From 6217dc5a0a230c3edb52e491b12e5403909d9754 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Fri, 9 Oct 2020 09:47:57 +0200 Subject: [PATCH] Removed Qcaml_ prefixes --- ao/lib/basis.ml | 4 ++-- ao/lib/basis.mli | 8 ++++---- ao/lib/basis_gaussian.ml | 10 +++++----- ao/lib/basis_gaussian.mli | 16 ++++++++-------- ao/lib/dune | 2 +- ao/test/ao_basis.ml | 13 ++++++------- ao/test/ao_basis_gaussian.ml | 17 ++++++++--------- common/lib/dune | 2 +- common/test/bitstring.ml | 2 +- common/test/math_functions.ml | 2 +- gaussian_basis/lib/atomic_shell.ml | 2 +- gaussian_basis/lib/atomic_shell.mli | 2 +- gaussian_basis/lib/atomic_shell_pair.ml | 2 +- gaussian_basis/lib/atomic_shell_pair.mli | 2 +- gaussian_basis/lib/atomic_shell_pair_couple.ml | 2 +- gaussian_basis/lib/atomic_shell_pair_couple.mli | 2 +- gaussian_basis/lib/basis.mli | 2 +- gaussian_basis/lib/contracted_shell.ml | 2 +- gaussian_basis/lib/contracted_shell.mli | 2 +- gaussian_basis/lib/contracted_shell_pair.ml | 2 +- gaussian_basis/lib/contracted_shell_pair.mli | 2 +- .../lib/contracted_shell_pair_couple.ml | 2 +- .../lib/contracted_shell_pair_couple.mli | 2 +- gaussian_basis/lib/dune | 2 +- gaussian_basis/lib/general_basis.ml | 4 ++-- gaussian_basis/lib/general_basis.mli | 4 ++-- gaussian_basis/lib/primitive_shell.ml | 2 +- gaussian_basis/lib/primitive_shell.mli | 2 +- gaussian_basis/lib/primitive_shell_pair.ml | 2 +- gaussian_basis/lib/primitive_shell_pair.mli | 2 +- .../lib/primitive_shell_pair_couple.ml | 2 +- .../lib/primitive_shell_pair_couple.mli | 2 +- gaussian_basis/test/general_basis.ml | 8 ++++---- gaussian_integrals/lib/dune | 2 +- gaussian_integrals/lib/electron_nucleus.ml | 8 ++++---- gaussian_integrals/lib/electron_nucleus.mli | 4 ++-- gaussian_integrals/lib/eri.ml | 4 ++-- gaussian_integrals/lib/eri_long_range.ml | 6 +++--- gaussian_integrals/lib/f12.ml | 4 ++-- gaussian_integrals/lib/f12_rr.ml | 4 ++-- gaussian_integrals/lib/kinetic.ml | 6 +++--- gaussian_integrals/lib/matrix_on_basis.mli | 4 ++-- gaussian_integrals/lib/multipole.ml | 6 +++--- gaussian_integrals/lib/multipole.mli | 4 ++-- gaussian_integrals/lib/one_electron_rr.ml | 6 +++--- gaussian_integrals/lib/orthonormalization.ml | 6 +++--- gaussian_integrals/lib/orthonormalization.mli | 4 ++-- gaussian_integrals/lib/overlap.ml | 6 +++--- gaussian_integrals/lib/overlap_primitives.ml | 2 +- gaussian_integrals/lib/screened_eri.ml | 6 +++--- .../lib/two_electron_integrals.ml | 8 ++++---- .../lib/two_electron_integrals.mli | 8 ++++---- gaussian_integrals/lib/two_electron_rr.ml | 4 ++-- .../lib/two_electron_rr_vectorized.ml | 6 +++--- gaussian_integrals/lib/zero_m_parameters.ml | 4 ++-- gaussian_integrals/test/general_basis.ml | 8 ++++---- linear_algebra/lib/dune | 2 +- linear_algebra/lib/four_idx_storage.ml | 2 +- linear_algebra/lib/spherical_to_cartesian.ml | 2 +- linear_algebra/lib/spherical_to_cartesian.mli | 2 +- linear_algebra/test/vector.ml | 2 +- operators/lib/dune | 2 +- particles/lib/dune | 2 +- particles/lib/electrons.ml | 2 +- particles/lib/electrons.mli | 2 +- particles/lib/element.ml | 2 +- particles/lib/element.mli | 2 +- particles/lib/mass.ml | 2 +- particles/lib/mass.mli | 2 +- particles/lib/nuclei.ml | 2 +- particles/lib/nuclei.mli | 2 +- particles/lib/xyz_ast.mli | 2 +- particles/lib/xyz_parser.mly | 2 +- particles/test/electrons.ml | 4 ++-- particles/test/nuclei.ml | 6 +++--- 75 files changed, 147 insertions(+), 149 deletions(-) diff --git a/ao/lib/basis.ml b/ao/lib/basis.ml index 8434c00..81b46f4 100644 --- a/ao/lib/basis.ml +++ b/ao/lib/basis.ml @@ -1,4 +1,4 @@ -open Qcaml_linear_algebra +open Linear_algebra type basis = | Unknown @@ -14,7 +14,7 @@ let of_nuclei_and_basis_filename ?(kind=`Gaussian) ?operators ?