Production/Stable

* automatic exclusion of atoms with zero radius from surface analysis
  (this creates artefacts especially with the triangulation in GITIM)
* Chacon-Tarazona support removed (contact developers to reintroduce it if needed)
* ready for integration in MDAKit (see https://github.com/MDAnalysis/MDAKits)
* version bump to 1.0.0

AUTHORS.md

@@ -0,0 +1,7 @@
+Marcello-Sega https://api.github.com/users/Marcello-Sega
+gyorgy-hantal https://api.github.com/users/gyorgy-hantal
+balazsfabian https://api.github.com/users/balazsfabian
+elija-feigl https://api.github.com/users/elija-feigl
+JakobMichl https://api.github.com/users/JakobMichl
+iuvenis https://api.github.com/users/iuvenis
+bnovak1 https://api.github.com/users/bnovak1

README.md

@@ -26,7 +26,6 @@ So far the following interface/phase identification methods have been implemente
 * GITIM 
 * SASA
 * Willard Chandler
-* Chacon Tarazona
 * DBSCAN filtering
 
 ## Supported formats
@@ -475,7 +474,5 @@ Depending on which algorithm you are using, you might also want to cite the foll
 
 [M. Sega and G. Hantal._Phys. Chem. Chem. Phys._ **29**, 18968-18974 (2017)](https://doi.org/10.1039/C7CP02918G) Phase and interface determination in computer simulations of liquid mixtures with high partial miscibility.
 
-[E. Chacón, P. Tarazona, Phys. Rev. Lett. **91**, 166103 (2003)](http://dx.doi.org/10.1103/PhysRevLett.91.166103) Intrinsic profiles beyond the capillary wave theory: A Monte Carlo study.
-
 [A. P. Willard, D. Chandler, J. Phys. Chem. B **114**,1954 (2010)](http://dx.doi.org/10.1021/jp909219k) Instantaneous Liquid Interfaces
 

README.rst

@@ -12,8 +12,8 @@ So far the following methods have been implemented:
 
 * ITIM
 * GITIM 
+* SASA
 * Willard Chandler
-* Chacon Tarazona
 * DBSCAN filtering
 
 ----

docs/source/conf.py

@@ -86,7 +86,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:

docs/source/index.rst

@@ -24,7 +24,6 @@
     ITIM
     GITIM
     WillardChandler
-    ChaconTarazona
     SimpleInterface
     observables
     datafiles

pytim/__init__.py

@@ -7,7 +7,6 @@
 from .gitim import GITIM
 from .sasa import SASA
 from .willard_chandler import WillardChandler
-from .chacon_tarazona import ChaconTarazona
 from . import observables, utilities, datafiles
 from .version import __version__
 import warnings

pytim/gitim.py

@@ -68,6 +68,10 @@ class GITIM(Interface):
                                     of the interface: 'generic' (default)
                                     or  'planar'
         :param bool centered:       Center the  :py:obj:`group`
+        :param bool include_zero_radius: if false (default) exclude atoms with zero radius
+                                    from the surface analysis (they are always included
+                                    in the cluster search, if present in the relevant
+                                    group) to avoid some artefacts.
         :param bool info:           Print additional info
         :param bool warnings:       Print warnings
         :param bool autoassign:     If true (default) detect the interface
@@ -124,6 +128,7 @@ def __init__(self,
                  max_layers=1,
                  radii_dict=None,
                  cluster_cut=None,
+                 include_zero_radius=False,
                  cluster_threshold_density=None,
                  extra_cluster_groups=None,
                  biggest_cluster_only=False,
@@ -155,6 +160,7 @@ def __init__(self,
         self.normal = None
         self.PDB = {}
         self.molecular = molecular
+        self.include_zero_radius = include_zero_radius
         sanity.assign_cluster_params(cluster_cut,
                                      cluster_threshold_density, extra_cluster_groups)
         sanity.check_multiple_layers_options()
@@ -254,7 +260,8 @@ def _assign_layers_setup(self):
         # then all atoms in the larges group are labelled as liquid-like
         self.label_group(self.cluster_group.atoms, beta=0.0)
 
-        alpha_group = self.cluster_group[:]
+        if self.include_zero_radius: alpha_group = self.cluster_group[:]
+        else: alpha_group = self.cluster_group[self.cluster_group.radii > 0.0]
 
         # TODO the successive layers analysis should be done by removing points
         # from the triangulation and updating the circumradius of the neighbors

pytim/interface.py

@@ -73,6 +73,9 @@ class Interface(object):
     autoassign, _autoassign =\
         _create_property('autoassign',
                          "(bool) assign layers every time a frame changes")
+    include_zero_radius, _include_zero_radius=\
+        _create_property('include_zero_radius',
+                         "(bool) include atoms with zero radius in the analysis (excluded by default)")
     cluster_threshold_density, _cluster_threshold_density =\
         _create_property('cluster_threshold_density',
                          "(float) threshold for the density-based filtering")

pytim/itim.py

@@ -56,6 +56,10 @@ class ITIM(Interface):
                                   search, if cluster_cut is not None
         :param Object extra_cluster_groups: Additional groups, to allow for
                                   mixed interfaces
+        :param bool include_zero_radius: if false (default) exclude atoms with zero radius
+                                  from the surface analysis (they are always included
+                                  in the cluster search, if present in the relevant
+                                  group) to avoid some artefacts.
         :param bool info:         Print additional info
         :param bool centered:     Center the  :py:obj:`group`
         :param bool warnings:     Print warnings
@@ -186,6 +190,7 @@ def __init__(self,
                  max_layers=1,
                  radii_dict=None,
                  cluster_cut=None,
+                 include_zero_radius=False,
                  cluster_threshold_density=None,
                  extra_cluster_groups=None,
                  info=False,
@@ -214,6 +219,7 @@ def __init__(self,
         self.normal = None
         self.PDB = {}
         self.molecular = molecular
+        self.include_zero_radius = include_zero_radius
 
         sanity.assign_cluster_params(cluster_cut,
                                      cluster_threshold_density, extra_cluster_groups)
@@ -294,6 +300,8 @@ def _assign_one_side(self,
             # atom here goes to 0 to #sorted_atoms, it is not a MDAnalysis
             # index/atom
             for atom in sorted_atoms:
+                if self.include_zero_radius == False and not (_radius[atom] > 0.0):
+                    continue
                 if self._seen[uplow][atom] != 0:
                     continue
 

pytim/observables/rdf.py

@@ -316,7 +316,7 @@ def sample(self, g1=None, g2=None, kargs1=None, kargs2=None):
         self.count += count
 
         box = self.universe.dimensions
-        self.volume += np.product(box[:3])
+        self.volume += np.prod(box[:3])
         self.nsamples += 1
         self.n_squared += len(self.g1) * len(self.g2)