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Anthony Scemama 2021-01-28 00:34:26 +01:00
parent d0f61750da
commit 8502befb65
67 changed files with 2621 additions and 936 deletions
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19
ao/README.org
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@ -1,24 +1,27 @@
#+TITLE: Atomic Orbitals
#+HTML_LINK_HOME: index.html
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/theme.setup
* Summary
#+name: synopsis
#+begin_src ocaml :export output raw
#+begin_src ocaml :exports none :results value
"Atomic basis set"
#+end_src
#+RESULTS: synopsis
: Atomic basis set
This modules contains the data structures used to characterize the
atomic basis set.
* Dune files :noexport:
** Generate dune files
Use [C-c C-c] on the code below to create the output for the dune files
#+header: :noweb strip-export
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var dune="lib/dune"
#+header: :var dunetest="test/dune"
#+begin_src python :exports none :results output none
@ -56,7 +59,7 @@ with open(dunetest,'w') as f:
** Dependencies
#+name: dependencies
#+begin_src elisp
#+begin_src elisp
(libraries
qcaml.common
qcaml.particles
@ -67,7 +70,7 @@ with open(dunetest,'w') as f:
#+end_src
** Modules without implementation
#+name: noimplementation
#+begin_src elisp
(modules_without_implementation ao_dim)
@ -86,4 +89,4 @@ with open(dunetest,'w') as f:

17
ao/basis.org
View File

@ -16,7 +16,7 @@
Data structure for Atomic Orbitals.
** Dimensions :noexports:
** Dimensions :noexport:
#+begin_src ocaml :tangle lib/ao_dim.mli :exports none
type t
@ -24,6 +24,7 @@ type t
** Polymorphic types
<<<~Basis.t~>>>
#+NAME: types
#+begin_src ocaml :tangle lib/basis_poly.mli
type t =
@ -37,6 +38,7 @@ type t =
** Types
<<<~Basis.t~>>>
#+begin_src ocaml :tangle (eval mli)
type t
type ao = Ao_dim.t
@ -63,17 +65,24 @@ open Common
#+begin_src ocaml :tangle (eval mli)
val of_nuclei_and_basis_filename :
?kind:[> `Gaussian ] -> ?operators:Operator.t list -> ?cartesian:bool ->
nuclei:Nuclei.t -> string -> t
?kind:[> `Gaussian ] ->
?operators:Operator.t list ->
?cartesian:bool ->
nuclei:Nuclei.t ->
string ->
t
#+end_src
|--------------------------------+------------------------------------------------------------------------------------------------------------------------|
| ~of_nuclei_and_basis_filename~ | Creates the data structure for the atomic orbitals basis from a molecule ~Nuclei.t~ and the name of the basis-set file |
|--------------------------------+------------------------------------------------------------------------------------------------------------------------|
Defaults:
- ~kind~ : ~`Gaussian~
- ~operators~ : ~[]~
- ~cartesian~ : ~false~
Example:
#+begin_example
let b = Ao.Basis.of_nuclei_and_basis_filename ~nuclei filename;;
val b : Ao.Basis.t = Gaussian Basis, spherical, 15 AOs
@ -113,6 +122,7 @@ val cartesian : t -> bool
val values : t -> Coordinate.t -> ao Vector.t
#+end_src
|---------------------+--------------------------------------------------|
| ~size~ | Number of atomic orbitals in the AO basis set |
| ~ao_basis~ | One-electron basis set |
| ~overlap~ | Overlap matrix |
@ -126,6 +136,7 @@ val values : t -> Coordinate.t -> ao Vector.t
| ~f12_over_r12_ints~ | Electron-electron potential integrals |
| ~cartesian~ | If true, use cartesian Gaussians (6d, 10f, ...) |
| ~values~ | Values of the AOs evaluated at a given point |
|---------------------+--------------------------------------------------|
#+begin_src ocaml :tangle (eval ml) :exports none

18
ao/basis_gaussian.org
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@ -16,11 +16,11 @@
Data structure for Gaussian Atomic Orbitals:
$$
\[
\chi_i(\mathbf{r}) = P_i(\mathbf{r}) \sum_k c_k \exp\left( -\alpha_k (\mathbf{r-R_A})^2 \right)
$$
\]
where the polynomial $P_Ai and the Gaussian part are both centered on
where the polynomial $P_i$ and the Gaussian part are both centered on
nucleus $A$.
** Type
@ -78,6 +78,7 @@ val overlap : t -> Overlap.t
val size : t -> int
#+end_src
|---------------------+--------------------------------------------------|
| ~basis~ | One-electron basis set |
| ~cartesian~ | If true, use cartesian Gaussians (6d, 10f, ...) |
| ~ee_ints~ | Electron-electron potential integrals |
@ -90,6 +91,7 @@ val size : t -> int
| ~ortho~ | Orthonormalization matrix of the overlap |
| ~overlap~ | Overlap matrix |
| ~size~ | Number of atomic orbitals |
|---------------------+--------------------------------------------------|
#+begin_src ocaml :tangle (eval ml) :exports none
let basis t = t.basis
@ -109,10 +111,14 @@ let size t = Matrix.dim1 (Lazy.force t.overlap)
** Computation
#+begin_src ocaml :tangle (eval mli)
val values : t -> Coordinate.t -> Gaussian.Basis.t Vector.t
val values : t ->
Coordinate.t ->
Gaussian.Basis.t Vector.t
#+end_src
|----------+--------------------------------------------------------------|
| ~values~ | Returns the values of all the AOs evaluated at a given point |
|----------+--------------------------------------------------------------|
#+begin_src ocaml :tangle (eval ml) :exports none
module Cs = Contracted_shell
@ -136,7 +142,8 @@ let values t point =
val make : basis:Gaussian.Basis.t ->
?operators:Operator.t list ->
?cartesian:bool ->
Nuclei.t -> t
Nuclei.t ->
t
#+end_src
Creates the data structure for atomic orbitals from a Gaussian basis and the
@ -146,6 +153,7 @@ val make : basis:Gaussian.Basis.t ->
- ~operators~ : ~[]~
- ~cartesian~ : ~false~
Example:
#+begin_example
let b = Ao.Basis_gaussian.make ~basis nuclei ;;
val b : Ao.Basis_gaussian.t = Gaussian Basis, spherical, 15 AOs

2
ao/lib/ao_dim.mli
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@ -1,4 +1,4 @@
(* Dimensions :noexports: *)
(* Dimensions :noexport: *)
(* [[file:~/QCaml/ao/basis.org::*Dimensions][Dimensions:1]] *)

11
ao/lib/basis.ml
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@ -12,13 +12,16 @@ open Common
(* | ~of_nuclei_and_basis_filename~ | Creates the data structure for the atomic orbitals basis from a molecule ~Nuclei.t~ and the name of the basis-set file |
(* |--------------------------------+------------------------------------------------------------------------------------------------------------------------|
* | ~of_nuclei_and_basis_filename~ | Creates the data structure for the atomic orbitals basis from a molecule ~Nuclei.t~ and the name of the basis-set file |
* |--------------------------------+------------------------------------------------------------------------------------------------------------------------|
*
* Defaults:
* - ~kind~ : ~`Gaussian~
* - ~operators~ : ~[]~
* - ~cartesian~ : ~false~
*
* Example:
* #+begin_example
* let b = Ao.Basis.of_nuclei_and_basis_filename ~nuclei filename;;
* val b : Ao.Basis.t = Gaussian Basis, spherical, 15 AOs
@ -42,7 +45,8 @@ let of_nuclei_and_basis_filename ?(kind=`Gaussian) ?operators ?(cartesian=false)
(* | ~size~ | Number of atomic orbitals in the AO basis set |
(* |---------------------+--------------------------------------------------|
* | ~size~ | Number of atomic orbitals in the AO basis set |
* | ~ao_basis~ | One-electron basis set |
* | ~overlap~ | Overlap matrix |
* | ~multipole~ | Multipole matrices |
@ -54,7 +58,8 @@ let of_nuclei_and_basis_filename ?(kind=`Gaussian) ?operators ?(cartesian=false)
* | ~f12_ints~ | Electron-electron potential integrals |
* | ~f12_over_r12_ints~ | Electron-electron potential integrals |
* | ~cartesian~ | If true, use cartesian Gaussians (6d, 10f, ...) |
* | ~values~ | Values of the AOs evaluated at a given point | *)
* | ~values~ | Values of the AOs evaluated at a given point |
* |---------------------+--------------------------------------------------| *)

13
ao/lib/basis.mli
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@ -1,5 +1,6 @@
(* Types *)
(* Types
*
* <<<~Basis.t~>>> *)
(* [[file:~/QCaml/ao/basis.org::*Types][Types:1]] *)
type t
@ -16,8 +17,12 @@ open Linear_algebra
(* [[file:~/QCaml/ao/basis.org::*Conversions][Conversions:1]] *)
val of_nuclei_and_basis_filename :
?kind:[> `Gaussian ] -> ?operators:Operator.t list -> ?cartesian:bool ->
nuclei:Nuclei.t -> string -> t
?kind:[> `Gaussian ] ->
?operators:Operator.t list ->
?cartesian:bool ->
nuclei:Nuclei.t ->
string ->
t
(* Conversions:1 ends here *)
(* Access *)

11
ao/lib/basis_gaussian.ml
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@ -24,7 +24,8 @@ type t =
(* | ~basis~ | One-electron basis set |
(* |---------------------+--------------------------------------------------|
* | ~basis~ | One-electron basis set |
* | ~cartesian~ | If true, use cartesian Gaussians (6d, 10f, ...) |
* | ~ee_ints~ | Electron-electron potential integrals |
* | ~ee_lr_ints~ | Electron-electron long-range potential integrals |
@ -35,7 +36,8 @@ type t =
* | ~multipole~ | Multipole matrices |
* | ~ortho~ | Orthonormalization matrix of the overlap |
* | ~overlap~ | Overlap matrix |
* | ~size~ | Number of atomic orbitals | *)
* | ~size~ | Number of atomic orbitals |
* |---------------------+--------------------------------------------------| *)
(* [[file:~/QCaml/ao/basis_gaussian.org::*Access][Access:2]] *)
@ -55,7 +57,9 @@ let size t = Matrix.dim1 (Lazy.force t.overlap)
(* | ~values~ | Returns the values of all the AOs evaluated at a given point | *)
(* |----------+--------------------------------------------------------------|
* | ~values~ | Returns the values of all the AOs evaluated at a given point |
* |----------+--------------------------------------------------------------| *)
(* [[file:~/QCaml/ao/basis_gaussian.org::*Computation][Computation:2]] *)
@ -83,6 +87,7 @@ let values t point =
* - ~operators~ : ~[]~
* - ~cartesian~ : ~false~
*
* Example:
* #+begin_example
* let b = Ao.Basis_gaussian.make ~basis nuclei ;;
* val b : Ao.Basis_gaussian.t = Gaussian Basis, spherical, 15 AOs

7
ao/lib/basis_gaussian.mli
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@ -35,7 +35,9 @@ val size : t -> int
(* [[file:~/QCaml/ao/basis_gaussian.org::*Computation][Computation:1]] *)
val values : t -> Coordinate.t -> Gaussian.Basis.t Vector.t
val values : t ->
Coordinate.t ->
Gaussian.Basis.t Vector.t
(* Computation:1 ends here *)
(* Creation *)
@ -45,7 +47,8 @@ val values : t -> Coordinate.t -> Gaussian.Basis.t Vector.t
val make : basis:Gaussian.Basis.t ->
?operators:Operator.t list ->
?cartesian:bool ->
Nuclei.t -> t
Nuclei.t ->
t
(* Creation:1 ends here *)
(* Printers *)

1
ao/lib/basis_poly.mli
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@ -1,5 +1,6 @@
(* Polymorphic types
*
* <<<~Basis.t~>>>
* #+NAME: types *)
(* [[file:~/QCaml/ao/basis.org::types][types]] *)

20
common/README.org
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@ -1,15 +1,15 @@
#+TITLE: Common
#+HTML_LINK_HOME: index.html
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/theme.setup
* Summary
#+name: synopsis
#+begin_src ocaml :export output raw
"Utility functions used by all the other directories."
#+begin_src ocaml :exports none :results value
"Utility functions used by all the other directories"
#+end_src
#+RESULTS: synopsis
: Utility functions used by all the other directories.
: Utility functions used by all the other directories
* Dune files :noexport:
@ -19,7 +19,7 @@
Use [C-c C-c] on the code below to create the output for the dune files
#+header: :noweb strip-export
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var dune="lib/dune"
#+header: :var dunetest="test/dune"
#+begin_src python :exports none :results output none
@ -56,7 +56,7 @@ with open(dunetest,'w') as f:
** Dependencies
#+name: dependencies
#+begin_src elisp
#+begin_src elisp
(libraries
str
zarith
@ -65,7 +65,7 @@ with open(dunetest,'w') as f:
#+end_src
** Modules without implementation
#+name: noimplementation
#+begin_src elisp
#+end_src
@ -76,7 +76,7 @@ with open(dunetest,'w') as f:
functionalities to OCaml, such as support for the ~popcnt~ instruction.
#+name: c-files
#+begin_src elisp
#+begin_src elisp
(c_names
util
)
@ -88,5 +88,5 @@ with open(dunetest,'w') as f:
** Parser
#+name: lex-yacc
#+begin_src elisp
#+begin_src elisp
#+end_src

4
common/angular_momentum.org
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@ -19,6 +19,7 @@
** Type
<<<~Angular_momentum.t~>>>
#+NAME: types
#+begin_src ocaml :tangle (eval mli)
type t =
@ -64,6 +65,7 @@ val to_string : t -> string
| ~to_int~ | Returns the $l_{max}$ value of the shell |
| ~to_string~ | Converts the angular momentum into a string |
Example:
#+begin_example
Angular_momentum.of_char 'p';;
- : Angular_momentum.t = P
@ -142,6 +144,7 @@ val zkey_array : kind -> Zkey.t array
| ~n_functions~ | Returns the number of cartesian functions in a shell. |
| ~zkey_array~ | Array of ~Zkey.t~, where each element is a a key associated with the the powers of $x,y,z$. |
Example:
#+begin_example
Angular_momentum.(n_functions D) ;;
- : int = 6
@ -245,6 +248,7 @@ val ( + ) : t -> t -> t
val ( - ) : t -> t -> t
#+end_src
Example:
#+begin_example
Angular_momentum.(D + P);;
- : Angular_momentum.t = F

