feat(md): add CSVR thermostat for NVT molecular dynamics#7461
Open
mintleaf84 wants to merge 6 commits into
Open
feat(md): add CSVR thermostat for NVT molecular dynamics#7461mintleaf84 wants to merge 6 commits into
mintleaf84 wants to merge 6 commits into
Conversation
Implement the Canonical Sampling through Velocity Rescaling (CSVR) thermostat as described in: G. Bussi, D. Donadio, M. Parrinello, J. Chem. Phys. 126, 014101 (2007) Features: - New thermostat option: md_thermostat = csvr - New parameter: md_csvr_tau (characteristic time scale) - Properly samples the canonical (NVT) ensemble - Simple implementation with only one parameter Implements deepmodeling#6941
- Add csvr option to md_thermostat parameter description - Add md_csvr_tau parameter documentation Implements deepmodeling#6941
Add CSVR thermostat test case to verlet_test.cpp: - Test position update correctness - Verify temperature is in reasonable range Implements deepmodeling#6941
mohanchen
added
Feature Discussed
YuLiu98
reviewed
Jun 19, 2026
| } | ||
|
|
||
| // Get degrees of freedom | ||
| int ndeg = frozen_freedom_; |
Collaborator
There was a problem hiding this comment.
frozen_freedom_ is FROZEN degree instead of atom degree.
Author
There was a problem hiding this comment.
Fixed. Changed to 3 * ucell.nat - frozen_freedom_.
YuLiu98
reviewed
Jun 20, 2026
| factor = exp(-1.0 / taut); | ||
| } | ||
|
|
||
| // Generate Gaussian random number |
Collaborator
There was a problem hiding this comment.
MD_func::gaussrand() can be used to generate Gaussian random number.
Author
There was a problem hiding this comment.
Fixed. Replaced with MD_func::gaussrand().
YuLiu98
reviewed
Jun 20, 2026
| sumnoises += r * r; | ||
| } | ||
|
|
||
| // CSVR core formula |
Collaborator
There was a problem hiding this comment.
This part can be more concise.
Add another factor:
double factor2 = (1-factor)*kin_target/kin_energy/ndeg;
......
double resample = factor + factor2 * (rr*rr+sumnoises ) + 2.0*rr*sqrt(factor*factor2);
Author
There was a problem hiding this comment.
Fixed. Simplified with factor2 variable.
- Fix degrees of freedom: use 3N - frozen_freedom instead of frozen_freedom - Use MD_func::gaussrand() instead of std::random for consistency - Simplify CSVR core formula with factor2 variable - Remove unused #include <random> Co-authored-by: monkeycode-ai <monkeycode-ai@chaitin.com> Co-authored-by: monkeycode-ai <monkeycode-ai@chaitin.com>
monkeycode-ai
Bot
force-pushed
the
feat-csvr-thermostat
branch
from
a26615f to
0ce1d85
Compare
Author
Code Change SummaryAll review comments have been addressed:
double factor2 = (1.0 - factor) * kin_target / kin_energy / ndeg;
double resample = factor + factor2 * (rr * rr + sumnoises) + 2.0 * rr * sqrt(factor * factor2); |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Reminder
Linked Issue
Implements #6941
Unit Tests and/or Case Tests for my changes
source/source_md/test/verlet_test.cpp[PASSED] 1 testWhat's changed?
Implement the Canonical Sampling through Velocity Rescaling (CSVR) thermostat as described in:
G. Bussi, D. Donadio, M. Parrinello, J. Chem. Phys. 126, 014101 (2007)
Features:
md_thermostat = csvrmd_csvr_tau(characteristic time scale, default: 100.0 fs)Usage:
Changed Files
source/source_io/module_parameter/md_parameter.hmd_csvr_tauparametersource/source_io/module_parameter/read_input_item_md.cppmd_csvr_tausource/source_md/verlet.happly_csvr()function declarationsource/source_md/verlet.cppsource/source_md/test/verlet_test.cppdocs/advanced/input_files/input-main.mdAny changes of core modules? (ignore if not applicable)
No changes to core modules. The modification is only in the MD module.