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TIMatch #1193

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4050eaf
Add 'surftension' command to calculate capillary-wave surface tension…
ndlevinzon Aug 31, 2026
3b2f864
Fix documentation typo in Action_SurfaceTension.cpp regarding agr/gnu…
ndlevinzon Aug 31, 2026
44a6fb6
Refactor output formatting in Action_SurfaceTension.cpp for clarity a…
ndlevinzon Aug 31, 2026
0b7379b
Implement 2-D FFT for height fields in Action_SurfaceTension
ndlevinzon Aug 31, 2026
ff489f3
Enhance 'surftension' command with new options and functionality
ndlevinzon Sep 23, 2026
6f46225
Update 'surftension' command to include 'out' alias and directory checks
ndlevinzon Aug 31, 2026
7e4d9e3
Refine documentation and formatting in Action_SurfaceTension
ndlevinzon Aug 31, 2026
2195e93
Enhance documentation in Action_SurfaceTension.cpp for clarity and de…
ndlevinzon Aug 31, 2026
787bd93
Add ST_Finite function to Action_SurfaceTension.cpp for finite number…
ndlevinzon Aug 31, 2026
6d45348
Update variable name in Action_SurfaceTension.h for clarity
ndlevinzon Aug 31, 2026
2dc336f
Initialize gamma and kappa variables in Action_SurfaceTension::Print …
ndlevinzon Aug 31, 2026
80af7dd
Update RunTest.sh for surftension tests with new input parameters and…
ndlevinzon Sep 2, 2026
581ce3f
Enhance 'surftension' command with output file prefix support and doc…
ndlevinzon Sep 23, 2026
ff994f1
Update surftension test files and parameters for improved accuracy
ndlevinzon Sep 2, 2026
5db8110
Update RunTest.sh and data files for dual frame analysis in surface t…
ndlevinzon Sep 2, 2026
82e79b9
Refactor README.md for improved clarity and structure
ndlevinzon Sep 23, 2026
8a2f97f
Add templatematch (timap) for TI-aligned residue libraries.
ndlevinzon Sep 14, 2026
6fddf2b
Update RunTest.sh permissions to make it executable
ndlevinzon Sep 14, 2026
2b43387
Add dual-topology support to templatematch for thermodynamic integration
ndlevinzon Sep 14, 2026
1dc02f5
Enhance documentation and implementation of dummy atoms in templatematch
ndlevinzon Sep 14, 2026
f4c6254
Add Exec_TIMatch for template matching in thermodynamic integration
ndlevinzon Sep 16, 2026
5a5633c
Refactor templatematch to timatch for clarity and consistency
ndlevinzon Sep 16, 2026
6f92ef2
Add Exec_TIMap implementation for template matching in thermodynamic …
ndlevinzon Sep 16, 2026
7ea4cd4
Refactor command and documentation from timatch to timap for consistency
ndlevinzon Sep 16, 2026
26f9cfc
Enhance timap functionality for amino-acid and nucleic-acid template …
ndlevinzon Sep 16, 2026
756967d
Implement series mode in timap for analog topology mapping
ndlevinzon Sep 22, 2026
c701918
Add new ModXNA fragments and update documentation for template matching
ndlevinzon Sep 22, 2026
bf3f0fd
Refactor and rename template matching components for clarity and cons…
ndlevinzon Sep 22, 2026
b9b4970
Update README and remove unused files for clarity and organization
ndlevinzon Sep 23, 2026
90b780f
Update documentation and improve Exec_TIMap functionality for templat…
ndlevinzon Sep 23, 2026
e0c3630
Fix return type in FmtFromFilename method for Exec_TIMap class
ndlevinzon Sep 23, 2026
9571bd3
Update README.md to correct terminology for Action_surftension and TIMap
ndlevinzon Sep 24, 2026
c65161c
Merge upstream master into TemplateMatch.
ndlevinzon Oct 9, 2026
aea3899
Move the timap manual entry to Topology File Commands.
ndlevinzon Oct 9, 2026
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2 changes: 1 addition & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -196,7 +196,7 @@ Enhancements to entropy calculation in original Action\_Gist.
Code for the CUDA version of the 'closest' Action.

* Nathan D. Levinzon (University of Utah, UT)
Action\surftension.
Action\_surftension and TIMap.

* Andrew Simmonett (National Institutes of Health)
Code for the reciprocal part of the particle mesh Ewald calculation (electrostatic and Lennard-Jones).
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