diff --git a/cmeutils/dynamics.py b/cmeutils/dynamics.py index a0d164b..32b6a4a 100644 --- a/cmeutils/dynamics.py +++ b/cmeutils/dynamics.py @@ -30,7 +30,7 @@ def msd_from_gsd( Choose from "window" or "direct". See Freud for the differences https://freud.readthedocs.io/en/latest/modules/msd.html#freud.msd.MSD """ - with gsd.hoomd.open(gsdfile, "rb") as trajectory: + with gsd.hoomd.open(gsdfile, "r") as trajectory: init_box = trajectory[start].configuration.box final_box = trajectory[stop].configuration.box assert all( diff --git a/cmeutils/gsd_utils.py b/cmeutils/gsd_utils.py index 569f094..c1ba685 100644 --- a/cmeutils/gsd_utils.py +++ b/cmeutils/gsd_utils.py @@ -21,12 +21,12 @@ def get_type_position( ---------- typename : str or list of str Name of particles of which to get the positions (found in - gsd.hoomd.Snapshot.particles.types) + gsd.hoomd.Frame.particles.types) If you want the positions of multiple types, pass in a list e.g., ['ca', 'c3'] gsd_file : str, default None Filename of the gsd trajectory - snap : gsd.hoomd.Snapshot, default None + snap : gsd.hoomd.Frame, default None Trajectory snapshot gsd_frame : int, default -1 Frame number to get positions from. Supports negative indexing. @@ -70,7 +70,7 @@ def get_all_types(gsd_file=None, snap=None, gsd_frame=-1): ---------- gsd_file : str, default None Filename of the gsd trajectory - snap : gsd.hoomd.Snapshot, default None + snap : gsd.hoomd.Frame, default None Trajectory snapshot gsd_frame : int, default -1 Frame number to get positions from. Supports negative indexing. @@ -94,7 +94,7 @@ def get_molecule_cluster(gsd_file=None, snap=None, gsd_frame=-1): ---------- gsd_file : str, default None Filename of the gsd trajectory - snap : gsd.hoomd.Snapshot, default None + snap : gsd.hoomd.Frame, default None Trajectory snapshot. gsd_frame : int, default -1 Frame number of gsd_file to use to compute clusters. @@ -125,13 +125,13 @@ def _validate_inputs(gsd_file, snap, gsd_frame): if gsd_file: assert isinstance(gsd_frame, int) try: - with gsd.hoomd.open(name=gsd_file, mode="rb") as f: + with gsd.hoomd.open(name=gsd_file, mode="r") as f: snap = f[gsd_frame] except Exception as e: print("Unable to open the gsd_file") raise e elif snap: - assert isinstance(snap, gsd.hoomd.Snapshot) + assert isinstance(snap, gsd.hoomd.Frame) return snap @@ -148,15 +148,15 @@ def snap_delete_types(snap, delete_types): Parameters ---------- - snap : gsd.hoomd.Snapshot + snap : gsd.hoomd.Frame The snapshot to read in Returns ------- - gsd.hoomd.Snapshot + gsd.hoomd.Frame The new snapshot with particles deleted. """ - new_snap = gsd.hoomd.Snapshot() + new_snap = gsd.hoomd.Frame() delete_ids = [snap.particles.types.index(i) for i in delete_types] selection = np.where(~np.isin(snap.particles.typeid, delete_ids))[0] new_snap.particles.N = len(selection) @@ -225,7 +225,7 @@ def update_rigid_snapshot(snapshot, mb_compound): Parameters ---------- - snapshot : gsd.hoomd.Snapshot + snapshot : gsd.hoomd.Frame The snapshot returned from create_hoomd_forcefield or create_hoomd_simulation in mBuild mb_compound : mbuild.Compound, required @@ -307,7 +307,7 @@ def ellipsoid_gsd(gsd_file, new_file, lpar, lperp): Value of lperp of the ellipsoids """ - with gsd.hoomd.open(new_file, "wb") as new_t: + with gsd.hoomd.open(new_file, "w") as new_t: with gsd.hoomd.open(gsd_file) as old_t: for snap in old_t: snap.particles.type_shapes = [ @@ -352,7 +352,7 @@ def xml_to_gsd(xmlfile, gsdfile): overwrite=True, ) hoomd.util.unquiet_status() - with gsd.hoomd.open(f.name) as t, gsd.hoomd.open(gsdfile, "wb") as newt: + with gsd.hoomd.open(f.name) as t, gsd.hoomd.open(gsdfile, "w") as newt: snap = t[0] bonds = snap.bonds.group bonds = bonds[np.lexsort((bonds[:, 1], bonds[:, 0]))] diff --git a/cmeutils/structure.py b/cmeutils/structure.py index 56a73b3..0b38457 100644 --- a/cmeutils/structure.py +++ b/cmeutils/structure.py @@ -37,7 +37,7 @@ def angle_distribution( Filename of the GSD trajectory. A_name, B_name, C_name : str