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awvwgk merged 2 commits into from
Apr 22, 2026
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Allow setting SCF parameters in ASE calculator #44

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Allow setting SCF parameters in ASE calculator
awvwgk Apr 18, 2026
54fa9c9
Minor changes
awvwgk Apr 19, 2026
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254 changes: 23 additions & 231 deletions docs/ase.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,19 +12,10 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"id": "81f0cb23",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/giulialuise/miniconda3/envs/skala/lib/python3.13/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
" from .autonotebook import tqdm as notebook_tqdm\n"
]
}
],
"outputs": [],
"source": [
"import numpy as np\n",
"from ase.build import molecule\n",
Expand All @@ -47,31 +38,17 @@
"- `basis`: Basis set for the calculation (e.g., \"def2-svp\", \"def2-tzvp\")\n",
"- `with_density_fit`: Enable density fitting for faster calculations\n",
"- `with_dftd3`: Include DFT-D3 dispersion correction (default: True)\n",
"- `verbose`: Control output verbosity (0-4)"
"- `verbose`: Control output verbosity (0-4)\n",
"- `with_retry`: Enable retry mechanism for SCF convergence (default: True)\n",
"- `ks_config`: Additional configuration options for the KS solver (e.g., convergence criteria)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": null,
"id": "37d38241",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Calculator parameters:\n",
" xc: skala\n",
" basis: def2-svp\n",
" with_density_fit: False\n",
" with_newton: False\n",
" with_dftd3: True\n",
" charge: None\n",
" multiplicity: None\n",
" verbose: 4\n"
]
}
],
"outputs": [],
"source": [
"# Create a water molecule\n",
"atoms = molecule(\"H2O\")\n",
Expand All @@ -97,120 +74,10 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": null,
"id": "3de5e444",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"System: uname_result(system='Linux', node='GCRAZGDL1498', release='6.8.0-1034-azure', version='#39~22.04.1-Ubuntu SMP Wed Aug 13 22:25:47 UTC 2025', machine='x86_64') Threads 24\n",
"Python 3.13.7 | packaged by conda-forge | (main, Sep 3 2025, 14:30:35) [GCC 14.3.0]\n",
"numpy 2.3.3 scipy 1.16.2 h5py 3.14.0\n",
"Date: Tue Oct 7 15:43:37 2025\n",
"PySCF version 2.9.0\n",
"PySCF path /home/giulialuise/miniconda3/envs/skala/lib/python3.13/site-packages/pyscf\n",
"\n",
"[CONFIG] conf_file None\n",
"[INPUT] verbose = 4\n",
"[INPUT] num. atoms = 3\n",
"[INPUT] num. electrons = 10\n",
"[INPUT] charge = 0\n",
"[INPUT] spin (= nelec alpha-beta = 2S) = 0\n",
"[INPUT] symmetry False subgroup None\n",
"[INPUT] Mole.unit = Angstrom\n",
"[INPUT] Symbol X Y Z unit X Y Z unit Magmom\n",
"[INPUT] 1 O 0.000000000000 0.000000000000 0.119262000000 AA 0.000000000000 0.000000000000 0.225372517068 Bohr 0.0\n",
"[INPUT] 2 H 0.000000000000 0.763239000000 -0.477047000000 AA 0.000000000000 1.442312677587 -0.901488178545 Bohr 0.0\n",
"[INPUT] 3 H 0.000000000000 -0.763239000000 -0.477047000000 AA 0.000000000000 -1.442312677587 -0.901488178545 Bohr 0.0\n",
"\n",
"nuclear repulsion = 9.08829376913928\n",
"number of shells = 12\n",
"number of NR pGTOs = 38\n",
"number of NR cGTOs = 24\n",
"basis = def2-svp\n",
"ecp = {}\n",
"CPU time: 1.87\n",
"/home/giulialuise/.cache/huggingface/hub/models--microsoft--skala/snapshots/9eedaca41deeaebe197bec77d1898f777770d3ef/skala-1.0.fun\n",
"Downloaded in 0.16 seconds\n",
"\n",
"\n",
"******** <class 'skala.pyscf.dft.SkalaRKS'> ********\n",
"method = SkalaRKS\n",
"initial guess = minao\n",
"damping factor = 0\n",
"level_shift factor = 0\n",
"DIIS = <class 'pyscf.scf.diis.CDIIS'>\n",
"diis_start_cycle = 1\n",
"diis_space = 8\n",
"diis_damp = 0\n",
"SCF conv_tol = 1e-09\n",
"SCF conv_tol_grad = None\n",
"SCF max_cycles = 50\n",
"direct_scf = True\n",
"direct_scf_tol = 1e-13\n",
"chkfile to save SCF result = /tmp/tmpcw83w2ua\n",
"max_memory 4000 MB (current use 736 MB)\n",
"XC library libxc version None\n",
" None\n",
"XC functionals = custom\n",
"radial grids: \n",
"Treutler-Ahlrichs [JCP 102, 346 (1995); DOI:10.1063/1.469408] (M4) radial grids\n",
"\n",
"becke partition: Becke, JCP 88, 2547 (1988); DOI:10.1063/1.454033\n",
"pruning grids: <function nwchem_prune at 0x764481e2b560>\n",
"grids dens level: 3\n",
"symmetrized grids: False\n",
"atomic radii adjust function: <function treutler_atomic_radii_adjust at 0x764476f1aca0>\n",
"small_rho_cutoff = 1e-07\n",
"Set gradient conv threshold to 3.16228e-05\n",
"Initial guess from minao.\n",
"tot grids = 33704\n",
"init E= -76.2302482032812\n",
" HOMO = -0.430502394424911 LUMO = -0.00557962018270088\n",
"cycle= 1 E= -76.1844346685567 delta_E= 0.0458 |g|= 0.818 |ddm|= 1.41\n",
" HOMO = -0.0571497729893296 LUMO = 0.092111968345332\n",
"cycle= 2 E= -75.9921484773828 delta_E= 0.192 |g|= 1.28 |ddm|= 1.4\n",
" HOMO = -0.266575634970147 LUMO = 0.0399392427556757\n",
"cycle= 3 E= -76.3081751739264 delta_E= -0.316 |g|= 0.0337 |ddm|= 0.956\n",
" HOMO = -0.25652282325852 LUMO = 0.0420512491571007\n",
"cycle= 4 E= -76.30841420647 delta_E= -0.000239 |g|= 0.0064 |ddm|= 0.0228\n",
" HOMO = -0.257181682273231 LUMO = 0.0406822667985362\n",
"cycle= 5 E= -76.3084203471352 delta_E= -6.14e-06 |g|= 0.00122 |ddm|= 0.00337\n",
" HOMO = -0.257376647610882 LUMO = 0.0405720409497939\n",
"cycle= 6 E= -76.3084205799498 delta_E= -2.33e-07 |g|= 3.1e-05 |ddm|= 0.000715\n",
" HOMO = -0.257386810929883 LUMO = 0.0405644826339652\n",
"cycle= 7 E= -76.3084206025217 delta_E= -2.26e-08 |g|= 3.89e-06 |ddm|= 3.08e-05\n",
" HOMO = -0.257387527784119 LUMO = 0.0405648211980371\n",
"cycle= 8 E= -76.3084205960069 delta_E= 6.51e-09 |g|= 3.05e-07 |ddm|= 3.24e-06\n",
" HOMO = -0.25738749260452 LUMO = 0.0405648168862294\n",
"cycle= 9 E= -76.3084206012037 delta_E= -5.2e-09 |g|= 3.17e-08 |ddm|= 2.17e-07\n",
" HOMO = -0.257387492441066 LUMO = 0.0405648161651567\n",
"cycle= 10 E= -76.3084206024703 delta_E= -1.27e-09 |g|= 2.04e-08 |ddm|= 1.73e-08\n",
" HOMO = -0.257387491334681 LUMO = 0.0405648167913778\n",
"cycle= 11 E= -76.3084206001009 delta_E= 2.37e-09 |g|= 1.44e-08 |ddm|= 7.84e-09\n",
" HOMO = -0.257387491019448 LUMO = 0.0405648174191108\n",
"cycle= 12 E= -76.3084205990203 delta_E= 1.08e-09 |g|= 1.38e-08 |ddm|= 4.07e-09\n",
" HOMO = -0.257387490637195 LUMO = 0.0405648176151493\n",
"cycle= 13 E= -76.3084206006191 delta_E= -1.6e-09 |g|= 2.06e-08 |ddm|= 7.24e-09\n",
" HOMO = -0.257387491245932 LUMO = 0.0405648173875793\n",
"cycle= 14 E= -76.3084206022113 delta_E= -1.59e-09 |g|= 1.76e-08 |ddm|= 4.61e-09\n",
" HOMO = -0.257387491753683 LUMO = 0.0405648174842908\n",
"cycle= 15 E= -76.3084205999321 delta_E= 2.28e-09 |g|= 2.05e-08 |ddm|= 4.88e-09\n",
" HOMO = -0.25738749162096 LUMO = 0.0405648180109603\n",
"cycle= 16 E= -76.3084206010219 delta_E= -1.09e-09 |g|= 1.75e-08 |ddm|= 3.15e-09\n",
" HOMO = -0.257387492013501 LUMO = 0.0405648177311237\n",
"cycle= 17 E= -76.3084206001081 delta_E= 9.14e-10 |g|= 1.46e-08 |ddm|= 3.2e-09\n",
" HOMO = -0.257387493925225 LUMO = 0.0405648195794535\n",
"Extra cycle E= -76.3084206016336 delta_E= -1.53e-09 |g|= 1.48e-08 |ddm|= 1.74e-08\n",
"converged SCF energy = -76.3084206016336\n",
"Dipole moment(X, Y, Z, Debye): -0.00000, 0.00000, -2.00440\n",
"Total energy: -2076.457890 eV\n",
