MULTEM 2.2.3

.gitignore

@@ -9,6 +9,7 @@
 *.wisdom
 *.exe
 *.dll
+*.asv
 *.7z
 *Copy*.cuh
 *Copy*.hpp

README.md

@@ -15,7 +15,7 @@ The Matlab interface is the recommended way for researchers.
 
 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 10.0** 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.
 
 Using precompile GUI interface
 =================================
@@ -36,9 +36,9 @@ The precompile mexfiles are only available for Windows operating system.
 
 Building MULTEM for Matlab
 =================================
-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.
+The following steps work using Matlab R2018a and CUDA 10.0. It assumes that Visual studio 2017 community, g++7.5 or Clang(Xcode 10.x) compiler is installed in your operating system. Additionally, Multem also requires fftw3, blas and lapack libraries.
 
-- 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.
+- First of all, you have to set a C++ compiler to Matlab by executing the following comand: `mex -setup cpp`. Be aware that Matlab 2018a 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`.
@@ -49,27 +49,25 @@ Troubleshooting
 
   **for Windows:**
 
-  	- Verify the installation of Visual studio 2015 professional.
-  	- Verify the installation of Cuda 8.0 (https://developer.nvidia.com/cuda-downloads).
+  	- Verify the installation of Visual studio 2017 community.
+  	- Verify the installation of Cuda 10.0 (https://developer.nvidia.com/cuda-downloads).
 
   **for Linux:**
 
-  	- 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:
+  	- Verify that gcc-7.5 and g++7.5 are the default compilers installed in your operating system. In Ubuntu, it can be installed by executing the following commands:
 
-  		* `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`
+		* `sudo apt-get install gcc-7.5 g++-7.5`
 
-  	- Verify the correct installation of Cuda 8.0 (https://developer.nvidia.com/cuda-downloads).
+  	- Verify the correct installation of Cuda 10.0 (https://developer.nvidia.com/cuda-downloads).
 
     - 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`
 
     - 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`
 
-- Verify the installation path of cuda 8.0, fftw3, blas and lapack. Their installation paths should be specified in the `MEX.m` file located at `matlab_functions`.
+- Verify the installation path of cuda 10.0, fftw3, blas and lapack. Their installation paths should be specified in the `MEX.m` file located at `matlab_functions`.
 
 **Please cite MULTEM in your publications if it helps your research:**
 

compile_mex_multem.m

@@ -3,16 +3,16 @@
 files = {'mex_lambda',...
         'mex_sigma',...
         'mex_gamma',...
-        'mex_fxeg_tabulated_data',...
+        'mex_fxeg_data',...
         'mex_feg',...
         'mex_fxg',...
-        'mex_Pr',...
-        'mex_Vz',...
-        'mex_Vr',...
-        'mex_Vp',...
+        'mex_pr',...
+        'mex_vz',...
+        'mex_vr',...
+        'mex_vp',...
         'mex_gmax',...
         'mex_min_spl',...
-        'mex_mrad_2_rAngs',...
+        'mex_mrad_2_rAng',...
         'mex_mrad_2_sigma',...
         'mex_fwhm_2_sigma',...
         'mex_hwhm_2_sigma',...        
@@ -31,9 +31,9 @@
         'mex_microscope_aberrations',...
         'mex_projected_potential',...
         'mex_transmission_function',...
-        'mex_wave_function',...
-        'mex_MULTEM'};
-    
+        'mex_multem',...
+        'mex_wave_function'};
+
 for file=files
   disp(['Compiling ' file{1}])
   run(['mex_files_multem/',file{1}])

crystalline_materials/Ag001_xtl.m

@@ -0,0 +1,23 @@
+function [atoms, lx, ly, lz, a, b, c, dz] = Ag001_xtl(na, nb, nc, ncu, rms3d)
+    xtl_parm.na = na;
+    xtl_parm.nb = nb;
+    xtl_parm.nc = nc;
+    a = 4.0853; 
+    b = 4.0853; 
+    c = 4.0853;
+    xtl_parm.a = a;
+    xtl_parm.b = b;
+    xtl_parm.c = c;
+    xtl_parm.nuLayer = 2;
+    occ = 1;
+    region = 0;
+    charge = 0;
+    % Ag = 47
+    % Z charge x y z rms3d occupancy region charge
+    xtl_parm.uLayer(1).atoms = [47, 0.0, 0.0, 0.0, rms3d, occ, region, charge; 47, 0.5, 0.5, 0.0, rms3d, occ, region, charge];
+    xtl_parm.uLayer(2).atoms = [47, 0.0, 0.5, 0.5, rms3d, occ, region, charge; 47, 0.5, 0.0, 0.5, rms3d, occ, region, charge];
+    atoms = il_crystal_by_lays(xtl_parm);
+
+    dz = xtl_parm.c/ncu;
+    lx = na*xtl_parm.a; ly = nb*xtl_parm.b; lz = nc*xtl_parm.c;
+end

