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Removed duplicated code

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This commit is contained in:
Anthony Scemama 2019-10-24 11:25:49 +02:00
parent dd98ac29fc
commit 0462e19117
16 changed files with 190 additions and 765 deletions
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10
Basis/AOBasis.ml
View File

@ -47,14 +47,8 @@ let make ~cartesian ~basis ?f12 nuclei =
) in
let f12_ints = lazy (
let f12 =
match f12 with
| Some f12 -> f12
| None -> failwith "Missing f12 factor"
in
F12.of_basis f12 basis
)
in
F12.of_basis basis
) in
{ basis ; overlap ; ortho ; eN_ints ; kin_ints ; ee_ints ; f12_ints ;
cartesian ;

2
Basis/AOBasis.mli
View File

@ -31,7 +31,7 @@ val cartesian : t -> bool
(** {1 Creators} *)
val make : cartesian:bool -> basis:Basis.t -> ?f12:F12.f12_factor -> Nuclei.t -> t
val make : cartesian:bool -> basis:Basis.t -> ?f12:F12factor.t -> Nuclei.t -> t
(** Creates the data structure for atomic orbitals from a {Basis.t} and the
molecular geometry {Nuclei.t} *)

19
Basis/ERI.ml
View File

@ -3,9 +3,10 @@
open Constants
open Util
module Csp = ContractedShellPair
module Cspc = ContractedShellPairCouple
module Zm = struct
module T = struct
let name = "Electron repulsion integrals"
@ -35,8 +36,20 @@ module Zm = struct
aux f 0 maxm;
result
let class_of_contracted_shell_pair_couple shell_pair_couple =
let shell_p = Cspc.shell_pair_p shell_pair_couple
and shell_q = Cspc.shell_pair_q shell_pair_couple
in
if Array.length (Csp.shell_pairs shell_p) +
(Array.length (Csp.shell_pairs shell_q)) < 4 then
TwoElectronRR.contracted_class_shell_pair_couple
~zero_m shell_pair_couple
else
TwoElectronRRVectorized.contracted_class_shell_pairs
~zero_m shell_p shell_q
end
module M = TwoElectronIntegralsNonSeparable.Make(Zm)
module M = TwoElectronIntegrals.Make(T)
include M

396
Basis/F12.ml
View File

@ -5,397 +5,23 @@
open Constants
let cutoff = integrals_cutoff
module Bs = Basis
module Cs = ContractedShell
module Csp = ContractedShellPair
module Cspc = ContractedShellPairCouple
module Fis = FourIdxStorage
module T = struct
include FourIdxStorage
type f12_factor =
{
expo_s : float ;
coef_g : float array;
expo_sg : float array;
expo_sg_inv : float array;
}
let make_gaussian_corr_factor expo_s coef_g expo_sg =
let expo_sg_inv =
Array.map (fun x -> 1. /. (x *. expo_s *. expo_s)) expo_sg
in
{
expo_s ; coef_g ; expo_sg ; expo_sg_inv
}
(* -1/expo_s *. exp (-expo_s r) *)
let gaussian_geminal expo_s =
let coef_g =
[| 0.3144 ; 0.3037 ; 0.1681 ; 0.09811 ; 0.06024 ; 0.03726 |]
|> Array.map (fun x -> -. x /. expo_s)
and expo_sg =
[| 0.2209 ; 1.004 ; 3.622 ; 12.16 ; 45.87 ; 254.4 |]
in
make_gaussian_corr_factor expo_s coef_g expo_sg
(* exp (-expo_s r) *)
let simple_gaussian_geminal expo_s =
let coef_g =
[| 0.3144 ; 0.3037 ; 0.1681 ; 0.09811 ; 0.06024 ; 0.03726 |]
and expo_sg =
[| 0.2209 ; 1.004 ; 3.622 ; 12.16 ; 45.87 ; 254.4 |]
in
make_gaussian_corr_factor expo_s coef_g expo_sg
(** r12 * exp ( -expo_s * r) *)
let gaussian_geminal_times_r12 expo_s =
let coef_g =
[| 0.2454 ; 0.2938 ; 0.1815 ; 0.11281 ; 0.07502 ; 0.05280 |]
and expo_sg =
[| 0.1824 ; 0.7118; 2.252 ; 6.474 ; 19.66 ; 77.92 |]
in make_gaussian_corr_factor expo_s coef_g expo_sg
(* exp (-expo_s r) *)
let simple_gaussian_geminal' expo_s =
let coef_g =
[|
-3.4793465193721626604883567779324948787689208984375 ;
-0.00571703486454788484955047422886309504974633455276489257812 ;
4.14878218728681513738365538301877677440643310546875 ;
0.202874298181392742623785352407139725983142852783203125 ;
0.0819187742387294803858566183407674543559551239013671875 ;
0.04225945671351955673644695821167260874062776565551757812 ;
|]
and expo_sg =
[|
0.63172472556807146570889699432882480323314666748046875;
26.3759196683467962429858744144439697265625;
0.63172102793029016876147352377302013337612152099609375;
7.08429025944207335641067402320913970470428466796875;
42.4442841447001910637482069432735443115234375;
391.44036073596890901171718724071979522705078125 ;
|]
in make_gaussian_corr_factor expo_s coef_g expo_sg
let one_over_r =
let coef_g = [|
841.88478132 ; 70.590185207 ; 18.3616020768 ; 7.2608642093 ;
3.57483416444 ; 2.01376031082 ; 1.24216542801 ; 0.81754348620 ;
0.564546514023 ; 0.404228610699 ; 0.297458536575 ; 0.223321219537 ;
0.169933732064 ; 0.130190978230 ; 0.099652303426 ; 0.075428246546 ;
0.0555635614051 ; 0.0386791283055 ; 0.0237550435652 ; 0.010006278387 ;
|]
and expo_sg_inv =
[| 84135.654509 ; 2971.58727634 ; 474.716025959 ; 130.676724560 ;
47.3938388887 ; 20.2078651631 ; 9.5411021938 ; 4.8109546955 ;
2.52795733067 ; 1.35894103210 ; 0.73586710268 ; 0.39557629706 ;
0.20785895177 ; 0.104809693858 ; 0.049485682527 ; 0.021099788990 ;
0.007652472186 ; 0.0021065225215 ; 0.0003365204879 ; 0.0000118855674 |]
in make_gaussian_corr_factor 1.0 coef_g expo_sg_inv
module Zero_m = struct
let name = "F12"
end
let class_of_contracted_shell_pair_couple f12 shell_pair_couple =
let f12_factor = F12factor.gaussian_geminal 1.0
let class_of_contracted_shell_pair_couple shell_pair_couple =
let g = f12_factor.F12factor.gaussian in
F12RR.contracted_class_shell_pair_couple
f12.expo_sg_inv f12.coef_g shell_pair_couple
let filter_contracted_shell_pairs f12 ?(cutoff=integrals_cutoff) shell_pairs =
List.map (fun pair ->
match Cspc.make ~cutoff pair pair with
| Some cspc ->
let cls = class_of_contracted_shell_pair_couple f12 cspc in
(pair, Zmap.fold (fun key value accu -> max (abs_float value) accu) cls 0. )
(* TODO \sum_k |coef_k * integral_k| *)
| None -> (pair, -1.)
) shell_pairs
|> List.filter (fun (_, schwartz_p_max) -> schwartz_p_max >= cutoff)
|> List.map fst
(* TODO
let filter_contracted_shell_pair_couples
?(cutoff=integrals_cutoff) shell_pair_couples =
List.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
*)
let store_class basis ?(cutoff=integrals_cutoff) data f12 contracted_shell_pair_couple cls =
let to_powers x =
let open Zkey in
match to_powers x with
| Three x -> x
| _ -> assert false
in
let shell_p = Cspc.shell_pair_p contracted_shell_pair_couple
and shell_q = Cspc.shell_pair_q contracted_shell_pair_couple
in
(*
let lambda_inv = -. 1. /. f12.expo_s in
*)
Array.iteri (fun i_c powers_i ->
let i_c = Cs.index (Csp.shell_a shell_p) + i_c + 1 in
let xi = to_powers powers_i in
Array.iteri (fun j_c powers_j ->
let j_c = Cs.index (Csp.shell_b shell_p) + j_c + 1 in
let xj = to_powers powers_j in
Array.iteri (fun k_c powers_k ->
let k_c = Cs.index (Csp.shell_a shell_q) + k_c + 1 in
let xk = to_powers powers_k in
Array.iteri (fun l_c powers_l ->
let l_c = Cs.index (Csp.shell_b shell_q) + l_c + 1 in
let xl = to_powers powers_l in
