Refactor atom density class (#48)

* Refactor Atoms_density class to AnalysisBase

* move the deprecated density class to bottom

* add doc for new atom density class

* Update tests/analysis/atom_density/test_atom_density.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* Update docs/analysis/atom_density.md

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

---------

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Author: robinzyb

docs/analysis/atom_density.md

@@ -44,13 +44,16 @@ Next, we move to the analysis of water density at interfaces.
 To perform the water density analysis, the indices of oxygen atoms between two interfaces are need to be specified, as shown in the `O_idx` of the above figure. Again, you can find the indices using the method `find_idx_from_range`, and put these indices (`List`) in the `inp_dict["density_type"]["idx_list"]`. Here, the `density_unit` should be set to `"water"` because the coordinates of oxygen atoms are treated as the positions of water molecules and are converted to water density through unit conversion.
 
 ## Usage
-Now, we import the analysis class `AtomDensity` and gather the following mentioned parameters.
+Now, we import the analysis class `AtomDensity` and gather the above mentioned parameters into a dictionary `inp`. Because the `AtomDensity` class is based on the `AnalysisBase` class from the MDAnalysis package, an `Universe` object is necessary to use the class.
+We recommend that users instantiate an `Universe` object by themselves as follows. The dictionary `inp` is not required.
 ```python
 from ectoolkits.analysis.atom_density import AtomDensity
 
-# from
-inp_dict={
+# The following input
+inp={
      "xyz_file": "./Hematite-pos-1.xyz", # the path to the xyz trajecotry.
+     "format": "XYZ", # could be other formats for trajectories. Please refer to MDAnalysis
+     # https://userguide.mdanalysis.org/stable/formats/index.html#id1
      "cell": [10.0564, 8.7091, 38.506, 90, 90, 90], # the cell parameters
      "surf2": [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43], # the interface on the right
      "surf1": [112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 12], # the interface on the left
@@ -74,9 +77,22 @@ inp_dict={
          ]
  }
 
-ad = AtomDensity(inp_dict)
+xyz_file = inp.get("xyz_file")
+fmt = inp.get("format", "XYZ")
+cell = inp.get("cell")
+cell = Cell.new(cell)
+u = Universe(xyz_file, format=fmt)
+u.atoms.dimensions = cell.cellpar()
+surf1 = inp.get("surf1")
+surf2 = inp.get("surf2")
+density_type = inp.get("density_type")
+ad = AtomDensity(atomgroup=u.atoms,
+                 surf1=surf1,
+                 surf2=surf2,
+                 density_type=density_type)
 ad.run()
 
+
 # detail information is accessible in
 ad.atom_density
 ad.atom_density_z
@@ -90,4 +106,40 @@ all_cent_density = ad.get_ave_density(width_list)
 ad.plot_density(sym=False)
 
 ```
-![density](./figures/density.png)
+![density](./figures/density.png)
+
+
+
+
+## Old inputs
+For users using the following old input. We recommend use the function `run_atom_density_analysis` to parse the input. The usage is present as follows:
+```python
+from ectoolkits.analysis.atom_density import run_atom_density_analysis
+
+# from
+inp_dict={
+     "xyz_file": "./Hematite-pos-1.xyz", # the path to the xyz trajecotry.
+     "cell": [10.0564, 8.7091, 38.506, 90, 90, 90], # the cell parameters
+     "surf2": [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43], # the interface on the right
+     "surf1": [112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 12], # the interface on the left
+     "density_type":[
+         {
+             "element": "O",
+             "idx_method": "manual",
+             "idx_list": O_idx,
+             "density_unit": "water",
+             "dz": 0.05,
+             "name": "O_density"
+             },
+         {
+             "element": "H",
+             "idx_method": "manual",
+             "idx_list": H_idx,
+             "density_unit": "water",
+             "dz": 0.05,
+             "name": "H_density"
+             }
+         ]
+ }
+
+ad = run_atom_density_analysis(input_dict)