update for release

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021-2023 Xing Zhang
+Copyright (c) 2021-2024 Xing Zhang
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

MANIFEST.in

@@ -1,9 +1,6 @@
 include MANIFEST.in
 include README.md setup.py LICENSE
 
-prune pyscfad/lib/build
+include pyscfad/geomopt/log.ini
 
-include pyscfad/lib/*.so
-include pyscfad/lib/*.dylib
-
-recursive-include pyscfad/lib *.c *.h
+global-exclude *.py[cod]

README.md

@@ -11,23 +11,11 @@ Installation
 ---
 * To install the latest release, use the following commands:
 ```
-# install cmake
-pip install cmake
-
-# install OpenMP runtime used with clang
-# On Linux:
-sudo apt update
-sudo apt install libomp-dev
-
-# On OSX:
-brew install libomp
-
-# install pyscf
-pip install 'pyscf @ git+https://github.com/fishjojo/pyscf.git@ad#egg=pyscf' 
-pip install 'pyscf-properties @ git+https://github.com/fishjojo/properties.git@ad' 
-
 # install pyscfad
 pip install pyscfad
+
+# install pyscfadlib, optional
+pip install pyscfadlib
 ```
 
 ---
@@ -36,32 +24,6 @@ pip install pyscfad
 pip install git+https://github.com/fishjojo/pyscfad.git
 ```
 
-* The dependencies can be installed via a predefined conda environment
-```
-conda env create -f environment.yml
-conda activate pyscfad_env
-```
-
-* Alternatively, the dependencies can be installed from source
-```
-pip install numpy scipy h5py
-pip install jax jaxlib jaxopt
-
-# install pyscf
-cd $HOME; git clone https://github.com/fishjojo/pyscf.git
-cd pyscf; git checkout ad 
-cd pyscf/lib; mkdir build 
-cd build; cmake ..; make
-
-export PYTHONPATH=$HOME/pyscf:$PYTHONPATH
-```
-
----
-* One can also run PySCFAD inside a docker container:
-```
-docker pull fishjojo/pyscfad:latest
-docker run -rm -t -i fishjojo/pyscfad:latest /bin/bash
-```
 
 Running examples
 ----------------
@@ -71,10 +33,4 @@ the following lines need to be added to
 the PySCF configure file($HOME/.pyscf\_conf.py)
 ```
 pyscfad = True
-pyscf_numpy_backend = 'jax'
-pyscf_scipy_linalg_backend = 'pyscfad'
-pyscf_scipy_backend = 'jax'
-# The followings are optional
-pyscfad_scf_implicit_diff = True
-pyscfad_ccsd_implicit_diff = True
 ```

examples/cc/00-simple.py

@@ -1,5 +1,3 @@
-import jax
-from pyscfad import gto, scf, cc
 '''
 Reference nuclear gradient
 [[0.0, 0.0, -1.15101379e-01]
@@ -8,10 +6,19 @@
 Note that without implicit differentiation turned on,
 the gradient will be initial guess dependent.
 '''
+import jax
+from pyscfad import gto, scf, cc
+from pyscfad import config
+
+# implicit differentiation of SCF iterations
+config.update('pyscfad_scf_implicit_diff', True)
+# implicit differentiation of CC iterations
+config.update('pyscfad_ccsd_implicit_diff', True)
+
 mol = gto.Mole()
 mol.atom = 'H 0. 0. 0.; F 0. 0. 1.1'
 mol.basis = 'ccpvdz'
-mol.verbose = 3
+mol.verbose = 4
 mol.incore_anyway = True
 mol.build()
 

examples/gw/01-rpa.py

@@ -1,12 +1,3 @@
-import jax
-from pyscf import df as pyscf_df
-from pyscfad import gto, dft, scf, df
-from pyscfad.gw import rpa
