{"id":3315,"date":"2021-05-10T21:18:03","date_gmt":"2021-05-10T21:18:03","guid":{"rendered":"https:\/\/er-c.org\/?page_id=3315"},"modified":"2021-05-12T08:50:07","modified_gmt":"2021-05-12T08:50:07","slug":"dr-probe-examples-reation-create-structure-models","status":"publish","type":"page","link":"https:\/\/er-c.org\/index.php\/software\/stem-stm-simulation\/dr-probe\/dr-probe-examples\/dr-probe-examples-reation\/dr-probe-examples-reation-create-structure-models\/","title":{"rendered":"Dr. Probe Examples Creation Create Structure Models"},"content":{"rendered":"\n\n<div id=\"wp-block-themeisle-blocks-slider-0c9de452\" class=\"wp-block-themeisle-blocks-slider glide\" data-per-view=\"1\" data-gap=\"0\" data-peek=\"0\" data-autoplay=\"4000\" data-height=\"300px\" data-hide-arrows=\"false\"><div class=\"glide__track\" data-glide-el=\"track\"><div class=\"glide__slides\"><div class=\"wp-block-themeisle-blocks-slider-item-wrapper glide__slide\" tabindex=\"0\"><figure><img decoding=\"async\" class=\"wp-block-themeisle-blocks-slider-item\" src=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/drprobe-teas_001.png\" alt=\"\" title=\"\" data-id=\"2358\"\/><\/figure><\/div><div class=\"wp-block-themeisle-blocks-slider-item-wrapper glide__slide\" tabindex=\"0\"><figure><img decoding=\"async\" class=\"wp-block-themeisle-blocks-slider-item\" src=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/drprobe-teas_002.png\" alt=\"\" title=\"\" data-id=\"2359\"\/><\/figure><\/div><div class=\"wp-block-themeisle-blocks-slider-item-wrapper glide__slide\" tabindex=\"0\"><figure><img decoding=\"async\" class=\"wp-block-themeisle-blocks-slider-item\" src=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/drprobe-teas_003.png\" alt=\"\" title=\"\" data-id=\"2360\"\/><\/figure><\/div><div class=\"wp-block-themeisle-blocks-slider-item-wrapper glide__slide\" tabindex=\"0\"><figure><img decoding=\"async\" class=\"wp-block-themeisle-blocks-slider-item\" src=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/drprobe-teas_004.png\" alt=\"\" title=\"\" data-id=\"2361\"\/><\/figure><\/div><div class=\"wp-block-themeisle-blocks-slider-item-wrapper glide__slide\" tabindex=\"0\"><figure><img decoding=\"async\" class=\"wp-block-themeisle-blocks-slider-item\" src=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/drprobe-teas_005.png\" alt=\"\" title=\"\" data-id=\"2362\"\/><\/figure><\/div><div class=\"wp-block-themeisle-blocks-slider-item-wrapper glide__slide\" tabindex=\"0\"><figure><img decoding=\"async\" class=\"wp-block-themeisle-blocks-slider-item\" src=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/drprobe-teas_006.png\" alt=\"\" title=\"\" data-id=\"2363\"\/><\/figure><\/div><div class=\"wp-block-themeisle-blocks-slider-item-wrapper glide__slide\" tabindex=\"0\"><figure><img decoding=\"async\" class=\"wp-block-themeisle-blocks-slider-item\" src=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/drprobe-teas_007.png\" alt=\"\" title=\"\" data-id=\"2364\"\/><\/figure><\/div><\/div><div class=\"glide__bullets\" data-glide-el=\"controls[nav]\"><button class=\"glide__bullet\" data-glide-dir=\"=0\"><\/button><button class=\"glide__bullet\" data-glide-dir=\"=1\"><\/button><button class=\"glide__bullet\" data-glide-dir=\"=2\"><\/button><button class=\"glide__bullet\" data-glide-dir=\"=3\"><\/button><button class=\"glide__bullet\" data-glide-dir=\"=4\"><\/button><button class=\"glide__bullet\" data-glide-dir=\"=5\"><\/button><button class=\"glide__bullet\" data-glide-dir=\"=6\"><\/button><\/div><\/div><\/div>\n\n\n\n\n\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<div\n\t\t\t\n\t\t\tclass=\"so-widget-sow-headline so-widget-sow-headline-default-feea9c97c678\"\n\t\t\t\n\t\t><div class=\"sow-headline-container \">\n\t\t\t\t\t\t\t<h1 class=\"sow-headline\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t<a href=\"https:\/\/er-c.org\/index.php\/software\/stem-stm-simulation\/dr-probe\/\" >\n\t\t\t\t\t\t\t\tDr. Probe<\/a>\t\t\t\t\t\t<\/h1>\n\t\t\t\t\t\t\t\t\t\t\t<div class=\"decoration\">\n\t\t\t\t\t\t<div class=\"decoration-inside\"><\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t\t\t\t<h3 class=\"sow-sub-headline\">\n\t\t\t\t\t\tHR(S)TEM image simulation package\t\t\t\t\t\t<\/h3>\n\t\t\t\t\t\t<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-themeisle-blocks-advanced-columns has-1-columns has-desktop-equal-layout has-tablet-equal-layout has-mobile-equal-layout