pymatgen.io.qchem package

This package implements modules for input and output to and from Qchem.

Submodules

pymatgen.io.qchem.inputs module

Classes for reading/manipulating/writing QChem input files.

class QCInput(molecule: Molecule | list[Molecule] | Literal['read'], rem: dict, opt: dict[str, list] | None = None, pcm: dict | None = None, solvent: dict | None = None, smx: dict | None = None, scan: dict[str, list] | None = None, van_der_waals: dict[str, float] | None = None, vdw_mode: str = 'atomic', plots: dict | None = None, nbo: dict | None = None, geom_opt: dict | None = None, cdft: list[list[dict]] | None = None, almo_coupling: list[list[tuple[int, int]]] | None = None, svp: dict | None = None, pcm_nonels: dict | None = None)[source]

Bases: InputFile

An object representing a QChem input file. QCInput attributes represent different sections of a QChem input file. To add a new section one needs to modify __init__, __str__, from_sting and add static methods to read and write the new section i.e. section_template and read_section. By design, there is very little (or no) checking that input parameters conform to the appropriate QChem format, this responsible lands on the user or a separate error handling software.

Parameters:
  • molecule (pymatgen Molecule object, list of Molecule objects, or "read") – Input molecule(s). molecule can be set as a pymatgen Molecule object, a list of such Molecule objects, or as the string “read”. “read” can be used in multi_job QChem input files where the molecule is read in from the previous calculation.

  • rem (dict) – A dictionary of all the input parameters for the rem section of QChem input file. Ex. rem = {‘method’: ‘rimp2’, ‘basis’: ‘6-31*G++’ … }

  • opt (dict of lists) – A dictionary of opt sections, where each opt section is a key and the corresponding values are a list of strings. Strings must be formatted as instructed by the QChem manual. The different opt sections are: CONSTRAINT, FIXED, DUMMY, and CONNECT Ex. opt = {“CONSTRAINT”: [“tors 2 3 4 5 25.0”, “tors 2 5 7 9 80.0”], “FIXED”: [“2 XY”]}

  • pcm (dict) – A dictionary of the PCM section, defining behavior for use of the polarizable continuum model. Ex: pcm = {“theory”: “cpcm”, “hpoints”: 194}

  • solvent (dict) – A dictionary defining the solvent parameters used with PCM. Ex: solvent = {“dielectric”: 78.39, “temperature”: 298.15}

  • smx (dict) – A dictionary defining solvent parameters used with the SMD method, a solvent method that adds short-range terms to PCM. Ex: smx = {“solvent”: “water”}

  • scan (dict of lists) – A dictionary of scan variables. Because two constraints of the same type are allowed (for instance, two torsions or two bond stretches), each TYPE of variable (stre, bend, tors) should be its own key in the dict, rather than each variable. Note that the total number of variable (sum of lengths of all lists) CANNOT be more than two. Ex. scan = {“stre”: [“3 6 1.5 1.9 0.1”], “tors”: [“1 2 3 4 -180 180 15”]}

  • van_der_waals (dict) – A dictionary of custom van der Waals radii to be used when constructing cavities for the PCM model or when computing, e.g. Mulliken charges. They keys are strs whose meaning depends on the value of vdw_mode, and the values are the custom radii in angstroms.

  • vdw_mode (str) – Method of specifying custom van der Waals radii - ‘atomic’ or ‘sequential’. In ‘atomic’ mode (default), dict keys represent the atomic number associated with each radius (e.g., 12 = carbon). In ‘sequential’ mode, dict keys represent the sequential position of a single specific atom in the input structure.

  • plots (dict) – A dictionary of all the input parameters for the plots section of the QChem input file.

  • nbo (dict) – A dictionary of all the input parameters for the nbo section of the QChem input file.

  • geom_opt (dict) – A dictionary of input parameters for the geom_opt section of the QChem input file. This section is required when using the new libopt3 geometry optimizer.

  • cdft (list of lists of dicts) –

    A list of lists of dictionaries, where each dictionary represents a charge constraint in the cdft section of the QChem input file.

    Each entry in the main list represents one state (allowing for multi-configuration calculations using constrained density functional theory - configuration interaction (CDFT-CI). Each state is represented by a list, which itself contains some number of constraints (dictionaries).

    Ex:

    1. For a single-state calculation with two constraints:

    cdft=[[

    {“value”: 1.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [2], “types”: [None]}, {“value”: 2.0, “coefficients”: [1.0, -1.0], “first_atoms”: [1, 17], “last_atoms”: [3, 19],

    ”types”: [“s”]}

    ]]

    Note that a type of None will default to a charge constraint (which can also be accessed by requesting a type of “c” or “charge”.

    2. For a multi-reference calculation: cdft=[

    [
    {“value”: 1.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27],

    ”types”: [“c”]},

    {“value”: 0.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27],

    ”types”: [“s”]},

    ], [

    {“value”: 0.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27],

    ”types”: [“c”]},

    {“value”: -1.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27],

    ”types”: [“s”]},

    ]

    ]

  • almo_coupling (list of lists of int 2-tuples) –

    A list of lists of int 2-tuples used for calculations of diabatization and state coupling calculations

    relying on the absolutely localized molecular orbitals (ALMO) methodology. Each entry in the main list represents a single state (two states are included in an ALMO calculation). Within a single state, each 2-tuple represents the charge and spin multiplicity of a single fragment.

    ex: almo=[
    [

    (1, 2), (0, 1)

    ], [

    (0, 1), (1, 2)

    ]

    ]

static almo_template(almo_coupling: list[list[tuple[int, int]]]) str[source]
Parameters:

almo – list of lists of int 2-tuples.

Returns:

(str)

static cdft_template(cdft: list[list[dict]]) str[source]
Parameters:

cdft – list of lists of dicts.

Returns:

(str)

static find_sections(string: str) list[source]

Find sections in the string.

Parameters:

string (str) – String

Returns:

List of sections.

static from_file(filename: str | Path) QCInput[source]

Create QcInput from file.

Parameters:

filename (str) – Filename

Returns:

QcInput

classmethod from_multi_jobs_file(filename: str) list[QCInput][source]

Create list of QcInput from a file.

Parameters:

filename (str) – Filename

Returns:

List of QCInput objects

classmethod from_str(string: str) QCInput[source]

Read QcInput from string.

Parameters:

string (str) – String input.

Returns:

QcInput

static geom_opt_template(geom_opt: dict) str[source]
Parameters:

() (geom_opt) –

Returns:

(str) geom_opt parameters.

get_str() str[source]

Return a string representation of an entire input file.

get_string(*args, **kwargs) str[source]

get_string is deprecated! Use get_str instead

static molecule_template(molecule: Molecule | list[Molecule] | Literal['read']) str[source]
Parameters:

molecule (Molecule, list of Molecules, or "read") –

Returns:

(str) Molecule template.

static multi_job_string(job_list: list[QCInput]) str[source]
Parameters:

() (job_list) – List of jobs.

Returns:

(str) String representation of multi job input file.

static nbo_template(nbo: dict) str[source]
Parameters:

() (nbo) –

Returns:

(str)

static opt_template(opt: dict[str, list]) str[source]

Optimization template.

Parameters:

() (opt) –

Returns:

(str)

static pcm_nonels_template(pcm_nonels: dict) str[source]

Template for the $pcm_nonels section.

Arg

pcm_nonels: dict of CMIRS parameters, e.g. {

“a”: “-0.006736”, “b”: “0.032698”, “c”: “-1249.6”, “d”: “-21.405”, “gamma”: “3.7”, “solvrho”: “0.05”, “delta”: 7, “gaulag_n”: 40,

}

Returns:

(str)

static pcm_template(pcm: dict) str[source]

Pcm run template.

Parameters:

() (pcm) –

Returns:

(str)

static plots_template(plots: dict) str[source]
Parameters:

() (plots) –

Returns:

(str)

static read_almo(string: str) list[list[tuple[int, int]]][source]

Read ALMO coupling parameters from string.

Parameters:

string (str) – String

Returns:

(list of lists of int 2-tuples) almo_coupling parameters

static read_cdft(string: str) list[list[dict]][source]

Read cdft parameters from string.

Parameters:

string (str) – String

Returns:

cdft parameters

Return type:

list[list[dict]]

static read_geom_opt(string: str) dict[source]

Read geom_opt parameters from string.

