Renamed ao_basis to ao

ao/lib/basis.ml

@@ -2,7 +2,7 @@ open Qcaml_linear_algebra
     
 type basis =
   | Unknown
-  | Gaussian of Ao_basis_gaussian.t
+  | Gaussian of Basis_gaussian.t
 
 type t =
   { ao_basis : basis  ;
@@ -17,7 +17,7 @@ let of_nuclei_and_basis_filename ?(kind=`Gaussian) ?operators ?(cartesian=false)
         Qcaml_gaussian_basis.Basis.of_nuclei_and_basis_filename  ~nuclei filename
       in
       let ao_basis = 
-        Gaussian (Ao_basis_gaussian.make ~basis ?operators ~cartesian nuclei )
+        Gaussian (Basis_gaussian.make ~basis ?operators ~cartesian nuclei )
       in
       { ao_basis ; cartesian }
   | _ -> failwith "of_nuclei_and_basis_filename needs to be called with `Gaussian"
@@ -29,13 +29,13 @@ let ao_basis t = t.ao_basis
                     
 let size t = 
   match t.ao_basis with
-  | Gaussian b -> Ao_basis_gaussian.size b
+  | Gaussian b -> Basis_gaussian.size b
   | _ -> not_implemented ()
 
 let overlap t =
   begin
     match t.ao_basis with
-    | Gaussian b -> Ao_basis_gaussian.overlap b
+    | Gaussian b -> Basis_gaussian.overlap b
     | _ -> not_implemented ()
   end
   |> Matrix.relabel
@@ -43,7 +43,7 @@ let overlap t =
 let multipole t =
   begin
     match t.ao_basis with
-    | Gaussian b -> Ao_basis_gaussian.multipole b
+    | Gaussian b -> Basis_gaussian.multipole b
     | _ -> not_implemented ()
   end
   |> Array.map Matrix.relabel
@@ -51,7 +51,7 @@ let multipole t =
 let ortho t =
   begin
     match t.ao_basis with
-    | Gaussian b -> Ao_basis_gaussian.ortho b
+    | Gaussian b -> Basis_gaussian.ortho b
     | _ -> not_implemented ()
   end
   |> Matrix.relabel
@@ -59,7 +59,7 @@ let ortho t =
 let eN_ints t =
   begin
     match t.ao_basis with
-    | Gaussian b -> Ao_basis_gaussian.eN_ints b
+    | Gaussian b -> Basis_gaussian.eN_ints b
     | _ -> not_implemented ()
   end
   |> Matrix.relabel
@@ -67,7 +67,7 @@ let eN_ints t =
 let kin_ints t =
   begin
     match t.ao_basis with
-    | Gaussian b -> Ao_basis_gaussian.kin_ints b
+    | Gaussian b -> Basis_gaussian.kin_ints b
     | _ -> not_implemented ()
   end
   |> Matrix.relabel
@@ -75,7 +75,7 @@ let kin_ints t =
 let ee_ints t =
   begin
     match t.ao_basis with
-    | Gaussian b -> Ao_basis_gaussian.ee_ints b
+    | Gaussian b -> Basis_gaussian.ee_ints b
     | _ -> not_implemented ()
   end
   |> Four_idx_storage.relabel
@@ -83,7 +83,7 @@ let ee_ints t =
 let ee_lr_ints t =
   begin
     match t.ao_basis with
-    | Gaussian b -> Ao_basis_gaussian.ee_lr_ints b
+    | Gaussian b -> Basis_gaussian.ee_lr_ints b
     | _ -> not_implemented ()
   end
   |> Four_idx_storage.relabel
@@ -91,7 +91,7 @@ let ee_lr_ints t =
 let f12_ints t =
   begin
     match t.ao_basis with
-    | Gaussian b -> Ao_basis_gaussian.f12_ints b
+    | Gaussian b -> Basis_gaussian.f12_ints b
     | _ -> not_implemented ()
   end
   |> Four_idx_storage.relabel
@@ -99,7 +99,7 @@ let f12_ints t =
 let f12_over_r12_ints t =
   begin
     match t.ao_basis with
-    | Gaussian b -> Ao_basis_gaussian.f12_over_r12_ints b
+    | Gaussian b -> Basis_gaussian.f12_over_r12_ints b
     | _ -> not_implemented ()
   end
   |> Four_idx_storage.relabel
@@ -110,7 +110,7 @@ let cartesian t = t.cartesian
 let values t point =
   begin
     match t.ao_basis with
-    | Gaussian b -> Ao_basis_gaussian.values b point
+    | Gaussian b -> Basis_gaussian.values b point
     | _ -> not_implemented ()
   end
   |> Vector.relabel

