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QML: Quantum Machine Learning

License: MIT License

Python 56.00% Fortran 44.00%

qml's Introduction

QML: A Python Toolkit for Quantum Machine Learning

QML is a Python2/3-compatible toolkit for representation learning of properties of molecules and solids.

Current list of contributors:

Anders S. Christensen (University of Basel)
Felix A. Faber (University of Basel)
Bing Huang (University of Basel)
Lars A. Bratholm (University of Copenhagen)
Alexandre Tkatchenko (University of Luxembourg)
Klaus-Robert Muller (Technische Universitat Berlin/Korea University)
O. Anatole von Lilienfeld (University of Basel)

1) Citing QML:

Until the preprint is available from arXiv, please cite this GitHub repository as:

AS Christensen, LA Bratholm, FA Faber, B Huang, A Tkatchenko, KR Muller, OA von Lilienfeld (2017) "QML: A Python Toolkit for Quantum Machine Learning" https://github.com/qmlcode/qml

2) Get help:

Documentation and installation instruction is found at: http://www.qmlcode.org/

3) License:

QML is freely available under the terms of the MIT license.

qml's People

Contributors

Stargazers

Watchers

Forkers

andersx larsbratholm liusong299 alpha-librae rsantana-isg clustersdata nimitkothari syyunn quantumgame amoliu mrauha chrinide cstein farnazh thegodone qiangzhongwork silviaamam ferchault charnley aliakbarrashidi berquist mikstr aebk2015 solertis zaspel binghuang2018 stone2015 wardlt anomishra jeffschriber somnambwl joshua-sexton rmeli yy692 thomascherickal m-andreeva onurcaylak linuxzhaoli gharib85 qshao laranea sgangoly inspectordidi nickcafferry kvkarandashev viniavila dom1l abhirup86 alphabstc occdaudio qml-uy1 biliu raghurama123 vinzenzhalhammer vanilsongomes yychuang lkampoli qianyaoyy zeroinfinite wesharrell trogstold takshan ybwei hongxiahao91 fermiq brendenpelkie python-repository-hub ujhin matt1h rkalescky meliao dkhan42 kangle2017 puckvg g-anush edmundgoodman hmcezar takafumi-shiraogawa abhi-raghav caguerra stophobia

qml's Issues

Documentation missing in FCHL

Documentation missing for kernel and kernel_args params in fchl_scalar_kernels

https://github.com/qmlcode/qml/blob/develop/qml/fchl/fchl_scalar_kernels.py#L49

I have a very quick question: Does the generate_fchl_acsf method, which I think generates the "FCHL19" representation, support periodic boundary conditions? I couldn't find a basis argument, but I thought I'd ask explicitly!

Cheers,

Marcel

pip3 install qml error

Hello everyone, I have never had problems installing with pip3 before. I have Ubuntu 18.04.4 LTS. Thanks

Collecting qml
Downloading https://files.pythonhosted.org/packages/7b/f3/c08d18659054cdf5e5dc531ee32ab20e6aa1d3772545837557828a03b1f5/qml-0.4.0.27.tar.gz (41kB)
100% |████████████████████████████████| 51kB 1.2MB/s
Building wheels for collected packages: qml
Running setup.py bdist_wheel for qml ... error
Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;file='/tmp/pip-build-b9e7yqyc/qml/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" bdist_wheel -d /tmp/tmpm3f7m3g3pip-wheel- --python-tag cp36:
MKL-discover: MKLROOT was not set
running bdist_wheel
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building extension "ffchl_module" sources
f2py options: ['--quiet']
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs.
adding 'build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers.f' to sources.
adding 'build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers2.f90' to sources.
building extension "farad_kernels" sources
f2py options: ['--quiet']
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs.
adding 'build/src.linux-x86_64-3.6/farad_kernels-f2pywrappers.f' to sources.
adding 'build/src.linux-x86_64-3.6/farad_kernels-f2pywrappers2.f90' to sources.
building extension "fcho_solve" sources
f2py options: ['--quiet']
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs.
adding 'build/src.linux-x86_64-3.6/fcho_solve-f2pywrappers.f' to sources.
building extension "fdistance" sources
f2py options: ['--quiet']
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs.
adding 'build/src.linux-x86_64-3.6/fdistance-f2pywrappers.f' to sources.
building extension "fkernels" sources
f2py options: ['--quiet']
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs.
adding 'build/src.linux-x86_64-3.6/fkernels-f2pywrappers.f' to sources.
building extension "fslatm" sources
f2py options: ['--quiet']
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs.
adding 'build/src.linux-x86_64-3.6/fslatm-f2pywrappers.f' to sources.
adding 'build/src.linux-x86_64-3.6/fslatm-f2pywrappers2.f90' to sources.
building extension "frepresentations" sources
f2py options: ['--quiet']
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs.
adding 'build/src.linux-x86_64-3.6/frepresentations-f2pywrappers.f' to sources.
adding 'build/src.linux-x86_64-3.6/frepresentations-f2pywrappers2.f90' to sources.
build_src: building npy-pkg config files
running build_py
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/qml
copying qml/compound.py -> build/lib.linux-x86_64-3.6/qml
copying qml/representations.py -> build/lib.linux-x86_64-3.6/qml
copying qml/data.py -> build/lib.linux-x86_64-3.6/qml
copying qml/alchemy.py -> build/lib.linux-x86_64-3.6/qml
copying qml/init.py -> build/lib.linux-x86_64-3.6/qml
copying qml/fchl.py -> build/lib.linux-x86_64-3.6/qml
copying qml/kernels.py -> build/lib.linux-x86_64-3.6/qml
copying qml/slatm.py -> build/lib.linux-x86_64-3.6/qml
copying qml/distance.py -> build/lib.linux-x86_64-3.6/qml
copying qml/math.py -> build/lib.linux-x86_64-3.6/qml
copying qml/wrappers.py -> build/lib.linux-x86_64-3.6/qml
copying qml/arad.py -> build/lib.linux-x86_64-3.6/qml
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
customize Gnu95FCompiler
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'ffchl_module' extension
compiling C sources
C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

creating build/temp.linux-x86_64-3.6/build
creating build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/build
creating build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6
compile options: '-Ibuild/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6 -I/home/graggi/.local/lib/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c'
extra options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
x86_64-linux-gnu-gcc: build/src.linux-x86_64-3.6/ffchl_modulemodule.c
x86_64-linux-gnu-gcc: build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c
compiling Fortran 90 module sources
creating build/temp.linux-x86_64-3.6/qml
Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
compile options: '-Ibuild/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6 -I/home/graggi/.local/lib/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c'
extra options: '-Jbuild/temp.linux-x86_64-3.6/qml -Ibuild/temp.linux-x86_64-3.6/qml'
extra f90 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
gfortran:f90: qml/ffchl_module.f90
qml/ffchl_module.f90:275:36:

   & t_width, d_width, cut_distance, order, pd, ang_norm2, &
                                  1

Warning: Unused dummy argument ‘cut_distance’ at (1) [-Wunused-dummy-argument]
compiling Fortran sources
Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
compile options: '-Ibuild/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6 -I/home/graggi/.local/lib/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c'
extra options: '-Jbuild/temp.linux-x86_64-3.6/qml -Ibuild/temp.linux-x86_64-3.6/qml'
extra f90 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
gfortran:f90: qml/ffchl_scalar_kernels.f90
extra f90 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
gfortran:f90: build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers2.f90
extra f77 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
gfortran:f77: build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers.f
/usr/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_modulemodule.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.o build/temp.linux-x86_64-3.6/qml/ffchl_module.o build/temp.linux-x86_64-3.6/qml/ffchl_scalar_kernels.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers2.o -L/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -lgfortran -o build/lib.linux-x86_64-3.6/qml/ffchl_module.cpython-36m-x86_64-linux-gnu.so -lgomp -lblas -llapack
/usr/bin/ld: cannot find -lblas
/usr/bin/ld: cannot find -llapack
collect2: error: ld returned 1 exit status
error: Command "/usr/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_modulemodule.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.o build/temp.linux-x86_64-3.6/qml/ffchl_module.o build/temp.linux-x86_64-3.6/qml/ffchl_scalar_kernels.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers2.o -L/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -lgfortran -o build/lib.linux-x86_64-3.6/qml/ffchl_module.cpython-36m-x86_64-linux-gnu.so -lgomp -lblas -llapack" failed with exit status 1

