10
0
mirror of https://github.com/LCPQ/quantum_package synced 2024-11-03 12:43:52 +01:00
quantum_package/ocaml/qp_create_ezfio_from_xyz.ml

664 lines
19 KiB
OCaml
Raw Normal View History

open Qputils
open Qptypes
open Core.Std
2014-08-27 16:38:13 +02:00
let spec =
let open Command.Spec in
empty
2015-05-02 14:50:23 +02:00
+> flag "o" (optional string)
2014-11-16 18:05:04 +01:00
~doc:"file Name of the created EZFIO file."
2014-08-27 16:38:13 +02:00
+> flag "b" (required string)
~doc:"string Name of basis set."
2014-08-27 16:38:13 +02:00
+> flag "c" (optional_with_default 0 int)
~doc:"int Total charge of the molecule. Default is 0."
+> flag "d" (optional_with_default 0. float)
~doc:"float Add dummy atoms. x * (covalent radii of the atoms)"
2015-05-02 14:50:23 +02:00
+> flag "m" (optional_with_default 1 int)
2014-11-16 18:05:04 +01:00
~doc:"int Spin multiplicity (2S+1) of the molecule. Default is 1."
2016-01-25 15:44:15 +01:00
+> flag "p" (optional string)
~doc:"string Name of the pseudopotential"
2016-01-27 00:19:08 +01:00
+> flag "cart" no_arg
~doc:" Compute AOs in the Cartesian basis set (6d, 10f, ...)"
2015-11-25 23:46:09 +01:00
+> anon ("xyz_file" %: file )
2014-08-27 16:38:13 +02:00
2016-01-25 15:44:15 +01:00
(** Handle dummy atoms placed on bonds *)
let dummy_centers ~threshold ~molecule ~nuclei =
let d =
Molecule.distance_matrix molecule
in
let n =
Array.length d
in
let nuclei =
Array.of_list nuclei
in
let rec aux accu = function
| (-1,_) -> accu
| (i,-1) -> aux accu (i-1,i-1)
| (i,j) when (i>j) ->
let new_accu =
let x,y =
Element.covalent_radius (nuclei.(i)).Atom.element |> Positive_float.to_float,
Element.covalent_radius (nuclei.(j)).Atom.element |> Positive_float.to_float
in
let r =
( x +. y ) *. threshold
in
if d.(i).(j) < r then
(i,x,j,y,d.(i).(j)) :: accu
else
accu
in aux new_accu (i,j-1)
| (i,j) when (i=j) -> aux accu (i,j-1)
| _ -> assert false
in
aux [] (n-1,n-1)
|> List.map ~f:(fun (i,x,j,y,r) ->
let f =
x /. (x +. y)
in
let u =
Point3d.of_tuple ~units:Units.Bohr
( nuclei.(i).Atom.coord.Point3d.x +.
(nuclei.(j).Atom.coord.Point3d.x -. nuclei.(i).Atom.coord.Point3d.x) *. f,
nuclei.(i).Atom.coord.Point3d.y +.
(nuclei.(j).Atom.coord.Point3d.y -. nuclei.(i).Atom.coord.Point3d.y) *. f,
nuclei.(i).Atom.coord.Point3d.z +.
(nuclei.(j).Atom.coord.Point3d.z -. nuclei.(i).Atom.coord.Point3d.z) *. f)
in
Atom.{ element = Element.X ; charge = Charge.of_int 0 ; coord = u }
)
2016-01-25 15:44:15 +01:00
(** Returns the list of available basis sets *)
2015-11-25 23:46:09 +01:00
let list_basis () =
let basis_list =
Qpackage.root ^ "/install/emsl/EMSL_api.py list_basis"
|> Unix.open_process_in
|> In_channel.input_lines
|> List.map ~f:(fun x ->
match String.split x ~on:'\'' with
| [] -> ""
| a :: []
| _ :: a :: _ -> String.strip a
)
in
List.sort basis_list ~cmp:String.ascending
2016-02-04 18:50:40 +01:00
|> String.concat ~sep:"\n"
2015-11-25 23:46:09 +01:00
2016-01-25 15:44:15 +01:00
(** Run the program *)
2016-01-27 00:19:08 +01:00
let run ?o b c d m p cart xyz_file =
2014-08-27 16:38:13 +02:00
(* Read molecule *)
let molecule =
(Molecule.of_xyz_file xyz_file ~charge:(Charge.of_int c)
~multiplicity:(Multiplicity.of_int m) )
2014-08-27 16:38:13 +02:00
in
let dummy =
dummy_centers ~threshold:d ~molecule ~nuclei:molecule.Molecule.nuclei
in
let nuclei =
molecule.Molecule.nuclei @ dummy
in
2014-11-16 18:05:04 +01:00
2016-01-25 15:44:15 +01:00
(**********
Basis set
**********)
let basis_table =
Hashtbl.Poly.create ()
in
2014-11-16 18:05:04 +01:00
(* Open basis set channels *)
let basis_channel element =
let key =
Element.to_string element
in
2014-11-16 18:05:04 +01:00
match Hashtbl.find basis_table key with
| Some in_channel ->
in_channel
2015-11-22 15:18:51 +01:00
| None ->
let msg =
Printf.sprintf "%s is not defined in basis %s.%!"
(Element.to_long_string element) b ;
in
failwith msg
2014-11-16 18:05:04 +01:00
in
Added /home/scemama/quantum_package/scripts/make_binary.sh make[1]: Entering directory `/home/scemama/quantum_package/src' cd AOs ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[2]: Entering directory `/home/scemama/quantum_package/src/AOs' make[3]: Entering directory `/home/scemama/quantum_package/src/AOs' make[3]: Leaving directory `/home/scemama/quantum_package/src/AOs' make[2]: Leaving directory `/home/scemama/quantum_package/src/AOs' cd BiInts ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[2]: Entering directory `/home/scemama/quantum_package/src/BiInts' make[3]: Entering directory `/home/scemama/quantum_package/src/BiInts' make[3]: Leaving directory `/home/scemama/quantum_package/src/BiInts' make[2]: Leaving directory `/home/scemama/quantum_package/src/BiInts' cd Bitmask ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[2]: Entering directory `/home/scemama/quantum_package/src/Bitmask' make[3]: Entering directory `/home/scemama/quantum_package/src/Bitmask' make[3]: Leaving directory `/home/scemama/quantum_package/src/Bitmask' make[2]: Leaving directory `/home/scemama/quantum_package/src/Bitmask' cd Dets ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[2]: Entering directory `/home/scemama/quantum_package/src/Dets' make[3]: Entering directory `/home/scemama/quantum_package/src/Dets' make[3]: Leaving directory `/home/scemama/quantum_package/src/Dets' make[2]: Leaving directory `/home/scemama/quantum_package/src/Dets' cd Electrons ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[2]: Entering directory `/home/scemama/quantum_package/src/Electrons' make[3]: Entering directory `/home/scemama/quantum_package/src/Electrons' make[3]: Leaving directory `/home/scemama/quantum_package/src/Electrons' make[2]: Leaving directory `/home/scemama/quantum_package/src/Electrons' cd Ezfio_files ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[2]: Entering directory `/home/scemama/quantum_package/src/Ezfio_files' make[3]: Entering directory `/home/scemama/quantum_package/src/Ezfio_files' make[3]: Leaving directory `/home/scemama/quantum_package/src/Ezfio_files' make[2]: Leaving directory `/home/scemama/quantum_package/src/Ezfio_files' cd Full_CI ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[2]: Entering directory `/home/scemama/quantum_package/src/Full_CI' make[3]: Entering directory `/home/scemama/quantum_package/src/Full_CI' make[3]: Leaving directory `/home/scemama/quantum_package/src/Full_CI' make[2]: Leaving directory `/home/scemama/quantum_package/src/Full_CI' cd Generators_full ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[2]: Entering directory `/home/scemama/quantum_package/src/Generators_full' make[3]: Entering directory `/home/scemama/quantum_package/src/Generators_full' make[3]: Leaving directory `/home/scemama/quantum_package/src/Generators_full' make[2]: Leaving directory `/home/scemama/quantum_package/src/Generators_full' cd Hartree_Fock ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[2]: Entering directory `/home/scemama/quantum_package/src/Hartree_Fock' make[3]: Entering directory `/home/scemama/quantum_package/src/Hartree_Fock' make[3]: Leaving directory `/home/scemama/quantum_package/src/Hartree_Fock' make[2]: Leaving directory `/home/scemama/quantum_package/src/Hartree_Fock' cd MOGuess ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[2]: Entering directory `/home/scemama/quantum_package/src/MOGuess' make[3]: Entering directory `/home/scemama/quantum_package/src/MOGuess' make[3]: Leaving directory `/home/scemama/quantum_package/src/MOGuess' make[2]: Leaving directory `/home/scemama/quantum_package/src/MOGuess' cd MonoInts ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[2]: Entering directory `/home/scemama/quantum_package/src/MonoInts' make[3]: Entering directory `/home/scemama/quantum_package/src/MonoInts' make[3]: Leaving directory `/home/scemama/quantum_package/src/MonoInts' make[2]: Leaving directory `/home/scemama/quantum_package/src/MonoInts' cd MOs ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[2]: Entering directory `/home/scemama/quantum_package/src/MOs' make[3]: Entering directory `/home/scemama/quantum_package/src/MOs' make[3]: Leaving directory `/home/scemama/quantum_package/src/MOs' make[2]: Leaving directory `/home/scemama/quantum_package/src/MOs' cd Nuclei ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[2]: Entering directory `/home/scemama/quantum_package/src/Nuclei' make[3]: Entering directory `/home/scemama/quantum_package/src/Nuclei' make[3]: Leaving directory `/home/scemama/quantum_package/src/Nuclei' make[2]: Leaving directory `/home/scemama/quantum_package/src/Nuclei' cd Output ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[2]: Entering directory `/home/scemama/quantum_package/src/Output' make[3]: Entering directory `/home/scemama/quantum_package/src/Output' make[3]: Leaving directory `/home/scemama/quantum_package/src/Output' make[2]: Leaving directory `/home/scemama/quantum_package/src/Output' cd Selectors_full ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[2]: Entering directory `/home/scemama/quantum_package/src/Selectors_full' make[3]: Entering directory `/home/scemama/quantum_package/src/Selectors_full' make[3]: Leaving directory `/home/scemama/quantum_package/src/Selectors_full' make[2]: Leaving directory `/home/scemama/quantum_package/src/Selectors_full' cd Utils ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[2]: Entering directory `/home/scemama/quantum_package/src/Utils' make[3]: Entering directory `/home/scemama/quantum_package/src/Utils' make[3]: Leaving directory `/home/scemama/quantum_package/src/Utils' make[2]: Leaving directory `/home/scemama/quantum_package/src/Utils' cd Molden ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[2]: Entering directory `/home/scemama/quantum_package/src/Molden' make[3]: Entering directory `/home/scemama/quantum_package/src/Molden' make[3]: Leaving directory `/home/scemama/quantum_package/src/Molden' make[2]: Leaving directory `/home/scemama/quantum_package/src/Molden' make[1]: Leaving directory `/home/scemama/quantum_package/src' make[1]: Entering directory `/home/scemama/quantum_package/ocaml' rm -f -- test_atom ocamlbuild -j 0 -syntax camlp4o -cflags "-g -warn-error A" -lflags "-g -warn-error A" -ocamlopt ocamlc.opt test_atom.byte -use-ocamlfind # No parallelism done ln -s test_atom.byte test_atom rm -f -- test_basis ocamlbuild -j 0 -syntax camlp4o -cflags "-g -warn-error A" -lflags "-g -warn-error A" -ocamlopt ocamlc.opt test_basis.byte -use-ocamlfind # No parallelism done ln -s test_basis.byte test_basis rm -f -- test_bitlist ocamlbuild -j 0 -syntax camlp4o -cflags "-g -warn-error A" -lflags "-g -warn-error A" -ocamlopt ocamlc.opt test_bitlist.byte -use-ocamlfind # No parallelism done ln -s test_bitlist.byte test_bitlist rm -f -- test_determinants ocamlbuild -j 0 -syntax camlp4o -cflags "-g -warn-error A" -lflags "-g -warn-error A" -ocamlopt ocamlc.opt test_determinants.byte -use-ocamlfind # No parallelism done ln -s test_determinants.byte test_determinants rm -f -- test_elements ocamlbuild -j 0 -syntax camlp4o -cflags "-g -warn-error A" -lflags "-g -warn-error A" -ocamlopt ocamlc.opt test_elements.byte -use-ocamlfind # No parallelism done ln -s test_elements.byte test_elements rm -f -- test_excitation ocamlbuild -j 0 -syntax camlp4o -cflags "-g -warn-error A" -lflags "-g -warn-error A" -ocamlopt ocamlc.opt test_excitation.byte -use-ocamlfind # No parallelism done ln -s test_excitation.byte test_excitation rm -f -- test_gto ocamlbuild -j 0 -syntax camlp4o -cflags "-g -warn-error A" -lflags "-g -warn-error A" -ocamlopt ocamlc.opt test_gto.byte -use-ocamlfind # No parallelism done ln -s test_gto.byte test_gto rm -f -- test_input ocamlbuild -j 0 -syntax camlp4o -cflags "-g -warn-error A" -lflags "-g -warn-error A" -ocamlopt ocamlc.opt test_input.byte -use-ocamlfind # No parallelism done ln -s test_input.byte test_input rm -f -- test_mo_label ocamlbuild -j 0 -syntax camlp4o -cflags "-g -warn-error A" -lflags "-g -warn-error A" -ocamlopt ocamlc.opt test_mo_label.byte -use-ocamlfind # No parallelism done ln -s test_mo_label.byte test_mo_label rm -f -- test_molecule ocamlbuild -j 0 -syntax camlp4o -cflags "-g -warn-error A" -lflags "-g -warn-error A" -ocamlopt ocamlc.opt test_molecule.byte -use-ocamlfind # No parallelism done ln -s test_molecule.byte test_molecule rm -f -- test_point3d ocamlbuild -j 0 -syntax camlp4o -cflags "-g -warn-error A" -lflags "-g -warn-error A" -ocamlopt ocamlc.opt test_point3d.byte -use-ocamlfind # No parallelism done ln -s test_point3d.byte test_point3d make -C /home/scemama/quantum_package/data executables make[2]: Entering directory `/home/scemama/quantum_package/data' cd /home/scemama/quantum_package/src ; make executables make[3]: Entering directory `/home/scemama/quantum_package/src' cd AOs ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[4]: Entering directory `/home/scemama/quantum_package/src/AOs' make[5]: Entering directory `/home/scemama/quantum_package/src/AOs' make[5]: Leaving directory `/home/scemama/quantum_package/src/AOs' make[4]: Leaving directory `/home/scemama/quantum_package/src/AOs' cd BiInts ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[4]: Entering directory `/home/scemama/quantum_package/src/BiInts' make[5]: Entering directory `/home/scemama/quantum_package/src/BiInts' make[5]: Leaving directory `/home/scemama/quantum_package/src/BiInts' make[4]: Leaving directory `/home/scemama/quantum_package/src/BiInts' cd Bitmask ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[4]: Entering directory `/home/scemama/quantum_package/src/Bitmask' make[5]: Entering directory `/home/scemama/quantum_package/src/Bitmask' make[5]: Leaving directory `/home/scemama/quantum_package/src/Bitmask' make[4]: Leaving directory `/home/scemama/quantum_package/src/Bitmask' cd