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Colvars / colvars Public

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Bias-exchange metadynamics implementation#734

Draft

giacomofiorin wants to merge 31 commits into

masterColvars/colvars:masterfrom

bias-exchangeColvars/colvars:bias-exchangeCopy head branch name to clipboard

Conversation Commits31 (31)Checks Files changed

Draft

Bias-exchange metadynamics implementation#734
giacomofiorin wants to merge 31 commits into
masterfrom
bias-exchange

Commits

Commits on Oct 18, 2024

Partial implementation of features restart (limited to active flag for now)
giacomofiorin
committed
Re-enable inactive colvars when writing a state
giacomofiorin
committed
Initial implementation of Tcl bias-exchange scripts
giacomofiorin
committed
Store name of object in base class (colvardeps)
giacomofiorin
committed
Allow reporting feature states to trajectory
giacomofiorin
committed
Set BE frequency from command
giacomofiorin
committed
Reactivate all variables (some may have been inactivated by dependency)
giacomofiorin
committed
Simplify manual definition of biases
giacomofiorin
committed
Create example folder and README
giacomofiorin
committed
Simplify input, add equilibrium run
giacomofiorin
committed
Re-enable thermostat
giacomofiorin
committed
Use narrower Gaussians, move upper wall closer
giacomofiorin
committed
Add trajectory post-processing script & basic documentation
giacomofiorin
committed
Some README updates, minor code tweaks
giacomofiorin
committed
Specify implementation constraints
giacomofiorin
committed
Add neutral bias to simplify bias-exchange protocol syntax
giacomofiorin
committed
Amend bemtd example to include neutral bias
giacomofiorin
committed
Small improvements
giacomofiorin
committed
Update post-processing script to correctly handle "neutral" biases
giacomofiorin
committed
Fix missing state I/O code for neutral bias
giacomofiorin
committed
Begin phasing out protocols where neutral replicas have no bias
giacomofiorin
committed
Some doc updates
giacomofiorin
committed
Modified load_trajectories.py script to write in output a unique trajectory sorted by time

fabsugar
authored and
giacomofiorin
committed
Use more precise type in return code setter
giacomofiorin
committed
Access bias energy and applied forces via scripting
giacomofiorin
committed
Use calcenergy & calcforces to avoid evolving the bias during exchanges
giacomofiorin
committed
Added step to header when writing output traj through load_trajectories.py

fabsugar
authored and
giacomofiorin
committed
Update formatting of feature state and ignore it in diffs
giacomofiorin
committed
Fix unused variable warning
giacomofiorin
committed
Silence hidden member warning
giacomofiorin
committed
Manually edit reference state files in tests to account for feature states
giacomofiorin
committed

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