List outputs (#454)

* Always return absolute filename

* Add output files property to calculations

* Save output files to CLI summary

* Save MD postprocessing filenames

* Add output files to missing CLI functions

* Fix Mixin tests

* Remove duplicate geomopt traj and fix output files

* Tidy building filenames

* Test output files

* Fix saving MD restart files

* Fix MD minimize filename

* Fix checking lists of output files

* Fix MD restart files list

* Fix inconsistent paths

* Fix local path

* Fix docstring

* Fix phonon output files

* Fix phonon output file tests

* Fix writing tuples in CLI summary

* Apply suggestions from code review

Co-authored-by: Jacob Wilkins <46597752+oerc0122@users.noreply.github.com>

* Update tests/utils.py

Co-authored-by: Jacob Wilkins <46597752+oerc0122@users.noreply.github.com>

* Use asserts for tests

* Fix when output dir is created

* Avoid rebuilding phonon files

---------

Co-authored-by: Jacob Wilkins <46597752+oerc0122@users.noreply.github.com>

Author: ElliottKasoar

janus_core/calculations/base.py

@@ -205,7 +205,7 @@ def __init__(
                 log_suffix,
                 param_prefix if file_prefix is None else "",
                 filename=self.log_kwargs["filename"],
-            ).absolute()
+            )
 
         self.log_kwargs.setdefault("name", calc_name)
         self.logger = config_logger(**self.log_kwargs)

janus_core/calculations/descriptors.py

@@ -183,10 +183,24 @@ def __init__(
                 check_calculator(image.calc, "get_descriptors")
 
         # Set output file
-        self.write_kwargs.setdefault("filename", None)
         self.write_kwargs["filename"] = self._build_filename(
-            "descriptors.extxyz", filename=self.write_kwargs["filename"]
-        ).absolute()
+            "descriptors.extxyz", filename=self.write_kwargs.get("filename")
+        )
+
+    @property
+    def output_files(self) -> None:
+        """
+        Dictionary of output file labels and paths.
+
+        Returns
+        -------
+        dict[str, PathLike]
+            Output file labels and paths.
+        """
+        return {
+            "log": self.log_kwargs["filename"] if self.logger else None,
+            "results": self.write_kwargs["filename"] if self.write_results else None,
+        }
 
     def run(self) -> None:
         """Calculate descriptors for structure(s)."""

janus_core/calculations/eos.py

@@ -246,27 +246,46 @@ def __init__(
         if not self.struct.calc:
             raise ValueError("Please attach a calculator to `struct`.")
 
-        if self.minimize and self.logger:
-            set_minimize_logging(
-                self.logger, self.minimize_kwargs, self.log_kwargs, track_carbon
-            )
+        set_minimize_logging(
+            self.logger, self.minimize_kwargs, self.log_kwargs, track_carbon
+        )
 
         # Set output files
-        self.write_kwargs.setdefault("filename", None)
         self.write_kwargs["filename"] = self._build_filename(
-            "generated.extxyz", filename=self.write_kwargs["filename"]
-        ).absolute()
+            "generated.extxyz", filename=self.write_kwargs.get("filename")
+        )
 
-        self.plot_kwargs.setdefault("filename", None)
         self.plot_kwargs["filename"] = self._build_filename(
-            "eos-plot.svg", filename=self.plot_kwargs["filename"]
-        ).absolute()
+            "eos-plot.svg", filename=self.plot_kwargs.get("filename")
+        )
+        self.fit_file = self._build_filename("eos-fit.dat")
+        self.raw_file = self._build_filename("eos-raw.dat")
 
         self.results = {}
         self.volumes = []
         self.energies = []
         self.lattice_scalars = empty(0)
 
+    @property
+    def output_files(self) -> None:
+        """
+        Dictionary of output file labels and paths.
+
+        Returns
+        -------
+        dict[str, PathLike]
+            Output file labels and paths.
+        """
+        return {
+            "log": self.log_kwargs["filename"] if self.logger else None,
+            "generated_structures": self.write_kwargs["filename"]
+            if self.write_structures
+            else None,
+            "plot": self.plot_kwargs["filename"] if self.plot_to_file else None,
+            "fit": self.fit_file if self.write_results else None,
+            "raw": self.raw_file if self.write_results else None,
+        }
+
     def run(self) -> EoSResults:
         """
         Calculate equation of state.
@@ -302,9 +321,8 @@ def run(self) -> EoSResults:
         self._calc_volumes_energies()
 
         if self.write_results:
-            eos_raw_file = f"{self.file_prefix}-eos-raw.dat"
-            build_file_dir(eos_raw_file)
-            with open(eos_raw_file, "w", encoding="utf8") as out:
+            build_file_dir(self.raw_file)
+            with open(self.raw_file, "w", encoding="utf8") as out:
                 print("#Lattice Scalar | Energy [eV] | Volume [Å^3] ", file=out)
                 for eos_data in zip(
                     self.lattice_scalars, self.energies, self.volumes, strict=True
@@ -330,9 +348,8 @@ def run(self) -> EoSResults:
             self.tracker.stop()
 
         if self.write_results:
-            eos_fit_file = f"{self.file_prefix}-eos-fit.dat"
-            build_file_dir(eos_fit_file)
-            with open(eos_fit_file, "w", encoding="utf8") as out:
+            build_file_dir(self.fit_file)
+            with open(self.fit_file, "w", encoding="utf8") as out:
                 print("#Bulk modulus [GPa] | Energy [eV] | Volume [Å^3] ", file=out)
                 print(bulk_modulus, e_0, v_0, file=out)
 

janus_core/calculations/geom_opt.py

@@ -233,25 +233,53 @@ def __init__(
             raise ValueError("Please attach a calculator to `struct`.")
 
         # Set output files
-        self.write_kwargs.setdefault("filename", None)
         self.write_kwargs["filename"] = self._build_filename(
-            "opt.extxyz", filename=self.write_kwargs["filename"]
-        ).absolute()
+            "opt.extxyz", filename=self.write_kwargs.get("filename")
+        )
 
         if self.write_traj:
+            if "trajectory" in self.opt_kwargs:
+                raise ValueError(
+                    "Please use traj_kwargs['filename'] to save the trajectory"
+                )
+
             self.traj_kwargs.setdefault(
                 "filename", self._build_filename("traj.extxyz").absolute()
             )
-            self.opt_kwargs.setdefault("trajectory", str(self.traj_kwargs["filename"]))
+            self.opt_kwargs["trajectory"] = str(self.traj_kwargs["filename"])
+
         elif self.traj_kwargs:
-            raise ValueError("traj_kwargs given, but trajectory writing not enabled.")
+            raise ValueError(
+                "traj_kwargs given, but trajectory writing not enabled via write_traj."
+            )
+
         elif "trajectory" in self.opt_kwargs:
             raise ValueError(
-                '"trajectory" given in opt_kwargs,but trajectory writing not enabled.'
+                "Please use write_traj, and optionally traj_kwargs['filename'] to "
+                "save the trajectory"
             )
+
         # Configure optimizer dynamics
         self.set_optimizer()
 
+    @property
+    def output_files(self) -> None:
+        """
+        Dictionary of output file labels and paths.
+
+        Returns
+        -------
+        dict[str, PathLike]
+            Output file labels and paths.
+        """
+        return {
+            "log": self.log_kwargs["filename"] if self.logger else None,
+            "optimized_structure": self.write_kwargs["filename"]
+            if self.write_results
+            else None,
+            "trajectory": self.traj_kwargs.get("filename"),
+        }
+
     def set_optimizer(self) -> None:
         """Set optimizer for geometry optimization."""
         self._set_functions()