9
1
mirror of https://github.com/QuantumPackage/qp2.git synced 2024-12-13 07:03:29 +01:00

Merge branch 'dev' into dev-lct

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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@ -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

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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 =

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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
;;

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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

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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_float x = x
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_float x = x
let to_int x = int_of_float x
let to_string x =
if x >= 0. then
Printf.sprintf "+%f" x

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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

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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 " "

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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
;

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@ -1,16 +1,16 @@
open Qptypes
open Core
open Sexplib.Std
type t =
{ sym : Symmetry.t ;
expo : AO_expo.t ;
} [@@deriving sexp]
{ sym : Symmetry.t ;
expo : AO_expo.t ;
} [@@deriving sexp]
let to_string p =
let { sym = s ; expo = e } = p in
Printf.sprintf "(%s, %22e)"
(Symmetry.to_string s)
(AO_expo.to_float e)
(Symmetry.to_string s)
(AO_expo.to_float e)
let of_sym_expo s e =

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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
;;

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@ -1,6 +1,5 @@
open Qputils;;
open Qptypes;;
open Core;;
include Input_ao_basis;;
include Input_bitmasks;;

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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 )
;;

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

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

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 =