fix dir rewrite in case of name conflict & remove test files
This commit is contained in:
Guilhem Fauré
parent
39082cb994
commit
cc3a2103d0
@ -31,6 +31,7 @@ class Configuration:
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unknown_char_replacement: str = "??" # Replaces unknown characters
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clear_log: bool = True # Clear log before every run instead of appending to
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clear_output: bool = True # Remove eventual output dir before running
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conflict_strategy: str = "prepend id" # Prepend or append : date, id or counter
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ignore_pattern: list[str] = [] # Ignore objects of which title match
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logfile: str = "log-spip2md.log" # File where logs will be written, relative to wd
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loglevel: str = "WARNING" # Minimum criticity of logs written in logfile
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@ -65,17 +65,14 @@ class SpipInterface:
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_depth: int # Equals `profondeur` for sections
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_fileprefix: str # String to prepend to written files
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_parentdir: str # Path from output dir to direct parent
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_dest_dir_conflict: bool = False # Whether another same-named directory exists
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_storage_parentdir: Optional[str] = None
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_storage_title: Optional[str] = None
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_url: Optional[str] = None # In case URL in frontmatter different of dest dir
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_style: tuple[int, ...] # _styles to apply to some elements of printed output
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# memo: dict[str, str] = {} # Memoïze values
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def dest_directory(self, prepend: str = "", append: str = "") -> str:
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raise NotImplementedError(
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f"Subclasses need to implement directory(), params:{prepend}{append}"
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)
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def dest_directory(self) -> str:
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raise NotImplementedError("Subclasses need to implement directory()")
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def dest_filename(self, prepend: str = "", append: str = "") -> str:
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raise NotImplementedError(
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@ -388,10 +385,32 @@ class RedactionalObject(WritableObject):
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text = text.replace(m.group(), path_link.format("", "NOT FOUND"), 1)
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return text
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# Modify this object’s title to prevent filename conflicts
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def conflict_title(self, conflict: str) -> None:
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if CFG.conflict_strategy == "prepend id":
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title: str = str(self._id) + "_" + self._title
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elif CFG.conflict_strategy == "append id":
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title: str = self._title + "_" + str(self._id)
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elif CFG.conflict_strategy == "prepend counter":
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m = match(r"([0-9]+)_" + self._title, conflict)
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if m is not None:
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title: str = str(int(m.group(1)) + 1) + "_" + self._title
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else:
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title: str = "1_" + self._title
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else: # Defaults to append counter
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m = match(self._title + r"_([0-9]+)$", conflict)
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if m is not None:
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title: str = self._title + "_" + str(int(m.group(1)) + 1)
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else:
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title: str = self._title + "_1"
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LOG.debug(f"Rewriting {self._title} title to {title}")
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self._title = title
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# Get slugified directory of this object
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def dest_directory(self) -> str:
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_id: str = str(self._id) + "-" if CFG.prepend_id else ""
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directory: str = self._parentdir + slugify(_id + self._title, max_length=100)
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slug: str = slugify(_id + self._title, max_length=100)
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directory: str = self._parentdir + slug
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if self._storage_title is not None or self._storage_parentdir is not None:
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self._url = directory
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directory: str = (
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@ -405,14 +424,6 @@ class RedactionalObject(WritableObject):
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max_length=100,
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)
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)
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# If directory already exists, append a number or increase appended number
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if self._dest_dir_conflict:
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self.style_print(f" -| {directory} ALREADY EXISTS")
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m = match(r"^(.+)_([0-9]+)$", directory)
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if m is not None:
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directory = m.group(1) + "_" + str(int(m.group(2)) + 1)
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else:
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directory += "_1"
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return directory + r"/"
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# Get filename of this object
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@ -585,12 +596,12 @@ class RedactionalObject(WritableObject):
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# Write object to output destination
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def write(self) -> str:
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# Make a directory for this object if there isn’t
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directory: str = self.dest_directory()
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try:
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makedirs(self.dest_directory())
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makedirs(directory)
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except FileExistsError:
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# Create a new directory if write is about to overwrite an existing file
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# or to write into a directory without the same fileprefix
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directory = self.dest_directory()
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for file in listdir(directory):
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LOG.debug(
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f"Testing if {type(self).__name__} `{self.dest_path()}` of prefix "
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@ -598,15 +609,12 @@ class RedactionalObject(WritableObject):
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+ f"of prefix `{file.split('.')[0]}` in `{self.dest_directory()}`"
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)
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if isfile(directory + file) and (
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self.dest_directory() + file == self.dest_path()
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directory + file == self.dest_path()
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or file.split(".")[0] != self._fileprefix
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):
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LOG.debug(
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f"Not writing {self._title} in {self.dest_directory()} along "
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+ file
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)
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self._dest_dir_conflict = True
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self.conflict_title(directory.split("/")[-1])
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makedirs(self.dest_directory())
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break
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# Write the content of this object into a file named as self.filename()
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with open(self.dest_path(), "w") as f:
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f.write(self.content())
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118
test/0.spip
118
test/0.spip
@ -1,118 +0,0 @@
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{{{Test {SPIP}}}}
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Un {petit} paragraphe {{d’introduction}}, { {{vraiment}} petit}.
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----
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{{{Une {liste} non ordonnée}}}
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- { {{E-mail:}} } aude.simon@irsamc.ups-tlse.fr
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- {{ {Address:} }} Laboratoire de Chimie et Physique Quantiques, IRSAMC, Université
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- { {{Office:}} } 220 Bâtiment 3R1B4
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- {{ {Phone:} }} +33 (0)5 61 55 60 33
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- { {{Fax:}} } +33 (0)5 61 55 60 65
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{{{Une autre {liste} non ordonnée}}}
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-* { {{E-mail:}} } aude.simon@irsamc.ups-tlse.fr
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-* {{ {Address:} }} Laboratoire de Chimie et Physique Quantiques, IRSAMC, Université
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-* { {{Office:}} } 220 Bâtiment 3R1B4
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-* {{ {Phone:} }} +33 (0)5 61 55 60 33
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-* { {{Fax:}} } +33 (0)5 61 55 60 65
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{{{Une {liste} ordonnée}}}
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-# { {{E-mail:}} } aude.simon@irsamc.ups-tlse.fr
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-# {{ {Address:} }} Laboratoire de Chimie et Physique Quantiques, IRSAMC, Université
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-# { {{Office:}} } 220 Bâtiment 3R1B4
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-# {{ {Phone:} }} +33 (0)5 61 55 60 33
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-# { {{Fax:}} } +33 (0)5 61 55 60 65
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----
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{{{Un paragraphe bien garni}}}
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Un lien [lark->https://lark-parser.readthedocs.io] dans un {paragraphe} en italique,
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avec un peu de {{gras}}, voire même du { {{gras}} dans de l’{{italique}} (en gras)}.
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Conclut par un {{ {Lorem ipsum} }} dolor sit amet, officia excepteur ex fugiat reprehenderit enim labore culpa sint ad nisi Lorem pariatur mollit ex esse exercitation amet. Nisi anim cupidatat excepteur officia.
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Reprehenderit nostrud nostrud ipsum Lorem est aliquip amet voluptate voluptate dolor minim nulla est accolade impromptue } proident. Du <code>def pythonCode(): pass</code> code python. Nostrud officia {{pariatur}} ut officia. Sit [un lien->https://google.com]irure elit esse lien [?wikipedia] ea nulla sunt ex occaecat texte <del>biffé</del> on dit barré non ? Reprehenderit commodo footnote[[content of footnote]] officia dolor Lorem duis laboris cupidatat officia voluptate.
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Culpa proident adipisicing id {nulla} nisi laboris ex in Lorem sunt duis officia eiusmod. Aliqua reprehenderit commodo ex non [excepteur] duis unexpected pipe | sunt velit enim. Voluptate laboris sint cupidatat {{strong then}}- dash ullamco ut ea consectetur et est culpa et culpa duis.
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----
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{{{Un petit tableau}}}
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||Test table|This is a test table||
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|{{Test}}|{{Result}}|
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|1=1|True|
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|2=1|False|
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|Life=Tacos|True|
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|World|False|
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---------------------------------
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{{{Un bout de {{poesie}}}}}
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<poesie>
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Lorem ipsum dolor sit amet, officia excepteur ex fugiat reprehenderit enim labore culpa sint ad nisi Lorem pariatur mollit ex esse exercitation amet. Nisi anim cupidatat excepteur officia. Reprehenderit nostrud nostrud ipsum Lorem est aliquip amet voluptate voluptate dolor minim nulla est proident. Nostrud officia pariatur ut officia. Sit irure elit esse ea nulla sunt ex occaecat reprehenderit commodo officia dolor Lorem duis laboris cupidatat officia voluptate.<img4523> Culpa proident adipisicing id nulla nisi laboris ex in Lorem sunt duis officia eiusmod. Aliqua reprehenderit commodo ex non excepteur duis sunt velit enim. Voluptate laboris sint cupidatat ullamco ut ea consectetur et est culpa et culpa duis.
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</poesie>
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{{{Cadre de code}}}
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<cadre>
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def spipParser():
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return False
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</cadre>
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{{{Citation sans balise fermante}}}
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<quote> Lorem ipsum dolor sit amet, qui minim labore adipisicing minim sint cillum sint consectetur cupidatat.
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----
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{{{ Lien en plusieurs langues }}}
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<multi>
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[fr]
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Retrouvez toutes nos publications sur :
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{{[HAL-LCPQ_SEM->https://hal.archives-ouvertes.fr/LCPQ_SEM/]}}
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[en]Find all our publications on :
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{{[HAL-LCPQ_SEM->https://hal.archives-ouvertes.fr/LCPQ_SEM/]}}
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[es]Recobre todas nuestras publicaciones sobre :
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{{[HAL-LCPQ_SEM->https://hal.archives-ouvertes.fr/LCPQ_SEM/]}}
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</multi>
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{{{ Titre multiligne avec beaucoup d’elements }}}
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{{{ {{[HAL-LCPQ_SEM->https://hal.archives-ouvertes.fr/LCPQ_SEM/]}}
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[en]Find all our publications on :
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||||
{{[HAL-LCPQ_SEM->https://hal.archives-ouvertes.fr/LCPQ_SEM/]}}
|
||||
[es]Recobre todas nuestras publicaciones sobre :
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{{[HAL-LCPQ_SEM->https://hal.archives-ouvertes.fr/LCPQ_SEM/]}} }}}
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----
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{{{Des images}}}
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<image1|left>
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À gauche.
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<image1|center>
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Au milieu.
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<image1|right>
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À droite.
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----------------------------------------------------------------------------
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Lone angle bracket < oh.
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Escaped \{ curly brace.
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FIN
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143
test/1.spip
143
test/1.spip
@ -1,143 +0,0 @@
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{{{Chargé de Recherche}}}
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{ {{E-mail:}} } aude.simon@irsamc.ups-tlse.fr
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{{ {Address:} }} Laboratoire de Chimie et Physique Quantiques, IRSAMC, Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse Cedex 4, France
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{ {{Office:}} } 220 Bâtiment 3R1B4
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{{ {Phone:} }} +33 (0)5 61 55 60 33
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{ {{Fax:}} } +33 (0)5 61 55 60 65
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Un lien [lark->https://lark-parser.readthedocs.io] dans un paragraphe.
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[lark->https://lark-parser.readthedocs.io]
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----
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---
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{{{Short CV}}}
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{{2010-current:}} Researcher at LCPQ (Univ. Toulouse III & CNRS), MAD Team
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{{2005 - 2009:}} Researcher at CESR (now IRAP,Univ. Toulouse III & CNRS )
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{{2003-2004:}} Post-Doc, University of Waterloo, Canada (T. B. McMahon's group)
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{{2000-2002: }} PhD, LCP Univ. Paris XI (supervision : P. Maître)
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| not
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| a
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| table
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---- ---
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<div style="text-align:center">
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{ multi
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[fr]
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Retrouvez toutes nos publications sur :
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{{[HAL-LCPQ_SEM->https://hal.archives-ouvertes.fr/LCPQ_SEM/]}}
|
||||
[en]Find all our publications on :
|
||||
{{[HAL-LCPQ_SEM->https://hal.archives-ouvertes.fr/LCPQ_SEM/]}}
|
||||
[es]Recobre todas nuestras publicaciones sobre :
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{{[HAL-LCPQ_SEM->https://hal.archives-ouvertes.fr/LCPQ_SEM/]}}
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multi }
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</div>
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----
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<hr noshade>
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<div style="text-align:center">
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{{{ <multi>
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[fr]
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Retrouvez toutes nos publications sur :
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{{[HAL-LCPQ_SEM->https://hal.archives-ouvertes.fr/LCPQ_SEM/]}}
|
||||
[en]Find all our publications on :
|
||||
{{[HAL-LCPQ_SEM->https://hal.archives-ouvertes.fr/LCPQ_SEM/]}}
|
||||
[es]Recobre todas nuestras publicaciones sobre :
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{{[HAL-LCPQ_SEM->https://hal.archives-ouvertes.fr/LCPQ_SEM/]}}
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</multi> }}}
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</div>
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<br>
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<object style="width:100%;height:800px;" type="text/html" data="https://haltools.archives-ouvertes.fr/Public/afficheRequetePubli.php?annee_publideb=2003&annee_publifin=2022&typdoc=('ART')&collection_exp=LCPQ_SEM&CB_auteur=oui&CB_titre=oui&CB_article=oui&langue=Anglais&tri_exp=annee_publi&tri_exp2=typdoc&tri_exp3=date_publi&ordre_aff=TA&Fen=Aff&css=https://www.lcpq.ups-tlse.fr/squelettes/css/charte-2/VisuCondense_nic.css"></object>
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{{{Research Interests}}}
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* {{Astrochemistry}} - Atmospheric Chemistry: interactions of PAH with ions, atoms (Si, Fe) and with molecular clusters ((H2O)n) ; PAH reactivity
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* {{Molecular Dynamics}} of large systems
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* Infrared and UV-visible {{Spectroscopy}} for large systems
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* {{Electronic Structure}} with DFT-based approach, in particular DFTB
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* Hybrid {{DFTB/Force Field approaches}}
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------------------------------------------------
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{{{Collaborations}}}
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I have collaborations through various projects:
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* ANR PARCS 2014-2017 (http://www.lcpq.ups-tlse.fr/anr-parcs) : C. Toubin (PhLAM, PCMT team, Univ. Lille) and J. Mascetti (ISM, Univ. Bordeaux I) : ANR PARCS
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* ERC Nanocosmos 2015-2020 (http://www.icmm.csic.es/nanocosmos/) : C. Joblin (IRAP/LCAR, Toulouse)
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* SWEET project 2016-2017 : J. -P. Champeaux (LCAR, Toulouse)
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* ANR PACHYNO 2017-2020 ((http://www.lcpq.ups-tlse.fr/anr-pachyno) : C. Falvo and Th. Pino (ISMO, Orsay), F. Calvo (LiPhy, Grenoble)
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Other collaborations :
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* Vincent Pauchard : CUNY Energy Institute, New-York
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||Test table|This is a test table||
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|{{Test}}|{{Result}}|
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|1=1|True|
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|2=1|False|
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|Life=Tacos|True|
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|World|False|
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----
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{{{Student Supervision (starting 2012)}}}
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{{Feb.- May 2012}} Charlotte Marshall, M2 ERASMUS-MUNDUS, Topic: "The laboratory investigation of PAHs of astrophysical interest" (supervision of the theoretical part)
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{{2013-2015:}} Christophe Iftner, PhD entitled "Modeling molecular clusters in cryogenic environment" (co-supervision with Fernand Spiegelman)
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{{April - June 2015:}} Guillaume Rouaut, M1, Topic : "Molecular dynamics and infrared spectra at finite temperature of PAH of astrophysical interest : isomerisations"
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{{2014-2016:}} Eric Michoulier, PhD entitled "Modeling the interactions of PAHs with interstellar water ice" (co-supervision with Céline Toubin, PhLAM, Lille)
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-* li 1
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-* li 2
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|{{Test}}|{{Result}}|
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|1=1|True|
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|2=1|False|
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|Life=Tacos|True|
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|World|False|
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{{January-June 2016:}} Guillaume Rouaut, M2, Topic : "Modeling molecular clusters in a cryogenic environment : structures, energetics and IR spectra"
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{{2015-2017:}} Sarah Rodriguez-Castillo, PhD entitled "Formation and destruction of interstellar PAHs: experience and theory" (thesis supervised by C. Joblin, supervision of the theoretical part)
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----
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{{{News and Research Highlights}}}
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* {{Water clusters embedded in an argon matrix : a DFTB/Force Field Study}}. Finite-temperature infrared spectra of water clusters - described at the SCC-DFTB level - embedded in an argon 'super-cluster' - described with a force field ( FF)- are determined and compared with experimental data.
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----
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{{{Des tags au hasard}}}
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<p>Du contenu simple</p>
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<p>Du contenu complexe, avec un [lien->https://google.com] dedans</p>
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<p align=justify>Du contenu simple mais dans un paragraphe justifié</p>
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<p align="justify">Du contenu simple mais dans un paragraphe justifié avec des guillemets</p>
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{{{Un paragraphe justifié}}}
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<p align="justify">Anthony Scemama, l'un des deux coordinateurs du CNRS pour le centre d'excellence européen H2020 [T.REX->https://trex-coe.eu/], répond aux questions de "CNRS Le Journal" sur la révolution exascale des supercalculateurs.</p>
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[Lien vers l'article->https://lejournal.cnrs.fr/articles/revolution-en-vue-pour-percer-les-secrets-de-la-matiere]
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from {{ A. Simon, C. Iftner, J. Mascetti, F. Spiegelman ’Water clusters in an argon matrix : infrared spectra from molecular dynamics simulations with a self-consistent charge density functional based tight binding/force field potential’ J. Phys. Chem. A 2015, 119, 2449-2467 (DOI : 10.1021/jp508533k)}}
|
||||
ABSTRACT: The present theoretical study aims at investigating the effects of an argon matrix on the structures, energetics, dynamics, and infrared (IR) spectra of small water clusters (H2O)n (n = 1−6). The potential energy surface is obtained from a hybrid selfconsistent charge density functional-based tight binding/force-field approach (SCCDFTB/FF) in which the water clusters are treated at the SCC-DFTB level and the matrix is modeled at the FF level by a cluster consisting of ∼340 Ar atoms with a face centered cubic (fcc) structure, namely (H2O)n/Ar. With respect to a pure FF scheme, this allows a quantum description of the molecular system embedded in the matrix, along with all-atom geometry optimization and molecular dynamics (MD) simulations of the (H2O)n/Ar system. Finite-temperature IR spectra are derived from the MD simulations. The SCC-DFTB/FF scheme is first benchmarked on (H2O)Arn clusters against correlated wave function results and DFT calculations performed in the present work, and against FF data available in the literature. Regarding (H2O)n/Ar systems, the geometries of the water clusters are found to adapt to the fcc environment, possibly leading to intermolecular distortion and matrix perturbation. Several energetical quantities are estimated to characterize the water clusters in the matrix. In the particular case of the water hexamer, substitution and insertion energies for the prism, bag, and cage are found to be lower than that for the 6-member ring isomer. Finite-temperature MD simulations show that the water monomer has a quasifree rotation motion at 13 K, in agreement with experimental data. In the case of the water dimer, the only large-amplitude motion is a distortion−rotation intermolecular motion, whereas only vibration motions around the nuclei equilibrium positions are observed for clusters with larger sizes. Regarding the IR spectra, we find that the matrix environment leads to redshifts of the stretching modes and almost no shift of the bending modes. This is in agreement with experimental data. Furthermore, in the case of the water monomer and dimer, the magnitudes of the computed shifts are in fair agreement with the experimental values. The complex case of the water hexamer, which presents several low-energy isomers, is discussed.
|
||||
|
||||
* {{Electronic Spectra of [FePAH]+ complexes in the Region of the Diffuse Interstellar Bands by means of multireference wavefunction calculations. }} This is done in collaboration with Nadia Ben Amor (GMO group).
|
||||
|
||||
from {{ M. Lanza, A. Simon, N. Ben Amor ’Electronic Spectroscopy of [FePAH]+ complexes in the Region of the Diffuse Interstellar Bands : Multireference Wavefunction Studies on [FeC6H6]+’ J. Phys. Chem. A 2015, 119, 6123-6130 (DOI : 10.1021/acs.jpca.5b00438)}}
|
||||
ABSTRACT: The low-energy states and electronic spectrum in the nearinfrared− visible region of [FeC6H6]+ are studied by theoretical approaches. An exhaustive exploration of the potential energy surface of [FeC6H6]+ is performed using the density functional theory method. The ground state is found to be a 4A1 state. The structures of the lowest energy states (4A2 and 4A1) are used to perform multireference wave function calculations by means of the multistate complete active space with perturbation at the second order method. Contrary to the density functional theory results (4A1 ground state), multireference perturbative calculations show that the 4A2 state is the ground state. The vertical electronic spectrum is computed and compared with the astronomical diffuse interstellar bands, a set of near-infrared-visible bands detected on the extinction curve in our and other galaxies. Many transitions are found in this domain, corresponding to d → d, d → 4s, or d → π* excitations, but few are allowed and, if they are, their oscillation strengths are small. Even though some band positions could match some of the observed bands, the relative intensities do not fit, making the contribution of the [Fe−C6H6]+ complexes to the diffuse interstellar bands questionable. This work, however, lays the foundation for the studies of polycyclic aromatic hydrocarbons (PAHs) complexed to Fe cations that are more likely to possess d → π* and π → π* transitions in the diffuse interstellar bands domain. PAH ligands indeed possess a larger number of π and π* orbitals, respectively, higher and lower in energy than those of C6H6, which are expected to lead to lower energy d → π* and π → π* transitions in [FePAH]+ than in [FeC6H6]+ complexes.
|
||||
74
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74
test/2.spip
@ -1,74 +0,0 @@
|
||||
|
||||
<img780|right>
|
||||
<h1>{{Chargé de Recherche}}</h1>
|
||||
|
||||
{ {{E-mail:}} } aude.simon@irsamc.ups-tlse.fr
|
||||
|
||||
<p align=justify>
|
||||
{ {{Address:}} } Laboratoire de Chimie et Physique Quantiques, IRSAMC, Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse Cedex 4, France
|
||||
|
||||
{ {{Office:}} } 220 Bâtiment 3R1B4
|
||||
|
||||
{ {{Phone:}} } +33 (0)5 61 55 60 33
|
||||
|
||||
{ {{Fax:}} } +33 (0)5 61 55 60 65
|
||||
_
|
||||
----
|
||||
|
||||
{{{Short CV}}}
|
||||
|
||||
{{2010-current:}} Researcher at LCPQ (Univ. Toulouse III & CNRS), MAD Team
|
||||
{{2005 - 2009:}} Researcher at CESR (now IRAP,Univ. Toulouse III & CNRS )
|
||||
{{2003-2004:}} Post-Doc, University of Waterloo, Canada (T. B. McMahon's group)
|
||||
{{2000-2002: }} PhD, LCP Univ. Paris XI (supervision : P. Maître)
|
||||
_
|
||||
----
|
||||
|
||||
{{{Research Interests}}}
|
||||
|
||||
<P align=justify>* {{Astrochemistry}} - Atmospheric Chemistry: interactions of PAH with ions, atoms (Si, Fe) and with molecular clusters ((H2O)n) ; PAH reactivity
|
||||
* {{Molecular Dynamics}} of large systems
|
||||
* Infrared and UV-visible {{Spectroscopy}} for large systems
|
||||
* {{Electronic Structure}} with DFT-based approach, in particular DFTB
|
||||
* Hybrid {{DFTB/Force Field approaches}}
|
||||
|
||||
_
|
||||
----
|
||||
|
||||
{{{Collaborations}}}
|
||||
|
||||
I have collaborations through various projects:
|
||||
* ANR PARCS 2014-2017 (http://www.lcpq.ups-tlse.fr/anr-parcs) : C. Toubin (PhLAM, PCMT team, Univ. Lille) and J. Mascetti (ISM, Univ. Bordeaux I) : ANR PARCS
|
||||
* ERC Nanocosmos 2015-2020 (http://www.icmm.csic.es/nanocosmos/) : C. Joblin (IRAP/LCAR, Toulouse)
|
||||
* SWEET project 2016-2017 : J. -P. Champeaux (LCAR, Toulouse)
|
||||
* ANR PACHYNO 2017-2020 ((http://www.lcpq.ups-tlse.fr/anr-pachyno) : C. Falvo and Th. Pino (ISMO, Orsay), F. Calvo (LiPhy, Grenoble)
|
||||
|
||||
Other collaborations :
|
||||
* Vincent Pauchard : CUNY Energy Institute, New-York
|
||||
_
|
||||
----
|
||||
|
||||
{{{Student Supervision (starting 2012)}}}
|
||||
|
||||
{{Feb.- May 2012}} Charlotte Marshall, M2 ERASMUS-MUNDUS, Topic: "The laboratory investigation of PAHs of astrophysical interest" (supervision of the theoretical part)
|
||||
{{2013-2015:}} Christophe Iftner, PhD entitled "Modeling molecular clusters in cryogenic environment" (co-supervision with Fernand Spiegelman)
|
||||
{{April - June 2015:}} Guillaume Rouaut, M1, Topic : "Molecular dynamics and infrared spectra at finite temperature of PAH of astrophysical interest : isomerisations"
|
||||
{{2014-2016:}} Eric Michoulier, PhD entitled "Modeling the interactions of PAHs with interstellar water ice" (co-supervision with Céline Toubin, PhLAM, Lille)
|
||||
{{January-June 2016:}} Guillaume Rouaut, M2, Topic : "Modeling molecular clusters in a cryogenic environment : structures, energetics and IR spectra"
|
||||
{{2015-2017:}} Sarah Rodriguez-Castillo, PhD entitled "Formation and destruction of interstellar PAHs: experience and theory" (thesis supervised by C. Joblin, supervision of the theoretical part)
|
||||
|
||||
_
|
||||
----
|
||||
|
||||
{{{News and Research Highlights}}}
|
||||
<P align=justify>* {{Water clusters embedded in an argon matrix : a DFTB/Force Field Study}}. Finite-temperature infrared spectra of water clusters - described at the SCC-DFTB level - embedded in an argon 'super-cluster' - described with a force field ( FF)- are determined and compared with experimental data.
|
||||
|
||||
<img816|center>
|
||||
<P align=justify> from {{ A. Simon, C. Iftner, J. Mascetti, F. Spiegelman ’Water clusters in an argon matrix : infrared spectra from molecular dynamics simulations with a self-consistent charge density functional based tight binding/force field potential’ J. Phys. Chem. A 2015, 119, 2449-2467 (DOI : 10.1021/jp508533k)}}
|
||||
<P align=justify> ABSTRACT: The present theoretical study aims at investigating the effects of an argon matrix on the structures, energetics, dynamics, and infrared (IR) spectra of small water clusters (H2O)n (n = 1−6). The potential energy surface is obtained from a hybrid selfconsistent charge density functional-based tight binding/force-field approach (SCCDFTB/FF) in which the water clusters are treated at the SCC-DFTB level and the matrix is modeled at the FF level by a cluster consisting of ∼340 Ar atoms with a face centered cubic (fcc) structure, namely (H2O)n/Ar. With respect to a pure FF scheme, this allows a quantum description of the molecular system embedded in the matrix, along with all-atom geometry optimization and molecular dynamics (MD) simulations of the (H2O)n/Ar system. Finite-temperature IR spectra are derived from the MD simulations. The SCC-DFTB/FF scheme is first benchmarked on (H2O)Arn clusters against correlated wave function results and DFT calculations performed in the present work, and against FF data available in the literature. Regarding (H2O)n/Ar systems, the geometries of the water clusters are found to adapt to the fcc environment, possibly leading to intermolecular distortion and matrix perturbation. Several energetical quantities are estimated to characterize the water clusters in the matrix. In the particular case of the water hexamer, substitution and insertion energies for the prism, bag, and cage are found to be lower than that for the 6-member ring isomer. Finite-temperature MD simulations show that the water monomer has a quasifree rotation motion at 13 K, in agreement with experimental data. In the case of the water dimer, the only large-amplitude motion is a distortion−rotation intermolecular motion, whereas only vibration motions around the nuclei equilibrium positions are observed for clusters with larger sizes. Regarding the IR spectra, we find that the matrix environment leads to redshifts of the stretching modes and almost no shift of the bending modes. This is in agreement with experimental data. Furthermore, in the case of the water monomer and dimer, the magnitudes of the computed shifts are in fair agreement with the experimental values. The complex case of the water hexamer, which presents several low-energy isomers, is discussed.
|
||||
|
||||
<P align=justify>* {{Electronic Spectra of [FePAH]+ complexes in the Region of the Diffuse Interstellar Bands by means of multireference wavefunction calculations. }} This is done in collaboration with Nadia Ben Amor (GMO group).
|
||||
|
||||
<img818|center>
|
||||
<P align=justify> from {{ M. Lanza, A. Simon, N. Ben Amor ’Electronic Spectroscopy of [FePAH]+ complexes in the Region of the Diffuse Interstellar Bands : Multireference Wavefunction Studies on [FeC6H6]+’ J. Phys. Chem. A 2015, 119, 6123-6130 (DOI : 10.1021/acs.jpca.5b00438)}}
|
||||
<P align=justify> ABSTRACT: The low-energy states and electronic spectrum in the nearinfrared− visible region of [FeC6H6]+ are studied by theoretical approaches. An exhaustive exploration of the potential energy surface of [FeC6H6]+ is performed using the density functional theory method. The ground state is found to be a 4A1 state. The structures of the lowest energy states (4A2 and 4A1) are used to perform multireference wave function calculations by means of the multistate complete active space with perturbation at the second order method. Contrary to the density functional theory results (4A1 ground state), multireference perturbative calculations show that the 4A2 state is the ground state. The vertical electronic spectrum is computed and compared with the astronomical diffuse interstellar bands, a set of near-infrared-visible bands detected on the extinction curve in our and other galaxies. Many transitions are found in this domain, corresponding to d → d, d → 4s, or d → π* excitations, but few are allowed and, if they are, their oscillation strengths are small. Even though some band positions could match some of the observed bands, the relative intensities do not fit, making the contribution of the [Fe−C6H6]+ complexes to the diffuse interstellar bands questionable. This work, however, lays the foundation for the studies of polycyclic aromatic hydrocarbons (PAHs) complexed to Fe cations that are more likely to possess d → π* and π → π* transitions in the diffuse interstellar bands domain. PAH ligands indeed possess a larger number of π and π* orbitals, respectively, higher and lower in energy than those of C6H6, which are expected to lead to lower energy d → π* and π → π* transitions in [FePAH]+ than in [FeC6H6]+ complexes.
|
||||
@ -1,5 +0,0 @@
|
||||
<quote>[L1 Parcours Spécial - Physique 1 ->https://cloud.irsamc.ups-tlse.fr/index.php/s/3yyo7J7gnPxdtQG]
|
||||
|
||||
----
|
||||
|
||||
[L3 Parcours Spécial Physique - Mécanique Quantique -> https://cloud.irsamc.ups-tlse.fr/index.php/s/Zr3Me25b5GWamN3]
|
||||
76
test/4.spip
76
test/4.spip
@ -1,76 +0,0 @@
|
||||
<doc1211|right>
|
||||
|
||||
<h1>{{Ph.D Student}}</h1>
|
||||
|
||||
{ {{E-mail:}} } fernand.louisnard[AT]irsamc.ups-tlse.fr
|
||||
|
||||
<p align=justify>
|
||||
{ {{Address:}} } Laboratoire de Chimie et Physique Quantiques, IRSAMC, Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse Cedex 4, France
|
||||
|
||||
{ {{Office:}} } 221 Building 3R1B4
|
||||
|
||||
{ {{Phone:}} }
|
||||
|
||||
{ {{Fax:}} }
|
||||
|
||||
---
|
||||
|
||||
{{{SHORT CV}}}
|
||||
|
||||
<p align=justify>
|
||||
{ {{2018 - 2021:}} } Ph.D in Theoretical chemistry
|
||||
Paul Sabatier University, {{Laboratoire de Chimie et Physique Quantiques (LCPQ)}}, Toulouse, FRANCE.
|
||||
Exploration of energetic landscapes and nuclear quantum effects: A Parallel-Tempering Path-Integral Molecular Dynamics approach.
|
||||
Director: Aude Simon
|
||||
Co-director: Jérôme Cuny
|
||||
<p align=justify>{ {{2017 - 2018}} } Master 2 in Theoretical chemistry and computational modelling,
|
||||
TCCM ERASMUS Mundus Master, Valencia, SPAIN.
|
||||
<p align=justify>{ {{2016 - 2017:}} } Master 1 in Theoretical chemistry and modelling,
|
||||
Paul Sabatier University, Toulouse, FRANCE.
|
||||
<p align=justify>{ {{2012 - 2015:}} } Bachelor in chemistry "Parcours spéciaux",
|
||||
Paul Sabatier University, Toulouse, FRANCE.
|
||||
|
||||
- [Full curriculum vitae (french)-> doc1215 ]
|
||||
|
||||
- [Full curriculum vitae (english)-> doc1214 ]
|
||||
|
||||
{{{RESEARCH ACTIVITIES}}}
|
||||
|
||||
<sjcycle393|rubrique|cycle|random=true|docs=830,831,832,833|fx=carousel|carouselvisible=2|carouselfluid=true|carouselslidedimension=100|timeout=2000|largeurmax=300>
|
||||
|
||||
<p align=justify>I am developping methods (Path Integral Molecular Dynamics (PIMD), asynchronous Replica Exchange Molecular Dynamics (REMD) and (Replica Exchange Path Integral Molecular Dynamics (PIREMD) to enhance Molecular Dynamic simulations on the [deMonNano->http://demon-nano.ups-tlse.fr/] code (which is a DFTB code) and the [deMon2k->http://demon-software.com/public_html/index.html] code (a DFT code). Using the right parallelization method for their implementation, they fit perfectly the architecture of supercomputers and show a great scaling peformance.
|
||||
|
||||
In the second part of my Ph.D I will use these methods to determine the impact of Nuclear Quantum Effects (NQEs) on:
|
||||
|
||||
- neutral and protonated water clusters
|
||||
- proton transfer on water clusters
|
||||
- the behavior of protons adsorbed on metals surfaces such as silver, gold or ruthenium
|
||||
- the absorption and emission properties of simple organic molecules in aqueous solvant.
|
||||
|
||||
- [Full publication list -> ******* ]
|
||||
|
||||
{{{TEACHING}}}
|
||||
|
||||
{{L1 Level:}}
|
||||
|
||||
-{{2018-2019 Physique}} S2 Rebondir (27h Cours/TD)
|
||||
|
||||
{{L2 Level:}}
|
||||
|
||||
-{{2018-2019 Atomistique et liaison chimique I}} L2 Parcours Spéciaux (4h Cours/TD)
|
||||
|
||||
{{L3 Level:}}
|
||||
|
||||
-{{2018-2020 Structure Géométrique et Réactivité}} L3 Chimie (14h TD) -{{2018-2020 Thermodynamique et Cinétique}} L3 Chimie (20h TP)
|
||||
|
||||
{{Schools:}}
|
||||
|
||||
-{{2019 Molecular Dynamics}} TCCM Winter School\} School for advanced sciences of Luchon, Luchon-Superbagnères, FRANCE
|
||||
|
||||
{{{ORAL COMMUNICATIONS}}}
|
||||
|
||||
-{{MPI implementation of the Parallel-Tempering Molecular Dynamics (PTMD) approach in deMon2k.}}
|
||||
F. Louisnard, J. Cuny, A. Simon
|
||||
19th deMon developpers Workshop, Fréjus (France), May 2019\} -{{Synchronous and Asynchronous implementation of the Parallel-Tempering Molecular Dynamics method in the codes deMonNano and deMon2k}}
|
||||
F. Louisnard, J. Cuny, A. Simon
|
||||
Les Toulousaines du Calcul Atomique et Moléculaire" –TouCAM, Toulouse (France), November 2019\}
|
||||
@ -1,27 +0,0 @@
|
||||
---
|
||||
authors:
|
||||
- 42
|
||||
date: 2012-04-24 15:00:00
|
||||
description: ''
|
||||
draft: false
|
||||
lang: fr
|
||||
lastmod: 2015-06-24 09:59:05
|
||||
publishDate: 2012-04-24 15:00:00
|
||||
title: "080. ModeÌ\x81lisation et simulation multi-eÌ\x81chelle au service du deÌ\x81\
|
||||
veloppement des Nano et BioNanoTechnologies"
|
||||
---
|
||||
|
||||
# 080. ModeÌlisation et simulation multi-eÌchelle au service du deÌveloppement des Nano et BioNanoTechnologies
|
||||
|
||||
Séminaire LCPQ
|
||||
|
||||
Salle de cours du 2ème étage
|
||||
|
||||
La modeÌlisation multi-eÌchelle vise aÌ€ donner une description des pheÌnomeÌ€nes physiques aÌ€ diffeÌrentes eÌchelles. Ce type de modeÌlisation est en plein expansion depuis une dizaine d’anneÌes pour l’eÌtude de nombreuses proprieÌteÌs (eÌlectroniques, optoeÌlectroniques, structurales, eÌnergeÌtiques, dynamiques, meÌcaniques, ...) de systeÌ€mes tant du monde du vivant que celui des mateÌriaux (et donc pourquoi pas pour des systeÌ€mes issus des deux domaines). Ces simulations permettent d’appreÌhender l’eÌtude de proprieÌteÌs du nano- au micromeÌ€tre, voire au delaÌ€, sur des temps pheÌnomeÌnologiques de la femto- aÌ€ la microseconde, voire au delaÌ€. Dans le domaine des mateÌriaux par exemple , il s’agira de deÌduire les proprieÌteÌs macroscopiques d’un mateÌriau aÌ€ partir de sa description aÌ€ l’eÌchelle la plus microscopique (l’atome), via des niveaux de description emboiÌ‚teÌs (la dynamique moleÌculaire, le Monte Carlo...). Tout le probleÌ€me est de lier ces diffeÌrents niveaux de description en utilisant la bonne information pour passer d’une eÌchelle aÌ€ l’autre.
|
||||
Dans ce cadre, je preÌsente quelques deÌveloppements meÌthodologiques et leur applications dans les domaines suivants :
|
||||
|
||||
i) Croissance des couches atomiques sur divers substrats ;
|
||||
ii) L'organisation supramoleÌculaire dans les films minces de polymeÌ€res
|
||||
conducteurs et les interfaces ;
|
||||
iii) Interactions moleÌculaires faibles et leur impacts dans le monde du vivant et celui des mateÌriaux .
|
||||
|
||||
@ -1,21 +0,0 @@
|
||||
---
|
||||
id: 1508
|
||||
authors:
|
||||
- 42
|
||||
date: 2012-03-08 14:00:00
|
||||
description: ''
|
||||
draft: false
|
||||
lang: fr
|
||||
lastmod: 2015-06-24 09:50:47
|
||||
publishDate: 2012-03-08 14:00:00
|
||||
title: 096. De la réactivité atome-diatome à la réactivité des clusters d'or
|
||||
---
|
||||
# 096. De la réactivité atome-diatome à la réactivité des clusters d'or
|
||||
|
||||
Séminaire LCPQ
|
||||
|
||||
Salle de cours (2ème étage)
|
||||
|
||||
L'exposeÌ qui traitera de l'eÌtude theÌorique de la reÌactiviteÌ de diffeÌrents systeÌ€mes se compose de deux parties. La premieÌ€re abordera la reÌactiviteÌ de systeÌ€mes atome-diatome d'inteÌreÌ‚t astrophysique impliquant des radicaux libres. La seconde portera sur la dissociation de H2 sur diffeÌrents “nano-objets†d'or.
|
||||
|
||||
Plus de détails dans le pdf ci-dessous...
|
||||
Loading…
Reference in New Issue
Block a user