Merge branch 'dev' of gitlab.com:scemama/QCaml into dev

ao/lib/basis.ml

@@ -16,7 +16,7 @@ let of_nuclei_and_basis_filename ?(kind=`Gaussian) ?operators ?(cartesian=false)
   match kind with
   | `Gaussian ->
       let basis =
-        Gaussian_basis.Basis.of_nuclei_and_basis_filename  ~nuclei filename
+        Gaussian.Basis.of_nuclei_and_basis_filename  ~nuclei filename
       in
       let ao_basis = 
         Gaussian (Basis_gaussian.make ~basis ?operators ~cartesian nuclei )

ao/lib/basis_gaussian.ml

@@ -1,9 +1,9 @@
 open Linear_algebra
-open Gaussian_basis
+open Gaussian
 open Gaussian_integrals
 open Operators
   
-module Basis = Gaussian_basis.Basis
+module Basis = Gaussian.Basis
 
 type t =
 {

ao/lib/basis_gaussian.mli

@@ -12,7 +12,7 @@ type t
 val size : t -> int
 (** Number of atomic orbitals *) 
 
-val basis : t -> Gaussian_basis.Basis.t
+val basis : t -> Gaussian.Basis.t
 (** One-electron basis set *)
 
 val overlap : t -> Overlap.t
@@ -45,14 +45,14 @@ val kin_ints : t -> Kinetic.t
 val cartesian : t -> bool
 (** If true, use cartesian Gaussians (6d, 10f, ...) *)
 
-val values : t -> Coordinate.t -> Gaussian_basis.Basis.t Vector.t
+val values : t -> Coordinate.t -> Gaussian.Basis.t Vector.t
 (** Values of the AOs evaluated at a given point *)
 
 
 
 (** {1 Creators} *)
 
-val make : basis:Gaussian_basis.Basis.t -> ?operators:Operator.t list ->
+val make : basis:Gaussian.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

@@ -6,7 +6,7 @@
  (libraries
         qcaml.common
         qcaml.particles
-        qcaml.gaussian_basis
+        qcaml.gaussian
         qcaml.gaussian_integrals
 	qcaml.operators
  )

ao/test/ao_basis_gaussian.ml

@@ -1,6 +1,6 @@
 open Alcotest
 open Gaussian_integrals
-open Gaussian_basis
+open Gaussian
 open Particles
 open Operators
 open Linear_algebra

common/lib/qcaml.ml

@@ -3,7 +3,7 @@ let name = "QCaml"
 
 let root =
   let rec chop = function
-    | [] -> raise Not_found
+    | [] -> []
     | x :: _ as l when x = name -> l
     | _ :: rest -> chop rest
   in

dune-project

@@ -27,7 +27,6 @@ in quantum chemistry.")
   (depends
     (ocaml (>= 4.10))
     (dune  (>= 1.10))
-    str
     lacaml
     getopt
     zarith

gaussian/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 gaussian_basis)
- (public_name qcaml.gaussian_basis)
+ (name gaussian)
+ (public_name qcaml.gaussian)
  (libraries
         str
         qcaml.common

gaussian/test/dune

@@ -3,6 +3,6 @@
  (libraries
   alcotest
   qcaml.particles
-  qcaml.gaussian_basis
+  qcaml.gaussian
  )
  (synopsis "Tests for Gaussian basis sets"))

gaussian/test/general_basis.ml

@@ -1,6 +1,6 @@
 open Common
 open Particles
-open Gaussian_basis
+open Gaussian
 open Alcotest
 
 let wd = Common.Qcaml.root ^ Filename.dir_sep ^ "test"

gaussian_integrals/lib/dune

@@ -7,7 +7,7 @@
         str
         qcaml.common
         qcaml.linear_algebra
-        qcaml.gaussian_basis
+        qcaml.gaussian
         qcaml.operators
  )
  (modules_without_implementation matrix_on_basis)

gaussian_integrals/lib/electron_nucleus.ml

@@ -3,7 +3,7 @@
 include Common
 include Particles
 include Linear_algebra
-include Gaussian_basis
+include Gaussian
 open Util
 open Constants
 

gaussian_integrals/lib/electron_nucleus.mli

@@ -9,7 +9,7 @@ $$ %}
 include module type of Matrix_on_basis
 
 open Particles
-open Gaussian_basis
+open Gaussian
 
 val of_basis_nuclei : basis:Basis.t -> Nuclei.t -> t
 (** Build from a {Basis.t} and the nuclei (coordinates and charges). *)

gaussian_integrals/lib/eri.ml

@@ -1,7 +1,7 @@
 (** Electron-electron repulsion integrals *)
 
 open Common
-open Gaussian_basis
+open Gaussian
 
 module Csp = Contracted_shell_pair
 module Cspc = Contracted_shell_pair_couple

gaussian_integrals/lib/eri_long_range.ml

@@ -3,7 +3,7 @@
 *)
 
 open Common
-open Gaussian_basis
+open Gaussian
 open Operators
 
 module Csp  = Contracted_shell_pair

gaussian_integrals/lib/f12_rr.ml

@@ -1,5 +1,5 @@
 open Common
-open Gaussian_basis
+open Gaussian
 
 module Am   = Angular_momentum
 module Asp  = Atomic_shell_pair

gaussian_integrals/lib/kinetic.ml

@@ -1,6 +1,6 @@
 open Common
 open Linear_algebra
-open Gaussian_basis
+open Gaussian
 open Util
 open Constants
 

gaussian_integrals/lib/matrix_on_basis.mli

@@ -1,6 +1,6 @@
 (** Signature for matrices built on the {!Basis.t} *)
 