Name(s) of particles that form the angle triplet - (found in gsd.hoomd.Snapshot.particles.types) + (found in gsd.hoomd.Frame.particles.types) They must be given in the same order as they form the angle start : int Starting frame index for accumulating bond lengths. @@ -78,7 +78,7 @@ def angle_distribution( elif degrees and theta_max is None: theta_max = 180 - trajectory = gsd.hoomd.open(gsd_file, mode="rb") + trajectory = gsd.hoomd.open(gsd_file, mode="r") name = "-".join([A_name, B_name, C_name]) name_rev = "-".join([C_name, B_name, A_name]) @@ -149,7 +149,7 @@ def bond_distribution( Filename of the GSD trajectory. A_name, B_name : str Name(s) of particles that form the bond pair - (found in gsd.hoomd.Snapshot.particles.types) + (found in gsd.hoomd.Frame.particles.types) start : int Starting frame index for accumulating bond lengths. Negative numbers index from the end. (default 0) @@ -179,7 +179,7 @@ def bond_distribution( If histogram is True, returns a 2D array of bin centers and bin heights. """ - trajectory = gsd.hoomd.open(gsd_file, mode="rb") + trajectory = gsd.hoomd.open(gsd_file, mode="r") name = "-".join([A_name, B_name]) name_rev = "-".join([B_name, A_name]) @@ -243,7 +243,7 @@ def dihedral_distribution( Filename of the GSD trajectory. A_name, B_name, C_name, D_name: str Name(s) of particles that form the dihedral quadruplett - (found in gsd.hoomd.Snapshot.particles.types) + (found in gsd.hoomd.Frame.particles.types) They must be given in the same order as they form the dihedral start : int Starting frame index for accumulating bond lengths. @@ -273,7 +273,7 @@ def dihedral_distribution( If histogram is True, returns a 2D array of bin centers and bin heights. """ - trajectory = gsd.hoomd.open(gsd_file, mode="rb") + trajectory = gsd.hoomd.open(gsd_file, mode="r") name = "-".join([A_name, B_name, C_name, D_name]) name_rev = "-".join([D_name, C_name, B_name, A_name]) @@ -391,7 +391,7 @@ def gsd_rdf( Filename of the GSD trajectory. A_name, B_name : str Name(s) of particles between which to calculate the RDF (found in - gsd.hoomd.Snapshot.particles.types) + gsd.hoomd.Frame.particles.types) start : int Starting frame index for accumulating the RDF. Negative numbers index from the end. (default 0) @@ -413,7 +413,7 @@ def gsd_rdf( ------- (freud.density.RDF, float) """ - with gsd.hoomd.open(gsdfile, mode="rb") as trajectory: + with gsd.hoomd.open(gsdfile, mode="r") as trajectory: snap = trajectory[0] if r_max is None: @@ -482,13 +482,13 @@ def get_centers(gsdfile, new_gsdfile): new_gsdfile : str Filename of new GSD for centers. """ - with gsd.hoomd.open(new_gsdfile, "wb") as new_traj, gsd.hoomd.open( - gsdfile, "rb" + with gsd.hoomd.open(new_gsdfile, "w") as new_traj, gsd.hoomd.open( + gsdfile, "r" ) as traj: snap = traj[0] cluster_idx = gsd_utils.get_molecule_cluster(snap=snap) for snap in traj: - new_snap = gsd.hoomd.Snapshot() + new_snap = gsd.hoomd.Frame() new_snap.configuration.box = snap.configuration.box f_box = freud.box.Box.from_box(snap.configuration.box) # Use the freud box to unwrap the particle positions @@ -640,7 +640,7 @@ def all_atom_rdf( ------- freud.density.RDF """ - with gsd.hoomd.open(gsdfile, mode="rb") as trajectory: + with gsd.hoomd.open(gsdfile, mode="r") as trajectory: snap = trajectory[start] if r_max is None: # Use a value just less than half the maximum box length. diff --git a/cmeutils/tests/base_test.py b/cmeutils/tests/base_test.py index 9551568..f9a93ee 100644 --- a/cmeutils/tests/base_test.py +++ b/cmeutils/tests/base_test.py @@ -31,13 +31,13 @@ def gsdfile_images(self, tmp_path): @pytest.fixture def snap(self, gsdfile): - with gsd.hoomd.open(name=gsdfile, mode="rb") as f: + with gsd.hoomd.open(name=gsdfile, mode="r") as f: snap = f[-1] return snap @pytest.fixture def snap_bond(self, gsdfile_bond): - with gsd.hoomd.open(name=gsdfile_bond, mode="rb") as f: + with gsd.hoomd.open(name=gsdfile_bond, mode="r") as f: snap = f[-1] return snap @@ -72,7 +72,7 @@ def p3ht_fresnel(self): def