Update dev docs

Author: shyuep

docs/changelog.md

@@ -7,6 +7,7 @@ nav_order: 2
 # Change Log
 
 ## 2025.4.14
+* SYMPREC is now properly rounded when they are modified by custodian.
 * PR #362 from @Andrew-S-Rosen (#362)
     Anytime that we modify NCORE, we should also unset NPAR if it's present in the INCAR file since NPAR takes precedence. This is done throughout Custodian, but there was one spot missing it. I added it in.
 * PR #356 from @esoteric-ephemera (#356)

docs/custodian.ansible.interpreter.md

@@ -36,7 +36,7 @@ Examples:
 Initializes a Modder from a list of supported actions.
 
 * **Parameters**
-  * **actions** (*[**Action**]*) – A sequence of supported actions. See
+  * **actions** ( *[**Action**]*) – A sequence of supported actions. See
     [`custodian.ansible.actions`](custodian.ansible.actions.md#module-custodian.ansible.actions). Default is None,
     which means only DictActions are supported.
   * **strict** (*bool*) – Indicating whether to use strict mode. In non-strict

docs/custodian.cp2k.interpreter.md

@@ -20,7 +20,7 @@ Initializes a Modder for Cp2kInput sets
 * **Parameters**
   * **filename** (*str*) – name of cp2k input file to modify. This file will be overwritten
     if actions are applied.
-  * **actions** (*[**Action**]*) – A sequence of supported actions. See
+  * **actions** ( *[**Action**]*) – A sequence of supported actions. See
     [`custodian.ansible.actions`](custodian.ansible.actions.md#module-custodian.ansible.actions). Default is None,
     which means DictActions and FileActions are supported.
   * **strict** (*bool*) – Indicating whether to use strict mode. In non-strict

docs/custodian.cp2k.jobs.md

@@ -37,7 +37,7 @@ of the static constructors. The defaults are usually fine too.
   * **backup** (*bool*) – Whether to backup the initial input files. If True,
     the input file will be copied with a
     “.orig” appended. Defaults to True.
-  * **settings_override** (*[**actions**]*) – A list of actions. See the Cp2kModder
+  * **settings_override** ( *[**actions**]*) – A list of actions. See the Cp2kModder
     in interpreter.py
   * **restart** (*bool*) – Whether to run in restart mode, i.e. this a continuation of
     a previous calculation. Default is False.

docs/custodian.custodian.md

@@ -52,11 +52,11 @@ every 30 x 10 = 300 seconds, i.e., 5 minutes. -->
 Initializes a Custodian from a list of jobs and error handlers.
 
 * **Parameters**
-  * **handlers** (*[**ErrorHandler**]*) – Error handlers. In order of priority of
+  * **handlers** ( *[**ErrorHandler**]*) – Error handlers. In order of priority of
     fixing.
-  * **jobs** (*[**Job**]*) – Sequence of Jobs to be run. Note that this can be
+  * **jobs** ( *[**Job**]*) – Sequence of Jobs to be run. Note that this can be
     any sequence or even a generator yielding jobs.
-  * **validators** (*[**Validator**]*) – Validators to ensure job success
+  * **validators** ( *[**Validator**]*) – Validators to ensure job success
   * **max_errors_per_job** (*int*) – Maximum number of errors per job allowed
     before exiting. Defaults to None, which means it is set to be
     equal to max_errors..

docs/custodian.feff.interpreter.md

@@ -15,7 +15,7 @@ Bases: [`Modder`](custodian.ansible.interpreter.md#custodian.ansible.interpreter
 A Modder for FeffInput sets
 
 * **Parameters**
-  * **actions** (*[**Action**]*) – A sequence of supported actions. See
+  * **actions** ( *[**Action**]*) – A sequence of supported actions. See
   * **actions** – A sequence of supported actions. See
     [`custodian.ansible.actions`](custodian.ansible.actions.md#module-custodian.ansible.actions). Default is None,
     which means DictActions and FileActions are supported.

docs/custodian.gaussian.handlers.md

@@ -41,17 +41,17 @@ 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 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)
 
@@ -71,13 +71,13 @@ Convert memory size between different units to megabytes (MB).
 
 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’)
 
@@ -110,7 +110,7 @@ Check if the job is nearing the walltime. If so, return True, else False.
 
 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.jdftx.jobs.md

@@ -0,0 +1,48 @@
+---
+layout: default
+title: custodian.jdftx.jobs.md
+nav_exclude: true
+---
+
+# custodian.jdftx.jobs module
+
+This module implements basic kinds of jobs for JDFTx runs.
+
+### *class* custodian.jdftx.jobs.JDFTxJob(jdftx_cmd, input_file='init.in', output_file='jdftx.out', stderr_file='std_err.txt')
+
+Bases: `Job`
+
+A basic JDFTx job. Runs whatever is in the working directory.
+
+* **Parameters:**
+  * **jdftx_cmd** (*str*) – Command to run JDFTx as a string.
+  * **input_file** (*str*) – Name of the file to use as input to JDFTx
+    executable. Defaults to “init.in”
+  * **output_file** (*str*) – Name of file to direct standard out to.
+    Defaults to “jdftx.out”.
+  * **stderr_file** (*str*) – Name of file to direct standard error to.
+    Defaults to “std_err.txt”.
+
+#### postprocess(directory='./') → None
+
+No post-processing required.
+
+#### run(directory='./')
+
+Perform the actual JDFTx run.
+
+## Returns:
+
+> (subprocess.Popen) Used for monitoring.
+
+#### setup(directory='./') → None
+
+No setup required.
+
+#### terminate(directory='./') → None
+
+Terminate JDFTx.
+
+#### *static* terminate_process(proc, timeout=5)
+
+Terminate a process gracefully, then forcefully if necessary.

docs/custodian.jdftx.md

@@ -0,0 +1,19 @@
+---
+layout: default
+title: custodian.jdftx.md
+nav_exclude: true
+---
+
+# custodian.jdftx package
+
+This package implements various JDFTx Jobs and Error Handlers.
+Used Cp2kJob developed by Nick Winner as a template.
+
+
+* [custodian.jdftx.jobs module](custodian.jdftx.jobs.md)
+  * [`JDFTxJob`](custodian.jdftx.jobs.md#custodian.jdftx.jobs.JDFTxJob)
+    * [`JDFTxJob.postprocess()`](custodian.jdftx.jobs.md#custodian.jdftx.jobs.JDFTxJob.postprocess)
+    * [`JDFTxJob.run()`](custodian.jdftx.jobs.md#custodian.jdftx.jobs.JDFTxJob.run)
+    * [`JDFTxJob.setup()`](custodian.jdftx.jobs.md#custodian.jdftx.jobs.JDFTxJob.setup)
+    * [`JDFTxJob.terminate()`](custodian.jdftx.jobs.md#custodian.jdftx.jobs.JDFTxJob.terminate)
+    * [`JDFTxJob.terminate_process()`](custodian.jdftx.jobs.md#custodian.jdftx.jobs.JDFTxJob.terminate_process)

docs/custodian.nwchem.jobs.md

@@ -17,7 +17,7 @@ A basic Nwchem job.
 Initializes a basic NwChem job.
 
 * **Parameters**
-  * **nwchem_cmd** (*[**str**]*) – Command to run Nwchem as a list of args. For
+  * **nwchem_cmd** ( *[**str**]*) – Command to run Nwchem as a list of args. For
     example, [“nwchem”].
   * **input_file** (*str*) – Input file to run. Defaults to “mol.nw”.
   * **output_file** (*str*) – Name of file to direct standard out to.
@@ -27,7 +27,7 @@ Initializes a basic NwChem job.
     Defaults to True.
   * **gzipped** (*bool*) – Deprecated. Please use the Custodian class’s
     gzipped_output option instead.
-  * **settings_override** (*[**dict**]*) – An ansible style list of dict to override changes.
+  * **settings_override** ( *[**dict**]*) – An ansible style list of dict to override changes.
     #TODO: Not implemented yet.
 
 ### postprocess()