More flexible command configuration

src/koopmans/base.py

@@ -0,0 +1,12 @@
+"""Pydantic base model to use throughout `koopmans`."""
+
+from pydantic import BaseModel as _BaseModel
+from pydantic import ConfigDict
+
+
+class BaseModel(_BaseModel):
+    """Base model with a modified default configuration."""
+
+    model_config = ConfigDict(extra="forbid",
+                              arbitrary_types_allowed=True,
+                              validate_assignment=True)

src/koopmans/calculators/_calculator.py

@@ -68,6 +68,7 @@ class CalculatorExt(utils.HasDirectory):
     ext_in: str = ''
     ext_out: str = ''
     parent_process: Workflow | None
+    code: str = ''
 
     def __init__(self, parent_process=None, engine=None, skip_qc: bool = False, **kwargs: Any):
         super().__init__(parent_process=parent_process, engine=engine)
@@ -205,9 +206,6 @@ def _pre_calculate(self):
         if self.directory.exists():
             utils.remove(self.directory)
 
-        # By default, check the corresponding program is installed
-        self.check_code_is_installed()
-
         # Copy over all files linked to this calculation
         self._fetch_linked_files()
 
@@ -249,18 +247,6 @@ def read_input(self, input_file: Optional[Path] = None):
             self.atoms = calc.atoms
             self.atoms.calc = self
 
-    def check_code_is_installed(self):
-        """Check that the corresponding code is installed."""
-        if self.command.path == Path():
-            executable_with_path = utils.find_executable(self.command.executable)
-            if executable_with_path is None:
-                raise OSError(f'`{self.command.executable}` is not installed')
-            self.command.path = executable_with_path.parent
-        else:
-            if not (self.command.path / self.command.executable).is_file():
-                raise OSError(f'`{self.command.executable}` is not installed')
-        return
-
     def write_alphas(self):
         """Write the screening parameters to a file."""
         raise NotImplementedError(

src/koopmans/calculators/_koopmans_cp.py

@@ -4,7 +4,6 @@
 
 import copy
 import math
-import os
 import pickle
 import xml.etree.ElementTree as ET
 from pathlib import Path
@@ -18,7 +17,6 @@
 
 from koopmans import bands, pseudopotentials, settings, utils
 from koopmans.cell import cell_follows_qe_conventions, cell_to_parameters
-from koopmans.commands import ParallelCommand
 from koopmans.files import File
 
 from ._calculator import (CalculatorABC, CalculatorCanEnforceSpinSym,
@@ -82,6 +80,7 @@ class KoopmansCPCalculator(CalculatorCanEnforceSpinSym, CalculatorExt, Espresso_
 
     ext_in = '.cpi'
     ext_out = '.cpo'
+    code = 'kcp'
 
     def __init__(self, atoms: Atoms, alphas: Optional[List[List[float]]] = None,
                  filling: Optional[List[List[bool]]] = None, **kwargs):
@@ -104,9 +103,6 @@ def __init__(self, atoms: Atoms, alphas: Optional[List[List[float]]] = None,
             if 'neldw' not in self.parameters:
                 self.parameters.neldw = self.parameters.nelec // 2
 
-        if not isinstance(self.command, ParallelCommand):
-            self.command = ParallelCommand(os.environ.get('ASE_ESPRESSO_KCP_COMMAND', self.command))
-
         if alphas is not None:
             self.alphas = alphas
         if filling is not None:

src/koopmans/calculators/_koopmans_ham.py

@@ -8,7 +8,6 @@
 from ase_koopmans.dft.kpoints import BandPath
 
 from koopmans import settings, utils
-from koopmans.commands import ParallelCommand
 
 from ._calculator import CalculatorABC, KCWannCalculator, ReturnsBandStructure
 
@@ -18,6 +17,7 @@ class KoopmansHamCalculator(KCWannCalculator, KoopmansHam, ReturnsBandStructure,
 
     ext_in = '.khi'
     ext_out = '.kho'
+    code = "kcw_ham"
 
     def __init__(self, atoms: Atoms, alphas: Optional[List[float]] = None, *args, **kwargs):
         # Define the valid settings
@@ -27,8 +27,6 @@ def __init__(self, atoms: Atoms, alphas: Optional[List[float]] = None, *args, **
         KoopmansHam.__init__(self, atoms=atoms)
         KCWannCalculator.__init__(self, *args, **kwargs)
 
