Core components of the pyiron integrated development environment (IDE) for computational materials science
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pyiron_base
The pyiron_base workflow manager provides the data storage and job management for the pyiron
project. As part of the modularization of the pyiron project in 2018, the monolithic code base
which started as pyCMW back in 2011 was split in pyiron_base and pyiron_atomistics. This split highlights the
separation of the technical complexity and workflow management in pyiron_base and the physics modelling for atomistic
simulation in pyiron_atomistics.
Features:
- Calculation which can be either simple python functions or external executables written in any programming language
can be wrapped in
pyiron_baseto enable parameter studies with thousands or millions of calculation. - The calculation can either be executed locally on the same computer or on high performance computing (HPC) resources. The python simple queuing system adapter pysqa is used to interface with the HPC queuing systems directly from python and the pympipool package is employed to assign dedicated resources like multiple CPU cores and GPUs to individual python functions.
- Scientific data is efficiently stored using the hierarchical data format (HDF) via the h5py python library and more specifically the h5io packages to match the python datatypes to the HDF5 data types.
With this functionality the pyiron_base workflow manager enables the rapid prototyping and up-scaling of parameter
studies for a wide range of scientific application. Starting from simulation codes written in Fortran without any Python
bindings, over more modern modelling codes written in C or C++ with Python bindings up to machine learning models
requiring GPU acceleration, the approach follows the same three steps:
- Implement a wrapper for the simulation code, which takes a set of input parameters calls the simulation code and
returns a set of output parameters. For a simulation code with python bindings this is achieved with the
wrap_python_function()function and for any external executable which requires file-based communication this is achieved with thecreate_job_class()function which requires only awrite_input()function and acollect_output()function to parse the input and output files of the external executable. Both functions return ajobobject. This is the central building block of thepyiron_baseworkflow manager. - Following the map-reduce pattern a series of
jobobjects are created and submitted to the available computing resources. When thepyiron_baseworkflow manager is executed directly on the login node of a HPC cluster, the calculation are directly submitted to the queuing system. Alternatively, thepyiron_baseworkflow manager also supports submission via an secure shell (SSH) connection to the HPC cluster. Still in contrast to many other workflow managers, thepyiron_baseworkflow manager does not require constant connection to the remote computing resources. Once thejobobjects are submitted the workflow can be shutdown. - Finally, after the execution of the individual
jobobjects is completed thepyiron_tableobject gathers the data of the individualjobobjects in a single table. The table is accessible aspandas.DataFrameso it is compatible to most machine learning and plotting libraries for further analysis.
Example:
As the pyiron_base workflow manager was developed as part of the pyiron project the
implementation of the quantum espresso density functional theory (DFT) simulation
code in the pyiron_base workflow manager is chosen as example. Still the same steps apply for any kind of simulation
code:
import os
import matplotlib.pyplot as plt
import numpy as np
from ase.build import bulk
from ase.calculators.espresso import Espresso
from ase.io import write
from pwtools import io
def write_input(input_dict, working_directory="."):
filename = os.path.join(working_directory, 'input.pwi')
os.makedirs(working_directory, exist_ok=True)
write(
filename=filename,
images=input_dict["structure"],
Crystal=True,
kpts=input_dict["kpts"],
input_data={"calculation": input_dict["calculation"]},
pseudopotentials=input_dict["pseudopotentials"],
tstress=True,
tprnfor=True
)
def collect_output(working_directory="."):
filename = os.path.join(working_directory, 'output.pwo')
try:
return {"structure": io.read_pw_md(filename)[-1].get_ase_atoms()}
except TypeError:
out = io.read_pw_scf(filename)
return {
"energy": out.etot,
"volume": out.volume,
}
def workflow(project, structure):
# Structure optimization
job_qe_minimize = pr.create.job.QEJob(job_name="qe_relax")
job_qe_minimize.input["calculation"] = "vc-relax"
job_qe_minimize.input.structure = structure
job_qe_minimize.run()
structure_opt = job_qe_minimize.output.structure
# Energy Volume Curve
energy_lst, volume_lst = [], []
for i, strain in enumerate(np.linspace(0.9, 1.1, 5)):
structure_strain = structure_opt.copy()
structure_strain = structure.copy()
structure_strain.set_cell(
structure_strain.cell * strain**(1/3),
scale_atoms=True
)
job_strain = pr.create.job.QEJob(
job_name="job_strain_" + str(i)
)
job_strain.input.structure = structure_strain
job_strain.run(delete_existing_job=True)
energy_lst.append(job_strain.output.energy)
volume_lst.append(job_strain.output.volume)
return {"volume": volume_lst, "energy": energy_lst}
from pyiron_base import Project
pr = Project("test")
pr.create_job_class(
class_name="QEJob",
write_input_funct=write_input,
collect_output_funct=collect_output,
default_input_dict={ # Default Parameter
"structure": None,
"pseudopotentials": {"Al": "Al.pbe-n-kjpaw_psl.1.0.0.UPF"},
"kpts": (3, 3, 3),
"calculation": "scf",
},
executable_str="mpirun -np 1 pw.x -in input.pwi > output.pwo",
)
job_workflow = pr.wrap_python_function(workflow)
job_workflow.input.project = pr
job_workflow.input.structure = bulk('Al', a=4.15, cubic=True)
job_workflow.run()
plt.plot(job_workflow.output.result["volume"], job_workflow.output.result["energy"])
plt.xlabel("Volume")
plt.ylabel("Energy")
After the definition of the write_input() and collect_output() function for the quantum espresso DFT simulation code
the workflow() function is defined to combine multiple quantum espresso DFT simulation. First the structure is
optimized to identify the equilibrium volume and afterwards five strains ranging from 90% to 110% are applied to
determine the bulk modulus. Finally, in the last few lines all the individual pieces are put together, by creating
QEJob the quantum espresso job class based on the write_input() and collect_output() function and then wrapping
the workflow() function using the wrap_python_function(). The whole workflow is executed when the run() function
is called. Afterwards the results are plotted using the matplotlib library.
Disclaimer
While we try to develop a stable and reliable software library, the development remains a opensource project under the BSD 3-Clause License without any warranties:
BSD 3-Clause License
Copyright (c) 2018, Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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