let key = Zkey.of_powers_twelve xi xj xk xl in
let value = Zmap.find cls key in
(*
lambda_inv *. (s.{i_c,j_c} *. s.{k_c,l_c} -. value)
lambda_inv *. value
*)
value
|> set_chem data i_c j_c k_c l_c
) (Cs.zkey_array (Csp.shell_b shell_q))
) (Cs.zkey_array (Csp.shell_a shell_q))
) (Cs.zkey_array (Csp.shell_b shell_p))
) (Cs.zkey_array (Csp.shell_a shell_p))
let of_basis_serial f12 basis =
let n = Bs.size basis
and shell = Bs.contracted_shells basis
in
let eri_array =
Fis.create ~size:n `Dense
(*
Fis.create ~size:n `Sparse
*)
in
let t0 = Unix.gettimeofday () in
let shell_pairs =
Csp.of_contracted_shell_array shell
|> filter_contracted_shell_pairs f12 ~cutoff
in
Printf.printf "%d significant shell pairs computed in %f seconds\n"
(List.length shell_pairs) (Unix.gettimeofday () -. t0);
let t0 = Unix.gettimeofday () in
let ishell = ref 0 in
List.iter (fun shell_p ->
let () =
if (Cs.index (Csp.shell_a shell_p) > !ishell) then
(ishell := Cs.index (Csp.shell_a shell_p) ; print_int !ishell ; print_newline ())
in
let sp =
Csp.shell_pairs shell_p
in
try
List.iter (fun shell_q ->
let () =
if Cs.index (Csp.shell_a shell_q) >
Cs.index (Csp.shell_a shell_p) then
raise Exit
in
let sq = Csp.shell_pairs shell_q in
let cspc =
if Array.length sp < Array.length sq then
Cspc.make ~cutoff shell_p shell_q
else
Cspc.make ~cutoff shell_q shell_p
in
match cspc with
| Some cspc ->
let cls =
class_of_contracted_shell_pair_couple f12 cspc
in
store_class basis ~cutoff eri_array f12 cspc cls
| None -> ()
) shell_pairs
with Exit -> ()
) shell_pairs ;
Printf.printf "Computed ERIs in %f seconds\n%!" (Unix.gettimeofday () -. t0);
eri_array
(* Parallel functions *)
let of_basis_parallel f12 basis =
let n = Bs.size basis
and shell = Bs.contracted_shells basis
in
let store_class_parallel
?(cutoff=integrals_cutoff) contracted_shell_pair_couple cls =
let to_powers x =
let open Zkey in
match to_powers x with
| Three x -> x
| _ -> assert false
in
let shell_p = Cspc.shell_pair_p contracted_shell_pair_couple
and shell_q = Cspc.shell_pair_q contracted_shell_pair_couple
in
let result = ref [] in
Array.iteri (fun i_c powers_i ->
let i_c = Cs.index (Csp.shell_a shell_p) + i_c + 1 in
let xi = to_powers powers_i in
Array.iteri (fun j_c powers_j ->
let j_c = Cs.index (Csp.shell_b shell_p) + j_c + 1 in
let xj = to_powers powers_j in
Array.iteri (fun k_c powers_k ->
let k_c = Cs.index (Csp.shell_a shell_q) + k_c + 1 in
let xk = to_powers powers_k in
Array.iteri (fun l_c powers_l ->
let l_c = Cs.index (Csp.shell_b shell_q) + l_c + 1 in
let xl = to_powers powers_l in
let key = Zkey.of_powers_twelve xi xj xk xl in
let value = Zmap.find cls key in
result := (i_c, j_c, k_c, l_c, value) :: !result
) (Cs.zkey_array (Csp.shell_b shell_q))
) (Cs.zkey_array (Csp.shell_a shell_q))
) (Cs.zkey_array (Csp.shell_b shell_p))
) (Cs.zkey_array (Csp.shell_a shell_p));
!result
in
let t0 = Unix.gettimeofday () in
let shell_pairs =
Csp.of_contracted_shell_array shell
|> filter_contracted_shell_pairs f12 ~cutoff
in
if Parallel.master then
Printf.printf "%d significant shell pairs computed in %f seconds\n"
(List.length shell_pairs) (Unix.gettimeofday () -. t0);
let t0 = Unix.gettimeofday () in
let ishell = ref max_int in
let input_stream = Stream.of_list (List.rev shell_pairs) in
let f shell_p =
let () =
if Parallel.rank < 2 && Cs.index (Csp.shell_a shell_p) < !ishell then
(ishell := Cs.index (Csp.shell_a shell_p) ; print_int !ishell ; print_newline ())
in
let sp =
Csp.shell_pairs shell_p
in
let result = ref [] in
try
List.iter (fun shell_q ->
let () =
if Cs.index (Csp.shell_a shell_q) >
Cs.index (Csp.shell_a shell_p) then
raise Exit
in
let sq = Csp.shell_pairs shell_q in
let cspc =
if Array.length sp < Array.length sq then
Cspc.make ~cutoff shell_p shell_q
else
Cspc.make ~cutoff shell_q shell_p
in
match cspc with
| Some cspc ->
let cls =
class_of_contracted_shell_pair_couple f12 cspc
in
result := (store_class_parallel ~cutoff cspc cls) :: !result;
| None -> ()
) shell_pairs;
raise Exit
with Exit -> List.concat !result |> Array.of_list
in
let eri_array =
if Parallel.master then
Fis.create ~size:n `Dense
else
Fis.create ~size:n `Dense
in
Farm.run ~ordered:false ~f input_stream
|> Stream.iter (fun l ->
Array.iter (fun (i_c,j_c,k_c,l_c,value) ->
(*
lambda_inv *. (s.{i_c,j_c} *. s.{k_c,l_c} -. value)
lambda_inv *. value
*)
value
|> set_chem eri_array i_c j_c k_c l_c) l);
if Parallel.master then
Printf.printf
"Computed %s Integrals in parallel in %f seconds\n%!" Zero_m.name (Unix.gettimeofday () -. t0);
Fis.broadcast eri_array
let of_basis =
match Parallel.size with
| 1 -> of_basis_serial
| _ -> of_basis_parallel
g.GaussianOperator.expo_sg_inv
g.GaussianOperator.coef_g
shell_pair_couple
end
module M = TwoElectronIntegrals.Make(T)
include M

