update ld1

docs/source/conf.py

@@ -20,8 +20,8 @@
 
 # -- Project information -----------------------------------------------------
 
-project = "WorkGraph Collections"
-copyright = "2023, Xing Wang"
+project = "ASE QuantumESPRESSO"
+copyright = "2024, Xing Wang"
 author = "Xing Wang"
 
 # The full version, including alpha/beta/rc tags

docs/source/installation.rst

@@ -7,7 +7,7 @@ The recommended method of installation is to use the Python package manager |pip
 
 .. code-block:: console
 
-    $ pip install git+https://github.com/superstar54/workgraph-collections.git
+    $ pip install ase-quantumespresso
 
 
 This will install the latest version.

src/ase_quantumespresso/__init__.py

@@ -5,4 +5,11 @@
 from .ld1 import Ld1Template
 
 
-__all__ = ["Espresso", "PwTemplate", "DosTemplate", "ProjwfcTemplate", "PpTemplate", "Ld1Template"]
+__all__ = [
+    "Espresso",
+    "PwTemplate",
+    "DosTemplate",
+    "ProjwfcTemplate",
+    "PpTemplate",
+    "Ld1Template",
+]

src/ase_quantumespresso/ld1.py

@@ -1,8 +1,9 @@
 from .namelist import NamelistTemplate
-import re
+
 
 class Ld1Template(NamelistTemplate):
     _label = "ld1"
+    outputname = "ld1.ld1o"
 
     def __init__(self):
         super().__init__(
@@ -13,6 +14,7 @@ def __init__(self):
 
     def write_input(self, profile, directory, atoms, parameters, properties):
         from ase.io.espresso_namelist.keys import ld1_keys
+
         # I removed the "test" key from ld1_keys, because it was causing the following error:
         # Error: reading number of pseudo wavefunctions (nwfs)
         ld1_keys.pop("test")
@@ -22,38 +24,11 @@ def write_input(self, profile, directory, atoms, parameters, properties):
         super().write_input(profile, directory, atoms, parameters, properties)
 
     def read_results(self, directory):
-        path = directory / "ld1.ld1o"
-        with open(path, "r") as f:
-            energy_data = parse_energy_totals(f.read())
-
-        return {"ld1": energy_data}
-
-
+        from .parsers.ld1 import Ld1Parser
 
-def parse_energy_totals(text):
-    # Pattern to find Etot and Etotps lines and capture relevant parts
-    etot_pattern = r"Etot\s+=\s+([-\d\.]+)\s+Ry,\s+([-\d\.]+)\s+Ha,\s+([-\d\.]+)\s+eV"
-    etotps_pattern = r"Etotps\s+=\s+([-\d\.]+)\s+Ry,\s+([-\d\.]+)\s+Ha,\s+([-\d\.]+)\s+eV"
-
-    # Search for patterns and extract values
-    etot_match = re.search(etot_pattern, text)
-    etotps_match = re.search(etotps_pattern, text)
-
-    # Structured data
-    energy_data = {}
-
-    if etot_match:
-        energy_data['Etot'] = {
-            'Ry': float(etot_match.group(1)),
-            'Ha': float(etot_match.group(2)),
-            'eV': float(etot_match.group(3))
-        }
-
-    if etotps_match:
-        energy_data['Etotps'] = {
-            'Ry': float(etotps_match.group(1)),
-            'Ha': float(etotps_match.group(2)),
-            'eV': float(etotps_match.group(3))
-        }
-
-    return energy_data
+        parser = Ld1Parser(directory, self.outputname)
+        exit_code = parser.parse()
+        results = parser.results
+        results["exit_code"] = exit_code
+        print("results", results)
+        return results

src/ase_quantumespresso/parsers/__init__.py

@@ -1,5 +1,6 @@
 from .pw import PwParser
 from .dos import DosParser
 from .projwfc import ProjwfcParser
+from .ld1 import Ld1Parser
 
