LCPQ/quantum_package
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Merge pull request #52 from scemama/master

Browse Source 
Accept cause Sooner is beter.
 Will fix the test bug on monday.
This commit is contained in:
Thomas Applencourt 2015-04-10 19:47:06 +02:00
commit 4d44c1b46d
82 changed files with 2718 additions and 1306 deletions
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5
.gitattributes vendored Normal file
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@ -0,0 +1,5 @@
*.irp.f linguist-language=IRPF90
*.f linguist-language=Fortran
*.ml linguist-language=Ocaml
*.sh linguist-language=Bash
*.py linguist-language=Python

2
.gitignore vendored
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@ -7,3 +7,5 @@ bin/
quantum_package_static.tar.gz
resultsFile
opam_installer.sh
*.mod
*.p

6
.travis.yml
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@ -1,5 +1,9 @@
sudo: true
language: python
python:
- "2.6"
before_script:
- sudo apt-get update
- sudo apt-get install gfortran liblapack-dev
@ -9,4 +13,4 @@ script:
- source ./quantum_package.rc
- cp ./src/Makefile.config.gfortran ./src/Makefile.config
- make build
- ./tests/unit_test/unit_test.py

3
INSTALL.md
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@ -6,8 +6,9 @@
* m4
* GNU make
* Fortran compiler (ifort or gfortran are tested)
* Python >= 2.7
* Python >= 2.6
* Bash
* Patch (for opam)
## Standard installation

2
Makefile
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@ -44,6 +44,6 @@ ocaml:
$(MAKE) ocaml/Qptypes.ml
veryclean:
rm -f EZFIO
rm -rf EZFIO
$(MAKE) EZFIO
$(MAKE) -C src veryclean

0
src/BiInts/ASSUMPTIONS.rst → data/ezfio_defaults/.empty
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1
data/ezfio_defaults/.gitignore vendored Normal file
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@ -0,0 +1 @@
*ezfio_interface_default

5
data/ezfio_defaults → data/ezfio_defaults/WILL_BE_DELETED.ezfio_default
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@ -43,11 +43,6 @@ all_singles
pt2_max 1.e-8
do_pt2_end False
cassd
n_det_max_cassd 10000
pt2_max 1.e-4
do_pt2_end True
hartree_fock
n_it_scf_max 200
thresh_scf 1.e-10

4
data/ezfio_defaults/cisd.ezfio_default Normal file
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@ -0,0 +1,4 @@
cisd_selected
n_det_max_cisd 10000
pt2_max 1.e-4

9
data/ezfio_defaults/determinants.ezfio_default Normal file
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@ -0,0 +1,9 @@
determinants
n_states 1
n_states_diag determinants_n_states
n_det_max_jacobi 1000
threshold_generators 0.99
threshold_selectors 0.999
read_wf false
s2_eig false
only_single_double_dm false

2
data/ezfio_defaults/properties.ezfio_default Normal file
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@ -0,0 +1,2 @@
properties
z_one_point 3.9

8
ocaml/Input.ml
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@ -2,16 +2,10 @@ open Qputils;;
open Qptypes;;
open Core.Std;;
include Input_ao_basis;;
include Input_bi_integrals;;
include Input_bitmasks;;
include Input_cisd_sc2;;
include Input_determinants;;
include Input_electrons;;
include Input_full_ci;;
include Input_hartree_fock;;
include Input_mo_basis;;
include Input_nuclei;;
include Input_auto_generated;;

127
ocaml/Input_cisd_sc2.ml
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@ -1,127 +0,0 @@
open Qptypes;;
open Qputils;;
open Core.Std;;
module Cisd_sc2 : sig
type t =
{ n_det_max_cisd_sc2 : Det_number_max.t;
pt2_max : PT2_energy.t;
do_pt2_end : bool;
} with 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 =
{ n_det_max_cisd_sc2 : Det_number_max.t;
pt2_max : PT2_energy.t;
do_pt2_end : bool;
} with sexp
;;
let get_default = Qpackage.get_ezfio_default "cisd_sc2_selected";;
let read_n_det_max_cisd_sc2 () =
if not (Ezfio.has_cisd_sc2_selected_n_det_max_cisd_sc2 ()) then
get_default "n_det_max_cisd_sc2"
|> Int.of_string
|> Ezfio.set_cisd_sc2_selected_n_det_max_cisd_sc2
;
Ezfio.get_cisd_sc2_selected_n_det_max_cisd_sc2 ()
|> Det_number_max.of_int
;;
let write_n_det_max_cisd_sc2 n =
Det_number_max.to_int n
|> Ezfio.set_cisd_sc2_selected_n_det_max_cisd_sc2
;;
let read_pt2_max () =
if not (Ezfio.has_cisd_sc2_selected_pt2_max ()) then
get_default "pt2_max"
|> Float.of_string
|> Ezfio.set_cisd_sc2_selected_pt2_max
;
Ezfio.get_cisd_sc2_selected_pt2_max ()
|> PT2_energy.of_float
;;
let write_pt2_max p =
PT2_energy.to_float p
|> Ezfio.set_cisd_sc2_selected_pt2_max
;;
let read_do_pt2_end () =
if not (Ezfio.has_cisd_sc2_selected_do_pt2_end ()) then
get_default "do_pt2_end"
|> Bool.of_string
|> Ezfio.set_cisd_sc2_selected_do_pt2_end
;
Ezfio.get_cisd_sc2_selected_do_pt2_end ()
;;
let write_do_pt2_end =
Ezfio.set_cisd_sc2_selected_do_pt2_end
;;
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 ();
}
;;
let write { n_det_max_cisd_sc2 ;
pt2_max ;
do_pt2_end ;
} =
write_n_det_max_cisd_sc2 n_det_max_cisd_sc2;
write_pt2_max pt2_max;
write_do_pt2_end do_pt2_end;
;;
let to_string b =
Printf.sprintf "
n_det_max_cisd_sc2 = %s
pt2_max = %s
do_pt2_end = %s
"
(Det_number_max.to_string b.n_det_max_cisd_sc2)
(PT2_energy.to_string b.pt2_max)
(Bool.to_string b.do_pt2_end)
;;
let to_rst b =
Printf.sprintf "
Stop when the `n_det` > `n_det_max_cisd_sc2` ::
n_det_max_cisd_sc2 = %s
Stop when -E(PT2) < `pt2_max` ::
pt2_max = %s
Compute E(PT2) at the end ::
do_pt2_end = %s
"
(Det_number_max.to_string b.n_det_max_cisd_sc2)
(PT2_energy.to_string b.pt2_max)
(Bool.to_string b.do_pt2_end)
|> Rst_string.of_string
;;
include Generic_input_of_rst;;
let of_rst = of_rst t_of_sexp;;
end

153
ocaml/Input_full_ci.ml
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@ -1,153 +0,0 @@
open Qptypes;;
open Qputils;;
open Core.Std;;
module Full_ci : sig
type t =
{ n_det_max_fci : Det_number_max.t;
pt2_max : PT2_energy.t;
do_pt2_end : bool;
var_pt2_ratio : Normalized_float.t;
} with 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 =
{ n_det_max_fci : Det_number_max.t;
pt2_max : PT2_energy.t;
do_pt2_end : bool;
var_pt2_ratio : Normalized_float.t;
} with sexp
;;
let get_default = Qpackage.get_ezfio_default "full_ci";;
let read_n_det_max_fci () =
if not (Ezfio.has_full_ci_n_det_max_fci ()) then
get_default "n_det_max_fci"
|> Int.of_string
|> Ezfio.set_full_ci_n_det_max_fci
;
Ezfio.get_full_ci_n_det_max_fci ()
|> Det_number_max.of_int
;;
let write_n_det_max_fci ndet =
Det_number_max.to_int ndet
|> Ezfio.set_full_ci_n_det_max_fci
;;
let read_var_pt2_ratio () =
if not (Ezfio.has_full_ci_var_pt2_ratio ()) then
get_default "var_pt2_ratio"
|> Float.of_string
|> Ezfio.set_full_ci_var_pt2_ratio
;
Ezfio.get_full_ci_var_pt2_ratio ()
|> Normalized_float.of_float
;;
let write_var_pt2_ratio ratio =
Normalized_float.to_float ratio
|> Ezfio.set_full_ci_var_pt2_ratio
;;
let read_pt2_max () =
if not (Ezfio.has_full_ci_pt2_max ()) then
get_default "pt2_max"
|> Float.of_string
|> Ezfio.set_full_ci_pt2_max
;
Ezfio.get_full_ci_pt2_max ()
|> PT2_energy.of_float
;;
let write_pt2_max pt2_max =
PT2_energy.to_float pt2_max
|> Ezfio.set_full_ci_pt2_max
;;
let read_do_pt2_end () =
if not (Ezfio.has_full_ci_do_pt2_end ()) then
get_default "do_pt2_end"
|> Bool.of_string
|> Ezfio.set_full_ci_do_pt2_end
;
Ezfio.get_full_ci_do_pt2_end ()
;;
let write_do_pt2_end =
Ezfio.set_full_ci_do_pt2_end
;;
let read () =
Some
{ n_det_max_fci = read_n_det_max_fci ();
pt2_max = read_pt2_max ();
do_pt2_end = read_do_pt2_end ();
var_pt2_ratio = read_var_pt2_ratio ();
}
;;
let write { n_det_max_fci ;
pt2_max ;
do_pt2_end ;
var_pt2_ratio ;
} =
write_n_det_max_fci n_det_max_fci;
write_pt2_max pt2_max;
write_do_pt2_end do_pt2_end;
write_var_pt2_ratio var_pt2_ratio;
;;
let to_string b =
Printf.sprintf "
n_det_max_fci = %s
pt2_max = %s
do_pt2_end = %s
var_pt2_ratio = %s
"
(Det_number_max.to_string b.n_det_max_fci)
(PT2_energy.to_string b.pt2_max)
(Bool.to_string b.do_pt2_end)
(Normalized_float.to_string b.var_pt2_ratio)
;;
let to_rst b =
Printf.sprintf "
Stop when the `n_det` > `n_det_max_fci` ::
n_det_max_fci = %s
Stop when -E(PT2) < `pt2_max` ::
pt2_max = %s
Compute E(PT2) at the end ::
do_pt2_end = %s
Target energy ratio variational/(variational+PT2) ::
var_pt2_ratio = %s
"
(Det_number_max.to_string b.n_det_max_fci)
(PT2_energy.to_string b.pt2_max)
(Bool.to_string b.do_pt2_end)
(Normalized_float.to_string b.var_pt2_ratio)
|> Rst_string.of_string
;;
include Generic_input_of_rst;;
let of_rst = of_rst t_of_sexp;;
end

128
ocaml/Input_hartree_fock.ml
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@ -1,128 +0,0 @@
open Qptypes;;
open Qputils;;
open Core.Std;;
module Hartree_fock : sig
type t =
{ n_it_scf_max : Strictly_positive_int.t;
thresh_scf : Threshold.t;
guess : MO_guess.t;
} with 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 =
{ n_it_scf_max : Strictly_positive_int.t;
thresh_scf : Threshold.t;
guess : MO_guess.t;
} with sexp
;;
let get_default = Qpackage.get_ezfio_default "hartree_fock";;
let read_n_it_scf_max () =
if not (Ezfio.has_hartree_fock_n_it_scf_max ()) then
get_default "n_it_scf_max"
|> Int.of_string
|> Ezfio.set_hartree_fock_n_it_scf_max
;
Ezfio.get_hartree_fock_n_it_scf_max ()
|> Strictly_positive_int.of_int
;;
let write_n_it_scf_max n_it_scf_max =
Strictly_positive_int.to_int n_it_scf_max
|> Ezfio.set_hartree_fock_n_it_scf_max
;;
let read_thresh_scf () =
if not (Ezfio.has_hartree_fock_thresh_scf()) then
get_default "thresh_scf"
|> Float.of_string
|> Ezfio.set_hartree_fock_thresh_scf
;
Ezfio.get_hartree_fock_thresh_scf ()
|> Threshold.of_float
;;
let write_thresh_scf thresh_scf =
Threshold.to_float thresh_scf
|> Ezfio.set_hartree_fock_thresh_scf
;;
let read_guess () =
if not (Ezfio.has_hartree_fock_guess ()) then
get_default "guess"
|> String.strip ~drop:(fun x -> x = '"')
|> Ezfio.set_hartree_fock_guess
;
Ezfio.get_hartree_fock_guess ()
|> MO_guess.of_string
;;
let write_guess guess =
MO_guess.to_string guess
|> Ezfio.set_hartree_fock_guess
;;
let read () =
Some
{ n_it_scf_max = read_n_it_scf_max ();
thresh_scf = read_thresh_scf ();
guess = read_guess ();
}
;;
let write { n_it_scf_max ;
thresh_scf ;
guess ;
} =
write_n_it_scf_max n_it_scf_max;
write_thresh_scf thresh_scf;
write_guess guess
;;
let to_string b =
Printf.sprintf "
n_it_scf_max = %s
thresh_scf = %s
guess = %s
"
(Strictly_positive_int.to_string b.n_it_scf_max)
(Threshold.to_string b.thresh_scf)
(MO_guess.to_string b.guess)
;;
let to_rst b =
Printf.sprintf "
Type of MO guess [ Huckel | HCore ] ::
guess = %s
Max number of SCF iterations ::
n_it_scf_max = %s
SCF convergence criterion (on energy) ::
thresh_scf = %s
"
(MO_guess.to_string b.guess)
(Strictly_positive_int.to_string b.n_it_scf_max)
(Threshold.to_string b.thresh_scf)
|> Rst_string.of_string
;;
include Generic_input_of_rst;;
let of_rst = of_rst t_of_sexp;;
end

26
ocaml/Input_mo_basis.ml
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@ -2,27 +2,21 @@ open Qptypes;;
open Qputils;;
open Core.Std;;
type t_mo =
{ mo_tot_num : MO_number.t ;
mo_label : MO_label.t;
mo_occ : MO_occ.t array;
mo_coef : (MO_coef.t array) array;
ao_md5 : MD5.t;
} with sexp
module Mo_basis : sig
type t =
{ mo_tot_num : MO_number.t ;
mo_label : MO_label.t;
mo_occ : MO_occ.t array;
mo_coef : (MO_coef.t array) array;
ao_md5 : MD5.t;
} with sexp
;;
type t = t_mo
val read : unit -> t option
val to_string : t -> string
val to_rst : t -> Rst_string.t
end = struct
type t =
{ mo_tot_num : MO_number.t ;
mo_label : MO_label.t;
mo_occ : MO_occ.t array;
mo_coef : (MO_coef.t array) array;
ao_md5 : MD5.t;
} with sexp
;;
type t = t_mo
let get_default = Qpackage.get_ezfio_default "mo_basis";;

30
ocaml/Qpackage.ml
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@ -71,8 +71,8 @@ let executables = lazy (
)
let get_ezfio_default directory data =
let filename = root^"/data/ezfio_defaults" in
let get_ezfio_default_in_file ~directory ~data ~filename =
let lines = In_channel.with_file filename ~f:(fun in_channel ->
In_channel.input_lines in_channel) in
let rec find_dir = function
@ -93,8 +93,10 @@ let get_ezfio_default directory data =
begin
match (String.lsplit2 ~on:' ' (String.strip line)) with
| Some (l,r) ->
if (l = data) then (String.lowercase (String.strip r))
else find_data rest
if (l = data) then
String.strip r
else
find_data rest
| None -> raise Not_found
end
| [] -> raise Not_found
@ -102,3 +104,23 @@ let get_ezfio_default directory data =
find_dir lines
|> find_data ;
;;
let get_ezfio_default directory data =
let dirname = root^"/data/ezfio_defaults/" in
let rec aux = function
| [] -> raise Not_found
| filename :: tail ->
let filename =
dirname^filename
in
try
get_ezfio_default_in_file ~directory ~data ~filename
with
| Not_found -> aux tail
in
Sys.readdir dirname
|> Array.to_list
|> aux
;;