Parameters:

string (str) – String

Returns:

(dict) geom_opt parameters.

static read_molecule(string: str) Molecule | list[Molecule] | Literal['read'][source]

Read molecule from string.

Parameters:

string (str) – String

Returns:

Molecule

static read_nbo(string: str) dict[source]

Read nbo parameters from string.

Parameters:

string (str) – String

Returns:

(dict) nbo parameters.

static read_opt(string: str) dict[str, list][source]

Read opt section from string.

Parameters:

string (str) – String

Returns:

(dict) Opt section

static read_pcm(string: str) dict[source]

Read pcm parameters from string.

Parameters:

string (str) – String

Returns:

(dict) PCM parameters

static read_pcm_nonels(string: str) dict[source]

Read pcm_nonels parameters from string.

Parameters:

string (str) – String

Returns:

(dict) PCM parameters

static read_plots(string: str) dict[source]

Read plots parameters from string.

Parameters:

string (str) – String

Returns:

(dict) plots parameters.

static read_rem(string: str) dict[source]

Parse rem from string.

Parameters:

string (str) – String

Returns:

(dict) rem

static read_scan(string: str) dict[str, list][source]

Read scan section from a string.

Parameters:

string – String to be parsed

Returns:

Dict representing Q-Chem scan section

static read_smx(string: str) dict[source]

Read smx parameters from string.

Parameters:

string (str) – String

Returns:

(dict) SMX parameters.

static read_solvent(string: str) dict[source]

Read solvent parameters from string.

Parameters:

string (str) – String

Returns:

(dict) Solvent parameters

static read_svp(string: str) dict[source]

Read svp parameters from string.

static read_vdw(string: str) tuple[str, dict][source]

Read van der Waals parameters from string.

Parameters:

string (str) – String

Returns:

(str, dict) vdW mode (‘atomic’ or ‘sequential’) and dict of van der Waals radii.

static rem_template(rem: dict) str[source]
Parameters:

() (rem) –

Returns:

(str)

static scan_template(scan: dict[str, list]) str[source]
Parameters:

scan (dict) – Dictionary with scan section information. Ex: {“stre”: [“3 6 1.5 1.9 0.1”], “tors”: [“1 2 3 4 -180 180 15”]}.

Returns:

String representing Q-Chem input format for scan section

static smx_template(smx: dict) str[source]
Parameters:

() (smx) –

Returns:

(str)

static solvent_template(solvent: dict) str[source]

Solvent template.

Parameters:

() (solvent) –

Returns:

(str)

static svp_template(svp: dict) str[source]

Template for the $svp section.

Parameters:
  • svp – dict of SVP parameters, e.g.

  • {"rhoiso" – “0.001”, “nptleb”: “1202”, “itrngr”: “2”, “irotgr”: “2”}

Returns:

the $svp section. Note that all parameters will be concatenated onto

a single line formatted as a FORTRAN namelist. This is necessary because the isodensity SS(V)PE model in Q-Chem calls a secondary code.

Return type:

str

static van_der_waals_template(radii: dict[str, float], mode: str = 'atomic') str[source]
Parameters:
  • radii (dict) – Dictionary with custom van der Waals radii, in Angstroms, keyed by either atomic number or sequential atom number (see ‘mode’ kwarg). Ex: {1: 1.20, 12: 1.70}

  • mode – ‘atomic’ or ‘sequential’. In ‘atomic’ mode (default), dict keys represent the atomic number associated with each radius (e.g., ‘12’ = carbon). In ‘sequential’ mode, dict keys represent the sequential position of a single specific atom in the input structure. NOTE: keys must be given as strings even though they are numbers!.

Returns:

String representing Q-Chem input format for van_der_waals section

static write_multi_job_file(job_list: list[QCInput], filename: str)[source]

Write a multijob file.

Parameters:
  • () (filename) – List of jobs.

  • () – Filename

pymatgen.io.qchem.outputs module

Parsers for Qchem output files.

class QCOutput(filename: str)[source]

Bases: MSONable

Class to parse QChem output files.

Parameters:

filename (str) – Filename to parse.

as_dict()[source]
Returns:

MSONable dict.

static multiple_outputs_from_file(filename, keep_sub_files=True)[source]

Parses a QChem output file with multiple calculations # 1.) Separates the output into sub-files

e.g. qcout -> qcout.0, qcout.1, qcout.2 … qcout.N a.) Find delimiter for multiple calculations b.) Make separate output sub-files

2.) Creates separate QCCalcs for each one from the sub-files.

check_for_structure_changes(mol1: Molecule, mol2: Molecule) str[source]

Compares connectivity of two molecules (using MoleculeGraph w/ OpenBabelNN). This function will work with two molecules with different atom orderings,

but for proper treatment, atoms should be listed in the same order.

Possible outputs include: - no_change: the bonding in the two molecules is identical - unconnected_fragments: the MoleculeGraph of mol1 is connected, but the

MoleculeGraph is mol2 is not connected

  • fewer_bonds: the MoleculeGraph of mol1 has more bonds (edges) than the MoleculeGraph of mol2

  • more_bonds: the MoleculeGraph of mol2 has more bonds (edges) than the MoleculeGraph of mol1

  • bond_change: this case catches any other non-identical MoleculeGraphs

Parameters:
  • mol1 – Pymatgen Molecule object to be compared.

  • mol2 – Pymatgen Molecule object to be compared.

Returns:

One of [“unconnected_fragments”, “fewer_bonds”, “more_bonds”, “bond_change”, “no_change”]

get_percentage(line: str, orbital: str) str[source]

Retrieve the percent character of an orbital.

Parameters:
  • line – Line containing orbital and percentage.

  • orbital – Type of orbital (s, p, d, f).

Returns:

Percentage of character.

Raises:

n/a

jump_to_header(lines: list[str], header: str) list[str][source]

Given a list of lines, truncate the start of the list so that the first line of the new list contains the header.

Parameters:
  • lines – List of lines.

  • header – Substring to match.

Returns:

Truncated lines.

Raises:

RuntimeError

nbo_parser(filename: str) dict[str, list[DataFrame]][source]

Parse all the important sections of NBO output.

Parameters:

filename – Path to QChem NBO output.

Returns:

Data frames of formatted output.

Raises:

RuntimeError

parse_hybridization_character(lines: list[str]) list[DataFrame][source]

Parse the hybridization character section of NBO output.

Parameters:

lines – QChem output lines.

Returns:

Data frames of formatted output.

Raises:

RuntimeError

parse_hyperbonds(lines: list[str]) list[DataFrame][source]

Parse the natural populations section of NBO output.

Parameters:

lines – QChem output lines.

Returns:

Data frame of formatted output.

Raises:

RuntimeError

parse_natural_populations(lines: list[str]) list[DataFrame][source]

Parse the natural populations section of NBO output.

Parameters:

lines – QChem output lines.

Returns:

Data frame of formatted output.

Raises:

RuntimeError

parse_perturbation_energy(lines: list[str]) list[DataFrame][source]

Parse the perturbation energy section of NBO output.

Parameters:

lines – QChem output lines.

Returns:

Data frame of formatted output.

Raises:

RuntimeError

z_int(string: str) int[source]

Convert string to integer. If string empty, return -1.

Parameters:

string – Input to be cast to int.

Returns:

Int representation.

Raises:

n/a

pymatgen.io.qchem.sets module

Input sets for Qchem.

class ForceSet(molecule: Molecule, basis_set: str = 'def2-tzvpd', scf_algorithm: str = 'diis', qchem_version: int = 5, dft_rung: int = 4, pcm_dielectric: float | None = None, isosvp_dielectric: float | None = None, smd_solvent: str | None = None, cmirs_solvent: Literal['water', 'acetonitrile', 'dimethyl sulfoxide', 'cyclohexane', 'benzene'] | None = None, custom_smd: str | None = None, max_scf_cycles: int = 100, plot_cubes: bool = False, nbo_params: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic', cdft_constraints: list[list[dict]] | None = None, overwrite_inputs: dict | None = None)[source]

Bases: QChemDictSet

QChemDictSet for a force (gradient) calculation.