78
Basis/F12factor.ml Normal file
View File

@ -0,0 +1,78 @@
(** Type for f12 correlation factors *)
open Constants
type t =
{
expo_s : float ;
gaussian : GaussianOperator.t
}
let make_gaussian_corr_factor expo_s coef_g expo_sg =
let expo_sg =
Array.map (fun x -> x *. expo_s *. expo_s) expo_sg
in
let gaussian = GaussianOperator.make coef_g expo_sg in
{ expo_s ; gaussian }
(* -1/expo_s *. exp (-expo_s r) *)
let gaussian_geminal expo_s =
let coef_g =
[| 0.3144 ; 0.3037 ; 0.1681 ; 0.09811 ; 0.06024 ; 0.03726 |]
|> Array.map (fun x -> -. x /. expo_s)
and expo_sg =
[| 0.2209 ; 1.004 ; 3.622 ; 12.16 ; 45.87 ; 254.4 |]
in
make_gaussian_corr_factor expo_s coef_g expo_sg
(* exp (-expo_s r) *)
let simple_gaussian_geminal expo_s =
let coef_g =
[| 0.3144 ; 0.3037 ; 0.1681 ; 0.09811 ; 0.06024 ; 0.03726 |]
and expo_sg =
[| 0.2209 ; 1.004 ; 3.622 ; 12.16 ; 45.87 ; 254.4 |]
in
make_gaussian_corr_factor expo_s coef_g expo_sg
(** r12 * exp ( -expo_s * r) *)
let gaussian_geminal_times_r12 expo_s =
let coef_g =
[| 0.2454 ; 0.2938 ; 0.1815 ; 0.11281 ; 0.07502 ; 0.05280 |]
and expo_sg =
[| 0.1824 ; 0.7118; 2.252 ; 6.474 ; 19.66 ; 77.92 |]
in make_gaussian_corr_factor expo_s coef_g expo_sg
(* exp (-expo_s r) *)
let simple_gaussian_geminal' expo_s =
let coef_g =
[|
-3.4793465193721626604883567779324948787689208984375 ;
-0.00571703486454788484955047422886309504974633455276489257812 ;
4.14878218728681513738365538301877677440643310546875 ;
0.202874298181392742623785352407139725983142852783203125 ;
0.0819187742387294803858566183407674543559551239013671875 ;
0.04225945671351955673644695821167260874062776565551757812 ;
|]
and expo_sg =
[|
0.63172472556807146570889699432882480323314666748046875;
26.3759196683467962429858744144439697265625;
0.63172102793029016876147352377302013337612152099609375;
7.08429025944207335641067402320913970470428466796875;
42.4442841447001910637482069432735443115234375;
391.44036073596890901171718724071979522705078125 ;
|]
in make_gaussian_corr_factor expo_s coef_g expo_sg

