From be5d2dd30c9ee249ba11be32679f9eabe95821e7 Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Mon, 23 Dec 2024 14:17:06 +0900
Subject: [PATCH 01/12] Set BUILD_WITHOUT_LAPACKE=ON as default

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index c178490f..3b2ad2ac 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -52,7 +52,7 @@ sdist.include = [
 PHONO3PY_USE_MTBLAS = {env="PHONO3PY_USE_MTBLAS", default="ON"}
 USE_CONDA_PATH = {env="USE_CONDA_PATH", default="ON"}
 PHONO3PY_USE_OMP = {env="PHONO3PY_USE_OMP", default="ON"}
-BUILD_WITHOUT_LAPACKE = {env="BUILD_WITHOUT_LAPACKE", default="OFF"}
+BUILD_WITHOUT_LAPACKE = {env="BUILD_WITHOUT_LAPACKE", default="ON"}
 
 [tool.setuptools_scm]
 write_to = "phono3py/_version.py"

From eb1ebe0cf29f5efbb91edeae32e7893fa6169d2a Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Mon, 23 Dec 2024 14:43:32 +0900
Subject: [PATCH 02/12] Update CMakeLists.txt

---
 CMakeLists.txt | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 11dc20d1..0e46d3fa 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -66,7 +66,9 @@ endif()
 message(STATUS "Build type: ${CMAKE_BUILD_TYPE}")
 message(STATUS "CMAKE_SYSTEM_PREFIX_PATH: ${CMAKE_SYSTEM_PREFIX_PATH}")
 
-if(USE_CONDA_PATH AND DEFINED ENV{CONDA_PREFIX})
+if((NOT BUILD_WITHOUT_LAPACKE)
+   AND USE_CONDA_PATH
+   AND DEFINED ENV{CONDA_PREFIX})
     message(STATUS "$ENV{CONDA_PREFIX}")
     set(CMAKE_MODULE_PATH $ENV{CONDA_PREFIX})
     set(MY_INCLUDES $ENV{CONDA_PREFIX}/include ${PROJECT_SOURCE_DIR}/c)

From 7b8f7a8d841de8634d583e670ad151a8a1b957a0 Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Mon, 23 Dec 2024 15:20:16 +0900
Subject: [PATCH 03/12] Define complex for VC

---
 c/lapack_wrapper.h | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/c/lapack_wrapper.h b/c/lapack_wrapper.h
index b18db54a..a2e30008 100644
--- a/c/lapack_wrapper.h
+++ b/c/lapack_wrapper.h
@@ -36,6 +36,20 @@
 #define __lapack_wrapper_H__
 
 #ifdef NO_INCLUDE_LAPACKE
+#if defined(_MSC_VER)
+typedef struct {
+    double real;
+    double imag;
+} lapack_complex_double;
+lapack_complex_double lapack_make_complex_double(double re, double im) {
+    lapack_complex_double c;
+    c.real = re;
+    c.imag = im;
+    return c;
+}
+#define lapack_complex_double_real(z) ((z).real)
+#define lapack_complex_double_imag(z) ((z).imag)
+#else
 #include <complex.h>
 #define lapack_complex_double double _Complex
 #ifdef CMPLX
@@ -46,6 +60,7 @@
 #define lapack_complex_double_real(z) (creal(z))
 #define lapack_complex_double_imag(z) (cimag(z))
 #endif
+#endif
 
 #if defined(MKL_BLAS) || defined(SCIPY_MKL_H)
 #include <mkl.h>

From 71dcf8410835fd57a453290cfaa156e2d331374d Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Mon, 23 Dec 2024 15:45:51 +0900
Subject: [PATCH 04/12] Define complex for VC

---
 c/lapack_wrapper.c |  5 +++--
 c/lapack_wrapper.h | 28 ++++++++++------------------
 2 files changed, 13 insertions(+), 20 deletions(-)

diff --git a/c/lapack_wrapper.c b/c/lapack_wrapper.c
index 166e2000..f8838cb1 100644
--- a/c/lapack_wrapper.c
+++ b/c/lapack_wrapper.c
@@ -38,7 +38,7 @@
 
 #define min(a, b) ((a) > (b) ? (b) : (a))
 
-#if (defined(MKL_BLAS) || defined(SCIPY_MKL_H)) && !defined(NO_INCLUDE_LAPACKE)
+#if defined(_MSC_VER) || defined(MKL_BLAS) || defined(SCIPY_MKL_H)
 lapack_complex_double lapack_make_complex_double(double re, double im) {
     lapack_complex_double z;
     z.real = re;
@@ -47,7 +47,8 @@ lapack_complex_double lapack_make_complex_double(double re, double im) {
 }
 #endif
 
-#if defined(MKL_BLAS) || defined(SCIPY_MKL_H) || defined(NO_INCLUDE_LAPACKE)
+#if defined(_MSC_VER) || defined(MKL_BLAS) || defined(SCIPY_MKL_H) || \
+    defined(NO_INCLUDE_LAPACKE)
 #ifndef LAPACKE_malloc
 #define LAPACKE_malloc(size) malloc(size)
 #endif
diff --git a/c/lapack_wrapper.h b/c/lapack_wrapper.h
index a2e30008..2c4178a4 100644
--- a/c/lapack_wrapper.h
+++ b/c/lapack_wrapper.h
@@ -35,21 +35,21 @@
 #ifndef __lapack_wrapper_H__
 #define __lapack_wrapper_H__
 
-#ifdef NO_INCLUDE_LAPACKE
+#if defined(_MSC_VER) || defined(MKL_BLAS) || defined(SCIPY_MKL_H)
 #if defined(_MSC_VER)
 typedef struct {
     double real;
     double imag;
 } lapack_complex_double;
-lapack_complex_double lapack_make_complex_double(double re, double im) {
-    lapack_complex_double c;
-    c.real = re;
-    c.imag = im;
-    return c;
-}
+#else
+#include <mkl.h>
+#define lapack_complex_double MKL_Complex16
+#endif
+lapack_complex_double lapack_make_complex_double(double re, double im);
 #define lapack_complex_double_real(z) ((z).real)
 #define lapack_complex_double_imag(z) ((z).imag)
 #else
+#if defined(NO_INCLUDE_LAPACKE)
 #include <complex.h>
 #define lapack_complex_double double _Complex
 #ifdef CMPLX
@@ -59,19 +59,11 @@ lapack_complex_double lapack_make_complex_double(double re, double im) {
 #endif
 #define lapack_complex_double_real(z) (creal(z))
 #define lapack_complex_double_imag(z) (cimag(z))
+#else
+#if !defined(MKL_BLAS) && !defined(SCIPY_MKL_H)
+#include <lapacke.h>
 #endif
 #endif
-
-#if defined(MKL_BLAS) || defined(SCIPY_MKL_H)
-#include <mkl.h>
-#define lapack_complex_double MKL_Complex16
-MKL_Complex16 lapack_make_complex_double(double re, double im);
-#define lapack_complex_double_real(z) ((z).real)
-#define lapack_complex_double_imag(z) ((z).imag)
-#endif
-
-#if !defined(MKL_BLAS) && !defined(SCIPY_MKL_H) && !defined(NO_INCLUDE_LAPACKE)
-#include <lapacke.h>
 #endif
 
 lapack_complex_double phonoc_complex_prod(const lapack_complex_double a,

From 0b677509b9969ee29a39213a6a6eb5f906b66aaa Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Mon, 23 Dec 2024 16:04:55 +0900
Subject: [PATCH 05/12] Remove unnecessary functions from _phono3py.cpp and
 phono3py.h

---
 c/_phono3py.cpp | 162 ------------------------------------------------
 c/phono3py.h    |  31 ---------
 2 files changed, 193 deletions(-)

diff --git a/c/_phono3py.cpp b/c/_phono3py.cpp
index a7017d66..52e7ff14 100644
--- a/c/_phono3py.cpp
+++ b/c/_phono3py.cpp
@@ -887,168 +887,6 @@ void py_get_triplets_integration_weights_with_sigma(
         num_triplets, frequencies, num_band, num_iw);
 }
 
-long py_get_grid_index_from_address(nb::ndarray<> py_address,
-                                    nb::ndarray<> py_D_diag) {
-    long *address;
-    long *D_diag;
-    long gp;
-
-    address = (long *)py_address.data();
-    D_diag = (long *)py_D_diag.data();
-
-    gp = ph3py_get_grid_index_from_address(address, D_diag);
-
-    return gp;
-}
-
-long py_get_ir_grid_map(nb::ndarray<> py_grid_mapping_table,
-                        nb::ndarray<> py_D_diag, nb::ndarray<> py_is_shift,
-                        nb::ndarray<> py_rotations) {
-    long *D_diag;
-    long *is_shift;
-    long(*rot)[3][3];
-    long num_rot;
-
-    long *grid_mapping_table;
-    long num_ir;
-
-    D_diag = (long *)py_D_diag.data();
-    is_shift = (long *)py_is_shift.data();
-    rot = (long(*)[3][3])py_rotations.data();
-    num_rot = (long)py_rotations.shape(0);
-    grid_mapping_table = (long *)py_grid_mapping_table.data();
-
-    num_ir = ph3py_get_ir_grid_map(grid_mapping_table, D_diag, is_shift, rot,
-                                   num_rot);
-    return num_ir;
-}
-
-void py_get_gr_grid_addresses(nb::ndarray<> py_gr_grid_addresses,
-                              nb::ndarray<> py_D_diag) {
-    long(*gr_grid_addresses)[3];
-    long *D_diag;
-
-    gr_grid_addresses = (long(*)[3])py_gr_grid_addresses.data();
-    D_diag = (long *)py_D_diag.data();
-
-    ph3py_get_gr_grid_addresses(gr_grid_addresses, D_diag);
-}
-
-long py_get_reciprocal_rotations(nb::ndarray<> py_rec_rotations,
-                                 nb::ndarray<> py_rotations,
-                                 long is_time_reversal) {
-    long(*rec_rotations)[3][3];
-    long(*rotations)[3][3];
-    long num_rot, num_rec_rot;
-
-    rec_rotations = (long(*)[3][3])py_rec_rotations.data();
-    rotations = (long(*)[3][3])py_rotations.data();
-    num_rot = (long)py_rotations.shape(0);
-
-    num_rec_rot = ph3py_get_reciprocal_rotations(rec_rotations, rotations,
-                                                 num_rot, is_time_reversal);
-
-    return num_rec_rot;
-}
-
-bool py_transform_rotations(nb::ndarray<> py_transformed_rotations,
-                            nb::ndarray<> py_rotations, nb::ndarray<> py_D_diag,
-                            nb::ndarray<> py_Q) {
-    long(*transformed_rotations)[3][3];
-    long(*rotations)[3][3];
-    long *D_diag;
-    long(*Q)[3];
-    long num_rot, succeeded;
-
-    transformed_rotations = (long(*)[3][3])py_transformed_rotations.data();
-    rotations = (long(*)[3][3])py_rotations.data();
-    D_diag = (long *)py_D_diag.data();
-    Q = (long(*)[3])py_Q.data();
-    num_rot = (long)py_transformed_rotations.shape(0);
-
-    succeeded = ph3py_transform_rotations(transformed_rotations, rotations,
-                                          num_rot, D_diag, Q);
-    if (succeeded) {
-        return true;
-    } else {
-        return false;
-    }
-}
-
-bool py_get_snf3x3(nb::ndarray<> py_D_diag, nb::ndarray<> py_P,
-                   nb::ndarray<> py_Q, nb::ndarray<> py_A) {
-    long *D_diag;
-    long(*P)[3];
-    long(*Q)[3];
-    long(*A)[3];
-    long succeeded;
-
-    D_diag = (long *)py_D_diag.data();
-    P = (long(*)[3])py_P.data();
-    Q = (long(*)[3])py_Q.data();
-    A = (long(*)[3])py_A.data();
-
-    succeeded = ph3py_get_snf3x3(D_diag, P, Q, A);
-    if (succeeded) {
-        return true;
-    } else {
-        return false;
-    }
-}
-
-long py_get_bz_grid_addresses(nb::ndarray<> py_bz_grid_addresses,
-                              nb::ndarray<> py_bz_map, nb::ndarray<> py_bzg2grg,
-                              nb::ndarray<> py_D_diag, nb::ndarray<> py_Q,
-                              nb::ndarray<> py_PS,
-                              nb::ndarray<> py_reciprocal_lattice, long type) {
-    long(*bz_grid_addresses)[3];
-    long *bz_map;
-    long *bzg2grg;
-    long *D_diag;
-    long(*Q)[3];
-    long *PS;
-    double(*reciprocal_lattice)[3];
-    long num_total_gp;
-
-    bz_grid_addresses = (long(*)[3])py_bz_grid_addresses.data();
-    bz_map = (long *)py_bz_map.data();
-    bzg2grg = (long *)py_bzg2grg.data();
-    D_diag = (long *)py_D_diag.data();
-    Q = (long(*)[3])py_Q.data();
-    PS = (long *)py_PS.data();
-    reciprocal_lattice = (double(*)[3])py_reciprocal_lattice.data();
-
-    num_total_gp =
-        ph3py_get_bz_grid_addresses(bz_grid_addresses, bz_map, bzg2grg, D_diag,
-                                    Q, PS, reciprocal_lattice, type);
-
-    return num_total_gp;
-}
-
-long py_rotate_bz_grid_addresses(long bz_grid_index, nb::ndarray<> py_rotation,
-                                 nb::ndarray<> py_bz_grid_addresses,
-                                 nb::ndarray<> py_bz_map,
-                                 nb::ndarray<> py_D_diag, nb::ndarray<> py_PS,
-                                 long type) {
-    long(*bz_grid_addresses)[3];
-    long(*rotation)[3];
-    long *bz_map;
-    long *D_diag;
-    long *PS;
-    long ret_bz_gp;
-
-    bz_grid_addresses = (long(*)[3])py_bz_grid_addresses.data();
-    rotation = (long(*)[3])py_rotation.data();
-    bz_map = (long *)py_bz_map.data();
-    D_diag = (long *)py_D_diag.data();
-    PS = (long *)py_PS.data();
-
-    ret_bz_gp = ph3py_rotate_bz_grid_index(
-        bz_grid_index, rotation, bz_grid_addresses, bz_map, D_diag, PS, type);
-
-    return ret_bz_gp;
-}
-
 long py_get_default_colmat_solver() {
 #if defined(MKL_BLAS) || defined(SCIPY_MKL_H) || !defined(NO_INCLUDE_LAPACKE)
     return (long)1;
diff --git a/c/phono3py.h b/c/phono3py.h
index 54247e24..351a7c3f 100644
--- a/c/phono3py.h
+++ b/c/phono3py.h
@@ -176,37 +176,6 @@ void ph3py_get_integration_weight_with_sigma(
     const double *frequency_points, const long num_band0,
     const long (*triplets)[3], const long num_triplets,
     const double *frequencies, const long num_band, const long tp_type);
-long ph3py_get_grid_index_from_address(const long address[3],
-                                       const long mesh[3]);
-void ph3py_get_gr_grid_addresses(long gr_grid_addresses[][3],
-                                 const long D_diag[3]);
-long ph3py_get_reciprocal_rotations(long rec_rotations[48][3][3],
-                                    const long (*rotations)[3][3],
-                                    const long num_rot,
-                                    const long is_time_reversal);
-long ph3py_transform_rotations(long (*transformed_rots)[3][3],
-                               const long (*rotations)[3][3],
-                               const long num_rot, const long D_diag[3],
-                               const long Q[3][3]);
-long ph3py_get_snf3x3(long D_diag[3], long P[3][3], long Q[3][3],
-                      const long A[3][3]);
-long ph3py_transform_rotations(long (*transformed_rots)[3][3],
-                               const long (*rotations)[3][3],
-                               const long num_rot, const long D_diag[3],
-                               const long Q[3][3]);
-long ph3py_get_ir_grid_map(long *ir_grid_map, const long D_diag[3],
-                           const long PS[3], const long (*grg_rotations)[3][3],
-                           const long num_rot);
-long ph3py_get_bz_grid_addresses(long (*bz_grid_addresses)[3], long *bz_map,
-                                 long *bzg2grg, const long D_diag[3],
-                                 const long Q[3][3], const long PS[3],
-                                 const double rec_lattice[3][3],
-                                 const long type);
-long ph3py_rotate_bz_grid_index(const long bz_grid_index,
-                                const long rotation[3][3],
-                                const long (*bz_grid_addresses)[3],
-                                const long *bz_map, const long D_diag[3],
-                                const long PS[3], const long bz_grid_type);
 void ph3py_symmetrize_collision_matrix(double *collision_matrix,
                                        const long num_column,
                                        const long num_temp,

From cd1e1e9407ef3b41f641e9f33e5661fac1f9c67c Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 24 Dec 2024 00:07:42 +0000
Subject: [PATCH 06/12] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.8.3 → v0.8.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.8.3...v0.8.4)
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ea69ffe6..69500ebe 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -11,7 +11,7 @@ repos:
     exclude: ^example/AlN-LDA/
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.8.3
+  rev: v0.8.4
   hooks:
   - id: ruff
     args: [ "--fix", "--show-fixes" ]

From 61712ee520ce37d1fbfc7bfe99571709b0ab43c7 Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Tue, 24 Dec 2024 13:30:05 +0900
Subject: [PATCH 07/12] Made D_diag's dtype=long

---
 phono3py/phonon/grid.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/phono3py/phonon/grid.py b/phono3py/phonon/grid.py
index c34bcc9f..5997de66 100644
--- a/phono3py/phonon/grid.py
+++ b/phono3py/phonon/grid.py
@@ -684,6 +684,7 @@ def _set_mesh_numbers(
                     self._D_diag = length2mesh(
                         length, self._lattice, rotations=symmetry_dataset.rotations
                     )
+                self._D_diag = np.array(self._D_diag, dtype="long")
         if num_values == 9:
             self._run_grg(
                 symmetry_dataset,

From b12248f384017d6ad81e9801576f6f8e19aac37b Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Tue, 24 Dec 2024 15:37:41 +0900
Subject: [PATCH 08/12] Show diagonalization information

---
 phono3py/conductivity/direct_solution.py | 47 ++++++++++++++++--------
 phono3py/conductivity/utils.py           |  2 +-
 2 files changed, 33 insertions(+), 16 deletions(-)

diff --git a/phono3py/conductivity/direct_solution.py b/phono3py/conductivity/direct_solution.py
index 8e3ec348..52f60c9b 100644
--- a/phono3py/conductivity/direct_solution.py
+++ b/phono3py/conductivity/direct_solution.py
@@ -177,10 +177,21 @@ def set_collision_matrix(self, collision_matrix):
         )
         self.collision_matrix = collision_matrix
 
-    def get_collision_eigenvalues(self):
+    @property
+    def collision_eigenvalues(self):
         """Return eigenvalues of collision matrix."""
         return self._collision_eigenvalues
 
+    def get_collision_eigenvalues(self):
+        """Return eigenvalues of collision matrix."""
+        warnings.warn(
+            "Use attribute, Conductivity_LBTE.collision_eigenvalues "
+            "instead of Conductivity_LBTE.get_collision_eigenvalues().",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        return self.collision_eigenvalues
+
     def get_frequencies_all(self):
         """Return phonon frequencies on GR-grid."""
         return self._frequencies[self._pp.bz_grid.grg2bzg]
@@ -690,12 +701,12 @@ def _symmetrize_collision_matrix(self):
             import phono3py._phono3py as phono3c
 
             if self._log_level:
-                sys.stdout.write("- Making collision matrix symmetric " "(built-in) ")
+                sys.stdout.write("- Making collision matrix symmetric (built-in) ")
                 sys.stdout.flush()
             phono3c.symmetrize_collision_matrix(self._collision_matrix)
         except ImportError:
             if self._log_level:
-                sys.stdout.write("- Making collision matrix symmetric " "(numpy) ")
+                sys.stdout.write("- Making collision matrix symmetric (numpy) ")
                 sys.stdout.flush()
 
             if self._is_reducible_collision_matrix:
@@ -819,14 +830,18 @@ def _get_Y(self, i_sigma, i_temp, weights, X):
 
         start = time.time()
 
-        if self._pinv_method == 0:
-            eig_str = "abs(eig)"
-        else:
-            eig_str = "eig"
-        print(
-            f"Calculating pseudo-inv by ignoring {eig_str}<{self._pinv_cutoff:<.1e}",
-            end="",
-        )
+        if self._log_level:
+            if self._pinv_method == 0:
+                eig_str = "abs(eig)"
+            else:
+                eig_str = "eig"
+            w = self._collision_eigenvalues[i_sigma, i_temp]
+            null_space = (np.abs(w) < self._pinv_cutoff).sum()
+            print(
+                f"Pseudo-inv by ignoring {null_space}/{len(w)} dims "
+                f"under {eig_str}<{self._pinv_cutoff:<.1e}",
+                end="",
+            )
         if solver in [0, 1, 2, 3, 4, 5]:
             if self._log_level:
                 print(" (np.dot) ", end="")
@@ -1866,13 +1881,14 @@ def diagonalize_collision_matrix(
         assert size == shape[1]
 
     solver = select_colmat_solver(pinv_solver)
+    trace = np.trace(collision_matrices[i_sigma, i_temp].reshape(size, size))
 
     # [1] dsyev: safer and slower than dsyevd and smallest memory usage
     # [2] dsyevd: faster than dsyev and largest memory usage
     if solver in [1, 2]:
         if log_level:
             routine = ["dsyev", "dsyevd"][solver - 1]
-            sys.stdout.write("Diagonalizing by lapacke %s... " % routine)
+            sys.stdout.write("Diagonalizing by lapacke %s ... " % routine)
             sys.stdout.flush()
         import phono3py._phono3py as phono3c
 
@@ -1890,14 +1906,14 @@ def diagonalize_collision_matrix(
         )  # only diagonalization
     elif solver == 3:  # np.linalg.eigh depends on dsyevd.
         if log_level:
-            sys.stdout.write("Diagonalizing by np.linalg.eigh... ")
+            sys.stdout.write("Diagonalizing by np.linalg.eigh ... ")
             sys.stdout.flush()
         col_mat = collision_matrices[i_sigma, i_temp].reshape(size, size)
         w, col_mat[:] = np.linalg.eigh(col_mat)
 
     elif solver == 4:  # fully scipy dsyev
         if log_level:
-            sys.stdout.write("Diagonalizing by " "scipy.linalg.lapack.dsyev... ")
+            sys.stdout.write("Diagonalizing by " "scipy.linalg.lapack.dsyev ... ")
             sys.stdout.flush()
         import scipy.linalg
 
@@ -1905,7 +1921,7 @@ def diagonalize_collision_matrix(
         w, _, info = scipy.linalg.lapack.dsyev(col_mat.T, overwrite_a=1)
     elif solver == 5:  # fully scipy dsyevd
         if log_level:
-            sys.stdout.write("Diagonalizing by " "scipy.linalg.lapack.dsyevd... ")
+            sys.stdout.write("Diagonalizing by " "scipy.linalg.lapack.dsyevd ... ")
             sys.stdout.flush()
         import scipy.linalg
 
@@ -1913,6 +1929,7 @@ def diagonalize_collision_matrix(
         w, _, info = scipy.linalg.lapack.dsyevd(col_mat.T, overwrite_a=1)
 
     if log_level:
+        print(f"delta={trace - w.sum():<.1e} ", end="")
         print("[%.3fs]" % (time.time() - start))
         sys.stdout.flush()
 
diff --git a/phono3py/conductivity/utils.py b/phono3py/conductivity/utils.py
index ebdf67c6..1b70ce99 100644
--- a/phono3py/conductivity/utils.py
+++ b/phono3py/conductivity/utils.py
@@ -550,7 +550,7 @@ def write_kappa(
         mfp = lbte.get_mean_free_path()
         boundary_mfp = lbte.boundary_mfp
 
-        coleigs = lbte.get_collision_eigenvalues()
+        coleigs = lbte.collision_eigenvalues
         # After kappa calculation, the variable is overwritten by unitary matrix
         unitary_matrix = lbte.collision_matrix
 

From 47aaab55d31482f9e0f5299bc9c74e79a3429ffe Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Tue, 24 Dec 2024 15:59:36 +0900
Subject: [PATCH 09/12] Show also trace in diagonalization of colmat

---
 phono3py/conductivity/direct_solution.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/phono3py/conductivity/direct_solution.py b/phono3py/conductivity/direct_solution.py
index 52f60c9b..8bca4a8b 100644
--- a/phono3py/conductivity/direct_solution.py
+++ b/phono3py/conductivity/direct_solution.py
@@ -838,7 +838,7 @@ def _get_Y(self, i_sigma, i_temp, weights, X):
             w = self._collision_eigenvalues[i_sigma, i_temp]
             null_space = (np.abs(w) < self._pinv_cutoff).sum()
             print(
-                f"Pseudo-inv by ignoring {null_space}/{len(w)} dims "
+                f"Pinv by ignoring {null_space}/{len(w)} dims "
                 f"under {eig_str}<{self._pinv_cutoff:<.1e}",
                 end="",
             )
@@ -1906,14 +1906,14 @@ def diagonalize_collision_matrix(
         )  # only diagonalization
     elif solver == 3:  # np.linalg.eigh depends on dsyevd.
         if log_level:
-            sys.stdout.write("Diagonalizing by np.linalg.eigh ... ")
+            sys.stdout.write("Diagonalize by np.linalg.eigh ")
             sys.stdout.flush()
         col_mat = collision_matrices[i_sigma, i_temp].reshape(size, size)
         w, col_mat[:] = np.linalg.eigh(col_mat)
 
     elif solver == 4:  # fully scipy dsyev
         if log_level:
-            sys.stdout.write("Diagonalizing by " "scipy.linalg.lapack.dsyev ... ")
+            sys.stdout.write("Diagonalize by scipy.linalg.lapack.dsyev ")
             sys.stdout.flush()
         import scipy.linalg
 
@@ -1921,7 +1921,7 @@ def diagonalize_collision_matrix(
         w, _, info = scipy.linalg.lapack.dsyev(col_mat.T, overwrite_a=1)
     elif solver == 5:  # fully scipy dsyevd
         if log_level:
-            sys.stdout.write("Diagonalizing by " "scipy.linalg.lapack.dsyevd ... ")
+            sys.stdout.write("Diagnalize by scipy.linalg.lapack.dsyevd ")
             sys.stdout.flush()
         import scipy.linalg
 
@@ -1929,7 +1929,7 @@ def diagonalize_collision_matrix(
         w, _, info = scipy.linalg.lapack.dsyevd(col_mat.T, overwrite_a=1)
 
     if log_level:
-        print(f"delta={trace - w.sum():<.1e} ", end="")
+        print(f"sum={w.sum():<.1e} d={trace - w.sum():<.1e} ", end="")
         print("[%.3fs]" % (time.time() - start))
         sys.stdout.flush()
 

From fb7f2bbe8f9d83e6389b4be032bbef7fe053ff54 Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Thu, 26 Dec 2024 10:02:00 +0900
Subject: [PATCH 10/12] Update github workflows for no-lapacke as default

---
 .../phono3py-pytest-conda-mkl-phphmtblas.yml  |  2 +-
 .../phono3py-pytest-conda-mkl-v2.yml          |  2 +-
 .../workflows/phono3py-pytest-conda-mkl.yml   |  2 +-
 .../phono3py-pytest-conda-phphmtblas.yml      |  2 +-
 ...=> phono3py-pytest-conda-with-lapacke.yml} |  4 +-
 .github/workflows/phono3py-pytest-conda.yml   |  4 +-
 doc/direct-solution.md                        | 36 ++++++---------
 doc/install.md                                | 46 ++++++++++---------
 8 files changed, 48 insertions(+), 50 deletions(-)
 rename .github/workflows/{phono3py-pytest-conda-nolapacke.yml => phono3py-pytest-conda-with-lapacke.yml} (86%)

diff --git a/.github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml b/.github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml
index 49e60dd4..2c149f50 100644
--- a/.github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml
+++ b/.github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml
@@ -42,7 +42,7 @@ jobs:
     - name: Install phono3py
       run: |
         conda activate test
-        PHPHCALC_USE_MTBLAS=ON pip install -e . -vvv
+        BUILD_WITHOUT_LAPACKE=OFF PHPHCALC_USE_MTBLAS=ON pip install -e . -vvv
     - name: Run pytest
       run: |
         conda activate test
diff --git a/.github/workflows/phono3py-pytest-conda-mkl-v2.yml b/.github/workflows/phono3py-pytest-conda-mkl-v2.yml
index c1e95df6..2ff17580 100644
--- a/.github/workflows/phono3py-pytest-conda-mkl-v2.yml
+++ b/.github/workflows/phono3py-pytest-conda-mkl-v2.yml
@@ -42,7 +42,7 @@ jobs:
     - name: Install phono3py
       run: |
         conda activate test
-        pip install -e . -vvv
+        BUILD_WITHOUT_LAPACKE=OFF pip install -e . -vvv
     - name: Run pytest
       run: |
         conda activate test
diff --git a/.github/workflows/phono3py-pytest-conda-mkl.yml b/.github/workflows/phono3py-pytest-conda-mkl.yml
index c1ae62de..15df9803 100644
--- a/.github/workflows/phono3py-pytest-conda-mkl.yml
+++ b/.github/workflows/phono3py-pytest-conda-mkl.yml
@@ -46,7 +46,7 @@ jobs:
     - name: Run pytest
       run: |
         conda activate test
-        pytest -v --cov=./ --cov-report=xml test
+        BUILD_WITHOUT_LAPACKE=OFF pytest -v --cov=./ --cov-report=xml test
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v3
       with:
diff --git a/.github/workflows/phono3py-pytest-conda-phphmtblas.yml b/.github/workflows/phono3py-pytest-conda-phphmtblas.yml
index cd4d625e..d7fde199 100644
--- a/.github/workflows/phono3py-pytest-conda-phphmtblas.yml
+++ b/.github/workflows/phono3py-pytest-conda-phphmtblas.yml
@@ -42,7 +42,7 @@ jobs:
     - name: Install phono3py
       run: |
         conda activate test
-        PHPHCALC_USE_MTBLAS=ON pip install -e . -vvv
+        BUILD_WITHOUT_LAPACKE=OFF PHPHCALC_USE_MTBLAS=ON pip install -e . -vvv
     - name: Run pytest
       run: |
         conda activate test
diff --git a/.github/workflows/phono3py-pytest-conda-nolapacke.yml b/.github/workflows/phono3py-pytest-conda-with-lapacke.yml
similarity index 86%
rename from .github/workflows/phono3py-pytest-conda-nolapacke.yml
rename to .github/workflows/phono3py-pytest-conda-with-lapacke.yml
index a114f4e4..ba6ea604 100644
--- a/.github/workflows/phono3py-pytest-conda-nolapacke.yml
+++ b/.github/workflows/phono3py-pytest-conda-with-lapacke.yml
@@ -24,7 +24,7 @@ jobs:
       run: |
         conda activate test
         conda install --yes python=${{ matrix.python-version }}
-        conda install --yes matplotlib-base pyyaml h5py scipy pytest spglib cmake c-compiler cxx-compiler
+        conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py scipy pytest spglib cmake c-compiler cxx-compiler
     - name: Install symfc develop branch
       run: |
         conda activate test
@@ -42,7 +42,7 @@ jobs:
     - name: Install phono3py
       run: |
         conda activate test
-        BUILD_WITHOUT_LAPACKE=ON pip install -e . -vvv
+        BUILD_WITHOUT_LAPACKE=OFF pip install -e . -vvv
     - name: Run pytest
       run: |
         conda activate test
diff --git a/.github/workflows/phono3py-pytest-conda.yml b/.github/workflows/phono3py-pytest-conda.yml
index 99b0a596..ac42faa9 100644
--- a/.github/workflows/phono3py-pytest-conda.yml
+++ b/.github/workflows/phono3py-pytest-conda.yml
@@ -25,13 +25,13 @@ jobs:
       run: |
         conda activate test
         conda install --yes python=${{ matrix.python-version }}
-        conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py "numpy>=2.1" scipy pytest spglib alm cmake c-compiler cxx-compiler pypolymlp
+        conda install --yes matplotlib-base pyyaml h5py "numpy>=2.1" scipy pytest spglib alm cmake c-compiler cxx-compiler pypolymlp
     - name: Install dependent packages for python == 3.9
       if: ${{ matrix.python-version == 3.9 }}
       run: |
         conda activate test
         conda install --yes python=${{ matrix.python-version }}
-        conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py scipy pytest spglib alm cmake c-compiler cxx-compiler
+        conda install --yes matplotlib-base pyyaml h5py scipy pytest spglib alm cmake c-compiler cxx-compiler
     - name: Install symfc develop branch
       run: |
         conda activate test
diff --git a/doc/direct-solution.md b/doc/direct-solution.md
index 2d716feb..54c8edf7 100644
--- a/doc/direct-solution.md
+++ b/doc/direct-solution.md
@@ -295,24 +295,23 @@ language implementation through the python C-API.
 
 ## Solver choice for diagonalization
 
-For larger systems, diagonalization of collision matrix takes longest time and
-requires large memory space. Phono3py relies on LAPACK for the diagonalization
-and so the performance is dependent on the choice of the diagonalization solver.
-
-Using multithreaded BLAS with many-core computing node, computing time may be
-well reduced and the calculation can finish in a realistic time. Currently
-scipy, numpy and LAPACKE can be used as the LAPACK wrapper in phono3py. Scipy
-and numpy distributed by anaconda are MKL linked, therefore MKL multithread BLAS
-is used through them. Multithreaded OpenBLAS is installed by conda and can be
-used via LAPACKE in phono3py. MKL LAPACK and BLAS are also able to be used via
-LAPACKE in phono3py with appropriate setting in `setup.py`.
-
-Using `--pinv-solver NUMBER`, one of the following solver is chosen:
-
-1. Lapacke `dsyev`: Smaller memory consumption than `dsyevd`, but slower. This
+Diagonalizing the collision matrix for larger systems is the most time-consuming
+step and requires significant memory. Phono3py uses LAPACK for diagonalization,
+making performance highly dependent on the solver choice. Utilizing
+multithreaded BLAS on many-core nodes can significantly reduce computation time,
+allowing calculations to complete within practical limits. Currently, Phono3py
+supports diagonalization via scipy, numpy, and LAPACKE as LAPACK wrappers.
+
+The default choice of the diagonalization solver is `scipy.linalg.lapack.dsyev`
+(`--pinv-solver=4`). Using `--pinv-solver NUMBER`, one of the following solvers
+is specified:
+
+1. (Only available when {ref}`compiling with LAPACKE <install_with_lapacke>`)
+   Lapacke `dsyev`: Smaller memory consumption than `dsyevd`, but slower. This
    is the default solver when MKL LAPACKE is integrated or scipy is not
    installed.
-2. Lapacke `dsyevd`: Larger memory consumption than `dsyev`, but faster. This is
+2. (Only available when {ref}`compiling with LAPACKE <install_with_lapacke>`)
+   Lapacke `dsyevd`: Larger memory consumption than `dsyev`, but faster. This is
    not considered as stable as `dsyev` but can be significantly faster than
    `dsyev` for solving large collision matrix. It is recommended to compare the
    result with that by `dsyev` solver using smaller collision matrix (e.g.,
@@ -323,8 +322,3 @@ Using `--pinv-solver NUMBER`, one of the following solver is chosen:
    LAPACKE is not integrated.
 5. Scipy's `dsyevd`: Similar to solver (2), this solver should be used
    carefully.
-
-```{note}
-`pinv-solver` =3, 4, and 5 are only available when phono3py is compiled
-without LAPACKE.
-```
diff --git a/doc/install.md b/doc/install.md
index 6ff25900..17b6de30 100644
--- a/doc/install.md
+++ b/doc/install.md
@@ -41,8 +41,9 @@ removed.
 If phono3py is compiled with a special compiler or special options, manual
 modification of `CMakeLists.txt` may be needed.
 
-- {ref}`Linear algebra library <install_lapacke>`: BLAS, LAPACK, and LAPACKE
 - {ref}`OpenMP library <install_openmp>`: For the multithreding support.
+- {ref}`Linear algebra library <install_lapacke>`: BLAS, LAPACK, and LAPACKE
+  (optional, see {ref}`install_with_lapacke`)
 
 These packages may be installed by the package manager of OS (e.g. `apt`) or
 conda environment. Automatic search of required libraries and flags that are
@@ -61,24 +62,6 @@ See an example at {ref}`install_an_example`. In the standard output, flags and
 libraries found by cmake are shown. Please carefully check if those
 configurations are expected ones or not.
 
-(install_without_lapacke)=
-### Building without linking LAPACKE
-
-**Experimental**
-
-To compile phono3py without linking LAPACKE in C, use the following command:
-
-```
-% BUILD_WITHOUT_LAPACKE=ON pip install -e . -vvv
-```
-
-When this option is enabled, linking to BLAS and LAPACKE libraries is not
-required, so installing these libraries for C compilation may not be necessary.
-However, since numpy and scipy rely on BLAS and LAPACK libraries, their runtime
-versions are still required.
-
-(install_an_example)=
-
 ## Installation instruction of latest development version of phono3py
 
 When using conda, `PYTHONPATH` should not be set if possible because potentially
@@ -122,7 +105,7 @@ wrong python libraries can be imported.
    % conda install numpy scipy h5py pyyaml matplotlib-base c-compiler cxx-compiler cmake spglib
    ```
 
-   Unless {ref}`install_without_lapacke`, the following packages will be
+   Unless {ref}`install_with_lapacke`, the following packages will be
    necessary to compile phono3py:
 
    ```bash
@@ -142,7 +125,7 @@ wrong python libraries can be imported.
    % conda install numpy scipy h5py pyyaml matplotlib-base c-compiler cxx-compiler spglib cmake
    ```
 
-   Unless {ref}`install_without_lapacke`, the following package will be
+   Unless {ref}`install_with_lapacke`, the following package will be
    necessary to compile phono3py:
 
    ```bash
@@ -185,6 +168,27 @@ LAPACK*E* is the C-wrapper of LAPACK and LAPACK relies on BLAS. Both
 single-thread or multithread BLAS can be used in phono3py. In the following,
 multiple different ways of installation of LAPACKE are explained.
 
+(install_with_lapacke)=
+#### Building with linking LAPACKE
+
+Phono3py can operate without linking to LAPACKE, which is the default
+compilation setting. However, it is also possible to compile Phono3py with
+LAPACKE support. When compiled this way, the diagonalization of the dynamical
+matrix is handled by LAPACK routines within the C code of Phono3py.
+Additionally, LAPACK is used for the diagonalization of the collision matrix
+in the direct solution.
+
+To compile phono3py with linking LAPACKE in C, use the following command:
+
+```
+% BUILD_WITHOUT_LAPACKE=OFF pip install -e . -vvv
+```
+
+For this, BLAS and LAPACKE libraries are required.
+
+(install_an_example)=
+
+
 #### OpenBLAS provided by conda
 
 The installation of LAPACKE is easy by conda. It is:

From 1184cc00c4da32597662c65ff0aa087f7988fdd4 Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Thu, 26 Dec 2024 10:11:06 +0900
Subject: [PATCH 11/12] Fix titles of github workflows

---
 .github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml | 2 +-
 .github/workflows/phono3py-pytest-conda-with-lapacke.yml   | 2 +-
 .github/workflows/phono3py-pytest-conda.yml                | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml b/.github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml
index 2c149f50..7a276266 100644
--- a/.github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml
+++ b/.github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml
@@ -1,4 +1,4 @@
-name: Pytest with mkl  sing BLAS for phph-calc
+name: Pytest with mkl using BLAS for phph-calc
 
 on:
   pull_request:
diff --git a/.github/workflows/phono3py-pytest-conda-with-lapacke.yml b/.github/workflows/phono3py-pytest-conda-with-lapacke.yml
index ba6ea604..09e41605 100644
--- a/.github/workflows/phono3py-pytest-conda-with-lapacke.yml
+++ b/.github/workflows/phono3py-pytest-conda-with-lapacke.yml
@@ -1,4 +1,4 @@
-name: Pytest without linking BLAS and LAPACK in C
+name: Pytest with linking BLAS and LAPACK in C
 
 on:
   pull_request:
diff --git a/.github/workflows/phono3py-pytest-conda.yml b/.github/workflows/phono3py-pytest-conda.yml
index ac42faa9..bc6e8e8d 100644
--- a/.github/workflows/phono3py-pytest-conda.yml
+++ b/.github/workflows/phono3py-pytest-conda.yml
@@ -1,4 +1,4 @@
-name: Pytest with openblas
+name: Pytest without using LAPACKE
 
 on:
   pull_request:

From 3a7458b207f1c28f29acf98f0c9dafbc69c54735 Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Thu, 26 Dec 2024 10:17:52 +0900
Subject: [PATCH 12/12] Set version 3.10.2

---
 doc/changelog.md    | 4 ++++
 doc/conf.py         | 2 +-
 phono3py/version.py | 2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/doc/changelog.md b/doc/changelog.md
index 85cc3446..3d22fee3 100644
--- a/doc/changelog.md
+++ b/doc/changelog.md
@@ -2,6 +2,10 @@
 
 # Change Log
 
+## Dec-26-2024: Version 3.10.2
+
+- `BUILD_WITHOUT_LAPACKE=ON` was made as the default compilation choice.
+
 ## Dec-23-2024: Version 3.10.1
 
 - Replace `dtype="int_"` by `dtype="long"`.
diff --git a/doc/conf.py b/doc/conf.py
index 319c91eb..3682b15e 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -60,7 +60,7 @@
 # The short X.Y version.
 version = "3.10"
 # The full version, including alpha/beta/rc tags.
-release = "3.10.1"
+release = "3.10.2"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/phono3py/version.py b/phono3py/version.py
index 97046b22..a589b5d7 100644
--- a/phono3py/version.py
+++ b/phono3py/version.py
@@ -34,4 +34,4 @@
 # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
-__version__ = "3.10.1"
+__version__ = "3.10.2"