diff --git a/larch/io/columnfile.py b/larch/io/columnfile.py
index 69b904bc5..735792571 100644
--- a/larch/io/columnfile.py
+++ b/larch/io/columnfile.py
@@ -612,6 +612,7 @@ def write_group(filename, group, scalars=None, arrays=None,
 
 def read_fdmnes(filename, **kwargs):
     """read [FDMNES](http://fdmnes.neel.cnrs.fr/) ascii files"""
+    shift_energy = kwargs.pop("shift_energy", True)
     group = read_ascii(filename, **kwargs)
     group.header_dict = dict(filetype='FDMNES', energy_units='eV')
     for headline in group.header:
@@ -622,7 +623,8 @@ def read_fdmnes(filename, **kwargs):
             vals_names = headline.split(" = ")[1].split(", ")
             group.header_dict.update(dict(zip(vals_names, vals)))
     group.name = f'FDMNES file {filename}'
-    group.energy += group.header_dict["E_edge"]
+    if shift_energy:
+        group.energy += group.header_dict["E_edge"]
     #fix _arrlabel -> arrlabel
     for ilab, lab in enumerate(group.array_labels):
         if lab.startswith("_"):
diff --git a/larch/xrd/struct2xas.py b/larch/xrd/struct2xas.py
index aa11542bd..0c7c31b8d 100644
--- a/larch/xrd/struct2xas.py
+++ b/larch/xrd/struct2xas.py
@@ -4,11 +4,15 @@
 """
 Struct2XAS: convert CIFs and XYZs files to FDMNES and FEFF inputs
 """
+
 # main imports
 import os
 import json
 import time
-import tempfile
+from dataclasses import dataclass
+from typing import Union, List  # , Any, Dict
+
+# import tempfile
 import numpy as np
 
 # pymatgen
@@ -19,7 +23,8 @@
 
 import larch.utils.logging as logging
 from larch.utils import mkdir, unixpath
-from larch.utils.strutils import fix_filename, unique_name, strict_ascii
+
+# from larch.utils.strutils import fix_filename, unique_name, strict_ascii
 from larch.site_config import user_larchdir
 from larch.io import read_ascii
 from larch.math.convolution1D import lin_gamma, conv
@@ -43,7 +48,7 @@
 __author__ = ["Beatriz G. Foschiani", "Mauro Rovezzi"]
 __email__ = ["beatrizgfoschiani@gmail.com", "mauro.rovezzi@esrf.fr"]
 __credits__ = ["Jade Chongsathapornpong", "Marius Retegan"]
-__version__ = "2023.3.0"
+__version__ = "2024.1.0"
 
 
 # initialize the logger
@@ -109,10 +114,21 @@ def structure_folders():
     return folders
 
 
+@dataclass
+class Job:
+    num: int  #: index of the job
+    description: str  #: description
+    type: Union[str, None]  #: 'fdmnes', 'feff'
+    timestamp: str  #: creation timestamp
+    path: Union[str, None]  #: path for the calculation
+
+
 class Struct2XAS:
     """Class to convert data from CIF and XYZ files to FDMNES and FEFF inputs"""
 
-    def __init__(self, file, abs_atom) -> None:
+    def __init__(
+        self, file: str, abs_atom: str, parent_path: Union[str, None] = None
+    ) -> None:
         """
 
         Arguments
@@ -134,7 +150,7 @@ def __init__(self, file, abs_atom) -> None:
             Structures from xyz files are always considered non-symmetric for
             the lack of lattice information. For creating the object from an
             XYZ file, a non-symmetric `structure` object from pymatgen is
-            generated (spacegroup: P1) from a `molecule` one via
+            generated (spacegroup: P1) from a `molecule` via
             :func:`xyz2struct`. The lattice parameters chosen for this
             structure are arbitrary and are based on the size of the molecule,
             as are the fractional coordinates. Therefore, the analysis of this
@@ -145,7 +161,6 @@ def __init__(self, file, abs_atom) -> None:
             For creating the object from cif file, a pymatgen structure is
             generated with symmetry information from cif file.
         """
-
         self.file = file
         self.abs_atom = abs_atom
         self.frame = 0
@@ -156,9 +171,18 @@ def __init__(self, file, abs_atom) -> None:
         self.nabs_sites = len(self.get_abs_sites())
         self.elems = self._get_elems()
         self.species = self._get_species()
-        self.parent_path = user_larchdir
+        if parent_path is None:
+            self.parent_path = user_larchdir
+        else:
+            self.parent_path = parent_path
         self.folders = structure_folders()
-        logger.info(
+        self.calc_path = None
+        self.njob = 0
+        self.jobs = []
+        self.tmpl_fdmnes = None
+        self.tmpl_feff = None
+        self.tmpl_sbatch = None
+        logger.debug(
             f"Frames: {self.nframes}, Absorbing sites: {self.nabs_sites}. (Indexes for frames and abs_sites start at 0)"
         )
 
@@ -243,9 +267,10 @@ def read_structure(self, file):
             self.molecules = None
             self.mol = None
             self.nframes = 1
-            self.cif = CifParser(self.file)
+            self.cif = CifParser(self.file, occupancy_tolerance=10, site_tolerance=5e-3)
             self.struct = Structure.from_file(self.file)
-            # self.struct = self.cif.get_structures()[0]  #: NOT WORKING!
+            # self.struct = self.cif.parse_structures()[0] #: TODO
+            # self.struct = self.cif.get_structures()[0]  #: DEPRECATED / NOT WORKING!
             logger.debug("structure created from a CIF file")
         elif self.file_ext == ".xyz":
             self.is_xyz = True
@@ -368,7 +393,7 @@ def get_abs_sites(self):
             The lists inside the list contain the following respective
             information:
             [
-            abs_idx,        # index identifier of the absorber site
+            abs_idx,         # index identifier of the absorber site
                              #     used by self.set_abs_site().
             species_string,  #  The specie for absorber sites.
             frac_coords,     # Fractional coordinate position
@@ -617,6 +642,7 @@ def get_coord_envs(self):
         """
         abs_sites = self.get_abs_sites()
         idx_abs_site = abs_sites[self.abs_site][-1]
+        coord_env_list = []
 
         if self.is_cif:
             from pymatgen.analysis.bond_valence import BVAnalyzer
@@ -641,7 +667,6 @@ def get_coord_envs(self):
             except ValueError:
                 valences = "undefined"
 
-            coord_env_list = []
             se = lgf.compute_structure_environments(
                 max_cn=6,
                 valences=valences,
@@ -658,32 +683,26 @@ def get_coord_envs(self):
                 strategy=strategy, structure_environments=se
             )
             coord_env_ce = lse.coordination_environments[idx_abs_site]
-            ngbs_sites = lse._all_nbs_sites
-            coord_env_list.append(
-                [
-                    f"Coord. Env. for Site {abs_sites[self.abs_site][0]}",
-                    coord_env_ce,
-                    ngbs_sites,
-                ]
-            )
+            coord_env = lse._all_nbs_sites
 
         if self.is_xyz:
             from pymatgen.analysis.local_env import CrystalNN
 
             obj = CrystalNN()
-            coord_env_list = []
+
             coord_env = obj.get_nn_info(self.struct, idx_abs_site)
             for site in coord_env:
                 site["site"].cart_coords = self.struct[site["site_index"]].coords
             coord_dict = obj.get_cn_dict(self.struct, idx_abs_site)
-            coord_env_list.append(
-                [
-                    f"Coord. Env. for Site {abs_sites[self.abs_site][0]}",
-                    {"ce_symbol": f"Elements Dict = {coord_dict}"},
-                    coord_env,
-                ]
-            )
+            coord_env_ce = {"ce_symbol": f"Elements Dict = {coord_dict}"}
 
+        coord_env_list.append(
+            [
+                f"Coord. Env. for Site {abs_sites[self.abs_site][0]}",
+                coord_env_ce,
+                coord_env,
+            ]
+        )
         return coord_env_list
 
     def get_coord_envs_info(self):
@@ -695,7 +714,11 @@ def get_coord_envs_info(self):
         abs_site_coord = self.get_abs_sites()[self.abs_site][4]
 
         elems_dist = []
-        for site in coord_env[2]:
+        sites = coord_env[2]
+        if len(sites) == 0:
+            logger.warning("Empty coordination environment")
+            return None
+        for site in sites:
             if self.is_cif:
                 coord_sym = [
                     coord_env[1][i]["ce_symbol"] for i in range(len(coord_env[1]))
@@ -768,20 +791,28 @@ def make_cluster(self, radius):
         return atoms
 
     def make_input_fdmnes(
-        self, radius=7, parent_path=None, template=None, green=True, **kwargs
+        self,
+        parent_path: str = None,
+        newjob: Union[str, None] = None,
+        template: str = None,
+        radius: float = 7,
+        green: str = True,
+        **kwargs,
     ):
         """
         Create a fdmnes input from a template.
 
         Arguments
         ---------
-        radius : float, [7]
-            radius for fdmnes calculation in Angstrom
         parent_path : str, [None]
             path to the parent directory where the input files are stored
-            if None it will create a temporary directory
+            (under `fdmnes` directory)
+        newjob : str or None [None]
+            if a string, a new job is created with the given description
         template : str, [None]
             full path to the template file
+        radius : float, [7]
+            radius for fdmnes calculation in Angstrom
         green : boolean [True]
             True: use `Green` (muffin-tin potentials, faster)
             False: use finite-difference method (slower)
@@ -792,28 +823,52 @@ def make_input_fdmnes(
         Returns
         -------
         None -> writes FDMNES input to disk
-        directory structure: {parent_path}/fdmnes/{self.file_name}/{self.abs_atom}/frame{self.frame}/site{self.abs_site}/
+        directory structure:
+          + {parent_path}
+          |+ fdmnes
+          ||+ {file_name}
+          |||+ {abs_atom}
+          ||||+ frame{nframe}
+          |||||+ site{abs_site}
+          ||||||+ job{njob}
 
         """
-        replacements = {}
-        replacements.update(**kwargs)
-        replacements["version"] = __version__
-
-        if template is None:
-            template = os.path.join(
-                os.path.dirname(os.path.realpath(__file__)), "templates", "fdmnes.tmpl"
-            )
-
         if parent_path is None:
-            parent_path = self.folders["fdmnes"]
-
-        self.outdir = os.path.join(
-            parent_path,
+            parent_path = self.parent_path
+
+        if (newjob is not None) or (self.njob == 0):
+            self.njob += 1
+            job = Job(
+                num=self.njob,
+                description=newjob,
+                type="fdmnes",
+                timestamp=_get_timestamp(),
+                path=None,
+            )
+            self.jobs.append(job)
+        else:
+            job = self.jobs[self.njob - 1]
+        calc_path = os.path.join(
+            "fdmnes",
             self.file_name,
             self.abs_atom,
             f"frame{self.frame}",
             f"site{self.abs_site}",
+            f"job{self.njob}",
         )
+        job.path = calc_path
+        self.outdir = os.path.join(parent_path, calc_path)
+        self.calc_path = calc_path
+
+        if template is None:
+            template = os.path.join(
+                os.path.dirname(os.path.realpath(__file__)), "templates", "fdmnes.tmpl"
+            )
+        assert os.path.isfile(template), "wrong template path"
+
+        replacements = {}
+        replacements.update(**kwargs)
+        replacements["version"] = __version__
 
         method = "green" if green else ""
         absorber = ""
@@ -928,7 +983,8 @@ def make_input_fdmnes(
         try:
             os.makedirs(self.outdir, mode=0o755)
         except FileExistsError:
-            pass
+            errmsg = f"`job{job.num}` already exists -> use `newjob` or remove it"
+            raise FileExistsError(errmsg)
 
         # Write the input file.
         fnout = os.path.join(self.outdir, "job_inp.txt")
@@ -940,17 +996,40 @@ def make_input_fdmnes(
         with open(os.path.join(self.outdir, "fdmfile.txt"), "w") as fp:
             fp.write("1\njob_inp.txt")
 
-        logger.info(f"written FDMNES input -> {fnout}")
+        logger.info(f"written input for `/{job.path}`")
+
+    def make_sbatch(self, template: str, **kwargs):
+        """Generates a SBATCH file (SLURM workload manager) using a template
+
+        Arguments
+        ---------
+        template: str
+            path to the SBATCH template file
+        **kwargs
+            keyword arguments to be replaced in the template file
+
+        Returns
+        -------
+        None: writes `job.sbatch`
+
+        """
+        assert os.path.isfile(template), "wrong template path"
+        batch_script = os.path.join(self.outdir, "job.sbatch")
+        with open(batch_script, "w") as fp, open(template) as tp:
+            fp.write(tp.read().format(**kwargs))
+            logger.info(f"written {fp.name}")
+        os.chmod(batch_script, 0o755)
 
     def make_input_feff(
         self,
-        radius=7,
-        parent_path=None,
-        template=None,
-        feff_comment="*",
-        edge="K",
-        sig2=None,
-        debye=None,
+        parent_path: str = None,
+        newjob: Union[str, None] = None,
+        template: str = None,
+        radius: float = 7,
+        feff_comment: str = "*",
+        edge: str = "K",
+        sig2: Union[float, None] = None,
+        debye: Union[List[float], None] = None,
         **kwargs,
     ):
         """
@@ -958,13 +1037,15 @@ def make_input_feff(
 
         Arguments
         ---------
-        radius : float, [7]
-            radius for feff calculation [Angstrom].
         parent_path : str, [None]
             path to the parent directory where the input files are stored
-            if None it will create a temporary directory
+            (under "feff" directory)
+        newjob : str or None [None]
+            if a string, a new job is created with the given description
         template : str, [None]
             full path to the template file
+        radius : float, [7]
+            radius for feff calculation [Angstrom].
         feff_coment : str, ["*"]
             comment character used in the input file
         sig2 : float or None, [None]
@@ -982,21 +1063,42 @@ def make_input_feff(
         Returns
         -------
         None -> writes FEFF input to disk
-        directory structure: {parent_path}/feff/{self.file_name}/{self.abs_atom}/frame{self.frame}/site{self.abs_site}/
+        directory structure:
+          + {parent_path}
+          |+ feff
+          ||+ {file_name}
+          |||+ {abs_atom}
+          ||||+ frame{nframe}
+          |||||+ site{abs_site}
+          ||||||+ job{njob}
         """
-        replacements = {}
-        replacements.update(**kwargs)
-        replacements["version"] = __version__
 
         if parent_path is None:
-            parent_path = self.folders["feff"]
-        self.outdir = os.path.join(
-            parent_path,
+            parent_path = self.parent_path
+
+        if (newjob is not None) or (self.njob == 0):
+            self.njob += 1
+            job = Job(
+                num=self.njob,
+                description=newjob,
+                type="fdmnes",
+                timestamp=_get_timestamp(),
+                path=None,
+            )
+            self.jobs.append(job)
+        else:
+            job = self.jobs[self.njob - 1]
+        calc_path = os.path.join(
+            "feff",
             self.file_name,
             self.abs_atom,
             f"frame{self.frame}",
             f"site{self.abs_site}",
+            f"job{self.njob}",
         )
+        job.path = calc_path
+        self.outdir = os.path.join(parent_path, calc_path)
+        self.calc_path = calc_path
 
         if template is None:
             template = os.path.join(
@@ -1004,6 +1106,11 @@ def make_input_feff(
                 "templates",
                 "feff_exafs.tmpl",
             )
+        assert os.path.isfile(template), "wrong template path"
+
+        replacements = {}
+        replacements.update(**kwargs)
+        replacements["version"] = __version__
 
         if sig2 is None:
             use_sig2 = "*"
@@ -1343,7 +1450,9 @@ def convolve_data(
     return group
 
 
-def save_cif_from_mp(api_key, material_id, parent_path=None):
+def save_cif_from_mp(
+    api_key: str, material_id: str, parent_path: str = None
+) -> list[str, str]:
     """Collect a CIF file from the Materials Project Database, given the material id
 
     Parameters
@@ -1353,8 +1462,8 @@ def save_cif_from_mp(api_key, material_id, parent_path=None):
     material id : str
         material id (format mp-xxxx) from Materials Project
     parent_path : str
-        path where to store the CIF files
-        if None, a temporary one is created
+        output where to store the CIF files
+        if None, user_larchdir + 'mp_structs' is used
 
     Returns
     -------
@@ -1377,7 +1486,7 @@ def save_cif_from_mp(api_key, material_id, parent_path=None):
     return [parent_path, outfn]
 
 
-def save_mp_structure(api_key, material_id, parent_path=None):
+def save_mp_structure(api_key: str, material_id: str, parent_path: str = None) -> str:
     """Save structure from Materials Project Database as json, given the material id
 
     Parameters
@@ -1387,7 +1496,7 @@ def save_mp_structure(api_key, material_id, parent_path=None):
     material id : str
         material id (format mp-xxxx) from Materials Project
     parent_path : str
-        path where to store the Structure files
+        output path where to store the Structure files
         if None, user_larchdir + 'mp_structs' is used
 
     Returns