Write charge in elementary charge unit (XML writer) (#794)

* make default charge to be written out elementary_charge instead of coulomb

* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci

* change default behavior for json writer

* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci

* add missing alias for atom restraint

* change the types check in json writer to be a awarning

* fix unit test

* Update gmso/core/atom_type.py

Co-authored-by: CalCraven <54594941+CalCraven@users.noreply.github.com>

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: CalCraven <54594941+CalCraven@users.noreply.github.com>

gmso/core/atom.py

@@ -67,6 +67,7 @@ class Atom(Site):
         Refer to https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html
         for more information.
         """,
+        alias="restraint",
     )
 
     model_config = ConfigDict(

gmso/core/atom_type.py

@@ -14,6 +14,7 @@
     unyt_compare,
     unyt_to_hashable,
 )
+from gmso.utils.units import GMSO_UnitRegistry
 
 
 class AtomType(ParametricPotential):
@@ -254,7 +255,9 @@ def validate_charge(cls, charge):
             warnings.warn(
                 UNIT_WARNING_STRING.format("Charges", "elementary charge")
             )
-            charge *= u.elementary_charge
+            charge *= u.Unit(
+                "elementary_charge", registry=GMSO_UnitRegistry().reg
+            )
         else:
             ensure_valid_dimensions(charge, u.elementary_charge)
 

gmso/core/forcefield.py

@@ -56,7 +56,7 @@ class ForceField(object):
         If true, perform a strict validation of the forcefield XML file
     greedy: bool, default=True
         If True, when using strict mode, fail on the first error/mismatch
-    backend: str, default="gmso"
+    backend: str, default="forcefield-utilities"
         Can be "gmso" or "forcefield-utilities". This will define the methods to
         load the forcefield.
 
@@ -579,6 +579,12 @@ def xml_from_forcefield_utilities(cls, filename):
         except:
             loader = FoyerFFs()
             ff = loader.load(filename).to_gmso_ff()
+            ff.units = {
+                "energy": "kJ",
+                "distance": "nm",
+                "mass": "amu",
+                "charge": "elementary_charge",
+            }
         return ff
 
     def to_xml(self, filename, overwrite=False, backend="gmso"):
@@ -647,7 +653,7 @@ def _xml_from_gmso(self, filename, overwrite=False):
                     "energy": "kJ",
                     "distance": "nm",
                     "mass": "amu",
-                    "charge": "coulomb",
+                    "charge": "elementary_charge",
                 },
             )
 

gmso/formats/json.py

@@ -21,7 +21,7 @@
 from gmso.formats.formats_registry import loads_as, saves_as
 
 
-def _to_json(top, types=False, update=True):
+def _to_json(top, types=True, update=False):
     """Return a json serializable dictionary from a topology.
 
     This method is used for json serializing the topology
@@ -30,7 +30,7 @@ def _to_json(top, types=False, update=True):
     ----------
     top: gmso.Topology, required
         The topology
-    types: bool, default=False
+    types: bool, default=True
         If true, include type info (i.e. Potentials)
     update: bool, default=False
         If true, update the topology before iterating through the files
@@ -41,9 +41,10 @@ def _to_json(top, types=False, update=True):
         A json serializable dictionary representing members of this Topology
     """
     if types and not top.is_typed():
-        raise ValueError(
+        warnings.warn(
             "Cannot incorporate types because the topology is not typed."
         )
+        types = False
 
     if not types and top.is_typed():
         warnings.warn(
@@ -282,7 +283,7 @@ def _from_json(json_dict):
 
 
 @saves_as(".json")
-def write_json(top, filename, **kwargs):
+def write_json(top, filename, types=True, update=False, **kwargs):
     """Save the topology as a JSON file.
 