-from pyscfad import config
-
-config.update('pyscfad_scf_implicit_diff', True)
-config.update('pyscfad_moleintor_opt', True)
-
 '''
 RPA e_tot, e_hf, e_corr =  -76.26428191794197 -75.95645187758402 -0.30783004035795963
 
@@ -39,6 +30,18 @@
 
 '''
 
+import jax
+from pyscf import df as pyscf_df
+from pyscfad import gto, dft, scf, df
+from pyscfad.gw import rpa
+from pyscfad import config
+
+config.update('pyscfad_scf_implicit_diff', True)
+# Using optimized C implementation for gradients calculations.
+# This requires the `pyscfadlib` package, which can be installed with
+# `pip install pyscfadlib`
+#config.update('pyscfad_moleintor_opt', True)
+
 mol = gto.Mole()
 mol.verbose = 4
 mol.atom = [

examples/mp/00-simple.py

@@ -1,15 +1,18 @@
+"""
+Analytic nuclear gradient for MP2 computed by auto-differentiation
+"""
 import jax
 import pyscf
 from pyscfad import gto, scf, mp
+from pyscfad import config
 
-"""
-Analytic nuclear gradient for MP2 computed by auto-differentiation
-"""
+# implicit differentiation of SCF iterations
+config.update('pyscfad_scf_implicit_diff', True)
 
 mol = gto.Mole()
-mol.atom = 'H 0 0 0; H 0 0 0.74'  # in Angstrom
+mol.atom = 'H 0 0 0; H 0 0 0.74'
 mol.basis = '631g'
-mol.verbose=5
+mol.verbose=4
 mol.build()
 
 def mp2(mol, dm0=None):

pyscfad/version.py

@@ -1 +1 @@
-__version__ = "0.1.2"
+__version__ = "0.1.4"

pyscfadlib/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021-2024 Xing Zhang
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+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.

pyscfadlib/MANIFEST.in

@@ -0,0 +1,15 @@
+include MANIFEST.in
+include README.md setup.py LICENSE
+
+recursive-include pyscfadlib/thirdparty *.so
+include pyscfadlib/*.so pyscfadlib/config.h.in
+
+# macos dynamic libraries
+include pyscfadlib/*.dylib
+include pyscfadlib/thirdparty/lib*/*.dylib
+
+# source code
+recursive-include pyscfadlib *.c *.h CMakeLists.txt
+
+global-exclude *.py[cod]
+prune pyscfadlib/build

pyscfadlib/README.md

@@ -0,0 +1,2 @@
+pyscfadlib is the support library for PySCFAD.
+It contains most of the C optimized code for derivative calculations.

pyscfadlib/pyproject.toml

@@ -0,0 +1,14 @@
+[tool.cibuildwheel]
+build-verbosity = 1
+container-engine = "docker"
+manylinux-x86_64-image = "manylinux2014"
+skip = ["pp*", "*musllinux*"]
+
+[tool.cibuildwheel.linux]
+archs = ["x86_64"]
+before-all = [
+    "ulimit -n 1024",
+    "ln -s libquadmath.so.0 /usr/lib64/libquadmath.so",
+    "yum install -y openblas-devel.x86_64",
+]
+repair-wheel-command = "auditwheel -v repair -w {dest_dir} {wheel}"

pyscfadlib/CMakeLists.txt → pyscfadlib/pyscfadlib/CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required (VERSION 3.18)
+cmake_minimum_required (VERSION 3.5)
 project (pyscfadlib)
 
 if (NOT CMAKE_BUILD_TYPE)
@@ -39,6 +39,18 @@ endif()
 
 set(CMAKE_INCLUDE_CURRENT_DIR ON)
 
+if (NOT BLAS_LIBRARIES)
+#enable_language(Fortran)
+find_package(BLAS)
+check_function_exists(ffsll HAVE_FFS)
+endif()
+
+if (NOT BLAS_LIBRARIES)
+  message(FATAL_ERROR "A required library with BLAS API not found.")
+else()
+  message(STATUS "BLAS libraries: ${BLAS_LIBRARIES}")
+endif()
+
 option(ENABLE_OPENMP "Compiling C extensions with openmp" ON)
 set(OPENMP_C_PROPERTIES "")
 if(ENABLE_OPENMP)
@@ -72,6 +84,9 @@ else ()
   set(CMAKE_INSTALL_RPATH "\$ORIGIN:\$ORIGIN/thirdparty/lib:\$ORIGIN/thirdparty/lib64")
 endif()
 
+add_subdirectory(np_helper)
+add_subdirectory(gto)
+add_subdirectory(vhf)
 add_subdirectory(vjp)
 
 set(C_LINK_TEMPLATE "<CMAKE_C_COMPILER> <CMAKE_SHARED_LIBRARY_C_FLAGS> <LANGUAGE_COMPILE_FLAGS> <LINK_FLAGS> <CMAKE_SHARED_LIBRARY_CREATE_C_FLAGS> -o <TARGET> <OBJECTS> <LINK_LIBRARIES>")
@@ -101,37 +116,9 @@ if(BUILD_LIBCINT)
         -DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR>
         -DCMAKE_INSTALL_LIBDIR:PATH=lib
         -DCMAKE_C_COMPILER:STRING=${CMAKE_C_COMPILER}
+        -DBLAS_LIBRARIES:STRING=${BLAS_LIBRARIES}
         -DCMAKE_C_CREATE_SHARED_LIBRARY:STRING=${C_LINK_TEMPLATE}
         -DBUILD_MARCH_NATIVE:STRING=${BUILD_MARCH_NATIVE}
   )
-  add_dependencies(cgto_vjp libcint)
-endif()
-
-option(BUILD_PYSCF_LIB "Building PySCF library" ON)
-
-set(patch_pyscf ${PROJECT_SOURCE_DIR}/apply_patch.sh pyscf.patch)
-
-if(BUILD_PYSCF_LIB)
-  ExternalProject_Add(pyscf
-    GIT_REPOSITORY https://github.com/pyscf/pyscf.git
-    GIT_TAG v2.3.0
-    PATCH_COMMAND ${patch_pyscf}
-    SOURCE_SUBDIR "pyscf/lib"
-    PREFIX ${PROJECT_BINARY_DIR}/thirdparty
-    INSTALL_DIR ${PROJECT_SOURCE_DIR}/thirdparty
-    CMAKE_ARGS
-            -DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR>
-            -DCMAKE_INSTALL_LIBDIR:PATH=lib
-            -DCMAKE_INSTALL_INCLUDEDIR:PATH=include/pyscf
-            -DCMAKE_C_COMPILER:STRING=${CMAKE_C_COMPILER}
-            -DBLA_VENDOR:STRING=${BLA_VENDOR}
-            -DENABLE_LIBXC:STRING=OFF
-            -DENABLE_XCFUN:STRING=OFF
-            #-DBUILD_LIBCINT:STRING=OFF
-  )
-  add_dependencies(cgto_vjp pyscf)
-  add_dependencies(np_helper_vjp pyscf)
-  add_dependencies(ao2mo_vjp pyscf)
-  add_dependencies(cvhf_vjp pyscf)
-  add_dependencies(cc_vjp pyscf)
+  add_dependencies(cgto libcint)
 endif()

pyscfadlib/pyscfadlib/copy_pyscf_lib.sh

@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+
+git clone https://github.com/pyscf/pyscf.git
+cd pyscf
+git checkout 'v2.3.0'
+
+cp -rf pyscf/lib/vhf ../vhf
+cp -rf pyscf/lib/gto ../gto
+cp -rf pyscf/lib/np_helper ../np_helper

pyscfadlib/pyscfadlib/gto/CMakeLists.txt

@@ -0,0 +1,26 @@
+# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
+#
+# 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.
+
+add_library(cgto SHARED 
+  fill_int2c.c fill_nr_3c.c fill_r_3c.c fill_int2e.c fill_r_4c.c
+  ft_ao.c ft_ao_deriv.c fill_grids_int2c.c
+  grid_ao_drv.c deriv1.c deriv2.c nr_ecp.c nr_ecp_deriv.c
+  autocode/auto_eval1.c)
+add_dependencies(cgto np_helper)
+
+set_target_properties(cgto PROPERTIES
+  LIBRARY_OUTPUT_DIRECTORY ${PROJECT_SOURCE_DIR})
+
+target_link_libraries(cgto cintad np_helper ${BLAS_LIBRARIES} ${OPENMP_C_PROPERTIES})
+