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tests_sphinx_sphinx_check_all.py
177 lines (162 loc) · 6.82 KB
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tests_sphinx_sphinx_check_all.py
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from pyiron_atomistics import Project
import numpy as np
import unittest
import os
class TestSphinx(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.file_location = os.path.dirname(os.path.abspath(__file__))
cls.project = Project('SPX_CHECK_ALL')
cls.a_Fe = 2.83
cls.a_Al = 4.024
@classmethod
def tearDownClass(cls):
cls.project.remove(enable=True)
def test_Fe_nonmag(self):
job = self.project.create_job(self.project.job_type.Sphinx, 'spx_Fe_nonmag')
job.structure = self.project.create.structure.ase.bulk('Fe', a=self.a_Fe)
job.calc_static()
job.run()
self.assertLess(
np.linalg.norm(job['output/generic/forces']),
1.0e-4,
'Forces wrong'
)
self.assertTrue(
np.allclose(
job.structure.positions,
job['output/generic/positions'][-1],
),
'Positions not correctly parsed'
)
self.assertTrue(
np.allclose(
job.structure.cell,
job['output/generic/cells'][-1]
),
'Cells not correctly parsed'
)
self.assertFalse(
'atom_spins' in job['output/generic/dft'].list_nodes(),
'spins present'
)
self.assertAlmostEqual(
job['output/generic/volume'][-1],
np.linalg.det(job.structure.cell),
4,
msg='Volume wrong'
)
self.assertTrue(
np.allclose(
job.structure.positions, job['output/generic/positions'][0]
),
'Positions not parsed properly'
)
job = self.project.create_job(self.project.job_type.Sphinx, 'spx_Fe_ferro')
job.structure = self.project.create.structure.ase.bulk('Fe', a=self.a_Fe)
job.structure.set_initial_magnetic_moments(len(job.structure) * [2])
job.calc_static()
job.run()
self.assertLess(
self.project.load('spx_Fe_ferro')['output/generic/energy_tot'][0],
self.project.load('spx_Fe_nonmag')['output/generic/energy_tot'][0],
'BCC Fe erromagnetic state has lower energy than nonmagnetic state'
)
def test_Fe_ferro_C(self):
job = self.project.create_job(self.project.job_type.Sphinx, 'spx_Fe_ferro_C')
job.structure = self.project.create.structure.ase.bulk('Fe', a=self.a_Fe)
job.structure.set_initial_magnetic_moments(len(job.structure) * [2])
job.structure += self.project.create_atoms(
elements=['C'], positions=[[0, 0, 0.5 * self.a_Fe]], magmoms=[0]
)
job.calc_static()
job.run()
self.assertTrue(
np.allclose(job.structure.positions, job['output/generic/positions'][-1]),
'Positions not correctly parsed'
)
job = self.project.create_job(self.project.job_type.Sphinx, 'spx_Al')
job.structure = self.project.create.structure.ase.bulk('Al', a=self.a_Al)
job.calc_static()
job.run()
job = job.restart(from_charge_density=False, from_wave_functions=False)
job.run()
self.assertTrue(
'spx_Al_restart' in list(self.project.job_table().job), 'restart job not found'
)
self.assertAlmostEqual(
self.project.load('spx_Al')['output/generic/energy_tot'][-1],
self.project.load('spx_Al_restart')['output/generic/energy_tot'][-1],
4,
msg='Energy value after restart too different'
)
def test_Al_minimize(self):
job = self.project.create_job(self.project.job_type.Sphinx, 'spx_Al_minimize')
job.structure = self.project.create.structure.ase.bulk('Al', a=self.a_Al, cubic=True)
job.structure.positions[0, 0] += 0.01
job.calc_minimize()
job.run()
E = job['output/generic/energy_tot']
self.assertGreater(E[0], E[-1], 'Energy not decreased')
def test_check_overlap(self):
job = self.project.create_job(self.project.job_type.Sphinx, 'spx_check_overlap')
job.structure = self.project.create.structure.ase.bulk('Fe', a=2.832)
job.set_check_overlap(False)
job.calc_static()
job.run()
def test_symmetry(self):
job = self.project.create_job(self.project.job_type.Sphinx, 'spx_symmetry')
job.structure = self.project.create.structure.ase.bulk('Fe', a=2.832)
job.fix_symmetry = False
job.calc_static()
job.run()
def test_Fe_ferro_constraint(self):
job = self.project.create_job(self.project.job_type.Sphinx, 'spx_Fe_ferro_constraint')
job.structure = self.project.create.structure.ase.bulk('Fe', a=self.a_Fe)
job.structure.set_initial_magnetic_moments(len(job.structure) * [2])
job.fix_spin_constraint = True
job.calc_static()
job.run()
self.assertTrue(
np.allclose(
job['output/generic/dft/atom_spins'],
job.structure.get_initial_magnetic_moments()
),
'Magnetic moments either not properly parsed or constraining not working'
)
def test_Al_save_memory(self):
job = self.project.create_job(self.project.job_type.Sphinx, 'spx_Al_save_memory')
job.structure = self.project.create.structure.ase.bulk('Al', a=self.a_Al)
job.input['SaveMemory'] = True
job.calc_static()
job.run()
def test_Al_interactive(self):
job = self.project.create_job(self.project.job_type.Sphinx, 'spx_Al_interactive')
job.structure = self.project.create.structure.ase.bulk('Al', a=self.a_Al)
job.structure.positions[0, 0] += 0.01
job.server.run_mode.interactive = True
job.calc_static()
minim = job.create_job(self.project.job_type.SxExtOptInteractive, 'sxextopt_Al')
minim.run()
def test_nonmodal2(self):
job = self.project.create_job(self.project.job_type.Sphinx, 'nonmodal2')
job.structure = self.project.create.structure.ase.bulk('Al', a=self.a_Al)
job.calc_static()
job.save()
job_reload = self.project.load(job.job_name)
job_reload.run()
self.assertTrue(job['output/generic/dft/bands_e_fermi'] is not None)
self.assertTrue(job_reload.status.finished)
def test_sxextopt_Fe(self):
spx = self.project.create_job('Sphinx', 'spx_sxextopt_Fe')
spx.structure = self.project.create.structure.ase.bulk('Fe', a=2)
spx.structure.set_initial_magnetic_moments(len(spx.structure) * [2])
spx.server.run_mode.interactive = True
spx.calc_static()
sxextopt = self.project.create_job('SxExtOptInteractive', 'sxextopt_Fe')
sxextopt.ref_job = spx
sxextopt.save()
sxextopt = self.project.load('sxextopt_Fe')
sxextopt.run()
if __name__ == "__main__":
unittest.main()