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update readme
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‎README.md

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@@ -37,7 +37,7 @@ The precompiled mexfiles are only available for Windows operating system and Ubu
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### Building MULTEM for Matlab
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The following steps have been tested and found to work with Matlab 2022b and CUDA 11.8. It is assumed that a C++ compiler such as Visual Studio 2019 Community, g++11.3 or Clang (Xcode 10.x) is installed on your operating system. Additionally, MULTEM also requires the fftw3, BLAS, and LAPACK libraries to be installed.The following steps have been tested and found to work with Matlab 2022b and CUDA 11.8. It is assumed that a C++ compiler such as Visual Studio 2019 Community, g++11.3 or Clang (Xcode 10.x) is installed on your operating system. Additionally, MULTEM also requires the fftw3, BLAS, and LAPACK libraries to be installed.
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The following steps have been tested and found to work with Matlab 2022b and CUDA 11.8. It is assumed that a C++ compiler such as Visual Studio 2022 Community, g++11.3 or Clang (Xcode 10.x) is installed on your operating system. Additionally, MULTEM also requires the fftw3, BLAS, and LAPACK libraries to be installed.The following steps have been tested and found to work with Matlab 2022b and CUDA 11.8. It is assumed that a C++ compiler such as Visual Studio 2022 Community, g++11.3 or Clang (Xcode 10.x) is installed on your operating system. Additionally, MULTEM also requires the fftw3, BLAS, and LAPACK libraries to be installed.
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- Firstly, a C++ compiler must be set for Matlab by executing the following command: `mex -setup cpp`. It is important to note that Matlab 2022b only supports the compilers listed above.
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- Next, add the following folders to the Matlab path: crystalline_materials, matlab_functions, and mex_bin.
@@ -50,7 +50,7 @@ The following steps have been tested and found to work with Matlab 2022b and CUD
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**for Windows:**
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- Verify the installation of Visual studio 2019 community.
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- Verify the installation of Visual studio 2022 community.
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- Verify the installation of Cuda 11.8 (https://developer.nvidia.com/cuda-downloads).
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**for Linux:**

‎compile_mex_multem.m

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for file=files
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disp(['Compiling ' file{1}])
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run(['mex_files_multem/',file{1}])
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end
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end
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% clc; clear all;
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% addpath('matlab_functions')
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% files = {'mex_incident_wave',...
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% 'mex_propagate',...
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% 'mex_microscope_aberrations',...
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% 'mex_projected_potential',...
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% 'mex_transmission_function',...
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% 'mex_multem',...
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% 'mex_wave_function',...
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% 'mex_apply_ctf'
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% };
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% for file=files
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% disp(['Compiling ' file{1}])
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% run(['mex_files_multem/',file{1}])
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% end

‎matlab_functions/ilm_mex.m

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CUDA_PATH = '/usr/local/cuda-10.0';
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end
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end
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% CUDA_PATH = 'C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v11.8';
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CUDA_PATH = ilm_replace_filesep(CUDA_PATH);
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%%%%%%%%%%%%%%%%%%%% get cuda version %%%%%%%%%%%%%%%%%%%%%%%
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CARD_86="-gencode=arch=compute_86,code=\"sm_86,compute_86\"";
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CARD_87="-gencode=arch=compute_87,code=\"sm_87,compute_87\"";
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CARD_MULT = join([CARD_35, CARD_50, CARD_60, CARD_70, CARD_75], ' ');
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CARD_MULT = join([CARD_50, CARD_60, CARD_70, CARD_75], ' ');
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if CUDA_VERSION_D >= 11.0
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CARD_MULT = join([CARD_MULT CARD_86, CARD_87], ' ');
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end

