#!/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 # 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 terminal = pn.widgets.Terminal( "Computational Molecular and Material Design Environment\n Authors:\n Universitas Pertamina\n Institut Teknologi Sumatera\n Masyarakat Komputasi Indonesia\n\n", options = {"cursorBlink": True}, height = 200, sizing_mode = 'stretch_width' ) # CMMDE software options software_btn = pn.widgets.MultiSelect(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.MultiChoice(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.MultiChoice(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') def run(event): os.makedirs(Name_input.value) os.chdir(Name_input.value) terminal.subprocess.run("cmmde.py","-i{}".format(editor.value),"-s{}".format(software[software_btn.value[0]]), "-j{}".format(job[job_btn.value[0]]), "-m{}".format(method[method_btn.value[0]])) Run_btn.on_click(run) # Post calculations post_btn = pn.widgets.MultiChoice(name="Post calculation",value=['Frequency calculation'], options=['Frequency calculation','Radial distribution function', 'Mean Square Displacement','Time-dependent calculation','Thermochemistry calculation']) post_calc = {'Frequency calculation':'freq', 'Radial distribution function':'rdf','Mean Square Displacement':'msd','Time-dependent calculation':'td','Thermochemistry':'thermo'} def post_calculation(event): os.makedirs(post_calc[post_btn.value[0]]) os.chdir(post_calc[post_btn.value[0]]) if post_calc[post_btn.value[0]] == 'thermo' and software[software_btn.value[0]] == 'orca': terminal.subprocess.run("cmmdepost.py","-j{}".format(post_calc[post_btn.value[0]]),"-s{}".format(software[software_btn.value[0]])) else: terminal.subprocess.run("cmmde.py","-i{}".format("../cmmd.xyz"),"-s{}".format(software[software_btn.value[0]]), "-j{}".format(post_calc[post_btn.value[0]]), "-m{}".format(method[method_btn.value[0]])) 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.subprocess.run("squeue") 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, terminal, terminal.subprocess.param.running,visual_btn,pn.Tabs(xyzviewer)], sidebar=[pn.Row(software_btn,height=200),Name_input,pn.Column(job_btn, height=400),pn.Column(method_btn,height=400),pn.Row(Run_btn,Progress_btn),pn.Column(post_btn,height=400),pn.Row(runpost_btn,Progress_btn)], header_background=accent, accent_base_color=accent ) if __name__.startswith("bokeh"): cmmde_gui().servable()