From e6d245e1b6202d3ae3fe458daaf5bf6a704770c3 Mon Sep 17 00:00:00 2001
From: Dylan <dbmorgan98@gmail.com>
Date: Tue, 19 Nov 2024 17:23:57 +0000
Subject: [PATCH 01/11] Started tests for parameters and small reconfigure

---
 dfttoolkit/utils/run_utils.py | 14 ++++++++++----
 tests/conftest.py             | 25 +++++++++++++++++++++++++
 tests/test_output.py          | 19 ++-----------------
 tests/test_parameters.py      | 18 ++++++++++++++++++
 4 files changed, 55 insertions(+), 21 deletions(-)
 create mode 100644 tests/test_parameters.py

diff --git a/dfttoolkit/utils/run_utils.py b/dfttoolkit/utils/run_utils.py
index 9400aca..ef1be1f 100644
--- a/dfttoolkit/utils/run_utils.py
+++ b/dfttoolkit/utils/run_utils.py
@@ -31,14 +31,20 @@ def no_repeat(
     def _no_repeat(func):
         @wraps(func)
         def wrapper(*args, **kwargs):
-            if not os.path.isdir(calc_dir):
-                raise ValueError(f"{calc_dir} is not a directory.")
+            # Override calc_dir in decorator call if given in func
+            if "calc_dir" in kwargs:
+                check_dir = kwargs["calc_dir"]
+            else:
+                check_dir = calc_dir
+
+            if not os.path.isdir(check_dir):
+                raise ValueError(f"{check_dir} is not a directory.")
             if force:
                 return func(*args, **kwargs)
-            if not os.path.isfile(f"{calc_dir}/{output_file}"):
+            if not os.path.isfile(f"{check_dir}/{output_file}"):
                 return func(*args, **kwargs)
             else:
-                print(f"aims.out already exists in {calc_dir}. Skipping calculation.")
+                print(f"aims.out already exists in {check_dir}. Skipping calculation.")
 
         return wrapper
 
diff --git a/tests/conftest.py b/tests/conftest.py
index 8e85d8a..61840ff 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,4 +1,7 @@
 import pytest
+import os
+import subprocess
+from dfttoolkit.utils.file_utils import aims_bin_path_prompt
 
 
 def pytest_addoption(parser):
@@ -21,3 +24,25 @@ def pytest_addoption(parser):
 @pytest.fixture(scope="session")
 def run_aims(request):
     return request.config.getoption("--run-aims")
+
+
+@pytest.fixture(scope="session")
+def aims_calc_dir(run_aims):
+    """
+    Run FHI-aims calculations using a custom binary if specified by --run-aims.
+
+    If the calculation has already been run (ie. if the directory
+    `custom_bin_aims_calcs` exists), the calculations will not be run again, unless the
+    user specifies `change_bin` as an option to --run-aims.
+    """
+
+    # Check if the directory already exists
+    if os.path.isdir("custom_bin_aims_calcs") and run_aims != "change_bin":
+        return "custom_bin_aims_calcs"
+    elif run_aims is not False:
+        cwd = os.path.dirname(os.path.realpath(__file__))
+        binary = aims_bin_path_prompt(run_aims, cwd)
+        subprocess.run(["bash", f"{cwd}/run_aims.sh", binary, str(run_aims)])
+        return "custom_bin_aims_calcs"
+    else:
+        return "default_aims_calcs"
diff --git a/tests/test_output.py b/tests/test_output.py
index 0f5c9f6..792313e 100644
--- a/tests/test_output.py
+++ b/tests/test_output.py
@@ -1,35 +1,20 @@
 import os
-import subprocess
 
 import numpy as np
 import pytest
 import yaml
 from dfttoolkit.output import AimsOutput
-from dfttoolkit.utils.file_utils import aims_bin_path_prompt
 
 
 class TestAimsOutput:
 
     @pytest.fixture(params=range(1, 11), autouse=True)
-    def aims_out(self, request, run_aims):
+    def aims_out(self, request, aims_calc_dir):
 
         cwd = os.path.dirname(os.path.realpath(__file__))
 
-        # Run the FHI-aims calculations if the run-aims option is specified but not if
-        # they already exist.
-        # Force it to run if the run-aims option is "change_bin"
-        # run_aims fixture is defined in conftest.py
-        if request.param == 1 and run_aims is not False:
-            binary = aims_bin_path_prompt(run_aims, cwd)
-            subprocess.run(["bash", f"{cwd}/run_aims.sh", binary, str(run_aims)])
-            aims_out_dir = "custom_bin_aims_calcs"
-        elif run_aims is not False:
-            aims_out_dir = "custom_bin_aims_calcs"
-        else:
-            aims_out_dir = "default_aims_calcs"
-
         self.ao = AimsOutput(
-            aims_out=f"{cwd}/fixtures/{aims_out_dir}/{str(request.param)}/aims.out"
+            aims_out=f"{cwd}/fixtures/{aims_calc_dir}/{str(request.param)}/aims.out"
         )
 
         with open(f"{cwd}/test_references.yaml", "r") as references:
diff --git a/tests/test_parameters.py b/tests/test_parameters.py
new file mode 100644
index 0000000..48c8d05
--- /dev/null
+++ b/tests/test_parameters.py
@@ -0,0 +1,18 @@
+import os
+import pytest
+from dfttoolkit.parameters import AimsControl
+
+
+# TODO Create generic test class with functions for all tests to inherit
+
+
+class TestAimsControl:
+
+    @pytest.fixture(params=range(1, 11), autouse=True)
+    def aims_control(self, request, aims_calc_dir):
+
+        cwd = os.path.dirname(os.path.realpath(__file__))
+
+        self.ac = AimsControl(
+            control_in=f"{cwd}/fixtures/{aims_calc_dir}/{str(request.param)}/control.in"
+        )

From 2d876f405c61afd92a569bc21e4cc0ebf04bdf10 Mon Sep 17 00:00:00 2001
From: Dylan Morgan <dbmorgan98@gmail.com>
Date: Thu, 21 Nov 2024 01:37:28 +0000
Subject: [PATCH 02/11] Continued adding parameter tests

