✨ PwOutput: Parse k-points from stdout as fallback

src/qe_tools/outputs/parsers/pw.py

@@ -59,6 +59,21 @@ def parse(content):
 )
 _HOMO_RE = re.compile(r"highest occupied level\s*\(ev\):\s*([\-\d.E+]+)")
 _TOTAL_ENERGY_RE = re.compile(r"!\s+total energy\s*=\s*([\-\d.E+]+)\s*Ry")
+_ALAT_RE = re.compile(r"lattice parameter \(alat\)\s*=\s*([\-\d.E+]+)\s*a\.u\.")
+
+# Captures the `number of k points= N` line plus the following
+# `cart. coord. in units 2pi/alat` block of `k( i ) = ( x y z ), wk = w` lines.
+# `[^\n]*` after the count tolerates trailing variants (`(tetrahedron method)`,
+# `Marzari-Vanderbilt smearing, ...`, or nothing).
+_KPOINTS_BLOCK_RE = re.compile(
+    r"number of k points=\s*(?P<nks>\d+)[^\n]*\n"
+    r"\s*cart\. coord\. in units 2pi/alat\s*\n"
+    r"(?P<rows>(?:\s*k\(\s*\d+\s*\)\s*=\s*\(\s*[\-\d.E+]+\s+[\-\d.E+]+\s+[\-\d.E+]+\s*\),\s*wk\s*=\s*[\-\d.E+]+\s*\n)+)"
+)
+_KPOINT_ROW_RE = re.compile(
+    r"k\(\s*\d+\s*\)\s*=\s*\(\s*([\-\d.E+]+)\s+([\-\d.E+]+)\s+([\-\d.E+]+)\s*\),"
+    r"\s*wk\s*=\s*([\-\d.E+]+)"
+)
 
 
 class PwStdoutParser(BaseStdoutParser):
@@ -85,4 +100,27 @@ def parse(content: str) -> dict:
         if energy_matches:
             parsed_data["total_energy"] = float(energy_matches[-1])
 
+        # k-points: take the last block, since vc-relax reprints after relaxation.
+        # The stdout values are in 2pi/alat; convert to 1/Å using `alat` (also from
+        # stdout, in bohr) so downstream Specs match the XML-derived units.
+        kpoint_blocks = list(_KPOINTS_BLOCK_RE.finditer(content))
+        alat_match = _ALAT_RE.search(content)
+        if kpoint_blocks and alat_match:
+            import math
+
+            from qe_tools import CONSTANTS
+
+            alat_ang = float(alat_match.group(1)) * CONSTANTS.bohr_to_ang
+            scale = 2 * math.pi / alat_ang
+            block = kpoint_blocks[-1]
+            cartesian = []
+            weights = []
+            for row in _KPOINT_ROW_RE.finditer(block.group("rows")):
+                kx, ky, kz, wk = (float(v) for v in row.groups())
+                cartesian.append([kx * scale, ky * scale, kz * scale])
+                weights.append(wk)
+            parsed_data["number_of_k_points"] = int(block.group("nks"))
+            parsed_data["k_points_cartesian"] = cartesian
+            parsed_data["k_points_weights"] = weights
+
         return parsed_data

src/qe_tools/outputs/pw.py

@@ -272,15 +272,26 @@ class _PwMapping:
     Only available when ``tot_magnetization`` is set in ``SYSTEM``.
     """
 
-    number_of_k_points: Annotated[int, Spec("xml.output.band_structure.nks")]
+    number_of_k_points: Annotated[
+        int,
+        Spec(
+            Coalesce(
+                "xml.output.band_structure.nks",
+                "stdout.number_of_k_points",
+            )
+        ),
+    ]
     """Number of k-points at which the Kohn-Sham states were computed."""
 
     k_points_weights: Annotated[
         list,
         Spec(
-            (
-                "xml.output.band_structure.ks_energies",
-                [lambda ks: ks["k_point"]["@weight"]],
+            Coalesce(
+                (
+                    "xml.output.band_structure.ks_energies",
+                    [lambda ks: ks["k_point"]["@weight"]],
+                ),
+                "stdout.k_points_weights",
             )
         ),
     ]
@@ -292,18 +303,24 @@ class _PwMapping:
     k_points_cartesian: Annotated[
         list,
         Spec(
-            (
-                "xml.output",
-                lambda output: [
-                    [
-                        kp
-                        * 2
-                        * math.pi
-                        / (output["atomic_structure"]["@alat"] * CONSTANTS.bohr_to_ang)
-                        for kp in ks["k_point"]["$"]
-                    ]
-                    for ks in output["band_structure"]["ks_energies"]
-                ],
+            Coalesce(
+                (
+                    "xml.output",
+                    lambda output: [
+                        [
+                            kp
+                            * 2
+                            * math.pi
+                            / (
+                                output["atomic_structure"]["@alat"]
+                                * CONSTANTS.bohr_to_ang
+                            )
+                            for kp in ks["k_point"]["$"]
+                        ]
+                        for ks in output["band_structure"]["ks_energies"]
+                    ],
+                ),
+                "stdout.k_points_cartesian",
             )
         ),
         Unit("1/angstrom"),

