{"id":3317,"date":"2021-05-10T21:19:31","date_gmt":"2021-05-10T21:19:31","guid":{"rendered":"https:\/\/er-c.org\/?page_id=3317"},"modified":"2021-05-12T11:46:29","modified_gmt":"2021-05-12T11:46:29","slug":"dr-probe-examples-reation-super-cell","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-super-cell\/","title":{"rendered":"Dr. Probe Examples Creation Super-Cell"},"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 the orthogonalization of a hexagonal atomic structure for TEM and STEM image simulations. Orthogonalzation is required for structure models where one of the cell angles is not 90 degrees. The material in this example is aluminum nitride (AlN) and we want to prepare a structure model for imaging along the [001] zone-axis of the crystal by using the program 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: #023d6b; \"\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: #eb5f73; \"\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:40px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<div style=\"height:80px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/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-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:40%\">\n<h5 class=\"h1\" style=\"text-align: left;\">Quick guide to structure model orthogonalization<\/h5>\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\">The steps required to orthogonalize 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: justify;\">1. Open the Dr. Probe command-line shell and prepare a folder structure for storing data.<\/p>\n\n&nbsp;\n<p style=\"text-align: justify;\">2. Obtain an initial unit cell or create one with BuildCell.<\/p>\n\n&nbsp;\n<p style=\"text-align: justify;\">3. Use CellMuncher to create an orthogonal structure model:<\/p>\n\n&nbsp;\n<p style=\"text-align: justify;\">&nbsp;&nbsp;&nbsp;&nbsp; 3a) Swap axis to bring the non-orthogonal plane in the <i>x<\/i>&#8211;<i>z<\/i> plane.<\/p>\n\n&nbsp;\n<p style=\"text-align: justify;\">&nbsp;&nbsp;&nbsp;&nbsp; 3b) Apply orthogonalization in the <i>x<\/i>&#8211;<i>z<\/i> plane.<\/p>\n\n&nbsp;\n<p style=\"text-align: justify;\">&nbsp;&nbsp;&nbsp;&nbsp; 3c) Reverse the initial swapping of axes.<\/p>\n\n&nbsp;\n<p style=\"text-align: justify;\">&nbsp;&nbsp;&nbsp;&nbsp; 3d) Wrap atoms into the new periodic unit.<\/p>\n\n&nbsp;\n<p style=\"text-align: justify;\">&nbsp;&nbsp;&nbsp;&nbsp; 3e) Remove close or duplicate atoms from the new cell.<\/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;\">Preparations<\/h5>\n&nbsp;\n<p style=\"text-align: justify;\">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\n&nbsp;\n<p style=\"text-align: justify;\">2. Create a working directory for storing data, e.g. <code>C:\\data\\aln\\001\\<\/code>.<\/p>\n\n&nbsp;\n<p style=\"text-align: justify;\">3. Switch to this directory within the command-line shell by typing<br><code>cd C:\\data\\aln\\001<\/code><\/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\" style=\"flex-basis:40%\">\n<h5 class=\"h1\" style=\"text-align: left;\">Initial structure file of hexagonal AlN<\/h5>\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\">The example is based on an initial structure data file as given by the text block below. Please copy the text block and save it as file <code>AlN-00.cel<\/code> or <strong><a href=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example.orthcel.AlN-00.zip\">download<\/a><\/strong> the initial structure file!<\/p>\n<h3>&nbsp;<\/h3>\n<img loading=\"lazy\" decoding=\"async\" class=\"alignnone wp-image-3613\" src=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/drprobe_primitive-cell-300x60.png\" alt=\"\" width=\"400\" height=\"79\" srcset=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/drprobe_primitive-cell-300x60.png 300w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/drprobe_primitive-cell.png 660w\" sizes=\"auto, (max-width: 400px) 100vw, 400px\" \/>\n<h3>&nbsp;<\/h3>\n<p class=\"sub1\" style=\"text-align: justify;\">Alternative you may create the structure file with the program BuildCell by the command<\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: left;\"><code>BuildCell --spacegroup=186\n        --lattice=3.110,3.110,4.980,90.0,90.0,120.0\n        --atom=Al,-0.333333,-0.666667,0.000000,1.0,0.300\n        --atom=N,-0.333333,-0.666667,0.3821,1.0,0.355\n        --output=AlN-00.cel<\/code><\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\">The structure data is taken from H. Schulz &amp; K.H. Thiemann, <em>Solid State Communications<\/em> <b>23<\/b> (1977) 815-818.<\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\">In [001] projection it displays as shown by the image on the right.