crystalline_materials/Al001_xtl.m

@@ -0,0 +1,23 @@
+function [atoms, lx, ly, lz, a, b, c, dz] = Al001_xtl(na, nb, nc, ncu, rms3d)
+    xtl_parm.na = na;
+    xtl_parm.nb = nb;
+    xtl_parm.nc = nc;
+    a = 4.0493; 
+    b = 4.0493; 
+    c = 4.0493;
+    xtl_parm.a = a;
+    xtl_parm.b = b;
+    xtl_parm.c = c;
+    xtl_parm.nuLayer = 2;
+    occ = 1;
+    region = 0;
+    charge = 0;
+    % Al = 13
+    % Z charge x y z rms3d occupancy region charge
+    xtl_parm.uLayer(1).atoms = [13, 0.0, 0.0, 0.0, rms3d, occ, region, charge; 13, 0.5, 0.5, 0.0, rms3d, occ, region, charge];
+    xtl_parm.uLayer(2).atoms = [13, 0.0, 0.5, 0.5, rms3d, occ, region, charge; 13, 0.5, 0.0, 0.5, rms3d, occ, region, charge];
+    atoms = il_crystal_by_lays(xtl_parm);
+
+    dz = xtl_parm.c/ncu;
+    lx = na*xtl_parm.a; ly = nb*xtl_parm.b; lz = nc*xtl_parm.c;
+end

crystalline_materials/Au001_xtl.m

@@ -0,0 +1,26 @@
+function [atoms, lx, ly, lz, a, b, c, dz] = Au001_xtl(na, nb, nc, ncu, rms3d)
+    xtl_parm.na = na;
+    xtl_parm.nb = nb;
+    xtl_parm.nc = nc;
+    a = 4.0780; 
+    b = 4.0780; 
+    c = 4.0780;
+    % a = 4.07003925431053; 
+    % b = a; 
+    % c = a;
+    xtl_parm.a = a;
+    xtl_parm.b = b;
+    xtl_parm.c = c;
+    xtl_parm.nuLayer = 2;
+    occ = 1;
+    region = 0;
+    charge = 0;
+    % Au = 79
+    % Z x y z rms3d occupancy charge
+    xtl_parm.uLayer(1).atoms = [79, 0.0, 0.0, 0.0, rms3d, occ, region, charge; 79, 0.5, 0.5, 0.0, rms3d, occ, region, charge];
+    xtl_parm.uLayer(2).atoms = [79, 0.0, 0.5, 0.5, rms3d, occ, region, charge; 79, 0.5, 0.0, 0.5, rms3d, occ, region, charge];
+    atoms = il_crystal_by_lays(xtl_parm);
+
+    dz = xtl_parm.c/ncu;
+    lx = na*xtl_parm.a; ly = nb*xtl_parm.b; lz = nc*xtl_parm.c;
+end

crystalline_materials/Au110_xtl.m

@@ -0,0 +1,23 @@
+function [atoms, lx, ly, lz, a, b, c, dz] = Au110_xtl(na, nb, nc, ncu, rms3d)
+    xtl_parm.na = na;
+    xtl_parm.nb = nb;
+    xtl_parm.nc = nc;
+    a = 4.0780/sqrt(2); 
+    b = 4.0780; 
+    c = 4.0780/sqrt(2);
+    xtl_parm.a = a;
+    xtl_parm.b = b;
+    xtl_parm.c = c;
+    xtl_parm.nuLayer = 2;
+    occ = 1;
+    region = 0;
+    charge = 0;
+    % Au = 79
+    % Z charge x y z rms3d occupancy region charge
+    xtl_parm.uLayer(1).atoms = [79, 0.00, 0.00, 0.00, rms3d, 1.0];
+    xtl_parm.uLayer(2).atoms = [79, 0.50, 0.50, 0.50, rms3d, 1.0];
+    atoms = il_crystal_by_lays(xtl_parm);
+
+    dz = xtl_parm.c/ncu;
+    lx = na*xtl_parm.a; ly = nb*xtl_parm.b; lz = nc*xtl_parm.c;
+end

crystalline_materials/Cu001_xtl.m

@@ -0,0 +1,23 @@
+function [atoms, lx, ly, lz, a, b, c, dz] = Cu001_xtl(na, nb, nc, ncu, rms3d)
+    xtl_parm.na = na;
+    xtl_parm.nb = nb;
+    xtl_parm.nc = nc;
+    a = 3.6150; 
+    b = 3.6150; 
+    c = 3.6150;
+    xtl_parm.a = a;
+    xtl_parm.b = b;
+    xtl_parm.c = c;
+    xtl_parm.nuLayer = 2;
+    occ = 1;
+    region = 0;
+    charge = 0;
+    % Cu = 29
+    % Z charge x y z rms3d occupancy region charge
+    xtl_parm.uLayer(1).atoms = [29, 0.0, 0.0, 0.0, rms3d, occ, region, charge; 29, 0.5, 0.5, 0.0, rms3d, occ, region, charge];
+    xtl_parm.uLayer(2).atoms = [29, 0.0, 0.5, 0.5, rms3d, occ, region, charge; 29, 0.5, 0.0, 0.5, rms3d, occ, region, charge];
+    atoms = il_crystal_by_lays(xtl_parm);
+
+    dz = xtl_parm.c/ncu;
+    lx = na*xtl_parm.a; ly = nb*xtl_parm.b; lz = nc*xtl_parm.c;
+end

crystalline_materials/Diamond110_xtl.m

@@ -0,0 +1,23 @@
+function [atoms, lx, ly, lz, a, b, c, dz] = Diamond110_xtl(na, nb, nc, ncu, rms3d)
+    xtl_parm.na = na;
+    xtl_parm.nb = nb;
+    xtl_parm.nc = nc;
+    a = 3.56/sqrt(2); 
+    b = 3.56; 
+    c = sqrt(2)*3.56/2;
+    xtl_parm.a = a;
+    xtl_parm.b = b;
+    xtl_parm.c = c;
+    xtl_parm.nuLayer = 2;
+    occ = 1;
+    region = 0;
+    charge = 0;
+    % C = 6
+    % Z x y z rms3d occupancy charge 
+    xtl_parm.uLayer(1).atoms = [6, 0.00, 0.00, 0.00, rms3d, occ, region, charge; 6, 0.50, 0.75, 0.00, rms3d, occ, region, charge];
+    xtl_parm.uLayer(2).atoms = [6, 0.00, 0.25, 0.50, rms3d, occ, region, charge; 6, 0.50, 0.50, 0.50, rms3d, occ, region, charge];
+    atoms = il_crystal_by_lays(xtl_parm);
+
+    dz = xtl_parm.c/ncu;
+    lx = na*xtl_parm.a; ly = nb*xtl_parm.b; lz = nc*xtl_parm.c;
+end

crystalline_materials/GaAs001_xtl.m

@@ -0,0 +1,26 @@
+function [atoms, lx, ly, lz, a, b, c, dz] = GaAs001_xtl(na, nb, nc, ncu, rms3d)
+    xtl_parm.na = na;
+    xtl_parm.nb = nb;
+    xtl_parm.nc = nc;
+    a = 5.6537; 
+    b = 5.6537; 
+    c = 5.6537;
+    xtl_parm.a = a;
+    xtl_parm.b = b;
+    xtl_parm.c = c;
+    xtl_parm.nuLayer = 4;
+    occ = 1;
+    region = 0;
+    charge = 0;
+    % Ga = 31, As = 33;
+    % Z charge x y z rms3d occupancy region charge
+    xtl_parm.uLayer(1).atoms = [31, 0.00, 0.00, 0.00, rms3d, occ, region, charge; 31, 0.50, 0.50, 0.00, rms3d, occ, region, charge]; %Ga
+    xtl_parm.uLayer(2).atoms = [33, 0.25, 0.25, 0.25, rms3d, occ, region, charge; 33, 0.75, 0.75, 0.25, rms3d, occ, region, charge]; %As
+    xtl_parm.uLayer(3).atoms = [31, 0.00, 0.50, 0.50, rms3d, occ, region, charge; 31, 0.50, 0.00, 0.50, rms3d, occ, region, charge]; %Ga
+    xtl_parm.uLayer(4).atoms = [33, 0.75, 0.25, 0.75, rms3d, occ, region, charge; 33, 0.25, 0.75, 0.75, rms3d, occ, region, charge]; %As
+
+    atoms = il_crystal_by_lays(xtl_parm);
+
+    dz = xtl_parm.c/ncu;
+    lx = na*xtl_parm.a; ly = nb*xtl_parm.b; lz = nc*xtl_parm.c;
+end

crystalline_materials/LaAlO3001_xtl.m

@@ -0,0 +1,24 @@
+function [atoms, lx, ly, lz, a, b, c, dz] = LaAlO3001_xtl(na, nb, nc, ncu, rms3d)
+    xtl_parm.na = na;
+    xtl_parm.nb = nb;
+    xtl_parm.nc = nc;
+    a = 3.7900; 
+    b = 3.79; 
+    c = 3.79;
+    xtl_parm.a = a;
+    xtl_parm.b = b;
+    xtl_parm.c = c;
+    xtl_parm.nuLayer = 2;
+    occ = 1;
+    region = 0;
+    charge = 0;
+    % Sr = 38, Ti = 22; O = 8
+    % La = 57, Al = 13; O = 8
+    % Z charge x y z rms3d occupancy region charge
+    xtl_parm.uLayer(1).atoms = [57, 0.0, 0.0, 0.0, rms3d, occ, region, charge; 8, 0.5, 0.5, 0.0, rms3d, occ, region, charge];
+    xtl_parm.uLayer(2).atoms = [8, 0.0, 0.5, 0.5, rms3d, occ, region, charge; 8, 0.5, 0.0, 0.5, rms3d, occ, region, charge; 13, 0.5, 0.5, 0.5, rms3d, occ, region, charge];
+    atoms = il_crystal_by_lays(xtl_parm);
+
+    dz = xtl_parm.c/ncu;
+    lx = na*xtl_parm.a; ly = nb*xtl_parm.b; lz = nc*xtl_parm.c;
+end

