Introduced AOBasis

.merlin

@@ -1,7 +1,9 @@
 PKG str unix bigarray lacaml
 S .
 S Nuclei
+S CI
 S Utils
 S Basis
 S SCF
+S MOBasis
 B _build/**

Basis/AOBasis.ml

@@ -0,0 +1,43 @@
+open Lacaml.D
+
+type t =
+{
+  basis         : Basis.t ;
+  overlap       : Overlap.t lazy_t;
+  ortho         : Orthonormalization.t lazy_t;
+  eN_ints       : NucInt.t lazy_t;
+  ee_ints       : ERI.t lazy_t;
+  kin_ints      : KinInt.t lazy_t;
+  cartesian     : bool;
+}
+
+let make ~cartesian ~basis nuclei =
+
+  let overlap = lazy (
+    Overlap.of_basis basis
+  ) in
+
+  let ortho = lazy (
+    Orthonormalization.make ~cartesian ~basis (Lazy.force overlap)
+  ) in
+
+  let eN_ints  = lazy (
+    NucInt.of_basis_nuclei ~basis nuclei
+  ) in
+
+  let kin_ints = lazy (
+    KinInt.of_basis basis
+  ) in
+
+  let ee_ints  = lazy (
+    ERI.of_basis basis
+  ) in
+
+  { basis ; overlap ; ortho ; eN_ints ; kin_ints ; ee_ints ;
+    cartesian ;
+  }
+
+
+
+
+

Basis/AOBasis.mli

@@ -0,0 +1,19 @@
+(** Data structure for Atomic Orbitals. *)
+
+type t =
+{
+  basis      : Basis.t ;                      (* One-electron basis set *)
+  overlap    : Overlap.t lazy_t;              (* Overlap matrix *)
+  ortho      : Orthonormalization.t lazy_t;   (* Orthonormalization matrix of the overlap *)
+  eN_ints    : NucInt.t lazy_t;               (* Electron-nucleus potential integrals *)
+  ee_ints    : ERI.t lazy_t;                  (* Electron-electron potential integrals *)
+  kin_ints   : KinInt.t lazy_t;               (* Kinetic energy integrals *)
+  cartesian  : bool ;                         (* If true, use cartesian Gaussians (6d, 10f, ...) *)
+}
+
+
+val make : cartesian:bool -> basis:Basis.t -> Nuclei.t -> t
+(** Creates the data structure for atomic orbitals from a {Basis.t} and the
+    molecular geometry {Nuclei.t} *)
+
+

Basis/KinInt.mli

@@ -0,0 +1,17 @@
+(** Electronic kinetic energy integrals, expressed as a matrix in a {Basis.t}.
+
+{%
+$$
+T_{ij} = \left \langle \chi_i \left| -\frac{1}{2} \Delta \right| \chi_j \right \rangle
+$$
+%}
+*)
+
+type t = Lacaml.D.Mat.t
+
+val of_basis : Basis.t -> t
+(** Build from a {Basis.t}. *)
+
+val to_file : filename:string -> t -> unit
+(** Write the integrals in a file. *)
+

Basis/NucInt.ml

@@ -41,7 +41,7 @@ let cutoff2 = cutoff *. cutoff
 exception NullIntegral
 
 
-let of_basis_nuclei basis nuclei =
+let of_basis_nuclei ~basis nuclei =
   let to_powers x = 
     let open Zkey in
     match to_powers x with

Basis/NucInt.mli

@@ -0,0 +1,15 @@
+(** Electron-Nucleus attractive potential integrals, expressed as a matrix in a {Basis.t}.
+
+{% $$
+V_{ij} = \left \langle \chi_i \left| \sum_A \frac{-Z_A}{ | \mathbf{r} - \mathbf{R}_A |} \right| \chi_j \right \rangle
+$$ %}
+
+*)
+
+type t = Lacaml.D.Mat.t
+
+val of_basis_nuclei : basis:Basis.t -> Nuclei.t -> t
+(** Build from a {Basis.t} and the nuclei (coordinates and charges). *)
+
+val to_file : filename:string -> t -> unit
+(** Write the integrals in a file. *)

SCF/Fock.ml

@@ -3,7 +3,6 @@ open Simulation
 open Constants
 
 
-
 type t =
   {
     fock     : Mat.t ;
@@ -12,11 +11,13 @@ type t =
     exchange : Mat.t ;
   }
 
-let make ~density simulation =
+module Ao = AOBasis
+
+let make ~density ao_basis =
   let m_P  = density
-  and m_T  = Lazy.force simulation.kin_ints
-  and m_V  = Lazy.force simulation.eN_ints
-  and m_G  = Lazy.force simulation.ee_ints
+  and m_T  = Lazy.force ao_basis.Ao.kin_ints
+  and m_V  = Lazy.force ao_basis.Ao.eN_ints
+  and m_G  = Lazy.force ao_basis.Ao.ee_ints
   in
   let nBas = Mat.dim1 m_T
   in

SCF/Guess.ml

@@ -7,43 +7,44 @@ type guess =
 
 type t = guess
 
-module Si = Simulation
+module Ao = AOBasis
 module El = Electrons
 
-let hcore_guess simulation = 
-  let eN_ints  = Lazy.force simulation.Si.eN_ints
-  and kin_ints = Lazy.force simulation.Si.kin_ints
+let hcore_guess ao_basis = 
+  let eN_ints  = Lazy.force ao_basis.Ao.eN_ints
+  and kin_ints = Lazy.force ao_basis.Ao.kin_ints
   in
   Mat.add eN_ints kin_ints
 
 
-let huckel_guess simulation =
+let huckel_guess ao_basis =
   let c = 0.5 *. 1.75 in
-  let ao_num = Basis.size simulation.Si.basis in
-  let eN_ints  = Lazy.force simulation.Si.eN_ints
-  and kin_ints = Lazy.force simulation.Si.kin_ints
-  and overlap  = Lazy.force simulation.Si.overlap
-  and m_X = Lazy.force simulation.Si.overlap_ortho
+  let ao_num = Basis.size ao_basis.Ao.basis in
+  let eN_ints  = Lazy.force ao_basis.Ao.eN_ints
+  and kin_ints = Lazy.force ao_basis.Ao.kin_ints
+  and overlap  = Lazy.force ao_basis.Ao.overlap
+  and m_X = Lazy.force ao_basis.Ao.ortho
   in
   let diag = Array.init (ao_num+1) (fun i -> if i=0 then 0. else
     eN_ints.{i,i} +. kin_ints.{i,i})
   in
 
-  let nocc = 
-    simulation.Si.electrons.El.n_alpha
-  in
-  let m_F = (Fock.make ~density:(gemm ~alpha:2. ~transb:`T ~k:nocc m_X m_X) simulation).Fock.fock in
-  for j=1 to ao_num do
-    for i=1 to ao_num do
-      if (i <> j) then
-        m_F.{i,j} <- c *. overlap.{i,j} *. (diag.(i) +. diag.(j)) (*TODO Pseudo *)
+  function 
+  | 0 -> invalid_arg "Huckel guess needs a non-zero number of occupied MOs."
+  | nocc ->
+    let m_F = (Fock.make ~density:(gemm ~alpha:2. ~transb:`T ~k:nocc m_X m_X) ao_basis).Fock.fock in
+    for j=1 to ao_num do
+      for i=1 to ao_num do
+        if (i <> j) then
+          m_F.{i,j} <- c *. overlap.{i,j} *. (diag.(i) +. diag.(j)) (*TODO Pseudo *)
+      done;
     done;
-  done;
-  m_F
+    m_F
 
-let make ~guess simulation = 
+
+let make ?(nocc=0) ~guess ao_basis = 
   match guess with
-  | `Hcore  -> Hcore  (hcore_guess  simulation)
-  | `Huckel -> Huckel (huckel_guess simulation)
+  | `Hcore  -> Hcore  (hcore_guess  ao_basis)
+  | `Huckel -> Huckel (huckel_guess ao_basis nocc)
 
 

SCF/Guess.mli

@@ -7,7 +7,7 @@ type guess =
 type t = guess
 
 
-val make : guess:[ `Hcore | `Huckel ] -> Simulation.t -> t
+val make : ?nocc:int -> guess:[ `Hcore | `Huckel ] -> AOBasis.t -> t
 
 
 

SCF/RHF.ml

@@ -1,37 +1,44 @@
 open Util
 open Lacaml.D
-open Simulation
+
+module Si = Simulation
+module El = Electrons
+module Ao = AOBasis
 
 let make ?guess:(guess=`Huckel) ?max_scf:(max_scf=64) ?level_shift:(level_shift=0.1)
   ?threshold_SCF:(threshold_SCF=1.e-5) simulation =
 
   (* Number of occupied MOs *)
   let nocc =
-    simulation.electrons.Electrons.n_alpha
+    simulation.Si.electrons.El.n_alpha
   in
 
   let nuclear_repulsion = 
-    simulation.nuclear_repulsion
+    simulation.Si.nuclear_repulsion
+  in
+  
+  let ao_basis = 
+    simulation.Si.ao_basis
   in
 
   (* Initial guess *)
   let guess = 
-    Guess.make ~guess simulation 
+    Guess.make ~nocc ~guess ao_basis
   in
 
   (* Orthogonalization matrix *)
   let m_X = 
-    Lazy.force simulation.overlap_ortho 
+    Lazy.force ao_basis.Ao.ortho
   in
 
 
   (* Overlap matrix *)
   let m_S =
-    Lazy.force  simulation.overlap
+    Lazy.force  ao_basis.Ao.overlap
   in
 
-  let m_T = Lazy.force simulation.kin_ints
-  and m_V = Lazy.force simulation.eN_ints
+  let m_T = Lazy.force ao_basis.Ao.kin_ints
+  and m_V = Lazy.force ao_basis.Ao.eN_ints
   in
 
   (* Level shift in MO basis *)
@@ -53,7 +60,7 @@ let make ?guess:(guess=`Huckel) ?max_scf:(max_scf=64) ?level_shift:(level_shift=
       (* Fock matrix in AO basis *)
       let m_F, m_Hc, m_J, m_K =
         let x = 
-          Fock.make  ~density:m_P  simulation
+          Fock.make  ~density:m_P  ao_basis
         in
         x.Fock.fock, x.Fock.core, x.Fock.coulomb, x.Fock.exchange
       in

Simulation.ml

@@ -1,15 +1,10 @@
 type t = {
-  charge : Charge.t;
-  electrons : Electrons.t ;
-  basis : Basis.t;
-  nuclei : Nuclei.t;
-  overlap : Overlap.t lazy_t;
-  overlap_ortho : Orthonormalization.t lazy_t;
-  eN_ints : NucInt.t lazy_t;
-  kin_ints : KinInt.t lazy_t;
-  ee_ints : ERI.t lazy_t;
+  charge            : Charge.t;
+  electrons         : Electrons.t ;
+  nuclei            : Nuclei.t;
+  basis             : Basis.t;
+  ao_basis          : AOBasis.t;
   nuclear_repulsion : float;
-  cartesian : bool;
 }
 
 let make ?cartesian:(cartesian=false)
@@ -26,21 +21,22 @@ let make ?cartesian:(cartesian=false)
   let electrons =
     Electrons.make ~multiplicity ~charge nuclei
   in
+
   let charge = 
     Charge.(Nuclei.charge nuclei + Electrons.charge electrons)
   in
-  let overlap = 
-    lazy (Overlap.of_basis basis)
+
+  let ao_basis = 
+    AOBasis.make ~basis ~cartesian nuclei
   in
+
+  let nuclear_repulsion = 
+    Nuclei.repulsion nuclei
+  in
+
   {
-    charge ; 
-    basis ; nuclei ; electrons ; overlap ;
-    overlap_ortho = lazy (Orthonormalization.make ~cartesian ~basis (Lazy.force overlap));
-    eN_ints  = lazy (NucInt.of_basis_nuclei basis nuclei);
-    kin_ints = lazy (KinInt.of_basis basis);
-    ee_ints  = lazy (ERI.of_basis basis);
-    nuclear_repulsion =  Nuclei.repulsion nuclei;
-    cartesian ;
+    charge ; basis ; nuclei ; electrons ; ao_basis ;
+    nuclear_repulsion ; 
   }
 
 

run_integrals.ml

@@ -36,10 +36,11 @@ let run ~out =
   print_float s.Simulation.nuclear_repulsion; print_newline ();
   print_endline @@ Basis.to_string  s.Simulation.basis;
 
-  let overlap  = Lazy.force s.Simulation.overlap  in
-  let eN_ints  = Lazy.force s.Simulation.eN_ints  in
-  let kin_ints = Lazy.force s.Simulation.kin_ints in
-  let ee_ints  = Lazy.force s.Simulation.ee_ints  in
+  let ao_basis = s.Simulation.ao_basis in
+  let overlap  = Lazy.force ao_basis.AOBasis.overlap  in
+  let eN_ints  = Lazy.force ao_basis.AOBasis.eN_ints  in
+  let kin_ints = Lazy.force ao_basis.AOBasis.kin_ints in
+  let ee_ints  = Lazy.force ao_basis.AOBasis.ee_ints  in
   Overlap.to_file ~filename:(out_file^".overlap") overlap;
   NucInt.to_file ~filename:(out_file^".nuc") eN_ints;
   KinInt.to_file ~filename:(out_file^".kin") kin_ints;