Parameters:
  • molecule (Pymatgen Molecule object) –

  • basis_set (str) – Basis set to use. (Default: “def2-tzvpd”)

  • scf_algorithm (str) – Algorithm to use for converging the SCF. Recommended choices are “DIIS”, “GDM”, and “DIIS_GDM”. Other algorithms supported by Qchem’s GEN_SCFMAN module will also likely perform well. Refer to the QChem manual for further details. (Default: “diis”)

  • qchem_version (int) – Which major version of Q-Chem will be run. Supports 5 and 6. (Default: 5)

  • dft_rung (int) –

    Select the rung on “Jacob’s Ladder of Density Functional Approximations” in order of increasing accuracy/cost. For each rung, we have prescribed one functional based on our experience, available benchmarks, and the suggestions of the Q-Chem manual: 1 (LSDA) = SPW92 2 (GGA) = B97-D3(BJ) 3 (metaGGA) = B97M-V 4 (hybrid metaGGA) = ωB97M-V 5 (double hybrid metaGGA) = ωB97M-(2).

    (Default: 4)

    To set a functional not given by one of the above, set the overwrite_inputs argument to {“method”:”<NAME OF FUNCTIONAL>”}

  • pcm_dielectric (float) –

    Dielectric constant to use for PCM implicit solvation model. (Default: None) If supplied, will set up the $pcm section of the input file for a C-PCM calculation. Other types of PCM calculations (e.g., IEF-PCM, SS(V)PE, etc.) may be requested by passing custom keywords to overwrite_inputs, e.g. overwrite_inputs = {“pcm”: {“theory”: “ssvpe”}} Refer to the QChem manual for further details on the models available.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • isosvp_dielectric (float) –

    Dielectric constant to use for isodensity SS(V)PE implicit solvation model. (Default: None). If supplied, will set solvent_method to “isosvp” and populate the $svp section of the input file with appropriate parameters.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • smd_solvent (str) –

    Solvent to use for SMD implicit solvation model. (Default: None) Examples include “water”, “ethanol”, “methanol”, and “acetonitrile”. Refer to the QChem manual for a complete list of solvents available. To define a custom solvent, set this argument to “custom” and populate custom_smd with the necessary parameters.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • cmirs_solvent (str) –

    Solvent to use for the CMIRS implicit solvation model. (Default: None). Only 5 solvents are presently available as of Q-Chem 6: “water”, “benzene”, “cyclohexane”, “dimethyl sulfoxide”, and “acetonitrile”. Note that selection of a solvent here will also populate the iso SS(V)PE dielectric constant, because CMIRS uses the isodensity SS(V)PE model to compute electrostatics.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • custom_smd (str) – List of parameters to define a custom solvent in SMD. (Default: None) Must be given as a string of seven comma separated values in the following order: “dielectric, refractive index, acidity, basicity, surface tension, aromaticity, electronegative halogenicity” Refer to the QChem manual for further details.

  • max_scf_cycles (int) – Maximum number of SCF iterations. (Default: 100)

  • plot_cubes (bool) – Whether to write CUBE files of the electron density. (Default: False)

  • vdw_mode ('atomic' | 'sequential') – Method of specifying custom van der Waals radii. Applies only if you are using overwrite_inputs to add a $van_der_waals section to the input. In ‘atomic’ mode (default), dict keys represent the atomic number associated with each radius (e.g., ‘12’ = carbon). In ‘sequential’ mode, dict keys represent the sequential position of a single specific atom in the input structure.

  • cdft_constraints (list of lists of dicts) –

    A list of lists of dictionaries, where each dictionary represents a charge constraint in the cdft section of the QChem input file.

    Each entry in the main list represents one state (allowing for multi-configuration calculations using constrained density functional theory - configuration interaction (CDFT-CI). Each state is represented by a list, which itself contains some number of constraints (dictionaries).

    Ex:

    1. For a single-state calculation with two constraints:

    cdft_constraints=[[
    {

    “value”: 1.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [2], “types”: [None]

    }, {

    ”value”: 2.0, “coefficients”: [1.0, -1.0], “first_atoms”: [1, 17], “last_atoms”: [3, 19], “types”: [“s”]

    }

    ]]

    Note that a type of None will default to a charge constraint (which can also be accessed by requesting a type of “c” or “charge”).

    2. For a CDFT-CI multi-reference calculation: cdft_constraints=[

    [
    {

    “value”: 1.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27], “types”: [“c”]

    }, {

    ”value”: 0.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27], “types”: [“s”]

    },

    ], [

    {

    “value”: 0.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27], “types”: [“c”]

    }, {

    ”value”: -1.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27], “types”: [“s”]

    },

    ]

    ]

  • overwrite_inputs (dict) –

    Dictionary of QChem input sections to add or overwrite variables. The currently available sections (keys) are rem, pcm, solvent, smx, opt, scan, van_der_waals, and plots. The value of each key is a dictionary of key value pairs relevant to that section. For example, to add a new variable to the rem section that sets symmetry to false, use

    overwrite_inputs = {“rem”: {“symmetry”: “false”}}

    Note that if something like basis is added to the rem dict it will overwrite the default basis.

    Note that supplying a van_der_waals section here will automatically modify the PCM “radii” setting to “read”.

    Note that all keys must be given as strings, even when they are numbers!

class FreqSet(molecule: Molecule, basis_set: str = 'def2-svpd', scf_algorithm: str = 'diis', qchem_version: int = 5, dft_rung: int = 4, pcm_dielectric: float | None = None, isosvp_dielectric: float | None = None, smd_solvent: str | None = None, cmirs_solvent: Literal['water', 'acetonitrile', 'dimethyl sulfoxide', 'cyclohexane', 'benzene'] | None = None, custom_smd: str | None = None, max_scf_cycles: int = 100, plot_cubes: bool = False, nbo_params: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic', cdft_constraints: list[list[dict]] | None = None, overwrite_inputs: dict | None = None)[source]

Bases: QChemDictSet

QChemDictSet for a frequency calculation.

Parameters:
  • molecule (Pymatgen Molecule object) –

  • basis_set (str) – Basis set to use. (Default: “def2-svpd”)

  • scf_algorithm (str) – Algorithm to use for converging the SCF. Recommended choices are “DIIS”, “GDM”, and “DIIS_GDM”. Other algorithms supported by Qchem’s GEN_SCFMAN module will also likely perform well. Refer to the QChem manual for further details. (Default: “diis”)

  • qchem_version (int) – Which major version of Q-Chem will be run. Supports 5 and 6. (Default: 5)

  • dft_rung (int) –

    Select the rung on “Jacob’s Ladder of Density Functional Approximations” in order of increasing accuracy/cost. For each rung, we have prescribed one functional based on our experience, available benchmarks, and the suggestions of the Q-Chem manual: 1 (LSDA) = SPW92 2 (GGA) = B97-D3(BJ) 3 (metaGGA) = B97M-V 4 (hybrid metaGGA) = ωB97M-V 5 (double hybrid metaGGA) = ωB97M-(2).

    (Default: 4)

    To set a functional not given by one of the above, set the overwrite_inputs argument to {“method”:”<NAME OF FUNCTIONAL>”}

  • pcm_dielectric (float) –

    Dielectric constant to use for PCM implicit solvation model. (Default: None) If supplied, will set up the $pcm section of the input file for a C-PCM calculation. Other types of PCM calculations (e.g., IEF-PCM, SS(V)PE, etc.) may be requested by passing custom keywords to overwrite_inputs, e.g. overwrite_inputs = {“pcm”: {“theory”: “ssvpe”}} Refer to the QChem manual for further details on the models available.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • isosvp_dielectric (float) –

    Dielectric constant to use for isodensity SS(V)PE implicit solvation model. (Default: None). If supplied, will set solvent_method to “isosvp” and populate the $svp section of the input file with appropriate parameters.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • smd_solvent (str) –

    Solvent to use for SMD implicit solvation model. (Default: None) Examples include “water”, “ethanol”, “methanol”, and “acetonitrile”. Refer to the QChem manual for a complete list of solvents available. To define a custom solvent, set this argument to “custom” and populate custom_smd with the necessary parameters.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • cmirs_solvent (str) –

    Solvent to use for the CMIRS implicit solvation model. (Default: None). Only 5 solvents are presently available as of Q-Chem 6: “water”, “benzene”, “cyclohexane”, “dimethyl sulfoxide”, and “acetonitrile”. Note that selection of a solvent here will also populate the iso SS(V)PE dielectric constant, because CMIRS uses the isodensity SS(V)PE model to compute electrostatics.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • custom_smd (str) – List of parameters to define a custom solvent in SMD. (Default: None) Must be given as a string of seven comma separated values in the following order: “dielectric, refractive index, acidity, basicity, surface tension, aromaticity, electronegative halogenicity” Refer to the QChem manual for further details.

  • max_scf_cycles (int) – Maximum number of SCF iterations. (Default: 100)

  • plot_cubes (bool) – Whether to write CUBE files of the electron density. (Default: False)

  • vdw_mode ('atomic' | 'sequential') – Method of specifying custom van der Waals radii. Applies only if you are using overwrite_inputs to add a $van_der_waals section to the input. In ‘atomic’ mode (default), dict keys represent the atomic number associated with each radius (e.g., ‘12’ = carbon). In ‘sequential’ mode, dict keys represent the sequential position of a single specific atom in the input structure.

  • cdft_constraints (list of lists of dicts) –

    A list of lists of dictionaries, where each dictionary represents a charge constraint in the cdft section of the QChem input file.

    Each entry in the main list represents one state (allowing for multi-configuration calculations using constrained density functional theory - configuration interaction (CDFT-CI). Each state is represented by a list, which itself contains some number of constraints (dictionaries).

    Ex:

    1. For a single-state calculation with two constraints:

    cdft_constraints=[[
    {

    “value”: 1.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [2], “types”: [None]

    }, {

    ”value”: 2.0, “coefficients”: [1.0, -1.0], “first_atoms”: [1, 17], “last_atoms”: [3, 19], “types”: [“s”]

    }

    ]]

    Note that a type of None will default to a charge constraint (which can also be accessed by requesting a type of “c” or “charge”).

    2. For a CDFT-CI multi-reference calculation: cdft_constraints=[

    [
    {

    “value”: 1.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27], “types”: [“c”]

    }, {

    ”value”: 0.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27], “types”: [“s”]

    },

    ], [

    {

    “value”: 0.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27], “types”: [“c”]

    }, {

    ”value”: -1.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27], “types”: [“s”]

    },

    ]

    ]

  • overwrite_inputs (dict) –

    Dictionary of QChem input sections to add or overwrite variables. The currently available sections (keys) are rem, pcm, solvent, smx, opt, scan, van_der_waals, and plots. The value of each key is a dictionary of key value pairs relevant to that section. For example, to add a new variable to the rem section that sets symmetry to false, use

    overwrite_inputs = {“rem”: {“symmetry”: “false”}}

    Note that if something like basis is added to the rem dict it will overwrite the default basis.

    Note that supplying a van_der_waals section here will automatically modify the PCM “radii” setting to “read”.

    Note that all keys must be given as strings, even when they are numbers!

class OptSet(molecule: Molecule, basis_set: str = 'def2-svpd', scf_algorithm: str = 'diis', qchem_version: int = 5, dft_rung: int = 4, pcm_dielectric: float | None = None, isosvp_dielectric: float | None = None, smd_solvent: str | None = None, cmirs_solvent: Literal['water', 'acetonitrile', 'dimethyl sulfoxide', 'cyclohexane', 'benzene'] | None = None, custom_smd: str | None = None, max_scf_cycles: int = 100, plot_cubes: bool = False, nbo_params: dict | None = None, opt_variables: dict[str, list] | None = None, geom_opt_max_cycles: int = 200, geom_opt: dict | None = None, cdft_constraints: list[list[dict]] | None = None, overwrite_inputs: dict | None = None)[source]

Bases: QChemDictSet

QChemDictSet for a geometry optimization.

Parameters:
  • molecule (Pymatgen Molecule object) –

  • job_type (str) – QChem job type to run. Valid options are “opt” for optimization, “sp” for single point, “freq” for frequency calculation, or “force” for force evaluation.

  • basis_set (str) – Basis set to use. (Default: “def2-svpd”)

  • scf_algorithm (str) – Algorithm to use for converging the SCF. Recommended choices are “DIIS”, “GDM”, and “DIIS_GDM”. Other algorithms supported by Qchem’s GEN_SCFMAN module will also likely perform well. Refer to the QChem manual for further details. (Default: “diis”)

  • qchem_version (int) – Which major version of Q-Chem will be run. Supports 5 and 6. (Default: 5)

  • dft_rung (int) –

    Select the rung on “Jacob’s Ladder of Density Functional Approximations” in order of increasing accuracy/cost. For each rung, we have prescribed one functional based on our experience, available benchmarks, and the suggestions of the Q-Chem manual: 1 (LSDA) = SPW92 2 (GGA) = B97-D3(BJ) 3 (metaGGA) = B97M-V 4 (hybrid metaGGA) = ωB97M-V 5 (double hybrid metaGGA) = ωB97M-(2).

    (Default: 4)

    To set a functional not given by one of the above, set the overwrite_inputs argument to {“method”:”<NAME OF FUNCTIONAL>”}

  • pcm_dielectric (float) –

    Dielectric constant to use for PCM implicit solvation model. (Default: None) If supplied, will set up the $pcm section of the input file for a C-PCM calculation. Other types of PCM calculations (e.g., IEF-PCM, SS(V)PE, etc.) may be requested by passing custom keywords to overwrite_inputs, e.g. overwrite_inputs = {“pcm”: {“theory”: “ssvpe”}} Refer to the QChem manual for further details on the models available.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • isosvp_dielectric (float) –

    Dielectric constant to use for isodensity SS(V)PE implicit solvation model. (Default: None). If supplied, will set solvent_method to “isosvp” and populate the $svp section of the input file with appropriate parameters.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • smd_solvent (str) –

    Solvent to use for SMD implicit solvation model. (Default: None) Examples include “water”, “ethanol”, “methanol”, and “acetonitrile”. Refer to the QChem manual for a complete list of solvents available. To define a custom solvent, set this argument to “custom” and populate custom_smd with the necessary parameters.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • cmirs_solvent (str) –

    Solvent to use for the CMIRS implicit solvation model. (Default: None). Only 5 solvents are presently available as of Q-Chem 6: “water”, “benzene”, “cyclohexane”, “dimethyl sulfoxide”, and “acetonitrile”. Note that selection of a solvent here will also populate the iso SS(V)PE dielectric constant, because CMIRS uses the isodensity SS(V)PE model to compute electrostatics.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • custom_smd (str) – List of parameters to define a custom solvent in SMD. (Default: None) Must be given as a string of seven comma separated values in the following order: “dielectric, refractive index, acidity, basicity, surface tension, aromaticity, electronegative halogenicity” Refer to the QChem manual for further details.

  • max_scf_cycles (int) – Maximum number of SCF iterations. (Default: 100)

  • geom_opt_max_cycles (int) – Maximum number of geometry optimization iterations. (Default: 200)

  • geom_opt (dict) – A dict containing parameters for the $geom_opt section of the Q-Chem input file, which control the new geometry optimizer available starting in version 5.4.2. The new optimizer remains under development but was officially released and became the default optimizer in Q-Chem version 6.0.0. Note that for version 5.4.2, the new optimizer must be explicitly requested by passing in a dictionary (empty or otherwise) for this input parameter. (Default: False)

  • plot_cubes (bool) – Whether to write CUBE files of the electron density. (Default: False)

  • vdw_mode ('atomic' | 'sequential') – Method of specifying custom van der Waals radii. Applies only if you are using overwrite_inputs to add a $van_der_waals section to the input. In ‘atomic’ mode (default), dict keys represent the atomic number associated with each radius (e.g., ‘12’ = carbon). In ‘sequential’ mode, dict keys represent the sequential position of a single specific atom in the input structure.

  • cdft_constraints (list of lists of dicts) –

    A list of lists of dictionaries, where each dictionary represents a charge constraint in the cdft section of the QChem input file.

    Each entry in the main list represents one state (allowing for multi-configuration calculations using constrained density functional theory - configuration interaction (CDFT-CI). Each state is represented by a list, which itself contains some number of constraints (dictionaries).

    Ex:

    1. For a single-state calculation with two constraints:

    cdft_constraints=[[
    {

    “value”: 1.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [2], “types”: [None]

    }, {

    ”value”: 2.0, “coefficients”: [1.0, -1.0], “first_atoms”: [1, 17], “last_atoms”: [3, 19], “types”: [“s”]

    }

    ]]

    Note that a type of None will default to a charge constraint (which can also be accessed by requesting a type of “c” or “charge”).

