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Moved 4-idx into FourIndex.mli

This commit is contained in:
Anthony Scemama 2019-03-21 00:44:10 +01:00
parent e226bd135e
commit 3874dd1d95
11 changed files with 257 additions and 135 deletions
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7
Basis/Basis.ml
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@ -1,8 +1,9 @@
type t =
{
size : int;
size : int;
contracted_shells : ContractedShell.t array ;
atomic_shells : AtomicShell.t array lazy_t;
general_basis : GeneralBasis.t ;
}
module As = AtomicShell
@ -10,6 +11,7 @@ module Cs = ContractedShell
module Gb = GeneralBasis
module Ps = PrimitiveShell
let general_basis t = t.general_basis
(** Returns an array of the basis set per atom *)
let of_nuclei_and_general_basis nucl bas =
@ -49,7 +51,8 @@ let of_nuclei_and_general_basis nucl bas =
|> List.sort (fun x y -> compare (As.index x) (As.index y))
|> Array.of_list
) in
{ contracted_shells ; atomic_shells ; size = !index_ }
{ contracted_shells ; atomic_shells ; size = !index_;
general_basis = bas }
let size x = x.size

2
Basis/Basis.mli
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@ -33,6 +33,8 @@ val atomic_shells : t -> AtomicShell.t array
val contracted_shells : t -> ContractedShell.t array
(** Returns all the contracted basis functions. *)
val general_basis : t -> GeneralBasis.t
(** Returns the [!GeneralBasis] that was used to build the current basis. *)
(** {2 Printers} *)

16
Basis/GeneralBasis.ml
View File

@ -78,18 +78,20 @@ let read filename =
loop ()
let read_many filenames =
let combine basis_list =
let h = Hashtbl.create 63 in
let l =
List.map read filenames
|> List.concat
in
List.iter (fun (k,v) ->
List.concat basis_list
|> List.iter (fun (k,v) ->
let l = Hashtbl.find_all h k in
Hashtbl.replace h k (Array.concat (v::l) )
) l;
) ;
Hashtbl.fold (fun k v accu -> (k, v)::accu) h []
let read_many filenames =
List.map read filenames
|> combine
let string_of_primitive ?id prim =
match id with

7
Basis/GeneralBasis.mli
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@ -51,6 +51,12 @@ val read : string -> t
*)
val combine : t list -> t
(** Combines the basis functions of each element among different basis sets.
Used to complement a basis with an auxiliary basis set.
*)
val read_many : string list -> t
(** Reads multiple basis set files and return an association list where
the key is an {!Element.t} and the value is the parsed basis set.
@ -58,6 +64,7 @@ val read_many : string list -> t
*)
val read_element : in_channel -> element_basis option
(** Reads an element from the input channel [ic]. For example,
{[

12
CI/CI.ml
View File

@ -592,12 +592,9 @@ let second_order_sum { det_space ; m_H ; m_S2 ; eigensystem ; n_states }
same_spin +. opposite_spin
in
let result =
Util.stream_range 0 (Array.length psi0 - 1)
|> Farm.run ~ordered:false ~f:det_contribution
|> Util.stream_fold (+.) 0.
in
Parallel.broadcast (lazy result)
Util.stream_range 0 (Array.length psi0 - 1)
|> Farm.run ~ordered:true ~f:det_contribution
|> Util.stream_to_list
let pt2_en ci =
@ -662,6 +659,7 @@ let pt2_en ci =
second_order_sum ci list_holes list_particles
i_o1_alfa i_o1_alfa w_alfa
|> List.fold_left (+.) 0.
@ -692,6 +690,7 @@ let pt2_mp ci =
second_order_sum ci list_holes list_particles
i_o1_alfa i_o1_alfa w_alfa
|> List.fold_left (+.) 0.
let variance ci =
@ -711,5 +710,6 @@ let variance ci =
second_order_sum ci list_holes list_particles
i_o1_alfa i_o1_alfa w_alfa
|> List.fold_left (+.) 0.