-open Gaussian_basis
+open Gaussian
 open Linear_algebra
 
 type t = (Basis.t, Basis.t) Matrix.t

gaussian_integrals/lib/multipole.ml

@@ -1,6 +1,6 @@
 open Common
 open Linear_algebra
-open Gaussian_basis
+open Gaussian
 open Constants
 
 type t = (Basis.t, Basis.t) Matrix.t array
@@ -222,3 +222,19 @@ let of_basis basis =
   Array.iter Matrix.detri_inplace result;
   result
 
+
+let to_file ~filename eni_array =
+  let n = Matrix.dim1 eni_array in
+  let eni_array = Matrix.to_bigarray_inplace eni_array in
+  let oc = open_out filename in
+    
+  for j=1 to n do
+    for i=1 to j do
+      let value = eni_array.{i,j} in
+      if (value <> 0.) then
+        Printf.fprintf oc " %5d %5d %20.15f\n" i j value;
+    done;
+  done;
+  close_out oc
+    
+

gaussian_integrals/lib/multipole.mli

@@ -10,7 +10,7 @@
 *)
 
 open Linear_algebra
-open Gaussian_basis
+open Gaussian
 
 type t = (Basis.t, Basis.t) Matrix.t array
 
@@ -60,3 +60,7 @@ val matrix_z4 : t -> (Basis.t, Basis.t) Matrix.t
 (** {% $$ \langle \chi_i | z^4 | \chi_j \rangle $$ %} *)
 
 val of_basis : Basis.t -> t
+
+val to_file : filename:string -> (Basis.t, Basis.t) Matrix.t -> unit                                                
+(** Write a matrix to a file *)
+

gaussian_integrals/lib/one_electron_rr.ml

@@ -2,7 +2,7 @@ open Common
 open Particles
 open Util
 open Constants
-open Gaussian_basis
+open Gaussian
 
 exception NullPair
 

gaussian_integrals/lib/orthonormalization.ml

@@ -1,6 +1,6 @@
 open Common
 open Linear_algebra
-open Gaussian_basis
+open Gaussian
 
 module Am  = Angular_momentum
 module Bs  = Basis

gaussian_integrals/lib/orthonormalization.mli

@@ -1,6 +1,6 @@
 (** Orthonormalization of the basis. *)
 
-open Gaussian_basis
+open Gaussian
 open Linear_algebra
 
 type t = (Basis.t, Basis.t) Matrix.t

gaussian_integrals/lib/overlap.ml

@@ -1,6 +1,6 @@
 open Common
 open Linear_algebra
-open Gaussian_basis
+open Gaussian
 open Util
 open Constants
 

gaussian_integrals/lib/screened_eri.ml

@@ -1,7 +1,7 @@
 (** Screened Electron-electron repulsion integrals (Yukawa potential). Required for F12/r12. *)
 
 open Common
-open Gaussian_basis
+open Gaussian
 open Operators
 
 module Csp  = Contracted_shell_pair

gaussian_integrals/lib/two_electron_integrals.ml

@@ -3,7 +3,7 @@
 
 open Common
 open Linear_algebra
-open Gaussian_basis
+open Gaussian
 open Operators
 
 open Constants

gaussian_integrals/lib/two_electron_integrals.mli

@@ -6,7 +6,7 @@
 *)
 
 open Common
-open Gaussian_basis
+open Gaussian
 open Linear_algebra
 open Operators
 

gaussian_integrals/lib/two_electron_rr.ml

@@ -1,5 +1,5 @@
 open Common
-open Gaussian_basis
+open Gaussian
 
 module Am   = Angular_momentum
 module Asp  = Atomic_shell_pair

gaussian_integrals/lib/two_electron_rr_vectorized.ml

@@ -1,5 +1,5 @@
 open Common
-open Gaussian_basis
+open Gaussian
 open Linear_algebra
 
 module Am   = Angular_momentum

gaussian_integrals/test/general_basis.ml

@@ -1,6 +1,6 @@
 open Common
 open Particles
-open Gaussian_basis
+open Gaussian
 open Alcotest
 
 let wd = Common.Qcaml.root ^ Filename.dir_sep ^ "test"

qcaml/lib/dune

@@ -6,7 +6,7 @@
  (libraries
         qcaml.common
         qcaml.particles
-        qcaml.gaussian_basis
+        qcaml.gaussian
         qcaml.gaussian_integrals
 	qcaml.operators
 	qcaml.ao

qcaml/lib/qcaml.ml

@@ -1,2 +1,8 @@
 module Common = Common
 module Ao = Ao
+module Gaussian = Gaussian
+module Gaussian_integrals = Gaussian_integrals
+module Linear_algebra = Linear_algebra
+module Operators = Operators
+module Particles = Particles
+

simulation/lib/dune

@@ -6,7 +6,7 @@
  (libraries
         qcaml.common
         qcaml.particles
-        qcaml.gaussian_basis
+        qcaml.gaussian
         qcaml.gaussian_integrals
 	qcaml.operators
 	qcaml.ao