Update dev docs

Author: shyuep

docs/custodian.gaussian.handlers.md

@@ -8,7 +8,7 @@ nav_exclude: true
 
 This module implements error handlers for Gaussian runs.
 
-### *class* custodian.gaussian.handlers.GaussianErrorHandler(input_file: str, output_file: str, stderr_file: str = 'stderr.txt', cart_coords: bool = True, scf_max_cycles: int = 100, opt_max_cycles: int = 100, job_type: str = 'normal', lower_functional: str | None = None, lower_basis_set: str | None = None, prefix: str = 'error', check_convergence: bool = True)
+## *class* custodian.gaussian.handlers.GaussianErrorHandler(input_file: str, output_file: str, stderr_file: str = ‘stderr.txt’, cart_coords: bool = True, scf_max_cycles: int = 100, opt_max_cycles: int = 100, job_type: str = ‘normal’, lower_functional: str | None = None, lower_basis_set: str | None = None, prefix: str = ‘error’, check_convergence: bool = True)
 
 Bases: `ErrorHandler`
 
@@ -41,19 +41,19 @@ Initialize the GaussianErrorHandler class.
     be monitored and plotted (convergence criteria versus cycle number) and
     saved to a file called ‘convergence.png’.
 
-#### GRID_NAMES *= ('finegrid', 'fine', 'superfinegrid', 'superfine', 'coarsegrid', 'coarse', 'sg1grid', 'sg1', 'pass0grid', 'pass0')*
+### GRID_NAMES *= (‘finegrid’, ‘fine’, ‘superfinegrid’, ‘superfine’, ‘coarsegrid’, ‘coarse’, ‘sg1grid’, ‘sg1’, ‘pass0grid’, ‘pass0’)*
 
-#### MEM_UNITS *= ('kb', 'mb', 'gb', 'tb', 'kw', 'mw', 'gw', 'tw')*
+### MEM_UNITS *= (‘kb’, ‘mb’, ‘gb’, ‘tb’, ‘kw’, ‘mw’, ‘gw’, ‘tw’)*
 
-#### activate_better_guess *= False*
+### activate_better_guess *= False*
 
-#### check(directory: str = './')
+### check(directory: str = ‘./’)
 
 Check for errors in the Gaussian output file.
 
-#### conv_criteria*: ClassVar* *= {'max_disp': re.compile('\\\\s+(Maximum Displacement)\\\\s+(-?\\\\d+.?\\\\d\*|.\*)\\\\s+(-?\\\\d+.?\\\\d\*)'), 'max_force': re.compile('\\\\s+(Maximum Force)\\\\s+(-?\\\\d+.?\\\\d\*|.\*)\\\\s+(-?\\\\d+.?\\\\d\*)'), 'rms_disp': re.compile('\\\\s+(RMS {5}Displacement)\\\\s+(-?\\\\d+.?\\\\d\*|.\*)\\\\s+(-?\\\\d+.?\\\\d\*)'), 'rms_force': re.compile('\\\\s+(RMS {5}Force)\\\\s+(-?\\\\d+.?\\\\d\*|.\*)\\\\s+(-?\\\\d+.?\\\\d\*)')}*
+### conv_criteria\*: ClassVar\* *= {‘max_disp’: re.compile(’\\s+(Maximum Displacement)\\s+(-?\\d+.?\\d\*|.\*)\\s+(-?\\d+.?\\d\*)’), ‘max_force’: re.compile(’\\s+(Maximum Force)\\s+(-?\\d+.?\\d\*|.\*)\\s+(-?\\d+.?\\d\*)’), ‘rms_disp’: re.compile(’\\s+(RMS {5}Displacement)\\s+(-?\\d+.?\\d\*|.\*)\\s+(-?\\d+.?\\d\*)’), ‘rms_force’: re.compile(’\\s+(RMS {5}Force)\\s+(-?\\d+.?\\d\*|.\*)\\s+(-?\\d+.?\\d\*)’)}*
 
-#### *static* convert_mem(mem: float, unit: str)
+### *static* convert_mem(mem: float, unit: str)
 
 Convert memory size between different units to megabytes (MB).
 
@@ -67,19 +67,19 @@ Convert memory size between different units to megabytes (MB).
 * **Return type:**
   float
 
-#### correct(directory: str = './')
+### correct(directory: str = ‘./’)
 
 Perform necessary actions to correct the errors in the Gaussian output.
 
