`chemparseplot.parse.eon.saddle_search`¶

Module Contents¶

Classes¶

EONSaddleStatus

Status codes returned by eOn saddle point searches.

Functions¶

`extract_saddle_gprd`	Extract saddle point geometry from GPRD log lines.
`_read_results_dat`	Reads and parses the results.dat file.
`_find_log_file`	Finds the most recent, valid log file within the eOn results directory.
`_extract_total_time`	Extracts the total run time from the log data.
`_extract_initial_energy`	Extracts the initial energy from the log data.
`_extract_saddle_info`	Extracts saddle point information (saddle_fmax and method) from the log data.
`_get_methods`
`parse_eon_saddle`	Parses eOn saddle point search results from a directory.

Data¶

log

API¶

chemparseplot.parse.eon.saddle_search.log¶: ‘getLogger(…)’

class chemparseplot.parse.eon.saddle_search.EONSaddleStatus(*args, **kwds)¶

Bases: enum.Enum

Status codes returned by eOn saddle point searches.

Added in version 0.0.3.

Initialization

GOOD¶: (0, ‘Success’)

INIT¶: (1, ‘Initial’)

BAD_NO_CONVEX¶: (2, ‘Initial displacement unable to reach convex region’)

BAD_HIGH_ENERGY¶: (3, ‘Barrier too high’)

BAD_MAX_CONCAVE_ITERATIONS¶: (4, ‘Too many iterations in concave region’)

BAD_MAX_ITERATIONS¶: (5, ‘Too many iterations’)

BAD_NOT_CONNECTED¶: (6, ‘Saddle is not connected to initial state’)

BAD_PREFACTOR¶: (7, ‘Prefactors not within window’)

BAD_HIGH_BARRIER¶: (8, ‘Energy barrier not within window’)

BAD_MINIMA¶: (9, ‘Minimizations from saddle did not converge’)

FAILED_PREFACTOR¶: (10, ‘Hessian calculation failed’)

POTENTIAL_FAILED¶: (11, ‘Potential failed’)

NONNEGATIVE_ABORT¶: (12, ‘Nonnegative initial mode, aborting’)

NONLOCAL_ABORT¶: (13, ‘Nonlocal abort’)

NEGATIVE_BARRIER¶: (14, ‘Negative barrier detected’)

BAD_MD_TRAJECTORY_TOO_SHORT¶: (15, ‘No reaction found during MD trajectory’)

BAD_NO_NEGATIVE_MODE_AT_SADDLE¶: (16, ‘Converged to stationary point with zero negative modes’)

BAD_NO_BARRIER¶: (17, ‘No forward barrier was found along minimized band’)

ZEROMODE_ABORT¶: (18, ‘Zero mode abort.’)

OPTIMIZER_ERROR¶: (19, ‘Optimizer error.’)

UNKNOWN¶: ()

__new__(value, description)¶

classmethod from_value(value)¶

chemparseplot.parse.eon.saddle_search.extract_saddle_gprd(log: list[str])¶: Extract saddle point geometry from GPRD log lines.

Added in version 0.0.3.

chemparseplot.parse.eon.saddle_search._read_results_dat(eresp: pathlib.Path) → dict¶

Reads and parses the results.dat file.

Args: eresp: Path to the eOn results directory.

Returns: A dictionary containing the parsed data from results.dat, or None if the file does not exist or the termination reason is not 0.

chemparseplot.parse.eon.saddle_search._find_log_file(eresp: pathlib.Path) → pathlib.Path | None¶

Finds the most recent, valid log file within the eOn results directory.

Args: eresp: Path to the eOn results directory.

Returns: Path to the chosen log file, or None if no suitable log file is found.

chemparseplot.parse.eon.saddle_search._extract_total_time(log_data: list[str]) → float¶

Extracts the total run time from the log data.

Args: log_data: A list of strings representing the lines of the log file.

Returns: The total run time in seconds as a float, or 0.0 if not found.

chemparseplot.parse.eon.saddle_search._extract_initial_energy(log_data: list[str]) → float¶

Extracts the initial energy from the log data.

Args: log_data: A list of strings representing the lines of the log file.

Returns: The initial energy as a float, or None if not found.

chemparseplot.parse.eon.saddle_search._extract_saddle_info(log_data: list[str], eresp: pathlib.Path, *, is_gprd: bool) → tuple[float, str]¶

Extracts saddle point information (saddle_fmax and method) from the log data.

Args: log_data: A list of strings representing the lines of the log file. eresp: Path to the eOn results directory. is_gprd: Boolean flag indicating whether the GPRD method was used.

Returns: A tuple containing: - saddle_fmax: The maximum force at the saddle point.

chemparseplot.parse.eon.saddle_search._get_methods(eresp: pathlib.Path) → rgpycrumbs.basetypes.DimerOpt¶

chemparseplot.parse.eon.saddle_search.parse_eon_saddle(eresp: pathlib.Path, rloc: rgpycrumbs.basetypes.SpinID) → rgpycrumbs.basetypes.SaddleMeasure¶

Parses eOn saddle point search results from a directory.