Add the gui code to main

.binder/environment.yml

@@ -0,0 +1,18 @@
+name: rdf
+channels:
+  - conda-forge
+dependencies:
+  - python >3.8
+  - conda-forge/label/pyscal_dev::pyscal
+  - rdflib
+  - pyyaml
+  - jupyterlab
+  - graphviz
+  - python-graphviz
+  - pyyaml
+  - ase 
+  - ipycytoscape
+  - voila
+  - plotly
+  - jupyterlab-dash
+  - networkx

example.ipynb

@@ -259,17 +259,53 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "id": "89e1aaca-34b3-472c-8002-1cc11d078f8d",
    "metadata": {
     "tags": []
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "['Al', 'Ni']\n"
+     ]
+    }
+   ],
    "source": [
     "struct_l12 = g.create_structure(\"l12\", element=['Al', 'Ni'], \n",
     "                         lattice_constant=3.57)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "17b9ad8b-bf22-4161-9864-40fa6d224d79",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "61a43f15c15e4a71a52599b4e6be62a3",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "CytoscapeWidget(cytoscape_layout={'name': 'cola', 'avoidOverlap': True, 'animate': True}, cytoscape_style=[{'s…"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "g.visualise()"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "e83523ad-f684-42fe-84e1-da8125201a0d",

pyscal_rdf/graph.py

@@ -365,6 +365,8 @@ def to_file(self, sample, filename=None, format="lammps-dump"):
             asesys = sys.to_ase()
             write(filename, asesys, format="vasp")
         else:
+            #asesys = sys.to_ase()
+            #write(filename, asesys, format=format)
             sys.to_file(filename, format=format)
 
     def serialize(self, filename, format='turtle'):

pyscal_rdf/gui/auto_query.py

@@ -0,0 +1,31 @@
+from ipywidgets import HBox, VBox, Layout
+from pyscal_rdf.gui.create import output, dropdown, button, checkbox, textbox, header, upload, text
+from pyscal_rdf.gui.properties import dataprops, options
+
+class AutoQuery:
+    def __init__(self, theme="teal"):
+        self.first_line = text("Find all samples with..")
+        self.property_dropdown = dropdown("", options, 
+                                          value="Bravais lattice ")
+        self.compare_options = dropdown("", [" equal to ", 
+                                                   " in between ",
+                                                   " equal to either "],
+                                       value=" equal to ")
+        self.compare_output = output(theme=theme)
+        self.input_output = output(theme=theme)
+        self.input_field_1 = textbox("", value="bcc", dtype="text")
+        self.input_field_2 = textbox("", value="", dtype="text")
+        self.run_button = button("Run query", theme=theme)
+        self.show_button = button("Show query", theme=theme)
+        self.result_output = output(theme=theme)
+        self.plot_structure_button = button("Plot structure", theme=theme)
+        self.visualise_graph_button = button("Visualise graph", theme=theme)
+        self.result_plotter = output(theme=theme)
+        self.w1 = HBox(children=[ self.property_dropdown, 
+                       self.compare_output,
+                       self.input_output])
+        self.panel = VBox(children=[self.first_line, 
+               self.w1,
+               HBox(children=[self.run_button, self.show_button]),
+               self.result_output,
+               self.result_plotter])

