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This commit is contained in:
Anthony Scemama 2018-03-22 00:29:14 +01:00
parent 69b1e10f00
commit 0face5817e
14 changed files with 203 additions and 156 deletions
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8
Basis/AtomicShellPair.ml
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@ -28,12 +28,14 @@ let make ?(cutoff=Constants.epsilon) atomic_shell_a atomic_shell_b =
let contracted_shell_pairs =
List.map (fun s_a ->
List.map (fun s_b ->
Csp.make ~cutoff s_a s_b
if Cs.index s_b <= Cs.index s_a then
Csp.make ~cutoff s_a s_b
else
None
) l_b
) l_a
|> List.concat
|> List.filter (function None -> false | _ -> true)
|> List.map (function None -> assert false | Some x -> x)
|> list_some
in
match contracted_shell_pairs with
| [] -> None

5
Basis/AtomicShellPairCouple.ml
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@ -1,3 +1,5 @@
open Util
type t =
{
atomic_shell_pair_p: AtomicShellPair.t ;
@ -32,8 +34,7 @@ let make ?(cutoff=Constants.epsilon) atomic_shell_pair_p atomic_shell_pair_q =
) (Asp.contracted_shell_pairs atomic_shell_pair_q)
) (Asp.contracted_shell_pairs atomic_shell_pair_p)
|> List.concat
|> List.filter (function None -> false | _ -> true)
|> List.map (function None -> assert false | Some x -> x)
|> list_some
in
match contracted_shell_pair_couples with
| [] -> None

2
Basis/ContractedShell.ml
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@ -75,6 +75,8 @@ let size_of_shell x = Array.length x.norm_coef_scale
let primitives x = x.prim
let zkey_array x = Ps.zkey_array x.prim.(0)
(** {2 Printers} *)

3
Basis/ContractedShell.mli
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@ -65,6 +65,9 @@ val norm_scales : t -> float array
val size_of_shell : t -> int
(** Number of contracted functions in the shell: length of {!norm_coef_scale}. *)
val zkey_array : t -> Zkey.t array
(** Returns the array of Zkeys associated with the contracted shell. *)
(** {2 Printers} *)

16
Basis/ContractedShellPair.ml
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@ -120,11 +120,17 @@ let cmp a b =
of contracted shells.
*)
let of_contracted_shell_array ?(cutoff=Constants.epsilon) basis =
Array.mapi (fun i shell_a ->
Array.mapi (fun j shell_b ->
make ~cutoff shell_a shell_b)
(Array.sub basis 0 (i+1))
) basis
let rec loop accu = function
| [] -> List.rev accu
| (s_a :: rest) as l ->
let new_accu =
(List.map (fun s_b -> make ~cutoff s_a s_b) l) :: accu
in loop new_accu rest
in
loop [] (Array.to_list basis)
|> List.concat
|> list_some
let equivalent x y =

16
Basis/ContractedShellPair.mli
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@ -22,18 +22,16 @@ val make : ?cutoff:float -> ContractedShell.t -> ContractedShell.t -> t option
The contracted shell pair contains the only pairs of primitives for which
the norm is greater than [cutoff].
If all the primitive shell pairs are not significant, the function returns
[None].
The function returns [None] if all the primitive shell pairs are not
significant, or if the index of the 1st primitive is smaller than the index
of the second primitive.
*)
val of_contracted_shell_array : ?cutoff:float -> ContractedShell.t array -> t option array array
(** Creates all possible contracted shell pairs from a list of contracted shells.
If a shell pair is not significant, sets the value to [None]:
{[
(of_contracted_shell_array p).(i).(j) = create p.(i) p.(j)
]}
val of_contracted_shell_array : ?cutoff:float -> ContractedShell.t array -> t list
(** Creates all possible contracted shell pairs from an array of contracted shells.
Only significant shell pairs are kept.
*)
val shell_a : t -> ContractedShell.t

5
Basis/ContractedShellPairCouple.ml
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@ -1,3 +1,5 @@
open Util
type t =
{
shell_pair_p: ContractedShellPair.t ;
@ -35,8 +37,7 @@ let make ?(cutoff=Constants.epsilon) shell_pair_p shell_pair_q =
) (Csp.coefs_and_shell_pairs shell_pair_q)
) (Csp.coefs_and_shell_pairs shell_pair_p)
|> List.concat
|> List.filter (function None -> false | _ -> true)
|> List.map (function None -> assert false | Some x -> x)
|> list_some
in
match coefs_and_shell_pair_couples with
| [] -> None

205
Basis/ERI.ml
View File

@ -7,6 +7,8 @@ open Bigarray
type t = (float, float32_elt, fortran_layout) Bigarray.Genarray.t
module Am = AngularMomentum
module As = AtomicShell
module Asp = AtomicShellPair
module Bs = Basis
module Cs = ContractedShell
module Csp = ContractedShellPair
@ -49,6 +51,15 @@ let contracted_class_shell_pairs_vec ?schwartz_p ?schwartz_q shell_p shell_q : f
TwoElectronRRVectorized.contracted_class_shell_pairs ~zero_m ?schwartz_p ?schwartz_q shell_p shell_q
let contracted_class_atomic_shell_pairs ?schwartz_p ?schwartz_q shell_p shell_q : float Zmap.t =
TwoElectronRR.contracted_class_atomic_shell_pairs ~zero_m ?schwartz_p ?schwartz_q shell_p shell_q
(*
let contracted_class_atomic_shell_pairs_vec ?schwartz_p ?schwartz_q shell_p shell_q : float Zmap.t =
TwoElectronRRVectorized.contracted_class_atomic_shell_pairs ~zero_m ?schwartz_p ?schwartz_q shell_p shell_q
*)
let cutoff2 = cutoff *. cutoff
(*
type n_cls = { n : int ; cls : Zkey.t array }
@ -78,6 +89,9 @@ let of_basis basis =
let n = Bs.size basis
and shell = Bs.contracted_shells basis
(*TODO
and atomic_shells = Bs.atomic_shells basis
*)
in
@ -85,34 +99,34 @@ let of_basis basis =
let shell_pairs =
Csp.of_contracted_shell_array shell
in
(*TODO
let atomic_shell_pairs =
Asp.of_atomic_shell_array ~cutoff atomic_shells
in
*)
(* Pre-compute diagonal integrals for Schwartz *)
let t0 = Unix.gettimeofday () in
let schwartz =
Array.map (fun pair_array -> Array.map (function
| None -> (Zmap.create 0, 0.)
| Some pair ->
let cls =
contracted_class_shell_pairs pair pair
in
(cls, Zmap.fold (fun key value accu -> max (abs_float value) accu) cls 0. )
) pair_array ) shell_pairs
List.map (fun pair ->
let cls =
contracted_class_shell_pairs pair pair
(*TODO
contracted_class_atomic_shell_pairs pair pair
*)
in
(pair, cls, 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)
in
let icount = ref 0 in
for i=0 to (Array.length shell) - 1 do
print_int (Cs.index shell.(i)) ; print_newline ();
for j=0 to i do
let schwartz_p, schwartz_p_max = schwartz.(i).(j) in
if (schwartz_p_max >= cutoff) then
icount := !icount + 1;
done;
done;
Printf.printf "%d shell pairs computed in %f seconds\n" !icount (Unix.gettimeofday () -. t0);
Printf.printf "%d shell pairs computed in %f seconds\n"
(List.length schwartz) (Unix.gettimeofday () -. t0);
(* Group shell pairs by common pairs of atoms *)
(* 4D data initialization *)
let eri_array =
@ -125,81 +139,86 @@ let of_basis basis =
let t0 = Unix.gettimeofday () in
let inn = ref 0 and out = ref 0 in
for i=0 to (Array.length shell) - 1 do
print_int (Cs.index shell.(i)) ; print_newline ();
for j=0 to i do
let schwartz_p, schwartz_p_max = schwartz.(i).(j) in
(*TODO
for i=0 to (Array.length atomic_shells) - 1 do
*)
let ishell = ref 0 in
List.iter (fun (shell_p, schwartz_p, schwartz_p_max) ->
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
(*TODO
Asp.atomic_shell_pairs shell_p
*)
in
try
if (schwartz_p_max < cutoff) then raise NullIntegral;
List.iter (fun (shell_q, schwartz_q, schwartz_q_max) ->
let () =
if Cs.index (Csp.shell_a shell_q) >
Cs.index (Csp.shell_a shell_p) then
raise Exit
in
let shell_p =
match shell_pairs.(i).(j) with
| None -> raise NullIntegral
| Some x -> x
in
