From 3a6e8265fef570fc239d65ffe002b383a7d61a0c Mon Sep 17 00:00:00 2001 From: fishjojo Date: Fri, 26 Jul 2024 19:33:14 -0700 Subject: [PATCH 1/3] fix canonical_orth, gmres --- LICENSE | 197 ++++++++++++++++++++++++++++ README.md | 13 +- pyscfad/_src/scipy/sparse/linalg.py | 12 +- pyscfad/lo/iao.py | 23 ++-- pyscfad/lo/pipek.py | 3 +- pyscfad/scf/addons.py | 4 +- pyscfad/util.py | 2 +- 7 files changed, 228 insertions(+), 26 deletions(-) diff --git a/LICENSE b/LICENSE index e41a3cce..be514fd7 100644 --- a/LICENSE +++ b/LICENSE @@ -19,3 +19,200 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + +--- + +This software contains code modified from PySCF, which is +licensed under the Apache-2.0 license. The original license terms +are as follows: + + Copyright 2014-2024 PySCF developers + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. For the purposes of this definition, + "control" means (i) the power, direct or indirect, to cause the + direction or management of such entity, whether by contract or + otherwise, or (ii) ownership of fifty percent (50%) or more of the + outstanding shares, or (iii) beneficial ownership of such entity. + + "You" (or "Your") shall mean an individual or Legal Entity + exercising permissions granted by this License. + + "Source" form shall mean the preferred form for making modifications, + including but not limited to software source code, documentation + source, and configuration files. + + "Object" form shall mean any form resulting from mechanical + transformation or translation of a Source form, including but + not limited to compiled object code, generated documentation, + and conversions to other media types. + + "Work" shall mean the work of authorship, whether in Source or + Object form, made available under the License, as indicated by a + copyright notice that is included in or attached to the work + (an example is provided in the Appendix below). + + "Derivative Works" shall mean any work, whether in Source or Object + form, that is based on (or derived from) the Work and for which the + editorial revisions, annotations, elaborations, or other modifications + represent, as a whole, an original work of authorship. For the purposes + of this License, Derivative Works shall not include works that remain + separable from, or merely link (or bind by name) to the interfaces of, + the Work and Derivative Works thereof. + + "Contribution" shall mean any work of authorship, including + the original version of the Work and any modifications or additions + to that Work or Derivative Works thereof, that is intentionally + submitted to Licensor for inclusion in the Work by the copyright owner + or by an individual or Legal Entity authorized to submit on behalf of + the copyright owner. For the purposes of this definition, "submitted" + means any form of electronic, verbal, or written communication sent + to the Licensor or its representatives, including but not limited to + communication on electronic mailing lists, source code control systems, + and issue tracking systems that are managed by, or on behalf of, the + Licensor for the purpose of discussing and improving the Work, but + excluding communication that is conspicuously marked or otherwise + designated in writing by the copyright owner as "Not a Contribution." + + "Contributor" shall mean Licensor and any individual or Legal Entity + on behalf of whom a Contribution has been received by Licensor and + subsequently incorporated within the Work. + + 2. Grant of Copyright License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + copyright license to reproduce, prepare Derivative Works