pyscal_rdf/gui/create.py

@@ -0,0 +1,103 @@
+import ipywidgets as widgets
+from ipywidgets import Layout
+from pyscal_rdf.gui.themes import themes
+import panel as pn
+pn.extension()
+
+def output(theme="teal"):
+    """
+    Create an ouput widget
+    """
+    output = widgets.Output(layout={'border': '1px solid %s'%themes[theme]["border"]})
+    return output
+
+def dropdown(description, options, value=None, disabled=False, tooltip="Select value", theme="teal"):
+    if value is None:
+        value = options[0]
+
+    dropdown = widgets.Dropdown(
+        options = options,
+        value = value,
+        description = description,
+        description_long = description,
+        disabled=disabled,
+        tooltip=tooltip,
+    )    
+    return dropdown
+
+def button(description, disabled=False, tooltip="Click me", theme="teal"):
+    button = widgets.Button(
+        description=description,
+        disabled=disabled,
+        button_style='',
+        tooltip=tooltip,
+    )
+    button.style.button_color = themes[theme]["button"]
+    return button
+
+def checkbox(description, value=True, theme="teal"):
+    checkbox = widgets.Checkbox(
+        value=value,
+        description=description,
+        disabled=False
+    )
+    return checkbox 
+
+def textbox(description, value, dtype, theme="teal", disabled=False, tooltip="Enter value"):
+    if dtype == "int":
+        inttext = widgets.IntText(
+            value=value,
+            description=description,
+            disabled=disabled,
+            tooltip=tooltip,
+        )
+        return inttext
+    elif dtype == "float":
+        inttext = widgets.FloatText(
+            value=value,
+            description=description,
+            disabled=disabled,
+            tooltip=tooltip,
+        )
+        return inttext
+    elif dtype == "text":
+        inttext = widgets.Text(
+            value=value,
+            description=description,
+            disabled=disabled,
+            tooltip=tooltip,
+        )
+        return inttext 
+    elif dtype == "textarea":
+        inttext = widgets.Textarea(
+            value=value,
+            description=description,
+            disabled=disabled,
+            tooltip=tooltip,
+            layout=Layout(width="auto", height="100%")
+        )
+        return inttext 
+
+def header(text, tooltip="", theme="teal"):
+    color = themes[theme]["header"]
+    header = widgets.HTML(value = f"<b><font color='{color}'>{text}</b>",tooltip=tooltip)
+    return header
+
+def text(text, tooltip="", theme="teal"):
+    color = themes[theme]["text"]
+    header = widgets.HTML(value = f"<font color='{color}'>{text}", tooltip=tooltip)
+    return header
+
+def upload(theme="teal", tooltip="Select file to upload"):
+    upload = widgets.FileUpload(
+        accept='',
+        multiple=False,
+        tooltip=tooltip,
+    )
+    return upload
+
+def download(filename, theme="teal"):
+    download = pn.widgets.FileDownload(file=filename, 
+                            embed=True)
+    return download
+

pyscal_rdf/gui/create_element.py

@@ -0,0 +1,29 @@
+from ipywidgets import HBox, VBox, Layout
+from pyscal_rdf.gui.create import dropdown, button, checkbox, textbox, header
+from pyscal.crystal_structures import elements, structures
+el_list = list(elements.keys())
+
+class CreateElement:
+    def __init__(self, theme="teal"):
+        #create widgets
+        self.dropdown = dropdown('Element', 
+                                 el_list, 
+                                 value="Fe", 
+                                 theme=theme)
+        self.run_button = button('Generate', 
+                                 theme=theme)
+        self.checkbox = checkbox('Add to graph', 
+                                 theme=theme)
+        self.repetition_box = textbox('Repetitions', 
+                                      value=1, 
+                                      theme=theme,
+                                      dtype="int")
+        self.text = "Create using element symbol"
+        self.header = header(self.text, 
+                             theme=theme, tooltip="create an element")
+        self.panel = VBox(children=[self.header,
+                                   self.dropdown,
+                                   self.checkbox,
+                                   self.repetition_box,
+                                   self.run_button])
+

pyscal_rdf/gui/create_gb.py

@@ -0,0 +1,42 @@
+from ipywidgets import HBox, VBox, Layout
+from pyscal_rdf.gui.create import output, dropdown, button, checkbox, textbox, header
+from pyscal.crystal_structures import elements, structures
+st_list = list(structures.keys())
+
+class CreateGB:
+    def __init__(self, theme="teal"):
+        #create widgets
+        self.axis_box = textbox('Axis', 
+                                value="0 0 1", 
+                                theme=theme,
+                                dtype="text",)
+        self.gb_plane_box = textbox('GB Plane', 
+                                value="3 -1 0", 
+                                theme=theme,
+                                dtype="text")
+        self.rep_box = textbox('Repetitions', 
+                                value="1 1 1", 
+                                theme=theme,
+                                dtype="text")
+        #self.sigma_dropdown = dropdown('Sigma', 
+        #                              value=5, 
+        #                              theme=theme,
+        #                             dtype="int")
+        self.sigma_button = button('Find sigma', 
+                                 theme=theme,
+                                 disabled=False,
+                                 tooltip="Calculate possible sigma values, only 10 results are shown")
+        self.gb_plane_button = button('Find possible GB planes', 
+                                 theme=theme,
+                                 disabled=False,
+                                 tooltip="Calculate possible gb plane, only 10 results are shown")
+        self.run_button = button('Generate', 
+                                 theme=theme,
+                                 disabled=True,
+                                 tooltip="Creating a structure using the above methods is necessary. Reading in a file does not work")
+        self.widget_list = [self.axis_box, self.sigma_button]
+        self.panel = HBox(children=self.widget_list)
+        self.sigma_dropdown = None
+        self.sigma_hb = None
+        self.gb_plane_dropdown = None
+        self.gb_plane_hb = None

