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| Introduction | ||
| ============ | ||
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| **MULTEM** is a collection of routines written in C++ with CUDA to perform accurate and fast multislice simulations for different TEM experiments as: HRTEM, STEM, ISTEM, ED, PED, CBED, ADF-TEM, ABF-HC, EFTEM and EELS. | ||
| **MULTEM** is a collection of routines written in C++ with CUDA to perform accurate and fast multislice simulations for different TEM experiments as: HRTEM, STEM, ISTEM, ED, PED, CBED, ADF-TEM, ABF-HC, EFTEM and EELS. It is developed by Ivan Lobato ([email protected]). | ||
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| Currently, there are three supported ways to use MULTEM: | ||
| - C++: using the library itself | ||
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| Remarks | ||
| ================================= | ||
| In order to use the GPU capability of MULTEM, you need a Nvidia Graphic card with **compute capability greater than 2.0** and **CUDA 8.0** installed in your operating system. You can check the compute capability of your graphic card using the following [nvidia website](https://developer.nvidia.com/cuda-gpus) | ||
| In order to use the GPU capability of MULTEM, you need a Nvidia Graphic card with **compute capability greater than 2.0** and **CUDA 8.0** installed in your operating system. You can check the compute capability of your graphic card using the following nvidia website: https://developer.nvidia.com/cuda-gpus. | ||
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| Using GUI interface | ||
| Using precompile GUI interface | ||
| ================================= | ||
| The precompile GUI interface is only available for Windows operating system. | ||
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@@ -34,18 +34,70 @@ The precompile mexfiles are only available for Windows operating system. | |
| - Add to the Matlab path the following folders: crystalline_materials, matlab_functions and mex_bin. | ||
| - Run the examples located in 'mex_examples_multem'. | ||
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| Compiling MULTEM for Matlab | ||
| Building MULTEM for Matlab | ||
| ================================= | ||
| The following steps work using Matlab R2017a and CUDA 8.0. It assumes that Visual studio 2015, g++4.9 or Clang compiler is installed in your operating system: | ||
| The following steps work using Matlab R2017a and CUDA 8.0. It assumes that Visual studio 2015 professional, g++4.9 or Clang(Xcode 8.x) compiler is installed in your operating system. Additionally, Multem also requires fftw3, blas and lapack libraries. | ||
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| - First of all, you have to add to the Matlab path the following folders: crystalline_materials, matlab_functions and mex_bin. | ||
| - First of all, you have to set a C++ compiler to Matlab by executing the following comand: `mex -setup cpp`. Be aware that Matlab 2017a only support the above compilers. | ||
| - Then add to the Matlab path the following folders: crystalline_materials, matlab_functions and mex_bin. | ||
| - Run the `compile_mex_multem.m` script. This will create the required executable files to run the examples. | ||
| - Run the examples located in `mex_examples_multem`. | ||
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| - Then you need to modify the `mex_CUDA_xxxx` file located in the `mex_files_multem` folder, which corresponds to your operating system: | ||
| 1. for Windows `mex_CUDA_win64` | ||
| 2. for Linux `mex_CUDA_glnxa64` | ||
| 3. for Mac `mex_CUDA_maci64` | ||
| Troubleshooting | ||
| ================================= | ||
| - If MULTEM do not compile with the above procedures, one of the following procedures might fix it | ||
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| - Go to the line which contains the following definition`NVCCFLAGS="$xxxxx ..."` and replace 'xxxxx' by 'SINGLE_CARD' or 'MULTI_CARD'. 'SINGLE_CARD'/'MULTI_CARD' defines the compute capability of your graphic card. | ||
| **for Windows:** | ||
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| - Verify the installation of Visual studio 2015 professional. | ||
| - Verify the installation of Cuda 8.0 (https://developer.nvidia.com/cuda-downloads). | ||
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| **for Linux:** | ||
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| - Verify that gcc-4.9 and g++4.9 are the default compilers installed in your operating system. In Ubuntu, it can be installed by executing the following commands: | ||
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| * `sudo add-apt-repository ppa:ubuntu-toolchain-r/test` | ||
| * `sudo apt-get update` | ||
| * `sudo apt-get install gcc-4.9 g++-4.9` | ||
| * `sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 60 --slave /usr/bin/g++ g++ /usr/bin/g++-4.9` | ||
