mirror of
https://github.com/LCPQ/quantum_package
synced 2024-11-19 04:22:36 +01:00
Merge branch 'master' of github.com:scemama/quantum_package
This commit is contained in:
commit
ac285a09d9
2
Makefile
2
Makefile
@ -45,5 +45,5 @@ ocaml:
|
|||||||
|
|
||||||
veryclean:
|
veryclean:
|
||||||
rm -rf EZFIO
|
rm -rf EZFIO
|
||||||
$(MAKE) EZFIO
|
rm -rf resultsFile
|
||||||
$(MAKE) -C src veryclean
|
$(MAKE) -C src veryclean
|
||||||
|
|||||||
@ -1,19 +1,19 @@
|
|||||||
bielec_integrals
|
bielec_integrals
|
||||||
read_ao_integrals False
|
read_ao_integrals false
|
||||||
read_mo_integrals False
|
read_mo_integrals false
|
||||||
write_ao_integrals False
|
write_ao_integrals false
|
||||||
write_mo_integrals False
|
write_mo_integrals false
|
||||||
threshold_ao 1.e-15
|
threshold_ao 1.e-15
|
||||||
threshold_mo 1.e-15
|
threshold_mo 1.e-15
|
||||||
direct False
|
direct false
|
||||||
|
|
||||||
cis_dressed
|
cis_dressed
|
||||||
n_state_cis 10
|
n_state_cis 10
|
||||||
n_core_cis 0
|
n_core_cis 0
|
||||||
n_act_cis mo_basis_mo_tot_num
|
n_act_cis mo_basis_mo_tot_num
|
||||||
mp2_dressing False
|
mp2_dressing false
|
||||||
standard_doubles True
|
standard_doubles true
|
||||||
en_2_2 False
|
en_2_2 false
|
||||||
|
|
||||||
determinants
|
determinants
|
||||||
n_states 1
|
n_states 1
|
||||||
@ -21,27 +21,27 @@ determinants
|
|||||||
n_det_max_jacobi 1000
|
n_det_max_jacobi 1000
|
||||||
threshold_generators 0.99
|
threshold_generators 0.99
|
||||||
threshold_selectors 0.999
|
threshold_selectors 0.999
|
||||||
read_wf False
|
read_wf false
|
||||||
s2_eig False
|
s2_eig false
|
||||||
only_single_double_dm False
|
only_single_double_dm false
|
||||||
|
|
||||||
full_ci
|
full_ci
|
||||||
n_det_max_fci 10000
|
n_det_max_fci 10000
|
||||||
n_det_max_fci_property 50000
|
n_det_max_fci_property 50000
|
||||||
pt2_max 1.e-4
|
pt2_max 1.e-4
|
||||||
do_pt2_end True
|
do_pt2_end true
|
||||||
var_pt2_ratio 0.75
|
var_pt2_ratio 0.75
|
||||||
|
|
||||||
cas_sd
|
cas_sd
|
||||||
n_det_max_cas_sd 100000
|
n_det_max_cas_sd 100000
|
||||||
pt2_max 1.e-4
|
pt2_max 1.e-4
|
||||||
do_pt2_end True
|
do_pt2_end true
|
||||||
var_pt2_ratio 0.75
|
var_pt2_ratio 0.75
|
||||||
|
|
||||||
all_singles
|
all_singles
|
||||||
n_det_max_fci 50000
|
n_det_max_fci 50000
|
||||||
pt2_max 1.e-8
|
pt2_max 1.e-8
|
||||||
do_pt2_end False
|
do_pt2_end false
|
||||||
|
|
||||||
hartree_fock
|
hartree_fock
|
||||||
n_it_scf_max 200
|
n_it_scf_max 200
|
||||||
@ -55,7 +55,7 @@ cisd_selected
|
|||||||
cisd_sc2_selected
|
cisd_sc2_selected
|
||||||
n_det_max_cisd_sc2 10000
|
n_det_max_cisd_sc2 10000
|
||||||
pt2_max 1.e-4
|
pt2_max 1.e-4
|
||||||
do_pt2_end True
|
do_pt2_end true
|
||||||
|
|
||||||
properties
|
properties
|
||||||
z_one_point 3.9
|
z_one_point 3.9
|
||||||
|
|||||||
@ -1,9 +0,0 @@
|
|||||||
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
|
|
||||||
@ -1,2 +0,0 @@
|
|||||||
properties
|
|
||||||
z_one_point 3.9
|
|
||||||
4
ocaml/.merlin
Normal file
4
ocaml/.merlin
Normal file
@ -0,0 +1,4 @@
|
|||||||
|
PKG core ZMQ cryptokit
|
||||||
|
B _build/
|
||||||
|
|
||||||
|
|
||||||
@ -4,7 +4,7 @@ open Core.Std;;
|
|||||||
|
|
||||||
include Input_ao_basis;;
|
include Input_ao_basis;;
|
||||||
include Input_bitmasks;;
|
include Input_bitmasks;;
|
||||||
include Input_determinants;;
|
include Input_determinants_by_hand;;
|
||||||
include Input_electrons;;
|
include Input_electrons;;
|
||||||
include Input_mo_basis;;
|
include Input_mo_basis;;
|
||||||
include Input_nuclei;;
|
include Input_nuclei;;
|
||||||
|
|||||||
@ -2,20 +2,14 @@ open Qptypes;;
|
|||||||
open Qputils;;
|
open Qputils;;
|
||||||
open Core.Std;;
|
open Core.Std;;
|
||||||
|
|
||||||
module Determinants : sig
|
module Determinants_by_hand : sig
|
||||||
type t =
|
type t =
|
||||||
{ n_int : N_int_number.t;
|
{ n_int : N_int_number.t;
|
||||||
bit_kind : Bit_kind.t;
|
bit_kind : Bit_kind.t;
|
||||||
mo_label : MO_label.t;
|
|
||||||
n_det : Det_number.t;
|
n_det : Det_number.t;
|
||||||
n_states : States_number.t;
|
n_states : States_number.t;
|
||||||
n_states_diag : States_number.t;
|
n_states_diag : States_number.t;
|
||||||
n_det_max_jacobi : Strictly_positive_int.t;
|
|
||||||
threshold_generators : Threshold.t;
|
|
||||||
threshold_selectors : Threshold.t;
|
|
||||||
read_wf : bool;
|
|
||||||
expected_s2 : Positive_float.t;
|
expected_s2 : Positive_float.t;
|
||||||
s2_eig : bool;
|
|
||||||
psi_coef : Det_coef.t array;
|
psi_coef : Det_coef.t array;
|
||||||
psi_det : Determinant.t array;
|
psi_det : Determinant.t array;
|
||||||
} with sexp
|
} with sexp
|
||||||
@ -28,16 +22,10 @@ end = struct
|
|||||||
type t =
|
type t =
|
||||||
{ n_int : N_int_number.t;
|
{ n_int : N_int_number.t;
|
||||||
bit_kind : Bit_kind.t;
|
bit_kind : Bit_kind.t;
|
||||||
mo_label : MO_label.t;
|
|
||||||
n_det : Det_number.t;
|
n_det : Det_number.t;
|
||||||
n_states : States_number.t;
|
n_states : States_number.t;
|
||||||
n_states_diag : States_number.t;
|
n_states_diag : States_number.t;
|
||||||
n_det_max_jacobi : Strictly_positive_int.t;
|
|
||||||
threshold_generators : Threshold.t;
|
|
||||||
threshold_selectors : Threshold.t;
|
|
||||||
read_wf : bool;
|
|
||||||
expected_s2 : Positive_float.t;
|
expected_s2 : Positive_float.t;
|
||||||
s2_eig : bool;
|
|
||||||
psi_coef : Det_coef.t array;
|
psi_coef : Det_coef.t array;
|
||||||
psi_det : Determinant.t array;
|
psi_det : Determinant.t array;
|
||||||
} with sexp
|
} with sexp
|
||||||
@ -77,22 +65,6 @@ end = struct
|
|||||||
|> Ezfio.set_determinants_bit_kind
|
|> Ezfio.set_determinants_bit_kind
|
||||||
;;
|
;;
|
||||||
|
|
||||||
|
|
||||||
let read_mo_label () =
|
|
||||||
if (not (Ezfio.has_determinants_mo_label ())) then
|
|
||||||
Ezfio.get_mo_basis_mo_label ()
|
|
||||||
|> Ezfio.set_determinants_mo_label
|
|
||||||
;
|
|
||||||
Ezfio.get_determinants_mo_label ()
|
|
||||||
|> MO_label.of_string
|
|
||||||
;;
|
|
||||||
|
|
||||||
let write_mo_label l =
|
|
||||||
MO_label.to_string l
|
|
||||||
|> Ezfio.set_determinants_mo_label
|
|
||||||
;;
|
|
||||||
|
|
||||||
|
|
||||||
let read_n_det () =
|
let read_n_det () =
|
||||||
if not (Ezfio.has_determinants_n_det ()) then
|
if not (Ezfio.has_determinants_n_det ()) then
|
||||||
Ezfio.set_determinants_n_det 1
|
Ezfio.set_determinants_n_det 1
|
||||||
@ -138,67 +110,6 @@ end = struct
|
|||||||
Ezfio.set_determinants_n_states_diag (max n_states n)
|
Ezfio.set_determinants_n_states_diag (max n_states n)
|
||||||
;;
|
;;
|
||||||
|
|
||||||
|
|
||||||
let read_n_det_max_jacobi () =
|
|
||||||
if not (Ezfio.has_determinants_n_det_max_jacobi ()) then
|
|
||||||
get_default "n_det_max_jacobi"
|
|
||||||
|> Int.of_string
|
|
||||||
|> Ezfio.set_determinants_n_det_max_jacobi
|
|
||||||
;
|
|
||||||
Ezfio.get_determinants_n_det_max_jacobi ()
|
|
||||||
|> Strictly_positive_int.of_int
|
|
||||||
;;
|
|
||||||
|
|
||||||
let write_n_det_max_jacobi n =
|
|
||||||
Strictly_positive_int.to_int n
|
|
||||||
|> Ezfio.set_determinants_n_det_max_jacobi
|
|
||||||
;;
|
|
||||||
|
|
||||||
|
|
||||||
let read_threshold_generators () =
|
|
||||||
if not (Ezfio.has_determinants_threshold_generators ()) then
|
|
||||||
get_default "threshold_generators"
|
|
||||||
|> Float.of_string
|
|
||||||
|> Ezfio.set_determinants_threshold_generators
|
|
||||||
;
|
|
||||||
Ezfio.get_determinants_threshold_generators ()
|
|
||||||
|> Threshold.of_float
|
|
||||||
;;
|
|
||||||
|
|
||||||
let write_threshold_generators t =
|
|
||||||
Threshold.to_float t
|
|
||||||
|> Ezfio.set_determinants_threshold_generators
|
|
||||||
;;
|
|
||||||
|
|
||||||
|
|
||||||
let read_threshold_selectors () =
|
|
||||||
if not (Ezfio.has_determinants_threshold_selectors ()) then
|
|
||||||
get_default "threshold_selectors"
|
|
||||||
|> Float.of_string
|
|
||||||
|> Ezfio.set_determinants_threshold_selectors
|
|
||||||
;
|
|
||||||
Ezfio.get_determinants_threshold_selectors ()
|
|
||||||
|> Threshold.of_float
|
|
||||||
;;
|
|
||||||
|
|
||||||
let write_threshold_selectors t =
|
|
||||||
Threshold.to_float t
|
|
||||||
|> Ezfio.set_determinants_threshold_selectors
|
|
||||||
;;
|
|
||||||
|
|
||||||
|
|
||||||
let read_read_wf () =
|
|
||||||
if not (Ezfio.has_determinants_read_wf ()) then
|
|
||||||
get_default "read_wf"
|
|
||||||
|> Bool.of_string
|
|
||||||
|> Ezfio.set_determinants_read_wf
|
|
||||||
;
|
|
||||||
Ezfio.get_determinants_read_wf ()
|
|
||||||
;;
|
|
||||||
|
|
||||||
let write_read_wf = Ezfio.set_determinants_read_wf ;;
|
|
||||||
|
|
||||||
|
|
||||||
let read_expected_s2 () =
|
let read_expected_s2 () =
|
||||||
if not (Ezfio.has_determinants_expected_s2 ()) then
|
if not (Ezfio.has_determinants_expected_s2 ()) then
|
||||||
begin
|
begin
|
||||||
@ -219,19 +130,6 @@ end = struct
|
|||||||
|> Ezfio.set_determinants_expected_s2
|
|> Ezfio.set_determinants_expected_s2
|
||||||
;;
|
;;
|
||||||
|
|
||||||
|
|
||||||
let read_s2_eig () =
|
|
||||||
if not (Ezfio.has_determinants_s2_eig ()) then
|
|
||||||
get_default "s2_eig"
|
|
||||||
|> Bool.of_string
|
|
||||||
|> Ezfio.set_determinants_s2_eig
|
|
||||||
;
|
|
||||||
Ezfio.get_determinants_s2_eig ()
|
|
||||||
;;
|
|
||||||
|
|
||||||
let write_s2_eig = Ezfio.set_determinants_s2_eig ;;
|
|
||||||
|
|
||||||
|
|
||||||
let read_psi_coef () =
|
let read_psi_coef () =
|
||||||
if not (Ezfio.has_determinants_psi_coef ()) then
|
if not (Ezfio.has_determinants_psi_coef ()) then
|
||||||
begin
|
begin
|
||||||
@ -315,16 +213,10 @@ end = struct
|
|||||||
Some
|
Some
|
||||||
{ n_int = read_n_int () ;
|
{ n_int = read_n_int () ;
|
||||||
bit_kind = read_bit_kind () ;
|
bit_kind = read_bit_kind () ;
|
||||||
mo_label = read_mo_label () ;
|
|
||||||
n_det = read_n_det () ;
|
n_det = read_n_det () ;
|
||||||
n_states = read_n_states () ;
|
n_states = read_n_states () ;
|
||||||
n_states_diag = read_n_states_diag () ;
|
n_states_diag = read_n_states_diag () ;
|
||||||
n_det_max_jacobi = read_n_det_max_jacobi () ;
|
|
||||||
threshold_generators = read_threshold_generators () ;
|
|
||||||
threshold_selectors = read_threshold_selectors () ;
|
|
||||||
read_wf = read_read_wf () ;
|
|
||||||
expected_s2 = read_expected_s2 () ;
|
expected_s2 = read_expected_s2 () ;
|
||||||
s2_eig = read_s2_eig () ;
|
|
||||||
psi_coef = read_psi_coef () ;
|
psi_coef = read_psi_coef () ;
|
||||||
psi_det = read_psi_det () ;
|
psi_det = read_psi_det () ;
|
||||||
}
|
}
|
||||||
@ -334,31 +226,19 @@ end = struct
|
|||||||
|
|
||||||
let write { n_int ;
|
let write { n_int ;
|
||||||
bit_kind ;
|
bit_kind ;
|
||||||
mo_label ;
|
|
||||||
n_det ;
|
n_det ;
|
||||||
n_states ;
|
n_states ;
|
||||||
n_states_diag ;
|
n_states_diag ;
|
||||||
n_det_max_jacobi ;
|
|
||||||
threshold_generators ;
|
|
||||||
threshold_selectors ;
|
|
||||||
read_wf ;
|
|
||||||
expected_s2 ;
|
expected_s2 ;
|
||||||
s2_eig ;
|
|
||||||
psi_coef ;
|
psi_coef ;
|
||||||
psi_det ;
|
psi_det ;
|
||||||
} =
|
} =
|
||||||
write_n_int n_int ;
|
write_n_int n_int ;
|
||||||
write_bit_kind bit_kind;
|
write_bit_kind bit_kind;
|
||||||
write_mo_label mo_label;
|
|
||||||
write_n_det n_det;
|
write_n_det n_det;
|
||||||
write_n_states n_states;
|
write_n_states n_states;
|
||||||
write_n_states_diag ~n_states:n_states n_states_diag;
|
write_n_states_diag ~n_states:n_states n_states_diag;
|
||||||
write_n_det_max_jacobi n_det_max_jacobi;
|
|
||||||
write_threshold_generators threshold_generators;
|
|
||||||
write_threshold_selectors threshold_selectors;
|
|
||||||
write_read_wf read_wf;
|
|
||||||
write_expected_s2 expected_s2;
|
write_expected_s2 expected_s2;
|
||||||
write_s2_eig s2_eig;
|
|
||||||
write_psi_coef ~n_det:n_det psi_coef ~n_states:n_states;
|
write_psi_coef ~n_det:n_det psi_coef ~n_states:n_states;
|
||||||
write_psi_det ~n_int:n_int ~n_det:n_det psi_det;
|
write_psi_det ~n_int:n_int ~n_det:n_det psi_det;
|
||||||
;;
|
;;
|
||||||
@ -399,35 +279,17 @@ end = struct
|
|||||||
|> String.concat_array ~sep:"\n"
|
|> String.concat_array ~sep:"\n"
|
||||||
in
|
in
|
||||||
Printf.sprintf "
|
Printf.sprintf "
|
||||||
Read the current wave function ::
|
|
||||||
|
|
||||||
read_wf = %s
|
|
||||||
|
|
||||||
Label of the MOs on which the determinants were computed ::
|
|
||||||
|
|
||||||
mo_label = %s
|
|
||||||
|
|
||||||
Force the selected wave function to be an eigenfunction of S^2.
|
Force the selected wave function to be an eigenfunction of S^2.
|
||||||
If true, input the expected value of S^2 ::
|
If true, input the expected value of S^2 ::
|
||||||
|
|
||||||
s2_eig = %s
|
|
||||||
expected_s2 = %s
|
expected_s2 = %s
|
||||||
|
|
||||||
Thresholds on generators and selectors (fraction of the norm) ::
|
|
||||||
|
|
||||||
threshold_generators = %s
|
|
||||||
threshold_selectors = %s
|
|
||||||
|
|
||||||
Number of requested states, and number of states used for the
|
Number of requested states, and number of states used for the
|
||||||
Davidson diagonalization ::
|
Davidson diagonalization ::
|
||||||
|
|
||||||
n_states = %s
|
n_states = %s
|
||||||
n_states_diag = %s
|
n_states_diag = %s
|
||||||
|
|
||||||
Maximum size of the Hamiltonian matrix that will be fully diagonalized ::
|
|
||||||
|
|
||||||
n_det_max_jacobi = %s
|
|
||||||
|
|
||||||
Number of determinants ::
|
Number of determinants ::
|
||||||
|
|
||||||
n_det = %s
|
n_det = %s
|
||||||
@ -436,15 +298,9 @@ Determinants ::
|
|||||||
|
|
||||||
%s
|
%s
|
||||||
"
|
"
|
||||||
(b.read_wf |> Bool.to_string)
|
|
||||||
(b.mo_label |> MO_label.to_string)
|
|
||||||
(b.s2_eig |> Bool.to_string)
|
|
||||||
(b.expected_s2 |> Positive_float.to_string)
|
(b.expected_s2 |> Positive_float.to_string)
|
||||||
(b.threshold_generators |> Threshold.to_string)
|
|
||||||
(b.threshold_selectors |> Threshold.to_string)
|
|
||||||
(b.n_states |> States_number.to_string)
|
(b.n_states |> States_number.to_string)
|
||||||
(b.n_states_diag |> States_number.to_string)
|
(b.n_states_diag |> States_number.to_string)
|
||||||
(b.n_det_max_jacobi |> Strictly_positive_int.to_string)
|
|
||||||
(b.n_det |> Det_number.to_string)
|
(b.n_det |> Det_number.to_string)
|
||||||
det_text
|
det_text
|
||||||
|> Rst_string.of_string
|
|> Rst_string.of_string
|
||||||
@ -456,31 +312,19 @@ Determinants ::
|
|||||||
Printf.sprintf "
|
Printf.sprintf "
|
||||||
n_int = %s
|
n_int = %s
|
||||||
bit_kind = %s
|
bit_kind = %s
|
||||||
mo_label = \"%s\"
|
|
||||||
n_det = %s
|
n_det = %s
|
||||||
n_states = %s
|
n_states = %s
|
||||||
n_states_diag = %s
|
n_states_diag = %s
|
||||||
n_det_max_jacobi = %s
|
|
||||||
threshold_generators = %s
|
|
||||||
threshold_selectors = %s
|
|
||||||
read_wf = %s
|
|
||||||
expected_s2 = %s
|
expected_s2 = %s
|
||||||
s2_eig = %s
|
|
||||||
psi_coef = %s
|
psi_coef = %s
|
||||||
psi_det = %s
|
psi_det = %s
|
||||||
"
|
"
|
||||||
(b.n_int |> N_int_number.to_string)
|
(b.n_int |> N_int_number.to_string)
|
||||||
(b.bit_kind |> Bit_kind.to_string)
|
(b.bit_kind |> Bit_kind.to_string)
|
||||||
(b.mo_label |> MO_label.to_string)
|
|
||||||
(b.n_det |> Det_number.to_string)
|
(b.n_det |> Det_number.to_string)
|
||||||
(b.n_states |> States_number.to_string)
|
(b.n_states |> States_number.to_string)
|
||||||
(b.n_states_diag |> States_number.to_string)
|
(b.n_states_diag |> States_number.to_string)
|
||||||
(b.n_det_max_jacobi |> Strictly_positive_int.to_string)
|
|
||||||
(b.threshold_generators |> Threshold.to_string)
|
|
||||||
(b.threshold_selectors |> Threshold.to_string)
|
|
||||||
(b.read_wf |> Bool.to_string)
|
|
||||||
(b.expected_s2 |> Positive_float.to_string)
|
(b.expected_s2 |> Positive_float.to_string)
|
||||||
(b.s2_eig |> Bool.to_string)
|
|
||||||
(b.psi_coef |> Array.to_list |> List.map ~f:Det_coef.to_string
|
(b.psi_coef |> Array.to_list |> List.map ~f:Det_coef.to_string
|
||||||
|> String.concat ~sep:", ")
|
|> String.concat ~sep:", ")
|
||||||
(b.psi_det |> Array.to_list |> List.map ~f:(Determinant.to_string
|
(b.psi_det |> Array.to_list |> List.map ~f:(Determinant.to_string
|
||||||
@ -35,7 +35,7 @@ default: $(ALL_TESTS) $(ALL_EXE) .gitignore
|
|||||||
executables: $(QPACKAGE_ROOT)/data/executables
|
executables: $(QPACKAGE_ROOT)/data/executables
|
||||||
|
|
||||||
$(QPACKAGE_ROOT)/data/executables:
|
$(QPACKAGE_ROOT)/data/executables:
|
||||||
$(QPACKAGE_ROOT)/scripts/create_executables_list.sh
|
$(QPACKAGE_ROOT)/scripts/create/create_executables_list.sh
|
||||||
|
|
||||||
external_libs:
|
external_libs:
|
||||||
opam install cryptokit core
|
opam install cryptokit core
|
||||||
|
|||||||
@ -13,10 +13,12 @@ let spec =
|
|||||||
~doc:"int Total charge of the molecule. Default is 0."
|
~doc:"int Total charge of the molecule. Default is 0."
|
||||||
+> flag "m" (optional_with_default 1 int)
|
+> flag "m" (optional_with_default 1 int)
|
||||||
~doc:"int Spin multiplicity (2S+1) of the molecule. Default is 1."
|
~doc:"int Spin multiplicity (2S+1) of the molecule. Default is 1."
|
||||||
|
+> flag "p" (optional_with_default 0 int)
|
||||||
|
~doc:"Using pseudo. Default is not (aka 0)"
|
||||||
+> anon ("xyz_file" %: string)
|
+> anon ("xyz_file" %: string)
|
||||||
;;
|
;;
|
||||||
|
|
||||||
let run ?o b c m xyz_file =
|
let run ?o b c m p xyz_file =
|
||||||
|
|
||||||
(* Read molecule *)
|
(* Read molecule *)
|
||||||
let molecule =
|
let molecule =
|
||||||
@ -60,8 +62,12 @@ let run ?o b c m xyz_file =
|
|||||||
| None -> (* Principal basis *)
|
| None -> (* Principal basis *)
|
||||||
let basis = elem_and_basis_name in
|
let basis = elem_and_basis_name in
|
||||||
let command =
|
let command =
|
||||||
|
if (p = 0) then
|
||||||
Qpackage.root ^ "/scripts/get_basis.sh \"" ^ temp_filename
|
Qpackage.root ^ "/scripts/get_basis.sh \"" ^ temp_filename
|
||||||
^ "\" \"" ^ basis ^"\""
|
^ "\" \"" ^ basis ^"\""
|
||||||
|
else
|
||||||
|
Qpackage.root ^ "/scripts/get_basis.sh \"" ^ temp_filename
|
||||||
|
^ "\" \"" ^ basis ^"\" pseudo"
|
||||||
in
|
in
|
||||||
begin
|
begin
|
||||||
let filename =
|
let filename =
|
||||||
@ -247,6 +253,9 @@ let run ?o b c m xyz_file =
|
|||||||
~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_expo) ;
|
~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_expo) ;
|
||||||
|
|
||||||
|
|
||||||
|
(* Doesn't work... *)
|
||||||
|
(* if p = 1 then Qpackage.root ^ "scripts/pseudo/put_pseudo_in_ezfio.py" ezfio_file.to_string; *)
|
||||||
|
|
||||||
match Input.Ao_basis.read () with
|
match Input.Ao_basis.read () with
|
||||||
| None -> failwith "Error in basis"
|
| None -> failwith "Error in basis"
|
||||||
| Some x -> Input.Ao_basis.write x
|
| Some x -> Input.Ao_basis.write x
|
||||||
@ -266,8 +275,8 @@ elements can be defined as follows:
|
|||||||
|
|
||||||
")
|
")
|
||||||
spec
|
spec
|
||||||
(fun o b c m xyz_file () ->
|
(fun o b c m p xyz_file () ->
|
||||||
run ?o b c m xyz_file )
|
run ?o b c m p xyz_file )
|
||||||
;;
|
;;
|
||||||
|
|
||||||
let () =
|
let () =
|
||||||
|
|||||||
1
scripts/.gitignore
vendored
1
scripts/.gitignore
vendored
@ -1,2 +1,3 @@
|
|||||||
*.pyc
|
*.pyc
|
||||||
*.pyo
|
*.pyo
|
||||||
|
docopt.py
|
||||||
@ -1,63 +0,0 @@
|
|||||||
#!/bin/bash
|
|
||||||
#
|
|
||||||
# usage:
|
|
||||||
# check_dependencies.sh MOs AOs Electrons
|
|
||||||
#
|
|
||||||
# Checks that the list of dependencies given in
|
|
||||||
# argument is consistent. If the dependencies
|
|
||||||
# are OK the exit code is 0, otherwise it is 1.
|
|
||||||
# If no argument is given, the dependencies are
|
|
||||||
# read in the Makefile.
|
|
||||||
# Thu Apr 3 01:44:23 CEST 2014
|
|
||||||
|
|
||||||
if [[ -z ${QPACKAGE_ROOT} ]]
|
|
||||||
then
|
|
||||||
print "The QPACKAGE_ROOT environment variable is not set."
|
|
||||||
print "Please reload the quantum_package.rc file."
|
|
||||||
exit -1
|
|
||||||
fi
|
|
||||||
source ${QPACKAGE_ROOT}/scripts/qp_include.sh
|
|
||||||
|
|
||||||
if [[ -z $1 ]]
|
|
||||||
then
|
|
||||||
exit 0
|
|
||||||
fi
|
|
||||||
|
|
||||||
if [[ $1 == "-" ]]
|
|
||||||
then
|
|
||||||
COMMAND_LINE=$(cat NEEDED_MODULES)
|
|
||||||
else
|
|
||||||
COMMAND_LINE=$(unique_list $@)
|
|
||||||
fi
|
|
||||||
|
|
||||||
for d in $COMMAND_LINE
|
|
||||||
do
|
|
||||||
if [[ ! -d ${QPACKAGE_ROOT}/src/$d ]]
|
|
||||||
then
|
|
||||||
echo Error: Directory $d does not exist
|
|
||||||
exit 2
|
|
||||||
fi
|
|
||||||
|
|
||||||
done
|
|
||||||
|
|
||||||
DEPS_LONG=""
|
|
||||||
for i in $COMMAND_LINE
|
|
||||||
do
|
|
||||||
DEPS_LONG+=" $i "
|
|
||||||
DEPS_LONG+=$(cat "${QPACKAGE_ROOT}/src/${i}/NEEDED_MODULES")
|
|
||||||
done
|
|
||||||
|
|
||||||
DEPS=$(unique_list $DEPS_LONG)
|
|
||||||
|
|
||||||
if [[ ! "$COMMAND_LINE" == "$DEPS" ]]
|
|
||||||
then
|
|
||||||
DEPS=$(${QPACKAGE_ROOT}/scripts/check_dependencies.sh ${DEPS})
|
|
||||||
fi
|
|
||||||
echo "$DEPS"
|
|
||||||
|
|
||||||
if [[ "$COMMAND_LINE" == "$DEPS" ]]
|
|
||||||
then
|
|
||||||
exit 0
|
|
||||||
else
|
|
||||||
exit 1
|
|
||||||
fi
|
|
||||||
@ -1,590 +0,0 @@
|
|||||||
"""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()
|
|
||||||
@ -70,9 +70,9 @@ def is_bool(str_):
|
|||||||
Take a string, if is a bool return the conversion into
|
Take a string, if is a bool return the conversion into
|
||||||
fortran and ocaml.
|
fortran and ocaml.
|
||||||
"""
|
"""
|
||||||
if "true" in str_.lower():
|
if "true" in str_.strip().lower():
|
||||||
return Type(None, "true", ".True.")
|
return Type(None, "true", ".True.")
