concat
in
@ -518,7 +498,7 @@ let run ?o b au c d m p cart xyz_file =
in
let result = do_work [] 1 nuclei
|> List.rev
|> List.map ~f:(fun (x,i) ->
|> List.map (fun (x,i) ->
try
let e =
match x.Atom.element with
@ -530,13 +510,13 @@ let run ?o b au c d m p cart xyz_file =
in
try
Basis.read_element (basis_channel key) i e
with Caml.Not_found ->
with Not_found ->
let key =
Element x.Atom.element
in
try
Basis.read_element (basis_channel key) i e
with Caml.Not_found ->
with Not_found ->
failwith (Printf.sprintf "Basis not found for atom %d (%s)" (Nucl_number.to_int i)
(Element.to_string x.Atom.element) )
with
@ -552,37 +532,38 @@ let run ?o b au c d m p cart xyz_file =
let ao_num = List.length long_basis in
Ezfio.set_ao_basis_ao_num ao_num;
Ezfio.set_ao_basis_ao_basis b;
let ao_prim_num = List.map long_basis ~f:(fun (_,g,_) -> List.length g.Gto.lc)
and ao_nucl = List.map long_basis ~f:(fun (_,_,n) -> Nucl_number.to_int n)
let ao_prim_num = List.map (fun (_,g,_) -> List.length g.Gto.lc) long_basis
and ao_nucl = List.map (fun (_,_,n) -> Nucl_number.to_int n) long_basis
and ao_power=
let l = List.map long_basis ~f:(fun (x,_,_) -> x) in
(List.map l ~f:(fun t -> Positive_int.to_int Symmetry.Xyz.(t.x)) )@
(List.map l ~f:(fun t -> Positive_int.to_int Symmetry.Xyz.(t.y)) )@
(List.map l ~f:(fun t -> Positive_int.to_int Symmetry.Xyz.(t.z)) )
let l = List.map (fun (x,_,_) -> x) long_basis in
(List.map (fun t -> Positive_int.to_int Symmetry.Xyz.(t.x)) l)@
(List.map (fun t -> Positive_int.to_int Symmetry.Xyz.(t.y)) l)@
(List.map (fun t -> Positive_int.to_int Symmetry.Xyz.(t.z)) l)
in
let ao_prim_num_max = List.fold ~init:0 ~f:(fun s x ->
let ao_prim_num_max = List.fold_left (fun s x ->
if x > s then x
else s) ao_prim_num
else s) 0 ao_prim_num
in
let gtos =
List.map long_basis ~f:(fun (_,x,_) -> x)
List.map (fun (_,x,_) -> x) long_basis
in
let create_expo_coef ec =
let coefs =
begin match ec with
| `Coefs -> List.map gtos ~f:(fun x->
List.map x.Gto.lc ~f:(fun (_,coef) -> AO_coef.to_float coef) )
| `Expos -> List.map gtos ~f:(fun x->
List.map x.Gto.lc ~f:(fun (prim,_) -> AO_expo.to_float
prim.GaussianPrimitive.expo) )
| `Coefs -> List.map (fun x->
List.map (fun (_,coef) ->
AO_coef.to_float coef) x.Gto.lc) gtos
| `Expos -> List.map (fun x->
List.map (fun (prim,_) -> AO_expo.to_float
prim.GaussianPrimitive.expo) x.Gto.lc) gtos
end
in
let rec get_n n accu = function
| [] -> List.rev accu
| h::tail ->
let y =
begin match List.nth h n with
begin match List.nth_opt h n with
| Some x -> x
| None -> 0.
end
@ -621,9 +602,10 @@ let run ?o b au c d m p cart xyz_file =
| ex ->
begin
begin
match Sys.is_directory ezfio_file with
| `Yes -> rmdir ezfio_file
| _ -> ()
try
if Sys.is_directory ezfio_file then
rmdir ezfio_file
with _ -> ()
end;
raise ex;
end
@ -730,7 +712,7 @@ If a file with the same name as the basis set exists, this file will be read. O
if basis = "show" then
begin
list_basis ()
|> List.iter ~f:print_endline;
|> List.iter print_endline;
exit 0
end;

