pymatgen.io.qchem.inputs module

Classes for reading/manipulating/writing QChem input files.

class QCInput(molecule: Union[pymatgen.core.structure.Molecule, Literal[read]], rem: Dict, opt: Optional[Dict[str, List]] = None, pcm: Optional[Dict] = None, solvent: Optional[Dict] = None, smx: Optional[Dict] = None, scan: Optional[Dict[str, List]] = None, van_der_waals: Optional[Dict[str, float]] = None, vdw_mode: str = 'atomic', plots: Optional[Dict] = None, nbo: Optional[Dict] = None)[source]

Bases: monty.json.MSONable

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 staticmethods 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 or "read") – Input molecule. molecule can be set as either a pymatgen Molecule object or as the str “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. Stings 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 construcing 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 QChem input file.

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

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) → pymatgen.io.qchem.inputs.QCInput[source]

Create QcInput from file. :param filename: Filename :type filename: str

Returns

QcInput

classmethod from_multi_jobs_file(filename: str) → List[pymatgen.io.qchem.inputs.QCInput][source]

Create list of QcInput from a file. :param filename: Filename :type filename: str

Returns

List of QCInput objects

classmethod from_string(string: str) → pymatgen.io.qchem.inputs.QCInput[source]

Read QcInput from string.

Parameters

string (str) – String input.

Returns

QcInput

static molecule_template(molecule: Union[pymatgen.core.structure.Molecule, Literal[read]]) → str[source]
Parameters

molecule (Molecule) – molecule

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_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_molecule(string: str) → Union[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_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_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 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

write_file(filename: str)[source]

Write QcInput to file.

Parameters

filename (str) – Filename

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

Write a multijob file.

Parameters

  • () (filename) – List of jobs.

  • () – Filename