test: fix the atom mapping of XYZ frames in the stub interfaces by HanatoK · Pull Request #985 · Colvars/colvars

HanatoK · 2026-10-22T21:02:32Z

Summary

When I was trying to implement PBC support for the stub test interfaces using Claude, it complained that the atom mapping is wrong in case of reading the XYZ trajectory files. This PR aims to fix the issue and regenerate all test reference files.

After fixing the atom mapping, there are four tests with exactly zero gradients, namely orientationangle, rmsd, rmsd_sym and tilt, which fail the debug_gradients() tests, so the reference files have to be perturbed to make the numerical comparison more robust.

Related issue(s)

N/A

Affected engine(s)

CPU and GPU stub interfaces

Author(s)

@HanatoK

Licensing

By submitting this pull request, I agree that my contribution will be included in Colvars repository and redistributed under the GNU Lesser General Public License (LGPL) version 3.

Note: NAMD, VMD and TinkerHP follow more restrictive licenses, e.g. the UIUC license. However, the terms of the LGPLv3 remain in effect for the copies of the Colvars code distributed alongside those packages.

Artificial Intelligence (AI)

Yes. This commit was prepared completely by using Claude Opus 5.5 and Claude Code. My conversion with Claude is attached.
2026-10-22-163419-pastedcontent-idc7a0.txt

Further information / links

The CPU and GPU stub proxies copied the positions of each XYZ frame into the atom slots in file order, but the slots are numbered in the order in which atoms are requested: the atoms of the Colvars configuration first, then all others. Every test whose first atom group was not atoms 1..N in increasing order computed its variables on the wrong coordinates (e.g. angle_harmonic-fixed used atoms 1-4 instead of 1, 4, 10, 11). read_frame_xyz() now reads each frame in atom ID order and copies the positions into the slots through atoms_ids, and writes the force files in atom ID order. The buffers are kept as member variables. The reference outputs of the 99 affected functional tests are regenerated. New values were spot-checked against an independent numpy calculation (distance_harmonic-fixed, angle_harmonic-fixed). With the correct coordinates, frame 0 of trajectory.xyz coincides with rmsd_atoms_refpos.xyz and with a permutation of da_flipped.xyz, a point where rmsd and orientationAngle are not differentiable and tilt has a zero gradient, so the debugGradients checks of rmsd, rmsd_sym, orientationangle and tilt failed. Both reference files are perturbed by a uniform random displacement of up to 0.01 A per coordinate (all atoms of rmsd_atoms_refpos.xyz, atoms 6-9 of da_flipped.xyz; seed 20261022), and the references of the 21 tests using them are regenerated. These files are used only by the stub tests; engine tests have their own copies. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

debug_gradients() compared each finite-difference change with the analytic one relative to the size of that component alone. For components that are nearly zero this ratio is dominated by the rounding errors of the CVC values (a few ulp), and its value depends on how the compiler evaluates floating-point expressions. distancez-axis-fitgroup_harmonic-fixed has a fitting-group component of 1.4e-12 next to others of up to 2.9e-7; its error was 4.9e-4 with Clang on x86_64, but 1.1e-3 with GCC on ARM64 (FMA contraction) and with Intel oneAPI (-fp-model=fast), failing both CI jobs. No step size helps: a larger one makes the truncation error dominate. Errors are now measured against at least 1e-3 times the largest change predicted by any gradient component of the CVC, in both the CPU and GPU code paths. Components larger than that are checked exactly as before; for smaller ones, an error is flagged if it exceeds about 1e-6 of the largest component. The largest predicted change is logged once per CVC. The fitting-group comparisons also gain the denominator floor that only the main-group one had, so that 0/0 can no longer produce a NaN that record_gradient_error() silently ignores. Injecting wrong gradients into the 61 functional tests that use debugGradients (uniform 1% scaling, 1% error on the largest, median or smallest component, sign flips, swapped components, missing fit gradients) gives the same detections as before, with no false alarms. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

jhenin · 2026-10-24T22:09:22Z

I see the issue in principle but I didn't expect it to matter in practice because in the caller code (run_colvars_test*.cpp) atoms are initialized in order:

    for (int ai = 0; ai < natoms; ai++) {
      proxy->init_atom(ai+1);
    }

Looking into it further...

