- save latest jupyter notebooks and function_nodes

.gitignore

@@ -9,3 +9,4 @@ _build/
 apidoc/
 .ipynb_checkpoints/
 test_times.dat
+.aider*

pyiron_workflow/node_library/atomistic/calculator/ase.py

@@ -1,7 +1,7 @@
-from pyiron_workflow.function import single_value_node, function_node
+from pyiron_workflow.function import function_node
 
 
-@single_value_node()
+@function_node()
 def static(atoms=None, engine=None, _internal=None, keys_to_store=None):
     from pyiron_workflow.node_library.atomistic.calculator.data import OutputCalcStatic
 

pyiron_workflow/node_library/atomistic/calculator/generic.py

@@ -1,4 +1,4 @@
-from pyiron_workflow.function import single_value_node
+from pyiron_workflow.function import function_node
 
 from pyiron_workflow.node_library.atomistic.calculator.data import (
     InputCalcMinimize,
@@ -7,7 +7,7 @@
 )
 
 
-@single_value_node("generic")
+@function_node("generic")
 def static(structure=None, engine=None):  # , keys_to_store=None):
     output = engine(
         structure=structure,

pyiron_workflow/node_library/atomistic/engine/ase.py

@@ -1,14 +1,14 @@
-from pyiron_workflow.function import single_value_node
+from pyiron_workflow.function import function_node
 
 
-@single_value_node("engine")
+@function_node("engine")
 def EMT():
     from ase.calculators.emt import EMT
 
     return EMT()
 
 
-@single_value_node("engine")
+@function_node("engine")
 def M3GNet():
     import matgl
     from matgl.ext.ase import M3GNetCalculator

pyiron_workflow/node_library/atomistic/engine/lammps.py

@@ -5,7 +5,7 @@
 
 # from pyiron_atomistics.atomistics.structure.atoms import Atoms
 
-from pyiron_workflow.function import single_value_node, function_node
+from pyiron_workflow.function import function_node, function_node
 from pyiron_workflow.workflow import Workflow
 
 from pyiron_workflow.node_library.atomistic.calculator.data import (
@@ -20,53 +20,53 @@
 from pyiron_atomistics.lammps.control import LammpsControl
 
 
-@single_value_node("calculator")
+@function_node("calculator")
 def Calc(parameters):
     from pyiron_atomistics.lammps.control import LammpsControl
 
     calculator = LammpsControl()
 
     if isinstance(parameters, InputCalcMD):
         calculator.calc_md(**parameters)
-        calculator._mode = "md"
+        calculator.mode = "md"
     elif isinstance(parameters, InputCalcMinimize):
         calculator.calc_minimize(**parameters)
-        calculator._mode = "minimize"
+        calculator.mode = "minimize"
     elif isinstance(parameters, InputCalcStatic):
         calculator.calc_static(**parameters)
-        calculator._mode = "static"
+        calculator.mode = "static"
     else:
         raise TypeError(f"Unexpected parameters type {parameters}")
 
     return calculator
 
 
-@single_value_node("calculator")
+@function_node("calculator")
 def CalcStatic(calculator_input: Optional[InputCalcStatic | dict] = None):
     calculator_kwargs = parse_input_kwargs(calculator_input, InputCalcStatic)
     calculator = LammpsControl()
     calculator.calc_static(**calculator_kwargs)
-    calculator._mode = "static"
+    calculator.mode = "static"
 
     return calculator
 
 
-@single_value_node("calculator")
+@function_node("calculator")
 def CalcMinimize(calculator_input: Optional[InputCalcMinimize | dict] = None):
     calculator_kwargs = parse_input_kwargs(calculator_input, InputCalcMinimize)
     calculator = LammpsControl()
     calculator.calc_minimize(**calculator_kwargs)
-    calculator._mode = "static"
+    calculator.mode = "static"
 
     return calculator
 
 
-@single_value_node("calculator")
+@function_node("calculator")
 def CalcMD(calculator_input: Optional[InputCalcMD | dict] = None):
     calculator_kwargs = parse_input_kwargs(calculator_input, InputCalcMD)
     calculator = LammpsControl()
     calculator.calc_md(**calculator_kwargs)
-    calculator._mode = "md"
+    calculator.mode = "md"
 
     return calculator
 
@@ -89,13 +89,13 @@ def InitLammps(structure=None, potential=None, calculator=None, working_director
 
     calculator.write_file(file_name="control.inp", cwd=working_directory)
     bla = "bla"
-    # print("Lammps_init: ", calculator._mode, bla)
+    # print("Lammps_init: ", calculator.mode, bla)
 
-    # return os.path.abspath(working_directory), calculator._mode, bla
+    # return os.path.abspath(working_directory), calculator.mode, bla
     return os.path.abspath(working_directory), bla
 
 
-@single_value_node("log")
+@function_node("log")
 def ParseLogFile(log_file):
     from pymatgen.io.lammps.outputs import parse_lammps_log
 
@@ -107,7 +107,7 @@ def ParseLogFile(log_file):
     return log
 
 
-@single_value_node("dump")
+@function_node("dump")
 def ParseDumpFile(dump_file):
     from pymatgen.io.lammps.outputs import parse_lammps_dumps
 
@@ -171,7 +171,7 @@ class GenericOutput:
     forces = []
 
 
-@single_value_node()
+@function_node()
 def Collect(
     out_dump,
     out_log,
@@ -194,7 +194,7 @@ def Collect(
     elif isinstance(calc_mode, (InputCalcMinimize, InputCalcMD, InputCalcStatic)):
         calc_mode = calc_mode.__class__.__name__.replace("InputCalc", "").lower()
     elif isinstance(calc_mode, LammpsControl):
-        calc_mode = calc_mode._mode
+        calc_mode = calc_mode.mode
     else:
         raise ValueError(f"Unexpected calc_mode {calc_mode}")
 
@@ -217,7 +217,7 @@ def Collect(
     return generic
 
 
-@single_value_node("potential")
+@function_node("potential")
 def Potential(structure, name=None, index=0):
     from pyiron_atomistics.lammps.potential import list_potentials as lp
 
@@ -232,7 +232,7 @@ def Potential(structure, name=None, index=0):
     return pot
 
 
-@single_value_node("potentials")
+@function_node("potentials")
 def ListPotentials(structure):
     from pyiron_atomistics.lammps.potential import list_potentials as lp
 

pyiron_workflow/node_library/atomistic/property/elastic.py

@@ -1,6 +1,6 @@
 import numpy as np
 
-from pyiron_workflow.function import single_value_node
+from pyiron_workflow.function import function_node
 from pyiron_workflow.node_library.dev_tools import wf_data_class
 from dataclasses import field
 
@@ -39,7 +39,7 @@ class DataStructureContainer:
     stress: list = field(default_factory=lambda: [])
 
 
-@single_value_node()
+@function_node()
 def elastic_constants(structure, calculator=None, engine=None):
     structure_table = generate_structures(structure).run()
 
@@ -63,7 +63,7 @@ def elastic_constants(structure, calculator=None, engine=None):
     return elastic
 
 
-@single_value_node()
+@function_node()
 def symmetry_analysis(structure, parameters: InputElasticTensor = InputElasticTensor()):
     out = OutputElasticSymmetryAnalysis(structure)
 
@@ -78,7 +78,7 @@ def symmetry_analysis(structure, parameters: InputElasticTensor = InputElasticTe
     return out
 
 
-@single_value_node("structures")
+@function_node("structures")
 def generate_structures(
     structure, parameters: InputElasticTensor = InputElasticTensor()
 ):
@@ -168,7 +168,7 @@ class OutputElasticAnalysis:
     C_eigval: np.ndarray = field(default_factory=lambda: np.zeros(0))
 
 
-@single_value_node("structures")
+@function_node("structures")
 def analyse_structures(
     data_df: DataStructureContainer,
     parameters: InputElasticTensor = InputElasticTensor(),

pyiron_workflow/node_library/atomistic/property/phonons.py

@@ -2,7 +2,7 @@
 
 
 # from pyiron_workflow.macro import Macro, macro_node
-from pyiron_workflow.function import single_value_node, function_node
+from pyiron_workflow.function import function_node, function_node
 from pyiron_workflow.node_library.dev_tools import wf_data_class, parse_input_kwargs
 
 
@@ -22,7 +22,7 @@ class InputPhonopyGenerateSupercells:
     max_distance: Optional[float] = None
 
 
-# @single_value_node()
+# @function_node()
 def generate_supercells(phonopy, parameters: InputPhonopyGenerateSupercells):
     from structuretoolkit.common import phonopy_to_atoms
 
@@ -32,7 +32,7 @@ def generate_supercells(phonopy, parameters: InputPhonopyGenerateSupercells):
     return supercells
 
 
-@single_value_node("parameters")
+@function_node("parameters")
 def PhonopyParameters(
     distance: float = 0.01,
     is_plusminus: Union[str, bool] = "auto",
@@ -89,7 +89,7 @@ def create_phonopy(
     return phonopy, out
 
 
-@single_value_node()
+@function_node()
 def get_dynamical_matrix(phonopy, q=[0, 0, 0]):
     import numpy as np
 
@@ -101,15 +101,15 @@ def get_dynamical_matrix(phonopy, q=[0, 0, 0]):
     return dynamical_matrix
 
 
-@single_value_node()
+@function_node()
 def get_eigenvalues(matrix):
     import numpy as np
 
     ew = np.linalg.eigvalsh(matrix)
     return ew
 
 
-@single_value_node()
+@function_node()
 def check_consistency(phonopy, tolerance: float = 1e-10):
     dyn_matrix = get_dynamical_matrix(phonopy).run()
     ew = get_eigenvalues(dyn_matrix).run()
@@ -123,7 +123,7 @@ def check_consistency(phonopy, tolerance: float = 1e-10):
     return has_imaginary_modes
 
 
-@single_value_node()
+@function_node()
 def get_total_dos(phonopy, mesh=3 * [10]):
     from pandas import DataFrame
 

pyiron_workflow/node_library/atomistic/structure/build.py

@@ -1,8 +1,8 @@
-from pyiron_workflow.function import single_value_node
+from pyiron_workflow.function import function_node
 from pyiron_workflow.workflow import Workflow
 
 
-@single_value_node("structure")
+@function_node("structure")
 def bulk(
     name,
     crystalstructure=None,
@@ -36,11 +36,11 @@ def cubic_bulk_cell(
         repeat,
     )
 
-    wf.structure = bulk(name=element, cubic=True)
-    wf.cell = repeat(structure=wf.structure, repeat_scalar=cell_size)
+    wf.bulk = bulk(name=element, cubic=True)
+    wf.cell = repeat(structure=wf.bulk, repeat_scalar=cell_size)
 
-    wf.cell_with_vacancies = create_vacancy(structure=wf.cell, index=vacancy_index)
-    return wf.cell_with_vacancies  # .outputs.structure
+    wf.structure = create_vacancy(structure=wf.cell, index=vacancy_index)
+    return wf.structure  # .outputs.structure
 
 
 nodes = [bulk, cubic_bulk_cell]

pyiron_workflow/node_library/atomistic/structure/calc.py

@@ -1,12 +1,12 @@
-from pyiron_workflow.function import single_value_node
+from pyiron_workflow.function import function_node
 from typing import Optional, Union
 
 # Huge savings when replacing pyiron_atomistics atoms class with ase one!! (> 5s vs 40 ms)
 # from pyiron_atomistics.atomistics.structure.atoms import Atoms
 from ase import Atoms
 
 
-@single_value_node("structure")
+@function_node("structure")
 def volume(structure: Optional[Atoms] = None) -> float:
     return structure.get_volume()
 

pyiron_workflow/node_library/atomistic/structure/transform.py

@@ -1,17 +1,17 @@
-from pyiron_workflow.function import single_value_node
+from pyiron_workflow.function import function_node
 from typing import Optional, Union
 
 # Huge savings when replacing pyiron_atomistics atoms class with ase one!! (> 5s vs 40 ms)
 # from pyiron_atomistics.atomistics.structure.atoms import Atoms
 from ase import Atoms
 
 
-@single_value_node("structure")
+@function_node("structure")
 def repeat(structure: Atoms, repeat_scalar: int = 1) -> Atoms:
     return structure.repeat(repeat_scalar)
 
 
-@single_value_node("structure")
+@function_node("structure")
 def apply_strain(
     structure: Optional[Atoms] = None, strain: Union[float, int] = 0
 ) -> Optional[Atoms]:
@@ -22,7 +22,7 @@ def apply_strain(
     return struct
 
 
-@single_value_node()
+@function_node()
 def create_vacancy(structure, index: int | None = 0):
     structure = structure.copy()
     if index is not None:
@@ -31,7 +31,7 @@ def create_vacancy(structure, index: int | None = 0):
     return structure
 
 
-@single_value_node("structure")
+@function_node("structure")
 def rotate_axis_angle(
     structure: Atoms,
     angle: float | int = 0,

pyiron_workflow/node_library/atomistic_codes.py

@@ -43,7 +43,7 @@ def Lammps(wf, structure=Atoms(), potential=None):
     wf.Collect = wf.create.atomistic.engine.lammps.Collect(
         out_dump=wf.ParseDumpFile.outputs.dump,
         out_log=wf.ParseLogFile.outputs.log,
-        calc_mode=wf.calc._mode,  # SVN gives output -> inject attribute getter node
+        calc_mode=wf.calc.mode,  # SVN gives output -> inject attribute getter node
     )
 
     return wf.Collect

pyiron_workflow/node_library/databases/elasticity.py

@@ -1,8 +1,8 @@
-from pyiron_workflow.function import single_value_node
+from pyiron_workflow.function import function_node
 from typing import Optional
 
 
-@single_value_node("dataframe")
+@function_node("dataframe")
 def de_jong(max_index: int | None = None, filename="ec.json"):
     """
     Expects the file to be the "ec.json" database referenced by: