Issue 1080 (#1088)

* Update fill_region bounds and docstring to be more explicit

* Fix type error caused by treating box as list

* fix backword none check

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* [pre-commit.ci] pre-commit autoupdate (#1089)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/psf/black: 22.12.0 → 23.1.0](psf/black@22.12.0...23.1.0)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

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

* Lammps lj unit charges (#1086)

* Produce n=2 when ports are not capped

* Add option to not scale charges in lj units, and update docs for consistency

* Update mbuild/formats/lammpsdata.py

Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>

---------

Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>

* Update fill_region bounds and docstring to be more explicit

* Fix type error caused by treating box as list

* fix backword none check

* Add unit tests for new errors

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Jennifer A Clark <jennifer.a.clark13@gmail.com>
Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>

Author: 4 people

mbuild/packing.py

@@ -316,9 +316,13 @@ def fill_region(
     fix_orientation : bool or list of bools
         Specify that compounds should not be rotated when filling the box,
         default=False.
-    bounds : list-like of floats [minx, miny, minz, maxx, maxy, maxz], units nm, default=None
-        Bounding within box to pack compounds, if you want to pack within a bounding
+    bounds : list-like of list-likes of floats [[min_x, min_y, min_z, max_x, max_y, max_z], ...], units nm, default=None
+        Bounding(s) within box to pack compound(s). To pack within a bounding
         area that is not the full extent of the region, bounds are required.
+        Each item of `compound` must have its own bound specified. Use `None`
+        to indicate a given compound is not bounded, e.g.
+        `[ [0., 0., 1., 2., 2., 2.], None]` to bound only the first element
+        of `compound` and not the second.
     temp_file : str, default=None
         File name to write PACKMOL raw output to.
     update_port_locations : bool, default=False
@@ -354,6 +358,23 @@ def fill_region(
                 "`compound`, `n_compounds`, and `fix_orientation` must be of "
                 "equal length."
             )
+    if bounds is not None:
+        if not isinstance(bounds, (list)):
+            raise TypeError(
+                "`bounds` must be a list of one or more bounding boxes "
+                "and/or `None` for each item in `compound`."
+            )
+        if len(bounds) != len(n_compounds):
+            raise ValueError(
+                "`compound` and `bounds` must be of equal length. Use `None` "
+                "for non-bounded items in `compound`."
+            )
+        for bound in bounds:
+            if not isinstance(bound, (Box, list)):
+                raise ValueError(
+                    "Each bound in `bounds` must be `None`, `Box`, or a "
+                    "list of [min_x, min_y, min_z, max_x, max_y, max_z]."
+                )
 
     # See if region is a single region or list
     my_regions = []
@@ -373,7 +394,7 @@ def fill_region(
             f"expected a list of type: list or mbuild.Box, was provided {region} of type: {type(region)}"
         )
     container = []
-    if not bounds:
+    if bounds is None:
         bounds = []
     for bound, reg in zip_longest(bounds, my_regions, fillvalue=None):
         if bound is None:

mbuild/tests/test_packing.py

@@ -138,6 +138,33 @@ def test_fill_region_incorrect_type(self, ethane):
                 compound=[ethane], n_compounds=[2], region=box1, bounds=None
             )
 
+    def test_fill_region_bounds_not_list(self, ethane):
+        box1 = Box(lengths=[2, 2, 2], angles=[90.0, 90.0, 90.0])
+        with pytest.raises(TypeError):
+            mb.fill_region(
+                compound=[ethane], n_compounds=[2], region=box1, bounds=box1
+            )
+
+    def test_fill_region_incorrect_bounds_amount(self, ethane, h2o):
+        box1 = Box(lengths=[2, 2, 2], angles=[90.0, 90.0, 90.0])
+        with pytest.raises(ValueError):
+            mb.fill_region(
+                compound=[ethane, h2o],
+                n_compounds=[2, 2],
+                region=box1,
+                bounds=[box1],
+            )
+
+    def test_fill_region_incorrect_bounds_types(self, ethane, h2o):
+        box1 = Box(lengths=[2, 2, 2], angles=[90.0, 90.0, 90.0])
+        with pytest.raises(ValueError):
+            mb.fill_region(
+                compound=[ethane, h2o],
+                n_compounds=[2, 2],
+                region=box1,
+                bounds=[1.0, 1.0, 1.0],
+            )
+
     def test_box_no_bound(self, ethane):
         box1 = Box(lengths=[2, 2, 2], angles=[90.0, 90.0, 90.0])
         mb.fill_region(