-__all__ = [PwParser, DosParser, ProjwfcParser]
+__all__ = [PwParser, DosParser, ProjwfcParser, Ld1Parser]

src/ase_quantumespresso/parsers/dos.py

@@ -4,7 +4,6 @@
 Modified from aiida-quantumespresso.parsers.dos.DosParser.
 """
 
-# from aiida_quantumespresso.calculations.pw import PwCalculation
 from aiida_quantumespresso.utils.mapping import get_logging_container
 from .exit_code import DosExitCodes
 from .base import BaseParser

src/ase_quantumespresso/parsers/exit_code.py

@@ -120,7 +120,7 @@ class PwExitCodes:
 
 
 @dataclass(frozen=True)
-class NamelistsCalculation:
+class NamelistsExitCodes:
     ERROR_OUTPUT_STDOUT_MISSING: ExitCode = ExitCode(
         302, "The folder did not contain the required stdout output file."
     )
@@ -139,14 +139,14 @@ class NamelistsCalculation:
 
 
 @dataclass(frozen=True)
-class DosExitCodes(NamelistsCalculation):
+class DosExitCodes(NamelistsExitCodes):
     ERROR_OUTPUT_STDOUT_MISSING: ExitCode = ExitCode(
         302, "The folder did not contain the required stdout output file."
     )
 
 
 @dataclass(frozen=True)
-class ProjwfcExitCodes(NamelistsCalculation):
+class ProjwfcExitCodes(NamelistsExitCodes):
     ERROR_NO_RETRIEVED_TEMPORARY_FOLDER: ExitCode = ExitCode(
         301, "The retrieved temporary folder could not be accessed."
     )

src/ase_quantumespresso/parsers/ld1.py

@@ -0,0 +1,80 @@
+# -*- coding: utf-8 -*-
+"""`Parser` implementation for the `ld1.x` code of Quantum ESPRESSO.
+
+"""
+
+from aiida_quantumespresso.utils.mapping import get_logging_container
+from .exit_code import NamelistsExitCodes
+from .base import BaseParser
+import re
+
+
+class Ld1Parser(BaseParser):
+    """`Parser` implementation for the `dos.x` calculation, modified from aiida-quantumespresso."""
+
+    success_string = "End of pseudopotential test"
+
+    def __init__(self, directory, outputname):
+        """Initialize the instance of `PwParser`."""
+        super().__init__(directory, output_filename=outputname)
+        self.outputname = outputname
+        self.exit_codes = NamelistsExitCodes()
+
+    def parse(self, **kwargs):
+        """Parse the retrieved files of a ``DosCalculation`` into output nodes."""
+
+        logs = get_logging_container()
+
+        _, parsed_stdout, logs = self.parse_stdout_from_retrieved(logs)
+
+        base_exit_code = self.check_base_errors(logs)
+        if base_exit_code:
+            return self.exit(base_exit_code, logs)
+
+        self.out("output_parameters", parsed_stdout)
+
+        if "ERROR_OUTPUT_STDOUT_INCOMPLETE" in logs.error:
+            return self.exit(self.exit_codes.ERROR_OUTPUT_STDOUT_INCOMPLETE, logs)
+
+        # Parse the Energy
+        filepath_dos = self.directory / self.outputname
+        try:
+            with open(filepath_dos, "r") as handle:
+                text = handle.read()
+                energy_data = parse_energy_totals(text)
+                self.out("ld1", energy_data)
+        except OSError:
+            return self.exit(self.exit_codes.ERROR_READING_DOS_FILE, logs)
+
+        return self.exit(logs=logs)
+
+
+def parse_energy_totals(text):
+    # Pattern to find Etot and Etotps lines and capture relevant parts
+    etot_pattern = r"Etot\s+=\s+([-\d\.]+)\s+Ry,\s+([-\d\.]+)\s+Ha,\s+([-\d\.]+)\s+eV"
+    etotps_pattern = (
+        r"Etotps\s+=\s+([-\d\.]+)\s+Ry,\s+([-\d\.]+)\s+Ha,\s+([-\d\.]+)\s+eV"
+    )
+
+    # Search for patterns and extract values
+    etot_match = re.search(etot_pattern, text)
+    etotps_match = re.search(etotps_pattern, text)
+
+    # Structured data
+    energy_data = {}
+
+    if etot_match:
+        energy_data["Etot"] = {
+            "Ry": float(etot_match.group(1)),
+            "Ha": float(etot_match.group(2)),
+            "eV": float(etot_match.group(3)),
+        }
+
+    if etotps_match:
+        energy_data["Etotps"] = {
+            "Ry": float(etotps_match.group(1)),
+            "Ha": float(etotps_match.group(2)),
+            "eV": float(etotps_match.group(3)),
+        }
+
+    return energy_data

src/ase_quantumespresso/parsers/projwfc.py

@@ -122,7 +122,6 @@ def parse(self, **kwargs):
         Dos_out["y"] = {"arrays": dos, "labels": "Dos", "units": "states/eV"}
         self.out("dos", Dos_out)
 
-        print("results: ", self.results.keys())
         return self.exit(logs=logs)
 
     def _parse_xml(self, retrieved_temporary_folder):

src/ase_quantumespresso/projwfc.py

@@ -20,5 +20,4 @@ def read_results(self, directory):
         exit_code = parser.parse()
         results = parser.results
         results["exit_code"] = exit_code
-        print("results: ", results.keys())
         return results

tests/test_ld1.py

@@ -0,0 +1,50 @@
+from ase_quantumespresso.espresso import Espresso, EspressoProfile
+from ase_quantumespresso.ld1 import Ld1Template
+
+input_data = {
+    "input": {
+        "title": "Pt",
+        "zed": 78.0,
+        "rel": 1,
+        "config": "[Xe] 4f13 6s1 6p0 5d9",
+        "iswitch": 3,
+        "dft": "PBE",
+    },
+    "inputp": {
+        "lpaw": True,
+        "use_xsd": False,
+        "pseudotype": 3,
+        "file_pseudopw": "Pt.star4f.pbe-n-kjpaw_psl.1.0.0.UPF",
+        "author": "Test",
+        "lloc": -1,
+        "rcloc": 2.4,
+        "which_augfun": "PSQ",
+        "rmatch_augfun_nc": True,
+        "nlcc": True,
+        "new_core_ps": True,
+        "rcore": 1.8,
+        "tm": True,
+    },
+}
+pseudo_potential_test_cards = """
+6
+6S  1  0  1.00  0.00  2.00  2.20  0.0
+6S  1  0  0.00  4.40  2.00  2.20  0.0
+6P  2  1  0.00  0.00  2.30  2.50  0.0
+6P  2  1  0.00  6.40  2.30  2.50  0.0
+5D  3  2  9.00  0.00  1.00  2.20  0.0
+5D  3  2  0.00  0.80  1.00  2.20  0.0
+"""
+
+
+def test_base_ld1():
+    profile = EspressoProfile(command="ld1.x", pseudo_dir=".")
+    calc = Espresso(
+        directory="calculatioin",
+        profile=profile,
+        template=Ld1Template(),
+        input_data=input_data,
+        pseudo_potential_test_cards=pseudo_potential_test_cards,
+    )
+    calc.get_property("ld1")
+    assert calc.results["exit_code"].status == 0

tests/test_pw.py

@@ -4,7 +4,7 @@
 def test_pw(bulk_si, pseudopotentials, pseudo_dir, pw_input_data):
     profile = EspressoProfile(command="pw.x", pseudo_dir=pseudo_dir)
     calc = Espresso(
-        directory="test",
+        directory="calculatioin",
         profile=profile,
         pseudopotentials=pseudopotentials,
         input_data=pw_input_data,