From c4340c96c6c8d387396d386fe3002b3f4e4417c8 Mon Sep 17 00:00:00 2001 From: Aditya Wibawa Sakti Date: Wed, 17 Aug 2022 14:34:36 +0700 Subject: [PATCH] mod gui --- cmmde_gui/gui.py | 58 ++++++++++++++++++++++++++---------------- cmmde_gui/ts_finder.py | 24 +++++++++++++++++ 2 files changed, 60 insertions(+), 22 deletions(-) create mode 100644 cmmde_gui/ts_finder.py diff --git a/cmmde_gui/gui.py b/cmmde_gui/gui.py index 0b40ff5..e180688 100755 --- a/cmmde_gui/gui.py +++ b/cmmde_gui/gui.py @@ -38,8 +38,8 @@ def cmmde_gui(): height = 500, disabled=True ) # CMMDE software options - software_main = pn.widgets.Select(name="Software selections",value='Orca',options=['Orca','GROMACS','Dcdftbmd','Quantum Espresso']) - software = {'Orca':'orca','GROMACS':'gromacs','Dcdftbmd':'dcdftb','Quantum Espresso':'qe'} + software_main = pn.widgets.Select(name="Software selections",value='Orca',options=['Orca','XTB','Dcdftbmd','Quantum Espresso','GROMACS']) + software = {'Orca':'orca','GROMACS':'gromacs','Dcdftbmd':'dcdftb','Quantum Espresso':'qe','XTB':'xtb'} # Orca card job_orca = pn.widgets.MultiSelect(name="Job selections",value=['Single point calculation'],options=['Single point calculation','Geometry optimization','Frequency calculation','TS optimizer','Nudged elastic band']) @@ -74,10 +74,12 @@ def cmmde_gui(): TextArea.value = TextArea.value + "\n" + "Perhitungan anda telah tersubmit!" # RunMessage = pn.widgets.StaticText() run_orca_btn.on_click(run_orca) + # CMMDE job options job_main = pn.widgets.MultiSelect(name="Job selections",value=['Single point calculation'],options=['Single point calculation','Geometry optimization','Frequency calculation']) job = {'Single point calculation':'sp','Geometry optimization':'opt','Frequency calculation':'freq'} + # CMMDE method options method_btn = pn.widgets.Select(name="Method selections",value='GFN2-xTB',options=['GFN2-xTB','GFN1-xTB','B3LYP/def2-svp','M06/def2-svp','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','B3LYP/def2-svp':'B3LYP def2-svp','M06/def2-svp':'M06 def2-svp'} @@ -166,40 +168,43 @@ def cmmde_gui(): 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','B3LYP/def2-svp']) post_method = {'GFN2-xTB':'XTB2', 'GFN1-xTB':'XTB1','DFTB2':'DFTB2','DFTB2-gammah':'DFTB2_gammah','DFTB3':'DFTB3','DFTB3-diag':'DFTB3-diag','B3LYP/def2-svp':'B3LYP def2-svp'} def post_calculation(event): - # terminal.clear() - Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value - os.chdir(Folder) + Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value + # terminal.clear() if post_calc[post_btn.value] == 'thermo' and post_software[post_software_main.value] == 'orca': # Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value - # os.chdir(Folder) - if not os.path.exists(post_calc[post_btn.value]): - os.makedirs(post_calc[post_btn.value]) - os.chdir(post_calc[post_btn.value]) - os.system("cp ../freq/cmmd.out .") + # os.chdir(Folder) + Post_folder = Folder + "/" + post_calc[post_btn.value] + if not os.path.exists(Post_folder): + os.makedirs(Post_folder) + os.chdir(Post_folder) + os.system("cp {}/freq/cmmd.out .".format(Folder)) cmd = subprocess.run(["cmmdepost.py","-j","{}".format(post_calc[post_btn.value]),"-s","{}".format(post_software[post_software_main.value])],capture_output=True,text=True) TextArea.value = TextArea.value + "\n" + cmd.stdout elif post_calc[post_btn.value] == 'ir' and post_software[post_software_main.value] == 'orca': # Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value # os.chdir(Folder) - if not os.path.exists(post_calc[post_btn.value]): - os.makedirs(post_calc[post_btn.value]) - os.chdir(post_calc[post_btn.value]) - os.system("cp ../freq/cmmd.out .") + Post_folder = Folder + "/" + post_calc[post_btn.value] + if not os.path.exists(Post_folder): + os.makedirs(Post_folder) + os.chdir(Post_folder) + os.system("cp {}/freq/cmmd.out .".format(Folder)) cmd = subprocess.run(["cmmdepost.py","-j","{}".format(post_calc[post_btn.value]),"-s","{}".format(post_software[post_software_main.value])]) TextArea.value = TextArea.value + "\n" + "Plot spektrum IR berhasil dilakukan" # terminal.subprocess.run("cmmdepost.py","-j{}".format(post_calc[post_btn.value]),"-s{}".format(post_software[post_software_main.value])) elif post_calc[post_btn.value] == 'opt' and post_software[post_software_main.value] == 'orca': # Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value # os.chdir(Folder) + os.chdir(Folder) cmd = subprocess.run(["cmmdepost.py","-j","{}".format(post_calc[post_btn.value]),"-s","{}".format(post_software[post_software_main.value]),"-m","{}".format(post_method[post_method_btn.value])],capture_output=True,text=True) TextArea.value = TextArea.value + "\n" + cmd.stdout else: # Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value # os.chdir(Folder) - if not os.path.exists(post_calc[post_btn.value]): - os.makedirs(post_calc[post_btn.value]) - os.chdir(post_calc[post_btn.value]) - list_commands = ["cmmde.py","-i","{}".format("../cmmd.xyz"),"-s","{}".format(post_software[post_software_main.value]),"-j","{}".format(post_calc[post_btn.value]),"-m","{}".format(post_method[post_method_btn.value])] + Post_folder = Folder + post_calc[post_btn.value] + if not os.path.exists(Post_folder): + os.makedirs(Post_folder) + os.chdir(Post_folder) + list_commands = ["cmmde.py","-i","{}/cmmd.xyz".format(Folder),"-s","{}".format(post_software[post_software_main.value]),"-j","{}".format(post_calc[post_btn.value]),"-m","{}".format(post_method[post_method_btn.value])] if dispersion_cor.value != 'None': new_commands = ["-disp","{}".format(dispersion_cor.value)] for i in new_commands: @@ -219,7 +224,6 @@ def cmmde_gui(): # 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 queue",button_type='primary') @@ -227,10 +231,20 @@ def cmmde_gui(): # Check the calculation progress def calc_progress(event): + Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value + os.chdir(Folder) + cmd = subprocess.run(["tail", "-n", "10", "cmmd.out"],capture_output=True,text=True) + TextArea.value = TextArea.value + "\n" + cmd.stdout + Checkcalc_btn_main = pn.widgets.Button(name="Check calculation",button_type='primary') + Checkcalc_btn_main.on_click(calc_progress) + + def calc_progress_post(event): + Folder = workdir + "/" + id_input.value + "/" + Molecule_input.value + post_calc[post_btn.value] + os.chdir(Folder) cmd = subprocess.run(["tail", "-n", "10", "cmmd.out"],capture_output=True,text=True) TextArea.value = TextArea.value + "\n" + cmd.stdout - Checkcalc_btn = pn.widgets.Button(name="Check calculation",button_type='primary') - Checkcalc_btn.on_click(calc_progress) + Checkcalc_btn_post = pn.widgets.Button(name="Check calculation",button_type='primary') + Checkcalc_btn_post.on_click(calc_progress_post) # # Download Button download_xyz = pn.widgets.FileDownload(file="cmmd.xyz",filename="optimized.xyz") download_slab = pn.widgets.FileDownload(file="slab.vasp",filename="slab.vasp") @@ -366,7 +380,7 @@ def cmmde_gui(): site="Computational Molecular and Material Design Environment", title="CMMDE", main=[TextArea, editor, xyzviewer], - 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_main,job_main,method_btn, dispersion_cor,solvent, pn.Row(Run_btn,Progress_btn),pn.Row(Checkcalc_btn,visual_btn),download_xyz,title="Main Calculation",collapsed=True),pn.Card(post_software_main,post_btn,post_method_btn,dispersion_cor,solvent,pn.Row(runpost_btn,Progress_btn),pn.Row(Checkcalc_btn,visual_btn),pn.Row(download_spec_raw,download_spec_plot),pn.Row(download_opt_raw,download_opt_plot),title="Post-Calculation",collapsed=True)], + 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_main,job_main,method_btn, dispersion_cor,solvent, pn.Row(Run_btn,Progress_btn),pn.Row(Checkcalc_btn_main,visual_btn),download_xyz,title="Main Calculation",collapsed=True),pn.Card(post_software_main,post_btn,post_method_btn,dispersion_cor,solvent,pn.Row(runpost_btn,Progress_btn),pn.Row(Checkcalc_btn_post),pn.Row(download_spec_raw,download_spec_plot),pn.Row(download_opt_raw,download_opt_plot),title="Post-Calculation",collapsed=True)], header_background=accent, accent_base_color=accent ) diff --git a/cmmde_gui/ts_finder.py b/cmmde_gui/ts_finder.py new file mode 100644 index 0000000..f89a307 --- /dev/null +++ b/cmmde_gui/ts_finder.py @@ -0,0 +1,24 @@ +import os +import panel as pn +import subprocess +def path(workdir,id_input,textarea): + reaktan_input = pn.widgets.FileInput(name="Struktur reaktan",accept='.xyz') + produk_input = pn.widgets.FileInput(name="Struktur produk", accept='.xyz') + path_name = pn.widgets.TextInput(name="Directory name") + alp = pn.widgets.TextInput(name="Bias energy",value="1.2") + kpush = pn.widgets.TextInput(name="Push force",value="0.003") + kpull = pn.widgets.TextInput(name="Pull force",value="-0.015") + ppull = pn.widgets.TextInput(name="Histogram bin",value="0.05") + def run_path(event): + reaktan_input.save("reaktan.xyz") + reaktan = "reaktan.xyz" + produk_input.save("produk.xyz") + produk = "produk.xyz" + Folder = workdir + "/" + id_input + "/" + path_name + if os.path.exists(Folder): + textarea = textarea + "Directory exists! Please change!" + else: + os.makedirs(Folder) + os.chdir(Folder) + cmd = subprocess.run(["cmmde.py","-s","xtb","-i","{}".format(reaktan),"-j","path","-produk","{}".format(produk),"-alp","{}".format(alp.value)]) +