The VASP Scripter AddOn

Transcription

1 The VASP Scripter AddOn Tutorial Version

2 The VASP Scripter AddOn: Tutorial Version Copyright QuantumWise A/S Atomistix ToolKit Copyright Notice All rights reserved. This publication may be freely redistributed in its full, unmodified form. No part of this publication may be incorporated or used in other publications without prior written permission from the publisher.

3 TABLE OF CONTENTS 1. Introduction Installing and configuring the VASP Scripter... 2 Installing the VASP Scripter... 2 Configuring the VASP Scripter How to use the VASP Scripter... 6 Overview... 6 Setup... 6 Accuracy... 8 Electrons... 9 Ions Properties Generating the VASP input files Setting up a NEB simulation for VASP Setting up the NEB object Generating the VASP NEB input files iii

4 CHAPTER 1. INTRODUCTION This tutorial shows how to use the graphical user interface in ATK, that is Virtual NanoLab (VNL), to set up VASP calculations. This plugin functionality is provided as a separate download, which can be installed through the AddOn Manager in VNL. The plugin can be used to generate VASP input files for a wide range of tasks, including total energy calculations, relaxations and NEB calculations. Important The VASP plugin is a tool that can ease the generation of correctly formatted input files for VASP. This tutorial is however not a user guide to VASP, nor does QuantumWise provide access to the VASP code. It is assumed that the user has already obtained and installed VASP from its official source, and is familiar with the code. Tip The source code to the plugin is provided, and you can make your own modifications to it, to add extra functionality. The code may also be used as inspiration for designing input interfaces for other software packages. To familiarize yourself with VNL in general, it is recommended to go through the VNL Tutorial. You are now ready to begin the tutorial. 1

5 CHAPTER 2. INSTALLING AND CONFIGURING THE VASP SCRIPTER INSTALLING THE VASP SCRIPTER To install the VASP Scripter, start VNL and from the main window open Help AddOn Manager. Select the VASP Scripter, and press the Install button. The VASP Scripter will now be downloaded from the QuantumWise server and installed. Note A note on definitions is in order. A "plugin" is a piece of code that adds a specific functionality to ATK. An "addon" is a collection of plugins. The VASP Scripter AddOn contains just one plugin - the VASP Scripter. Tip On Linux, the addon is installed in the directory vnl/lib/python2.6/site-packages/addons/vaspscripter (on Windows the directory is vnl/lib/site-packages/addons/vaspscripter) inside the ATK installation directory, where you can browse and edit the source code for the addon. CONFIGURING THE VASP SCRIPTER The first time you use the VASP Scripter, you will need to configure it by specifying the location of the VASP pseudopotential (PP) libraries. This step can be skipped, in case the PP libraries are not installed on the machine where you run VNL. You will however then have to create your POTCAR file manually. 2

6 Tip Even if VASP is not configured to run on the platform where you use VNL, you can still copy the PP libraries over to it, in order to have the plugin generate the POTCAR files properly. The plugin does not attempt to launch VASP, it just looks for the PP files. Important The PP libraries are not provided by QuantumWise; they should have been given to you when you obtained your VASP license. STARTING THE VASP SCRIPTER Start the VASP Scripter by selecting Tools Custom Scripter from the VNL main menu. This opens a Custom Scripter window. From the top menu select Scripters VASP and the VASP Scripter will open. Next open the Database tool from the VNL main menu. Select the AgGaS2 configuration, and drag-and-drop it onto the VASP Scripter window. This will focus the "Configuration" tab in the VASP Scripter. Note If you happen to have incomplete VASP PP libraries, please make sure that the selected configuration only contains elements for which you have PPs available. CONFIGURE THE PSEUDOPOTENTIAL LIBRARIES Select the "Setup" tab. 3

7 Note that the Pseudopotential version line in the lower half of the window indicates that for the element(s) in your atomic configuration, "no pseudopotentials are found". Indeed, you have not yet specified the correct path to your PPs. To do so, click on the Manage pseudopotential directories... button. This opens a new dialog For each type of PP and exchange-correlation functional (e.g. Ultra-soft-LDA or PAW-PBE), you can individually change the path to the directory containing the corresponding library. Do not try typing in the path; instead, use the Change... buttons. 4

