LCPQ/QCaml
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Anthony Scemama 2021-01-01 16:39:33 +01:00
parent 28e6fda242
commit 73a5cf6ca2
38 changed files with 6151 additions and 200 deletions
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12
Makefile
View File

@ -1,12 +1,18 @@
# Frontend to dune. # Frontend to dune.
DIRS=$(shell ls */README.org | sed "s|/README.org||g")
DOCS=$(patsubst %, docs/%.html, $(DIRS))
.PHONY: default build install uninstall test clean .PHONY: default build install uninstall test clean
default: build default: tangle build doc
tangle:
doc: docs/%.html: %/README.org
- ./bin/tangle.sh $*
- ./bin/build_doc.sh $*
doc: $(DOCS)
build: build:
dune build dune build

3
ao/lib/basis.ml
View File

@ -21,7 +21,8 @@ let of_nuclei_and_basis_filename ?(kind=`Gaussian) ?operators ?(cartesian=false)
{ ao_basis ; cartesian } { ao_basis ; cartesian }
| _ -> failwith "of_nuclei_and_basis_filename needs to be called with `Gaussian" | _ -> failwith "of_nuclei_and_basis_filename needs to be called with `Gaussian"
let not_implemented = Util.not_implemented let not_implemented () =
Util.not_implemented "Only Gaussian is implemented"
let ao_basis t = t.ao_basis let ao_basis t = t.ao_basis

2
bin/build_doc.sh
View File

@ -24,4 +24,6 @@ CONFIG="--load docs/htmlize.el --load docs/config.el"
emacs --batch $CONFIG docs/${DIR}.org -f org-html-export-to-html emacs --batch $CONFIG docs/${DIR}.org -f org-html-export-to-html
rm docs/${DIR}.org

79
bin/tangle.sh
View File

@ -14,88 +14,11 @@ fi
DIR=${1%/} DIR=${1%/}
cat << EOF > ${PWD}/tmpfile_$DIR
(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"))
(org-babel-tangle)
EOF
cd $DIR cd $DIR
for i in *.org for i in *.org
do do
echo "--- $i ----" echo "--- $i ----"
emacs --batch ./$i --load=../tmpfile_$DIR emacs --batch ./$i --load=../docs/config_tangle.el -f org-babel-tangle
done done
rm ../tmpfile_$DIR

8
common/lib/charge.ml
View File

@ -3,11 +3,11 @@
(* This type should be used for all charges in the program (electrons, nuclei,...). *) (* This type should be used for all charges in the program (electrons, nuclei,...). *)
(* [[file:../charge.org::*Type][Type:2]] *) (* [[file:~/QCaml/common/charge.org::*Type][Type:2]] *)
type t = float type t = float
(* Type:2 ends here *) (* Type:2 ends here *)
(* [[file:../charge.org::*Conversions][Conversions:2]] *) (* [[file:~/QCaml/common/charge.org::*Conversions][Conversions:2]] *)
external of_float : float -> t = "%identity" external of_float : float -> t = "%identity"
external to_float : t -> float = "%identity" external to_float : t -> float = "%identity"
@ -25,7 +25,7 @@ let to_string x =
"0.0" "0.0"
(* Conversions:2 ends here *) (* Conversions:2 ends here *)
(* [[file:../charge.org::*Simple operations][Simple operations:2]] *) (* [[file:~/QCaml/common/charge.org::*Simple%20operations][Simple operations:2]] *)
let gen_op op = let gen_op op =
fun a b -> fun a b ->
op (to_float a) (to_float b) op (to_float a) (to_float b)
@ -39,7 +39,7 @@ let ( / ) = gen_op ( /. )
let is_null t = t == 0. let is_null t = t == 0.
(* Simple operations:2 ends here *) (* Simple operations:2 ends here *)
(* [[file:../charge.org::*Printers][Printers:2]] *) (* [[file:~/QCaml/common/charge.org::*Printers][Printers:2]] *)
let pp ppf x = let pp ppf x =
Format.fprintf ppf "@[%s@]" (to_string x) Format.fprintf ppf "@[%s@]" (to_string x)
(* Printers:2 ends here *) (* Printers:2 ends here *)

