pymatgen.io.vasp.sets module

This module defines the VaspInputSet abstract base class and a concrete implementation for the parameters developed and tested by the core team of pymatgen, including the Materials Virtual Lab, Materials Project and the MIT high throughput project. The basic concept behind an input set is to specify a scheme to generate a consistent set of VASP inputs from a structure without further user intervention. This ensures comparability across runs.

Read the following carefully before implementing new input sets:

  1. 99% of what needs to be done can be done by specifying user_incar_settings to override some of the defaults of various input sets. Unless there is an extremely good reason to add a new set, DO NOT add one. E.g., if you want to turn the hubbard U off, just set “LDAU”: False as a user_incar_setting.

  2. All derivative input sets should inherit from one of the usual MPRelaxSet or MITRelaxSet, and proper superclass delegation should be used where possible. In particular, you are not supposed to implement your own as_dict or from_dict for derivative sets unless you know what you are doing. Improper overriding the as_dict and from_dict protocols is the major cause of implementation headaches. If you need an example, look at how the MPStaticSet or MPNonSCFSets are constructed.

The above are recommendations. The following are UNBREAKABLE rules: 1. All input sets must take in a structure or list of structures as the first

argument.

  1. user_incar_settings, user_kpoints_settings and user_<whatever>_settings are ABSOLUTE. Any new sets you implement must obey this. If a user wants to override your settings, you assume he knows what he is doing. Do not magically override user supplied settings. You can issue a warning if you think the user is wrong.

  2. All input sets must save all supplied args and kwargs as instance variables. E.g., self.my_arg = my_arg and self.kwargs = kwargs in the __init__. This ensures the as_dict and from_dict work correctly.

exception BadInputSetWarning[source]

Bases: UserWarning

class DictSet(structure, config_dict, files_to_transfer=None, user_incar_settings=None, user_kpoints_settings=None, user_potcar_settings=None, constrain_total_magmom=False, sort_structure=True, potcar_functional='PBE', force_gamma=False, reduce_structure=None, vdw=None, use_structure_charge=False, standardize=False, sym_prec=0.1, international_monoclinic=True)[source]

Bases: pymatgen.io.vasp.sets.VaspInputSet

Concrete implementation of VaspInputSet that is initialized from a dict settings. This allows arbitrary settings to be input. In general, this is rarely used directly unless there is a source of settings in yaml format (e.g., from a REST interface). It is typically used by other VaspInputSets for initialization.

Special consideration should be paid to the way the MAGMOM initialization for the INCAR is done. The initialization differs depending on the type of structure and the configuration settings. The order in which the magmom is determined is as follows:

  1. If the site itself has a magmom setting, that is used.

  2. If the species on the site has a spin setting, that is used.

  3. If the species itself has a particular setting in the config file, that is used, e.g., Mn3+ may have a different magmom than Mn4+.

  4. Lastly, the element symbol itself is checked in the config file. If there are no settings, VASP’s default of 0.6 is used.

Parameters
  • structure (Structure) – The Structure to create inputs for.

  • config_dict (dict) – The config dictionary to use.

  • files_to_transfer (dict) – A dictionary of {filename: filepath}. This allows the transfer of files from a previous calculation.

  • user_incar_settings (dict) –

    User INCAR settings. This allows a user to override INCAR settings, e.g., setting a different MAGMOM for various elements or species. Note that in the new scheme, ediff_per_atom and hubbard_u are no longer args. Instead, the config_dict supports EDIFF_PER_ATOM and EDIFF keys. The former scales with # of atoms, the latter does not. If both are present, EDIFF is preferred. To force such settings, just supply user_incar_settings={“EDIFF”: 1e-5, “LDAU”: False} for example. The keys ‘LDAUU’, ‘LDAUJ’, ‘LDAUL’ are special cases since pymatgen defines different values depending on what anions are present in the structure, so these keys can be defined in one of two ways, e.g. either {“LDAUU”:{“O”:{“Fe”:5}}} to set LDAUU for Fe to 5 in an oxide, or {“LDAUU”:{“Fe”:5}} to set LDAUU to 5 regardless of the input structure.

    If a None value is given, that key is unset. For example, {“ENCUT”: None} will remove ENCUT from the incar settings.

  • user_kpoints_settings (dict or Kpoints) – Allow user to override kpoints setting by supplying a dict E.g., {“reciprocal_density”: 1000}. User can also supply Kpoints object. Default is None.

  • (dict (user_potcar_settings) – Allow user to override POTCARs. E.g., {“Gd”: “Gd_3”}. This is generally not recommended. Default is None.

  • constrain_total_magmom (bool) – Whether to constrain the total magmom (NUPDOWN in INCAR) to be the sum of the expected MAGMOM for all species. Defaults to False.

  • sort_structure (bool) – Whether to sort the structure (using the default sort order of electronegativity) before generating input files. Defaults to True, the behavior you would want most of the time. This ensures that similar atomic species are grouped together.

  • potcar_functional (str) – Functional to use. Default (None) is to use the functional in Potcar.DEFAULT_FUNCTIONAL. Valid values: “PBE”, “PBE_52”, “PBE_54”, “LDA”, “LDA_52”, “LDA_54”, “PW91”, “LDA_US”, “PW91_US”.

  • force_gamma (bool) – Force gamma centered kpoint generation. Default (False) is to use the Automatic Density kpoint scheme, which will use the Gamma centered generation scheme for hexagonal cells, and Monkhorst-Pack otherwise.

  • reduce_structure (None/str) – Before generating the input files, generate the reduced structure. Default (None), does not alter the structure. Valid values: None, “niggli”, “LLL”.

  • vdw – Adds default parameters for van-der-Waals functionals supported by VASP to INCAR. Supported functionals are: DFT-D2, undamped DFT-D3, DFT-D3 with Becke-Jonson damping, Tkatchenko-Scheffler, Tkatchenko-Scheffler with iterative Hirshfeld partitioning, MBD@rSC, dDsC, Dion’s vdW-DF, DF2, optPBE, optB88, optB86b and rVV10.

  • use_structure_charge (bool) – If set to True, then the public variable used for setting the overall charge of the structure (structure.charge) is used to set the NELECT variable in the INCAR Default is False (structure’s overall charge is not used)

  • standardize (float) – Whether to standardize to a primitive standard cell. Defaults to False.

