Compare two checkpoint files.
usage: compare.py [-h] [--reset] chk1 chk1
| chk1 | checkpoint file 1 |
| chk2 | checkpoint file 2 |
| --reset=False | reset checkpoint files first |
Module author: Adam Gagorik <adam.gagorik@gmail.com>
Extend a set of simulations.
usage: extend [-h] [--ok] [-r] [--add ADD] [--set SET] [--print PSTEP]
[--stub STUB]
[name]
| name | output file name |
| --ok=False | turn off dry run |
| -r=False | search recursivly |
| --add=0 | steps to add to iterations.real |
| --set | set iterations.real to new value |
| set iterations.print to new value | |
| --stub=ext.{i} | simulation job name stub |
Module author: Adam Gagorik <adam.gagorik@gmail.com>
Create a bash script for submitting simulations.
usage: script [-h] [--stub STUB] [--mode {runs,parts,all}] [--depth DEPTH]
[--comment]
[name]
| name | output file name |
| --stub={relpath} | |
| simulation job name stub | |
| --mode=all | directory search mode |
| --depth | search depth |
| --comment=False | |
| comment custom command | |
Module author: Adam Gagorik <adam.gagorik@gmail.com>
Reset a checkpoint file to be more like a new simulation.
usage: reset.py [-h] [--elecs] [--holes] [--notraps] [--nodefects] [--nofix]
[input] [output]
| ifile | input file |
| ofile | output file |
| --elecs=False | keep electrons |
| --holes=False | keep holes |
| --notraps=False | |
| delete traps | |
| --nodefects=False | |
| delete defects | |
| --nofix=False | do not fix traps |
Module author: Adam Gagorik <adam.gagorik@gmail.com>
scan a working variable - simply set a parameter in the input file equal to a python list or numpy array. For example, voltage.right = [-1, -2, -3]
usage: scan.py [-h] [--real int] [--fresh int] [--equil int] [--print int]
[--sort] [--key {None,abs}] [--reverse] [--mode str]
[--job JOB] [--stub STUB] [--fmt FMT]
[template]
| template | template input file name |
| --real | iterations.real when –fresh or –equil are not set |
| --fresh | override iterations.real for fresh runs |
| --equil | override iterations.real for equilibrated runs |
| --print=1000 | iterations.print |
| --sort=False | sort the working variable values |
| --key | key for sorting working variable values (None or abs) |
| --reverse=False | |
| reverse the working variable values | |
| --mode | what to do (gen or scan) |
| --job=run | stub to use in command script |
| --stub={working}_{value} | |
| stub to use for directories; you can use {working}, {value}, {i} in the string | |
| --fmt | value format string in stub |
Module author: Adam Gagorik <adam.gagorik@gmail.com>
Search for dat files and report on their progress.
usage: done [-h] [-r] [-d] [stub]
| stub | regex for system searching |
| -r=False | search recursivly |
| -d=False | show which simulations are not done |
Module author: Adam Gagorik <adam.gagorik@gmail.com>