Skip to content

Commit

Permalink
Merge pull request #19 from aiidateam/release-1.1.2
Browse files Browse the repository at this point in the history 
Release 1.1.2
  • Loading branch information
@giovannipizzi
giovannipizzi committed Nov 21, 2018
2 parents 4ef986c + c053cb5 commit 0a5306a
Show file tree
Hide file tree
Showing 7 changed files with 255 additions and 6 deletions.
2 changes: 1 addition & 1 deletion qe_tools/__init__.py
View file
@@ -1,3 +1,3 @@
from .parsers import PwInputFile, CpInputFile

__version__ = "1.1.1"
__version__ = "1.1.2"
74 changes: 70 additions & 4 deletions qe_tools/parsers/qeinputparser.py
View file
Expand Up @@ -339,8 +339,8 @@ def str2val(valstr):
try:
val = conversion_fn(valstr)
except ValueError as error:
print('Error converting {} to a value'.format(repr(valstr)))
raise error
raise ValueError('Error converting {} to a value'.format(
repr(valstr)))
if val is None:
raise ValueError('Unable to convert {} to a python variable.\n'
'NOTE: Support for algebraic expressions is not yet '
Expand Down Expand Up @@ -403,8 +403,22 @@ def parse_namelists(txt):
for nmlst, blockstr in namelist_re.findall(txt):
# ...extract the key value pairs, storing them each in nmlst_dict,...
nmlst_dict = {}
for key, valstr in key_value_re.findall(blockstr):
nmlst_dict[key.lower()] = str2val(valstr)
# I split the lines, putting back a \n at the end (I want
# to have it otherwise lines not ending with a comma are ignored)
blocklines = blockstr.splitlines()
# Remove comments on each line, and then put back the \n
# Note that strip_comment does not want \n in the string!
blocklines = [
"{}\n".format(strip_comment(line)) for line in blocklines
]

for blockline in blocklines:
for key, valstr in key_value_re.findall(blockline):
if key.lower() in nmlst_dict:
raise ValueError(
"Key {} found more than once in namelist {}".format(
key.lower(), nmlst))
nmlst_dict[key.lower()] = str2val(valstr)
# ...and, store nmlst_dict as a value in params_dict with the namelist
# as the key.
if len(nmlst_dict.keys()) > 0:
Expand Down Expand Up @@ -1185,3 +1199,55 @@ def get_structure_from_qeinput(filepath=None,
species=atomic_species,
cell=cell.tolist(),
atom_names=atomic_positions['names'])


def strip_comment(string,
comment_characters=('!', ),
quote_characters=('"', "'")):
"""
Return the string only until the first comment (if any), but makes
sure to ignore comments if inside a string
Note: it expects to get a SINGLE line, without newline characters
Note: it does not cope with escaping of quotes
:param string: the string to check
:param comment_characters: a list or tuple of accepted comment characters
:param quote_characters: a list or tuple of accepted valid string characters
"""
new_string = [] # Will contain individual charachters of the new string

in_string = False
string_quote = None # Will contain the specific character used to enter
# this string: this avoids that 'aaa" is considered as
# the string containing the three characters aaa

for char in string:
if char == '\n':
raise ValueError(
"I still cannot cope with newlines in the string...")
# Check if we are entering/existing a string
if in_string and char == string_quote:
#print("EXIT")
in_string = False
string_quote = None
elif not in_string and char in quote_characters:
#print("ENTER")
in_string = True
string_quote = char
#print(char, in_string, string_quote)

# We found a comment, return until here (without the comment)
if not in_string and char in comment_characters:
return "".join(new_string)

new_string.append(char)

# If we are here, no comments where found
if in_string:
raise ValueError(
"String >>{}<< is not closed, it was open with the {} char".format(
string, string_quote))
# I just return the same string, even if this would be equivalent to "".join(new_string)
return string
2 changes: 1 addition & 1 deletion setup.json
View file
Expand Up @@ -32,5 +32,5 @@
"license": "MIT License",
"name": "qe-tools",
"url": "https://github.com/aiidateam/qe-tools",
"version": "1.1.1"
"version": "1.1.2"
}
29 changes: 29 additions & 0 deletions tests/data/example_comment_in_namelist.in
View file
@@ -0,0 +1,29 @@
&control
pseudo_dir = 'pseudo/'
calculation = 'scf',
prefix = 'Si_exc1',
/
&system
ibrav = 0
! ibrav = -3,
celldm(1) = 20.385647759,
nat = 1,
ntyp = 1,
ecutwfc = 30
/
&electrons
/

ATOMIC_SPECIES
Si 28.086 Si.pbe-n-rrkjus_psl.1.0.0.UPF

ATOMIC_POSITIONS {bohr}
Si 0. 0. 0.