has-default-gap has-vertical-unset\" id=\"wp-block-themeisle-blocks-advanced-columns-27948cc6\"><div class=\"wp-block-themeisle-blocks-advanced-columns-overlay\"><\/div><div class=\"innerblocks-wrap\">\n<div class=\"wp-block-themeisle-blocks-advanced-column\" id=\"wp-block-themeisle-blocks-advanced-column-cf76d8a1\">\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-9d6595d7 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:10%\"><\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:80%\">\n<div class=\"wp-block-buttons is-content-justification-center is-layout-flex wp-block-buttons-is-layout-flex\">\n<div class=\"wp-block-button is-style-fill\"><a class=\"wp-block-button__link has-background\" href=\"https:\/\/er-c.org\/index.php\/software\/open-source-in-house-solutions\/dr-probe\/dr-probe-download\/\" style=\"background-color:#023d6b\">Download<\/a><\/div>\n\n\n\n<div class=\"wp-block-button is-style-fill\"><a class=\"wp-block-button__link has-background\" href=\"https:\/\/er-c.org\/index.php\/software\/open-source-in-house-solutions\/dr-probe\/dr-probe-installation\/\" style=\"background-color:#023d6b\">Installation<\/a><\/div>\n\n\n\n<div class=\"wp-block-button is-style-fill\"><a class=\"wp-block-button__link has-background\" href=\"https:\/\/er-c.org\/index.php\/software\/open-source-in-house-solutions\/dr-probe\/dr-probe-registration\/\" style=\"background-color:#023d6b\">Registration<\/a><\/div>\n\n\n\n<div class=\"wp-block-button is-style-fill\"><a class=\"wp-block-button__link has-background\" href=\"https:\/\/er-c.org\/index.php\/software\/open-source-in-house-solutions\/dr-probe\/dr-probe-documentation\/\" style=\"background-color:#023d6b\">Documentation<\/a><\/div>\n\n\n\n<div class=\"wp-block-button is-style-outline is-style-outline--1\"><a class=\"wp-block-button__link has-white-background-color has-background\" href=\"https:\/\/er-c.org\/index.php\/software\/open-source-in-house-solutions\/dr-probe\/dr-probe-examples\/\">Examples<\/a><\/div>\n\n\n\n<div class=\"wp-block-button is-style-fill\"><a class=\"wp-block-button__link has-background\" href=\"https:\/\/er-c.org\/index.php\/software\/open-source-in-house-solutions\/dr-probe\/dr-probe-development\/\" style=\"background-color:#023d6b\">Development<\/a><\/div>\n<\/div>\n\n\n\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n<div\n\t\t\t\n\t\t\tclass=\"so-widget-sow-features so-widget-sow-features-default-51eddc7803e1\"\n\t\t\t\n\t\t><ul\n\tclass=\"sow-features-list\n\tsow-features-responsive\">\n\n\t\t\t<li\n\t\t\tclass=\"sow-features-feature sow-icon-container-position-top\"\n\t\t\tstyle=\"display: flex; flex-direction: column; width: calc(25% - 25px);\"\n\t\t>\n\t\t\t\n\t\t\t\t\t\t<a\t\t\t\tclass=\"sow-icon-container sow-container-round\"\n\t\t\t\tstyle=\"color: #eb5f73; \"\n\t\t\t\ttitle=\"Structure model creation and manipulation\"\n\t\t\t\t\t\t\t\t\thref=\"https:\/\/er-c.org\/index.php\/software\/stem-stm-simulation\/dr-probe\/dr-probe-examples\/dr-probe-examples-reation\/\"\n\t\t\t\t\t\t\t\t>\n\t\t\t\t<span class=\"sow-icon-fontawesome sow-far\" data-sow-icon=\"&#xf185;\"\n\t\tstyle=\"font-size: 30px; color: #FFFFFF\" \n\t\taria-hidden=\"true\"><\/span>\t\t\t<\/a>\n\n\t\t\t<div class=\"textwidget\">\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<h6 class=\"sow-features-feature-title\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t<a\n\t\t\t\t\t\t\t\thref=\"https:\/\/er-c.org\/index.php\/software\/stem-stm-simulation\/dr-probe\/dr-probe-examples\/dr-probe-examples-reation\/\"\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t>\n\t\t\t\t\t\t\tStructure model creation and manipulation\t\t\t\t\t\t\t<\/a>\n\t\t\t\t\t\t\t\t\t\t\t\t<\/h6>\n\t\t\t\t\n\t\t\t\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t<\/li>\n\n\t\t\t<li\n\t\t\tclass=\"sow-features-feature sow-icon-container-position-top\"\n\t\t\tstyle=\"display: flex; flex-direction: column; width: calc(25% - 25px);\"\n\t\t>\n\t\t\t\n\t\t\t\t\t\t<a\t\t\t\tclass=\"sow-icon-container sow-container-round\"\n\t\t\t\tstyle=\"color: #023d6b; \"\n\t\t\t\ttitle=\"Simulations with the Dr. Probe GUI\"\n\t\t\t\t\t\t\t\t\thref=\"https:\/\/er-c.org\/index.php\/software\/stem-stm-simulation\/dr-probe\/dr-probe-examples\/dr-probe-examples-gui\/\"\n\t\t\t\t\t\t\t\t>\n\t\t\t\t<span class=\"sow-icon-ionicons\" data-sow-icon=\"&#xf35c;\"\n\t\tstyle=\"font-size: 30px; color: #FFFFFF\" \n\t\taria-hidden=\"true\"><\/span>\t\t\t<\/a>\n\n\t\t\t<div