mirror of https://gitlab.com/scemama/QCaml.git
MP2 OK
This commit is contained in:
parent
28e6fda242
commit
73a5cf6ca2
16
Makefile
16
Makefile
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@ -1,13 +1,19 @@
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# Frontend to dune.
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DIRS=$(shell ls */README.org | sed "s|/README.org||g")
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DOCS=$(patsubst %, docs/%.html, $(DIRS))
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.PHONY: default build install uninstall test clean
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default: build
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default: tangle build doc
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docs/%.html: %/README.org
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- ./bin/tangle.sh $*
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- ./bin/build_doc.sh $*
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doc: $(DOCS)
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tangle:
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doc:
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build:
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dune build
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@ -21,7 +21,8 @@ let of_nuclei_and_basis_filename ?(kind=`Gaussian) ?operators ?(cartesian=false)
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{ ao_basis ; cartesian }
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| _ -> failwith "of_nuclei_and_basis_filename needs to be called with `Gaussian"
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let not_implemented = Util.not_implemented
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let not_implemented () =
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Util.not_implemented "Only Gaussian is implemented"
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let ao_basis t = t.ao_basis
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@ -23,5 +23,7 @@ done
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CONFIG="--load docs/htmlize.el --load docs/config.el"
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emacs --batch $CONFIG docs/${DIR}.org -f org-html-export-to-html
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rm docs/${DIR}.org
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@ -14,88 +14,11 @@ fi
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DIR=${1%/}
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cat << EOF > ${PWD}/tmpfile_$DIR
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(package-initialize)
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(add-to-list 'package-archives
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'("gnu" . "https://elpa.gnu.org/packages/"))
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(add-to-list 'package-archives
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'("melpa-stable" . "https://stable.melpa.org/packages/"))
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(add-to-list 'package-archives
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'("melpa" . "https://melpa.org/packages/"))
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(setq package-archive-priorities '(("melpa-stable" . 100)
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("melpa" . 50)
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("gnu" . 10)))
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(require 'cl)
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(let* ((required-packages
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'(dash
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htmlize
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ess
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evil
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gnuplot
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tuareg
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tramp
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bibtex-completion
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org-ref
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org-gnome
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org-evil
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org-bullets
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org-mime
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magit
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rustic
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auctex))
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(missing-packages (remove-if #'package-installed-p required-packages)))
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(when missing-packages
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(message "Missing packages: %s" missing-packages)
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(package-refresh-contents)
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(dolist (pkg missing-packages)
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(package-install pkg)
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(message "Package %s has been installed" pkg))))
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(setq org-alphabetical-lists t)
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(setq org-src-fontify-natively t)
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(setq org-src-preserve-indentation t)
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(setq org-confirm-babel-evaluate nil)
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(org-babel-do-load-languages
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'org-babel-load-languages
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'(
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(emacs-lisp . t)
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(shell . t)
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(python . t)
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(C . t)
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(ocaml . t)
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(gnuplot . t)
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(latex . t)
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(ditaa . t)
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(dot . t)
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(org . t)
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(makefile . t)
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))
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(setq pwd (file-name-directory buffer-file-name))
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(setq name (file-name-nondirectory (substring buffer-file-name 0 -4)))
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(setq lib (concat pwd "lib/"))
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(setq testdir (concat pwd "test/"))
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(setq mli (concat lib name ".mli"))
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(setq ml (concat lib name ".ml"))
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(setq c (concat lib name ".c"))
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(setq test-ml (concat testdir name ".ml"))
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(org-babel-tangle)
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EOF
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cd $DIR
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for i in *.org
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do
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echo "--- $i ----"
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emacs --batch ./$i --load=../tmpfile_$DIR
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emacs --batch ./$i --load=../docs/config_tangle.el -f org-babel-tangle
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done
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rm ../tmpfile_$DIR
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@ -3,11 +3,11 @@
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(* This type should be used for all charges in the program (electrons, nuclei,...). *)
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(* [[file:../charge.org::*Type][Type:2]] *)
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(* [[file:~/QCaml/common/charge.org::*Type][Type:2]] *)
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type t = float
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(* Type:2 ends here *)
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(* [[file:../charge.org::*Conversions][Conversions:2]] *)
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(* [[file:~/QCaml/common/charge.org::*Conversions][Conversions:2]] *)
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external of_float : float -> t = "%identity"
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external to_float : t -> float = "%identity"
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@ -25,7 +25,7 @@ let to_string x =
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"0.0"
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(* Conversions:2 ends here *)
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(* [[file:../charge.org::*Simple operations][Simple operations:2]] *)
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(* [[file:~/QCaml/common/charge.org::*Simple%20operations][Simple operations:2]] *)
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let gen_op op =
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fun a b ->
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op (to_float a) (to_float b)
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@ -39,7 +39,7 @@ let ( / ) = gen_op ( /. )
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let is_null t = t == 0.
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(* Simple operations:2 ends here *)
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(* [[file:../charge.org::*Printers][Printers:2]] *)
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(* [[file:~/QCaml/common/charge.org::*Printers][Printers:2]] *)
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let pp ppf x =
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Format.fprintf ppf "@[%s@]" (to_string x)
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(* Printers:2 ends here *)
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@ -1,14 +1,14 @@
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(* Type *)
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(* [[file:../charge.org::*Type][Type:1]] *)
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(* [[file:~/QCaml/common/charge.org::*Type][Type:1]] *)
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type t
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(* Type:1 ends here *)
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(* Conversions *)
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(* [[file:../charge.org::*Conversions][Conversions:1]] *)
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(* [[file:~/QCaml/common/charge.org::*Conversions][Conversions:1]] *)
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val of_float : float -> t
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val to_float : t -> float
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@ -22,7 +22,7 @@ val to_string: t -> string
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(* Simple operations *)
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(* [[file:../charge.org::*Simple operations][Simple operations:1]] *)
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(* [[file:~/QCaml/common/charge.org::*Simple%20operations][Simple operations:1]] *)
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val ( + ) : t -> t -> t
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val ( - ) : t -> t -> t
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val ( * ) : t -> float -> t
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@ -33,6 +33,6 @@ val is_null : t -> bool
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(* Printers *)
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(* [[file:../charge.org::*Printers][Printers:1]] *)
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(* [[file:~/QCaml/common/charge.org::*Printers][Printers:1]] *)
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val pp : Format.formatter -> t -> unit
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(* Printers:1 ends here *)
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@ -39,7 +39,7 @@ let leadz i = leadz i |> Int32.to_int
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* | ~pow~ | Fast implementation of the power function for small integer powers |
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* | ~chop~ | In ~chop a f~, evaluate ~f~ only if the absolute value of ~a~ is larger than ~Constants.epsilon~, and return ~a *. f ()~. |
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* | ~float_of_int_fast~ | Faster implementation of float_of_int for small positive ints |
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* | ~not_implemented~ | Fails with error message if some functionality is not implemented |
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* | ~not_implemented~ | Fails if some functionality is not implemented |
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* | ~of_some~ | Extracts the value of an option | *)
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@ -123,8 +123,9 @@ let chop f g =
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else f *. (g ())
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let not_implemented () =
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failwith "Not implemented"
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exception Not_implemented of string
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let not_implemented string =
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raise (Not_implemented string)
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let of_some = function
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@ -35,8 +35,11 @@ val chop : float -> (unit -> float) -> float
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val pow : float -> int -> float
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val float_of_int_fast : int -> float
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val not_implemented : unit -> 'a
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val of_some : 'a option -> 'a
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exception Not_implemented of string
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val not_implemented : string -> 'a
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(* @raise Not_implemented. *)
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(* General functions:1 ends here *)
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(* Functions related to the Boys function *)