‎matlab_functions/mex_CUDA_win64.xml

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<config
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Name="NVIDIA CUDA Compiler"
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ShortName="nvcc"
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HostCompiler="MSVCPP160"
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HostCompiler="MSVCPP190"
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Manufacturer="NVIDIA"
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Version="XXX_CUDA_VER"
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Language="CUDA"
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INCLUDE="-I&quot;$MATLABROOT\extern\include&quot;"
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ARCH_FLAGS="XXX_ARCH_FLAGS"
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NVCC_FLAGS="--std=c++14 --default-stream per-thread --expt-extended-lambda --expt-relaxed-constexpr $ARCH_FLAGS"
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NVCC_FLAGS="--std=c++14 --default-stream per-thread --expt-extended-lambda --expt-relaxed-constexpr -allow-unsupported-compiler $ARCH_FLAGS"
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COMPILER="nvcc"
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COMPFLAGS="--compiler-options=/Zp8,/GR,/bigobj,/W3,/EHs,/nologo,/MD,/arch:AVX2 $NVCC_FLAGS"
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<and>
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<envVarExists name="ProgramFiles(x86)" />
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<fileExists name="$$\Microsoft Visual Studio\Installer\vswhere.exe" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[16.0,17.0)&quot; -products Microsoft.VisualStudio.Product.Enterprise -property installationPath -format value" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[17.0,18.0)&quot; -products Microsoft.VisualStudio.Product.Enterprise -property installationPath -format value" />
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<cmdReturns name="set &quot;vcroot=$$&quot;&amp;for /f &quot;delims= &quot; %a in ('type &quot;$$\VC\Auxiliary\Build\Microsoft.VCToolsVersion.default.txt&quot;') do @if exist &quot;$$\VC\Tools\MSVC\%a\bin\HostX64\x64\cl.exe&quot; call echo %vcroot%" />
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</and>
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<and>
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<envVarExists name="ProgramFiles(x86)" />
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<fileExists name="$$\Microsoft Visual Studio\Installer\vswhere.exe" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[16.0,17.0)&quot; -products Microsoft.VisualStudio.Product.Professional -property installationPath -format value" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[17.0,18.0)&quot; -products Microsoft.VisualStudio.Product.Professional -property installationPath -format value" />
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<cmdReturns name="set &quot;vcroot=$$&quot;&amp;for /f &quot;delims= &quot; %a in ('type &quot;$$\VC\Auxiliary\Build\Microsoft.VCToolsVersion.default.txt&quot;') do @if exist &quot;$$\VC\Tools\MSVC\%a\bin\HostX64\x64\cl.exe&quot; call echo %vcroot%" />
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</and>
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<and>
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<envVarExists name="ProgramFiles(x86)" />
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<fileExists name="$$\Microsoft Visual Studio\Installer\vswhere.exe" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[16.0,17.0)&quot; -products Microsoft.VisualStudio.Product.Community -property installationPath -format value" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[17.0,18.0)&quot; -products Microsoft.VisualStudio.Product.Community -property installationPath -format value" />
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<cmdReturns name="set &quot;vcroot=$$&quot;&amp;for /f &quot;delims= &quot; %a in ('type &quot;$$\VC\Auxiliary\Build\Microsoft.VCToolsVersion.default.txt&quot;') do @if exist &quot;$$\VC\Tools\MSVC\%a\bin\HostX64\x64\cl.exe&quot; call echo %vcroot%" />
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</and>
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</or>
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<and>
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<envVarExists name="ProgramFiles(x86)" />
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<fileExists name="$$\Microsoft Visual Studio\Installer\vswhere.exe" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[16.0,17.0)&quot; -products Microsoft.VisualStudio.Product.Enterprise -property installationPath -format value" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[17.0,18.0)&quot; -products Microsoft.VisualStudio.Product.Enterprise -property installationPath -format value" />
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</and>
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<and>
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<envVarExists name="ProgramFiles(x86)" />
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<fileExists name="$$\Microsoft Visual Studio\Installer\vswhere.exe" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[16.0,17.0)&quot; -products Microsoft.VisualStudio.Product.Professional -property installationPath -format value" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[17.0,18.0)&quot; -products Microsoft.VisualStudio.Product.Professional -property installationPath -format value" />
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</and>
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<and>
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<envVarExists name="ProgramFiles(x86)" />
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<fileExists name="$$\Microsoft Visual Studio\Installer\vswhere.exe" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[16.0,17.0)&quot; -products Microsoft.VisualStudio.Product.Community -property installationPath -format value" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[17.0,18.0)&quot; -products Microsoft.VisualStudio.Product.Community -property installationPath -format value" />
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</and>
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</or>
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</VSINSTALLDIR>
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<and>
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<envVarExists name="ProgramFiles(x86)" />
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<fileExists name="$$\Microsoft Visual Studio\Installer\vswhere.exe" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[16.0,17.0)&quot; -products Microsoft.VisualStudio.Product.Enterprise -property installationPath -format value" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[17.0,18.0)&quot; -products Microsoft.VisualStudio.Product.Enterprise -property installationPath -format value" />
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<cmdReturns name="set &quot;vcroot=$$&quot;&amp;for /f &quot;delims= &quot; %a in ('type &quot;$$\VC\Auxiliary\Build\Microsoft.VCToolsVersion.default.txt&quot;') do @if exist &quot;$$\VC\Tools\MSVC\%a\bin\HostX64\x64\cl.exe&quot; call echo %vcroot%\VC\Tools\MSVC\%a" />
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</and>
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<and>
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<envVarExists name="ProgramFiles(x86)" />
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<fileExists name="$$\Microsoft Visual Studio\Installer\vswhere.exe" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[16.0,17.0)&quot; -products Microsoft.VisualStudio.Product.Professional -property installationPath -format value" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[17.0,18.0)&quot; -products Microsoft.VisualStudio.Product.Professional -property installationPath -format value" />
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<cmdReturns name="set &quot;vcroot=$$&quot;&amp;for /f &quot;delims= &quot; %a in ('type &quot;$$\VC\Auxiliary\Build\Microsoft.VCToolsVersion.default.txt&quot;') do @if exist &quot;$$\VC\Tools\MSVC\%a\bin\HostX64\x64\cl.exe&quot; call echo %vcroot%\VC\Tools\MSVC\%a" />
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</and>
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<and>
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<envVarExists name="ProgramFiles(x86)" />
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<fileExists name="$$\Microsoft Visual Studio\Installer\vswhere.exe" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[16.0,17.0)&quot; -products Microsoft.VisualStudio.Product.Community -property installationPath -format value" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[17.0,18.0)&quot; -products Microsoft.VisualStudio.Product.Community -property installationPath -format value" />
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<cmdReturns name="set &quot;vcroot=$$&quot;&amp;for /f &quot;delims= &quot; %a in ('type &quot;$$\VC\Auxiliary\Build\Microsoft.VCToolsVersion.default.txt&quot;') do @if exist &quot;$$\VC\Tools\MSVC\%a\bin\HostX64\x64\cl.exe&quot; call echo %vcroot%\VC\Tools\MSVC\%a" />
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</and>
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</or>
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<and>
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<envVarExists name="ProgramFiles(x86)" />
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<fileExists name="$$\Microsoft Visual Studio\Installer\vswhere.exe" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[16.0,17.0)&quot; -products Microsoft.VisualStudio.Product.Enterprise -property installationPath -format value" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[17.0,18.0)&quot; -products Microsoft.VisualStudio.Product.Enterprise -property installationPath -format value" />
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<fileExists name="$$\VC\Auxiliary\Build\vcvarsall.bat" />
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<dirExists name="$$"/>
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</and>
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<and>
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<envVarExists name="ProgramFiles(x86)" />
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<fileExists name="$$\Microsoft Visual Studio\Installer\vswhere.exe" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[16.0,17.0)&quot; -products Microsoft.VisualStudio.Product.Professional -property installationPath -format value" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[17.0,18.0)&quot; -products Microsoft.VisualStudio.Product.Professional -property installationPath -format value" />
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<fileExists name="$$\VC\Auxiliary\Build\vcvarsall.bat" />
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<dirExists name="$$"/>
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</and>
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<and>
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<envVarExists name="ProgramFiles(x86)" />
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<fileExists name="$$\Microsoft Visual Studio\Installer\vswhere.exe" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[16.0,17.0)&quot; -products Microsoft.VisualStudio.Product.Community -property installationPath -format value" />
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<cmdReturns name="&quot;$$\\vswhere.exe&quot; -version &quot;[17.0,18.0)&quot; -products Microsoft.VisualStudio.Product.Community -property installationPath -format value" />
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<fileExists name="$$\VC\Auxiliary\Build\vcvarsall.bat" />
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<dirExists name="$$"/>
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</and>