(cartesian=false) match kind with | `Gaussian -> let basis = - Qcaml_gaussian_basis.Basis.of_nuclei_and_basis_filename ~nuclei filename + Gaussian_basis.Basis.of_nuclei_and_basis_filename ~nuclei filename in let ao_basis = Gaussian (Basis_gaussian.make ~basis ?operators ~cartesian nuclei ) diff --git a/ao/lib/basis.mli b/ao/lib/basis.mli index ac3086a..4fdd054 100644 --- a/ao/lib/basis.mli +++ b/ao/lib/basis.mli @@ -1,9 +1,9 @@ (** Data structure for Atomic Orbitals. *) -open Qcaml_common -open Qcaml_particles -open Qcaml_operators -open Qcaml_linear_algebra +open Common +open Particles +open Operators +open Linear_algebra type basis = | Unknown diff --git a/ao/lib/basis_gaussian.ml b/ao/lib/basis_gaussian.ml index 3b1ecd1..36ee919 100644 --- a/ao/lib/basis_gaussian.ml +++ b/ao/lib/basis_gaussian.ml @@ -1,9 +1,9 @@ -open Qcaml_linear_algebra -open Qcaml_gaussian_basis -open Qcaml_gaussian_integrals -open Qcaml_operators +open Linear_algebra +open Gaussian_basis +open Gaussian_integrals +open Operators -module Basis = Qcaml_gaussian_basis.Basis +module Basis = Gaussian_basis.Basis type t = { diff --git a/ao/lib/basis_gaussian.mli b/ao/lib/basis_gaussian.mli index 98d162b..9b62166 100644 --- a/ao/lib/basis_gaussian.mli +++ b/ao/lib/basis_gaussian.mli @@ -1,9 +1,9 @@ (** Data structure for Atomic Orbitals. *) -open Qcaml_common -open Qcaml_particles -open Qcaml_linear_algebra -open Qcaml_gaussian_integrals -open Qcaml_operators +open Common +open Particles +open Linear_algebra +open Gaussian_integrals +open Operators type t @@ -12,7 +12,7 @@ type t val size : t -> int (** Number of atomic orbitals *) -val basis : t -> Qcaml_gaussian_basis.Basis.t +val basis : t -> Gaussian_basis.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 -> Qcaml_gaussian_basis.Basis.t Vector.t +val values : t -> Coordinate.t -> Gaussian_basis.Basis.t Vector.t (** Values of the AOs evaluated at a given point *) (** {1 Creators} *) -val make : basis:Qcaml_gaussian_basis.Basis.t -> ?operators:Operator.t list -> +val make : basis: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} *) diff --git a/ao/lib/dune b/ao/lib/dune index 766f400..379db74 100644 --- a/ao/lib/dune +++ b/ao/lib/dune @@ -1,7 +1,7 @@ ; 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) + (name ao) (public_name qcaml.ao) (libraries qcaml.common diff --git a/ao/test/ao_basis.ml b/ao/test/ao_basis.ml index a655f4e..2a8d359 100644 --- a/ao/test/ao_basis.ml +++ b/ao/test/ao_basis.ml @@ -1,11 +1,10 @@ open Alcotest -open Qcaml_common -open Qcaml_particles -open Qcaml_operators -open Qcaml_linear_algebra -open Qcaml_ao.Basis +open Particles +open Operators +open Linear_algebra +open Ao.Basis -let wd = Qcaml.root ^ Filename.dir_sep ^ "test" +let wd = Common.Qcaml.root ^ Filename.dir_sep ^ "test" let make_tests name t = @@ -90,7 +89,7 @@ let tests = let rs = 0.5 in let operators = [ Operator.of_range_separation rs ] in let ao_basis = - Qcaml_ao.Basis.of_nuclei_and_basis_filename ~kind:`Gaussian + Ao.Basis.of_nuclei_and_basis_filename ~kind:`Gaussian ~operators ~cartesian:false ~nuclei basis_filename in make_tests "water" ao_basis ; diff --git a/ao/test/ao_basis_gaussian.ml b/ao/test/ao_basis_gaussian.ml index 750c4dd..b68d948 100644 --- a/ao/test/ao_basis_gaussian.ml +++ b/ao/test/ao_basis_gaussian.ml @@ -1,13 +1,12 @@ open Alcotest -open Qcaml_common -open Qcaml_gaussian_integrals -open Qcaml_gaussian_basis -open Qcaml_particles -open Qcaml_operators -open Qcaml_linear_algebra -open Qcaml_ao.Basis_gaussian +open Gaussian_integrals +open Gaussian_basis +open Particles +open Operators +open Linear_algebra +open Ao.Basis_gaussian -let wd = Qcaml.root ^ Filename.dir_sep ^ "test" +let wd = Common.Qcaml.root ^ Filename.dir_sep ^ "test" let make_tests name t = @@ -92,7 +91,7 @@ let tests = let rs = 0.5 in let operators = [ Operator.of_range_separation rs ] in let ao_basis = - Qcaml_ao.Basis_gaussian.make ~basis ~operators nuclei + Ao.Basis_gaussian.make ~basis ~operators nuclei in make_tests "water" ao_basis ; diff --git a/common/lib/dune b/common/lib/dune index fa52323..fda41f1 100644 --- a/common/lib/dune +++ b/common/lib/dune @@ -1,7 +1,7 @@ ; 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_common) + (name common) (public_name qcaml.common) (libraries str diff --git a/common/test/bitstring.ml b/common/test/bitstring.ml index 2ef6896..453c6ee 100644 --- a/common/test/bitstring.ml +++ b/common/test/bitstring.ml @@ -1,4 +1,4 @@ -open Qcaml_common.Bitstring +open Common.Bitstring let check msg x = Alcotest.