crystalline_materials/Mo001_xtl.m

@@ -0,0 +1,23 @@
+function [atoms, lx, ly, lz, a, b, c, dz] = Mo001_xtl(na, nb, nc, ncu, rms3d)
+    xtl_parm.na = na;
+    xtl_parm.nb = nb;
+    xtl_parm.nc = nc;
+    a = 3.1470; 
+    b = 3.1470; 
+    c = 3.1470;
+    xtl_parm.a = a;
+    xtl_parm.b = b;
+    xtl_parm.c = c;
+    xtl_parm.nuLayer = 2;
+    occ = 1;
+    region = 0;
+    charge = 0;
+    % Mo = 42
+    % Z charge x y z rms3d occupancy region charge
+    xtl_parm.uLayer(1).atoms = [42, 0.0, 0.0, 0.0, rms3d, occ, region, charge];
+    xtl_parm.uLayer(2).atoms = [42, 0.5, 0.5, 0.5, rms3d, occ, region, charge];
+    atoms = il_crystal_by_lays(xtl_parm);
+
+    dz = xtl_parm.c/ncu;
+    lx = na*xtl_parm.a; ly = nb*xtl_parm.b; lz = nc*xtl_parm.c;
+end

crystalline_materials/PdH001_xtl.m

@@ -0,0 +1,25 @@
+function [atoms, lx, ly, lz, a, b, c, dz] = PdH001_xtl(na, nb, nc, ncu, rms3d)
+    xtl_parm.na = na;
+    xtl_parm.nb = nb;
+    xtl_parm.nc = nc;
+    a = 4.025; 
+    b = 4.025; 
+    c = 4.025;
+    xtl_parm.a = a;
+    xtl_parm.b = b;
+    xtl_parm.c = c;
+    xtl_parm.nuLayer = 2;
+    occ = 1;
+    region = 0;
+    charge = 0;
+    % Pd = 46, H = 1
+    % Z charge x y z rms3d occupancy region charge
+    xtl_parm.uLayer(1).atoms = [46, 0.0, 0.0, 0.0, rms3d, occ, region, charge; 46, 0.5, 0.5, 0.0, rms3d, occ, region, charge;...
+                               1, 0.5, 0.0, 0.0, rms3d, occ, region, charge; 1, 0.0, 0.5, 0.0, rms3d, occ, region, charge];
+    xtl_parm.uLayer(2).atoms = [46, 0.0, 0.5, 0.5, rms3d, occ, region, charge; 46, 0.5, 0.0, 0.5, rms3d, occ, region, charge;...
+                               1, 0.0, 0.0, 0.5, rms3d, occ, region, charge; 1, 0.5, 0.5, 0.5, rms3d, occ, region, charge];
+    atoms = il_crystal_by_lays(xtl_parm);
+
+    dz = xtl_parm.c/ncu;
+    lx = na*xtl_parm.a; ly = nb*xtl_parm.b; lz = nc*xtl_parm.c;
+end

crystalline_materials/Primitive_xtl.m

@@ -0,0 +1,24 @@
+function [atoms, lx, ly, lz, a, b, c, dz] = Primitive_xtl(na, nb, nc, ncu, rms3d)
+    xtl_parm.na = na;
+    xtl_parm.nb = nb;
+    xtl_parm.nc = nc;
+    a = 4.0780; 
+    b = 4.0780; 
+    c = 4.0780;
+    a = 6.50; 
+    b = 6.50;
+    xtl_parm.a = a;
+    xtl_parm.b = b;
+    xtl_parm.c = c;
+    xtl_parm.nuLayer = 1;
+    occ = 1;
+    region = 0;
+    charge = 0;
+    % Au = 79
+    % Z charge x y z rms3d occupancy region charge
+    xtl_parm.uLayer(1).atoms = [79, 0.5, 0.5, 0.0, rms3d, occ, region, charge];
+    atoms = il_crystal_by_lays(xtl_parm);
+
+    dz = xtl_parm.c/ncu;
+    lx = na*xtl_parm.a; ly = nb*xtl_parm.b; lz = nc*xtl_parm.c;
+end