mirror of
https://github.com/QuantumPackage/qp2.git
synced 2024-08-29 20:23:40 +02:00
Merge pull request #26 from QuantumPackage/dev-lcpq
OCaml Core is not needed anymore
This commit is contained in:
commit
da1f0766dc
@ -291,7 +291,7 @@ OCaml
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.. code:: bash
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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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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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}
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PACKAGES=""
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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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|
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while true ; do
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while true ; do
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case "$1" in
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case "$1" in
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4
ocaml/.gitignore
vendored
4
ocaml/.gitignore
vendored
@ -9,13 +9,12 @@ Input_ao_two_e_erf_ints.ml
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Input_ao_two_e_ints.ml
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Input_ao_two_e_ints.ml
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Input_auto_generated.ml
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Input_auto_generated.ml
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Input_becke_numerical_grid.ml
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Input_becke_numerical_grid.ml
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Input_champ.ml
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Input_davidson.ml
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Input_davidson.ml
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Input_density_for_dft.ml
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Input_density_for_dft.ml
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Input_determinants.ml
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Input_determinants.ml
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Input_dft_keywords.ml
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Input_dft_keywords.ml
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Input_dressing.ml
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Input_dressing.ml
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Input_firth_order_der.ml
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Input_ijkl_ints_in_r3.ml
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Input_mo_one_e_ints.ml
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Input_mo_one_e_ints.ml
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Input_mo_two_e_erf_ints.ml
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Input_mo_two_e_erf_ints.ml
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Input_mo_two_e_ints.ml
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Input_mo_two_e_ints.ml
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@ -23,6 +22,7 @@ Input_nuclei.ml
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Input_perturbation.ml
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Input_perturbation.ml
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Input_pseudo.ml
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Input_pseudo.ml
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Input_scf_utils.ml
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Input_scf_utils.ml
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Input_variance.ml
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qp_create_ezfio
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qp_create_ezfio
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qp_create_ezfio.native
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qp_create_ezfio.native
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qp_edit
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qp_edit
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@ -1,4 +1,4 @@
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open Core
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open Sexplib.Std
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exception AtomError of string
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exception AtomError of string
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@ -11,20 +11,20 @@ type t =
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(** Read xyz coordinates of the atom *)
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(** Read xyz coordinates of the atom *)
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let of_string ~units s =
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let of_string ~units s =
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let buffer = s
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let buffer = s
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|> String.split ~on:' '
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|> String_ext.split ~on:' '
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|> List.filter ~f:(fun x -> x <> "")
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|> List.filter (fun x -> x <> "")
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in
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in
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match buffer with
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match buffer with
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| [ name; charge; x; y; z ] ->
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| [ name; charge; x; y; z ] ->
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{ element = Element.of_string name ;
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{ element = Element.of_string name ;
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charge = Charge.of_string charge ;
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charge = Charge.of_string charge ;
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coord = Point3d.of_string ~units (String.concat [x; y; z] ~sep:" ")
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coord = Point3d.of_string ~units (String.concat " " [x; y; z] )
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}
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}
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| [ name; x; y; z ] ->
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| [ name; x; y; z ] ->
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let e = Element.of_string name in
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let e = Element.of_string name in
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{ element = e ;
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{ element = e ;
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charge = Element.to_charge e;
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charge = Element.to_charge e;
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coord = Point3d.of_string ~units (String.concat [x; y; z] ~sep:" ")
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coord = Point3d.of_string ~units (String.concat " " [x; y; z])
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}
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}
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| _ -> raise (AtomError s)
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| _ -> raise (AtomError s)
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@ -33,7 +33,7 @@ let to_string ~units a =
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[ Element.to_string a.element ;
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[ Element.to_string a.element ;
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Charge.to_string a.charge ;
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Charge.to_string a.charge ;
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Point3d.to_string ~units a.coord ]
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Point3d.to_string ~units a.coord ]
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|> String.concat ~sep:" "
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|> String.concat " "
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let to_xyz a =
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let to_xyz a =
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12
ocaml/Bit.ml
12
ocaml/Bit.ml
@ -1,4 +1,4 @@
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open Core;;
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open Sexplib.Std
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(*
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(*
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Type for bits
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Type for bits
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@ -16,31 +16,31 @@ type t =
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let to_string = function
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let to_string = function
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| Zero -> "0"
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| Zero -> "0"
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| One -> "1"
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| One -> "1"
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;;
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let and_operator a b =
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let and_operator a b =
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match a, b with
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match a, b with
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| Zero, _ -> Zero
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| Zero, _ -> Zero
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| _, Zero -> Zero
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| _, Zero -> Zero
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| _, _ -> One
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| _, _ -> One
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;;
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let or_operator a b =
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let or_operator a b =
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match a, b with
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match a, b with
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| One, _ -> One
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| One, _ -> One
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| _, One -> One
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| _, One -> One
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| _, _ -> Zero
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| _, _ -> Zero
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;;
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let xor_operator a b =
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let xor_operator a b =
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match a, b with
|
match a, b with
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| One, Zero -> One
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| One, Zero -> One
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| Zero, One -> One
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| Zero, One -> One
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| _, _ -> Zero
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| _, _ -> Zero
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;;
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let not_operator = function
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let not_operator = function
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| One -> Zero
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| One -> Zero
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| Zero -> One
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| Zero -> One
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;;
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@ -1,5 +1,4 @@
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open Qptypes
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open Qptypes
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open Core
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(*
|
(*
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Type for bits strings
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Type for bits strings
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@ -22,15 +21,15 @@ let to_string b =
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let of_string ?(zero='0') ?(one='1') s =
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let of_string ?(zero='0') ?(one='1') s =
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String.to_list s
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List.init (String.length s) (String.get s)
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|> List.rev_map ~f:( fun c ->
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|> List.rev_map ( fun c ->
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if (c = zero) then Bit.Zero
|
if (c = zero) then Bit.Zero
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||||||
else if (c = one) then Bit.One
|
else if (c = one) then Bit.One
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else (failwith ("Error in bitstring ") ) )
|
else (failwith ("Error in bitstring ") ) )
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|
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let of_string_mp s =
|
let of_string_mp s =
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String.to_list s
|
List.init (String.length s) (String.get s)
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|> List.rev_map ~f:(function
|
|> List.rev_map (function
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||||||
| '-' -> Bit.Zero
|
| '-' -> Bit.Zero
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||||||
| '+' -> Bit.One
|
| '+' -> Bit.One
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||||||
| _ -> failwith ("Error in bitstring ") )
|
| _ -> failwith ("Error in bitstring ") )
|
||||||
@ -44,7 +43,7 @@ let of_int64 i =
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| 1L -> Bit.One :: accu |> List.rev
|
| 1L -> Bit.One :: accu |> List.rev
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||||||
| i ->
|
| i ->
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let b =
|
let b =
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match (Int64.bit_and i 1L ) with
|
match (Int64.logand i 1L ) with
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||||||
| 0L -> Bit.Zero
|
| 0L -> Bit.Zero
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||||||
| 1L -> Bit.One
|
| 1L -> Bit.One
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| _ -> raise (Failure "i land 1 not in (0,1)")
|
| _ -> raise (Failure "i land 1 not in (0,1)")
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@ -70,18 +69,18 @@ let to_int64 l =
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let rec do_work accu = function
|
let rec do_work accu = function
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| [] -> accu
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| [] -> accu
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| Bit.Zero::tail -> do_work Int64.(shift_left accu 1) tail
|
| Bit.Zero::tail -> do_work Int64.(shift_left accu 1) tail
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| 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
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||||||
in do_work Int64.zero (List.rev l)
|
in do_work Int64.zero (List.rev l)
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|
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||||||
|
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||||||
(* Create a bit list from a list of int64 *)
|
(* Create a bit list from a list of int64 *)
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||||||
let of_int64_list l =
|
let of_int64_list l =
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List.map ~f:of_int64 l
|
List.map of_int64 l
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||||||
|> List.concat
|
|> List.concat
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||||||
|
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||||||
(* Create a bit list from an array of int64 *)
|
(* Create a bit list from an array of int64 *)
|
||||||
let of_int64_array l =
|
let of_int64_array l =
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Array.map ~f:of_int64 l
|
Array.map of_int64 l
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|> Array.to_list
|
|> Array.to_list
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||||||
|> List.concat
|
|> List.concat
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||||||
|
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@ -116,7 +115,7 @@ let to_int64_list l =
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in
|
in
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let l = do_work [] [] 1 l
|
let l = do_work [] [] 1 l
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in
|
in
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List.rev_map ~f:to_int64 l
|
List.rev_map to_int64 l
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|
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(* Create an array of int64 from a bit list *)
|
(* Create an array of int64 from a bit list *)
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let to_int64_array l =
|
let to_int64_array l =
|
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@ -127,8 +126,8 @@ let to_int64_array l =
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|||||||
let of_mo_number_list n_int l =
|
let of_mo_number_list n_int l =
|
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let n_int = N_int_number.to_int n_int in
|
let n_int = N_int_number.to_int n_int in
|
||||||
let length = n_int*64 in
|
let length = n_int*64 in
|
||||||
let a = Array.create length (Bit.Zero) in
|
let a = Array.make length (Bit.Zero) in
|
||||||
List.iter ~f:(fun i-> a.((MO_number.to_int i)-1) <- Bit.One) l;
|
List.iter (fun i-> a.((MO_number.to_int i)-1) <- Bit.One) l;
|
||||||
Array.to_list a
|
Array.to_list a
|
||||||
|
|
||||||
|
|
||||||
@ -183,10 +182,10 @@ let not_operator b = logical_operator1 Bit.not_operator b
|
|||||||
|
|
||||||
|
|
||||||
let popcnt 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.One -> accu+1
|
||||||
| Bit.Zero -> accu
|
| Bit.Zero -> accu
|
||||||
)
|
) 0 b
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
@ -1,14 +1,14 @@
|
|||||||
open Core
|
open Sexplib.Std
|
||||||
|
|
||||||
type t = float [@@deriving sexp]
|
type t = float [@@deriving sexp]
|
||||||
|
|
||||||
let of_float x = x
|
let of_float x = x
|
||||||
let of_int i = Float.of_int i
|
let of_int i = float_of_int i
|
||||||
let of_string s = Float.of_string s
|
let of_string s = float_of_string s
|
||||||
|
|
||||||
|
|
||||||
let to_float x = x
|
let to_float x = x
|
||||||
let to_int x = Float.to_int x
|
let to_int x = int_of_float x
|
||||||
let to_string x =
|
let to_string x =
|
||||||
if x >= 0. then
|
if x >= 0. then
|
||||||
Printf.sprintf "+%f" x
|
Printf.sprintf "+%f" x
|
||||||
|
@ -1,4 +1,4 @@
|
|||||||
open Core
|
open Sexplib.Std
|
||||||
open Qptypes
|
open Qptypes
|
||||||
|
|
||||||
exception ElementError of string
|
exception ElementError of string
|
||||||
@ -14,7 +14,7 @@ type t =
|
|||||||
[@@deriving sexp]
|
[@@deriving sexp]
|
||||||
|
|
||||||
let of_string x =
|
let of_string x =
|
||||||
match (String.capitalize (String.lowercase x)) with
|
match (String.capitalize_ascii (String.lowercase_ascii x)) with
|
||||||
| "X" | "Dummy" -> X
|
| "X" | "Dummy" -> X
|
||||||
| "H" | "Hydrogen" -> H
|
| "H" | "Hydrogen" -> H
|
||||||
| "He" | "Helium" -> He
|
| "He" | "Helium" -> He
|
||||||
|
@ -1,4 +1,3 @@
|
|||||||
open Core
|
|
||||||
open Qptypes
|
open Qptypes
|
||||||
|
|
||||||
module Hole = struct
|
module Hole = struct
|
||||||
@ -56,7 +55,7 @@ let to_string = function
|
|||||||
"," ;
|
"," ;
|
||||||
(MO_class.to_string (Particle.to_mo_class p));
|
(MO_class.to_string (Particle.to_mo_class p));
|
||||||
"]"]
|
"]"]
|
||||||
|> String.concat ~sep:" "
|
|> String.concat " "
|
||||||
| Double (h1,p1,h2,p2) ->
|
| Double (h1,p1,h2,p2) ->
|
||||||
[ "Double Exc. : [" ;
|
[ "Double Exc. : [" ;
|
||||||
(MO_class.to_string (Hole.to_mo_class h1));
|
(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));
|
(MO_class.to_string (Particle.to_mo_class p2));
|
||||||
"]"]
|
"]"]
|
||||||
|> String.concat ~sep:" "
|
|> String.concat " "
|
||||||
|
|
||||||
|
|
||||||
|
@ -1,5 +1,6 @@
|
|||||||
(** CONTRL *)
|
(** CONTRL *)
|
||||||
type scftyp_t = RHF | ROHF | MCSCF | NONE
|
type scftyp_t = RHF | ROHF | MCSCF | NONE
|
||||||
|
|
||||||
let string_of_scftyp = function
|
let string_of_scftyp = function
|
||||||
| RHF -> "RHF"
|
| RHF -> "RHF"
|
||||||
| ROHF -> "ROHF"
|
| ROHF -> "ROHF"
|
||||||
@ -79,14 +80,14 @@ let read_until_found f tries =
|
|||||||
begin
|
begin
|
||||||
try
|
try
|
||||||
Some (read_mos x f)
|
Some (read_mos x f)
|
||||||
with Caml.Not_found ->
|
with Not_found ->
|
||||||
None
|
None
|
||||||
end
|
end
|
||||||
) None tries
|
) None tries
|
||||||
in
|
in
|
||||||
match result with
|
match result with
|
||||||
| Some mos -> mos
|
| Some mos -> mos
|
||||||
| None -> raise Caml.Not_found