Failed building wheel for qml
Running setup.py clean for qml
Failed to build qml
Installing collected packages: qml
Running setup.py install for qml ... error
Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;file='/tmp/pip-build-b9e7yqyc/qml/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-0kdli_b1-record/install-record.txt --single-version-externally-managed --compile --user --prefix=:
MKL-discover: MKLROOT was not set
running install
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building extension "ffchl_module" sources
f2py options: ['--quiet']
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs.
adding 'build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers.f' to sources.
adding 'build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers2.f90' to sources.
building extension "farad_kernels" sources
f2py options: ['--quiet']
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs.
adding 'build/src.linux-x86_64-3.6/farad_kernels-f2pywrappers.f' to sources.
adding 'build/src.linux-x86_64-3.6/farad_kernels-f2pywrappers2.f90' to sources.
building extension "fcho_solve" sources
f2py options: ['--quiet']
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs.
adding 'build/src.linux-x86_64-3.6/fcho_solve-f2pywrappers.f' to sources.
building extension "fdistance" sources
f2py options: ['--quiet']
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs.
adding 'build/src.linux-x86_64-3.6/fdistance-f2pywrappers.f' to sources.
building extension "fkernels" sources
f2py options: ['--quiet']
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs.
adding 'build/src.linux-x86_64-3.6/fkernels-f2pywrappers.f' to sources.
building extension "fslatm" sources
f2py options: ['--quiet']
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs.
adding 'build/src.linux-x86_64-3.6/fslatm-f2pywrappers.f' to sources.
adding 'build/src.linux-x86_64-3.6/fslatm-f2pywrappers2.f90' to sources.
building extension "frepresentations" sources
f2py options: ['--quiet']
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs.
adding 'build/src.linux-x86_64-3.6/frepresentations-f2pywrappers.f' to sources.
adding 'build/src.linux-x86_64-3.6/frepresentations-f2pywrappers2.f90' to sources.
build_src: building npy-pkg config files
running build_py
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/qml
copying qml/compound.py -> build/lib.linux-x86_64-3.6/qml
copying qml/representations.py -> build/lib.linux-x86_64-3.6/qml
copying qml/data.py -> build/lib.linux-x86_64-3.6/qml
copying qml/alchemy.py -> build/lib.linux-x86_64-3.6/qml
copying qml/init.py -> build/lib.linux-x86_64-3.6/qml
copying qml/fchl.py -> build/lib.linux-x86_64-3.6/qml
copying qml/kernels.py -> build/lib.linux-x86_64-3.6/qml
copying qml/slatm.py -> build/lib.linux-x86_64-3.6/qml
copying qml/distance.py -> build/lib.linux-x86_64-3.6/qml
copying qml/math.py -> build/lib.linux-x86_64-3.6/qml
copying qml/wrappers.py -> build/lib.linux-x86_64-3.6/qml
copying qml/arad.py -> build/lib.linux-x86_64-3.6/qml
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
customize Gnu95FCompiler
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'ffchl_module' extension
compiling C sources
C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

creating build/temp.linux-x86_64-3.6/build
creating build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/build
creating build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6
compile options: '-Ibuild/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6 -I/home/graggi/.local/lib/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c'
extra options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
x86_64-linux-gnu-gcc: build/src.linux-x86_64-3.6/ffchl_modulemodule.c
x86_64-linux-gnu-gcc: build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c
compiling Fortran 90 module sources
creating build/temp.linux-x86_64-3.6/qml
Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
compile options: '-Ibuild/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6 -I/home/graggi/.local/lib/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c'
extra options: '-Jbuild/temp.linux-x86_64-3.6/qml -Ibuild/temp.linux-x86_64-3.6/qml'
extra f90 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
gfortran:f90: qml/ffchl_module.f90
qml/ffchl_module.f90:275:36:

     & t_width, d_width, cut_distance, order, pd, ang_norm2, &
                                    1
Warning: Unused dummy argument ‘cut_distance’ at (1) [-Wunused-dummy-argument]
compiling Fortran sources
Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
compile options: '-Ibuild/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6 -I/home/graggi/.local/lib/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c'
extra options: '-Jbuild/temp.linux-x86_64-3.6/qml -Ibuild/temp.linux-x86_64-3.6/qml'
extra f90 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
gfortran:f90: qml/ffchl_scalar_kernels.f90
extra f90 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
gfortran:f90: build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers2.f90
extra f77 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
gfortran:f77: build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers.f
/usr/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_modulemodule.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.o build/temp.linux-x86_64-3.6/qml/ffchl_module.o build/temp.linux-x86_64-3.6/qml/ffchl_scalar_kernels.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers2.o -L/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -lgfortran -o build/lib.linux-x86_64-3.6/qml/ffchl_module.cpython-36m-x86_64-linux-gnu.so -lgomp -lblas -llapack
/usr/bin/ld: cannot find -lblas
/usr/bin/ld: cannot find -llapack
collect2: error: ld returned 1 exit status
error: Command "/usr/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_modulemodule.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.o build/temp.linux-x86_64-3.6/qml/ffchl_module.o build/temp.linux-x86_64-3.6/qml/ffchl_scalar_kernels.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers2.o -L/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -lgfortran -o build/lib.linux-x86_64-3.6/qml/ffchl_module.cpython-36m-x86_64-linux-gnu.so -lgomp -lblas -llapack" failed with exit status 1

----------------------------------------

Command "/usr/bin/python3 -u -c "import setuptools, tokenize;file='/tmp/pip-build-b9e7yqyc/qml/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-0kdli_b1-record/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /tmp/pip-build-b9e7yqyc/qml/

Remove most of qml7 xyz files

There is no reason to have more than a few. If many is needed for a test we can include a pickle with coordinates / nuclear charges

i having a very hard time installing qml. compiler issue?

hello. as the title says, im having a hard time. i believe im having compiler issues. every time i try to install this program on any of my systems i run into issues. i happen to have access to a computer with the intel compilers via ssh, and on that computer i was able to install using the option for intel compiler. im using python 2.7.15. here's what i normally get:

(ipml_env) isaiahk@DESKTOP-BSK29S8:~$ python -m pip install qml
Collecting qml
  Using cached https://files.pythonhosted.org/packages/89/70/4ca9ef42f192676ad3e15a590fc127581908445ce8a1a94e8ad50622f96d/qml-0.4.0.17.tar.gz
Building wheels for collected packages: qml
  Running setup.py bdist_wheel for qml ... error
  Complete output from command /home/isaiahk/anaconda3/envs/ipml_env/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-SwJZIR/qml/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/pip-wheel-kv_sBe --python-tag cp27:
  MKL-discover: MKLROOT was not set
  running bdist_wheel
  running build
  running config_cc
  unifing config_cc, config, build_clib, build_ext, build commands --compiler options
  running config_fc
  unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
  running build_src
  build_src
  building extension "ffchl_module" sources
  f2py options: ['--quiet']
    adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/fortranobject.c' to sources.
    adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7' to include_dirs.
    adding 'build/src.linux-x86_64-2.7/ffchl_module-f2pywrappers.f' to sources.
    adding 'build/src.linux-x86_64-2.7/ffchl_module-f2pywrappers2.f90' to sources.
  building extension "farad_kernels" sources
  f2py options: ['--quiet']
    adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/fortranobject.c' to sources.
    adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7' to include_dirs.
    adding 'build/src.linux-x86_64-2.7/farad_kernels-f2pywrappers.f' to sources.
    adding 'build/src.linux-x86_64-2.7/farad_kernels-f2pywrappers2.f90' to sources.
  building extension "fcho_solve" sources
  f2py options: ['--quiet']
    adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/fortranobject.c' to sources.
    adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7' to include_dirs.
    adding 'build/src.linux-x86_64-2.7/fcho_solve-f2pywrappers.f' to sources.
  building extension "fdistance" sources
  f2py options: ['--quiet']
    adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/fortranobject.c' to sources.
    adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7' to include_dirs.
    adding 'build/src.linux-x86_64-2.7/fdistance-f2pywrappers.f' to sources.
  building extension "fkernels" sources
  f2py options: ['--quiet']
    adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/fortranobject.c' to sources.
    adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7' to include_dirs.
    adding 'build/src.linux-x86_64-2.7/fkernels-f2pywrappers.f' to sources.
  building extension "fslatm" sources
  f2py options: ['--quiet']
    adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/fortranobject.c' to sources.
    adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7' to include_dirs.
    adding 'build/src.linux-x86_64-2.7/fslatm-f2pywrappers.f' to sources.
    adding 'build/src.linux-x86_64-2.7/fslatm-f2pywrappers2.f90' to sources.
  building extension "frepresentations" sources
  f2py options: ['--quiet']
    adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/fortranobject.c' to sources.
    adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7' to include_dirs.
    adding 'build/src.linux-x86_64-2.7/frepresentations-f2pywrappers.f' to sources.
    adding 'build/src.linux-x86_64-2.7/frepresentations-f2pywrappers2.f90' to sources.
  build_src: building npy-pkg config files
  running build_py
  creating build/lib.linux-x86_64-2.7
  creating build/lib.linux-x86_64-2.7/qml
  copying qml/__init__.py -> build/lib.linux-x86_64-2.7/qml
  copying qml/alchemy.py -> build/lib.linux-x86_64-2.7/qml
  copying qml/arad.py -> build/lib.linux-x86_64-2.7/qml
  copying qml/compound.py -> build/lib.linux-x86_64-2.7/qml
  copying qml/data.py -> build/lib.linux-x86_64-2.7/qml
  copying qml/distance.py -> build/lib.linux-x86_64-2.7/qml
  copying qml/fchl.py -> build/lib.linux-x86_64-2.7/qml
  copying qml/kernels.py -> build/lib.linux-x86_64-2.7/qml
  copying qml/math.py -> build/lib.linux-x86_64-2.7/qml
  copying qml/representations.py -> build/lib.linux-x86_64-2.7/qml
  copying qml/slatm.py -> build/lib.linux-x86_64-2.7/qml
  copying qml/wrappers.py -> build/lib.linux-x86_64-2.7/qml
  running build_ext
  customize UnixCCompiler
  customize UnixCCompiler using build_ext
  get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
  customize Gnu95FCompiler
  Found executable /usr/bin/gfortran
  customize Gnu95FCompiler
  customize Gnu95FCompiler using build_ext
  get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
  customize Gnu95FCompiler
  customize Gnu95FCompiler
  customize Gnu95FCompiler using build_ext
  building 'ffchl_module' extension
  compiling C sources
  C compiler: gcc -pthread -B /home/isaiahk/anaconda3/envs/ipml_env/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC

  creating build/temp.linux-x86_64-2.7/build
  creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7
  creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/build
  creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7
  compile options: '-Ibuild/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7 -I/home/isaiahk/.local/lib/python2.7/site-packages/numpy/core/include -I/home/isaiahk/anaconda3/envs/ipml_env/include/python2.7 -c'
  extra options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
  gcc: build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/fortranobject.c
  gcc: build/src.linux-x86_64-2.7/ffchl_modulemodule.c
  compiling Fortran 90 module sources
  creating build/temp.linux-x86_64-2.7/qml
  Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
  Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
  Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
  compile options: '-Ibuild/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7 -I/home/isaiahk/.local/lib/python2.7/site-packages/numpy/core/include -I/home/isaiahk/anaconda3/envs/ipml_env/include/python2.7 -c'
  extra options: '-Jbuild/temp.linux-x86_64-2.7/qml -Ibuild/temp.linux-x86_64-2.7/qml'
  extra f90 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
  gfortran:f90: qml/ffchl_module.f90
  qml/ffchl_module.f90:275:36:

       & t_width, d_width, cut_distance, order, pd, ang_norm2, &
                                      1
  Warning: Unused dummy argument ‘cut_distance’ at (1) [-Wunused-dummy-argument]
  compiling Fortran sources
  Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
  Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
  Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
  compile options: '-Ibuild/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7 -I/home/isaiahk/.local/lib/python2.7/site-packages/numpy/core/include -I/home/isaiahk/anaconda3/envs/ipml_env/include/python2.7 -c'
  extra options: '-Jbuild/temp.linux-x86_64-2.7/qml -Ibuild/temp.linux-x86_64-2.7/qml'
  extra f90 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
  gfortran:f90: qml/ffchl_scalar_kernels.f90
  extra f90 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
  gfortran:f90: build/src.linux-x86_64-2.7/ffchl_module-f2pywrappers2.f90
  extra f77 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
  gfortran:f77: build/src.linux-x86_64-2.7/ffchl_module-f2pywrappers.f
  /usr/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/ffchl_modulemodule.o build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/fortranobject.o build/temp.linux-x86_64-2.7/qml/ffchl_module.o build/temp.linux-x86_64-2.7/qml/ffchl_scalar_kernels.o build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/ffchl_module-f2pywrappers.o build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/ffchl_module-f2pywrappers2.o -L/usr/lib/gcc/x86_64-linux-gnu/5 -L/usr/lib/gcc/x86_64-linux-gnu/5 -L/home/isaiahk/anaconda3/envs/ipml_env/lib -lpython2.7 -lgfortran -o build/lib.linux-x86_64-2.7/qml/ffchl_module.so -lgomp -lblas -llapack
  /usr/bin/ld: cannot find -lblas
  /usr/bin/ld: cannot find -llapack
  collect2: error: ld returned 1 exit status
  /usr/bin/ld: cannot find -lblas
  /usr/bin/ld: cannot find -llapack
  collect2: error: ld returned 1 exit status
  error: Command "/usr/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/ffchl_modulemodule.o build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/fortranobject.o build/temp.linux-x86_64-2.7/qml/ffchl_module.o build/temp.linux-x86_64-2.7/qml/ffchl_scalar_kernels.o build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/ffchl_module-f2pywrappers.o build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/ffchl_module-f2pywrappers2.o -L/usr/lib/gcc/x86_64-linux-gnu/5 -L/usr/lib/gcc/x86_64-linux-gnu/5 -L/home/isaiahk/anaconda3/envs/ipml_env/lib -lpython2.7 -lgfortran -o build/lib.linux-x86_64-2.7/qml/ffchl_module.so -lgomp -lblas -llapack" failed with exit status 1

  ----------------------------------------
  Failed building wheel for qml
  Running setup.py clean for qml
Failed to build qml
Installing collected packages: qml
  Running setup.py install for qml ... error
    Complete output from command /home/isaiahk/anaconda3/envs/ipml_env/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-SwJZIR/qml/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-yXoY8m/install-record.txt --single-version-externally-managed --compile:
    MKL-discover: MKLROOT was not set
    running install
    running build
    running config_cc
    unifing config_cc, config, build_clib, build_ext, build commands --compiler options
    running config_fc
    unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
    running build_src
    build_src
    building extension "ffchl_module" sources
    f2py options: ['--quiet']
      adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/fortranobject.c' to sources.
      adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7' to include_dirs.
      adding 'build/src.linux-x86_64-2.7/ffchl_module-f2pywrappers.f' to sources.
      adding 'build/src.linux-x86_64-2.7/ffchl_module-f2pywrappers2.f90' to sources.
    building extension "farad_kernels" sources
    f2py options: ['--quiet']
      adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/fortranobject.c' to sources.
      adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7' to include_dirs.
      adding 'build/src.linux-x86_64-2.7/farad_kernels-f2pywrappers.f' to sources.
      adding 'build/src.linux-x86_64-2.7/farad_kernels-f2pywrappers2.f90' to sources.
    building extension "fcho_solve" sources
    f2py options: ['--quiet']
      adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/fortranobject.c' to sources.
      adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7' to include_dirs.
      adding 'build/src.linux-x86_64-2.7/fcho_solve-f2pywrappers.f' to sources.
    building extension "fdistance" sources
    f2py options: ['--quiet']
      adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/fortranobject.c' to sources.
      adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7' to include_dirs.
      adding 'build/src.linux-x86_64-2.7/fdistance-f2pywrappers.f' to sources.
    building extension "fkernels" sources
    f2py options: ['--quiet']
      adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/fortranobject.c' to sources.
      adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7' to include_dirs.
      adding 'build/src.linux-x86_64-2.7/fkernels-f2pywrappers.f' to sources.
    building extension "fslatm" sources
    f2py options: ['--quiet']
      adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/fortranobject.c' to sources.
      adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7' to include_dirs.
      adding 'build/src.linux-x86_64-2.7/fslatm-f2pywrappers.f' to sources.
      adding 'build/src.linux-x86_64-2.7/fslatm-f2pywrappers2.f90' to sources.
    building extension "frepresentations" sources
    f2py options: ['--quiet']
      adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/fortranobject.c' to sources.
      adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7' to include_dirs.
      adding 'build/src.linux-x86_64-2.7/frepresentations-f2pywrappers.f' to sources.
      adding 'build/src.linux-x86_64-2.7/frepresentations-f2pywrappers2.f90' to sources.
    build_src: building npy-pkg config files
    running build_py
    creating build/lib.linux-x86_64-2.7
    creating build/lib.linux-x86_64-2.7/qml
    copying qml/__init__.py -> build/lib.linux-x86_64-2.7/qml
    copying qml/alchemy.py -> build/lib.linux-x86_64-2.7/qml
    copying qml/arad.py -> build/lib.linux-x86_64-2.7/qml
    copying qml/compound.py -> build/lib.linux-x86_64-2.7/qml
    copying qml/data.py -> build/lib.linux-x86_64-2.7/qml
    copying qml/distance.py -> build/lib.linux-x86_64-2.7/qml
    copying qml/fchl.py -> build/lib.linux-x86_64-2.7/qml
    copying qml/kernels.py -> build/lib.linux-x86_64-2.7/qml
    copying qml/math.py -> build/lib.linux-x86_64-2.7/qml
    copying qml/representations.py -> build/lib.linux-x86_64-2.7/qml
    copying qml/slatm.py -> build/lib.linux-x86_64-2.7/qml
    copying qml/wrappers.py -> build/lib.linux-x86_64-2.7/qml
    running build_ext
    customize UnixCCompiler
    customize UnixCCompiler using build_ext
    get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
    customize Gnu95FCompiler
    Found executable /usr/bin/gfortran
    customize Gnu95FCompiler
    customize Gnu95FCompiler using build_ext
    get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
    customize Gnu95FCompiler
    customize Gnu95FCompiler
    customize Gnu95FCompiler using build_ext
    building 'ffchl_module' extension
    compiling C sources
    C compiler: gcc -pthread -B /home/isaiahk/anaconda3/envs/ipml_env/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC

    creating build/temp.linux-x86_64-2.7/build
    creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7
    creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/build
    creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7
    compile options: '-Ibuild/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7 -I/home/isaiahk/.local/lib/python2.7/site-packages/numpy/core/include -I/home/isaiahk/anaconda3/envs/ipml_env/include/python2.7 -c'
    extra options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
    gcc: build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/fortranobject.c
    gcc: build/src.linux-x86_64-2.7/ffchl_modulemodule.c
    compiling Fortran 90 module sources
    creating build/temp.linux-x86_64-2.7/qml
    Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
    Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
    Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
    compile options: '-Ibuild/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7 -I/home/isaiahk/.local/lib/python2.7/site-packages/numpy/core/include -I/home/isaiahk/anaconda3/envs/ipml_env/include/python2.7 -c'
    extra options: '-Jbuild/temp.linux-x86_64-2.7/qml -Ibuild/temp.linux-x86_64-2.7/qml'
    extra f90 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
    gfortran:f90: qml/ffchl_module.f90
    qml/ffchl_module.f90:275:36:

         & t_width, d_width, cut_distance, order, pd, ang_norm2, &
                                        1
    Warning: Unused dummy argument ‘cut_distance’ at (1) [-Wunused-dummy-argument]
    compiling Fortran sources
    Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
    Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
    Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
    compile options: '-Ibuild/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7 -I/home/isaiahk/.local/lib/python2.7/site-packages/numpy/core/include -I/home/isaiahk/anaconda3/envs/ipml_env/include/python2.7 -c'
    extra options: '-Jbuild/temp.linux-x86_64-2.7/qml -Ibuild/temp.linux-x86_64-2.7/qml'
    extra f90 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
    gfortran:f90: qml/ffchl_scalar_kernels.f90
    extra f90 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
    gfortran:f90: build/src.linux-x86_64-2.7/ffchl_module-f2pywrappers2.f90
    extra f77 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
    gfortran:f77: build/src.linux-x86_64-2.7/ffchl_module-f2pywrappers.f
    /usr/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/ffchl_modulemodule.o build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/fortranobject.o build/temp.linux-x86_64-2.7/qml/ffchl_module.o build/temp.linux-x86_64-2.7/qml/ffchl_scalar_kernels.o build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/ffchl_module-f2pywrappers.o build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/ffchl_module-f2pywrappers2.o -L/usr/lib/gcc/x86_64-linux-gnu/5 -L/usr/lib/gcc/x86_64-linux-gnu/5 -L/home/isaiahk/anaconda3/envs/ipml_env/lib -lpython2.7 -lgfortran -o build/lib.linux-x86_64-2.7/qml/ffchl_module.so -lgomp -lblas -llapack
    /usr/bin/ld: cannot find -lblas
    /usr/bin/ld: cannot find -llapack
    collect2: error: ld returned 1 exit status
    /usr/bin/ld: cannot find -lblas
    /usr/bin/ld: cannot find -llapack
    collect2: error: ld returned 1 exit status
    error: Command "/usr/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/ffchl_modulemodule.o build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/fortranobject.o build/temp.linux-x86_64-2.7/qml/ffchl_module.o build/temp.linux-x86_64-2.7/qml/ffchl_scalar_kernels.o build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/ffchl_module-f2pywrappers.o build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/ffchl_module-f2pywrappers2.o -L/usr/lib/gcc/x86_64-linux-gnu/5 -L/usr/lib/gcc/x86_64-linux-gnu/5 -L/home/isaiahk/anaconda3/envs/ipml_env/lib -lpython2.7 -lgfortran -o build/lib.linux-x86_64-2.7/qml/ffchl_module.so -lgomp -lblas -llapack" failed with exit status 1

    ----------------------------------------
Command "/home/isaiahk/anaconda3/envs/ipml_env/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-SwJZIR/qml/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-yXoY8m/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-SwJZIR/qml/

some things that ive tried already:
i installed gfortran
pip is up to date

Merge in qmlcode/tutorials notebooks

The tutorial could be converted to ipython notebooks and added to the docs.

FCHL python/fortran interface bug

The same fortran function is called two different places in the code, using different parameters.

https://github.com/qmlcode/qml/blob/develop/qml/fchl/fchl_scalar_kernels.py#L132

https://github.com/qmlcode/qml/blob/develop/qml/fchl/fchl_kernels.py#L148

One has a verbose flag and one does not, so one of them must be wrong?

Possible race condition in symmetric global kernel

Jimmy found this

ModuleNotFoundError: No module named 'numpy'

Collecting qml@ git+https://github.com/qmlcode/qml@a7921c9176b9498dcce096efad0883271706d633
  Cloning https://github.com/qmlcode/qml (to revision a7921c9176b9498dcce096efad0883271706d633) to /tmp/pip-install-4nhanz7h/qml_b8a84c0a43fb4a789769c5dfb049f2df
  Running command git clone --quiet https://github.com/qmlcode/qml /tmp/pip-install-4nhanz7h/qml_b8a84c0a43fb4a789769c5dfb049f2df
  Running command git rev-parse -q --verify 'sha^a7921c9176b9498dcce096efad0883271706d633'
  Running command git fetch -q https://github.com/qmlcode/qml a7921c9176b9498dcce096efad0883271706d633
  Running command git checkout -q a7921c9176b9498dcce096efad0883271706d633
  Resolved https://github.com/qmlcode/qml to commit a7921c9176b9498dcce096efad0883271706d633
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error
  
  Ã Getting requirements to build wheel did not run successfully.
  â exit code: 1
  â°â> [20 lines of output]
      Traceback (most recent call last):
        File "/home/berenger/src/MLKRR/venv/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/home/berenger/src/MLKRR/venv/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/home/berenger/src/MLKRR/venv/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
          return hook(config_settings)
                 ^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-0it_nql3/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 325, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=['wheel'])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-0it_nql3/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 295, in _get_build_requires
          self.run_setup()
        File "/tmp/pip-build-env-0it_nql3/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 487, in run_setup
          super().run_setup(setup_script=setup_script)
        File "/tmp/pip-build-env-0it_nql3/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 311, in run_setup
          exec(code, locals())
        File "<string>", line 2, in <module>
      ModuleNotFoundError: No module named 'numpy'
      [end of output]

move qml.ml.* python modules to qml.*

On second thought it seems unnecessary to type qml.ml.respresentations, rather than qml.representations.

Anybody against me moving it back to it's former dir?

QML install error, MKLROOT not set?

Hi all,
When attempting to install the QML package for python 3.8.3 an error returned. I've followed the installation guide for intel compilers and have installed ifort, mkl, numpy and scikit-learn. Looking through the message it says that MKLROOT is not set. Checking in system variables confirms this. There is a variable for ifort_compiler20 and mkl_serial, probably indicating succesfull installation.

What should mklroot be set to and is it the problem in this situation?

