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Merge pull request #2 from TApplencourt/master

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Add EZFIO.cfg
This commit is contained in:
Anthony Scemama 2015-03-30 18:59:31 +02:00
commit 98da6c7a3e
33 changed files with 1404 additions and 750 deletions
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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

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
data/ezfio_defaults/.empty Normal file
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9
data/ezfio_defaults/bi_integrals.ezfio_default Normal file
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@ -0,0 +1,9 @@
bielec_integrals
read_ao_integrals False
read_mo_integrals False
write_ao_integrals False
write_mo_integrals False
threshold_ao 1.e-15
threshold_mo 1.e-15
direct False

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

5
data/ezfio_defaults/cisd_sc2.ezfio_default Normal file
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@ -0,0 +1,5 @@
cisd_sc2_selected
n_det_max_cisd_sc2 10000
pt2_max 1.e-4
do_pt2_end True

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

0
data/ezfio_defaults → data/ezfio_defaults/q_package.ezfio_default
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2
ocaml/Input.ml
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@ -7,6 +7,7 @@ include Input_ao_basis;;
include Input_bi_integrals;;
include Input_bitmasks;;
include Input_cisd_sc2;;
include Input_cisd_sc2_selected;;
include Input_determinants;;
include Input_electrons;;
include Input_full_ci;;
@ -14,4 +15,3 @@ include Input_hartree_fock;;
include Input_mo_basis;;
include Input_nuclei;;

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.lowercase (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
;;

6
ocaml/qp_edit.ml
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@ -13,6 +13,7 @@ type keyword =
| Ao_basis
| Bielec_integrals
| Cisd_sc2
| Cisd_sc2_selected
| Determinants
| Electrons
| Full_ci
@ -26,6 +27,7 @@ let keyword_to_string = function
| Ao_basis -> "AO basis"
| Bielec_integrals -> "Two electron integrals"
| Cisd_sc2 -> "CISD (SC)^2"
| Cisd_sc2_selected -> "CISD (SC)^2 selected"
| Determinants -> "Determinants"
| Electrons -> "Electrons"
| Full_ci -> "Selected Full-CI"
@ -80,6 +82,8 @@ let get s =
f Electrons.(read, to_rst)
| Cisd_sc2 ->
f Cisd_sc2.(read, to_rst)
| Cisd_sc2_selected ->
f Cisd_sc2_selected.(read, to_rst)
| Nuclei ->
f Nuclei.(read, to_rst)
| Ao_basis ->
@ -129,6 +133,7 @@ let set str s =
| Full_ci -> write Full_ci.(of_rst, write) s
| Electrons -> write Electrons.(of_rst, write) s
| Cisd_sc2 -> write Cisd_sc2.(of_rst, write) s
| Cisd_sc2_selected -> write Cisd_sc2_selected.(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
@ -179,6 +184,7 @@ let run check_only ezfio_filename =
Bielec_integrals ;
Hartree_fock ;
Cisd_sc2 ;
Cisd_sc2_selected ;
Full_ci ;
Mo_basis;
Determinants ;

333
scripts/ezfio_interface.py
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@ -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"] == "output":
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 += 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()

5
scripts/ezfio_interface/convert_ezfio.sh Normal file
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#!/bin/bash
# Convert a old ezfio file (with option.irp.f ezfio_default)
# into a new EZFIO.cfg type
mv $1/Hartree_Fock $1/hartree_fock
mv $1/hartree_Fock/thresh_SCF $1/hartree_fock/thresh_scf