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| - Run the `compile_mex_multem.m` script. This will create the required executable files to run the examples. | ||
| - Run the examples located in 'mex_examples_multem'. | ||
| - Verify the correct installation of Cuda 8.0 (https://developer.nvidia.com/cuda-downloads). | ||
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| - Verify the installation of fftw3 libraries. In Ubuntu, it can be installed by executing the following command: | ||
| * `sudo apt-get install libfftw3-dev libfftw3-doc` | ||
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| - Verify the installation of blas and lapack libraries. In Ubuntu, it can be installed by executing the following command: | ||
| * `sudo apt-get install libblas-dev liblapack-dev` | ||
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| - Verify the intallation path of cuda 8.0, fftw3, blas and lapack. Their installation path should be specified in the `MEX.m` file located at `matlab_functions`. | ||
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| **Please cite MULTEM in your publications if it helps your research:** | ||
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| @article{LVAV16_1, | ||
| Author = {I.Lobato and S.Van Aert and J.Verbeeck}, | ||
| Journal = {Ultramicroscopy}, | ||
| Title = {Progress and new advances in simulating electron microscopy datasets using MULTEM}, | ||
| Year = {2016}, | ||
| volume = {168}, | ||
| pages = {17-27} | ||
| } | ||
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| @article{LD15_2, | ||
| Author = {I. Lobato and D. Van Dyck}, | ||
| Journal = {Ultramicroscopy}, | ||
| Title = {MULTEM: A new multislice program to perform accurate and fast electron diffraction and imaging simulations using Graphics Processing Units with CUDA}, | ||
| Year = {2015}, | ||
| volume = {156}, | ||
| pages = {9-17} | ||
| } | ||
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| **if you use our parameterization of the electronscattering factors, please cite the following article:** | ||
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| @Article{LD14_1, | ||
| Title = {{An accurate parameterization for the scattering factors, electron densities and electrostatic potentials for neutral atoms that obey all physical constraints}}, | ||
| Author = {I. Lobato and D. Van Dyck}, | ||
| Journal = {Acta Crystallographica Section A}, | ||
| Year = {2014}, | ||
| Pages = {636-649}, | ||
| Volume = {70} | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
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| addpath([ pwd '/matlab_functions']) | ||
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| files = {'mex_lambda',... | ||
| 'mex_sigma',... | ||
| 'mex_gamma',... | ||
| 'mex_fxeg_tabulated_data',... | ||
| 'mex_feg',... | ||
| 'mex_fxg',... | ||
| 'mex_Pr',... | ||
| 'mex_Vz',... | ||
| 'mex_Vr',... | ||
| 'mex_Vp',... | ||
| 'mex_mrad_2_rAngs',... | ||
| 'mex_scherzer_defocus',... | ||
| 'mex_scherzer_aperture',... | ||
| 'mex_crystal_by_lays',... | ||
| 'mex_rdf_3d',... | ||
| 'mex_amorp_spec',... | ||
| 'mex_add_amorp_lay',... | ||
| 'mex_spec_rot',... | ||
| 'mex_spec_planes',... | ||
| 'mex_spec_slicing',... | ||
| 'mex_incident_wave',... | ||
| files = {'mex_incident_wave',... | ||
| 'mex_propagate',... | ||
| 'mex_microscope_aberrations',... | ||
| 'mex_projected_potential',... | ||
| 'mex_transmission_function',... | ||
| 'mex_transmission_function',... | ||
| 'mex_wave_function',... | ||
| 'mex_MULTEM'}; | ||
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| for file=files | ||
| disp(['Compiling ' file{1}]) | ||
| run(['mex_files_multem/',file{1}]) | ||
| end | ||
| end | ||
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| % addpath([ pwd '/matlab_functions']) | ||
| % | ||
| % files = {'mex_lambda',... | ||
| % 'mex_sigma',... | ||
| % 'mex_gamma',... | ||
| % 'mex_fxeg_tabulated_data',... | ||
| % 'mex_feg',... | ||
| % 'mex_fxg',... | ||
| % 'mex_Pr',... | ||
| % 'mex_Vz',... | ||
| % 'mex_Vr',... | ||
| % 'mex_Vp',... | ||
| % 'mex_gmax',... | ||
| % 'mex_min_spl',... | ||
| % 'mex_mrad_2_rAngs',... | ||
| % 'mex_mrad_2_sigma',... | ||
| % 'mex_fwhm_2_sigma',... | ||
| % 'mex_hwhm_2_sigma',... | ||
| % 'mex_iehwgd_2_sigma',... | ||
| % 'mex_scherzer_defocus',... | ||
| % 'mex_scherzer_aperture',... | ||
| % 'mex_crystal_by_lays',... | ||
| % 'mex_rdf_3d',... | ||
| % 'mex_amorp_spec',... | ||
| % 'mex_add_amorp_lay',... | ||
| % 'mex_spec_rot',... | ||
| % 'mex_spec_planes',... | ||
| % 'mex_spec_slicing',... | ||
| % 'mex_incident_wave',... | ||
| % 'mex_propagate',... | ||
| % 'mex_microscope_aberrations',... | ||
| % 'mex_projected_potential',... | ||
| % 'mex_transmission_function',... | ||
| % 'mex_wave_function',... | ||
| % 'mex_MULTEM'}; | ||
| % | ||
| % for file=files | ||
| % disp(['Compiling ' file{1}]) | ||
| % run(['mex_files_multem/',file{1}]) | ||
| % end |
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