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@ -53,10 +53,10 @@ def cmmde_gui(): |
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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,.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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# 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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@ -77,8 +77,8 @@ def cmmde_gui(): |
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jobs = ",".join(job_list) |
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if editor.value == "": |
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FileInput.save("geom.xyz") |
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geom = "geom.xyz" |
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FileInput.save(FileInput.filename) |
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geom = FileInput.filename |
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else: |
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geom = editor.value |
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@ -171,11 +171,12 @@ def cmmde_gui(): |
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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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Material_input = pn.widgets.TextInput(name="Material name") |
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Material_upload = pn.widgets.FileInput(title='Input structure') |
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def materialinput(event): |
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if Material_upload.value is not None: |
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Material_upload.save("POSCAR") |
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Material_upload.param.watch(materialinput,'value') |
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# def materialinput(event): |
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# if Material_upload.value is not None: |
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# Material_upload.save("POSCAR") |
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# Material_upload.param.watch(materialinput,'value') |
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# Generate material folder button |
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materialdir_btn = pn.widgets.Button(name="Generate work directory",type="primary") |
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@ -192,9 +193,11 @@ def cmmde_gui(): |
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TextWarning.value = "Successfully create the directory!" |
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materialdir_btn.on_click(materialgen) |
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def slab_builder(event): |
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Folder = workdir + "/" + id_input.value + "/" + Material_input.value |
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os.chdir(Folder) |
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Material_upload.save("POSCAR") |
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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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@ -214,11 +217,30 @@ def cmmde_gui(): |
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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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filename_solute = pn.widgets.TextInput(title="Solute name") |
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filename_solvent = pn.widgets.TextInput(title="Solvent name") |
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solute_upload = pn.widgets.FileInput(accept=".xyz",multiple=True) |
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solvent_upload = pn.widgets.FileInput(accept=".xyz") |
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def SolutionBuilder(event): |
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solute = filename_solute.value.split(",") |
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for i in solute: |
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solute_folder = workdir + "/" + id_input.value + "/" + "{}".format(i) |
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os.makedirs(i) |
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os.chdir(i) |
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solute_upload.save(solute_upload.filename) |
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solvent = filename_solvent.value |
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solvent_folder = workdir + "/" + id_input.value + "/" + solvent |
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os.chdir("../{}".format(solvent_folder)) |
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solvent_upload.save(solvent_upload.filename) |
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os.chdir("../") |
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cmd = subprocess.run(["cmmde.py","-s","gromacs","-mt","{}".format(solute_folder)]) |
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solvent = filename_solvent.value |
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solvent_upload.save(solvent_upload.filename) |
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@ -229,7 +251,10 @@ def cmmde_gui(): |
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def visualize(event): |
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xyzview = py3Dmol.view() |
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Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value |
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if Material_input.value == "": |
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Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value |
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else: |
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Folder = workdir + "/" + id_input.value + "/" + Material_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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@ -266,7 +291,7 @@ def cmmde_gui(): |
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site="CMMDE-GUI", |
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title="CMMDE Editor", |
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main=[TextArea, editor, xyzviewer], |
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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(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),pn.Card(software_btn,job_btn,method_btn,pn.Row(Run_btn,Progress_btn),pn.Row(Checkcalc_btn,visual_btn),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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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),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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