From a748e52dacb2f85d5b4cdfd53af9ab7e97cddd66 Mon Sep 17 00:00:00 2001
From: Michele Nottoli <michele.nottoli@gmail.com>
Date: Fri, 3 Nov 2023 14:47:46 +0100
Subject: [PATCH] Options working.
---
gext/descriptors.py | 4 +-
gext/fitting.py | 77 +++++++++++++++++++++++++-------
gext/main.py | 28 ++++++++----
tests/test_descriptor_fitting.py | 10 +++--
4 files changed, 88 insertions(+), 31 deletions(-)
diff --git a/gext/descriptors.py b/gext/descriptors.py
index 1d6fe48..f1f6657 100644
--- a/gext/descriptors.py
+++ b/gext/descriptors.py
@@ -1,9 +1,9 @@
-"""Module which provides functions to compute descriptors."""
+"""Module which provides functionality to compute descriptors."""
import numpy as np
from scipy.spatial.distance import pdist
-class Distance():
+class Distance:
"""Distance matrix descriptors."""
diff --git a/gext/fitting.py b/gext/fitting.py
index 6dfd0de..3c6adb7 100644
--- a/gext/fitting.py
+++ b/gext/fitting.py
@@ -1,21 +1,66 @@
-"""Module that defines fitting functions."""
+"""Module which provides functionality to perform fitting."""
from typing import List
import numpy as np
+import abc
+
+class AbstractFitting(abc.ABC):
+
+ def __init__(self, **kwargs):
+ self.set_options(**kwargs)
+
+ @abc.abstractmethod
+ def set_options(self, **kwargs):
+ """Base method for setting options."""
+
+ @abc.abstractmethod
+ def compute(self, vectors: List[np.ndarray], target:np.ndarray):
+ """Base method for computing new fitting coefficients."""
+
+ def linear_combination(self, vectors: List[np.ndarray],
+ coefficients: np. ndarray) -> np.ndarray:
+ """Given a set of vectors (or matrices) and the corresponding
+ coefficients, build their linear combination."""
+ result = np.zeros(vectors[0].shape, dtype=np.float64)
+ for coeff, vector in zip(coefficients, vectors):
+ result += vector*coeff
+ return result
+
+class LeastSquare(AbstractFitting):
-def linear(vectors: List[np.ndarray], target: np.ndarray):
"""Simple least square minimization fitting."""
- matrix = np.vstack(vectors).T
- coefficients, _, _, _ = np.linalg.lstsq(matrix, target, rcond=None)
- return np.array(coefficients, dtype=np.float64)
-
-def quasi_time_reversible():
- """Time reversible least square minimization fitting."""
-
-def linear_combination(vectors: List[np.ndarray], coefficients: np.ndarray) -> np.ndarray:
- """Given a set of vectors (or matrices) and the corresponding
- coefficients, build their linear combination."""
- result = np.zeros(vectors[0].shape, dtype=np.float64)
- for coeff, vector in zip(coefficients, vectors):
- result += vector*coeff
- return result
+
+ supported_options = {
+ "regularization": 0.0,
+ }
+
+ def set_options(self, **kwargs):
+ self.options = {}
+ for key, value in kwargs.items():
+ if key in self.supported_options:
+ self.options[key] = value
+ else:
+ raise ValueError(f"Unsupported option: {key}")
+
+ for option, default_value in self.supported_options.items():
+ if not option in self.options:
+ self.options[option] = default_value
+
+ if self.options["regularization"] < 0 \
+ or self.options["regularization"] > 100:
+ raise ValueError("Unsupported value for regularization")
+
+ def compute(self, vectors: List[np.ndarray], target: np.ndarray):
+ """Given a set of vectors and a target return the fitting
+ coefficients."""
