mirror of https://gitlab.com/scemama/QCaml.git
Documentation
This commit is contained in:
parent
c23821e098
commit
8918f49302
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@ -0,0 +1,28 @@
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let () =
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try Topdirs.dir_directory (Sys.getenv "OCAML_TOPLEVEL_PATH")
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with Not_found -> ()
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;;
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#use "topfind";;
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#require "lacaml";;
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#directory "_build";;
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#directory "_build/Utils";;
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#directory "_build/Basis";;
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#directory "_build/HartreeFock";;
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#load "Powers.cmo";;
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#load "Zkey.cmo";;
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#load "AngularMomentum.cmo";;
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#load "Constants.cmo";;
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#load "Util.cmo";;
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#load "Coordinate.cmo";;
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#load "Zmap.cmo";;
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#load "Zkey.cmo";;
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#load "ContractedShell.cmo";;
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#load "ShellPair.cmo";;
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#load "TwoElectronRR.cmo";;
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#load "ERI.cmo";;
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#use "topfind";;
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@ -10,6 +10,8 @@ module Bs = Basis
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module Cs = ContractedShell
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module Csp = ContractedShellPair
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let cutoff = integrals_cutoff
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(** (00|00)^m : Fundamental electron repulsion integral
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$ \int \int \phi_p(r1) 1/r_{12} \phi_q(r2) dr_1 dr_2 $
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@ -11,6 +11,7 @@ module Sp = ShellPair
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type t = Mat.t
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let cutoff = integrals_cutoff
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(** Computes all the kinetic integrals of the contracted shell pair *)
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let contracted_class shell_a shell_b : float Zmap.t =
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@ -33,6 +33,8 @@ let contracted_class_shell_pair shell_p geometry: float Zmap.t =
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OneElectronRR.contracted_class_shell_pair ~zero_m shell_p geometry
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let cutoff = integrals_cutoff
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let cutoff2 = cutoff *. cutoff
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exception NullIntegral
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@ -10,11 +10,6 @@ module Csp = ContractedShellPair
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module Po = Powers
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module Sp = ShellPair
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(** In chop f g, evaluate g only if f is non zero, and return f *. (g ()) *)
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let chop f g =
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if (abs_float f) < cutoff then 0.
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else f *. (g ())
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(** Horizontal and Vertical Recurrence Relations (HVRR) *)
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@ -84,7 +79,7 @@ let hvrr_one_e angMom_a angMom_b
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let bm = Po.decr xyz angMom_b in
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let h1 = hrr ap bm in
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let f2 = Co.get xyz center_ab in
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if abs_float f2 < cutoff then h1 else
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if abs_float f2 < integrals_cutoff then h1 else
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let h2 = hrr angMom_a bm in
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h1 +. f2 *. h2
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@ -130,7 +125,7 @@ let contracted_class_shell_pair ~zero_m shell_p geometry : float Zmap.t =
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let coef_prod = shell_p.Csp.coef.(ab) in
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(** Screening on the product of coefficients *)
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if abs_float coef_prod < 1.e-3 *. cutoff then
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if abs_float coef_prod < 1.e-3 *. integrals_cutoff then
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raise NullPair;
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@ -11,6 +11,8 @@ module Cs = ContractedShell
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module Csp = ContractedShellPair
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module Sp = ShellPair
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let cutoff = integrals_cutoff
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(** Computes all the overlap integrals of the contracted shell pair *)
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let contracted_class shell_a shell_b : float Zmap.t =
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@ -45,7 +47,7 @@ let contracted_class shell_a shell_b : float Zmap.t =
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shell_p.Csp.coef.(ab)
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in
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(** Screening on thr product of coefficients *)
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if (abs_float coef_prod) > 1.e-4*.cutoff then
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if (abs_float coef_prod) > 1.e-3*.cutoff then
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begin
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let expo_inv =
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shell_p.Csp.expo_inv.(ab)
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@ -1,5 +1,4 @@
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open Util
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open Constants
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module Am = AngularMomentum
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module Co = Coordinate
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@ -8,8 +7,7 @@ module Csp = ContractedShellPair
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module Sp = ShellPair
