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Merge branch 'master' of gitlab.com:scemama/QCaml

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Anthony Scemama 2020-03-27 18:24:08 +01:00
commit 2d1e6672d5
43 changed files with 39535 additions and 220 deletions
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108
Basis/AOBasis.ml
View File

@ -3,26 +3,28 @@ open Util
type t =
{
basis : Basis.t ;
overlap : Overlap.t lazy_t;
ortho : Orthonormalization.t lazy_t;
eN_ints : NucInt.t lazy_t;
kin_ints : KinInt.t lazy_t;
ee_ints : ERI.t lazy_t;
f12_ints : F12.t lazy_t;
f12_over_r12_ints : ScreenedERI.t lazy_t;
cartesian : bool;
basis : Basis.t ;
overlap : Overlap.t lazy_t;
ortho : Orthonormalization.t lazy_t;
eN_ints : NucInt.t lazy_t;
kin_ints : KinInt.t lazy_t;
ee_ints : ERI.t lazy_t;
ee_lr_ints : ERI_lr.t lazy_t;
f12_ints : F12.t lazy_t;
f12_over_r12_ints : ScreenedERI.t lazy_t;
cartesian : bool ;
}
let basis t = t.basis
let overlap t = Lazy.force t.overlap
let ortho t = Lazy.force t.ortho
let eN_ints t = Lazy.force t.eN_ints
let kin_ints t = Lazy.force t.kin_ints
let ee_ints t = Lazy.force t.ee_ints
let f12_ints t = Lazy.force t.f12_ints
let basis t = t.basis
let overlap t = Lazy.force t.overlap
let ortho t = Lazy.force t.ortho
let eN_ints t = Lazy.force t.eN_ints
let kin_ints t = Lazy.force t.kin_ints
let ee_ints t = Lazy.force t.ee_ints
let ee_lr_ints t = Lazy.force t.ee_lr_ints
let f12_ints t = Lazy.force t.f12_ints
let f12_over_r12_ints t = Lazy.force t.f12_over_r12_ints
let cartesian t = t.cartesian
let cartesian t = t.cartesian
@ -48,45 +50,58 @@ let make ~cartesian ~basis ?f12 nuclei =
ERI.of_basis basis
) in
let ee_lr_ints = lazy (
ERI_lr.of_basis basis
) in
let f12_ints = lazy (
F12.of_basis basis
F12.of_basis basis
) in
let f12_over_r12_ints = lazy (
ScreenedERI.of_basis basis
) in
{ basis ; overlap ; ortho ; eN_ints ; kin_ints ; ee_ints ; f12_ints ; f12_over_r12_ints ;
cartesian ;
{ basis ; overlap ; ortho ; eN_ints ; kin_ints ; ee_ints ;
ee_lr_ints ; f12_ints ; f12_over_r12_ints ; cartesian ;
}
let test_case t =
let test_case name t =
let check_matrix title a r =
let a = Mat.to_array a in
Array.iteri (fun i x ->
let message =
Printf.sprintf "%s line %d" title i
in
Alcotest.(check (array (float 1.e-10))) message a.(i) x
) (Mat.to_array r)
Mat.to_array r
|> Array.iteri (fun i x ->
let message =
Printf.sprintf "%s line %d" title i
in
Alcotest.(check (array (float 1.e-10))) message a.(i) x
)
in
let check_eri title a r =
let f { ERI.i_r1 ; j_r2 ; k_r1 ; l_r2 ; value } =
(i_r1, (j_r2, (k_r1, (l_r2, value))))
(i_r1, (j_r2, (k_r1, (l_r2, value))))
in
let a = ERI.to_list a |> List.map f
and r = ERI.to_list r |> List.map f
let a = ERI.to_list a |> List.rev_map f |> List.rev in
let r = ERI.to_list r |> List.rev_map f |> List.rev in
Alcotest.(check (list (pair int (pair int (pair int (pair int (float 1.e-10))))))) "ERI" a r
in
let check_eri_lr title a r =
let f { ERI_lr.i_r1 ; j_r2 ; k_r1 ; l_r2 ; value } =
(i_r1, (j_r2, (k_r1, (l_r2, value))))
in
Alcotest.(check (list (pair int (pair int (pair int (pair int (float 1.e-12))))))) "ERI" a r
let a = ERI_lr.to_list a |> List.rev_map f |> List.rev in
let r = ERI_lr.to_list r |> List.rev_map f |> List.rev in
Alcotest.(check (list (pair int (pair int (pair int (pair int (float 1.e-10))))))) "ERI_lr" a r
in
let test_overlap () =
let reference =
sym_matrix_of_file "test_files/ao_overlap.ref"
sym_matrix_of_file ("test_files/"^name^"_overlap.ref")
in
let overlap =
Lazy.force t.overlap |> Overlap.matrix
@ -96,7 +111,7 @@ let test_case t =
let test_eN_ints () =
let reference =
sym_matrix_of_file "test_files/ao_nuc.ref"
sym_matrix_of_file ("test_files/"^name^"_nuc.ref")
in
let eN_ints =
Lazy.force t.eN_ints |> NucInt.matrix
@ -106,7 +121,7 @@ let test_case t =
let test_kin_ints () =
let reference =
sym_matrix_of_file "test_files/ao_kin.ref"
sym_matrix_of_file ("test_files/"^name^"_kin.ref")
in
let kin_ints =
Lazy.force t.kin_ints |> KinInt.matrix
@ -116,19 +131,32 @@ let test_case t =
let test_ee_ints () =
let reference =
ERI.of_file "test_files/ao_eri.ref" ~sparsity:`Dense ~size:(Basis.size t.basis)
ERI.of_file ("test_files/"^name^"_eri.ref") ~sparsity:`Dense ~size:(Basis.size t.basis)
in
let ee_ints =
Lazy.force t.ee_ints
Lazy.force t.ee_ints
in
check_eri "ee_ints" ee_ints reference
;
in
let test_ee_lr_ints () =
let reference =
ERI_lr.of_file ("test_files/"^name^"_eri_lr.ref") ~sparsity:`Dense
~size:(Basis.size t.basis)
in
let ee_lr_ints =
Lazy.force t.ee_lr_ints
in
check_eri_lr "ee_lr_ints" ee_lr_ints reference
in
[
"Overlap", `Quick, test_overlap;
"eN_ints", `Quick, test_eN_ints;
"kin_ints", `Quick, test_kin_ints;
"ee_ints", `Quick, test_ee_ints;
"Overlap", `Quick, test_overlap;
"eN_ints", `Quick, test_eN_ints;
"kin_ints", `Quick, test_kin_ints;
"ee_ints", `Quick, test_ee_ints;
"ee_lr_ints", `Quick, test_ee_lr_ints;
]

