Skip to content

Deprecate "enableFitGradients no" #869

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
HanatoK wants to merge 5 commits into
base: master
Choose a base branch
from
Open

Deprecate "enableFitGradients no" #869

Show file tree
Hide file tree
Changes from 2 commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
cd0dd63
test: add new tests with "enableFitGradients yes"
HanatoK Oct 17, 2025
f2af1d8
fix: add a warning when fit gradients are disabled when it should not
HanatoK Oct 17, 2025
f5bd1e7
doc: Update fit gradient documentation
jhenin Apr 2, 2026
fb7c29e
test: remove enablefitgradients no from unit tests
jhenin Apr 2, 2026
69f9036
fix: cvmodule pointer
jhenin Apr 2, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion doc/colvars-refman-main.tex
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5277,7 +5277,7 @@
By default, these terms are calculated and included in the total gradients;
if this option is set to \texttt{off}, they are neglected.
In the case of a minimum RMSD component, this flag is automatically disabled because the contributions of those derivatives to the gradients cancel out; other types of variable will require projecting each of the gradients of the variable onto each of the gradients of the roto-translation.
When \refkey{fittingGroup}{atom-group|fittingGroup} is enabled, the computation is a $O(n^{(\rm fit)}+n^{(\rm main)})$ loop for all variables, including RMSDs.
When \refkey{fittingGroup}{atom-group|fittingGroup} is enabled, the computation is a $O(n^{(\rm fit)}+n^{(\rm main)})$ loop for all variables, including RMSDs. \textbf{In general, this option should be always on, unless you are sure that the forces acting on the fitting group are zero.}
}

\end{itemize}
Expand Down
6 changes: 6 additions & 0 deletions src/colvaratoms.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -928,6 +928,12 @@ int cvm::atom_group::parse_fitting_options(std::string const &group_conf) {
if (b_fit_gradients && (is_enabled(f_ag_center) || is_enabled(f_ag_rotate))) {
enable(f_ag_fit_gradients);
}

if (!b_fit_gradients && (is_enabled(f_ag_center) || is_enabled(f_ag_rotate))) {
cvm::log(
"Warning: the fit gradients are manually disabled, which shouldn't be, "
"unless you are sure that the forces on the fitting group are exactly zero.\n");
}
}

return COLVARS_OK;
Expand Down
19 changes: 19 additions & 0 deletions ...stancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out.colvars.state
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
configuration {
step 5
dt 1.000000e+00
version 2025-08-30
units real
}

colvar {
name one
x ( 0.33441046606706 , -0.91019936379702 , 2.0964658373033 )
}

restraint {
configuration {
step 5
name harmonic1
}
}

6 changes: 6 additions & 0 deletions ...istancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out.colvars.traj
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
# step one fa_one
0 ( -7.80793674955774e-01 , 8.33518131317475e-01 , -1.96571381488752e+00 ) ( 3.12317469982310e-03 , -3.33407252526990e-03 , 7.86285525955008e-03 )
1 ( 6.86565235316166e-01 , -1.48641743515745e-01 , 2.08948541877886e+00 ) ( -2.74626094126467e-03 , 5.94566974062980e-04 , -8.35794167511546e-03 )
2 ( 3.52200355643387e-01 , -1.08894793069560e+00 , 2.11108938189417e+00 ) ( -1.40880142257355e-03 , 4.35579172278241e-03 , -8.44435752757668e-03 )
3 ( 5.06865358123474e-01 , 6.04575068548870e-01 , 2.23263820221945e+00 ) ( -2.02746143249390e-03 , -2.41830027419548e-03 , -8.93055280887779e-03 )
4 ( 3.34410466067062e-01 , -9.10199363797018e-01 , 2.09646583730325e+00 ) ( -1.33764186426825e-03 , 3.64079745518807e-03 , -8.38586334921301e-03 )
104 changes: 104 additions & 0 deletions ...istancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out_forces_0.dat
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,104 @@
2.232492500000e-04 2.230500000000e-03 3.787500000000e-04
2.232492500000e-04 2.230500000000e-03 3.787500000000e-04
2.232492500000e-04 2.230500000000e-03 3.787500000000e-04
2.232492500000e-04 2.230500000000e-03 3.787500000000e-04
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
-2.232492500000e-04 -2.230500000000e-03 -3.787500000000e-04
-2.232492500000e-04 -2.230500000000e-03 -3.787500000000e-04
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
-2.232492500000e-04 -2.230500000000e-03 -3.787500000000e-04
-2.232492500000e-04 -2.230500000000e-03 -3.787500000000e-04
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
104 changes: 104 additions & 0 deletions ...istancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out_forces_1.dat
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,104 @@
-1.785032500000e-04 -2.195105000000e-03 -9.521625000000e-05
-1.785032500000e-04 -2.195105000000e-03 -9.521625000000e-05
-1.785032500000e-04 -2.195105000000e-03 -9.521625000000e-05
-1.785032500000e-04 -2.195105000000e-03 -9.521625000000e-05
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
1.785032500000e-04 2.195105000000e-03 9.521625000000e-05
1.785032500000e-04 2.195105000000e-03 9.521625000000e-05
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
1.785032500000e-04 2.195105000000e-03 9.521625000000e-05
1.785032500000e-04 2.195105000000e-03 9.521625000000e-05
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
0.000000000000e+00 0.000000000000e+00 0.000000000000e+00
Loading