    2. For a CDFT-CI multi-reference calculation: cdft_constraints=[

    [
    {

    “value”: 1.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27], “types”: [“c”]

    }, {

    ”value”: 0.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27], “types”: [“s”]

    },

    ], [

    {

    “value”: 0.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27], “types”: [“c”]

    }, {

    ”value”: -1.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27], “types”: [“s”]

    },

    ]

    ]

  • overwrite_inputs (dict) –

    Dictionary of QChem input sections to add or overwrite variables. The currently available sections (keys) are rem, pcm, solvent, smx, opt, scan, van_der_waals, and plots. The value of each key is a dictionary of key value pairs relevant to that section. For example, to add a new variable to the rem section that sets symmetry to false, use

    overwrite_inputs = {“rem”: {“symmetry”: “false”}}

    Note that if something like basis is added to the rem dict it will overwrite the default basis.

    Note that supplying a van_der_waals section here will automatically modify the PCM “radii” setting to “read”.

    Note that all keys must be given as strings, even when they are numbers!

  • vdw_mode – Method of specifying custom van der Waals radii. Applies only if you are using overwrite_inputs to add a $van_der_waals section to the input. In ‘atomic’ mode (default), dict keys represent the atomic number associated with each radius (e.g., ‘12’ = carbon). In ‘sequential’ mode, dict keys represent the sequential position of a single specific atom in the input structure.

class PESScanSet(molecule: Molecule, basis_set: str = 'def2-svpd', scf_algorithm: str = 'diis', qchem_version: int = 5, dft_rung: int = 4, pcm_dielectric: float | None = None, isosvp_dielectric: float | None = None, smd_solvent: str | None = None, cmirs_solvent: Literal['water', 'acetonitrile', 'dimethyl sulfoxide', 'cyclohexane', 'benzene'] | None = None, custom_smd: str | None = None, max_scf_cycles: int = 100, plot_cubes: bool = False, nbo_params: dict | None = None, opt_variables: dict[str, list] | None = None, scan_variables: dict[str, list] | None = None, overwrite_inputs: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic')[source]

Bases: QChemDictSet

QChemDictSet for a potential energy surface scan (PES_SCAN) calculation, used primarily to identify possible transition states or to sample different geometries. Note: Because there are no defaults that can be used for a PES scan (the variables are completely dependent on the molecular structure), by default scan_variables = None. However, a PES Scan job should not be run with less than one variable (or more than two variables).

Parameters:
  • molecule (Pymatgen Molecule object) –

  • opt_variables (dict) –

    A dictionary of opt sections, where each opt section is a key and the corresponding values are a list of strings. Strings must be formatted as instructed by the QChem manual. The different opt sections are: CONSTRAINT, FIXED, DUMMY, and CONNECT.

    Ex. opt = {“CONSTRAINT”: [“tors 2 3 4 5 25.0”, “tors 2 5 7 9 80.0”], “FIXED”: [“2 XY”]}

  • scan_variables (dict) –

    A dictionary of scan variables. Because two constraints of the same type are allowed (for instance, two torsions or two bond stretches), each TYPE of variable (stre, bend, tors) should be its own key in the dict, rather than each variable. Note that the total number of variable (sum of lengths of all lists) CANNOT be more than two.

    Ex. scan_variables = {“stre”: [“3 6 1.5 1.9 0.1”], “tors”: [“1 2 3 4 -180 180 15”]}

  • basis_set (str) – Basis set to use. (Default: “def2-svpd”)

  • scf_algorithm (str) – Algorithm to use for converging the SCF. Recommended choices are “DIIS”, “GDM”, and “DIIS_GDM”. Other algorithms supported by Qchem’s GEN_SCFMAN module will also likely perform well. Refer to the QChem manual for further details. (Default: “diis”)

  • qchem_version (int) – Which major version of Q-Chem will be run. Supports 5 and 6. (Default: 5)

  • dft_rung (int) –

    Select the rung on “Jacob’s Ladder of Density Functional Approximations” in order of increasing accuracy/cost. For each rung, we have prescribed one functional based on our experience, available benchmarks, and the suggestions of the Q-Chem manual: 1 (LSDA) = SPW92 2 (GGA) = B97-D3(BJ) 3 (metaGGA) = B97M-V 4 (hybrid metaGGA) = ωB97M-V 5 (double hybrid metaGGA) = ωB97M-(2)

    (Default: 4)

    To set a functional not given by one of the above, set the overwrite_inputs argument to {“method”:”<NAME OF FUNCTIONAL>”}

  • pcm_dielectric (float) –

    Dielectric constant to use for PCM implicit solvation model. (Default: None) If supplied, will set up the $pcm section of the input file for a C-PCM calculation. Other types of PCM calculations (e.g., IEF-PCM, SS(V)PE, etc.) may be requested by passing custom keywords to overwrite_inputs, e.g. overwrite_inputs = {“pcm”: {“theory”: “ssvpe”}} Refer to the QChem manual for further details on the models available.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • isosvp_dielectric (float) –

    Dielectric constant to use for isodensity SS(V)PE implicit solvation model. (Default: None). If supplied, will set solvent_method to “isosvp” and populate the $svp section of the input file with appropriate parameters.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • smd_solvent (str) –

    Solvent to use for SMD implicit solvation model. (Default: None) Examples include “water”, “ethanol”, “methanol”, and “acetonitrile”. Refer to the QChem manual for a complete list of solvents available. To define a custom solvent, set this argument to “custom” and populate custom_smd with the necessary parameters.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • cmirs_solvent (str) –

    Solvent to use for the CMIRS implicit solvation model. (Default: None). Only 5 solvents are presently available as of Q-Chem 6: “water”, “benzene”, “cyclohexane”, “dimethyl sulfoxide”, and “acetonitrile”. Note that selection of a solvent here will also populate the iso SS(V)PE dielectric constant, because CMIRS uses the isodensity SS(V)PE model to compute electrostatics.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • custom_smd (str) – List of parameters to define a custom solvent in SMD. (Default: None) Must be given as a string of seven comma separated values in the following order: “dielectric, refractive index, acidity, basicity, surface tension, aromaticity, electronegative halogenicity” Refer to the QChem manual for further details.

  • max_scf_cycles (int) – Maximum number of SCF iterations. (Default: 100)

  • plot_cubes (bool) – Whether to write CUBE files of the electron density. (Default: False)

  • overwrite_inputs (dict) –

    Dictionary of QChem input sections to add or overwrite variables. The currently available sections (keys) are rem, pcm, solvent, smx, opt, scan, van_der_waals, and plots. The value of each key is a dictionary of key value pairs relevant to that section. For example, to add a new variable to the rem section that sets symmetry to false, use

    overwrite_inputs = {“rem”: {“symmetry”: “false”}}

    Note that if something like basis is added to the rem dict it will overwrite the default basis.

    Note that supplying a van_der_waals section here will automatically modify the PCM “radii” setting to “read”.

    Note that all keys must be given as strings, even when they are numbers!

  • vdw_mode ('atomic' | 'sequential') – Method of specifying custom van der Waals radii. Applies only if you are using overwrite_inputs to add a $van_der_waals section to the input. In ‘atomic’ mode (default), dict keys represent the atomic number associated with each radius (e.g., ‘12’ = carbon). In ‘sequential’ mode, dict keys represent the sequential position of a single specific atom in the input structure.

class QChemDictSet(molecule: Molecule, job_type: str, basis_set: str, scf_algorithm: str, qchem_version: int = 5, dft_rung: int = 4, pcm_dielectric: float | None = None, isosvp_dielectric: float | None = None, smd_solvent: str | None = None, cmirs_solvent: Literal['water', 'acetonitrile', 'dimethyl sulfoxide', 'cyclohexane', 'benzene'] | None = None, custom_smd: str | None = None, opt_variables: dict[str, list] | None = None, scan_variables: dict[str, list] | None = None, max_scf_cycles: int = 100, geom_opt_max_cycles: int = 200, plot_cubes: bool = False, nbo_params: dict | None = None, geom_opt: dict | None = None, cdft_constraints: list[list[dict]] | None = None, almo_coupling_states: list[list[tuple[int, int]]] | None = None, overwrite_inputs: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic', extra_scf_print: bool = False)[source]

Bases: QCInput

Build a QCInput given all the various input parameters. Can be extended by standard implementations below.