  • sym_prec (float) – Tolerance for symmetry finding.

  • international_monoclinic (bool) – Whether to use international convention (vs Curtarolo) for monoclinic. Defaults True.

incar

Incar object

kpoints

Writes out a KPOINTS file using the fully automated grid method. Uses Gamma centered meshes for hexagonal cells and Monk grids otherwise.

Algorithm:

Uses a simple approach scaling the number of divisions along each reciprocal lattice vector proportional to its length.

nelect

Gets the default number of electrons for a given structure.

poscar

Poscar object

structure
write_input(output_dir, make_dir_if_not_present=True, include_cif=False)[source]

Writes a set of VASP input to a directory.

Parameters
  • output_dir (str) – Directory to output the VASP input files

  • make_dir_if_not_present (bool) – Set to True if you want the directory (and the whole path) to be created if it is not present.

  • include_cif (bool) – Whether to write a CIF file in the output directory for easier opening by VESTA.

class MITMDSet(structure, start_temp, end_temp, nsteps, time_step=2, spin_polarized=False, **kwargs)[source]

Bases: pymatgen.io.vasp.sets.MITRelaxSet

Clas for writing a vasp md run. This DOES NOT do multiple stage runs.

Parameters
  • structure (Structure) – Input structure.

  • start_temp (int) – Starting temperature.

  • end_temp (int) – Final temperature.

  • nsteps (int) – Number of time steps for simulations. NSW parameter.

  • time_step (int) – The time step for the simulation. The POTIM parameter. Defaults to 2fs.

  • spin_polarized (bool) – Whether to do spin polarized calculations. The ISPIN parameter. Defaults to False.

  • **kwargs – Other kwargs supported by DictSet.

kpoints

Writes out a KPOINTS file using the fully automated grid method. Uses Gamma centered meshes for hexagonal cells and Monk grids otherwise.

Algorithm:

Uses a simple approach scaling the number of divisions along each reciprocal lattice vector proportional to its length.

class MITNEBSet(structures, unset_encut=False, **kwargs)[source]

Bases: pymatgen.io.vasp.sets.MITRelaxSet

Class for writing NEB inputs. Note that EDIFF is not on a per atom basis for this input set.

Parameters
  • unset_encut (bool) – Whether to unset ENCUT.

  • **kwargs – Other kwargs supported by DictSet.

poscar

Poscar object

poscars
write_input(output_dir, make_dir_if_not_present=True, write_cif=False, write_path_cif=False, write_endpoint_inputs=False)[source]

NEB inputs has a special directory structure where inputs are in 00, 01, 02, ….

Parameters
  • output_dir (str) – Directory to output the VASP input files

  • make_dir_if_not_present (bool) – Set to True if you want the directory (and the whole path) to be created if it is not present.

  • write_cif (bool) – If true, writes a cif along with each POSCAR.

  • write_path_cif (bool) – If true, writes a cif for each image.

  • write_endpoint_inputs (bool) – If true, writes input files for running endpoint calculations.

class MITRelaxSet(structure, **kwargs)[source]

Bases: pymatgen.io.vasp.sets.DictSet

Standard implementation of VaspInputSet utilizing parameters in the MIT High-throughput project. The parameters are chosen specifically for a high-throughput project, which means in general pseudopotentials with fewer electrons were chosen.

Please refer:

