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https://github.com/pfloos/quack
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GoDuck qcaml
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GoDuck
62
GoDuck
@ -1,18 +1,68 @@
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#! /bin/bash
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function help() {
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cat << EOF
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Usage:
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./qcaml-tools/quack_input -b <string> [-c <int>] [-f] [-h] [-m <int>]
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[-r <int>] -x <string> [--]
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Arguments:
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Options:
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-b --basis=<string> Name of the file containing the basis set
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-c --charge=<int> Total charge of the molecule. Specify negative
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charges with 'm' instead of the minus sign,
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for example m1 instead of -1. Default is
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0
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-f --frozen-core Freeze core MOs. Default is false
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-h --help Prints the help message.
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-m --multiplicity=<int> Spin multiplicity (2S+1). Default is singlet
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-r --rydberg=<int> Number of Rydberg electrons. Default is 0
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-x --xyz=<string> Name of the file containing the nuclear
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coordinates in xyz format
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Description:
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Prepares the input data for QuAcK.
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Writes \$QUACK_DIR/input/basis and \$QUACK_DIR/input/molecule.
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If \$QUACK_DIR is not set, \$QUACK_DIR is replaces by the current
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directory.
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Usage:
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$(basename $0) [-h|--help]
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Options:
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-h --help Prints the help message
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EOF
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exit 0
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}
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set -e
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if [ $# -ne 2 ]
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if [ $# -ne 2 ] || [ $# -ne 4 ]
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then
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echo "You need two arguments [Molecule] [Basis] !!"
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echo "You need at least two arguments [Molecule] [Basis] [Charge] [Multiplicity]"
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fi
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if [ $# = 2 ]
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then
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cp examples/molecule."$1" input/molecule
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cp examples/basis."$1"."$2" input/basis
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cp basis/"$2" input/basis.qcaml
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# ./bin/IntPak
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./qcaml-tools/quack_integrals -x mol/${1}.xyz -b basis/${2}
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./qcaml-tools/quack_input -x mol/${1}.xyz -b basis/${2}
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./bin/QuAcK
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fi
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if [ $# = 4 ]
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then
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./qcaml-tools/quack_integrals -x mol/${1}.xyz -b basis/${2}
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./qcaml-tools/quack_input -x mol/${1}.xyz -b basis/${2} -c ${3} -m ${4}
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./bin/QuAcK
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fi
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BIN
qcaml-tools/GoDuck
Executable file
BIN
qcaml-tools/GoDuck
Executable file
Binary file not shown.
185
qcaml-tools/GoDuck.ml
Normal file
185
qcaml-tools/GoDuck.ml
Normal file
@ -0,0 +1,185 @@
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let quack_dir =
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try Sys.getenv "QUACK_ROOT" with
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Not_found -> "."
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let quack_input = quack_dir ^ "/input/"
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let quack_mol = quack_dir ^ "/mol/"
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let quack_basis = quack_dir ^ "/basis/"
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let quack_int = quack_dir ^ "/int/"
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let quack_basis_filename = quack_input ^ "basis"
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let quack_molecule_filename = quack_input ^ "molecule"
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module Command_line = Qcaml.Common.Command_line
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module Util = Qcaml.Common.Util
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let () =
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let open Command_line in
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begin
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set_header_doc (Sys.argv.(0) ^ " - QuAcK command");
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set_description_doc "Prepares the input data for QuAcK.
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Writes $QUACK_ROOT/input/basis and $QUACK_ROOT/input/molecule.
