From 9a18b8b31d28a9db04d2812cd48ced711375ae55 Mon Sep 17 00:00:00 2001 From: Qiming Sun Date: Sat, 1 Jun 2024 09:31:06 -0700 Subject: [PATCH] Update for 2.6 release --- source/install.rst | 19 +++++++++++++------ source/interface/geomopt.rst | 2 +- source/user/geomopt.rst | 8 ++++---- source/user/gto.rst | 2 ++ source/version.rst | 4 ++++ 5 files changed, 24 insertions(+), 11 deletions(-) diff --git a/source/install.rst b/source/install.rst index 7f5428376..9e742156f 100644 --- a/source/install.rst +++ b/source/install.rst @@ -3,8 +3,8 @@ Install PySCF ************* -1) Install with `pip` (easiest method) -====================================== +1) Install with `pip` +===================== This is the recommended way to install PySCF for non-developers:: $ pip install --prefer-binary pyscf @@ -16,8 +16,15 @@ PySCF via pip, you can upgrade it to the new version with:: $ pip install --upgrade pyscf -.. note:: - Since PySCF version 2.1, the Linux wheels require manylinux2010 (for x86_64) or manylinux2014 (for aarch64). So the pip version should >= 19.3 for installing on Linux. +Some theoretical models developed in recent years are only available in the +pyscf-forge package. To access these modules, you can install the pyscf-forge package:: + + $ pip install pyscf-forge + +Certain modules are maintained as extensions of PySCF (see also `Install extensions`_). +To install all PySCF functionalities, you can execute the command:: + + $ pip install pyscf[all] 2) Build from source with `pip` @@ -38,7 +45,7 @@ list of prerequisites. If you would like to tune the CMake compilation parameters, you can set them with the environment variable `CMAKE_CONFIGURE_ARGS`, for example:: - $ export CMAKE_CONFIGURE_ARGS="-DBUILD_MARCH_NATIVE=ON" + $ export CMAKE_CONFIGURE_ARGS="-DBUILD_MARCH_NATIVE=ON -DBLA_VENDOR=Intel10_64lp_seq" See :ref:`cmake_options` for more details about CMake configuration. @@ -56,7 +63,7 @@ Prerequisites for manual install are * CMake >= 3.10 * Python >= 3.7 * Numpy >= 1.13 - * Scipy >= 0.19 + * Scipy >= 1.3 * h5py >= 2.7 You can download the latest version of PySCF (or the development diff --git a/source/interface/geomopt.rst b/source/interface/geomopt.rst index 901a3ff2e..7c12cf936 100644 --- a/source/interface/geomopt.rst +++ b/source/interface/geomopt.rst @@ -17,7 +17,7 @@ The following example shows how to optimize the structure of the N\ :sub:`2`\ m mol = gto.M(atom='N 0 0 0; N 0 0 1.2', basis='ccpvdz') mf = scf.RHF(mol) mol_eq = optimize(mf) - print(mol_eq.atom_coords()) + print(mol_eq.tostring()) Examples ======== diff --git a/source/user/geomopt.rst b/source/user/geomopt.rst index 24f11c3fc..bf696d2a0 100644 --- a/source/user/geomopt.rst +++ b/source/user/geomopt.rst @@ -26,23 +26,23 @@ and :mod:`pyscf.geomopt.berny_solver`:: # geometric from pyscf.geomopt.geometric_solver import optimize mol_eq = optimize(mf, maxsteps=100) - print(mol_eq.atom_coords()) + print(mol_eq.tostring()) # pyberny from pyscf.geomopt.berny_solver import optimize mol_eq = optimize(mf, maxsteps=100) - print(mol_eq.atom_coords()) + print(mol_eq.tostring()) The second way is to create an :func:`optimizer` from the :class:`Gradients` class:: # geometric mol_eq = mf.Gradients().optimizer(solver='geomeTRIC').kernel() - print(mol_eq.atom_coords()) + print(mol_eq.tostring()) # pyberny mol_eq = mf.Gradients().optimizer(solver='berny').kernel() - print(mol_eq.atom_coords()) + print(mol_eq.tostring()) For the ``geomeTRIC`` backend, the convergence criteria are controlled by the following parameters:: diff --git a/source/user/gto.rst b/source/user/gto.rst index 0a5be9b7d..0bfb6f1fb 100644 --- a/source/user/gto.rst +++ b/source/user/gto.rst @@ -166,6 +166,8 @@ This function returns a (N,3) array for the coordinates of each atom:: [0. 1. 0.] [0. 0. 1.]] +Please note the unit is Bohr by default. You can assign the keyword argument +`unit='Ang'` to change the unit to Angstrom. Ghost atoms can also be specified when inputting the geometry. See :source:`examples/gto/03-ghost_atom.py` for examples. diff --git a/source/version.rst b/source/version.rst index 5a94fed19..6935e0381 100644 --- a/source/version.rst +++ b/source/version.rst @@ -7,6 +7,8 @@ Version history =============== ============ Version Release date =============== ============ +2.6.0_ 2024-06-01 +2.5.0_ 2024-02-03 2.4.0_ 2023-10-16 2.3.0_ 2023-07-04 2.2.0_ 2023-03-09 @@ -71,6 +73,8 @@ Version Release date 1.0 alpha 1 2015-04-07 =============== ============ +.. _2.6.0: https://github.com/pyscf/pyscf/releases/tag/v2.6.0 +.. _2.5.0: https://github.com/pyscf/pyscf/releases/tag/v2.5.0 .. _2.4.0: https://github.com/pyscf/pyscf/releases/tag/v2.4.0 .. _2.3.0: https://github.com/pyscf/pyscf/releases/tag/v2.3.0 .. _2.2.0: https://github.com/pyscf/pyscf/releases/tag/v2.2.0