39
Basis/GaussianOperator.ml Normal file
View File

@ -0,0 +1,39 @@
(** Representation for two-electron operators expressed in a Gaussian basis set. *)
open Constants
type t =
{
coef_g : float array;
expo_sg : float array;
expo_sg_inv : float array;
}
let make coef_g expo_sg =
let expo_sg_inv =
Array.map (fun x -> 1. /. x ) expo_sg
in
{ coef_g ; expo_sg ; expo_sg_inv }
let one_over_r =
let coef_g = [|
841.88478132 ; 70.590185207 ; 18.3616020768 ; 7.2608642093 ;
3.57483416444 ; 2.01376031082 ; 1.24216542801 ; 0.81754348620 ;
0.564546514023 ; 0.404228610699 ; 0.297458536575 ; 0.223321219537 ;
0.169933732064 ; 0.130190978230 ; 0.099652303426 ; 0.075428246546 ;
0.0555635614051 ; 0.0386791283055 ; 0.0237550435652 ; 0.010006278387 ;
|]
and expo_sg =
[| 84135.654509 ; 2971.58727634 ; 474.716025959 ; 130.676724560 ;
47.3938388887 ; 20.2078651631 ; 9.5411021938 ; 4.8109546955 ;
2.52795733067 ; 1.35894103210 ; 0.73586710268 ; 0.39557629706 ;
0.20785895177 ; 0.104809693858 ; 0.049485682527 ; 0.021099788990 ;
0.007652472186 ; 0.0021065225215 ; 0.0003365204879 ; 0.0000118855674 |]
in make coef_g expo_sg

26
Basis/TwoElectronIntegralsNonSeparable.ml → Basis/TwoElectronIntegrals.ml
View File

@ -1,5 +1,4 @@
(** Two electron integral functor for operators that are not separable among %{ $(x,y,z)$ %}.
It is parameterized by the [zero_m] function.
(** Two electron integrals
*)
open Constants
@ -11,30 +10,18 @@ module Csp = ContractedShellPair
module Cspc = ContractedShellPairCouple
module Fis = FourIdxStorage
module type Zero_mType =
module type TwoEI_structure =
sig
val name : string
val zero_m : Zero_m_parameters.t -> float array
val class_of_contracted_shell_pair_couple : ContractedShellPairCouple.t -> float Zmap.t
end
module Make(Zero_m : Zero_mType) = struct
module Make(T : TwoEI_structure) = struct
include FourIdxStorage
let zero_m = Zero_m.zero_m
let class_of_contracted_shell_pair_couple shell_pair_couple =
let shell_p = Cspc.shell_pair_p shell_pair_couple
and shell_q = Cspc.shell_pair_q shell_pair_couple
in
if Array.length (Csp.shell_pairs shell_p) +
(Array.length (Csp.shell_pairs shell_q)) < 4 then
TwoElectronRR.contracted_class_shell_pair_couple
~zero_m shell_pair_couple
else
TwoElectronRRVectorized.contracted_class_shell_pairs
~zero_m shell_p shell_q
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 ->
@ -283,6 +270,7 @@ module Make(Zero_m : Zero_mType) = struct
else
Fis.create ~size:n `Dense
in
Farm.run ~ordered:true ~f input_stream
|> Stream.iter (fun l ->
Array.iter (fun (i_c,j_c,k_c,l_c,value) ->
@ -290,7 +278,7 @@ module Make(Zero_m : Zero_mType) = struct
if Parallel.master then
Printf.printf
"Computed %s Integrals in parallel in %f seconds\n%!" Zero_m.name (Unix.gettimeofday () -. t0);
"Computed %s Integrals in parallel in %f seconds\n%!" T.name (Unix.gettimeofday () -. t0);
Fis.broadcast eri_array

19
Basis/TwoElectronIntegralsNonSeparable.mli → Basis/TwoElectronIntegrals.mli
View File

@ -6,27 +6,20 @@
*)
module type Zero_mType =
module type TwoEI_structure =
sig
val name : string
(** Name of the kind of integrals, for printing purposes. *)
val zero_m : Zero_m_parameters.t -> float array
(** The returned float array contains all the {% $(00|00)^m$ %} values, where
[m] is the index of the array.
- [maxm] : Maximum total angular momentum
- [expo_pq_inv] : {% $1/p + 1/q$ %} where {% $p$ %} and {% $q$ %} are the
exponents of {% $\phi_p$ %} and {% $\phi_q$ %}
- [norm_pq_sq] : square of the distance between the centers of
{% $\phi_p$ %} and {% $\phi_q$ %}
val class_of_contracted_shell_pair_couple : ContractedShellPairCouple.t -> float Zmap.t
(** Returns an integral class from a couple of contracted shells.
The results is stored in a Zmap.
*)
end
module Make : functor (Zero_m : Zero_mType) ->
module Make : functor (T : TwoEI_structure) ->
sig
include module type of FourIdxStorage