let sp =
Csp.shell_pairs shell_p
in
for k=0 to i do
for l=0 to k do
let schwartz_q, schwartz_q_max = schwartz.(k).(l) in
try
if schwartz_p_max *. schwartz_q_max < cutoff2 then
raise NullIntegral;
if schwartz_p_max *. schwartz_q_max < cutoff2 then
raise NullIntegral;
let shell_q =
match shell_pairs.(k).(l) with
| None -> raise NullIntegral
| Some x -> x
in
let sq =
Csp.shell_pairs shell_q
(*TODO
Asp.atomic_shell_pairs shell_q
*)
in
let sq =
Csp.shell_pairs shell_q
in
let swap =
let swap =
Array.length sp > Array.length sq
in
in
(* Compute all the integrals of the class *)
let cls =
if swap then
if (Array.length sp) + (Array.length sq) < 4 then
contracted_class_shell_pairs ~schwartz_p:schwartz_q ~schwartz_q:schwartz_p shell_q shell_p
(* Compute all the integrals of the class *)
let cls =
if swap then
(*TODO
contracted_class_atomic_shell_pairs ~schwartz_p:schwartz_q ~schwartz_q:schwartz_p shell_q shell_p
*)
if (Array.length sp) + (Array.length sq) < 4 then
contracted_class_shell_pairs ~schwartz_p:schwartz_q ~schwartz_q:schwartz_p shell_q shell_p
else
contracted_class_shell_pairs_vec ~schwartz_p:schwartz_q ~schwartz_q:schwartz_p shell_q shell_p
else
contracted_class_shell_pairs_vec ~schwartz_p:schwartz_q ~schwartz_q:schwartz_p shell_q shell_p
else
if (Array.length sp) + (Array.length sq) < 4 then
contracted_class_shell_pairs ~schwartz_p ~schwartz_q shell_p shell_q
else
contracted_class_shell_pairs_vec ~schwartz_p ~schwartz_q shell_p shell_q
in
in
(* Write the data in the output file *)
Array.iteri (fun i_c powers_i ->
let i_c = Cs.index shell.(i) + i_c + 1 in
let xi = to_powers powers_i in
Array.iteri (fun j_c powers_j ->
let j_c = Cs.index shell.(j) + j_c + 1 in
let xj = to_powers powers_j in
Array.iteri (fun k_c powers_k ->
let k_c = Cs.index shell.(k) + k_c + 1 in
let xk = to_powers powers_k in
Array.iteri (fun l_c powers_l ->
let l_c = Cs.index shell.(l) + l_c + 1 in
let xl = to_powers powers_l in
let key =
if swap then
Zkey.of_powers_twelve xk xl xi xj
else
Zkey.of_powers_twelve xi xj xk xl
in
let value =
Zmap.find cls key
in
(* Write the data in the output file *)
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 =
if swap then
Zkey.of_powers_twelve xk xl xi xj
else
Zkey.of_powers_twelve xi xj xk xl
in
let value =
Zmap.find cls key
in
eri_array.{i_c,k_c,j_c,l_c} <- value;
eri_array.{j_c,k_c,i_c,l_c} <- value;
eri_array.{i_c,l_c,j_c,k_c} <- value;
@ -208,21 +227,19 @@ let of_basis basis =
eri_array.{k_c,j_c,l_c,i_c} <- value;
eri_array.{l_c,i_c,k_c,j_c} <- value;
eri_array.{l_c,j_c,k_c,i_c} <- value;
if (abs_float value > cutoff) then
(inn := !inn + 1;
)
else
out := !out + 1;
) Am.(zkey_array (Singlet (Cs.ang_mom shell.(l))))
) Am.(zkey_array (Singlet (Cs.ang_mom shell.(k))))
) Am.(zkey_array (Singlet (Cs.ang_mom shell.(j))))
) Am.(zkey_array (Singlet (Cs.ang_mom shell.(i))))
if (abs_float value > cutoff) then
(inn := !inn + 1;
)
else
out := !out + 1;
) (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))
with NullIntegral -> ()
done;
done;
with NullIntegral -> ()
done;
done;
) schwartz
with Exit -> ()
) schwartz;
Printf.printf "In: %d Out:%d\n" !inn !out ;
Printf.printf "Computed ERIs in %f seconds\n%!" (Unix.gettimeofday () -. t0);
eri_array

2
Basis/PrimitiveShell.ml
View File

@ -84,3 +84,5 @@ let norm_scales x = Lazy.force x.norm_scales
let size_of_shell x = Array.length (norm_scales x)
let zkey_array x = Am.(zkey_array (Singlet (x.ang_mom)))

3
Basis/PrimitiveShell.mli
View File

@ -61,3 +61,6 @@ val norm_scales : t -> float array
val size_of_shell : t -> int
(** Number of functions in the shell. *)
val zkey_array : t -> Zkey.t array
(** Returns the array of Zkeys associated with the primitive shell. *)

78
Basis/PrimitiveShellPair.ml
View File

@ -65,57 +65,57 @@ let create_make_of p_a p_b =
function p_a ->
let norm_coef_a =
Ps.normalization p_a
let norm_coef_a =
Ps.normalization p_a
in
let alpha_a =
Co.( Ps.exponent p_a |. Ps.center p_a )
in
function p_b ->
let normalization =
norm_coef_a *. Ps.normalization p_b
in
let alpha_a =
Co.( Ps.exponent p_a |. Ps.center p_a )
let exponent =
Ps.exponent p_a +. Ps.exponent p_b
in
function p_b ->
let exponent_inv = 1. /. exponent in
let normalization =
norm_coef_a *. Ps.normalization p_b
let normalization =
let argexpo =
Ps.exponent p_a *. Ps.exponent p_b *. a_minus_b_sq *. exponent_inv
in
normalization *. (pi *. exponent_inv)**1.5 *. exp (-. argexpo)
in
function cutoff ->
if abs_float normalization > cutoff then (
let beta_b =
Co.( Ps.exponent p_b |. Ps.center p_b )
in
let exponent =
Ps.exponent p_a +. Ps.exponent p_b
let center =
Co.(exponent_inv |. (alpha_a |+ beta_b))
in
let exponent_inv = 1. /. exponent in
let normalization =
let argexpo =
Ps.exponent p_a *. Ps.exponent p_b *. a_minus_b_sq *. exponent_inv
in
normalization *. (pi *. exponent_inv)**1.5 *. exp (-. argexpo)
let center_minus_a =
Co.(center |- Ps.center p_a)
in
function cutoff ->
Some {
ang_mom ;
exponent ; exponent_inv ; center ; center_minus_a ; a_minus_b ;
a_minus_b_sq ; normalization ; norm_scales ; shell_a = p_a;
shell_b = p_b }
if abs_float normalization > cutoff then (
let beta_b =
Co.( Ps.exponent p_b |. Ps.center p_b )
in
let center =
Co.(exponent_inv |. (alpha_a |+ beta_b))
in
let center_minus_a =
Co.(center |- Ps.center p_a)
in
Some {
ang_mom ;
exponent ; exponent_inv ; center ; center_minus_a ; a_minus_b ;
a_minus_b_sq ; normalization ; norm_scales ; shell_a = p_a;
shell_b = p_b }
)
else None
)
else None
let make p_a p_b =

3
Basis/PrimitiveShellPair.mli
View File

@ -48,8 +48,7 @@ val create_make_of : PrimitiveShell.t -> PrimitiveShell.t ->
are pre-computed.
The result is None if the normalization coefficient of the resulting
function is below the cutoff, given as a last argument.
function is below the cutoff given as a last argument.
*)
val ang_mom : t -> AngularMomentum.t

9
Utils/Util.ml
View File

@ -152,6 +152,15 @@ let boys_function ~maxm t =
end
(** {2 List functions} *)
let list_some l =
List.filter (function None -> false | _ -> true) l
|> List.map (function Some x -> x | _ -> assert false)
(** {2 Linear algebra} *)
let array_sum a =
Array.fold_left ( +. ) 0. a

4
Utils/Util.mli
View File

@ -57,6 +57,10 @@ val array_product : float array -> float
(** Returns the product of all the elements of the array *)
(** {2 Extension of the List module} *)
val list_some : 'a option list -> 'a list
(** {2 Linear algebra } *)
val diagonalize_symm : Lacaml.D.mat -> Lacaml.D.mat * Lacaml.D.vec