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@ -213,8 +213,11 @@ val chop : float -> (unit -> float) -> float
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val pow : float -> int -> float
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val float_of_int_fast : int -> float
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val not_implemented : unit -> 'a
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val of_some : 'a option -> 'a
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exception Not_implemented of string
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val not_implemented : string -> 'a
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(* @raise Not_implemented. *)
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#+end_src
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| ~fact~ | Factorial function. |
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@ -223,7 +226,7 @@ val of_some : 'a option -> 'a
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| ~pow~ | Fast implementation of the power function for small integer powers |
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| ~chop~ | In ~chop a f~, evaluate ~f~ only if the absolute value of ~a~ is larger than ~Constants.epsilon~, and return ~a *. f ()~. |
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||||
| ~float_of_int_fast~ | Faster implementation of float_of_int for small positive ints |
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||||
| ~not_implemented~ | Fails with error message if some functionality is not implemented |
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||||
| ~not_implemented~ | Fails if some functionality is not implemented |
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| ~of_some~ | Extracts the value of an option |
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#+begin_src ocaml :tangle (eval ml) :exports none
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@ -306,8 +309,9 @@ let chop f g =
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else f *. (g ())
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let not_implemented () =
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failwith "Not implemented"
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exception Not_implemented of string
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let not_implemented string =
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raise (Not_implemented string)
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||||
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let of_some = function
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|
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@ -0,0 +1,239 @@
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|||
<?xml version="1.0" encoding="utf-8"?>
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
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||||
<head>
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||||
<!-- 2021-01-01 Fri 16:38 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
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||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>Atomic Orbitals</title>
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<meta name="generator" content="Org mode" />
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<meta name="author" content="Anthony Scemama" />
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<style type="text/css">
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<!--/*--><![CDATA[/*><!--*/
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.title { text-align: center;
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margin-bottom: .2em; }
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.subtitle { text-align: center;
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font-size: medium;
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font-weight: bold;
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margin-top:0; }
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.todo { font-family: monospace; color: red; }
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.done { font-family: monospace; color: green; }
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||||
.priority { font-family: monospace; color: orange; }
|
||||
.tag { background-color: #eee; font-family: monospace;
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padding: 2px; font-size: 80%; font-weight: normal; }
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.timestamp { color: #bebebe; }
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.timestamp-kwd { color: #5f9ea0; }
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.org-right { margin-left: auto; margin-right: 0px; text-align: right; }
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.org-left { margin-left: 0px; margin-right: auto; text-align: left; }
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.org-center { margin-left: auto; margin-right: auto; text-align: center; }
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.underline { text-decoration: underline; }
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#postamble p, #preamble p { font-size: 90%; margin: .2em; }
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p.verse { margin-left: 3%; }
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pre {
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border: 1px solid #ccc;
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||||
box-shadow: 3px 3px 3px #eee;
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||||
padding: 8pt;
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||||
font-family: monospace;
|
||||
overflow: auto;
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||||
margin: 1.2em;
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||||
}
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||||
pre.src {
|
||||
position: relative;
|
||||
overflow: auto;
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||||
padding-top: 1.2em;
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||||
}
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pre.src:before {
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||||
display: none;
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||||
position: absolute;
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||||
background-color: white;
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||||
top: -10px;
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||||
right: 10px;
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||||
padding: 3px;
|
||||
border: 1px solid black;
|
||||
}
|
||||
pre.src:hover:before { display: inline;}
|
||||
/* Languages per Org manual */
|
||||
pre.src-asymptote:before { content: 'Asymptote'; }
|
||||
pre.src-awk:before { content: 'Awk'; }
|
||||
pre.src-C:before { content: 'C'; }
|
||||
/* pre.src-C++ doesn't work in CSS */
|
||||
pre.src-clojure:before { content: 'Clojure'; }
|
||||
pre.src-css:before { content: 'CSS'; }
|
||||
pre.src-D:before { content: 'D'; }
|
||||
pre.src-ditaa:before { content: 'ditaa'; }
|
||||
pre.src-dot:before { content: 'Graphviz'; }
|
||||
pre.src-calc:before { content: 'Emacs Calc'; }
|
||||
pre.src-emacs-lisp:before { content: 'Emacs Lisp'; }
|
||||
pre.src-fortran:before { content: 'Fortran'; }
|
||||
pre.src-gnuplot:before { content: 'gnuplot'; }
|
||||
pre.src-haskell:before { content: 'Haskell'; }
|
||||
pre.src-hledger:before { content: 'hledger'; }
|
||||
pre.src-java:before { content: 'Java'; }
|
||||
pre.src-js:before { content: 'Javascript'; }
|
||||
pre.src-latex:before { content: 'LaTeX'; }
|
||||
pre.src-ledger:before { content: 'Ledger'; }
|
||||
pre.src-lisp:before { content: 'Lisp'; }
|
||||
pre.src-lilypond:before { content: 'Lilypond'; }
|
||||
pre.src-lua:before { content: 'Lua'; }
|
||||
pre.src-matlab:before { content: 'MATLAB'; }
|
||||
pre.src-mscgen:before { content: 'Mscgen'; }
|
||||
pre.src-ocaml:before { content: 'Objective Caml'; }
|
||||
pre.src-octave:before { content: 'Octave'; }
|
||||
pre.src-org:before { content: 'Org mode'; }
|
||||
pre.src-oz:before { content: 'OZ'; }
|
||||
pre.src-plantuml:before { content: 'Plantuml'; }
|
||||
pre.src-processing:before { content: 'Processing.js'; }
|
||||
pre.src-python:before { content: 'Python'; }
|
||||
pre.src-R:before { content: 'R'; }
|
||||
pre.src-ruby:before { content: 'Ruby'; }
|
||||
pre.src-sass:before { content: 'Sass'; }
|
||||
pre.src-scheme:before { content: 'Scheme'; }
|
||||
pre.src-screen:before { content: 'Gnu Screen'; }
|
||||
pre.src-sed:before { content: 'Sed'; }
|
||||
pre.src-sh:before { content: 'shell'; }
|
||||
pre.src-sql:before { content: 'SQL'; }
|
||||
pre.src-sqlite:before { content: 'SQLite'; }
|
||||
/* additional languages in org.el's org-babel-load-languages alist */
|
||||
pre.src-forth:before { content: 'Forth'; }
|
||||
pre.src-io:before { content: 'IO'; }
|
||||
pre.src-J:before { content: 'J'; }
|
||||
pre.src-makefile:before { content: 'Makefile'; }
|
||||
pre.src-maxima:before { content: 'Maxima'; }
|
||||
pre.src-perl:before { content: 'Perl'; }
|
||||
pre.src-picolisp:before { content: 'Pico Lisp'; }
|
||||
pre.src-scala:before { content: 'Scala'; }
|
||||
pre.src-shell:before { content: 'Shell Script'; }
|
||||
pre.src-ebnf2ps:before { content: 'ebfn2ps'; }
|
||||
/* additional language identifiers per "defun org-babel-execute"
|
||||
in ob-*.el */
|
||||
pre.src-cpp:before { content: 'C++'; }
|
||||
pre.src-abc:before { content: 'ABC'; }
|
||||
pre.src-coq:before { content: 'Coq'; }
|
||||
pre.src-groovy:before { content: 'Groovy'; }
|
||||
/* additional language identifiers from org-babel-shell-names in
|
||||
ob-shell.el: ob-shell is the only babel language using a lambda to put
|
||||
the execution function name together. */
|
||||
pre.src-bash:before { content: 'bash'; }
|
||||
pre.src-csh:before { content: 'csh'; }
|
||||
pre.src-ash:before { content: 'ash'; }
|
||||
pre.src-dash:before { content: 'dash'; }
|
||||
pre.src-ksh:before { content: 'ksh'; }
|
||||
pre.src-mksh:before { content: 'mksh'; }
|
||||
pre.src-posh:before { content: 'posh'; }
|
||||
/* Additional Emacs modes also supported by the LaTeX listings package */
|
||||
pre.src-ada:before { content: 'Ada'; }
|
||||
pre.src-asm:before { content: 'Assembler'; }
|
||||
pre.src-caml:before { content: 'Caml'; }
|
||||
pre.src-delphi:before { content: 'Delphi'; }
|
||||
pre.src-html:before { content: 'HTML'; }
|
||||
pre.src-idl:before { content: 'IDL'; }
|
||||
pre.src-mercury:before { content: 'Mercury'; }
|
||||
pre.src-metapost:before { content: 'MetaPost'; }
|
||||
pre.src-modula-2:before { content: 'Modula-2'; }
|
||||
pre.src-pascal:before { content: 'Pascal'; }
|
||||
pre.src-ps:before { content: 'PostScript'; }
|
||||
pre.src-prolog:before { content: 'Prolog'; }
|
||||
pre.src-simula:before { content: 'Simula'; }
|
||||
pre.src-tcl:before { content: 'tcl'; }
|
||||
pre.src-tex:before { content: 'TeX'; }
|
||||
pre.src-plain-tex:before { content: 'Plain TeX'; }
|
||||
pre.src-verilog:before { content: 'Verilog'; }
|
||||
pre.src-vhdl:before { content: 'VHDL'; }
|
||||
pre.src-xml:before { content: 'XML'; }
|
||||
pre.src-nxml:before { content: 'XML'; }
|
||||
/* add a generic configuration mode; LaTeX export needs an additional
|
||||
(add-to-list 'org-latex-listings-langs '(conf " ")) in .emacs */
|
||||
pre.src-conf:before { content: 'Configuration File'; }
|
||||
|
||||
table { border-collapse:collapse; }
|
||||
caption.t-above { caption-side: top; }
|
||||
caption.t-bottom { caption-side: bottom; }
|
||||
td, th { vertical-align:top; }
|
||||
th.org-right { text-align: center; }
|
||||
th.org-left { text-align: center; }
|
||||
th.org-center { text-align: center; }
|
||||
td.org-right { text-align: right; }
|
||||
td.org-left { text-align: left; }
|
||||
td.org-center { text-align: center; }
|
||||
dt { font-weight: bold; }
|
||||
.footpara { display: inline; }
|
||||
.footdef { margin-bottom: 1em; }
|
||||
.figure { padding: 1em; }
|
||||
.figure p { text-align: center; }
|
||||
.equation-container {
|
||||
display: table;
|
||||
text-align: center;
|
||||
width: 100%;
|
||||
}
|
||||
.equation {
|
||||
vertical-align: middle;
|
||||
}
|
||||
.equation-label {
|
||||
display: table-cell;
|
||||
text-align: right;
|
||||
vertical-align: middle;
|
||||
}
|
||||
.inlinetask {
|
||||
padding: 10px;
|
||||
border: 2px solid gray;
|
||||
margin: 10px;
|
||||
background: #ffffcc;
|
||||
}
|
||||
#org-div-home-and-up
|
||||
{ text-align: right; font-size: 70%; white-space: nowrap; }
|
||||
textarea { overflow-x: auto; }
|
||||
.linenr { font-size: smaller }
|
||||
.code-highlighted { background-color: #ffff00; }
|
||||
.org-info-js_info-navigation { border-style: none; }
|
||||
#org-info-js_console-label
|
||||
{ font-size: 10px; font-weight: bold; white-space: nowrap; }
|
||||
.org-info-js_search-highlight
|
||||
{ background-color: #ffff00; color: #000000; font-weight: bold; }
|
||||
.org-svg { width: 90%; }
|
||||
/*]]>*/-->
|
||||
</style>
|
||||
<link rel="stylesheet" type="text/css" href="https://fniessen.github.io/org-html-themes/src/readtheorg_theme/css/htmlize.css"/>
|
||||
<link rel="stylesheet" type="text/css" href="https://fniessen.github.io/org-html-themes/src/readtheorg_theme/css/readtheorg.css"/>
|
||||
<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.3/jquery.min.js"></script>
|
||||
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
|
||||
<script type="text/javascript" src="https://fniessen.github.io/org-html-themes/src/lib/js/jquery.stickytableheaders.min.js"></script>
|
||||
<script type="text/javascript" src="https://fniessen.github.io/org-html-themes/src/readtheorg_theme/js/readtheorg.js"></script>
|
||||
<script type="text/javascript">
|
||||
// @license magnet:?xt=urn:btih:e95b018ef3580986a04669f1b5879592219e2a7a&dn=public-domain.txt Public Domain
|
||||
<!--/*--><![CDATA[/*><!--*/
|
||||
function CodeHighlightOn(elem, id)
|
||||
{
|
||||
var target = document.getElementById(id);
|
||||
if(null != target) {
|
||||
elem.classList.add("code-highlighted");
|
||||
target.classList.add("code-highlighted");
|
||||
}
|
||||
}
|
||||
function CodeHighlightOff(elem, id)
|
||||
{
|
||||
var target = document.getElementById(id);
|
||||
if(null != target) {
|
||||
elem.classList.remove("code-highlighted");
|
||||
target.classList.remove("code-highlighted");
|
||||
}
|
||||
}
|
||||
/*]]>*///-->
|
||||
// @license-end
|
||||
</script>
|
||||
</head>
|
||||
<body>
|
||||
<div id="content">
|
||||
<h1 class="title">Atomic Orbitals</h1>
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-ocaml" id="orgb54ee80"><span class="org-string">"Atomic basis set"</span>
|
||||
</pre>
|
||||
</div>
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: Anthony Scemama</p>
|
||||
<p class="date">Created: 2021-01-01 Fri 16:38</p>
|
||||
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
</html>
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -71,6 +71,7 @@ with class 'color and highest min-color value."