The error message is:

Collecting qml
Using cached https://files.pythonhosted.org/packages/7b/f3/c08d18659054cdf5e5dc531ee32ab20e6aa1d3772545837557828a03b1f5/qml-0.4.0.27.tar.gz
Installing collected packages: qml
Running setup.py install for qml ... error
ERROR: Command errored out with exit status 1:
command: 'c:\users\BRS\appdata\local\programs\python\python38\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\BRS\AppData\Local\Temp\pip-install-gn9koii5\qml\setup.py'"'"'; file='"'"'C:\Users\BRS\AppData\Local\Temp\pip-install-gn9koii5\qml\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' build --compiler=intelem --fcompiler=intelem install --record 'C:\Users\BRS\AppData\Local\Temp\pip-record-537c7i8_\install-record.txt' --single-version-externally-managed --compile --user --prefix=
cwd: C:\Users\BRS\AppData\Local\Temp\pip-install-gn9koii5\qml
Complete output (103 lines):
MKL-discover: MKLROOT was not set
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building extension "ffchl_module" sources
f2py options: ['--quiet']
adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8\fortranobject.c' to sources.
adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8' to include_dirs.
adding 'build\src.win-amd64-3.8\ffchl_module-f2pywrappers.f' to sources.
adding 'build\src.win-amd64-3.8\ffchl_module-f2pywrappers2.f90' to sources.
building extension "farad_kernels" sources
f2py options: ['--quiet']
adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8\fortranobject.c' to sources.
adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8' to include_dirs.
adding 'build\src.win-amd64-3.8\farad_kernels-f2pywrappers.f' to sources.
adding 'build\src.win-amd64-3.8\farad_kernels-f2pywrappers2.f90' to sources.
building extension "fcho_solve" sources
f2py options: ['--quiet']
adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8\fortranobject.c' to sources.
adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8' to include_dirs.
adding 'build\src.win-amd64-3.8\fcho_solve-f2pywrappers.f' to sources.
building extension "fdistance" sources
f2py options: ['--quiet']
adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8\fortranobject.c' to sources.
adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8' to include_dirs.
adding 'build\src.win-amd64-3.8\fdistance-f2pywrappers.f' to sources.
building extension "fkernels" sources
f2py options: ['--quiet']
adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8\fortranobject.c' to sources.
adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8' to include_dirs.
adding 'build\src.win-amd64-3.8\fkernels-f2pywrappers.f' to sources.
building extension "fslatm" sources
f2py options: ['--quiet']
adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8\fortranobject.c' to sources.
adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8' to include_dirs.
adding 'build\src.win-amd64-3.8\fslatm-f2pywrappers.f' to sources.
adding 'build\src.win-amd64-3.8\fslatm-f2pywrappers2.f90' to sources.
building extension "frepresentations" sources
f2py options: ['--quiet']
adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8\fortranobject.c' to sources.
adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8' to include_dirs.
adding 'build\src.win-amd64-3.8\frepresentations-f2pywrappers.f' to sources.
adding 'build\src.win-amd64-3.8\frepresentations-f2pywrappers2.f90' to sources.
build_src: building npy-pkg config files
running build_py
creating build\lib.win-amd64-3.8
creating build\lib.win-amd64-3.8\qml
copying qml\alchemy.py -> build\lib.win-amd64-3.8\qml
copying qml\arad.py -> build\lib.win-amd64-3.8\qml
copying qml\compound.py -> build\lib.win-amd64-3.8\qml
copying qml\data.py -> build\lib.win-amd64-3.8\qml
copying qml\distance.py -> build\lib.win-amd64-3.8\qml
copying qml\fchl.py -> build\lib.win-amd64-3.8\qml
copying qml\kernels.py -> build\lib.win-amd64-3.8\qml
copying qml\math.py -> build\lib.win-amd64-3.8\qml
copying qml\representations.py -> build\lib.win-amd64-3.8\qml
copying qml\slatm.py -> build\lib.win-amd64-3.8\qml
copying qml\wrappers.py -> build\lib.win-amd64-3.8\qml
copying qml_init_.py -> build\lib.win-amd64-3.8\qml
running build_ext
Could not locate executable icc
Could not locate executable ecc
customize IntelEM64TCCompiler
customize IntelEM64TCCompiler using build_ext
customize IntelEM64TFCompiler
Could not locate executable ifort
Could not locate executable efort
Could not locate executable efc
Traceback (most recent call last):
File "", line 1, in
File "C:\Users\BRS\AppData\Local\Temp\pip-install-gn9koii5\qml\setup.py", line 172, in
setup_pepytools()
File "C:\Users\BRS\AppData\Local\Temp\pip-install-gn9koii5\qml\setup.py", line 140, in setup_pepytools
setup(
File "c:\users\BRS\appdata\local\programs\python\python38\lib\site-packages\numpy\distutils\core.py", line 171, in setup
return old_setup(**new_attr)
File "c:\users\BRS\appdata\local\programs\python\python38\lib\site-packages\setuptools_init_.py", line 145, in setup
return distutils.core.setup(**attrs)
File "c:\users\BRS\appdata\local\programs\python\python38\lib\distutils\core.py", line 148, in setup
dist.run_commands()
File "c:\users\BRS\appdata\local\programs\python\python38\lib\distutils\dist.py", line 966, in run_commands
self.run_command(cmd)
File "c:\users\BRS\appdata\local\programs\python\python38\lib\distutils\dist.py", line 985, in run_command
cmd_obj.run()
File "c:\users\BRS\appdata\local\programs\python\python38\lib\site-packages\numpy\distutils\command\build.py", line 42, in run
old_build.run(self)
File "c:\users\BRS\appdata\local\programs\python\python38\lib\distutils\command\build.py", line 135, in run
self.run_command(cmd_name)
File "c:\users\BRS\appdata\local\programs\python\python38\lib\distutils\cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "c:\users\BRS\appdata\local\programs\python\python38\lib\distutils\dist.py", line 985, in run_command
cmd_obj.run()
File "c:\users\BRS\appdata\local\programs\python\python38\lib\site-packages\numpy\distutils\command\build_ext.py", line 239, in run
fcompiler.customize(self.distribution)
File "c:\users\BRS\appdata\local\programs\python\python38\lib\site-packages\numpy\distutils\fcompiler_init_.py", line 463, in customize
self.find_executables()
File "c:\users\BRS\appdata\local\programs\python\python38\lib\site-packages\numpy\distutils\fcompiler_init_.py", line 352, in find_executables
raise CompilerNotFound('%s: f90 nor f77' % ctype)
numpy.distutils.fcompiler.CompilerNotFound: intelem: f90 nor f77
----------------------------------------
ERROR: Command errored out with exit status 1: 'c:\users\BRS\appdata\local\programs\python\python38\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\BRS\AppData\Local\Temp\pip-install-gn9koii5\qml\setup.py'"'"'; file='"'"'C:\Users\BRS\AppData\Local\Temp\pip-install-gn9koii5\qml\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' build --compiler=intelem --fcompiler=intelem install --record 'C:\Users\BRS\AppData\Local\Temp\pip-record-537c7i8_\install-record.txt' --single-version-externally-managed --compile --user --prefix= Check the logs for full command output.

I'm new to python, help would be greatly appreciated.

UnicodeDecodeError from setup.py

probably my setup, but happens on both my macbook and linux desktop at work (both with python 3)

p setup.py install --prefix=/Users/strange/qmlcode
MKL-discover: MKLROOT was not set
Traceback (most recent call last):
File "setup.py", line 170, in
setup_pepytools()
File "setup.py", line 149, in setup_pepytools
long_description = readme(),
File "setup.py", line 134, in readme
return f.read()
File "/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/encodings/ascii.py", line 26, in decode
return codecs.ascii_decode(input, self.errors)[0]

Following seems to fix it:

diff --git a/setup.py b/setup.py
index 495f7e8..2ce0397 100755
--- a/setup.py
+++ b/setup.py
@@ -130,7 +130,7 @@ ext_fslatm = Extension(name = 'fslatm',
 
 # use README.md as long description
 def readme():
-    with open('README.md') as f:
+    with open('README.md', encoding='latin1') as f:
         return f.read()

OpenMP problem in acsf generation with gradients

The subroutine fgenerate_acsf_and_gradients causes problems when the size of the representation is over a certain size (nTs=15, nRs2=15, nRs3=15 makes it not work). The bug doesn't seem to be reproducible on every computer.

BoB generation

The generation of a BoB representation via
$ qml.representations.generate_bob
requires the variable "atomtypes" as third argument which is not used by the function.

Installation fails on Windows systems with the error: invalid numeric argument '/Wno-maybe-uninitialized'

When installing qmlcode on a windows system, pip install qml, the installation fails with the error:

 cl : Command line error D8021 : invalid numeric argument '/Wno-maybe-uninitialized'
error: Command "C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.29.30037\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -Ibuild\src.win-amd64-3.9\build\src.win-amd64-3.9\fchl -IC:\raghav\env_dftb\lib\site-packages\numpy\core\include -IC:\raghav\env_dftb\include -Ic:\users\davinder kumar\appdata\local\programs\python\python39\include -Ic:\users\davinder kumar\appdata\local\programs\python\python39\include -IC:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.29.30037\include /Tcbuild\src.win-amd64-3.9\fchl\ffchl_modulemodule.c /Fobuild\temp.win-amd64-3.9\Release\build\src.win-amd64-3.9\fchl\ffchl_modulemodule.obj -O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp" failed with exit status 2

Is this a problem due to lack of some installed requirement?

Installation broken in fresh virtual environments

Description

The QML library cannot be installed in an environment where NumPy is not already installed, for example a fresh virtual environment when installing another project which uses QML as a dependency.