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module Po = Powers
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let debug=false
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let cutoff = Constants.integrals_cutoff
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let cutoff2 = cutoff *. cutoff
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exception NullQuartet
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@ -11,7 +11,7 @@ module Po = Powers
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exception NullQuartet
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exception Found
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let cutoff = Constants.cutoff
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let cutoff = Constants.integrals_cutoff
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let cutoff2 = cutoff *. cutoff
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let at_least_one_valid arr =
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7
Makefile
7
Makefile
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@ -11,7 +11,9 @@ MLLFILES=$(wildcard */*.mll) $(wildcard *.mll) Utils/math_functions.c
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MLYFILES=$(wildcard */*.mly) $(wildcard *.mly)
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MLFILES= $(wildcard */*.ml) $(wildcard *.ml)
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MLIFILES=$(wildcard */*.mli) $(wildcard *.mli)
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ALL_EXE=$(patsubst %.ml,%.native,$(wildcard run_*.ml))
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ALL_NATIVE=$(patsubst %.ml,%.native,$(wildcard run_*.ml))
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ALL_BYTE=$(patsubst %.ml,%.byte,$(wildcard run_*.ml))
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ALL_EXE=$(ALL_BYTE) $(ALL_NATIVE)
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.PHONY: default
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@ -32,7 +34,6 @@ doc: qpackage.odocl
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%.byte: $(MLFILES) $(MLIFILES) $(MLLFILES) $(MLYFILES)
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rm -f -- $*
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$(OCAMLBUILD) $*.byte -use-ocamlfind $(PKGS)
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ln -s $*.byte $*
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%.native: $(MLFILES) $(MLIFILES) $(MLLFILES) $(MLYFILES)
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rm -f -- $*
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@ -42,12 +43,10 @@ doc: qpackage.odocl
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%.p.native: $(MLFILES) $(MLIFILES) $(MLLFILES) $(MLYFILES)
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rm -f -- $*
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$(OCAMLBUILD) $*.p.native -use-ocamlfind $(PKGS)
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ln -s $*.p.native $*
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%.p.byte: $(MLFILES) $(MLIFILES) $(MLLFILES) $(MLYFILES)
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rm -f -- $*
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$(OCAMLBUILD) -ocamlc ocamlcp $*.byte -use-ocamlfind $(PKGS)
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ln -s $*.byte $*
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clean:
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rm -rf _build $(ALL_EXE) $(ALL_TESTS) *.native *.byte
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@ -141,7 +141,7 @@ let covalent_radius x =
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| Te -> 1.38 | I -> 1.39 | Xe -> 1.40 | Pt -> 1.30
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in
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Constants.a0 *. (result x)
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|> Radius.of_float
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|> NonNegativeFloat.of_float
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let vdw_radius x =
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@ -162,7 +162,7 @@ let vdw_radius x =
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| Te -> 2.06 | I -> 1.98 | Xe -> 2.16 | Pt -> 1.75
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in
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Constants.a0 *. (result x)
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|> Radius.of_float
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|> NonNegativeFloat.of_float
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let mass c =
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@ -20,6 +20,6 @@ val to_int : t -> int
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val of_int : int -> t
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val to_charge : t -> Charge.t
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val of_charge : Charge.t -> t
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val covalent_radius : t -> Radius.t
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val vdw_radius : t -> Radius.t
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val covalent_radius : t -> NonNegativeFloat.t
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val vdw_radius : t -> NonNegativeFloat.t
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val mass : t -> Mass.t
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@ -1 +1 @@
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include PositiveFloat
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include NonNegativeFloat
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@ -1,12 +1 @@
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type t = {
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x : float ;
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y : float ;
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z : float ;
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}
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let make { Point.x ; y ; z } = { x ; y ; z }
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(* = %identity *)
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include Bohr
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@ -1,3 +1,5 @@
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(** 3D point in cartesian coordinates, where units are Angstroms. *)
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type t = private {
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x : float ;
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y : float ;
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@ -7,4 +9,3 @@ type t = private {
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val make : Point.t -> t
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@ -0,0 +1,87 @@
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(** Azimuthal quantum number, represented as s,p,d,... *)
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type t = S | P | D | F | G | H | I | J | K | L | M | N | O
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exception AngularMomentumError of string
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(** Raised when the {!AngularMomentum.t} element can't be created.