8
common/bitstring.org
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@ -96,6 +96,7 @@ end
** Type
<<<~Bitstring.t~>>>
#+begin_src ocaml :tangle (eval mli)
type t
#+end_src
@ -186,6 +187,7 @@ check_bool "of_x" true (one_x = (of_int x));
check_bool "of_z" true (one_x = (of_z (Z.of_int x)));
#+end_src
Example:
#+begin_example
Bitstring.of_int 15;;
- : Bitstring.t =
@ -231,6 +233,7 @@ let testbit = function
| Many x -> Many.testbit x
#+end_src
Example:
#+begin_example
Bitstring.(shift_left (of_int 15) 2);;
- : Bitstring.t =
@ -296,6 +299,7 @@ let lognot = function
#+end_src
Example:
#+begin_example
Bitstring.(logor (of_int 15) (of_int 73));;
- : Bitstring.t =
@ -333,6 +337,7 @@ let plus_one = function
#+end_src
Example:
#+begin_example
Bitstring.(plus_one (of_int 15));;
- : Bitstring.t =
@ -362,6 +367,7 @@ let popcount = function
#+end_src
Example:
#+begin_example
Bitstring.(trailing_zeros (of_int 12));;
- : int = 2
@ -387,6 +393,7 @@ let rec to_list ?(accu=[]) = function
check_bool "to_list" true ([ 1 ; 3 ; 4 ; 6 ] = (to_list (of_int 45)));
#+end_src
Example:
#+begin_example
Bitstring.(to_list (of_int 45));;
- : int list = [1; 3; 4; 6]
@ -412,6 +419,7 @@ let permutations m n =
aux (Util.binom n m) (minus_one (shift_left_one n m)) []
#+end_src
Example:
#+begin_example
Bitstring.permutations 2 4;;
- : Bitstring.t list =

1
common/charge.org
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@ -17,6 +17,7 @@
** Type
<<<~Charge.t~>>>
#+begin_src ocaml :tangle (eval mli)
type t
#+end_src

12
common/command_line.org
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@ -59,7 +59,7 @@ let multiplicity =
in
#+end_src
** Type
** Types
#+NAME:type
#+begin_src ocaml :tangle (eval mli)
@ -67,7 +67,9 @@ type short_opt = char
type long_opt = string
type optional = Mandatory | Optional
type documentation = string
type argument = With_arg of string | Without_arg | With_opt_arg of string
type argument = | With_arg of string
| Without_arg
| With_opt_arg of string
type description = {
short: short_opt ;
@ -79,9 +81,9 @@ type description = {
#+end_src
- Short option: in the command line, a dash with a single character
- <<<Short option>>>: in the command line, a dash with a single character
(ex: =ls -l=)
- Long option: in the command line, two dashes with a word
- <<<Long option>>>: in the command line, two dashes with a word
(ex: =ls --directory=)
- Command-line options can be ~Mandatory~ or ~Optional~
- Documentation of the option is used in the help function
@ -163,6 +165,7 @@ let output_text t =
Function to build the short description of the command-line
arguments, such as
Example:
#+begin_example
my_program -b <string> [-h] [-u <float>] -x <string> [--]
#+end_example
@ -184,6 +187,7 @@ let output_short x =
Function to build the long description of the command-line
arguments, such as
Example:
#+begin_example
-x --xyz=<string> Name of the file containing the nuclear
coordinates in xyz format

1
common/constants.org
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@ -13,7 +13,6 @@
:PROPERTIES:
:header-args: :noweb yes :comments both
:END:
All constants used in the program.
** Thresholds

18
common/coordinate.org
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@ -22,6 +22,7 @@
** Type
<<<~Coordinate.t~>>>
#+NAME: types
#+begin_src ocaml :tangle (eval mli)
type bohr
@ -62,7 +63,7 @@ type axis = X | Y | Z
#+begin_src ocaml :tangle (eval mli)
val make : 'a point -> t
val make_angstrom : 'a point -> angstrom point
val zero : bohr point
val zero : bohr point
#+end_src
| ~make~ | Creates a point in atomic units |
@ -114,14 +115,15 @@ val ( |+ ) : t -> t -> t
val ( |- ) : t -> t -> t
#+end_src
| ~neg~ | Negative of a point |
| ~get~ | Extracts the projection of the coordinate on an axis |
| ~dot~ | Dot product |
| ~norm~ | $\ell{^2}$ norm of the vector |
| ~¦.~ | Scales the vector by a constant |
| ~¦+~ | Adds two vectors |
| ~¦-~ | Subtracts two vectors |
| ~neg~ | Negative of a point |
| ~get~ | Extracts the projection of the coordinate on an axis |
| ~dot~ | Dot product |
| ~norm~ | $\ell{^2}$ norm of the vector |
| $\vert .$ | Scales the vector by a constant |
| $\vert +$ | Adds two vectors |
| $\vert -$ | Subtracts two vectors |
Example:
#+begin_example
Coordinate.neg { x=1. ; y=2. ; z=3. } ;;
- : Coordinate.t = -1.0000 -2.0000 -3.0000

5
common/lib/angular_momentum.ml
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@ -31,6 +31,7 @@ open Powers
* | ~to_int~ | Returns the $l_{max}$ value of the shell |
* | ~to_string~ | Converts the angular momentum into a string |
*
* Example:
* #+begin_example
* Angular_momentum.of_char 'p';;
* - : Angular_momentum.t = P
@ -105,6 +106,7 @@ let of_int = function
(* | ~n_functions~ | Returns the number of cartesian functions in a shell. |
* | ~zkey_array~ | Array of ~Zkey.t~, where each element is a a key associated with the the powers of $x,y,z$. |
*
* Example:
* #+begin_example
* Angular_momentum.(n_functions D) ;;
* - : int = 6
@ -204,7 +206,8 @@ let zkey_array a =
(* #+begin_example
(* Example:
* #+begin_example
* Angular_momentum.(D + P);;
* - : Angular_momentum.t = F
*

1
common/lib/angular_momentum.mli
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@ -1,5 +1,6 @@
(* Type
*
* <<<~Angular_momentum.t~>>>
* #+NAME: types *)
(* [[file:~/QCaml/common/angular_momentum.org::types][types]] *)

12
common/lib/bitstring.ml
View File

@ -114,7 +114,8 @@ let of_z x =
(* #+begin_example
(* Example:
* #+begin_example
* Bitstring.of_int 15;;
* - : Bitstring.t =
* ++++------------------------------------------------------------
@ -201,7 +202,8 @@ let plus_one = function
(* #+begin_example
(* Example:
* #+begin_example
* Bitstring.(plus_one (of_int 15));;
* - : Bitstring.t =
* ----+-----------------------------------------------------------
@ -233,7 +235,8 @@ let popcount = function
(* #+begin_example
(* Example:
* #+begin_example
* Bitstring.(trailing_zeros (of_int 12));;
* - : int = 2
*
@ -257,7 +260,8 @@ let rec to_list ?(accu=[]) = function
(* #+begin_example
(* Example:
* #+begin_example
* Bitstring.(to_list (of_int 45));;
* - : int list = [1; 3; 4; 6]
* #+end_example *)

5
common/lib/bitstring.mli
View File

@ -1,5 +1,6 @@
(* Type *)
(* Type
*
* <<<~Bitstring.t~>>> *)
(* [[file:~/QCaml/common/bitstring.org::*Type][Type:1]] *)
type t

5
common/lib/charge.mli
View File

@ -1,5 +1,6 @@
(* Type *)
(* Type
*
* <<<~Charge.t~>>> *)
(* [[file:~/QCaml/common/charge.org::*Type][Type:1]] *)
type t

14
common/lib/command_line.ml
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@ -1,8 +1,8 @@
(* - Short option: in the command line, a dash with a single character
(* - <<<Short option>>>: in the command line, a dash with a single character
* (ex: =ls -l=)
* - Long option: in the command line, two dashes with a word
* - <<<Long option>>>: in the command line, two dashes with a word
* (ex: =ls --directory=)
* - Command-line options can be ~Mandatory~ or ~Optional~
* - Documentation of the option is used in the help function
@ -11,12 +11,14 @@
* (~git --log[=<n>]~) *)
(* [[file:~/QCaml/common/command_line.org::*Type][Type:2]] *)
(* [[file:~/QCaml/common/command_line.org::*Types][Types:2]] *)
type short_opt = char
type long_opt = string
type optional = Mandatory | Optional
type documentation = string
type argument = With_arg of string | Without_arg | With_opt_arg of string
type argument = | With_arg of string
| Without_arg
| With_opt_arg of string
type description = {
short: short_opt ;
@ -25,7 +27,7 @@ type description = {
doc : documentation ;
arg : argument ;
}
(* Type:2 ends here *)
(* Types:2 ends here *)
(* Mutable attributes
*
@ -96,6 +98,7 @@ let output_text t =
(* Function to build the short description of the command-line
* arguments, such as
*
* Example:
* #+begin_example
* my_program -b <string> [-h] [-u <float>] -x <string> [--]
* #+end_example *)
@ -120,6 +123,7 @@ let output_short x =
(* Function to build the long description of the command-line
* arguments, such as
*
* Example:
* #+begin_example
* -x --xyz=<string> Name of the file containing the nuclear
* coordinates in xyz format

6
common/lib/command_line.mli
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@ -1,4 +1,4 @@
(* Type
(* Types
*
* #+NAME:type *)
@ -7,7 +7,9 @@ type short_opt = char
type long_opt = string
type optional = Mandatory | Optional
type documentation = string
type argument = With_arg of string | Without_arg | With_opt_arg of string
type argument = | With_arg of string
| Without_arg
| With_opt_arg of string
type description = {
short: short_opt ;

15
common/lib/coordinate.ml
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@ -53,14 +53,15 @@ let angstrom_to_bohr { x ; y ; z } =
(* | ~neg~ | Negative of a point |
* | ~get~ | Extracts the projection of the coordinate on an axis |
* | ~dot~ | Dot product |
* | ~norm~ | $\ell{^2}$ norm of the vector |
* | ~¦.~ | Scales the vector by a constant |
* | ~¦+~ | Adds two vectors |
* | ~¦-~ | Subtracts two vectors |
(* | ~neg~ | Negative of a point |
* | ~get~ | Extracts the projection of the coordinate on an axis |
* | ~dot~ | Dot product |
* | ~norm~ | $\ell{^2}$ norm of the vector |
* | $\vert .$ | Scales the vector by a constant |
* | $\vert +$ | Adds two vectors |
* | $\vert -$ | Subtracts two vectors |
*
* Example:
* #+begin_example
* Coordinate.neg { x=1. ; y=2. ; z=3. } ;;
* - : Coordinate.t = -1.0000 -2.0000 -3.0000

3
common/lib/coordinate.mli
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@ -1,5 +1,6 @@
(* Type
*
* <<<~Coordinate.t~>>>
* #+NAME: types *)
(* [[file:~/QCaml/common/coordinate.org::types][types]] *)
@ -25,7 +26,7 @@ type axis = X | Y | Z
(* [[file:~/QCaml/common/coordinate.org::*Creation][Creation:1]] *)
val make : 'a point -> t
val make_angstrom : 'a point -> angstrom point
val zero : bohr point
val zero : bohr point
(* Creation:1 ends here *)
(* Conversion *)

5
common/lib/non_negative_float.mli
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@ -1,5 +1,6 @@
(* Type *)
(* Type
*
* <<<~Non_negative_float.t~>> *)
(* [[file:~/QCaml/common/non_negative_float.org::*Type][Type:1]] *)
type t = private float

10
common/lib/powers.ml
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@ -8,13 +8,14 @@ type t = {
x : int ;
y : int ;
z : int ;
tot : int ;
tot : int ;
}
(* Type:2 ends here *)
(* #+begin_example
(* Example:
* #+begin_example
* Powers.of_int_tuple (2,3,1);;
* - : Powers.t = x^2 + y^3 + z^1
*
@ -24,9 +25,9 @@ type t = {
(* [[file:~/QCaml/common/powers.org::*Conversions][Conversions:2]] *)
let of_int_tuple t =
let of_int_tuple t =
let result =
match t with
match t with
| (x,y,z) -> { x ; y ; z ; tot=x+y+z }
in
if result.x < 0 ||
@ -46,6 +47,7 @@ let to_int_tuple { x ; y ; z ; _ } = (x,y,z)
* | ~incr~ | Returns a new ~Powers.t~ with the power on the given axis incremented |
* | ~decr~ | Returns a new ~Powers.t~ with the power on the given axis decremented. As opposed to ~of_int_tuple~, the values may become negative|
*
* Example:
* #+begin_example
* Powers.get Coordinate.Y (Powers.of_int_tuple (2,3,1));;
* - : int = 3

9
common/lib/powers.mli
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@ -1,12 +1,13 @@
(* Type *)
(* Type
*
* <<<~Powers.t~>>> *)
(* [[file:~/QCaml/common/powers.org::*Type][Type:1]] *)
type t = private {
x : int ;
y : int ;
z : int ;
tot : int ;
tot : int ;
}
(* Type:1 ends here *)
@ -23,7 +24,7 @@ val to_int_tuple : t -> int * int * int
(* [[file:~/QCaml/common/powers.org::*Operations][Operations:1]] *)
val get : Coordinate.axis -> t -> int
val incr : Coordinate.axis -> t -> t
val incr : Coordinate.axis -> t -> t
val decr : Coordinate.axis -> t -> t
(* Operations:1 ends here *)

5
common/lib/range.mli
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@ -1,5 +1,6 @@
(* Type *)
(* Type
*
* <<<~Range.t~>>> *)
(* [[file:~/QCaml/common/range.org::*Type][Type:1]] *)
type t

5
common/lib/spin.mli
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@ -1,5 +1,6 @@
(* Type *)
(* Type
*
* <<<~Spin.t~>>> *)
(* [[file:~/QCaml/common/spin.org::*Type][Type:1]] *)
type t = Alfa | Beta

7
common/lib/util.ml
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@ -1,5 +1,6 @@
(* [[file:~/QCaml/common/util.org::*Erf][Erf:3]] *)
external erf_float : float -> float = "erf_float_bytecode" "erf_float" [@@unboxed] [@@noalloc]
external erf_float : float -> float
= "erf_float_bytecode" "erf_float" [@@unboxed] [@@noalloc]
(* Erf:3 ends here *)
(* [[file:~/QCaml/common/util.org::*Erfc][Erfc:3]] *)
@ -7,7 +8,8 @@ external erfc_float : float -> float = "erfc_float_bytecode" "erfc_float" [@@unb
(* Erfc:3 ends here *)
(* [[file:~/QCaml/common/util.org::*Gamma][Gamma:3]] *)
external gamma_float : float -> float = "gamma_float_bytecode" "gamma_float" [@@unboxed] [@@noalloc]
external gamma_float : float -> float
= "gamma_float_bytecode" "gamma_float" [@@unboxed] [@@noalloc]
(* Gamma:3 ends here *)
(* [[file:~/QCaml/common/util.org::*Popcnt][Popcnt:3]] *)
@ -362,6 +364,7 @@ let stream_fold f init stream =
* | ~pp_float_2darray_size~ | Printer for matrices with size |
* | ~pp_bitstring~ | Printer for bit strings (used by ~Bitstring~ module) |
*
* Example:
* #+begin_example
* pp_float_array_size:
* [ 6: 1.000000 1.732051 1.732051 1.000000 1.732051 1.000000 ]

