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lammps/tools/i-pi/ipi/tests/test_contraction.py
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test_contraction.py
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"""Tests ring polymer contraction.
Copyright (C) 2013, Joshua More and Michele Ceriotti
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http.//www.gnu.org/licenses/>.
"""
import sys
sys.path.append("../")
sys.path.append("../../")
from ipi.utils import nmtransform
import numpy as np
from numpy.testing import assert_almost_equal as assert_equals
def check_up_and_down_scaling(n, q):
"""Check if q expanding and then contracting a ring polymer is a no-op.
Args:
n: The number of beads in the scaled ring polymer.
q: The original position array.
"""
rescale = nmtransform.nm_rescale(q.shape[0], n)
print "Initial position of the beads:"
print q, q.shape, (q.shape[0], n)
# rescale up to the n beads
beads_n = rescale.b1tob2(q)
print "Upscaled to %d beads:"%n
print beads_n, beads_n.shape
beads_final = rescale.b2tob1(beads_n)
print "Final position of the beads:"
print beads_final
assert_equals(q, beads_final)
return beads_n
def check_rpc_consistency(n, q):
"""Check if q expanding and then contracting a ring polymer is a no-op.
Args:
n: The number of beads in the scaled ring polymer.
q: The original position array.
"""
rescale1 = nmtransform.nm_rescale(q.shape[0], n)
rescale2 = nmtransform.nm_rescale(n,q.shape[0])
beads_n=rescale1.b1tob2(q)
beads_1=rescale1.b2tob1(beads_n)
beads_2=rescale2.b1tob2(beads_n)
assert_equals(beads_1, beads_2)
def check_centroid_pos(n, q):
"""Check if expanding and then contracting a ring polymer
maintains the centroid.
Args:
n: The number of beads in the scaled ring polymer.
q: The original position array.
"""
beads_big = check_up_and_down_scaling(n, q)
rescale_big = nmtransform.mk_rs_matrix(n, 1)
rescale_q = nmtransform.mk_rs_matrix(q.shape[0], 1)
centroid_big = np.dot(rescale_big, beads_big)
centroid_q = np.dot(rescale_q, q)
assert_equals(centroid_q, centroid_big)
numbers_to_check = range(10, 56, 9)
def test_1_to_n():
"""One bead tests."""
for n in numbers_to_check:
q = np.array([[0.0,0.0,0.0, 1.0,0.0,0.0]])
yield check_up_and_down_scaling, n, q
yield check_rpc_consistency, n, q
yield check_centroid_pos, n, q
def test_2_to_n():
"""Two bead tests."""
for n in numbers_to_check:
q = np.array([[0.0,0.0,0.0, 1.0,0.0,0.0],
[0.0,0.1,0.0, 1.0,0.1,0.0]])
yield check_up_and_down_scaling, n, q
yield check_rpc_consistency, n, q
yield check_centroid_pos, n, q
def test_3_to_n():
"""Three bead tests."""
for n in numbers_to_check:
q = np.array([[0.0, 0.0,0.0, 1.0, 0.0,0.0],
[0.0, 0.1,0.0, 1.0, 0.1,0.0],
[0.0,-0.1,0.0, 1.0,-0.1,0.0]])
yield check_up_and_down_scaling, n, q
yield check_rpc_consistency, n, q
yield check_centroid_pos, n, q
def test_4_to_n():
"""Four bead tests."""
for n in numbers_to_check:
q = np.array([[0.0, 0.0,0.0, 1.0, 0.0,0.0],
[0.0, 0.1,0.0, 1.0, 0.1,0.0],
[0.0, 0.2,0.0, 1.0, 0.2,0.0],
[0.0,-0.1,0.0, 1.0,-0.1,0.0]])
yield check_up_and_down_scaling, n, q
yield check_rpc_consistency, n, q
yield check_centroid_pos, n, q
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