Merge branch 'flatironinstitute:master' into master

.github/workflows/python.yml

@@ -148,7 +148,7 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Install GCC and make
-      run: C:\msys64\usr\bin\bash.exe -lc "pacman -Sy --noconfirm make mingw-w64-x86_64-toolchain"
+      run: C:\msys64\usr\bin\bash.exe -lc "pacman -Sy --noconfirm make mingw-w64-x86_64-toolchain mingw-w64-x86_64-gcc-fortran mingw-w64-x86_64-gcc-libgfortran mingw-w64-x86_64-gcc-libs mingw-w64-x86_64-gcc-lto-dump  mingw-w64-x86_64-gcc-objc"
 
     - name: Build and Test Python 3.6
       uses: actions/setup-python@v3

.gitignore

@@ -22,3 +22,5 @@ lib/*
 *.log
 *.sh
 sbatch*
+*.obj
+make.inc

.readthedocs.yaml

@@ -0,0 +1,24 @@
+# .readthedocs.yml
+# "Read the Docs" doc-hosting website configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required (for this file format)
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+# Build all formats
+formats: all
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  install:
+    - requirements: docs/requirements.txt

AUTHORS

@@ -1,13 +1,18 @@
-Authors of FMM3D:
+FMM3D development team
 
-Zydrunas Gimbutas 
+Travis Askham
+Alex Barnett
+Zydrunas Gimbutas
 Leslie Greengard <[email protected]>
 Libin Lu
+Jeremy Magland 
+Dhairya Malhotra
 Manas Rachh <[email protected]>
 Vladimir Rokhlin
+Michael O'Neil
+Felipe Vico
 
-Jeremy Magland contributed support for python interface
+The contributions of Alex Barnett, Leslie Greengard, 
+Libin Lu, Jeremy Magland, Dhairya Malhotra, and Manas Rachh are 
+works made for hire for The Simons Foundation, Inc.
 
-Michael O'Neil contributed multiple scattering codes
-
-Dhairya Malhotra contributed [Scientific computing template library SCTL] (https://github.com/dmalhotra/SCTL)

CONTRIBUTING

@@ -0,0 +1,37 @@
+Contributions of source code, documentations, and fixes are happily
+accepted via GitHub merge requests. 
+If you are planning a large contribution, we encourage you to discuss
+the concept on a GitHub issue, or a merge request.
+
+FMM3D is distributed under the Apache License, Version 2.0 (see LICENSE).  
+The act of submitting a pull request or patch (with or without an explicit
+Signed-off-by tag) will be understood as an affirmation of the
+following:
+
+  Developer's Certificate of Origin 1.1
+
+  By making a contribution to this project, I certify that:
+
+  (a) The contribution was created in whole or in part by me and I
+      have the right to submit it under the open source license
+      indicated in the file; or
+
+  (b) The contribution is based upon previous work that, to the best
+      of my knowledge, is covered under an appropriate open source
+      license and I have the right under that license to submit that
+      work with modifications, whether created in whole or in part
+      by me, under the same open source license (unless I am
+      permitted to submit under a different license), as indicated
+      in the file; or
+
+  (c) The contribution was provided directly to me by some other
+      person who certified (a), (b) or (c) and I have not modified
+      it.
+
+  (d) I understand and agree that this project and the contribution
+      are public and that a record of the contribution (including all
+      personal information I submit with it, including my sign-off) is
+      maintained indefinitely and may be redistributed consistent with
+      this project or the open source license(s) involved.
+
+

LICENSE

@@ -1,20 +1,35 @@
-Copyright (C) 2019-2020 The Simons Foundation, Inc., Zydrunas Gimbutas, 
-and Vladimir Rokhlin - All Rights Reserved.
-
-FMM3D is 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
+Copyright (C) 2019-2023 The Simons Foundation, Inc., FMM3D Development Team 
+(see AUTHORS) - All Rights Reserved.
 
+FMM3D as a whole is 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.
+
+This product bundles the file "src/Common/dlaran.f", 
+which is available under a modified "3-Clause BSD" license. 
+For details, see src/Common/dlaran.f.
+This product bundles the files "src/Common/dfft.f", "src/Helmholtz/hwts3e.f",
+"src/Helmholtz/hwts_3d_iprec0.txt",
+"src/Helmholtz/hwts_3d_iprec1.txt",
+"src/Helmholtz/hwts_3d_iprec2.txt",
+"src/Helmholtz/hwts_3d_iprec3.txt",
+"src/Helmholtz/hwts_3d_iprec4.txt",
+"src/Helmholtz/hnumfour.f",
+"src/Helmholtz/hnumphys.f",
+"src/Laplace/lwtsexp_sep1.f", and
+"src/Laplace/lwtsexp_sep2.f",
+which are available under the public domain. See each file for details.
 
