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Merge pull request #148 from bastonero/examples/aiida
`Examples`: add a sscha-aiida example
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‎Examples/sscha_and_aiida/README.md‎

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# Instructions
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We provide here the script `run_aiida_sscha.py`, which performs a thermal expansion calculation using SSCHA and aiida-quantumespresso.
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It is preferable to execute the example that you already have some experience with both the SSCHA and AiiDA-QuantumEspresso codes. Nevertheless, you can try following the instructions and to run the example.
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## Installation
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We recommend to install all the packages via `mamba` (which is based on top of `conda`). After having installed `mamba`, you can simply run the following:
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```console
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> mamba create -n aiida-sscha -c conda-forge python gfortran libblas lapack openmpi julia openmpi-mpicc pip numpy scipy spglib aiida-core
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> pip install ase quippy-ase cellconstructor python-sscha aiida-quantumespresso aiida-pseudo
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> mamba activate aiida-sscha
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```
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Then, you should configure an AiiDA profile in order to use the example script (see also Prerequisites section).
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## Prerequisites
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You need to have installed in the same environment:
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- `python-sscha`
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- `cellconstructor`
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- `aiida-core`
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- `aiida-quantumespresso`
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For the AiiDA part, it is essential the dameon is running and you have:
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1. Configured a computer where to run the code (e.g. on your own laptop; see `aiida-core` docs for further details)
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2. Configured a code for the `pw.x` binary, related to the computer (see `aiida-quantumespresso` docs for further details)
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3. Installed a pseupopotentials library via `aiida-pseudo`. E.g. `aiida-pseudo install -x PBEsol -v 1.3`
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Please refer to the aiida-core and aiida-quantumespresso for further installation instruction.
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## How-to run
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Open the `run_aiida_sscha.py` and change the data according to your needs and local installation. Then simply
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```console
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> python run_aiida_sscha.py > run_aiida_sscha.log
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```
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Usually an actual production run would take a while. We suggest to use instead
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```console
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> nohup python run_aiida_sscha.py > run_aiida_sscha.log &
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```
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or a submit script at glance.

‎Examples/sscha_and_aiida/run_aiida_sscha.py‎

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"""Example of an actual AiiDA-powered SSCHA run."""
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import os
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import numpy as np
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from cellconstructor.Phonons import Phonons
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from sscha.aiida_ensemble import AiiDAEnsemble
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from sscha.SchaMinimizer import SSCHA_Minimizer
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from sscha.Relax import SSCHA
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from sscha.Utilities import IOInfo
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from aiida import load_profile
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from aiida_quantumespresso.common.types import ElectronicType
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load_profile()
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# =========== DEFINITION OF INPUTS =============== #
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np.random.seed(0)
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# Define the temperature range (in K)
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t_start = 300
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t_end = 800
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delta_t = 50
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target_pressure = 0
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number_q_irreducible = 4
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kpoints_distance = 0.4 # kpoints mesh
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number_of_configurations = 100
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max_iterations = 15
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data_directory = './minimization'
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pw_code_label = 'pw_7.2@hlrn-gottingen'
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dyn_filepath = './harmonic_dyn/dynamical-matrix-'
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directory_output = "./thermal_expansion"
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aiida_inputs = dict(
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pw_code_label=pw_code_label,
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protocol='precise',
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overrides={
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'pseudo_family': 'SSSP/1.3/PBEsol/precision',
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'kpoints_distance': 0.4,
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'pw':{
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'parameters':{
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'SYSTEM':{
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# ...
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},
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'ELECTRONS':{
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'mixing_beta': 0.7
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},
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},
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'settings':{
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'cmdline': ['-nk', '8']
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},
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}
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},
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options={
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'resources':{
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'num_machines': 1,
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'num_mpiprocs_per_machine': 96,
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'num_cores_per_mpiproc': 1
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},
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# 'account': 'myproject',
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'max_wallclock_seconds': int(1*60*60),
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},
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electronic_type=ElectronicType.INSULATOR,
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# group_label='Group/Where/To/Add/PwNodes', # You need to create it first
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)
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# =========== DEFINITION OF INPUTS =============== #
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dyn = Phonons(dyn_filepath, number_q_irreducible)
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dyn.ForcePositiveDefinite()
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dyn.Symmetrize()
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if not os.path.exists(directory_output):
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os.makedirs("./thermal_expansion")
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# We cycle over several temperatures
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t = t_start
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volumes = []
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temperatures = []
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while t <= t_end:
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# Change the temperature
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ensemble = AiiDAEnsemble(dyn, t)
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minim = SSCHA_Minimizer(ensemble)
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minim.set_minimization_step(0.1)
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relax = SSCHA(
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minimizer=minim,
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aiida_inputs=aiida_inputs,
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N_configs=number_of_configurations,
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max_pop=max_iterations,
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save_ensemble=True,
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)
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# Setup the I/O
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ioinfo = IOInfo()
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ioinfo.SetupSaving( os.path.join(directory_output, "minim_t{}".format(t)))
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relax.setup_custom_functions( custom_function_post = ioinfo.CFP_SaveAll)
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# Run the NPT simulation
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relax.vc_relax(
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target_press = target_pressure,
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restart_from_ens = False,
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ensemble_loc = f'ensembles_T{t}'
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)
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# Save the volume and temperature
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volumes.append(relax.minim.dyn.structure.get_volume())
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temperatures.append(t)
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# Start the next simulation from the converged value at this temperature
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relax.minim.dyn.save_qe(os.path.join(directory_output, f"sscha_T{t}_dyn"))
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dyn = relax.minim.dyn
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# Print in standard output
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relax.minim.finalize()
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# Update the temperature
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t += delta_t
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# Save the thermal expansion
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np.savetxt(os.path.join(directory_output, "thermal_expansion.dat"),
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np.transpose([temperatures, volumes]),
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header = "Temperature [K]; Volume [A^3]")

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