dftd3 1.3.0__tar.gz → 1.3.2__tar.gz

{dftd3-1.3.0 → dftd3-1.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dftd3
-Version: 1.3.0
+Version: 1.3.2
 Summary: Python API of the DFT-D3 project
 License: LGPL-3.0-or-later
 Classifier: Intended Audience :: Science/Research
@@ -12,6 +12,7 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Scientific/Engineering :: Chemistry
 Classifier: Topic :: Scientific/Engineering :: Physics
 Project-URL: repository, https://github.com/dftd3/simple-dftd3
@@ -254,7 +255,7 @@ Now you are ready to use ``dftd3``, check if you can import it with
    >>> import dftd3
    >>> from dftd3.library import get_api_version
    >>> get_api_version()
-   '1.3.0'
+   '1.3.2'
 
 
 Building the extension module

{dftd3-1.3.0 → dftd3-1.3.2}/README.rst

@@ -222,7 +222,7 @@ Now you are ready to use ``dftd3``, check if you can import it with
    >>> import dftd3
    >>> from dftd3.library import get_api_version
    >>> get_api_version()
-   '1.3.0'
+   '1.3.2'
 
 
 Building the extension module

{dftd3-1.3.0 → dftd3-1.3.2}/dftd3/__init__.py

@@ -18,4 +18,4 @@
 # make sure we have a CFFI available
 import cffi
 
-__version__ = "1.3.0"
+__version__ = "1.3.2"

{dftd3-1.3.0 → dftd3-1.3.2}/meson.build

@@ -19,7 +19,7 @@
 project(
   'dftd3',
   'c',
-  version: '1.3.0',
+  version: '1.3.2',
   license: 'LGPL-3.0-or-later',
   meson_version: '>=0.55,!=1.8.0',
   default_options: [

{dftd3-1.3.0 → dftd3-1.3.2}/pyproject.toml

@@ -9,7 +9,7 @@ build-backend = "mesonpy"
 
 [project]
 name = "dftd3"
-version = "1.3.0"
+version = "1.3.2"
 description = "Python API of the DFT-D3 project"
 readme = "README.rst"
 license.text = "LGPL-3.0-or-later"
@@ -25,6 +25,7 @@ classifiers = [
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: 3.14",
   "Topic :: Scientific/Engineering :: Chemistry",
   "Topic :: Scientific/Engineering :: Physics",
 ]

{dftd3-1.3.0 → dftd3-1.3.2}/subprojects/s-dftd3/.github/workflows/build.yml

@@ -181,7 +181,7 @@ jobs:
          --no-rebuild
          --num-processes 1
          --suite s-dftd3
-         -t 2
+         -t 10
       env:
         OMP_NUM_THREADS: 1,2,1
 

{dftd3-1.3.0 → dftd3-1.3.2}/subprojects/s-dftd3/.github/workflows/wheel.yml

@@ -92,7 +92,7 @@ jobs:
             cibw-${{ runner.os }}-
 
       - name: Install cibuildwheel
-        run: python -m pip install "cibuildwheel==2.23.4"
+        run: python -m pip install "cibuildwheel==3.4.1"
 
       - name: Download sdist
         uses: actions/download-artifact@v4
@@ -156,9 +156,43 @@ jobs:
           tag: ${{ github.ref }}
           overwrite: true
 
-      - name: Publish to PyPI
-        if: ${{ github.event_name == 'release' }}
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_TOKEN }}
+  publish-to-pypi:
+    name: Publish to PyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+      - sdist
+      - wheels
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/dftd3
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download sdist
+      uses: actions/download-artifact@v4
+      with:
+        name: dftd3-python-sdist
+        path: dist/
+
+    - name: Download manylinux wheels
+      uses: actions/download-artifact@v4
+      with:
+        name: dftd3-python-ubuntu-latest
+        path: dist/
+
+    - name: Download windows wheels
+      uses: actions/download-artifact@v4
+      with:
+        name: dftd3-python-windows-latest
+        path: dist/
+
+    - name: Download osx wheels
+      uses: actions/download-artifact@v4
+      with:
+        name: dftd3-python-macos-14
+        path: dist/
+
+    - name: Publish distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

{dftd3-1.3.0 → dftd3-1.3.2}/subprojects/s-dftd3/CMakeLists.txt

@@ -19,7 +19,7 @@ cmake_minimum_required(VERSION 3.14)
 project(
   "s-dftd3"
   LANGUAGES "Fortran"
-  VERSION "1.3.0"
+  VERSION "1.3.2"
   DESCRIPTION "Simple reimplementation of the DFT-D3 dispersion model"
 )
 

