diff --git a/Makefile b/Makefile index ec555670..4aa24d00 100644 --- a/Makefile +++ b/Makefile @@ -45,5 +45,5 @@ ocaml: veryclean: rm -rf EZFIO - $(MAKE) EZFIO + rm -rf resultsFile $(MAKE) -C src veryclean diff --git a/data/ezfio_defaults/determinants.ezfio_default b/data/ezfio_defaults/determinants.ezfio_default deleted file mode 100644 index 2cfbe3ea..00000000 --- a/data/ezfio_defaults/determinants.ezfio_default +++ /dev/null @@ -1,9 +0,0 @@ -determinants - n_states 1 - n_states_diag determinants_n_states - n_det_max_jacobi 1000 - threshold_generators 0.99 - threshold_selectors 0.999 - read_wf false - s2_eig false - only_single_double_dm false diff --git a/data/ezfio_defaults/properties.ezfio_default b/data/ezfio_defaults/properties.ezfio_default deleted file mode 100644 index ce06d413..00000000 --- a/data/ezfio_defaults/properties.ezfio_default +++ /dev/null @@ -1,2 +0,0 @@ -properties - z_one_point 3.9 diff --git a/ocaml/Input.ml b/ocaml/Input.ml index 01bb54a0..5e012996 100644 --- a/ocaml/Input.ml +++ b/ocaml/Input.ml @@ -4,8 +4,8 @@ open Core.Std;; include Input_ao_basis;; include Input_bitmasks;; -include Input_determinants;; +include Input_determinants_by_hand;; include Input_electrons;; include Input_mo_basis;; include Input_nuclei;; -include Input_auto_generated;; \ No newline at end of file +include Input_auto_generated;; diff --git a/ocaml/Input_determinants.ml b/ocaml/Input_determinants_by_hand.ml similarity index 73% rename from ocaml/Input_determinants.ml rename to ocaml/Input_determinants_by_hand.ml index 9af2b7c0..4c0453e6 100644 --- a/ocaml/Input_determinants.ml +++ b/ocaml/Input_determinants_by_hand.ml @@ -2,20 +2,14 @@ open Qptypes;; open Qputils;; open Core.Std;; -module Determinants : sig +module Determinants_by_hand : sig type t = { n_int : N_int_number.t; bit_kind : Bit_kind.t; - mo_label : MO_label.t; n_det : Det_number.t; n_states : States_number.t; n_states_diag : States_number.t; - n_det_max_jacobi : Strictly_positive_int.t; - threshold_generators : Threshold.t; - threshold_selectors : Threshold.t; - read_wf : bool; expected_s2 : Positive_float.t; - s2_eig : bool; psi_coef : Det_coef.t array; psi_det : Determinant.t array; } with sexp @@ -28,16 +22,10 @@ end = struct type t = { n_int : N_int_number.t; bit_kind : Bit_kind.t; - mo_label : MO_label.t; n_det : Det_number.t; n_states : States_number.t; n_states_diag : States_number.t; - n_det_max_jacobi : Strictly_positive_int.t; - threshold_generators : Threshold.t; - threshold_selectors : Threshold.t; - read_wf : bool; expected_s2 : Positive_float.t; - s2_eig : bool; psi_coef : Det_coef.t array; psi_det : Determinant.t array; } with sexp @@ -77,22 +65,6 @@ end = struct |> Ezfio.set_determinants_bit_kind ;; - - let read_mo_label () = - if (not (Ezfio.has_determinants_mo_label ())) then - Ezfio.get_mo_basis_mo_label () - |> Ezfio.set_determinants_mo_label - ; - Ezfio.get_determinants_mo_label () - |> MO_label.of_string - ;; - - let write_mo_label l = - MO_label.to_string l - |> Ezfio.set_determinants_mo_label - ;; - - let read_n_det () = if not (Ezfio.has_determinants_n_det ()) then Ezfio.set_determinants_n_det 1 @@ -138,67 +110,6 @@ end = struct Ezfio.set_determinants_n_states_diag (max n_states n) ;; - - let read_n_det_max_jacobi () = - if not (Ezfio.has_determinants_n_det_max_jacobi ()) then - get_default "n_det_max_jacobi" - |> Int.of_string - |> Ezfio.set_determinants_n_det_max_jacobi - ; - Ezfio.get_determinants_n_det_max_jacobi () - |> Strictly_positive_int.of_int - ;; - - let write_n_det_max_jacobi n = - Strictly_positive_int.to_int n - |> Ezfio.set_determinants_n_det_max_jacobi - ;; - - - let read_threshold_generators () = - if not (Ezfio.has_determinants_threshold_generators ()) then - get_default "threshold_generators" - |> Float.of_string - |> Ezfio.set_determinants_threshold_generators - ; - Ezfio.get_determinants_threshold_generators () - |> Threshold.of_float - ;; - - let write_threshold_generators t = - Threshold.to_float t - |> Ezfio.set_determinants_threshold_generators - ;; - - - let read_threshold_selectors () = - if not (Ezfio.has_determinants_threshold_selectors ()) then - get_default "threshold_selectors" - |> Float.of_string - |> Ezfio.set_determinants_threshold_selectors - ; - Ezfio.get_determinants_threshold_selectors () - |> Threshold.of_float - ;; - - let write_threshold_selectors t = - Threshold.to_float t - |> Ezfio.set_determinants_threshold_selectors - ;; - - - let read_read_wf () = - if not (Ezfio.has_determinants_read_wf ()) then - get_default "read_wf" - |> Bool.of_string - |> Ezfio.set_determinants_read_wf - ; - Ezfio.get_determinants_read_wf () - ;; - - let write_read_wf = Ezfio.set_determinants_read_wf ;; - - let read_expected_s2 () = if not (Ezfio.has_determinants_expected_s2 ()) then begin @@ -219,19 +130,6 @@ end = struct |> Ezfio.set_determinants_expected_s2 ;; - - let read_s2_eig () = - if not (Ezfio.has_determinants_s2_eig ()) then - get_default "s2_eig" - |> Bool.of_string - |> Ezfio.set_determinants_s2_eig - ; - Ezfio.get_determinants_s2_eig () - ;; - - let write_s2_eig = Ezfio.set_determinants_s2_eig ;; - - let read_psi_coef () = if not (Ezfio.has_determinants_psi_coef ()) then begin @@ -315,16 +213,10 @@ end = struct Some { n_int = read_n_int () ; bit_kind = read_bit_kind () ; - mo_label = read_mo_label () ; n_det = read_n_det () ; n_states = read_n_states () ; n_states_diag = read_n_states_diag () ; - n_det_max_jacobi = read_n_det_max_jacobi () ; - threshold_generators = read_threshold_generators () ; - threshold_selectors = read_threshold_selectors () ; - read_wf = read_read_wf () ; expected_s2 = read_expected_s2 () ; - s2_eig = read_s2_eig () ; psi_coef = read_psi_coef () ; psi_det = read_psi_det () ; } @@ -334,31 +226,19 @@ end = struct let write { n_int ; bit_kind ; - mo_label ; n_det ; n_states ; n_states_diag ; - n_det_max_jacobi ; - threshold_generators ; - threshold_selectors ; - read_wf ; expected_s2 ; - s2_eig ; psi_coef ; psi_det ; } = write_n_int n_int ; write_bit_kind bit_kind; - write_mo_label mo_label; write_n_det n_det; write_n_states n_states; write_n_states_diag ~n_states:n_states n_states_diag; - write_n_det_max_jacobi n_det_max_jacobi; - write_threshold_generators threshold_generators; - write_threshold_selectors threshold_selectors; - write_read_wf read_wf; write_expected_s2 expected_s2; - write_s2_eig s2_eig; write_psi_coef ~n_det:n_det psi_coef ~n_states:n_states; write_psi_det ~n_int:n_int ~n_det:n_det psi_det; ;; @@ -399,35 +279,17 @@ end = struct |> String.concat_array ~sep:"\n" in Printf.sprintf " -Read the current wave function :: - - read_wf = %s - -Label of the MOs on which the determinants were computed :: - - mo_label = %s - Force the selected wave function to be an eigenfunction of S^2. If true, input the expected value of S^2 :: - s2_eig = %s expected_s2 = %s -Thresholds on generators and selectors (fraction of the norm) :: - - threshold_generators = %s - threshold_selectors = %s - Number of requested states, and number of states used for the Davidson diagonalization :: n_states = %s n_states_diag = %s -Maximum size of the Hamiltonian matrix that will be fully diagonalized :: - - n_det_max_jacobi = %s - Number of determinants :: n_det = %s @@ -436,15 +298,9 @@ Determinants :: %s " - (b.read_wf |> Bool.to_string) - (b.mo_label |> MO_label.to_string) - (b.s2_eig |> Bool.to_string) (b.expected_s2 |> Positive_float.to_string) - (b.threshold_generators |> Threshold.to_string) - (b.threshold_selectors |> Threshold.to_string) (b.n_states |> States_number.to_string) (b.n_states_diag |> States_number.to_string) - (b.n_det_max_jacobi |> Strictly_positive_int.to_string) (b.n_det |> Det_number.to_string) det_text |> Rst_string.of_string @@ -456,31 +312,19 @@ Determinants :: Printf.sprintf " n_int = %s bit_kind = %s -mo_label = \"%s\" n_det = %s n_states = %s n_states_diag = %s -n_det_max_jacobi = %s -threshold_generators = %s -threshold_selectors = %s -read_wf = %s expected_s2 = %s -s2_eig = %s psi_coef = %s psi_det = %s " (b.n_int |> N_int_number.to_string) (b.bit_kind |> Bit_kind.to_string) - (b.mo_label |> MO_label.to_string) (b.n_det |> Det_number.to_string) (b.n_states |> States_number.to_string) (b.n_states_diag |> States_number.to_string) - (b.n_det_max_jacobi |> Strictly_positive_int.to_string) - (b.threshold_generators |> Threshold.to_string) - (b.threshold_selectors |> Threshold.to_string) - (b.read_wf |> Bool.to_string) (b.expected_s2 |> Positive_float.to_string) - (b.s2_eig |> Bool.to_string) (b.psi_coef |> Array.to_list |> List.map ~f:Det_coef.to_string |> String.concat ~sep:", ") (b.psi_det |> Array.to_list |> List.map ~f:(Determinant.to_string diff --git a/ocaml/Makefile b/ocaml/Makefile index eaa8e382..ce932bfc 100644 --- a/ocaml/Makefile +++ b/ocaml/Makefile @@ -35,7 +35,7 @@ default: $(ALL_TESTS) $(ALL_EXE) .gitignore executables: $(QPACKAGE_ROOT)/data/executables $(QPACKAGE_ROOT)/data/executables: - $(QPACKAGE_ROOT)/scripts/create_executables_list.sh + $(QPACKAGE_ROOT)/scripts/create/create_executables_list.sh external_libs: opam install cryptokit core diff --git a/ocaml/qp_create_ezfio_from_xyz.ml b/ocaml/qp_create_ezfio_from_xyz.ml index dfc9b4bd..8370fb1f 100644 --- a/ocaml/qp_create_ezfio_from_xyz.ml +++ b/ocaml/qp_create_ezfio_from_xyz.ml @@ -5,18 +5,20 @@ open Core.Std;; let spec = let open Command.Spec in empty - +> flag "o" (optional string) + +> flag "o" (optional string) ~doc:"file Name of the created EZFIO file." +> flag "b" (required string) ~doc:"string Name of basis set." +> flag "c" (optional_with_default 0 int) ~doc:"int Total charge of the molecule. Default is 0." - +> flag "m" (optional_with_default 1 int) + +> flag "m" (optional_with_default 1 int) ~doc:"int Spin multiplicity (2S+1) of the molecule. Default is 1." + +> flag "p" (optional_with_default 0 int) + ~doc:"Using pseudo. Default is not (aka 0)" +> anon ("xyz_file" %: string) ;; -let run ?o b c m xyz_file = +let run ?o b c m p xyz_file = (* Read molecule *) let molecule = @@ -60,8 +62,12 @@ let run ?o b c m xyz_file = | None -> (* Principal basis *) let basis = elem_and_basis_name in let command = + if (p = 0) then Qpackage.root ^ "/scripts/get_basis.sh \"" ^ temp_filename ^ "\" \"" ^ basis ^"\"" + else + Qpackage.root ^ "/scripts/get_basis.sh \"" ^ temp_filename + ^ "\" \"" ^ basis ^"\" pseudo" in begin let filename = @@ -246,7 +252,10 @@ let run ?o b c m xyz_file = Ezfio.set_ao_basis_ao_expo(Ezfio.ezfio_array_of_list ~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_expo) ; - + + (* Doesn't work... *) + (* if p = 1 then Qpackage.root ^ "scripts/pseudo/put_pseudo_in_ezfio.py" ezfio_file.to_string; *) + match Input.Ao_basis.read () with | None -> failwith "Error in basis" | Some x -> Input.Ao_basis.write x @@ -266,8 +275,8 @@ elements can be defined as follows: ") spec - (fun o b c m xyz_file () -> - run ?o b c m xyz_file ) + (fun o b c m p xyz_file () -> + run ?o b c m p xyz_file ) ;; let () = diff --git a/scripts/.gitignore b/scripts/.gitignore index 52e4e611..e456a8d3 100644 --- a/scripts/.gitignore +++ b/scripts/.gitignore @@ -1,2 +1,3 @@ *.pyc *.pyo +docopt.py \ No newline at end of file diff --git a/scripts/check_dependencies.sh b/scripts/check_dependencies.sh deleted file mode 100755 index f21dbc40..00000000 --- a/scripts/check_dependencies.sh +++ /dev/null @@ -1,63 +0,0 @@ -#!/bin/bash -# -# usage: -# check_dependencies.sh MOs AOs Electrons -# -# Checks that the list of dependencies given in -# argument is consistent. If the dependencies -# are OK the exit code is 0, otherwise it is 1. -# If no argument is given, the dependencies are -# read in the Makefile. -# Thu Apr 3 01:44:23 CEST 2014 - -if [[ -z ${QPACKAGE_ROOT} ]] -then - print "The QPACKAGE_ROOT environment variable is not set." - print "Please reload the quantum_package.rc file." - exit -1 -fi -source ${QPACKAGE_ROOT}/scripts/qp_include.sh - -if [[ -z $1 ]] -then - exit 0 -fi - -if [[ $1 == "-" ]] -then - COMMAND_LINE=$(cat NEEDED_MODULES) -else - COMMAND_LINE=$(unique_list $@) -fi - -for d in $COMMAND_LINE -do - if [[ ! -d ${QPACKAGE_ROOT}/src/$d ]] - then - echo Error: Directory $d does not exist - exit 2 - fi - -done - -DEPS_LONG="" -for i in $COMMAND_LINE -do - DEPS_LONG+=" $i " - DEPS_LONG+=$(cat "${QPACKAGE_ROOT}/src/${i}/NEEDED_MODULES") -done - -DEPS=$(unique_list $DEPS_LONG) - -if [[ ! "$COMMAND_LINE" == "$DEPS" ]] -then - DEPS=$(${QPACKAGE_ROOT}/scripts/check_dependencies.sh ${DEPS}) -fi -echo "$DEPS" - -if [[ "$COMMAND_LINE" == "$DEPS" ]] -then - exit 0 -else - exit 1 -fi diff --git a/scripts/docopt.py b/scripts/docopt.py deleted file mode 100755 index 59830d53..00000000 --- a/scripts/docopt.py +++ /dev/null @@ -1,590 +0,0 @@ -"""Pythonic command-line interface parser that will make you smile. - - * http://docopt.org - * Repository and issue-tracker: https://github.com/docopt/docopt - * Licensed under terms of MIT license (see LICENSE-MIT) - * Copyright (c) 2013 Vladimir Keleshev, vladimir@keleshev.com - -""" -import sys -import re - - -__all__ = ['docopt'] -__version__ = '0.6.1' - - -class DocoptLanguageError(Exception): - - """Error in construction of usage-message by developer.""" - - -class DocoptExit(SystemExit): - - """Exit in case user invoked program with incorrect arguments.""" - - usage = '' - - def __init__(self, message=''): - SystemExit.__init__(self, (message + '\n' + self.usage).strip()) - - -class Pattern(object): - - def __eq__(self, other): - return repr(self) == repr(other) - - def __hash__(self): - return hash(repr(self)) - - def fix(self): - self.fix_identities() - self.fix_repeating_arguments() - return self - - def fix_identities(self, uniq=None): - """Make pattern-tree tips point to same object if they are equal.""" - if not hasattr(self, 'children'): - return self - uniq = list(set(self.flat())) if uniq is None else uniq - for i, child in enumerate(self.children): - if not hasattr(child, 'children'): - assert child in uniq - self.children[i] = uniq[uniq.index(child)] - else: - child.fix_identities(uniq) - - def fix_repeating_arguments(self): - """Fix elements that should accumulate/increment values.""" - either = [list(child.children) for child in transform(self).children] - for case in either: - for e in [child for child in case if case.count(child) > 1]: - if isinstance( - e, - Argument) or isinstance( - e, - Option) and e.argcount: - if e.value is None: - e.value = [] - elif not isinstance(e.value, list): - e.value = e.value.split() - if isinstance( - e, - Command) or isinstance( - e, - Option) and e.argcount == 0: - e.value = 0 - return self - - -def transform(pattern): - """Expand pattern into an (almost) equivalent one, but with single Either. - - Example: ((-a | -b) (-c | -d)) => (-a -c | -a -d | -b -c | -b -d) - Quirks: [-a] => (-a), (-a...) => (-a -a) - - """ - result = [] - groups = [[pattern]] - while groups: - children = groups.pop(0) - parents = [Required, Optional, OptionsShortcut, Either, OneOrMore] - if any(t in map(type, children) for t in parents): - child = [c for c in children if type(c) in parents][0] - children.remove(child) - if isinstance(child, Either): - for c in child.children: - groups.append([c] + children) - elif isinstance(child, OneOrMore): - groups.append(child.children * 2 + children) - else: - groups.append(child.children + children) - else: - result.append(children) - return Either(*[Required(*e) for e in result]) - - -class LeafPattern(Pattern): - - """Leaf/terminal node of a pattern tree.""" - - def __init__(self, name, value=None): - self.name, self.value = name, value - - def __repr__(self): - return '%s(%r, %r)' % (self.__class__.__name__, self.name, self.value) - - def flat(self, *types): - return [self] if not types or type(self) in types else [] - - def match(self, left, collected=None): - collected = [] if collected is None else collected - pos, match = self.single_match(left) - if match is None: - return False, left, collected - left_ = left[:pos] + left[pos + 1:] - same_name = [a for a in collected if a.name == self.name] - if type(self.value) in (int, list): - if isinstance(self.value, int): - increment = 1 - else: - increment = ([match.value] if isinstance(match.value, str) - else match.value) - if not same_name: - match.value = increment - return True, left_, collected + [match] - same_name[0].value += increment - return True, left_, collected - return True, left_, collected + [match] - - -class BranchPattern(Pattern): - - """Branch/inner node of a pattern tree.""" - - def __init__(self, *children): - self.children = list(children) - - def __repr__(self): - return '%s(%s)' % (self.__class__.__name__, - ', '.join(repr(a) for a in self.children)) - - def flat(self, *types): - if type(self) in types: - return [self] - return sum([child.flat(*types) for child in self.children], []) - - -class Argument(LeafPattern): - - def single_match(self, left): - for n, pattern in enumerate(left): - if isinstance(pattern, Argument): - return n, Argument(self.name, pattern.value) - return None, None - - @classmethod - def parse(class_, source): - name = re.findall('(<\S*?>)', source)[0] - value = re.findall('\[default: (.*)\]', source, flags=re.I) - return class_(name, value[0] if value else None) - - -class Command(Argument): - - def __init__(self, name, value=False): - self.name, self.value = name, value - - def single_match(self, left): - for n, pattern in enumerate(left): - if isinstance(pattern, Argument): - if pattern.value == self.name: - return n, Command(self.name, True) - else: - break - return None, None - - -class Option(LeafPattern): - - def __init__(self, short=None, long=None, argcount=0, value=False): - assert argcount in (0, 1) - self.short, self.long, self.argcount = short, long, argcount - self.value = None if value is False and argcount else value - - @classmethod - def parse(class_, option_description): - short, long, argcount, value = None, None, 0, False - options, _, description = option_description.strip().partition(' ') - options = options.replace(',', ' ').replace('=', ' ') - for s in options.split(): - if s.startswith('--'): - long = s - elif s.startswith('-'): - short = s - else: - argcount = 1 - if argcount: - matched = re.findall('\[default: (.*)\]', description, flags=re.I) - value = matched[0] if matched else None - return class_(short, long, argcount, value) - - def single_match(self, left): - for n, pattern in enumerate(left): - if self.name == pattern.name: - return n, pattern - return None, None - - @property - def name(self): - return self.long or self.short - - def __repr__(self): - return 'Option(%r, %r, %r, %r)' % (self.short, self.long, - self.argcount, self.value) - - -class Required(BranchPattern): - - def match(self, left, collected=None): - collected = [] if collected is None else collected - l = left - c = collected - for pattern in self.children: - matched, l, c = pattern.match(l, c) - if not matched: - return False, left, collected - return True, l, c - - -class Optional(BranchPattern): - - def match(self, left, collected=None): - collected = [] if collected is None else collected - for pattern in self.children: - m, left, collected = pattern.match(left, collected) - return True, left, collected - - -class OptionsShortcut(Optional): - - """Marker/placeholder for [options] shortcut.""" - - -class OneOrMore(BranchPattern): - - def match(self, left, collected=None): - assert len(self.children) == 1 - collected = [] if collected is None else collected - l = left - c = collected - l_ = None - matched = True - times = 0 - while matched: - # could it be that something didn't match but changed l or c? - matched, l, c = self.children[0].match(l, c) - times += 1 if matched else 0 - if l_ == l: - break - l_ = l - if times >= 1: - return True, l, c - return False, left, collected - - -class Either(BranchPattern): - - def match(self, left, collected=None): - collected = [] if collected is None else collected - outcomes = [] - for pattern in self.children: - matched, _, _ = outcome = pattern.match(left, collected) - if matched: - outcomes.append(outcome) - if outcomes: - return min(outcomes, key=lambda outcome: len(outcome[1])) - return False, left, collected - - -class Tokens(list): - - def __init__(self, source, error=DocoptExit): - self += source.split() if hasattr(source, 'split') else source - self.error = error - - @staticmethod - def from_pattern(source): - source = re.sub(r'([\[\]\(\)\|]|\.\.\.)', r' \1 ', source) - source = [s for s in re.split('\s+|(\S*<.*?>)', source) if s] - return Tokens(source, error=DocoptLanguageError) - - def move(self): - return self.pop(0) if len(self) else None - - def current(self): - return self[0] if len(self) else None - - -def parse_long(tokens, options): - """long ::= '--' chars [ ( ' ' | '=' ) chars ] ;""" - long, eq, value = tokens.move().partition('=') - assert long.startswith('--') - value = None if eq == value == '' else value - similar = [o for o in options if o.long == long] - if tokens.error is DocoptExit and similar == []: # if no exact match - similar = [o for o in options if o.long and o.long.startswith(long)] - if len(similar) > 1: # might be simply specified ambiguously 2+ times? - raise tokens.error('%s is not a unique prefix: %s?' % - (long, ', '.join(o.long for o in similar))) - elif len(similar) < 1: - argcount = 1 if eq == '=' else 0 - o = Option(None, long, argcount) - options.append(o) - if tokens.error is DocoptExit: - o = Option(None, long, argcount, value if argcount else True) - else: - o = Option(similar[0].short, similar[0].long, - similar[0].argcount, similar[0].value) - if o.argcount == 0: - if value is not None: - raise tokens.error('%s must not have an argument' % o.long) - else: - if value is None: - if tokens.current() in [None, '--']: - raise tokens.error('%s requires argument' % o.long) - value = tokens.move() - if tokens.error is DocoptExit: - o.value = value if value is not None else True - return [o] - - -def parse_shorts(tokens, options): - """shorts ::= '-' ( chars )* [ [ ' ' ] chars ] ;""" - token = tokens.move() - assert token.startswith('-') and not token.startswith('--') - left = token.lstrip('-') - parsed = [] - while left != '': - short, left = '-' + left[0], left[1:] - similar = [o for o in options if o.short == short] - if len(similar) > 1: - raise tokens.error('%s is specified ambiguously %d times' % - (short, len(similar))) - elif len(similar) < 1: - o = Option(short, None, 0) - options.append(o) - if tokens.error is DocoptExit: - o = Option(short, None, 0, True) - else: # why copying is necessary here? - o = Option(short, similar[0].long, - similar[0].argcount, similar[0].value) - value = None - if o.argcount != 0: - if left == '': - if tokens.current() in [None, '--']: - raise tokens.error('%s requires argument' % short) - value = tokens.move() - else: - value = left - left = '' - if tokens.error is DocoptExit: - o.value = value if value is not None else True - parsed.append(o) - return parsed - - -def parse_pattern(source, options): - tokens = Tokens.from_pattern(source) - result = parse_expr(tokens, options) - if tokens.current() is not None: - raise tokens.error('unexpected ending: %r' % ' '.join(tokens)) - return Required(*result) - - -def parse_expr(tokens, options): - """expr ::= seq ( '|' seq )* ;""" - seq = parse_seq(tokens, options) - if tokens.current() != '|': - return seq - result = [Required(*seq)] if len(seq) > 1 else seq - while tokens.current() == '|': - tokens.move() - seq = parse_seq(tokens, options) - result += [Required(*seq)] if len(seq) > 1 else seq - return [Either(*result)] if len(result) > 1 else result - - -def parse_seq(tokens, options): - """seq ::= ( atom [ '...' ] )* ;""" - result = [] - while tokens.current() not in [None, ']', ')', '|']: - atom = parse_atom(tokens, options) - if tokens.current() == '...': - atom = [OneOrMore(*atom)] - tokens.move() - result += atom - return result - - -def parse_atom(tokens, options): - """atom ::= '(' expr ')' | '[' expr ']' | 'options' - | long | shorts | argument | command ; - """ - token = tokens.current() - result = [] - if token in '([': - tokens.move() - matching, pattern = {'(': [')', Required], '[': [']', Optional]}[token] - result = pattern(*parse_expr(tokens, options)) - if tokens.move() != matching: - raise tokens.error("unmatched '%s'" % token) - return [result] - elif token == 'options': - tokens.move() - return [OptionsShortcut()] - elif token.startswith('--') and token != '--': - return parse_long(tokens, options) - elif token.startswith('-') and token not in ('-', '--'): - return parse_shorts(tokens, options) - elif token.startswith('<') and token.endswith('>') or token.isupper(): - return [Argument(tokens.move())] - else: - return [Command(tokens.move())] - - -def parse_argv(tokens, options, options_first=False): - """Parse command-line argument vector. - - If options_first: - argv ::= [ long | shorts ]* [ argument ]* [ '--' [ argument ]* ] ; - else: - argv ::= [ long | shorts | argument ]* [ '--' [ argument ]* ] ; - - """ - parsed = [] - while tokens.current() is not None: - if tokens.current() == '--': - return parsed + [Argument(None, v) for v in tokens] - elif tokens.current().startswith('--'): - parsed += parse_long(tokens, options) - elif tokens.current().startswith('-') and tokens.current() != '-': - parsed += parse_shorts(tokens, options) - elif options_first: - return parsed + [Argument(None, v) for v in tokens] - else: - parsed.append(Argument(None, tokens.move())) - return parsed - - -def parse_defaults(doc): - defaults = [] - for s in parse_section('options:', doc): - # FIXME corner case "bla: options: --foo" - _, _, s = s.partition(':') # get rid of "options:" - split = re.split('\n[ \t]*(-\S+?)', '\n' + s)[1:] - split = [s1 + s2 for s1, s2 in zip(split[::2], split[1::2])] - options = [Option.parse(s) for s in split if s.startswith('-')] - defaults += options - return defaults - - -def parse_section(name, source): - pattern = re.compile('^([^\n]*' + name + '[^\n]*\n?(?:[ \t].*?(?:\n|$))*)', - re.IGNORECASE | re.MULTILINE) - return [s.strip() for s in pattern.findall(source)] - - -def formal_usage(section): - _, _, section = section.partition(':') # drop "usage:" - pu = section.split() - return '( ' + ' '.join(') | (' if s == pu[0] else s for s in pu[1:]) + ' )' - - -def extras(help, version, options, doc): - if help and any((o.name in ('-h', '--help')) and o.value for o in options): - print(doc.strip("\n")) - sys.exit() - if version and any(o.name == '--version' and o.value for o in options): - print(version) - sys.exit() - - -class Dict(dict): - - def __repr__(self): - return '{%s}' % ',\n '.join('%r: %r' % i for i in sorted(self.items())) - - -def docopt(doc, argv=None, help=True, version=None, options_first=False): - """Parse `argv` based on command-line interface described in `doc`. - - `docopt` creates your command-line interface based on its - description that you pass as `doc`. Such description can contain - --options, , commands, which could be - [optional], (required), (mutually | exclusive) or repeated... - - Parameters - ---------- - doc : str - Description of your command-line interface. - argv : list of str, optional - Argument vector to be parsed. sys.argv[1:] is used if not - provided. - help : bool (default: True) - Set to False to disable automatic help on -h or --help - options. - version : any object - If passed, the object will be printed if --version is in - `argv`. - options_first : bool (default: False) - Set to True to require options precede positional arguments, - i.e. to forbid options and positional arguments intermix. - - Returns - ------- - args : dict - A dictionary, where keys are names of command-line elements - such as e.g. "--verbose" and "", and values are the - parsed values of those elements. - - Example - ------- - >>> from docopt import docopt - >>> doc = ''' - ... Usage: - ... my_program tcp [--timeout=] - ... my_program serial [--baud=] [--timeout=] - ... my_program (-h | --help | --version) - ... - ... Options: - ... -h, --help Show this screen and exit. - ... --baud= Baudrate [default: 9600] - ... ''' - >>> argv = ['tcp', '127.0.0.1', '80', '--timeout', '30'] - >>> docopt(doc, argv) - {'--baud': '9600', - '--help': False, - '--timeout': '30', - '--version': False, - '': '127.0.0.1', - '': '80', - 'serial': False, - 'tcp': True} - - See also - -------- - * For video introduction see http://docopt.org - * Full documentation is available in README.rst as well as online - at https://github.com/docopt/docopt#readme - - """ - argv = sys.argv[1:] if argv is None else argv - - usage_sections = parse_section('usage:', doc) - if len(usage_sections) == 0: - raise DocoptLanguageError('"usage:" (case-insensitive) not found.') - if len(usage_sections) > 1: - raise DocoptLanguageError('More than one "usage:" (case-insensitive).') - DocoptExit.usage = usage_sections[0] - - options = parse_defaults(doc) - pattern = parse_pattern(formal_usage(DocoptExit.usage), options) - # [default] syntax for argument is disabled - # for a in pattern.flat(Argument): - # same_name = [d for d in arguments if d.name == a.name] - # if same_name: - # a.value = same_name[0].value - argv = parse_argv(Tokens(argv), list(options), options_first) - pattern_options = set(pattern.flat(Option)) - for options_shortcut in pattern.flat(OptionsShortcut): - doc_options = parse_defaults(doc) - options_shortcut.children = list(set(doc_options) - pattern_options) - # if any_options: - # options_shortcut.children += [Option(o.short, o.long, o.argcount) - # for o in argv if type(o) is Option] - extras(help, version, argv, doc) - matched, left, collected = pattern.fix().match(argv) - if matched and left == []: # better error message if left? - return Dict((a.name, a.value) for a in (pattern.flat() + collected)) - raise DocoptExit() diff --git a/scripts/ezfio_interface/ei_handler.py b/scripts/ezfio_interface/ei_handler.py index a02b13d5..6d18d071 100755 --- a/scripts/ezfio_interface/ei_handler.py +++ b/scripts/ezfio_interface/ei_handler.py @@ -70,9 +70,9 @@ def is_bool(str_): Take a string, if is a bool return the conversion into fortran and ocaml. """ - if "true" in str_.lower(): + if "true" in str_.strip().lower(): return Type(None, "true", ".True.") - elif "false" in str_.lower(): + elif "false" in str_.strip().lower(): return Type(None, "false", ".False") else: raise TypeError @@ -112,6 +112,8 @@ def get_type_dict(): # ~#~#~#~#~#~#~#~ # fancy_type['integer'] = Type(None, "int", "integer") + fancy_type['integer*8'] = Type(None, "int", "integer*8") + fancy_type['int'] = Type(None, "int", "integer") fancy_type['float'] = Type(None, "float", "double precision") @@ -121,7 +123,7 @@ def get_type_dict(): fancy_type['bool'] = Type(None, "bool", "logical") fancy_type['character*(32)'] = Type(None, "string", "character*(32)") - fancy_type['character*(60)'] = Type(None, "string", "character*(60)") + fancy_type['character*(64)'] = Type(None, "string", "character*(68)") fancy_type['character*(256)'] = Type(None, "string", "character*(256)") # ~#~#~#~#~#~#~#~ # @@ -203,7 +205,7 @@ def get_dict_config_file(config_file_path, module_lower): - ezfio_name : Will be the name of the file - ezfio_dir : Will be the folder who containt the ezfio_name * /ezfio_dir/ezfio_name - * equal to MODULE_lower name for the moment. + * equal to MODULE_lower name by default. - interface : The provider is a imput or a output - default : The default value /!\ stored in a Type named type! if interface == output @@ -216,7 +218,7 @@ def get_dict_config_file(config_file_path, module_lower): d = defaultdict(dict) l_info_required = ["doc", "interface"] - l_info_optional = ["ezfio_name", "size"] + l_info_optional = ["ezfio_dir", "ezfio_name", "size"] # ~#~#~#~#~#~#~#~#~#~#~ # # L o a d _ C o n f i g # @@ -238,10 +240,8 @@ def get_dict_config_file(config_file_path, module_lower): pvd = section.lower() # Create the dictionary who containt the value per default - d_default = {"ezfio_name": pvd} - - # Set the ezfio_dir - d[pvd]["ezfio_dir"] = module_lower + d_default = {"ezfio_name": pvd, + "ezfio_dir": module_lower} # Check if type if avalaible type_ = config_file.get(section, "type") @@ -269,7 +269,7 @@ def get_dict_config_file(config_file_path, module_lower): d[pvd][option] = d_default[option] # If interface is input we need a default value information - if d[pvd]["interface"] == "input": + if d[pvd]["interface"].lower() == "input": try: default_raw = config_file.get(section, "default") except ConfigParser.NoOptionError: @@ -294,6 +294,7 @@ def create_ezfio_provider(dict_ezfio_cfg): default size} create the a list who containt all the code for the provider + output = output_dict_info['ezfio_dir' return [code, ...] """ from ezfio_generate_provider import EZFIO_Provider diff --git a/scripts/ezfio_interface/ezfio_generate_ocaml.py b/scripts/ezfio_interface/ezfio_generate_ocaml.py index 25b6c55f..37b6c6ad 100755 --- a/scripts/ezfio_interface/ezfio_generate_ocaml.py +++ b/scripts/ezfio_interface/ezfio_generate_ocaml.py @@ -1,7 +1,13 @@ #!/usr/bin/env python +""" +This programme generate all the +ocaml template needed by qp_edit + +You can see `ezfio_generate_provider.py` +for an example of utilisation +""" import sys -import os # If type in **kwargs from ei_handler import Type diff --git a/scripts/ezfio_interface/ezfio_generate_provider.py b/scripts/ezfio_interface/ezfio_generate_provider.py index af4fcd6a..7f3c8441 100755 --- a/scripts/ezfio_interface/ezfio_generate_provider.py +++ b/scripts/ezfio_interface/ezfio_generate_provider.py @@ -45,7 +45,7 @@ END_PROVIDER self.set_write() for v in self.values: if not v: - msg = "Error : %s is not set in ezfio_with_default.py" % (v) + msg = "Error : %s is not set in EZFIO.cfg" % (v) print >>sys.stderr, msg sys.exit(1) return self.data % self.__dict__ diff --git a/scripts/prepare_ezfio.sh b/scripts/ezfio_interface/prepare_ezfio.sh similarity index 100% rename from scripts/prepare_ezfio.sh rename to scripts/ezfio_interface/prepare_ezfio.sh diff --git a/scripts/ezfio_interface/qp_convert_ezfio_v1_to_v2.sh b/scripts/ezfio_interface/qp_convert_ezfio_v1_to_v2.sh new file mode 100755 index 00000000..3ef9a5f3 --- /dev/null +++ b/scripts/ezfio_interface/qp_convert_ezfio_v1_to_v2.sh @@ -0,0 +1,36 @@ +#!/bin/bash +# Convert a old ezfio file (with option.irp.f ezfio_default) +# into a new EZFIO.cfg type + +# Hartree Fock +# Changin the case, don't know if is needed or not + +echo "Will tranform qp_v1.*_ezfio to qp_v2.*_ezfio" +echo "All action are irrevocable! And is by choice" +echo "You need to stop to use a old version! Plz..." + +echo "Change thresh_SCF > thresh_scf0" +mv $1/hartree_Fock/thresh_SCF $1/hartree_fock/thresh_scf 2> /dev/null + +# Set disk_acess +echo "Change {read,write}_ao_integrals > disk_access_ao_integrals" + +biint=$1/bielec_integrals + +if [[ -f $biint/read_ao_integrals ]]; then + if [[ `cat $1/bielec_integrals/read_ao_integrals` -eq "T" ]] + then + echo "Read" > $biint/disk_access_ao_integrals + + elif [[ `cat $biint/write_ao_integrals` -eq "T" ]] + then + echo "Write" > $biint/disk_access_ao_integrals + + else + echo "None" > $biint/disk_access_ao_integrals + + fi + rm $biint/read_ao_integrals $biint/write_ao_integrals $biint/write_ao_intergals 2> /dev/null +fi + +echo "Done" \ No newline at end of file diff --git a/scripts/ezfio_interface/qp_convert_output_to_ezfio.py b/scripts/ezfio_interface/qp_convert_output_to_ezfio.py new file mode 100755 index 00000000..400def37 --- /dev/null +++ b/scripts/ezfio_interface/qp_convert_output_to_ezfio.py @@ -0,0 +1,302 @@ +#!