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*)
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val of_char : char -> t
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(** Returns an {!AngularMomentum.t} when a shell is given as a character (case
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insensitive).
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Example:
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[AngularMomentum.of_char 'p' -> AngularMomentum.P]
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*)
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val to_string : t -> string
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(**
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[AngularMomentum.(to_string D) -> "D"]
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*)
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val to_char : t -> char
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(**
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[AngularMomentum.(to_char D) -> 'D']
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*)
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val to_int : t -> int
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(**
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Returns the l{_max} value of the shell.
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Example:
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[AngularMomentum.of_int 3 -> AngularMomentum.F]
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*)
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val of_int : int -> t
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(**
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Opposite of {!of_int}.
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Example:
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[AngularMomentum.of_int 3 -> AngularMomentum.F]
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*)
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type kind =
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Singlet of t
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| Doublet of (t * t)
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| Triplet of (t * t * t)
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| Quartet of (t * t * t * t)
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val n_functions : t -> int
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(** Number of cartesian functions in shell.
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Example:
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[AngularMomentum.n_functions D -> 6]
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*)
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val zkey_array : kind -> Zkey.t array
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(** Array of {!Zkey.t}, where each element is a a key associated with the
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the powers of x,y,z.
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Example:
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{[
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AngularMomentum.( zkey_array Doublet (P,S) ) ->
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[| {Zkey.left = 0; right = 1125899906842624} ;
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{Zkey.left = 0; right = 1099511627776} ;
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{Zkey.left = 0; right = 1073741824} |]
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=
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let s,x,y,z =
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Powers.( of_int_tuple (0,0,0),
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of_int_tuple (1,0,0),
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of_int_tuple (0,1,0),
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of_int_tuple (0,0,1) )
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in
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Array.map (fun (a,b) -> {!Zkey.of_powers_six} a b)
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[| (x,s) ; (y,s) ; (z,s) |]
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]}
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*)
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@ -5,8 +5,7 @@ type t = {
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}
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let make { Point.x ; y ; z } = { x ; y ; z }
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(* = %identity *)
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external make : Point.t -> t = "%identity"
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@ -1,3 +1,5 @@
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(** 3D point in cartesian coordinates, where units are atomic units (Bohr). *)
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type t = private {
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x : float ;
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y : float ;
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@ -1,4 +1,5 @@
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let cutoff = 1.e-15
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let integrals_cutoff = 1.e-15
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let epsilon = 1.e-20
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(** Constants *)
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let pi = acos (-1.)
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@ -7,5 +8,5 @@ let sq_pi_over_two = sq_pi *. 0.5
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let pi_inv = 1. /. pi
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let two_over_sq_pi = 2. /. (sqrt pi)
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let a0 = 0.529_177_210_67
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let a0 = 0.529_177_210_671_2
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let a0_inv = 1. /. a0
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|
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@ -1,8 +1,26 @@
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val cutoff : float
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val epsilon : float
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(** Value below which a float is considered null. Default is 10{^-20}. *)
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val integrals_cutoff : float
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(** Cutoff value for integrals. Default is 10{^-15}. *)
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val pi : float
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(** pi = 3.141_592_653_589_793_12 *)
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val sq_pi : float
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(** [sqrt pi] *)
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val sq_pi_over_two : float
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(** [(sqrt pi) /. 2.] *)
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val pi_inv : float
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(** [ 1. /. pi ] *)
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val two_over_sq_pi : float
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(** [ 2. /. (sqrt pi) ] *)
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val a0 : float
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(** Bohr radius : a{_0} = 0.529_177_210_671_2 Angstrom *)
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val a0_inv : float
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(** [ 1. /. a0 ] *)
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|
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@ -1,12 +1,6 @@
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type point = Point.t
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type bohr = Bohr.t
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type angstrom = Angstrom.t
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let a_to_b a = Constants.a0_inv *. a
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let b_to_a b = Constants.a0 *. b
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let bohr_to_angstrom { Bohr.x ; y ; z } =
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let b_to_a b = Constants.a0 *. b in
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Angstrom.make
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{
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Point.