|
||||||
elif "false" in str_.lower():
|
elif "false" in str_.strip().lower():
|
||||||
return Type(None, "false", ".False")
|
return Type(None, "false", ".False")
|
||||||
else:
|
else:
|
||||||
raise TypeError
|
raise TypeError
|
||||||
@ -112,6 +112,8 @@ def get_type_dict():
|
|||||||
# ~#~#~#~#~#~#~#~ #
|
# ~#~#~#~#~#~#~#~ #
|
||||||
|
|
||||||
fancy_type['integer'] = Type(None, "int", "integer")
|
fancy_type['integer'] = Type(None, "int", "integer")
|
||||||
|
fancy_type['integer*8'] = Type(None, "int", "integer*8")
|
||||||
|
|
||||||
fancy_type['int'] = Type(None, "int", "integer")
|
fancy_type['int'] = Type(None, "int", "integer")
|
||||||
|
|
||||||
fancy_type['float'] = Type(None, "float", "double precision")
|
fancy_type['float'] = Type(None, "float", "double precision")
|
||||||
@ -121,7 +123,7 @@ def get_type_dict():
|
|||||||
fancy_type['bool'] = Type(None, "bool", "logical")
|
fancy_type['bool'] = Type(None, "bool", "logical")
|
||||||
|
|
||||||
fancy_type['character*(32)'] = Type(None, "string", "character*(32)")
|
fancy_type['character*(32)'] = Type(None, "string", "character*(32)")
|
||||||
fancy_type['character*(60)'] = Type(None, "string", "character*(60)")
|
fancy_type['character*(64)'] = Type(None, "string", "character*(68)")
|
||||||
fancy_type['character*(256)'] = Type(None, "string", "character*(256)")
|
fancy_type['character*(256)'] = Type(None, "string", "character*(256)")
|
||||||
|
|
||||||
# ~#~#~#~#~#~#~#~ #
|
# ~#~#~#~#~#~#~#~ #
|
||||||
@ -203,7 +205,7 @@ def get_dict_config_file(config_file_path, module_lower):
|
|||||||
- ezfio_name : Will be the name of the file
|
- ezfio_name : Will be the name of the file
|
||||||
- ezfio_dir : Will be the folder who containt the ezfio_name
|
- ezfio_dir : Will be the folder who containt the ezfio_name
|
||||||
* /ezfio_dir/ezfio_name
|
* /ezfio_dir/ezfio_name
|
||||||
* equal to MODULE_lower name for the moment.
|
* equal to MODULE_lower name by default.
|
||||||
- interface : The provider is a imput or a output
|
- interface : The provider is a imput or a output
|
||||||
- default : The default value /!\ stored in a Type named type!
|
- default : The default value /!\ stored in a Type named type!
|
||||||
if interface == output
|
if interface == output
|
||||||
@ -216,7 +218,7 @@ def get_dict_config_file(config_file_path, module_lower):
|
|||||||
|
|
||||||
d = defaultdict(dict)
|
d = defaultdict(dict)
|
||||||
l_info_required = ["doc", "interface"]
|
l_info_required = ["doc", "interface"]
|
||||||
l_info_optional = ["ezfio_name", "size"]
|
l_info_optional = ["ezfio_dir", "ezfio_name", "size"]
|
||||||
|
|
||||||
# ~#~#~#~#~#~#~#~#~#~#~ #
|
# ~#~#~#~#~#~#~#~#~#~#~ #
|
||||||
# L o a d _ C o n f i g #
|
# L o a d _ C o n f i g #
|
||||||
@ -238,10 +240,8 @@ def get_dict_config_file(config_file_path, module_lower):
|
|||||||
pvd = section.lower()
|
pvd = section.lower()
|
||||||
|
|
||||||
# Create the dictionary who containt the value per default
|
# Create the dictionary who containt the value per default
|
||||||
d_default = {"ezfio_name": pvd}
|
d_default = {"ezfio_name": pvd,
|
||||||
|
"ezfio_dir": module_lower}
|
||||||
# Set the ezfio_dir
|
|
||||||
d[pvd]["ezfio_dir"] = module_lower
|
|
||||||
|
|
||||||
# Check if type if avalaible
|
# Check if type if avalaible
|
||||||
type_ = config_file.get(section, "type")
|
type_ = config_file.get(section, "type")
|
||||||
@ -269,7 +269,7 @@ def get_dict_config_file(config_file_path, module_lower):
|
|||||||
d[pvd][option] = d_default[option]
|
d[pvd][option] = d_default[option]
|
||||||
|
|
||||||
# If interface is input we need a default value information
|
# If interface is input we need a default value information
|
||||||
if d[pvd]["interface"] == "input":
|
if d[pvd]["interface"].lower() == "input":
|
||||||
try:
|
try:
|
||||||
default_raw = config_file.get(section, "default")
|
default_raw = config_file.get(section, "default")
|
||||||
except ConfigParser.NoOptionError:
|
except ConfigParser.NoOptionError:
|
||||||
@ -294,6 +294,7 @@ def create_ezfio_provider(dict_ezfio_cfg):
|
|||||||
default
|
default
|
||||||
size}
|
size}
|
||||||
create the a list who containt all the code for the provider
|
create the a list who containt all the code for the provider
|
||||||
|
output = output_dict_info['ezfio_dir'
|
||||||
return [code, ...]
|
return [code, ...]
|
||||||
"""
|
"""
|
||||||
from ezfio_generate_provider import EZFIO_Provider
|
from ezfio_generate_provider import EZFIO_Provider
|
||||||
|
|||||||
@ -1,7 +1,13 @@
|
|||||||
#!/usr/bin/env python
|
#!/usr/bin/env python
|
||||||
|
"""
|
||||||
|
This programme generate all the
|
||||||
|
ocaml template needed by qp_edit
|
||||||
|
|
||||||
|
You can see `ezfio_generate_provider.py`
|
||||||
|
for an example of utilisation
|
||||||
|
"""
|
||||||
|
|
||||||
import sys
|
import sys
|
||||||
import os
|
|
||||||
|
|
||||||
# If type in **kwargs
|
# If type in **kwargs
|
||||||
from ei_handler import Type
|
from ei_handler import Type
|
||||||
|
|||||||
@ -45,7 +45,7 @@ END_PROVIDER
|
|||||||
self.set_write()
|
self.set_write()
|
||||||
for v in self.values:
|
for v in self.values:
|
||||||
if not v:
|
if not v:
|
||||||
msg = "Error : %s is not set in ezfio_with_default.py" % (v)
|
msg = "Error : %s is not set in EZFIO.cfg" % (v)
|
||||||
print >>sys.stderr, msg
|
print >>sys.stderr, msg
|
||||||
sys.exit(1)
|
sys.exit(1)
|
||||||
return self.data % self.__dict__
|
return self.data % self.__dict__
|
||||||
|
|||||||
36
scripts/ezfio_interface/qp_convert_ezfio_v1_to_v2.sh
Executable file
36
scripts/ezfio_interface/qp_convert_ezfio_v1_to_v2.sh
Executable file
@ -0,0 +1,36 @@
|
|||||||
|
#!/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
|
||||||
|
|
||||||
|
echo "Will tranform qp_v1.*_ezfio to qp_v2.*_ezfio"
|
||||||
|
echo "All action are irrevocable! And is by choice"
|
||||||
|
echo "You need to stop to use a old version! Plz..."
|
||||||
|
|
||||||
|
echo "Change thresh_SCF > thresh_scf0"
|
||||||
|
mv $1/hartree_Fock/thresh_SCF $1/hartree_fock/thresh_scf 2> /dev/null
|
||||||
|
|
||||||
|
# Set disk_acess
|
||||||
|
echo "Change {read,write}_ao_integrals > disk_access_ao_integrals"
|
||||||
|
|
||||||
|
biint=$1/bielec_integrals
|
||||||
|
|
||||||
|
if [[ -f $biint/read_ao_integrals ]]; then
|
||||||
|
if [[ `cat $1/bielec_integrals/read_ao_integrals` -eq "T" ]]
|
||||||
|
then
|
||||||
|
echo "Read" > $biint/disk_access_ao_integrals
|
||||||
|
|
||||||
|
elif [[ `cat $biint/write_ao_integrals` -eq "T" ]]
|
||||||
|
then
|
||||||
|
echo "Write" > $biint/disk_access_ao_integrals
|
||||||
|
|
||||||
|
else
|
||||||
|
echo "None" > $biint/disk_access_ao_integrals
|
||||||
|
|
||||||
|
fi
|
||||||
|
rm $biint/read_ao_integrals $biint/write_ao_integrals $biint/write_ao_intergals 2> /dev/null
|
||||||
|
fi
|
||||||
|
|
||||||
|
echo "Done"
|
||||||
302
scripts/ezfio_interface/qp_convert_output_to_ezfio.py
Executable file
302
scripts/ezfio_interface/qp_convert_output_to_ezfio.py
Executable file
@ -0,0 +1,302 @@
|
|||||||
|
#!/usr/bin/env python
|
||||||
|
"""
|
||||||
|
This function acceep
|
||||||
|
|
||||||
|
Usage:
|
||||||
|
qp_convert_output_to_ezfio.py <file.out> [--ezfio=<folder.ezfio>]
|
||||||
|
|
||||||
|
Option:
|
||||||
|
file.out is the file to check (like gamess.out)
|
||||||
|
folder.ezfio is the name you whant for the ezfio
|
||||||
|
(by default is file.out.ezfio)
|
||||||
|
|
||||||
|
"""
|
||||||
|
|
||||||
|
|
||||||
|
import sys
|
||||||
|
import os
|
||||||
|
from functools import reduce
|
||||||
|
|
||||||
|
|
||||||
|
# ~#~#~#~#~#~#~#~ #
|
||||||
|
# Add to the path #
|
||||||
|
# ~#~#~#~#~#~#~#~ #
|
||||||
|
|
||||||
|
|
||||||
|
try:
|
||||||
|
QPACKAGE_ROOT = os.environ["QPACKAGE_ROOT"]
|
||||||
|
except:
|
||||||
|
print "Error: QPACKAGE_ROOT environment variable not found."
|
||||||
|
sys.exit(1)
|
||||||
|
else:
|
||||||
|
sys.path = [QPACKAGE_ROOT + "/EZFIO/Python",
|
||||||
|
QPACKAGE_ROOT + "/resultsFile",
|
||||||
|
QPACKAGE_ROOT + "/scripts"] + sys.path
|
||||||
|
|
||||||
|
# ~#~#~#~#~#~ #
|
||||||
|
# I m p o r t #
|
||||||
|
# ~#~#~#~#~#~ #
|
||||||
|
|
||||||
|
from ezfio import ezfio
|
||||||
|
|
||||||
|
|
||||||
|
try:
|
||||||
|
from resultsFile import *
|
||||||
|
except:
|
||||||
|
print "Error: resultsFile Python library not installed"
|
||||||
|
sys.exit(1)
|
||||||
|
|
||||||
|
from docopt import docopt
|
||||||
|
|
||||||
|
# _
|
||||||
|
# |_ ._ _ _|_ o _ ._
|
||||||
|
# | |_| | | (_ |_ | (_) | |
|
||||||
|
#
|
||||||
|
|
||||||
|
|
||||||
|
def write_ezfio(res, filename):
|
||||||
|
|
||||||
|
res.clean_uncontractions()
|
||||||
|
ezfio.set_file(filename)
|
||||||
|
|
||||||
|
# _
|
||||||
|
# |_ | _ _ _|_ ._ _ ._ _
|
||||||
|
# |_ | (/_ (_ |_ | (_) | | _>
|
||||||
|
#
|
||||||
|
ezfio.set_electrons_elec_alpha_num(res.num_alpha)
|
||||||
|
ezfio.set_electrons_elec_beta_num(res.num_beta)
|
||||||
|
|
||||||
|
#
|
||||||
|
# |\ | _ | _ o
|
||||||
|
# | \| |_| (_ | (/_ |
|
||||||
|
#
|
||||||
|
|
||||||
|
# ~#~#~#~ #
|
||||||
|
# I n i t #
|
||||||
|
# ~#~#~#~ #
|
||||||
|
|
||||||
|
charge = []
|
||||||
|
coord_x = []
|
||||||
|
coord_y = []
|
||||||
|
coord_z = []
|
||||||
|
|
||||||
|
# ~#~#~#~#~#~#~ #
|
||||||
|
# P a r s i n g #
|
||||||
|
# ~#~#~#~#~#~#~ #
|
||||||
|
|
||||||
|
for a in res.geometry:
|
||||||
|
charge.append(a.charge)
|
||||||
|
if res.units == 'BOHR':
|
||||||
|
coord_x.append(a.coord[0])
|
||||||
|
coord_y.append(a.coord[1])
|
||||||
|
coord_z.append(a.coord[2])
|
||||||
|
else:
|
||||||
|
coord_x.append(a.coord[0] / a0)
|
||||||
|
coord_y.append(a.coord[1] / a0)
|
||||||
|
coord_z.append(a.coord[2] / a0)
|
||||||
|
|
||||||
|
# ~#~#~#~#~ #
|
||||||
|
# W r i t e #
|
||||||
|
# ~#~#~#~#~ #
|
||||||
|
|
||||||
|
ezfio.set_nuclei_nucl_num(len(res.geometry))
|
||||||
|
ezfio.set_nuclei_nucl_charge(charge)
|
||||||
|
|
||||||
|
# Transformt H1 into H
|
||||||
|
import re
|
||||||
|
p = re.compile(ur'(\d*)$')
|
||||||
|
label = [p.sub("", x.name).capitalize() for x in res.geometry]
|
||||||
|
ezfio.set_nuclei_nucl_label(label)
|
||||||
|
|
||||||
|
ezfio.set_nuclei_nucl_coord(coord_x + coord_y + coord_z)
|
||||||
|
|
||||||
|
# _
|
||||||
|
# /\ _ _ |_) _. _ o _
|
||||||
|
# /--\ (_) _> |_) (_| _> | _>
|
||||||
|
#
|
||||||
|
|
||||||
|
# ~#~#~#~ #
|
||||||
|
# I n i t #
|
||||||
|
# ~#~#~#~ #
|
||||||
|
|
||||||
|
import string
|
||||||
|
at = []
|
||||||
|
num_prim = []
|
||||||
|
power_x = []
|
||||||
|
power_y = []
|
||||||
|
power_z = []
|
||||||
|
coefficient = []
|
||||||
|
exponent = []
|
||||||
|
|
||||||
|
res.clean_contractions()
|
||||||
|
res.convert_to_cartesian()
|
||||||
|
|
||||||
|
# ~#~#~#~#~#~#~ #
|
||||||
|
# P a r s i n g #
|
||||||
|
# ~#~#~#~#~#~#~ #
|
||||||
|
|
||||||
|
for b in res.basis:
|
||||||
|
c = b.center
|
||||||
|
for i, atom in enumerate(res.geometry):
|
||||||
|
if atom.coord == c:
|
||||||
|
at.append(i + 1)
|
||||||
|
num_prim.append(len(b.prim))
|
||||||
|
s = b.sym
|
||||||
|
power_x.append(string.count(s, "x"))
|
||||||
|
power_y.append(string.count(s, "y"))
|
||||||
|
power_z.append(string.count(s, "z"))
|
||||||
|
coefficient.append(b.coef)
|
||||||
|
exponent.append([p.expo for p in b.prim])
|
||||||
|
|
||||||
|
# ~#~#~#~#~ #
|
||||||
|
# W r i t e #
|
||||||
|
# ~#~#~#~#~ #
|
||||||
|
|
||||||
|
ezfio.set_ao_basis_ao_num(len(res.basis))
|
||||||
|
ezfio.set_ao_basis_ao_nucl(at)
|
||||||
|
ezfio.set_ao_basis_ao_prim_num(num_prim)
|
||||||
|
ezfio.set_ao_basis_ao_power(power_x + power_y + power_z)
|
||||||
|
|
||||||
|
# ~#~#~#~#~#~#~ #
|
||||||
|
# P a r s i n g #
|
||||||
|
# ~#~#~#~#~#~#~ #
|
||||||
|
|
||||||
|
prim_num_max = ezfio.get_ao_basis_ao_prim_num_max()
|
||||||
|
|
||||||
|
for i in range(len(res.basis)):
|
||||||
|
coefficient[
|
||||||
|
i] += [0. for j in range(len(coefficient[i]), prim_num_max)]
|
||||||
|
exponent[i] += [0. for j in range(len(exponent[i]), prim_num_max)]
|
||||||
|
|
||||||
|
coefficient = reduce(lambda x, y: x + y, coefficient, [])
|
||||||
|
exponent = reduce(lambda x, y: x + y, exponent, [])
|
||||||
|
|
||||||
|
coef = []
|
||||||
|
expo = []
|
||||||
|
for i in range(prim_num_max):
|
||||||
|
for j in range(i, len(coefficient), prim_num_max):
|
||||||
|
coef.append(coefficient[j])
|
||||||
|
expo.append(exponent[j])
|
||||||
|
|
||||||
|
# ~#~#~#~#~ #
|
||||||
|
# W r i t e #
|
||||||
|
# ~#~#~#~#~ #
|
||||||
|
|
||||||
|
ezfio.set_ao_basis_ao_coef(coef)
|
||||||
|
ezfio.set_ao_basis_ao_expo(expo)
|
||||||
|
ezfio.set_ao_basis_ao_basis("Read by resultsFile")
|
||||||
|
|
||||||
|
# _
|
||||||
|
# |\/| _ _ |_) _. _ o _
|
||||||
|
# | | (_) _> |_) (_| _> | _>
|
||||||
|
#
|
||||||
|
|
||||||
|
# ~#~#~#~ #
|
||||||
|
# I n i t #
|
||||||
|
# ~#~#~#~ #
|
||||||
|
|
||||||
|
MoTag = res.determinants_mo_type
|
||||||
|
ezfio.set_mo_basis_mo_label('Orthonormalized')
|
||||||
|
MO_type = MoTag
|
||||||
|
allMOs = res.mo_sets[MO_type]
|
||||||
|
|
||||||
|
# ~#~#~#~#~#~#~ #
|
||||||
|
# P a r s i n g #
|
||||||
|
# ~#~#~#~#~#~#~ #
|
||||||
|
|
||||||
|
try:
|
||||||
|
closed = [(allMOs[i].eigenvalue, i) for i in res.closed_mos]
|
||||||
|
active = [(allMOs[i].eigenvalue, i) for i in res.active_mos]
|
||||||
|
virtual = [(allMOs[i].eigenvalue, i) for i in res.virtual_mos]
|
||||||
|
except:
|
||||||
|
closed = []
|
||||||
|
virtual = []
|
||||||
|
active = [(allMOs[i].eigenvalue, i) for i in range(len(allMOs))]
|
||||||
|
|
||||||
|
closed = map(lambda x: x[1], closed)
|
||||||
|
active = map(lambda x: x[1], active)
|
||||||
|
virtual = map(lambda x: x[1], virtual)
|
||||||
|
MOindices = closed + active + virtual
|
||||||
|
|
||||||
|
MOs = []
|
||||||
|
for i in MOindices:
|
||||||
|
MOs.append(allMOs[i])
|
||||||
|
|
||||||
|
mo_tot_num = len(MOs)
|
||||||
|
while len(MOindices) < mo_tot_num:
|
||||||
|
MOindices.append(len(MOindices))
|
||||||
|
|
||||||
|
MOmap = list(MOindices)
|
||||||
|
for i in range(len(MOindices)):
|
||||||
|
MOmap[i] = MOindices.index(i)
|
||||||
|
|
||||||
|
energies = []
|
||||||
|
for i in xrange(mo_tot_num):
|
||||||
|
energies.append(MOs[i].eigenvalue)
|
||||||
|
|
||||||
|
if res.occ_num is not None:
|
||||||
|
OccNum = []
|
||||||
|
for i in MOindices:
|
||||||
|
OccNum.append(res.occ_num[MO_type][i])
|
||||||
|
|
||||||
|
while len(OccNum) < mo_tot_num:
|
||||||
|
OccNum.append(0.)
|
||||||
|
|
||||||
|
MoMatrix = []
|
||||||
|
sym0 = [i.sym for i in res.mo_sets[MO_type]]
|
||||||
|
sym = [i.sym for i in res.mo_sets[MO_type]]
|
||||||
|
for i in xrange(len(sym)):
|
||||||
|
sym[MOmap[i]] = sym0[i]
|
||||||
|
|
||||||
|
MoMatrix = []
|
||||||
|
for i in xrange(len(MOs)):
|
||||||
|
m = MOs[i]
|
||||||
|
for coef in m.vector:
|
||||||
|
MoMatrix.append(coef)
|
||||||
|
|
||||||
|
while len(MoMatrix) < len(MOs[0].vector) ** 2:
|
||||||
|
MoMatrix.append(0.)
|
||||||
|
|
||||||
|
# ~#~#~#~#~ #
|
||||||
|
# W r i t e #
|
||||||
|
# ~#~#~#~#~ #
|
||||||
|
|
||||||
|
ezfio.set_mo_basis_mo_tot_num(mo_tot_num)
|
||||||
|
ezfio.set_mo_basis_mo_occ(OccNum)
|
||||||
|
ezfio.set_mo_basis_mo_coef(MoMatrix)
|
||||||
|
|
||||||
|
# ______ _
|
||||||
|
# | ___ \ | |
|
||||||
|
# | |_/ /__ ___ _ _ __| | ___
|
||||||
|
# | __/ __|/ _ \ | | |/ _` |/ _ \
|
||||||
|
# | | \__ \ __/ |_| | (_| | (_) |
|
||||||
|
# \_| |___/\___|\__,_|\__,_|\___/
|
||||||
|
#
|
||||||
|
|
||||||
|
ezfio.set_pseudo_integrals_do_pseudo(False)
|
||||||
|
|
||||||
|
|
||||||
|
def get_full_path(file_path):
|
||||||
|
file_path = os.path.expanduser(file_path)
|
||||||
|
file_path = os.path.expandvars(file_path)
|
||||||
|
file_path = os.path.abspath(file_path)
|
||||||
|
return file_path
|
||||||
|
|
||||||
|
if __name__ == '__main__':
|
||||||
|
arguments = docopt(__doc__)
|
||||||
|
|
||||||
|
file_ = get_full_path(arguments['<file.out>'])
|
||||||
|
|
||||||
|
if arguments["--ezfio"]:
|
||||||
|
ezfio_file = get_full_path(arguments["--ezfio"])
|
||||||
|
else:
|
||||||
|
ezfio_file = "{0}.ezfio".format(file_)
|
||||||
|
|
||||||
|
try:
|
||||||
|
res_file = getFile(file_)
|
||||||
|
except:
|
||||||
|
raise
|
||||||
|
else:
|
||||||
|
print file_, 'recognized as', str(res_file).split('.')[-1].split()[0]
|
||||||
|
|
||||||
|
write_ezfio(res_file, ezfio_file)
|
||||||
@ -4,14 +4,16 @@ open Core.Std;;
|
|||||||
|
|
||||||
(** Interactive editing of the input.
|
(** Interactive editing of the input.
|
||||||
|
|
||||||
@author A. Scemama
|
WARNING
|
||||||
|
This file is autogenerad by
|
||||||
|
`${{QP_ROOT}}/script/ezfio_interface/ei_handler.py`
|
||||||
*)
|
*)
|
||||||
|
|
||||||
|
|
||||||
(** Keywords used to define input sections *)
|
(** Keywords used to define input sections *)
|
||||||
type keyword =
|
type keyword =
|
||||||
| Ao_basis
|
| Ao_basis
|
||||||
| Determinants
|
| Determinants_by_hand
|
||||||
| Electrons
|
| Electrons
|
||||||
| Mo_basis
|
| Mo_basis
|
||||||
| Nuclei
|
| Nuclei
|
||||||
@ -21,7 +23,7 @@ type keyword =
|
|||||||
|
|
||||||
let keyword_to_string = function
|
let keyword_to_string = function
|
||||||
| Ao_basis -> "AO basis"
|
| Ao_basis -> "AO basis"
|
||||||
| Determinants -> "Determinants"
|
| Determinants_by_hand -> "Determinants_by_hand"
|
||||||
| Electrons -> "Electrons"
|
| Electrons -> "Electrons"
|
||||||
| Mo_basis -> "MO basis"
|
| Mo_basis -> "MO basis"
|
||||||
| Nuclei -> "Molecule"
|
| Nuclei -> "Molecule"
|
||||||
@ -72,8 +74,8 @@ let get s =
|
|||||||
f Nuclei.(read, to_rst)
|
f Nuclei.(read, to_rst)
|
||||||
| Ao_basis ->
|
| Ao_basis ->
|
||||||
f Ao_basis.(read, to_rst)
|
f Ao_basis.(read, to_rst)
|
||||||
| Determinants ->
|
| Determinants_by_hand ->
|
||||||
f Determinants.(read, to_rst)
|
f Determinants_by_hand.(read, to_rst)
|
||||||
{section_to_rst}
|
{section_to_rst}
|
||||||
end
|
end
|
||||||
with
|
with
|
||||||
@ -114,7 +116,7 @@ let set str s =
|
|||||||
match s with
|
match s with
|
||||||
{write}
|
{write}
|
||||||
| Electrons -> write Electrons.(of_rst, write) s
|
| Electrons -> write Electrons.(of_rst, write) s
|
||||||
| Determinants -> write Determinants.(of_rst, write) s
|
| Determinants_by_hand -> write Determinants_by_hand.(of_rst, write) s
|
||||||
| Nuclei -> write Nuclei.(of_rst, write) s
|
| Nuclei -> write Nuclei.(of_rst, write) s
|
||||||
| Ao_basis -> () (* TODO *)
|
| Ao_basis -> () (* TODO *)
|
||||||
| Mo_basis -> () (* TODO *)
|
| Mo_basis -> () (* TODO *)
|
||||||
@ -162,7 +164,7 @@ let run check_only ezfio_filename =
|
|||||||
Electrons ;
|
Electrons ;
|
||||||
{tasks}
|
{tasks}
|
||||||
Mo_basis;
|
Mo_basis;
|
||||||
Determinants ;
|
Determinants_by_hand ;
|
||||||
]
|
]
|
||||||
in
|
in
|
||||||
|
|
||||||
|
|||||||
27
scripts/ezfio_interface/upgrade_1.0_2.0.sh
Executable file
27
scripts/ezfio_interface/upgrade_1.0_2.0.sh
Executable file
@ -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
|
||||||
@ -90,13 +90,19 @@ END_PROVIDER
|
|||||||
self.default = t
|
self.default = t
|
||||||
|
|
||||||
def get_default(self):
|
def get_default(self):
|
||||||
filename = '/'.join( [os.environ['QPACKAGE_ROOT'], 'data',
|
mypath = '/'.join( [os.environ['QPACKAGE_ROOT'], 'data',
|
||||||
'ezfio_defaults',
|
'ezfio_defaults'] )
|
||||||
'WILL_BE_DELETED.ezfio_default'] )
|
|
||||||
|
|
||||||
|
from os import listdir
|
||||||
|
from os.path import isfile, join
|
||||||
|
onlyfiles = [ join(mypath,f) for f in listdir(mypath) if isfile(join(mypath,f)) ]
|
||||||
|
|
||||||
|
lines = []
|
||||||
|
for filename in onlyfiles:
|
||||||
file = open(filename,'r')
|
file = open(filename,'r')
|
||||||
lines = file.readlines()
|
lines.extend(file.readlines())
|
||||||
file.close()
|
file.close()
|
||||||
|
|
||||||
k=-1
|
k=-1
|
||||||
# Search directory
|
# Search directory
|
||||||
for k,line in enumerate(lines):
|
for k,line in enumerate(lines):
|
||||||
|
|||||||
@ -1,7 +1,7 @@
|
|||||||
#!/usr/bin/env python
|
#!/usr/bin/env python
|
||||||
|
|
||||||
import os
|
import os
|
||||||
file = open(os.environ["QPACKAGE_ROOT"]+'/src/Dets/H_apply_template.f','r')
|
file = open(os.environ["QPACKAGE_ROOT"]+'/src/Determinants/H_apply_template.f','r')
|
||||||
template = file.read()
|
template = file.read()
|
||||||
file.close()
|
file.close()
|
||||||
|
|
||||||
@ -104,7 +104,7 @@ class H_apply(object):
|
|||||||
endif
|
endif
|
||||||
SOFT_TOUCH psi_det psi_coef N_det
|
SOFT_TOUCH psi_det psi_coef N_det
|
||||||
"""
|
"""
|
||||||
s["printout_now"] = """write(output_Dets,*) &
|
s["printout_now"] = """write(output_determinants,*) &
|
||||||
100.*float(i_generator)/float(N_det_generators), '% in ', wall_1-wall_0, 's'"""
|
100.*float(i_generator)/float(N_det_generators), '% in ', wall_1-wall_0, 's'"""
|
||||||
self.data = s
|
self.data = s
|
||||||
|
|
||||||
@ -211,9 +211,9 @@ class H_apply(object):
|
|||||||
delta_pt2(k) = 0.d0
|
delta_pt2(k) = 0.d0
|
||||||
pt2_old(k) = 0.d0
|
pt2_old(k) = 0.d0
|
||||||
enddo
|
enddo
|
||||||
write(output_Dets,'(A12, X, A8, 3(2X, A9), 2X, A8, 2X, A8, 2X, A8)') &
|
write(output_determinants,'(A12, X, A8, 3(2X, A9), 2X, A8, 2X, A8, 2X, A8)') &
|
||||||
'N_generators', 'Norm', 'Delta PT2', 'PT2', 'Est. PT2', 'secs'
|
'N_generators', 'Norm', 'Delta PT2', 'PT2', 'Est. PT2', 'secs'
|
||||||
write(output_Dets,'(A12, X, A8, 3(2X, A9), 2X, A8, 2X, A8, 2X, A8)') &
|
write(output_determinants,'(A12, X, A8, 3(2X, A9), 2X, A8, 2X, A8, 2X, A8)') &
|
||||||
'============', '========', '=========', '=========', '=========', &
|
'============', '========', '=========', '=========', '=========', &
|
||||||
'========='
|
'========='
|
||||||
"""
|
"""
|
||||||
@ -226,7 +226,7 @@ class H_apply(object):
|
|||||||
"""
|
"""
|
||||||
self.data["printout_now"] = """
|
self.data["printout_now"] = """
|
||||||
do k=1,N_st
|
do k=1,N_st
|
||||||
write(output_Dets,'(I10, 4(2X, F9.6), 2X, F8.1)') &
|
write(output_determinants,'(I10, 4(2X, F9.6), 2X, F8.1)') &
|
||||||
i_generator, norm_psi(k), delta_pt2(k), pt2(k), &
|
i_generator, norm_psi(k), delta_pt2(k), pt2(k), &
|
||||||
pt2(k)/(norm_psi(k)*norm_psi(k)), &
|
pt2(k)/(norm_psi(k)*norm_psi(k)), &
|
||||||
wall_1-wall_0
|
wall_1-wall_0
|
||||||
@ -258,7 +258,7 @@ class H_apply(object):
|
|||||||
! SOFT_TOUCH psi_det psi_coef N_det
|
! SOFT_TOUCH psi_det psi_coef N_det
|
||||||
selection_criterion_min = min(selection_criterion_min, maxval(select_max))*0.1d0
|
selection_criterion_min = min(selection_criterion_min, maxval(select_max))*0.1d0
|
||||||
selection_criterion = selection_criterion_min
|
selection_criterion = selection_criterion_min
|
||||||
call write_double(output_Dets,selection_criterion,'Selection criterion')
|
call write_double(output_determinants,selection_criterion,'Selection criterion')
|
||||||
"""
|
"""
|
||||||
self.data["keys_work"] = """
|
self.data["keys_work"] = """
|
||||||
e_2_pert_buffer = 0.d0
|
e_2_pert_buffer = 0.d0
|
||||||
|
|||||||
@ -42,9 +42,14 @@ then
|
|||||||
echo "ERROR"
|
echo "ERROR"
|
||||||
exit 1
|
exit 1
|
||||||
fi
|
fi
|
||||||
${EMSL_API_ROOT}/EMSL_api.py get_basis_data --treat_l --save --path="${tmpfile}" --basis="${basis}" $atoms
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
pseudo="$1"
|
||||||
|
shift
|
||||||
|
|
||||||
|
if [[ -z $pseudo ]]
|
||||||
|
then
|
||||||
|
${EMSL_API_ROOT}/EMSL_api.py get_basis_data --treat_l --save --path="${tmpfile}" --basis="${basis}"
|
||||||
|
else
|
||||||
|
${EMSL_API_ROOT}/EMSL_api.py get_basis_data --save --path="${tmpfile}" --basis="${basis}" --db_path="${EMSL_API_ROOT}/db/Pseudo.db"
|
||||||
|
fi
|
||||||
|
|
||||||
|
|||||||
@ -8,8 +8,8 @@ CURL_URL="http://qmcchem.ups-tlse.fr/files/scemama/${CURL}.tar.bz2"
|
|||||||
|
|
||||||
if [[ -z ${QPACKAGE_ROOT} ]]
|
if [[ -z ${QPACKAGE_ROOT} ]]
|
||||||
then
|
then
|
||||||
print "The QPACKAGE_ROOT environment variable is not set."