|
| None -> raise Not_found
|
||||||
|
|
||||||
let read_natural_mos f =
|
let read_natural_mos f =
|
||||||
let tries = [
|
let tries = [
|
||||||
@ -116,7 +117,7 @@ type guess_t =
|
|||||||
| Natural of (int*string)
|
| Natural of (int*string)
|
||||||
|
|
||||||
let guess_of_string s =
|
let guess_of_string s =
|
||||||
match String.lowercase s with
|
match String.lowercase_ascii s with
|
||||||
| "huckel" -> Huckel
|
| "huckel" -> Huckel
|
||||||
| "hcore" -> Hcore
|
| "hcore" -> Hcore
|
||||||
| _ -> raise (Invalid_argument "Bad MO guess")
|
| _ -> raise (Invalid_argument "Bad MO guess")
|
||||||
@ -430,7 +431,7 @@ let create_cas_input ?(vecfile="") ~guess ~nstate s n_e n_a =
|
|||||||
in
|
in
|
||||||
try
|
try
|
||||||
string_of_guess (Natural (norb, vecfile))
|
string_of_guess (Natural (norb, vecfile))
|
||||||
with Caml.Not_found ->
|
with Not_found ->
|
||||||
string_of_guess (Canonical (norb, vecfile))
|
string_of_guess (Canonical (norb, vecfile))
|
||||||
end
|
end
|
||||||
;
|
;
|
||||||
|
@ -1,16 +1,16 @@
|
|||||||
open Qptypes
|
open Qptypes
|
||||||
open Core
|
open Sexplib.Std
|
||||||
|
|
||||||
type t =
|
type t =
|
||||||
{ sym : Symmetry.t ;
|
{ sym : Symmetry.t ;
|
||||||
expo : AO_expo.t ;
|
expo : AO_expo.t ;
|
||||||
} [@@deriving sexp]
|
} [@@deriving sexp]
|
||||||
|
|
||||||
let to_string p =
|
let to_string p =
|
||||||
let { sym = s ; expo = e } = p in
|
let { sym = s ; expo = e } = p in
|
||||||
Printf.sprintf "(%s, %22e)"
|
Printf.sprintf "(%s, %22e)"
|
||||||
(Symmetry.to_string s)
|
(Symmetry.to_string s)
|
||||||
(AO_expo.to_float e)
|
(AO_expo.to_float e)
|
||||||
|
|
||||||
|
|
||||||
let of_sym_expo s e =
|
let of_sym_expo s e =
|
||||||
|
@ -1,5 +1,6 @@
|
|||||||
open Core;;
|
open Sexplib
|
||||||
open Qptypes;;
|
open Sexplib.Std
|
||||||
|
open Qptypes
|
||||||
|
|
||||||
|
|
||||||
let fail_msg str (ex,range) =
|
let fail_msg str (ex,range) =
|
||||||
@ -15,25 +16,25 @@ let fail_msg str (ex,range) =
|
|||||||
let start_pos = range.start_pos.offset
|
let start_pos = range.start_pos.offset
|
||||||
and end_pos = range.end_pos.offset
|
and end_pos = range.end_pos.offset
|
||||||
in
|
in
|
||||||
let pre = String.sub ~pos:0 ~len:start_pos str
|
let pre = String.sub str 0 start_pos
|
||||||
and mid = String.sub ~pos:start_pos ~len:(end_pos-start_pos) str
|
and mid = String.sub str start_pos (end_pos-start_pos)
|
||||||
and post = String.sub ~pos:(end_pos)
|
and post = String.sub str (end_pos)
|
||||||
~len:((String.length str)-(end_pos)) str
|
((String.length str)-(end_pos))
|
||||||
in
|
in
|
||||||
let str = Printf.sprintf "%s ## %s ## %s" pre mid post
|
let str = Printf.sprintf "%s ## %s ## %s" pre mid post
|
||||||
in
|
in
|
||||||
let str = String.tr str ~target:'(' ~replacement:' '
|
let str = String_ext.tr str ~target:'(' ~replacement:' '
|
||||||
|> String.split ~on:')'
|
|> String_ext.split ~on:')'
|
||||||
|> List.map ~f:String.strip
|
|> List.map String_ext.strip
|
||||||
|> List.filter ~f:(fun x ->
|
|> List.filter (fun x ->
|
||||||
match String.substr_index x ~pos:0 ~pattern:"##" with
|
match String_ext.substr_index ~pos:0 ~pattern:"##" x with
|
||||||
| None -> false
|
| None -> false
|
||||||
| Some _ -> true
|
| Some _ -> true
|
||||||
)
|
)
|
||||||
|> String.concat ~sep:"\n"
|
|> String.concat "\n"
|
||||||
in
|
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 =
|
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
|
match ( Sexp.of_string_conv sexp t_of_sexp ) with
|
||||||
| `Result r -> Some r
|
| `Result r -> Some r
|
||||||
| `Error ex -> ( fail_msg sexp ex; None)
|
| `Error ex -> ( fail_msg sexp ex; None)
|
||||||
;;
|
|
||||||
|
|
||||||
let of_rst t_of_sexp s =
|
let of_rst t_of_sexp s =
|
||||||
Rst_string.to_string s
|
Rst_string.to_string s
|
||||||
|> String.split ~on:'\n'
|
|> String_ext.split ~on:'\n'
|
||||||
|> List.filter ~f:(fun line ->
|
|> List.filter (fun line -> String.contains line '=')
|
||||||
String.contains line '=')
|
|> List.map (fun line ->
|
||||||
|> List.map ~f:(fun line ->
|
|
||||||
"("^(
|
"("^(
|
||||||
String.tr line ~target:'=' ~replacement:' '
|
String_ext.tr ~target:'=' ~replacement:' ' line
|
||||||
)^")" )
|
)^")" )
|
||||||
|> String.concat
|
|> String.concat ""
|
||||||
|> evaluate_sexp t_of_sexp
|
|> evaluate_sexp t_of_sexp
|
||||||
;;
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
@ -1,6 +1,5 @@
|
|||||||
open Qputils;;
|
open Qputils;;
|
||||||
open Qptypes;;
|
open Qptypes;;
|
||||||
open Core;;
|
|
||||||
|
|
||||||
include Input_ao_basis;;
|
include Input_ao_basis;;
|
||||||
include Input_bitmasks;;
|
include Input_bitmasks;;
|
||||||
|
@ -1,6 +1,6 @@
|
|||||||
open Qptypes;;
|
open Qptypes;;
|
||||||
open Qputils;;
|
open Qputils;;
|
||||||
open Core;;
|
open Sexplib.Std;;
|
||||||
|
|
||||||
module Ao_basis : sig
|
module Ao_basis : sig
|
||||||
type t =
|
type t =
|
||||||
@ -52,13 +52,13 @@ end = struct
|
|||||||
let read_ao_prim_num () =
|
let read_ao_prim_num () =
|
||||||
Ezfio.get_ao_basis_ao_prim_num ()
|
Ezfio.get_ao_basis_ao_prim_num ()
|
||||||
|> Ezfio.flattened_ezfio
|
|> Ezfio.flattened_ezfio
|
||||||
|> Array.map ~f:AO_prim_number.of_int
|
|> Array.map AO_prim_number.of_int
|
||||||
;;
|
;;
|
||||||
|
|
||||||
let read_ao_prim_num_max () =
|
let read_ao_prim_num_max () =
|
||||||
Ezfio.get_ao_basis_ao_prim_num ()
|
Ezfio.get_ao_basis_ao_prim_num ()
|
||||||
|> Ezfio.flattened_ezfio
|
|> 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
|
|> AO_prim_number.of_int
|
||||||
;;
|
;;
|
||||||
|
|
||||||
@ -66,42 +66,42 @@ end = struct
|
|||||||
let nmax = Nucl_number.get_max () in
|
let nmax = Nucl_number.get_max () in
|
||||||
Ezfio.get_ao_basis_ao_nucl ()
|
Ezfio.get_ao_basis_ao_nucl ()
|
||||||
|> Ezfio.flattened_ezfio
|
|> 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 read_ao_power () =
|
||||||
let x = Ezfio.get_ao_basis_ao_power () in
|
let x = Ezfio.get_ao_basis_ao_power () in
|
||||||
let dim = x.Ezfio.dim.(0) in
|
let dim = x.Ezfio.dim.(0) in
|
||||||
let data = Ezfio.flattened_ezfio x 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
|
for i=1 to dim
|
||||||
do
|
do
|
||||||
if (data.(i-1) > 0) then
|
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
|
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
|
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;
|
done;
|
||||||
Array.map ~f:Symmetry.Xyz.of_string result
|
Array.map Symmetry.Xyz.of_string result
|
||||||
;;
|
;;
|
||||||
|
|
||||||
let read_ao_coef () =
|
let read_ao_coef () =
|
||||||
Ezfio.get_ao_basis_ao_coef ()
|
Ezfio.get_ao_basis_ao_coef ()
|
||||||
|> Ezfio.flattened_ezfio
|
|> Ezfio.flattened_ezfio
|
||||||
|> Array.map ~f:AO_coef.of_float
|
|> Array.map AO_coef.of_float
|
||||||
;;
|
;;
|
||||||
|
|
||||||
let read_ao_expo () =
|
let read_ao_expo () =
|
||||||
Ezfio.get_ao_basis_ao_expo ()
|
Ezfio.get_ao_basis_ao_expo ()
|
||||||
|> Ezfio.flattened_ezfio
|
|> Ezfio.flattened_ezfio
|
||||||
|> Array.map ~f:AO_expo.of_float
|
|> Array.map AO_expo.of_float
|
||||||
;;
|
;;
|
||||||
|
|
||||||
let read_ao_cartesian () =
|
let read_ao_cartesian () =
|
||||||
if not (Ezfio.has_ao_basis_ao_cartesian ()) then
|
if not (Ezfio.has_ao_basis_ao_cartesian ()) then
|
||||||
get_default "ao_cartesian"
|
get_default "ao_cartesian"
|
||||||
|> Bool.of_string
|
|> bool_of_string
|
||||||
|> Ezfio.set_ao_basis_ao_cartesian
|
|> Ezfio.set_ao_basis_ao_cartesian
|
||||||
;
|
;
|
||||||
Ezfio.get_ao_basis_ao_cartesian ()
|
Ezfio.get_ao_basis_ao_cartesian ()
|
||||||
@ -110,10 +110,10 @@ end = struct
|
|||||||
let to_long_basis b =
|
let to_long_basis b =
|
||||||
let ao_num = AO_number.to_int b.ao_num in
|
let ao_num = AO_number.to_int b.ao_num in
|
||||||
let gto_array = Array.init (AO_number.to_int b.ao_num)
|
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 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 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 ;
|
let prim = { GaussianPrimitive.sym = s ;
|
||||||
GaussianPrimitive.expo = b.ao_expo.(ao_num*j+i)
|
GaussianPrimitive.expo = b.ao_expo.(ao_num*j+i)
|
||||||
}
|
}
|
||||||
@ -178,14 +178,14 @@ end = struct
|
|||||||
in
|
in
|
||||||
let ao_prim_num =
|
let ao_prim_num =
|
||||||
Array.to_list 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
|
in
|
||||||
Ezfio.set_ao_basis_ao_prim_num (Ezfio.ezfio_array_of_list
|
Ezfio.set_ao_basis_ao_prim_num (Ezfio.ezfio_array_of_list
|
||||||
~rank:1 ~dim:[| ao_num |] ~data:ao_prim_num) ;
|
~rank:1 ~dim:[| ao_num |] ~data:ao_prim_num) ;
|
||||||
|
|
||||||
let ao_nucl =
|
let ao_nucl =
|
||||||
Array.to_list ao_nucl
|
Array.to_list ao_nucl
|
||||||
|> List.map ~f:Nucl_number.to_int
|
|> List.map Nucl_number.to_int
|
||||||
in
|
in
|
||||||
Ezfio.set_ao_basis_ao_nucl(Ezfio.ezfio_array_of_list
|
Ezfio.set_ao_basis_ao_nucl(Ezfio.ezfio_array_of_list
|
||||||
~rank:1 ~dim:[| ao_num |] ~data:ao_nucl) ;
|
~rank:1 ~dim:[| ao_num |] ~data:ao_nucl) ;
|
||||||
@ -193,9 +193,9 @@ end = struct
|
|||||||
let ao_power =
|
let ao_power =
|
||||||
let l = Array.to_list ao_power in
|
let l = Array.to_list ao_power in
|
||||||
List.concat [
|
List.concat [
|
||||||
(List.map ~f:(fun a -> Positive_int.to_int a.Symmetry.Xyz.x) l) ;
|
(List.map (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 (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.z) l) ]
|
||||||
in
|
in
|
||||||
Ezfio.set_ao_basis_ao_power(Ezfio.ezfio_array_of_list
|
Ezfio.set_ao_basis_ao_power(Ezfio.ezfio_array_of_list
|
||||||
~rank:2 ~dim:[| ao_num ; 3 |] ~data:ao_power) ;
|
~rank:2 ~dim:[| ao_num ; 3 |] ~data:ao_power) ;
|
||||||
@ -204,14 +204,14 @@ end = struct
|
|||||||
|
|
||||||
let ao_coef =
|
let ao_coef =
|
||||||
Array.to_list ao_coef
|
Array.to_list ao_coef
|
||||||
|> List.map ~f:AO_coef.to_float
|
|> List.map AO_coef.to_float
|
||||||
in
|
in
|
||||||
Ezfio.set_ao_basis_ao_coef(Ezfio.ezfio_array_of_list
|
Ezfio.set_ao_basis_ao_coef(Ezfio.ezfio_array_of_list
|
||||||
~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_coef) ;
|
~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_coef) ;
|
||||||
|
|
||||||
let ao_expo =
|
let ao_expo =
|
||||||
Array.to_list ao_expo
|
Array.to_list ao_expo
|
||||||
|> List.map ~f:AO_expo.to_float
|
|> List.map AO_expo.to_float
|
||||||
in
|
in
|
||||||
Ezfio.set_ao_basis_ao_expo(Ezfio.ezfio_array_of_list
|
Ezfio.set_ao_basis_ao_expo(Ezfio.ezfio_array_of_list
|
||||||
~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_expo) ;
|
~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_expo) ;
|
||||||
@ -271,58 +271,56 @@ end = struct
|
|||||||
| Some (s', g', n') ->
|
| Some (s', g', n') ->
|
||||||
if s <> s' || n <> n' then find2 (s,g,n) a (i+1)
|
if s <> s' || n <> n' then find2 (s,g,n) a (i+1)
|
||||||
else
|
else
|
||||||
let lc = List.map ~f:(fun (prim, _) -> prim) g.Gto.lc
|
let lc = List.map (fun (prim, _) -> prim) g.Gto.lc
|
||||||
and lc' = List.map ~f:(fun (prim, _) -> prim) g'.Gto.lc
|
and lc' = List.map (fun (prim, _) -> prim) g'.Gto.lc
|
||||||
in
|
in
|
||||||
if lc <> lc' then find2 (s,g,n) a (i+1) else (a.(i) <- None ; i)
|
if lc <> lc' then find2 (s,g,n) a (i+1) else (a.(i) <- None ; i)
|
||||||
in
|
in
|
||||||
find x a 0
|
find x a 0
|
||||||
in
|
in
|
||||||
let search_array = Array.map ~f:(fun i -> Some i) unordered_basis in
|
let search_array = Array.map (fun i -> Some i) unordered_basis in
|
||||||
Array.map ~f:(fun x -> find x search_array) ordered_basis
|
Array.map (fun x -> find x search_array) ordered_basis
|
||||||
;;
|
;;
|
||||||
|
|
||||||
|
|
||||||
let of_long_basis long_basis name ao_cartesian =
|
let of_long_basis long_basis name ao_cartesian =
|
||||||
let ao_num = List.length long_basis |> AO_number.of_int in
|
let ao_num = List.length long_basis |> AO_number.of_int in
|
||||||
let ao_prim_num =
|
let ao_prim_num =
|
||||||
List.map long_basis ~f:(fun (_,g,_) -> List.length g.Gto.lc
|
List.map (fun (_,g,_) -> List.length g.Gto.lc
|
||||||
|> AO_prim_number.of_int )
|
|> AO_prim_number.of_int ) long_basis
|
||||||
|> Array.of_list
|
|> Array.of_list
|
||||||
and ao_nucl =
|
and ao_nucl =
|
||||||
List.map long_basis ~f:(fun (_,_,n) -> n)
|
List.map (fun (_,_,n) -> n) long_basis
|
||||||
|> Array.of_list
|
|> Array.of_list
|
||||||
and ao_power =
|
and ao_power =
|
||||||
List.map ~f:(fun (x,_,_) -> x) long_basis
|
List.map (fun (x,_,_) -> x) long_basis
|
||||||
|> Array.of_list
|
|> Array.of_list
|
||||||
in
|
in
|
||||||
let ao_prim_num_max = Array.fold ~init:0 ~f:(fun s x ->
|
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)
|
if AO_prim_number.to_int x > s then AO_prim_number.to_int x else s) 0
|
||||||
ao_prim_num
|
ao_prim_num
|
||||||
|> AO_prim_number.of_int
|
|> AO_prim_number.of_int
|
||||||
in
|
in
|
||||||
|
|
||||||
let gtos =
|
let gtos =
|
||||||
List.map long_basis ~f:(fun (_,x,_) -> x)
|
List.map (fun (_,x,_) -> x) long_basis
|
||||||
in
|
in
|
||||||
let create_expo_coef ec =
|
let create_expo_coef ec =
|
||||||
let coefs =
|
let coefs =
|
||||||
begin match ec with
|
begin match ec with
|
||||||
| `Coefs -> List.map gtos ~f:(fun x->
|
| `Coefs -> List.map (fun x->
|
||||||
List.map x.Gto.lc ~f:(fun (_,coef) -> AO_coef.to_float coef) )
|
List.map (fun (_,coef) -> AO_coef.to_float coef) x.Gto.lc ) gtos
|
||||||
| `Expos -> List.map gtos ~f:(fun x->
|
| `Expos -> List.map (fun x->
|
||||||
List.map x.Gto.lc ~f:(fun (prim,_) -> AO_expo.to_float
|
List.map (fun (prim,_) -> AO_expo.to_float
|
||||||
prim.GaussianPrimitive.expo) )
|
prim.GaussianPrimitive.expo) x.Gto.lc ) gtos
|
||||||
end
|
end
|
||||||
in
|
in
|
||||||
let rec get_n n accu = function
|
let rec get_n n accu = function
|
||||||
| [] -> List.rev accu
|
| [] -> List.rev accu
|
||||||
| h::tail ->
|
| h::tail ->
|
||||||
let y =
|
let y =
|
||||||
begin match List.nth h n with
|
try List.nth h n
|
||||||
| Some x -> x
|
with _ -> 0.
|
||||||
| None -> 0.
|
|
||||||
end
|
|
||||||
in
|
in
|
||||||
get_n n (y::accu) tail
|
get_n n (y::accu) tail
|
||||||
in
|
in
|
||||||
@ -335,10 +333,10 @@ end = struct
|
|||||||
|
|
||||||
let ao_coef = create_expo_coef `Coefs
|
let ao_coef = create_expo_coef `Coefs
|
||||||
|> Array.of_list
|
|> Array.of_list
|
||||||
|> Array.map ~f:AO_coef.of_float
|
|> Array.map AO_coef.of_float
|
||||||
and ao_expo = create_expo_coef `Expos
|
and ao_expo = create_expo_coef `Expos
|
||||||
|> Array.of_list
|
|> Array.of_list
|
||||||
|> Array.map ~f:AO_expo.of_float
|
|> Array.map AO_expo.of_float
|
||||||
in
|
in
|
||||||
{ ao_basis = name ;
|
{ ao_basis = name ;
|
||||||
ao_num ; ao_prim_num ; ao_prim_num_max ; ao_nucl ;
|
ao_num ; ao_prim_num ; ao_prim_num_max ; ao_nucl ;
|
||||||
@ -347,17 +345,17 @@ end = struct
|
|||||||
|
|
||||||
let reorder b =
|
let reorder b =
|
||||||
let order = ordering b in
|
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
|
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
|
and ao_num = AO_number.to_int b.ao_num in
|
||||||
let ao_coef =
|
let ao_coef =
|
||||||
Array.init ao_prim_num_max ~f:(fun i ->
|
Array.init ao_prim_num_max (fun i ->
|
||||||
f @@ Array.init ao_num ~f:(fun j -> b.ao_coef.(i*ao_num + j) )
|
f @@ Array.init ao_num (fun j -> b.ao_coef.(i*ao_num + j) )
|
||||||
) |> Array.to_list |> Array.concat
|
) |> Array.to_list |> Array.concat
|
||||||
in
|
in
|
||||||
let ao_expo =
|
let ao_expo =
|
||||||
Array.init ao_prim_num_max ~f:(fun i ->
|
Array.init ao_prim_num_max (fun i ->
|
||||||
f @@ Array.init ao_num ~f:(fun j -> b.ao_expo.(i*ao_num + j) )
|
f @@ Array.init ao_num (fun j -> b.ao_expo.(i*ao_num + j) )
|
||||||
) |> Array.to_list |> Array.concat
|
) |> Array.to_list |> Array.concat
|
||||||
in
|
in
|
||||||
{ b with
|
{ b with
|
||||||
@ -373,7 +371,7 @@ end = struct
|
|||||||
|
|
||||||
let to_rst b =
|
let to_rst b =
|
||||||
let print_sym =
|
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) ) )
|
fun i -> ( (i+1),b.ao_nucl.(i),b.ao_power.(i) ) )
|
||||||
in
|
in
|
||||||
let rec do_work = function
|
let rec do_work = function
|
||||||
@ -383,7 +381,7 @@ end = struct
|
|||||||
(Symmetry.Xyz.to_string x)
|
(Symmetry.Xyz.to_string x)
|
||||||
)::(do_work tail)
|
)::(do_work tail)
|
||||||
in do_work l
|
in do_work l
|
||||||
|> String.concat
|
|> String.concat ""
|
||||||
in
|
in
|
||||||
|
|
||||||
let short_basis = to_basis b in
|
let short_basis = to_basis b in
|
||||||
@ -408,11 +406,11 @@ Basis set (read-only) ::
|
|||||||
======= ========= ===========
|
======= ========= ===========
|
||||||
|
|
||||||
" (AO_basis_name.to_string b.ao_basis)
|
" (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
|
(Basis.to_string short_basis
|
||||||
|> String.split ~on:'\n'
|
|> String_ext.split ~on:'\n'
|
||||||
|> List.map ~f:(fun x-> " "^x)
|
|> List.map (fun x-> " "^x)
|
||||||
|> String.concat ~sep:"\n"
|
|> String.concat "\n"
|
||||||
) print_sym
|
) print_sym
|
||||||
|
|
||||||
|> Rst_string.of_string
|
|> Rst_string.of_string
|
||||||
@ -420,14 +418,14 @@ Basis set (read-only) ::
|
|||||||
|
|
||||||
let read_rst s =
|
let read_rst s =
|
||||||
let s = Rst_string.to_string s
|
let s = Rst_string.to_string s
|
||||||
|> String.split ~on:'\n'
|
|> String_ext.split ~on:'\n'
|
||||||
in
|
in
|
||||||
let rec extract_basis = function
|
let rec extract_basis = function
|
||||||
| [] -> failwith "Error in basis set"
|
| [] -> failwith "Error in basis set"
|
||||||
| line :: tail ->
|
| line :: tail ->
|
||||||
let line = String.strip line in
|
let line = String.trim line in
|
||||||
if line = "Basis set (read-only) ::" then
|
if line = "Basis set (read-only) ::" then
|
||||||
String.concat tail ~sep:"\n"
|
String.concat "\n" tail
|
||||||
else
|
else
|
||||||
extract_basis tail
|
extract_basis tail
|
||||||
in
|
in
|
||||||
@ -450,17 +448,17 @@ md5 = %s
|
|||||||
(AO_basis_name.to_string b.ao_basis)
|
(AO_basis_name.to_string b.ao_basis)
|
||||||
(AO_number.to_string b.ao_num)
|
(AO_number.to_string b.ao_num)
|
||||||
(b.ao_prim_num |> Array.to_list |> List.map
|
(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)
|
(AO_prim_number.to_string b.ao_prim_num_max)
|
||||||
(b.ao_nucl |> Array.to_list |> List.map ~f:Nucl_number.to_string |>
|
(b.ao_nucl |> Array.to_list |> List.map Nucl_number.to_string |>
|
||||||
String.concat ~sep:", ")
|
String.concat ", ")
|
||||||
(b.ao_power |> Array.to_list |> List.map ~f:(fun x->
|
(b.ao_power |> Array.to_list |> List.map (fun x->
|
||||||
"("^(Symmetry.Xyz.to_string x)^")" )|> String.concat ~sep:", ")
|
"("^(Symmetry.Xyz.to_string x)^")" )|> String.concat ", ")
|
||||||
(b.ao_coef |> Array.to_list |> List.map ~f:AO_coef.to_string
|
(b.ao_coef |> Array.to_list |> List.map AO_coef.to_string
|
||||||
|> String.concat ~sep:", ")
|
|> String.concat ", ")
|
||||||
(b.ao_expo |> Array.to_list |> List.map ~f:AO_expo.to_string
|
(b.ao_expo |> Array.to_list |> List.map AO_expo.to_string
|
||||||
|> String.concat ~sep:", ")
|
|> String.concat ", ")
|
||||||
(b.ao_cartesian |> Bool.to_string)
|
(b.ao_cartesian |> string_of_bool)
|
||||||
(to_md5 b |> MD5.to_string )
|
(to_md5 b |> MD5.to_string )
|
||||||
|
|
||||||
;;
|
;;
|
||||||
|
@ -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
|
|
||||||
|
|
||||||
|
|
@ -1,6 +1,6 @@
|
|||||||
open Qptypes;;
|
open Qptypes
|
||||||
open Qputils;;
|
open Qputils
|
||||||
open Core;;
|
open Sexplib.Std
|
||||||
|
|
||||||
module Bitmasks : sig
|
module Bitmasks : sig
|
||||||
type t =
|
type t =
|
||||||
@ -59,7 +59,7 @@ end = struct
|
|||||||
|
|
||||||
let full_mask n_int =
|
let full_mask n_int =
|
||||||
let range = "[1-"^
|
let range = "[1-"^
|
||||||
(Int.to_string (Ezfio.get_mo_basis_mo_num ()))^"]"
|
(string_of_int (Ezfio.get_mo_basis_mo_num ()))^"]"
|
||||||
in
|
in
|
||||||
MO_class.create_active range
|
MO_class.create_active range
|
||||||
|> MO_class.to_bitlist n_int
|
|> MO_class.to_bitlist n_int
|
||||||
@ -75,7 +75,7 @@ end = struct
|
|||||||
full_mask n_int
|
full_mask n_int
|
||||||
in
|
in
|
||||||
let result = [ act ; act ; act ; act ; act ; act ]
|
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 )
|
let y = Bitlist.to_int64_list x in y@y )
|
||||||
|> List.concat
|
|> List.concat
|
||||||
in
|
in
|
||||||
@ -107,7 +107,7 @@ end = struct
|
|||||||
full_mask n_int
|
full_mask n_int
|
||||||
in
|
in
|
||||||
let result = [ act ; act ]
|
let result = [ act ; act ]
|
||||||
|> List.map ~f:(fun x ->
|
|> List.map (fun x ->
|
||||||
let y = Bitlist.to_int64_list x in y@y )
|
let y = Bitlist.to_int64_list x in y@y )
|
||||||
|> List.concat
|
|> List.concat
|
||||||
in
|
in
|
||||||
@ -147,12 +147,12 @@ cas = %s
|
|||||||
(Bit_kind.to_string b.bit_kind)
|
(Bit_kind.to_string b.bit_kind)
|
||||||
(Bitmask_number.to_string b.n_mask_gen)
|
(Bitmask_number.to_string b.n_mask_gen)
|
||||||
(Array.to_list b.generators
|
(Array.to_list b.generators
|
||||||
|> List.map ~f:(fun x-> Int64.to_string x)
|
|> List.map (fun x-> Int64.to_string x)
|
||||||
|> String.concat ~sep:", ")
|
|> String.concat ", ")
|
||||||
(Bitmask_number.to_string b.n_mask_cas)
|
(Bitmask_number.to_string b.n_mask_cas)
|
||||||
(Array.to_list b.cas
|
(Array.to_list b.cas
|
||||||
|> List.map ~f:(fun x-> Int64.to_string x)
|
|> List.map (fun x-> Int64.to_string x)
|
||||||
|> String.concat ~sep:", ")
|
|> String.concat ", ")
|
||||||
end
|
end
|
||||||
|
|
||||||
|
|
||||||
|
@ -1,6 +1,6 @@
|
|||||||
open Qptypes;;
|
open Qptypes;;
|
||||||
open Qputils;;
|
open Qputils;;
|
||||||
open Core;;
|
open Sexplib.Std;;
|
||||||
|
|
||||||
module Determinants_by_hand : sig
|
module Determinants_by_hand : sig
|
||||||
type t =
|
type t =
|
||||||
@ -112,7 +112,7 @@ end = struct
|
|||||||
begin
|
begin
|
||||||
Ezfio.set_determinants_n_states n_states;
|
Ezfio.set_determinants_n_states n_states;
|
||||||
let data =
|
let data =
|
||||||
Array.create n_states 1.
|
Array.make n_states 1.