Parameters:
  • molecule (Pymatgen Molecule object) – Molecule to run QChem on.

  • job_type (str) – QChem job type to run. Valid options are “opt” for optimization, “sp” for single point, “freq” for frequency calculation, or “force” for force evaluation.

  • basis_set (str) – Basis set to use. For example, “def2-tzvpd”.

  • scf_algorithm (str) – Algorithm to use for converging the SCF. Recommended choices are “DIIS”, “GDM”, and “DIIS_GDM”. Other algorithms supported by Qchem’s GEN_SCFMAN module will also likely perform well. Refer to the QChem manual for further details.

  • qchem_version (int) – Which major version of Q-Chem will be run. Supports 5 and 6. (Default: 5)

  • dft_rung (int) –

    Select the rung on “Jacob’s Ladder of Density Functional Approximations” in order of increasing accuracy/cost. For each rung, we have prescribed one functional based on our experience, available benchmarks, and the suggestions of the Q-Chem manual: 1 (LSDA) = SPW92 2 (GGA) = B97-D3(BJ) 3 (metaGGA) = B97M-V 4 (hybrid metaGGA) = ωB97M-V 5 (double hybrid metaGGA) = ωB97M-(2).

    (Default: 4)

    To set a functional not given by one of the above, set the overwrite_inputs argument to {“method”:”<NAME OF FUNCTIONAL>”}

  • pcm_dielectric (float) –

    Dielectric constant to use for PCM implicit solvation model. (Default: None) If supplied, will set up the $pcm section of the input file for a C-PCM calculation. Other types of PCM calculations (e.g., IEF-PCM, SS(V)PE, etc.) may be requested by passing custom keywords to overwrite_inputs, e.g. overwrite_inputs = {“pcm”: {“theory”: “ssvpe”}} Refer to the QChem manual for further details on the models available.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • isosvp_dielectric (float) –

    Dielectric constant to use for isodensity SS(V)PE implicit solvation model. (Default: None). If supplied, will set solvent_method to “isosvp” and populate the $svp section of the input file with appropriate parameters.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • smd_solvent (str) –

    Solvent to use for SMD implicit solvation model. (Default: None) Examples include “water”, “ethanol”, “methanol”, and “acetonitrile”. Refer to the QChem manual for a complete list of solvents available. To define a custom solvent, set this argument to “custom” and populate custom_smd with the necessary parameters.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • cmirs_solvent (str) –

    Solvent to use for the CMIRS implicit solvation model. (Default: None). Only 5 solvents are presently available as of Q-Chem 6: “water”, “benzene”, “cyclohexane”, “dimethyl sulfoxide”, and “acetonitrile”. Note that selection of a solvent here will also populate the iso SS(V)PE dielectric constant, because CMIRS uses the isodensity SS(V)PE model to compute electrostatics.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • custom_smd (str) – List of parameters to define a custom solvent in SMD. (Default: None) Must be given as a string of seven comma separated values in the following order: “dielectric, refractive index, acidity, basicity, surface tension, aromaticity, electronegative halogenicity” Refer to the QChem manual for further details.

  • opt_variables (dict) –

    A dictionary of opt sections, where each opt section is a key and the corresponding values are a list of strings. Strings must be formatted as instructed by the QChem manual. The different opt sections are: CONSTRAINT, FIXED, DUMMY, and CONNECT.

    Ex. opt = {“CONSTRAINT”: [“tors 2 3 4 5 25.0”, “tors 2 5 7 9 80.0”], “FIXED”: [“2 XY”]}

  • scan_variables (dict) –

    A dictionary of scan variables. Because two constraints of the same type are allowed (for instance, two torsions or two bond stretches), each TYPE of variable (stre, bend, tors) should be its own key in the dict, rather than each variable. Note that the total number of variable (sum of lengths of all lists) CANNOT be more than two.

    Ex. scan_variables = {“stre”: [“3 6 1.5 1.9 0.1”], “tors”: [“1 2 3 4 -180 180 15”]}

  • max_scf_cycles (int) – Maximum number of SCF iterations. (Default: 100)

  • geom_opt_max_cycles (int) – Maximum number of geometry optimization iterations. (Default: 200)

  • plot_cubes (bool) – Whether to write CUBE files of the electron density. (Default: False)

  • nbo_params (dict) – A dict containing the desired NBO params. Note that a key:value pair of “version”:7 will trigger NBO7 analysis. Otherwise, NBO5 analysis will be performed, including if an empty dict is passed. Besides a key of “version”, all other key:value pairs will be written into the $nbo section of the QChem input file. (Default: False)

  • geom_opt (dict) – A dict containing parameters for the $geom_opt section of the Q-Chem input file, which control the new geometry optimizer available starting in version 5.4.2. The new optimizer remains under development but was officially released and became the default optimizer in Q-Chem version 6.0.0. Note that for version 5.4.2, the new optimizer must be explicitly requested by passing in a dictionary (empty or otherwise) for this input parameter. (Default: False)

  • vdw_mode ('atomic' | 'sequential') –

    Method of specifying custom van der Waals radii. Applies only if you are using overwrite_inputs to add a $van_der_waals section to the input. In ‘atomic’ mode (default), dict keys represent the atomic number associated with each radius (e.g., ‘12’ = carbon). In ‘sequential’ mode, dict keys represent the sequential position of a single specific atom in the input structure.

    cdft_constraints (list of lists of dicts):

    A list of lists of dictionaries, where each dictionary represents a charge constraint in the cdft section of the QChem input file.

    Each entry in the main list represents one state (allowing for multi-configuration calculations using constrained density functional theory - configuration interaction (CDFT-CI). Each state is represented by a list, which itself contains some number of constraints (dictionaries).

    Ex:

    1. For a single-state calculation with two constraints:

    cdft_constraints=[[
    {

    “value”: 1.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [2], “types”: [None]

    }, {

    ”value”: 2.0, “coefficients”: [1.0, -1.0], “first_atoms”: [1, 17], “last_atoms”: [3, 19], “types”: [“s”]

    }

    ]]

    Note that a type of None will default to a charge constraint (which can also be accessed by requesting a type of “c” or “charge”).

    2. For a CDFT-CI multi-reference calculation: cdft_constraints=[

    [
    {

    “value”: 1.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27], “types”: [“c”]

    }, {

    ”value”: 0.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27], “types”: [“s”]

    },

    ], [

    {

    “value”: 0.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27], “types”: [“c”]

    }, {

    ”value”: -1.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27], “types”: [“s”]

    },

    ]

    ]

  • cdft_constraints (list[list[dict]]) – A list of lists of dictionaries, where each

  • almo_coupling_states (list of lists of int 2-tuples) –

    A list of lists of int 2-tuples used for calculations of diabatization and state coupling calculations relying on the absolutely localized molecular orbitals (ALMO) methodology. Each entry in the main list represents a single state (two states are included in an ALMO calculation). Within a single state, each 2-tuple represents the charge and spin multiplicity of a single fragment. ex: almo_coupling_states=[

    [

    (1, 2), (0, 1)

    ], [

    (0, 1), (1, 2)

    ]

    ]

  • overwrite_inputs (dict) –

    Dictionary of QChem input sections to add or overwrite variables. The currently available sections (keys) are rem, pcm, solvent, smx, opt, scan, van_der_waals, and plots. The value of each key is a dictionary of key value pairs relevant to that section. For example, to add a new variable to the rem section that sets symmetry to false, use

    overwrite_inputs = {“rem”: {“symmetry”: “false”}}

    Note that if something like basis is added to the rem dict it will overwrite the default basis.

    Note that supplying a van_der_waals section here will automatically modify the PCM “radii” setting to “read”.

    Note that all keys must be given as strings, even when they are numbers!

  • vdw_mode – Method of specifying custom van der Waals radii. Applies only if you are using overwrite_inputs to add a $van_der_waals section to the input. In ‘atomic’ mode (default), dict keys represent the atomic number associated with each radius (e.g., ‘12’ = carbon). In ‘sequential’ mode, dict keys represent the sequential position of a single specific atom in the input structure.