|
echo "The QPACKAGE_ROOT environment variable is not set."
|
||||||
print "Please reload the quantum_package.rc file."
|
echo "Please reload the quantum_package.rc file."
|
||||||
exit -1
|
exit -1
|
||||||
fi
|
fi
|
||||||
|
|
||||||
21
scripts/install/install_docopt.sh
Executable file
21
scripts/install/install_docopt.sh
Executable file
@ -0,0 +1,21 @@
|
|||||||
|
#!/bin/bash
|
||||||
|
#
|
||||||
|
# Installs docopt
|
||||||
|
# lundi 27 avril 2015, 16:51:34 (UTC+0200)
|
||||||
|
|
||||||
|
DOCOPT="docopt.py"
|
||||||
|
DOCOPT_URL="https://raw.githubusercontent.com/docopt/docopt/master/${DOCOPT}"
|
||||||
|
|
||||||
|
if [[ -z ${QPACKAGE_ROOT} ]]
|
||||||
|
then
|
||||||
|
echo "The QPACKAGE_ROOT environment variable is not set."
|
||||||
|
echo "Please reload the quantum_package.rc file."
|
||||||
|
exit -1
|
||||||
|
fi
|
||||||
|
|
||||||
|
cd ${QPACKAGE_ROOT}
|
||||||
|
|
||||||
|
rm -f -- scripts/${DOCOPT}{,c}
|
||||||
|
${QPACKAGE_ROOT}/scripts/fetch_from_web.py ${DOCOPT_URL} ${DOCOPT}
|
||||||
|
|
||||||
|
mv ${DOCOPT} scripts/${DOCOPT}
|
||||||
@ -8,8 +8,8 @@ URL="https://github.com/LCPQ/${BASE}/archive/master.tar.gz"
|
|||||||
|
|
||||||
if [[ -z ${QPACKAGE_ROOT} ]]
|
if [[ -z ${QPACKAGE_ROOT} ]]
|
||||||
then
|
then
|
||||||
print "The QPACKAGE_ROOT environment variable is not set."
|
echo "The QPACKAGE_ROOT environment variable is not set."
|
||||||
print "Please reload the quantum_package.rc file."
|
echo "Please reload the quantum_package.rc file."
|
||||||
exit -1
|
exit -1
|
||||||
fi
|
fi
|
||||||
|
|
||||||
@ -8,8 +8,8 @@ URL="https://github.com/LCPQ/${BASE}/archive/master.tar.gz"
|
|||||||
|
|
||||||
if [[ -z ${QPACKAGE_ROOT} ]]
|
if [[ -z ${QPACKAGE_ROOT} ]]
|
||||||
then
|
then
|
||||||
print "The QPACKAGE_ROOT environment variable is not set."
|
echo "The QPACKAGE_ROOT environment variable is not set."
|
||||||
print "Please reload the quantum_package.rc file."
|
echo "Please reload the quantum_package.rc file."
|
||||||
exit -1
|
exit -1
|
||||||
fi
|
fi
|
||||||
|
|
||||||
@ -30,7 +30,7 @@ Build failed for module $MODULE
|
|||||||
"
|
"
|
||||||
fi
|
fi
|
||||||
fi
|
fi
|
||||||
${QPACKAGE_ROOT}/scripts/create_gitignore.sh
|
${QPACKAGE_ROOT}/scripts/module/create_gitignore.sh
|
||||||
cd ${OLDPWD}
|
cd ${OLDPWD}
|
||||||
done
|
done
|
||||||
${QPACKAGE_ROOT}/scripts/create_executables_list.sh
|
${QPACKAGE_ROOT}/scripts/module/create_executables_list.sh
|
||||||
@ -13,8 +13,9 @@ source ${QPACKAGE_ROOT}/scripts/qp_include.sh
|
|||||||
function do_clean()
|
function do_clean()
|
||||||
{
|
{
|
||||||
rm -rf -- \
|
rm -rf -- \
|
||||||
IRPF90_temp IRPF90_man Makefile.depend $(cat NEEDED_MODULES) include \
|
IRPF90_temp IRPF90_man Makefile.depend \
|
||||||
ezfio_interface.irp.f irpf90.make irpf90_entities tags $(ls_exe)
|
$(module_handler.py print_genealogy) include \
|
||||||
|
ezfio_interface.irp.f irpf90.make irpf90_entities tags $(ls_exe) *.mod
|
||||||
}
|
}
|
||||||
|
|
||||||
if [[ -z $1 ]]
|
if [[ -z $1 ]]
|
||||||
@ -14,7 +14,9 @@ source ${QPACKAGE_ROOT}/scripts/qp_include.sh
|
|||||||
|
|
||||||
check_current_dir_is_module
|
check_current_dir_is_module
|
||||||
|
|
||||||
OUTPUT=$(${QPACKAGE_ROOT}/scripts/check_dependencies.sh $@)
|
OUTPUT=$(module_handler.py check_dependencies $@)
|
||||||
echo ${OUTPUT} > NEEDED_MODULES
|
|
||||||
|
|
||||||
|
|
||||||
|
if [[ $? -eq 0 ]]
|
||||||
|
then
|
||||||
|
echo $@ > NEEDED_CHILDREN_MODULES
|
||||||
|
fi
|
||||||
202
scripts/module/module_handler.py
Executable file
202
scripts/module/module_handler.py
Executable file
@ -0,0 +1,202 @@
|
|||||||
|
#!/usr/bin/env python
|
||||||
|
# -*- coding: utf-8 -*-
|
||||||
|
|
||||||
|
"""
|
||||||
|
Create the NEEDED_MODULE
|
||||||
|
aka the genealogy (children module, subchildren module and so on),
|
||||||
|
of a NEEDED_CHILDREN_MODULES file
|
||||||
|
|
||||||
|
Usage:
|
||||||
|
module_handler.py print_genealogy [<NEEDED_CHILDREN_MODULES>]
|
||||||
|
module_handler.py check_dependencies [<module_name>...]
|
||||||
|
module_handler.py create_png [<NEEDED_CHILDREN_MODULES>]
|
||||||
|
|
||||||
|
Options:
|
||||||
|
print_genealogy Print the genealogy of the NEEDED_CHILDREN_MODULES
|
||||||
|
aka (children, subchildren, etc)
|
||||||
|
create_png Create a png of the file
|
||||||
|
NEEDED_CHILDREN_MODULES The path of NEEDED_CHILDREN_MODULES
|
||||||
|
by default try to open the file in the current path
|
||||||
|
"""
|
||||||
|
|
||||||
|
from docopt import docopt
|
||||||
|
|
||||||
|
import os
|
||||||
|
import sys
|
||||||
|
import os.path
|
||||||
|
from functools import wraps
|
||||||
|
|
||||||
|
|
||||||
|
def cache(func):
|
||||||
|
"""
|
||||||
|
A decorator for lazy evaluation off true function
|
||||||
|
"""
|
||||||
|
saved = {}
|
||||||
|
|
||||||
|
@wraps(func)
|
||||||
|
def newfunc(*args):
|
||||||
|
if args in saved:
|
||||||
|
return saved[args]
|
||||||
|
|
||||||
|
result = func(*args)
|
||||||
|
saved[args] = result
|
||||||
|
return result
|
||||||
|
return newfunc
|
||||||
|
|
||||||
|
|
||||||
|
@cache
|
||||||
|
def get_dict_genealogy():
|
||||||
|
"""Loop over MODULE in QPACKAGE_ROOT/src, open all the NEEDED_CHILDREN_MODULES
|
||||||
|
and create a dict[MODULE] = [sub module needed, ...]
|
||||||
|
"""
|
||||||
|
d_ref = dict()
|
||||||
|
|
||||||
|
qpackage_root = os.environ['QPACKAGE_ROOT']
|
||||||
|
dir_ = os.path.join(qpackage_root, 'src')
|
||||||
|
|
||||||
|
for o in os.listdir(dir_):
|
||||||
|
|
||||||
|
try:
|
||||||
|
with open(os.path.join(dir_, o, "NEEDED_CHILDREN_MODULES"), "r") as f:
|
||||||
|
l_children = f.read().split()
|
||||||
|
except IOError:
|
||||||
|
pass
|
||||||
|
else:
|
||||||
|
d_ref[o] = l_children
|
||||||
|
|
||||||
|
return d_ref
|
||||||
|
|
||||||
|
|
||||||
|
def module_genealogy(path):
|
||||||
|
"""
|
||||||
|
Take a name of a NEEDED_CHILDREN_MODULES
|
||||||
|
and return a list of all the {sub, subsub, ...}children
|
||||||
|
"""
|
||||||
|
try:
|
||||||
|
with open(path, "r") as f:
|
||||||
|
l_children = f.read().split()
|
||||||
|
except IOError as e:
|
||||||
|
print >> sys.stderr, e
|
||||||
|
sys.exit(1)
|
||||||
|
else:
|
||||||
|
|
||||||
|
needed_module = get_it_and_children(l_children)
|
||||||
|
|
||||||
|
return needed_module
|
||||||
|
|
||||||
|
|
||||||
|
def get_it_and_children(l_module):
|
||||||
|
"""
|
||||||
|
From a list of module return the module and all of the genealogy
|
||||||
|
"""
|
||||||
|
d_ref = get_dict_genealogy()
|
||||||
|
|
||||||
|
l = []
|
||||||
|
for module in l_module:
|
||||||
|
if module not in l:
|
||||||
|
l.append(module)
|
||||||
|
try:
|
||||||
|
l.extend(get_it_and_children(d_ref[module]))
|
||||||
|
except KeyError:
|
||||||
|
print >> sys.stderr, "`{0}` in not a good submodule name".format(module)
|
||||||
|
print >> sys.stderr, "Check the corresponding NEEDED_CHILDREN_MODULES"
|
||||||
|
sys.exit(1)
|
||||||
|
|
||||||
|
return list(set(l))
|
||||||
|
|
||||||
|
|
||||||
|
def get_all_children(l_module):
|
||||||
|
"""
|
||||||
|
From a list of module return all the genealogy
|
||||||
|
"""
|
||||||
|
|
||||||
|
it_and_all = get_it_and_children(l_module)
|
||||||
|
return [children for children in it_and_all if children not in l_module]
|
||||||
|
|
||||||
|
|
||||||
|
def reduce_(l_module):
|
||||||
|
"""
|
||||||
|
Take a l_module and try to find the lower combinaitions
|
||||||
|
of module with the same genealogy
|
||||||
|
"""
|
||||||
|
import itertools
|
||||||
|
d_ref = get_dict_genealogy()
|
||||||
|
|
||||||
|
target_genealogy = sorted(get_all_children(l_module))
|
||||||
|
|
||||||
|
for i in xrange(len(d_ref)):
|
||||||
|
for c in itertools.combinations(d_ref, i):
|
||||||
|
|
||||||
|
guess_genealogy = sorted(get_it_and_children(d_ref, c))
|
||||||
|
|
||||||
|
if target_genealogy == guess_genealogy:
|
||||||
|
return c
|
||||||
|
|
||||||
|
|
||||||
|
def create_png_from_path(path):
|
||||||
|
" Change a path like this into a module list"
|
||||||
|
"path = /home/razoa/quantum_package/src/Molden/NEEDED_CHILDREN_MODULES"
|
||||||
|
|
||||||
|
l_module = os.path.split(path)[0].split("/")[-1]
|
||||||
|
create_png([l_module])
|
||||||
|
|
||||||
|
|
||||||
|
def create_png(l_module):
|
||||||
|
"""Create the png of the dependancy tree for a l_module"""
|
||||||
|
|
||||||
|
# Init
|
||||||
|
import pydot
|
||||||
|
all_ready_done = []
|
||||||
|
|
||||||
|
def draw_module_edge(module, l_children):
|
||||||
|
"Draw all the module recursifly"
|
||||||
|
|
||||||
|
if module not in all_ready_done:
|
||||||
|
for children in l_children:
|
||||||
|
# Add Edge
|
||||||
|
edge = pydot.Edge(module, children)
|
||||||
|
graph.add_edge(edge)
|
||||||
|
# Recurs
|
||||||
|
draw_module_edge(children, d_ref[children])
|
||||||
|
all_ready_done.append(module)
|
||||||
|
|
||||||
|
# Init
|
||||||
|
graph = pydot.Dot(graph_type='digraph')
|
||||||
|
d_ref = get_dict_genealogy()
|
||||||
|
|
||||||
|
# Create all the edge
|
||||||
|
for module in l_module:
|
||||||
|
node_a = pydot.Node(module, fontcolor="red")
|
||||||
|
graph.add_node(node_a)
|
||||||
|
draw_module_edge(module, d_ref[module])
|
||||||
|
|
||||||
|
# Save
|
||||||
|
path = '{0}.png'.format("_".join(l_module))
|
||||||
|
print "png saved in {0}".format(path)
|
||||||
|
graph.write_png(path)
|
||||||
|
|
||||||
|
if __name__ == '__main__':
|
||||||
|
|
||||||
|
arguments = docopt(__doc__)
|
||||||
|
|
||||||
|
if not arguments['<NEEDED_CHILDREN_MODULES>']:
|
||||||
|
dir_ = os.getcwd()
|
||||||
|
path = os.path.join(dir_, "NEEDED_CHILDREN_MODULES")
|
||||||
|
else:
|
||||||
|
path = os.path.abspath(arguments['<NEEDED_CHILDREN_MODULES>'])
|
||||||
|
path = os.path.expanduser(path)
|
||||||
|
path = os.path.expandvars(path)
|
||||||
|
|
||||||
|
if arguments['print_genealogy']:
|
||||||
|
l_all_needed_molule = module_genealogy(path)
|
||||||
|
print " ".join(sorted(l_all_needed_molule))
|
||||||
|
|
||||||
|
elif arguments["check_dependencies"]:
|
||||||
|
l_module = arguments['<module_name>']
|
||||||
|
if l_module:
|
||||||
|
l_all_needed_molule = get_it_and_children(l_module)
|
||||||
|
else:
|
||||||
|
l_all_needed_molule = module_genealogy(path)
|
||||||
|
|
||||||
|
elif arguments["create_png"]:
|
||||||
|
create_png_from_path(path)
|
||||||
2125
scripts/module/pydot.py
Normal file
2125
scripts/module/pydot.py
Normal file
File diff suppressed because it is too large
Load Diff
@ -71,7 +71,7 @@ debug "Module does not already exist: OK"
|
|||||||
|
|
||||||
|
|
||||||
# Set up dependencies
|
# Set up dependencies
|
||||||
ALL_MODULES="${NEEDED_MODULES}"
|
ALL_MODULES="$(cat NEEDED_MODULES)"
|
||||||
echo "Select which modules you are sure you will need: (press q to quit)"
|
echo "Select which modules you are sure you will need: (press q to quit)"
|
||||||
NEEDED_MODULES=""
|
NEEDED_MODULES=""
|
||||||
select M in ${ALL_MODULES}
|
select M in ${ALL_MODULES}
|
||||||
@ -117,7 +117,7 @@ debug "Module directory is created."
|
|||||||
|
|
||||||
|
|
||||||
# Create the Makefile
|
# Create the Makefile
|
||||||
"${QPACKAGE_ROOT}/scripts/create_Makefile.sh" || fail "Unable to create Makefile"
|
"${QPACKAGE_ROOT}/scripts/module/create_Makefile.sh" || fail "Unable to create Makefile"
|
||||||
if [[ ! -f Makefile ]]
|
if [[ ! -f Makefile ]]
|
||||||
then
|
then
|
||||||
fail "Makefile was not created"
|
fail "Makefile was not created"
|
||||||
@ -125,8 +125,8 @@ fi
|
|||||||
debug "Makefile created"
|
debug "Makefile created"
|
||||||
|
|
||||||
# Create the NEEDED_MODULES file
|
# Create the NEEDED_MODULES file
|
||||||
"${QPACKAGE_ROOT}/scripts/create_Needed_modules.sh" ${NEEDED_MODULES} || fail "Unable to create the NEEDED_MODULES file"
|
"${QPACKAGE_ROOT}/scripts/module/create_Needed_modules.sh" ${NEEDED_MODULES} || fail "Unable to create the NEEDED_MODULES file"
|
||||||
if [[ ! -f NEEDED_MODULES ]]
|
if [[ ! -f NEEDED_CHILDREN_MODULES ]]
|
||||||
then
|
then
|
||||||
fail "NEEDED_MODULES was not created"
|
fail "NEEDED_MODULES was not created"
|
||||||
fi
|
fi
|
||||||
@ -135,7 +135,7 @@ debug "NEEDED_MODULES created"
|
|||||||
|
|
||||||
|
|
||||||
# Create rst templates
|
# Create rst templates
|
||||||
"${QPACKAGE_ROOT}/scripts/create_rst_templates.sh" || fail "Unable to create rst templates"
|
"${QPACKAGE_ROOT}/scripts/module/create_rst_templates.sh" || fail "Unable to create rst templates"
|
||||||
|
|
||||||
|
|
||||||
# Update module list in main NEEDED_MODULES
|
# Update module list in main NEEDED_MODULES
|
||||||
118
scripts/pseudo/elts_num_ele.py
Normal file
118
scripts/pseudo/elts_num_ele.py
Normal file
@ -0,0 +1,118 @@
|
|||||||
|
name_to_elec = {"H": 1,
|
||||||
|
"He": 2,
|
||||||
|
"Li": 3,
|
||||||
|
"Be": 4,
|
||||||
|
"B": 5,
|
||||||
|
"C": 6,
|
||||||
|
"N": 7,
|
||||||
|
"O": 8,
|
||||||
|
"F": 9,
|
||||||
|
"Ne": 10,
|
||||||
|
"Na": 11,
|
||||||
|
"Mg": 12,
|
||||||
|
"Al": 13,
|
||||||
|
"Si": 14,
|
||||||
|
"P": 15,
|
||||||
|
"S": 16,
|
||||||
|
"Cl": 17,
|
||||||
|
"Ar": 18,
|
||||||
|
"K": 19,
|
||||||
|
"Ca": 20,
|
||||||
|
"Sc": 21,
|
||||||
|
"Ti": 22,
|
||||||
|
"V": 23,
|
||||||
|
"Cr": 24,
|
||||||
|
"Mn": 25,
|
||||||
|
"Fe": 26,
|
||||||
|
"Co": 27,
|
||||||
|
"Ni": 28,
|
||||||
|
"Cu": 29,
|
||||||
|
"Zn": 30,
|
||||||
|
"Ga": 31,
|
||||||
|
"Ge": 32,
|
||||||
|
"As": 33,
|
||||||
|
"Se": 34,
|
||||||
|
"Br": 35,
|
||||||
|
"Kr": 36,
|
||||||
|
"Rb": 37,
|
||||||
|
"Sr": 38,
|
||||||
|
"Y": 39,
|
||||||
|
"Zr": 40,
|
||||||
|
"Nb": 41,
|
||||||
|
"Mo": 42,
|
||||||
|
"Tc": 43,
|
||||||
|
"Ru": 44,
|
||||||
|
"Rh": 45,
|
||||||
|
"Pd": 46,
|
||||||
|
"Ag": 47,
|
||||||
|
"Cd": 48,
|
||||||
|
"In": 49,
|
||||||
|
"Sn": 50,
|
||||||
|
"Sb": 51,
|
||||||
|
"Te": 52,
|
||||||
|
"I": 53,
|
||||||
|
"Xe": 54,
|
||||||
|
"Cs": 55,
|
||||||
|
"Ba": 56,
|
||||||
|
"La": 57,
|
||||||
|
"Ce": 58,
|
||||||
|
"Pr": 59,
|
||||||
|
"Nd": 60,
|
||||||
|
"Pm": 61,
|
||||||
|
"Sm": 62,
|
||||||
|
"Eu": 63,
|
||||||
|
"Gd": 64,
|
||||||
|
"Tb": 65,
|
||||||
|
"Dy": 66,
|
||||||
|
"Ho": 67,
|
||||||
|
"Er": 68,
|
||||||
|
"Tm": 69,
|
||||||
|
"Yb": 70,
|
||||||
|
"Lu": 71,
|
||||||
|
"Hf": 72,
|
||||||
|
"Ta": 73,
|
||||||
|
"W": 74,
|
||||||
|
"Re": 75,
|
||||||
|
"Os": 76,
|
||||||
|
"Ir": 77,
|
||||||
|
"Pt": 78,
|
||||||
|
"Au": 79,
|
||||||
|
"Hg": 80,
|
||||||
|
"Tl": 81,
|
||||||
|
"Pb": 82,
|
||||||
|
"Bi": 83,
|
||||||
|
"Po": 84,
|
||||||
|
"At": 85,
|
||||||
|
"Rn": 86,
|
||||||
|
"Fr": 87,
|
||||||
|
"Ra": 88,
|
||||||
|
"Ac": 89,
|
||||||
|
"Th": 90,
|
||||||
|
"Pa": 91,
|
||||||
|
"U": 92,
|
||||||
|
"Np": 93,
|
||||||
|
"Pu": 94,
|
||||||
|
"Am": 95,
|
||||||
|
"Cm": 96,
|
||||||
|
"Bk": 97,
|
||||||
|
"Cf": 98,
|
||||||
|
"Es": 99,
|
||||||
|
"Fm": 100,
|
||||||
|
"Md": 101,
|
||||||
|
"No": 102,
|
||||||
|
"Lr": 103,
|
||||||
|
"Rf": 104,
|
||||||
|
"Db": 105,
|
||||||
|
"Sg": 106,
|
||||||
|
"Bh": 107,
|
||||||
|
"Hs": 108,
|
||||||
|
"Mt": 109,
|
||||||
|
"Ds": 110,
|
||||||
|
"Rg": 111,
|
||||||
|
"Cn": 112,
|
||||||
|
"Uut": 113,
|
||||||
|
"Fl": 114,
|
||||||
|
"Uup": 115,
|
||||||
|
"Lv": 116,
|
||||||
|
"Uus": 117,
|
||||||
|
"Uuo": 118}
|
||||||
338
scripts/pseudo/put_pseudo_in_ezfio.py
Executable file
338
scripts/pseudo/put_pseudo_in_ezfio.py
Executable file
@ -0,0 +1,338 @@
|
|||||||
|
#!/usr/bin/env python
|
||||||
|
# -*- coding: utf-8 -*-
|
||||||
|
"""
|
||||||
|
Create the pseudo potential for a given atom
|
||||||
|
|
||||||
|
Usage:
|
||||||
|
put_pseudo_in_ezfio.py <ezfio_path>
|
||||||
|
|
||||||
|
Help:
|
||||||
|
atom is the Abreviation of the atom
|
||||||
|
"""
|
||||||
|
|
||||||
|
|
||||||
|
import os
|
||||||
|
import sys
|
||||||
|
from docopt import docopt
|
||||||
|
|
||||||
|
from subprocess import Popen, PIPE
|
||||||
|
|
||||||
|
qpackage_root = os.environ['QPACKAGE_ROOT']
|
||||||
|
|
||||||
|
EZFIO = "{0}/EZFIO".format(qpackage_root)
|
||||||
|
sys.path = [EZFIO + "/Python"] + sys.path
|
||||||
|
|
||||||
|
from ezfio import ezfio
|
||||||
|
|
||||||
|
import re
|
||||||
|
p = re.compile(ur'\|(\d+)><\d+\|')
|
||||||
|
|
||||||
|
|
||||||
|
def get_pseudo_str(l_atom):
|
||||||
|
"""
|
||||||
|
Run EMSL_local for geting the str of the speudo potential
|
||||||
|
|
||||||
|
str_ele :
|
||||||
|
Element Symbol: Na
|
||||||
|
Number of replaced protons: 10
|
||||||
|
Number of projectors: 2
|
||||||
|
|
||||||
|
Pseudopotential data:
|
||||||
|
|
||||||
|
Local component:
|
||||||
|
Coeff. r^n Exp.
|
||||||
|
1.00000000 -1 5.35838717
|
||||||
|
5.35838717 1 3.67918975
|
||||||
|
-2.07764789 0 1.60507673
|
||||||
|
|
||||||
|
Non-local component:
|
||||||
|
Coeff. r^n Exp. Proj.
|
||||||
|
10.69640234 0 1.32389367 |0><0|
|
||||||
|
10.11238853 0 1.14052020 |1><1|
|
||||||
|
"""
|
||||||
|
|
||||||
|
EMSL_root = "{0}/EMSL_Basis/".format(qpackage_root)
|
||||||
|
EMSL_path = "{0}/EMSL_api.py".format(EMSL_root)
|
||||||
|
db_path = "{0}/db/Pseudo.db".format(EMSL_root)
|
||||||
|
|
||||||
|
str_ = ""
|
||||||
|
|
||||||
|
for a in l_atom:
|
||||||
|
l_cmd_atom = ["--atom", a]
|
||||||
|
|
||||||
|
l_cmd_head = [EMSL_path, "get_basis_data",
|
||||||
|
"--db_path", db_path,
|
||||||
|
"--basis", "BFD-Pseudo"]
|
||||||
|
|
||||||
|
process = Popen(l_cmd_head + l_cmd_atom, stdout=PIPE, stderr=PIPE)
|
||||||
|
|
||||||
|
stdout, _ = process.communicate()
|
||||||
|
str_ += stdout.strip() + "\n"
|
||||||
|
|
||||||
|
return str_
|
||||||
|
|
||||||
|
|
||||||
|
def get_v_n_dz_local(str_ele):
|
||||||
|
"""
|
||||||
|
From a str_ele of the pseudo (aka only one ele in the str)
|
||||||
|
get the list ussefull for the Local potential : v_k n_k and dz_k
|
||||||
|
"""
|
||||||
|
l_v_k = []
|
||||||
|
l_n_k = []
|
||||||
|
l_dz_k = []
|
||||||
|
|
||||||
|
for l in str_ele.splitlines():
|
||||||
|
try:
|
||||||
|
v, n, dz = l.split()
|
||||||
|
v = float(v)
|
||||||
|
n = int(n)
|
||||||
|
dz = float(dz)
|
||||||
|
except ValueError:
|
||||||
|
pass
|
||||||
|
else:
|
||||||
|
l_v_k.append(v)
|
||||||
|
l_n_k.append(n)
|
||||||
|
l_dz_k.append(dz)
|
||||||
|
|
||||||
|
return l_v_k, l_n_k, l_dz_k
|
||||||
|
|
||||||
|
|
||||||
|
def get_v_n_dz_l_nonlocal(str_ele):
|
||||||
|
"""
|
||||||
|
From a str_ele of the pseudo (aka only one ele in the str)
|
||||||
|
get the list ussefull for the non Local potential
|
||||||
|
v_kl (v, l)
|
||||||
|
n_k (v, l)
|
||||||
|
dz_k (dz ,l)
|
||||||
|
"""
|
||||||
|
l_v_kl = []
|
||||||
|
l_n_kl = []
|
||||||
|
l_dz_kl = []
|
||||||
|
|
||||||
|
for l in str_ele.splitlines():
|
||||||
|
try:
|
||||||
|
v, n, dz, proj = l.split()
|
||||||
|
v = float(v)
|
||||||
|
n = int(n)
|
||||||
|
dz = float(dz)
|
||||||
|
l = int(p.match(proj).group(1))
|
||||||
|
|
||||||
|
except ValueError:
|
||||||
|
pass
|
||||||
|
else:
|
||||||
|
l_v_kl.append([v])
|
||||||
|
l_n_kl.append([n])
|
||||||
|
l_dz_kl.append([dz])
|
||||||
|
|
||||||
|
if not l_v_kl:
|
||||||
|
l_v_kl.append([0.])
|
||||||
|
l_n_kl.append([0])
|
||||||
|
l_dz_kl.append([0.])