ao/lib/basis.mli

@@ -7,7 +7,7 @@ open Qcaml_linear_algebra
 
 type basis =
   | Unknown
-  | Gaussian of Ao_basis_gaussian.t
+  | Gaussian of Basis_gaussian.t
 
 type t 
 
@@ -59,5 +59,5 @@ val values : t -> Coordinate.t -> 'a Vector.t
 val of_nuclei_and_basis_filename :
   ?kind:[> `Gaussian ] -> ?operators:Operator.t list -> ?cartesian:bool ->
   nuclei:Nuclei.t -> string -> t
-(** Creates the data structure for atomic orbitals from a {Basis.t} and the
-    molecular geometry {Nuclei.t} *)
+(** Creates the data structure for the atomic orbitals basis from a molecule
+    {Nuclei.t} and the name of the basis-set file *)

ao/lib/basis_gaussian.ml

@@ -3,6 +3,8 @@ open Qcaml_gaussian_basis
 open Qcaml_gaussian_integrals
 open Qcaml_operators
   
+module Basis = Qcaml_gaussian_basis.Basis
+
 type t =
 {
   basis              :  Basis.t                     ;

ao/lib/basis_gaussian.mli

@@ -2,7 +2,6 @@
 open Qcaml_common
 open Qcaml_particles
 open Qcaml_linear_algebra
-open Qcaml_gaussian_basis
 open Qcaml_gaussian_integrals
 open Qcaml_operators
   
@@ -13,7 +12,7 @@ type t
 val size : t -> int
 (** Number of atomic orbitals *) 
 
-val basis : t -> Basis.t
+val basis : t -> Qcaml_gaussian_basis.Basis.t
 (** One-electron basis set *)
 
 val overlap : t -> Overlap.t
@@ -46,14 +45,14 @@ val kin_ints : t -> Kinetic.t
 val cartesian : t -> bool
 (** If true, use cartesian Gaussians (6d, 10f, ...) *)
 
-val values : t -> Coordinate.t -> Basis.t Vector.t
+val values : t -> Coordinate.t -> Qcaml_gaussian_basis.Basis.t Vector.t
 (** Values of the AOs evaluated at a given point *)
 
 
 
 (** {1 Creators} *)
 
-val make : basis:Basis.t -> ?operators:Operator.t list -> ?cartesian:bool
-  -> Nuclei.t -> t
-(** Creates the data structure for atomic orbitals from a {Basis.t} and the
+val make : basis:Qcaml_gaussian_basis.Basis.t -> ?operators:Operator.t list ->
+  ?cartesian:bool -> Nuclei.t -> t
+(** Creates the data structure for atomic orbitals from a Gaussian basis and the
     molecular geometry {Nuclei.t} *)

ao/lib/dune

@@ -1,8 +1,8 @@
 ; name = name of the supermodule that will wrap all source files as submodules
 ; public_name = name of the library for ocamlfind and opam
 (library
- (name qcaml_ao_basis)
- (public_name qcaml.ao_basis)
+ (name qcaml_ao)
+ (public_name qcaml.ao)
  (libraries
         qcaml.common
         qcaml.particles

ao/test/ao_basis.ml

@@ -1,10 +1,9 @@
 open Alcotest
 open Qcaml_common
-open Qcaml_ao_basis
 open Qcaml_particles
 open Qcaml_operators
 open Qcaml_linear_algebra
-open Ao_basis
+open Qcaml_ao.Basis
 
 let wd = Qcaml.root ^ Filename.dir_sep ^ "test"
  
@@ -91,7 +90,7 @@ let tests =
     let rs = 0.5 in
     let operators = [ Operator.of_range_separation rs ] in
     let ao_basis = 
-      Ao_basis.of_nuclei_and_basis_filename ~kind:`Gaussian
+      Qcaml_ao.Basis.of_nuclei_and_basis_filename ~kind:`Gaussian
         ~operators ~cartesian:false ~nuclei basis_filename
     in
     make_tests "water" ao_basis ;

ao/test/ao_basis_gaussian.ml

@@ -2,11 +2,10 @@ open Alcotest
 open Qcaml_common
 open Qcaml_gaussian_integrals
 open Qcaml_gaussian_basis
-open Qcaml_ao_basis
 open Qcaml_particles
 open Qcaml_operators
 open Qcaml_linear_algebra
-open Ao_basis_gaussian
+open Qcaml_ao.Basis_gaussian
 
 let wd = Qcaml.root ^ Filename.dir_sep ^ "test"
  
