`chemparseplot.parse.eon.saddle_search`#

Module Contents#

Classes#

`EonSaddleResults`	Parsed subset of `results.dat` needed for saddle post-processing.
`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[source]#: ‘getLogger(…)’

class chemparseplot.parse.eon.saddle_search.EonSaddleResults[source]#

Parsed subset of results.dat needed for saddle post-processing.

termination_status: str#: None

pes_calls: int | None#: None

iter_steps: int | None#: None

saddle_energy: float | None#: None

property terminal_only: bool#

class chemparseplot.parse.eon.saddle_search.EONSaddleStatus(*args, **kwds)[source]#

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)[source]#

chemparseplot.parse.eon.saddle_search.extract_saddle_gprd(log: list[str])[source]#: 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) → chemparseplot.parse.eon.saddle_search.EonSaddleResults | None[source]#

Reads and parses the results.dat file.

Args: eresp: Path to the eOn results directory.

Returns: Parsed results data, or None if the file does not exist.

chemparseplot.parse.eon.saddle_search._find_log_file(eresp: pathlib.Path) → pathlib.Path | None[source]#

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[source]#

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[source]#

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][source]#

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[source]#

chemparseplot.parse.eon.saddle_search.parse_eon_saddle(eresp: pathlib.Path, rloc: rgpycrumbs.basetypes.SpinID) → rgpycrumbs.basetypes.SaddleMeasure[source]#

Parses eOn saddle point search results from a directory.