|
||||||
|
|
||||||
|
return l_v_kl, l_n_kl, l_dz_kl
|
||||||
|
|
||||||
|
|
||||||
|
def get_zeff_alpha_beta(str_ele):
|
||||||
|
"""
|
||||||
|
Return the the zeff, alpha num elec and beta num elec
|
||||||
|
Assert ezfio_set_file alredy defined
|
||||||
|
"""
|
||||||
|
|
||||||
|
import re
|
||||||
|
|
||||||
|
# ___
|
||||||
|
# | ._ o _|_
|
||||||
|
# _|_ | | | |_
|
||||||
|
#
|
||||||
|
|
||||||
|
# ~#~#~#~#~#~#~ #
|
||||||
|
# s t r _ e l e #
|
||||||
|
# ~#~#~#~#~#~#~ #
|
||||||
|
|
||||||
|
# m = re.search('Element Symbol: ([a-zA-Z]+)', str_ele)
|
||||||
|
# name = m.group(1).capitalize()
|
||||||
|
name = str_ele.split("\n")[0].strip().capitalize()
|
||||||
|
|
||||||
|
m = re.search('Number of replaced protons: (\d+)', str_ele)
|
||||||
|
z_remove = int(m.group(1))
|
||||||
|
|
||||||
|
# _
|
||||||
|
# |_) _. ._ _ _
|
||||||
|
# | (_| | _> (/_
|
||||||
|
#
|
||||||
|
|
||||||
|
from elts_num_ele import name_to_elec
|
||||||
|
z = name_to_elec[name]
|
||||||
|
|
||||||
|
z_eff = z - z_remove
|
||||||
|
|
||||||
|
alpha = (z_remove / 2)
|
||||||
|
beta = (z_remove / 2)
|
||||||
|
|
||||||
|
# _
|
||||||
|
# |_) _ _|_ ._ ._
|
||||||
|
# | \ (/_ |_ |_| | | |
|
||||||
|
#
|
||||||
|
|
||||||
|
return [z_eff, alpha, beta]
|
||||||
|
|
||||||
|
|
||||||
|
def add_zero(array, size, type):
|
||||||
|
for add in xrange(len(array), size):
|
||||||
|
array.append([type(0)])
|
||||||
|
|
||||||
|
return array
|
||||||
|
|
||||||
|
|
||||||
|
def make_it_square(matrix, dim, type=float):
|
||||||
|
"""
|
||||||
|
matix the matrix to squate
|
||||||
|
dim array [lmax, kmax]
|
||||||
|
type the null value you want
|
||||||
|
[[[28.59107316], [19.37583724]], [[50.25646328]]]
|
||||||
|
=>
|
||||||
|
[[[28.59107316], [19.37583724]], [[50.25646328], [0.0]]]
|
||||||
|
"""
|
||||||
|
|
||||||
|
lmax = dim[0]
|
||||||
|
kmax = dim[1]
|
||||||
|
|
||||||
|
for l_list in matrix:
|
||||||
|
|
||||||
|
l_list = add_zero(l_list, lmax, type)
|
||||||
|
|
||||||
|
for k_list in list_:
|
||||||
|
k_list = add_zero(k_list, kmax, type)
|
||||||
|
|
||||||
|
return matrix
|
||||||
|
|
||||||
|
if __name__ == "__main__":
|
||||||
|
arguments = docopt(__doc__)
|
||||||
|
# ___
|
||||||
|
# | ._ o _|_
|
||||||
|
# _|_ | | | |_
|
||||||
|
#
|
||||||
|
|
||||||
|
# ~#~#~#~#~ #
|
||||||
|
# E Z F I O #
|
||||||
|
# ~#~#~#~#~ #
|
||||||
|
|
||||||
|
ezfio_path = arguments["<ezfio_path>"]
|
||||||
|
ezfio_path = os.path.expanduser(ezfio_path)
|
||||||
|
ezfio_path = os.path.expandvars(ezfio_path)
|
||||||
|
ezfio_path = os.path.abspath(ezfio_path)
|
||||||
|
|
||||||
|
ezfio.set_file("{0}".format(ezfio_path))
|
||||||
|
|
||||||
|
# ~#~#~#~#~#~#~#~#~#~#~ #
|
||||||
|
# P s e u d o _ d a t a #
|
||||||
|
# ~#~#~#~#~#~#~#~#~#~#~ #
|
||||||
|
|
||||||
|
l_ele = ezfio.get_nuclei_nucl_label()
|
||||||
|
str_ = get_pseudo_str(l_ele)
|
||||||
|
|
||||||
|
# _
|
||||||
|
# |_) _. ._ _ _
|
||||||
|
# | (_| | _> (/_
|
||||||
|
#
|
||||||
|
|
||||||
|
l_str_ele = [str_ele for str_ele in str_.split("Element Symbol: ")
|
||||||
|
if str_ele]
|
||||||
|
|
||||||
|
for i in "l_zeff v_k n_k dz_k v_kl n_kl dz_kl".split():
|
||||||
|
exec("{0} = []".format(i))
|
||||||
|
|
||||||
|
alpha_tot = 0
|
||||||
|
beta_tot = 0
|
||||||
|
|
||||||
|
for str_ele in l_str_ele:
|
||||||
|
|
||||||
|
# ~#~#~#~#~ #
|
||||||
|
# S p l i t #
|
||||||
|
# ~#~#~#~#~ #
|
||||||
|
|
||||||
|
l = str_ele.find("Local component:")
|
||||||
|
nl = str_ele.find("Non-local component")
|
||||||
|
|
||||||
|
# ~#~#~#~#~ #
|
||||||
|
# L o c a l #
|
||||||
|
# ~#~#~#~#~ #
|
||||||
|
|
||||||
|
l_v, l_n, l_dz = get_v_n_dz_local(str_ele[l:nl])
|
||||||
|
|
||||||
|
v_k.append(l_v)
|
||||||
|
n_k.append(l_n)
|
||||||
|
dz_k.append(l_dz)
|
||||||
|
|
||||||
|
# ~#~#~#~#~#~#~#~#~ #
|
||||||
|
# N o n _ L o c a l #
|
||||||
|
# ~#~#~#~#~#~#~#~#~ #
|
||||||
|
|
||||||
|
l_v_kl, l_n_kl, l_dz_kl = get_v_n_dz_l_nonlocal(str_ele[nl:])
|
||||||
|
|
||||||
|
v_kl.append(l_v_kl)
|
||||||
|
n_kl.append(l_n_kl)
|
||||||
|
dz_kl.append(l_dz_kl)
|
||||||
|
|
||||||
|
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
|
||||||
|
# Z _ e f f , a l p h a / b e t a _ e l e c #
|
||||||
|
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
|
||||||
|
|
||||||
|
zeff, alpha, beta = get_zeff_alpha_beta(str_ele)
|
||||||
|
|
||||||
|
alpha_tot += alpha
|
||||||
|
beta_tot += beta
|
||||||
|
l_zeff.append(zeff)
|
||||||
|
# _
|
||||||
|
# /\ _| _| _|_ _ _ _ _|_ o _
|
||||||
|
# /--\ (_| (_| |_ (_) (/_ /_ | | (_)
|
||||||
|
#
|
||||||
|
|
||||||
|
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
|
||||||
|
# Z _ e f f , a l p h a / b e t a _ e l e c #
|
||||||
|
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
|
||||||
|
|
||||||
|
ezfio.nuclei_nucl_charge = l_zeff
|
||||||
|
|
||||||
|
alpha_tot = ezfio.get_electrons_elec_alpha_num() - alpha_tot
|
||||||
|
beta_tot = ezfio.get_electrons_elec_beta_num() - beta_tot
|
||||||
|
|
||||||
|
ezfio.electrons_elec_alpha_num = alpha_tot
|
||||||
|
ezfio.electrons_elec_beta_num = beta_tot
|
||||||
|
|
||||||
|
# Change all the array 'cause EZFIO
|
||||||
|
# v_kl (v, l) => v_kl(l,v)
|
||||||
|
# v_kl => zip(*_v_kl)
|
||||||
|
# [[7.0, 79.74474797, -49.45159098], [1.0, 5.41040609, -4.60151975]]
|
||||||
|
# [(7.0, 1.0), (79.74474797, 5.41040609), (-49.45159098, -4.60151975)]
|
||||||
|
|
||||||
|
# ~#~#~#~#~ #
|
||||||
|
# L o c a l #
|
||||||
|
# ~#~#~#~#~ #
|
||||||
|
|
||||||
|
klocmax = max([len(i) for i in v_k])
|
||||||
|
ezfio.pseudo_intergrals_klocmax = klocmax
|
||||||
|
|
||||||
|
ezfio.pseudo_intergrals_v_k = zip(*v_k)
|
||||||
|
ezfio.pseudo_intergrals_n_k = zip(*n_k)
|
||||||
|
ezfio.pseudo_intergrals_dz_k = zip(*dz_k)
|
||||||
|
|
||||||
|
# ~#~#~#~#~#~#~#~#~ #
|
||||||
|
# N o n _ L o c a l #
|
||||||
|
# ~#~#~#~#~#~#~#~#~ #
|
||||||
|
|
||||||
|
lmax = max([len(i) for i in v_kl])
|
||||||
|
kmax = max([len(sublist) for list_ in v_kl for sublist in list_])
|
||||||
|
|
||||||
|
ezfio.pseudo_intergrals_lmaxpo = lmax
|
||||||
|
ezfio.pseudo_intergrals_kmax = kmax
|
||||||
|
|
||||||
|
v_kl = make_it_square(v_kl, [lmax, kmax])
|
||||||
|
n_kl = make_it_square(n_kl, [lmax, kmax], int)
|
||||||
|
dz_kl = make_it_square(dz_kl, [lmax, kmax])
|
||||||
|
|
||||||
|
ezfio.pseudo_intergrals_v_kl = zip(*v_kl)
|
||||||
|
ezfio.pseudo_intergrals_n_kl = zip(*n_kl)
|
||||||
|
ezfio.pseudo_intergrals_dz_kl = zip(*dz_kl)
|
||||||
|
|
||||||
|
ezfio.pseudo_intergrals_do_pseudo = True
|
||||||
@ -1,210 +0,0 @@
|
|||||||
#!/usr/bin/env python
|
|
||||||
|
|
||||||
import sys,os
|
|
||||||
try:
|
|
||||||
QPACKAGE_ROOT = os.environ["QPACKAGE_ROOT"]
|
|
||||||
except:
|
|
||||||
print "Error: QPACKAGE_ROOT environment variable not found."
|
|
||||||
sys.exit(1)
|
|
||||||
|
|
||||||
sys.path = [ QPACKAGE_ROOT+"/EZFIO/Python", QPACKAGE_ROOT+"/resultsFile" ]+sys.path
|
|
||||||
from ezfio import ezfio
|
|
||||||
import ezfio as ez
|
|
||||||
print "EZFIO: ", os.path.dirname(ez.__file__)
|
|
||||||
|
|
||||||
try:
|
|
||||||
from resultsFile import *
|
|
||||||
except:
|
|
||||||
print "Error: resultsFile Python library not installed"
|
|
||||||
sys.exit(1)
|
|
||||||
|
|
||||||
|
|
||||||
def write_ezfioFile(res,filename):
|
|
||||||
res.clean_uncontractions()
|
|
||||||
ezfio.set_file(filename)
|
|
||||||
|
|
||||||
# Electrons
|
|
||||||
ezfio.set_electrons_elec_alpha_num(res.num_alpha)
|
|
||||||
ezfio.set_electrons_elec_beta_num(res.num_beta)
|
|
||||||
|
|
||||||
# Nuclei
|
|
||||||
ezfio.set_nuclei_nucl_num(len(res.geometry))
|
|
||||||
charge = []
|
|
||||||
coord = []
|
|
||||||
coord_x = []
|
|
||||||
coord_y = []
|
|
||||||
coord_z = []
|
|
||||||
for a in res.geometry:
|
|
||||||
charge.append(a.charge)
|
|
||||||
if res.units == 'BOHR':
|
|
||||||
coord_x.append(a.coord[0])
|
|
||||||
coord_y.append(a.coord[1])
|
|
||||||
coord_z.append(a.coord[2])
|
|
||||||
else:
|
|
||||||
coord_x.append(a.coord[0]/a0)
|
|
||||||
coord_y.append(a.coord[1]/a0)
|
|
||||||
coord_z.append(a.coord[2]/a0)
|
|
||||||
ezfio.set_nuclei_nucl_charge(charge)
|
|
||||||
label = map(lambda x: x.name, res.geometry)
|
|
||||||
ezfio.set_nuclei_nucl_label(label)
|
|
||||||
ezfio.set_nuclei_nucl_coord(coord_x+coord_y+coord_z)
|
|
||||||
|
|
||||||
# Basis
|
|
||||||
basis = res.uncontracted_basis
|
|
||||||
geom = res.geometry
|
|
||||||
|
|
||||||
res.clean_contractions()
|
|
||||||
# AO Basis
|
|
||||||
import string
|
|
||||||
at = []
|
|
||||||
num_prim = []
|
|
||||||
magnetic_number = []
|
|
||||||
angular_number = []
|
|
||||||
power_x = []
|
|
||||||
power_y = []
|
|
||||||
power_z = []
|
|
||||||
coefficient = []
|
|
||||||
exponent = []
|
|
||||||
res.convert_to_cartesian()
|
|
||||||
for b in res.basis:
|
|
||||||
c = b.center
|
|
||||||
for i,atom in enumerate(res.geometry):
|
|
||||||
if atom.coord == c:
|
|
||||||
at.append(i+1)
|
|
||||||
num_prim.append(len(b.prim))
|
|
||||||
s = b.sym
|
|
||||||
power_x.append( string.count(s,"x") )
|
|
||||||
power_y.append( string.count(s,"y") )
|
|
||||||
power_z.append( string.count(s,"z") )
|
|
||||||
coefficient.append( b.coef )
|
|
||||||
exponent.append( [ p.expo for p in b.prim ] )
|
|
||||||
ezfio.set_ao_basis_ao_num(len(res.basis))
|
|
||||||
ezfio.set_ao_basis_ao_nucl(at)
|
|
||||||
ezfio.set_ao_basis_ao_prim_num(num_prim)
|
|
||||||
ezfio.set_ao_basis_ao_power(power_x+power_y+power_z)
|
|
||||||
prim_num_max = ezfio.get_ao_basis_ao_prim_num_max()
|
|
||||||
len_res_basis = len(res.basis)
|
|
||||||
for i in range(len(res.basis)):
|
|
||||||
coefficient[i] += [ 0. for j in range(len(coefficient[i]),prim_num_max) ]
|
|
||||||
exponent[i] += [ 0. for j in range(len(exponent[i]),prim_num_max) ]
|
|
||||||
coefficient = reduce(lambda x, y: x+y, coefficient, [])
|
|
||||||
exponent = reduce(lambda x, y: x+y, exponent, [])
|
|
||||||
coef = []
|
|
||||||
expo = []
|
|
||||||
for i in range(prim_num_max):
|
|
||||||
for j in range(i,len(coefficient),prim_num_max):
|
|
||||||
coef.append ( coefficient[j] )
|
|
||||||
expo.append ( exponent[j] )
|
|
||||||
ezfio.set_ao_basis_ao_coef(coef)
|
|
||||||
ezfio.set_ao_basis_ao_expo(expo)
|
|
||||||
ezfio.set_ao_basis_ao_basis("Read by resultsFile")
|
|
||||||
|
|
||||||
|
|
||||||
# MO
|
|
||||||
MoTag = res.determinants_mo_type
|
|
||||||
ezfio.set_mo_basis_mo_label('Orthonormalized')
|
|
||||||
MO_type = MoTag
|
|
||||||
allMOs = res.mo_sets[MO_type]
|
|
||||||
|
|
||||||
|
|
||||||
try:
|
|
||||||
closed = [ (allMOs[i].eigenvalue,i) for i in res.closed_mos ]
|
|
||||||
active = [ (allMOs[i].eigenvalue,i) for i in res.active_mos ]
|
|
||||||
virtual =[ (allMOs[i].eigenvalue,i) for i in res.virtual_mos ]
|
|
||||||
except:
|
|
||||||
closed = []
|
|
||||||
virtual = []
|
|
||||||
active = [ (allMOs[i].eigenvalue,i) for i in range(len(allMOs)) ]
|
|
||||||
|
|
||||||
# closed.sort()
|
|
||||||
# active.sort()
|
|
||||||
# virtual.sort()
|
|
||||||
closed = map( lambda x: x[1], closed)
|
|
||||||
active = map( lambda x: x[1], active)
|
|
||||||
virtual = map( lambda x: x[1], virtual)
|
|
||||||
MOindices = closed + active + virtual
|
|
||||||
|
|
||||||
MOs = []
|
|
||||||
for i in MOindices:
|
|
||||||
MOs.append(allMOs[i])
|
|
||||||
|
|
||||||
mo_tot_num = len(MOs)
|
|
||||||
while len(MOindices) < mo_tot_num:
|
|
||||||
MOindices.append(len(MOindices))
|
|
||||||
|
|
||||||
MOmap = list(MOindices)
|
|
||||||
for i in range(len(MOindices)):
|
|
||||||
MOmap[i] = MOindices.index(i)
|
|
||||||
|
|
||||||
energies = []
|
|
||||||
for i in xrange(mo_tot_num):
|
|
||||||
energies.append(MOs[i].eigenvalue)
|
|
||||||
|
|
||||||
if res.occ_num is not None:
|
|
||||||
OccNum = []
|
|
||||||
for i in MOindices:
|
|
||||||
OccNum.append(res.occ_num[MO_type][i])
|
|
||||||
|
|
||||||
while len(OccNum) < mo_tot_num:
|
|
||||||
OccNum.append(0.)
|
|
||||||
|
|
||||||
MoMatrix = []
|
|
||||||
sym0 = [ i.sym for i in res.mo_sets[MO_type] ]
|
|
||||||
sym = [ i.sym for i in res.mo_sets[MO_type] ]
|
|
||||||
for i in xrange(len(sym)):
|
|
||||||
sym[MOmap[i]] = sym0[i]
|
|
||||||
|
|
||||||
MoMatrix = []
|
|
||||||
for i in xrange(len(MOs)):
|
|
||||||
m = MOs[i]
|
|
||||||
for coef in m.vector:
|
|
||||||
MoMatrix.append(coef)
|
|
||||||
|
|
||||||
while len(MoMatrix) < len(MOs[0].vector)**2:
|
|
||||||
MoMatrix.append(0.)
|
|
||||||
|
|
||||||
mo = []
|
|
||||||
for i in MOindices:
|
|
||||||
mo.append(res.mo_sets[MoTag][i])
|
|
||||||
|
|
||||||
if len(mo) < mo_tot_num:
|
|
||||||
newmo = orbital()
|
|
||||||
newmo.eigenvalue = 0.
|
|
||||||
newmo.vector = [0. for i in range(mo_tot_num)]
|
|
||||||
newmo.vector[len(mo)] = 1.
|
|
||||||
while len(mo) < mo_tot_num:
|
|
||||||
mo.append(newmo)
|
|
||||||
Energies = [ m.eigenvalue for m in mo ]
|
|
||||||
|
|
||||||
ezfio.set_mo_basis_mo_tot_num(mo_tot_num)
|
|
||||||
ezfio.set_mo_basis_mo_occ(OccNum)
|
|
||||||
ezfio.set_mo_basis_mo_coef(MoMatrix)
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
if __name__ == '__main__':
|
|
||||||
# Check command line
|
|
||||||
|
|
||||||
det_threshold = 0.
|
|
||||||
|
|
||||||
if len(sys.argv) == 2:
|
|
||||||
State=0
|
|
||||||
elif len(sys.argv) == 3:
|
|
||||||
State=int(sys.argv[2])
|
|
||||||
else:
|
|
||||||
print "usage: "+sys.argv[0]+" file.out [state]"
|
|
||||||
sys.exit(2)
|
|
||||||
|
|
||||||
firstArg = sys.argv[1]
|
|
||||||
|
|
||||||
file = getFile(firstArg)
|
|
||||||
print firstArg, 'recognized as', str(file).split('.')[-1].split()[0]
|
|
||||||
|
|
||||||
filename = firstArg+".ezfio"
|
|
||||||
write_ezfioFile(file,filename)
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
@ -35,9 +35,10 @@ function check_current_dir_is_module()
|
|||||||
exit -1
|
exit -1
|
||||||
fi
|
fi
|
||||||
}
|
}
|
||||||
if [[ -f NEEDED_MODULES ]]
|
|
||||||
|
if [[ -f NEEDED_CHILDREN_MODULES ]]
|
||||||
then
|
then
|
||||||
NEEDED_MODULES=$(cat NEEDED_MODULES)
|
NEEDED_MODULES=$(module_handler.py print_genealogy NEEDED_CHILDREN_MODULES)
|
||||||
fi
|
fi
|
||||||
|
|
||||||
# List of executables in the current directory
|
# List of executables in the current directory
|
||||||
|
|||||||
@ -14,7 +14,7 @@ check_current_dir_is_module
|
|||||||
|
|
||||||
# Check if the NEEDED_MODULES file is consistent
|
# Check if the NEEDED_MODULES file is consistent
|
||||||
INCLUDE_DIRS="${NEEDED_MODULES} include"
|
INCLUDE_DIRS="${NEEDED_MODULES} include"
|
||||||
NEEDED_MODULES_OK=$( ${QPACKAGE_ROOT}/scripts/check_dependencies.sh ${NEEDED_MODULES} )
|
NEEDED_MODULES_OK=$(module_handler.py check_dependencies ${NEEDED_MODULES} )
|
||||||
if [[ $? -ne 0 ]]
|
if [[ $? -ne 0 ]]
|
||||||
then
|
then
|
||||||
error "
|
error "
|
||||||
@ -28,7 +28,7 @@ fi
|
|||||||
# Check if README.rst exists
|
# Check if README.rst exists
|
||||||
if [[ ! -f README.rst ]]
|
if [[ ! -f README.rst ]]
|
||||||
then
|
then
|
||||||
${QPACKAGE_ROOT}/scripts/create_rst_templates.sh
|
${QPACKAGE_ROOT}/scripts/module/create_rst_templates.sh
|
||||||
error "
|
error "
|
||||||
README.rst was not present, so I created a
|
README.rst was not present, so I created a
|
||||||
default one for you.
|
default one for you.
|
||||||
@ -62,7 +62,7 @@ then
|
|||||||
fi
|
fi
|
||||||
|
|
||||||
# Update Makefile.depend
|
# Update Makefile.depend
|
||||||
${QPACKAGE_ROOT}/scripts/create_Makefile_depend.sh
|
${QPACKAGE_ROOT}/scripts/module/create_Makefile_depend.sh
|
||||||
|
|
||||||
# Update EZFIO interface
|
# Update EZFIO interface
|
||||||
${QPACKAGE_ROOT}/scripts/ezfio_interface/ei_handler.py
|
${QPACKAGE_ROOT}/scripts/ezfio_interface/ei_handler.py
|
||||||
|
|||||||
@ -52,7 +52,7 @@ ${IRPF90_VERSION}.
|
|||||||
|
|
||||||
IRPF90 version >= ${IRPF90_REQUIRED_VERSION} is required.
|
IRPF90 version >= ${IRPF90_REQUIRED_VERSION} is required.
|
||||||
To upgrade IRPF90, run :
|
To upgrade IRPF90, run :
|
||||||
${QPACKAGE_ROOT}/scripts/upgrade_irpf90.sh
|
${QPACKAGE_ROOT}/scripts/upgrade/upgrade_irpf90.sh
|
||||||
"
|
"
|
||||||
else
|
else
|
||||||
info "irpf90 version is OK"
|
info "irpf90 version is OK"
|
||||||
@ -75,7 +75,7 @@ then
|
|||||||
Current EZFIO version : ${EZFIO_VERSION}
|
Current EZFIO version : ${EZFIO_VERSION}
|
||||||
EZFIO version >= ${EZFIO_REQUIRED_VERSION} is required.
|
EZFIO version >= ${EZFIO_REQUIRED_VERSION} is required.
|
||||||
To upgrade EZFIO, run :
|
To upgrade EZFIO, run :
|
||||||
${QPACKAGE_ROOT}/scripts/upgrade_ezfio.sh
|
${QPACKAGE_ROOT}/scripts/upgrade/upgrade_ezfio.sh
|
||||||
"
|
"
|
||||||
else
|
else
|
||||||
info "EZFIO version is OK"
|
info "EZFIO version is OK"
|
||||||
|
|||||||
@ -83,7 +83,7 @@ def update_needed(data):
|
|||||||
"""Read the NEEDED_MODULES file, and replace the data with it.
|
"""Read the NEEDED_MODULES file, and replace the data with it.
|
||||||
Create the links to the GitHub pages."""
|
Create the links to the GitHub pages."""
|
||||||
|
|
||||||
file = open('NEEDED_MODULES', 'r')
|
file = open('NEEDED_CHILDREN_MODULES', 'r')
|
||||||
modules = file.read()
|
modules = file.read()
|
||||||
file.close()
|
file.close()
|
||||||
|
|
||||||
|
|||||||
@ -12,7 +12,7 @@ fi
|
|||||||
cd -- ${QPACKAGE_ROOT}
|
cd -- ${QPACKAGE_ROOT}
|
||||||
mv -- ${QPACKAGE_ROOT}/EZFIO ${QPACKAGE_ROOT}/EZFIO.old
|
mv -- ${QPACKAGE_ROOT}/EZFIO ${QPACKAGE_ROOT}/EZFIO.old
|
||||||
|
|
||||||
${QPACKAGE_ROOT}/scripts/install_ezfio.sh
|
${QPACKAGE_ROOT}/scripts/install/install_ezfio.sh
|
||||||
|
|
||||||
if [[ $? -eq 0 ]]
|
if [[ $? -eq 0 ]]
|
||||||
then
|
then
|
||||||
@ -12,7 +12,7 @@ fi
|
|||||||
cd -- ${QPACKAGE_ROOT}
|
cd -- ${QPACKAGE_ROOT}
|
||||||
mv -f -- ${QPACKAGE_ROOT}/irpf90 ${QPACKAGE_ROOT}/irpf90.old
|
mv -f -- ${QPACKAGE_ROOT}/irpf90 ${QPACKAGE_ROOT}/irpf90.old
|
||||||
|
|
||||||
${QPACKAGE_ROOT}/scripts/install_irpf90.sh
|
${QPACKAGE_ROOT}/scripts/install/install_irpf90.sh
|
||||||
|
|
||||||
if [[ $? -eq 0 ]]
|
if [[ $? -eq 0 ]]
|
||||||
then
|
then
|
||||||
@ -17,8 +17,10 @@ export QPACKAGE_ROOT=\$( cd \$(dirname "\${BASH_SOURCE}") ; pwd -P )
|
|||||||
export LD_LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LD_LIBRARY_PATH}
|
export LD_LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LD_LIBRARY_PATH}
|
||||||
export LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LIBRARY_PATH}
|
export LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LIBRARY_PATH}
|
||||||
export C_INCLUDE_PATH="\${QPACKAGE_ROOT}"/include:\${C_INCLUDE_PATH}
|
export C_INCLUDE_PATH="\${QPACKAGE_ROOT}"/include:\${C_INCLUDE_PATH}
|
||||||
export PYTHONPATH=\${PYTHONPATH}:"\${QPACKAGE_ROOT}"/scripts:"\${QPACKAGE_ROOT}"/scripts/ezfio_interface
|
|
||||||
export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/scripts:"\${QPACKAGE_ROOT}"/scripts/ezfio_interface
|
export PYTHONPATH=\${PYTHONPATH}\$(find "${QPACKAGE_ROOT}"/scripts -type d -printf ":%p")
|
||||||
|
|
||||||
|
export PATH=\${PATH}\$(find "${QPACKAGE_ROOT}"/scripts -type d -printf ":%p")
|
||||||
export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/bin
|
export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/bin
|
||||||
export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/ocaml
|
export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/ocaml
|
||||||
source "\${QPACKAGE_ROOT}"/bin/irpman &> /dev/null
|
source "\${QPACKAGE_ROOT}"/bin/irpman &> /dev/null
|
||||||
@ -28,37 +30,29 @@ EOF
|
|||||||
source quantum_package.rc
|
source quantum_package.rc
|
||||||
|
|
||||||
echo "${BLUE}===== Installing IRPF90 ===== ${BLACK}"
|
echo "${BLUE}===== Installing IRPF90 ===== ${BLACK}"
|
||||||
${QPACKAGE_ROOT}/scripts/install_irpf90.sh | tee install_irpf90.log
|
${QPACKAGE_ROOT}/scripts/install/install_irpf90.sh | tee ${QPACKAGE_ROOT}/install_logs/install_irpf90.log
|
||||||
if [[ ! -d ${QPACKAGE_ROOT}/irpf90 ]]
|
if [[ ! -d ${QPACKAGE_ROOT}/irpf90 ]] || [[ ! -x ${QPACKAGE_ROOT}/bin/irpf90 ]] || [[ ! -x ${QPACKAGE_ROOT}/bin/irpman ]]
|
||||||
then
|
|
||||||
echo $RED "Error in IRPF90 installation" $BLACK
|
|
||||||
exit 1
|
|
||||||
fi
|
|
||||||
|
|
||||||
if [[ ! -x ${QPACKAGE_ROOT}/bin/irpf90 ]]
|
|
||||||
then
|
|
||||||
echo $RED "Error in IRPF90 installation" $BLACK
|
|
||||||
exit 1
|
|
||||||
fi
|
|
||||||
|
|
||||||
if [[ ! -x ${QPACKAGE_ROOT}/bin/irpman ]]
|
|
||||||
then
|
then
|
||||||
echo $RED "Error in IRPF90 installation" $BLACK
|
echo $RED "Error in IRPF90 installation" $BLACK
|
||||||
exit 1
|
exit 1
|
||||||
fi
|
fi
|
||||||
|
|
||||||
|
mkdir -p ${QPACKAGE_ROOT}/install_logs
|
||||||
|
|
||||||
echo "${BLUE}===== Installing Zlib ===== ${BLACK}"
|
echo "${BLUE}===== Installing Zlib ===== ${BLACK}"
|
||||||
${QPACKAGE_ROOT}/scripts/install_zlib.sh | tee install_zlib.log
|
${QPACKAGE_ROOT}/scripts/install/install_zlib.sh | tee ${QPACKAGE_ROOT}/install_logs/install_zlib.log
|
||||||
|
|
||||||
echo "${BLUE}===== Installing Curl ===== ${BLACK}"
|
echo "${BLUE}===== Installing Curl ===== ${BLACK}"
|
||||||
${QPACKAGE_ROOT}/scripts/install_curl.sh | tee install_curl.log
|
${QPACKAGE_ROOT}/scripts/install/install_curl.sh | tee ${QPACKAGE_ROOT}/install_logs/install_curl.log
|
||||||
|
|
||||||
echo "${BLUE}===== Installing M4 ===== ${BLACK}"
|
echo "${BLUE}===== Installing M4 ===== ${BLACK}"
|
||||||
${QPACKAGE_ROOT}/scripts/install_m4.sh | tee install_m4.log
|
${QPACKAGE_ROOT}/scripts/install/install_m4.sh | tee ${QPACKAGE_ROOT}/install_logs/install_m4.log
|
||||||
|
|
||||||
|
echo "${BLUE}===== Installing Docopt ===== ${BLACK}"
|
||||||
|
${QPACKAGE_ROOT}/scripts/install/install_docopt.sh | tee ${QPACKAGE_ROOT}/install_logs/install_docopt.log
|
||||||
|
|
||||||
echo "${BLUE}===== Installing EMSL Basis set library ===== ${BLACK}"
|
echo "${BLUE}===== Installing EMSL Basis set library ===== ${BLACK}"
|
||||||
${QPACKAGE_ROOT}/scripts/install_emsl.sh | tee install_emsl.log
|
${QPACKAGE_ROOT}/scripts/install/install_emsl.sh | tee ${QPACKAGE_ROOT}/install_logs/install_emsl.log
|
||||||
|
|
||||||
if [[ ! -d ${QPACKAGE_ROOT}/EMSL_Basis ]]
|
if [[ ! -d ${QPACKAGE_ROOT}/EMSL_Basis ]]
|
||||||
then
|
then
|
||||||
@ -68,7 +62,7 @@ fi
|
|||||||
|
|
||||||
echo "${BLUE}===== Installing EZFIO ===== ${BLACK}"
|
echo "${BLUE}===== Installing EZFIO ===== ${BLACK}"
|
||||||
|
|
||||||
${QPACKAGE_ROOT}/scripts/install_ezfio.sh | tee install_ezfio.log
|
${QPACKAGE_ROOT}/scripts/install/install_ezfio.sh | tee ${QPACKAGE_ROOT}/install_logs/install_ezfio.log
|
||||||
if [[ ! -d ${QPACKAGE_ROOT}/EZFIO ]]
|
if [[ ! -d ${QPACKAGE_ROOT}/EZFIO ]]
|
||||||
then
|
then
|
||||||
echo $RED "Error in EZFIO installation" $BLACK
|
echo $RED "Error in EZFIO installation" $BLACK
|
||||||
@ -78,7 +72,7 @@ fi
|
|||||||
|
|
||||||
echo "${BLUE}===== Installing Ocaml compiler and libraries ===== ${BLACK}"
|
echo "${BLUE}===== Installing Ocaml compiler and libraries ===== ${BLACK}"
|
||||||
rm -f -- ocaml/Qptypes.ml
|
rm -f -- ocaml/Qptypes.ml
|
||||||
${QPACKAGE_ROOT}/scripts/install_ocaml.sh | tee install_ocaml.log
|
${QPACKAGE_ROOT}/scripts/install/install_ocaml.sh | tee ${QPACKAGE_ROOT}/install_logs/install_ocaml.log
|
||||||
|
|
||||||
if [[ ! -f ${QPACKAGE_ROOT}/ocaml/Qptypes.ml ]]
|
if [[ ! -f ${QPACKAGE_ROOT}/ocaml/Qptypes.ml ]]
|
||||||
then
|
then
|
||||||
@ -87,7 +81,7 @@ then
|
|||||||
fi
|
fi
|
||||||
|
|
||||||
echo "${BLUE}===== Installing resultsFile Python library ===== ${BLACK}"
|
echo "${BLUE}===== Installing resultsFile Python library ===== ${BLACK}"
|
||||||
${QPACKAGE_ROOT}/scripts/install_resultsFile.sh
|
${QPACKAGE_ROOT}/scripts/install/install_resultsFile.sh
|
||||||
if [[ ! -d ${QPACKAGE_ROOT}/resultsFile ]]
|
if [[ ! -d ${QPACKAGE_ROOT}/resultsFile ]]
|
||||||
then
|
then
|
||||||
echo $RED "Error in resultsFile installation" $BLACK
|
echo $RED "Error in resultsFile installation" $BLACK
|
||||||
@ -106,8 +100,7 @@ source ${QPACKAGE_ROOT}/quantum_package.rc
|
|||||||
" $BLACK
|
" $BLACK
|
||||||
|
|
||||||
|
|
||||||
mkdir -p ${QPACKAGE_ROOT}/install_logs
|
|
||||||
mv ${QPACKAGE_ROOT}/*.log ${QPACKAGE_ROOT}/install_logs/
|
|
||||||
|
|
||||||
if [[ $1 == "--robot" ]] ;
|
if [[ $1 == "--robot" ]] ;
|
||||||
then
|
then
|
||||||
|
|||||||
@ -1,8 +1 @@
|
|||||||
* The atomic orbitals are normalized:
|
|
||||||
|
|
||||||
.. math::
|
|
||||||
|
|
||||||
\int \left(\chi_i({\bf r}) \right)^2 dr = 1
|
|
||||||
|
|
||||||
* The AO coefficients in the EZFIO files are not necessarily normalized and are normalized after reading
|
* The AO coefficients in the EZFIO files are not necessarily normalized and are normalized after reading
|
||||||
* The AO coefficients and exponents are ordered in increasing order of exponents
|
|
||||||
|
|||||||
1
src/AOs/NEEDED_CHILDREN_MODULES
Normal file
1
src/AOs/NEEDED_CHILDREN_MODULES
Normal file
@ -0,0 +1 @@
|
|||||||
|
Nuclei
|
||||||
@ -1,2 +0,0 @@
|
|||||||
Ezfio_files Nuclei Output Utils
|
|
||||||
|
|
||||||
@ -17,21 +17,19 @@ The AO coefficients are normalized as:
|
|||||||
|
|
||||||
{\tilde c}_{ki} = \frac{c_{ki}}{ \int \left( (x-X_A)^a (y-Y_A)^b (z-Z_A)^c e^{-\gamma_{ki} |{\bf r} - {\bf R}_A|^2} \right)^2} dr
|
{\tilde c}_{ki} = \frac{c_{ki}}{ \int \left( (x-X_A)^a (y-Y_A)^b (z-Z_A)^c e^{-\gamma_{ki} |{\bf r} - {\bf R}_A|^2} \right)^2} dr
|
||||||
|
|
||||||
|
Warning: ``ao_coef`` contains the AO coefficients given in input. These do not
|
||||||
|
include the normalization constant of the AO. The ``ao_coef_normalized`` includes
|
||||||
|
this normalization factor.