102
CI/F12CI.ml Normal file
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@ -0,0 +1,102 @@
open Lacaml.D
type t =
{
mo_basis : MOBasis.t ;
aux_basis : MOBasis.t ;
det_space : DeterminantSpace.t ;
ci : CI.t ;
}
let ci t = t.ci
let mo_basis t = t.mo_basis
let det_space t = t.det_space
let mo_class t = DeterminantSpace.mo_class @@ det_space t
let f12_integrals mo_basis =
let two_e_ints = MOBasis.two_e_ints mo_basis in
( (fun i j _ -> 0.),
(fun i j k l s s' ->
if s' = Spin.other s then
ERI.get_phys two_e_ints i j k l
else
(ERI.get_phys two_e_ints i j k l) -.
(ERI.get_phys two_e_ints i j l k)
) )
let h_ij mo_basis ki kj =
let integrals =
List.map (fun f -> f mo_basis)
[ CI.h_integrals ]
in
CIMatrixElement.make integrals ki kj
|> List.hd
let f_ij mo_basis ki kj =
let integrals =
List.map (fun f -> f mo_basis)
[ f12_integrals ]
in
CIMatrixElement.make integrals ki kj
|> List.hd
let dressing_vector ci =
let mo_basis = DeterminantSpace.mo_basis ci.CI.det_space in
let i_o1_alfa = h_ij mo_basis in
let alfa_o2_i = f_ij mo_basis in
let w_alfa _ _ = 1. in
let mo_class = CI.mo_class ci in
let list_holes = List.concat
[ MOClass.inactive_mos mo_class ; MOClass.active_mos mo_class ]
and list_particles = MOClass.auxiliary_mos mo_class
in
CI.second_order_sum ci list_holes list_particles
i_o1_alfa alfa_o2_i w_alfa
|> Vec.of_list
let make ~simulation ?(frozen_core=true) ~mo_basis ~aux_basis_filename () =
let mo_num = MOBasis.size mo_basis in
(* Add auxiliary basis set *)
let s =
let charge = Charge.to_int @@ Simulation.charge simulation
and multiplicity = Electrons.multiplicity @@ Simulation.electrons simulation
and nuclei = Simulation.nuclei simulation
in
let general_basis =
Basis.general_basis @@ Simulation.basis simulation
in
GeneralBasis.combine [
general_basis ; GeneralBasis.read aux_basis_filename
]
|> Basis.of_nuclei_and_general_basis nuclei
|> Simulation.make ~charge ~multiplicity ~nuclei
in
let aux_basis =
MOBasis.of_mo_basis s mo_basis
in
let det_space =
DeterminantSpace.fci_f12_of_mo_basis aux_basis ~frozen_core mo_num
in
let ci = CI.make det_space in
{ mo_basis ; aux_basis ; det_space ; ci }

106
MOBasis/MOBasis.ml
View File

@ -20,6 +20,7 @@ type t =
mo_coef : Mat.t; (* Matrix of the MO coefficients in the AO basis *)
eN_ints : NucInt.t lazy_t; (* Electron-nucleus potential integrals *)
ee_ints : ERI.t lazy_t; (* Electron-electron potential integrals *)
f12_ints : F12.t lazy_t; (* F12 integrals *)
kin_ints : KinInt.t lazy_t; (* Kinetic energy integrals *)
one_e_ints : Mat.t lazy_t; (* Kinetic energy integrals *)
}
@ -37,6 +38,7 @@ let eN_ints t = Lazy.force t.eN_ints
let ee_ints t = Lazy.force t.ee_ints
let kin_ints t = Lazy.force t.kin_ints
let two_e_ints t = Lazy.force t.ee_ints
let f12_ints t = Lazy.force t.f12_ints
let one_e_ints t = Lazy.force t.one_e_ints
let mo_energies t =
@ -64,99 +66,6 @@ let ao_matrix_of_mo_matrix ~mo_coef ~ao_overlap mo_matrix =
x_o_xt ~x:sc ~o:mo_matrix
let four_index_transform ~mo_coef eri_ao =
let ao_num = Mat.dim1 mo_coef in
let mo_num = Mat.dim2 mo_coef in
let eri_mo =
ERI.create ~size:mo_num `Dense
in
let mo_num_2 = mo_num * mo_num in
let ao_num_2 = ao_num * ao_num in
let ao_mo_num = ao_num * mo_num in
let range_mo = list_range 1 mo_num in
let range_ao = list_range 1 ao_num in
let u = Mat.create mo_num_2 mo_num
and o = Mat.create ao_num ao_num_2
and p = Mat.create ao_num_2 mo_num
and q = Mat.create ao_mo_num mo_num
in
if Parallel.master then Printf.eprintf "4-idx transformation \n%!";
let task delta =
Mat.fill u 0.;
List.iter (fun l ->
if abs_float mo_coef.{l,delta} > epsilon then
begin
let jk = ref 0 in
List.iter (fun k ->
List.iter (fun j ->
incr jk;
ERI.get_chem_all_i eri_ao ~j ~k ~l
|> Array.iteri (fun i x -> o.{i+1,!jk} <- x)
) range_ao
) range_ao;
(* o_i_jk *)
let p =
gemm ~transa:`T ~c:p o mo_coef
(* p_jk_alpha = \sum_i o_i_jk c_i_alpha *)
in
let p' =
Bigarray.reshape_2 (Bigarray.genarray_of_array2 p) ao_num ao_mo_num
(* p_j_kalpha *)
in
let q =
gemm ~transa:`T ~c:q p' mo_coef
(* q_kalpha_beta = \sum_j p_j_kalpha c_j_beta *)
in
let q' =
Bigarray.reshape_2 (Bigarray.genarray_of_array2 q) ao_num mo_num_2
(* q_k_alphabeta = \sum_j p_j_kalpha c_j_beta *)
in
ignore @@
gemm ~transa:`T ~beta:1. ~alpha:mo_coef.{l,delta} ~c:u q' mo_coef ;
(* u_alphabeta_gamma = \sum_k q_k_alphabeta c_k_gamma *)
end
) range_ao;
let u =
Bigarray.reshape
(Bigarray.genarray_of_array2 u)
[| mo_num ; mo_num ; mo_num |]
|> Bigarray.array3_of_genarray
in
let result = ref [] in
List.iter (fun gamma ->
List.iter (fun beta ->
List.iter (fun alpha ->
let x = u.{alpha,beta,gamma} in
if x <> 0. then
result := (alpha, beta, gamma, delta, x) :: !result;
) (list_range 1 beta)
) range_mo
) (list_range 1 delta);
Array.of_list !result
in
let n = ref 0 in
Stream.of_list range_mo
|> Farm.run ~f:task ~ordered:false
|> Stream.iter (fun l ->
if Parallel.master then (Printf.eprintf "\r%d / %d%!" !n mo_num; incr n);
Array.iter (fun (alpha, beta, gamma, delta, x) ->
ERI.set_chem eri_mo alpha beta gamma delta x) l);
if Parallel.master then Printf.eprintf "\n";
Parallel.broadcast (lazy eri_mo)
let make ~simulation ~mo_type ~mo_occupation ~mo_coef () =
let ao_basis =
Si.ao_basis simulation
@ -164,7 +73,7 @@ let make ~simulation ~mo_type ~mo_occupation ~mo_coef () =
let eN_ints = lazy (
AOBasis.eN_ints ao_basis
|> NucInt.matrix
|> mo_matrix_of_ao_matrix ~mo_coef
|> mo_matrix_of_ao_matrix ~mo_coef
|> NucInt.of_matrix
)
and kin_ints = lazy (
@ -175,7 +84,11 @@ let make ~simulation ~mo_type ~mo_occupation ~mo_coef () =
)
and ee_ints = lazy (
AOBasis.ee_ints ao_basis
|> four_index_transform ~mo_coef
|> ERI.four_index_transform mo_coef
)
and f12_ints = lazy (
AOBasis.f12_ints ao_basis
|> F12.four_index_transform mo_coef
)
in
let one_e_ints = lazy (
@ -183,7 +96,8 @@ let make ~simulation ~mo_type ~mo_occupation ~mo_coef () =
(KinInt.matrix @@ Lazy.force kin_ints) )
in
{ simulation ; mo_type ; mo_occupation ; mo_coef ;
eN_ints ; ee_ints ; kin_ints ; one_e_ints }
eN_ints ; ee_ints ; kin_ints ; one_e_ints ;
f12_ints }

3
MOBasis/MOBasis.mli
View File

@ -46,6 +46,9 @@ val one_e_ints : t -> Mat.t
val two_e_ints : t -> ERI.t
(** Electron-electron repulsion integrals *)
val f12_ints : t -> F12.t
(** F12 integrals *)
val size : t -> int
(** Number of molecular orbitals in the basis *)

