mirror of
https://github.com/LCPQ/quantum_package
synced 2024-06-21 12:42:13 +02:00
Anthony Scemama
f6a5e40b6e
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
291 lines
8.8 KiB
OCaml
291 lines
8.8 KiB
OCaml
open Qputils;;
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open Qptypes;;
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open Core.Std;;
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let spec =
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let open Command.Spec in
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empty
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+> flag "o" (optional string)
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~doc:"file Name of the created EZFIO file."
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+> flag "b" (required string)
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~doc:"string Name of basis set."
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+> flag "c" (optional_with_default 0 int)
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~doc:"int Total charge of the molecule. Default is 0."
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+> flag "m" (optional_with_default 1 int)
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~doc:"int Spin multiplicity (2S+1) of the molecule. Default is 1."
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+> anon ("xyz_file" %: string)
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;;
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let run ?o b c m xyz_file =
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(* Read molecule *)
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let molecule =
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(Molecule.of_xyz_file xyz_file ~charge:(Charge.of_int c)
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~multiplicity:(Multiplicity.of_int m) )
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in
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let nuclei = molecule.Molecule.nuclei in
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let basis_table = Hashtbl.Poly.create () in
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(* Open basis set channels *)
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let basis_channel element =
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let key = Element.to_string element in
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match Hashtbl.find basis_table key with
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| Some in_channel ->
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in_channel
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| None ->
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begin
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Printf.printf "%s is not defined in basis %s.\nEnter alternate basis : %!"
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(Element.to_long_string element) b ;
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let bas =
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match In_channel.input_line stdin with
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| Some line -> String.strip line |> String.lowercase
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| None -> failwith "Aborted"
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in
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let new_channel = In_channel.create
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(Qpackage.root ^ "/data/basis/" ^ bas)
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in
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Hashtbl.add_exn basis_table ~key:key ~data:new_channel;
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new_channel
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end
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in
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let temp_filename =
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Filename.temp_file "qp_create_" ".basis"
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in
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let rec build_basis = function
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| [] -> ()
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| elem_and_basis_name :: rest ->
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begin
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match (String.lsplit2 ~on:':' elem_and_basis_name) with
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| None -> (* Principal basis *)
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let basis = elem_and_basis_name in
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let command =
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let rec apply accu = function
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| [] -> accu
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| atom::rest ->
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let new_accu =
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accu ^ " " ^ (Element.to_string atom)
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in
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apply new_accu rest
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in
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let accu =
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Qpackage.root ^ "/scripts/get_basis.sh \"" ^ temp_filename
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^ "\" " ^ basis
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in
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List.map nuclei ~f:(fun x -> x.Atom.element)
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|> apply accu
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in
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begin
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let filename =
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Unix.open_process_in command
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|> In_channel.input_all
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|> String.strip
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in
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let new_channel =
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In_channel.create filename
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in
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Unix.unlink filename;
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List.iter nuclei ~f:(fun elem->
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let key = Element.to_string elem.Atom.element
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in
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match Hashtbl.add basis_table ~key:key ~data:new_channel with
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| `Ok -> ()
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| `Duplicate -> ()
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)
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end
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| Some (key, basis) -> (*Aux basis *)
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begin
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let elem = Element.of_string key
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and basis = String.lowercase basis
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in
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let key = Element.to_string elem
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in
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let command =
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Qpackage.root ^ "/scripts/get_basis.sh \"" ^ temp_filename ^
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"\" " ^ basis ^ " " ^ key
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in
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begin
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let filename =
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Unix.open_process_in command
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|> In_channel.input_all
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|> String.strip
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in
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let new_channel =
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In_channel.create filename
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in
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Unix.unlink filename;
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match Hashtbl.add basis_table ~key:key ~data:new_channel with
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| `Ok -> ()
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| `Duplicate -> failwith ("Duplicate definition of basis for "^(Element.to_long_string elem))
|
|
end
|
|
end
|
|
end;
|
|
build_basis rest
|
|
in
|
|
String.split ~on:'|' b
|
|
|> List.rev_map ~f:String.strip
|
|
|> build_basis;
|
|
|
|
(* 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");
|
|
|
|
(* Create EZFIO *)
|
|
Ezfio.set_file ezfio_file;
|
|
|
|
(* 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 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
|
|
Basis.read_element (basis_channel x.Atom.element) i x.Atom.element
|
|
with
|
|
| End_of_file ->
|
|
begin
|
|
let alt_channel = basis_channel x.Atom.element in
|
|
try
|
|
Basis.read_element alt_channel i x.Atom.element
|
|
with
|
|
End_of_file -> failwith
|
|
("Element "^(Element.to_string x.Atom.element)^" not found")
|
|
end
|
|
)
|
|
|> List.concat
|
|
in
|
|
(* close all in_channels *)
|
|
result
|
|
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)) )
|
|
in
|
|
let ao_prim_num_max = List.fold ~init:0 ~f:(fun s x ->
|
|
if x > s then x
|
|
else s) ao_prim_num
|
|
in
|
|
let gtos = List.map long_basis ~f:(fun (_,x,_) -> x) 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
|
|
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) ;
|
|
|
|
|
|
match Input.Ao_basis.read () with
|
|
| None -> failwith "Error in basis"
|
|
| Some x -> Input.Ao_basis.write x
|
|
|
|
;;
|
|
|
|
let command =
|
|
Command.basic
|
|
~summary: "Quantum Package command"
|
|
~readme:(fun () -> "
|
|
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:
|
|
|
|
-b \"cc-pcvdz | H:cc-pvdz | C:6-31g\"
|
|
|
|
")
|
|
spec
|
|
(fun o b c m xyz_file () ->
|
|
run ?o b c m xyz_file )
|
|
;;
|
|
|
|
let () =
|
|
Command.run command
|
|
;;
|
|
|
|
|
|
|