---
 dfttoolkit/parameters.py                      |  22 ++-
 dfttoolkit/utils/__init__.py                  |   0
 tests/__init__.py                             |   0
 tests/conftest.py                             |   8 +
 .../manipulated_aims_files/1/control.in       | 145 +++++++++++++++++
 .../manipulated_aims_files/10/control.in      |  88 +++++++++++
 .../manipulated_aims_files/2/control.in       | 147 +++++++++++++++++
 .../manipulated_aims_files/3/control.in       | 148 ++++++++++++++++++
 .../manipulated_aims_files/4/control.in       |  87 ++++++++++
 .../manipulated_aims_files/5/control.in       | 144 +++++++++++++++++
 .../manipulated_aims_files/6/control.in       |  88 +++++++++++
 .../manipulated_aims_files/7/control.in       | 148 ++++++++++++++++++
 .../manipulated_aims_files/8/control.in       |  92 +++++++++++
 .../manipulated_aims_files/9/control.in       | 145 +++++++++++++++++
 tests/test_parameters.py                      |  41 ++++-
 15 files changed, 1293 insertions(+), 10 deletions(-)
 delete mode 100644 dfttoolkit/utils/__init__.py
 delete mode 100644 tests/__init__.py
 create mode 100644 tests/fixtures/manipulated_aims_files/1/control.in
 create mode 100644 tests/fixtures/manipulated_aims_files/10/control.in
 create mode 100644 tests/fixtures/manipulated_aims_files/2/control.in
 create mode 100644 tests/fixtures/manipulated_aims_files/3/control.in
 create mode 100644 tests/fixtures/manipulated_aims_files/4/control.in
 create mode 100644 tests/fixtures/manipulated_aims_files/5/control.in
 create mode 100644 tests/fixtures/manipulated_aims_files/6/control.in
 create mode 100644 tests/fixtures/manipulated_aims_files/7/control.in
 create mode 100644 tests/fixtures/manipulated_aims_files/8/control.in
 create mode 100644 tests/fixtures/manipulated_aims_files/9/control.in

diff --git a/dfttoolkit/parameters.py b/dfttoolkit/parameters.py
index 7e73993..d919dd5 100644
--- a/dfttoolkit/parameters.py
+++ b/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
@@ -75,7 +75,9 @@ 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.
 
@@ -83,6 +85,10 @@ def remove_keywords(self, *args: str) -> None:
         ----------
         *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:
@@ -90,8 +96,16 @@ def remove_keywords(self, *args: str) -> None:
                 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:
         """
diff --git a/dfttoolkit/utils/__init__.py b/dfttoolkit/utils/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/tests/__init__.py b/tests/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/tests/conftest.py b/tests/conftest.py
index 61840ff..cbe9132 100644
--- a/tests/conftest.py
+++ b/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
diff --git a/tests/fixtures/manipulated_aims_files/1/control.in b/tests/fixtures/manipulated_aims_files/1/control.in
new file mode 100644
index 0000000..e6e1181
--- /dev/null
+++ b/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
diff --git a/tests/fixtures/manipulated_aims_files/10/control.in b/tests/fixtures/manipulated_aims_files/10/control.in
new file mode 100644
index 0000000..1c60dd8
--- /dev/null
+++ b/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
diff --git a/tests/fixtures/manipulated_aims_files/2/control.in b/tests/fixtures/manipulated_aims_files/2/control.in
new file mode 100644
index 0000000..12bd563
--- /dev/null
+++ b/tests/fixtures/manipulated_aims_files/2/control.in
@@ -0,0 +1,147 @@
+spin                         collinear
+default_initial_moment       1
+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
diff --git a/tests/fixtures/manipulated_aims_files/3/control.in b/tests/fixtures/manipulated_aims_files/3/control.in
new file mode 100644
index 0000000..7d015f1
--- /dev/null
+++ b/tests/fixtures/manipulated_aims_files/3/control.in
@@ -0,0 +1,148 @@
+spin                         collinear
+default_initial_moment       1
+include_spin_orbit           non_self_consistent
+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
diff --git a/tests/fixtures/manipulated_aims_files/4/control.in b/tests/fixtures/manipulated_aims_files/4/control.in
new file mode 100644
index 0000000..d00339a
--- /dev/null
+++ b/tests/fixtures/manipulated_aims_files/4/control.in
@@ -0,0 +1,87 @@
+################################################################################
+#
+#  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
diff --git a/tests/fixtures/manipulated_aims_files/5/control.in b/tests/fixtures/manipulated_aims_files/5/control.in
new file mode 100644
index 0000000..286b7b1
--- /dev/null
+++ b/tests/fixtures/manipulated_aims_files/5/control.in
@@ -0,0 +1,144 @@
+################################################################################
+#
+#  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
diff --git a/tests/fixtures/manipulated_aims_files/6/control.in b/tests/fixtures/manipulated_aims_files/6/control.in
new file mode 100644
index 0000000..330436c
--- /dev/null
+++ b/tests/fixtures/manipulated_aims_files/6/control.in
@@ -0,0 +1,88 @@
+relax_unit_cell              full
+################################################################################
+#
+#  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
diff --git a/tests/fixtures/manipulated_aims_files/7/control.in b/tests/fixtures/manipulated_aims_files/7/control.in
new file mode 100644
index 0000000..fe0b9f0
--- /dev/null
+++ b/tests/fixtures/manipulated_aims_files/7/control.in
@@ -0,0 +1,148 @@
+sc_accuracy_rho              1e-10
+sc_accuracy_eev              1e-6
+sc_accuracy_etot             1e-12
+sc_accuracy_forces           1e-8
+################################################################################
+#
+#  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
diff --git a/tests/fixtures/manipulated_aims_files/8/control.in b/tests/fixtures/manipulated_aims_files/8/control.in
new file mode 100644
index 0000000..287e2e9
--- /dev/null
+++ b/tests/fixtures/manipulated_aims_files/8/control.in
@@ -0,0 +1,92 @@
+sc_iter_limit                10
+sc_accuracy_rho              1e-10
+sc_accuracy_eev              1e-6
+sc_accuracy_etot             1e-12
+sc_accuracy_forces           1e-8
+################################################################################
+#
+#  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
diff --git a/tests/fixtures/manipulated_aims_files/9/control.in b/tests/fixtures/manipulated_aims_files/9/control.in
new file mode 100644
index 0000000..3dd43b6
--- /dev/null
+++ b/tests/fixtures/manipulated_aims_files/9/control.in
@@ -0,0 +1,145 @@
+hse_unit                     b
+################################################################################
+#
+#  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
diff --git a/tests/test_parameters.py b/tests/test_parameters.py
index 48c8d05..5f85a89 100644
--- a/tests/test_parameters.py
+++ b/tests/test_parameters.py
@@ -1,18 +1,47 @@
 import os
+import shutil
 import pytest
 from dfttoolkit.parameters import AimsControl
 
 
-# TODO Create generic test class with functions for all tests to inherit
-
-
 class TestAimsControl:
 
     @pytest.fixture(params=range(1, 11), autouse=True)
     def aims_control(self, request, aims_calc_dir):
-
-        cwd = os.path.dirname(os.path.realpath(__file__))
+        self.cwd = os.path.dirname(os.path.realpath(__file__))
 
         self.ac = AimsControl(
-            control_in=f"{cwd}/fixtures/{aims_calc_dir}/{str(request.param)}/control.in"
+            control_in=f"{self.cwd}/fixtures/{aims_calc_dir}/{str(request.param)}"
+            "/control.in"
         )
+
+        # Read reference
+        with open(
+            f"{self.cwd}/fixtures/manipulated_aims_files/{str(request.param)}"
+            "/control.in",
+            "r",
+        ) as f:
+            self.removed_keywords_control_ref = f.readlines()
+
+    @property
+    def _aims_fixture_no(self) -> int:
+        return int(self.ac.path.split("/")[-2])
+
+    def test_remove_keywords_overwrite(self, tmp_dir):
+        control_path = tmp_dir / "control.in"
+        shutil.copy(self.ac.path, control_path)
+        ac = AimsControl(control_in=str(control_path))
+        ac.remove_keywords("xc", "relax_geometry", "k_grid", output="overwrite")
+
+        assert "".join(self.removed_keywords_control_ref) == control_path.read_text()
+
+    def test_remove_keywords_print(self, capfd):
+        self.ac.remove_keywords("xc", "relax_geometry", "k_grid", output="print")
+
+        out, err = capfd.readouterr()
+
+        # print(out)
+        # print("".join(self.removed_keywords_control_ref))
+
+        assert out == print("".join(self.removed_keywords_control_ref))
+        assert err == ""