|
||||||
|
|
||||||
|
The AOs are also sorted by increasing exponent to accelerate the calculation of
|
||||||
|
the two electron integrals.
|
||||||
|
|
||||||
Assumptions
|
Assumptions
|
||||||
===========
|
===========
|
||||||
|
|
||||||
.. Do not edit this section. It was auto-generated from the
|
.. Do not edit this section. It was auto-generated from the
|
||||||
.. NEEDED_MODULES file.
|
.. NEEDED_MODULES file.
|
||||||
|
|
||||||
* The atomic orbitals are normalized:
|
|
||||||
|
|
||||||
.. math::
|
|
||||||
|
|
||||||
\int \left(\chi_i({\bf r}) \right)^2 dr = 1
|
|
||||||
|
|
||||||
* The AO coefficients in the EZFIO files are not necessarily normalized and are normalized after reading
|
|
||||||
* The AO coefficients and exponents are ordered in increasing order of exponents
|
|
||||||
|
|
||||||
|
|
||||||
Needed Modules
|
Needed Modules
|
||||||
==============
|
==============
|
||||||
@ -39,10 +37,7 @@ Needed Modules
|
|||||||
.. Do not edit this section. It was auto-generated from the
|
.. Do not edit this section. It was auto-generated from the
|
||||||
.. NEEDED_MODULES file.
|
.. NEEDED_MODULES file.
|
||||||
|
|
||||||
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
|
|
||||||
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
|
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
|
||||||
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
|
|
||||||
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
|
|
||||||
|
|
||||||
Documentation
|
Documentation
|
||||||
=============
|
=============
|
||||||
@ -70,45 +65,41 @@ Documentation
|
|||||||
Overlap between atomic basis functions:
|
Overlap between atomic basis functions:
|
||||||
:math:`\int \chi_i(r) \chi_j(r) dr)`
|
:math:`\int \chi_i(r) \chi_j(r) dr)`
|
||||||
|
|
||||||
`ao_coef <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L21>`_
|
`ao_coef <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L62>`_
|
||||||
Coefficients, exponents and powers of x,y and z
|
AO Coefficients, read from input. Those should not be used directly, as
|
||||||
|
the MOs are expressed on the basis of **normalized** AOs.
|
||||||
|
|
||||||
`ao_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L157>`_
|
`ao_coef_normalized <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L84>`_
|
||||||
Transposed ao_coef and ao_expo
|
Coefficients including the AO normalization
|
||||||
|
|
||||||
`ao_coef_unnormalized <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L116>`_
|
`ao_coef_normalized_ordered <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L107>`_
|
||||||
Coefficients, exponents and powers of x,y and z as in the EZFIO file
|
Sorted primitives to accelerate 4 index MO transformation
|
||||||
ao_coef(i,j) = coefficient of the jth primitive on the ith ao
|
|
||||||
|
`ao_coef_normalized_ordered_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L133>`_
|
||||||
|
Transposed ao_coef_normalized_ordered
|
||||||
|
|
||||||
|
`ao_expo <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L41>`_
|
||||||
|
AO Exponents read from input
|
||||||
|
|
||||||
|
`ao_expo_ordered <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L108>`_
|
||||||
|
Sorted primitives to accelerate 4 index MO transformation
|
||||||
|
|
||||||
|
`ao_expo_ordered_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L147>`_
|
||||||
|
Transposed ao_expo_ordered
|
||||||
|
|
||||||
|
`ao_l <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L162>`_
|
||||||
ao_l = l value of the AO: a+b+c in x^a y^b z^c
|
ao_l = l value of the AO: a+b+c in x^a y^b z^c
|
||||||
|
|
||||||
`ao_expo <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L20>`_
|
`ao_l_char <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L163>`_
|
||||||
Coefficients, exponents and powers of x,y and z
|
|
||||||
|
|
||||||
`ao_expo_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L158>`_
|
|
||||||
Transposed ao_coef and ao_expo
|
|
||||||
|
|
||||||
`ao_expo_unsorted <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L117>`_
|
|
||||||
Coefficients, exponents and powers of x,y and z as in the EZFIO file
|
|
||||||
ao_coef(i,j) = coefficient of the jth primitive on the ith ao
|
|
||||||
ao_l = l value of the AO: a+b+c in x^a y^b z^c
|
ao_l = l value of the AO: a+b+c in x^a y^b z^c
|
||||||
|
|
||||||
`ao_l <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L118>`_
|
`ao_l_char_space <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L311>`_
|
||||||
Coefficients, exponents and powers of x,y and z as in the EZFIO file
|
|
||||||
ao_coef(i,j) = coefficient of the jth primitive on the ith ao
|
|
||||||
ao_l = l value of the AO: a+b+c in x^a y^b z^c
|
|
||||||
|
|
||||||
`ao_l_char <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L119>`_
|
|
||||||
Coefficients, exponents and powers of x,y and z as in the EZFIO file
|
|
||||||
ao_coef(i,j) = coefficient of the jth primitive on the ith ao
|
|
||||||
ao_l = l value of the AO: a+b+c in x^a y^b z^c
|
|
||||||
|
|
||||||
`ao_l_char_space <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L309>`_
|
|
||||||
Undocumented
|
Undocumented
|
||||||
|
|
||||||
`ao_md5 <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L400>`_
|
`ao_md5 <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L403>`_
|
||||||
MD5 key characteristic of the AO basis
|
MD5 key characteristic of the AO basis
|
||||||
|
|
||||||
`ao_nucl <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L207>`_
|
`ao_nucl <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L209>`_
|
||||||
Index of the nuclei on which the ao is centered
|
Index of the nuclei on which the ao is centered
|
||||||
|
|
||||||
`ao_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L1>`_
|
`ao_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L1>`_
|
||||||
@ -118,35 +109,35 @@ Documentation
|
|||||||
Number of atomic orbitals
|
Number of atomic orbitals
|
||||||
|
|
||||||
`ao_power <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L19>`_
|
`ao_power <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L19>`_
|
||||||
Coefficients, exponents and powers of x,y and z
|
Powers of x,y and z read from input
|
||||||
|
|
||||||
`ao_prim_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L175>`_
|
`ao_prim_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L177>`_
|
||||||
Number of primitives per atomic orbital
|
Number of primitives per atomic orbital
|
||||||
|
|
||||||
`ao_prim_num_max <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L197>`_
|
`ao_prim_num_max <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L199>`_
|
||||||
Undocumented
|
Undocumented
|
||||||
|
|
||||||
`ao_prim_num_max_align <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L198>`_
|
`ao_prim_num_max_align <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L200>`_
|
||||||
Undocumented
|
Undocumented
|
||||||
|
|
||||||
`l_to_charater <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L216>`_
|
`l_to_charater <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L218>`_
|
||||||
character corresponding to the "L" value of an AO orbital
|
character corresponding to the "L" value of an AO orbital
|
||||||
|
|
||||||
`n_aos_max <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L229>`_
|
`n_aos_max <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L231>`_
|
||||||
Number of AOs per atom
|
Number of AOs per atom
|
||||||
|
|
||||||
`nucl_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L242>`_
|
`nucl_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L244>`_
|
||||||
List of AOs attached on each atom
|
List of AOs attached on each atom
|
||||||
|
|
||||||
`nucl_list_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L260>`_
|
`nucl_list_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L262>`_
|
||||||
Index of the shell type Aos and of the corresponding Aos
|
Index of the shell type Aos and of the corresponding Aos
|
||||||
Per convention, for P,D,F and G AOs, we take the index
|
Per convention, for P,D,F and G AOs, we take the index
|
||||||
of the AO with the the corresponding power in the "X" axis
|
of the AO with the the corresponding power in the "X" axis
|
||||||
|
|
||||||
`nucl_n_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L228>`_
|
`nucl_n_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L230>`_
|
||||||
Number of AOs per atom
|
Number of AOs per atom
|
||||||
|
|
||||||
`nucl_num_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L261>`_
|
`nucl_num_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L263>`_
|
||||||
Index of the shell type Aos and of the corresponding Aos
|
Index of the shell type Aos and of the corresponding Aos
|
||||||
Per convention, for P,D,F and G AOs, we take the index
|
Per convention, for P,D,F and G AOs, we take the index
|
||||||
of the AO with the the corresponding power in the "X" axis
|
of the AO with the the corresponding power in the "X" axis
|
||||||
|
|||||||
@ -21,8 +21,8 @@
|
|||||||
!$OMP overlap_x,overlap_y, overlap_z, overlap, &
|
!$OMP overlap_x,overlap_y, overlap_z, overlap, &
|
||||||
!$OMP alpha, beta,i,j,c) &
|
!$OMP alpha, beta,i,j,c) &
|
||||||
!$OMP SHARED(nucl_coord,ao_power,ao_prim_num, &
|
!$OMP SHARED(nucl_coord,ao_power,ao_prim_num, &
|
||||||
!$OMP ao_overlap_x,ao_overlap_y,ao_overlap_z,ao_overlap,ao_num,ao_coef_transp,ao_nucl, &
|
!$OMP ao_overlap_x,ao_overlap_y,ao_overlap_z,ao_overlap,ao_num,ao_coef_normalized_ordered_transp,ao_nucl, &
|
||||||
!$OMP ao_expo_transp,dim1)
|
!$OMP ao_expo_ordered_transp,dim1)
|
||||||
do j=1,ao_num
|
do j=1,ao_num
|
||||||
A_center(1) = nucl_coord( ao_nucl(j), 1 )
|
A_center(1) = nucl_coord( ao_nucl(j), 1 )
|
||||||
A_center(2) = nucl_coord( ao_nucl(j), 2 )
|
A_center(2) = nucl_coord( ao_nucl(j), 2 )
|
||||||
@ -44,12 +44,12 @@
|
|||||||
power_B(2) = ao_power( i, 2 )
|
power_B(2) = ao_power( i, 2 )
|
||||||
power_B(3) = ao_power( i, 3 )
|
power_B(3) = ao_power( i, 3 )
|
||||||
do n = 1,ao_prim_num(j)
|
do n = 1,ao_prim_num(j)
|
||||||
alpha = ao_expo_transp(n,j)
|
alpha = ao_expo_ordered_transp(n,j)
|
||||||
!DEC$ VECTOR ALIGNED
|
!DEC$ VECTOR ALIGNED
|
||||||
do l = 1, ao_prim_num(i)
|
do l = 1, ao_prim_num(i)
|
||||||
beta = ao_expo_transp(l,i)
|
beta = ao_expo_ordered_transp(l,i)
|
||||||
call overlap_gaussian_xyz(A_center,B_center,alpha,beta,power_A,power_B,overlap_x,overlap_y,overlap_z,overlap,dim1)
|
call overlap_gaussian_xyz(A_center,B_center,alpha,beta,power_A,power_B,overlap_x,overlap_y,overlap_z,overlap,dim1)
|
||||||
c = ao_coef_transp(n,j) * ao_coef_transp(l,i)
|
c = ao_coef_normalized_ordered_transp(n,j) * ao_coef_normalized_ordered_transp(l,i)
|
||||||
ao_overlap(i,j) += c * overlap
|
ao_overlap(i,j) += c * overlap
|
||||||
ao_overlap_x(i,j) += c * overlap_x
|
ao_overlap_x(i,j) += c * overlap_x
|
||||||
ao_overlap_y(i,j) += c * overlap_y
|
ao_overlap_y(i,j) += c * overlap_y
|
||||||
@ -84,8 +84,8 @@ BEGIN_PROVIDER [ double precision, ao_overlap_abs,(ao_num_align,ao_num) ]
|
|||||||
!$OMP overlap_x,overlap_y, overlap_z, overlap, &
|
!$OMP overlap_x,overlap_y, overlap_z, overlap, &
|
||||||
!$OMP alpha, beta,i,j,dx) &
|
!$OMP alpha, beta,i,j,dx) &
|
||||||
!$OMP SHARED(nucl_coord,ao_power,ao_prim_num, &
|
!$OMP SHARED(nucl_coord,ao_power,ao_prim_num, &
|
||||||
!$OMP ao_overlap_abs,ao_num,ao_coef_transp,ao_nucl, &
|
!$OMP ao_overlap_abs,ao_num,ao_coef_normalized_ordered_transp,ao_nucl, &
|
||||||
!$OMP ao_expo_transp,dim1,lower_exp_val)
|
!$OMP ao_expo_ordered_transp,dim1,lower_exp_val)
|
||||||
do j=1,ao_num
|
do j=1,ao_num
|
||||||
A_center(1) = nucl_coord( ao_nucl(j), 1 )
|
A_center(1) = nucl_coord( ao_nucl(j), 1 )
|
||||||
A_center(2) = nucl_coord( ao_nucl(j), 2 )
|
A_center(2) = nucl_coord( ao_nucl(j), 2 )
|
||||||
@ -104,14 +104,14 @@ BEGIN_PROVIDER [ double precision, ao_overlap_abs,(ao_num_align,ao_num) ]
|
|||||||
power_B(2) = ao_power( i, 2 )
|
power_B(2) = ao_power( i, 2 )
|
||||||
power_B(3) = ao_power( i, 3 )
|
power_B(3) = ao_power( i, 3 )
|
||||||
do n = 1,ao_prim_num(j)
|
do n = 1,ao_prim_num(j)
|
||||||
alpha = ao_expo_transp(n,j)
|
alpha = ao_expo_ordered_transp(n,j)
|
||||||
!DEC$ VECTOR ALIGNED
|
!DEC$ VECTOR ALIGNED
|
||||||
do l = 1, ao_prim_num(i)
|
do l = 1, ao_prim_num(i)
|
||||||
beta = ao_expo_transp(l,i)
|
beta = ao_expo_ordered_transp(l,i)
|
||||||
call overlap_x_abs(A_center(1),B_center(1),alpha,beta,power_A(1),power_B(1),overlap_x,lower_exp_val,dx,dim1)
|
call overlap_x_abs(A_center(1),B_center(1),alpha,beta,power_A(1),power_B(1),overlap_x,lower_exp_val,dx,dim1)
|
||||||
call overlap_x_abs(A_center(2),B_center(2),alpha,beta,power_A(2),power_B(2),overlap_y,lower_exp_val,dx,dim1)
|
call overlap_x_abs(A_center(2),B_center(2),alpha,beta,power_A(2),power_B(2),overlap_y,lower_exp_val,dx,dim1)
|
||||||
call overlap_x_abs(A_center(3),B_center(3),alpha,beta,power_A(3),power_B(3),overlap_z,lower_exp_val,dx,dim1)
|
call overlap_x_abs(A_center(3),B_center(3),alpha,beta,power_A(3),power_B(3),overlap_z,lower_exp_val,dx,dim1)
|
||||||
ao_overlap_abs(i,j) += abs(ao_coef_transp(n,j) * ao_coef_transp(l,i)) * overlap_x * overlap_y * overlap_z
|
ao_overlap_abs(i,j) += abs(ao_coef_normalized_ordered_transp(n,j) * ao_coef_normalized_ordered_transp(l,i)) * overlap_x * overlap_y * overlap_z
|
||||||
enddo
|
enddo
|
||||||
enddo
|
enddo
|
||||||
enddo
|
enddo
|
||||||
|
|||||||
@ -17,20 +17,15 @@
|
|||||||
END_PROVIDER
|
END_PROVIDER
|
||||||
|
|
||||||
BEGIN_PROVIDER [ integer, ao_power, (ao_num_align,3) ]
|
BEGIN_PROVIDER [ integer, ao_power, (ao_num_align,3) ]
|
||||||
&BEGIN_PROVIDER [ double precision, ao_expo, (ao_num_align,ao_prim_num_max) ]
|
|
||||||
&BEGIN_PROVIDER [ double precision, ao_coef, (ao_num_align,ao_prim_num_max) ]
|
|
||||||
implicit none
|
implicit none
|
||||||
|
|
||||||
BEGIN_DOC
|
BEGIN_DOC
|
||||||
! Coefficients, exponents and powers of x,y and z
|
! Powers of x,y and z read from input
|
||||||
END_DOC
|
END_DOC
|
||||||
PROVIDE ezfio_filename
|
PROVIDE ezfio_filename
|
||||||
|
|
||||||
double precision, allocatable :: buffer(:,:)
|
|
||||||
allocate ( buffer(ao_num,ao_prim_num_max) )
|
|
||||||
integer :: ibuffer(ao_num,3)
|
|
||||||
integer :: i,j,k
|
integer :: i,j,k
|
||||||
character*(128) :: give_ao_character_space
|
integer, allocatable :: ibuffer(:,:)
|
||||||
|
allocate ( ibuffer(ao_num,3) )
|
||||||
ibuffer = 0
|
ibuffer = 0
|
||||||
call ezfio_get_ao_basis_ao_power(ibuffer)
|
call ezfio_get_ao_basis_ao_power(ibuffer)
|
||||||
ao_power = 0
|
ao_power = 0
|
||||||
@ -39,6 +34,20 @@ END_PROVIDER
|
|||||||
ao_power(i,j) = ibuffer(i,j)
|
ao_power(i,j) = ibuffer(i,j)
|
||||||
enddo
|
enddo
|
||||||
enddo
|
enddo
|
||||||
|
deallocate(ibuffer)
|
||||||
|
|
||||||
|
END_PROVIDER
|
||||||
|
|
||||||
|
BEGIN_PROVIDER [ double precision, ao_expo, (ao_num_align,ao_prim_num_max) ]
|
||||||
|
implicit none
|
||||||
|
BEGIN_DOC
|
||||||
|
! AO Exponents read from input
|
||||||
|
END_DOC
|
||||||
|
PROVIDE ezfio_filename
|
||||||
|
|
||||||
|
double precision, allocatable :: buffer(:,:)
|
||||||
|
allocate ( buffer(ao_num,ao_prim_num_max) )
|
||||||
|
integer :: i,j,k
|
||||||
ao_expo = 0.d0
|
ao_expo = 0.d0
|
||||||
buffer = 0.d0
|
buffer = 0.d0
|
||||||
call ezfio_get_ao_basis_ao_expo(buffer)
|
call ezfio_get_ao_basis_ao_expo(buffer)
|
||||||
@ -47,7 +56,20 @@ END_PROVIDER
|
|||||||
ao_expo(i,j) = buffer(i,j)
|
ao_expo(i,j) = buffer(i,j)
|
||||||
enddo
|
enddo
|
||||||
enddo
|
enddo
|
||||||
|
deallocate(buffer)
|
||||||
|
END_PROVIDER
|
||||||
|
|
||||||
|
BEGIN_PROVIDER [ double precision, ao_coef, (ao_num_align,ao_prim_num_max) ]
|
||||||
|
implicit none
|
||||||
|
BEGIN_DOC
|
||||||
|
! AO Coefficients, read from input. Those should not be used directly, as
|
||||||
|
! the MOs are expressed on the basis of **normalized** AOs.