‎mex_examples_multem/example_MULTEM_HRTEM.m

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%%%%%%%%%%%%%%%%%%%%% Set system configuration %%%%%%%%%%%%%%%%%%%%%
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input_multem.system_conf.precision = 1; % eP_Float = 1, eP_double = 2
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input_multem.system_conf.device = 1; % eD_CPU = 1, eD_GPU = 2
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input_multem.system_conf.device = 2; % eD_CPU = 1, eD_GPU = 2
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input_multem.system_conf.cpu_nthread = 1;
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input_multem.system_conf.gpu_device = 0;
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input_multem.phi = 0.0; % Till ilumination (�)
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%%%%%%%%%%%%%%%%%%%%%% Illumination model %%%%%%%%%%%%%%%%%%%%%%%%%%
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input_multem.illumination_model = 2; % 1: coherente mode, 2: Partial coherente mode, 3: transmission cross coefficient, 4: Numerical integration
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input_multem.illumination_model = 1; % 1: coherente mode, 2: Partial coherente mode, 3: transmission cross coefficient, 4: Numerical integration
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input_multem.temporal_spatial_incoh = 1; % 1: Temporal and Spatial, 2: Temporal, 3: Spatial
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%%%%%%%%%%%%%%%%%%%%%%%% Objective lens %%%%%%%%%%%%%%%%%%%%%%%%

‎src/gpu_fcns.cuh

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// phase factor 2d
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template <class TGrid, class T>
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__global__ void exp_r_factor_2d(TGrid grid_2d, Value_type<TGrid> gx,
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Value_type<TGrid> gy, rVector<T> psi_i, rVector<T> psi_o, scaling)
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Value_type<TGrid> gy, rVector<T> psi_i, rVector<T> psi_o, bool scaling)
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{
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int iy = threadIdx.x + blockIdx.x*blockDim.x;
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int ix = threadIdx.y + blockIdx.y*blockDim.y;

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