From 9c852e4e3a9873564b114336aa578d6c6811aacc Mon Sep 17 00:00:00 2001
From: Dylan Morgan <dbmorgan98@gmail.com>
Date: Thu, 21 Nov 2024 01:40:36 +0000
Subject: [PATCH 03/11] Type hint fixes

---
 dfttoolkit/utils/math_utils.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/dfttoolkit/utils/math_utils.py b/dfttoolkit/utils/math_utils.py
index c8af90b..04a3061 100644
--- a/dfttoolkit/utils/math_utils.py
+++ b/dfttoolkit/utils/math_utils.py
@@ -1,5 +1,6 @@
-from typing import Union
 from copy import deepcopy
+from typing import Union
+
 import numpy as np
 import numpy.typing as npt
 import scipy
@@ -405,7 +406,7 @@ def apply_hann_window(data):
     return windowed_data
 
 
-def norm_matrix_by_dagonal(matrix: np.array) -> np.array:
+def norm_matrix_by_dagonal(matrix: npt.NDArray) -> npt.NDArray:
     """
     Norms a matrix such that the diagonal becomes 1.
 
@@ -437,7 +438,7 @@ def norm_matrix_by_dagonal(matrix: np.array) -> np.array:
     return new_matrix
 
 
-def mae(delta: np.ndarray) -> float:
+def mae(delta: np.ndarray) -> np.floating:
     """
     Calculated the mean absolute error from a list of value differnces.
 
@@ -455,7 +456,7 @@ def mae(delta: np.ndarray) -> float:
     return np.mean(np.abs(delta))
 
 
-def rel_mae(delta: np.ndarray, target_val: np.ndarray) -> float:
+def rel_mae(delta: np.ndarray, target_val: np.ndarray) -> np.floating:
     """
     Calculated the relative mean absolute error from a list of value differnces,
     given the target values.

From 092075a2af953be4ac43abd158075a60750dfd2c Mon Sep 17 00:00:00 2001
From: Dylan Morgan <dbmorgan98@gmail.com>
Date: Thu, 21 Nov 2024 01:41:02 +0000
Subject: [PATCH 04/11] Added default imports

---
 dfttoolkit/__init__.py | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/dfttoolkit/__init__.py b/dfttoolkit/__init__.py
index e69de29..c4f5b04 100644
--- a/dfttoolkit/__init__.py
+++ b/dfttoolkit/__init__.py
@@ -0,0 +1,38 @@
+from .benchmarking import BenchmarkAims
+from .custom_ase import CustomAims
+from .friction import FrictionTensor
+from .geometry import AimsGeometry, VaspGeometry, XSFGeometry, XYZGeometry
+from .output import AimsOutput, ELSIOutput
+from .parameters import AimsControl
+from .trajectory import MDTrajectory
+from .utils import math_utils, units
+from .utils.file_utils import aims_bin_path_prompt, check_required_files
+from .utils.geometry_utils import read_xyz_animation
+from .utils.periodic_table import PeriodicTable
+from .utils.run_utils import no_repeat
+from .vibrations import AimsVibrations, VaspVibrations
+from .visualise import VisualiseAims
+
+__all__ = [
+    "BenchmarkAims",
+    "CustomAims",
+    "FrictionTensor",
+    "AimsGeometry",
+    "VaspGeometry",
+    "XSFGeometry",
+    "XYZGeometry",
+    "AimsOutput",
+    "ELSIOutput",
+    "AimsControl",
+    "MDTrajectory",
+    "math_utils",
+    "units",
+    "aims_bin_path_prompt",
+    "check_required_files",
+    "read_xyz_animation",
+    "PeriodicTable",
+    "no_repeat",
+    "AimsVibrations",
+    "VaspVibrations",
+    "VisualiseAims",
+]

From 4f31086223162ef3df6e9ddcb3d3d18f84f57c80 Mon Sep 17 00:00:00 2001
From: Dylan <dbmorgan98@gmail.com>
Date: Thu, 21 Nov 2024 16:24:12 +0000
Subject: [PATCH 05/11] Added BaseParser tests

---
 dfttoolkit/base_parser.py                     |   2 +-
 .../elsi_files/D_spin_01_kpt_000001.csc       | Bin 0 -> 8024 bytes
 tests/test_base.py                            |  97 ++++++++++++++++++
 3 files changed, 98 insertions(+), 1 deletion(-)
 create mode 100644 tests/fixtures/elsi_files/D_spin_01_kpt_000001.csc
 create mode 100644 tests/test_base.py

diff --git a/dfttoolkit/base_parser.py b/dfttoolkit/base_parser.py
index 38332f6..336a3e4 100644
--- a/dfttoolkit/base_parser.py
+++ b/dfttoolkit/base_parser.py
@@ -27,7 +27,7 @@ def __init__(self, supported_files, **kwargs):
 
             # Check if the file path exists
             if not os.path.isfile(kwargs[kwarg]):
-                raise ValueError(f"{kwargs[kwarg]} does not exist.")
+                raise FileNotFoundError(f"{kwargs[kwarg]} does not exist.")
 
             # Store the file paths
             self.file_paths[kwarg] = kwargs[kwarg]
diff --git a/tests/fixtures/elsi_files/D_spin_01_kpt_000001.csc b/tests/fixtures/elsi_files/D_spin_01_kpt_000001.csc
new file mode 100644
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HcmV?d00001