|
||||||
|> Array.to_list
|
|> Array.to_list
|
||||||
in
|
in
|
||||||
Ezfio.ezfio_array_of_list ~rank:1 ~dim:[| n_states |] ~data
|
Ezfio.ezfio_array_of_list ~rank:1 ~dim:[| n_states |] ~data
|
||||||
@ -126,7 +126,7 @@ end = struct
|
|||||||
|> States_number.to_int
|
|> States_number.to_int
|
||||||
in
|
in
|
||||||
let data =
|
let data =
|
||||||
Array.map ~f:Positive_float.to_float data
|
Array.map Positive_float.to_float data
|
||||||
|> Array.to_list
|
|> Array.to_list
|
||||||
in
|
in
|
||||||
Ezfio.ezfio_array_of_list ~rank:1 ~dim:[| n_states |] ~data
|
Ezfio.ezfio_array_of_list ~rank:1 ~dim:[| n_states |] ~data
|
||||||
@ -142,21 +142,21 @@ end = struct
|
|||||||
begin
|
begin
|
||||||
let data =
|
let data =
|
||||||
Array.init n_states (fun _ -> 1./.(float_of_int n_states))
|
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
|
in
|
||||||
write_state_average_weight data
|
write_state_average_weight data
|
||||||
end;
|
end;
|
||||||
let result =
|
let result =
|
||||||
Ezfio.get_determinants_state_average_weight ()
|
Ezfio.get_determinants_state_average_weight ()
|
||||||
|> Ezfio.flattened_ezfio
|
|> Ezfio.flattened_ezfio
|
||||||
|> Array.map ~f:Positive_float.of_float
|
|> Array.map Positive_float.of_float
|
||||||
in
|
in
|
||||||
if Array.length result = n_states then
|
if Array.length result = n_states then
|
||||||
result
|
result
|
||||||
else
|
else
|
||||||
let data =
|
let data =
|
||||||
Array.init n_states (fun _ -> 1./.(float_of_int n_states))
|
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
|
in
|
||||||
(write_state_average_weight data; data)
|
(write_state_average_weight data; data)
|
||||||
;;
|
;;
|
||||||
@ -189,18 +189,18 @@ end = struct
|
|||||||
|> States_number.to_int
|
|> States_number.to_int
|
||||||
in
|
in
|
||||||
Ezfio.ezfio_array_of_list ~rank:2 ~dim:[| 1 ; n_states |]
|
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
|
|> Ezfio.set_determinants_psi_coef
|
||||||
end;
|
end;
|
||||||
Ezfio.get_determinants_psi_coef ()
|
Ezfio.get_determinants_psi_coef ()
|
||||||
|> Ezfio.flattened_ezfio
|
|> 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 write_psi_coef ~n_det ~n_states c =
|
||||||
let n_det = Det_number.to_int n_det
|
let n_det = Det_number.to_int n_det
|
||||||
and c = Array.to_list c
|
and c = Array.to_list c
|
||||||
|> List.map ~f:Det_coef.to_float
|
|> List.map Det_coef.to_float
|
||||||
and n_states =
|
and n_states =
|
||||||
States_number.to_int n_states
|
States_number.to_int n_states
|
||||||
in
|
in
|
||||||
@ -242,9 +242,9 @@ end = struct
|
|||||||
assert (n_int = dim.(0));
|
assert (n_int = dim.(0));
|
||||||
assert (dim.(1) = 2);
|
assert (dim.(1) = 2);
|
||||||
assert (dim.(2) = (Det_number.to_int (read_n_det ())));
|
assert (dim.(2) = (Det_number.to_int (read_n_det ())));
|
||||||
List.init dim.(2) ~f:(fun i ->
|
List.init dim.(2) (fun i ->
|
||||||
Array.sub ~pos:(2*n_int*i) ~len:(2*n_int) data)
|
Array.sub data (2*n_int*i) (2*n_int) )
|
||||||
|> List.map ~f:(Determinant.of_int64_array
|
|> List.map (Determinant.of_int64_array
|
||||||
~n_int:(N_int_number.of_int n_int)
|
~n_int:(N_int_number.of_int n_int)
|
||||||
~alpha:n_alpha ~beta:n_beta )
|
~alpha:n_alpha ~beta:n_beta )
|
||||||
|> Array.of_list
|
|> Array.of_list
|
||||||
@ -332,18 +332,19 @@ end = struct
|
|||||||
else
|
else
|
||||||
"0."
|
"0."
|
||||||
)
|
)
|
||||||
|> String.concat_array ~sep:"\t"
|
|> Array.to_list |> String.concat "\t"
|
||||||
in
|
in
|
||||||
Array.init ndet ~f:(fun i ->
|
Array.init ndet (fun i ->
|
||||||
Printf.sprintf " %s\n%s\n"
|
Printf.sprintf " %s\n%s\n"
|
||||||
(coefs_string i)
|
(coefs_string i)
|
||||||
(Determinant.to_string ~mo_num:mo_num b.psi_det.(i)
|
(Determinant.to_string ~mo_num:mo_num b.psi_det.(i)
|
||||||
|> String.split ~on:'\n'
|
|> String_ext.split ~on:'\n'
|
||||||
|> List.map ~f:(fun x -> " "^x)
|
|> List.map (fun x -> " "^x)
|
||||||
|> String.concat ~sep:"\n"
|
|> String.concat "\n"
|
||||||
)
|
)
|
||||||
)
|
)
|
||||||
|> String.concat_array ~sep:"\n"
|
|> Array.to_list
|
||||||
|
|> String.concat "\n"
|
||||||
in
|
in
|
||||||
Printf.sprintf "
|
Printf.sprintf "
|
||||||
Force the selected wave function to be an eigenfunction of S^2.
|
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.expected_s2 |> Positive_float.to_string)
|
||||||
(b.n_det |> Det_number.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
|
det_text
|
||||||
|> Rst_string.of_string
|
|> Rst_string.of_string
|
||||||
;;
|
;;
|
||||||
@ -388,11 +389,11 @@ psi_det = %s
|
|||||||
(b.n_det |> Det_number.to_string)
|
(b.n_det |> Det_number.to_string)
|
||||||
(b.n_states |> States_number.to_string)
|
(b.n_states |> States_number.to_string)
|
||||||
(b.expected_s2 |> Positive_float.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.state_average_weight |> Array.to_list |> List.map Positive_float.to_string |> String.concat ",")
|
||||||
(b.psi_coef |> Array.to_list |> List.map ~f:Det_coef.to_string
|
(b.psi_coef |> Array.to_list |> List.map Det_coef.to_string
|
||||||
|> String.concat ~sep:", ")
|
|> String.concat ", ")
|
||||||
(b.psi_det |> Array.to_list |> List.map ~f:(Determinant.to_string
|
(b.psi_det |> Array.to_list |> List.map (Determinant.to_string
|
||||||
~mo_num) |> String.concat ~sep:"\n\n")
|
~mo_num) |> String.concat "\n\n")
|
||||||
;;
|
;;
|
||||||
|
|
||||||
let of_rst r =
|
let of_rst r =
|
||||||
@ -400,33 +401,36 @@ psi_det = %s
|
|||||||
in
|
in
|
||||||
|
|
||||||
(* Split into header and determinants data *)
|
(* 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
|
in
|
||||||
let (header, dets) =
|
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
|
in
|
||||||
|
|
||||||
(* Handle header *)
|
(* Handle header *)
|
||||||
let header = r
|
let header = r
|
||||||
|> String.split ~on:'\n'
|
|> String_ext.split ~on:'\n'
|
||||||
|> List.filter ~f:(fun line ->
|
|> List.filter (fun line ->
|
||||||
if (line = "") then
|
if (line = "") then
|
||||||
false
|
false
|
||||||
else
|
else
|
||||||
( (String.contains line '=') && (line.[0] = ' ') )
|
( (String.contains line '=') && (line.[0] = ' ') )
|
||||||
)
|
)
|
||||||
|> List.map ~f:(fun line ->
|
|> List.map (fun line ->
|
||||||
"("^(
|
"("^(
|
||||||
String.tr line ~target:'=' ~replacement:' '
|
String_ext.tr line ~target:'=' ~replacement:' '
|
||||||
|> String.strip
|
|> String.trim
|
||||||
)^")" )
|
)^")" )
|
||||||
|> String.concat
|
|> String.concat ""
|
||||||
in
|
in
|
||||||
|
|
||||||
(* Handle determinant coefs *)
|
(* Handle determinant coefs *)
|
||||||
let dets = match ( dets
|
let dets = match ( dets
|
||||||
|> String.split ~on:'\n'
|
|> String_ext.split ~on:'\n'
|
||||||
|> List.map ~f:(String.strip)
|
|> List.map String.trim
|
||||||
) with
|
) with
|
||||||
| _::lines -> lines
|
| _::lines -> lines
|
||||||
| _ -> failwith "Error in determinants"
|
| _ -> failwith "Error in determinants"
|
||||||
@ -438,8 +442,8 @@ psi_det = %s
|
|||||||
| ""::""::tail -> read_coefs accu tail
|
| ""::""::tail -> read_coefs accu tail
|
||||||
| ""::c::tail ->
|
| ""::c::tail ->
|
||||||
let c =
|
let c =
|
||||||
String.split ~on:'\t' c
|
String_ext.split ~on:'\t' c
|
||||||
|> List.map ~f:(fun x -> Det_coef.of_float (Float.of_string x))
|
|> List.map (fun x -> Det_coef.of_float (Float.of_string x))
|
||||||
|> Array.of_list
|
|> Array.of_list
|
||||||
in
|
in
|
||||||
read_coefs (c::accu) tail
|
read_coefs (c::accu) tail
|
||||||
@ -450,15 +454,15 @@ psi_det = %s
|
|||||||
read_coefs [] dets
|
read_coefs [] dets
|
||||||
in
|
in
|
||||||
let nstates =
|
let nstates =
|
||||||
List.hd_exn buffer
|
List.hd buffer
|
||||||
|> Array.length
|
|> Array.length
|
||||||
in
|
in
|
||||||
let extract_state i =
|
let extract_state i =
|
||||||
let i =
|
let i =
|
||||||
i-1
|
i-1
|
||||||
in
|
in
|
||||||
List.map ~f:(fun x -> Det_coef.to_string x.(i)) buffer
|
List.map (fun x -> Det_coef.to_string x.(i)) buffer
|
||||||
|> String.concat ~sep:" "
|
|> String.concat " "
|
||||||
in
|
in
|
||||||
let rec build_result = function
|
let rec build_result = function
|
||||||
| 1 -> extract_state 1
|
| 1 -> extract_state 1
|
||||||
@ -492,21 +496,12 @@ psi_det = %s
|
|||||||
| _::tail -> read_dets accu tail
|
| _::tail -> read_dets accu tail
|
||||||
in
|
in
|
||||||
let dets =
|
let dets =
|
||||||
List.map ~f:String.rev dets
|
List.map String_ext.rev dets
|
||||||
in
|
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 =
|
let a =
|
||||||
read_dets [] dets
|
read_dets [] dets
|
||||||
|> String.concat
|
|> String.concat ""
|
||||||
in
|
in
|
||||||
Gc.set control;
|
|
||||||
"(psi_det ("^a^"))"
|
"(psi_det ("^a^"))"
|
||||||
in
|
in
|
||||||
|
|
||||||
@ -520,7 +515,7 @@ psi_det = %s
|
|||||||
Printf.sprintf "(n_states %d)" (States_number.to_int @@ read_n_states ())
|
Printf.sprintf "(n_states %d)" (States_number.to_int @@ read_n_states ())
|
||||||
in
|
in
|
||||||
let s =
|
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
|
in
|
||||||
|
|
||||||
|
|
||||||
@ -603,16 +598,16 @@ psi_det = %s
|
|||||||
States_number.to_int det.n_states
|
States_number.to_int det.n_states
|
||||||
in
|
in
|
||||||
Range.to_int_list range
|
Range.to_int_list range
|
||||||
|> List.iter ~f:(fun istate ->
|
|> List.iter (fun istate ->
|
||||||
if istate > n_states then
|
if istate > n_states then
|
||||||
failwith "State to extract should not be greater than n_states")
|
failwith "State to extract should not be greater than n_states")
|
||||||
;
|
;
|
||||||
let sorted_list =
|
let sorted_list =
|
||||||
Range.to_int_list range
|
Range.to_int_list range
|
||||||
|> List.sort ~compare
|
|> List.sort compare
|
||||||
in
|
in
|
||||||
let state_shift = ref 0 in
|
let state_shift = ref 0 in
|
||||||
List.iter ~f:(fun istate ->
|
List.iter (fun istate ->
|
||||||
let j =
|
let j =
|
||||||
istate - 1
|
istate - 1
|
||||||
in
|
in
|
||||||
|
@ -1,6 +1,6 @@
|
|||||||
open Qptypes;;
|
open Qptypes
|
||||||
open Qputils;;
|
open Qputils
|
||||||
open Core;;
|
open Sexplib.Std
|
||||||
|
|
||||||
module Electrons : sig
|
module Electrons : sig
|
||||||
type t =
|
type t =
|
||||||
|
@ -1,6 +1,6 @@
|
|||||||
open Qptypes
|
open Qptypes
|
||||||
open Qputils
|
open Qputils
|
||||||
open Core
|
open Sexplib.Std
|
||||||
|
|
||||||
|
|
||||||
module Mo_basis : sig
|
module Mo_basis : sig
|
||||||
@ -38,9 +38,10 @@ end = struct
|
|||||||
|
|
||||||
let reorder b ordering =
|
let reorder b ordering =
|
||||||
{ b with mo_coef =
|
{ b with mo_coef =
|
||||||
Array.map ~f:(fun mo ->
|
Array.map (fun mo ->
|
||||||
Array.init ~f:(fun i -> mo.(ordering.(i))) (Array.length mo) )
|
Array.init (Array.length mo)
|
||||||
b.mo_coef
|
(fun i -> mo.(ordering.(i)))
|
||||||
|
) b.mo_coef
|
||||||
}
|
}
|
||||||
|
|
||||||
let read_ao_md5 () =
|
let read_ao_md5 () =
|
||||||
@ -73,7 +74,7 @@ end = struct
|
|||||||
begin
|
begin
|
||||||
let mo_num = MO_number.to_int (read_mo_num ()) in
|
let mo_num = MO_number.to_int (read_mo_num ()) in
|
||||||
let data =
|
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
|
|> Array.to_list
|
||||||
in
|
in
|
||||||
Ezfio.ezfio_array_of_list ~rank:1
|
Ezfio.ezfio_array_of_list ~rank:1
|
||||||
@ -81,7 +82,7 @@ end = struct
|
|||||||
|> Ezfio.set_mo_basis_mo_class
|
|> Ezfio.set_mo_basis_mo_class
|
||||||
end;
|
end;
|
||||||
Ezfio.flattened_ezfio (Ezfio.get_mo_basis_mo_class () )
|
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 () =
|
let read_mo_occ () =
|
||||||
@ -90,7 +91,7 @@ end = struct
|
|||||||
let elec_alpha_num = Ezfio.get_electrons_elec_alpha_num ()
|
let elec_alpha_num = Ezfio.get_electrons_elec_alpha_num ()
|
||||||
and elec_beta_num = Ezfio.get_electrons_elec_beta_num ()
|
and elec_beta_num = Ezfio.get_electrons_elec_beta_num ()
|
||||||
and mo_num = MO_number.to_int (read_mo_num ()) in
|
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.
|
if (i<elec_beta_num) then 2.
|
||||||
else if (i < elec_alpha_num) then 1.
|
else if (i < elec_alpha_num) then 1.
|
||||||
else 0.) |> Array.to_list in
|
else 0.) |> Array.to_list in
|
||||||
@ -99,18 +100,18 @@ end = struct
|
|||||||
|> Ezfio.set_mo_basis_mo_occ
|
|> Ezfio.set_mo_basis_mo_occ
|
||||||
end;
|
end;
|
||||||
Ezfio.flattened_ezfio (Ezfio.get_mo_basis_mo_occ () )
|
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 read_mo_coef () =
|
||||||
let a = Ezfio.get_mo_basis_mo_coef ()
|
let a = Ezfio.get_mo_basis_mo_coef ()
|
||||||
|> Ezfio.flattened_ezfio
|
|> Ezfio.flattened_ezfio
|
||||||
|> Array.map ~f:MO_coef.of_float
|
|> Array.map MO_coef.of_float
|
||||||
in
|
in
|
||||||
let mo_num = read_mo_num () |> MO_number.to_int in
|
let mo_num = read_mo_num () |> MO_number.to_int in
|
||||||
let ao_num = (Array.length a)/mo_num in
|
let ao_num = (Array.length a)/mo_num in
|
||||||
Array.init mo_num ~f:(fun j ->
|
Array.init mo_num (fun j ->
|
||||||
Array.sub ~pos:(j*ao_num) ~len:(ao_num) a
|
Array.sub a (j*ao_num) (ao_num)
|
||||||
)
|
)
|
||||||
|
|
||||||
|
|
||||||
@ -136,14 +137,14 @@ end = struct
|
|||||||
| 1 ->
|
| 1 ->
|
||||||
let header = [ Printf.sprintf " #%15d" (imin+1) ; ] in
|
let header = [ Printf.sprintf " #%15d" (imin+1) ; ] in
|
||||||
let new_lines =
|
let new_lines =
|
||||||
List.init ao_num ~f:(fun i ->
|
List.init ao_num (fun i ->
|
||||||
Printf.sprintf " %3d %15.10f " (i+1)
|
Printf.sprintf " %3d %15.10f " (i+1)
|
||||||
(MO_coef.to_float mo_coef.(imin ).(i)) )
|
(MO_coef.to_float mo_coef.(imin ).(i)) )
|
||||||
in header @ new_lines
|
in header @ new_lines
|
||||||
| 2 ->
|
| 2 ->
|
||||||
let header = [ Printf.sprintf " #%15d %15d" (imin+1) (imin+2) ; ] in
|
let header = [ Printf.sprintf " #%15d %15d" (imin+1) (imin+2) ; ] in
|
||||||
let new_lines =
|
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)
|
Printf.sprintf " %3d %15.10f %15.10f" (i+1)
|
||||||
(MO_coef.to_float mo_coef.(imin ).(i))
|
(MO_coef.to_float mo_coef.(imin ).(i))
|
||||||
(MO_coef.to_float mo_coef.(imin+1).(i)) )
|
(MO_coef.to_float mo_coef.(imin+1).(i)) )
|
||||||
@ -152,7 +153,7 @@ end = struct
|
|||||||
let header = [ Printf.sprintf " #%15d %15d %15d"
|
let header = [ Printf.sprintf " #%15d %15d %15d"
|
||||||
(imin+1) (imin+2) (imin+3); ] in
|
(imin+1) (imin+2) (imin+3); ] in
|
||||||
let new_lines =
|
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)
|
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 ).(i))
|
||||||
(MO_coef.to_float mo_coef.(imin+1).(i))
|
(MO_coef.to_float mo_coef.(imin+1).(i))
|
||||||
@ -162,7 +163,7 @@ end = struct
|
|||||||
let header = [ Printf.sprintf " #%15d %15d %15d %15d"
|
let header = [ Printf.sprintf " #%15d %15d %15d %15d"
|
||||||
(imin+1) (imin+2) (imin+3) (imin+4) ; ] in
|
(imin+1) (imin+2) (imin+3) (imin+4) ; ] in
|
||||||
let new_lines =
|
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)
|
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 ).(i))
|
||||||
(MO_coef.to_float mo_coef.(imin+1).(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"
|
let header = [ Printf.sprintf " #%15d %15d %15d %15d %15d"
|
||||||
(imin+1) (imin+2) (imin+3) (imin+4) (imin+5) ; ] in
|
(imin+1) (imin+2) (imin+3) (imin+4) (imin+5) ; ] in
|
||||||
let new_lines =
|
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)
|
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 ).(i))
|
||||||
(MO_coef.to_float mo_coef.(imin+1).(i))
|
(MO_coef.to_float mo_coef.(imin+1).(i))
|
||||||
@ -185,11 +186,11 @@ end = struct
|
|||||||
in
|
in
|
||||||
let rec create_list accu i =
|
let rec create_list accu i =
|
||||||
if (i+4 < mo_num) then
|
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
|
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
|
in
|
||||||
create_list [] 0 |> String.concat ~sep:"\n\n"
|
create_list [] 0 |> String.concat "\n\n"
|
||||||
|
|
||||||
|
|
||||||
let to_rst b =
|
let to_rst b =
|
||||||
@ -224,13 +225,13 @@ mo_coef = %s
|
|||||||
(MO_label.to_string b.mo_label)
|
(MO_label.to_string b.mo_label)
|
||||||
(MO_number.to_string b.mo_num)
|
(MO_number.to_string b.mo_num)
|
||||||
(b.mo_class |> Array.to_list |> List.map
|
(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
|
(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
|
(b.mo_coef |> Array.map
|
||||||
~f:(fun x-> Array.map ~f:MO_coef.to_string x |> String.concat_array
|
(fun x-> Array.map MO_coef.to_string x |>
|
||||||
~sep:"," ) |>
|
Array.to_list |> String.concat "," ) |>
|
||||||
String.concat_array ~sep:"\n" )
|
Array.to_list |> String.concat "\n" )
|
||||||
|
|
||||||
|
|
||||||
let write_mo_num n =
|
let write_mo_num n =
|
||||||
@ -245,7 +246,7 @@ mo_coef = %s
|
|||||||
|
|
||||||
let write_mo_class a =
|
let write_mo_class a =
|
||||||
let mo_num = Array.length a in
|
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
|
|> Array.to_list
|
||||||
in Ezfio.ezfio_array_of_list ~rank:1 ~dim:[| mo_num |] ~data
|
in Ezfio.ezfio_array_of_list ~rank:1 ~dim:[| mo_num |] ~data
|
||||||
|> Ezfio.set_mo_basis_mo_class
|
|> Ezfio.set_mo_basis_mo_class
|
||||||
@ -253,7 +254,7 @@ mo_coef = %s
|
|||||||
|
|
||||||
let write_mo_occ a =
|
let write_mo_occ a =
|
||||||
let mo_num = Array.length a in
|
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
|
|> Array.to_list
|
||||||
in Ezfio.ezfio_array_of_list ~rank:1 ~dim:[| mo_num |] ~data
|
in Ezfio.ezfio_array_of_list ~rank:1 ~dim:[| mo_num |] ~data
|
||||||
|> Ezfio.set_mo_basis_mo_occ
|
|> Ezfio.set_mo_basis_mo_occ
|
||||||
@ -268,7 +269,7 @@ mo_coef = %s
|
|||||||
let mo_num = Array.length a in
|
let mo_num = Array.length a in
|
||||||
let ao_num = Array.length a.(0) in
|
