Added simulation

This commit is contained in:
Anthony Scemama 2021-01-01 11:46:11 +01:00
parent f45423a9ba
commit 92c23f042f
12 changed files with 300 additions and 56 deletions

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@ -65,6 +65,7 @@ val ( + ) : t -> t -> t
val ( - ) : t -> t -> t
val ( * ) : t -> float -> t
val ( / ) : t -> float -> t
val is_null : t -> bool
#+end_src
#+begin_src ocaml :tangle (eval ml) :exports none
@ -77,6 +78,8 @@ let ( + ) = gen_op ( +. )
let ( - ) = gen_op ( -. )
let ( * ) = gen_op ( *. )
let ( / ) = gen_op ( /. )
let is_null t = t == 0.
#+end_src
** Printers
@ -87,6 +90,6 @@ val pp : Format.formatter -> t -> unit
#+begin_src ocaml :tangle (eval ml) :exports none
let pp ppf x =
Format.fprintf ppf "@[+%s@]" (to_string x)
Format.fprintf ppf "@[%s@]" (to_string x)
#+end_src

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@ -3,11 +3,11 @@
(* This type should be used for all charges in the program (electrons, nuclei,...). *)
(* [[file:~/QCaml/common/charge.org::*Type][Type:2]] *)
(* [[file:../charge.org::*Type][Type:2]] *)
type t = float
(* Type:2 ends here *)
(* [[file:~/QCaml/common/charge.org::*Conversions][Conversions:2]] *)
(* [[file:../charge.org::*Conversions][Conversions:2]] *)
external of_float : float -> t = "%identity"
external to_float : t -> float = "%identity"
@ -25,7 +25,7 @@ let to_string x =
"0.0"
(* Conversions:2 ends here *)
(* [[file:~/QCaml/common/charge.org::*Simple%20operations][Simple operations:2]] *)
(* [[file:../charge.org::*Simple operations][Simple operations:2]] *)
let gen_op op =
fun a b ->
op (to_float a) (to_float b)
@ -35,9 +35,11 @@ let ( + ) = gen_op ( +. )
let ( - ) = gen_op ( -. )
let ( * ) = gen_op ( *. )
let ( / ) = gen_op ( /. )
let is_null t = t == 0.
(* Simple operations:2 ends here *)
(* [[file:~/QCaml/common/charge.org::*Printers][Printers:2]] *)
(* [[file:../charge.org::*Printers][Printers:2]] *)
let pp ppf x =
Format.fprintf ppf "@[+%s@]" (to_string x)
Format.fprintf ppf "@[%s@]" (to_string x)
(* Printers:2 ends here *)

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@ -1,14 +1,14 @@
(* Type *)
(* [[file:~/QCaml/common/charge.org::*Type][Type:1]] *)
(* [[file:../charge.org::*Type][Type:1]] *)
type t
(* Type:1 ends here *)
(* Conversions *)
(* [[file:~/QCaml/common/charge.org::*Conversions][Conversions:1]] *)
(* [[file:../charge.org::*Conversions][Conversions:1]] *)
val of_float : float -> t
val to_float : t -> float
@ -22,16 +22,17 @@ val to_string: t -> string
(* Simple operations *)
(* [[file:~/QCaml/common/charge.org::*Simple%20operations][Simple operations:1]] *)
(* [[file:../charge.org::*Simple operations][Simple operations:1]] *)
val ( + ) : t -> t -> t
val ( - ) : t -> t -> t
val ( * ) : t -> float -> t
val ( / ) : t -> float -> t
val ( / ) : t -> float -> t
val is_null : t -> bool
(* Simple operations:1 ends here *)
(* Printers *)
(* [[file:~/QCaml/common/charge.org::*Printers][Printers:1]] *)
(* [[file:../charge.org::*Printers][Printers:1]] *)
val pp : Format.formatter -> t -> unit
(* Printers:1 ends here *)

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@ -119,13 +119,33 @@ let to_xyz_string t =
(* | ~repulsion~ | Nuclear repulsion energy, in atomic units |
(* | ~formula~ | Returns the chemical formula |
* | ~repulsion~ | Nuclear repulsion energy, in atomic units |
* | ~charge~ | Sum of the charges of the nuclei |
* | ~small_core~ | Number of core electrons in the small core model |
* | ~large_core~ | Number of core electrons in the large core model | *)
(* [[file:../nuclei.org::*Query][Query:2]] *)
let formula t =
let dict = Hashtbl.create 67 in
Array.iter (fun (e,_) ->
let e = Element.to_string e in
let value =
try (Hashtbl.find dict e) + 1
with Not_found -> 1
in
Hashtbl.replace dict e value
) t;
Hashtbl.to_seq_keys dict
|> List.of_seq
|> List.sort String.compare
|> List.fold_left (fun accu key ->
let x = Hashtbl.find dict key in
accu ^ key ^ "_{" ^ (string_of_int x) ^ "}") ""
let repulsion nuclei =
let get_charge e =
Element.to_charge e

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@ -24,10 +24,11 @@ val to_string : t -> string
val of_filename : string -> t
(* Conversion:1 ends here *)
(* Query *)
(* TODO Query *)
(* [[file:../nuclei.org::*Query][Query:1]] *)
val formula : t -> string
val repulsion : t -> float
val charge : t -> Charge.t
val small_core : t -> int

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@ -24,7 +24,9 @@ type t = (Element.t * Coordinate.t) array
#+end_src
#+begin_src ocaml :tangle (eval ml) :exports none
<<types>>
open Common
type t = (Element.t * Coordinate.t) array
open Xyz_ast
#+end_src
@ -312,21 +314,42 @@ let to_xyz_string t =
|> String.concat "\n"
#+end_src
** Query
** TODO Query
#+begin_src ocaml :tangle (eval mli)
val formula : t -> string
val repulsion : t -> float
val charge : t -> Charge.t
val small_core : t -> int
val large_core : t -> int
#+end_src
| ~formula~ | Returns the chemical formula |
| ~repulsion~ | Nuclear repulsion energy, in atomic units |
| ~charge~ | Sum of the charges of the nuclei |
| ~small_core~ | Number of core electrons in the small core model |
| ~large_core~ | Number of core electrons in the large core model |
#+begin_src ocaml :tangle (eval ml) :exports none
let formula t =
let dict = Hashtbl.create 67 in
Array.iter (fun (e,_) ->
let e = Element.to_string e in
let value =
try (Hashtbl.find dict e) + 1
with Not_found -> 1
in
Hashtbl.replace dict e value
) t;
Hashtbl.to_seq_keys dict
|> List.of_seq
|> List.sort String.compare
|> List.fold_left (fun accu key ->
let x = Hashtbl.find dict key in
accu ^ key ^ "_{" ^ (string_of_int x) ^ "}") ""
let repulsion nuclei =
let get_charge e =
Element.to_charge e

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@ -10,14 +10,15 @@
: Main QCaml entry point
* Dune files :noexport:
* File generation :noexport:
Use [C-c C-c] on the code below to create the output for the dune files
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 dune="lib/dune"
#+header: :var mlfile="lib/qcaml.ml"
#+header: :var dunetest="test/dune"
#+header: :var dependencies=dependencies
#+begin_src python :exports none :results output none
@ -26,13 +27,15 @@ synopsis = """
<<synopsis>>
"""
dependencies = '\n '.join(map(lambda x: x[0], dependencies))
excluded_modules = [ "top" ]
dependencies = '\n '.join([x[0] for x in dependencies if x[0].replace("qcaml.","") not in excluded_modules])
with open(dune,'w') as f:
f.write(f"""
(library
(name {name})
(public_name qcaml.{name})
(name qcaml)
(public_name qcaml)
(synopsis {synopsis} )
(libraries
{dependencies}
@ -41,19 +44,29 @@ with open(dune,'w') as f:
<<c-files>>
)
<<lex-yacc>>
""".replace("qcaml.qcaml","qcaml"))
""")
with open(dunetest,'w') as f:
f.write(f"""
(library
(name test_{name})
(synopsis "Test for {name} library")
(name test_qcaml)
(synopsis "Test for qcaml library")
(libraries
alcotest
qcaml.{name}
qcaml
)
)
""".replace("qcaml.qcaml","qcaml"))
""")
with open(mlfile,'w') as f:
s = dependencies.split()
s = [x.replace("qcaml.","") for x in s ]
s = [x.capitalize() for x in s]
s = [ f"module {x} = {x}\n" for x in s ]
s = ''.join(s)
f.write("(* Auto-generated by qcaml/README.org *)\n")
f.write(s)
#+end_src
@ -63,7 +76,6 @@ grep "public_name" ../*/lib/dune | grep -v "qcaml)" | cut -d ' ' -f 3 | tr ')' '
#+end_src
#+RESULTS: dependencies
| (libraries |
| qcaml.ao |
| qcaml.common |
| qcaml.gaussian |
@ -74,4 +86,4 @@ grep "public_name" ../*/lib/dune | grep -v "qcaml)" | cut -d ' ' -f 3 | tr ')' '
| qcaml.particles |
| qcaml.perturbation |
| qcaml.simulation |
| ) |
| qcaml.top |

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@ -1,3 +1,4 @@
(* Auto-generated by qcaml/README.org *)
module Ao = Ao
module Common = Common
module Gaussian = Gaussian

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@ -1,7 +1,10 @@
(* [[file:../simulation.org::*Simulation][Simulation:2]] *)
open Common
open Particles
open Operators
(* Simulation:2 ends here *)
(* [[file:../simulation.org::*Type][Type:2]] *)
type t = {
charge : Charge.t;
electrons : Electrons.t;
@ -9,19 +12,42 @@ type t = {
ao_basis : Ao.Basis.t;
operators : Operator.t list;
}
(* Type:2 ends here *)
(* | ~nuclei~ | Nuclear coordinates used in the smiulation |
* | ~charge~ | Total charge (electrons + nuclei) |
* | ~electrons~ | Electrons used in the simulation |
* | ~ao_basis~ | Atomic basis set |
* | ~nuclear_repulsion~ | Nuclear repulsion energy |
* | ~operators~ | List of extra operators (range-separation, f12, etc) | *)
(* [[file:../simulation.org::*Access][Access:2]] *)
let nuclei t = t.nuclei
let charge t = t.charge
let electrons t = t.electrons
let ao_basis t = t.ao_basis
let nuclear_repulsion t = Nuclei.repulsion @@ nuclei t
let operators t = t.operators
(* Access:2 ends here *)
let make ?(multiplicity=1)
?(charge=0)
?(operators=[])
~nuclei
ao_basis
(* Defaults:
* - multiplicity : ~1~
* - charge : ~0~
* - operators : ~[]~ *)
(* [[file:../simulation.org::*Creation][Creation:2]] *)
let make
?(multiplicity=1)
?(charge=0)
?(operators=[])
~nuclei
ao_basis
=
(* Tune Garbage Collector *)
@ -36,10 +62,14 @@ let make ?(multiplicity=1)
Charge.(Nuclei.charge nuclei + Electrons.charge electrons)
in
{
charge ; nuclei ; electrons ; ao_basis ;
operators
}
{ charge ; nuclei ; electrons ; ao_basis ; operators}
(* Creation:2 ends here *)
(* [[file:../simulation.org::*Printers][Printers:2]] *)
let pp ppf t =
let formula = Nuclei.formula t.nuclei in
let n_aos = Ao.Basis.size t.ao_basis in
let n_ops = List.length t.operators in
Format.fprintf ppf "@[@[%s@], @[%a@], @[%d AOs@], @[%d operators@]@]"
formula Electrons.pp t.electrons n_aos n_ops
(* Printers:2 ends here *)

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@ -1,32 +1,50 @@
(* Contains the state of a simulation *)
(* Simulation
* :PROPERTIES:
* :header-args: :noweb yes :comments both
* :END:
*
* Contains the state of the simulation.
*
* #+NAME: open *)
(* [[file:../simulation.org::open][open]] *)
open Common
open Particles
open Operators
(* open ends here *)
(* Type
*
* #+NAME: types *)
(* [[file:../simulation.org::types][types]] *)
type t
(* types ends here *)
val nuclei : t -> Nuclei.t
(** Nuclear coordinates used in the smiulation *)
(* Access *)
val charge : t -> Charge.t
(** Total charge (electrons + nuclei) *)
val electrons : t -> Electrons.t
(** Electrons used in the simulation *)
val ao_basis : t -> Ao.Basis.t
(** Atomic basis set *)
(* [[file:../simulation.org::*Access][Access:1]] *)
val nuclei : t -> Nuclei.t
val charge : t -> Charge.t
val electrons : t -> Electrons.t
val ao_basis : t -> Ao.Basis.t
val nuclear_repulsion : t -> float
(** Nuclear repulsion energy *)
val operators : t -> Operator.t list
(* Access:1 ends here *)
val operators : t -> Operator.t list
(** List of extra operators (range-separation, f12, etc) *)
(* Creation *)
(** {1 Creation} *)
(* [[file:../simulation.org::*Creation][Creation:1]] *)
val make : ?multiplicity:int -> ?charge:int ->
?operators:Operator.t list-> nuclei:Nuclei.t ->
Ao.Basis.t -> t
(* Creation:1 ends here *)
(* Printers *)
(* [[file:../simulation.org::*Printers][Printers:1]] *)
val pp : Format.formatter -> t -> unit
(* Printers:1 ends here *)

