Espresso: streamline file copying / additional recipes (#1974)

## Summary of Changes

This pull request introduces several improvements and new features to
Quacc Espresso, enhancing the user experience and expanding its
capabilities:

**Streamlined Input/Output Naming:**

- Quacc Espresso now enforces predefined names for **all** input and
output files removing the little freedom users had for this. This
ensures consistency across different calculations and reduce the
potential for errors.

**Intelligent File Copying:**

- When users provide a prev_dir argument, Quacc will now determines
which files to copy based on the binary and input data. This will reduce
the amount of data being copied overall, I think this was one of your
suggestions on a previous merge request.

**New Recipes for Electron-Phonon Calculations:**

- Two new recipes have been added to perform electron-phonon
calculations and Fourier interpolation of the phonon potential. It's a
little step toward future compatibility with codes such as EPW.

Some tests have been modified to be more robust, some internal functions
have been modified as well.

note to self: the two recipes have to be added to the list of recipes

### Checklist

- [ ] I have read the ["Guidelines"
section](https://quantum-accelerators.github.io/quacc/dev/contributing.html#guidelines)
of the contributing guide. Don't lie! 😉
- [ ] My PR is on a custom branch and is _not_ named `main`.
- [ ] I have added relevant, comprehensive [unit
tests](https://quantum-accelerators.github.io/quacc/dev/contributing.html#unit-tests).

### Notes

- Your PR will likely not be merged without proper and thorough tests.
- If you are an external contributor, you will see a comment from
[@buildbot-princeton](https://github.com/buildbot-princeton). This is
solely for the maintainers.
- When your code is ready for review, ping one of the [active
maintainers](https://quantum-accelerators.github.io/quacc/about/contributors.html#active-maintainers).

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Andrew S. Rosen <asrosen93@gmail.com>

docs/user/recipes/recipes_list.md

@@ -197,9 +197,11 @@ The list of available quacc recipes is shown below. The "Req'd Extras" column sp
 | Espresso Post Processing | `#!Python @job`  | [quacc.recipes.espresso.core.post_processing_job][] |              |
 | Espresso Phonon          | `#!Python @job`  | [quacc.recipes.espresso.phonons.phonon_job][]       |              |
 | Espresso Grid Phonon     | `#!Python @flow` | [quacc.recipes.espresso.phonons.grid_phonon_flow][] |              |
-| Espresso q2r             | `#!Python @job`  | [quacc.recipes.espresso.phonons.q2r_job][]          |              |
-| Espresso matdyn          | `#!Python @job`  | [quacc.recipes.espresso.phonons.matdyn_job][]       |              |
+| Espresso Q2R             | `#!Python @job`  | [quacc.recipes.espresso.phonons.q2r_job][]          |              |
+| Espresso Matdyn          | `#!Python @job`  | [quacc.recipes.espresso.phonons.matdyn_job][]       |              |
 | Espresso Phonon DOS Flow | `#!Python @flow` | [quacc.recipes.espresso.phonons.phonon_dos_flow][]  |              |
+| Espresso DVSCF Q2R       | `#!Python @job`  | [quacc.recipes.espresso.phonons.dvscf_q2r_job][]    |              |
+| Espresso PostAHC         | `#!Python @job`  | [quacc.recipes.espresso.phonons.postahc_job][]      |              |
 | Espresso Non-SCF         | `#!Python @job`  | [quacc.recipes.espresso.core.non_scf_job][]         |              |
 | Espresso DOS             | `#!Python @job`  | [quacc.recipes.espresso.dos.dos_job][]              |              |
 | Espresso DOS Flow        | `#!Python @flow` | [quacc.recipes.espresso.dos.dos_flow][]             |              |

src/quacc/calculators/espresso/espresso.py

@@ -28,7 +28,7 @@
     get_pseudopotential_info,
     remove_conflicting_kpts_kspacing,
 )
-from quacc.utils.dicts import recursive_dict_merge
+from quacc.utils.dicts import Remove, recursive_dict_merge, remove_dict_entries
 from quacc.utils.files import load_yaml_calc
 
 if TYPE_CHECKING:
@@ -38,7 +38,8 @@
 
 
 class EspressoTemplate(EspressoTemplate_):
-    """This is a wrapper around the ASE Espresso template that allows for the use of
+    """
+    A wrapper around the ASE Espresso template that allows for the use of
     other binaries such as pw.x, ph.x, cp.x, etc.
     """
 
@@ -72,6 +73,8 @@ def __init__(
 
         self.binary = binary
 
+        self._ase_known_binary = self.binary in ALL_KEYS
+
         self.test_run = test_run
 
         self.nruns = 0
@@ -125,13 +128,16 @@ def write_input(
                 properties=properties,
                 **parameters,
             )
-        elif self.binary == "ph":
+        elif self.binary in ["ph", "phcg"]:
             with Path.open(directory / self.inputname, "w") as fd:
                 write_espresso_ph(fd=fd, properties=properties, **parameters)
         else:
             with Path.open(directory / self.inputname, "w") as fd:
                 write_fortran_namelist(
-                    fd, binary=self.binary, properties=properties, **parameters
+                    fd,
+                    binary=self.binary if self._ase_known_binary else None,
+                    properties=properties,
+                    **parameters,
                 )
 
     def execute(self, *args: Any, **kwargs: Any) -> None:
@@ -203,7 +209,7 @@ def read_results(self, directory: Path | str) -> dict[str, Any]:
         if self.binary == "pw":
             atoms = read(directory / self.outputname, format="espresso-out")
             results = dict(atoms.calc.properties())
-        elif self.binary == "ph":
+        elif self.binary in ["ph", "phcg"]:
             with Path.open(directory / self.outputname, "r") as fd:
                 results = read_espresso_ph(fd)
         elif self.binary == "dos":
@@ -218,13 +224,7 @@ def read_results(self, directory: Path | str) -> dict[str, Any]:
                 energy = lines[1:, 0]
                 dos = lines[1:, 1]
                 pdos = lines[1:, 2]
-            results = {
-                "projwfc_results": {
-                    "energy": energy,
-                    "dos": dos,
-                    "pdos": pdos,
-                }
-            }
+            results = {"projwfc_results": {"energy": energy, "dos": dos, "pdos": pdos}}
         elif self.binary == "matdyn":
             fldos = Path(directory, "matdyn.dos")
             if fldos.exists():
@@ -267,7 +267,7 @@ def _output_handler(
         outkeys = espresso_prepare_dir(espresso_outdir, self.binary)
 
         input_data = parameters.get("input_data", {})
-        input_data = recursive_dict_merge(input_data, outkeys)
+        input_data = recursive_dict_merge(input_data, outkeys, verbose=True)
 
         parameters["input_data"] = input_data
 
@@ -291,7 +291,23 @@ def _sanity_checks(self, parameters: dict[str, Any]) -> None:
         """
         input_data = parameters.get("input_data", {})
 
-        if self.binary == "ph":
+        if self.binary == "pw":
+            system = input_data.get("system", {})
+
+            occupations = system.get("occupations", "fixed")
+            smearing = system.get("smearing", None)
+            degauss = system.get("degauss", None)
+
+            if occupations == "fixed" and not (smearing is None and degauss is None):
+                LOGGER.warning(
+                    "The occupations are set to 'fixed' but smearing or degauss is also set. This will be ignored."
+                )
+                system["smearing"] = Remove
+                system["degauss"] = Remove
+
+            parameters["input_data"]["system"] = system
+
+        elif self.binary in ["ph", "phcg"]:
             input_ph = input_data.get("inputph", {})
             qpts = parameters.get("qpts", (0, 0, 0))
 
@@ -322,14 +338,13 @@ def _sanity_checks(self, parameters: dict[str, Any]) -> None:
             parameters["input_data"]["inputph"] = input_ph
             parameters["qpts"] = qpts
 
-        return parameters
+        return remove_dict_entries(parameters, remove_trigger=Remove)
 
 
 class Espresso(Espresso_):
     """
-    This is a wrapper around the ASE Espresso calculator that adjusts input_data
+    A wrapper around the ASE Espresso calculator that adjusts input_data
     parameters and allows for the use of presets.
-
     Templates are used to set the binary and input/output file names.
     """
 
@@ -385,21 +400,21 @@ def __init__(
         self._user_calc_params = {}
 
         template = template or EspressoTemplate("pw")
+
+        self._binary = template.binary
+
         full_path = Path(
-            SETTINGS.ESPRESSO_BIN_DIR, SETTINGS.ESPRESSO_BINARIES[template.binary]
+            SETTINGS.ESPRESSO_BIN_DIR, SETTINGS.ESPRESSO_BINARIES[self._binary]
         )
         self._bin_path = str(full_path)
-        self._binary = template.binary
 
-        if self._binary in ALL_KEYS:
+        if template._ase_known_binary:
             self._cleanup_params()
         else:
             LOGGER.warning(
                 f"the binary you requested, `{self._binary}`, is not supported by ASE. This means that presets and usual checks will not be carried out, your `input_data` must be provided in nested format."
             )
 
-            template.binary = None
-
             self.kwargs["input_data"] = Namelist(self.kwargs.get("input_data"))
             self._user_calc_params = self.kwargs