/usr/bin/env python +""" +This function acceep + +Usage: + qp_convert_output_to_ezfio.py [--ezfio=] + +Option: + file.out is the file to check (like gamess.out) + folder.ezfio is the name you whant for the ezfio + (by default is file.out.ezfio) + +""" + + +import sys +import os +from functools import reduce + + +# ~#~#~#~#~#~#~#~ # +# Add to the path # +# ~#~#~#~#~#~#~#~ # + + +try: + QPACKAGE_ROOT = os.environ["QPACKAGE_ROOT"] +except: + print "Error: QPACKAGE_ROOT environment variable not found." + sys.exit(1) +else: + sys.path = [QPACKAGE_ROOT + "/EZFIO/Python", + QPACKAGE_ROOT + "/resultsFile", + QPACKAGE_ROOT + "/scripts"] + sys.path + +# ~#~#~#~#~#~ # +# I m p o r t # +# ~#~#~#~#~#~ # + +from ezfio import ezfio + + +try: + from resultsFile import * +except: + print "Error: resultsFile Python library not installed" + sys.exit(1) + +from docopt import docopt + +# _ +# |_ ._ _ _|_ o _ ._ +# | |_| | | (_ |_ | (_) | | +# + + +def write_ezfio(res, filename): + + res.clean_uncontractions() + ezfio.set_file(filename) + + # _ + # |_ | _ _ _|_ ._ _ ._ _ + # |_ | (/_ (_ |_ | (_) | | _> + # + ezfio.set_electrons_elec_alpha_num(res.num_alpha) + ezfio.set_electrons_elec_beta_num(res.num_beta) + + # + # |\ | _ | _ o + # | \| |_| (_ | (/_ | + # + + # ~#~#~#~ # + # I n i t # + # ~#~#~#~ # + + charge = [] + coord_x = [] + coord_y = [] + coord_z = [] + + # ~#~#~#~#~#~#~ # + # P a r s i n g # + # ~#~#~#~#~#~#~ # + + for a in res.geometry: + charge.append(a.charge) + if res.units == 'BOHR': + coord_x.append(a.coord[0]) + coord_y.append(a.coord[1]) + coord_z.append(a.coord[2]) + else: + coord_x.append(a.coord[0] / a0) + coord_y.append(a.coord[1] / a0) + coord_z.append(a.coord[2] / a0) + + # ~#~#~#~#~ # + # W r i t e # + # ~#~#~#~#~ # + + ezfio.set_nuclei_nucl_num(len(res.geometry)) + ezfio.set_nuclei_nucl_charge(charge) + + # Transformt H1 into H + import re + p = re.compile(ur'(\d*)$') + label = [p.sub("", x.name).capitalize() for x in res.geometry] + ezfio.set_nuclei_nucl_label(label) + + ezfio.set_nuclei_nucl_coord(coord_x + coord_y + coord_z) + + # _ + # /\ _ _ |_) _. _ o _ + # /--\ (_) _> |_) (_| _> | _> + # + + # ~#~#~#~ # + # I n i t # + # ~#~#~#~ # + + import string + at = [] + num_prim = [] + power_x = [] + power_y = [] + power_z = [] + coefficient = [] + exponent = [] + + res.clean_contractions() + res.convert_to_cartesian() + + # ~#~#~#~#~#~#~ # + # P a r s i n g # + # ~#~#~#~#~#~#~ # + + for b in res.basis: + c = b.center + for i, atom in enumerate(res.geometry): + if atom.coord == c: + at.append(i + 1) + num_prim.append(len(b.prim)) + s = b.sym + power_x.append(string.count(s, "x")) + power_y.append(string.count(s, "y")) + power_z.append(string.count(s, "z")) + coefficient.append(b.coef) + exponent.append([p.expo for p in b.prim]) + + # ~#~#~#~#~ # + # W r i t e # + # ~#~#~#~#~ # + + ezfio.set_ao_basis_ao_num(len(res.basis)) + ezfio.set_ao_basis_ao_nucl(at) + ezfio.set_ao_basis_ao_prim_num(num_prim) + ezfio.set_ao_basis_ao_power(power_x + power_y + power_z) + + # ~#~#~#~#~#~#~ # + # P a r s i n g # + # ~#~#~#~#~#~#~ # + + prim_num_max = ezfio.get_ao_basis_ao_prim_num_max() + + for i in range(len(res.basis)): + coefficient[ + i] += [0. for j in range(len(coefficient[i]), prim_num_max)] + exponent[i] += [0. for j in range(len(exponent[i]), prim_num_max)] + + coefficient = reduce(lambda x, y: x + y, coefficient, []) + exponent = reduce(lambda x, y: x + y, exponent, []) + + coef = [] + expo = [] + for i in range(prim_num_max): + for j in range(i, len(coefficient), prim_num_max): + coef.append(coefficient[j]) + expo.append(exponent[j]) + + # ~#~#~#~#~ # + # W r i t e # + # ~#~#~#~#~ # + + ezfio.set_ao_basis_ao_coef(coef) + ezfio.set_ao_basis_ao_expo(expo) + ezfio.set_ao_basis_ao_basis("Read by resultsFile") + + # _ + # |\/| _ _ |_) _. _ o _ + # | | (_) _> |_) (_| _> | _> + # + + # ~#~#~#~ # + # I n i t # + # ~#~#~#~ # + + MoTag = res.determinants_mo_type + ezfio.set_mo_basis_mo_label('Orthonormalized') + MO_type = MoTag + allMOs = res.mo_sets[MO_type] + + # ~#~#~#~#~#~#~ # + # P a r s i n g # + # ~#~#~#~#~#~#~ # + + try: + closed = [(allMOs[i].eigenvalue, i) for i in res.closed_mos] + active = [(allMOs[i].eigenvalue, i) for i in res.active_mos] + virtual = [(allMOs[i].eigenvalue, i) for i in res.virtual_mos] + except: + closed = [] + virtual = [] + active = [(allMOs[i].eigenvalue, i) for i in range(len(allMOs))] + + closed = map(lambda x: x[1], closed) + active = map(lambda x: x[1], active) + virtual = map(lambda x: x[1], virtual) + MOindices = closed + active + virtual + + MOs = [] + for i in MOindices: + MOs.append(allMOs[i]) + + mo_tot_num = len(MOs) + while len(MOindices) < mo_tot_num: + MOindices.append(len(MOindices)) + + MOmap = list(MOindices) + for i in range(len(MOindices)): + MOmap[i] = MOindices.index(i) + + energies = [] + for i in xrange(mo_tot_num): + energies.append(MOs[i].eigenvalue) + + if res.occ_num is not None: + OccNum = [] + for i in MOindices: + OccNum.append(res.occ_num[MO_type][i]) + + while len(OccNum) < mo_tot_num: + OccNum.append(0.) + + MoMatrix = [] + sym0 = [i.sym for i in res.mo_sets[MO_type]] + sym = [i.sym for i in res.mo_sets[MO_type]] + for i in xrange(len(sym)): + sym[MOmap[i]] = sym0[i] + + MoMatrix = [] + for i in xrange(len(MOs)): + m = MOs[i] + for coef in m.vector: + MoMatrix.append(coef) + + while len(MoMatrix) < len(MOs[0].vector) ** 2: + MoMatrix.append(0.) + + # ~#~#~#~#~ # + # W r i t e # + # ~#~#~#~#~ # + + ezfio.set_mo_basis_mo_tot_num(mo_tot_num) + ezfio.set_mo_basis_mo_occ(OccNum) + ezfio.set_mo_basis_mo_coef(MoMatrix) + + # ______ _ + # | ___ \ | | + # | |_/ /__ ___ _ _ __| | ___ + # | __/ __|/ _ \ | | |/ _` |/ _ \ + # | | \__ \ __/ |_| | (_| | (_) | + # \_| |___/\___|\__,_|\__,_|\___/ + # + + ezfio.set_pseudo_integrals_do_pseudo(False) + + +def get_full_path(file_path): + file_path = os.path.expanduser(file_path) + file_path = os.path.expandvars(file_path) + file_path = os.path.abspath(file_path) + return file_path + +if __name__ == '__main__': + arguments = docopt(__doc__) + + file_ = get_full_path(arguments['']) + + if arguments["--ezfio"]: + ezfio_file = get_full_path(arguments["--ezfio"]) + else: + ezfio_file = "{0}.ezfio".format(file_) + + try: + res_file = getFile(file_) + except: + raise + else: + print file_, 'recognized as', str(res_file).split('.')[-1].split()[0] + + write_ezfio(res_file, ezfio_file) diff --git a/scripts/ezfio_interface/qp_edit_template b/scripts/ezfio_interface/qp_edit_template index 8d52acfd..2990a193 100644 --- a/scripts/ezfio_interface/qp_edit_template +++ b/scripts/ezfio_interface/qp_edit_template @@ -4,14 +4,16 @@ open Core.Std;; (** Interactive editing of the input. -@author A. Scemama +WARNING +This file is autogenerad by +`${{QP_ROOT}}/script/ezfio_interface/ei_handler.py` *) (** Keywords used to define input sections *) type keyword = | Ao_basis -| Determinants +| Determinants_by_hand | Electrons | Mo_basis | Nuclei @@ -20,11 +22,11 @@ type keyword = let keyword_to_string = function -| Ao_basis -> "AO basis" -| Determinants -> "Determinants" -| Electrons -> "Electrons" -| Mo_basis -> "MO basis" -| Nuclei -> "Molecule" +| Ao_basis -> "AO basis" +| Determinants_by_hand -> "Determinants_by_hand" +| Electrons -> "Electrons" +| Mo_basis -> "MO basis" +| Nuclei -> "Molecule" {keywords_to_string} ;; @@ -72,8 +74,8 @@ let get s = f Nuclei.(read, to_rst) | Ao_basis -> f Ao_basis.(read, to_rst) - | Determinants -> - f Determinants.(read, to_rst) + | Determinants_by_hand -> + f Determinants_by_hand.(read, to_rst) {section_to_rst} end with @@ -114,7 +116,7 @@ let set str s = match s with {write} | Electrons -> write Electrons.(of_rst, write) s - | Determinants -> write Determinants.(of_rst, write) s + | Determinants_by_hand -> write Determinants_by_hand.(of_rst, write) s | Nuclei -> write Nuclei.(of_rst, write) s | Ao_basis -> () (* TODO *) | Mo_basis -> () (* TODO *) @@ -162,7 +164,7 @@ let run check_only ezfio_filename = Electrons ; {tasks} Mo_basis; - Determinants ; + Determinants_by_hand ; ] in diff --git a/scripts/ezfio_interface/upgrade_1.0_2.0.sh b/scripts/ezfio_interface/upgrade_1.0_2.0.sh new file mode 100755 index 00000000..ec0ab770 --- /dev/null +++ b/scripts/ezfio_interface/upgrade_1.0_2.0.sh @@ -0,0 +1,27 @@ +#!/bin/bash +# Convert a old ezfio file (with option.irp.f ezfio_default) +# into a new EZFIO.cfg type + +# Hartree Fock +# Changin the case, don't know if is needed or not +mv $1/Hartree_Fock $1/hartree_fock 2> /dev/null + +mv $1/hartree_Fock/thresh_SCF $1/hartree_fock/thresh_scf 2> /dev/null + +# BiInts +mv $1/bi_integrals $1/bielect_integrals 2> /dev/null + +if [ -f $1/bielect_integrals/read_ao_integrals ]; then + if [ `cat $1/bielect_integrals/read_ao_integrals` -eq "True" ] + then + echo "Read" > $1/bielect_integrals/disk_access_ao_integrals + + elif [ `cat bielect_integrals/write_ao_integrals` -eq "True" ] + then + echo "Write" > $1/bielect_integrals/disk_access_ao_integrals + + else + echo "None" > $1/bielect_integrals/disk_access_ao_integrals + + fi +fi \ No newline at end of file diff --git a/scripts/ezfio_with_default.py b/scripts/ezfio_with_default.py index 1b5f01a8..a2dfa430 100755 --- a/scripts/ezfio_with_default.py +++ b/scripts/ezfio_with_default.py @@ -90,13 +90,19 @@ END_PROVIDER self.default = t def get_default(self): - filename = '/'.join( [os.environ['QPACKAGE_ROOT'], 'data', - 'ezfio_defaults', - 'WILL_BE_DELETED.ezfio_default'] ) + mypath = '/'.join( [os.environ['QPACKAGE_ROOT'], 'data', + 'ezfio_defaults'] ) + + from os import listdir + from os.path import isfile, join + onlyfiles = [ join(mypath,f) for f in listdir(mypath) if isfile(join(mypath,f)) ] + + lines = [] + for filename in onlyfiles: + file = open(filename,'r') + lines.extend(file.readlines()) + file.close() - file = open(filename,'r') - lines = file.readlines() - file.close() k=-1 # Search directory for k,line in enumerate(lines): diff --git a/scripts/generate_h_apply.py b/scripts/generate_h_apply.py index 280c9f72..072a8f1e 100755 --- a/scripts/generate_h_apply.py +++ b/scripts/generate_h_apply.py @@ -1,7 +1,7 @@ #!/usr/bin/env python import os -file = open(os.environ["QPACKAGE_ROOT"]+'/src/Dets/H_apply_template.f','r') +file = open(os.environ["QPACKAGE_ROOT"]+'/src/Determinants/H_apply_template.f','r') template = file.read() file.close() @@ -104,7 +104,7 @@ class H_apply(object): endif SOFT_TOUCH psi_det psi_coef N_det """ - s["printout_now"] = """write(output_Dets,*) & + s["printout_now"] = """write(output_determinants,*) & 100.*float(i_generator)/float(N_det_generators), '% in ', wall_1-wall_0, 's'""" self.data = s @@ -211,9 +211,9 @@ class H_apply(object): delta_pt2(k) = 0.d0 pt2_old(k) = 0.d0 enddo - write(output_Dets,'(A12, X, A8, 3(2X, A9), 2X, A8, 2X, A8, 2X, A8)') & + write(output_determinants,'(A12, X, A8, 3(2X, A9), 2X, A8, 2X, A8, 2X, A8)') & 'N_generators', 'Norm', 'Delta PT2', 'PT2', 'Est. PT2', 'secs' - write(output_Dets,'(A12, X, A8, 3(2X, A9), 2X, A8, 2X, A8, 2X, A8)') & + write(output_determinants,'(A12, X, A8, 3(2X, A9), 2X, A8, 2X, A8, 2X, A8)') & '============', '========', '=========', '=========', '=========', & '=========' """ @@ -226,7 +226,7 @@ class H_apply(object): """ self.data["printout_now"] = """ do k=1,N_st - write(output_Dets,'(I10, 4(2X, F9.6), 2X, F8.1)') & + write(output_determinants,'(I10, 4(2X, F9.6), 2X, F8.1)') & i_generator, norm_psi(k), delta_pt2(k), pt2(k), & pt2(k)/(norm_psi(k)*norm_psi(k)), & wall_1-wall_0 @@ -258,7 +258,7 @@ class H_apply(object): ! SOFT_TOUCH psi_det psi_coef N_det selection_criterion_min = min(selection_criterion_min, maxval(select_max))*0.1d0 selection_criterion = selection_criterion_min - call write_double(output_Dets,selection_criterion,'Selection criterion') + call write_double(output_determinants,selection_criterion,'Selection criterion') """ self.data["keys_work"] = """ e_2_pert_buffer = 0.d0 diff --git a/scripts/get_basis.sh b/scripts/get_basis.sh index 51b0a4f0..a2f07e4e 100755 --- a/scripts/get_basis.sh +++ b/scripts/get_basis.sh @@ -42,9 +42,14 @@ then echo "ERROR" exit 1 fi -${EMSL_API_ROOT}/EMSL_api.py get_basis_data --treat_l --save --path="${tmpfile}" --basis="${basis}" $atoms - - +pseudo="$1" +shift +if [[ -z $pseudo ]] +then + ${EMSL_API_ROOT}/EMSL_api.py get_basis_data --treat_l --save --path="${tmpfile}" --basis="${basis}" +else + ${EMSL_API_ROOT}/EMSL_api.py get_basis_data --save --path="${tmpfile}" --basis="${basis}" --db_path="${EMSL_API_ROOT}/db/Pseudo.db" +fi diff --git a/scripts/install_curl.sh b/scripts/install/install_curl.sh similarity index 83% rename from scripts/install_curl.sh rename to scripts/install/install_curl.sh index 20033f77..b2e47481 100755 --- a/scripts/install_curl.sh +++ b/scripts/install/install_curl.sh @@ -8,8 +8,8 @@ CURL_URL="http://qmcchem.ups-tlse.fr/files/scemama/${CURL}.tar.bz2" if [[ -z ${QPACKAGE_ROOT} ]] then - print "The QPACKAGE_ROOT environment variable is not set." - print "Please reload the quantum_package.rc file." + echo "The QPACKAGE_ROOT environment variable is not set." + echo "Please reload the quantum_package.rc file." exit -1 fi diff --git a/scripts/install/install_docopt.sh b/scripts/install/install_docopt.sh new file mode 100755 index 00000000..6f799c47 --- /dev/null +++ b/scripts/install/install_docopt.sh @@ -0,0 +1,21 @@ +#!/bin/bash +# +# Installs docopt +# lundi 27 avril 2015, 16:51:34 (UTC+0200) + +DOCOPT="docopt.py" +DOCOPT_URL="https://raw.githubusercontent.com/docopt/docopt/master/${DOCOPT}" + +if [[ -z ${QPACKAGE_ROOT} ]] +then + echo "The QPACKAGE_ROOT environment variable is not set." + echo "Please reload the quantum_package.rc file." + exit -1 +fi + +cd ${QPACKAGE_ROOT} + +rm -f -- scripts/${DOCOPT}{,c} +${QPACKAGE_ROOT}/scripts/fetch_from_web.py ${DOCOPT_URL} ${DOCOPT} + +mv ${DOCOPT} scripts/${DOCOPT} \ No newline at end of file diff --git a/scripts/install_emsl.sh b/scripts/install/install_emsl.sh similarity index 79% rename from scripts/install_emsl.sh rename to scripts/install/install_emsl.sh index dff002a1..b01afb6e 100755 --- a/scripts/install_emsl.sh +++ b/scripts/install/install_emsl.sh @@ -8,8 +8,8 @@ URL="https://github.com/LCPQ/${BASE}/archive/master.tar.gz" if [[ -z ${QPACKAGE_ROOT} ]] then - print "The QPACKAGE_ROOT environment variable is not set." - print "Please reload the quantum_package.rc file." + echo "The QPACKAGE_ROOT environment variable is not set." + echo "Please reload the quantum_package.rc file." exit -1 fi diff --git a/scripts/install_ezfio.sh b/scripts/install/install_ezfio.sh similarity index 77% rename from scripts/install_ezfio.sh rename to scripts/install/install_ezfio.sh index 0f7a6505..c0033ca8 100755 --- a/scripts/install_ezfio.sh +++ b/scripts/install/install_ezfio.sh @@ -8,8 +8,8 @@ URL="https://github.com/LCPQ/${BASE}/archive/master.tar.gz" if [[ -z ${QPACKAGE_ROOT} ]] then - print "The QPACKAGE_ROOT environment variable is not set." - print "Please reload the quantum_package.rc file." + echo "The QPACKAGE_ROOT environment variable is not set." + echo "Please reload the quantum_package.rc file." exit -1 fi diff --git a/scripts/install_irpf90.sh b/scripts/install/install_irpf90.sh similarity index 100% rename from scripts/install_irpf90.sh rename to scripts/install/install_irpf90.sh diff --git a/scripts/install_m4.sh b/scripts/install/install_m4.sh similarity index 100% rename from scripts/install_m4.sh rename to scripts/install/install_m4.sh diff --git a/scripts/install_ocaml.sh b/scripts/install/install_ocaml.sh similarity index 100% rename from scripts/install_ocaml.sh rename to scripts/install/install_ocaml.sh diff --git a/scripts/install_resultsFile.sh b/scripts/install/install_resultsFile.sh similarity index 100% rename from scripts/install_resultsFile.sh rename to scripts/install/install_resultsFile.sh diff --git a/scripts/install_zlib.sh b/scripts/install/install_zlib.sh similarity index 100% rename from scripts/install_zlib.sh rename to scripts/install/install_zlib.sh diff --git a/scripts/build_modules.sh b/scripts/module/build_modules.sh similarity index 84% rename from scripts/build_modules.sh rename to scripts/module/build_modules.sh index c3e0cda5..1b69a920 100755 --- a/scripts/build_modules.sh +++ b/scripts/module/build_modules.sh @@ -30,7 +30,7 @@ Build failed for module $MODULE " fi fi - ${QPACKAGE_ROOT}/scripts/create_gitignore.sh + ${QPACKAGE_ROOT}/scripts/module/create_gitignore.sh cd ${OLDPWD} done -${QPACKAGE_ROOT}/scripts/create_executables_list.sh +${QPACKAGE_ROOT}/scripts/module/create_executables_list.sh diff --git a/scripts/clean_modules.sh b/scripts/module/clean_modules.sh similarity index 83% rename from scripts/clean_modules.sh rename to scripts/module/clean_modules.sh index cc25cede..608e0161 100755 --- a/scripts/clean_modules.sh +++ b/scripts/module/clean_modules.sh @@ -13,8 +13,9 @@ source ${QPACKAGE_ROOT}/scripts/qp_include.sh function do_clean() { rm -rf -- \ - IRPF90_temp IRPF90_man Makefile.depend $(cat NEEDED_MODULES) include \ - ezfio_interface.irp.f irpf90.make irpf90_entities tags $(ls_exe) + IRPF90_temp IRPF90_man Makefile.depend \ + $(module_handler.py print_genealogy) include \ + ezfio_interface.irp.f irpf90.make irpf90_entities tags $(ls_exe) *.mod } if [[ -z $1 ]] diff --git a/scripts/create_Makefile.sh b/scripts/module/create_Makefile.sh similarity index 100% rename from scripts/create_Makefile.sh rename to scripts/module/create_Makefile.sh diff --git a/scripts/create_Makefile_depend.sh b/scripts/module/create_Makefile_depend.sh similarity index 100% rename from scripts/create_Makefile_depend.sh rename to scripts/module/create_Makefile_depend.sh diff --git a/scripts/create_Needed_modules.sh b/scripts/module/create_Needed_modules.sh similarity index 77% rename from scripts/create_Needed_modules.sh rename to scripts/module/create_Needed_modules.sh index 026eadab..61ea5839 100755 --- a/scripts/create_Needed_modules.sh +++ b/scripts/module/create_Needed_modules.sh @@ -14,7 +14,9 @@ source ${QPACKAGE_ROOT}/scripts/qp_include.sh check_current_dir_is_module -OUTPUT=$(${QPACKAGE_ROOT}/scripts/check_dependencies.sh $@) -echo ${OUTPUT} > NEEDED_MODULES - +OUTPUT=$(module_handler.py check_dependencies $@) +if [[ $? -eq 0 ]] +then + echo $@ > NEEDED_CHILDREN_MODULES +fi \ No newline at end of file diff --git a/scripts/create_executables_list.sh b/scripts/module/create_executables_list.sh similarity index 100% rename from scripts/create_executables_list.sh rename to scripts/module/create_executables_list.sh diff --git a/scripts/create_gitignore.sh b/scripts/module/create_gitignore.sh similarity index 100% rename from scripts/create_gitignore.sh rename to scripts/module/create_gitignore.sh diff --git a/scripts/create_rst_templates.sh b/scripts/module/create_rst_templates.sh similarity index 100% rename from scripts/create_rst_templates.sh rename to scripts/module/create_rst_templates.sh diff --git a/scripts/module/module_handler.py b/scripts/module/module_handler.py new file mode 100755 index 00000000..3bc1d0e4 --- /dev/null +++ b/scripts/module/module_handler.py @@ -0,0 +1,202 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +""" +Create the NEEDED_MODULE + aka the genealogy (children module, subchildren module and so on), +of a NEEDED_CHILDREN_MODULES file + +Usage: + module_handler.py print_genealogy [] + module_handler.py check_dependencies [...] + module_handler.py create_png [] + +Options: + print_genealogy Print the genealogy of the NEEDED_CHILDREN_MODULES + aka (children, subchildren, etc) + create_png Create a png of the file + NEEDED_CHILDREN_MODULES The path of NEEDED_CHILDREN_MODULES + by default try to open the file in the current path +""" + +from docopt import docopt + +import os +import sys +import os.path +from functools import wraps + + +def cache(func): + """ + A decorator for lazy evaluation off true function + """ + saved = {} + + @wraps(func) + def newfunc(*args): + if args in saved: + return saved[args] + + result = func(*args) + saved[args] = result + return result + return newfunc + + +@cache +def get_dict_genealogy(): + """Loop over MODULE in QPACKAGE_ROOT/src, open all the NEEDED_CHILDREN_MODULES + and create a dict[MODULE] = [sub module needed, ...] + """ + d_ref = dict() + + qpackage_root = os.environ['QPACKAGE_ROOT'] + dir_ = os.path.join(qpackage_root, 'src') + + for o in os.listdir(dir_): + + try: + with open(os.path.join(dir_, o, "NEEDED_CHILDREN_MODULES"), "r") as f: + l_children = f.read().split() + except IOError: + pass + else: + d_ref[o] = l_children + + return d_ref + + +def module_genealogy(path): + """ + Take a name of a NEEDED_CHILDREN_MODULES + and return a list of all the {sub, subsub, ...}children + """ + try: + with open(path, "r") as f: + l_children = f.read().split() + except IOError as e: + print >> sys.stderr, e + sys.exit(1) + else: + + needed_module = get_it_and_children(l_children) + + return needed_module + + +def get_it_and_children(l_module): + """ + From a list of module return the module and all of the genealogy + """ + d_ref = get_dict_genealogy() + + l = [] + for module in l_module: + if module not in l: + l.append(module) + try: + l.extend(get_it_and_children(d_ref[module])) + except KeyError: + print >> sys.stderr, "`{0}` in not a good submodule name".format(module) + print >> sys.stderr, "Check the corresponding NEEDED_CHILDREN_MODULES" + sys.exit(1) + + return list(set(l)) + + +def get_all_children(l_module): + """ + From a list of module return all the genealogy + """ + + it_and_all = get_it_and_children(l_module) + return [children for children in it_and_all if children not in l_module] + + +def reduce_(l_module): + """ + Take a l_module and try to find the lower combinaitions + of module with the same genealogy + """ + import itertools + d_ref = get_dict_genealogy() + + target_genealogy = sorted(get_all_children(l_module)) + + for i in xrange(len(d_ref)): + for c in itertools.combinations(d_ref, i): + + guess_genealogy = sorted(get_it_and_children(d_ref, c)) + + if target_genealogy == guess_genealogy: + return c + + +def create_png_from_path(path): + " Change a path like this into a module list" + "path = /home/razoa/quantum_package/src/Molden/NEEDED_CHILDREN_MODULES" + + l_module = os.path.split(path)[0].split("/")[-1] + create_png([l_module]) + + +def create_png(l_module): + """Create the png of the dependancy tree for a l_module""" + + # Init + import pydot + all_ready_done = [] + + def draw_module_edge(module, l_children): + "Draw all the module recursifly" + + if module not in all_ready_done: + for children in l_children: + # Add Edge + edge = pydot.Edge(module, children) + graph.add_edge(edge) + # Recurs + draw_module_edge(children, d_ref[children]) + all_ready_done.append(module) + + # Init + graph = pydot.Dot(graph_type='digraph') + d_ref = get_dict_genealogy() + + # Create all the edge + for module in l_module: + node_a = pydot.Node(module, fontcolor="red") + graph.add_node(node_a) + draw_module_edge(module, d_ref[module]) + + # Save + path = '{0}.png'.format("_".join(l_module)) + print "png saved in {0}".format(path) + graph.write_png(path) + +if __name__ == '__main__': + + arguments = docopt(__doc__) + + if not arguments['']: + dir_ = os.getcwd() + path = os.path.join(dir_, "NEEDED_CHILDREN_MODULES") + else: + path = os.path.abspath(arguments['']) + path = os.path.expanduser(path) + path = os.path.expandvars(path) + + if arguments['print_genealogy']: + l_all_needed_molule = module_genealogy(path) + print " ".join(sorted(l_all_needed_molule)) + + elif arguments["check_dependencies"]: + l_module = arguments[''] + if l_module: + l_all_needed_molule = get_it_and_children(l_module) + else: + l_all_needed_molule = module_genealogy(path) + + elif arguments["create_png"]: + create_png_from_path(path) diff --git a/scripts/module/pydot.py b/scripts/module/pydot.py new file mode 100644 index 00000000..c788c137 --- /dev/null +++ b/scripts/module/pydot.py @@ -0,0 +1,2125 @@ +# -*- coding: Latin-1 -*- +"""Graphviz's dot language Python interface. + +This module provides with a full interface to create handle modify +and process graphs in Graphviz's dot language. + +References: + +pydot Homepage: http://code.google.com/p/pydot/ +Graphviz: http://www.graphviz.org/ +DOT Language: http://www.graphviz.org/doc/info/lang.html + +Programmed and tested with Graphviz 2.26.3 and Python 2.6 on OSX 10.6.4 + +Copyright (c) 2005-2011 Ero Carrera + +Distributed under MIT license [http://opensource.org/licenses/mit-license.html]. +""" + +__author__ = 'Ero Carrera' +__version__ = '1.0.*' +__license__ = 'MIT' + +import os +import re +import subprocess +import tempfile +import copy +import sys + +try: + import dot_parser +except Exception as e: + print >> sys.stderr, "Couldn't import dot_parser, loading of dot files will not be possible." + + +GRAPH_ATTRIBUTES = set(['Damping', 'K', 'URL', 'aspect', 'bb', 'bgcolor', + 'center', 'charset', 'clusterrank', 'colorscheme', 'comment', 'compound', + 'concentrate', 'defaultdist', 'dim', 'dimen', 'diredgeconstraints', + 'dpi', 'epsilon', 'esep', 'fontcolor', 'fontname', 'fontnames', + 'fontpath', 'fontsize', 'id', 'label', 'labeljust', 'labelloc', + 'landscape', 'layers', 'layersep', 'layout', 'levels', 'levelsgap', + 'lheight', 'lp', 'lwidth', 'margin', 'maxiter', 'mclimit', 'mindist', + 'mode', 'model', 'mosek', 'nodesep', 'nojustify', 'normalize', 'nslimit', + 'nslimit1', 'ordering', 'orientation', 'outputorder', 'overlap', + 'overlap_scaling', 'pack', 'packmode', 'pad', 'page', 'pagedir', + 'quadtree', 'quantum', 'rankdir', 'ranksep', 'ratio', 'remincross', + 'repulsiveforce', 'resolution', 'root', 'rotate', 'searchsize', 'sep', + 'showboxes', 'size', 'smoothing', 'sortv', 'splines', 'start', + 'stylesheet', 'target', 'truecolor', 'viewport', 'voro_margin', + # for subgraphs + 'rank']) + + +EDGE_ATTRIBUTES = set(['URL', + 'arrowhead', + 'arrowsize', + 'arrowtail', + 'color', + 'colorscheme', + 'comment', + 'constraint', + 'decorate', + 'dir', + 'edgeURL', + 'edgehref', + 'edgetarget', + 'edgetooltip', + 'fontcolor', + 'fontname', + 'fontsize', + 'headURL', + 'headclip', + 'headhref', + 'headlabel', + 'headport', + 'headtarget', + 'headtooltip', + 'href', + 'id', + 'label', + 'labelURL', + 'labelangle', + 'labeldistance', + 'labelfloat', + 'labelfontcolor', + 'labelfontname', + 'labelfontsize', + 'labelhref', + 'labeltarget', + 'labeltooltip', + 'layer', + 'len', + 'lhead', + 'lp', + 'ltail', + 'minlen', + 'nojustify', + 'penwidth', + 'pos', + 'samehead', + 'sametail', + 'showboxes', + 'style', + 'tailURL', + 'tailclip', + 'tailhref', + 'taillabel', + 'tailport', + 'tailtarget', + 'tailtooltip', + 'target', + 'tooltip', + 'weight', + 'rank']) + + +NODE_ATTRIBUTES = set(['URL', 'color', 'colorscheme', 'comment', + 'distortion', 'fillcolor', 'fixedsize', 'fontcolor', 'fontname', + 'fontsize', 'group', 'height', 'id', 'image', 'imagescale', 'label', + 'labelloc', 'layer', 'margin', 'nojustify', 'orientation', 'penwidth', + 'peripheries', 'pin', 'pos', 'rects', 'regular', 'root', 'samplepoints', + 'shape', 'shapefile', 'showboxes', 'sides', 'skew', 'sortv', 'style', + 'target', 'tooltip', 'vertices', 'width', 'z', + # The following are attributes dot2tex + 'texlbl', 'texmode']) + + +CLUSTER_ATTRIBUTES = set(['K', + 'URL', + 'bgcolor', + 'color', + 'colorscheme', + 'fillcolor', + 'fontcolor', + 'fontname', + 'fontsize', + 'label', + 'labeljust', + 'labelloc', + 'lheight', + 'lp', + 'lwidth', + 'nojustify', + 'pencolor', + 'penwidth', + 'peripheries', + 'sortv', + 'style', + 'target', + 'tooltip']) + + +# +# Extented version of ASPN's Python Cookbook Recipe: +# Frozen dictionaries. +# http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/414283 +# +# This version freezes dictionaries used as values within dictionaries. +# +class frozendict(dict): + + def _blocked_attribute(obj): + raise AttributeError("A frozendict cannot be modified.") + _blocked_attribute = property(_blocked_attribute) + + __delitem__ = __setitem__ = clear = _blocked_attribute + pop = popitem = setdefault = update = _blocked_attribute + + def __new__(cls, *args, **kw): + new = dict.__new__(cls) + + args_ = [] + for arg in args: + if isinstance(arg, dict): + arg = copy.copy(arg) + for k, v in arg.iteritems(): + if isinstance(v, frozendict): + arg[k] = v + elif isinstance(v, dict): + arg[k] = frozendict(v) + elif isinstance(v, list): + v_ = list() + for elm in v: + if isinstance(elm, dict): + v_.append(frozendict(elm)) + else: + v_.append(elm) + arg[k] = tuple(v_) + args_.append(arg) + else: + args_.append(arg) + + dict.__init__(new, *args_, **kw) + return new + + def __init__(self, *args, **kw): + pass + + def __hash__(self): + try: + return self._cached_hash + except AttributeError: + h = self._cached_hash = hash(tuple(sorted(self.iteritems()))) + return h + + def __repr__(self): + return "frozendict(%s)" % dict.__repr__(self) + + +dot_keywords = ['graph', 'subgraph', 'digraph', 'node', 'edge', 'strict'] + +id_re_alpha_nums = re.compile('^[_a-zA-Z][a-zA-Z0-9_,]*$', re.UNICODE) +id_re_alpha_nums_with_ports = re.compile( + '^[_a-zA-Z][a-zA-Z0-9_,:\"]*[a-zA-Z0-9_,\"]+$', + re.UNICODE) +id_re_num = re.compile('^[0-9,]+$', re.UNICODE) +id_re_with_port = re.compile('^([^:]*):([^:]*)$', re.UNICODE) +id_re_dbl_quoted = re.compile('^\".*\"$', re.S | re.UNICODE) +id_re_html = re.compile('^<.*>$', re.S | re.UNICODE) + + +def needs_quotes(s): + """Checks whether a string is a dot language ID. + + It will check whether the string is solely composed + by the characters allowed in an ID or not. + If the string is one of the reserved keywords it will + need quotes too but the user will need to add them + manually. + """ + + # If the name is a reserved keyword it will need quotes but pydot + # can't tell when it's being used as a keyword or when it's simply + # a name. Hence the user needs to supply the quotes when an element + # would use a reserved keyword as name. This function will return + # false indicating that a keyword string, if provided as-is, won't + # need quotes. + if s in dot_keywords: + return False + + chars = [ord(c) for c in s if ord(c) > 0x7f or ord(c) == 0] + if chars and not id_re_dbl_quoted.match(s) and not id_re_html.match(s): + return True + + for test_re in [ + id_re_alpha_nums, + id_re_num, + id_re_dbl_quoted, + id_re_html, + id_re_alpha_nums_with_ports]: + if test_re.match(s): + return False + + m = id_re_with_port.match(s) + if m: + return needs_quotes(m.group(1)) or needs_quotes(m.group(2)) + + return True + + +def quote_if_necessary(s): + + if isinstance(s, bool): + if s is True: + return 'True' + return 'False' + + if not isinstance(s, basestring): + return s + + if not s: + return s + + if needs_quotes(s): + replace = {'"': r'\"', + "\n": r'\n', + "\r": r'\r'} + for (a, b) in replace.items(): + s = s.replace(a, b) + + return '"' + s + '"' + + return s + + +def graph_from_dot_data(data): + """Load graph as defined by data in DOT format. + + The data is assumed to be in DOT format. It will + be parsed and a Dot class will be returned, + representing the graph. + """ + + return dot_parser.parse_dot_data(data) + + +def graph_from_dot_file(path): + """Load graph as defined by a DOT file. + + The file is assumed to be in DOT format. It will + be loaded, parsed and a Dot class will be returned, + representing the graph. + """ + + fd = file(path, 'rb') + data = fd.read() + fd.close() + + return graph_from_dot_data(data) + + +def graph_from_edges(edge_list, node_prefix='', directed=False): + """Creates a basic graph out of an edge list. + + The edge list has to be a list of tuples representing + the nodes connected by the edge. + The values can be anything: bool, int, float, str. + + If the graph is undirected by default, it is only + calculated from one of the symmetric halves of the matrix. + """ + + if directed: + graph = Dot(graph_type='digraph') + + else: + graph = Dot(graph_type='graph') + + for edge in edge_list: + + if isinstance(edge[0], str): + src = node_prefix + edge[0] + else: + src = node_prefix + str(edge[0]) + + if isinstance(edge[1], str): + dst = node_prefix + edge[1] + else: + dst = node_prefix + str(edge[1]) + + e = Edge(src, dst) + graph.add_edge(e) + + return graph + + +def graph_from_adjacency_matrix(matrix, node_prefix=u'', directed=False): + """Creates a basic graph out of an adjacency matrix. + + The matrix has to be a list of rows of values + representing an adjacency matrix. + The values can be anything: bool, int, float, as long + as they can evaluate to True or False. + """ + + node_orig = 1 + + if directed: + graph = Dot(graph_type='digraph') + else: + graph = Dot(graph_type='graph') + + for row in matrix: + if not directed: + skip = matrix.index(row) + r = row[skip:] + else: + skip = 0 + r = row + node_dest = skip + 1 + + for e in r: + if e: + graph.add_edge( + Edge(node_prefix + node_orig, + node_prefix + node_dest)) + node_dest += 1 + node_orig += 1 + + return graph + + +def graph_from_incidence_matrix(matrix, node_prefix='', directed=False): + """Creates a basic graph out of an incidence matrix. + + The matrix has to be a list of rows of values + representing an incidence matrix. + The values can be anything: bool, int, float, as long + as they can evaluate to True or False. + """ + + node_orig = 1 + + if directed: + graph = Dot(graph_type='digraph') + else: + graph = Dot(graph_type='graph') + + for row in matrix: + nodes = [] + c = 1 + + for node in row: + if node: + nodes.append(c * node) + c += 1 + nodes.sort() + + if len(nodes) == 2: + graph.add_edge( + Edge(node_prefix + abs(nodes[0]), + node_prefix + nodes[1])) + + if not directed: + graph.set_simplify(True) + + return graph + + +def __find_executables(path): + """Used by find_graphviz + + path - single directory as a string + + If any of the executables are found, it will return a dictionary + containing the program names as keys and their paths as values. + + Otherwise returns None + """ + + success = False + progs = { + 'dot': '', + 'twopi': '', + 'neato': '', + 'circo': '', + 'fdp': '', + 'sfdp': ''} + + was_quoted = False + path = path.strip() + if path.startswith('"') and path.endswith('"'): + path = path[1:-1] + was_quoted = True + + if os.path.isdir(path): + + for prg in progs.iterkeys(): + + if progs[prg]: + continue + + if os.path.exists(os.path.join(path, prg)): + + if was_quoted: + progs[prg] = '"' + os.path.join(path, prg) + '"' + else: + progs[prg] = os.path.join(path, prg) + + success = True + + elif os.path.exists(os.path.join(path, prg + '.exe')): + + if was_quoted: + progs[prg] = '"' + os.path.join(path, prg + '.exe') + '"' + else: + progs[prg] = os.path.join(path, prg + '.exe') + + success = True + + if success: + + return progs + + else: + + return None + + +# The multi-platform version of this 'find_graphviz' function was +# contributed by Peter Cock +# +def find_graphviz(): + """Locate Graphviz's executables in the system. + + Tries three methods: + + First: Windows Registry (Windows only) + This requires Mark Hammond's pywin32 is installed. + + Secondly: Search the path + It will look for 'dot', 'twopi' and 'neato' in all the directories + specified in the PATH environment variable. + + Thirdly: Default install location (Windows only) + It will look for 'dot', 'twopi' and 'neato' in the default install + location under the "Program Files" directory. + + It will return a dictionary containing the program names as keys + and their paths as values. + + If this fails, it returns None. + """ + + # Method 1 (Windows only) + # + if os.sys.platform == 'win32': + + HKEY_LOCAL_MACHINE = 0x80000002 + KEY_QUERY_VALUE = 0x0001 + + RegOpenKeyEx = None + RegQueryValueEx = None + RegCloseKey = None + + try: + import win32api + import win32con + RegOpenKeyEx = win32api.RegOpenKeyEx + RegQueryValueEx = win32api.RegQueryValueEx + RegCloseKey = win32api.RegCloseKey + + except ImportError: + # Print a messaged suggesting they install these? + # + pass + + try: + import ctypes + + def RegOpenKeyEx(key, subkey, opt, sam): + result = ctypes.c_uint(0) + ctypes.windll.advapi32.RegOpenKeyExA( + key, + subkey, + opt, + sam, + ctypes.byref(result)) + return result.value + + def RegQueryValueEx(hkey, valuename): + data_type = ctypes.c_uint(0) + data_len = ctypes.c_uint(1024) + data = ctypes.create_string_buffer(1024) + + res = ctypes.windll.advapi32.RegQueryValueExA( + hkey, + valuename, + 0, + ctypes.byref(data_type), + data, + ctypes.byref(data_len)) + + return data.value + + RegCloseKey = ctypes.windll.advapi32.RegCloseKey + + except ImportError: + # Print a messaged suggesting they install these? + # + pass + + if RegOpenKeyEx is not None: + + # Get the GraphViz install path from the registry + # + hkey = None + potentialKeys = [ + "SOFTWARE\\ATT\\Graphviz", + "SOFTWARE\\AT&T Research Labs\\Graphviz", + ] + for potentialKey in potentialKeys: + + try: + hkey = RegOpenKeyEx(HKEY_LOCAL_MACHINE, + potentialKey, 0, KEY_QUERY_VALUE) + + if hkey is not None: + path = RegQueryValueEx(hkey, "InstallPath") + RegCloseKey(hkey) + + # The regitry variable might exist, left by old installations + # but with no value, in those cases we keep + # searching... + if not path: + continue + + # Now append the "bin" subdirectory: + # + path = os.path.join(path, "bin") + progs = __find_executables(path) + if progs is not None: + # print "Used Windows registry" + return progs + + except Exception as excp: + #raise excp + pass + else: + break + + # Method 2 (Linux, Windows etc) + # + if 'PATH' in os.environ: + + for path in os.environ['PATH'].split(os.pathsep): + progs = __find_executables(path) + if progs is not None: + # print "Used path" + return progs + + # Method 3 (Windows only) + # + if os.sys.platform == 'win32': + + # Try and work out the equivalent of "C:\Program Files" on this + # machine (might be on drive D:, or in a different language) + # + + if 'PROGRAMFILES' in os.environ: + + # Note, we could also use the win32api to get this + # information, but win32api may not be installed. + + path = os.path.join( + os.environ['PROGRAMFILES'], + 'ATT', + 'GraphViz', + 'bin') + + else: + + # Just in case, try the default... + path = r"C:\Program Files\att\Graphviz\bin" + + progs = __find_executables(path) + + if progs is not None: + + # print "Used default install location" + return progs + + for path in ( + '/usr/bin', '/usr/local/bin', + '/opt/local/bin', + '/opt/bin', '/sw/bin', '/usr/share', + '/Applications/Graphviz.app/Contents/MacOS/'): + + progs = __find_executables(path) + if progs is not None: + # print "Used path" + return progs + + # Failed to find GraphViz + # + return None + + +class Common: + + """Common information to several classes. + + Should not be directly used, several classes are derived from + this one. + """ + + def __getstate__(self): + + dict = copy.copy(self.obj_dict) + + return dict + + def __setstate__(self, state): + + self.obj_dict = state + + def __get_attribute__(self, attr): + """Look for default attributes for this node""" + + attr_val = self.obj_dict['attributes'].get(attr, None) + + if attr_val is None: + # get the defaults for nodes/edges + + default_node_name = self.obj_dict['type'] + + # The defaults for graphs are set on a node named 'graph' + if default_node_name in ('subgraph', 'digraph', 'cluster'): + default_node_name = 'graph' + + g = self.get_parent_graph() + if g is not None: + defaults = g.get_node(default_node_name) + else: + return None + + # Multiple defaults could be set by having repeated 'graph [...]' + # 'node [...]', 'edge [...]' statements. In such case, if the + # same attribute is set in different statements, only the first + # will be returned. In order to get all, one would call the + # get_*_defaults() methods and handle those. Or go node by node + # (of the ones specifying defaults) and modify the attributes + # individually. + # + if not isinstance(defaults, (list, tuple)): + defaults = [defaults] + + for default in defaults: + attr_val = default.obj_dict['attributes'].get(attr, None) + if attr_val: + return attr_val + else: + return attr_val + + return None + + def set_parent_graph(self, parent_graph): + + self.obj_dict['parent_graph'] = parent_graph + + def get_parent_graph(self): + + return self.obj_dict.get('parent_graph', None) + + def set(self, name, value): + """Set an attribute value by name. + + Given an attribute 'name' it will set its value to 'value'. + There's always the possibility of using the methods: + + set_'name'(value) + + which are defined for all the existing attributes. + """ + + self.obj_dict['attributes'][name] = value + + def get(self, name): + """Get an attribute value by name. + + Given an attribute 'name' it will get its value. + There's always the possibility of using the methods: + + get_'name'() + + which are defined for all the existing attributes. + """ + + return self.obj_dict['attributes'].get(name, None) + + def get_attributes(self): + """""" + + return self.obj_dict['attributes'] + + def set_sequence(self, seq): + + self.obj_dict['sequence'] = seq + + def get_sequence(self): + + return self.obj_dict['sequence'] + + def create_attribute_methods(self, obj_attributes): + + # for attr in self.obj_dict['attributes']: + for attr in obj_attributes: + + # Generate all the Setter methods. + # + self.