let ao_num = Array.length a.(0) in
|
||||||
let data =
|
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) a
|
||||||
|> Array.to_list
|
|> Array.to_list
|
||||||
|> List.concat
|
|> List.concat
|
||||||
|
@ -1,6 +1,6 @@
|
|||||||
open Qptypes;;
|
open Qptypes;;
|
||||||
open Qputils;;
|
open Qputils;;
|
||||||
open Core;;
|
open Sexplib.Std;;
|
||||||
|
|
||||||
module Nuclei_by_hand : sig
|
module Nuclei_by_hand : sig
|
||||||
type t =
|
type t =
|
||||||
@ -41,7 +41,7 @@ end = struct
|
|||||||
let read_nucl_label () =
|
let read_nucl_label () =
|
||||||
Ezfio.get_nuclei_nucl_label ()
|
Ezfio.get_nuclei_nucl_label ()
|
||||||
|> Ezfio.flattened_ezfio
|
|> Ezfio.flattened_ezfio
|
||||||
|> Array.map ~f:Element.of_string
|
|> Array.map Element.of_string
|
||||||
;;
|
;;
|
||||||
|
|
||||||
let write_nucl_label ~nucl_num labels =
|
let write_nucl_label ~nucl_num labels =
|
||||||
@ -50,7 +50,7 @@ end = struct
|
|||||||
in
|
in
|
||||||
let labels =
|
let labels =
|
||||||
Array.to_list labels
|
Array.to_list labels
|
||||||
|> List.map ~f:Element.to_string
|
|> List.map Element.to_string
|
||||||
in
|
in
|
||||||
Ezfio.ezfio_array_of_list ~rank:1
|
Ezfio.ezfio_array_of_list ~rank:1
|
||||||
~dim:[| nucl_num |] ~data:labels
|
~dim:[| nucl_num |] ~data:labels
|
||||||
@ -61,7 +61,7 @@ end = struct
|
|||||||
let read_nucl_charge () =
|
let read_nucl_charge () =
|
||||||
Ezfio.get_nuclei_nucl_charge ()
|
Ezfio.get_nuclei_nucl_charge ()
|
||||||
|> Ezfio.flattened_ezfio
|
|> Ezfio.flattened_ezfio
|
||||||
|> Array.map ~f:Charge.of_float
|
|> Array.map Charge.of_float
|
||||||
;;
|
;;
|
||||||
|
|
||||||
let write_nucl_charge ~nucl_num charges =
|
let write_nucl_charge ~nucl_num charges =
|
||||||
@ -70,7 +70,7 @@ end = struct
|
|||||||
in
|
in
|
||||||
let charges =
|
let charges =
|
||||||
Array.to_list charges
|
Array.to_list charges
|
||||||
|> List.map ~f:Charge.to_float
|
|> List.map Charge.to_float
|
||||||
in
|
in
|
||||||
Ezfio.ezfio_array_of_list ~rank:1
|
Ezfio.ezfio_array_of_list ~rank:1
|
||||||
~dim:[| nucl_num |] ~data:charges
|
~dim:[| nucl_num |] ~data:charges
|
||||||
@ -85,7 +85,7 @@ end = struct
|
|||||||
|> Ezfio.flattened_ezfio
|
|> Ezfio.flattened_ezfio
|
||||||
in
|
in
|
||||||
let zero = Point3d.of_string Units.Bohr "0. 0. 0." 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)
|
for i=0 to (nucl_num-1)
|
||||||
do
|
do
|
||||||
result.(i) <- Point3d.({ x=raw_data.(i);
|
result.(i) <- Point3d.({ x=raw_data.(i);
|
||||||
@ -101,9 +101,9 @@ end = struct
|
|||||||
in
|
in
|
||||||
let coord = Array.to_list coord in
|
let coord = Array.to_list coord in
|
||||||
let coord =
|
let coord =
|
||||||
(List.map ~f:(fun x-> x.Point3d.x) coord) @
|
(List.map (fun x-> x.Point3d.x) coord) @
|
||||||
(List.map ~f:(fun x-> x.Point3d.y) coord) @
|
(List.map (fun x-> x.Point3d.y) coord) @
|
||||||
(List.map ~f:(fun x-> x.Point3d.z) coord)
|
(List.map (fun x-> x.Point3d.z) coord)
|
||||||
in
|
in
|
||||||
Ezfio.ezfio_array_of_list ~rank:2
|
Ezfio.ezfio_array_of_list ~rank:2
|
||||||
~dim:[| nucl_num ; 3 |] ~data:coord
|
~dim:[| nucl_num ; 3 |] ~data:coord
|
||||||
@ -160,11 +160,11 @@ nucl_coord = %s
|
|||||||
"
|
"
|
||||||
(Nucl_number.to_string b.nucl_num)
|
(Nucl_number.to_string b.nucl_num)
|
||||||
(b.nucl_label |> Array.to_list |> List.map
|
(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
|
(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
|
(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 "
|
( Printf.sprintf " %d\n "
|
||||||
nucl_num
|
nucl_num
|
||||||
) :: (
|
) :: (
|
||||||
List.init nucl_num ~f:(fun i->
|
List.init nucl_num (fun i->
|
||||||
Printf.sprintf " %-3s %d %s"
|
Printf.sprintf " %-3s %d %s"
|
||||||
(b.nucl_label.(i) |> Element.to_string)
|
(b.nucl_label.(i) |> Element.to_string)
|
||||||
(b.nucl_charge.(i) |> Charge.to_int )
|
(b.nucl_charge.(i) |> Charge.to_int )
|
||||||
(b.nucl_coord.(i) |> Point3d.to_string ~units:Units.Angstrom) )
|
(b.nucl_coord.(i) |> Point3d.to_string ~units:Units.Angstrom) )
|
||||||
) |> String.concat ~sep:"\n"
|
) |> String.concat "\n"
|
||||||
in
|
in
|
||||||
Printf.sprintf "
|
Printf.sprintf "
|
||||||
Nuclear coordinates in xyz format (Angstroms) ::
|
Nuclear coordinates in xyz format (Angstroms) ::
|
||||||
@ -192,16 +192,15 @@ Nuclear coordinates in xyz format (Angstroms) ::
|
|||||||
|
|
||||||
let of_rst s =
|
let of_rst s =
|
||||||
let l = Rst_string.to_string s
|
let l = Rst_string.to_string s
|
||||||
|> String.split ~on:'\n'
|
|> String_ext.split ~on:'\n'
|
||||||
in
|
in
|
||||||
(* Find lines containing the xyz data *)
|
(* Find lines containing the xyz data *)
|
||||||
let rec extract_begin = function
|
let rec extract_begin = function
|
||||||
| [] -> raise Caml.Not_found
|
| [] -> raise Not_found
|
||||||
| line::tail ->
|
| line::tail ->
|
||||||
let line = String.strip line in
|
let line = String.trim line in
|
||||||
if (String.length line > 3) &&
|
if (String.length line > 3) &&
|
||||||
(String.sub line ~pos:((String.length line)-2)
|
(String.sub line ((String.length line)-2) 2 = "::") then
|
||||||
~len:2 = "::") then
|
|
||||||
tail
|
tail
|
||||||
else
|
else
|
||||||
extract_begin tail
|
extract_begin tail
|
||||||
@ -213,12 +212,12 @@ Nuclear coordinates in xyz format (Angstroms) ::
|
|||||||
| _ :: nucl_num :: title :: lines ->
|
| _ :: nucl_num :: title :: lines ->
|
||||||
begin
|
begin
|
||||||
let nucl_num = nucl_num
|
let nucl_num = nucl_num
|
||||||
|> String.strip
|
|> String.trim
|
||||||
|> Int.of_string
|
|> int_of_string
|
||||||
|> Nucl_number.of_int ~max:nmax
|
|> Nucl_number.of_int ~max:nmax
|
||||||
and lines = Array.of_list lines
|
and lines = Array.of_list lines
|
||||||
in
|
in
|
||||||
List.init (Nucl_number.to_int nucl_num) ~f:(fun i ->
|
List.init (Nucl_number.to_int nucl_num) (fun i ->
|
||||||
Atom.of_string Units.Angstrom lines.(i))
|
Atom.of_string Units.Angstrom lines.(i))
|
||||||
end
|
end
|
||||||
| _ -> failwith "Error in xyz format"
|
| _ -> failwith "Error in xyz format"
|
||||||
@ -227,12 +226,12 @@ Nuclear coordinates in xyz format (Angstroms) ::
|
|||||||
let result =
|
let result =
|
||||||
{ nucl_num = List.length atom_list
|
{ nucl_num = List.length atom_list
|
||||||
|> Nucl_number.of_int ~max:nmax;
|
|> Nucl_number.of_int ~max:nmax;
|
||||||
nucl_label = List.map atom_list ~f:(fun x ->
|
nucl_label = List.map (fun x ->
|
||||||
x.Atom.element) |> Array.of_list ;
|
x.Atom.element) atom_list |> Array.of_list ;
|
||||||
nucl_charge = List.map atom_list ~f:(fun x ->
|
nucl_charge = List.map (fun x ->
|
||||||
x.Atom.charge ) |> Array.of_list ;
|
x.Atom.charge ) atom_list |> Array.of_list ;
|
||||||
nucl_coord = List.map atom_list ~f:(fun x ->
|
nucl_coord = List.map (fun x ->
|
||||||
x.Atom.coord ) |> Array.of_list ;
|
x.Atom.coord ) atom_list |> Array.of_list ;
|
||||||
}
|
}
|
||||||
in Some result
|
in Some result
|
||||||
;;
|
;;
|
||||||
|
@ -1,5 +1,6 @@
|
|||||||
open Core
|
|
||||||
open Qptypes
|
open Qptypes
|
||||||
|
open Sexplib.Std
|
||||||
|
|
||||||
|
|
||||||
type t =
|
type t =
|
||||||
| Core of MO_number.t list
|
| Core of MO_number.t list
|
||||||
@ -12,8 +13,8 @@ type t =
|
|||||||
|
|
||||||
let to_string x =
|
let to_string x =
|
||||||
let print_list l =
|
let print_list l =
|
||||||
let s = List.map ~f:(fun x-> MO_number.to_int x |> string_of_int )l
|
let s = List.map (fun x-> MO_number.to_int x |> string_of_int ) l
|
||||||
|> (String.concat ~sep:", ")
|
|> (String.concat ", ")
|
||||||
in
|
in
|
||||||
"("^s^")"
|
"("^s^")"
|
||||||
in
|
in
|
||||||
@ -32,7 +33,7 @@ let to_string x =
|
|||||||
|
|
||||||
|
|
||||||
let of_string s =
|
let of_string s =
|
||||||
match (String.lowercase s) with
|
match (String.lowercase_ascii s) with
|
||||||
| "core" -> Core []
|
| "core" -> Core []
|
||||||
| "inactive" -> Inactive []
|
| "inactive" -> Inactive []
|
||||||
| "active" -> Active []
|
| "active" -> Active []
|
||||||
@ -42,7 +43,7 @@ let of_string s =
|
|||||||
|
|
||||||
|
|
||||||
let _mo_number_list_of_range range =
|
let _mo_number_list_of_range range =
|
||||||
Range.of_string range |> List.map ~f:MO_number.of_int
|
Range.of_string range |> List.map MO_number.of_int
|
||||||
|
|
||||||
|
|
||||||
let create_core range = Core (_mo_number_list_of_range range)
|
let create_core range = Core (_mo_number_list_of_range range)
|
||||||
|
@ -1,4 +1,4 @@
|
|||||||
open Core;;
|
open Sexplib.Std
|
||||||
|
|
||||||
type t =
|
type t =
|
||||||
| Guess
|
| Guess
|
||||||
@ -8,7 +8,7 @@ type t =
|
|||||||
| Orthonormalized
|
| Orthonormalized
|
||||||
| None
|
| None
|
||||||
[@@deriving sexp]
|
[@@deriving sexp]
|
||||||
;;
|
|
||||||
|
|
||||||
let to_string = function
|
let to_string = function
|
||||||
| Guess -> "Guess"
|
| Guess -> "Guess"
|
||||||
@ -20,7 +20,7 @@ let to_string = function
|
|||||||
;;
|
;;
|
||||||
|
|
||||||
let of_string s =
|
let of_string s =
|
||||||
match String.lowercase (String.strip s) with
|
match String.lowercase_ascii (String.trim s) with
|
||||||
| "guess" -> Guess
|
| "guess" -> Guess
|
||||||
| "canonical" -> Canonical
|
| "canonical" -> Canonical
|
||||||
| "natural" -> Natural
|
| "natural" -> Natural
|
||||||
|
@ -1,4 +1,4 @@
|
|||||||
open Core
|
open Sexplib.Std
|
||||||
open Qptypes
|
open Qptypes
|
||||||
|
|
||||||
(** New job : Request to create a new multi-tasked job *)
|
(** New job : Request to create a new multi-tasked job *)
|
||||||
@ -161,7 +161,7 @@ end = struct
|
|||||||
}
|
}
|
||||||
let create ~state ~tasks = { state = State.of_string state ; tasks }
|
let create ~state ~tasks = { state = State.of_string state ; tasks }
|
||||||
let to_string x =
|
let to_string x =
|
||||||
Printf.sprintf "add_task %s %s" (State.to_string x.state) (String.concat ~sep:"|" x.tasks)
|
Printf.sprintf "add_task %s %s" (State.to_string x.state) (String.concat "|" x.tasks)
|
||||||
end
|
end
|
||||||
|
|
||||||
|
|
||||||
@ -193,12 +193,12 @@ end = struct
|
|||||||
}
|
}
|
||||||
let create ~state ~task_ids =
|
let create ~state ~task_ids =
|
||||||
{ state = State.of_string state ;
|
{ state = State.of_string state ;
|
||||||
task_ids = List.map ~f:Id.Task.of_int task_ids
|
task_ids = List.map Id.Task.of_int task_ids
|
||||||
}
|
}
|
||||||
let to_string x =
|
let to_string x =
|
||||||
Printf.sprintf "del_task %s %s"
|
Printf.sprintf "del_task %s %s"
|
||||||
(State.to_string x.state)
|
(State.to_string x.state)
|
||||||
(String.concat ~sep:"|" @@ List.map ~f:Id.Task.to_string x.task_ids)
|
(String.concat "|" @@ List.map Id.Task.to_string x.task_ids)
|
||||||
end
|
end
|
||||||
|
|
||||||
|
|
||||||
@ -219,7 +219,7 @@ end = struct
|
|||||||
else "done"
|
else "done"
|
||||||
in
|
in
|
||||||
Printf.sprintf "del_task_reply %s %s"
|
Printf.sprintf "del_task_reply %s %s"
|
||||||
more (String.concat ~sep:"|" @@ List.map ~f:Id.Task.to_string x.task_ids)
|
more (String.concat "|" @@ List.map Id.Task.to_string x.task_ids)
|
||||||
end
|
end
|
||||||
|
|
||||||
|
|
||||||
@ -303,11 +303,11 @@ end = struct
|
|||||||
"get_tasks_reply ok"
|
"get_tasks_reply ok"
|
||||||
let to_string_list x =
|
let to_string_list x =
|
||||||
"get_tasks_reply ok" :: (
|
"get_tasks_reply ok" :: (
|
||||||
List.map x ~f:(fun (task_id, task) ->
|
List.map (fun (task_id, task) ->
|
||||||
match task_id with
|
match task_id with
|
||||||
| Some task_id -> Printf.sprintf "%d %s" (Id.Task.to_int task_id) task
|
| Some task_id -> Printf.sprintf "%d %s" (Id.Task.to_int task_id) task
|
||||||
| None -> Printf.sprintf "0 terminate"
|
| None -> Printf.sprintf "0 terminate"
|
||||||
) )
|
) x )
|
||||||
|
|
||||||
end
|
end
|
||||||
|
|
||||||
@ -408,14 +408,14 @@ end = struct
|
|||||||
let create ~state ~client_id ~task_ids =
|
let create ~state ~client_id ~task_ids =
|
||||||
{ client_id = Id.Client.of_int client_id ;
|
{ client_id = Id.Client.of_int client_id ;
|
||||||
state = State.of_string state ;
|
state = State.of_string state ;
|
||||||
task_ids = List.map ~f:Id.Task.of_int task_ids;
|
task_ids = List.map Id.Task.of_int task_ids;
|
||||||
}
|
}
|
||||||
|
|
||||||
let to_string x =
|
let to_string x =
|
||||||
Printf.sprintf "task_done %s %d %s"
|
Printf.sprintf "task_done %s %d %s"
|
||||||
(State.to_string x.state)
|
(State.to_string x.state)
|
||||||
(Id.Client.to_int x.client_id)
|
(Id.Client.to_int x.client_id)
|
||||||
(String.concat ~sep:"|" @@ List.map ~f:Id.Task.to_string x.task_ids)
|
(String.concat "|" @@ List.map Id.Task.to_string x.task_ids)
|
||||||
end
|
end
|
||||||
|
|
||||||
(** Terminate *)
|
(** Terminate *)
|
||||||
@ -460,7 +460,7 @@ end = struct
|
|||||||
type t = string
|
type t = string
|
||||||
let create x = x
|
let create x = x
|
||||||
let to_string x =
|
let to_string x =
|
||||||
String.concat ~sep:" " [ "error" ; x ]
|
String.concat " " [ "error" ; x ]
|
||||||
end
|
end
|
||||||
|
|
||||||
|
|
||||||
|
@ -62,7 +62,7 @@ let name m =
|
|||||||
try
|
try
|
||||||
let i = List.assoc e accu in
|
let i = List.assoc e accu in
|
||||||
build_list ( (e,i+1)::(List.remove_assoc e accu) ) rest
|
build_list ( (e,i+1)::(List.remove_assoc e accu) ) rest
|
||||||
with Caml.Not_found -> build_list ( (e,1)::accu ) rest
|
with Not_found -> build_list ( (e,1)::accu ) rest
|
||||||
end
|
end
|
||||||
| [] -> accu
|
| [] -> accu
|
||||||
in
|
in
|
||||||
@ -207,7 +207,7 @@ let distance_matrix molecule =
|
|||||||
|
|
||||||
|
|
||||||
|
|
||||||
open Core ;;
|
|
||||||
include To_md5
|
include To_md5
|
||||||
let to_md5 = to_md5 sexp_of_t
|
let to_md5 = to_md5 sexp_of_t
|
||||||
|
|
||||||
|
@ -1,10 +1,11 @@
|
|||||||
open Core;;
|
open Qptypes
|
||||||
open Qptypes ;;
|
open Sexplib.Std
|
||||||
|
|
||||||
type t = Strictly_positive_int.t [@@deriving sexp]
|
type t = Strictly_positive_int.t [@@deriving sexp]
|
||||||
|
|
||||||
let of_int = Strictly_positive_int.of_int ;;
|
let of_int = Strictly_positive_int.of_int
|
||||||
let to_int = Strictly_positive_int.to_int ;;
|
|
||||||
|
let to_int = Strictly_positive_int.to_int
|
||||||
|
|
||||||
let to_string m =
|
let to_string m =
|
||||||
match (to_int m) with
|
match (to_int m) with
|
||||||
@ -18,7 +19,7 @@ let to_string m =
|
|||||||
| 8 -> "Octet"
|
| 8 -> "Octet"
|
||||||
| 9 -> "Nonet"
|
| 9 -> "Nonet"
|
||||||
| i -> Printf.sprintf "%d-et" i
|
| i -> Printf.sprintf "%d-et" i
|
||||||
;;
|
|
||||||
|
|
||||||
let of_alpha_beta a b =
|
let of_alpha_beta a b =
|
||||||
let a = Elec_alpha_number.to_int a
|
let a = Elec_alpha_number.to_int a
|
||||||
@ -26,11 +27,11 @@ let of_alpha_beta a b =
|
|||||||
in
|
in
|
||||||
assert (a >= b);
|
assert (a >= b);
|
||||||
of_int (1 + a - b)
|
of_int (1 + a - b)
|
||||||
;;
|
|
||||||
|
|
||||||
let to_alpha_beta ne m =
|
let to_alpha_beta ne m =
|
||||||
let ne = Elec_number.to_int ne in
|
let ne = Elec_number.to_int ne in
|
||||||
let nb = (ne-(to_int m)+1)/2 in
|
let nb = (ne-(to_int m)+1)/2 in
|
||||||
let na = ne - nb in
|
let na = ne - nb in
|
||||||
(Elec_alpha_number.of_int na, Elec_beta_number.of_int nb)
|
(Elec_alpha_number.of_int na, Elec_beta_number.of_int nb)
|
||||||
;;
|
|
||||||
|
@ -1,5 +1,5 @@
|
|||||||
open Core;;
|
open Qptypes
|
||||||
open Qptypes;;
|
open Sexplib.Std
|
||||||
|
|
||||||
type t = {
|
type t = {
|
||||||
x : float ;
|
x : float ;
|
||||||
@ -21,10 +21,10 @@ let of_string ~units s =
|
|||||||
| Units.Angstrom -> Units.angstrom_to_bohr
|
| Units.Angstrom -> Units.angstrom_to_bohr
|
||||||
in
|
in
|
||||||
let l = s
|
let l = s
|
||||||
|> String.split ~on:' '
|
|> String_ext.split ~on:' '
|
||||||
|> List.filter ~f:(fun x -> x <> "")
|
|> List.filter (fun x -> x <> "")
|
||||||
|> List.map ~f:Float.of_string
|
|> List.map float_of_string
|
||||||
|> Array.of_list
|
|> Array.of_list
|
||||||
in
|
in
|
||||||
{ x = l.(0) *. f ;
|
{ x = l.(0) *. f ;
|
||||||
y = l.(1) *. f ;
|
y = l.(1) *. f ;
|
||||||
|
@ -1,5 +1,3 @@
|
|||||||
open Core
|
|
||||||
|
|
||||||
type t =
|
type t =
|
||||||
{
|
{
|
||||||
title: string;
|
title: string;
|
||||||
@ -7,14 +5,14 @@ type t =
|
|||||||
cur_value : float;
|
cur_value : float;
|
||||||
end_value : float;
|
end_value : float;
|
||||||
bar_length : int;
|
bar_length : int;
|
||||||
init_time : Time.t;
|
init_time : float;
|
||||||
dirty : bool;
|
dirty : bool;
|
||||||
next : Time.t;
|
next : float;
|
||||||
}
|
}
|
||||||
|
|
||||||
let init ?(bar_length=20) ?(start_value=0.) ?(end_value=1.) ~title =
|
let init ?(bar_length=20) ?(start_value=0.) ?(end_value=1.) ~title =
|
||||||
{ title ; start_value ; end_value ; bar_length ; cur_value=start_value ;
|
{ title ; start_value ; end_value ; bar_length ; cur_value=start_value ;
|
||||||
init_time= Time.now () ; dirty = false ; next = Time.now () }
|
init_time= Unix.time () ; dirty = false ; next = Unix.time () }
|
||||||
|
|
||||||
let update ~cur_value bar =
|
let update ~cur_value bar =
|
||||||
{ bar with cur_value ; dirty=true }
|
{ bar with cur_value ; dirty=true }
|
||||||
@ -40,23 +38,23 @@ let display_tty bar =
|
|||||||
|> Float.to_int
|
|> Float.to_int
|
||||||
in
|
in
|
||||||
let hashes =
|
let hashes =
|
||||||
String.init bar.bar_length ~f:(fun i ->
|
String.init bar.bar_length (fun i ->
|
||||||
if (i < n_hashes) then '#'
|
if (i < n_hashes) then '#'
|
||||||
else ' '
|
else ' '
|
||||||
)
|
)
|
||||||
in
|
in
|
||||||
let now =
|
let now =
|
||||||
Time.now ()
|
Unix.time ()
|
||||||
in
|
in
|
||||||
let running_time =
|
let running_time =
|
||||||
Time.abs_diff now bar.init_time
|
now -. bar.init_time
|
||||||
in
|
in
|
||||||
Printf.eprintf "%s : [%s] %4.1f%% | %10s\r%!"
