TIMatch - #1193

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ndlevinzon wants to merge 32 commits into

Amber-MD:masterfrom

ndlevinzon:TemplateMatch

Commits on Sep 22, 2026

Commits on Sep 23, 2026

Enhance 'surftension' command with new options and functionality

ndlevinzon
and
cursoragent
committed
ff489f3
Update 'surftension' command to include 'out' alias and directory checks
ndlevinzon
committed
6f46225
Refine documentation and formatting in Action_SurfaceTension
ndlevinzon
committed
7e4d9e3
Enhance documentation in Action_SurfaceTension.cpp for clarity and detail
ndlevinzon
committed
2195e93
Add ST_Finite function to Action_SurfaceTension.cpp for finite number checks
ndlevinzon
committed
787bd93
Update variable name in Action_SurfaceTension.h for clarity
ndlevinzon
committed
6d45348
Initialize gamma and kappa variables in Action_SurfaceTension::Print for improved clarity
ndlevinzon
committed
2dc336f
Update RunTest.sh for surftension tests with new input parameters and output files
ndlevinzon
committed
80af7dd
Enhance 'surftension' command with output file prefix support and documentation updates

ndlevinzon
and
cursoragent
committed
581ce3f
Update surftension test files and parameters for improved accuracy
ndlevinzon
committed
ff994f1
Update RunTest.sh and data files for dual frame analysis in surface tension tests
ndlevinzon
committed
5db8110
Refactor README.md for improved clarity and structure

ndlevinzon
and
cursoragent
committed
82e79b9
Add templatematch (timap) for TI-aligned residue libraries.
ndlevinzon
committed
8a2f97f
Update RunTest.sh permissions to make it executable
ndlevinzon
committed
6fddf2b
Add dual-topology support to templatematch for thermodynamic integration
ndlevinzon
committed
2b43387
Enhance documentation and implementation of dummy atoms in templatematch
ndlevinzon
committed
1dc02f5
Add Exec_TIMatch for template matching in thermodynamic integration
ndlevinzon
committed
f4c6254
Refactor templatematch to timatch for clarity and consistency
ndlevinzon
committed
5a5633c
Add Exec_TIMap implementation for template matching in thermodynamic integration
ndlevinzon
committed
6f92ef2
Refactor command and documentation from timatch to timap for consistency
ndlevinzon
committed
7ea4cd4
Enhance timap functionality for amino-acid and nucleic-acid template matching
ndlevinzon
committed
26f9cfc
Implement series mode in timap for analog topology mapping
ndlevinzon
committed
756967d
Add new ModXNA fragments and update documentation for template matching
ndlevinzon
committed
c701918
Refactor and rename template matching components for clarity and consistency
ndlevinzon
committed
bf3f0fd
Update README and remove unused files for clarity and organization
ndlevinzon
committed
b9b4970
Update documentation and improve Exec_TIMap functionality for template matching
ndlevinzon
committed
90b780f
Fix return type in FmtFromFilename method for Exec_TIMap class
ndlevinzon
committed
e0c3630

Commits on Sep 24, 2026

Update README.md to correct terminology for Action_surftension and TIMap
ndlevinzon
committed
9571bd3

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TIMatch - #1193

TIMatch#1193
ndlevinzon wants to merge 32 commits into
Amber-MD:masterfrom
ndlevinzon:TemplateMatch

Commits on Sep 22, 2026

Add 'surftension' command to calculate capillary-wave surface tension of a liquid slab

Fix documentation typo in Action_SurfaceTension.cpp regarding agr/gnu keywords

Refactor output formatting in Action_SurfaceTension.cpp for clarity and consistency

Implement 2-D FFT for height fields in Action_SurfaceTension

Commits on Sep 23, 2026

Enhance 'surftension' command with new options and functionality

Update 'surftension' command to include 'out' alias and directory checks

Refine documentation and formatting in Action_SurfaceTension

Enhance documentation in Action_SurfaceTension.cpp for clarity and detail

Add ST_Finite function to Action_SurfaceTension.cpp for finite number checks

Update variable name in Action_SurfaceTension.h for clarity

Initialize gamma and kappa variables in Action_SurfaceTension::Print for improved clarity

Update RunTest.sh for surftension tests with new input parameters and output files

Enhance 'surftension' command with output file prefix support and documentation updates

Update surftension test files and parameters for improved accuracy

Update RunTest.sh and data files for dual frame analysis in surface tension tests

Refactor README.md for improved clarity and structure

Add templatematch (timap) for TI-aligned residue libraries.

Update RunTest.sh permissions to make it executable

Add dual-topology support to templatematch for thermodynamic integration

Enhance documentation and implementation of dummy atoms in templatematch

Add Exec_TIMatch for template matching in thermodynamic integration

Refactor templatematch to timatch for clarity and consistency

Add Exec_TIMap implementation for template matching in thermodynamic integration

Refactor command and documentation from timatch to timap for consistency

Enhance timap functionality for amino-acid and nucleic-acid template matching

Implement series mode in timap for analog topology mapping

Add new ModXNA fragments and update documentation for template matching

Refactor and rename template matching components for clarity and consistency

Update README and remove unused files for clarity and organization

Update documentation and improve Exec_TIMap functionality for template matching

Fix return type in FmtFromFilename method for Exec_TIMap class

Commits on Sep 24, 2026

Update README.md to correct terminology for Action_surftension and TIMap