pyscal_rdf/gui/create_structure.py

@@ -0,0 +1,46 @@
+from ipywidgets import HBox, VBox, Layout
+from pyscal_rdf.gui.create import output, dropdown, button, checkbox, textbox, header
+from pyscal.crystal_structures import elements, structures
+st_list = list(structures.keys())
+el_list = ["H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne", "Na", "Mg", "Al", "Si", "P", "S", "Cl", "K", "Ar", "Ca", "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Ni", "Co", "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", "I", "Te", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg", "Tl", "Pb", "Bi", "Th", "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt", "Ds", "Rg", "Cn", "Nh", "Fl", "Mc", "Lv", "Ts", "Og"]
+
+class CreateStructure:
+    def __init__(self, theme="teal"):
+        #create widgets
+        self.dropdown = dropdown('Structure', 
+                                 st_list, 
+                                 value="bcc", 
+                                 theme=theme)
+        self.run_button = button('Generate', 
+                                 theme=theme)
+        self.checkbox = checkbox('Add to graph', 
+                                 theme=theme)
+        self.repetition_box = textbox('Repetitions', 
+                                      value=1, 
+                                      theme=theme,
+                                     dtype="int")
+        self.lattice_parameter_box = textbox('LatticeParameter', 
+                                      value=1, 
+                                      theme=theme,
+                                      dtype="float")
+        self.element_box = dropdown('Element', 
+                                 el_list, 
+                                 value="Fe", 
+                                 theme=theme)
+        self.element_box_2 = dropdown('Element', 
+                                 el_list, 
+                                 value="Al", 
+                                 theme=theme,
+                                 disabled=True)
+
+        self.text = "Create a bulk structure"
+        self.header = header(self.text, theme=theme)
+        self.panel = VBox(children=[self.header,
+                                   self.dropdown,
+                                   self.checkbox,
+                                   self.repetition_box,
+                                   self.lattice_parameter_box,
+                                   self.element_box,
+                                   self.element_box_2, 
+                                   self.run_button])
+

pyscal_rdf/gui/create_vacancy.py

@@ -0,0 +1,21 @@
+from ipywidgets import HBox, VBox, Layout
+from pyscal_rdf.gui.create import output, dropdown, button, checkbox, textbox, header
+from pyscal.crystal_structures import elements, structures
+st_list = list(structures.keys())
+
+class CreateVacancy:
+    def __init__(self, theme="teal"):
+        #create widgets
+        self.vacancy_dropdown = dropdown('Add vacancy', 
+                                ["concentration", "number"], 
+                                theme=theme,
+                                )
+        self.vacancy_box = textbox('', 
+                                value="0", 
+                                theme=theme,
+                                dtype="text")
+        self.run_button = button('Generate', 
+                                 theme=theme,
+                                 disabled=True,
+                                 tooltip="Add either vacancy concentration or number")
+        self.panel = VBox(children=[HBox(children=[self.vacancy_dropdown, self.vacancy_box]), self.run_button])

pyscal_rdf/gui/ontology.py

@@ -0,0 +1,11 @@
+from ipywidgets import HBox, VBox, Layout
+from pyscal_rdf.gui.create import output, dropdown, button, checkbox, textbox, header, upload
+
+class Ontology:
+    def __init__(self, theme="teal"):
+        #create widgets
+        self.text = "pyscal-rdf uses the Computational Material Sample Ontology"
+        self.header = header(self.text, theme=theme)
+        self.output = output()
+        self.panel = VBox(children=[self.header, 
+                                    self.output])