__setattr__( + 'set_' + + attr, + lambda x, + a=attr: self.obj_dict['attributes'].__setitem__( + a, + x)) + + # Generate all the Getter methods. + # + self.__setattr__( + 'get_' + attr, + lambda a=attr: self.__get_attribute__(a)) + + +class Error(Exception): + + """General error handling class. + """ + + def __init__(self, value): + self.value = value + + def __str__(self): + return self.value + + +class InvocationException(Exception): + + """To indicate that a ploblem occurred while running any of the GraphViz executables. + """ + + def __init__(self, value): + self.value = value + + def __str__(self): + return self.value + + +class Node(object, Common): + + """A graph node. + + This class represents a graph's node with all its attributes. + + node(name, attribute=value, ...) + + name: node's name + + All the attributes defined in the Graphviz dot language should + be supported. + """ + + def __init__(self, name='', obj_dict=None, **attrs): + + # + # Nodes will take attributes of all other types because the defaults + # for any GraphViz object are dealt with as if they were Node definitions + # + + if obj_dict is not None: + + self.obj_dict = obj_dict + + else: + + self.obj_dict = dict() + + # Copy the attributes + # + self.obj_dict['attributes'] = dict(attrs) + self.obj_dict['type'] = 'node' + self.obj_dict['parent_graph'] = None + self.obj_dict['parent_node_list'] = None + self.obj_dict['sequence'] = None + + # Remove the compass point + # + port = None + if isinstance(name, basestring) and not name.startswith('"'): + idx = name.find(':') + if idx > 0 and idx + 1 < len(name): + name, port = name[:idx], name[idx:] + + if isinstance(name, (long, int)): + name = str(name) + + self.obj_dict['name'] = quote_if_necessary(name) + self.obj_dict['port'] = port + + self.create_attribute_methods(NODE_ATTRIBUTES) + + def set_name(self, node_name): + """Set the node's name.""" + + self.obj_dict['name'] = node_name + + def get_name(self): + """Get the node's name.""" + + return self.obj_dict['name'] + + def get_port(self): + """Get the node's port.""" + + return self.obj_dict['port'] + + def add_style(self, style): + + styles = self.obj_dict['attributes'].get('style', None) + if not styles and style: + styles = [style] + else: + styles = styles.split(',') + styles.append(style) + + self.obj_dict['attributes']['style'] = ','.join(styles) + + def to_string(self): + """Returns a string representation of the node in dot language. + """ + + # RMF: special case defaults for node, edge and graph properties. + # + node = quote_if_necessary(self.obj_dict['name']) + + node_attr = list() + + for attr, value in self.obj_dict['attributes'].iteritems(): + if value is not None: + node_attr.append('%s=%s' % (attr, quote_if_necessary(value))) + else: + node_attr.append(attr) + + # No point in having nodes setting any defaults if the don't set + # any attributes... + # + if node in ('graph', 'node', 'edge') and len(node_attr) == 0: + return '' + + node_attr = ', '.join(node_attr) + + if node_attr: + node += ' [' + node_attr + ']' + + return node + ';' + + +class Edge(object, Common): + + """A graph edge. + + This class represents a graph's edge with all its attributes. + + edge(src, dst, attribute=value, ...) + + src: source node's name + dst: destination node's name + + All the attributes defined in the Graphviz dot language should + be supported. + + Attributes can be set through the dynamically generated methods: + + set_[attribute name], i.e. set_label, set_fontname + + or directly by using the instance's special dictionary: + + Edge.obj_dict['attributes'][attribute name], i.e. + + edge_instance.obj_dict['attributes']['label'] + edge_instance.obj_dict['attributes']['fontname'] + + """ + + def __init__(self, src='', dst='', obj_dict=None, **attrs): + + if isinstance(src, (list, tuple)) and dst == '': + src, dst = src + + if obj_dict is not None: + + self.obj_dict = obj_dict + + else: + + self.obj_dict = dict() + + # Copy the attributes + # + self.obj_dict['attributes'] = dict(attrs) + self.obj_dict['type'] = 'edge' + self.obj_dict['parent_graph'] = None + self.obj_dict['parent_edge_list'] = None + self.obj_dict['sequence'] = None + + if isinstance(src, Node): + src = src.get_name() + + if isinstance(dst, Node): + dst = dst.get_name() + + points = (quote_if_necessary(src), quote_if_necessary(dst)) + + self.obj_dict['points'] = points + + self.create_attribute_methods(EDGE_ATTRIBUTES) + + def get_source(self): + """Get the edges source node name.""" + + return self.obj_dict['points'][0] + + def get_destination(self): + """Get the edge's destination node name.""" + + return self.obj_dict['points'][1] + + def __hash__(self): + + return hash(hash(self.get_source()) + hash(self.get_destination())) + + def __eq__(self, edge): + """Compare two edges. + + If the parent graph is directed, arcs linking + node A to B are considered equal and A->B != B->A + + If the parent graph is undirected, any edge + connecting two nodes is equal to any other + edge connecting the same nodes, A->B == B->A + """ + + if not isinstance(edge, Edge): + raise Error("Can't compare and edge to a non-edge object.") + + if self.get_parent_graph().get_top_graph_type() == 'graph': + + # If the graph is undirected, the edge has neither + # source nor destination. + # + if ((self.get_source() == edge.get_source() and self.get_destination() == edge.get_destination()) or ( + edge.get_source() == self.get_destination() and edge.get_destination() == self.get_source())): + return True + + else: + + if self.get_source() == edge.get_source( + ) and self.get_destination() == edge.get_destination(): + return True + + return False + + def parse_node_ref(self, node_str): + + if not isinstance(node_str, str): + return node_str + + if node_str.startswith('"') and node_str.endswith('"'): + + return node_str + + node_port_idx = node_str.rfind(':') + + if node_port_idx > 0 and node_str[0] == '"' and node_str[ + node_port_idx - + 1] == '"': + + return node_str + + if node_port_idx > 0: + + a = node_str[:node_port_idx] + b = node_str[node_port_idx + 1:] + + node = quote_if_necessary(a) + + node += ':' + quote_if_necessary(b) + + return node + + return node_str + + def to_string(self): + """Returns a string representation of the edge in dot language. + """ + + src = self.parse_node_ref(self.get_source()) + dst = self.parse_node_ref(self.get_destination()) + + if isinstance(src, frozendict): + edge = [Subgraph(obj_dict=src).to_string()] + elif isinstance(src, (int, long)): + edge = [str(src)] + else: + edge = [src] + + if (self.get_parent_graph() and + self.get_parent_graph().get_top_graph_type() and + self.get_parent_graph().get_top_graph_type() == 'digraph'): + + edge.append('->') + + else: + edge.append('--') + + if isinstance(dst, frozendict): + edge.append(Subgraph(obj_dict=dst).to_string()) + elif isinstance(dst, (int, long)): + edge.append(str(dst)) + else: + edge.append(dst) + + edge_attr = list() + + for attr, value in self.obj_dict['attributes'].iteritems(): + + if value is not None: + edge_attr.append('%s=%s' % (attr, quote_if_necessary(value))) + else: + edge_attr.append(attr) + + edge_attr = ', '.join(edge_attr) + + if edge_attr: + edge.append(' [' + edge_attr + ']') + + return ' '.join(edge) + ';' + + +class Graph(object, Common): + + """Class representing a graph in Graphviz's dot language. + + This class implements the methods to work on a representation + of a graph in Graphviz's dot language. + + graph( graph_name='G', graph_type='digraph', + strict=False, suppress_disconnected=False, attribute=value, ...) + + graph_name: + the graph's name + graph_type: + can be 'graph' or 'digraph' + suppress_disconnected: + defaults to False, which will remove from the + graph any disconnected nodes. + simplify: + if True it will avoid displaying equal edges, i.e. + only one edge between two nodes. removing the + duplicated ones. + + All the attributes defined in the Graphviz dot language should + be supported. + + Attributes can be set through the dynamically generated methods: + + set_[attribute name], i.e. set_size, set_fontname + + or using the instance's attributes: + + Graph.obj_dict['attributes'][attribute name], i.e. + + graph_instance.obj_dict['attributes']['label'] + graph_instance.obj_dict['attributes']['fontname'] + """ + + def __init__( + self, + graph_name='G', + obj_dict=None, + graph_type='digraph', + strict=False, + suppress_disconnected=False, + simplify=False, + **attrs): + + if obj_dict is not None: + self.obj_dict = obj_dict + + else: + + self.obj_dict = dict() + + self.obj_dict['attributes'] = dict(attrs) + + if graph_type not in ['graph', 'digraph']: + raise Error( + 'Invalid type "%s". Accepted graph types are: graph, digraph, subgraph' % + graph_type) + + self.obj_dict['name'] = quote_if_necessary(graph_name) + self.obj_dict['type'] = graph_type + + self.obj_dict['strict'] = strict + self.obj_dict['suppress_disconnected'] = suppress_disconnected + self.obj_dict['simplify'] = simplify + + self.obj_dict['current_child_sequence'] = 1 + self.obj_dict['nodes'] = dict() + self.obj_dict['edges'] = dict() + self.obj_dict['subgraphs'] = dict() + + self.set_parent_graph(self) + + self.create_attribute_methods(GRAPH_ATTRIBUTES) + + def get_graph_type(self): + + return self.obj_dict['type'] + + def get_top_graph_type(self): + + parent = self + while True: + parent_ = parent.get_parent_graph() + if parent_ == parent: + break + parent = parent_ + + return parent.obj_dict['type'] + + def set_graph_defaults(self, **attrs): + + self.add_node(Node('graph', **attrs)) + + def get_graph_defaults(self, **attrs): + + graph_nodes = self.get_node('graph') + + if isinstance(graph_nodes, (list, tuple)): + return [node.get_attributes() for node in graph_nodes] + + return graph_nodes.get_attributes() + + def set_node_defaults(self, **attrs): + + self.add_node(Node('node', **attrs)) + + def get_node_defaults(self, **attrs): + + graph_nodes = self.get_node('node') + + if isinstance(graph_nodes, (list, tuple)): + return [node.get_attributes() for node in graph_nodes] + + return graph_nodes.get_attributes() + + def set_edge_defaults(self, **attrs): + + self.add_node(Node('edge', **attrs)) + + def get_edge_defaults(self, **attrs): + + graph_nodes = self.get_node('edge') + + if isinstance(graph_nodes, (list, tuple)): + return [node.get_attributes() for node in graph_nodes] + + return graph_nodes.get_attributes() + + def set_simplify(self, simplify): + """Set whether to simplify or not. + + If True it will avoid displaying equal edges, i.e. + only one edge between two nodes. removing the + duplicated ones. + """ + + self.obj_dict['simplify'] = simplify + + def get_simplify(self): + """Get whether to simplify or not. + + Refer to set_simplify for more information. + """ + + return self.obj_dict['simplify'] + + def set_type(self, graph_type): + """Set the graph's type, 'graph' or 'digraph'.""" + + self.obj_dict['type'] = graph_type + + def get_type(self): + """Get the graph's type, 'graph' or 'digraph'.""" + + return self.obj_dict['type'] + + def set_name(self, graph_name): + """Set the graph's name.""" + + self.obj_dict['name'] = graph_name + + def get_name(self): + """Get the graph's name.""" + + return self.obj_dict['name'] + + def set_strict(self, val): + """Set graph to 'strict' mode. + + This option is only valid for top level graphs. + """ + + self.obj_dict['strict'] = val + + def get_strict(self, val): + """Get graph's 'strict' mode (True, False). + + This option is only valid for top level graphs. + """ + + return self.obj_dict['strict'] + + def set_suppress_disconnected(self, val): + """Suppress disconnected nodes in the output graph. + + This option will skip nodes in the graph with no incoming or outgoing + edges. This option works also for subgraphs and has effect only in the + current graph/subgraph. + """ + + self.obj_dict['suppress_disconnected'] = val + + def get_suppress_disconnected(self, val): + """Get if suppress disconnected is set. + + Refer to set_suppress_disconnected for more information. + """ + + return self.obj_dict['suppress_disconnected'] + + def get_next_sequence_number(self): + + seq = self.obj_dict['current_child_sequence'] + + self.obj_dict['current_child_sequence'] += 1 + + return seq + + def add_node(self, graph_node): + """Adds a node object to the graph. + + It takes a node object as its only argument and returns + None. + """ + + if not isinstance(graph_node, Node): + raise TypeError( + 'add_node() received a non node class object: ' + + str(graph_node)) + + node = self.get_node(graph_node.get_name()) + + if not node: + + self.obj_dict['nodes'][ + graph_node.get_name()] = [ + graph_node.obj_dict] + + #self.node_dict[graph_node.get_name()] = graph_node.attributes + graph_node.set_parent_graph(self.get_parent_graph()) + + else: + + self.obj_dict['nodes'][ + graph_node.get_name()].append( + graph_node.obj_dict) + + graph_node.set_sequence(self.get_next_sequence_number()) + + def del_node(self, name, index=None): + """Delete a node from the graph. + + Given a node's name all node(s) with that same name + will be deleted if 'index' is not specified or set + to None. + If there are several nodes with that same name and + 'index' is given, only the node in that position + will be deleted. + + 'index' should be an integer specifying the position + of the node to delete. If index is larger than the + number of nodes with that name, no action is taken. + + If nodes are deleted it returns True. If no action + is taken it returns False. + """ + + if isinstance(name, Node): + name = name.get_name() + + if name in self.obj_dict['nodes']: + + if index is not None and index < len(self.obj_dict['nodes'][name]): + del self.obj_dict['nodes'][name][index] + return True + else: + del self.obj_dict['nodes'][name] + return True + + return False + + def get_node(self, name): + """Retrieve a node from the graph. + + Given a node's name the corresponding Node + instance will be returned. + + If one or more nodes exist with that name a list of + Node instances is returned. + An empty list is returned otherwise. + """ + + match = list() + + if name in self.obj_dict['nodes']: + + match.extend([Node(obj_dict=obj_dict) + for obj_dict in self.obj_dict['nodes'][name]]) + + return match + + def get_nodes(self): + """Get the list of Node instances.""" + + return self.get_node_list() + + def get_node_list(self): + """Get the list of Node instances. + + This method returns the list of Node instances + composing the graph. + """ + + node_objs = list() + + for node, obj_dict_list in self.obj_dict['nodes'].iteritems(): + node_objs.extend([Node(obj_dict=obj_d) for obj_d in obj_dict_list]) + + return node_objs + + def add_edge(self, graph_edge): + """Adds an edge object to the graph. + + It takes a edge object as its only argument and returns + None. + """ + + if not isinstance(graph_edge, Edge): + raise TypeError( + 'add_edge() received a non edge class object: ' + + str(graph_edge)) + + edge_points = (graph_edge.get_source(), graph_edge.get_destination()) + + if edge_points in self.obj_dict['edges']: + + edge_list = self.obj_dict['edges'][edge_points] + edge_list.append(graph_edge.obj_dict) + + else: + + self.obj_dict['edges'][edge_points] = [graph_edge.obj_dict] + + graph_edge.set_sequence(self.get_next_sequence_number()) + + graph_edge.set_parent_graph(self.get_parent_graph()) + + def del_edge(self, src_or_list, dst=None, index=None): + """Delete an edge from the graph. + + Given an edge's (source, destination) node names all + matching edges(s) will be deleted if 'index' is not + specified or set to None. + If there are several matching edges and 'index' is + given, only the edge in that position will be deleted. + + 'index' should be an integer specifying the position + of the edge to delete. If index is larger than the + number of matching edges, no action is taken. + + If edges are deleted it returns True. If no action + is taken it returns False. + """ + + if isinstance(src_or_list, (list, tuple)): + if dst is not None and isinstance(dst, (int, long)): + index = dst + src, dst = src_or_list + else: + src, dst = src_or_list, dst + + if isinstance(src, Node): + src = src.get_name() + + if isinstance(dst, Node): + dst = dst.get_name() + + if (src, dst) in self.obj_dict['edges']: + + if index is not None and index < len( + self.obj_dict['edges'][ + (src, dst)]): + del self.obj_dict['edges'][(src, dst)][index] + return True + else: + del self.obj_dict['edges'][(src, dst)] + return True + + return False + + def get_edge(self, src_or_list, dst=None): + """Retrieved an edge from the graph. + + Given an edge's source and destination the corresponding + Edge instance(s) will be returned. + + If one or more edges exist with that source and destination + a list of Edge instances is returned. + An empty list is returned otherwise. + """ + + if isinstance(src_or_list, (list, tuple)) and dst is None: + edge_points = tuple(src_or_list) + edge_points_reverse = (edge_points[1], edge_points[0]) + else: + edge_points = (src_or_list, dst) + edge_points_reverse = (dst, src_or_list) + + match = list() + + if edge_points in self.obj_dict['edges'] or ( + self.get_top_graph_type() == 'graph' and edge_points_reverse in self.obj_dict['edges']): + + edges_obj_dict = self.obj_dict['edges'].get( + edge_points, + self.obj_dict['edges'].get(edge_points_reverse, None)) + + for edge_obj_dict in edges_obj_dict: + match.append( + Edge( + edge_points[0], + edge_points[1], + obj_dict=edge_obj_dict)) + + return match + + def get_edges(self): + return self.get_edge_list() + + def get_edge_list(self): + """Get the list of Edge instances. + + This method returns the list of Edge instances + composing the graph. + """ + + edge_objs = list() + + for edge, obj_dict_list in self.obj_dict['edges'].iteritems(): + edge_objs.extend([Edge(obj_dict=obj_d) for obj_d in obj_dict_list]) + + return edge_objs + + def add_subgraph(self, sgraph): + """Adds an subgraph object to the graph. + + It takes a subgraph object as its only argument and returns + None. + """ + + if not isinstance( + sgraph, + Subgraph) and not isinstance( + sgraph, + Cluster): + raise TypeError( + 'add_subgraph() received a non subgraph class object:' + + str(sgraph)) + + if sgraph.get_name() in self.obj_dict['subgraphs']: + + sgraph_list = self.obj_dict['subgraphs'][sgraph.get_name()] + sgraph_list.append(sgraph.obj_dict) + + else: + self.obj_dict['subgraphs'][sgraph.get_name()] = [sgraph.obj_dict] + + sgraph.set_sequence(self.get_next_sequence_number()) + + sgraph.set_parent_graph(self.get_parent_graph()) + + def get_subgraph(self, name): + """Retrieved a subgraph from the graph. + + Given a subgraph's name the corresponding + Subgraph instance will be returned. + + If one or more subgraphs exist with the same name, a list of + Subgraph instances is returned. + An empty list is returned otherwise. + """ + + match = list() + + if name in self.obj_dict['subgraphs']: + + sgraphs_obj_dict = self.obj_dict['subgraphs'].get(name) + + for obj_dict_list in sgraphs_obj_dict: + #match.extend( Subgraph( obj_dict = obj_d ) for obj_d in obj_dict_list ) + match.append(Subgraph(obj_dict=obj_dict_list)) + + return match + + def get_subgraphs(self): + + return self.get_subgraph_list() + + def get_subgraph_list(self): + """Get the list of Subgraph instances. + + This method returns the list of Subgraph instances + in the graph. + """ + + sgraph_objs = list() + + for sgraph, obj_dict_list in self.obj_dict['subgraphs'].iteritems(): + sgraph_objs.extend([Subgraph(obj_dict=obj_d) + for obj_d in obj_dict_list]) + + return sgraph_objs + + def set_parent_graph(self, parent_graph): + + self.obj_dict['parent_graph'] = parent_graph + + for obj_list in self.obj_dict['nodes'].itervalues(): + for obj in obj_list: + obj['parent_graph'] = parent_graph + + for obj_list in self.obj_dict['edges'].itervalues(): + for obj in obj_list: + obj['parent_graph'] = parent_graph + + for obj_list in self.obj_dict['subgraphs'].itervalues(): + for obj in obj_list: + Graph(obj_dict=obj).set_parent_graph(parent_graph) + + def to_string(self): + """Returns a string representation of the graph in dot language. + + It will return the graph and all its subelements in string from. + """ + + graph = list() + + if self.obj_dict.get('strict', None) is not None: + + if self == self.get_parent_graph() and self.obj_dict['strict']: + + graph.append('strict ') + + if self.obj_dict['name'] == '': + if 'show_keyword' in self.obj_dict and self.obj_dict[ + 'show_keyword']: + graph.append('subgraph {\n') + else: + graph.append('{\n') + else: + graph.append( + '%s %s {\n' % + (self.obj_dict['type'], self.obj_dict['name'])) + + for attr in self.obj_dict['attributes'].iterkeys(): + + if self.obj_dict['attributes'].get(attr, None) is not None: + + val = self.obj_dict['attributes'].get(attr) + if val is not None: + graph.append('%s=%s' % (attr, quote_if_necessary(val))) + else: + graph.append(attr) + + graph.append(';\n') + + edges_done = set() + + edge_obj_dicts = list() + for e in self.obj_dict['edges'].itervalues(): + edge_obj_dicts.extend(e) + + if edge_obj_dicts: + edge_src_set, edge_dst_set = zip( + *[obj['points'] for obj in edge_obj_dicts]) + edge_src_set, edge_dst_set = set(edge_src_set), set(edge_dst_set) + else: + edge_src_set, edge_dst_set = set(), set() + + node_obj_dicts = list() + for e in self.obj_dict['nodes'].itervalues(): + node_obj_dicts.extend(e) + + sgraph_obj_dicts = list() + for sg in self.obj_dict['subgraphs'].itervalues(): + sgraph_obj_dicts.extend(sg) + + obj_list = sorted([(obj['sequence'], obj) for obj in ( + edge_obj_dicts + node_obj_dicts + sgraph_obj_dicts)]) + + for idx, obj in obj_list: + + if obj['type'] == 'node': + + node = Node(obj_dict=obj) + + if self.obj_dict.get('suppress_disconnected', False): + + if (node.get_name() not in edge_src_set and + node.get_name() not in edge_dst_set): + + continue + + graph.append(node.to_string() + '\n') + + elif obj['type'] == 'edge': + + edge = Edge(obj_dict=obj) + + if self.obj_dict.get('simplify', False) and edge in edges_done: + continue + + graph.append(edge.to_string() + '\n') + edges_done.add(edge) + + else: + + sgraph = Subgraph(obj_dict=obj) + + graph.append(sgraph.to_string() + '\n') + + graph.append('}\n') + + return ''.join(graph) + + +class Subgraph(Graph): + + """Class representing a subgraph in Graphviz's dot language. + + This class implements the methods to work on a representation + of a subgraph in Graphviz's dot language. + + subgraph(graph_name='subG', suppress_disconnected=False, attribute=value, ...) + + graph_name: + the subgraph's name + suppress_disconnected: + defaults to false, which will remove from the + subgraph any disconnected nodes. + All the attributes defined in the Graphviz dot language should + be supported. + + Attributes can be set through the dynamically generated methods: + + set_[attribute name], i.e. set_size, set_fontname + + or using the instance's attributes: + + Subgraph.obj_dict['attributes'][attribute name], i.e. + + subgraph_instance.obj_dict['attributes']['label'] + subgraph_instance.obj_dict['attributes']['fontname'] + """ + + # RMF: subgraph should have all the attributes of graph so it can be passed + # as a graph to all methods + # + def __init__( + self, + graph_name='', + obj_dict=None, + suppress_disconnected=False, + simplify=False, + **attrs): + + Graph.__init__( + self, + graph_name=graph_name, + obj_dict=obj_dict, + suppress_disconnected=suppress_disconnected, + simplify=simplify, + **attrs) + + if obj_dict is None: + + self.obj_dict['type'] = 'subgraph' + + +class Cluster(Graph): + + """Class representing a cluster in Graphviz's dot language. + + This class implements the methods to work on a representation + of a cluster in Graphviz's dot language. + + cluster(graph_name='subG', suppress_disconnected=False, attribute=value, ...) + + graph_name: + the cluster's name (the string 'cluster' will be always prepended) + suppress_disconnected: + defaults to false, which will remove from the + cluster any disconnected nodes. + All the attributes defined in the Graphviz dot language should + be supported. + + Attributes can be set through the dynamically generated methods: + + set_[attribute name], i.e. set_color, set_fontname + + or using the instance's attributes: + + Cluster.obj_dict['attributes'][attribute name], i.e. + + cluster_instance.obj_dict['attributes']['label'] + cluster_instance.obj_dict['attributes']['fontname'] + """ + + def __init__( + self, + graph_name='subG', + obj_dict=None, + suppress_disconnected=False, + simplify=False, + **attrs): + + Graph.__init__( + self, + graph_name=graph_name, + obj_dict=obj_dict, + suppress_disconnected=suppress_disconnected, + simplify=simplify, + **attrs) + + if obj_dict is None: + + self.obj_dict['type'] = 'subgraph' + self.obj_dict['name'] = 'cluster_' + graph_name + + self.create_attribute_methods(CLUSTER_ATTRIBUTES) + + +class Dot(Graph): + + """A container for handling a dot language file. + + This class implements methods to write and process + a dot language file. It is a derived class of + the base class 'Graph'. + """ + + def __init__(self, *argsl, **argsd): + Graph.__init__(self, *argsl, **argsd) + + self.shape_files = list() + + self.progs = None + + self.formats = [ + 'canon', + 'cmap', + 'cmapx', + 'cmapx_np', + 'dia', + 'dot', + 'fig', + 'gd', + 'gd2', + 'gif', + 'hpgl', + 'imap', + 'imap_np', + 'ismap', + 'jpe', + 'jpeg', + 'jpg', + 'mif', + 'mp', + 'pcl', + 'pdf', + 'pic', + 'plain', + 'plain-ext', + 'png', + 'ps', + 'ps2', + 'svg', + 'svgz', + 'vml', + 'vmlz', + 'vrml', + 'vtx', + 'wbmp', + 'xdot', + 'xlib'] + + self.prog = 'dot' + + # Automatically creates all the methods enabling the creation + # of output in any of the supported formats. + for frmt in self.formats: + self.__setattr__( + 'create_' + frmt, + lambda f=frmt, + prog=self.prog: self.create( + format=f, + prog=prog)) + f = self.__dict__['create_' + frmt] + f.__doc__ = '''Refer to the docstring accompanying the 'create' method for more information.''' + + for frmt in self.formats + ['raw']: + self.__setattr__( + 'write_' + frmt, + lambda path, + f=frmt, + prog=self.prog: self.write( + path, + format=f, + prog=prog)) + + f = self.__dict__['write_' + frmt] + f.__doc__ = '''Refer to the docstring accompanying the 'write' method for more information.''' + + def __getstate__(self): + + dict = copy.copy(self.obj_dict) + + return dict + + def __setstate__(self, state): + + self.obj_dict = state + + def set_shape_files(self, file_paths): + """Add the paths of the required image files. + + If the graph needs graphic objects to be used as shapes or otherwise + those need to be in the same folder as the graph is going to be rendered + from. Alternatively the absolute path to the files can be specified when + including the graphics in the graph. + + The files in the location pointed to by the path(s) specified as arguments + to this method will be copied to the same temporary location where the + graph is going to be rendered. + """ + + if isinstance(file_paths, basestring): + self.shape_files.append(file_paths) + + if isinstance(file_paths, (list, tuple)): + self.shape_files.extend(file_paths) + + def set_prog(self, prog): + """Sets the default program. + + Sets the default program in charge of processing + the dot file into a graph. + """ + self.prog = prog + + def set_graphviz_executables(self, paths): + """This method allows to manually specify the location of the GraphViz executables. + + The argument to this method should be a dictionary where the keys are as follows: + + {'dot': '', 'twopi': '', 'neato': '', 'circo': '', 'fdp': ''} + + and the values are the paths to the corresponding executable, including the name + of the executable itself. + """ + + self.progs = paths + + def write(self, path, prog=None, format='raw'): + """Writes a graph to a file. + + Given a filename 'path' it will open/create and truncate + such file and write on it a representation of the graph + defined by the dot object and in the format specified by + 'format'. + The format 'raw' is used to dump the string representation + of the Dot object, without further processing. + The output can be processed by any of graphviz tools, defined + in 'prog', which defaults to 'dot' + Returns True or False according to the success of the write + operation. + + There's also the preferred possibility of using: + + write_'format'(path, prog='program') + + which are automatically defined for all the supported formats. + [write_ps(), write_gif(), write_dia(), ...] + """ + + if prog is None: + prog = self.prog + + dot_fd = file(path, "w+b") + if format == 'raw': + data = self.to_string() + if isinstance(data, basestring): + if not isinstance(data, unicode): + try: + data = unicode(data, 'utf-8') + except: + pass + + try: + data = data.encode('utf-8') + except: + pass + dot_fd.write(data) + else: + dot_fd.write(self.create(prog, format)) + dot_fd.close() + + return True + + def create(self, prog=None, format='ps'): + """Creates and returns a Postscript representation of the graph. + + create will write the graph to a temporary dot file and process + it with the program given by 'prog' (which defaults to 'twopi'), + reading the Postscript output and returning it as a string is the + operation is successful. + On failure None is returned. + + There's also the preferred possibility of using: + + create_'format'(prog='program') + + which are automatically defined for all the supported formats. + [create_ps(), create_gif(), create_dia(), ...] + + If 'prog' is a list instead of a string the fist item is expected + to be the program name, followed by any optional command-line + arguments for it: + + [ 'twopi', '-Tdot', '-s10' ] + """ + + if prog is None: + prog = self.prog + + if isinstance(prog, (list, tuple)): + prog, args = prog[0], prog[1:] + else: + args = [] + + if self.progs is None: + self.progs = find_graphviz() + if self.progs is None: + raise InvocationException( + 'GraphViz\'s executables not found') + + if prog not in self.progs: + raise InvocationException( + 'GraphViz\'s executable "%s" not found' % prog) + + if not os.path.exists( + self.progs[prog]) or not os.path.isfile( + self.progs[prog]): + raise InvocationException( + 'GraphViz\'s executable "%s" is not a file or doesn\'t exist' % + self.progs[prog]) + + tmp_fd, tmp_name = tempfile.mkstemp() + os.close(tmp_fd) + self.write(tmp_name) + tmp_dir = os.path.dirname(tmp_name) + + # For each of the image files... + # + for img in self.shape_files: + + # Get its data + # + f = file(img, 'rb') + f_data = f.read() + f.close() + + # And copy it under a file with the same name in the temporary directory + # + f = file(os.path.join(tmp_dir, os.path.basename(img)), 'wb') + f.write(f_data) + f.close() + + cmdline = [self.progs[prog], '-T' + format, tmp_name] + args + + p = subprocess.Popen( + cmdline, + cwd=tmp_dir, + stderr=subprocess.PIPE, stdout=subprocess.PIPE) + + stderr = p.stderr + stdout = p.stdout + + stdout_output = list() + while True: + data = stdout.read() + if not data: + break + stdout_output.append(data) + stdout.close() + + stdout_output = ''.join(stdout_output) + + if not stderr.closed: + stderr_output = list() + while True: + data = stderr.read() + if not data: + break + stderr_output.append(data) + stderr.close() + + if stderr_output: + stderr_output = ''.join(stderr_output) + + #pid, status = os.waitpid(p.pid, 0) + status = p.wait() + + if status != 0: + raise InvocationException( + 'Program terminated with status: %d. stderr follows: %s' % ( + status, stderr_output)) + elif stderr_output: + print stderr_output + + # For each of the image files... + # + for img in self.shape_files: + + # remove it + # + os.unlink(os.path.join(tmp_dir, os.path.basename(img))) + + os.unlink(tmp_name) + + return stdout_output diff --git a/scripts/create_module.sh b/scripts/module/qp_create_module.sh similarity index 85% rename from scripts/create_module.sh rename to scripts/module/qp_create_module.sh index dbddc3d3..1a456e67 100755 --- a/scripts/create_module.sh +++ b/scripts/module/qp_create_module.sh @@ -71,7 +71,7 @@ debug "Module does not already exist: OK" # Set up dependencies -ALL_MODULES="${NEEDED_MODULES}" +ALL_MODULES="$(cat NEEDED_MODULES)" echo "Select which modules you are sure you will need: (press q to quit)" NEEDED_MODULES="" select M in ${ALL_MODULES} @@ -117,7 +117,7 @@ debug "Module directory is created." # Create the Makefile -"${QPACKAGE_ROOT}/scripts/create_Makefile.sh" || fail "Unable to create Makefile" +"${QPACKAGE_ROOT}/scripts/module/create_Makefile.sh" || fail "Unable to create Makefile" if [[ ! -f Makefile ]] then fail "Makefile was not created" @@ -125,8 +125,8 @@ fi debug "Makefile created" # Create the NEEDED_MODULES file -"${QPACKAGE_ROOT}/scripts/create_Needed_modules.sh" ${NEEDED_MODULES} || fail "Unable to create the NEEDED_MODULES file" -if [[ ! -f NEEDED_MODULES ]] +"${QPACKAGE_ROOT}/scripts/module/create_Needed_modules.sh" ${NEEDED_MODULES} || fail "Unable to create the NEEDED_MODULES file" +if [[ ! -f NEEDED_CHILDREN_MODULES ]] then fail "NEEDED_MODULES was not created" fi @@ -135,7 +135,7 @@ debug "NEEDED_MODULES created" # Create rst templates -"${QPACKAGE_ROOT}/scripts/create_rst_templates.sh" || fail "Unable to create rst