"Total energy: -76.308421 Hartree\n"
]
}
],
"outputs": [],
"source": [
"# Calculate the total energy\n",
"energy_eV = atoms.get_potential_energy() # eV\n",
Expand All @@ -232,33 +99,15 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": null,
"id": "b2cc79b6",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{'with_density_fit': True, 'verbose': 0}\n",
"Changed parameters: {'with_density_fit': True, 'verbose': 0}\n",
"\n",
"Current calculator parameters:\n",
" xc: skala\n",
" basis: def2-svp\n",
" with_density_fit: True\n",
" with_newton: False\n",
" with_dftd3: True\n",
" charge: None\n",
" multiplicity: None\n",
" verbose: 0\n",
"<skala.ase.calculator.Skala object at 0x7643f91ae900>\n"
]
}
],
"outputs": [],
"source": [
"# Update calculator settings\n",
"changed_params = atoms.calc.set(with_density_fit=True, verbose=0)\n",
"changed_params = atoms.calc.set(\n",
" with_density_fit=True, verbose=0, ks_config={\"conv_tol\": 1e-6}\n",
")\n",
"print(changed_params)\n",
"print(f\"Changed parameters: {changed_params}\")\n",
"\n",
Expand All @@ -282,25 +131,10 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": null,
"id": "be609051",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"/home/giulialuise/.cache/huggingface/hub/models--microsoft--skala/snapshots/9eedaca41deeaebe197bec77d1898f777770d3ef/skala-1.0.fun\n",
"Downloaded in 0.10 seconds\n",
"Forces on atoms (eV/Å):\n",
" Atom 1 (O): [ 0.0000, 0.0000, -0.5867]\n",
" Atom 2 (H): [ -0.0000, -0.6148, 0.2933]\n",
" Atom 3 (H): [ 0.0000, 0.6148, 0.2933]\n",
"\n",
"Maximum force component: 0.6148 eV/Å\n"
]
}
],
"outputs": [],
"source": [
"# Calculate forces\n",
"forces = atoms.get_forces() # eV/Å\n",
Expand Down Expand Up @@ -328,27 +162,10 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": null,
"id": "cb74929f",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
" Step Time Energy fmax\n",
"LBFGSLineSearch: 0 15:43:56 -2076.458638 0.681230\n",
"LBFGSLineSearch: 1 15:44:02 -2076.466242 0.308524\n",
"LBFGSLineSearch: 2 15:44:13 -2076.467743 0.153213\n",
"LBFGSLineSearch: 3 15:44:26 -2076.468485 0.002282\n",
"Optimization completed in 3 steps\n",
"Initial energy: -2076.458638 eV\n",
"Final energy: -2076.468485 eV\n",
"Energy change: -0.009847 eV\n",
"Maximum final force: 0.0023 eV/Å\n"
]
}
],
"outputs": [],
"source": [
"# Store initial geometry for comparison\n",
"initial_positions = atoms.positions.copy()\n",
Expand Down Expand Up @@ -382,19 +199,10 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": null,
"id": "192bdbfa",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Dipole moment vector (Debye): [ -0.0000, 0.0000, -0.4200]\n",
"Dipole moment magnitude: 0.4200 Debye\n"
]
}
],
"outputs": [],
"source": [
"# Calculate dipole moment\n",
"dipole = atoms.get_dipole_moment() # Debye\n",
Expand All @@ -417,26 +225,10 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": null,
"id": "11a8bbd0",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Methane molecule:\n",
"Chemical formula: CH4\n",
"Number of atoms: 5\n",
"/home/giulialuise/.cache/huggingface/hub/models--microsoft--skala/snapshots/9eedaca41deeaebe197bec77d1898f777770d3ef/skala-1.0.fun\n",
"Downloaded in 0.11 seconds\n",
"\n",
"Calculation results:\n",
"Total energy: -1102.070344 eV\n",
"Maximum force: 0.351115 eV/Å\n"
]
}
],
"outputs": [],
"source": [
"# Create a methane molecule\n",
"atoms = molecule(\"CH4\")\n",
Expand Down Expand Up @@ -497,7 +289,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.13.7"
"version": "3.13.5"
}
},
"nbformat": 4,
Expand Down
14 changes: 13 additions & 1 deletion src/skala/ase/calculator.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@

from skala.functional.base import ExcFunctionalBase
from skala.pyscf import SkalaKS
from skala.pyscf.retry import retry_scf


class Skala(Calculator): # type: ignore[misc]
Expand Down Expand Up @@ -43,9 +44,11 @@ class Skala(Calculator): # type: ignore[misc]
"auxbasis": None,
"with_newton": False,
"with_dftd3": True,
"with_retry": True,
"charge": None,
"multiplicity": None,
"verbose": 0,
"ks_config": None,
}

_mol: gto.Mole | None = None
Expand All @@ -72,6 +75,10 @@ def set(self, **kwargs: Any) -> dict[str, Any]:
self._ks.verbose = verbose
self._ks.base.verbose = verbose

if "ks_config" in changed_parameters and self.parameters.ks_config is not None:
if self._ks is not None:
self._ks.base(**self.parameters.ks_config)

if (
"charge" in changed_parameters
or "multiplicity" in changed_parameters
Expand Down Expand Up @@ -165,12 +172,17 @@ def calculate(
auxbasis=self.parameters.auxbasis,
with_newton=bool(self.parameters.with_newton),
with_dftd3=bool(self.parameters.with_dftd3),
ks_config=self.parameters.ks_config,
).nuc_grad_method()
self._ks = grad_method
else:
self._ks.reset(self._mol)

energy = self._ks.base.kernel()
if self.parameters.with_retry:
self._ks.base, _ = retry_scf(self._ks.base)
energy = self._ks.base.e_tot
else:
energy = self._ks.base.kernel()
gradient = self._ks.kernel()

self.results["energy"] = float(energy) * Hartree
Expand Down
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