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added a line to tools/README and fixed the alphabetical ordering in docs

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tanmoy.7989
2019-09-09 02:04:59 -07:00
parent f41a1f8303
commit 91a1971977
2 changed files with 16 additions and 14 deletions
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29
doc/src/Tools.txt
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@ -486,6 +486,21 @@ README for more info on Pizza.py and how to use these scripts.
:line
replica tool :h4,link(replica)
The tools/replica directory contains the reorder_remd_traj python script which
can be used to reorder the replica trajectories (resulting from the use of the
temper command) according to temperature. This will produce discontinuous
trajectories with all frames at the same temperature in each trajectory.
Additional options can be used to calculate the canonical configurational
log-weight for each frame at each temperature using the pymbar package. See
the README.md file for further details. Try out the peptide example provided.
This tool was written by Tanmoy Sanyal, while at the Shell lab
at UC Santa Barbara. (tanmoy dot 7989 at gmail.com)
:line
reax tool :h4,link(reax_tool)
The reax sub-directory contains stand-alone codes that can
@ -551,17 +566,3 @@ See the README file for details.
These files were provided by Vikas Varshney (vv0210 at gmail.com)
:line
replica tool :h4,link(replica)
The tools/replica directory contains the reorder_remd_traj python script which
can be used to reorder the replica trajectories (resulting from the use of the
temper command) according to temperature. This will produce discontinuous
trajectories with all frames at the same temperature in each trajectory.
Additional options can be used to calculate the canonical configurational
log-weight for each frame at each temperature using the pymbar package. See
the README.md file for further details. Try out the peptide example provided.
This tool was written by Tanmoy Sanyal, while at the Shell lab
at UC Santa Barbara. (tanmoy dot 7989 at gmail.com)

1
tools/README
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@ -38,6 +38,7 @@ polybond Python tool for programmable polymer bonding
pymol_asphere convert LAMMPS output of ellipsoids to PyMol format
python Python scripts for post-processing LAMMPS output
reax Tools for analyzing output of ReaxFF simulations
replica tool to reorder LAMMPS replica trajectories according to temperature
smd convert Smooth Mach Dynamics triangles to VTK
spin perform a cubic polynomial interpolation of a GNEB MEP
vim add-ons to VIM editor for editing LAMMPS input scripts