A Jain, G. Hautier, C. Moore, S. P. Ong, C. Fischer, T. Mueller,
K. A. Persson, G. Ceder. A high-throughput infrastructure for density
functional theory calculations. Computational Materials Science,
2011, 50(8), 2295-2310. doi:10.1016/j.commatsci.2011.02.023
CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF': 1e-05, 'ENCUT': 520, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'ISYM': 0, 'LDAU': True, 'LDAUJ': {'F': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'O': {'Ag': 0, 'Co': 0, 'Cr': 0, 'Cu': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Nb': 0, 'Ni': 0, 'Re': 0, 'Ta': 0, 'V': 0, 'W': 0}, 'S': {'Fe': 0, 'Mn': 0}}, 'LDAUL': {'F': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'O': {'Ag': 2, 'Co': 2, 'Cr': 2, 'Cu': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Nb': 2, 'Ni': 2, 'Re': 2, 'Ta': 2, 'V': 2, 'W': 2}, 'S': {'Fe': 2, 'Mn': 2.5}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'O': {'Ag': 1.5, 'Co': 3.4, 'Cr': 3.5, 'Cu': 4, 'Fe': 4.0, 'Mn': 3.9, 'Mo': 4.38, 'Nb': 1.5, 'Ni': 6, 'Re': 2, 'Ta': 2, 'V': 3.1, 'W': 4.0}, 'S': {'Fe': 1.9, 'Mn': 2.5}}, 'LORBIT': '11', 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 5, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 200, 'NELMIN': 6, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'length': 25}, 'POTCAR': {'Ac': {'hash': 'd6854224d20e3de6e6fd7399503791d1', 'symbol': 'Ac'}, 'Ag': {'hash': 'e8ffa02fe3f3a51338ac1ac91ae968b9', 'symbol': 'Ag'}, 'Al': {'hash': 'a6fd9a46aec185f4ad2acd0cbe4ae2fa', 'symbol': 'Al'}, 'Ar': {'hash': 'e782fc6292623b396091bf8b871c272f', 'symbol': 'Ar'}, 'As': {'hash': '8005364db225a254e52cba350bedd032', 'symbol': 'As'}, 'Au': {'hash': 'a9182d436a13194b744640ac940ab9b0', 'symbol': 'Au'}, 'B': {'hash': '18ed2875dfa6305324cec3d7d59273ae', 'symbol': 'B'}, 'Ba': {'hash': 'c0477913afb63dfae3439f3534fbf0ed', 'symbol': 'Ba_sv'}, 'Be': {'hash': 'fb974e44d56a8c62c6bbd1a1eb70c3a7', 'symbol': 'Be'}, 'Bi': {'hash': 'e29661c79d59abae3b3ba69eae24b1a5', 'symbol': 'Bi'}, 'Br': {'hash': '40f9594b4506684a69158c8975cfb9d6', 'symbol': 'Br'}, 'C': {'hash': 'c0a8167dbb174fe492a3db7f5006c0f8', 'symbol': 'C'}, 'Ca': {'hash': 'eb006721e214c04b3c13146e81b3a27d', 'symbol': 'Ca_sv'}, 'Cd': {'hash': '0506b2d0ac28d5fe2b5ced77a701aa86', 'symbol': 'Cd'}, 'Ce': {'hash': 'ff3a09f2ff91798e58eb4b9854e9be4a', 'symbol': 'Ce'}, 'Cl': {'hash': '779b9901046c78fe51c5d80224642aeb', 'symbol': 'Cl'}, 'Co': {'hash': 'b169bca4e137294d2ab3df8cbdd09083', 'symbol': 'Co'}, 'Cr': {'hash': '82c14307937c7509fda4e9bc023d243d', 'symbol': 'Cr'}, 'Cs': {'hash': '096b53a7d80cc0086976bcda50d536e5', 'symbol': 'Cs_sv'}, 'Cu': {'hash': '8ca4e43a30de0c397e51f16bbb20d678', 'symbol': 'Cu'}, 'Dy': {'hash': 'd4a05220ab0a2d4c03a76872ea724a1e', 'symbol': 'Dy_3'}, 'Er': {'hash': 'daa65a04877317f8c3c593ddeaa8a132', 'symbol': 'Er_3'}, 'Eu': {'hash': 'd466d046adf21f6146ee9644049ea268', 'symbol': 'Eu'}, 'F': {'hash': '180141c33d032bfbfff30b3bea9d23dd', 'symbol': 'F'}, 'Fe': {'hash': '9530da8244e4dac17580869b4adab115', 'symbol': 'Fe'}, 'Ga': {'hash': '6e0b9d58412b1bfcd7252aff13d476c2', 'symbol': 'Ga'}, 'Gd': {'hash': '1f0d42b1e5f6769d319d3f247992aeb9', 'symbol': 'Gd'}, 'Ge': {'hash': '79e788788c31e196a460553010512d3f', 'symbol': 'Ge'}, 'H': {'hash': 'bb43c666e3d36577264afe07669e9582', 'symbol': 'H'}, 'He': {'hash': '47f9434aa3db96c85d7c4b3e4c2df09b', 'symbol': 'He'}, 'Hf': {'hash': 'b113f150cbf9c736f8244a6c25b0482e', 'symbol': 'Hf'}, 'Hg': {'hash': 'c2f15dfb5fd53396c5427635e5019160', 'symbol': 'Hg'}, 'Ho': {'hash': '661891464a27e87cf7e1324dd1893b77', 'symbol': 'Ho_3'}, 'I': {'hash': 'f4ff16a495dd361ff5824ee61b418bb0', 'symbol': 'I'}, 'In': {'hash': '7df38c0cdb4e6d9a9b93f09d690bb3ae', 'symbol': 'In'}, 'Ir': {'hash': 'dbcf7dcc6f4fb40df7b3d26904f60a66', 'symbol': 'Ir'}, 'K': {'hash': '3e84f86d37f203a4fb01de36af57e430', 'symbol': 'K_sv'}, 'Kr': {'hash': '39b9b85ae3982e6c012fb549b2840ce5', 'symbol': 'Kr'}, 'La': {'hash': '9b3ce03d18f7c0b40471a817ff91b287', 'symbol': 'La'}, 'Li': {'hash': '65e83282d1707ec078c1012afbd05be8', 'symbol': 'Li'}, 'Lu': {'hash': 'd40a90babf1224b88ffb4c3273ac3848', 'symbol': 'Lu_3'}, 'Mg': {'hash': '1771eb72adbbfa6310d66e7517e49930', 'symbol': 'Mg'}, 'Mn': {'hash': 'd082dba29b57ab59b3165e605dbf71b8', 'symbol': 'Mn'}, 'Mo': {'hash': '84e18fd84a98e3d7fa8f055952410df0', 'symbol': 'Mo_pv'}, 'N': {'hash': 'b98fd027ddebc67da4063ff2cabbc04b', 'symbol': 'N'}, 'Na': {'hash': '1a89e79f7e21d99e8cf5788979f6a987', 'symbol': 'Na'}, 'Nb': {'hash': '7bcee99a4dc3094be0f9fd7961c02966', 'symbol': 'Nb_pv'}, 'Nd': {'hash': '0c64e63070cee837c967283fffa001df', 'symbol': 'Nd'}, 'Ne': {'hash': '52064eee378b9e37a295a674f1c278f0', 'symbol': 'Ne'}, 'Ni': {'hash': '653f5772e68b2c7fd87ffd1086c0d710', 'symbol': 'Ni'}, 'Np': {'hash': '20cb30b714200c4db870550b288ac4cd', 'symbol': 'Np'}, 'O': {'hash': '7a25bc5b9a5393f46600a4939d357982', 'symbol': 'O'}, 'Os': {'hash': '35c2cb48d48a9c38c40fb82bbe70626d', 'symbol': 'Os'}, 'P': {'hash': '7dc3393307131ae67785a0cdacb61d5f', 'symbol': 'P'}, 'Pa': {'hash': 'a1fdb1089d0727f415416ec8082246ba', 'symbol': 'Pa'}, 'Pb': {'hash': '704c2c967247d7f84090d2536c91877d', 'symbol': 'Pb'}, 'Pd': {'hash': 'a395eb3aaf2fcab12fac3030a1146f61', 'symbol': 'Pd'}, 'Pm': {'hash': 'a2c9485ea86b2a7cf175077e6e5c7b3e', 'symbol': 'Pm'}, 'Pr': {'hash': '92f191499bf5346ea652bb806350ad87', 'symbol': 'Pr'}, 'Pt': {'hash': 'a604ea3c6a9cc23c739b762f625cf449', 'symbol': 'Pt'}, 'Pu': {'hash': 'f1d01e845dccc52d448679911f301a73', 'symbol': 'Pu'}, 'Rb': {'hash': 'e447c648d870b066b3514e6b800727ab', 'symbol': 'Rb_pv'}, 'Re': {'hash': '72385e193c92a8acfe17ea49004c2be1', 'symbol': 'Re'}, 'Rh': {'hash': '2c3dba3fcc6058ca1b1cfa75e45084bc', 'symbol': 'Rh'}, 'Ru': {'hash': '7925f4d4b68076d70af7cd86eef9ba8d', 'symbol': 'Ru_pv'}, 'S': {'hash': 'd368db6899d8839859bbee4811a42a88', 'symbol': 'S'}, 'Sb': {'hash': 'd82c022b02fc5344e85bd1909f9ee3e7', 'symbol': 'Sb'}, 'Sc': {'hash': 'dc386f505ad0c43385a7715b4111cb75', 'symbol': 'Sc_sv'}, 'Se': {'hash': '67a8804ede9f1112726e3d136978ef19', 'symbol': 'Se'}, 'Si': {'hash': 'b2b0ea6feb62e7cde209616683b8f7f5', 'symbol': 'Si'}, 'Sm': {'hash': 'e5e274e7cd99602ca81d146155abdf88', 'symbol': 'Sm_3'}, 'Sn': {'hash': '849b0795e148f93113a06be8fd5f5001', 'symbol': 'Sn_d'}, 'Sr': {'hash': 'ca6a5429c120a0ab705824386a76fe5b', 'symbol': 'Sr_sv'}, 'Ta': {'hash': 'd4e2cfe9338ef80da592d5bb9dc782c7', 'symbol': 'Ta'}, 'Tb': {'hash': '0790955c547003956c0fd4f080f7f508', 'symbol': 'Tb_3'}, 'Tc': {'hash': '9592642886319309a39d55c5717c6f48', 'symbol': 'Tc'}, 'Te': {'hash': '72719856e22fb1d3032df6f96d98a0f2', 'symbol': 'Te'}, 'Th': {'hash': 'aea79f322180fa6f0bfa74cb2a156dcf', 'symbol': 'Th'}, 'Ti': {'hash': 'c617e8b539c3f44a0ab6e8da2a92d318', 'symbol': 'Ti'}, 'Tl': {'hash': '2aa0d5406aaab7ebfbc761da382f1352', 'symbol': 'Tl'}, 'Tm': {'hash': '94a07cb7949b01305cb161da0cbfb492', 'symbol': 'Tm_3'}, 'U': {'hash': '72702eabbb1bc02b4167590dc848ed5d', 'symbol': 'U'}, 'V': {'hash': '7f1297a2e1d963e2a4d81b61f85e4ded', 'symbol': 'V_pv'}, 'W': {'hash': '2a33e0d5c700640535f60ac0a12177ab', 'symbol': 'W_pv'}, 'Xe': {'hash': '338472e581f58b41d37c002a5e22353b', 'symbol': 'Xe'}, 'Y': {'hash': '4ed187e77cd54f198bb88020278b143d', 'symbol': 'Y_sv'}, 'Yb': {'hash': '9f472bd422f640710f7d93e2d9ce89f4', 'symbol': 'Yb'}, 'Zn': {'hash': 'e35ee27f8483a63bb68dbc236a343af3', 'symbol': 'Zn'}, 'Zr': {'hash': 'd221d2c0bac4f8e81af2f5c42a314274', 'symbol': 'Zr'}}}
class MPHSEBSSet(structure, user_incar_settings=None, added_kpoints=None, mode='Gap', reciprocal_density=None, copy_chgcar=True, kpoints_line_density=20, **kwargs)[source]

Bases: pymatgen.io.vasp.sets.MPHSERelaxSet

Implementation of a VaspInputSet for HSE band structure computations. Remember that HSE band structures must be self-consistent in VASP. A band structure along symmetry lines for instance needs BOTH a uniform grid with appropriate weights AND a path along the lines with weight 0.

Thus, the “Uniform” mode is just like regular static SCF but allows adding custom kpoints (e.g., corresponding to known VBM/CBM) to the uniform grid that have zero weight (e.g., for better gap estimate).

The “Gap” mode behaves just like the “Uniform” mode, however, if starting from a previous calculation, the VBM and CBM k-points will automatically be added to added_kpoints.

The “Line” mode is just like Uniform mode, but additionally adds k-points along symmetry lines with zero weight.

Parameters
  • structure (Structure) – Structure to compute

  • user_incar_settings (dict) – A dict specifying additional incar settings

  • added_kpoints (list) – a list of kpoints (list of 3 number list) added to the run. The k-points are in fractional coordinates

  • mode (str) – “Line” - generate k-points along symmetry lines for bandstructure. “Uniform” - generate uniform k-points grid.

  • reciprocal_density (int) – k-point density to use for uniform mesh.

  • copy_chgcar (bool) – Whether to copy the CHGCAR of a previous run.

  • kpoints_line_density (int) – k-point density for high symmetry lines

  • **kwargs (dict) – Any other parameters to pass into DictSet.

classmethod from_prev_calc(prev_calc_dir, **kwargs)[source]

Generate a set of Vasp input files for HSE calculations from a directory of previous Vasp run.

Parameters
  • prev_calc_dir (str) – Directory containing the outputs (vasprun.xml and OUTCAR) of previous vasp run.

  • **kwargs – All kwargs supported by MPHSEBSStaticSet, other than prev_structure which is determined from the previous calc dir.

kpoints

Writes out a KPOINTS file using the fully automated grid method. Uses Gamma centered meshes for hexagonal cells and Monk grids otherwise.

Algorithm:

Uses a simple approach scaling the number of divisions along each reciprocal lattice vector proportional to its length.

override_from_prev_calc(prev_calc_dir='.')[source]

Update the input set to include settings from a previous calculation.

Parameters

prev_calc_dir (str) – The path to the previous calculation directory.

Returns

The input set with the settings (structure, k-points, incar, etc) updated using the previous VASP run.

class MPHSERelaxSet(structure, **kwargs)[source]

Bases: pymatgen.io.vasp.sets.DictSet

Same as the MPRelaxSet, but with HSE parameters.

CONFIG = {'INCAR': {'ALGO': 'All', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'HFSCREEN': 0.2, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': 0, 'ISPIN': 2, 'LHFCALC': True, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 5, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'PRECFOCK': 'Fast', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 50}, 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}}
class MPMDSet(structure, start_temp, end_temp, nsteps, spin_polarized=False, **kwargs)[source]

Bases: pymatgen.io.vasp.sets.MPRelaxSet

This a modified version of the old MITMDSet pre 2018/03/12.

This set serves as the basis for the amorphous skyline paper.

  1. Aykol, M.; Dwaraknath, S. S.; Sun, W.; Persson, K. A. Thermodynamic Limit for Synthesis of Metastable Inorganic Materials. Sci. Adv. 2018, 4 (4).

Class for writing a vasp md run. This DOES NOT do multiple stage runs. Precision remains normal, to increase accuracy of stress tensor.

Parameters
  • structure (Structure) – Input structure.

  • start_temp (int) – Starting temperature.

  • end_temp (int) – Final temperature.

  • nsteps (int) – Number of time steps for simulations. NSW parameter.

  • time_step (int) – The time step for the simulation. The POTIM parameter. Defaults to 2fs.

  • spin_polarized (bool) – Whether to do spin polarized calculations. The ISPIN parameter. Defaults to False.

  • **kwargs – Other kwargs supported by DictSet.

kpoints

Writes out a KPOINTS file using the fully automated grid method. Uses Gamma centered meshes for hexagonal cells and Monk grids otherwise.

Algorithm:

Uses a simple approach scaling the number of divisions along each reciprocal lattice vector proportional to its length.

class MPMetalRelaxSet(structure, **kwargs)[source]

Bases: pymatgen.io.vasp.sets.MPRelaxSet

Implementation of VaspInputSet utilizing parameters in the public Materials Project, but with tuning for metals. Key things are a denser k point density, and a

CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 5, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}}
class MPNMRSet(structure, mode='cs', isotopes=None, prev_incar=None, reciprocal_density=100, **kwargs)[source]

Bases: pymatgen.io.vasp.sets.MPStaticSet

Init a MPNMRSet.

Parameters
  • structure (Structure) – Structure to compute

  • mode (str) – The NMR calculation to run “cs”: for Chemical Shift “efg” for Electric Field Gradient

  • isotopes (list) – list of Isotopes for quadrupole moments

  • prev_incar (Incar) – Incar file from previous run.

  • reciprocal_density (int) – density of k-mesh by reciprocal volume (defaults to 100)

  • **kwargs – kwargs supported by MPStaticSet.

incar

Incar object

class MPNonSCFSet(structure, prev_incar=None, mode='line', nedos=2001, reciprocal_density=100, sym_prec=0.1, kpoints_line_density=20, optics=False, copy_chgcar=True, nbands_factor=1.2, small_gap_multiply=None, **kwargs)[source]

Bases: pymatgen.io.vasp.sets.MPRelaxSet

Init a MPNonSCFSet. Typically, you would use the classmethod from_prev_calc to initialize from a previous SCF run.

Parameters
  • structure (Structure) – Structure to compute

  • prev_incar (Incar/string) – Incar file from previous run.

  • mode (str) – Line, Uniform or Boltztrap mode supported.

  • nedos (int) – nedos parameter. Default to 2001.

  • reciprocal_density (int) – density of k-mesh by reciprocal volume (defaults to 100)

  • sym_prec (float) – Symmetry precision (for Uniform mode).

  • kpoints_line_density (int) – Line density for Line mode.

  • optics (bool) – whether to add dielectric function

  • copy_chgcar – Whether to copy the old CHGCAR when starting from a previous calculation.

  • nbands_factor (float) – Multiplicative factor for NBANDS when starting from a previous calculation. Choose a higher number if you are doing an LOPTICS calculation.

  • small_gap_multiply ([float, float]) – When starting from a previous calculation, if the gap is less than 1st index, multiply the default reciprocal_density by the 2nd index.

  • **kwargs – kwargs supported by MPRelaxSet.

classmethod from_prev_calc(prev_calc_dir, **kwargs)[source]

Generate a set of Vasp input files for NonSCF calculations from a directory of previous static Vasp run.

Parameters
  • prev_calc_dir (str) – The directory contains the outputs( vasprun.xml and OUTCAR) of previous vasp run.

  • **kwargs – All kwargs supported by MPNonSCFSet, other than structure, prev_incar and prev_chgcar which are determined from the prev_calc_dir.

incar

Incar object

kpoints

Writes out a KPOINTS file using the fully automated grid method. Uses Gamma centered meshes for hexagonal cells and Monk grids otherwise.

Algorithm:

Uses a simple approach scaling the number of divisions along each reciprocal lattice vector proportional to its length.

override_from_prev_calc(prev_calc_dir='.')[source]

Update the input set to include settings from a previous calculation.

Parameters

prev_calc_dir (str) – The path to the previous calculation directory.

Returns

The input set with the settings (structure, k-points, incar, etc) updated using the previous VASP run.

class MPRelaxSet(structure, **kwargs)[source]

Bases: pymatgen.io.vasp.sets.DictSet

Implementation of VaspInputSet utilizing parameters in the public Materials Project. Typically, the pseudopotentials chosen contain more electrons than the MIT parameters, and the k-point grid is ~50% more dense. The LDAUU parameters are also different due to the different psps used, which result in different fitted values.

CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 5, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}}
class MPSOCSet(structure, saxis=(0, 0, 1), copy_chgcar=True, nbands_factor=1.2, reciprocal_density=100, small_gap_multiply=None, magmom=None, **kwargs)[source]

Bases: pymatgen.io.vasp.sets.MPStaticSet

An input set for running spin-orbit coupling (SOC) calculations.

Parameters
  • structure (Structure) – the structure must have the ‘magmom’ site property and each magnetic moment value must have 3 components. eg: magmom = [[0,0,2], ...]

  • saxis (tuple) – magnetic moment orientation

  • copy_chgcar – Whether to copy the old CHGCAR. Defaults to True.

  • nbands_factor (float) – Multiplicative factor for NBANDS. Choose a higher number if you are doing an LOPTICS calculation.

  • reciprocal_density (int) – density of k-mesh by reciprocal volume.

  • small_gap_multiply ([float, float]) – If the gap is less than 1st index, multiply the default reciprocal_density by the 2nd index.

  • magmom (list[list[float]]) – Override for the structure magmoms.

  • **kwargs – kwargs supported by MPStaticSet.

classmethod from_prev_calc(prev_calc_dir, **kwargs)[source]

Generate a set of Vasp input files for SOC calculations from a directory of previous static Vasp run. SOC calc requires all 3 components for MAGMOM for each atom in the structure.

Parameters
  • prev_calc_dir (str) – The directory contains the outputs( vasprun.xml and OUTCAR) of previous vasp run.

  • **kwargs – All kwargs supported by MPSOCSet, other than structure, prev_incar and prev_chgcar which are determined from the prev_calc_dir.

incar

Incar object

override_from_prev_calc(prev_calc_dir='.')[source]

Update the input set to include settings from a previous calculation.

Parameters

prev_calc_dir (str) – The path to the previous calculation directory.

Returns

The input set with the settings (structure, k-points, incar, etc) updated using the previous VASP run.

class MPStaticSet(structure, prev_incar=None, prev_kpoints=None, lepsilon=False, lcalcpol=False, reciprocal_density=100, small_gap_multiply=None, **kwargs)[source]

Bases: pymatgen.io.vasp.sets.MPRelaxSet

Run a static calculation.

Parameters
  • structure (Structure) – Structure from previous run.

  • prev_incar (Incar) – Incar file from previous run.

  • prev_kpoints (Kpoints) – Kpoints from previous run.

  • lepsilon (bool) – Whether to add static dielectric calculation

  • reciprocal_density (int) – For static calculations, we usually set the reciprocal density by volume. This is a convenience arg to change that, rather than using user_kpoints_settings. Defaults to 100, which is ~50% more than that of standard relaxation calculations.

  • small_gap_multiply ([float, float]) – If the gap is less than 1st index, multiply the default reciprocal_density by the 2nd index.

  • **kwargs – kwargs supported by MPRelaxSet.

classmethod from_prev_calc(prev_calc_dir, **kwargs)[source]

Generate a set of Vasp input files for static calculations from a directory of previous Vasp run.

Parameters
  • prev_calc_dir (str) – Directory containing the outputs( vasprun.xml and OUTCAR) of previous vasp run.

  • **kwargs – All kwargs supported by MPStaticSet, other than prev_incar and prev_structure and prev_kpoints which are determined from the prev_calc_dir.

incar

Incar object

kpoints

Writes out a KPOINTS file using the fully automated grid method. Uses Gamma centered meshes for hexagonal cells and Monk grids otherwise.

Algorithm:

Uses a simple approach scaling the number of divisions along each reciprocal lattice vector proportional to its length.

override_from_prev_calc(prev_calc_dir='.')[source]

Update the input set to include settings from a previous calculation.

Parameters

prev_calc_dir (str) – The path to the previous calculation directory.

Returns

The input set with the settings (structure, k-points, incar, etc) updated using the previous VASP run.

class MVLElasticSet(structure, potim=0.015, **kwargs)[source]

Bases: pymatgen.io.vasp.sets.MPRelaxSet

MVL denotes VASP input sets that are implemented by the Materials Virtual Lab (http://www.materialsvirtuallab.org) for various research.

This input set is used to calculate elastic constants in VASP. It is used in the following work:

Z. Deng, Z. Wang, I.-H. Chu, J. Luo, S. P. Ong.
“Elastic Properties of Alkali Superionic Conductor Electrolytes
from First Principles Calculations”, J. Electrochem. Soc.
2016, 163(2), A67-A74. doi: 10.1149/2.0061602jes

To read the elastic constants, you may use the Outcar class which parses the elastic constants.

Parameters
  • scale (float) – POTIM parameter. The default of 0.015 is usually fine, but some structures may require a smaller step.

  • user_incar_settings (dict) – A dict specifying additional incar settings.

class MVLGBSet(structure, k_product=40, slab_mode=False, is_metal=True, **kwargs)[source]

Bases: pymatgen.io.vasp.sets.MPRelaxSet

Class for writing a vasp input files for grain boundary calculations, slab or bulk.

Parameters
  • structure (Structure) – provide the structure

  • k_product – Kpoint number * length for a & b directions, also for c direction in bulk calculations. Default to 40.

  • slab_mode (bool) – Defaults to False. Use default (False) for a bulk supercell. Use True if you are performing calculations on a slab-like (i.e., surface) of the GB, for example, when you are calculating the work of separation.

  • is_metal (bool) – Defaults to True. This determines whether an ISMEAR of 1 is used (for metals) or not (for insulators and semiconductors) by default. Note that it does not override user_incar_settings, which can be set by the user to be anything desired.

  • **kwargs – Other kwargs supported by MPRelaxSet.

incar

Incar object

kpoints

k_product, default to 40, is kpoint number * length for a & b directions, also for c direction in bulk calculations Automatic mesh & Gamma is the default setting.

class MVLGWSet(structure, prev_incar=None, nbands=None, potcar_functional='PBE_54', reciprocal_density=100, mode='STATIC', copy_wavecar=True, nbands_factor=5, ncores=16, **kwargs)[source]

Bases: pymatgen.io.vasp.sets.DictSet

MVL denotes VASP input sets that are implemented by the Materials Virtual Lab (http://www.materialsvirtuallab.org) for various research. This is a flexible input set for GW calculations.

Note that unlike all other input sets in this module, the PBE_54 series of functional is set as the default. These have much improved performance for GW calculations.

A typical sequence is mode=”STATIC” -> mode=”DIAG” -> mode=”GW” -> mode=”BSE”. For all steps other than the first one (static), the recommendation is to use from_prev_calculation on the preceding run in the series.

Parameters
  • structure (Structure) – Input structure.

  • prev_incar (Incar/string) – Incar file from previous run.

  • mode (str) – Supported modes are “STATIC” (default), “DIAG”, “GW”, and “BSE”.

  • nbands (int) – For subsequent calculations, it is generally recommended to perform NBANDS convergence starting from the NBANDS of the previous run for DIAG, and to use the exact same NBANDS for GW and BSE. This parameter is used by from_previous_calculation to set nband.

  • potcar_functional (str) – Defaults to “PBE_54”.

  • copy_wavecar – Whether to copy the old WAVECAR, WAVEDER and associated files when starting from a previous calculation.

  • nbands_factor (int) – Multiplicative factor for NBANDS when starting from a previous calculation. Only applies if mode==”DIAG”. Need to be tested for convergence.

  • ncores (int) – Numbers of cores used for the calculation. VASP will alter NBANDS if it was not dividable by ncores. Only applies if mode==”DIAG”.

  • **kwargs – All kwargs supported by DictSet. Typically, user_incar_settings is a commonly used option.