8
common/lib/charge.mli
View File

@ -1,14 +1,14 @@
(* Type *) (* Type *)
(* [[file:../charge.org::*Type][Type:1]] *) (* [[file:~/QCaml/common/charge.org::*Type][Type:1]] *)
type t type t
(* Type:1 ends here *) (* Type:1 ends here *)
(* Conversions *) (* Conversions *)
(* [[file:../charge.org::*Conversions][Conversions:1]] *) (* [[file:~/QCaml/common/charge.org::*Conversions][Conversions:1]] *)
val of_float : float -> t val of_float : float -> t
val to_float : t -> float val to_float : t -> float
@ -22,7 +22,7 @@ val to_string: t -> string
(* Simple operations *) (* Simple operations *)
(* [[file:../charge.org::*Simple operations][Simple operations:1]] *) (* [[file:~/QCaml/common/charge.org::*Simple%20operations][Simple operations:1]] *)
val ( + ) : t -> t -> t val ( + ) : t -> t -> t
val ( - ) : t -> t -> t val ( - ) : t -> t -> t
val ( * ) : t -> float -> t val ( * ) : t -> float -> t
@ -33,6 +33,6 @@ val is_null : t -> bool
(* Printers *) (* Printers *)
(* [[file:../charge.org::*Printers][Printers:1]] *) (* [[file:~/QCaml/common/charge.org::*Printers][Printers:1]] *)
val pp : Format.formatter -> t -> unit val pp : Format.formatter -> t -> unit
(* Printers:1 ends here *) (* Printers:1 ends here *)

7
common/lib/util.ml
View File

@ -39,7 +39,7 @@ let leadz i = leadz i |> Int32.to_int
* | ~pow~ | Fast implementation of the power function for small integer powers | * | ~pow~ | Fast implementation of the power function for small integer powers |
* | ~chop~ | In ~chop a f~, evaluate ~f~ only if the absolute value of ~a~ is larger than ~Constants.epsilon~, and return ~a *. f ()~. | * | ~chop~ | In ~chop a f~, evaluate ~f~ only if the absolute value of ~a~ is larger than ~Constants.epsilon~, and return ~a *. f ()~. |
* | ~float_of_int_fast~ | Faster implementation of float_of_int for small positive ints | * | ~float_of_int_fast~ | Faster implementation of float_of_int for small positive ints |
* | ~not_implemented~ | Fails with error message if some functionality is not implemented | * | ~not_implemented~ | Fails if some functionality is not implemented |
* | ~of_some~ | Extracts the value of an option | *) * | ~of_some~ | Extracts the value of an option | *)
@ -123,8 +123,9 @@ let chop f g =
else f *. (g ()) else f *. (g ())
let not_implemented () = exception Not_implemented of string
failwith "Not implemented" let not_implemented string =
raise (Not_implemented string)
let of_some = function let of_some = function

5
common/lib/util.mli
View File

@ -35,8 +35,11 @@ val chop : float -> (unit -> float) -> float
val pow : float -> int -> float val pow : float -> int -> float
val float_of_int_fast : int -> float val float_of_int_fast : int -> float
val not_implemented : unit -> 'a
val of_some : 'a option -> 'a val of_some : 'a option -> 'a
exception Not_implemented of string
val not_implemented : string -> 'a
(* @raise Not_implemented. *)
(* General functions:1 ends here *) (* General functions:1 ends here *)
(* Functions related to the Boys function *) (* Functions related to the Boys function *)

12
common/util.org
View File

@ -213,8 +213,11 @@ val chop : float -> (unit -> float) -> float
val pow : float -> int -> float val pow : float -> int -> float
val float_of_int_fast : int -> float val float_of_int_fast : int -> float
val not_implemented : unit -> 'a
val of_some : 'a option -> 'a val of_some : 'a option -> 'a
exception Not_implemented of string
val not_implemented : string -> 'a
(* @raise Not_implemented. *)
#+end_src #+end_src
| ~fact~ | Factorial function. | | ~fact~ | Factorial function. |
@ -223,7 +226,7 @@ val of_some : 'a option -> 'a
| ~pow~ | Fast implementation of the power function for small integer powers | | ~pow~ | Fast implementation of the power function for small integer powers |
| ~chop~ | In ~chop a f~, evaluate ~f~ only if the absolute value of ~a~ is larger than ~Constants.epsilon~, and return ~a *. f ()~. | | ~chop~ | In ~chop a f~, evaluate ~f~ only if the absolute value of ~a~ is larger than ~Constants.epsilon~, and return ~a *. f ()~. |
| ~float_of_int_fast~ | Faster implementation of float_of_int for small positive ints | | ~float_of_int_fast~ | Faster implementation of float_of_int for small positive ints |
| ~not_implemented~ | Fails with error message if some functionality is not implemented | | ~not_implemented~ | Fails if some functionality is not implemented |
| ~of_some~ | Extracts the value of an option | | ~of_some~ | Extracts the value of an option |
#+begin_src ocaml :tangle (eval ml) :exports none #+begin_src ocaml :tangle (eval ml) :exports none
@ -306,8 +309,9 @@ let chop f g =
else f *. (g ()) else f *. (g ())
let not_implemented () = exception Not_implemented of string
failwith "Not implemented" let not_implemented string =
raise (Not_implemented string)
let of_some = function let of_some = function

239
docs/ao.html Normal file
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@ -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>Atomic Orbitals</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; }
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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");
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/*]]>*///-->
// @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>

2339
docs/common.html Normal file
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File diff suppressed because it is too large Load Diff

1
docs/config.el
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@ -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-output-type 'css) ; default: 'inline-css
(setq org-html-htmlize-font-prefix "org-") ; default: "org-" (setq org-html-htmlize-font-prefix "org-") ; default: "org-"
(setq org-confirm-babel-evaluate nil)
(setq c "c") (setq c "c")
(setq ml "ml") (setq ml "ml")

71
docs/config_tangle.el Executable file
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@ -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"))

239
docs/gaussian.html Normal file
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@ -0,0 +1,239 @@
<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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<h1 class="title">Gaussian</h1>
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<pre class="src src-ocaml" id="org5fcfd15"><span class="org-string">"Gaussian basis sets"</span>
</pre>
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<p class="author">Author: Anthony Scemama</p>
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<h1 class="title">Gaussian integrals</h1>
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<pre class="src src-ocaml" id="orgf36fc27"><span class="org-string">"Integrals on the Gaussian basis sets"</span>
</pre>
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<p class="author">Author: Anthony Scemama</p>
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<h1 class="title">Linear Algebra</h1>
<div class="org-src-container">
<pre class="src src-ocaml" id="org6e8c657"><span class="org-string">"Linear algebra utilities of QCaml libraries."</span>
</pre>
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<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>
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<div id="content">
<h1 class="title">Molecular orbitals</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org9d1c0a9">1. Frozen core</a>
<ul>
<li><a href="#org1c7c95a">1.1. Type</a></li>
<li><a href="#orgb2586e7">1.2. Creation</a></li>
<li><a href="#org482997a">1.3. Access</a></li>
<li><a href="#orga5d7816">1.4. Printers</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div class="org-src-container">
<pre class="src src-ocaml" id="org7d44fe6"><span class="org-string">"Molecular orbitals"</span>
</pre>
</div>
<div id="outline-container-org9d1c0a9" class="outline-2">
<h2 id="org9d1c0a9"><span class="section-number-2">1</span> Frozen core</h2>
<div class="outline-text-2" id="text-1">
<p>
Defines how the core electrons are frozen, for each atom.
</p>
</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">-&gt;</span> <span class="org-tuareg-font-lock-module">Particles.Nuclei.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</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">-&gt;</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">-&gt;</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">-&gt;</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">-&gt;</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">-&gt;</span> t <span class="org-tuareg-font-lock-operator">-&gt;</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>
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<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>
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<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">-&gt;</span> <span class="org-tuareg-font-lock-module">Mo.Basis.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span> t
</pre>
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</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 : &lt;abstr&gt;
</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">-&gt;</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">-&gt;</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">-&gt;</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">-&gt;</span> t <span class="org-tuareg-font-lock-operator">-&gt;</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>

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<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">-&gt;</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">-&gt;</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">-&gt;</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">-&gt;</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">-&gt;</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">-&gt;</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">-&gt;</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">-&gt;</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">-&gt;</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">-&gt;</span>
<span class="org-tuareg-font-lock-module">Ao.Basis.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</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">-&gt;</span> t <span class="org-tuareg-font-lock-operator">-&gt;</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>

2
gaussian_integrals/lib/multipole.ml
View File

@ -32,7 +32,7 @@ let matrix t = function
| "x4" -> t.(12) | "x4" -> t.(12)
| "y4" -> t.(13) | "y4" -> t.(13)
| "z4" -> t.(14) | "z4" -> t.(14)
| _ -> Util.not_implemented () | _ -> Util.not_implemented "Multipole"

