Customize oxygen pseudo supported (#234)

This change allow to pass oxygen pseudopotenital, if not provide, the
default oxygen pseudopotentieal will be used.

aiida_sssp_workflow/cli/run.py

@@ -32,6 +32,24 @@
 @options.OverridableOption(
     "--pw-code", "pw_code", type=types.CodeParamType(entry_point="quantumespresso.pw")
 )(required=True)
+@click.option(
+    "--oxygen-pseudo",
+    "oxygen_pseudo",
+    type=click.Path(exists=True),
+    help="Oxygen pseudo to use for oxides precision measure workflow.",
+)
+@click.option(
+    "--oxygen-ecutwfc",
+    "oxygen_ecutwfc",
+    type=click.FLOAT,
+    help="Oxygen ecutwfc to use for oxides precision measure workflow.",
+)
+@click.option(
+    "--oxygen-ecutrho",
+    "oxygen_ecutrho",
+    type=click.FLOAT,
+    help="Oxygen ecutrho to use for oxides precision measure workflow.",
+)
 @options.OverridableOption(
     "--pw-code-large-memory",
     "pw_code_large_memory",
@@ -115,6 +133,9 @@ def launch(
     walltime,
     num_mpiprocs,
     pseudo,
+    oxygen_pseudo,
+    oxygen_ecutwfc,
+    oxygen_ecutrho,
     clean_workdir,
     daemon,
     comment,
@@ -240,6 +261,19 @@ def launch(
     if pw_code_large_memory:
         inputs["pw_code_large_memory"] = pw_code_large_memory
 
+    if oxygen_pseudo:
+        if not (oxygen_ecutwfc and oxygen_ecutrho):
+            echo.echo_critical(
+                "oxygen_ecutwfc and oxygen_ecutrho must be provided if using custmized oxygen pseudo."
+            )
+
+        with open(oxygen_pseudo, "rb") as stream:
+            oxygen_pseudo = UpfData(stream)
+
+        inputs["measure"]["oxygen_pseudo"] = oxygen_pseudo
+        inputs["measure"]["oxygen_ecutwfc"] = orm.Float(oxygen_ecutwfc)
+        inputs["measure"]["oxygen_ecutrho"] = orm.Float(oxygen_ecutrho)
+
     if len(configuration) == 0:
         pass
     elif len(configuration) == 1:

aiida_sssp_workflow/workflows/measure/__init__.py

@@ -32,6 +32,9 @@ def define(cls, spec):
                     help='The `pw.x` code use for the `PwCalculation`.')
         spec.input('pseudo', valid_type=UpfData, required=True,
                     help='Pseudopotential to be verified')
+        spec.input('oxygen_pseudo', valid_type=UpfData, required=False)
+        spec.input('oxygen_ecutwfc', valid_type=orm.Float, required=False)
+        spec.input('oxygen_ecutrho', valid_type=orm.Float, required=False)
         spec.input('protocol', valid_type=orm.Str, required=True,
                     help='The protocol which define input calculation parameters.')
         spec.input('wavefunction_cutoff', valid_type=orm.Float, required=True, help='The wavefunction cutoff.')
@@ -48,10 +51,17 @@ def _get_pw_cutoff(
         """Get cutoff pair, if strcture contains oxygen or nitrogen, need
         to use the max between pseudo cutoff and the O/N cutoff.
         """
+        if "oxygen_pseudo" in self.inputs:
+            o_ecutwfc = self.inputs.oxygen_ecutwfc.value
+            o_ecutrho = self.inputs.oxygen_ecutrho.value
+        else:
+            o_ecutwfc = self._O_ECUTWFC
+            o_ecutrho = self._O_ECUTRHO
+
         elements = set(structure.get_symbols_set())
         if "O" in elements:
-            ecutwfc = max(ecutwfc, self._O_ECUTWFC)
-            ecutrho = max(ecutrho, self._O_ECUTRHO)
+            ecutwfc = max(ecutwfc, o_ecutwfc)
+            ecutrho = max(ecutrho, o_ecutrho)
 
         if "N" in elements:
             ecutwfc = max(ecutwfc, self._N_ECUTWFC)

aiida_sssp_workflow/workflows/measure/precision.py

@@ -83,7 +83,10 @@ def _setup_pseudo_and_configuration(self):
         # for the oxide, need to pseudo of oxygen,
         # the pseudo is the one select after the oxygen verification and
         # store in the `statics/upf/O.**.upf`
-        pseudo_O = get_pseudo_O()
+        if "oxygen_pseudo" in self.inputs:
+            pseudo_O = self.inputs.oxygen_pseudo
+        else:
+            pseudo_O = get_pseudo_O()
         self.ctx.pseudos_oxide = {
             self.ctx.element: self.inputs.pseudo,
             "O": pseudo_O,