Instead, adapt colvarproxy_stub::read_frame_xyz to read all coords from XYZ then extract relevant coords. Also write force output as XYZ trajectory file.

jhenin · 2026-10-24T23:10:46Z

I see several issues: the test runners added all atoms as Colvars atoms, which is unnecessary and unrealistic. Instead I made the XYZ parser more flexible to allow for loading coordinates from a yet unknown system size.

I made the force output an XYZ trajectory file for consistency, to be able to inspect in VMD, and to reduce the number of files.

HanatoK · 2026-10-24T23:24:25Z

@jhenin The new changes break the GPU stub test. I got the following error:

colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units.
colvars: Trying to read partial positions with invalid atom group pointer
terminate called without an active exception

Since this is a fork of colvarproxy stubs, we need to keep them in sync, which is much easier if the file structure is similar

jhenin · 2026-10-25T20:21:46Z

I have now adapted the GPU test as well. For that, I took out the colvarproxy_stubs_gpu class from the run_colvars_test_cuda sources to make it easier to compare the two implementations.

The next step, ideally, would be merging the two codes altogether (the stubs classes, and the test runners) and conditionally including the GPU-related parts. That would remove a lot of duplicated code and help with future maintenance, but I'm not sure it is worth the effort.

HanatoK · 2026-10-26T15:04:04Z

I have now adapted the GPU test as well. For that, I took out the colvarproxy_stubs_gpu class from the run_colvars_test_cuda sources to make it easier to compare the two implementations.

The next step, ideally, would be merging the two codes altogether (the stubs classes, and the test runners) and conditionally including the GPU-related parts. That would remove a lot of duplicated code and help with future maintenance, but I'm not sure it is worth the effort.

Thanks! However, after refactoring the code, the GPU stub interface fails to compile on HIP:

/opt/rocm/bin/amdclang++ -DCOLVARS_HIP -DLEPTON -I/home/hanatok/HDD/Documents/git/colvars/tests/functional_gpu/../../src -I/home/hanatok/HDD/Documents/git/colvars/tests/functional_gpu -O3 -DNDEBUG -MD -MT CMakeFiles/colvars_stubs_gpu.dir/home/hanatok/HDD/Documents/git/colvars/misc_interfaces/stubs/colvarproxy_stub_gpu.cpp.o -MF CMakeFiles/colvars_stubs_gpu.dir/home/hanatok/HDD/Documents/git/colvars/misc_interfaces/stubs/colvarproxy_stub_gpu.cpp.o.d -o CMakeFiles/colvars_stubs_gpu.dir/home/hanatok/HDD/Documents/git/colvars/misc_interfaces/stubs/colvarproxy_stub_gpu.cpp.o -c /home/hanatok/HDD/Documents/git/colvars/misc_interfaces/stubs/colvarproxy_stub_gpu.cpp
In file included from /home/hanatok/HDD/Documents/git/colvars/misc_interfaces/stubs/colvarproxy_stub_gpu.cpp:16:
/home/hanatok/HDD/Documents/git/colvars/tests/functional_gpu/../../src/colvar_gpu_support.h:23:10: fatal error: 'hip/hip_runtime.h' file not found
   23 | #include <hip/hip_runtime.h>
      |          ^~~~~~~~~~~~~~~~~~~
1 error generated.

The CUDA stub interface is good and the tests are all passed locally.

I am looking into the changes to the CMakeLists.txt file to see if I can fix the HIP issue.

HanatoK · 2026-10-26T15:21:10Z

I have now adapted the GPU test as well. For that, I took out the colvarproxy_stubs_gpu class from the run_colvars_test_cuda sources to make it easier to compare the two implementations.
The next step, ideally, would be merging the two codes altogether (the stubs classes, and the test runners) and conditionally including the GPU-related parts. That would remove a lot of duplicated code and help with future maintenance, but I'm not sure it is worth the effort.

