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Merge remote-tracking branch 'upstream/master'

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Thomas Applencourt 2014-12-01 15:28:03 +01:00
commit 3159ebe8b3
25 changed files with 485 additions and 312 deletions
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15
Makefile
View File

@ -28,13 +28,14 @@ EZFIO: bin/irpf90
bin/irpf90:
$(info $(BLUE)===== Fetching IRPF90 from the web ===== $(BLACK))
@sleep 1
@$(FETCH_FROM_WEB) "$(WWW_SERVER)/$(IRPF90_TGZ)" $(IRPF90_TGZ) || \
(echo Unable to download IRPF90 : $(WWW_SERVER)/$(IRPF90_TGZ) ; exit 1)
tar -zxf $(IRPF90_TGZ) && rm $(IRPF90_TGZ)
$(MAKE) -C irpf90 | tee install_irpf90.log
rm -rf -- $$PWD/bin/irpf90 $$PWD/bin/irpman
ln -s $$PWD/irpf90/bin/irpf90 $$PWD/bin/irpf90
ln -s $$PWD/irpf90/bin/irpman $$PWD/bin/irpman
#@$(FETCH_FROM_WEB) "$(WWW_SERVER)/$(IRPF90_TGZ)" $(IRPF90_TGZ) || \
# (echo Unable to download IRPF90 : $(WWW_SERVER)/$(IRPF90_TGZ) ; exit 1)
#tar -zxf $(IRPF90_TGZ) && rm $(IRPF90_TGZ)
#$(MAKE) -C irpf90 | tee install_irpf90.log
#rm -rf -- $$PWD/bin/irpf90 $$PWD/bin/irpman
echo $$PWD/irpf90/bin/irpf90 $$\@ > $$PWD/bin/irpf90
echo $$PWD/irpf90/bin/irpman $$\@ > $$PWD/bin/irpman
chmod +x $$PWD/bin/irpf90 $$PWD/bin/irpman
doc:
$(MAKE) -C doc

2
data/ezfio_defaults
View File

@ -18,7 +18,7 @@ cis_dressed
determinants
n_states 1
n_states_diag determinants_n_states
n_det_max_jacobi 5000
n_det_max_jacobi 1000
threshold_generators 0.99
threshold_selectors 0.999
read_wf False

60
ocaml/Generic_input_of_rst.ml Normal file
View File

@ -0,0 +1,60 @@
open Core.Std;;
open Qptypes;;
let fail_msg str (ex,range) =
let msg = match ex with
| Failure msg -> msg
| _ -> raise ex
in
let range = match range with
| Sexp.Annotated.Atom (range,_) -> range
| Sexp.Annotated.List (range,_,_) -> range
in
let open Sexp.Annotated in
let start_pos = range.start_pos.offset
and end_pos = range.end_pos.offset
in
let pre = String.sub ~pos:0 ~len:start_pos str
and mid = String.sub ~pos:start_pos ~len:(end_pos-start_pos) str
and post = String.sub ~pos:(end_pos)
~len:((String.length str)-(end_pos)) str
in
let str = Printf.sprintf "%s ## %s ## %s" pre mid post
in
let str = String.tr str ~target:'(' ~replacement:' '
|> String.split ~on:')'
|> List.map ~f:String.strip
|> List.filter ~f:(fun x ->
match String.substr_index x ~pos:0 ~pattern:"##" with
| None -> false
| Some _ -> true
)
|> String.concat ~sep:"\n"
in
Printf.eprintf "Error: (%s)\n\n %s\n\n" msg str;
;;
let evaluate_sexp t_of_sexp s =
let sexp = ("("^s^")") in
match ( Sexp.of_string_conv sexp t_of_sexp ) with
| `Result r -> Some r
| `Error ex -> ( fail_msg sexp ex; None)
;;
let of_rst t_of_sexp s =
Rst_string.to_string s
|> String.split ~on:'\n'
|> List.filter ~f:(fun line ->
String.contains line '=')
|> List.map ~f:(fun line ->
"("^(
String.tr line ~target:'=' ~replacement:' '
)^")" )
|> String.concat
|> evaluate_sexp t_of_sexp
;;