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@ -15,7 +9,10 @@ let bohr_to_angstrom { Bohr.x ; y ; z } =
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z = b_to_a z ;
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}
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let angstrom_to_bohr { Angstrom.x ; y ; z } =
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let a_to_b a = Constants.a0_inv *. a in
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Bohr.make
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{
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Point.
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|
@ -24,3 +21,4 @@ let angstrom_to_bohr { Angstrom.x ; y ; z } =
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z = a_to_b z ;
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}
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|
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|
|
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|
|
@ -1,3 +1,6 @@
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(** Coordinate_type can be Bohr or Angstrom. This module provides the conversion
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functions from {!Bohr.t} to {!Angstrom.t} and from {!Angstrom.t} to {!Bohr.t} *)
|
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type bohr = Bohr.t
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type angstrom = Angstrom.t
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|
|
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|
@ -0,0 +1,17 @@
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(** Information related to electrons. *)
|
||||
|
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type t = {
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n_alpha : int ; (** Number of alpha electrons *)
|
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n_beta : int ; (** Number of beta electrons *)
|
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multiplicity : int; (** Spin multiplicity: 2S+1 *)
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}
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||||
|
||||
|
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val make : ?multiplicity:int -> ?charge:int -> Nuclei.t -> t
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(** Creates the data relative to electrons for a molecular system
|
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described by {!Nuclei.t} for a given total charge and spin multiplicity.
|
||||
@param multiplicity default is 1
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@param charge default is 0
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@raise Invalid_argument if the spin multiplicity is not compatible with
|
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the molecule and the total charge.
|
||||
*)
|
||||
|
|
@ -5,6 +5,7 @@ let of_float x =
|
|||
x
|
||||
|
||||
external to_float : t -> float = "%identity"
|
||||
external unsafe_of_float : float -> t = "%identity"
|
||||
|
||||
let to_string x =
|
||||
let f = to_float x in string_of_float f
|
||||
|
|
@ -1 +0,0 @@
|
|||
include PositiveFloat
|
||||
|
|
@ -1,13 +1,22 @@
|
|||
(** Functions from libm *)
|
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external erf_float : float -> float = "erf_float_bytecode" "erf_float" [@@unboxed] [@@noalloc]
|
||||
external erfc_float : float -> float = "erfc_float_bytecode" "erfc_float" [@@unboxed] [@@noalloc]
|
||||
external gamma_float : float -> float = "gamma_float_bytecode" "gamma_float" [@@unboxed] [@@noalloc]
|
||||
(** All utilities which should be included in all source files are defined here *)
|
||||
|
||||
(** {1 Functions from libm} *)
|
||||
|
||||
open Constants
|
||||
open Lacaml.D
|
||||
|
||||
let factmax = 150
|
||||
|
||||
external erf_float : float -> float = "erf_float_bytecode" "erf_float"
|
||||
[@@unboxed] [@@noalloc]
|
||||
|
||||
external erfc_float : float -> float = "erfc_float_bytecode" "erfc_float"
|
||||
[@@unboxed] [@@noalloc]
|
||||
|
||||
external gamma_float : float -> float = "gamma_float_bytecode" "gamma_float"
|
||||
[@@unboxed] [@@noalloc]
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
|
@ -79,8 +88,6 @@ let fact_memo =
|
|||
|
||||
|
||||
|
||||
(** Factorial function.
|
||||
@raise Invalid_argument for negative or arguments >100. *)
|
||||
let fact = function
|
||||
| i when (i < 0) ->
|
||||
raise (Invalid_argument "Argument of factorial should be non-negative")
|
||||
|
|
@ -89,24 +96,23 @@ let fact = function
|
|||
| i -> fact_memo.(i)
|
||||
|
||||
|
||||
|
||||
(** Integer powers of floats *)
|
||||
let rec pow a = function
|
||||
| 0 -> 1.
