mirror of
https://github.com/QuantumPackage/qp2.git
synced 2024-12-11 22:23:31 +01:00
Removed core
This commit is contained in:
parent
a145334269
commit
09eab3db06
@ -291,7 +291,7 @@ OCaml
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.. code:: bash
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opam install ocamlbuild cryptokit zmq core sexplib ppx_sexp_conv ppx_deriving getopt
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opam install ocamlbuild cryptokit zmq sexplib ppx_sexp_conv ppx_deriving getopt
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EZFIO
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2
configure
vendored
2
configure
vendored
@ -60,7 +60,7 @@ function execute () {
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}
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PACKAGES=""
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OCAML_PACKAGES="ocamlbuild cryptokit zmq core.v0.11.3 sexplib ppx_sexp_conv ppx_deriving getopt"
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OCAML_PACKAGES="ocamlbuild cryptokit zmq sexplib ppx_sexp_conv ppx_deriving getopt"
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while true ; do
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case "$1" in
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@ -80,14 +80,14 @@ let read_until_found f tries =
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begin
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try
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Some (read_mos x f)
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with Caml.Not_found ->
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with Not_found ->
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None
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end
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) None tries
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in
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match result with
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| Some mos -> mos
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| None -> raise Caml.Not_found
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| None -> raise Not_found
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let read_natural_mos f =
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let tries = [
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@ -431,7 +431,7 @@ let create_cas_input ?(vecfile="") ~guess ~nstate s n_e n_a =
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in
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try
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string_of_guess (Natural (norb, vecfile))
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with Caml.Not_found ->
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with Not_found ->
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string_of_guess (Canonical (norb, vecfile))
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end
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;
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@ -1,6 +1,5 @@
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open Qputils;;
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open Qptypes;;
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open Core;;
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include Input_ao_basis;;
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include Input_bitmasks;;
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@ -1,6 +1,6 @@
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open Qptypes;;
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open Qputils;;
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open Core;;
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open Sexplib.Std;;
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module Ao_basis : sig
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type t =
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@ -52,13 +52,13 @@ end = struct
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let read_ao_prim_num () =
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Ezfio.get_ao_basis_ao_prim_num ()
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|> Ezfio.flattened_ezfio
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|> Array.map ~f:AO_prim_number.of_int
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|> Array.map AO_prim_number.of_int
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;;
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let read_ao_prim_num_max () =
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Ezfio.get_ao_basis_ao_prim_num ()
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|> Ezfio.flattened_ezfio
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|> Array.fold ~f:(fun x y -> if x>y then x else y) ~init:0
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|> Array.fold_left (fun x y -> if x>y then x else y) 0
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|> AO_prim_number.of_int
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;;
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@ -66,42 +66,42 @@ end = struct
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let nmax = Nucl_number.get_max () in
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Ezfio.get_ao_basis_ao_nucl ()
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|> Ezfio.flattened_ezfio
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|> Array.map ~f:(fun x-> Nucl_number.of_int ~max:nmax x)
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|> Array.map (fun x-> Nucl_number.of_int ~max:nmax x)
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;;
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let read_ao_power () =
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let x = Ezfio.get_ao_basis_ao_power () in
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let dim = x.Ezfio.dim.(0) in
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let data = Ezfio.flattened_ezfio x in
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let result = Array.init dim ~f:(fun x -> "") in
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let result = Array.init dim (fun x -> "") in
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for i=1 to dim
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do
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if (data.(i-1) > 0) then
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result.(i-1) <- result.(i-1)^"x"^(Int.to_string data.(i-1));
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result.(i-1) <- result.(i-1)^"x"^(string_of_int data.(i-1));
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if (data.(dim+i-1) > 0) then
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result.(i-1) <- result.(i-1)^"y"^(Int.to_string data.(dim+i-1));
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result.(i-1) <- result.(i-1)^"y"^(string_of_int data.(dim+i-1));
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if (data.(2*dim+i-1) > 0) then
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result.(i-1) <- result.(i-1)^"z"^(Int.to_string data.(2*dim+i-1));
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result.(i-1) <- result.(i-1)^"z"^(string_of_int data.(2*dim+i-1));
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done;
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Array.map ~f:Symmetry.Xyz.of_string result
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Array.map Symmetry.Xyz.of_string result
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;;
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let read_ao_coef () =
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Ezfio.get_ao_basis_ao_coef ()