Dets ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[4]: Entering directory `/home/scemama/quantum_package/src/Dets' make[5]: Entering directory `/home/scemama/quantum_package/src/Dets' make[5]: Leaving directory `/home/scemama/quantum_package/src/Dets' make[4]: Leaving directory `/home/scemama/quantum_package/src/Dets' cd Electrons ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[4]: Entering directory `/home/scemama/quantum_package/src/Electrons' make[5]: Entering directory `/home/scemama/quantum_package/src/Electrons' make[5]: Leaving directory `/home/scemama/quantum_package/src/Electrons' make[4]: Leaving directory `/home/scemama/quantum_package/src/Electrons' cd Ezfio_files ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[4]: Entering directory `/home/scemama/quantum_package/src/Ezfio_files' make[5]: Entering directory `/home/scemama/quantum_package/src/Ezfio_files' make[5]: Leaving directory `/home/scemama/quantum_package/src/Ezfio_files' make[4]: Leaving directory `/home/scemama/quantum_package/src/Ezfio_files' cd Full_CI ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[4]: Entering directory `/home/scemama/quantum_package/src/Full_CI' make[5]: Entering directory `/home/scemama/quantum_package/src/Full_CI' make[5]: Leaving directory `/home/scemama/quantum_package/src/Full_CI' make[4]: Leaving directory `/home/scemama/quantum_package/src/Full_CI' cd Generators_full ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[4]: Entering directory `/home/scemama/quantum_package/src/Generators_full' make[5]: Entering directory `/home/scemama/quantum_package/src/Generators_full' make[5]: Leaving directory `/home/scemama/quantum_package/src/Generators_full' make[4]: Leaving directory `/home/scemama/quantum_package/src/Generators_full' cd Hartree_Fock ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[4]: Entering directory `/home/scemama/quantum_package/src/Hartree_Fock' make[5]: Entering directory `/home/scemama/quantum_package/src/Hartree_Fock' make[5]: Leaving directory `/home/scemama/quantum_package/src/Hartree_Fock' make[4]: Leaving directory `/home/scemama/quantum_package/src/Hartree_Fock' cd MOGuess ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[4]: Entering directory `/home/scemama/quantum_package/src/MOGuess' make[5]: Entering directory `/home/scemama/quantum_package/src/MOGuess' make[5]: Leaving directory `/home/scemama/quantum_package/src/MOGuess' make[4]: Leaving directory `/home/scemama/quantum_package/src/MOGuess' cd MonoInts ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[4]: Entering directory `/home/scemama/quantum_package/src/MonoInts' make[5]: Entering directory `/home/scemama/quantum_package/src/MonoInts' make[5]: Leaving directory `/home/scemama/quantum_package/src/MonoInts' make[4]: Leaving directory `/home/scemama/quantum_package/src/MonoInts' cd MOs ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[4]: Entering directory `/home/scemama/quantum_package/src/MOs' make[5]: Entering directory `/home/scemama/quantum_package/src/MOs' make[5]: Leaving directory `/home/scemama/quantum_package/src/MOs' make[4]: Leaving directory `/home/scemama/quantum_package/src/MOs' cd Nuclei ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[4]: Entering directory `/home/scemama/quantum_package/src/Nuclei' make[5]: Entering directory `/home/scemama/quantum_package/src/Nuclei' make[5]: Leaving directory `/home/scemama/quantum_package/src/Nuclei' make[4]: Leaving directory `/home/scemama/quantum_package/src/Nuclei' cd Output ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[4]: Entering directory `/home/scemama/quantum_package/src/Output' make[5]: Entering directory `/home/scemama/quantum_package/src/Output' make[5]: Leaving directory `/home/scemama/quantum_package/src/Output' make[4]: Leaving directory `/home/scemama/quantum_package/src/Output' cd Selectors_full ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[4]: Entering directory `/home/scemama/quantum_package/src/Selectors_full' make[5]: Entering directory `/home/scemama/quantum_package/src/Selectors_full' make[5]: Leaving directory `/home/scemama/quantum_package/src/Selectors_full' make[4]: Leaving directory `/home/scemama/quantum_package/src/Selectors_full' cd Utils ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[4]: Entering directory `/home/scemama/quantum_package/src/Utils' make[5]: Entering directory `/home/scemama/quantum_package/src/Utils' make[5]: Leaving directory `/home/scemama/quantum_package/src/Utils' make[4]: Leaving directory `/home/scemama/quantum_package/src/Utils' cd Molden ; make -j $(cat /proc/cpuinfo | grep MHz | wc -l) make[4]: Entering directory `/home/scemama/quantum_package/src/Molden' make[5]: Entering directory `/home/scemama/quantum_package/src/Molden' make[5]: Leaving directory `/home/scemama/quantum_package/src/Molden' make[4]: Leaving directory `/home/scemama/quantum_package/src/Molden' rm -f executables ; \ for EXE in $(find /home/scemama/quantum_package/src -perm /u+x -type f | grep -e "/home/scemama/quantum_package/src/[^/]*/[^/]*$" |sort ) ; \ do printf "%-30s %s\n" $(basename $EXE) $EXE | sed "s|/home/scemama/quantum_package|\$QPACKAGE_ROOT|g" >> executables ;\ done make[3]: Leaving directory `/home/scemama/quantum_package/src' mv /home/scemama/quantum_package/src/executables . make[2]: Leaving directory `/home/scemama/quantum_package/data' rm -f -- qp_basis_clean ocamlbuild -j 0 -syntax camlp4o -cflags "-g -warn-error A" -lflags "-g -warn-error A" -ocamlopt ocamlc.opt qp_basis_clean.native -use-ocamlfind # No parallelism done ln -s qp_basis_clean.native qp_basis_clean rm -f -- qp_create_ezfio_from_xyz ocamlbuild -j 0 -syntax camlp4o -cflags "-g -warn-error A" -lflags "-g -warn-error A" -ocamlopt ocamlc.opt qp_create_ezfio_from_xyz.native -use-ocamlfind # No parallelism done ln -s qp_create_ezfio_from_xyz.native qp_create_ezfio_from_xyz rm -f -- qp_edit ocamlbuild -j 0 -syntax camlp4o -cflags "-g -warn-error A" -lflags "-g -warn-error A" -ocamlopt ocamlc.opt qp_edit.native -use-ocamlfind # No parallelism done ln -s qp_edit.native qp_edit rm -f -- qp_print ocamlbuild -j 0 -syntax camlp4o -cflags "-g -warn-error A" -lflags "-g -warn-error A" -ocamlopt ocamlc.opt qp_print.native -use-ocamlfind # No parallelism done ln -s qp_print.native qp_print rm -f -- qp_run ocamlbuild -j 0 -syntax camlp4o -cflags "-g -warn-error A" -lflags "-g -warn-error A" -ocamlopt ocamlc.opt qp_run.native -use-ocamlfind # No parallelism done ln -s qp_run.native qp_run rm -f -- qp_set_ddci ocamlbuild -j 0 -syntax camlp4o -cflags "-g -warn-error A" -lflags "-g -warn-error A" -ocamlopt ocamlc.opt qp_set_ddci.native -use-ocamlfind # No parallelism done ln -s qp_set_ddci.native qp_set_ddci rm -f -- qp_set_mo_class ocamlbuild -j 0 -syntax camlp4o -cflags "-g -warn-error A" -lflags "-g -warn-error A" -ocamlopt ocamlc.opt qp_set_mo_class.native -use-ocamlfind # No parallelism done ln -s qp_set_mo_class.native qp_set_mo_class make[1]: Leaving directory `/home/scemama/quantum_package/ocaml' Creating root of static directory Copying binary files /home/scemama/quantum_package Copying dynamic libraries Copying EMSL_Basis directory Copying scripts directory Creating quantum_package.rc Creating the archive Done : /home/scemama/quantum_package/quantum_package_static.tar.gz
2015-01-16 00:48:09 +01:00
let temp_filename =
Filename.temp_file "qp_create_" ".basis"
in
2015-11-22 15:18:51 +01:00
let () =
Sys.remove temp_filename
in
let fetch_channel basis =
let command =
2016-01-25 15:44:15 +01:00
Qpackage.root ^ "/scripts/get_basis.sh \"" ^ temp_filename
^ "." ^ basis ^ "\" \"" ^ basis ^"\""
in
2016-01-25 23:38:07 +01:00
let long_basis =
Qpackage.root ^ "/data/basis/" ^ basis
in
match
Sys.is_file basis,
Sys.is_file long_basis
with
| `Yes, _ -> In_channel.create basis
| `No , `Yes -> In_channel.create long_basis
| _ ->
begin
let filename =
Unix.open_process_in command
|> In_channel.input_all
|> String.strip
in
let new_channel =
In_channel.create filename
in
Unix.unlink filename;
new_channel
end
in
2014-11-16 18:05:04 +01:00
let rec build_basis = function
| [] -> ()
| elem_and_basis_name :: rest ->
begin
match (String.lsplit2 ~on:':' elem_and_basis_name) with
| None -> (* Principal basis *)
begin
let basis =
elem_and_basis_name
2014-11-16 18:05:04 +01:00
in
2015-01-12 16:58:22 +01:00
let new_channel =
fetch_channel basis
2015-01-12 16:58:22 +01:00
in
List.iter nuclei ~f:(fun elem->
let key =
Element.to_string elem.Atom.element
2014-11-16 18:05:04 +01:00
in
match Hashtbl.add basis_table ~key:key ~data:new_channel with
| `Ok -> ()
| `Duplicate -> ()
)
end
| Some (key, basis) -> (*Aux basis *)
begin
let elem =
Element.of_string key
and basis =
String.lowercase basis
2014-11-16 18:05:04 +01:00
in
let key =
Element.to_string elem
2014-11-16 18:05:04 +01:00
in
let new_channel =
fetch_channel basis
2015-01-12 16:58:22 +01:00
in
begin
match Hashtbl.add basis_table ~key:key ~data:new_channel with
| `Ok -> ()
| `Duplicate -> failwith ("Duplicate definition of basis for "^(Element.to_long_string elem))
end
end
2014-11-16 18:05:04 +01:00
end;
build_basis rest
in
2015-01-12 16:58:22 +01:00
String.split ~on:'|' b
2014-11-16 18:05:04 +01:00
|> List.rev_map ~f:String.strip
|> build_basis;
2014-08-27 16:38:13 +02:00
2016-01-25 15:44:15 +01:00
(***************
Pseudopotential
***************)
let pseudo_table =
Hashtbl.Poly.create ()
in
(* Open pseudo channels *)
let pseudo_channel element =
let key =
Element.to_string element
in
Hashtbl.find pseudo_table key
in
let temp_filename =
Filename.temp_file "qp_create_" ".pseudo"
in
let () =
Sys.remove temp_filename
in
let fetch_channel pseudo =
2016-01-25 23:38:07 +01:00
let long_pseudo =
Qpackage.root ^ "/data/pseudo/" ^ pseudo
in
match
Sys.is_file pseudo,
Sys.is_file long_pseudo
with
| `Yes, _ -> In_channel.create pseudo
| `No , `Yes -> In_channel.create long_pseudo
2016-01-25 15:44:15 +01:00
| _ -> failwith ("Pseudo file "^pseudo^" not found.")
in
let rec build_pseudo = function
| [] -> ()
| elem_and_pseudo_name :: rest ->
begin
match (String.lsplit2 ~on:':' elem_and_pseudo_name) with
| None -> (* Principal pseudo *)
begin
let pseudo =
elem_and_pseudo_name
in
let new_channel =
fetch_channel pseudo
in
List.iter nuclei ~f:(fun elem->
let key =
Element.to_string elem.Atom.element
in
match Hashtbl.add pseudo_table ~key:key ~data:new_channel with
| `Ok -> ()
| `Duplicate -> ()
)
end
| Some (key, pseudo) -> (*Aux pseudo *)
begin
let elem =
Element.of_string key
and pseudo =
String.lowercase pseudo
in
let key =
Element.to_string elem
in
let new_channel =
fetch_channel pseudo
in
begin
match Hashtbl.add pseudo_table ~key:key ~data:new_channel with
| `Ok -> ()
| `Duplicate -> failwith ("Duplicate definition of pseudo for "^(Element.to_long_string elem))
end
end
end;
build_pseudo rest
in
let () =
match p with
| None -> ()
| Some p ->
String.split ~on:'|' p
|> List.rev_map ~f:String.strip
|> build_pseudo
in
2014-08-27 16:38:13 +02:00
(* Build EZFIO File name *)
let ezfio_file =
match o with
| Some x -> x
| None ->
begin
match String.rsplit2 ~on:'.' xyz_file with
| Some (x,"xyz") -> x^".ezfio"
| _ -> xyz_file^".ezfio"
end
in
if Sys.file_exists_exn ezfio_file then
failwith (ezfio_file^" already exists");
let write_file () =
(* Create EZFIO *)
Ezfio.set_file ezfio_file;
(* Write Pseudo *)
let pseudo =
List.map nuclei ~f:(fun x ->
match pseudo_channel x.Atom.element with
| Some channel -> Pseudo.read_element channel x.Atom.element
| None -> Pseudo.empty x.Atom.element
)
in
2016-01-25 15:44:15 +01:00
let molecule =
let n_elec_to_remove =
List.fold pseudo ~init:0 ~f:(fun accu x ->
accu + (Positive_int.to_int x.Pseudo.n_elec))
2016-01-25 15:44:15 +01:00
in
{ Molecule.elec_alpha =
(Elec_alpha_number.to_int molecule.Molecule.elec_alpha)
- n_elec_to_remove/2
|> Elec_alpha_number.of_int;
Molecule.elec_beta =
(Elec_beta_number.to_int molecule.Molecule.elec_beta)
- (n_elec_to_remove - n_elec_to_remove/2)
|> Elec_beta_number.of_int;
Molecule.nuclei =
let charges =
List.map pseudo ~f:(fun x -> Positive_int.to_int x.Pseudo.n_elec
|> Float.of_int)
|> Array.of_list
in
List.mapi molecule.Molecule.nuclei ~f:(fun i x ->
{ x with Atom.charge = (Charge.to_float x.Atom.charge) -. charges.(i)
|> Charge.of_float }
)
}
2016-01-25 15:44:15 +01:00
in
let nuclei =
molecule.Molecule.nuclei @ dummy
2016-01-25 15:44:15 +01:00
in
(* Write Electrons *)
Ezfio.set_electrons_elec_alpha_num ( Elec_alpha_number.to_int
molecule.Molecule.elec_alpha ) ;
Ezfio.set_electrons_elec_beta_num ( Elec_beta_number.to_int
molecule.Molecule.elec_beta ) ;
(* Write Nuclei *)
let labels =
List.map ~f:(fun x->Element.to_string x.Atom.element) nuclei
and charges =
List.map ~f:(fun x-> Atom.(Charge.to_float x.charge)) nuclei
and coords =
(List.map ~f:(fun x-> x.Atom.coord.Point3d.x) nuclei) @
(List.map ~f:(fun x-> x.Atom.coord.Point3d.y) nuclei) @
(List.map ~f:(fun x-> x.Atom.coord.Point3d.z) nuclei) in
let nucl_num = (List.length labels) in
Ezfio.set_nuclei_nucl_num nucl_num ;
Ezfio.set_nuclei_nucl_label (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| nucl_num |] ~data:labels);
Ezfio.set_nuclei_nucl_charge (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| nucl_num |] ~data:charges);
Ezfio.set_nuclei_nucl_coord (Ezfio.ezfio_array_of_list
~rank:2 ~dim:[| nucl_num ; 3 |] ~data:coords);
(* Write pseudopotential *)
let () =
match p with
| None -> Ezfio.set_pseudo_do_pseudo false
| _ -> Ezfio.set_pseudo_do_pseudo true
in
let klocmax =
List.fold pseudo ~init:0 ~f:(fun accu x ->
2016-01-25 15:44:15 +01:00