4
ocaml/qp_run.ml
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@ -20,6 +20,10 @@ let run exe ezfio_file =
Printf.printf "===============\nQuantum Package\n===============\n\n";
Printf.printf "Date : %s\n\n%!" (Time.to_string time_start);
match (Sys.command ("qp_edit -c "^ezfio_file)) with
| 0 -> ()
| i -> failwith "Error: Input inconsistent\n";
;
let exe =
match (List.find ~f:(fun (x,_) -> x = exe) executables) with
| None -> assert false

34
ocaml/qptypes_generator.ml
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@ -150,19 +150,41 @@ end = struct
let to_string = function
| Huckel -> \"Huckel\"
| HCore -> \"HCore\"
| HCore -> \"Hcore\"
let of_string s =
let s =
String.lowercase s
in
match s with
| \"huckel\" -> Huckel
| \"hcore\" -> HCore
| \"Huckel\" -> Huckel
| \"Hcore\" -> HCore
| _ -> failwith (\"Wrong Guess type : \"^s)
end
module Disk_access : sig
type t with sexp
val to_string : t -> string
val of_string : string -> t
end = struct
type t =
| Read
| Write
| None
with sexp
let to_string = function
| Read -> \"Read\"
| Write -> \"Write\"
| None -> \"None\"
let of_string s =
match s with
| \"Read\" -> Read
| \"Write\" -> Write
| \"None\" -> None
| _ -> failwith (\"Wrong IO type : \"^s)
end
"
;;
let template = format_of_string "

177
ocaml/test_input.ml
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@ -1,177 +0,0 @@
open Qptypes;;
let test_ao () =
Ezfio.set_file "F2.ezfio" ;
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);
;;
let test_bielec_intergals () =
Ezfio.set_file "F2.ezfio" ;
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 = match Input.Bielec_integrals.of_rst rst with
| Some x -> x
| None -> assert false
in
if (b = b2) then
print_endline "OK"
else
print_endline "rst failed";
;;
let test_bitmasks () =
Ezfio.set_file "F2.ezfio" ;
let b = match Input.Bitmasks.read () with
| Some x -> x
| None -> assert false
in
print_endline (Input.Bitmasks.to_string b);
;;
let test_dets () =
Ezfio.set_file "F2.ezfio" ;
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 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
print_endline "Failed"
;;
let test_cisd_sc2 () =
Ezfio.set_file "F2.ezfio" ;
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 = match Input.Cisd_sc2.of_rst rst with
| Some x -> x
| None -> assert false
in
if (b = b2) then
print_endline "OK"
else
print_endline "rst failed";
;;
let test_electrons () =
Ezfio.set_file "F2.ezfio" ;
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 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"
;;
let test_fci () =
Ezfio.set_file "F2.ezfio" ;
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 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 = b2) then
print_endline "OK"
else
print_endline "Failed in rst"
;;
let test_hf () =
Ezfio.set_file "F2.ezfio" ;
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 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 = b2) then
print_endline "OK"
else
print_endline "Failed in rst"
;;
let test_mo () =
Ezfio.set_file "F2.ezfio" ;
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 = match Input.Nuclei.read () with
| Some x -> x
| None -> assert false
in
let rst = Input.Nuclei.to_rst b 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 = b2) then
print_endline "OK"
else
print_endline "Failed in rst"
;;
(*
test_ao ();;
test_bitmasks ();
test_cis ();
test_cisd_sc2 ();
test_dets ();
test_hf ();;
test_mo ();;
test_nucl ();
test_bielec_intergals ();;
test_electrons();
*)
test_dets ();

2
scripts/create_rst_templates.sh
View File

@ -12,6 +12,8 @@ fi
source ${QPACKAGE_ROOT}/scripts/qp_include.sh
check_current_dir_is_module
MODULE=$(basename $PWD)
README="True"
if [[ -f README.rst ]]

590
scripts/docopt.py Executable file
View File

@ -0,0 +1,590 @@
"""Pythonic command-line interface parser that will make you smile.
* http://docopt.org
* Repository and issue-tracker: https://github.com/docopt/docopt
* Licensed under terms of MIT license (see LICENSE-MIT)
* Copyright (c) 2013 Vladimir Keleshev, vladimir@keleshev.com
"""
import sys
import re
__all__ = ['docopt']
__version__ = '0.6.1'
class DocoptLanguageError(Exception):
"""Error in construction of usage-message by developer."""
class DocoptExit(SystemExit):
"""Exit in case user invoked program with incorrect arguments."""
usage = ''
def __init__(self, message=''):
SystemExit.__init__(self, (message + '\n' + self.usage).strip())
class Pattern(object):
def __eq__(self, other):
return repr(self) == repr(other)
def __hash__(self):
return hash(repr(self))
def fix(self):
self.fix_identities()
self.fix_repeating_arguments()
return self
def fix_identities(self, uniq=None):
"""Make pattern-tree tips point to same object if they are equal."""
if not hasattr(self, 'children'):
return self
uniq = list(set(self.flat())) if uniq is None else uniq
for i, child in enumerate(self.children):
if not hasattr(child, 'children'):
assert child in uniq
self.children[i] = uniq[uniq.index(child)]
else:
child.fix_identities(uniq)
def fix_repeating_arguments(self):
"""Fix elements that should accumulate/increment values."""
either = [list(child.children) for child in transform(self).children]
for case in either:
for e in [child for child in case if case.count(child) > 1]:
if isinstance(
e,
Argument) or isinstance(
e,
Option) and e.argcount:
if e.value is None:
e.value = []
elif not isinstance(e.value, list):
e.value = e.value.split()
if isinstance(
e,
Command) or isinstance(
e,
Option) and e.argcount == 0:
e.value = 0
return self
def transform(pattern):
"""Expand pattern into an (almost) equivalent one, but with single Either.
Example: ((-a | -b) (-c | -d)) => (-a -c | -a -d | -b -c | -b -d)
Quirks: [-a] => (-a), (-a...) => (-a -a)
"""
result = []
groups = [[pattern]]
while groups:
children = groups.pop(0)
parents = [Required, Optional, OptionsShortcut, Either, OneOrMore]
if any(t in map(type, children) for t in parents):
child = [c for c in children if type(c) in parents][0]
children.remove(child)
if isinstance(child, Either):
for c in child.children:
groups.append([c] + children)
elif isinstance(child, OneOrMore):
groups.append(child.children * 2 + children)
else:
groups.append(child.children + children)
else:
result.append(children)
return Either(*[Required(*e) for e in result])
class LeafPattern(Pattern):
"""Leaf/terminal node of a pattern tree."""
def __init__(self, name, value=None):
self.name, self.value = name, value
def __repr__(self):
return '%s(%r, %r)' % (self.__class__.__name__, self.name, self.value)
def flat(self, *types):
return [self] if not types or type(self) in types else []
def match(self, left, collected=None):
collected = [] if collected is None else collected
pos, match = self.single_match(left)
if match is None:
return False, left, collected
left_ = left[:pos] + left[pos + 1:]
same_name = [a for a in collected if a.name == self.name]
if type(self.value) in (int, list):
if isinstance(self.value, int):
increment = 1
else:
increment = ([match.value] if isinstance(match.value, str)
else match.value)
if not same_name:
match.value = increment
return True, left_, collected + [match]
same_name[0].value += increment
return True, left_, collected
return True, left_, collected + [match]
class BranchPattern(Pattern):
"""Branch/inner node of a pattern tree."""
def __init__(self, *children):
self.children = list(children)
def __repr__(self):
return '%s(%s)' % (self.__class__.__name__,
', '.join(repr(a) for a in self.children))
def flat(self, *types):
if type(self) in types:
return [self]
return sum([child.flat(*types) for child in self.children], [])
class Argument(LeafPattern):
def single_match(self, left):
for n, pattern in enumerate(left):
if isinstance(pattern, Argument):
return n, Argument(self.name, pattern.value)
return None, None
@classmethod
def parse(class_, source):
name = re.findall('(<\S*?>)', source)[0]
value = re.findall('\[default: (.*)\]', source, flags=re.I)
return class_(name, value[0] if value else None)
class Command(Argument):
def __init__(self, name, value=False):
self.name, self.value = name, value
def single_match(self, left):
for n, pattern in enumerate(left):
if isinstance(pattern, Argument):
if pattern.value == self.name:
return n, Command(self.name, True)
else:
break
return None, None
class Option(LeafPattern):
def __init__(self, short=None, long=None, argcount=0, value=False):
assert argcount in (0, 1)
self.short, self.long, self.argcount = short, long, argcount
self.value = None if value is False and argcount else value
@classmethod
def parse(class_, option_description):
short, long, argcount, value = None, None, 0, False
options, _, description = option_description.strip().partition(' ')
options = options.replace(',', ' ').replace('=', ' ')
for s in options.split():
if s.startswith('--'):
long = s
elif s.startswith('-'):
short = s
else:
argcount = 1
if argcount:
matched = re.findall('\[default: (.*)\]', description, flags=re.I)
value = matched[0] if matched else None
return class_(short, long, argcount, value)
def single_match(self, left):
for n, pattern in enumerate(left):
if self.name == pattern.name:
return n, pattern
return None, None
@property
def name(self):
return self.long or self.short
def __repr__(self):
return 'Option(%r, %r, %r, %r)' % (self.short, self.long,
self.argcount, self.value)
class Required(BranchPattern):
def match(self, left, collected=None):
collected = [] if collected is None else collected
l = left
c = collected
for pattern in self.children:
matched, l, c = pattern.match(l, c)
if not matched:
return False, left, collected
return True, l, c
class Optional(BranchPattern):
def match(self, left, collected=None):
collected = [] if collected is None else collected
for pattern in self.children:
m, left, collected = pattern.match(left, collected)
return True, left, collected
class OptionsShortcut(Optional):
"""Marker/placeholder for [options] shortcut."""
class OneOrMore(BranchPattern):
def match(self, left, collected=None):
assert len(self.children) == 1
collected = [] if collected is None else collected
l = left
c = collected
l_ = None
matched = True
times = 0
while matched:
# could it be that something didn't match but changed l or c?
matched, l, c = self.children[0].match(l, c)
times += 1 if matched else 0
if l_ == l:
break
l_ = l
if times >= 1:
return True, l, c
return False, left, collected
class Either(BranchPattern):
def match(self, left, collected=None):
collected = [] if collected is None else collected
outcomes = []
for pattern in self.children:
matched, _, _ = outcome = pattern.match(left, collected)
if matched:
outcomes.append(outcome)
if outcomes:
return min(outcomes, key=lambda outcome: len(outcome[1]))
return False, left, collected
class Tokens(list):
def __init__(self, source, error=DocoptExit):
self += source.split() if hasattr(source, 'split') else source
self.error = error
@staticmethod
def from_pattern(source):
source = re.sub(r'([\[\]\(\)\|]|\.\.\.)', r' \1 ', source)
source = [s for s in re.split('\s+|(\S*<.*?>)', source) if s]
return Tokens(source, error=DocoptLanguageError)
def move(self):
return self.pop(0) if len(self) else None
def current(self):
return self[0] if len(self) else None
def parse_long(tokens, options):
"""long ::= '--' chars [ ( ' ' | '=' ) chars ] ;"""
long, eq, value = tokens.move().partition('=')
assert long.startswith('--')
value = None if eq == value == '' else value
similar = [o for o in options if o.long == long]
if tokens.error is DocoptExit and similar == []: # if no exact match
similar = [o for o in options if o.long and o.long.startswith(long)]
if len(similar) > 1: # might be simply specified ambiguously 2+ times?
raise tokens.error('%s is not a unique prefix: %s?' %
(long, ', '.join(o.long for o in similar)))
elif len(similar) < 1:
argcount = 1 if eq == '=' else 0
o = Option(None, long, argcount)
options.append(o)
if tokens.error is DocoptExit:
o = Option(None, long, argcount, value if argcount else True)
else:
o = Option(similar[0].short, similar[0].long,
similar[0].argcount, similar[0].value)
if o.argcount == 0:
if value is not None:
raise tokens.error('%s must not have an argument' % o.long)
else:
if value is None:
if tokens.current() in [None, '--']:
raise tokens.error('%s requires argument' % o.long)
value = tokens.move()
if tokens.error is DocoptExit:
o.value = value if value is not None else True
return [o]
def parse_shorts(tokens, options):
"""shorts ::= '-' ( chars )* [ [ ' ' ] chars ] ;"""
token = tokens.move()
assert token.startswith('-') and not token.startswith('--')
left = token.lstrip('-')
parsed = []
while left != '':
short, left = '-' + left[0], left[1:]
similar = [o for o in options if o.short == short]
if len(similar) > 1:
raise tokens.error('%s is specified ambiguously %d times' %
(short, len(similar)))
elif len(similar) < 1:
o = Option(short, None, 0)
options.append(o)
if tokens.error is DocoptExit:
o = Option(short, None, 0, True)
else: # why copying is necessary here?
o = Option(short, similar[0].long,
similar[0].argcount, similar[0].value)
value = None
if o.argcount != 0:
if left == '':
if tokens.current() in [None, '--']:
raise tokens.error('%s requires argument' % short)
value = tokens.move()
else:
value = left
left = ''
if tokens.error is DocoptExit:
o.value = value if value is not None else True
parsed.append(o)
return parsed
def parse_pattern(source, options):
tokens = Tokens.from_pattern(source)
result = parse_expr(tokens, options)
if tokens.current() is not None:
raise tokens.error('unexpected ending: %r' % ' '.join(tokens))
return Required(*result)
def parse_expr(tokens, options):
"""expr ::= seq ( '|' seq )* ;"""
seq = parse_seq(tokens, options)
if tokens.current() != '|':
return seq
result = [Required(*seq)] if len(seq) > 1 else seq
while tokens.current() == '|':
tokens.move()
seq = parse_seq(tokens, options)
result += [Required(*seq)] if len(seq) > 1 else seq
return [Either(*result)] if len(result) > 1 else result
def parse_seq(tokens, options):
"""seq ::= ( atom [ '...' ] )* ;"""
result = []
while tokens.current() not in [None, ']', ')', '|']:
atom = parse_atom(tokens, options)
if tokens.current() == '...':
atom = [OneOrMore(*atom)]
tokens.move()
result += atom
return result
def parse_atom(tokens, options):
"""atom ::= '(' expr ')' | '[' expr ']' | 'options'
| long | shorts | argument | command ;
"""
token = tokens.current()
result = []
if token in '([':
tokens.move()
matching, pattern = {'(': [')', Required], '[': [']', Optional]}[token]
result = pattern(*parse_expr(tokens, options))
if tokens.move() != matching:
raise tokens.error("unmatched '%s'" % token)
return [result]
elif token == 'options':
tokens.move()
return [OptionsShortcut()]
elif token.startswith('--') and token != '--':
return parse_long(tokens, options)
elif token.startswith('-') and token not in ('-', '--'):
return parse_shorts(tokens, options)
elif token.startswith('<') and token.endswith('>') or token.isupper():
return [Argument(tokens.move())]
else:
return [Command(tokens.move())]
def parse_argv(tokens, options, options_first=False):
"""Parse command-line argument vector.
If options_first:
argv ::= [ long | shorts ]* [ argument ]* [ '--' [ argument ]* ] ;
else:
argv ::= [ long | shorts | argument ]* [ '--' [ argument ]* ] ;
"""
parsed = []
while tokens.current() is not None:
if tokens.current() == '--':
return parsed + [Argument(None, v) for v in tokens]
elif tokens.current().startswith('--'):
parsed += parse_long(tokens, options)
elif tokens.current().startswith('-') and tokens.current() != '-':
parsed += parse_shorts(tokens, options)
elif options_first:
return parsed + [Argument(None, v) for v in tokens]
else:
parsed.append(Argument(None, tokens.move()))
return parsed
def parse_defaults(doc):
defaults = []
for s in parse_section('options:', doc):
# FIXME corner case "bla: options: --foo"
_, _, s = s.partition(':') # get rid of "options:"
split = re.split('\n[ \t]*(-\S+?)', '\n' + s)[1:]
split = [s1 + s2 for s1, s2 in zip(split[::2], split[1::2])]
options = [Option.parse(s) for s in split if s.startswith('-')]
defaults += options
return defaults
def parse_section(name, source):
pattern = re.compile('^([^\n]*' + name + '[^\n]*\n?(?:[ \t].*?(?:\n|$))*)',
re.IGNORECASE | re.MULTILINE)
return [s.strip() for s in pattern.findall(source)]
def formal_usage(section):
_, _, section = section.partition(':') # drop "usage:"
pu = section.split()
return '( ' + ' '.join(') | (' if s == pu[0] else s for s in pu[1:]) + ' )'
def extras(help, version, options, doc):
if help and any((o.name in ('-h', '--help')) and o.value for o in options):
print(doc.strip("\n"))
sys.exit()
if version and any(o.name == '--version' and o.value for o in options):
print(version)
sys.exit()
class Dict(dict):
def __repr__(self):
return '{%s}' % ',\n '.join('%r: %r' % i for i in sorted(self.items()))
def docopt(doc, argv=None, help=True, version=None, options_first=False):
"""Parse `argv` based on command-line interface described in `doc`.
`docopt` creates your command-line interface based on its
description that you pass as `doc`. Such description can contain
--options, <positional-argument>, commands, which could be
[optional], (required), (mutually | exclusive) or repeated...
Parameters
----------
doc : str
Description of your command-line interface.
argv : list of str, optional
Argument vector to be parsed. sys.argv[1:] is used if not
provided.
help : bool (default: True)
Set to False to disable automatic help on -h or --help
options.
version : any object
If passed, the object will be printed if --version is in
`argv`.
options_first : bool (default: False)
Set to True to require options precede positional arguments,
i.e. to forbid options and positional arguments intermix.
Returns
-------
args : dict
A dictionary, where keys are names of command-line elements
such as e.g. "--verbose" and "<path>", and values are the
parsed values of those elements.
Example
-------
>>> from docopt import docopt
>>> doc = '''
... Usage:
... my_program tcp <host> <port> [--timeout=<seconds>]
... my_program serial <port> [--baud=<n>] [--timeout=<seconds>]
... my_program (-h | --help | --version)
...
... Options:
... -h, --help Show this screen and exit.
... --baud=<n> Baudrate [default: 9600]
... '''
>>> argv = ['tcp', '127.0.0.1', '80', '--timeout', '30']
>>> docopt(doc, argv)
{'--baud': '9600',
'--help': False,
'--timeout': '30',
'--version': False,
'<host>': '127.0.0.1',
'<port>': '80',
'serial': False,
'tcp': True}
See also
--------
* For video introduction see http://docopt.org
* Full documentation is available in README.rst as well as online
at https://github.com/docopt/docopt#readme
"""
argv = sys.argv[1:] if argv is None else argv
usage_sections = parse_section('usage:', doc)
if len(usage_sections) == 0:
raise DocoptLanguageError('"usage:" (case-insensitive) not found.')
if len(usage_sections) > 1:
raise DocoptLanguageError('More than one "usage:" (case-insensitive).')
DocoptExit.usage = usage_sections[0]
options = parse_defaults(doc)
pattern = parse_pattern(formal_usage(DocoptExit.usage), options)
# [default] syntax for argument is disabled
# for a in pattern.flat(Argument):
# same_name = [d for d in arguments if d.name == a.name]
# if same_name:
# a.value = same_name[0].value
argv = parse_argv(Tokens(argv), list(options), options_first)
pattern_options = set(pattern.flat(Option))
for options_shortcut in pattern.flat(OptionsShortcut):
doc_options = parse_defaults(doc)
options_shortcut.children = list(set(doc_options) - pattern_options)
# if any_options:
# options_shortcut.children += [Option(o.short, o.long, o.argcount)
# for o in argv if type(o) is Option]
extras(help, version, argv, doc)
matched, left, collected = pattern.fix().match(argv)
if matched and left == []: # better error message if left?
return Dict((a.name, a.value) for a in (pattern.flat() + collected))
raise DocoptExit()

333
scripts/ezfio_interface.py
View File

@ -1,333 +0,0 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Take a path in argv
Check if EZFIO.cfg exists.
EZFIO.cfg are in MODULE directories.
create : ezfio_interface.irp.f
folder_ezfio_inteface_config
Example EZFIO.cfg:
```
[thresh_SCF]
doc: Threshold on the convergence of the Hartree Fock energy
type: Threshold
default: 1.e-10
[do_pt2_end]
type: logical
doc: If true, compute the PT2 at the end of the selection
default: true
```
"""
import sys
import os
import os.path
import ConfigParser
from collections import defaultdict
from collections import namedtuple
Type = namedtuple('Type', 'ocaml fortran')
def bool_convertor(b):
return ( b.lower() in [ "true", ".true." ] )
def get_type_dict():
"""
This function makes the correspondance between the type of value read in
ezfio.cfg into the f90 and Ocam Type
return fancy_type[fancy_type] = namedtuple('Type', 'ocaml fortran')
For example fancy_type['Ndet'].fortran = interger
.ocaml = int
"""
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
# Dict to change ocaml LowLevel type into FortranLowLevel type
ocaml_to_fortran = {"int": "integer",
"float": "double precision",
"logical": "logical",
"string": "character*60"}
fancy_type = defaultdict(dict)
# ~#~#~#~#~#~#~#~ #
# R a w _ t y p e #
# ~#~#~#~#~#~#~#~ #
fancy_type['integer'] = Type("int", "integer")
fancy_type['int'] = Type("int", "integer")
fancy_type['float'] = Type("float", "double precision")
fancy_type['double precision'] = Type("float", "double precision")
fancy_type['logical'] = Type("bool", "logical")
fancy_type['bool'] = Type("bool", "logical")
# ~#~#~#~#~#~#~#~ #
# q p _ t y p e s #
# ~#~#~#~#~#~#~#~ #
src = os.environ['QPACKAGE_ROOT'] + "/ocaml/qptypes_generator.ml"
with open(src, "r") as f:
l = [i for i in f.read().splitlines() if i.strip().startswith("*")]
for i in l:
ocaml_fancy_type = i.split()[1].strip()
ocaml_type = i.split()[3]
fortran_type = ocaml_to_fortran[ocaml_type]
fancy_type[ocaml_fancy_type] = Type(ocaml_type, fortran_type)
return dict(fancy_type)
type_dict = get_type_dict()
def get_dict_config_file(config_file_path, module_lower):
"""
Input:
config_file_path is the config file path
(for example FULL_PATH/EZFIO.cfg)
module_lower is the MODULE name lowered
(Ex fullci)
Return a dict d[provider_name] = {type,
doc,
ezfio_name,
ezfio_dir,
interface,
default}
Type : Is a fancy_type named typle who containt fortran and ocaml type
doc : Is the doc
ezfio_name : Will be the name of the file
ezfio_dir : Will be the folder who containt the ezfio_name
* /ezfio_dir/ezfio_name
* equal to MODULE_lower name for the moment.
interface : The provider is a imput or a output
if is a output:
default : The default value
"""
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
d = defaultdict(dict)
l_info_required = ["doc", "interface"]
l_info_optional = ["ezfio_name"]
# ~#~#~#~#~#~#~#~#~#~#~ #
# L o a d _ C o n f i g #
# ~#~#~#~#~#~#~#~#~#~#~ #
config_file = ConfigParser.ConfigParser()
config_file.readfp(open(config_file_path))
# ~#~#~#~#~#~#~#~#~ #
# F i l l _ d i c t #
# ~#~#~#~#~#~#~#~#~ #
def error(o, p, c):
"o option ; p provider_name ;c config_file_path"
print "You need a {0} for {1} in {2}".format(o, p, c)
for section in config_file.sections():
# pvd = provider
pvd = section.lower()
# Create the dictionary who containt the value per default
d_default = {"ezfio_name": pvd}
# Set the ezfio_dir
d[pvd]["ezfio_dir"] = module_lower
# Check if type if avalaible
type_ = config_file.get(section, "type")
if type_ not in type_dict:
print "{0} not avalaible. Choose in:".format(type_)
print ", ".join([i for i in type_dict])
sys.exit(1)
else:
d[pvd]["type"] = type_dict[type_]
# Fill the dict with REQUIRED information
for option in l_info_required:
try:
d[pvd][option] = config_file.get(section, option)
except ConfigParser.NoOptionError:
error(option, pvd, config_file_path)
sys.exit(1)
# Fill the dict with OPTIONAL information
for option in l_info_optional:
try:
d[pvd][option] = config_file.get(section, option).lower()
except ConfigParser.NoOptionError:
d[pvd][option] = d_default[option]
# If interface is output we need a default value information
if d[pvd]["interface"] == "input":
try:
d[pvd]["default"] = config_file.get(section, "default")
except ConfigParser.NoOptionError:
error("default", pvd, config_file_path)
sys.exit(1)
return dict(d)
def create_ezfio_provider(dict_ezfio_cfg):
"""
From dict d[provider_name] = {type,
doc,
ezfio_name,
ezfio_dir,
interface,
default}
create the a list who containt all the code for the provider
return [code, ...]
"""
from ezfio_with_default import EZFIO_Provider
dict_code_provider = dict()
ez_p = EZFIO_Provider()
for provider_name, dict_info in dict_ezfio_cfg.iteritems():
if "default" in dict_info:
ez_p.set_type(dict_info['type'].fortran)
ez_p.set_name(provider_name)
ez_p.set_doc(dict_info['doc'])
ez_p.set_ezfio_dir(dict_info['ezfio_dir'])
ez_p.set_ezfio_name(dict_info['ezfio_name'])
ez_p.set_default(dict_info['default'])
ez_p.set_output("output_%s" % dict_info['ezfio_dir'])
dict_code_provider[provider_name] = str(ez_p)
return dict_code_provider
def save_ezfio_provider(path_head, dict_code_provider):
"""
Write in path_head/"ezfio_interface.irp.f" the value of dict_code_provider
"""
path = "{0}/ezfio_interface.irp.f".format(path_head)
# print "Path = {}".format(path)
try:
f = open(path, "r")
except IOError:
old_output = ""
else:
old_output = f.read()
f.close()
output = "! DO NOT MODIFY BY HAND\n" + \
"! Created by $QPACKAGE_ROOT/scripts/ezfio_interface.py\n" + \
"! from file {0}/EZFIO.cfg\n".format(path_head) + \
"\n"
for provider_name, code in dict_code_provider.iteritems():
output += str(code) + "\n"
if output != old_output:
with open(path, "w") as f:
f.write(output)
def create_ezfio_config(dict_ezfio_cfg, opt, module_lower):
"""
From dict_ezfio_cfg[provider_name] = {type, default, ezfio_name,ezfio_dir,doc}
Return the string ezfio_interface_config
"""
result = [module_lower]
lenmax = max([len(i) for i in dict_ezfio_cfg]) + 2
l = sorted(dict_ezfio_cfg.keys())
for provider_name in l:
provider_info = dict_ezfio_cfg[provider_name]
s = " {0} {1}".format(
provider_name.lower().ljust(lenmax),
provider_info["type"].fortran)
result.append(s)
return "\n".join(result)
def save_ezfio_config(module_lower, str_ezfio_config):
"""
Write the str_ezfio_config in
$QPACKAGE_ROOT/EZFIO/{0}.ezfio_interface_config".format(module_lower)
"""
ezfio_dir = "{0}/EZFIO".format(os.environ['QPACKAGE_ROOT'])
path = "{0}/config/{1}.ezfio_interface_config".format(ezfio_dir,
module_lower)
# print "Path = {}".format(path)
try:
f = open(path, "r")
except IOError:
old_output = ""
else:
old_output = f.read()
f.close()
if str_ezfio_config != old_output:
with open(path, "w") as f:
f.write(str_ezfio_config)
def main():
"""
Two condition:
-Take the EZFIO.cfg path in arg
or
-Look if EZFIO.cfg is present in the pwd
"""
try:
config_file_path = sys.argv[1]
except:
config_file_path = "EZFIO.cfg"
if "EZFIO.cfg" not in os.listdir(os.getcwd()):
sys.exit(0)
config_file_path = os.path.expanduser(config_file_path)
config_file_path = os.path.expandvars(config_file_path)
config_file_path = os.path.abspath(config_file_path)
# print config_file_path
path_dirname = os.path.dirname(config_file_path)
module = [i for i in path_dirname.split("/") if i][-1]
module_lower = module.lower()
# print "Read {0}".format(config_file_path)
dict_info_provider = get_dict_config_file(config_file_path, module_lower)
# print "Generating the ezfio_interface.irp.f: \n"
d_config = create_ezfio_provider(dict_info_provider)
# print "Saving the ezfio_interface.irp.f"
save_ezfio_provider(path_dirname, d_config)
# print "Generating the ezfio_config"
config_ezfio = create_ezfio_config(dict_info_provider, "config", module_lower)
# print "Saving ezfio_config"
save_ezfio_config(module_lower, config_ezfio)
if __name__ == "__main__":
main()

27
scripts/ezfio_interface/convert_ezfio.sh Executable file
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@ -0,0 +1,27 @@
#!/bin/bash
# Convert a old ezfio file (with option.irp.f ezfio_default)
# into a new EZFIO.cfg type
# Hartree Fock
# Changin the case, don't know if is needed or not
mv $1/Hartree_Fock $1/hartree_fock 2> /dev/null
mv $1/hartree_Fock/thresh_SCF $1/hartree_fock/thresh_scf 2> /dev/null
# BiInts
mv $1/bi_integrals $1/bielect_integrals 2> /dev/null
if [ -f $1/bielect_integrals/read_ao_integrals ]; then
if [ `cat $1/bielect_integrals/read_ao_integrals` -eq "True" ]
then
echo "Read" > $1/bielect_integrals/disk_access_ao_integrals
elif [ `cat bielect_integrals/write_ao_integrals` -eq "True" ]
then
echo "Write" > $1/bielect_integrals/disk_access_ao_integrals
else
echo "None" > $1/bielect_integrals/disk_access_ao_integrals
fi
fi

