def setUp(self):
from pele.optimize import mylbfgs
self.natoms = 10
self.coords = np.random.uniform(-1, 1., 3 * self.natoms) * self.natoms ** (-1. / 3)
self.pot = LJ()
ret = mylbfgs(self.coords, self.pot, tol=2.)
self.coords = ret.coords
self.E = self.pot.getEnergy(self.coords)
self.Egrad, self.grad = self.pot.getEnergyGradient(self.coords)
def test_LJ(natoms=12, **kwargs): # pragma: no cover
from pele.potentials.lj import LJ
from pele.optimize import mylbfgs
import pele.utils.rotations as rot
from pele.mindist.permutational_alignment import permuteArray
import random
quench = mylbfgs
lj = LJ()
X1 = np.random.uniform(-1, 1, [natoms * 3]) * (float(natoms))**(1. / 3)
# quench X1
ret = quench(X1, lj)
X1 = ret.coords
X2 = np.random.uniform(-1, 1, [natoms * 3]) * (float(natoms))**(1. / 3)
# make X2 a rotation of X1
print("testing with", natoms,
"atoms, with X2 a rotated and permuted isomer of X1")
aa = rot.random_aa()
rot_mx = rot.aa2mx(aa)
for j in range(natoms):
i = 3 * j
X2[i:i + 3] = np.dot(rot_mx, X1[i:i + 3])
perm = list(range(natoms))
random.shuffle(perm)
print(perm)
X2 = permuteArray(X2, perm)
import copy
X1i = copy.copy(X1)
X2i = copy.copy(X2)
print("******************************")
print("testing normal LJ ISOMER")
print("******************************")
test(X1, X2, lj, **kwargs)
print("******************************")
print("testing normal LJ non isomer")
print("******************************")
X2 = np.random.uniform(-1, 1, [natoms * 3]) * (float(natoms))**(1. / 3)
ret = quench(X2, lj)
X2 = ret.coords
Y = X1.reshape([-1, 3])
Y += np.random.random(3)
X1[:] = Y.flatten()
test(X1, X2, lj, **kwargs)
distinit = np.linalg.norm(X1 - X2)
print("distinit", distinit)
def setUp(self):
self.natoms = 10
self.coords = np.random.uniform(-1, 1., 3 * self.natoms) * self.natoms ** (-1. / 3)
self.pot = LJ()
self.E = self.pot.getEnergy(self.coords)
self.Egrad, self.grad = self.pot.getEnergyGradient(self.coords)
self.ilist = [] # np.zeros([self.natoms*(self.natoms-1)/2, 2])
k = 0
for i in range(self.natoms):
for j in range(i):
k += 1
self.ilist.append([i, j])
self.ilist = np.array(self.ilist)
"""
an example for finding the minimum distance and best alignment
between two lennard jones clusters
"""
from __future__ import print_function
from builtins import range
import numpy as np
from pele.potentials.lj import LJ
from pele.optimize import lbfgs_py
from pele.mindist import MinPermDistAtomicCluster
pot = LJ()
natoms = 40
# get two random quenched structures to compare
coords1 = np.random.rand(natoms * 3) * natoms ** (1. / 3) * 1.5
coords2 = np.random.rand(natoms * 3) * natoms ** (1. / 3) * 1.5
ret1 = lbfgs_py(coords1, pot)
ret2 = lbfgs_py(coords2, pot)
coords1 = ret1.coords
coords2 = ret2.coords
# all the atoms are permutable
permlist = [list(range(natoms))]
mindist = MinPermDistAtomicCluster(niter=100, permlist=permlist, verbose=False)
dist, newcoords1, newcoords2 = mindist(coords1, coords2)
print("")