|
Printf.eprintf "%s : [%s] %4.1f%% | %8.0f s\r%!"
|
||||||
bar.title
|
bar.title
|
||||||
hashes
|
hashes
|
||||||
percent
|
percent
|
||||||
(Time.Span.to_string running_time);
|
running_time;
|
||||||
{ bar with dirty = false ; next = Time.add now (Time.Span.of_sec 0.1) }
|
{ bar with dirty = false ; next = now +. 0.1 }
|
||||||
|
|
||||||
|
|
||||||
let display_file bar =
|
let display_file bar =
|
||||||
@ -65,19 +63,19 @@ let display_file bar =
|
|||||||
(bar.end_value -. bar.start_value)
|
(bar.end_value -. bar.start_value)
|
||||||
in
|
in
|
||||||
let running_time =
|
let running_time =
|
||||||
Time.abs_diff (Time.now ()) bar.init_time
|
(Unix.time ()) -. bar.init_time
|
||||||
in
|
in
|
||||||
Printf.eprintf "%5.2f %% in %20s \n%!"
|
Printf.eprintf "%5.2f %% in %20.0f seconds \n%!"
|
||||||
percent
|
percent
|
||||||
(Time.Span.to_string running_time);
|
running_time;
|
||||||
{ bar with dirty = false ; next = Time.add (Time.now ()) (Time.Span.of_sec 10.) }
|
{ bar with dirty = false ; next = (Unix.time ()) +. 10. }
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
let display bar =
|
let display bar =
|
||||||
if (not bar.dirty) then
|
if (not bar.dirty) then
|
||||||
bar
|
bar
|
||||||
else if (Time.now () < bar.next) then
|
else if (Unix.time () < bar.next) then
|
||||||
bar
|
bar
|
||||||
else
|
else
|
||||||
begin
|
begin
|
||||||
|
@ -1,4 +1,4 @@
|
|||||||
open Core
|
open Sexplib.Std
|
||||||
open Qptypes
|
open Qptypes
|
||||||
|
|
||||||
|
|
||||||
@ -81,12 +81,12 @@ let to_string_local = function
|
|||||||
| t ->
|
| t ->
|
||||||
"Local component:" ::
|
"Local component:" ::
|
||||||
( Printf.sprintf "%20s %8s %20s" "Coeff." "r^n" "Exp." ) ::
|
( Printf.sprintf "%20s %8s %20s" "Coeff." "r^n" "Exp." ) ::
|
||||||
( List.map t ~f:(fun (l,c) -> Printf.sprintf "%20f %8d %20f"
|
( List.map (fun (l,c) -> Printf.sprintf "%20f %8d %20f"
|
||||||
(AO_coef.to_float c)
|
(AO_coef.to_float c)
|
||||||
(R_power.to_int l.GaussianPrimitive_local.r_power)
|
(R_power.to_int l.GaussianPrimitive_local.r_power)
|
||||||
(AO_expo.to_float l.GaussianPrimitive_local.expo)
|
(AO_expo.to_float l.GaussianPrimitive_local.expo)
|
||||||
) )
|
) t )
|
||||||
|> String.concat ~sep:"\n"
|
|> String.concat "\n"
|
||||||
|
|
||||||
|
|
||||||
(** Transform the non-local component of the pseudopotential to a string *)
|
(** Transform the non-local component of the pseudopotential to a string *)
|
||||||
@ -95,7 +95,7 @@ let to_string_non_local = function
|
|||||||
| t ->
|
| t ->
|
||||||
"Non-local component:" ::
|
"Non-local component:" ::
|
||||||
( Printf.sprintf "%20s %8s %20s %8s" "Coeff." "r^n" "Exp." "Proj") ::
|
( Printf.sprintf "%20s %8s %20s %8s" "Coeff." "r^n" "Exp." "Proj") ::
|
||||||
( List.map t ~f:(fun (l,c) ->
|
( List.map (fun (l,c) ->
|
||||||
let p =
|
let p =
|
||||||
Positive_int.to_int l.GaussianPrimitive_non_local.proj
|
Positive_int.to_int l.GaussianPrimitive_non_local.proj
|
||||||
in
|
in
|
||||||
@ -104,8 +104,8 @@ let to_string_non_local = function
|
|||||||
(R_power.to_int l.GaussianPrimitive_non_local.r_power)
|
(R_power.to_int l.GaussianPrimitive_non_local.r_power)
|
||||||
(AO_expo.to_float l.GaussianPrimitive_non_local.expo)
|
(AO_expo.to_float l.GaussianPrimitive_non_local.expo)
|
||||||
p p
|
p p
|
||||||
) )
|
) t )
|
||||||
|> String.concat ~sep:"\n"
|
|> String.concat "\n"
|
||||||
|
|
||||||
(** Transform the Pseudopotential to a string *)
|
(** Transform the Pseudopotential to a string *)
|
||||||
let to_string t =
|
let to_string t =
|
||||||
@ -116,29 +116,30 @@ let to_string t =
|
|||||||
:: to_string_local t.local
|
:: to_string_local t.local
|
||||||
:: to_string_non_local t.non_local
|
:: to_string_non_local t.non_local
|
||||||
:: []
|
:: []
|
||||||
|> List.filter ~f:(fun x -> x <> "")
|
|> List.filter (fun x -> x <> "")
|
||||||
|> String.concat ~sep:"\n"
|
|> String.concat "\n"
|
||||||
|
|
||||||
|
|
||||||
(** Find an element in the file *)
|
(** Find an element in the file *)
|
||||||
let find in_channel element =
|
let find in_channel element =
|
||||||
In_channel.seek in_channel 0L;
|
seek_in in_channel 0;
|
||||||
|
|
||||||
let loop, element_read, old_pos =
|
let loop, element_read, old_pos =
|
||||||
ref true,
|
ref true,
|
||||||
ref None,
|
ref None,
|
||||||
ref (In_channel.pos in_channel)
|
ref (pos_in in_channel)
|
||||||
in
|
in
|
||||||
|
|
||||||
while !loop
|
while !loop
|
||||||
do
|
do
|
||||||
try
|
try
|
||||||
let buffer =
|
let buffer =
|
||||||
old_pos := In_channel.pos in_channel;
|
old_pos := pos_in in_channel;
|
||||||
match In_channel.input_line in_channel with
|
try
|
||||||
| Some line -> String.split ~on:' ' line
|
input_line in_channel
|
||||||
|> List.hd_exn
|
|> String_ext.split ~on:' '
|
||||||
| None -> raise End_of_file
|
|> List.hd
|
||||||
|
with _ -> raise End_of_file
|
||||||
in
|
in
|
||||||
element_read := Some (Element.of_string buffer);
|
element_read := Some (Element.of_string buffer);
|
||||||
loop := !element_read <> (Some element)
|
loop := !element_read <> (Some element)
|
||||||
@ -146,7 +147,7 @@ let find in_channel element =
|
|||||||
| Element.ElementError _ -> ()
|
| Element.ElementError _ -> ()
|
||||||
| End_of_file -> loop := false
|
| End_of_file -> loop := false
|
||||||
done ;
|
done ;
|
||||||
In_channel.seek in_channel !old_pos;
|
seek_in in_channel !old_pos;
|
||||||
!element_read
|
!element_read
|
||||||
|
|
||||||
|
|
||||||
@ -156,13 +157,13 @@ let read_element in_channel element =
|
|||||||
| Some e when e = element ->
|
| Some e when e = element ->
|
||||||
begin
|
begin
|
||||||
let rec read result =
|
let rec read result =
|
||||||
match In_channel.input_line in_channel with
|
try
|
||||||
| None -> result
|
let line = input_line in_channel in
|
||||||
| Some line ->
|
if (String.trim line = "") then
|
||||||
if (String.strip line = "") then
|
|
||||||
result
|
result
|
||||||
else
|
else
|
||||||
read (line::result)
|
read (line::result)
|
||||||
|
with _ -> result
|
||||||
in
|
in
|
||||||
|
|
||||||
let data =
|
let data =
|
||||||
@ -171,20 +172,20 @@ let read_element in_channel element =
|
|||||||
in
|
in
|
||||||
|
|
||||||
let debug_data =
|
let debug_data =
|
||||||
String.concat ~sep:"\n" data
|
String.concat "\n" data
|
||||||
in
|
in
|
||||||
|
|
||||||
let decode_first_line = function
|
let decode_first_line = function
|
||||||
| first_line :: rest ->
|
| first_line :: rest ->
|
||||||
begin
|
begin
|
||||||
let first_line_split =
|
let first_line_split =
|
||||||
String.split first_line ~on:' '
|
String_ext.split first_line ~on:' '
|
||||||
|> List.filter ~f:(fun x -> (String.strip x) <> "")
|
|> List.filter (fun x -> (String.trim x) <> "")
|
||||||
in
|
in
|
||||||
match first_line_split with
|
match first_line_split with
|
||||||
| e :: "GEN" :: n :: p ->
|
| e :: "GEN" :: n :: p ->
|
||||||
{ element = Element.of_string e ;
|
{ element = Element.of_string e ;
|
||||||
n_elec = Int.of_string n |> Positive_int.of_int ;
|
n_elec = int_of_string n |> Positive_int.of_int ;
|
||||||
local = [] ;
|
local = [] ;
|
||||||
non_local = []
|
non_local = []
|
||||||
}, rest
|
}, rest
|
||||||
@ -200,18 +201,18 @@ let read_element in_channel element =
|
|||||||
| (n,line::rest) ->
|
| (n,line::rest) ->
|
||||||
begin
|
begin
|
||||||
match
|
match
|
||||||
String.split line ~on:' '
|
String_ext.split line ~on:' '
|
||||||
|> List.filter ~f:(fun x -> String.strip x <> "")
|
|> List.filter (fun x -> String.trim x <> "")
|
||||||
with
|
with
|
||||||
| c :: i :: e :: [] ->
|
| c :: i :: e :: [] ->
|
||||||
let i =
|
let i =
|
||||||
Int.of_string i
|
int_of_string i
|
||||||
in
|
in
|
||||||
let elem =
|
let elem =
|
||||||
( create_primitive
|
( create_primitive
|
||||||
(Float.of_string e |> AO_expo.of_float)
|
(float_of_string e |> AO_expo.of_float)
|
||||||
(i-2 |> R_power.of_int),
|
(i-2 |> R_power.of_int),
|
||||||
Float.of_string c |> AO_coef.of_float
|
float_of_string c |> AO_coef.of_float
|
||||||
)
|
)
|
||||||
in
|
in
|
||||||
loop create_primitive (elem::accu) (n-1, rest)
|
loop create_primitive (elem::accu) (n-1, rest)
|
||||||
@ -230,8 +231,8 @@ let read_element in_channel element =
|
|||||||
match data with
|
match data with
|
||||||
| n :: rest ->
|
| n :: rest ->
|
||||||
let n =
|
let n =
|
||||||
String.strip n
|
String.trim n
|
||||||
|> Int.of_string
|
|> int_of_string
|
||||||
|> Positive_int.of_int
|
|> Positive_int.of_int
|
||||||
in
|
in
|
||||||
decode_local_n n rest
|
decode_local_n n rest
|
||||||
@ -250,8 +251,8 @@ let read_element in_channel element =
|
|||||||
match data with
|
match data with
|
||||||
| n :: rest ->
|
| n :: rest ->
|
||||||
let n =
|
let n =
|
||||||
String.strip n
|
String.trim n
|
||||||
|> Int.of_string
|
|> int_of_string
|
||||||
|> Positive_int.of_int
|
|> Positive_int.of_int
|
||||||
in
|
in
|
||||||
let result =
|
let result =
|
||||||
|
@ -1,45 +1,45 @@
|
|||||||
open Core;;
|
open Qptypes
|
||||||
open Qptypes;;
|
open Qputils
|
||||||
open Qputils;;
|
|
||||||
|
|
||||||
(** Variables related to the quantum package installation *)
|
(** Variables related to the quantum package installation *)
|
||||||
|
|
||||||
let root =
|
let root =
|
||||||
match (Sys.getenv "QP_ROOT") with
|
match (Sys.getenv_opt "QP_ROOT") with
|
||||||
| None -> failwith "QP_ROOT environment variable is not set.
|
| None -> failwith "QP_ROOT environment variable is not set.
|
||||||
Please source the quantum_package.rc file."
|
Please source the quantum_package.rc file."
|
||||||
| Some x -> x
|
| Some x -> x
|
||||||
;;
|
|
||||||
|
|
||||||
let bit_kind_size = lazy (
|
let bit_kind_size = lazy (
|
||||||
let filename = root^"/src/bitmask/bitmasks_module.f90" in
|
let filename = root^"/src/bitmask/bitmasks_module.f90" in
|
||||||
if not (Sys.file_exists_exn filename) then
|
if not (Sys.file_exists filename) then
|
||||||
raise (Failure ("File "^filename^" not found"));
|
raise (Failure ("File "^filename^" not found"));
|
||||||
|
|
||||||
let in_channel = In_channel.create filename in
|
let in_channel = open_in filename in
|
||||||
let lines = In_channel.input_lines in_channel in
|
let lines = input_lines in_channel in
|
||||||
In_channel.close in_channel;
|
close_in in_channel;
|
||||||
|
|
||||||
let rec get_data = function
|
let rec get_data = function
|
||||||
| [] -> raise (Failure ("bit_kind_size not found in "^filename))
|
| [] -> raise (Failure ("bit_kind_size not found in "^filename))
|
||||||
| line::tail ->
|
| line::tail ->
|
||||||
let line =
|
let line =
|
||||||
begin match String.split ~on:'!' line |> List.hd with
|
try
|
||||||
| Some x -> x
|
String_ext.split ~on:'!' line
|
||||||
| None -> ""
|
|> List.hd
|
||||||
end in
|
with _ -> line
|
||||||
begin match (String.rsplit2 ~on:':' line) with
|
in
|
||||||
| Some (_ ,buffer) ->
|
begin match (String_ext.rsplit2 ~on:':' line) with
|
||||||
begin match (String.split ~on:'=' buffer |> List.map ~f:String.strip) with
|
| Some (_ ,buffer) ->
|
||||||
| ["bit_kind_size"; x] ->
|
begin match (String_ext.split ~on:'=' buffer |> List.map String.trim) with
|
||||||
Int.of_string x |> Bit_kind_size.of_int
|
| ["bit_kind_size"; x] ->
|
||||||
| _ -> get_data tail
|
int_of_string x |> Bit_kind_size.of_int
|
||||||
end
|
| _ -> get_data tail
|
||||||
| _ -> get_data tail
|
end
|
||||||
end
|
| _ -> get_data tail
|
||||||
|
end
|
||||||
in
|
in
|
||||||
get_data lines )
|
get_data lines )
|
||||||
;;
|
|
||||||
|
|
||||||
let bit_kind = lazy (
|
let bit_kind = lazy (
|
||||||
Lazy.force bit_kind_size
|
Lazy.force bit_kind_size
|
||||||
@ -47,23 +47,26 @@ let bit_kind = lazy (
|
|||||||
|> fun x -> x / 8
|
|> fun x -> x / 8
|
||||||
|> Bit_kind.of_int
|
|> Bit_kind.of_int
|
||||||
)
|
)
|
||||||
;;
|
|
||||||
|
|
||||||
let executables = lazy (
|
let executables = lazy (
|
||||||
let filename = root^"/data/executables"
|
let filename = root^"/data/executables" in
|
||||||
and func in_channel =
|
let lines =
|
||||||
In_channel.input_lines in_channel
|
let in_channel = open_in filename in
|
||||||
|> List.map ~f:(fun x ->
|
let result = input_lines in_channel in
|
||||||
let e = String.split ~on:' ' x
|
close_in in_channel;
|
||||||
|> List.filter ~f:(fun x -> x <> "")
|
result
|
||||||
|
in
|
||||||
|
lines
|
||||||
|
|> List.map (fun x ->
|
||||||
|
let e = String_ext.split ~on:' ' x
|
||||||
|
|> List.filter (fun x -> x <> "")
|
||||||
in
|
in
|
||||||
match e with
|
match e with
|
||||||
| [a;b] -> (a,String.substr_replace_all ~pattern:"$QP_ROOT" ~with_:root b)
|
| [a;b] -> (a,String_ext.substr_replace_all ~pattern:"$QP_ROOT" ~with_:root b)
|
||||||
| _ -> ("","")
|
| _ -> ("","")
|
||||||
)
|
)
|
||||||
in
|
|> List.sort (fun (x,_) (y,_) ->
|
||||||
In_channel.with_file filename ~f:func
|
|
||||||
|> List.sort ~compare:(fun (x,_) (y,_) ->
|
|
||||||
if x < y then -1
|
if x < y then -1
|
||||||
else if x > y then 1
|
else if x > y then 1
|
||||||
else 0)
|
else 0)
|
||||||
@ -72,33 +75,37 @@ let executables = lazy (
|
|||||||
|
|
||||||
|
|
||||||
let get_ezfio_default_in_file ~directory ~data ~filename =
|
let get_ezfio_default_in_file ~directory ~data ~filename =
|
||||||
let lines = In_channel.with_file filename ~f:(fun in_channel ->
|
let lines =
|
||||||
In_channel.input_lines in_channel) in
|
let in_channel = open_in filename in
|
||||||
|
let result = input_lines in_channel in
|
||||||
|
close_in in_channel;
|
||||||
|
result
|
||||||
|
in
|
||||||
let rec find_dir = function
|
let rec find_dir = function
|
||||||
| line :: rest ->
|
| line :: rest ->
|
||||||
if ((String.strip line) = directory) then
|
if ((String.trim line) = directory) then
|
||||||
rest
|
rest
|
||||||
else
|
else
|
||||||
find_dir rest
|
find_dir rest
|
||||||
| [] -> raise Caml.Not_found
|
| [] -> raise Not_found
|
||||||
in
|
in
|
||||||
let rec find_data = function
|
let rec find_data = function
|
||||||
| line :: rest ->
|
| line :: rest ->
|
||||||
if (line = "") then
|
if (line = "") then
|
||||||
raise Caml.Not_found
|
raise Not_found
|
||||||
else if (line.[0] <> ' ') then
|
else if (line.[0] <> ' ') then
|
||||||
raise Caml.Not_found
|
raise Not_found
|
||||||
else
|
else
|
||||||
begin
|
begin
|
||||||
match (String.lsplit2 ~on:' ' (String.strip line)) with
|
match (String_ext.lsplit2 ~on:' ' (String.trim line)) with
|
||||||
| Some (l,r) ->
|
| Some (l,r) ->
|
||||||
if (l = data) then
|
if (l = data) then
|
||||||
String.strip r
|
String.trim r
|
||||||
else
|
else
|
||||||
find_data rest
|
find_data rest
|
||||||
| None -> raise Caml.Not_found
|
| None -> raise Not_found
|
||||||
end
|
end
|
||||||
| [] -> raise Caml.Not_found
|
| [] -> raise Not_found
|
||||||
in
|
in
|
||||||
find_dir lines
|
find_dir lines
|
||||||
|> find_data ;
|
|> find_data ;
|
||||||
@ -111,7 +118,7 @@ let get_ezfio_default directory data =
|
|||||||
| [] ->
|
| [] ->
|
||||||
begin
|
begin
|
||||||
Printf.printf "%s/%s not found\n%!" directory data;
|
Printf.printf "%s/%s not found\n%!" directory data;
|
||||||
raise Caml.Not_found
|
raise Not_found
|
||||||
end
|
end
|
||||||
| filename :: tail ->
|
| filename :: tail ->
|
||||||
let filename =
|
let filename =
|
||||||
@ -120,7 +127,7 @@ let get_ezfio_default directory data =
|
|||||||
try
|
try
|
||||||
get_ezfio_default_in_file ~directory ~data ~filename
|
get_ezfio_default_in_file ~directory ~data ~filename
|
||||||
with
|
with
|
||||||
| Caml.Not_found -> aux tail
|
| Not_found -> aux tail
|
||||||
in
|
in
|
||||||
Sys.readdir dirname
|
Sys.readdir dirname
|
||||||
|> Array.to_list
|
|> Array.to_list
|
||||||
@ -131,10 +138,7 @@ let ezfio_work ezfio_file =
|
|||||||
let result =
|
let result =
|
||||||
Filename.concat ezfio_file "work"
|
Filename.concat ezfio_file "work"
|
||||||
in
|
in
|
||||||
begin
|
if not (Sys.file_exists result) then
|
||||||
match Sys.is_directory result with
|
( Ezfio.set_file ezfio_file ; Ezfio.set_work_empty false);
|
||||||
| `Yes -> ()
|
|
||||||
| _ -> ( Ezfio.set_file ezfio_file ; Ezfio.set_work_empty false)
|
|
||||||
end;
|
|
||||||
result
|
result
|
||||||
;;
|
;;
|
||||||
|
@ -42,3 +42,14 @@ let rmdir dirname =
|
|||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
let input_lines ic =
|
||||||
|
let n = in_channel_length ic in
|
||||||
|
let s = Bytes.create n in
|
||||||
|
really_input ic s 0 n;
|
||||||
|
close_in ic;
|
||||||
|
Bytes.to_string s
|
||||||
|
|> String_ext.split ~on:'\n'
|
||||||
|
|
||||||
|
|
||||||
|
let string_of_string s = s
|
||||||
|
|
||||||
|
@ -83,7 +83,7 @@ let pop_task ~client_id q =
|
|||||||
}
|
}
|
||||||
and found =
|
and found =
|
||||||
try Some (TasksMap.find task_id q.tasks)
|
try Some (TasksMap.find task_id q.tasks)
|
||||||
with Caml.Not_found -> None
|
with Not_found -> None
|
||||||
in new_q, Some task_id, found
|
in new_q, Some task_id, found
|
||||||
| [] -> q, None, None
|
| [] -> q, None, None
|
||||||
|
|
||||||
@ -104,7 +104,7 @@ let end_task ~task_id ~client_id q =
|
|||||||
let () =
|
let () =
|
||||||
let client_id_check =
|
let client_id_check =
|
||||||
try RunningMap.find task_id running with
|
try RunningMap.find task_id running with
|
||||||
Caml.Not_found -> failwith "Task already finished"
|
Not_found -> failwith "Task already finished"
|
||||||
in
|
in
|
||||||
assert (client_id_check = client_id)
|
assert (client_id_check = client_id)
|
||||||
in
|
in
|
||||||
|
@ -3,27 +3,6 @@ include String
|
|||||||
(** Split a string on a given character *)
|
(** Split a string on a given character *)
|
||||||
let split ?(on=' ') str =
|
let split ?(on=' ') str =
|
||||||
split_on_char on str
|
split_on_char on str
|
||||||
(*
|
|
||||||
let rec do_work ?(accu=[]) ?(left="") = function
|
|
||||||
| "" -> List.rev (left::accu)
|
|
||||||
| s ->
|
|
||||||
let new_s =
|
|
||||||
(length s) - 1
|
|
||||||
|> sub s 1
|
|
||||||
in
|
|
||||||
if (s.[0] = on) then
|
|
||||||
let new_accu =
|
|
||||||
left :: accu
|
|
||||||
in
|
|
||||||
do_work ~accu:new_accu new_s
|
|
||||||
else
|
|
||||||
let new_left =
|
|
||||||
concat "" [ left ; make 1 s.[0] ]
|
|
||||||
in
|
|
||||||
do_work ~accu ~left:new_left new_s
|
|
||||||
in
|
|
||||||
do_work str
|
|
||||||
*)
|
|
||||||
|
|
||||||
|
|
||||||
(** Strip blanks on the left of a string *)
|
(** Strip blanks on the left of a string *)
|
||||||
@ -88,7 +67,7 @@ let lsplit2_exn ?(on=' ') s =
|
|||||||
(** Split a string in two pieces when a character is found the 1st time from the right *)
|
(** Split a string in two pieces when a character is found the 1st time from the right *)
|
||||||
let rsplit2_exn ?(on=' ') s =
|
let rsplit2_exn ?(on=' ') s =
|
||||||
let length =
|
let length =
|
||||||
String.length s
|
String.length s
|
||||||
in
|
in
|
||||||
let rec do_work i =
|
let rec do_work i =
|
||||||
if (i = -1) then
|
if (i = -1) then
|
||||||
@ -101,7 +80,7 @@ let rsplit2_exn ?(on=' ') s =
|
|||||||
else
|
else
|
||||||
do_work (i-1)
|
do_work (i-1)
|
||||||
in
|
in
|
||||||
do_work length
|
do_work (length-1)
|
||||||
|
|
||||||
|
|
||||||
let lsplit2 ?(on=' ') s =
|
let lsplit2 ?(on=' ') s =
|
||||||
@ -123,6 +102,15 @@ let to_list s =
|
|||||||
|> Array.to_list
|
|> Array.to_list
|
||||||
|
|
||||||
|
|
||||||
|
let of_list l =
|
||||||
|
let a = Array.of_list l in
|
||||||
|
String.init (Array.length a) (fun i -> a.(i))
|
||||||
|
|
||||||
|
let rev s =
|
||||||
|
to_list s
|
||||||
|
|> List.rev
|
||||||
|
|> of_list
|
||||||
|
|
||||||
let fold ~init ~f s =
|
let fold ~init ~f s =
|
||||||
to_list s
|
to_list s
|
||||||
|> List.fold_left f init
|
|> List.fold_left f init
|
||||||
@ -140,3 +128,23 @@ let is_prefix ~prefix s =
|
|||||||
|
|
||||||
let of_char c =
|
let of_char c =
|
||||||
String.make 1 c
|
String.make 1 c
|
||||||
|
|
||||||
|
let tr ~target ~replacement s =
|
||||||
|
String.map (fun c -> if c = target then replacement else c) s
|
||||||
|
|
||||||
|
|
||||||
|
let substr_index ?(pos=0) ~pattern s =
|
||||||
|
try
|
||||||
|
let regexp =
|
||||||
|
Str.regexp pattern
|
||||||
|
in
|
||||||
|
Some (Str.search_forward regexp s pos)
|
||||||
|
with Not_found -> None
|
||||||
|
|
||||||
|
|
||||||
|
let substr_replace_all ~pattern ~with_ s =
|
||||||
|
let regexp =
|
||||||
|
Str.regexp pattern
|
||||||
|
in
|
||||||
|
Str.global_replace regexp with_ s
|
||||||
|
|
||||||
|
@ -33,7 +33,7 @@ type t =
|
|||||||
|
|
||||||
let debug_env =
|
let debug_env =
|
||||||
try
|
try
|
||||||
Sys.getenv "QP_TASK_DEBUG"; true
|
Sys.getenv "QP_TASK_DEBUG" = "1"
|
||||||
with Not_found -> false
|
with Not_found -> false
|
||||||
|
|
||||||
|
|
||||||
|
@ -1,4 +1,4 @@
|
|||||||
true: package(core,cryptokit,zmq,str,ppx_sexp_conv,ppx_deriving,getopt)
|
true: package(cryptokit,zmq,str,sexplib,ppx_sexp_conv,ppx_deriving,getopt)
|
||||||
true: thread
|
true: thread
|
||||||
false: profile
|
false: profile
|
||||||
<*byte> : linkdep(c_bindings.o), custom
|
<*byte> : linkdep(c_bindings.o), custom
|
||||||
|
@ -4,9 +4,8 @@ SHA1=$(git log -1 | head -1 | cut -d ' ' -f 2)
|
|||||||
DATE=$(git log -1 | grep Date | cut -d ':' -f 2-)
|
DATE=$(git log -1 | grep Date | cut -d ':' -f 2-)
|
||||||
MESSAGE=$(git log -1 | tail -1 | sed 's/"/\\"/g')
|
MESSAGE=$(git log -1 | tail -1 | sed 's/"/\\"/g')
|
||||||
cat << EOF > Git.ml
|
cat << EOF > Git.ml
|
||||||
open Core
|
let sha1 = "$SHA1" |> String.trim
|
||||||
let sha1 = "$SHA1" |> String_ext.strip
|
let date = "$DATE" |> String.trim
|
||||||
let date = "$DATE" |> String_ext.strip
|
let message = "$MESSAGE" |> String.trim
|
||||||
let message = "$MESSAGE" |> String_ext.strip
|
|
||||||
EOF
|
EOF
|
||||||
|
|
||||||
|
@ -1,4 +1,3 @@
|
|||||||
open Core
|
|
||||||
open Qptypes
|
open Qptypes
|
||||||
open Element
|
open Element
|
||||||
|
|
||||||
@ -6,22 +5,22 @@ let () =
|
|||||||
let indices =
|
let indices =
|
||||||
Array.init 78 (fun i -> i)
|
Array.init 78 (fun i -> i)
|
||||||
in
|
in
|
||||||
Out_channel.with_file (Qpackage.root ^ "/data/list_element.txt")
|
let out_channel =
|
||||||
~f:(fun out_channel ->
|
open_out (Qpackage.root ^ "/data/list_element.txt")
|
||||||
Array.init 110 ~f:(fun i ->
|
in
|
||||||
let element =
|
Array.init 110 (fun i ->
|
||||||
try
|
let element =
|
||||||
Some (of_charge (Charge.of_int i))
|
try
|
||||||
with
|
Some (of_charge (Charge.of_int i))
|
||||||
| _ -> None
|
with
|
||||||
in
|
| _ -> None
|
||||||
match element with
|
in
|
||||||
| None -> ""
|
match element with
|
||||||
| Some x -> Printf.sprintf "%3d %3s %s %f\n"
|
| None -> ""
|
||||||
i (to_string x) (to_long_string x) (Positive_float.to_float @@ mass x )
|
| Some x -> Printf.sprintf "%3d %3s %s %f\n"
|
||||||
)
|
i (to_string x) (to_long_string x) (Positive_float.to_float @@ mass x )
|
||||||
|> Array.to_list
|
|
||||||
|> String.concat ~sep:""
|
|
||||||
|> Out_channel.output_string out_channel
|
|
||||||
)
|
)
|
||||||
|
|> Array.to_list
|
||||||
|
|> String.concat ""
|
||||||
|
|> Printf.fprintf out_channel "%s"
|
||||||
|
|
||||||
|
@ -1,6 +1,6 @@
|
|||||||
open Qputils
|
open Qputils
|
||||||
open Qptypes
|
open Qptypes
|
||||||
open Core
|
open Sexplib.Std
|
||||||
|
|
||||||
type element =
|
type element =
|
||||||
| Element of Element.t
|
| Element of Element.t
|
||||||
@ -38,7 +38,7 @@ let dummy_centers ~threshold ~molecule ~nuclei =
|
|||||||
| _ -> assert false
|
| _ -> assert false
|
||||||
in
|
in
|
||||||
aux [] (n-1,n-1)
|
aux [] (n-1,n-1)
|
||||||
|> List.map ~f:(fun (i,x,j,y,r) ->
|
|> List.map (fun (i,x,j,y,r) ->
|
||||||
let f =
|
let f =
|
||||||
x /. (x +. y)
|
x /. (x +. y)
|
||||||
in
|
in
|
||||||
@ -58,22 +58,22 @@ let dummy_centers ~threshold ~molecule ~nuclei =
|
|||||||
(** Returns the list of available basis sets *)
|
(** Returns the list of available basis sets *)
|
||||||
let list_basis () =
|
let list_basis () =
|
||||||
let basis_list =
|
let basis_list =
|
||||||
let ic = Pervasives.open_in (Qpackage.root ^ "/data/basis/00_README.rst") in
|
let ic = open_in (Qpackage.root ^ "/data/basis/00_README.rst") in
|
||||||
let n = Pervasives.in_channel_length ic in
|
let n = in_channel_length ic in
|
||||||
let s = Bytes.create n in
|
let s = Bytes.create n in
|
||||||
Pervasives.really_input ic s 0 n;
|
really_input ic s 0 n;
|
||||||
Pervasives.close_in ic;
|
close_in ic;
|
||||||
Bytes.to_string s
|
Bytes.to_string s
|
||||||
|> String.split ~on:'\n'
|
|> String_ext.split ~on:'\n'
|
||||||
|> List.filter ~f:(fun line -> String.length line > 1 && line.[0] <> '#')
|
|> List.filter (fun line -> String.length line > 1 && line.[0] <> '#')
|
||||||
|> List.map ~f:(fun line ->
|
|> List.map (fun line ->
|
||||||
match String.split ~on:'\'' line with
|
match String_ext.split ~on:'\'' line with
|
||||||
| file :: name :: descr :: _ ->
|
| file :: name :: descr :: _ ->
|
||||||
Printf.sprintf "%s\n %s\n %s\n\n" file name (String.strip descr)
|
Printf.sprintf "%s\n %s\n %s\n\n" file name (String.trim descr)
|
||||||
| _ -> assert false
|
| _ -> assert false
|
||||||
)
|
)
|
||||||
in
|
in
|
||||||
List.sort basis_list ~compare:String.ascending
|
List.sort compare basis_list
|
||||||
|
|
||||||
|
|
||||||
(** Run the program *)
|
(** Run the program *)
|
||||||
@ -101,7 +101,7 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
**********)
|
**********)
|
||||||
|
|
||||||
let basis_table =
|
let basis_table =
|
||||||
Hashtbl.Poly.create ()
|
Hashtbl.create 63
|
||||||
in
|
in
|
||||||
|
|
||||||
(* Open basis set channels *)
|
(* Open basis set channels *)
|
||||||
@ -111,10 +111,7 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
| Element e -> Element.to_string e
|
| Element e -> Element.to_string e
|
||||||
| Int_elem (i,e) -> Printf.sprintf "%d,%s" (Nucl_number.to_int i) (Element.to_string e)
|
| Int_elem (i,e) -> Printf.sprintf "%d,%s" (Nucl_number.to_int i) (Element.to_string e)
|
||||||
in
|
in
|
||||||
match Hashtbl.find basis_table key with
|
Hashtbl.find basis_table key
|
||||||
| Some in_channel ->
|
|
||||||
in_channel
|
|
||||||
| None -> raise Caml.Not_found
|
|
||||||
in
|
in
|
||||||
|
|
||||||
let temp_filename =
|
let temp_filename =
|
||||||
@ -129,11 +126,11 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
Qpackage.root ^ "/data/basis/" ^ basis
|
Qpackage.root ^ "/data/basis/" ^ basis
|
||||||
in
|
in
|
||||||
match
|
match
|
||||||
Sys.is_file basis,
|
Sys.file_exists basis,
|
||||||
Sys.is_file long_basis
|
Sys.file_exists long_basis
|
||||||
with
|
with
|
||||||
| `Yes, _ -> In_channel.create basis
|
| true , _ -> open_in basis
|
||||||
| `No , `Yes -> In_channel.create long_basis
|
| false, true -> open_in long_basis
|
||||||
| _ -> failwith ("Basis "^basis^" not found")
|
| _ -> failwith ("Basis "^basis^" not found")
|
||||||
in
|
in
|
||||||
|
|
||||||
@ -141,7 +138,7 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
| [] -> ()
|
| [] -> ()
|
||||||
| elem_and_basis_name :: rest ->
|
| elem_and_basis_name :: rest ->
|
||||||
begin
|
begin
|
||||||
match (String.lsplit2 ~on:':' elem_and_basis_name) with
|
match (String_ext.lsplit2 ~on:':' elem_and_basis_name) with
|
||||||
| None -> (* Principal basis *)
|
| None -> (* Principal basis *)
|
||||||
begin
|
begin
|
||||||
let basis =
|
let basis =
|
||||||
@ -150,14 +147,12 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
let new_channel =
|
let new_channel =
|
||||||
fetch_channel basis
|
fetch_channel basis
|
||||||
in
|
in
|
||||||
List.iter nuclei ~f:(fun elem->
|
List.iter (fun elem->
|
||||||
let key =
|
let key =
|
||||||
Element.to_string elem.Atom.element
|
Element.to_string elem.Atom.element
|
||||||
in
|
in
|
||||||
match Hashtbl.add basis_table ~key:key ~data:new_channel with
|
Hashtbl.add basis_table key new_channel
|
||||||
| `Ok -> ()
|
) nuclei
|
||||||
| `Duplicate -> ()
|
|
||||||
)
|
|
||||||
end
|
end
|
||||||
| Some (key, basis) -> (*Aux basis *)
|
| Some (key, basis) -> (*Aux basis *)
|
||||||
begin
|
begin
|
||||||
@ -166,12 +161,12 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
Element (Element.of_string key)
|
Element (Element.of_string key)
|
||||||
with Element.ElementError _ ->
|
with Element.ElementError _ ->
|
||||||
let result =
|
let result =
|
||||||
match (String.split ~on:',' key) with
|
match (String_ext.split ~on:',' key) with
|
||||||
| i :: k :: [] -> (Nucl_number.of_int @@ int_of_string i, Element.of_string k)
|
| i :: k :: [] -> (Nucl_number.of_int @@ int_of_string i, Element.of_string k)
|
||||||
| _ -> failwith "Expected format is int,Element:basis"
|
| _ -> failwith "Expected format is int,Element:basis"
|
||||||
in Int_elem result
|
in Int_elem result
|
||||||
and basis =
|
and basis =
|
||||||
String.lowercase basis
|
String.lowercase_ascii basis
|
||||||
in
|
in
|
||||||
let key =
|
let key =
|
||||||
match elem with
|
match elem with
|
||||||
@ -181,23 +176,13 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
let new_channel =
|
let new_channel =
|
||||||
fetch_channel basis
|
fetch_channel basis
|
||||||
in
|
in
|
||||||
begin
|
Hashtbl.add basis_table key new_channel
|
||||||
match Hashtbl.add basis_table ~key:key ~data:new_channel with
|
|
||||||
| `Ok -> ()
|
|
||||||
| `Duplicate ->
|
|
||||||
let e =
|
|
||||||
match elem with
|
|
||||||
| Element e -> e
|
|
||||||
| Int_elem (_,e) -> e
|
|
||||||
in
|
|
||||||
failwith ("Duplicate definition of basis for "^(Element.to_long_string e))
|
|
||||||
end
|
|
||||||
end
|
end
|
||||||
end;
|
end;
|
||||||
build_basis rest
|
build_basis rest
|
||||||
in
|
in
|
||||||
String.split ~on:'|' b
|
String_ext.split ~on:'|' b
|
||||||
|> List.rev_map ~f:String.strip
|
|> List.rev_map String.trim
|
||||||
|> build_basis;
|
|> build_basis;
|
||||||
|
|
||||||
|
|
||||||
@ -207,7 +192,7 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
***************)
|
***************)
|
||||||
|
|
||||||
let pseudo_table =
|
let pseudo_table =
|
||||||
Hashtbl.Poly.create ()
|
Hashtbl.create 63
|
||||||
in
|
in
|
||||||
|
|
||||||
(* Open pseudo channels *)
|
(* Open pseudo channels *)
|
||||||
@ -215,7 +200,7 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
let key =
|
let key =
|
||||||
Element.to_string element
|
Element.to_string element
|
||||||
in
|
in
|
||||||
Hashtbl.find pseudo_table key
|
Hashtbl.find_opt pseudo_table key
|
||||||
in
|
in
|
||||||
let temp_filename =
|
let temp_filename =
|
||||||
Filename.temp_file "qp_create_" ".pseudo"
|
Filename.temp_file "qp_create_" ".pseudo"
|
||||||
@ -229,11 +214,11 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
Qpackage.root ^ "/data/pseudo/" ^ pseudo
|
Qpackage.root ^ "/data/pseudo/" ^ pseudo
|
||||||
in
|
in
|
||||||
match
|
match
|
||||||
Sys.is_file pseudo,
|
Sys.file_exists pseudo,
|
||||||
Sys.is_file long_pseudo
|
Sys.file_exists long_pseudo
|
||||||
with
|
with
|
||||||
| `Yes, _ -> In_channel.create pseudo
|
| true , _ -> open_in pseudo
|
||||||
| `No , `Yes -> In_channel.create long_pseudo
|
| false, true-> open_in long_pseudo
|
||||||
| _ -> failwith ("Pseudo file "^pseudo^" not found.")
|
| _ -> failwith ("Pseudo file "^pseudo^" not found.")