<\/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 size-medium wp-image-3615\" src=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example.orthcel.AlN-300x197.png\" alt=\"\" width=\"300\" height=\"197\" srcset=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example.orthcel.AlN-300x197.png 300w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example.orthcel.AlN-1024x672.png 1024w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example.orthcel.AlN-768x504.png 768w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example.orthcel.AlN-1536x1008.png 1536w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example.orthcel.AlN-2048x1344.png 2048w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example.orthcel.AlN-580x380.png 580w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example.orthcel.AlN-150x100.png 150w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/>\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-3616\" src=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example.orthcel.construction-300x211.png\" alt=\"\" width=\"400\" height=\"281\" srcset=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example.orthcel.construction-300x211.png 300w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example.orthcel.construction.png 400w\" sizes=\"auto, (max-width: 400px) 100vw, 400px\" \/>\n\n\n\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\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;\">Calculation of the orthogonal cell dimensions<\/h5>\n<p style=\"text-align: justify;\">&nbsp;<\/p>\n<p class=\"sub1\" style=\"text-align: justify;\">By orthogonalizing a structure model, we try to find a (usually larger) periodic unit of the structure, where all cell axes are oriented with 90 degree angles against each other. In the present example of AlN, where the angle between <i>a<\/i>&#8211; and <i>b<\/i>-axis is 120 degrees, the orthogonalization is a mere 2-dimensional problem, as illustrated below, because the angles <em>alpha<\/em> between the <em>x<\/em>&#8211; and <em>z<\/em>-axis, and <em>beta<\/em> between the <em>y<\/em>&#8211; and <em>z<\/em>-axis are both 90 degree already.<\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\">In this case, an orthogonal unit cell is found with the new basis vectors <em><b>a<\/b>&#8216;<\/em> = <em><b>a<\/b><\/em> and <em><b>b<\/b>&#8216;<\/em> = 2<em><b>b<\/b><\/em> &#8211; <em><b>a<\/b><\/em>.<\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\">In general, the solution is not alway as simple, in particular, when the angle <em>gamma<\/em> is not 120 deg, or when the original lattice constants are not equal, i.e. <em>a<\/em> \u2260 <em>b<\/em>. In such general cases, the solution requires a linear combination with very large multiples of the original lattice vectors to span a perfectly periodic new unit. There are also cases, where even no exact solution exists. It may be possible to finde approximate solutions.<\/p>\n\n&nbsp;\n<p class=\"sub1\" style=\"text-align: justify;\">The following sequence of operations with the program CellMuncher will transform the hexagonal AlN structure model into a model with an orthorhombic unit cell.<\/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-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:40%\">\n<p style=\"text-align: left;\"><strong>1. Swap the <em>y<\/em>&#8211; and <em>z<\/em>-axes of the initial structure, since CellMuncher applies its orthogonalization routine to the plane containing the <em>beta<\/em> angle only.<\/strong><\/p>\n<p style=\"text-align: left;\"><br><code>CellMuncher -f AlN-00.cel -o AlN-01.cel --swap-axes=yz<\/code><\/p>\n\n&nbsp;\n<p style=\"text-align: left;\"><strong>2. Apply the orthogonalization:<\/strong><\/p>\n<p style=\"text-align: left;\"><br><code>CellMuncher -f AlN-01.cel -o AlN-02.cel --orthogonalize-plane=xz,2<\/code><\/p>\n<p style=\"text-align: justify;\"><br>Note: The number specified at the end of the command-line argument limits the possible periodic repeat of the original cell to find orthogonal substitutions. If no solution is found within this bound, CellMuncher will abort. In this case you should rather use the CellMuncher option <code>--create-block<\/code> to cut an orthogonal block from the initial structure (see the <strong><a href=\"https:\/\/er-c.org\/index.php\/software\/stem-stm-simulation\/dr-probe\/dr-probe-documentation\/dr-probe-documentation-cellmuncher\/\">CellMuncher documentation<\/a><\/strong>). The option <code>--create-block<\/code> is the most direct way of creating an orthogonal super-cell of any given structure. However, it requires a few pre-calculation to select a proper block, depending very much on the details of the input structure.<\/p>\n\n&nbsp;\n<p style=\"text-align: justify;\"><strong>3. Swap axes again to get back to the original orientation of the structure.<\/strong><\/p>\n<p style=\"text-align: justify;\"><br><code>CellMuncher -f AlN-02.cel -o AlN-03.cel --swap-axes=yz<\/code><\/p>\n<p style=\"text-align: justify;\"><br>In this step, we already obtain the final super-cell of this example, which is now orthogonal and as the size of <em>a<\/em> = 0.3110 nm, <em>b<\/em> = 0.5387 nm, and <em>c<\/em> = 0.4980 nm.