From 6467f81cc46dfbeeebe189be60dfd425fc8c1d21 Mon Sep 17 00:00:00 2001
From: Christoph Groth <christoph.groth@cea.fr>
Date: Wed, 22 May 2013 16:03:12 +0200
Subject: [PATCH] hamiltonian_submatrix: eliminate zeros in sparse matrices
---
kwant/_system.pyx | 52 +++++++++++++++++++++++++++++------------------
1 file changed, 32 insertions(+), 20 deletions(-)
diff --git a/kwant/_system.pyx b/kwant/_system.pyx
index d14f075b..9e4ea271 100644
--- a/kwant/_system.pyx
+++ b/kwant/_system.pyx
@@ -31,6 +31,7 @@ def make_sparse(ham, args, CGraph gr, diag,
cdef complex [:, :] h
cdef gint [:, :] rows_cols
cdef complex [:] data
+ cdef complex value
matrix = ta.matrix
@@ -59,10 +60,12 @@ def make_sparse(ham, args, CGraph gr, diag,
raise ValueError(msg.format(fs, fs))
for i in xrange(h.shape[0]):
for j in xrange(h.shape[1]):
- data[k] = h[i, j]
- rows_cols[0, k] = i + to_off[n_ts]
- rows_cols[1, k] = j + from_off[n_fs]
- k += 1
+ value = h[i, j]
+ if value != 0:
+ data[k] = value
+ rows_cols[0, k] = i + to_off[n_ts]
+ rows_cols[1, k] = j + from_off[n_fs]
+ k += 1
nbors = gr.out_neighbors(fs)
for ts in nbors.data[:nbors.size]:
@@ -74,12 +77,15 @@ def make_sparse(ham, args, CGraph gr, diag,
raise ValueError(msg.format(fs, ts))
for i in xrange(h.shape[0]):
for j in xrange(h.shape[1]):
- data[k] = h[i, j]
- rows_cols[0, k] = i + to_off[n_ts]
- rows_cols[1, k] = j + from_off[n_fs]
- k += 1
+ value = h[i, j]
+ if value != 0:
+ data[k] = value
+ rows_cols[0, k] = i + to_off[n_ts]
+ rows_cols[1, k] = j + from_off[n_fs]
+ k += 1
- return sp.coo_matrix((data, rows_cols), shape=(to_off[-1], from_off[-1]))
+ return sp.coo_matrix((data[:k], rows_cols[:, :k]),
+ shape=(to_off[-1], from_off[-1]))
@cython.boundscheck(False)
@@ -93,6 +99,7 @@ def make_sparse_full(ham, args, CGraph gr, diag,
cdef complex [:, :] h
cdef gint [:, :] rows_cols
cdef complex [:] data
+ cdef complex value
matrix = ta.matrix
n = gr.num_nodes
@@ -116,10 +123,12 @@ def make_sparse_full(ham, args, CGraph gr, diag,
raise ValueError(msg.format(fs, fs))
for i in xrange(h.shape[0]):
for j in xrange(h.shape[1]):
- data[k] = h[i, j]
- rows_cols[0, k] = i + to_off[fs]
- rows_cols[1, k] = j + from_off[fs]
- k += 1
+ value = h[i, j]
+ if value != 0:
+ data[k] = value
+ rows_cols[0, k] = i + to_off[fs]
+ rows_cols[1, k] = j + from_off[fs]
+ k += 1
nbors = gr.out_neighbors(fs)
for ts in nbors.data[:nbors.size]:
@@ -130,13 +139,16 @@ def make_sparse_full(ham, args, CGraph gr, diag,
raise ValueError(msg.format(fs, ts))
for i in xrange(h.shape[0]):
for j in xrange(h.shape[1]):
- data[k] = h[i, j]
- data[k + 1] = h[i, j].conjugate()
- rows_cols[1, k + 1] = rows_cols[0, k] = i + to_off[ts]
- rows_cols[0, k + 1] = rows_cols[1, k] = j + from_off[fs]
- k += 2
-
- return sp.coo_matrix((data, rows_cols), shape=(to_off[-1], from_off[-1]))
+ value = h[i, j]
+ if value != 0:
+ data[k] = value
+ data[k + 1] = h[i, j].conjugate()
+ rows_cols[1, k + 1] = rows_cols[0, k] = i + to_off[ts]
+ rows_cols[0, k + 1] = rows_cols[1, k] = j + from_off[fs]
+ k += 2
+
+ return sp.coo_matrix((data[:k], rows_cols[:, :k]),
+ shape=(to_off[-1], from_off[-1]))
@cython.boundscheck(False)
--
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