templates" +"${QPACKAGE_ROOT}/scripts/module/create_rst_templates.sh" || fail "Unable to create rst templates" # Update module list in main NEEDED_MODULES diff --git a/scripts/pseudo/elts_num_ele.py b/scripts/pseudo/elts_num_ele.py new file mode 100644 index 00000000..3c4ad09f --- /dev/null +++ b/scripts/pseudo/elts_num_ele.py @@ -0,0 +1,118 @@ +name_to_elec = {"H": 1, + "He": 2, + "Li": 3, + "Be": 4, + "B": 5, + "C": 6, + "N": 7, + "O": 8, + "F": 9, + "Ne": 10, + "Na": 11, + "Mg": 12, + "Al": 13, + "Si": 14, + "P": 15, + "S": 16, + "Cl": 17, + "Ar": 18, + "K": 19, + "Ca": 20, + "Sc": 21, + "Ti": 22, + "V": 23, + "Cr": 24, + "Mn": 25, + "Fe": 26, + "Co": 27, + "Ni": 28, + "Cu": 29, + "Zn": 30, + "Ga": 31, + "Ge": 32, + "As": 33, + "Se": 34, + "Br": 35, + "Kr": 36, + "Rb": 37, + "Sr": 38, + "Y": 39, + "Zr": 40, + "Nb": 41, + "Mo": 42, + "Tc": 43, + "Ru": 44, + "Rh": 45, + "Pd": 46, + "Ag": 47, + "Cd": 48, + "In": 49, + "Sn": 50, + "Sb": 51, + "Te": 52, + "I": 53, + "Xe": 54, + "Cs": 55, + "Ba": 56, + "La": 57, + "Ce": 58, + "Pr": 59, + "Nd": 60, + "Pm": 61, + "Sm": 62, + "Eu": 63, + "Gd": 64, + "Tb": 65, + "Dy": 66, + "Ho": 67, + "Er": 68, + "Tm": 69, + "Yb": 70, + "Lu": 71, + "Hf": 72, + "Ta": 73, + "W": 74, + "Re": 75, + "Os": 76, + "Ir": 77, + "Pt": 78, + "Au": 79, + "Hg": 80, + "Tl": 81, + "Pb": 82, + "Bi": 83, + "Po": 84, + "At": 85, + "Rn": 86, + "Fr": 87, + "Ra": 88, + "Ac": 89, + "Th": 90, + "Pa": 91, + "U": 92, + "Np": 93, + "Pu": 94, + "Am": 95, + "Cm": 96, + "Bk": 97, + "Cf": 98, + "Es": 99, + "Fm": 100, + "Md": 101, + "No": 102, + "Lr": 103, + "Rf": 104, + "Db": 105, + "Sg": 106, + "Bh": 107, + "Hs": 108, + "Mt": 109, + "Ds": 110, + "Rg": 111, + "Cn": 112, + "Uut": 113, + "Fl": 114, + "Uup": 115, + "Lv": 116, + "Uus": 117, + "Uuo": 118} diff --git a/scripts/pseudo/put_pseudo_in_ezfio.py b/scripts/pseudo/put_pseudo_in_ezfio.py new file mode 100755 index 00000000..87db7845 --- /dev/null +++ b/scripts/pseudo/put_pseudo_in_ezfio.py @@ -0,0 +1,338 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +""" +Create the pseudo potential for a given atom + +Usage: + put_pseudo_in_ezfio.py + +Help: + atom is the Abreviation of the atom +""" + + +import os +import sys +from docopt import docopt + +from subprocess import Popen, PIPE + +qpackage_root = os.environ['QPACKAGE_ROOT'] + +EZFIO = "{0}/EZFIO".format(qpackage_root) +sys.path = [EZFIO + "/Python"] + sys.path + +from ezfio import ezfio + +import re +p = re.compile(ur'\|(\d+)><\d+\|') + + +def get_pseudo_str(l_atom): + """ + Run EMSL_local for geting the str of the speudo potential + + str_ele : + Element Symbol: Na + Number of replaced protons: 10 + Number of projectors: 2 + + Pseudopotential data: + + Local component: + Coeff. r^n Exp. + 1.00000000 -1 5.35838717 + 5.35838717 1 3.67918975 + -2.07764789 0 1.60507673 + + Non-local component: + Coeff. r^n Exp. Proj. + 10.69640234 0 1.32389367 |0><0| + 10.11238853 0 1.14052020 |1><1| + """ + + EMSL_root = "{0}/EMSL_Basis/".format(qpackage_root) + EMSL_path = "{0}/EMSL_api.py".format(EMSL_root) + db_path = "{0}/db/Pseudo.db".format(EMSL_root) + + str_ = "" + + for a in l_atom: + l_cmd_atom = ["--atom", a] + + l_cmd_head = [EMSL_path, "get_basis_data", + "--db_path", db_path, + "--basis", "BFD-Pseudo"] + + process = Popen(l_cmd_head + l_cmd_atom, stdout=PIPE, stderr=PIPE) + + stdout, _ = process.communicate() + str_ += stdout.strip() + "\n" + + return str_ + + +def get_v_n_dz_local(str_ele): + """ + From a str_ele of the pseudo (aka only one ele in the str) + get the list ussefull for the Local potential : v_k n_k and dz_k + """ + l_v_k = [] + l_n_k = [] + l_dz_k = [] + + for l in str_ele.splitlines(): + try: + v, n, dz = l.split() + v = float(v) + n = int(n) + dz = float(dz) + except ValueError: + pass + else: + l_v_k.append(v) + l_n_k.append(n) + l_dz_k.append(dz) + + return l_v_k, l_n_k, l_dz_k + + +def get_v_n_dz_l_nonlocal(str_ele): + """ + From a str_ele of the pseudo (aka only one ele in the str) + get the list ussefull for the non Local potential + v_kl (v, l) + n_k (v, l) + dz_k (dz ,l) + """ + l_v_kl = [] + l_n_kl = [] + l_dz_kl = [] + + for l in str_ele.splitlines(): + try: + v, n, dz, proj = l.split() + v = float(v) + n = int(n) + dz = float(dz) + l = int(p.match(proj).group(1)) + + except ValueError: + pass + else: + l_v_kl.append([v]) + l_n_kl.append([n]) + l_dz_kl.append([dz]) + + if not l_v_kl: + l_v_kl.append([0.]) + l_n_kl.append([0]) + l_dz_kl.append([0.]) + + return l_v_kl, l_n_kl, l_dz_kl + + +def get_zeff_alpha_beta(str_ele): + """ + Return the the zeff, alpha num elec and beta num elec + Assert ezfio_set_file alredy defined + """ + + import re + + # ___ + # | ._ o _|_ + # _|_ | | | |_ + # + + # ~#~#~#~#~#~#~ # + # s t r _ e l e # + # ~#~#~#~#~#~#~ # + +# m = re.search('Element Symbol: ([a-zA-Z]+)', str_ele) +# name = m.group(1).capitalize() + name = str_ele.split("\n")[0].strip().capitalize() + + m = re.search('Number of replaced protons: (\d+)', str_ele) + z_remove = int(m.group(1)) + + # _ + # |_) _. ._ _ _ + # | (_| | _> (/_ + # + + from elts_num_ele import name_to_elec + z = name_to_elec[name] + + z_eff = z - z_remove + + alpha = (z_remove / 2) + beta = (z_remove / 2) + + # _ + # |_) _ _|_ ._ ._ + # | \ (/_ |_ |_| | | | + # + + return [z_eff, alpha, beta] + + +def add_zero(array, size, type): + for add in xrange(len(array), size): + array.append([type(0)]) + + return array + + +def make_it_square(matrix, dim, type=float): + """ + matix the matrix to squate + dim array [lmax, kmax] + type the null value you want + [[[28.59107316], [19.37583724]], [[50.25646328]]] + => + [[[28.59107316], [19.37583724]], [[50.25646328], [0.0]]] + """ + + lmax = dim[0] + kmax = dim[1] + + for l_list in matrix: + + l_list = add_zero(l_list, lmax, type) + + for k_list in list_: + k_list = add_zero(k_list, kmax, type) + + return matrix + +if __name__ == "__main__": + arguments = docopt(__doc__) + # ___ + # | ._ o _|_ + # _|_ | | | |_ + # + + # ~#~#~#~#~ # + # E Z F I O # + # ~#~#~#~#~ # + + ezfio_path = arguments[""] + ezfio_path = os.path.expanduser(ezfio_path) + ezfio_path = os.path.expandvars(ezfio_path) + ezfio_path = os.path.abspath(ezfio_path) + + ezfio.set_file("{0}".format(ezfio_path)) + + # ~#~#~#~#~#~#~#~#~#~#~ # + # P s e u d o _ d a t a # + # ~#~#~#~#~#~#~#~#~#~#~ # + + l_ele = ezfio.get_nuclei_nucl_label() + str_ = get_pseudo_str(l_ele) + + # _ + # |_) _. ._ _ _ + # | (_| | _> (/_ + # + + l_str_ele = [str_ele for str_ele in str_.split("Element Symbol: ") + if str_ele] + + for i in "l_zeff v_k n_k dz_k v_kl n_kl dz_kl".split(): + exec("{0} = []".format(i)) + + alpha_tot = 0 + beta_tot = 0 + + for str_ele in l_str_ele: + + # ~#~#~#~#~ # + # S p l i t # + # ~#~#~#~#~ # + + l = str_ele.find("Local component:") + nl = str_ele.find("Non-local component") + + # ~#~#~#~#~ # + # L o c a l # + # ~#~#~#~#~ # + + l_v, l_n, l_dz = get_v_n_dz_local(str_ele[l:nl]) + + v_k.append(l_v) + n_k.append(l_n) + dz_k.append(l_dz) + + # ~#~#~#~#~#~#~#~#~ # + # N o n _ L o c a l # + # ~#~#~#~#~#~#~#~#~ # + + l_v_kl, l_n_kl, l_dz_kl = get_v_n_dz_l_nonlocal(str_ele[nl:]) + + v_kl.append(l_v_kl) + n_kl.append(l_n_kl) + dz_kl.append(l_dz_kl) + + # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ # + # Z _ e f f , a l p h a / b e t a _ e l e c # + # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ # + + zeff, alpha, beta = get_zeff_alpha_beta(str_ele) + + alpha_tot += alpha + beta_tot += beta + l_zeff.append(zeff) + # _ + # /\ _| _| _|_ _ _ _ _|_ o _ + # /--\ (_| (_| |_ (_) (/_ /_ | | (_) + # + + # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ # + # Z _ e f f , a l p h a / b e t a _ e l e c # + # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ # + + ezfio.nuclei_nucl_charge = l_zeff + + alpha_tot = ezfio.get_electrons_elec_alpha_num() - alpha_tot + beta_tot = ezfio.get_electrons_elec_beta_num() - beta_tot + + ezfio.electrons_elec_alpha_num = alpha_tot + ezfio.electrons_elec_beta_num = beta_tot + + # Change all the array 'cause EZFIO + # v_kl (v, l) => v_kl(l,v) + # v_kl => zip(*_v_kl) + # [[7.0, 79.74474797, -49.45159098], [1.0, 5.41040609, -4.60151975]] + # [(7.0, 1.0), (79.74474797, 5.41040609), (-49.45159098, -4.60151975)] + + # ~#~#~#~#~ # + # L o c a l # + # ~#~#~#~#~ # + + klocmax = max([len(i) for i in v_k]) + ezfio.pseudo_intergrals_klocmax = klocmax + + ezfio.pseudo_intergrals_v_k = zip(*v_k) + ezfio.pseudo_intergrals_n_k = zip(*n_k) + ezfio.pseudo_intergrals_dz_k = zip(*dz_k) + + # ~#~#~#~#~#~#~#~#~ # + # N o n _ L o c a l # + # ~#~#~#~#~#~#~#~#~ # + + lmax = max([len(i) for i in v_kl]) + kmax = max([len(sublist) for list_ in v_kl for sublist in list_]) + + ezfio.pseudo_intergrals_lmaxpo = lmax + ezfio.pseudo_intergrals_kmax = kmax + + v_kl = make_it_square(v_kl, [lmax, kmax]) + n_kl = make_it_square(n_kl, [lmax, kmax], int) + dz_kl = make_it_square(dz_kl, [lmax, kmax]) + + ezfio.pseudo_intergrals_v_kl = zip(*v_kl) + ezfio.pseudo_intergrals_n_kl = zip(*n_kl) + ezfio.pseudo_intergrals_dz_kl = zip(*dz_kl) + + ezfio.pseudo_intergrals_do_pseudo = True diff --git a/scripts/qp_convert.py b/scripts/qp_convert.py deleted file mode 100755 index ab008e9e..00000000 --- a/scripts/qp_convert.py +++ /dev/null @@ -1,210 +0,0 @@ -#!/usr/bin/env python - -import sys,os -try: - QPACKAGE_ROOT = os.environ["QPACKAGE_ROOT"] -except: - print "Error: QPACKAGE_ROOT environment variable not found." - sys.exit(1) - -sys.path = [ QPACKAGE_ROOT+"/EZFIO/Python", QPACKAGE_ROOT+"/resultsFile" ]+sys.path -from ezfio import ezfio -import ezfio as ez -print "EZFIO: ", os.path.dirname(ez.__file__) - -try: - from resultsFile import * -except: - print "Error: resultsFile Python library not installed" - sys.exit(1) - - -def write_ezfioFile(res,filename): - res.clean_uncontractions() - ezfio.set_file(filename) - -# Electrons - ezfio.set_electrons_elec_alpha_num(res.num_alpha) - ezfio.set_electrons_elec_beta_num(res.num_beta) - -# Nuclei - ezfio.set_nuclei_nucl_num(len(res.geometry)) - charge = [] - coord = [] - coord_x = [] - coord_y = [] - coord_z = [] - for a in res.geometry: - charge.append(a.charge) - if res.units == 'BOHR': - coord_x.append(a.coord[0]) - coord_y.append(a.coord[1]) - coord_z.append(a.coord[2]) - else: - coord_x.append(a.coord[0]/a0) - coord_y.append(a.coord[1]/a0) - coord_z.append(a.coord[2]/a0) - ezfio.set_nuclei_nucl_charge(charge) - label = map(lambda x: x.name, res.geometry) - ezfio.set_nuclei_nucl_label(label) - ezfio.set_nuclei_nucl_coord(coord_x+coord_y+coord_z) - -# Basis - basis = res.uncontracted_basis - geom = res.geometry - - res.clean_contractions() - # AO Basis - import string - at = [] - num_prim = [] - magnetic_number = [] - angular_number = [] - power_x = [] - power_y = [] - power_z = [] - coefficient = [] - exponent = [] - res.convert_to_cartesian() - for b in res.basis: - c = b.center - for i,atom in enumerate(res.geometry): - if atom.coord == c: - at.append(i+1) - num_prim.append(len(b.prim)) - s = b.sym - power_x.append( string.count(s,"x") ) - power_y.append( string.count(s,"y") ) - power_z.append( string.count(s,"z") ) - coefficient.append( b.coef ) - exponent.append( [ p.expo for p in b.prim ] ) - ezfio.set_ao_basis_ao_num(len(res.basis)) - ezfio.set_ao_basis_ao_nucl(at) - ezfio.set_ao_basis_ao_prim_num(num_prim) - ezfio.set_ao_basis_ao_power(power_x+power_y+power_z) - prim_num_max = ezfio.get_ao_basis_ao_prim_num_max() - len_res_basis = len(res.basis) - for i in range(len(res.basis)): - coefficient[i] += [ 0. for j in range(len(coefficient[i]),prim_num_max) ] - exponent[i] += [ 0. for j in range(len(exponent[i]),prim_num_max) ] - coefficient = reduce(lambda x, y: x+y, coefficient, []) - exponent = reduce(lambda x, y: x+y, exponent, []) - coef = [] - expo = [] - for i in range(prim_num_max): - for j in range(i,len(coefficient),prim_num_max): - coef.append ( coefficient[j] ) - expo.append ( exponent[j] ) - ezfio.set_ao_basis_ao_coef(coef) - ezfio.set_ao_basis_ao_expo(expo) - ezfio.set_ao_basis_ao_basis("Read by resultsFile") - - -# MO - MoTag = res.determinants_mo_type - ezfio.set_mo_basis_mo_label('Orthonormalized') - MO_type = MoTag - allMOs = res.mo_sets[MO_type] - - - try: - closed = [ (allMOs[i].eigenvalue,i) for i in res.closed_mos ] - active = [ (allMOs[i].eigenvalue,i) for i in res.active_mos ] - virtual =[ (allMOs[i].eigenvalue,i) for i in res.virtual_mos ] - except: - closed = [] - virtual = [] - active = [ (allMOs[i].eigenvalue,i) for i in range(len(allMOs)) ] - -# closed.sort() -# active.sort() -# virtual.sort() - closed = map( lambda x: x[1], closed) - active = map( lambda x: x[1], active) - virtual = map( lambda x: x[1], virtual) - MOindices = closed + active + virtual - - MOs = [] - for i in MOindices: - MOs.append(allMOs[i]) - - mo_tot_num = len(MOs) - while len(MOindices) < mo_tot_num: - MOindices.append(len(MOindices)) - - MOmap = list(MOindices) - for i in range(len(MOindices)): - MOmap[i] = MOindices.index(i) - - energies = [] - for i in xrange(mo_tot_num): - energies.append(MOs[i].eigenvalue) - - if res.occ_num is not None: - OccNum = [] - for i in MOindices: - OccNum.append(res.occ_num[MO_type][i]) - - while len(OccNum) < mo_tot_num: - OccNum.append(0.) - - MoMatrix = [] - sym0 = [ i.sym for i in res.mo_sets[MO_type] ] - sym = [ i.sym for i in res.mo_sets[MO_type] ] - for i in xrange(len(sym)): - sym[MOmap[i]] = sym0[i] - - MoMatrix = [] - for i in xrange(len(MOs)): - m = MOs[i] - for coef in m.vector: - MoMatrix.append(coef) - - while len(MoMatrix) < len(MOs[0].vector)**2: - MoMatrix.append(0.) - - mo = [] - for i in MOindices: - mo.append(res.mo_sets[MoTag][i]) - - if len(mo) < mo_tot_num: - newmo = orbital() - newmo.eigenvalue = 0. - newmo.vector = [0. for i in range(mo_tot_num)] - newmo.vector[len(mo)] = 1. - while len(mo) < mo_tot_num: - mo.append(newmo) - Energies = [ m.eigenvalue for m in mo ] - - ezfio.set_mo_basis_mo_tot_num(mo_tot_num) - ezfio.set_mo_basis_mo_occ(OccNum) - ezfio.set_mo_basis_mo_coef(MoMatrix) - - - - -if __name__ == '__main__': - # Check command line - - det_threshold = 0. - - if len(sys.argv) == 2: - State=0 - elif len(sys.argv) == 3: - State=int(sys.argv[2]) - else: - print "usage: "+sys.argv[0]+" file.out [state]" - sys.exit(2) - - firstArg = sys.argv[1] - - file = getFile(firstArg) - print firstArg, 'recognized as', str(file).split('.')[-1].split()[0] - - filename = firstArg+".ezfio" - write_ezfioFile(file,filename) - - - - - diff --git a/scripts/qp_include.sh b/scripts/qp_include.sh index 467baca8..8e2d4f9f 100644 --- a/scripts/qp_include.sh +++ b/scripts/qp_include.sh @@ -35,9 +35,10 @@ function check_current_dir_is_module() exit -1 fi } -if [[ -f NEEDED_MODULES ]] + +if [[ -f NEEDED_CHILDREN_MODULES ]] then - NEEDED_MODULES=$(cat NEEDED_MODULES) + NEEDED_MODULES=$(module_handler.py print_genealogy NEEDED_CHILDREN_MODULES) fi # List of executables in the current directory diff --git a/scripts/run_Makefile_common.sh b/scripts/run_Makefile_common.sh index 82e898ac..859cc8d0 100755 --- a/scripts/run_Makefile_common.sh +++ b/scripts/run_Makefile_common.sh @@ -14,7 +14,7 @@ check_current_dir_is_module # Check if the NEEDED_MODULES file is consistent INCLUDE_DIRS="${NEEDED_MODULES} include" -NEEDED_MODULES_OK=$( ${QPACKAGE_ROOT}/scripts/check_dependencies.sh ${NEEDED_MODULES} ) +NEEDED_MODULES_OK=$(module_handler.py check_dependencies ${NEEDED_MODULES} ) if [[ $? -ne 0 ]] then error " @@ -28,7 +28,7 @@ fi # Check if README.rst exists if [[ ! -f README.rst ]] then - ${QPACKAGE_ROOT}/scripts/create_rst_templates.sh + ${QPACKAGE_ROOT}/scripts/module/create_rst_templates.sh error " README.rst was not present, so I created a default one for you. @@ -62,7 +62,7 @@ then fi # Update Makefile.depend -${QPACKAGE_ROOT}/scripts/create_Makefile_depend.sh +${QPACKAGE_ROOT}/scripts/module/create_Makefile_depend.sh # Update EZFIO interface - ${QPACKAGE_ROOT}/scripts/ezfio_interface/ei_handler.py +${QPACKAGE_ROOT}/scripts/ezfio_interface/ei_handler.py diff --git a/scripts/run_Makefile_global.sh b/scripts/run_Makefile_global.sh index fc9e168a..869172a2 100755 --- a/scripts/run_Makefile_global.sh +++ b/scripts/run_Makefile_global.sh @@ -52,7 +52,7 @@ ${IRPF90_VERSION}. IRPF90 version >= ${IRPF90_REQUIRED_VERSION} is required. To upgrade IRPF90, run : - ${QPACKAGE_ROOT}/scripts/upgrade_irpf90.sh + ${QPACKAGE_ROOT}/scripts/upgrade/upgrade_irpf90.sh " else info "irpf90 version is OK" @@ -75,7 +75,7 @@ then Current EZFIO version : ${EZFIO_VERSION} EZFIO version >= ${EZFIO_REQUIRED_VERSION} is required. To upgrade EZFIO, run : - ${QPACKAGE_ROOT}/scripts/upgrade_ezfio.sh + ${QPACKAGE_ROOT}/scripts/upgrade/upgrade_ezfio.sh " else info "EZFIO version is OK" diff --git a/scripts/update_README.py b/scripts/update_README.py index 0f32404d..177d57a4 100755 --- a/scripts/update_README.py +++ b/scripts/update_README.py @@ -83,7 +83,7 @@ def update_needed(data): """Read the NEEDED_MODULES file, and replace the data with it. Create the links to the GitHub pages.""" - file = open('NEEDED_MODULES', 'r') + file = open('NEEDED_CHILDREN_MODULES', 'r') modules = file.read() file.close() diff --git a/scripts/upgrade_ezfio.sh b/scripts/upgrade/upgrade_ezfio.sh similarity index 91% rename from scripts/upgrade_ezfio.sh rename to scripts/upgrade/upgrade_ezfio.sh index 4a9af403..c35a2dbd 100755 --- a/scripts/upgrade_ezfio.sh +++ b/scripts/upgrade/upgrade_ezfio.sh @@ -12,7 +12,7 @@ fi cd -- ${QPACKAGE_ROOT} mv -- ${QPACKAGE_ROOT}/EZFIO ${QPACKAGE_ROOT}/EZFIO.old -${QPACKAGE_ROOT}/scripts/install_ezfio.sh +${QPACKAGE_ROOT}/scripts/install/install_ezfio.sh if [[ $? -eq 0 ]] then diff --git a/scripts/upgrade_irpf90.sh b/scripts/upgrade/upgrade_irpf90.sh similarity index 91% rename from scripts/upgrade_irpf90.sh rename to scripts/upgrade/upgrade_irpf90.sh index 5735754f..dea48014 100755 --- a/scripts/upgrade_irpf90.sh +++ b/scripts/upgrade/upgrade_irpf90.sh @@ -12,7 +12,7 @@ fi cd -- ${QPACKAGE_ROOT} mv -f -- ${QPACKAGE_ROOT}/irpf90 ${QPACKAGE_ROOT}/irpf90.old -${QPACKAGE_ROOT}/scripts/install_irpf90.sh +${QPACKAGE_ROOT}/scripts/install/install_irpf90.sh if [[ $? -eq 0 ]] then diff --git a/setup_environment.sh b/setup_environment.sh index be4bae64..657573c0 100755 --- a/setup_environment.sh +++ b/setup_environment.sh @@ -17,8 +17,10 @@ export QPACKAGE_ROOT=\$( cd \$(dirname "\${BASH_SOURCE}") ; pwd -P ) export LD_LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LD_LIBRARY_PATH} export LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LIBRARY_PATH} export C_INCLUDE_PATH="\${QPACKAGE_ROOT}"/include:\${C_INCLUDE_PATH} -export PYTHONPATH=\${PYTHONPATH}:"\${QPACKAGE_ROOT}"/scripts:"\${QPACKAGE_ROOT}"/scripts/ezfio_interface -export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/scripts:"\${QPACKAGE_ROOT}"/scripts/ezfio_interface + +export PYTHONPATH=\${PYTHONPATH}\$(find "${QPACKAGE_ROOT}"/scripts -type d -printf ":%p") + +export PATH=\${PATH}\$(find "${QPACKAGE_ROOT}"/scripts -type d -printf ":%p") export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/bin export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/ocaml source "\${QPACKAGE_ROOT}"/bin/irpman &> /dev/null @@ -28,37 +30,29 @@ EOF source quantum_package.rc echo "${BLUE}===== Installing IRPF90 ===== ${BLACK}" -${QPACKAGE_ROOT}/scripts/install_irpf90.sh | tee install_irpf90.log -if [[ ! -d ${QPACKAGE_ROOT}/irpf90 ]] -then - echo $RED "Error in IRPF90 installation" $BLACK - exit 1 -fi - -if [[ ! -x ${QPACKAGE_ROOT}/bin/irpf90 ]] -then - echo $RED "Error in IRPF90 installation" $BLACK - exit 1 -fi - -if [[ ! -x ${QPACKAGE_ROOT}/bin/irpman ]] +${QPACKAGE_ROOT}/scripts/install/install_irpf90.sh | tee ${QPACKAGE_ROOT}/install_logs/install_irpf90.log +if [[ ! -d ${QPACKAGE_ROOT}/irpf90 ]] || [[ ! -x ${QPACKAGE_ROOT}/bin/irpf90 ]] || [[ ! -x ${QPACKAGE_ROOT}/bin/irpman ]] then echo $RED "Error in IRPF90 installation" $BLACK exit 1 fi +mkdir -p ${QPACKAGE_ROOT}/install_logs echo "${BLUE}===== Installing Zlib ===== ${BLACK}" -${QPACKAGE_ROOT}/scripts/install_zlib.sh | tee install_zlib.log +${QPACKAGE_ROOT}/scripts/install/install_zlib.sh | tee ${QPACKAGE_ROOT}/install_logs/install_zlib.log echo "${BLUE}===== Installing Curl ===== ${BLACK}" -${QPACKAGE_ROOT}/scripts/install_curl.sh | tee install_curl.log +${QPACKAGE_ROOT}/scripts/install/install_curl.sh | tee ${QPACKAGE_ROOT}/install_logs/install_curl.log echo "${BLUE}===== Installing M4 ===== ${BLACK}" -${QPACKAGE_ROOT}/scripts/install_m4.sh | tee install_m4.log +${QPACKAGE_ROOT}/scripts/install/install_m4.sh | tee ${QPACKAGE_ROOT}/install_logs/install_m4.log + +echo "${BLUE}===== Installing Docopt ===== ${BLACK}" +${QPACKAGE_ROOT}/scripts/install/install_docopt.sh | tee ${QPACKAGE_ROOT}/install_logs/install_docopt.log echo "${BLUE}===== Installing EMSL Basis set library ===== ${BLACK}" -${QPACKAGE_ROOT}/scripts/install_emsl.sh | tee install_emsl.log +${QPACKAGE_ROOT}/scripts/install/install_emsl.sh | tee ${QPACKAGE_ROOT}/install_logs/install_emsl.log if [[ ! -d ${QPACKAGE_ROOT}/EMSL_Basis ]] then @@ -68,7 +62,7 @@ fi echo "${BLUE}===== Installing EZFIO ===== ${BLACK}" -${QPACKAGE_ROOT}/scripts/install_ezfio.sh | tee install_ezfio.log +${QPACKAGE_ROOT}/scripts/install/install_ezfio.sh | tee ${QPACKAGE_ROOT}/install_logs/install_ezfio.log if [[ ! -d ${QPACKAGE_ROOT}/EZFIO ]] then echo $RED "Error in EZFIO installation" $BLACK @@ -78,7 +72,7 @@ fi echo "${BLUE}===== Installing Ocaml compiler and libraries ===== ${BLACK}" rm -f -- ocaml/Qptypes.ml -${QPACKAGE_ROOT}/scripts/install_ocaml.sh | tee install_ocaml.log +${QPACKAGE_ROOT}/scripts/install/install_ocaml.sh | tee ${QPACKAGE_ROOT}/install_logs/install_ocaml.log if [[ ! -f ${QPACKAGE_ROOT}/ocaml/Qptypes.ml ]] then @@ -87,7 +81,7 @@ then fi echo "${BLUE}===== Installing resultsFile Python library ===== ${BLACK}" -${QPACKAGE_ROOT}/scripts/install_resultsFile.sh +${QPACKAGE_ROOT}/scripts/install/install_resultsFile.sh if [[ ! -d ${QPACKAGE_ROOT}/resultsFile ]] then echo $RED "Error in resultsFile installation" $BLACK @@ -106,8 +100,7 @@ source ${QPACKAGE_ROOT}/quantum_package.rc " $BLACK -mkdir -p ${QPACKAGE_ROOT}/install_logs -mv ${QPACKAGE_ROOT}/*.log ${QPACKAGE_ROOT}/install_logs/ + if [[ $1 == "--robot" ]] ; then diff --git a/src/AOs/NEEDED_CHILDREN_MODULES b/src/AOs/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..2c80725f --- /dev/null +++ b/src/AOs/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Nuclei diff --git a/src/AOs/NEEDED_MODULES b/src/AOs/NEEDED_MODULES deleted file mode 100644 index 9f7ccbcc..00000000 --- a/src/AOs/NEEDED_MODULES +++ /dev/null @@ -1,2 +0,0 @@ -Ezfio_files Nuclei Output Utils - diff --git a/src/AOs/README.rst b/src/AOs/README.rst index 5978e16f..f5cb8707 100644 --- a/src/AOs/README.rst +++ b/src/AOs/README.rst @@ -37,10 +37,7 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `Ezfio_files `_ * `Nuclei `_ -* `Output `_ -* `Utils `_ Documentation ============= diff --git a/src/Bielec_integrals/NEEDED_CHILDREN_MODULES b/src/Bielec_integrals/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..24979463 --- /dev/null +++ b/src/Bielec_integrals/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +MonoInts Bitmask diff --git a/src/Bielec_integrals/NEEDED_MODULES b/src/Bielec_integrals/NEEDED_MODULES deleted file mode 100644 index 5f709ce4..00000000 --- a/src/Bielec_integrals/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Bitmask Electrons Ezfio_files MOs Nuclei Output Utils MonoInts diff --git a/src/Bielec_integrals/README.rst b/src/Bielec_integrals/README.rst index 38dc9e96..6e17f2b7 100644 --- a/src/Bielec_integrals/README.rst +++ b/src/Bielec_integrals/README.rst @@ -16,15 +16,8 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Bitmask `_ -* `Electrons `_ -* `Ezfio_files `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ * `MonoInts `_ +* `Bitmask `_ Documentation ============= diff --git a/src/Bitmask/NEEDED_CHILDREN_MODULES b/src/Bitmask/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..b936db90 --- /dev/null +++ b/src/Bitmask/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +MOs diff --git a/src/Bitmask/NEEDED_MODULES b/src/Bitmask/NEEDED_MODULES deleted file mode 100644 index 190f8c6e..00000000 --- a/src/Bitmask/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Electrons Ezfio_files MOs Nuclei Output Utils diff --git a/src/Bitmask/README.rst b/src/Bitmask/README.rst index b8e3aa57..395efc52 100644 --- a/src/Bitmask/README.rst +++ b/src/Bitmask/README.rst @@ -40,13 +40,7 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Electrons `_ -* `Ezfio_files `_ * `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ Documentation ============= diff --git a/src/CAS_SD/NEEDED_CHILDREN_MODULES b/src/CAS_SD/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..f7264a0f --- /dev/null +++ b/src/CAS_SD/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Perturbation Selectors_full Generators_CAS diff --git a/src/CAS_SD/NEEDED_MODULES b/src/CAS_SD/NEEDED_MODULES deleted file mode 100644 index cbf44be7..00000000 --- a/src/CAS_SD/NEEDED_MODULES +++ /dev/null @@ -1,2 +0,0 @@ -AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Generators_CAS Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils - diff --git a/src/CAS_SD/README.rst b/src/CAS_SD/README.rst index 0dc4ea56..2e56e56e 100644 --- a/src/CAS_SD/README.rst +++ b/src/CAS_SD/README.rst @@ -24,21 +24,7 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `Dets `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Generators_CAS `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ * `Perturbation `_ -* `Properties `_ * `Selectors_full `_ -* `Utils `_ +* `Generators_CAS `_ diff --git a/src/CID/NEEDED_CHILDREN_MODULES b/src/CID/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..afc8cfd4 --- /dev/null +++ b/src/CID/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Selectors_full SingleRefMethod diff --git a/src/CID/NEEDED_MODULES b/src/CID/NEEDED_MODULES deleted file mode 100644 index ac8e21ab..00000000 --- a/src/CID/NEEDED_MODULES +++ /dev/null @@ -1,3 +0,0 @@ -AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Selectors_full SingleRefMethod Utils - - diff --git a/src/CID/README.rst b/src/CID/README.rst index 6adc4dcd..5d2fa851 100644 --- a/src/CID/README.rst +++ b/src/CID/README.rst @@ -15,21 +15,8 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `Dets `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ * `Selectors_full `_ * `SingleRefMethod `_ -* `Utils `_ Documentation ============= diff --git a/src/CID_SC2_selected/NEEDED_CHILDREN_MODULES b/src/CID_SC2_selected/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..7be053d7 --- /dev/null +++ b/src/CID_SC2_selected/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +CID_selected diff --git a/src/CID_SC2_selected/NEEDED_MODULES b/src/CID_SC2_selected/NEEDED_MODULES deleted file mode 100644 index 42d83610..00000000 --- a/src/CID_SC2_selected/NEEDED_MODULES +++ /dev/null @@ -1,2 +0,0 @@ -AOs Bielec_integrals Bitmask CISD CISD_selected Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils - diff --git a/src/CID_SC2_selected/README.rst b/src/CID_SC2_selected/README.rst index 720b6385..ec9e7a3f 100644 --- a/src/CID_SC2_selected/README.rst +++ b/src/CID_SC2_selected/README.rst @@ -19,23 +19,5 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `CISD `_ -* `CISD_selected `_ -* `Dets `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Perturbation `_ -* `Properties `_ -* `Selectors_full `_ -* `SingleRefMethod `_ -* `Utils `_ +* `CID_selected `_ diff --git a/src/CID_selected/NEEDED_CHILDREN_MODULES b/src/CID_selected/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..1e0c52c2 --- /dev/null +++ b/src/CID_selected/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Perturbation CID diff --git a/src/CID_selected/NEEDED_MODULES b/src/CID_selected/NEEDED_MODULES deleted file mode 100644 index b27ab85e..00000000 --- a/src/CID_selected/NEEDED_MODULES +++ /dev/null @@ -1,2 +0,0 @@ -AOs Bielec_integrals Bitmask CISD Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils - diff --git a/src/CID_selected/README.rst b/src/CID_selected/README.rst index 2ee45ac6..50cc701f 100644 --- a/src/CID_selected/README.rst +++ b/src/CID_selected/README.rst @@ -22,22 +22,6 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `CISD `_ -* `Dets `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ * `Perturbation `_ -* `Properties `_ -* `Selectors_full `_ -* `SingleRefMethod `_ -* `Utils `_ +* `CID `_ diff --git a/src/CIS/NEEDED_CHILDREN_MODULES b/src/CIS/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..afc8cfd4 --- /dev/null +++ b/src/CIS/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Selectors_full SingleRefMethod diff --git a/src/CIS/NEEDED_MODULES b/src/CIS/NEEDED_MODULES deleted file mode 100644 index 010e60f5..00000000 --- a/src/CIS/NEEDED_MODULES +++ /dev/null @@ -1,2 +0,0 @@ -AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Selectors_full SingleRefMethod Utils - diff --git a/src/CIS/README.rst b/src/CIS/README.rst index e9ba93db..e3b2478a 100644 --- a/src/CIS/README.rst +++ b/src/CIS/README.rst @@ -31,19 +31,6 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `Dets `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ * `Selectors_full `_ * `SingleRefMethod `_ -* `Utils `_ diff --git a/src/CISD/NEEDED_CHILDREN_MODULES b/src/CISD/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..afc8cfd4 --- /dev/null +++ b/src/CISD/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Selectors_full SingleRefMethod diff --git a/src/CISD/NEEDED_MODULES b/src/CISD/NEEDED_MODULES deleted file mode 100644 index 010e60f5..00000000 --- a/src/CISD/NEEDED_MODULES +++ /dev/null @@ -1,2 +0,0 @@ -AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Selectors_full SingleRefMethod Utils - diff --git a/src/CISD/README.rst b/src/CISD/README.rst index 07528e59..68ab4cfb 100644 --- a/src/CISD/README.rst +++ b/src/CISD/README.rst @@ -15,21 +15,8 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `Dets `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ * `Selectors_full `_ * `SingleRefMethod `_ -* `Utils `_ Documentation ============= diff --git a/src/CISD_SC2_selected/NEEDED_CHILDREN_MODULES b/src/CISD_SC2_selected/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..fa61747b --- /dev/null +++ b/src/CISD_SC2_selected/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +CISD_selected diff --git a/src/CISD_SC2_selected/NEEDED_MODULES b/src/CISD_SC2_selected/NEEDED_MODULES deleted file mode 100644 index 42d83610..00000000 --- a/src/CISD_SC2_selected/NEEDED_MODULES +++ /dev/null @@ -1,2 +0,0 @@ -AOs Bielec_integrals Bitmask CISD CISD_selected Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils - diff --git a/src/CISD_SC2_selected/README.rst b/src/CISD_SC2_selected/README.rst index 25f4368f..b4f4fac1 100644 --- a/src/CISD_SC2_selected/README.rst +++ b/src/CISD_SC2_selected/README.rst @@ -19,23 +19,5 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `CISD `_ * `CISD_selected `_ -* `Dets `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Perturbation `_ -* `Properties `_ -* `Selectors_full `_ -* `SingleRefMethod `_ -* `Utils `_ diff --git a/src/CISD_selected/NEEDED_CHILDREN_MODULES b/src/CISD_selected/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..2b104007 --- /dev/null +++ b/src/CISD_selected/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Perturbation CISD diff --git a/src/CISD_selected/NEEDED_MODULES b/src/CISD_selected/NEEDED_MODULES deleted file mode 100644 index b27ab85e..00000000 --- a/src/CISD_selected/NEEDED_MODULES +++ /dev/null @@ -1,2 +0,0 @@ -AOs Bielec_integrals Bitmask CISD Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils - diff --git a/src/CISD_selected/README.rst b/src/CISD_selected/README.rst index 1ba5f9c5..a72c5a21 100644 --- a/src/CISD_selected/README.rst +++ b/src/CISD_selected/README.rst @@ -28,22 +28,6 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `CISD `_ -* `Dets `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ * `Perturbation `_ -* `Properties `_ -* `Selectors_full `_ -* `SingleRefMethod `_ -* `Utils `_ +* `CISD `_ diff --git a/src/DDCI_selected/NEEDED_CHILDREN_MODULES b/src/DDCI_selected/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..f7264a0f --- /dev/null +++ b/src/DDCI_selected/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Perturbation Selectors_full Generators_CAS diff --git a/src/DDCI_selected/NEEDED_MODULES b/src/DDCI_selected/NEEDED_MODULES deleted file mode 100644 index cbf44be7..00000000 --- a/src/DDCI_selected/NEEDED_MODULES +++ /dev/null @@ -1,2 +0,0 @@ -AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Generators_CAS Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils - diff --git a/src/DDCI_selected/README.rst b/src/DDCI_selected/README.rst index db75b101..9cfdbefa 100644 --- a/src/DDCI_selected/README.rst +++ b/src/DDCI_selected/README.rst @@ -19,21 +19,7 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `Dets `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Generators_CAS `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ * `Perturbation `_ -* `Properties `_ * `Selectors_full `_ -* `Utils `_ +* `Generators_CAS `_ diff --git a/src/Dets/ASSUMPTIONS.rst b/src/Determinants/ASSUMPTIONS.rst similarity index 100% rename from src/Dets/ASSUMPTIONS.rst rename to src/Determinants/ASSUMPTIONS.rst diff --git a/src/Determinants/EZFIO.cfg b/src/Determinants/EZFIO.cfg new file mode 100644 index 00000000..5f63404b --- /dev/null +++ b/src/Determinants/EZFIO.cfg @@ -0,0 +1,103 @@ +[N_states] +type: States_number +doc: Number of states to consider +interface: input +default: 1 + +[N_det_max_jacobi] +type: Strictly_positive_int +doc: Maximum number of determinants diagonalized by Jacobi +interface: input +default: 1000 + +[read_wf] +type: logical +doc: If true, read the wave function from the EZFIO file +interface: input +default: False + +[only_single_double_dm] +type: logical +doc: If true, The One body DM is calculated with ignoring the Double<->Doubles extra diag elements +interface: input +default: False + +[s2_eig] +type: logical +doc: Force the wave function to be an eigenfunction of S^2 +interface: input +default: False + +[threshold_generators] +type: Threshold +doc: Thresholds on generators (fraction of the norm) +interface: input +default: 0.99 + +[threshold_selectors] +type: Threshold +doc: Thresholds on selectors (fraction of the norm) +interface: input +default: 0.999 + + +# Only create the ezfio_config, (no Input_* and no PROVIDER) + +[n_states_diag] +type: integer +doc: n_states_diag +interface: Ocaml + +[n_int] +interface: OCaml +doc: n_int +type: N_int_number + +[bit_kind] +interface: OCaml +doc: bit_kind +type: Bit_kind + +[mo_label] +interface: OCaml +doc: o_label +type: character*(64) + +[n_det] +interface: OCaml +doc: n_det +type: integer + +[psi_coef] +interface: OCaml +doc: psi_coef +type: double precision +size: (determinants_n_det,determinants_n_states) + +[psi_det] +interface: OCaml +doc: psi_det +type: integer*8 +size: (determinants_n_int*determinants_bit_kind/8,2,determinants_n_det) + +[det_num] +interface: OCaml +doc: det_num +type: integer + +[det_occ] +interface: OCaml +doc: det_occ +type: integer +size: (electrons_elec_alpha_num,determinants_det_num,2) + +[det_coef] +interface: OCaml +doc: det_coef +type: double precision +size: (determinants_det_num) + +[expected_s2] +interface: OCaml +doc: expcted_s2 +type: double precision \ No newline at end of file diff --git a/src/Dets/H_apply.irp.f b/src/Determinants/H_apply.irp.f similarity index 100% rename from src/Dets/H_apply.irp.f rename to src/Determinants/H_apply.irp.f diff --git a/src/Dets/H_apply_template.f b/src/Determinants/H_apply_template.f similarity index 100% rename from src/Dets/H_apply_template.f rename to src/Determinants/H_apply_template.f diff --git a/src/Dets/Makefile b/src/Determinants/Makefile similarity index 100% rename from src/Dets/Makefile rename to src/Determinants/Makefile diff --git a/src/Determinants/NEEDED_CHILDREN_MODULES b/src/Determinants/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..afc397de --- /dev/null +++ b/src/Determinants/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Bielec_integrals diff --git a/src/Dets/README.rst b/src/Determinants/README.rst similarity index 76% rename from src/Dets/README.rst rename to src/Determinants/README.rst index cbc1c352..37baa392 100644 --- a/src/Dets/README.rst +++ b/src/Determinants/README.rst @@ -32,16 +32,7 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ * `Bielec_integrals `_ -* `Bitmask `_ -* `Electrons `_ -* `Ezfio_files `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ Documentation ============= @@ -49,7 +40,7 @@ Documentation .