8 Tip If your PP libraries all reside in sub-directories of a common reference directory, you can facilitate the process by first selecting this directory on the first line, and then clicking Apply. This will append the conventional sub-directory names to the reference directory. (If your sub-directories are named differently, you will still need to select them individually, however, the reference directory will then be used as a starting point.) When you click OK, your directory choices are stored for future use in the file PPdirconfig.json in the plugin installation directory. The Pseudopotential version line on the Setup tab should now change, reflecting the available choices for the pseudopotential. To make sure you have specified the correct directories for each type of PP, you can go over the different exchange-correlation (XC) functionals and the PP types, and make sure none of them displays the no pseudopotential found message on the Pseudopotential version line. (Only the basic XC types need to be checked, i.e. LDA, PBE and GGA-91.) 5

9 CHAPTER 3. HOW TO USE THE VASP SCRIPTER OVERVIEW Open the VASP Scripter with the AgGaS2 structure, as illustrated in the section called Starting the VASP Scripter. You will see a number of tabs which control different aspects of a VASP simulation. Setup (set the type of calculation to be performed, the exchange-correlation functional, and the pseudopotentials) Accuracy (set the energy cut-off, k-point sampling, and other accuracy parameters) Electrons (set further parameters for calculating electronic states at given ionic positions) Ions (control the behavior during ionic motion, optimization/relaxation or molecular dynamics) Properties (select desired properties to be calculated) Configuration (shows the initial atomic positions, created with other VNL tools) Tip Most of the controls in each tab have context help; hover the mouse pointer over the control to see it. In the following you will learn about each tab in a little more detail. SETUP First switch to the Setup tab. 6

10 SELECTING THE TASK Presently, the Scripter can be used for setting up the following types of VASP calculations: Structural optimization (relaxation) Static self-consistent (SC) runs Static non-self-consistent runs; you will need to provide a charge density file (CHGCAR) from a previous self-consistent calculation (see the the section called Properties ). Molecular dynamics Nudged Elastic Band, (requires that a NEB configuration is dropped onto the Scripter) Note Charged super cells are not presently supported. 7

11 EXCHANGE-CORRELATION Use the corresponding drop-down lists to select the exchange-correlation functional and pseudopotential type, and use the checkbox to specify whether spin-orbit coupling should be included or not. To perform a spin-polarized calculation, select the proper exchange-correlation functional from the drop box (e.g. LSDA or SPBE instead of LDA or PBE). The choice will be reflected by the state of the "Spin polarized" checkbox. Tip Including spin-orbit interaction results in a much more intensive computation, in part due to limitations of VASP. For a scalar-relativistic calculation, keep the "Spin-orbit coupling" checkbox unchecked. ELEMENT-SPECIFIC SETTINGS The drop-down box will list the elements in your selected configuration. If any of these elements has more than one variant of a pseudopotential (e.g. differing by whether semi-core states are treated as valence electrons or not), you can select which version you want to use via the checkboxes that are displayed in this case. If you have selected an XC functional that uses on-site terms (e.g. LDA+U), you can specify the on-site parameters and the quantum number l of the orbitals to which these parameters would be applied for each species. Use l=-1 to turn the on-site potential off. ACCURACY Next switch to the Accuracy tab. 8

12 Here, you can select the general precision settings (VASP's PREC tag, defining the FFT meshes and the default energy cut-off), and the size and type of the k-point sampling mesh. The number of divisions along each unit vector can be chosen independently, or you can use the buttons on the right to quickly make the mesh more dense or sparse. You can manually set the energy cutoff for the plane-wave basis set (e.g. if you need to keep it constant across a series of calculations involving different structures with different elements); otherwise the general precision setting will determine the default cut-off, depending on the elements in your configuration. ELECTRONS On the Electrons tab, you select the minimization algorithm to be used for optimizing electronic states and the charge density, and the number of bands to include. Note The "Very Fast (RMM-DIIS)" algorithm may lead to incorrect results unless a large number of bands is used. 9

13 In the Smearing box you select the algorithm to broaden the step-like Fermi distribution, and the broadening width Sigma (if applicable). In the Convergence box you select the minimum and maximum number of electronic iterations, and the energy change between iterations that will be used as the stopping criterion. 10

14 Note The electronic stopping criterion also defines the default value for the ionic stopping criterion. IONS If you have selected Structural optimization as the task on the Setup tab, the Ions tab will look like below: You can select how many and how large steps you want to take, the algorithm to use for performing the relaxation, and which of the cell parameters (volume, shape and/or internal parameters) are allowed to relax. Note It is not possible to fix the cell shape and relax both volume and internal positions in a single VASP run. If you make this selection, the Scripter will change it for you. The stopping criterion for the relaxation is, by default, the energy change equal to 10x the electronic stopping criterion. You can specify a different criterion on the Ions tab, either in terms of energy change or in terms of forces. PROPERTIES In the present version of the VASP Scripter, the only available options on the Properties tab are to save the wave functions (to a binary file WAVECAR), and saving the charge density (to a file CHG for visualization and to a file CHGCAR for performing a subsequent non-self-consistent calculation). 11

15 GENERATING THE VASP INPUT FILES Once you are satisfied with your settings, select the directory where you want to save the VASP files, and press the save button in the top left corner (or select Save from the menu). The Scripter will write the VASP input files to this directory, overwriting any existing files (make sure you have selected the correct directory!). You should now be able to use the generated files to launch a VASP calculation, either directly in the directory where they were saved, or by copying this directory to a different machine where VASP is installed. 12

16 CHAPTER 4. SETTING UP A NEB SIMULATION FOR VASP The following example illustrates how to setup a Nudged Elastic Band calculation from the VASP Scripter. The example you will consider is the adsorption of hydrogen on a Si (100) 2x1 surface. SETTING UP THE NEB OBJECT Note You will use the new "Builder 2012" in VNL to set up the calculation. In ATK 11.8 this builder is still in a prototype state, with limited functionality. It will be released in its full version in ATK 12.2 with many new functions for building geometries. Start the preview edition of the new Builder by selecting Tools Builder 2012 from the menu in the VNL main window. Download and save the script (si100-2x1.py). # Set up lattice vector_a = [7.68, 0.00, 0.00]*Angstrom vector_b = [0.00, 3.84, 0.00]*Angstrom vector_c = [0.00, 0.00, 21.00]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements elements = [Hydrogen, Hydrogen, Hydrogen, Hydrogen, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Hydrogen, Hydrogen] # Define coordinates cartesian_coordinates = [[ , , ], [ , , ], [ , , ], [ , , ], [ , , ], [ , , ], [ , , ], [ , , ], [ , , ], [ , , ], [ , , ], [ , , ], [ , , ], 13

17 # Set up configuration bulk_configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, cartesian_coordinates=cartesian_coordinates ) [ , , ], [ , , ], [ , , ], [ , , ], [ , , ], [ , , ], [ , , ], [ , , ], [ , , ]]*Angstrom Click the Add button in the lower panel of the Builder and select Add from Files... Import the file si100-2x1.py using the file browser. Tip Alternatively, you can highlight the script text in this tutorial and drag and drop the text directly onto the Builder window. Another possibility is to drag and drop the file from the file browser in the VNL main window. Note The geometry in si100-2x1.py was built in a few easy steps with the ATK12.2 version of the builder. Select the added "Bulk" configuration in the lower panel (called the stash) and press the Copy button. This adds a copy of the configuration to the stash. The new configuration is now the active configuration. Next select the two upper hydrogen atoms (those on the bottom are just to passivate the inactive surface) by holding down Ctrl while clicking on them with the left mouse button. Open the Translate tool in the tool panel on the right. Set the z-distance to 3 Angstrom and press "Apply". 14

18 Next open the Edit Z-matrix tool (also on the tool panel). Set the distance between the hydrogen atoms to 0.7 Ångström - corresponding to a free hydrogen molecule - and press Enter. Note that the last selected atom moves, while the first remains fixed. You have now defined the initial and final states of the reaction path. The next step is to set up the NEB configuration by inserting a number of images between these states. To this end, open the Create Nudged Elastic Band tool in the right-hand panel. Select the two configurations by first clicking the initial Si(100) configuration in the stash. Then click the second configuration (the one with the free hydrogen molecule) while holding down Ctrl. Set the maximum distance between images to 0.5 Ångström in the tool panel. Press the Create NEB button. The NEB object will now be built and added to the stash, as illustrated below. Push the play button to see the different initial configurations in the reaction pathway. 15

19 GENERATING THE VASP NEB INPUT FILES To set up the a NEB calculation with VASP, open the VASP Scripter. Then drag the NEB configuration from the stash onto the VASP Scripter. Now set up the appropriate calculation parameters at each tab. When you are done, select the directory where the NEB calculation should be saved and press "Save". You are now ready to perform the NEB optimization using VASP. 16