mod README

README.md

@@ -22,9 +22,6 @@ CMMDE is a set of tools based on Python for running computational jobs, as well
 
 Tahap kedua peluncuran CMMDE, didahului workshop: 
 
-**Senin, 15 Agustus 2022 (10:00 WIB):**</br>
-Penyiapan Server Komputasi</br>
-Tautan: [https://mki.ac/CMMD-server](https://mki.ac/CMMD-server)
 
 **Selasa, 16 Agustus 2022 (13:00 WIB):**</br>
 Workshop on Text-Based CMMDE</br>
@@ -40,6 +37,9 @@ Launching Consortium on Computational Science Development</br>
 (Konsorsium Pengembangan Sains Komputasi)</br>
 Tautan: [https://mki.ac/cmsd-launch]( https://mki.ac/cmsd-launch)
 
+**Kamis, 18 Agustus 2022 (13:00 WIB):**</br>
+Penyiapan Server Komputasi</br>
+Tautan: [https://mki.ac/CMMD-server](https://mki.ac/CMMD-server)
 Informasi lebih lanjut: cmmde@mki.or.id
 
 

bin/cmmdepost.py

@@ -63,7 +63,7 @@ ev2kcal = 23.060541945329334
 Ha2kj = 2625.5
 ev2kj = 96
 # Analisis Output
-
+method = opt.method
 if opt.job == 'sp' and opt.software == 'orca' and not (opt.method == 'XTB' or opt.method == 'XTB2'):
     if os.path.isfile('cmmd.out'):
         with open('cmmd.out','r') as f:
@@ -101,6 +101,7 @@ elif opt.job == 'sp' and opt.software == 'orca':
 if opt.job == 'opt' and opt.software == 'orca':
     Energy = []
     Gradient = []
+    TotalEnergy = []
     if os.path.isfile('cmmd.out'):
         with open('cmmd.out','r') as f:
             for line in f:
@@ -110,35 +111,48 @@ if opt.job == 'opt' and opt.software == 'orca':
                 if "Current gradient" in line:
                     arr = line.split()
                     Gradient.append(float(arr[4]))
-        Optstep = range(0,len(Energy))
+                if "TOTAL ENERGY" in line:
-
-        with open('cmmd.out','r') as f:
-            lines = f.readlines()
-            occ = []
-            energy = []
-            for index,line in enumerate(lines):
-                if 'Basis Dimension' in line:
                     arr = line.split()
-                    NBas = int(arr[4])
+                    TotalEnergy.append(float(arr[3]))
-                if 'ORBITAL ENERGIES' in line:
+        Optstep = range(0,len(Energy))
-                    for i in range(NBas):
+        print("Total energi elektronik = {} Hartree = {} kJ/mol".format(TotalEnergy[-1],TotalEnergy[-1]*Ha2kj))
-                        arr = lines[index+i+4].split()
+        if method != "XTB1" and method != "xtb1" and method != "XTB2" and method != "xtb2" and method != "XTB" and method != "xtb":
-                        occ.append(arr[1])
+            with open('cmmd.out','r') as f:
-                        energy.append(float(arr[3]))
+                lines = f.readlines()
-            Eocc = []
+                occ = []
-            Evir = []
+                energy = []
-            for energy in energy:
+                for index,line in enumerate(lines):
-                if energy > 0:
+                    if 'Basis Dimension' in line:
-                    Evir.append(energy)
+                        arr = line.split()
-                if energy < 0:
+                        NBas = int(arr[4])
-                    Eocc.append(energy)
+                    if 'ORBITAL ENERGIES' in line:
-            E_HOMO = max(Eocc)
+                        for i in range(NBas):
-            E_LUMO = min(Evir)
+                            arr = lines[index+i+4].split()
-            print('######INFORMASI ENERGI HOMO & LUMO######')
+                            occ.append(arr[1])
-            print('Energi HOMO = {:.2f} eV'.format(E_HOMO))
+                            energy.append(float(arr[3]))
-            print('Energi LUMO = {:.2f} eV'.format(E_LUMO))
+                Eocc = []
-            print('Gap HOMO-LUMO = {:.2f} eV'.format(E_LUMO-E_HOMO))
+                Evir = []
-
+                for energy in energy:
+                    if energy > 0:
+                        Evir.append(energy)
+                    if energy < 0:
+                        Eocc.append(energy)
+                E_HOMO = max(Eocc)
+                E_LUMO = min(Evir)
+                print('######INFORMASI ENERGI HOMO & LUMO######')
+                print('Energi HOMO = {:.2f} eV'.format(E_HOMO))
+                print('Energi LUMO = {:.2f} eV'.format(E_LUMO))
+                print('Gap HOMO-LUMO = {:.2f} eV'.format(E_LUMO-E_HOMO))
+        else:
+            Gaps = []
+            with open("cmmd.out", 'r') as f:
+                print('######INFORMASI ENERGI HOMO & LUMO######')
+                for line in f:
+                    if "GAP" in line:
+                        arr = line.split()
+                        Gaps.append(float(arr[3]))
+            print("Gap HOMO-LUMO = {:.2f} eV".format(Gaps[-1]))
+                
         with open('optimized.dat','w') as fout:
             print("#Step Energy Gradient", file=fout)
             for optstep,energy,gradient in zip(Optstep,Energy,Gradient):

