Continued adding parameter tests

dfttoolkit/parameters.py

@@ -1,4 +1,4 @@
-from typing import List
+from typing import List, Literal, Union
 
 import dfttoolkit.utils.file_utils as fu
 from dfttoolkit.base_parser import BaseParser
@@ -75,23 +75,37 @@ def add_keywords(self, **kwargs: dict) -> None:
         # TODO finish this
         raise NotImplementedError
 
-    def remove_keywords(self, *args: str) -> None:
+    def remove_keywords(
+        self, *args: str, output: Literal["overwrite", "print", "return"] = "return"
+    ) -> Union[None, List[str]]:
         """
         Remove keywords from the control.in file.
 
         Parameters
         ----------
         *args : str
             Keywords to be removed from the control.in file.
+        output : Literal['overwrite', 'print', 'return'], default='overwrite'
+            Overwrite the original file, print the modified file to STDOUT, or return
+            the modified file as a list of '\\n' separated strings.
+
         """
 
         for keyword in args:
             for i, line in enumerate(self.lines):
                 if keyword in line:
                     self.lines.pop(i)
 
-        with open(self.path, "w") as f:
-            f.writelines(self.lines)
+        match output:
+            case "overwrite":
+                with open(self.path, "w") as f:
+                    f.writelines(self.lines)
+
+            case "print":
+                print(*self.lines, sep="")
+
+            case "return":
+                return self.lines
 
     def get_keywords(self) -> dict:
         """

tests/conftest.py

@@ -46,3 +46,11 @@ def aims_calc_dir(run_aims):
         return "custom_bin_aims_calcs"
     else:
         return "default_aims_calcs"
+
+
+@pytest.fixture(scope="session")
+def tmp_dir(tmp_path_factory):
+    """Temporary directory for all tests to write files to"""
+
+    d = tmp_path_factory.mktemp("tmp")
+    return d

tests/fixtures/manipulated_aims_files/1/control.in

@@ -0,0 +1,145 @@
+output_level                 full
+################################################################################
+#
+#  FHI-aims code project
+#  VB, Fritz-Haber Institut, 2009
+#
+#  Suggested "light" defaults for O atom (to be pasted into control.in file)
+#  Be sure to double-check any results obtained with these settings for post-processing,
+#  e.g., with the "tight" defaults and larger basis sets.
+#
+################################################################################
+  species        O
+#     global species definitions
+    nucleus             8
+    mass                15.9994
+#
+    l_hartree           4
+#
+    cut_pot             3.5  1.5  1.0
+    basis_dep_cutoff    1e-4
+#
+    radial_base         36 5.0
+    radial_multiplier   1
+     angular_grids specified
+      division   0.2659   50
+      division   0.4451  110
+      division   0.6052  194
+      division   0.7543  302
+#      division   0.8014  434
+#      division   0.8507  590
+#      division   0.8762  770
+#      division   0.9023  974
+#      division   1.2339 1202
+#      outer_grid 974
+      outer_grid 302
+################################################################################
+#
+#  Definition of "minimal" basis
+#
+################################################################################
+#     valence basis states
+    valence      2  s   2.
+    valence      2  p   4.
+#     ion occupancy
+    ion_occ      2  s   1.
+    ion_occ      2  p   3.
+################################################################################
+#
+#  Suggested additional basis functions. For production calculations, 
+#  uncomment them one after another (the most important basis functions are
+#  listed first).
+#
+#  Constructed for dimers: 1.0 A, 1.208 A, 1.5 A, 2.0 A, 3.0 A
+#
+################################################################################
+#  "First tier" - improvements: -699.05 meV to -159.38 meV
+     hydro 2 p 1.8
+     hydro 3 d 7.6
+     hydro 3 s 6.4
+#  "Second tier" - improvements: -49.91 meV to -5.39 meV
+#     hydro 4 f 11.6
+#     hydro 3 p 6.2
+#     hydro 3 d 5.6
+#     hydro 5 g 17.6
+#     hydro 1 s 0.75
+#  "Third tier" - improvements: -2.83 meV to -0.50 meV
+#     ionic 2 p auto
+#     hydro 4 f 10.8
+#     hydro 4 d 4.7
+#     hydro 2 s 6.8
+#  "Fourth tier" - improvements: -0.40 meV to -0.12 meV
+#     hydro 3 p 5
+#     hydro 3 s 3.3
+#     hydro 5 g 15.6
+#     hydro 4 f 17.6
+#     hydro 4 d 14
+# Further basis functions - -0.08 meV and below
+#     hydro 3 s 2.1
+#     hydro 4 d 11.6
+#     hydro 3 p 16
+#     hydro 2 s 17.2
+################################################################################
+#
+#  FHI-aims code project
+#  VB, Fritz-Haber Institut, 2009
+#
+#  Suggested "light" defaults for H atom (to be pasted into control.in file)
+#  Be sure to double-check any results obtained with these settings for post-processing,
+#  e.g., with the "tight" defaults and larger basis sets.
+#
+################################################################################
+  species        H
+#     global species definitions
+    nucleus             1
+    mass                1.00794
+#
+    l_hartree           4
+#
+    cut_pot             3.5  1.5  1.0
+    basis_dep_cutoff    1e-4
+#     
+    radial_base         24 5.0
+    radial_multiplier   1
+    angular_grids       specified
+      division   0.2421   50
+      division   0.3822  110
+      division   0.4799  194
+      division   0.5341  302
+#      division   0.5626  434
+#      division   0.5922  590
+#      division   0.6542  770
+#      division   0.6868 1202
+#      outer_grid  770
+      outer_grid  302
+################################################################################
+#
+#  Definition of "minimal" basis
+#
+################################################################################
+#     valence basis states
+    valence      1  s   1.
+#     ion occupancy
+    ion_occ      1  s   0.5
+################################################################################
+#
+#  Suggested additional basis functions. For production calculations, 
+#  uncomment them one after another (the most important basis functions are
+#  listed first).
+#
+#  Basis constructed for dimers: 0.5 A, 0.7 A, 1.0 A, 1.5 A, 2.5 A
+#
+################################################################################
+#  "First tier" - improvements: -1014.90 meV to -62.69 meV
+     hydro 2 s 2.1
+     hydro 2 p 3.5
+#  "Second tier" - improvements: -12.89 meV to -1.83 meV
+#     hydro 1 s 0.85
+#     hydro 2 p 3.7
+#     hydro 2 s 1.2
+#     hydro 3 d 7
+#  "Third tier" - improvements: -0.25 meV to -0.12 meV
+#     hydro 4 f 11.2
+#     hydro 3 p 4.8
+#     hydro 4 d 9
+#     hydro 3 s 3.2

