From 5df8e62253709c8d0410d3c1b06f17ed1820f4d4 Mon Sep 17 00:00:00 2001
From: Pranab Das <31024886+pranabdas@users.noreply.github.com>
Date: Sat, 23 May 2026 15:50:08 +0800
Subject: [PATCH 01/19] SOF-7915: refactor espresso structure parser to use
 pymatgen

ASE parser is limited to ibrav==0, requires intermediate POSCAR generation.
---
 express/parsers/structure.py | 55 +++++++++---------------------------
 pyproject.toml               |  8 +++---
 2 files changed, 17 insertions(+), 46 deletions(-)

diff --git a/express/parsers/structure.py b/express/parsers/structure.py
index b1b6c3e6..dfcda6d8 100644
--- a/express/parsers/structure.py
+++ b/express/parsers/structure.py
@@ -1,9 +1,8 @@
-import io
 import json
 
 import pymatgen as mg
 from pymatgen.core.structure import Structure
-from ase.io import read, write
+from pymatgen.io.pwscf import PWInput
 from jarvis.core.atoms import Atoms
 from jarvis.io.vasp.inputs import Poscar
 
@@ -38,22 +37,16 @@ def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self.structure_string = kwargs.get("structure_string")
         self.structure_format = kwargs.get("structure_format")
+        self.cell_type = kwargs.get("cell_type", "original")  # original, primitive or conventional
 
-        # convert espresso input into poscar
+        # convert espresso input into pymatgen.core.structure
         if self.structure_format == "espresso-in":
-            self.structure_format = "poscar"
-            self.structure_string = self.espresso_input_to_poscar(self.structure_string)
-
+            self.structure = PWInput.from_str(self.structure_string).structure
         # convert jarvis-db-entry JSON into poscar
-        if self.structure_format == "jarvis-db-entry":
-            self.structure_format = "poscar"
+        elif self.structure_format == "jarvis-db-entry":
             self.structure_string = self.jarvis_db_entry_json_to_poscar(self.structure_string)
-
-        # cell_type is either original, primitive or conventional
-        self.cell_type = kwargs.get("cell_type", "original")
-
-        # Initialize structure class
-        if self.structure_format == "pymatgen.core.structure":
+            self.structure = Structure.from_str(self.structure_string, "poscar")
+        elif self.structure_format == "pymatgen.core.structure":
             structure_as_dict = json.loads(self.structure_string)
             self.structure = Structure.from_dict(structure_as_dict)
         else:
@@ -63,7 +56,7 @@ def __init__(self, *args, **kwargs):
             self.structure = STRUCTURE_MAP[self.cell_type](self.structure)
 
         # keep only one atom inside the basis in order to have the original lattice type
-        self.lattice_only_structure = self.structure.copy() # deepcopy
+        self.lattice_only_structure = self.structure.copy()  # deepcopy
         self.lattice_only_structure.remove_sites(range(1, len(self.structure.sites)))
 
     def lattice_vectors(self):
@@ -178,16 +171,15 @@ def basis(self):
         for i, site in enumerate(self.structure.sites):
             if not site.is_ordered:
                 raise ValueError(
-                   f"Disordered site at {site.frac_coords.tolist()} with "
-                   f"occupancy {site.species} is not supported."
+                    f"Disordered site at {site.frac_coords.tolist()} with "
+                    f"occupancy {site.species} is not supported."
                 )
 
             # Use specie.symbol to strip oxidation state (e.g. "Li0+" → "Li", "O2-" → "O")
             elements.append({"id": i, "value": site.specie.symbol})
-            coordinates.append({
-                "id": i,
-                "value": self._round(site.frac_coords.tolist(), PRECISION_MAP["coordinates_crystal"])
-            })
+            coordinates.append(
+                {"id": i, "value": self._round(site.frac_coords.tolist(), PRECISION_MAP["coordinates_crystal"])}
+            )
         return {"units": "crystal", "elements": elements, "coordinates": coordinates}
 
     def space_group_symbol(self):
@@ -240,27 +232,6 @@ def atomic_constraints(self):
         """
         return self.structure.site_properties.get("selective_dynamics")
 
-    def espresso_input_to_poscar(self, espresso_input):
-        """
-        Extracts structure from espresso input file and returns in poscar format.
-
-        Args:
-            espresso_input (str): input file content
-
-        Returns:
-            str: poscar
-        """
-        input_ = io.StringIO()
-        input_.write(espresso_input)
-        input_.seek(0)
-        atoms = read(input_, format="espresso-in")
-        output_ = io.StringIO()
-        write(output_, atoms, format="vasp", vasp5=True)
-        content = output_.getvalue()
-        input_.close()
-        output_.close()
-        return content
-
     def jarvis_db_entry_json_to_poscar(self, jarvis_db_entry_json_str):
         """
         Extracts structure from jarvis atoms dictionary and returns in poscar format.
diff --git a/pyproject.toml b/pyproject.toml
index cd333d3b..c1893fd2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,10 +15,10 @@ classifiers = [
     "Topic :: Software Development",
 ]
 dependencies = [
-    "pymatgen>=2023.8.10",
-    "ase>=3.17.0",
-    "mat3ra-esse>=2026.3.25.post0",
-    "jarvis-tools>=2023.12.12",
+    "pymatgen>=2025.10.7",
+    "ase>=3.28.0",
+    "mat3ra-esse>=2026.5.18.post3",
+    "jarvis-tools>=2026.4.2",
     # To avoid module 'numpy.linalg._umath_linalg' has no attribute '_ilp64' in Colab
     "numpy>=1.24.4,<2",
 ]

From 9829d63f49183fdc0a5b4a2a1d4f9c1ddc8c9e85 Mon Sep 17 00:00:00 2001
From: Pranab Das <31024886+pranabdas@users.noreply.github.com>
Date: Sat, 23 May 2026 16:27:27 +0800
Subject: [PATCH 02/19] use qe-tools to parse structure from espresso-in

---
 express/parsers/structure.py | 10 ++++++++--
 pyproject.toml               |  5 +++--
 2 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/express/parsers/structure.py b/express/parsers/structure.py
index dfcda6d8..e42b6539 100644
--- a/express/parsers/structure.py
+++ b/express/parsers/structure.py
@@ -2,7 +2,7 @@
 
 import pymatgen as mg
 from pymatgen.core.structure import Structure
-from pymatgen.io.pwscf import PWInput
+from qe_tools.parsers import PwInputFile
 from jarvis.core.atoms import Atoms
 from jarvis.io.vasp.inputs import Poscar
 
@@ -41,7 +41,13 @@ def __init__(self, *args, **kwargs):
 
         # convert espresso input into pymatgen.core.structure
         if self.structure_format == "espresso-in":
-            self.structure = PWInput.from_str(self.structure_string).structure
+            parsed = PwInputFile(self.structure_string)
+            self.structure = Structure(
+                lattice=parsed.structure["cell"],
+                species=parsed.structure["atom_names"],
+                coords=parsed.structure["positions"],
+                coords_are_cartesian=True,
+            )
         # convert jarvis-db-entry JSON into poscar
         elif self.structure_format == "jarvis-db-entry":
             self.structure_string = self.jarvis_db_entry_json_to_poscar(self.structure_string)
diff --git a/pyproject.toml b/pyproject.toml
index c1893fd2..b97682c4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,12 +15,13 @@ classifiers = [
     "Topic :: Software Development",
 ]
 dependencies = [
-    "pymatgen>=2025.10.7",
     "ase>=3.28.0",
-    "mat3ra-esse>=2026.5.18.post3",
     "jarvis-tools>=2026.4.2",
+    "mat3ra-esse>=2026.5.18.post3",
     # To avoid module 'numpy.linalg._umath_linalg' has no attribute '_ilp64' in Colab
     "numpy>=1.24.4,<2",
+    "pymatgen>=2025.10.7",
+    "qe-tools==2.3.0",
 ]
 