class=\"textwidget\">\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<h6 class=\"sow-features-feature-title\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t<a\n\t\t\t\t\t\t\t\thref=\"https:\/\/er-c.org\/index.php\/software\/stem-stm-simulation\/dr-probe\/dr-probe-examples\/dr-probe-examples-gui\/\"\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t>\n\t\t\t\t\t\t\tSimulations with the Dr. Probe GUI\t\t\t\t\t\t\t<\/a>\n\t\t\t\t\t\t\t\t\t\t\t\t<\/h6>\n\t\t\t\t\n\t\t\t\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t<\/li>\n\n\t\t\t<li\n\t\t\tclass=\"sow-features-feature sow-icon-container-position-top\"\n\t\t\tstyle=\"display: flex; flex-direction: column; width: calc(25% - 25px);\"\n\t\t>\n\t\t\t\n\t\t\t\t\t\t<a\t\t\t\tclass=\"sow-icon-container sow-container-round\"\n\t\t\t\tstyle=\"color: #023d6b; \"\n\t\t\t\ttitle=\"Simulations with the Dr. Probe command-line tools\"\n\t\t\t\t\t\t\t\t\thref=\"https:\/\/er-c.org\/index.php\/software\/stem-stm-simulation\/dr-probe\/dr-probe-examples\/dr-probe-examples-cl\/\"\n\t\t\t\t\t\t\t\t>\n\t\t\t\t<span class=\"sow-icon-ionicons\" data-sow-icon=\"&#xf394;\"\n\t\tstyle=\"font-size: 30px; color: #FFFFFF\" \n\t\taria-hidden=\"true\"><\/span>\t\t\t<\/a>\n\n\t\t\t<div class=\"textwidget\">\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<h6 class=\"sow-features-feature-title\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t<a\n\t\t\t\t\t\t\t\thref=\"https:\/\/er-c.org\/index.php\/software\/stem-stm-simulation\/dr-probe\/dr-probe-examples\/dr-probe-examples-cl\/\"\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t>\n\t\t\t\t\t\t\tSimulations with the Dr. Probe command-line tools\t\t\t\t\t\t\t<\/a>\n\t\t\t\t\t\t\t\t\t\t\t\t<\/h6>\n\t\t\t\t\n\t\t\t\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t<\/li>\n\n\t\t\t<li\n\t\t\tclass=\"sow-features-feature sow-icon-container-position-top\"\n\t\t\tstyle=\"display: flex; flex-direction: column; width: calc(25% - 25px);\"\n\t\t>\n\t\t\t\n\t\t\t\t\t\t<a\t\t\t\tclass=\"sow-icon-container sow-container-round\"\n\t\t\t\tstyle=\"color: #023d6b; \"\n\t\t\t\ttitle=\"Publications\"\n\t\t\t\t\t\t\t\t\thref=\"https:\/\/er-c.org\/index.php\/software\/stem-stm-simulation\/dr-probe\/dr-probe-examples\/dr-probe-examples-publications\/\"\n\t\t\t\t\t\t\t\t>\n\t\t\t\t<span class=\"sow-icon-fontawesome sow-far\" data-sow-icon=\"&#xf0c5;\"\n\t\tstyle=\"font-size: 30px; color: #FFFFFF\" \n\t\taria-hidden=\"true\"><\/span>\t\t\t<\/a>\n\n\t\t\t<div class=\"textwidget\">\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<h6 class=\"sow-features-feature-title\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t<a\n\t\t\t\t\t\t\t\thref=\"https:\/\/er-c.org\/index.php\/software\/stem-stm-simulation\/dr-probe\/dr-probe-examples\/dr-probe-examples-publications\/\"\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t>\n\t\t\t\t\t\t\tPublications\t\t\t\t\t\t\t<\/a>\n\t\t\t\t\t\t\t\t\t\t\t\t<\/h6>\n\t\t\t\t\n\t\t\t\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t<\/li>\n\n\t<\/ul>\n<\/div>\n\n\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<hr>\n&nbsp;\n<p style=\"text-align: center;\">We describe here how to create atomic structure data for TEM and STEM image simulations in a different crystallographic orientation than the original structure model. The material in this example is the cubic perovskite SrTiO<sub>3<\/sub>, and we want to prepare structure data for imaging along the [110] zone-axis by using the two command-line tools BuildCell and CellMuncher.<\/p>\n\n&nbsp;\n<hr>\n\n\n\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n<div\n\t\t\t\n\t\t\tclass=\"so-widget-sow-features so-widget-sow-features-default-7972f72d0523\"\n\t\t\t\n\t\t><ul\n\tclass=\"sow-features-list\n\tsow-features-responsive\">\n\n\t\t\t<li\n\t\t\tclass=\"sow-features-feature sow-icon-container-position-top\"\n\t\t\tstyle=\"display: flex; flex-direction: column; width: calc(33.333% - 25px);\"\n\t\t>\n\t\t\t\n\t\t\t\t\t\t<a\t\t\t\tclass=\"sow-icon-container sow-container-square\"\n\t\t\t\tstyle=\"color: #023d6b; \"\n\t\t\t\ttitle=\"Structure models for TEM and STEM simulations\"\n\t\t\t\t\t\t\t\t\thref=\"https:\/\/er-c.org\/index.php\/software\/stem-stm-simulation\/dr-probe\/dr-probe-examples\/dr-probe-examples-reation\/dr-probe-examples-reation-structure-models\/\"\n\t\t\t\t\t\t\t\t>\n\t\t\t\t<span class=\"sow-icon-fontawesome sow-far\" data-sow-icon=\"&#xf044;\"\n\t\tstyle=\"font-size: 20px; color: #FFFFFF\" \n\t\taria-hidden=\"true\"><\/span>\t\t\t<\/a>\n\n\t\t\t<div class=\"textwidget\">\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<h6 class=\"sow-features-feature-title\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t<a\n\t\t\t\t\t\t\t\thref=\"https:\/\/er-c.org\/index.php\/software\/stem-stm-simulation\/dr-probe\/dr-probe-examples\/dr-probe-examples-reation\/dr-probe-examples-reation-structure-models\/\"\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t>\n\t\t\t\t\t\t\tStructure models for TEM and STEM simulations\t\t\t\t\t\t\t<\/a>\n\t\t\t\t\t\t\t\t\t\t\t\t<\/h6>\n\t\t\t\t\n\t\t\t\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t<\/li>\n\n\t\t\t<li\n\t\t\tclass=\"sow-features-feature sow-icon-container-position-top\"\n\t\t\tstyle=\"display: flex; flex-direction: column; width: calc(33.333% - 25px);\"\n\t\t>\n\t\t\t\n\t\t\t\t\t\t<a\t\t\t\tclass=\"sow-icon-container sow-container-square\"\n\t\t\t\tstyle=\"color: #eb5f73; \"\n\t\t\t\ttitle=\"Create atomic structure models of SrTiO3[110] for TEM and STEM simulations\"\n\t\t\t\t\t\t\t\t\thref=\"https:\/\/er-c.org\/index.php\/software\/stem-stm-simulation\/dr-probe\/dr-probe-examples\/dr-probe-examples-reation\/dr-probe-examples-reation-create-structure-models\/\"\n\t\t\t\t\t\t\t\t>\n\t\t\t\t<span class=\"sow-icon-fontawesome sow-far\" data-sow-icon=\"&#xf044;\"\n\t\tstyle=\"font-size: 20px; color: #FFFFFF\" \n\t\taria-hidden=\"true\"><\/span>\t\t\t<\/a>\n\n\t\t\t<div class=\"textwidget\">\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<h6 class=\"sow-features-feature-title\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t<a\n\t\t\t\t\t\t\t\thref=\"https:\/\/er-c.org\/index.php\/software\/stem-stm-simulation\/dr-probe\/dr-probe-examples\/dr-probe-examples-reation\/dr-probe-examples-reation-create-structure-models\/\"\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t>\n\t\t\t\t\t\t\tCreate atomic structure models of SrTiO3[110] for TEM and STEM simulations\t\t\t\t\t\t\t<\/a>\n\t\t\t\t\t\t\t\t\t\t\t\t<\/h6>\n\t\t\t\t\n\t\t\t\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t<\/li>\n\n\t\t\t<li\n\t\t\tclass=\"sow-features-feature sow-icon-container-position-top\"\n\t\t\tstyle=\"display: flex; flex-direction: column; width: calc(33.333% - 25px);\"\n\t\t>\n\t\t\t\n\t\t\t\t\t\t<a\t\t\t\tclass=\"sow-icon-container sow-container-square\"\n\t\t\t\tstyle=\"color: #023d6b; \"\n\t\t\t\ttitle=\"Make an orthogonal super-cell of hexagonal AIN\"\n\t\t\t\t\t\t\t\t\thref=\"https:\/\/er-c.org\/index.php\/software\/stem-stm-simulation\/dr-probe\/dr-probe-examples\/dr-probe-examples-reation\/dr-probe-examples-reation-super-cell\/\"\n\t\t\t\t\t\t\t\t>\n\t\t\t\t<span class=\"sow-icon-fontawesome sow-far\" data-sow-icon=\"&#xf044;\"\n\t\tstyle=\"font-size: 20px; color: #FFFFFF\" \n\t\taria-hidden=\"true\"><\/span>\t\t\t<\/a>\n\n\t\t\t<div class=\"textwidget\">\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<h6 class=\"sow-features-feature-title\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t<a\n\t\t\t\t\t\t\t\thref=\"https:\/\/er-c.org\/index.php\/software\/stem-stm-simulation\/dr-probe\/dr-probe-examples\/dr-probe-examples-reation\/dr-probe-examples-reation-super-cell\/\"\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t>\n\t\t\t\t\t\t\tMake an orthogonal super-cell of hexagonal AIN\t\t\t\t\t\t\t<\/a>\n\t\t\t\t\t\t\t\t\t\t\t\t<\/h6>\n\t\t\t\t\n\t\t\t\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t<\/li>\n\n\t<\/ul>\n<\/div>\n\n\n<div style=\"height:80px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<div class=\"wp-block-columns has-background is-layout-flex wp-container-core-columns-is-layout-9d6595d7 wp-block-columns-is-layout-flex\" style=\"background-color:#ebebeb\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:40%\">\n<h5 class=\"h1\" style=\"text-align: left;\">Quick guide to structure file creation for multislice simulations<\/h5>\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\">The steps required to create and adopt a structure model for STEM and TEM image simulations are listed here in short. More detailed explanations are given below.<\/p>\n\n&nbsp;\n<p style=\"text-align: left;\">1. Open the command-line shell and prepare a folder structure for storing data.<\/p>\n\n&nbsp;\n<p style=\"text-align: left;\">2. Create a unit-cell with BuildCell.<\/p>\n\n&nbsp;\n<p style=\"text-align: left;\">3. Orient (rotate) the unit-cell to the desired zone axis with CellMuncher.