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If $QUACK_ROOT is not set, $QUACK_ROOT is replaces by the current
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directory.";
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set_specs
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[ { short='b' ; long="basis" ; opt=Mandatory;
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arg=With_arg "<string>";
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doc="Name of the file containing the basis set in the $QUACK_ROOT/basis/ directory"; } ;
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{ short='x' ; long="xyz" ; opt=Mandatory;
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arg=With_arg "<string>";
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doc="Name of the file containing the nuclear coordinates in xyz format in the $QUACK_ROOT/mol/ directory without the .xyz extension"; } ;
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{ short='m' ; long="multiplicity" ; opt=Optional;
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arg=With_arg "<int>";
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doc="Spin multiplicity (2S+1). Default is singlet"; } ;
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{ short='c' ; long="charge" ; opt=Optional;
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arg=With_arg "<int>";
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doc="Total charge of the molecule. Specify negative charges with 'm' instead of the minus sign, for example m1 instead of -1. Default is 0"; } ;
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{ short='f' ; long="frozen-core" ; opt=Optional;
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arg=Without_arg ;
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doc="Freeze core MOs. Default is false"; } ;
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{ short='r' ; long="rydberg" ; opt=Optional;
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arg=With_arg "<int>" ;
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doc="Number of Rydberg electrons. Default is 0"; } ;
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{ short='u' ; long="range-separation" ; opt=Optional;
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arg=With_arg "<float>";
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doc="Range-separation parameter."; } ;
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]
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end;
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(* Handle options *)
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let basis_file =
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quack_basis ^ (Util.of_some @@ Command_line.get "basis")
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in
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let nuclei_file =
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quack_mol ^ (Util.of_some @@ Command_line.get "xyz") ^ ".xyz"
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in
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let frozen_core = Command_line.get_bool "frozen-core" in
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let charge =
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match Command_line.get "charge" with
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| Some x -> ( if x.[0] = 'm' then
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~- (int_of_string (String.sub x 1 (String.length x - 1)))
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else
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int_of_string x )
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| None -> 0
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in
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let multiplicity =
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match Command_line.get "multiplicity" with
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| Some x -> int_of_string x
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| None -> 1
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in
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let rydberg =
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match Command_line.get "rydberg" with
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| Some x -> int_of_string x
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| None -> 0
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in
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let range_separation =
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match Command_line.get "range-separation" with
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| None -> None
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| Some mu -> Some (float_of_string mu)
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in
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let nuclei =
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Qcaml.Particles.Nuclei.of_xyz_file nuclei_file
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in
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let electrons =
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Qcaml.Particles.Electrons.of_atoms ~multiplicity ~charge nuclei
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in
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let basis =
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Qcaml.Gaussian.Basis.of_nuclei_and_basis_filename ~nuclei basis_file
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in
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let print_basis nuclei basis =
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let oc = open_out quack_basis_filename in
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let ocf = Format.formatter_of_out_channel oc in
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let g_basis = Qcaml.Gaussian.Basis.general_basis basis in
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let dict =
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Array.to_list nuclei
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|> List.mapi (fun i (e, _) ->
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(i+1), List.assoc e g_basis
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)
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in
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List.iter (fun (i,b) ->
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Format.fprintf ocf "%d %d\n" i (Array.length b);
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Array.iter (fun x ->
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Format.fprintf ocf "%a" Qcaml.Gaussian.General_basis.pp_gcs x) b
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) dict;
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close_out oc
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in
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print_basis nuclei basis;
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let print_molecule nuclei electrons =
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let oc = open_out quack_molecule_filename in
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let nat = Array.length nuclei in
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let nela = Qcaml.Particles.Electrons.n_alfa electrons in
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let nelb = Qcaml.Particles.Electrons.n_beta electrons in
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let ncore =
