From a38e601fcb1331deaf9333211ee6fcc5b80b4c9c Mon Sep 17 00:00:00 2001 From: sebastiankloth Date: Thu, 3 Nov 2022 16:20:04 +0100 Subject: [PATCH] Adjusted functions to work with new pbc_poits --- mdevaluate/distribution.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/mdevaluate/distribution.py b/mdevaluate/distribution.py index a4bda18..5f7a27c 100644 --- a/mdevaluate/distribution.py +++ b/mdevaluate/distribution.py @@ -4,7 +4,7 @@ from .coordinates import rotate_axis, polar_coordinates, spherical_coordinates from .atoms import next_neighbors from .autosave import autosave_data from .utils import runningmean -from .pbc import pbc_diff, pbc_points, make_PBC +from .pbc import pbc_diff, pbc_points from .logging import logger from scipy import spatial @@ -144,7 +144,7 @@ def rdf(atoms_a, atoms_b=None, bins=None, box=None, kind=None, chunksize=50000, def pbc_tree_rdf(atoms_a, atoms_b=None, bins=None, box=None, exclude=0, returnx=False, **kwargs): if box is None: box = atoms_a.box.diagonal() - all_coords = pbc_points(pbc_diff(atoms_b,box=box), box, thickness=np.amax(bins)+0.1, center=0) + all_coords = pbc_points(atoms_b, box, thickness=np.amax(bins)+0.1) to_tree = spatial.cKDTree(all_coords) dist = to_tree.query(pbc_diff(atoms_a,box=box),k=len(atoms_b), distance_upper_bound=np.amax(bins)+0.1)[0].flatten() dist = dist[dist < np.inf] @@ -159,8 +159,8 @@ def pbc_tree_rdf(atoms_a, atoms_b=None, bins=None, box=None, exclude=0, returnx= def pbc_spm_rdf(atoms_a, atoms_b=None, bins=None, box=None, exclude=0, returnx=False, **kwargs): if box is None: - box = atoms_a.box.diagonal() - all_coords = pbc_points(pbc_diff(atoms_b,box=box), box, thickness=np.amax(bins)+0.1, center=0) + box = atoms_a.box + all_coords = pbc_points(atoms_b, box, thickness=np.amax(bins)+0.1) to_tree = spatial.cKDTree(all_coords) if all_coords.nbytes/1024**3 * len(atoms_a) < 2: from_tree = spatial.cKDTree(pbc_diff(atoms_a,box=box)) @@ -361,7 +361,7 @@ def next_neighbor_distribution(atoms, reference=None, number_of_neighbors=4, bin def hbonds(D, H, A, box, DA_lim=0.35, HA_lim=0.35, min_cos=np.cos(30*np.pi/180), full_output=False): def dist_DltA(D, H, A, box, max_dist=0.35): - ppoints, pind = make_PBC(D, box, thickness=max_dist+0.1, index=True) + ppoints, pind = pbc_points(D, box, thickness=max_dist+0.1, index=True) Dtree = cKDTree(ppoints) Atree = cKDTree(A) pairs = Dtree.sparse_distance_matrix(Atree, max_dist, output_type='ndarray') @@ -371,7 +371,7 @@ def hbonds(D, H, A, box, DA_lim=0.35, HA_lim=0.35, min_cos=np.cos(30*np.pi/180), return pairs def dist_AltD(D, H, A, box, max_dist=0.35): - ppoints, pind = make_PBC(A, box, thickness=max_dist+0.1, index=True) + ppoints, pind = pbc_points(A, box, thickness=max_dist+0.1, index=True) Atree = cKDTree(ppoints) Dtree = cKDTree(D) pairs = Atree.sparse_distance_matrix(Dtree, max_dist, output_type='ndarray')