Nuclei for T2

Basis/ERI.ml

@@ -3,7 +3,7 @@
 open Util
 open Constants
 
-type t = FourIdxStorage.t
+include FourIdxStorage
 
 
 module Am  = AngularMomentum
@@ -16,14 +16,6 @@ module Cspc = ContractedShellPairCouple
 module Fis = FourIdxStorage
 
 
-let get_chem = Fis.get_chem
-let get_phys = Fis.get_phys
-
-let set_chem = Fis.set_chem
-let set_phys = Fis.set_phys
-
-let to_file = Fis.to_file
-
 let cutoff = integrals_cutoff
 
 

Basis/ERI.mli

@@ -1,6 +1,6 @@
 (** Electron repulsion intergals. *)
 
-type t 
+include module type of FourIdxStorage
 
 (*
 val filter_atomic_shell_pairs : ?cutoff:float -> AtomicShellPair.t list -> AtomicShellPair.t  list
@@ -13,16 +13,7 @@ val filter_contracted_shell_pairs : ?cutoff:float -> ContractedShellPair.t list
 val class_of_contracted_shell_pair_couple : ContractedShellPairCouple.t -> float Zmap.t
 (** Computes all the ERI of the class built from a couple of contracted shell pairs. *)
 
-
-val get_chem : t -> int -> int -> int -> int -> float
-(** Get an integral using the Chemist's convention {% $(ij|kl)$ %}. *)
-
-val get_phys : t -> int -> int -> int -> int -> float
-(** Get an integral using the Physicist's convention {% $\langle ij|kl \rangle$ %}. *)
-
 val of_basis : Basis.t -> t
 (** Compute all ERI's for a given {!Basis.t}. *)
 
-val to_file : ?cutoff:float -> filename:string -> t -> unit
-(** Write the ERI's to a file, using the Physicist's convention. *)
 

Nuclei/Nuclei.ml

@@ -25,6 +25,12 @@ let of_xyz_file filename =
 
 
 
+let of_zmt_string buffer =
+  Zmatrix.of_string buffer
+  |> Zmatrix.to_xyz
+  |> Array.map (fun (e,x,y,z) -> (e, Coordinate.angstrom_to_bohr (Angstrom.make {Point.x ; y ; z} )))
+    
+
 let of_zmt_file filename =
   let ic = open_in filename in
   let rec aux accu =
@@ -36,9 +42,7 @@ let of_zmt_file filename =
       List.rev accu
       |> String.concat "\n"
   in aux []
-  |> Zmatrix.of_string
-  |> Zmatrix.to_xyz
-  |> Array.map (fun (e,x,y,z) -> (e, Coordinate.angstrom_to_bohr (Angstrom.make {Point.x ; y ; z} )))
+  |> of_zmt_string
     
 
 let to_string atoms =
@@ -92,3 +96,30 @@ let charge nuclei =
     0 nuclei 
   |> Charge.of_int
 
+
+let to_xyz_string t =
+  [ string_of_int (Array.length t) ; "" ] @
+  ( Array.mapi (fun i (e, coord) ->
+         let coord =
+           Coordinate.bohr_to_angstrom coord
+         in
+         Printf.sprintf " %5s   %12.6f  %12.6f  %12.6f"
+            (Element.to_string e) coord.Angstrom.x coord.Angstrom.y coord.Angstrom.z
+       ) t 
+    |> Array.to_list )
+  |> String.concat "\n"
+
+
+let to_t2_string t =
+  [ "# nAt nEl nCore nRyd" ;
+    Printf.sprintf "  %d   %d  %d     0" (Array.length t)
+    (Array.fold_left (+) 0 (Array.map (fun (e,_) -> Element.to_int e) t) )
+    (2 * Array.length t); 
+    "# Znuc   x            y           z" ]
+  @ (Array.mapi (fun i (e, coord) ->
+         Printf.sprintf " %5f    %12.6f  %12.6f  %12.6f"
+            (Element.to_int e |> float_of_int)  coord.Bohr.x coord.Bohr.y coord.Bohr.z
+       ) t 
+    |> Array.to_list )
+  |> String.concat "\n"
+

Nuclei/Nuclei.mli

@@ -8,6 +8,9 @@ type t = (Element.t * Bohr.t) array
 val of_xyz_file : string -> t
 (** Create from a file, in [xyz] format. *)
 
+val of_zmt_string : string -> t
+(** Create from a string, in z-matrix format. *)
+
 val of_zmt_file : string -> t
 (** Create from a file, in z-matrix format. *)
 