Thanks! However, after refactoring the code, the GPU stub interface fails to compile on HIP:
/opt/rocm/bin/amdclang++ -DCOLVARS_HIP -DLEPTON -I/home/hanatok/HDD/Documents/git/colvars/tests/functional_gpu/../../src -I/home/hanatok/HDD/Documents/git/colvars/tests/functional_gpu -O3 -DNDEBUG -MD -MT CMakeFiles/colvars_stubs_gpu.dir/home/hanatok/HDD/Documents/git/colvars/misc_interfaces/stubs/colvarproxy_stub_gpu.cpp.o -MF CMakeFiles/colvars_stubs_gpu.dir/home/hanatok/HDD/Documents/git/colvars/misc_interfaces/stubs/colvarproxy_stub_gpu.cpp.o.d -o CMakeFiles/colvars_stubs_gpu.dir/home/hanatok/HDD/Documents/git/colvars/misc_interfaces/stubs/colvarproxy_stub_gpu.cpp.o -c /home/hanatok/HDD/Documents/git/colvars/misc_interfaces/stubs/colvarproxy_stub_gpu.cpp
In file included from /home/hanatok/HDD/Documents/git/colvars/misc_interfaces/stubs/colvarproxy_stub_gpu.cpp:16:
/home/hanatok/HDD/Documents/git/colvars/tests/functional_gpu/../../src/colvar_gpu_support.h:23:10: fatal error: 'hip/hip_runtime.h' file not found
   23 | #include <hip/hip_runtime.h>
      |          ^~~~~~~~~~~~~~~~~~~
1 error generated.
The CUDA stub interface is good and the tests are all passed locally.

I am looking into the changes to the CMakeLists.txt file to see if I can fix the HIP issue.

Should be fixed in commit 0faff29.

Copilot

🟡 Changes recommended

One or more issues must be addressed before approval.

2 open issues

What changed in this PR

This PR corrects XYZ atom mapping in the testing stub, updates GPU stub build integration, and refreshes regression references for the corrected coordinates.

Changes:

Map XYZ coordinates and exported forces by atom ID rather than registration order.
Adjust GPU stub compilation and error/debug logging.
Perturb reference geometries to avoid zero-gradient cases and regenerate expected outputs.

