diff --git a/src/alchemlyb/workflows/abfe.py b/src/alchemlyb/workflows/abfe.py index 95441643..e6cef074 100644 --- a/src/alchemlyb/workflows/abfe.py +++ b/src/alchemlyb/workflows/abfe.py @@ -113,13 +113,13 @@ def read(self): f'Reading {len(u_nk)} lines of u_nk from {file}') u_nk_list.append(u_nk) except Exception as exc: - msg = f'Error reading read u_nk from {file}.\n{exc}' + msg = f'Error reading read u_nk from {file}.' if self.ignore_warnings: - self.logger.exception(msg + + self.logger.exception(msg + f'\n{exc}\n' + 'This exception is being ignored because ignore_warnings=True.') else: self.logger.error(msg) - raise ValueError(msg) + raise ValueError(msg) from exc try: dhdl = self._extract_dHdl(file, T=self.T) @@ -127,13 +127,13 @@ def read(self): f'Reading {len(dhdl)} lines of dhdl from {file}') dHdl_list.append(dhdl) except Exception as exc: - msg = f'Error reading read dhdl from {file}.\n{exc}' + msg = f'Error reading read dhdl from {file}.' if self.ignore_warnings: - self.logger.exception(msg + + self.logger.exception(msg + f'\n{exc}\n' + 'This exception is being ignored because ignore_warnings=True.') else: self.logger.error(msg) - raise ValueError(msg) + raise ValueError(msg) from exc # Sort the files according to the state self.logger.info('Sort files according to the u_nk.') @@ -181,8 +181,9 @@ def run(self, skiptime=0, uncorr='dhdl', threshold=50, with the specified number of points in the time plot. The number of time points (an integer) must be provided. Specify as ``None`` will not do the convergence analysis. Default: None. By default, 'MBAR' - estimator will be used for convergence analysis. If the dataset - does not contain u_nk, please run + estimator will be used for convergence analysis, as it is + usually the fastest converging method. If the dataset does not + contain u_nk, please run meth:`~alchemlyb.workflows.ABFE.check_convergence` manually with estimator='TI'.