tests/outputs/fixtures/pw/default_xml_220603/pw.out

@@ -86,7 +86,12 @@
 
 --- SYMMETRIES REMOVED ---
 
---- K-POINTS REMOVED ---
+     number of k points=     4  Marzari-Vanderbilt smearing, width (Ry)=  0.0100
+                       cart. coord. in units 2pi/alat
+        k(    1) = (   0.0000000   0.0000000   0.0000000), wk =   0.2500000
+        k(    2) = (   0.0000000   0.0000000  -0.6123724), wk =   0.2500000
+        k(    3) = (   0.0000000  -0.5773503   0.2041241), wk =   0.7500000
+        k(    4) = (   0.0000000  -0.5773503  -0.4082483), wk =   0.7500000
 
 --- MEMORY INFO REMOVED ---
 

tests/outputs/fixtures/pw/default_xml_250521/pw.out

@@ -95,6 +95,11 @@
      F                 7.00    18.99840     F ( 1.00)
      Li                3.00     6.94100     Li( 1.00)
 
+     number of k points=     2  Marzari-Vanderbilt smearing, width (Ry)=  0.0100
+                       cart. coord. in units 2pi/alat
+        k(    1) = (   0.0000000   0.0000000   0.0000000), wk =   1.0000000
+        k(    2) = (  -0.5000000   0.0000000   0.0000000), wk =   1.0000000
+
      Dense  grid:    50733 G-vectors     FFT dimensions: (  45,  45,  45)
 
      Smooth grid:    17941 G-vectors     FFT dimensions: (  36,  36,  36)

tests/outputs/test_pw_output.py

@@ -1,5 +1,6 @@
 from pathlib import Path
 
+import numpy as np
 import pytest
 
 from qe_tools.outputs.pw import PwOutput
@@ -99,6 +100,44 @@ def test_total_energy_nscf_clobber():
     )
 
 
+def test_k_points_stdout_xml_agree():
+    """Stdout-derived k-points agree with the XML values within stdout's printed precision.
+
+    QE prints k-points in `cart. coord. in units 2pi/alat` to 7 digits and `alat` to
+    5 digits, so cartesian coordinates in 1/Å can only match the XML at ~1e-3.
+    """
+    pw_directory = Path(__file__).parent / "fixtures" / "pw" / "default_xml_211101"
+
+    pw_out = PwOutput.from_dir(pw_directory)
+
+    assert pw_out.get_output("k_points_weights") == pytest.approx(
+        pw_out.raw_outputs["stdout"]["k_points_weights"]
+    )
+    np.testing.assert_allclose(
+        pw_out.get_output("k_points_cartesian"),
+        pw_out.raw_outputs["stdout"]["k_points_cartesian"],
+        atol=1e-3,
+    )
+
+
+def test_k_points_stdout_fallback_without_xml():
+    """`PwOutput.from_files(stdout=...)` exposes k-point outputs via the stdout fallback."""
+    stdout_file = (
+        Path(__file__).parent / "fixtures" / "pw" / "default_xml_211101" / "pw.out"
+    )
+
+    pw_out = PwOutput.from_files(stdout=stdout_file)
+
+    assert "xml" not in pw_out.raw_outputs
+    assert pw_out.get_output("number_of_k_points") == 2
+    assert len(pw_out.get_output("k_points_weights")) == pw_out.get_output(
+        "number_of_k_points"
+    )
+    assert len(pw_out.get_output("k_points_cartesian")) == pw_out.get_output(
+        "number_of_k_points"
+    )
+
+
 def test_insulator_homo(robust_data_regression_check):
     """Test stdout-derived `highest_occupied_level` from an insulator SCF."""
 

tests/outputs/test_pw_output/test_default_xml_211101_.yml

@@ -101,6 +101,17 @@ base_outputs:
 raw_outputs:
   stdout:
     code_version: '7.0'
+    k_points_cartesian:
+    - - 0.0
+      - 0.0
+      - 0.0
+    - - 0.8124187117851777
+      - 0.4690501057329147
+      - 0.33166847673261757
+    k_points_weights:
+    - 1.0
+    - 1.0
+    number_of_k_points: 2
     total_energy: -22.13271119
     volume_bohr3: 275.9279
     wall_time_seconds: 1.96