diff --git a/tests/test_base.py b/tests/test_base.py
new file mode 100644
index 0000000..a22ceb3
--- /dev/null
+++ b/tests/test_base.py
@@ -0,0 +1,97 @@
+from dfttoolkit.base_parser import BaseParser
+import pytest
+
+
+@pytest.fixture
+def elsi_csc(cwd):
+    yield f"{cwd}/fixtures/elsi_files/D_spin_01_kpt_000001.csc"
+
+
+@pytest.fixture(autouse=True)
+def base_parser(default_calc_dir, elsi_csc):
+    bp = BaseParser(
+        ["aims_out", "control_in", "elsi_out"],
+        aims_out=f"{default_calc_dir}/aims.out",
+        control_in=f"{default_calc_dir}/control.in",
+        elsi_out=elsi_csc,
+    )
+    yield bp
+
+
+def test_check_supported_file(default_calc_dir):
+
+    with pytest.raises(ValueError):
+        BaseParser(
+            ["aims_out", "elsi_in"],
+            aims_out=f"{default_calc_dir}/aims.out",
+            control_in=f"{default_calc_dir}/control.in",
+        )
+
+    with pytest.raises(ValueError):
+        BaseParser(
+            ["aims.out", "control.in"],
+            aims_out=f"{default_calc_dir}/aims.out",
+            control_in=f"{default_calc_dir}/control.in",
+        )
+
+
+def test_check_file_exists(default_calc_dir):
+    with pytest.raises(FileNotFoundError):
+        BaseParser(
+            ["aims_out", "control_in"],
+            aims_out=f"{default_calc_dir}/aims.out",
+            control_in="./control.in",
+        )
+
+
+def test_store_file_paths(base_parser, default_calc_dir, cwd):
+    assert base_parser.file_paths == {
+        "aims_out": f"{default_calc_dir}/aims.out",
+        "control_in": f"{default_calc_dir}/control.in",
+        "elsi_out": f"{cwd}/fixtures/elsi_files/D_spin_01_kpt_000001.csc",
+    }
+
+
+def test_read_binary_content(base_parser):
+    assert isinstance(base_parser.file_contents["elsi_out"], bytes) is True
+
+
+def test_read_txt_content(elsi_csc, base_parser, default_calc_dir):
+    with open(elsi_csc, "rb") as f:
+        assert base_parser.file_contents["elsi_out"] == f.read()
+
+    with open(f"{default_calc_dir}/aims.out", "r") as f:
+        assert base_parser.file_contents["aims_out"] == f.readlines()
+
+    with open(f"{default_calc_dir}/control.in", "r") as f:
+        assert base_parser.file_contents["control_in"] == f.readlines()
+
+
+def test__str__(base_parser, default_calc_dir):
+    base_parser.lines = base_parser.file_contents["aims_out"]
+    with open(f"{default_calc_dir}/aims.out", "r") as f:
+        ao_lines = f.readlines()
+
+    assert str(base_parser) == "".join(ao_lines)
+
+    base_parser.lines = base_parser.file_contents["control_in"]
+    with open(f"{default_calc_dir}/control.in", "r") as f:
+        ci_lines = f.readlines()
+
+    assert str(base_parser) == "".join(ci_lines)
+
+
+def test__str__error(base_parser):
+    # TODO maybe change to read the file as None or "" rather than just setting the attr
+    base_parser.lines = None
+    with pytest.raises(ValueError):
+        str(base_parser)
+
+    base_parser.lines = ""
+    with pytest.raises(ValueError):
+        str(base_parser)
+
+
+def test_properties():
+    # TODO
+    pass

From c8e235793fa9797bf8d45257a6bc4eae52c18296 Mon Sep 17 00:00:00 2001
From: Dylan <dbmorgan98@gmail.com>
Date: Thu, 21 Nov 2024 16:25:23 +0000
Subject: [PATCH 06/11] Minor formatting changes

---
 dfttoolkit/output.py | 18 ++++++++--------
 tests/test_output.py | 51 +++++++++++++++++---------------------------
 2 files changed, 29 insertions(+), 40 deletions(-)

diff --git a/dfttoolkit/output.py b/dfttoolkit/output.py
index 1b49606..923a76e 100644
--- a/dfttoolkit/output.py
+++ b/dfttoolkit/output.py
@@ -1323,33 +1323,33 @@ def read_elsi_as_csc(
 
         # Get the column pointer
         end = 128 + self.n_basis * 8
-        col_ptr = np.frombuffer(self.lines[128:end], dtype=np.int64)
-        col_ptr = np.append(col_ptr, self.n_non_zero + 1)
-        col_ptr -= 1
+        col_i = np.frombuffer(self.lines[128:end], dtype=np.int64)
+        col_i = np.append(col_i, self.n_non_zero + 1)
+        col_i -= 1
 
         # Get the row index
         start = end + self.n_non_zero * 4
-        row_idx = np.array(np.frombuffer(self.lines[end:start], dtype=np.int32))
-        row_idx -= 1
+        row_i = np.array(np.frombuffer(self.lines[end:start], dtype=np.int32))
+        row_i -= 1
 
         if header[2] == 0:  # real
-            nnz_val = np.frombuffer(
+            nnz = np.frombuffer(
                 self.lines[start : start + self.n_non_zero * 8],
                 dtype=np.float64,
             )
 
         else:  # complex
-            nnz_val = np.frombuffer(
+            nnz = np.frombuffer(
                 self.lines[start : start + self.n_non_zero * 16],
                 dtype=np.complex128,
             )
 
         if csc_format:
             return sp.csc_matrix(
-                (nnz_val, row_idx, col_ptr), shape=(self.n_basis, self.n_basis)
+                (nnz, row_i, col_i), shape=(self.n_basis, self.n_basis)
             )
 
         else:
             return sp.csc_matrix(
-                (nnz_val, row_idx, col_ptr), shape=(self.n_basis, self.n_basis)
+                (nnz, row_i, col_i), shape=(self.n_basis, self.n_basis)
             ).toarray()
diff --git a/tests/test_output.py b/tests/test_output.py
index 792313e..d08505a 100644
--- a/tests/test_output.py
+++ b/tests/test_output.py
@@ -2,28 +2,21 @@
 
 import numpy as np
 import pytest
-import yaml
 from dfttoolkit.output import AimsOutput
 
 
 class TestAimsOutput:
+    @property
+    def _aims_fixture_no(self) -> int:
+        return int(self.ao.path.split("/")[-2])
 
     @pytest.fixture(params=range(1, 11), autouse=True)
-    def aims_out(self, request, aims_calc_dir):
-
-        cwd = os.path.dirname(os.path.realpath(__file__))
+    def aims_out(self, cwd, request, aims_calc_dir):
 
         self.ao = AimsOutput(
             aims_out=f"{cwd}/fixtures/{aims_calc_dir}/{str(request.param)}/aims.out"
         )
 
-        with open(f"{cwd}/test_references.yaml", "r") as references:
-            self.ref_data = yaml.safe_load(references)
-
-    @property
-    def _aims_fixture_no(self) -> int:
-        return int(self.ao.path.split("/")[-2])
-
     def test_get_number_of_atoms(self):
         if self._aims_fixture_no in [4, 6, 8, 10]:
             assert self.ao.get_number_of_atoms() == 2
@@ -49,12 +42,12 @@ def test_check_exit_normal(self):
         else:
             assert self.ao.check_exit_normal() is True
 
-    def test_get_time_per_scf(self):
+    def test_get_time_per_scf(self, ref_data):
         # Fail if the absolute tolerance between any values in test vs. reference array is
         # greater than 2e-3
         assert np.allclose(
             self.ao.get_time_per_scf(),
-            self.ref_data["timings"][self._aims_fixture_no - 1],
+            ref_data["timings"][self._aims_fixture_no - 1],
             atol=2e-3,
         )
 
@@ -84,14 +77,14 @@ def test_get_change_of_total_energy_1(self):
             < 1e-8
         )
 
-    def test_get_change_of_total_energy_2(self):
+    def test_get_change_of_total_energy_2(self, ref_data):
         """Get every energy change"""
 