To reproduce

python3 -m venv venv
source venv/bin/activate
pip install qml

If NumPy is installed beforehand, then it works

python3 -m venv venv
source venv/bin/activate
pip install numpy
pip install qml

How to fix

NumPy should be specified as a dependency in the setup configuration.

Segmentation fault for test_krr_bob on macOS

The test test_krr_bob produces a segmentation fault on macOS (10.14):

================================================================================== test session starts ===================================================================================
platform darwin -- Python 3.6.9, pytest-5.1.2, py-1.8.0, pluggy-0.13.0 -- /Users/rmeli/miniconda3/envs/qml/bin/python
cachedir: .pytest_cache
rootdir: /Users/rmeli/Documents/git/software/qml
collected 90 items                                                                                                                                                                       

test/test_acsf.py::test_acsf_1 PASSED                                                                                                                                              [  1%]
test/test_acsf.py::test_acsf_2 PASSED                                                                                                                                              [  2%]
test/test_acsf_linear_angles.py::test_fchl_acsf PASSED                                                                                                                             [  3%]
test/test_acsf_linear_angles.py::test_acsf PASSED                                                                                                                                  [  4%]
test/test_arad.py::test_arad PASSED                                                                                                                                                [  5%]
test/test_armp.py::test_set_representation PASSED                                                                                                                                  [  6%]
test/test_armp.py::test_set_properties PASSED                                                                                                                                      [  7%]
test/test_armp.py::test_set_descriptor PASSED                                                                                                                                      [  8%]
test/test_armp.py::test_fit_1 PASSED                                                                                                                                               [ 10%]
test/test_armp.py::test_fit_2 PASSED                                                                                                                                               [ 11%]
test/test_armp.py::test_fit_3 PASSED                                                                                                                                               [ 12%]
test/test_armp.py::test_fit_4 PASSED                                                                                                                                               [ 13%]
test/test_armp.py::test_score_3 PASSED                                                                                                                                             [ 14%]
test/test_armp.py::test_predict_3 PASSED                                                                                                                                           [ 15%]
test/test_armp.py::test_predict_fromxyz PASSED                                                                                                                                     [ 16%]
test/test_armp.py::test_retraining PASSED                                                                                                                                          [ 17%]
test/test_compound.py::test_compound PASSED                                                                                                                                        [ 18%]
test/test_distance.py::test_manhattan PASSED                                                                                                                                       [ 20%]
test/test_distance.py::test_l2 PASSED                                                                                                                                              [ 21%]
test/test_distance.py::test_p PASSED                                                                                                                                               [ 22%]
test/test_energy_krr_atomic_cmat.py::test_krr_gaussian_local_cmat PASSED                                                                                                           [ 23%]
test/test_energy_krr_atomic_cmat.py::test_krr_laplacian_local_cmat PASSED                                                                                                          [ 24%]
test/test_energy_krr_bob.py::test_krr_bob Fatal Python error: Segmentation fault

Thread 0x000070000e7bf000 (most recent call first):
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/threading.py", line 295 in wait
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/queue.py", line 164 in get
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/tensorflow/python/summary/writer/event_file_writer.py", line 159 in run
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/threading.py", line 916 in _bootstrap_inner
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/threading.py", line 884 in _bootstrap

Current thread 0x0000000113a955c0 (most recent call first):
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/qml/representations/representations.py", line 314 in generate_bob
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/qml/utils/compound.py", line 249 in generate_bob
  File "/Users/rmeli/Documents/git/software/qml/test/test_energy_krr_bob.py", line 74 in test_krr_bob
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/python.py", line 170 in pytest_pyfunc_call
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/callers.py", line 187 in _multicall
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/manager.py", line 86 in <lambda>
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/manager.py", line 92 in _hookexec
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/hooks.py", line 286 in __call__
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/python.py", line 1423 in runtest
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/runner.py", line 117 in pytest_runtest_call
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/callers.py", line 187 in _multicall
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/manager.py", line 86 in <lambda>
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/manager.py", line 92 in _hookexec
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/hooks.py", line 286 in __call__
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/runner.py", line 192 in <lambda>
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/runner.py", line 220 in from_call
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/runner.py", line 192 in call_runtest_hook
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/runner.py", line 167 in call_and_report
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/runner.py", line 87 in runtestprotocol
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/runner.py", line 72 in pytest_runtest_protocol
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/callers.py", line 187 in _multicall
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/manager.py", line 86 in <lambda>
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/manager.py", line 92 in _hookexec
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/hooks.py", line 286 in __call__
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/main.py", line 256 in pytest_runtestloop
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/callers.py", line 187 in _multicall
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/manager.py", line 86 in <lambda>
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/manager.py", line 92 in _hookexec
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/hooks.py", line 286 in __call__
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/main.py", line 235 in _main
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/main.py", line 191 in wrap_session
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/main.py", line 228 in pytest_cmdline_main
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/callers.py", line 187 in _multicall
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/manager.py", line 86 in <lambda>
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/manager.py", line 92 in _hookexec
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/hooks.py", line 286 in __call__
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/config/__init__.py", line 78 in main
  File "/Users/rmeli/miniconda3/envs/qml/bin/pytest", line 10 in <module>
[1]    18142 segmentation fault  pytest -v

The segmentation fault comes from subroutine fgenerate_bob in frepresentations.f90 when called by def generate_bob in representations.py.

Installation

Installation on develop branch.

conda create -n qml python=3.6 ipython
conda activate qml
pip install numpy scipy pandoc ase pandas scikit-learn tensorflow pytest
python setup.py build
python setup.py install

Remove Dataprovider from data/ remove ASE dependency

As said in title. These are superseeded by the QMLearn interface.

This will also remove the dependency on ASE, as far as I can see.

Any downsides to this @larsbratholm ?

wheel problem

The python version is python3.10.
And the ERROR: Could not build wheels for qml, which is required to install pyproject.toml-based projects

Look into using dask for distributed computations

http://dask.pydata.org/en/latest/

Problems with installation

I try to install qml in the centos machine with intel 2017/2020 compiler and python3.

Then error as below:
raise CompilerNotFound()
numpy.distutils.fcompiler.CompilerNotFound
And I also tried to install with default: error as below:
/tmp/ccC5eEBN.s: Assembler messages:
/tmp/ccC5eEBN.s:422: Error: suffix or operands invalid for vpcmpgtq' /tmp/ccC5eEBN.s:423: Error: suffix or operands invalid for vpcmpgtq'
/tmp/ccC5eEBN.s:424: Error: suffix or operands invalid for vpand' /tmp/ccC5eEBN.s:425: Error: suffix or operands invalid for vpand'
/tmp/ccC5eEBN.s:426: Error: no such instruction: vperm2i128 $32,%ymm1,%ymm0,%ymm2' /tmp/ccC5eEBN.s:427: Error: no such instruction: vperm2i128 $49,%ymm1,%ymm0,%ymm0'
/tmp/ccC5eEBN.s:428: Error: suffix or operands invalid for vpshufd' /tmp/ccC5eEBN.s:429: Error: suffix or operands invalid for vpshufd'
/tmp/ccC5eEBN.s:430: Error: suffix or operands invalid for vpunpcklqdq' /tmp/ccC5eEBN.s:431: Error: suffix or operands invalid for vpaddd'
/tmp/ccC5eEBN.s:436: Error: no such instruction: vperm2i128 $33,%ymm1,%ymm4,%ymm0' /tmp/ccC5eEBN.s:438: Error: suffix or operands invalid for vpaddd'
/tmp/ccC5eEBN.s:440: Error: no such instruction: `vperm2i128 $33,%ymm1,%ymm0,%ymm2'
error: Command "gcc -pthread -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -I/opt/netcdf/include -fPIC -Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7 -I/opt/python3.7/Python-3.7.1/lib/python3.7/site-packages/numpy/core/include -I/opt/python3.7/Python-3.7.1/include/python3.7m -c build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/fortranobject.c -o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/fortranobject.o -MMD -MF build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/fortranobject.o.d -O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp" failed with exit status 1.

I really need help! Thanks a lot!

Change examples/tutorials to jupyter notebooks

The current ones are in markdown. It would probably be better to change these to notebooks so people can edit them and that they are automatically updated with code changes.

Create notebook from the ./examples

The folder contains some simple examples of running neural networks. This should be extended and rewritten as notebooks.

Time taken to import qml modules

Hello,

It might just be me, but I was recently timing / profiling some reasonably fast code and noticed that the bottleneck was the qml import. I then ran a file containing only the two imports that were causing the bottleneck, i.e. import.py containing:

from qml.kernels import gaussian_kernel
from qml.math import cho_solve

and it took my reasonably crap laptop 4s to run that. Is it just me or could there be some hefty imports in those modules?

Thanks,
Puck

FCHL example uses old notation

The FCHL documentation for using kernels does currently not match the code. E.g. the second argument of get_atomic_symmetric_kernels is verbose in the code, but sigma in the example.

