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Ivanlh20Ivanlh20
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fix the coherent partial envelop function for TEM
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+48
-48
lines changed

‎matlab_functions/ilm_read_ap_cif.m

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@@ -1,5 +1,5 @@
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% Read atomic positions from cif file
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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function [atoms, lx, ly, lz] = ilm_read_ap_cif(path, rmsd_3d_0, pbc, na, nb, nc)
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if(nargin<6)
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nc = 1;

‎matlab_functions/ilm_read_lat_parm_cif.m

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@@ -1,5 +1,5 @@
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% Read lattice parameter from cif file
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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function [a, b, c] = ilm_read_lat_parm_cif(path)
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str_file = fileread(path);
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str_file = strtrim(strsplit(str_file, '\n'));

‎mex_examples_multem/example_MULTEM_CBED.m

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@@ -1,7 +1,7 @@
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% output_multislice = input_multem.ilc_multem perform TEM simulation
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% Convergent beam electron diffraction (CBED) simulation
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_MULTEM_CBEI.m

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@@ -1,7 +1,7 @@
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% output_multislice = input_multem.ilc_multem perform TEM simulation
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% Convergent beam electron Imaging (CBEI) simulation
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_MULTEM_ED.m

+1-1
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@@ -1,7 +1,7 @@
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% output_multislice = input_multem.ilc_multem perform TEM simulation
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% Electron diffraction (ED) simulation
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_MULTEM_EELS.m

+1-1
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@@ -1,7 +1,7 @@
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% output_multislice = input_multem.ilc_multem perform TEM simulation
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% STEM electron energy loss spectroscopy (EELS) simulation
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_MULTEM_EFTEM.m

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@@ -1,7 +1,7 @@
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% output_multislice = input_multem.ilc_multem perform TEM simulation
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% Energy filtered transmission electron microscopy (EFTEM) simulation
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_MULTEM_EWFS.m

+1-1
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@@ -1,7 +1,7 @@
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% output_multislice = input_multem.ilc_multem perform TEM simulation
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% Exit wave real space (EWRS) simulation
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_MULTEM_EWFS_till_illumination.m

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@@ -1,7 +1,7 @@
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% output_multislice = input_multem.ilc_multem perform TEM simulation
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% Exit wave real space (EWRS) simulation
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
4-
% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_MULTEM_EWRS.m

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@@ -1,7 +1,7 @@
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% output_multislice = input_multem.ilc_multem perform TEM simulation
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% Exit wave real space (EWRS) simulation
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
4-
% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_MULTEM_EWRS_till_illumination.m

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@@ -1,7 +1,7 @@
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% output_multislice = input_multem.ilc_multem perform TEM simulation
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% Exit wave real space (EWRS) simulation
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
4-
% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_MULTEM_HCTEM.m

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@@ -1,7 +1,7 @@
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% output_multislice = input_multem.ilc_multem perform TEM simulation
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% Hollow cone transmission electron microscopy (HCTEM) simulation
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_MULTEM_HRTEM.m

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@@ -1,7 +1,7 @@
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% output_multislice = input_multem.ilc_multem perform TEM simulation
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% High resolution transmission electron microscopy (HRTEM) simulation
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_MULTEM_ISTEM.m

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@@ -1,7 +1,7 @@
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% output_multislice = input_multem.ilc_multem perform TEM simulation
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% Imaging scanning transmission electron microscopy (ISTEM) simulation
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_MULTEM_PED.m

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@@ -4,7 +4,7 @@
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%
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
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%
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_MULTEM_STEM.m

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@@ -1,7 +1,7 @@
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% output_multislice = input_multem.ilc_multem perform TEM simulation
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% Scanning transmission electron microscopy (STEM) simulation
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_MULTEM_STEM_EELS.m

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@@ -1,7 +1,7 @@
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% output_multislice = input_multem.ilc_multem perform TEM simulation
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% STEM electron energy loss spectroscopy (EELS) simulation
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_MULTEM_STEM_matrix_detector.m

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% output_multislice = input_multem.ilc_multem perform TEM simulation
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% Scanning transmission electron microscopy (STEM) simulation
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_add_amorphous_layer.m

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@@ -1,4 +1,4 @@
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_amorphous_specimen.m

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@@ -1,4 +1,4 @@
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_apply_ctf.m

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% output_multislice = input_multem.ilc_multem perform TEM simulation
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% inclusion of TEM aberrerations into a exitwve simulation
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_beam_self_interaction.m

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% output_multislice = input_multem.ilc_multem perform TEM simulation
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_crystal_by_layers.m

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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_feg.m

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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_fxg.m

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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_incident_wave_1.m

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% output_multislice = input_multem.ilc_multem perform TEM simulation
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% Incident wave simulation
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_incident_wave_2.m

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% output_multislice = input_multem.ilc_multem perform TEM simulation
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% Incident wave simulation
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_incident_wave_3.m

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% output_multislice = input_multem.ilc_multem perform TEM simulation
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% Incident wave simulation
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_incident_wave_4.m

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% output_multislice = input_multem.ilc_multem perform TEM simulation
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% Incident wave simulation
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) '/mex_bin'])

‎mex_examples_multem/example_microscope_aberrations.m

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% output_multislice = input_multem.ilc_multem perform TEM simulation
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% inclusion of TEM aberrerations into a exitwve simulation
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_pr.m

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@@ -1,4 +1,4 @@
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_projected_potential.m

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@@ -1,4 +1,4 @@
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_propagate.m

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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_specimen_creation_from_cif_file.m

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% Specimen creation
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear all;clc;
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‎mex_examples_multem/example_specimen_planes.m

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@@ -1,4 +1,4 @@
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_specimen_rotation.m

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%
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% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
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%
7-
% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_specimen_slicing_rotation.m

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@@ -1,4 +1,4 @@
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_specimen_slicing_show.m

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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_specimen_slicing_with_amorphous_layer.m

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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_specimen_slicing_zone_axis.m

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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_specimen_subslicing.m

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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_transmission_function.m

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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_vp.m

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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_vr.m

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@@ -1,4 +1,4 @@
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_vz.m

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@@ -1,4 +1,4 @@
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% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>
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clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])

‎mex_examples_multem/example_wave_function.m

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@@ -1,6 +1,6 @@
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% output_multislice = input_multem.ilc_multem perform TEM simulation
22
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
3-
% Copyright 2021 Ivan Lobato <Ivanlh20@gmail.com>clear; clc;
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% Copyright 2023 Ivan Lobato <Ivanlh20@gmail.com>clear; clc;
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addpath([fileparts(pwd) filesep 'mex_bin'])
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addpath([fileparts(pwd) filesep 'crystalline_materials'])

‎src/cgpu_fcns.cuh

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@@ -2019,10 +2019,10 @@ namespace mt
20192019
{
20202020
T_r chi = g2*(lens.c_c_30*g2+lens.c_c_10);
20212021
T_r c = c_Pi*lens.si_theta_c*lens.ti_iehwgd;
2022-
T_r u = 1.0 + 2*c*c*g2;
2022+
T_r u = 1.0 + c*c*g2;
20232023

20242024
c = c_Pi*lens.ti_iehwgd*lens.lambda*g2;
2025-
T_r temp_inc = 0.5*c*c;
2025+
T_r temp_inc = 0.25*c*c;
20262026

20272027
c = c_Pi*lens.si_theta_c*(lens.c_30*lens.lambda2*g2-lens.c_10);
20282028
T_r spa_inc = c*c*g2;

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