9
common/lib/util.mli
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@ -1,13 +1,16 @@
(* [[file:~/QCaml/common/util.org::*Erf][Erf:2]] *)
external erf_float : float -> float = "erf_float_bytecode" "erf_float" [@@unboxed] [@@noalloc]
external erf_float : float -> float
= "erf_float_bytecode" "erf_float" [@@unboxed] [@@noalloc]
(* Erf:2 ends here *)
(* [[file:~/QCaml/common/util.org::*Erfc][Erfc:2]] *)
external erfc_float : float -> float = "erfc_float_bytecode" "erfc_float" [@@unboxed] [@@noalloc]
external erfc_float : float -> float
= "erfc_float_bytecode" "erfc_float" [@@unboxed] [@@noalloc]
(* Erfc:2 ends here *)
(* [[file:~/QCaml/common/util.org::*Gamma][Gamma:2]] *)
external gamma_float : float -> float = "gamma_float_bytecode" "gamma_float" [@@unboxed] [@@noalloc]
external gamma_float : float -> float
= "gamma_float_bytecode" "gamma_float" [@@unboxed] [@@noalloc]
(* Gamma:2 ends here *)
(* [[file:~/QCaml/common/util.org::*Popcnt][Popcnt:2]] *)

5
common/lib/zkey.mli
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@ -1,5 +1,6 @@
(* Types *)
(* Types
*
* <<<~Zkey.t~>>> *)
(* [[file:~/QCaml/common/zkey.org::*Types][Types:1]] *)
type t

5
common/lib/zmap.mli
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@ -1,5 +1,6 @@
(* Type *)
(* Type
*
* <<<~Zmap.t~>>> *)
(* [[file:~/QCaml/common/zmap.org::*Type][Type:1]] *)
include module type of Hashtbl.Make(Zkey)

1
common/non_negative_float.org
View File

@ -16,6 +16,7 @@
** Type
<<<~Non_negative_float.t~>>
#+begin_src ocaml :tangle (eval mli)
type t = private float
#+end_src

23
common/powers.org
View File

@ -7,34 +7,35 @@
(setq ml (concat lib name ".ml"))
(setq test-ml (concat testdir name ".ml"))
(org-babel-tangle)
#+end_src
#+end_src
* Powers
:PROPERTIES:
:header-args: :noweb yes :comments both
:END:
Contains powers of x, y and z describing the polynomials in atomic basis sets.
Contains powers of $x$, $y$ and $z$ describing the polynomials in atomic basis sets.
** Type
<<<~Powers.t~>>>
#+begin_src ocaml :tangle (eval mli)
type t = private {
x : int ;
y : int ;
z : int ;
tot : int ;
tot : int ;
}
#+end_src
~tot~ always contains ~x+y+z~.
#+begin_src ocaml :tangle (eval ml) :exports none
type t = {
x : int ;
y : int ;
z : int ;
tot : int ;
tot : int ;
}
#+end_src
@ -42,9 +43,10 @@ type t = {
#+begin_src ocaml :tangle (eval mli)
val of_int_tuple : int * int * int -> t
val to_int_tuple : t -> int * int * int
val to_int_tuple : t -> int * int * int
#+end_src
Example:
#+begin_example
Powers.of_int_tuple (2,3,1);;
- : Powers.t = x^2 + y^3 + z^1
@ -54,9 +56,9 @@ Powers.(to_int_tuple (of_int_tuple (2,3,1)));;
#+end_example
#+begin_src ocaml :tangle (eval ml) :exports none
let of_int_tuple t =
let of_int_tuple t =
let result =
match t with
match t with
| (x,y,z) -> { x ; y ; z ; tot=x+y+z }
in
if result.x < 0 ||
@ -67,14 +69,14 @@ let of_int_tuple t =
result
let to_int_tuple { x ; y ; z ; _ } = (x,y,z)
let to_int_tuple { x ; y ; z ; _ } = (x,y,z)
#+end_src
** Operations
#+begin_src ocaml :tangle (eval mli)
val get : Coordinate.axis -> t -> int
val incr : Coordinate.axis -> t -> t
val incr : Coordinate.axis -> t -> t
val decr : Coordinate.axis -> t -> t
#+end_src
@ -82,6 +84,7 @@ val decr : Coordinate.axis -> t -> t
| ~incr~ | Returns a new ~Powers.t~ with the power on the given axis incremented |
| ~decr~ | Returns a new ~Powers.t~ with the power on the given axis decremented. As opposed to ~of_int_tuple~, the values may become negative|
Example:
#+begin_example
Powers.get Coordinate.Y (Powers.of_int_tuple (2,3,1));;
- : int = 3

1
common/range.org
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@ -24,6 +24,7 @@
** Type
<<<~Range.t~>>>
#+begin_src ocaml :tangle (eval mli)
type t
#+end_src

1
common/spin.org
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@ -18,6 +18,7 @@
** Type
<<<~Spin.t~>>>
#+begin_src ocaml :tangle (eval mli)
type t = Alfa | Beta
#+end_src

9
common/test/bitstring.ml
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@ -19,7 +19,8 @@ check_bool "of_z" true (one_x = (of_z (Z.of_int x)));
(* #+begin_example
(* Example:
* #+begin_example
* Bitstring.(shift_left (of_int 15) 2);;
* - : Bitstring.t =
* --++++----------------------------------------------------------
@ -59,7 +60,8 @@ check_bool "testbit6" false (testbit (of_z (Z.of_int 8)) 4);
(* #+begin_example
(* Example:
* #+begin_example
* Bitstring.(logor (of_int 15) (of_int 73));;
* - : Bitstring.t =
* ++++--+---------------------------------------------------------
@ -90,7 +92,8 @@ check_bool "to_list" true ([ 1 ; 3 ; 4 ; 6 ] = (to_list (of_int 45)));
(* #+begin_example
(* Example:
* #+begin_example
* Bitstring.permutations 2 4;;
* - : Bitstring.t list =
* [++--------------------------------------------------------------;

16
common/util.org
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@ -53,11 +53,13 @@ CAMLprim double erf_float(double x) {
#+end_src
#+begin_src ocaml :tangle (eval mli)
external erf_float : float -> float = "erf_float_bytecode" "erf_float" [@@unboxed] [@@noalloc]
external erf_float : float -> float
= "erf_float_bytecode" "erf_float" [@@unboxed] [@@noalloc]
#+end_src
#+begin_src ocaml :tangle (eval ml) :exports none
external erf_float : float -> float = "erf_float_bytecode" "erf_float" [@@unboxed] [@@noalloc]
external erf_float : float -> float
= "erf_float_bytecode" "erf_float" [@@unboxed] [@@noalloc]
#+end_src
*** Erfc
@ -73,7 +75,8 @@ CAMLprim double erfc_float(double x) {
#+end_src
#+begin_src ocaml :tangle (eval mli)
external erfc_float : float -> float = "erfc_float_bytecode" "erfc_float" [@@unboxed] [@@noalloc]
external erfc_float : float -> float
= "erfc_float_bytecode" "erfc_float" [@@unboxed] [@@noalloc]
#+end_src
#+begin_src ocaml :tangle (eval ml) :exports none
@ -94,11 +97,13 @@ CAMLprim double gamma_float(double x) {
#+end_src
#+begin_src ocaml :tangle (eval mli)
external gamma_float : float -> float = "gamma_float_bytecode" "gamma_float" [@@unboxed] [@@noalloc]
external gamma_float : float -> float
= "gamma_float_bytecode" "gamma_float" [@@unboxed] [@@noalloc]
#+end_src
#+begin_src ocaml :tangle (eval ml) :exports none
external gamma_float : float -> float = "gamma_float_bytecode" "gamma_float" [@@unboxed] [@@noalloc]
external gamma_float : float -> float
= "gamma_float_bytecode" "gamma_float" [@@unboxed] [@@noalloc]
#+end_src
*** Popcnt
@ -627,6 +632,7 @@ val pp_bitstring : int -> Format.formatter -> Z.t -> unit
| ~pp_float_2darray_size~ | Printer for matrices with size |
| ~pp_bitstring~ | Printer for bit strings (used by ~Bitstring~ module) |
Example:
#+begin_example
pp_float_array_size:
[ 6: 1.000000 1.732051 1.732051 1.000000 1.732051 1.000000 ]

2
common/zkey.org
View File

@ -21,6 +21,7 @@
The small integers x, y and z are stored compactly in this 126-bits
space:
Example:
#+begin_example
Left Right
3 [--------------------------------------------------------------] [------------------|---------------|---------------|---------------]
@ -41,6 +42,7 @@
** Types
<<<~Zkey.t~>>>
#+begin_src ocaml :tangle (eval mli)
type t

1
common/zmap.org
View File

@ -18,6 +18,7 @@
** Type
<<<~Zmap.t~>>>
#+begin_src ocaml :tangle (eval mli)
include module type of Hashtbl.Make(Zkey)
#+end_src