<\/p>\n\n&nbsp;\n<p style=\"text-align: justify;\"><strong>4. Since some of the atomic sites may be placed out of the cell bounds, we wrap them back periodically into the range [0,1) for all three dimensions.<\/strong><\/p>\n<p style=\"text-align: justify;\"><br><code>CellMuncher -f AlN-03.cel -o AlN-04.cel --periodic=x --periodic=y --periodic=z<\/code><\/p>\n\n&nbsp;\n<p style=\"text-align: justify;\"><strong>5. Finally, we remove close or duplicate atoms from the cell.<\/strong><\/p>\n<p style=\"text-align: justify;\"><br><code>CellMuncher -f AlN-04.cel -o AlN_001.cel --remove-close-atoms=0.2<\/code><\/p>\n<p style=\"text-align: justify;\"><br>The value specified with the option <code>--remove-close-atoms<\/code> denotes the minimum allowed interatomic distance in the structure. A value of 0.2 \u00c5 is usually sufficient.<\/p>\n\n&nbsp;\n<p style=\"text-align: justify;\">The structure obtained after the transformtion to an orthorhombic cell is shown left in three different projections.<\/p>\n\n&nbsp;\n<p style=\"text-align: justify;\"><code>The structure definition file <a href=\"https:\/\/er-c.org\/barthel\/data\/Example.orthcel.AlN-orth.zip\">AlN_001.cel<\/a> obtained after the above transformations to an orthorhombic cell is listed on the right.<\/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-3617\" src=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example.orthcel.AlN-orth-300x135.png\" alt=\"\" width=\"400\" height=\"180\" srcset=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example.orthcel.AlN-orth-300x135.png 300w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/Example.orthcel.AlN-orth.png 600w\" sizes=\"auto, (max-width: 400px) 100vw, 400px\" \/>\n\n\n\n<div style=\"height:100px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<img loading=\"lazy\" decoding=\"async\" class=\"alignnone wp-image-3618\" src=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/drporbe_supercell-300x92.jpg\" alt=\"\" width=\"400\" height=\"122\" srcset=\"https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/drporbe_supercell-300x92.jpg 300w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/drporbe_supercell-1024x312.jpg 1024w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/drporbe_supercell-768x234.jpg 768w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/drporbe_supercell-1536x469.jpg 1536w, https:\/\/er-c.org\/wp-content\/uploads\/2021\/05\/drporbe_supercell.jpg 1672w\" sizes=\"auto, (max-width: 400px) 100vw, 400px\" \/>\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\" style=\"flex-basis:40%\">\n<h5 class=\"h1\" style=\"text-align: left;\">Summary of commands:<\/h5>\n<h6><code><\/code>&nbsp;<\/h6>\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<h6>&nbsp;<\/h6>\n<p class=\"sub1\" style=\"text-align: left;\"><code>BuildCell --spacegroup=186 --lattice=3.110,3.110,4.980,90.0,90.0,120.0 --atom=Al,-0.333333,-0.666667,0.000000,1.0,0.300 --atom=N,-0.333333,-0.666667,0.3821,1.0,0.355 --output=AlN-00.cel<\/code><code><\/code><\/p>\n<h6>&nbsp;<\/h6>\n<p class=\"sub1\" style=\"text-align: left;\"><code>CellMuncher -f AlN-00.cel -o AlN-01.cel --swap-axes=yz<br><\/code><\/p>\n<h6>&nbsp;<\/h6>\n<p class=\"sub1\" style=\"text-align: left;\"><code>\tCellMuncher -f AlN-01.cel -o AlN-02.cel --orthogonalize-plane=xz,2<\/code><\/p>\n<h6>&nbsp;<\/h6>\n<p class=\"sub1\" style=\"text-align: left;\"><code>CellMuncher -f AlN-02.cel -o AlN-03.cel --swap-axes=yz<\/code><\/p>\n<h6>&nbsp;<\/h6>\n<p class=\"sub1\" style=\"text-align: left;\"><code>CellMuncher -f AlN-03.cel -o AlN-04.cel --periodic=x --periodic=y --periodic=z<\/code><\/p>\n<h6>&nbsp;<\/h6>\n<p class=\"sub1\" style=\"text-align: left;\"><code>CellMuncher -f AlN-04.cel -o AlN_001.cel --remove-close-atoms=0.2 --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-vertically-aligned-top 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<h6><code><\/code>&nbsp;&nbsp;<\/h6>\n<p class=\"sub1\" style=\"text-align: justify;\">Use the command<\/p>\n<h6><code><\/code>&nbsp;&nbsp;<\/h6>\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<h6 style=\"text-align: justify;\"><code><\/code>&nbsp;&nbsp; <\/h6>\n<p class=\"sub1\" style=\"text-align: justify;\">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<h6 style=\"text-align: justify;\"><code><\/code>&nbsp;&nbsp; <\/h6>\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\n<code><\/code> &nbsp; <code><\/code>\n<\/div>\n<\/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-3317","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/er-c.org\/index.php\/wp-json\/wp\/v2\/pages\/3317","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=3317"}],"version-history":[{"count":21,"href":"https:\/\/er-c.org\/index.php\/wp-json\/wp\/v2\/pages\/3317\/revisions"}],"predecessor-version":[{"id":3641,"href":"https:\/\/er-c.org\/index.php\/wp-json\/wp\/v2\/pages\/3317\/revisions\/3641"}],"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=3317"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}