<\/p>\n\n&nbsp;\n<p style=\"text-align: left;\">4. Center the atoms in the structure slices by shifting along the <i>c<\/i> (<i>z<\/i>) axis. Shift atoms also away from the <i>x<\/i> and <i>y<\/i> boundaries of the cell.<\/p>\n\n&nbsp;\n<p style=\"text-align: left;\">5. Extend the cell (periodically) for frozen-lattice simulations.<\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:10%\"><\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:40%\">\n<h1>&nbsp;<\/h1>\n<h5 class=\"h1\" style=\"text-align: left;\">Preparations<\/h5>\n<h6>&nbsp;<\/h6>\n&nbsp;\n<p style=\"text-align: left;\">1. Start the console or command-line shell. On Windows OS you may use the Dr. Probe command-line shell or add the Dr. Probe installation folder to your environmental PATH variable.<\/p>\n<h6>&nbsp;<\/h6>\n<p style=\"text-align: left;\">2. Create a working directory for storing data, e.g. <code>C:\\data\\sto\\110\\<\/code>.<\/p>\n<h6>&nbsp;<\/h6>\n<p style=\"text-align: left;\">3. Switch to this directory within the command-line shell by typing<br><code>cd C:\\data\\sto\\110<\/code><\/p>\n<h6>&nbsp;<\/h6>\n<p style=\"text-align: left;\">4. Create a sub-folder which will hold the structure data by typing<br><code>md cel<\/code><code><\/code><\/p>\n<h6>&nbsp;<\/h6>\n<p style=\"text-align: left;\">If you prefer organizing your files in a different way, adopt the file names below accordingly.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-9d6595d7 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-vertically-aligned-center is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:40%\">\n<img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-medium wp-image-3575\" src=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/STO_001_persp-300x279.png\" alt=\"\" width=\"300\" height=\"279\" srcset=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/STO_001_persp-300x279.png 300w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/STO_001_persp.png 501w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/>\n<p style=\"text-align: center;\">The structure parameters are taken from Abramov et <em>al<\/em>. [1].<\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:10%\"><\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:40%\">\n<h4 class=\"h1\" style=\"text-align: left;\">Creating a SrTiO<sub>3<\/sub> unit-cell<\/h4>\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\">Crystal unit cells can be created with the tool BuildCell. For the case of SrTiO<sub>3<\/sub> we fill a primitive cubic cell with atoms and assign thermal vibration parameters. For such simple unit cells you may alternatively write the <strong><a href=\"https:\/\/er-c.org\/index.php\/software\/stem-stm-simulation\/dr-probe\/dr-probe-documentation\/dr-probe-documentation-celslc\/dr-probe-documentation-celslc-input\/\">CEL file<\/a><\/strong> manually.<\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: left;\"><code>BuildCell --spacegroup=221 --lattice=3.901,3.901,3.901,90.0,90.0,90.0\n        --atom=Sr,0.0,0.0,0.0,1.0,0.62 --atom=Ti,0.5,0.5,0.5,1.0,0.44\n        --atom=O,0.0,0.5,0.5,1.0,0.71 --output=cel\\STO_001.cel<\/code><\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\">The result is written into the file <code>cel\\STO_001.cel<\/code> and should look like the text below. <a href=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example00.STO_001.cel.zip\"><strong>(Download)<\/strong><\/a><\/p>\n\n&nbsp;\n\n<img loading=\"lazy\" decoding=\"async\" class=\"alignnone wp-image-3574\" src=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/drprobe_super-cell-300x69.jpg\" alt=\"\" width=\"500\" height=\"115\" srcset=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/drprobe_super-cell-300x69.jpg 300w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/drprobe_super-cell-1024x235.jpg 1024w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/drprobe_super-cell-768x176.jpg 768w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/drprobe_super-cell-1536x352.jpg 1536w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/drprobe_super-cell.jpg 1674w\" sizes=\"auto, (max-width: 500px) 100vw, 500px\" \/>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns has-background is-layout-flex wp-container-core-columns-is-layout-9d6595d7 wp-block-columns-is-layout-flex\" style=\"background-color:#ebebeb\">\n<div class=\"wp-block-column is-vertically-aligned-center