 [project.optional-dependencies]

From 1a1177d139108098379dd6d0ded55c01d8e7b5db Mon Sep 17 00:00:00 2001
From: Pranab Das <31024886+pranabdas@users.noreply.github.com>
Date: Sat, 23 May 2026 17:29:22 +0800
Subject: [PATCH 03/19] add tests for espresso-in parser

---
 tests/.gitattributes                          |  1 +
 tests/fixtures/structural/references.py       | 22 ++++++
 .../structural/test-005/pw_si_ibrav0.in       |  3 +
 .../structural/test-005/pw_si_ibrav2.in       |  3 +
 tests/unit/parsers/test_structure_parser.py   | 70 ++++++++++++++++++-
 5 files changed, 96 insertions(+), 3 deletions(-)
 create mode 100644 tests/fixtures/structural/test-005/pw_si_ibrav0.in
 create mode 100644 tests/fixtures/structural/test-005/pw_si_ibrav2.in

diff --git a/tests/.gitattributes b/tests/.gitattributes
index 816d8cd1..9dc05008 100644
--- a/tests/.gitattributes
+++ b/tests/.gitattributes
@@ -5,3 +5,4 @@ fixtures/vasp/** filter=lfs diff=lfs merge=lfs -text
 fixtures/data.py filter=lfs diff=lfs merge=lfs -text
 fixtures/pyML/test-001/*.JSON filter=lfs diff=lfs merge=lfs -text
 *.cif filter=lfs diff=lfs merge=lfs -text
+fixtures/structural/test-005/*.in filter=lfs diff=lfs merge=lfs -text
diff --git a/tests/fixtures/structural/references.py b/tests/fixtures/structural/references.py
index d49591bc..6d502f7b 100644
--- a/tests/fixtures/structural/references.py
+++ b/tests/fixtures/structural/references.py
@@ -29,3 +29,25 @@
         {"id": 8, "value": [0.333333330, 0.666666670, 0.666666670]},
     ],
 }
+
+# ibrav=0 silicon with explicit CELL_PARAMETERS
+SI_IBRAV0_BASIS = {
+    "units": "crystal",
+    "elements": [{"id": 0, "value": "Si"}, {"id": 1, "value": "Si"}],
+    "coordinates": [
+        {"id": 0, "value": [0.0, 0.0, 0.0]},
+        {"id": 1, "value": [0.25, 0.25, 0.25]},
+    ],
+}
+
+# ibrav=2 with FCC lattice, qe-tools produces symmetry equivalent but non-identical basis
+SI_IBRAV2_BASIS = {
+    "units": "crystal",
+    "elements": [{"id": 0, "value": "Si"}, {"id": 1, "value": "Si"}],
+    "coordinates": [
+        {"id": 0, "value": [0.0, 0.0, 0.0]},
+        {"id": 1, "value": [-0.25, 0.75, -0.25]},
+    ],
+}
+
+SI_PRIMITIVE_LATTICE_A = 3.867  # Angstrom
diff --git a/tests/fixtures/structural/test-005/pw_si_ibrav0.in b/tests/fixtures/structural/test-005/pw_si_ibrav0.in
new file mode 100644
index 00000000..6598c17f
--- /dev/null
+++ b/tests/fixtures/structural/test-005/pw_si_ibrav0.in
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:4e67b5144b55e13e136098191e0c30ccb660f9436dd688dc276f8ceaf829622f
+size 628
diff --git a/tests/fixtures/structural/test-005/pw_si_ibrav2.in b/tests/fixtures/structural/test-005/pw_si_ibrav2.in
new file mode 100644
index 00000000..f33c51cf
--- /dev/null
+++ b/tests/fixtures/structural/test-005/pw_si_ibrav2.in
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d4448b4dd80296a2dda8fe82ed2aa54e12c785d7c0047f1dc2b8632bb05c4605
+size 590
diff --git a/tests/unit/parsers/test_structure_parser.py b/tests/unit/parsers/test_structure_parser.py
index e77631ad..0a37781b 100644
--- a/tests/unit/parsers/test_structure_parser.py
+++ b/tests/unit/parsers/test_structure_parser.py
@@ -1,7 +1,7 @@
 import os
 
 from tests.unit import UnitTestBase
-from tests.fixtures.structural.references import LI_CIF_BASIS
+from tests.fixtures.structural.references import LI_CIF_BASIS, SI_IBRAV0_BASIS, SI_IBRAV2_BASIS, SI_PRIMITIVE_LATTICE_A
 from express.parsers.structure import StructureParser
 
 LI_CIF_PATH = os.path.join(os.path.dirname(__file__), "..", "..", "fixtures", "structural", "test-004", "Li.cif")
@@ -10,6 +10,14 @@
     os.path.dirname(__file__), "..", "..", "fixtures", "structural", "test-004", "SrLaCoO4.cif"
 )
 
+SI_IBRAV0_PATH = os.path.join(
+    os.path.dirname(__file__), "..", "..", "fixtures", "structural", "test-005", "pw_si_ibrav0.in"
+)
+
+SI_IBRAV2_PATH = os.path.join(
+    os.path.dirname(__file__), "..", "..", "fixtures", "structural", "test-005", "pw_si_ibrav2.in"
+)
+
 
 def _read_file(path):
     with open(path) as f:
@@ -46,12 +54,12 @@ class DisorderedStructureParserTest(UnitTestBase):
     when basis() is called on a structure with disordered (mixed-occupancy) sites.
 
     The SrLaCoO4 CIF has Sr2+ and La3+ sharing the same Wyckoff 4e site
-    with occupancy 0.5 each — a canonical disordered case.
+    with occupancy 0.5 each, a disordered case.
     """
 
     def setUp(self):
         super().setUp()
-        # Parsing itself succeeds — pymatgen can load disordered structures.
+        # Parsing itself succeeds as pymatgen can load disordered structures.
         # The error is raised lazily when basis() is called.
         self.parser = StructureParser(
             structure_string=_read_file(DISORDERED_CIF_PATH),
@@ -72,3 +80,59 @@ def test_basis_raises_for_disordered_site(self):
         self.assertIn("is not supported", error)
         self.assertIn("occupancy", error)
         self.assertIn("0.361", error)
+
+
+class EspressoInIbrav0StructureParserTest(UnitTestBase):
+    """Tests that StructureParser correctly parses espresso-in files with ibrav=0
+    and explicit CELL_PARAMETERS.
+    The primitive lattice constant is 3.867 Angstrom."""
+
+    def setUp(self):
+        super().setUp()
+        self.parser = StructureParser(
+            structure_string=_read_file(SI_IBRAV0_PATH),
+            structure_format="espresso-in",
+        )
+
+    def tearDown(self):
+        super().tearDown()
+
+    def test_basis(self):
+        self.assertDeepAlmostEqual(self.parser.basis(), SI_IBRAV0_BASIS, places=5)
+
+    def test_formula(self):
+        self.assertEqual(self.parser.formula(), "Si2")
+
+    def test_lattice_bravais_type(self):
+        self.assertEqual(self.parser.lattice_bravais()["type"], "FCC")
+
+    def test_lattice_parameter_a(self):
+        self.assertAlmostEqual(self.parser.lattice_bravais()["a"], SI_PRIMITIVE_LATTICE_A, places=3)
+
+
+class EspressoInIbrav2StructureParserTest(UnitTestBase):
+    """Tests that StructureParser correctly parses espresso-in files with ibrav=2
+    (FCC) defined via celldm(1), without explicit CELL_PARAMETERS.
+    The primitive lattice constant is 3.867 Angstrom."""
+
+    def setUp(self):
+        super().setUp()
+        self.parser = StructureParser(
+            structure_string=_read_file(SI_IBRAV2_PATH),
+            structure_format="espresso-in",
+        )
+
+    def tearDown(self):
+        super().tearDown()
+
+    def test_basis(self):
+        self.assertDeepAlmostEqual(self.parser.basis(), SI_IBRAV2_BASIS, places=5)
+
+    def test_formula(self):
+        self.assertEqual(self.parser.formula(), "Si2")
+
+    def test_lattice_bravais_type(self):
+        self.assertEqual(self.parser.lattice_bravais()["type"], "FCC")
+
+    def test_lattice_parameter_a(self):
+        self.assertAlmostEqual(self.parser.lattice_bravais()["a"], SI_PRIMITIVE_LATTICE_A, places=3)

From 9bac1b54daf282c2a8269c4e08a320660ab69cf9 Mon Sep 17 00:00:00 2001
From: Pranab Das <31024886+pranabdas@users.noreply.github.com>
Date: Thu, 28 May 2026 21:13:55 +0800
Subject: [PATCH 04/19] implement qe pw input parser using made

---
 .../parsers/apps/espresso/pw_input_file.py    | 166 ++++++++++++++++++
 express/parsers/structure.py                  |   2 +-
 pyproject.toml                                |   5 +-
 tests/fixtures/structural/references.py       |  13 +-
 tests/unit/parsers/test_structure_parser.py   |   6 +-
 5 files changed, 172 insertions(+), 20 deletions(-)
 create mode 100644 express/parsers/apps/espresso/pw_input_file.py

diff --git a/express/parsers/apps/espresso/pw_input_file.py b/express/parsers/apps/espresso/pw_input_file.py
new file mode 100644
index 00000000..f106aa85
--- /dev/null
+++ b/express/parsers/apps/espresso/pw_input_file.py
@@ -0,0 +1,166 @@
+import math
+import re
+from typing import List, Optional, Tuple
+
+from mat3ra.esse.models.properties_directory.structural.lattice import LatticeSchema
+from mat3ra.made.cell.primitive_cell import get_primitive_lattice_vectors_from_config
+
+BOHR_TO_ANGSTROM = 0.529177210903
+
+# Maps QE ibrav codes → made/esse Bravais type strings
+IBRAV_TO_LATTICE_TYPE = {
+    1:  "CUB",
+    2:  "FCC",
+    3:  "BCC",  -3: "BCC",
+    4:  "HEX",
+    5:  "RHL",  -5: "RHL",
+    6:  "TET",
+    7:  "BCT",
+    8:  "ORC",
+    9:  "ORCC", -9: "ORCC",
+    10: "ORCF",
+    11: "ORCI",
+    12: "MCL",  -12: "MCL",
+    13: "MCLC",
+    14: "TRI",
+}
+
+
+def _strip_comments(text: str) -> str:
+    text = re.sub(r"!.*$", "", text, flags=re.MULTILINE)
+    text = re.sub(r"#.*$", "", text, flags=re.MULTILINE)
+    return text
+
+
+def _parse_namelist(text: str, name: str) -> dict:
+    """Extract key=value pairs from a Fortran namelist block &NAME ... /"""
+    match = re.search(rf"&{name}\s*([\s\S]*?)\/", text, re.IGNORECASE)
+    if not match:
+        return {}
+    block = match.group(1)
+    result = {}
+    # Regular key=value pairs
+    for k, v in re.findall(r"(\w+)\s*=\s*([^,\n/=]+)", block):
+        result[k.strip().lower()] = v.strip()
+    # celldm(N) with explicit index
+    for n, v in re.findall(r"celldm\s*\(\s*(\d+)\s*\)\s*=\s*([^,\n/]+)", block, re.IGNORECASE):
+        result[f"celldm{n}"] = v.strip()
+    return result
+
+
+def _get_cell_from_ibrav(system: dict) -> List[List[float]]:
+    ibrav = int(system.get("ibrav", 0))
+    lattice_type = IBRAV_TO_LATTICE_TYPE.get(ibrav)
+    if lattice_type is None:
+        raise ValueError(f"Unsupported ibrav={ibrav}")
+
+    has_celldm = "celldm1" in system
+
+    if has_celldm:
+        a = float(system["celldm1"]) * BOHR_TO_ANGSTROM
+        b = a * float(system.get("celldm2", 1))
+        c = a * float(system.get("celldm3", 1))
+        # celldm(4,5,6) are cosines → convert to degrees
+        alpha = math.degrees(math.acos(float(system.get("celldm4", 0))))
+        beta  = math.degrees(math.acos(float(system.get("celldm5", 0))))
+        gamma = math.degrees(math.acos(float(system.get("celldm6", 0))))
+    else:
+        a = float(system.get("a", 1))
+        b = float(system.get("b", a))
+        c = float(system.get("c", a))
+        alpha = math.degrees(math.acos(float(system["cosbc"]))) if "cosbc" in system else float(system.get("alpha", 90))
+        beta  = math.degrees(math.acos(float(system["cosac"]))) if "cosac" in system else float(system.get("beta",  90))
+        gamma = math.degrees(math.acos(float(system["cosab"]))) if "cosab" in system else float(system.get("gamma", 90))
+
+    lattice_config = LatticeSchema(type=lattice_type, a=a, b=b, c=c, alpha=alpha, beta=beta, gamma=gamma)
+
+    return get_primitive_lattice_vectors_from_config(lattice_config)
+
+
+def _parse_cell_parameters(text: str, celldm1_angstrom: Optional[float]) -> List[List[float]]:
+    match = re.search(
+        r"CELL_PARAMETERS\s*[{(]?\s*(\w+)\s*[)}]?\s*\n"
+        r"((?:[ \t]*[-\d.eEdD+]+[ \t]+[-\d.eEdD+]+[ \t]+[-\d.eEdD+]+[ \t]*\n?){3})",
+        text, re.IGNORECASE,
+    )
+    if not match:
+        raise ValueError("CELL_PARAMETERS card not found")
+    units = match.group(1).lower()
+    rows = [list(map(float, line.split())) for line in match.group(2).strip().splitlines()]
+    if units == "bohr":
+        rows = [[v * BOHR_TO_ANGSTROM for v in row] for row in rows]
+    elif units == "alat":
+        if not celldm1_angstrom:
+            raise ValueError("alat units require celldm(1)")
+        rows = [[v * celldm1_angstrom for v in row] for row in rows]
+    return rows  # angstrom: use as-is
+
+
+def _parse_atomic_positions(
+    text: str, cell: List[List[float]], celldm1_angstrom: Optional[float]
+) -> Tuple[List[str], List[List[float]]]:
+    match = re.search(
+        r"ATOMIC_POSITIONS\s*[{(]?\s*(\w+)\s*[)}]?\s*\n"
+        r"((?:[ \t]*\w+[ \t]+[-\d.eEdD+]+[ \t]+[-\d.eEdD+]+[ \t]+[-\d.eEdD+]+.*\n?)+)",
+        text, re.IGNORECASE,
+    )
+    if not match:
+        raise ValueError("ATOMIC_POSITIONS card not found")
+    units = match.group(1).lower()
+    names, positions = [], []
+    for line in match.group(2).strip().splitlines():
+        parts = line.split()
+        if len(parts) < 4:
+            continue
+        symbol = parts[0]
+        coords = list(map(float, parts[1:4]))
+        if units == "crystal":
+            # fractional → Cartesian: coords_cart[j] = sum_i frac[i] * cell[i][j]
+            coords = [
+                sum(coords[i] * cell[i][j] for i in range(3))
+                for j in range(3)
+            ]
+        elif units == "bohr":
+            coords = [v * BOHR_TO_ANGSTROM for v in coords]
+        elif units == "alat":
+            if not celldm1_angstrom:
+                raise ValueError("alat units require celldm(1)")
+            coords = [v * celldm1_angstrom for v in coords]
+        names.append(symbol)
+        positions.append(coords)
+    return names, positions
+
+
+class PwInputFile:
+    """
+    QE pw.x input parser.
+    Uses get_primitive_lattice_vectors_from_config() from mat3ra.made for ibrav != 0.
+
+    self.structure dict keys match qe-tools PwInputFile.structure:
+        cell        - 3x3 list of lists (Angstrom)
+        atom_names  - list of element symbols
+        positions   - list of Cartesian coords (Angstrom)
+    """
+
+    def __init__(self, input_text: str):
+        text = _strip_comments(input_text)
+        system = _parse_namelist(text, "SYSTEM")
+        ibrav = int(system.get("ibrav", 0))
+
+        celldm1_angstrom = (
+            float(system["celldm1"]) * BOHR_TO_ANGSTROM if "celldm1" in system else None
+        )
+
+        cell = (
+            _parse_cell_parameters(text, celldm1_angstrom)
+            if ibrav == 0
+            else _get_cell_from_ibrav(system)   # ← delegates to made
+        )
+
+        atom_names, positions = _parse_atomic_positions(text, cell, celldm1_angstrom)
+
+        self.structure = {
+            "cell": cell,
+            "atom_names": atom_names,
+            "positions": positions,
+        }
diff --git a/express/parsers/structure.py b/express/parsers/structure.py
index e42b6539..a4c231d7 100644
--- a/express/parsers/structure.py
+++ b/express/parsers/structure.py
@@ -2,7 +2,7 @@
 