23
Basis/AOBasis.mli
View File

@ -1,31 +1,34 @@
(** Data structure for Atomic Orbitals. *)
type t
type t
(** {1 Accessors} *)
val basis : t -> Basis.t
val basis : t -> Basis.t
(** One-electron basis set *)
val overlap : t -> Overlap.t
val overlap : t -> Overlap.t
(** Overlap matrix *)
val ortho : t -> Orthonormalization.t
val ortho : t -> Orthonormalization.t
(** Orthonormalization matrix of the overlap *)
val eN_ints : t -> NucInt.t
val eN_ints : t -> NucInt.t
(** Electron-nucleus potential integrals *)
val ee_ints : t -> ERI.t
val ee_ints : t -> ERI.t
(** Electron-electron potential integrals *)
val f12_ints : t -> F12.t
val ee_lr_ints : t -> ERI_lr.t
(** Electron-electron long-range potential integrals *)
val f12_ints : t -> F12.t
(** Electron-electron potential integrals *)
val kin_ints : t -> KinInt.t
val kin_ints : t -> KinInt.t
(** Kinetic energy integrals *)
val cartesian : t -> bool
val cartesian : t -> bool
(** If true, use cartesian Gaussians (6d, 10f, ...) *)
@ -38,4 +41,4 @@ val make : cartesian:bool -> basis:Basis.t -> ?f12:F12factor.t -> Nuclei.t ->
(** {2 Tests} *)
val test_case : t -> unit Alcotest.test_case list
val test_case : string -> t -> unit Alcotest.test_case list

3
Basis/AtomicShellPair.ml
View File

@ -26,7 +26,7 @@ let make ?(cutoff=Constants.epsilon) atomic_shell_a atomic_shell_b =
in
let contracted_shell_pairs =
List.map (fun s_a ->
List.concat_map (fun s_a ->
List.map (fun s_b ->
if Cs.index s_b <= Cs.index s_a then
Csp.make ~cutoff s_a s_b
@ -34,7 +34,6 @@ let make ?(cutoff=Constants.epsilon) atomic_shell_a atomic_shell_b =
None
) l_b
) l_a
|> List.concat
|> list_some
in
match contracted_shell_pairs with

3
Basis/AtomicShellPairCouple.ml
View File

@ -28,12 +28,11 @@ let make ?(cutoff=Constants.epsilon) atomic_shell_pair_p atomic_shell_pair_q =
and atomic_shell_d = Asp.atomic_shell_b atomic_shell_pair_q
in
let contracted_shell_pair_couples =
List.map (fun ap_ab ->
List.concat_map (fun ap_ab ->
List.map (fun ap_cd ->
ContractedShellPairCouple.make ~cutoff ap_ab ap_cd
) (Asp.contracted_shell_pairs atomic_shell_pair_q)
) (Asp.contracted_shell_pairs atomic_shell_pair_p)
|> List.concat
|> list_some
in
match contracted_shell_pair_couples with

3
Basis/ContractedShellPairCouple.ml
View File

@ -29,14 +29,13 @@ let make ?(cutoff=Constants.epsilon) shell_pair_p shell_pair_q =
in
let cutoff = 1.e-3 *. cutoff in
let coefs_and_shell_pair_couples =
List.map (fun (c_ab, sp_ab) ->
List.concat_map (fun (c_ab, sp_ab) ->
List.map (fun (c_cd, sp_cd) ->
let coef_prod = c_ab *. c_cd in
if abs_float coef_prod < cutoff then None
else Some (coef_prod, Pspc.make sp_ab sp_cd)
) (Csp.coefs_and_shell_pairs shell_pair_q)
) (Csp.coefs_and_shell_pairs shell_pair_p)
|> List.concat
|> list_some
in
match coefs_and_shell_pair_couples with

8
Basis/ERI.ml
View File

@ -15,10 +15,10 @@ module T = struct
let zero_m z =
let expo_pq_inv = z.expo_p_inv +. z.expo_q_inv in
assert (expo_pq_inv <> 0.);
let exp_pq = 1. /. expo_pq_inv in
let expo_pq = 1. /. expo_pq_inv in
let t =
if z.norm_pq_sq > integrals_cutoff then
z.norm_pq_sq *. exp_pq
z.norm_pq_sq *. expo_pq
else 0.
in
let maxm = z.maxm in
@ -28,11 +28,11 @@ module T = struct
| l ->
begin
result.(k) <- result.(k) *. accu;
let new_accu = -. accu *. exp_pq in
let new_accu = -. accu *. expo_pq in
(aux [@tailcall]) new_accu (k+1) (l-1)
end
in
let f = two_over_sq_pi *. (sqrt exp_pq) in
let f = two_over_sq_pi *. (sqrt expo_pq) in
aux f 0 maxm;
result

8
Basis/TwoElectronIntegrals.ml
View File

@ -24,7 +24,7 @@ module Make(T : TwoEI_structure) = struct
let class_of_contracted_shell_pair_couple = T.class_of_contracted_shell_pair_couple
let filter_contracted_shell_pairs ?(cutoff=integrals_cutoff) shell_pairs =
List.map (fun pair ->
List.rev_map (fun pair ->
match Cspc.make ~cutoff pair pair with
| Some cspc ->
let cls = class_of_contracted_shell_pair_couple cspc in
@ -33,20 +33,20 @@ module Make(T : TwoEI_structure) = struct
| None -> (pair, -1.)
) shell_pairs
|> List.filter (fun (_, schwartz_p_max) -> schwartz_p_max >= cutoff)
|> List.map fst
|> List.rev_map fst
(* TODO
let filter_contracted_shell_pair_couples
?(cutoff=integrals_cutoff) shell_pair_couples =
List.map (fun pair ->
List.rev_map (fun pair ->
let cls =
class_of_contracted_shell_pairs pair pair
in
(pair, Zmap.fold (fun key value accu -> max (abs_float value) accu) cls 0. )
) shell_pairs
|> List.filter (fun (_, schwartz_p_max) -> schwartz_p_max >= cutoff)
|> List.map fst
|> List.rev_map fst
*)