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|> Ezfio.flattened_ezfio
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|> Array.map ~f:AO_coef.of_float
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|> Array.map AO_coef.of_float
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;;
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let read_ao_expo () =
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Ezfio.get_ao_basis_ao_expo ()
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|> Ezfio.flattened_ezfio
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|> Array.map ~f:AO_expo.of_float
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|> Array.map AO_expo.of_float
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;;
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let read_ao_cartesian () =
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if not (Ezfio.has_ao_basis_ao_cartesian ()) then
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get_default "ao_cartesian"
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|> Bool.of_string
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|> bool_of_string
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|> Ezfio.set_ao_basis_ao_cartesian
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;
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Ezfio.get_ao_basis_ao_cartesian ()
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@ -110,10 +110,10 @@ end = struct
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let to_long_basis b =
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let ao_num = AO_number.to_int b.ao_num in
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let gto_array = Array.init (AO_number.to_int b.ao_num)
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~f:(fun i ->
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(fun i ->
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let s = Symmetry.Xyz.to_symmetry b.ao_power.(i) in
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let ao_prim_num = AO_prim_number.to_int b.ao_prim_num.(i) in
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let prims = List.init ao_prim_num ~f:(fun j ->
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let prims = List.init ao_prim_num (fun j ->
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let prim = { GaussianPrimitive.sym = s ;
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GaussianPrimitive.expo = b.ao_expo.(ao_num*j+i)
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}
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@ -178,14 +178,14 @@ end = struct
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in
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let ao_prim_num =
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Array.to_list ao_prim_num
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|> List.map ~f:AO_prim_number.to_int
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|> List.map AO_prim_number.to_int
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in
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Ezfio.set_ao_basis_ao_prim_num (Ezfio.ezfio_array_of_list
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~rank:1 ~dim:[| ao_num |] ~data:ao_prim_num) ;
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let ao_nucl =
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Array.to_list ao_nucl
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|> List.map ~f:Nucl_number.to_int
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|> List.map Nucl_number.to_int
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in
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Ezfio.set_ao_basis_ao_nucl(Ezfio.ezfio_array_of_list
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~rank:1 ~dim:[| ao_num |] ~data:ao_nucl) ;
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@ -193,9 +193,9 @@ end = struct
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let ao_power =
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let l = Array.to_list ao_power in
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List.concat [
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(List.map ~f:(fun a -> Positive_int.to_int a.Symmetry.Xyz.x) l) ;
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(List.map ~f:(fun a -> Positive_int.to_int a.Symmetry.Xyz.y) l) ;
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(List.map ~f:(fun a -> Positive_int.to_int a.Symmetry.Xyz.z) l) ]
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(List.map (fun a -> Positive_int.to_int a.Symmetry.Xyz.x) l) ;
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(List.map (fun a -> Positive_int.to_int a.Symmetry.Xyz.y) l) ;
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(List.map (fun a -> Positive_int.to_int a.Symmetry.Xyz.z) l) ]
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in
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Ezfio.set_ao_basis_ao_power(Ezfio.ezfio_array_of_list
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~rank:2 ~dim:[| ao_num ; 3 |] ~data:ao_power) ;
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@ -204,14 +204,14 @@ end = struct
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let ao_coef =
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Array.to_list ao_coef
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|> List.map ~f:AO_coef.to_float
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|> List.map AO_coef.to_float
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in
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Ezfio.set_ao_basis_ao_coef(Ezfio.ezfio_array_of_list
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~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_coef) ;
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let ao_expo =
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Array.to_list ao_expo
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|> List.map ~f:AO_expo.to_float
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|> List.map AO_expo.to_float
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in
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Ezfio.set_ao_basis_ao_expo(Ezfio.ezfio_array_of_list
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~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_expo) ;
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@ -271,58 +271,56 @@ end = struct
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| Some (s', g', n') ->
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if s <> s' || n <> n' then find2 (s,g,n) a (i+1)
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else
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let lc = List.map ~f:(fun (prim, _) -> prim) g.Gto.lc
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and lc' = List.map ~f:(fun (prim, _) -> prim) g'.Gto.lc
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let lc = List.map (fun (prim, _) -> prim) g.Gto.lc
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and lc' = List.map (fun (prim, _) -> prim) g'.Gto.lc
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in
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if lc <> lc' then find2 (s,g,n) a (i+1) else (a.(i) <- None ; i)
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in
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find x a 0
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in
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let search_array = Array.map ~f:(fun i -> Some i) unordered_basis in
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Array.map ~f:(fun x -> find x search_array) ordered_basis
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let search_array = Array.map (fun i -> Some i) unordered_basis in