|
||||||
|
END_DOC
|
||||||
|
PROVIDE ezfio_filename
|
||||||
|
|
||||||
|
double precision, allocatable :: buffer(:,:)
|
||||||
|
allocate ( buffer(ao_num,ao_prim_num_max) )
|
||||||
|
integer :: i,j,k
|
||||||
ao_coef = 0.d0
|
ao_coef = 0.d0
|
||||||
buffer = 0.d0
|
buffer = 0.d0
|
||||||
call ezfio_get_ao_basis_ao_coef(buffer)
|
call ezfio_get_ao_basis_ao_coef(buffer)
|
||||||
@ -56,13 +78,17 @@ END_PROVIDER
|
|||||||
ao_coef(i,j) = buffer(i,j)
|
ao_coef(i,j) = buffer(i,j)
|
||||||
enddo
|
enddo
|
||||||
enddo
|
enddo
|
||||||
|
|
||||||
deallocate(buffer)
|
deallocate(buffer)
|
||||||
|
END_PROVIDER
|
||||||
|
|
||||||
! Normalization of the AO coefficients
|
BEGIN_PROVIDER [ double precision, ao_coef_normalized, (ao_num_align,ao_prim_num_max) ]
|
||||||
! ------------------------------------
|
implicit none
|
||||||
|
BEGIN_DOC
|
||||||
|
! Coefficients including the AO normalization
|
||||||
|
END_DOC
|
||||||
double precision :: norm, norm2,overlap_x,overlap_y,overlap_z,C_A(3)
|
double precision :: norm, norm2,overlap_x,overlap_y,overlap_z,C_A(3)
|
||||||
integer :: l, powA(3), nz
|
integer :: l, powA(3), nz
|
||||||
|
integer :: i,j
|
||||||
nz=100
|
nz=100
|
||||||
C_A(1) = 0.d0
|
C_A(1) = 0.d0
|
||||||
C_A(2) = 0.d0
|
C_A(2) = 0.d0
|
||||||
@ -73,80 +99,73 @@ END_PROVIDER
|
|||||||
powA(3) = ao_power(i,3)
|
powA(3) = ao_power(i,3)
|
||||||
do j=1,ao_prim_num(i)
|
do j=1,ao_prim_num(i)
|
||||||
call overlap_gaussian_xyz(C_A,C_A,ao_expo(i,j),ao_expo(i,j),powA,powA,overlap_x,overlap_y,overlap_z,norm,nz)
|
call overlap_gaussian_xyz(C_A,C_A,ao_expo(i,j),ao_expo(i,j),powA,powA,overlap_x,overlap_y,overlap_z,norm,nz)
|
||||||
ao_coef(i,j) = ao_coef(i,j)/sqrt(norm)
|
ao_coef_normalized(i,j) = ao_coef(i,j)/sqrt(norm)
|
||||||
enddo
|
enddo
|
||||||
enddo
|
enddo
|
||||||
|
END_PROVIDER
|
||||||
|
|
||||||
|
BEGIN_PROVIDER [ double precision, ao_coef_normalized_ordered, (ao_num_align,ao_prim_num_max) ]
|
||||||
|
&BEGIN_PROVIDER [ double precision, ao_expo_ordered, (ao_num_align,ao_prim_num_max) ]
|
||||||
|
implicit none
|
||||||
|
BEGIN_DOC
|
||||||
|
! Sorted primitives to accelerate 4 index MO transformation
|
||||||
|
END_DOC
|
||||||
|
|
||||||
! Sorting of the exponents for efficient integral calculations
|
|
||||||
integer :: iorder(ao_prim_num_max)
|
integer :: iorder(ao_prim_num_max)
|
||||||
double precision :: d(ao_prim_num_max,2)
|
double precision :: d(ao_prim_num_max,2)
|
||||||
|
integer :: i,j
|
||||||
do i=1,ao_num
|
do i=1,ao_num
|
||||||
do j=1,ao_prim_num(i)
|
do j=1,ao_prim_num(i)
|
||||||
iorder(j) = j
|
iorder(j) = j
|
||||||
d(j,1) = ao_expo(i,j)
|
d(j,1) = ao_expo(i,j)
|
||||||
d(j,2) = ao_coef(i,j)
|
d(j,2) = ao_coef_normalized(i,j)
|
||||||
enddo
|
enddo
|
||||||
call dsort(d(1,1),iorder,ao_prim_num(i))
|
call dsort(d(1,1),iorder,ao_prim_num(i))
|
||||||
call dset_order(d(1,2),iorder,ao_prim_num(i))
|
call dset_order(d(1,2),iorder,ao_prim_num(i))
|
||||||
do j=1,ao_prim_num(i)
|
do j=1,ao_prim_num(i)
|
||||||
ao_expo(i,j) = d(j,1)
|
ao_expo_ordered(i,j) = d(j,1)
|
||||||
ao_coef(i,j) = d(j,2)
|
ao_coef_normalized_ordered(i,j) = d(j,2)
|
||||||
enddo
|
enddo
|
||||||
enddo
|
enddo
|
||||||
END_PROVIDER
|
END_PROVIDER
|
||||||
|
|
||||||
|
|
||||||
BEGIN_PROVIDER [ double precision, ao_coef_transp, (ao_prim_num_max_align,ao_num) ]
|
BEGIN_PROVIDER [ double precision, ao_coef_normalized_ordered_transp, (ao_prim_num_max_align,ao_num) ]
|
||||||
&BEGIN_PROVIDER [ double precision, ao_expo_transp, (ao_prim_num_max_align,ao_num) ]
|
|
||||||
implicit none
|
implicit none
|
||||||
BEGIN_DOC
|
BEGIN_DOC
|
||||||
! Transposed ao_coef and ao_expo
|
! Transposed ao_coef_normalized_ordered
|
||||||
END_DOC
|
END_DOC
|
||||||
integer :: i,j
|
integer :: i,j
|
||||||
do j=1, ao_num
|
do j=1, ao_num
|
||||||
do i=1, ao_prim_num_max
|
do i=1, ao_prim_num_max
|
||||||
ao_coef_transp(i,j) = ao_coef(j,i)
|
ao_coef_normalized_ordered_transp(i,j) = ao_coef_normalized_ordered(j,i)
|
||||||
ao_expo_transp(i,j) = ao_expo(j,i)
|
|
||||||
enddo
|
enddo
|
||||||
enddo
|
enddo
|
||||||
|
|
||||||
|
|
||||||
END_PROVIDER
|
END_PROVIDER
|
||||||
|
|
||||||
BEGIN_PROVIDER [ double precision, ao_coef_unnormalized, (ao_num_align,ao_prim_num_max) ]
|
BEGIN_PROVIDER [ double precision, ao_expo_ordered_transp, (ao_prim_num_max_align,ao_num) ]
|
||||||
&BEGIN_PROVIDER [ double precision, ao_expo_unsorted, (ao_num_align,ao_prim_num_max) ]
|
implicit none
|
||||||
&BEGIN_PROVIDER [ integer, ao_l, (ao_num) ]
|
BEGIN_DOC
|
||||||
|
! Transposed ao_expo_ordered
|
||||||
|
END_DOC
|
||||||
|
integer :: i,j
|
||||||
|
do j=1, ao_num
|
||||||
|
do i=1, ao_prim_num_max
|
||||||
|
ao_expo_ordered_transp(i,j) = ao_expo_ordered(j,i)
|
||||||
|
enddo
|
||||||
|
enddo
|
||||||
|
|
||||||
|
END_PROVIDER
|
||||||
|
|
||||||
|
|
||||||
|
BEGIN_PROVIDER [ integer, ao_l, (ao_num) ]
|
||||||
&BEGIN_PROVIDER [ character*(128), ao_l_char, (ao_num) ]
|
&BEGIN_PROVIDER [ character*(128), ao_l_char, (ao_num) ]
|
||||||
implicit none
|
implicit none
|
||||||
|
|
||||||
BEGIN_DOC
|
BEGIN_DOC
|
||||||
! Coefficients, exponents and powers of x,y and z as in the EZFIO file
|
|
||||||
! ao_coef(i,j) = coefficient of the jth primitive on the ith ao
|
|
||||||
! ao_l = l value of the AO: a+b+c in x^a y^b z^c
|
! ao_l = l value of the AO: a+b+c in x^a y^b z^c
|
||||||
END_DOC
|
END_DOC
|
||||||
PROVIDE ezfio_filename
|
integer :: i
|
||||||
|
|
||||||
double precision, allocatable :: buffer(:,:)
|
|
||||||
allocate ( buffer(ao_num,ao_prim_num_max) )
|
|
||||||
integer :: i,j,k
|
|
||||||
character*(128) :: give_ao_character_space
|
|
||||||
buffer = 0.d0
|
|
||||||
call ezfio_get_ao_basis_ao_expo(buffer)
|
|
||||||
do j = 1, ao_prim_num_max
|
|
||||||
do i = 1, ao_num
|
|
||||||
ao_expo_unsorted(i,j) = buffer(i,j)
|
|
||||||
enddo
|
|
||||||
enddo
|
|
||||||
|
|
||||||
buffer = 0.d0
|
|
||||||
call ezfio_get_ao_basis_ao_coef(buffer)
|
|
||||||
do j = 1, ao_prim_num_max
|
|
||||||
do i = 1, ao_num
|
|
||||||
ao_coef_unnormalized(i,j) = buffer(i,j)
|
|
||||||
enddo
|
|
||||||
enddo
|
|
||||||
deallocate(buffer)
|
|
||||||
|
|
||||||
do i=1,ao_num
|
do i=1,ao_num
|
||||||
ao_l(i) = ao_power(i,1) + ao_power(i,2) + ao_power(i,3)
|
ao_l(i) = ao_power(i,1) + ao_power(i,2) + ao_power(i,3)
|
||||||
ao_l_char(i) = l_to_charater(ao_l(i))
|
ao_l_char(i) = l_to_charater(ao_l(i))
|
||||||
@ -154,23 +173,6 @@ END_PROVIDER
|
|||||||
END_PROVIDER
|
END_PROVIDER
|
||||||
|
|
||||||
|
|
||||||
BEGIN_PROVIDER [ double precision, ao_coef_transp, (ao_prim_num_max_align,ao_num) ]
|
|
||||||
&BEGIN_PROVIDER [ double precision, ao_expo_transp, (ao_prim_num_max_align,ao_num) ]
|
|
||||||
implicit none
|
|
||||||
BEGIN_DOC
|
|
||||||
! Transposed ao_coef and ao_expo
|
|
||||||
END_DOC
|
|
||||||
integer :: i,j
|
|
||||||
do j=1, ao_num
|
|
||||||
do i=1, ao_prim_num_max
|
|
||||||
ao_coef_transp(i,j) = ao_coef(j,i)
|
|
||||||
ao_expo_transp(i,j) = ao_expo(j,i)
|
|
||||||
enddo
|
|
||||||
enddo
|
|
||||||
|
|
||||||
|
|
||||||
END_PROVIDER
|
|
||||||
|
|
||||||
|
|
||||||
BEGIN_PROVIDER [ integer, ao_prim_num, (ao_num_align) ]
|
BEGIN_PROVIDER [ integer, ao_prim_num, (ao_num_align) ]
|
||||||
implicit none
|
implicit none
|
||||||
@ -397,6 +399,7 @@ END_PROVIDER
|
|||||||
ao_l_char_space(i) = give_ao_character_space
|
ao_l_char_space(i) = give_ao_character_space
|
||||||
enddo
|
enddo
|
||||||
END_PROVIDER
|
END_PROVIDER
|
||||||
|
|
||||||
BEGIN_PROVIDER [ character*(32), ao_md5 ]
|
BEGIN_PROVIDER [ character*(32), ao_md5 ]
|
||||||
BEGIN_DOC
|
BEGIN_DOC
|
||||||
! MD5 key characteristic of the AO basis
|
! MD5 key characteristic of the AO basis
|
||||||
|
|||||||
1
src/Bielec_integrals/NEEDED_CHILDREN_MODULES
Normal file
1
src/Bielec_integrals/NEEDED_CHILDREN_MODULES
Normal file
@ -0,0 +1 @@
|
|||||||
|
MonoInts Bitmask
|
||||||
@ -1 +0,0 @@
|
|||||||
AOs Bitmask Electrons Ezfio_files MOs Nuclei Output Utils MonoInts
|
|
||||||
@ -16,15 +16,8 @@ Needed Modules
|
|||||||
.. Do not edit this section. It was auto-generated from the
|
.. Do not edit this section. It was auto-generated from the
|
||||||
.. NEEDED_MODULES file.
|
.. NEEDED_MODULES file.
|
||||||
|
|
||||||
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
|
|
||||||
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
|
|
||||||
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
|
|
||||||
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
|
|
||||||
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
|
|
||||||
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
|
|
||||||
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
|
|
||||||
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
|
|
||||||
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
|
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
|
||||||
|
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
|
||||||
|
|
||||||
Documentation
|
Documentation
|
||||||
=============
|
=============
|
||||||
|
|||||||
@ -42,24 +42,24 @@ double precision function ao_bielec_integral(i,j,k,l)
|
|||||||
|
|
||||||
do p = 1, ao_prim_num(i)
|
do p = 1, ao_prim_num(i)
|
||||||
double precision :: coef1
|
double precision :: coef1
|
||||||
coef1 = ao_coef_transp(p,i)
|
coef1 = ao_coef_normalized_ordered_transp(p,i)
|
||||||
do q = 1, ao_prim_num(j)
|
do q = 1, ao_prim_num(j)
|
||||||
double precision :: coef2
|
double precision :: coef2
|
||||||
coef2 = coef1*ao_coef_transp(q,j)
|
coef2 = coef1*ao_coef_normalized_ordered_transp(q,j)
|
||||||
double precision :: p_inv,q_inv
|
double precision :: p_inv,q_inv
|
||||||
call give_explicit_poly_and_gaussian(P_new,P_center,pp,fact_p,iorder_p,&
|
call give_explicit_poly_and_gaussian(P_new,P_center,pp,fact_p,iorder_p,&
|
||||||
ao_expo_transp(p,i),ao_expo_transp(q,j), &
|
ao_expo_ordered_transp(p,i),ao_expo_ordered_transp(q,j), &
|
||||||
I_power,J_power,I_center,J_center,dim1)
|
I_power,J_power,I_center,J_center,dim1)
|
||||||
p_inv = 1.d0/pp
|
p_inv = 1.d0/pp
|
||||||
do r = 1, ao_prim_num(k)
|
do r = 1, ao_prim_num(k)
|
||||||
double precision :: coef3
|
double precision :: coef3
|
||||||
coef3 = coef2*ao_coef_transp(r,k)
|
coef3 = coef2*ao_coef_normalized_ordered_transp(r,k)
|
||||||
do s = 1, ao_prim_num(l)
|
do s = 1, ao_prim_num(l)
|
||||||
double precision :: coef4
|
double precision :: coef4
|
||||||
coef4 = coef3*ao_coef_transp(s,l)
|
coef4 = coef3*ao_coef_normalized_ordered_transp(s,l)
|
||||||
double precision :: general_primitive_integral
|
double precision :: general_primitive_integral
|
||||||
call give_explicit_poly_and_gaussian(Q_new,Q_center,qq,fact_q,iorder_q,&
|
call give_explicit_poly_and_gaussian(Q_new,Q_center,qq,fact_q,iorder_q,&
|
||||||
ao_expo_transp(r,k),ao_expo_transp(s,l), &
|
ao_expo_ordered_transp(r,k),ao_expo_ordered_transp(s,l), &
|
||||||
K_power,L_power,K_center,L_center,dim1)
|
K_power,L_power,K_center,L_center,dim1)
|
||||||
q_inv = 1.d0/qq
|
q_inv = 1.d0/qq
|
||||||
integral = general_primitive_integral(dim1, &
|
integral = general_primitive_integral(dim1, &
|
||||||
@ -82,15 +82,15 @@ double precision function ao_bielec_integral(i,j,k,l)
|
|||||||
double precision :: ERI
|
double precision :: ERI
|
||||||
|
|
||||||
do p = 1, ao_prim_num(i)
|
do p = 1, ao_prim_num(i)
|
||||||
coef1 = ao_coef_transp(p,i)
|
coef1 = ao_coef_normalized_ordered_transp(p,i)
|
||||||
do q = 1, ao_prim_num(j)
|
do q = 1, ao_prim_num(j)
|
||||||
coef2 = coef1*ao_coef_transp(q,j)
|
coef2 = coef1*ao_coef_normalized_ordered_transp(q,j)
|
||||||
do r = 1, ao_prim_num(k)
|
do r = 1, ao_prim_num(k)
|
||||||
coef3 = coef2*ao_coef_transp(r,k)
|
coef3 = coef2*ao_coef_normalized_ordered_transp(r,k)
|
||||||
do s = 1, ao_prim_num(l)
|
do s = 1, ao_prim_num(l)
|
||||||
coef4 = coef3*ao_coef_transp(s,l)
|
coef4 = coef3*ao_coef_normalized_ordered_transp(s,l)
|
||||||
integral = ERI( &
|
integral = ERI( &
|
||||||
ao_expo_transp(p,i),ao_expo_transp(q,j),ao_expo_transp(r,k),ao_expo_transp(s,l),&
|
ao_expo_ordered_transp(p,i),ao_expo_ordered_transp(q,j),ao_expo_ordered_transp(r,k),ao_expo_ordered_transp(s,l),&
|
||||||
I_power(1),J_power(1),K_power(1),L_power(1), &
|
I_power(1),J_power(1),K_power(1),L_power(1), &
|
||||||
I_power(2),J_power(2),K_power(2),L_power(2), &
|
I_power(2),J_power(2),K_power(2),L_power(2), &
|
||||||
I_power(3),J_power(3),K_power(3),L_power(3))
|
I_power(3),J_power(3),K_power(3),L_power(3))
|
||||||
@ -149,12 +149,12 @@ double precision function ao_bielec_integral_schwartz_accel(i,j,k,l)
|
|||||||
|
|
||||||
schwartz_kl(0,0) = 0.d0
|
schwartz_kl(0,0) = 0.d0
|
||||||
do r = 1, ao_prim_num(k)
|
do r = 1, ao_prim_num(k)
|
||||||
coef1 = ao_coef_transp(r,k)*ao_coef_transp(r,k)
|
coef1 = ao_coef_normalized_ordered_transp(r,k)*ao_coef_normalized_ordered_transp(r,k)
|
||||||
schwartz_kl(0,r) = 0.d0
|
schwartz_kl(0,r) = 0.d0
|
||||||
do s = 1, ao_prim_num(l)
|
do s = 1, ao_prim_num(l)
|
||||||
coef2 = coef1 * ao_coef_transp(s,l) * ao_coef_transp(s,l)
|
coef2 = coef1 * ao_coef_normalized_ordered_transp(s,l) * ao_coef_normalized_ordered_transp(s,l)
|
||||||
call give_explicit_poly_and_gaussian(Q_new,Q_center,qq,fact_q,iorder_q,&
|
call give_explicit_poly_and_gaussian(Q_new,Q_center,qq,fact_q,iorder_q,&
|
||||||
ao_expo_transp(r,k),ao_expo_transp(s,l), &
|
ao_expo_ordered_transp(r,k),ao_expo_ordered_transp(s,l), &
|
||||||
K_power,L_power,K_center,L_center,dim1)
|
K_power,L_power,K_center,L_center,dim1)
|
||||||
q_inv = 1.d0/qq
|
q_inv = 1.d0/qq
|
||||||
schwartz_kl(s,r) = general_primitive_integral(dim1, &
|
schwartz_kl(s,r) = general_primitive_integral(dim1, &
|
||||||
@ -168,13 +168,13 @@ double precision function ao_bielec_integral_schwartz_accel(i,j,k,l)
|
|||||||
|
|
||||||
do p = 1, ao_prim_num(i)
|
do p = 1, ao_prim_num(i)
|
||||||
double precision :: coef1
|
double precision :: coef1
|
||||||
coef1 = ao_coef_transp(p,i)
|
coef1 = ao_coef_normalized_ordered_transp(p,i)
|
||||||
do q = 1, ao_prim_num(j)
|
do q = 1, ao_prim_num(j)
|
||||||
double precision :: coef2
|
double precision :: coef2
|
||||||
coef2 = coef1*ao_coef_transp(q,j)
|
coef2 = coef1*ao_coef_normalized_ordered_transp(q,j)
|
||||||
double precision :: p_inv,q_inv
|
double precision :: p_inv,q_inv
|
||||||
call give_explicit_poly_and_gaussian(P_new,P_center,pp,fact_p,iorder_p,&
|
call give_explicit_poly_and_gaussian(P_new,P_center,pp,fact_p,iorder_p,&
|
||||||
ao_expo_transp(p,i),ao_expo_transp(q,j), &
|
ao_expo_ordered_transp(p,i),ao_expo_ordered_transp(q,j), &
|
||||||
I_power,J_power,I_center,J_center,dim1)
|
I_power,J_power,I_center,J_center,dim1)
|
||||||
p_inv = 1.d0/pp
|
p_inv = 1.d0/pp
|
||||||
schwartz_ij = general_primitive_integral(dim1, &
|
schwartz_ij = general_primitive_integral(dim1, &
|
||||||
@ -189,16 +189,16 @@ double precision function ao_bielec_integral_schwartz_accel(i,j,k,l)
|
|||||||
cycle
|
cycle
|
||||||
endif
|
endif
|
||||||
double precision :: coef3
|
double precision :: coef3
|
||||||
coef3 = coef2*ao_coef_transp(r,k)
|
coef3 = coef2*ao_coef_normalized_ordered_transp(r,k)
|
||||||
do s = 1, ao_prim_num(l)
|
do s = 1, ao_prim_num(l)
|
||||||
double precision :: coef4
|
double precision :: coef4
|
||||||
if (schwartz_kl(s,r)*schwartz_ij < thresh) then
|
if (schwartz_kl(s,r)*schwartz_ij < thresh) then
|
||||||
cycle
|
cycle
|
||||||
endif
|
endif
|
||||||
coef4 = coef3*ao_coef_transp(s,l)
|
coef4 = coef3*ao_coef_normalized_ordered_transp(s,l)
|
||||||
double precision :: general_primitive_integral
|
double precision :: general_primitive_integral
|
||||||
call give_explicit_poly_and_gaussian(Q_new,Q_center,qq,fact_q,iorder_q,&
|
call give_explicit_poly_and_gaussian(Q_new,Q_center,qq,fact_q,iorder_q,&
|
||||||
ao_expo_transp(r,k),ao_expo_transp(s,l), &
|
ao_expo_ordered_transp(r,k),ao_expo_ordered_transp(s,l), &
|
||||||
K_power,L_power,K_center,L_center,dim1)
|
K_power,L_power,K_center,L_center,dim1)
|
||||||
q_inv = 1.d0/qq
|
q_inv = 1.d0/qq
|
||||||
integral = general_primitive_integral(dim1, &
|
integral = general_primitive_integral(dim1, &
|
||||||
@ -222,12 +222,12 @@ double precision function ao_bielec_integral_schwartz_accel(i,j,k,l)
|
|||||||
|
|
||||||
schwartz_kl(0,0) = 0.d0
|
schwartz_kl(0,0) = 0.d0
|
||||||
do r = 1, ao_prim_num(k)
|
do r = 1, ao_prim_num(k)
|
||||||
coef1 = ao_coef_transp(r,k)*ao_coef_transp(r,k)
|
coef1 = ao_coef_normalized_ordered_transp(r,k)*ao_coef_normalized_ordered_transp(r,k)
|
||||||
schwartz_kl(0,r) = 0.d0
|
schwartz_kl(0,r) = 0.d0
|
||||||
do s = 1, ao_prim_num(l)
|
do s = 1, ao_prim_num(l)
|
||||||
coef2 = coef1*ao_coef_transp(s,l)*ao_coef_transp(s,l)
|
coef2 = coef1*ao_coef_normalized_ordered_transp(s,l)*ao_coef_normalized_ordered_transp(s,l)
|
||||||
schwartz_kl(s,r) = ERI( &
|
schwartz_kl(s,r) = ERI( &
|
||||||
ao_expo_transp(r,k),ao_expo_transp(s,l),ao_expo_transp(r,k),ao_expo_transp(s,l),&
|
ao_expo_ordered_transp(r,k),ao_expo_ordered_transp(s,l),ao_expo_ordered_transp(r,k),ao_expo_ordered_transp(s,l),&
|
||||||
K_power(1),L_power(1),K_power(1),L_power(1), &
|
K_power(1),L_power(1),K_power(1),L_power(1), &
|
||||||
K_power(2),L_power(2),K_power(2),L_power(2), &
|
K_power(2),L_power(2),K_power(2),L_power(2), &
|
||||||
K_power(3),L_power(3),K_power(3),L_power(3)) * &
|
K_power(3),L_power(3),K_power(3),L_power(3)) * &
|
||||||
@ -238,11 +238,11 @@ double precision function ao_bielec_integral_schwartz_accel(i,j,k,l)
|
|||||||
enddo
|
enddo
|
||||||
|
|
||||||
do p = 1, ao_prim_num(i)
|
do p = 1, ao_prim_num(i)
|
||||||
coef1 = ao_coef_transp(p,i)
|
coef1 = ao_coef_normalized_ordered_transp(p,i)
|
||||||
do q = 1, ao_prim_num(j)
|
do q = 1, ao_prim_num(j)
|
||||||
coef2 = coef1*ao_coef_transp(q,j)
|
coef2 = coef1*ao_coef_normalized_ordered_transp(q,j)
|
||||||
schwartz_ij = ERI( &
|
schwartz_ij = ERI( &
|
||||||
ao_expo_transp(p,i),ao_expo_transp(q,j),ao_expo_transp(p,i),ao_expo_transp(q,j),&
|
ao_expo_ordered_transp(p,i),ao_expo_ordered_transp(q,j),ao_expo_ordered_transp(p,i),ao_expo_ordered_transp(q,j),&
|
||||||
I_power(1),J_power(1),I_power(1),J_power(1), &
|
I_power(1),J_power(1),I_power(1),J_power(1), &
|
||||||
I_power(2),J_power(2),I_power(2),J_power(2), &
|
I_power(2),J_power(2),I_power(2),J_power(2), &
|
||||||
I_power(3),J_power(3),I_power(3),J_power(3))*coef2*coef2
|
I_power(3),J_power(3),I_power(3),J_power(3))*coef2*coef2
|
||||||
@ -253,14 +253,14 @@ double precision function ao_bielec_integral_schwartz_accel(i,j,k,l)
|
|||||||
if (schwartz_kl(0,r)*schwartz_ij < thresh) then
|
if (schwartz_kl(0,r)*schwartz_ij < thresh) then
|
||||||
cycle
|
cycle
|
||||||
endif
|
endif
|
||||||
coef3 = coef2*ao_coef_transp(r,k)
|
coef3 = coef2*ao_coef_normalized_ordered_transp(r,k)
|
||||||
do s = 1, ao_prim_num(l)
|
do s = 1, ao_prim_num(l)
|
||||||
if (schwartz_kl(s,r)*schwartz_ij < thresh) then
|
if (schwartz_kl(s,r)*schwartz_ij < thresh) then
|
||||||
cycle
|
cycle
|
||||||
endif
|
endif
|
||||||
coef4 = coef3*ao_coef_transp(s,l)
|
coef4 = coef3*ao_coef_normalized_ordered_transp(s,l)
|
||||||
integral = ERI( &
|
integral = ERI( &
|
||||||
ao_expo_transp(p,i),ao_expo_transp(q,j),ao_expo_transp(r,k),ao_expo_transp(s,l),&
|
ao_expo_ordered_transp(p,i),ao_expo_ordered_transp(q,j),ao_expo_ordered_transp(r,k),ao_expo_ordered_transp(s,l),&
|
||||||
I_power(1),J_power(1),K_power(1),L_power(1), &
|
I_power(1),J_power(1),K_power(1),L_power(1), &
|
||||||
I_power(2),J_power(2),K_power(2),L_power(2), &
|
I_power(2),J_power(2),K_power(2),L_power(2), &
|
||||||
I_power(3),J_power(3),K_power(3),L_power(3))
|
I_power(3),J_power(3),K_power(3),L_power(3))
|
||||||
|
|||||||
1
src/Bitmask/NEEDED_CHILDREN_MODULES
Normal file
1
src/Bitmask/NEEDED_CHILDREN_MODULES
Normal file
@ -0,0 +1 @@
|
|||||||
|
MOs
|
||||||
@ -1 +0,0 @@
|
|||||||
AOs Electrons Ezfio_files MOs Nuclei Output Utils
|
|
||||||
@ -40,13 +40,7 @@ Needed Modules
|
|||||||
.. Do not edit this section. It was auto-generated from the
|
.. Do not edit this section. It was auto-generated from the
|
||||||
.. NEEDED_MODULES file.
|
.. NEEDED_MODULES file.
|
||||||
|
|
||||||
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
|
|
||||||
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
|
|
||||||
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
|
|
||||||
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
|
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
|
||||||
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
|
|
||||||
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
|
|
||||||
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
|
|
||||||
|
|
||||||
Documentation
|
Documentation
|
||||||
=============
|
=============
|
||||||
|
|||||||
1
src/CAS_SD/NEEDED_CHILDREN_MODULES
Normal file
1
src/CAS_SD/NEEDED_CHILDREN_MODULES
Normal file
@ -0,0 +1 @@
|
|||||||
|
Perturbation Selectors_full Generators_CAS
|
||||||
@ -1,2 +0,0 @@
|
|||||||
AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Generators_CAS Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils
|
|
||||||
|
|
||||||
@ -24,21 +24,7 @@ Needed Modules
|
|||||||
.. Do not edit this section. It was auto-generated from the
|
.. Do not edit this section. It was auto-generated from the
|
||||||
.. NEEDED_MODULES file.
|
.. NEEDED_MODULES file.
|
||||||
|
|
||||||
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
|
|
||||||
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
|
|
||||||
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
|
|
||||||
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
|
|
||||||
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
|
|
||||||
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
|
|
||||||
* `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_
|
|
||||||
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
|
|
||||||
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
|
|
||||||
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
|
|
||||||
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
|
|
||||||
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
|
|
||||||
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
|
|
||||||
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
|
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
|
||||||
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
|
|
||||||
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
|
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
|
||||||
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
|
* `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_
|
||||||
|
|
||||||
|
|||||||
1
src/CID/NEEDED_CHILDREN_MODULES
Normal file
1
src/CID/NEEDED_CHILDREN_MODULES
Normal file
@ -0,0 +1 @@
|
|||||||
|
Selectors_full SingleRefMethod
|
||||||
@ -1,3 +0,0 @@
|
|||||||
AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Selectors_full SingleRefMethod Utils
|
|
||||||
|
|
||||||
|
|
||||||
@ -15,21 +15,8 @@ Needed Modules
|
|||||||
.. Do not edit this section. It was auto-generated from the
|
.. Do not edit this section. It was auto-generated from the
|
||||||
.. NEEDED_MODULES file.
|
.. NEEDED_MODULES file.
|
||||||
|
|
||||||
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
|
|
||||||
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
|
|
||||||
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
|
|
||||||
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
|
|
||||||
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
|
|
||||||
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
|
|
||||||
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
|
|
||||||
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
|
|
||||||
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
|
|
||||||
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
|
|
||||||
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
|
|
||||||
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
|
|
||||||
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
|
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
|
||||||
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
|
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
|
||||||
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
|
|
||||||
|
|
||||||
Documentation
|
Documentation
|
||||||
=============
|
=============
|
||||||
|
|||||||
1
src/CID_SC2_selected/NEEDED_CHILDREN_MODULES
Normal file
1
src/CID_SC2_selected/NEEDED_CHILDREN_MODULES
Normal file
@ -0,0 +1 @@
|
|||||||
|
CID_selected
|
||||||
@ -1,2 +0,0 @@
|
|||||||
AOs Bielec_integrals Bitmask CISD CISD_selected Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils
|
|
||||||
|
|
||||||
@ -19,23 +19,5 @@ Needed Modules
|
|||||||
.. Do not edit this section. It was auto-generated from the
|
.. Do not edit this section. It was auto-generated from the
|
||||||
.. NEEDED_MODULES file.
|
.. NEEDED_MODULES file.
|
||||||
|
|
||||||
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
|
* `CID_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected>`_
|
||||||
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
|
|
||||||
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
|
|
||||||
* `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
|
|
||||||
* `CISD_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected>`_
|
|
||||||
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
|
|
||||||
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
|
|
||||||
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
|
|
||||||
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
|
|
||||||
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
|
|
||||||
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
|
|
||||||
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
|
|
||||||
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
|
|
||||||
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
|
|
||||||
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
|
|
||||||
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
|
|
||||||
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
|
|
||||||
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
|
|
||||||
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
|
|
||||||
|
|
||||||
|
|||||||
1
src/CID_selected/NEEDED_CHILDREN_MODULES
Normal file
1
src/CID_selected/NEEDED_CHILDREN_MODULES
Normal file
@ -0,0 +1 @@
|
|||||||
|
Perturbation CID
|
||||||
@ -1,2 +0,0 @@
|
|||||||
AOs Bielec_integrals Bitmask CISD Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils
|
|
||||||
|
|
||||||
@ -22,22 +22,6 @@ Needed Modules
|
|||||||
.. Do not edit this section. It was auto-generated from the
|
.. Do not edit this section. It was auto-generated from the
|
||||||
.. NEEDED_MODULES file.
|
.. NEEDED_MODULES file.
|
||||||
|
|
||||||
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
|
|
||||||
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
|
|
||||||
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
|
|
||||||
* `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
|
|
||||||
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
|
|
||||||
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
|
|
||||||
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
|
|
||||||
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
|
|
||||||
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
|
|
||||||
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
|
|
||||||
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
|
|
||||||
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
|
|
||||||
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
|
|
||||||
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
|
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
|
||||||
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
|
* `CID <http://github.com/LCPQ/quantum_package/tree/master/src/CID>`_
|
||||||
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
|
|
||||||
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
|
|
||||||
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
|
|
||||||
|
|
||||||
|
|||||||
1
src/CIS/NEEDED_CHILDREN_MODULES
Normal file
1
src/CIS/NEEDED_CHILDREN_MODULES
Normal file
@ -0,0 +1 @@
|
|||||||
|
Selectors_full SingleRefMethod
|
||||||
@ -1,2 +0,0 @@
|
|||||||
AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Selectors_full SingleRefMethod Utils
|
|
||||||
|
|
||||||
@ -31,19 +31,6 @@ Needed Modules
|
|||||||
.. Do not edit this section. It was auto-generated from the
|
.. Do not edit this section. It was auto-generated from the
|
||||||
.. NEEDED_MODULES file.
|
.. NEEDED_MODULES file.
|
||||||
|
|
||||||
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
|
|
||||||
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
|
|
||||||
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
|
|
||||||
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
|
|
||||||
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
|
|
||||||
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
|
|
||||||
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
|
|
||||||
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
|
|
||||||
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
|
|
||||||
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
|
|
||||||
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
|
|
||||||
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
|
|
||||||
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
|
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
|
||||||
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
|
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
|
||||||
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
|
|
||||||
|
|
||||||
|
|||||||
1
src/CISD/NEEDED_CHILDREN_MODULES
Normal file
1
src/CISD/NEEDED_CHILDREN_MODULES
Normal file
@ -0,0 +1 @@
|
|||||||
|
Selectors_full SingleRefMethod
|
||||||
@ -1,2 +0,0 @@
|
|||||||
AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Selectors_full SingleRefMethod Utils
|
|
||||||
|
|
||||||
@ -15,21 +15,8 @@ Needed Modules
|
|||||||
.. Do not edit this section. It was auto-generated from the
|
.. Do not edit this section. It was auto-generated from the
|
||||||
.. NEEDED_MODULES file.
|
.. NEEDED_MODULES file.
