def test_input():
from numpy import array, all, abs
from pylada.error import ValueError
from pylada.gulp import Functional
functional = Functional()
functional.morse['Ti', 'O'] = [1.0279493, 3.640737, 1.88265, 0, 25]
functional.morse['Ti', 'Ti'] = [0.00567139, 1.5543, 4.18784, 0, 25]
functional.morse['O', 'O'] = [0.00567139, 1.5543, 4.18784, 0, 25]
# should fail since no interaction enabled yet.
try: functional.input_string()
except ValueError: pass
else: raise Exception()
functional.morse.enabled = True
string = functional.input_string().splitlines()
assert string[:2] == [''] * 2
assert string[2] == 'morse'
assert string[3].split()[:4] == ['O', 'core'] * 2
assert all(abs(array( string[3].split()[4:], dtype='float64')
- functional.morse['O', 'O'] ) < 1e-3)
assert string[4].split()[:4] == ['Ti', 'core'] * 2
assert all(abs(array( string[4].split()[4:], dtype='float64')
- functional.morse['Ti', 'Ti'] ) < 1e-3)
assert string[5].split()[:4] == ['O', 'core', 'Ti', 'core']
assert all(abs(array( string[5].split()[4:], dtype='float64')
- functional.morse['Ti', 'O'] ) < 1e-3)
def test():
""" Tests file setup. """
from tempfile import mkdtemp
from os.path import exists
from shutil import rmtree
from quantities import eV
from pylada.gulp import Functional
from pylada.crystal import Structure
from pylada.tools import create_directory
functional = Functional()
functional.qeq = True
functional.morse.enabled = True
functional.morse['Ti', 'O'] = [1.0279493, 3.640737, 1.88265, 0, 25]
functional.morse['Ti', 'Ti'] = [0.00567139, 1.5543, 4.18784, 0, 25]
functional.morse['O', 'O'] = [0.00567139, 1.5543, 4.18784, 0, 25]
structure = Structure( 4.6391, 0, 0,
0, 4.6391, 0,
0, 0, 2.97938,
scale=1, symmgroup=136 ) \
.add_atom(0, 0, 0, 'Ti', asymmetric=True) \
.add_atom(2.31955, 2.31955, 1.48969, 'Ti', asymmetric=False) \
.add_atom(1.42027, 1.42027, 0, 'O', asymmetric=True) \
.add_atom(-1.42027, -1.42027, 0, 'O', asymmetric=False) \
.add_atom(-0.899275, 0.899275, 1.48969, 'O', asymmetric=False) \
.add_atom(0.899275, -0.899275, 1.48969, 'O', asymmetric=False)
directory = mkdtemp()
if directory == '/tmp/test/':
if exists(directory): rmtree(directory)
create_directory(directory)
try:
result = functional(structure, directory)
assert result._finished
assert result.success
assert not result.optimize
assert not result.conp
assert abs(result.energy + 9.84502039*eV) < 1e-5
finally:
if directory != '/tmp/test/': rmtree(directory)
def test_repr():
""" Test representability. """
from numpy import all, array, abs
from pylada.gulp import Functional
functional = Functional()
b = {}; exec(repr(functional)) in b; b = b['functional']
assert not b.morse.enabled
assert not b.opti
assert not b.conv
assert not b.conp
assert not b.isotropic
assert not b.cellonly
assert not b.buckingham.enabled
assert len(b.morse) == 0
assert len(b.buckingham) == 0
functional.morse['Ti', 'O'] = [1.0279493, 3.640737, 1.88265, 0, 25]
functional.morse['Ti', 'Ti'] = [0.00567139, 1.5543, 4.18784, 0, 25]
functional.morse['O', 'O'] = [0.00567139, 1.5543, 4.18784, 0, 25]
b = {}; exec(repr(functional)) in b; b = b['functional']
assert not b.morse.enabled
assert not b.opti
assert not b.conv
assert not b.conp
assert not b.isotropic
assert not b.cellonly
assert len(b.morse) == 3
assert not b.buckingham.enabled
assert len(b.buckingham) == 0
assert all(abs(array( functional.morse['Ti', 'O'])
- [1.0279493, 3.640737, 1.88265, 0, 25] ) < 1e-4)
assert all(abs(array( functional.morse['Ti', 'Ti'])
- [0.00567139, 1.5543, 4.18784, 0, 25] ) < 1e-4)
assert all(abs(array( functional.morse['O', 'O'])