187
docs/ao.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-01-20 Wed 23:52 -->
<!-- 2021-01-28 Thu 00:21 -->
<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>
@ -193,12 +193,29 @@
.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>
<link rel="stylesheet" title="Standard" href="qcaml.css" type="text/css" />
<script type="text/javascript" src="org-info.js">
// @license magnet:?xt=urn:btih:1f739d935676111cfff4b4693e3816e664797050&amp;dn=gpl-3.0.txt GPL-v3-or-Later
// @license-end
</script>
<script type="text/javascript">
// @license magnet:?xt=urn:btih:1f739d935676111cfff4b4693e3816e664797050&amp;dn=gpl-3.0.txt GPL-v3-or-Later
<!--/*--><![CDATA[/*><!--*/
org_html_manager.set("TOC_DEPTH", "4");
org_html_manager.set("LINK_HOME", "index.html");
org_html_manager.set("LINK_UP", "");
org_html_manager.set("LOCAL_TOC", "1");
org_html_manager.set("VIEW_BUTTONS", "0");
org_html_manager.set("MOUSE_HINT", "underline");
org_html_manager.set("FIXED_TOC", "0");
org_html_manager.set("TOC", "1");
org_html_manager.set("VIEW", "info");
org_html_manager.setup(); // activate after the parameters are set
/*]]>*///-->
// @license-end
</script>
<script type="text/javascript">
// @license magnet:?xt=urn:btih:e95b018ef3580986a04669f1b5879592219e2a7a&dn=public-domain.txt Public Domain
<!--/*--><![CDATA[/*><!--*/
@ -255,38 +272,43 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org372d71d">1. Gaussian basis</a>
<li><a href="#org10034f2">1. Summary</a></li>
<li><a href="#org5474da5">2. Gaussian basis</a>
<ul>
<li><a href="#org569cf0d">1.1. Type</a></li>
<li><a href="#org1cc0115">1.2. Access</a></li>
<li><a href="#org8d029c7">1.3. Computation</a></li>
<li><a href="#orge9b9a74">1.4. Creation</a></li>
<li><a href="#orgd376854">1.5. Printers</a></li>
<li><a href="#org7b7dfc2">2.1. Type</a></li>
<li><a href="#org9115219">2.2. Access</a></li>
<li><a href="#org7028216">2.3. Computation</a></li>
<li><a href="#org1f24daa">2.4. Creation</a></li>
<li><a href="#orge8bdd89">2.5. Printers</a></li>
</ul>
</li>
<li><a href="#org0efb0c2">2. Basis</a>
<li><a href="#org6b9a069">3. Basis</a>
<ul>
<li><a href="#orgfc56091">2.1. Dimensions&#xa0;&#xa0;&#xa0;<span class="tag"><span class="noexports">noexports</span></span></a></li>
<li><a href="#orga0a6bd2">2.2. Polymorphic types</a></li>
<li><a href="#orgf9a3143">2.3. Types</a></li>
<li><a href="#org1a171c4">2.4. Conversions</a></li>
<li><a href="#org3f1b82a">2.5. Access</a></li>
<li><a href="#org2155877">2.6. Printers</a></li>
<li><a href="#org68c3519">3.1. Polymorphic types</a></li>
<li><a href="#org5764372">3.2. Types</a></li>
<li><a href="#org6ea365f">3.3. Conversions</a></li>
<li><a href="#org867b16c">3.4. Access</a></li>
<li><a href="#orgf5a488a">3.5. Printers</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div class="org-src-container">
<pre class="src src-ocaml" id="org60f1a39"><span class="org-string">"Atomic basis set"</span>
</pre>
</div>
<div id="outline-container-org372d71d" class="outline-2">
<h2 id="org372d71d"><span class="section-number-2">1</span> Gaussian basis</h2>
<div id="outline-container-org10034f2" class="outline-2">
<h2 id="org10034f2"><span class="section-number-2">1</span> Summary</h2>
<div class="outline-text-2" id="text-1">
<p>
This modules contains the data structures used to characterize the
atomic basis set.
</p>
</div>
</div>
<div id="outline-container-org5474da5" class="outline-2">
<h2 id="org5474da5"><span class="section-number-2">2</span> Gaussian basis</h2>
<div class="outline-text-2" id="text-2">
<p>
Data structure for Gaussian Atomic Orbitals:
</p>
@ -297,19 +319,19 @@ Data structure for Gaussian Atomic Orbitals:
</p>
<p>
where the polynomial $P<sub>Ai</sub> and the Gaussian part are both centered on
where the polynomial \(P_i\) and the Gaussian part are both centered on
nucleus \(A\).
</p>
</div>
<div id="outline-container-org569cf0d" class="outline-3">
<h3 id="org569cf0d"><span class="section-number-3">1.1</span> Type</h3>
<div class="outline-text-3" id="text-1-1">
<div id="outline-container-org7b7dfc2" class="outline-3">
<h3 id="org7b7dfc2"><span class="section-number-3">2.1</span> Type</h3>
<div class="outline-text-3" id="text-2-1">
<p>
<a id="org99abab3"><code>Gaussian_basis.t</code></a>
<a id="org8bd4ea5"><code>Gaussian_basis.t</code></a>
</p>
<div class="org-src-container">
<pre class="src src-ocaml" id="orgfe8c01d"><span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Common</span>
<pre class="src src-ocaml" id="org5bf215b"><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">Linear_algebra</span>
<span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Gaussian_integrals</span>
@ -321,9 +343,9 @@ nucleus \(A\).
</div>
</div>
<div id="outline-container-org1cc0115" class="outline-3">
<h3 id="org1cc0115"><span class="section-number-3">1.2</span> Access</h3>
<div class="outline-text-3" id="text-1-2">
<div id="outline-container-org9115219" class="outline-3">
<h3 id="org9115219"><span class="section-number-3">2.2</span> Access</h3>
<div class="outline-text-3" id="text-2-2">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">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">Gaussian.Basis.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">cartesian</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> bool
@ -413,11 +435,13 @@ nucleus \(A\).
</div>
</div>
<div id="outline-container-org8d029c7" class="outline-3">
<h3 id="org8d029c7"><span class="section-number-3">1.3</span> Computation</h3>
<div class="outline-text-3" id="text-1-3">
<div id="outline-container-org7028216" class="outline-3">
<h3 id="org7028216"><span class="section-number-3">2.3</span> Computation</h3>
<div class="outline-text-3" id="text-2-3">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">values</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">Coordinate.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Gaussian.Basis.</span>t <span class="org-tuareg-font-lock-module">Vector.</span>t
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">values</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">Coordinate.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span>
<span class="org-tuareg-font-lock-module">Gaussian.Basis.</span>t <span class="org-tuareg-font-lock-module">Vector.</span>t
</pre>
</div>
@ -439,14 +463,15 @@ nucleus \(A\).
</div>
</div>
<div id="outline-container-orge9b9a74" class="outline-3">
<h3 id="orge9b9a74"><span class="section-number-3">1.4</span> Creation</h3>
<div class="outline-text-3" id="text-1-4">
<div id="outline-container-org1f24daa" class="outline-3">
<h3 id="org1f24daa"><span class="section-number-3">2.4</span> Creation</h3>
<div class="outline-text-3" id="text-2-4">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">make</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-label">basis</span><span class="org-tuareg-font-lock-operator">:</span><span class="org-tuareg-font-lock-module">Gaussian.Basis.</span>t <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">?cartesian</span><span class="org-tuareg-font-lock-operator">:</span>bool <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-operator">-&gt;</span> t
<span class="org-tuareg-font-lock-module">Nuclei.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span>
t
</pre>
</div>
@ -463,16 +488,19 @@ Defaults:
<li><code>cartesian</code> : <code>false</code></li>
</ul>
<pre class="example" id="org3eab3c8">
<p>
Example:
</p>
<pre class="example" id="orgb9ea620">
let b = Ao.Basis_gaussian.make ~basis nuclei ;;
val b : Ao.Basis_gaussian.t = Gaussian Basis, spherical, 15 AOs
</pre>
</div>
</div>
<div id="outline-container-orgd376854" class="outline-3">
<h3 id="orgd376854"><span class="section-number-3">1.5</span> Printers</h3>
<div class="outline-text-3" id="text-1-5">
<div id="outline-container-orge8bdd89" class="outline-3">
<h3 id="orge8bdd89"><span class="section-number-3">2.5</span> Printers</h3>
<div class="outline-text-3" id="text-2-5">
<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>
@ -481,23 +509,22 @@ val b : Ao.Basis_gaussian.t = Gaussian Basis, spherical, 15 AOs
</div>
</div>
<div id="outline-container-org0efb0c2" class="outline-2">
<h2 id="org0efb0c2"><span class="section-number-2">2</span> Basis</h2>
<div class="outline-text-2" id="text-2">
<div id="outline-container-org6b9a069" class="outline-2">
<h2 id="org6b9a069"><span class="section-number-2">3</span> Basis</h2>
<div class="outline-text-2" id="text-3">
<p>
Data structure for Atomic Orbitals.
</p>
</div>
<div id="outline-container-orgfc56091" class="outline-3">
<h3 id="orgfc56091"><span class="section-number-3">2.1</span> Dimensions&#xa0;&#xa0;&#xa0;<span class="tag"><span class="noexports">noexports</span></span></h3>
</div>
<div id="outline-container-orga0a6bd2" class="outline-3">
<h3 id="orga0a6bd2"><span class="section-number-3">2.2</span> Polymorphic types</h3>
<div class="outline-text-3" id="text-2-2">
<div id="outline-container-org68c3519" class="outline-3">
<h3 id="org68c3519"><span class="section-number-3">3.1</span> Polymorphic types</h3>
<div class="outline-text-3" id="text-3-1">
<p>
<a id="org221aabc"><code>Basis.t</code></a>
</p>
<div class="org-src-container">
<pre class="src src-ocaml" id="org7556cac"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span> <span class="org-tuareg-font-lock-operator">=</span>
<pre class="src src-ocaml" id="org7f2805d"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span> <span class="org-tuareg-font-lock-operator">=</span>
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">Unknown</span>
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">Gaussian</span> <span class="org-keyword">of</span> <span class="org-tuareg-font-lock-module">Basis_gaussian.</span>t
</pre>
@ -505,9 +532,12 @@ Data structure for Atomic Orbitals.
</div>
</div>
<div id="outline-container-orgf9a3143" class="outline-3">
<h3 id="orgf9a3143"><span class="section-number-3">2.3</span> Types</h3>
<div class="outline-text-3" id="text-2-3">
<div id="outline-container-org5764372" class="outline-3">
<h3 id="org5764372"><span class="section-number-3">3.2</span> Types</h3>
<div class="outline-text-3" id="text-3-2">
<p>
<a id="orgaf9bd07"><code>Basis.t</code></a>
</p>
<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>
<span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">ao</span> <span class="org-tuareg-font-lock-operator">=</span> <span class="org-tuareg-font-lock-module">Ao_dim.</span>t
@ -521,13 +551,17 @@ Data structure for Atomic Orbitals.
</div>
</div>
<div id="outline-container-org1a171c4" class="outline-3">
<h3 id="org1a171c4"><span class="section-number-3">2.4</span> Conversions</h3>
<div class="outline-text-3" id="text-2-4">
<div id="outline-container-org6ea365f" class="outline-3">
<h3 id="org6ea365f"><span class="section-number-3">3.3</span> Conversions</h3>
<div class="outline-text-3" id="text-3-3">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_nuclei_and_basis_filename</span> <span class="org-tuareg-font-lock-operator">:</span>
<span class="org-tuareg-font-lock-label">?kind</span><span class="org-tuareg-font-lock-operator">:[&gt;</span> <span class="org-tuareg-font-lock-constructor">`Gaussian</span> <span class="org-tuareg-font-lock-operator">]</span> <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">?cartesian</span><span class="org-tuareg-font-lock-operator">:</span>bool <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> string <span class="org-tuareg-font-lock-operator">-&gt;</span> t
<span class="org-tuareg-font-lock-label">?kind</span><span class="org-tuareg-font-lock-operator">:[&gt;</span> <span class="org-tuareg-font-lock-constructor">`Gaussian</span> <span class="org-tuareg-font-lock-operator">]</span> <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">?cartesian</span><span class="org-tuareg-font-lock-operator">:</span>bool <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>
string <span class="org-tuareg-font-lock-operator">-&gt;</span>
t
</pre>
</div>
@ -556,16 +590,19 @@ Defaults:
<li><code>cartesian</code> : <code>false</code></li>
</ul>
<pre class="example" id="orgd1e8c0c">
<p>
Example:
</p>
<pre class="example" id="org65a225c">
let b = Ao.Basis.of_nuclei_and_basis_filename ~nuclei filename;;
val b : Ao.Basis.t = Gaussian Basis, spherical, 15 AOs
</pre>
</div>
</div>
<div id="outline-container-org3f1b82a" class="outline-3">
<h3 id="org3f1b82a"><span class="section-number-3">2.5</span> Access</h3>
<div class="outline-text-3" id="text-2-5">
<div id="outline-container-org867b16c" class="outline-3">
<h3 id="org867b16c"><span class="section-number-3">3.4</span> Access</h3>
<div class="outline-text-3" id="text-3-4">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">size</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">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">Basis_poly.</span>t
@ -662,9 +699,9 @@ val b : Ao.Basis.t = Gaussian Basis, spherical, 15 AOs
</div>
<div id="outline-container-org2155877" class="outline-3">
<h3 id="org2155877"><span class="section-number-3">2.6</span> Printers</h3>
<div class="outline-text-3" id="text-2-6">
<div id="outline-container-orgf5a488a" class="outline-3">
<h3 id="orgf5a488a"><span class="section-number-3">3.5</span> Printers</h3>
<div class="outline-text-3" id="text-3-5">
<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>
@ -675,7 +712,7 @@ val b : Ao.Basis.t = Gaussian Basis, spherical, 15 AOs
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-20 Wed 23:52</p>
<p class="date">Created: 2021-01-28 Thu 00:21</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