14
Basis/TwoElectronRR.ml
View File

@ -301,7 +301,7 @@ let rec hvrr_two_e
let contracted_class_shell_pair_couple ~zero_m shell_pair_couple : float Zmap.t =
let contracted_class_shell_pair_couple ~zero_m ?mu_erf shell_pair_couple : float Zmap.t =
let maxm = Am.to_int (Cspc.ang_mom shell_pair_couple) in
@ -340,12 +340,11 @@ let contracted_class_shell_pair_couple ~zero_m shell_pair_couple : float Zmap.t
let norm_pq_sq = Co.dot center_pq center_pq in
let expo_p_inv = Psp.exponent_inv sp_ab in
let expo_q_inv = Psp.exponent_inv sp_cd in
let normalization = Psp.normalization sp_ab *. Psp.normalization sp_cd in
let zero = Zp.zero zero_m in
let zero = Zp.zero ?mu_erf zero_m in
let zero_m_array = zero_m
{ zero with
maxm ; expo_p_inv ; expo_q_inv ; norm_pq_sq ;
center_pq ; center_pa ; center_qc ; normalization ;
center_pq ; center_pa ; center_qc ;
}
in
@ -412,7 +411,7 @@ let contracted_class_shell_pair_couple ~zero_m shell_pair_couple : float Zmap.t
let contracted_class_atomic_shell_pair_couple ~zero_m atomic_shell_pair_couple : float Zmap.t =
let contracted_class_atomic_shell_pair_couple ~zero_m ?mu_erf atomic_shell_pair_couple : float Zmap.t =
let maxm = Am.to_int (Aspc.ang_mom atomic_shell_pair_couple) in
@ -454,13 +453,12 @@ let contracted_class_atomic_shell_pair_couple ~zero_m atomic_shell_pair_couple :
let center_pa = Psp.center_minus_a sp_ab in
let norm_pq_sq = Co.dot center_pq center_pq in
let expo_q_inv = Psp.exponent_inv sp_cd in
let normalization = Psp.normalization sp_ab *. Psp.normalization sp_cd in
let zero = Zp.zero zero_m in
let zero = Zp.zero ?mu_erf zero_m in
let zero_m_array = zero_m
{ zero with
maxm ; expo_p_inv ; expo_q_inv ; norm_pq_sq ;
center_pq ; center_pa ; center_qc ; normalization ;
center_pq ; center_pa ; center_qc ;
}
in

17
Basis/TwoElectronRRVectorized.ml
View File

@ -24,7 +24,7 @@ let at_least_one_valid arr =
Array.iter (fun x -> if (abs_float x > cutoff) then raise Found) arr ; false
with Found -> true
type fou_idx_intermediate =
type four_idx_intermediate =
{
expo_b : float array;
expo_d : float array;
@ -577,7 +577,7 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
let contracted_class_shell_pairs ~zero_m ?schwartz_p ?schwartz_q shell_p shell_q : float Zmap.t =
let contracted_class_shell_pairs ~zero_m ?mu_erf ?schwartz_p ?schwartz_q shell_p shell_q : float Zmap.t =
let sp = Csp.shell_pairs shell_p
and sq = Csp.shell_pairs shell_q
@ -651,16 +651,13 @@ let contracted_class_shell_pairs ~zero_m ?schwartz_p ?schwartz_q shell_p shell_q
let norm_pq_sq =
Co.dot center_pq center_pq
in
let normalization = Psp.normalization sp.(i-1) *.
Psp.normalization sq.(i-1)
in
let zero = Zp.zero zero_m in
let zero = Zp.zero ?mu_erf zero_m in
let zero_m_array =
zero_m
{zero with
expo_p_inv ; expo_q_inv ; norm_pq_sq ;
center_pq ; center_pa ; center_qc ; normalization ;
center_pq ; center_pa ; center_qc ;
}
in
zero_m_array.(0)
@ -786,15 +783,11 @@ let contracted_class_shell_pairs ~zero_m ?schwartz_p ?schwartz_q shell_p shell_q
let norm_pq_sq =
x *. x +. y *. y +. z *. z
in
let normalization = Psp.normalization shell_ab *.
Psp.normalization shell_cd
in
let zero = Zp.zero zero_m in
let zero = Zp.zero ?mu_erf zero_m in
zero_m {zero with
maxm ; expo_p_inv ; expo_q_inv ; norm_pq_sq ;
center_pq = Coordinate.make Coordinate.{x ; y ; z} ;
center_pa ; center_qc = center_qc_tmp.(cd) ;
normalization ;
}
) sq
in

8
Basis/Zero_m_parameters.ml
View File

@ -3,25 +3,27 @@ type t =
expo_p_inv : float ;
expo_q_inv : float ;
norm_pq_sq : float ;
normalization : float ;
maxm : int ;
center_pq : Coordinate.t ;
center_pa : Coordinate.t ;
center_qc : Coordinate.t ;
f12_factor : F12factor.t option;
mu_erf : float option;
zero_m_func : t -> float array ;
}
let zero ?f12_factor zero_m_func =
let zero ?f12_factor ?mu_erf zero_m_func =
{
zero_m_func ;
f12_factor ;
mu_erf;
maxm=0 ;
expo_p_inv = 0.;
expo_q_inv = 0.;
norm_pq_sq = 0.;
normalization = 0.;
center_pq = Coordinate.zero ;
center_pa = Coordinate.zero ;
center_qc = Coordinate.zero ;
}