is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:40%\">\n<h5 class=\"h1\" style=\"text-align: left;\">Orientation of the unit cell along [110]<\/h5>\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\">Orient the unit cell along the [110] zone axis using the <code>--create-block<\/code> option of CellMuncher. Take care to extend the periodic unit, such that the tilted structure is again periodic in an orthorhombic cell along the new crystal axes. This is simple for initially cubic cells as in the present case. The new cell dimensions along x and z will be by a factor of square root of 2 larger than the cubic cell: <em>a&#8217; = c&#8217; = a * Sqrt<\/em>(2). Use at least 6 digits precision for the new cell dimensions in order to prevent round-off problems.<\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: left;\"><code>CellMuncher -f cel\\STO_001.cel -o cel\\tmp1.cel --create-block=1,1,0,0,0,1,0.55168472,0.3901,0.55168472<\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:10%\"><\/div>\n\n\n\n<div class=\"wp-block-column is-vertically-aligned-center is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:40%\">\n<img loading=\"lazy\" decoding=\"async\" class=\"alignnone wp-image-3597 size-medium\" src=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/STO_110_persp-1-300x230.png\" alt=\"\" width=\"300\" height=\"230\" srcset=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/STO_110_persp-1-300x230.png 300w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/STO_110_persp-1-1024x785.png 1024w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/STO_110_persp-1-768x589.png 768w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/STO_110_persp-1-1536x1177.png 1536w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/STO_110_persp-1.png 1644w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/>\n<p style=\"text-align: center;\">The size of the new cell is a&#8217;=0.55168472nm, b&#8217;=0.3901nm, c&#8217;=0.55168472nm and it contains 2 of the original SrTiO<sub>3<\/sub> units, i.e. 2 Sr atoms, 2 Ti atoms and 6 O atoms.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-9d6595d7 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-vertically-aligned-center is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:40%\">\n<img loading=\"lazy\" decoding=\"async\" class=\"alignnone wp-image-3586\" src=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example00.STO_110-300x210.png\" alt=\"\" width=\"400\" height=\"280\" srcset=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example00.STO_110-300x210.png 300w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example00.STO_110.png 400w\" sizes=\"auto, (max-width: 400px) 100vw, 400px\" \/>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:10%\"><\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:40%\">\n<h5 class=\"h1\" style=\"text-align: left;\">Center atomic planes to structure slices<\/h5>\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\">The current super-cell file <code>cel\\tmp1.cel<\/code> should look as in the image above but may contain more than the desired 10 atoms (= 2 original unit SrTiO<sub>3<\/sub> cells) due to round-off errors during the block cutting.<\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\">Next, we translate all atoms by half an atomic plane along each cell dimension. This step prevents later possible numerical round-off errors, e.g. during the subsequent distribution of the super-cell atoms into 4 equidistant slices along <em>z<\/em>. The translation by half atomic planes should be done always, when atoms are placed at the termination planes of object slices.<\/p>\n<p class=\"sub1\" style=\"text-align: justify;\"><br>For the current example of SrTiO<sub>3<\/sub> [110] the fractional shifts by half planes along each axis are (0.125, 0.25, 0.125). Note that other structures will require different fractional shifts. The fractional shift should be 1\/(2<em>N<\/em><sub>p<\/sub>), where <em>N<\/em><sub>p<\/sub> is the number of atomic planes along a cell axis.<\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: left;\"><code>CellMuncher -f cel\\tmp1.cel -o cel\\tmp2.cel -T x,0.125 -T y,0.25 -T z,0.125<\/code><\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\">We now wrap the fractional atomic site coordinates back to the interval [0,1).