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CAS+EN2 in the presence of auxiliary basis OK

This commit is contained in:
Anthony Scemama 2019-03-20 19:18:36 +01:00
parent 08e8b494ea
commit 4c5bade8fb
12 changed files with 262 additions and 64 deletions
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7
Basis/Basis.ml
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@ -91,3 +91,10 @@ let of_nuclei_and_basis_filename ~nuclei filename =
of_nuclei_and_general_basis nuclei general_basis
let of_nuclei_and_basis_filenames ~nuclei filenames =
let general_basis =
GeneralBasis.read_many filenames
in
of_nuclei_and_general_basis nuclei general_basis

5
Basis/Basis.mli
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@ -18,6 +18,11 @@ val of_nuclei_and_basis_filename : nuclei:Nuclei.t -> string -> t
from a file.
*)
val of_nuclei_and_basis_filenames : nuclei:Nuclei.t -> string list -> t
(** Same as {!of_nuclei_and_general_basis}, but taking the {!GeneralBasis.t}
from multiple files.
*)
val size : t -> int
(** Number of contracted basis functions. *)

12
Basis/GeneralBasis.ml
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@ -78,6 +78,18 @@ let read filename =
loop ()
let read_many filenames =
let h = Hashtbl.create 63 in
let l =
List.map read filenames
|> List.concat
in
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 string_of_primitive ?id prim =
match id with

7
Basis/GeneralBasis.mli
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@ -51,6 +51,13 @@ val read : string -> t
*)
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.
This function is usually used to add an auxiliary basis set.
*)
val read_element : in_channel -> element_basis option
(** Reads an element from the input channel [ic]. For example,
{[

9
CI/CI.ml
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@ -394,7 +394,7 @@ let make ?(n_states=1) det_space =
Matrix.mm ~transa:`T m_H psi
in
let eigenvectors, eigenvalues =
Davidson.make ~threshold:1.e-12 ~n_states diagonal matrix_prod
Davidson.make ~threshold:1.e-6 ~n_states diagonal matrix_prod
in
let eigenvalues = Vec.map (fun x -> x +. e_shift) eigenvalues in
eigenvectors, eigenvalues
@ -415,9 +415,12 @@ let second_order_sum { det_space ; m_H ; m_S2 ; eigensystem ; n_states }
let cls = MOClass.mo_class_array mo_class in
Util.list_range 1 (MOBasis.size mo_basis)
|> List.filter (fun i -> match cls.(i) with
| MOClass.Deleted _
| MOClass.Inactive _
| MOClass.Active _
| MOClass.Virtual _ -> true
| MOClass.Auxiliary _
| MOClass.Deleted _
| MOClass.Core _ -> false
| _ -> true
)
|> Array.of_list
in

