Instruction:
Write a Python 3 function that can
create a virtual molecule by unique atoms the centriods of the equivalent atoms and the farthest atom.

Response:
def _virtual_molecule(self, mol, ilabels, eq_atoms):
        """
        Create a virtual molecule by unique atoms, the centriods of the
        equivalent atoms

        Args:
            mol: The molecule. OpenBabel OBMol object
            ilables: inchi label map
            eq_atoms: equivalent atom labels
            farthest_group_idx: The equivalent atom group index in which
                there is the farthest atom to the centroid

        Return:
            The virtual molecule
        """
        vmol = ob.OBMol()

        non_unique_atoms = set([a for g in eq_atoms for a in g])
        all_atoms = set(range(1, len(ilabels) + 1))
        unique_atom_labels = sorted(all_atoms - non_unique_atoms)

        #try to align molecules using unique atoms
        for i in unique_atom_labels:
            orig_idx = ilabels[i-1]
            oa1 = mol.GetAtom(orig_idx)
            a1 = vmol.NewAtom()
            a1.SetAtomicNum(oa1.GetAtomicNum())
            a1.SetVector(oa1.GetVector())

        #try to align using centroids of the equivalent atoms
        if vmol.NumAtoms() < 3:
            for symm in eq_atoms:
                c1x, c1y, c1z = self._group_centroid(mol, ilabels, symm)
                min_distance = float("inf")
                for i in range(1, vmol.NumAtoms()+1):
                    va = vmol.GetAtom(i)
                    distance = math.sqrt((c1x - va.x())**2 + (c1y - va.y())**2
                                         + (c1z - va.z())**2)
                    if distance < min_distance:
                        min_distance = distance
                if min_distance > 0.2:
                    a1 = vmol.NewAtom()
                    a1.SetAtomicNum(9)
                    a1.SetVector(c1x, c1y, c1z)

        return vmol


Instruction:
Can you generate the documentation for the following Python 3 function
def _align_heavy_atoms(mol1, mol2, vmol1, vmol2, ilabel1, ilabel2,
                           eq_atoms):
        """
        Align the label of topologically identical atoms of second molecule
        towards first molecule

        Args:
            mol1: First molecule. OpenBabel OBMol object
            mol2: Second molecule. OpenBabel OBMol object
            vmol1: First virtual molecule constructed by centroids. OpenBabel
                OBMol object
            vmol2: First virtual molecule constructed by centroids. OpenBabel
                OBMol object
            ilabel1: inchi label map of the first molecule
            ilabel2: inchi label map of the second molecule
            eq_atoms: equivalent atom lables

        Return:
            corrected inchi labels of heavy atoms of the second molecule
        """

        nvirtual = vmol1.NumAtoms()
        nheavy = len(ilabel1)

        for i in ilabel2:  # add all heavy atoms
            a1 = vmol1.NewAtom()
            a1.SetAtomicNum(1)
            a1.SetVector(0.0, 0.0, 0.0)  # useless, just to pair with vmol2
            oa2 = mol2.GetAtom(i)
            a2 = vmol2.NewAtom()
            a2.SetAtomicNum(1)
            # align using the virtual atoms, these atoms are not
            # used to align, but match by positions
            a2.SetVector(oa2.GetVector())

        aligner = ob.OBAlign(False, False)
        aligner.SetRefMol(vmol1)
        aligner.SetTargetMol(vmol2)
        aligner.Align()
        aligner.UpdateCoords(vmol2)

        canon_mol1 = ob.OBMol()
        for i in ilabel1:
            oa1 = mol1.GetAtom(i)
            a1 = canon_mol1.NewAtom()
            a1.SetAtomicNum(oa1.GetAtomicNum())
            a1.SetVector(oa1.GetVector())

        aligned_mol2 = ob.OBMol()
        for i in range(nvirtual + 1, nvirtual + nheavy + 1):
            oa2 = vmol2.GetAtom(i)
            a2 = aligned_mol2.NewAtom()
            a2.SetAtomicNum(oa2.GetAtomicNum())
            a2.SetVector(oa2.GetVector())

        canon_label2 = list(range(1, nheavy+1))
        for symm in eq_atoms:
            for i in symm:
                canon_label2[i-1] = -1
        for symm in eq_atoms:
            candidates1 = list(symm)
            candidates2 = list(symm)
            for c2 in candidates2:
                distance = 99999.0
                canon_idx = candidates1[0]
                a2 = aligned_mol2.GetAtom(c2)
                for c1 in candidates1:
                    a1 = canon_mol1.GetAtom(c1)
                    d = a1.GetDistance(a2)
                    if d < distance:
                        distance = d
                        canon_idx = c1
                canon_label2[c2-1] = canon_idx
                candidates1.remove(canon_idx)

        canon_inchi_orig_map2 = [(canon, inchi, orig)
                                 for canon, inchi, orig in
                                 zip(canon_label2, list(range(1, nheavy + 1)),
                                     ilabel2)]
        canon_inchi_orig_map2.sort(key=lambda m: m[0])
        heavy_atom_indices2 = tuple([x[2] for x in canon_inchi_orig_map2])
        return heavy_atom_indices2

Response: Align the label of topologically identical atoms of first molecule with second molecule.


Instruction:
Write a Python 3 script to
align the label of topologically identical atoms of the first molecule with the second molecule.

Response:
def _align_hydrogen_atoms(mol1, mol2, heavy_indices1,
                              heavy_indices2):
        """
        Align the label of topologically identical atoms of second molecule
        towards first molecule

        Args:
            mol1: First molecule. OpenBabel OBMol object
            mol2: Second molecule. OpenBabel OBMol object
            heavy_indices1: inchi label map of the first molecule
            heavy_indices2: label map of the second molecule

        Return:
            corrected label map of all atoms of the second molecule
        """
        num_atoms = mol2.NumAtoms()
        all_atom = set(range(1, num_atoms+1))
        hydrogen_atoms1 = all_atom - set(heavy_indices1)
        hydrogen_atoms2 = all_atom - set(heavy_indices2)
        label1 = heavy_indices1 + tuple(hydrogen_atoms1)
        label2 = heavy_indices2 + tuple(hydrogen_atoms2)

        cmol1 = ob.OBMol()
        for i in label1:
            oa1 = mol1.GetAtom(i)
            a1 = cmol1.NewAtom()
            a1.SetAtomicNum(oa1.GetAtomicNum())
            a1.SetVector(oa1.GetVector())
        cmol2 = ob.OBMol()
        for i in label2:
            oa2 = mol2.GetAtom(i)
            a2 = cmol2.NewAtom()
            a2.SetAtomicNum(oa2.GetAtomicNum())
            a2.SetVector(oa2.GetVector())

        aligner = ob.OBAlign(False, False)
        aligner.SetRefMol(cmol1)
        aligner.SetTargetMol(cmol2)
        aligner.Align()
        aligner.UpdateCoords(cmol2)

        hydrogen_label2 = []
        hydrogen_label1 = list(range(len(heavy_indices1) + 1, num_atoms + 1))
        for h2 in range(len(heavy_indices2) + 1, num_atoms + 1):
            distance = 99999.0
            idx = hydrogen_label1[0]
            a2 = cmol2.GetAtom(h2)
            for h1 in hydrogen_label1:
                a1 = cmol1.GetAtom(h1)
                d = a1.GetDistance(a2)
                if d < distance:
                    distance = d
                    idx = h1
            hydrogen_label2.append(idx)
            hydrogen_label1.remove(idx)

        hydrogen_orig_idx2 = label2[len(heavy_indices2):]
        hydrogen_canon_orig_map2 = [(canon, orig) for canon, orig
                                    in zip(hydrogen_label2,
                                           hydrogen_orig_idx2)]
        hydrogen_canon_orig_map2.sort(key=lambda m: m[0])
        hydrogen_canon_indices2 = [x[1] for x in hydrogen_canon_orig_map2]

        canon_label1 = label1
        canon_label2 = heavy_indices2 + tuple(hydrogen_canon_indices2)

        return canon_label1, canon_label2


Instruction:
Can you create a Python 3 function that
returns the elements of the atoms in the specified order

Response:
def _get_elements(mol, label):
        """
        The the elements of the atoms in the specified order

        Args:
            mol: The molecule. OpenBabel OBMol object.
            label: The atom indices. List of integers.

        Returns:
            Elements. List of integers.
        """
        elements = [int(mol.GetAtom(i).GetAtomicNum()) for i in label]
        return elements


Instruction:
Implement a function in Python 3 to
return True if the molecule is a linear one.

Response:
def _is_molecule_linear(self, mol):
        """
        Is the molecule a linear one

        Args:
            mol: The molecule. OpenBabel OBMol object.

        Returns:
            Boolean value.
        """
        if mol.NumAtoms() < 3:
            return True
        a1 = mol.GetAtom(1)
        a2 = mol.GetAtom(2)
        for i in range(3, mol.NumAtoms()+1):
            angle = float(mol.GetAtom(i).GetAngle(a2, a1))
            if angle < 0.0:
                angle = -angle
            if angle > 90.0:
                angle = 180.0 - angle
            if angle > self._angle_tolerance:
                return False
        return True


Instruction:
How would you explain what the following Python 3 function does
def get_molecule_hash(self, mol):
        obmol = BabelMolAdaptor(mol).openbabel_mol
        inchi = self._inchi_labels(obmol)[2]
        return inchi

Response: Return inchi as molecular hash


Instruction:
Can you tell what is the following Python 3 function doing
def fit(self, mol1, mol2):
        return self.get_rmsd(mol1, mol2) < self._tolerance

Response:
Fit two molecules.

        Args:
            mol1: First molecule. OpenBabel OBMol or pymatgen Molecule object
            mol2: Second molecule. OpenBabel OBMol or pymatgen Molecule object

        Returns:
            A boolean value indicates whether two molecules are the same.


Instruction:
Can you generate a brief explanation for the following Python 3 code
def get_rmsd(self, mol1, mol2):
        label1, label2 = self._mapper.uniform_labels(mol1, mol2)
        if label1 is None or label2 is None:
            return float("Inf")
        return self._calc_rms(mol1, mol2, label1, label2)

Response: Get the RMSD between two molecules.


Instruction:
Explain what the following Python 3 code does
def _calc_rms(mol1, mol2, clabel1, clabel2):
        obmol1 = BabelMolAdaptor(mol1).openbabel_mol
        obmol2 = BabelMolAdaptor(mol2).openbabel_mol

        cmol1 = ob.OBMol()
        for i in clabel1:
            oa1 = obmol1.GetAtom(i)
            a1 = cmol1.NewAtom()
            a1.SetAtomicNum(oa1.GetAtomicNum())
            a1.SetVector(oa1.GetVector())
        cmol2 = ob.OBMol()
        for i in clabel2:
            oa2 = obmol2.GetAtom(i)
            a2 = cmol2.NewAtom()
            a2.SetAtomicNum(oa2.GetAtomicNum())
            a2.SetVector(oa2.GetVector())

        aligner = ob.OBAlign(True, False)
        aligner.SetRefMol(cmol1)
        aligner.SetTargetMol(cmol2)
        aligner.Align()
        return aligner.GetRMSD()

Response: Calculates the RMSD of the two Molecules.