         # Fail if the absolute tolerance between any values in test vs. reference array is
         # greater than 1e-10
         assert np.allclose(
             self.ao.get_change_of_total_energy(n_occurrence=None),
-            self.ref_data["energy_diffs"][self._aims_fixture_no - 1],
+            ref_data["energy_diffs"][self._aims_fixture_no - 1],
             atol=1e-8,
         )
 
@@ -127,7 +120,7 @@ def test_get_change_of_total_energy_3(self):
 
     #     assert np.allclose(
     #         self.ao.get_change_of_total_energy(n_occurrence=1),
-    #         self.ref_data['all_energies'][self.aims_fixture_no(self.ao) - 1],
+    #         ref_data['all_energies'][self.aims_fixture_no(self.ao) - 1],
     #         atol=1e-10,
     #     )
 
@@ -157,15 +150,11 @@ def test_check_spin_polarised(self):
         else:
             assert self.ao.check_spin_polarised() is False
 
-    def test_get_convergence_parameters(self):
+    def test_get_convergence_parameters(self, ref_data):
         if self._aims_fixture_no in [7, 8]:
-            assert (
-                self.ao.get_convergence_parameters() == self.ref_data["conv_params"][1]
-            )
+            assert self.ao.get_convergence_parameters() == ref_data["conv_params"][1]
         else:
-            assert (
-                self.ao.get_convergence_parameters() == self.ref_data["conv_params"][0]
-            )
+            assert self.ao.get_convergence_parameters() == ref_data["conv_params"][0]
 
     def test_get_final_energy(self):
         final_energies = [
@@ -221,25 +210,25 @@ def compare_n_initial_ks_states():
     # TODO
     # def test_get_all_ks_eigenvalues(self):
     #     if self._aims_fixture_no == 1:
-    #         for key in self.ref_data["eigenvalues"].keys():
+    #         for key in ref_data["eigenvalues"].keys():
     #             # Check the values are within tolerance and that keys match
     #             assert np.allclose(
     #                 self.ao.get_all_ks_eigenvalues()[key],
-    #                 self.ref_data["eigenvalues"][key],
+    #                 ref_data["eigenvalues"][key],
     #                 atol=1e-8,
     #             )
 
     #     elif self._aims_fixture_no in [2, 3]:
     #         spin_up, spin_down = self.ao.get_all_ks_eigenvalues()
 
-    #         for key in self.ref_data["su_eigenvalues"].keys():
+    #         for key in ref_data["su_eigenvalues"].keys():
     #             # Check the values are within tolerance and that keys match
     #             assert np.allclose(
-    #                 spin_up[key], self.ref_data["su_eigenvalues"][key], atol=1e-8
+    #                 spin_up[key], ref_data["su_eigenvalues"][key], atol=1e-8
     #             )
     #             # Repeat for spin_down
     #             assert np.allclose(
-    #                 spin_down[key], self.ref_data["sd_eigenvalues"][key], atol=1e-8
+    #                 spin_down[key], ref_data["sd_eigenvalues"][key], atol=1e-8
     #             )
 
     #     else:
@@ -249,13 +238,13 @@ def compare_n_initial_ks_states():
     # TODO
     # def get_final_ks_eigenvalues_test(self):
 
-    def test_get_pert_soc_ks_eigenvalues(self):
+    def test_get_pert_soc_ks_eigenvalues(self, ref_data):
         if self._aims_fixture_no == 3:
-            for key in self.ref_data["pert_soc_eigenvalues"].keys():
+            for key in ref_data["pert_soc_eigenvalues"].keys():
                 # Check the values are within tolerance and that keys match
                 assert np.allclose(
                     self.ao.get_pert_soc_ks_eigenvalues()[key],
-                    self.ref_data["pert_soc_eigenvalues"][key],
+                    ref_data["pert_soc_eigenvalues"][key],
                     atol=1e-8,
                 )
 

From 9e5ec6194c87dbe8d174c1875b1c087c8a9b7898 Mon Sep 17 00:00:00 2001
From: Dylan <dbmorgan98@gmail.com>
Date: Thu, 21 Nov 2024 16:25:34 +0000
Subject: [PATCH 07/11] Dependency updates

---
 poetry.lock | 379 +++++++++++++++++++++++++---------------------------
 1 file changed, 185 insertions(+), 194 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index f2b8838..55596ac 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -249,76 +249,65 @@ files = [
 
 [[package]]
 name = "contourpy"
-version = "1.3.0"
+version = "1.3.1"
 description = "Python library for calculating contours of 2D quadrilateral grids"
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 files = [
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-    {file = "contourpy-1.3.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:76c905ef940a4474a6289c71d53122a4f77766eef23c03cd57016ce19d0f7b42"},
-    {file = "contourpy-1.3.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:92f8557cbb07415a4d6fa191f20fd9d2d9eb9c0b61d1b2f52a8926e43c6e9af7"},
-    {file = "contourpy-1.3.0-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:36f965570cff02b874773c49bfe85562b47030805d7d8360748f3eca570f4cab"},
-    {file = "contourpy-1.3.0-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:cacd81e2d4b6f89c9f8a5b69b86490152ff39afc58a95af002a398273e5ce589"},
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 [package.dependencies]
@@ -333,73 +322,73 @@ test-no-images = ["pytest", "pytest-cov", "pytest-rerunfailures", "pytest-xdist"
 
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 [package.dependencies]
@@ -513,59 +502,61 @@ test = ["pytest (>=6)"]
 
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 optional = false
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+    {file = "fonttools-4.55.0-cp39-cp39-musllinux_1_2_aarch64.whl", hash = "sha256:a656652e1f5d55b9728937a7e7d509b73d23109cddd4e89ee4f49bde03b736c6"},
+    {file = "fonttools-4.55.0-cp39-cp39-musllinux_1_2_x86_64.whl", hash = "sha256:f50a1f455902208486fbca47ce33054208a4e437b38da49d6721ce2fef732fcf"},
+    {file = "fonttools-4.55.0-cp39-cp39-win32.whl", hash = "sha256:161d1ac54c73d82a3cded44202d0218ab007fde8cf194a23d3dd83f7177a2f03"},
+    {file = "fonttools-4.55.0-cp39-cp39-win_amd64.whl", hash = "sha256:ca7fd6987c68414fece41c96836e945e1f320cda56fc96ffdc16e54a44ec57a2"},
+    {file = "fonttools-4.55.0-py3-none-any.whl", hash = "sha256:12db5888cd4dd3fcc9f0ee60c6edd3c7e1fd44b7dd0f31381ea03df68f8a153f"},
+    {file = "fonttools-4.55.0.tar.gz", hash = "sha256:7636acc6ab733572d5e7eec922b254ead611f1cdad17be3f0be7418e8bfaca71"},
 ]
 
 [package.extras]
@@ -662,22 +653,22 @@ tests = ["coverage[toml]", "pytest", "pytest-cov", "pytest-mock"]
 