118
CI/DeterminantSpace.ml
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@ -226,15 +226,15 @@ let fock_diag det_space det =
alfa, beta
let cas_of_mo_basis mo_basis n m =
let spin_of_mo_basis mo_basis f =
let s = MOBasis.simulation mo_basis in
let e = Simulation.electrons s in
let n_alfa = Electrons.n_alfa e
and n_beta = Electrons.n_beta e in
let det_a =
Ss.cas_of_mo_basis mo_basis n_alfa n m
and det_b =
Ss.cas_of_mo_basis mo_basis n_beta n m
let det_a = f n_alfa
and det_b = f n_beta
in
let mo_class = Ss.mo_class det_a in
let determinants =
@ -248,8 +248,31 @@ let cas_of_mo_basis mo_basis n m =
Format.printf "Number of determinants : %d %d %d\n%!"
n_det_alfa n_det_beta ndet;
Spin (det_alfa, det_beta)
in
{ n_alfa ; n_beta ; mo_class ; mo_basis ; determinants }
let arbitrary_of_mo_basis mo_basis f =
let s = MOBasis.simulation mo_basis in
let e = Simulation.electrons s in
let n_alfa = Electrons.n_alfa e
and n_beta = Electrons.n_beta e in
let det_a = f n_alfa
and det_b = f n_beta
in
let mo_class = Ss.mo_class det_a in
let determinants =
let det_alfa = Ss.spin_determinants det_a
and det_beta = Ss.spin_determinants det_b
in
let n_det_beta = Array.length det_beta in
let n_det_alfa = Array.length det_alfa in
let ndet = n_det_alfa * n_det_beta in
Format.printf "Number of determinants : %d %d %d\n%!"
n_det_alfa n_det_beta ndet;
(*
let det = Array.make n_det_alfa
(Array.init n_det_beta (fun i -> i))
in
@ -261,49 +284,70 @@ let cas_of_mo_basis mo_basis n m =
Arbitrary {
det_alfa ; det_beta ; det ; index_start
}
*)
in
{ n_alfa ; n_beta ; mo_class ; mo_basis ; determinants }
let cas_of_mo_basis mo_basis n m =
let f n_alfa =
Ss.cas_of_mo_basis mo_basis n_alfa n m
in
spin_of_mo_basis mo_basis f
let fci_of_mo_basis ?(frozen_core=true) mo_basis =
let f n_alfa =
Ss.fci_of_mo_basis ~frozen_core mo_basis n_alfa
in
spin_of_mo_basis mo_basis f
let fci_f12_of_mo_basis ?(frozen_core=true) mo_basis mo_num =
let s = MOBasis.simulation mo_basis in
let e = Simulation.electrons s in
let n_alfa = Electrons.n_alfa e
and n_beta = Electrons.n_beta e in
let det_a =
Ss.fci_of_mo_basis ~frozen_core mo_basis n_alfa
and det_b =
Ss.fci_of_mo_basis ~frozen_core mo_basis n_beta
let n_core =
if frozen_core then
(Nuclei.small_core @@ Simulation.nuclei @@ MOBasis.simulation mo_basis) / 2
else 0
in
let mo_class = Ss.mo_class det_a in
let determinants =
let det_alfa = Ss.spin_determinants det_a
and det_beta = Ss.spin_determinants det_b
in
let n_det_beta = Array.length det_beta in
let n_det_alfa = Array.length det_alfa in
let n, m =
(n_alfa + n_beta - n_core),
(mo_num - n_core)
in
let f n_alfa =
Ss.cas_of_mo_basis mo_basis n_alfa n m
in
let r =
spin_of_mo_basis mo_basis f
in
{ r with mo_class =
MOClass.to_list r.mo_class
|> List.map (fun i ->
match i with
| MOClass.Virtual i when i > mo_num -> MOClass.Auxiliary i
| i -> i)
|> MOClass.of_list }
let ndet = n_det_alfa * n_det_beta in
Format.printf "Number of determinants : %d %d %d\n%!"
n_det_alfa n_det_beta ndet;
Spin (det_alfa, det_beta)
(*
let det = Array.make n_det_alfa
(Array.init n_det_beta (fun i -> i))
in
let index_start = Array.init (n_det_alfa+1) (fun i -> i*n_det_beta) in
let ndet = (index_start.(n_det_alfa)) in
Format.printf "Number of determinants : %d %d %d\n%!"
n_det_alfa n_det_beta ndet;
Arbitrary {
det_alfa ; det_beta ; det ; index_start
let cas_f12_of_mo_basis mo_basis n m mo_num =
let f n_alfa =
Ss.cas_of_mo_basis mo_basis n_alfa n m
in
let r =
spin_of_mo_basis mo_basis f
in
{ r with mo_class =
MOClass.to_list r.mo_class
|> List.map (fun i ->
match i with
| MOClass.Virtual i when i > mo_num -> MOClass.Auxiliary i
| i -> i)
|> MOClass.of_list
}
*)
in
{ n_alfa ; n_beta ; mo_class ; mo_basis ; determinants }
let pp_det_space ppf t =

11
CI/DeterminantSpace.mli
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@ -57,7 +57,16 @@ val fci_of_mo_basis : ?frozen_core:bool -> MOBasis.t -> t
*)
val cas_of_mo_basis : MOBasis.t -> int -> int -> t
(** Creates a CAS(n,m) space of determinants.
(** Creates a CAS(n,m) space of determinants. *)
val fci_f12_of_mo_basis : ?frozen_core:bool -> MOBasis.t -> int -> t
(** Creates the active space to perform a FCI-F12 with an
auxiliary basis set. *)
val cas_f12_of_mo_basis : MOBasis.t -> int -> int -> int -> t
(** [cas_of_mo_basis mo_basis m n mo_num] Creates a CAS(n,m) space
of determinants with an auxiliary basis set defined as the MOs from
[mo_num+1] to [MOBasis.size mo_basis].
*)
(** {2 Printing} *)