CELL_PARAMETERS {alat}
-1.0 1.0 1.0
1.0 -1.0 1.0
1.0 1.0 -1.0

K_POINTS {automatic}
6 6 6 1 1 1
38 changes: 38 additions & 0 deletions tests/data/example_ibrav0_error_multiplekeys.in
View file
@@ -0,0 +1,38 @@
&CONTROL
calculation = 'scf'
outdir = './out/'
prefix = 'aiida'
pseudo_dir = './pseudo/'
restart_mode = 'from_scratch'
tprnfor = .true.
tstress = .true.
tstress = .true.
verbosity = 'high'
wf_collect = .true.
/
&SYSTEM
ecutrho = 3.2000000000d+02
ecutwfc = 4.0000000000d+01
ibrav = 0
nat = 5
ntyp = 3
/
&ELECTRONS
conv_thr = 1.0000000000d-10
/
ATOMIC_SPECIES
Ba 137.327 Ba.pbesol-spn-rrkjus_psl.0.2.3-tot-pslib030.UPF
O 15.9994 O.pbesol-n-rrkjus_psl.0.1-tested-pslib030.UPF
Ti 47.867 Ti.pbesol-spn-rrkjus_psl.0.2.3-tot-pslib030.UPF
ATOMIC_POSITIONS angstrom
Ba 0.0000000000 0.0000000000 0.0000000000
Ti 2.0000000000 2.0000000000 2.0000000000
O 2.0000000000 2.0000000000 0.0000000000
O 2.0000000000 0.0000000000 2.0000000000
O 0.0000000000 2.0000000000 2.0000000000
K_POINTS automatic
2 2 2 0 0 0
CELL_PARAMETERS angstrom
4.0000000000 0.0000000000 0.0000000000
0.0000000000 4.0000000000 0.0000000000
0.0000000000 0.0000000000 4.0000000000
104 changes: 104 additions & 0 deletions tests/data/ref/example_comment_in_namelist.json
View file
@@ -0,0 +1,104 @@
{
"atomic_positions": {
"fixed_coords": [
[
false,
false,
false
]
],
"names": [
"Si"
],
"positions": [
[
0.0,
0.0,
0.0
]
],
"units": "bohr"
},
"atomic_species": {
"masses": [
28.086
],
"names": [
"Si"
],
"pseudo_file_names": [
"Si.pbe-n-rrkjus_psl.1.0.0.UPF"
]
},
"cell": [
[
-10.787620176406609,
10.787620176406609,
10.787620176406609
],
[
10.787620176406609,
-10.787620176406609,
10.787620176406609
],
[
10.787620176406609,
10.787620176406609,
-10.787620176406609
]
],
"cell_parameters": {
"cell": [
[
-1.0,
1.0,
1.0
],
[
1.0,
-1.0,
1.0
],
[
1.0,
1.0,
-1.0
]
],
"units": "alat"
},
"k_points": {
"offset": [
0.5,
0.5,
0.5
],
"points": [
6,
6,
6
],
"type": "automatic"
},
"namelists": {
"CONTROL": {
"calculation": "scf",
"prefix": "Si_exc1",
"pseudo_dir": "pseudo/"
},
"SYSTEM": {
"celldm(1)": 20.385647759,
"ecutwfc": 30,
"ibrav": 0,
"nat": 1,
"ntyp": 1
}
},
"positions_angstrom": [
[
0.0,
0.0,
0.0
]
]
}
12 changes: 12 additions & 0 deletions tests/test_parsers.py
View file
Expand Up @@ -197,9 +197,21 @@ def singletest(self, label, parser='pw'):
############################################################################
## Here start the tests
############################################################################
def test_example_comment_in_namelist(self):
self.singletest(label='example_comment_in_namelist')

def test_example_ibrav0(self):
self.singletest(label='example_ibrav0')

def test_example_ibrav0_error_multiplekeys(self):
# It should raise because there is twice the same key in a namelist
with self.assertRaises(ValueError) as exception_obj:
self.singletest(label='example_ibrav0_error_multiplekeys')

# It should complain about 'tstress' being found multiple times
the_exception = exception_obj.exception
self.assertIn("tstress", str(the_exception))

def test_example_ibrav0_uppercaseunits(self):
self.singletest(label='example_ibrav0_uppercaseunits')

Expand Down

0 comments on commit 0a5306a

Please sign in to comment.