 [[package]]
 name = "jedi"
-version = "0.19.1"
+version = "0.19.2"
 description = "An autocompletion tool for Python that can be used for text editors."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "jedi-0.19.1-py2.py3-none-any.whl", hash = "sha256:e983c654fe5c02867aef4cdfce5a2fbb4a50adc0af145f70504238f18ef5e7e0"},
-    {file = "jedi-0.19.1.tar.gz", hash = "sha256:cf0496f3651bc65d7174ac1b7d043eff454892c708a87d1b683e57b569927ffd"},
+    {file = "jedi-0.19.2-py2.py3-none-any.whl", hash = "sha256:a8ef22bde8490f57fe5c7681a3c83cb58874daf72b4784de3cce5b6ef6edb5b9"},
+    {file = "jedi-0.19.2.tar.gz", hash = "sha256:4770dc3de41bde3966b02eb84fbcf557fb33cce26ad23da12c742fb50ecb11f0"},
 ]
 
 [package.dependencies]
-parso = ">=0.8.3,<0.9.0"
+parso = ">=0.8.4,<0.9.0"
 
 [package.extras]
 docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alabaster (==0.7.12)", "babel (==2.9.1)", "chardet (==4.0.0)", "commonmark (==0.8.1)", "docutils (==0.17.1)", "future (==0.18.2)", "idna (==2.10)", "imagesize (==1.2.0)", "mock (==1.0.1)", "packaging (==20.9)", "pyparsing (==2.4.7)", "pytz (==2021.1)", "readthedocs-sphinx-ext (==2.1.4)", "recommonmark (==0.5.0)", "requests (==2.25.1)", "six (==1.15.0)", "snowballstemmer (==2.1.0)", "sphinx (==1.8.5)", "sphinx-rtd-theme (==0.4.3)", "sphinxcontrib-serializinghtml (==1.1.4)", "sphinxcontrib-websupport (==1.2.4)", "urllib3 (==1.26.4)"]
 qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"]
-testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
+testing = ["Django", "attrs", "colorama", "docopt", "pytest (<9.0.0)"]
 
 [[package]]
 name = "jinja2"
@@ -1197,13 +1188,13 @@ files = [
 
 [[package]]
 name = "packaging"
-version = "24.1"
+version = "24.2"
 description = "Core utilities for Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "packaging-24.1-py3-none-any.whl", hash = "sha256:5b8f2217dbdbd2f7f384c41c628544e6d52f2d0f53c6d0c3ea61aa5d1d7ff124"},
-    {file = "packaging-24.1.tar.gz", hash = "sha256:026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002"},
+    {file = "packaging-24.2-py3-none-any.whl", hash = "sha256:09abb1bccd265c01f4a3aa3f7a7db064b36514d2cba19a2f694fe6150451a759"},
+    {file = "packaging-24.2.tar.gz", hash = "sha256:c228a6dc5e932d346bc5739379109d49e8853dd8223571c7c5b55260edc0b97f"},
 ]
 
 [[package]]
@@ -1404,13 +1395,13 @@ diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pyright"
-version = "1.1.387"
+version = "1.1.389"
 description = "Command line wrapper for pyright"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "pyright-1.1.387-py3-none-any.whl", hash = "sha256:6a1f495a261a72e12ad17e20d1ae3df4511223c773b19407cfa006229b1b08a5"},
-    {file = "pyright-1.1.387.tar.gz", hash = "sha256:577de60224f7fe36505d5b181231e3a395d427b7873be0bbcaa962a29ea93a60"},
+    {file = "pyright-1.1.389-py3-none-any.whl", hash = "sha256:41e9620bba9254406dc1f621a88ceab5a88af4c826feb4f614d95691ed243a60"},
+    {file = "pyright-1.1.389.tar.gz", hash = "sha256:716bf8cc174ab8b4dcf6828c3298cac05c5ed775dda9910106a5dcfe4c7fe220"},
 ]
 
 [package.dependencies]
@@ -1887,13 +1878,13 @@ widechars = ["wcwidth"]
 
 [[package]]
 name = "tomli"
-version = "2.0.2"
+version = "2.1.0"
 description = "A lil' TOML parser"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "tomli-2.0.2-py3-none-any.whl", hash = "sha256:2ebe24485c53d303f690b0ec092806a085f07af5a5aa1464f3931eec36caaa38"},
-    {file = "tomli-2.0.2.tar.gz", hash = "sha256:d46d457a85337051c36524bc5349dd91b1877838e2979ac5ced3e710ed8a60ed"},
+    {file = "tomli-2.1.0-py3-none-any.whl", hash = "sha256:a5c57c3d1c56f5ccdf89f6523458f60ef716e210fc47c4cfb188c5ba473e0391"},
+    {file = "tomli-2.1.0.tar.gz", hash = "sha256:3f646cae2aec94e17d04973e4249548320197cfabdf130015d023de4b74d8ab8"},
 ]
 
 [[package]]

From a7ebfa9ef5d3323594b88b889fe0a226e6546512 Mon Sep 17 00:00:00 2001
From: Dylan <dbmorgan98@gmail.com>
Date: Thu, 21 Nov 2024 16:26:37 +0000
Subject: [PATCH 08/11] Added parameter tests and small restructure

---
 dfttoolkit/parameters.py   |  7 +++-
 tests/conftest.py          | 29 +++++++++++---
 tests/test_parameters.py   | 53 ++++++++++++++++----------
 tests/test_references.yaml | 42 +++++++++++++++++++++
 tests/test_utils.py        | 77 ++++++++++++++++++--------------------
 5 files changed, 142 insertions(+), 66 deletions(-)

diff --git a/dfttoolkit/parameters.py b/dfttoolkit/parameters.py
index d919dd5..f8d5a25 100644
--- a/dfttoolkit/parameters.py
+++ b/dfttoolkit/parameters.py
@@ -85,10 +85,15 @@ def remove_keywords(
         ----------
         *args : str
             Keywords to be removed from the control.in file.
-        output : Literal['overwrite', 'print', 'return'], default='overwrite'
+        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.
 
+        Returns
+        -------
+        Union[None, List[str]]
+            If output is "return", the modified file is returned as a list of '\\n'
+            separated strings.
         """
 
         for keyword in args:
diff --git a/tests/conftest.py b/tests/conftest.py
index cbe9132..27fad60 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,6 +1,8 @@
-import pytest
 import os
 import subprocess
+
+import pytest
+import yaml
 from dfttoolkit.utils.file_utils import aims_bin_path_prompt
 
 
@@ -23,7 +25,7 @@ def pytest_addoption(parser):
 
 @pytest.fixture(scope="session")
 def run_aims(request):
-    return request.config.getoption("--run-aims")
+    yield request.config.getoption("--run-aims")
 
 
 @pytest.fixture(scope="session")
@@ -43,9 +45,9 @@ def aims_calc_dir(run_aims):
         cwd = os.path.dirname(os.path.realpath(__file__))
         binary = aims_bin_path_prompt(run_aims, cwd)
         subprocess.run(["bash", f"{cwd}/run_aims.sh", binary, str(run_aims)])
-        return "custom_bin_aims_calcs"
+        yield "custom_bin_aims_calcs"
     else:
-        return "default_aims_calcs"
+        yield "default_aims_calcs"
 
 
 @pytest.fixture(scope="session")
@@ -53,4 +55,21 @@ def tmp_dir(tmp_path_factory):
     """Temporary directory for all tests to write files to"""
 
     d = tmp_path_factory.mktemp("tmp")
-    return d
+    yield d
+
+
+@pytest.fixture(scope="session")
+def ref_data():
+    cwd = os.path.dirname(os.path.realpath(__file__))
+    with open(f"{cwd}/test_references.yaml", "r") as references:
+        yield yaml.safe_load(references)
+
+
+@pytest.fixture(scope="session")
+def cwd():
+    yield os.path.dirname(os.path.realpath(__file__))
+
+
+@pytest.fixture(scope="session")
+def default_calc_dir(cwd):
+    yield f"{cwd}/fixtures/default_aims_calcs/1/"
diff --git a/tests/test_parameters.py b/tests/test_parameters.py
index 5f85a89..e6dd4f3 100644
--- a/tests/test_parameters.py
+++ b/tests/test_parameters.py
@@ -1,47 +1,62 @@
 import os
 import shutil
+
 import pytest
+import yaml
 from dfttoolkit.parameters import AimsControl
 
 
 class TestAimsControl:
+    @property
+    def aims_fixture_no(self) -> int:
+        return int(self.ac.path.split("/")[-2])
 
     @pytest.fixture(params=range(1, 11), autouse=True)
-    def aims_control(self, request, aims_calc_dir):
-        self.cwd = os.path.dirname(os.path.realpath(__file__))
-
+    def aims_control(self, cwd, request, aims_calc_dir):
         self.ac = AimsControl(
-            control_in=f"{self.cwd}/fixtures/{aims_calc_dir}/{str(request.param)}"
+            control_in=f"{cwd}/fixtures/{aims_calc_dir}/{str(request.param)}"
             "/control.in"
         )
 
-        # Read reference
+    @pytest.fixture
+    def ref_files(self, cwd):
         with open(
-            f"{self.cwd}/fixtures/manipulated_aims_files/{str(request.param)}"
-            "/control.in",
+            f"{cwd}/fixtures/manipulated_aims_files/{self.aims_fixture_no}/control.in",
             "r",
         ) as f:
-            self.removed_keywords_control_ref = f.readlines()
+            yield f.readlines()
 
-    @property
-    def _aims_fixture_no(self) -> int:
-        return int(self.ac.path.split("/")[-2])
+    def test_initialise_parameters(self, cwd):
+        with open(
+            f"{cwd}/fixtures/default_aims_calcs/{self.aims_fixture_no}/control.in",
+            "r",
+        ) as f:
+            assert self.ac.lines == f.readlines()
 
-    def test_remove_keywords_overwrite(self, tmp_dir):
+        assert self.ac.lines == self.ac.file_contents["control_in"]
+        assert self.ac.supported_files == ["control_in"]
+        assert self.ac.supported_files == self.ac._supported_files
+        assert self.ac.path.endswith("control.in")
+
+    def test_remove_keywords_overwrite(self, tmp_dir, ref_files):
         control_path = tmp_dir / "control.in"
         shutil.copy(self.ac.path, control_path)
         ac = AimsControl(control_in=str(control_path))
         ac.remove_keywords("xc", "relax_geometry", "k_grid", output="overwrite")
 
-        assert "".join(self.removed_keywords_control_ref) == control_path.read_text()
+        assert "".join(ref_files) == control_path.read_text()
 
-    def test_remove_keywords_print(self, capfd):
+    def test_remove_keywords_print(self, capsys, ref_files):
         self.ac.remove_keywords("xc", "relax_geometry", "k_grid", output="print")
+        out, err = capsys.readouterr()
 
-        out, err = capfd.readouterr()
+        assert out == "".join(ref_files) + "\n"
+        assert err == ""
 
-        # print(out)
-        # print("".join(self.removed_keywords_control_ref))
+    def test_remove_keywords_return(self, ref_files):
+        control = self.ac.remove_keywords("xc", "relax_geometry", "k_grid")
+        assert control == ref_files
 
-        assert out == print("".join(self.removed_keywords_control_ref))
-        assert err == ""
+    def test_get_keywords(self, ref_data):
+        keywords = self.ac.get_keywords()
+        assert keywords == ref_data["keywords"][self.aims_fixture_no - 1]
diff --git a/tests/test_references.yaml b/tests/test_references.yaml
index 6bc4c34..c76687a 100644
--- a/tests/test_references.yaml
+++ b/tests/test_references.yaml
@@ -122,6 +122,48 @@ energy_diffs:
   0.01499, -0.002865, 0.0002206, 7.186e-05, 6.018e-06]
 - [-2.158, -0.07087, 0.04834, 0.1184, -0.003943, 0.0103, -0.001032, 0.004801, 0.002519,
   0.001141, 7.119e-06]
+keywords:
+- { "xc": "pbe", "output_level": "full" }
+- {
+      "xc": "pbe",
+      "spin": "collinear",
+      "default_initial_moment": "1",
+      "output_level": "full",
+  }
+- {
+      "xc": "pbe",
+      "spin": "collinear",
+      "default_initial_moment": "1",
+      "include_spin_orbit": "non_self_consistent",
+      "output_level": "full",
+  }
+- { "xc": "pbe", "k_grid": "1 1 1" }
+- { "xc": "pbe", "relax_geometry": "bfgs 5e-3" }
+- {
+      "xc": "pbe",
+      "k_grid": "8 8 8",
+      "relax_geometry": "bfgs 5e-3",
+      "relax_unit_cell": "full",
+  }
+- {
+      "xc": "pbe",
+      "relax_geometry": "bfgs 5e-3",
+      "sc_accuracy_rho": "1e-10",
+      "sc_accuracy_eev": "1e-6",
+      "sc_accuracy_etot": "1e-12",
+      "sc_accuracy_forces": "1e-8",
+  }
+- {
+      "xc": "pbe",
+      "k_grid": "1 1 1",
+      "sc_iter_limit": "10",
+      "sc_accuracy_rho": "1e-10",
+      "sc_accuracy_eev": "1e-6",
+      "sc_accuracy_etot": "1e-12",
+      "sc_accuracy_forces": "1e-8",
+  }
+- { "xc": "hse06 0.11", "hse_unit": "b" }
+- { "xc": "hse06 0.11", "hse_unit": "b", "k_grid": "8 8 8" }
 pert_soc_eigenvalues:
   eigenvalue_eV: [-511.262291, -511.262291, -25.174078, -25.174077, -13.017798, -13.017797,
     -9.204901, -9.2049, -7.069313, -7.069308, 0.067805, 0.067807, 2.733286, 2.733288,
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 8d57230..54d2f62 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -3,50 +3,45 @@
 from dfttoolkit.utils.run_utils import no_repeat
 
 
-class TestNoRepeat:
+def test_specified_dir_not_found():
+    @no_repeat(calc_dir="bogus")
+    def to_be_decorated():
+        return True
 
-    calc_dir = (
-        f"{os.path.dirname(os.path.realpath(__file__))}/fixtures/default_aims_calcs/1"
-    )
+    with pytest.raises(ValueError) as excinfo:
+        to_be_decorated()
 