36
ocaml/Input_ao_basis.ml
View File

@ -4,7 +4,7 @@ open Core.Std;;
module Ao_basis : sig
type t =
{ ao_basis : string ;
{ ao_basis : AO_basis_name.t;
ao_num : AO_number.t ;
ao_prim_num : AO_prim_number.t array;
ao_prim_num_max : AO_prim_number.t;
@ -14,13 +14,13 @@ module Ao_basis : sig
ao_expo : AO_expo.t array;
} with sexp
;;
val read : unit -> t
val read : unit -> t option
val to_string : t -> string
val to_md5 : t -> MD5.t
val to_rst : t -> Rst_string.t
end = struct
type t =
{ ao_basis : string ;
{ ao_basis : AO_basis_name.t;
ao_num : AO_number.t ;
ao_prim_num : AO_prim_number.t array;
ao_prim_num_max : AO_prim_number.t;
@ -34,10 +34,8 @@ end = struct
let get_default = Qpackage.get_ezfio_default "ao_basis";;
let read_ao_basis () =
if not (Ezfio.has_ao_basis_ao_basis ()) then
Ezfio.set_ao_basis_ao_basis ""
;
Ezfio.get_ao_basis_ao_basis ()
|> AO_basis_name.of_string
;;
let read_ao_num () =
@ -95,15 +93,19 @@ end = struct
;;
let read () =
{ ao_basis = read_ao_basis ();
ao_num = read_ao_num () ;
ao_prim_num = read_ao_prim_num ();
ao_prim_num_max = read_ao_prim_num_max ();
ao_nucl = read_ao_nucl ();
ao_power = read_ao_power ();
ao_coef = read_ao_coef () ;
ao_expo = read_ao_expo () ;
}
if (Ezfio.has_ao_basis_ao_basis ()) then
Some
{ ao_basis = read_ao_basis ();
ao_num = read_ao_num () ;
ao_prim_num = read_ao_prim_num ();
ao_prim_num_max = read_ao_prim_num_max ();
ao_nucl = read_ao_nucl ();
ao_power = read_ao_power ();
ao_coef = read_ao_coef () ;
ao_expo = read_ao_expo () ;
}
else
None
;;
let to_long_basis b =
@ -171,7 +173,7 @@ Basis set ::
%s
======= ========= ===========
" b.ao_basis
" (AO_basis_name.to_string b.ao_basis)
(Basis.to_string short_basis
|> String.split ~on:'\n'
|> List.map ~f:(fun x-> " "^x)
@ -213,7 +215,7 @@ ao_coef = %s
ao_expo = %s
md5 = %s
"
b.ao_basis
(AO_basis_name.to_string b.ao_basis)
(AO_number.to_string b.ao_num)
(b.ao_prim_num |> Array.to_list |> List.map
~f:(AO_prim_number.to_string) |> String.concat ~sep:", " )

22
ocaml/Input_bi_integrals.ml
View File

@ -13,11 +13,11 @@ module Bielec_integrals : sig
direct : bool;
} with sexp
;;
val read : unit -> t
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
val of_rst : Rst_string.t -> t option
end = struct
type t =
{ read_ao_integrals : bool;
@ -150,7 +150,7 @@ end = struct
if (result.read_mo_integrals &&
result.write_mo_integrals) then
failwith "Read and Write MO integrals are both true.";
result
Some result
;;
let write b =
@ -220,20 +220,8 @@ Direct calculation of integrals ::
|> Rst_string.of_string
;;
let of_rst s =
let s = Rst_string.to_string s
|> String.split ~on:'\n'
|> List.filter ~f:(fun line ->
String.contains line '=')
|> List.map ~f:(fun line ->
"("^(
String.tr line ~target:'=' ~replacement:' '
)^")" )
|> String.concat
in
Sexp.of_string ("("^s^")")
|> t_of_sexp
;;
include Generic_input_of_rst;;
let of_rst = of_rst t_of_sexp;;
end

16
ocaml/Input_bitmasks.ml
View File

@ -10,7 +10,7 @@ module Bitmasks : sig
generators : int64 array;
} with sexp
;;
val read : unit -> t
val read : unit -> t option
val to_string : t -> string
end = struct
type t =
@ -77,11 +77,15 @@ end = struct
;;
let read () =
{ n_int = read_n_int ();
bit_kind = read_bit_kind ();
n_mask_gen = read_n_mask_gen ();
generators = read_generators ();
}
if (Ezfio.has_mo_basis_mo_tot_num ()) then
Some
{ n_int = read_n_int ();
bit_kind = read_bit_kind ();
n_mask_gen = read_n_mask_gen ();
generators = read_generators ();
}
else
None
;;
let to_string b =

8
ocaml/Input_cis.ml
View File

@ -12,9 +12,10 @@ module Cis_dressed : sig
en_2_2 : bool;
} with sexp
;;
val read : unit -> t
val read : unit -> t option
val to_string : t -> string
val to_rst : t -> Rst_string.t
val of_rst : Rst_string.t -> t option
end = struct
type t =
{ n_state_cis : States_number.t;
@ -85,6 +86,7 @@ end = struct
;;
let read () =
Some
{ n_state_cis = read_n_state_cis ();
n_core_cis = read_n_core_cis ();
n_act_cis = read_n_act_cis ();
@ -145,6 +147,10 @@ Epstein-Nesbet 2x2 diagonalization ::
|> Rst_string.of_string
;;
include Generic_input_of_rst;;
let of_rst = of_rst t_of_sexp;;
end

23
ocaml/Input_cisd_sc2.ml
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@ -9,11 +9,11 @@ module Cisd_sc2 : sig
do_pt2_end : bool;
} with sexp
;;
val read : unit -> t
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
val of_rst : Rst_string.t -> t option
end = struct
type t =
{ n_det_max_cisd_sc2 : Det_number_max.t;
@ -71,6 +71,7 @@ end = struct
let read () =
Some
{ n_det_max_cisd_sc2 = read_n_det_max_cisd_sc2 ();
pt2_max = read_pt2_max ();
do_pt2_end = read_do_pt2_end ();
@ -118,22 +119,8 @@ Compute E(PT2) at the end ::
|> Rst_string.of_string
;;
let of_rst s =
let s = Rst_string.to_string s
|> String.split ~on:'\n'
|> List.filter ~f:(fun line ->
String.contains line '=')
|> List.map ~f:(fun line ->
"("^(
String.tr line ~target:'=' ~replacement:' '
)^")" )
|> String.concat
in
Sexp.of_string ("("^s^")")
|> t_of_sexp
;;
include Generic_input_of_rst;;
let of_rst = of_rst t_of_sexp;;
end