131
simulation/simulation.org Normal file
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@ -0,0 +1,131 @@
#+begin_src elisp tangle: no :results none :exports none
(setq pwd (file-name-directory buffer-file-name))
(setq name (file-name-nondirectory (substring buffer-file-name 0 -4)))
(setq lib (concat pwd "lib/"))
(setq testdir (concat pwd "test/"))
(setq mli (concat lib name ".mli"))
(setq ml (concat lib name ".ml"))
(setq test-ml (concat testdir name ".ml"))
(org-babel-tangle)
#+end_src
* Simulation
:PROPERTIES:
:header-args: :noweb yes :comments both
:END:
Contains the state of the simulation.
#+NAME: open
#+begin_src ocaml :tangle (eval mli)
open Common
open Particles
open Operators
#+end_src
#+begin_src ocaml :tangle (eval ml) :exports none
<<open>>
#+end_src
** Type
#+NAME: types
#+begin_src ocaml :tangle (eval mli)
type t
#+end_src
#+begin_src ocaml :tangle (eval ml) :exports none
type t = {
charge : Charge.t;
electrons : Electrons.t;
nuclei : Nuclei.t;
ao_basis : Ao.Basis.t;
operators : Operator.t list;
}
#+end_src
** Access
#+begin_src ocaml :tangle (eval mli)
val nuclei : t -> Nuclei.t
val charge : t -> Charge.t
val electrons : t -> Electrons.t
val ao_basis : t -> Ao.Basis.t
val nuclear_repulsion : t -> float
val operators : t -> Operator.t list
#+end_src
| ~nuclei~ | Nuclear coordinates used in the smiulation |
| ~charge~ | Total charge (electrons + nuclei) |
| ~electrons~ | Electrons used in the simulation |
| ~ao_basis~ | Atomic basis set |
| ~nuclear_repulsion~ | Nuclear repulsion energy |
| ~operators~ | List of extra operators (range-separation, f12, etc) |
#+begin_src ocaml :tangle (eval ml) :exports none
let nuclei t = t.nuclei
let charge t = t.charge
let electrons t = t.electrons
let ao_basis t = t.ao_basis
let nuclear_repulsion t = Nuclei.repulsion @@ nuclei t
let operators t = t.operators
#+end_src
** Creation
#+begin_src ocaml :tangle (eval mli)
val make : ?multiplicity:int -> ?charge:int ->
?operators:Operator.t list-> nuclei:Nuclei.t ->
Ao.Basis.t -> t
#+end_src
Defaults:
- multiplicity : ~1~
- charge : ~0~
- operators : ~[]~
#+begin_src ocaml :tangle (eval ml) :exports none
let make
?(multiplicity=1)
?(charge=0)
?(operators=[])
~nuclei
ao_basis
=
(* Tune Garbage Collector *)
let gc = Gc.get () in
Gc.set { gc with space_overhead = 1000 };
let electrons =
Electrons.of_atoms ~multiplicity ~charge nuclei
in
let charge =
Charge.(Nuclei.charge nuclei + Electrons.charge electrons)
in
{ charge ; nuclei ; electrons ; ao_basis ; operators}
#+end_src
** Printers
#+begin_src ocaml :tangle (eval mli)
val pp : Format.formatter -> t -> unit
#+end_src
#+begin_src ocaml :tangle (eval ml) :exports none
let pp ppf t =
let formula = Nuclei.formula t.nuclei in
let n_aos = Ao.Basis.size t.ao_basis in
let n_ops = List.length t.operators in
Format.fprintf ppf "@[@[%s@], @[%a@], @[%d AOs@], @[%d operators@]@]"
formula Electrons.pp t.electrons n_aos n_ops
#+end_src
#+RESULTS:
: Line 2, characters 16-30:
: 2 | let formula = Nuclei.formula t.nuclei in
: ^^^^^^^^^^^^^^
: Error: Unbound module Nuclei

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@ -11,7 +11,9 @@ let printers =
"Common.Zkey.pp" ;
"Particles.Electrons.pp" ;
"Particles.Element.pp" ;
"Particles.Nuclei.pp" ;
"Particles.Zmatrix.pp" ;
"Simulation.Simulation.pp" ;
]