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base: IPKM:c09549902a06f3241bafa2d6c7a61e2e9cf7b15f
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IPKM:mdeval_dev
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compare: IPKM:33c4756e34d75cd322ed50cb4d30cfac3088d9fa
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IPKM:mdeval_dev
IPKM:main

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src/mdevaluate/extra/free_energy_landscape.py
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@ -4,6 +4,7 @@ from typing import Optional
import numpy as np import numpy as np
from numpy.typing import ArrayLike, NDArray from numpy.typing import ArrayLike, NDArray
from numpy.polynomial.polynomial import Polynomial as Poly from numpy.polynomial.polynomial import Polynomial as Poly
import math
from scipy.spatial import KDTree from scipy.spatial import KDTree
import pandas as pd import pandas as pd
import multiprocessing as mp import multiprocessing as mp
@ -48,7 +49,7 @@ def _pbc_points_reduced(
def _build_tree(points, box, r_max, pore_geometry): def _build_tree(points, box, r_max, pore_geometry):
if np.all(np.diag(np.diag(box)) == box): if np.all(np.diag(np.diag(box)) == box):
tree = KDTree(points % box, boxsize=box) tree = KDTree(points, boxsize=box)
points_pbc_index = None points_pbc_index = None
else: else:
points_pbc, points_pbc_index = _pbc_points_reduced( points_pbc, points_pbc_index = _pbc_points_reduced(
@ -78,7 +79,8 @@ def occupation_matrix(
z_bins = np.arange(0, box[2][2] + edge_length, edge_length) z_bins = np.arange(0, box[2][2] + edge_length, edge_length)
bins = [x_bins, y_bins, z_bins] bins = [x_bins, y_bins, z_bins]
# Trajectory is split for parallel computing # Trajectory is split for parallel computing
indices = np.array_split(frame_indices, nodes) size = math.ceil(len(frame_indices) / nodes)
indices = [frame_indices[i : i + size] for i in range(0, len(frame_indices), size)]
pool = mp.Pool(nodes) pool = mp.Pool(nodes)
results = pool.map( results = pool.map(
partial(_calc_histogram, trajectory=trajectory, bins=bins), indices partial(_calc_histogram, trajectory=trajectory, bins=bins), indices
@ -272,11 +274,7 @@ def distance_resolved_energies(
def find_energy_maxima( def find_energy_maxima(
energy_df: pd.DataFrame, energy_df: pd.DataFrame, r_min: float, r_max: float
r_min: float,
r_max: float,
r_eval: float = None,
degree: int = 2,
) -> pd.DataFrame: ) -> pd.DataFrame:
distances = [] distances = []
energies = [] energies = []
@ -285,9 +283,6 @@ def find_energy_maxima(
x = np.array(data_d["r"]) x = np.array(data_d["r"])
y = np.array(data_d["energy"]) y = np.array(data_d["energy"])
mask = (x >= r_min) * (x <= r_max) mask = (x >= r_min) * (x <= r_max)
p3 = Poly.fit(x[mask], y[mask], deg=degree) p3 = Poly.fit(x[mask], y[mask], deg=2)
if r_eval is None: energies.append(np.max(p3(np.linspace(r_min, r_max, 1000))))
energies.append(np.max(p3(np.linspace(r_min, r_max, 1000))))
else:
energies.append(p3(r_eval))
return pd.DataFrame({"d": distances, "energy": energies}) return pd.DataFrame({"d": distances, "energy": energies})