let x =
List.length x.Pseudo.local
in
if (x > accu) then x
else accu
)
and lmax =
List.fold pseudo ~init:0 ~f:(fun accu x ->
let x =
List.fold x.Pseudo.non_local ~init:0 ~f:(fun accu (x,_) ->
let x =
Positive_int.to_int x.Pseudo.Primitive_non_local.proj
in
if (x > accu) then x
else accu
)
2016-01-25 15:44:15 +01:00
in
if (x > accu) then x
else accu
)
in
let kmax =
Array.init (lmax+1) ~f:(fun i->
List.map pseudo ~f:(fun x ->
List.filter x.Pseudo.non_local ~f:(fun (y,_) ->
(Positive_int.to_int y.Pseudo.Primitive_non_local.proj) = i)
|> List.length )
|> List.fold ~init:0 ~f:(fun accu x ->
if accu > x then accu else x)
)
|> Array.fold ~init:0 ~f:(fun accu i ->
if i > accu then i else accu)
2016-01-25 22:45:23 +01:00
in
let () =
Ezfio.set_pseudo_pseudo_klocmax klocmax;
Ezfio.set_pseudo_pseudo_kmax kmax;
Ezfio.set_pseudo_pseudo_lmax lmax;
let tmp_array_v_k, tmp_array_dz_k, tmp_array_n_k =
Array.make_matrix ~dimx:klocmax ~dimy:nucl_num 0. ,
Array.make_matrix ~dimx:klocmax ~dimy:nucl_num 0. ,
Array.make_matrix ~dimx:klocmax ~dimy:nucl_num 0
2016-01-25 22:45:23 +01:00
in
List.iteri pseudo ~f:(fun j x ->
List.iteri x.Pseudo.local ~f:(fun i (y,c) ->
tmp_array_v_k.(i).(j) <- AO_coef.to_float c;
let y, z =
AO_expo.to_float y.Pseudo.Primitive_local.expo,
R_power.to_int y.Pseudo.Primitive_local.r_power
in
tmp_array_dz_k.(i).(j) <- y;
tmp_array_n_k.(i).(j) <- z;
)
);
let concat_2d tmp_array =
let data =
Array.map tmp_array ~f:Array.to_list
|> Array.to_list
|> List.concat
in
Ezfio.ezfio_array_of_list ~rank:2 ~dim:[|nucl_num ; klocmax|] ~data
in
concat_2d tmp_array_v_k
|> Ezfio.set_pseudo_pseudo_v_k ;
concat_2d tmp_array_dz_k
|> Ezfio.set_pseudo_pseudo_dz_k;
concat_2d tmp_array_n_k
|> Ezfio.set_pseudo_pseudo_n_k;
let tmp_array_v_kl, tmp_array_dz_kl, tmp_array_n_kl =
Array.init (lmax+1) ~f:(fun _ ->
(Array.make_matrix ~dimx:kmax ~dimy:nucl_num 0. )),
Array.init (lmax+1) ~f:(fun _ ->
(Array.make_matrix ~dimx:kmax ~dimy:nucl_num 0. )),
Array.init (lmax+1) ~f:(fun _ ->
(Array.make_matrix ~dimx:kmax ~dimy:nucl_num 0 ))
in
List.iteri pseudo ~f:(fun j x ->
let last_idx =
Array.create ~len:(lmax+1) 0
in
List.iter x.Pseudo.non_local ~f:(fun (y,c) ->
let k, y, z =
Positive_int.to_int y.Pseudo.Primitive_non_local.proj,
AO_expo.to_float y.Pseudo.Primitive_non_local.expo,
R_power.to_int y.Pseudo.Primitive_non_local.r_power
in
let i =
last_idx.(k)
in
tmp_array_v_kl.(k).(i).(j) <- AO_coef.to_float c;
tmp_array_dz_kl.(k).(i).(j) <- y;
tmp_array_n_kl.(k).(i).(j) <- z;
last_idx.(k) <- i+1;
)
);
let concat_3d tmp_array =
let data =
Array.map tmp_array ~f:(fun x ->
Array.map x ~f:Array.to_list
|> Array.to_list
|> List.concat)
|> Array.to_list
|> List.concat
in
Ezfio.ezfio_array_of_list ~rank:3 ~dim:[|nucl_num ; kmax ; lmax+1|] ~data
in
concat_3d tmp_array_v_kl
|> Ezfio.set_pseudo_pseudo_v_kl ;
concat_3d tmp_array_dz_kl
|> Ezfio.set_pseudo_pseudo_dz_kl ;
concat_3d tmp_array_n_kl
|> Ezfio.set_pseudo_pseudo_n_kl ;
2016-01-25 22:45:23 +01:00
in
2016-01-25 15:44:15 +01:00
(* Write Basis set *)
let basis =
let nmax =
Nucl_number.get_max ()
in
let rec do_work (accu:(Atom.t*Nucl_number.t) list) (n:int) = function
| [] -> accu
| e::tail ->
let new_accu =
(e,(Nucl_number.of_int ~max:nmax n))::accu
in
do_work new_accu (n+1) tail
in
let result = do_work [] 1 nuclei
|> List.rev
|> List.map ~f:(fun (x,i) ->
try
let e =
match x.Atom.element with
| Element.X -> Element.H
| e -> e
in
Basis.read_element (basis_channel x.Atom.element) i e
with
| End_of_file -> failwith
("Element "^(Element.to_string x.Atom.element)^" not found in basis set.")