tests/outputs/test_pw_output/test_default_xml_220603_.yml

@@ -117,6 +117,25 @@ base_outputs:
 raw_outputs:
   stdout:
     code_version: '7.1'
+    k_points_cartesian:
+    - - 0.0
+      - 0.0
+      - 0.0
+    - - 0.0
+      - 0.0
+      - -0.9950055926815952
+    - - 0.0
+      - -0.9381003739495717
+      - 0.33166847673261757
+    - - 0.0
+      - -0.9381003739495717
+      - -0.6633371159489775
+    k_points_weights:
+    - 0.25
+    - 0.25
+    - 0.75
+    - 0.75
+    number_of_k_points: 4
     total_energy: -22.65373597
     volume_bohr3: 275.9279
     wall_time_seconds: 2.02

tests/outputs/test_pw_output/test_default_xml_230310_.yml

@@ -169,6 +169,61 @@ raw_outputs:
   stdout:
     code_version: '7.2'
     highest_occupied_level: 9.0922
+    k_points_cartesian:
+    - - 0.0
+      - 0.0
+      - 0.0
+    - - -0.5577988981584857
+      - -0.3220453424463573
+      - 0.11177181862660332
+    - - 1.1155977963169714
+      - 0.6440906848927146
+      - -0.22354363725320664
+    - - -0.5577988981584857
+      - 0.3220453424463573
+      - 0.22354363725320664
+    - - 1.1155977963169714
+      - 1.2881813697854292
+      - -0.11177181862660332
+    - - 0.5577988981584857
+      - 0.9661360273390719
+      - 0.0
+    - - 1.1155977963169714
+      - -0.6440906848927146
+      - -0.44708714779493075
+    - - 0.0
+      - 0.0
+      - 0.33531545587981
+    - - 1.673396694475457
+      - 0.9661360273390719
+      - 0.0
+    - - 1.1155977963169714
+      - 0.6440906848927146
+      - 0.11177181862660332
+    - - 1.673396694475457
+      - -0.9661360273390719
+      - -0.33531545587981
+    - - 1.1155977963169714
+      - -1.2881813697854292
+      - -0.22354363725320664
+    - - 0.0
+      - 0.0
+      - -0.6706307850481373
+    k_points_weights:
+    - 0.03125
+    - 0.1875
+    - 0.09375
+    - 0.1875
+    - 0.375
+    - 0.1875
+    - 0.09375
+    - 0.0625
+    - 0.1875
+    - 0.1875
+    - 0.1875
+    - 0.1875
+    - 0.03125
+    number_of_k_points: 13
     total_energy: -396.09758618
     volume_bohr3: 217.1091
     wall_time_seconds: 100.44

tests/outputs/test_pw_output/test_default_xml_240411_.yml

@@ -153,6 +153,61 @@ base_outputs:
 raw_outputs:
   stdout:
     code_version: 7.3.1
+    k_points_cartesian:
+    - - 0.0
+      - 0.0
+      - 0.0
+    - - -0.0
+      - -0.0
+      - 0.49963377062181
+    - - 0.0
+      - 0.0
+      - -0.9992677037273625
+    - - -0.0
+      - 0.47105921720715943
+      - -0.16654453604602257
+    - - -0.0
+      - 0.47105921720715943
+      - 0.3330892345757875
+    - - 0.0
+      - 0.47105921720715943
+      - -1.165812239773385
+    - - 0.0
+      - 0.47105921720715943
+      - -0.666178469151575
+    - - 0.0
+      - -0.9421184344143189
+      - 0.3330892345757875
+    - - 0.0
+      - -0.9421184344143189
+      - 0.8327230051975975
+    - - 0.0
+      - -0.9421184344143189
+      - -0.666178469151575
+    - - 0.40794923180574794
+      - -1.1776480430178984
+      - 0.16654453604602257
+    - - 0.40794923180574794
+      - -1.1776480430178984
+      - 0.666178469151575
+    - - 0.40794923180574794
+      - -1.1776480430178984
+      - -0.3330892345757875
+    k_points_weights:
+    - 0.03125
+    - 0.0625
+    - 0.03125
+    - 0.1875
+    - 0.1875
+    - 0.1875
+    - 0.1875
+    - 0.09375
+    - 0.1875
+    - 0.09375
+    - 0.375
+    - 0.1875
+    - 0.1875
+    number_of_k_points: 13
     total_energy: -22.66279398
     volume_bohr3: 272.4124
     wall_time_seconds: 2.51

tests/outputs/test_pw_output/test_default_xml_250521_.yml

@@ -152,6 +152,17 @@ base_outputs:
 raw_outputs:
   stdout:
     code_version: '7.5'
+    k_points_cartesian:
+    - - 0.0
+      - 0.0
+      - 0.0
+    - - -0.7795511497938687
+      - 0.0
+      - 0.0
+    k_points_weights:
+    - 1.0
+    - 1.0
+    number_of_k_points: 2
     total_energy: -252.68718165
     volume_bohr3: 441.6841
     wall_time_seconds: 2.33