tests/fixtures/manipulated_aims_files/10/control.in

@@ -0,0 +1,88 @@
+hse_unit                     b
+################################################################################
+#
+#  FHI-aims code project
+#  VB, Fritz-Haber Institut, 2009
+#
+#  Suggested "light" defaults for Si atom (to be pasted into control.in file)
+#  Be sure to double-check any results obtained with these settings for post-processing,
+#  e.g., with the "tight" defaults and larger basis sets.
+#
+#  2020/09/08 Added f function to "light" after reinspection of Delta test outcomes.
+#             This was done for all of Al-Cl and is a tricky decision since it makes
+#             "light" calculations measurably more expensive for these elements.
+#             Nevertheless, outcomes for P, S, Cl (and to some extent, Si) appear
+#             to justify this choice.
+#
+################################################################################
+  species        Si
+#     global species definitions
+    nucleus             14
+    mass                28.0855
+#
+    l_hartree           4
+#
+    cut_pot             3.5          1.5  1.0
+    basis_dep_cutoff    1e-4
+#
+    radial_base         42 5.0
+    radial_multiplier   1
+    angular_grids       specified
+      division   0.5866   50
+      division   0.9616  110
+      division   1.2249  194
+      division   1.3795  302
+#      division   1.4810  434
+#      division   1.5529  590
+#      division   1.6284  770
+#      division   1.7077  974
+#      division   2.4068 1202
+#      outer_grid   974
+      outer_grid 302
+################################################################################
+#
+#  Definition of "minimal" basis
+#
+################################################################################
+#     valence basis states
+    valence      3  s   2.
+    valence      3  p   2.
+#     ion occupancy
+    ion_occ      3  s   1.
+    ion_occ      3  p   1.
+################################################################################
+#
+#  Suggested additional basis functions. For production calculations, 
+#  uncomment them one after another (the most important basis functions are
+#  listed first).
+#
+#  Constructed for dimers: 1.75 A, 2.0 A, 2.25 A, 2.75 A, 3.75 A
+#
+################################################################################
+#  "First tier" - improvements: -571.96 meV to -37.03 meV
+     hydro 3 d 4.2
+     hydro 2 p 1.4
+     hydro 4 f 6.2
+     ionic 3 s auto
+#  "Second tier" - improvements: -16.76 meV to -3.03 meV
+#     hydro 3 d 9
+#     hydro 5 g 9.4
+#     hydro 4 p 4
+#     hydro 1 s 0.65
+#  "Third tier" - improvements: -3.89 meV to -0.60 meV
+#     ionic 3 d auto
+#     hydro 3 s 2.6
+#     hydro 4 f 8.4
+#     hydro 3 d 3.4
+#     hydro 3 p 7.8
+#  "Fourth tier" - improvements: -0.33 meV to -0.11 meV
+#     hydro 2 p 1.6
+#     hydro 5 g 10.8
+#     hydro 5 f 11.2
+#     hydro 3 d 1
+#     hydro 4 s 4.5
+#  Further basis functions that fell out of the optimization - noise
+#  level... < -0.08 meV
+#     hydro 4 d 6.6
+#     hydro 5 g 16.4
+#     hydro 4 d 9