49
MOBasis/MOClass.ml
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@ -1,19 +1,21 @@
type mo_class =
| Core of int (* Always doubly occupied *)
| Inactive of int (* With 0,1 or 2 holes *)
| Active of int (* With 0,1 or 2 holes or particles *)
| Virtual of int (* With 0,1 or 2 particles *)
| Deleted of int (* Always unoccupied *)
| Core of int (* Always doubly occupied *)
| Inactive of int (* With 0,1 or 2 holes *)
| Active of int (* With 0,1 or 2 holes or particles *)
| Virtual of int (* With 0,1 or 2 particles *)
| Deleted of int (* Always unoccupied *)
| Auxiliary of int (* Auxiliary basis function *)
type t = mo_class list
let pp_mo_occ ppf = function
| Core i -> Format.fprintf ppf "@[Core %d@]" i
| Inactive i -> Format.fprintf ppf "@[Inactive %d@]" i
| Active i -> Format.fprintf ppf "@[Active %d@]" i
| Virtual i -> Format.fprintf ppf "@[Virtual %d@]" i
| Deleted i -> Format.fprintf ppf "@[Deleted %d@]" i
| Core i -> Format.fprintf ppf "@[Core %d@]" i
| Inactive i -> Format.fprintf ppf "@[Inactive %d@]" i
| Active i -> Format.fprintf ppf "@[Active %d@]" i
| Virtual i -> Format.fprintf ppf "@[Virtual %d@]" i
| Deleted i -> Format.fprintf ppf "@[Deleted %d@]" i
| Auxiliary i -> Format.fprintf ppf "@[Auxiliary %d@]" i
@ -62,6 +64,14 @@ let deleted_mos t =
|> Util.list_some
let virtual_mos t =
List.map (fun x ->
match x with
| Auxiliary i -> Some i
| _ -> None ) t
|> Util.list_some
let mo_class_array t =
let sze = List.length t + 1 in
let result = Array.make sze (Deleted 0) in
@ -72,6 +82,7 @@ let mo_class_array t =
| Active i -> result.(i) <- Active i
| Virtual i -> result.(i) <- Virtual i
| Deleted i -> result.(i) <- Deleted i
| Auxiliary i -> result.(i) <- Auxiliary i
) t;
result
@ -96,15 +107,22 @@ let fci ?(frozen_core=true) mo_basis =
let cas_sd mo_basis n m =
let mo_num = MOBasis.size mo_basis in
let n_alfa = MOBasis.simulation mo_basis |> Simulation.electrons |> Electrons.n_alfa in
let n_beta = MOBasis.simulation mo_basis |> Simulation.electrons |> Electrons.n_alfa in
let n_beta = MOBasis.simulation mo_basis |> Simulation.electrons |> Electrons.n_beta in
let n_unpaired = n_alfa - n_beta in
let last_inactive = n_alfa - (n + n_unpaired)/2 in
let n_alfa_in_cas = (n - n_unpaired)/2 in
let last_inactive = n_alfa - n_alfa_in_cas in
let last_active = last_inactive + m in
let ncore = (Nuclei.small_core @@ Simulation.nuclei @@ MOBasis.simulation mo_basis) / 2 in
let ncore =
(Nuclei.small_core @@ Simulation.nuclei @@ MOBasis.simulation mo_basis) / 2
|> min last_inactive
in
of_list (
List.concat [
Util.list_range 1 ncore
|> List.map (fun i -> Core i) ;
if ncore > 0 then
Util.list_range 1 ncore
|> List.map (fun i -> Core i)
else
[] ;
Util.list_range (ncore+1) last_inactive
|> List.map (fun i -> Inactive i) ;
Util.list_range (last_inactive+1) last_active
@ -114,3 +132,4 @@ let cas_sd mo_basis n m =
]
)

11
MOBasis/MOClass.mli
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@ -1,11 +1,12 @@
(** CI Classes of MOs : active, inactive, etc *)
type mo_class =
| Core of int (* Always doubly occupied *)
| Inactive of int (* With 0,1 or 2 holes *)
| Active of int (* With 0,1 or 2 holes or particles *)
| Virtual of int (* With 0,1 or 2 particles *)
| Deleted of int (* Always unoccupied *)
| Core of int (* Always doubly occupied *)
| Inactive of int (* With 0,1 or 2 holes *)
| Active of int (* With 0,1 or 2 holes or particles *)
| Virtual of int (* With 0,1 or 2 particles *)
| Deleted of int (* Always unoccupied *)
| Auxiliary of int (* Function of the auxiliary basis set *)
type t

4
Simulation.ml
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@ -47,12 +47,12 @@ let make ?cartesian:(cartesian=false)
}
let of_filenames ?cartesian:(cartesian=false) ?multiplicity:(multiplicity=1) ?charge:(charge=0) ~nuclei basis_filename =
let of_filenames ?(cartesian=false) ?(multiplicity=1) ?(charge=0) ~nuclei ?(aux_basis_filenames=[]) basis_filename =
let nuclei =
Nuclei.of_filename nuclei
in
let basis =
Basis.of_nuclei_and_basis_filename ~nuclei basis_filename
Basis.of_nuclei_and_basis_filenames ~nuclei (basis_filename :: aux_basis_filenames)
in
lazy (make ~cartesian ~charge ~multiplicity ~nuclei basis)
|> Parallel.broadcast

4
Simulation.mli
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@ -26,4 +26,6 @@ val make :
val of_filenames :
?cartesian:bool ->
?multiplicity:int -> ?charge:int -> nuclei:string -> string -> t
?multiplicity:int -> ?charge:int -> nuclei:string ->
?aux_basis_filenames:string list -> string -> t

89
run_fci_f12.ml Normal file
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@ -0,0 +1,89 @@
let () =
let open Command_line in
begin
set_header_doc (Sys.argv.(0) ^ " - QCaml command");
set_description_doc "Runs a Hartree-Fock calculation";
set_specs
[ { short='b' ; long="basis" ; opt=Mandatory;
arg=With_arg "<string>";
doc="Name of the file containing the basis set"; } ;
{ short='a' ; long="aux_basis" ; opt=Mandatory;
arg=With_arg "<string>";
doc="Name of the file containing the auxiliary basis set"; } ;
{ short='x' ; long="xyz" ; opt=Mandatory;
arg=With_arg "<string>";
doc="Name of the file containing the nuclear coordinates in xyz format"; } ;
{ short='m' ; long="multiplicity" ; opt=Optional;
arg=With_arg "<int>";
doc="Spin multiplicity (2S+1). Default is singlet"; } ;
{ short='c' ; long="charge" ; opt=Optional;
arg=With_arg "<int>";
doc="Total charge of the molecule. Default is 0"; } ;
]
end;
(* 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 nuclei_file = Util.of_some @@ Command_line.get "xyz" in
let charge =
match Command_line.get "charge" with
| Some x -> int_of_string x
| None -> 0
in
let multiplicity =
match Command_line.get "multiplicity" with
| Some x -> int_of_string x
| None -> 1
in
let ppf =
if Parallel.master then Format.std_formatter
else Printing.ppf_dev_null
in
let s' =
Simulation.of_filenames ~charge ~multiplicity ~nuclei:nuclei_file basis_file
in
let hf = HartreeFock.make s' in
Format.fprintf ppf "@[%a@]@." HartreeFock.pp_hf hf;
let mos' =
MOBasis.of_hartree_fock hf
in
let mo_num =
MOBasis.size mos'
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 s2 = Util.xt_o_x ~o:(CI.s2_matrix ci) ~x:(CI.eigenvectors ci) in
Util.list_range 1 (DeterminantSpace.size space)
|> List.iter (fun i -> Format.printf "@[%f@]@;" s2.{i,i});
*)