File	Description
tests/input_files/tilt_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/tilt_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/spinangle_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/spinangle_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/selfcoordnum-pairlist-large_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/selfcoordnum-pairlist_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/selfcoordnum_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/selfcoordnum_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/rmsd-fitgroup_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/rmsd-fitgroup_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/rmsd_sym_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/rmsd_sym_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/rmsd_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/rmsd_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/rmsd_atoms_refpos.xyz	Updated as part of this pull request.
tests/input_files/protein_cvs/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/protein_cvs/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/polar_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/polar_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/orientationproj-fitgroup_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/orientationproj-fitgroup_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/orientationproj-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/orientationproj-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/orientationproj_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/orientationproj_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/orientationangle-fitgroup_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/orientationangle-fitgroup_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/orientationangle_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/orientationangle_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/orientation-fitgroup_harmonic-ori-moving/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/orientation-fitgroup_harmonic-ori-moving-enableFitGradients/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/orientation-fitgroup_harmonic-ori-fixed-enableFitGradients/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/orientation_harmonic-ori-moving/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/orientation_harmonic-ori-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/orientation_harmonic-ori-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/inertiaz_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/inertiaz_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/inertia_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/inertia_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/hbond_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/gyration_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/gyration_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/groupcoord-aniso_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/groupcoord-aniso_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/groupcoord_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/groupcoord_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/eulerangles_harmonic-fixed-euler/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/eigenvector-normalized_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/eigenvector-normalized_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/eigenvector-difference_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/eigenvector-difference_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/eigenvector_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/eigenvector_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distancez-fitgroup_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distancez-fitgroup_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distancez-axis-fitgroup_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distancez-axis_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distancez-axis_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distancez_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distancez_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distancexy-fitgroup_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distancexy-fitgroup_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distancexy-axis_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distancexy-axis_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distancewalls/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distancewalls/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distancewalls-compatible/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distancewalls-compatible/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distancevec_harmonic-dvec-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distancevec_harmonic-dvec-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distancepairs_linear-distancepairs/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distancepairs_histogramrestraint-dp/AutoDiff/test_out.hr.hist.dat	Updated as part of this pull request.
tests/input_files/distancepairs_histogramrestraint-dp/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distanceinv_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distanceinv_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distancedir_harmonic-ddir-moving/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distancedir_harmonic-ddir-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distancedir_harmonic-ddir-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-wall-bypassExtended-off/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-wall-bypassExtended-off/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-runave/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-runave/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-grid-expand_metadynamics/AutoDiff/test_out.pmf	Updated as part of this pull request.
tests/input_files/distance-grid-expand_metadynamics/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-grid-expand_metadynamics/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-grid_metadynamics/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-grid_metadynamics/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-grid_metadynamics-wt/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-grid_metadynamics-wt/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-grid_metadynamics-ti/AutoDiff/test_out.metadynamics1.ti.count	Updated as part of this pull request.
tests/input_files/distance-grid_metadynamics-ti/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-grid_metadynamics-ti/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-grid_metadynamics-sigmas/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-grid_metadynamics-sigmas/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-grid_metadynamics-rebinfromgrids/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-grid_metadynamics-rebinfromgrids/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-grid_metadynamics-rebin/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-grid_metadynamics-rebin/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-grid_histogram/AutoDiff/test_out.histogram1.dat	Updated as part of this pull request.
tests/input_files/distance-grid_histogram/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-grid_histogram/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-grid_histogram-customgrid/AutoDiff/test_out.histogram1.dat	Updated as part of this pull request.
tests/input_files/distance-grid_histogram-customgrid/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-grid_histogram-customgrid/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-grid_harmonic-k-moving/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-grid_harmonic-k-moving/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-grid_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-grid_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-grid_harmonic-fixed-ti/AutoDiff/test_out.harmonic1.ti.count	Updated as part of this pull request.
tests/input_files/distance-grid_harmonic-fixed-ti/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-grid_harmonic-fixed-ti/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-grid_harmonic-centers-moving/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-grid_harmonic-centers-moving/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-grid_harmonic-centers-moving-ti/AutoDiff/test_out.harmonic1.ti.count	Updated as part of this pull request.
tests/input_files/distance-grid_harmonic-centers-moving-ti/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-grid_harmonic-centers-moving-ti/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-grid_abf/AutoDiff/test_out.count	Updated as part of this pull request.
tests/input_files/distance-grid_abf/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-grid_abf/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-grid_abf-customgrid/AutoDiff/test_out.count	Updated as part of this pull request.
tests/input_files/distance-grid_abf-customgrid/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-grid_abf-customgrid/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-extended/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-extended/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-extended-grid_histogram/AutoDiff/test_out.histogram1.dat	Updated as part of this pull request.
tests/input_files/distance-extended-grid_histogram/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-extended-grid_histogram/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-extended-grid_histogram-bypassExtended/AutoDiff/test_out.histogram1.dat	Updated as part of this pull request.
tests/input_files/distance-extended-grid_histogram-bypassExtended/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-extended-grid_histogram-bypassExtended/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-dihedral_histogram2d-periodic/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-dihedral_histogram2d-periodic/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test_out.histogram1.dat	Updated as part of this pull request.
tests/input_files/distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance-coeffs_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance-coeffs_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance_metadynamics-customgrid/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance_metadynamics-customgrid/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance_linear-k-moving/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance_linear-k-moving/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance_linear-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance_linear-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance_histogram-customgrid/AutoDiff/test_out.histogram1.dat	Updated as part of this pull request.
tests/input_files/distance_histogram-customgrid/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance_histogram-customgrid/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance_harmonicwalls-upper-k-moving/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance_harmonicwalls-upper-k-moving/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance_harmonicwalls-upper-k-moving-decoupling/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance_harmonicwalls-upper-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance_harmonicwalls-upper-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance_harmonicwalls-k-moving/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance_harmonicwalls-k-moving/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance_harmonicwalls-both-k-moving/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance_harmonicwalls-both-k-moving/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance_harmonicwalls-both-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance_harmonicwalls-both-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance_harmonic-k-moving/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance_harmonic-k-moving/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance_harmonic-k-moving-stages/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance_harmonic-k-moving-stages/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance_harmonic-centers-moving/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance_harmonic-centers-moving/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance_harmonic-centers-moving-stages/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance_harmonic-centers-moving-stages/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance_harmonic-centers-moving-full/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance_harmonic-centers-moving-full/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/distance_abmd/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/distance_abmd/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/dipolemagnitude_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/dipoleangle_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/dipoleangle_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/dihedralwalls/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/dihedralwalls/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/dihedral_histogram-customgrid-periodic/AutoDiff/test_out.histogram1.dat	Updated as part of this pull request.
tests/input_files/dihedral_histogram-customgrid-periodic/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/dihedral_histogram-customgrid-periodic/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/dihedral_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/dihedral_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/da_flipped.xyz	Updated as part of this pull request.
tests/input_files/customfunction_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/customfunction_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/coordnum-pairlist-large_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/coordnum-pairlist-large_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/coordnum-pairlist_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/coordnum-pairlist_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/coordnum-group2centeronly_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/coordnum-group2centeronly_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/coordnum-aniso-pairlist_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/coordnum-aniso_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/coordnum-aniso_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/coordnum_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/coordnum_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/input_files/angle_harmonic-fixed/AutoDiff/test_out.colvars.traj	Updated as part of this pull request.
tests/input_files/angle_harmonic-fixed/AutoDiff/test_out.colvars.state	Updated as part of this pull request.
tests/functional/run_colvars_test.cpp	Updated as part of this pull request.
tests/functional_gpu/CMakeLists.txt	Updated as part of this pull request.
src/colvarmodule.cpp	Updated as part of this pull request.
src/colvaratoms_gpu.cpp	Updated as part of this pull request.
misc_interfaces/stubs/colvarproxy_stub.h	Updated as part of this pull request.
misc_interfaces/stubs/colvarproxy_stub.cpp	Updated as part of this pull request.

