Bias-exchange metadynamics implementation#734

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giacomofiorin wants to merge 31 commits intomasterfrom bias-exchange

+1,593-58

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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Bias-exchange metadynamics implementation#734

Commits on Oct 18, 2024

Partial implementation of features restart (limited to active flag for now)

Re-enable inactive colvars when writing a state

Initial implementation of Tcl bias-exchange scripts

Store name of object in base class (colvardeps)

Allow reporting feature states to trajectory

Set BE frequency from command

Reactivate all variables (some may have been inactivated by dependency)

Simplify manual definition of biases

Create example folder and README

Simplify input, add equilibrium run

Re-enable thermostat

Use narrower Gaussians, move upper wall closer

Add trajectory post-processing script & basic documentation

Some README updates, minor code tweaks

Specify implementation constraints

Add neutral bias to simplify bias-exchange protocol syntax

Amend bemtd example to include neutral bias

Small improvements

Update post-processing script to correctly handle "neutral" biases

Fix missing state I/O code for neutral bias

Begin phasing out protocols where neutral replicas have no bias

Some doc updates

Modified load_trajectories.py script to write in output a unique trajectory sorted by time

Use more precise type in return code setter

Access bias energy and applied forces via scripting

Use calcenergy & calcforces to avoid evolving the bias during exchanges

Added step to header when writing output traj through load_trajectories.py

Update formatting of feature state and ignore it in diffs

Fix unused variable warning

Silence hidden member warning

Manually edit reference state files in tests to account for feature states