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -`copy_h_apply_buffer_to_wf `_ +`copy_h_apply_buffer_to_wf `_ Copies the H_apply buffer to psi_coef. You need to touch psi_det, psi_coef and N_det after calling this function. After calling this subroutine, N_det, psi_det and psi_coef need to be touched @@ -60,18 +51,18 @@ Documentation `fill_h_apply_buffer_no_selection `_ Fill the H_apply buffer with determiants for CISD -`h_apply_buffer_allocated `_ +`h_apply_buffer_allocated `_ Buffer of determinants/coefficients/perturbative energy for H_apply. Uninitialized. Filled by H_apply subroutines. -`h_apply_buffer_lock `_ +`h_apply_buffer_lock `_ Buffer of determinants/coefficients/perturbative energy for H_apply. Uninitialized. Filled by H_apply subroutines. -`resize_h_apply_buffer `_ +`resize_h_apply_buffer `_ Undocumented -`cisd_sc2 `_ +`cisd_sc2 `_ CISD+SC2 method :: take off all the disconnected terms of a CISD (selected or not) .br dets_in : bitmasks corresponding to determinants @@ -87,25 +78,25 @@ Documentation .br Initial guess vectors are not necessarily orthonormal -`connected_to_ref `_ +`connected_to_ref `_ Undocumented -`connected_to_ref_by_mono `_ +`connected_to_ref_by_mono `_ Undocumented -`det_search_key `_ +`det_search_key `_ Return an integer*8 corresponding to a determinant index for searching -`get_index_in_psi_det_sorted_bit `_ +`get_index_in_psi_det_sorted_bit `_ Returns the index of the determinant in the ``psi_det_sorted_bit`` array -`is_in_wavefunction `_ +`is_in_wavefunction `_ True if the determinant ``det`` is in the wave function -`occ_pattern_search_key `_ +`occ_pattern_search_key `_ Return an integer*8 corresponding to a determinant index for searching -`do_mono_excitation `_ +`do_mono_excitation `_ Apply the mono excitation operator : a^{dager}_(i_particle) a_(i_hole) of spin = ispin on key_in ispin = 1 == alpha @@ -113,13 +104,13 @@ Documentation i_ok = 1 == the excitation is possible i_ok = -1 == the excitation is not possible -`davidson_converged `_ +`davidson_converged `_ True if the Davidson algorithm is converged -`davidson_criterion `_ +`davidson_criterion `_ Can be : [ energy | residual | both | wall_time | cpu_time | iterations ] -`davidson_diag `_ +`davidson_diag `_ Davidson diagonalization. .br dets_in : bitmasks corresponding to determinants @@ -137,7 +128,7 @@ Documentation .br Initial guess vectors are not necessarily orthonormal -`davidson_diag_hjj `_ +`davidson_diag_hjj `_ Davidson diagonalization with specific diagonal elements of the H matrix .br H_jj : specific diagonal H matrix elements to diagonalize de Davidson @@ -157,49 +148,49 @@ Documentation .br Initial guess vectors are not necessarily orthonormal -`davidson_iter_max `_ +`davidson_iter_max `_ Max number of Davidson iterations -`davidson_sze_max `_ +`davidson_sze_max `_ Max number of Davidson sizes -`davidson_threshold `_ +`davidson_threshold `_ Can be : [ energy | residual | both | wall_time | cpu_time | iterations ] -`one_body_dm_mo `_ +`one_body_dm_mo `_ One-body density matrix -`one_body_dm_mo_alpha `_ +`one_body_dm_mo_alpha `_ Alpha and beta one-body density matrix for each state -`one_body_dm_mo_beta `_ +`one_body_dm_mo_beta `_ Alpha and beta one-body density matrix for each state -`one_body_single_double_dm_mo_alpha `_ +`one_body_single_double_dm_mo_alpha `_ Alpha and beta one-body density matrix for each state -`one_body_single_double_dm_mo_beta `_ +`one_body_single_double_dm_mo_beta `_ Alpha and beta one-body density matrix for each state -`one_body_spin_density_mo `_ +`one_body_spin_density_mo `_ rho(alpha) - rho(beta) -`save_natural_mos `_ +`save_natural_mos `_ Save natural orbitals, obtained by diagonalization of the one-body density matrix in the MO basis -`set_natural_mos `_ +`set_natural_mos `_ Set natural orbitals, obtained by diagonalization of the one-body density matrix in the MO basis -`state_average_weight `_ +`state_average_weight `_ Weights in the state-average calculation of the density matrix -`det_svd `_ +`det_svd `_ Computes the SVD of the Alpha x Beta determinant coefficient matrix -`filter_3_highest_electrons `_ +`filter_3_highest_electrons `_ Returns a determinant with only the 3 highest electrons -`int_of_3_highest_electrons `_ +`int_of_3_highest_electrons `_ Returns an integer*8 as : .br |_<--- 21 bits ---><--- 21 bits ---><--- 21 bits --->| @@ -210,158 +201,158 @@ Documentation in descending order .br -`max_degree_exc `_ +`max_degree_exc `_ Maximum degree of excitation in the wf -`n_det `_ +`n_det `_ Number of determinants in the wave function -`psi_average_norm_contrib `_ +`psi_average_norm_contrib `_ Contribution of determinants to the state-averaged density -`psi_average_norm_contrib_sorted `_ +`psi_average_norm_contrib_sorted `_ Wave function sorted by determinants contribution to the norm (state-averaged) -`psi_coef `_ +`psi_coef `_ The wave function coefficients. Initialized with Hartree-Fock if the EZFIO file is empty -`psi_coef_sorted `_ +`psi_coef_sorted `_ Wave function sorted by determinants contribution to the norm (state-averaged) -`psi_coef_sorted_ab `_ +`psi_coef_sorted_ab `_ Determinants on which we apply . They are sorted by the 3 highest electrons in the alpha part, then by the 3 highest electrons in the beta part to accelerate the research of connected determinants. -`psi_coef_sorted_bit `_ +`psi_coef_sorted_bit `_ Determinants on which we apply for perturbation. They are sorted by determinants interpreted as integers. Useful to accelerate the search of a random determinant in the wave function. -`psi_det `_ +`psi_det `_ The wave function determinants. Initialized with Hartree-Fock if the EZFIO file is empty -`psi_det_size `_ +`psi_det_size `_ Size of the psi_det/psi_coef arrays -`psi_det_sorted `_ +`psi_det_sorted `_ Wave function sorted by determinants contribution to the norm (state-averaged) -`psi_det_sorted_ab `_ +`psi_det_sorted_ab `_ Determinants on which we apply . They are sorted by the 3 highest electrons in the alpha part, then by the 3 highest electrons in the beta part to accelerate the research of connected determinants. -`psi_det_sorted_bit `_ +`psi_det_sorted_bit `_ Determinants on which we apply for perturbation. They are sorted by determinants interpreted as integers. Useful to accelerate the search of a random determinant in the wave function. -`psi_det_sorted_next_ab `_ +`psi_det_sorted_next_ab `_ Determinants on which we apply . They are sorted by the 3 highest electrons in the alpha part, then by the 3 highest electrons in the beta part to accelerate the research of connected determinants. -`read_dets `_ +`read_dets `_ Reads the determinants from the EZFIO file -`save_wavefunction `_ +`save_wavefunction `_ Save the wave function into the EZFIO file -`save_wavefunction_general `_ +`save_wavefunction_general `_ Save the wave function into the EZFIO file -`save_wavefunction_unsorted `_ +`save_wavefunction_unsorted `_ Save the wave function into the EZFIO file -`sort_dets_by_3_highest_electrons `_ +`sort_dets_by_3_highest_electrons `_ Determinants on which we apply . They are sorted by the 3 highest electrons in the alpha part, then by the 3 highest electrons in the beta part to accelerate the research of connected determinants. -`sort_dets_by_det_search_key `_ +`sort_dets_by_det_search_key `_ Determinants are sorted are sorted according to their det_search_key. Useful to accelerate the search of a random determinant in the wave function. -`double_exc_bitmask `_ +`double_exc_bitmask `_ double_exc_bitmask(:,1,i) is the bitmask for holes of excitation 1 double_exc_bitmask(:,2,i) is the bitmask for particles of excitation 1 double_exc_bitmask(:,3,i) is the bitmask for holes of excitation 2 double_exc_bitmask(:,4,i) is the bitmask for particles of excitation 2 for a given couple of hole/particle excitations i. -`n_double_exc_bitmasks `_ +`n_double_exc_bitmasks `_ Number of double excitation bitmasks -`n_single_exc_bitmasks `_ +`n_single_exc_bitmasks `_ Number of single excitation bitmasks -`single_exc_bitmask `_ +`single_exc_bitmask `_ single_exc_bitmask(:,1,i) is the bitmask for holes single_exc_bitmask(:,2,i) is the bitmask for particles for a given couple of hole/particle excitations i. -`ci_eigenvectors `_ +`ci_eigenvectors `_ Eigenvectors/values of the CI matrix -`ci_eigenvectors_s2 `_ +`ci_eigenvectors_s2 `_ Eigenvectors/values of the CI matrix -`ci_electronic_energy `_ +`ci_electronic_energy `_ Eigenvectors/values of the CI matrix -`ci_energy `_ +`ci_energy `_ N_states lowest eigenvalues of the CI matrix -`diag_algorithm `_ +`diag_algorithm `_ Diagonalization algorithm (Davidson or Lapack) -`diagonalize_ci `_ +`diagonalize_ci `_ Replace the coefficients of the CI states by the coefficients of the eigenstates of the CI matrix -`ci_sc2_eigenvectors `_ +`ci_sc2_eigenvectors `_ Eigenvectors/values of the CI matrix -`ci_sc2_electronic_energy `_ +`ci_sc2_electronic_energy `_ Eigenvectors/values of the CI matrix -`ci_sc2_energy `_ +`ci_sc2_energy `_ N_states_diag lowest eigenvalues of the CI matrix -`diagonalize_ci_sc2 `_ +`diagonalize_ci_sc2 `_ Replace the coefficients of the CI states_diag by the coefficients of the eigenstates of the CI matrix -`threshold_convergence_sc2 `_ +`threshold_convergence_sc2 `_ convergence of the correlation energy of SC2 iterations -`ci_eigenvectors_mono `_ +`ci_eigenvectors_mono `_ Eigenvectors/values of the CI matrix -`ci_eigenvectors_s2_mono `_ +`ci_eigenvectors_s2_mono `_ Eigenvectors/values of the CI matrix -`ci_electronic_energy_mono `_ +`ci_electronic_energy_mono `_ Eigenvectors/values of the CI matrix -`diagonalize_ci_mono `_ +`diagonalize_ci_mono `_ Replace the coefficients of the CI states by the coefficients of the eigenstates of the CI matrix -`apply_mono `_ +`apply_mono `_ Undocumented -`filter_connected `_ +`filter_connected `_ Filters out the determinants that are not connected by H .br returns the array idx which contains the index of the @@ -372,7 +363,7 @@ Documentation .br idx(0) is the number of determinants that interact with key1 -`filter_connected_davidson `_ +`filter_connected_davidson `_ Filters out the determinants that are not connected by H returns the array idx which contains the index of the determinants in the array key1 that interact @@ -381,7 +372,7 @@ Documentation idx(0) is the number of determinants that interact with key1 key1 should come from psi_det_sorted_ab. -`filter_connected_i_h_psi0 `_ +`filter_connected_i_h_psi0 `_ returns the array idx which contains the index of the .br determinants in the array key1 that interact @@ -390,7 +381,7 @@ Documentation .br idx(0) is the number of determinants that interact with key1 -`filter_connected_i_h_psi0_sc2 `_ +`filter_connected_i_h_psi0_sc2 `_ standard filter_connected_i_H_psi but returns in addition .br the array of the index of the non connected determinants to key1 @@ -401,7 +392,7 @@ Documentation .br to repeat the excitations -`filter_connected_sorted_ab `_ +`filter_connected_sorted_ab `_ Filters out the determinants that are not connected by H returns the array idx which contains the index of the determinants in the array key1 that interact @@ -410,197 +401,197 @@ Documentation .br Determinants are taken from the psi_det_sorted_ab array -`put_gess `_ +`put_gess `_ Undocumented -`det_to_occ_pattern `_ +`det_to_occ_pattern `_ Transform a determinant to an occupation pattern -`make_s2_eigenfunction `_ +`make_s2_eigenfunction `_ Undocumented -`n_occ_pattern `_ +`n_occ_pattern `_ array of the occ_pattern present in the wf psi_occ_pattern(:,1,j) = jth occ_pattern of the wave function : represent all the single occupation psi_occ_pattern(:,2,j) = jth occ_pattern of the wave function : represent all the double occupation -`occ_pattern_to_dets `_ +`occ_pattern_to_dets `_ Generate all possible determinants for a give occ_pattern -`occ_pattern_to_dets_size `_ +`occ_pattern_to_dets_size `_ Number of possible determinants for a given occ_pattern -`psi_occ_pattern `_ +`psi_occ_pattern `_ array of the occ_pattern present in the wf psi_occ_pattern(:,1,j) = jth occ_pattern of the wave function : represent all the single occupation psi_occ_pattern(:,2,j) = jth occ_pattern of the wave function : represent all the double occupation -`rec_occ_pattern_to_dets `_ +`rec_occ_pattern_to_dets `_ Undocumented -`n_states_diag `_ +`n_states_diag `_ Number of states to consider for the diagonalization -`pouet `_ +`pouet `_ Undocumented -`routine `_ +`routine `_ Undocumented -`idx_cas `_ +`idx_cas `_ CAS wave function, defined from the application of the CAS bitmask on the determinants. idx_cas gives the indice of the CAS determinant in psi_det. -`idx_non_cas `_ +`idx_non_cas `_ Set of determinants which are not part of the CAS, defined from the application of the CAS bitmask on the determinants. idx_non_cas gives the indice of the determinant in psi_det. -`n_det_cas `_ +`n_det_cas `_ CAS wave function, defined from the application of the CAS bitmask on the determinants. idx_cas gives the indice of the CAS determinant in psi_det. -`n_det_non_cas `_ +`n_det_non_cas `_ Set of determinants which are not part of the CAS, defined from the application of the CAS bitmask on the determinants. idx_non_cas gives the indice of the determinant in psi_det. -`psi_cas `_ +`psi_cas `_ CAS wave function, defined from the application of the CAS bitmask on the determinants. idx_cas gives the indice of the CAS determinant in psi_det. -`psi_cas_coef `_ +`psi_cas_coef `_ CAS wave function, defined from the application of the CAS bitmask on the determinants. idx_cas gives the indice of the CAS determinant in psi_det. -`psi_cas_coef_sorted_bit `_ +`psi_cas_coef_sorted_bit `_ CAS determinants sorted to accelerate the search of a random determinant in the wave function. -`psi_cas_sorted_bit `_ +`psi_cas_sorted_bit `_ CAS determinants sorted to accelerate the search of a random determinant in the wave function. -`psi_non_cas `_ +`psi_non_cas `_ Set of determinants which are not part of the CAS, defined from the application of the CAS bitmask on the determinants. idx_non_cas gives the indice of the determinant in psi_det. -`psi_non_cas_coef `_ +`psi_non_cas_coef `_ Set of determinants which are not part of the CAS, defined from the application of the CAS bitmask on the determinants. idx_non_cas gives the indice of the determinant in psi_det. -`psi_non_cas_coef_sorted_bit `_ +`psi_non_cas_coef_sorted_bit `_ CAS determinants sorted to accelerate the search of a random determinant in the wave function. -`psi_non_cas_sorted_bit `_ +`psi_non_cas_sorted_bit `_ CAS determinants sorted to accelerate the search of a random determinant in the wave function. -`bi_elec_ref_bitmask_energy `_ +`bi_elec_ref_bitmask_energy `_ Energy of the reference bitmask used in Slater rules -`kinetic_ref_bitmask_energy `_ +`kinetic_ref_bitmask_energy `_ Energy of the reference bitmask used in Slater rules -`mono_elec_ref_bitmask_energy `_ +`mono_elec_ref_bitmask_energy `_ Energy of the reference bitmask used in Slater rules -`nucl_elec_ref_bitmask_energy `_ +`nucl_elec_ref_bitmask_energy `_ Energy of the reference bitmask used in Slater rules -`ref_bitmask_energy `_ +`ref_bitmask_energy `_ Energy of the reference bitmask used in Slater rules -`expected_s2 `_ +`expected_s2 `_ Expected value of S2 : S*(S+1) -`get_s2 `_ +`get_s2 `_ Returns -`get_s2_u0 `_ +`get_s2_u0 `_ Undocumented -`s2_values `_ +`s2_values `_ array of the averaged values of the S^2 operator on the various states -`s_z `_ +`s_z `_ z component of the Spin -`s_z2_sz `_ +`s_z2_sz `_ z component of the Spin -`prog_save_casino `_ +`prog_save_casino `_ Undocumented -`save_casino `_ +`save_casino `_ Undocumented -`save_dets_qmcchem `_ +`save_dets_qmcchem `_ Undocumented -`save_for_qmc `_ +`save_for_qmc `_ Undocumented -`save_natorb `_ +`save_natorb `_ Undocumented -`a_operator `_ +`a_operator `_ Needed for diag_H_mat_elem -`ac_operator `_ +`ac_operator `_ Needed for diag_H_mat_elem -`decode_exc `_ +`decode_exc `_ Decodes the exc arrays returned by get_excitation. h1,h2 : Holes p1,p2 : Particles s1,s2 : Spins (1:alpha, 2:beta) degree : Degree of excitation -`det_connections `_ +`det_connections `_ Build connection proxy between determinants -`diag_h_mat_elem `_ +`diag_h_mat_elem `_ Computes -`get_double_excitation `_ +`get_double_excitation `_ Returns the two excitation operators between two doubly excited determinants and the phase -`get_excitation `_ +`get_excitation `_ Returns the excitation operators between two determinants and the phase -`get_excitation_degree `_ +`get_excitation_degree `_ Returns the excitation degree between two determinants -`get_excitation_degree_vector `_ +`get_excitation_degree_vector `_ Applies get_excitation_degree to an array of determinants -`get_mono_excitation `_ +`get_mono_excitation `_ Returns the excitation operator between two singly excited determinants and the phase -`get_occ_from_key `_ +`get_occ_from_key `_ Returns a list of occupation numbers from a bitstring -`h_u_0 `_ +`h_u_0 `_ Computes v_0 = H|u_0> .br n : number of determinants .br H_jj : array of -`i_h_j `_ +`i_h_j `_ Returns where i and j are determinants -`i_h_j_verbose `_ +`i_h_j_verbose `_ Returns where i and j are determinants -`i_h_psi `_ +`i_h_psi `_ for the various Nstates -`i_h_psi_sc2 `_ +`i_h_psi_sc2 `_ for the various Nstate .br returns in addition @@ -613,7 +604,7 @@ Documentation .br to repeat the excitations -`i_h_psi_sc2_verbose `_ +`i_h_psi_sc2_verbose `_ for the various Nstate .br returns in addition @@ -626,73 +617,73 @@ Documentation .br to repeat the excitations -`i_h_psi_sec_ord `_ +`i_h_psi_sec_ord `_ for the various Nstates -`n_con_int `_ +`n_con_int `_ Number of integers to represent the connections between determinants -`create_wf_of_psi_svd_matrix `_ +`create_wf_of_psi_svd_matrix `_ Matrix of wf coefficients. Outer product of alpha and beta determinants -`generate_all_alpha_beta_det_products `_ +`generate_all_alpha_beta_det_products `_ Create a wave function from all possible alpha x beta determinants -`get_index_in_psi_det_alpha_unique `_ +`get_index_in_psi_det_alpha_unique `_ Returns the index of the determinant in the ``psi_det_alpha_unique`` array -`get_index_in_psi_det_beta_unique `_ +`get_index_in_psi_det_beta_unique `_ Returns the index of the determinant in the ``psi_det_beta_unique`` array -`n_det_alpha_unique `_ +`n_det_alpha_unique `_ Unique alpha determinants -`n_det_beta_unique `_ +`n_det_beta_unique `_ Unique beta determinants -`psi_det_alpha `_ +`psi_det_alpha `_ List of alpha determinants of psi_det -`psi_det_alpha_unique `_ +`psi_det_alpha_unique `_ Unique alpha determinants -`psi_det_beta `_ +`psi_det_beta `_ List of beta determinants of psi_det -`psi_det_beta_unique `_ +`psi_det_beta_unique `_ Unique beta determinants -`psi_svd_alpha `_ +`psi_svd_alpha `_ SVD wave function -`psi_svd_beta `_ +`psi_svd_beta `_ SVD wave function -`psi_svd_coefs `_ +`psi_svd_coefs `_ SVD wave function -`psi_svd_matrix `_ +`psi_svd_matrix `_ Matrix of wf coefficients. Outer product of alpha and beta determinants -`psi_svd_matrix_columns `_ +`psi_svd_matrix_columns `_ Matrix of wf coefficients. Outer product of alpha and beta determinants -`psi_svd_matrix_rows `_ +`psi_svd_matrix_rows `_ Matrix of wf coefficients. Outer product of alpha and beta determinants -`psi_svd_matrix_values `_ +`psi_svd_matrix_values `_ Matrix of wf coefficients. Outer product of alpha and beta determinants -`spin_det_search_key `_ +`spin_det_search_key `_ Return an integer*8 corresponding to a determinant index for searching -`write_spindeterminants `_ +`write_spindeterminants `_ Undocumented -`cisd `_ +`cisd `_ Undocumented -`h_matrix_all_dets `_ +`h_matrix_all_dets `_ H matrix on the basis of the slater determinants defined by psi_det diff --git a/src/Dets/SC2.irp.f b/src/Determinants/SC2.irp.f similarity index 89% rename from src/Dets/SC2.irp.f rename to src/Determinants/SC2.irp.f index 8a6c10d7..440b2870 100644 --- a/src/Dets/SC2.irp.f +++ b/src/Determinants/SC2.irp.f @@ -43,10 +43,10 @@ subroutine CISD_SC2(dets_in,u_in,energies,dim_in,sze,N_st,Nint,convergence) allocate (doubles(Nint,2,sze),e_corr_array(sze),H_jj_ref(sze),H_jj_dressed(sze),& index_double(sze), degree_exc(sze), hij_double(sze)) - call write_time(output_Dets) - write(output_Dets,'(A)') '' - write(output_Dets,'(A)') 'CISD SC2' - write(output_Dets,'(A)') '========' + call write_time(output_determinants) + write(output_determinants,'(A)') '' + write(output_determinants,'(A)') 'CISD SC2' + write(output_determinants,'(A)') '========' !$OMP PARALLEL DEFAULT(NONE) & !$OMP SHARED(sze,N_st, & !$OMP H_jj_ref,Nint,dets_in,u_in) & @@ -175,7 +175,7 @@ subroutine CISD_SC2(dets_in,u_in,energies,dim_in,sze,N_st,Nint,convergence) enddo deallocate (H_matrix_tmp, eigenvalues, eigenvectors) else - call davidson_diag_hjj(dets_in,u_in,H_jj_dressed,energies,dim_in,sze,N_st,Nint,output_Dets) + call davidson_diag_hjj(dets_in,u_in,H_jj_dressed,energies,dim_in,sze,N_st,Nint,output_determinants) endif e_corr_double = 0.d0 @@ -184,18 +184,18 @@ subroutine CISD_SC2(dets_in,u_in,energies,dim_in,sze,N_st,Nint,convergence) e_corr_array(i) = u_in(index_double(i),1)*inv_c0 * hij_double(i) e_corr_double += e_corr_array(i) enddo - write(output_Dets,'(A,I3)') 'SC2 Iteration ', iter - write(output_Dets,'(A)') '------------------' - write(output_Dets,'(A)') '' - write(output_Dets,'(A)') '===== ================' - write(output_Dets,'(A)') 'State Energy ' - write(output_Dets,'(A)') '===== ================' + write(output_determinants,'(A,I3)') 'SC2 Iteration ', iter + write(output_determinants,'(A)') '------------------' + write(output_determinants,'(A)') '' + write(output_determinants,'(A)') '===== ================' + write(output_determinants,'(A)') 'State Energy ' + write(output_determinants,'(A)') '===== ================' do i=1,N_st - write(output_Dets,'(I5,X,F16.10)') i, energies(i)+nuclear_repulsion + write(output_determinants,'(I5,X,F16.10)') i, energies(i)+nuclear_repulsion enddo - write(output_Dets,'(A)') '===== ================' - write(output_Dets,'(A)') '' - call write_double(output_Dets,(e_corr_double - e_corr_double_before),& + write(output_determinants,'(A)') '===== ================' + write(output_determinants,'(A)') '' + call write_double(output_determinants,(e_corr_double - e_corr_double_before),& 'Delta(E_corr)') converged = dabs(e_corr_double - e_corr_double_before) < convergence converged = converged .or. abort_here @@ -206,7 +206,7 @@ subroutine CISD_SC2(dets_in,u_in,energies,dim_in,sze,N_st,Nint,convergence) enddo - call write_time(output_Dets) + call write_time(output_determinants) deallocate (doubles,e_corr_array,H_jj_ref,H_jj_dressed, & index_double, degree_exc, hij_double) diff --git a/src/Dets/connected_to_ref.irp.f b/src/Determinants/connected_to_ref.irp.f similarity index 100% rename from src/Dets/connected_to_ref.irp.f rename to src/Determinants/connected_to_ref.irp.f diff --git a/src/Dets/create_excitations.irp.f b/src/Determinants/create_excitations.irp.f similarity index 100% rename from src/Dets/create_excitations.irp.f rename to src/Determinants/create_excitations.irp.f diff --git a/src/Dets/davidson.irp.f b/src/Determinants/davidson.irp.f similarity index 100% rename from src/Dets/davidson.irp.f rename to src/Determinants/davidson.irp.f diff --git a/src/Dets/density_matrix.irp.f b/src/Determinants/density_matrix.irp.f similarity index 100% rename from src/Dets/density_matrix.irp.f rename to src/Determinants/density_matrix.irp.f diff --git a/src/Dets/det_svd.irp.f b/src/Determinants/det_svd.irp.f similarity index 100% rename from src/Dets/det_svd.irp.f rename to src/Determinants/det_svd.irp.f diff --git a/src/Dets/determinants.irp.f b/src/Determinants/determinants.irp.f similarity index 98% rename from src/Dets/determinants.irp.f rename to src/Determinants/determinants.irp.f index 104b868e..a70d0fe8 100644 --- a/src/Dets/determinants.irp.f +++ b/src/Determinants/determinants.irp.f @@ -25,7 +25,7 @@ BEGIN_PROVIDER [ integer, N_det ] else N_det = 1 endif - call write_int(output_dets,N_det,'Number of determinants') + call write_int(output_determinants,N_det,'Number of determinants') ASSERT (N_det > 0) END_PROVIDER @@ -58,7 +58,7 @@ BEGIN_PROVIDER [ integer, psi_det_size ] psi_det_size = 1 endif psi_det_size = max(psi_det_size,10000) - call write_int(output_dets,psi_det_size,'Dimension of the psi arrays') + call write_int(output_determinants,psi_det_size,'Dimension of the psi arrays') END_PROVIDER @@ -727,7 +727,7 @@ subroutine save_wavefunction_general(ndet,nstates,psidet,dim_psicoef,psicoef) enddo call ezfio_set_determinants_psi_coef(psi_coef_save) - call write_int(output_dets,ndet,'Saved determinants') + call write_int(output_determinants,ndet,'Saved determinants') call stop_progress deallocate (psi_coef_save) end diff --git a/src/Dets/determinants_bitmasks.irp.f b/src/Determinants/determinants_bitmasks.irp.f similarity index 100% rename from src/Dets/determinants_bitmasks.irp.f rename to src/Determinants/determinants_bitmasks.irp.f diff --git a/src/Dets/diagonalize_CI.irp.f b/src/Determinants/diagonalize_CI.irp.f similarity index 92% rename from src/Dets/diagonalize_CI.irp.f rename to src/Determinants/diagonalize_CI.irp.f index 55612920..0e697ab3 100644 --- a/src/Dets/diagonalize_CI.irp.f +++ b/src/Determinants/diagonalize_CI.irp.f @@ -23,12 +23,12 @@ BEGIN_PROVIDER [ double precision, CI_energy, (N_states_diag) ] integer :: j character*(8) :: st - call write_time(output_Dets) + call write_time(output_determinants) do j=1,N_states_diag CI_energy(j) = CI_electronic_energy(j) + nuclear_repulsion write(st,'(I4)') j - call write_double(output_Dets,CI_energy(j),'Energy of state '//trim(st)) - call write_double(output_Dets,CI_eigenvectors_s2(j),'S^2 of state '//trim(st)) + call write_double(output_determinants,CI_energy(j),'Energy of state '//trim(st)) + call write_double(output_determinants,CI_eigenvectors_s2(j),'S^2 of state '//trim(st)) enddo END_PROVIDER @@ -51,7 +51,7 @@ END_PROVIDER if (diag_algorithm == "Davidson") then call davidson_diag(psi_det,CI_eigenvectors,CI_electronic_energy, & - size(CI_eigenvectors,1),N_det,N_states_diag,N_int,output_Dets) + size(CI_eigenvectors,1),N_det,N_states_diag,N_int,output_determinants) else if (diag_algorithm == "Lapack") then diff --git a/src/Dets/diagonalize_CI_SC2.irp.f b/src/Determinants/diagonalize_CI_SC2.irp.f similarity index 92% rename from src/Dets/diagonalize_CI_SC2.irp.f rename to src/Determinants/diagonalize_CI_SC2.irp.f index 81931a62..97161ad3 100644 --- a/src/Dets/diagonalize_CI_SC2.irp.f +++ b/src/Determinants/diagonalize_CI_SC2.irp.f @@ -6,11 +6,11 @@ BEGIN_PROVIDER [ double precision, CI_SC2_energy, (N_states_diag) ] integer :: j character*(8) :: st - call write_time(output_Dets) + call write_time(output_determinants) do j=1,N_states_diag CI_SC2_energy(j) = CI_SC2_electronic_energy(j) + nuclear_repulsion write(st,'(I4)') j - call write_double(output_Dets,CI_SC2_energy(j),'Energy of state '//trim(st)) + call write_double(output_determinants,CI_SC2_energy(j),'Energy of state '//trim(st)) enddo END_PROVIDER diff --git a/src/Dets/diagonalize_CI_mono.irp.f b/src/Determinants/diagonalize_CI_mono.irp.f similarity index 99% rename from src/Dets/diagonalize_CI_mono.irp.f rename to src/Determinants/diagonalize_CI_mono.irp.f index a3c5b103..1c9a4de3 100644 --- a/src/Dets/diagonalize_CI_mono.irp.f +++ b/src/Determinants/diagonalize_CI_mono.irp.f @@ -16,7 +16,7 @@ if (diag_algorithm == "Davidson") then call davidson_diag(psi_det,CI_eigenvectors_mono,CI_electronic_energy, & - size(CI_eigenvectors_mono,1),N_det,N_states_diag,N_int,output_Dets) + size(CI_eigenvectors_mono,1),N_det,N_states_diag,N_int,output_determinants) else if (diag_algorithm == "Lapack") then diff --git a/src/Dets/excitations_utils.irp.f b/src/Determinants/excitations_utils.irp.f similarity index 100% rename from src/Dets/excitations_utils.irp.f rename to src/Determinants/excitations_utils.irp.f diff --git a/src/Dets/filter_connected.irp.f b/src/Determinants/filter_connected.irp.f similarity index 100% rename from src/Dets/filter_connected.irp.f rename to src/Determinants/filter_connected.irp.f diff --git a/src/Dets/guess_doublet.irp.f b/src/Determinants/guess_doublet.irp.f similarity index 100% rename from src/Dets/guess_doublet.irp.f rename to src/Determinants/guess_doublet.irp.f diff --git a/src/Dets/guess_singlet.irp.f b/src/Determinants/guess_singlet.irp.f similarity index 100% rename from src/Dets/guess_singlet.irp.f rename to src/Determinants/guess_singlet.irp.f diff --git a/src/Dets/guess_triplet.irp.f b/src/Determinants/guess_triplet.irp.f similarity index 100% rename from src/Dets/guess_triplet.irp.f rename to src/Determinants/guess_triplet.irp.f diff --git a/src/Dets/occ_pattern.irp.f b/src/Determinants/occ_pattern.irp.f similarity index 99% rename from src/Dets/occ_pattern.irp.f rename to src/Determinants/occ_pattern.irp.f index 29d0dacf..a0fd4a3c 100644 --- a/src/Dets/occ_pattern.irp.f +++ b/src/Determinants/occ_pattern.irp.f @@ -333,7 +333,7 @@ subroutine make_s2_eigenfunction ! enddo ! enddo ! !TODO DEBUG - call write_int(output_dets,N_det_new, 'Added deteminants for S^2') + call write_int(output_determinants,N_det_new, 'Added deteminants for S^2') end diff --git a/src/Determinants/options.irp.f b/src/Determinants/options.irp.f new file mode 100644 index 00000000..d4283128 --- /dev/null +++ b/src/Determinants/options.irp.f @@ -0,0 +1,22 @@ +BEGIN_PROVIDER [ integer, N_states_diag ] + implicit none + BEGIN_DOC +! Number of states to consider for the diagonalization + END_DOC + + logical :: has + PROVIDE ezfio_filename + call ezfio_has_determinants_n_states_diag(has) + if (has) then + call ezfio_get_determinants_n_states_diag(N_states_diag) + else + N_states_diag = N_states + endif + + call write_time(output_determinants) + call write_int(output_determinants, N_states_diag, & + 'N_states_diag') + + +END_PROVIDER + diff --git a/src/Dets/program_beginer_determinants.irp.f b/src/Determinants/program_beginer_determinants.irp.f similarity index 100% rename from src/Dets/program_beginer_determinants.irp.f rename to src/Determinants/program_beginer_determinants.irp.f diff --git a/src/Dets/psi_cas.irp.f b/src/Determinants/psi_cas.irp.f similarity index 97% rename from src/Dets/psi_cas.irp.f rename to src/Determinants/psi_cas.irp.f index 299e5e8f..8ca081d6 100644 --- a/src/Dets/psi_cas.irp.f +++ b/src/Determinants/psi_cas.irp.f @@ -38,7 +38,7 @@ use bitmasks enddo endif enddo - call write_int(output_dets,N_det_cas, 'Number of determinants in the CAS') + call write_int(output_determinants,N_det_cas, 'Number of determinants in the CAS') END_PROVIDER diff --git a/src/Dets/ref_bitmask.irp.f b/src/Determinants/ref_bitmask.irp.f similarity index 100% rename from src/Dets/ref_bitmask.irp.f rename to src/Determinants/ref_bitmask.irp.f diff --git a/src/Dets/s2.irp.f b/src/Determinants/s2.irp.f similarity index 100% rename from src/Dets/s2.irp.f rename to src/Determinants/s2.irp.f diff --git a/src/Dets/save_for_casino.irp.f b/src/Determinants/save_for_casino.irp.f similarity index 100% rename from src/Dets/save_for_casino.irp.f rename to src/Determinants/save_for_casino.irp.f diff --git a/src/Dets/save_for_qmcchem.irp.f b/src/Determinants/save_for_qmcchem.irp.f similarity index 94% rename from src/Dets/save_for_qmcchem.irp.f rename to src/Determinants/save_for_qmcchem.irp.f index 7dea70c6..b707ff7c 100644 --- a/src/Dets/save_for_qmcchem.irp.f +++ b/src/Determinants/save_for_qmcchem.irp.f @@ -32,7 +32,7 @@ subroutine save_dets_qmcchem deallocate(occ_tmp) ! OMP END PARALLEL call ezfio_set_determinants_det_occ(occ) - call write_int(output_dets,N_det,'Determinants saved for QMC') + call write_int(output_determinants,N_det,'Determinants saved for QMC') deallocate(occ) open(unit=31,file=trim(ezfio_filename)//'/mo_basis/mo_classif') write(31,'(I1)') 1 diff --git a/src/Dets/save_natorb.irp.f b/src/Determinants/save_natorb.irp.f similarity index 100% rename from src/Dets/save_natorb.irp.f rename to src/Determinants/save_natorb.irp.f diff --git a/src/Dets/slater_rules.irp.f b/src/Determinants/slater_rules.irp.f similarity index 100% rename from src/Dets/slater_rules.irp.f rename to src/Determinants/slater_rules.irp.f diff --git a/src/Dets/spindeterminants.ezfio_config b/src/Determinants/spindeterminants.ezfio_config similarity index 100% rename from src/Dets/spindeterminants.ezfio_config rename to src/Determinants/spindeterminants.ezfio_config diff --git a/src/Dets/spindeterminants.irp.f b/src/Determinants/spindeterminants.irp.f similarity index 100% rename from src/Dets/spindeterminants.irp.f rename to src/Determinants/spindeterminants.irp.f diff --git a/src/Dets/truncate_wf.irp.f b/src/Determinants/truncate_wf.irp.f similarity index 100% rename from src/Dets/truncate_wf.irp.f rename to src/Determinants/truncate_wf.irp.f diff --git a/src/Dets/utils.irp.f b/src/Determinants/utils.irp.f similarity index 100% rename from src/Dets/utils.irp.f rename to src/Determinants/utils.irp.f diff --git a/src/Dets/NEEDED_MODULES b/src/Dets/NEEDED_MODULES deleted file mode 100644 index 824c75ed..00000000 --- a/src/Dets/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Bielec_integrals Bitmask Electrons Ezfio_files MonoInts MOs Nuclei Output Utils diff --git a/src/Dets/determinants.ezfio_config b/src/Dets/determinants.ezfio_config deleted file mode 100644 index 0937502a..00000000 --- a/src/Dets/determinants.ezfio_config +++ /dev/null @@ -1,20 +0,0 @@ -determinants - n_int integer - bit_kind integer - mo_label character*(64) - n_det integer - n_states integer - n_states_diag integer - psi_coef double precision (determinants_n_det,determinants_n_states) - psi_det integer*8 (determinants_n_int*determinants_bit_kind/8,2,determinants_n_det) - n_det_max_jacobi integer - threshold_generators double precision - threshold_selectors double precision - det_num integer - det_occ integer (electrons_elec_alpha_num,determinants_det_num,2) - det_coef double precision (determinants_det_num) - read_wf logical - expected_s2 double precision - s2_eig logical - only_single_double_dm logical - diff --git a/src/Dets/options.irp.f b/src/Dets/options.irp.f deleted file mode 100644 index dda5c04a..00000000 --- a/src/Dets/options.irp.f +++ /dev/null @@ -1,61 +0,0 @@ -BEGIN_SHELL [ /usr/bin/python ] -from ezfio_with_default import EZFIO_Provider -T = EZFIO_Provider() -T.set_type ( "integer" ) -T.set_name ( "N_states" ) -T.set_doc ( "Number of states to consider" ) -T.set_ezfio_dir ( "determinants" ) -T.set_ezfio_name( "N_states" ) -T.set_output ( "output_dets" ) -print T - - -T.set_name ( "N_det_max_jacobi" ) -T.set_doc ( "Maximum number of determinants diagonalized by Jacobi" ) -T.set_ezfio_name( "N_det_max_jacobi" ) -print T - -T.set_type ( "logical" ) -T.set_name ( "read_wf" ) -T.set_doc ( "If true, read the wave function from the EZFIO file" ) -T.set_ezfio_name( "read_wf" ) -T.set_output ( "output_dets" ) -print T - -T.set_type ( "logical" ) -T.set_name ( "only_single_double_dm" ) -T.set_doc ( "If true, The One body DM is calculated with ignoring the Double<->Doubles extra diag elements" ) -T.set_ezfio_name( "only_single_double_dm" ) -T.set_output ( "output_dets" ) -print T - - -T.set_name ( "s2_eig" ) -T.set_doc ( "Force the wave function to be an eigenfunction of S^2" ) -T.set_ezfio_name( "s2_eig" ) -print T - -END_SHELL - -BEGIN_PROVIDER [ integer, N_states_diag ] - implicit none - BEGIN_DOC -! Number of states to consider for the diagonalization - END_DOC - - logical :: has - PROVIDE ezfio_filename - call ezfio_has_determinants_n_states_diag(has) - if (has) then - call ezfio_get_determinants_n_states_diag(N_states_diag) - else - N_states_diag = N_states - endif - - call write_time(output_dets) - call write_int(output_dets, N_states_diag, & - 'N_states_diag') - - -END_PROVIDER - diff --git a/src/Electrons/NEEDED_CHILDREN_MODULES b/src/Electrons/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..83260f86 --- /dev/null +++ b/src/Electrons/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Output diff --git a/src/Electrons/NEEDED_MODULES b/src/Electrons/NEEDED_MODULES deleted file mode 100644 index e9594555..00000000 --- a/src/Electrons/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -Ezfio_files Output Utils diff --git a/src/Electrons/README.rst b/src/Electrons/README.rst index ffd6d21b..e71a552d 100644 --- a/src/Electrons/README.rst +++ b/src/Electrons/README.rst @@ -24,9 +24,7 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `Ezfio_files `_ * `Output `_ -* `Utils `_ Documentation ============= diff --git a/src/Utils/NEEDED_MODULES b/src/Ezfio_files/NEEDED_CHILDREN_MODULES similarity index 100% rename from src/Utils/NEEDED_MODULES rename to src/Ezfio_files/NEEDED_CHILDREN_MODULES diff --git a/src/Ezfio_files/README.rst b/src/Ezfio_files/README.rst index 274eff11..e0ef23da 100644 --- a/src/Ezfio_files/README.rst +++ b/src/Ezfio_files/README.rst @@ -30,3 +30,4 @@ Documentation + diff --git a/src/FCIdump/NEEDED_CHILDREN_MODULES b/src/FCIdump/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..aae89501 --- /dev/null +++ b/src/FCIdump/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Determinants diff --git a/src/FCIdump/NEEDED_MODULES b/src/FCIdump/NEEDED_MODULES deleted file mode 100644 index 7f2f0ca8..00000000 --- a/src/FCIdump/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files MonoInts MOs Nuclei Output Utils diff --git a/src/FCIdump/README.rst b/src/FCIdump/README.rst index 1fdd9660..8a467b16 100644 --- a/src/FCIdump/README.rst +++ b/src/FCIdump/README.rst @@ -21,15 +21,5 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `Dets `_ -* `Electrons `_ -* `Ezfio_files `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ +* `Determinants `_ diff --git a/src/Full_CI/NEEDED_CHILDREN_MODULES b/src/Full_CI/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..04ce9e78 --- /dev/null +++ b/src/Full_CI/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Perturbation Selectors_full Generators_full diff --git a/src/Full_CI/NEEDED_MODULES b/src/Full_CI/NEEDED_MODULES deleted file mode 100644 index 5e074d3c..00000000 --- a/src/Full_CI/NEEDED_MODULES +++ /dev/null @@ -1,2 +0,0 @@ -AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Generators_full Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils - diff --git a/src/Full_CI/README.rst b/src/Full_CI/README.rst index 0b37ca69..51bb05d2 100644 --- a/src/Full_CI/README.rst +++ b/src/Full_CI/README.rst @@ -24,21 +24,7 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `Dets `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Generators_full `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ * `Perturbation `_ -* `Properties `_ * `Selectors_full `_ -* `Utils `_ +* `Generators_full `_ diff --git a/src/Generators_CAS/NEEDED_CHILDREN_MODULES b/src/Generators_CAS/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..aae89501 --- /dev/null +++ b/src/Generators_CAS/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Determinants diff --git a/src/Generators_CAS/NEEDED_MODULES b/src/Generators_CAS/NEEDED_MODULES deleted file mode 100644 index 7f2f0ca8..00000000 --- a/src/Generators_CAS/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files MonoInts MOs Nuclei Output Utils diff --git a/src/Generators_CAS/README.rst b/src/Generators_CAS/README.rst index 53e8c5a0..b729212c 100644 --- a/src/Generators_CAS/README.rst +++ b/src/Generators_CAS/README.rst @@ -43,15 +43,5 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `Dets `_ -* `Electrons `_ -* `Ezfio_files `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ +* `Determinants `_ diff --git a/src/Generators_CAS/generators.irp.f b/src/Generators_CAS/generators.irp.f index 511877a0..f47341de 100644 --- a/src/Generators_CAS/generators.irp.f +++ b/src/Generators_CAS/generators.irp.f @@ -7,7 +7,7 @@ BEGIN_PROVIDER [ integer, N_det_generators ] END_DOC integer :: i,k,l logical :: good - call write_time(output_dets) + call write_time(output_determinants) N_det_generators = 0 do i=1,N_det do l=1,n_cas_bitmask @@ -28,7 +28,7 @@ BEGIN_PROVIDER [ integer, N_det_generators ] endif enddo N_det_generators = max(N_det_generators,1) - call write_int(output_dets,N_det_generators,'Number of generators') + call write_int(output_determinants,N_det_generators,'Number of generators') END_PROVIDER BEGIN_PROVIDER [ integer(bit_kind), psi_det_generators, (N_int,2,psi_det_size) ] diff --git a/src/Generators_full/NEEDED_CHILDREN_MODULES b/src/Generators_full/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..54f54203 --- /dev/null +++ b/src/Generators_full/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Determinants Hartree_Fock diff --git a/src/Generators_full/NEEDED_MODULES b/src/Generators_full/NEEDED_MODULES deleted file mode 100644 index 7d973bce..00000000 --- a/src/Generators_full/NEEDED_MODULES +++ /dev/null @@ -1,2 +0,0 @@ -AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Utils - diff --git a/src/Generators_full/README.rst b/src/Generators_full/README.rst index a8492dbc..e558f48b 100644 --- a/src/Generators_full/README.rst +++ b/src/Generators_full/README.rst @@ -11,25 +11,25 @@ Documentation .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -`degree_max_generators `_ +`degree_max_generators `_ Max degree of excitation (respect to HF) of the generators -`n_det_generators `_ +`n_det_generators `_ For Single reference wave functions, the number of generators is 1 : the Hartree-Fock determinant -`psi_coef_generators `_ +`psi_coef_generators `_ For Single reference wave functions, the generator is the Hartree-Fock determinant -`psi_det_generators `_ +`psi_det_generators `_ For Single reference wave functions, the generator is the Hartree-Fock determinant -`select_max `_ +`select_max `_ Memo to skip useless selectors -`size_select_max `_ +`size_select_max `_ Size of the select_max array @@ -40,17 +40,6 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `Dets `_ -* `Electrons `_ -* `Ezfio_files `_ +* `Determinants `_ * `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ diff --git a/src/Generators_full/generators.irp.f b/src/Generators_full/generators.irp.f index 4d261acd..a61fc5c5 100644 --- a/src/Generators_full/generators.irp.f +++ b/src/Generators_full/generators.irp.f @@ -1,17 +1,5 @@ use bitmasks -BEGIN_SHELL [ /usr/bin/python ] -from ezfio_with_default import EZFIO_Provider -T = EZFIO_Provider() -T.set_type ( "double precision" ) -T.set_name ( "threshold_generators" ) -T.set_doc ( "Percentage of the norm of the state-averaged wave function to consider for the generators" ) -T.set_ezfio_dir ( "determinants" ) -T.set_ezfio_name( "threshold_generators" ) -T.set_output ( "output_dets" ) -print T -END_SHELL - BEGIN_PROVIDER [ integer, N_det_generators ] implicit none BEGIN_DOC @@ -20,7 +8,7 @@ BEGIN_PROVIDER [ integer, N_det_generators ] END_DOC integer :: i double precision :: norm - call write_time(output_dets) + call write_time(output_determinants) norm = 0.d0 N_det_generators = N_det do i=1,N_det @@ -31,7 +19,7 @@ BEGIN_PROVIDER [ integer, N_det_generators ] endif enddo N_det_generators = max(N_det_generators,1) - call write_int(output_dets,N_det_generators,'Number of generators') + call write_int(output_determinants,N_det_generators,'Number of generators') END_PROVIDER BEGIN_PROVIDER [ integer(bit_kind), psi_det_generators, (N_int,2,psi_det_size) ] diff --git a/src/Generators_restart/NEEDED_CHILDREN_MODULES b/src/Generators_restart/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..aae89501 --- /dev/null +++ b/src/Generators_restart/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Determinants diff --git a/src/Generators_restart/NEEDED_MODULES b/src/Generators_restart/NEEDED_MODULES deleted file mode 100644 index 7f2f0ca8..00000000 --- a/src/Generators_restart/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files MonoInts MOs Nuclei Output Utils diff --git a/src/Generators_restart/generators.irp.f b/src/Generators_restart/generators.irp.f index 2e0bc375..0a82e6f9 100644 --- a/src/Generators_restart/generators.irp.f +++ b/src/Generators_restart/generators.irp.f @@ -13,7 +13,7 @@ BEGIN_PROVIDER [ integer, N_det_generators ] N_det_generators = N_det ifirst = 1 endif - call write_int(output_dets,N_det_generators,'Number of generators') + call write_int(output_determinants,N_det_generators,'Number of generators') END_PROVIDER diff --git a/src/Hartree_Fock/NEEDED_CHILDREN_MODULES b/src/Hartree_Fock/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..b779faec --- /dev/null +++ b/src/Hartree_Fock/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Bielec_integrals MOGuess diff --git a/src/Hartree_Fock/NEEDED_MODULES b/src/Hartree_Fock/NEEDED_MODULES deleted file mode 100644 index 8f7f21c6..00000000 --- a/src/Hartree_Fock/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Bielec_integrals Bitmask Electrons Ezfio_files MonoInts MOGuess MOs Nuclei Output Utils diff --git a/src/Hartree_Fock/README.rst b/src/Hartree_Fock/README.rst index a1030e4a..2b470e9f 100644 --- a/src/Hartree_Fock/README.rst +++ b/src/Hartree_Fock/README.rst @@ -10,17 +10,8 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ * `Bielec_integrals `_ -* `Bitmask `_ -* `Electrons `_ -* `Ezfio_files `_ -* `MonoInts `_ * `MOGuess `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ Documentation ============= diff --git a/src/MOGuess/NEEDED_CHILDREN_MODULES b/src/MOGuess/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..88d7352e --- /dev/null +++ b/src/MOGuess/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +MonoInts diff --git a/src/MOGuess/NEEDED_MODULES b/src/MOGuess/NEEDED_MODULES deleted file mode 100644 index 59b334d4..00000000 --- a/src/MOGuess/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Electrons Ezfio_files MonoInts MOs Nuclei Output Utils diff --git a/src/MOGuess/README.rst b/src/MOGuess/README.rst index cb1702ab..771825ee 100644 --- a/src/MOGuess/README.rst +++ b/src/MOGuess/README.rst @@ -8,14 +8,7 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Electrons `_ -* `Ezfio_files `_ * `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ Documentation ============= diff --git a/src/MOs/NEEDED_CHILDREN_MODULES b/src/MOs/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..4692ec21 --- /dev/null +++ b/src/MOs/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +AOs Electrons diff --git a/src/MOs/NEEDED_MODULES b/src/MOs/NEEDED_MODULES deleted file mode 100644 index 5ca73603..00000000 --- a/src/MOs/NEEDED_MODULES +++ /dev/null @@ -1,3 +0,0 @@ -AOs Electrons Ezfio_files Nuclei Output Utils - - diff --git a/src/MOs/README.rst b/src/MOs/README.rst index d7a869b4..5086e4b8 100644 --- a/src/MOs/README.rst +++ b/src/MOs/README.rst @@ -26,10 +26,6 @@ Needed Modules * `AOs `_ * `Electrons `_ -* `Ezfio_files `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ Documentation ============= diff --git a/src/MP2/NEEDED_CHILDREN_MODULES b/src/MP2/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..d26e4dee --- /dev/null +++ b/src/MP2/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Perturbation Selectors_full SingleRefMethod diff --git a/src/MP2/NEEDED_MODULES b/src/MP2/NEEDED_MODULES deleted file mode 100644 index 076746d1..00000000 --- a/src/MP2/NEEDED_MODULES +++ /dev/null @@ -1,2 +0,0 @@ -AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils - diff --git a/src/MP2/README.rst b/src/MP2/README.rst index 92d915b6..f68d5936 100644 --- a/src/MP2/README.rst +++ b/src/MP2/README.rst @@ -19,21 +19,7 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `Dets `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ * `Perturbation `_ -* `Properties `_ * `Selectors_full `_ * `SingleRefMethod `_ -* `Utils `_ diff --git a/src/MRCC/NEEDED_CHILDREN_MODULES b/src/MRCC/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..04ce9e78 --- /dev/null +++ b/src/MRCC/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Perturbation Selectors_full Generators_full diff --git a/src/MRCC/NEEDED_MODULES b/src/MRCC/NEEDED_MODULES deleted file mode 100644 index 5e074d3c..00000000 --- a/src/MRCC/NEEDED_MODULES +++ /dev/null @@ -1,2 +0,0 @@ -AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Generators_full Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils - diff --git a/src/MRCC/README.rst b/src/MRCC/README.rst index 702d19aa..38137667 100644 --- a/src/MRCC/README.rst +++ b/src/MRCC/README.rst @@ -8,23 +8,9 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `Dets `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Generators_full `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ * `Perturbation `_ -* `Properties `_ * `Selectors_full `_ -* `Utils `_ +* `Generators_full `_ Documentation ============= diff --git a/src/MRCC/mrcc_utils.irp.f b/src/MRCC/mrcc_utils.irp.f index d33b7902..9b4add38 100644 --- a/src/MRCC/mrcc_utils.irp.f +++ b/src/MRCC/mrcc_utils.irp.f @@ -94,7 +94,7 @@ END_PROVIDER stop 'use Lapack' ! call davidson_diag(psi_det,CI_eigenvectors_dressed,CI_electronic_energy_dressed, & -! size(CI_eigenvectors_dressed,1),N_det,N_states_diag,N_int,output_Dets) +! size(CI_eigenvectors_dressed,1),N_det,N_states_diag,N_int,output_determinants) else if (diag_algorithm == "Lapack") then @@ -137,7 +137,7 @@ BEGIN_PROVIDER [ double precision, CI_energy_dressed, (N_states_diag) ] integer :: j character*(8) :: st - call write_time(output_Dets) + call write_time(output_determinants) do j=1,N_states_diag CI_energy_dressed(j) = CI_electronic_energy_dressed(j) + nuclear_repulsion enddo diff --git a/src/Makefile b/src/Makefile index 237b3ae4..93b5234f 100644 --- a/src/Makefile +++ b/src/Makefile @@ -12,21 +12,21 @@ EZFIO=$(EZFIO_DIR)/lib/libezfio_irp.a default: ezfio - $(QPACKAGE_ROOT)/scripts/build_modules.sh $(ALL_MODULES) + $(QPACKAGE_ROOT)/scripts/module/build_modules.sh $(ALL_MODULES) veryclean: - $(QPACKAGE_ROOT)/scripts/clean_modules.sh $(ALL_MODULES) + $(QPACKAGE_ROOT)/scripts/module/clean_modules.sh $(ALL_MODULES) # Define the dict [type in EZFIO.cfg] = ocaml type , f90 type # If you change the qptypes_generator.ml, you need to rm this # For simplicity add this to the veryclean rule - rm $(QPACKAGE_ROOT)/scripts/ezfio_interface/fancy_type.p + rm -f $(QPACKAGE_ROOT)/scripts/ezfio_interface/fancy_type.p $(ALL_MODULES): ezfio - $(QPACKAGE_ROOT)/scripts/build_modules.sh $@ + $(QPACKAGE_ROOT)/scripts/module/build_modules.sh $@ # Define the EZFIO rules $(EZFIO): $(wildcard $(QPACKAGE_ROOT)/src/*/*.ezfio_config) $(wildcard $(QPACKAGE_ROOT)/src/*/EZFIO.cfg) - $(QPACKAGE_ROOT)/scripts/prepare_ezfio.sh + $(QPACKAGE_ROOT)/scripts/ezfio_interface/prepare_ezfio.sh cd $(EZFIO_DIR);\ export FC="$(FC)" ; export FCFLAGS="$(FCFLAGS)" ; export IRPF90="$(IRPF90)" ;\ $(MAKE) ;\ diff --git a/src/Makefile.common b/src/Makefile.common index eddaa481..606e6f7c 100644 --- a/src/Makefile.common +++ b/src/Makefile.common @@ -18,8 +18,8 @@ default: all .gitignore # Include the user's config include $(QPACKAGE_ROOT)/src/Makefile.config -# Create the NEEDED_MODULES variable, needed for IRPF90 -NEEDED_MODULES=$(shell cat NEEDED_MODULES) +# Create the NEEDED_CHILDREN_MODULES variable, needed for IRPF90 +NEEDED_CHILDREN_MODULES=$(shell module_handler.py print_genealogy) # Check and update dependencies include Makefile.depend @@ -28,7 +28,7 @@ include Makefile.depend # Define the Makefile common variables EZFIO_DIR=$(QPACKAGE_ROOT)/EZFIO EZFIO=$(EZFIO_DIR)/lib/libezfio_irp.a -INCLUDE_DIRS=$(NEEDED_MODULES) include +INCLUDE_DIRS=$(NEEDED_CHILDREN_MODULES) include clean_links: rm -f $(INCLUDE_DIRS) $$(basename $$PWD) @@ -36,7 +36,7 @@ clean_links: LIB+=$(EZFIO) $(MKL) IRPF90+=$(patsubst %, -I %, $(INCLUDE_DIRS)) $(IRPF90_FLAGS) -irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO) NEEDED_MODULES $(wildcard *.py) +irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO) NEEDED_CHILDREN_MODULES $(wildcard *.py) - $(IRPF90) - update_README.py @@ -45,7 +45,7 @@ include irpf90.make endif .gitignore: - $(QPACKAGE_ROOT)/scripts/create_gitignore.sh + $(QPACKAGE_ROOT)/scripts/create/create_gitignore.sh # Frequent typos clena: clean diff --git a/src/Molden/NEEDED_CHILDREN_MODULES b/src/Molden/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..b936db90 --- /dev/null +++ b/src/Molden/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +MOs diff --git a/src/Molden/NEEDED_MODULES b/src/Molden/NEEDED_MODULES deleted file mode 100644 index 190f8c6e..00000000 --- a/src/Molden/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Electrons Ezfio_files MOs Nuclei Output Utils diff --git a/src/Molden/README.rst b/src/Molden/README.rst index d0e2343d..128a020a 100644 --- a/src/Molden/README.rst +++ b/src/Molden/README.rst @@ -31,11 +31,5 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Electrons `_ -* `Ezfio_files `_ * `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ diff --git a/src/MonoInts/Makefile b/src/MonoInts/Makefile index 06dc50ff..b1f3b02c 100644 --- a/src/MonoInts/Makefile +++ b/src/MonoInts/Makefile @@ -3,4 +3,4 @@ SRC= OBJ= -include $(QPACKAGE_ROOT)/src/Makefile.common +include $(QPACKAGE_ROOT)/src/Makefile.common \ No newline at end of file diff --git a/src/MonoInts/NEEDED_CHILDREN_MODULES b/src/MonoInts/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..be46a359 --- /dev/null +++ b/src/MonoInts/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +MOs Pseudo_integrals diff --git a/src/MonoInts/NEEDED_MODULES b/src/MonoInts/NEEDED_MODULES deleted file mode 100644 index 67230c44..00000000 --- a/src/MonoInts/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Electrons Ezfio_files MOs Nuclei Output Utils diff --git a/src/MonoInts/README.rst b/src/MonoInts/README.rst index fdbb086b..ac4983a9 100644 --- a/src/MonoInts/README.rst +++ b/src/MonoInts/README.rst @@ -4,13 +4,8 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Electrons `_ -* `Ezfio_files `_ * `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ +* `Pseudo_integrals `_ Documentation ============= @@ -69,38 +64,38 @@ Documentation `ao_nucl_elec_integral `_ interaction nuclear electron -`ao_nucl_elec_integral_per_atom `_ +`ao_nucl_elec_integral_per_atom `_ ao_nucl_elec_integral_per_atom(i,j,k) = - where Rk is the geometry of the kth atom -`give_polynom_mult_center_mono_elec `_ +`give_polynom_mult_center_mono_elec `_ Undocumented -`i_x1_pol_mult_mono_elec `_ +`i_x1_pol_mult_mono_elec `_ Undocumented -`i_x2_pol_mult_mono_elec `_ +`i_x2_pol_mult_mono_elec `_ Undocumented -`int_gaus_pol `_ +`int_gaus_pol `_ Undocumented -`nai_pol_mult `_ +`nai_pol_mult `_ Undocumented -`v_e_n `_ +`v_e_n `_ Undocumented -`v_phi `_ +`v_phi `_ Undocumented -`v_r `_ +`v_r `_ Undocumented -`v_theta `_ +`v_theta `_ Undocumented -`wallis `_ +`wallis `_ Undocumented `mo_nucl_elec_integral `_ diff --git a/src/MonoInts/pot_ao_ints.irp.f b/src/MonoInts/pot_ao_ints.irp.f index 32e98a2c..c93301e5 100644 --- a/src/MonoInts/pot_ao_ints.irp.f +++ b/src/MonoInts/pot_ao_ints.irp.f @@ -4,65 +4,74 @@ END_DOC implicit none double precision :: alpha, beta, gama, delta - integer :: i_c,num_A,num_B - double precision :: A_center(3),B_center(3),C_center(3) - integer :: power_A(3),power_B(3) - integer :: i,j,k,l,n_pt_in,m - double precision ::overlap_x,overlap_y,overlap_z,overlap,dx,NAI_pol_mult - integer :: nucl_numC - ! Important for OpenMP + integer :: num_A,num_B + double precision :: A_center(3),B_center(3),C_center(3) + integer :: power_A(3),power_B(3) + integer :: i,j,k,l,n_pt_in,m + double precision ::overlap_x,overlap_y,overlap_z,overlap,dx,NAI_pol_mult - ao_nucl_elec_integral = 0.d0 + if (do_pseudo.eqv..TRUE.) then + ao_nucl_elec_integral = ao_nucl_elec_integral_pseudo + else + ao_nucl_elec_integral = 0.d0 + endif + ! _ + ! /| / |_) + ! | / | \ + ! - !$OMP PARALLEL & - !$OMP DEFAULT (NONE) & - !$OMP PRIVATE (i,j,k,l,m,alpha,beta,A_center,B_center,C_center,power_A,power_B, & - !$OMP num_A,num_B,Z,c,n_pt_in) & - !$OMP SHARED (ao_num,ao_prim_num,ao_expo_ordered_transp,ao_power,ao_nucl,nucl_coord,ao_coef_normalized_ordered_transp, & - !$OMP n_pt_max_integrals,ao_nucl_elec_integral,nucl_num,nucl_charge) - n_pt_in = n_pt_max_integrals - !$OMP DO SCHEDULE (guided) - do j = 1, ao_num - power_A(1)= ao_power(j,1) - power_A(2)= ao_power(j,2) - power_A(3)= ao_power(j,3) - num_A = ao_nucl(j) - A_center(1) = nucl_coord(num_A,1) - A_center(2) = nucl_coord(num_A,2) - A_center(3) = nucl_coord(num_A,3) - do i = 1, ao_num - power_B(1)= ao_power(i,1) - power_B(2)= ao_power(i,2) - power_B(3)= ao_power(i,3) - num_B = ao_nucl(i) - B_center(1) = nucl_coord(num_B,1) - B_center(2) = nucl_coord(num_B,2) - B_center(3) = nucl_coord(num_B,3) - do l=1,ao_prim_num(j) - alpha = ao_expo_ordered_transp(l,j) - do m=1,ao_prim_num(i) - beta = ao_expo_ordered_transp(m,i) - c = 0.d0 - do k = 1, nucl_num - double precision :: Z,c - Z = nucl_charge(k) - C_center(1) = nucl_coord(k,1) - C_center(2) = nucl_coord(k,2) - C_center(3) = nucl_coord(k,3) - c = c+Z*NAI_pol_mult(A_center,B_center,power_A,power_B,alpha,beta,C_center,n_pt_in) - enddo - ao_nucl_elec_integral(i,j) = ao_nucl_elec_integral(i,j) - & - ao_coef_normalized_ordered_transp(l,j)*ao_coef_normalized_ordered_transp(m,i)*c + !$OMP PARALLEL & + !$OMP DEFAULT (NONE) & + !$OMP PRIVATE (i,j,k,l,m,alpha,beta,A_center,B_center,C_center,power_A,power_B, & + !$OMP num_A,num_B,Z,c,n_pt_in) & + !$OMP SHARED (ao_num,ao_prim_num,ao_expo_ordered_transp,ao_power,ao_nucl,nucl_coord,ao_coef_normalized_ordered_transp, & + !$OMP n_pt_max_integrals,ao_nucl_elec_integral,nucl_num,nucl_charge) + + n_pt_in = n_pt_max_integrals + + !$OMP DO SCHEDULE (guided) + + do j = 1, ao_num + num_A = ao_nucl(j) + power_A(1:3)= ao_power(j,1:3) + A_center(1:3) = nucl_coord(num_A,1:3) + + do i = 1, ao_num + + num_B = ao_nucl(i) + power_B(1:3)= ao_power(i,1:3) + B_center(1:3) = nucl_coord(num_B,1:3) + + do l=1,ao_prim_num(j) + alpha = ao_expo_ordered_transp(l,j) + + do m=1,ao_prim_num(i) + beta = ao_expo_ordered_transp(m,i) + + double precision :: c + c = 0.d0 + + do k = 1, nucl_num + double precision :: Z + Z = nucl_charge(k) + + C_center(1:3) = nucl_coord(k,1:3) + + c = c - Z*NAI_pol_mult(A_center,B_center,power_A,power_B,alpha,beta,C_center,n_pt_in) + + enddo + ao_nucl_elec_integral(i,j) = ao_nucl_elec_integral(i,j) + & + ao_coef_normalized_ordered_transp(l,j)*ao_coef_normalized_ordered_transp(m,i)*c + enddo + enddo enddo - enddo enddo - enddo + !$OMP END DO !$OMP END PARALLEL -END_PROVIDER - + END_PROVIDER BEGIN_PROVIDER [ double precision, ao_nucl_elec_integral_per_atom, (ao_num_align,ao_num,nucl_num)] BEGIN_DOC @@ -76,7 +85,6 @@ END_PROVIDER integer :: power_A(3),power_B(3) integer :: i,j,k,l,n_pt_in,m double precision ::overlap_x,overlap_y,overlap_z,overlap,dx,NAI_pol_mult - integer :: nucl_numC ! Important for OpenMP ao_nucl_elec_integral_per_atom = 0.d0 diff --git a/src/NEEDED_MODULES b/src/NEEDED_MODULES index efe8b8f8..4533ccfe 100644 --- a/src/NEEDED_MODULES +++ b/src/NEEDED_MODULES @@ -1 +1 @@ -AOs Bielec_integrals Bitmask CID CID_SC2_selected CID_selected CIS CISD CISD_selected CISD_SC2_selected Dets Electrons Ezfio_files Full_CI Generators_full Hartree_Fock MOGuess MonoInts MOs MP2 Nuclei Output Selectors_full Utils Molden FCIdump Generators_CAS CAS_SD DDCI_selected MRCC +AOs Bielec_integrals Bitmask CID CID_SC2_selected CID_selected CIS CISD CISD_selected CISD_SC2_selected Determinants Electrons Ezfio_files Full_CI Generators_full Hartree_Fock MOGuess MonoInts MOs MP2 Nuclei Output Selectors_full Utils Molden FCIdump Generators_CAS CAS_SD DDCI_selected MRCC Pseudo_integrals diff --git a/src/Nuclei/NEEDED_CHILDREN_MODULES b/src/Nuclei/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..83260f86 --- /dev/null +++ b/src/Nuclei/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Output diff --git a/src/Nuclei/NEEDED_MODULES b/src/Nuclei/NEEDED_MODULES deleted file mode 100644 index 516a2a11..00000000 --- a/src/Nuclei/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -Ezfio_files Utils Output diff --git a/src/Nuclei/README.rst b/src/Nuclei/README.rst index b21d02ee..aaad706d 100644 --- a/src/Nuclei/README.rst +++ b/src/Nuclei/README.rst @@ -12,8 +12,6 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `Ezfio_files `_ -* `Utils `_ * `Output `_ Documentation diff --git a/src/Output/NEEDED_CHILDREN_MODULES b/src/Output/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..dcdb5f86 --- /dev/null +++ b/src/Output/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Ezfio_files Utils diff --git a/src/Output/NEEDED_MODULES b/src/Output/NEEDED_MODULES deleted file mode 100644 index 5d0065cc..00000000 --- a/src/Output/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -Utils diff --git a/src/Output/README.rst b/src/Output/README.rst index adcae302..5fe93f50 100644 --- a/src/Output/README.rst +++ b/src/Output/README.rst @@ -31,6 +31,7 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. +* `Ezfio_files `_ * `Utils `_ Documentation diff --git a/src/Output/output.irp.f b/src/Output/output.irp.f index d227dda8..85f5cc0e 100644 --- a/src/Output/output.irp.f +++ b/src/Output/output.irp.f @@ -19,7 +19,7 @@ BEGIN_SHELL [ /bin/bash ] BEGIN_DOC ! Output file for $NAME END_DOC - PROVIDE output_wall_time_0 output_cpu_time_0 + PROVIDE output_wall_time_0 output_cpu_time_0 ezfio_filename integer :: getUnitAndOpen call ezfio_set_output_empty(.False.) IRP_IF COARRAY diff --git a/src/Perturbation/NEEDED_CHILDREN_MODULES b/src/Perturbation/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..e29a6721 --- /dev/null +++ b/src/Perturbation/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Properties Hartree_Fock diff --git a/src/Perturbation/NEEDED_MODULES b/src/Perturbation/NEEDED_MODULES deleted file mode 100644 index 4fa6ff4b..00000000 --- a/src/Perturbation/NEEDED_MODULES +++ /dev/null @@ -1,2 +0,0 @@ -AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Properties Utils - diff --git a/src/Perturbation/selection.irp.f b/src/Perturbation/selection.irp.f index 4230293a..77313888 100644 --- a/src/Perturbation/selection.irp.f +++ b/src/Perturbation/selection.irp.f @@ -135,7 +135,7 @@ subroutine remove_small_contributions if (N_removed > 0) then N_det = N_det - N_removed SOFT_TOUCH N_det psi_det psi_coef - call write_int(output_dets,N_removed, 'Removed determinants') + call write_int(output_determinants,N_removed, 'Removed determinants') endif end diff --git a/src/Properties/EZFIO.cfg b/src/Properties/EZFIO.cfg new file mode 100644 index 00000000..d230011d --- /dev/null +++ b/src/Properties/EZFIO.cfg @@ -0,0 +1,5 @@ +[z_one_point] +type: double precision +doc: z point on which the integrated delta rho is calculated +interface: input +default: 3.9 \ No newline at end of file diff --git a/src/Properties/NEEDED_CHILDREN_MODULES b/src/Properties/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..aae89501 --- /dev/null +++ b/src/Properties/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Determinants diff --git a/src/Properties/NEEDED_MODULES b/src/Properties/NEEDED_MODULES deleted file mode 100644 index 9095dbdf..00000000 --- a/src/Properties/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files MonoInts MOs Nuclei Output Utils diff --git a/src/Properties/options.irp.f b/src/Properties/options.irp.f deleted file mode 100644 index 0fd5a4c1..00000000 --- a/src/Properties/options.irp.f +++ /dev/null @@ -1,13 +0,0 @@ -BEGIN_SHELL [ /usr/bin/python ] -from ezfio_with_default import EZFIO_Provider -T = EZFIO_Provider() -T.set_type ( "double precision" ) -T.set_name ( "z_one_point" ) -T.set_doc ( "z point on which the integrated delta rho is calculated" ) -T.set_ezfio_dir ( "properties" ) -T.set_ezfio_name( "z_one_point" ) -T.set_output ( "output_full_ci" ) -print T - -END_SHELL - diff --git a/src/Properties/properties.ezfio_config b/src/Properties/properties.ezfio_config deleted file mode 100644 index 018b56d0..00000000 --- a/src/Properties/properties.ezfio_config +++ /dev/null @@ -1,2 +0,0 @@ -properties - z_one_point double precision diff --git a/src/Ezfio_files/NEEDED_MODULES b/src/Pseudo_integrals/ASSUMPTIONS.rst similarity index 100% rename from src/Ezfio_files/NEEDED_MODULES rename to src/Pseudo_integrals/ASSUMPTIONS.rst diff --git a/src/Pseudo_integrals/EZFIO.cfg b/src/Pseudo_integrals/EZFIO.cfg new file mode 100644 index 00000000..f56bc325 --- /dev/null +++ b/src/Pseudo_integrals/EZFIO.cfg @@ -0,0 +1,5 @@ +[do_pseudo] +type: logical +doc: Using pseudo potential integral of not +interface: input +default: False \ No newline at end of file diff --git a/src/Pseudo_integrals/Makefile b/src/Pseudo_integrals/Makefile new file mode 100644 index 00000000..5cf11b78 --- /dev/null +++ b/src/Pseudo_integrals/Makefile @@ -0,0 +1,6 @@ +# Define here all new external source files and objects.Don't forget to prefix the +# object files with IRPF90_temp/ +SRC=int.f90 +OBJ=IRPF90_temp/int.o + +include $(QPACKAGE_ROOT)/src/Makefile.common diff --git a/src/Pseudo_integrals/NEEDED_CHILDREN_MODULES b/src/Pseudo_integrals/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..88c6f86b --- /dev/null +++ b/src/Pseudo_integrals/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +AOs Electrons diff --git a/src/Pseudo_integrals/README.rst b/src/Pseudo_integrals/README.rst new file mode 100644 index 00000000..08076556 --- /dev/null +++ b/src/Pseudo_integrals/README.rst @@ -0,0 +1,24 @@ +======================= +Pseudo_integrals Module +======================= + +Documentation +============= + +.. Do not edit this section. It was auto-generated from the +.. NEEDED_MODULES file. + +`ao_nucl_elec_integral_pseudo `_ + interaction nuclear electron + + + +Needed Modules +============== + +.. Do not edit this section. It was auto-generated from the +.. NEEDED_MODULES file. + +* `AOs `_ +* `Electrons `_ + diff --git a/src/Pseudo_integrals/int.f90 b/src/Pseudo_integrals/int.f90 new file mode 100644 index 00000000..be806b3f --- /dev/null +++ b/src/Pseudo_integrals/int.f90 @@ -0,0 +1,2101 @@ +!! Vps= +!! +!! with: Vloc(C)=\sum_{k=1}^klocmax v_k rC**n_k exp(-dz_k rC**2) +!! Vpp(C)=\sum_{l=0}^lmax\sum_{k=1}^kmax v_kl rC**n_kl exp(-dz_kl rC**2)*|l> 0 factor* P_l^|m|(cos(theta)) cos (|m| phi) +! m = 0 1/sqrt(2) *factor* P_l^0(cos(theta)) +! m < 0 factor* P_l^|m|(cos(theta)) sin (|m| phi) +! +! x=cos(theta) + + double precision function ylm_real(l,m,x,phi) + implicit double precision (a-h,o-z) + DIMENSION PM(0:100,0:100) + MM=100 + pi=dacos(-1.d0) + iabs_m=iabs(m) + if(iabs_m.gt.l)stop 'm must be between -l and l' + factor= dsqrt( ((2*l+1)*fact(l-iabs_m))/(4.d0*pi*fact(l+iabs_m)) ) + if(dabs(x).gt.1.d0)then + print*,'pb. in ylm_no' + print*,'x=',x + stop + endif + call LPMN(MM,l,l,X,PM) + plm=PM(iabs_m,l) + coef=factor*plm + if(m.gt.0)ylm_real=dsqrt(2.d0)*coef*dcos(iabs_m*phi) + if(m.eq.0)ylm_real=coef + if(m.lt.0)ylm_real=dsqrt(2.d0)*coef*dsin(iabs_m*phi) + + fourpi=4.d0*dacos(-1.d0) + if(l.eq.0)ylm_real=dsqrt(1.d0/fourpi) + + xchap=dsqrt(1.d0-x**2)*dcos(phi) + ychap=dsqrt(1.d0-x**2)*dsin(phi) + zchap=x + if(l.eq.1.and.m.eq.1)ylm_real=dsqrt(3.d0/fourpi)*xchap + if(l.eq.1.and.m.eq.0)ylm_real=dsqrt(3.d0/fourpi)*zchap + if(l.eq.1.and.m.eq.-1)ylm_real=dsqrt(3.d0/fourpi)*ychap + + if(l.eq.2.and.m.eq.2)ylm_real=dsqrt(15.d0/16.d0/pi)*(xchap**2-ychap**2) + if(l.eq.2.and.m.eq.1)ylm_real=dsqrt(15.d0/fourpi)*xchap*zchap + if(l.eq.2.and.m.eq.0)ylm_real=dsqrt(5.d0/16.d0/pi)*(-xchap**2-ychap**2+2.d0*zchap**2) + if(l.eq.2.and.m.eq.-1)ylm_real=dsqrt(15.d0/fourpi)*ychap*zchap + if(l.eq.2.and.m.eq.-2)ylm_real=dsqrt(15.d0/fourpi)*xchap*ychap + + if(l.gt.2)stop 'l > 2 not coded!' + + end +! _ +! | | +! __ __ _ __ ___ ___ _ _ __| | ___ +! \ \ / / | '_ \/ __|/ _ \ | | |/ _` |/ _ \ +! \ V / | |_) \__ \ __/ |_| | (_| | (_) | +! \_/ | .__/|___/\___|\__,_|\____|\___/ +! | | +! |_| + +!! Routine Vpseudo is based on formumla (66) +!! of Kahn Baybutt TRuhlar J.Chem.Phys. vol.65 3826 (1976): +!! +!! Vpseudo= (4pi)**2* \sum_{l=0}^lmax \sum_{m=-l}^{l} +!! \sum{lambda=0}^{l+nA} \sum_{mu=-lambda}^{lambda} +!! \sum{k1=0}^{nAx} \sum{k2=0}^{nAy} \sum{k3=0}^{nAz} +!! binom(nAx,k1)*binom(nAy,k2)*binom(nAz,k3)* Y_{lambda mu}(AC_unit) +!! *CAx**(nAx-k1)*CAy**(nAy-k2)*CAz**(nAz-k3)* +!! bigI(lambda,mu,l,m,k1,k2,k3) +!! \sum{lambdap=0}^{l+nB} \sum_{mup=-lambdap}^{lambdap} +!! \sum{k1p=0}^{nBx} \sum{k2p=0}^{nBy} \sum{k3p=0}^{nBz} +!! binom(nBx,k1p)*binom(nBy,k2p)*binom(nBz,k3p)* Y_{lambdap mup}(BC_unit) +!! *CBx**(nBx-k1p)*CBy**(nBy-k2p)*CBz**(nBz-k3p)* +!! bigI(lambdap,mup,l,m,k1p,k2p,k3p)* +!! \sum_{k=1}^{kmax} v_kl(k,l)* +!! bigR(lambda,lambdap,k1+k2+k3+k1p+k2p+k3p+n_kl(k,l),g_a,g_b,AC,BC,dz_kl(k,l)) +!! +!! nA=nAx+nAy+nAz +!! nB=nBx+nBy+nBz +!! AC=|A-C| +!! AC_x= A_x-C_x, etc. +!! BC=|B-C| +!! AC_unit= vect(AC)/AC +!! BC_unit= vect(BC)/BC +!! bigI(lambda,mu,l,m,k1,k2,k3)= +!! \int dOmega Y_{lambda mu}(Omega) xchap^k1 ychap^k2 zchap^k3 Y_{l m}(Omega) +!! +!! bigR(lambda,lambdap,N,g_a,g_b,gamm_k,AC,BC) +!! = exp(-g_a* AC**2 -g_b* BC**2) * int_prod_bessel_loc(ktot+2,g_a+g_b+dz_k(k),l,dreal) +!! /int dx x^{ktot} exp(-g_k)*x**2) M_lambda(2 g_k D x) + +double precision function Vpseudo & +(lmax,kmax,v_kl,n_kl,dz_kl,a,n_a,g_a,b,n_b,g_b,c) +implicit none + +! ___ +! | ._ ._ _|_ +! _|_ | | |_) |_| |_ +! | +double precision, intent(in) :: a(3),g_a,b(3),g_b,c(3) +integer, intent(in) :: lmax,kmax,n_kl(kmax,0:lmax) +integer, intent(in) :: n_a(3),n_b(3) +double precision, intent(in) :: v_kl(kmax,0:lmax),dz_kl(kmax,0:lmax) + +! +! | _ _ _. | _ +! |_ (_) (_ (_| | (/_ +! + +double precision :: fourpi,f,prod,prodp,binom,accu,bigR,bigI,ylm +double precision :: theta_AC0,phi_AC0,theta_BC0,phi_BC0,ac,bc,big +double precision :: areal,freal,breal,t1,t2,int_prod_bessel, int_prod_bessel_num_soph_p +double precision :: arg + +integer :: ntot,ntotA,m,mu,mup,k1,k2,k3,ntotB,k1p,k2p,k3p,lambda,lambdap,ktot +integer :: l,k, nkl_max + +! _ +! |_) o _ _. ._ ._ _. +! |_) | (_| (_| | | (_| \/ +! _| / + +double precision, allocatable :: array_coefs_A(:,:,:) +double precision, allocatable :: array_coefs_B(:,:,:) + +double precision, allocatable :: array_R(:,:,:,:,:) +double precision, allocatable :: array_I_A(:,:,:,:,:) +double precision, allocatable :: array_I_B(:,:,:,:,:) + + +! _ +! / _. | _ | +! \_ (_| | (_ |_| | +! + +if (kmax.eq.1.and.lmax.eq.0.and.v_kl(1,0).eq.0.d0) then + Vpseudo=0.d0 + return +end if + +fourpi=4.d0*dacos(-1.d0) +ac=dsqrt((a(1)-c(1))**2+(a(2)-c(2))**2+(a(3)-c(3))**2) +bc=dsqrt((b(1)-c(1))**2+(b(2)-c(2))**2+(b(3)-c(3))**2) +arg=g_a*ac**2+g_b*bc**2 + +if(arg.gt.-dlog(1.d-20))then + Vpseudo=0.d0 + return +endif + +freal=dexp(-arg) + +areal=2.d0*g_a*ac +breal=2.d0*g_b*bc +ntotA=n_a(1)+n_a(2)+n_a(3) +ntotB=n_b(1)+n_b(2)+n_b(3) +ntot=ntotA+ntotB + +nkl_max=4 +!=!=!=!=!=!=!=!=!=! +! A l l o c a t e ! +!=!=!=!=!=!=!=!=!=! + +allocate (array_coefs_A(0:ntot,0:ntot,0:ntot)) +allocate (array_coefs_B(0:ntot,0:ntot,0:ntot)) + +allocate (array_R(0:ntot+nkl_max,kmax,0:lmax,0:lmax+ntot,0:lmax+ntot)) + +allocate (array_I_A(0:lmax+ntot,-(lmax+ntot):lmax+ntot,0:ntot,0:ntot,0:ntot)) + +allocate (array_I_B(0:lmax+ntot,-(lmax+ntot):lmax+ntot,0:ntot,0:ntot,0:ntot)) + +if(ac.eq.0.d0.and.bc.eq.0.d0)then + + + !=!=!=!=!=! + ! I n i t ! + !=!=!=!=!=! + + accu=0.d0 + + !=!=!=!=!=!=!=! + ! c a l c u l ! + !=!=!=!=!=!=!=! + + do k=1,kmax + do l=0,lmax + ktot=ntot+n_kl(k,l) + do m=-l,l + prod=bigI(0,0,l,m,n_a(1),n_a(2),n_a(3)) + prodp=bigI(0,0,l,m,n_b(1),n_b(2),n_b(3)) + + accu=accu+prod*prodp*v_kl(k,l)*int_prod_bessel_num_soph_p(ktot+2,g_a+g_b+dz_kl(k,l),0,0,areal,breal,arg) + + enddo + enddo + enddo + + !=!=!=!=! + ! E n d ! + !=!=!=!=! + + Vpseudo=accu*fourpi + +else if(ac.ne.0.d0.and.bc.ne.0.d0)then + + !=!=!=!=!=! + ! I n i t ! + !=!=!=!=!=! + + f=fourpi**2 + + theta_AC0=dacos( (a(3)-c(3))/ac ) + phi_AC0=datan2((a(2)-c(2))/ac,(a(1)-c(1))/ac) + theta_BC0=dacos( (b(3)-c(3))/bc ) + phi_BC0=datan2((b(2)-c(2))/bc,(b(1)-c(1))/bc) + + + + + do ktot=0,ntotA+ntotB+nkl_max + do lambda=0,lmax+ntotA + do lambdap=0,lmax+ntotB + do k=1,kmax + do l=0,lmax + array_R(ktot,k,l,lambda,lambdap)= int_prod_bessel_num_soph_p(ktot+2,g_a+g_b+dz_kl(k,l),lambda,lambdap,areal,breal,arg) + enddo + enddo + enddo + enddo + enddo + + do k1=0,n_a(1) + do k2=0,n_a(2) + do k3=0,n_a(3) + array_coefs_A(k1,k2,k3)=binom(n_a(1),k1)*binom(n_a(2),k2)*binom(n_a(3),k3) & + *(c(1)-a(1))**(n_a(1)-k1)*(c(2)-a(2))**(n_a(2)-k2)*(c(3)-a(3))**(n_a(3)-k3) + enddo + enddo + enddo + + do k1p=0,n_b(1) + do k2p=0,n_b(2) + do k3p=0,n_b(3) + array_coefs_B(k1p,k2p,k3p)=binom(n_b(1),k1p)*binom(n_b(2),k2p)*binom(n_b(3),k3p) & + *(c(1)-b(1))**(n_b(1)-k1p)*(c(2)-b(2))**(n_b(2)-k2p)*(c(3)-b(3))**(n_b(3)-k3p) + enddo + enddo + enddo + + !=!=!=!=!=!=!=! + ! c a l c u l ! + !=!=!=!=!=!=!=! + + accu=0.d0 + do l=0,lmax + do m=-l,l + + do lambda=0,l+ntotA + do mu=-lambda,lambda + do k1=0,n_a(1) + do k2=0,n_a(2) + do k3=0,n_a(3) + array_I_A(lambda,mu,k1,k2,k3)=bigI(lambda,mu,l,m,k1,k2,k3) + enddo + enddo + enddo + enddo + enddo + + do lambdap=0,l+ntotB + do mup=-lambdap,lambdap + do k1p=0,n_b(1) + do k2p=0,n_b(2) + do k3p=0,n_b(3) + array_I_B(lambdap,mup,k1p,k2p,k3p)=bigI(lambdap,mup,l,m,k1p,k2p,k3p) + enddo + enddo + enddo + enddo + enddo + + do lambda=0,l+ntotA + do mu=-lambda,lambda + + do k1=0,n_a(1) + do k2=0,n_a(2) + do k3=0,n_a(3) + + prod=ylm(lambda,mu,theta_AC0,phi_AC0)*array_coefs_A(k1,k2,k3)*array_I_A(lambda,mu,k1,k2,k3) + + do lambdap=0,l+ntotB + do mup=-lambdap,lambdap + + do k1p=0,n_b(1) + do k2p=0,n_b(2) + do k3p=0,n_b(3) + + prodp=ylm(lambdap,mup,theta_BC0,phi_BC0)*array_coefs_B(k1p,k2p,k3p)*array_I_B(lambdap,mup,k1p,k2p,k3p) + + do k=1,kmax + ktot=k1+k2+k3+k1p+k2p+k3p+n_kl(k,l) + accu=accu+prod*prodp*v_kl(k,l)*array_R(ktot,k,l,lambda,lambdap) + enddo + + enddo + enddo + enddo + + enddo + enddo + + enddo + enddo + enddo + + enddo + enddo + + enddo + enddo + + !