pymatgen.io.qchem.inputs module

Classes for reading/manipulating/writing QChem input files.

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[pymatgen.io.qchem.inputs.QCInput][source]

Create list of QcInput from a file.

Parameters:: filename (str) – Filename
Returns:: List of QCInput objects

classmethod from_string(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_string()[source]: Return a string representation of an entire input file.

static molecule_template(molecule: Molecule | list[pymatgen.core.structure.Molecule] | Literal['read']) → str[source]

Parameters:: molecule (Molecule, list of Molecules, or "read") –
Returns:: (str) Molecule template.

static multi_job_string(job_list: list[pymatgen.io.qchem.inputs.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:: (list of lists of dicts) cdft parameters

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[pymatgen.core.structure.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[pymatgen.io.qchem.inputs.QCInput], filename: str)[source]

Write a multijob file.

Parameters:

() (filename) – List of jobs.
() – Filename