From cd2750c164a5a9af33c74b9898cfbbf32724ce95 Mon Sep 17 00:00:00 2001
From: Joseph Weston <joseph@weston.cloud>
Date: Tue, 10 Sep 2019 13:31:18 +0200
Subject: [PATCH] add a deprecation warning to "hamiltonian" for vectorized
systems
Update internal uses of 'hamiltonian' to suppress this warning
and add a TODO to update to the new API.
---
kwant/builder.py | 7 +++++
kwant/operator.pyx | 11 ++++++--
kwant/tests/test_builder.py | 53 ++++++++++++++++++++++++++-----------
3 files changed, 54 insertions(+), 17 deletions(-)
diff --git a/kwant/builder.py b/kwant/builder.py
index 9a0bfcff..31019c34 100644
--- a/kwant/builder.py
+++ b/kwant/builder.py
@@ -2048,6 +2048,13 @@ class _VectorizedFinalizedBuilderMixin(_FinalizedBuilderMixin):
't' (< 0) then the associated hopping is stored in term '-t - 1'.
"""
def hamiltonian(self, i, j, *args, params=None):
+ warnings.warn(
+ "Querying individual matrix elements with 'hamiltonian' is "
+ "deprecated, and now takes O(log N) time where N is the number "
+ "of matrix elements per hamiltonian term. Query many matrix "
+ "elements at once using 'hamiltonian_term'.",
+ KwantDeprecationWarning
+ )
site_offsets = np.cumsum([0] + [len(s) for s in self.site_arrays])
if i == j:
which_term = self._onsite_term_by_site_id[i]
diff --git a/kwant/operator.pyx b/kwant/operator.pyx
index 8de1cad8..2a3e71ed 100644
--- a/kwant/operator.pyx
+++ b/kwant/operator.pyx
@@ -13,6 +13,7 @@ import cython
from operator import itemgetter
import functools as ft
import collections
+import warnings
import numpy as np
import tinyarray as ta
@@ -25,7 +26,9 @@ from .graph.core import DisabledFeatureError, NodeDoesNotExistError
from .graph.defs cimport gint
from .graph.defs import gint_dtype
from .system import is_infinite, Site
-from ._common import UserCodeError, get_parameters, deprecate_args
+from ._common import (
+ UserCodeError, KwantDeprecationWarning, get_parameters, deprecate_args
+)
################ Generic Utility functions
@@ -699,7 +702,11 @@ cdef class _LocalOperator:
return mat
offsets, norbs = _get_all_orbs(self.where, self._site_ranges)
- return BlockSparseMatrix(self.where, offsets, norbs, get_ham)
+ # TODO: update operators to use 'hamiltonian_term' rather than
+ # 'hamiltonian'.
+ with warnings.catch_warnings():
+ warnings.simplefilter("ignore", category=KwantDeprecationWarning)
+ return BlockSparseMatrix(self.where, offsets, norbs, get_ham)
def __getstate__(self):
return (
diff --git a/kwant/tests/test_builder.py b/kwant/tests/test_builder.py
index 575d0caf..253c9d7c 100644
--- a/kwant/tests/test_builder.py
+++ b/kwant/tests/test_builder.py
@@ -20,7 +20,7 @@ from numpy.testing import assert_almost_equal
import kwant
from kwant import builder, system
-from kwant._common import ensure_rng
+from kwant._common import ensure_rng, KwantDeprecationWarning
def test_bad_keys():
@@ -590,12 +590,16 @@ def test_hamiltonian_evaluation(vectorize):
for i in range(len(tags)):
site = fsyst.sites[i]
assert site in sites
- assert fsyst.hamiltonian(i, i) == f_onsite(site)
+ with warnings.catch_warnings():
+ warnings.filterwarnings("ignore", category=KwantDeprecationWarning)
+ assert fsyst.hamiltonian(i, i) == f_onsite(site)
for t, h in fsyst.graph:
tsite = fsyst.sites[t]
hsite = fsyst.sites[h]
- assert fsyst.hamiltonian(t, h) == f_hopping(tsite, hsite)
+ with warnings.catch_warnings():
+ warnings.filterwarnings("ignore", category=KwantDeprecationWarning)
+ assert fsyst.hamiltonian(t, h) == f_hopping(tsite, hsite)
# test when user-function raises errors
def onsite_raises(site):
@@ -608,13 +612,18 @@ def test_hamiltonian_evaluation(vectorize):
a, b = hop
# exceptions are converted to kwant.UserCodeError and we add our message
with raises(kwant.UserCodeError) as exc_info:
- fsyst.hamiltonian(a, a)
+ with warnings.catch_warnings():
+ warnings.filterwarnings("ignore", category=KwantDeprecationWarning)
+ fsyst.hamiltonian(a, a)
msg = 'Error occurred in user-supplied value function "onsite_raises"'
assert msg in str(exc_info.value)
for hop in [(a, b), (b, a)]:
with raises(kwant.UserCodeError) as exc_info:
- fsyst.hamiltonian(*hop)
+ with warnings.catch_warnings():
+ # Ignore deprecation warnings for 'hamiltonian'
+ warnings.filterwarnings("ignore", category=KwantDeprecationWarning)
+ fsyst.hamiltonian(*hop)
msg = ('Error occurred in user-supplied '
'value function "hopping_raises"')
assert msg in str(exc_info.value)
@@ -682,14 +691,18 @@ def test_vectorized_hamiltonian_evaluation():
for i in range(len(tags)):
site = fsyst_vectorized.sites[i]
assert site in sites
- assert (
- fsyst_vectorized.hamiltonian(i, i)
- == fsyst_simple.hamiltonian(i, i))
+ with warnings.catch_warnings():
+ warnings.filterwarnings("ignore", category=KwantDeprecationWarning)
+ assert (
+ fsyst_vectorized.hamiltonian(i, i)
+ == fsyst_simple.hamiltonian(i, i))
for t, h in fsyst_vectorized.graph:
- assert (
- fsyst_vectorized.hamiltonian(t, h)
- == fsyst_simple.hamiltonian(t, h))
+ with warnings.catch_warnings():
+ warnings.filterwarnings("ignore", category=KwantDeprecationWarning)
+ assert (
+ fsyst_vectorized.hamiltonian(t, h)
+ == fsyst_simple.hamiltonian(t, h))
# Test infinite system, including hoppings that go both ways into
# the next cell
@@ -1419,15 +1432,25 @@ def test_argument_passing(vectorize):
# test that mixing 'args' and 'params' raises TypeError
with raises(TypeError):
- syst.hamiltonian(0, 0, *(2, 1), params=dict(p1=2, p2=1))
+ with warnings.catch_warnings():
+ warnings.filterwarnings("ignore", category=KwantDeprecationWarning)
+ syst.hamiltonian(0, 0, *(2, 1), params=dict(p1=2, p2=1))
+
with raises(TypeError):
- inf_syst.hamiltonian(0, 0, *(2, 1), params=dict(p1=2, p2=1))
+ with warnings.catch_warnings():
+ warnings.filterwarnings("ignore", category=KwantDeprecationWarning)
+ inf_syst.hamiltonian(0, 0, *(2, 1), params=dict(p1=2, p2=1))
# Missing parameters raises TypeError
with raises(TypeError):
- syst.hamiltonian(0, 0, params=dict(p1=2))
+ with warnings.catch_warnings():
+ warnings.filterwarnings("ignore", category=KwantDeprecationWarning)
+ syst.hamiltonian(0, 0, params=dict(p1=2))
+
with raises(TypeError):
- syst.hamiltonian_submatrix(params=dict(p1=2))
+ with warnings.catch_warnings():
+ warnings.filterwarnings("ignore", category=KwantDeprecationWarning)
+ syst.hamiltonian_submatrix(params=dict(p1=2))
# test that passing parameters without default values works, and that
# passing parameters with default values fails
--
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