  • extra_scf_print (bool) – Whether to store extra information generated from the SCF cycle. If switched on, the Fock Matrix, coefficients of MO and the density matrix will be stored.

write(input_file: str)[source]
Parameters:

input_file (str) – Filename.

class SinglePointSet(molecule: Molecule, basis_set: str = 'def2-tzvpd', scf_algorithm: str = 'diis', qchem_version: int = 5, dft_rung: int = 4, pcm_dielectric: float | None = None, isosvp_dielectric: float | None = None, smd_solvent: str | None = None, cmirs_solvent: Literal['water', 'acetonitrile', 'dimethyl sulfoxide', 'cyclohexane', 'benzene'] | None = None, custom_smd: str | None = None, max_scf_cycles: int = 100, plot_cubes: bool = False, nbo_params: dict | None = None, vdw_mode: Literal['atomic', 'sequential'] = 'atomic', cdft_constraints: list[list[dict]] | None = None, almo_coupling_states: list[list[tuple[int, int]]] | None = None, extra_scf_print: bool = False, overwrite_inputs: dict | None = None)[source]

Bases: QChemDictSet

QChemDictSet for a single point calculation.

Parameters:
  • molecule (Pymatgen Molecule object) –

  • job_type (str) – QChem job type to run. Valid options are “opt” for optimization, “sp” for single point, “freq” for frequency calculation, or “force” for force evaluation.

  • basis_set (str) – Basis set to use. (Default: “def2-tzvpd”)

  • scf_algorithm (str) – Algorithm to use for converging the SCF. Recommended choices are “DIIS”, “GDM”, and “DIIS_GDM”. Other algorithms supported by Qchem’s GEN_SCFMAN module will also likely perform well. Refer to the QChem manual for further details. (Default: “diis”)

  • qchem_version (int) – Which major version of Q-Chem will be run. Supports 5 and 6. (Default: 5)

  • dft_rung (int) –

    Select the rung on “Jacob’s Ladder of Density Functional Approximations” in order of increasing accuracy/cost. For each rung, we have prescribed one functional based on our experience, available benchmarks, and the suggestions of the Q-Chem manual: 1 (LSDA) = SPW92 2 (GGA) = B97-D3(BJ) 3 (metaGGA) = B97M-V 4 (hybrid metaGGA) = ωB97M-V 5 (double hybrid metaGGA) = ωB97M-(2).

    (Default: 4)

    To set a functional not given by one of the above, set the overwrite_inputs argument to {“method”:”<NAME OF FUNCTIONAL>”}

  • pcm_dielectric (float) –

    Dielectric constant to use for PCM implicit solvation model. (Default: None) If supplied, will set up the $pcm section of the input file for a C-PCM calculation. Other types of PCM calculations (e.g., IEF-PCM, SS(V)PE, etc.) may be requested by passing custom keywords to overwrite_inputs, e.g. overwrite_inputs = {“pcm”: {“theory”: “ssvpe”}} Refer to the QChem manual for further details on the models available.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • isosvp_dielectric (float) –

    Dielectric constant to use for isodensity SS(V)PE implicit solvation model. (Default: None). If supplied, will set solvent_method to “isosvp” and populate the $svp section of the input file with appropriate parameters. Note that due to limitations in Q-Chem, use of the ISOSVP or CMIRS solvent models will disable the GEN_SCFMAN algorithm, which may limit compatible choices for scf_algorithm.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • smd_solvent (str) –

    Solvent to use for SMD implicit solvation model. (Default: None) Examples include “water”, “ethanol”, “methanol”, and “acetonitrile”. Refer to the QChem manual for a complete list of solvents available. To define a custom solvent, set this argument to “custom” and populate custom_smd with the necessary parameters.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • cmirs_solvent (str) –

    Solvent to use for the CMIRS implicit solvation model. (Default: None). Only 5 solvents are presently available as of Q-Chem 6: “water”, “benzene”, “cyclohexane”, “dimethyl sulfoxide”, and “acetonitrile”. Note that selection of a solvent here will also populate the iso SS(V)PE dielectric constant, because CMIRS uses the isodensity SS(V)PE model to compute electrostatics. Note also that due to limitations in Q-Chem, use of the ISOSVP or CMIRS solvent models will disable the GEN_SCFMAN algorithm, which may limit compatible choices for scf_algorithm.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • custom_smd (str) – List of parameters to define a custom solvent in SMD. (Default: None) Must be given as a string of seven comma separated values in the following order: “dielectric, refractive index, acidity, basicity, surface tension, aromaticity, electronegative halogenicity” Refer to the QChem manual for further details.

  • max_scf_cycles (int) – Maximum number of SCF iterations. (Default: 100)

  • plot_cubes (bool) – Whether to write CUBE files of the electron density. (Default: False)

  • cdft_constraints (list of lists of dicts) –

    A list of lists of dictionaries, where each dictionary represents a charge constraint in the cdft section of the QChem input file.

    Each entry in the main list represents one state (allowing for multi-configuration calculations using constrained density functional theory - configuration interaction (CDFT-CI). Each state is represented by a list, which itself contains some number of constraints (dictionaries).

    Ex:

    1. For a single-state calculation with two constraints:

    cdft_constraints=[[
    {

    “value”: 1.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [2], “types”: [None]

    }, {

    ”value”: 2.0, “coefficients”: [1.0, -1.0], “first_atoms”: [1, 17], “last_atoms”: [3, 19], “types”: [“s”]

    }

    ]]

    Note that a type of None will default to a charge constraint (which can also be accessed by requesting a type of “c” or “charge”).

    2. For a CDFT-CI multi-reference calculation: cdft_constraints=[

    [
    {

    “value”: 1.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27], “types”: [“c”]

    }, {

    ”value”: 0.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27], “types”: [“s”]

    },

    ], [

    {

    “value”: 0.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27], “types”: [“c”]

    }, {

    ”value”: -1.0, “coefficients”: [1.0], “first_atoms”: [1], “last_atoms”: [27], “types”: [“s”]

    },

    ]

    ]

  • almo_coupling_states (list of lists of int 2-tuples) –

    A list of lists of int 2-tuples used for calculations of diabatization and state coupling calculations relying on the absolutely localized molecular orbitals (ALMO) methodology. Each entry in the main list represents a single state (two states are included in an ALMO calculation). Within a single state, each 2-tuple represents the charge and spin multiplicity of a single fragment. ex: almo_coupling_states=[

    [

    (1, 2), (0, 1)

    ], [

    (0, 1), (1, 2)

    ]

    ]

  • vdw_mode ('atomic' | 'sequential') – Method of specifying custom van der Waals radii. Applies only if you are using overwrite_inputs to add a $van_der_waals section to the input. In ‘atomic’ mode (default), dict keys represent the atomic number associated with each radius (e.g., ‘12’ = carbon). In ‘sequential’ mode, dict keys represent the sequential position of a single specific atom in the input structure.

  • overwrite_inputs (dict) –

    Dictionary of QChem input sections to add or overwrite variables. The currently available sections (keys) are rem, pcm, solvent, smx, opt, scan, van_der_waals, and plots. The value of each key is a dictionary of key value pairs relevant to that section. For example, to add a new variable to the rem section that sets symmetry to false, use

    overwrite_inputs = {“rem”: {“symmetry”: “false”}}

    Note that if something like basis is added to the rem dict it will overwrite the default basis.

    Note that supplying a van_der_waals section here will automatically modify the PCM “radii” setting to “read”.

    Note that all keys must be given as strings, even when they are numbers!

  • vdw_mode – Method of specifying custom van der Waals radii. Applies only if you are using overwrite_inputs to add a $van_der_waals section to the input. In ‘atomic’ mode (default), dict keys represent the atomic number associated with each radius (e.g., ‘12’ = carbon). In ‘sequential’ mode, dict keys represent the sequential position of a single specific atom in the input structure.

  • extra_scf_print (bool) – Whether to store extra information generated from the SCF cycle. If switched on, the Fock Matrix, coefficients of MO and the density matrix will be stored.

class TransitionStateSet(molecule: Molecule, basis_set: str = 'def2-svpd', scf_algorithm: str = 'diis', qchem_version: int = 5, dft_rung: int = 4, pcm_dielectric: float | None = None, isosvp_dielectric: float | None = None, smd_solvent: str | None = None, cmirs_solvent: Literal['water', 'acetonitrile', 'dimethyl sulfoxide', 'cyclohexane', 'benzene'] | None = None, custom_smd: str | None = None, max_scf_cycles: int = 100, plot_cubes: bool = False, nbo_params: dict | None = None, opt_variables: dict[str, list] | None = None, geom_opt_max_cycles: int = 200, geom_opt: dict | None = None, overwrite_inputs: dict | None = None, vdw_mode='atomic')[source]

Bases: QChemDictSet

QChemDictSet for a transition-state search.

