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Merged
merged 18 commits into from
May 12, 2025
Merged

Support D4S #3

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de18cfc
support d4s
wxj6000 May 7, 2025
7d2a77c
remove tmp file
wxj6000 May 7, 2025
5347d6e
Merge branch 'master' into d4s
wxj6000 May 11, 2025
2ae8017
upgrade dftd4
wxj6000 May 11, 2025
06c2de9
update compilation tool
wxj6000 May 11, 2025
d31fa80
gcc-9
wxj6000 May 11, 2025
2a31211
gcc-10
wxj6000 May 11, 2025
67e6eb1
update tools
wxj6000 May 11, 2025
aa3c039
gcc
wxj6000 May 11, 2025
748f735
rollback dftd4 version
wxj6000 May 11, 2025
fbb1a2f
bugfix dftd4
wxj6000 May 11, 2025
59c0717
wb97x
wxj6000 May 11, 2025
3abc21a
d4s gradient
wxj6000 May 12, 2025
fb407a2
grad=True
wxj6000 May 12, 2025
102cb8a
add warning
wxj6000 May 12, 2025
56a3b0f
add test for wb97x
wxj6000 May 12, 2025
420c8d3
unit test for wb97x
wxj6000 May 12, 2025
85ade10
unit test
wxj6000 May 12, 2025
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17 changes: 12 additions & 5 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -18,10 +18,17 @@ jobs:
python-version: ${{ matrix.python-version }}
- name: Install
run: |
sudo apt-get install -y libopenblas-dev
pip install .
pip install pytest
sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get update
sudo apt install gcc-10 g++-10 gfortran-10
sudo update-alternatives \
--install /usr/bin/gcc gcc /usr/bin/gcc-10 100 \
--slave /usr/bin/gfortran gfortran /usr/bin/gfortran-10 \
--slave /usr/bin/gcov gcov /usr/bin/gcov-10
sudo apt-get install -y libopenblas-dev
pip install .
pip install pytest
- name: Test
run: |
export PYSCF_EXT_PATH=$(pwd):$PYSCF_EXT_PATH
pytest -s pyscf/dispersion
export PYSCF_EXT_PATH=$(pwd):$PYSCF_EXT_PATH
pytest -s pyscf/dispersion
6 changes: 5 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -62,8 +62,12 @@ Makefile
cmake_install.cmake
pyscf/lib/deps
pyscf/lib/config.h

pyscf/lib/cmake/
pyscf/lib/pkgconfig/
pyscf/lib/libdftd4.*
pyscf/lib/libs-dftd3.*
settings.py
*.cmake

# Memoization and caching
tmp/
Expand Down
53 changes: 34 additions & 19 deletions pyscf/dispersion/dftd4.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,9 @@ class _d4_restype(ctypes.Structure):
libdftd4.dftd4_new_error.restype = _d4_p
libdftd4.dftd4_new_structure.restype = _d4_p
libdftd4.dftd4_new_d4_model.restype = _d4_p
libdftd4.dftd4_new_d4s_model.restype = _d4_p
libdftd4.dftd4_custom_d4_model.restype = _d4_p
libdftd4.dftd4_custom_d4s_model.restype = _d4_p
libdftd4.dftd4_load_rational_damping.restype = _d4_p
libdftd4.dftd4_new_rational_damping.restype = _d4_p

Expand All @@ -40,18 +42,22 @@ def error_check(err):
raise RuntimeError(message.value.decode())

class DFTD4Dispersion(lib.StreamObject):
def __init__(self, mol, xc, ga=None, gc=None, wf=None, atm=False):
def __init__(self, mol, xc, version='d4', ga=None, gc=None, wf=None, atm=False):
xc_lc = xc.lower().encode()
self._disp = None
self._mol = None
self._param = None

log = lib.logger.new_logger(mol)
# https://github.com/dftd4/dftd4/pull/276
if xc_lc == 'wb97x':
log.warn('The previous wb97x is renamed as wb97x-2008. Now D4 dispersion for wb97x is the replacement of vv10 in wb97x-v. See https://github.com/dftd4/dftd4/blob/main/README.md')
coords = np.asarray(mol.atom_coords(), dtype=np.double, order='C')
charge = np.array([mol.charge], dtype=np.double)
nuc_types = [gto.charge(mol.atom_symbol(ia))
for ia in range(mol.natm)]
nuc_types = np.asarray(nuc_types, dtype=np.int32)

