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246 lines
12 KiB
246 lines
12 KiB
#!/usr/bin/env python3 |
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# pylint: disable=missing-function-docstring |
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from __future__ import print_function |
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import panel as pn |
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from panel_chemistry.widgets import JSMEEditor |
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from panel.interact import interact |
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import os |
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import sys |
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from panel_chemistry.pane import NGLViewer |
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from panel_chemistry.pane.ngl_viewer import EXTENSIONS |
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import py3Dmol |
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from panel_chemistry.pane import Py3DMol |
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import subprocess |
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import uuid |
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# from iodata import IOData |
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def test_can_construct(): |
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JSMEEditor() |
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def cmmde_gui(): |
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geom = '' |
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pn.extension("jsme", sizing_mode="stretch_width") |
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editor = JSMEEditor(value = " ",height=500,format="smiles",subscriptions=['smiles']) |
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# Terminal widget |
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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\n", |
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height = 500, disabled=True |
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) |
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# CMMDE software options |
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software_btn = pn.widgets.Select(name="Software selections",value='Orca',options=['Orca','GROMACS','Dcdftbmd','Quantum Espresso']) |
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software = {'Orca':'orca','GROMACS':'gromacs','Dcdftbmd':'dcdftb','Quantum Espresso':'qe'} |
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# CMMDE job options |
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job_btn = pn.widgets.MultiSelect(name="Job selections",value=['Single point calculation'],options=['Single point calculation','Geometry optimization','Frequency calculation','Molecular dynamics','Metadynamics']) |
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job = {'Single point calculation':'sp','Geometry optimization':'opt','Frequency calculation':'freq','Molecular dynamics':'md','Metadynamics':'mtd'} |
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# CMMDE method options |
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method_btn = pn.widgets.Select(name="Method selections",value='GFN2-xTB',options=['GFN2-xTB','GFN1-xTB','DFTB2','DFTB2-gammah','DFTB3','DFTB3-diag']) |
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method = {'GFN2-xTB':'XTB2', 'GFN1-xTB':'XTB1','DFTB2':'DFTB2','DFTB2-gammah':'DFTB2_gammah','DFTB3':'DFTB3','DFTB3-diag':'DFTB3-diag'} |
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# Name your molecule/Material |
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Name_input = pn.widgets.TextInput(name="Molecule name") |
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id_input = pn.widgets.TextInput(name="Input your name") |
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workdir = os.getenv("HOME") + "/" + "scr" |
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# File input (if you don't want to draw the structure) |
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FileInput = pn.widgets.FileInput(title='Input structure',accept='.xyz, .vasp, CONTCAR, POSCAR, .pdb') |
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def fileinput(event): |
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if FileInput.value is not None: |
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FileInput.save("geom.xyz") |
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FileInput.param.watch(fileinput,'value') |
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# CMMDE running button |
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Run_btn = pn.widgets.Button(name="Run CMMDE!",button_type='primary') |
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# RunMessage = pn.widgets.StaticText() |
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charge = pn.widgets.TextInput(name="Charge",value="0") |
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mult = pn.widgets.TextInput(name="Spin multiplicity",value="1") |
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def run(event): |
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# RunMessage.value = " " |
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# terminal.clear() |
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# unik = str(uuid.uuid4().hex) |
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Folder = workdir + "/" + id_input.value + "/" + Name_input.value |
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os.chdir(Folder) |
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job_list = [job[i] for i in job_btn.value] |
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jobs = ",".join(job_list) |
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if editor == JSMEEditor(value=" "): |
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geom = save(FileInput.filename) |
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else: |
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geom = editor.value |
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TextArea.value = TextArea.value + "\n" + "Mempersiapkan Struktur 3 Dimensi!" |
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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) |
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#terminal.subprocess.run("cmmde.py","-i{}".format(editor.value),"-s{}".format(software[software_btn.value]), "-j{}".format(jobs), "-m{}".format(method[method_btn.value])) |
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TextArea.value = TextArea.value + "\n" + "Perhitungan anda telah tersubmit!" |
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# RunMessage.value = "Perhitungan telah tersubmit!" |
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Run_btn.on_click(run) |
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# Check directory button |
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checkdir_btn = pn.widgets.Button(name="Generate work directory",type="primary") |
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TextWarning = pn.widgets.StaticText() |
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def checkdir(event): |
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Folder = workdir + "/" + id_input.value + "/" + Name_input.value |
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isExist = os.path.exists(Folder) |
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TextWarning.value = "" |
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if isExist: |
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TextWarning.value = "Directory exists! Change the molecule name!" |
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else: |
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os.makedirs(Folder) |
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TextWarning.value = "Successfully create the directory!" |
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checkdir_btn.on_click(checkdir) |
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# Post calculations |
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post_calc = {'Frequency calculation':'freq', 'Radial distribution function':'rdf','Mean Square Displacement':'msd','Time-dependent calculation':'td','Thermochemistry calculation':'thermo'} |
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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']) |
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# Post Calculation CMMDE software options |
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post_software_btn = pn.widgets.Select(name="Software selections for post calculations",value='Orca',options=['Orca','GROMACS','Dcdftbmd','Quantum Espresso']) |
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post_software = {'Orca':'orca','GROMACS':'gromacs','Dcdftbmd':'dcdftb','Quantum Espresso':'qe'} |
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# Post CMMDE method options |
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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']) |
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post_method = {'GFN2-xTB':'XTB2', 'GFN1-xTB':'XTB1','DFTB2':'DFTB2','DFTB2-gammah':'DFTB2_gammah','DFTB3':'DFTB3','DFTB3-diag':'DFTB3-diag'} |
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def post_calculation(event): |
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# terminal.clear() |
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if post_calc[post_btn.value] == 'thermo' and post_software[post_software_btn.value] == 'orca': |