@@ -24,3 +27,5 @@ val repulsion : t -> float
 val charge : t -> Charge.t
 (** Sum of the charges of the nuclei. *)
 
+val to_xyz_string  : t -> string
+val to_t2_string  : t -> string

SCF/Fock.ml

@@ -14,6 +14,8 @@ type t =
 
 module Ao = AOBasis
 
+
+
 let make ~density ao_basis =
   let m_P  = density
   and m_T  = Lazy.force ao_basis.Ao.kin_ints |> KinInt.matrix 
@@ -27,6 +29,57 @@ let make ~density ao_basis =
   and m_J = Array.make_matrix nBas nBas 0.
   and m_K = Array.make_matrix nBas nBas 0.
   in
+(*
+  let permutations  i j k l  =
+    let result =
+      [  [| i ; j ; k ; l |] ; 
+         [| i ; l ; k ; j |] ; 
+         [| k ; j ; i ; l |] ; 
+         [| k ; l ; i ; j |] ; 
+         [| j ; i ; l ; k |] ; 
+         [| j ; k ; l ; i |] ; 
+         [| l ; i ; j ; k |] ; 
+         [| l ; k ; j ; i |] ] 
+    in
+    if i<>k && j<>l && i<>j && k<>l then
+      result
+    else
+      List.map Zkey.of_int_array result
+      |> List.sort_uniq Pervasives.compare 
+      |> List.map Zkey.to_int_array
+  in
+  let sum = ref 0 in
+  ERI.to_stream m_G
+  |> Stream.iter (fun { ERI.i_r1 ; j_r2 ; k_r1 ; l_r2 ; value } ->
+     permutations i_r1 j_r2 k_r1 l_r2 
+     |> List.iter ( fun ijkl ->
+        let mu     = ijkl.(0)
+        and nu     = ijkl.(2)
+        and lambda = ijkl.(1)
+        and sigma  = ijkl.(3)
+        in
+        incr sum;
+        let p = m_P.{lambda,sigma} in
+        if abs_float p > epsilon then
+          let m_Jnu = m_J.(nu-1) in
+          m_Jnu.(mu-1) <- m_Jnu.(mu-1) +. p *. value )
+     );
+
+  Printf.printf "%d %d\n%!" !sum (nBas*nBas*nBas*nBas);
+*)
+  for sigma = 1 to nBas do
+    for nu = 1 to nBas do
+      let m_Jnu = m_J.(nu-1) in
+      for lambda = 1 to nBas do
+        let p = m_P.{lambda,sigma} in
+        for mu = 1 to nBas do
+          m_Jnu.(mu-1) <- m_Jnu.(mu-1) +.  p *. 
+                        ERI.get_phys m_G mu lambda nu sigma
+        done
+      done
+    done
+  done;
+    (*
   for sigma = 1 to nBas do
     for nu = 1 to nBas do
       let m_Jnu = m_J.(nu-1) in
@@ -45,6 +98,13 @@ let make ~density ao_basis =
       done
     done
   done;
+  for nu = 1 to nBas do
+    for mu = 1 to nu-1 do
+      m_J.(mu-1).(nu-1) <- m_J.(nu-1).(mu-1);
+    done
+  done;
+     *)
+
   for nu = 1 to nBas do
     let m_Knu = m_K.(nu-1) in
     for sigma = 1 to nBas do
@@ -58,12 +118,9 @@ let make ~density ao_basis =
                           ERI.get_phys m_G mu lambda sigma nu
           done
       done
-    done
-  done;
-  for nu = 1 to nBas do
+    done;
     for mu = 1 to nu-1 do
-      m_J.(mu-1).(nu-1) <- m_J.(nu-1).(mu-1);
-      m_K.(mu-1).(nu-1) <- m_K.(nu-1).(mu-1);
+      m_K.(mu-1).(nu-1) <- m_Knu.(mu-1);
     done
   done;
   let m_J =  Mat.of_array m_J

Utils/FourIdxStorage.ml

@@ -173,7 +173,7 @@ let to_stream d =
   and k = ref 1
   and l = ref 1
   in
-  let f _ =
+  let f_dense _ =
     i := !i+1;
     if !i > !k then begin
       i := 1;
@@ -195,7 +195,7 @@ let to_stream d =
      else
        None
   in
-  Stream.from f
+  Stream.from f_dense
     
 
 (** Write all integrals to a file with the <ij|kl> convention *)