47
CI/CI.ml
View File

@ -97,10 +97,12 @@ let create_matrix_arbitrary f det_space =
in
let singles =
List.filter (fun (i,d,det_j) -> d < 2) doubles
|> List.map (fun (i,_,det_j) -> (i,det_j))
|> List.rev_map (fun (i,_,det_j) -> (i,det_j))
|> List.rev
in
let doubles =
List.map (fun (i,_,det_j) -> (i,det_j)) doubles
List.rev_map (fun (i,_,det_j) -> (i,det_j)) doubles
|> List.rev
in
(singles, doubles)
) det_beta
@ -262,10 +264,12 @@ let create_matrix_spin ?(nmax=2) f det_space =
in
let singles =
List.filter (fun (i,d,det_j) -> d < 2) doubles
|> List.map (fun (i,_,det_j) -> (i,det_j))
|> List.rev_map (fun (i,_,det_j) -> (i,det_j))
|> List.rev
in
let doubles =
List.map (fun (i,_,det_j) -> (i,det_j)) doubles
List.rev_map (fun (i,_,det_j) -> (i,det_j)) doubles
|> List.rev
in
(singles, doubles, triples)
) b
@ -292,13 +296,16 @@ let create_matrix_spin ?(nmax=2) f det_space =
in
let triples =
List.map (fun (i,_,det_j) -> (i,det_j)) triples
List.rev_map (fun (i,_,det_j) -> (i,det_j)) triples
|> List.rev
in
let doubles =
List.map (fun (i,_,det_j) -> (i,det_j)) doubles
List.rev_map (fun (i,_,det_j) -> (i,det_j)) doubles
|> List.rev
in
let singles =
List.map (fun (i,_,det_j) -> (i,det_j)) singles
List.rev_map (fun (i,_,det_j) -> (i,det_j)) singles
|> List.rev
in
(singles, doubles, triples)
) b
@ -769,7 +776,8 @@ let second_order_sum { det_space ; m_H ; m_S2 ; eigensystem ; n_states }
in
let psi_filtered =
List.map (fun i -> psi0.(i)) psi_filtered_idx
List.rev_map (fun i -> psi0.(i)) psi_filtered_idx
|> List.rev
in
let psi_h_alfa alfa =
@ -896,39 +904,34 @@ let second_order_sum2 { det_space ; m_H ; m_S2 ; eigensystem ; n_states }
Ds.determinants_array det_space
|> Array.to_list
|> List.map (fun det_i ->
|> List.concat_map (fun det_i ->
[ Spin.Alfa ; Spin.Beta ]
|> List.map (fun spin ->
List.map (fun particle ->
|> List.concat_map (fun spin ->
List.concat_map (fun particle ->
List.map (fun hole ->
[ [ Determinant.single_excitation spin hole particle det_i ] ;
List.map (fun particle' ->
List.concat_map (fun particle' ->
List.map (fun hole' ->
Determinant.double_excitation
spin hole particle
spin hole' particle' det_i
) list_holes
) list_particles
|> List.concat
;
List.map (fun particle' ->
List.concat_map (fun particle' ->
List.map (fun hole' ->
Determinant.double_excitation
spin hole particle
(Spin.other spin) hole' particle' det_i
) list_holes
) list_particles
|> List.concat
]
|> List.concat
) list_holes
) list_particles
|> List.concat
)
|> List.concat
)
|> List.concat
|> List.concat
|> List.filter (fun alfa -> not (Determinant.is_none alfa))
|> List.sort_uniq compare
in
@ -988,16 +991,16 @@ let is_external det_space =
Determinant.alfa a
|> Spindeterminant.bitstring
in
let n_a =
Bitstring.(popcount @@ logand inactive_mask alfa)
let n_a =
Bitstring.(popcount @@ logand inactive_mask alfa)
in
match n_a with
| 0 | 1 | 2 ->
| 0 | 1 | 2 ->
let beta =
Determinant.beta a
|> Spindeterminant.bitstring
in
n_a + Bitstring.(popcount @@ logand inactive_mask beta) < 3
n_a + Bitstring.(popcount @@ logand inactive_mask beta) < 3
| _ -> false

6
CI/DeterminantSpace.ml
View File

@ -323,10 +323,11 @@ let fci_f12_of_mo_basis mo_basis ~frozen_core mo_num =
in
{ r with mo_class =
MOClass.to_list r.mo_class
|> List.map (fun i ->
|> List.rev_map (fun i ->
match i with
| MOClass.Virtual i when i > mo_num -> MOClass.Auxiliary i
| i -> i)
|> List.rev
|> MOClass.of_list }
@ -339,10 +340,11 @@ let cas_f12_of_mo_basis mo_basis ~frozen_core n m mo_num =
in
{ r with mo_class =
MOClass.to_list r.mo_class
|> List.map (fun i ->
|> List.rev_map (fun i ->
match i with
| MOClass.Virtual i when i > mo_num -> MOClass.Auxiliary i
| i -> i)
|> List.rev
|> MOClass.of_list
}

6
CI/Excitation.ml
View File

@ -76,7 +76,7 @@ let multiple_of_spindet t t' =
else
Phase.Neg
in
(phase, List.map2 (fun hole particle -> (hole, particle)) holes (List.rev particles) )
(phase, List.rev @@ List.rev_map2 (fun hole particle -> (hole, particle)) holes (List.rev particles) )
let double_of_spindet t t' =
@ -99,8 +99,8 @@ let multiple_of_det t t' =
in
let phase = Phase.add pa pb in
Multiple (phase, List.concat [
List.map (fun (hole, particle) -> { hole ; particle ; spin=Spin.Alfa }) a ;
List.map (fun (hole, particle) -> { hole ; particle ; spin=Spin.Beta }) b ])
List.rev @@ List.rev_map (fun (hole, particle) -> { hole ; particle ; spin=Spin.Alfa }) a ;
List.rev @@ List.rev_map (fun (hole, particle) -> { hole ; particle ; spin=Spin.Beta }) b ])
let double_of_det t t' =

3
CI/Spindeterminant.ml
View File

@ -93,7 +93,8 @@ let holes_particles_of t t' =
let holes = Bitstring.logand (bitstring t) x |> Bitstring.to_list
and particles = Bitstring.logand (bitstring t') x |> Bitstring.to_list
in
List.map2 (fun h p -> (h,p)) holes particles
List.rev_map2 (fun h p -> (h,p)) holes particles
|> List.rev
let set_phase p = function

4
CI/SpindeterminantSpace.ml
View File

@ -30,8 +30,8 @@ let fci_of_mo_basis ~frozen_core mo_basis elec_num =
let spin_determinants =
Bitstring.permtutations elec_num mo_num
|> List.filter (fun b -> Bitstring.logand neg_active_mask b = occ_mask)
|> List.map (fun b -> Spindeterminant.of_bitstring b)
|> Array.of_list
|> Array.map (fun b -> Spindeterminant.of_bitstring b)
in
{ elec_num ; mo_basis ; mo_class ; spin_determinants }
@ -54,8 +54,8 @@ let cas_of_mo_basis mo_basis ~frozen_core elec_num n m =
let spin_determinants =
Bitstring.permtutations elec_num mo_num
|> List.filter (fun b -> Bitstring.logand neg_active_mask b = occ_mask)
|> List.map (fun b -> Spindeterminant.of_bitstring b)
|> Array.of_list
|> Array.map (fun b -> Spindeterminant.of_bitstring b)
in
{ elec_num ; mo_basis ; mo_class ; spin_determinants }

2
INSTALL.md
View File

@ -1,7 +1,7 @@
# Generic installation
```bash
opam install lacaml mpi getopt alcotest zarith
opam install ocamlbuild lacaml mpi getopt alcotest zarith
```

10
MOBasis/HF12.ml
View File

@ -67,10 +67,11 @@ let array_4_init d1 d2 d3 d4 fx =
SharedMemory.create Bigarray.Float64 [| d1;d2;d3;d4 |]
in
Util.list_range 1 d4
|> List.map (fun l ->
|> List.rev_map (fun l ->
Util.list_range 1 d3
|> List.map (fun k -> (k,l)) )
|> List.rev_map (fun k -> (k,l)) )
|> List.concat
|> List.rev
|> Stream.of_list
|> Farm.run ~f ~ordered:false
|> Stream.iter (fun (k,l,x) ->
@ -133,10 +134,11 @@ let array_5_init d1 d2 d3 d4 d5 fx =
SharedMemory.create Bigarray.Float64 [| d1;d2;d3;d4;d5 |]
in
Util.list_range 1 d5
|> List.map (fun m ->
|> List.rev_map (fun m ->
Util.list_range 1 d4
|> List.map (fun l -> (l,m)) )
|> List.rev_map (fun l -> (l,m)) )
|> List.concat
|> List.rev
|> Stream.of_list
|> Farm.run ~f ~ordered:false
|> Stream.iter (fun (l,m,x) ->

18
MOBasis/MOClass.ml
View File

@ -34,51 +34,45 @@ let to_list t = t
let core_mos t =
List.map (fun x ->
List.filter_map (fun x ->
match x with
| Core i -> Some i
| _ -> None) t
|> Util.list_some
let inactive_mos t =
List.map (fun x ->
List.filter_map (fun x ->
match x with
| Inactive i -> Some i
| _ -> None ) t
|> Util.list_some
let active_mos t =
List.map (fun x ->
List.filter_map (fun x ->
match x with
| Active i -> Some i
| _ -> None ) t
|> Util.list_some
let virtual_mos t =
List.map (fun x ->
List.filter_map (fun x ->
match x with
| Virtual i -> Some i
| _ -> None ) t
|> Util.list_some
let deleted_mos t =
List.map (fun x ->
List.filter_map (fun x ->
match x with
| Deleted i -> Some i
| _ -> None ) t
|> Util.list_some
let auxiliary_mos t =
List.map (fun x ->
List.filter_map (fun x ->
match x with
| Auxiliary i -> Some i
| _ -> None ) t
|> Util.list_some
let mo_class_array t =

2
Notebooks/F12_matrix.ipynb
View File

@ -9724,7 +9724,7 @@
"metadata": {
"celltoolbar": "Raw Cell Format",
"kernelspec": {
"display_name": "OCaml 4.07.1",
"display_name": "OCaml default",
"language": "OCaml",
"name": "ocaml-jupyter"
},

2
Notebooks/SpVec.ipynb
View File

@ -1746,7 +1746,7 @@
"metadata": {
"celltoolbar": "Raw Cell Format",
"kernelspec": {
"display_name": "OCaml 4.07.1",
"display_name": "OCaml default",
"language": "OCaml",
"name": "ocaml-jupyter"
},

159
Notebooks/TemplateQCaml.ipynb Normal file
View File

@ -0,0 +1,159 @@
{
"cells": [
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"val png_image : string -> unit = <fun>\n"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"- : unit = ()\n",
"Findlib has been successfully loaded. Additional directives:\n",
" #require \"package\";; to load a package\n",
" #list;; to list the available packages\n",
" #camlp4o;; to load camlp4 (standard syntax)\n",
" #camlp4r;; to load camlp4 (revised syntax)\n",
" #predicates \"p,q,...\";; to set these predicates\n",
" Topfind.reset();; to force that packages will be reloaded\n",
" #thread;; to enable threads\n",
"\n",
"- : unit = ()\n"
]
},
{
"data": {
"text/plain": [
"val png_image : string -> Jupyter_notebook.display_id = <fun>\n"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"let png_image = print_endline ;;\n",
"\n",
"(* --------- *)\n",
"\n",
"#cd \"/home/scemama/QCaml\";;\n",
"#use \"topfind\";;\n",
"#require \"jupyter.notebook\";;\n",
"\n",
"let png_image name = \n",
" Jupyter_notebook.display_file ~base64:true \"image/png\" (\"Notebooks/images/\"^name)\n",
";;\n",
"\n",
"#require \"lacaml.top\";;\n",
"#require \"alcotest\";;\n",
"#require \"str\";;\n",
"#require \"bigarray\";;\n",
"#require \"zarith\";;\n",
"#require \"getopt\";;\n",
"#directory \"_build\";;\n",
"#directory \"_build/Basis\";;\n",
"#directory \"_build/CI\";;\n",
"#directory \"_build/MOBasis\";;\n",
"#directory \"_build/Nuclei\";;\n",
"#directory \"_build/Parallel\";;\n",
"#directory \"_build/Perturbation\";;\n",
"#directory \"_build/SCF\";;\n",
"#directory \"_build/Utils\";;\n"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"File Constants.cmo is not a bytecode object file.\n",
"File Util.cma is not a bytecode object file.\n",
"File Matrix.cmo is not a bytecode object file.\n",
"File Simulation.cmo is not a bytecode object file.\n",
"File Spindeterminant.cmo is not a bytecode object file.\n",
"File Determinant.cmo is not a bytecode object file.\n",
"File HartreeFock.cmo is not a bytecode object file.\n",
"File MOBasis.cmo is not a bytecode object file.\n",
"File F12CI.cmo is not a bytecode object file.\n"
]
}
],
"source": [
"#load \"Constants.cmo\";;\n",
"#load_rec \"Util.cma\";;\n",
"#load_rec \"Matrix.cmo\";;\n",
"#load_rec \"Simulation.cmo\";;\n",
"#load_rec \"Spindeterminant.cmo\";;\n",
"#load_rec \"Determinant.cmo\";;\n",
"#load_rec \"HartreeFock.cmo\";;\n",
"#load_rec \"MOBasis.cmo\";;\n",
"#load_rec \"F12CI.cmo\";;"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"#install_printer AngularMomentum.pp_string ;;\n",
"#install_printer Basis.pp ;;\n",
"#install_printer Charge.pp ;;\n",
"#install_printer Coordinate.pp ;;\n",
"#install_printer Vector.pp;;\n",
"#install_printer Matrix.pp;;\n",
"#install_printer Util.pp_float_2darray;;\n",
"#install_printer Util.pp_float_array;;\n",
"#install_printer Util.pp_matrix;;\n",
"#install_printer HartreeFock.pp ;;\n",
"#install_printer Fock.pp ;;\n",
"#install_printer MOClass.pp ;;\n",
"let pp_mo ppf t = MOBasis.pp ~start:1 ~finish:0 ppf t ;;\n",
"#install_printer pp_mo;;\n",
"(*\n",
"#install_printer DeterminantSpace.pp;;\n",
"*)\n",
"#install_printer SpindeterminantSpace.pp;;\n",
"#install_printer Bitstring.pp;;\n",
"\n",
"(* --------- *)\n",
"\n",
"open Lacaml.D\n"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "OCaml default",
"language": "OCaml",
"name": "ocaml-jupyter"
},
"language_info": {
"codemirror_mode": "text/x-ocaml",
"file_extension": ".ml",
"mimetype": "text/x-ocaml",
"name": "OCaml",
"nbconverter_exporter": null,
"pygments_lexer": "OCaml",
"version": "4.07.1"
}
},
"nbformat": 4,
"nbformat_minor": 4
}

1
SCF/Guess.ml
View File

@ -66,7 +66,6 @@ let test_case ao_basis =
Lacaml.D.Mat.add
(AOBasis.eN_ints ao_basis |> NucInt.matrix)
(AOBasis.kin_ints ao_basis |> KinInt.matrix)
|> Conventions.rephase
|> Lacaml.D.Mat.to_array
in
Array.iteri (fun i x ->

10
Simulation.ml
View File

@ -5,6 +5,7 @@ type t = {
basis : Basis.t;
ao_basis : AOBasis.t;
f12 : F12factor.t option;
mu_erf : float option;
nuclear_repulsion : float;
}
@ -14,12 +15,14 @@ let electrons t = t.electrons
let basis t = t.basis
let ao_basis t = t.ao_basis
let nuclear_repulsion t = t.nuclear_repulsion
let mu_erf t = t.mu_erf
let f12 t = t.f12
let make ?cartesian:(cartesian=false)
?multiplicity:(multiplicity=1)
?charge:(charge=0)
?f12
?mu_erf
~nuclei
basis
=
@ -45,18 +48,19 @@ let make ?cartesian:(cartesian=false)
in
{
charge ; basis ; nuclei ; electrons ; ao_basis ; f12 ;
charge ; basis ; nuclei ; electrons ; ao_basis ; f12 ; mu_erf ;
nuclear_repulsion ;
}
let of_filenames ?(cartesian=false) ?(multiplicity=1) ?(charge=0) ?f12 ~nuclei ?(aux_basis_filenames=[]) basis_filename =
let of_filenames ?(cartesian=false) ?(multiplicity=1) ?(charge=0) ?f12 ?mu_erf ~nuclei ?(aux_basis_filenames=[]) basis_filename =
let nuclei =
Nuclei.of_filename nuclei
in
let basis =
Basis.of_nuclei_and_basis_filenames ~nuclei (basis_filename :: aux_basis_filenames)
in
lazy (make ?f12 ~cartesian ~charge ~multiplicity ~nuclei basis)
lazy (make ?mu_erf ?f12 ~cartesian ~charge ~multiplicity ~nuclei basis)
|> Parallel.broadcast

7
Simulation.mli
View File

@ -21,15 +21,18 @@ val nuclear_repulsion : t -> float
val f12 : t -> F12factor.t option
(** f12 correlation factor *)
val mu_erf : t -> float option
(** Range-separation parameter of the electron repulsion integrals potential *)
(** {1 Creation} *)
val make :
?cartesian:bool ->
?multiplicity:int -> ?charge:int -> ?f12:F12factor.t ->
nuclei:Nuclei.t -> Basis.t -> t
?mu_erf:float -> nuclei:Nuclei.t -> Basis.t -> t
val of_filenames :
?cartesian:bool ->
?multiplicity:int -> ?charge:int -> ?f12:F12factor.t ->
nuclei:string -> ?aux_basis_filenames:string list -> string -> t
?mu_erf: float -> nuclei:string -> ?aux_basis_filenames:string list -> string -> t