_{Review effort: Balanced}

Copilot

🔵 Needs a closer look

The scientific baseline changes and GPU stub integration require domain review and numerical validation, including CUDA/HIP runtime checks of atom mapping and applied forces unavailable in this environment.

No open issues 🎉

2 resolved since last review

_{Review effort: Balanced}

giacomofiorin

Useful improvements, should we want to use the stub interface beyond the original tests inputs.

HanatoK force-pushed the test_stub_pbc branch from 52cbae3 to cbae5be Compare October 22, 2026 21:03

HanatoK and others added 2 commits October 22, 2026 16:46

HanatoK force-pushed the test_stub_pbc branch from ab78cdd to 6bc7070 Compare October 22, 2026 21:46

HanatoK requested review from giacomofiorin and jhenin October 23, 2026 14:41

jhenin added 2 commits October 25, 2026 01:00

test: do not add all atoms in functional tests

103b48e

Instead, adapt colvarproxy_stub::read_frame_xyz to read all coords from XYZ then extract relevant coords. Also write force output as XYZ trajectory file.

test: Update output for new force XYZ traj format

7c632e8

jhenin added 2 commits October 25, 2026 09:48

refactor: move colvarproxy_stubs_gpu to own files

ab90278

Since this is a fork of colvarproxy stubs, we need to keep them in sync, which is much easier if the file structure is similar

test: harmonize CPU and GPU functional tests

399e496

build: fix the HIP build of the GPU stub test interface

0faff29

giacomofiorin requested a balanced review from Copilot October 26, 2026 21:00

Copilot started reviewing on behalf of giacomofiorin October 26, 2026 21:01

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Copilot AI reviewed Oct 26, 2026

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Comment thread misc_interfaces/stubs/colvarproxy_stub.cpp Resolved

Comment thread misc_interfaces/stubs/colvarproxy_stub.cpp Resolved

HanatoK added 2 commits October 27, 2026 10:13

fix: compare the .xyz files in compare_test.sh

9bda051

fix: check out-of-bound atom IDs when reading XYZ files in stubs

d4d02f6

giacomofiorin requested a balanced review from Copilot October 29, 2026 14:35

Copilot started reviewing on behalf of giacomofiorin October 29, 2026 14:35

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jhenin approved these changes Oct 30, 2026

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giacomofiorin approved these changes Oct 30, 2026

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giacomofiorin merged commit c5b5804 into Colvars:master Oct 30, 2026
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test: fix the atom mapping of XYZ frames in the stub interfaces - #985

test: fix the atom mapping of XYZ frames in the stub interfaces#985
giacomofiorin merged 9 commits into
Colvars:masterfrom
HanatoK:test_stub_pbc

HanatoK commented Oct 22, 2026 •

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HanatoK commented Oct 22, 2026 •

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