37
ocaml/qp_run.ml
View File

@ -46,7 +46,7 @@ let run slave ?prefix exe ezfio_file =
in
let time_start =
Core.Time.now ()
Unix.time ()
in
if (not (Sys.file_exists ezfio_file)) then
@ -65,7 +65,15 @@ let run slave ?prefix exe ezfio_file =
failwith ("Executable "^exe^" not found")
end;
Printf.printf "%s\n" (Core.Time.to_string time_start);
let tm = Unix.localtime time_start in
Printf.printf "Date: %2.2d/%2.2d/%4d %2.2d:%2.2d:%2.2d\n"
tm.Unix.tm_mday
(tm.Unix.tm_mon+1)
(tm.Unix.tm_year+1900)
(tm.Unix.tm_hour + if tm.Unix.tm_isdst then 1 else 0)
tm.Unix.tm_min
tm.Unix.tm_sec
;
Printf.printf "===============\nQuantum Package\n===============\n\n";
Printf.printf "Git Commit: %s\n" Git.message;
Printf.printf "Git Date : %s\n" Git.date;
@ -89,10 +97,12 @@ let run slave ?prefix exe ezfio_file =
if slave then
try
let address =
Core.In_channel.read_all qp_run_address_filename
|> String.trim
let ic = open_in qp_run_address_filename in
let result = input_line ic in
close_in ic;
String.trim result
in
Unix.putenv "QP_RUN_ADDRESS_MASTER" address
Unix.putenv "QP_RUN_ADDRESS_MASTER" address;
with Sys_error _ -> failwith "No master is not running"
in
@ -110,8 +120,11 @@ let run slave ?prefix exe ezfio_file =
Unix.putenv "QP_RUN_ADDRESS" address;
let () =
if (not slave) then
Core.Out_channel.with_file qp_run_address_filename ~f:(
fun oc -> Core.Out_channel.output_lines oc [address])
begin
let oc = open_out qp_run_address_filename in
Printf.fprintf oc "%s\n" address;
close_out oc;
end
in
@ -135,9 +148,13 @@ let run slave ?prefix exe ezfio_file =
if (not slave) then
Sys.remove qp_run_address_filename;
let duration = Core.Time.diff (Core.Time.now()) time_start
|> Core.Time.Span.to_string in
Printf.printf "Wall time : %s\n\n" duration;
let duration = Unix.time () -. time_start |> Unix.gmtime in
let open Unix in
let d, h, m, s =
duration.tm_yday, duration.tm_hour, duration.tm_min, duration.tm_sec
in
Printf.printf "Wall time: %d:%2.2d:%2.2d" (d*24+h) m s ;
Printf.printf "\n\n";
if (exit_code <> 0) then
exit exit_code

13
scripts/ezfio_interface/ei_handler.py
View File

@ -556,7 +556,7 @@ def create_ocaml_input(dict_ezfio_cfg, module_lower):
template += ["open Qptypes;;",
"open Qputils;;",
"open Core;;",
"open Sexplib.Std;;",
"",
"module {0} : sig".format(module_lower.capitalize())]
@ -611,7 +611,16 @@ def create_ocaml_input(dict_ezfio_cfg, module_lower):
"",
"end"]
return "\n".join(template)
result = "\n".join(template)
result = result.replace("String.of_string","string_of_string")
result = result.replace("String.to_string","string_of_string")
result = result.replace("Int.of_string","int_of_string")
result = result.replace("Int.to_string","string_of_int")
result = result.replace("Float.of_string","float_of_string")
result = result.replace("Float.to_string","string_of_float")
result = result.replace("Bool.of_string","bool_of_string")
result = result.replace("Bool.to_string","string_of_bool")
return result
def save_ocaml_input(module_lower, str_ocaml_input):

1
scripts/ezfio_interface/ezfio_generate_ocaml.py
View File

@ -352,7 +352,6 @@ class EZFIO_ocaml(object):
l_template = ['open Qputils;;',
'open Qptypes;;',
'open Core;;',
'']
for m in self.l_module_lower:

58
scripts/ezfio_interface/qp_edit_template
View File

@ -4,7 +4,7 @@
open Qputils
open Qptypes
open Core
open Sexplib.Std
(** Interactive editing of the input.
@ -53,7 +53,7 @@ Editing file `%s`
let make_header kw =
let s = keyword_to_string kw in
let l = String.length s in
"\n\n"^s^"\n"^(String.init l ~f:(fun _ -> '='))^"\n\n"
"\n\n"^s^"\n"^(String.init l (fun _ -> '='))^"\n\n"
@ -92,19 +92,19 @@ let get s =
(** Applies the changes from the string [str] corresponding to section [s] *)
let set str s =
let header = (make_header s) in
match String.substr_index ~pos:0 ~pattern:header str with
match String_ext.substr_index ~pos:0 ~pattern:header str with
| None -> ()
| Some idx ->
begin
let index_begin = idx + (String.length header) in
let index_end =
match ( String.substr_index ~pos:(index_begin+(String.length header)+1)
match ( String_ext.substr_index ~pos:(index_begin+(String.length header)+1)
~pattern:"==" str) with
| Some i -> i
| None -> String.length str
in
let l = index_end - index_begin in
let str = String.sub ~pos:index_begin ~len:l str
let str = String.sub str index_begin l
|> Rst_string.of_string
in
let write (of_rst,w) s =
@ -132,11 +132,11 @@ let set str s =
let create_temp_file ezfio_filename fields =
let temp_filename = Filename.temp_file "qp_edit_" ".rst" in
begin
Out_channel.with_file temp_filename ~f:(fun out_channel ->
(file_header ezfio_filename) :: (List.map ~f:get fields)
|> String.concat ~sep:"\n"
|> Out_channel.output_string out_channel
);
let oc = open_out temp_filename in
(file_header ezfio_filename) :: (List.map get fields)
|> String.concat "\n"
|> Printf.fprintf oc "%s";
close_out oc;
at_exit (fun () -> Sys.remove temp_filename);
temp_filename
end
@ -155,20 +155,19 @@ let run check_only ?ndet ?state ezfio_filename =
in
(* Open EZFIO *)
if (not (Sys.file_exists_exn ezfio_filename)) then
if (not (Sys.file_exists ezfio_filename)) then
failwith (ezfio_filename^" does not exists");
Ezfio.set_file ezfio_filename;
(* Clean qp_stop status *)
[ "qpstop" ; "qpkill" ]
|> List.iter ~f:(fun f ->
|> List.iter (fun f ->
let stopfile =
Filename.concat (Qpackage.ezfio_work ezfio_filename) f
in
match Sys.file_exists stopfile with
| `Yes -> Sys.remove stopfile
| _ -> ()
if Sys.file_exists stopfile then
Sys.remove stopfile
);
(* Reorder basis set *)
@ -180,7 +179,7 @@ let run check_only ?ndet ?state ezfio_filename =
in
let ordering = Input.Ao_basis.ordering aos in
let test = Array.copy ordering in
Array.sort ~compare test ;
Array.sort compare test ;
if test <> ordering then
begin
Printf.eprintf "Warning: Basis set is not properly ordered. Redordering.\n";
@ -212,7 +211,7 @@ let run check_only ?ndet ?state ezfio_filename =
(*
let output = (file_header ezfio_filename) :: (
List.map ~f:get [
List.map get [
Ao_basis ;
Mo_basis ;
])
@ -238,24 +237,28 @@ let run check_only ?ndet ?state ezfio_filename =
(* Open the temp file with external editor *)
let editor =
match Sys.getenv "EDITOR" with
| Some editor -> editor
| None -> "vi"
try Sys.getenv "EDITOR"
with Not_found -> "vi"
in
match check_only with
| true -> ()
| false ->
Printf.sprintf "%s %s" editor temp_filename
|> Sys.command_exn
|> Sys.command |> ignore
;
(* Re-read the temp file *)
let temp_string =
In_channel.with_file temp_filename ~f:(fun in_channel ->
In_channel.input_all in_channel)
let ic = open_in temp_filename in
let result =
input_lines ic
|> String.concat "\n"
in
List.iter ~f:(fun x -> set temp_string x) tasks
close_in ic;
result
in
List.iter (fun x -> set temp_string x) tasks
@ -281,7 +284,8 @@ let create_backup ezfio_filename =
tar -cf .backup.tar --exclude=\"work/*\" %s && (mv .backup.tar %s || rm .backup.tar)
"
ezfio_filename ezfio_filename backup_filename
|> Sys.command_exn
|> Sys.command
|> ignore
with _ -> ()
@ -290,10 +294,10 @@ let restore_backup ezfio_filename =
let filename =
Printf.sprintf "%s/work/backup.tar" ezfio_filename
in
if Sys.file_exists_exn filename then
if Sys.file_exists filename then
begin
Printf.sprintf "tar -xf %s" filename
|> Sys.command_exn;
|> Sys.command |> ignore;
remove_backup ezfio_filename
end