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Array.map (fun x -> find x search_array) ordered_basis
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;;
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let of_long_basis long_basis name ao_cartesian =
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let ao_num = List.length long_basis |> AO_number.of_int in
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let ao_prim_num =
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List.map long_basis ~f:(fun (_,g,_) -> List.length g.Gto.lc
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|> AO_prim_number.of_int )
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List.map (fun (_,g,_) -> List.length g.Gto.lc
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|> AO_prim_number.of_int ) long_basis
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|> Array.of_list
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and ao_nucl =
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List.map long_basis ~f:(fun (_,_,n) -> n)
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List.map (fun (_,_,n) -> n) long_basis
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|> Array.of_list
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and ao_power =
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List.map ~f:(fun (x,_,_) -> x) long_basis
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List.map (fun (x,_,_) -> x) long_basis
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|> Array.of_list
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in
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let ao_prim_num_max = Array.fold ~init:0 ~f:(fun s x ->
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if AO_prim_number.to_int x > s then AO_prim_number.to_int x else s)
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let ao_prim_num_max = Array.fold_left (fun s x ->
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if AO_prim_number.to_int x > s then AO_prim_number.to_int x else s) 0
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ao_prim_num
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|> AO_prim_number.of_int
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in
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let gtos =
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List.map long_basis ~f:(fun (_,x,_) -> x)
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List.map (fun (_,x,_) -> x) long_basis
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in
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let create_expo_coef ec =
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let coefs =
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begin match ec with
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| `Coefs -> List.map gtos ~f:(fun x->
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List.map x.Gto.lc ~f:(fun (_,coef) -> AO_coef.to_float coef) )
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| `Expos -> List.map gtos ~f:(fun x->
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List.map x.Gto.lc ~f:(fun (prim,_) -> AO_expo.to_float
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prim.GaussianPrimitive.expo) )
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| `Coefs -> List.map (fun x->
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List.map (fun (_,coef) -> AO_coef.to_float coef) x.Gto.lc ) gtos
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| `Expos -> List.map (fun x->
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List.map (fun (prim,_) -> AO_expo.to_float
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prim.GaussianPrimitive.expo) x.Gto.lc ) gtos
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end
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in
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let rec get_n n accu = function
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| [] -> List.rev accu
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| h::tail ->
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let y =
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begin match List.nth h n with
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| Some x -> x
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| None -> 0.
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end
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try List.nth h n
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with _ -> 0.
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in
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get_n n (y::accu) tail
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in
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@ -335,10 +333,10 @@ end = struct
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let ao_coef = create_expo_coef `Coefs
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|> Array.of_list
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|> Array.map ~f:AO_coef.of_float
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|> Array.map AO_coef.of_float
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and ao_expo = create_expo_coef `Expos
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|> Array.of_list
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|> Array.map ~f:AO_expo.of_float
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|> Array.map AO_expo.of_float
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in
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{ ao_basis = name ;
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ao_num ; ao_prim_num ; ao_prim_num_max ; ao_nucl ;
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@ -347,17 +345,17 @@ end = struct
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let reorder b =
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let order = ordering b in
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let f a = Array.init (Array.length a) ~f:(fun i -> a.(order.(i))) in
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let f a = Array.init (Array.length a) (fun i -> a.(order.(i))) in
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let ao_prim_num_max = AO_prim_number.to_int b.ao_prim_num_max
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and ao_num = AO_number.to_int b.ao_num in
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let ao_coef =
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Array.init ao_prim_num_max ~f:(fun i ->
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f @@ Array.init ao_num ~f:(fun j -> b.ao_coef.(i*ao_num + j) )
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Array.init ao_prim_num_max (fun i ->
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f @@ Array.init ao_num (fun j -> b.ao_coef.(i*ao_num + j) )
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) |> Array.to_list |> Array.concat
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in
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let ao_expo =
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Array.init ao_prim_num_max ~f:(fun i ->
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f @@ Array.init ao_num ~f:(fun j -> b.ao_expo.(i*ao_num + j) )
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Array.init ao_prim_num_max (fun i ->
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f @@ Array.init ao_num (fun j -> b.ao_expo.(i*ao_num + j) )
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) |> Array.to_list |> Array.concat
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in
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{ b with
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@ -373,7 +371,7 @@ end = struct
