Merge branch 'main' into 700-lammpswrite-updates

.github/workflows/CI.yaml

@@ -16,6 +16,7 @@ jobs:
     name: GMSO Tests
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
         os: [macOS-latest, ubuntu-latest]
         python-version: ["3.8", "3.9"]

.pre-commit-config.yaml

@@ -16,12 +16,12 @@ repos:
     - id: trailing-whitespace
       exclude: 'setup.cfg'
 - repo: https://github.com/psf/black
-  rev: 22.10.0
+  rev: 22.12.0
   hooks:
     - id: black
       args: [--line-length=80]
 - repo: https://github.com/pycqa/isort
-  rev: 5.10.1
+  rev: 5.11.1
   hooks:
     - id: isort
       name: isort (python)

README.md

@@ -14,23 +14,26 @@ To learn more, get started, or contribute, check out our [Documentation](https:/
   <img src="docs/images/mosdef_graphic_gmso.png?raw=true" alt="GMSO within the MoSDeF Ecosystem" width="500" height="500"/>
 </p>
 
-This is an example using `mBuild` and `Foyer` to build a `GMSO` topology through [`ParmEd`](https://parmed.github.io/ParmEd/html/index.html) and write out to [`LAMMPS`](https://docs.lammps.org/).
+This is an example using `mBuild` and `Foyer` to build a `GMSO` topology and write out to [`LAMMPS`](https://docs.lammps.org/).
 ```python
 import foyer
+import forcefield_utilities as ffutils
 from mbuild.lib.molecules import Ethane
-from gmso.external.convert_parmed import from_parmed
+from gmso.external.convert_mbuild import from_mbuild
+from gmso.parameterization import apply
 from gmso.formats.lammpsdata import write_lammpsdata
 # Start with a mBuild compound
 mb_ethane = Ethane()
-oplsaa = foyer.Forcefield(name='oplsaa')
+oplsaa = ffutils.FoyerFFs().load('oplsaa').to_gmso_ff()
 # atomtype the system with foyer, and convert the resulting structure to a topology
-typed_ethane = from_parmed(oplsaa.apply(mb_ethane))
-typed_ethane.name = 'ethane'
+gmso_ethane = from_mbuild(mb_ethane)
+apply(top=gmso_ethane,
+      forcefields=oplsaa,
+      identify_connections=True)
 # Write out lammps datafile
-write_lammpsdata(typed_ethane, filename='ethane.lammps', atom_style='full')
+write_lammpsdata(gmso_ethane, filename='ethane.lammps', atom_style='full')
 ```
 
-
 Introduction
 ------------
 
@@ -107,19 +110,36 @@ For full, detailed instructions, refer to the [documentation for installation](h
 conda install -c conda-forge gmso
 ```
 
-### `pip` installation quickstart
-_Note: `GMSO` is not on `pypi` currently, but its dependencies are._
+### Installing from source
 
-```bash
-git clone  https://github.com/mosdef-hub/gmso.git
+Dependencies of GMSO are listed in the files ``environment.yml`` (lightweight environment specification containing minimal dependencies) and ``environment-dev.yml`` (comprehensive environment specification including optional and testing packages for developers).
+The ``gmso`` or ``gmso-dev`` conda environments can be created with
+
+
+```.. code-block:: bash
+git clone https://github.com/mosdef-hub/gmso.git
 cd gmso
-pip install -r requirements.txt
-pip install -e .
+# for gmso conda environment
+conda env create -f environment.yml
+conda activate gmso
+
+# for gmso-dev
+conda env create -f environment-dev.yml
+conda activate gmso-dev
+
+# install a non-editable version of gmso
+pip install .
 ```
 
-`pip` quickstart will install `GMSO` in [`editable` mode](https://pip.pypa.io/en/stable/reference/pip_install/#editable-installs), which means that as you edit the source code of `GMSO` those edits will be reflected in your installation.
+### Install an editable version from source
 
+Once all dependencies have been installed and the ``conda`` environment has been created, the ``GMSO`` itself can be installed.
 
+``` code-block:: bash
+cd gmso
+conda activate gmso-dev # or gmso depending on your installation
+pip install -e .
+```
 Documentation
 -------------
 

gmso/core/topology.py

@@ -1158,18 +1158,6 @@ def get_index(self, member):
 
         return index
 
-    def _reindex_connection_types(self, ref):
-        """Re-generate the indices of the connection types in the topology."""
-        if ref not in self._index_refs:
-            raise GMSOError(
-                f"cannot reindex {ref}. It should be one of "
-                f"{ANGLE_TYPE_DICT}, {BOND_TYPE_DICT}, "
-                f"{ANGLE_TYPE_DICT}, {DIHEDRAL_TYPE_DICT}, {IMPROPER_TYPE_DICT},"
-                f"{PAIRPOTENTIAL_TYPE_DICT}"
-            )
-        for i, ref_member in enumerate(self._set_refs[ref].keys()):
-            self._index_refs[ref][ref_member] = i
-
     def get_forcefield(self):
         """Get an instance of gmso.ForceField out of this topology
 
@@ -1399,6 +1387,8 @@ def save(self, filename, overwrite=False, **kwargs):
         **kwargs:
             The arguments to specific file savers listed below(as extensions):
             * json: types, update, indent
+            * gro: precision
+            * lammps/lammpsdata: atom_style
         """
         if not isinstance(filename, Path):
             filename = Path(filename).resolve()

gmso/formats/__init__.py

@@ -4,10 +4,10 @@
 from .formats_registry import LoadersRegistry, SaversRegistry
 from .gro import read_gro, write_gro
 from .gsd import write_gsd
-from .json import save_json
+from .json import write_json
 from .lammpsdata import write_lammpsdata
 from .mcf import write_mcf
-from .mol2 import from_mol2
+from .mol2 import read_mol2
 from .top import write_top
 from .xyz import read_xyz, write_xyz
 

gmso/formats/json.py

@@ -282,7 +282,7 @@ def _from_json(json_dict):
 
 
 @saves_as(".json")
-def save_json(top, filename, **kwargs):
+def write_json(top, filename, **kwargs):
     """Save the topology as a JSON file.
 
     Parameters

gmso/formats/mol2.py

@@ -12,7 +12,7 @@
 
 
 @loads_as(".mol2")
-def from_mol2(filename, site_type="atom"):
+def read_mol2(filename, site_type="atom"):
     """Read in a TRIPOS mol2 file format into a gmso topology object.
 
     Creates a Topology from a mol2 file structure. This will read in the

gmso/formats/top.py

@@ -21,9 +21,23 @@
 
 
 @saves_as(".top")
-def write_top(top, filename, top_vars=None, simplify_check=False):
-    """Write a gmso.core.Topology object to a GROMACS topology (.TOP) file."""
-    pot_types = _validate_compatibility(top, simplify_check)
+def write_top(top, filename, top_vars=None):
+    """Write a gmso.core.Topology object to a GROMACS topology (.TOP) file.
+
+    Parameters
+    ----------
+    top : gmso.Topology
+        A typed Topology Object
+    filename : str
+        Path of the output file
+
+    Notes
+    -----
+    See https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html for
+    a full description of the top file format. This method is a work in progress and do not currently
+    support the full GROMACS specs.
+    """
+    pot_types = _validate_compatibility(top)
     top_vars = _get_top_vars(top, top_vars)
 
     # Sanity checks
@@ -262,9 +276,9 @@ def _accepted_potentials():
     return accepted_potentials
 
 
-def _validate_compatibility(top, simplify_check):
+def _validate_compatibility(top):
     """Check compatability of topology object with GROMACS TOP format."""
-    pot_types = check_compatibility(top, _accepted_potentials(), simplify_check)
+    pot_types = check_compatibility(top, _accepted_potentials())
     return pot_types
 
 

gmso/utils/compatibility.py

@@ -5,7 +5,7 @@
 from gmso.exceptions import EngineIncompatibilityError
 
 
-def check_compatibility(topology, accepted_potentials, simplify_check=False):
+def check_compatibility(topology, accepted_potentials):
     """
     Compare the potentials in a topology against a list of accepted potential templates.
 
@@ -15,8 +15,7 @@ def check_compatibility(topology, accepted_potentials, simplify_check=False):
         The topology whose potentials to check.
     accepted_potentials: list
         A list of gmso.Potential objects to check against
-    simplify_check : bool, optional, default=False
-        Simplify the sympy expression check, aka, only compare the expression string
+
     Returns
     -------
     potential_forms_dict: dict
@@ -30,7 +29,8 @@ def check_compatibility(topology, accepted_potentials, simplify_check=False):
         # filter_by=PotentialFilters.UNIQUE_NAME_CLASS
     ):
         potential_form = _check_single_potential(
-            atom_type, accepted_potentials, simplify_check
+            atom_type,
+            accepted_potentials,
         )
         if not potential_form:
             raise EngineIncompatibilityError(
@@ -43,7 +43,8 @@ def check_compatibility(topology, accepted_potentials, simplify_check=False):
         # filter_by=PotentialFilters.UNIQUE_NAME_CLASS
     ):
         potential_form = _check_single_potential(
-            connection_type, accepted_potentials, simplify_check
+            connection_type,
+            accepted_potentials,
         )
         if not potential_form:
             raise EngineIncompatibilityError(
@@ -55,14 +56,18 @@ def check_compatibility(topology, accepted_potentials, simplify_check=False):
     return potential_forms_dict
 
 
-def _check_single_potential(potential, accepted_potentials, simplify_check):
+def _check_single_potential(potential, accepted_potentials):
     """Check to see if a single given potential is in the list of accepted potentials."""
+    ind_var = potential.independent_variables
+    u_dims = {para.units.dimensions for para in potential.parameters.values()}
     for ref in accepted_potentials:
-        if ref.independent_variables == potential.independent_variables:
-            if simplify_check:
-                if str(ref.expression) == str(potential.expression):
-                    return {potential: ref.name}
+        ref_ind_var = ref.independent_variables
+        ref_u_dims = set(ref.expected_parameters_dimensions.values())
+        if len(ind_var) == len(ref_ind_var) and u_dims == ref_u_dims:
+            if str(ref.expression) == str(potential.expression):
+                return {potential: ref.name}
             else:
+                print("Simpify", ref, potential)
                 if sympy.simplify(ref.expression - potential.expression) == 0:
                     return {potential: ref.name}
     return False