Merge branch 'master' of git://github.com/TApplencourt/quantum_package into TApplencourt-master

ocaml/Input.ml

@@ -2,15 +2,10 @@ open Qputils;;
 open Qptypes;;
 open Core.Std;;
 
-
 include Input_ao_basis;;
-include Input_bielec_integrals;;
 include Input_bitmasks;;
-include Input_cisd_sc2_selected;;
 include Input_determinants;;
 include Input_electrons;;
-include Input_full_ci;;
-include Input_hartree_fock;;
 include Input_mo_basis;;
 include Input_nuclei;;
-
+include Input_auto_generated;;

scripts/docopt.py

@@ -0,0 +1,590 @@
+"""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, <positional-argument>, 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 "<path>", and values are the
+        parsed values of those elements.
+
+    Example
+    -------
+    >>> from docopt import docopt
+    >>> doc = '''
+    ... Usage:
+    ...     my_program tcp <host> <port> [--timeout=<seconds>]
+    ...     my_program serial <port> [--baud=<n>] [--timeout=<seconds>]
+    ...     my_program (-h | --help | --version)
+    ...
+    ... Options:
+    ...     -h, --help  Show this screen and exit.
+    ...     --baud=<n>  Baudrate [default: 9600]
+    ... '''
+    >>> argv = ['tcp', '127.0.0.1', '80', '--timeout', '30']
+    >>> docopt(doc, argv)
+    {'--baud': '9600',
+     '--help': False,
+     '--timeout': '30',
+     '--version': False,
+     '<host>': '127.0.0.1',
+     '<port>': '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()

scripts/ezfio_interface/ei_handler.py

@@ -1,26 +1,42 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
-Take a path in argv
-Check if EZFIO.cfg exists.
-EZFIO.cfg are in MODULE directories.
-create : ezfio_interface.irp.f
-         folder_ezfio_inteface_config
-Ezfio_dir : is equal to MODULE.lower!
+Welcom the ei_handler.
+We will create all the ezfio related stuff from a EZFIO.cfg file.
 
+Usage:
+    ei_handler.py [--path] [--irpf90] [--ezfio_config] [--ocaml] [--ezfio_default] [--global]
+
+By default all the option are executed.
+
+Options:
+    -h --help
+    --path             The path of the `EZFIO.cfg`, by default will look in the ${pwd}
+    --irpf90           Create the `ezfio_interface.ipf90`
+                             who containt all the provider needed
+                             (aka all with the `interface: input` parameter)
+                             in `${pwd}`
+    --ezfio_config     Create the `${module_lower}_ezfio_interface_config` in
+                             `${QPACKAGE_ROOT}/EZFIO/config/`
+                       This file is needed by *EZFIO* to create the `libezfio.so`
+    --ocaml            Create the `Input_module.lower.ml` for the *qp_edit*
+    --ezfio_default    Create the `${module_lower}_ezfio_interface_default` in
+                             `${QPACKAGE_ROOT}/data/ezfio_defaults` needed by
+                             the ocaml
+    --global           Create all the stuff who need all the EZFIO.cfg
 
 Format specification :
-    [provider_name] : the name of the provider in irp.f90
-    - doc        : Is the doc
-    - Type       : Is a fancy_type support by the ocaml
-    - ezfio_name : Will be the name of the file for the ezfio
-        (optional by default is the name of the provider)
-    - interface  : The provider is a imput or a output
-    - default : The default value if interface == input:
-    - size : Is the string read in ezfio.cgf who containt the size information
-             (like 1 or =sum(ao_num) or (ao_num,3) )
+    [provider_name]  | the name of the provider in irp.f90
+    doc:{str}        | Is the doc
+    Type:{str}       | Is a fancy_type support by the ocaml
+    ezfio_name:{str} | Will be the name of the file for the ezfio
+                       (optional by default is the name of the provider)
+    interface:{str}  | The provider is a imput or a output
+    default:{str}    | The default value if interface == input:
+    size:{str}       | the size information
+                        (like 1 or =sum(ao_num) or (ao_num,3) )
 