self.natm = mol.natm
if isinstance(mol, gto.Mole):
lattice = lib.c_null_ptr()
Expand All @@ -71,20 +77,29 @@ def __init__(self, mol, xc, ga=None, gc=None, wf=None, atm=False):
lattice, periodic,
)
error_check(err)
if ga is None and gc is None and wf is None:
self._disp = libdftd4.dftd4_new_d4_model(err, self._mol)
if version.lower() == 'd4':
if ga is None and gc is None and wf is None:
self._disp = libdftd4.dftd4_new_d4_model(err, self._mol)
else:
# Default from DFTD4 repo, https://github.com/dftd4/dftd4/blob/main/python/dftd4/interface.py#L290
if ga is None: ga = 3.0
if gc is None: gc = 2.0
if wf is None: wf = 6.0
self._disp = libdftd4.dftd4_custom_d4_model(err, self._mol,
ctypes.c_double(ga),
ctypes.c_double(gc),
ctypes.c_double(wf))
elif version.lower() == 'd4s':
if ga is None and gc is None:
self._disp = libdftd4.dftd4_new_d4s_model(err, self._mol)
else:
if ga is None: ga = 3.0
if gc is None: gc = 2.0
self._disp = libdftd4.dftd4_custom_d4s_model(err, self._mol,
ctypes.c_double(ga),
ctypes.c_double(gc))
else:
# Default from DFTD4 repo, https://github.com/dftd4/dftd4/blob/main/python/dftd4/interface.py#L290
if ga is None:
ga = 3.0
if gc is None:
gc = 2.0
if wf is None:
wf = 6.0
self._disp = libdftd4.dftd4_custom_d4_model(err, self._mol,
ctypes.c_double(ga),
ctypes.c_double(gc),
ctypes.c_double(wf))
raise ValueError('version must be d4 or d4s')
error_check(err)
self._param = libdftd4.dftd4_load_rational_damping(
err,
Expand All @@ -107,10 +122,10 @@ def __del__(self):
def set_param(self, s8, a1, a2, s6=1.0, s9=1.0, alp=16.0):
self._param = libdftd4.dftd4_new_rational_damping(
ctypes.c_double(s6),
ctypes.c_double(s8),
ctypes.c_double(s9),
ctypes.c_double(a1),
ctypes.c_double(a2),
ctypes.c_double(s8),
ctypes.c_double(s9),
ctypes.c_double(a1),
ctypes.c_double(a2),
ctypes.c_double(alp))
return

Expand Down
86 changes: 84 additions & 2 deletions pyscf/dispersion/tests/test_d4.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,10 +25,16 @@ def test_d4_unknown_xc():

def test_d4_energy():
mol = pyscf.M(atom='H 0 0 0; H 0 0 1')
model = DFTD4Dispersion(mol, xc='WB97X')
model = DFTD4Dispersion(mol, xc='WB97X-2008')
out = model.get_dispersion()
assert abs(out['energy'] - -2.21334459527e-05) < 1e-10

def test_wb97x_d4_energy():
mol = pyscf.M(atom='H 0 0 0; H 0 0 1')
model = DFTD4Dispersion(mol, xc='WB97X')
out = model.get_dispersion()
assert abs(out['energy'] - -0.00027002) < 1e-8

def test_d4_gradients():
mol = pyscf.M(atom='H 0 0 0; H 0 0 1')
model = DFTD4Dispersion(mol, xc='HF')
Expand All @@ -39,6 +45,82 @@ def test_d4_gradients():

def test_d4_with_pbc():
mol = pyscf.M(atom='H 0 0 0; H 0 0 1', a=np.eye(3)*2)
model = DFTD4Dispersion(mol, xc='WB97X')
model = DFTD4Dispersion(mol, xc='WB97X-2008')
out = model.get_dispersion()
assert abs(out['energy'] - -0.002715970438476524) < 1e-10

def test_d4s_energy():
''' Test copied from DFTD4
'''
mol = pyscf.M(
atom="""
Na -1.855282634 3.586705153 -2.417637293
H 4.401780235 0.023388444 -4.954577493
O -2.987060334 4.762520654 1.270433015
H 0.799808860 1.411034556 -5.046553216
F -4.206474694 1.842757675 4.550380848
H -3.543561218 -3.188356651 1.462400217
H 2.700321601 1.068184525 -1.732346503
O 3.731140888 -2.070015433 2.231609376
N -1.753068192 0.359514171 1.053234061
H 5.417557885 -1.578818300 1.753940027
H -2.234628682 -2.138565050 4.109222857
Cl 1.015658662 -3.219521545 -3.360509630
B 2.421192557 0.266264350 -3.918624743
B -3.025260988 2.536678890 2.316649847
N -2.004389486 -2.292351369 2.197828073
Al 1.122265541 -1.369420070 0.484550554
"""
)
model = DFTD4Dispersion(mol, xc="TPSS", version="d4s")
out = model.get_dispersion()
assert abs(out['energy'] - -0.016049411775539424) < 1.0e-7

def test_d4s_gradient():
''' Test copied from DFTD4
'''
mol = pyscf.M(
atom="""
H -1.795376258 -3.778664229 -1.078835583
S -2.682788333 0.388926662 1.662148652
B 0.114846497 1.488579332 3.656603965
O -1.079988795 -0.162591216 -4.557030658
Mg 0.603028329 4.088161496 -0.025893731
H -1.225340893 -1.799813824 -3.707731733
H -1.334609820 -4.248190824 2.727919027
H -0.162780825 2.412679941 5.690306951
Si 2.878024440 -0.331205250 1.883113735
H 0.684893279 0.327902040 -4.205476937
B -1.209197735 -2.872537625 0.940642042
Li -3.255726045 2.212410929 -2.867155493
F -1.831474682 5.205272937 -2.269762706
H 4.908858657 -1.925765619 2.990699194
H 1.268062422 -2.604093417 0.551628052
S 4.119569763 1.598928667 -1.391174777
""",
spin=1
)
ref = np.array(
[
[-1.04361222e-04, -1.65054791e-04, -1.36662175e-04],
[-1.41500522e-03, +1.89282651e-04, +2.16639105e-04],
[-1.18067839e-04, +4.50543787e-04, +1.50087553e-03],
[+3.37690080e-04, -4.10348598e-04, -3.02311767e-04],
[+4.39892308e-04, +1.54862493e-03, +1.33655085e-04],
[+1.31259180e-06, -7.51721105e-05, -1.39848135e-04],
[-4.61111364e-05, -1.65382677e-04, +1.81820530e-04],
[-1.94292825e-05, +7.21791149e-05, +1.79879351e-04],
[+1.14226323e-03, -6.08455689e-04, +6.24007890e-04],
[+6.95738570e-05, -1.86718359e-05, -1.25837081e-04],
[-1.66091884e-04, -1.03519307e-03, -1.71797180e-04],
[-1.29925668e-03, +6.18658801e-05, -6.30138324e-04],
[-1.58991399e-04, +5.73306273e-04, -2.35799582e-04],
[+2.90056077e-04, -2.14985916e-04, +1.62430848e-04],
[+6.43808246e-05, -3.35585457e-04, -2.45131168e-04],
[+9.82145702e-04, +1.33047503e-04, -1.01178292e-03],
]
)

model = DFTD4Dispersion(mol, xc="BLYP", version="d4s")
out = model.get_dispersion(grad=True)
assert np.linalg.norm(out['gradient'] - ref) < 1.0e-7
8 changes: 6 additions & 2 deletions pyscf/lib/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,8 @@
cmake_minimum_required (VERSION 3.5)
project (pyscf-dispersion)

set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -cpp -ffree-line-length-none -Wall")

include(ExternalProject)
# statically compile deps mctc mstore
ExternalProject_Add(dftd3_static
Expand Down Expand Up @@ -46,23 +48,25 @@ add_dependencies(dftd3 dftd3_static)
# statically compile deps mctc mstore
ExternalProject_Add(dftd4_static
GIT_REPOSITORY "https://github.com/dftd4/dftd4"
GIT_TAG v3.7.0
GIT_TAG cf1af36a0f89fdaa2faa15def912148db9f7cb07
GIT_SHALLOW FALSE
GIT_PROGRESS TRUE
PREFIX ${PROJECT_BINARY_DIR}/deps
INSTALL_DIR ${PROJECT_SOURCE_DIR}/deps
CMAKE_ARGS -DWITH_OpenMP=OFF
-DCMAKE_Fortran_FLAGS=-cpp\ -ffree-line-length-none\ -Wall
-DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR>
-DCMAKE_INSTALL_LIBDIR:PATH=lib
)
ExternalProject_Add(dftd4
GIT_REPOSITORY "https://github.com/dftd4/dftd4"
GIT_TAG v3.7.0
GIT_TAG cf1af36a0f89fdaa2faa15def912148db9f7cb07
GIT_SHALLOW FALSE
GIT_PROGRESS TRUE
PREFIX ${PROJECT_BINARY_DIR}/deps
INSTALL_DIR ${PROJECT_SOURCE_DIR}/deps
CMAKE_ARGS -DWITH_OpenMP=OFF -DBUILD_SHARED_LIBS=ON
-DCMAKE_Fortran_FLAGS=-cpp\ -ffree-line-length-none\ -Wall
-DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR>
-DCMAKE_INSTALL_LIBDIR:PATH=${PROJECT_SOURCE_DIR}
)
Expand Down