=!=!=!=! + ! E n d ! + !=!=!=!=! + + Vpseudo=f*accu + +else if(ac.eq.0.d0.and.bc.ne.0.d0)then + + !=!=!=!=!=! + ! I n i t ! + !=!=!=!=!=! + + f=fourpi**1.5d0 + theta_BC0=dacos( (b(3)-c(3))/bc ) + phi_BC0=datan2((b(2)-c(2))/bc,(b(1)-c(1))/bc) + + areal=2.d0*g_a*ac + breal=2.d0*g_b*bc + freal=dexp(-g_a*ac**2-g_b*bc**2) + + do ktot=0,ntotA+ntotB+nkl_max + do lambdap=0,lmax+ntotB + do k=1,kmax + do l=0,lmax + + array_R(ktot,k,l,0,lambdap)= int_prod_bessel_num_soph_p(ktot+2,g_a+g_b+dz_kl(k,l),0,lambdap,areal,breal,arg) + enddo + enddo + enddo + enddo + + do k1p=0,n_b(1) + do k2p=0,n_b(2) + do k3p=0,n_b(3) + + array_coefs_B(k1p,k2p,k3p)=binom(n_b(1),k1p)*binom(n_b(2),k2p)*binom(n_b(3),k3p) & + *(c(1)-b(1))**(n_b(1)-k1p)*(c(2)-b(2))**(n_b(2)-k2p)*(c(3)-b(3))**(n_b(3)-k3p) + enddo + enddo + enddo + + !=!=!=!=!=!=!=! + ! c a l c u l ! + !=!=!=!=!=!=!=! + + accu=0.d0 + do l=0,lmax + do m=-l,l + + do lambdap=0,l+ntotB + do mup=-lambdap,lambdap + do k1p=0,n_b(1) + do k2p=0,n_b(2) + do k3p=0,n_b(3) + array_I_B(lambdap,mup,k1p,k2p,k3p)=bigI(lambdap,mup,l,m,k1p,k2p,k3p) + enddo + enddo + enddo + enddo + enddo + + prod=bigI(0,0,l,m,n_a(1),n_a(2),n_a(3)) + + do lambdap=0,l+ntotB + do mup=-lambdap,lambdap + do k1p=0,n_b(1) + do k2p=0,n_b(2) + do k3p=0,n_b(3) + + prodp=array_coefs_B(k1p,k2p,k3p)*ylm(lambdap,mup,theta_BC0,phi_BC0)*array_I_B(lambdap,mup,k1p,k2p,k3p) + + do k=1,kmax + + ktot=ntotA+k1p+k2p+k3p+n_kl(k,l) + accu=accu+prod*prodp*v_kl(k,l)*array_R(ktot,k,l,0,lambdap) + + enddo + + enddo + enddo + enddo + enddo + enddo + enddo + enddo + + !=!=!=!=! + ! E n d ! + !=!=!=!=! + + Vpseudo=f*accu + +else if(ac.ne.0.d0.and.bc.eq.0.d0)then + + !=!=!=!=!=! + ! I n i t ! + !=!=!=!=!=! + + f=fourpi**1.5d0 + theta_AC0=dacos( (a(3)-c(3))/ac ) + phi_AC0=datan2((a(2)-c(2))/ac,(a(1)-c(1))/ac) + + areal=2.d0*g_a*ac + breal=2.d0*g_b*bc + freal=dexp(-g_a*ac**2-g_b*bc**2) + + do ktot=0,ntotA+ntotB+nkl_max + do lambda=0,lmax+ntotA + do k=1,kmax + do l=0,lmax + + array_R(ktot,k,l,lambda,0)= int_prod_bessel_num_soph_p(ktot+2,g_a+g_b+dz_kl(k,l),lambda,0,areal,breal,arg) + enddo + enddo + enddo + enddo + + do k1=0,n_a(1) + do k2=0,n_a(2) + do k3=0,n_a(3) + + array_coefs_A(k1,k2,k3)=binom(n_a(1),k1)*binom(n_a(2),k2)*binom(n_a(3),k3) & + *(c(1)-a(1))**(n_a(1)-k1)*(c(2)-a(2))**(n_a(2)-k2)*(c(3)-a(3))**(n_a(3)-k3) + + enddo + enddo + enddo + + !=!=!=!=!=!=!=! + ! c a l c u l ! + !=!=!=!=!=!=!=! + + accu=0.d0 + do l=0,lmax + do m=-l,l + + do lambda=0,l+ntotA + do mu=-lambda,lambda + do k1=0,n_a(1) + do k2=0,n_a(2) + do k3=0,n_a(3) + array_I_A(lambda,mu,k1,k2,k3)=bigI(lambda,mu,l,m,k1,k2,k3) + enddo + enddo + enddo + enddo + enddo + + do lambda=0,l+ntotA + do mu=-lambda,lambda + do k1=0,n_a(1) + do k2=0,n_a(2) + do k3=0,n_a(3) + + prod=array_coefs_A(k1,k2,k3)*ylm(lambda,mu,theta_AC0,phi_AC0)*array_I_A(lambda,mu,k1,k2,k3) + prodp=bigI(0,0,l,m,n_b(1),n_b(2),n_b(3)) + + do k=1,kmax + ktot=k1+k2+k3+ntotB+n_kl(k,l) + accu=accu+prod*prodp*v_kl(k,l)*array_R(ktot,k,l,lambda,0) + enddo + + enddo + enddo + enddo + enddo + enddo + + enddo + enddo + + !=!=!=!=! + ! E n d ! + !=!=!=!=! + + Vpseudo=f*accu +endif + +! _ +! |_ o ._ _. | o _ _ +! | | | | (_| | | _> (/_ +! + deallocate (array_R, array_I_A, array_I_B) + deallocate (array_coefs_A, array_coefs_B) + return +end + +! _ +! | | +!__ __ _ __ ___ ___ _ _ __| | ___ _ __ _ _ _ __ ___ +!\ \ / / | '_ \/ __|/ _ \ | | |/ _` |/ _ \ | '_ \| | | | '_ ` _ \ +! \ V / | |_) \__ \ __/ |_| | (_| | (_) | | | | | |_| | | | | | | +! \_/ | .__/|___/\___|\__,_|\__,_|\___/ |_| |_|\__,_|_| |_| |_| +! | | +! |_| + +double precision function Vpseudo_num(npts,rmax,lmax,kmax,v_kl,n_kl,dz_kl,a,n_a,g_a,b,n_b,g_b,c) +implicit none + + +! ___ +! | ._ ._ _|_ +! _|_ | | |_) |_| |_ +! | +double precision, intent(in) :: a(3),g_a,b(3),g_b,c(3) +integer, intent(in) :: lmax,kmax,npts +integer, intent(in) :: n_a(3),n_b(3), n_kl(kmax,0:lmax) +double precision, intent(in) :: v_kl(kmax,0:lmax),dz_kl(kmax,0:lmax) +double precision, intent(in) :: rmax + +! +! | _ _ _. | _ +! |_ (_) (_ (_| | (/_ +! + +integer :: l,m,k,kk +double precision ac(3),bc(3) +double precision dr,sum,rC +double precision overlap_orb_ylm_brute + +! _ +! / _. | _ | +! \_ (_| | (_ |_| | +! + +do l=1,3 + ac(l)=a(l)-c(l) + bc(l)=b(l)-c(l) +enddo + +dr=rmax/npts +sum=0.d0 +do l=0,lmax + do m=-l,l + do k=1,npts + rC=(k-1)*dr+dr/2.d0 + do kk=1,kmax + sum=sum+dr*v_kl(kk,l)*rC**(n_kl(kk,l)+2)*dexp(-dz_kl(kk,l)*rC**2) & + *overlap_orb_ylm_brute(npts,rC,n_a,ac,g_a,l,m) & + *overlap_orb_ylm_brute(npts,rC,n_b,bc,g_b,l,m) + enddo + enddo + enddo +enddo +Vpseudo_num=sum +return +end +!! Routine Vloc is a variation of formumla (66) +!! of Kahn Baybutt TRuhlar J.Chem.Phys. vol.65 3826 (1976) +!! without the projection operator +!! +!! Vloc= (4pi)**3/2* \sum_{k=1}^{klocmax} \sum_{l=0}^lmax \sum_{m=-l}^{l} +!!\sum{k1=0}^{nAx} \sum{k2=0}^{nAy} \sum{k3=0}^{nAz} +!! binom(nAx,k1)*binom(nAy,k2)*binom(nAz,k3) +!! *CAx**(nAx-k1)*CAy**(nAy-k2)*CAz**(nAz-k3)* +!! \sum{k1p=0}^{nBx} \sum{k2p=0}^{nBy} \sum{k3p=0}^{nBz} +!! binom(nBx,k1p)*binom(nBy,k2p)*binom(nBz,k3p) +!! *CBx**(nBx-k1p)*CBy**(nBy-k2p)*CBz**(nBz-k3p)* +!!\sum_{l=0}^lmax \sum_{m=-l}^{l} + +!! bigI(0,0,l,m,k1+k1p,k2+k2p,k3+k3p)*Y_{l m}(D_unit) +!! *v_k(k)* bigR(lambda,k1+k2+k3+k1p+k2p+k3p+n_k(k),g_a,g_b,AC,BC,dz_k(k)) +!! +!! nA=nAx+nAy+nAz +!! nB=nBx+nBy+nBz +!! D=(g_a AC+g_b BC) +!! D_unit= vect(D)/D +!! AC_x= A_x-C_x, etc. +!! BC=|B-C| +!! AC_unit= vect(AC)/AC +!! BC_unit= vect(BC)/BCA +!! +!! bigR(lambda,g_a,g_b,g_k,AC,BC) +!! = exp(-g_a* AC**2 -g_b* BC**2)* +!! I_loc= \int dx x**l *exp(-gam*x**2) M_n(ax) l=ktot+2 gam=g_a+g_b+dz_k(k) a=dreal n=l +!! M_n(x) modified spherical bessel function + + +double precision function Vloc(klocmax,v_k,n_k,dz_k,a,n_a,g_a,b,n_b,g_b,c) +implicit none +integer klocmax_max,lmax_max,ntot_max +parameter (klocmax_max=10,lmax_max=2) +parameter (ntot_max=10) +integer klocmax +double precision v_k(klocmax_max),dz_k(klocmax_max),crochet,bigA +integer n_k(klocmax_max) +double precision a(3),g_a,b(3),g_b,c(3),d(3) +integer n_a(3),n_b(3),ntotA,ntotB,ntot,m +integer i,l,k,ktot,k1,k2,k3,k1p,k2p,k3p +double precision f,fourpi,ac,bc,freal,d2,dreal,theta_DC0,phi_DC0 +double precision,allocatable :: array_R_loc(:,:,:) +double precision,allocatable :: array_coefs(:,:,:,:,:,:) +double precision int_prod_bessel_loc,binom,accu,prod,ylm,bigI,arg + + fourpi=4.d0*dacos(-1.d0) + f=fourpi**1.5d0 + ac=dsqrt((a(1)-c(1))**2+(a(2)-c(2))**2+(a(3)-c(3))**2) + bc=dsqrt((b(1)-c(1))**2+(b(2)-c(2))**2+(b(3)-c(3))**2) + arg=g_a*ac**2+g_b*bc**2 + if(arg.gt.-dlog(10.d-20))then + Vloc=0.d0 + return + endif + + ntotA=n_a(1)+n_a(2)+n_a(3) + ntotB=n_b(1)+n_b(2)+n_b(3) + ntot=ntotA+ntotB + + if(ac.eq.0.d0.and.bc.eq.0.d0)then + accu=0.d0 + + do k=1,klocmax + accu=accu+v_k(k)*crochet(n_k(k)+2+ntot,g_a+g_b+dz_k(k)) + enddo + Vloc=accu*fourpi*bigI(0,0,0,0,n_a(1)+n_b(1),n_a(2)+n_b(2),n_a(3)+n_b(3)) + !bigI frequantly is null + return + endif + + freal=dexp(-g_a*ac**2-g_b*bc**2) + + d2=0.d0 + do i=1,3 + d(i)=g_a*(a(i)-c(i))+g_b*(b(i)-c(i)) + d2=d2+d(i)**2 + enddo + d2=dsqrt(d2) + dreal=2.d0*d2 + + theta_DC0=dacos(d(3)/d2) + phi_DC0=datan2(d(2)/d2,d(1)/d2) + +allocate (array_R_loc(-2:ntot_max+klocmax_max,klocmax_max,0:ntot_max)) +allocate (array_coefs(0:ntot_max,0:ntot_max,0:ntot_max,0:ntot_max,0:ntot_max,0:ntot_max)) + + do ktot=-2,ntotA+ntotB+klocmax + do l=0,ntot + do k=1,klocmax + array_R_loc(ktot,k,l)=freal*int_prod_bessel_loc(ktot+2,g_a+g_b+dz_k(k),l,dreal) + enddo + enddo + enddo + + do k1=0,n_a(1) + do k2=0,n_a(2) + do k3=0,n_a(3) + do k1p=0,n_b(1) + do k2p=0,n_b(2) + do k3p=0,n_b(3) + array_coefs(k1,k2,k3,k1p,k2p,k3p)=binom(n_a(1),k1)*binom(n_a(2),k2)*binom(n_a(3),k3) & + *(c(1)-a(1))**(n_a(1)-k1)*(c(2)-a(2))**(n_a(2)-k2)*(c(3)-a(3))**(n_a(3)-k3) & + *binom(n_b(1),k1p)*binom(n_b(2),k2p)*binom(n_b(3),k3p) & + *(c(1)-b(1))**(n_b(1)-k1p)*(c(2)-b(2))**(n_b(2)-k2p)*(c(3)-b(3))**(n_b(3)-k3p) + enddo + enddo + enddo + enddo + enddo + enddo + + accu=0.d0 + do k=1,klocmax + do k1=0,n_a(1) + do k2=0,n_a(2) + do k3=0,n_a(3) + do k1p=0,n_b(1) + do k2p=0,n_b(2) + do k3p=0,n_b(3) + + do l=0,ntot + do m=-l,l + prod=ylm(l,m,theta_DC0,phi_DC0)*array_coefs(k1,k2,k3,k1p,k2p,k3p) & + *bigI(l,m,0,0,k1+k1p,k2+k2p,k3+k3p) + ktot=k1+k2+k3+k1p+k2p+k3p+n_k(k) + accu=accu+prod*v_k(k)*array_R_loc(ktot,k,l) + enddo + enddo + + enddo + enddo + enddo + enddo + enddo + enddo + enddo + Vloc=f*accu + + deallocate (array_R_loc) + deallocate (array_coefs) +end + +double precision function bigA(i,j,k) +implicit none +integer i,j,k +double precision fourpi,dblefact +fourpi=4.d0*dacos(-1.d0) +bigA=0.d0 +if(mod(i,2).eq.1)return +if(mod(j,2).eq.1)return +if(mod(k,2).eq.1)return +bigA=fourpi*dblefact(i-1)*dblefact(j-1)*dblefact(k-1)/dblefact(i+j+k+1) +end +!! +!! I_{lambda,mu,l,m}^{k1,k2,k3} = /int dOmega Y_{lambda mu} xchap^k1 ychap^k2 zchap^k3 Y_{lm} +!! + +double precision function bigI(lambda,mu,l,m,k1,k2,k3) +implicit none +integer lambda,mu,l,m,k1,k2,k3 +integer k,i,kp,ip +double precision pi,sum,factor1,factor2,cylm,cylmp,bigA,binom,fact,coef_pm +pi=dacos(-1.d0) + +if(mu.gt.0.and.m.gt.0)then +sum=0.d0 +factor1=dsqrt((2*lambda+1)*fact(lambda-iabs(mu))/(4.d0*pi*fact(lambda+iabs(mu)))) +factor2=dsqrt((2*l+1)*fact(l-iabs(m))/(4.d0*pi*fact(l+iabs(m)))) +do k=0,mu/2 + do i=0,lambda-mu + do kp=0,m/2 + do ip=0,l-m + cylm=(-1.d0)**k*factor1*dsqrt(2.d0)*binom(mu,2*k)*fact(mu+i)/fact(i)*coef_pm(lambda,i+mu) + cylmp=(-1.d0)**kp*factor2*dsqrt(2.d0)*binom(m,2*kp)*fact(m+ip)/fact(ip)*coef_pm(l,ip+m) + sum=sum+cylm*cylmp*bigA(mu-2*k+m-2*kp+k1,2*k+2*kp+k2,i+ip+k3) + enddo + enddo + enddo +enddo +bigI=sum +return +endif + +if(mu.eq.0.and.m.eq.0)then +factor1=dsqrt((2*lambda+1)/(4.d0*pi)) +factor2=dsqrt((2*l+1)/(4.d0*pi)) +sum=0.d0 +do i=0,lambda + do ip=0,l + cylm=factor1*coef_pm(lambda,i) + cylmp=factor2*coef_pm(l,ip) + sum=sum+cylm*cylmp*bigA(k1,k2,i+ip+k3) + enddo +enddo +bigI=sum +return +endif + +if(mu.eq.0.and.m.gt.0)then +factor1=dsqrt((2*lambda+1)/(4.d0*pi)) +factor2=dsqrt((2*l+1)*fact(l-iabs(m))/(4.d0*pi*fact(l+iabs(m)))) +sum=0.d0 +do i=0,lambda + do kp=0,m/2 + do ip=0,l-m + cylm=factor1*coef_pm(lambda,i) + cylmp=(-1.d0)**kp*factor2*dsqrt(2.d0)*binom(m,2*kp)*fact(m+ip)/fact(ip)*coef_pm(l,ip+m) + sum=sum+cylm*cylmp*bigA(m-2*kp+k1,2*kp+k2,i+ip+k3) + enddo + enddo +enddo +bigI=sum +return +endif + +if(mu.gt.0.and.m.eq.0)then +sum=0.d0 +factor1=dsqrt((2*lambda+1)*fact(lambda-iabs(mu))/(4.d0*pi*fact(lambda+iabs(mu)))) +factor2=dsqrt((2*l+1)/(4.d0*pi)) +do k=0,mu/2 + do i=0,lambda-mu + do ip=0,l + cylm=(-1.d0)**k*factor1*dsqrt(2.d0)*binom(mu,2*k)*fact(mu+i)/fact(i)*coef_pm(lambda,i+mu) + cylmp=factor2*coef_pm(l,ip) + sum=sum+cylm*cylmp*bigA(mu-2*k +k1,2*k +k2,i+ip +k3) + enddo + enddo +enddo +bigI=sum +return +endif + +if(mu.lt.0.and.m.lt.0)then +mu=-mu +m=-m +factor1=dsqrt((2*lambda+1)*fact(lambda-iabs(mu))/(4.d0*pi*fact(lambda+iabs(mu)))) +factor2=dsqrt((2*l+1)*fact(l-iabs(m))/(4.d0*pi*fact(l+iabs(m)))) +sum=0.d0 +do k=0,(mu-1)/2 + do i=0,lambda-mu + do kp=0,(m-1)/2 + do ip=0,l-m + cylm=(-1.d0)**k*factor1*dsqrt(2.d0)*binom(mu,2*k+1)*fact(mu+i)/fact(i)*coef_pm(lambda,i+mu) + cylmp=(-1.d0)**kp*factor2*dsqrt(2.d0)*binom(m,2*kp+1)*fact(m+ip)/fact(ip)*coef_pm(l,ip+m) + sum=sum+cylm*cylmp*bigA(mu-(2*k+1)+m-(2*kp+1)+k1,(2*k+1)+(2*kp+1)+k2,i+ip+k3) + enddo + enddo + enddo +enddo +mu=-mu +m=-m +bigI=sum +return +endif + +if(mu.eq.0.and.m.lt.0)then +m=-m +factor1=dsqrt((2*lambda+1)/(4.d0*pi)) +factor2=dsqrt((2*l+1)*fact(l-iabs(m))/(4.d0*pi*fact(l+iabs(m)))) +sum=0.d0 +do i=0,lambda + do kp=0,(m-1)/2 + do ip=0,l-m + cylm=factor1*coef_pm(lambda,i) + cylmp=(-1.d0)**kp*factor2*dsqrt(2.d0)*binom(m,2*kp+1)*fact(m+ip)/fact(ip)*coef_pm(l,ip+m) + sum=sum+cylm*cylmp*bigA(m-(2*kp+1)+k1,2*kp+1+k2,i+ip+k3) + enddo + enddo +enddo +m=-m +bigI=sum +return +endif + +if(mu.lt.0.and.m.eq.0)then +sum=0.d0 +mu=-mu +factor1=dsqrt((2*lambda+1)*fact(lambda-iabs(mu))/(4.d0*pi*fact(lambda+iabs(mu)))) +factor2=dsqrt((2*l+1)/(4.d0*pi)) +do k=0,(mu-1)/2 + do i=0,lambda-mu + do ip=0,l + cylm=(-1.d0)**k*factor1*dsqrt(2.d0)*binom(mu,2*k+1)*fact(mu+i)/fact(i)*coef_pm(lambda,i+mu) + cylmp=factor2*coef_pm(l,ip) + sum=sum+cylm*cylmp*bigA(mu-(2*k+1)+k1,2*k+1+k2,i+ip+k3) + enddo + enddo +enddo +mu=-mu +bigI=sum +return +endif + +if(mu.gt.0.and.m.lt.0)then +sum=0.d0 +factor1=dsqrt((2*lambda+1)*fact(lambda-iabs(mu))/(4.d0*pi*fact(lambda+iabs(mu)))) +factor2=dsqrt((2*l+1)*fact(l-iabs(m))/(4.d0*pi*fact(l+iabs(m)))) +m=-m +do k=0,mu/2 + do i=0,lambda-mu + do kp=0,(m-1)/2 + do ip=0,l-m + cylm=(-1.d0)**k*factor1*dsqrt(2.d0)*binom(mu,2*k)*fact(mu+i)/fact(i)*coef_pm(lambda,i+mu) + cylmp=(-1.d0)**kp*factor2*dsqrt(2.d0)*binom(m,2*kp+1)*fact(m+ip)/fact(ip)*coef_pm(l,ip+m) + sum=sum+cylm*cylmp*bigA(mu-2*k+m-(2*kp+1)+k1,2*k+2*kp+1+k2,i+ip+k3) + enddo + enddo + enddo +enddo +m=-m +bigI=sum +return +endif + +if(mu.lt.0.and.m.gt.0)then +mu=-mu +factor1=dsqrt((2*lambda+1)*fact(lambda-iabs(mu))/(4.d0*pi*fact(lambda+iabs(mu)))) +factor2=dsqrt((2*l+1)*fact(l-iabs(m))/(4.d0*pi*fact(l+iabs(m)))) +sum=0.d0 +do k=0,(mu-1)/2 + do i=0,lambda-mu + do kp=0,m/2 + do ip=0,l-m + cylm=(-1.d0)**k*factor1*dsqrt(2.d0)*binom(mu,2*k+1)*fact(mu+i)/fact(i)*coef_pm(lambda,i+mu) + cylmp=(-1.d0)**kp*factor2*dsqrt(2.d0)*binom(m,2*kp)*fact(m+ip)/fact(ip)*coef_pm(l,ip+m) + sum=sum+cylm*cylmp*bigA(mu-(2*k+1)+m-2*kp+k1,2*k+1+2*kp+k2,i+ip+k3) + enddo + enddo + enddo +enddo +bigI=sum +mu=-mu +return +endif + +stop 'pb in bigI!' +end + +double precision function crochet(n,g) +implicit none +integer n +double precision g,pi,dblefact,expo +pi=dacos(-1.d0) +expo=0.5d0*dfloat(n+1) +crochet=dblefact(n-1)/(2.d0*g)**expo +if(mod(n,2).eq.0)crochet=crochet*dsqrt(pi/2.d0) +end + +!! +!! overlap= = /int dOmega Ylm (x-center_x)**nx*(y-center_y)**nx*(z-center)**nx +!! *exp(-g*(r-center)**2) +!! +double precision function overlap_orb_ylm_brute(npts,r,npower_orb,center_orb,g_orb,l,m) +implicit none +integer npower_orb(3),l,m,i,j,npts +double precision u,g_orb,du,dphi,term,orb_phi,ylm_real,sintheta,r_orb,phi,center_orb(3) +double precision x_orb,y_orb,z_orb,twopi,r +twopi=2.d0*dacos(-1.d0) +du=2.d0/npts +dphi=twopi/npts +overlap_orb_ylm_brute=0.d0 +do i=1,npts + u=-1.d0+du*(i-1)+du/2.d0 + sintheta=dsqrt(1.d0-u**2) + do j=1,npts + phi=dphi*(j-1)+dphi/2.d0 + x_orb=r*dcos(phi)*sintheta + y_orb=r*dsin(phi)*sintheta + z_orb=r*u + term=orb_phi(x_orb,y_orb,z_orb,npower_orb,center_orb,g_orb)*ylm_real(l,m,u,phi) + overlap_orb_ylm_brute= overlap_orb_ylm_brute+term*du*dphi + enddo +enddo +end + +double precision function overlap_orb_ylm_grid(nptsgrid,r_orb,npower_orb,center_orb,g_orb,l,m) +implicit none +!! PSEUDOS +integer nptsgridmax,nptsgrid +double precision coefs_pseudo,ptsgrid +parameter(nptsgridmax=50) +common/pseudos/coefs_pseudo(nptsgridmax),ptsgrid(nptsgridmax,3) +!!!!! +integer npower_orb(3),l,m,i +double precision x,g_orb,two_pi,dx,dphi,term,orb_phi,ylm_real,sintheta,r_orb,phi,center_orb(3) +double precision x_orb,y_orb,z_orb,twopi,pi,cosphi,sinphi,xbid +pi=dacos(-1.d0) +twopi=2.d0*pi +overlap_orb_ylm_grid=0.d0 +do i=1,nptsgrid + x_orb=r_orb*ptsgrid(i,1) + y_orb=r_orb*ptsgrid(i,2) + z_orb=r_orb*ptsgrid(i,3) + x=ptsgrid(i,3) + phi=datan2(ptsgrid(i,2),ptsgrid(i,1)) + term=orb_phi(x_orb,y_orb,z_orb,npower_orb,center_orb,g_orb)*ylm_real(l,m,x,phi) + overlap_orb_ylm_grid= overlap_orb_ylm_grid+coefs_pseudo(i)*term +enddo +overlap_orb_ylm_grid=2.d0*twopi*overlap_orb_ylm_grid +end + +! Y_l^m(theta,phi) = i^(m+|m|) ([(2l+1)*(l-|m|)!]/[4pi*(l+|m|)!])^1/2 P_l^|m|(cos(theta)) exp(i m phi) +! l=0,1,2,.... +! m=0,1,...,l +! Here: +! n=l (n=0,1,...) +! m=0,1,...,n +! x=cos(theta) 0 < x < 1 +! +! +! This routine computes: PM(m,n) for n=0,...,N (number N in input) and m=0,..,n + +! Exemples (see 'Associated Legendre Polynomilas wikipedia') +! P_{0}^{0}(x)=1 +! P_{1}^{-1}(x)=-1/2 P_{1}^{1}(x) +! P_{1}^{0}(x)=x +! P_{1}^{1}(x)=-(1-x^2)^{1/2} +! P_{2}^{-2}(x)=1/24 P_{2}^{2}(x) +! P_{2}^{-1}(x)=-1/6 P_{2}^{1}(x) +! P_{2}^{0}(x)=1/2 (3x^{2}-1) +! P_{2}^{1}(x)=-3x(1-x^2)^{1/2} +! P_{2}^{2}(x)=3(1-x^2) + + + SUBROUTINE LPMN(MM,M,N,X,PM) +! +! Here N = LMAX +! Here M= MMAX (we take M=LMAX in input) +! +! ===================================================== +! Purpose: Compute the associated Legendre functions Pmn(x) +! Input : x --- Argument of Pmn(x) +! m --- Order of Pmn(x), m = 0,1,2,...,n +! n --- Degree of Pmn(x), n = 0,1,2,...,N +! mm --- Physical dimension of PM +! Output: PM(m,n) --- Pmn(x) +! ===================================================== +! + IMPLICIT DOUBLE PRECISION (P,X) + DIMENSION PM(0:MM,0:(N+1)) + DO 10 I=0,N + DO 10 J=0,M +10 PM(J,I)=0.0D0 + PM(0,0)=1.0D0 + IF (DABS(X).EQ.1.0D0) THEN + DO 15 I=1,N +15 PM(0,I)=X**I + RETURN + ENDIF + LS=1 + IF (DABS(X).GT.1.0D0) LS=-1 + XQ=DSQRT(LS*(1.0D0-X*X)) + XS=LS*(1.0D0-X*X) + DO 30 I=1,M +30 PM(I,I)=-LS*(2.0D0*I-1.0D0)*XQ*PM(I-1,I-1) + DO 35 I=0,M +35 PM(I,I+1)=(2.0D0*I+1.0D0)*X*PM(I,I) + + DO 40 I=0,M + DO 40 J=I+2,N + PM(I,J)=((2.0D0*J-1.0D0)*X*PM(I,J-1)- (I+J-1.0D0)*PM(I,J-2))/(J-I) +40 CONTINUE + END + + +! Y_l^m(theta,phi) = i^(m+|m|) ([(2l+1)*(l-|m|)!]/[4pi*(l+|m|)!])^1/2 +! P_l^|m|(cos(theta)) exp(i m phi) + + subroutine erreur(x,n,rmoy,error) + implicit double precision(a-h,o-z) + dimension x(n) +! calcul de la moyenne + rmoy=0.d0 + do i=1,n + rmoy=rmoy+x(i) + enddo + rmoy=rmoy/dfloat(n) +! calcul de l'erreur + error=0.d0 + do i=1,n + error=error+(x(i)-rmoy)**2 + enddo + if(n.gt.1)then + rn=dfloat(n) + rn1=dfloat(n-1) + error=dsqrt(error)/dsqrt(rn*rn1) + else + write(2,*)'Seulement un block Erreur nondefinie' + error=0.d0 + endif + end + + subroutine initpseudos(nptsgrid) + implicit none + integer nptsgridmax,nptsgrid,ik + double precision coefs_pseudo,ptsgrid + double precision p,q,r,s + parameter(nptsgridmax=50) + common/pseudos/coefs_pseudo(nptsgridmax),ptsgrid(nptsgridmax,3) + + p=1.d0/dsqrt(2.d0) + q=1.d0/dsqrt(3.d0) + r=1.d0/dsqrt(11.d0) + s=3.d0/dsqrt(11.d0) + + if(nptsgrid.eq.4)then + + ptsgrid(1,1)=q + ptsgrid(1,2)=q + ptsgrid(1,3)=q + + ptsgrid(2,1)=q + ptsgrid(2,2)=-q + ptsgrid(2,3)=-q + + ptsgrid(3,1)=-q + ptsgrid(3,2)=q + ptsgrid(3,3)=-q + + ptsgrid(4,1)=-q + ptsgrid(4,2)=-q + ptsgrid(4,3)=q + + do ik=1,4 + coefs_pseudo(ik)=1.d0/4.d0 + enddo + return + endif + + ptsgrid(1,1)=1.d0 + ptsgrid(1,2)=0.d0 + ptsgrid(1,3)=0.d0 + + ptsgrid(2,1)=-1.d0 + ptsgrid(2,2)=0.d0 + ptsgrid(2,3)=0.d0 + + ptsgrid(3,1)=0.d0 + ptsgrid(3,2)=1.d0 + ptsgrid(3,3)=0.d0 + + ptsgrid(4,1)=0.d0 + ptsgrid(4,2)=-1.d0 + ptsgrid(4,3)=0.d0 + + ptsgrid(5,1)=0.d0 + ptsgrid(5,2)=0.d0 + ptsgrid(5,3)=1.d0 + + ptsgrid(6,1)=0.d0 + ptsgrid(6,2)=0.d0 + ptsgrid(6,3)=-1.d0 + + do ik=1,6 + coefs_pseudo(ik)=1.d0/6.d0 + enddo + + if(nptsgrid.eq.6)return + + ptsgrid(7,1)=p + ptsgrid(7,2)=p + ptsgrid(7,3)=0.d0 + + ptsgrid(8,1)=p + ptsgrid(8,2)=-p + ptsgrid(8,3)=0.d0 + + ptsgrid(9,1)=-p + ptsgrid(9,2)=p + ptsgrid(9,3)=0.d0 + + ptsgrid(10,1)=-p + ptsgrid(10,2)=-p + ptsgrid(10,3)=0.d0 + + ptsgrid(11,1)=p + ptsgrid(11,2)=0.d0 + ptsgrid(11,3)=p + + ptsgrid(12,1)=p + ptsgrid(12,2)=0.d0 + ptsgrid(12,3)=-p + + ptsgrid(13,1)=-p + ptsgrid(13,2)=0.d0 + ptsgrid(13,3)=p + + ptsgrid(14,1)=-p + ptsgrid(14,2)=0.d0 + ptsgrid(14,3)=-p + + ptsgrid(15,1)=0.d0 + ptsgrid(15,2)=p + ptsgrid(15,3)=p + + ptsgrid(16,1)=0.d0 + ptsgrid(16,2)=p + ptsgrid(16,3)=-p + + ptsgrid(17,1)=0.d0 + ptsgrid(17,2)=-p + ptsgrid(17,3)=p + + ptsgrid(18,1)=0.d0 + ptsgrid(18,2)=-p + ptsgrid(18,3)=-p + + do ik=1,6 + coefs_pseudo(ik)=1.d0/30.d0 + enddo + do ik=7,18 + coefs_pseudo(ik)=1.d0/15.d0 + enddo + + if(nptsgrid.eq.18)return + + ptsgrid(19,1)=q + ptsgrid(19,2)=q + ptsgrid(19,3)=q + + ptsgrid(20,1)=-q + ptsgrid(20,2)=q + ptsgrid(20,3)=q + + ptsgrid(21,1)=q + ptsgrid(21,2)=-q + ptsgrid(21,3)=q + + ptsgrid(22,1)=q + ptsgrid(22,2)=q + ptsgrid(22,3)=-q + + ptsgrid(23,1)=-q + ptsgrid(23,2)=-q + ptsgrid(23,3)=q + + ptsgrid(24,1)=-q + ptsgrid(24,2)=q + ptsgrid(24,3)=-q + + ptsgrid(25,1)=q + ptsgrid(25,2)=-q + ptsgrid(25,3)=-q + + ptsgrid(26,1)=-q + ptsgrid(26,2)=-q + ptsgrid(26,3)=-q + + do ik=1,6 + coefs_pseudo(ik)=1.d0/21.d0 + enddo + do ik=7,18 + coefs_pseudo(ik)=4.d0/105.d0 + enddo + do ik=19,26 + coefs_pseudo(ik)=27.d0/840.d0 + enddo + + if(nptsgrid.eq.26)return + + ptsgrid(27,1)=r + ptsgrid(27,2)=r + ptsgrid(27,3)=s + + ptsgrid(28,1)=r + ptsgrid(28,2)=-r + ptsgrid(28,3)=s + + ptsgrid(29,1)=-r + ptsgrid(29,2)=r + ptsgrid(29,3)=s + + ptsgrid(30,1)=-r + ptsgrid(30,2)=-r + ptsgrid(30,3)=s + + ptsgrid(31,1)=r + ptsgrid(31,2)=r + ptsgrid(31,3)=-s + + ptsgrid(32,1)=r + ptsgrid(32,2)=-r + ptsgrid(32,3)=-s + + ptsgrid(33,1)=-r + ptsgrid(33,2)=r + ptsgrid(33,3)=-s + + ptsgrid(34,1)=-r + ptsgrid(34,2)=-r + ptsgrid(34,3)=-s + + ptsgrid(35,1)=r + ptsgrid(35,2)=s + ptsgrid(35,3)=r + + ptsgrid(36,1)=-r + ptsgrid(36,2)=s + ptsgrid(36,3)=r + + ptsgrid(37,1)=r + ptsgrid(37,2)=s + ptsgrid(37,3)=-r + + ptsgrid(38,1)=-r + ptsgrid(38,2)=s + ptsgrid(38,3)=-r + + ptsgrid(39,1)=r + ptsgrid(39,2)=-s + ptsgrid(39,3)=r + + ptsgrid(40,1)=r + ptsgrid(40,2)=-s + ptsgrid(40,3)=-r + + ptsgrid(41,1)=-r + ptsgrid(41,2)=-s + ptsgrid(41,3)=r + + ptsgrid(42,1)=-r + ptsgrid(42,2)=-s + ptsgrid(42,3)=-r + + ptsgrid(43,1)=s + ptsgrid(43,2)=r + ptsgrid(43,3)=r + + ptsgrid(44,1)=s + ptsgrid(44,2)=r + ptsgrid(44,3)=-r + + ptsgrid(45,1)=s + ptsgrid(45,2)=-r + ptsgrid(45,3)=r + + ptsgrid(46,1)=s + ptsgrid(46,2)=-r + ptsgrid(46,3)=-r + + ptsgrid(47,1)=-s + ptsgrid(47,2)=r + ptsgrid(47,3)=r + + ptsgrid(48,1)=-s + ptsgrid(48,2)=r + ptsgrid(48,3)=-r + + ptsgrid(49,1)=-s + ptsgrid(49,2)=-r + ptsgrid(49,3)=r + + ptsgrid(50,1)=-s + ptsgrid(50,2)=-r + ptsgrid(50,3)=-r + + do ik=1,6 + coefs_pseudo(ik)=4.d0/315.d0 + enddo + do ik=7,18 + coefs_pseudo(ik)=64.d0/2835.d0 + enddo + do ik=19,26 + coefs_pseudo(ik)=27.d0/1280.d0 + enddo + do ik=27,50 + coefs_pseudo(ik)=14641.d0/725760.d0 + enddo + + if(nptsgrid.eq.50)return + + write(*,*)'Grid for pseudos not available!' + write(*,*)'N=4-6-18-26-50 only!' + stop + end + +double precision function dblefact(n) +implicit none +integer :: n,k +double precision prod +dblefact=1.d0 + +if(n.lt.0)return +if(mod(n,2).eq.1)then + prod=1.d0 + do k=1,n,2 + prod=prod*dfloat(k) + enddo + dblefact=prod + return + endif + if(mod(n,2).eq.0)then + prod=1.d0 + do k=2,n,2 + prod=prod*dfloat(k) + enddo + dblefact=prod + return + endif +end +!! +!! R_{lambda,lamba',N}= exp(-ga_a AC**2 -g_b BC**2) /int_{0}{+infty} r**(2+n) exp(-(g_a+g_b+g_k)r**2) +!! * M_{lambda}( 2g_a ac r) M_{lambda'}(2g_b bc r) +!! + double precision function bigR(lambda,lambdap,n,g_a,g_b,ac,bc,g_k) + implicit none + integer lambda,lambdap,n,npts,i + double precision g_a,g_b,ac,bc,g_k,arg,factor,delta1,delta2,cc,rmax,dr,sum,x1,x2,r + double precision bessel_mod + arg=g_a*ac**2+g_b*bc**2 + factor=dexp(-arg) + delta1=2.d0*g_a*ac + delta2=2.d0*g_b*bc + cc=g_a+g_b+g_k + if(cc.eq.0.d0)stop 'pb. in bigR' + rmax=dsqrt(-dlog(10.d-20)/cc) + npts=500 + dr=rmax/npts + sum=0.d0 + do i=1,npts + r=(i-1)*dr + x1=delta1*r + x2=delta2*r + sum=sum+dr*r**(n+2)*dexp(-cc*r**2)*bessel_mod(x1,lambda)*bessel_mod(x2,lambdap) + enddo + bigR=sum*factor + end + + double precision function bessel_mod(x,n) + implicit none + integer n + double precision x,bessel_mod_exp,bessel_mod_recur + if(x.le.0.8d0)then + bessel_mod=bessel_mod_exp(n,x) + else + bessel_mod=bessel_mod_recur(n,x) + endif + end + + recursive function bessel_mod_recur(n,x) result(a) + implicit none + integer n + double precision x,a,bessel_mod_exp + if(x.le.0.8d0)then + a=bessel_mod_exp(n,x) + return + endif + if(n.eq.0)a=dsinh(x)/x + if(n.eq.1)a=(x*dcosh(x)-dsinh(x))/x**2 + if(n.ge.2)a=bessel_mod_recur(n-2,x)-(2*n-1)/x*bessel_mod_recur(n-1,x) + end + + double precision function bessel_mod_exp(n,x) + implicit none + integer n,k + double precision x,coef,accu,fact,dblefact + accu=0.d0 + do k=0,10 + coef=1.d0/fact(k)/dblefact(2*(n+k)+1) + accu=accu+(x**2/2.d0)**k*coef + enddo + bessel_mod_exp=x**n*accu + end + +! double precision function bessel_mod(x,n) +! IMPLICIT DOUBLE PRECISION (A-H,O-Z) +! parameter(NBESSMAX=100) +! dimension SI(0:NBESSMAX),DI(0:NBESSMAX) +! if(n.lt.0.or.n.gt.NBESSMAX)stop 'pb with argument of bessel_mod' +! CALL SPHI(N,X,NBESSMAX,SI,DI) +! bessel_mod=si(n) +! end + + SUBROUTINE SPHI(N,X,NMAX,SI,DI) +! +! ======================================================== +! Purpose: Compute modified spherical Bessel functions +! of the first kind, in(x) and in'(x) +! Input : x --- Argument of in(x) +! n --- Order of in(x) ( n = 0,1,2,... ) +! Output: SI(n) --- in(x) +! DI(n) --- in'(x) +! NM --- Highest order computed +! Routines called: +! MSTA1 and MSTA2 for computing the starting +! point for backward recurrence +! ======================================================== +! + IMPLICIT DOUBLE PRECISION (A-H,O-Z) + DIMENSION SI(0:NMAX),DI(0:NMAX) + NM=N + IF (DABS(X).LT.1.0D-100) THEN + DO 10 K=0,N + SI(K)=0.0D0 +10 DI(K)=0.0D0 + SI(0)=1.0D0 + DI(1)=0.333333333333333D0 + RETURN + ENDIF + SI(0)=DSINH(X)/X + SI(1)=-(DSINH(X)/X-DCOSH(X))/X + SI0=SI(0) + IF (N.GE.2) THEN + M=MSTA1(X,200) + + write(34,*)'m=',m + + IF (M.LT.N) THEN + NM=M + ELSE + M=MSTA2(X,N,15) + write(34,*)'m=',m + ENDIF + F0=0.0D0 + F1=1.0D0-100 + DO 15 K=M,0,-1 + F=(2.0D0*K+3.0D0)*F1/X+F0 + IF (K.LE.NM) SI(K)=F + F0=F1 +15 F1=F + CS=SI0/F + write(34,*)'cs=',cs + DO 20 K=0,NM +20 SI(K)=CS*SI(K) + ENDIF + DI(0)=SI(1) + DO 25 K=1,NM +25 DI(K)=SI(K-1)-(K+1.0D0)/X*SI(K) + RETURN + END + + + INTEGER FUNCTION MSTA1(X,MP) +! +! =================================================== +! Purpose: Determine the starting point for backward +! recurrence such that the magnitude of +! Jn(x) at that point is about 10^(-MP) +! Input : x --- Argument of Jn(x) +! MP --- Value of magnitude +! Output: MSTA1 --- Starting point +! =================================================== +! + IMPLICIT DOUBLE PRECISION (A-H,O-Z) + A0=DABS(X) + N0=INT(1.1*A0)+1 + F0=ENVJ(N0,A0)-MP + N1=N0+5 + F1=ENVJ(N1,A0)-MP + DO 10 IT=1,20 + NN=N1-(N1-N0)/(1.0D0-F0/F1) + F=ENVJ(NN,A0)-MP + IF(ABS(NN-N1).LT.1) GO TO 20 + N0=N1 + F0=F1 + N1=NN + 10 F1=F + 20 MSTA1=NN + RETURN + END + + + INTEGER FUNCTION MSTA2(X,N,MP) +! +! =================================================== +! Purpose: Determine the starting point for backward +! recurrence such that all Jn(x) has MP +! significant digits +! Input : x --- Argument of Jn(x) +! n --- Order of Jn(x) +! MP --- Significant digit +! Output: MSTA2 --- Starting point +! =================================================== +! + IMPLICIT DOUBLE PRECISION (A-H,O-Z) + A0=DABS(X) + HMP=0.5D0*MP + EJN=ENVJ(N,A0) + IF (EJN.LE.HMP) THEN + OBJ=MP + N0=INT(1.1*A0) + ELSE + OBJ=HMP+EJN + N0=N + ENDIF + F0=ENVJ(N0,A0)-OBJ + N1=N0+5 + F1=ENVJ(N1,A0)-OBJ + DO 10 IT=1,20 + NN=N1-(N1-N0)/(1.0D0-F0/F1) + F=ENVJ(NN,A0)-OBJ + IF (iABS(NN-N1).LT.1) GO TO 20 + N0=N1 + F0=F1 + N1=NN +10 F1=F +20 MSTA2=NN+10 + RETURN + END + + double precision FUNCTION ENVJ(N,X) + DOUBLE PRECISION X + integer N + ENVJ=0.5D0*DLOG10(6.28D0*N)-N*DLOG10(1.36D0*X/N) + RETURN + END + +!c Computation of real spherical harmonics Ylm(theta,phi) +!c +!c l=0,1,.... +!c m=-l,l +!c +!c m>0: Y_lm = sqrt(2) ([(2l+1)*(l-|m|)!]/[4pi*(l+|m|)!])^1/2 P_l^|m|(cos(theta)) cos(m phi) +!c m=0: Y_l0 = ([(2l+1)*(l-|m|)!]/[4pi*(l+|m|)!])^1/2 P_l^0 (cos(theta)) +!c m<0: Y_lm = sqrt(2) ([(2l+1)*(l-|m|)!]/[4pi*(l+|m|)!])^1/2 P_l^|m|(cos(theta)) sin(|m|phi) + +!Examples(wikipedia http://en.wikipedia.org/wiki/Table_of_spherical_harmonics#Real_spherical_harmonics) + +! l = 0 + +! Y_00 = \sqrt{1/(4pi)} + +! l = 1 + +! Y_1-1= \sqrt{3/(4pi)} y/r +! Y_10 = \sqrt{3/(4pi)} z/r +! Y_11 = \sqrt{3/(4pi)} x/r +! +! l = 2 +! +! Y_2,-2= 1/2 \sqrt{15/pi} xy/r^2 +! Y_2,-1= 1/2 \sqrt{15/pi} yz/r^2 +! Y_20 = 1/4 \sqrt{15/pi} (-x^2-y^2 +2z^2)/r^2 +! Y_21 = 1/2 \sqrt{15/pi} zx/r^2 +! Y_22 = 1/4 \sqrt{15/pi} (x^2-y^2)/r^2 +! +!c +double precision function ylm(l,m,theta,phi) +implicit none +integer l,m +double precision theta,phi,pm,factor,pi,x,fact,sign +DIMENSION PM(0:100,0:100) +pi=dacos(-1.d0) +x=dcos(theta) +sign=(-1.d0)**m +CALL LPMN(100,l,l,X,PM) +factor=dsqrt( (2*l+1)*fact(l-iabs(m)) /(4.d0*pi*fact(l+iabs(m))) ) +if(m.gt.0)ylm=sign*dsqrt(2.d0)*factor*pm(m,l)*dcos(dfloat(m)*phi) +if(m.eq.0)ylm=factor*pm(m,l) +if(m.lt.0)ylm=sign*dsqrt(2.d0)*factor*pm(iabs(m),l)*dsin(dfloat(iabs(m))*phi) +end + +!c Explicit representation of Legendre polynomials P_n(x) +!! +!! P_n0(x) = P_n(x)= \sum_{k=0}^n a_k x^k +!! +!! with a_k= 2^n binom(n,k) binom( (n+k-1)/2, n ) +!! coef_pm(n,k) is the k_th coefficient of P_n(x) +double precision function coef_pm(n,k) +implicit none +integer n,k +double precision arg,binom,binom_gen +if(n.eq.0.and.k.ne.0)stop 'coef_pm not defined' +if(n.eq.0.and.k.eq.0)then +coef_pm=1.d0 +return +endif +arg=0.5d0*dfloat(n+k-1) +coef_pm=2.d0**n*binom(n,k)*binom_gen(arg,n) +end + +!! Ylm_bis uses the series expansion of Ylm in xchap^i ychap^j zchap^k +!! xchap=x/r etc. +!c m>0: Y_lm = sqrt(2)*factor* P_l^|m|(cos(theta)) cos(m phi) +!c m=0: Y_l0 = factor* P_l^0 (cos(theta)) +!c m<0: Y_lm = sqrt(2) factor* P_l^|m|(cos(theta)) sin(|m|phi) +!c factor= ([(2l+1)*(l-|m|)!]/[4pi*(l+|m|)!])^1/2 + +!! P_l^m (x) = (-1)**m (1-x**2)^m/2 d^m/dx^m P_l(x) m >0 or 0 +!! the series expansion of P_m (x) is known +!! +!! sin(theta)**m cos(mphi) = \sum_0^[m/2] binom(m,2k) x^(m-2k) y^2k (-1)**k (easy to proove with +!! Moivre formula) +!! (here x = xchap...) +!! +!! Ylm m> 0 = \sum_{k=0}^[m/2] \sum_{i=0}^(l-m) c_ki x^(m-2k) y^2k z^i +!! +!! c_ki= (-1)^k sqrt(2)*factor*binom(m,2k)*(m+i)!/i!*coef_pm(l,i+m) +!! +!! Ylm m< 0 = \sum_{k=0}^[(m-1)/2] \sum_{i=0}^(l-m) c_ki x^(m-(2k+1)) y^(2k+1) z^i +!! +!! c_ki= (-1)^k sqrt(2)*factor*binom(m,2k+1)*(m+i)!/i!*coef_pm(l,i+m) + + +double precision function ylm_bis(l,m,theta,phi) +implicit none +integer l,m,k,i +double precision x,y,z,theta,phi,sum,factor,pi,binom,fact,coef_pm,cylm +pi=dacos(-1.d0) +x=dsin(theta)*dcos(phi) +y=dsin(theta)*dsin(phi) +z=dcos(theta) +factor=dsqrt((2*l+1)*fact(l-iabs(m))/(4.d0*pi*fact(l+iabs(m)))) +if(m.gt.0)then +sum=0.d0 +do k=0,m/2 + do i=0,l-m + cylm=(-1.d0)**k*factor*dsqrt(2.d0)*binom(m,2*k)*fact(m+i)/fact(i)*coef_pm(l,i+m) + sum=sum+cylm*x**(m-2*k)*y**(2*k)*z**i + enddo +enddo +ylm_bis=sum +return +endif +if(m.eq.0)then +sum=0.d0 +do i=0,l + sum=sum+factor*coef_pm(l,i)*z**i +enddo +ylm_bis=sum +return +endif +if(m.lt.0)then +m=-m +sum=0.d0 +do k=0,(m-1)/2 + do i=0,l-m + cylm=(-1.d0)**k*factor*dsqrt(2.d0)*binom(m,2*k+1)*fact(m+i)/fact(i)*coef_pm(l,i+m) + sum=sum+cylm*x**(m-(2*k+1))*y**(2*k+1)*z**i + enddo +enddo +ylm_bis=sum +m=-m +return +endif +end + +!c +!c Computation of associated Legendre Polynomials PM(m,n) for n=0,...,N +!c Here: +!c n=l (n=0,1,...) +!c m=0,1,...,n +!c x=cos(theta) 0 < x < 1 +!c +!c This routine computes: PM(m,n) for n=0,...,N (number N in input) and m=0,..,n +!c Exemples (see 'Associated Legendre Polynomilas wikipedia') +!c P_{0}^{0}(x)=1 +!c P_{1}^{-1}(x)=-1/2 P_{1}^{1}(x) +!c P_{1}^{0}(x)=x +!c P_{1}^{1}(x)=-(1-x^2)^{1/2} +!c P_{2}^{-2}(x)=1/24 P_{2}^{2}(x) +!c P_{2}^{-1}(x)=-1/6 P_{2}^{1}(x) +!c P_{2}^{0}(x)=1/2 (3x^{2}-1) +!c P_{2}^{1}(x)=-3x(1-x^2)^{1/2} +!c P_{2}^{2}(x)=3(1-x^2) +!c +!c Explicit representation: +!! +!! P_n0(x) = P_n(x)= \sum_{k=0}^n a_k x^k +!! +!! with a_k= 2^n binom(n,k) binom( (n+k-1)/2, n ) + +double precision function binom(i,j) + implicit none + integer :: i,j + double precision :: fact + binom = fact(i)/(fact(j)*fact(i-j)) +end + +double precision function binom_gen(alpha,n) + implicit none + integer :: n,k + double precision :: fact,alpha,prod + prod=1.d0 + do k=0,n-1 + prod=prod*(alpha-k) + binom_gen = prod/(fact(n)) + enddo +end + +double precision function test_int(g_a,g_b,g_c,ac,bc) +implicit none +double precision factor,g_a,g_b,g_c,ac,bc,x,dx,sum,alpha,beta,pi +integer i,npts +pi=dacos(-1.d0) +factor=0.5d0*pi/(g_a*g_b*ac*bc*dsqrt(g_a+g_b+g_c))*dexp(-g_a*ac**2-g_b*bc**2) +npts=2000 +dx=20.d0/npts +sum=0.d0 +alpha=(2.d0*g_a*ac+2.d0*g_b*bc)/dsqrt(g_c+g_a+g_b) +beta=(2.d0*g_b*bc-2.d0*g_b*bc)/dsqrt(g_c+g_a+g_b) +do i=1,npts + x=(i-1)*dx+0.5d0*dx + sum=sum+dx*dexp(-x**2)*(dcosh(alpha*x)-dcosh(beta*x)) +enddo +test_int=factor*sum +end + +recursive function fact1(n,a) result(x) +implicit none +integer n +double precision a,x,erf +if(n.eq.0)then +x=dsqrt(dacos(-1.d0))/2.d0*erf(a) +return +endif +if(n.eq.1)then +x=1.d0-dexp(-a**2) +return +endif +if(mod(n,2).eq.0)x=0.5d0*dfloat(n-1)*fact1(n-2,a)+a**n*dexp(-a**2) +if(mod(n,2).eq.1)x=0.5d0*dfloat(n-1)*fact1(n-2,a)+0.5d0*a**(n-1)*dexp(-a**2) +end + + double precision FUNCTION ERF(X) + implicit double precision(a-h,o-z) + IF(X.LT.0.d0)THEN + ERF=-GAMMP(.5d0,X**2) + ELSE + ERF=GAMMP(.5d0,X**2) + ENDIF + RETURN + END + + double precision function coef_nk(n,k) + implicit none + integer n,k + double precision gam,dblefact,fact + gam=dblefact(2*(n+k)+1) + coef_nk=1.d0/(2.d0**k*fact(k)*gam) + end + +!! Calculation of +!! +!! I= \int dx x**l *exp(-gam*x**2) M_n(ax) M_m(bx) +!! +!! M_n(x) modified spherical bessel function +!! + double precision function int_prod_bessel(l,gam,n,m,a,b) + implicit none + integer n,k,m,q,l,kcp + double precision gam,dblefact,fact,pi,a,b + double precision int,intold,sum,coef_nk,crochet + logical done + + if(a.ne.0.d0.and.b.ne.0.d0)then + q=0 + intold=-1.d0 + int=0.d0 + done=.false. + kcp=0 + do while (.not.done) + kcp=kcp+1 + sum=0.d0 + do k=0,q + sum=sum+coef_nk(n,k)*coef_nk(m,q-k)*a**(n+2*k)*b**(m-2*k+2*q) + enddo + int=int+sum*crochet(2*q+n+m+l,gam) + if(dabs(int-intold).lt.1d-15)then + done=.true. + else + q=q+1 + intold=int + endif + enddo + int_prod_bessel=int + if(kcp.gt.100) then + print*,"l",l + print*, "gam", gam + print*, "n", n + print*, "m", m + print*, "a", a + print*, "b", b + print*, "kcp", kcp + print*,'**WARNING** bad convergence in int_prod_bessel' + endif + return + endif + + if(a.eq.0.d0.and.b.ne.0.d0)then + if(n.ne.0)then + int_prod_bessel=0.d0 + return + endif + q=0 + intold=-1.d0 + int=0.d0 + done=.false. + kcp=0 + do while (.not.done) + kcp=kcp+1 + int=int+coef_nk(m,q)*b**(m+2*q)*crochet(2*q+m+l,gam) + if(dabs(int-intold).lt.1d-15)then + done=.true. + else + q=q+1 + intold=int + endif + enddo + int_prod_bessel=int + if(kcp.gt.100)stop '**WARNING** bad convergence in int_prod_bessel' + return + endif + + if(a.ne.0.d0.and.b.eq.0.d0)then + if(m.ne.0)then + int_prod_bessel=0.d0 + return + endif + q=0 + intold=-1.d0 + int=0.d0 + done=.false. + kcp=0 + do while (.not.done) + kcp=kcp+1 + int=int+coef_nk(n,q)*a**(n+2*q)*crochet(2*q+n+l,gam) + if(dabs(int-intold).lt.1d-15)then + done=.true. + else + q=q+1 + intold=int + endif + enddo + int_prod_bessel=int + if(kcp.gt.100)stop '**WARNING** bad convergence in int_prod_bessel' + return + endif + + if(a.eq.0.d0.and.b.eq.0.d0)then + if(n.ne.0.or.m.ne.0)then + int_prod_bessel=0.d0 + return + endif + int_prod_bessel=crochet(l,gam) + return + endif + + stop 'pb in int_prod_bessel!!' + end + + +double precision function int_prod_bessel_num_soph_p(l,gam,n,m,a,b,arg) + implicit none + integer :: n,m,l + double precision :: gam,a,b,arg,arg_new + double precision :: bessel_mod,factor + logical :: not_done + double precision :: bigA,xold,x,dx,accu,intnew,intold,intold2,u,v,freal + integer :: iter, i, nI, n0 + double precision :: eps + + u=(a+b)/(2.d0*dsqrt(gam)) + arg_new=u**2-arg + freal=dexp(arg_new) + v=u/dsqrt(gam) + + bigA=v+dsqrt(-dlog(1.d-15)/gam) + n0=5 + accu=0.d0 + dx=bigA/(float(n0)-1.d0) + iter=0 + do i=1,n0 + x=(float(i)-1.d0)*dx + accu=accu+x**l*dexp(-gam*(x-v)**2)*bessel_mod(a*x,n)*bessel_mod(b*x,m)*dexp(-(a+b)*x) + enddo + +accu=accu*freal +intold=accu*dx + +eps=1.d-08 +nI=n0-1 +dx=dx/2.d0 +not_done=.true. + +do while(not_done) + iter=iter+1 + accu=0.d0 + do i=1,nI + x=dx+(float(i)-1.d0)*2.d0*dx + accu=accu+dx*x**l*dexp(-gam*(x-v)**2)*bessel_mod(a*x,n)*bessel_mod(b*x,m)*dexp(-(a+b)*x) + enddo + accu=accu*freal + intnew=intold/2.d0+accu + if(iter.gt.1.and.dabs(intnew-intold).lt.eps.and.dabs(intnew-intold2).lt.eps)then + not_done=.false. + else + intold2=intold + intold=intnew + dx=dx/2.d0 + nI=2*nI + endif +enddo +int_prod_bessel_num_soph_p=intold +end + +!! Calculation of +!! +!! I= \int dx x**l *exp(-gam*x**2) M_n(ax) +!! +!! M_n(x) modified spherical bessel function +!! + double precision function int_prod_bessel_loc(l,gam,n,a) + implicit none + integer n,k,l,kcp + double precision gam,a + double precision int,intold,coef_nk,crochet + logical done + k=0 + intold=-1.d0 + int=0.d0 + done=.false. + kcp=0 + do while (.not.done) + kcp=kcp+1 + int=int+coef_nk(n,k)*a**(n+2*k)*crochet(2*k+n+l,gam) + if(dabs(int-intold).lt.1d-15)then + done=.true. + else + k=k+1 + intold=int + endif + enddo + int_prod_bessel_loc=int + if(kcp.gt.100)print*,'**WARNING** bad convergence in int_prod_bessel' + end + + double precision function int_prod_bessel_num(l,gam,n,m,a,b) + implicit none + integer n,m,l,i,npoints + double precision gam,a,b + double precision sum,dx,x,bessel_mod + sum=0.d0 + npoints=20000 + dx=30.d0/npoints + do i=1,npoints + x=(i-1)*dx+0.5d0*dx + sum=sum+dx*x**l*dexp(-gam*x**2)*bessel_mod(a*x,n)*bessel_mod(b*x,m) + enddo + int_prod_bessel_num=sum + end + + + diff --git a/src/Pseudo_integrals/pot_ao_ints_pseudo.irp.f b/src/Pseudo_integrals/pot_ao_ints_pseudo.irp.f new file mode 100644 index 00000000..37dc7591 --- /dev/null +++ b/src/Pseudo_integrals/pot_ao_ints_pseudo.irp.f @@ -0,0 +1,167 @@ + BEGIN_PROVIDER [ double precision, ao_nucl_elec_integral_pseudo, (ao_num_align,ao_num)] + BEGIN_DOC +! interaction nuclear electron + END_DOC + implicit none + double precision :: alpha, beta, gama, delta + integer :: num_A,num_B + double precision :: A_center(3),B_center(3),C_center(3) + integer :: power_A(3),power_B(3) + integer :: i,j,k,l,n_pt_in,m + double precision :: Vloc, Vpseudo + + double precision :: cpu_1, cpu_2, wall_1, wall_2, wall_0 + integer :: thread_num + + ao_nucl_elec_integral_pseudo = 0.d0 + + ! + ! | _ _ _. | + ! |_ (_) (_ (_| | + ! + !! Parameters of the local part of pseudo: + + integer klocmax + integer, allocatable :: n_k(:,:) + double precision, allocatable :: v_k(:,:), dz_k(:,:) + + call ezfio_get_pseudo_integrals_klocmax(klocmax) + + allocate(n_k(nucl_num,klocmax),v_k(nucl_num,klocmax), dz_k(nucl_num,klocmax)) + + call ezfio_get_pseudo_integrals_v_k(v_k) + call ezfio_get_pseudo_integrals_n_k(n_k) + call ezfio_get_pseudo_integrals_dz_k(dz_k) + + !! Dump array + integer, allocatable :: n_k_dump(:) + double precision, allocatable :: v_k_dump(:), dz_k_dump(:) + + allocate(n_k_dump(1:klocmax), v_k_dump(1:klocmax), dz_k_dump(1:klocmax)) + + + ! + ! |\ | _ ._ | _ _ _. | + ! | \| (_) | | | (_) (_ (_| | + ! + !! Parameters of non local part of pseudo: + + integer :: kmax,lmax + integer, allocatable :: n_kl(:,:,:) + double precision, allocatable :: v_kl(:,:,:), dz_kl(:,:,:) + + call ezfio_get_pseudo_integrals_lmaxpo(lmax) + call ezfio_get_pseudo_integrals_kmax(kmax) + !lmax plus one -> lmax + lmax = lmax - 1 + + allocate(n_kl(nucl_num,kmax,0:lmax), v_kl(nucl_num,kmax,0:lmax), dz_kl(nucl_num,kmax,0:lmax)) + + call ezfio_get_pseudo_integrals_n_kl(n_kl) + call ezfio_get_pseudo_integrals_v_kl(v_kl) + call ezfio_get_pseudo_integrals_dz_kl(dz_kl) + + + !! Dump array + integer, allocatable :: n_kl_dump(:,:) + double precision, allocatable :: v_kl_dump(:,:), dz_kl_dump(:,:) + + allocate(n_kl_dump(kmax,0:lmax), v_kl_dump(kmax,0:lmax), dz_kl_dump(kmax,0:lmax)) + + ! _ + ! / _. | _ | + ! \_ (_| | (_ |_| | + ! + + write(output_monoints,*) 'Providing the nuclear electron pseudo integrals ' + + call wall_time(wall_1) + call cpu_time(cpu_1) + + !