CONFIG = {'INCAR': {'ALGO': 'Normal', 'EDIFF': 1e-08, 'IBRION': -1, 'ICHARG': 1, 'ISMEAR': 0, 'ISPIN': 2, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': True, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 5, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'PREC': 'Accurate', 'SIGMA': 0.01}, 'KPOINTS': {'reciprocal_density': 100}, 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag_sv_GW', 'Al': 'Al_GW', 'Ar': 'Ar_GW', 'As': 'As_GW', 'At': 'At_d_GW', 'Au': 'Au_sv_GW', 'B': 'B_GW', 'Ba': 'Ba_sv_GW', 'Be': 'Be_sv_GW', 'Bi': 'Bi_d_GW', 'Br': 'Br_GW', 'C': 'C_GW', 'Ca': 'Ca_sv_GW', 'Cd': 'Cd_sv_GW', 'Ce': 'Ce_GW', 'Cl': 'Cl_GW', 'Co': 'Co_sv_GW', 'Cr': 'Cr_sv_GW', 'Cs': 'Cs_sv_GW', 'Cu': 'Cu_sv_GW', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F_GW', 'Fe': 'Fe_sv_GW', 'Ga': 'Ga_d_GW', 'Gd': 'Gd', 'Ge': 'Ge_d_GW', 'H': 'H_GW', 'He': 'He_GW', 'Hf': 'Hf_sv_GW', 'Hg': 'Hg_sv_GW', 'Ho': 'Ho_3', 'I': 'I_GW', 'In': 'In_d_GW', 'Ir': 'Ir_sv_GW', 'K': 'K_sv_GW', 'Kr': 'Kr_GW', 'La': 'La_GW', 'Li': 'Li_sv_GW', 'Lu': 'Lu_3', 'Mg': 'Mg_sv_GW', 'Mn': 'Mn_sv_GW', 'Mo': 'Mo_sv_GW', 'N': 'N_GW', 'Na': 'Na_sv_GW', 'Nb': 'Nb_sv_GW', 'Nd': 'Nd_3', 'Ne': 'Ne_GW', 'Ni': 'Ni_sv_GW', 'Np': 'Np', 'O': 'O_GW', 'Os': 'Os_sv_GW', 'P': 'P_GW', 'Pa': 'Pa', 'Pb': 'Pb_d_GW', 'Pd': 'Pd_sv_GW', 'Pm': 'Pm_3', 'Po': 'Po_d_GW', 'Pr': 'Pr_3', 'Pt': 'Pt_sv_GW', 'Pu': 'Pu', 'Rb': 'Rb_sv_GW', 'Re': 'Re_sv_GW', 'Rh': 'Rh_sv_GW', 'Rn': 'Rn_d_GW', 'Ru': 'Ru_sv_GW', 'S': 'S_GW', 'Sb': 'Sb_d_GW', 'Sc': 'Sc_sv_GW', 'Se': 'Se_GW', 'Si': 'Si_GW', 'Sm': 'Sm_3', 'Sn': 'Sn_d_GW', 'Sr': 'Sr_sv_GW', 'Ta': 'Ta_sv_GW', 'Tb': 'Tb_3', 'Tc': 'Tc_sv_GW', 'Te': 'Te_GW', 'Th': 'Th', 'Ti': 'Ti_sv_GW', 'Tl': 'Tl_d_GW', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_sv_GW', 'W': 'W_sv_GW', 'Xe': 'Xe_GW', 'Y': 'Y_sv_GW', 'Yb': 'Yb_2', 'Zn': 'Zn_sv_GW', 'Zr': 'Zr_sv_GW'}}
SUPPORTED_MODES = ('DIAG', 'GW', 'STATIC', 'BSE')
classmethod from_prev_calc(prev_calc_dir, mode='DIAG', **kwargs)[source]

Generate a set of Vasp input files for GW or BSE calculations from a directory of previous Exact Diag Vasp run.

Parameters
  • prev_calc_dir (str) – The directory contains the outputs( vasprun.xml of previous vasp run.

  • mode (str) – Supported modes are “STATIC”, “DIAG” (default), “GW”, and “BSE”.

  • **kwargs – All kwargs supported by MVLGWSet, other than structure, prev_incar and mode, which are determined from the prev_calc_dir.

incar

Incar object

kpoints

Generate gamma center k-points mesh grid for GW calc, which is requested by GW calculation.

override_from_prev_calc(prev_calc_dir='.')[source]

Update the input set to include settings from a previous calculation.

Parameters

prev_calc_dir (str) – The path to the previous calculation directory.

Returns

The input set with the settings (structure, k-points, incar, etc) updated using the previous VASP run.

class MVLNPTMDSet(structure, start_temp, end_temp, nsteps, time_step=2, spin_polarized=False, **kwargs)[source]

Bases: pymatgen.io.vasp.sets.MITMDSet

Class for writing a vasp md run in NPT ensemble.

Notes

To eliminate Pulay stress, the default ENCUT is set to a rather large value of ENCUT, which is 1.5 * ENMAX.

Parameters
  • structure (Structure) – input structure.

  • start_temp (int) – Starting temperature.

  • end_temp (int) – Final temperature.

  • nsteps (int) – Number of time steps for simulations. NSW parameter.

  • time_step (int) – The time step for the simulation. The POTIM parameter. Defaults to 2fs.

  • spin_polarized (bool) – Whether to do spin polarized calculations. The ISPIN parameter. Defaults to False.

  • **kwargs – Other kwargs supported by DictSet.

class MVLRelax52Set(structure, potcar_functional='PBE_52', **kwargs)[source]

Bases: pymatgen.io.vasp.sets.DictSet

Implementation of VaspInputSet utilizing the public Materials Project parameters for INCAR & KPOINTS and VASP’s recommended PAW potentials for POTCAR.

Keynotes from VASP manual:
  1. Recommended potentials for calculations using vasp.5.2+

  2. If dimers with short bonds are present in the compound (O2, CO,

    N2, F2, P2, S2, Cl2), it is recommended to use the h potentials. Specifically, C_h, O_h, N_h, F_h, P_h, S_h, Cl_h

  3. Released on Oct 28, 2018 by VASP. Please refer to VASP

    Manual 1.2, 1.3 & 10.2.1 for more details.

Parameters
  • structure (Structure) – input structure.

  • potcar_functional (str) – choose from “PBE_52” and “PBE_54”.

  • **kwargs – Other kwargs supported by DictSet.

CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF_PER_ATOM': 5e-05, 'ENCUT': 520, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': -5, 'ISPIN': 2, 'LDAU': True, 'LDAUJ': {'F': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}, 'O': {'Co': 0, 'Cr': 0, 'Fe': 0, 'Mn': 0, 'Mo': 0, 'Ni': 0, 'V': 0, 'W': 0}}, 'LDAUL': {'F': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}, 'O': {'Co': 2, 'Cr': 2, 'Fe': 2, 'Mn': 2, 'Mo': 2, 'Ni': 2, 'V': 2, 'W': 2}}, 'LDAUPRINT': 1, 'LDAUTYPE': 2, 'LDAUU': {'F': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}, 'O': {'Co': 3.32, 'Cr': 3.7, 'Fe': 5.3, 'Mn': 3.9, 'Mo': 4.38, 'Ni': 6.2, 'V': 3.25, 'W': 6.2}}, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 5, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Am': 'Am', 'Ar': 'Ar', 'As': 'As', 'At': 'At_d', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be', 'Bi': 'Bi_d', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Cm': 'Cm', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu_2', 'F': 'F', 'Fe': 'Fe', 'Fr': 'Fr_sv', 'Ga': 'Ga_d', 'Gd': 'Gd_3', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg', 'Mn': 'Mn_pv', 'Mo': 'Mo_sv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_sv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni', 'Np': 'Np', 'O': 'O', 'Os': 'Os', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Po': 'Po_d', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Ra': 'Ra_sv', 'Rb': 'Rb_sv', 'Re': 'Re', 'Rh': 'Rh_pv', 'Rn': 'Rn', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_sv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_sv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}}
class MVLScanRelaxSet(structure, potcar_functional='PBE_52', **kwargs)[source]

Bases: pymatgen.io.vasp.sets.MPRelaxSet

Class for writing a relax input set using Strongly Constrained and Appropriately Normed (SCAN) semilocal density functional.

Notes

  1. This functional is only available from VASP.5.4.3 upwards.

2. Meta-GGA calculations require POTCAR files that include information on the kinetic energy density of the core-electrons, i.e. “PBE_52” or “PBE_54”. Make sure the POTCAR including the following lines (see VASP wiki for more details):

$ grep kinetic POTCAR kinetic energy-density mkinetic energy-density pseudized kinetic energy density (partial)

Parameters
  • structure (Structure) – input structure.

  • potcar_functional (str) – choose from “PBE_52” and “PBE_54”.

  • vdw (str) – set “rVV10” to enable SCAN+rVV10, which is a versatile van der Waals density functional by combing the SCAN functional with the rVV10 non-local correlation functional.

  • **kwargs – Other kwargs supported by DictSet.

class MVLSlabSet(structure, k_product=50, bulk=False, auto_dipole=False, set_mix=True, sort_structure=True, **kwargs)[source]

Bases: pymatgen.io.vasp.sets.MPRelaxSet

Class for writing a set of slab vasp runs, including both slabs (along the c direction) and orient unit cells (bulk), to ensure the same KPOINTS, POTCAR and INCAR criterion.

Parameters
  • k_product – default to 50, kpoint number * length for a & b directions, also for c direction in bulk calculations

  • bulk (bool) – Set to True for bulk calculation. Defaults to False.

  • **kwargs – Other kwargs supported by DictSet.

as_dict(verbosity=2)[source]

A JSON serializable dict representation of an object.

kpoints
k_product, default to 50, is kpoint number * length for a & b

directions, also for c direction in bulk calculations

Automatic mesh & Gamma is the default setting.

class VaspInputSet[source]

Bases: monty.json.MSONable

Base class representing a set of Vasp input parameters with a structure supplied as init parameters. Typically, you should not inherit from this class. Start from DictSet or MPRelaxSet or MITRelaxSet.

all_input
as_dict(verbosity=2)[source]

A JSON serializable dict representation of an object.

get_vasp_input() → pymatgen.io.vasp.inputs.VaspInput[source]
Returns

VaspInput

incar

Incar object

kpoints

Kpoints object

poscar

Poscar object

potcar

Potcar object.

potcar_symbols

List of POTCAR symbols.

write_input(output_dir, make_dir_if_not_present=True, include_cif=False)[source]

Writes a set of VASP input to a directory.

Parameters
  • output_dir (str) – Directory to output the VASP input files

  • make_dir_if_not_present (bool) – Set to True if you want the directory (and the whole path) to be created if it is not present.

  • include_cif (bool) – Whether to write a CIF file in the output directory for easier opening by VESTA.

batch_write_input(structures, vasp_input_set=<class 'pymatgen.io.vasp.sets.MPRelaxSet'>, output_dir='.', make_dir_if_not_present=True, subfolder=None, sanitize=False, include_cif=False, **kwargs)[source]

Batch write vasp input for a sequence of structures to output_dir, following the format output_dir/{group}/{formula}_{number}.

Parameters
  • structures ([Structure]) – Sequence of Structures.

  • vasp_input_set (VaspInputSet) – VaspInputSet class that creates vasp input files from structures. Note that a class should be supplied. Defaults to MPRelaxSet.

  • output_dir (str) – Directory to output files. Defaults to current directory “.”.

  • make_dir_if_not_present (bool) – Create the directory if not present. Defaults to True.

  • subfolder (callable) – Function to create subdirectory name from structure. Defaults to simply “formula_count”.

  • sanitize (bool) – Boolean indicating whether to sanitize the structure before writing the VASP input files. Sanitized output are generally easier for viewing and certain forms of analysis. Defaults to False.

  • include_cif (bool) – Whether to output a CIF as well. CIF files are generally better supported in visualization programs.

  • **kwargs – Additional kwargs are passed to the vasp_input_set class in addition to structure.

get_structure_from_prev_run(vasprun, outcar=None)[source]

Process structure from previous run.

Parameters
  • vasprun (Vasprun) – Vasprun that contains the final structure from previous run.

  • outcar (Outcar) – Outcar that contains the magnetization info from previous run.

Returns

Returns the magmom-decorated structure that can be passed to get Vasp input files, e.g. get_kpoints.

get_vasprun_outcar(path, parse_dos=True, parse_eigen=True)[source]
standardize_structure(structure, sym_prec=0.1, international_monoclinic=True)[source]

Get the symmetrically standardized structure.

Parameters
  • structure (Structure) – The structure.

  • sym_prec (float) – Tolerance for symmetry finding for standardization.

  • international_monoclinic (bool) – Whether to use international convention (vs Curtarolo) for monoclinic. Defaults True.

Returns

The symmetrized structure.