823
scripts/ezfio_interface/ei_handler.py Executable file
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@ -0,0 +1,823 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Welcom the ei_handler.
We will create all the ezfio related stuff from a EZFIO.cfg file.
Usage:
ei_handler.py [--path] [--irpf90] [--ezfio_config] [--ocaml] [--ezfio_default] [--global]
By default all the option are executed.
Options:
-h --help
--path The path of the `EZFIO.cfg`, by default will look in the ${pwd}
--irpf90 Create the `ezfio_interface.irpf90`
which contains all the providers needed
(aka all with the `interface: input` parameter)
in `${pwd}`
--ezfio_config Create the `${module_lower}_ezfio_interface_config` in
`${QPACKAGE_ROOT}/EZFIO/config/`
This file is needed by *EZFIO* to create the `libezfio.so`
--ocaml Create the `Input_module.lower.ml` for the *qp_edit*
--ezfio_default Create the `${module_lower}_ezfio_interface_default` in
`${QPACKAGE_ROOT}/data/ezfio_defaults` needed by
the ocaml
--global Create all the stuff who need all the EZFIO.cfg
Format specification :
[provider_name] | the name of the provider in irp.f90
doc:{str} | Is the doc
Type:{str} | Is a fancy_type supported by the ocaml
ezfio_name:{str} | Will be the name of the file for the ezfio
(optional by default is the name of the provider)
interface:{str} | The provider is a imput or a output
default:{str} | The default value if interface == input:
size:{str} | the size information
(like 1 or =sum(ao_num) or (ao_num,3) )
Example of EZFIO.cfg:
```
[thresh_SCF]
doc: Threshold on the convergence of the Hartree Fock energy
type: Threshold
default: 1.e-10
interface: input
size: 1
[energy]
type: double precision
doc: Calculated HF energy
interface: output
```
"""
from docopt import docopt
import sys
import os
import os.path
import ConfigParser
from collections import defaultdict
from collections import namedtuple
Type = namedtuple('Type', 'fancy ocaml fortran')
def is_bool(str_):
"""
Take a string, if is a bool return the conversion into
fortran and ocaml.
"""
if str_.lower() in ['true', '.true.']:
return Type(None, "true", ".True.")
elif str_.lower() in ['false', '.false.']:
return Type(None, "false", ".False")
else:
raise TypeError
def get_type_dict():
"""
This function makes the correspondance between the type of value read in
ezfio.cfg into the f90 and Ocaml Type
return fancy_type[fancy_type] = namedtuple('Type', 'ocaml fortran')
For example fancy_type['Ndet'].fortran = interger
.ocaml = int
"""
# ~#~#~#~#~ #
# P i c l e #
# ~#~#~#~#~ #
import cPickle as pickle
from os import listdir
qpackage_root = os.environ['QPACKAGE_ROOT']
fancy_type_pickle = qpackage_root + "/scripts/ezfio_interface/fancy_type.p"
if fancy_type_pickle in listdir(os.getcwd()):
fancy_type = pickle.load(open(fancy_type_pickle, "rb"))
return fancy_type
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
fancy_type = defaultdict(dict)
# ~#~#~#~#~#~#~#~ #
# R a w _ t y p e #
# ~#~#~#~#~#~#~#~ #
fancy_type['integer'] = Type(None, "int", "integer")
fancy_type['int'] = Type(None, "int", "integer")
fancy_type['float'] = Type(None, "float", "double precision")
fancy_type['double precision'] = Type(None, "float", "double precision")
fancy_type['logical'] = Type(None, "bool", "logical")
fancy_type['bool'] = Type(None, "bool", "logical")
fancy_type['character*(32)'] = Type(None, "string", "character*(32)")
fancy_type['character*(60)'] = Type(None, "string", "character*(60)")
fancy_type['character*(256)'] = Type(None, "string", "character*(256)")
# ~#~#~#~#~#~#~#~ #
# q p _ t y p e s #
# ~#~#~#~#~#~#~#~ #
# Dict to change ocaml LowLevel type into FortranLowLevel type
ocaml_to_fortran = {"int": "integer",
"float": "double precision",
"logical": "logical",
"string": "character*32"}
# Read and parse qptype generate
src = qpackage_root + "/ocaml/qptypes_generator.ml"
with open(src, "r") as f:
r = f.read()
# Generate
l_gen = [i for i in r.splitlines() if i.strip().startswith("*")]
# Untouch
b = r.find('let untouched = "')
e = r.find(';;', b)
l_un = [
i for i in r[
b:e].splitlines() if i.strip().startswith("module")]
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
# q p _ t y p e s _ g e n e r a t e #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
# Read the fancy_type, the ocaml. and convert the ocaml to the fortran
for i in l_gen + l_un:
str_fancy_type = i.split()[1].strip()
str_ocaml_type = i.split()[3]
if str_ocaml_type != 'sig':
str_fortran_type = ocaml_to_fortran[str_ocaml_type]
else:
str_fortran_type = 'character*(32)'
str_ocaml_type = 'string'
fancy_type[str_fancy_type] = Type(str_fancy_type,
str_ocaml_type,
str_fortran_type)
# ~#~#~#~#~#~#~#~ #
# F i n a l i z e #
# ~#~#~#~#~#~#~#~ #
pickle.dump(dict(fancy_type), open(fancy_type_pickle, "wb"))
return dict(fancy_type)
type_dict = get_type_dict()
def get_dict_config_file(config_file_path, module_lower):
"""
Input:
config_file_path is the config file path
(for example FULL_PATH/EZFIO.cfg)
module_lower is the MODULE name lowered
(Ex fullci)
Return a dict d[provider_name] = {type,
doc,
ezfio_name,
ezfio_dir,
size,
interface,
default}
- Type : Is a Type named tuple who containt
fortran and ocaml type
- doc : Is the doc
- ezfio_name : Will be the name of the file
- ezfio_dir : Will be the folder who containt the ezfio_name
* /ezfio_dir/ezfio_name
* equal to MODULE_lower name for the moment.
- interface : The provider is a imput or a output
- default : The default value /!\ stored in a Type named type!
if interface == output
- size : Is the string read in ezfio.cgf who containt the size information
(like 1 or =sum(ao_num))
"""
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
d = defaultdict(dict)
l_info_required = ["doc", "interface"]
l_info_optional = ["ezfio_name", "size"]
# ~#~#~#~#~#~#~#~#~#~#~ #
# L o a d _ C o n f i g #
# ~#~#~#~#~#~#~#~#~#~#~ #
config_file = ConfigParser.ConfigParser()
config_file.readfp(open(config_file_path))
# ~#~#~#~#~#~#~#~#~ #
# F i l l _ d i c t #
# ~#~#~#~#~#~#~#~#~ #
def error(o, p, c):
"o option ; p provider_name ;c config_file_path"
print "You need a {0} for {1} in {2}".format(o, p, c)
for section in config_file.sections():
# pvd = provider
pvd = section.lower()
# Create the dictionary who containt the value per default
d_default = {"ezfio_name": pvd}
# Set the ezfio_dir
d[pvd]["ezfio_dir"] = module_lower
# Check if type if avalaible
type_ = config_file.get(section, "type")
if type_ not in type_dict:
print "{0} not avalaible. Choose in:".format(type_)
print ", ".join(sorted([i for i in type_dict]))
sys.exit(1)
else:
d[pvd]["type"] = type_dict[type_]
# Fill the dict with REQUIRED information
for option in l_info_required:
try:
d[pvd][option] = config_file.get(section, option)
except ConfigParser.NoOptionError:
error(option, pvd, config_file_path)
sys.exit(1)
# Fill the dict with OPTIONAL information
for option in l_info_optional:
try:
d[pvd][option] = config_file.get(section, option).lower()
except ConfigParser.NoOptionError:
if option in d_default:
d[pvd][option] = d_default[option]
# If interface is input we need a default value information
if d[pvd]["interface"] == "input":
try:
default_raw = config_file.get(section, "default")
except ConfigParser.NoOptionError:
error("default", pvd, config_file_path)
sys.exit(1)
try:
d[pvd]["default"] = is_bool(default_raw)
except TypeError:
d[pvd]["default"] = Type(None, default_raw, default_raw)
return dict(d)
def create_ezfio_provider(dict_ezfio_cfg):
"""
From dict d[provider_name] = {type,
doc,
ezfio_name,
ezfio_dir,
interface,
default
size}
create the a list who containt all the code for the provider
return [code, ...]
"""
from ezfio_generate_provider import EZFIO_Provider
dict_code_provider = dict()
ez_p = EZFIO_Provider()
for provider_name, dict_info in dict_ezfio_cfg.iteritems():
if "default" in dict_info:
ez_p.set_type(dict_info['type'].fortran)
ez_p.set_name(provider_name)
ez_p.set_doc(dict_info['doc'])
ez_p.set_ezfio_dir(dict_info['ezfio_dir'])
ez_p.set_ezfio_name(dict_info['ezfio_name'])
ez_p.set_output("output_%s" % dict_info['ezfio_dir'])
dict_code_provider[provider_name] = str(ez_p) + "\n"
return dict_code_provider
def save_ezfio_provider(path_head, dict_code_provider):
"""
Write in path_head/"ezfio_interface.irp.f" the value of dict_code_provider
"""
path = "{0}/ezfio_interface.irp.f".format(path_head)
try:
f = open(path, "r")
except IOError:
old_output = ""
else:
old_output = f.read()
f.close()
l_output = ["! DO NOT MODIFY BY HAND",
"! Created by $QPACKAGE_ROOT/scripts/ezfio_interface.py",
"! from file {0}/EZFIO.cfg".format(path_head),
"\n"]
l_output += [code for code in dict_code_provider.values()]
output = "\n".join(l_output)
if output != old_output:
with open(path, "w+") as f:
f.write(output)
def create_ezfio_stuff(dict_ezfio_cfg, config_or_default="config"):
"""
From dict_ezfio_cfg[provider_name] = {type, default, ezfio_name,ezfio_dir,doc}
Return the string ezfio_interface_config
"""
def size_format_to_ezfio(size_raw):
"""
If size_raw == "=" is a formula -> do nothing; return
If the value are between parenthses -> do nothing; return
Else put it in parenthsesis
"""
size_raw = str(size_raw)
if any([size_raw.startswith('='),
size_raw.startswith("(") and size_raw.endswith(")")]):
size_convert = size_raw
else:
size_convert = "({0})".format(size_raw)
return size_convert
def create_format_string(size):
"""
Take a size number and
return the string format for being right align with this offset
"""
return "{{0:<{0}}}".format(size).format
# ~#~#~#~#~#~#~#~#~#~#~# #
# F o r m a t _ i n f o #
# ~#~#~#~#~#~#~#~#~#~#~# #
lenmax_name = max([len(i) for i in dict_ezfio_cfg])
lenmax_type = max([len(i["type"].fortran)
for i in dict_ezfio_cfg.values()])
str_name_format = create_format_string(lenmax_name + 2)
str_type_format = create_format_string(lenmax_type + 2)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
# C r e a t e _ t h e _ s t r i n g #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
# Checking is many ezfio_dir provided
l_ezfio_dir = [d['ezfio_dir'] for d in dict_ezfio_cfg.values()]
if not l_ezfio_dir.count(l_ezfio_dir[0]) == len(l_ezfio_dir):
print >> sys.stderr, "You have many ezfio_dir. Not supported yet"
raise TypeError
else:
result = [l_ezfio_dir[0]]
for provider_name, provider_info in sorted(dict_ezfio_cfg.iteritems()):
# Get the value from dict
name_raw = provider_info["ezfio_name"].lower()
fortran_type_raw = provider_info["type"].fortran
if "size" in provider_info and not provider_info["size"] == "1":
size_raw = provider_info["size"]
else:
size_raw = None
# It is the last so we don't need to right align it
str_size = size_format_to_ezfio(size_raw) if size_raw else ""
# Get the string in to good format (left align and co)
str_name = str_name_format(name_raw)
str_fortran_type = str_type_format(fortran_type_raw)
# Return the string
if config_or_default == "config":
s = " {0} {1} {2}".format(str_name, str_fortran_type, str_size)
elif config_or_default == "default":
try:
str_value = provider_info["default"].ocaml
except KeyError:
continue
else:
s = " {0} {1}".format(str_name, str_value)
else:
raise KeyError
# Append
result.append(s)
return "\n".join(result)
def create_ezfio_config(dict_ezfio_cfg):
return create_ezfio_stuff(dict_ezfio_cfg,
config_or_default="config")
def save_ezfio_config(module_lower, str_ezfio_config):
"""
Write the str_ezfio_config in
"$QPACKAGE_ROOT/EZFIO/{0}.ezfio_interface_config".format(module_lower)
"""
root_ezfio = "{0}/EZFIO".format(os.environ['QPACKAGE_ROOT'])
path = "{0}/config/{1}.ezfio_interface_config".format(root_ezfio,
module_lower)
try:
f = open(path, "r")
except IOError:
old_output = ""
else:
old_output = f.read()
f.close()
if str_ezfio_config != old_output:
with open(path, "w+") as f:
f.write(str_ezfio_config)
def create_ezfio_default(dict_ezfio_cfg):
return create_ezfio_stuff(dict_ezfio_cfg,
config_or_default="default")
def save_ezfio_default(module_lower, str_ezfio_default):
"""
Write the str_ezfio_config in
"$QPACKAGE_ROOT/data/ezfio_defaults/{0}.ezfio_interface_default".format(module_lower)
"""
root_ezfio_default = "{0}/data/ezfio_defaults/".format(
os.environ['QPACKAGE_ROOT'])
path = "{0}/{1}.ezfio_interface_default".format(root_ezfio_default,
module_lower)
try:
f = open(path, "r")
except IOError:
old_output = ""
else:
old_output = f.read()
f.close()
if str_ezfio_default != old_output:
with open(path, "w+") as f:
f.write(str_ezfio_default)
def create_ocaml_input(dict_ezfio_cfg, module_lower):
# ~#~#~#~# #
# I n i t #
# ~#~#~#~# #
from ezfio_generate_ocaml import EZFIO_ocaml
l_ezfio_name = []
l_type = []
l_doc = []
for k, v in dict_ezfio_cfg.iteritems():
if v['interface'] == "input":
l_ezfio_name.append(v['ezfio_name'])
l_type.append(v["type"])
l_doc.append(v["doc"])
if not l_ezfio_name:
raise ValueError
e_glob = EZFIO_ocaml(l_ezfio_name=l_ezfio_name,
l_type=l_type,
l_doc=l_doc)
# ~#~#~#~#~#~#~#~# #
# C r e a t i o n #
# ~#~#~#~#~#~#~#~# #
template = ['(* =~=~ *)',
'(* Init *)',
'(* =~=~ *)',
""]
template += ["open Qptypes;;",
"open Qputils;;",
"open Core.Std;;",
"",
"module {0} : sig".format(module_lower.capitalize())]
template += [e_glob.create_type()]
template += [" 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"]
template += [e_glob.create_type()]
template += ['',
' let get_default = Qpackage.get_ezfio_default "{0}";;'.format(module_lower),
'']
template += ['(* =~=~=~=~=~=~==~=~=~=~=~=~ *)',
'(* Generate Special Function *)',
'(* =~=~=~==~=~~=~=~=~=~=~=~=~ *)',
""]
for provider_name, d_val in sorted(dict_ezfio_cfg.iteritems()):
if 'default' not in d_val:
continue
ezfio_dir = d_val["ezfio_dir"]
ezfio_name = d_val["ezfio_name"]
e = EZFIO_ocaml(ezfio_dir=ezfio_dir,
ezfio_name=ezfio_name,
type=d_val["type"])
template += [e.create_read(),
e.create_write(),
""]
template += ['(* =~=~=~=~=~=~=~=~=~=~=~=~ *)',
'(* Generate Global Function *)',
'(* =~=~=~=~=~=~=~=~=~=~=~=~ *)',
""]
template += [e_glob.create_read_global(),
e_glob.create_write_global(),
e_glob.create_to_string(),
e_glob.create_to_rst()]
template += [" include Generic_input_of_rst;;",
" let of_rst = of_rst t_of_sexp;;",
"",
"end"]
return "\n".join(template)
def save_ocaml_input(module_lower, str_ocaml_input):
"""
Write the str_ocaml_input in
$QPACKAGE_ROOT/ocaml/Input_{0}.ml".format(module_lower)
"""
path = "{0}/ocaml/Input_{1}.ml".format(os.environ['QPACKAGE_ROOT'],
module_lower)
try:
f = open(path, "r")
except IOError:
old_output = ""
else:
old_output = f.read()
f.close()
if str_ocaml_input != old_output:
with open(path, "w+") as f:
f.write(str_ocaml_input)
def get_l_module_lower():
"""
Get all module who have EZFIO.cfg with input data
(NB `search` in all the ligne and `match` only in one)
"""
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
mypath = "{0}/src".format(os.environ['QPACKAGE_ROOT'])
# ~#~#~#~#~#~#~#~ #
# L _ f o l d e r #
# ~#~#~#~#~#~#~#~ #
from os import listdir
from os.path import isdir, join, exists
l_folder = [f for f in listdir(mypath) if isdir(join(mypath, f))]
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
# L _ m o d u l e _ l o w e r #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
l_module_lower = []
import re
p = re.compile(ur'interface:\s+input')
for f in l_folder:
path = "{0}/{1}/EZFIO.cfg".format(mypath, f)
if exists(path):
with open(path, 'r') as file_:
if p.search(file_.read()):
l_module_lower.append(f.lower())
# ~#~#~#~#~#~ #
# R e t u r n #
# ~#~#~#~#~#~ #
return l_module_lower
def create_ocaml_input_global():
"""
Check for all the EZFIO.cfg get the module lower
then create incule {module_lower}.ml
"""
# ~#~#~#~# #
# I n i t #
# ~#~#~#~# #
l_module_lower = get_l_module_lower()
# ~#~#~#~#~#~#~#~# #
# C r e a t i o n #
# ~#~#~#~#~#~#~#~# #
from ezfio_generate_ocaml import EZFIO_ocaml
qpackage_root = os.environ['QPACKAGE_ROOT']
path = qpackage_root + "/scripts/ezfio_interface/qp_edit_template"
with open(path, "r") as f:
template_raw = f.read()
e = EZFIO_ocaml(l_module_lower=l_module_lower)
template = template_raw.format(keywords=e.create_qp_keywords(),
keywords_to_string=e.create_qp_keywords_to_string(),
section_to_rst=e.create_qp_section_to_rst(),
write=e.create_qp_write(),
tasks=e.create_qp_tasks())
input_auto = e.create_input_auto_generated()
return (template, input_auto)
def save_ocaml_input_auto(str_ocaml_input_global):
"""
Write the str_ocaml_input in
$QPACKAGE_ROOT/ocaml/Input_auto_generated.ml
"""
path = "{0}/ocaml/Input_auto_generated.ml".format(os.environ['QPACKAGE_ROOT'])
try:
f = open(path, "r")
except IOError:
old_output = ""
else:
old_output = f.read()
f.close()
if str_ocaml_input_global != old_output:
with open(path, "w+") as f:
f.write(str_ocaml_input_global)
def save_ocaml_qp_edit(str_ocaml_qp_edit):
"""
Write the str_ocaml_qp_edit in
$QPACKAGE_ROOT/ocaml/qp_edit.ml
"""
path = "{0}/ocaml/qp_edit.ml".format(os.environ['QPACKAGE_ROOT'])
try:
f = open(path, "r")
except IOError:
old_output = ""
else:
old_output = f.read()
f.close()
if str_ocaml_qp_edit != old_output:
with open(path, "w+") as f:
f.write(str_ocaml_qp_edit)
if __name__ == "__main__":
arguments = docopt(__doc__)
# ___
# | ._ o _|_
# _|_ | | | |_
#
if not arguments["--global"]:
if not arguments["--path"]:
config_file_path = "EZFIO.cfg"
if "EZFIO.cfg" not in os.listdir(os.getcwd()):
sys.exit(0)
else:
config_file_path = arguments["path"]
# Get the full path
config_file_path = os.path.expanduser(config_file_path)
config_file_path = os.path.expandvars(config_file_path)
config_file_path = os.path.abspath(config_file_path)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
# G e t _ m o d u l e _ d i r #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
path_dirname = os.path.dirname(config_file_path)
module = [i for i in path_dirname.split("/") if i][-1]
module_lower = module.lower()
# Because we only authorise this right now!
ezfio_dir = module_lower
dict_ezfio_cfg = get_dict_config_file(config_file_path, ezfio_dir)
# _
# / _ _| _ _ _ ._ _ ._ _. _|_ o _ ._
# \_ (_) (_| (/_ (_| (/_ | | (/_ | (_| |_ | (_) | |
# _|
# ~#~#~#~#~#~#~#~#~#~ #
# W h a t _ t o _ d o #
# ~#~#~#~#~#~#~#~#~#~ #
if any([arguments[i] for i in ["--irpf90",
"--ezfio_config",
"--ocaml",
"--ezfio_default",
"--global"]]):
# User changer somme argument, do what he want
do_all = False
else:
# Do all the stuff
do_all = True
# ~#~#~#~#~#~#~ #
# I R P . f 9 0 #
# ~#~#~#~#~#~#~ #
if do_all or arguments["--irpf90"]:
l_str_code = create_ezfio_provider(dict_ezfio_cfg)
save_ezfio_provider(path_dirname, l_str_code)
# ~#~#~#~#~#~#~#~#~#~#~#~ #
# e z f i o _ c o n f i g #
# ~#~#~#~#~#~#~#~#~#~#~#~ #
if do_all or arguments["--ezfio_config"]:
str_ezfio_config = create_ezfio_config(dict_ezfio_cfg)
save_ezfio_config(module_lower, str_ezfio_config)
# ~#~#~#~#~#~#
# O c a m l #
# ~#~#~#~#~#~#
if do_all or arguments["--ocaml"]:
try:
str_ocaml_input = create_ocaml_input(dict_ezfio_cfg, module_lower)
except ValueError:
pass
else:
save_ocaml_input(module_lower, str_ocaml_input)
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# e z f i o _ d e f a u l t #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
if do_all or arguments["--ezfio_default"]:
str_ezfio_default = create_ezfio_default(dict_ezfio_cfg)
save_ezfio_default(module_lower, str_ezfio_default)
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# e z f i o _ d e f a u l t #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
if do_all or arguments["--global"]:
str_ocaml_qp_edit, str_ocaml_input_auto = create_ocaml_input_global()
save_ocaml_input_auto(str_ocaml_input_auto)
save_ocaml_qp_edit(str_ocaml_qp_edit)