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if frozen_core then
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Qcaml.Particles.Nuclei.small_core nuclei
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else 0
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in
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let nryd = rydberg in
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Printf.fprintf oc "# nAt nEla nElb nCore nRyd\n";
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Printf.fprintf oc " %4d %4d %4d %5d %4d\n" nat nela nelb ncore nryd;
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Printf.fprintf oc "# Znuc x y z\n";
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let open Qcaml.Common.Coordinate in
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Array.iter (fun (element, coord) ->
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Printf.fprintf oc "%3s %16.10f %16.10f %16.10f\n"
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(Qcaml.Particles.Element.to_string element)
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coord.x coord.y coord.z
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) nuclei;
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close_out oc
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in
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print_molecule nuclei electrons;
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let operators =
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match range_separation with
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| None -> []
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| Some mu -> [ Qcaml.Operators.Operator.of_range_separation mu ]
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in
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let ao_basis =
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Qcaml.Ao.Basis.of_nuclei_and_basis_filename ~kind:`Gaussian
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~operators ~cartesian:true ~nuclei basis_file
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in
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let overlap = Qcaml.Ao.Basis.overlap ao_basis in
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let eN_ints = Qcaml.Ao.Basis.eN_ints ao_basis in
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let kin_ints = Qcaml.Ao.Basis.kin_ints ao_basis in
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let ee_ints = Qcaml.Ao.Basis.ee_ints ao_basis in
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let multipole = Qcaml.Ao.Basis.multipole ao_basis in
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let x_mat = Qcaml.Gaussian_integrals.Multipole.matrix_x multipole in
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let y_mat = Qcaml.Gaussian_integrals.Multipole.matrix_y multipole in
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let z_mat = Qcaml.Gaussian_integrals.Multipole.matrix_z multipole in
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Qcaml.Gaussian_integrals.Overlap.to_file ~filename:(quack_int ^ "Ov.dat") overlap;
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Qcaml.Gaussian_integrals.Electron_nucleus.to_file ~filename:(quack_int ^ "Nuc.dat") eN_ints;
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Qcaml.Gaussian_integrals.Kinetic.to_file ~filename:(quack_int ^ "Kin.dat") kin_ints;
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Qcaml.Gaussian_integrals.Eri.to_file ~filename:(quack_int ^ "ERI.dat") ee_ints;
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Qcaml.Gaussian_integrals.Multipole.to_file ~filename:(quack_int ^ "x.dat") x_mat;
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Qcaml.Gaussian_integrals.Multipole.to_file ~filename:(quack_int ^ "y.dat") y_mat;
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Qcaml.Gaussian_integrals.Multipole.to_file ~filename:(quack_int ^ "z.dat") z_mat;
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match range_separation with
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| Some _mu ->
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Qcaml.Gaussian_integrals.Eri_long_range.to_file ~filename:(quack_int ^ "ERI_lr.dat") (Qcaml.Ao.Basis.ee_lr_ints ao_basis)
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| None -> ()
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.NOTPARALLEL:
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TARGETS=quack_input \
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quack_integrals
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quack_integrals \
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GoDuck
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.PHONY: default build install uninstall test clean
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(names
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quack_input
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quack_integrals
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GoDuck
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)
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(libraries
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qcaml
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let quack_dir =
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try Sys.getenv "QUACK_DIR" with
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try Sys.getenv "QUACK_ROOT" with
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Not_found -> "."
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let quack_basis_filename = quack_dir ^ "/input/basis"
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begin
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set_header_doc (Sys.argv.(0) ^ " - QuAcK command");
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set_description_doc "Prepares the input data for QuAcK.
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Writes $QUACK_DIR/input/basis and $QUACK_DIR/input/molecule.
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If $QUACK_DIR is not set, $QUACK_DIR is replaces by the current
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Writes $QUACK_ROOT/input/basis and $QUACK_ROOT/input/molecule.
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If $QUACK_ROOT is not set, $QUACK_ROOT is replaces by the current
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directory.";
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set_specs
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[ { short='b' ; long="basis" ; opt=Mandatory;
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let quack_dir =
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try Sys.getenv "QUACK_DIR" with
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try Sys.getenv "QUACK_ROOT" with
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Not_found -> "."
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module Command_line = Qcaml.Common.Command_line
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@ -245,7 +245,7 @@ program QuAcK
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else
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call system('./GoQCaml')
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! call system('./GoQCaml')
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call read_integrals(nBas,S,T,V,Hc,ERI_AO)
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call read_dipole_integrals(nBas,dipole_int)
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