71
ocaml/Input_determinants.ml
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@ -19,11 +19,11 @@ module Determinants : sig
psi_coef : Det_coef.t array;
psi_det : Determinant.t array;
} with sexp
val read : unit -> t
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
val of_rst : Rst_string.t -> t option
end = struct
type t =
{ n_int : N_int_number.t;
@ -131,9 +131,11 @@ end = struct
|> States_number.of_int
;;
let write_n_states_diag n =
States_number.to_int n
|> Ezfio.set_determinants_n_states_diag
let write_n_states_diag ~n_states n =
let n_states = States_number.to_int n_states
and n = States_number.to_int n
in
Ezfio.set_determinants_n_states_diag (max n_states n)
;;
@ -232,20 +234,27 @@ end = struct
let read_psi_coef () =
if not (Ezfio.has_determinants_psi_coef ()) then
Ezfio.ezfio_array_of_list ~rank:1 ~dim:[| 1 |] ~data:[1.]
|> Ezfio.set_determinants_psi_coef
;
begin
let n_states =
read_n_states ()
|> States_number.to_int
in
Ezfio.ezfio_array_of_list ~rank:2 ~dim:[| 1 ; n_states |]
~data:(List.init n_states ~f:(fun i -> if (i=0) then 1. else 0. ))
|> Ezfio.set_determinants_psi_coef
end;
Ezfio.get_determinants_psi_coef ()
|> Ezfio.flattened_ezfio
|> Array.map ~f:Det_coef.of_float
;;
let write_psi_coef ~n_det c =
let write_psi_coef ~n_det ~n_states c =
let n_det = Det_number.to_int n_det
and c = Array.to_list c
|> List.map ~f:Det_coef.to_float
and n_states = States_number.to_int n_states
in
Ezfio.ezfio_array_of_list ~rank:1 ~dim:[| n_det |] ~data:c
Ezfio.ezfio_array_of_list ~rank:2 ~dim:[| n_det ; n_states |] ~data:c
|> Ezfio.set_determinants_psi_coef
;;
@ -302,21 +311,25 @@ end = struct
let read () =
{ n_int = read_n_int () ;
bit_kind = read_bit_kind () ;
mo_label = read_mo_label () ;
n_det = read_n_det () ;
n_states = read_n_states () ;
n_states_diag = read_n_states_diag () ;
n_det_max_jacobi = read_n_det_max_jacobi () ;
threshold_generators = read_threshold_generators () ;
threshold_selectors = read_threshold_selectors () ;
read_wf = read_read_wf () ;
expected_s2 = read_expected_s2 () ;
s2_eig = read_s2_eig () ;
psi_coef = read_psi_coef () ;
psi_det = read_psi_det () ;
}
if (Ezfio.has_mo_basis_mo_tot_num ()) then
Some
{ n_int = read_n_int () ;
bit_kind = read_bit_kind () ;
mo_label = read_mo_label () ;
n_det = read_n_det () ;
n_states = read_n_states () ;
n_states_diag = read_n_states_diag () ;
n_det_max_jacobi = read_n_det_max_jacobi () ;
threshold_generators = read_threshold_generators () ;
threshold_selectors = read_threshold_selectors () ;
read_wf = read_read_wf () ;
expected_s2 = read_expected_s2 () ;
s2_eig = read_s2_eig () ;
psi_coef = read_psi_coef () ;
psi_det = read_psi_det () ;
}
else
None
;;
let write { n_int ;
@ -339,14 +352,14 @@ end = struct
write_mo_label mo_label;
write_n_det n_det;
write_n_states n_states;
write_n_states_diag n_states_diag;
write_n_states_diag ~n_states:n_states n_states_diag;
write_n_det_max_jacobi n_det_max_jacobi;
write_threshold_generators threshold_generators;
write_threshold_selectors threshold_selectors;
write_read_wf read_wf;
write_expected_s2 expected_s2;
write_s2_eig s2_eig;
write_psi_coef ~n_det:n_det psi_coef;
write_psi_coef ~n_det:n_det psi_coef ~n_states:n_states;
write_psi_det ~n_int:n_int ~n_det:n_det psi_det;
;;
@ -538,8 +551,8 @@ psi_det = %s
and n_int = Printf.sprintf "(n_int %d)" (N_int_number.get_max ()) in
let s = String.concat [ header ; bitkind ; n_int ; psi_coef ; psi_det]
in
Sexp.of_string ("("^s^")")
|> t_of_sexp
Generic_input_of_rst.evaluate_sexp t_of_sexp s
;;
end

30
ocaml/Input_electrons.ml
View File

@ -8,12 +8,12 @@ module Electrons : sig
elec_beta_num : Elec_beta_number.t;
} with sexp
;;
val read : unit -> t
val read : unit -> t option
val write : t -> unit
val read_elec_num : unit -> Elec_number.t
val to_string : t -> string
val to_rst : t -> Rst_string.t
val of_rst : Rst_string.t -> t
val of_rst : Rst_string.t -> t option
end = struct
type t =
{ elec_alpha_num : Elec_alpha_number.t;
@ -53,9 +53,13 @@ end = struct
let read () =
{ elec_alpha_num = read_elec_alpha_num ();
elec_beta_num = read_elec_beta_num ();
}
if (Ezfio.has_electrons_elec_alpha_num ()) then
Some
{ elec_alpha_num = read_elec_alpha_num ();
elec_beta_num = read_elec_beta_num ();
}
else
None
;;
let write { elec_alpha_num ; elec_beta_num } =
@ -91,20 +95,8 @@ elec_num = %s
(Elec_number.to_string (read_elec_num ()))
;;
let of_rst s =
let s = Rst_string.to_string s
|> String.split ~on:'\n'
|> List.filter ~f:(fun line ->
String.contains line '=')
|> List.map ~f:(fun line ->
"("^(
String.tr line ~target:'=' ~replacement:' '
)^")" )
|> String.concat
in
Sexp.of_string ("("^s^")")
|> t_of_sexp
;;
include Generic_input_of_rst;;
let of_rst = of_rst t_of_sexp;;
end