create_frame(i, add_bonds, images, seed=42): np.random.seed(seed) - s = gsd.hoomd.Snapshot() + s = gsd.hoomd.Frame() s.configuration.step = i s.particles.N = 5 s.particles.types = ["A", "B"] @@ -93,7 +93,7 @@ def create_frame(i, add_bonds, images, seed=42): def create_gsd(filename, add_bonds=False, images=False): - with gsd.hoomd.open(name=filename, mode="wb") as f: + with gsd.hoomd.open(name=filename, mode="w") as f: f.extend( [ create_frame(i, add_bonds=add_bonds, images=images) diff --git a/cmeutils/tests/test_gsd.py b/cmeutils/tests/test_gsd.py index a463c1a..7691a35 100644 --- a/cmeutils/tests/test_gsd.py +++ b/cmeutils/tests/test_gsd.py @@ -33,7 +33,7 @@ class TestGSD(BaseTest): def test_ellipsoid_gsd(self, butane_gsd): ellipsoid_gsd(butane_gsd, "ellipsoid.gsd", 0.5, 1.0) - with gsd.hoomd.open(name="ellipsoid.gsd", mode="rb") as f: + with gsd.hoomd.open(name="ellipsoid.gsd", mode="r") as f: snap = f[-1] assert snap.particles.type_shapes[0]["type"] == "Ellipsoid" diff --git a/cmeutils/visualize.py b/cmeutils/visualize.py index dce6a8f..41e9def 100644 --- a/cmeutils/visualize.py +++ b/cmeutils/visualize.py @@ -31,13 +31,13 @@ def __init__( gsd_file : str, required Path to a GSD file to load frame : int, optional, default 0 - The frame of the GSD file to load the gsd.hoomd.Snapshot + The frame of the GSD file to load the gsd.hoomd.Frame view_axis : np.ndarray (3,), optional, default (1, 0, 0) Sets the fresnel.camera attributes of camrea position and direction color_dict : dict, optional, default None Set colors for particle types diameter_scale : float, optional default 0.30 - Scale the diameter values stored in gsd.hoomd.Snapshot + Scale the diameter values stored in gsd.hoomd.Frame height : float, optional default 10 Sets the fresnel.camera height attriubute Acts like a zoom where larger values zooms out @@ -62,7 +62,7 @@ def __init__( upwrap_positions: bool, optional, default False If True, the particle positions are unwrapped in the image This requires the GSD file snapshot contain accurate values for - gsd.hoomd.Snapshot.particles.image + gsd.hoomd.Frame.particles.image device, fresnel.Device(), optional Set the device to be used by the scene and in rendering. show_box: bool, optional, default True @@ -113,7 +113,7 @@ def frame(self, frame): @property def snapshot(self): - """gsd.hoomd.Snapshot loaded from the GSD file. + """gsd.hoomd.Frame loaded from the GSD file. The snapshot loaded depends on FresnelGSD.frame """ return self._snapshot @@ -154,7 +154,7 @@ def set_type_color(self, particle_type, color): """ if particle_type not in set(self.particle_types): raise ValueError( - f"Particle type of {particle_type} is not in the Snapshot" + f"Particle type of {particle_type} is not in the Frame" ) self._color_dict[particle_type] = color @@ -163,7 +163,7 @@ def unwrap_positions(self): """If set to True, then positions of the particles are unwrapped before creating the image. This requires that the GSD file snapshots contain accurate - image values (gsd.hoomd.Snapshot.particles.image + image values (gsd.hoomd.Frame.particles.image """ return self._unwrap_positions @@ -290,7 +290,7 @@ def positions(self): @property def radius(self): """Sets the size of the particles. - Determined by the gsd.hoomd.Snapshot.particles.diameter + Determined by the gsd.hoomd.Frame.particles.diameter values and FresnelGSD.diameter_scale """ return self.snapshot.particles.diameter * self.diameter_scale diff --git a/environment-dev.yml b/environment-dev.yml index c8d9243..582cb24 100644 --- a/environment-dev.yml +++ b/environment-dev.yml @@ -3,8 +3,8 @@ channels: - conda-forge dependencies: - fresnel - - freud - - gsd=2.9 + - freud>=2.13.1 + - gsd>=3.0 - hoomd<4.0=*cpu* - mbuild - numpy diff --git a/environment.yml b/environment.yml index 519a469..ef6cecc 100644 --- a/environment.yml +++ b/environment.yml @@ -3,8 +3,8 @@ channels: - conda-forge dependencies: - fresnel - - freud - - gsd=2.9 + - freud>=2.13.1 + - gsd>=3.0 - hoomd<4.0=*cpu* - mbuild - numpy