Created a new unified flow module for RSS.

autoplex/auto/rss/rss_default_configuration.yaml

@@ -0,0 +1,152 @@
+# General Parameters
+tag: 'Si'
+train_from_scratch: true
+resume_from_previous_state:
+  test_error:
+  pre_database_dir:
+  mlip_path:
+  isolated_atom_energies:
+
+# Buildcell Parameters
+generated_struct_numbers:
+  - 8000
+  - 2000
+buildcell_options:
+  - NFORM: '{2,4,6,8}'
+    SYMMOPS: '1-4'
+    MINSEP: '1.5 Ti-Ti=2.5-2.8 Ti-O=1.3-1.6 O-O=1.9-2.2'
+  - NFORM: '{3,5,7}'
+    SYMMOPS: '1-4'
+    MINSEP: '1.5 Ti-Ti=2.5-2.8 Ti-O=1.3-1.6 O-O=1.9-2.2'
+fragment_file: null
+fragment_numbers: null
+num_processes_buildcell: 128
+
+# Sampling Parameters
+num_of_initial_selected_structs:
+  - 80
+  - 20
+num_of_rss_selected_structs: 100
+initial_selection_enabled: true
+rss_selection_method: 'bcur2i'
+bcur_params:
+  soap_paras:
+    l_max: 12
+    n_max: 12
+    atom_sigma: 0.0875
+    cutoff: 10.5
+    cutoff_transition_width: 1.0
+    zeta: 4.0
+    average: true
+    species: true
+  frac_of_bcur: 0.8
+  bolt_max_num: 3000
+random_seed: null
+
+# DFT Labelling Parameters
+include_isolated_atom: true
+isolatedatom_box:
+  - 20.0
+  - 20.0
+  - 20.0
+e0_spin: false
+include_dimer: true
+dimer_box:
+  - 20.0
+  - 20.0
+  - 20.0
+dimer_range:
+  - 1.0
+  - 5.0
+dimer_num: 41
+custom_incar:
+  ISMEAR: 0
+  SIGMA: 0.05
+  PREC: 'Accurate'
+  ADDGRID: '.TRUE.'
+  EDIFF: 1e-7
+  NELM: 250
+  LWAVE: '.FALSE.'
+  LCHARG: '.FALSE.'
+  ALGO: 'Normal'
+  AMIX: null
+  LREAL: '.FALSE.'
+  ISYM: 0
+  ENCUT: 520.0
+  KSPACING: 0.20
+  GGA: 'PS'
+  KPAR: 8
+  NCORE: 16
+  LSCALAPACK: '.FALSE.'
+  LPLANE: '.FALSE.'
+custom_potcar:
+  Ti: 'Ti'
+vasp_ref_file: 'vasp_ref.extxyz'
+
+# Data Preprocessing Parameters
+config_types:
+  - 'initial'
+  - 'traj_early'
+  - 'traj'
+rss_group:
+  - 'traj'
+test_ratio: 0.1
+regularization: false
+scheme: 'linear-hull'
+reg_minmax:
+  - [0.1, 1]
+  - [0.001, 0.1]
+  - [0.0316, 0.316]
+  - [0.0632, 0.632]
+distillation: false
+force_max: null
+force_label: null
+pre_database_dir: null
+
+# MLIP Parameters
+mlip_type: 'GAP'
+ref_energy_name: 'REF_energy'
+ref_force_name: 'REF_forces'
+ref_virial_name: 'REF_virial'
+auto_delta: true
+num_processes_fit: 32
+device_for_fitting: 'cpu'
+fit_kwargs:
+  twob:
+    cutoff: 5.0
+    n_sparse: 15
+    theta_uniform: 1.0
+  threeb:
+    cutoff: 3.0
+  soap:
+    l_max: 10
+    n_max: 10
+    atom_sigma: 0.5
+    n_sparse: 2500
+    cutoff: 5.0
+  general:
+    three_body: false
+
+# RSS Exploration Parameters
+scalar_pressure_method: 'uniform'
+scalar_exp_pressure: 100
+scalar_pressure_exponential_width: 0.2
+scalar_pressure_low: 0
+scalar_pressure_high: 50
+max_steps: 300
+force_tol: 0.01
+stress_tol: 0.01
+stop_criterion: 0.01
+max_iteration_number: 25
+num_groups: 6
+initial_kt: 0.3
+current_iter_index: 1
+hookean_repul: true
+hookean_paras:
+  '(8, 8)': [1000, 1.3]
+  '(8, 22)': [1000, 0.9]
+  '(22, 22)': [1000, 1.7]
+keep_symmetry: false
+write_traj: true
+num_processes_rss: 128
+device_for_rss: 'cpu'

autoplex/data/common/flows.py

@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-from dataclasses import dataclass
+from dataclasses import dataclass, field
 from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
@@ -237,7 +237,7 @@ def static_run_and_convert(
 
 
 @dataclass
-class DFTStaticMaker(Maker):
+class DFTStaticLabelling(Maker):
     """
     Maker to set up and run VASP static calculations for input structures, including bulk, isolated atoms, and dimers.
 
@@ -247,66 +247,78 @@ class DFTStaticMaker(Maker):
     ----------
     name: str
         Name of the flow.
-    isolated_atom : bool, optional
-        Whether to perform calculations for isolated atoms. Default is False.
-    isolated_species : list[str], optional
+    isolated_atom: bool
+        If true, perform single-point calculations for isolated atoms. Default is False.
+    isolated_species: list[str]
         List of species for which to perform isolated atom calculations. If None,
         species will be automatically derived from the 'structures' list. Default is None.
-    e0_spin : bool, optional
-        Whether to include spin polarization in isolated atom and dimer calculations.
+    e0_spin: bool
+        If true, include spin polarization in isolated atom and dimer calculations.
         Default is False.
-    dimer : bool, optional
-        Whether to perform calculations for dimers. Default is False.
-    dimer_species : list[str], optional
+    isolatedatom_box: list[float]
+        List of the lattice constants for a isolated_atom configuration.
+    dimer: bool
+        If true, perform single-point calculations for dimers. Default is False.
+    dimer_box: list[float]
+        The lattice constants of a dimer box.
+    dimer_species: list[str]
         List of species for which to perform dimer calculations. If None, species
         will be derived from the 'structures' list. Default is None.
-    dimer_range : list[float], optional
-        Range of distances for dimer calculations. Default is [0.8, 4.8].
-    dimer_num : int, optional
-        Number of different distances to consider for dimer calculations. Default is 22.
-    custom_set : dict, optional
+    dimer_range: list[float]
+        Range of distances for dimer calculations.
+    dimer_num: int
+        Number of different distances to consider for dimer calculations.
+    custom_incar: dict
         Dictionary of custom VASP input parameters. If provided, will update the
         default parameters. Default is None.
+    custom_potcar: dict
+        Dictionary of POTCAR settings to update. Keys are element symbols, values are the desired POTCAR labels.
+        Default is None.
 
     Returns
     -------
-    Response
-        A Response object containing the VASP jobs and the directories where
-        the calculations were set up.
-
+    dict
+        A dictionary containing:
+        - 'dirs_of_vasp': List of directories containing VASP data.
+        - 'config_type': List of configuration types corresponding to each directory.
     """
 
-    name: str = "DFT single-point calculations"
+    name: str = "do_dft_labelling"
     isolated_atom: bool = False
     isolated_species: list[str] | None = None
     e0_spin: bool = False
+    isolatedatom_box: list[float] = field(default_factory=lambda: [20, 20, 20])
     dimer: bool = False
+    dimer_box: list[float] = field(default_factory=lambda: [20, 20, 20])
     dimer_species: list[str] | None = None
     dimer_range: list[float] | None = None
     dimer_num: int = 21
-    custom_set: dict | None = None
+    custom_incar: dict | None = None
+    custom_potcar: dict | None = None
 
     @job
     def make(
         self,
-        structures: list[Structure],
-        config_types: list[str] | None = None,
+        structures: list,
+        config_type: str | None = None,
     ):
         """
         Maker to set up and run VASP static calculations.
 