-Example EZFIO.cfg:
+Example of EZFIO.cfg:
 ```
 [thresh_SCF]
 doc: Threshold on the convergence of the Hartree Fock energy
@@ -34,8 +50,8 @@ type: double precision
 doc: Calculated HF energy
 interface: output
 ```
-
 """
+from docopt import docopt
 
 import sys
 import os
@@ -79,7 +95,6 @@ def get_type_dict():
     from os import listdir
 
     qpackage_root = os.environ['QPACKAGE_ROOT']
-
     fancy_type_pickle = qpackage_root + "/scripts/ezfio_interface/fancy_type.p"
 
     if fancy_type_pickle in listdir(os.getcwd()):
@@ -131,7 +146,9 @@ def get_type_dict():
         b = r.find('let untouched = "')
         e = r.find(';;', b)
 
-        l_un = [i for i in r[b:e].splitlines() if i.strip().startswith("module")]
+        l_un = [
+            i for i in r[
+                b:e].splitlines() if i.strip().startswith("module")]
 
     # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
     # q p _ t y p e s _ g e n e r a t e #
@@ -280,7 +297,6 @@ def create_ezfio_provider(dict_ezfio_cfg):
     return [code, ...]
     """
     from ezfio_generate_provider import EZFIO_Provider
-
     dict_code_provider = dict()
 
     ez_p = EZFIO_Provider()
@@ -473,7 +489,7 @@ def save_ezfio_default(module_lower, str_ezfio_default):
             f.write(str_ezfio_default)
 
 
-def create_ocaml_input(dict_ezfio_cfg,module_lower):
+def create_ocaml_input(dict_ezfio_cfg, module_lower):
 
     # ~#~#~#~# #
     #  I n i t #
@@ -586,72 +602,180 @@ def save_ocaml_input(module_lower, str_ocaml_input):
             f.write(str_ocaml_input)
 
 
-def main():
+def create_ocaml_input_global():
     """
-    Two condition:
-        -Take the EZFIO.cfg path in arg
-        or
-        -Look if EZFIO.cfg is present in the pwd
-
-    Return : - ezfio_interface.irp.f
-             - folder_ezfio_inteface_config
+    Check for all the EZFIO.cfg get the module lower
+    then create incule {module_lower}.ml
     """
 
     # ~#~#~#~# #
     #  I n i t #
     # ~#~#~#~# #
 
+    from os import listdir
+    from os.path import isdir, join, exists
+
+    mypath = "{0}/src".format(os.environ['QPACKAGE_ROOT'])
+
+    onlyfodler = [f for f in listdir(mypath) if isdir(join(mypath, f))]
+
+    l_module_lower = [f.lower() for f in onlyfodler
+                      if exists("{0}/{1}/EZFIO.cfg".format(mypath, f))]
+
+    # ~#~#~#~#~#~#~#~# #
+    #  C r e a t i o n #
+    # ~#~#~#~#~#~#~#~# #
+
+    from ezfio_generate_ocaml import EZFIO_ocaml
+
+    qpackage_root = os.environ['QPACKAGE_ROOT']
+    path = qpackage_root + "/scripts/ezfio_interface/qp_edit_template"
+
+    with open(path, "r") as f:
+        template_raw = f.read()
+
+    e = EZFIO_ocaml(l_module_lower=l_module_lower)
+
+    template = template_raw.format(keywords=e.create_qp_keywords(),
+                                   keywords_to_string=e.create_qp_keywords_to_string(),
+                                   section_to_rst=e.create_qp_section_to_rst(),
+                                   write=e.create_qp_write(),
+                                   tasks=e.create_qp_tasks())
+
+    input_auto = e.create_input_auto_generated()
+
+    return (template, input_auto)
+
+
+def save_ocaml_input_auto(str_ocaml_input_global):
+    """
+    Write the str_ocaml_input in
+    $QPACKAGE_ROOT/ocaml/Input_auto_generated.ml
+    """
+
+    path = "{0}/ocaml/Input_auto_generated.ml".format(os.environ['QPACKAGE_ROOT'])
+
     try:
-        config_file_path = sys.argv[1]
-    except:
-        config_file_path = "EZFIO.cfg"
-        if "EZFIO.cfg" not in os.listdir(os.getcwd()):
-            sys.exit(0)
+        f = open(path, "r")
+    except IOError:
+        old_output = ""
+    else:
+        old_output = f.read()
+        f.close()
 