|
||||||
in
|
in
|
||||||
|
|
||||||
@ -241,7 +226,7 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
| [] -> ()
|
| [] -> ()
|
||||||
| elem_and_pseudo_name :: rest ->
|
| elem_and_pseudo_name :: rest ->
|
||||||
begin
|
begin
|
||||||
match (String.lsplit2 ~on:':' elem_and_pseudo_name) with
|
match (String_ext.lsplit2 ~on:':' elem_and_pseudo_name) with
|
||||||
| None -> (* Principal pseudo *)
|
| None -> (* Principal pseudo *)
|
||||||
begin
|
begin
|
||||||
let pseudo =
|
let pseudo =
|
||||||
@ -250,21 +235,19 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
let new_channel =
|
let new_channel =
|
||||||
fetch_channel pseudo
|
fetch_channel pseudo
|
||||||
in
|
in
|
||||||
List.iter nuclei ~f:(fun elem->
|
List.iter (fun elem->
|
||||||
let key =
|
let key =
|
||||||
Element.to_string elem.Atom.element
|
Element.to_string elem.Atom.element
|
||||||
in
|
in
|
||||||
match Hashtbl.add pseudo_table ~key:key ~data:new_channel with
|
Hashtbl.add pseudo_table key new_channel
|
||||||
| `Ok -> ()
|
) nuclei
|
||||||
| `Duplicate -> ()
|
|
||||||
)
|
|
||||||
end
|
end
|
||||||
| Some (key, pseudo) -> (*Aux pseudo *)
|
| Some (key, pseudo) -> (*Aux pseudo *)
|
||||||
begin
|
begin
|
||||||
let elem =
|
let elem =
|
||||||
Element.of_string key
|
Element.of_string key
|
||||||
and pseudo =
|
and pseudo =
|
||||||
String.lowercase pseudo
|
String.lowercase_ascii pseudo
|
||||||
in
|
in
|
||||||
let key =
|
let key =
|
||||||
Element.to_string elem
|
Element.to_string elem
|
||||||
@ -272,11 +255,7 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
let new_channel =
|
let new_channel =
|
||||||
fetch_channel pseudo
|
fetch_channel pseudo
|
||||||
in
|
in
|
||||||
begin
|
Hashtbl.add pseudo_table key new_channel
|
||||||
match Hashtbl.add pseudo_table ~key:key ~data:new_channel with
|
|
||||||
| `Ok -> ()
|
|
||||||
| `Duplicate -> failwith ("Duplicate definition of pseudo for "^(Element.to_long_string elem))
|
|
||||||
end
|
|
||||||
end
|
end
|
||||||
end;
|
end;
|
||||||
build_pseudo rest
|
build_pseudo rest
|
||||||
@ -285,8 +264,8 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
match p with
|
match p with
|
||||||
| None -> ()
|
| None -> ()
|
||||||
| Some p ->
|
| Some p ->
|
||||||
String.split ~on:'|' p
|
String_ext.split ~on:'|' p
|
||||||
|> List.rev_map ~f:String.strip
|
|> List.rev_map String.trim
|
||||||
|> build_pseudo
|
|> build_pseudo
|
||||||
in
|
in
|
||||||
|
|
||||||
@ -296,13 +275,13 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
| Some x -> x
|
| Some x -> x
|
||||||
| None ->
|
| None ->
|
||||||
begin
|
begin
|
||||||
match String.rsplit2 ~on:'.' xyz_file with
|
match String_ext.rsplit2 ~on:'.' xyz_file with
|
||||||
| Some (x,"xyz")
|
| Some (x,"xyz")
|
||||||
| Some (x,"zmt") -> x^".ezfio"
|
| Some (x,"zmt") -> x^".ezfio"
|
||||||
| _ -> xyz_file^".ezfio"
|
| _ -> xyz_file^".ezfio"
|
||||||
end
|
end
|
||||||
in
|
in
|
||||||
if Sys.file_exists_exn ezfio_file then
|
if Sys.file_exists ezfio_file then
|
||||||
failwith (ezfio_file^" already exists");
|
failwith (ezfio_file^" already exists");
|
||||||
|
|
||||||
let write_file () =
|
let write_file () =
|
||||||
@ -311,17 +290,17 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
|
|
||||||
(* Write Pseudo *)
|
(* Write Pseudo *)
|
||||||
let pseudo =
|
let pseudo =
|
||||||
List.map nuclei ~f:(fun x ->
|
List.map (fun x ->
|
||||||
match pseudo_channel x.Atom.element with
|
match pseudo_channel x.Atom.element with
|
||||||
| Some channel -> Pseudo.read_element channel x.Atom.element
|
| Some channel -> Pseudo.read_element channel x.Atom.element
|
||||||
| None -> Pseudo.empty x.Atom.element
|
| None -> Pseudo.empty x.Atom.element
|
||||||
)
|
) nuclei
|
||||||
in
|
in
|
||||||
|
|
||||||
let molecule =
|
let molecule =
|
||||||
let n_elec_to_remove =
|
let n_elec_to_remove =
|
||||||
List.fold pseudo ~init:0 ~f:(fun accu x ->
|
List.fold_left (fun accu x ->
|
||||||
accu + (Positive_int.to_int x.Pseudo.n_elec))
|
accu + (Positive_int.to_int x.Pseudo.n_elec)) 0 pseudo
|
||||||
in
|
in
|
||||||
{ Molecule.elec_alpha =
|
{ Molecule.elec_alpha =
|
||||||
(Elec_alpha_number.to_int molecule.Molecule.elec_alpha)
|
(Elec_alpha_number.to_int molecule.Molecule.elec_alpha)
|
||||||
@ -333,14 +312,14 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
|> Elec_beta_number.of_int;
|
|> Elec_beta_number.of_int;
|
||||||
Molecule.nuclei =
|
Molecule.nuclei =
|
||||||
let charges =
|
let charges =
|
||||||
List.map pseudo ~f:(fun x -> Positive_int.to_int x.Pseudo.n_elec
|
List.map (fun x -> Positive_int.to_int x.Pseudo.n_elec
|
||||||
|> Float.of_int)
|
|> Float.of_int) pseudo
|
||||||
|> Array.of_list
|
|> Array.of_list
|
||||||
in
|
in
|
||||||
List.mapi molecule.Molecule.nuclei ~f:(fun i x ->
|
List.mapi (fun i x ->
|
||||||
{ x with Atom.charge = (Charge.to_float x.Atom.charge) -. charges.(i)
|
{ x with Atom.charge = (Charge.to_float x.Atom.charge) -. charges.(i)
|
||||||
|> Charge.of_float }
|
|> Charge.of_float }
|
||||||
)
|
) molecule.Molecule.nuclei
|
||||||
}
|
}
|
||||||
in
|
in
|
||||||
let nuclei =
|
let nuclei =
|
||||||
@ -356,13 +335,13 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
|
|
||||||
(* Write Nuclei *)
|
(* Write Nuclei *)
|
||||||
let labels =
|
let labels =
|
||||||
List.map ~f:(fun x->Element.to_string x.Atom.element) nuclei
|
List.map (fun x->Element.to_string x.Atom.element) nuclei
|
||||||
and charges =
|
and charges =
|
||||||
List.map ~f:(fun x-> Atom.(Charge.to_float x.charge)) nuclei
|
List.map (fun x-> Atom.(Charge.to_float x.charge)) nuclei
|
||||||
and coords =
|
and coords =
|
||||||
(List.map ~f:(fun x-> x.Atom.coord.Point3d.x) nuclei) @
|
(List.map (fun x-> x.Atom.coord.Point3d.x) nuclei) @
|
||||||
(List.map ~f:(fun x-> x.Atom.coord.Point3d.y) nuclei) @
|
(List.map (fun x-> x.Atom.coord.Point3d.y) nuclei) @
|
||||||
(List.map ~f:(fun x-> x.Atom.coord.Point3d.z) nuclei) in
|
(List.map (fun x-> x.Atom.coord.Point3d.z) nuclei) in
|
||||||
let nucl_num = (List.length labels) in
|
let nucl_num = (List.length labels) in
|
||||||
Ezfio.set_nuclei_nucl_num nucl_num ;
|
Ezfio.set_nuclei_nucl_num nucl_num ;
|
||||||
Ezfio.set_nuclei_nucl_label (Ezfio.ezfio_array_of_list
|
Ezfio.set_nuclei_nucl_label (Ezfio.ezfio_array_of_list
|
||||||
@ -381,40 +360,41 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
in
|
in
|
||||||
|
|
||||||
let klocmax =
|
let klocmax =
|
||||||
List.fold pseudo ~init:0 ~f:(fun accu x ->
|
List.fold_left (fun accu x ->
|
||||||
let x =
|
let x =
|
||||||
List.length x.Pseudo.local
|
List.length x.Pseudo.local
|
||||||
in
|
in
|
||||||
if (x > accu) then x
|
if (x > accu) then x
|
||||||
else accu
|
else accu
|
||||||
)
|
) 0 pseudo
|
||||||
and lmax =
|
and lmax =
|
||||||
List.fold pseudo ~init:0 ~f:(fun accu x ->
|
List.fold_left (fun accu x ->
|
||||||
let x =
|
let x =
|
||||||
List.fold x.Pseudo.non_local ~init:0 ~f:(fun accu (x,_) ->
|
List.fold_left (fun accu (x,_) ->
|
||||||
let x =
|
let x =
|
||||||
Positive_int.to_int x.Pseudo.GaussianPrimitive_non_local.proj
|
Positive_int.to_int x.Pseudo.GaussianPrimitive_non_local.proj
|
||||||
in
|
in
|
||||||
if (x > accu) then x
|
if (x > accu) then x
|
||||||
else accu
|
else accu
|
||||||
)
|
) 0 x.Pseudo.non_local
|
||||||
in
|
in
|
||||||
if (x > accu) then x
|
if (x > accu) then x
|
||||||
else accu
|
else accu
|
||||||
)
|
) 0 pseudo
|
||||||
in
|
in
|
||||||
|
|
||||||
let kmax =
|
let kmax =
|
||||||
Array.init (lmax+1) ~f:(fun i->
|
Array.init (lmax+1) (fun i->
|
||||||
List.map pseudo ~f:(fun x ->
|
List.map (fun x ->
|
||||||
List.filter x.Pseudo.non_local ~f:(fun (y,_) ->
|
List.filter (fun (y,_) ->
|
||||||
(Positive_int.to_int y.Pseudo.GaussianPrimitive_non_local.proj) = i)
|
(Positive_int.to_int y.Pseudo.GaussianPrimitive_non_local.proj) = i)
|
||||||
|> List.length )
|
x.Pseudo.non_local
|
||||||
|> List.fold ~init:0 ~f:(fun accu x ->
|
|> List.length ) pseudo
|
||||||
if accu > x then accu else x)
|
|> List.fold_left (fun accu x ->
|
||||||
)
|
if accu > x then accu else x) 0
|
||||||
|> Array.fold ~init:0 ~f:(fun accu i ->
|
)
|
||||||
if i > accu then i else accu)
|
|> Array.fold_left (fun accu i ->
|
||||||
|
if i > accu then i else accu) 0
|
||||||
in
|
in
|
||||||
|
|
||||||
|
|
||||||
@ -423,12 +403,12 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
Ezfio.set_pseudo_pseudo_kmax kmax;
|
Ezfio.set_pseudo_pseudo_kmax kmax;
|
||||||
Ezfio.set_pseudo_pseudo_lmax lmax;
|
Ezfio.set_pseudo_pseudo_lmax lmax;
|
||||||
let tmp_array_v_k, tmp_array_dz_k, tmp_array_n_k =
|
let tmp_array_v_k, tmp_array_dz_k, tmp_array_n_k =
|
||||||
Array.make_matrix ~dimx:klocmax ~dimy:nucl_num 0. ,
|
Array.make_matrix klocmax nucl_num 0. ,
|
||||||
Array.make_matrix ~dimx:klocmax ~dimy:nucl_num 0. ,
|
Array.make_matrix klocmax nucl_num 0. ,
|
||||||
Array.make_matrix ~dimx:klocmax ~dimy:nucl_num 0
|
Array.make_matrix klocmax nucl_num 0
|
||||||
in
|
in
|
||||||
List.iteri pseudo ~f:(fun j x ->
|
List.iteri (fun j x ->
|
||||||
List.iteri x.Pseudo.local ~f:(fun i (y,c) ->
|
List.iteri (fun i (y,c) ->
|
||||||
tmp_array_v_k.(i).(j) <- AO_coef.to_float c;
|
tmp_array_v_k.(i).(j) <- AO_coef.to_float c;
|
||||||
let y, z =
|
let y, z =
|
||||||
AO_expo.to_float y.Pseudo.GaussianPrimitive_local.expo,
|
AO_expo.to_float y.Pseudo.GaussianPrimitive_local.expo,
|
||||||
@ -436,11 +416,11 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
in
|
in
|
||||||
tmp_array_dz_k.(i).(j) <- y;
|
tmp_array_dz_k.(i).(j) <- y;
|
||||||
tmp_array_n_k.(i).(j) <- z;
|
tmp_array_n_k.(i).(j) <- z;
|
||||||
)
|
) x.Pseudo.local
|
||||||
);
|
) pseudo ;
|
||||||
let concat_2d tmp_array =
|
let concat_2d tmp_array =
|
||||||
let data =
|
let data =
|
||||||
Array.map tmp_array ~f:Array.to_list
|
Array.map Array.to_list tmp_array
|
||||||
|> Array.to_list
|
|> Array.to_list
|
||||||
|> List.concat
|
|> List.concat
|
||||||
in
|
in
|
||||||
@ -454,18 +434,18 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
|> Ezfio.set_pseudo_pseudo_n_k;
|
|> Ezfio.set_pseudo_pseudo_n_k;
|
||||||
|
|
||||||
let tmp_array_v_kl, tmp_array_dz_kl, tmp_array_n_kl =
|
let tmp_array_v_kl, tmp_array_dz_kl, tmp_array_n_kl =
|
||||||
Array.init (lmax+1) ~f:(fun _ ->
|
Array.init (lmax+1) (fun _ ->
|
||||||
(Array.make_matrix ~dimx:kmax ~dimy:nucl_num 0. )),
|
(Array.make_matrix kmax nucl_num 0. )),
|
||||||
Array.init (lmax+1) ~f:(fun _ ->
|
Array.init (lmax+1) (fun _ ->
|
||||||
(Array.make_matrix ~dimx:kmax ~dimy:nucl_num 0. )),
|
(Array.make_matrix kmax nucl_num 0. )),
|
||||||
Array.init (lmax+1) ~f:(fun _ ->
|
Array.init (lmax+1) (fun _ ->
|
||||||
(Array.make_matrix ~dimx:kmax ~dimy:nucl_num 0 ))
|
(Array.make_matrix kmax nucl_num 0 ))
|
||||||
in
|
in
|
||||||
List.iteri pseudo ~f:(fun j x ->
|
List.iteri (fun j x ->
|
||||||
let last_idx =
|
let last_idx =
|
||||||
Array.create ~len:(lmax+1) 0
|
Array.make (lmax+1) 0
|
||||||
in
|
in
|
||||||
List.iter x.Pseudo.non_local ~f:(fun (y,c) ->
|
List.iter (fun (y,c) ->
|
||||||
let k, y, z =
|
let k, y, z =
|
||||||
Positive_int.to_int y.Pseudo.GaussianPrimitive_non_local.proj,
|
Positive_int.to_int y.Pseudo.GaussianPrimitive_non_local.proj,
|
||||||
AO_expo.to_float y.Pseudo.GaussianPrimitive_non_local.expo,
|
AO_expo.to_float y.Pseudo.GaussianPrimitive_non_local.expo,
|
||||||
@ -478,14 +458,14 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
tmp_array_dz_kl.(k).(i).(j) <- y;
|
tmp_array_dz_kl.(k).(i).(j) <- y;
|
||||||
tmp_array_n_kl.(k).(i).(j) <- z;
|
tmp_array_n_kl.(k).(i).(j) <- z;
|
||||||
last_idx.(k) <- i+1;
|
last_idx.(k) <- i+1;
|
||||||
)
|
) x.Pseudo.non_local
|
||||||
);
|
) pseudo ;
|
||||||
let concat_3d tmp_array =
|
let concat_3d tmp_array =
|
||||||
let data =
|
let data =
|
||||||
Array.map tmp_array ~f:(fun x ->
|
Array.map (fun x ->
|
||||||
Array.map x ~f:Array.to_list
|
Array.map Array.to_list x
|
||||||
|> Array.to_list
|
|> Array.to_list
|
||||||
|> List.concat)
|
|> List.concat) tmp_array
|
||||||
|> Array.to_list
|
|> Array.to_list
|
||||||
|> List.concat
|
|> List.concat
|
||||||
in
|
in
|
||||||
@ -518,7 +498,7 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
in
|
in
|
||||||
let result = do_work [] 1 nuclei
|
let result = do_work [] 1 nuclei
|
||||||
|> List.rev
|
|> List.rev
|
||||||
|> List.map ~f:(fun (x,i) ->
|
|> List.map (fun (x,i) ->
|
||||||
try
|
try
|
||||||
let e =
|
let e =
|
||||||
match x.Atom.element with
|
match x.Atom.element with
|
||||||
@ -530,13 +510,13 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
in
|
in
|
||||||
try
|
try
|
||||||
Basis.read_element (basis_channel key) i e
|
Basis.read_element (basis_channel key) i e
|
||||||
with Caml.Not_found ->
|
with Not_found ->
|
||||||
let key =
|
let key =
|
||||||
Element x.Atom.element
|
Element x.Atom.element
|
||||||
in
|
in
|
||||||
try
|
try
|
||||||
Basis.read_element (basis_channel key) i e
|
Basis.read_element (basis_channel key) i e
|
||||||
with Caml.Not_found ->
|
with Not_found ->
|
||||||
failwith (Printf.sprintf "Basis not found for atom %d (%s)" (Nucl_number.to_int i)
|
failwith (Printf.sprintf "Basis not found for atom %d (%s)" (Nucl_number.to_int i)
|
||||||
(Element.to_string x.Atom.element) )
|
(Element.to_string x.Atom.element) )
|
||||||
with
|
with
|
||||||
@ -552,37 +532,38 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
let ao_num = List.length long_basis in
|
let ao_num = List.length long_basis in
|
||||||
Ezfio.set_ao_basis_ao_num ao_num;
|
Ezfio.set_ao_basis_ao_num ao_num;
|
||||||
Ezfio.set_ao_basis_ao_basis b;
|
Ezfio.set_ao_basis_ao_basis b;
|
||||||
let ao_prim_num = List.map long_basis ~f:(fun (_,g,_) -> List.length g.Gto.lc)
|
let ao_prim_num = List.map (fun (_,g,_) -> List.length g.Gto.lc) long_basis
|
||||||
and ao_nucl = List.map long_basis ~f:(fun (_,_,n) -> Nucl_number.to_int n)
|
and ao_nucl = List.map (fun (_,_,n) -> Nucl_number.to_int n) long_basis
|
||||||
and ao_power=
|
and ao_power=
|
||||||
let l = List.map long_basis ~f:(fun (x,_,_) -> x) in
|
let l = List.map (fun (x,_,_) -> x) long_basis in
|
||||||
(List.map l ~f:(fun t -> Positive_int.to_int Symmetry.Xyz.(t.x)) )@
|
(List.map (fun t -> Positive_int.to_int Symmetry.Xyz.(t.x)) l)@
|
||||||
(List.map l ~f:(fun t -> Positive_int.to_int Symmetry.Xyz.(t.y)) )@
|
(List.map (fun t -> Positive_int.to_int Symmetry.Xyz.(t.y)) l)@
|
||||||
(List.map l ~f:(fun t -> Positive_int.to_int Symmetry.Xyz.(t.z)) )
|
(List.map (fun t -> Positive_int.to_int Symmetry.Xyz.(t.z)) l)
|
||||||
in
|
in
|
||||||
let ao_prim_num_max = List.fold ~init:0 ~f:(fun s x ->
|
let ao_prim_num_max = List.fold_left (fun s x ->
|
||||||
if x > s then x
|
if x > s then x
|
||||||
else s) ao_prim_num
|
else s) 0 ao_prim_num
|
||||||
in
|
in
|
||||||
let gtos =
|
let gtos =
|
||||||
List.map long_basis ~f:(fun (_,x,_) -> x)
|
List.map (fun (_,x,_) -> x) long_basis
|
||||||
in
|
in
|
||||||
|
|
||||||
let create_expo_coef ec =
|
let create_expo_coef ec =
|
||||||
let coefs =
|
let coefs =
|
||||||
begin match ec with
|
begin match ec with
|
||||||
| `Coefs -> List.map gtos ~f:(fun x->
|
| `Coefs -> List.map (fun x->
|
||||||
List.map x.Gto.lc ~f:(fun (_,coef) -> AO_coef.to_float coef) )
|
List.map (fun (_,coef) ->
|
||||||
| `Expos -> List.map gtos ~f:(fun x->
|
AO_coef.to_float coef) x.Gto.lc) gtos
|
||||||
List.map x.Gto.lc ~f:(fun (prim,_) -> AO_expo.to_float
|
| `Expos -> List.map (fun x->
|
||||||
prim.GaussianPrimitive.expo) )
|
List.map (fun (prim,_) -> AO_expo.to_float
|
||||||
|
prim.GaussianPrimitive.expo) x.Gto.lc) gtos
|
||||||
end
|
end
|
||||||
in
|
in
|
||||||
let rec get_n n accu = function
|
let rec get_n n accu = function
|
||||||
| [] -> List.rev accu
|
| [] -> List.rev accu
|
||||||
| h::tail ->
|
| h::tail ->
|
||||||
let y =
|
let y =
|
||||||
begin match List.nth h n with
|
begin match List.nth_opt h n with
|
||||||
| Some x -> x
|
| Some x -> x
|
||||||
| None -> 0.
|
| None -> 0.
|
||||||
end
|
end
|
||||||
@ -621,9 +602,10 @@ let run ?o b au c d m p cart xyz_file =
|
|||||||
| ex ->
|
| ex ->
|
||||||
begin
|
begin
|
||||||
begin
|
begin
|
||||||
match Sys.is_directory ezfio_file with
|
try
|
||||||
| `Yes -> rmdir ezfio_file
|
if Sys.is_directory ezfio_file then
|
||||||
| _ -> ()
|
rmdir ezfio_file
|
||||||
|
with _ -> ()
|
||||||
end;
|
end;
|
||||||
raise ex;
|
raise ex;
|
||||||
end
|
end
|
||||||
@ -730,7 +712,7 @@ If a file with the same name as the basis set exists, this file will be read. O
|
|||||||
if basis = "show" then
|
if basis = "show" then
|
||||||
begin
|
begin
|
||||||
list_basis ()
|
list_basis ()
|
||||||
|> List.iter ~f:print_endline;
|
|> List.iter print_endline;
|
||||||
exit 0
|
exit 0
|
||||||
end;
|
end;
|
||||||
|
|
||||||
|
@ -46,7 +46,7 @@ let run slave ?prefix exe ezfio_file =
|
|||||||
in
|
in
|
||||||
|
|
||||||
let time_start =
|
let time_start =
|
||||||
Core.Time.now ()
|
Unix.time ()
|
||||||
in
|
in
|
||||||
|
|
||||||
if (not (Sys.file_exists ezfio_file)) then
|
if (not (Sys.file_exists ezfio_file)) then
|
||||||
@ -65,7 +65,15 @@ let run slave ?prefix exe ezfio_file =
|
|||||||
failwith ("Executable "^exe^" not found")
|
failwith ("Executable "^exe^" not found")
|
||||||
end;
|
end;
|
||||||
|
|
||||||
Printf.printf "%s\n" (Core.Time.to_string time_start);
|
let tm = Unix.localtime time_start in
|
||||||
|
Printf.printf "Date: %2.2d/%2.2d/%4d %2.2d:%2.2d:%2.2d\n"
|
||||||
|
tm.Unix.tm_mday
|
||||||
|
(tm.Unix.tm_mon+1)
|
||||||
|
(tm.Unix.tm_year+1900)
|
||||||
|
(tm.Unix.tm_hour + if tm.Unix.tm_isdst then 1 else 0)
|
||||||
|
tm.Unix.tm_min
|
||||||
|
tm.Unix.tm_sec
|
||||||
|
;
|
||||||
Printf.printf "===============\nQuantum Package\n===============\n\n";
|
Printf.printf "===============\nQuantum Package\n===============\n\n";
|
||||||
Printf.printf "Git Commit: %s\n" Git.message;
|
Printf.printf "Git Commit: %s\n" Git.message;
|
||||||
Printf.printf "Git Date : %s\n" Git.date;
|
Printf.printf "Git Date : %s\n" Git.date;
|
||||||
@ -89,10 +97,12 @@ let run slave ?prefix exe ezfio_file =
|
|||||||
if slave then
|
if slave then
|
||||||
try
|
try
|
||||||
let address =
|
let address =
|
||||||
Core.In_channel.read_all qp_run_address_filename
|
let ic = open_in qp_run_address_filename in
|
||||||
|> String.trim
|
let result = input_line ic in
|
||||||
|
close_in ic;
|
||||||
|
String.trim result
|
||||||
in
|
in
|
||||||
Unix.putenv "QP_RUN_ADDRESS_MASTER" address
|
Unix.putenv "QP_RUN_ADDRESS_MASTER" address;
|
||||||
with Sys_error _ -> failwith "No master is not running"
|
with Sys_error _ -> failwith "No master is not running"
|
||||||
in
|
in
|
||||||
|
|
||||||
@ -110,8 +120,11 @@ let run slave ?prefix exe ezfio_file =
|
|||||||
Unix.putenv "QP_RUN_ADDRESS" address;
|
Unix.putenv "QP_RUN_ADDRESS" address;
|
||||||
let () =
|
let () =
|
||||||
if (not slave) then
|
if (not slave) then
|
||||||
Core.Out_channel.with_file qp_run_address_filename ~f:(
|
begin
|
||||||
fun oc -> Core.Out_channel.output_lines oc [address])
|
let oc = open_out qp_run_address_filename in
|
||||||
|
Printf.fprintf oc "%s\n" address;
|
||||||
|
close_out oc;
|
||||||
|
end
|
||||||
in
|
in
|
||||||
|
|
||||||
|
|
||||||
@ -135,9 +148,13 @@ let run slave ?prefix exe ezfio_file =
|
|||||||
if (not slave) then
|
if (not slave) then
|
||||||
Sys.remove qp_run_address_filename;
|
Sys.remove qp_run_address_filename;
|
||||||
|
|
||||||
let duration = Core.Time.diff (Core.Time.now()) time_start
|
let duration = Unix.time () -. time_start |> Unix.gmtime in
|
||||||
|> Core.Time.Span.to_string in
|
let open Unix in
|
||||||
Printf.printf "Wall time : %s\n\n" duration;
|
let d, h, m, s =
|
||||||
|
duration.tm_yday, duration.tm_hour, duration.tm_min, duration.tm_sec
|
||||||
|
in
|
||||||
|
Printf.printf "Wall time: %d:%2.2d:%2.2d" (d*24+h) m s ;
|
||||||
|
Printf.printf "\n\n";
|
||||||
if (exit_code <> 0) then
|
if (exit_code <> 0) then
|
||||||
exit exit_code
|
exit exit_code
|
||||||
|
|
||||||
|
@ -556,7 +556,7 @@ def create_ocaml_input(dict_ezfio_cfg, module_lower):
|
|||||||
|
|
||||||
template += ["open Qptypes;;",
|
template += ["open Qptypes;;",
|
||||||
"open Qputils;;",
|
"open Qputils;;",
|
||||||
"open Core;;",
|
"open Sexplib.Std;;",
|
||||||
"",
|
"",
|
||||||
"module {0} : sig".format(module_lower.capitalize())]
|
"module {0} : sig".format(module_lower.capitalize())]
|
||||||
|
|
||||||
@ -611,7 +611,16 @@ def create_ocaml_input(dict_ezfio_cfg, module_lower):
|
|||||||
"",
|
"",
|
||||||
"end"]
|
"end"]
|
||||||
|
|
||||||
return "\n".join(template)
|
result = "\n".join(template)
|
||||||
|
result = result.replace("String.of_string","string_of_string")
|
||||||
|
result = result.replace("String.to_string","string_of_string")
|
||||||
|
result = result.replace("Int.of_string","int_of_string")
|
||||||
|
result = result.replace("Int.to_string","string_of_int")
|
||||||
|
result = result.replace("Float.of_string","float_of_string")
|
||||||
|
result = result.replace("Float.to_string","string_of_float")
|
||||||
|
result = result.replace("Bool.of_string","bool_of_string")
|
||||||
|
result = result.replace("Bool.to_string","string_of_bool")
|
||||||
|
return result
|
||||||
|
|
||||||
|
|
||||||
def save_ocaml_input(module_lower, str_ocaml_input):
|
def save_ocaml_input(module_lower, str_ocaml_input):
|
||||||
|
@ -352,7 +352,6 @@ class EZFIO_ocaml(object):
|
|||||||
|
|
||||||
l_template = ['open Qputils;;',
|
l_template = ['open Qputils;;',
|
||||||
'open Qptypes;;',
|
'open Qptypes;;',
|
||||||
'open Core;;',
|
|
||||||
'']
|
'']
|
||||||
|
|
||||||
for m in self.l_module_lower:
|
for m in self.l_module_lower:
|
||||||
|
@ -4,7 +4,7 @@
|
|||||||
|
|
||||||
open Qputils
|
open Qputils
|
||||||
open Qptypes
|
open Qptypes
|
||||||
open Core
|
open Sexplib.Std
|
||||||
|
|
||||||
(** Interactive editing of the input.
|
(** Interactive editing of the input.
|
||||||
|
|
||||||
@ -53,7 +53,7 @@ Editing file `%s`
|
|||||||
let make_header kw =
|
let make_header kw =
|
||||||
let s = keyword_to_string kw in
|
let s = keyword_to_string kw in
|
||||||
let l = String.length s in
|
let l = String.length s in
|
||||||
"\n\n"^s^"\n"^(String.init l ~f:(fun _ -> '='))^"\n\n"
|
"\n\n"^s^"\n"^(String.init l (fun _ -> '='))^"\n\n"
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
@ -92,19 +92,19 @@ let get s =
|
|||||||
(** Applies the changes from the string [str] corresponding to section [s] *)
|
(** Applies the changes from the string [str] corresponding to section [s] *)
|
||||||
let set str s =
|
let set str s =
|
||||||
let header = (make_header s) in
|
let header = (make_header s) in
|
||||||
match String.substr_index ~pos:0 ~pattern:header str with
|
match String_ext.substr_index ~pos:0 ~pattern:header str with
|
||||||
| None -> ()
|
| None -> ()
|
||||||
| Some idx ->
|
| Some idx ->
|
||||||
begin
|
begin
|
||||||
let index_begin = idx + (String.length header) in
|
let index_begin = idx + (String.length header) in
|
||||||
let index_end =
|
let index_end =
|
||||||
match ( String.substr_index ~pos:(index_begin+(String.length header)+1)
|
match ( String_ext.substr_index ~pos:(index_begin+(String.length header)+1)
|
||||||
~pattern:"==" str) with
|
~pattern:"==" str) with
|
||||||
| Some i -> i
|
| Some i -> i
|
||||||
| None -> String.length str
|
| None -> String.length str
|
||||||
in
|
in
|
||||||
let l = index_end - index_begin in
|
let l = index_end - index_begin in
|
||||||
let str = String.sub ~pos:index_begin ~len:l str
|
let str = String.sub str index_begin l
|
||||||
|> Rst_string.of_string
|
|> Rst_string.of_string
|
||||||
in
|
in
|
||||||
let write (of_rst,w) s =
|
let write (of_rst,w) s =
|
||||||
@ -132,11 +132,11 @@ let set str s =
|
|||||||
let create_temp_file ezfio_filename fields =
|
let create_temp_file ezfio_filename fields =
|
||||||
let temp_filename = Filename.temp_file "qp_edit_" ".rst" in
|
let temp_filename = Filename.temp_file "qp_edit_" ".rst" in
|
||||||
begin
|
begin
|
||||||
Out_channel.with_file temp_filename ~f:(fun out_channel ->
|
let oc = open_out temp_filename in
|
||||||
(file_header ezfio_filename) :: (List.map ~f:get fields)
|
(file_header ezfio_filename) :: (List.map get fields)
|
||||||
|> String.concat ~sep:"\n"
|
|> String.concat "\n"
|
||||||
|> Out_channel.output_string out_channel
|
|> Printf.fprintf oc "%s";
|
||||||
);
|
close_out oc;
|
||||||
at_exit (fun () -> Sys.remove temp_filename);
|
at_exit (fun () -> Sys.remove temp_filename);
|
||||||
temp_filename
|
temp_filename
|
||||||
end
|
end
|
||||||
@ -155,20 +155,19 @@ let run check_only ?ndet ?state ezfio_filename =
|
|||||||
in
|
in
|
||||||
|
|
||||||
(* Open EZFIO *)
|
(* Open EZFIO *)
|
||||||
if (not (Sys.file_exists_exn ezfio_filename)) then
|
if (not (Sys.file_exists ezfio_filename)) then
|
||||||
failwith (ezfio_filename^" does not exists");
|
failwith (ezfio_filename^" does not exists");
|
||||||
|
|
||||||
Ezfio.set_file ezfio_filename;
|
Ezfio.set_file ezfio_filename;
|
||||||
|
|
||||||
(* Clean qp_stop status *)
|
(* Clean qp_stop status *)
|
||||||
[ "qpstop" ; "qpkill" ]
|
[ "qpstop" ; "qpkill" ]
|
||||||
|> List.iter ~f:(fun f ->
|
|> List.iter (fun f ->
|
||||||
let stopfile =
|
let stopfile =
|
||||||
Filename.concat (Qpackage.ezfio_work ezfio_filename) f
|
Filename.concat (Qpackage.ezfio_work ezfio_filename) f
|
||||||
in
|
in
|
||||||
match Sys.file_exists stopfile with
|
if Sys.file_exists stopfile then
|
||||||
| `Yes -> Sys.remove stopfile
|
Sys.remove stopfile
|
||||||
| _ -> ()
|
|
||||||
);
|
);
|
||||||
|
|
||||||
(* Reorder basis set *)
|
(* Reorder basis set *)
|
||||||
@ -180,7 +179,7 @@ let run check_only ?ndet ?state ezfio_filename =
|
|||||||
in
|
in
|
||||||
let ordering = Input.Ao_basis.ordering aos in
|
let ordering = Input.Ao_basis.ordering aos in
|
||||||
let test = Array.copy ordering in
|
let test = Array.copy ordering in
|
||||||
Array.sort ~compare test ;
|
Array.sort compare test ;
|
||||||
if test <> ordering then
|
if test <> ordering then
|
||||||
begin
|
begin
|
||||||
Printf.eprintf "Warning: Basis set is not properly ordered. Redordering.\n";
|
Printf.eprintf "Warning: Basis set is not properly ordered. Redordering.\n";
|
||||||
@ -212,7 +211,7 @@ let run check_only ?ndet ?state ezfio_filename =
|
|||||||
|
|
||||||
(*
|
(*
|
||||||
let output = (file_header ezfio_filename) :: (
|
let output = (file_header ezfio_filename) :: (
|
||||||
List.map ~f:get [
|
List.map get [
|
||||||
Ao_basis ;
|
Ao_basis ;
|
||||||
Mo_basis ;
|
Mo_basis ;
|
||||||
])
|
])
|
||||||
@ -238,24 +237,28 @@ let run check_only ?ndet ?state ezfio_filename =
|
|||||||
|
|
||||||
(* Open the temp file with external editor *)
|
(* Open the temp file with external editor *)
|
||||||
let editor =
|
let editor =
|
||||||
match Sys.getenv "EDITOR" with
|
try Sys.getenv "EDITOR"
|
||||||
| Some editor -> editor
|
with Not_found -> "vi"
|
||||||
| None -> "vi"
|
|
||||||
in
|
in
|
||||||
|
|
||||||
match check_only with
|
match check_only with
|
||||||
| true -> ()
|
| true -> ()
|
||||||
| false ->
|
| false ->
|
||||||
Printf.sprintf "%s %s" editor temp_filename
|
Printf.sprintf "%s %s" editor temp_filename
|
||||||
|> Sys.command_exn
|
|> Sys.command |> ignore
|
||||||
;
|
;
|
||||||
|
|
||||||
(* Re-read the temp file *)
|
(* Re-read the temp file *)
|
||||||
let temp_string =
|
let temp_string =
|
||||||
In_channel.with_file temp_filename ~f:(fun in_channel ->
|
let ic = open_in temp_filename in
|
||||||
In_channel.input_all in_channel)
|
let result =
|
||||||
|
input_lines ic
|
||||||
|
|> String.concat "\n"
|
||||||
|
in
|
||||||
|
close_in ic;
|
||||||
|
result
|
||||||
in
|
in
|
||||||
List.iter ~f:(fun x -> set temp_string x) tasks
|
List.iter (fun x -> set temp_string x) tasks
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
@ -281,7 +284,8 @@ let create_backup ezfio_filename =
|
|||||||
tar -cf .backup.tar --exclude=\"work/*\" %s && (mv .backup.tar %s || rm .backup.tar)
|
tar -cf .backup.tar --exclude=\"work/*\" %s && (mv .backup.tar %s || rm .backup.tar)
|
||||||
"
|
"
|
||||||
ezfio_filename ezfio_filename backup_filename
|
ezfio_filename ezfio_filename backup_filename
|
||||||
|> Sys.command_exn
|
|> Sys.command
|
||||||
|
|> ignore
|
||||||
with _ -> ()
|
with _ -> ()
|
||||||
|
|
||||||
|
|
||||||
@ -290,10 +294,10 @@ let restore_backup ezfio_filename =
|
|||||||
let filename =
|
let filename =
|
||||||
Printf.sprintf "%s/work/backup.tar" ezfio_filename
|
Printf.sprintf "%s/work/backup.tar" ezfio_filename
|
||||||
in
|
in
|
||||||
if Sys.file_exists_exn filename then
|
if Sys.file_exists filename then
|
||||||
begin
|
begin
|
||||||
Printf.sprintf "tar -xf %s" filename
|
Printf.sprintf "tar -xf %s" filename
|
||||||
|> Sys.command_exn;
|
|> Sys.command |> ignore;
|
||||||
remove_backup ezfio_filename
|
remove_backup ezfio_filename
|
||||||
end
|
end
|
||||||
|
|
||||||
|
@ -1,14 +1,15 @@
|
|||||||
#!/usr/bin/env python2
|
#!/usr/bin/env python2
|
||||||
|
|
||||||
import os
|
import os
|
||||||
|
from qp_path import QP_SRC
|
||||||
|
|
||||||
Pert_dir = os.environ["QP_ROOT"]+"/src/perturbation/"
|
Pert_dir = os.path.join(QP_SRC,"perturbation")
|
||||||
|
|
||||||
perturbations = []
|
perturbations = []
|
||||||
|
|
||||||
for filename in filter(lambda x: x.endswith(".irp.f"), os.listdir(Pert_dir)):
|
for filename in filter(lambda x: x.endswith(".irp.f"), os.listdir(Pert_dir)):
|
||||||
|
|
||||||
filename = Pert_dir+filename
|
filename = os.path.join(Pert_dir,filename)
|
||||||
file = open(filename,'r')
|
file = open(filename,'r')
|
||||||
lines = file.readlines()
|
lines = file.readlines()
|
||||||
file.close()
|
file.close()
|
||||||
|
@ -70,7 +70,7 @@ subroutine run_stochastic_cipsi
|
|||||||
write(*,'(A)') '--------------------------------------------------------------------------------'
|
write(*,'(A)') '--------------------------------------------------------------------------------'
|
||||||
|
|
||||||
|
|
||||||
to_select = N_det
|
to_select = N_det*int(sqrt(dble(N_states)))
|
||||||
to_select = max(N_states_diag, to_select)
|
to_select = max(N_states_diag, to_select)
|
||||||
|
|
||||||
pt2 = 0.d0
|
pt2 = 0.d0
|
||||||
|
@ -408,10 +408,6 @@ subroutine davidson_diag_hjj_sjj(dets_in,u_in,H_jj,s2_out,energies,dim_in,sze,N_
|
|||||||
! Compute s_kl = <u_k | S_l> = <u_k| S2 |u_l>
|
! Compute s_kl = <u_k | S_l> = <u_k| S2 |u_l>
|
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! -------------------------------------------
|
! -------------------------------------------
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|
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! call dgemm('T','N', shift2, shift2, sze, &
|
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! 1.d0, U, size(U,1), S, size(S,1), &
|
|
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! 0.d0, s_, size(s_,1))
|
|
||||||
|
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!$OMP PARALLEL DO DEFAULT(SHARED) PRIVATE(i,j,k)
|
!$OMP PARALLEL DO DEFAULT(SHARED) PRIVATE(i,j,k)
|
||||||
do j=1,shift2
|
do j=1,shift2
|
||||||
do i=1,shift2
|
do i=1,shift2
|
||||||
@ -438,8 +434,13 @@ subroutine davidson_diag_hjj_sjj(dets_in,u_in,H_jj,s2_out,energies,dim_in,sze,N_
|
|||||||
do k=1,shift2
|
do k=1,shift2
|
||||||
h_p(k,k) = h_p(k,k) + S_z2_Sz - expected_s2
|
h_p(k,k) = h_p(k,k) + S_z2_Sz - expected_s2
|
||||||
enddo
|
enddo
|
||||||
alpha = 0.1d0
|
if (only_expected_s2) then
|
||||||
h_p = h + alpha*h_p
|
alpha = 0.1d0
|
||||||
|
h_p = h + alpha*h_p
|
||||||
|
else
|
||||||
|
alpha = 0.0001d0
|
||||||
|
h_p = h + alpha*h_p
|
||||||
|
endif
|
||||||
else
|
else
|
||||||
h_p = h
|
h_p = h
|
||||||
alpha = 0.d0
|
alpha = 0.d0
|
||||||
|
@ -48,7 +48,7 @@ program fci
|
|||||||
else
|
else
|
||||||
PROVIDE mo_two_e_integrals_in_map
|
PROVIDE mo_two_e_integrals_in_map
|
||||||
|
|
||||||
call run_slave_cipsi
|
call run_slave_cipsi
|
||||||
|
|
||||||
endif
|
endif
|
||||||
end
|
end
|
||||||
|
@ -45,9 +45,9 @@ BEGIN_PROVIDER [ double precision, mo_coef, (ao_num,mo_num) ]
|
|||||||
BEGIN_DOC
|
BEGIN_DOC
|
||||||
! Molecular orbital coefficients on |AO| basis set
|
! Molecular orbital coefficients on |AO| basis set
|
||||||
!
|
!
|
||||||
! mo_coef(i,j) = coefficient of the i-th |AO| on the jth mo
|
! mo_coef(i,j) = coefficient of the i-th |AO| on the jth |MO|
|
||||||
!
|
!
|
||||||
! mo_label : Label characterizing the MOS (local, canonical, natural, etc)
|
! mo_label : Label characterizing the |MOs| (local, canonical, natural, etc)
|
||||||
END_DOC
|
END_DOC
|
||||||
integer :: i, j
|
integer :: i, j
|
||||||
double precision, allocatable :: buffer(:,:)
|
double precision, allocatable :: buffer(:,:)
|
||||||
|
@ -1,7 +1,7 @@
|
|||||||
BEGIN_PROVIDER [ double precision, eigenvectors_Fock_matrix_mo, (ao_num,mo_num) ]
|
BEGIN_PROVIDER [ double precision, eigenvectors_Fock_matrix_mo, (ao_num,mo_num) ]
|
||||||
implicit none
|
implicit none
|
||||||
BEGIN_DOC
|
BEGIN_DOC
|
||||||
! Eigenvectors of the Fock matrix in the MO basis obtained with level shift.
|
! Eigenvectors of the Fock matrix in the |MO| basis obtained with level shift.
|
||||||
END_DOC
|
END_DOC
|
||||||
|
|
||||||
integer :: i,j
|
integer :: i,j
|
||||||
|
Loading…
Reference in New Issue
Block a user