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Stop using PDB because its precision is too low
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,118 @@ | ||
| #!/usr/bin/env python2 | ||
| # -*- coding: utf-8 -*- | ||
| ########################################################################### | ||
| # Copyright (c), The AiiDA team. All rights reserved. # | ||
| # This file is part of the AiiDA code. # | ||
| # # | ||
| # The code is hosted on GitHub at https://github.com/cp2k/aiida-cp2k # | ||
| # For further information on the license, see the LICENSE.txt file # | ||
| # For further information please visit http://www.aiida.net # | ||
| ########################################################################### | ||
| from __future__ import print_function | ||
|
|
||
| import sys | ||
| import ase.build | ||
| import numpy as np | ||
| from utils import wait_for_calc | ||
|
|
||
| from aiida import load_dbenv, is_dbenv_loaded | ||
| from aiida.backends import settings | ||
| if not is_dbenv_loaded(): | ||
| load_dbenv(profile=settings.AIIDADB_PROFILE) | ||
|
|
||
| from aiida.common.example_helpers import test_and_get_code # noqa | ||
| from aiida.orm.data.structure import StructureData # noqa | ||
| from aiida.orm.data.parameter import ParameterData # noqa | ||
| from aiida.orm.data.singlefile import SinglefileData # noqa | ||
|
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||
|
|
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| # ============================================================================== | ||
| if len(sys.argv) != 2: | ||
| print("Usage: test_precision.py <code_name>") | ||
| sys.exit(1) | ||
|
|
||
| codename = sys.argv[1] | ||
| code = test_and_get_code(codename, expected_code_type='cp2k') | ||
|
|
||
| print("Testing structure roundtrip precision ase->aiida->cp2k->aiida->ase...") | ||
|
|
||
| # calc object | ||
| calc = code.new_calc() | ||
|
|
||
| # structure | ||
| epsilon = 1e-10 # expected precision in Angstrom | ||
| dist = 0.74 + epsilon | ||
| atoms = ase.Atoms('H2', positions=[(0, 0, 0), (0, 0, dist)], cell=[4, 4, 4]) | ||
| structure = StructureData(ase=atoms) | ||
| calc.use_structure(structure) | ||
|
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||
|
|
||
| # parameters | ||
| parameters = ParameterData(dict={ | ||
| 'GLOBAL': { | ||
| 'RUN_TYPE': 'MD', | ||
| }, | ||
| 'MOTION': { | ||
| 'MD': { | ||
| 'TIMESTEP': 0.0, # do not move atoms | ||
| 'STEPS': 1, | ||
| }, | ||
| }, | ||
| 'FORCE_EVAL': { | ||
| 'METHOD': 'Quickstep', | ||
| 'DFT': { | ||
| 'BASIS_SET_FILE_NAME': 'BASIS_MOLOPT', | ||
| 'SCF': { | ||
| 'MAX_SCF': 1, | ||
| }, | ||
| 'XC': { | ||
| 'XC_FUNCTIONAL': { | ||
| '_': 'LDA', | ||
| }, | ||
| }, | ||
| }, | ||
| 'SUBSYS': { | ||
| 'KIND': { | ||
| '_': 'DEFAULT', | ||
| 'BASIS_SET': 'DZVP-MOLOPT-SR-GTH', | ||
| 'POTENTIAL': 'GTH-LDA', | ||
| }, | ||
| }, | ||
| }, | ||
| }) | ||
| calc.use_parameters(parameters) | ||
|
|
||
| # resources | ||
| calc.set_max_wallclock_seconds(3*60) # 3 min | ||
| calc.set_resources({"num_machines": 1}) | ||
|
|
||
| # store and submit | ||
| calc.store_all() | ||
| calc.submit() | ||
| print("submitted calculation: PK=%s" % calc.pk) | ||
|
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| wait_for_calc(calc) | ||
|
|
||
| # check structure preservation | ||
| atoms2 = calc.out.output_structure.get_ase() | ||
|
|
||
| # zeros should be preserved exactly | ||
| if np.all(atoms2.positions[0] == 0.0): | ||
| print("OK, zeros in structure were preserved exactly") | ||
| else: | ||
| print("ERROR!") | ||
| print("Zeros in structure changed: ", atoms2.positions[0]) | ||
| sys.exit(3) | ||
|
|
||
| # other values should be preserved with epsilon precision | ||
| dist2 = atoms2.get_distance(0, 1) | ||
| if abs(dist2 - dist) < epsilon: | ||
| print("OK, structure preserved with %.1e Angstrom precision" % epsilon) | ||
| else: | ||
| print("ERROR!") | ||
| print("Structure changed by %e Angstrom" % abs(dist - dist2)) | ||
| sys.exit(3) | ||
|
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| sys.exit(0) | ||
|
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| # EOF |