{dftd3-1.3.0 → dftd3-1.3.2}/subprojects/s-dftd3/doc/comparison.rst

@@ -70,6 +70,10 @@ A list of projects currently using this DFT-D3 implementation is given here.
   All-electron electronic structure theory with numeric atom-centered orbitals.\ :footcite:`blum2009`
 `VASP <https://www.vasp.at/>`_: (since 6.6.0)
   The Vienna Ab initio Simulation Package: atomic scale materials modelling from first principles.\ :footcite:`kresse1999`
+`REST <https://gitee.com/RESTGroup/rest>`_:
+  Rust-based Electronic Structure Toolkit is a next-generation electronic structure calculation platform
+  developed by the Research Center for Chemical Theory (RCCT) at Fudan University.
+  Provides Rust bindings in `dftd3-rs <https://github.com/RESTGroup/dftd3-rs>`_.
 
 If your project is using *s-dftd3* feel free to add your project to this list.
 

{dftd3-1.3.0 → dftd3-1.3.2}/subprojects/s-dftd3/fpm.toml

@@ -1,15 +1,15 @@
 name = "s-dftd3"
-version = "1.3.0"
+version = "1.3.2"
 license = "LGPL-3.0-or-later"
 maintainer = ["@awvwgk"]
 author = ["Sebastian Ehlert"]
-copyright = "2019-2022 Sebastian Ehlert"
+copyright = "2019-2026 Sebastian Ehlert"
 description = "Simple reimplementation of the DFT-D3 method"
 keywords = ["dispersion-correction", "quantum-chemistry"]
 
 [dependencies]
 mctc-lib.git = "https://github.com/grimme-lab/mctc-lib"
-mctc-lib.tag = "v0.4.1"
+mctc-lib.tag = "v0.5.0"
 
 [dev-dependencies]
 mstore.git = "https://github.com/grimme-lab/mstore"

{dftd3-1.3.0 → dftd3-1.3.2}/subprojects/s-dftd3/meson.build

@@ -17,7 +17,7 @@
 project(
   's-dftd3',
   'fortran',
-  version: '1.3.0',
+  version: '1.3.2',
   license: 'LGPL-3.0-or-later',
   meson_version: '>=0.55,!=1.8.0',
   default_options: [

{dftd3-1.3.0 → dftd3-1.3.2}/subprojects/s-dftd3/python/README.rst

@@ -222,7 +222,7 @@ Now you are ready to use ``dftd3``, check if you can import it with
    >>> import dftd3
    >>> from dftd3.library import get_api_version
    >>> get_api_version()
-   '1.3.0'
+   '1.3.2'
 
 
 Building the extension module

{dftd3-1.3.0 → dftd3-1.3.2}/subprojects/s-dftd3/python/dftd3/__init__.py

@@ -18,4 +18,4 @@
 # make sure we have a CFFI available
 import cffi
 
-__version__ = "1.3.0"
+__version__ = "1.3.2"

{dftd3-1.3.0 → dftd3-1.3.2}/subprojects/s-dftd3/python/meson.build

@@ -19,7 +19,7 @@
 project(
   'dftd3',
   'c',
-  version: '1.3.0',
+  version: '1.3.2',
   license: 'LGPL-3.0-or-later',
   meson_version: '>=0.55,!=1.8.0',
   default_options: [

{dftd3-1.3.0 → dftd3-1.3.2}/subprojects/s-dftd3/python/pyproject.toml

@@ -9,7 +9,7 @@ build-backend = "mesonpy"
 
 [project]
 name = "dftd3"
-version = "1.3.0"
+version = "1.3.2"
 description = "Python API of the DFT-D3 project"
 readme = "README.rst"
 license.text = "LGPL-3.0-or-later"
@@ -25,6 +25,7 @@ classifiers = [
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: 3.14",
   "Topic :: Scientific/Engineering :: Chemistry",
   "Topic :: Scientific/Engineering :: Physics",
 ]

{dftd3-1.3.0 → dftd3-1.3.2}/subprojects/s-dftd3/src/dftd3/api.f90

@@ -964,7 +964,7 @@ end subroutine set_gcp_realspace_cutoff
 subroutine delete_gcp_api(vgcp) &
       & bind(C, name=namespace//"delete_gcp")
    type(c_ptr), intent(inout) :: vgcp
-   type(vp_error), pointer :: gcp
+   type(vp_gcp), pointer :: gcp
 
    if (c_associated(vgcp)) then
       call c_f_pointer(vgcp, gcp)

{dftd3-1.3.0 → dftd3-1.3.2}/subprojects/s-dftd3/src/dftd3/damping/atm.f90

@@ -329,9 +329,9 @@ subroutine get_atm_dispersion_derivs(mol, trans, cutoff, s9, rs9, alp, rvdw, c6,
                   energy_local(jat) = energy_local(jat) - dE/3.0_wp
                   energy_local(kat) = energy_local(kat) - dE/3.0_wp
 
-                  gradient_local(:, iat) = gradient_local(:, iat) - dGij - dGik
-                  gradient_local(:, jat) = gradient_local(:, jat) + dGij - dGjk
-                  gradient_local(:, kat) = gradient_local(:, kat) + dGik + dGjk
+                  gradient_local(:, iat) = gradient_local(:, iat) - (dGij + dGik) * triple
+                  gradient_local(:, jat) = gradient_local(:, jat) + (dGij - dGjk) * triple
+                  gradient_local(:, kat) = gradient_local(:, kat) + (dGik + dGjk) * triple
 
                   do ic = 1, 3
                      do jc = 1, 3

{dftd3-1.3.0 → dftd3-1.3.2}/subprojects/s-dftd3/src/dftd3/disp.f90

@@ -99,6 +99,7 @@ subroutine get_dispersion_atomic(mol, disp, param, cutoff, energies, gradient, s
    call param%get_dispersion3(mol, lattr, cutoff%disp3, disp%rvdw, disp%r4r2, c6, dc6dcn, &
       & energies, dEdcn, gradient, sigma)
    if (grad) then
+      call get_lattice_points(mol%periodic, mol%lattice, cutoff%cn, lattr)
       call add_coordination_number_derivs(mol, lattr, cutoff%cn, disp%rcov, dEdcn, &
          & gradient, sigma)
    end if

{dftd3-1.3.0 → dftd3-1.3.2}/subprojects/s-dftd3/src/dftd3/version.f90

@@ -24,10 +24,10 @@ module dftd3_version
 
 
    !> String representation of the s-dftd3 version
-   character(len=*), parameter :: dftd3_version_string = "1.3.0"
+   character(len=*), parameter :: dftd3_version_string = "1.3.2"
 
    !> Numeric representation of the s-dftd3 version
-   integer, parameter :: dftd3_version_compact(3) = [1, 3, 0]
+   integer, parameter :: dftd3_version_compact(3) = [1, 3, 2]
 
 
 contains

{dftd3-1.3.0 → dftd3-1.3.2}/subprojects/s-dftd3/subprojects/mctc-lib.wrap

@@ -1,4 +1,4 @@
 [wrap-git]
 directory = mctc-lib
 url = https://github.com/grimme-lab/mctc-lib
-revision = v0.4.1
+revision = v0.5.1

{dftd3-1.3.0 → dftd3-1.3.2}/subprojects/s-dftd3/subprojects/toml-f.wrap

@@ -1,4 +1,4 @@
 [wrap-git]
 directory = toml-f
 url = https://github.com/toml-f/toml-f
-revision = v0.4.2
+revision = v0.5.0

{dftd3-1.3.0 → dftd3-1.3.2}/subprojects/s-dftd3/test/unit/test_periodic.f90

@@ -51,10 +51,10 @@ subroutine collect_periodic(testsuite)
       & new_unittest("M06L-D3(0)", test_m06ld3zero_cyanamide), &
       & new_unittest("rPW86PBE-D3(0)", test_rpw86pbed3zero_co2), &
       & new_unittest("revSSB-D3(0)", test_revssbd3zero_cytosine), &
-      ! new_unittest("HSEsol-D3(BJ)-ATM", test_hsesold3bjatm_oxacb), &
+      & new_unittest("HSEsol-D3(BJ)-ATM", test_hsesold3bjatm_oxacb), &
       ! new_unittest("PWGGA-D3(BJ)-ATM", test_pwggad3bjatm_pyrazine), &
-      ! new_unittest("B3PW91-D3(0)-ATM", test_b3pw91d3zeroatm_urea), &
-      ! new_unittest("RPBE-D3(0)-ATM", test_rpbed3zeroatm_hexamine) &
+      & new_unittest("B3PW91-D3(0)-ATM", test_b3pw91d3zeroatm_urea), &
+      & new_unittest("RPBE-D3(0)-ATM", test_rpbed3zeroatm_hexamine), &
       & new_unittest("revPBE-D3(BJ)", test_revpbed3bj_1d), &
       & new_unittest("BP86-D3(0)", test_bp86d3zero_2d) &
       & ]
@@ -90,7 +90,7 @@ subroutine test_dftd3_gen(error, mol, param, ref)
 end subroutine test_dftd3_gen
 
 
-subroutine test_numgrad(error, mol, param)
+subroutine test_numgrad(error, mol, param, thr_in)
 
    !> Error handling
    type(error_type), allocatable, intent(out) :: error
@@ -101,37 +101,112 @@ subroutine test_numgrad(error, mol, param)
    !> Damping parameters
    class(damping_param), intent(in) :: param
 
+   !> Gradient threshold
+   real(wp), intent(in), optional :: thr_in
+
    integer :: iat, ic
    type(d3_model) :: d3
-   real(wp) :: energy, er, el, sigma(3, 3)
+   real(wp) :: energy, er, el, sigma(3, 3), thr_grad, numerr
    real(wp), allocatable :: gradient(:, :), numgrad(:, :)
    real(wp), parameter :: step = 1.0e-6_wp
+   logical :: tight
 
    allocate(gradient(3, mol%nat), numgrad(3, mol%nat))
    call new_d3_model(d3, mol)
+   thr_grad = thr2
+   if (present(thr_in)) thr_grad = thr_in
+   tight = present(thr_in)
 
    do iat = 1, mol%nat
       do ic = 1, 3
-         mol%xyz(ic, iat) = mol%xyz(ic, iat) + step
-         call get_dispersion(mol, d3, param, cutoff, er)
-         mol%xyz(ic, iat) = mol%xyz(ic, iat) - 2*step
-         call get_dispersion(mol, d3, param, cutoff, el)
-         mol%xyz(ic, iat) = mol%xyz(ic, iat) + step
-         numgrad(ic, iat) = 0.5_wp*(er - el)/step
+         if (tight) then
+            call ridders_cartesian(ic, iat, numgrad(ic, iat), numerr)
+         else
+            mol%xyz(ic, iat) = mol%xyz(ic, iat) + step
+            call get_dispersion(mol, d3, param, cutoff, er)
+            mol%xyz(ic, iat) = mol%xyz(ic, iat) - 2*step
+            call get_dispersion(mol, d3, param, cutoff, el)
+            mol%xyz(ic, iat) = mol%xyz(ic, iat) + step
+            numgrad(ic, iat) = 0.5_wp*(er - el)/step
+         end if
       end do
    end do
 
    call get_dispersion(mol, d3, param, cutoff, energy, gradient, sigma)
 
-   if (any(abs(gradient - numgrad) > thr2)) then
+   if (any(abs(gradient - numgrad) > thr_grad)) then
       call test_failed(error, "Gradient of dispersion energy does not match")
       print'(3es21.14)', gradient-numgrad
    end if
 
+contains
+
+subroutine ridders_cartesian(ic, iat, deriv, err)
+
+   integer, intent(in) :: ic, iat
+   real(wp), intent(out) :: deriv, err
+
+   integer, parameter :: max_tab = 10
+   real(wp), parameter :: initial_step = 1.0e-4_wp
+   real(wp), parameter :: step_div = sqrt(2.0_wp)
+   real(wp), parameter :: step_div_2 = step_div**2
+   integer :: iter, order
+   real(wp) :: table(max_tab, max_tab), factor, err_est, prev_deriv, prev_err
+   real(wp) :: h, x0
+
+   x0 = mol%xyz(ic, iat)
+   h = initial_step
+   err = huge(1.0_wp)
+   prev_err = err
+
+   mol%xyz(ic, iat) = x0 + h
+   call get_dispersion(mol, d3, param, cutoff, er)
+   mol%xyz(ic, iat) = x0 - h
+   call get_dispersion(mol, d3, param, cutoff, el)
+   table(1, 1) = 0.5_wp*(er - el)/h
+   deriv = table(1, 1)
+   prev_deriv = deriv
+
+   do iter = 2, max_tab
+      h = h / step_div
+      mol%xyz(ic, iat) = x0 + h
+      call get_dispersion(mol, d3, param, cutoff, er)
+      mol%xyz(ic, iat) = x0 - h
+      call get_dispersion(mol, d3, param, cutoff, el)
+      table(iter, 1) = 0.5_wp*(er - el)/h
+
+      factor = step_div_2
+      do order = 1, iter - 1
+         factor = factor * step_div_2
+         table(iter, order + 1) = (factor*table(iter, order) &
+            & - table(iter - 1, order))/(factor - 1.0_wp)
+         err_est = max(abs(table(iter, order + 1) - table(iter, order)), &
+            & abs(table(iter, order + 1) - table(iter - 1, order)))
+         if (err_est <= err) then
+            err = err_est
+            deriv = table(iter, order + 1)
+         end if
+      end do
+
+      if (abs(table(iter, iter) - table(iter - 1, iter - 1)) >= 2*err &
+         & .and. iter > 2) then
+         deriv = prev_deriv
+         err = prev_err
+         exit
+      end if
+
+      prev_deriv = deriv
+      prev_err = err
+   end do
+
+   mol%xyz(ic, iat) = x0
+
+end subroutine ridders_cartesian
+
 end subroutine test_numgrad
 
 
-subroutine test_numsigma(error, mol, param)
+subroutine test_numsigma(error, mol, param, thr_in)
 
    !> Error handling
    type(error_type), allocatable, intent(out) :: error
@@ -142,44 +217,131 @@ subroutine test_numsigma(error, mol, param)
    !> Damping parameters
    class(damping_param), intent(in) :: param
 
+   !> Strain derivative threshold
+   real(wp), intent(in), optional :: thr_in
+
    integer :: ic, jc
    type(d3_model) :: d3
    real(wp) :: energy, er, el, sigma(3, 3), eps(3, 3), numsigma(3, 3), lattice(3, 3)
+   real(wp) :: thr_sigma, numerr
    real(wp), allocatable :: gradient(:, :), xyz(:, :)
    real(wp), parameter :: unity(3, 3) = reshape(&
       & [1, 0, 0, 0, 1, 0, 0, 0, 1], shape(unity))
    real(wp), parameter :: step = 1.0e-7_wp
+   logical :: tight
 
    allocate(gradient(3, mol%nat), xyz(3, mol%nat))
    call new_d3_model(d3, mol)
+   thr_sigma = thr3
+   if (present(thr_in)) thr_sigma = thr_in
+   tight = present(thr_in)
 
    eps(:, :) = unity
    xyz(:, :) = mol%xyz
    lattice(:, :) = mol%lattice
    do ic = 1, 3
       do jc = 1, 3
-         eps(jc, ic) = eps(jc, ic) + step
-         mol%xyz(:, :) = matmul(eps, xyz)
-         mol%lattice(:, :) = matmul(eps, lattice)
-         call get_dispersion(mol, d3, param, cutoff, er)
-         eps(jc, ic) = eps(jc, ic) - 2*step
-         mol%xyz(:, :) = matmul(eps, xyz)
-         mol%lattice(:, :) = matmul(eps, lattice)
-         call get_dispersion(mol, d3, param, cutoff, el)
-         eps(jc, ic) = eps(jc, ic) + step
-         mol%xyz(:, :) = xyz
-         mol%lattice(:, :) = lattice
-         numsigma(jc, ic) = 0.5_wp*(er - el)/step
+         if (tight) then
+            call ridders_strain(ic, jc, numsigma(jc, ic), numerr)
+         else
+            eps(jc, ic) = eps(jc, ic) + step
+            mol%xyz(:, :) = matmul(eps, xyz)
+            mol%lattice(:, :) = matmul(eps, lattice)
+            call get_dispersion(mol, d3, param, cutoff, er)
+            eps(jc, ic) = eps(jc, ic) - 2*step
+            mol%xyz(:, :) = matmul(eps, xyz)
+            mol%lattice(:, :) = matmul(eps, lattice)
+            call get_dispersion(mol, d3, param, cutoff, el)
+            eps(jc, ic) = eps(jc, ic) + step
+            mol%xyz(:, :) = xyz
+            mol%lattice(:, :) = lattice
+            numsigma(jc, ic) = 0.5_wp*(er - el)/step
+         end if
       end do
    end do
 
    call get_dispersion(mol, d3, param, cutoff, energy, gradient, sigma)
 
-   if (any(abs(sigma - numsigma) > thr3)) then
+   if (any(abs(sigma - numsigma) > thr_sigma)) then
       call test_failed(error, "Strain derivatives do not match")
       print'(3es21.14)', sigma-numsigma
    end if
 
+contains
+
+subroutine ridders_strain(ic, jc, deriv, err)
+
+   integer, intent(in) :: ic, jc
+   real(wp), intent(out) :: deriv, err
+
+   integer, parameter :: max_tab = 10
+   real(wp), parameter :: initial_step = 5.0e-8_wp
+   real(wp), parameter :: step_div = sqrt(2.0_wp)
+   real(wp), parameter :: step_div_2 = step_div**2
+   integer :: iter, order
+   real(wp) :: table(max_tab, max_tab), factor, err_est, prev_deriv, prev_err
+   real(wp) :: h
+
+   h = initial_step
+   err = huge(1.0_wp)
+   prev_err = err
+
+   call strain_energy(ic, jc, h, er)
+   call strain_energy(ic, jc, -h, el)
+   table(1, 1) = 0.5_wp*(er - el)/h
+   deriv = table(1, 1)
+   prev_deriv = deriv
+
+   do iter = 2, max_tab
+      h = h / step_div
+      call strain_energy(ic, jc, h, er)
+      call strain_energy(ic, jc, -h, el)
+      table(iter, 1) = 0.5_wp*(er - el)/h
+
+      factor = step_div_2
+      do order = 1, iter - 1
+         factor = factor * step_div_2
+         table(iter, order + 1) = (factor*table(iter, order) &
+            & - table(iter - 1, order))/(factor - 1.0_wp)
+         err_est = max(abs(table(iter, order + 1) - table(iter, order)), &
+            & abs(table(iter, order + 1) - table(iter - 1, order)))
+         if (err_est <= err) then
+            err = err_est
+            deriv = table(iter, order + 1)
+         end if
+      end do
+
+      if (abs(table(iter, iter) - table(iter - 1, iter - 1)) >= 2*err &
+         & .and. iter > 2) then
+         deriv = prev_deriv
+         err = prev_err
+         exit
+      end if
+
+      prev_deriv = deriv
+      prev_err = err
+   end do
+
+   mol%xyz(:, :) = xyz
+   mol%lattice(:, :) = lattice
+
+end subroutine ridders_strain
+
+subroutine strain_energy(ic, jc, step, energy)
+
+   integer, intent(in) :: ic, jc
+   real(wp), intent(in) :: step
+   real(wp), intent(out) :: energy
+   real(wp) :: strain(3, 3)
+
+   strain(:, :) = unity
+   strain(jc, ic) = strain(jc, ic) + step
+   mol%xyz(:, :) = matmul(strain, xyz)
+   mol%lattice(:, :) = matmul(strain, lattice)
+   call get_dispersion(mol, d3, param, cutoff, energy)
+
+end subroutine strain_energy
+
 end subroutine test_numsigma
 
 
@@ -340,7 +502,7 @@ subroutine test_hsesold3bjatm_oxacb(error)
 
    call get_structure(mol, "X23", "oxacb")
    call new_rational_damping(param, inp)
-   call test_numgrad(error, mol, param)
+   call test_numgrad(error, mol, param, 1.0e-11_wp)
 
 end subroutine test_hsesold3bjatm_oxacb
 
@@ -358,7 +520,7 @@ subroutine test_pwggad3bjatm_pyrazine(error)
 
    call get_structure(mol, "X23", "pyrazine")
    call new_rational_damping(param, inp)
-   call test_numsigma(error, mol, param)
+   call test_numsigma(error, mol, param, 1.0e-8_wp)
 
 end subroutine test_pwggad3bjatm_pyrazine
 
@@ -376,7 +538,7 @@ subroutine test_b3pw91d3zeroatm_urea(error)
 
    call get_structure(mol, "X23", "urea")
    call new_zero_damping(param, inp)
-   call test_numgrad(error, mol, param)
+   call test_numgrad(error, mol, param, 1.0e-11_wp)
 
 end subroutine test_b3pw91d3zeroatm_urea
 
@@ -394,7 +556,7 @@ subroutine test_rpbed3zeroatm_hexamine(error)
 
    call get_structure(mol, "X23", "hexamine")
    call new_zero_damping(param, inp)
-   call test_numsigma(error, mol, param)
+   call test_numsigma(error, mol, param, 1.0e-8_wp)
 
 end subroutine test_rpbed3zeroatm_hexamine