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let to_rst b =
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let print_sym =
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let l = List.init (Array.length b.ao_power) ~f:(
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let l = List.init (Array.length b.ao_power) (
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fun i -> ( (i+1),b.ao_nucl.(i),b.ao_power.(i) ) )
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in
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let rec do_work = function
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@ -383,7 +381,7 @@ end = struct
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(Symmetry.Xyz.to_string x)
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)::(do_work tail)
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in do_work l
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|> String.concat
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|> String.concat ""
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in
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let short_basis = to_basis b in
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@ -408,11 +406,11 @@ Basis set (read-only) ::
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======= ========= ===========
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" (AO_basis_name.to_string b.ao_basis)
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(Bool.to_string b.ao_cartesian)
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(string_of_bool b.ao_cartesian)
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(Basis.to_string short_basis
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|> String.split ~on:'\n'
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|> List.map ~f:(fun x-> " "^x)
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|> String.concat ~sep:"\n"
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|> String_ext.split ~on:'\n'
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|> List.map (fun x-> " "^x)
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|> String.concat "\n"
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) print_sym
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|> Rst_string.of_string
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@ -420,14 +418,14 @@ Basis set (read-only) ::
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let read_rst s =
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let s = Rst_string.to_string s
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|> String.split ~on:'\n'
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|> String_ext.split ~on:'\n'
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in
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let rec extract_basis = function
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| [] -> failwith "Error in basis set"
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| line :: tail ->
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let line = String.strip line in
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let line = String.trim line in
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if line = "Basis set (read-only) ::" then
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String.concat tail ~sep:"\n"
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String.concat "\n" tail
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else
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extract_basis tail
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in
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@ -450,17 +448,17 @@ md5 = %s
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(AO_basis_name.to_string b.ao_basis)
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(AO_number.to_string b.ao_num)
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(b.ao_prim_num |> Array.to_list |> List.map
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~f:(AO_prim_number.to_string) |> String.concat ~sep:", " )
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(AO_prim_number.to_string) |> String.concat ", " )
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(AO_prim_number.to_string b.ao_prim_num_max)
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(b.ao_nucl |> Array.to_list |> List.map ~f:Nucl_number.to_string |>
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String.concat ~sep:", ")
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(b.ao_power |> Array.to_list |> List.map ~f:(fun x->
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"("^(Symmetry.Xyz.to_string x)^")" )|> String.concat ~sep:", ")
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(b.ao_coef |> Array.to_list |> List.map ~f:AO_coef.to_string
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|> String.concat ~sep:", ")
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(b.ao_expo |> Array.to_list |> List.map ~f:AO_expo.to_string
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|> String.concat ~sep:", ")
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(b.ao_cartesian |> Bool.to_string)
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(b.ao_nucl |> Array.to_list |> List.map Nucl_number.to_string |>
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String.concat ", ")
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(b.ao_power |> Array.to_list |> List.map (fun x->
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"("^(Symmetry.Xyz.to_string x)^")" )|> String.concat ", ")
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(b.ao_coef |> Array.to_list |> List.map AO_coef.to_string
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|> String.concat ", ")
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(b.ao_expo |> Array.to_list |> List.map AO_expo.to_string
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|> String.concat ", ")
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(b.ao_cartesian |> string_of_bool)
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(to_md5 b |> MD5.to_string )
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;;
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|
@ -1,228 +0,0 @@
|
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open Qptypes;;
|
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open Qputils;;
|
||||
open Core;;
|
||||
|
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module Bielec_integrals : sig
|
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type t =
|
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{ read_ao_integrals : bool;
|
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read_mo_integrals : bool;
|
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write_ao_integrals : bool;
|
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write_mo_integrals : bool;
|
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threshold_ao : Threshold.t;
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threshold_mo : Threshold.t;
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direct : bool;
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} [@@deriving sexp]
|
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;;
|
||||
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
|
||||
|
||||
|
@ -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
|
||||
|
||||
|
||||
|
@ -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
|
||||
|
@ -1,6 +1,6 @@
|
||||
open Qptypes;;
|
||||
open Qputils;;
|
||||
open Core;;
|
||||
open Qptypes
|
||||
open Qputils
|
||||
open Sexplib.Std
|
||||
|
||||
module Electrons : sig
|
||||
type t =
|
||||
|
@ -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
|
||||
|
@ -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
|
||||