100
Utils/FourIdxStorage.ml
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@ -1,4 +1,6 @@
open Util
open Lacaml.D
open Constants
let max_index = 1 lsl 14
@ -260,3 +262,101 @@ let to_list data =
in
append []
let four_index_transform coef source =
let ao_num = Mat.dim1 coef in
let mo_num = Mat.dim2 coef in
let destination =
match source.four_index with
| Dense _ -> create ~size:mo_num `Dense
| Sparse _ -> create ~size:mo_num `Sparse
in
let mo_num_2 = mo_num * mo_num in
let ao_num_2 = ao_num * ao_num in
let ao_mo_num = ao_num * mo_num in
let range_mo = list_range 1 mo_num in
let range_ao = list_range 1 ao_num in
let u = Mat.create mo_num_2 mo_num
and o = Mat.create ao_num ao_num_2
and p = Mat.create ao_num_2 mo_num
and q = Mat.create ao_mo_num mo_num
in
if Parallel.master then Printf.eprintf "4-idx transformation \n%!";
let task delta =
Mat.fill u 0.;
List.iter (fun l ->
if abs_float coef.{l,delta} > epsilon then
begin
let jk = ref 0 in
List.iter (fun k ->
List.iter (fun j ->
incr jk;
get_chem_all_i source ~j ~k ~l
|> Array.iteri (fun i x -> o.{i+1,!jk} <- x)
) range_ao
) range_ao;
(* o_i_jk *)
let p =
gemm ~transa:`T ~c:p o coef
(* p_jk_alpha = \sum_i o_i_jk c_i_alpha *)
in
let p' =
Bigarray.reshape_2 (Bigarray.genarray_of_array2 p) ao_num ao_mo_num
(* p_j_kalpha *)
in
let q =
gemm ~transa:`T ~c:q p' coef
(* q_kalpha_beta = \sum_j p_j_kalpha c_j_beta *)
in
let q' =
Bigarray.reshape_2 (Bigarray.genarray_of_array2 q) ao_num mo_num_2
(* q_k_alphabeta = \sum_j p_j_kalpha c_j_beta *)
in
ignore @@
gemm ~transa:`T ~beta:1. ~alpha:coef.{l,delta} ~c:u q' coef ;
(* u_alphabeta_gamma = \sum_k q_k_alphabeta c_k_gamma *)
end
) range_ao;
let u =
Bigarray.reshape
(Bigarray.genarray_of_array2 u)
[| mo_num ; mo_num ; mo_num |]
|> Bigarray.array3_of_genarray
in
let result = ref [] in
List.iter (fun gamma ->
List.iter (fun beta ->
List.iter (fun alpha ->
let x = u.{alpha,beta,gamma} in
if x <> 0. then
result := (alpha, beta, gamma, delta, x) :: !result;
) (list_range 1 beta)
) range_mo
) (list_range 1 delta);
Array.of_list !result
in
let n = ref 0 in
Stream.of_list range_mo
|> Farm.run ~f:task ~ordered:false
|> Stream.iter (fun l ->
if Parallel.master then (Printf.eprintf "\r%d / %d%!" !n mo_num; incr n);
Array.iter (fun (alpha, beta, gamma, delta, x) ->
set_chem destination alpha beta gamma delta x) l);
if Parallel.master then Printf.eprintf "\n";
Parallel.broadcast (lazy destination)

4
Utils/FourIdxStorage.mli
View File

@ -7,6 +7,8 @@ There are two kinds of ordering of indices:
*)
open Lacaml.D
type t
type element = (** Element for the stream *)
@ -54,6 +56,8 @@ val to_stream : t -> element Stream.t
val to_list : t -> element list
(** Retrun the data structure as a list. *)
val four_index_transform : Mat.t -> t -> t
(** Perform a four-index transformation *)
(** {2 I/O} *)

33
run_fci_f12.ml
View File

@ -2,7 +2,7 @@ let () =
let open Command_line in
begin
set_header_doc (Sys.argv.(0) ^ " - QCaml command");
set_description_doc "Runs a Hartree-Fock calculation";
set_description_doc "Runs a F12-Full CI calculation";
set_specs
[ { short='b' ; long="basis" ; opt=Mandatory;
arg=With_arg "<string>";
@ -29,7 +29,7 @@ let () =
(* Handle options *)
let basis_file = Util.of_some @@ Command_line.get "basis" in
let aux_basis_file = Util.of_some @@ Command_line.get "aux_basis" in
let aux_basis_filename = Util.of_some @@ Command_line.get "aux_basis" in
let nuclei_file = Util.of_some @@ Command_line.get "xyz" in
@ -50,37 +50,22 @@ let () =
else Printing.ppf_dev_null
in
let s' =
let simulation =
Simulation.of_filenames ~charge ~multiplicity ~nuclei:nuclei_file basis_file
in
let hf = HartreeFock.make s' in
let hf = HartreeFock.make simulation in
Format.fprintf ppf "@[%a@]@." HartreeFock.pp_hf hf;
let mos' =
let mo_basis =
MOBasis.of_hartree_fock hf
in
let mo_num =
MOBasis.size mos'
let fcif12 =
F12CI.make ~simulation ~frozen_core:false ~mo_basis ~aux_basis_filename ()
in
let s =
Simulation.of_filenames ~charge ~multiplicity ~nuclei:nuclei_file
~aux_basis_filenames:[aux_basis_file] basis_file
in
let mos =
MOBasis.of_mo_basis s mos'
in
let space =
DeterminantSpace.fci_f12_of_mo_basis mos ~frozen_core:false mo_num
in
let ci = CI.make space in
Format.fprintf ppf "FCI energy : %20.16f@." ((CI.eigenvalues ci).{1} +. Simulation.nuclear_repulsion s);
let ci = F12CI.ci fcif12 in
Format.fprintf ppf "FCI energy : %20.16f@." ((CI.eigenvalues ci).{1} +. Simulation.nuclear_repulsion simulation);
(*
let s2 = Util.xt_o_x ~o:(CI.s2_matrix ci) ~x:(CI.eigenvectors ci) in
Util.list_range 1 (DeterminantSpace.size space)