483
scripts/ezfio_interface/ezfio_generate_ocaml.py Executable file
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@ -0,0 +1,483 @@
#!/usr/bin/env python
import sys
import os
# If type in **kwargs
from ei_handler import Type
class EZFIO_ocaml(object):
def __init__(self, **kwargs):
for k, v in kwargs.iteritems():
try:
exec "self.{0} = {1}".format(k, v)
except NameError:
exec "self.{0} = '{1}'".format(k, v)
@property
def Ocaml_type(self):
return self.type.ocaml.capitalize()
@property
def ocaml_type(self):
return self.type.ocaml
@property
def fancy_type(self):
return self.type.fancy
def check_if_init(self, l_arg, name):
for i in l_arg:
try:
exec "self.{0}".format(i)
except AttributeError:
msg = "You need to provide a '{0}' for creating {1}"
raise KeyError(msg.format(i, name))
def create_read(self):
'''
You need to instantiate the EZFIO_ocaml with this keyword argument
ezfio_dir = str
ezfio_name = str
type = Named_tuple(fancy_type, ocaml_type, fortrant_type)
Return the read template
'''
# ~#~#~#~#~#~#~#~ #
# C h e c k i n g #
# ~#~#~#~#~#~#~#~ #
self.check_if_init(["ezfio_dir", "ezfio_name", "type"],
sys._getframe().f_code.co_name)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
# C r e a t e _ t e m pl a t e #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
l_template = [
'(* Read snippet for {self.ezfio_name} *)',
'let read_{self.ezfio_name} () =',
' if not (Ezfio.has_{self.ezfio_dir}_{self.ezfio_name} ()) then',
' get_default "{self.ezfio_name}"',
' |> {self.Ocaml_type}.of_string',
' |> Ezfio.set_{self.ezfio_dir}_{self.ezfio_name}',
' ;',
' Ezfio.get_{self.ezfio_dir}_{self.ezfio_name} ()']
if self.fancy_type:
l_template += [" |> {self.fancy_type}.of_{self.ocaml_type}"]
l_template += [";;"]
template = "\n ".join(l_template)
# ~#~#~#~#~#~ #
# R e n d e r #
# ~#~#~#~#~#~ #
template_rendered = template.format(**locals())
# ~#~#~#~#~#~ #
# R e t u r n #
# ~#~#~#~#~#~ #
return template_rendered
def create_write(self):
'''
You need to instantiate the EZFIO_ocaml with this keyword argument
ezfio_dir = str
ezfio_name = str
type = Named_tuple(fancy_type, ocaml_type, fortrant_type)
Return the read template
'''
# ~#~#~#~#~#~#~#~ #
# C h e c k i n g #
# ~#~#~#~#~#~#~#~ #
self.check_if_init(["ezfio_dir", "ezfio_name", "type"],
sys._getframe().f_code.co_name)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
# C r e a t e _ t e m pl a t e #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
l_template = ['(* Write snippet for {self.ezfio_name} *)']
if self.fancy_type:
l_template += ['let write_{self.ezfio_name} var = ',
' {self.fancy_type}.to_{self.ocaml_type} var',
' |> Ezfio.set_{self.ezfio_dir}_{self.ezfio_name}']
else:
l_template += ['let write_{self.ezfio_name} =',
' Ezfio.set_{self.ezfio_dir}_{self.ezfio_name}']
l_template += [';;']
template = "\n ".join(l_template)
# ~#~#~#~#~#~ #
# R e n d e r #
# ~#~#~#~#~#~ #
template_rendered = template.format(**locals())
# ~#~#~#~#~#~ #
# R e t u r n #
# ~#~#~#~#~#~ #
return template_rendered
def create_type(self):
'''
You need to instantiate the EZFIO_ocaml with this keyword argument
l_ezfio_name = [provider_name, ...]
l_type = [Named_tuple(fancy_type, ocaml_type, fortrant_type), ...]
Return the type template
'''
# ~#~#~#~#~#~#~#~ #
# C h e c k i n g #
# ~#~#~#~#~#~#~#~ #
self.check_if_init(["l_ezfio_name", "l_type"],
sys._getframe().f_code.co_name)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
# C r e a t e _ t e m pl a t e #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
l_template = ["(* Generate type *)",
"type t = ",
" {"]
for p, t in zip(self.l_ezfio_name, self.l_type):
if t.fancy:
l_template += [" {0:<30} : {1}.t;".format(p, t.fancy)]
else:
l_template += [" {0:<30} : {1};".format(p, t.ocaml)]
l_template += [" } with sexp",
";;"]
# ~#~#~#~#~#~ #
# R e t u r n #
# ~#~#~#~#~#~ #
return "\n ".join(l_template)
def create_read_global(self):
'''
You need to instantiate the EZFIO_ocaml with this keyword argument
l_ezfio_name = [ezfio_name, ...]
Return the read_global template
'''
# ~#~#~#~#~#~#~#~ #
# C h e c k i n g #
# ~#~#~#~#~#~#~#~ #
self.check_if_init(["l_ezfio_name"],
sys._getframe().f_code.co_name)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
# C r e a t e _ t e m pl a t e #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
l_template = ["(* Read all *)",
"let read() = ",
" Some",
" {"]
l_template += [" {0:<30} = read_{0} ();".format(p)
for p in self.l_ezfio_name]
l_template += [" }",
";;"]
# ~#~#~#~#~#~ #
# R e t u r n #
# ~#~#~#~#~#~ #
return "\n ".join(l_template)
def create_write_global(self):
'''
You need to instantiate the EZFIO_ocaml with this keyword argument
l_ezfio_name = [provider_name, ...]
Return the type template
'''
# ~#~#~#~#~#~#~#~ #
# C h e c k i n g #
# ~#~#~#~#~#~#~#~ #
self.check_if_init(["l_ezfio_name"],
sys._getframe().f_code.co_name)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
# C r e a t e _ t e m pl a t e #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
l_template = ["(* Write all *)",
"let write{ "]
l_template += [" {0};".format(p) for p in self.l_ezfio_name]
l_template += [" } ="]
l_template += [" write_{0:<30} {0};".format(p)
for p in self.l_ezfio_name]
l_template += [";;"]
# ~#~#~#~#~#~ #
# R e t u r n #
# ~#~#~#~#~#~ #
return "\n ".join(l_template)
def create_to_string(self):
'''
You need to instantiate the EZFIO_ocaml with this keyword argument
l_ezfio_name = [provider_name, ...]
l_type = [Named_tuple(fancy_type, ocaml_type, fortrant_type), ...]
Return the type template
'''
# ~#~#~#~#~#~#~#~ #
# C h e c k i n g #
# ~#~#~#~#~#~#~#~ #
self.check_if_init(["l_ezfio_name", "l_type"],
sys._getframe().f_code.co_name)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
# C r e a t e _ t e m pl a t e #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
l_template = ['(* to_string*)',
'let to_string b =',
' Printf.sprintf "']
l_template += ["{0} = %s".format(p) for p in self.l_ezfio_name]
l_template += ['"']
for p, t in zip(self.l_ezfio_name, self.l_type):
if t.fancy:
str_ = t.fancy
else:
str_ = t.ocaml.capitalize()
l_template += [" ({0}.to_string b.{1})".format(str_, p)]
l_template += [";;"]
# ~#~#~#~#~#~ #
# R e t u r n #
# ~#~#~#~#~#~ #
return "\n ".join(l_template)
def create_to_rst(self):
'''
You need to instantiate the EZFIO_ocaml with this keyword argument
l_ezfio_name = [provider_name, ...]
l_type = [Named_tuple(fancy_type, ocaml_type, fortrant_type), ...]
Return the type template
'''
# ~#~#~#~#~#~#~#~ #
# C h e c k i n g #
# ~#~#~#~#~#~#~#~ #
self.check_if_init(["l_ezfio_name", "l_type", "l_doc"],
sys._getframe().f_code.co_name)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
# C r e a t e _ t e m pl a t e #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
l_template = ['(* to_rst*)',
'let to_rst b =',
' Printf.sprintf "']
for p, d in zip(self.l_ezfio_name, self.l_doc):
l_template += ["{0} ::".format(d),
"",
" {0} = %s".format(p),
""]
l_template += ['"']
for p, t in zip(self.l_ezfio_name, self.l_type):
if t.fancy:
str_ = t.fancy
else:
str_ = t.ocaml.capitalize()
l_template += [" ({0}.to_string b.{1})".format(str_, p)]
l_template += ["|> Rst_string.of_string",
";;"]
# ~#~#~#~#~#~ #
# R e t u r n #
# ~#~#~#~#~#~ #
return "\n ".join(l_template)
def create_input_auto_generated(self):
"""
Generate the include of all the Input_module.lower template
"""
# ~#~#~#~#~#~#~#~ #
# C h e c k i n g #
# ~#~#~#~#~#~#~#~ #
self.check_if_init(["l_module_lower"],
sys._getframe().f_code.co_name)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
# C r e a t e _ t e m pl a t e #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
l_template = ['open Qputils;;',
'open Qptypes;;',
'open Core.Std;;',
'']
for m in self.l_module_lower:
l_template += ["include Input_{0}".format(m)]
# ~#~#~#~#~#~ #
# R e t u r n #
# ~#~#~#~#~#~ #
return "\n".join(l_template)
def create_qp_keywords(self):
"""
Generate keywords template
"""
# ~#~#~#~#~#~#~#~ #
# C h e c k i n g #
# ~#~#~#~#~#~#~#~ #
self.check_if_init(["l_module_lower"],
sys._getframe().f_code.co_name)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
# C r e a t e _ t e m pl a t e #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
l_template = ["| {0}".format(m.capitalize())
for m in self.l_module_lower]
# ~#~#~#~#~#~ #
# R e t u r n #
# ~#~#~#~#~#~ #
return "\n".join(l_template)
def create_qp_keywords_to_string(self):
"""
Generate keywords to string template
"""
# ~#~#~#~#~#~#~#~ #
# C h e c k i n g #
# ~#~#~#~#~#~#~#~ #
self.check_if_init(["l_module_lower"],
sys._getframe().f_code.co_name)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
# C r e a t e _ t e m pl a t e #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
l_template = ['| {0} -> "{0}"'.format(m.capitalize())
for m in self.l_module_lower]
# ~#~#~#~#~#~ #
# R e t u r n #
# ~#~#~#~#~#~ #
return "\n".join(l_template)
def create_qp_section_to_rst(self):
"""
Generate section to rst
"""
# ~#~#~#~#~#~#~#~ #
# C h e c k i n g #
# ~#~#~#~#~#~#~#~ #
self.check_if_init(["l_module_lower"],
sys._getframe().f_code.co_name)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
# C r e a t e _ t e m pl a t e #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
l_template = []
for m in self.l_module_lower:
m_cap = m.capitalize()
l_template += [" | {0} ->".format(m_cap),
" f {0}.(read, to_rst)".format(m_cap)]
# ~#~#~#~#~#~ #
# R e t u r n #
# ~#~#~#~#~#~ #
return "\n".join(l_template)
def create_qp_write(self):
"""
Generate write
"""
# ~#~#~#~#~#~#~#~ #
# C h e c k i n g #
# ~#~#~#~#~#~#~#~ #
self.check_if_init(["l_module_lower"],
sys._getframe().f_code.co_name)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
# C r e a t e _ t e m pl a t e #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
str_ = " | {0} -> write {0}.(of_rst, write) s"
l_template = [str_.format(m.capitalize()) for m in self.l_module_lower]
# ~#~#~#~#~#~ #
# R e t u r n #
# ~#~#~#~#~#~ #
return "\n".join(l_template)
def create_qp_tasks(self):
"""
Generate taks
"""
# ~#~#~#~#~#~#~#~ #
# C h e c k i n g #
# ~#~#~#~#~#~#~#~ #
self.check_if_init(["l_module_lower"],
sys._getframe().f_code.co_name)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
# C r e a t e _ t e m pl a t e #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
l_template = [" {0} ; ".format(m.capitalize())
for m in self.l_module_lower]
# ~#~#~#~#~#~ #
# R e t u r n #
# ~#~#~#~#~#~ #
return "\n".join(l_template)

98
scripts/ezfio_interface/ezfio_generate_provider.py Executable file
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@ -0,0 +1,98 @@
#!/usr/bin/env python
__author__ = "Applencourt PEP8"
__date__ = "jeudi 26 mars 2015, 12:49:35 (UTC+0100)"
"""
Creates the provider of a variable that has to be
fetched from the EZFIO file.
"""
import sys
class EZFIO_Provider(object):
data = """
BEGIN_PROVIDER [ %(type)s, %(name)s ]
implicit none
BEGIN_DOC
! %(doc)s
END_DOC
logical :: has
PROVIDE ezfio_filename
call ezfio_has_%(ezfio_dir)s_%(ezfio_name)s(has)
if (has) then
call ezfio_get_%(ezfio_dir)s_%(ezfio_name)s(%(name)s)
else
print *, '%(ezfio_dir)s/%(ezfio_name)s not found in EZFIO file'
stop 1
endif
%(write)s
END_PROVIDER
""".strip()
write_correspondance = {"integer": "write_int",
"logical": "write_bool",
"double precision": "write_double"}
def __init__(self):
self.values = "type doc name ezfio_dir ezfio_name write output".split()
for v in self.values:
exec "self.{0} = None".format(v)
def __repr__(self):
self.set_write()
for v in self.values:
if not v:
msg = "Error : %s is not set in ezfio_with_default.py" % (v)
print >>sys.stderr, msg
sys.exit(1)
return self.data % self.__dict__
def set_write(self):
self.write = ""
if self.type in self.write_correspondance:
write = self.write_correspondance[self.type]
output = self.output
name = self.name
l_write = ["",
" call write_time(%(output)s)",
" call %(write)s(%(output)s, %(name)s, &",
" '%(name)s')",
""]
self.write = "\n".join(l_write) % locals()
def set_type(self, t):
self.type = t.lower()
def set_doc(self, t):
self.doc = t.strip().replace('\n', '\n! ')
def set_name(self, t):
self.name = t
def set_ezfio_dir(self, t):
self.ezfio_dir = t.lower()
def set_ezfio_name(self, t):
self.ezfio_name = t.lower()
def set_output(self, t):
self.output = t
def test_module():
T = EZFIO_Provider()
T.set_type("double precision")
T.set_name("thresh_SCF")
T.set_doc("Threshold on the convergence of the Hartree Fock energy")
T.set_ezfio_dir("Hartree_Fock")
T.set_ezfio_name("thresh_SCF")
T.set_output("output_Hartree_Fock")
print T
if __name__ == '__main__':
test_module()

39
ocaml/qp_edit.ml → scripts/ezfio_interface/qp_edit_template
View File

@ -11,27 +11,21 @@ open Core.Std;;
(** Keywords used to define input sections *)
type keyword =
| Ao_basis
| Bielec_integrals
| Cisd_sc2
| Determinants
| Electrons
| Full_ci
| Hartree_fock
| Mo_basis
| Nuclei
{keywords}
;;
let keyword_to_string = function
| Ao_basis -> "AO basis"
| Bielec_integrals -> "Two electron integrals"
| Cisd_sc2 -> "CISD (SC)^2"
| Determinants -> "Determinants"
| Electrons -> "Electrons"
| Full_ci -> "Selected Full-CI"
| Hartree_fock -> "Hartree-Fock"
| Mo_basis -> "MO basis"
| Nuclei -> "Molecule"
| Ao_basis -> "AO basis"
| Determinants -> "Determinants"
| Electrons -> "Electrons"
| Mo_basis -> "MO basis"
| Nuclei -> "Molecule"
{keywords_to_string}
;;
@ -70,24 +64,17 @@ let get s =
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)
{section_to_rst}
end
with
| Sys_error msg -> (Printf.eprintf "Info: %s\n%!" msg ; "")
@ -125,11 +112,8 @@ let set str 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
{write}
| 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 *)
@ -176,10 +160,7 @@ let run check_only ezfio_filename =
Nuclei ;
Ao_basis;
Electrons ;
Bielec_integrals ;
Hartree_fock ;
Cisd_sc2 ;
Full_ci ;
{tasks}
Mo_basis;
Determinants ;
]

7
scripts/ezfio_with_default.py
View File

@ -90,7 +90,10 @@ END_PROVIDER
self.default = t
def get_default(self):
filename = '/'.join( [os.environ['QPACKAGE_ROOT'], 'data', 'ezfio_defaults'] )
filename = '/'.join( [os.environ['QPACKAGE_ROOT'], 'data',
'ezfio_defaults',
'WILL_BE_DELETED.ezfio_default'] )
file = open(filename,'r')
lines = file.readlines()
file.close()
@ -115,6 +118,8 @@ END_PROVIDER
true = True
false= False
try:
true = True
false = False
v_eval = eval(v)
except:
v = "call ezfio_get_%(v)s(%(name)s)"%locals()

2
scripts/prepare_ezfio.sh
View File

@ -9,7 +9,7 @@ echo "=-=-=-=-=-=-=-=-=-=-=-"
for dir in ${QPACKAGE_ROOT}/src/*/
do
cd $dir || exit -1
${QPACKAGE_ROOT}/scripts/ezfio_interface.py
${QPACKAGE_ROOT}/scripts/ezfio_interface/ei_handler.py
done
# For old-style directories. Will be removed some day...

3
scripts/run_Makefile_common.sh
View File

@ -65,5 +65,4 @@ fi
${QPACKAGE_ROOT}/scripts/create_Makefile_depend.sh
# Update EZFIO interface
${QPACKAGE_ROOT}/scripts/ezfio_interface.py
${QPACKAGE_ROOT}/scripts/ezfio_interface/ei_handler.py

14
setup_environment.sh
View File

@ -17,8 +17,8 @@ export QPACKAGE_ROOT=\$( cd \$(dirname "\${BASH_SOURCE}") ; pwd -P )
export LD_LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LD_LIBRARY_PATH}
export LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LIBRARY_PATH}
export C_INCLUDE_PATH="\${QPACKAGE_ROOT}"/include:\${C_INCLUDE_PATH}
export PYTHONPATH=\${PYTHONPATH}:"\${QPACKAGE_ROOT}"/scripts
export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/scripts
export PYTHONPATH=\${PYTHONPATH}:"\${QPACKAGE_ROOT}"/scripts:"\${QPACKAGE_ROOT}"/scripts/ezfio_interface
export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/scripts:"\${QPACKAGE_ROOT}"/scripts/ezfio_interface
export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/bin
export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/ocaml
source "\${QPACKAGE_ROOT}"/bin/irpman &> /dev/null
@ -48,16 +48,6 @@ then
fi
echo "${BLUE}===== Installing EZFIO ===== ${BLACK}"
${QPACKAGE_ROOT}/scripts/install_ezfio.sh | tee install_ezfio.log
if [[ ! -d ${QPACKAGE_ROOT}/EZFIO ]]
then
echo $RED "Error in EZFIO installation" $BLACK
exit 1
fi
echo "${BLUE}===== Installing Zlib ===== ${BLACK}"
${QPACKAGE_ROOT}/scripts/install_zlib.sh | tee install_zlib.log

9
src/BiInts/bi_integrals.ezfio_config
View File

@ -1,9 +0,0 @@
bielec_integrals
read_ao_integrals logical
read_mo_integrals logical
write_ao_integrals logical
write_mo_integrals logical
threshold_ao double precision
threshold_mo double precision
direct logical

46
src/BiInts/options.irp.f
View File

@ -1,46 +0,0 @@
BEGIN_SHELL [ /usr/bin/python ]
from ezfio_with_default import EZFIO_Provider
T = EZFIO_Provider()
T.set_type ( "logical" )
T.set_name ( "do_direct_integrals" )
T.set_doc ( "If true, compute integrals on the fly" )
T.set_ezfio_dir ( "bielec_integrals" )
T.set_ezfio_name( "direct" )
T.set_output ( "output_biints" )
print T
T.set_type ( "logical" )
T.set_name ( "write_mo_integrals" )
T.set_doc ( "If true, write MO integrals in EZFIO" )
T.set_ezfio_name( "write_mo_integrals" )
print T
T.set_name ( "write_ao_integrals" )
T.set_doc ( "If true, write AO integrals in EZFIO" )
T.set_ezfio_name( "write_ao_integrals" )
print T
T.set_name ( "read_mo_integrals" )
T.set_doc ( "If true, read MO integrals in EZFIO" )
T.set_ezfio_name( "read_mo_integrals" )
print T
T.set_name ( "read_ao_integrals" )
T.set_doc ( "If true, read AO integrals in EZFIO" )
T.set_ezfio_name( "read_ao_integrals" )
print T
T.set_type ( "double precision" )
T.set_name ( "ao_integrals_threshold" )
T.set_doc ( "If <pq|rs> < ao_integrals_threshold, <pq|rs> = 0" )
T.set_ezfio_name( "threshold_ao" )
print T
T.set_name ( "mo_integrals_threshold" )
T.set_doc ( "If <ij|kl> < mo_integrals_threshold, <ij|kl> = 0" )
T.set_ezfio_name( "threshold_mo" )
print T
END_SHELL

0
src/Bielec_integrals/ASSUMPTIONS.rst Normal file
View File

32
src/Bielec_integrals/EZFIO.cfg Normal file
View File

@ -0,0 +1,32 @@
[do_direct_integrals]
type: logical
doc: Compute integrals on the fly
interface: input
default: False
ezfio_name: direct
[disk_access_mo_integrals]
type: Disk_access
doc: Read/Write MO integrals from/to disk [ Write | Read | None ]
interface: input
default: None
[disk_access_ao_integrals]
type: Disk_access
doc: Read/Write AO integrals from/to disk [ Write | Read | None ]
interface: input
default: None
[ao_integrals_threshold]
type: Threshold
doc: If |<pq|rs>| < ao_integrals_threshold then <pq|rs> is zero
interface: input
default: 1.e-15
ezfio_name: threshold_ao
[mo_integrals_threshold]
type: Threshold
doc: If |<ij|kl>| < ao_integrals_threshold then <pq|rs> is zero
interface: input
default: 1.e-15
ezfio_name: threshold_mo

0
src/BiInts/Makefile → src/Bielec_integrals/Makefile
View File

0
src/BiInts/NEEDED_MODULES → src/Bielec_integrals/NEEDED_MODULES
View File

0
src/BiInts/README.rst → src/Bielec_integrals/README.rst
View File

29
src/BiInts/ao_bi_integrals.irp.f → src/Bielec_integrals/ao_bi_integrals.irp.f
View File

@ -319,13 +319,6 @@ subroutine compute_ao_bielec_integrals(j,k,l,sze,buffer_value)
end
BEGIN_PROVIDER [ logical, ao_bielec_integrals_in_map ]
implicit none
use map_module
@ -356,7 +349,7 @@ BEGIN_PROVIDER [ logical, ao_bielec_integrals_in_map ]
integer :: load_ao_integrals
print*,'Reading the AO integrals'
if (load_ao_integrals(trim(ezfio_filename)//'/work/ao_integrals.bin') == 0) then
write(output_BiInts,*) 'AO integrals provided'
write(output_bielec_integrals,*) 'AO integrals provided'
ao_bielec_integrals_in_map = .True.
return
endif
@ -374,7 +367,7 @@ BEGIN_PROVIDER [ logical, ao_bielec_integrals_in_map ]
PROVIDE progress_bar
call omp_init_lock(lock)
lmax = ao_num*(ao_num+1)/2
write(output_BiInts,*) 'Providing the AO integrals'
write(output_bielec_integrals,*) 'Providing the AO integrals'
call wall_time(wall_0)
call wall_time(wall_1)
call cpu_time(cpu_1)
@ -385,7 +378,7 @@ BEGIN_PROVIDER [ logical, ao_bielec_integrals_in_map ]
!$OMP DEFAULT(NONE) &
!$OMP SHARED (ao_num, jl_pairs, ao_integrals_map,thresh, &
!$OMP cpu_1,wall_1,lock, lmax,n_centers,ao_nucl, &
!$OMP ao_overlap_abs,ao_overlap,output_BiInts,abort_here, &
!$OMP ao_overlap_abs,ao_overlap,output_bielec_integrals,abort_here, &
!$OMP wall_0,progress_bar,progress_value)
allocate(buffer_i(size_buffer))
@ -452,7 +445,7 @@ IRP_ENDIF
if (thread_num == 0) then
if (wall_2 - wall_0 > 1.d0) then
wall_0 = wall_2
write(output_BiInts,*) 100.*float(kk)/float(lmax), '% in ', &
write(output_bielec_integrals,*) 100.*float(kk)/float(lmax), '% in ', &
wall_2-wall_1, 's', map_mb(ao_integrals_map) ,'MB'
progress_value = dble(map_mb(ao_integrals_map))
endif
@ -469,21 +462,21 @@ IRP_ENDIF
stop 'Aborting in AO integrals calculation'
endif
IRP_IF COARRAY
write(output_BiInts,*) 'Communicating the map'
write(output_bielec_integrals,*) 'Communicating the map'
call communicate_ao_integrals()
IRP_ENDIF COARRAY
write(output_BiInts,*) 'Sorting the map'
write(output_bielec_integrals,*) 'Sorting the map'
call map_sort(ao_integrals_map)
call cpu_time(cpu_2)
call wall_time(wall_2)
integer(map_size_kind) :: get_ao_map_size, ao_map_size
ao_map_size = get_ao_map_size()
write(output_BiInts,*) 'AO integrals provided:'
write(output_BiInts,*) ' Size of AO map : ', map_mb(ao_integrals_map) ,'MB'
write(output_BiInts,*) ' Number of AO integrals :', ao_map_size
write(output_BiInts,*) ' cpu time :',cpu_2 - cpu_1, 's'
write(output_BiInts,*) ' wall time :',wall_2 - wall_1, 's ( x ', (cpu_2-cpu_1)/(wall_2-wall_1+tiny(1.d0)), ' )'
write(output_bielec_integrals,*) 'AO integrals provided:'
write(output_bielec_integrals,*) ' Size of AO map : ', map_mb(ao_integrals_map) ,'MB'
write(output_bielec_integrals,*) ' Number of AO integrals :', ao_map_size
write(output_bielec_integrals,*) ' cpu time :',cpu_2 - cpu_1, 's'
write(output_bielec_integrals,*) ' wall time :',wall_2 - wall_1, 's ( x ', (cpu_2-cpu_1)/(wall_2-wall_1+tiny(1.d0)), ' )'
ao_bielec_integrals_in_map = .True.
if (write_ao_integrals) then

0
src/BiInts/gauss_legendre.irp.f → src/Bielec_integrals/gauss_legendre.irp.f
View File

4
src/BiInts/map_integrals.irp.f → src/Bielec_integrals/map_integrals.irp.f
View File

@ -13,7 +13,7 @@ BEGIN_PROVIDER [ type(map_type), ao_integrals_map ]
call bielec_integrals_index(ao_num,ao_num,ao_num,ao_num,key_max)
sze = key_max
call map_init(ao_integrals_map,sze)
write(output_BiInts,*) 'AO map initialized'
write(output_bielec_integrals,*) 'AO map initialized'
END_PROVIDER
subroutine bielec_integrals_index(i,j,k,l,i1)
@ -244,7 +244,7 @@ BEGIN_PROVIDER [ type(map_type), mo_integrals_map ]
call bielec_integrals_index(mo_tot_num,mo_tot_num,mo_tot_num,mo_tot_num,key_max)
sze = key_max
call map_init(mo_integrals_map,sze)
write(output_BiInts,*) 'MO map initialized'
write(output_bielec_integrals,*) 'MO map initialized'
END_PROVIDER
subroutine insert_into_ao_integrals_map(n_integrals, &

22
src/BiInts/mo_bi_integrals.irp.f → src/Bielec_integrals/mo_bi_integrals.irp.f
View File