Utils/FourIdxStorage.mli

@@ -25,12 +25,22 @@ val create : size:int -> [< `Dense | `Sparse ] -> t
 
 (** {2 Accessors} *)
 val get_chem : t -> int -> int -> int -> int -> float
+(** Get an integral using the Chemist's convention {% $(ij|kl)$ %}. *)
+
 val get_phys : t -> int -> int -> int -> int -> float
+(** Get an integral using the Physicist's convention {% $\langle ij|kl \rangle$ %}. *)
+
 val set_chem : t -> int -> int -> int -> int -> float -> unit
+(** Set an integral using the Chemist's convention {% $(ij|kl)$ %}. *)
+
 val set_phys : t -> int -> int -> int -> int -> float -> unit
+(** Set an integral using the Physicist's convention {% $\langle ij|kl \rangle$ %}. *)
 
 val to_stream : t -> element Stream.t
+(** Fetch all integrals from a stream. *)
+
 
 (** {2 I/O} *)
+
 val to_file : ?cutoff:float -> filename:string -> t -> unit
 (** Write the data to file, using the physicist's ordering. *)

Utils/Zkey.ml

@@ -31,6 +31,7 @@ let (<+) z x =
 
 type kind = 
   | Three  of  Powers.t
+  | Four   of (int * int * int * int)
   | Six    of (Powers.t * Powers.t)
   | Nine   of (Powers.t * Powers.t * Powers.t)
   | Twelve of (Powers.t * Powers.t * Powers.t * Powers.t)
@@ -42,6 +43,13 @@ let of_powers_three { x=a ; y=b ; z=c ; _ } =
   );
   make 3 a <+ b <+ c
 
+let of_int_four i j k l =
+  assert (
+    let alpha = i lor j lor k lor l in
+    alpha >= 0 && alpha < (1 lsl 15)
+  );
+  make 4 i <+ j <+ k <+ l
+
 let of_powers_six   { x=a ; y=b ; z=c ; _ } { x=d ; y=e ; z=f ; _ } =
   assert (
     let alpha = a lor b lor c lor d lor e lor f in
@@ -76,12 +84,18 @@ let of_powers a =
   | Six    (a,b)     -> of_powers_six    a b
   | Twelve (a,b,c,d) -> of_powers_twelve a b c d
   | Nine   (a,b,c)   -> of_powers_nine   a b c
+  | _                -> invalid_arg "of_powers"
 
 
 let mask10 = 0x3ff
 and mask15 = 0x7fff
 
 
+let of_int_array = function
+| [| a ; b ; c ; d |] -> of_int_four a b c d
+| _ -> invalid_arg "of_int_array"
+
+
 (** Transform the Zkey into an int array *)
 let to_int_array { left ; right ; kind }  = 
   match kind with
@@ -91,6 +105,13 @@ let to_int_array { left ; right ; kind }  =
                   mask15 land  right
                |]
 
+  | 4  -> [|
+                  mask15 land (right lsr 45) ;
+                  mask15 land (right lsr 30) ;
+                  mask15 land (right lsr 15) ;
+                  mask15 land  right
+               |]
+
   | 6  -> [| 
                   mask10 land (right lsr 50) ;
                   mask10 land (right lsr 40) ;
@@ -180,6 +201,7 @@ let to_powers { left ; right ; kind } =
                   mask10 land (right lsr 10) ,
                   mask10 land  right )
                )
+
   | _ -> invalid_arg (__FILE__^": to_powers")
 
 

Utils/Zkey.mli

@@ -33,6 +33,9 @@ val to_string : t -> string
 val of_powers_three  : Powers.t -> t
 (** Create from a {!Powers.t}. *)
 
+val of_int_four  : int -> int -> int -> int -> t
+(** Create from four integers. *)
+
 val of_powers_six    : Powers.t -> Powers.t -> t
 (** Create from two {!Powers.t}. *)
 
@@ -44,6 +47,7 @@ val of_powers_twelve : Powers.t -> Powers.t -> Powers.t -> Powers.t -> t
 
 type kind =
   | Three  of  Powers.t
+  | Four   of (int * int * int * int)
   | Six    of (Powers.t * Powers.t)
   | Nine   of (Powers.t * Powers.t * Powers.t)
   | Twelve of (Powers.t * Powers.t * Powers.t * Powers.t)
@@ -54,6 +58,9 @@ val of_powers : kind -> t
 val to_int_array : t -> int array
 (** Convert to an int array. *)
 
+val of_int_array : int array -> t
+(** Convert from an int array. *)
+
 val to_powers : t -> kind
 
 (** {1 Functions for hash tables} *)