CoreDev
/
CMMDE
4
1
Fork 0
Code Issues 2 Pull Requests Packages Projects Releases Wiki Activity

edit README

Browse Source
Aditya Wibawa Sakti 2 years ago
parent f473e7b09c
commit d3eea9cc7d
2 changed files with 90 additions and 44 deletions
Whitespace
Show all changes Ignore whitespace when comparing lines Ignore changes in amount of whitespace Ignore changes in whitespace at EOL
Split View
Diff Options
Show Stats Download Patch File Download Diff File
  1. 20
      bin/cmmdepost.py
  2. 114
      cmmde_gui/gui.py

20
bin/cmmdepost.py
Unescape View File

@ -201,12 +201,9 @@ if opt.job == 'ir' and opt.software == 'orca':
if "Final Gibbs free energy" in line:
arr = line.split()
Gibbs = float(arr[5])
if "Total entropy" in line:
arr = line.split()
Entropy = float(arr[4])
if "Temperature" in line:
arr = line.split()
Temperature = float(arr[2])
# if "Total entropy" in line:
# arr = line.split()
# Entropy = float(arr[4])
if "IR SPECTRUM" in line:
for i in range(NFreq):
arr = lines[index+6+i].split()
@ -247,12 +244,9 @@ if opt.job == 'thermo' and opt.software == 'orca':
if "Final Gibbs free energy" in line:
arr = line.split()
Gibbs = float(arr[5])
if "Total entropy" in line:
arr = line.split()
Entropy = float(arr[4])
if "Temperature" in line:
arr = line.split()
Temperature = float(arr[2])
# if "Total entropy" in line:
# arr = line.split()
# Entropy = float(arr[4])
if "Non-thermal (ZPE)" in line:
arr = line.split()
ZPE = float(arr[3])
@ -325,7 +319,7 @@ if opt.job == 'thermo' and opt.software == 'orca':
print('')
print('######INFORMASI BESARAN TERMOKIMIA######')
print("Entalpi (H) = {} Hartree = {} kj/mol".format(Enthalpy,Enthalpy*Ha2kj))
print("Entropi (S) = {} Hartree/K = {} J/(mol K)".format(Entropy/Temperature,Entropy*Ha2kj/Temperature*1000))
# print("Entropi (S) = {} Hartree/K = {} J/(mol K)".format(Entropy/Temperature,Entropy*Ha2kj/Temperature*1000))
print("Energi bebas Gibbs (G) = {} Hartree = {} kJ/mol".format(Gibbs,Gibbs*Ha2kj))
else:

114
cmmde_gui/gui.py
Unescape View File

@ -16,8 +16,8 @@ import uuid
# from iodata import IOData
def test_can_construct():
JSMEEditor()
# def test_can_construct():
# JSMEEditor()
def cmmde_gui():
@ -27,28 +27,62 @@ def cmmde_gui():
editor = JSMEEditor(value = " ",height=500,format="smiles",subscriptions=['smiles'])
# Name your molecule
Molecule_input = pn.widgets.TextInput(name="Molecule name")
id_input = pn.widgets.TextInput(name="Input your name")
charge = pn.widgets.TextInput(name="Charge",value="0")
mult = pn.widgets.TextInput(name="Spin multiplicity",value="1")
workdir = os.getenv("HOME") + "/" + "scr"
# Terminal widget
TextArea= pn.widgets.TextAreaInput(value = "Computational Molecular and Material Design Environment\n Authors:\n Universitas Pertamina\n Institut Teknologi Sumatera\n Masyarakat Komputasi Indonesia\n\nSupported by:\n Konsorsium Pengembangan Sains Komputasi\n",
TextArea= pn.widgets.TextAreaInput(value = "Computational Molecular and Material Design Environment\n Authors:\n Universitas Pertamina\n Institut Teknologi Sumatera\n Institut Teknologi Bandung\n Masyarakat Komputasi Indonesia\n\nSupported by:\n Konsorsium Pengembangan Sains Komputasi\n",
height = 500, disabled=True
)
# CMMDE software options
software_btn = pn.widgets.Select(name="Software selections",value='Orca',options=['Orca','GROMACS','Dcdftbmd','Quantum Espresso'])
software_main = pn.widgets.Select(name="Software selections",value='Orca',options=['Orca','GROMACS','Dcdftbmd','Quantum Espresso'])
software = {'Orca':'orca','GROMACS':'gromacs','Dcdftbmd':'dcdftb','Quantum Espresso':'qe'}
# 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_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'}
dispersion_cor = pn.widgets.Select(name="Dispersion corrections",value='None',options=['None','D3','D3BJ','D4'])
solvent = pn.widgets.Select(name='Solvent',value='None',options=['None','water','acetone','acetonitrile','aniline','benzaldehyde','benzene','CH2Cl2','CHCl3','CS2','dioxane','DMF','ethanol','ether','ethylacetate','furane','hexadecane','hexane','ocatnol','octanol(wet)','phenol','toluene','THF'])
run_orca_btn = pn.widgets.Button(name="Run Orca!",button_type='primary')
def run_orca(event):
# RunMessage.value = " "
# terminal.clear()
# unik = str(uuid.uuid4().hex)
Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value
os.chdir(Folder)
job_list = [job[i] for i in job_orca.value]
jobs = ",".join(job_list)
if editor.value == "":
FileInput.save("geom.xyz")
geom = "geom.xyz"
else:
geom = editor.value
TextArea.value = TextArea.value + "\n" + "Mempersiapkan Struktur 3 Dimensi!"
cmd = subprocess.run(["cmmde.py","-i","{}".format(geom),"-s","orca","-j","{}".format(jobs),"-m","{}".format(method[method_orca.value]),"-c","{}".format(charge.value),"-mult","{}".format(mult.value)],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 = pn.widgets.StaticText()
run_orca_btn.on_click(run_orca)
# CMMDE job options
job_btn = pn.widgets.MultiSelect(name="Job selections",value=['Single point calculation'],options=['Single point calculation','Geometry optimization','Frequency calculation','Molecular dynamics','Metadynamics'])
job = {'Single point calculation':'sp','Geometry optimization':'opt','Frequency calculation':'freq','Molecular dynamics':'md','Metadynamics':'mtd'}
job_main = pn.widgets.MultiSelect(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'}
# 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','B3LYP/def2-svp'])
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'}
method_btn = pn.widgets.Select(name="Method selections",value='GFN2-xTB',options=['GFN2-xTB','GFN1-xTB','B3LYP/def2-svp','M06/def2-svp','DFTB2','DFTB2-gammah','DFTB3','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','M06/def2-svp':'M06 def2-svp'}
# Name your molecule/Material
Molecule_input = pn.widgets.TextInput(name="Molecule name")
id_input = pn.widgets.TextInput(name="Input your name")
workdir = os.getenv("HOME") + "/" + "scr"
# File input (if you don't want to draw the structure)
@ -61,8 +95,7 @@ def cmmde_gui():
# CMMDE running button
Run_btn = pn.widgets.Button(name="Run CMMDE!",button_type='primary')
# RunMessage = pn.widgets.StaticText()
charge = pn.widgets.TextInput(name="Charge",value="0")
mult = pn.widgets.TextInput(name="Spin multiplicity",value="1")
def run(event):
# RunMessage.value = " "
# terminal.clear()
@ -73,7 +106,7 @@ def cmmde_gui():
os.chdir(Folder)
job_list = [job[i] for i in job_btn.value]
job_list = [job[i] for i in job_main.value]
jobs = ",".join(job_list)
if editor.value == "":
@ -83,8 +116,17 @@ def cmmde_gui():
geom = editor.value
TextArea.value = TextArea.value + "\n" + "Mempersiapkan Struktur 3 Dimensi!"
cmd = subprocess.run(["cmmde.py","-i","{}".format(geom),"-s","{}".format(software[software_btn.value]),"-j","{}".format(jobs),"-m","{}".format(method[method_btn.value]),"-c","{}".format(charge.value),"-mult","{}".format(mult.value)],capture_output=True,text=True)
#terminal.subprocess.run("cmmde.py","-i{}".format(editor.value),"-s{}".format(software[software_btn.value]), "-j{}".format(jobs), "-m{}".format(method[method_btn.value]))
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)]
if dispersion_cor.value != 'None':
new_commands = ["-disp","{}".format(dispersion_cor.value)]
for i in new_commands:
list_commands.append(i)
if solvent.value != 'None':
new_commands = ["-solvent","{}".format(solvent.value)]
for i in new_commands:
list_commands.append(i)
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!"
@ -118,8 +160,8 @@ def cmmde_gui():