-#### error_defs*: ClassVar* *= {'A syntax error was detected in the input line.': 'syntax', 'Atom specifications unexpectedly found in input stream.': 'found_coords', 'Bad file opened by FileIO': 'bad_file', 'Convergence failure': 'scf_convergence', 'End of file in ZSymb': 'zmatrix', 'End of file reading connectivity.': 'coords', 'Error in internal coordinate system': 'internal_coords', 'FileIO operation on non-existent file.': 'missing_file', 'FormBX had a problem': 'linear_bend', 'Inv3 failed in PCMMkU': 'solute_solvent_surface', 'Linear angle in Tors.': 'linear_bend', 'No data on chk file.': 'empty_file', 'Optimization stopped': 'opt_steps', 'Out-of-memory error in routine': 'insufficient_mem', 'The combination of multiplicity ([0-9]+) and \\\\s+? ([0-9]+) electrons is impossible.': 'charge', 'There are no atoms in this input structure !': 'missing_mol', 'Z-matrix optimization but no Z-matrix variables.': 'coord_inputs'}*
+### error_defs\*: ClassVar\* *= {‘A syntax error was detected in the input line.’: ‘syntax’, ‘Atom specifications unexpectedly found in input stream.’: ‘found_coords’, ‘Bad file opened by FileIO’: ‘bad_file’, ‘Convergence failure’: ‘scf_convergence’, ‘End of file in ZSymb’: ‘zmatrix’, ‘End of file reading connectivity.’: ‘coords’, ‘Error in internal coordinate system’: ‘internal_coords’, ‘FileIO operation on non-existent file.’: ‘missing_file’, ‘FormBX had a problem’: ‘linear_bend’, ‘Inv3 failed in PCMMkU’: ‘solute_solvent_surface’, ‘Linear angle in Tors.’: ‘linear_bend’, ‘No data on chk file.’: ‘empty_file’, ‘Optimization stopped’: ‘opt_steps’, ‘Out-of-memory error in routine’: ‘insufficient_mem’, ‘The combination of multiplicity ([0-9]+) and \\s+? ([0-9]+) electrons is impossible.’: ‘charge’, ‘There are no atoms in this input structure !’: ‘missing_mol’, ‘Z-matrix optimization but no Z-matrix variables.’: ‘coord_inputs’}*
 
-#### error_patt *= re.compile('Optimization stopped|Convergence failure|FormBX had a problem|Linear angle in Tors.|Inv3 failed in PCMMkU|Error in internal coordinate system|End of file in ZSymb|There are no atoms in this input str)*
+### error_patt *= re.compile(‘Optimization stopped|Convergence failure|FormBX had a problem|Linear angle in Tors.|Inv3 failed in PCMMkU|Error in internal coordinate system|End of file in ZSymb|There are no atoms in this input str)*
 
-#### grid_patt *= re.compile('(-?\\\\d{5})')*
+### grid_patt *= re.compile(‘(-?\\d{5})’)*
 
-#### recom_mem_patt *= re.compile('Use %mem=([0-9]+)MW to provide the minimum amount of memory required to complete this step.')*
+### recom_mem_patt *= re.compile(‘Use %mem=([0-9]+)MW to provide the minimum amount of memory required to complete this step.’)*
 
-### *class* custodian.gaussian.handlers.WallTimeErrorHandler(wall_time: int, buffer_time: int, input_file: str, output_file: str, stderr_file: str = 'stderr.txt', prefix: str = 'error')
+## *class* custodian.gaussian.handlers.WallTimeErrorHandler(wall_time: int, buffer_time: int, input_file: str, output_file: str, stderr_file: str = ‘stderr.txt’, prefix: str = ‘error’)
 
 Bases: `ErrorHandler`
 
@@ -102,15 +102,15 @@ Initialize the WalTimeErrorHandler class.
     which means a series of error.1.tar.gz, error.2.tar.gz, … will be
     generated.
 
-#### check(directory: str = './')
+### check(directory: str = ‘./’)
 
 Check if the job is nearing the walltime. If so, return True, else False.
 
-#### correct(directory: str = './')
+### correct(directory: str = ‘./’)
 
 Perform the corrections.
 
-#### is_monitor*: bool* *= True*
+### is_monitor\*: bool\* *= True*
 
 This class property indicates whether the error handler is a monitor,
 i.e., a handler that monitors a job as it is running. If a

docs/custodian.gaussian.jobs.md

@@ -8,7 +8,7 @@ nav_exclude: true
 
 This module implements basic kinds of jobs for Gaussian runs.
 
-### *class* custodian.gaussian.jobs.GaussianJob(gaussian_cmd: str, input_file: str, output_file: str, stderr_file: str = 'stderr.txt', suffix: str = '', backup: bool = True)
+## *class* custodian.gaussian.jobs.GaussianJob(gaussian_cmd: str, input_file: str, output_file: str, stderr_file: str = ‘stderr.txt’, suffix: str = ‘’, backup: bool = True)
 
 Bases: `Job`
 
@@ -26,7 +26,7 @@ A basic Gaussian job.
   * **backup** (*bool*) – Whether to backup the input file. If True, the input will be
     copied with a “.orig” appended to the name. Defaults to True.
 
-#### *classmethod* generate_better_guess(gaussian_cmd: str, input_file: str, output_file: str, stderr_file: str = 'stderr.txt', backup: bool = True, cart_coords: bool = True, directory: str = './')
+### *classmethod* generate_better_guess(gaussian_cmd: str, input_file: str, output_file: str, stderr_file: str = ‘stderr.txt’, backup: bool = True, cart_coords: bool = True, directory: str = ‘./’)
 
 Generate a better initial guess for a Gaussian calculation (optimization or
 SCF run). This is done by running the job at a lower level of theory
@@ -46,15 +46,15 @@ generated by the previous job.
 * **Yields:**
   *GaussianJob* – The Gaussian job instance.
 
-#### postprocess(directory: str = './')
+### postprocess(directory: str = ‘./’)
 
 Perform any postprocessing of the Gaussian run. This includes making a copy
 of the input and output file if a suffix is specified.
 
 * **Parameters:**
   **directory** (*str*) – Directory where the job was run. Defaults to ‘./’.
 
-#### run(directory: str = './')
+### run(directory: str = ‘./’)
 
 Perform the actual Gaussian run.
 
@@ -65,15 +65,15 @@ Perform the actual Gaussian run.
 * **Return type:**
   subprocess.Popen
 
-#### setup(directory: str = './')
+### setup(directory: str = ‘./’)
 
 Perform initial setup for the job, i.e., make a backup of the input file if
 requested.
 
 * **Parameters:**
   **directory** (*str*) – Directory where the job will be run. Defaults to ‘./’.
 
-#### terminate(directory: str = './')
+### terminate(directory: str = ‘./’)
 
 Terminate the Gaussian job.
 

docs/custodian.gaussian.md

@@ -8,7 +8,6 @@ nav_exclude: true
 
 This package implements various Gaussian Jobs and Error Handlers.
 
-
 * [custodian.gaussian.handlers module](custodian.gaussian.handlers.md)
   * [`GaussianErrorHandler`](custodian.gaussian.handlers.md#custodian.gaussian.handlers.GaussianErrorHandler)
     * [`GaussianErrorHandler.GRID_NAMES`](custodian.gaussian.handlers.md#custodian.gaussian.handlers.GaussianErrorHandler.GRID_NAMES)

docs/custodian.vasp.utils.md

@@ -8,29 +8,30 @@ nav_exclude: true
 
 Utility methods for VASP error handlers.
 
-### custodian.vasp.utils.increase_k_point_density(kpoints: Kpoints | dict | float, structure: Structure, factor: float = 0.1, max_inc: int = 500, min_kpoints: int = 1, force_gamma: bool = True)
+## custodian.vasp.utils.increase_k_point_density(kpoints: Kpoints | dict | float, structure: Structure, factor: float = 0.1, max_inc: int = 500, min_kpoints: int = 1, force_gamma: bool = True)
 
 Inputs:
 : kpoints (Kpoints, dict, float, int) :
-  : If a dict or Kpoints object: original Kpoints used in the calculation
-    If a float: the original KSPACING used in the calculation
-  <br/>
-  structure (Structure) : associated structure
-  factor (float) : factor used to increase k-point density.
-  <br/>
-  > The first increase uses approximately (1 + factor) higher k-point density.
-  > The second increase: ~ (1 + 2\*factor) higher k-kpoint density, etc.
-  max_inc (int)
-  : before giving up
-  <br/>
-  min_kpoints (int): The minimum permitted number of k-points.
-  : Can be useful if using the tetrahedron method, where
-    at least 4 k-points are needed.
-  <br/>
-  force_gamma (bool) = True: whether to use Gamma-centered or
-  : Monkhorst-Pack grids
+: If a dict or Kpoints object: original Kpoints used in the calculation
+If a float: the original KSPACING used in the calculation
+<br/>
+structure (Structure) : associated structure
+factor (float) : factor used to increase k-point density.
+<br/>
+
+> The first increase uses approximately (1 + factor) higher k-point density.
+> The second increase: ~ (1 + 2\*factor) higher k-kpoint density, etc.
+> max_inc (int)
+> : before giving up
+> <br/>
+> min_kpoints (int): The minimum permitted number of k-points.
+> : Can be useful if using the tetrahedron method, where
+> at least 4 k-points are needed.
+> <br/>
+> force_gamma (bool) = True: whether to use Gamma-centered or
+> : Monkhorst-Pack grids
 
 Outputs:
 : dict :
-  : The new Kpoints object / KSPACING consistent with constraints.
-    If an empty dict, no new k-point mesh could be found.
+: The new Kpoints object / KSPACING consistent with constraints.
+If an empty dict, no new k-point mesh could be found.

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "custodian"
-version = "2024.6.24"
+version = "2024.10.14"
 description = "A simple JIT job management framework in Python."
 authors = [
     { name = "Janosh Riebesell", email = "[email protected]" },