From 53bca8fc923cc3531f33574dccbc26190654ea86 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Wed, 13 Sep 2017 17:37:54 +0200 Subject: [PATCH] Fixed EZFIO.cfg --- ocaml/Input_ao_basis.ml | 387 +++++++++++---------------------- plugins/Hartree_Fock/EZFIO.cfg | 6 - src/AO_Basis/EZFIO.cfg | 6 + 3 files changed, 132 insertions(+), 267 deletions(-) diff --git a/ocaml/Input_ao_basis.ml b/ocaml/Input_ao_basis.ml index 348ddd7f..e01ca713 100644 --- a/ocaml/Input_ao_basis.ml +++ b/ocaml/Input_ao_basis.ml @@ -1,101 +1,38 @@ +(* =~=~ *) +(* Init *) +(* =~=~ *) + open Qptypes;; open Qputils;; open Core;; module Ao_basis : sig - type t = - { ao_basis : AO_basis_name.t; - ao_num : AO_number.t ; - ao_prim_num : AO_prim_number.t array; - ao_prim_num_max : AO_prim_number.t; - ao_nucl : Nucl_number.t array; - ao_power : Symmetry.Xyz.t array; - ao_coef : AO_coef.t array; - ao_expo : AO_expo.t array; - ao_cartesian : bool; - } [@@deriving sexp] - ;; - val read : unit -> t option +(* Generate type *) + type t = + { + threshold_overlap_ao_eigenvalues : Threshold.t; + } [@@deriving sexp] + ;; + val read : unit -> t option + val write : t-> unit val to_string : t -> string - val to_basis : t -> Basis.t - val write : t -> unit - val to_md5 : t -> MD5.t val to_rst : t -> Rst_string.t + val of_rst : Rst_string.t -> t option end = struct - type t = - { ao_basis : AO_basis_name.t; - ao_num : AO_number.t ; - ao_prim_num : AO_prim_number.t array; - ao_prim_num_max : AO_prim_number.t; - ao_nucl : Nucl_number.t array; - ao_power : Symmetry.Xyz.t array; - ao_coef : AO_coef.t array; - ao_expo : AO_expo.t array; - ao_cartesian : bool; - } [@@deriving sexp] - ;; +(* Generate type *) + type t = + { + threshold_overlap_ao_eigenvalues : Threshold.t; + } [@@deriving sexp] + ;; let get_default = Qpackage.get_ezfio_default "ao_basis";; - let read_ao_basis () = - Ezfio.get_ao_basis_ao_basis () - |> AO_basis_name.of_string - ;; - - let read_ao_num () = - Ezfio.get_ao_basis_ao_num () - |> AO_number.of_int - ;; - - let read_ao_prim_num () = - Ezfio.get_ao_basis_ao_prim_num () - |> Ezfio.flattened_ezfio - |> Array.map ~f: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 - |> AO_prim_number.of_int - ;; - - let read_ao_nucl () = - 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) - ;; - - 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 - 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)); - if (data.(dim+i-1) > 0) then - result.(i-1) <- result.(i-1)^"y"^(Int.to_string 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)); - done; - Array.map ~f: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 - ;; - - let read_ao_expo () = - Ezfio.get_ao_basis_ao_expo () - |> Ezfio.flattened_ezfio - |> Array.map ~f:AO_expo.of_float - ;; +(* =~=~=~=~=~=~==~=~=~=~=~=~ *) +(* Generate Special Function *) +(* =~=~=~==~=~~=~=~=~=~=~=~=~ *) +(* Read snippet for ao_cartesian *) let read_ao_cartesian () = if not (Ezfio.has_ao_basis_ao_cartesian ()) then get_default "ao_cartesian" @@ -104,191 +41,119 @@ end = struct ; Ezfio.get_ao_basis_ao_cartesian () ;; - - 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 -> - 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 prim = { GaussianPrimitive.sym = s ; - GaussianPrimitive.expo = b.ao_expo.(ao_num*j+i) - } - in - let coef = b.ao_coef.(ao_num*j+i) in - (prim,coef) - ) in - Gto.of_prim_coef_list prims - ) - in - let rec do_work accu sym gto nucl = - match (sym, gto, nucl) with - | (s::srest, g::grest, n::nrest) -> - do_work ((s,g,n)::accu) srest grest nrest - | ([],[],[]) -> List.rev accu - | _ -> assert false - in - do_work [] - (Array.to_list b.ao_power) - (Array.to_list gto_array) - (Array.to_list b.ao_nucl) - ;; - let to_basis b = - to_long_basis b - |> Long_basis.to_basis - ;; - - let to_md5 b = - let short_basis = to_basis b in - Basis.to_md5 short_basis - ;; - - - - let write_md5 b = - to_md5 b - |> MD5.to_string - |> Ezfio.set_ao_basis_ao_md5 +(* Write snippet for ao_cartesian *) + let write_ao_cartesian = + Ezfio.set_ao_basis_ao_cartesian ;; - let write_ao_basis name = - AO_basis_name.to_string name - |> Ezfio.set_ao_basis_ao_basis +(* Read snippet for ao_prim_num_max *) + let read_ao_prim_num_max () = + if not (Ezfio.has_ao_basis_ao_prim_num_max ()) then + get_default "ao_prim_num_max" + |> Int.of_string + |> Ezfio.set_ao_basis_ao_prim_num_max + ; + Ezfio.get_ao_basis_ao_prim_num_max () + ;; +(* Write snippet for ao_prim_num_max *) + let write_ao_prim_num_max = + Ezfio.set_ao_basis_ao_prim_num_max ;; - let write b = - let { ao_basis ; - ao_num ; - ao_prim_num ; - ao_prim_num_max ; - ao_nucl ; - ao_power ; - ao_coef ; - ao_expo ; - ao_cartesian ; - } = b - in - write_md5 b ; - write_ao_basis ao_basis; +(* Read snippet for integral_kinetic *) + let read_integral_kinetic () = + if not (Ezfio.has_ao_basis_integral_kinetic ()) then + get_default "integral_kinetic" + |> Float.of_string + |> Ezfio.set_ao_basis_integral_kinetic + ; + Ezfio.get_ao_basis_integral_kinetic () + ;; +(* Write snippet for integral_kinetic *) + let write_integral_kinetic = + Ezfio.set_ao_basis_integral_kinetic ;; - - let read () = - if (Ezfio.has_ao_basis_ao_basis ()) then - begin - let result = - { ao_basis = read_ao_basis (); - ao_num = read_ao_num () ; - ao_prim_num = read_ao_prim_num (); - ao_prim_num_max = read_ao_prim_num_max (); - ao_nucl = read_ao_nucl (); - ao_power = read_ao_power (); - ao_coef = read_ao_coef () ; - ao_expo = read_ao_expo () ; - ao_cartesian = read_ao_cartesian () ; - } - in - to_md5 result - |> MD5.to_string - |> Ezfio.set_ao_basis_ao_md5 ; - Some result - end - else - None +(* Read snippet for integral_nuclear *) + let read_integral_nuclear () = + if not (Ezfio.has_ao_basis_integral_nuclear ()) then + get_default "integral_nuclear" + |> Float.of_string + |> Ezfio.set_ao_basis_integral_nuclear + ; + Ezfio.get_ao_basis_integral_nuclear () ;; - - - let to_rst b = - let print_sym = - let l = List.init (Array.length b.ao_power) ~f:( - fun i -> ( (i+1),b.ao_nucl.(i),b.ao_power.(i) ) ) in - let rec do_work = function - | [] -> [] - | (i,n,x)::tail -> - (Printf.sprintf " %5d %6d %-8s\n" i (Nucl_number.to_int n) (Symmetry.Xyz.to_string x)):: - (do_work tail) - in do_work l - |> String.concat - in - - let short_basis = to_basis b in - Printf.sprintf " -Name of the AO basis :: - - ao_basis = %s - -Cartesian coordinates (6d,10f,...) :: - - ao_cartesian = %s - -Basis set (read-only) :: - -%s - - -======= ========= =========== - Basis Nucleus Symmetries -======= ========= =========== -%s -======= ========= =========== - -" (AO_basis_name.to_string b.ao_basis) - (Bool.to_string b.ao_cartesian) - (Basis.to_string short_basis - |> String.split ~on:'\n' - |> List.map ~f:(fun x-> " "^x) - |> String.concat ~sep:"\n" - ) print_sym - - |> Rst_string.of_string +(* Write snippet for integral_nuclear *) + let write_integral_nuclear = + Ezfio.set_ao_basis_integral_nuclear ;; - let read_rst s = - let s = Rst_string.to_string s - |> String.split ~on:'\n' - in - let rec extract_basis = function - | [] -> failwith "Error in basis set" - | line :: tail -> - let line = String.strip line in - if line = "Basis set (read-only) ::" then - String.concat tail ~sep:"\n" - else - extract_basis tail - in - extract_basis s +(* Read snippet for integral_overlap *) + let read_integral_overlap () = + if not (Ezfio.has_ao_basis_integral_overlap ()) then + get_default "integral_overlap" + |> Float.of_string + |> Ezfio.set_ao_basis_integral_overlap + ; + Ezfio.get_ao_basis_integral_overlap () + ;; +(* Write snippet for integral_overlap *) + let write_integral_overlap = + Ezfio.set_ao_basis_integral_overlap ;; - let to_string b = - Printf.sprintf " -ao_basis = %s -ao_num = %s -ao_prim_num = %s -ao_prim_num_max = %s -ao_nucl = %s -ao_power = %s -ao_coef = %s -ao_expo = %s -ao_cartesian = %s -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 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) - (to_md5 b |> MD5.to_string ) - +(* Read snippet for threshold_overlap_ao_eigenvalues *) + let read_threshold_overlap_ao_eigenvalues () = + if not (Ezfio.has_ao_basis_threshold_overlap_ao_eigenvalues ()) then + get_default "threshold_overlap_ao_eigenvalues" + |> Float.of_string + |> Ezfio.set_ao_basis_threshold_overlap_ao_eigenvalues + ; + Ezfio.get_ao_basis_threshold_overlap_ao_eigenvalues () + |> Threshold.of_float + ;; +(* Write snippet for threshold_overlap_ao_eigenvalues *) + let write_threshold_overlap_ao_eigenvalues var = + Threshold.to_float var + |> Ezfio.set_ao_basis_threshold_overlap_ao_eigenvalues ;; -end +(* =~=~=~=~=~=~=~=~=~=~=~=~ *) +(* Generate Global Function *) +(* =~=~=~=~=~=~=~=~=~=~=~=~ *) + +(* Read all *) + let read() = + Some + { + threshold_overlap_ao_eigenvalues = read_threshold_overlap_ao_eigenvalues (); + } + ;; +(* Write all *) + let write{ + threshold_overlap_ao_eigenvalues; + } = + write_threshold_overlap_ao_eigenvalues threshold_overlap_ao_eigenvalues; + ;; +(* to_string*) + let to_string b = + Printf.sprintf " + threshold_overlap_ao_eigenvalues = %s + " + (Threshold.to_string b.threshold_overlap_ao_eigenvalues) + ;; +(* to_rst*) + let to_rst b = + Printf.sprintf " + Threshold on the magnitude of the smallest eigenvalues of the overlap matrix in the AO basis :: + + threshold_overlap_ao_eigenvalues = %s + + " + (Threshold.to_string b.threshold_overlap_ao_eigenvalues) + |> Rst_string.of_string + ;; + include Generic_input_of_rst;; + let of_rst = of_rst t_of_sexp;; + +end \ No newline at end of file diff --git a/plugins/Hartree_Fock/EZFIO.cfg b/plugins/Hartree_Fock/EZFIO.cfg index a3e97d32..7f67d961 100644 --- a/plugins/Hartree_Fock/EZFIO.cfg +++ b/plugins/Hartree_Fock/EZFIO.cfg @@ -1,9 +1,3 @@ -[threshold_overlap_ao_eigenvalues] -type: Threshold -doc: Threshold on the magnitude of the smallest eigenvalues of the overlap matrix in the AO basis -interface: ezfio,provider,ocaml -default: 1.e-6 - [max_dim_diis] type: integer doc: Maximum size of the DIIS extrapolation procedure diff --git a/src/AO_Basis/EZFIO.cfg b/src/AO_Basis/EZFIO.cfg index 9e548514..e02f791e 100644 --- a/src/AO_Basis/EZFIO.cfg +++ b/src/AO_Basis/EZFIO.cfg @@ -76,3 +76,9 @@ size: (ao_basis.ao_num,ao_basis.ao_num) interface: ezfio default: false +[threshold_overlap_ao_eigenvalues] +type: Threshold +doc: Threshold on the magnitude of the smallest eigenvalues of the overlap matrix in the AO basis +interface: ezfio,provider,ocaml +default: 1.e-6 +