|
|||
|
||||
(setq org-html-htmlize-output-type 'css) ; default: 'inline-css
|
||||
(setq org-html-htmlize-font-prefix "org-") ; default: "org-"
|
||||
(setq org-confirm-babel-evaluate nil)
|
||||
|
||||
(setq c "c")
|
||||
(setq ml "ml")
|
||||
|
|
|
|||
|
|
@ -0,0 +1,71 @@
|
|||
;; Thanks to Tobias's answer on Emacs Stack Exchange:
|
||||
;; https://emacs.stackexchange.com/questions/38437/org-mode-batch-export-missing-syntax-highlighting
|
||||
|
||||
(package-initialize)
|
||||
(add-to-list 'package-archives
|
||||
'("gnu" . "https://elpa.gnu.org/packages/"))
|
||||
(add-to-list 'package-archives
|
||||
'("melpa-stable" . "https://stable.melpa.org/packages/"))
|
||||
(add-to-list 'package-archives
|
||||
'("melpa" . "https://melpa.org/packages/"))
|
||||
(setq package-archive-priorities '(("melpa-stable" . 100)
|
||||
("melpa" . 50)
|
||||
("gnu" . 10)))
|
||||
(require 'cl)
|
||||
(let* ((required-packages
|
||||
'(dash
|
||||
htmlize
|
||||
ess
|
||||
evil
|
||||
gnuplot
|
||||
tuareg
|
||||
tramp
|
||||
bibtex-completion
|
||||
org-ref
|
||||
org-gnome
|
||||
org-evil
|
||||
org-bullets
|
||||
org-mime
|
||||
magit
|
||||
rustic
|
||||
auctex))
|
||||
|
||||
(missing-packages (remove-if #'package-installed-p required-packages)))
|
||||
(when missing-packages
|
||||
(message "Missing packages: %s" missing-packages)
|
||||
(package-refresh-contents)
|
||||
(dolist (pkg missing-packages)
|
||||
(package-install pkg)
|
||||
(message "Package %s has been installed" pkg))))
|
||||
|
||||
(setq org-alphabetical-lists t)
|
||||
(setq org-src-fontify-natively t)
|
||||
|
||||
(setq org-src-preserve-indentation t)
|
||||
(setq org-confirm-babel-evaluate nil)
|
||||
|
||||
(org-babel-do-load-languages
|
||||
'org-babel-load-languages
|
||||
'(
|
||||
(emacs-lisp . t)
|
||||
(shell . t)
|
||||
(python . t)
|
||||
(C . t)
|
||||
(ocaml . t)
|
||||
(gnuplot . t)
|
||||
(latex . t)
|
||||
(ditaa . t)
|
||||
(dot . t)
|
||||
(org . t)
|
||||
(makefile . t)
|
||||
))
|
||||
|
||||
(setq pwd (file-name-directory buffer-file-name))
|
||||
(setq name (file-name-nondirectory (substring buffer-file-name 0 -4)))
|
||||
(setq lib (concat pwd "lib/"))
|
||||
(setq testdir (concat pwd "test/"))
|
||||
(setq mli (concat lib name ".mli"))
|
||||
(setq ml (concat lib name ".ml"))
|
||||
(setq c (concat lib name ".c"))
|
||||
(setq test-ml (concat testdir name ".ml"))
|
||||
|
||||
|
|
@ -0,0 +1,239 @@
|
|||
<?xml version="1.0" encoding="utf-8"?>
|
||||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
|
||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
|
||||
<!-- 2021-01-01 Fri 16:38 -->
|
||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<title>Gaussian</title>
|
||||
<meta name="generator" content="Org mode" />
|
||||
<meta name="author" content="Anthony Scemama" />
|
||||
<style type="text/css">
|
||||
<!--/*--><![CDATA[/*><!--*/
|
||||
.title { text-align: center;
|
||||
margin-bottom: .2em; }
|
||||
.subtitle { text-align: center;
|
||||
font-size: medium;
|
||||
font-weight: bold;
|
||||
margin-top:0; }
|
||||
.todo { font-family: monospace; color: red; }
|
||||
.done { font-family: monospace; color: green; }
|
||||
.priority { font-family: monospace; color: orange; }
|
||||
.tag { background-color: #eee; font-family: monospace;
|
||||
padding: 2px; font-size: 80%; font-weight: normal; }
|
||||
.timestamp { color: #bebebe; }
|
||||
.timestamp-kwd { color: #5f9ea0; }
|
||||
.org-right { margin-left: auto; margin-right: 0px; text-align: right; }
|
||||
.org-left { margin-left: 0px; margin-right: auto; text-align: left; }
|
||||
.org-center { margin-left: auto; margin-right: auto; text-align: center; }
|
||||
.underline { text-decoration: underline; }
|
||||
#postamble p, #preamble p { font-size: 90%; margin: .2em; }
|
||||
p.verse { margin-left: 3%; }
|
||||
pre {
|
||||
border: 1px solid #ccc;
|
||||
box-shadow: 3px 3px 3px #eee;
|
||||
padding: 8pt;
|
||||
font-family: monospace;
|
||||
overflow: auto;
|
||||
margin: 1.2em;
|
||||
}
|
||||
pre.src {
|
||||
position: relative;
|
||||
overflow: auto;
|
||||
padding-top: 1.2em;
|
||||
}
|
||||
pre.src:before {
|
||||
display: none;
|
||||
position: absolute;
|
||||
background-color: white;
|
||||
top: -10px;
|
||||
right: 10px;
|
||||
padding: 3px;
|
||||
border: 1px solid black;
|
||||
}
|
||||
pre.src:hover:before { display: inline;}
|
||||
/* Languages per Org manual */
|
||||
pre.src-asymptote:before { content: 'Asymptote'; }
|
||||
pre.src-awk:before { content: 'Awk'; }
|
||||
pre.src-C:before { content: 'C'; }
|
||||
/* pre.src-C++ doesn't work in CSS */
|
||||
pre.src-clojure:before { content: 'Clojure'; }
|
||||
pre.src-css:before { content: 'CSS'; }
|
||||
pre.src-D:before { content: 'D'; }
|
||||
pre.src-ditaa:before { content: 'ditaa'; }
|
||||
pre.src-dot:before { content: 'Graphviz'; }
|
||||
pre.src-calc:before { content: 'Emacs Calc'; }
|
||||
pre.src-emacs-lisp:before { content: 'Emacs Lisp'; }
|
||||
pre.src-fortran:before { content: 'Fortran'; }
|
||||
pre.src-gnuplot:before { content: 'gnuplot'; }
|
||||
pre.src-haskell:before { content: 'Haskell'; }
|
||||
pre.src-hledger:before { content: 'hledger'; }
|
||||
pre.src-java:before { content: 'Java'; }
|
||||
pre.src-js:before { content: 'Javascript'; }
|
||||
pre.src-latex:before { content: 'LaTeX'; }
|
||||
pre.src-ledger:before { content: 'Ledger'; }
|
||||
pre.src-lisp:before { content: 'Lisp'; }
|
||||
pre.src-lilypond:before { content: 'Lilypond'; }
|
||||
pre.src-lua:before { content: 'Lua'; }
|
||||
pre.src-matlab:before { content: 'MATLAB'; }
|
||||
pre.src-mscgen:before { content: 'Mscgen'; }
|
||||
pre.src-ocaml:before { content: 'Objective Caml'; }
|
||||
pre.src-octave:before { content: 'Octave'; }
|
||||
pre.src-org:before { content: 'Org mode'; }
|
||||
pre.src-oz:before { content: 'OZ'; }
|
||||
pre.src-plantuml:before { content: 'Plantuml'; }
|
||||
pre.src-processing:before { content: 'Processing.js'; }
|
||||
pre.src-python:before { content: 'Python'; }
|
||||
pre.src-R:before { content: 'R'; }
|
||||
pre.src-ruby:before { content: 'Ruby'; }
|
||||
pre.src-sass:before { content: 'Sass'; }
|
||||
pre.src-scheme:before { content: 'Scheme'; }
|
||||
pre.src-screen:before { content: 'Gnu Screen'; }
|
||||
pre.src-sed:before { content: 'Sed'; }
|
||||
pre.src-sh:before { content: 'shell'; }
|
||||
pre.src-sql:before { content: 'SQL'; }
|
||||
pre.src-sqlite:before { content: 'SQLite'; }
|
||||
/* additional languages in org.el's org-babel-load-languages alist */
|
||||
pre.src-forth:before { content: 'Forth'; }
|
||||
pre.src-io:before { content: 'IO'; }
|
||||
pre.src-J:before { content: 'J'; }
|
||||
pre.src-makefile:before { content: 'Makefile'; }
|
||||
pre.src-maxima:before { content: 'Maxima'; }
|
||||
pre.src-perl:before { content: 'Perl'; }
|
||||
pre.src-picolisp:before { content: 'Pico Lisp'; }
|
||||
pre.src-scala:before { content: 'Scala'; }
|
||||
pre.src-shell:before { content: 'Shell Script'; }
|
||||
pre.src-ebnf2ps:before { content: 'ebfn2ps'; }
|
||||
/* additional language identifiers per "defun org-babel-execute"
|
||||
in ob-*.el */
|
||||
pre.src-cpp:before { content: 'C++'; }
|
||||
pre.src-abc:before { content: 'ABC'; }
|
||||
pre.src-coq:before { content: 'Coq'; }
|
||||
pre.src-groovy:before { content: 'Groovy'; }
|
||||
/* additional language identifiers from org-babel-shell-names in
|
||||
ob-shell.el: ob-shell is the only babel language using a lambda to put
|
||||
the execution function name together. */
|
||||
pre.src-bash:before { content: 'bash'; }
|
||||
pre.src-csh:before { content: 'csh'; }
|
||||
pre.src-ash:before { content: 'ash'; }
|
||||
pre.src-dash:before { content: 'dash'; }
|
||||
pre.src-ksh:before { content: 'ksh'; }
|
||||
pre.src-mksh:before { content: 'mksh'; }
|
||||
pre.src-posh:before { content: 'posh'; }
|
||||
/* Additional Emacs modes also supported by the LaTeX listings package */
|
||||
pre.src-ada:before { content: 'Ada'; }
|
||||
pre.src-asm:before { content: 'Assembler'; }
|
||||
pre.src-caml:before { content: 'Caml'; }
|
||||
pre.src-delphi:before { content: 'Delphi'; }
|
||||
pre.src-html:before { content: 'HTML'; }
|
||||
pre.src-idl:before { content: 'IDL'; }
|
||||
pre.src-mercury:before { content: 'Mercury'; }
|
||||
pre.src-metapost:before { content: 'MetaPost'; }
|
||||
pre.src-modula-2:before { content: 'Modula-2'; }
|
||||
pre.src-pascal:before { content: 'Pascal'; }
|
||||
pre.src-ps:before { content: 'PostScript'; }
|
||||
pre.src-prolog:before { content: 'Prolog'; }
|
||||
pre.src-simula:before { content: 'Simula'; }
|
||||
pre.src-tcl:before { content: 'tcl'; }
|
||||
pre.src-tex:before { content: 'TeX'; }
|
||||
pre.src-plain-tex:before { content: 'Plain TeX'; }
|
||||
pre.src-verilog:before { content: 'Verilog'; }
|
||||
pre.src-vhdl:before { content: 'VHDL'; }
|
||||
pre.src-xml:before { content: 'XML'; }
|
||||
pre.src-nxml:before { content: 'XML'; }
|
||||
/* add a generic configuration mode; LaTeX export needs an additional
|
||||
(add-to-list 'org-latex-listings-langs '(conf " ")) in .emacs */
|
||||
pre.src-conf:before { content: 'Configuration File'; }
|
||||
|
||||
table { border-collapse:collapse; }
|
||||
caption.t-above { caption-side: top; }
|
||||
caption.t-bottom { caption-side: bottom; }
|
||||
td, th { vertical-align:top; }
|
||||
th.org-right { text-align: center; }
|
||||
th.org-left { text-align: center; }
|
||||
th.org-center { text-align: center; }
|
||||
td.org-right { text-align: right; }
|
||||
td.org-left { text-align: left; }
|
||||
td.org-center { text-align: center; }
|
||||
dt { font-weight: bold; }
|
||||
.footpara { display: inline; }
|
||||
.footdef { margin-bottom: 1em; }
|
||||
.figure { padding: 1em; }
|
||||
.figure p { text-align: center; }
|
||||
.equation-container {
|
||||
display: table;
|
||||
text-align: center;
|
||||
width: 100%;
|
||||
}
|
||||
.equation {
|
||||
vertical-align: middle;
|
||||
}
|
||||
.equation-label {
|
||||
display: table-cell;
|
||||
text-align: right;
|
||||
vertical-align: middle;
|
||||
}
|
||||
.inlinetask {
|
||||
padding: 10px;
|
||||
border: 2px solid gray;
|
||||
margin: 10px;
|
||||
background: #ffffcc;
|
||||
}
|
||||
#org-div-home-and-up
|
||||
{ text-align: right; font-size: 70%; white-space: nowrap; }
|
||||
textarea { overflow-x: auto; }
|
||||
.linenr { font-size: smaller }
|
||||
.code-highlighted { background-color: #ffff00; }
|
||||
.org-info-js_info-navigation { border-style: none; }
|
||||
#org-info-js_console-label
|
||||
{ font-size: 10px; font-weight: bold; white-space: nowrap; }
|
||||
.org-info-js_search-highlight
|
||||
{ background-color: #ffff00; color: #000000; font-weight: bold; }
|
||||
.org-svg { width: 90%; }
|
||||
/*]]>*/-->
|
||||
</style>
|
||||
<link rel="stylesheet" type="text/css" href="https://fniessen.github.io/org-html-themes/src/readtheorg_theme/css/htmlize.css"/>
|
||||
<link rel="stylesheet" type="text/css" href="https://fniessen.github.io/org-html-themes/src/readtheorg_theme/css/readtheorg.css"/>
|
||||
<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.3/jquery.min.js"></script>
|
||||
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
|
||||
<script type="text/javascript" src="https://fniessen.github.io/org-html-themes/src/lib/js/jquery.stickytableheaders.min.js"></script>
|
||||
<script type="text/javascript" src="https://fniessen.github.io/org-html-themes/src/readtheorg_theme/js/readtheorg.js"></script>
|
||||
<script type="text/javascript">
|
||||
// @license magnet:?xt=urn:btih:e95b018ef3580986a04669f1b5879592219e2a7a&dn=public-domain.txt Public Domain
|
||||
<!--/*--><![CDATA[/*><!--*/
|
||||
function CodeHighlightOn(elem, id)
|
||||
{
|
||||
var target = document.getElementById(id);
|
||||
if(null != target) {
|
||||
elem.classList.add("code-highlighted");
|
||||
target.classList.add("code-highlighted");
|
||||
}
|
||||
}
|
||||
function CodeHighlightOff(elem, id)
|
||||
{
|
||||
var target = document.getElementById(id);