-    config_file_path = os.path.expanduser(config_file_path)
-    config_file_path = os.path.expandvars(config_file_path)
-    config_file_path = os.path.abspath(config_file_path)
+    if str_ocaml_input_global != old_output:
+        with open(path, "w+") as f:
+            f.write(str_ocaml_input_global)
 
-    # ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
-    #  G e t _ m o d u l e _ d i r #
-    # ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
 
-    path_dirname = os.path.dirname(config_file_path)
-    module = [i for i in path_dirname.split("/") if i][-1]
-    module_lower = module.lower()
+def save_ocaml_qp_edit(str_ocaml_qp_edit):
+    """
+    Write the str_ocaml_qp_edit in
+    $QPACKAGE_ROOT/ocaml/qp_edit.ml
+    """
 
-    # Because we only authorise this right now!
-    ezfio_dir = module_lower
-    dict_ezfio_cfg = get_dict_config_file(config_file_path, ezfio_dir)
+    path = "{0}/ocaml/qp_edit.ml".format(os.environ['QPACKAGE_ROOT'])
 
-    # ~#~#~#~#~#~#
-    #  O c a m l #
-    # ~#~#~#~#~#~#
+    try:
+        f = open(path, "r")
+    except IOError:
+        old_output = ""
+    else:
+        old_output = f.read()
+        f.close()
 
-    str_ocaml_input = create_ocaml_input(dict_ezfio_cfg, module_lower)
-    save_ocaml_input(module_lower, str_ocaml_input)
-
-    # ~#~#~#~#~#~#~#~#
-    #  I R P . f 9 0 #
-    # ~#~#~#~#~#~#~#~#
-
-    l_str_code = create_ezfio_provider(dict_ezfio_cfg)
-    save_ezfio_provider(path_dirname, l_str_code)
-
-    # ~#~#~#~#~#~#~#~#~#~#~#~# #
-    #  e z f i o _ c o n f i g #
-    # ~#~#~#~#~#~#~#~#~#~#~#~# #
-
-    str_ezfio_config = create_ezfio_config(dict_ezfio_cfg)
-    save_ezfio_config(module_lower, str_ezfio_config)
-
-    # ~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
-    #  e z f i o _  d e f a u l t #
-    # ~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
-
-    str_ezfio_default = create_ezfio_default(dict_ezfio_cfg)
-    save_ezfio_default(module_lower, str_ezfio_default)
+    if str_ocaml_qp_edit != old_output:
+        with open(path, "w+") as f:
+            f.write(str_ocaml_qp_edit)
 
 
 if __name__ == "__main__":
-    main()
+    arguments = docopt(__doc__)
+
+    # ___
+    #  |  ._  o _|_
+    # _|_ | | |  |_
+    #
+
+    if not arguments["--global"]:
+        if not arguments["--path"]:
+            config_file_path = "EZFIO.cfg"
+            if "EZFIO.cfg" not in os.listdir(os.getcwd()):
+                sys.exit(0)
+        else:
+            config_file_path = arguments["path"]
+
+        # Get the full path
+        config_file_path = os.path.expanduser(config_file_path)
+        config_file_path = os.path.expandvars(config_file_path)
+        config_file_path = os.path.abspath(config_file_path)
+
+        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
+        #  G e t _ m o d u l e _ d i r #
+        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
+
+        path_dirname = os.path.dirname(config_file_path)
+        module = [i for i in path_dirname.split("/") if i][-1]
+        module_lower = module.lower()
+
+        # Because we only authorise this right now!
+        ezfio_dir = module_lower
+        dict_ezfio_cfg = get_dict_config_file(config_file_path, ezfio_dir)
+
+    #  _
+    # /   _   _|  _     _   _  ._   _  ._ _. _|_ o  _  ._
+    # \_ (_) (_| (/_   (_| (/_ | | (/_ | (_|  |_ | (_) | |
+    #                   _|
+
+    # ~#~#~#~#~#~#~#~#~#~ #
+    # W h a t _ t o _ d o #
+    # ~#~#~#~#~#~#~#~#~#~ #
+    if any([arguments[i] for i in ["--irpf90",
+                                   "--ezfio_config",
+                                   "--ocaml",
+                                   "--ezfio_default",
+                                   "--global"]]):
+        # User changer somme argument, do what he want
+        do_all = False
+    else:
+        # Do all the stuff
+        do_all = True
+
+    # ~#~#~#~#~#~#~ #
+    # I R P . f 9 0 #
+    # ~#~#~#~#~#~#~ #
+
+    if do_all or arguments["--irpf90"]:
+        l_str_code = create_ezfio_provider(dict_ezfio_cfg)
+        save_ezfio_provider(path_dirname, l_str_code)
+
+    # ~#~#~#~#~#~#~#~#~#~#~#~ #
+    # e z f i o _ c o n f i g #
+    # ~#~#~#~#~#~#~#~#~#~#~#~ #
+
+    if do_all or arguments["--ezfio_config"]:
+        str_ezfio_config = create_ezfio_config(dict_ezfio_cfg)
+        save_ezfio_config(module_lower, str_ezfio_config)
+
+    # ~#~#~#~#~#~#
+    # O c a m l #
+    # ~#~#~#~#~#~#
+    if do_all or arguments["--ocaml"]:
+        str_ocaml_input = create_ocaml_input(dict_ezfio_cfg, module_lower)
+        save_ocaml_input(module_lower, str_ocaml_input)
+
+    # ~#~#~#~#~#~#~#~#~#~#~#~#~ #
+    # e z f i o _ d e f a u l t #
+    # ~#~#~#~#~#~#~#~#~#~#~#~#~ #
+    if do_all or arguments["--ezfio_default"]:
+        str_ezfio_default = create_ezfio_default(dict_ezfio_cfg)
+        save_ezfio_default(module_lower, str_ezfio_default)
+
+    # ~#~#~#~#~#~#~#~#~#~#~#~#~ #
+    # e z f i o _ d e f a u l t #
+    # ~#~#~#~#~#~#~#~#~#~#~#~#~ #
+
+    if do_all or arguments["--global"]:
+        str_ocaml_qp_edit, str_ocaml_input_auto = create_ocaml_input_global()
+        save_ocaml_input_auto(str_ocaml_input_auto)
+        save_ocaml_qp_edit(str_ocaml_qp_edit)

scripts/ezfio_interface/ezfio_generate_ocaml.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 
 import sys
+import os
 
 # If type in **kwargs
 from ei_handler import Type
@@ -227,7 +228,8 @@ class EZFIO_ocaml(object):
                       "let write{ "]
         l_template += ["           {0};".format(p) for p in self.l_ezfio_name]
         l_template += ["         } ="]
-        l_template += ["  write_{0:<30} {0};".format(p) for p in self.l_ezfio_name]
+        l_template += ["  write_{0:<30} {0};".format(p)
+                       for p in self.l_ezfio_name]
         l_template += [";;"]
 
         # ~#~#~#~#~#~ #
@@ -324,3 +326,158 @@ class EZFIO_ocaml(object):
         # R e t u r n #
         # ~#~#~#~#~#~ #
         return "\n   ".join(l_template)
+
+    def create_input_auto_generated(self):
+        """
+        Generate the include of all the Input_module.lower template
+        """
+
+        # ~#~#~#~#~#~#~#~ #
+        # C h e c k i n g #
+        # ~#~#~#~#~#~#~#~ #
+
+        self.check_if_init(["l_module_lower"],
+                           sys._getframe().f_code.co_name)
+
+        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
+        # C r e a t e _ t e m pl a t e #
+        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
+
+        l_template = ['open Qputils;;',
+                      'open Qptypes;;',
+                      'open Core.Std;;',
+                      '']
+
+        for m in self.l_module_lower:
+            l_template += ["include Input_{0}".format(m)]
+
+        # ~#~#~#~#~#~ #
+        # R e t u r n #
+        # ~#~#~#~#~#~ #
+
+        return "\n".join(l_template)
+
+    def create_qp_keywords(self):
+        """
+        Generate keywords template
+        """
+
+        # ~#~#~#~#~#~#~#~ #
+        # C h e c k i n g #
+        # ~#~#~#~#~#~#~#~ #
+
+        self.check_if_init(["l_module_lower"],
+                           sys._getframe().f_code.co_name)
+
+        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
+        # C r e a t e _ t e m pl a t e #
+        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
+
+        l_template = ["| {0}".format(m.capitalize())
+                      for m in self.l_module_lower]
+
+        # ~#~#~#~#~#~ #
+        # R e t u r n #
+        # ~#~#~#~#~#~ #
+
+        return "\n".join(l_template)
+
+    def create_qp_keywords_to_string(self):
+        """
+        Generate keywords to string template
+        """
+
+        # ~#~#~#~#~#~#~#~ #
+        # C h e c k i n g #
+        # ~#~#~#~#~#~#~#~ #
+
+        self.check_if_init(["l_module_lower"],
+                           sys._getframe().f_code.co_name)
+
+        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
+        # C r e a t e _ t e m pl a t e #
+        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
+
+        l_template = ['| {0} -> "{0}"'.format(m.capitalize())
+                      for m in self.l_module_lower]
+
+        # ~#~#~#~#~#~ #
+        # R e t u r n #
+        # ~#~#~#~#~#~ #
+
+        return "\n".join(l_template)
+
+    def create_qp_section_to_rst(self):
+        """
+        Generate section to rst
+        """
+        # ~#~#~#~#~#~#~#~ #
+        # C h e c k i n g #
+        # ~#~#~#~#~#~#~#~ #
+
+        self.check_if_init(["l_module_lower"],
+                           sys._getframe().f_code.co_name)
+
+        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
+        # C r e a t e _ t e m pl a t e #
+        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
+
+        l_template = []
+        for m in self.l_module_lower:
+            m_cap = m.capitalize()
+            l_template += ["         | {0} ->".format(m_cap),
+                           "           f {0}.(read, to_rst)".format(m_cap)]
+
+        # ~#~#~#~#~#~ #
+        # R e t u r n #
+        # ~#~#~#~#~#~ #
+
+        return "\n".join(l_template)
+
+    def create_qp_write(self):
+        """
+        Generate write
+        """
+        # ~#~#~#~#~#~#~#~ #
+        # C h e c k i n g #
+        # ~#~#~#~#~#~#~#~ #
+
+        self.check_if_init(["l_module_lower"],
+                           sys._getframe().f_code.co_name)
+
+        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
+        # C r e a t e _ t e m pl a t e #
+        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
+
+        str_ = "        | {0} -> write {0}.(of_rst, write) s"
+        l_template = [str_.format(m.capitalize()) for m in self.l_module_lower]
+
+        # ~#~#~#~#~#~ #
+        # R e t u r n #
+        # ~#~#~#~#~#~ #
+
+        return "\n".join(l_template)
+
+    def create_qp_tasks(self):
+        """
+        Generate taks
+        """
+        # ~#~#~#~#~#~#~#~ #
+        # C h e c k i n g #
+        # ~#~#~#~#~#~#~#~ #
+
+        self.check_if_init(["l_module_lower"],
+                           sys._getframe().f_code.co_name)
+
+        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
+        # C r e a t e _ t e m pl a t e #
+        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
+
+        l_template = ["      {0} ; ".format(m.capitalize())
+                      for m in self.l_module_lower]
+
+        # ~#~#~#~#~#~ #
+        # R e t u r n #
+        # ~#~#~#~#~#~ #
+
+        return "\n".join(l_template)

scripts/ezfio_interface/qp_edit_template

@@ -11,27 +11,21 @@ open Core.Std;;
 (** Keywords used to define input sections *)
 type keyword = 
 | Ao_basis
-| Bielec_integrals
-| Cisd_sc2_selected
 | Determinants
 | Electrons
-| Full_ci
-| Hartree_fock
 | Mo_basis
 | Nuclei
+{keywords}
 ;;
 
 
 let keyword_to_string = function
 | Ao_basis          -> "AO basis"
-| Bielec_integrals  -> "Two electron integrals"
-| Cisd_sc2_selected -> "CISD (SC)^2"
 | Determinants      -> "Determinants"
 | Electrons         -> "Electrons"
-| Full_ci           -> "Selected Full-CI"
-| Hartree_fock      -> "Hartree-Fock"
 | Mo_basis          -> "MO basis"
 | Nuclei            -> "Molecule"
+{keywords_to_string}
 ;;
 
 
@@ -70,24 +64,17 @@ let get s =
       begin
          let open Input in
          match s with
-         | Full_ci ->
-           f Full_ci.(read, to_rst)
-         | Hartree_fock ->
-           f Hartree_fock.(read, to_rst)
          | Mo_basis ->
            f Mo_basis.(read, to_rst)
          | Electrons ->
            f Electrons.(read, to_rst)
-         | Cisd_sc2_selected -> 
-           f Cisd_sc2_selected.(read, to_rst)
          | Nuclei ->
            f Nuclei.(read, to_rst)
          | Ao_basis ->
            f Ao_basis.(read, to_rst)
-         | Bielec_integrals -> 
-           f Bielec_integrals.(read, to_rst)
          | Determinants ->
            f Determinants.(read, to_rst)
+{section_to_rst}
       end
     with
     | Sys_error msg -> (Printf.eprintf "Info: %s\n%!" msg ; "")
@@ -125,11 +112,8 @@ let set str s =
       in
       let open Input in
         match s with
-        | Hartree_fock     -> write Hartree_fock.(of_rst, write) s
-        | Full_ci          -> write Full_ci.(of_rst, write) s
+{write}
         | Electrons        -> write Electrons.(of_rst, write) s
-        | Cisd_sc2_selected -> write Cisd_sc2_selected.(of_rst, write) s
-        | Bielec_integrals -> write Bielec_integrals.(of_rst, write) s
         | Determinants     -> write Determinants.(of_rst, write) s
         | Nuclei           -> write Nuclei.(of_rst, write) s
         | Ao_basis         -> () (* TODO *)
@@ -176,10 +160,7 @@ let run check_only ezfio_filename =
       Nuclei ;
       Ao_basis;
       Electrons ;
-      Bielec_integrals ;
-      Hartree_fock ;
-      Cisd_sc2_selected ;
-      Full_ci ;
+{tasks}
       Mo_basis;
       Determinants ;
   ]

src/CISD_SC2_selected/EZFIO.cfg

@@ -19,11 +19,11 @@ default: 0.0001
 
 [energy]
 type: double precision
-doc: "Calculated Full CI energy"
+doc: Calculated CISD_SC2 energy of ground_state
 interface: output
 
 [energy_pt2]
 type: double precision
-doc: "Calculated Full CI energy"
+doc: Calculated CISD_SC2 energy+pt2 of ground_state
 interface: output
 

src/CISD_SC2_selected/cisd_sc2_selection.irp.f

@@ -62,6 +62,13 @@ program cisd_sc2_selected
     if (abort_all) then
       exit
     endif
+
+    ! =~=~=~=~=~=~=~=~=~=~=~=~=~!
+    ! W r i t e _ o n _ d i s k !
+    ! =~=~=~=~=~=~=~=~=~=~=~=~=~!
+
+    call ezfio_set_full_ci_energy(CI_SC2_energy(1))
+
   enddo
   N_det = min(n_det_max_cisd_sc2,N_det)
   davidson_threshold = 1.d-10
@@ -98,6 +105,12 @@ program cisd_sc2_selected
     print*,'Degree of excitation of this determinant : ',degree
     
    enddo
+
+    ! =~=~=~=~=~=~=~=~=~=~=~=~=~!
+    ! W r i t e _ o n _ d i s k !
+    ! =~=~=~=~=~=~=~=~=~=~=~=~=~!
+
+    call ezfio_set_full_ci_energy_pt2(CI_SC2_energy(i)+pt2(i)* (1.d0 + norm_pert) - H_pert_diag(i))
   endif
   call save_wavefunction
   deallocate(pt2,norm_pert,H_pert_diag)

src/MRCC/NEEDED_MODULES

@@ -1,2 +1,2 @@
-AOs BiInts Bitmask CAS_SD_selected Dets Electrons Ezfio_files Generators_CAS Generators_full Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils
+AOs Bielec_integrals Bitmask CAS_SD_selected Dets Electrons Ezfio_files Generators_CAS Generators_full Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils