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fix: preserve HR data when wrapping HContainer with external data_array #7536

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Merged
mohanchen merged 1 commit into from
Jun 30, 2026
Merged

fix: preserve HR data when wrapping HContainer with external data_array #7536

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4 changes: 3 additions & 1 deletion source/source_lcao/module_hcontainer/hcontainer.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,9 @@ HContainer<T>::HContainer(const HContainer<T>& HR_in, T* data_array)
this->allocated_size = 0;
this->atom_pairs = HR_in.atom_pairs;
// data of HR_in will not be copied, please call add() after this constructor to copy data.
this->allocate(this->wrapper_pointer, true);
// Only zero memory when allocating fresh data (data_array==nullptr);
// when wrapping existing data (data_array!=nullptr), preserve the original content.
this->allocate(this->wrapper_pointer, data_array == nullptr);
// tmp terms not copied
}

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32 changes: 32 additions & 0 deletions tests/03_NAO_multik/scf_out_hsr_spin2/INPUT
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Original file line number Diff line number Diff line change
@@ -0,0 +1,32 @@
INPUT_PARAMETERS
#Parameters (1.General)
suffix autotest
calculation scf

nbands 6
symmetry 0
pseudo_dir ../../PP_ORB
orbital_dir ../../PP_ORB
gamma_only 0

nspin 2

#Parameters (2.Iteration)
ecutwfc 20
scf_thr 1e-8
scf_nmax 1

#Parameters (3.Basis)
basis_type lcao

#Parameters (4.Smearing)
smearing_method gauss
smearing_sigma 0.002

#Parameters (5.Mixing)
mixing_type broyden
mixing_beta 0.7
mixing_gg0 0.0

out_mat_hs2 1 5
ks_solver scalapack_gvx
4 changes: 4 additions & 0 deletions tests/03_NAO_multik/scf_out_hsr_spin2/KPT
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@@ -0,0 +1,4 @@
K_POINTS
0
Gamma
2 1 1 0 0 0
1 change: 1 addition & 0 deletions tests/03_NAO_multik/scf_out_hsr_spin2/README
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@@ -0,0 +1 @@
test the output of H(R)/S(R) matrix with nspin=2; Note: delete OUT folder before testing!
22 changes: 22 additions & 0 deletions tests/03_NAO_multik/scf_out_hsr_spin2/STRU
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@@ -0,0 +1,22 @@
ATOMIC_SPECIES
Si 14 Si_dojo_nsoc.upf upf201

NUMERICAL_ORBITAL
Si_dojo_6au_sz.orb

LATTICE_CONSTANT
15.3 // add lattice constant

LATTICE_VECTORS
0.0 0.5 0.5
0.5 0.0 0.5
0.5 0.5 0.0

ATOMIC_POSITIONS
Direct

Si // Element type
0.0 // magnetism
2
0.00 0.00 0.00 1 1 1 mag 1.0
0.25 0.25 0.25 1 1 1 mag -1.0
229 changes: 229 additions & 0 deletions tests/03_NAO_multik/scf_out_hsr_spin2/hrs1_nao.csr.ref
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--- Ionic Step 1 ---
# print H matrix in real space H(R)
2 # number of spin directions
1 # spin index
8 # number of localized basis
13 # number of Bravais lattice vector R

user_defined_lattice
8.09641
0 0.5 0.5
0.5 0 0.5
0.5 0.5 0
Si
2
Direct
0 0 0
0.25 0.25 0.25

#----------------------------------------------------------------------#
# CSR Format #
# The outer loop corresponds to the number of Bravais lattice vectors. #
# The first line contains the index of the Bravais lattice vector #
# (Rx, Ry, Rz), followed by the number of non-zero elements. #
# The subsequent lines consist of three blocks of data, which are #
# values, column indices, row pointers. #
#----------------------------------------------------------------------#

-1 0 0 48
# CSR values
-1.11792e-04 7.16241e-04 -3.82452e-06 -7.16241e-04 -3.37629e-02 8.00872e-03
8.00872e-03 -8.00872e-03 -7.16241e-04 2.12235e-03 -2.46427e-05 -2.57041e-03
-5.50669e-03 -1.91945e-03 -1.96652e-02 1.96652e-02 -3.82452e-06 2.46427e-05
-4.45692e-04 -2.46427e-05 -5.50669e-03 -1.96652e-02 -1.91945e-03 1.96652e-02
7.16241e-04 -2.57041e-03 2.46427e-05 2.12235e-03 5.50669e-03 1.96652e-02
1.96652e-02 -1.91945e-03 -1.12382e-04 7.21513e-04 3.79778e-06 -7.21513e-04
-7.21513e-04 2.16956e-03 2.43147e-05 -2.61966e-03 3.79778e-06 -2.43147e-05
-4.48512e-04 2.43147e-05 7.21513e-04 -2.61966e-03 -2.43147e-05 2.16956e-03
# CSR column indices
0 1 2 3 4 5 6 7 0 1 2 3 4 5 6 7
0 1 2 3 4 5 6 7 0 1 2 3 4 5 6 7
4 5 6 7 4 5 6 7 4 5 6 7 4 5 6 7
# CSR row pointers
0 8 16 24 32 36 40 44 48

-1 0 1 32
# CSR values
-1.11792e-04 7.16241e-04 7.16241e-04 3.82452e-06 -7.16241e-04 2.12235e-03
2.57041e-03 2.46427e-05 -7.16241e-04 2.57041e-03 2.12235e-03 2.46427e-05
3.82452e-06 -2.46427e-05 -2.46427e-05 -4.45692e-04 -1.12382e-04 7.21513e-04
7.21513e-04 -3.79778e-06 -7.21513e-04 2.16956e-03 2.61966e-03 -2.43147e-05
-7.21513e-04 2.61966e-03 2.16956e-03 -2.43147e-05 -3.79778e-06 2.43147e-05
2.43147e-05 -4.48512e-04
# CSR column indices
0 1 2 3 0 1 2 3 0 1 2 3 0 1 2 3
4 5 6 7 4 5 6 7 4 5 6 7 4 5 6 7
# CSR row pointers
0 4 8 12 16 20 24 28 32

-1 1 0 32
# CSR values
-1.11792e-04 -3.82452e-06 7.16241e-04 -7.16241e-04 -3.82452e-06 -4.45692e-04
2.46427e-05 -2.46427e-05 -7.16241e-04 -2.46427e-05 2.12235e-03 -2.57041e-03
7.16241e-04 2.46427e-05 -2.57041e-03 2.12235e-03 -1.12382e-04 3.79778e-06
7.21513e-04 -7.21513e-04 3.79778e-06 -4.48512e-04 -2.43147e-05 2.43147e-05
-7.21513e-04 2.43147e-05 2.16956e-03 -2.61966e-03 7.21513e-04 -2.43147e-05
-2.61966e-03 2.16956e-03
# CSR column indices
0 1 2 3 0 1 2 3 0 1 2 3 0 1 2 3
4 5 6 7 4 5 6 7 4 5 6 7 4 5 6 7
# CSR row pointers
0 4 8 12 16 20 24 28 32

0 -1 0 48
# CSR values
-1.11792e-04 7.16241e-04 -7.16241e-04 -3.82452e-06 -3.37629e-02 8.00872e-03
-8.00872e-03 8.00872e-03 -7.16241e-04 2.12235e-03 -2.57041e-03 -2.46427e-05
-5.50669e-03 -1.91945e-03 1.96652e-02 -1.96652e-02 7.16241e-04 -2.57041e-03
2.12235e-03 2.46427e-05 5.50669e-03 1.96652e-02 -1.91945e-03 1.96652e-02
-3.82452e-06 2.46427e-05 -2.46427e-05 -4.45692e-04 -5.50669e-03 -1.96652e-02
1.96652e-02 -1.91945e-03 -1.12382e-04 7.21513e-04 -7.21513e-04 3.79778e-06
-7.21513e-04 2.16956e-03 -2.61966e-03 2.43147e-05 7.21513e-04 -2.61966e-03
2.16956e-03 -2.43147e-05 3.79778e-06 -2.43147e-05 2.43147e-05 -4.48512e-04
# CSR column indices
0 1 2 3 4 5 6 7 0 1 2 3 4 5 6 7
0 1 2 3 4 5 6 7 0 1 2 3 4 5 6 7
4 5 6 7 4 5 6 7 4 5 6 7 4 5 6 7
# CSR row pointers
0 8 16 24 32 36 40 44 48

0 -1 1 32
# CSR values
-1.11792e-04 7.16241e-04 3.82452e-06 7.16241e-04 -7.16241e-04 2.12235e-03
2.46427e-05 2.57041e-03 3.82452e-06 -2.46427e-05 -4.45692e-04 -2.46427e-05
-7.16241e-04 2.57041e-03 2.46427e-05 2.12235e-03 -1.12382e-04 7.21513e-04
-3.79778e-06 7.21513e-04 -7.21513e-04 2.16956e-03 -2.43147e-05 2.61966e-03
-3.79778e-06 2.43147e-05 -4.48512e-04 2.43147e-05 -7.21513e-04 2.61966e-03
-2.43147e-05 2.16956e-03
# CSR column indices
0 1 2 3 0 1 2 3 0 1 2 3 0 1 2 3
4 5 6 7 4 5 6 7 4 5 6 7 4 5 6 7
# CSR row pointers
0 4 8 12 16 20 24 28 32

0 0 -1 48
# CSR values
-1.11792e-04 3.82452e-06 -7.16241e-04 -7.16241e-04 -3.37629e-02 -8.00872e-03
-8.00872e-03 -8.00872e-03 3.82452e-06 -4.45692e-04 2.46427e-05 2.46427e-05
5.50669e-03 -1.91945e-03 -1.96652e-02 -1.96652e-02 7.16241e-04 -2.46427e-05
2.12235e-03 2.57041e-03 5.50669e-03 -1.96652e-02 -1.91945e-03 -1.96652e-02
7.16241e-04 -2.46427e-05 2.57041e-03 2.12235e-03 5.50669e-03 -1.96652e-02
-1.96652e-02 -1.91945e-03 -1.12382e-04 -3.79778e-06 -7.21513e-04 -7.21513e-04
-3.79778e-06 -4.48512e-04 -2.43147e-05 -2.43147e-05 7.21513e-04 2.43147e-05
2.16956e-03 2.61966e-03 7.21513e-04 2.43147e-05 2.61966e-03 2.16956e-03
# CSR column indices
0 1 2 3 4 5 6 7 0 1 2 3 4 5 6 7
0 1 2 3 4 5 6 7 0 1 2 3 4 5 6 7
4 5 6 7 4 5 6 7 4 5 6 7 4 5 6 7
# CSR row pointers
0 8 16 24 32 36 40 44 48

0 0 0 40
# CSR values
-5.43126e-01 -3.37629e-02 -8.00872e-03 8.00872e-03 8.00872e-03 8.04017e-01
5.50669e-03 -1.91945e-03 1.96652e-02 1.96652e-02 8.04017e-01 -5.50669e-03
1.96652e-02 -1.91945e-03 -1.96652e-02 8.04017e-01 -5.50669e-03 1.96652e-02
-1.96652e-02 -1.91945e-03 -3.37629e-02 5.50669e-03 -5.50669e-03 -5.50669e-03
-4.69258e-01 -8.00872e-03 -1.91945e-03 1.96652e-02 1.96652e-02 8.75227e-01
8.00872e-03 1.96652e-02 -1.91945e-03 -1.96652e-02 8.75227e-01 8.00872e-03
1.96652e-02 -1.96652e-02 -1.91945e-03 8.75227e-01
# CSR column indices
0 4 5 6 7 1 4 5 6 7 2 4 5 6 7 3
4 5 6 7 0 1 2 3 4 0 1 2 3 5 0 1
2 3 6 0 1 2 3 7
# CSR row pointers
0 5 10 15 20 25 30 35 40

0 0 1 48
# CSR values
-1.11792e-04 3.82452e-06 7.16241e-04 7.16241e-04 3.82452e-06 -4.45692e-04
-2.46427e-05 -2.46427e-05 -7.16241e-04 2.46427e-05 2.12235e-03 2.57041e-03
-7.16241e-04 2.46427e-05 2.57041e-03 2.12235e-03 -3.37629e-02 5.50669e-03
5.50669e-03 5.50669e-03 -1.12382e-04 -3.79778e-06 7.21513e-04 7.21513e-04
-8.00872e-03 -1.91945e-03 -1.96652e-02 -1.96652e-02 -3.79778e-06 -4.48512e-04
2.43147e-05 2.43147e-05 -8.00872e-03 -1.96652e-02 -1.91945e-03 -1.96652e-02
-7.21513e-04 -2.43147e-05 2.16956e-03 2.61966e-03 -8.00872e-03 -1.96652e-02
-1.96652e-02 -1.91945e-03 -7.21513e-04 -2.43147e-05 2.61966e-03 2.16956e-03
# CSR column indices
0 1 2 3 0 1 2 3 0 1 2 3 0 1 2 3
0 1 2 3 4 5 6 7 0 1 2 3 4 5 6 7
0 1 2 3 4 5 6 7 0 1 2 3 4 5 6 7
# CSR row pointers
0 4 8 12 16 24 32 40 48

0 1 -1 32
# CSR values
-1.11792e-04 -7.16241e-04 3.82452e-06 -7.16241e-04 7.16241e-04 2.12235e-03
-2.46427e-05 2.57041e-03 3.82452e-06 2.46427e-05 -4.45692e-04 2.46427e-05
7.16241e-04 2.57041e-03 -2.46427e-05 2.12235e-03 -1.12382e-04 -7.21513e-04
-3.79778e-06 -7.21513e-04 7.21513e-04 2.16956e-03 2.43147e-05 2.61966e-03
-3.79778e-06 -2.43147e-05 -4.48512e-04 -2.43147e-05 7.21513e-04 2.61966e-03
2.43147e-05 2.16956e-03
# CSR column indices
0 1 2 3 0 1 2 3 0 1 2 3 0 1 2 3
4 5 6 7 4 5 6 7 4 5 6 7 4 5 6 7
# CSR row pointers
0 4 8 12 16 20 24 28 32

0 1 0 48
# CSR values
-1.11792e-04 -7.16241e-04 7.16241e-04 -3.82452e-06 7.16241e-04 2.12235e-03
-2.57041e-03 2.46427e-05 -7.16241e-04 -2.57041e-03 2.12235e-03 -2.46427e-05
-3.82452e-06 -2.46427e-05 2.46427e-05 -4.45692e-04 -3.37629e-02 -5.50669e-03
5.50669e-03 -5.50669e-03 -1.12382e-04 -7.21513e-04 7.21513e-04 3.79778e-06
8.00872e-03 -1.91945e-03 1.96652e-02 -1.96652e-02 7.21513e-04 2.16956e-03
-2.61966e-03 -2.43147e-05 -8.00872e-03 1.96652e-02 -1.91945e-03 1.96652e-02
-7.21513e-04 -2.61966e-03 2.16956e-03 2.43147e-05 8.00872e-03 -1.96652e-02
1.96652e-02 -1.91945e-03 3.79778e-06 2.43147e-05 -2.43147e-05 -4.48512e-04
# CSR column indices
0 1 2 3 0 1 2 3 0 1 2 3 0 1 2 3
0 1 2 3 4 5 6 7 0 1 2 3 4 5 6 7
0 1 2 3 4 5 6 7 0 1 2 3 4 5 6 7
# CSR row pointers
0 4 8 12 16 24 32 40 48

1 -1 0 32
# CSR values
-1.11792e-04 -3.82452e-06 -7.16241e-04 7.16241e-04 -3.82452e-06 -4.45692e-04
-2.46427e-05 2.46427e-05 7.16241e-04 2.46427e-05 2.12235e-03 -2.57041e-03
-7.16241e-04 -2.46427e-05 -2.57041e-03 2.12235e-03 -1.12382e-04 3.79778e-06
-7.21513e-04 7.21513e-04 3.79778e-06 -4.48512e-04 2.43147e-05 -2.43147e-05
7.21513e-04 -2.43147e-05 2.16956e-03 -2.61966e-03 -7.21513e-04 2.43147e-05
-2.61966e-03 2.16956e-03
# CSR column indices
0 1 2 3 0 1 2 3 0 1 2 3 0 1 2 3
4 5 6 7 4 5 6 7 4 5 6 7 4 5 6 7
# CSR row pointers
0 4 8 12 16 20 24 28 32

1 0 -1 32
# CSR values
-1.11792e-04 -7.16241e-04 -7.16241e-04 3.82452e-06 7.16241e-04 2.12235e-03
2.57041e-03 -2.46427e-05 7.16241e-04 2.57041e-03 2.12235e-03 -2.46427e-05
3.82452e-06 2.46427e-05 2.46427e-05 -4.45692e-04 -1.12382e-04 -7.21513e-04
-7.21513e-04 -3.79778e-06 7.21513e-04 2.16956e-03 2.61966e-03 2.43147e-05
7.21513e-04 2.61966e-03 2.16956e-03 2.43147e-05 -3.79778e-06 -2.43147e-05
-2.43147e-05 -4.48512e-04
# CSR column indices
0 1 2 3 0 1 2 3 0 1 2 3 0 1 2 3
4 5 6 7 4 5 6 7 4 5 6 7 4 5 6 7
# CSR row pointers
0 4 8 12 16 20 24 28 32

1 0 0 48
# CSR values
-1.11792e-04 -7.16241e-04 -3.82452e-06 7.16241e-04 7.16241e-04 2.12235e-03
2.46427e-05 -2.57041e-03 -3.82452e-06 -2.46427e-05 -4.45692e-04 2.46427e-05
-7.16241e-04 -2.57041e-03 -2.46427e-05 2.12235e-03 -3.37629e-02 -5.50669e-03
-5.50669e-03 5.50669e-03 -1.12382e-04 -7.21513e-04 3.79778e-06 7.21513e-04
8.00872e-03 -1.91945e-03 -1.96652e-02 1.96652e-02 7.21513e-04 2.16956e-03
-2.43147e-05 -2.61966e-03 8.00872e-03 -1.96652e-02 -1.91945e-03 1.96652e-02
3.79778e-06 2.43147e-05 -4.48512e-04 -2.43147e-05 -8.00872e-03 1.96652e-02
1.96652e-02 -1.91945e-03 -7.21513e-04 -2.61966e-03 2.43147e-05 2.16956e-03
# CSR column indices
0 1 2 3 0 1 2 3 0 1 2 3 0 1 2 3
0 1 2 3 4 5 6 7 0 1 2 3 4 5 6 7
0 1 2 3 4 5 6 7 0 1 2 3 4 5 6 7
# CSR row pointers
0 4 8 12 16 24 32 40 48

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