(check bool) msg true x diff --git a/common/test/math_functions.ml b/common/test/math_functions.ml index 5894dcb..3e9c8a2 100644 --- a/common/test/math_functions.ml +++ b/common/test/math_functions.ml @@ -1,4 +1,4 @@ -open Qcaml_common.Util +open Common.Util open Alcotest let test_external () = diff --git a/gaussian_basis/lib/atomic_shell.ml b/gaussian_basis/lib/atomic_shell.ml index 523eabe..1d2f37a 100644 --- a/gaussian_basis/lib/atomic_shell.ml +++ b/gaussian_basis/lib/atomic_shell.ml @@ -1,4 +1,4 @@ -open Qcaml_common +open Common type t = { expo : float array array; diff --git a/gaussian_basis/lib/atomic_shell.mli b/gaussian_basis/lib/atomic_shell.mli index bf0ce0d..9b1860b 100644 --- a/gaussian_basis/lib/atomic_shell.mli +++ b/gaussian_basis/lib/atomic_shell.mli @@ -30,7 +30,7 @@ where: type t -open Qcaml_common +open Common val make : ?index:int -> Contracted_shell.t array -> t (** Creates a contracted shell from a list of coefficients and primitives. *) diff --git a/gaussian_basis/lib/atomic_shell_pair.ml b/gaussian_basis/lib/atomic_shell_pair.ml index 05fa850..10d6956 100644 --- a/gaussian_basis/lib/atomic_shell_pair.ml +++ b/gaussian_basis/lib/atomic_shell_pair.ml @@ -1,4 +1,4 @@ -open Qcaml_common +open Common type t = { diff --git a/gaussian_basis/lib/atomic_shell_pair.mli b/gaussian_basis/lib/atomic_shell_pair.mli index 9c564c8..a72e3ca 100644 --- a/gaussian_basis/lib/atomic_shell_pair.mli +++ b/gaussian_basis/lib/atomic_shell_pair.mli @@ -3,7 +3,7 @@ type t -open Qcaml_common +open Common val make : ?cutoff:float -> Atomic_shell.t -> Atomic_shell.t -> t option diff --git a/gaussian_basis/lib/atomic_shell_pair_couple.ml b/gaussian_basis/lib/atomic_shell_pair_couple.ml index 703a07d..2ed3d53 100644 --- a/gaussian_basis/lib/atomic_shell_pair_couple.ml +++ b/gaussian_basis/lib/atomic_shell_pair_couple.ml @@ -1,4 +1,4 @@ -open Qcaml_common +open Common type t = { diff --git a/gaussian_basis/lib/atomic_shell_pair_couple.mli b/gaussian_basis/lib/atomic_shell_pair_couple.mli index 94f167a..cf46c7f 100644 --- a/gaussian_basis/lib/atomic_shell_pair_couple.mli +++ b/gaussian_basis/lib/atomic_shell_pair_couple.mli @@ -13,7 +13,7 @@ acting on different electrons, since they will be coupled by a two-electron oper type t -open Qcaml_common +open Common val make : ?cutoff:float -> Atomic_shell_pair.t -> Atomic_shell_pair.t -> t option (** Creates an atomic shell pair couple using two atomic shell pairs. diff --git a/gaussian_basis/lib/basis.mli b/gaussian_basis/lib/basis.mli index da5f8c7..f258f8d 100644 --- a/gaussian_basis/lib/basis.mli +++ b/gaussian_basis/lib/basis.mli @@ -2,7 +2,7 @@ type t -open Qcaml_particles +open Particles val of_nuclei_and_general_basis : Nuclei.t -> General_basis.t -> t (** Takes an array of {!Nuclei.t}, and a {!GeneralBasis.t} (such as cc-pVDZ diff --git a/gaussian_basis/lib/contracted_shell.ml b/gaussian_basis/lib/contracted_shell.ml index f558ee6..b3846f1 100644 --- a/gaussian_basis/lib/contracted_shell.ml +++ b/gaussian_basis/lib/contracted_shell.ml @@ -1,4 +1,4 @@ -open Qcaml_common +open Common type t = { expo : float array; diff --git a/gaussian_basis/lib/contracted_shell.mli b/gaussian_basis/lib/contracted_shell.mli index 45ace7d..ec80fdc 100644 --- a/gaussian_basis/lib/contracted_shell.mli +++ b/gaussian_basis/lib/contracted_shell.mli @@ -28,7 +28,7 @@ where: type t -open Qcaml_common +open Common val make : ?index:int -> (float * Primitive_shell.t) array -> t (** Creates a contracted shell from a list of coefficients and primitives. *) diff --git a/gaussian_basis/lib/contracted_shell_pair.ml b/gaussian_basis/lib/contracted_shell_pair.ml index 1946cb1..438ec05 100644 --- a/gaussian_basis/lib/contracted_shell_pair.ml +++ b/gaussian_basis/lib/contracted_shell_pair.ml @@ -1,4 +1,4 @@ -open Qcaml_common +open Common type t = { diff --git a/gaussian_basis/lib/contracted_shell_pair.mli b/gaussian_basis/lib/contracted_shell_pair.mli index 0750ee4..9ad9f27 100644 --- a/gaussian_basis/lib/contracted_shell_pair.mli +++ b/gaussian_basis/lib/contracted_shell_pair.mli @@ -13,7 +13,7 @@ A contracted shell pair is a product of two {!Contracted_shell.t}: type t -open Qcaml_common +open Common val make : ?cutoff:float -> Contracted_shell.t -> Contracted_shell.t -> t option (** Creates an contracted shell pair {% $\varphi_{ab}$ %} from a contracted diff --git a/gaussian_basis/lib/contracted_shell_pair_couple.ml b/gaussian_basis/lib/contracted_shell_pair_couple.ml index 2df01fe..7df7c6a 100644 --- a/gaussian_basis/lib/contracted_shell_pair_couple.ml +++ b/gaussian_basis/lib/contracted_shell_pair_couple.ml @@ -1,4 +1,4 @@ -open Qcaml_common +open Common type t = { diff --git a/gaussian_basis/lib/contracted_shell_pair_couple.mli b/gaussian_basis/lib/contracted_shell_pair_couple.mli index 7680bfb..24d615d 100644 --- a/gaussian_basis/lib/contracted_shell_pair_couple.mli +++ b/gaussian_basis/lib/contracted_shell_pair_couple.mli @@ -13,7 +13,7 @@ acting on different electrons, since they will be coupled by a two-electron oper type t -open Qcaml_common +open Common val make : ?cutoff:float -> Contracted_shell_pair.t -> Contracted_shell_pair.t -> t option (** Creates a contracted shell pair couple using two contracted shell pairs. diff --git a/gaussian_basis/lib/dune b/gaussian_basis/lib/dune index bc8f66e..3922710 100644 --- a/gaussian_basis/lib/dune +++ b/gaussian_basis/lib/dune @@ -1,7 +1,7 @@ ; 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_gaussian_basis) + (name gaussian_basis) (public_name qcaml.gaussian_basis) (libraries str diff --git a/gaussian_basis/lib/general_basis.ml b/gaussian_basis/lib/general_basis.ml index fc6a819..c1e67c6 100644 --- a/gaussian_basis/lib/general_basis.ml +++ b/gaussian_basis/lib/general_basis.ml @@ -1,7 +1,7 @@ (** General basis set read from a file *) -open Qcaml_common -open Qcaml_particles +open Common +open Particles type primitive = { diff --git a/gaussian_basis/lib/general_basis.mli b/gaussian_basis/lib/general_basis.mli index b2f4376..f087e6c 100644 --- a/gaussian_basis/lib/general_basis.mli +++ b/gaussian_basis/lib/general_basis.mli @@ -28,8 +28,8 @@ are created by picking the data from the general basis set. This data structure simplifies the creation of the atomic basis set. *) -open Qcaml_common -open Qcaml_particles +open Common +open Particles type primitive = private { diff --git a/gaussian_basis/lib/primitive_shell.ml b/gaussian_basis/lib/primitive_shell.ml index 794142c..2ce25fb 100644 --- a/gaussian_basis/lib/primitive_shell.ml +++ b/gaussian_basis/lib/primitive_shell.ml @@ -1,4 +1,4 @@ -open Qcaml_common +open Common open Util open Constants diff --git a/gaussian_basis/lib/primitive_shell.mli b/gaussian_basis/lib/primitive_shell.mli index 8647b62..02581eb 100644 --- a/gaussian_basis/lib/primitive_shell.mli +++ b/gaussian_basis/lib/primitive_shell.mli @@ -20,7 +20,7 @@ where: type t -open Qcaml_common +open Common val to_string : t -> string (** Pretty-printing of the primitive shell in a string. *) diff --git a/gaussian_basis/lib/primitive_shell_pair.ml b/gaussian_basis/lib/primitive_shell_pair.ml index b64df39..cc13fe0 100644 --- a/gaussian_basis/lib/primitive_shell_pair.ml +++ b/gaussian_basis/lib/primitive_shell_pair.ml @@ -1,4 +1,4 @@ -open Qcaml_common +open Common open Constants diff --git a/gaussian_basis/lib/primitive_shell_pair.mli b/gaussian_basis/lib/primitive_shell_pair.mli index be2ec7e..78da50d 100644 --- a/gaussian_basis/lib/primitive_shell_pair.mli +++ b/gaussian_basis/lib/primitive_shell_pair.mli @@ -37,7 +37,7 @@ References: type t -open Qcaml_common +open Common val make : Primitive_shell.t -> Primitive_shell.t -> t (** Creates a primitive shell pair using two primitive shells. *) diff --git a/gaussian_basis/lib/primitive_shell_pair_couple.ml b/gaussian_basis/lib/primitive_shell_pair_couple.ml index 2b51122..5508fb2 100644 --- a/gaussian_basis/lib/primitive_shell_pair_couple.ml +++ b/gaussian_basis/lib/primitive_shell_pair_couple.ml @@ -1,4 +1,4 @@ -open Qcaml_common +open Common type t = { diff --git a/gaussian_basis/lib/primitive_shell_pair_couple.mli