330
Basis/TwoElectronIntegralsSeparable.ml
View File

@ -1,330 +0,0 @@
(** Two electron integral functor for operators that are separable among %{ $(x,y,z)$ %}.
It is parameterized by the [zero_m] function.
*)
open Constants
let cutoff = integrals_cutoff
module Bs = Basis
module Cs = ContractedShell
module Csp = ContractedShellPair
module Cspc = ContractedShellPairCouple
module Fis = FourIdxStorage
include FourIdxStorage
(** Exponent of the geminal *)
let expo_s = 1.0
(** Coefficients and exponents of the Gaussian fit of the Slater Geminal*)
let coef_g =
[| 0.3144 ; 0.3037 ; 0.1681 ; 0.09811 ; 0.06024 ; 0.03726 |]
let expo_sg_inv =
Array.map (fun x -> 1. /. (x *. expo_s *. expo_s))
[| 0.2209 ; 1.004 ; 3.622 ; 12.16 ; 45.87 ; 254.4 |]
(*
Fit of 1/r:
let coef_g = [|
841.88478132 ; 70.590185207 ; 18.3616020768 ; 7.2608642093 ;
3.57483416444 ; 2.01376031082 ; 1.24216542801 ; 0.81754348620 ;
0.564546514023 ; 0.404228610699 ; 0.297458536575 ; 0.223321219537 ;
0.169933732064 ; 0.130190978230 ; 0.099652303426 ; 0.075428246546 ;
0.0555635614051 ; 0.0386791283055 ; 0.0237550435652 ; 0.010006278387 ;
|]
let expo_sg_inv =
Array.map (fun x -> 1. /. (x *. expo_s *. expo_s))
[| 84135.654509 ; 2971.58727634 ; 474.716025959 ; 130.676724560 ;
47.3938388887 ; 20.2078651631 ; 9.5411021938 ; 4.8109546955 ;
2.52795733067 ; 1.35894103210 ; 0.73586710268 ; 0.39557629706 ;
0.20785895177 ; 0.104809693858 ; 0.049485682527 ; 0.021099788990 ;
0.007652472186 ; 0.0021065225215 ; 0.0003365204879 ; 0.0000118855674 |]
*)
let class_of_contracted_shell_pair_couple shell_pair_couple =
F12RR.contracted_class_shell_pair_couple
expo_sg_inv coef_g shell_pair_couple
module Zero_m = struct
let name = "F12"
end
let filter_contracted_shell_pairs ?(cutoff=integrals_cutoff) shell_pairs =
List.map (fun pair ->
match Cspc.make ~cutoff pair pair with
| Some cspc ->
let cls = class_of_contracted_shell_pair_couple cspc in
(pair, Zmap.fold (fun key value accu -> max (abs_float value) accu) cls 0. )
(* TODO \sum_k |coef_k * integral_k| *)
| None -> (pair, -1.)
) shell_pairs
|> List.filter (fun (_, schwartz_p_max) -> schwartz_p_max >= cutoff)
|> List.map fst
(* TODO
let filter_contracted_shell_pair_couples
?(cutoff=integrals_cutoff) shell_pair_couples =
List.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
*)
let store_class ?(cutoff=integrals_cutoff) data contracted_shell_pair_couple cls =
let to_powers x =
let open Zkey in
match to_powers x with
| Three x -> x
| _ -> assert false
in
let shell_p = Cspc.shell_pair_p contracted_shell_pair_couple
and shell_q = Cspc.shell_pair_q contracted_shell_pair_couple
in
Array.iteri (fun i_c powers_i ->
let i_c = Cs.index (Csp.shell_a shell_p) + i_c + 1 in
let xi = to_powers powers_i in
Array.iteri (fun j_c powers_j ->
let j_c = Cs.index (Csp.shell_b shell_p) + j_c + 1 in
let xj = to_powers powers_j in
Array.iteri (fun k_c powers_k ->
let k_c = Cs.index (Csp.shell_a shell_q) + k_c + 1 in
let xk = to_powers powers_k in
Array.iteri (fun l_c powers_l ->
let l_c = Cs.index (Csp.shell_b shell_q) + l_c + 1 in
let xl = to_powers powers_l in
let key = Zkey.of_powers_twelve xi xj xk xl in
let value = Zmap.find cls key in
set_chem data i_c j_c k_c l_c value
) (Cs.zkey_array (Csp.shell_b shell_q))
) (Cs.zkey_array (Csp.shell_a shell_q))
) (Cs.zkey_array (Csp.shell_b shell_p))
) (Cs.zkey_array (Csp.shell_a shell_p))
let of_basis_serial basis =
let n = Bs.size basis
and shell = Bs.contracted_shells basis
in
let eri_array =
Fis.create ~size:n `Dense
(*
Fis.create ~size:n `Sparse
*)
in
let t0 = Unix.gettimeofday () in
let shell_pairs =
Csp.of_contracted_shell_array shell
|> filter_contracted_shell_pairs ~cutoff
in
Printf.printf "%d significant shell pairs computed in %f seconds\n"
(List.length shell_pairs) (Unix.gettimeofday () -. t0);
