CMMDE/cmmde_gui/gui.py

#!/usr/bin/env python3
# pylint: disable=missing-function-docstring
from __future__ import print_function
import panel as pn

from panel_chemistry.widgets import JSMEEditor
from panel.interact import interact
import os
import sys
from panel_chemistry.pane import NGLViewer
from panel_chemistry.pane.ngl_viewer import EXTENSIONS
import py3Dmol
from panel_chemistry.pane import Py3DMol
import subprocess
import uuid
# from iodata import IOData


def test_can_construct():
    JSMEEditor()


def cmmde_gui():
    geom = ''
    pn.extension("jsme", sizing_mode="stretch_width")
    
    editor = JSMEEditor(value = " ",height=500,format="smiles",subscriptions=['smiles'])
    
     

# 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\n",
        height = 500
        )
# CMMDE software options
    software_btn = pn.widgets.Select(name="Software selections",value='Orca',options=['Orca','GROMACS','Dcdftbmd','Quantum Espresso'])
    software = {'Orca':'orca','GROMACS':'gromacs','Dcdftbmd':'dcdftb','Quantum Espresso':'qe'}


# 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'}

# 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 = {'GFN2-xTB':'XTB2', 'GFN1-xTB':'XTB1','DFTB2':'DFTB2','DFTB2-gammah':'DFTB2_gammah','DFTB3':'DFTB3','DFTB3-diag':'DFTB3-diag'}

# Name your molecule/Materialmaterial
    Name_input = pn.widgets.TextInput(name="Molecule name")

# CMMDE running button
    Run_btn = pn.widgets.Button(name="Run CMMDE!",button_type='primary')
    # RunMessage = pn.widgets.StaticText()
  
    def run(event):
        # RunMessage.value = " "
        # terminal.clear()
        unik = str(uuid.uuid4().hex)
        
        Folder = Name_input.value + "_" + unik
        os.makedirs(Folder)
        os.chdir(Folder)

        
        job_list = [job[i] for i in job_btn.value] 
        jobs = ",".join(job_list)
        cmd = subprocess.run(["cmmde.py","-i","{}".format(editor.value),"-s","{}".format(software[software_btn.value]),"-j","{}".format(jobs),"-m","{}".format(method[method_btn.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]))
        TextArea.value = TextArea.value + "\n" + cmd.stdout
        

        # RunMessage.value = "Perhitungan telah tersubmit!"



    Run_btn.on_click(run)

# Post calculations
    post_calc = {'Frequency calculation':'freq', 'Radial distribution function':'rdf','Mean Square Displacement':'msd','Time-dependent calculation':'td','Thermochemistry calculation':'thermo'}
    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 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 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'])
    post_method = {'GFN2-xTB':'XTB2', 'GFN1-xTB':'XTB1','DFTB2':'DFTB2','DFTB2-gammah':'DFTB2_gammah','DFTB3':'DFTB3','DFTB3-diag':'DFTB3-diag'}
    def post_calculation(event):
        # terminal.clear()
        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]))  
        else:
            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]))
            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)
# Check the progress
    def progress(event):
        # terminal.clear()
        # terminal.subprocess.run("squeue")
        cmd = subprocess.run(["squeue"],capture_output=True,text=True)
        TextArea.value = TextArea.value + "\n" + cmd.stdout
        


    Progress_btn = pn.widgets.Button(name="Check calculation",button_type='primary')    
    Progress_btn.on_click(progress)

# Visualize the results
    xyzview = py3Dmol.view()
    xyzview.setBackgroundColor('0xeeeeee')
    xyzview.zoomTo()
    xyzviewer = Py3DMol(xyzview, height=400, sizing_mode="stretch_width",name="CMMDE viewer")
    def visualize(event):
        with open('cmmd.xyz','r') as f:
            xyz = f.read()
        xyzview.addModel(xyz,'xyz')
        xyzview.setStyle('stick')
        xyzviewer.object = xyzview
        
    # xyzviewer.object = xyzview

    visual_btn = pn.widgets.Button(name="Visualize!", button_type='primary')
    visual_btn.on_click(visualize)

    def set_background(color='0xeeeeee'):
        xyzview.setBackgroundColor(color)
        xyzviewer.param.trigger("object")
    set_background("#e6f6ff")

    accent = "#0072B5"

    # background = pn.widgets.ColorPicker(value="#e6f6ff", name="Background")
    # pn.bind(set_background, color=background, watch=True)     
    # def set_style(style="stick"):
    #     xyzview.setStyle({style: {}})
    #     xyzview.zoomTo()
    #     xyzviewer.param.trigger("object")
    
    # set_style("stick")
    # style=pn.widgets.RadioButtonGroup(value="stick", options=["stick", "sphere"], name="Style", button_type="success")
    # set_style=pn.bind(set_style, style=style, watch=True) 
    
       
#### Wrap them all together ##########       
    
    return pn.template.MaterialTemplate(
        site="CMMDE-GUI",
        title="CMMDE Editor",
        main=[editor, TextArea, visual_btn, pn.Tabs(xyzviewer)],
        sidebar=[pn.Row(software_btn),Name_input,pn.Card(job_btn,method_btn,pn.Row(Run_btn,Progress_btn),title="Main Calculation",collapsed=True),pn.Card(post_btn,post_software_btn,post_method_btn,pn.Row(runpost_btn,Progress_btn),title="Post Calculation",collapsed=True)],
        header_background=accent, accent_base_color=accent
    )    


if __name__.startswith("bokeh"):
    cmmde_gui().servable()