767
docs/common.html
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165
docs/gaussian.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Gaussian</title>
@ -193,12 +193,29 @@
.org-svg { width: 90%; }
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</style>
<link rel="stylesheet" type="text/css" href="https://fniessen.github.io/org-html-themes/src/readtheorg_theme/css/htmlize.css"/>
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<link rel="stylesheet" title="Standard" href="qcaml.css" type="text/css" />
<script type="text/javascript" src="org-info.js">
// @license magnet:?xt=urn:btih:1f739d935676111cfff4b4693e3816e664797050&amp;dn=gpl-3.0.txt GPL-v3-or-Later
// @license-end
</script>
<script type="text/javascript">
// @license magnet:?xt=urn:btih:1f739d935676111cfff4b4693e3816e664797050&amp;dn=gpl-3.0.txt GPL-v3-or-Later
<!--/*--><![CDATA[/*><!--*/
org_html_manager.set("TOC_DEPTH", "4");
org_html_manager.set("LINK_HOME", "index.html");
org_html_manager.set("LINK_UP", "");
org_html_manager.set("LOCAL_TOC", "1");
org_html_manager.set("VIEW_BUTTONS", "0");
org_html_manager.set("MOUSE_HINT", "underline");
org_html_manager.set("FIXED_TOC", "0");
org_html_manager.set("TOC", "1");
org_html_manager.set("VIEW", "info");
org_html_manager.setup(); // activate after the parameters are set
/*]]>*///-->
// @license-end
</script>
<script type="text/javascript">
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@ -255,42 +272,42 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org493bb5e">1. Atomic shell</a>
<li><a href="#orgf3ada33">1. Summmary</a></li>
<li><a href="#org7457529">2. Atomic shell</a>
<ul>
<li><a href="#org8b57b46">1.1. Type</a></li>
<li><a href="#org6ce19dc">1.2. Access</a></li>
<li><a href="#orgd728205">1.3. Creation</a></li>
<li><a href="#orgae3aa50">1.4. Printers</a></li>
<li><a href="#org0e4fe4d">2.1. Type</a></li>
<li><a href="#orgde1bce4">2.2. Access</a></li>
<li><a href="#org24b2b8e">2.3. Creation</a></li>
<li><a href="#orge729f26">2.4. Printers</a></li>
</ul>
</li>
<li><a href="#orgb8a46dc">2. Atomic shell pair couple</a>
<li><a href="#org8871eba">3. Atomic shell pair couple</a>
<ul>
<li><a href="#orgda54231">2.1. Type</a></li>
<li><a href="#orgce726a0">2.2. Access</a></li>
<li><a href="#org9a8f8ee">2.3. Creation</a></li>
<li><a href="#org4eb55a5">2.4. Printers</a></li>
<li><a href="#org1019362">3.1. Type</a></li>
<li><a href="#org2371d45">3.2. Access</a></li>
<li><a href="#org9169380">3.3. Creation</a></li>
<li><a href="#orgadedc00">3.4. Printers</a></li>
</ul>
</li>
<li><a href="#org9d5af05">3. Atomic shell pair</a>
<li><a href="#org750192c">4. Atomic shell pair</a>
<ul>
<li><a href="#orgc038806">3.1. Type</a></li>
<li><a href="#org66f13a3">3.2. Access</a></li>
<li><a href="#orgbe94db4">3.3. Creation</a></li>
<li><a href="#org5f9e64f">3.4. Printers</a></li>
<li><a href="#org6b2bebd">4.1. Type</a></li>
<li><a href="#org0967ce4">4.2. Access</a></li>
<li><a href="#org176c31a">4.3. Creation</a></li>
<li><a href="#org3f5a744">4.4. Printers</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div class="org-src-container">
<pre class="src src-ocaml" id="orgb7f41e9"><span class="org-string">"Gaussian basis sets"</span>
</pre>
</div>
<div id="outline-container-orgf3ada33" class="outline-2">
<h2 id="orgf3ada33"><span class="section-number-2">1</span> Summmary</h2>
</div>
<div id="outline-container-org493bb5e" class="outline-2">
<h2 id="org493bb5e"><span class="section-number-2">1</span> Atomic shell</h2>
<div class="outline-text-2" id="text-1">
<div id="outline-container-org7457529" class="outline-2">
<h2 id="org7457529"><span class="section-number-2">2</span> Atomic shell</h2>
<div class="outline-text-2" id="text-2">
<p>
Set of contracted Gaussians differing only by the powers of \(x\), \(y\) and \(z\), with a
constant <code>Angular_momentum.t</code>, all centered on the same point.
@ -322,9 +339,9 @@ particular powers of \(x,y,z\) (<code>PrimitiveShell.norm_coef_scale</code>)</li
</div>
<div id="outline-container-org8b57b46" class="outline-3">
<h3 id="org8b57b46"><span class="section-number-3">1.1</span> Type</h3>
<div class="outline-text-3" id="text-1-1">
<div id="outline-container-org0e4fe4d" class="outline-3">
<h3 id="org0e4fe4d"><span class="section-number-3">2.1</span> Type</h3>
<div class="outline-text-3" id="text-2-1">
<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>
@ -334,9 +351,9 @@ particular powers of \(x,y,z\) (<code>PrimitiveShell.norm_coef_scale</code>)</li
</div>
</div>
<div id="outline-container-org6ce19dc" class="outline-3">
<h3 id="org6ce19dc"><span class="section-number-3">1.2</span> Access</h3>
<div class="outline-text-3" id="text-1-2">
<div id="outline-container-orgde1bce4" class="outline-3">
<h3 id="orgde1bce4"><span class="section-number-3">2.2</span> Access</h3>
<div class="outline-text-3" id="text-2-2">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">ang_mom</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">Angular_momentum.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">center</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">Coordinate.</span>t
@ -412,15 +429,15 @@ particular powers of \(x,y,z\) (<code>PrimitiveShell.norm_coef_scale</code>)</li
</tbody>
</table>
<pre class="example" id="org62fa36c">
<pre class="example" id="org37e8ada">
</pre>
</div>
</div>
<div id="outline-container-orgd728205" class="outline-3">
<h3 id="orgd728205"><span class="section-number-3">1.3</span> Creation</h3>
<div class="outline-text-3" id="text-1-3">
<div id="outline-container-org24b2b8e" class="outline-3">
<h3 id="org24b2b8e"><span class="section-number-3">2.3</span> Creation</h3>
<div class="outline-text-3" id="text-2-3">
<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">?index</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-module">Contracted_shell.</span>t array <span class="org-tuareg-font-lock-operator">-&gt;</span> t
@ -451,9 +468,9 @@ particular powers of \(x,y,z\) (<code>PrimitiveShell.norm_coef_scale</code>)</li
</div>
</div>
<div id="outline-container-orgae3aa50" class="outline-3">
<h3 id="orgae3aa50"><span class="section-number-3">1.4</span> Printers</h3>
<div class="outline-text-3" id="text-1-4">
<div id="outline-container-orge729f26" class="outline-3">
<h3 id="orge729f26"><span class="section-number-3">2.4</span> Printers</h3>
<div class="outline-text-3" id="text-2-4">
<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>
@ -462,9 +479,9 @@ particular powers of \(x,y,z\) (<code>PrimitiveShell.norm_coef_scale</code>)</li
</div>
</div>
<div id="outline-container-orgb8a46dc" class="outline-2">
<h2 id="orgb8a46dc"><span class="section-number-2">2</span> Atomic shell pair couple</h2>
<div class="outline-text-2" id="text-2">
<div id="outline-container-org8871eba" class="outline-2">
<h2 id="org8871eba"><span class="section-number-2">3</span> Atomic shell pair couple</h2>
<div class="outline-text-2" id="text-3">
<p>
An atomic shell pair couple is the cartesian product between two sets of functions, one
set over electron one and one set over electron two. Both sets are atomic shell
@ -479,9 +496,9 @@ acting on different electrons, since they will be coupled by a two-electron oper
</div>
<div id="outline-container-orgda54231" class="outline-3">
<h3 id="orgda54231"><span class="section-number-3">2.1</span> Type</h3>
<div class="outline-text-3" id="text-2-1">
<div id="outline-container-org1019362" class="outline-3">
<h3 id="org1019362"><span class="section-number-3">3.1</span> Type</h3>
<div class="outline-text-3" id="text-3-1">
<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>
@ -491,9 +508,9 @@ acting on different electrons, since they will be coupled by a two-electron oper
</div>
</div>
<div id="outline-container-orgce726a0" class="outline-3">
<h3 id="orgce726a0"><span class="section-number-3">2.2</span> Access</h3>
<div class="outline-text-3" id="text-2-2">
<div id="outline-container-org2371d45" class="outline-3">
<h3 id="org2371d45"><span class="section-number-3">3.2</span> Access</h3>
<div class="outline-text-3" id="text-3-2">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">ang_mom</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">Angular_momentum.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">atomic_shell_a</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">Atomic_shell.</span>t
@ -577,9 +594,9 @@ acting on different electrons, since they will be coupled by a two-electron oper
</div>
</div>
<div id="outline-container-org9a8f8ee" class="outline-3">
<h3 id="org9a8f8ee"><span class="section-number-3">2.3</span> Creation</h3>
<div class="outline-text-3" id="text-2-3">
<div id="outline-container-org9169380" class="outline-3">
<h3 id="org9169380"><span class="section-number-3">3.3</span> Creation</h3>
<div class="outline-text-3" id="text-3-3">
<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">?cutoff</span><span class="org-tuareg-font-lock-operator">:</span>float <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Atomic_shell_pair.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Atomic_shell_pair.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span> t option
</pre>
@ -604,15 +621,15 @@ Default cutoff is \(\epsilon\).
</tbody>
</table>
<pre class="example" id="org2b8686b">
<pre class="example" id="org6444454">
</pre>
</div>
</div>
<div id="outline-container-org4eb55a5" class="outline-3">
<h3 id="org4eb55a5"><span class="section-number-3">2.4</span> Printers</h3>
<div class="outline-text-3" id="text-2-4">
<div id="outline-container-orgadedc00" class="outline-3">
<h3 id="orgadedc00"><span class="section-number-3">3.4</span> Printers</h3>
<div class="outline-text-3" id="text-3-4">
<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>
@ -621,9 +638,9 @@ Default cutoff is \(\epsilon\).
</div>
</div>
<div id="outline-container-org9d5af05" class="outline-2">
<h2 id="org9d5af05"><span class="section-number-2">3</span> Atomic shell pair</h2>
<div class="outline-text-2" id="text-3">
<div id="outline-container-org750192c" class="outline-2">
<h2 id="org750192c"><span class="section-number-2">4</span> Atomic shell pair</h2>
<div class="outline-text-2" id="text-4">
<p>
Data structure to represent pairs of atomic shells. The products of
functions in the shell pair are one-electron functions.
@ -634,9 +651,9 @@ An atomic shell pair is an array of pairs of contracted shells.
</p>
</div>
<div id="outline-container-orgc038806" class="outline-3">
<h3 id="orgc038806"><span class="section-number-3">3.1</span> Type</h3>
<div class="outline-text-3" id="text-3-1">
<div id="outline-container-org6b2bebd" class="outline-3">
<h3 id="org6b2bebd"><span class="section-number-3">4.1</span> Type</h3>
<div class="outline-text-3" id="text-4-1">
<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>
@ -646,9 +663,9 @@ An atomic shell pair is an array of pairs of contracted shells.
</div>
</div>
<div id="outline-container-org66f13a3" class="outline-3">
<h3 id="org66f13a3"><span class="section-number-3">3.2</span> Access</h3>
<div class="outline-text-3" id="text-3-2">
<div id="outline-container-org0967ce4" class="outline-3">
<h3 id="org0967ce4"><span class="section-number-3">4.2</span> Access</h3>
<div class="outline-text-3" id="text-4-2">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">atomic_shell_a</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">Atomic_shell.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">atomic_shell_b</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">Atomic_shell.</span>t
@ -714,9 +731,9 @@ An atomic shell pair is an array of pairs of contracted shells.
</div>
</div>
<div id="outline-container-orgbe94db4" class="outline-3">
<h3 id="orgbe94db4"><span class="section-number-3">3.3</span> Creation</h3>
<div class="outline-text-3" id="text-3-3">
<div id="outline-container-org176c31a" class="outline-3">
<h3 id="org176c31a"><span class="section-number-3">4.3</span> Creation</h3>
<div class="outline-text-3" id="text-4-3">
<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">?cutoff</span><span class="org-tuareg-font-lock-operator">:</span>float <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Atomic_shell.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Atomic_shell.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span> t option
</pre>
@ -748,9 +765,9 @@ If an atomic shell pair is not significant, sets the value to <code>None</code>.
</div>
</div>
<div id="outline-container-org5f9e64f" class="outline-3">
<h3 id="org5f9e64f"><span class="section-number-3">3.4</span> Printers</h3>
<div class="outline-text-3" id="text-3-4">
<div id="outline-container-org3f5a744" class="outline-3">
<h3 id="org3f5a744"><span class="section-number-3">4.4</span> Printers</h3>
<div class="outline-text-3" id="text-4-4">
<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>
@ -761,7 +778,7 @@ If an atomic shell pair is not significant, sets the value to <code>None</code>.
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-20 Wed 23:52</p>
<p class="date">Created: 2021-01-27 Wed 23:44</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

47
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@ -3,7 +3,7 @@
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<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Gaussian integrals</title>
@ -193,12 +193,29 @@
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<link rel="stylesheet" type="text/css" href="https://fniessen.github.io/org-html-themes/src/readtheorg_theme/css/htmlize.css"/>
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org_html_manager.set("TOC_DEPTH", "4");
org_html_manager.set("LINK_HOME", "index.html");
org_html_manager.set("LINK_UP", "");
org_html_manager.set("LOCAL_TOC", "1");
org_html_manager.set("VIEW_BUTTONS", "0");
org_html_manager.set("MOUSE_HINT", "underline");
org_html_manager.set("FIXED_TOC", "0");
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@ -229,14 +246,22 @@
<a accesskey="H" href="index.html"> HOME </a>
</div><div id="content">
<h1 class="title">Gaussian integrals</h1>
<div class="org-src-container">
<pre class="src src-ocaml" id="org2519248"><span class="org-string">"Integrals on the Gaussian basis sets"</span>
</pre>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orge4d21a1">1. Summmary</a></li>
</ul>
</div>
</div>
<div id="outline-container-orge4d21a1" class="outline-2">
<h2 id="orge4d21a1"><span class="section-number-2">1</span> Summmary</h2>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-20 Wed 23:52</p>
<p class="date">Created: 2021-01-27 Wed 23:44</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

63
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@ -3,7 +3,7 @@
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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@ -193,12 +193,29 @@
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<link rel="stylesheet" type="text/css" href="https://fniessen.github.io/org-html-themes/src/readtheorg_theme/css/htmlize.css"/>
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<script type="text/javascript" src="org-info.js">
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<script type="text/javascript">
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org_html_manager.setup(); // activate after the parameters are set
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@ -223,24 +240,20 @@
</script>
</head>
<body>
<div id="content">
<div id="org-div-home-and-up">
<a accesskey="h" href=""> UP </a>
|
<a accesskey="H" href="index.html"> HOME </a>
</div><div id="content">
<h1 class="title">QCaml documentation</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org5057d67">1. Documentation of Modules</a></li>
</ul>
</div>
</div>
<div id="orga362751" class="figure">
<p><img src="./chamo_bg.png" alt="chamo_bg.png" />
<div id="orgde12e86" class="figure">
<p><img src="./chamo_bg.png" alt="chamo_bg.png" width="400px" />
</p>
</div>
<p>
QCaml is an OCaml library for writing quantum chemistry codes.
QCaml is an OCaml library for writing quantum chemistry codes.
It is written using literate programming with org-mode.
</p>
@ -259,9 +272,11 @@ This loads all the sub-libraries provided with QCaml, and installs
the pretty printers.
</p>
<div id="outline-container-org5057d67" class="outline-2">
<h2 id="org5057d67"><span class="section-number-2">1</span> Documentation of Modules</h2>
<div class="outline-text-2" id="text-1">
<p>
<b>List of modules</b>
</p>
<ul class="org-ul">
<li><a href="./ao.html">Ao</a></li>
<li><a href="./common.html">Common</a></li>
@ -277,11 +292,9 @@ the pretty printers.
<li><a href="./top.html">Top</a></li>
</ul>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-08 Fri 23:16</p>
<p class="date">Created: 2021-01-27 Wed 23:36</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

14
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@ -1,9 +1,10 @@
#+TITLE: QCaml documentation
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/theme.setup
#+ATTR_HTML: :width 400px
[[./chamo_bg.png]]
QCaml is an OCaml library for writing quantum chemistry codes.
QCaml is an OCaml library for writing quantum chemistry codes.
It is written using literate programming with org-mode.
To use it interactively in the top level or in a Jupyter or org-mode
@ -15,13 +16,14 @@
This loads all the sub-libraries provided with QCaml, and installs
the pretty printers.
* Documentation of Modules
*List of modules*
#+NAME: modules
#+begin_src sh :exports none
ls ../*/README.org \
| cut -d '/' -f 2
| cut -d '/' -f 2
#+end_src
#+NAME: list

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@ -193,12 +193,29 @@
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<h1 class="title">Linear Algebra</h1>
<div class="org-src-container">
<pre class="src src-ocaml" id="org3aac483"><span class="org-string">"Linear algebra utilities of QCaml libraries."</span>
</pre>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org6e14c98">1. Summmary</a></li>
</ul>
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<div id="outline-container-org6e14c98" class="outline-2">
<h2 id="org6e14c98"><span class="section-number-2">1</span> Summmary</h2>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-20 Wed 23:52</p>
<p class="date">Created: 2021-01-27 Wed 23:44</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
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@ -3,7 +3,7 @@
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<title>Molecular orbitals</title>
@ -193,12 +193,29 @@
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@ -233,36 +250,36 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org1294b69">1. Frozen core</a>
<li><a href="#orgdaf938b">1. Summmary</a></li>
<li><a href="#org9acb3b3">2. Frozen core</a>
<ul>
<li><a href="#org6b6a0df">1.1. Type</a></li>
<li><a href="#orgd41d207">1.2. Creation</a></li>
<li><a href="#org9bc8cb6">1.3. Access</a></li>
<li><a href="#orga5ea7e6">1.4. Printers</a></li>
<li><a href="#org64a252c">2.1. Type</a></li>
<li><a href="#org987723c">2.2. Creation</a></li>
<li><a href="#orgc89d6d7">2.3. Access</a></li>
<li><a href="#org5c73928">2.4. Printers</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div class="org-src-container">
<pre class="src src-ocaml" id="org7099c5c"><span class="org-string">"Molecular orbitals"</span>
</pre>
<div id="outline-container-orgdaf938b" class="outline-2">
<h2 id="orgdaf938b"><span class="section-number-2">1</span> Summmary</h2>
</div>
<div id="outline-container-org1294b69" class="outline-2">
<h2 id="org1294b69"><span class="section-number-2">1</span> Frozen core</h2>
<div class="outline-text-2" id="text-1">
<div id="outline-container-org9acb3b3" class="outline-2">
<h2 id="org9acb3b3"><span class="section-number-2">2</span> Frozen core</h2>
<div class="outline-text-2" id="text-2">
<p>
Defines how the core electrons are frozen, for each atom.
</p>
</div>
<div id="outline-container-org6b6a0df" class="outline-3">
<h3 id="org6b6a0df"><span class="section-number-3">1.1</span> Type</h3>
<div class="outline-text-3" id="text-1-1">
<div id="outline-container-org64a252c" class="outline-3">
<h3 id="org64a252c"><span class="section-number-3">2.1</span> Type</h3>
<div class="outline-text-3" id="text-2-1">
<div class="org-src-container">
<pre class="src src-ocaml" id="orgea93a5d"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">kind</span> <span class="org-tuareg-font-lock-operator">=</span>
<pre class="src src-ocaml" id="org92bd127"><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
@ -276,9 +293,9 @@ Defines how the core electrons are frozen, for each atom.
</div>
</div>
<div id="outline-container-orgd41d207" class="outline-3">
<h3 id="orgd41d207"><span class="section-number-3">1.2</span> Creation</h3>
<div class="outline-text-3" id="text-1-2">
<div id="outline-container-org987723c" class="outline-3">
<h3 id="org987723c"><span class="section-number-3">2.2</span> Creation</h3>
<div class="outline-text-3" id="text-2-2">
<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
@ -313,7 +330,7 @@ Defines how the core electrons are frozen, for each atom.
</tbody>
</table>
<pre class="example" id="org033fa67">
<pre class="example" id="org8539b48">
let f = Frozen_core.(make Small nuclei) ;;
val f : Frozen_core.t = [|0; 2; 2; 0|]
@ -323,9 +340,9 @@ val f : Frozen_core.t = [|0; 2; 2; 0|]
</div>
</div>
<div id="outline-container-org9bc8cb6" class="outline-3">
<h3 id="org9bc8cb6"><span class="section-number-3">1.3</span> Access</h3>
<div class="outline-text-3" id="text-1-3">
<div id="outline-container-orgc89d6d7" class="outline-3">
<h3 id="orgc89d6d7"><span class="section-number-3">2.3</span> Access</h3>
<div class="outline-text-3" id="text-2-3">
<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
@ -353,7 +370,7 @@ val f : Frozen_core.t = [|0; 2; 2; 0|]
</tbody>
</table>
<pre class="example" id="org5c22144">
<pre class="example" id="org5deb173">
Frozen_core.num_elec f ;;
- : int = 4
@ -363,9 +380,9 @@ Frozen_core.num_mos f ;;
</div>
</div>
<div id="outline-container-orga5ea7e6" class="outline-3">
<h3 id="orga5ea7e6"><span class="section-number-3">1.4</span> Printers</h3>
<div class="outline-text-3" id="text-1-4">
<div id="outline-container-org5c73928" class="outline-3">
<h3 id="org5c73928"><span class="section-number-3">2.4</span> Printers</h3>
<div class="outline-text-3" id="text-2-4">
<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>
@ -376,7 +393,7 @@ Frozen_core.num_mos f ;;
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-20 Wed 23:52</p>
<p class="date">Created: 2021-01-27 Wed 23:44</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
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255
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
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<title>Common</title>
@ -193,12 +193,29 @@
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@ -255,76 +272,76 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org775ffd4">1. Electrons</a>
<li><a href="#orgc3aa2b1">1. Summmary</a></li>
<li><a href="#orgf4a663e">2. Electrons</a>
<ul>
<li><a href="#org8d7eb03">1.1. Type</a></li>
<li><a href="#org828c0b4">1.2. Creation</a></li>
<li><a href="#org7990560">1.3. Access</a></li>
<li><a href="#orge31a496">1.4. Printers</a></li>
<li><a href="#org810810a">1.5. Tests</a></li>
<li><a href="#org88e7967">2.1. Type</a></li>
<li><a href="#org376ca80">2.2. Creation</a></li>
<li><a href="#orgd1d110c">2.3. Access</a></li>
<li><a href="#org1d2a3d7">2.4. Printers</a></li>
<li><a href="#org7b61e24">2.5. Tests</a></li>
</ul>
</li>
<li><a href="#org192b2be">2. Element</a>
<li><a href="#org918ae65">3. Element</a>
<ul>
<li><a href="#org8abd3f7">2.1. Type</a></li>
<li><a href="#orgfb1e8c0">2.2. Conversion</a></li>
<li><a href="#org7920ab5">2.3. Database information</a></li>
<li><a href="#orgd9e4111">2.4. Printers</a></li>
<li><a href="#org8889a68">3.1. Type</a></li>
<li><a href="#orgc639e8c">3.2. Conversion</a></li>
<li><a href="#org8706da1">3.3. Database information</a></li>
<li><a href="#org95418b5">3.4. Printers</a></li>
</ul>
</li>
<li><a href="#org683f181">3. Atomic mass</a></li>
<li><a href="#org69bdfa4">4. Nuclei</a>
<li><a href="#orgc544cb3">4. Atomic mass</a></li>
<li><a href="#org0dcc52f">5. Nuclei</a>
<ul>
<li><a href="#orgd713019">4.1. Type</a></li>
<li><a href="#org4bd7221">4.2. xyz file lexer/parser</a>
<li><a href="#org83b7fcb">5.1. Type</a></li>
<li><a href="#orgcba845a">5.2. xyz file lexer/parser</a>
<ul>
<li><a href="#org7281519">4.2.1. Lexer</a></li>
<li><a href="#org0b56536">4.2.2. Parser</a></li>
<li><a href="#org196ee2a">5.2.1. Lexer</a></li>
<li><a href="#orgda1a58a">5.2.2. Parser</a></li>
</ul>
</li>
<li><a href="#orgf5cc2de">4.3. Conversion</a></li>
<li><a href="#org070bc98">4.4. <span class="todo TODO">TODO</span> Query</a></li>
<li><a href="#org1ab3f3a">4.5. Printers</a></li>
<li><a href="#org59045e6">4.6. Tests</a></li>
<li><a href="#org4bc334a">5.3. Conversion</a></li>
<li><a href="#org259e4f9">5.4. <span class="todo TODO">TODO</span> Query</a></li>
<li><a href="#org606af7e">5.5. Printers</a></li>
<li><a href="#orgcd3169c">5.6. Tests</a></li>
</ul>
</li>
<li><a href="#org35f99d4">5. Z-matrix</a>
<li><a href="#orgf9d75ec">6. Z-matrix</a>
<ul>
<li><a href="#org74ef0d8">5.1. Type</a></li>
<li><a href="#org4b91a4e">5.2. Conversion</a></li>
<li><a href="#orgbec757c">5.3. Printers</a></li>
<li><a href="#org2ee988d">6.1. Type</a></li>
<li><a href="#org0a2b5eb">6.2. Conversion</a></li>
<li><a href="#org36acab9">6.3. Printers</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div class="org-src-container">
<pre class="src src-ocaml" id="org5e7fdf1"><span class="org-string">"Information relative to particles (electrons and nuclei)."</span>
</pre>
</div>
<div id="outline-container-orgc3aa2b1" class="outline-2">
<h2 id="orgc3aa2b1"><span class="section-number-2">1</span> Summmary</h2>
</div>
<div id="outline-container-org775ffd4" class="outline-2">
<h2 id="org775ffd4"><span class="section-number-2">1</span> Electrons</h2>
<div class="outline-text-2" id="text-1">
<div id="outline-container-orgf4a663e" class="outline-2">
<h2 id="orgf4a663e"><span class="section-number-2">2</span> Electrons</h2>
<div class="outline-text-2" id="text-2">
<p>
Data structure which contains the number of &alpha; and &beta; electrons.
</p>
</div>
<div id="outline-container-org8d7eb03" class="outline-3">
<h3 id="org8d7eb03"><span class="section-number-3">1.1</span> Type</h3>
<div class="outline-text-3" id="text-1-1">
<div id="outline-container-org88e7967" class="outline-3">
<h3 id="org88e7967"><span class="section-number-3">2.1</span> Type</h3>
<div class="outline-text-3" id="text-2-1">
<div class="org-src-container">
<pre class="src src-ocaml" id="org777e0db"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
<pre class="src src-ocaml" id="org380f263"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
</pre>
</div>
</div>
</div>
<div id="outline-container-org828c0b4" class="outline-3">
<h3 id="org828c0b4"><span class="section-number-3">1.2</span> Creation</h3>
<div class="outline-text-3" id="text-1-2">
<div id="outline-container-org376ca80" class="outline-3">
<h3 id="org376ca80"><span class="section-number-3">2.2</span> Creation</h3>
<div class="outline-text-3" id="text-2-2">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Common</span>
@ -355,16 +372,16 @@ Data structure which contains the number of &alpha; and &beta; electrons.
<tr>
<td class="org-left"><code>of_atoms</code></td>
<td class="org-left">Creates the data relative to electrons for a molecular system described by <a href="#orgc195f64"><code>Nuclei.t</code></a> for a given total charge and spin multiplicity.</td>
<td class="org-left">Creates the data relative to electrons for a molecular system described by <a href="#org117d80f"><code>Nuclei.t</code></a> for a given total charge and spin multiplicity.</td>
</tr>
</tbody>
</table>
</div>
</div>
<div id="outline-container-org7990560" class="outline-3">
<h3 id="org7990560"><span class="section-number-3">1.3</span> Access</h3>
<div class="outline-text-3" id="text-1-3">
<div id="outline-container-orgd1d110c" class="outline-3">
<h3 id="orgd1d110c"><span class="section-number-3">2.3</span> Access</h3>
<div class="outline-text-3" id="text-2-3">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">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">n_elec</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> int
@ -412,9 +429,9 @@ Data structure which contains the number of &alpha; and &beta; electrons.
</div>
</div>
<div id="outline-container-orge31a496" class="outline-3">
<h3 id="orge31a496"><span class="section-number-3">1.4</span> Printers</h3>
<div class="outline-text-3" id="text-1-4">
<div id="outline-container-org1d2a3d7" class="outline-3">
<h3 id="org1d2a3d7"><span class="section-number-3">2.4</span> Printers</h3>
<div class="outline-text-3" id="text-2-4">
<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>
@ -422,24 +439,24 @@ Data structure which contains the number of &alpha; and &beta; electrons.
</div>
</div>
<div id="outline-container-org810810a" class="outline-3">
<h3 id="org810810a"><span class="section-number-3">1.5</span> Tests</h3>
<div id="outline-container-org7b61e24" class="outline-3">
<h3 id="org7b61e24"><span class="section-number-3">2.5</span> Tests</h3>
</div>
</div>
<div id="outline-container-org192b2be" class="outline-2">
<h2 id="org192b2be"><span class="section-number-2">2</span> Element</h2>
<div class="outline-text-2" id="text-2">
<div id="outline-container-org918ae65" class="outline-2">
<h2 id="org918ae65"><span class="section-number-2">3</span> Element</h2>
<div class="outline-text-2" id="text-3">
<p>
Chemical elements.
</p>
</div>
<div id="outline-container-org8abd3f7" class="outline-3">
<h3 id="org8abd3f7"><span class="section-number-3">2.1</span> Type</h3>
<div class="outline-text-3" id="text-2-1">
<div id="outline-container-org8889a68" class="outline-3">
<h3 id="org8889a68"><span class="section-number-3">3.1</span> Type</h3>
<div class="outline-text-3" id="text-3-1">
<div class="org-src-container">
<pre class="src src-ocaml" id="orgc857d0f"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span> <span class="org-tuareg-font-lock-operator">=</span>
<pre class="src src-ocaml" id="org2343857"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span> <span class="org-tuareg-font-lock-operator">=</span>
<span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">X</span>
<span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">H</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">He</span>
<span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Li</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Be</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">B</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">C</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">N</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">O</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">F</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Ne</span>
@ -456,9 +473,9 @@ Chemical elements.
</div>
</div>
<div id="outline-container-orgfb1e8c0" class="outline-3">
<h3 id="orgfb1e8c0"><span class="section-number-3">2.2</span> Conversion</h3>
<div class="outline-text-3" id="text-2-2">
<div id="outline-container-orgc639e8c" class="outline-3">
<h3 id="orgc639e8c"><span class="section-number-3">3.2</span> Conversion</h3>
<div class="outline-text-3" id="text-3-2">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_string</span> <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">-&gt;</span> t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">to_string</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> string
@ -518,7 +535,7 @@ Chemical elements.
</tbody>
</table>
<pre class="example" id="org6c6cf9f">
<pre class="example" id="orgce999ba">
Element.of_string "Fe" ;;
- : Element.t = Particles.Element.Fe
@ -537,9 +554,9 @@ Element.(to_string Fe);;
</div>
</div>
<div id="outline-container-org7920ab5" class="outline-3">
<h3 id="org7920ab5"><span class="section-number-3">2.3</span> Database information</h3>
<div class="outline-text-3" id="text-2-3">
<div id="outline-container-org8706da1" class="outline-3">
<h3 id="org8706da1"><span class="section-number-3">3.3</span> Database information</h3>
<div class="outline-text-3" id="text-3-3">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">covalent_radius</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">Non_negative_float.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">vdw_radius</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">Non_negative_float.</span>t
@ -587,9 +604,9 @@ Element.(to_string Fe);;
</div>
</div>
<div id="outline-container-orgd9e4111" class="outline-3">
<h3 id="orgd9e4111"><span class="section-number-3">2.4</span> Printers</h3>
<div class="outline-text-3" id="text-2-4">
<div id="outline-container-org95418b5" class="outline-3">
<h3 id="org95418b5"><span class="section-number-3">3.4</span> Printers</h3>
<div class="outline-text-3" id="text-3-4">
<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
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">pp_long</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
@ -599,34 +616,34 @@ Element.(to_string Fe);;
</div>
</div>
<div id="outline-container-org683f181" class="outline-2">
<h2 id="org683f181"><span class="section-number-2">3</span> Atomic mass</h2>
<div class="outline-text-2" id="text-3">
<div id="outline-container-orgc544cb3" class="outline-2">
<h2 id="orgc544cb3"><span class="section-number-2">4</span> Atomic mass</h2>
<div class="outline-text-2" id="text-4">
<p>
Atomic mass, a non-negative float.
</p>
<div class="org-src-container">
<pre class="src src-ocaml" id="org7467a2c"><span class="org-tuareg-font-lock-governing">include</span> <span class="org-tuareg-font-lock-governing">module type of</span> <span class="org-tuareg-font-lock-module">Common.Non_negative_float</span>
<pre class="src src-ocaml" id="orgb21935a"><span class="org-tuareg-font-lock-governing">include</span> <span class="org-tuareg-font-lock-governing">module type of</span> <span class="org-tuareg-font-lock-module">Common.Non_negative_float</span>
</pre>
</div>
</div>
</div>
<div id="outline-container-org69bdfa4" class="outline-2">
<h2 id="org69bdfa4"><span class="section-number-2">4</span> Nuclei</h2>
<div class="outline-text-2" id="text-4">
<div id="outline-container-org0dcc52f" class="outline-2">
<h2 id="org0dcc52f"><span class="section-number-2">5</span> Nuclei</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-orgd713019" class="outline-3">
<h3 id="orgd713019"><span class="section-number-3">4.1</span> Type</h3>
<div class="outline-text-3" id="text-4-1">
<div id="outline-container-org83b7fcb" class="outline-3">
<h3 id="org83b7fcb"><span class="section-number-3">5.1</span> Type</h3>
<div class="outline-text-3" id="text-5-1">
<p>
<a id="orgc195f64"><code>Nuclei.t</code></a>
<a id="org117d80f"><code>Nuclei.t</code></a>
</p>
<div class="org-src-container">
<pre class="src src-ocaml" id="orgf7c74d8"><span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Common</span>
<pre class="src src-ocaml" id="org9b85d6c"><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">type</span> <span class="org-type">t</span> <span class="org-tuareg-font-lock-operator">=</span> <span class="org-tuareg-font-lock-operator">(</span><span class="org-tuareg-font-lock-module">Element.</span>t <span class="org-tuareg-font-lock-operator">*</span> <span class="org-tuareg-font-lock-module">Coordinate.</span>t<span class="org-tuareg-font-lock-operator">)</span> array
</pre>
@ -634,13 +651,13 @@ Atomic mass, a non-negative float.
</div>
</div>
<div id="outline-container-org4bd7221" class="outline-3">
<h3 id="org4bd7221"><span class="section-number-3">4.2</span> xyz file lexer/parser</h3>
<div class="outline-text-3" id="text-4-2">
<div id="outline-container-orgcba845a" class="outline-3">
<h3 id="orgcba845a"><span class="section-number-3">5.2</span> xyz file lexer/parser</h3>
<div class="outline-text-3" id="text-5-2">
</div>
<div id="outline-container-org7281519" class="outline-4">
<h4 id="org7281519"><span class="section-number-4">4.2.1</span> Lexer</h4>
<div class="outline-text-4" id="text-4-2-1">
<div id="outline-container-org196ee2a" class="outline-4">
<h4 id="org196ee2a"><span class="section-number-4">5.2.1</span> Lexer</h4>
<div class="outline-text-4" id="text-5-2-1">
<p>
<code>nuclei_lexer.mll</code> contains the description of the lexemes used in
an xyz file.
@ -692,9 +709,9 @@ rule read_all <span class="org-tuareg-font-lock-operator">=</span> parse
</div>
</div>
<div id="outline-container-org0b56536" class="outline-4">
<h4 id="org0b56536"><span class="section-number-4">4.2.2</span> Parser</h4>
<div class="outline-text-4" id="text-4-2-2">
<div id="outline-container-orgda1a58a" class="outline-4">
<h4 id="orgda1a58a"><span class="section-number-4">5.2.2</span> Parser</h4>
<div class="outline-text-4" id="text-5-2-2">
<p>
<code>xyz_parser.mly</code> parses nuclear coordinates in xyz format.
</p>
@ -812,9 +829,9 @@ an <code>xyz_file</code> data structure.
</div>
</div>
<div id="outline-container-orgf5cc2de" class="outline-3">
<h3 id="orgf5cc2de"><span class="section-number-3">4.3</span> Conversion</h3>
<div class="outline-text-3" id="text-4-3">
<div id="outline-container-org4bc334a" class="outline-3">
<h3 id="org4bc334a"><span class="section-number-3">5.3</span> Conversion</h3>
<div class="outline-text-3" id="text-5-3">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_xyz_string</span> <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">-&gt;</span> t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">to_xyz_string</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> string
@ -872,9 +889,9 @@ an <code>xyz_file</code> data structure.
</div>
</div>
<div id="outline-container-org070bc98" class="outline-3">
<h3 id="org070bc98"><span class="section-number-3">4.4</span> <span class="todo TODO">TODO</span> Query</h3>
<div class="outline-text-3" id="text-4-4">
<div id="outline-container-org259e4f9" class="outline-3">
<h3 id="org259e4f9"><span class="section-number-3">5.4</span> <span class="todo TODO">TODO</span> Query</h3>
<div class="outline-text-3" id="text-5-4">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">formula</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> string
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">repulsion</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> float
@ -922,9 +939,9 @@ an <code>xyz_file</code> data structure.
</div>
</div>
<div id="outline-container-org1ab3f3a" class="outline-3">
<h3 id="org1ab3f3a"><span class="section-number-3">4.5</span> Printers</h3>
<div class="outline-text-3" id="text-4-5">
<div id="outline-container-org606af7e" class="outline-3">
<h3 id="org606af7e"><span class="section-number-3">5.5</span> Printers</h3>
<div class="outline-text-3" id="text-5-5">
<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>
@ -932,32 +949,32 @@ an <code>xyz_file</code> data structure.
</div>
</div>
<div id="outline-container-org59045e6" class="outline-3">
<h3 id="org59045e6"><span class="section-number-3">4.6</span> Tests</h3>
<div id="outline-container-orgcd3169c" class="outline-3">
<h3 id="orgcd3169c"><span class="section-number-3">5.6</span> Tests</h3>
</div>
</div>
<div id="outline-container-org35f99d4" class="outline-2">
<h2 id="org35f99d4"><span class="section-number-2">5</span> Z-matrix</h2>
<div class="outline-text-2" id="text-5">
<div id="outline-container-orgf9d75ec" class="outline-2">
<h2 id="orgf9d75ec"><span class="section-number-2">6</span> Z-matrix</h2>
<div class="outline-text-2" id="text-6">
<p>
Z-matrix representation of nuclear coordinates.
</p>
</div>
<div id="outline-container-org74ef0d8" class="outline-3">
<h3 id="org74ef0d8"><span class="section-number-3">5.1</span> Type</h3>
<div class="outline-text-3" id="text-5-1">
<div id="outline-container-org2ee988d" class="outline-3">
<h3 id="org2ee988d"><span class="section-number-3">6.1</span> Type</h3>
<div class="outline-text-3" id="text-6-1">
<div class="org-src-container">
<pre class="src src-ocaml" id="org7111155"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
<pre class="src src-ocaml" id="org2500b30"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
</pre>
</div>
</div>
</div>
<div id="outline-container-org4b91a4e" class="outline-3">
<h3 id="org4b91a4e"><span class="section-number-3">5.2</span> Conversion</h3>
<div class="outline-text-3" id="text-5-2">
<div id="outline-container-org0a2b5eb" class="outline-3">
<h3 id="org0a2b5eb"><span class="section-number-3">6.2</span> Conversion</h3>
<div class="outline-text-3" id="text-6-2">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_string</span> <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">-&gt;</span> t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">to_xyz</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-operator">(</span><span class="org-tuareg-font-lock-module">Element.</span>t <span class="org-tuareg-font-lock-operator">*</span> float <span class="org-tuareg-font-lock-operator">*</span> float <span class="org-tuareg-font-lock-operator">*</span> float<span class="org-tuareg-font-lock-operator">)</span> array
@ -991,7 +1008,7 @@ Z-matrix representation of nuclear coordinates.
</tbody>
</table>
<pre class="example" id="org4da0c8d">
<pre class="example" id="org4442d9d">
let zmt = Zmatrix.of_string "
n
n 1 nn
@ -1036,9 +1053,9 @@ H -0.568803 -0.793910 1.726048"
</div>
<div id="outline-container-orgbec757c" class="outline-3">
<h3 id="orgbec757c"><span class="section-number-3">5.3</span> Printers</h3>
<div class="outline-text-3" id="text-5-3">
<div id="outline-container-org36acab9" class="outline-3">
<h3 id="org36acab9"><span class="section-number-3">6.3</span> Printers</h3>
<div class="outline-text-3" id="text-6-3">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">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>
@ -1049,7 +1066,7 @@ H -0.568803 -0.793910 1.726048"
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-20 Wed 23:52</p>
<p class="date">Created: 2021-01-27 Wed 23:44</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