let t0 = Unix.gettimeofday () in
let ishell = ref 0 in
List.iter (fun shell_p ->
let () =
if (Cs.index (Csp.shell_a shell_p) > !ishell) then
(ishell := Cs.index (Csp.shell_a shell_p) ; print_int !ishell ; print_newline ())
in
let sp =
Csp.shell_pairs shell_p
in
try
List.iter (fun shell_q ->
let () =
if Cs.index (Csp.shell_a shell_q) >
Cs.index (Csp.shell_a shell_p) then
raise Exit
in
let sq = Csp.shell_pairs shell_q in
let cspc =
if Array.length sp < Array.length sq then
Cspc.make ~cutoff shell_p shell_q
else
Cspc.make ~cutoff shell_q shell_p
in
match cspc with
| Some cspc ->
let cls =
class_of_contracted_shell_pair_couple cspc
in
store_class ~cutoff eri_array cspc cls
| None -> ()
) shell_pairs
with Exit -> ()
) shell_pairs ;
Printf.printf "Computed ERIs in %f seconds\n%!" (Unix.gettimeofday () -. t0);
eri_array
(* Parallel functions *)
let of_basis_parallel basis =
let n = Bs.size basis
and shell = Bs.contracted_shells basis
in
let store_class_parallel
?(cutoff=integrals_cutoff) contracted_shell_pair_couple cls =
let to_powers x =
let open Zkey in
match to_powers x with
| Three x -> x
| _ -> assert false
in
let shell_p = Cspc.shell_pair_p contracted_shell_pair_couple
and shell_q = Cspc.shell_pair_q contracted_shell_pair_couple
in
let result = ref [] in
Array.iteri (fun i_c powers_i ->
let i_c = Cs.index (Csp.shell_a shell_p) + i_c + 1 in
let xi = to_powers powers_i in
Array.iteri (fun j_c powers_j ->
let j_c = Cs.index (Csp.shell_b shell_p) + j_c + 1 in
let xj = to_powers powers_j in
Array.iteri (fun k_c powers_k ->
let k_c = Cs.index (Csp.shell_a shell_q) + k_c + 1 in
let xk = to_powers powers_k in
Array.iteri (fun l_c powers_l ->
let l_c = Cs.index (Csp.shell_b shell_q) + l_c + 1 in
let xl = to_powers powers_l in
let key = Zkey.of_powers_twelve xi xj xk xl in
let value = Zmap.find cls key in
result := (i_c, j_c, k_c, l_c, value) :: !result
) (Cs.zkey_array (Csp.shell_b shell_q))
) (Cs.zkey_array (Csp.shell_a shell_q))
) (Cs.zkey_array (Csp.shell_b shell_p))
) (Cs.zkey_array (Csp.shell_a shell_p));
!result
in
let t0 = Unix.gettimeofday () in
let shell_pairs =
Csp.of_contracted_shell_array shell
|> filter_contracted_shell_pairs ~cutoff
in
if Parallel.master then
Printf.printf "%d significant shell pairs computed in %f seconds\n"
(List.length shell_pairs) (Unix.gettimeofday () -. t0);
let t0 = Unix.gettimeofday () in
let ishell = ref max_int in
let input_stream = Stream.of_list (List.rev shell_pairs) in
let f shell_p =
let () =
if Parallel.rank < 2 && Cs.index (Csp.shell_a shell_p) < !ishell then
(ishell := Cs.index (Csp.shell_a shell_p) ; print_int !ishell ; print_newline ())
in
let sp =
Csp.shell_pairs shell_p
in
let result = ref [] in
try
List.iter (fun shell_q ->
let () =
if Cs.index (Csp.shell_a shell_q) >
Cs.index (Csp.shell_a shell_p) then
raise Exit
in
let sq = Csp.shell_pairs shell_q in
let cspc =
if Array.length sp < Array.length sq then
Cspc.make ~cutoff shell_p shell_q
else
Cspc.make ~cutoff shell_q shell_p
in
match cspc with
| Some cspc ->
let cls =
class_of_contracted_shell_pair_couple cspc
in
result := (store_class_parallel ~cutoff cspc cls) :: !result;
| None -> ()
) shell_pairs;
raise Exit
with Exit -> List.concat !result |> Array.of_list
in
let eri_array =
if Parallel.master then
Fis.create ~size:n `Dense
else
Fis.create ~size:0 `Dense
in
Farm.run ~ordered:true ~f input_stream
|> Stream.iter (fun l ->
Array.iter (fun (i_c,j_c,k_c,l_c,value) ->
set_chem eri_array i_c j_c k_c l_c value) l);
if Parallel.master then
Printf.printf
"Computed %s Integrals in parallel in %f seconds\n%!" Zero_m.name (Unix.gettimeofday () -. t0);
Parallel.broadcast (lazy eri_array)
let of_basis =
match Parallel.size with
| 1 -> of_basis_serial
| _ -> of_basis_parallel