-    def test_specified_dir_not_found(self):
-        @no_repeat(calc_dir="bogus")
-        def to_be_decorated():
-            return True
-
-        with pytest.raises(ValueError) as excinfo:
-            to_be_decorated()
-
-        assert "bogus is not a directory." == str(excinfo.value)
-
-    @pytest.mark.parametrize(
-        ("calc_dir", "force", "expected"),
-        [
-            ("./", False, True),
-            (
-                f"{os.path.dirname(os.path.realpath(__file__))}/fixtures/default_aims_calcs/1",
-                True,
-                True,
-            ),
-        ],
-    )
-    def test_default_dir_no_args(self, calc_dir, force, expected):
-        @no_repeat(calc_dir=calc_dir, force=force)
-        def to_be_decorated():
-            return True
+    assert "bogus is not a directory." == str(excinfo.value)
 
-        assert to_be_decorated() == expected
 
-    def test_no_repeat(self, capfd):
-        @no_repeat(calc_dir=self.calc_dir)
-        def to_be_decorated():
-            return True
+@pytest.mark.parametrize(
+    ("default_calc_dir", "force", "expected"),
+    [
+        ("./", False, True),
+        (
+            f"{os.path.dirname(os.path.realpath(__file__))}/fixtures/default_aims_calcs/1",
+            True,
+            True,
+        ),
+    ],
+)
+def test_default_dir_no_args(default_calc_dir, force, expected):
+    @no_repeat(calc_dir=default_calc_dir, force=force)
+    def to_be_decorated():
+        return True
 
-        to_be_decorated()
+    assert to_be_decorated() == expected
 
-        out, err = capfd.readouterr()
-        assert (
-            out
-            == f"aims.out already exists in {self.calc_dir}. Skipping calculation.\n"
-        )
-        assert err == ""
+
+def test_no_repeat(capfd, default_calc_dir):
+    @no_repeat(calc_dir=default_calc_dir)
+    def to_be_decorated():
+        return True
+
+    to_be_decorated()
+
+    out, err = capfd.readouterr()
+    assert (
+        out == f"aims.out already exists in {default_calc_dir}. Skipping calculation.\n"
+    )
+    assert err == ""

From 3ed39bedc999a384ba6d5a65bee11de7df48ffd2 Mon Sep 17 00:00:00 2001
From: Dylan <dbmorgan98@gmail.com>
Date: Fri, 22 Nov 2024 12:29:32 +0000
Subject: [PATCH 09/11] Commented __init__ import and __all__

---
 dfttoolkit/__init__.py | 74 +++++++++++++++++++++---------------------
 1 file changed, 37 insertions(+), 37 deletions(-)

diff --git a/dfttoolkit/__init__.py b/dfttoolkit/__init__.py
index c4f5b04..833fa3c 100644
--- a/dfttoolkit/__init__.py
+++ b/dfttoolkit/__init__.py
@@ -1,38 +1,38 @@
-from .benchmarking import BenchmarkAims
-from .custom_ase import CustomAims
-from .friction import FrictionTensor
-from .geometry import AimsGeometry, VaspGeometry, XSFGeometry, XYZGeometry
-from .output import AimsOutput, ELSIOutput
-from .parameters import AimsControl
-from .trajectory import MDTrajectory
-from .utils import math_utils, units
-from .utils.file_utils import aims_bin_path_prompt, check_required_files
-from .utils.geometry_utils import read_xyz_animation
-from .utils.periodic_table import PeriodicTable
-from .utils.run_utils import no_repeat
-from .vibrations import AimsVibrations, VaspVibrations
-from .visualise import VisualiseAims
+# from .benchmarking import BenchmarkAims
+# from .custom_ase import CustomAims
+# from .friction import FrictionTensor
+# from .geometry import AimsGeometry, VaspGeometry, XSFGeometry, XYZGeometry
+# from .output import AimsOutput, ELSIOutput
+# from .parameters import AimsControl
+# from .trajectory import MDTrajectory
+# from .utils import math_utils, units
+# from .utils.file_utils import aims_bin_path_prompt, check_required_files
+# from .utils.geometry_utils import read_xyz_animation
+# from .utils.periodic_table import PeriodicTable
+# from .utils.run_utils import no_repeat
+# from .vibrations import AimsVibrations, VaspVibrations
+# from .visualise import VisualiseAims
 
-__all__ = [
-    "BenchmarkAims",
-    "CustomAims",
-    "FrictionTensor",
-    "AimsGeometry",
-    "VaspGeometry",
-    "XSFGeometry",
-    "XYZGeometry",
-    "AimsOutput",
-    "ELSIOutput",
-    "AimsControl",
-    "MDTrajectory",
-    "math_utils",
-    "units",
-    "aims_bin_path_prompt",
-    "check_required_files",
-    "read_xyz_animation",
-    "PeriodicTable",
-    "no_repeat",
-    "AimsVibrations",
-    "VaspVibrations",
-    "VisualiseAims",
-]
+# __all__ = [
+#     "BenchmarkAims",
+#     "CustomAims",
+#     "FrictionTensor",
+#     "AimsGeometry",
+#     "VaspGeometry",
+#     "XSFGeometry",
+#     "XYZGeometry",
+#     "AimsOutput",
+#     "ELSIOutput",
+#     "AimsControl",
+#     "MDTrajectory",
+#     "math_utils",
+#     "units",
+#     "aims_bin_path_prompt",
+#     "check_required_files",
+#     "read_xyz_animation",
+#     "PeriodicTable",
+#     "no_repeat",
+#     "AimsVibrations",
+#     "VaspVibrations",
+#     "VisualiseAims",
+# ]

From d3e59152b86c3946fea0cf2dc7e6d5b365d8c4a4 Mon Sep 17 00:00:00 2001
From: Dylan <dbmorgan98@gmail.com>
Date: Fri, 22 Nov 2024 12:30:22 +0000
Subject: [PATCH 10/11] Removed unnecessary imports

---
 tests/test_parameters.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tests/test_parameters.py b/tests/test_parameters.py
index e6dd4f3..05a6d53 100644
--- a/tests/test_parameters.py
+++ b/tests/test_parameters.py
@@ -1,8 +1,6 @@
-import os
 import shutil
 
 import pytest
-import yaml
 from dfttoolkit.parameters import AimsControl
 
 

From 48cd901c2e5f9878ed8c4c70102de17d9f587d2b Mon Sep 17 00:00:00 2001
From: Dylan <dbmorgan98@gmail.com>
Date: Fri, 22 Nov 2024 12:51:39 +0000
Subject: [PATCH 11/11] Added pypi repository for publishing

---
 .github/workflows/pypi.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pypi.yaml b/.github/workflows/pypi.yaml
index 844f1c0..8ec2de1 100644
--- a/.github/workflows/pypi.yaml
+++ b/.github/workflows/pypi.yaml
@@ -52,7 +52,7 @@ jobs:
     environment:
       name: pypi
       # OPTIONAL: uncomment and update to include your PyPI project URL in the deployment status:
-      # url: https://pypi.org/p/YOURPROJECT
+      url: https://pypi.org/project/dfttoolkit/
 
     steps:
       - name: Retrieve release distributions