Support GSD 3 (#739)

* fix mass value in from_parmed * specify gsd version < 3.0 * add support for gsd >= 3.0 * revert convert_parmed changes * change > to >= * change Snapshot to Frame; update gsd minimum version * use hoomd.Snapshot in isinstance * remove gsd major version var * Pin numpy to 1.24.2 to fix breaking string comparison to unyt array --------- Co-authored-by: CalCraven <[email protected]>
mosdef-hub · Jun 27, 2023 · 4bac8e5 · 4bac8e5
1 parent e488a03
commit 4bac8e5
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Showing 4 changed files with 16 additions and 18 deletions.
diff --git a/environment-dev.yml b/environment-dev.yml
@@ -3,7 +3,7 @@ channels:
   - conda-forge
 dependencies:
   - python>=3.8
-  - numpy
+  - numpy=1.24.2
   - sympy
   - unyt<=2.9.2
   - boltons
@@ -15,7 +15,7 @@ dependencies:
   - openbabel>=3.0.0
   - foyer>=0.11.3
   - forcefield-utilities>=0.2.1
-  - gsd>=2.0
+  - gsd>=2.9
   - parmed>=3.4.3
   - pytest-cov
   - codecov

diff --git a/environment.yml b/environment.yml
@@ -3,7 +3,7 @@ channels:
   - conda-forge
 dependencies:
   - python>=3.8
-  - numpy
+  - numpy=1.24.2
   - sympy
   - unyt<=2.9.2
   - boltons

diff --git a/gmso/external/convert_hoomd.py b/gmso/external/convert_hoomd.py
@@ -90,7 +90,7 @@ def to_gsd_snapshot(
 
     Return
     ------
-    gsd_snapshot : gsd.hoomd.Snapshot
+    gsd_snapshot : gsd.hoomd.Frame
         Converted hoomd Snapshot.
     base_units : dict
         Based units dictionary utilized during the conversion.
@@ -102,8 +102,7 @@ def to_gsd_snapshot(
     read force field parameters from a Foyer XML file.
     """
     base_units = _validate_base_units(base_units, top, auto_scale)
-
-    gsd_snapshot = gsd.hoomd.Snapshot()
+    gsd_snapshot = gsd.hoomd.Frame()
 
     gsd_snapshot.configuration.step = 0
     gsd_snapshot.configuration.dimensions = 3
@@ -202,7 +201,6 @@ def to_hoomd_snapshot(
     read force field parameters from a Foyer XML file.
     """
     base_units = _validate_base_units(base_units, top, auto_scale)
-
     hoomd_snapshot = hoomd.Snapshot()
 
     # Write box information
@@ -257,7 +255,7 @@ def _parse_particle_information(
 
     Parameters
     ----------
-    snapshot : gsd.hoomd.Snapshot or hoomd.Snapshot
+    snapshot : gsd.hoomd.Frame or hoomd.Snapshot
         The target Snapshot object.
     top : gmso.Topology
         Topology object holding system information.
@@ -313,7 +311,7 @@ def _parse_particle_information(
         snapshot.particles.typeid[0:] = typeids
         snapshot.particles.mass[0:] = masses
         snapshot.particles.charge[0:] = charges / charge_factor
-    elif isinstance(snapshot, gsd.hoomd.Snapshot):
+    elif isinstance(snapshot, gsd.hoomd.Frame):
         snapshot.particles.N = top.n_sites
         snapshot.particles.types = unique_types
         snapshot.particles.position = xyz
@@ -360,7 +358,7 @@ def _parse_pairs_information(
         snapshot.pairs.group[:] = np.reshape(pairs, (-1, 2))
         snapshot.pairs.types = pair_types
         snapshot.pairs.typeid[:] = pair_typeids
-    elif isinstance(snapshot, gsd.hoomd.Snapshot):
+    elif isinstance(snapshot, gsd.hoomd.Frame):
         snapshot.pairs.N = len(pairs)
         snapshot.pairs.group = np.reshape(pairs, (-1, 2))
         snapshot.pairs.types = pair_types
@@ -372,7 +370,7 @@ def _parse_bond_information(snapshot, top):
 
     Parameters
     ----------
-    snapshot : gsd.hoomd.Snapshot or hoomd.Snapshot
+    snapshot : gsd.hoomd.Frame or hoomd.Snapshot
         The target Snapshot object.
     top : gmso.Topology
         Topology object holding system information
@@ -406,7 +404,7 @@ def _parse_bond_information(snapshot, top):
         snapshot.bonds.types = unique_bond_types
         snapshot.bonds.typeid[0:] = bond_typeids
         snapshot.bonds.group[0:] = bond_groups
-    elif isinstance(snapshot, gsd.hoomd.Snapshot):
+    elif isinstance(snapshot, gsd.hoomd.Frame):
         snapshot.bonds.types = unique_bond_types
         snapshot.bonds.typeid = bond_typeids
         snapshot.bonds.group = bond_groups
@@ -419,7 +417,7 @@ def _parse_angle_information(snapshot, top):
 
     Parameters
     ----------
-    snapshot : gsd.hoomd.Snapshot or hoomd.Snapshot
+    snapshot : gsd.hoomd.Frame or hoomd.Snapshot
         The target Snapshot object.
     top : gmso.Topology
         Topology object holding system information
@@ -453,7 +451,7 @@ def _parse_angle_information(snapshot, top):
         snapshot.angles.types = unique_angle_types
         snapshot.angles.typeid[0:] = angle_typeids
         snapshot.angles.group[0:] = np.reshape(angle_groups, (-1, 3))
-    elif isinstance(snapshot, gsd.hoomd.Snapshot):
+    elif isinstance(snapshot, gsd.hoomd.Frame):
         snapshot.angles.types = unique_angle_types
         snapshot.angles.typeid = angle_typeids
         snapshot.angles.group = np.reshape(angle_groups, (-1, 3))
@@ -467,7 +465,7 @@ def _parse_dihedral_information(snapshot, top):
 
     Parameters
     ----------
-    snapshot : gsd.hoomd.Snapshot or hoomd.Snapshot
+    snapshot : gsd.hoomd.Frame or hoomd.Snapshot
         The target Snapshot object.
     top : gmso.Topology
         Topology object holding system information
@@ -499,7 +497,7 @@ def _parse_dihedral_information(snapshot, top):
         snapshot.dihedrals.types = unique_dihedral_types
         snapshot.dihedrals.typeid[0:] = dihedral_typeids
         snapshot.dihedrals.group[0:] = np.reshape(dihedral_groups, (-1, 4))
-    elif isinstance(snapshot, gsd.hoomd.Snapshot):
+    elif isinstance(snapshot, gsd.hoomd.Frame):
         snapshot.dihedrals.types = unique_dihedral_types
         snapshot.dihedrals.typeid = dihedral_typeids
         snapshot.dihedrals.group = np.reshape(dihedral_groups, (-1, 4))
@@ -547,7 +545,7 @@ def _parse_improper_information(snapshot, top):
         snapshot.impropers.types = unique_improper_types
         snapshot.impropers.typeid[0:] = improper_typeids
         snapshot.impropers.group[0:] = np.reshape(improper_groups, (-1, 4))
-    elif isinstance(snapshot, gsd.hoomd.Snapshot):
+    elif isinstance(snapshot, gsd.hoomd.Frame):
         snapshot.impropers.types = unique_improper_types
         snapshot.impropers.typeid = improper_typeids
         snapshot.impropers.group = np.reshape(improper_groups, (-1, 4))

diff --git a/gmso/formats/gsd.py b/gmso/formats/gsd.py
@@ -57,5 +57,5 @@ def write_gsd(
         shift_coords=shift_coords,
         parse_special_pairs=write_special_pairs,
     )[0]
-    with gsd.hoomd.open(filename, mode="wb") as gsd_file:
+    with gsd.hoomd.open(filename, mode="w") as gsd_file:
         gsd_file.append(gsd_snapshot)