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make number parsing more robust
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@eimrek
eimrek committed Oct 17, 2023
1 parent ee3f7d7 commit 7cc0725
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Showing 4 changed files with 311 additions and 72 deletions.
119 changes: 47 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 +14,23 @@
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 +386,20 @@ 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 +433,27 @@ 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 +538,21 @@ 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 +564,25 @@ 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
36 changes: 36 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 +1,36 @@
&control
outdir = './out_nacl'
prefix = 'nacl'
calculation = 'scf'
tprnfor = .true.
tstress = .true.
pseudo_dir = './pseudo/'
/
&system
ibrav = 0
nat = 8
ntyp = 2
ecutwfc = 70.0
/
&electrons
diagonalization = 'david'
conv_thr = 1.0d-9
/
ATOMIC_SPECIES
Na 22.98976928 Na.paw.z_9.ld1.psl.v1.0.0-low.upf
Cl 35.453 Cl.pbe-n-rrkjus_psl.1.0.0.UPF
ATOMIC_POSITIONS crystal
Na 0.0000000000000000 0.0000000000000000 0.0000000000000000
Na 0.0000000000000000 0.5000000000000000 0.5000000000000000
Na 0.5000000000000000 0.0000000000000000 0.5000000000000000
Na 0.5000000000000000 0.5000000000000000 0.0000000000000000
Cl 0.5000000000000000 0.5000000000000000 0.5000000000000000
Cl 0.5000000000000000 0.0000000000000000 0.0000000000000000
Cl 0.0000000000000000 0.5000000000000000 0.0000000000000000
Cl 0.0000000000000000 0.0000000000000000 0.5000000000000000
CELL_PARAMETERS angstrom
5.6903014761756712 0 0
0 5.6903014761756712 0
0 0 5.6903014761756712
K_POINTS automatic
8 8 8 1 1 1
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