-------
-
+References
+===========
 Also, if you find this library useful, or it helps you in creating
 software or publications, please acknowledge that fact by citing this
 repository along with the author names, and any corresponding journal

docs/conf.py

@@ -12,16 +12,11 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys
-import os
-import sphinx.ext.autodoc
+#import sphinx.ext.autodoc
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0, os.path.abspath('..'))
-sys.path.append(os.path.abspath('sphinxext'))
-sys.path.insert(0,os.path.abspath('../../texext'))
 
 # -- General configuration ------------------------------------------------
 
@@ -33,12 +28,11 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
+#    'sphinx.ext.autodoc',
     'sphinx.ext.todo',
     'sphinx.ext.napoleon',
     'sphinx.ext.mathjax',
-#    'sphinx.ext.autosectionlabel',   # needs v 1.4; can :ref: other files w/o this; removed 7/29/18
-    'texext',
+    'sphinx_math_dollar',
     'sphinxcontrib.bibtex',
 ]
 
@@ -77,7 +71,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:

docs/fortran-c.rst

@@ -355,7 +355,7 @@ and the associated pressure
 Here $x_{j}$ are the source locations,
 $\sigma_{j}$ are the Stokeslet densities,
 $\nu_{j}$ are the stresslet orientation vectors, $\mu_{j}$ 
-are the stresslet densities, and rhw xollwxrion of $x$ 
+are the stresslet densities, and the locations $x$ 
 at which the velocity and its gradient are evaluated are referred to
 as the evaluation points.
 

docs/install.rst

@@ -114,7 +114,8 @@ In order to disable multi-threading, append ``OMP=OFF`` to the make task.
 
 In order to use the optimized direct evaluation kernels (this
 automatically turns on multithreading as well), append ``FAST_KER=ON`` to
-the make task. This option is currently *not* supported on Windows.
+the make task. The optimized direct kernel evaluation rotuines require
+gcc version 9 or higher. This option is currently *not* supported on Windows.
 
 
 All of these different libraries are
@@ -175,7 +176,7 @@ usage examples for the Python wrappers.
 .. note::
    On windows, you will need to update ``distutils.cfg`` located in 
    ``(PYTHON_INSTALL_DIR)\Lib\distutils`` and set it to::
-
+ 
        [build]
        compiler=mingw32
 
@@ -212,14 +213,21 @@ First make sure you have MATLAB installed.
 
 Then run ``make matlab`` (after copying over the operating
 system specific make.inc.* file to make.inc) which links the .m files to
-the .c file in the matlab folder.
+the .c file in the matlab folder. 
 
 To run tests, you can run ``matlab test_hfmm3d.m`` and 
 ``matlab test_lfmm3d.m`` and it should return with $0$ crashes.
 
 Example codes for demonstrating the Helmholtz and Laplace
 interfaces are ``hfmm3d_example.m`` and ``lfmm3d_example.m``.
 
+In order to build the MATLAB routines with the optimized direct kernel 
+evaluation routines on a Mac, we recommend building mex with gcc
+instead of clang. The relevant xml files for configuring mex to use
+gcc can be found at https://github.com/danfortunato/matlab-gcc.
+Follow the instructions there to configure mex with gcc, and set
+CC = ``gcc-<version number>`` in your make.inc file. 
+
 
 Tips for installing dependencies
 **********************************
@@ -262,16 +270,16 @@ Then do::
 On Windows
 ~~~~~~~~~~~~~~~
 
-Download 64 bit mingw (available `here <https://sourceforge.net/projects/mingw-w64/files/mingw-w64/mingw-w64-release/>`_).
+Download 64 bit mingw (Available at https://sourceforge.net/projects/mingw-w64/files/mingw-w64/mingw-w64-release/).
 Recommended version is ``gcc-8.1.0``, ``x86_64-posix-seh``.
 Follow the install instructions and append to the environment variable ``PATH`` the
 location of the bin directory of your mingw installation.
 
 Download  and install ``make`` for windows 
-(Available `here <http://gnuwin32.sourceforge.net/packages/make.htm>`_).
+(Available at http://gnuwin32.sourceforge.net/packages/make.htm).
 
 Download and install ``git`` for windows
-(Available `here <https://git-scm.com/download/win>`_).
+(Available at https://git-scm.com/download/win).
 
 Tips for installing optional dependencies
 ******************************************

docs/requirements.txt

@@ -1,2 +1,3 @@
 texext
 sphinxcontrib.bibtex
+sphinx_rtd_theme

julia/AUTHORS

@@ -0,0 +1,17 @@
+FMM3D development team
+
+Travis Askham
+Alex Barnett
+Zydrunas Gimbutas
+Leslie Greengard <[email protected]>
+Libin Lu
+Jeremy Magland 
+Dhairya Malhotra
+Manas Rachh <[email protected]>
+Vladimir Rokhlin
+Michael O'Neil 
+
+The contributions of Alex Barnett, Leslie Greengard, 
+Libin Lu, Jeremy Magland, Dhairya Malhotra, and Manas Rachh are 
+works made for hire for The Simons Foundation, Inc.
+

julia/LICENSE

@@ -0,0 +1,36 @@
+Copyright (C) 2019-2023 The Simons Foundation, Inc., FMM3D Development Team 
+(see AUTHORS) - All Rights Reserved.
+
+FMM3D as a whole is 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.
+
+This product bundles the file "src/Common/dlaran.f", 
+which is available under a modified "3-Clause BSD" license. 
+For details, see src/Common/dlaran.f.
+This product bundles the files "src/Common/dfft.f", "src/Helmholtz/hwts3e.f",
+"src/Helmholtz/hwts_3d_iprec0.txt",
+"src/Helmholtz/hwts_3d_iprec1.txt",
+"src/Helmholtz/hwts_3d_iprec2.txt",
+"src/Helmholtz/hwts_3d_iprec3.txt",
+"src/Helmholtz/hwts_3d_iprec4.txt",
+"src/Helmholtz/hnumfour.f",
+"src/Helmholtz/hnumphys.f",
+"src/Laplace/lwtsexp_sep1.f", and
+"src/Laplace/lwtsexp_sep2.f",
+which are available under the public domain. See each file for details.
+
+References
+===========
+Also, if you find this library useful, or it helps you in creating
+software or publications, please acknowledge that fact by citing this
+repository along with the author names, and any corresponding journal
+article.

make.inc.icc

@@ -1,7 +1,7 @@
 CC=icc
 CXX=icpc
 FC=ifort
-FFLAGS= -fPIC -O3 -march=native -funroll-loops -mkl 
+FFLAGS= -fPIC -O3 -march=native -funroll-loops -mkl -w 
 LIBS=-lm 
 CLIBS = -lm -ldl -lifcore
 

make.inc.macos.gnu

@@ -1,6 +1,6 @@
 # makefile overrides
 # OS:       macOS
-# Compiler: gfortran X.X
+# Compiler: gfortran X.X/Clang
 # OpenMP:   enabled
 #
 
@@ -22,8 +22,6 @@ OMPLIBS = -lgomp
 # MATLAB interface:
 FDIR=$$(dirname `gfortran --print-file-name libgfortran.dylib`)
 MFLAGS +=-L${FDIR}
-MEX = $(shell ls -d /Applications/MATLAB_R20**.app)/bin/mex
-#LIBS = -lm -lstdc++.6
-#MEXLIBS= -lm -lstdc++.6 -lgfortran -ldl
+MEX = $(shell ls -d /Applications/MATLAB_R* | sort | tail -1)/bin/mex
 
 

make.inc.macos.intel

@@ -7,7 +7,8 @@
 CC=icc
 CXX=icpc
 FC=ifort
-FFLAGS= -fPIC -O3 -march=native -funroll-loops -mkl -std=legacy 
+
+FFLAGS= -fPIC -O3 -march=native -funroll-loops -mkl -std=legacy -w 
 LIBS=
 #CLIBS = -lm -ldl -lifcore
 CLIBS = -lm -ldl
@@ -26,6 +27,11 @@ endif
 #  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
 
 OMPFLAGS = -qopenmp
-OMPLIBS = 
+OMPLIBS = -qopenmp
+
+# MATLAB interface:
+FDIR=$$(dirname `gfortran --print-file-name libgfortran.dylib`)
+MFLAGS +=-L${FDIR}
+MEX = $(shell ls -d /Applications/MATLAB_R* | sort | tail -1)/bin/mex