add locate_api method and explicitly use validator

sparc/api.py

@@ -14,7 +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
+        # 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/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 .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):

sparc/sparc_parsers/aimd.py

@@ -18,9 +18,6 @@
 from ..api import SparcAPI
 from .utils import strip_comments
 
-# TODO: should allow user to select the api
-defaultAPI = SparcAPI()
-
 
 @reader
 def _read_aimd(fileobj):

sparc/sparc_parsers/inpt.py

@@ -11,20 +11,20 @@
 
 
 @reader
-def _read_inpt(fileobj):
+def _read_inpt(fileobj, validator=defaultAPI):
     contents = fileobj.read()
     # label = get_label(fileobj, ".ion")
     data, comments = strip_comments(contents)
     # We do not read the cell at this time!
 
     # find the index for all atom type lines. They should be at the
     # top of their block
-    inpt_blocks = read_block_input(data, validator=defaultAPI)
+    inpt_blocks = read_block_input(data, validator=validator)
     return {"inpt": {"params": inpt_blocks, "comments": comments}}
 
 
 @writer
-def _write_inpt(fileobj, data_dict):
+def _write_inpt(fileobj, data_dict, validator=defaultAPI):
     if "inpt" not in data_dict:
         raise ValueError("Your dict does not contain inpt section!")
 
@@ -45,7 +45,7 @@ def _write_inpt(fileobj, data_dict):
     params = inpt_dict["params"]
     for key, val in params.items():
         # TODO: can we add a multiline argument?
-        val_string = defaultAPI.convert_value_to_string(key, val)
+        val_string = validator.convert_value_to_string(key, val)
         if (val_string.count("\n") > 0) or (
             key
             in [

sparc/sparc_parsers/ion.py

@@ -24,17 +24,17 @@
     strip_comments,
 )
 
-# TODO: should allow user to select the api
-defaultAPI = SparcAPI()
-
 
 class InvalidSortingComment(ValueError):
     def __init__(self, message):
         self.message = message
 
 
+defaultAPI = SparcAPI()
+
+
 @reader
-def _read_ion(fileobj):
+def _read_ion(fileobj, validator=defaultAPI):
     """
     Read information from the .ion file. Note, this method does not return an atoms object,
     but rather return a dict. Thus the label option is not necessary to keep
@@ -54,7 +54,7 @@ def _read_ion(fileobj):
     # find the index for all atom type lines. They should be at the top of their block
     atom_type_bounds = [i for i, x in enumerate(data) if "ATOM_TYPE" in x] + [len(data)]
     atom_blocks = [
-        read_block_input(data[start:end], validator=defaultAPI)
+        read_block_input(data[start:end], validator=validator)
         for start, end in zip(atom_type_bounds[:-1], atom_type_bounds[1:])
     ]
 
@@ -71,6 +71,7 @@ def _read_ion(fileobj):
 def _write_ion(
     fileobj,
     data_dict,
+    validator=defaultAPI,
 ):
     """
     Writes the ion file content from the atom_dict
@@ -133,7 +134,7 @@ def _write_ion(
             if val is None:
                 continue
 
-            val_string = defaultAPI.convert_value_to_string(key, val)
+            val_string = validator.convert_value_to_string(key, val)
             # print(val_string)
             # TODO: make sure 1 line is accepted
             # TODO: write pads to vector lines

sparc/utils.py

@@ -1,21 +1,19 @@
 """Utilities that are loosely related to core sparc functionalities
 """
-import os
 import io
-import tempfile
+import os
 import shutil
+import tempfile
 from pathlib import Path
 from typing import List, Optional, Union
 from warnings import warn
 
-
 import numpy as np
 
 from .api import SparcAPI
 from .docparser import SPARCDocParser
 
 
-
 def deprecated(message):
     def decorator(func):
         def new_func(*args, **kwargs):
@@ -127,6 +125,7 @@ def cprint(content, color=None, bold=False, underline=False, **kwargs):
     print(output, **kwargs)
     return
 
+
 def locate_api(json_file=None, doc_path=None):
     """Find the default api in the following order
     1) User-provided json file path
@@ -137,10 +136,10 @@ def locate_api(json_file=None, doc_path=None):
     if json_file is not None:
         api = SparcAPI(json_file)
         return api
-    
+
     if doc_path is None:
         doc_path = os.environ.get("SPARC_DOC_PATH", None)
-        
+
     if doc_path is not None:
         with tempfile.TemporaryDirectory() as tmpdir:
             tmpdir = Path(tmpdir)