@ -31,7 +31,7 @@ BEGIN_PROVIDER [ logical, mo_bielec_integrals_in_map ]
integer :: load_mo_integrals
print*,'Reading the MO integrals'
if (load_mo_integrals(trim(ezfio_filename)//'/work/mo_integrals.bin') == 0) then
write(output_BiInts,*) 'MO integrals provided'
write(output_bielec_integrals,*) 'MO integrals provided'
return
endif
endif
@ -84,8 +84,8 @@ subroutine add_integrals_to_map(mask_ijkl)
call bitstring_to_list( mask_ijkl(1,4), list_ijkl(1,4), n_l, N_int )
size_buffer = min(ao_num*ao_num*ao_num,16000000)
write(output_BiInts,*) 'Providing the molecular integrals '
write(output_BiInts,*) 'Buffers : ', 8.*(mo_tot_num_align*(n_j)*(n_k+1) + mo_tot_num_align +&
write(output_bielec_integrals,*) 'Providing the molecular integrals '
write(output_bielec_integrals,*) 'Buffers : ', 8.*(mo_tot_num_align*(n_j)*(n_k+1) + mo_tot_num_align +&
ao_num+ao_num*ao_num+ size_buffer*3)/(1024*1024), 'MB / core'
call wall_time(wall_1)
@ -99,7 +99,7 @@ subroutine add_integrals_to_map(mask_ijkl)
!$OMP wall_0,thread_num) &
!$OMP DEFAULT(NONE) &
!$OMP SHARED(size_buffer,ao_num,mo_tot_num,n_i,n_j,n_k,n_l,mo_tot_num_align,&
!$OMP mo_coef_transp,output_BiInts, &
!$OMP mo_coef_transp,output_bielec_integrals, &
!$OMP mo_coef_transp_is_built, list_ijkl, &
!$OMP mo_coef_is_built, wall_1, abort_here, &
!$OMP mo_coef,mo_integrals_threshold,ao_integrals_map,mo_integrals_map,progress_bar,progress_value)
@ -272,7 +272,7 @@ IRP_ENDIF
if (thread_num == 0) then
if (wall_2 - wall_0 > 1.d0) then
wall_0 = wall_2
write(output_BiInts,*) 100.*float(l1)/float(ao_num), '% in ', &
write(output_bielec_integrals,*) 100.*float(l1)/float(ao_num), '% in ', &
wall_2-wall_1, 's', map_mb(mo_integrals_map) ,'MB'
progress_value = dble(map_mb(mo_integrals_map))
@ -291,7 +291,7 @@ IRP_ENDIF
stop 'Aborting in MO integrals calculation'
endif
IRP_IF COARRAY
write(output_BiInts,*) 'Communicating the map'
write(output_bielec_integrals,*) 'Communicating the map'
call communicate_mo_integrals()
IRP_ENDIF
call map_unique(mo_integrals_map)
@ -304,11 +304,11 @@ IRP_ENDIF
deallocate(list_ijkl)
write(output_BiInts,*)'Molecular integrals provided:'
write(output_BiInts,*)' Size of MO map ', map_mb(mo_integrals_map) ,'MB'
write(output_BiInts,*)' Number of MO integrals: ', mo_map_size
write(output_BiInts,*)' cpu time :',cpu_2 - cpu_1, 's'
write(output_BiInts,*)' wall time :',wall_2 - wall_1, 's ( x ', (cpu_2-cpu_1)/(wall_2-wall_1), ')'
write(output_bielec_integrals,*)'Molecular integrals provided:'
write(output_bielec_integrals,*)' Size of MO map ', map_mb(mo_integrals_map) ,'MB'
write(output_bielec_integrals,*)' Number of MO integrals: ', mo_map_size
write(output_bielec_integrals,*)' cpu time :',cpu_2 - cpu_1, 's'
write(output_bielec_integrals,*)' wall time :',wall_2 - wall_1, 's ( x ', (cpu_2-cpu_1)/(wall_2-wall_1), ')'
if (write_mo_integrals) then
call dump_mo_integrals(trim(ezfio_filename)//'/work/mo_integrals.bin')

41
src/Bielec_integrals/read_write.irp.f Normal file
View File

@ -0,0 +1,41 @@
BEGIN_PROVIDER [ logical, read_ao_integrals ]
&BEGIN_PROVIDER [ logical, read_mo_integrals ]
&BEGIN_PROVIDER [ logical, write_ao_integrals ]
&BEGIN_PROVIDER [ logical, write_mo_integrals ]
BEGIN_DOC
! One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals
END_DOC
implicit none
if (disk_access_ao_integrals.EQ.'Read') then
read_ao_integrals = .True.
write_ao_integrals = .False.
else if (disk_access_ao_integrals.EQ.'Write') then
read_ao_integrals = .False.
write_ao_integrals = .True.
else if (disk_access_ao_integrals.EQ.'None') then
read_ao_integrals = .False.
write_ao_integrals = .False.
else if (disk_access_mo_integrals.EQ.'Read') then
read_mo_integrals = .True.
write_mo_integrals = .False.
else if (disk_access_mo_integrals.EQ.'Write') then
read_mo_integrals = .False.
write_mo_integrals = .True.
else if (disk_access_mo_integrals.EQ.'None') then
read_mo_integrals = .False.
write_mo_integrals = .False.
else
print *, 'bielec_integrals/disk_acces not of a the good type'
stop "1"
endif
END_PROVIDER

2
src/CAS_SD/NEEDED_MODULES
View File

@ -1,2 +1,2 @@
AOs BiInts Bitmask Dets Electrons Ezfio_files Generators_CAS Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils
AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Generators_CAS Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils

2
src/CID/NEEDED_MODULES
View File

@ -1,3 +1,3 @@
AOs BiInts Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Selectors_full SingleRefMethod Utils
AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Selectors_full SingleRefMethod Utils

2
src/CID_SC2_selected/NEEDED_MODULES
View File

@ -1,2 +1,2 @@
AOs BiInts Bitmask CISD CISD_selected Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils
AOs Bielec_integrals Bitmask CISD CISD_selected Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils

2
src/CID_selected/NEEDED_MODULES
View File

@ -1,2 +1,2 @@
AOs BiInts Bitmask CISD Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils
AOs Bielec_integrals Bitmask CISD Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils

2
src/CIS/NEEDED_MODULES
View File

@ -1,2 +1,2 @@
AOs BiInts Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Selectors_full SingleRefMethod Utils
AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Selectors_full SingleRefMethod Utils

2
src/CISD/NEEDED_MODULES
View File

@ -1,2 +1,2 @@
AOs BiInts Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Selectors_full SingleRefMethod Utils
AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Selectors_full SingleRefMethod Utils

29
src/CISD_SC2_selected/EZFIO.cfg Normal file
View File

@ -0,0 +1,29 @@
[N_det_max_cisd_sc2]
type: Det_number_max
doc: Max number of determinants
interface: input
default: 10000
[do_pt2_end]
type: logical
doc: If true, compute the PT2 at the end of the selection
interface: input
default: true
[PT2_max]
type: PT2_energy
doc: The selection process stops when the largest PT2 (for all the states) is lower
than abs(pt2_max)
interface: input
default: 0.0001
[energy]
type: double precision
doc: Calculated CISD_SC2 energy of ground_state
interface: output
[energy_pt2]
type: double precision
doc: Calculated CISD_SC2 energy+pt2 of ground_state
interface: output

2
src/CISD_SC2_selected/NEEDED_MODULES
View File

@ -1,2 +1,2 @@
AOs BiInts Bitmask CISD CISD_selected Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils
AOs Bielec_integrals Bitmask CISD CISD_selected Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils

4
src/CISD_SC2_selected/cisd_sc2.ezfio_config
View File

@ -1,4 +0,0 @@
cisd_sc2_selected
n_det_max_cisd_sc2 integer
pt2_max double precision
do_pt2_end logical

14
src/CISD_SC2_selected/cisd_sc2_selection.irp.f
View File

@ -62,12 +62,20 @@ program cisd_sc2_selected
if (abort_all) then
exit
endif
! =~=~=~=~=~=~=~=~=~=~=~=~=~!
! W r i t e _ o n _ d i s k !
! =~=~=~=~=~=~=~=~=~=~=~=~=~!
call ezfio_set_full_ci_energy(CI_SC2_energy(1))
enddo
N_det = min(n_det_max_cisd_sc2,N_det)
davidson_threshold = 1.d-10
touch N_det psi_det psi_coef davidson_threshold davidson_criterion
call diagonalize_CI_SC2
pt2 = 0.d0
if(do_pt2_end)then
threshold_selectors = 1.d0
call H_apply_PT2(pt2, norm_pert, H_pert_diag, N_st)
@ -97,6 +105,12 @@ program cisd_sc2_selected
print*,'Degree of excitation of this determinant : ',degree
enddo
! =~=~=~=~=~=~=~=~=~=~=~=~=~!
! W r i t e _ o n _ d i s k !
! =~=~=~=~=~=~=~=~=~=~=~=~=~!
call ezfio_set_full_ci_energy_pt2(CI_SC2_energy(i)+pt2(i)* (1.d0 + norm_pert) - H_pert_diag(i))
endif
call save_wavefunction
deallocate(pt2,norm_pert,H_pert_diag)

51
src/CISD_SC2_selected/options.irp.f
View File

@ -1,51 +0,0 @@
BEGIN_PROVIDER [ integer, n_det_max_cisd_sc2 ]
implicit none
BEGIN_DOC
! Get n_det_max_cisd_sc2 from EZFIO file
END_DOC
logical :: has_n_det_max_cisd_sc2
PROVIDE ezfio_filename
call ezfio_has_cisd_sc2_selected_n_det_max_cisd_sc2(has_n_det_max_cisd_sc2)
if (has_n_det_max_cisd_sc2) then
call ezfio_get_cisd_sc2_selected_n_det_max_cisd_sc2(n_det_max_cisd_sc2)
else
n_det_max_cisd_sc2 = 1000
call ezfio_set_cisd_sc2_selected_n_det_max_cisd_sc2(n_det_max_cisd_sc2)
endif
print*,'n_det_max_cisd_sc2 = ',n_det_max_cisd_sc2
END_PROVIDER
BEGIN_PROVIDER [ double precision , pt2_max ]
implicit none
BEGIN_DOC
! Get pt2_max from EZFIO file
END_DOC
logical :: has_pt2_max
PROVIDE ezfio_filename
call ezfio_has_cisd_sc2_selected_pt2_max(has_pt2_max)
if (has_pt2_max) then
call ezfio_get_cisd_sc2_selected_pt2_max(pt2_max)
else
pt2_max = 1.d-3
call ezfio_set_cisd_sc2_selected_pt2_max(pt2_max)
endif
print*,'pt2_max = ',pt2_max
END_PROVIDER
BEGIN_PROVIDER [ logical, do_pt2_end ]
implicit none
BEGIN_DOC
! Get do_pt2_end from EZFIO file
END_DOC
logical :: has_do_pt2_end
PROVIDE ezfio_filename
call ezfio_has_cisd_sc2_selected_do_pt2_end(has_do_pt2_end)
if (has_do_pt2_end) then
call ezfio_get_cisd_sc2_selected_do_pt2_end(do_pt2_end)
else
do_pt2_end = .True.
call ezfio_set_cisd_sc2_selected_do_pt2_end(do_pt2_end)
endif
print*,'do_pt2_end = ',do_pt2_end
END_PROVIDER

2
src/CISD_selected/NEEDED_MODULES
View File

@ -1,2 +1,2 @@
AOs BiInts Bitmask CISD Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils
AOs Bielec_integrals Bitmask CISD Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils

2
src/DDCI_selected/NEEDED_MODULES
View File

@ -1,2 +1,2 @@
AOs BiInts Bitmask Dets Electrons Ezfio_files Generators_CAS Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils
AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Generators_CAS Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils

2
src/Dets/NEEDED_MODULES
View File

@ -1 +1 @@
AOs BiInts Bitmask Electrons Ezfio_files MonoInts MOs Nuclei Output Utils
AOs Bielec_integrals Bitmask Electrons Ezfio_files MonoInts MOs Nuclei Output Utils

23
src/Dets/det_svd.irp.f
View File

@ -3,7 +3,7 @@ program det_svd
BEGIN_DOC
! Computes the SVD of the Alpha x Beta determinant coefficient matrix
END_DOC
integer :: i,j
integer :: i,j,k
read_wf = .True.
TOUCH read_wf
@ -40,17 +40,22 @@ program det_svd
print *, 'N_det_alpha = ', N_det_alpha_unique
print *, 'N_det_beta = ', N_det_beta_unique
print *, ''
! do i=1,N_det_alpha_unique
! do j=1,N_det_beta_unique
! print *, i,j,psi_svd_matrix(i,j,:)
! enddo
! enddo
print *, ''
call diagonalize_ci
print *, 'Energy = ', ci_energy
do i=1,N_det_alpha_unique
do j=1,N_det_beta_unique
do k=1,N_states
if (dabs(psi_svd_matrix(i,j,k)) < 1.d-15) then
psi_svd_matrix(i,j,k) = 0.d0
endif
enddo
enddo
enddo
print *, ''
print *, psi_svd_coefs(1:20,1)
! call save_wavefunction
call save_wavefunction
end

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

@ -42,8 +42,10 @@ subroutine save_dets_qmcchem
enddo
close(31)
call system('gzip -f '//trim(ezfio_filename)//'/mo_basis/mo_classif')
end
program save_for_qmc
call save_dets_qmcchem
call write_spindeterminants
end

4
src/Dets/spindeterminants.ezfio_config
View File

@ -7,4 +7,8 @@ spindeterminants
psi_det_alpha integer*8 (spindeterminants_n_int*spindeterminants_bit_kind/8,spindeterminants_n_det_alpha)
psi_det_beta integer*8 (spindeterminants_n_int*spindeterminants_bit_kind/8,spindeterminants_n_det_beta)
psi_coef_matrix double precision (spindeterminants_n_det_alpha,spindeterminants_n_det_beta,spindeterminants_n_states)
n_svd_coefs integer
psi_svd_alpha double precision (spindeterminants_n_det_alpha,spindeterminants_n_svd_coefs,spindeterminants_n_states)
psi_svd_beta double precision (spindeterminants_n_det_beta,spindeterminants_n_svd_coefs,spindeterminants_n_states)
psi_svd_coefs double precision (spindeterminants_n_svd_coefs,spindeterminants_n_states)

51
src/Dets/spindeterminants.irp.f
View File

@ -26,7 +26,7 @@ subroutine write_spindeterminants
enddo
call ezfio_set_spindeterminants_psi_det_alpha(psi_det_alpha_unique)
deallocate(tmpdet)
allocate(tmpdet(N_int2,N_det_beta_unique))
do i=1,N_det_beta_unique
do k=1,N_int
@ -38,7 +38,54 @@ subroutine write_spindeterminants
enddo
call ezfio_set_spindeterminants_psi_det_beta(psi_det_beta_unique)
deallocate(tmpdet)
call ezfio_set_spindeterminants_psi_coef_matrix(psi_svd_matrix)
integer :: n_svd_coefs
double precision :: norm, f
f = 1.d0/dble(N_states)
norm = 1.d0
do n_svd_coefs=1,N_det_alpha_unique
do k=1,N_states
norm -= psi_svd_coefs(n_svd_coefs,k)*psi_svd_coefs(n_svd_coefs,k)
enddo
if (norm < 1.d-6) then
exit
endif
enddo
n_svd_coefs -= 1
call ezfio_set_spindeterminants_n_svd_coefs(n_svd_coefs)
double precision, allocatable :: dtmp(:,:,:)
allocate(dtmp(N_det_alpha_unique,n_svd_coefs,N_states))
do k=1,N_states
do j=1,n_svd_coefs
do i=1,N_det_alpha_unique
dtmp(i,j,k) = psi_svd_alpha(i,j,k)
enddo
enddo
enddo
call ezfio_set_spindeterminants_psi_svd_alpha(dtmp)
deallocate(dtmp)
allocate(dtmp(N_det_beta_unique,n_svd_coefs,N_states))
do k=1,N_states
do j=1,n_svd_coefs
do i=1,N_det_beta_unique
dtmp(i,j,k) = psi_svd_beta(i,j,k)
enddo
enddo
enddo
call ezfio_set_spindeterminants_psi_svd_beta(dtmp)
deallocate(dtmp)
allocate(dtmp(n_svd_coefs,N_states,1))
do k=1,N_states
do j=1,n_svd_coefs
dtmp(j,k,1) = psi_svd_coefs(j,k)
enddo
enddo
call ezfio_set_spindeterminants_psi_svd_coefs(dtmp)
deallocate(dtmp)
end

