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| #!/usr/bin/env python | ||
| # coding: utf-8 | ||
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| # # Quantum Espresso SCF calcuation via API | ||
| # | ||
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| # In[1]: | ||
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| from utils.settings import ENDPOINT_ARGS, ACCOUNT_ID | ||
| from utils.generic import display_JSON | ||
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| from exabyte_api_client.endpoints.workflows import WorkflowEndpoints | ||
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| # In[2]: | ||
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| # Initialize a helper class to interact with WorkflowEndpoints | ||
| endpoint = WorkflowEndpoints(*ENDPOINT_ARGS) | ||
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| # In[3]: | ||
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| # payload for workflow creation | ||
| BODY = { | ||
| "name": "Silicon-SCF-bash-REST", | ||
| "subworkflows": [ | ||
| { | ||
| "name": "QE-SCF", | ||
| "application": { | ||
| "name": "shell", | ||
| "version": "4.2.46", | ||
| "build": "Default", | ||
| "isDefault": "true", | ||
| "summary": "Shell Script", | ||
| "shortName": "sh", | ||
| }, | ||
| "properties": ["total_energy", "fermi_energy"], | ||
| "units": [ | ||
| { | ||
| "type": "execution", | ||
| "application": { | ||
| "name": "shell", | ||
| "version": "4.2.46", | ||
| "build": "Default", | ||
| "isDefault": "true", | ||
| "summary": "Shell Script", | ||
| "shortName": "sh", | ||
| }, | ||
| "head": "true", | ||
| "input": [ | ||
| { | ||
| "content": "#!/bin/bash\n# ---------------------- CLUSTER PARAMETERS ---------------------- #\n#PBS -N Silicon-SCF\n#PBS -j oe\n#PBS -l nodes=1\n#PBS -l ppn=4\n#PBS -q OR\n#PBS -l walltime=00:00:30:00\n#PBS -A seminar-espresso-tutorials\n# ------------------------- INPUT FILES -------------------------- #\n# switch to the job working directory\ncd $PBS_O_WORKDIR\n\nBASE_URL='https://github.com/pranabdas/espresso/raw/next/src'\nIN_FILE='pw.scf.silicon.in'\nPP_FILE='Si.pz-vbc.UPF'\n\n# get QE input file\nwget ${BASE_URL}/silicon/${IN_FILE} -O ${IN_FILE}\n\n# get pseudopotential file\nwget ${BASE_URL}/pseudos/${PP_FILE} -O ${PP_FILE}\n\n# delete pseudo_dir from input file and provide via env\nsed -i '/^\\s*pseudo_dir/d' ${IN_FILE}\nexport ESPRESSO_PSEUDO='./'\n\n# --------------------------- RUN JOB ---------------------------- #\n# load required module\nmodule add espresso/63-i-174-impi-044\n\n# run the calculation\nmpirun -np $PBS_NP pw.x -in ${IN_FILE} | tee ${IN_FILE%*.in}.out\n\n# ----------------------------- END ------------------------------ #\n", | ||
| "name": "pbs-Silicon-scf.sh", | ||
| } | ||
| ], | ||
| "name": "Silicon-SCF.sh", | ||
| "executable": { | ||
| "isDefault": "true", | ||
| "monitors": ["standard_output"], | ||
| "results": [ | ||
| "atomic_forces", | ||
| "band_gaps", | ||
| "band_structure", | ||
| "density_of_states", | ||
| "fermi_energy", | ||
| "phonon_dispersions", | ||
| "phonon_dos", | ||
| "pressure", | ||
| "stress_tensor", | ||
| "total_energy", | ||
| "total_energy_contributions", | ||
| "total_force", | ||
| "zero_point_energy", | ||
| "final_structure", | ||
| "magnetic_moments", | ||
| "reaction_energy_barrier", | ||
| "reaction_energy_profile", | ||
| "potential_profile", | ||
| "charge_density_profile", | ||
| ], | ||
| "name": "sh", | ||
| }, | ||
| "flavor": { | ||
| "isDefault": "true", | ||
| "input": [{"name": "hello_world.sh"}], | ||
| "monitors": ["standard_output"], | ||
| "applicationName": "shell", | ||
| "executableName": "sh", | ||
| "name": "hello_world", | ||
| "executable": { | ||
| "isDefault": "true", | ||
| "monitors": ["standard_output"], | ||
| "results": [ | ||
| "atomic_forces", | ||
| "band_gaps", | ||
| "band_structure", | ||
| "density_of_states", | ||
| "fermi_energy", | ||
| "phonon_dispersions", | ||
| "phonon_dos", | ||
| "pressure", | ||
| "stress_tensor", | ||
| "total_energy", | ||
| "total_energy_contributions", | ||
| "total_force", | ||
| "zero_point_energy", | ||
| "final_structure", | ||
| "magnetic_moments", | ||
| "reaction_energy_barrier", | ||
| "reaction_energy_profile", | ||
| "potential_profile", | ||
| "charge_density_profile", | ||
| ], | ||
| "name": "sh", | ||
| }, | ||
| }, | ||
| } | ||
| ], | ||
| "compute": { | ||
| "ppn": 4, | ||
| "nodes": 1, | ||
| "queue": "OR", | ||
| "timeLimit": "01:00:00", | ||
| "notify": "n", | ||
| "cluster": {"fqdn": "master-production-20160630-cluster-001.exabyte.io"}, | ||
| }, | ||
| } | ||
| ], | ||
| } | ||
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| # In[4]: | ||
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| response = endpoint.create(BODY) | ||
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| # In[ ]: | ||
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