Parameters:
  • molecule (Pymatgen Molecule object) –

  • basis_set (str) – Basis set to use. (Default: “def2-svpd”)

  • scf_algorithm (str) – Algorithm to use for converging the SCF. Recommended choices are “DIIS”, “GDM”, and “DIIS_GDM”. Other algorithms supported by Qchem’s GEN_SCFMAN module will also likely perform well. Refer to the QChem manual for further details. (Default: “diis”)

  • qchem_version (int) – Which major version of Q-Chem will be run. Supports 5 and 6. (Default: 5)

  • dft_rung (int) –

    Select the rung on “Jacob’s Ladder of Density Functional Approximations” in order of increasing accuracy/cost. For each rung, we have prescribed one functional based on our experience, available benchmarks, and the suggestions of the Q-Chem manual: 1 (LSDA) = SPW92 2 (GGA) = B97-D3(BJ) 3 (metaGGA) = B97M-V 4 (hybrid metaGGA) = ωB97M-V 5 (double hybrid metaGGA) = ωB97M-(2).

    (Default: 4)

    To set a functional not given by one of the above, set the overwrite_inputs argument to {“method”:”<NAME OF FUNCTIONAL>”}

  • pcm_dielectric (float) –

    Dielectric constant to use for PCM implicit solvation model. (Default: None) If supplied, will set up the $pcm section of the input file for a C-PCM calculation. Other types of PCM calculations (e.g., IEF-PCM, SS(V)PE, etc.) may be requested by passing custom keywords to overwrite_inputs, e.g. overwrite_inputs = {“pcm”: {“theory”: “ssvpe”}} Refer to the QChem manual for further details on the models available.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • isosvp_dielectric (float) –

    Dielectric constant to use for isodensity SS(V)PE implicit solvation model. (Default: None). If supplied, will set solvent_method to “isosvp” and populate the $svp section of the input file with appropriate parameters.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • smd_solvent (str) –

    Solvent to use for SMD implicit solvation model. (Default: None) Examples include “water”, “ethanol”, “methanol”, and “acetonitrile”. Refer to the QChem manual for a complete list of solvents available. To define a custom solvent, set this argument to “custom” and populate custom_smd with the necessary parameters.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • cmirs_solvent (str) –

    Solvent to use for the CMIRS implicit solvation model. (Default: None). Only 5 solvents are presently available as of Q-Chem 6: “water”, “benzene”, “cyclohexane”, “dimethyl sulfoxide”, and “acetonitrile”. Note that selection of a solvent here will also populate the iso SS(V)PE dielectric constant, because CMIRS uses the isodensity SS(V)PE model to compute electrostatics.

    Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.

  • custom_smd (str) – List of parameters to define a custom solvent in SMD. (Default: None) Must be given as a string of seven comma separated values in the following order: “dielectric, refractive index, acidity, basicity, surface tension, aromaticity, electronegative halogenicity” Refer to the QChem manual for further details.

  • max_scf_cycles (int) – Maximum number of SCF iterations. (Default: 100)

  • geom_opt_max_cycles (int) – Maximum number of geometry optimization iterations. (Default: 200)

  • geom_opt (dict) – A dict containing parameters for the $geom_opt section of the Q-Chem input file, which control the new geometry optimizer available starting in version 5.4.2. The new optimizer remains under development but was officially released and became the default optimizer in Q-Chem version 6.0.0. Note that for version 5.4.2, the new optimizer must be explicitly requested by passing in a dictionary (empty or otherwise) for this input parameter. (Default: False)

  • plot_cubes (bool) – Whether to write CUBE files of the electron density. (Default: False)

  • overwrite_inputs (dict) –

    Dictionary of QChem input sections to add or overwrite variables. The currently available sections (keys) are rem, pcm, solvent, smx, opt, scan, van_der_waals, and plots. The value of each key is a dictionary of key value pairs relevant to that section. For example, to add a new variable to the rem section that sets symmetry to false, use

    overwrite_inputs = {“rem”: {“symmetry”: “false”}}

    Note that if something like basis is added to the rem dict it will overwrite the default basis.

    Note that supplying a van_der_waals section here will automatically modify the PCM “radii” setting to “read”.

    Note that all keys must be given as strings, even when they are numbers!

  • vdw_mode ('atomic' | 'sequential') – Method of specifying custom van der Waals radii. Applies only if you are using overwrite_inputs to add a $van_der_waals section to the input. In ‘atomic’ mode (default), dict keys represent the atomic number associated with each radius (e.g., ‘12’ = carbon). In ‘sequential’ mode, dict keys represent the sequential position of a single specific atom in the input structure.

pymatgen.io.qchem.utils module

Utilities for Qchem io.

lower_and_check_unique(dict_to_check)[source]

Takes a dictionary and makes all the keys lower case. Also converts all numeric values (floats, ints) to str and replaces “jobtype” with “job_type” just so that key specifically can be called elsewhere without ambiguity. Finally, ensures that multiple identical keys, that differed only due to different capitalizations, are not present. If there are multiple equivalent keys, an Exception is raised.

Parameters:

dict_to_check (dict) – The dictionary to check and standardize

Returns:

An identical dictionary but with all keys made

lower case and no identical keys present.

Return type:

to_return (dict)

process_parsed_coords(coords)[source]

Takes a set of parsed coordinates, which come as an array of strings, and returns a numpy array of floats.

process_parsed_fock_matrix(fock_matrix)[source]

The Fock matrix is parsed as a list, while it should actually be a square matrix, this function takes the list of finds the right dimensions in order to reshape the matrix.

process_parsed_hess(hess_data)[source]

Takes the information contained in a HESS file and converts it into the format of the machine-readable 132.0 file which can be printed out to be read into subsequent optimizations.

read_matrix_pattern(header_pattern, footer_pattern, elements_pattern, text, postprocess=<class 'str'>)[source]

Parse a matrix to get the quantities in a numpy array.

read_pattern(text_str, patterns, terminate_on_match=False, postprocess=<class 'str'>)[source]

General pattern reading on an input string.

Parameters:
  • text_str (str) – the input string to search for patterns

  • patterns (dict) – A dict of patterns, e.g., {“energy”: r”energy\(sigma->0\)\s+=\s+([\d\-.]+)”}.

  • terminate_on_match (bool) – Whether to terminate when there is at least one match in each key in pattern.

  • postprocess (callable) – A post processing function to convert all matches. Defaults to str, i.e., no change.

Renders accessible:

Any attribute in patterns. For example, {“energy”: r”energy\(sigma->0\)\s+=\s+([\d\-.]+)”} will set the value of matches[“energy”] = [[-1234], [-3453], …], to the results from regex and postprocess. Note that the returned values are lists of lists, because you can grep multiple items on one line.

read_table_pattern(text_str, header_pattern, row_pattern, footer_pattern, postprocess=<class 'str'>, attribute_name=None, last_one_only=False)[source]

Parse table-like data. A table composes of three parts: header, main body, footer. All the data matches “row pattern” in the main body will be returned.

Parameters:
  • text_str (str) – the input string to search for patterns

  • header_pattern (str) – The regular expression pattern matches the table header. This pattern should match all the text immediately before the main body of the table. For multiple sections table match the text until the section of interest. MULTILINE and DOTALL options are enforced, as a result, the “.” meta-character will also match “n” in this section.

  • row_pattern (str) – The regular expression matches a single line in the table. Capture interested field using regular expression groups.

  • footer_pattern (str) – The regular expression matches the end of the table. E.g. a long dash line.

  • postprocess (callable) – A post processing function to convert all matches. Defaults to str, i.e., no change.

  • attribute_name (str) – Name of this table. If present the parsed data will be attached to “data. e.g. self.data[“efg”] = […]

  • last_one_only (bool) – All the tables will be parsed, if this option is set to True, only the last table will be returned. The enclosing list will be removed. i.e. Only a single table will be returned. Default to be True.

Returns:

List of tables. 1) A table is a list of rows. 2) A row if either a list of attribute values in case the capturing group is defined without name in row_pattern, or a dict in case that named capturing groups are defined by row_pattern.