2
src/FCIdump/NEEDED_MODULES
View File

@ -1 +1 @@
AOs BiInts Bitmask Dets Electrons Ezfio_files MonoInts MOs Nuclei Output Utils
AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files MonoInts MOs Nuclei Output Utils

6
src/Full_CI/EZFIO.cfg
View File

@ -18,7 +18,7 @@ default: true
[PT2_max]
type: PT2_energy
doc: The selection process stops when the largest PT2 (for all the state is lower
doc: The selection process stops when the largest PT2 (for all the state) is lower
than pt2_max in absolute value
interface: input
default: 0.0001
@ -32,11 +32,11 @@ default: 0.75
[energy]
type: double precision
doc: "Calculated Full CI energy"
doc: Calculated Selected FCI energy
interface: output
[energy_pt2]
type: double precision
doc: "Calculated Full CI energy"
doc: Calculated FCI energy + PT2
interface: output

2
src/Full_CI/NEEDED_MODULES
View File

@ -1,2 +1,2 @@
AOs BiInts Bitmask Dets Electrons Ezfio_files Generators_full Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils
AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Generators_full Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils

2
src/Generators_CAS/NEEDED_MODULES
View File

@ -1 +1 @@
AOs BiInts Bitmask Dets Electrons Ezfio_files MonoInts MOs Nuclei Output Utils
AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files MonoInts MOs Nuclei Output Utils

2
src/Generators_full/NEEDED_MODULES
View File

@ -1,2 +1,2 @@
AOs BiInts Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Utils
AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Utils

2
src/Generators_restart/NEEDED_MODULES
View File

@ -1 +1 @@
AOs BiInts Bitmask Dets Electrons Ezfio_files MonoInts MOs Nuclei Output Utils
AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files MonoInts MOs Nuclei Output Utils

22
src/Hartree_Fock/EZFIO.cfg Normal file
View File

@ -0,0 +1,22 @@
[thresh_scf]
type: Threshold
doc: Threshold on the convergence of the Hartree Fock energy
interface: input
default: 1.e-10
[n_it_scf_max]
type: Strictly_positive_int
doc: Maximum number of SCF iterations
interface: input
default: 200
[mo_guess_type]
type: MO_guess
doc: Initial MO guess. Can be [ Huckel | HCore ]
interface: input
default: Huckel
[energy]
type: double precision
doc: Calculated HF energy
interface: output

2
src/Hartree_Fock/NEEDED_MODULES
View File

@ -1 +1 @@
AOs BiInts Bitmask Electrons Ezfio_files MonoInts MOGuess MOs Nuclei Output Utils
AOs Bielec_integrals Bitmask Electrons Ezfio_files MonoInts MOGuess MOs Nuclei Output Utils

6
src/Hartree_Fock/hartree_fock.ezfio_config
View File

@ -1,6 +0,0 @@
hartree_fock
thresh_scf double precision
n_it_scf_max integer
energy double precision
guess character*(32)

35
src/Hartree_Fock/options.irp.f
View File

@ -1,35 +0,0 @@
BEGIN_SHELL [ /usr/bin/python ]
from ezfio_with_default import EZFIO_Provider
T = EZFIO_Provider()
T.set_type ( "double precision" )
T.set_name ( "thresh_SCF" )
T.set_doc ( "Threshold on the convergence of the Hartree Fock energy" )
T.set_ezfio_dir ( "Hartree_Fock" )
T.set_ezfio_name( "thresh_SCF" )
T.set_output ( "output_Hartree_Fock" )
print T
T = EZFIO_Provider()
T.set_type ( "integer" )
T.set_name ( "n_it_scf_max" )
T.set_doc ( "Maximum number of SCF iterations" )
T.set_ezfio_dir ( "Hartree_Fock" )
T.set_ezfio_name( "n_it_scf_max" )
T.set_output ( "output_Hartree_Fock" )
print T
T = EZFIO_Provider()
T.set_type ( "character*(32)" )
T.set_name ( "mo_guess_type" )
T.set_doc ( "Initial MO guess. Can be [ Huckel | HCore ]" )
T.set_ezfio_dir ( "Hartree_Fock" )
T.set_ezfio_name( "guess" )
T.set_output ( "output_Hartree_Fock" )
print T
END_SHELL

2
src/MP2/NEEDED_MODULES
View File

@ -1,2 +1,2 @@
AOs BiInts Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils
AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils

5
src/MRCC/EZFIO.cfg
View File

@ -1,5 +1,4 @@
[energy]
type: double precision
doc: "Calculated MRCC energy"
interface: output
doc: Calculated MRCC energy
interface: output

2
src/MRCC/NEEDED_MODULES
View File

@ -1,2 +1,2 @@
AOs BiInts Bitmask Dets Electrons Ezfio_files Generators_full Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils
AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Generators_full Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils

87
src/MRCC/README.rst
View File

@ -1,82 +1,9 @@
E(CAS+SD) = -3.93510180989509
-0.726935163332
++++----
++++----
0.685482292841
+++-+---
+++-+---
0.0409791961003
++-+-+--
++-+-+--
c2*c3/c1 = -0.038642391672
-0.996413146877
++++----
++++----
-0.0598366139154
++-+-+--
+++-+---
-0.0598366139154
+++-+---
++-+-+--
=======
0.706616635698
+++-+---
+++-+---
-0.692594178414
++++----
++++----
-0.0915716740265
++-+-+--
+++-+---
-0.0915716740265
+++-+---
++-+-+--
0.0461418323107
++-+-+--
++-+-+--
-0.0458957789452
++--++--
++--++--
----
0.713102867186
++++----
++++----
-0.688067688244
+++-+---
+++-+---
0.089262694488
+++-+---
++-+-+--
0.089262694488
++-+-+--
+++-+---
-0.0459510603899
++-+-+--
++-+-+--
===========
MRCC Module
===========
Needed Modules
==============
Documentation
=============

2
src/NEEDED_MODULES
View File

@ -1 +1 @@
AOs BiInts Bitmask CID CID_SC2_selected CID_selected CIS CISD CISD_selected CISD_SC2_selected Dets Electrons Ezfio_files Full_CI Generators_full Hartree_Fock MOGuess MonoInts MOs MP2 Nuclei Output Selectors_full Utils Molden FCIdump Generators_CAS CAS_SD DDCI_selected MRCC
AOs Bielec_integrals Bitmask CID CID_SC2_selected CID_selected CIS CISD CISD_selected CISD_SC2_selected Dets Electrons Ezfio_files Full_CI Generators_full Hartree_Fock MOGuess MonoInts MOs MP2 Nuclei Output Selectors_full Utils Molden FCIdump Generators_CAS CAS_SD DDCI_selected MRCC

2
src/Perturbation/NEEDED_MODULES
View File

@ -1,2 +1,2 @@
AOs BiInts Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Properties Utils
AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Properties Utils

2
src/Properties/NEEDED_MODULES
View File

@ -1 +1 @@
AOs BiInts Bitmask Dets Electrons Ezfio_files MonoInts MOs Nuclei Output Utils
AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files MonoInts MOs Nuclei Output Utils

2
src/Selectors_full/NEEDED_MODULES
View File

@ -1,2 +1,2 @@
AOs BiInts Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Utils
AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Utils

2
src/Selectors_no_sorted/NEEDED_MODULES
View File

@ -1 +1 @@
AOs BiInts Bitmask Dets Electrons Ezfio_files MonoInts MOs Nuclei Output Utils
AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files MonoInts MOs Nuclei Output Utils

309
tests/unit_test/unit_test.py Executable file
View File

@ -0,0 +1,309 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import unittest
import subprocess
import os
import sys
qpackage_root = os.environ['QPACKAGE_ROOT']
EZFIO = "{0}/EZFIO".format(qpackage_root)
sys.path = [EZFIO + "/Python"] + sys.path
from ezfio import ezfio
from collections import defaultdict
# ~#~#~ #
# O p t #
# ~#~#~ #
precision = 5.e-8
# A test get a geo file and a basis file.
# A global dict containt the result for this test
# A test return True or Raise a error !
# More ezfio condition you set, beter it is
# You cannot order the test flow.
# So if you dont whant to remarque on test (for example the HF), set
# a global variable and check for it
global has_hf_alredy
has_hf_alredy = False
global filename_check
def init_folder(geo, basis, mult=1, ezfio_name=None):
'''
Take a geo in arg (aka a existing geo.xyz in test/)
And create the geo.ezfio with the adeguate basis and multipliciti
DO NOT CHECK IS THE EZFIO FOLDER ALREADY EXIST
'''
cmd = "cp {0}/tests/{1}.xyz .".format(qpackage_root, geo)
subprocess.check_call([cmd], shell=True)
if not ezfio_name:
ezfio_name = geo
cmd = "qp_create_ezfio_from_xyz -b {0} -m {1} {2}.xyz -o {3}.ezfio"
subprocess.check_call([cmd.format(basis, mult, geo, ezfio_name)],
shell=True)
def get_error_message(l_exepected, l_cur):
l_msg = ["Need {0} get {1} error is {2}".format(i, j, abs(i - j))
for i, j in zip(l_exepected, l_cur)]
return "\n".join(l_msg)
# _
# / |_ _ _ | o ._ ._ _|_
# \_ | | (/_ (_ |< | | | |_) |_| |_
# |
def check_disk_acess(geo, basis, mult=1):
import uuid
filename = str(uuid.uuid4())
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
init_folder(geo, basis, mult, ezfio_name=filename)
ezfio.set_file("{0}.ezfio".format(filename))
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# S e t _ p a r a m e t e r #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# Test 1
ezfio.bielec_integrals_disk_access_ao_integrals = "Write"
cmd = "qp_edit -c {0}.ezfio".format(filename)
subprocess.check_call([cmd], shell=True)
# Test 2
ezfio.bielec_integrals_disk_access_ao_integrals = "IculeAcess"
cmd = "qp_edit -c {0}.ezfio".format(filename)
try:
subprocess.check_call([cmd], shell=True)
return_code = False
except subprocess.CalledProcessError:
return_code = True
# ~#~#~#~#~#~#~#~ #
# F i n a l i z e #
# ~#~#~#~#~#~#~#~ #
if return_code:
subprocess.call(["rm -R {0}.ezfio".format(filename)], shell=True)
return return_code
def check_mo_guess(geo, basis, mult=1):
import uuid
filename = str(uuid.uuid4())
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
init_folder(geo, basis, mult, ezfio_name=filename)
ezfio.set_file("{0}.ezfio".format(filename))
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# S e t _ p a r a m e t e r #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# Test 1
ezfio.hartree_fock_mo_guess_type = "Huckel"
cmd = "qp_edit -c {0}.ezfio".format(filename)
subprocess.check_call([cmd], shell=True)
# Test 2
ezfio.hartree_fock_mo_guess_type = "IculeGuess"
cmd = "qp_edit -c {0}.ezfio".format(filename)
try:
subprocess.check_call([cmd], shell=True)
return_code = False
except subprocess.CalledProcessError:
return_code = True
# ~#~#~#~#~#~#~#~ #
# F i n a l i z e #
# ~#~#~#~#~#~#~#~ #
if return_code:
subprocess.call(["rm -R {0}.ezfio".format(filename)], shell=True)
return return_code
# _
# / |_ _ _ | _. | _ _
# \_ | | (/_ (_ |< \/ (_| | |_| (/_ _>
#
def run_hf(geo, basis, mult=1):
"""
Run a simle by default hf
EZFIO path = geo.ezfio
"""
# ~#~#~#~#~#~#~#~#~#~ #
# R e f _ e n e r g y #
# ~#~#~#~#~#~#~#~#~#~ #
ref_energy = defaultdict(dict)
ref_energy["sto-3g"]["methane"] = -39.7267433402
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
# G l o b a l _ v a r i a b l e #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
global has_hf_alredy
has_hf_alredy = True
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
init_folder(geo, basis, mult)
ezfio.set_file("{0}.ezfio".format(geo))
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# S e t _ p a r a m e t e r #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
ezfio.bielec_integrals_direct = False
ezfio.bielec_integrals_threshold_ao = 1.e-15
ezfio.bielec_integrals_disk_access_ao_integrals = "None"
ezfio.bielec_integrals_threshold_mo = 1.e-15
ezfio.bielec_integrals_disk_access_mo_integrals = "None"
ezfio.hartree_fock_mo_guess_type = "Huckel"
ezfio.hartree_fock_thresh_scf = 1.e-10
ezfio.hartree_fock_n_it_scf_max = 100
# ~#~#~ #
# R u n #
# ~#~#~ #
cmd = "qp_run SCF {0}.ezfio/".format(geo)
subprocess.check_call([cmd], shell=True)
# ~#~#~#~#~ #
# C h e c k #
# ~#~#~#~#~ #
cur_e = ezfio.get_hartree_fock_energy()
ref_e = ref_energy[basis][geo]
if abs(cur_e - ref_e) <= precision:
return True
else:
raise ValueError(get_error_message([ref_e], [cur_e]))
def run_full_ci_10k_pt2_end(geo, basis):
"""
Run a Full_ci with 10k with the TruePT2
EZFIO path = geo.ezfio
"""
# ~#~#~#~#~#~#~#~#~#~ #
# R e f _ e n e r g y #
# ~#~#~#~#~#~#~#~#~#~ #
ref_energy_var = defaultdict(dict)
ref_energy_pt2 = defaultdict(dict)
ref_energy_var["sto-3g"]["methane"] = -0.398058753535695E+02
ref_energy_pt2["sto-3g"]["methane"] = -0.398059182483741E+02
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
ezfio.set_file("{0}.ezfio".format(geo))
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# S e t _ p a r a m e t e r #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
ezfio.full_ci_do_pt2_end = True
ezfio.full_ci_n_det_max_fci = 10000
ezfio.full_ci_pt2_max = 1.e-8
# ~#~#~ #
# R u n #
# ~#~#~ #
cmd = "qp_run full_ci {0}.ezfio/".format(geo)
subprocess.check_call([cmd], shell=True)
# ~#~#~#~#~ #
# C h e c k #
# ~#~#~#~#~ #
cur_var = ezfio.get_full_ci_energy()
cur_pt2 = ezfio.get_full_ci_energy_pt2()
ref_var = ref_energy_var[basis][geo]
ref_pt2 = ref_energy_pt2[basis][geo]
t = [abs(cur_var - ref_var) <= precision,
abs(cur_pt2 - ref_pt2) <= precision]
if all(t):
return True
else:
raise ValueError(get_error_message([ref_var, ref_pt2],
[cur_var, cur_pt2]))
def hf_then_10k_test(geo, basis):
if not has_hf_alredy:
run_hf(geo, basis)
try:
run_full_ci_10k_pt2_end(geo, basis)
return_code = True
except:
return_code = False
# ~#~#~#~#~#~#~#~ #
# F i n a l i z e #
# ~#~#~#~#~#~#~#~ #
if return_code:
subprocess.call(["rm -R {0}.ezfio".format(geo)], shell=True)
return return_code
# ___
# | _ _ _|_
# | (/_ _> |_
#
class ValueTest(unittest.TestCase):
def test_full_ci_10k_pt2_end(self):
self.assertTrue(hf_then_10k_test("methane", "sto-3g"))
class InputTest(unittest.TestCase):
def test_check_disk_acess(self):
self.assertTrue(check_disk_acess("methane", "un-ccemd-ref"))
def test_check_mo_guess(self):
self.assertTrue(check_mo_guess("methane", "maug-cc-pVDZ"))
if __name__ == '__main__':
unittest.main()