<\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: left;\"><code>CellMuncher -f cel\\tmp2.cel -o cel\\tmp3.cel --periodic=x --periodic=y --periodic=z --cif<\/code><\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\">Previous round-off errors occurring with block cutting will now be cured by removing atoms which are closer than a small threshold distance to other atoms. As threshold, usually 0.2 \u00c5 are sufficient.<\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: left;\"><code>CellMuncher -f cel\\tmp3.cel -o cel\\STO_110.cel --remove-close-atoms=0.2 --cif<\/code><\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\">The result of the above procedure up to this point is shown in the figure on the left.<\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\">This super-cell can be the input for a coherent TEM image calculation using Debye-Waller factors to describe thermal diffuse scattering (TDS).<\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\"><strong><a href=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example00.STO_110.cel.zip\">Download <\/a><\/strong>the SrTiO<sub>3<\/sub> [110] super-cell for TEM simulations.<\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\">For STEM image simulations or TEM image simulations approximating TDS by a frozen lattice (frozen phonons) approach, please proceed to the next step!<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns has-background is-layout-flex wp-container-core-columns-is-layout-9d6595d7 wp-block-columns-is-layout-flex\" style=\"background-color:#ebebeb\">\n<div class=\"wp-block-column is-vertically-aligned-center is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:40%\">\n<h5 class=\"h1\" style=\"text-align: left;\">Extend the super-cell by 3 x 4<\/h5>\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\">We repeat the SrTiO<sub>3<\/sub> [110] super-cell 3 times along <i>x<\/i> and 4 times along <i>y<\/i>.<\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: left;\"><code>CellMuncher -f cel\\STO_110.cel -o cel\\STO_110_3x4.cel --repeat=x,3 --repeat=y,4 --cif<\/code><\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\">The size of the new super-cell is now <em>a<\/em> = 1.6569 nm, <em>b<\/em> = 1.562 nm, and <em>c<\/em> = 0.5523 nm, and it contains 24 of the original SrTiO<sub>3<\/sub> unit cells projected along the [110] zone-axis.<\/p>\n<p style=\"text-align: justify;\">&nbsp;<\/p>\n<p class=\"sub1\" style=\"text-align: justify;\">An increased <i>x<\/i>&#8211; and <i>y<\/i>-dimension of the super-cell allows us to introduce aperiodic atomic displacements in a frozen-lattice approach. It should be done if severe artifacts can be expected due to the real-space wrap-around of the spreading wave function with increasing object thickness. You should adopt the number of repeats to your simulation. As a general rule of thumb: calculations for thicker objects require also a larger super-cell along <i>x<\/i> and <i>y<\/i>.<\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\">An image of the 3&#215;4 extended SrTiO<sub>3<\/sub> [110] super-cell is shown in the figure on the right.<\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\">The extended super-cell can be used for small-scale STEM image simulations. It should give reasonable results for a specimen thickness below 40 nm.<\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\"><strong><a href=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example00.STO_110_3x4.cel.zip\">Download<\/a> <\/strong>the extended SrTiO<sub>3<\/sub> [110] super-cell for STEM simulations.<\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:10%\"><\/div>\n\n\n\n<div class=\"wp-block-column is-vertically-aligned-center is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:40%\">\n<img loading=\"lazy\" decoding=\"async\" class=\"alignnone wp-image-3593 size-full\" src=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example00.STO_110_3x4-1.png\" alt=\"\" width=\"400\" height=\"316\" srcset=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example00.STO_110_3x4-1.png 400w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example00.STO_110_3x4-1-300x237.png 300w\" sizes=\"auto, (max-width: 400px) 100vw, 400px\" \/>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-9d6595d7 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-vertically-aligned-center is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:40%\">\n<h5 class=\"h1\" style=\"text-align: left;\">Summary of commands:<\/h5>\n\u00a0\n<p class=\"sub1\" style=\"text-align: justify;\">Following is the complete sequence of all commands used above. You may copy this sequence and execute it by one call from a batch file or shell script.