Instruction:
Write a Python 3 function that can
group molecules by structural equality.

Response:
def group_molecules(self, mol_list):
        """
        Group molecules by structural equality.

        Args:
            mol_list: List of OpenBabel OBMol or pymatgen objects

        Returns:
            A list of lists of matched molecules
            Assumption: if s1=s2 and s2=s3, then s1=s3
            This may not be true for small tolerances.
        """
        mol_hash = [(i, self._mapper.get_molecule_hash(m))
                    for i, m in enumerate(mol_list)]
        mol_hash.sort(key=lambda x: x[1])

        #Use molecular hash to pre-group molecules.
        raw_groups = tuple([tuple([m[0] for m in g]) for k, g
                            in itertools.groupby(mol_hash,
                                                 key=lambda x: x[1])])

        group_indices = []
        for rg in raw_groups:
            mol_eq_test = [(p[0], p[1], self.fit(mol_list[p[0]],
                                                 mol_list[p[1]]))
                           for p in itertools.combinations(sorted(rg), 2)]
            mol_eq = set([(p[0], p[1]) for p in mol_eq_test if p[2]])
            not_alone_mols = set(itertools.chain.from_iterable(mol_eq))
            alone_mols = set(rg) - not_alone_mols
            group_indices.extend([[m] for m in alone_mols])
            while len(not_alone_mols) > 0:
                current_group = {not_alone_mols.pop()}
                while len(not_alone_mols) > 0:
                    candidate_pairs = set(
                        [tuple(sorted(p)) for p
                         in itertools.product(current_group, not_alone_mols)])
                    mutual_pairs = candidate_pairs & mol_eq
                    if len(mutual_pairs) == 0:
                        break
                    mutual_mols = set(itertools.chain
                                      .from_iterable(mutual_pairs))
                    current_group |= mutual_mols
                    not_alone_mols -= mutual_mols
                group_indices.append(sorted(current_group))

        group_indices.sort(key=lambda x: (len(x), -x[0]), reverse=True)
        all_groups = [[mol_list[i] for i in g] for g in group_indices]
        return all_groups


Instruction:
Make a summary of the following Python 3 code
def nmltostring(nml):
    if not isinstance(nml,dict):
      raise ValueError("nml should be a dict !")

    curstr = ""
    for key,group in nml.items():
       namelist = ["&" + key]
       for k, v in group.items():
         if isinstance(v, list) or isinstance(v, tuple):
           namelist.append(k + " = " + ",".join(map(str, v)) + ",")
         elif is_string(v):
           namelist.append(k + " = '" + str(v) + "',")
         else:
           namelist.append(k + " = " + str(v) + ",")
       namelist.append("/")

       curstr = curstr + "\n".join(namelist) + "\n"

    return curstr

Response: Convert a dictionary representing a Fortran namelist into a string.


Instruction:
Write a Python 3 function that can
initialize an instance from an AbinitTask instance.

Response:
def from_node(cls, task):
        """Initialize an instance from an :class:`AbinitTask` instance."""
        new = super().from_node(task)

        new.update(
            executable=task.executable,
            #executable_version:
            #task_events=
            pseudos=[p.as_dict() for p in task.input.pseudos],
            #input=task.input
        )

        new.register_gridfs_files(
            run_abi=(task.input_file.path, "t"),
            run_abo=(task.output_file.path, "t"),
        )

        return new


Instruction:
Can you tell what is the following Python 3 function doing
def parse(self, filename):
        with abiinspect.YamlTokenizer(filename) as r:
            doc = r.next_doc_with_tag("!Autoparal")
            try:
                d = yaml.safe_load(doc.text_notag)
                return ParalHints(info=d["info"], confs=d["configurations"])
            except:
                import traceback
                sexc = traceback.format_exc()
                err_msg = "Wrong YAML doc:\n%s\n\nException:\n%s" % (doc.text, sexc)
                self.add_error(err_msg)
                logger.critical(err_msg)
                raise self.Error(err_msg)

Response: Read the AutoParal section from filename.


Instruction:
Here you have a function in Python 3, explain what it does
def from_mpi_omp_lists(cls, mpi_procs, omp_threads):
        info = {}
        confs = [ParalConf(mpi_ncpus=p, omp_ncpus=p, efficiency=1.0)
                 for p, t in product(mpi_procs, omp_threads)]

        return cls(info, confs)

Response: Build a list of Parallel configurations from two lists containing the number of MPI processes and number of OpenMP threads.


Instruction:
Can you generate a brief explanation for the following Python 3 code
def select_with_condition(self, condition, key=None):
        condition = Condition.as_condition(condition)
        new_confs = []

        for conf in self:
            # Select the object on which condition is applied
            obj = conf if key is None else AttrDict(conf[key])
            add_it = condition(obj=obj)
            #if key is "vars": print("conf", conf, "added:", add_it)
            if add_it: new_confs.append(conf)

        self._confs = new_confs

Response: Select all the configurations that satisfy the given condition.


Instruction:
Write a Python 3 function that can
sort the configurations in place. items with highest efficiency come first

Response:
def sort_by_efficiency(self, reverse=True):
        """Sort the configurations in place. items with highest efficiency come first"""
        self._confs.sort(key=lambda c: c.efficiency, reverse=reverse)
        return self


Instruction:
Can you tell what is the following Python 3 function doing
def sort_by_speedup(self, reverse=True):
        self._confs.sort(key=lambda c: c.speedup, reverse=reverse)
        return self

Response: Sort the configurations in place. items with highest speedup come first


Instruction:
Explain what the following Python 3 code does
def sort_by_mem_per_proc(self, reverse=False):
        # Avoid sorting if mem_per_cpu is not available.
        if any(c.mem_per_proc > 0.0 for c in self):
            self._confs.sort(key=lambda c: c.mem_per_proc, reverse=reverse)
        return self

Response: Sort the configurations in place. items with lowest memory per proc come first.


Instruction:
How would you explain what the following Python 3 function does
def get_ordered_with_policy(self, policy, max_ncpus):
        # Build new list since we are gonna change the object in place.
        hints = self.__class__(self.info, confs=[c for c in self if c.num_cores <= max_ncpus])

        # First select the configurations satisfying the condition specified by the user (if any)
        bkp_hints = hints.copy()
        if policy.condition:
            logger.info("Applying condition %s" % str(policy.condition))
            hints.select_with_condition(policy.condition)

            # Undo change if no configuration fullfills the requirements.
            if not hints:
                hints = bkp_hints
                logger.warning("Empty list of configurations after policy.condition")

        # Now filter the configurations depending on the values in vars
        bkp_hints = hints.copy()
        if policy.vars_condition:
            logger.info("Applying vars_condition %s" % str(policy.vars_condition))
            hints.select_with_condition(policy.vars_condition, key="vars")

            # Undo change if no configuration fullfills the requirements.
            if not hints:
                hints = bkp_hints
                logger.warning("Empty list of configurations after policy.vars_condition")

        if len(policy.autoparal_priorities) == 1:
            # Example: hints.sort_by_speedup()
            if policy.autoparal_priorities[0] in ['efficiency', 'speedup', 'mem_per_proc']:
                getattr(hints, "sort_by_" + policy.autoparal_priorities[0])()
            elif isinstance(policy.autoparal_priorities[0], collections.Mapping):
                if policy.autoparal_priorities[0]['meta_priority'] == 'highest_speedup_minimum_efficiency_cutoff':
                    min_efficiency = policy.autoparal_priorities[0].get('minimum_efficiency', 1.0)
                    hints.select_with_condition({'efficiency': {'$gte': min_efficiency}})
                    hints.sort_by_speedup()
        else:
            hints = hints.multidimensional_optimization(priorities=policy.autoparal_priorities)
            if len(hints) == 0: raise ValueError("len(hints) == 0")

        #TODO: make sure that num_cores == 1 is never selected when we have more than one configuration
        #if len(hints) > 1:
        #    hints.select_with_condition(dict(num_cores={"$eq": 1)))

        # Return final (orderded ) list of configurations (best first).
        return hints

Response: Returns a new list of all the configurations in the current set according to the given TaskPolicy.


Instruction:
Write a Python 3 function that can
convert an object obj into a TaskPolicy. Accepts a dict - like object containing the key - value pairs as keys and the value - value pairs as values.

Response:
def as_policy(cls, obj):
        """
        Converts an object obj into a `:class:`TaskPolicy. Accepts:

            * None
            * TaskPolicy
            * dict-like object
        """
        if obj is None:
            # Use default policy.
            return TaskPolicy()
        else:
            if isinstance(obj, cls):
                return obj
            elif isinstance(obj, collections.abc.Mapping):
                return cls(**obj)
            else:
                raise TypeError("Don't know how to convert type %s to %s" % (type(obj), cls))


Instruction:
Here you have a function in Python 3, explain what it does
def from_user_config(cls):
        global _USER_CONFIG_TASKMANAGER
        if _USER_CONFIG_TASKMANAGER is not None:
            return _USER_CONFIG_TASKMANAGER

        # Try in the current directory then in user configuration directory.
        path = os.path.join(os.getcwd(), cls.YAML_FILE)
        if not os.path.exists(path):
            path = os.path.join(cls.USER_CONFIG_DIR, cls.YAML_FILE)

        if not os.path.exists(path):
            raise RuntimeError(colored(
		"\nCannot locate %s neither in current directory nor in %s\n"
                "!!! PLEASE READ THIS: !!!\n"
                "To use AbiPy to run jobs this file must be present\n"
                "It provides a description of the cluster/computer you are running on\n"
                "Examples are provided in abipy/data/managers." % (cls.YAML_FILE, path), color="red"))

        _USER_CONFIG_TASKMANAGER = cls.from_file(path)
        return _USER_CONFIG_TASKMANAGER

Response: Initialize the TaskManager from the user - supplied configuration file.


Instruction:
Write a Python 3 script to
read the configuration parameters from the Yaml file filename.

Response:
def from_file(cls, filename):
        """Read the configuration parameters from the Yaml file filename."""
        try:
            with open(filename, "r") as fh:
                return cls.from_dict(yaml.safe_load(fh))
        except Exception as exc:
            print("Error while reading TaskManager parameters from %s\n" % filename)
            raise


Instruction:
Here you have a function in Python 3, explain what it does
def as_manager(cls, obj):
        if isinstance(obj, cls): return obj
        if obj is None: return cls.from_user_config()

        if is_string(obj):
            if os.path.exists(obj):
                return cls.from_file(obj)
            else:
                return cls.from_string(obj)

        elif isinstance(obj, collections.abc.Mapping):
            return cls.from_dict(obj)
        else:
            raise TypeError("Don't know how to convert type %s to TaskManager" % type(obj))

Response: Convert obj into TaskManager instance. Accepts string filepath dictionary TaskManager object. Accepts string filepath TaskManager object. Accepts dictionary TaskManager object. Accepts None.