21
Utils/AngularMomentum.ml
View File

@ -107,19 +107,19 @@ let zkey_array a =
begin
match a with
| Singlet l1 ->
List.map (fun x -> Zkey.of_powers_three x) (keys_1d @@ to_int l1)
List.rev_map (fun x -> Zkey.of_powers_three x) (keys_1d @@ to_int l1)
| Doublet (l1, l2) ->
List.map (fun a ->
List.map (fun b -> Zkey.of_powers_six a b) (keys_1d @@ to_int l2)
List.rev_map (fun a ->
List.rev_map (fun b -> Zkey.of_powers_six a b) (keys_1d @@ to_int l2)
) (keys_1d @@ to_int l1)
|> List.concat
| Triplet (l1, l2, l3) ->
List.map (fun a ->
List.map (fun b ->
List.map (fun c ->
List.rev_map (fun a ->
List.rev_map (fun b ->
List.rev_map (fun c ->
Zkey.of_powers_nine a b c) (keys_1d @@ to_int l3)
) (keys_1d @@ to_int l2)
|> List.concat
@ -128,10 +128,10 @@ let zkey_array a =
| Quartet (l1, l2, l3, l4) ->
List.map (fun a ->
List.map (fun b ->
List.map (fun c ->
List.map (fun d ->
List.rev_map (fun a ->
List.rev_map (fun b ->
List.rev_map (fun c ->
List.rev_map (fun d ->
Zkey.of_powers_twelve a b c d) (keys_1d @@ to_int l4)
) (keys_1d @@ to_int l3)
|> List.concat
@ -140,6 +140,7 @@ let zkey_array a =
) (keys_1d @@ to_int l1)
|> List.concat
end
|> List.rev
|> Array.of_list
in
Hashtbl.add zkey_array_memo a result;

2
Utils/Davidson.ml
View File

@ -117,7 +117,7 @@ let make
in
let residual_norms = List.map nrm2 u_proposed in
let residual_norms = List.rev @@ List.rev_map nrm2 u_proposed in
let residual_norm =
List.fold_left (fun accu i -> accu +. i *. i) 0. residual_norms
|> sqrt

21
Utils/Matrix.ml
View File

@ -80,11 +80,12 @@ let sparse_of_computed ?(threshold=epsilon) = function
| Computed {m ; n ; f} ->
Sparse { m ; n ; v=Array.init n (fun j ->
Util.list_range 1 m
|> List.map (fun i ->
|> List.rev_map (fun i ->
let x = f i (j+1) in
if abs_float x > threshold then Some (i, x)
else None)
|> Util.list_some
|> List.rev
|> Vector.sparse_of_assoc_list m
) }
| _ -> invalid_arg "Expected a computed matrix"
@ -176,7 +177,7 @@ let outer_product ?(threshold=epsilon) v1 v2 =
in
let v =
Array.init (Vector.dim v2) (fun j ->
List.map (fun (i, x) ->
List.rev_map (fun (i, x) ->
let z = x *. v'.{j+1} in
if abs_float z < threshold then
None
@ -184,6 +185,7 @@ let outer_product ?(threshold=epsilon) v1 v2 =
Some (i, z)
) v
|> Util.list_some
|> List.rev
|> Vector.sparse_of_assoc_list (Vector.dim v1)
)
in
@ -500,22 +502,23 @@ let split_cols nrows = function
Mat.to_col_vecs a
|> Array.to_list
|> Util.list_pack nrows
|> List.map (fun l ->
|> List.rev_map (fun l ->
Dense (Mat.of_col_vecs @@ Array.of_list l) )
|> List.rev
end
| Sparse a ->
begin
Array.to_list a.v
|> Util.list_pack nrows
|> List.map Array.of_list
|> List.map (fun v -> Sparse { m=a.m ; n= Array.length v ; v })
|> List.rev_map Array.of_list
|> List.rev_map (fun v -> Sparse { m=a.m ; n= Array.length v ; v })
end
| Computed a ->
begin
Util.list_range 0 (a.n-1)
|> Util.list_pack nrows
|> List.map Array.of_list
|> List.map (fun v -> Computed { m=a.m ; n= Array.length v ; f = (fun i j -> a.f i (j+v.(0)) ) })
|> List.rev_map Array.of_list
|> List.rev_map (fun v -> Computed { m=a.m ; n= Array.length v ; f = (fun i j -> a.f i (j+v.(0)) ) })
end
@ -534,7 +537,9 @@ let join_cols l =
| [] -> Sparse { m=0 ; n=0 ; v=[| |] }
| (Dense a) :: rest -> aux_dense [] ((Dense a) :: rest)
| (Sparse a) :: rest -> aux_sparse 0 0 [] ((Sparse a) :: rest)
| (Computed a) :: rest -> aux_sparse 0 0 [] (List.map sparse_of_computed ( (Computed a) :: rest ))
| (Computed a) :: rest -> aux_sparse 0 0 []
(List.rev_map sparse_of_computed ( (Computed a) :: rest )
|> List.rev)
in aux (List.rev l)

59
Utils/Util.ml
View File

@ -133,34 +133,37 @@ let fact = function
| i -> fact_memo.(i)
let binom_func n k =
(*TODO : slow function *)
assert (n >= k);
let rec aux n k =
if k = 0 || k = n then
1
else
aux (n-1) (k-1) + aux (n-1) k
in aux n k
let binom =
let memo =
Array.init 64 (fun n -> Array.init 64 (fun k ->
if n >= k then binom_func n k else 0) )
let m =
Array.make_matrix 64 64 0
in
for n=0 to Array.length m - 1 do
m.(n).(0) <- 1;
m.(n).(n) <- 1;
for k=1 to (n - 1) do
m.(n).(k) <- m.(n-1).(k-1) + m.(n-1).(k)
done
done;
m
in
fun n k ->
if n < 64 then
begin
assert (n >= k);
let rec f n k =
assert (k >= 0);
assert (n >= k);
if k = 0 || k = n then
1
else if n < 64 then
memo.(n).(k)
end
else
binom_func n k
f (n-1) (k-1) + f (n-1) k
in f
let binom_float n k =
binom n k
|> float_of_int_fast
let rec pow a = function
| 0 -> 1.
| 1 -> a
@ -206,29 +209,26 @@ let boys_function ~maxm t =
let result =
Array.init (maxm+1) (fun m -> 1. /. float_of_int (2*m+1))
in
(*
assert (abs_float t > 1.e-10);
*)
if t <> 0. then
begin
let power_t_inv = (maxm+maxm+1) in
try
let fmax =
let t_inv = sqrt (1. /. t) in
let n = float_of_int maxm in
let dm = 0.5 +. n in
let f = (pow t_inv (maxm+maxm+1) ) in
let f = (pow t_inv power_t_inv ) in
match classify_float f with
| FP_normal -> (incomplete_gamma dm t) *. 0.5 *. f
| FP_zero
| FP_subnormal -> 0.
| _ -> invalid_arg "zero_m overflow"
| _ -> raise Exit
in
let emt = exp (-. t) in
result.(maxm) <- fmax;
for n=maxm-1 downto 0 do
result.(n) <- ( (t+.t) *. result.(n+1) +. emt) *. result.(n)
done
end;
result
done;
result
with Exit -> result
end
@ -241,7 +241,8 @@ let of_some = function
let list_some l =
List.filter (function None -> false | _ -> true) l
|> List.map (function Some x -> x | _ -> assert false)
|> List.rev_map (function Some x -> x | _ -> assert false)
|> List.rev
let list_range first last =