|
||||
if(null != target) {
|
||||
elem.classList.remove("code-highlighted");
|
||||
target.classList.remove("code-highlighted");
|
||||
}
|
||||
}
|
||||
/*]]>*///-->
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|
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<h1 class="title">Molecular orbitals</h1>
|
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<li><a href="#orgb2586e7">1.2. Creation</a></li>
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<pre class="src src-ocaml" id="org7d44fe6"><span class="org-string">"Molecular orbitals"</span>
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||||
Defines how the core electrons are frozen, for each atom.
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||||
</div>
|
||||
|
||||
<div id="outline-container-org1c7c95a" class="outline-3">
|
||||
<h3 id="org1c7c95a"><span class="section-number-3">1.1</span> Type</h3>
|
||||
<div class="outline-text-3" id="text-1-1">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-ocaml" id="org2ed636d"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">kind</span> <span class="org-tuareg-font-lock-operator">=</span>
|
||||
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">All_electron</span>
|
||||
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">Small</span>
|
||||
<span class="org-tuareg-font-lock-operator">|</span> Large
|
||||
</pre>
|
||||
</div>
|
||||
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
|
||||
</pre>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb2586e7" class="outline-3">
|
||||
<h3 id="orgb2586e7"><span class="section-number-3">1.2</span> Creation</h3>
|
||||
<div class="outline-text-3" id="text-1-2">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">make</span> <span class="org-tuareg-font-lock-operator">:</span> kind <span class="org-tuareg-font-lock-operator">-></span> <span class="org-tuareg-font-lock-module">Particles.Nuclei.</span>t <span class="org-tuareg-font-lock-operator">-></span> t
|
||||
|
||||
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_int_list</span> <span class="org-tuareg-font-lock-operator">:</span> int list <span class="org-tuareg-font-lock-operator">-></span> t
|
||||
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_int_array</span> <span class="org-tuareg-font-lock-operator">:</span> int array <span class="org-tuareg-font-lock-operator">-></span> t
|
||||
</pre>
|
||||
</div>
|
||||
|
||||
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
<col class="org-left" />
|
||||
|
||||
<col class="org-left" />
|
||||
</colgroup>
|
||||
<tbody>
|
||||
<tr>
|
||||
<td class="org-left"><code>make</code></td>
|
||||
<td class="org-left">Creates a <code>Frozen_core.t</code> with the same kind for all atoms</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>of_int_array</code></td>
|
||||
<td class="org-left">Creates a <code>Frozen_core.t</code> giving the number of frozen electrons per atom</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>of_int_list</code></td>
|
||||
<td class="org-left">Creates a <code>Frozen_core.t</code> giving the number of frozen electrons per atom</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
|
||||
<pre class="example" id="org7332159">
|
||||
let f = Frozen_core.(make Small nuclei) ;;
|
||||
val f : Frozen_core.t = [|0; 2; 2; 0|]
|
||||
|
||||
let f = Frozen_core.(of_int_list [0; 2; 2; 0])
|
||||
val f : Frozen_core.t = [|0; 2; 2; 0|]
|
||||
</pre>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org482997a" class="outline-3">
|
||||
<h3 id="org482997a"><span class="section-number-3">1.3</span> Access</h3>
|
||||
<div class="outline-text-3" id="text-1-3">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">num_elec</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> int
|
||||
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">num_mos</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> int
|
||||
</pre>
|
||||
</div>
|
||||
|
||||
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
<col class="org-left" />
|
||||
|
||||
<col class="org-left" />
|
||||
</colgroup>
|
||||
<tbody>
|
||||
<tr>
|
||||
<td class="org-left"><code>num_elec</code></td>
|
||||
<td class="org-left">Number of frozen electrons</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>num_mos</code></td>
|
||||
<td class="org-left">Number of frozen molecular orbitals</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
|
||||
<pre class="example" id="org1d3352f">
|
||||
Frozen_core.num_elec f ;;
|
||||
- : int = 4
|
||||
|
||||
Frozen_core.num_mos f ;;
|
||||
- : int = 2
|
||||
</pre>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orga5d7816" class="outline-3">
|
||||
<h3 id="orga5d7816"><span class="section-number-3">1.4</span> Printers</h3>
|
||||
<div class="outline-text-3" id="text-1-4">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">pp</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Format.</span>formatter <span class="org-tuareg-font-lock-operator">-></span> t <span class="org-tuareg-font-lock-operator">-></span> unit
|
||||
</pre>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: Anthony Scemama</p>
|
||||
<p class="date">Created: 2021-01-01 Fri 16:38</p>
|
||||
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
</html>
|
||||
|
|
@ -0,0 +1,239 @@
|
|||
<?xml version="1.0" encoding="utf-8"?>
|
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|
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|
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|
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|
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|
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
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<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<title>Operators</title>
|
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<meta name="generator" content="Org mode" />
|
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<meta name="author" content="Anthony Scemama" />
|
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<style type="text/css">
|
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#postamble p, #preamble p { font-size: 90%; margin: .2em; }
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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/* additional language identifiers per "defun org-babel-execute"
|
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in ob-*.el */
|
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|
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|
||||
ob-shell.el: ob-shell is the only babel language using a lambda to put
|
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the execution function name together. */
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/* Additional Emacs modes also supported by the LaTeX listings package */
|
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|
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|
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|
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|
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|
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|
||||
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|
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pre.src-ps:before { content: 'PostScript'; }
|
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|
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|
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|
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|
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|
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|
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|
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/* add a generic configuration mode; LaTeX export needs an additional
|
||||
(add-to-list 'org-latex-listings-langs '(conf " ")) in .emacs */
|
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|
||||
|
||||
table { border-collapse:collapse; }
|
||||
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|
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|
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|
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|
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|
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|
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|
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dt { font-weight: bold; }
|
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|
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.footdef { margin-bottom: 1em; }
|
||||
.figure { padding: 1em; }
|
||||
.figure p { text-align: center; }
|
||||
.equation-container {
|
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display: table;
|
||||
text-align: center;
|
||||
width: 100%;
|
||||
}
|
||||
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|
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|
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}
|
||||
.equation-label {
|
||||
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|
||||
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|
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|
||||
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|
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.inlinetask {
|
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|
||||
border: 2px solid gray;
|
||||
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|
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|
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}
|
||||
#org-div-home-and-up
|
||||
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|
||||
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|
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|
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|
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|
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#org-info-js_console-label
|
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|
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.org-info-js_search-highlight
|
||||
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
||||
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|
||||
</head>
|
||||
<body>
|
||||
<div id="content">
|
||||
<h1 class="title">Operators</h1>
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-ocaml" id="org0a9530e"><span class="org-string">"Parameteried operators, such as F12 and range-separation"</span>
|
||||
</pre>
|
||||
</div>
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: Anthony Scemama</p>
|
||||
<p class="date">Created: 2021-01-01 Fri 16:38</p>
|
||||
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
</html>
|
||||
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Load Diff
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</head>
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<body>
|
||||
<div id="content">
|
||||
<h1 class="title">Perturbation</h1>
|
||||
<div id="table-of-contents">
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#org4a19d89">1. MP2</a>
|
||||
<ul>
|
||||
<li><a href="#org9ac9790">1.1. Type</a></li>
|
||||
<li><a href="#org0b288bd">1.2. Creation</a></li>
|
||||
<li><a href="#org0bf5c08">1.3. Access</a></li>
|
||||
<li><a href="#org10bdc37">1.4. Printers</a></li>
|
||||
<li><a href="#org38093b0">1.5. Tests</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-ocaml" id="org8cc608d"><span class="org-string">"Perturbation theory"</span>
|
||||
</pre>
|
||||
</div>
|
||||
|
||||
|
||||
<div id="outline-container-org4a19d89" class="outline-2">
|
||||
<h2 id="org4a19d89"><span class="section-number-2">1</span> MP2</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org9ac9790" class="outline-3">
|
||||
<h3 id="org9ac9790"><span class="section-number-3">1.1</span> Type</h3>
|
||||