|
||||||
|
|
||||||
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
|
|
||||||
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
|
|
||||||
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
|
|
||||||
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
|
|
||||||
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
|
|
||||||
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
|
|
||||||
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
|
|
||||||
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
|
|
||||||
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
|
|
||||||
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
|
|
||||||
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
|
|
||||||
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
|
|
||||||
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
|
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
|
||||||
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
|
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
|
||||||
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
|
|
||||||
|
|
||||||
Documentation
|
Documentation
|
||||||
=============
|
=============
|
||||||
|
|||||||
1
src/CISD_SC2_selected/NEEDED_CHILDREN_MODULES
Normal file
1
src/CISD_SC2_selected/NEEDED_CHILDREN_MODULES
Normal file
@ -0,0 +1 @@
|
|||||||
|
CISD_selected
|
||||||
@ -1,2 +0,0 @@
|
|||||||
AOs Bielec_integrals Bitmask CISD CISD_selected Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils
|
|
||||||
|
|
||||||
@ -19,23 +19,5 @@ Needed Modules
|
|||||||
.. Do not edit this section. It was auto-generated from the
|
.. Do not edit this section. It was auto-generated from the
|
||||||
.. NEEDED_MODULES file.
|
.. NEEDED_MODULES file.
|
||||||
|
|
||||||
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
|
|
||||||
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
|
|
||||||
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
|
|
||||||
* `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
|
|
||||||
* `CISD_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected>`_
|
* `CISD_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected>`_
|
||||||
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
|
|
||||||
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
|
|
||||||
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
|
|
||||||
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
|
|
||||||
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
|
|
||||||
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
|
|
||||||
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
|
|
||||||
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
|
|
||||||
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
|
|
||||||
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
|
|
||||||
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
|
|
||||||
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
|
|
||||||
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
|
|
||||||
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
|
|
||||||
|
|
||||||
|
|||||||
1
src/CISD_selected/NEEDED_CHILDREN_MODULES
Normal file
1
src/CISD_selected/NEEDED_CHILDREN_MODULES
Normal file
@ -0,0 +1 @@
|
|||||||
|
Perturbation CISD
|
||||||
@ -1,2 +0,0 @@
|
|||||||
AOs Bielec_integrals Bitmask CISD Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils
|
|
||||||
|
|
||||||
@ -28,22 +28,6 @@ Needed Modules
|
|||||||
.. Do not edit this section. It was auto-generated from the
|
.. Do not edit this section. It was auto-generated from the
|
||||||
.. NEEDED_MODULES file.
|
.. NEEDED_MODULES file.
|
||||||
|
|
||||||
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
|
|
||||||
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
|
|
||||||
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
|
|
||||||
* `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
|
|
||||||
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
|
|
||||||
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
|
|
||||||
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
|
|
||||||
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
|
|
||||||
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
|
|
||||||
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
|
|
||||||
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
|
|
||||||
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
|
|
||||||
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
|
|
||||||
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
|
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
|
||||||
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
|
* `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
|
||||||
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
|
|
||||||
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
|
|
||||||
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
|
|
||||||
|
|
||||||
|
|||||||
1
src/DDCI_selected/NEEDED_CHILDREN_MODULES
Normal file
1
src/DDCI_selected/NEEDED_CHILDREN_MODULES
Normal file
@ -0,0 +1 @@
|
|||||||
|
Perturbation Selectors_full Generators_CAS
|
||||||
@ -1,2 +0,0 @@
|
|||||||
AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Generators_CAS Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils
|
|
||||||
|
|
||||||
@ -19,21 +19,7 @@ Needed Modules
|
|||||||
.. Do not edit this section. It was auto-generated from the
|
.. Do not edit this section. It was auto-generated from the
|
||||||
.. NEEDED_MODULES file.
|
.. NEEDED_MODULES file.
|
||||||
|
|
||||||
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
|
|
||||||
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
|
|
||||||
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
|
|
||||||
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
|
|
||||||
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
|
|
||||||
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
|
|
||||||
* `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_
|
|
||||||
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
|
|
||||||
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
|
|
||||||
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
|
|
||||||
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
|
|
||||||
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
|
|
||||||
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
|
|
||||||
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
|
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
|
||||||
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
|
|
||||||
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
|
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
|
||||||
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
|
* `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_
|
||||||
|
|
||||||
|
|||||||
103
src/Determinants/EZFIO.cfg
Normal file
103
src/Determinants/EZFIO.cfg
Normal file
@ -0,0 +1,103 @@
|
|||||||
|
[N_states]
|
||||||
|
type: States_number
|
||||||
|
doc: Number of states to consider
|
||||||
|
interface: input
|
||||||
|
default: 1
|
||||||
|
|
||||||
|
[N_det_max_jacobi]
|
||||||
|
type: Strictly_positive_int
|
||||||
|
doc: Maximum number of determinants diagonalized by Jacobi
|
||||||
|
interface: input
|
||||||
|
default: 1000
|
||||||
|
|
||||||
|
[read_wf]
|
||||||
|
type: logical
|
||||||
|
doc: If true, read the wave function from the EZFIO file
|
||||||
|
interface: input
|
||||||
|
default: False
|
||||||
|
|
||||||
|
[only_single_double_dm]
|
||||||
|
type: logical
|
||||||
|
doc: If true, The One body DM is calculated with ignoring the Double<->Doubles extra diag elements
|
||||||
|
interface: input
|
||||||
|
default: False
|
||||||
|
|
||||||
|
[s2_eig]
|
||||||
|
type: logical
|
||||||
|
doc: Force the wave function to be an eigenfunction of S^2
|
||||||
|
interface: input
|
||||||
|
default: False
|
||||||
|
|
||||||
|
[threshold_generators]
|
||||||
|
type: Threshold
|
||||||
|
doc: Thresholds on generators (fraction of the norm)
|
||||||
|
interface: input
|
||||||
|
default: 0.99
|
||||||
|
|
||||||
|
[threshold_selectors]
|
||||||
|
type: Threshold
|
||||||
|
doc: Thresholds on selectors (fraction of the norm)
|
||||||
|
interface: input
|
||||||
|
default: 0.999
|
||||||
|
|
||||||
|
|
||||||
|
# Only create the ezfio_config, (no Input_* and no PROVIDER)
|
||||||
|
|
||||||
|
[n_states_diag]
|
||||||
|
type: integer
|
||||||
|
doc: n_states_diag
|
||||||
|
interface: Ocaml
|
||||||
|
|
||||||
|
[n_int]
|
||||||
|
interface: OCaml
|
||||||
|
doc: n_int
|
||||||
|
type: N_int_number
|
||||||
|
|
||||||
|
[bit_kind]
|
||||||
|
interface: OCaml
|
||||||
|
doc: bit_kind
|
||||||
|
type: Bit_kind
|
||||||
|
|
||||||
|
[mo_label]
|
||||||
|
interface: OCaml
|
||||||
|
doc: o_label
|
||||||
|
type: character*(64)
|
||||||
|
|
||||||
|
[n_det]
|
||||||
|
interface: OCaml
|
||||||
|
doc: n_det
|
||||||
|
type: integer
|
||||||
|
|
||||||
|
[psi_coef]
|
||||||
|
interface: OCaml
|
||||||
|
doc: psi_coef
|
||||||
|
type: double precision
|
||||||
|
size: (determinants_n_det,determinants_n_states)
|
||||||
|
|
||||||
|
[psi_det]
|
||||||
|
interface: OCaml
|
||||||
|
doc: psi_det
|
||||||
|
type: integer*8
|
||||||
|
size: (determinants_n_int*determinants_bit_kind/8,2,determinants_n_det)
|
||||||
|
|
||||||
|
[det_num]
|
||||||
|
interface: OCaml
|
||||||
|
doc: det_num
|
||||||
|
type: integer
|
||||||
|
|
||||||
|
[det_occ]
|
||||||
|
interface: OCaml
|
||||||
|
doc: det_occ
|
||||||
|
type: integer
|
||||||
|
size: (electrons_elec_alpha_num,determinants_det_num,2)
|
||||||
|
|
||||||
|
[det_coef]
|
||||||
|
interface: OCaml
|
||||||
|
doc: det_coef
|
||||||
|
type: double precision
|
||||||
|
size: (determinants_det_num)
|
||||||
|
|
||||||
|
[expected_s2]
|
||||||
|
interface: OCaml
|
||||||
|
doc: expcted_s2
|
||||||
|
type: double precision
|
||||||
@ -181,8 +181,43 @@ subroutine copy_H_apply_buffer_to_wf
|
|||||||
call normalize(psi_coef,N_det)
|
call normalize(psi_coef,N_det)
|
||||||
SOFT_TOUCH N_det psi_det psi_coef
|
SOFT_TOUCH N_det psi_det psi_coef
|
||||||
|
|
||||||
|
call debug_unicity_of_determinants
|
||||||
end
|
end
|
||||||
|
|
||||||
|
subroutine debug_unicity_of_determinants
|
||||||
|
implicit none
|
||||||
|
BEGIN_DOC
|
||||||
|
! This subroutine checks that there are no repetitions in the wave function
|
||||||
|
END_DOC
|
||||||
|
logical :: same, failed
|
||||||
|
integer :: i,k
|
||||||
|
print *, "======= DEBUG UNICITY ========="
|
||||||
|
failed = .False.
|
||||||
|
do i=2,N_det
|
||||||
|
same = .True.
|
||||||
|
do k=1,N_int
|
||||||
|
if ( psi_det_sorted_bit(k,1,i) /= psi_det_sorted_bit(k,1,i-1) ) then
|
||||||
|
same = .False.
|
||||||
|
exit
|
||||||
|
endif
|
||||||
|
if ( psi_det_sorted_bit(k,2,i) /= psi_det_sorted_bit(k,2,i-1) ) then
|
||||||
|
same = .False.
|
||||||
|
exit
|
||||||
|
endif
|
||||||
|
enddo
|
||||||
|
if (same) then
|
||||||
|
failed = .True.
|
||||||
|
call debug_det(psi_det_sorted_bit(1,1,i))
|
||||||
|
endif
|
||||||
|
enddo
|
||||||
|
|
||||||
|
if (failed) then
|
||||||
|
print *, '======= Determinants not unique : Failed ! ========='
|
||||||
|
stop
|
||||||
|
else
|
||||||
|
print *, '======= Determinants are unique : OK ! ========='
|
||||||
|
endif
|
||||||
|
end
|
||||||
|
|
||||||
subroutine fill_H_apply_buffer_no_selection(n_selected,det_buffer,Nint,iproc)
|
subroutine fill_H_apply_buffer_no_selection(n_selected,det_buffer,Nint,iproc)
|
||||||
use bitmasks
|
use bitmasks
|
||||||
1
src/Determinants/NEEDED_CHILDREN_MODULES
Normal file
1
src/Determinants/NEEDED_CHILDREN_MODULES
Normal file
@ -0,0 +1 @@
|
|||||||
|
Bielec_integrals
|
||||||
@ -32,16 +32,7 @@ Needed Modules
|
|||||||
.. Do not edit this section. It was auto-generated from the
|
.. Do not edit this section. It was auto-generated from the
|
||||||
.. NEEDED_MODULES file.
|
.. NEEDED_MODULES file.
|
||||||
|
|
||||||
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
|
|
||||||
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
|
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
|
||||||
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
|
|
||||||
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
|
|
||||||
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
|
|
||||||
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
|
|
||||||
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
|
|
||||||
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
|
|
||||||
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
|
|
||||||
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
|
|
||||||
|
|
||||||
Documentation
|
Documentation
|
||||||
=============
|
=============
|
||||||
@ -49,26 +40,29 @@ Documentation
|
|||||||
.. Do not edit this section. It was auto-generated from the
|
.. Do not edit this section. It was auto-generated from the
|
||||||
.. NEEDED_MODULES file.
|
.. NEEDED_MODULES file.
|
||||||
|
|
||||||
`copy_h_apply_buffer_to_wf <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L100>`_
|
`copy_h_apply_buffer_to_wf <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/H_apply.irp.f#L100>`_
|
||||||
Copies the H_apply buffer to psi_coef. You need to touch psi_det, psi_coef and N_det
|
Copies the H_apply buffer to psi_coef. You need to touch psi_det, psi_coef and N_det
|
||||||
after calling this function.
|
after calling this function.
|
||||||
After calling this subroutine, N_det, psi_det and psi_coef need to be touched
|
After calling this subroutine, N_det, psi_det and psi_coef need to be touched
|
||||||
|
|
||||||
`fill_h_apply_buffer_no_selection <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L187>`_
|
`debug_unicity_of_determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L187>`_
|
||||||
|
This subroutine checks that there are no repetitions in the wave function
|
||||||
|
|
||||||
|
`fill_h_apply_buffer_no_selection <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L222>`_
|
||||||
Fill the H_apply buffer with determiants for CISD
|
Fill the H_apply buffer with determiants for CISD
|
||||||
|
|
||||||
`h_apply_buffer_allocated <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L15>`_
|
`h_apply_buffer_allocated <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/H_apply.irp.f#L15>`_
|
||||||
Buffer of determinants/coefficients/perturbative energy for H_apply.
|
Buffer of determinants/coefficients/perturbative energy for H_apply.
|
||||||
Uninitialized. Filled by H_apply subroutines.
|
Uninitialized. Filled by H_apply subroutines.
|
||||||
|
|
||||||
`h_apply_buffer_lock <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L16>`_
|
`h_apply_buffer_lock <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/H_apply.irp.f#L16>`_
|
||||||
Buffer of determinants/coefficients/perturbative energy for H_apply.
|
Buffer of determinants/coefficients/perturbative energy for H_apply.
|
||||||
Uninitialized. Filled by H_apply subroutines.
|
Uninitialized. Filled by H_apply subroutines.
|
||||||
|
|
||||||
`resize_h_apply_buffer <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L48>`_
|
`resize_h_apply_buffer <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/H_apply.irp.f#L48>`_
|
||||||
Undocumented
|
Undocumented
|
||||||
|
|
||||||
`cisd_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/SC2.irp.f#L1>`_
|
`cisd_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/SC2.irp.f#L1>`_
|
||||||
CISD+SC2 method :: take off all the disconnected terms of a CISD (selected or not)
|
CISD+SC2 method :: take off all the disconnected terms of a CISD (selected or not)
|
||||||
.br
|
.br
|
||||||
dets_in : bitmasks corresponding to determinants
|
dets_in : bitmasks corresponding to determinants
|
||||||
@ -84,25 +78,25 @@ Documentation
|
|||||||
.br
|
.br
|
||||||
Initial guess vectors are not necessarily orthonormal
|
Initial guess vectors are not necessarily orthonormal
|
||||||
|
|
||||||
`connected_to_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L155>`_
|
`connected_to_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/connected_to_ref.irp.f#L155>`_
|
||||||
Undocumented
|
Undocumented
|
||||||
|
|
||||||
`connected_to_ref_by_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L253>`_
|
`connected_to_ref_by_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/connected_to_ref.irp.f#L253>`_
|
||||||
Undocumented
|
Undocumented
|
||||||
|
|
||||||
`det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L1>`_
|
`det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/connected_to_ref.irp.f#L1>`_
|
||||||
Return an integer*8 corresponding to a determinant index for searching
|
Return an integer*8 corresponding to a determinant index for searching
|
||||||
|
|
||||||
`get_index_in_psi_det_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L48>`_
|
`get_index_in_psi_det_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/connected_to_ref.irp.f#L48>`_
|
||||||
Returns the index of the determinant in the ``psi_det_sorted_bit`` array
|
Returns the index of the determinant in the ``psi_det_sorted_bit`` array
|
||||||
|
|
||||||
`is_in_wavefunction <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L34>`_
|
`is_in_wavefunction <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/connected_to_ref.irp.f#L34>`_
|
||||||
True if the determinant ``det`` is in the wave function
|
True if the determinant ``det`` is in the wave function
|
||||||
|
|
||||||
`occ_pattern_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L17>`_
|
`occ_pattern_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/connected_to_ref.irp.f#L17>`_
|
||||||
Return an integer*8 corresponding to a determinant index for searching
|
Return an integer*8 corresponding to a determinant index for searching
|
||||||
|
|
||||||
`do_mono_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/create_excitations.irp.f#L1>`_
|
`do_mono_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/create_excitations.irp.f#L1>`_
|
||||||
Apply the mono excitation operator : a^{dager}_(i_particle) a_(i_hole) of spin = ispin
|
Apply the mono excitation operator : a^{dager}_(i_particle) a_(i_hole) of spin = ispin
|
||||||
on key_in
|
on key_in
|
||||||
ispin = 1 == alpha
|
ispin = 1 == alpha
|
||||||
@ -110,13 +104,13 @@ Documentation
|
|||||||
i_ok = 1 == the excitation is possible
|
i_ok = 1 == the excitation is possible
|
||||||
i_ok = -1 == the excitation is not possible
|
i_ok = -1 == the excitation is not possible
|
||||||
|
|
||||||
`davidson_converged <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L382>`_
|
`davidson_converged <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/davidson.irp.f#L382>`_
|
||||||
True if the Davidson algorithm is converged
|
True if the Davidson algorithm is converged
|
||||||
|
|
||||||
`davidson_criterion <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L372>`_
|
`davidson_criterion <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/davidson.irp.f#L372>`_
|
||||||
Can be : [ energy | residual | both | wall_time | cpu_time | iterations ]
|
Can be : [ energy | residual | both | wall_time | cpu_time | iterations ]
|
||||||
|
|
||||||
`davidson_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L18>`_
|
`davidson_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/davidson.irp.f#L18>`_
|
||||||
Davidson diagonalization.
|
Davidson diagonalization.
|
||||||
.br
|
.br
|
||||||
dets_in : bitmasks corresponding to determinants
|
dets_in : bitmasks corresponding to determinants
|
||||||
@ -134,7 +128,7 @@ Documentation
|
|||||||
.br
|
.br
|
||||||
Initial guess vectors are not necessarily orthonormal
|
Initial guess vectors are not necessarily orthonormal
|
||||||
|
|
||||||
`davidson_diag_hjj <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L68>`_
|
`davidson_diag_hjj <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/davidson.irp.f#L68>`_
|
||||||
Davidson diagonalization with specific diagonal elements of the H matrix
|
Davidson diagonalization with specific diagonal elements of the H matrix
|
||||||
.br
|
.br
|
||||||
H_jj : specific diagonal H matrix elements to diagonalize de Davidson
|
H_jj : specific diagonal H matrix elements to diagonalize de Davidson
|
||||||
@ -154,49 +148,49 @@ Documentation
|
|||||||
.br
|
.br
|
||||||
Initial guess vectors are not necessarily orthonormal
|
Initial guess vectors are not necessarily orthonormal
|
||||||
|
|
||||||
`davidson_iter_max <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L1>`_
|
`davidson_iter_max <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/davidson.irp.f#L1>`_
|
||||||
Max number of Davidson iterations
|
Max number of Davidson iterations
|
||||||
|
|
||||||
`davidson_sze_max <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L9>`_
|
`davidson_sze_max <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/davidson.irp.f#L9>`_
|
||||||
Max number of Davidson sizes
|
Max number of Davidson sizes
|
||||||
|
|
||||||
`davidson_threshold <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L373>`_
|
`davidson_threshold <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/davidson.irp.f#L373>`_
|
||||||
Can be : [ energy | residual | both | wall_time | cpu_time | iterations ]
|
Can be : [ energy | residual | both | wall_time | cpu_time | iterations ]
|
||||||
|
|
||||||
`one_body_dm_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L164>`_
|
`one_body_dm_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/density_matrix.irp.f#L164>`_
|
||||||
One-body density matrix
|
One-body density matrix
|
||||||
|
|
||||||
`one_body_dm_mo_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L1>`_
|
`one_body_dm_mo_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/density_matrix.irp.f#L1>`_
|
||||||
Alpha and beta one-body density matrix for each state
|
Alpha and beta one-body density matrix for each state
|
||||||
|
|
||||||
`one_body_dm_mo_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L2>`_
|
`one_body_dm_mo_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/density_matrix.irp.f#L2>`_
|
||||||
Alpha and beta one-body density matrix for each state
|
Alpha and beta one-body density matrix for each state
|
||||||
|
|
||||||
`one_body_single_double_dm_mo_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L80>`_
|
`one_body_single_double_dm_mo_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/density_matrix.irp.f#L80>`_
|
||||||
Alpha and beta one-body density matrix for each state
|
Alpha and beta one-body density matrix for each state
|
||||||
|
|
||||||
`one_body_single_double_dm_mo_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L81>`_
|
`one_body_single_double_dm_mo_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/density_matrix.irp.f#L81>`_
|
||||||
Alpha and beta one-body density matrix for each state
|
Alpha and beta one-body density matrix for each state
|
||||||
|
|
||||||
`one_body_spin_density_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L172>`_
|
`one_body_spin_density_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/density_matrix.irp.f#L172>`_
|
||||||
rho(alpha) - rho(beta)
|
rho(alpha) - rho(beta)
|
||||||
|
|
||||||
`save_natural_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L196>`_
|
`save_natural_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/density_matrix.irp.f#L196>`_
|
||||||
Save natural orbitals, obtained by diagonalization of the one-body density matrix in the MO basis
|
Save natural orbitals, obtained by diagonalization of the one-body density matrix in the MO basis
|
||||||
|
|
||||||
`set_natural_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L180>`_
|
`set_natural_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/density_matrix.irp.f#L180>`_
|
||||||
Set natural orbitals, obtained by diagonalization of the one-body density matrix in the MO basis
|
Set natural orbitals, obtained by diagonalization of the one-body density matrix in the MO basis
|
||||||
|
|
||||||
`state_average_weight <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L207>`_
|
`state_average_weight <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/density_matrix.irp.f#L207>`_
|
||||||
Weights in the state-average calculation of the density matrix
|
Weights in the state-average calculation of the density matrix
|
||||||
|
|
||||||
`det_svd <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/det_svd.irp.f#L1>`_
|
`det_svd <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/det_svd.irp.f#L1>`_
|
||||||
Computes the SVD of the Alpha x Beta determinant coefficient matrix
|
Computes the SVD of the Alpha x Beta determinant coefficient matrix
|
||||||
|
|
||||||
`filter_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L426>`_
|
`filter_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L426>`_
|
||||||
Returns a determinant with only the 3 highest electrons
|
Returns a determinant with only the 3 highest electrons
|
||||||
|
|
||||||
`int_of_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L391>`_
|
`int_of_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L391>`_
|
||||||
Returns an integer*8 as :
|
Returns an integer*8 as :
|
||||||
.br
|
.br
|
||||||
|_<--- 21 bits ---><--- 21 bits ---><--- 21 bits --->|
|
|_<--- 21 bits ---><--- 21 bits ---><--- 21 bits --->|
|
||||||
@ -207,158 +201,158 @@ Documentation
|
|||||||
in descending order
|
in descending order
|
||||||
.br
|
.br
|
||||||
|
|
||||||
`max_degree_exc <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L32>`_
|
`max_degree_exc <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L32>`_
|
||||||
Maximum degree of excitation in the wf
|
Maximum degree of excitation in the wf
|
||||||
|
|
||||||
`n_det <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L3>`_
|
`n_det <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L3>`_
|
||||||
Number of determinants in the wave function
|
Number of determinants in the wave function
|
||||||
|
|
||||||
`psi_average_norm_contrib <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L276>`_
|
`psi_average_norm_contrib <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L276>`_
|
||||||
Contribution of determinants to the state-averaged density
|
Contribution of determinants to the state-averaged density
|
||||||
|
|
||||||
`psi_average_norm_contrib_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L306>`_
|
`psi_average_norm_contrib_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L306>`_
|
||||||
Wave function sorted by determinants contribution to the norm (state-averaged)
|
Wave function sorted by determinants contribution to the norm (state-averaged)
|
||||||
|
|
||||||
`psi_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L230>`_
|
`psi_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L230>`_
|
||||||
The wave function coefficients. Initialized with Hartree-Fock if the EZFIO file
|
The wave function coefficients. Initialized with Hartree-Fock if the EZFIO file
|
||||||
is empty
|
is empty
|
||||||
|
|
||||||
`psi_coef_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L305>`_
|
`psi_coef_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L305>`_
|
||||||
Wave function sorted by determinants contribution to the norm (state-averaged)
|
Wave function sorted by determinants contribution to the norm (state-averaged)
|
||||||
|
|
||||||
`psi_coef_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L453>`_
|
`psi_coef_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L453>`_
|
||||||
Determinants on which we apply <i|H|j>.
|
Determinants on which we apply <i|H|j>.
|
||||||
They are sorted by the 3 highest electrons in the alpha part,
|
They are sorted by the 3 highest electrons in the alpha part,
|
||||||
then by the 3 highest electrons in the beta part to accelerate
|
then by the 3 highest electrons in the beta part to accelerate
|
||||||
the research of connected determinants.
|
the research of connected determinants.
|
||||||
|
|
||||||
`psi_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L336>`_
|
`psi_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L336>`_
|
||||||
Determinants on which we apply <i|H|psi> for perturbation.
|
Determinants on which we apply <i|H|psi> for perturbation.
|
||||||
They are sorted by determinants interpreted as integers. Useful
|
They are sorted by determinants interpreted as integers. Useful
|
||||||
to accelerate the search of a random determinant in the wave
|
to accelerate the search of a random determinant in the wave
|
||||||
function.
|
function.
|
||||||
|
|
||||||
`psi_det <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L65>`_
|
`psi_det <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L65>`_
|
||||||
The wave function determinants. Initialized with Hartree-Fock if the EZFIO file
|
The wave function determinants. Initialized with Hartree-Fock if the EZFIO file
|
||||||
is empty
|
is empty
|
||||||
|
|
||||||
`psi_det_size <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L47>`_
|
`psi_det_size <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L47>`_
|
||||||
Size of the psi_det/psi_coef arrays
|
Size of the psi_det/psi_coef arrays
|
||||||
|
|
||||||
`psi_det_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L304>`_
|
`psi_det_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L304>`_
|
||||||
Wave function sorted by determinants contribution to the norm (state-averaged)
|
Wave function sorted by determinants contribution to the norm (state-averaged)
|
||||||
|
|
||||||
`psi_det_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L452>`_
|
`psi_det_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L452>`_
|
||||||
Determinants on which we apply <i|H|j>.
|
Determinants on which we apply <i|H|j>.
|
||||||
They are sorted by the 3 highest electrons in the alpha part,
|
They are sorted by the 3 highest electrons in the alpha part,
|
||||||
then by the 3 highest electrons in the beta part to accelerate
|
then by the 3 highest electrons in the beta part to accelerate
|
||||||
the research of connected determinants.
|
the research of connected determinants.
|
||||||
|
|
||||||
`psi_det_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L335>`_
|
`psi_det_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L335>`_
|
||||||
Determinants on which we apply <i|H|psi> for perturbation.
|
Determinants on which we apply <i|H|psi> for perturbation.
|
||||||
They are sorted by determinants interpreted as integers. Useful
|
They are sorted by determinants interpreted as integers. Useful
|
||||||
to accelerate the search of a random determinant in the wave
|
to accelerate the search of a random determinant in the wave
|
||||||
function.
|
function.
|
||||||
|
|
||||||
`psi_det_sorted_next_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L454>`_
|
`psi_det_sorted_next_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L454>`_
|
||||||
Determinants on which we apply <i|H|j>.
|
Determinants on which we apply <i|H|j>.
|
||||||
They are sorted by the 3 highest electrons in the alpha part,
|
They are sorted by the 3 highest electrons in the alpha part,
|
||||||
then by the 3 highest electrons in the beta part to accelerate
|
then by the 3 highest electrons in the beta part to accelerate
|
||||||
the research of connected determinants.
|
the research of connected determinants.
|
||||||
|
|
||||||
`read_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L583>`_
|
`read_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L583>`_
|
||||||
Reads the determinants from the EZFIO file
|
Reads the determinants from the EZFIO file
|
||||||
|
|
||||||
`save_wavefunction <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L630>`_
|
`save_wavefunction <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L630>`_
|
||||||
Save the wave function into the EZFIO file
|
Save the wave function into the EZFIO file
|
||||||
|
|
||||||
`save_wavefunction_general <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L649>`_
|
`save_wavefunction_general <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L649>`_
|
||||||
Save the wave function into the EZFIO file
|
Save the wave function into the EZFIO file
|
||||||
|
|
||||||
`save_wavefunction_unsorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L640>`_
|
`save_wavefunction_unsorted <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L640>`_
|
||||||
Save the wave function into the EZFIO file
|
Save the wave function into the EZFIO file
|
||||||
|
|
||||||
`sort_dets_by_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L474>`_
|
`sort_dets_by_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L474>`_
|
||||||
Determinants on which we apply <i|H|j>.
|
Determinants on which we apply <i|H|j>.
|
||||||
They are sorted by the 3 highest electrons in the alpha part,
|
They are sorted by the 3 highest electrons in the alpha part,
|
||||||
then by the 3 highest electrons in the beta part to accelerate
|
then by the 3 highest electrons in the beta part to accelerate
|
||||||
the research of connected determinants.
|
the research of connected determinants.
|
||||||
|
|
||||||
`sort_dets_by_det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L349>`_
|
`sort_dets_by_det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L349>`_
|
||||||
Determinants are sorted are sorted according to their det_search_key.
|
Determinants are sorted are sorted according to their det_search_key.
|
||||||
Useful to accelerate the search of a random determinant in the wave
|
Useful to accelerate the search of a random determinant in the wave
|
||||||
function.
|
function.
|
||||||
|
|
||||||
`double_exc_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants_bitmasks.irp.f#L40>`_
|
`double_exc_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants_bitmasks.irp.f#L40>`_
|
||||||
double_exc_bitmask(:,1,i) is the bitmask for holes of excitation 1
|
double_exc_bitmask(:,1,i) is the bitmask for holes of excitation 1
|
||||||
double_exc_bitmask(:,2,i) is the bitmask for particles of excitation 1
|
double_exc_bitmask(:,2,i) is the bitmask for particles of excitation 1
|
||||||
double_exc_bitmask(:,3,i) is the bitmask for holes of excitation 2
|
double_exc_bitmask(:,3,i) is the bitmask for holes of excitation 2
|
||||||
double_exc_bitmask(:,4,i) is the bitmask for particles of excitation 2
|
double_exc_bitmask(:,4,i) is the bitmask for particles of excitation 2
|
||||||
for a given couple of hole/particle excitations i.