)
|> List.concat
in
(* close all in_channels *)
result
2015-11-22 15:18:51 +01:00
in
let long_basis = Long_basis.of_basis basis in
let ao_num = List.length long_basis in
Ezfio.set_ao_basis_ao_num ao_num;
Ezfio.set_ao_basis_ao_basis b;
let ao_prim_num = List.map long_basis ~f:(fun (_,g,_) -> List.length g.Gto.lc)
and ao_nucl = List.map long_basis ~f:(fun (_,_,n) -> Nucl_number.to_int n)
and ao_power=
let l = List.map long_basis ~f:(fun (x,_,_) -> x) in
(List.map l ~f:(fun t -> Positive_int.to_int Symmetry.Xyz.(t.x)) )@
(List.map l ~f:(fun t -> Positive_int.to_int Symmetry.Xyz.(t.y)) )@
(List.map l ~f:(fun t -> Positive_int.to_int Symmetry.Xyz.(t.z)) )
2014-09-18 17:01:43 +02:00
in
let ao_prim_num_max = List.fold ~init:0 ~f:(fun s x ->
if x > s then x
else s) ao_prim_num
2014-09-18 17:01:43 +02:00
in
let gtos =
List.map long_basis ~f:(fun (_,x,_) -> x)
2014-09-18 17:01:43 +02:00
in
let create_expo_coef ec =
let coefs =
begin match ec with
| `Coefs -> List.map gtos ~f:(fun x->
List.map x.Gto.lc ~f:(fun (_,coef) -> AO_coef.to_float coef) )
| `Expos -> List.map gtos ~f:(fun x->
List.map x.Gto.lc ~f:(fun (prim,_) -> AO_expo.to_float
prim.Primitive.expo) )
end
in
let rec get_n n accu = function
| [] -> List.rev accu
| h::tail ->
let y =
begin match List.nth h n with
| Some x -> x
| None -> 0.
end
in
get_n n (y::accu) tail
in
let rec build accu = function
| n when n=ao_prim_num_max -> accu
| n -> build ( accu @ (get_n n [] coefs) ) (n+1)
in
build [] 0
in
let ao_coef = create_expo_coef `Coefs
and ao_expo = create_expo_coef `Expos
in
let () =
Ezfio.set_ao_basis_ao_prim_num (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| ao_num |] ~data:ao_prim_num) ;
Ezfio.set_ao_basis_ao_nucl(Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| ao_num |] ~data:ao_nucl) ;
Ezfio.set_ao_basis_ao_power(Ezfio.ezfio_array_of_list
~rank:2 ~dim:[| ao_num ; 3 |] ~data:ao_power) ;
Ezfio.set_ao_basis_ao_coef(Ezfio.ezfio_array_of_list
~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_coef) ;
Ezfio.set_ao_basis_ao_expo(Ezfio.ezfio_array_of_list
~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_expo) ;
Ezfio.set_ao_basis_ao_cartesian(cart);
in
match Input.Ao_basis.read () with
| None -> failwith "Error in basis"
| Some x -> Input.Ao_basis.write x
2014-09-17 23:47:13 +02:00
in
2016-01-25 15:44:15 +01:00
let () =
try write_file () with
| ex ->
begin
begin
match Sys.is_directory ezfio_file with
| `Yes -> rmdir ezfio_file
| _ -> ()
end;
raise ex;
end
in ()
2015-01-06 19:12:17 +01:00
2014-08-27 16:38:13 +02:00
let command =
Command.basic
~summary: "Quantum Package command"
2014-11-16 18:05:04 +01:00
~readme:(fun () -> "
2015-11-25 23:46:09 +01:00
=== Available basis sets ===
" ^ (list_basis ()) ^ "
============================
2015-11-24 17:31:22 +01:00
Creates an EZFIO directory from a standard xyz file. The basis set is defined
as a single string if all the atoms are taken from the same basis set,
otherwise specific elements can be defined as follows:
2014-11-16 18:05:04 +01:00
2015-01-12 16:58:22 +01:00
-b \"cc-pcvdz | H:cc-pvdz | C:6-31g\"
2014-11-16 18:05:04 +01:00
2015-11-24 17:31:22 +01:00
If a file with the same name as the basis set exists, this file will be read.
Otherwise, the basis set is obtained from the database.
2015-11-25 23:46:09 +01:00
" )
2014-08-27 16:38:13 +02:00
spec
2016-01-27 00:19:08 +01:00
(fun o b c d m p cart xyz_file () ->
run ?o b c d m p cart xyz_file )
2014-08-27 16:38:13 +02:00
let () =
Command.run command
2014-08-27 16:38:13 +02:00