$OMP PARALLEL & + !$OMP DEFAULT (NONE) & + !$OMP PRIVATE (i,j,k,l,m,alpha,beta,A_center,B_center,C_center,power_A,power_B, & + !$OMP num_A,num_B,Z,c,n_pt_in, & + !$OMP v_k_dump,n_k_dump, dz_k_dump, n_kl_dump, v_kl_dump, dz_kl_dump, & + !$OMP wall_0,wall_2,thread_num, output_monoints) & + !$OMP SHARED (ao_num,ao_prim_num,ao_expo_ordered_transp,ao_power,ao_nucl,nucl_coord,ao_coef_normalized_ordered_transp, & + !$OMP ao_nucl_elec_integral_pseudo,nucl_num,nucl_charge, & + !$OMP klocmax,lmax,kmax,v_k,n_k, dz_k, n_kl, v_kl, dz_kl, & + !$OMP wall_1) + + !$OMP DO SCHEDULE (guided) + + do j = 1, ao_num + + num_A = ao_nucl(j) + power_A(1:3)= ao_power(j,1:3) + A_center(1:3) = nucl_coord(num_A,1:3) + + do i = 1, ao_num + + num_B = ao_nucl(i) + power_B(1:3)= ao_power(i,1:3) + B_center(1:3) = nucl_coord(num_B,1:3) + + do l=1,ao_prim_num(j) + alpha = ao_expo_ordered_transp(l,j) + + do m=1,ao_prim_num(i) + beta = ao_expo_ordered_transp(m,i) + double precision :: c + c = 0.d0 + + do k = 1, nucl_num + double precision :: Z + Z = nucl_charge(k) + + C_center(1:3) = nucl_coord(k,1:3) + + v_k_dump = v_k(k,1:klocmax) + n_k_dump = n_k(k,1:klocmax) + dz_k_dump = dz_k(k,1:klocmax) + + c = c + Vloc(klocmax, v_k_dump,n_k_dump, dz_k_dump, & + A_center,power_A,alpha,B_center,power_B,beta,C_center) + + + n_kl_dump = n_kl(k,1:kmax,0:lmax) + v_kl_dump = v_kl(k,1:kmax,0:lmax) + dz_kl_dump = dz_kl(k,1:kmax,0:lmax) + + c = c + Vpseudo(lmax,kmax,v_kl_dump,n_kl_dump,dz_kl_dump,A_center,power_A,alpha,B_center,power_B,beta,C_center) + + enddo + ao_nucl_elec_integral_pseudo(i,j) = ao_nucl_elec_integral_pseudo(i,j) + & + ao_coef_normalized_ordered_transp(l,j)*ao_coef_normalized_ordered_transp(m,i)*c + enddo + enddo + enddo + + call wall_time(wall_2) + if (thread_num == 0) then + if (wall_2 - wall_0 > 1.d0) then + wall_0 = wall_2 + write(output_monoints,*) 100.*float(j)/float(ao_num), '% in ', & + wall_2-wall_1, 's' + endif + endif + enddo + + !$OMP END DO + !$OMP END PARALLEL + + +! _ +! | \ _ _. | | _ _ _. _|_ _ +! |_/ (/_ (_| | | (_) (_ (_| |_ (/_ +! + + deallocate(n_k,v_k, dz_k) + deallocate(n_k_dump,v_k_dump, dz_k_dump) + + deallocate(n_kl,v_kl, dz_kl) + deallocate(n_kl_dump,v_kl_dump, dz_kl_dump) + + +END_PROVIDER diff --git a/src/Pseudo_integrals/pseudo.ezfio_config b/src/Pseudo_integrals/pseudo.ezfio_config new file mode 100644 index 00000000..a01bc2c0 --- /dev/null +++ b/src/Pseudo_integrals/pseudo.ezfio_config @@ -0,0 +1,10 @@ +pseudo_integrals + klocmax integer + v_k double precision (nuclei_nucl_num,pseudo_integrals_klocmax) + n_k integer (nuclei_nucl_num,pseudo_integrals_klocmax) + dz_k double precision (nuclei_nucl_num,pseudo_integrals_klocmax) + lmaxpo integer + kmax integer + v_kl double precision (nuclei_nucl_num,pseudo_integrals_kmax,pseudo_integrals_lmaxpo) + n_kl integer (nuclei_nucl_num,pseudo_integrals_kmax,pseudo_integrals_lmaxpo) + dz_kl double precision (nuclei_nucl_num,pseudo_integrals_kmax,pseudo_integrals_lmaxpo) diff --git a/src/Selectors_full/NEEDED_CHILDREN_MODULES b/src/Selectors_full/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..54f54203 --- /dev/null +++ b/src/Selectors_full/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Determinants Hartree_Fock diff --git a/src/Selectors_full/NEEDED_MODULES b/src/Selectors_full/NEEDED_MODULES deleted file mode 100644 index 7d973bce..00000000 --- a/src/Selectors_full/NEEDED_MODULES +++ /dev/null @@ -1,2 +0,0 @@ -AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Utils - diff --git a/src/Selectors_full/README.rst b/src/Selectors_full/README.rst index aaa07bbd..11286fce 100644 --- a/src/Selectors_full/README.rst +++ b/src/Selectors_full/README.rst @@ -123,38 +123,38 @@ Documentation .br n_double_selectors = number of double excitations in the selectors determinants -`n_det_selectors `_ +`n_det_selectors `_ For Single reference wave functions, the number of selectors is 1 : the Hartree-Fock determinant -`psi_selectors `_ +`psi_selectors `_ Determinants on which we apply for perturbation. -`psi_selectors_ab `_ +`psi_selectors_ab `_ Determinants on which we apply . They are sorted by the 3 highest electrons in the alpha part, then by the 3 highest electrons in the beta part to accelerate the research of connected determinants. -`psi_selectors_coef `_ +`psi_selectors_coef `_ Determinants on which we apply for perturbation. -`psi_selectors_coef_ab `_ +`psi_selectors_coef_ab `_ Determinants on which we apply . They are sorted by the 3 highest electrons in the alpha part, then by the 3 highest electrons in the beta part to accelerate the research of connected determinants. -`psi_selectors_diag_h_mat `_ +`psi_selectors_diag_h_mat `_ Diagonal elements of the H matrix for each selectors -`psi_selectors_next_ab `_ +`psi_selectors_next_ab `_ Determinants on which we apply . They are sorted by the 3 highest electrons in the alpha part, then by the 3 highest electrons in the beta part to accelerate the research of connected determinants. -`psi_selectors_size `_ +`psi_selectors_size `_ Undocumented @@ -165,17 +165,6 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `Dets `_ -* `Electrons `_ -* `Ezfio_files `_ +* `Determinants `_ * `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ diff --git a/src/Selectors_full/selectors.irp.f b/src/Selectors_full/selectors.irp.f index 986241f5..73ae6371 100644 --- a/src/Selectors_full/selectors.irp.f +++ b/src/Selectors_full/selectors.irp.f @@ -1,17 +1,5 @@ use bitmasks -BEGIN_SHELL [ /usr/bin/python ] -from ezfio_with_default import EZFIO_Provider -T = EZFIO_Provider() -T.set_type ( "double precision" ) -T.set_name ( "threshold_selectors" ) -T.set_doc ( "Percentage of the norm of the state-averaged wave function to consider for the selectors" ) -T.set_ezfio_dir ( "determinants" ) -T.set_ezfio_name( "threshold_selectors" ) -T.set_output ( "output_dets" ) -print T -END_SHELL - BEGIN_PROVIDER [ integer, psi_selectors_size ] implicit none psi_selectors_size = psi_det_size @@ -25,7 +13,7 @@ BEGIN_PROVIDER [ integer, N_det_selectors] END_DOC integer :: i double precision :: norm - call write_time(output_dets) + call write_time(output_determinants) norm = 0.d0 N_det_selectors = N_det do i=1,N_det @@ -36,7 +24,7 @@ BEGIN_PROVIDER [ integer, N_det_selectors] endif enddo N_det_selectors = max(N_det_selectors,1) - call write_int(output_dets,N_det_selectors,'Number of selectors') + call write_int(output_determinants,N_det_selectors,'Number of selectors') END_PROVIDER BEGIN_PROVIDER [ integer(bit_kind), psi_selectors, (N_int,2,psi_selectors_size) ] diff --git a/src/Selectors_no_sorted/NEEDED_CHILDREN_MODULES b/src/Selectors_no_sorted/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..aae89501 --- /dev/null +++ b/src/Selectors_no_sorted/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Determinants diff --git a/src/Selectors_no_sorted/NEEDED_MODULES b/src/Selectors_no_sorted/NEEDED_MODULES deleted file mode 100644 index 7f2f0ca8..00000000 --- a/src/Selectors_no_sorted/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files MonoInts MOs Nuclei Output Utils diff --git a/src/Selectors_no_sorted/selectors.irp.f b/src/Selectors_no_sorted/selectors.irp.f index d6c20804..8080e99c 100644 --- a/src/Selectors_no_sorted/selectors.irp.f +++ b/src/Selectors_no_sorted/selectors.irp.f @@ -15,11 +15,11 @@ BEGIN_PROVIDER [ integer, N_det_selectors] END_DOC integer :: i double precision :: norm - call write_time(output_dets) + call write_time(output_determinants) norm = 0.d0 N_det_selectors = N_det N_det_selectors = max(N_det_selectors,1) - call write_int(output_dets,N_det_selectors,'Number of selectors') + call write_int(output_determinants,N_det_selectors,'Number of selectors') END_PROVIDER diff --git a/src/SingleRefMethod/NEEDED_CHILDREN_MODULES b/src/SingleRefMethod/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..bf459a13 --- /dev/null +++ b/src/SingleRefMethod/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Bitmask diff --git a/src/SingleRefMethod/NEEDED_MODULES b/src/SingleRefMethod/NEEDED_MODULES deleted file mode 100644 index bdcbdf7d..00000000 --- a/src/SingleRefMethod/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Bitmask Electrons Ezfio_files MOs Nuclei Output Utils diff --git a/src/Utils/NEEDED_CHILDREN_MODULES b/src/Utils/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..8b137891 --- /dev/null +++ b/src/Utils/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ + diff --git a/src/Utils/README.rst b/src/Utils/README.rst index 68a4f080..ff16f3ed 100644 --- a/src/Utils/README.rst +++ b/src/Utils/README.rst @@ -160,6 +160,39 @@ Documentation `rint_sum `_ Needed for the calculation of two-electron integrals. +`a_coef `_ + Undocumented + +`b_coef `_ + Undocumented + +`ddfact2 `_ + Undocumented + +`erf0 `_ + Undocumented + +`gammln `_ + Undocumented + +`gammp `_ + Undocumented + +`gcf `_ + Undocumented + +`gser `_ + Undocumented + +`rinteg `_ + Undocumented + +`rintgauss `_ + Undocumented + +`sabpartial `_ + Undocumented + `overlap_a_b_c `_ Undocumented diff --git a/src/Properties/need.irp.f b/src/Utils/need.irp.f similarity index 100% rename from src/Properties/need.irp.f rename to src/Utils/need.irp.f diff --git a/tests/HBO.out b/tests/HBO.out new file mode 100644 index 00000000..ab71c53f --- /dev/null +++ b/tests/HBO.out @@ -0,0 +1,619 @@ +----- GAMESS execution script ----- +This job is running on host LPQLX15 +under operating system Linux at jeudi 16 avril 2015, 11:11:32 (UTC+0200) +Available scratch disk space (Kbyte units) at beginning of the job is +Filesystem 1K-blocks Used Available Use% Mounted on +/dev/sda1 464085784 81207016 359281456 19% / + + Distributed Data Interface kickoff program. + Initiating 1 compute processes on 1 nodes to run the following command: + /usr/local/gamess/gamess.01.x HBO + + ****************************************************** + * GAMESS VERSION = 22 FEB 2006 (R5) * + * FROM IOWA STATE UNIVERSITY * + * M.W.SCHMIDT, K.K.BALDRIDGE, J.A.BOATZ, S.T.ELBERT, * + * M.S.GORDON, J.H.JENSEN, S.KOSEKI, N.MATSUNAGA, * + * K.A.NGUYEN, S.J.SU, T.L.WINDUS, * + * TOGETHER WITH M.DUPUIS, J.A.MONTGOMERY * + * J.COMPUT.CHEM. 14, 1347-1363(1993) * + ***************** AMD 64 BIT VERSION ***************** + + SINCE 1993, STUDENTS AND POSTDOCS WORKING AT IOWA STATE UNIVERSITY + AND ALSO IN THEIR VARIOUS JOBS AFTER LEAVING ISU HAVE MADE IMPORTANT + CONTRIBUTIONS TO THE CODE: + IVANA ADAMOVIC, CHRISTINE AIKENS, YURI ALEXEEV, POOJA ARORA, ROB BELL, + PRADIPTA BANDYOPADHYAY, BRETT BODE, GALINA CHABAN, WEI CHEN, + CHEOL HO CHOI, PAUL DAY, TIM DUDLEY, DMITRI FEDOROV, GRAHAM FLETCHER, + MARK FREITAG, KURT GLAESEMANN, GRANT MERRILL, TAKESHI NAGATA, + HEATHER NETZLOFF, BOSILJKA NJEGIC, RYAN OLSON, MIKE PAK, JIM SHOEMAKER, + LYUDMILA SLIPCHENKO, JIE SONG, TETSUYA TAKETSUGU, SIMON WEBB. + + ADDITIONAL CODE HAS BEEN PROVIDED BY COLLABORATORS IN OTHER GROUPS: + IOWA STATE UNIVERSITY: JOE IVANIC, KLAUS RUEDENBERG + UNIVERSITY OF TOKYO: KIMIHIKO HIRAO, HARUYUKI NAKANO, TAKAHITO + NAKAJIMA, TAKAO TSUNEDA, MUNEAKI KAMIYA, SUSUMU YANAGISAWA, + KIYOSHI YAGI + UNIVERSITY OF SOUTHERN DENMARK: FRANK JENSEN + UNIVERSITY OF IOWA: VISVALDAS KAIRYS, HUI LI + NATIONAL INST. OF STANDARDS AND TECHNOLOGY: WALT STEVENS, DAVID GARMER + UNIVERSITY OF PISA: BENEDETTA MENNUCCI, JACOPO TOMASI + UNIVERSITY OF MEMPHIS: HENRY KURTZ, PRAKASHAN KORAMBATH + UNIVERSITY OF ALBERTA: MARIUSZ KLOBUKOWSKI + UNIVERSITY OF NEW ENGLAND: MARK SPACKMAN + MIE UNIVERSITY: HIROAKI UMEDA + MICHIGAN STATE UNIVERSITY: + KAROL KOWALSKI, MARTA WLOCH, PIOTR PIECUCH + UNIVERSITY OF SILESIA: MONIKA MUSIAL, STANISLAW KUCHARSKI + FACULTES UNIVERSITAIRES NOTRE-DAME DE LA PAIX: + OLIVIER QUINET, BENOIT CHAMPAGNE + UNIVERSITY OF CALIFORNIA - SANTA BARBARA: BERNARD KIRTMAN + INSTITUTE FOR MOLECULAR SCIENCE: KAZUYA ISHIMURA AND SHIGERU NAGASE + UNIVERSITY OF NOTRE DAME: DAN CHIPMAN + KYUSHU UNIVERSITY: + FENG LONG GU, JACEK KORCHOWIEC, MARCIN MAKOWSKI, AND YURIKO AOKI + PENNSYLVANIA STATE UNIVERSITY: + TZVETELIN IORDANOV, CHET SWALINA, SHARON HAMMES-SCHIFFER + + EXECUTION OF GAMESS BEGUN Thu Apr 16 11:11:32 2015 + + ECHO OF THE FIRST FEW INPUT CARDS - + INPUT CARD> + INPUT CARD> $CONTRL + INPUT CARD> RUNTYP=ENERGY + INPUT CARD> MULT=1 + INPUT CARD> SCFTYP=ROHF + INPUT CARD> $END + INPUT CARD> + INPUT CARD> $GUESS + INPUT CARD> GUESS=HCORE + INPUT CARD> $END + INPUT CARD> + INPUT CARD> $DATA + INPUT CARD> HBO + INPUT CARD>C1 + INPUT CARD>H 1.0 0. 0. 0. + INPUT CARD>S 3 + INPUT CARD> 1 18.7311370 0.0334946 + INPUT CARD> 2 2.8253944 0.2347269 + INPUT CARD> 3 0.6401217 0.8137573 + INPUT CARD>S 1 + INPUT CARD> 1 0.1612778 1.0000000 + INPUT CARD> + INPUT CARD>B 5.0 1.1660 0. 0. + INPUT CARD>S 4 + INPUT CARD> 1 330.7528500 0.0179942 + INPUT CARD> 2 49.8438650 0.1246937 + INPUT CARD> 3 11.1170540 0.4343354 + INPUT CARD> 4 2.9227243 0.5609794 + INPUT CARD>L 3 + INPUT CARD> 1 5.6812646 -0.1303871 0.0637429 + INPUT CARD> 2 1.4544046 -0.2514344 0.2761331 + INPUT CARD> 3 0.4283786 1.2051292 0.7773866 + INPUT CARD>L 1 + INPUT CARD> 1 0.1442192 1.0000000 1.0000000 + INPUT CARD> + INPUT CARD>B 8.0 2.3660 0. 0. + INPUT CARD>S 4 + INPUT CARD> 1 883.2728600 0.0175506 + INPUT CARD> 2 133.1292800 0.1228292 + INPUT CARD> 3 29.9064080 0.4348836 + INPUT CARD> 4 7.9786772 0.5600108 + INPUT CARD>L 3 + INPUT CARD> 1 16.1944470 -0.1134010 0.0685453 + INPUT CARD> 2 3.7800860 -0.1772865 0.3312254 + INPUT CARD> 3 1.0709836 1.1504079 0.7346079 + INPUT CARD>L 1 + INPUT CARD> 1 0.2838798 1.0000000 1.0000000 + INPUT CARD> + INPUT CARD> $END + + ..... DONE SETTING UP THE RUN ..... + 1000000 WORDS OF MEMORY AVAILABLE + + + RUN TITLE + --------- + HBO + + THE POINT GROUP OF THE MOLECULE IS C1 + THE ORDER OF THE PRINCIPAL AXIS IS 0 + + ATOM ATOMIC COORDINATES (BOHR) + CHARGE X Y Z + H 1.0 0.0000000000 0.0000000000 0.0000000000 + B 5.0 2.2034205017 0.0000000000 0.0000000000 + B 8.0 4.4710916869 0.0000000000 0.0000000000 + + INTERNUCLEAR DISTANCES (ANGS.) + ------------------------------ + + H B B + + 1 H 0.0000000 1.1660000 * 2.3660000 * + 2 B 1.1660000 * 0.0000000 1.2000000 * + 3 B 2.3660000 * 1.2000000 * 0.0000000 + + ATOMIC BASIS SET + ---------------- + THE CONTRACTED PRIMITIVE FUNCTIONS HAVE BEEN UNNORMALIZED + THE CONTRACTED BASIS FUNCTIONS ARE NOW NORMALIZED TO UNITY + + SHELL TYPE PRIMITIVE EXPONENT CONTRACTION COEFFICIENT(S) + + H + + 1 S 1 18.7311370 0.033494602358 + 1 S 2 2.8253944 0.234726916524 + 1 S 3 0.6401217 0.813757357284 + + 2 S 4 0.1612778 1.000000000000 + + B + + 3 S 5 330.7528500 0.017994199122 + 3 S 6 49.8438650 0.124693693914 + 3 S 7 11.1170540 0.434335378802 + 3 S 8 2.9227243 0.560979372621 + + 4 L 9 5.6812646 -0.130387101955 0.063742897507 + 4 L 10 1.4544046 -0.251434403769 0.276133089199 + 4 L 11 0.4283786 1.205129218067 0.777386569593 + + 5 L 12 0.1442192 1.000000000000 1.000000000000 + + B + + 6 S 13 883.2728600 0.017550600144 + 6 S 14 133.1292800 0.122829201010 + 6 S 15 29.9064080 0.434883603578 + 6 S 16 7.9786772 0.560010804607 + + 7 L 17 16.1944470 -0.113401005792 0.068545299729 + 7 L 18 3.7800860 -0.177286509055 0.331225398691 + 7 L 19 1.0709836 1.150407958755 0.734607897097 + + 8 L 20 0.2838798 1.000000000000 1.000000000000 + + TOTAL NUMBER OF BASIS SET SHELLS = 8 + NUMBER OF CARTESIAN GAUSSIAN BASIS FUNCTIONS = 20 + NUMBER OF ELECTRONS = 14 + CHARGE OF MOLECULE = 0 + SPIN MULTIPLICITY = 1 + NUMBER OF OCCUPIED ORBITALS (ALPHA) = 7 + NUMBER OF OCCUPIED ORBITALS (BETA ) = 7 + TOTAL NUMBER OF ATOMS = 3 + THE NUCLEAR REPULSION ENERGY IS 21.6977130101 + + THIS MOLECULE IS RECOGNIZED AS BEING LINEAR. + + $CONTRL OPTIONS + --------------- + SCFTYP=ROHF RUNTYP=ENERGY EXETYP=RUN + MPLEVL= 0 CITYP =NONE CCTYP =NONE VBTYP =NONE + MULT = 1 ICHARG= 0 NZVAR = 0 COORD =UNIQUE + PP =NONE RELWFN=NONE LOCAL =NONE NUMGRD= F + ISPHER= -1 NOSYM = 0 MAXIT = 30 UNITS =ANGS + PLTORB= F MOLPLT= F AIMPAC= F FRIEND= + NPRINT= 7 IREST = 0 GEOM =INPUT + NORMF = 0 NORMP = 0 ITOL = 20 ICUT = 9 + INTTYP=BEST GRDTYP=BEST QMTTOL= 1.0E-06 + + $SYSTEM OPTIONS + --------------- + REPLICATED MEMORY= 1000000 WORDS (ON EVERY NODE). + DISTRIBUTED MEMDDI= 0 MILLION WORDS IN AGGREGATE, + MEMDDI DISTRIBUTED OVER 1 PROCESSORS IS 0 WORDS/PROCESSOR. + TOTAL MEMORY REQUESTED ON EACH PROCESSOR= 1000000 WORDS. + TIMLIM= 525600.00 MINUTES, OR 365.00 DAYS. + PARALL= F BALTYP= NXTVAL KDIAG= 0 COREFL= F + + ---------------- + PROPERTIES INPUT + ---------------- + + MOMENTS FIELD POTENTIAL DENSITY + IEMOM = 1 IEFLD = 0 IEPOT = 0 IEDEN = 0 + WHERE =COMASS WHERE =NUCLEI WHERE =NUCLEI WHERE =NUCLEI + OUTPUT=BOTH OUTPUT=BOTH OUTPUT=BOTH OUTPUT=BOTH + IEMINT= 0 IEFINT= 0 IEDINT= 0 + MORB = 0 + EXTRAPOLATION IN EFFECT + SOSCF IN EFFECT + ORBITAL PRINTING OPTION: NPREO= 1 20 2 1 + + ------------------------------- + INTEGRAL TRANSFORMATION OPTIONS + ------------------------------- + NWORD = 0 CUTOFF = 1.0E-09 + MPTRAN = 0 DIRTRF = F + AOINTS =DUP + + ---------------------- + INTEGRAL INPUT OPTIONS + ---------------------- + NOPK = 1 NORDER= 0 SCHWRZ= F + + ------------------------------------------ + THE POINT GROUP IS C1 , NAXIS= 0, ORDER= 1 + ------------------------------------------ + + DIMENSIONS OF THE SYMMETRY SUBSPACES ARE + A = 20 + + ..... DONE SETTING UP THE RUN ..... + STEP CPU TIME = 0.01 TOTAL CPU TIME = 0.0 ( 0.0 MIN) + TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 100.00% + + ******************** + 1 ELECTRON INTEGRALS + ******************** + ...... END OF ONE-ELECTRON INTEGRALS ...... + STEP CPU TIME = 0.00 TOTAL CPU TIME = 0.0 ( 0.0 MIN) + TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 100.00% + + ------------- + GUESS OPTIONS + ------------- + GUESS =HCORE NORB = 0 NORDER= 0 + MIX = F PRTMO = F PUNMO = F + TOLZ = 1.0E-08 TOLE = 1.0E-05 + SYMDEN= F PURIFY= F + + INITIAL GUESS ORBITALS GENERATED BY HCORE ROUTINE. + + SYMMETRIES FOR INITIAL GUESS ORBITALS FOLLOW. ALPHA SET(S). + 7 ORBITALS ARE OCCUPIED ( 2 CORE ORBITALS). + 3=A 4=A 5=A 6=A 7=A 8=A 9=A + 10=A 11=A 12=A 13=A 14=A 15=A 16=A + 17=A + + SYMMETRIES FOR INITIAL GUESS ORBITALS FOLLOW. BETA SET(S). + 7 ORBITALS ARE OCCUPIED ( 2 CORE ORBITALS). + 3=A 4=A 5=A 6=A 7=A 8=A 9=A + 10=A 11=A 12=A 13=A 14=A 15=A 16=A + 17=A + ...... END OF INITIAL ORBITAL SELECTION ...... + STEP CPU TIME = 0.00 TOTAL CPU TIME = 0.0 ( 0.0 MIN) + TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 100.00% + + ---------------------- + AO INTEGRAL TECHNOLOGY + ---------------------- + S,P,L SHELL ROTATED AXIS INTEGRALS, REPROGRAMMED BY + KAZUYA ISHIMURA (IMS) AND JOSE SIERRA (SYNSTAR). + S,P,D,L SHELL ROTATED AXIS INTEGRALS PROGRAMMED BY + KAZUYA ISHIMURA (INSTITUTE FOR MOLECULAR SCIENCE). + S,P,D,F,G SHELL TO TOTAL QUARTET ANGULAR MOMENTUM SUM 5, + ERIC PROGRAM BY GRAHAM FLETCHER (ELORET AND NASA ADVANCED + SUPERCOMPUTING DIVISION, AMES RESEARCH CENTER). + S,P,D,F,G,L SHELL GENERAL RYS QUADRATURE PROGRAMMED BY + MICHEL DUPUIS (PACIFIC NORTHWEST NATIONAL LABORATORY). + + -------------------- + 2 ELECTRON INTEGRALS + -------------------- + + THE -PK- OPTION IS OFF, THE INTEGRALS ARE NOT IN SUPERMATRIX FORM. + STORING 15000 INTEGRALS/RECORD ON DISK, USING 12 BYTES/INTEGRAL. + TWO ELECTRON INTEGRAL EVALUATION REQUIRES 89392 WORDS OF MEMORY. + II,JST,KST,LST = 1 1 1 1 NREC = 1 INTLOC = 1 + II,JST,KST,LST = 2 1 1 1 NREC = 1 INTLOC = 2 + II,JST,KST,LST = 3 1 1 1 NREC = 1 INTLOC = 7 + II,JST,KST,LST = 4 1 1 1 NREC = 1 INTLOC = 22 + II,JST,KST,LST = 5 1 1 1 NREC = 1 INTLOC = 169 + II,JST,KST,LST = 6 1 1 1 NREC = 1 INTLOC = 678 + II,JST,KST,LST = 7 1 1 1 NREC = 1 INTLOC = 1045 + II,JST,KST,LST = 8 1 1 1 NREC = 1 INTLOC = 3095 + TOTAL NUMBER OF NONZERO TWO-ELECTRON INTEGRALS = 7058 + 1 INTEGRAL RECORDS WERE STORED ON DISK FILE 8. + ...... END OF TWO-ELECTRON INTEGRALS ..... + STEP CPU TIME = 0.01 TOTAL CPU TIME = 0.0 ( 0.0 MIN) + TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 100.00% + + --------------------------- + ROHF SCF CALCULATION + --------------------------- + + NUCLEAR ENERGY = 21.6977130101 + MAXIT = 30 NPUNCH= 2 MULT= 1 + EXTRAP=T DAMP=F SHIFT=F RSTRCT=F DIIS=F SOSCF=T + DENSITY MATRIX CONV= 1.00E-05 + ROHF CANONICALIZATION PARAMETERS + C-C O-O V-V + ALPHA -0.5000 0.5000 1.5000 + BETA 1.5000 0.5000 -0.5000 + SOSCF WILL OPTIMIZE 91 ORBITAL ROTATION ANGLES. SOGTOL= 2.500E-01 + MEMORY REQUIRED FOR UHF/ROHF STEP= 34446 WORDS. + + ITER EX TOTAL ENERGY E CHANGE DENSITY CHANGE ORB. GRAD + 1 0 -89.6780199978 -89.6780199978 13.802827629 0.000000000 + 2 1 -86.8672057689 2.8108142288 13.697658380 1.147034737 + 3 2 -90.7237904418 -3.8565846728 6.184375907 0.885015488 + 4 3 -88.5602746012 2.1635158406 6.139277282 0.784307787 + 5 0 -90.8787176080 -2.3184430069 2.371801774 0.897367372 + ---------------START SECOND ORDER SCF--------------- + 6 1 -99.6901335684 -8.8114159604 0.589370704 0.247448832 + 7 2 -99.6027127341 0.0874208344 0.282419417 0.261235193 + 8 3 -100.0104700579 -0.4077573239 0.097896975 0.028403161 + 9 4 -100.0166758568 -0.0062057989 0.041892588 0.022623440 + 10 5 -100.0185127886 -0.0018369318 0.005554114 0.004257220 + 11 6 -100.0185731832 -0.0000603946 0.002182788 0.001537483 + 12 7 -100.0185817542 -0.0000085710 0.000686329 0.000164155 + 13 8 -100.0185822279 -0.0000004737 0.000159733 0.000052231 + 14 9 -100.0185822583 -0.0000000304 0.000031771 0.000009807 + 15 10 -100.0185822589 -0.0000000006 0.000003729 0.000001197 + 16 11 -100.0185822589 -0.0000000000 0.000000462 0.000000205 + + ----------------- + DENSITY CONVERGED + ----------------- + + FINAL ROHF ENERGY IS -100.0185822589 AFTER 16 ITERATIONS + + -------------------- + SPIN SZ = 0.000 + S-SQUARED = -0.000 + -------------------- + + ------------ + EIGENVECTORS + ------------ + + 1 2 3 4 5 + -20.5358 -7.6507 -1.3450 -0.6694 -0.6084 + A A A A A + 1 H 1 S 0.000344 -0.001283 0.014215 0.292154 0.137956 + 2 H 1 S 0.009984 0.010621 -0.040706 0.189877 0.183728 + 3 B 2 S 0.001078 0.993835 -0.103615 -0.167500 0.038365 + 4 B 2 S 0.003671 0.056948 0.125777 0.229996 -0.092389 + 5 B 2 X 0.000735 0.002873 0.178961 -0.173521 -0.351664 + 6 B 2 Y 0.000000 0.000000 0.000000 0.000000 0.000000 + 7 B 2 Z 0.000000 0.000000 0.000000 0.000000 0.000000 + 8 B 2 S 0.007386 -0.022682 0.028991 0.265728 0.011974 + 9 B 2 X 0.019131 0.008736 -0.072950 -0.150274 0.027354 + 10 B 2 Y 0.000000 0.000000 0.000000 0.000000 0.000000 + 11 B 2 Z 0.000000 0.000000 0.000000 0.000000 0.000000 + 12 O 3 S 0.992054 -0.001164 -0.212590 0.045561 -0.066200 + 13 O 3 S 0.053959 0.001671 0.432154 -0.104949 0.138600 + 14 O 3 X -0.002799 -0.001577 -0.143624 -0.191121 0.522743 + 15 O 3 Y 0.000000 0.000000 0.000000 0.000000 0.000000 + 16 O 3 Z 0.000000 0.000000 0.000000 0.000000 0.000000 + 17 O 3 S -0.038715 -0.006953 0.509977 -0.099891 0.303790 + 18 O 3 X 0.008857 0.005154 -0.052386 -0.130143 0.293535 + 19 O 3 Y 0.000000 0.000000 0.000000 0.000000 0.000000 + 20 O 3 Z 0.000000 0.000000 0.000000 0.000000 0.000000 + + 6 7 8 9 10 + -0.5169 -0.5169 0.1699 0.1699 0.2267 + A A A A A + 1 H 1 S 0.000000 0.000000 0.000000 0.000000 -0.150419 + 2 H 1 S 0.000000 0.000000 0.000000 0.000000 -1.466998 + 3 B 2 S 0.000000 0.000000 0.000000 0.000000 -0.144359 + 4 B 2 S 0.000000 0.000000 0.000000 0.000000 -0.048306 + 5 B 2 X 0.000000 0.000000 0.000000 0.000000 -0.139034 + 6 B 2 Y -0.083449 0.221695 0.137663 0.278557 0.000000 + 7 B 2 Z 0.221695 0.083449 0.278557 -0.137663 0.000000 + 8 B 2 S 0.000000 0.000000 0.000000 0.000000 2.027943 + 9 B 2 X 0.000000 0.000000 0.000000 0.000000 -0.144405 + 10 B 2 Y -0.050412 0.133928 0.379815 0.768545 0.000000 + 11 B 2 Z 0.133928 0.050412 0.768545 -0.379815 0.000000 + 12 O 3 S 0.000000 0.000000 0.000000 0.000000 0.053464 + 13 O 3 S 0.000000 0.000000 0.000000 0.000000 -0.086787 + 14 O 3 X 0.000000 0.000000 0.000000 0.000000 0.153448 + 15 O 3 Y -0.190568 0.506276 -0.136229 -0.275656 0.000000 + 16 O 3 Z 0.506276 0.190568 -0.275656 0.136229 0.000000 + 17 O 3 S 0.000000 0.000000 0.000000 0.000000 -0.606405 + 18 O 3 X 0.000000 0.000000 0.000000 0.000000 0.320500 + 19 O 3 Y -0.148054 0.393331 -0.221558 -0.448317 0.000000 + 20 O 3 Z 0.393331 0.148054 -0.448317 0.221558 0.000000 + + 11 12 13 14 15 + 0.4316 0.7045 0.7045 0.7350 1.1048 + A A A A A + 1 H 1 S -0.197856 0.000000 0.000000 0.585371 -0.661822 + 2 H 1 S 2.428044 0.000000 0.000000 1.162180 1.538010 + 3 B 2 S 0.027852 0.000000 0.000000 0.045321 0.010878 + 4 B 2 S -0.331748 0.000000 0.000000 0.814476 1.936129 + 5 B 2 X 0.288153 0.000000 0.000000 -0.704191 0.333782 + 6 B 2 Y 0.000000 0.097971 1.207126 0.000000 0.000000 + 7 B 2 Z 0.000000 1.207126 -0.097971 0.000000 0.000000 + 8 B 2 S 0.216139 0.000000 0.000000 -1.451072 -1.909797 + 9 B 2 X 2.635346 0.000000 0.000000 2.283710 0.676105 + 10 B 2 Y 0.000000 -0.085320 -1.051252 0.000000 0.000000 + 11 B 2 Z 0.000000 -1.051252 0.085320 0.000000 0.000000 + 12 O 3 S 0.086152 0.000000 0.000000 0.027095 0.050912 + 13 O 3 S -0.030658 0.000000 0.000000 -0.048038 -0.187902 + 14 O 3 X 0.005711 0.000000 0.000000 -0.124028 0.248507 + 15 O 3 Y 0.000000 -0.002880 -0.035481 0.000000 0.000000 + 16 O 3 Z 0.000000 -0.035481 0.002880 0.000000 0.000000 + 17 O 3 S -1.936881 0.000000 0.000000 -0.740239 -0.345357 + 18 O 3 X 0.485099 0.000000 0.000000 -0.079803 0.535249 + 19 O 3 Y 0.000000 0.000732 0.009020 0.000000 0.000000 + 20 O 3 Z 0.000000 0.009020 -0.000732 0.000000 0.000000 + + 16 17 18 19 20 + 1.2423 1.3557 1.3557 1.4100 2.2399 + A A A A A + 1 H 1 S 0.719124 0.000000 0.000000 0.725323 -0.157789 + 2 H 1 S -1.191244 0.000000 0.000000 -0.477445 -1.225214 + 3 B 2 S 0.105177 0.000000 0.000000 -0.060885 -0.141177 + 4 B 2 S 0.511585 0.000000 0.000000 0.050787 -0.875118 + 5 B 2 X 1.035905 0.000000 0.000000 0.780799 -0.452459 + 6 B 2 Y 0.000000 0.002283 0.015609 0.000000 0.000000 + 7 B 2 Z 0.000000 0.015609 -0.002283 0.000000 0.000000 + 8 B 2 S 1.010217 0.000000 0.000000 0.112107 -0.746938 + 9 B 2 X -0.643431 0.000000 0.000000 -0.134607 -2.362585 + 10 B 2 Y 0.000000 -0.058566 -0.400461 0.000000 0.000000 + 11 B 2 Z 0.000000 -0.400461 0.058566 0.000000 0.000000 + 12 O 3 S 0.065107 0.000000 0.000000 0.020195 0.012799 + 13 O 3 S -0.268804 0.000000 0.000000 -0.067586 -1.977025 + 14 O 3 X -0.440790 0.000000 0.000000 0.885097 0.119422 + 15 O 3 Y 0.000000 -0.143987 -0.984542 0.000000 0.000000 + 16 O 3 Z 0.000000 -0.984542 0.143987 0.000000 0.000000 + 17 O 3 S -0.423279 0.000000 0.000000 -0.263857 4.377413 + 18 O 3 X 1.480677 0.000000 0.000000 -0.527277 -1.336333 + 19 O 3 Y 0.000000 0.174511 1.193260 0.000000 0.000000 + 20 O 3 Z 0.000000 1.193260 -0.174511 0.000000 0.000000 + ...... END OF ROHF CALCULATION ...... + STEP CPU TIME = 0.00 TOTAL CPU TIME = 0.0 ( 0.0 MIN) + TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 100.00% + + ---------------------------------------------------------------- + PROPERTY VALUES FOR THE ROHF SELF-CONSISTENT FIELD WAVEFUNCTION + ---------------------------------------------------------------- + + ----------------- + ENERGY COMPONENTS + ----------------- + + WAVEFUNCTION NORMALIZATION = 1.0000000000 + + ONE ELECTRON ENERGY = -179.7468005131 + TWO ELECTRON ENERGY = 58.0305052441 + NUCLEAR REPULSION ENERGY = 21.6977130101 + ------------------ + TOTAL ENERGY = -100.0185822589 + + ELECTRON-ELECTRON POTENTIAL ENERGY = 58.0305052441 + NUCLEUS-ELECTRON POTENTIAL ENERGY = -279.7201121919 + NUCLEUS-NUCLEUS POTENTIAL ENERGY = 21.6977130101 + ------------------ + TOTAL POTENTIAL ENERGY = -199.9918939377 + TOTAL KINETIC ENERGY = 99.9733116788 + VIRIAL RATIO (V/T) = 2.0004528267 + + ...... PI ENERGY ANALYSIS ...... + + ENERGY ANALYSIS: + FOCK ENERGY= -63.6857886983 + BARE H ENERGY= -179.7468005131 + ELECTRONIC ENERGY = -121.7162946057 + KINETIC ENERGY= 99.9733116788 + N-N REPULSION= 21.6977130101 + TOTAL ENERGY= -100.0185815956 + SIGMA PART(1+2)= -104.7962806542 + (K,V1,2)= 92.4442005381 -240.4183928275 43.1779116353 + PI PART(1+2)= -16.9200139514 + (K,V1,2)= 7.5291111407 -39.3017193643 14.8525942722 + SIGMA SKELETON, ERROR= -83.0985676441 -0.0000000000 + MIXED PART= 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 + ...... END OF PI ENERGY ANALYSIS ...... + + --------------------------------------- + MULLIKEN AND LOWDIN POPULATION ANALYSES + --------------------------------------- + + MULLIKEN ATOMIC POPULATION IN EACH MOLECULAR ORBITAL + + 1 2 3 4 5 + + 2.000000 2.000000 2.000000 2.000000 2.000000 + + 1 0.000109 0.002431 -0.009540 0.732140 0.208060 + 2 0.004773 2.000884 0.269059 0.988894 0.366310 + 3 1.995118 -0.003315 1.740481 0.278967 1.425630 + + 6 7 + + 2.000000 2.000000 + + 1 0.000000 0.000000 + 2 0.420558 0.420558 + 3 1.579442 1.579442 + + ATOMIC SPIN POPULATION (ALPHA MINUS BETA) + ATOM MULL.POP. LOW.POP. + 1 H 0.000000 0.000000 + 2 B 0.000000 0.000000 + 3 B 0.000000 0.000000 + + ----- POPULATIONS IN EACH AO ----- + MULLIKEN LOWDIN + 1 H 1 S 0.51411 0.47971 + 2 H 1 S 0.41909 0.48591 + 3 B 2 S 1.99770 1.98102 + 4 B 2 S 0.45972 0.43762 + 5 B 2 X 0.70045 0.64124 + 6 B 2 Y 0.25163 0.23600 + 7 B 2 Z 0.25163 0.23600 + 8 B 2 S 0.37344 0.43074 + 9 B 2 X 0.09860 0.36418 + 10 B 2 Y 0.16892 0.22234 + 11 B 2 Z 0.16892 0.22234 + 12 O 3 S 1.99590 1.99380 + 13 O 3 S 0.85319 0.83536 + 14 O 3 X 0.99185 0.94649 + 15 O 3 Y 0.86458 0.82908 + 16 O 3 Z 0.86458 0.82908 + 17 O 3 S 1.06945 0.76118 + 18 O 3 X 0.52649 0.64275 + 19 O 3 Y 0.71487 0.71259 + 20 O 3 Z 0.71487 0.71259 + + ----- MULLIKEN ATOMIC OVERLAP POPULATIONS ----- + (OFF-DIAGONAL ELEMENTS NEED TO BE MULTIPLIED BY 2) + + 1 2 3 + + 1 0.5637982 + 2 0.3833280 3.4279422 + 3 -0.0139266 0.6597650 7.9499266 + + TOTAL MULLIKEN AND LOWDIN ATOMIC POPULATIONS + ATOM MULL.POP. CHARGE LOW.POP. CHARGE + 1 H 0.933200 0.066800 0.965622 0.034378 + 2 B 4.471035 0.528965 4.771474 0.228526 + 3 B 8.595765 -0.595765 8.262905 -0.262905 + + ------------------------------- + BOND ORDER AND VALENCE ANALYSIS BOND ORDER THRESHOLD=0.050 + ------------------------------- + + BOND BOND BOND + ATOM PAIR DIST ORDER ATOM PAIR DIST ORDER ATOM PAIR DIST ORDER + 1 2 1.166 0.974 2 3 1.200 2.151 + + TOTAL BONDED FREE + ATOM VALENCE VALENCE VALENCE + 1 H 0.969 0.969 -0.000 + 2 B 3.125 3.125 -0.000 + 3 B 2.145 2.145 -0.000 + + ----------------------------------------- + ATOMIC SPIN DENSITY AT THE NUCLEUS (A.U.) + ----------------------------------------- + SPIN DENS ALPHA DENS BETA DENS + 1 H 1.0 0.0000000 0.19961 0.19961 + 2 B 5.0 0.0000000 30.17561 30.17561 + 3 B 8.0 0.0000000 131.78303 131.78303 + + --------------------- + ELECTROSTATIC MOMENTS + --------------------- + + POINT 1 X Y Z (BOHR) CHARGE + 3.418988 0.000000 0.000000 -0.00 (A.U.) + DX DY DZ /D/ (DEBYE) + -3.311042 0.000000 0.000000 3.311042 + ...... END OF PROPERTY EVALUATION ...... + STEP CPU TIME = 0.00 TOTAL CPU TIME = 0.0 ( 0.0 MIN) + TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 100.00% + 440000 WORDS OF DYNAMIC MEMORY USED + EXECUTION OF GAMESS TERMINATED NORMALLY Thu Apr 16 11:11:32 2015 + DDI: 1128 bytes (0.0 MB / 0 MWords) used by master data server. + + ---------------------------------------- + CPU timing information for all processes + ======================================== + 0: 0.029395 + 0.008325 = 0.037720 + ---------------------------------------- + ddikick.x: exited gracefully. +----- accounting info ----- +jeudi 16 avril 2015, 11:11:35 (UTC+0200) +Files used on the master node LPQLX15 were: +-rw-rw-r-- 1 razoa razoa 8438 avril 16 11:11 /tmp/gamess/HBO.dat +-rw-r--r-- 1 razoa razoa 1404 avril 16 11:11 /tmp/gamess/HBO.F05 +-rw-rw-r-- 1 razoa razoa 180016 avril 16 11:11 /tmp/gamess/HBO.F08 +-rw-rw-r-- 1 razoa razoa 4711680 avril 16 11:11 /tmp/gamess/HBO.F10 +0.104u 0.077s 0:03.22 5.2% 0+0k 0+16io 0pf+0w diff --git a/tests/unit_test/unit_test.py b/tests/unit_test/unit_test.py index eb9b1e79..f9049d82 100755 --- a/tests/unit_test/unit_test.py +++ b/tests/unit_test/unit_test.py @@ -62,7 +62,6 @@ def get_error_message(l_exepected, l_cur): # / |_ _ _ | o ._ ._ _|_ # \_ | | (/_ (_ |< | | | |_) |_| |_ # | - def check_disk_acess(geo, basis, mult=1): import uuid @@ -147,8 +146,6 @@ def check_mo_guess(geo, basis, mult=1): # / |_ _ _ | _. | _ _ # \_ | | (/_ (_ |< \/ (_| | |_| (/_ _> # - - def run_hf(geo, basis, mult=1): """ Run a simle by default hf @@ -190,6 +187,8 @@ def run_hf(geo, basis, mult=1): ezfio.hartree_fock_thresh_scf = 1.e-10 ezfio.hartree_fock_n_it_scf_max = 100 + ezfio.pseudo_integrals_do_pseudo = False + # ~#~#~ # # R u n # # ~#~#~ # @@ -286,6 +285,56 @@ def hf_then_10k_test(geo, basis): return return_code +# _ +# / |_ _ _ | _. ._ _ _ ._ _ ._ _|_ +# \_ | | (/_ (_ |< (_| |_) (_ (_) | | \/ (/_ | |_ +# | | __ +def check_convert(path_out): + ''' + Path_out is the out_file + ''' + + # ~#~#~#~#~#~#~#~#~#~ # + # R e f _ e n e r g y # + # ~#~#~#~#~#~#~#~#~#~ # + + ref_energy = defaultdict(dict) + + ref_energy["HBO.out"] = -100.0185822589 + + # ~#~#~#~#~#~#~#~#~#~#~#~#~ # + # S e t _ p a r a m e t e r # + # ~#~#~#~#~#~#~#~#~#~#~#~#~ # + + cmd = "cp {0}/tests/{1} .".format(qpackage_root, path_out) + subprocess.check_call([cmd], shell=True) + + cmd = "qp_convert_output_to_ezfio.py {0}".format(path_out) + subprocess.check_call([cmd], shell=True) + + # Test 2 + cmd = "qp_edit -c {0}.ezfio".format(path_out) + subprocess.check_call([cmd], shell=True) + + cmd = "qp_run SCF {0}.ezfio".format(path_out) + subprocess.check_call([cmd], shell=True) + + # ~#~#~#~#~ # + # C h e c k # + # ~#~#~#~#~ # + + ezfio.set_file("{0}.ezfio".format(path_out)) + + cur_e = ezfio.get_hartree_fock_energy() + ref_e = ref_energy[path_out] + + if abs(cur_e - ref_e) <= precision: + subprocess.call(["rm {0}".format(path_out)], shell=True) + subprocess.call(["rm -R {0}.ezfio".format(path_out)], shell=True) + return True + else: + raise ValueError(get_error_message([ref_e], [cur_e])) + # ___ # | _ _ _|_ # | (/_ _> |_ @@ -295,6 +344,9 @@ class ValueTest(unittest.TestCase): def test_full_ci_10k_pt2_end(self): self.assertTrue(hf_then_10k_test("methane", "sto-3g")) + def test_check_convert_hf_energy(self): + self.assertTrue(check_convert("HBO.out")) + class InputTest(unittest.TestCase):