         Parameters
         ----------
-        structures : list[Structure], optional
+        structures : list[Structure] | list[list[Structure]]
             List of structures for which to run the VASP static calculations. If None,
             no bulk calculations will be performed. Default is None.
-        config_types : list[str], optional
-            List of configuration types corresponding to the structures. If provided,
-            should have the same length as the 'structures' list. If None, defaults
+        config_type : str
+            Configuration types corresponding to the structures. If None, defaults
             to 'bulk'. Default is None.
         """
         job_list = []
 
+        if isinstance(structures[0], list):
+            structures = flatten(structures, recursive=False)
+
         dirs: dict[str, list[str]] = {"dirs_of_vasp": [], "config_type": []}
 
         default_custom_set = {
@@ -336,8 +348,8 @@ def make(
             "AMIN": None,
         }
 
-        if self.custom_set is not None:
-            default_custom_set.update(self.custom_set)
+        if self.custom_incar is not None:
+            default_custom_set.update(self.custom_incar)
 
         custom_set = default_custom_set
 
@@ -358,13 +370,16 @@ def make(
             run_vasp_kwargs={"handlers": custom_handlers},
         )
 
+        if self.custom_potcar is not None:
+            st_m = update_user_potcar_settings(st_m, potcar_updates=self.custom_potcar)
+
         if structures:
             for idx, struct in enumerate(structures):
                 static_job = st_m.make(structure=struct)
                 static_job.name = f"static_bulk_{idx}"
                 dirs["dirs_of_vasp"].append(static_job.output.dir_name)
-                if config_types:
-                    dirs["config_type"].append(config_types[idx])
+                if config_type:
+                    dirs["config_type"].append(config_type)
                 else:
                     dirs["config_type"].append("bulk")
                 job_list.append(static_job)
@@ -380,12 +395,18 @@ def make(
                     syms = ElementCollection(atoms).get_species()
 
                 for idx, sym in enumerate(syms):
-                    lattice = Lattice.orthorhombic(20.0, 20.5, 21.0)
+                    lattice = Lattice.orthorhombic(
+                        self.isolatedatom_box[0],
+                        self.isolatedatom_box[1],
+                        self.isolatedatom_box[2],
+                    )
                     isolated_atom_struct = Structure(lattice, [sym], [[0.0, 0.0, 0.0]])
                     static_job = st_m.make(structure=isolated_atom_struct)
                     static_job.name = f"static_isolated_{idx}"
                     static_job = update_user_incar_settings(
-                        static_job, {"KSPACING": 2.0}
+                        # static_job, {"KSPACING": 100.0, "ALGO": "All", "KPAR": 1, "NBANDS": 20}
+                        static_job,
+                        {"KSPACING": 100.0, "ALGO": "All", "KPAR": 1},
                     )
 
                     if self.e0_spin:
@@ -419,7 +440,11 @@ def make(
                                 self.dimer_num - 1 + 0.000000000001
                             )
 
-                        lattice = Lattice.orthorhombic(15.0, 15.5, 16.0)
+                        lattice = Lattice.orthorhombic(
+                            self.dimer_box[0],
+                            self.dimer_box[1],
+                            self.dimer_box[2],
+                        )
                         dimer_struct = Structure(
                             lattice,
                             [pair[0], pair[1]],
@@ -430,7 +455,9 @@ def make(
                         static_job = st_m.make(structure=dimer_struct)
                         static_job.name = f"static_dimer_{dimer_i}"
                         static_job = update_user_incar_settings(
-                            static_job, {"KSPACING": 2.0}
+                            # static_job, {"KSPACING": 100.0, "ALGO": "All", "KPAR": 1, "NBANDS": 20}
+                            static_job,
+                            {"KSPACING": 100.0, "ALGO": "All", "KPAR": 1},
                         )
 
                         if self.e0_spin: