VASP: Implement get_input_file_dict()

jan-janssen commented 4 months ago

The get_input_file_dict() returns a dictionary with the following structure:

{
    "files_to_create": {"file_name": "file_content_as_single_string"},
    "files_to_copy": {"file_name": "file_source"},
}

With this unification the write_input() function can be replace with a standardised function for all codes:

def write_input(self):
    """
    Call routines that generate the code specific input files
    Returns:
    """
    input_dict = self.get_input_file_dict()
    for file_name, content in input_dict["files_to_create"].items():
        with open(os.path.join(self.working_directory, file_name), "w") as f:
            f.writelines(content)
    for file_name, source in input_dict["files_to_copy"].items():
        shutil.copy(source, os.path.join(self.working_directory, file_name))

coveralls commented 4 months ago

Pull Request Test Coverage Report for Build 9444468421

Details

67 of 74 (90.54%) changed or added relevant lines in 3 files are covered.
76 unchanged lines in 2 files lost coverage.
Overall coverage decreased (-0.02%) to 71.167%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/vasp/potential.py	5	7	71.43%
pyiron_atomistics/vasp/base.py	22	27	81.48%
<!--	Total:	67	74	90.54%	-->

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/vasp/structure.py	4	97.98%
pyiron_atomistics/vasp/base.py	72	66.36%
<!--	Total:	76	-->

Totals
Change from base Build 9438715818:	-0.02%
Covered Lines:	10680
Relevant Lines:	15007

Pull Request Test Coverage Report for Build 9444530779

Details

61 of 68 (89.71%) changed or added relevant lines in 3 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage decreased (-0.02%) to 71.167%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/vasp/potential.py	5	7	71.43%
pyiron_atomistics/vasp/base.py	16	21	76.19%
<!--	Total:	61	68	89.71%	-->

Totals
Change from base Build 9438715818:	-0.02%
Covered Lines:	10680
Relevant Lines:	15007

Pull Request Test Coverage Report for Build 9471869531

Warning: This coverage report may be inaccurate.

This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.

For more information on this, see Tracking coverage changes with pull request builds.
To avoid this issue with future PRs, see these Recommended CI Configurations.
For a quick fix, rebase this PR at GitHub. Your next report should be accurate.

Details

68 of 72 (94.44%) changed or added relevant lines in 3 files are covered.
218 unchanged lines in 2 files lost coverage.
Overall coverage decreased (-0.02%) to 71.164%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/vasp/base.py	23	25	92.0%
pyiron_atomistics/vasp/potential.py	5	7	71.43%
<!--	Total:	68	72	94.44%	-->

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/dft/bader.py	4	92.73%
pyiron_atomistics/vasp/base.py	214	66.03%
<!--	Total:	218	-->

Totals
Change from base Build 9438715818:	-0.02%
Covered Lines:	10681
Relevant Lines:	15009

💛 - Coveralls

jan-janssen commented 4 months ago

@samwaseda As we already discussed a very similar pull request for LAMMPS https://github.com/pyiron/pyiron_atomistics/pull/1446 I just added you as an additional reviewer here.

coveralls commented 4 months ago

Pull Request Test Coverage Report for Build 9472795099

Warning: This coverage report may be inaccurate.

This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.

For more information on this, see Tracking coverage changes with pull request builds.
To avoid this issue with future PRs, see these Recommended CI Configurations.
For a quick fix, rebase this PR at GitHub. Your next report should be accurate.

Details

68 of 72 (94.44%) changed or added relevant lines in 3 files are covered.
218 unchanged lines in 2 files lost coverage.
Overall coverage decreased (-0.02%) to 71.164%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/vasp/base.py	23	25	92.0%
pyiron_atomistics/vasp/potential.py	5	7	71.43%
<!--	Total:	68	72	94.44%	-->

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/dft/bader.py	4	92.73%
pyiron_atomistics/vasp/base.py	214	66.03%
<!--	Total:	218	-->

Totals
Change from base Build 9438715818:	-0.02%
Covered Lines:	10681
Relevant Lines:	15009

💛 - Coveralls

coveralls commented 4 months ago

Pull Request Test Coverage Report for Build 9476641099

Details

68 of 72 (94.44%) changed or added relevant lines in 3 files are covered.
3 unchanged lines in 1 file lost coverage.
Overall coverage decreased (-0.02%) to 71.164%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/vasp/base.py	23	25	92.0%
pyiron_atomistics/vasp/potential.py	5	7	71.43%
<!--	Total:	68	72	94.44%	-->

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/vasp/base.py	3	66.03%
<!--	Total:	3		-->

Totals
Change from base Build 9450521916:	-0.02%
Covered Lines:	10681
Relevant Lines:	15009

💛 - Coveralls

coveralls commented 4 months ago

Pull Request Test Coverage Report for Build 9476744849

Details

68 of 72 (94.44%) changed or added relevant lines in 3 files are covered.
3 unchanged lines in 1 file lost coverage.
Overall coverage decreased (-0.02%) to 71.164%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/vasp/base.py	23	25	92.0%
pyiron_atomistics/vasp/potential.py	5	7	71.43%
<!--	Total:	68	72	94.44%	-->

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/vasp/base.py	3	66.03%
<!--	Total:	3		-->

Totals
Change from base Build 9450521916:	-0.02%
Covered Lines:	10681
Relevant Lines:	15009

💛 - Coveralls

coveralls commented 4 months ago

Pull Request Test Coverage Report for Build 9477144844

Details

62 of 69 (89.86%) changed or added relevant lines in 3 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage decreased (-0.02%) to 71.181%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/vasp/potential.py	5	7	71.43%
pyiron_atomistics/vasp/base.py	17	22	77.27%
<!--	Total:	62	69	89.86%	-->

Totals
Change from base Build 9477094720:	-0.02%
Covered Lines:	10695
Relevant Lines:	15025

💛 - Coveralls

jan-janssen commented 4 months ago

Define a calculate() function which can be submitted using an pympipool.Executor:

from pympipool import Executor
import os
import posixpath
import shutil
import subprocess
from pyiron_atomistics import Project
from pyiron_atomistics.vasp.output import parse_vasp_output

def calculate_vasp(working_directory, input_file_dict, executable_dict, collect_output_kwargs):
    os.makedirs(working_directory, exist_ok=True)
    for file_name, content in input_file_dict["files_to_create"].items():
        with open(os.path.join(working_directory, file_name), "w") as f:
            f.writelines(content)
    for file_name, source in input_file_dict["files_to_copy"].items():
        shutil.copy(source, os.path.join(working_directory, file_name))
    _ = subprocess.run(
        executable_dict["command"],
        cwd=working_directory,
        shell=executable_dict["shell"],
        stdout=subprocess.PIPE,
        stderr=subprocess.STDOUT,
        universal_newlines=True,
        check=True,
    )
    return parse_vasp_output(
        working_directory=working_directory,
        **collect_output_kwargs,
    )

pr = Project("test")
pr.remove_jobs(recursive=True, silently=True)
job = pr.create.job.Vasp("vasp")
job.structure = pr.create.structure.ase.bulk("Al", cubic=True)
job.validate_ready_to_run()

executable, shell = job.executable.get_input_for_subprocess_call(
    cores=job.server.cores, threads=job.server.threads, gpus=job.server.gpus
)
with Executor(backend="mpi") as exe:
    future = exe.submit(
        calculate_vasp, 
        working_directory="tmp", 
        input_file_dict=job.get_input_file_dict(), 
        executable_dict={
            "command": executable,
            "shell": shell,
        }, 
        collect_output_kwargs={
            "sorted_indices": job.sorted_indices,
            "structure": job.structure,
        },
    )
    output_dict = future.result()

job._python_only_job = True
job.save()
job._store_output(output_dict=output_dict)

job_reload = pr.load(job.job_name)
print(job_reload.output.energy_pot)

jan-janssen commented 4 months ago

Waiting for https://github.com/pyiron/pyiron_base/pull/1472

coveralls commented 4 months ago

Pull Request Test Coverage Report for Build 9609405373

Details

67 of 73 (91.78%) changed or added relevant lines in 3 files are covered.
133 unchanged lines in 4 files lost coverage.
Overall coverage decreased (-0.1%) to 71.064%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/vasp/potential.py	5	7	71.43%
pyiron_atomistics/vasp/base.py	22	26	84.62%
<!--	Total:	67	73	91.78%	-->

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/vasp/base.py	17	61.73%
pyiron_atomistics/lammps/output.py	21	87.18%
pyiron_atomistics/lammps/interactive.py	22	45.59%
pyiron_atomistics/lammps/base.py	73	79.85%
<!--	Total:	133	-->

Totals
Change from base Build 9609409415:	-0.1%
Covered Lines:	10676
Relevant Lines:	15023

💛 - Coveralls

coveralls commented 4 months ago

Pull Request Test Coverage Report for Build 9609413711

Details

67 of 73 (91.78%) changed or added relevant lines in 3 files are covered.
17 unchanged lines in 1 file lost coverage.
Overall coverage decreased (-0.1%) to 71.057%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/vasp/potential.py	5	7	71.43%
pyiron_atomistics/vasp/base.py	22	26	84.62%
<!--	Total:	67	73	91.78%	-->

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/vasp/base.py	17	61.73%
<!--	Total:	17		-->

Totals
Change from base Build 9609409415:	-0.1%
Covered Lines:	10677
Relevant Lines:	15026

pyiron / pyiron_atomistics