-        self.command = ParallelCommand(f'kcw.x -in PREFIX{self.ext_in} > PREFIX{self.ext_out} 2>&1')
-
         # Store the alphas
         self.alphas = alphas
 

src/koopmans/calculators/_koopmans_screen.py

@@ -5,7 +5,6 @@
 from ase_koopmans.calculators.espresso import KoopmansScreen
 
 from koopmans import settings, utils
-from koopmans.commands import ParallelCommandWithPostfix
 
 from ._calculator import CalculatorABC, KCWannCalculator
 
@@ -15,6 +14,7 @@ class KoopmansScreenCalculator(KCWannCalculator, KoopmansScreen, CalculatorABC):
 
     ext_in = '.ksi'
     ext_out = '.kso'
+    code = "kcw_screen"
 
     def __init__(self, atoms: Atoms, *args, **kwargs):
         # Define the valid settings
@@ -25,8 +25,6 @@ def __init__(self, atoms: Atoms, *args, **kwargs):
         KCWannCalculator.__init__(self, *args, **kwargs)
         super().__init__(*args, **kwargs)
 
-        self.command = ParallelCommandWithPostfix(f'kcw.x -in PREFIX{self.ext_in} > PREFIX{self.ext_out} 2>&1')
-
     def _pre_calculate(self):
         # Check eps infinity
         kpoints = [self.parameters.mp1, self.parameters.mp2, self.parameters.mp3]

src/koopmans/calculators/_ph.py

@@ -4,7 +4,6 @@
 from ase_koopmans import Atoms
 from ase_koopmans.calculators.espresso import EspressoPh
 
-from koopmans.commands import ParallelCommand
 from koopmans.settings import PhSettingsDict
 
 from ._calculator import CalculatorABC, CalculatorExt
@@ -15,6 +14,7 @@ class PhCalculator(CalculatorExt, EspressoPh, CalculatorABC):
 
     ext_in = '.phi'
     ext_out = '.pho'
+    code = "ph"
 
     def __init__(self, atoms: Atoms, *args, **kwargs):
         self.parameters = PhSettingsDict()
@@ -24,8 +24,6 @@ def __init__(self, atoms: Atoms, *args, **kwargs):
         EspressoPh.__init__(self, atoms=atoms)
         CalculatorExt.__init__(self, *args, **kwargs)
 
-        self.command = ParallelCommand(f'ph.x -in PREFIX{self.ext_in} > PREFIX{self.ext_out} 2>&1')
-
     def is_converged(self):
         """Return True; a ph calculation is never not "converged"."""
         return True

src/koopmans/calculators/_projwfc.py

@@ -1,7 +1,6 @@
 """projwfc.x calculator module for koopmans."""
 
 import copy
-import os
 import re
 from pathlib import Path
 from typing import Dict, List, Optional
@@ -14,7 +13,6 @@
 from upf_tools import UPFDict
 
 from koopmans import pseudopotentials
-from koopmans.commands import Command, ParallelCommand
 from koopmans.files import File
 from koopmans.settings import ProjwfcSettingsDict
 
@@ -26,6 +24,7 @@ class ProjwfcCalculator(CalculatorExt, Projwfc, CalculatorABC):
 
     ext_in = '.pri'
     ext_out = '.pro'
+    code = "projwfc"
 
     def __init__(self, atoms: Atoms, *args, **kwargs):
         # Define the valid settings
@@ -36,9 +35,6 @@ def __init__(self, atoms: Atoms, *args, **kwargs):
         Projwfc.__init__(self, atoms=atoms)
         CalculatorExt.__init__(self, *args, **kwargs)
 
-        if not isinstance(self.command, Command):
-            self.command = ParallelCommand(os.environ.get('ASE_PROJWFC_COMMAND', self.command))
-
         # We need pseudopotentials and pseudo dir in order to work out the number of valence electrons for each
         # element, and therefore what pDOS files to expect. We also need spin-polarized to know if the pDOS files will
         # contain columns for each spin channel

src/koopmans/calculators/_pw.py

@@ -1,14 +1,11 @@
 """pw calculator module for koopmans."""
 
-import os
-
 import numpy as np
 from ase_koopmans import Atoms
 from ase_koopmans.calculators.espresso import Espresso
 from ase_koopmans.dft.kpoints import BandPath
 
 from koopmans.cell import cell_follows_qe_conventions, cell_to_parameters
-from koopmans.commands import Command, ParallelCommandWithPostfix
 from koopmans.settings import PWSettingsDict
 
 from ._calculator import CalculatorABC, CalculatorExt, ReturnsBandStructure
@@ -19,6 +16,7 @@ class PWCalculator(CalculatorExt, Espresso, ReturnsBandStructure, CalculatorABC)
 
     ext_in = '.pwi'
     ext_out = '.pwo'
+    code = "pw"
 
     def __init__(self, atoms: Atoms, *args, **kwargs):
         # Define the valid settings
@@ -28,10 +26,6 @@ def __init__(self, atoms: Atoms, *args, **kwargs):
         Espresso.__init__(self, atoms=atoms)
         CalculatorExt.__init__(self, *args, **kwargs)
 
-        if not isinstance(self.command, Command):
-            self.command = ParallelCommandWithPostfix(os.environ.get(
-                'ASE_ESPRESSO_COMMAND', self.command))
-
     def _pre_calculate(self):
         # Update ibrav and celldms
         if cell_follows_qe_conventions(self.atoms.cell):

src/koopmans/calculators/_pw2wannier.py

@@ -1,11 +1,8 @@
 """pw2wannier calculator module for koopmans."""
 
