feat: add slip length information to post of Gamma.py

apex/core/property/Gamma.py

@@ -267,11 +267,12 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                                                             np.array([relax_a, relax_b, relax_c]))
                         norm_length = np.linalg.norm(slip_vector_cartesian, 2)
                         frac_slip_vec = np.array([norm_length, 0, 0])
-                    except:
+                    except Exception:
                         raise RuntimeError(
                             'Only int | float or '
                             'Sequence[int | float, int | float, int | float] is allowed for the input_length'
                         )
+                self.slip_length = frac_slip_vec[0]
                 # get displaced structure
                 for obtained_slab in self.__displace_slab_generator(slab,
                                                                     disp_vector=frac_slip_vec,
@@ -299,6 +300,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                     # vasp.perturb_xz('POSCAR', 'POSCAR', self.pert_xz)
                     # record miller
                     dumpfn(self.plane_miller, "miller.json")
+                    dumpfn(self.slip_length, 'slip_length.json')
                     count += 1
                 os.chdir(cwd)
 
@@ -546,12 +548,11 @@ def _compute_lower(self, output_file, all_tasks, all_res):
                 + str(self.displace_direction)
             )
             """
-            ptr_data += "No_task: \tDisplacement \tStacking_Fault_E(J/m^2) EpA(eV) slab_equi_EpA(eV)\n"
+            ptr_data += "No_task: \tDisplacement \tDisplace_Length(\AA) \tStacking_Fault_E(J/m^2) EpA(eV) slab_equi_EpA(eV)\n"
             all_tasks.sort()
             n_steps = len(all_tasks) - 1
-            task_result_slab_equi = loadfn(
-                os.path.join(all_tasks[0], "result_task.json")
-            )
+            task_result_slab_equi = loadfn(os.path.join(all_tasks[0], "result_task.json"))
+            slip_length = loadfn(os.path.join(all_tasks[0], "slip_length.json"))
             for ii in all_tasks:
                 task_result = loadfn(os.path.join(ii, "result_task.json"))
                 natoms = np.sum(task_result["atom_numbs"])
@@ -581,16 +582,17 @@ def _compute_lower(self, output_file, all_tasks, all_res):
                         / AA
                         * Cf
                 )
-
+                frac = int(ii[-4:]) / n_steps
                 miller_index = loadfn(os.path.join(ii, "miller.json"))
-                ptr_data += "%-25s     %7.2f   %7.3f    %8.3f %8.3f\n" % (
+                ptr_data += "%-25s    %7.2f   %7.3f  %7.3f    %8.3f %8.3f\n" % (
                     str(miller_index) + "-" + structure_dir + ":",
-                    int(ii[-4:]) / n_steps,
+                    frac,
+                    (slip_length * frac),
                     sfe,
                     epa,
                     equi_epa_slab,
                 )
-                res_data[int(ii[-4:]) / n_steps] = [sfe, epa, equi_epa]
+                res_data[frac] = [(slip_length * frac), sfe, epa, equi_epa]
 
         else:
             if "init_data_path" not in self.parameter:

apex/reporter/property_report.py

@@ -396,28 +396,33 @@ class GammaReport(PropertyReport):
     @staticmethod
     def plotly_graph(res_data: dict, name: str, **kwargs) -> [go, go.layout]:
         displ = []
+        displ_length = []
         fault_en = []
         struct_en = []
         equi_en = []
         for k, v in res_data.items():
             displ.append(k)
-            fault_en.append(v[0])
-            struct_en.append((v[1]))
-            equi_en.append(v[2])
+            displ_length.append(v[0])
+            fault_en.append(v[1])
+            struct_en.append((v[2]))
+            equi_en.append(v[3])
         df = pd.DataFrame({
             "displacement": displ,
+            "displace_length": displ_length,
             "fault_en": fault_en
         })
         trace = go.Scatter(
             name=name,
             x=df['displacement'],
+            # x=df['displace_length'],
             y=df['fault_en'],
             mode='lines+markers'
         )
         layout = go.Layout(
             title='Stacking Fault Energy (Gamma Line)',
             xaxis=dict(
                 title_text="Displacement",
+                # title_text="Displace_Length (Å)",
                 title_font=dict(
                     size=18,
                     color="#7f7f7f"
@@ -437,16 +442,19 @@ def plotly_graph(res_data: dict, name: str, **kwargs) -> [go, go.layout]:
     @staticmethod
     def dash_table(res_data: dict, decimal: int = 3, **kwargs) -> dash_table.DataTable:
         displ = []
+        displ_length = []
         fault_en = []
         struct_en = []
         equi_en = []
         for k, v in res_data.items():
             displ.append(float(k))
-            fault_en.append(v[0])
-            struct_en.append((v[1]))
-            equi_en.append(v[2])
+            displ_length.append(v[0])
+            fault_en.append(v[1])
+            struct_en.append((v[2]))
+            equi_en.append(v[3])
         df = pd.DataFrame({
             "Displace": round_format(displ, decimal),
+            "Slip_Length (Å)": round_format(displ_length, decimal),
             "E_Fault (J/m^2)": round_format(fault_en, decimal),
             "E_Slab (eV)": round_format(struct_en, decimal),
             "E_Equilib (eV)": round_format(equi_en, decimal)

apex/reporter/relaxation_report.py

@@ -54,9 +54,9 @@ def dash_table(res_data: dict, decimal: int = 3, **kwargs) -> dash_table.DataTab
         df = pd.DataFrame({
             "Conf": conf_list,
             "Equi E (eV)": equi_en,
-            "Cell Vector length a (\AA)": cell_vec_a,
-            "Cell Vector length b (\AA)": cell_vec_b,
-            "Cell Vector length c (\AA)": cell_vec_c,
+            "Cell Vector length a (Å)": cell_vec_a,
+            "Cell Vector length b (Å)": cell_vec_b,
+            "Cell Vector length c (Å)": cell_vec_c,
             "Space Group Symbol": space_group_symbol,
             "Space Group Number": space_group_number,
             "Point Group Symbol": point_group_symbol,

tests/output/gamma_00/task.000000/slip_length.json

@@ -0,0 +1 @@
+5.075764016067081

tests/output/gamma_00/task.000001/slip_length.json

@@ -0,0 +1 @@
+5.075764016067081

tests/output/gamma_00/task.000002/slip_length.json

@@ -0,0 +1 @@
+5.075764016067081