- [0.00567139, 1.5543, 4.18784, 0, 25] ) < 1e-4)
functional.morse.enabled = True
functional.opti = True
functional.cellonly = True
b = {}; exec(repr(functional)) in b; b = b['functional']
assert b.morse.enabled
assert b.opti
assert not b.conv
assert not b.conp
assert not b.isotropic
assert not b.buckingham.enabled
assert len(b.buckingham) == 0
assert b.cellonly
assert len(b.morse) == 3
assert all(abs(array( functional.morse['Ti', 'O'])
- [1.0279493, 3.640737, 1.88265, 0, 25] ) < 1e-4)
assert all(abs(array( functional.morse['Ti', 'Ti'])
- [0.00567139, 1.5543, 4.18784, 0, 25] ) < 1e-4)
assert all(abs(array( functional.morse['O', 'O'])
- [0.00567139, 1.5543, 4.18784, 0, 25] ) < 1e-4)
def test_filesetup():
""" Tests file setup. """
from tempfile import mkdtemp
from os.path import exists, join, samefile, lexists
from shutil import rmtree
from pylada.gulp import Functional
from pylada.crystal import Structure
from pylada.tools import create_directory, get_section_from_file
functional = Functional()
functional.morse.enabled = True
functional.morse['Ti', 'O'] = [1.0279493, 3.640737, 1.88265, 0, 25]
functional.morse['Ti', 'Ti'] = [0.00567139, 1.5543, 4.18784, 0, 25]
functional.morse['O', 'O'] = [0.00567139, 1.5543, 4.18784, 0, 25]
structure = Structure( 4.6391, 0, 0,
0, 4.6391, 0,
0, 0, 2.97938,
scale=1, symmgroup=136 ) \
.add_atom(0, 0, 0, 'Ti', asymmetric=True) \
.add_atom(2.31955, 2.31955, 1.48969, 'Ti', asymmetric=False) \
.add_atom(1.42027, 1.42027, 0, 'O', asymmetric=True) \
.add_atom(-1.42027, -1.42027, 0, 'O', asymmetric=False) \
.add_atom(-0.899275, 0.899275, 1.48969, 'O', asymmetric=False) \
.add_atom(0.899275, -0.899275, 1.48969, 'O', asymmetric=False)
directory = mkdtemp()
if directory == '/tmp/test/':
if exists(directory): rmtree(directory)
create_directory(directory)
try:
iterator = functional.iter(structure, outdir=directory)
assert exists(directory)
assert not exists(join(directory, 'gulp.out'))
assert not exists(join(directory, 'gulp.in'))
assert not exists(join(directory, 'gulp.err'))
program = iterator.next()
assert exists(join(directory, 'gulp.out'))
assert exists(join(directory, 'gulp.in'))
assert not exists(join(directory, 'gulp.err'))
with open(join(directory, 'gulp.out'), 'r') as file:
get_section_from_file(file, 'input file')
get_section_from_file(file, 'functional')
rmtree(directory)
create_directory(directory)
workdir = join(directory, 'wtf')
iterator = functional.iter( structure, outdir=directory,
workdir=workdir )
assert exists(directory)
assert not exists(join(directory, 'gulp.out'))
assert not exists(join(directory, 'gulp.in'))
assert not exists(join(directory, 'gulp.err'))
program = iterator.next()
assert exists(join(directory, 'gulp.out'))
assert exists(join(directory, 'gulp.in'))
assert not exists(join(directory, 'gulp.err'))
with open(join(directory, 'gulp.out'), 'r') as file:
get_section_from_file(file, 'input file')
get_section_from_file(file, 'functional')
assert samefile(workdir, join(directory, 'workdir'))
assert exists(join(workdir, 'gulp.out'))
assert samefile(join(workdir, 'gulp.out'), join(directory, 'gulp.out'))
assert exists(join(workdir, 'gulp.in'))
assert not samefile(join(workdir, 'gulp.in'), join(directory, 'gulp.in'))
assert lexists(join(workdir, 'gulp.err'))
assert exists(join(directory, '.pylada_is_running'))
program.onfinish()
assert not exists(join(directory, '.pylada_is_running'))
assert exists(workdir)
assert exists(join(directory, 'workdir'))
assert samefile(join(workdir, 'gulp.out'), join(directory, 'gulp.out'))
finally:
if directory != '/tmp/test/': rmtree(directory)
