mirror of
https://github.com/LCPQ/quantum_package
synced 2024-08-25 14:01:46 +02:00
Added Molecule.of_xyz_file
This commit is contained in:
parent
9bffc0883b
commit
caafe823be
@ -1,3 +1,5 @@
|
|||||||
|
#TODO : Opam auto-installer in makefile
|
||||||
|
|
||||||
# Check if QPACKAGE_ROOT is defined
|
# Check if QPACKAGE_ROOT is defined
|
||||||
|
|
||||||
ifndef QPACKAGE_ROOT
|
ifndef QPACKAGE_ROOT
|
||||||
|
@ -33,13 +33,13 @@ let of_string s =
|
|||||||
| [ name; charge; x; y; z ] ->
|
| [ name; charge; x; y; z ] ->
|
||||||
{ element = Element.of_string name ;
|
{ element = Element.of_string name ;
|
||||||
charge = Charge.of_string charge ;
|
charge = Charge.of_string charge ;
|
||||||
coord = Point3d.of_string (String.concat [x; y; z] ?sep:(Some " "))
|
coord = Point3d.of_string (String.concat [x; y; z] ~sep:" ")
|
||||||
}
|
}
|
||||||
| [ name; x; y; z ] ->
|
| [ name; x; y; z ] ->
|
||||||
let e = Element.of_string name in
|
let e = Element.of_string name in
|
||||||
{ element = e ;
|
{ element = e ;
|
||||||
charge = Charge.of_int (Element.charge e);
|
charge = Charge.of_int (Element.charge e);
|
||||||
coord = Point3d.of_string (String.concat [x; y; z] ?sep:(Some " "))
|
coord = Point3d.of_string (String.concat [x; y; z] ~sep:" ")
|
||||||
}
|
}
|
||||||
| _ -> raise (AtomError s)
|
| _ -> raise (AtomError s)
|
||||||
;;
|
;;
|
||||||
|
@ -91,7 +91,7 @@ let find in_channel element =
|
|||||||
;;
|
;;
|
||||||
|
|
||||||
let read_basis_of_element in_channel element =
|
let read_basis_of_element in_channel element =
|
||||||
find in_channel element ;
|
ignore (find in_channel element) ;
|
||||||
read_basis in_channel ;
|
read_basis in_channel ;
|
||||||
;;
|
;;
|
||||||
|
|
||||||
@ -100,5 +100,5 @@ let to_string { sym = sym ; lc = lc } =
|
|||||||
let f (p,c) = Printf.sprintf "( %s, %f )" (Primitive.to_string p) c
|
let f (p,c) = Printf.sprintf "( %s, %f )" (Primitive.to_string p) c
|
||||||
in
|
in
|
||||||
Printf.sprintf "[ %s : %s ]" (Symmetry.to_string sym)
|
Printf.sprintf "[ %s : %s ]" (Symmetry.to_string sym)
|
||||||
(String.concat (List.map ~f:f lc) ?sep:(Some ", "))
|
(String.concat (List.map ~f:f lc) ~sep:", ")
|
||||||
;;
|
;;
|
||||||
|
@ -9,7 +9,7 @@ type t = {
|
|||||||
elec_beta : Positive_int.t ;
|
elec_beta : Positive_int.t ;
|
||||||
}
|
}
|
||||||
|
|
||||||
let charge { nuclei ; elec_alpha ; elec_beta } =
|
let get_charge { nuclei ; elec_alpha ; elec_beta } =
|
||||||
let result = Positive_int.(to_int elec_alpha + to_int elec_beta) in
|
let result = Positive_int.(to_int elec_alpha + to_int elec_beta) in
|
||||||
let rec nucl_charge = function
|
let rec nucl_charge = function
|
||||||
| a::rest -> Atom.(Charge.to_float a.charge) +. nucl_charge rest
|
| a::rest -> Atom.(Charge.to_float a.charge) +. nucl_charge rest
|
||||||
@ -18,12 +18,12 @@ let charge { nuclei ; elec_alpha ; elec_beta } =
|
|||||||
nucl_charge nuclei -. (Float.of_int result)
|
nucl_charge nuclei -. (Float.of_int result)
|
||||||
;;
|
;;
|
||||||
|
|
||||||
let multiplicity m =
|
let get_multiplicity m =
|
||||||
Multiplicity.of_alpha_beta m.elec_alpha m.elec_beta
|
Multiplicity.of_alpha_beta m.elec_alpha m.elec_beta
|
||||||
;;
|
;;
|
||||||
|
|
||||||
let name m =
|
let name m =
|
||||||
let cm = Float.to_int (charge m) in
|
let cm = Float.to_int (get_charge m) in
|
||||||
let c =
|
let c =
|
||||||
match cm with
|
match cm with
|
||||||
| 0 -> ""
|
| 0 -> ""
|
||||||
@ -32,7 +32,7 @@ let name m =
|
|||||||
| i when i>1 -> Printf.sprintf " (%d+)" i
|
| i when i>1 -> Printf.sprintf " (%d+)" i
|
||||||
| i -> Printf.sprintf " (%d-)" (-i)
|
| i -> Printf.sprintf " (%d-)" (-i)
|
||||||
in
|
in
|
||||||
let mult = Multiplicity.to_string (multiplicity m) in
|
let mult = Multiplicity.to_string (get_multiplicity m) in
|
||||||
let { nuclei ; elec_alpha ; elec_beta } = m in
|
let { nuclei ; elec_alpha ; elec_beta } = m in
|
||||||
let rec build_list accu = function
|
let rec build_list accu = function
|
||||||
| a::rest ->
|
| a::rest ->
|
||||||
@ -67,35 +67,47 @@ let to_string m =
|
|||||||
let n = List.length nuclei in
|
let n = List.length nuclei in
|
||||||
let title = name m in
|
let title = name m in
|
||||||
[ Int.to_string n ; title ] @ (List.map ~f:Atom.to_string nuclei)
|
[ Int.to_string n ; title ] @ (List.map ~f:Atom.to_string nuclei)
|
||||||
|> String.concat ?sep:(Some "\n")
|
|> String.concat ~sep:"\n"
|
||||||
;;
|
;;
|
||||||
|
|
||||||
let of_xyz_string s charge' multiplicity' =
|
let of_xyz_string
|
||||||
|
?(charge=0) ?(multiplicity=(Multiplicity.of_int 1))
|
||||||
|
s =
|
||||||
let l = String.split s ~on:'\n'
|
let l = String.split s ~on:'\n'
|
||||||
|> List.filter ~f:(fun x -> x <> "")
|
|> List.filter ~f:(fun x -> x <> "")
|
||||||
|> List.map ~f:Atom.of_string
|
|> List.map ~f:Atom.of_string
|
||||||
in
|
in
|
||||||
let ne = ( charge {
|
let ne = ( get_charge {
|
||||||
nuclei=l ;
|
nuclei=l ;
|
||||||
elec_alpha=(Positive_int.of_int 0) ;
|
elec_alpha=(Positive_int.of_int 0) ;
|
||||||
elec_beta=(Positive_int.of_int 0) }
|
elec_beta=(Positive_int.of_int 0) }
|
||||||
|> Float.to_int
|
|> Float.to_int
|
||||||
)- charge'
|
)- charge
|
||||||
|> Positive_int.of_int
|
|> Positive_int.of_int
|
||||||
in
|
in
|
||||||
let (na,nb) = Multiplicity.to_alpha_beta ne multiplicity' in
|
let (na,nb) = Multiplicity.to_alpha_beta ne multiplicity in
|
||||||
let result =
|
let result =
|
||||||
{ nuclei = l ;
|
{ nuclei = l ;
|
||||||
elec_alpha = (Positive_int.of_int na) ;
|
elec_alpha = (Positive_int.of_int na) ;
|
||||||
elec_beta = (Positive_int.of_int nb) }
|
elec_beta = (Positive_int.of_int nb) }
|
||||||
in
|
in
|
||||||
if ((multiplicity result) <> multiplicity') then
|
if ((get_multiplicity result) <> multiplicity) then
|
||||||
let msg = Printf.sprintf
|
let msg = Printf.sprintf
|
||||||
"With %d electrons multiplicity %d is impossible"
|
"With %d electrons multiplicity %d is impossible"
|
||||||
(Positive_int.to_int ne)
|
(Positive_int.to_int ne)
|
||||||
(Multiplicity.to_int multiplicity')
|
(Multiplicity.to_int multiplicity)
|
||||||
in
|
in
|
||||||
raise (MultiplicityError msg);
|
raise (MultiplicityError msg);
|
||||||
else () ;
|
else () ;
|
||||||
result
|
result
|
||||||
;;
|
;;
|
||||||
|
|
||||||
|
|
||||||
|
let of_xyz_file
|
||||||
|
?(charge=0) ?(multiplicity=(Multiplicity.of_int 1))
|
||||||
|
filename =
|
||||||
|
let (_,buffer) = In_channel.read_all filename
|
||||||
|
|> String.lsplit2_exn ~on:'\n' in
|
||||||
|
let (_,buffer) = String.lsplit2_exn buffer ~on:'\n' in
|
||||||
|
of_xyz_string ~charge:charge ~multiplicity:multiplicity buffer
|
||||||
|
;;
|
||||||
|
@ -10,14 +10,18 @@ H 1.0 0.54386314 0.00000000 -0.92559535
|
|||||||
"
|
"
|
||||||
in
|
in
|
||||||
|
|
||||||
try ignore (Molecule.of_xyz_string xyz 1 (Strictly_positive_int.of_int 1))
|
|
||||||
with
|
|
||||||
| Molecule.MultiplicityError _ -> print_string "OK\n"
|
|
||||||
;
|
|
||||||
print_string "---\n";
|
print_string "---\n";
|
||||||
let m = Molecule.of_xyz_string xyz 0 (Strictly_positive_int.of_int 1)
|
begin
|
||||||
|
try (
|
||||||
|
ignore (Molecule.of_xyz_string xyz ~multiplicity:(Multiplicity.of_int 2)) ;
|
||||||
|
print_string "Failed in MultiplicityError\n" )
|
||||||
|
with
|
||||||
|
| Molecule.MultiplicityError _ -> print_string "MultiplicityError OK\n"
|
||||||
|
end ;
|
||||||
|
print_string "---\n";
|
||||||
|
let m = Molecule.of_xyz_string xyz
|
||||||
in print_endline (Molecule.name m) ;
|
in print_endline (Molecule.name m) ;
|
||||||
let m = Molecule.of_xyz_string xyz 1 (Strictly_positive_int.of_int 2)
|
let m = Molecule.of_xyz_string xyz ~charge:1 ~multiplicity:(Multiplicity.of_int 2)
|
||||||
in print_endline (Molecule.name m) ;
|
in print_endline (Molecule.name m) ;
|
||||||
|
|
||||||
let xyz =
|
let xyz =
|
||||||
@ -27,9 +31,14 @@ O 1.65102147 0.00000000 -2.35602344
|
|||||||
H 0.54386314 0.00000000 -0.92559535
|
H 0.54386314 0.00000000 -0.92559535
|
||||||
"
|
"
|
||||||
in
|
in
|
||||||
let m = Molecule.of_xyz_string xyz (-2) (Strictly_positive_int.of_int 1)
|
let m = Molecule.of_xyz_string xyz ~charge:(-2)
|
||||||
in print_endline (Molecule.name m) ;
|
in print_endline (Molecule.name m) ;
|
||||||
|
print_endline (Molecule.to_string m);
|
||||||
|
print_string "---------\n";
|
||||||
|
|
||||||
|
let m = Molecule.of_xyz_file "c2h6.xyz" in
|
||||||
print_string (Molecule.to_string m);
|
print_string (Molecule.to_string m);
|
||||||
|
|
||||||
;;
|
;;
|
||||||
|
|
||||||
test_molecule ();;
|
test_molecule ();;
|
||||||
|
Loading…
Reference in New Issue
Block a user