mod gui

cmmde_gui/gui.py

@@ -42,7 +42,7 @@ def cmmde_gui():
     software = {'Orca':'orca','GROMACS':'gromacs','Dcdftbmd':'dcdftb','Quantum Espresso':'qe','XTB':'xtb'}
 
 # Orca card
-    job_orca = pn.widgets.MultiSelect(name="Job selections",value=['Single point calculation'],options=['Single point calculation','Geometry optimization','Frequency calculation','TS optimizer','Nudged elastic band'])
+    job_orca = pn.widgets.Select(name="Job selections",value=['Single point calculation'],options=['Single point calculation','Geometry optimization','Frequency calculation','TS optimizer','Nudged elastic band'])
     job_orca_dict = {'Single point calculation':'sp','Geometry optimization':'opt','Frequency calculation':'freq','TS optimizer':'ts','Nudged elastic band':'neb'} 
     method_orca = pn.widgets.Select(name="Method selections",value='GFN2-xTB',options=['GFN2-xTB','GFN1-xTB','B3LYP/def2-svp','M06/def2-svp'])
     method_orca_dict = {'GFN2-xTB':'XTB2', 'GFN1-xTB':'XTB1','DFTB2':'DFTB2','DFTB2-gammah':'DFTB2_gammah','DFTB3':'DFTB3','DFTB3-diag':'DFTB3-diag','B3LYP/def2-svp':'B3LYP def2-svp','M06/def2-svp':'M06 def2-svp'}
@@ -76,7 +76,7 @@ def cmmde_gui():
     run_orca_btn.on_click(run_orca)
 
 # CMMDE job options
-    job_main = pn.widgets.MultiSelect(name="Job selections",value=['Single point calculation'],options=['Single point calculation','Geometry optimization','Frequency calculation'])
+    job_main = pn.widgets.Select(name="Job selections",value='Single point calculation',options=['Single point calculation','Geometry optimization','Frequency calculation'])
     job = {'Single point calculation':'sp','Geometry optimization':'opt','Frequency calculation':'freq'}
 
 
@@ -103,16 +103,16 @@ def cmmde_gui():
         # terminal.clear()
         # unik = str(uuid.uuid4().hex)
         
-        
+        # job_list = [job[i] for i in job_main.value] 
-        Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value 
+        # jobs = ",".join(job_list)
+        Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value + "/" + job[job_main.value] 
+        if not os.path.exists(Folder):
+            os.makedirs(Folder)
         if os.path.exists("{}/geom.smi".format(Folder)):
             os.system("rm {}/geom.smi".format(Folder))
         os.chdir(Folder)
 
         
-        job_list = [job[i] for i in job_main.value] 
-        jobs = ",".join(job_list)
-        
         if editor.value == "":
             FileInput.save("geom.xyz")
             geom = "geom.xyz"
@@ -120,7 +120,7 @@ def cmmde_gui():
             geom = editor.value
             
         TextArea.value = TextArea.value + "\n" + "Mempersiapkan Struktur 3 Dimensi!"
-        list_commands = ["cmmde.py","-i","{}".format(geom),"-s","{}".format(software[software_main.value]),"-j","{}".format(jobs),"-m","{}".format(method[method_btn.value]),"-c","{}".format(charge.value),"-mult","{}".format(mult.value)]
+        list_commands = ["cmmde.py","-i","{}".format(geom),"-s","{}".format(software[software_main.value]),"-j","{}".format(job[job_main.value]),"-m","{}".format(method[method_btn.value]),"-c","{}".format(charge.value),"-mult","{}".format(mult.value)]
         if dispersion_cor.value != 'None':
             new_commands = ["-disp","{}".format(dispersion_cor.value)]
             for i in new_commands:  
@@ -132,11 +132,10 @@ def cmmde_gui():
         cmd = subprocess.run(list_commands,capture_output=True,text=True)
         #terminal.subprocess.run("cmmde.py","-i{}".format(editor.value),"-s{}".format(software[software_main.value]), "-j{}".format(jobs), "-m{}".format(method[method_btn.value]))
         TextArea.value = TextArea.value + "\n" + "Perhitungan anda telah tersubmit!"
-        
 
