Merge pull request #38 from alchem0x2A/master

Allow choosing API versions in SparcBundle and SPARC calculator

.github/workflows/installation_test.yml

@@ -46,6 +46,7 @@ jobs:
         # python -m pytest -svv tests/ --cov=sparc --cov-report=json --cov-report=html
         export SPARC_TESTS_DIR="./SPARC-master/tests"
         export ASE_SPARC_COMMAND="mpirun -n 1 sparc"
+        export SPARC_DOC_PATH="./SPARC-master/doc"
         coverage run -a -m pytest -svv tests/
         coverage json --omit="tests/*.py"
         coverage html --omit="tests/*.py"

sparc/api.py

@@ -14,6 +14,7 @@
 class SparcAPI:
     def __init__(self, json_api=None):
         """Initialize the API from a json file"""
+        # TODO: like ase io, adapt to both file and fio
         if json_api is None:
             json_api = Path(default_json_api)
         else:

sparc/calculator.py

@@ -10,7 +10,7 @@
 
 from .api import SparcAPI
 from .io import SparcBundle
-from .utils import _find_default_sparc, deprecated, h2gpts
+from .utils import _find_default_sparc, deprecated, h2gpts, locate_api
 
 # Below are a list of ASE-compatible calculator input parameters that are
 # in Angstrom/eV units
@@ -24,7 +24,6 @@
     "nbands",
 ]
 
-
 defaultAPI = SparcAPI()
 
 
@@ -54,6 +53,8 @@ def __init__(
         command=None,
         psp_dir=None,
         log="sparc.log",
+        sparc_json_file=None,
+        sparc_doc_path=None,
         **kwargs,
     ):
         # Initialize the calculator but without restart.
@@ -73,12 +74,14 @@ def __init__(
         if label is None:
             label = "SPARC" if restart is None else None
 
+        self.validator = locate_api(json_file=sparc_json_file, doc_path=sparc_doc_path)
         self.sparc_bundle = SparcBundle(
             directory=Path(self.directory),
             mode="w",
             atoms=self.atoms,
             label=label,
             psp_dir=psp_dir,
+            validator=self.validator,
         )
 
         # Try restarting from an old calculation and set results
@@ -432,14 +435,15 @@ def get_fermi_level(self):
 
     def _detect_sparc_version(self):
         """Run a short sparc test to determine which sparc is used"""
-        # TODO: complete the implementation
+        command = self._make_command()
+
         return None
 
     def _sanitize_kwargs(self, kwargs):
         """Convert known parameters from"""
         # print(kwargs)
         # TODO: versioned validator
-        validator = defaultAPI
+        validator = self.validator
         valid_params = {}
         special_params = self.default_params.copy()
         # TODO: how about overwriting the default parameters?
@@ -469,7 +473,7 @@ def _convert_special_params(self, atoms=None):
         h <--> gpts <--> FD_GRID, only when None of FD_GRID / ECUT or MESH_SPACING is provided
         """
         converted_sparc_params = {}
-        validator = defaultAPI
+        validator = self.validator
         params = self.special_params.copy()
 
         # xc --> EXCHANGE_CORRELATION

sparc/docparser.py

@@ -290,6 +290,7 @@ def to_dict(self):
     @classmethod
     def json_from_directory(cls, directory=".", include_subdirs=True, **kwargs):
         """Recursively add parameters from all Manual files"""
+        directory = Path(directory)
         root_dict = cls(directory=directory, **kwargs).to_dict()
         if include_subdirs:
             for sub_manual_tex in directory.glob("*/Manual*.tex"):

sparc/io.py

@@ -16,21 +16,22 @@
 from ase.calculators.singlepoint import SinglePointDFTCalculator
 from ase.units import GPa, Hartree
 
+# various io formatters
+from .api import SparcAPI
 from .common import psp_dir as default_psp_dir
 from .download_data import is_psp_download_complete
 from .sparc_parsers.aimd import _read_aimd
 from .sparc_parsers.atoms import atoms_to_dict, dict_to_atoms
 from .sparc_parsers.geopt import _read_geopt
 from .sparc_parsers.inpt import _read_inpt, _write_inpt
-
-# various io formatters
 from .sparc_parsers.ion import _read_ion, _write_ion
 from .sparc_parsers.out import _read_out
 from .sparc_parsers.pseudopotential import copy_psp_file, parse_psp8_header
 from .sparc_parsers.static import _read_static
-from .utils import deprecated, string2index
+from .utils import deprecated, string2index, locate_api
 
 # from .sparc_parsers.ion import read_ion, write_ion
+defaultAPI = SparcAPI()
 
 
 class SparcBundle:
@@ -67,6 +68,7 @@ def __init__(
         atoms=None,
         label=None,
         psp_dir=None,
+        validator=defaultAPI,
     ):
         self.directory = Path(directory)
         self.mode = mode.lower()
@@ -85,6 +87,7 @@ def __init__(
         # Sorting should be consistent across the whole bundle!
         self.sorting = None
         self.last_image = -1
+        self.validator = validator
 
     def _find_files(self):
         """Find all files matching '{label}.*'"""
@@ -187,8 +190,8 @@ def _read_ion_and_inpt(self):
         This method should be rarely used
         """
         f_ion, f_inpt = self._indir(".ion"), self._indir(".inpt")
-        ion_data = _read_ion(f_ion)
-        inpt_data = _read_inpt(f_inpt)
+        ion_data = _read_ion(f_ion, validator=self.validator)
+        inpt_data = _read_inpt(f_inpt, validator=self.validator)
         merged_data = {**ion_data, **inpt_data}
         return dict_to_atoms(merged_data)
 
@@ -254,8 +257,8 @@ def _write_ion_and_inpt(
                     target_fname = copy_psp_file(origin_psp, target_dir)
                     block["PSEUDO_POT"] = target_fname
 
-        _write_ion(self._indir(".ion"), data_dict)
-        _write_inpt(self._indir(".inpt"), data_dict)
+        _write_ion(self._indir(".ion"), data_dict, validator=self.validator)
+        _write_inpt(self._indir(".inpt"), data_dict, validator=self.validator)
         return
 
     def read_raw_results(self, include_all_files=False):
@@ -673,7 +676,9 @@ def read_sparc(filename, index=-1, include_all_files=False, **kwargs):
     with embedded calculator result.
 
     """
-    sb = SparcBundle(directory=filename)
+    # We rely on minimal api version choose, i.e. default or set from env
+    api = locate_api()
+    sb = SparcBundle(directory=filename, validator=api)
     atoms_or_images = sb.convert_to_ase(
         index=index, include_all_files=include_all_files, **kwargs
     )
@@ -690,7 +695,8 @@ def write_sparc(filename, images, **kwargs):
         if len(images) > 1:
             raise ValueError("SPARC format only supports writing one atoms object!")
         atoms = images[0]
-    sb = SparcBundle(directory=filename, mode="w")
+    api = locate_api()
+    sb = SparcBundle(directory=filename, mode="w", validator=api)
     sb._write_ion_and_inpt(atoms, **kwargs)
     return
 
@@ -704,8 +710,9 @@ def read_ion(filename, **kwargs):
 
     The returned Atoms object of read_ion method only contains the initial positions
     """
+    api = locate_api()
     parent_dir = Path(filename).parent
-    sb = SparcBundle(directory=parent_dir)
+    sb = SparcBundle(directory=parent_dir, validator=api)
     atoms = sb._read_ion_and_inpt()
     return atoms
 
@@ -720,7 +727,8 @@ def write_ion(filename, atoms, **kwargs):
     """
     label = Path(filename).with_suffix("").name
     parent_dir = Path(filename).parent
-    sb = SparcBundle(directory=parent_dir, label=label, mode="w")
+    api = locate_api()
+    sb = SparcBundle(directory=parent_dir, label=label, mode="w", validator=api)
     sb._write_ion_and_inpt(atoms, **kwargs)
     return atoms
 
@@ -730,7 +738,8 @@ def read_static(filename, index=-1, **kwargs):
     The reader works only when other files (.ion, .inpt) exist.
     """
     parent_dir = Path(filename).parent
-    sb = SparcBundle(directory=parent_dir)
+    api = locate_api()
+    sb = SparcBundle(directory=parent_dir, validator=api)
     atoms_or_images = sb.convert_to_ase(index=index, **kwargs)
     return atoms_or_images
 
@@ -740,7 +749,8 @@ def read_geopt(filename, index=-1, **kwargs):
     The reader works only when other files (.ion, .inpt) exist.
     """
     parent_dir = Path(filename).parent
-    sb = SparcBundle(directory=parent_dir)
+    api = locate_api()
+    sb = SparcBundle(directory=parent_dir, validator=api)
     atoms_or_images = sb.convert_to_ase(index=index, **kwargs)
     return atoms_or_images
 
@@ -750,7 +760,8 @@ def read_aimd(filename, index=-1, **kwargs):
     The reader works only when other files (.ion, .inpt) exist.
     """
     parent_dir = Path(filename).parent
-    sb = SparcBundle(directory=parent_dir)
+    api = locate_api()
+    sb = SparcBundle(directory=parent_dir, validator=api)
     atoms_or_images = sb.convert_to_ase(index=index, **kwargs)
     return atoms_or_images