 import pymatgen as mg
 from pymatgen.core.structure import Structure
-from qe_tools.parsers import PwInputFile
+from express.parsers.apps.espresso.pw_input_file import PwInputFile
 from jarvis.core.atoms import Atoms
 from jarvis.io.vasp.inputs import Poscar
 
diff --git a/pyproject.toml b/pyproject.toml
index 2ab645f1..dc3a238d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,14 +15,11 @@ classifiers = [
     "Topic :: Software Development",
 ]
 dependencies = [
-    "pymatgen>=2023.8.10",
-    "ase>=3.17.0",
     "mat3ra-esse>=2026.5.27.post0",
+    "mat3ra-made @ git+https://github.com/exabyte-io/made.git@f80df56b6b404ce1d5482e6d850e60f10041a8f5",
     "jarvis-tools>=2023.12.12",
     # To avoid module 'numpy.linalg._umath_linalg' has no attribute '_ilp64' in Colab
     "numpy>=1.24.4,<2",
-    "pymatgen>=2025.10.7",
-    "qe-tools==2.3.0",
 ]
 
 [project.optional-dependencies]
diff --git a/tests/fixtures/structural/references.py b/tests/fixtures/structural/references.py
index 6d502f7b..6d26ed96 100644
--- a/tests/fixtures/structural/references.py
+++ b/tests/fixtures/structural/references.py
@@ -30,8 +30,7 @@
     ],
 }
 
-# ibrav=0 silicon with explicit CELL_PARAMETERS
-SI_IBRAV0_BASIS = {
+SI_IBRAV_BASIS = {
     "units": "crystal",
     "elements": [{"id": 0, "value": "Si"}, {"id": 1, "value": "Si"}],
     "coordinates": [
@@ -40,14 +39,4 @@
     ],
 }
 
-# ibrav=2 with FCC lattice, qe-tools produces symmetry equivalent but non-identical basis
-SI_IBRAV2_BASIS = {
-    "units": "crystal",
-    "elements": [{"id": 0, "value": "Si"}, {"id": 1, "value": "Si"}],
-    "coordinates": [
-        {"id": 0, "value": [0.0, 0.0, 0.0]},
-        {"id": 1, "value": [-0.25, 0.75, -0.25]},
-    ],
-}
-
 SI_PRIMITIVE_LATTICE_A = 3.867  # Angstrom
diff --git a/tests/unit/parsers/test_structure_parser.py b/tests/unit/parsers/test_structure_parser.py
index 0a37781b..969f269a 100644
--- a/tests/unit/parsers/test_structure_parser.py
+++ b/tests/unit/parsers/test_structure_parser.py
@@ -1,7 +1,7 @@
 import os
 
 from tests.unit import UnitTestBase
-from tests.fixtures.structural.references import LI_CIF_BASIS, SI_IBRAV0_BASIS, SI_IBRAV2_BASIS, SI_PRIMITIVE_LATTICE_A
+from tests.fixtures.structural.references import LI_CIF_BASIS, SI_IBRAV_BASIS, SI_PRIMITIVE_LATTICE_A
 from express.parsers.structure import StructureParser
 
 LI_CIF_PATH = os.path.join(os.path.dirname(__file__), "..", "..", "fixtures", "structural", "test-004", "Li.cif")
@@ -98,7 +98,7 @@ def tearDown(self):
         super().tearDown()
 
     def test_basis(self):
-        self.assertDeepAlmostEqual(self.parser.basis(), SI_IBRAV0_BASIS, places=5)
+        self.assertDeepAlmostEqual(self.parser.basis(), SI_IBRAV_BASIS, places=5)
 
     def test_formula(self):
         self.assertEqual(self.parser.formula(), "Si2")
@@ -126,7 +126,7 @@ def tearDown(self):
         super().tearDown()
 
     def test_basis(self):
-        self.assertDeepAlmostEqual(self.parser.basis(), SI_IBRAV2_BASIS, places=5)
+        self.assertDeepAlmostEqual(self.parser.basis(), SI_IBRAV_BASIS, places=5)
 
     def test_formula(self):
         self.assertEqual(self.parser.formula(), "Si2")

From e141f3cb088b3da597ba57c8d14db373650e216b Mon Sep 17 00:00:00 2001
From: Pranab Das <31024886+pranabdas@users.noreply.github.com>
Date: Thu, 28 May 2026 21:18:12 +0800
Subject: [PATCH 05/19] fix made[tools] dependency

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index dc3a238d..ef94061e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,7 +16,7 @@ classifiers = [
 ]
 dependencies = [
     "mat3ra-esse>=2026.5.27.post0",
-    "mat3ra-made @ git+https://github.com/exabyte-io/made.git@f80df56b6b404ce1d5482e6d850e60f10041a8f5",
+    "mat3ra-made[tools] @ git+https://github.com/exabyte-io/made.git@f80df56b6b404ce1d5482e6d850e60f10041a8f5",
     "jarvis-tools>=2023.12.12",
     # To avoid module 'numpy.linalg._umath_linalg' has no attribute '_ilp64' in Colab
     "numpy>=1.24.4,<2",

From 52a13cc167b7464e0f1c343ed6204cb7e4bc35e5 Mon Sep 17 00:00:00 2001
From: Pranab Das <31024886+pranabdas@users.noreply.github.com>
Date: Thu, 28 May 2026 22:04:41 +0800
Subject: [PATCH 06/19] bump made

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index ef94061e..0978a7e2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,7 +16,7 @@ classifiers = [
 ]
 dependencies = [
     "mat3ra-esse>=2026.5.27.post0",
-    "mat3ra-made[tools] @ git+https://github.com/exabyte-io/made.git@f80df56b6b404ce1d5482e6d850e60f10041a8f5",
+    "mat3ra-made[tools] @ git+https://github.com/exabyte-io/made.git@190beb96c97d066396a5433b4a640442c49a73f9",
     "jarvis-tools>=2023.12.12",
     # To avoid module 'numpy.linalg._umath_linalg' has no attribute '_ilp64' in Colab
     "numpy>=1.24.4,<2",

From 94555a98b61f531ed8008748a735ae102ccc37f5 Mon Sep 17 00:00:00 2001
From: Pranab Das <31024886+pranabdas@users.noreply.github.com>
Date: Wed, 3 Jun 2026 23:35:28 +0800
Subject: [PATCH 07/19] use BOHR_TO_ANGSTROM contstant via utils

---
 express/parsers/apps/espresso/pw_input_file.py | 11 +++++------
 pyproject.toml                                 |  2 +-
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/express/parsers/apps/espresso/pw_input_file.py b/express/parsers/apps/espresso/pw_input_file.py
index f106aa85..b1781f87 100644
--- a/express/parsers/apps/espresso/pw_input_file.py
+++ b/express/parsers/apps/espresso/pw_input_file.py
@@ -4,8 +4,7 @@
 
 from mat3ra.esse.models.properties_directory.structural.lattice import LatticeSchema
 from mat3ra.made.cell.primitive_cell import get_primitive_lattice_vectors_from_config
-
-BOHR_TO_ANGSTROM = 0.529177210903
+from mat3ra.utils.constants import COEFFICIENTS
 
 # Maps QE ibrav codes → made/esse Bravais type strings
 IBRAV_TO_LATTICE_TYPE = {
@@ -57,7 +56,7 @@ def _get_cell_from_ibrav(system: dict) -> List[List[float]]:
     has_celldm = "celldm1" in system
 
     if has_celldm:
-        a = float(system["celldm1"]) * BOHR_TO_ANGSTROM
+        a = float(system["celldm1"]) * COEFFICIENTS["BOHR_TO_ANGSTROM"]
         b = a * float(system.get("celldm2", 1))
         c = a * float(system.get("celldm3", 1))
         # celldm(4,5,6) are cosines → convert to degrees
@@ -88,7 +87,7 @@ def _parse_cell_parameters(text: str, celldm1_angstrom: Optional[float]) -> List
     units = match.group(1).lower()
     rows = [list(map(float, line.split())) for line in match.group(2).strip().splitlines()]
     if units == "bohr":
-        rows = [[v * BOHR_TO_ANGSTROM for v in row] for row in rows]
+        rows = [[v * COEFFICIENTS["BOHR_TO_ANGSTROM"] for v in row] for row in rows]
     elif units == "alat":
         if not celldm1_angstrom:
             raise ValueError("alat units require celldm(1)")
@@ -121,7 +120,7 @@ def _parse_atomic_positions(
                 for j in range(3)
             ]
         elif units == "bohr":
-            coords = [v * BOHR_TO_ANGSTROM for v in coords]
+            coords = [v * COEFFICIENTS["BOHR_TO_ANGSTROM"] for v in coords]
         elif units == "alat":
             if not celldm1_angstrom:
                 raise ValueError("alat units require celldm(1)")
@@ -148,7 +147,7 @@ def __init__(self, input_text: str):
         ibrav = int(system.get("ibrav", 0))
 
         celldm1_angstrom = (
-            float(system["celldm1"]) * BOHR_TO_ANGSTROM if "celldm1" in system else None
+            float(system["celldm1"]) * COEFFICIENTS["BOHR_TO_ANGSTROM"] if "celldm1" in system else None
         )
 
         cell = (
diff --git a/pyproject.toml b/pyproject.toml
index 0978a7e2..00546194 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,7 +16,7 @@ classifiers = [
 ]
 dependencies = [
     "mat3ra-esse>=2026.5.27.post0",
-    "mat3ra-made[tools] @ git+https://github.com/exabyte-io/made.git@190beb96c97d066396a5433b4a640442c49a73f9",
+    "mat3ra-made[tools] @ git+https://github.com/exabyte-io/made.git@e5fa168b942f73623fed986dde7a5ba55c6f9821",
     "jarvis-tools>=2023.12.12",
     # To avoid module 'numpy.linalg._umath_linalg' has no attribute '_ilp64' in Colab
     "numpy>=1.24.4,<2",

From a93bb057d85fb3cf15de7d4fdc3dbbe891be4b81 Mon Sep 17 00:00:00 2001
From: Pranab Das <31024886+pranabdas@users.noreply.github.com>
Date: Thu, 4 Jun 2026 00:00:29 +0800
Subject: [PATCH 08/19] replace strip_comments with
 remove_comments_from_source_code from mat3ra-utils

---
 express/parsers/apps/espresso/pw_input_file.py | 9 ++-------
 pyproject.toml                                 | 2 +-
 2 files changed, 3 insertions(+), 8 deletions(-)

diff --git a/express/parsers/apps/espresso/pw_input_file.py b/express/parsers/apps/espresso/pw_input_file.py
index b1781f87..e55efbdb 100644
--- a/express/parsers/apps/espresso/pw_input_file.py
+++ b/express/parsers/apps/espresso/pw_input_file.py
@@ -5,6 +5,7 @@
 from mat3ra.esse.models.properties_directory.structural.lattice import LatticeSchema
 from mat3ra.made.cell.primitive_cell import get_primitive_lattice_vectors_from_config
 from mat3ra.utils.constants import COEFFICIENTS
+from mat3ra.utils.string import remove_comments_from_source_code
 
 # Maps QE ibrav codes → made/esse Bravais type strings
 IBRAV_TO_LATTICE_TYPE = {
@@ -25,12 +26,6 @@
 }
 
 
-def _strip_comments(text: str) -> str:
-    text = re.sub(r"!.*$", "", text, flags=re.MULTILINE)
-    text = re.sub(r"#.*$", "", text, flags=re.MULTILINE)
-    return text
-
-
 def _parse_namelist(text: str, name: str) -> dict:
     """Extract key=value pairs from a Fortran namelist block &NAME ... /"""
     match = re.search(rf"&{name}\s*([\s\S]*?)\/", text, re.IGNORECASE)
@@ -142,7 +137,7 @@ class PwInputFile:
     """
 
     def __init__(self, input_text: str):
-        text = _strip_comments(input_text)
+        text = remove_comments_from_source_code(input_text, language="fortran")
         system = _parse_namelist(text, "SYSTEM")
         ibrav = int(system.get("ibrav", 0))
 
diff --git a/pyproject.toml b/pyproject.toml
index 00546194..c3f02310 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,7 +16,7 @@ classifiers = [
 ]
 dependencies = [
     "mat3ra-esse>=2026.5.27.post0",
-    "mat3ra-made[tools] @ git+https://github.com/exabyte-io/made.git@e5fa168b942f73623fed986dde7a5ba55c6f9821",
+    "mat3ra-made[tools] @ git+https://github.com/exabyte-io/made.git@9f24bff67b63dc5d4c55c0c89509e72743ad1258",
     "jarvis-tools>=2023.12.12",
     # To avoid module 'numpy.linalg._umath_linalg' has no attribute '_ilp64' in Colab
     "numpy>=1.24.4,<2",

From b019cab728dbacdae17ef5072f817db1f57474f9 Mon Sep 17 00:00:00 2001
From: Pranab Das <31024886+pranabdas@users.noreply.github.com>
Date: Sat, 6 Jun 2026 00:30:36 +0800
Subject: [PATCH 09/19] refactor after moving parsers to parsers repo

---
 .../parsers/apps/espresso/pw_input_file.py    | 95 ++-----------------
 pyproject.toml                                |  3 +-
 2 files changed, 11 insertions(+), 87 deletions(-)

diff --git a/express/parsers/apps/espresso/pw_input_file.py b/express/parsers/apps/espresso/pw_input_file.py
index e55efbdb..4c8ecab6 100644
--- a/express/parsers/apps/espresso/pw_input_file.py
+++ b/express/parsers/apps/espresso/pw_input_file.py
@@ -1,11 +1,11 @@
 import math
-import re
-from typing import List, Optional, Tuple
+from typing import List
 
 from mat3ra.esse.models.properties_directory.structural.lattice import LatticeSchema
 from mat3ra.made.cell.primitive_cell import get_primitive_lattice_vectors_from_config
 from mat3ra.utils.constants import COEFFICIENTS
 from mat3ra.utils.string import remove_comments_from_source_code
+from mat3ra.parsers.applications.espresso.pw_x.stdin.parser import EspressoPwxStdinParser
 
 # Maps QE ibrav codes → made/esse Bravais type strings
 IBRAV_TO_LATTICE_TYPE = {
@@ -26,22 +26,6 @@
 }
 
 
-def _parse_namelist(text: str, name: str) -> dict:
-    """Extract key=value pairs from a Fortran namelist block &NAME ... /"""
-    match = re.search(rf"&{name}\s*([\s\S]*?)\/", text, re.IGNORECASE)
-    if not match:
-        return {}
-    block = match.group(1)
-    result = {}
-    # Regular key=value pairs
-    for k, v in re.findall(r"(\w+)\s*=\s*([^,\n/=]+)", block):
-        result[k.strip().lower()] = v.strip()
-    # celldm(N) with explicit index
-    for n, v in re.findall(r"celldm\s*\(\s*(\d+)\s*\)\s*=\s*([^,\n/]+)", block, re.IGNORECASE):
-        result[f"celldm{n}"] = v.strip()
-    return result
-
-
 def _get_cell_from_ibrav(system: dict) -> List[List[float]]:
     ibrav = int(system.get("ibrav", 0))
     lattice_type = IBRAV_TO_LATTICE_TYPE.get(ibrav)
@@ -71,87 +55,26 @@ def _get_cell_from_ibrav(system: dict) -> List[List[float]]:
     return get_primitive_lattice_vectors_from_config(lattice_config)
 
 
-def _parse_cell_parameters(text: str, celldm1_angstrom: Optional[float]) -> List[List[float]]:
-    match = re.search(
-        r"CELL_PARAMETERS\s*[{(]?\s*(\w+)\s*[)}]?\s*\n"
-        r"((?:[ \t]*[-\d.eEdD+]+[ \t]+[-\d.eEdD+]+[ \t]+[-\d.eEdD+]+[ \t]*\n?){3})",
-        text, re.IGNORECASE,
-    )
-    if not match:
-        raise ValueError("CELL_PARAMETERS card not found")
-    units = match.group(1).lower()
-    rows = [list(map(float, line.split())) for line in match.group(2).strip().splitlines()]
-    if units == "bohr":
-        rows = [[v * COEFFICIENTS["BOHR_TO_ANGSTROM"] for v in row] for row in rows]
-    elif units == "alat":
-        if not celldm1_angstrom:
-            raise ValueError("alat units require celldm(1)")
-        rows = [[v * celldm1_angstrom for v in row] for row in rows]
-    return rows  # angstrom: use as-is
-
-
-def _parse_atomic_positions(
-    text: str, cell: List[List[float]], celldm1_angstrom: Optional[float]
-) -> Tuple[List[str], List[List[float]]]:
-    match = re.search(
-        r"ATOMIC_POSITIONS\s*[{(]?\s*(\w+)\s*[)}]?\s*\n"
-        r"((?:[ \t]*\w+[ \t]+[-\d.eEdD+]+[ \t]+[-\d.eEdD+]+[ \t]+[-\d.eEdD+]+.*\n?)+)",
-        text, re.IGNORECASE,
-    )
-    if not match:
-        raise ValueError("ATOMIC_POSITIONS card not found")
-    units = match.group(1).lower()
-    names, positions = [], []
-    for line in match.group(2).strip().splitlines():
-        parts = line.split()
-        if len(parts) < 4:
-            continue
-        symbol = parts[0]
-        coords = list(map(float, parts[1:4]))
-        if units == "crystal":
-            # fractional → Cartesian: coords_cart[j] = sum_i frac[i] * cell[i][j]
-            coords = [
-                sum(coords[i] * cell[i][j] for i in range(3))
-                for j in range(3)
-            ]
-        elif units == "bohr":
-            coords = [v * COEFFICIENTS["BOHR_TO_ANGSTROM"] for v in coords]
-        elif units == "alat":
-            if not celldm1_angstrom:
-                raise ValueError("alat units require celldm(1)")
-            coords = [v * celldm1_angstrom for v in coords]
-        names.append(symbol)
-        positions.append(coords)
-    return names, positions
-
-
 class PwInputFile:
-    """
-    QE pw.x input parser.
-    Uses get_primitive_lattice_vectors_from_config() from mat3ra.made for ibrav != 0.
-
-    self.structure dict keys match qe-tools PwInputFile.structure:
-        cell        - 3x3 list of lists (Angstrom)
-        atom_names  - list of element symbols
-        positions   - list of Cartesian coords (Angstrom)
-    """
-
     def __init__(self, input_text: str):
         text = remove_comments_from_source_code(input_text, language="fortran")
-        system = _parse_namelist(text, "SYSTEM")
+        parser = EspressoPwxStdinParser(text)
+
+        system = parser.get_namelist_as_dict("SYSTEM")
         ibrav = int(system.get("ibrav", 0))
 
         celldm1_angstrom = (
             float(system["celldm1"]) * COEFFICIENTS["BOHR_TO_ANGSTROM"] if "celldm1" in system else None
         )
 
+        # Delegate to the new parser method if ibrav == 0, else build from ibrav
         cell = (
-            _parse_cell_parameters(text, celldm1_angstrom)
+            parser.get_card_cell_parameters(celldm1_angstrom)
             if ibrav == 0
-            else _get_cell_from_ibrav(system)   # ← delegates to made
+            else _get_cell_from_ibrav(system)
         )
 
-        atom_names, positions = _parse_atomic_positions(text, cell, celldm1_angstrom)
+        atom_names, positions = parser.get_card_atomic_positions(cell, celldm1_angstrom)
 
         self.structure = {
             "cell": cell,
diff --git a/pyproject.toml b/pyproject.toml
index c3f02310..c4fb6923 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,7 +16,8 @@ classifiers = [
 ]
 dependencies = [
     "mat3ra-esse>=2026.5.27.post0",
-    "mat3ra-made[tools] @ git+https://github.com/exabyte-io/made.git@9f24bff67b63dc5d4c55c0c89509e72743ad1258",
+    "mat3ra-made[tools] @ git+https://github.com/exabyte-io/made.git@97cd8a9a9f9898446ebffc5881919ef236849a1b",
+    "mat3ra-parsers @ git+https://github.com/exabyte-io/parsers.git@d850566958a32b323ee345a93c6d57d4caf9a359",
     "jarvis-tools>=2023.12.12",
     # To avoid module 'numpy.linalg._umath_linalg' has no attribute '_ilp64' in Colab
     "numpy>=1.24.4,<2",

From 9e2b20eb7d736b8412d60f81bda27183900ff423 Mon Sep 17 00:00:00 2001
From: Pranab Das <31024886+pranabdas@users.noreply.github.com>
Date: Fri, 12 Jun 2026 22:15:53 +0800
Subject: [PATCH 10/19] use updated parser to get_namelist

---
 express/parsers/apps/espresso/pw_input_file.py | 14 ++++----------
 pyproject.toml                                 |  4 ++--
 2 files changed, 6 insertions(+), 12 deletions(-)

diff --git a/express/parsers/apps/espresso/pw_input_file.py b/express/parsers/apps/espresso/pw_input_file.py
index 4c8ecab6..624c235f 100644
--- a/express/parsers/apps/espresso/pw_input_file.py
+++ b/express/parsers/apps/espresso/pw_input_file.py
@@ -60,19 +60,13 @@ def __init__(self, input_text: str):
         text = remove_comments_from_source_code(input_text, language="fortran")
         parser = EspressoPwxStdinParser(text)
 
-        system = parser.get_namelist_as_dict("SYSTEM")
+        system = parser.get_namelist("SYSTEM")
         ibrav = int(system.get("ibrav", 0))
 
-        celldm1_angstrom = (
-            float(system["celldm1"]) * COEFFICIENTS["BOHR_TO_ANGSTROM"] if "celldm1" in system else None
-        )
+        celldm1_angstrom = float(system["celldm1"]) * COEFFICIENTS["BOHR_TO_ANGSTROM"] if "celldm1" in system else None
 
-        # Delegate to the new parser method if ibrav == 0, else build from ibrav
-        cell = (
-            parser.get_card_cell_parameters(celldm1_angstrom)
-            if ibrav == 0
-            else _get_cell_from_ibrav(system)
-        )
+        # Delegate crystal lattice calculation based on ibrav value
+        cell = parser.get_card_cell_parameters(celldm1_angstrom) if ibrav == 0 else _get_cell_from_ibrav(system)
 
         atom_names, positions = parser.get_card_atomic_positions(cell, celldm1_angstrom)
 
diff --git a/pyproject.toml b/pyproject.toml
index c4fb6923..038f99e1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,8 +16,8 @@ classifiers = [
 ]
 dependencies = [
     "mat3ra-esse>=2026.5.27.post0",
-    "mat3ra-made[tools] @ git+https://github.com/exabyte-io/made.git@97cd8a9a9f9898446ebffc5881919ef236849a1b",
-    "mat3ra-parsers @ git+https://github.com/exabyte-io/parsers.git@d850566958a32b323ee345a93c6d57d4caf9a359",
+    "mat3ra-made[tools] @ git+https://github.com/exabyte-io/made.git@774c0c2c54c5f175291ea026411de1ee8405d825",
+    "mat3ra-parsers @ git+https://github.com/exabyte-io/parsers.git@6f8601a2bdd3aac155f9743b2c53dfc73c4c69a4",
     "jarvis-tools>=2023.12.12",
     # To avoid module 'numpy.linalg._umath_linalg' has no attribute '_ilp64' in Colab
     "numpy>=1.24.4,<2",

From 7be6036fd661b8b9011f5eed6a862d002f86124c Mon Sep 17 00:00:00 2001
From: Pranab Das <31024886+pranabdas@users.noreply.github.com>
Date: Sat, 13 Jun 2026 13:12:41 +0800
Subject: [PATCH 11/19] refactor parser changes

---
 express/parsers/apps/espresso/pw_input_file.py | 4 ++--
 pyproject.toml                                 | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/express/parsers/apps/espresso/pw_input_file.py b/express/parsers/apps/espresso/pw_input_file.py
index 624c235f..b6d10897 100644
--- a/express/parsers/apps/espresso/pw_input_file.py
+++ b/express/parsers/apps/espresso/pw_input_file.py
@@ -5,7 +5,7 @@
 from mat3ra.made.cell.primitive_cell import get_primitive_lattice_vectors_from_config
 from mat3ra.utils.constants import COEFFICIENTS
 from mat3ra.utils.string import remove_comments_from_source_code
-from mat3ra.parsers.applications.espresso.pw_x.stdin.parser import EspressoPwxStdinParser
+from mat3ra.parsers.applications.espresso.pwin import EspressoPwinParser
 
 # Maps QE ibrav codes → made/esse Bravais type strings
 IBRAV_TO_LATTICE_TYPE = {
@@ -58,7 +58,7 @@ def _get_cell_from_ibrav(system: dict) -> List[List[float]]:
 class PwInputFile:
     def __init__(self, input_text: str):
         text = remove_comments_from_source_code(input_text, language="fortran")
-        parser = EspressoPwxStdinParser(text)
+        parser = EspressoPwinParser(text)
 
         system = parser.get_namelist("SYSTEM")
         ibrav = int(system.get("ibrav", 0))
diff --git a/pyproject.toml b/pyproject.toml
index e7f22491..2b08459e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,8 +16,8 @@ classifiers = [
 ]
 dependencies = [
     "mat3ra-esse>=2026.6.12",
-    "mat3ra-made[tools] @ git+https://github.com/exabyte-io/made.git@774c0c2c54c5f175291ea026411de1ee8405d825",
-    "mat3ra-parsers @ git+https://github.com/exabyte-io/parsers.git@6f8601a2bdd3aac155f9743b2c53dfc73c4c69a4",
+    "mat3ra-made[tools] @ git+https://github.com/exabyte-io/made.git@1b18d807cea0d34b4551baa1da6cc2827298193b",
+    "mat3ra-parsers @ git+https://github.com/exabyte-io/parsers.git@63f0bf323035a1c9b294494af3accdb0333baf38",
     "jarvis-tools>=2023.12.12",
     # To avoid module 'numpy.linalg._umath_linalg' has no attribute '_ilp64' in Colab
     "numpy>=1.24.4,<2",

From 04c1f910f2135aef9411464753e5a3156e484697 Mon Sep 17 00:00:00 2001
From: Pranab Das <31024886+pranabdas@users.noreply.github.com>
Date: Sat, 13 Jun 2026 13:44:18 +0800
Subject: [PATCH 12/19] bump parser

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 2b08459e..0859a1ec 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ classifiers = [
 dependencies = [
     "mat3ra-esse>=2026.6.12",
     "mat3ra-made[tools] @ git+https://github.com/exabyte-io/made.git@1b18d807cea0d34b4551baa1da6cc2827298193b",
-    "mat3ra-parsers @ git+https://github.com/exabyte-io/parsers.git@63f0bf323035a1c9b294494af3accdb0333baf38",
+    "mat3ra-parsers @ git+https://github.com/exabyte-io/parsers.git@372a7fd31ee27ada9216221a970fce608878a5a8",
     "jarvis-tools>=2023.12.12",
     # To avoid module 'numpy.linalg._umath_linalg' has no attribute '_ilp64' in Colab
     "numpy>=1.24.4,<2",

From 13da531b83402c10f23835b7a4347c5d7f4f02aa Mon Sep 17 00:00:00 2001
From: Pranab Das <31024886+pranabdas@users.noreply.github.com>
Date: Sat, 13 Jun 2026 15:42:12 +0800
Subject: [PATCH 13/19] bump parsers

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 0859a1ec..1bd2ade0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ classifiers = [
 dependencies = [
     "mat3ra-esse>=2026.6.12",
     "mat3ra-made[tools] @ git+https://github.com/exabyte-io/made.git@1b18d807cea0d34b4551baa1da6cc2827298193b",
-    "mat3ra-parsers @ git+https://github.com/exabyte-io/parsers.git@372a7fd31ee27ada9216221a970fce608878a5a8",
+    "mat3ra-parsers @ git+https://github.com/exabyte-io/parsers.git@0edfda94b01e357aafc8851873c13d7b688857c1",
     "jarvis-tools>=2023.12.12",
     # To avoid module 'numpy.linalg._umath_linalg' has no attribute '_ilp64' in Colab
     "numpy>=1.24.4,<2",

From c8a5252f893c664bb813c49a7fae78c6c9a4f24d Mon Sep 17 00:00:00 2001
From: Pranab Das <31024886+pranabdas@users.noreply.github.com>
Date: Sat, 13 Jun 2026 21:49:07 +0800
Subject: [PATCH 14/19] update parsers

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 1bd2ade0..3dab5fb1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ classifiers = [
 dependencies = [
     "mat3ra-esse>=2026.6.12",
     "mat3ra-made[tools] @ git+https://github.com/exabyte-io/made.git@1b18d807cea0d34b4551baa1da6cc2827298193b",
-    "mat3ra-parsers @ git+https://github.com/exabyte-io/parsers.git@0edfda94b01e357aafc8851873c13d7b688857c1",
+    "mat3ra-parsers @ git+https://github.com/exabyte-io/parsers.git@988851514c1a4ca387def281ee7a63b4f70435f8",
     "jarvis-tools>=2023.12.12",
     # To avoid module 'numpy.linalg._umath_linalg' has no attribute '_ilp64' in Colab
     "numpy>=1.24.4,<2",

From c0be22841062adba27c54b5d72df0a389cb2c57a Mon Sep 17 00:00:00 2001
From: Pranab Das <31024886+pranabdas@users.noreply.github.com>
Date: Sat, 13 Jun 2026 22:17:02 +0800
Subject: [PATCH 15/19] update parsers

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 3dab5fb1..2e9d5afc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ classifiers = [
 dependencies = [
     "mat3ra-esse>=2026.6.12",
     "mat3ra-made[tools] @ git+https://github.com/exabyte-io/made.git@1b18d807cea0d34b4551baa1da6cc2827298193b",
-    "mat3ra-parsers @ git+https://github.com/exabyte-io/parsers.git@988851514c1a4ca387def281ee7a63b4f70435f8",
+    "mat3ra-parsers @ git+https://github.com/exabyte-io/parsers.git@b50bb00e41be4682c8420288fbd0f731808cdbb8",
     "jarvis-tools>=2023.12.12",
     # To avoid module 'numpy.linalg._umath_linalg' has no attribute '_ilp64' in Colab
     "numpy>=1.24.4,<2",

From 01565af4f5f1090b055c806cd52968ea3c979c50 Mon Sep 17 00:00:00 2001
From: Pranab Das <31024886+pranabdas@users.noreply.github.com>
Date: Sat, 20 Jun 2026 00:55:31 +0800
Subject: [PATCH 16/19] update parser class

---
 express/parsers/apps/espresso/pw_input_file.py | 4 ++--
 pyproject.toml                                 | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/express/parsers/apps/espresso/pw_input_file.py b/express/parsers/apps/espresso/pw_input_file.py
index b6d10897..624c235f 100644
--- a/express/parsers/apps/espresso/pw_input_file.py
+++ b/express/parsers/apps/espresso/pw_input_file.py
@@ -5,7 +5,7 @@
 from mat3ra.made.cell.primitive_cell import get_primitive_lattice_vectors_from_config
 from mat3ra.utils.constants import COEFFICIENTS
 from mat3ra.utils.string import remove_comments_from_source_code
-from mat3ra.parsers.applications.espresso.pwin import EspressoPwinParser
+from mat3ra.parsers.applications.espresso.pw_x.stdin.parser import EspressoPwxStdinParser
 
 # Maps QE ibrav codes → made/esse Bravais type strings
 IBRAV_TO_LATTICE_TYPE = {
@@ -58,7 +58,7 @@ def _get_cell_from_ibrav(system: dict) -> List[List[float]]:
 class PwInputFile:
     def __init__(self, input_text: str):
         text = remove_comments_from_source_code(input_text, language="fortran")
-        parser = EspressoPwinParser(text)
+        parser = EspressoPwxStdinParser(text)
 
         system = parser.get_namelist("SYSTEM")
         ibrav = int(system.get("ibrav", 0))
diff --git a/pyproject.toml b/pyproject.toml
index 2e9d5afc..a13a1a21 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,8 +16,8 @@ classifiers = [
 ]
 dependencies = [
     "mat3ra-esse>=2026.6.12",
-    "mat3ra-made[tools] @ git+https://github.com/exabyte-io/made.git@1b18d807cea0d34b4551baa1da6cc2827298193b",
-    "mat3ra-parsers @ git+https://github.com/exabyte-io/parsers.git@b50bb00e41be4682c8420288fbd0f731808cdbb8",
+    "mat3ra-made[tools] @ git+https://github.com/exabyte-io/made.git@bdfa37a451f0364cee1602bcec723fb878fdfc0a",
+    "mat3ra-parsers @ git+https://github.com/exabyte-io/parsers.git@30182b7f967024d31ff03dc39dcbdc33faf89722",
     "jarvis-tools>=2023.12.12",
     # To avoid module 'numpy.linalg._umath_linalg' has no attribute '_ilp64' in Colab
     "numpy>=1.24.4,<2",

From 59ea4b1404eee695a88999a1b2eccdf7570bc1e5 Mon Sep 17 00:00:00 2001
From: Pranab Das <31024886+pranabdas@users.noreply.github.com>
Date: Sat, 20 Jun 2026 00:59:45 +0800
Subject: [PATCH 17/19] remove espresso comments by chaining fortran and python
 comments

---
 express/parsers/apps/espresso/pw_input_file.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/express/parsers/apps/espresso/pw_input_file.py b/express/parsers/apps/espresso/pw_input_file.py
index 624c235f..d96c289a 100644
--- a/express/parsers/apps/espresso/pw_input_file.py
+++ b/express/parsers/apps/espresso/pw_input_file.py
@@ -57,7 +57,9 @@ def _get_cell_from_ibrav(system: dict) -> List[List[float]]:
 
 class PwInputFile:
     def __init__(self, input_text: str):
-        text = remove_comments_from_source_code(input_text, language="fortran")
+        text = remove_comments_from_source_code(
+            remove_comments_from_source_code(input_text, language="fortran"), language="python"
+        )
         parser = EspressoPwxStdinParser(text)
 
         system = parser.get_namelist("SYSTEM")

From 26d8d618b18ff1277372eed8b36d1ec9c273d6f0 Mon Sep 17 00:00:00 2001
From: Pranab Das <31024886+pranabdas@users.noreply.github.com>
Date: Sat, 20 Jun 2026 01:00:03 +0800
Subject: [PATCH 18/19] chore: bump gh actions/checkout

---
 .github/workflows/cicd.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/cicd.yml b/.github/workflows/cicd.yml
index 698755f8..5696ef99 100644
--- a/.github/workflows/cicd.yml
+++ b/.github/workflows/cicd.yml
@@ -16,12 +16,12 @@ jobs:
 
     steps:
       - name: Checkout this repository
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         with:
           lfs: true
 
       - name: Checkout actions repository
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         with:
           repository: Exabyte-io/actions
           token: ${{ secrets.BOT_GITHUB_TOKEN }}
@@ -43,12 +43,12 @@ jobs:
 
     steps:
       - name: Checkout this repository
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         with:
           lfs: true
 
       - name: Checkout actions repository
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         with:
           repository: Exabyte-io/actions
           token: ${{ secrets.BOT_GITHUB_TOKEN }}
@@ -71,13 +71,13 @@ jobs:
 
     steps:
       - name: Checkout this repository
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         with:
           lfs: true
           fetch-tags: true
 
       - name: Checkout actions repository
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         with:
           repository: Exabyte-io/actions
           token: ${{ secrets.BOT_GITHUB_TOKEN }}

From 6980e3af8fb940a7c51907f656897855d16ce79d Mon Sep 17 00:00:00 2001
From: Pranab Das <31024886+pranabdas@users.noreply.github.com>
Date: Sat, 20 Jun 2026 10:59:08 +0800
Subject: [PATCH 19/19] update parsers lib

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index a13a1a21..7d94a56b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ classifiers = [
 dependencies = [
     "mat3ra-esse>=2026.6.12",
     "mat3ra-made[tools] @ git+https://github.com/exabyte-io/made.git@bdfa37a451f0364cee1602bcec723fb878fdfc0a",
-    "mat3ra-parsers @ git+https://github.com/exabyte-io/parsers.git@30182b7f967024d31ff03dc39dcbdc33faf89722",
+    "mat3ra-parsers @ git+https://github.com/exabyte-io/parsers.git@09184533d422d47945073849106bdf1ac5c878ac",
     "jarvis-tools>=2023.12.12",
     # To avoid module 'numpy.linalg._umath_linalg' has no attribute '_ilp64' in Colab
     "numpy>=1.24.4,<2",