         # RunMessage.value = "Perhitungan telah tersubmit!"
 
-
+    download_xyz = pn.widgets.FileDownload(file="{}/cmmd.xyz".format(workdir+"/"+id_input.value+"/"+Molecule_input.value+"/"+job[job_main.value]),filename="optimized.xyz")
 
     Run_btn.on_click(run)
 
@@ -206,7 +205,7 @@ def cmmde_gui():
             if not os.path.exists(Post_folder):
                 os.makedirs(Post_folder)
             os.chdir(Post_folder)
-            list_commands = ["cmmde.py","-i","{}/cmmd.xyz".format(Folder),"-s","{}".format(post_software[post_software_main.value]),"-j","{}".format(post_calc[post_btn.value]),"-m","{}".format(post_method[post_method_btn.value])]
+            list_commands = ["cmmde.py","-i","{}/cmmd.xyz".format(Folder+"/"+job[job_main.value]),"-s","{}".format(post_software[post_software_main.value]),"-j","{}".format(post_calc[post_btn.value]),"-m","{}".format(post_method[post_method_btn.value])]
             if dispersion_cor.value != 'None':
                 new_commands = ["-disp","{}".format(dispersion_cor.value)]
                 for i in new_commands:  
@@ -233,7 +232,7 @@ def cmmde_gui():
 
 # Check the calculation progress
     def calc_progress(event):
-        Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value 
+        Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value + "/" + job[job_main.value] 
         os.chdir(Folder)
         cmd = subprocess.run(["tail", "-n", "10", "cmmd.out"],capture_output=True,text=True)
         TextArea.value = TextArea.value + "\n" + cmd.stdout 
@@ -247,13 +246,6 @@ def cmmde_gui():
         TextArea.value = TextArea.value + "\n" + cmd.stdout 
     Checkcalc_btn_post = pn.widgets.Button(name="Check post-calculation",button_type='primary')
     Checkcalc_btn_post.on_click(calc_progress_post)
-# # Download Button
-    download_xyz = pn.widgets.FileDownload(file="cmmd.xyz",filename="optimized.xyz")
-    download_slab = pn.widgets.FileDownload(file="slab.vasp",filename="slab.vasp")
-    download_spec_plot = pn.widgets.FileDownload(file="IR.pdf",filename="IR.pdf")
-    download_spec_raw = pn.widgets.FileDownload(file="IR_fit.dat",filename="IR_fit.dat")
-    download_opt_plot = pn.widgets.FileDownload(file="optimized.pdf",filename="optimized.pdf")
-    download_opt_raw = pn.widgets.FileDownload(file="optimized.dat",filename="optimized.dat")
 # Slab Builder
     hkl_input = pn.widgets.TextInput(name="Miller index (hkl)",placeholder="Example: 100")
     size_input = pn.widgets.TextInput(name="Dimension",placeholder="Example: 2x2")
@@ -270,7 +262,13 @@ def cmmde_gui():
     # Generate material folder button
     materialdir_btn = pn.widgets.Button(name="Generate work directory",type="primary")
     
+# # Download Button
     
+    download_slab = pn.widgets.FileDownload(file="{}/slab.vasp",filename="slab.vasp")
+    download_spec_plot = pn.widgets.FileDownload(file="IR.pdf",filename="IR.pdf")
+    download_spec_raw = pn.widgets.FileDownload(file="IR_fit.dat".format(workdir+"/"+id_input.value+"/"+Molecule_input.value+"/"+"ir"),filename="IR_fit.dat")
+    download_opt_plot = pn.widgets.FileDownload(file="optimized.pdf",filename="optimized.pdf")
+    download_opt_raw = pn.widgets.FileDownload(file="optimized.dat",filename="optimized.dat")
     def materialgen(event):
         Folder = workdir + "/" + id_input.value + "/" + Material_input.value 
         isExist = os.path.exists(Folder)
@@ -341,7 +339,7 @@ def cmmde_gui():
         xyzview = py3Dmol.view()
         
         if Material_input.value == "":
-            Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value 
+            Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value + "/" + job[job_main.value] 
         else:
             Folder = workdir + "/" + id_input.value + "/" + Material_input.value
         os.chdir(Folder)