5
scripts/perturbation.py
View File

@ -1,14 +1,15 @@
#!/usr/bin/env python2
import os
from qp_path import QP_SRC
Pert_dir = os.environ["QP_ROOT"]+"/src/perturbation/"
Pert_dir = os.path.join(QP_SRC,"perturbation")
perturbations = []
for filename in filter(lambda x: x.endswith(".irp.f"), os.listdir(Pert_dir)):
filename = Pert_dir+filename
filename = os.path.join(Pert_dir,filename)
file = open(filename,'r')
lines = file.readlines()
file.close()

2
src/cipsi/stochastic_cipsi.irp.f
View File

@ -70,7 +70,7 @@ subroutine run_stochastic_cipsi
write(*,'(A)') '--------------------------------------------------------------------------------'
to_select = N_det
to_select = N_det*int(sqrt(dble(N_states)))
to_select = max(N_states_diag, to_select)
pt2 = 0.d0

9
src/davidson/diagonalization_hs2_dressed.irp.f
View File

@ -408,10 +408,6 @@ subroutine davidson_diag_hjj_sjj(dets_in,u_in,H_jj,s2_out,energies,dim_in,sze,N_
! Compute s_kl = <u_k | S_l> = <u_k| S2 |u_l>
! -------------------------------------------
! call dgemm('T','N', shift2, shift2, sze, &
! 1.d0, U, size(U,1), S, size(S,1), &
! 0.d0, s_, size(s_,1))
!$OMP PARALLEL DO DEFAULT(SHARED) PRIVATE(i,j,k)
do j=1,shift2
do i=1,shift2
@ -438,8 +434,13 @@ subroutine davidson_diag_hjj_sjj(dets_in,u_in,H_jj,s2_out,energies,dim_in,sze,N_
do k=1,shift2
h_p(k,k) = h_p(k,k) + S_z2_Sz - expected_s2
enddo
if (only_expected_s2) then
alpha = 0.1d0
h_p = h + alpha*h_p
else
alpha = 0.0001d0
h_p = h + alpha*h_p
endif
else
h_p = h
alpha = 0.d0

4
src/mo_basis/mos.irp.f
View File

@ -45,9 +45,9 @@ BEGIN_PROVIDER [ double precision, mo_coef, (ao_num,mo_num) ]
BEGIN_DOC
! Molecular orbital coefficients on |AO| basis set
!
! mo_coef(i,j) = coefficient of the i-th |AO| on the jth mo
! mo_coef(i,j) = coefficient of the i-th |AO| on the jth |MO|
!
! mo_label : Label characterizing the MOS (local, canonical, natural, etc)
! mo_label : Label characterizing the |MOs| (local, canonical, natural, etc)
END_DOC
integer :: i, j
double precision, allocatable :: buffer(:,:)

2
src/scf_utils/diagonalize_fock.irp.f
View File

@ -1,7 +1,7 @@
BEGIN_PROVIDER [ double precision, eigenvectors_Fock_matrix_mo, (ao_num,mo_num) ]
implicit none
BEGIN_DOC
! Eigenvectors of the Fock matrix in the MO basis obtained with level shift.
! Eigenvectors of the Fock matrix in the |MO| basis obtained with level shift.
END_DOC
integer :: i,j