Update abacus_dos_run and abacus_run_md

Author: ahxbcn

src/abacusagent/modules/submodules/dos.py

@@ -334,8 +334,8 @@ def plot_pdos_species(shifted_energy, orbitals, output_dir, nspin, dpi):
             plt.plot(shifted_energy, -pdos_data[1::2], label=f'{species_name} ' + r'$\downarrow$', linestyle='--', linewidth=1.0)
 
     plt.axvline(x=0, color='black', linestyle=':', linewidth=1.0)
-    plt.xlabel('Energy/eV', fontsize=10)
-    plt.ylabel('States/eV', fontsize=10)
+    plt.xlabel('Energy (eV)', fontsize=10)
+    plt.ylabel(r"States ($eV^{-1}$)", fontsize=10)
     plt.xlim(max(min(shifted_energy), -20), min(20, max(shifted_energy)))
     if nspin == 1:
         plt.ylim(bottom=0)
@@ -382,7 +382,7 @@ def plot_pdos_species_shell(shifted_energy, orbitals, output_dir, nspin, dpi):
 
         ax.axvline(x=0, color='black', linestyle=':', linewidth=1.0)
         ax.set_title(f'PDOS for {species}', fontsize=12, pad=10)
-        ax.set_ylabel('States/eV', fontsize=10)
+        ax.set_ylabel(r"States ($eV^{-1}$)", fontsize=10)
         ax.set_xlim(max(min(shifted_energy), -20), min(20, max(shifted_energy)))
         #if nspin == 1:
         #    ax.set_ylim(bottom=0)
@@ -391,7 +391,7 @@ def plot_pdos_species_shell(shifted_energy, orbitals, output_dir, nspin, dpi):
 
         #ax.set_ylim(bottom=0)
 
-    axes[-1].set_xlabel('Energy/eV', fontsize=10)
+    axes[-1].set_xlabel('Energy (eV)', fontsize=10)
 
     plt.tight_layout()
     pdos_pic_file = os.path.join(output_dir, 'PDOS.png')
@@ -460,13 +460,13 @@ def plot_pdos_species_orbital(shifted_energy, orbitals, output_dir, nspin, label
             ax.set_xlim(max(min(shifted_energy), -20), min(20, max(shifted_energy)))
             if nspin == 1:
                 ax.set_ylim(bottom=0)
-            ax.set_ylabel('States/eV', fontsize=10)
+            ax.set_ylabel(r"States ($eV^{-1}$)", fontsize=10)
             ax.legend(fontsize=8, ncol=nspin)
             ax.grid(alpha=0.3)
 
             subplot_count += 1
 
-    axes[-1].set_xlabel('Energy/eV', fontsize=10)
+    axes[-1].set_xlabel('Energy (eV)', fontsize=10)
 
     plt.tight_layout()
     pdos_pic_file = os.path.join(output_dir, 'PDOS.png')
@@ -500,8 +500,8 @@ def plot_dos(file_path: List[Path],
         plt.plot(energy, dos, linestyle='-', label='spin up')
         plt.plot(energy, -dos_dn, linestyle='--', label='spin down')
     plt.axvline(x=0, color='k', linestyle='--', alpha=0.5)
-    plt.xlabel('Energy/eV')
-    plt.ylabel('States/ev')
+    plt.xlabel('Energy (eV)')
+    plt.ylabel(r'States ($eV^{-1}$)')
     plt.title('Density of States')
     plt.grid(True, alpha=0.3)
     plt.xlim(x_min, x_max)

src/abacusagent/modules/submodules/md.py

@@ -8,8 +8,7 @@
 from abacustest.lib_prepare.abacus import ReadInput, WriteInput, AbacusStru
 
 from abacusagent.init_mcp import mcp
-from abacusagent.modules.util.comm import generate_work_path, link_abacusjob, run_abacus
-from abacusagent.modules.submodules.abacus import abacus_collect_data
+from abacusagent.modules.util.comm import generate_work_path, link_abacusjob, run_abacus, collect_metrics
 
 
 def get_last_md_stru(md_stru_outputdir: Path) -> Path:
@@ -181,7 +180,7 @@ def abacus_run_md(
 
         run_abacus(work_path)
 
-        metrics = abacus_collect_data(work_path)['collected_metrics']
+        metrics = collect_metrics(work_path)
         suffix = input_params.get('suffix', 'ABACUS')
         md_traj_file, traj_frame_nums = convert_md_dump_to_ase_traj(Path(os.path.join(work_path, f'OUT.{suffix}/MD_dump')).absolute())
         return {'md_work_path': work_path,