640
scripts/ezfio_interface/ei_handler.py Executable file
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#!/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
Ezfio_dir : is equal to MODULE.lower!
Format specification :
[provider_name] : the name of the provider in irp.f90
- doc : Is the doc
- Type : Is a fancy_type support by the ocaml
- ezfio_name : Will be the name of the file for the ezfio
(optional by default is the name of the provider)
- interface : The provider is a imput or a output
- default : The default value if interface == input:
- size : Is the string read in ezfio.cgf who containt the size information
(like 1 or =sum(ao_num) or (ao_num,3) )
Example 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
```
"""
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 convert into
fortran and ocaml one.
"""
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 Ocam 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['MO_guess'] = Type("MO_guess", "string", "character*(32)")
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
src = qpackage_root + "/ocaml/qptypes_generator.ml"
with open(src, "r") as f:
l = [i for i in f.read().splitlines() if i.strip().startswith("*")]
# Read the fancy_type, the ocaml. and convert the ocam to the fortran
for i in l:
str_fancy_type = i.split()[1].strip()
str_ocaml_type = i.split()[3]
str_fortran_type = ocaml_to_fortran[str_ocaml_type]
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)
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_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_provider = []
l_type = []
l_doc = []
for k, v in dict_ezfio_cfg.iteritems():
if v['interface'] == "input":
l_provider.append(k)
l_type.append(v["type"])
l_doc.append(v["doc"])
e_glob = EZFIO_ocaml(l_provider=l_provider,
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 "full_ci";;',
'']
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 main():
"""
Two condition:
-Take the EZFIO.cfg path in arg
or
-Look if EZFIO.cfg is present in the pwd
Return : - ezfio_interface.irp.f
- folder_ezfio_inteface_config
"""
# ~#~#~#~# #
# I n i t #
# ~#~#~#~# #
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)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
# 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 c a m l #
# ~#~#~#~#~#~#
str_ocaml_input = create_ocaml_input(dict_ezfio_cfg, module_lower)
save_ocaml_input(module_lower, str_ocaml_input)
# ~#~#~#~#~#~#~#~#
# I R P . f 9 0 #
# ~#~#~#~#~#~#~#~#
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 #
# ~#~#~#~#~#~#~#~#~#~#~#~# #
str_ezfio_config = create_ezfio_config(dict_ezfio_cfg)
save_ezfio_config(module_lower, str_ezfio_config)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
# e z f i o _ d e f a u l t #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
str_ezfio_default = create_ezfio_default(dict_ezfio_cfg)
save_ezfio_default(module_lower, str_ezfio_default)
if __name__ == "__main__":
main()

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scripts/ezfio_interface/ezfio_generate_ocaml.py Executable file
View File

@ -0,0 +1,326 @@
#!/usr/bin/env python
import sys
# 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_provider = [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_provider", "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_provider, 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_provider = [provider_name, ...]
Return the read_global template
'''
# ~#~#~#~#~#~#~#~ #
# C h e c k i n g #
# ~#~#~#~#~#~#~#~ #
self.check_if_init(["l_provider"],
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_provider]
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_provider = [provider_name, ...]
Return the type template
'''
# ~#~#~#~#~#~#~#~ #
# C h e c k i n g #
# ~#~#~#~#~#~#~#~ #
self.check_if_init(["l_provider"],
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_provider]
l_template += [" } ="]
l_template += [" write_{0:<30} {0};".format(p) for p in self.l_provider]
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_provider = [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_provider", "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_provider]
l_template += ['"']
for p, t in zip(self.l_provider, 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_provider = [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_provider", "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_provider, self.l_doc):
l_template += ["{0} ::".format(d),
"",
" {0} = %s".format(p),
""]
l_template += ['"']
for p, t in zip(self.l_provider, 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)

96
scripts/ezfio_interface/ezfio_generate_provider.py Executable file
View File

@ -0,0 +1,96 @@
#!/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.
"""
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()

17
scripts/ezfio_with_default.py
View File

@ -90,10 +90,19 @@ END_PROVIDER
self.default = t
def get_default(self):
filename = '/'.join( [os.environ['QPACKAGE_ROOT'], 'data', 'ezfio_defaults'] )
file = open(filename,'r')
lines = file.readlines()
file.close()
from os import listdir
from os.path import isfile, join
mypath = '/'.join( [os.environ['QPACKAGE_ROOT'], 'data', 'ezfio_defaults','/'])
onlyfiles = [ f for f in listdir(mypath) if isfile(join(mypath,f)) ]
lines= []
for filename in onlyfiles:
file = open(mypath+filename,'r')
lines.extend(file.readlines()[:])
file.close()
# Search directory
for k,line in enumerate(lines):
if line[0] != ' ':

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

4
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

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: Get n_det_max_cisd_sc2 from EZFIO file
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 state) is lower
than pt2_max in absolute value
interface: input
default: 0.0001
[energy]
type: double precision
doc: "Calculated Full CI energy"
interface: output
[energy_pt2]
type: double precision
doc: "Calculated Full CI energy"
interface: output

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

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

16
src/Full_CI/EZFIO.cfg
View File

@ -1,42 +1,42 @@
[N_det_max_fci]
type: Det_number_max
doc: Max number of determinants in the wave function
interface: output
interface: input
default: 10000
[N_det_max_fci_property]
type: Det_number_max
doc: Max number of determinants in the wave function when you select for a given property
interface: output
interface: input
default: 10000
[do_pt2_end]
type: logical
doc: If true, compute the PT2 at the end of the selection
interface: output
interface: input
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: output
interface: input
default: 0.0001
[var_pt2_ratio]
type: Normalized_float
doc: The selection process stops when the energy ratio variational/(variational+PT2)
is equal to var_pt2_ratio
interface: output
interface: input
default: 0.75
[energy]
type: double precision
doc: "Calculated Full CI energy"
interface: input
interface: output
[energy_pt2]
type: double precision
doc: "Calculated Full CI energy"
interface: input
interface: output

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

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

181
tests/unit_test/unit_test.py Executable file
View File

@ -0,0 +1,181 @@
#!/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 = 1.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
def init_folder(geo, basis, mult=1):
'''
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)
cmd = "qp_create_ezfio_from_xyz -b {0} -m {1} {2}.xyz".format(basis,
mult,
geo)
subprocess.check_call([cmd], shell=True)
def get_error_message(l_exepected, l_cur):
l_msg = ["Need {0} get {1}".format(i,j) for i,j in zip(l_exepected,l_cur)]
return "\n".join(l_msg)
def run_hf(geo, basis):
"""
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)
ezfio.set_file("{0}.ezfio".format(geo))
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# S e t _ p a r a m e t e r #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
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 run_big_test(geo, basis):
if not has_hf_alredy:
run_hf(geo, basis)
run_full_ci_10k_pt2_end(geo, basis)
return True
class SimplisticTest(unittest.TestCase):
def test_full_ci_10k_pt2_end(self):
self.assertTrue(run_big_test("methane", "sto-3g"))
if __name__ == '__main__':
unittest.main()