27
ocaml/Input_full_ci.ml
View File

@ -9,11 +9,11 @@ module Full_ci : sig
do_pt2_end : bool;
} with sexp
;;
val read : unit -> t
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
val of_rst : Rst_string.t -> t option
end = struct
type t =
{ n_det_max_fci : Det_number_max.t;
@ -69,9 +69,10 @@ end = struct
let read () =
{ n_det_max_fci = read_n_det_max_fci ();
pt2_max = read_pt2_max ();
do_pt2_end = read_do_pt2_end ();
Some
{ n_det_max_fci = read_n_det_max_fci ();
pt2_max = read_pt2_max ();
do_pt2_end = read_do_pt2_end ();
}
;;
@ -117,20 +118,8 @@ Compute E(PT2) at the end ::
|> Rst_string.of_string
;;
let of_rst s =
let s = Rst_string.to_string s
|> String.split ~on:'\n'
|> List.filter ~f:(fun line ->
String.contains line '=')
|> List.map ~f:(fun line ->
"("^(
String.tr line ~target:'=' ~replacement:' '
)^")" )
|> String.concat
in
Sexp.of_string ("("^s^")")
|> t_of_sexp
;;
include Generic_input_of_rst;;
let of_rst = of_rst t_of_sexp;;
end

22
ocaml/Input_hartree_fock.ml
View File

@ -8,11 +8,11 @@ module Hartree_fock : sig
thresh_scf : Threshold.t;
} with sexp
;;
val read : unit -> t
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
val of_rst : Rst_string.t -> t option
end = struct
type t =
{ n_it_scf_max : Strictly_positive_int.t;
@ -54,6 +54,7 @@ end = struct
let read () =
Some
{ n_it_scf_max = read_n_it_scf_max ();
thresh_scf = read_thresh_scf ();
}
@ -93,21 +94,8 @@ SCF convergence criterion (on energy) ::
|> Rst_string.of_string
;;
let of_rst s =
let s = Rst_string.to_string s
|> String.split ~on:'\n'
|> List.filter ~f:(fun line ->
String.contains line '=')
|> List.map ~f:(fun line ->
"("^(
String.tr line ~target:'=' ~replacement:' '
)^")" )
|> String.concat
in
Sexp.of_string ("("^s^")")
|> t_of_sexp
;;
include Generic_input_of_rst;;
let of_rst = of_rst t_of_sexp;;
end

16
ocaml/Input_mo_basis.ml
View File

@ -10,7 +10,7 @@ module Mo_basis : sig
mo_coef : (MO_coef.t array) array;
} with sexp
;;
val read : unit -> t
val read : unit -> t option
val to_string : t -> string
val to_rst : t -> Rst_string.t
end = struct
@ -68,11 +68,15 @@ end = struct
;;
let read () =
{ mo_tot_num = read_mo_tot_num ();
mo_label = read_mo_label () ;
mo_occ = read_mo_occ ();
mo_coef = read_mo_coef ();
}
if (Ezfio.has_mo_basis_mo_tot_num ()) then
Some
{ mo_tot_num = read_mo_tot_num ();
mo_label = read_mo_label () ;
mo_occ = read_mo_occ ();
mo_coef = read_mo_coef ();
}
else
None
;;
let mo_coef_to_string mo_coef =

38
ocaml/Input_nuclei.ml
View File

@ -10,11 +10,11 @@ module Nuclei : sig
nucl_coord : Point3d.t array;
} with sexp
;;
val read : unit -> t
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
val of_rst : Rst_string.t -> t option
end = struct
type t =
{ nucl_num : Nucl_number.t ;
@ -111,11 +111,15 @@ end = struct
let read () =
{ nucl_num = read_nucl_num ();
nucl_label = read_nucl_label () ;
nucl_charge = read_nucl_charge ();
nucl_coord = read_nucl_coord ();
}
if (Ezfio.has_nuclei_nucl_num ()) then
Some
{ nucl_num = read_nucl_num ();
nucl_label = read_nucl_label () ;
nucl_charge = read_nucl_charge ();
nucl_coord = read_nucl_coord ();
}
else
None
;;
let write { nucl_num ;
@ -203,15 +207,17 @@ Nuclear coordinates in xyz format (Angstroms) ::
| _ -> failwith "Error in xyz format"
in
(* Create the Nuclei.t data structure *)
{ nucl_num = List.length atom_list
|> Nucl_number.of_int ~max:nmax;
nucl_label = List.map atom_list ~f:(fun x ->
x.Atom.element) |> Array.of_list ;
nucl_charge = List.map atom_list ~f:(fun x ->
x.Atom.charge ) |> Array.of_list ;
nucl_coord = List.map atom_list ~f:(fun x ->
x.Atom.coord ) |> Array.of_list ;
}
let result =
{ nucl_num = List.length atom_list
|> Nucl_number.of_int ~max:nmax;
nucl_label = List.map atom_list ~f:(fun x ->
x.Atom.element) |> Array.of_list ;
nucl_charge = List.map atom_list ~f:(fun x ->
x.Atom.charge ) |> Array.of_list ;
nucl_coord = List.map atom_list ~f:(fun x ->
x.Atom.coord ) |> Array.of_list ;
}
in Some result
;;
end