|
for a given couple of hole/particle excitations i.
|
||||||
|
|
||||||
`n_double_exc_bitmasks <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants_bitmasks.irp.f#L31>`_
|
`n_double_exc_bitmasks <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants_bitmasks.irp.f#L31>`_
|
||||||
Number of double excitation bitmasks
|
Number of double excitation bitmasks
|
||||||
|
|
||||||
`n_single_exc_bitmasks <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants_bitmasks.irp.f#L8>`_
|
`n_single_exc_bitmasks <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants_bitmasks.irp.f#L8>`_
|
||||||
Number of single excitation bitmasks
|
Number of single excitation bitmasks
|
||||||
|
|
||||||
`single_exc_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants_bitmasks.irp.f#L17>`_
|
`single_exc_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants_bitmasks.irp.f#L17>`_
|
||||||
single_exc_bitmask(:,1,i) is the bitmask for holes
|
single_exc_bitmask(:,1,i) is the bitmask for holes
|
||||||
single_exc_bitmask(:,2,i) is the bitmask for particles
|
single_exc_bitmask(:,2,i) is the bitmask for particles
|
||||||
for a given couple of hole/particle excitations i.
|
for a given couple of hole/particle excitations i.
|
||||||
|
|
||||||
`ci_eigenvectors <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L37>`_
|
`ci_eigenvectors <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI.irp.f#L37>`_
|
||||||
Eigenvectors/values of the CI matrix
|
Eigenvectors/values of the CI matrix
|
||||||
|
|
||||||
`ci_eigenvectors_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L38>`_
|
`ci_eigenvectors_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI.irp.f#L38>`_
|
||||||
Eigenvectors/values of the CI matrix
|
Eigenvectors/values of the CI matrix
|
||||||
|
|
||||||
`ci_electronic_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L36>`_
|
`ci_electronic_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI.irp.f#L36>`_
|
||||||
Eigenvectors/values of the CI matrix
|
Eigenvectors/values of the CI matrix
|
||||||
|
|
||||||
`ci_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L18>`_
|
`ci_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI.irp.f#L18>`_
|
||||||
N_states lowest eigenvalues of the CI matrix
|
N_states lowest eigenvalues of the CI matrix
|
||||||
|
|
||||||
`diag_algorithm <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L1>`_
|
`diag_algorithm <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI.irp.f#L1>`_
|
||||||
Diagonalization algorithm (Davidson or Lapack)
|
Diagonalization algorithm (Davidson or Lapack)
|
||||||
|
|
||||||
`diagonalize_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L96>`_
|
`diagonalize_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI.irp.f#L96>`_
|
||||||
Replace the coefficients of the CI states by the coefficients of the
|
Replace the coefficients of the CI states by the coefficients of the
|
||||||
eigenstates of the CI matrix
|
eigenstates of the CI matrix
|
||||||
|
|
||||||
`ci_sc2_eigenvectors <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_SC2.irp.f#L27>`_
|
`ci_sc2_eigenvectors <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_SC2.irp.f#L27>`_
|
||||||
Eigenvectors/values of the CI matrix
|
Eigenvectors/values of the CI matrix
|
||||||
|
|
||||||
`ci_sc2_electronic_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_SC2.irp.f#L26>`_
|
`ci_sc2_electronic_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_SC2.irp.f#L26>`_
|
||||||
Eigenvectors/values of the CI matrix
|
Eigenvectors/values of the CI matrix
|
||||||
|
|
||||||
`ci_sc2_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_SC2.irp.f#L1>`_
|
`ci_sc2_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_SC2.irp.f#L1>`_
|
||||||
N_states_diag lowest eigenvalues of the CI matrix
|
N_states_diag lowest eigenvalues of the CI matrix
|
||||||
|
|
||||||
`diagonalize_ci_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_SC2.irp.f#L46>`_
|
`diagonalize_ci_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_SC2.irp.f#L46>`_
|
||||||
Replace the coefficients of the CI states_diag by the coefficients of the
|
Replace the coefficients of the CI states_diag by the coefficients of the
|
||||||
eigenstates of the CI matrix
|
eigenstates of the CI matrix
|
||||||
|
|
||||||
`threshold_convergence_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_SC2.irp.f#L18>`_
|
`threshold_convergence_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_SC2.irp.f#L18>`_
|
||||||
convergence of the correlation energy of SC2 iterations
|
convergence of the correlation energy of SC2 iterations
|
||||||
|
|
||||||
`ci_eigenvectors_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_mono.irp.f#L2>`_
|
`ci_eigenvectors_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_mono.irp.f#L2>`_
|
||||||
Eigenvectors/values of the CI matrix
|
Eigenvectors/values of the CI matrix
|
||||||
|
|
||||||
`ci_eigenvectors_s2_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_mono.irp.f#L3>`_
|
`ci_eigenvectors_s2_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_mono.irp.f#L3>`_
|
||||||
Eigenvectors/values of the CI matrix
|
Eigenvectors/values of the CI matrix
|
||||||
|
|
||||||
`ci_electronic_energy_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_mono.irp.f#L1>`_
|
`ci_electronic_energy_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_mono.irp.f#L1>`_
|
||||||
Eigenvectors/values of the CI matrix
|
Eigenvectors/values of the CI matrix
|
||||||
|
|
||||||
`diagonalize_ci_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_mono.irp.f#L59>`_
|
`diagonalize_ci_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_mono.irp.f#L59>`_
|
||||||
Replace the coefficients of the CI states by the coefficients of the
|
Replace the coefficients of the CI states by the coefficients of the
|
||||||
eigenstates of the CI matrix
|
eigenstates of the CI matrix
|
||||||
|
|
||||||
`apply_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/excitations_utils.irp.f#L1>`_
|
`apply_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/excitations_utils.irp.f#L1>`_
|
||||||
Undocumented
|
Undocumented
|
||||||
|
|
||||||
`filter_connected <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L2>`_
|
`filter_connected <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/filter_connected.irp.f#L2>`_
|
||||||
Filters out the determinants that are not connected by H
|
Filters out the determinants that are not connected by H
|
||||||
.br
|
.br
|
||||||
returns the array idx which contains the index of the
|
returns the array idx which contains the index of the
|
||||||
@ -369,7 +363,7 @@ Documentation
|
|||||||
.br
|
.br
|
||||||
idx(0) is the number of determinants that interact with key1
|
idx(0) is the number of determinants that interact with key1
|
||||||
|
|
||||||
`filter_connected_davidson <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L163>`_
|
`filter_connected_davidson <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/filter_connected.irp.f#L163>`_
|
||||||
Filters out the determinants that are not connected by H
|
Filters out the determinants that are not connected by H
|
||||||
returns the array idx which contains the index of the
|
returns the array idx which contains the index of the
|
||||||
determinants in the array key1 that interact
|
determinants in the array key1 that interact
|
||||||
@ -378,7 +372,7 @@ Documentation
|
|||||||
idx(0) is the number of determinants that interact with key1
|
idx(0) is the number of determinants that interact with key1
|
||||||
key1 should come from psi_det_sorted_ab.
|
key1 should come from psi_det_sorted_ab.
|
||||||
|
|
||||||
`filter_connected_i_h_psi0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L293>`_
|
`filter_connected_i_h_psi0 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/filter_connected.irp.f#L293>`_
|
||||||
returns the array idx which contains the index of the
|
returns the array idx which contains the index of the
|
||||||
.br
|
.br
|
||||||
determinants in the array key1 that interact
|
determinants in the array key1 that interact
|
||||||
@ -387,7 +381,7 @@ Documentation
|
|||||||
.br
|
.br
|
||||||
idx(0) is the number of determinants that interact with key1
|
idx(0) is the number of determinants that interact with key1
|
||||||
|
|
||||||
`filter_connected_i_h_psi0_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L392>`_
|
`filter_connected_i_h_psi0_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/filter_connected.irp.f#L392>`_
|
||||||
standard filter_connected_i_H_psi but returns in addition
|
standard filter_connected_i_H_psi but returns in addition
|
||||||
.br
|
.br
|
||||||
the array of the index of the non connected determinants to key1
|
the array of the index of the non connected determinants to key1
|
||||||
@ -398,7 +392,7 @@ Documentation
|
|||||||
.br
|
.br
|
||||||
to repeat the excitations
|
to repeat the excitations
|
||||||
|
|
||||||
`filter_connected_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L101>`_
|
`filter_connected_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/filter_connected.irp.f#L101>`_
|
||||||
Filters out the determinants that are not connected by H
|
Filters out the determinants that are not connected by H
|
||||||
returns the array idx which contains the index of the
|
returns the array idx which contains the index of the
|
||||||
determinants in the array key1 that interact
|
determinants in the array key1 that interact
|
||||||
@ -407,197 +401,197 @@ Documentation
|
|||||||
.br
|
.br
|
||||||
Determinants are taken from the psi_det_sorted_ab array
|
Determinants are taken from the psi_det_sorted_ab array
|
||||||
|
|
||||||
`put_gess <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/guess_triplet.irp.f#L1>`_
|
`put_gess <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/guess_triplet.irp.f#L1>`_
|
||||||
Undocumented
|
Undocumented
|
||||||
|
|
||||||
`det_to_occ_pattern <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L2>`_
|
`det_to_occ_pattern <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/occ_pattern.irp.f#L2>`_
|
||||||
Transform a determinant to an occupation pattern
|
Transform a determinant to an occupation pattern
|
||||||
|
|
||||||
`make_s2_eigenfunction <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L251>`_
|
`make_s2_eigenfunction <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/occ_pattern.irp.f#L251>`_
|
||||||
Undocumented
|
Undocumented
|
||||||
|
|
||||||
`n_occ_pattern <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L143>`_
|
`n_occ_pattern <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/occ_pattern.irp.f#L143>`_
|
||||||
array of the occ_pattern present in the wf
|
array of the occ_pattern present in the wf
|
||||||
psi_occ_pattern(:,1,j) = jth occ_pattern of the wave function : represent all the single occupation
|
psi_occ_pattern(:,1,j) = jth occ_pattern of the wave function : represent all the single occupation
|
||||||
psi_occ_pattern(:,2,j) = jth occ_pattern of the wave function : represent all the double occupation
|
psi_occ_pattern(:,2,j) = jth occ_pattern of the wave function : represent all the double occupation
|
||||||
|
|
||||||
`occ_pattern_to_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L42>`_
|
`occ_pattern_to_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/occ_pattern.irp.f#L42>`_
|
||||||
Generate all possible determinants for a give occ_pattern
|
Generate all possible determinants for a give occ_pattern
|
||||||
|
|
||||||
`occ_pattern_to_dets_size <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L20>`_
|
`occ_pattern_to_dets_size <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/occ_pattern.irp.f#L20>`_
|
||||||
Number of possible determinants for a given occ_pattern
|
Number of possible determinants for a given occ_pattern
|
||||||
|
|
||||||
`psi_occ_pattern <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L142>`_
|
`psi_occ_pattern <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/occ_pattern.irp.f#L142>`_
|
||||||
array of the occ_pattern present in the wf
|
array of the occ_pattern present in the wf
|
||||||
psi_occ_pattern(:,1,j) = jth occ_pattern of the wave function : represent all the single occupation
|
psi_occ_pattern(:,1,j) = jth occ_pattern of the wave function : represent all the single occupation
|
||||||
psi_occ_pattern(:,2,j) = jth occ_pattern of the wave function : represent all the double occupation
|
psi_occ_pattern(:,2,j) = jth occ_pattern of the wave function : represent all the double occupation
|
||||||
|
|
||||||
`rec_occ_pattern_to_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L102>`_
|
`rec_occ_pattern_to_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/occ_pattern.irp.f#L102>`_
|
||||||
Undocumented
|
Undocumented
|
||||||
|
|
||||||
`n_states_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/options.irp.f#L40>`_
|
`n_states_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/options.irp.f#L1>`_
|
||||||
Number of states to consider for the diagonalization
|
Number of states to consider for the diagonalization
|
||||||
|
|
||||||
`pouet <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/program_beginer_determinants.irp.f#L1>`_
|
`pouet <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/program_beginer_determinants.irp.f#L1>`_
|
||||||
Undocumented
|
Undocumented
|
||||||
|
|
||||||
`routine <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/program_beginer_determinants.irp.f#L7>`_
|
`routine <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/program_beginer_determinants.irp.f#L7>`_
|
||||||
Undocumented
|
Undocumented
|
||||||
|
|
||||||
`idx_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L5>`_
|
`idx_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L5>`_
|
||||||
CAS wave function, defined from the application of the CAS bitmask on the
|
CAS wave function, defined from the application of the CAS bitmask on the
|
||||||
determinants. idx_cas gives the indice of the CAS determinant in psi_det.
|
determinants. idx_cas gives the indice of the CAS determinant in psi_det.
|
||||||
|
|
||||||
`idx_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L62>`_
|
`idx_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L62>`_
|
||||||
Set of determinants which are not part of the CAS, defined from the application
|
Set of determinants which are not part of the CAS, defined from the application
|
||||||
of the CAS bitmask on the determinants.
|
of the CAS bitmask on the determinants.
|
||||||
idx_non_cas gives the indice of the determinant in psi_det.
|
idx_non_cas gives the indice of the determinant in psi_det.
|
||||||
|
|
||||||
`n_det_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L6>`_
|
`n_det_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L6>`_
|
||||||
CAS wave function, defined from the application of the CAS bitmask on the
|
CAS wave function, defined from the application of the CAS bitmask on the
|
||||||
determinants. idx_cas gives the indice of the CAS determinant in psi_det.
|
determinants. idx_cas gives the indice of the CAS determinant in psi_det.
|
||||||
|
|
||||||
`n_det_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L63>`_
|
`n_det_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L63>`_
|
||||||
Set of determinants which are not part of the CAS, defined from the application
|
Set of determinants which are not part of the CAS, defined from the application
|
||||||
of the CAS bitmask on the determinants.
|
of the CAS bitmask on the determinants.
|
||||||
idx_non_cas gives the indice of the determinant in psi_det.
|
idx_non_cas gives the indice of the determinant in psi_det.
|
||||||
|
|
||||||
`psi_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L3>`_
|
`psi_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L3>`_
|
||||||
CAS wave function, defined from the application of the CAS bitmask on the
|
CAS wave function, defined from the application of the CAS bitmask on the
|
||||||
determinants. idx_cas gives the indice of the CAS determinant in psi_det.
|
determinants. idx_cas gives the indice of the CAS determinant in psi_det.
|
||||||
|
|
||||||
`psi_cas_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L4>`_
|
`psi_cas_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L4>`_
|
||||||
CAS wave function, defined from the application of the CAS bitmask on the
|
CAS wave function, defined from the application of the CAS bitmask on the
|
||||||
determinants. idx_cas gives the indice of the CAS determinant in psi_det.
|
determinants. idx_cas gives the indice of the CAS determinant in psi_det.
|
||||||
|
|
||||||
`psi_cas_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L47>`_
|
`psi_cas_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L47>`_
|
||||||
CAS determinants sorted to accelerate the search of a random determinant in the wave
|
CAS determinants sorted to accelerate the search of a random determinant in the wave
|
||||||
function.
|
function.
|
||||||
|
|
||||||
`psi_cas_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L46>`_
|
`psi_cas_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L46>`_
|
||||||
CAS determinants sorted to accelerate the search of a random determinant in the wave
|
CAS determinants sorted to accelerate the search of a random determinant in the wave
|
||||||
function.
|
function.
|
||||||
|
|
||||||
`psi_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L60>`_
|
`psi_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L60>`_
|
||||||
Set of determinants which are not part of the CAS, defined from the application
|
Set of determinants which are not part of the CAS, defined from the application
|
||||||
of the CAS bitmask on the determinants.
|
of the CAS bitmask on the determinants.
|
||||||
idx_non_cas gives the indice of the determinant in psi_det.
|
idx_non_cas gives the indice of the determinant in psi_det.
|
||||||
|
|
||||||
`psi_non_cas_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L61>`_
|
`psi_non_cas_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L61>`_
|
||||||
Set of determinants which are not part of the CAS, defined from the application
|
Set of determinants which are not part of the CAS, defined from the application
|
||||||
of the CAS bitmask on the determinants.
|
of the CAS bitmask on the determinants.
|
||||||
idx_non_cas gives the indice of the determinant in psi_det.
|
idx_non_cas gives the indice of the determinant in psi_det.
|
||||||
|
|
||||||
`psi_non_cas_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L100>`_
|
`psi_non_cas_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L100>`_
|
||||||
CAS determinants sorted to accelerate the search of a random determinant in the wave
|
CAS determinants sorted to accelerate the search of a random determinant in the wave
|
||||||
function.
|
function.
|
||||||
|
|
||||||
`psi_non_cas_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L99>`_
|
`psi_non_cas_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L99>`_
|
||||||
CAS determinants sorted to accelerate the search of a random determinant in the wave
|
CAS determinants sorted to accelerate the search of a random determinant in the wave
|
||||||
function.
|
function.
|
||||||
|
|
||||||
`bi_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L5>`_
|
`bi_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ref_bitmask.irp.f#L5>`_
|
||||||
Energy of the reference bitmask used in Slater rules
|
Energy of the reference bitmask used in Slater rules
|
||||||
|
|
||||||
`kinetic_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L3>`_
|
`kinetic_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ref_bitmask.irp.f#L3>`_
|
||||||
Energy of the reference bitmask used in Slater rules
|
Energy of the reference bitmask used in Slater rules
|
||||||
|
|
||||||
`mono_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L2>`_
|
`mono_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ref_bitmask.irp.f#L2>`_
|
||||||
Energy of the reference bitmask used in Slater rules
|
Energy of the reference bitmask used in Slater rules
|
||||||
|
|
||||||
`nucl_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L4>`_
|
`nucl_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ref_bitmask.irp.f#L4>`_
|
||||||
Energy of the reference bitmask used in Slater rules
|
Energy of the reference bitmask used in Slater rules
|
||||||
|
|
||||||
`ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L1>`_
|
`ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ref_bitmask.irp.f#L1>`_
|
||||||
Energy of the reference bitmask used in Slater rules
|
Energy of the reference bitmask used in Slater rules
|
||||||
|
|
||||||
`expected_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L48>`_
|
`expected_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/s2.irp.f#L48>`_
|
||||||
Expected value of S2 : S*(S+1)
|
Expected value of S2 : S*(S+1)
|
||||||
|
|
||||||
`get_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L1>`_
|
`get_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/s2.irp.f#L1>`_
|
||||||
Returns <S^2>
|
Returns <S^2>
|
||||||
|
|
||||||
`get_s2_u0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L82>`_
|
`get_s2_u0 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/s2.irp.f#L82>`_
|
||||||
Undocumented
|
Undocumented
|
||||||
|
|
||||||
`s2_values <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L67>`_
|
`s2_values <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/s2.irp.f#L67>`_
|
||||||
array of the averaged values of the S^2 operator on the various states
|
array of the averaged values of the S^2 operator on the various states
|
||||||
|
|
||||||
`s_z <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L36>`_
|
`s_z <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/s2.irp.f#L36>`_
|
||||||
z component of the Spin
|
z component of the Spin
|
||||||
|
|
||||||
`s_z2_sz <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L37>`_
|
`s_z2_sz <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/s2.irp.f#L37>`_
|
||||||
z component of the Spin
|
z component of the Spin
|
||||||
|
|
||||||
`prog_save_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_for_casino.irp.f#L266>`_
|
`prog_save_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/save_for_casino.irp.f#L266>`_
|
||||||
Undocumented
|
Undocumented
|
||||||
|
|
||||||
`save_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_for_casino.irp.f#L1>`_
|
`save_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/save_for_casino.irp.f#L1>`_
|
||||||
Undocumented
|
Undocumented
|
||||||
|
|
||||||
`save_dets_qmcchem <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_for_qmcchem.irp.f#L1>`_
|
`save_dets_qmcchem <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/save_for_qmcchem.irp.f#L1>`_
|
||||||
Undocumented
|
Undocumented
|
||||||
|
|
||||||
`save_for_qmc <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_for_qmcchem.irp.f#L48>`_
|
`save_for_qmc <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/save_for_qmcchem.irp.f#L48>`_
|
||||||
Undocumented
|
Undocumented
|
||||||
|
|
||||||
`save_natorb <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_natorb.irp.f#L1>`_
|
`save_natorb <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/save_natorb.irp.f#L1>`_
|
||||||
Undocumented
|
Undocumented
|
||||||
|
|
||||||
`a_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L962>`_
|
`a_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L962>`_
|
||||||
Needed for diag_H_mat_elem
|
Needed for diag_H_mat_elem
|
||||||
|
|
||||||
`ac_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1007>`_
|
`ac_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L1007>`_
|
||||||
Needed for diag_H_mat_elem
|
Needed for diag_H_mat_elem
|
||||||
|
|
||||||
`decode_exc <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L76>`_
|
`decode_exc <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L76>`_
|
||||||
Decodes the exc arrays returned by get_excitation.
|
Decodes the exc arrays returned by get_excitation.
|
||||||
h1,h2 : Holes
|
h1,h2 : Holes
|
||||||
p1,p2 : Particles
|
p1,p2 : Particles
|
||||||
s1,s2 : Spins (1:alpha, 2:beta)
|
s1,s2 : Spins (1:alpha, 2:beta)
|
||||||
degree : Degree of excitation
|
degree : Degree of excitation
|
||||||
|
|
||||||
`det_connections <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1139>`_
|
`det_connections <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L1139>`_
|
||||||
Build connection proxy between determinants
|
Build connection proxy between determinants
|
||||||
|
|
||||||
`diag_h_mat_elem <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L900>`_
|
`diag_h_mat_elem <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L900>`_
|
||||||
Computes <i|H|i>
|
Computes <i|H|i>
|
||||||
|
|
||||||
`get_double_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L141>`_
|
`get_double_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L141>`_
|
||||||
Returns the two excitation operators between two doubly excited determinants and the phase
|
Returns the two excitation operators between two doubly excited determinants and the phase
|
||||||
|
|
||||||
`get_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L30>`_
|
`get_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L30>`_
|
||||||
Returns the excitation operators between two determinants and the phase
|
Returns the excitation operators between two determinants and the phase
|
||||||
|
|
||||||
`get_excitation_degree <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1>`_
|
`get_excitation_degree <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L1>`_
|
||||||
Returns the excitation degree between two determinants
|
Returns the excitation degree between two determinants
|
||||||
|
|
||||||
`get_excitation_degree_vector <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L816>`_
|
`get_excitation_degree_vector <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L816>`_
|
||||||
Applies get_excitation_degree to an array of determinants
|
Applies get_excitation_degree to an array of determinants
|
||||||
|
|
||||||
`get_mono_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L274>`_
|
`get_mono_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L274>`_
|
||||||
Returns the excitation operator between two singly excited determinants and the phase
|
Returns the excitation operator between two singly excited determinants and the phase
|
||||||
|
|
||||||
`get_occ_from_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1055>`_
|
`get_occ_from_key <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L1055>`_
|
||||||
Returns a list of occupation numbers from a bitstring
|
Returns a list of occupation numbers from a bitstring
|
||||||
|
|
||||||
`h_u_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1071>`_
|
`h_u_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L1071>`_
|
||||||
Computes v_0 = H|u_0>
|
Computes v_0 = H|u_0>
|
||||||
.br
|
.br
|
||||||
n : number of determinants
|
n : number of determinants
|
||||||
.br
|
.br
|
||||||
H_jj : array of <j|H|j>
|
H_jj : array of <j|H|j>
|
||||||
|
|
||||||
`i_h_j <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L355>`_
|
`i_h_j <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L355>`_
|
||||||
Returns <i|H|j> where i and j are determinants
|
Returns <i|H|j> where i and j are determinants
|
||||||
|
|
||||||
`i_h_j_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L492>`_
|
`i_h_j_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L492>`_
|
||||||
Returns <i|H|j> where i and j are determinants
|
Returns <i|H|j> where i and j are determinants
|
||||||
|
|
||||||
`i_h_psi <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L631>`_
|
`i_h_psi <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L631>`_
|
||||||
<key|H|psi> for the various Nstates
|
<key|H|psi> for the various Nstates
|
||||||
|
|
||||||
`i_h_psi_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L713>`_
|
`i_h_psi_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L713>`_
|
||||||
<key|H|psi> for the various Nstate
|
<key|H|psi> for the various Nstate
|
||||||
.br
|
.br
|
||||||
returns in addition
|
returns in addition
|
||||||
@ -610,7 +604,7 @@ Documentation
|
|||||||
.br
|
.br
|
||||||
to repeat the excitations
|
to repeat the excitations
|
||||||
|
|
||||||
`i_h_psi_sc2_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L760>`_
|
`i_h_psi_sc2_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L760>`_
|
||||||
<key|H|psi> for the various Nstate
|
<key|H|psi> for the various Nstate
|
||||||
.br
|
.br
|
||||||
returns in addition
|
returns in addition
|
||||||
@ -623,73 +617,73 @@ Documentation
|
|||||||
.br
|
.br
|
||||||
to repeat the excitations
|
to repeat the excitations
|
||||||
|
|
||||||
`i_h_psi_sec_ord <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L666>`_
|
`i_h_psi_sec_ord <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L666>`_
|
||||||
<key|H|psi> for the various Nstates
|
<key|H|psi> for the various Nstates
|
||||||
|
|
||||||
`n_con_int <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1131>`_
|
`n_con_int <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L1131>`_
|
||||||
Number of integers to represent the connections between determinants
|
Number of integers to represent the connections between determinants
|
||||||
|
|
||||||
`create_wf_of_psi_svd_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L473>`_
|
`create_wf_of_psi_svd_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L473>`_
|
||||||
Matrix of wf coefficients. Outer product of alpha and beta determinants
|
Matrix of wf coefficients. Outer product of alpha and beta determinants
|
||||||
|
|
||||||
`generate_all_alpha_beta_det_products <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L528>`_
|
`generate_all_alpha_beta_det_products <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L528>`_
|
||||||
Create a wave function from all possible alpha x beta determinants
|
Create a wave function from all possible alpha x beta determinants
|
||||||
|
|
||||||
`get_index_in_psi_det_alpha_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L131>`_
|
`get_index_in_psi_det_alpha_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L131>`_
|
||||||
Returns the index of the determinant in the ``psi_det_alpha_unique`` array
|
Returns the index of the determinant in the ``psi_det_alpha_unique`` array
|
||||||
|
|
||||||
`get_index_in_psi_det_beta_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L212>`_
|
`get_index_in_psi_det_beta_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L212>`_
|
||||||
Returns the index of the determinant in the ``psi_det_beta_unique`` array
|
Returns the index of the determinant in the ``psi_det_beta_unique`` array
|
||||||
|
|
||||||
`n_det_alpha_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L54>`_
|
`n_det_alpha_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L54>`_
|
||||||
Unique alpha determinants
|
Unique alpha determinants
|
||||||
|
|
||||||
`n_det_beta_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L91>`_
|
`n_det_beta_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L91>`_
|
||||||
Unique beta determinants
|
Unique beta determinants
|
||||||
|
|
||||||
`psi_det_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L25>`_
|
`psi_det_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L25>`_
|
||||||
List of alpha determinants of psi_det
|
List of alpha determinants of psi_det
|
||||||
|
|
||||||
`psi_det_alpha_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L53>`_
|
`psi_det_alpha_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L53>`_
|
||||||
Unique alpha determinants
|
Unique alpha determinants
|
||||||
|
|
||||||
`psi_det_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L39>`_
|
`psi_det_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L39>`_
|
||||||
List of beta determinants of psi_det
|
List of beta determinants of psi_det
|
||||||
|
|
||||||
`psi_det_beta_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L90>`_
|
`psi_det_beta_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L90>`_
|
||||||
Unique beta determinants
|
Unique beta determinants
|
||||||
|
|
||||||
`psi_svd_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L568>`_
|
`psi_svd_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L568>`_
|
||||||
SVD wave function
|
SVD wave function
|
||||||
|
|
||||||
`psi_svd_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L569>`_
|
`psi_svd_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L569>`_
|
||||||
SVD wave function
|
SVD wave function
|
||||||
|
|
||||||
`psi_svd_coefs <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L570>`_
|
`psi_svd_coefs <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L570>`_
|
||||||
SVD wave function
|
SVD wave function
|
||||||
|
|
||||||
`psi_svd_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L457>`_
|
`psi_svd_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L457>`_
|
||||||
Matrix of wf coefficients. Outer product of alpha and beta determinants
|
Matrix of wf coefficients. Outer product of alpha and beta determinants
|
||||||
|
|
||||||
`psi_svd_matrix_columns <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L398>`_
|
`psi_svd_matrix_columns <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L398>`_
|
||||||
Matrix of wf coefficients. Outer product of alpha and beta determinants
|
Matrix of wf coefficients. Outer product of alpha and beta determinants
|
||||||
|
|
||||||
`psi_svd_matrix_rows <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L397>`_
|
`psi_svd_matrix_rows <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L397>`_
|
||||||
Matrix of wf coefficients. Outer product of alpha and beta determinants
|
Matrix of wf coefficients. Outer product of alpha and beta determinants
|
||||||
|
|
||||||
`psi_svd_matrix_values <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L396>`_
|
`psi_svd_matrix_values <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L396>`_
|
||||||
Matrix of wf coefficients. Outer product of alpha and beta determinants
|
Matrix of wf coefficients. Outer product of alpha and beta determinants
|
||||||
|
|
||||||
`spin_det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L9>`_
|
`spin_det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L9>`_
|
||||||
Return an integer*8 corresponding to a determinant index for searching
|
Return an integer*8 corresponding to a determinant index for searching
|
||||||
|
|
||||||
`write_spindeterminants <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L294>`_
|
`write_spindeterminants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L294>`_
|
||||||
Undocumented
|
Undocumented
|
||||||
|
|
||||||
`cisd <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/truncate_wf.irp.f#L1>`_
|
`cisd <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/truncate_wf.irp.f#L1>`_
|
||||||
Undocumented
|
Undocumented
|
||||||
|
|
||||||
`h_matrix_all_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/utils.irp.f#L1>`_
|
`h_matrix_all_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/utils.irp.f#L1>`_
|
||||||
H matrix on the basis of the slater determinants defined by psi_det
|
H matrix on the basis of the slater determinants defined by psi_det
|
||||||
|
|
||||||
|
|
||||||
Some files were not shown because too many files have changed in this diff Show More
Loading…
Reference in New Issue
Block a user