Space in -pthread arguments fails compilation

I followed Installing via with Intel compilers instructions and got this error:

ifort: error #10236: File not found:  ' -lpthread'

I've look at the compiling command and realise that was a extra space in the pthread argument.

https://github.com/qmlcode/qml/blob/master/setup.py#L41
https://github.com/qmlcode/qml/blob/master/setup.py#L28

I'm attaching the patch to fix that.
remove_pthread_extra_space.patch.txt

git apply remove_pthread_extra_space.patch.txt

Issue when giving integer values to fchl kernel functions

There's a bug in the fchl kernel functions if some parameters are integers. E.g. https://github.com/qmlcode/qml/blob/develop/qml/fchl/fchl_kernel_functions.py#L38

The numpy array will be an integer array and the subsequent transformations will be rounded to integer values. To fix, the line above should explicitely have dtype=float added. There might be more similar cases in the file.

Any documents about the use of FCHL19?

Hi,

It is a great work of the FCHL19 in https://arxiv.org/pdf/1909.01946.pdf
I searched the source code and had no idea where FCHL19 located. Is that possible to provide a basic example of the FCHL19?

Thanks,
Xinyu

Installation with Intel compiler fails

I have Intel Parallel Studio XE installed, and with it comes the Fortran Compiler 19.1 Update 3,
so using the intel install, I still get
File "C:\Python\Lib\site-packages\numpy\distutils\fcompiler\__init__.py", line 352, in find_executables raise CompilerNotFound('%s: f90 nor f77' % ctype) numpy.distutils.fcompiler.CompilerNotFound: intelem: f90 nor f77

What am I doing wrong?

import error

Python 3.9.9 (main, Dec 1 2021, 16:36:40)
[GCC 7.5.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

import qml
Traceback (most recent call last):
File "", line 1, in
File "/user/kijsdc/.local/lib/python3.9/site-packages/qml/init.py", line 37, in
from .compound import Compound
File "/user/kijsdc/.local/lib/python3.9/site-packages/qml/compound.py", line 30, in
from .representations import generate_coulomb_matrix
File "/user/kijsdc/.local/lib/python3.9/site-packages/qml/representations.py", line 28, in
from .frepresentations import fgenerate_coulomb_matrix
ImportError: /user/kijsdc/.local/lib/python3.9/site-packages/qml/frepresentations.cpython-39-x86_64-linux-gnu.so: undefined symbol: dsyev_

I need your help. please help me...

Doc issue (Mac Fortran support)

I was looking through the documentation to try it out. :-)

"Clang Fortran compiler" was mentioned here: http://www.qmlcode.org/installation.html#note-on-apple-mac-support

I think you mean that the "GCC Fortran compiler, gfortran" through homebrew does not include OpenMP support.

AFAIK, there is no Clang Fortran compiler.

You can get a gfortran from here, which I think includes the OpenMP support: http://hpc.sourceforge.net

Unable to install.

PS /home/rokejulianlockhart> pip3 install qml                   
Defaulting to user installation because normal site-packages is not writeable
Collecting qml
  Downloading qml-0.4.0.27.tar.gz (41 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 41.5/41.5 kB 1.2 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [25 lines of output]
      /tmp/pip-install-dd8zsoyi/qml_0fd0b7dd68194f79a7665a153691ee9d/setup.py:4: DeprecationWarning:
      
        `numpy.distutils` is deprecated since NumPy 1.23.0, as a result
        of the deprecation of `distutils` itself. It will be removed for
        Python >= 3.12. For older Python versions it will remain present.
        It is recommended to use `setuptools < 60.0` for those Python versions.
        For more details, see:
          https://numpy.org/devdocs/reference/distutils_status_migration.html
      
      
        from numpy.distutils.core import Extension, setup
      MKL-discover: MKLROOT was not set
      running egg_info
      running build_src
      INFO: build_src
      INFO: building extension "ffchl_module" sources
      INFO: f2py options: ['--quiet']
      INFO: f2py:> build/src.linux-x86_64-3.10/ffchl_modulemodule.c
      creating build
      creating build/src.linux-x86_64-3.10
      appenddecl: "dimension" not implemented.
      appenddecl: "dimension" not implemented.
      INFO:   adding 'build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fortranobject.c' to sources.
      INFO:   adding 'build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10' to include_dirs.
      error: file '/usr/lib64/python3.10/site-packages/numpy/f2py/src/fortranobject.c' does not exist
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
NativeCommandExitException: Program "pip3" ended with non-zero exit code: 1.
PS /home/rokejulianlockhart>

Verbose options for output

Some functions (mosly my own) always print output. Change behavior to only print if

verbose=True

is given as kwarg.

Add OSX to travis build

Here's an example of how to make a build matrix:

https://github.com/RMeli/irc/blob/master/.travis.yml

If the system is OSX or linux is then detected in the install scripts like so:

https://github.com/RMeli/irc/blob/master/.travis/before_install.sh

Compiler warnings

Remove any compiler warnings. Please post any compiler warnings you see in this thread!

Anaconda deployment

Build anaconda package and deploy it to anaconda cloud in travis. Docs on how to do this: https://conda.io/docs/user-guide/tutorials/build-pkgs-skeleton.html

Include compiler and link information in help

Doing help(qml) should include what f2py compiler was used (gfortran, ifort) and also what lib was used (mkl,blas,lapack).

@andersx said this was easy to include.

Remove all of Anders' stale branches

I'm on it

Error in test_armp.py//test_predict_fromxyz()

I had a mysterious test-fail. Seems like about 4 in 100 trial runs of the function in the title results in AssertionError (see output below).

I checked the printout and the number seem to vary ever so slightly and sometimes they are a bit above the threshold in np.isclose. I think rtol can simply be relaxed.

Pinging @SilviaAmAm @larsbratholm

Best,
Anders

andersx@nuke:~/dev/qml/gradient_kernel/test$ for i in $(seq 1 100); do python3 test_armp.py; done
2019-01-29 14:12:25.852190: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:12:31.543292: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:12:36.596743: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:12:41.695897: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:12:46.699178: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:12:51.896631: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:12:57.019773: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:13:02.016708: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:13:07.118745: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:13:12.030586: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:13:17.021577: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:13:21.881790: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:13:26.781928: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:13:31.817703: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:13:36.761721: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:13:41.757300: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:13:46.878520: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:13:51.886971: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:13:56.880519: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:14:01.952509: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:14:06.905798: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:14:11.792043: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:14:16.888623: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:14:21.966927: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:14:27.006712: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:14:32.458704: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:14:37.459119: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:14:42.656408: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:14:47.625612: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
Traceback (most recent call last):
  File "test_armp.py", line 308, in <module>
    test_predict_fromxyz()
  File "test_armp.py", line 231, in test_predict_fromxyz
    assert np.all(np.isclose(pred1, pred2, rtol=1.e-6))
AssertionError
2019-01-29 14:14:51.274565: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:14:56.231079: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:15:01.157808: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:15:06.427084: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:15:11.550079: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:15:16.739757: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:15:21.893527: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:15:26.889951: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:15:31.932909: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:15:37.024012: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:15:42.240176: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:15:48.002732: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
Traceback (most recent call last):
  File "test_armp.py", line 308, in <module>
    test_predict_fromxyz()
  File "test_armp.py", line 231, in test_predict_fromxyz
    assert np.all(np.isclose(pred1, pred2, rtol=1.e-6))
AssertionError
2019-01-29 14:15:52.242681: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:15:57.495700: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:16:02.606738: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:16:07.551746: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:16:12.523331: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:16:17.488134: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:16:22.563080: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:16:27.482621: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:16:32.612148: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:16:37.605385: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:16:42.644832: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:16:47.902066: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:16:53.091282: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:16:58.162367: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:17:03.169611: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:17:08.074685: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:17:13.014483: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:17:17.901797: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:17:22.916826: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
Traceback (most recent call last):
  File "test_armp.py", line 308, in <module>
    test_predict_fromxyz()
  File "test_armp.py", line 231, in test_predict_fromxyz
    assert np.all(np.isclose(pred1, pred2, rtol=1.e-6))
AssertionError
2019-01-29 14:17:26.786505: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:17:31.989765: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:17:37.135199: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:17:42.093665: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:17:46.974069: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:17:51.911819: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:17:56.848259: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
Traceback (most recent call last):
  File "test_armp.py", line 308, in <module>
    test_predict_fromxyz()
  File "test_armp.py", line 231, in test_predict_fromxyz
    assert np.all(np.isclose(pred1, pred2, rtol=1.e-6))
AssertionError
2019-01-29 14:18:00.691744: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
Traceback (most recent call last):
  File "test_armp.py", line 308, in <module>
    test_predict_fromxyz()
  File "test_armp.py", line 231, in test_predict_fromxyz
    assert np.all(np.isclose(pred1, pred2, rtol=1.e-6))
AssertionError
2019-01-29 14:18:04.548890: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:18:09.580368: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:18:14.534102: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:18:19.456988: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:18:25.042760: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:18:29.987893: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:18:34.885835: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:18:39.856855: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:18:44.779206: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:18:49.854183: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:18:54.852524: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:18:59.785425: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:19:04.820802: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:19:09.745178: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:19:14.667206: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:19:19.676176: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:19:24.918473: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:19:30.202376: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:19:35.403360: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:19:40.453957: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:19:45.314655: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:19:50.135643: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:19:55.088372: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:20:00.040717: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:20:04.950036: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:20:09.858293: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:20:14.732765: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:20:19.830306: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
Traceback (most recent call last):
  File "test_armp.py", line 308, in <module>
    test_predict_fromxyz()
  File "test_armp.py", line 231, in test_predict_fromxyz
    assert np.all(np.isclose(pred1, pred2, rtol=1.e-6))
AssertionError
2019-01-29 14:20:23.726169: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:20:28.885089: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:20:33.836026: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-01-29 14:20:38.848189: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA

handling topology only molecules [feature request]

Hello,

Would it be possible in some way to update the method in order to
also work with dimension 1 molecules (i.e. only the molecular graph).

Please forgive me if this is a stupid question.

Regards,
Francois.

Update docs to restructure

QML on Apple silicon

Is there a way to build this into a MacBook Air with Apple Silicon (M1)? I'm trying, but there were a lot of errors complaining
the lack of a FORTRAN compiler. Here is my output of python setup.py build --help-fcompiler

Gnu95FCompiler instance properties:
  archiver        = ['/opt/homebrew/bin/gfortran', '-cr']
  compile_switch  = '-c'
  compiler_f77    = ['/opt/homebrew/bin/gfortran', '-Wall', '-g', '-ffixed-
                    form', '-fno-second-underscore', '-fPIC', '-O3', '-funroll
                    -loops']
  compiler_f90    = ['/opt/homebrew/bin/gfortran', '-Wall', '-g', '-fno-
                    second-underscore', '-fPIC', '-O3', '-funroll-loops']
  compiler_fix    = ['/opt/homebrew/bin/gfortran', '-Wall', '-g', '-ffixed-
                    form', '-fno-second-underscore', '-Wall', '-g', '-fno-
                    second-underscore', '-fPIC', '-O3', '-funroll-loops']
  libraries       = ['gfortran']
  library_dirs    =
                    ['/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/
                    aarch64-apple-darwin21/11',
                    '/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/a
                    arch64-apple-darwin21/11/../../..',
                    '/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/a
                    arch64-apple-darwin21/11/../../..']
  linker_exe      = ['/opt/homebrew/bin/gfortran', '-Wall', '-Wall']
  linker_so       = ['/opt/homebrew/bin/gfortran', '-Wall', '-g', '-Wall', '
                    -g', '-undefined', 'dynamic_lookup', '-bundle']
  object_switch   = '-o '
  ranlib          = ['/opt/homebrew/bin/gfortran']
  version         = LooseVersion ('11')
  version_cmd     = ['/opt/homebrew/bin/gfortran', '-dumpversion']
Fortran compilers found:
  --fcompiler=gnu95  GNU Fortran 95 compiler (11)
Compilers available for this platform, but not found:
  --fcompiler=absoft  Absoft Corp Fortran Compiler
  --fcompiler=g95     G95 Fortran Compiler
  --fcompiler=gnu     GNU Fortran 77 compiler
  --fcompiler=ibm     IBM XL Fortran Compiler
  --fcompiler=intel   Intel Fortran Compiler for 32-bit apps
  --fcompiler=nag     NAGWare Fortran 95 Compiler
  --fcompiler=nagfor  NAG Fortran Compiler
  --fcompiler=pg      Portland Group Fortran Compiler
Compilers not available on this platform:
  --fcompiler=arm       Arm Compiler
  --fcompiler=compaq    Compaq Fortran Compiler
  --fcompiler=flang     Portland Group Fortran LLVM Compiler
  --fcompiler=fujitsu   Fujitsu Fortran Compiler
  --fcompiler=hpux      HP Fortran 90 Compiler
  --fcompiler=intele    Intel Fortran Compiler for Itanium apps
  --fcompiler=intelem   Intel Fortran Compiler for 64-bit apps
  --fcompiler=intelev   Intel Visual Fortran Compiler for Itanium apps
  --fcompiler=intelv    Intel Visual Fortran Compiler for 32-bit apps
  --fcompiler=intelvem  Intel Visual Fortran Compiler for 64-bit apps
  --fcompiler=lahey     Lahey/Fujitsu Fortran 95 Compiler
  --fcompiler=mips      MIPSpro Fortran Compiler
  --fcompiler=none      Fake Fortran compiler
  --fcompiler=nv        NVIDIA HPC SDK
  --fcompiler=pathf95   PathScale Fortran Compiler
  --fcompiler=sun       Sun or Forte Fortran 95 Compiler
  --fcompiler=vast      Pacific-Sierra Research Fortran 90 Compiler
For compiler details, run 'config_fc --verbose' setup command.```

It's worth to mention that I have `gfortran` installed from `brew`, and an Anaconda environment with many tools, including `pip`.

BoB seg faulting on MacOS

When I run generate_bob, either through the Compound class or just the representation, it is throwing a seg fault. I have installed qml (through pip3) as well as the Fortran compiler (brew install gcc).

Some basic functionality for the Compound class

It's not a bug but rather an enhancement / feature request : when creating mol objects using the Compound class to then generate a Coulomb matrix with mol.generate_coulomb_matrix, we have to specify the desired size of the Coulomb matrix with the size argument. It would be nice if properties such as the number of atoms were available in the Compound class. Currently I'm working around this by reading in the coordinates and atom types from the xyz files myself and generating Coulomb matrices using the representations.generate_coulomb_matrix function instead.

NameError: name 'Compound' is not defined

Dataset downloaders

Hi everybody,

I'm Michael Eickenberg. I came to visit Basel in December 2016 to work with Samuel on the scattering transform for electronic densities. In the context of this, I started an open source software package in which I wanted to gather all sorts of machine learning algorithms for molecule property estimation. Alas it only got to having some nice dataset downloaders (the scattering transform itself, which I wanted to also put in this package, is now being rolled out in a different package - let me know if anybody is interested in alpha-testing it).

Unfortunately, I don't think CheML is ever going to rise to Quantum Chemistry Machine Learning Glory, since I don't have time to work on it. So please feel free to use anything useful you find in CheML for this package. For example, https://github.com/CheML/CheML/blob/master/cheml/datasets.py has mechanisms for loading datasets and downloading them if they are not present. This is very convenient for showing off examples, because it abstracts away all the data procuration process.

Michael

Add license information to all files, re-update author list

Everything should be explicitly MIT licensed.
Additionally, some co-authors seem to have vanished in an earlier commit: 8f16e47#diff-04c6e90faac2675aa89e2176d2eec7d8

Add examples/documentation for Aglaia module

Does it make sense to include some code to get people started?

Problem with installing QML on MAC

I have Mac with Sierra OS. I have installed BLAS, LAPACK as well as ASE and gnu compilers from macport. When I try python setup.py install I get:
resetting extension 'farad_kernels' language from '/opt/local/bin/gfortran-mp-7' to 'f77'.
resetting extension 'fcho_solve' language from '/opt/local/bin/gfortran-mp-7' to 'f77'.
resetting extension 'fdistance' language from '/opt/local/bin/gfortran-mp-7' to 'f77'.
resetting extension 'fkernels' language from '/opt/local/bin/gfortran-mp-7' to 'f77'.
resetting extension 'frepresentations' language from '/opt/local/bin/gfortran-mp-7' to 'f77'.
customize Gnu95FCompiler
Could not locate executable gfortran
Could not locate executable f95
customize NAGFCompiler
customize AbsoftFCompiler
Could not locate executable f90
Could not locate executable f77
customize IBMFCompiler
Could not locate executable xlf90
Could not locate executable xlf
customize IntelFCompiler
Could not locate executable ifort
Could not locate executable ifc
customize GnuFCompiler
Could not locate executable g77
customize G95FCompiler
Could not locate executable g95
customize PGroupFCompiler
Could not locate executable pgfortran
don't know how to compile Fortran code on platform 'posix'
warning: build_ext: f77_compiler=None is not available.

building 'farad_kernels' extension
error: extension 'farad_kernels' has Fortran sources but no Fortran compiler found
bash-3.2$

I have give the full path in setup.py for FORTRAN = "/opt/local/bin/gfortran-mp-7"

Please let me know what I need to do to resolve the issue.