+ matrix = np.vstack(vectors).T
+ coefficients, _, _, _ = np.linalg.lstsq(matrix, target, rcond=None)
+ return np.array(coefficients, dtype=np.float64)
+
+class QuasiTimeReversible(AbstractFitting):
+
+ def set_options(**kwargs):
+ """TODO"""
+
+ def compute(self):
+ """Time reversible least square minimization fitting."""
diff --git a/gext/main.py b/gext/main.py
index b924b3b..c7aac97 100644
--- a/gext/main.py
+++ b/gext/main.py
@@ -4,7 +4,7 @@ from typing import Optional
import numpy as np
from . import grassmann
-from . import fitting
+from .fitting import LeastSquare, QuasiTimeReversible
from .descriptors import Distance, Coulomb
from .buffer import CircularBuffer
@@ -22,7 +22,7 @@ class Extrapolator:
"verbose": False,
"nsteps": 6,
"descriptor": "distance",
- "fitting": "linear",
+ "fitting": "leastsquare",
}
self.nelectrons = nelectrons
@@ -71,6 +71,14 @@ class Extrapolator:
raise ValueError("Unsupported descriptor")
self.descriptor_calculator.set_options(**descriptor_options)
+ if self.options["fitting"] == "leastsquare":
+ self.fitting_calculator = LeastSquare()
+ elif self.options["fitting"] == "qtr":
+ self.fitting_calculator = QuasiTimeReversible()
+ else:
+ raise ValueError("Unsupported descriptor")
+ self.fitting_calculator.set_options(**fitting_options)
+
def load_data(self, coords: np.ndarray, coeff: np.ndarray,
overlap: np.ndarray):
"""Load a new data point in the extrapolator."""
@@ -87,22 +95,24 @@ class Extrapolator:
def guess(self, coords: np.ndarray, overlap = None) -> np.ndarray:
"""Get a new electronic density to be used as a guess."""
- prev_descriptors = self.descriptors.get(self.options["nsteps"])
+ n = min(self.options["nsteps"], self.descriptors.count)
+
+ prev_descriptors = self.descriptors.get(n)
descriptor = self._compute_descriptor(coords)
- fit_coefficients = fitting.linear(prev_descriptors, descriptor)
+ fit_coefficients = self.fitting_calculator.compute(prev_descriptors, descriptor)
- gammas = self.gammas.get(self.options["nsteps"])
- gamma = fitting.linear_combination(gammas, fit_coefficients)
+ gammas = self.gammas.get(n)
+ gamma = self.fitting_calculator.linear_combination(gammas, fit_coefficients)
- fit_descriptor = fitting.linear_combination(prev_descriptors, fit_coefficients)
+ fit_descriptor = self.fitting_calculator.linear_combination(prev_descriptors, fit_coefficients)
if self.options["verbose"]:
print("error on descriptor:", \
np.linalg.norm(fit_descriptor - descriptor, ord=np.inf))
if overlap is None:
- overlaps = self.overlaps.get(self.options["nsteps"])
- overlap = fitting.linear_combination(overlaps, fit_coefficients)
+ overlaps = self.overlaps.get(n)
+ overlap = self.fitting_calculator.linear_combination(overlaps, fit_coefficients)
inverse_sqrt_overlap = self._inverse_sqrt_overlap(overlap)
else:
inverse_sqrt_overlap = self._inverse_sqrt_overlap(overlap)
diff --git a/tests/test_descriptor_fitting.py b/tests/test_descriptor_fitting.py
index 493a532..cc8c42b 100644
--- a/tests/test_descriptor_fitting.py
+++ b/tests/test_descriptor_fitting.py
@@ -35,10 +35,12 @@ def test_descriptor_fitting(datafile):
descriptors = extrapolator.descriptors.get(10)
target = descriptors[-1]
+ fitting_calculator = gext.fitting.LeastSquare()
+
for start in range(0, 9):
vectors = descriptors[start:-1]
- fit_coefficients = gext.fitting.linear(vectors, target)
- fitted_target = gext.fitting.linear_combination(vectors, fit_coefficients)
+ fit_coefficients = fitting_calculator.compute(vectors, target)
+ fitted_target = fitting_calculator.linear_combination(vectors, fit_coefficients)
errors.append(np.linalg.norm(target - fitted_target, ord=np.inf))
assert errors[0] < errors[-1]
@@ -47,7 +49,7 @@ def test_descriptor_fitting(datafile):
# used for the fitting
vectors = descriptors[:-1]
vectors[0] = target
- fit_coefficients = gext.fitting.linear(vectors, target)
- fitted_target = gext.fitting.linear_combination(vectors, fit_coefficients)
+ fit_coefficients = fitting_calculator.compute(vectors, target)
+ fitted_target = fitting_calculator.linear_combination(vectors, fit_coefficients)
assert np.linalg.norm(target - fitted_target, ord=np.inf) < SMALL
--
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