4
ocaml/Makefile
View File

@ -10,8 +10,8 @@ endif
LIBS=
PKGS=
OCAMLCFLAGS="-g"
OCAMLBUILD=ocamlbuild -j 0 -syntax camlp4o -cflags $(OCAMLCFLAGS) -lflags $(OCAMLCFLAGS)
OCAMLCFLAGS="-g -warn-error A"
OCAMLBUILD=ocamlbuild -j 0 -syntax camlp4o -cflags $(OCAMLCFLAGS) -lflags $(OCAMLCFLAGS) -ocamlopt ocamlc.opt
MLFILES=$(wildcard *.ml) ezfio.ml Qptypes.ml
MLIFILES=$(wildcard *.mli)
ALL_TESTS=$(patsubst %.ml,%.byte,$(wildcard test_*.ml))

3
ocaml/README.rst
View File

@ -8,5 +8,6 @@ with the user.
All executables start with `qp_` and all tests start with `test_`. Modules
file names start with a capital letter.
Info on how to extend the `qp_edit` tool is given in `README_qp_edit.rst`.
Info on how to extend the `qp_edit` tool is given in
`README_qp_edit.rst <https://github.com/LCPQ/quantum_package/blob/master/ocaml/README_qp_edit.rst>`_.

43
ocaml/README_qp_edit.rst
View File

@ -23,9 +23,8 @@ of the block.
;;
val read : unit -> t
val write : t -> unit
val to_string : t -> string
val to_rst : t -> Rst_string.t
val of_rst : Rst_string.t -> t
val of_rst : Rst_string.t -> t option
end = struct
type t =
{ r_x : Type_of_x.t
@ -42,12 +41,14 @@ of the block.
end
The following functions need to be defined::
The following functions need to be defined
.. code-block:: ocaml
val read : unit -> t
val write : t -> unit
val to_rst : t -> Rst_string.t
val of_rst : Rst_string.t -> t
val of_rst : Rst_string.t -> t option
The type `t` has to be defined in a same way in the `sig` and the `struct`.
@ -135,26 +136,12 @@ Finally, create the functions to write an RST string as
;;
and you can use this function to read it back:
and you can use the generic `of_rst` function to read it back:
.. code-block:: ocaml
let of_rst s =
let s = Rst_string.to_string s
|> String.split ~on:'\n'
|> List.filter ~f:(fun line ->
String.contains line '=')
|> List.map ~f:(fun line ->
"("^(
String.tr line ~target:'=' ~replacement:' '
)^")" )
|> String.concat
in
Sexp.of_string ("("^s^")")
|> t_of_sexp
;;
include Generic_input_of_rst;;
let of_rst = of_rst t_of_sexp;;
@ -201,10 +188,11 @@ vim search strings are given in brackets.
let get s =
let header = (make_header s)
and rst = match s with
and rst = let open Input in
match s with
...
| New_keyword ->
Input.New_keyword.(to_rst (read ()))
New_keyword.(to_rst (read ()))
...
@ -212,9 +200,10 @@ vim search strings are given in brackets.
.. code-block:: ocaml
match s with
...
| New_keyword ->
Input.New_keyword.(write (of_rst str))
let open Input in
match s with
...
| New_keyword -> write New_keyword.(of_rst, write)
...
;;

105
ocaml/qp_create_ezfio_from_xyz.ml
View File

@ -6,29 +6,85 @@ let spec =
let open Command.Spec in
empty
+> flag "o" (optional string)
~doc:"file Name of the created EZFIO file"
~doc:"file Name of the created EZFIO file."
+> flag "b" (required string)
~doc:"name Basis set."
~doc:"definition of basis set."
+> flag "c" (optional_with_default 0 int)
~doc:"int Total charge of the molecule. Default is 0."
+> flag "m" (optional_with_default 1 int)
~doc:"int Spin multiplicity (2S+1) of the molecule. Default is 1"
~doc:"int Spin multiplicity (2S+1) of the molecule. Default is 1."
+> anon ("xyz_file" %: string)
;;
let run ?o b c m xyz_file =
(* Open basis set channel *)
let basis_channel =
In_channel.create
(Qpackage.root ^ "/data/basis/" ^ (String.lowercase b))
in
(* Read molecule *)
let molecule =
(Molecule.of_xyz_file xyz_file ~charge:(Charge.of_int c)
~multiplicity:(Multiplicity.of_int m) )
in
let nuclei = molecule.Molecule.nuclei in
let basis_table = Hashtbl.Poly.create () in
(* Open basis set channels *)
let basis_channel element =
let key = Element.to_string element in
match Hashtbl.find basis_table key with
| Some in_channel ->
in_channel
| None ->
begin
Printf.printf "%s is not defined in basis %s.\nEnter alternate basis : %!"
(Element.to_long_string element) b ;
let bas =
match In_channel.input_line stdin with
| Some line -> String.strip line |> String.lowercase
| None -> failwith "Aborted"
in
let new_channel = In_channel.create
(Qpackage.root ^ "/data/basis/" ^ bas)
in
Hashtbl.add_exn basis_table ~key:key ~data:new_channel;
new_channel
end
in
let rec build_basis = function
| [] -> ()
| elem_and_basis_name :: rest ->
begin
match (String.lsplit2 ~on:':' elem_and_basis_name) with
| None -> (* Principal basis *)
begin
let new_channel = In_channel.create
(Qpackage.root ^ "/data/basis/" ^ elem_and_basis_name)
in
List.iter nuclei ~f:(fun x->
let key = Element.to_string x.Atom.element
in
match Hashtbl.add basis_table ~key:key ~data:new_channel with
| `Ok -> ()
| `Duplicate -> ()
)
end
| Some (key, basis) -> (*Aux basis *)
begin
let elem = Element.of_string key
and basis = String.lowercase basis
in
let new_channel = In_channel.create
(Qpackage.root ^ "/data/basis/" ^ basis)
in
match Hashtbl.add basis_table ~key:key ~data:new_channel with
| `Ok -> ()
| `Duplicate -> failwith ("Duplicate definition of basis for "^(Element.to_long_string elem))
end
end;
build_basis rest
in
String.split ~on:' ' b
|> List.rev_map ~f:String.strip
|> build_basis;
(* Build EZFIO File name *)
let ezfio_file =
@ -54,7 +110,6 @@ let run ?o b c m xyz_file =
molecule.Molecule.elec_beta ) ;
(* Write Nuclei *)
let nuclei = molecule.Molecule.nuclei in
let labels =
List.map ~f:(fun x->Element.to_string x.Atom.element) nuclei
and charges =
@ -74,17 +129,31 @@ let run ?o b c m xyz_file =
(* Write Basis set *)
let basis =
let nmax = Nucl_number.get_max () in
let rec do_work (accu:(Atom.t*Nucl_number.t) list) (n:int) = function
| [] -> accu
| e::tail -> let new_accu = (e,(Nucl_number.of_int ~max:nmax n))::accu in
| e::tail ->
let new_accu = (e,(Nucl_number.of_int ~max:nmax n))::accu in
do_work new_accu (n+1) tail
in
do_work [] 1 nuclei
let result = do_work [] 1 nuclei
|> List.rev
|> List.map ~f:(fun (x,i) ->
Basis.read_element basis_channel i x.Atom.element)
try
Basis.read_element (basis_channel x.Atom.element) i x.Atom.element
with
| End_of_file ->
begin
let alt_channel = basis_channel x.Atom.element in
Basis.read_element alt_channel i x.Atom.element
end
| _ -> assert false
)
|> List.concat
in
(* close all in_channels *)
result
in
let long_basis = Long_basis.of_basis basis in
let ao_num = List.length long_basis in
@ -150,8 +219,14 @@ let run ?o b c m xyz_file =
let command =
Command.basic
~summary: "Quantum Package command"
~readme:(fun () ->
"Creates an EZFIO directory from a standard xyz file
~readme:(fun () -> "
Creates an EZFIO directory from a standard xyz file.
The basis set is defined as a single string if all the
atoms are taken from the same basis set, otherwise specific
elements can be defined as follows:
-b \"cc-pcvdz H:cc-pvdz C:6-31g\"
")
spec
(fun o b c m xyz_file () ->

140
ocaml/qp_edit.ml
View File

@ -43,77 +43,93 @@ let make_header kw =
;;
let get s =
let header = (make_header s)
and rst = match s with
| Full_ci ->
Input.Full_ci.(to_rst (read ()))
| Hartree_fock ->
Input.Hartree_fock.(to_rst (read ()))
| Mo_basis ->
Input.Mo_basis.(to_rst (read ()))
| Electrons ->
Input.Electrons.(to_rst (read ()))
| Determinants ->
Input.Determinants.(to_rst (read ()))
| Cisd_sc2 ->
Input.Cisd_sc2.(to_rst (read ()))
| Nuclei ->
Input.Nuclei.(to_rst (read ()))
| Ao_basis ->
Input.Ao_basis.(to_rst (read ()))
| Bielec_integrals ->
Input.Bielec_integrals.(to_rst (read ()))
in header^(Rst_string.to_string rst)
let header = (make_header s) in
let f (read,to_rst) =
match read () with
| Some text -> header ^ (Rst_string.to_string (to_rst text))
| None -> ""
in
let rst =
try
begin
let open Input in
match s with
| Full_ci ->
f Full_ci.(read, to_rst)
| Hartree_fock ->
f Hartree_fock.(read, to_rst)
| Mo_basis ->
f Mo_basis.(read, to_rst)
| Electrons ->
f Electrons.(read, to_rst)
| Cisd_sc2 ->
f Cisd_sc2.(read, to_rst)
| Nuclei ->
f Nuclei.(read, to_rst)
| Ao_basis ->
f Ao_basis.(read, to_rst)
| Bielec_integrals ->
f Bielec_integrals.(read, to_rst)
| Determinants ->
f Determinants.(read, to_rst)
end
with
| Sys_error msg -> (Printf.eprintf "Info: %s\n%!" msg ; "")
in
rst
;;
let set str s =
let header = (make_header s) in
let index_begin = String.substr_index_exn ~pos:0 ~pattern:header str in
let index_begin = index_begin + (String.length header) in
let index_end =
match ( String.substr_index ~pos:(index_begin+(String.length header)+1)
~pattern:"==" str) with
| Some i -> i
| None -> String.length str
in
let l = index_end - index_begin in
let str = String.sub ~pos:index_begin ~len:l str
|> Rst_string.of_string
in
match s with
(*
| Mo_basis ->
*)
| Hartree_fock ->
Input.Hartree_fock.(write (of_rst str ))
| Full_ci ->
Input.Full_ci.(write (of_rst str))
| Electrons ->
Input.Electrons.(write (of_rst str))
| Determinants ->
Input.Determinants.(write (of_rst str))
| Cisd_sc2 ->
Input.Cisd_sc2.(write (of_rst str))
| Nuclei ->
Input.Nuclei.(write (of_rst str))
| Bielec_integrals ->
Input.Bielec_integrals.(write (of_rst str))
(*
| Ao_basis ->
*)
match String.substr_index ~pos:0 ~pattern:header str with
| None -> ()
| Some idx ->
begin
let index_begin = idx + (String.length header) in
let index_end =
match ( String.substr_index ~pos:(index_begin+(String.length header)+1)
~pattern:"==" str) with
| Some i -> i
| None -> String.length str
in
let l = index_end - index_begin in
let str = String.sub ~pos:index_begin ~len:l str
|> Rst_string.of_string
in
let write (of_rst,w) s =
try
match of_rst str with
| Some data -> w data
| None -> ()
with
| _ -> (Printf.eprintf "Info: Read error in %s\n%!"
(keyword_to_string s))
in
let open Input in
match s with
| Hartree_fock -> write Hartree_fock.(of_rst, write) s
| Full_ci -> write Full_ci.(of_rst, write) s
| Electrons -> write Electrons.(of_rst, write) s
| Cisd_sc2 -> write Cisd_sc2.(of_rst, write) s
| Bielec_integrals -> write Bielec_integrals.(of_rst, write) s
| Determinants -> write Determinants.(of_rst, write) s
| Nuclei -> write Nuclei.(of_rst, write) s
| Ao_basis -> () (* TODO *)
| Mo_basis -> () (* TODO *)
end
;;
let create_temp_file ezfio_filename fields =
let temp_filename = Filename.temp_file "qp_edit_" ".rst" in
Out_channel.with_file temp_filename ~f:(fun out_channel ->
(file_header ezfio_filename) :: (List.map ~f:get fields)
|> String.concat ~sep:"\n"
|> Out_channel.output_string out_channel
);
temp_filename
begin
Out_channel.with_file temp_filename ~f:(fun out_channel ->
(file_header ezfio_filename) :: (List.map ~f:get fields)
|> String.concat ~sep:"\n"
|> Out_channel.output_string out_channel
)
end
; temp_filename
;;
let run ezfio_filename =

10
ocaml/qp_print.ml
View File

@ -51,7 +51,10 @@ let run_i ~action ezfio_filename =
let compute_charge () =
let input = Input.Electrons.read () in
let input = match Input.Electrons.read () with
| Some x -> x
| None -> assert false
in
let nucl_charge = Ezfio.get_nuclei_nucl_charge ()
|> Ezfio.flattened_ezfio |> Array.map ~f:(Float.to_int)
and n_alpha = input.Input.Electrons.elec_alpha_num
@ -63,7 +66,10 @@ let run_i ~action ezfio_filename =
in
let compute_multiplicity () =
let input = Input.Electrons.read () in
let input = match Input.Electrons.read () with
| Some x -> x
| None -> assert false
in
let n_alpha = input.Input.Electrons.elec_alpha_num
and n_beta = input.Input.Electrons.elec_beta_num
in Multiplicity.of_alpha_beta n_alpha n_beta

9
ocaml/qptypes_generator.ml
View File

@ -100,6 +100,9 @@ let input_data = "
* Rst_string : string
* AO_basis_name : string
assert (x <> \"\") ;
"
;;
@ -228,9 +231,9 @@ let parse_input_ezfio input=
and (min, max) = String.lsplit2_exn ~on:':' c
and msg = d
in
let name :: typ :: ezfio_func :: min :: max :: msg :: [] =
match (name :: typ :: ezfio_func :: min :: max :: msg :: []) with
| l -> List.map ~f:String.strip l
let (name, typ, ezfio_func, min, max, msg) =
match (List.map [ name ; typ ; ezfio_func ; min ; max ; msg ] ~f:String.strip) with
| [ name ; typ ; ezfio_func ; min ; max ; msg ] -> (name, typ, ezfio_func, min, max, msg)
| _ -> assert false
in
Printf.sprintf ezfio_template

4
ocaml/test_basis.ml
View File

@ -9,12 +9,12 @@ let test_module () =
In_channel.create (Qpackage.root^"/data/basis/"^(String.lowercase b))
in
(*
let molecule =
let xyz_file = "F2.xyz" in
Molecule.of_xyz_file xyz_file
in
let nuclei = molecule.Molecule.nuclei in
*)
let basis =
(Basis.read_element basis_channel (Nucl_number.of_int 1) Element.F) @

90
ocaml/test_input.ml
View File

@ -2,7 +2,9 @@ open Qptypes;;
let test_ao () =
Ezfio.set_file "F2.ezfio" ;
let b = Input.Ao_basis.read ()
let b = match Input.Ao_basis.read () with
| Some x -> x
| None -> assert false
in
print_endline (Input.Ao_basis.to_string b);
print_endline (Input.Ao_basis.to_rst b |> Rst_string.to_string);
@ -10,13 +12,18 @@ let test_ao () =
let test_bielec_intergals () =
Ezfio.set_file "F2.ezfio" ;
let b = Input.Bielec_integrals.read ()
let b = match Input.Bielec_integrals.read () with
| Some x -> x
| None -> assert false
in
let output = Input.Bielec_integrals.to_string b
in
print_endline output;
let rst = Input.Bielec_integrals.to_rst b in
let b2 = Input.Bielec_integrals.of_rst rst in
let b2 = match Input.Bielec_integrals.of_rst rst with
| Some x -> x
| None -> assert false
in
if (b = b2) then
print_endline "OK"
else
@ -25,26 +32,35 @@ let test_bielec_intergals () =
let test_bitmasks () =
Ezfio.set_file "F2.ezfio" ;
let b = Input.Bitmasks.read ()
let b = match Input.Bitmasks.read () with
| Some x -> x
| None -> assert false
in
print_endline (Input.Bitmasks.to_string b);
;;
let test_cis () =
Ezfio.set_file "F2.ezfio" ;
let b = Input.Cis_dressed.read ()
let b = match Input.Cis_dressed.read () with
| Some x -> x
| None -> assert false
in
print_endline (Input.Cis_dressed.to_string b);
;;
let test_dets () =
Ezfio.set_file "F2.ezfio" ;
let b = Input.Determinants.read ()
let b = match Input.Determinants.read () with
| Some x -> x
| None -> assert false
in
print_endline (Input.Determinants.to_rst b |> Rst_string.to_string ) ;
print_endline (Input.Determinants.sexp_of_t b |> Sexplib.Sexp.to_string ) ;
let r = Input.Determinants.to_rst b in
let b2 = Input.Determinants.of_rst r in
let rst = Input.Determinants.to_rst b in
let b2 = match Input.Determinants.of_rst rst with
| Some x -> x
| None -> assert false
in
if (b2 = b) then
print_endline "OK"
else
@ -53,11 +69,16 @@ let test_dets () =
let test_cisd_sc2 () =
Ezfio.set_file "F2.ezfio" ;
let b = Input.Cisd_sc2.read ()
let b = match Input.Cisd_sc2.read () with
| Some x -> x
| None -> assert false
in
print_endline (Input.Cisd_sc2.to_string b);
let rst = Input.Cisd_sc2.to_rst b in
let b2 = Input.Cisd_sc2.of_rst rst in
let b2 = match Input.Cisd_sc2.of_rst rst with
| Some x -> x
| None -> assert false
in
if (b = b2) then
print_endline "OK"
else
@ -67,12 +88,17 @@ let test_cisd_sc2 () =
let test_electrons () =
Ezfio.set_file "F2.ezfio" ;
let b = Input.Electrons.read ()
let b = match Input.Electrons.read () with
| Some x -> x
| None -> assert false
in
print_endline (Input.Electrons.to_string b);
let rst = Input.Electrons.to_rst b in
let new_b = Input.Electrons.of_rst rst in
if (b = new_b) then
let b2 = match Input.Electrons.of_rst rst with
| Some x -> x
| None -> assert false
in
if (b = b2) then
print_endline "OK"
else
print_endline "Failed in rst"
@ -80,13 +106,18 @@ let test_electrons () =
let test_fci () =
Ezfio.set_file "F2.ezfio" ;
let b = Input.Full_ci.read ()
let b = match Input.Full_ci.read () with
| Some x -> x
| None -> assert false
in
print_endline (Input.Full_ci.to_string b);
let rst = Input.Full_ci.to_rst b in
let new_b = Input.Full_ci.of_rst rst in
let b2 = match Input.Full_ci.of_rst rst with
| Some x -> x
| None -> assert false
in
print_endline (Input.Full_ci.to_string b);
if (b = new_b) then
if (b = b2) then
print_endline "OK"
else
print_endline "Failed in rst"
@ -94,13 +125,18 @@ let test_fci () =
let test_hf () =
Ezfio.set_file "F2.ezfio" ;
let b = Input.Hartree_fock.read ()
let b = match Input.Hartree_fock.read () with
| Some x -> x
| None -> assert false
in
print_endline (Input.Hartree_fock.to_string b);
let rst = Input.Hartree_fock.to_rst b in
let new_b = Input.Hartree_fock.of_rst rst in
let b2 = match Input.Hartree_fock.of_rst rst with
| Some x -> x
| None -> assert false
in
print_endline (Input.Hartree_fock.to_string b);
if (b = new_b) then
if (b = b2) then
print_endline "OK"
else
print_endline "Failed in rst"
@ -108,18 +144,26 @@ let test_hf () =
let test_mo () =
Ezfio.set_file "F2.ezfio" ;
let b = Input.Mo_basis.read ()
let b = match Input.Mo_basis.read () with
| Some x -> x
| None -> assert false
in
print_endline (Input.Mo_basis.to_string b);
;;
let test_nucl () =
Ezfio.set_file "F2.ezfio" ;
let b = Input.Nuclei.read () in
let b = match Input.Nuclei.read () with
| Some x -> x
| None -> assert false
in
let rst = Input.Nuclei.to_rst b in
let new_b = Input.Nuclei.of_rst rst in
let b2 = match Input.Nuclei.of_rst rst with
| Some x -> x
| None -> assert false
in
print_endline (Input.Nuclei.to_string b);
if (b = new_b) then
if (b = b2) then
print_endline "OK"
else
print_endline "Failed in rst"

2
src/Dets/determinants.irp.f
View File

@ -149,7 +149,7 @@ END_PROVIDER
duplicate(i) = .False.
enddo
do i=1,N_det
do i=1,N_det-1
if (duplicate(i)) then
cycle
endif

1
src/Perturbation/selection.irp.f
View File

@ -148,7 +148,6 @@ subroutine make_s2_eigenfunction
integer, parameter :: bufsze = 1000
logical, external :: is_in_wavefunction
print *, irp_here
! !TODO DEBUG
! do i=1,N_det
! do j=i+1,N_det