|
||||
| 1 -> a
|
||||
| 2 -> a *. a
|
||||
| 3 -> a *. a *. a
|
||||
| -1 -> 1. /. a
|
||||
| n when (n<0) -> pow (1./.a) (-n)
|
||||
| n ->
|
||||
| n when n > 0 ->
|
||||
let b = pow a (n / 2) in
|
||||
b *. b *. (if n mod 2 = 0 then 1. else a)
|
||||
;;
|
||||
| n when n < 0 -> pow (1./.a) (-n)
|
||||
| _ -> assert false
|
||||
|
||||
|
||||
|
||||
|
||||
(** In chop f g, evaluate g only if f is non zero, and return f *. (g ()) *)
|
||||
let chop f g =
|
||||
if (abs_float f) < cutoff then 0.
|
||||
if (abs_float f) < Constants.epsilon then 0.
|
||||
else f *. (g ())
|
||||
|
||||
|
||||
|
|
@ -162,7 +168,7 @@ let diagonalize_symm h =
|
|||
in
|
||||
v, result
|
||||
|
||||
let xt_o_x o x =
|
||||
let xt_o_x ~o ~x =
|
||||
gemm o x
|
||||
|> gemm ~transa:`T x
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,67 @@
|
|||
(** All utilities which should be included in all source files are defined here *)
|
||||
|
||||
(** {1 Functions from libm} *)
|
||||
|
||||
external erf_float : float -> float = "erf_float_bytecode" "erf_float"
|
||||
[@@unboxed] [@@noalloc]
|
||||
(** Error function [erf] from [libm] *)
|
||||
|
||||
external erfc_float : float -> float = "erfc_float_bytecode" "erfc_float"
|
||||
[@@unboxed] [@@noalloc]
|
||||
(** Complementary error function [erfc] from [libm] *)
|
||||
|
||||
external gamma_float : float -> float = "gamma_float_bytecode" "gamma_float"
|
||||
[@@unboxed] [@@noalloc]
|
||||
(** Gamma function [gamma] from [libm] *)
|
||||
|
||||
|
||||
|
||||
(** {1 General functions} *)
|
||||
|
||||
val fact : int -> float
|
||||
(** Factorial function.
|
||||
@raise Invalid_argument for negative arguments or arguments >100.
|
||||
*)
|
||||
|
||||
val pow : float -> int -> float
|
||||
(** Fast implementation of the power function for small integer powers *)
|
||||
|
||||
val chop : float -> (unit -> float) -> float
|
||||
(** In [chop a f], evaluate [f] only if the absolute value of [a] is larger
|
||||
than {!Constants.epsilon}, and return [a *. f ()].
|
||||
*)
|
||||
|
||||
|
||||
|
||||
(** {1 Functions related to the Boys function} *)
|
||||
|
||||
val incomplete_gamma : alpha:float -> float -> float
|
||||
(** {{:https://en.wikipedia.org/wiki/Incomplete_gamma_function}
|
||||
Lower incomplete gamma function}
|
||||
@raise Failure when the calculation doesn't converge.
|
||||
*)
|
||||
|
||||
val boys_function : maxm:int -> float -> float array
|
||||
(** {{:https://link.springer.com/article/10.1007/s10910-005-9023-3}
|
||||
Generalized Boys function}.
|
||||
@param maxm Maximum total angular momentum.
|
||||
*)
|
||||
|
||||
|
||||
(** {1 Extension of the Array module} *)
|
||||
|
||||
val array_sum : float array -> float
|
||||
(** Returns the sum of all the elements of the array *)
|
||||
|
||||
val array_product : float array -> float
|
||||
(** Returns the product of all the elements of the array *)
|
||||
|
||||
|
||||
(** {1 Linear algebra } *)
|
||||
|
||||
val diagonalize_symm : Lacaml.D.mat -> Lacaml.D.mat * Lacaml.D.vec
|
||||
(** Diagonalize a symmetric matrix. Returns the eigenvectors and the eigenvalues. *)
|
||||
|
||||
val xt_o_x : o:Lacaml.D.mat -> x:Lacaml.D.mat -> Lacaml.D.mat
|
||||
(** Computes X{^T}.O.X *)
|
||||
|
||||
Loading…
Reference in New Issue