2
Simulation.ml
View File

@ -4,7 +4,7 @@ type t = {
nuclei : Nuclei.t;
basis : Basis.t;
ao_basis : AOBasis.t;
f12 : F12.f12_factor option;
f12 : F12factor.t option;
nuclear_repulsion : float;
}

6
Simulation.mli
View File

@ -18,18 +18,18 @@ val ao_basis : t -> AOBasis.t
val nuclear_repulsion : t -> float
(** Nuclear repulsion energy *)
val f12 : t -> F12.f12_factor option
val f12 : t -> F12factor.t option
(** f12 correlation factor *)
(** {1 Creation} *)
val make :
?cartesian:bool ->
?multiplicity:int -> ?charge:int -> ?f12:F12.f12_factor ->
?multiplicity:int -> ?charge:int -> ?f12:F12factor.t ->
nuclei:Nuclei.t -> Basis.t -> t
val of_filenames :
?cartesian:bool ->
?multiplicity:int -> ?charge:int -> ?f12:F12.f12_factor ->
?multiplicity:int -> ?charge:int -> ?f12:F12factor.t ->
nuclei:string -> ?aux_basis_filenames:string list -> string -> t

2
Utils/Util.ml
View File

@ -32,6 +32,8 @@ external leadz : int64 -> int32 = "leadz_bytecode" "leadz"
[@@unboxed] [@@noalloc]
(** bsf instruction *)
external vfork : unit -> int = "unix_vfork" "unix_vfork"
let leadz i = leadz i |> Int32.to_int

2
Utils/Util.mli
View File

@ -16,6 +16,8 @@ external gamma_float : float -> float = "gamma_float_bytecode" "gamma_float"
[@@unboxed] [@@noalloc]
(** Gamma function [gamma] from [libm] *)
external vfork : unit -> int = "unix_vfork" "unix_vfork"
(*
external popcnt : int64 -> int32 = "popcnt_bytecode" "popcnt"
[@@unboxed] [@@noalloc]

11
Utils/math_functions.c
View File

@ -72,3 +72,14 @@ CAMLprim value leadz_bytecode(value i)
return copy_int32(__builtin_clzll (i));
}
#include <unistd.h>
CAMLprim value unix_vfork(value unit)
{
int ret;
ret = vfork();
return Val_int(ret);
}

11
run_fci_f12.ml
View File

@ -26,9 +26,11 @@ let () =
arg=With_arg "<int>";
doc="Total charge of the molecule. Default is 0"; } ;
(*
{ short='e' ; long="expo" ; opt=Optional;
arg=With_arg "<float>";
doc="Exponent of the Gaussian geminal"; } ;
*)
{ short='s' ; long="state" ; opt=Optional;
arg=With_arg "<int>";
@ -49,11 +51,13 @@ let () =
| None -> 0
in
(*
let expo =
match Command_line.get "expo" with
| Some x -> float_of_string x
| None -> 1.0
in
*)
let state =
match Command_line.get "state" with
@ -72,8 +76,13 @@ let () =
else Printing.ppf_dev_null
in
(*
let f12 =
F12.gaussian_geminal expo
F12factor.gaussian_geminal expo
in
*)
let f12 =
F12factor.gaussian_geminal 1.0
in
let simulation =

2
run_integrals.ml
View File

@ -27,7 +27,7 @@ let run ~out =
| Some x -> x
in
let f12 = F12.gaussian_geminal 1.0 in
let f12 = F12factor.gaussian_geminal 1.0 in
let s =
Simulation.of_filenames ~nuclei:nuclei_file ~f12 basis_file
in