<div class="outline-text-3" id="text-1-1">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
|
||||
</pre>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0b288bd" class="outline-3">
|
||||
<h3 id="org0b288bd"><span class="section-number-3">1.2</span> Creation</h3>
|
||||
<div class="outline-text-3" id="text-1-2">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">make</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-label">frozen_core</span><span class="org-tuareg-font-lock-operator">:</span><span class="org-tuareg-font-lock-module">Mo.Frozen_core.</span>t <span class="org-tuareg-font-lock-operator">-></span> <span class="org-tuareg-font-lock-module">Mo.Basis.</span>t <span class="org-tuareg-font-lock-operator">-></span> t
|
||||
</pre>
|
||||
</div>
|
||||
|
||||
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
<col class="org-left" />
|
||||
|
||||
<col class="org-left" />
|
||||
</colgroup>
|
||||
<tbody>
|
||||
<tr>
|
||||
<td class="org-left"><code>make</code></td>
|
||||
<td class="org-left">Creates an MP2 data structure</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
|
||||
<pre class="example" id="org3955144">
|
||||
let mp2 =
|
||||
Mp2.make ~frozen_core:(Mo.Frozen_core.(make Small molecule)) mo_basis
|
||||
;;
|
||||
- : Mp2.t : <abstr>
|
||||
</pre>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0bf5c08" class="outline-3">
|
||||
<h3 id="org0bf5c08"><span class="section-number-3">1.3</span> Access</h3>
|
||||
<div class="outline-text-3" id="text-1-3">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">energy</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> float
|
||||
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">mo_basis</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> <span class="org-tuareg-font-lock-module">Mo.Basis.</span>t
|
||||
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">frozen_core</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> <span class="org-tuareg-font-lock-module">Mo.Frozen_core.</span>t
|
||||
</pre>
|
||||
</div>
|
||||
|
||||
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
<col class="org-left" />
|
||||
|
||||
<col class="org-left" />
|
||||
</colgroup>
|
||||
<tbody>
|
||||
<tr>
|
||||
<td class="org-left"><code>energy</code></td>
|
||||
<td class="org-left">Returns the MP2 energy</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>mo_basis</code></td>
|
||||
<td class="org-left">Returns the MO basis on which the MP2 energy was computed</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>frozen_core</code></td>
|
||||
<td class="org-left">Returns the frozen<sub>core</sub> scheme used to compute the MP2 energy</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
|
||||
<pre class="example" id="orgabe71c7">
|
||||
|
||||
</pre>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org10bdc37" class="outline-3">
|
||||
<h3 id="org10bdc37"><span class="section-number-3">1.4</span> Printers</h3>
|
||||
<div class="outline-text-3" id="text-1-4">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">pp</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Format.</span>formatter <span class="org-tuareg-font-lock-operator">-></span> t <span class="org-tuareg-font-lock-operator">-></span> unit
|
||||
</pre>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org38093b0" class="outline-3">
|
||||
<h3 id="org38093b0"><span class="section-number-3">1.5</span> Tests</h3>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: Anthony Scemama</p>
|
||||
<p class="date">Created: 2021-01-01 Fri 16:38</p>
|
||||
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
</html>
|
||||
|
|
@ -0,0 +1,368 @@
|
|||
<?xml version="1.0" encoding="utf-8"?>
|
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
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</head>
|
||||
<body>
|
||||
<div id="content">
|
||||
<h1 class="title">Simulation</h1>
|
||||
<div id="table-of-contents">
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#orgf303bc5">1. Simulation</a>
|
||||
<ul>
|
||||
<li><a href="#org2e878c8">1.1. Type</a></li>
|
||||
<li><a href="#org0ad2cbd">1.2. Access</a></li>
|
||||
<li><a href="#orgee1bf18">1.3. Creation</a></li>
|
||||
<li><a href="#org7e516a7">1.4. Printers</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-ocaml" id="orgd63cdb3"><span class="org-string">"Data describing a simulation (AOs, operators, nuclear coordinate,...)"</span>
|
||||
</pre>
|
||||
</div>
|
||||
|
||||
|
||||
<div id="outline-container-orgf303bc5" class="outline-2">
|
||||
<h2 id="orgf303bc5"><span class="section-number-2">1</span> Simulation</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
<p>
|
||||
Contains the state of the simulation.
|
||||
</p>
|
||||
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-ocaml" id="orgb80da13"><span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Common</span>
|
||||
<span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Particles</span>
|
||||
<span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Operators</span>
|
||||
</pre>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2e878c8" class="outline-3">
|
||||
<h3 id="org2e878c8"><span class="section-number-3">1.1</span> Type</h3>
|
||||
<div class="outline-text-3" id="text-1-1">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-ocaml" id="orgd92e1cd"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
|
||||
</pre>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0ad2cbd" class="outline-3">
|
||||
<h3 id="org0ad2cbd"><span class="section-number-3">1.2</span> Access</h3>
|
||||
<div class="outline-text-3" id="text-1-2">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">nuclei</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> <span class="org-tuareg-font-lock-module">Nuclei.</span>t
|
||||
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">charge</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> <span class="org-tuareg-font-lock-module">Charge.</span>t
|
||||
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">electrons</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> <span class="org-tuareg-font-lock-module">Electrons.</span>t
|
||||
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">ao_basis</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> <span class="org-tuareg-font-lock-module">Ao.Basis.</span>t
|
||||
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">nuclear_repulsion</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> float
|
||||
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">operators</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> <span class="org-tuareg-font-lock-module">Operator.</span>t list
|
||||
</pre>
|
||||
</div>
|
||||
|
||||
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
<col class="org-left" />
|
||||
|
||||
<col class="org-left" />
|
||||
</colgroup>
|
||||
<tbody>
|
||||
<tr>
|
||||
<td class="org-left"><code>nuclei</code></td>
|
||||
<td class="org-left">Nuclear coordinates used in the smiulation</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>charge</code></td>
|
||||
<td class="org-left">Total charge (electrons + nuclei)</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>electrons</code></td>
|
||||
<td class="org-left">Electrons used in the simulation</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>ao_basis</code></td>
|
||||
<td class="org-left">Atomic basis set</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>nuclear_repulsion</code></td>
|
||||
<td class="org-left">Nuclear repulsion energy</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td class="org-left"><code>operators</code></td>
|
||||
<td class="org-left">List of extra operators (range-separation, f12, etc)</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgee1bf18" class="outline-3">
|
||||
<h3 id="orgee1bf18"><span class="section-number-3">1.3</span> Creation</h3>
|
||||
<div class="outline-text-3" id="text-1-3">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">make</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-label">?multiplicity</span><span class="org-tuareg-font-lock-operator">:</span>int <span class="org-tuareg-font-lock-operator">-></span> <span class="org-tuareg-font-lock-label">?charge</span><span class="org-tuareg-font-lock-operator">:</span>int <span class="org-tuareg-font-lock-operator">-></span>
|
||||
<span class="org-tuareg-font-lock-label">?operators</span><span class="org-tuareg-font-lock-operator">:</span><span class="org-tuareg-font-lock-module">Operator.</span>t list<span class="org-tuareg-font-lock-operator">-></span> <span class="org-tuareg-font-lock-label">nuclei</span><span class="org-tuareg-font-lock-operator">:</span><span class="org-tuareg-font-lock-module">Nuclei.</span>t <span class="org-tuareg-font-lock-operator">-></span>
|
||||
<span class="org-tuareg-font-lock-module">Ao.Basis.</span>t <span class="org-tuareg-font-lock-operator">-></span> t
|
||||
</pre>
|
||||
</div>
|
||||
|
||||
<p>
|
||||
Defaults:
|
||||
</p>
|
||||
<ul class="org-ul">
|
||||
<li>multiplicity : <code>1</code></li>
|
||||
<li>charge : <code>0</code></li>
|
||||
<li>operators : <code>[]</code></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org7e516a7" class="outline-3">
|
||||
<h3 id="org7e516a7"><span class="section-number-3">1.4</span> Printers</h3>
|
||||
<div class="outline-text-3" id="text-1-4">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">pp</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Format.</span>formatter <span class="org-tuareg-font-lock-operator">-></span> t <span class="org-tuareg-font-lock-operator">-></span> unit
|
||||
</pre>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: Anthony Scemama</p>
|
||||
<p class="date">Created: 2021-01-01 Fri 16:38</p>
|
||||
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
</html>
|
||||
|
|
@ -32,7 +32,7 @@ let matrix t = function
|
|||
| "x4" -> t.(12)
|
||||
| "y4" -> t.(13)
|
||||
| "z4" -> t.(14)
|
||||
| _ -> Util.not_implemented ()
|
||||
| _ -> Util.not_implemented "Multipole"
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -95,18 +95,14 @@ let mo_class_array t =
|
|||
|
||||
let fci ~frozen_core mo_basis =
|
||||
let mo_num = Basis.size mo_basis in
|
||||
let ncore = (Nuclei.small_core @@ Simulation.nuclei @@ Basis.simulation mo_basis) / 2 in
|
||||
let ncore = Frozen_core.num_mos frozen_core in
|
||||
of_list (
|
||||
if frozen_core then
|
||||
List.concat [
|
||||
Util.list_range 1 ncore
|
||||
|> List.map (fun i -> Core i) ;
|
||||
Util.list_range (ncore+1) mo_num
|
||||
|> List.map (fun i -> Active i)
|
||||
]
|
||||
else
|
||||
Util.list_range 1 mo_num
|
||||
|> List.map (fun i -> Active i)
|
||||
)
|
||||
|
||||
let cas_sd mo_basis ~frozen_core n m =
|
||||
|
|
@ -117,19 +113,11 @@ let cas_sd mo_basis ~frozen_core n m =
|
|||
let n_alfa_in_cas = (n - n_unpaired)/2 + n_unpaired in
|
||||
let last_inactive = n_alfa - n_alfa_in_cas in
|
||||
let last_active = last_inactive + m in
|
||||
let ncore =
|
||||
if frozen_core then
|
||||
(Nuclei.small_core @@ Simulation.nuclei @@ Basis.simulation mo_basis) / 2
|
||||
|> min last_inactive
|
||||
else 0
|
||||
in
|
||||
let ncore = min (Frozen_core.num_mos frozen_core) last_inactive in
|
||||
of_list (
|
||||
List.concat [
|
||||
if ncore > 0 then
|
||||
Util.list_range 1 ncore
|
||||
|> List.map (fun i -> Core i)
|
||||
else
|
||||
[] ;
|
||||
Util.list_range 1 ncore
|
||||
|> List.map (fun i -> Core i) ;
|
||||
Util.list_range (ncore+1) last_inactive
|
||||
|> List.map (fun i -> Inactive i) ;
|
||||
Util.list_range (last_inactive+1) last_active
|
||||
|
|
|
|||
|
|
@ -15,12 +15,12 @@ val of_list : mo_class list -> t
|
|||
|
||||
val to_list : t -> mo_class list
|
||||
|
||||
val fci : frozen_core:bool -> Basis.t -> t
|
||||
val fci : frozen_core:Frozen_core.t -> Basis.t -> t
|
||||
(** Creates the MO classes for FCI calculations : all [Active]. The
|
||||
[n] lowest MOs are [Core] if [frozen_core = true].