of, + publicly display, publicly perform, sublicense, and distribute the + Work and such Derivative Works in Source or Object form. + + 3. Grant of Patent License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + (except as stated in this section) patent license to make, have made, + use, offer to sell, sell, import, and otherwise transfer the Work, + where such license applies only to those patent claims licensable + by such Contributor that are necessarily infringed by their + Contribution(s) alone or by combination of their Contribution(s) + with the Work to which such Contribution(s) was submitted. If You + institute patent litigation against any entity (including a + cross-claim or counterclaim in a lawsuit) alleging that the Work + or a Contribution incorporated within the Work constitutes direct + or contributory patent infringement, then any patent licenses + granted to You under this License for that Work shall terminate + as of the date such litigation is filed. + + 4. Redistribution. You may reproduce and distribute copies of the + Work or Derivative Works thereof in any medium, with or without + modifications, and in Source or Object form, provided that You + meet the following conditions: + + (a) You must give any other recipients of the Work or + Derivative Works a copy of this License; and + + (b) You must cause any modified files to carry prominent notices + stating that You changed the files; and + + (c) You must retain, in the Source form of any Derivative Works + that You distribute, all copyright, patent, trademark, and + attribution notices from the Source form of the Work, + excluding those notices that do not pertain to any part of + the Derivative Works; and + + (d) If the Work includes a "NOTICE" text file as part of its + distribution, then any Derivative Works that You distribute must + include a readable copy of the attribution notices contained + within such NOTICE file, excluding those notices that do not + pertain to any part of the Derivative Works, in at least one + of the following places: within a NOTICE text file distributed + as part of the Derivative Works; within the Source form or + documentation, if provided along with the Derivative Works; or, + within a display generated by the Derivative Works, if and + wherever such third-party notices normally appear. The contents + of the NOTICE file are for informational purposes only and + do not modify the License. You may add Your own attribution + notices within Derivative Works that You distribute, alongside + or as an addendum to the NOTICE text from the Work, provided + that such additional attribution notices cannot be construed + as modifying the License. + + You may add Your own copyright statement to Your modifications and + may provide additional or different license terms and conditions + for use, reproduction, or distribution of Your modifications, or + for any such Derivative Works as a whole, provided Your use, + reproduction, and distribution of the Work otherwise complies with + the conditions stated in this License. + + 5. Submission of Contributions. Unless You explicitly state otherwise, + any Contribution intentionally submitted for inclusion in the Work + by You to the Licensor shall be under the terms and conditions of + this License, without any additional terms or conditions. + Notwithstanding the above, nothing herein shall supersede or modify + the terms of any separate license agreement you may have executed + with Licensor regarding such Contributions. + + 6. Trademarks. This License does not grant permission to use the trade + names, trademarks, service marks, or