4
Utils/Vector.ml
View File

@ -91,8 +91,8 @@ let sparse_of_vec ?(threshold=epsilon) v =
let sparse_of_assoc_list n v =
Sparse { n ;
v = List.map (fun (index, value) -> {index ; value}) v
|> Array.of_list
v = Array.of_list v
|> Array.map (fun (index, value) -> {index ; value})
}

13
run_integrals.ml
View File

@ -1,6 +1,7 @@
let out_file : string option ref = ref None
let basis_file : string option ref = ref None
let nuclei_file : string option ref = ref None
let mu_erf : float option ref = ref None
let speclist = [
@ -8,6 +9,8 @@ let speclist = [
"File containing the atomic basis set") ;
( "-x" , Arg.String (fun x -> nuclei_file := Some x),
"File containing the nuclear coordinates") ;
( "-m" , Arg.Float (fun x -> mu_erf := Some x),
"Value of mu, the range separation factor.") ;
]
let run () =
@ -19,10 +22,11 @@ let run () =
match !nuclei_file with
| None -> raise (Invalid_argument "Coordinate file should be specified with -x")
| Some x -> x
and mu_erf = !mu_erf
in
let s =
Simulation.of_filenames ~nuclei:nuclei_file basis_file
Simulation.of_filenames ?mu_erf ~nuclei:nuclei_file basis_file
in
print_endline @@ Nuclei.to_string @@ Simulation.nuclei s;
@ -38,8 +42,11 @@ let run () =
Overlap.to_file ~filename:("Ov.dat") overlap;
NucInt.to_file ~filename:("Nuc.dat") eN_ints;
KinInt.to_file ~filename:("Kin.dat") kin_ints;
ERI.to_file ~filename:("ERI.dat") ee_ints;
()
ERI.to_file ~filename:("ERI.dat") ee_ints;
match mu_erf with
| Some mu_erf ->
ERI_lr.to_file ~filename:("ERI_lr.dat") (AOBasis.ee_lr_ints ao_basis)
| None -> ()
let () =

72
run_tests.ml
View File

@ -1,32 +1,54 @@
let () =
(* H2O / cc-pVDZ *)
let test_integrals_water, test_guess_water =
let basis_file = "test_files/cc-pvdz"
and nuclei_file = "test_files/water.xyz"
in
let simulation_closed_shell =
Simulation.of_filenames ~charge:0 ~multiplicity:1 ~nuclei:nuclei_file basis_file
in
let ao_basis =
Simulation.ao_basis simulation_closed_shell
in
(fun () -> AOBasis.test_case "water" ao_basis),
(fun () -> Guess.test_case ao_basis);
in
(* LiH / cc-pVTZ *)
let test_integrals_lih =
let basis_file = "test_files/cc-pvdz"
and nuclei_file = "test_files/lih.xyz"
in
let simulation_closed_shell =
Simulation.of_filenames ~mu_erf:0.5 ~charge:0 ~cartesian:true ~multiplicity:1 ~nuclei:nuclei_file basis_file
in
let ao_basis =
Simulation.ao_basis simulation_closed_shell
in
(fun () -> AOBasis.test_case "lih" ao_basis)
in
Alcotest.run "Unit tests" [
"Util", Util.test_case ();
"Bitstring", Bitstring.test_case ();
"Spindeterminant", Spindeterminant.test_case ();
"Determinant", Determinant.test_case ();
"Excitation", Excitation.test_case ();
"Sparse vectors", Vector.test_case ();
"Sparse matrices", Matrix.test_case ();
"Cholesky", Cholesky.test_case ();
];
"Util", Util.test_case ();
"Bitstring", Bitstring.test_case ();
"Spindeterminant", Spindeterminant.test_case ();
"Determinant", Determinant.test_case ();
"Excitation", Excitation.test_case ();
"Sparse vectors", Vector.test_case ();
"Sparse matrices", Matrix.test_case ();
"Cholesky", Cholesky.test_case ();
"Guess water", test_guess_water ();
"AO Integrals water", test_integrals_water ();
"AO Integrals LiH", test_integrals_lih ();
]
let basis_file = "test_files/cc-pvdz"
and nuclei_file = "test_files/h2o.xyz"
in
let simulation_closed_shell =
Simulation.of_filenames ~charge:0 ~multiplicity:1 ~nuclei:nuclei_file basis_file
in
let ao_basis =
Simulation.ao_basis simulation_closed_shell
in
Alcotest.run "Water, cc-pVDZ" [
"AO_Basis", AOBasis.test_case ao_basis;
"Guess", Guess.test_case ao_basis;
]

5
test_files/lih.xyz Normal file
View File

@ -0,0 +1,5 @@
2
LiH
Li 0.000000 0.000000 0.000000
H 0.000000 0.000000 1.639920

5964
test_files/lih_eri.ref Normal file
View File

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5964
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test_files/lih_kin.ref Normal file
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test_files/ao_nuc.ref → test_files/water_nuc.ref
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test_files/ao_overlap.ref → test_files/water_overlap.ref
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