@@ -93,7 +92,7 @@ let tests =
     let rs = 0.5 in
     let operators = [ Operator.of_range_separation rs ] in
     let ao_basis = 
-      Ao_basis_gaussian.make ~basis ~operators nuclei
+      Qcaml_ao.Basis_gaussian.make ~basis ~operators nuclei
     in
     make_tests "water" ao_basis ;
 

ao/test/dune

@@ -5,6 +5,6 @@
   qcaml.common
   qcaml.linear_algebra
   qcaml.gaussian_integrals
-  qcaml.ao_basis
+  qcaml.ao
  )
  (synopsis "Tests for the AO basis"))

qcaml/dune

@@ -1,15 +0,0 @@
-; name = name of the supermodule that will wrap all source files as submodules
-; public_name = name of the library for ocamlfind and opam
-(library
- (name qcaml)
- (public_name qcaml)
- (libraries
-        qcaml.common
-        qcaml.particles
-        qcaml.gaussian_basis
-        qcaml.gaussian_integrals
-	qcaml.operators
-	qcaml.ao_basis
-	qcaml.simulation
- )
- (synopsis "Main QCaml entry point"))

qcaml/qcaml.ml

@@ -1,10 +0,0 @@
-module Ao_basis = Qcaml_ao_basis
-module Common = Qcaml_common
-module Gaussian_basis = Qcaml_gaussian_basis
-module Gaussian_integrals = Qcaml_gaussian_integrals
-module Linear_algebra = Qcaml_linear_algebra
-module Operators = Qcaml_operators
-module Particles = Qcaml_particles
-module Simulation = Qcaml_simulation
-
-

simulation/lib/dune

@@ -1,14 +0,0 @@
-; name = name of the supermodule that will wrap all source files as submodules
-; public_name = name of the library for ocamlfind and opam
-(library
- (name qcaml_simulation)
- (public_name qcaml.simulation)
- (libraries
-        qcaml.common
-        qcaml.particles
-        qcaml.gaussian_basis
-        qcaml.gaussian_integrals
-	qcaml.operators
-	qcaml.ao_basis
- )
- (synopsis "Characterizes a simulation."))

simulation/lib/simulation.ml

@@ -1,46 +0,0 @@
-open Qcaml_common
-open Qcaml_particles
-open Qcaml_ao_basis
-open Qcaml_operators
-    
-type t = {
-  charge            : Charge.t;
-  electrons         : Electrons.t;
-  nuclei            : Nuclei.t;
-  ao_basis          : Ao_basis.t;
-  operators         : Operator.t list;
-}
-
-let nuclei            t = t.nuclei
-let charge            t = t.charge
-let electrons         t = t.electrons
-let ao_basis          t = t.ao_basis
-let nuclear_repulsion t = Nuclei.repulsion @@ nuclei t
-let operators         t = t.operators
-
-let make ?(multiplicity=1)
-      ?(charge=0)
-      ?(operators=[])
-      ~nuclei
-      ao_basis
-  =
-
-  (* Tune Garbage Collector *)
-  let gc = Gc.get () in
-  Gc.set { gc with space_overhead = 1000  };
-
-  let electrons =
-    Electrons.of_atoms ~multiplicity ~charge nuclei
-  in
-
-  let charge = 
-    Charge.(Nuclei.charge nuclei + Electrons.charge electrons)
-  in
-
-  {
-    charge ; nuclei ; electrons ; ao_basis ; 
-    operators
-  }
-
-
-

simulation/lib/simulation.mli

@@ -1,33 +0,0 @@
-(* Contains the state of a simulation *)
-
-open Qcaml_common
-open Qcaml_particles
-open Qcaml_ao_basis
-open Qcaml_operators
-    
-type t
-
-val nuclei : t -> Nuclei.t
-(** Nuclear coordinates used in the smiulation *)
-
-val charge : t -> Charge.t
-(** Total charge (electrons + nuclei) *)
-
-val electrons : t -> Electrons.t
-(** Electrons used in the simulation *)
-
-val ao_basis : t -> Ao_basis.t
-(** Atomic basis set *)
-
-val nuclear_repulsion : t -> float
-(** Nuclear repulsion energy *)
-
-val operators : t -> Operator.t list
-(** List of extra operators (range-separation, f12, etc) *)
-
-(** {1 Creation} *)
-
-val make : ?multiplicity:int -> ?charge:int -> 
-  ?operators:Operator.t list-> nuclei:Nuclei.t ->
-  Ao_basis.t -> t
-