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Lourdes Horace

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Aug 5, 2024, 4:08:04 AM8/5/24
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VASPis a density-functional theory code using pseudopotentials orthe projector-augmented wave method and a plane wave basis set. Thisinterface makes it possible to use VASP as a calculator in ASE, andalso to use ASE as a post-processor for an already performed VASPcalculation.

You need to add an environment variable which contains instructionson how to execute VASP. This must be stored as either ASE_VASP_COMMANDor VASP_COMMAND (the latter for legacy reasons). This could looksomething like this:


The following environment variable can be used to automatically copy thevan der Waals kernel to the calculation directory. The kernel is needed forvdW calculations, see VASP vdW wiki, for more details. The kernel is lookedfor whenever luse_vdw=True.


Net charge per unit cell given inunits of the elementary charge, asan alternative to specifyingnelect. Note: Thenow-deprecated net_chargeparameter worked just like this onebut with the sign inverted.


For parameters in the list without default value given, VASP will setthe default value. Most of the parameters used in the VASP INCAR fileare allowed keywords. See the official VASP manual for more details.Input arguments specific to the VTST add-ons for VASP are also supported.


For many elements, VASP is distributed with a choice ofpseudopotential setups. These may be hard/soft variants of thepseudopotential or include additional valence electrons.Three base setups are provided:


will treat the Ga atom in position 3 (i.e. the fourth atom) of theatoms object as special, with an additional 10 d-block valenceelectrons, while other Ga atoms use the default 3-electron setup andother elements use their own default setups. The positional index maybe quoted as a string (e.g. '3': 'Ga_d').


In this example the initial magnetic moments are assigned to the atomswhen defining the Atoms object. The calculator will detect that at leastone of the atoms has a non-zero magnetic moment and a spin-polarizedcalculation will automatically be performed. The ASE generated INCARfile will look like:


Alternatively, the k-point density can be set in the INCAR file withthese flags as described in the VASP manual. Ifkspacing is set, the ASE calculator will not write out a KPOINTSfile.


In VASP it is possible to define an automatic grid and shift the origin point.This function is not currently included in the ASE calculator. The same result can be achieved by using ase.dft.kpoints.monkhorst_pack() to generate an explicit list of k-points (see below) and simply adding a constant vector to the matrix.For example,


If an n-by-3 or n-by-4 array is used for kpts,this is interpreted as a list of n explicit k-points and an appropriate KPOINTS file is generated.The fourth column, if provided, sets the sample weighting of each point.Otherwise, all points are weighted equally.


Usually in these cases it is desirable to set the reciprocal parameter to True,so that the k-point vectors are given relative to the reciprocal lattice.Otherwise, they are taken as being in Cartesian space.


However, ASE offers a convenient ASE specific keyword to enable these, by using a dictionary construction, through theldau_luj keyword. If the user does not explicitly set ldau=False, then ldau=True will automaticallybe set if ldau_luj is set.For example:


Only Monkhorst-Pack and Gamma-centered k-point sampling are supportedfor restart at the moment. Some INCAR parameters may not beimplemented for restart yet. Please report any problems to the ASE mailinglist.


The restart parameter can be used , as the name suggest to continue a job from where aprevious calculation finished. Furthermore, it can be used to extract data froman already performed calculation. For example, to get the total potential energyof the sodium chloride molecule in the previous section, without performing any additionalcalculations, in the directory of the previous calculation do:


The results from the Vasp calculator can exported as a dictionary, which can then be saved in a JSON format,which enables easy and compressed sharing and storing of the input & outputs ofa VASP calculation. The following methods of Vasp can be used for this purpose:


At a later stage, that file can be used to restore a the input and (simple) output parameters of a calculation,without the need to copy around all the VASP specific files, using either the ase.io.jsonio.read_json() functionor the Vasp fromdict() method.


The dictionary object, which is created from the todict() method, also contains information about the ASEand VASP version which was used at the time of the calculation, through thease_version and vasp_version keys.


The ASE calculator contains no information about the wavefunctions or charge densities, so these are NOT storedin the dictionary or JSON file, and therefore results may vary on a restarted calculation.


Vibrational analysis can be performed using the Vibrationsclass or using the VASP internals (e.g. with IBRION=5).When using IBRION=5-8, the corresponding vibrationalanalysis can be represented by retrieving a VibrationsDataobject from the calculator using ase.calculators.vasp.Vasp.get_vibrations().From the OUTCAR, the energies of all modes can be retrieved usingase.calculators.vasp.Vasp.read_vib_freq().


We can use the directory keyword to control the folder in which the calculationstake place, and keep a more structured folder structure. The following script does theinitial calculations, in order to construct the band structure for silicon


As this calculation might be longer, depending on your system, it maybe more convenient to split the plotting into a separate file, as allof the VASP data is written to files. The plotting can then be achievedby using the restart keyword, in a second script


The Vasp calculator also allows for quick access to the Density of States (DOS), through the ASE DOS module, see DOS.Quick access to this function, however, can be found by using the get_dos() function:


Because VASP is a licensed software, we need to give users explicit access to the VASP modules on Quest. VASP provides Quest admins with access to a portal where we can use the e-mail associated with your VASP access/license to verify that you can use VASP on Quest. Please send an e-mail to quest...@northwestern.edu stating both that you would like to use VASP on Quest and the e-mail address associated with your VASP access/license.


Once you have received confirmation that you have been given access to use the VASP modules on Quest, you can start to run VASP simulations. Please find examples of running VASP 5.4.4 on Quest below. We provide two examples. The first is for the VASP 5.4.4 install that is available through the default set of modules. The second is for a new build of VASP (against newer OpenMPI and Intel Compilers) that is available through specifying an additional non-default module location.


We are working to provide a new build of VASP 5.4.4 which uses newer OpenMPI and Intel Compilers. This build can be used on Quest but is available through specifying an additional non-default module location.


You may find that you or your lab wants to have your own build of VASP. To help with this, we provide a Bash build script which will load the appropriate modules for building VASP and an appropriate makefile.include for building VASP on Quest.


The following Bash script can be used to build VASP in combination with makefile.include below. This makefile.include will produce the following programs: vasp_gam, vasp_ncl, and vasp_std. Please note that we are not including any build templates for compiling VASP with beef, vtst, etc. If you need help compiling your own copy of VASP on Quest with any of these additional libraries/extensions, you can reach out to us at quest...@northwestern.edu for support.


The following Bash script can be used to build VASP in combination with makefile.include below. This makefile.include will produce the following programs: vasp_gam, vasp_ncl, vasp_std, vasp_gpu_ncl, and vasp_gpu. Please note that we are not including any build templates for compiling VASP with beef, vtst, etc. If you need help compiling your own copy of VASP on Quest with any of these additional libraries/extensions, you can reach out to us at quest...@northwestern.edu for support.


The following Bash script can be used to build VASP with HDF5 enabled in combination with makefile.include below. This makefile.include will produce the following programs: vasp_gam, vasp_ncl, vasp_std. Please note that we are not including any build templates for compiling VASP with beef, vtst, etc. If you need help compiling your own copy of VASP on Quest with any of these additional libraries/extensions, you can reach out to us at quest...@northwestern.edu for support.


The following Bash script can be used to build VASP with GPU support enabled in combination with makefile.include below. This makefile.include will produce the following programs: vasp_gam, vasp_ncl, vasp_std. Please note that we are not including any build templates for compiling VASP with beef, vtst, etc. If you need help compiling your own copy of VASP on Quest with any of these additional libraries/extensions, you can reach out to us at quest...@northwestern.edu for support.


SPOSCAR is the perfect supercell structure, phonopy_disp.yamlcontains the information on displacements, and POSCAR-number arethe supercells with atomic displacements. POSCAR-numbercorresponds to the different atomic displacements written inphonopy_disp.yaml.


Force constants are calculated using the structure filesPOSCAR-number (from forces on atoms) or using the SPOSCARfile. In the case of VASP, the calculations for the finitedisplacement method can be proceeded just using thePOSCAR-number files as POSCAR of VASP calculations. Anexample of the INCAR is as follows:


To activate non-analytical term correction, BORN (optional) isrequired. This file contains the information of Born effective chargeand dielectric constant. These physical values are also obtained fromthe first-principles calculations, e.g., by using VASP, pwscf, etc. Inthe case of VASP, an example of INCAR will be as shown below:

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