post_calc = {'Frequency calculation':'freq', 'Radial distribution function':'rdf','Mean Square Displacement':'msd','Time-dependent calculation':'td','Thermochemistry calculation':'thermo','Optimized energy':'opt','IR plot':'ir'}
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','IR plot'])
# 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'}
post_software_main = pn.widgets.Select(name="Software selections for post calculations",value='Orca',options=['Orca','Dcdftbmd','Quantum Espresso'])
post_software = {'Orca':'orca','Dcdftbmd':'dcdftb','Quantum Espresso':'qe'}
# Post CMMDE method options
post_method_btn = pn.widgets.Select(name="Method selections for post calculations",value='GFN2-xTB',options=['GFN2-xTB','GFN1-xTB','DFTB2','DFTB2-gammah','DFTB3','DFTB3-diag','B3LYP/def2-svp'])
post_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'}
@ -127,37 +169,47 @@ def cmmde_gui():
# terminal.clear()
Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value
os.chdir(Folder)
if post_calc[post_btn.value] == 'thermo' and post_software[post_software_btn.value] == 'orca':
if post_calc[post_btn.value] == 'thermo' and post_software[post_software_main.value] == 'orca':
# Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value
# os.chdir(Folder)
if not os.path.exists(post_calc[post_btn.value]):
os.makedirs(post_calc[post_btn.value])
os.chdir(post_calc[post_btn.value])
os.system("cp ../freq/cmmd.out .")
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)
cmd = subprocess.run(["cmmdepost.py","-j","{}".format(post_calc[post_btn.value]),"-s","{}".format(post_software[post_software_main.value])],capture_output=True,text=True)
TextArea.value = TextArea.value + "\n" + cmd.stdout
elif post_calc[post_btn.value] == 'ir' and post_software[post_software_btn.value] == 'orca':
elif post_calc[post_btn.value] == 'ir' and post_software[post_software_main.value] == 'orca':
# Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value
# os.chdir(Folder)
if not os.path.exists(post_calc[post_btn.value]):
os.makedirs(post_calc[post_btn.value])
os.chdir(post_calc[post_btn.value])
os.system("cp ../freq/cmmd.out .")
cmd = subprocess.run(["cmmdepost.py","-j","{}".format(post_calc[post_btn.value]),"-s","{}".format(post_software[post_software_btn.value])])
cmd = subprocess.run(["cmmdepost.py","-j","{}".format(post_calc[post_btn.value]),"-s","{}".format(post_software[post_software_main.value])])
TextArea.value = TextArea.value + "\n" + "Plot spektrum IR berhasil dilakukan"
# 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':
# terminal.subprocess.run("cmmdepost.py","-j{}".format(post_calc[post_btn.value]),"-s{}".format(post_software[post_software_main.value]))
elif post_calc[post_btn.value] == 'opt' and post_software[post_software_main.value] == 'orca':
# Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value
# os.chdir(Folder)
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)
cmd = subprocess.run(["cmmdepost.py","-j","{}".format(post_calc[post_btn.value]),"-s","{}".format(post_software[post_software_main.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 + "/" + Molecule_input.value
# os.chdir(Folder)
os.makedirs(post_calc[post_btn.value])
if not os.path.exists(post_calc[post_btn.value]):
os.makedirs(post_calc[post_btn.value])
os.chdir(post_calc[post_btn.value])
cmd = subprocess.run(["cmmde.py","-i","{}".format("../cmmd.xyz"),"-s","{}".format(post_software[post_software_btn.value]),"-j","{}".format(post_calc[post_btn.value]),"-m","{}".format(post_method[post_method_btn.value])],capture_output=True,text=True)
# terminal.subprocess.run("cmmde.py","-i{}".format("../cmmd.xyz"),"-s{}".format(post_software[post_software_btn.value]), "-j{}".format(post_calc[post_btn.value]), "-m{}".format(post_method[post_method_btn.value]))
list_commands = ["cmmde.py","-i","{}".format("../cmmd.xyz"),"-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:
list_commands.append(i)
if solvent.value != 'None':
new_commands = ["-solvent","{}".format(solvent.value)]
for i in new_commands:
list_commands.append(i)
cmd = subprocess.run(list_commands,capture_output=True,text=True)
# terminal.subprocess.run("cmmde.py","-i{}".format("../cmmd.xyz"),"-s{}".format(post_software[post_software_main.value]), "-j{}".format(post_calc[post_btn.value]), "-m{}".format(post_method[post_method_btn.value]))
TextArea.value = TextArea.value + "\n" + cmd.stdout
runpost_btn = pn.widgets.Button(name="Run post calculation!",button_type='primary')
runpost_btn.on_click(post_calculation)
@ -314,7 +366,7 @@ def cmmde_gui():
site="Computational Molecular and Material Design Environment",
title="CMMDE",
main=[TextArea, editor, xyzviewer],
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,TextWarning, pn.Card(Material_upload,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(software_btn,job_btn,method_btn,pn.Row(Run_btn,Progress_btn),pn.Row(Checkcalc_btn,visual_btn),download_xyz,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),pn.Row(download_spec_raw,download_spec_plot),pn.Row(download_opt_raw,download_opt_plot),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,TextWarning, pn.Card(Material_upload,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(software_main,job_main,method_btn, dispersion_cor,solvent, pn.Row(Run_btn,Progress_btn),pn.Row(Checkcalc_btn,visual_btn),download_xyz,title="Main Calculation",collapsed=True),pn.Card(post_software_main,post_btn,post_method_btn,dispersion_cor,solvent,pn.Row(runpost_btn,Progress_btn),pn.Row(Checkcalc_btn,visual_btn),pn.Row(download_spec_raw,download_spec_plot),pn.Row(download_opt_raw,download_opt_plot),title="Post-Calculation",collapsed=True)],
header_background=accent, accent_base_color=accent
)

Write Preview
Loading…
Cancel
Save