├── .clang-format ├── .gitignore ├── Authors.txt ├── CMakeLists.txt ├── FindFFTW.cmake ├── License.txt ├── Quaternions ├── QUATERNION_LIST_36864_Orient ├── QUATERNION_LIST_4608_Orient └── QUATERNION_LIST_576_Orient ├── README.md ├── autotuner.cpp ├── bioem.cpp ├── bioem_algorithm.h ├── bioem_cuda.cu ├── doc ├── _static │ └── __empty__ ├── _templates │ └── __empty__ ├── _themes │ └── sphinx_rtd_theme │ │ ├── __init__.py │ │ ├── breadcrumbs.html │ │ ├── footer.html │ │ ├── layout.html │ │ ├── layout.html~ │ │ ├── search.html │ │ ├── searchbox.html │ │ ├── static │ │ ├── css │ │ │ ├── badge_only.css │ │ │ └── theme.css │ │ ├── fonts │ │ │ ├── FontAwesome.otf │ │ │ ├── Inconsolata-Bold.ttf │ │ │ ├── Inconsolata-Regular.ttf │ │ │ ├── Lato-Bold.ttf │ │ │ ├── Lato-BoldItalic.ttf │ │ │ ├── Lato-Italic.ttf │ │ │ ├── Lato-Regular.ttf │ │ │ ├── RobotoSlab-Bold.ttf │ │ │ ├── RobotoSlab-Regular.ttf │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ ├── fontawesome-webfont.woff │ │ │ └── fontawesome-webfont.woff2 │ │ └── js │ │ │ ├── modernizr.min.js │ │ │ └── theme.js │ │ ├── theme.conf │ │ └── versions.html ├── bib_manual.bib ├── conf.py ├── exts │ ├── .gitignore │ └── inpar.py ├── img │ ├── Fig1_10Dec.pdf │ ├── Fig1_10Dec.svg │ ├── ModComp.pdf │ └── ModComp.svg ├── index.rst ├── make.bat └── require.txt ├── include ├── MersenneTwister.h ├── autotuner.h ├── bioem.h ├── bioem_cuda.h ├── bioem_cuda_internal.h ├── defs.h ├── map.h ├── model.h ├── mrc.h ├── param.h └── timer.h ├── main.cpp ├── map.cpp ├── model.cpp ├── param.cpp └── timer.cpp /.clang-format: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/.clang-format -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/.gitignore -------------------------------------------------------------------------------- /Authors.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/Authors.txt -------------------------------------------------------------------------------- /CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/CMakeLists.txt -------------------------------------------------------------------------------- /FindFFTW.cmake: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/FindFFTW.cmake -------------------------------------------------------------------------------- /License.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/License.txt -------------------------------------------------------------------------------- /Quaternions/QUATERNION_LIST_36864_Orient: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/Quaternions/QUATERNION_LIST_36864_Orient -------------------------------------------------------------------------------- /Quaternions/QUATERNION_LIST_4608_Orient: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/Quaternions/QUATERNION_LIST_4608_Orient -------------------------------------------------------------------------------- /Quaternions/QUATERNION_LIST_576_Orient: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/Quaternions/QUATERNION_LIST_576_Orient -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/README.md -------------------------------------------------------------------------------- /autotuner.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/autotuner.cpp -------------------------------------------------------------------------------- /bioem.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/bioem.cpp -------------------------------------------------------------------------------- /bioem_algorithm.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/bioem_algorithm.h -------------------------------------------------------------------------------- /bioem_cuda.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/bioem_cuda.cu -------------------------------------------------------------------------------- /doc/_static/__empty__: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /doc/_templates/__empty__: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/__init__.py -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/breadcrumbs.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/breadcrumbs.html -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/footer.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/footer.html -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/layout.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/layout.html -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/layout.html~: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/layout.html~ -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/search.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/search.html -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/searchbox.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/searchbox.html -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/static/css/badge_only.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/static/css/badge_only.css -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/static/css/theme.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/static/css/theme.css -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/static/fonts/FontAwesome.otf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/static/fonts/FontAwesome.otf -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/static/fonts/Inconsolata-Bold.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/static/fonts/Inconsolata-Bold.ttf -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/static/fonts/Inconsolata-Regular.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/static/fonts/Inconsolata-Regular.ttf -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/static/fonts/Lato-Bold.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/static/fonts/Lato-Bold.ttf -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/static/fonts/Lato-BoldItalic.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/static/fonts/Lato-BoldItalic.ttf -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/static/fonts/Lato-Italic.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/static/fonts/Lato-Italic.ttf -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/static/fonts/Lato-Regular.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/static/fonts/Lato-Regular.ttf -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/static/fonts/RobotoSlab-Bold.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/static/fonts/RobotoSlab-Bold.ttf -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/static/fonts/RobotoSlab-Regular.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/static/fonts/RobotoSlab-Regular.ttf -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.eot: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.eot -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.svg -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.ttf -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff2 -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/static/js/modernizr.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/static/js/modernizr.min.js -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/static/js/theme.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/static/js/theme.js -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/theme.conf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/theme.conf -------------------------------------------------------------------------------- /doc/_themes/sphinx_rtd_theme/versions.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/_themes/sphinx_rtd_theme/versions.html -------------------------------------------------------------------------------- /doc/bib_manual.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/bib_manual.bib -------------------------------------------------------------------------------- /doc/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/conf.py -------------------------------------------------------------------------------- /doc/exts/.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | -------------------------------------------------------------------------------- /doc/exts/inpar.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/exts/inpar.py -------------------------------------------------------------------------------- /doc/img/Fig1_10Dec.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/img/Fig1_10Dec.pdf -------------------------------------------------------------------------------- /doc/img/Fig1_10Dec.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/img/Fig1_10Dec.svg -------------------------------------------------------------------------------- /doc/img/ModComp.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/img/ModComp.pdf -------------------------------------------------------------------------------- /doc/img/ModComp.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/img/ModComp.svg -------------------------------------------------------------------------------- /doc/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/index.rst -------------------------------------------------------------------------------- /doc/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/doc/make.bat -------------------------------------------------------------------------------- /doc/require.txt: -------------------------------------------------------------------------------- 1 | sphinxcontrib-bibtex 2 | 3 | -------------------------------------------------------------------------------- /include/MersenneTwister.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/include/MersenneTwister.h -------------------------------------------------------------------------------- /include/autotuner.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/include/autotuner.h -------------------------------------------------------------------------------- /include/bioem.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/include/bioem.h -------------------------------------------------------------------------------- /include/bioem_cuda.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/include/bioem_cuda.h -------------------------------------------------------------------------------- /include/bioem_cuda_internal.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/include/bioem_cuda_internal.h -------------------------------------------------------------------------------- /include/defs.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/include/defs.h -------------------------------------------------------------------------------- /include/map.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/include/map.h -------------------------------------------------------------------------------- /include/model.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/include/model.h -------------------------------------------------------------------------------- /include/mrc.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/include/mrc.h -------------------------------------------------------------------------------- /include/param.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/include/param.h -------------------------------------------------------------------------------- /include/timer.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/include/timer.h -------------------------------------------------------------------------------- /main.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/main.cpp -------------------------------------------------------------------------------- /map.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/map.cpp -------------------------------------------------------------------------------- /model.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/model.cpp -------------------------------------------------------------------------------- /param.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/param.cpp -------------------------------------------------------------------------------- /timer.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bio-phys/BioEM/HEAD/timer.cpp --------------------------------------------------------------------------------