product names of the Licensor, + except as required for reasonable and customary use in describing the + origin of the Work and reproducing the content of the NOTICE file. + + 7. Disclaimer of Warranty. Unless required by applicable law or + agreed to in writing, Licensor provides the Work (and each + Contributor provides its Contributions) on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or + implied, including, without limitation, any warranties or conditions + of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A + PARTICULAR PURPOSE. You are solely responsible for determining the + appropriateness of using or redistributing the Work and assume any + risks associated with Your exercise of permissions under this License. + + 8. Limitation of Liability. In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + + END OF TERMS AND CONDITIONS diff --git a/README.md b/README.md index 01a7b64e..02ce3903 100644 --- a/README.md +++ b/README.md @@ -23,12 +23,15 @@ pip install pyscfad ``` pip install git+https://github.com/fishjojo/pyscfad.git ``` +The dependent C library `pyscfadlib` can be compiled from source following the instruction +[here](https://fishjojo.github.io/pyscfad/getting_started/install.html#installing-pyscfadlib). -`pyscfad` depends on `pyscf>=2.3.0`. -Other dependencies include -`numpy>=1.17`, `scipy`, `h5py`, -`pyscfadlib`, -`jax>=0.3.25` and `jaxlib>=0.3.25`. + +`pyscfad` depends on +`numpy`, `scipy`, +`pyscf>=2.3.0`, +`pyscfadlib>=0.1.4`, +`jax>=0.4.14`, and `jaxlib>=0.4.14`. Citing PySCFAD -------------- diff --git a/pyscfad/_src/scipy/sparse/linalg.py b/pyscfad/_src/scipy/sparse/linalg.py index 979b1e1f..8f16bfaf 100644 --- a/pyscfad/_src/scipy/sparse/linalg.py +++ b/pyscfad/_src/scipy/sparse/linalg.py @@ -1,5 +1,6 @@ from functools import reduce import numpy +import scipy from scipy.sparse.linalg import LinearOperator, eigsh from scipy.sparse.linalg import gmres as scipy_gmres from pyscfad import ops @@ -24,9 +25,14 @@ def gmres(A_or_matvec, b, x0=None, *, else: A = numpy.array(ops.to_numpy(A_or_matvec)) - u, info = scipy_gmres(A, b.ravel(), x0=x0, rtol=tol, atol=atol, - restart=restart, maxiter=maxiter, M=M, - callback=callback, callback_type=callback_type) + if scipy.__version__ < '1.12': + u, info = scipy_gmres(A, b.ravel(), x0=x0, tol=tol, atol=atol, + restart=restart, maxiter=maxiter, M=M, + callback=callback, callback_type=callback_type) + else: + u, info = scipy_gmres(A, b.ravel(), x0=x0, rtol=tol, atol=atol, + restart=restart, maxiter=maxiter, M=M, + callback=callback, callback_type=callback_type) if info > 0: raise RuntimeError(f'scipy gmres failed to converge in {info} iterations.') elif info < 0: diff --git a/pyscfad/lo/iao.py b/pyscfad/lo/iao.py index b0064ce2..54ab3fae 100644 --- a/pyscfad/lo/iao.py +++ b/pyscfad/lo/iao.py @@ -1,11 +1,11 @@ +from jax import scipy as jsp from pyscf import __config__ -from pyscf.lib import logger from pyscf.gto import format_atom from pyscf.data.elements import is_ghost_atom -from jax import numpy as np -from jax import scipy +from pyscfad import numpy as np +from pyscfad.lib import logger from pyscfad import gto -from .orth import vec_lowdin +from pyscfad.lo.orth import vec_lowdin MINAO = getattr(__config__, 'lo_iao_minao', 'minao') @@ -23,25 +23,22 @@ def iao(mol, orbocc, minao=MINAO, kpts=None, lindep_threshold=1e-8): s2 = pmol.pbc_intor('int1e_ovlp', hermi=1, kpts=kpts) s12 = pbcgto.cell.intor_cross('int1e_ovlp', mol, pmol, kpts=kpts) else: - #s1 is the one electron overlap integrals (coulomb integrals) s1 = mol.intor_symmetric('int1e_ovlp') - #s2 is the same as s1 except in minao s2 = pmol.intor_symmetric('int1e_ovlp') - #overlap integrals of the two molecules s12 = gto.mole.intor_cross('int1e_ovlp', mol, pmol) def make_iaos(s1, s2, s12, mo): s21 = s12.conj().T # s2 is overlap in minimal reference basis and should never be singular: - s2cd = scipy.linalg.cho_factor(s2) - ctild = scipy.linalg.cho_solve(s2cd, np.dot(s21, mo)) + s2cd = jsp.linalg.cho_factor(s2) + ctild = jsp.linalg.cho_solve(s2cd, np.dot(s21, mo)) try: - s1cd = scipy.linalg.cho_factor(s1) - p12 = scipy.linalg.cho_solve(s1cd, s12) - ctild = scipy.linalg.cho_solve(s1cd, np.dot(s12, ctild)) + s1cd = jsp.linalg.cho_factor(s1) + p12 = jsp.linalg.cho_solve(s1cd, s12) + ctild = jsp.linalg.cho_solve(s1cd, np.dot(s12, ctild)) # s1 can be singular in large basis sets: Use canonical orthogonalization in this case: except Exception: # pylint: disable=broad-exception-caught - from pyscf.scf import addons + from pyscfad.scf import addons x = addons.canonical_orth_(s1, lindep_threshold) p12 = np.linalg.multi_dot((x, x.conj().T, s12)) ctild = np.dot(p12, ctild) diff --git a/pyscfad/lo/pipek.py b/pyscfad/lo/pipek.py index 6d70e0e6..2701fc65 100644 --- a/pyscfad/lo/pipek.py +++ b/pyscfad/lo/pipek.py @@ -3,7 +3,7 @@ import jax from pyscf.lo import pipek as pyscf_pipek from pyscfad import numpy as np -from pyscfad.ops import vmap, jit +from pyscfad.ops import vmap from pyscfad.implicit_diff import make_implicit_diff from pyscfad.soscf.ciah import extract_rotation from pyscfad.tools.linear_solver import gen_gmres @@ -77,7 +77,6 @@ def cost_function(x, mol, mo_coeff, pop_method='mulliken', exponent=2): pop = atomic_pops(mol, mo_coeff, pop_method) return -(np.einsum('xii->xi', pop)**exponent).sum() -@partial(jit, static_argnames=('pop_method', 'exponent')) def _opt_cond(x, mol, mo_coeff, pop_method='mulliken', exponent=2): g = jax.grad(cost_function, 0)(x, mol, mo_coeff, pop_method, exponent) return g diff --git a/pyscfad/scf/addons.py b/pyscfad/scf/addons.py index 3961504f..94913d9b 100644 --- a/pyscfad/scf/addons.py +++ b/pyscfad/scf/addons.py @@ -1,6 +1,6 @@ from functools import wraps -from pyscf import numpy as np from pyscf.scf import addons as pyscf_addons +from pyscfad import numpy as np from pyscfad import scipy @wraps(pyscf_addons.canonical_orth_) @@ -9,7 +9,7 @@ def canonical_orth_(S, thr=1e-7): normlz = np.power(np.diag(S), -0.5) Snorm = np.dot(np.diag(normlz), np.dot(S, np.diag(normlz))) # Form vectors for normalized overlap matrix - Sval, Svec = scipy.linalg.eigh(Snorm, deg_thresh=1e-12) + Sval, Svec = scipy.linalg.eigh(Snorm) X = Svec[:,Sval>=thr] / np.sqrt(Sval[Sval>=thr]) # Plug normalization back in X = np.dot(np.diag(normlz), X) diff --git a/pyscfad/util.py b/pyscfad/util.py index 3729d61d..11023206 100644 --- a/pyscfad/util.py +++ b/pyscfad/util.py @@ -23,7 +23,7 @@ def pytree_node(leaf_names, num_args=0, exclude_aux_name=()): exclude_aux_name : tuple, default=() A set of static attribute names that are not used for comparing the pytrees. Note that ``jax.jit`` recompiles the function for input - pytrees with differen static attribute values. + pytrees with different static attribute values. Notes ----- From 434f3fa149a85346836998603adaecdb614b0e0c Mon Sep 17 00:00:00 2001 From: fishjojo Date: Fri, 26 Jul 2024 20:37:35 -0700 Subject: [PATCH 2/3] Release 0.1.7 --- CHANGELOG.md | 16 ++++++++++++++++ pyscfad/version.py | 2 +- pyscfadlib/pyscfadlib/version.py | 2 +- 3 files changed, 18 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a0075b97..8436d0f7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,21 @@ # Change log +## pyscfad 0.1.7 (July 26, 2024) + +* Changes + * Drop support to Python 3.8. + * Add `pytree.PytreeNode`. + * Adapt class definition using `PytreeNode`. + * Add `util.to_pyscf`. + * Update `gto.mole._moleintor_jvp` for shell slicing. + * Add `scipy.linalg.eigh` JAX primitive for CPU. + * Improve `lo.orth.lowdin` gradient stability. + +* Bug fixes + * Fix example `dft/01-DFT+U.py`. + * Fix `scf.addons.canonical_orth_`. + * Fix GMRES solver for scipy versions before 1.12. + ## pyscfad 0.1.6 (June 27, 2024) * Changes * Update GMRES solver according to scipy updates. diff --git a/pyscfad/version.py b/pyscfad/version.py index 0a8da882..f1380eed 100644 --- a/pyscfad/version.py +++ b/pyscfad/version.py @@ -1 +1 @@ -__version__ = "0.1.6" +__version__ = "0.1.7" diff --git a/pyscfadlib/pyscfadlib/version.py b/pyscfadlib/pyscfadlib/version.py index 2fb25139..124e4620 100644 --- a/pyscfadlib/pyscfadlib/version.py +++ b/pyscfadlib/pyscfadlib/version.py @@ -1 +1 @@ -__version__ = '0.1.6' +__version__ = '0.1.7' From 08b57daa3279f915591a89810b04535682aaba32 Mon Sep 17 00:00:00 2001 From: Xing Zhang Date: Sat, 27 Jul 2024 22:10:40 -0700 Subject: [PATCH 3/3] fix release pipeline (#43) --- .github/workflows/publish_pyscfadlib.yml | 11 ++++++----- pyscfadlib/pyproject.toml | 8 ++++++-- pyscfadlib/pyscfadlib/CMakeLists.txt | 4 ++++ 3 files changed, 16 insertions(+), 7 deletions(-) diff --git a/.github/workflows/publish_pyscfadlib.yml b/.github/workflows/publish_pyscfadlib.yml index 0827464a..c918aaa5 100644 --- a/.github/workflows/publish_pyscfadlib.yml +++ b/.github/workflows/publish_pyscfadlib.yml @@ -19,7 +19,7 @@ jobs: - uses: actions/checkout@v4 - name: Build wheels - uses: pypa/cibuildwheel@v2.16.5 + uses: pypa/cibuildwheel@v2.19.2 env: CIBW_ARCHS_LINUX: "x86_64" CMAKE_CONFIGURE_ARGS: "-DWITH_F12=OFF" @@ -35,14 +35,15 @@ jobs: build_wheel_macos_x86: name: Build macos_x86 wheels - runs-on: macos-12 + runs-on: macos-13 steps: - uses: actions/checkout@v4 - name: Build wheels - uses: pypa/cibuildwheel@v2.16.5 + uses: pypa/cibuildwheel@v2.19.2 env: + MACOSX_DEPLOYMENT_TARGET: "10.14" CMAKE_CONFIGURE_ARGS: "-DWITH_F12=OFF" with: package-dir: pyscfadlib @@ -64,10 +65,10 @@ jobs: - uses: actions/checkout@v4 - name: Build wheels - uses: pypa/cibuildwheel@v2.16.5 + uses: pypa/cibuildwheel@v2.19.2 env: CMAKE_CONFIGURE_ARGS: "-DWITH_F12=OFF" - CMAKE_OSX_ARCHITECTURES: arm64 + CMAKE_OSX_ARCHITECTURES: arm64;x86_64 with: package-dir: pyscfadlib output-dir: pyscfadlib/wheelhouse diff --git a/pyscfadlib/pyproject.toml b/pyscfadlib/pyproject.toml index feed643f..d6a5375d 100644 --- a/pyscfadlib/pyproject.toml +++ b/pyscfadlib/pyproject.toml @@ -1,13 +1,17 @@ +[build-system] +requires = ["setuptools >= 61.0", "wheel", "cmake>=3.18", "nanobind"] +build-backend = "setuptools.build_meta" + [tool.cibuildwheel] build-verbosity = 1 test-requires = ["pytest", "pyscf>=2.3"] test-command = "pytest {package}/test" -test-skip = "cp38-macosx_arm64 cp311-macosx_arm64" +test-skip = "cp311-macosx_arm64" container-engine = "docker" manylinux-x86_64-image = "manylinux2014" -skip = ["pp*", "*musllinux*", "*universal2"] +skip = ["pp*", "*musllinux*"] [tool.cibuildwheel.linux] archs = ["x86_64"] diff --git a/pyscfadlib/pyscfadlib/CMakeLists.txt b/pyscfadlib/pyscfadlib/CMakeLists.txt index 9a595a2b..7c2b3988 100644 --- a/pyscfadlib/pyscfadlib/CMakeLists.txt +++ b/pyscfadlib/pyscfadlib/CMakeLists.txt @@ -28,6 +28,10 @@ endif() set(CMAKE_C_FLAGS "-Wall ${CMAKE_C_FLAGS}") set(CMAKE_CXX_FLAGS "-Wall ${CMAKE_CXX_FLAGS}") +#if (APPLE) +# set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -faligned-allocation") +#endif() + option(BUILD_MARCH_NATIVE "gcc flag -march=native" off) if (BUILD_MARCH_NATIVE) include(CheckCCompilerFlag)