     Parameters
@@ -291,11 +292,17 @@ def write_json(top, filename, **kwargs):
         The topology to save
     filename: str, pathlib.Path
         The file to save to topology to, must be suffixed with .json
+    types: bool, default=True
+        If true, include type info (i.e. Potentials)
+    update: bool, default=False
+        If true, update the topology before iterating through the files
     **kwargs: dict
         The keyword arguments to _to_json and json.dump methods
     """
     json_dict = _to_json(
-        top, update=kwargs.pop("update", True), types=kwargs.pop("types", False)
+        top,
+        update=update,
+        types=types,
     )
     if not isinstance(filename, Path):
         filename = Path(filename).resolve()

gmso/tests/test_serialization.py

@@ -224,7 +224,7 @@ def test_serialization_unsupported_file_format(self, ethane_from_scratch):
             ethane_from_scratch.save("ethane_from_scratch.zip")
 
     def test_serialization_untyped_with_types_info(self, ethane_from_scratch):
-        with pytest.raises(ValueError):
+        with pytest.warns(UserWarning):
             ethane_from_scratch.save("ethane_from_scratch.json", types=True)
 
     def test_serialization_overwrite(self, ethane_from_scratch):

gmso/utils/units.py

@@ -82,22 +82,26 @@ def default_reg():
 
 def register_general_units(reg: u.UnitRegistry):
     """Register units that are generally useful to a basic unyt UnitSystem."""
-    conversion = 1 * getattr(u.physical_constants, "elementary_charge").value
-    dim = u.dimensions.current_mks * u.dimensions.time
+    elementary_charge_conversion = (
+        1 * getattr(u.physical_constants, "elementary_charge").value
+    )
+    charge_dim = u.dimensions.current_mks * u.dimensions.time
     reg.add(
         "elementary_charge",
-        conversion,
-        dim,
+        elementary_charge_conversion,
+        charge_dim,
         r"\rm{e}",
     )  # proton charge
-    conversion = (
+
+    kb_conversion = (
         1 * getattr(u.physical_constants, "boltzmann_constant_mks").value
     )
-    dim = u.dimensions.energy / u.dimensions.temperature
+    kb_dim = u.dimensions.energy / u.dimensions.temperature
     reg.add(
-        "kb", base_value=conversion, dimensions=dim, tex_repr=r"\rm{kb}"
+        "kb", base_value=kb_conversion, dimensions=kb_dim, tex_repr=r"\rm{kb}"
     )  # boltzmann temperature
-    conversion = (
+
+    bohr_rad_conversion = (
         4
         * np.pi
         * getattr(u.physical_constants, "reduced_planck_constant").value ** 2
@@ -107,30 +111,35 @@ def register_general_units(reg: u.UnitRegistry):
             * getattr(u.physical_constants, "electron_mass").value
         )
     )
-    dim = u.dimensions.length
+    bohr_rad_dim = u.dimensions.length
     reg.add(
-        "a0", base_value=conversion, dimensions=dim, tex_repr=r"\rm{a0}"
+        "a0",
+        base_value=bohr_rad_conversion,
+        dimensions=bohr_rad_dim,
+        tex_repr=r"\rm{a0}",
     )  # bohr radius
-    conversion = (
+
+    hartree_conversion = (
         getattr(u.physical_constants, "reduced_planck_constant").value ** 2
         / u.Unit("a0", registry=reg).base_value ** 2
         / getattr(u.physical_constants, "electron_mass").value
     )
-    dim = u.dimensions.energy
+    hartree_dim = u.dimensions.energy
     reg.add(
         "Ehartree",
-        base_value=conversion,
-        dimensions=dim,
+        base_value=hartree_conversion,
+        dimensions=hartree_dim,
         tex_repr=r"\rm{Ehartree}",
     )  # Hartree energy
-    conversion = np.sqrt(
+
+    static_coulomb_conversion = np.sqrt(
         10**9 / (4 * np.pi * getattr(u.physical_constants, "eps_0").value)
     )
-    dim = u.dimensions.charge
+    charge_dim = u.dimensions.charge
     reg.add(
         "Statcoulomb_charge",
-        base_value=conversion,
-        dimensions=dim,
+        base_value=static_coulomb_conversion,
+        dimensions=charge_dim,
         tex_repr=r"\rm{Statcoulomb_charge}",
     )  # Static charge