<\/p>\n\n\u00a0\n<p class=\"sub1\" style=\"text-align: left;\"><code>BuildCell --spacegroup=221 \n--lattice=3.901,3.901,3.901,90.0,90.0,90.0 \n--atom=Sr,0.0,0.0,0.0,1.0,0.62 --atom=Ti,0.5,0.5,0.5,1.0,0.44 \n--atom=O,0.0,0.5,0.5,1.0,0.71 --output=cel\\STO_001.cel<\/code><\/p>\n\n\u00a0\n<p class=\"sub1\" style=\"text-align: left;\"><code><\/code><code>CellMuncher -f cel\\STO_001.cel -o cel\\tmp1.cel --create-block=1,1,0,0,0,1,0.551685,0.3901,0.551685<\/code><\/p>\n\n\u00a0\n<p class=\"sub1\" style=\"text-align: left;\"><code><\/code><code>CellMuncher -f cel\\tmp1.cel -o cel\\tmp2.cel -T x,0.125 -T y,0.25 -T z,0.125 --cif<\/code><\/p>\n\n\u00a0\n<p class=\"sub1\" style=\"text-align: left;\"><code><\/code><code>CellMuncher -f cel\\tmp2.cel -o cel\\tmp3.cel --periodic=x --periodic=y --periodic=z --cif<\/code><\/p>\n\n\u00a0\n<p class=\"sub1\" style=\"text-align: left;\"><code><\/code><code>CellMuncher -f cel\\tmp3.cel -o cel\\STO_110.cel --remove-close-atoms=0.2 --cif<\/code><\/p>\n\n\u00a0\n<p class=\"sub1\" style=\"text-align: left;\"><code><\/code><code>CellMuncher -f cel\\STO_110.cel -o cel\\STO_110_3x4.cel --repeat=x,3 --repeat=y,4 --cif <\/code><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:10%\"><\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:40%\">\n<h5 class=\"h1\" style=\"text-align: left;\">Translation from CEL to CIF for visualization<\/h5>\n&nbsp;\n<p class=\"sub1\" style=\"text-align: left;\">Use the command<\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: left;\"><code>CellMuncher -f dummy-file-name.cel -o dummy-file-name.cif -w CIF<\/code><\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: left;\">for translating from the <strong><a href=\"https:\/\/er-c.org\/index.php\/software\/stem-stm-simulation\/dr-probe\/dr-probe-documentation\/dr-probe-documentation-celslc\/dr-probe-documentation-celslc-input\/\">CEL file<\/a><\/strong> format to CIF. You can open the resulting CIF file directly with the program <strong><a href=\"http:\/\/jp-minerals.org\/vesta\/en\/\" target=\"_blank\" rel=\"noopener\">VESTA<\/a><\/strong> to visualize the structure.<\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\">Note that the <i>B<\/i><sub>iso<\/sub> values in the CIF output of CellMuncher is on a wrong scale. Correct these values before using the CIF file in simulations.<\/p>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-columns has-background is-layout-flex wp-container-core-columns-is-layout-9d6595d7 wp-block-columns-is-layout-flex\" style=\"background-color:#ebebeb\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<h5 class=\"h1\" style=\"text-align: left;\">References<\/h5>\n&nbsp;\n<p style=\"text-align: left;\">[1] Yu.A. Abramov, V.G. Tsirel&#8217;son, V.E. Zavodnik, S.A. Ivanov, and I.D. Brown, <em>Acta Cryst. B<\/em> <strong>51<\/strong> (1995) p. 942. doi: <strong><a href=\"https:\/\/doi.org\/10.1107\/S0108768195003752\" target=\"_blank\" rel=\"noopener\">10.1107\/S0108768195003752<\/a><\/strong><\/p>\n<\/div>\n<\/div>\n\n\n\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:10%\"><\/div>\n<\/div>\n<\/div>\n<\/div><\/div>\n\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":2,"featured_media":0,"parent":3283,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"templates\/builder-fullwidth-std.php","meta":{"_themeisle_gutenberg_block_has_review":false,"footnotes":""},"class_list":["post-3315","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/er-c.org\/index.php\/wp-json\/wp\/v2\/pages\/3315","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/er-c.org\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/er-c.org\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/er-c.org\/index.php\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/er-c.org\/index.php\/wp-json\/wp\/v2\/comments?post=3315"}],"version-history":[{"count":31,"href":"https:\/\/er-c.org\/index.php\/wp-json\/wp\/v2\/pages\/3315\/revisions"}],"predecessor-version":[{"id":3611,"href":"https:\/\/er-c.org\/index.php\/wp-json\/wp\/v2\/pages\/3315\/revisions\/3611"}],"up":[{"embeddable":true,"href":"https:\/\/er-c.org\/index.php\/wp-json\/wp\/v2\/pages\/3283"}],"wp:attachment":[{"href":"https:\/\/er-c.org\/index.php\/wp-json\/wp\/v2\/media?parent=3315"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}