Skip to content

Commit

Permalink
fix the coherent partial envelop function for TEM
Browse files Browse the repository at this point in the history
  • Loading branch information
@Ivanlh20
Ivanlh20 committed Jan 10, 2023
1 parent be8903f commit 3f55109
Show file tree
Hide file tree
Showing 47 changed files with 48 additions and 48 deletions.
2 changes: 1 addition & 1 deletion matlab_functions/ilm_read_ap_cif.m
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
% Read atomic positions from cif file
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>
function [atoms, lx, ly, lz] = ilm_read_ap_cif(path, rmsd_3d_0, pbc, na, nb, nc)
if(nargin<6)
nc = 1;
Expand Down
2 changes: 1 addition & 1 deletion matlab_functions/ilm_read_lat_parm_cif.m
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
% Read lattice parameter from cif file
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>
function [a, b, c] = ilm_read_lat_parm_cif(path)
str_file = fileread(path);
str_file = strtrim(strsplit(str_file, '\n'));
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_MULTEM_CBED.m
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
% output_multislice = input_multem.ilc_multem perform TEM simulation
% Convergent beam electron diffraction (CBED) simulation
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_MULTEM_CBEI.m
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
% output_multislice = input_multem.ilc_multem perform TEM simulation
% Convergent beam electron Imaging (CBEI) simulation
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_MULTEM_ED.m
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
% output_multislice = input_multem.ilc_multem perform TEM simulation
% Electron diffraction (ED) simulation
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_MULTEM_EELS.m
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
% output_multislice = input_multem.ilc_multem perform TEM simulation
% STEM electron energy loss spectroscopy (EELS) simulation
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_MULTEM_EFTEM.m
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
% output_multislice = input_multem.ilc_multem perform TEM simulation
% Energy filtered transmission electron microscopy (EFTEM) simulation
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_MULTEM_EWFS.m
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
% output_multislice = input_multem.ilc_multem perform TEM simulation
% Exit wave real space (EWRS) simulation
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_MULTEM_EWFS_till_illumination.m
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
% output_multislice = input_multem.ilc_multem perform TEM simulation
% Exit wave real space (EWRS) simulation
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_MULTEM_EWRS.m
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
% output_multislice = input_multem.ilc_multem perform TEM simulation
% Exit wave real space (EWRS) simulation
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_MULTEM_EWRS_till_illumination.m
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
% output_multislice = input_multem.ilc_multem perform TEM simulation
% Exit wave real space (EWRS) simulation
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_MULTEM_HCTEM.m
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
% output_multislice = input_multem.ilc_multem perform TEM simulation
% Hollow cone transmission electron microscopy (HCTEM) simulation
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_MULTEM_HRTEM.m
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
% output_multislice = input_multem.ilc_multem perform TEM simulation
% High resolution transmission electron microscopy (HRTEM) simulation
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_MULTEM_ISTEM.m
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
% output_multislice = input_multem.ilc_multem perform TEM simulation
% Imaging scanning transmission electron microscopy (ISTEM) simulation
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_MULTEM_PED.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
%
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
%
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_MULTEM_STEM.m
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
% output_multislice = input_multem.ilc_multem perform TEM simulation
% Scanning transmission electron microscopy (STEM) simulation
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_MULTEM_STEM_EELS.m
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
% output_multislice = input_multem.ilc_multem perform TEM simulation
% STEM electron energy loss spectroscopy (EELS) simulation
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_MULTEM_STEM_matrix_detector.m
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
% output_multislice = input_multem.ilc_multem perform TEM simulation
% Scanning transmission electron microscopy (STEM) simulation
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_add_amorphous_layer.m
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_amorphous_specimen.m
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_apply_ctf.m
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
% output_multislice = input_multem.ilc_multem perform TEM simulation
% inclusion of TEM aberrerations into a exitwve simulation
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_beam_self_interaction.m
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
% output_multislice = input_multem.ilc_multem perform TEM simulation
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_crystal_by_layers.m
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_feg.m
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_fxg.m
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_incident_wave_1.m
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
% output_multislice = input_multem.ilc_multem perform TEM simulation
% Incident wave simulation
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_incident_wave_2.m
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
% output_multislice = input_multem.ilc_multem perform TEM simulation
% Incident wave simulation
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_incident_wave_3.m
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
% output_multislice = input_multem.ilc_multem perform TEM simulation
% Incident wave simulation
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_incident_wave_4.m
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
% output_multislice = input_multem.ilc_multem perform TEM simulation
% Incident wave simulation
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) '/mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_microscope_aberrations.m
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
% output_multislice = input_multem.ilc_multem perform TEM simulation
% inclusion of TEM aberrerations into a exitwve simulation
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_pr.m
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_projected_potential.m
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_propagate.m
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_specimen_creation_from_cif_file.m
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
% Specimen creation
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear all;clc;

Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_specimen_planes.m
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_specimen_rotation.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
%
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
%
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_specimen_slicing_rotation.m
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_specimen_slicing_show.m
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_specimen_slicing_with_amorphous_layer.m
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_specimen_slicing_zone_axis.m
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_specimen_subslicing.m
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_transmission_function.m
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_vp.m
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_vr.m
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_vz.m
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
% Copyright 2021 Ivan Lobato <[email protected]>
% Copyright 2023 Ivan Lobato <[email protected]>

clear; clc;
addpath([fileparts(pwd) filesep 'mex_bin'])
Expand Down
2 changes: 1 addition & 1 deletion mex_examples_multem/example_wave_function.m
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
% output_multislice = input_multem.ilc_multem perform TEM simulation
% All parameters of the input_multem structure are explained in ilm_dflt_input_multem()
% Copyright 2021 Ivan Lobato <[email protected]>clear; clc;
% Copyright 2023 Ivan Lobato <[email protected]>clear; clc;

addpath([fileparts(pwd) filesep 'mex_bin'])
addpath([fileparts(pwd) filesep 'crystalline_materials'])
Expand Down
4 changes: 2 additions & 2 deletions src/cgpu_fcns.cuh
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2019,10 +2019,10 @@ namespace mt
{
T_r chi = g2*(lens.c_c_30*g2+lens.c_c_10);
T_r c = c_Pi*lens.si_theta_c*lens.ti_iehwgd;
T_r u = 1.0 + 2*c*c*g2;
T_r u = 1.0 + c*c*g2;

c = c_Pi*lens.ti_iehwgd*lens.lambda*g2;
T_r temp_inc = 0.5*c*c;
T_r temp_inc = 0.25*c*c;

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

0 comments on commit 3f55109

Please sign in to comment.