b/gaussian_basis/lib/primitive_shell_pair_couple.mli index b721603..35eefa2 100644 --- a/gaussian_basis/lib/primitive_shell_pair_couple.mli +++ b/gaussian_basis/lib/primitive_shell_pair_couple.mli @@ -13,7 +13,7 @@ acting on different electrons, since they will be coupled by a two-electron oper type t -open Qcaml_common +open Common val make : Primitive_shell_pair.t -> Primitive_shell_pair.t -> t (** Creates a primitive shell pair couple using two primitive shell pairs. diff --git a/gaussian_basis/test/general_basis.ml b/gaussian_basis/test/general_basis.ml index f262a43..c0df59d 100644 --- a/gaussian_basis/test/general_basis.ml +++ b/gaussian_basis/test/general_basis.ml @@ -1,9 +1,9 @@ -open Qcaml_common -open Qcaml_particles -open Qcaml_gaussian_basis +open Common +open Particles +open Gaussian_basis open Alcotest -let wd = Qcaml.root ^ Filename.dir_sep ^ "test" +let wd = Common.Qcaml.root ^ Filename.dir_sep ^ "test" let test_read () = let oxygen = Element.of_string "O" in diff --git a/gaussian_integrals/lib/dune b/gaussian_integrals/lib/dune index d5c4472..8bde0cc 100644 --- a/gaussian_integrals/lib/dune +++ b/gaussian_integrals/lib/dune @@ -1,7 +1,7 @@ ; 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_gaussian_integrals) + (name gaussian_integrals) (public_name qcaml.gaussian_integrals) (libraries str diff --git a/gaussian_integrals/lib/electron_nucleus.ml b/gaussian_integrals/lib/electron_nucleus.ml index 9be045c..022db9b 100644 --- a/gaussian_integrals/lib/electron_nucleus.ml +++ b/gaussian_integrals/lib/electron_nucleus.ml @@ -1,9 +1,9 @@ (** Electron-nucleus repulsion integrals *) -include Qcaml_common -include Qcaml_particles -include Qcaml_linear_algebra -include Qcaml_gaussian_basis +include Common +include Particles +include Linear_algebra +include Gaussian_basis open Util open Constants diff --git a/gaussian_integrals/lib/electron_nucleus.mli b/gaussian_integrals/lib/electron_nucleus.mli index 12ee05f..cc3c1d1 100644 --- a/gaussian_integrals/lib/electron_nucleus.mli +++ b/gaussian_integrals/lib/electron_nucleus.mli @@ -8,8 +8,8 @@ $$ %} include module type of Matrix_on_basis -open Qcaml_particles -open Qcaml_gaussian_basis +open Particles +open Gaussian_basis val of_basis_nuclei : basis:Basis.t -> Nuclei.t -> t (** Build from a {Basis.t} and the nuclei (coordinates and charges). *) diff --git a/gaussian_integrals/lib/eri.ml b/gaussian_integrals/lib/eri.ml index b8c7640..b04d279 100644 --- a/gaussian_integrals/lib/eri.ml +++ b/gaussian_integrals/lib/eri.ml @@ -1,7 +1,7 @@ (** Electron-electron repulsion integrals *) -open Qcaml_common -open Qcaml_gaussian_basis +open Common +open Gaussian_basis module Csp = Contracted_shell_pair module Cspc = Contracted_shell_pair_couple diff --git a/gaussian_integrals/lib/eri_long_range.ml b/gaussian_integrals/lib/eri_long_range.ml index 101d556..c524396 100644 --- a/gaussian_integrals/lib/eri_long_range.ml +++ b/gaussian_integrals/lib/eri_long_range.ml @@ -2,9 +2,9 @@ See Eq(52) in 10.1039/b605188j *) -open Qcaml_common -open Qcaml_gaussian_basis -open Qcaml_operators +open Common +open Gaussian_basis +open Operators module Csp = Contracted_shell_pair module Cspc = Contracted_shell_pair_couple diff --git a/gaussian_integrals/lib/f12.ml b/gaussian_integrals/lib/f12.ml index 1f9b69e..8a4c678 100644 --- a/gaussian_integrals/lib/f12.ml +++ b/gaussian_integrals/lib/f12.ml @@ -2,8 +2,8 @@ It is parameterized by the [zero_m] function. *) -open Qcaml_common -open Qcaml_operators +open Common +open Operators open Constants let cutoff = integrals_cutoff diff --git a/gaussian_integrals/lib/f12_rr.ml b/gaussian_integrals/lib/f12_rr.ml index 5af2337..bd72dec 100644 --- a/gaussian_integrals/lib/f12_rr.ml +++ b/gaussian_integrals/lib/f12_rr.ml @@ -1,5 +1,5 @@ -open Qcaml_common -open Qcaml_gaussian_basis +open Common +open Gaussian_basis module Am = Angular_momentum module Asp = Atomic_shell_pair diff --git a/gaussian_integrals/lib/kinetic.ml b/gaussian_integrals/lib/kinetic.ml index 594cd54..5bbc75d 100644 --- a/gaussian_integrals/lib/kinetic.ml +++ b/gaussian_integrals/lib/kinetic.ml @@ -1,6 +1,6 @@ -open Qcaml_common -open Qcaml_linear_algebra -open Qcaml_gaussian_basis +open Common +open Linear_algebra +open Gaussian_basis open Util open Constants diff --git a/gaussian_integrals/lib/matrix_on_basis.mli b/gaussian_integrals/lib/matrix_on_basis.mli index c02f4b2..41a4a37 100644 --- a/gaussian_integrals/lib/matrix_on_basis.mli +++ b/gaussian_integrals/lib/matrix_on_basis.mli @@ -1,7 +1,7 @@ (** Signature for matrices built on the {!Basis.t} *) -open Qcaml_gaussian_basis -open Qcaml_linear_algebra +open Gaussian_basis +open Linear_algebra type t = (Basis.t, Basis.t) Matrix.t diff --git a/gaussian_integrals/lib/multipole.ml b/gaussian_integrals/lib/multipole.ml index 7668fbb..b8e92ea 100644 --- a/gaussian_integrals/lib/multipole.ml +++ b/gaussian_integrals/lib/multipole.ml @@ -1,6 +1,6 @@ -open Qcaml_common -open Qcaml_linear_algebra -open Qcaml_gaussian_basis +open Common +open Linear_algebra +open Gaussian_basis open Constants type t = (Basis.t, Basis.t) Matrix.t array diff --git a/gaussian_integrals/lib/multipole.mli b/gaussian_integrals/lib/multipole.mli index 5a88a8e..cbeeae8 100644 --- a/gaussian_integrals/lib/multipole.mli +++ b/gaussian_integrals/lib/multipole.mli @@ -9,8 +9,8 @@ *) -open Qcaml_linear_algebra -open Qcaml_gaussian_basis +open Linear_algebra +open Gaussian_basis type t = (Basis.t, Basis.t) Matrix.t array diff --git a/gaussian_integrals/lib/one_electron_rr.ml b/gaussian_integrals/lib/one_electron_rr.ml index 5425b30..0636d5c 100644 --- a/gaussian_integrals/lib/one_electron_rr.ml +++ b/gaussian_integrals/lib/one_electron_rr.ml @@ -1,8 +1,8 @@ -open Qcaml_common -open Qcaml_particles +open Common +open Particles open Util open Constants -open Qcaml_gaussian_basis +open Gaussian_basis exception NullPair diff --git a/gaussian_integrals/lib/orthonormalization.ml b/gaussian_integrals/lib/orthonormalization.ml index a28fc36..1d1c1c6 100644 --- a/gaussian_integrals/lib/orthonormalization.ml +++ b/gaussian_integrals/lib/orthonormalization.ml @@ -1,6 +1,6 @@ -open Qcaml_common -open Qcaml_linear_algebra -open Qcaml_gaussian_basis +open Common +open Linear_algebra +open Gaussian_basis module Am = Angular_momentum module Bs = Basis diff --git a/gaussian_integrals/lib/orthonormalization.mli b/gaussian_integrals/lib/orthonormalization.mli index bc69a4c..6e8d8b6 100644 --- a/gaussian_integrals/lib/orthonormalization.mli +++ b/gaussian_integrals/lib/orthonormalization.mli @@ -1,7 +1,7 @@ (** Orthonormalization of the basis. *) -open Qcaml_gaussian_basis -open Qcaml_linear_algebra +open Gaussian_basis +open Linear_algebra type t = (Basis.t, Basis.t) Matrix.t diff --git a/gaussian_integrals/lib/overlap.ml b/gaussian_integrals/lib/overlap.ml index c5427da..b22bd89 100644 --- a/gaussian_integrals/lib/overlap.ml +++ b/gaussian_integrals/lib/overlap.ml @@ -1,6 +1,6 @@ -open Qcaml_common -open Qcaml_linear_algebra -open Qcaml_gaussian_basis +open Common +open Linear_algebra +open Gaussian_basis open Util open Constants diff --git a/gaussian_integrals/lib/overlap_primitives.ml b/gaussian_integrals/lib/overlap_primitives.ml index 902b2b0..92e46dc 100644 --- a/gaussian_integrals/lib/overlap_primitives.ml +++ b/gaussian_integrals/lib/overlap_primitives.ml @@ -1,4 +1,4 @@ -open Qcaml_common +open Common open Util diff --git a/gaussian_integrals/lib/screened_eri.ml b/gaussian_integrals/lib/screened_eri.ml index 2016e82..28573b3 100644 --- a/gaussian_integrals/lib/screened_eri.ml +++ b/gaussian_integrals/lib/screened_eri.ml @@ -1,8 +1,8 @@ (** Screened Electron-electron repulsion integrals (Yukawa potential). Required for F12/r12. *) -open Qcaml_common -open Qcaml_gaussian_basis -open Qcaml_operators +open Common +open Gaussian_basis +open Operators module Csp = Contracted_shell_pair module Cspc = Contracted_shell_pair_couple diff --git a/gaussian_integrals/lib/two_electron_integrals.ml b/gaussian_integrals/lib/two_electron_integrals.ml index 100ba7b..6601792 100644 --- a/gaussian_integrals/lib/two_electron_integrals.ml +++ b/gaussian_integrals/lib/two_electron_integrals.ml @@ -1,10 +1,10 @@ (** Two electron integrals *) -open Qcaml_common -open Qcaml_linear_algebra -open Qcaml_gaussian_basis -open Qcaml_operators +open Common +open Linear_algebra +open Gaussian_basis +open Operators open Constants let cutoff = integrals_cutoff diff --git a/gaussian_integrals/lib/two_electron_integrals.mli b/gaussian_integrals/lib/two_electron_integrals.mli index ba1ed14..d78a7fd 100644 --- a/gaussian_integrals/lib/two_electron_integrals.mli +++ b/gaussian_integrals/lib/two_electron_integrals.mli @@ -5,10 +5,10 @@ *) -open Qcaml_common -open Qcaml_gaussian_basis -open Qcaml_linear_algebra -open Qcaml_operators +open Common +open Gaussian_basis +open Linear_algebra +open Operators module type Two_ei_structure = sig diff --git a/gaussian_integrals/lib/two_electron_rr.ml b/gaussian_integrals/lib/two_electron_rr.ml index 4e6c482..1dac495 100644 --- a/gaussian_integrals/lib/two_electron_rr.ml +++ b/gaussian_integrals/lib/two_electron_rr.ml @@ -1,5 +1,5 @@ -open Qcaml_common -open Qcaml_gaussian_basis +open Common +open Gaussian_basis module Am = Angular_momentum module Asp = Atomic_shell_pair diff --git a/gaussian_integrals/lib/two_electron_rr_vectorized.ml b/gaussian_integrals/lib/two_electron_rr_vectorized.ml index 72ede4a..789d9ea 100644 --- a/gaussian_integrals/lib/two_electron_rr_vectorized.ml +++ b/gaussian_integrals/lib/two_electron_rr_vectorized.ml @@ -1,6 +1,6 @@ -open Qcaml_common -open Qcaml_gaussian_basis -open Qcaml_linear_algebra +open Common +open Gaussian_basis +open Linear_algebra module Am = Angular_momentum module Co = Coordinate diff --git a/gaussian_integrals/lib/zero_m_parameters.ml b/gaussian_integrals/lib/zero_m_parameters.ml index 996771d..a94efaa 100644 --- a/gaussian_integrals/lib/zero_m_parameters.ml +++ b/gaussian_integrals/lib/zero_m_parameters.ml @@ -1,5 +1,5 @@ -open Qcaml_common -open Qcaml_operators +open Common +open Operators type t = { diff --git a/gaussian_integrals/test/general_basis.ml b/gaussian_integrals/test/general_basis.ml index faf4dc8..59dd7a7 100644 --- a/gaussian_integrals/test/general_basis.ml +++ b/gaussian_integrals/test/general_basis.ml @@ -1,9 +1,9 @@ -open Qcaml_common -open Qcaml_particles -open Qcaml_gaussian_basis +open Common +open Particles +open Gaussian_basis open Alcotest -let wd = Qcaml.root ^ Filename.dir_sep ^ "test" +let wd = Common.Qcaml.root ^ Filename.dir_sep ^ "test" let test_read () = let oxygen = Element.of_string "O" in diff --git a/linear_algebra/lib/dune b/linear_algebra/lib/dune index 1423256..365a5c3 100644 --- a/linear_algebra/lib/dune +++ b/linear_algebra/lib/dune @@ -1,7 +1,7 @@ ; 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_linear_algebra) + (name linear_algebra) (public_name qcaml.linear_algebra) (libraries qcaml.common diff --git a/linear_algebra/lib/four_idx_storage.ml b/linear_algebra/lib/four_idx_storage.ml index b61ac85..5c97ea8 100644 --- a/linear_algebra/lib/four_idx_storage.ml +++ b/linear_algebra/lib/four_idx_storage.ml @@ -1,4 +1,4 @@ -open Qcaml_common +open Common let max_index = 1 lsl 14 diff --git a/linear_algebra/lib/spherical_to_cartesian.ml b/linear_algebra/lib/spherical_to_cartesian.ml index 9c76407..f89d9a9 100644 --- a/linear_algebra/lib/spherical_to_cartesian.ml +++ b/linear_algebra/lib/spherical_to_cartesian.ml @@ -1,4 +1,4 @@ -open Qcaml_common +open Common module Am = Angular_momentum diff --git a/linear_algebra/lib/spherical_to_cartesian.mli b/linear_algebra/lib/spherical_to_cartesian.mli index ae62078..65a3bea 100644 --- a/linear_algebra/lib/spherical_to_cartesian.mli +++ b/linear_algebra/lib/spherical_to_cartesian.mli @@ -1,6 +1,6 @@ (** Conversion from spherical coordinate to cartesian corrdinates. *) -open Qcaml_common +open Common type num_cartesian_ao type num_spherical_ao diff --git a/linear_algebra/test/vector.ml b/linear_algebra/test/vector.ml index fca07ca..99fee9e 100644 --- a/linear_algebra/test/vector.ml +++ b/linear_algebra/test/vector.ml @@ -1,4 +1,4 @@ -open Qcaml_linear_algebra +open Linear_algebra open Alcotest open Lacaml.D diff --git a/operators/lib/dune b/operators/lib/dune index 2ca47b9..4b7d2b2 100644 --- a/operators/lib/dune +++ b/operators/lib/dune @@ -1,7 +1,7 @@ ; 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_operators) + (name operators) (public_name qcaml.operators) (libraries str diff --git a/particles/lib/dune b/particles/lib/dune index 35d7d1d..2424274 100644 --- a/particles/lib/dune +++ b/particles/lib/dune @@ -1,7 +1,7 @@ ; 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_particles) + (name particles) (public_name qcaml.particles) (libraries str diff --git a/particles/lib/electrons.ml b/particles/lib/electrons.ml index 970845b..0c382c7 100644 --- a/particles/lib/electrons.ml +++ b/particles/lib/electrons.ml @@ -1,6 +1,6 @@ (** Number of {% $\alpha$ %} and {% $\beta$ %} electrons *) -open Qcaml_common +open Common type t = { n_alfa : int ; diff --git a/particles/lib/electrons.mli b/particles/lib/electrons.mli index 6775380..eb66b1b 100644 --- a/particles/lib/electrons.mli +++ b/particles/lib/electrons.mli @@ -1,6 +1,6 @@ (** Information related to electrons. *) -open Qcaml_common +open Common type t diff --git a/particles/lib/element.ml b/particles/lib/element.ml index c85b2ad..65dbdeb 100644 --- a/particles/lib/element.ml +++ b/particles/lib/element.ml @@ -1,4 +1,4 @@ -open Qcaml_common +open Common exception ElementError of string diff --git a/particles/lib/element.mli b/particles/lib/element.mli index 3463903..0133206 100644 --- a/particles/lib/element.mli +++ b/particles/lib/element.mli @@ -1,6 +1,6 @@ (** Chemical elements. *) -open Qcaml_common +open Common exception ElementError of string diff --git a/particles/lib/mass.ml b/particles/lib/mass.ml index 112464f..3fec2d3 100644 --- a/particles/lib/mass.ml +++ b/particles/lib/mass.ml @@ -1,3 +1,3 @@ (** Atomic mass. *) -include Qcaml_common.Non_negative_float +include Common.Non_negative_float diff --git a/particles/lib/mass.mli b/particles/lib/mass.mli index ff76a11..cd230dc 100644 --- a/particles/lib/mass.mli +++ b/particles/lib/mass.mli @@ -1,3 +1,3 @@ (** Atomic mass. *) -include module type of Qcaml_common.Non_negative_float +include module type of Common.Non_negative_float diff --git a/particles/lib/nuclei.ml b/particles/lib/nuclei.ml index ae028f7..d5de19e 100644 --- a/particles/lib/nuclei.ml +++ b/particles/lib/nuclei.ml @@ -1,4 +1,4 @@ -open Qcaml_common +open Common open Xyz_ast type t = (Element.t * Coordinate.t) array diff --git a/particles/lib/nuclei.mli b/particles/lib/nuclei.mli index 6349d79..1947b5a 100644 --- a/particles/lib/nuclei.mli +++ b/particles/lib/nuclei.mli @@ -2,7 +2,7 @@ of tuples ({!Element.t}, {!Coordinate.t}). *) -open Qcaml_common +open Common type t = (Element.t * Coordinate.t) array diff --git a/particles/lib/xyz_ast.mli b/particles/lib/xyz_ast.mli index 335f0ad..2205522 100644 --- a/particles/lib/xyz_ast.mli +++ b/particles/lib/xyz_ast.mli @@ -1,7 +1,7 @@ (** When an [xyz] file is read by the [Xyz_parser.mly], it is converted into an {!xyz_file} data structure. *) -open Qcaml_common +open Common type nucleus = { diff --git a/particles/lib/xyz_parser.mly b/particles/lib/xyz_parser.mly index adc4bd0..3b54b6d 100644 --- a/particles/lib/xyz_parser.mly +++ b/particles/lib/xyz_parser.mly @@ -1,7 +1,7 @@ /* Parses nuclear coordinates in xyz format */ %{ -open Qcaml_common +open Common let make_angstrom x y z = Coordinate.(make_angstrom { diff --git a/particles/test/electrons.ml b/particles/test/electrons.ml index d8aae87..c60a834 100644 --- a/particles/test/electrons.ml +++ b/particles/test/electrons.ml @@ -1,5 +1,5 @@ -open Qcaml_common -open Qcaml_particles +open Common +open Particles open Alcotest diff --git a/particles/test/nuclei.ml b/particles/test/nuclei.ml index 74a83ac..1366a69 100644 --- a/particles/test/nuclei.ml +++ b/particles/test/nuclei.ml @@ -1,8 +1,8 @@ -open Qcaml_common -open Qcaml_particles +open Common +open Particles open Alcotest -let wd = Qcaml.root ^ Filename.dir_sep ^ "test" +let wd = Common.Qcaml.root ^ Filename.dir_sep ^ "test" let test_xyz molecule length repulsion charge core = let xyz = Nuclei.of_xyz_file (wd^Filename.dir_sep^molecule^".xyz") in