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Several improvements to colvar component classes #643

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merged 15 commits into from
Mar 12, 2024
Merged

Several improvements to colvar component classes #643

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3faab97
Separate creation and initialization of colvar components
giacomofiorin Nov 29, 2023
b5465a7
Make simple scalar metrics the default, and only override it when needed
giacomofiorin Dec 1, 2023
85e7a40
Update inheritance metadata
giacomofiorin Dec 12, 2023
070773b
List forceNoPBC as an option for all components in the doc
giacomofiorin Dec 3, 2023
504d5bd
Honor the value of forceNoPBC when comparing values of distanceVec va…
giacomofiorin Dec 4, 2023
a039cd8
Remove flag from test input that was absent in reference run
giacomofiorin Dec 5, 2023
ce3fb4e
Condense most implementations of cvc::apply_force() into a single fun…
giacomofiorin Dec 7, 2023
1e80955
Remove some member functions from public scope
giacomofiorin Dec 8, 2023
728a002
Initialize some plain old data in header
giacomofiorin Dec 8, 2023
139ee35
Use shared pointers to handle the components of one colvar
giacomofiorin Dec 8, 2023
415ea65
Integrate periodicity check in cvc::init()
giacomofiorin Dec 8, 2023
e4d30ce
Appease compiler warning
giacomofiorin Dec 12, 2023
ccdd474
Return early if critical errors are raised in path CV initialization …
giacomofiorin Mar 8, 2024
3957f1e
Make some CVs (PCVs and NN-based CVs) more robust.
HanatoK Mar 12, 2024
a196302
Doc formatting minor fixes
giacomofiorin Mar 12, 2024
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12 changes: 6 additions & 6 deletions doc/colvars-code-refs.bib
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Expand Up @@ -102,9 +102,9 @@ @article {Ebrahimi2022
% Moving frame of reference
% Optimal rotation via flexible fitting
% orientationAngle colvar component (derived from orientation)
% orientationProj colvar component (derived from orientation)
% spinAngle colvar component (derived from orientation)
% tilt colvar component (derived from orientation)
% orientationProj colvar component (derived from orientationAngle)
% spinAngle colvar component (derived from tilt)
% tilt colvar component (derived from orientationProj)
% alpha colvar component
% dihedralPC colvar component
% cartesian colvar component
Expand Down Expand Up @@ -161,9 +161,9 @@ @article{Fu2016

% polarTheta colvar component
% polarPhi colvar component
% eulerPhi colvar component (derived from orientation)
% eulerTheta colvar component (derived from orientation)
% eulerPsi colvar component (derived from orientation)
% eulerPhi colvar component (derived from orientation_angle)
% eulerTheta colvar component (derived from orientation_angle)
% eulerPsi colvar component (derived from orientation_angle)
@article{Fu2017,
author = {Fu, Haohao and Cai, Wensheng and H\'enin, J\'er\^ome and Roux, Beno\^it and Chipot, Christophe},
title = {New Coarse Variables for the Accurate Determination of Standard Binding Free Energies},
Expand Down
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