-import os
-
 from ase_koopmans import Atoms
 from ase_koopmans.calculators.espresso import PW2Wannier
 
-from koopmans.commands import ParallelCommand
 from koopmans.settings import PW2WannierSettingsDict
 
 from ._calculator import CalculatorABC, CalculatorExt
@@ -16,6 +13,7 @@ class PW2WannierCalculator(CalculatorExt, PW2Wannier, CalculatorABC):
 
     ext_in = '.p2wi'
     ext_out = '.p2wo'
+    code = "pw2wannier90"
 
     def __init__(self, atoms: Atoms, *args, **kwargs):
         self.parameters = PW2WannierSettingsDict()
@@ -24,8 +22,6 @@ def __init__(self, atoms: Atoms, *args, **kwargs):
         PW2Wannier.__init__(self, atoms=atoms)
         CalculatorExt.__init__(self, *args, **kwargs)
 
-        self.command = ParallelCommand(os.environ.get('ASE_PW2WANNIER_COMMAND', self.command))
-
     def is_converged(self):
         """Return True; a PW2Wannier calculation is never not "converged"."""
         return True

src/koopmans/calculators/_wann2kc.py

@@ -3,7 +3,6 @@
 from ase_koopmans import Atoms
 from ase_koopmans.calculators.espresso import Wann2KC
 
-from koopmans.commands import ParallelCommandWithPostfix
 from koopmans.settings import Wann2KCSettingsDict
 
 from ._calculator import CalculatorABC, KCWannCalculator
@@ -14,6 +13,7 @@ class Wann2KCCalculator(KCWannCalculator, Wann2KC, CalculatorABC):
 
     ext_in = '.w2ki'
     ext_out = '.w2ko'
+    code = "kcw_wannier"
 
     def __init__(self, atoms: Atoms, *args, **kwargs):
         # Define the valid settings
@@ -23,8 +23,6 @@ def __init__(self, atoms: Atoms, *args, **kwargs):
         Wann2KC.__init__(self, atoms=atoms)
         KCWannCalculator.__init__(self, *args, **kwargs)
 
-        self.command = ParallelCommandWithPostfix(f'kcw.x -in PREFIX{self.ext_in} > PREFIX{self.ext_out} 2>&1')
-
     def is_converged(self):
         """Return True; a Wann2KC calculation is never not "converged"."""
         return True

src/koopmans/calculators/_wann2kcp.py

@@ -1,11 +1,8 @@
 """wann2kcp calculator module for koopmans."""
 
-import os
-
 from ase_koopmans import Atoms
 from ase_koopmans.calculators.espresso import Wann2KCP
 
-from koopmans.commands import ParallelCommand
 from koopmans.settings import Wann2KCPSettingsDict
 
 from ._calculator import CalculatorABC, CalculatorExt
@@ -16,6 +13,7 @@ class Wann2KCPCalculator(CalculatorExt, Wann2KCP, CalculatorABC):
 
     ext_in = '.wki'
     ext_out = '.wko'
+    code = "wann2kcp"
 
     def __init__(self, atoms: Atoms, *args, **kwargs):
         self.parameters = Wann2KCPSettingsDict()
@@ -24,8 +22,6 @@ def __init__(self, atoms: Atoms, *args, **kwargs):
         Wann2KCP.__init__(self, atoms=atoms)
         CalculatorExt.__init__(self, *args, **kwargs)
 
-        self.command = ParallelCommand(os.environ.get('ASE_WANN2KCP_COMMAND', self.command))
-
     def is_converged(self):
         """Return True; a Wann2KCP calculation is never not "converged"."""
         return True

src/koopmans/calculators/_wannier90.py

@@ -1,11 +1,8 @@
 """wannier90 calculator module for koopmans."""
 
-import os
-
 from ase_koopmans import Atoms
 from ase_koopmans.calculators.wannier90 import Wannier90
 
-from koopmans.commands import Command
 from koopmans.settings import Wannier90SettingsDict
 from koopmans.utils import CalculatorNotConvergedWarning, warn
 
@@ -17,6 +14,7 @@ class Wannier90Calculator(CalculatorExt, Wannier90, CalculatorABC):
 
     ext_in = '.win'
     ext_out = '.wout'
+    code = "wannier90"
 
     def __init__(self, atoms: Atoms, *args, **kwargs):
         # Define the list of parameters
@@ -26,9 +24,6 @@ def __init__(self, atoms: Atoms, *args, **kwargs):
         Wannier90.__init__(self, atoms=atoms)
         CalculatorExt.__init__(self, *args, **kwargs)
 
-        # Set up the command for running this calculator
-        self.command = Command(os.environ.get('ASE_WANNIER90_COMMAND', self.command))
-
     def is_converged(self):
         """Return True if the calculation is converged."""
         return self.results['convergence']