20
mo/lib/class.ml
View File

@ -95,18 +95,14 @@ let mo_class_array t =
let fci ~frozen_core mo_basis = let fci ~frozen_core mo_basis =
let mo_num = Basis.size mo_basis in 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 ( of_list (
if frozen_core then
List.concat [ List.concat [
Util.list_range 1 ncore Util.list_range 1 ncore
|> List.map (fun i -> Core i) ; |> List.map (fun i -> Core i) ;
Util.list_range (ncore+1) mo_num Util.list_range (ncore+1) mo_num
|> List.map (fun i -> Active i) |> 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 = 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 n_alfa_in_cas = (n - n_unpaired)/2 + n_unpaired in
let last_inactive = n_alfa - n_alfa_in_cas in let last_inactive = n_alfa - n_alfa_in_cas in
let last_active = last_inactive + m in let last_active = last_inactive + m in
let ncore = let ncore = min (Frozen_core.num_mos frozen_core) last_inactive in
if frozen_core then
(Nuclei.small_core @@ Simulation.nuclei @@ Basis.simulation mo_basis) / 2
|> min last_inactive
else 0
in
of_list ( of_list (
List.concat [ List.concat [
if ncore > 0 then Util.list_range 1 ncore
Util.list_range 1 ncore |> List.map (fun i -> Core i) ;
|> List.map (fun i -> Core i)
else
[] ;
Util.list_range (ncore+1) last_inactive Util.list_range (ncore+1) last_inactive
|> List.map (fun i -> Inactive i) ; |> List.map (fun i -> Inactive i) ;
Util.list_range (last_inactive+1) last_active Util.list_range (last_inactive+1) last_active

4
mo/lib/class.mli
View File

@ -15,12 +15,12 @@ val of_list : mo_class list -> t
val to_list : t -> mo_class list 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 (** Creates the MO classes for FCI calculations : all [Active]. The
[n] lowest MOs are [Core] if [frozen_core = true]. [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 (** [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], calculations. lowest MOs are [Core], then all the next MOs are [Inactive],
then [Active], then [Virtual]. then [Active], then [Virtual].

8
mo/lib/frozen_core.ml
View File

@ -1,4 +1,4 @@
(* [[file:../frozen_core.org::*Type][Type:3]] *) (* [[file:~/QCaml/mo/frozen_core.org::*Type][Type:3]] *)
type kind = type kind =
| All_electron | All_electron
| Small | Small
@ -21,7 +21,7 @@ type t = int array
* #+end_example *) * #+end_example *)
(* [[file:../frozen_core.org::*Creation][Creation:2]] *) (* [[file:~/QCaml/mo/frozen_core.org::*Creation][Creation:2]] *)
let make_ae nuclei = let make_ae nuclei =
Array.map (fun _ -> 0) nuclei Array.map (fun _ -> 0) nuclei
@ -56,7 +56,7 @@ let of_int_list = Array.of_list
* #+end_example *) * #+end_example *)
(* [[file:../frozen_core.org::*Access][Access:2]] *) (* [[file:~/QCaml/mo/frozen_core.org::*Access][Access:2]] *)
let num_elec t = let num_elec t =
Array.fold_left ( + ) 0 t Array.fold_left ( + ) 0 t
@ -64,7 +64,7 @@ let num_mos t =
(num_elec t) / 2 (num_elec t) / 2
(* Access:2 ends here *) (* Access:2 ends here *)
(* [[file:../frozen_core.org::*Printers][Printers:2]] *) (* [[file:~/QCaml/mo/frozen_core.org::*Printers][Printers:2]] *)
let pp ppf t = let pp ppf t =
Format.fprintf ppf "@[[|"; Format.fprintf ppf "@[[|";
Array.iter (fun x -> Format.fprintf ppf "@,@[%d@]" x) t; Array.iter (fun x -> Format.fprintf ppf "@,@[%d@]" x) t;

10
mo/lib/frozen_core.mli
View File

@ -2,21 +2,21 @@
* *
* #+NAME: types *) * #+NAME: types *)
(* [[file:../frozen_core.org::types][types]] *) (* [[file:~/QCaml/mo/frozen_core.org::types][types]] *)
type kind = type kind =
| All_electron | All_electron
| Small | Small
| Large | Large
(* types ends here *) (* types ends here *)
(* [[file:../frozen_core.org::*Type][Type:2]] *) (* [[file:~/QCaml/mo/frozen_core.org::*Type][Type:2]] *)
type t type t
(* Type:2 ends here *) (* Type:2 ends here *)
(* Creation *) (* 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 make : kind -> Particles.Nuclei.t -> t
val of_int_list : int list -> t val of_int_list : int list -> t
@ -26,7 +26,7 @@ val of_int_array : int array -> t
(* Access *) (* Access *)
(* [[file:../frozen_core.org::*Access][Access:1]] *) (* [[file:~/QCaml/mo/frozen_core.org::*Access][Access:1]] *)
val num_elec : t -> int val num_elec : t -> int
val num_mos : t -> int val num_mos : t -> int
(* Access:1 ends here *) (* Access:1 ends here *)
@ -34,6 +34,6 @@ val num_mos : t -> int
(* Printers *) (* Printers *)
(* [[file:../frozen_core.org::*Printers][Printers:1]] *) (* [[file:~/QCaml/mo/frozen_core.org::*Printers][Printers:1]] *)
val pp : Format.formatter -> t -> unit val pp : Format.formatter -> t -> unit
(* Printers:1 ends here *) (* Printers:1 ends here *)

8
particles/lib/nuclei.ml
View File

@ -1,4 +1,4 @@
(* [[file:../nuclei.org::*Type][Type:2]] *) (* [[file:~/QCaml/particles/nuclei.org::*Type][Type:2]] *)
open Common open Common
type t = (Element.t * Coordinate.t) array 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 | *) * | ~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 of_xyz_lexbuf lexbuf =
let data = let data =
Xyz_parser.input Nuclei_lexer.read_all lexbuf 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 | *) * | ~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 formula t =
let dict = Hashtbl.create 67 in let dict = Hashtbl.create 67 in
Array.iter (fun (e,_) -> 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 Array.fold_left (fun accu (e,_) -> accu + (Element.large_core e)) 0 a
(* Query:2 ends here *) (* Query:2 ends here *)
(* [[file:../nuclei.org::*Printers][Printers:2]] *) (* [[file:~/QCaml/particles/nuclei.org::*Printers][Printers:2]] *)
let pp ppf t = let pp ppf t =
Format.fprintf ppf "@[%s@]" (to_string t) Format.fprintf ppf "@[%s@]" (to_string t)
(* Printers:2 ends here *) (* Printers:2 ends here *)

8
particles/lib/nuclei.mli
View File

@ -2,7 +2,7 @@
* *
* #+NAME: types *) * #+NAME: types *)
(* [[file:../nuclei.org::types][types]] *) (* [[file:~/QCaml/particles/nuclei.org::types][types]] *)
open Common open Common
type t = (Element.t * Coordinate.t) array type t = (Element.t * Coordinate.t) array
@ -11,7 +11,7 @@ type t = (Element.t * Coordinate.t) array
(* Conversion *) (* Conversion *)
(* [[file:../nuclei.org::*Conversion][Conversion:1]] *) (* [[file:~/QCaml/particles/nuclei.org::*Conversion][Conversion:1]] *)
val of_xyz_string : string -> t val of_xyz_string : string -> t
val to_xyz_string : t -> string val to_xyz_string : t -> string
val of_xyz_file : string -> t val of_xyz_file : string -> t
@ -27,7 +27,7 @@ val of_filename : string -> t
(* TODO Query *) (* TODO Query *)
(* [[file:../nuclei.org::*Query][Query:1]] *) (* [[file:~/QCaml/particles/nuclei.org::*Query][Query:1]] *)
val formula : t -> string val formula : t -> string
val repulsion : t -> float val repulsion : t -> float
val charge : t -> Charge.t val charge : t -> Charge.t
@ -38,6 +38,6 @@ val large_core : t -> int
(* Printers *) (* Printers *)
(* [[file:../nuclei.org::*Printers][Printers:1]] *) (* [[file:~/QCaml/particles/nuclei.org::*Printers][Printers:1]] *)
val pp : Format.formatter -> t -> unit val pp : Format.formatter -> t -> unit
(* Printers:1 ends here *) (* Printers:1 ends here *)

2
particles/lib/nuclei_lexer.mll
View File

@ -4,7 +4,7 @@
* an xyz file. *) * an xyz file. *)
(* [[file:../nuclei.org::*Lexer][Lexer:1]] *) (* [[file:~/QCaml/particles/nuclei.org::*Lexer][Lexer:1]] *)
{ {
open Xyz_parser open Xyz_parser
} }