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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) |
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TextArea.value = TextArea.value + "\n" + cmd.stdout |
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# terminal.subprocess.run("cmmdepost.py","-j{}".format(post_calc[post_btn.value]),"-s{}".format(post_software[post_software_btn.value])) |
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else: |
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Folder = workdir + "/" + id_input.value + "/" + Name_input.value |
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os.chdir(Folder) |
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os.makedirs(post_calc[post_btn.value]) |
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os.chdir(post_calc[post_btn.value]) |
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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) |
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# 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])) |
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TextArea.value = TextArea.value + "\n" + cmd.stdout |
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runpost_btn = pn.widgets.Button(name="Run post calculation!",button_type='primary') |
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runpost_btn.on_click(post_calculation) |
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# Check the queue progress |
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def progress(event): |
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# terminal.clear() |
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# terminal.subprocess.run("squeue") |
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cmd = subprocess.run(["squeue"],capture_output=True,text=True) |
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TextArea.value = TextArea.value + "\n" + cmd.stdout |
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Progress_btn = pn.widgets.Button(name="Check queue",button_type='primary') |
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Progress_btn.on_click(progress) |
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# Check the calculation progress |
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def calc_progress(event): |
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cmd = subprocess.run(["tail", "-n", "10", "cmmd.out"],capture_output=True,text=True) |
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TextArea.value = TextArea.value + "\n" + cmd.stdout |
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Checkcalc_btn = pn.widgets.Button(name="Check calculation",button_type='primary') |
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Checkcalc_btn.on_click(calc_progress) |
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# # Download Button |
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download_xyz = pn.widgets.FileDownload(file="cmmd.xyz",filename="cmmd.xyz") |
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download_slab = pn.widgets.FileDownload(file="slab.vasp",filename="slab.vasp") |
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# Slab Builder |
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hkl_input = pn.widgets.TextInput(name="Miller index (hkl)",placeholder="Example: 100") |
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size_input = pn.widgets.TextInput(name="Dimension",placeholder="Example: 2x2") |
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layer_input = pn.widgets.TextInput(name="Layer",placeholder="Example: 2") |
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slabbuilder_btn = pn.widgets.Button(name="Build it!",button_type="primary") |
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def slab_builder(event): |
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Folder = workdir + "/" + id_input.value + "/" + Name_input.value |
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os.chdir(Folder) |
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os.system("mv geom.xyz POSCAR") |
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hkl = hkl_input.value |
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size = size_input.value |
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layer = layer_input.value |
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cmd = subprocess.run(["cmmdepre.py","-j","surface","-hkl","{}".format(hkl),"-s","{}".format(size),"-n","{}".format(layer),"-i","POSCAR"]) |
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os.system("mv slab_{}.xyz cmmd.xyz".format(hkl)) |
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os.system("mv slab_{}.vasp slab.vasp".format(hkl)) |
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cmd = subprocess.run(["echo","({})-surface construction done!".format(hkl)],capture_output=True,text=True) |
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TextArea.value = TextArea.value + "\n" + cmd.stdout |
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# xyzview = py3Dmol.view() |
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# with open('slab_{}.xyz'.format(hkl),'r') as f: |
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# xyz = f.read() |
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# xyzview.addModel(xyz,'xyz') |
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# xyzview.setStyle('stick') |
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# xyzviewer.object = xyzview |
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slabbuilder_btn.on_click(slab_builder) |
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# Solution Builder |
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# fileinput_solute = pn.widgets.FileInput(accept=".xyz",multiple=True) |
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# fileinput_solvent = pn.widgets.FileInput(accept=".xyz") |
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# def SolutionBuilder(event): |
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# solute = fileinput_solute.value |
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# solvent = fileinput_solute.value |
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# Visualize the results |
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xyzview = py3Dmol.view() |
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xyzviewer = Py3DMol(xyzview, height=400, sizing_mode="stretch_width",name="CMMDE viewer") |
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def visualize(event): |
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xyzview = py3Dmol.view() |
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Folder = workdir + "/" + id_input.value + "/" + Name_input.value |
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os.chdir(Folder) |
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with open('cmmd.xyz','r') as f: |
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xyz = f.read() |
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xyzview.addModel(xyz,'xyz') |
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xyzview.setStyle('stick') |
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xyzviewer.object = xyzview |
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visual_btn = pn.widgets.Button(name="Visualize!", button_type='primary') |
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visual_btn.on_click(visualize) |
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def set_background(color='0xeeeeee'): |
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xyzview.setBackgroundColor(color) |
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xyzviewer.param.trigger("object") |
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set_background("#e6f6ff") |
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accent = "#0072B5" |
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# background = pn.widgets.ColorPicker(value="#e6f6ff", name="Background") |
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# pn.bind(set_background, color=background, watch=True) |
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# def set_style(style="stick"): |
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# xyzview.setStyle({style: {}}) |
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# xyzview.zoomTo() |
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# xyzviewer.param.trigger("object") |
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# set_style("stick") |
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# style=pn.widgets.RadioButtonGroup(value="stick", options=["stick", "sphere"], name="Style", button_type="success") |
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# set_style=pn.bind(set_style, style=style, watch=True) |
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#### Wrap them all together ########## |
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return pn.template.MaterialTemplate( |
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site="CMMDE-GUI", |
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title="CMMDE Editor", |
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main=[editor, TextArea, pn.Tabs(xyzviewer)], |
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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)], |
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header_background=accent, accent_base_color=accent |
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) |
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if __name__.startswith("bokeh"): |
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cmmde_gui().servable()
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