91
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@ -3,7 +3,7 @@
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@ -193,12 +193,29 @@
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@ -233,32 +250,32 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org9499b78">1. MP2</a>
<li><a href="#org4e3f766">1. Summmary</a></li>
<li><a href="#org8e4d6b3">2. MP2</a>
<ul>
<li><a href="#org7af70d6">1.1. Type</a></li>
<li><a href="#orgc9fb258">1.2. Creation</a></li>
<li><a href="#org874a939">1.3. Access</a></li>
<li><a href="#org4363bab">1.4. Printers</a></li>
<li><a href="#org9eebbb5">1.5. Tests</a></li>
<li><a href="#orgafa22a1">2.1. Type</a></li>
<li><a href="#org0f17f3c">2.2. Creation</a></li>
<li><a href="#org6a18ed1">2.3. Access</a></li>
<li><a href="#orgb49bc14">2.4. Printers</a></li>
<li><a href="#orgd6b373f">2.5. Tests</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div class="org-src-container">
<pre class="src src-ocaml" id="org4748522"><span class="org-string">"Perturbation theory"</span>
</pre>
<div id="outline-container-org4e3f766" class="outline-2">
<h2 id="org4e3f766"><span class="section-number-2">1</span> Summmary</h2>
</div>
<div id="outline-container-org9499b78" class="outline-2">
<h2 id="org9499b78"><span class="section-number-2">1</span> MP2</h2>
<div class="outline-text-2" id="text-1">
<div id="outline-container-org8e4d6b3" class="outline-2">
<h2 id="org8e4d6b3"><span class="section-number-2">2</span> MP2</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org7af70d6" class="outline-3">
<h3 id="org7af70d6"><span class="section-number-3">1.1</span> Type</h3>
<div class="outline-text-3" id="text-1-1">
<div id="outline-container-orgafa22a1" class="outline-3">
<h3 id="orgafa22a1"><span class="section-number-3">2.1</span> Type</h3>
<div class="outline-text-3" id="text-2-1">
<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>
@ -266,9 +283,9 @@
</div>
</div>
<div id="outline-container-orgc9fb258" class="outline-3">
<h3 id="orgc9fb258"><span class="section-number-3">1.2</span> Creation</h3>
<div class="outline-text-3" id="text-1-2">
<div id="outline-container-org0f17f3c" class="outline-3">
<h3 id="org0f17f3c"><span class="section-number-3">2.2</span> Creation</h3>
<div class="outline-text-3" id="text-2-2">
<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>
@ -290,7 +307,7 @@
</tbody>
</table>
<pre class="example" id="orgb08821b">
<pre class="example" id="orgb30baf6">
let mp2 =
Perturbation.Mp2.make ~frozen_core:(Mo.Frozen_core.(make Small nuclei)) mo_basis
;;
@ -299,9 +316,9 @@ val mp2 : Perturbation.Mp2.t = E(MP2)=-0.185523
</div>
</div>
<div id="outline-container-org874a939" class="outline-3">
<h3 id="org874a939"><span class="section-number-3">1.3</span> Access</h3>
<div class="outline-text-3" id="text-1-3">
<div id="outline-container-org6a18ed1" class="outline-3">
<h3 id="org6a18ed1"><span class="section-number-3">2.3</span> Access</h3>
<div class="outline-text-3" id="text-2-3">
<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
@ -335,15 +352,15 @@ val mp2 : Perturbation.Mp2.t = E(MP2)=-0.185523
</tbody>
</table>
<pre class="example" id="org487f614">
<pre class="example" id="org02ea73d">
</pre>
</div>
</div>
<div id="outline-container-org4363bab" class="outline-3">
<h3 id="org4363bab"><span class="section-number-3">1.4</span> Printers</h3>
<div class="outline-text-3" id="text-1-4">
<div id="outline-container-orgb49bc14" class="outline-3">
<h3 id="orgb49bc14"><span class="section-number-3">2.4</span> Printers</h3>
<div class="outline-text-3" id="text-2-4">
<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>
@ -351,14 +368,14 @@ val mp2 : Perturbation.Mp2.t = E(MP2)=-0.185523
</div>
</div>
<div id="outline-container-org9eebbb5" class="outline-3">
<h3 id="org9eebbb5"><span class="section-number-3">1.5</span> Tests</h3>
<div id="outline-container-orgd6b373f" class="outline-3">
<h3 id="orgd6b373f"><span class="section-number-3">2.5</span> Tests</h3>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-20 Wed 23:52</p>
<p class="date">Created: 2021-01-27 Wed 23:44</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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color: #b8860b;
}
.org-org-level-3 {
/* org-level-3 */
color: #a020f0;
}
.org-org-level-4 {
/* org-level-4 */
color: #b22222;
}
.org-org-level-5 {
/* org-level-5 */
color: #228b22;
}
.org-org-level-6 {
/* org-level-6 */
color: #5f9ea0;
}
.org-org-level-7 {
/* org-level-7 */
color: #da70d6;
}
.org-org-level-8 {
/* org-level-8 */
color: #bc8f8f;
}
.org-org-link {
/* org-link */
color: #a020f0;
text-decoration: underline;
}
.org-org-property-value {
}
.org-org-scheduled-previously {
/* org-scheduled-previously */
color: #b22222;
}
.org-org-scheduled-today {
/* org-scheduled-today */
color: #006400;
}
.org-org-sexp-date {
/* org-sexp-date */
color: #a020f0;
}
.org-org-special-keyword {
/* org-special-keyword */
color: #bc8f8f;
}
.org-org-table {
/* org-table */
color: #0000ff;
}
.org-org-tag {
/* org-tag */
font-weight: bold;
}
.org-org-target {
/* org-target */
text-decoration: underline;
}
.org-org-time-grid {
/* org-time-grid */
color: #b8860b;
}
.org-org-todo {
/* org-todo */
color: #ff0000;
}
.org-org-upcoming-deadline {
/* org-upcoming-deadline */
color: #b22222;
}
.org-org-verbatim {
/* org-verbatim */
color: #7f7f7f;
text-decoration: underline;
}
.org-org-warning {
/* org-warning */
color: #ff0000;
font-weight: bold;
}
.org-outline-1 {
/* outline-1 */
color: #0000ff;
}
.org-outline-2 {
/* outline-2 */
color: #b8860b;
}
.org-outline-3 {
/* outline-3 */
color: #a020f0;
}
.org-outline-4 {
/* outline-4 */
color: #b22222;
}
.org-outline-5 {
/* outline-5 */
color: #228b22;
}
.org-outline-6 {
/* outline-6 */
color: #5f9ea0;
}
.org-outline-7 {
/* outline-7 */
color: #da70d6;
}
.org-outline-8 {
/* outline-8 */
color: #bc8f8f;
}
.outline-text-1, .outline-text-2, .outline-text-3, .outline-text-4, .outline-text-5, .outline-text-6 {
/* Add more spacing between section. Padding, so that folding with org-info.js works as expected. */
}
.org-preprocessor {
/* font-lock-preprocessor-face */
color: #da70d6;
}
.org-query-replace {
/* query-replace */
color: #b0e2ff;
background-color: #cd00cd;
}
.org-regexp-grouping-backslash {
/* font-lock-regexp-grouping-backslash */
font-weight: bold;
}
.org-regexp-grouping-construct {
/* font-lock-regexp-grouping-construct */
font-weight: bold;
}
.org-region {
/* region */
background-color: #eedc82;
}
.org-rmail-highlight {
}
.org-scroll-bar {
/* scroll-bar */
background-color: #bfbfbf;
}
.org-secondary-selection {
/* secondary-selection */
background-color: #ffff00;
}
.org-shadow {
/* shadow */
color: #7f7f7f;
}
.org-show-paren-match {
/* show-paren-match */
background-color: #40e0d0;
}
.org-show-paren-mismatch {
/* show-paren-mismatch */
color: #ffffff;
background-color: #a020f0;
}
.org-string {
/* font-lock-string-face */
color: #bc8f8f;
}
.org-texinfo-heading {
/* texinfo-heading */
color: #0000ff;
}
.org-tool-bar {
/* tool-bar */
color: #000000;
background-color: #bfbfbf;
}
.org-tooltip {
/* tooltip */
color: #000000;
background-color: #ffffe0;
}
.org-trailing-whitespace {
/* trailing-whitespace */
background-color: #ff0000;
}
.org-type {
/* font-lock-type-face */
color: #228b22;
}
.org-underline {
/* underline */
text-decoration: underline;
}
.org-variable-name {
/* font-lock-variable-name-face */
color: #b8860b;
}
.org-variable-pitch {
}
.org-vertical-border {
}
.org-warning {
/* font-lock-warning-face */
color: #ff0000;
font-weight: bold;
}
.rss_box {}
.rss_title, rss_title a {}
.rss_items {}
.rss_item a:link, .rss_item a:visited, .rss_item a:active {}
.rss_item a:hover {}
.rss_date {}
pre.src {
position: static;
overflow: visible;
padding-top: 1.2em;
}
label.org-src-name {
font-size: 80%;
font-style: italic;
}
#show_source {margin: 0; padding: 0;}
#postamble {
font-size: 75%;
min-width: 700px;
max-width: 80%;
line-height: 14pt;
margin-left: 20px;
margin-top: 10px;
padding: .2em;
background-color: #ffffff;
z-index: -1000;
}
} /* END OF @media all */
@media screen
{
#table-of-contents {
position: fixed;
margin-top: 105px;
float: right;
border: 1px solid #red;
max-width: 50%;
overflow: auto;
}
} /* END OF @media screen */

8
docs/qcaml.setup Normal file
View File

@ -0,0 +1,8 @@
# -*- mode: org; -*-
#+INFOJS_OPT: toc:t mouse:underline path:org-info.js
#+HTML_HEAD: <link rel="stylesheet" title="Standard" href="qcaml.css" type="text/css" />
#+OPTIONS: H:4 num:t toc:t \n:nil @:t ::t |:t ^:t -:t f:t *:t <:t

7
docs/theme.setup Normal file
View File

@ -0,0 +1,7 @@
# -*- mode: org; -*-
#+HTML_LINK_HOME: index.html
#+SETUPFILE: qcaml.setup
# SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup

47
docs/top.html
View File

@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-01-20 Wed 23:52 -->
<!-- 2021-01-28 Thu 00:32 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Top-level</title>
@ -193,12 +193,29 @@
.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>
<link rel="stylesheet" title="Standard" href="qcaml.css" type="text/css" />
<script type="text/javascript" src="org-info.js">
// @license magnet:?xt=urn:btih:1f739d935676111cfff4b4693e3816e664797050&amp;dn=gpl-3.0.txt GPL-v3-or-Later
// @license-end
</script>
<script type="text/javascript">
// @license magnet:?xt=urn:btih:1f739d935676111cfff4b4693e3816e664797050&amp;dn=gpl-3.0.txt GPL-v3-or-Later
<!--/*--><![CDATA[/*><!--*/
org_html_manager.set("TOC_DEPTH", "4");
org_html_manager.set("LINK_HOME", "index.html");
org_html_manager.set("LINK_UP", "");
org_html_manager.set("LOCAL_TOC", "1");
org_html_manager.set("VIEW_BUTTONS", "0");
org_html_manager.set("MOUSE_HINT", "underline");
org_html_manager.set("FIXED_TOC", "0");
org_html_manager.set("TOC", "1");
org_html_manager.set("VIEW", "info");
org_html_manager.setup(); // activate after the parameters are set
/*]]>*///-->
// @license-end
</script>
<script type="text/javascript">
// @license magnet:?xt=urn:btih:e95b018ef3580986a04669f1b5879592219e2a7a&dn=public-domain.txt Public Domain
<!--/*--><![CDATA[/*><!--*/
@ -229,14 +246,22 @@
<a accesskey="H" href="index.html"> HOME </a>
</div><div id="content">
<h1 class="title">Top-level</h1>
<div class="org-src-container">
<pre class="src src-ocaml" id="orgfc71223"><span class="org-string">"Installs pretty printers for top-level."</span>
</pre>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org55c0065">1. Summmary</a></li>
</ul>
</div>
</div>
<div id="outline-container-org55c0065" class="outline-2">
<h2 id="org55c0065"><span class="section-number-2">1</span> Summmary</h2>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-20 Wed 23:52</p>
<p class="date">Created: 2021-01-28 Thu 00:32</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

17
gaussian/README.org
View File

@ -1,9 +1,10 @@
#+TITLE: Gaussian
#+HTML_LINK_HOME: index.html
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/theme.setup
* Summmary
#+name: synopsis
#+begin_src ocaml :export output raw
#+begin_src ocaml :exports none :results value
"Gaussian basis sets"
#+end_src
@ -12,13 +13,13 @@
* Dune files :noexport:
** Generate dune files
Use [C-c C-c] on the code below to create the output for the dune files
#+header: :noweb strip-export
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var dune="lib/dune"
#+header: :var dunetest="test/dune"
#+begin_src python :exports none :results output none
@ -56,7 +57,7 @@ with open(dunetest,'w') as f:
** Dependencies
#+name: dependencies
#+begin_src elisp
#+begin_src elisp
(libraries
qcaml.common
qcaml.particles
@ -64,7 +65,7 @@ with open(dunetest,'w') as f:
#+end_src
** Modules without implementation
#+name: noimplementation
#+begin_src elisp
#+end_src
@ -82,4 +83,4 @@ with open(dunetest,'w') as f:

17
gaussian_integrals/README.org
View File

@ -1,9 +1,10 @@
#+TITLE: Gaussian integrals
#+HTML_LINK_HOME: index.html
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/theme.setup
* Summmary
#+name: synopsis
#+begin_src ocaml :export output raw
#+begin_src ocaml :exports none :results value
"Integrals on the Gaussian basis sets"
#+end_src
@ -12,13 +13,13 @@
* Dune files :noexport:
** Generate dune files
Use [C-c C-c] on the code below to create the output for the dune files
#+header: :noweb strip-export
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var dune="lib/dune"
#+header: :var dunetest="test/dune"
#+begin_src python :exports none :results output none
@ -56,7 +57,7 @@ with open(dunetest,'w') as f:
** Dependencies
#+name: dependencies
#+begin_src elisp
#+begin_src elisp
(libraries
qcaml.common
qcaml.linear_algebra
@ -66,7 +67,7 @@ with open(dunetest,'w') as f:
#+end_src
** Modules without implementation
#+name: noimplementation
#+begin_src elisp
(modules_without_implementation matrix_on_basis)
@ -85,4 +86,4 @@ with open(dunetest,'w') as f:

21
linear_algebra/README.org
View File

@ -1,24 +1,25 @@
#+TITLE: Linear Algebra
#+HTML_LINK_HOME: index.html
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/theme.setup
* Summmary
#+name: synopsis
#+begin_src ocaml :export output raw
"Linear algebra utilities of QCaml libraries."
#+begin_src ocaml :exports none :results value
"Linear algebra utilities of QCaml libraries"
#+end_src
#+RESULTS: synopsis
: Linear algebra utilities of QCaml libraries.
: Linear algebra utilities of QCaml libraries
* Dune files :noexport:
** Generate dune files
Use [C-c C-c] on the code below to create the output for the dune files
#+header: :noweb strip-export
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var dune="lib/dune"
#+header: :var dunetest="test/dune"
#+begin_src python :exports none :results output none
@ -56,7 +57,7 @@ with open(dunetest,'w') as f:
** Dependencies
#+name: dependencies
#+begin_src elisp
#+begin_src elisp
(libraries
qcaml.common
lacaml
@ -64,7 +65,7 @@ with open(dunetest,'w') as f:
#+end_src
** Modules without implementation
#+name: noimplementation
#+begin_src elisp
#+end_src
@ -82,4 +83,4 @@ with open(dunetest,'w') as f:

17
mo/README.org
View File

@ -1,9 +1,10 @@
#+TITLE: Molecular orbitals
#+HTML_LINK_HOME: index.html
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/theme.setup
* Summmary
#+name: synopsis
#+begin_src ocaml :export output raw
#+begin_src ocaml :exports none :results value
"Molecular orbitals"
#+end_src
@ -12,13 +13,13 @@
* Dune files :noexport:
** Generate dune files
Use [C-c C-c] on the code below to create the output for the dune files
#+header: :noweb strip-export
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var dune="lib/dune"
#+header: :var dunetest="test/dune"
#+begin_src python :exports none :results output none
@ -56,14 +57,14 @@ with open(dunetest,'w') as f:
** Dependencies
#+name: dependencies
#+begin_src elisp
#+begin_src elisp
(libraries
qcaml.simulation
)
#+end_src
** Modules without implementation
#+name: noimplementation
#+begin_src elisp
#+end_src
@ -81,4 +82,4 @@ with open(dunetest,'w') as f:

17
operators/README.org
View File

@ -1,9 +1,10 @@
#+TITLE: Operators
#+HTML_LINK_HOME: index.html
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/theme.setup
* Summmary
#+name: synopsis
#+begin_src ocaml :export output raw
#+begin_src ocaml :exports none :results value
"Parameteried operators, such as F12 and range-separation"
#+end_src
@ -12,13 +13,13 @@
* Dune files :noexport:
** Generate dune files
Use [C-c C-c] on the code below to create the output for the dune files
#+header: :noweb strip-export
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var dune="lib/dune"
#+header: :var dunetest="test/dune"
#+begin_src python :exports none :results output none
@ -56,14 +57,14 @@ with open(dunetest,'w') as f:
** Dependencies
#+name: dependencies
#+begin_src elisp
#+begin_src elisp
(libraries
qcaml.common
)
#+end_src
** Modules without implementation
#+name: noimplementation
#+begin_src elisp
#+end_src
@ -81,4 +82,4 @@ with open(dunetest,'w') as f:

21
particles/README.org
View File

@ -1,24 +1,25 @@
#+TITLE: Common
#+HTML_LINK_HOME: index.html
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/theme.setup
* Summmary
#+name: synopsis
#+begin_src ocaml :export output raw
"Information relative to particles (electrons and nuclei)."
#+begin_src ocaml :exports none :results value
"Information relative to particles (electrons and nuclei)"
#+end_src
#+RESULTS: synopsis
: Information relative to particles (electrons and nuclei).
: Information relative to particles (electrons and nuclei)
* Dune files :noexport:
** Generate dune files
Use [C-c C-c] on the code below to create the output for the dune files
#+header: :noweb strip-export
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var dune="lib/dune"
#+header: :var dunetest="test/dune"
#+begin_src python :exports none :results output none
@ -56,14 +57,14 @@ with open(dunetest,'w') as f:
** Dependencies
#+name: dependencies
#+begin_src elisp
#+begin_src elisp
(libraries
qcaml.common
)
#+end_src
** Modules without implementation
#+name: noimplementation
#+begin_src elisp
(modules_without_implementation
@ -92,4 +93,4 @@ with open(dunetest,'w') as f:

17
perturbation/README.org
View File

@ -1,9 +1,10 @@
#+TITLE: Perturbation
#+HTML_LINK_HOME: index.html
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/theme.setup
* Summmary
#+name: synopsis
#+begin_src ocaml :export output raw
#+begin_src ocaml :exports none :results value
"Perturbation theory"
#+end_src
@ -12,13 +13,13 @@
* Dune files :noexport:
** Generate dune files
Use [C-c C-c] on the code below to create the output for the dune files
#+header: :noweb strip-export
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var dune="lib/dune"
#+header: :var dunetest="test/dune"
#+begin_src python :exports none :results output none
@ -56,7 +57,7 @@ with open(dunetest,'w') as f:
** Dependencies
#+name: dependencies
#+begin_src elisp
#+begin_src elisp
(libraries
qcaml.simulation
qcaml.mo
@ -64,7 +65,7 @@ with open(dunetest,'w') as f:
#+end_src
** Modules without implementation
#+name: noimplementation
#+begin_src elisp
#+end_src
@ -82,4 +83,4 @@ with open(dunetest,'w') as f:

11
qcaml/README.org
View File

@ -1,9 +1,10 @@
#+TITLE: QCaml
#+HTML_LINK_HOME: index.html
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/theme.setup
* Summmary
#+name: synopsis
#+begin_src ocaml :export output raw
#+begin_src ocaml :exports none :results value
"Main QCaml entry point"
#+end_src
@ -12,12 +13,12 @@
* File generation :noexport:
Use [C-c C-c] on the code below. This will create the dune files
and the =qcaml.ml= file.
#+header: :noweb yes
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var dune="lib/dune"
#+header: :var mlfile="lib/qcaml.ml"
#+header: :var dunetest="test/dune"

17
simulation/README.org
View File

@ -1,9 +1,10 @@
#+TITLE: Simulation
#+HTML_LINK_HOME: index.html
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/theme.setup
* Summmary
#+name: synopsis
#+begin_src ocaml :export output raw
#+begin_src ocaml :exports none :results value
"Data describing a simulation (AOs, operators, nuclear coordinate,...)"
#+end_src
@ -12,13 +13,13 @@
* Dune files :noexport:
** Generate dune files
Use [C-c C-c] on the code below to create the output for the dune files
#+header: :noweb strip-export
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var dune="lib/dune"
#+header: :var dunetest="test/dune"
#+begin_src python :exports none :results output none
@ -56,7 +57,7 @@ with open(dunetest,'w') as f:
** Dependencies
#+name: dependencies
#+begin_src elisp
#+begin_src elisp
(libraries
qcaml.common
qcaml.particles
@ -68,7 +69,7 @@ with open(dunetest,'w') as f:
#+end_src
** Modules without implementation
#+name: noimplementation
#+begin_src elisp
#+end_src
@ -86,4 +87,4 @@ with open(dunetest,'w') as f:

14
top/README.org
View File

@ -1,15 +1,15 @@
#+TITLE: Top-level
#+HTML_LINK_HOME: index.html
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/theme.setup
* Summmary
#+name: synopsis
#+begin_src ocaml :export output raw
"Installs pretty printers for top-level."
#+begin_src ocaml :exports none :results value
"Installs pretty printers for top-level"
#+end_src
#+RESULTS: synopsis
: Installs pretty printers for top-level.
: Installs pretty printers for top-level
* Dune files :noexport:
@ -19,7 +19,7 @@
Use [C-c C-c] on the code below to create the output for the dune files
#+header: :noweb strip-export
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var name=(file-name-directory buffer-file-name)
#+begin_src python :exports none :results output none
name = name.split('/')[-2]
synopsis = """
@ -34,7 +34,7 @@ with open("lib/dune",'w') as f:
(synopsis {synopsis} )
(modes byte)
(libraries
compiler-libs.toplevel
compiler-libs.toplevel
qcaml
)
)