From c76c9b8c784e785f88711f90b678a94ff032b801 Mon Sep 17 00:00:00 2001
From: Michele Nottoli <michele.nottoli@gmail.com>
Date: Thu, 19 Oct 2023 17:00:11 +0200
Subject: [PATCH] Switched to descriptors.
---
grext/buffer.py | 2 +-
grext/descriptors.py | 12 ++++++++++++
grext/main.py | 13 ++++++++++---
3 files changed, 23 insertions(+), 4 deletions(-)
create mode 100644 grext/descriptors.py
diff --git a/grext/buffer.py b/grext/buffer.py
index f734505..c5ce6bc 100644
--- a/grext/buffer.py
+++ b/grext/buffer.py
@@ -8,7 +8,7 @@ class CircularBuffer:
"""Circular buffer to store the last `n` matrices."""
- def __init__(self, n: int, shape: Tuple[int, int]):
+ def __init__(self, n: int, shape: Tuple[int, ...]):
self.n = n
self.shape = shape
self.buffer = [np.zeros(shape, dtype=np.float64) for _ in range(n)]
diff --git a/grext/descriptors.py b/grext/descriptors.py
new file mode 100644
index 0000000..87fbd99
--- /dev/null
+++ b/grext/descriptors.py
@@ -0,0 +1,12 @@
+"""Module which provides functions to compute descriptors."""
+
+import numpy as np
+from scipy.spatial.distance import pdist
+
+def distance(coords: np.ndarray) -> np.ndarray:
+ """Compute the distance matric as a descriptor."""
+ return pdist(coords, metric="euclidean")
+
+def coulomb(coords: np.ndarray) -> np.ndarray:
+ """Compute the Coulomb matrix as a descriptor."""
+ return 1.0/distance(coords)
diff --git a/grext/main.py b/grext/main.py
index 25d9861..1bf9adc 100644
--- a/grext/main.py
+++ b/grext/main.py
@@ -5,6 +5,7 @@ import numpy as np
from . import grassmann
from . import fitting
+from . import descriptors
from .buffer import CircularBuffer
class Extrapolator:
@@ -25,7 +26,8 @@ class Extrapolator:
self.gammas = CircularBuffer(self.nsteps, (self.nelectrons, self.nbasis))
self.overlaps = CircularBuffer(self.nsteps, (self.nbasis, self.nbasis))
- self.coords = CircularBuffer(self.nsteps, (self.natoms, 3))
+ self.descriptors = CircularBuffer(self.nsteps,
+ ((self.natoms - 1)*self.natoms//2, ))
self.tangent: Optional[np.ndarray] = None
@@ -39,11 +41,12 @@ class Extrapolator:
self._set_tangent(coeff)
self.gammas.push(self._grassmann_log(coeff))
- self.coords.push(coords)
+ self.descriptors.push(self._compute_descriptor(coords))
self.overlaps.push(overlap)
def guess(self, coords: np.ndarray, overlap: Optional[np.ndarray]):
"""Get a new electronic density to be used as a guess."""
+ descriptor = self._compute_descriptor(coords)
coefficients = fitting.linear()
def _get_tangent(self) -> np.ndarray:
@@ -77,7 +80,11 @@ class Extrapolator:
tangent = self._get_tangent()
return grassmann.exp(gamma, tangent)
- def _sqrt_overlap(self, overlap):
+ def _sqrt_overlap(self, overlap) -> np.ndarray:
"""Compute the square root of the overlap matrix."""
q, s, vt = np.linalg.svd(overlap, full_matrices=False)
return q @ np.diag(np.sqrt(s)) @ vt
+
+ def _compute_descriptor(self, coords) -> np.ndarray:
+ """Given a set of coordinates compute the corresponding descriptor."""
+ return descriptors.distance(coords)
--
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