Emit warnings for empty Ag and user grid in DensityAnalysis

package/AUTHORS

@@ -152,6 +152,7 @@ Chronological list of authors
   - Mieczyslaw Torchala
   - Haochuan Chen
   - Karthikeyan Singaravelan
+
 2021
   - Aditya Kamath
 

package/CHANGELOG

@@ -21,6 +21,8 @@ The rules for this file:
   * 2.0.0
 
 Fixes
+
+  * UserWarning displayed when empty atomgroup is given to DensityAnalysis (Issue #3055)
   * atommethods (_get_prev/next_residues_by_resid) returns empty residue group 
     when given empty residue group (Issue #3089)
   * MOL2 files without bonds can now be read and written (Issue #3057)

package/MDAnalysis/analysis/density.py

@@ -369,6 +369,7 @@ class DensityAnalysis(AnalysisBase):
     .. versionchanged:: 2.0.0
        :func:`_set_user_grid` is now a method of :class:`DensityAnalysis`.
     """
+
     def __init__(self, atomgroup, delta=1.0,
                  metadata=None, padding=2.0,
                  gridcenter=None,
@@ -383,7 +384,18 @@ def __init__(self, atomgroup, delta=1.0,
         self._ydim = ydim
         self._zdim = zdim
 
+    def _checkinput(self):
+        if len(self._atomgroup) == 0:
+            msg = ("No atoms in selection over whole trajectory")
+            warnings.warn(msg)
+            logger.warning(msg)
+            return 1
+        else:
+            return 0
+
     def _prepare(self):
+        if _checkinput(self) == 1:
+            return
         coord = self._atomgroup.positions
         if self._gridcenter is not None:
             # Issue 2372: padding is ignored, defaults to 2.0 therefore warn
@@ -424,6 +436,8 @@ def _prepare(self):
         self.density = None
 
     def _single_frame(self):
+        if _checkinput(self) == 1:
+            return
         h, _ = np.histogramdd(self._atomgroup.positions,
                               bins=self._bins, range=self._arange,
                               normed=False)
@@ -434,6 +448,8 @@ def _single_frame(self):
         self._grid += h
 
     def _conclude(self):
+        if _checkinput(self) == 1:
+            return
         # average:
         self._grid /= float(self.n_frames)
         density = Density(grid=self._grid, edges=self._edges,
@@ -487,8 +503,8 @@ def _set_user_grid(gridcenter, xdim, ydim, zdim, smin, smax):
             raise ValueError("xdim, ydim, and zdim must be numbers") from err
 
         # Set min/max by shifting by half the edge length of each dimension
-        umin = gridcenter - xyzdim/2
-        umax = gridcenter + xyzdim/2
+        umin = gridcenter - xyzdim / 2
+        umax = gridcenter + xyzdim / 2
 
         # Here we test if coords of selection fall outside of the defined grid
         # if this happens, we warn users they may want to resize their grids
@@ -657,7 +673,7 @@ def __init__(self, *args, **kwargs):
 
         parameters = kwargs.pop('parameters', {})
         if (len(args) > 0 and isinstance(args[0], str) or
-            isinstance(kwargs.get('grid', None), str)):
+                isinstance(kwargs.get('grid', None), str)):
             # try to be smart: when reading from a file then it is likely that
             # this is a density
             parameters.setdefault('isDensity', True)
@@ -695,7 +711,8 @@ def _check_set_unit(self, u):
         # all this unit crap should be a class...
         try:
             for unit_type, value in u.items():
-                if value is None:  # check here, too iffy to use dictionary[None]=None
+                # check here, too iffy to use dictionary[None]=None
+                if value is None:
                     self.units[unit_type] = None
                     continue
                 try:
@@ -763,7 +780,8 @@ def convert_length(self, unit='Angstrom'):
         """
         if unit == self.units['length']:
             return
-        cvnfact = units.get_conversion_factor('length', self.units['length'], unit)
+        cvnfact = units.get_conversion_factor(
+            'length', self.units['length'], unit)
         self.edges = [x * cvnfact for x in self.edges]
         self.units['length'] = unit
         self._update()  # needed to recalculate midpoints and origin
@@ -814,8 +832,8 @@ def convert_density(self, unit='Angstrom'):
         if unit == self.units['density']:
             return
         try:
-            self.grid *= units.get_conversion_factor('density',
-                                                     self.units['density'], unit)
+            self.grid *= units.get_conversion_factor(
+                'density', self.units['density'], unit)
         except KeyError:
             errmsg = (f"The name of the unit ({unit} supplied) must be one "
                       f"of:\n{units.conversion_factor['density'].keys()}")
@@ -827,4 +845,5 @@ def __repr__(self):
             grid_type = 'density'
         else:
             grid_type = 'histogram'
-        return '<Density ' + grid_type + ' with ' + str(self.grid.shape) + ' bins>'
+        return '<Density ' + grid_type + ' with ' + \
+            str(self.grid.shape) + ' bins>'