cmmde_gui/gui.py

@@ -42,11 +42,11 @@ def cmmde_gui():
     job = {'Single point calculation':'sp','Geometry optimization':'opt','Frequency calculation':'freq','Molecular dynamics':'md','Metadynamics':'mtd'}
 
 # CMMDE method options
-    method_btn = pn.widgets.Select(name="Method selections",value='GFN2-xTB',options=['GFN2-xTB','GFN1-xTB','DFTB2','DFTB2-gammah','DFTB3','DFTB3-diag'])
+    method_btn = pn.widgets.Select(name="Method selections",value='GFN2-xTB',options=['GFN2-xTB','GFN1-xTB','DFTB2','DFTB2-gammah','DFTB3','DFTB3-diag','B3LYP/def2-svp'])
-    method = {'GFN2-xTB':'XTB2', 'GFN1-xTB':'XTB1','DFTB2':'DFTB2','DFTB2-gammah':'DFTB2_gammah','DFTB3':'DFTB3','DFTB3-diag':'DFTB3-diag'}
+    method = {'GFN2-xTB':'XTB2', 'GFN1-xTB':'XTB1','DFTB2':'DFTB2','DFTB2-gammah':'DFTB2_gammah','DFTB3':'DFTB3','DFTB3-diag':'DFTB3-diag','B3LYP/def2-svp':'B3LYP def2-svp'}
 
 # Name your molecule/Material
-    Name_input = pn.widgets.TextInput(name="Molecule name")
+    Molecule_input = pn.widgets.TextInput(name="Molecule name")
     id_input = pn.widgets.TextInput(name="Input your name")
     workdir = os.getenv("HOME") + "/" + "scr"
     
@@ -68,7 +68,7 @@ def cmmde_gui():
         # terminal.clear()
         # unik = str(uuid.uuid4().hex)
         
-        Folder = workdir + "/" + id_input.value + "/" + Name_input.value 
+        Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value 
         
         os.chdir(Folder)
 
@@ -96,7 +96,7 @@ def cmmde_gui():
     checkdir_btn = pn.widgets.Button(name="Generate work directory",type="primary")
     TextWarning = pn.widgets.StaticText()
     def checkdir(event):
-        Folder = workdir + "/" + id_input.value + "/" + Name_input.value 
+        Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value 
         isExist = os.path.exists(Folder)
         TextWarning.value = ""
         if isExist:
@@ -110,9 +110,11 @@ def cmmde_gui():
 
 
 
+
+
 # Post calculations
-    post_calc = {'Frequency calculation':'freq', 'Radial distribution function':'rdf','Mean Square Displacement':'msd','Time-dependent calculation':'td','Thermochemistry calculation':'thermo'}
+    post_calc = {'Frequency calculation':'freq', 'Radial distribution function':'rdf','Mean Square Displacement':'msd','Time-dependent calculation':'td','Thermochemistry calculation':'thermo','Optimized energy':'opt'}
-    post_btn = pn.widgets.Select(name="Job Selection",value='Frequency calculation', options=['Frequency calculation','Radial distribution function', 'Mean Square Displacement','Time-dependent calculation','Thermochemistry calculation'])
+    post_btn = pn.widgets.Select(name="Job Selection",value='Frequency calculation', options=['Frequency calculation','Radial distribution function', 'Mean Square Displacement','Time-dependent calculation','Thermochemistry calculation','Optimized energy'])
 # Post Calculation CMMDE software options
     post_software_btn = pn.widgets.Select(name="Software selections for post calculations",value='Orca',options=['Orca','GROMACS','Dcdftbmd','Quantum Espresso'])
     post_software = {'Orca':'orca','GROMACS':'gromacs','Dcdftbmd':'dcdftb','Quantum Espresso':'qe'}
@@ -124,9 +126,12 @@ def cmmde_gui():
         if post_calc[post_btn.value] == 'thermo' and post_software[post_software_btn.value] == 'orca':
             cmd = subprocess.run(["cmmdepost.py","-j","{}".format(post_calc[post_btn.value]),"-s","{}".format(post_software[post_software_btn.value])],capture_output=True,text=True)
             TextArea.value = TextArea.value + "\n" + cmd.stdout
-            # terminal.subprocess.run("cmmdepost.py","-j{}".format(post_calc[post_btn.value]),"-s{}".format(post_software[post_software_btn.value]))  
+            # terminal.subprocess.run("cmmdepost.py","-j{}".format(post_calc[post_btn.value]),"-s{}".format(post_software[post_software_btn.value]))
+        elif post_calc[post_btn.value] == 'opt' and post_software[post_software_btn.value] == 'orca':
+            cmd = subprocess.run(["cmmdepost.py","-j","{}".format(post_calc[post_btn.value]),"-s","{}".format(post_software[post_software_btn.value]),"-m","{}".format(post_method[post_method_btn.value])],capture_output=True,text=True)
+            TextArea.value = TextArea.value + "\n" + cmd.stdout  
         else:
-            Folder = workdir + "/" + id_input.value + "/" + Name_input.value 
+            Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value 
             os.chdir(Folder) 
             os.makedirs(post_calc[post_btn.value])
             os.chdir(post_calc[post_btn.value])
@@ -163,8 +168,24 @@ def cmmde_gui():
     size_input = pn.widgets.TextInput(name="Dimension",placeholder="Example: 2x2")
     layer_input = pn.widgets.TextInput(name="Layer",placeholder="Example: 2")
     slabbuilder_btn = pn.widgets.Button(name="Build it!",button_type="primary")
+    Material_input = pn.widgets.TextInput(name="Material name")
+    
+    # Generate material folder button
+    materialdir_btn = pn.widgets.Button(name="Generate work directory",type="primary")
+    TextWarning = pn.widgets.StaticText()
+    def materialgen(event):
+        Folder = workdir + "/" + id_input.value + "/" + Material_input.value 
+        isExist = os.path.exists(Folder)
+        TextWarning.value = ""
+        if isExist:
+            TextWarning.value = "Directory exists! Change the material name!"
+        else:
+            os.makedirs(Folder)
+            TextWarning.value = "Successfully create the directory!"
+
+    materialdir_btn.on_click(materialgen)
     def slab_builder(event):
-        Folder = workdir + "/" + id_input.value + "/" + Name_input.value 
+        Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value 
         os.chdir(Folder)
         os.system("mv geom.xyz POSCAR")
         hkl = hkl_input.value
@@ -190,7 +211,7 @@ def cmmde_gui():
     # def SolutionBuilder(event):
     #     solute = fileinput_solute.value
     #     solvent = fileinput_solute.value
-    
+
 
 
 # Visualize the results
@@ -200,7 +221,7 @@ def cmmde_gui():
     def visualize(event):
         xyzview = py3Dmol.view()
         
-        Folder = workdir + "/" + id_input.value + "/" + Name_input.value 
+        Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value 
         os.chdir(Folder)
         with open('cmmd.xyz','r') as f:
             xyz = f.read()
@@ -237,7 +258,7 @@ def cmmde_gui():
         site="CMMDE-GUI",
         title="CMMDE Editor",
         main=[editor, TextArea, pn.Tabs(xyzviewer)],
-        sidebar=[pn.Card(id_input,Name_input,charge,mult,checkdir_btn,TextWarning,pn.Card(FileInput,title="Upload molecule",collapsed=True),pn.Card(pn.Card(FileInput,title="Unit cell",collapsed=True),hkl_input,size_input,layer_input,pn.Row(slabbuilder_btn,visual_btn),pn.Row(download_xyz,download_slab),title="Surface Builder",collapsed=True),title="Pre-Calculation",collapsed=True),pn.Card(pn.Card(software_btn,job_btn,method_btn,pn.Row(Run_btn,Progress_btn),pn.Row(Checkcalc_btn,visual_btn),title="General calculation",collapsed=True),title="Main Calculation",collapsed=True),pn.Card(post_software_btn,post_btn,post_method_btn,pn.Row(runpost_btn,Progress_btn),pn.Row(Checkcalc_btn,visual_btn),title="Post-Calculation",collapsed=True)],
+        sidebar=[pn.Card(id_input,title="User information",collapsed=True),pn.Card(Molecule_input,charge,mult,checkdir_btn,TextWarning,pn.Card(FileInput,title="Upload molecule",collapsed=True),title="Molecule information",collapsed=True),pn.Card(Material_input, materialdir_btn, pn.Card(FileInput,title="Unit cell",collapsed=True),hkl_input,size_input,layer_input,pn.Row(slabbuilder_btn,visual_btn),pn.Row(download_xyz,download_slab),title="Surface Builder",collapsed=True),pn.Card(pn.Card(software_btn,job_btn,method_btn,pn.Row(Run_btn,Progress_btn),pn.Row(Checkcalc_btn,visual_btn),title="General calculation",collapsed=True),title="Main Calculation",collapsed=True),pn.Card(post_software_btn,post_btn,post_method_btn,pn.Row(runpost_btn,Progress_btn),pn.Row(Checkcalc_btn,visual_btn),title="Post-Calculation",collapsed=True)],
         header_background=accent, accent_base_color=accent
     )