Instruction:
Given the following Python 3 function, write the documentation
def from_dict(cls, d):
        return cls(**{k: v for k, v in d.items() if k in cls.ENTRIES})

Response: Create an instance from a dictionary.


Instruction:
How would you code a function in Python 3 to
return a new TaskManager with the same parameters as self but replace the QueueAdapter with a ShellAdapter with mpi_procs so that we can submit the job with passing through the queue.

Response:
def to_shell_manager(self, mpi_procs=1):
        """
        Returns a new `TaskManager` with the same parameters as self but replace the :class:`QueueAdapter`
        with a :class:`ShellAdapter` with mpi_procs so that we can submit the job without passing through the queue.
        """
        my_kwargs = copy.deepcopy(self._kwargs)
        my_kwargs["policy"] = TaskPolicy(autoparal=0)

        # On BlueGene we need at least two qadapters.
        # One for running jobs on the computing nodes and another one
        # for running small jobs on the fronted. These two qadapters
        # will have different enviroments and different executables.
        # If None of the q-adapters has qtype==shell, we change qtype to shell
        # and we return a new Manager for sequential jobs with the same parameters as self.
        # If the list contains a qadapter with qtype == shell, we ignore the remaining qadapters
        # when we build the new Manager.
        has_shell_qad = False
        for d in my_kwargs["qadapters"]:
            if d["queue"]["qtype"] == "shell": has_shell_qad = True
        if has_shell_qad:
            my_kwargs["qadapters"] = [d for d in my_kwargs["qadapters"] if d["queue"]["qtype"] == "shell"]

        for d in my_kwargs["qadapters"]:
            d["queue"]["qtype"] = "shell"
            d["limits"]["min_cores"] = mpi_procs
            d["limits"]["max_cores"] = mpi_procs

            # If shell_runner is specified, replace mpi_runner with shell_runner
            # in the script used to run jobs on the frontend.
            # On same machines based on Slurm, indeed, mpirun/mpiexec is not available
            # and jobs should be executed with `srun -n4 exec` when running on the computing nodes
            # or with `exec` when running in sequential on the frontend.
            if "job" in d and "shell_runner" in d["job"]:
                shell_runner = d["job"]["shell_runner"]
                #print("shell_runner:", shell_runner, type(shell_runner))
                if not shell_runner or shell_runner == "None": shell_runner = ""
                d["job"]["mpi_runner"] = shell_runner
                #print("shell_runner:", shell_runner)

        #print(my_kwargs)
        new = self.__class__(**my_kwargs)
        new.set_mpi_procs(mpi_procs)

        return new


Instruction:
How would you implement a function in Python 3 that
returns a new TaskManager with fixed MPI processes and OpenMP threads.

Response:
def new_with_fixed_mpi_omp(self, mpi_procs, omp_threads):
        """
        Return a new `TaskManager` in which autoparal has been disabled.
        The jobs will be executed with `mpi_procs` MPI processes and `omp_threads` OpenMP threads.
        Useful for generating input files for benchmarks.
        """
        new = self.deepcopy()
        new.policy.autoparal = 0
        new.set_mpi_procs(mpi_procs)
        new.set_omp_threads(omp_threads)
        return new


Instruction:
Given the following Python 3 function, write the documentation
def select_qadapter(self, pconfs):
        # Order the list of configurations according to policy.
        policy, max_ncpus = self.policy, self.max_cores
        pconfs = pconfs.get_ordered_with_policy(policy, max_ncpus)

        if policy.precedence == "qadapter":

            # Try to run on the qadapter with the highest priority.
            for qadpos, qad in enumerate(self.qads):
                possible_pconfs = [pc for pc in pconfs if qad.can_run_pconf(pc)]

                if qad.allocation == "nodes":
                #if qad.allocation in ["nodes", "force_nodes"]:
                    # Select the configuration divisible by nodes if possible.
                    for pconf in possible_pconfs:
                        if pconf.num_cores % qad.hw.cores_per_node == 0:
                            return self._use_qadpos_pconf(qadpos, pconf)

                # Here we select the first one.
                if possible_pconfs:
                    return self._use_qadpos_pconf(qadpos, possible_pconfs[0])

        elif policy.precedence == "autoparal_conf":
            # Try to run on the first pconf irrespectively of the priority of the qadapter.
            for pconf in pconfs:
                for qadpos, qad in enumerate(self.qads):

                    if qad.allocation == "nodes" and not pconf.num_cores % qad.hw.cores_per_node == 0:
                        continue # Ignore it. not very clean

                    if qad.can_run_pconf(pconf):
                        return self._use_qadpos_pconf(qadpos, pconf)

        else:
            raise ValueError("Wrong value of policy.precedence = %s" % policy.precedence)

        # No qadapter could be found
        raise RuntimeError("Cannot find qadapter for this run!")

Response: Given a list of parallel configurations and a list of ParalHints object with the optimal configuration select an appropriate QueueAdapter.


Instruction:
Write a Python 3 function that can
write the submission script. Return the path of the script.

Response:
def write_jobfile(self, task, **kwargs):
        """
        Write the submission script. Return the path of the script

        ================  ============================================
        kwargs            Meaning
        ================  ============================================
        exec_args         List of arguments passed to task.executable.
                          Default: no arguments.

        ================  ============================================
        """
        script = self.qadapter.get_script_str(
            job_name=task.name,
            launch_dir=task.workdir,
            executable=task.executable,
            qout_path=task.qout_file.path,
            qerr_path=task.qerr_file.path,
            stdin=task.files_file.path,
            stdout=task.log_file.path,
            stderr=task.stderr_file.path,
            exec_args=kwargs.pop("exec_args", []),
        )

        # Write the script.
        with open(task.job_file.path, "w") as fh:
            fh.write(script)
            task.job_file.chmod(0o740)
            return task.job_file.path


Instruction:
Given the following Python 3 function, write the documentation
def launch(self, task, **kwargs):
        if task.status == task.S_LOCKED:
            raise ValueError("You shall not submit a locked task!")

        # Build the task
        task.build()

        # Pass information on the time limit to Abinit (we always assume ndtset == 1)
        if isinstance(task, AbinitTask):
            args = kwargs.get("exec_args", [])
            if args is None: args = []
            args = args[:]
            args.append("--timelimit %s" % qu.time2slurm(self.qadapter.timelimit))
            kwargs["exec_args"] = args

        # Write the submission script
        script_file = self.write_jobfile(task, **kwargs)

        # Submit the task and save the queue id.
        try:
            qjob, process = self.qadapter.submit_to_queue(script_file)
            task.set_status(task.S_SUB, msg='Submitted to queue')
            task.set_qjob(qjob)
            return process

        except self.qadapter.MaxNumLaunchesError as exc:
            # TODO: Here we should try to switch to another qadapter
            # 1) Find a new parallel configuration in those stored in task.pconfs
            # 2) Change the input file.
            # 3) Regenerate the submission script
            # 4) Relaunch
            task.set_status(task.S_ERROR, msg="max_num_launches reached: %s" % str(exc))
            raise

Response: This method is used to submit the task to the queue and return the Process object.


Instruction:
Write a Python 3 function for
comparing Abinit version to version_string with operator op

Response:
def compare_version(self, version_string, op):
        """Compare Abinit version to `version_string` with operator `op`"""
        from pkg_resources import parse_version
        from monty.operator import operator_from_str
        op = operator_from_str(op)
        return op(parse_version(self.version), parse_version(version_string))


Instruction:
How would you implement a function in Python 3 that
converts a MyTimedelta object into a MyTimedelta object.

Response:
def as_timedelta(cls, delta):
        """Convert delta into a MyTimedelta object."""
        # Cannot monkey patch the __class__ and must pass through __new__ as the object is immutable.
        if isinstance(delta, cls): return delta
        return cls(delta.days, delta.seconds, delta.microseconds)


Instruction:
Write a Python 3 script to
return the runtime time of the task

Response:
def get_runtime(self):
        """:class:`timedelta` with the run-time, None if the Task is not running"""
        if self.start is None: return None

        if self.end is None:
            delta = datetime.datetime.now() - self.start
        else:
            delta = self.end - self.start

        return MyTimedelta.as_timedelta(delta)


Instruction:
Can you generate a brief explanation for the following Python 3 code
def get_time_inqueue(self):
        if self.submission is None: return None

        if self.start is None:
            delta = datetime.datetime.now() - self.submission
        else:
            delta = self.start - self.submission
            # This happens when we read the exact start datetime from the ABINIT log file.
            if delta.total_seconds() < 0: delta = datetime.timedelta(seconds=0)

        return MyTimedelta.as_timedelta(delta)

Response: Returns the time spent in the Queue.


Instruction:
Can you generate a brief explanation for the following Python 3 code
def set_workdir(self, workdir, chroot=False):
        if not chroot and hasattr(self, "workdir") and self.workdir != workdir:
            raise ValueError("self.workdir != workdir: %s, %s" % (self.workdir,  workdir))

        self.workdir = os.path.abspath(workdir)

        # Files required for the execution.
        self.input_file = File(os.path.join(self.workdir, "run.abi"))
        self.output_file = File(os.path.join(self.workdir, "run.abo"))
        self.files_file = File(os.path.join(self.workdir, "run.files"))
        self.job_file = File(os.path.join(self.workdir, "job.sh"))
        self.log_file = File(os.path.join(self.workdir, "run.log"))
        self.stderr_file = File(os.path.join(self.workdir, "run.err"))
        self.start_lockfile = File(os.path.join(self.workdir, "__startlock__"))
        # This file is produced by Abinit if nprocs > 1 and MPI_ABORT.
        self.mpiabort_file = File(os.path.join(self.workdir, "__ABI_MPIABORTFILE__"))

        # Directories with input|output|temporary data.
        self.wdir = Directory(self.workdir)
        self.indir = Directory(os.path.join(self.workdir, "indata"))
        self.outdir = Directory(os.path.join(self.workdir, "outdata"))
        self.tmpdir = Directory(os.path.join(self.workdir, "tmpdata"))

        # stderr and output file of the queue manager. Note extensions.
        self.qerr_file = File(os.path.join(self.workdir, "queue.qerr"))
        self.qout_file = File(os.path.join(self.workdir, "queue.qout"))

Response: Set the working directory for this instance.


Instruction:
Can you create a Python 3 function that
sets the : class : Work associated to this Task.

Response:
def set_work(self, work):
        """Set the :class:`Work` associated to this `Task`."""
        if not hasattr(self, "_work"):
            self._work = work
        else:
            if self._work != work:
                raise ValueError("self._work != work")


Instruction:
Can you create a Python 3 function that
returns the position of the task in the flow.

Response:
def pos(self):
        """The position of the task in the :class:`Flow`"""
        for i, task in enumerate(self.work):
            if self == task:
                return self.work.pos, i
        raise ValueError("Cannot find the position of %s in flow %s" % (self, self.flow))


Instruction:
Write a Python 3 script for
setting the values of the ABINIT variables in the input file. Return dict with old values.

Response:
def set_vars(self, *args, **kwargs):
        """
        Set the values of the ABINIT variables in the input file. Return dict with old values.
        """
        kwargs.update(dict(*args))
        old_values = {vname: self.input.get(vname) for vname in kwargs}
        self.input.set_vars(**kwargs)
        if kwargs or old_values:
            self.history.info("Setting input variables: %s" % str(kwargs))
            self.history.info("Old values: %s" % str(old_values))

        return old_values


Instruction:
Write a Python 3 script to
construct the input file of the calculation.

Response:
def make_input(self, with_header=False):
        """Construct the input file of the calculation."""
        s = str(self.input)
        if with_header: s = str(self) + "\n" + s
        return s


Instruction:
Implement a function in Python 3 to
return the path of the input file with extension ext.

Response:
def ipath_from_ext(self, ext):
        """
        Returns the path of the input file with extension ext.
        Use it when the file does not exist yet.
        """
        return os.path.join(self.workdir, self.prefix.idata + "_" + ext)


Instruction:
Create a Python 3 function to
return the path of the output file with extension ext.

Response:
def opath_from_ext(self, ext):
        """
        Returns the path of the output file with extension ext.
        Use it when the file does not exist yet.
        """
        return os.path.join(self.workdir, self.prefix.odata + "_" + ext)


Instruction:
Write a Python 3 function that can
cancel the job. Returns 1 if the job was cancelled. Returns 0 if the job was cancelled. Returns 1 if the job was cancelled. Returns 0 if the job was not done. Returns 1 if the job was cancelled. Returns 0 if the job was not done. Returns 1 if the job was cancelled. Returns 0 if the job was not done.

Response:
def cancel(self):
        """Cancel the job. Returns 1 if job was cancelled."""
        if self.queue_id is None: return 0
        if self.status >= self.S_DONE: return 0

        exit_status = self.manager.cancel(self.queue_id)
        if exit_status != 0:
            logger.warning("manager.cancel returned exit_status: %s" % exit_status)
            return 0

        # Remove output files and reset the status.
        self.history.info("Job %s cancelled by user" % self.queue_id)
        self.reset()
        return 1


Instruction:
Write a Python 3 function for
disabling autoparal and force execution with mpi_procs MPI processes and omp_threads OpenMP threads. Useful for generating benchmarks.

Response:
def with_fixed_mpi_omp(self, mpi_procs, omp_threads):
        """
        Disable autoparal and force execution with `mpi_procs` MPI processes
        and `omp_threads` OpenMP threads. Useful for generating benchmarks.
        """
        manager = self.manager if hasattr(self, "manager") else self.flow.manager
        self.manager = manager.new_with_fixed_mpi_omp(mpi_procs, omp_threads)


Instruction:
Make a summary of the following Python 3 code
def fix_ofiles(self):
        filepaths = self.outdir.list_filepaths()
        #logger.info("in fix_ofiles with filepaths %s" % list(filepaths))

        old2new = FilepathFixer().fix_paths(filepaths)

        for old, new in old2new.items():
            self.history.info("will rename old %s to new %s" % (old, new))
            os.rename(old, new)

Response: This method is called when the task reaches S_OK. It will rename all of the files in the output directory to the new ones.


Instruction:
Create a Python 3 function for
calling by restart once the task has finished preparing the task for restarting.

Response:
def _restart(self, submit=True):
        """
        Called by restart once we have finished preparing the task for restarting.

        Return:
            True if task has been restarted
        """
        self.set_status(self.S_READY, msg="Restarted on %s" % time.asctime())

        # Increase the counter.
        self.num_restarts += 1
        self.history.info("Restarted, num_restarts %d" % self.num_restarts)

        # Reset datetimes
        self.datetimes.reset()

        # Remove the lock file
        self.start_lockfile.remove()

        if submit:
            # Relaunch the task.
            fired = self.start()
            if not fired: self.history.warning("Restart failed")
        else:
            fired = False

        return fired


Instruction:
Can you write a function in Python 3 where it
checks if child process has terminated. Set and return returncode attribute.

Response:
def poll(self):
        """Check if child process has terminated. Set and return returncode attribute."""
        self._returncode = self.process.poll()

        if self._returncode is not None:
            self.set_status(self.S_DONE, "status set to Done")

        return self._returncode


Instruction:
Can you generate the documentation for the following Python 3 function
def wait(self):
        self._returncode = self.process.wait()
        try:
            self.process.stderr.close()
        except:
            pass
        self.set_status(self.S_DONE, "status set to Done")

        return self._returncode

Response: Wait for child process to terminate. Set and return returncode attribute.


Instruction:
Write a Python 3 function for
interacting with process and return stdout and stderr data.

Response:
def communicate(self, input=None):
        """
        Interact with process: Send data to stdin. Read data from stdout and stderr, until end-of-file is reached.
        Wait for process to terminate. The optional input argument should be a string to be sent to the
        child process, or None, if no data should be sent to the child.

        communicate() returns a tuple (stdoutdata, stderrdata).
        """
        stdoutdata, stderrdata = self.process.communicate(input=input)
        self._returncode = self.process.returncode
        self.set_status(self.S_DONE, "status set to Done")

        return stdoutdata, stderrdata


Instruction:
Write a Python 3 script for
resetting the status of the current queue manager.

Response:
def reset(self):
        """
        Reset the task status. Mainly used if we made a silly mistake in the initial
        setup of the queue manager and we want to fix it and rerun the task.

        Returns:
            0 on success, 1 if reset failed.
        """
        # Can only reset tasks that are done.
        # One should be able to reset 'Submitted' tasks (sometimes, they are not in the queue
        # and we want to restart them)
        #if self.status != self.S_SUB and self.status < self.S_DONE: return 1

        # Remove output files otherwise the EventParser will think the job is still running
        self.output_file.remove()
        self.log_file.remove()
        self.stderr_file.remove()
        self.start_lockfile.remove()
        self.qerr_file.remove()
        self.qout_file.remove()
        if self.mpiabort_file.exists:
            self.mpiabort_file.remove()

        self.set_status(self.S_INIT, msg="Reset on %s" % time.asctime())
        self.num_restarts = 0
        self.set_qjob(None)

        # Reset finalized flags.
        self.work.finalized = False
        self.flow.finalized = False

        return 0


Instruction:
Make a summary of the following Python 3 code
def lock(self, source_node):
        if self.status != self.S_INIT:
            raise ValueError("Trying to lock a task with status %s" % self.status)

        self._status = self.S_LOCKED
        self.history.info("Locked by node %s", source_node)

Response: Lock the task, source is the :class:`Node` that applies the lock.


Instruction:
Write a Python 3 function for
unlocking the task and set its status to S_READY.

Response:
def unlock(self, source_node, check_status=True):
        """
        Unlock the task, set its status to `S_READY` so that the scheduler can submit it.
        source_node is the :class:`Node` that removed the lock
        Call task.check_status if check_status is True.
        """
        if self.status != self.S_LOCKED:
            raise RuntimeError("Trying to unlock a task with status %s" % self.status)

        self._status = self.S_READY
        if check_status: self.check_status()
        self.history.info("Unlocked by %s", source_node)


Instruction:
Can you generate the documentation for the following Python 3 function
def set_status(self, status, msg):
        # truncate string if it's long. msg will be logged in the object and we don't want to waste memory.
        if len(msg) > 2000:
            msg = msg[:2000]
            msg += "\n... snip ...\n"

        # Locked files must be explicitly unlocked
        if self.status == self.S_LOCKED or status == self.S_LOCKED:
            err_msg = (
                 "Locked files must be explicitly unlocked before calling set_status but\n"
                 "task.status = %s, input status = %s" % (self.status, status))
            raise RuntimeError(err_msg)

        status = Status.as_status(status)

        changed = True
        if hasattr(self, "_status"):
            changed = (status != self._status)

        self._status = status

        if status == self.S_RUN:
            # Set datetimes.start when the task enters S_RUN
            if self.datetimes.start is None:
                self.datetimes.start = datetime.datetime.now()

        # Add new entry to history only if the status has changed.
        if changed:
            if status == self.S_SUB:
                self.datetimes.submission = datetime.datetime.now()
                self.history.info("Submitted with MPI=%s, Omp=%s, Memproc=%.1f [Gb] %s " % (
                    self.mpi_procs, self.omp_threads, self.mem_per_proc.to("Gb"), msg))

            elif status == self.S_OK:
                self.history.info("Task completed %s", msg)

            elif status == self.S_ABICRITICAL:
                self.history.info("Status set to S_ABI_CRITICAL due to: %s", msg)

            else:
                self.history.info("Status changed to %s. msg: %s", status, msg)

        #######################################################
        # The section belows contains callbacks that should not
        # be executed if we are in spectator_mode
        #######################################################
        if status == self.S_DONE:
            # Execute the callback
            self._on_done()

        if status == self.S_OK:
            # Finalize the task.
            if not self.finalized:
                self._on_ok()

                # here we remove the output files of the task and of its parents.
                if self.gc is not None and self.gc.policy == "task":
                    self.clean_output_files()

            if self.status == self.S_OK:
                # Because _on_ok might have changed the status.
                self.send_signal(self.S_OK)

        return status

Response: Sets the status of the current task and returns the status of the task.


Instruction:
Here you have a function in Python 3, explain what it does
def check_status(self):
        # 1) see it the job is blocked
        # 2) see if an error occured at submitting the job the job was submitted, TODO these problems can be solved
        # 3) see if there is output
        # 4) see if abinit reports problems
        # 5) see if both err files exist and are empty
        # 6) no output and no err files, the job must still be running
        # 7) try to find out what caused the problems
        # 8) there is a problem but we did not figure out what ...
        # 9) the only way of landing here is if there is a output file but no err files...

        # 1) A locked task can only be unlocked by calling set_status explicitly.
        # an errored task, should not end up here but just to be sure
        black_list = (self.S_LOCKED, self.S_ERROR)
        #if self.status in black_list: return self.status

        # 2) Check the returncode of the job script
        if self.returncode != 0:
            msg = "job.sh return code: %s\nPerhaps the job was not submitted properly?" % self.returncode
            return self.set_status(self.S_QCRITICAL, msg=msg)

        # If we have an abort file produced by Abinit
        if self.mpiabort_file.exists:
            return self.set_status(self.S_ABICRITICAL, msg="Found ABINIT abort file")

        # Analyze the stderr file for Fortran runtime errors.
        # getsize is 0 if the file is empty or it does not exist.
        err_msg = None
        if self.stderr_file.getsize() != 0:
            err_msg = self.stderr_file.read()

        # Analyze the stderr file of the resource manager runtime errors.
        # TODO: Why are we looking for errors in queue.qerr?
        qerr_info = None
        if self.qerr_file.getsize() != 0:
            qerr_info = self.qerr_file.read()

        # Analyze the stdout file of the resource manager (needed for PBS !)
        qout_info = None
        if self.qout_file.getsize():
            qout_info = self.qout_file.read()

        # Start to check ABINIT status if the output file has been created.
        #if self.output_file.getsize() != 0:
        if self.output_file.exists:
            try:
                report = self.get_event_report()
            except Exception as exc:
                msg = "%s exception while parsing event_report:\n%s" % (self, exc)
                return self.set_status(self.S_ABICRITICAL, msg=msg)

            if report is None:
                return self.set_status(self.S_ERROR, msg="got None report!")

            if report.run_completed:
                # Here we  set the correct timing data reported by Abinit
                self.datetimes.start = report.start_datetime
                self.datetimes.end = report.end_datetime

                # Check if the calculation converged.
                not_ok = report.filter_types(self.CRITICAL_EVENTS)
                if not_ok:
                    return self.set_status(self.S_UNCONVERGED, msg='status set to unconverged based on abiout')
                else:
                    return self.set_status(self.S_OK, msg="status set to ok based on abiout")

            # Calculation still running or errors?
            if report.errors:
                # Abinit reported problems
                logger.debug('Found errors in report')
                for error in report.errors:
                    logger.debug(str(error))
                    try:
                        self.abi_errors.append(error)
                    except AttributeError:
                        self.abi_errors = [error]

                # The job is unfixable due to ABINIT errors
                logger.debug("%s: Found Errors or Bugs in ABINIT main output!" % self)
                msg = "\n".join(map(repr, report.errors))
                return self.set_status(self.S_ABICRITICAL, msg=msg)

            # 5)
            if self.stderr_file.exists and not err_msg:
                if self.qerr_file.exists and not qerr_info:
                    # there is output and no errors
                    # The job still seems to be running
                    return self.set_status(self.S_RUN, msg='there is output and no errors: job still seems to be running')

        # 6)
        if not self.output_file.exists:
            logger.debug("output_file does not exists")
            if not self.stderr_file.exists and not self.qerr_file.exists:
                # No output at allThe job is still in the queue.
                return self.status

        # 7) Analyze the files of the resource manager and abinit and execution err (mvs)
        # MG: This section has been disabled: several portability issues
        # Need more robust logic in error_parser, perhaps logic provided by users via callbacks.
        if False and (qerr_info or qout_info):
            from pymatgen.io.abinit.scheduler_error_parsers import get_parser
            scheduler_parser = get_parser(self.manager.qadapter.QTYPE, err_file=self.qerr_file.path,
                                          out_file=self.qout_file.path, run_err_file=self.stderr_file.path)

            if scheduler_parser is None:
                return self.set_status(self.S_QCRITICAL,
                                       msg="Cannot find scheduler_parser for qtype %s" % self.manager.qadapter.QTYPE)

            scheduler_parser.parse()

            if scheduler_parser.errors:
                # Store the queue errors in the task
                self.queue_errors = scheduler_parser.errors
                # The job is killed or crashed and we know what happened
                msg = "scheduler errors found:\n%s" % str(scheduler_parser.errors)
                return self.set_status(self.S_QCRITICAL, msg=msg)

            elif lennone(qerr_info) > 0:
                # if only qout_info, we are not necessarily in QCRITICAL state,
                # since there will always be info in the qout file
                self.history.info('Found unknown message in the queue qerr file: %s' % str(qerr_info))
                #try:
                #    rt = self.datetimes.get_runtime().seconds
                #except:
                #    rt = -1.0
                #tl = self.manager.qadapter.timelimit
                #if rt > tl:
                #    msg += 'set to error : runtime (%s) exceded walltime (%s)' % (rt, tl)
                #    print(msg)
                #    return self.set_status(self.S_ERROR, msg=msg)
                # The job may be killed or crashed but we don't know what happened
                # It may also be that an innocent message was written to qerr, so we wait for a while
                # it is set to QCritical, we will attempt to fix it by running on more resources

        # 8) analyzing the err files and abinit output did not identify a problem
        # but if the files are not empty we do have a problem but no way of solving it:
        # The job is killed or crashed but we don't know what happend
        # it is set to QCritical, we will attempt to fix it by running on more resources
        if err_msg:
            msg = 'Found error message:\n %s' % str(err_msg)
            self.history.warning(msg)
            #return self.set_status(self.S_QCRITICAL, msg=msg)

        # 9) if we still haven't returned there is no indication of any error and the job can only still be running
        # but we should actually never land here, or we have delays in the file system ....
        # print('the job still seems to be running maybe it is hanging without producing output... ')

        # Check time of last modification.
        if self.output_file.exists and \
           (time.time() - self.output_file.get_stat().st_mtime > self.manager.policy.frozen_timeout):
            msg = "Task seems to be frozen, last change more than %s [s] ago" % self.manager.policy.frozen_timeout
            return self.set_status(self.S_ERROR, msg=msg)

        # Handle weird case in which either run.abo, or run.log have not been produced
        #if self.status not in (self.S_INIT, self.S_READY) and (not self.output.file.exists or not self.log_file.exits):
        #    msg = "Task have been submitted but cannot find the log file or the output file"
        #    return self.set_status(self.S_ERROR, msg)

        return self.set_status(self.S_RUN, msg='final option: nothing seems to be wrong, the job must still be running')

Response: This function checks the status of the job and returns the status of the job.


Instruction:
Can you generate the documentation for the following Python 3 function
def out_to_in(self, out_file):
        in_file = os.path.basename(out_file).replace("out", "in", 1)
        dest = os.path.join(self.indir.path, in_file)

        if os.path.exists(dest) and not os.path.islink(dest):
            logger.warning("Will overwrite %s with %s" % (dest, out_file))

        os.rename(out_file, dest)
        return dest

Response: Move an output file to the output data directory of the Task and rename it so that ABINIT will read it as an input data file.


Instruction:
Write a Python 3 function for
linking the specified file to the destination file.

Response:
def inlink_file(self, filepath):
        """
        Create a symbolic link to the specified file in the
        directory containing the input files of the task.
        """
        if not os.path.exists(filepath):
            logger.debug("Creating symbolic link to not existent file %s" % filepath)

        # Extract the Abinit extension and add the prefix for input files.
        root, abiext = abi_splitext(filepath)

        infile = "in_" + abiext
        infile = self.indir.path_in(infile)

        # Link path to dest if dest link does not exist.
        # else check that it points to the expected file.
        self.history.info("Linking path %s --> %s" % (filepath, infile))

        if not os.path.exists(infile):
            os.symlink(filepath, infile)
        else:
            if os.path.realpath(infile) != filepath:
                raise self.Error("infile %s does not point to filepath %s" % (infile, filepath))


Instruction:
Create a Python 3 function for
creating symbolic links to the output files produced by other tasks.

Response:
def make_links(self):
        """
        Create symbolic links to the output files produced by the other tasks.

        .. warning::

            This method should be called only when the calculation is READY because
            it uses a heuristic approach to find the file to link.
        """
        for dep in self.deps:
            filepaths, exts = dep.get_filepaths_and_exts()

            for path, ext in zip(filepaths, exts):
                logger.info("Need path %s with ext %s" % (path, ext))
                dest = self.ipath_from_ext(ext)

                if not os.path.exists(path):
                    # Try netcdf file.
                    # TODO: this case should be treated in a cleaner way.
                    path += ".nc"
                    if os.path.exists(path): dest += ".nc"

                if not os.path.exists(path):
                    raise self.Error("%s: %s is needed by this task but it does not exist" % (self, path))

                if path.endswith(".nc") and not dest.endswith(".nc"): # NC --> NC file
                    dest += ".nc"

                # Link path to dest if dest link does not exist.
                # else check that it points to the expected file.
                logger.debug("Linking path %s --> %s" % (path, dest))
                if not os.path.exists(dest):
                    os.symlink(path, dest)
                else:
                    # check links but only if we haven't performed the restart.
                    # in this case, indeed we may have replaced the file pointer with the
                    # previous output file of the present task.
                    if os.path.realpath(dest) != path and self.num_restarts == 0:
                        raise self.Error("\nDestination:\n %s\ndoes not point to path:\n %s" % (dest, path))


Instruction:
Can you write a function in Python 3 where it
gets the event report for the given source.

Response:
def get_event_report(self, source="log"):
        """
        Analyzes the main logfile of the calculation for possible Errors or Warnings.
        If the ABINIT abort file is found, the error found in this file are added to
        the output report.

        Args:
            source: "output" for the main output file,"log" for the log file.

        Returns:
            :class:`EventReport` instance or None if the source file file does not exist.
        """
        # By default, we inspect the main log file.
        ofile = {
            "output": self.output_file,
            "log": self.log_file}[source]

        parser = events.EventsParser()

        if not ofile.exists:
            if not self.mpiabort_file.exists:
                return None
            else:
                # ABINIT abort file without log!
                abort_report = parser.parse(self.mpiabort_file.path)
                return abort_report

        try:
            report = parser.parse(ofile.path)
            #self._prev_reports[source] = report

            # Add events found in the ABI_MPIABORTFILE.
            if self.mpiabort_file.exists:
                logger.critical("Found ABI_MPIABORTFILE!!!!!")
                abort_report = parser.parse(self.mpiabort_file.path)
                if len(abort_report) != 1:
                    logger.critical("Found more than one event in ABI_MPIABORTFILE")

                # Weird case: empty abort file, let's skip the part
                # below and hope that the log file contains the error message.
                #if not len(abort_report): return report

                # Add it to the initial report only if it differs
                # from the last one found in the main log file.
                last_abort_event = abort_report[-1]
                if report and last_abort_event != report[-1]:
                    report.append(last_abort_event)
                else:
                    report.append(last_abort_event)

            return report

        #except parser.Error as exc:
        except Exception as exc:
            # Return a report with an error entry with info on the exception.
            msg = "%s: Exception while parsing ABINIT events:\n %s" % (ofile, str(exc))
            self.set_status(self.S_ABICRITICAL, msg=msg)
            return parser.report_exception(ofile.path, exc)


Instruction:
Write a Python 3 function that can
return a NodeResults instance.

Response:
def get_results(self, **kwargs):
        """
        Returns :class:`NodeResults` instance.
        Subclasses should extend this method (if needed) by adding
        specialized code that performs some kind of post-processing.
        """
        # Check whether the process completed.
        if self.returncode is None:
            raise self.Error("return code is None, you should call wait, communicate or poll")

        if self.status is None or self.status < self.S_DONE:
            raise self.Error("Task is not completed")

        return self.Results.from_node(self)


Instruction:
Create a Python 3 function for
renaming a file located in datadir.

Response:
def rename(self, src_basename, dest_basename, datadir="outdir"):
        """
        Rename a file located in datadir.

        src_basename and dest_basename are the basename of the source file
        and of the destination file, respectively.
        """
        directory = {
            "indir": self.indir,
            "outdir": self.outdir,
            "tmpdir": self.tmpdir,
        }[datadir]

        src = directory.path_in(src_basename)
        dest = directory.path_in(dest_basename)

        os.rename(src, dest)


Instruction:
Given the following Python 3 function, write the documentation
def build(self, *args, **kwargs):
        # Create dirs for input, output and tmp data.
        self.indir.makedirs()
        self.outdir.makedirs()
        self.tmpdir.makedirs()

        # Write files file and input file.
        if not self.files_file.exists:
            self.files_file.write(self.filesfile_string)

        self.input_file.write(self.make_input())
        self.manager.write_jobfile(self)

Response: Creates the working directory and the input files of the Task.


Instruction:
Can you generate a brief explanation for the following Python 3 code
def remove_files(self, *filenames):
        filenames = list_strings(filenames)

        for dirpath, dirnames, fnames in os.walk(self.workdir):
            for fname in fnames:
                if fname in filenames:
                    filepath = os.path.join(dirpath, fname)
                    os.remove(filepath)

Response: Remove all the files listed in filenames.


Instruction:
Explain what the following Python 3 code does
def clean_output_files(self, follow_parents=True):
        paths = []
        if self.status != self.S_OK:
            logger.warning("Calling task.clean_output_files on a task whose status != S_OK")

        # Remove all files in tmpdir.
        self.tmpdir.clean()

        # Find the file extensions that should be preserved since these files are still
        # needed by the children who haven't reached S_OK
        except_exts = set()
        for child in self.get_children():
            if child.status == self.S_OK: continue
            # Find the position of self in child.deps and add the extensions.
            i = [dep.node for dep in child.deps].index(self)
            except_exts.update(child.deps[i].exts)

        # Remove the files in the outdir of the task but keep except_exts.
        exts = self.gc.exts.difference(except_exts)
        #print("Will remove its extensions: ", exts)
        paths += self.outdir.remove_exts(exts)
        if not follow_parents: return paths

        # Remove the files in the outdir of my parents if all the possible dependencies have been fulfilled.
        for parent in self.get_parents():

            # Here we build a dictionary file extension --> list of child nodes requiring this file from parent
            # e.g {"WFK": [node1, node2]}
            ext2nodes = collections.defaultdict(list)
            for child in parent.get_children():
                if child.status == child.S_OK: continue
                i = [d.node for d in child.deps].index(parent)
                for ext in child.deps[i].exts:
                    ext2nodes[ext].append(child)

            # Remove extension only if no node depends on it!
            except_exts = [k for k, lst in ext2nodes.items() if lst]
            exts = self.gc.exts.difference(except_exts)
            #print("%s removes extensions %s from parent node %s" % (self, exts, parent))
            paths += parent.outdir.remove_exts(exts)

        self.history.info("Removed files: %s" % paths)
        return paths

Response: This method removes all the output files that are needed by the task and all its children.


Instruction:
Given the following Python 3 function, write the documentation
def start(self, **kwargs):
        if self.status >= self.S_SUB:
            raise self.Error("Task status: %s" % str(self.status))

        if self.start_lockfile.exists:
            self.history.warning("Found lock file: %s" % self.start_lockfile.path)
            return 0

        self.start_lockfile.write("Started on %s" % time.asctime())

        self.build()
        self._setup()

        # Add the variables needed to connect the node.
        for d in self.deps:
            cvars = d.connecting_vars()
            self.history.info("Adding connecting vars %s" % cvars)
            self.set_vars(cvars)

            # Get (python) data from other nodes
            d.apply_getters(self)

        # Automatic parallelization
        if kwargs.pop("autoparal", True) and hasattr(self, "autoparal_run"):
            try:
                self.autoparal_run()
            #except QueueAdapterError as exc:
            #    # If autoparal cannot find a qadapter to run the calculation raises an Exception
            #    self.history.critical(exc)
            #    msg = "Error while trying to run autoparal in task:%s\n%s" % (repr(task), straceback())
            #    cprint(msg, "yellow")
            #    self.set_status(self.S_QCRITICAL, msg=msg)
            #    return 0
            except Exception as exc:
                # Sometimes autoparal_run fails because Abinit aborts
                # at the level of the parser e.g. cannot find the spacegroup
                # due to some numerical noise in the structure.
                # In this case we call fix_abicritical and then we try to run autoparal again.
                self.history.critical("First call to autoparal failed with `%s`. Will try fix_abicritical" % exc)
                msg = "autoparal_fake_run raised:\n%s" % straceback()
                logger.critical(msg)

                fixed = self.fix_abicritical()
                if not fixed:
                    self.set_status(self.S_ABICRITICAL, msg="fix_abicritical could not solve the problem")
                    return 0

                try:
                    self.autoparal_run()
                    self.history.info("Second call to autoparal succeeded!")
                    #cprint("Second call to autoparal succeeded!", "green")

                except Exception as exc:
                    self.history.critical("Second call to autoparal failed with %s. Cannot recover!", exc)
                    msg = "Tried autoparal again but got:\n%s" % straceback()
                    cprint(msg, "red")
                    self.set_status(self.S_ABICRITICAL, msg=msg)
                    return 0

        # Start the calculation in a subprocess and return.
        self._process = self.manager.launch(self, **kwargs)
        return 1

Response: Starts the calculation by performing the necessary steps.


Instruction:
Can you generate the documentation for the following Python 3 function
def start_and_wait(self, *args, **kwargs):
        self.start(*args, **kwargs)
        retcode = self.wait()
        return retcode

Response: Start the task and wait for completion.


Instruction:
Make a summary of the following Python 3 code
def get_graphviz(self, engine="automatic", graph_attr=None, node_attr=None, edge_attr=None):
        # https://www.graphviz.org/doc/info/
        from graphviz import Digraph
        fg = Digraph("task", # filename="task_%s.gv" % os.path.basename(self.workdir),
            engine="dot" if engine == "automatic" else engine)

        # Set graph attributes.
        #fg.attr(label="%s@%s" % (self.__class__.__name__, self.relworkdir))
        fg.attr(label=repr(self))
        #fg.attr(fontcolor="white", bgcolor='purple:pink')
        #fg.attr(rankdir="LR", pagedir="BL")
        #fg.attr(constraint="false", pack="true", packMode="clust")
        fg.node_attr.update(color='lightblue2', style='filled')

        # Add input attributes.
        if graph_attr is not None:
            fg.graph_attr.update(**graph_attr)
        if node_attr is not None:
            fg.node_attr.update(**node_attr)
        if edge_attr is not None:
            fg.edge_attr.update(**edge_attr)

        def node_kwargs(node):
            return dict(
                #shape="circle",
                color=node.color_hex,
                label=(str(node) if not hasattr(node, "pos_str") else
                    node.pos_str + "\n" + node.__class__.__name__),
            )

        edge_kwargs = dict(arrowType="vee", style="solid")
        cluster_kwargs = dict(rankdir="LR", pagedir="BL", style="rounded", bgcolor="azure2")

        # Build cluster with tasks.
        cluster_name = "cluster%s" % self.work.name
        with fg.subgraph(name=cluster_name) as wg:
            wg.attr(**cluster_kwargs)
            wg.attr(label="%s (%s)" % (self.__class__.__name__, self.name))
            wg.node(self.name, **node_kwargs(self))

            # Connect task to children.
            for child in self.get_children():
                # Test if child is in the same work.
                myg = wg if child in self.work else fg
                myg.node(child.name, **node_kwargs(child))
                # Find file extensions required by this task
                i = [dep.node for dep in child.deps].index(self)
                edge_label = "+".join(child.deps[i].exts)
                myg.edge(self.name, child.name, label=edge_label, color=self.color_hex,
                         **edge_kwargs)

            # Connect task to parents
            for parent in self.get_parents():
                # Test if parent is in the same work.
                myg = wg if parent in self.work else fg
                myg.node(parent.name, **node_kwargs(parent))
                # Find file extensions required by self (task)
                i = [dep.node for dep in self.deps].index(parent)
                edge_label = "+".join(self.deps[i].exts)
                myg.edge(parent.name, self.name, label=edge_label, color=parent.color_hex,
                         **edge_kwargs)

        # Treat the case in which we have a work producing output for other tasks.
        #for work in self:
        #    children = work.get_children()
        #    if not children: continue
        #    cluster_name = "cluster%s" % work.name
        #    seen = set()
        #    for child in children:
        #        # This is not needed, too much confusing
        #        #fg.edge(cluster_name, child.name, color=work.color_hex, **edge_kwargs)
        #        # Find file extensions required by work
        #        i = [dep.node for dep in child.deps].index(work)
        #        for ext in child.deps[i].exts:
        #            out = "%s (%s)" % (ext, work.name)
        #            fg.node(out)
        #            fg.edge(out, child.name, **edge_kwargs)
        #            key = (cluster_name, out)
        #            if key not in seen:
        #                fg.edge(cluster_name, out, color=work.color_hex, **edge_kwargs)
        #                seen.add(key)

        return fg

Response: Generate a task graph in the DOT language.


Instruction:
Implement a function in Python 3 to
create an instance of AbinitTask from an input.

Response:
def from_input(cls, input, workdir=None, manager=None):
        """
        Create an instance of `AbinitTask` from an ABINIT input.

        Args:
            ainput: `AbinitInput` object.
            workdir: Path to the working directory.
            manager: :class:`TaskManager` object.
        """
        return cls(input, workdir=workdir, manager=manager)


Instruction:
Write a Python 3 script to
build a Task with a temporary workdir.

Response:
def temp_shell_task(cls, inp, mpi_procs=1, workdir=None, manager=None):
        """
        Build a Task with a temporary workdir. The task is executed via the shell with 1 MPI proc.
        Mainly used for invoking Abinit to get important parameters needed to prepare the real task.

        Args:
            mpi_procs: Number of MPI processes to use.
        """
        # Build a simple manager to run the job in a shell subprocess
        import tempfile
        workdir = tempfile.mkdtemp() if workdir is None else workdir
        if manager is None: manager = TaskManager.from_user_config()

        # Construct the task and run it
        task = cls.from_input(inp, workdir=workdir, manager=manager.to_shell_manager(mpi_procs=mpi_procs))
        task.set_name('temp_shell_task')
        return task


Instruction:
Given the following Python 3 function, write the documentation
def setup(self):
        def rename_file(afile):
            """Helper function to rename :class:`File` objects. Return string for logging purpose."""
            # Find the index of the last file (if any).
            # TODO: Maybe it's better to use run.abo --> run(1).abo
            fnames = [f for f in os.listdir(self.workdir) if f.startswith(afile.basename)]
            nums = [int(f) for f in [f.split("_")[-1] for f in fnames] if f.isdigit()]
            last = max(nums) if nums else 0
            new_path = afile.path + "_" + str(last+1)

            os.rename(afile.path, new_path)
            return "Will rename %s to %s" % (afile.path, new_path)

        logs = []
        if self.output_file.exists: logs.append(rename_file(self.output_file))
        if self.log_file.exists: logs.append(rename_file(self.log_file))

        if logs:
            self.history.info("\n".join(logs))

Response: This function is called by Abinit when the application is ready to start the process.


Instruction:
Make a summary of the following Python 3 code
def cycle_class(self):
        if isinstance(self, RelaxTask):
            return abiinspect.Relaxation
        elif isinstance(self, GsTask):
            return abiinspect.GroundStateScfCycle
        elif self.is_dfpt_task:
            return abiinspect.D2DEScfCycle

        return None

Response: Returns the subclass of ScfCycle associated to the task or None if no SCF algorithm is associated to the task.


Instruction:
Write a Python 3 script for
returning a string with the list of files and prefixes needed to execute ABINIT.

Response:
def filesfile_string(self):
        """String with the list of files and prefixes needed to execute ABINIT."""
        lines = []
        app = lines.append
        pj = os.path.join

        app(self.input_file.path)                 # Path to the input file
        app(self.output_file.path)                # Path to the output file
        app(pj(self.workdir, self.prefix.idata))  # Prefix for input data
        app(pj(self.workdir, self.prefix.odata))  # Prefix for output data
        app(pj(self.workdir, self.prefix.tdata))  # Prefix for temporary data

        # Paths to the pseudopotential files.
        # Note that here the pseudos **must** be sorted according to znucl.
        # Here we reorder the pseudos if the order is wrong.
        ord_pseudos = []

        znucl = [specie.number for specie in
                 self.input.structure.types_of_specie]

        for z in znucl:
            for p in self.pseudos:
                if p.Z == z:
                    ord_pseudos.append(p)
                    break
            else:
                raise ValueError("Cannot find pseudo with znucl %s in pseudos:\n%s" % (z, self.pseudos))

        for pseudo in ord_pseudos:
            app(pseudo.path)

        return "\n".join(lines)


Instruction:
Implement a function in Python 3 to
true if the task is a GS Task and uses paral_kgb with the given value.

Response:
def uses_paral_kgb(self, value=1):
        """True if the task is a GS Task and uses paral_kgb with the given value."""
        paral_kgb = self.get_inpvar("paral_kgb", 0)
        # paral_kgb is used only in the GS part.
        return paral_kgb == value and isinstance(self, GsTask)


Instruction:
Can you write a function in Python 3 where it
changes the input structure.

Response:
def _change_structure(self, new_structure):
        """Change the input structure."""
        # Compare new and old structure for logging purpose.
        # TODO: Write method of structure to compare self and other and return a dictionary
        old_structure = self.input.structure
        old_lattice = old_structure.lattice

        abc_diff = np.array(new_structure.lattice.abc) - np.array(old_lattice.abc)
        angles_diff = np.array(new_structure.lattice.angles) - np.array(old_lattice.angles)
        cart_diff = new_structure.cart_coords - old_structure.cart_coords
        displs = np.array([np.sqrt(np.dot(v, v)) for v in cart_diff])

        recs, tol_angle, tol_length = [], 10**-2, 10**-5

        if np.any(np.abs(angles_diff) > tol_angle):
            recs.append("new_agles - old_angles = %s" % angles_diff)

        if np.any(np.abs(abc_diff) > tol_length):
            recs.append("new_abc - old_abc = %s" % abc_diff)

        if np.any(np.abs(displs) > tol_length):
            min_pos, max_pos = displs.argmin(), displs.argmax()
            recs.append("Mean displ: %.2E, Max_displ: %.2E (site %d), min_displ: %.2E (site %d)" %
                (displs.mean(), displs[max_pos], max_pos, displs[min_pos], min_pos))

        self.history.info("Changing structure (only significant diffs are shown):")
        if not recs:
            self.history.info("Input and output structure seems to be equal within the given tolerances")
        else:
            for rec in recs:
                self.history.info(rec)

        self.input.set_structure(new_structure)


Instruction:
Write a Python 3 function that can
find an optimal set of parameters for the execution of the task This method can change the ABINIT input variables and/or the submission parameters e.g. the number of CPUs for MPI and OpenMp. Set: self.pconfs where pconfs is a :class:`ParalHints` object with the configuration reported by autoparal and optimal is the optimal configuration selected. Returns 0 if success

Response:
def autoparal_run(self):
        """
        Find an optimal set of parameters for the execution of the task
        This method can change the ABINIT input variables and/or the
        submission parameters e.g. the number of CPUs for MPI and OpenMp.

        Set:
           self.pconfs where pconfs is a :class:`ParalHints` object with the configuration reported by
           autoparal and optimal is the optimal configuration selected.
           Returns 0 if success
        """
        policy = self.manager.policy

        if policy.autoparal == 0: # or policy.max_ncpus in [None, 1]:
            logger.info("Nothing to do in autoparal, returning (None, None)")
            return 0

        if policy.autoparal != 1:
            raise NotImplementedError("autoparal != 1")

        ############################################################################
        # Run ABINIT in sequential to get the possible configurations with max_ncpus
        ############################################################################

        # Set the variables for automatic parallelization
        # Will get all the possible configurations up to max_ncpus
        # Return immediately if max_ncpus == 1
        max_ncpus = self.manager.max_cores
        if max_ncpus == 1: return 0

        autoparal_vars = dict(autoparal=policy.autoparal, max_ncpus=max_ncpus, mem_test=0)
        self.set_vars(autoparal_vars)

        # Run the job in a shell subprocess with mpi_procs = 1
        # we don't want to make a request to the queue manager for this simple job!
        # Return code is always != 0
        process = self.manager.to_shell_manager(mpi_procs=1).launch(self)
        self.history.pop()
        retcode = process.wait()
        # To avoid: ResourceWarning: unclosed file <_io.BufferedReader name=87> in py3k
        process.stderr.close()
        #process.stdout.close()

        # Remove the variables added for the automatic parallelization
        self.input.remove_vars(list(autoparal_vars.keys()))

        ##############################################################
        # Parse the autoparal configurations from the main output file
        ##############################################################
        parser = ParalHintsParser()
        try:
            pconfs = parser.parse(self.output_file.path)
        except parser.Error:
            # In principle Abinit should have written a complete log file
            # because we called .wait() but sometimes the Yaml doc is incomplete and
            # the parser raises. Let's wait 5 secs and then try again.
            time.sleep(5)
            try:
                pconfs = parser.parse(self.output_file.path)
            except parser.Error:
                logger.critical("Error while parsing Autoparal section:\n%s" % straceback())
                return 2

        ######################################################
        # Select the optimal configuration according to policy
        ######################################################
        optconf = self.find_optconf(pconfs)

        ####################################################
        # Change the input file and/or the submission script
        ####################################################
        self.set_vars(optconf.vars)

        # Write autoparal configurations to JSON file.
        d = pconfs.as_dict()
        d["optimal_conf"] = optconf
        json_pretty_dump(d, os.path.join(self.workdir, "autoparal.json"))

        ##############
        # Finalization
        ##############
        # Reset the status, remove garbage files ...
        self.set_status(self.S_INIT, msg='finished autoparal run')

        # Remove the output file since Abinit likes to create new files
        # with extension .outA, .outB if the file already exists.
        os.remove(self.output_file.path)
        os.remove(self.log_file.path)
        os.remove(self.stderr_file.path)

        return 0


Instruction:
Implement a function in Python 3 to
find the optimal Parallel configuration.

Response:
def find_optconf(self, pconfs):
        """Find the optimal Parallel configuration."""
        # Save pconfs for future reference.
        self.set_pconfs(pconfs)

        # Select the partition on which we'll be running and set MPI/OMP cores.
        optconf = self.manager.select_qadapter(pconfs)
        return optconf


Instruction:
Explain what the following Python 3 code does
def fix_abicritical(self):
        event_handlers = self.event_handlers
        if not event_handlers:
            self.set_status(status=self.S_ERROR, msg='Empty list of event handlers. Cannot fix abi_critical errors')
            return 0

        count, done = 0, len(event_handlers) * [0]

        report = self.get_event_report()
        if report is None:
            self.set_status(status=self.S_ERROR, msg='get_event_report returned None')
            return 0

        # Note we have loop over all possible events (slow, I know)
        # because we can have handlers for Error, Bug or Warning
        # (ideally only for CriticalWarnings but this is not done yet)
        for event in report:
            for i, handler in enumerate(self.event_handlers):

                if handler.can_handle(event) and not done[i]:
                    logger.info("handler %s will try to fix event %s" % (handler, event))
                    try:
                        d = handler.handle_task_event(self, event)
                        if d:
                            done[i] += 1
                            count += 1

                    except Exception as exc:
                        logger.critical(str(exc))

        if count:
            self.reset_from_scratch()
            return 1

        self.set_status(status=self.S_ERROR, msg='We encountered AbiCritical events that could not be fixed')
        return 0

Response:
method to fix crashes and error caused by abinit
            returns 1 if task has been fixed else 0


Instruction:
Create a Python 3 function to
parse the timer data in the main output file of Abinit.

Response:
def parse_timing(self):
        """
        Parse the timer data in the main output file of Abinit.
        Requires timopt /= 0 in the input file (usually timopt = -1)

        Return: :class:`AbinitTimerParser` instance, None if error.
        """
        from .abitimer import AbinitTimerParser
        parser = AbinitTimerParser()
        read_ok = parser.parse(self.output_file.path)
        if read_ok:
            return parser
        return None


Instruction:
Create a Python 3 function for
opening the HIST file located in the in self. outdir. Returns None if file could not be opened.

Response:
def open_hist(self):
        """
        Open the HIST file located in the in self.outdir.
        Returns :class:`HistFile` object, None if file could not be found or file is not readable.
        """
        if not self.hist_path:
            if self.status == self.S_OK:
                logger.critical("%s reached S_OK but didn't produce a HIST file in %s" % (self, self.outdir))
            return None

        # Open the HIST file
        from abipy.dynamics.hist import HistFile
        try:
            return HistFile(self.hist_path)
        except Exception as exc:
            logger.critical("Exception while reading HIST file at %s:\n%s" % (self.hist_path, str(exc)))
            return None


Instruction:
Can you generate the documentation for the following Python 3 function
def open_gsr(self):
        gsr_path = self.gsr_path
        if not gsr_path:
            if self.status == self.S_OK:
                logger.critical("%s reached S_OK but didn't produce a GSR file in %s" % (self, self.outdir))
            return None

        # Open the GSR file.
        from abipy.electrons.gsr import GsrFile
        try:
            return GsrFile(gsr_path)
        except Exception as exc:
            logger.critical("Exception while reading GSR file at %s:\n%s" % (gsr_path, str(exc)))
            return None

Response: Open the GSR file located in the in self. outdir. Returns None if file could not be opened.


Instruction:
Here you have a function in Python 3, explain what it does
def inspect(self, **kwargs):
        try:
            scf_cycle = abiinspect.GroundStateScfCycle.from_file(self.output_file.path)
        except IOError:
            return None

        if scf_cycle is not None:
            if "title" not in kwargs: kwargs["title"] = str(self)
            return scf_cycle.plot(**kwargs)

        return None

Response: Plot the SCF cycle results with matplotlib.


Instruction:
Write a Python 3 script to
set up the NSCF calculations for this task.

Response:
def setup(self):
        """
        NSCF calculations should use the same FFT mesh as the one employed in the GS task
        (in principle, it's possible to interpolate inside Abinit but tests revealed some numerical noise
        Here we change the input file of the NSCF task to have the same FFT mesh.
        """
        for dep in self.deps:
            if "DEN" in dep.exts:
                parent_task = dep.node
                break
        else:
            raise RuntimeError("Cannot find parent node producing DEN file")

        with parent_task.open_gsr() as gsr:
            den_mesh = 3 * [None]
            den_mesh[0] = gsr.reader.read_dimvalue("number_of_grid_points_vector1")
            den_mesh[1] = gsr.reader.read_dimvalue("number_of_grid_points_vector2")
            den_mesh[2] = gsr.reader.read_dimvalue("number_of_grid_points_vector3")
            if self.ispaw:
                self.set_vars(ngfftdg=den_mesh)
            else:
                self.set_vars(ngfft=den_mesh)

        super().setup()


Instruction:
Can you generate a brief explanation for the following Python 3 code
def restart(self):
        restart_file = None

        # Try to restart from the WFK file if possible.
        # FIXME: This part has been disabled because WFK=IO is a mess if paral_kgb == 1
        # This is also the reason why I wrote my own MPI-IO code for the GW part!
        wfk_file = self.outdir.has_abiext("WFK")
        if False and wfk_file:
            irdvars = irdvars_for_ext("WFK")
            restart_file = self.out_to_in(wfk_file)

        # Fallback to DEN file. Note that here we look for out_DEN instead of out_TIM?_DEN
        # This happens when the previous run completed and task.on_done has been performed.
        # ********************************************************************************
        # Note that it's possible to have an undetected error if we have multiple restarts
        # and the last relax died badly. In this case indeed out_DEN is the file produced
        # by the last run that has executed on_done.
        # ********************************************************************************
        if restart_file is None:
            for ext in ("", ".nc"):
                out_den = self.outdir.path_in("out_DEN" + ext)
                if os.path.exists(out_den):
                    irdvars = irdvars_for_ext("DEN")
                    restart_file = self.out_to_in(out_den)
                    break

        if restart_file is None:
            # Try to restart from the last TIM?_DEN file.
            # This should happen if the previous run didn't complete in clean way.
            # Find the last TIM?_DEN file.
            last_timden = self.outdir.find_last_timden_file()
            if last_timden is not None:
                if last_timden.path.endswith(".nc"):
                    ofile = self.outdir.path_in("out_DEN.nc")
                else:
                    ofile = self.outdir.path_in("out_DEN")
                os.rename(last_timden.path, ofile)
                restart_file = self.out_to_in(ofile)
                irdvars = irdvars_for_ext("DEN")

        if restart_file is None:
            # Don't raise RestartError as we can still change the structure.
            self.history.warning("Cannot find the WFK|DEN|TIM?_DEN file to restart from.")
        else:
            # Add the appropriate variable for restarting.
            self.set_vars(irdvars)
            self.history.info("Will restart from %s", restart_file)

        # FIXME Here we should read the HIST file but restartxf if broken!
        #self.set_vars({"restartxf": -1})

        # Read the relaxed structure from the GSR file and change the input.
        self._change_structure(self.get_final_structure())

        # Now we can resubmit the job.
        return self._restart()

Response: Restart the structure relaxation for the current entry.


Instruction:
Write a Python 3 script to
plot the evolution of the structural relaxation with matplotlib.

Response:
def inspect(self, **kwargs):
        """
        Plot the evolution of the structural relaxation with matplotlib.

        Args:
            what: Either "hist" or "scf". The first option (default) extracts data
                from the HIST file and plot the evolution of the structural
                parameters, forces, pressures and energies.
                The second option, extracts data from the main output file and
                plot the evolution of the SCF cycles (etotal, residuals, etc).

        Returns:
            `matplotlib` figure, None if some error occurred.
        """
        what = kwargs.pop("what", "hist")

        if what == "hist":
            # Read the hist file to get access to the structure.
            with self.open_hist() as hist:
                return hist.plot(**kwargs) if hist else None

        elif what == "scf":
            # Get info on the different SCF cycles
            relaxation = abiinspect.Relaxation.from_file(self.output_file.path)
            if "title" not in kwargs: kwargs["title"] = str(self)
            return relaxation.plot(**kwargs) if relaxation is not None else None

        else:
            raise ValueError("Wrong value for what %s" % what)


Instruction:
Can you tell what is the following Python 3 function doing
def fix_ofiles(self):
        super().fix_ofiles()

        # Find the last TIM?_DEN file.
        last_timden = self.outdir.find_last_timden_file()
        if last_timden is None:
            logger.warning("Cannot find TIM?_DEN files")
            return

        # Rename last TIMDEN with out_DEN.
        ofile = self.outdir.path_in("out_DEN")
        if last_timden.path.endswith(".nc"): ofile += ".nc"
        self.history.info("Renaming last_denfile %s --> %s" % (last_timden.path, ofile))
        os.rename(last_timden.path, ofile)

Response: Fixes the file names in the out_DEN file and the TIM1_DEN file.


Instruction:
Can you generate the documentation for the following Python 3 function
def make_links(self):
        for dep in self.deps:
            for d in dep.exts:

                if d == "DDK":
                    ddk_task = dep.node
                    out_ddk = ddk_task.outdir.has_abiext("DDK")
                    if not out_ddk:
                        raise RuntimeError("%s didn't produce the DDK file" % ddk_task)

                    # Get (fortran) idir and costruct the name of the 1WF expected by Abinit
                    rfdir = list(ddk_task.input["rfdir"])
                    if rfdir.count(1) != 1:
                        raise RuntimeError("Only one direction should be specifned in rfdir but rfdir = %s" % rfdir)

                    idir = rfdir.index(1) + 1
                    ddk_case = idir + 3 * len(ddk_task.input.structure)

                    infile = self.indir.path_in("in_1WF%d" % ddk_case)
                    os.symlink(out_ddk, infile)

                elif d in ("WFK", "WFQ"):
                    gs_task = dep.node
                    out_wfk = gs_task.outdir.has_abiext(d)
                    if not out_wfk:
                        raise RuntimeError("%s didn't produce the %s file" % (gs_task, d))

                    if d == "WFK":
                        bname = "in_WFK"
                    elif d == "WFQ":
                        bname = "in_WFQ"
                    else:
                        raise ValueError("Don't know how to handle `%s`" % d)

                    if not os.path.exists(self.indir.path_in(bname)):
                            os.symlink(out_wfk, self.indir.path_in(bname))

                elif d == "DEN":
                    gs_task = dep.node
                    out_wfk = gs_task.outdir.has_abiext("DEN")
                    if not out_wfk:
                        raise RuntimeError("%s didn't produce the DEN file" % gs_task)
                    if not os.path.exists(self.indir.path_in("in_DEN")):
                        os.symlink(out_wfk, self.indir.path_in("in_DEN"))

                elif d == "1WF":
                    gs_task = dep.node
                    out_wfk = gs_task.outdir.has_abiext("1WF")
                    if not out_wfk:
                        raise RuntimeError("%s didn't produce the 1WF file" % gs_task)
                    dest = self.indir.path_in("in_" + out_wfk.split("_")[-1])
                    if not os.path.exists(dest):
                        os.symlink(out_wfk, dest)

                elif d == "1DEN":
                    gs_task = dep.node
                    out_wfk = gs_task.outdir.has_abiext("DEN")
                    if not out_wfk:
                        raise RuntimeError("%s didn't produce the 1DEN file" % gs_task)
                    dest = self.indir.path_in("in_" + out_wfk.split("_")[-1])
                    if not os.path.exists(dest):
                        os.symlink(out_wfk, dest)

                else:
                    raise ValueError("Don't know how to handle extension: %s" % str(dep.exts))

Response: Replace the default behaviour of make_links. More specifically this method is used to connect DFPT calculation to DDK files.


Instruction:
Implement a Python 3 function for
restarting the wavefunctions and density files.

Response:
def restart(self):
        """
        DFPT calculations can be restarted only if we have the 1WF file or the 1DEN file.
        from which we can read the first-order wavefunctions or the first order density.
        Prefer 1WF over 1DEN since we can reuse the wavefunctions.
        """
        # Abinit adds the idir-ipert index at the end of the file and this breaks the extension
        # e.g. out_1WF4, out_DEN4. find_1wf_files and find_1den_files returns the list of files found
        restart_file, irdvars = None, None

        # Highest priority to the 1WF file because restart is more efficient.
        wf_files = self.outdir.find_1wf_files()
        if wf_files is not None:
            restart_file = wf_files[0].path
            irdvars = irdvars_for_ext("1WF")
            if len(wf_files) != 1:
                restart_file = None
                self.history.critical("Found more than one 1WF file in outdir. Restart is ambiguous!")

        if restart_file is None:
            den_files = self.outdir.find_1den_files()
            if den_files is not None:
                restart_file = den_files[0].path
                irdvars = {"ird1den": 1}
                if len(den_files) != 1:
                    restart_file = None
                    self.history.critical("Found more than one 1DEN file in outdir. Restart is ambiguous!")

        if restart_file is None:
            # Raise because otherwise restart is equivalent to a run from scratch --> infinite loop!
            raise self.RestartError("%s: Cannot find the 1WF|1DEN file to restart from." % self)

        # Move file.
        self.history.info("Will restart from %s", restart_file)
        restart_file = self.out_to_in(restart_file)

        # Add the appropriate variable for restarting.
        self.set_vars(irdvars)

        # Now we can resubmit the job.
        return self._restart()