2
particles/lib/xyz_ast.mli
View File

@ -4,7 +4,7 @@
* an ~xyz_file~ data structure. *) * an ~xyz_file~ data structure. *)
(* [[file:../nuclei.org::*Parser][Parser:2]] *) (* [[file:~/QCaml/particles/nuclei.org::*Parser][Parser:2]] *)
open Common open Common
type nucleus = type nucleus =

2
particles/test/nuclei.ml
View File

@ -1,7 +1,7 @@
(* Tests *) (* Tests *)
(* [[file:../nuclei.org::*Tests][Tests:1]] *) (* [[file:~/QCaml/particles/nuclei.org::*Tests][Tests:1]] *)
open Common open Common
open Particles open Particles
open Alcotest open Alcotest

131
perturbation/lib/mp2.ml
View File

@ -1,21 +1,31 @@
(* [[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 open Linear_algebra
type t = float 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 = let inactives =
List.filter (fun i -> List.filter (fun i ->
match i with Mo.Class.Inactive _ -> true | _ -> false) mo_class 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 match i with Mo.Class.Virtual _ -> true | _ -> false) mo_class
in in
let rmp2 () = List.fold_left (fun accu b ->
List.fold_left (fun accu b -> match b with Mo.Class.Virtual b ->
match b with Mo.Class.Virtual b -> let eps = -. (epsilon%.(b)) in
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 +. accu +.
List.fold_left (fun accu a -> List.fold_left (fun accu j ->
match a with Mo.Class.Virtual a -> match j with Mo.Class.Inactive j ->
let eps = eps -. (epsilon%.(a)) in let eps = eps +. epsilon%.(j) in
accu +. accu +.
List.fold_left (fun accu j -> List.fold_left (fun accu i ->
match j with Mo.Class.Inactive j -> match i with Mo.Class.Inactive i ->
let eps = eps +. epsilon%.(j) in let eps = eps +. epsilon%.(i) in
accu +. let ijab = Four_idx_storage.get_phys eri i j a b
List.fold_left (fun accu i -> and abji = Four_idx_storage.get_phys eri a b j i in
match i with Mo.Class.Inactive i -> let abij = ijab in
let eps = eps +. epsilon%.(i) in accu +. ijab *. ( abij +. abij -. abji) /. eps
let ijab = Four_idx_storage.get_phys eri i j a b | _ -> accu
and abji = Four_idx_storage.get_phys eri a b j i in ) 0. inactives
let abij = ijab in | _ -> accu
accu +. ijab *. ( abij +. abij -. abji) /. eps ) 0. inactives
| _ -> accu | _ -> accu
) 0. inactives
| _ -> accu
) 0. inactives
| _ -> accu
) 0. virtuals
| _ -> accu
) 0. virtuals ) 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 in
let energy =
match Mo.Hartree_fock.kind hf with match Mo.Basis.mo_type mo_basis with
| Mo.Hartree_fock.RHF -> rmp2 () | RHF -> make_rmp2 mo_basis mo_class
| _ -> failwith "Not implemented" | 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 *)

29
perturbation/lib/mp2.mli Normal file
View File

@ -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 *)

180
perturbation/mp2.org Normal file
View File

@ -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

17
perturbation/test/mp2.ml
View File

@ -1,3 +1,7 @@
(* Tests *)
(* [[file:~/QCaml/perturbation/mp2.org::*Tests][Tests:1]] *)
open Alcotest open Alcotest
open Particles open Particles
@ -16,12 +20,19 @@ let tests =
Ao.Basis.of_nuclei_and_basis_filename ~kind:`Gaussian Ao.Basis.of_nuclei_and_basis_filename ~kind:`Gaussian
~cartesian:false ~nuclei basis_filename ~cartesian:false ~nuclei basis_filename
in in
let simulation = Simulation.make ~nuclei ao_basis in let simulation = Simulation.make ~nuclei ao_basis in
let hf = Mo.Hartree_fock.make ~guess:`Huckel simulation in let hf = Mo.Hartree_fock.make ~guess:`Huckel simulation in
Format.printf "%a" (Mo.Hartree_fock.pp) hf; Format.printf "%a" (Mo.Hartree_fock.pp) hf;
check (float 2.e-10) "Energy" (-76.0267987005) (Mo.Hartree_fock.energy 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) check (float 1.e-9) "MP2" (-0.2016211415) (e_mp2)
] ]
(* Tests:1 ends here *)

10
simulation/lib/simulation.ml
View File

@ -1,10 +1,10 @@
(* [[file:../simulation.org::*Simulation][Simulation:2]] *) (* [[file:~/QCaml/simulation/simulation.org::*Simulation][Simulation:2]] *)
open Common open Common
open Particles open Particles
open Operators open Operators
(* Simulation:2 ends here *) (* Simulation:2 ends here *)
(* [[file:../simulation.org::*Type][Type:2]] *) (* [[file:~/QCaml/simulation/simulation.org::*Type][Type:2]] *)
type t = { type t = {
charge : Charge.t; charge : Charge.t;
electrons : Electrons.t; electrons : Electrons.t;
@ -24,7 +24,7 @@ type t = {
* | ~operators~ | List of extra operators (range-separation, f12, etc) | *) * | ~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 nuclei t = t.nuclei
let charge t = t.charge let charge t = t.charge
let electrons t = t.electrons let electrons t = t.electrons
@ -41,7 +41,7 @@ let operators t = t.operators
* - operators : ~[]~ *) * - operators : ~[]~ *)
(* [[file:../simulation.org::*Creation][Creation:2]] *) (* [[file:~/QCaml/simulation/simulation.org::*Creation][Creation:2]] *)
let make let make
?(multiplicity=1) ?(multiplicity=1)
?(charge=0) ?(charge=0)
@ -65,7 +65,7 @@ let make
{ charge ; nuclei ; electrons ; ao_basis ; operators} { charge ; nuclei ; electrons ; ao_basis ; operators}
(* Creation:2 ends here *) (* Creation:2 ends here *)
(* [[file:../simulation.org::*Printers][Printers:2]] *) (* [[file:~/QCaml/simulation/simulation.org::*Printers][Printers:2]] *)
let pp ppf t = let pp ppf t =
let formula = Nuclei.formula t.nuclei in let formula = Nuclei.formula t.nuclei in
let n_aos = Ao.Basis.size t.ao_basis in let n_aos = Ao.Basis.size t.ao_basis in

10
simulation/lib/simulation.mli
View File

@ -7,7 +7,7 @@
* *
* #+NAME: open *) * #+NAME: open *)
(* [[file:../simulation.org::open][open]] *) (* [[file:~/QCaml/simulation/simulation.org::open][open]] *)
open Common open Common
open Particles open Particles
open Operators open Operators
@ -17,14 +17,14 @@ open Operators
* *
* #+NAME: types *) * #+NAME: types *)
(* [[file:../simulation.org::types][types]] *) (* [[file:~/QCaml/simulation/simulation.org::types][types]] *)
type t type t
(* types ends here *) (* types ends here *)
(* Access *) (* Access *)
(* [[file:../simulation.org::*Access][Access:1]] *) (* [[file:~/QCaml/simulation/simulation.org::*Access][Access:1]] *)
val nuclei : t -> Nuclei.t val nuclei : t -> Nuclei.t
val charge : t -> Charge.t val charge : t -> Charge.t
val electrons : t -> Electrons.t val electrons : t -> Electrons.t
@ -36,7 +36,7 @@ val operators : t -> Operator.t list
(* Creation *) (* Creation *)
(* [[file:../simulation.org::*Creation][Creation:1]] *) (* [[file:~/QCaml/simulation/simulation.org::*Creation][Creation:1]] *)
val make : ?multiplicity:int -> ?charge:int -> val make : ?multiplicity:int -> ?charge:int ->
?operators:Operator.t list-> nuclei:Nuclei.t -> ?operators:Operator.t list-> nuclei:Nuclei.t ->
Ao.Basis.t -> t Ao.Basis.t -> t
@ -45,6 +45,6 @@ val make : ?multiplicity:int -> ?charge:int ->
(* Printers *) (* Printers *)
(* [[file:../simulation.org::*Printers][Printers:1]] *) (* [[file:~/QCaml/simulation/simulation.org::*Printers][Printers:1]] *)
val pp : Format.formatter -> t -> unit val pp : Format.formatter -> t -> unit
(* Printers:1 ends here *) (* Printers:1 ends here *)

2
top/lib/install_printers.ml
View File

@ -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 = let printers =
[ [
"Common.Angular_momentum.pp" ; "Common.Angular_momentum.pp" ;