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131 lines
6.4 KiB
131 lines
6.4 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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# 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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terminal = pn.widgets.Terminal( |
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"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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options = {"cursorBlink": True}, |
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height = 200, sizing_mode = 'stretch_width' |
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) |
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# CMMDE software options |
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software_btn = pn.widgets.MultiSelect(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.MultiChoice(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.MultiChoice(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/Materialmaterial |
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Name_input = pn.widgets.TextInput(name="Molecule name") |
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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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def run(event): |
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os.makedirs(Name_input.value) |
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os.chdir(Name_input.value) |
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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]])) |
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Run_btn.on_click(run) |
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# Post calculations |
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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']) |
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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 Calculation CMMDE software options |
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post_software_btn = pn.widgets.MultiSelect(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.MultiChoice(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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if post_calc[post_btn.value[0]] == 'thermo' and post_software[post_software_btn.value[0]] == 'orca': |
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terminal.subprocess.run("cmmdepost.py","-j{}".format(post_calc[post_btn.value[0]]),"-s{}".format(post_software[post_software_btn.value[0]])) |
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else: |
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os.makedirs(post_calc[post_btn.value[0]]) |
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os.chdir(post_calc[post_btn.value[0]]) |
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terminal.subprocess.run("cmmde.py","-i{}".format("../cmmd.xyz"),"-s{}".format(post_software[post_software_btn.value[0]]), "-j{}".format(post_calc[post_btn.value[0]]), "-m{}".format(post_method[post_method_btn.value[0]])) |
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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 progress |
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def progress(event): |
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terminal.subprocess.run("squeue") |
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Progress_btn = pn.widgets.Button(name="Check calculation",button_type='primary') |
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Progress_btn.on_click(progress) |
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# Visualize the results |
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xyzview = py3Dmol.view() |
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xyzview.setBackgroundColor('0xeeeeee') |
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xyzview.zoomTo() |
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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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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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# 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, terminal, terminal.subprocess.param.running,visual_btn,pn.Tabs(xyzviewer)], |
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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(post_software_btn,height=200),pn.Row(post_method_btn,height=400),pn.Row(runpost_btn,Progress_btn)], |
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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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