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Fix input parser for cell parameters with integers (#71)
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The input parser would except for input files that define cell parameters
using integers instead of floats. The regex is updated to accept integers
in addition to floats. Furthermore, the regexes are slightly refactored
factoring out the pattern for valid numbers which was repeated multiple
times.
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@eimrek
eimrek authored Oct 18, 2023
1 parent ee3f7d7 commit efe4472
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Showing 4 changed files with 154 additions and 72 deletions.
120 changes: 48 additions & 72 deletions src/qe_tools/parsers/_input_base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,10 +14,24 @@
from .._qe_version import parse_version
from ..exceptions import InputValidationError, ParsingError

RE_FLAGS = re.M | re.X | re.I
RE_FLAGS = re.MULTILINE | re.VERBOSE | re.IGNORECASE

__all__ = tuple() # type: Tuple[str, ...]

NUMBER_PATTERN = r"""
(?:
[-|+]? # Plus or minus in front of the number (optional)
(?:\d* # optional decimal in the beginning .0001 is ok, for example
[\.] # There has to be a dot followed by
\d+) # at least one decimal
| # OR
(?:\d+ # at least one decimal, followed by
[\.]? # an optional dot
\d*) # followed by optional decimals
(?:[E|e|d|D][+|-]?\d+)? # optional exponents E+03, e-05, d0, D0
)
"""


class _BaseInputFile:
"""
Expand Down Expand Up @@ -373,34 +387,20 @@ def str01_to_bool(s):
# Define re for the card block.
# NOTE: This will match card block lines w/ or w/out force modifications.
atomic_positions_block_re = re.compile(
r"""
fr"""
^ \s* ATOMIC_POSITIONS \s* # Atomic positions start with that string
[{(]? \s* (?P<units>\S+?)? \s* [)}]? \s* $\n # The units are after the string in optional brackets
(?P<block> # This is the block of positions
[{{(]? \s* (?P<units>\S+?)? \s* [)}}]? \s* $\n # The units are after the string in optional brackets
(?P<block> # This is the block of positions
(
(
\s* # White space in front of the element spec is ok
(
[A-Za-z]+[A-Za-z0-9]{0,2} # Element spec
[A-Za-z]+[A-Za-z0-9]{{0,2}} # Element spec
(
\s+ # White space in front of the number
[-|+]? # Plus or minus in front of the number (optional)
(
(
\d* # optional decimal in the beginning .0001 is ok, for example
[\.] # There has to be a dot followed by
\d+ # at least one decimal
)
| # OR
(
\d+ # at least one decimal, followed by
[\.]? # an optional dot ( both 1 and 1. are fine)
\d* # And optional number of decimals (1.00001)
) # followed by optional decimals
)
([E|e|d|D][+|-]?\d+)? # optional exponents E+03, e-05
){3} # I expect three float values
((\s+[0-1]){3}\s*)? # Followed by optional ifpos
{NUMBER_PATTERN}
){{3}} # I expect three float values
((\s+[0-1]){{3}}\s*)? # Followed by optional ifpos
\s* # Followed by optional white space
|
\#.* # If a line is commented out, that is also ok
Expand Down Expand Up @@ -434,30 +434,27 @@ def str01_to_bool(s):

# Define re for atomic positions without force modifications.
atomic_positions_w_constraints_re = re.compile(
r"""
^ # Linestart
[ \t]* # Optional white space
(?P<name>[A-Za-z]+[A-Za-z0-9]{0,2})\s+ # get the symbol, max 3 chars, starting with a char
(?P<x> # Get x
[\-|\+]?(\d*[\.]\d+ | \d+[\.]?\d*)
([E|e|d|D][+|-]?\d+)?
fr"""
^ # Linestart
[ \t]* # Optional white space
(?P<name>[A-Za-z]+[A-Za-z0-9]{{0,2}})\s+ # get the symbol, max 3 chars, starting with a char
(?P<x> # Get x
{NUMBER_PATTERN}
)
[ \t]+
(?P<y> # Get y
[\-|\+]?(\d*[\.]\d+ | \d+[\.]?\d*)
([E|e|d|D][+|-]?\d+)?
(?P<y> # Get y
{NUMBER_PATTERN}
)
[ \t]+
(?P<z> # Get z
[\-|\+]?(\d*[\.]\d+ | \d+[\.]?\d*)
([E|e|d|D][+|-]?\d+)?
(?P<z> # Get z
{NUMBER_PATTERN}
)
[ \t]*
(?P<fx>[01]?) # Get fx
(?P<fx>[01]?) # Get fx
[ \t]*
(?P<fy>[01]?) # Get fx
(?P<fy>[01]?) # Get fx
[ \t]*
(?P<fz>[01]?) # Get fx
(?P<fz>[01]?) # Get fx
""", re.X | re.M
)
# Find the card block and extract units and the lines of the block.
Expand Down Expand Up @@ -542,39 +539,21 @@ def _parse_cell_parameters(txt):
"""
# Define re for the card block.
cell_parameters_block_re = re.compile(
r"""
fr"""
^ [ \t]*
CELL_PARAMETERS [ \t]*
[{(]? \s* (?P<units>[a-z]*) \s* [)}]? \s* [\n]
[{{(]? \s* (?P<units>[a-z]*) \s* [)}}]? \s* [\n]
(?P<block>
(
(
\s* # White space in front of the element spec is ok
\s* # White space in front is ok
(
# First number
(
[-|+]? # Plus or minus in front of the number (optional)
(\d* # optional decimal in the beginning .0001 is ok, for example
[\.] # There has to be a dot followed by
\d+) # at least one decimal
| # OR
(\d+ # at least one decimal, followed by
[\.]? # an optional dot
\d*) # followed by optional decimals
([E|e|d|D][+|-]?\d+)? # optional exponents E+03, e-05, d0, D0
(
\s+ # White space between numbers
[-|+]? # Plus or minus in front of the number (optional)
(\d* # optional decimal in the beginning .0001 is ok, for example
[\.] # There has to be a dot followed by
\d+) # at least one decimal
| # OR
(\d+ # at least one decimal, followed by
[\.]? # an optional dot
\d*) # followed by optional decimals
([E|e|d|D][+|-]?\d+)? # optional exponents E+03, e-05, d0, D0
){2} # I expect three float values
{NUMBER_PATTERN}
\s+
{NUMBER_PATTERN}
\s+
{NUMBER_PATTERN}
)
|
\#
Expand All @@ -586,28 +565,25 @@ def _parse_cell_parameters(txt):
\s* # A line only containing white space
)
[\n] # line break at the end
){3} # I need exactly 3 vectors
){{3}} # I need exactly 3 vectors
)
""", RE_FLAGS
)

cell_vector_regex = re.compile(
r"""
fr"""
^ # Linestart
[ \t]* # Optional white space
(?P<x> # Get x
[\-|\+]? ( \d*[\.]\d+ | \d+[\.]?\d*)
([E|e|d|D][+|-]?\d+)?
{NUMBER_PATTERN}
)
[ \t]+
(?P<y> # Get y
[\-|\+]? (\d*[\.]\d+ | \d+[\.]?\d*)
([E|e|d|D][+|-]?\d+)?
{NUMBER_PATTERN}
)
[ \t]+
(?P<z> # Get z
[\-|\+]? (\d*[\.]\d+ | \d+[\.]?\d*)
([E|e|d|D][+|-]?\d+)?
{NUMBER_PATTERN}
)
""", re.X | re.M
)
Expand Down
15 changes: 15 additions & 0 deletions tests/data/lattice_ibrav0_cell_parameters_int.in
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Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
&control
calculation = 'scf'
/
&system
ibrav = 0
/
ATOMIC_SPECIES
Na 22.99 Na.upf
ATOMIC_POSITIONS crystal
Na 0.0 0.0 0.0
CELL_PARAMETERS angstrom
5.7 0 0
0 5.7 0
0 0 5.7
K_POINTS gamma
88 changes: 88 additions & 0 deletions tests/data/ref/lattice_ibrav0_cell_parameters_int.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,88 @@
{
"atomic_positions": {
"fixed_coords": [
[
false,
false,
false
]
],
"names": [
"Na"
],
"positions": [
[
0.0,
0.0,
0.0
]
],
"units": "crystal"
},
"atomic_species": {
"masses": [
22.99
],
"names": [
"Na"
],
"pseudo_file_names": [
"Na.upf"
]
},
"cell": [
[
5.7,
0.0,
0.0
],
[
0.0,
5.7,
0.0
],
[
0.0,
0.0,
5.7
]
],
"cell_parameters": {
"cell": [
[
5.7,
0.0,
0.0
],
[
0.0,
5.7,
0.0
],
[
0.0,
0.0,
5.7
]
],
"units": "angstrom"
},
"k_points": {
"type": "gamma"
},
"namelists": {
"CONTROL": {
"calculation": "scf"
},
"SYSTEM": {
"ibrav": 0
}
},
"positions_angstrom": [
[
0.0,
0.0,
0.0
]
]
}
3 changes: 3 additions & 0 deletions tests/test_parsers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -222,6 +222,9 @@ def test_lattice_ibrav0_cell_parameters_ang(self):
def test_lattice_ibrav0_cell_parameters_celldm(self):
self.singletest(label='lattice_ibrav0_cell_parameters_celldm')

def test_lattice_ibrav0_cell_parameters_int(self):
self.singletest(label='lattice_ibrav0_cell_parameters_int')

def test_lattice_ibrav1(self):
self.singletest(label='lattice_ibrav1')

Expand Down

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