|
||||
*)
|
||||
|
||||
val cas_sd: Basis.t -> frozen_core:bool -> int -> int -> t
|
||||
val cas_sd: Basis.t -> frozen_core:Frozen_core.t -> int -> int -> t
|
||||
(** [cas_sd mo_basis n m ] creates the MO classes for CAS(n,m) + SD
|
||||
calculations. lowest MOs are [Core], then all the next MOs are [Inactive],
|
||||
then [Active], then [Virtual].
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
(* [[file:../frozen_core.org::*Type][Type:3]] *)
|
||||
(* [[file:~/QCaml/mo/frozen_core.org::*Type][Type:3]] *)
|
||||
type kind =
|
||||
| All_electron
|
||||
| Small
|
||||
|
|
@ -21,7 +21,7 @@ type t = int array
|
|||
* #+end_example *)
|
||||
|
||||
|
||||
(* [[file:../frozen_core.org::*Creation][Creation:2]] *)
|
||||
(* [[file:~/QCaml/mo/frozen_core.org::*Creation][Creation:2]] *)
|
||||
let make_ae nuclei =
|
||||
Array.map (fun _ -> 0) nuclei
|
||||
|
||||
|
|
@ -56,7 +56,7 @@ let of_int_list = Array.of_list
|
|||
* #+end_example *)
|
||||
|
||||
|
||||
(* [[file:../frozen_core.org::*Access][Access:2]] *)
|
||||
(* [[file:~/QCaml/mo/frozen_core.org::*Access][Access:2]] *)
|
||||
let num_elec t =
|
||||
Array.fold_left ( + ) 0 t
|
||||
|
||||
|
|
@ -64,7 +64,7 @@ let num_mos t =
|
|||
(num_elec t) / 2
|
||||
(* Access:2 ends here *)
|
||||
|
||||
(* [[file:../frozen_core.org::*Printers][Printers:2]] *)
|
||||
(* [[file:~/QCaml/mo/frozen_core.org::*Printers][Printers:2]] *)
|
||||
let pp ppf t =
|
||||
Format.fprintf ppf "@[[|";
|
||||
Array.iter (fun x -> Format.fprintf ppf "@,@[%d@]" x) t;
|
||||
|
|
|
|||
|
|
@ -2,21 +2,21 @@
|
|||
*
|
||||
* #+NAME: types *)
|
||||
|
||||
(* [[file:../frozen_core.org::types][types]] *)
|
||||
(* [[file:~/QCaml/mo/frozen_core.org::types][types]] *)
|
||||
type kind =
|
||||
| All_electron
|
||||
| Small
|
||||
| Large
|
||||
(* types ends here *)
|
||||
|
||||
(* [[file:../frozen_core.org::*Type][Type:2]] *)
|
||||
(* [[file:~/QCaml/mo/frozen_core.org::*Type][Type:2]] *)
|
||||
type t
|
||||
(* Type:2 ends here *)
|
||||
|
||||
(* Creation *)
|
||||
|
||||
|
||||
(* [[file:../frozen_core.org::*Creation][Creation:1]] *)
|
||||
(* [[file:~/QCaml/mo/frozen_core.org::*Creation][Creation:1]] *)
|
||||
val make : kind -> Particles.Nuclei.t -> t
|
||||
|
||||
val of_int_list : int list -> t
|
||||
|
|
@ -26,7 +26,7 @@ val of_int_array : int array -> t
|
|||
(* Access *)
|
||||
|
||||
|
||||
(* [[file:../frozen_core.org::*Access][Access:1]] *)
|
||||
(* [[file:~/QCaml/mo/frozen_core.org::*Access][Access:1]] *)
|
||||
val num_elec : t -> int
|
||||
val num_mos : t -> int
|
||||
(* Access:1 ends here *)
|
||||
|
|
@ -34,6 +34,6 @@ val num_mos : t -> int
|
|||
(* Printers *)
|
||||
|
||||
|
||||
(* [[file:../frozen_core.org::*Printers][Printers:1]] *)
|
||||
(* [[file:~/QCaml/mo/frozen_core.org::*Printers][Printers:1]] *)
|
||||
val pp : Format.formatter -> t -> unit
|
||||
(* Printers:1 ends here *)
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
(* [[file:../nuclei.org::*Type][Type:2]] *)
|
||||
(* [[file:~/QCaml/particles/nuclei.org::*Type][Type:2]] *)
|
||||
open Common
|
||||
|
||||
type t = (Element.t * Coordinate.t) array
|
||||
|
|
@ -15,7 +15,7 @@ open Xyz_ast
|
|||
* | ~of_filename~ | Detects the type of file (xyz, z-matrix) and reads the file | *)
|
||||
|
||||
|
||||
(* [[file:../nuclei.org::*Conversion][Conversion:2]] *)
|
||||
(* [[file:~/QCaml/particles/nuclei.org::*Conversion][Conversion:2]] *)
|
||||
let of_xyz_lexbuf lexbuf =
|
||||
let data =
|
||||
Xyz_parser.input Nuclei_lexer.read_all lexbuf
|
||||
|
|
@ -126,7 +126,7 @@ let to_xyz_string t =
|
|||
* | ~large_core~ | Number of core electrons in the large core model | *)
|
||||
|
||||
|
||||
(* [[file:../nuclei.org::*Query][Query:2]] *)
|
||||
(* [[file:~/QCaml/particles/nuclei.org::*Query][Query:2]] *)
|
||||
let formula t =
|
||||
let dict = Hashtbl.create 67 in
|
||||
Array.iter (fun (e,_) ->
|
||||
|
|
@ -176,7 +176,7 @@ let large_core a =
|
|||
Array.fold_left (fun accu (e,_) -> accu + (Element.large_core e)) 0 a
|
||||
(* Query:2 ends here *)
|
||||
|
||||
(* [[file:../nuclei.org::*Printers][Printers:2]] *)
|
||||
(* [[file:~/QCaml/particles/nuclei.org::*Printers][Printers:2]] *)
|
||||
let pp ppf t =
|
||||
Format.fprintf ppf "@[%s@]" (to_string t)
|
||||
(* Printers:2 ends here *)
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
*
|
||||
* #+NAME: types *)
|
||||
|
||||
(* [[file:../nuclei.org::types][types]] *)
|
||||
(* [[file:~/QCaml/particles/nuclei.org::types][types]] *)
|
||||
open Common
|
||||
|
||||
type t = (Element.t * Coordinate.t) array
|
||||
|
|
@ -11,7 +11,7 @@ type t = (Element.t * Coordinate.t) array
|
|||
(* Conversion *)
|
||||
|
||||
|
||||
(* [[file:../nuclei.org::*Conversion][Conversion:1]] *)
|
||||
(* [[file:~/QCaml/particles/nuclei.org::*Conversion][Conversion:1]] *)
|
||||
val of_xyz_string : string -> t
|
||||
val to_xyz_string : t -> string
|
||||
val of_xyz_file : string -> t
|
||||
|
|
@ -27,7 +27,7 @@ val of_filename : string -> t
|
|||
(* TODO Query *)
|
||||
|
||||
|
||||
(* [[file:../nuclei.org::*Query][Query:1]] *)
|
||||
(* [[file:~/QCaml/particles/nuclei.org::*Query][Query:1]] *)
|
||||
val formula : t -> string
|
||||
val repulsion : t -> float
|
||||
val charge : t -> Charge.t
|
||||
|
|
@ -38,6 +38,6 @@ val large_core : t -> int
|
|||
(* Printers *)
|
||||
|
||||
|
||||
(* [[file:../nuclei.org::*Printers][Printers:1]] *)
|
||||
(* [[file:~/QCaml/particles/nuclei.org::*Printers][Printers:1]] *)
|
||||
val pp : Format.formatter -> t -> unit
|
||||
(* Printers:1 ends here *)
|
||||
|
|
|
|||
|
|
@ -4,7 +4,7 @@
|
|||
* an xyz file. *)
|
||||
|
||||
|
||||
(* [[file:../nuclei.org::*Lexer][Lexer:1]] *)
|
||||
(* [[file:~/QCaml/particles/nuclei.org::*Lexer][Lexer:1]] *)
|
||||
{
|
||||
open Xyz_parser
|
||||
}
|
||||
|
|
|
|||
|
|
@ -4,7 +4,7 @@
|
|||
* an ~xyz_file~ data structure. *)
|
||||
|
||||
|
||||
(* [[file:../nuclei.org::*Parser][Parser:2]] *)
|
||||
(* [[file:~/QCaml/particles/nuclei.org::*Parser][Parser:2]] *)
|
||||
open Common
|
||||
|
||||
type nucleus =
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
(* Tests *)
|
||||
|
||||
|
||||
(* [[file:../nuclei.org::*Tests][Tests:1]] *)
|
||||
(* [[file:~/QCaml/particles/nuclei.org::*Tests][Tests:1]] *)
|
||||
open Common
|
||||
open Particles
|
||||
open Alcotest
|
||||
|
|
|
|||
|
|
@ -1,21 +1,31 @@
|
|||
open Linear_algebra
|
||||
|
||||
type t = float
|
||||
(* [[file:~/QCaml/perturbation/mp2.org::*Type][Type:2]] *)
|
||||
type t = {
|
||||
energy : float ;
|
||||
mo_basis : Mo.Basis.t ;
|
||||
frozen_core : Mo.Frozen_core.t ;
|
||||
}
|
||||
(* Type:2 ends here *)
|
||||
|
||||
|
||||
|
||||
(* | ~make~ | Creates an MP2 data structure |
|
||||
*
|
||||
* #+begin_example
|
||||
* let mp2 =
|
||||
* Mp2.make ~frozen_core:(Mo.Frozen_core.(make Small molecule)) mo_basis
|
||||
* ;;
|
||||
* - : Mp2.t : <abstr>
|
||||
* #+end_example *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/perturbation/mp2.org::*Creation][Creation:2]] *)
|
||||
open Linear_algebra
|
||||
|
||||
let make_rmp2 mo_basis mo_class =
|
||||
|
||||
let epsilon = Mo.Basis.mo_energies mo_basis in
|
||||
let eri = Mo.Basis.ee_ints mo_basis in
|
||||
|
||||
let make ~frozen_core hf =
|
||||
let mo_basis =
|
||||
Mo.Basis.of_hartree_fock hf
|
||||
in
|
||||
let epsilon =
|
||||
Mo.Basis.mo_energies mo_basis
|
||||
in
|
||||
let mo_class =
|
||||
Mo.Class.cas_sd mo_basis ~frozen_core 0 0
|
||||
|> Mo.Class.to_list
|
||||
in
|
||||
let eri =
|
||||
Mo.Basis.ee_ints mo_basis
|
||||
in
|
||||
let inactives =
|
||||
List.filter (fun i ->
|
||||
match i with Mo.Class.Inactive _ -> true | _ -> false) mo_class
|
||||
|
|
@ -24,39 +34,70 @@ let make ~frozen_core hf =
|
|||
match i with Mo.Class.Virtual _ -> true | _ -> false) mo_class
|
||||
in
|
||||
|
||||
let rmp2 () =
|
||||
List.fold_left (fun accu b ->
|
||||
match b with Mo.Class.Virtual b ->
|
||||
let eps = -. (epsilon%.(b)) in
|
||||
List.fold_left (fun accu b ->
|
||||
match b with Mo.Class.Virtual b ->
|
||||
let eps = -. (epsilon%.(b)) in
|
||||
accu +.
|
||||
List.fold_left (fun accu a ->
|
||||
match a with Mo.Class.Virtual a ->
|
||||
let eps = eps -. (epsilon%.(a)) in
|
||||
accu +.
|
||||
List.fold_left (fun accu a ->
|
||||
match a with Mo.Class.Virtual a ->
|
||||
let eps = eps -. (epsilon%.(a)) in
|
||||
accu +.
|
||||
List.fold_left (fun accu j ->
|
||||
match j with Mo.Class.Inactive j ->
|
||||
let eps = eps +. epsilon%.(j) in
|
||||
accu +.
|
||||
List.fold_left (fun accu i ->
|
||||
match i with Mo.Class.Inactive i ->
|
||||
let eps = eps +. epsilon%.(i) in
|
||||
let ijab = Four_idx_storage.get_phys eri i j a b
|
||||
and abji = Four_idx_storage.get_phys eri a b j i in
|
||||
let abij = ijab in
|
||||
accu +. ijab *. ( abij +. abij -. abji) /. eps
|
||||
| _ -> accu
|
||||
) 0. inactives
|
||||
| _ -> accu
|
||||
) 0. inactives
|
||||
| _ -> accu
|
||||
) 0. virtuals
|
||||
| _ -> accu
|
||||
List.fold_left (fun accu j ->
|
||||
match j with Mo.Class.Inactive j ->
|
||||
let eps = eps +. epsilon%.(j) in
|
||||
accu +.
|
||||
List.fold_left (fun accu i ->
|
||||
match i with Mo.Class.Inactive i ->
|
||||
let eps = eps +. epsilon%.(i) in
|
||||
let ijab = Four_idx_storage.get_phys eri i j a b
|
||||
and abji = Four_idx_storage.get_phys eri a b j i in
|
||||
let abij = ijab in
|
||||
accu +. ijab *. ( abij +. abij -. abji) /. eps
|
||||
| _ -> accu
|
||||
) 0. inactives
|
||||
| _ -> accu
|
||||
) 0. inactives
|
||||
| _ -> accu
|
||||
) 0. virtuals
|
||||
| _ -> accu
|
||||
) 0. virtuals
|
||||
|
||||
|
||||
let make ~frozen_core mo_basis =
|
||||
|
||||
let mo_class =
|
||||
Mo.Class.cas_sd mo_basis ~frozen_core 0 0
|
||||
|> Mo.Class.to_list
|
||||
in
|
||||
|
||||
|
||||
match Mo.Hartree_fock.kind hf with
|
||||
| Mo.Hartree_fock.RHF -> rmp2 ()
|
||||
| _ -> failwith "Not implemented"
|
||||
let energy =
|
||||
match Mo.Basis.mo_type mo_basis with
|
||||
| RHF -> make_rmp2 mo_basis mo_class
|
||||
| ROHF -> Common.Util.not_implemented "ROHF MP2"
|
||||
| UHF -> Common.Util.not_implemented "UHF MP2"
|
||||
| _ -> invalid_arg "MP2 needs RHF or ROHF MOs"
|
||||
in
|
||||
{ energy ; mo_basis ; frozen_core }
|
||||
(* Creation:2 ends here *)
|
||||
|
||||
|
||||
|
||||
(* | ~energy~ | Returns the MP2 energy |
|
||||
* | ~mo_basis~ | Returns the MO basis on which the MP2 energy was computed |
|
||||
* | ~frozen_core~ | Returns the frozen_core scheme used to compute the MP2 energy |
|
||||
*
|
||||
* #+begin_example
|
||||
*
|
||||
* #+end_example *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/perturbation/mp2.org::*Access][Access:2]] *)
|
||||
let energy t = t.energy
|
||||
let mo_basis t = t.mo_basis
|
||||
let frozen_core t = t.frozen_core
|
||||
(* Access:2 ends here *)
|
||||
|
||||
(* [[file:~/QCaml/perturbation/mp2.org::*Printers][Printers:2]] *)
|
||||
let pp ppf t =
|
||||
Format.fprintf ppf "@[E(MP2)=%f@]" t.energy
|
||||
(* Printers:2 ends here *)
|
||||
|
|
|
|||
|
|
@ -0,0 +1,29 @@
|
|||
(* Type *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/perturbation/mp2.org::*Type][Type:1]] *)
|
||||
type t
|
||||
(* Type:1 ends here *)
|
||||
|
||||
(* Creation *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/perturbation/mp2.org::*Creation][Creation:1]] *)
|
||||
val make : frozen_core:Mo.Frozen_core.t -> Mo.Basis.t -> t
|
||||
(* Creation:1 ends here *)
|
||||
|
||||
(* Access *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/perturbation/mp2.org::*Access][Access:1]] *)
|
||||
val energy : t -> float
|
||||
val mo_basis : t -> Mo.Basis.t
|
||||
val frozen_core : t -> Mo.Frozen_core.t
|
||||
(* Access:1 ends here *)
|
||||
|
||||
(* Printers *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/perturbation/mp2.org::*Printers][Printers:1]] *)
|
||||
val pp : Format.formatter -> t -> unit
|
||||
(* Printers:1 ends here *)
|
||||
|
|
@ -0,0 +1,180 @@
|
|||
#+begin_src elisp tangle: no :results none :exports none
|
||||
(setq pwd (file-name-directory buffer-file-name))
|
||||
(setq name (file-name-nondirectory (substring buffer-file-name 0 -4)))
|
||||
(setq lib (concat pwd "lib/"))
|
||||
(setq testdir (concat pwd "test/"))
|
||||
(setq mli (concat lib name ".mli"))
|
||||
(setq ml (concat lib name ".ml"))
|
||||
(setq test-ml (concat testdir name ".ml"))
|
||||
(org-babel-tangle)
|
||||
#+end_src
|
||||
|
||||
* MP2
|
||||
:PROPERTIES:
|
||||
:header-args: :noweb yes :comments both
|
||||
:END:
|
||||
|
||||
** Type
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
type t
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
type t = {
|
||||
energy : float ;
|
||||
mo_basis : Mo.Basis.t ;
|
||||
frozen_core : Mo.Frozen_core.t ;
|
||||
}
|
||||
#+end_src
|
||||
|
||||
** Creation
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val make : frozen_core:Mo.Frozen_core.t -> Mo.Basis.t -> t
|
||||
#+end_src
|
||||
|
||||
| ~make~ | Creates an MP2 data structure |
|
||||
|
||||
#+begin_example
|
||||
let mp2 =
|
||||
Mp2.make ~frozen_core:(Mo.Frozen_core.(make Small molecule)) mo_basis
|
||||
;;
|
||||
- : Mp2.t : <abstr>
|
||||
#+end_example
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
open Linear_algebra
|
||||
|
||||
let make_rmp2 mo_basis mo_class =
|
||||
|
||||
let epsilon = Mo.Basis.mo_energies mo_basis in
|
||||
let eri = Mo.Basis.ee_ints mo_basis in
|
||||
|
||||
let inactives =
|
||||
List.filter (fun i ->
|
||||
match i with Mo.Class.Inactive _ -> true | _ -> false) mo_class
|
||||
and virtuals =
|
||||
List.filter (fun i ->
|
||||
match i with Mo.Class.Virtual _ -> true | _ -> false) mo_class
|
||||
in
|
||||
|
||||
List.fold_left (fun accu b ->
|
||||
match b with Mo.Class.Virtual b ->
|
||||
let eps = -. (epsilon%.(b)) in
|
||||
accu +.
|
||||
List.fold_left (fun accu a ->
|
||||
match a with Mo.Class.Virtual a ->
|
||||
let eps = eps -. (epsilon%.(a)) in
|
||||
accu +.
|
||||
List.fold_left (fun accu j ->
|
||||
match j with Mo.Class.Inactive j ->
|
||||
let eps = eps +. epsilon%.(j) in
|
||||
accu +.
|
||||
List.fold_left (fun accu i ->
|
||||
match i with Mo.Class.Inactive i ->
|
||||
let eps = eps +. epsilon%.(i) in
|
||||
let ijab = Four_idx_storage.get_phys eri i j a b
|
||||
and abji = Four_idx_storage.get_phys eri a b j i in
|
||||
let abij = ijab in
|
||||
accu +. ijab *. ( abij +. abij -. abji) /. eps
|
||||
| _ -> accu
|
||||
) 0. inactives
|
||||
| _ -> accu
|
||||
) 0. inactives
|
||||
| _ -> accu
|
||||
) 0. virtuals
|
||||
| _ -> accu
|
||||
) 0. virtuals
|
||||
|
||||
|
||||
let make ~frozen_core mo_basis =
|
||||
|
||||
let mo_class =
|
||||
Mo.Class.cas_sd mo_basis ~frozen_core 0 0
|
||||
|> Mo.Class.to_list
|
||||
in
|
||||
|
||||
let energy =
|
||||
match Mo.Basis.mo_type mo_basis with
|
||||
| RHF -> make_rmp2 mo_basis mo_class
|
||||
| ROHF -> Common.Util.not_implemented "ROHF MP2"
|
||||
| UHF -> Common.Util.not_implemented "UHF MP2"
|
||||
| _ -> invalid_arg "MP2 needs RHF or ROHF MOs"
|
||||
in
|
||||
{ energy ; mo_basis ; frozen_core }
|
||||
#+end_src
|
||||
|
||||
** Access
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val energy : t -> float
|
||||
val mo_basis : t -> Mo.Basis.t
|
||||
val frozen_core : t -> Mo.Frozen_core.t
|
||||
#+end_src
|
||||
|
||||
| ~energy~ | Returns the MP2 energy |
|
||||
| ~mo_basis~ | Returns the MO basis on which the MP2 energy was computed |
|
||||
| ~frozen_core~ | Returns the frozen_core scheme used to compute the MP2 energy |
|
||||
|
||||
#+begin_example
|
||||
|
||||
#+end_example
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
let energy t = t.energy
|
||||
let mo_basis t = t.mo_basis
|
||||
let frozen_core t = t.frozen_core
|
||||
#+end_src
|
||||
|
||||
|
||||
** Printers
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val pp : Format.formatter -> t -> unit
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
let pp ppf t =
|
||||
Format.fprintf ppf "@[E(MP2)=%f@]" t.energy
|
||||
#+end_src
|
||||
|
||||
** Tests
|
||||
|
||||
#+begin_src ocaml :tangle (eval test-ml) :exports none
|
||||
open Alcotest
|
||||
open Particles
|
||||
|
||||
let wd = Common.Qcaml.root ^ Filename.dir_sep ^ "test"
|
||||
|
||||
let tests =
|
||||
[ "HF Water", `Quick, fun () ->
|
||||
let nuclei =
|
||||
wd ^ Filename.dir_sep ^ "water.xyz"
|
||||
|> Nuclei.of_xyz_file
|
||||
in
|
||||
let basis_filename =
|
||||
wd ^ Filename.dir_sep ^ "cc-pvdz"
|
||||
in
|
||||
let ao_basis =
|
||||
Ao.Basis.of_nuclei_and_basis_filename ~kind:`Gaussian
|
||||
~cartesian:false ~nuclei basis_filename
|
||||
in
|
||||
|
||||
let simulation = Simulation.make ~nuclei ao_basis in
|
||||
|
||||
let hf = Mo.Hartree_fock.make ~guess:`Huckel simulation in
|
||||
Format.printf "%a" (Mo.Hartree_fock.pp) hf;
|
||||
check (float 2.e-10) "Energy" (-76.0267987005) (Mo.Hartree_fock.energy hf);
|
||||
|
||||
let mo_basis = Mo.Basis.of_hartree_fock hf in
|
||||
|
||||
let frozen_core = Mo.Frozen_core.(make Small nuclei) in
|
||||
|
||||
let e_mp2 = Perturbation.Mp2.make ~frozen_core mo_basis in
|
||||
|
||||
check (float 1.e-9) "MP2" (-0.2016211415) (e_mp2)
|
||||
]
|
||||
|
||||
#+end_src
|
||||
|
||||
|
|
@ -1,3 +1,7 @@
|
|||
(* Tests *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/perturbation/mp2.org::*Tests][Tests:1]] *)
|
||||
open Alcotest
|
||||
open Particles
|
||||
|
||||
|
|
@ -16,12 +20,19 @@ let tests =
|
|||
Ao.Basis.of_nuclei_and_basis_filename ~kind:`Gaussian
|
||||
~cartesian:false ~nuclei basis_filename
|
||||
in
|
||||
|
||||
let simulation = Simulation.make ~nuclei ao_basis in
|
||||
|
||||
let hf = Mo.Hartree_fock.make ~guess:`Huckel simulation in
|
||||
Format.printf "%a" (Mo.Hartree_fock.pp) hf;
|
||||
check (float 2.e-10) "Energy" (-76.0267987005) (Mo.Hartree_fock.energy hf);
|
||||
let e_mp2 = Perturbation.Mp2.make ~frozen_core:true hf in
|
||||
Printf.printf "%s\n" (string_of_float e_mp2);
|
||||
|
||||
let mo_basis = Mo.Basis.of_hartree_fock hf in
|
||||
|
||||
let frozen_core = Mo.Frozen_core.(make Small nuclei) in
|
||||
|
||||
let e_mp2 = Perturbation.Mp2.make ~frozen_core mo_basis in
|
||||
|
||||
check (float 1.e-9) "MP2" (-0.2016211415) (e_mp2)
|
||||
]
|
||||
|
||||
(* Tests:1 ends here *)
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
(* [[file:../simulation.org::*Simulation][Simulation:2]] *)
|
||||
(* [[file:~/QCaml/simulation/simulation.org::*Simulation][Simulation:2]] *)
|
||||
open Common
|
||||
open Particles
|
||||
open Operators
|
||||
(* Simulation:2 ends here *)
|
||||
|
||||
(* [[file:../simulation.org::*Type][Type:2]] *)
|
||||
(* [[file:~/QCaml/simulation/simulation.org::*Type][Type:2]] *)
|
||||
type t = {
|
||||
charge : Charge.t;
|
||||
electrons : Electrons.t;
|
||||
|
|
@ -24,7 +24,7 @@ type t = {
|
|||
* | ~operators~ | List of extra operators (range-separation, f12, etc) | *)
|
||||
|
||||
|
||||
(* [[file:../simulation.org::*Access][Access:2]] *)
|
||||
(* [[file:~/QCaml/simulation/simulation.org::*Access][Access:2]] *)
|
||||
let nuclei t = t.nuclei
|
||||
let charge t = t.charge
|
||||
let electrons t = t.electrons
|
||||
|
|
@ -41,7 +41,7 @@ let operators t = t.operators
|
|||
* - operators : ~[]~ *)
|
||||
|
||||
|
||||
(* [[file:../simulation.org::*Creation][Creation:2]] *)
|
||||
(* [[file:~/QCaml/simulation/simulation.org::*Creation][Creation:2]] *)
|
||||
let make
|
||||
?(multiplicity=1)
|
||||
?(charge=0)
|
||||
|
|
@ -65,7 +65,7 @@ let make
|
|||
{ charge ; nuclei ; electrons ; ao_basis ; operators}
|
||||
(* Creation:2 ends here *)
|
||||
|
||||
(* [[file:../simulation.org::*Printers][Printers:2]] *)
|
||||
(* [[file:~/QCaml/simulation/simulation.org::*Printers][Printers:2]] *)
|
||||
let pp ppf t =
|
||||
let formula = Nuclei.formula t.nuclei in
|
||||
let n_aos = Ao.Basis.size t.ao_basis in
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@
|
|||
*
|
||||
* #+NAME: open *)
|
||||
|
||||
(* [[file:../simulation.org::open][open]] *)
|
||||
(* [[file:~/QCaml/simulation/simulation.org::open][open]] *)
|
||||
open Common
|
||||
open Particles
|
||||
open Operators
|
||||
|
|
@ -17,14 +17,14 @@ open Operators
|
|||
*
|
||||
* #+NAME: types *)
|
||||
|
||||
(* [[file:../simulation.org::types][types]] *)
|
||||
(* [[file:~/QCaml/simulation/simulation.org::types][types]] *)
|
||||
type t
|
||||
(* types ends here *)
|
||||
|
||||
(* Access *)
|
||||
|
||||
|
||||
(* [[file:../simulation.org::*Access][Access:1]] *)
|
||||
(* [[file:~/QCaml/simulation/simulation.org::*Access][Access:1]] *)
|
||||
val nuclei : t -> Nuclei.t
|
||||
val charge : t -> Charge.t
|
||||
val electrons : t -> Electrons.t
|
||||
|
|
@ -36,7 +36,7 @@ val operators : t -> Operator.t list
|
|||
(* Creation *)
|
||||
|
||||
|
||||
(* [[file:../simulation.org::*Creation][Creation:1]] *)
|
||||
(* [[file:~/QCaml/simulation/simulation.org::*Creation][Creation:1]] *)
|
||||
val make : ?multiplicity:int -> ?charge:int ->
|
||||
?operators:Operator.t list-> nuclei:Nuclei.t ->
|
||||
Ao.Basis.t -> t
|
||||
|
|
@ -45,6 +45,6 @@ val make : ?multiplicity:int -> ?charge:int ->
|
|||
(* Printers *)
|
||||
|
||||
|
||||
(* [[file:../simulation.org::*Printers][Printers:1]] *)
|
||||
(* [[file:~/QCaml/simulation/simulation.org::*Printers][Printers:1]] *)
|
||||
val pp : Format.formatter -> t -> unit
|
||||
(* Printers:1 ends here *)
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
(* [[file:../install_printers.org::*Intall printers][Intall printers:3]] *)
|
||||
(* [[file:~/QCaml/top/install_printers.org::*Intall%20printers][Intall printers:3]] *)
|
||||
let printers =
|
||||
[
|
||||
"Common.Angular_momentum.pp" ;
|
||||
|
|
|
|||
Loading…
Reference in New Issue