From cd0dd6391d2c39d360ac9ce51e9f22671869ce28 Mon Sep 17 00:00:00 2001 From: HanatoK Date: Fri, 17 Oct 2025 11:04:41 -0500 Subject: [PATCH 1/5] test: add new tests with "enableFitGradients yes" --- .../AutoDiff/test_out.colvars.state | 19 ++++ .../AutoDiff/test_out.colvars.traj | 6 + .../AutoDiff/test_out_forces_0.dat | 104 ++++++++++++++++++ .../AutoDiff/test_out_forces_1.dat | 104 ++++++++++++++++++ .../AutoDiff/test_out_forces_2.dat | 104 ++++++++++++++++++ .../AutoDiff/test_out_forces_3.dat | 104 ++++++++++++++++++ .../AutoDiff/test_out_forces_4.dat | 104 ++++++++++++++++++ .../test.in | 41 +++++++ .../AutoDiff/test_out.colvars.state | 19 ++++ .../AutoDiff/test_out.colvars.traj | 6 + .../AutoDiff/test_out_forces_0.dat | 104 ++++++++++++++++++ .../AutoDiff/test_out_forces_1.dat | 104 ++++++++++++++++++ .../AutoDiff/test_out_forces_2.dat | 104 ++++++++++++++++++ .../AutoDiff/test_out_forces_3.dat | 104 ++++++++++++++++++ .../AutoDiff/test_out_forces_4.dat | 104 ++++++++++++++++++ .../test.in | 32 ++++++ .../AutoDiff/test_out.colvars.state | 22 ++++ .../AutoDiff/test_out.colvars.traj | 6 + .../AutoDiff/test_out_forces_0.dat | 104 ++++++++++++++++++ .../AutoDiff/test_out_forces_1.dat | 104 ++++++++++++++++++ .../AutoDiff/test_out_forces_2.dat | 104 ++++++++++++++++++ .../AutoDiff/test_out_forces_3.dat | 104 ++++++++++++++++++ .../AutoDiff/test_out_forces_4.dat | 104 ++++++++++++++++++ .../test.in | 40 +++++++ .../AutoDiff/test_out.colvars.state | 19 ++++ .../AutoDiff/test_out.colvars.traj | 6 + .../AutoDiff/test_out_forces_0.dat | 104 ++++++++++++++++++ .../AutoDiff/test_out_forces_1.dat | 104 ++++++++++++++++++ .../AutoDiff/test_out_forces_2.dat | 104 ++++++++++++++++++ .../AutoDiff/test_out_forces_3.dat | 104 ++++++++++++++++++ .../AutoDiff/test_out_forces_4.dat | 104 ++++++++++++++++++ .../test.in | 33 ++++++ .../AutoDiff/test_out.colvars.state | 19 ++++ .../AutoDiff/test_out.colvars.traj | 6 + .../AutoDiff/test_out_forces_0.dat | 104 ++++++++++++++++++ .../AutoDiff/test_out_forces_1.dat | 104 ++++++++++++++++++ .../AutoDiff/test_out_forces_2.dat | 104 ++++++++++++++++++ .../AutoDiff/test_out_forces_3.dat | 104 ++++++++++++++++++ .../AutoDiff/test_out_forces_4.dat | 104 ++++++++++++++++++ .../test.in | 32 ++++++ 40 files changed, 2906 insertions(+) create mode 100644 tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out.colvars.state create mode 100644 tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out.colvars.traj create mode 100644 tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out_forces_0.dat create mode 100644 tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out_forces_1.dat create mode 100644 tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out_forces_2.dat create mode 100644 tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out_forces_3.dat create mode 100644 tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out_forces_4.dat create mode 100644 tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/test.in create mode 100644 tests/input_files/orientation-fitgroup_harmonic-ori-fixed-enableFitGradients/AutoDiff/test_out.colvars.state create mode 100644 tests/input_files/orientation-fitgroup_harmonic-ori-fixed-enableFitGradients/AutoDiff/test_out.colvars.traj create mode 100644 tests/input_files/orientation-fitgroup_harmonic-ori-fixed-enableFitGradients/AutoDiff/test_out_forces_0.dat create mode 100644 tests/input_files/orientation-fitgroup_harmonic-ori-fixed-enableFitGradients/AutoDiff/test_out_forces_1.dat create mode 100644 tests/input_files/orientation-fitgroup_harmonic-ori-fixed-enableFitGradients/AutoDiff/test_out_forces_2.dat create mode 100644 tests/input_files/orientation-fitgroup_harmonic-ori-fixed-enableFitGradients/AutoDiff/test_out_forces_3.dat create mode 100644 tests/input_files/orientation-fitgroup_harmonic-ori-fixed-enableFitGradients/AutoDiff/test_out_forces_4.dat create mode 100644 tests/input_files/orientation-fitgroup_harmonic-ori-fixed-enableFitGradients/test.in create mode 100644 tests/input_files/orientation-fitgroup_harmonic-ori-moving-enableFitGradients/AutoDiff/test_out.colvars.state create mode 100644 tests/input_files/orientation-fitgroup_harmonic-ori-moving-enableFitGradients/AutoDiff/test_out.colvars.traj create mode 100644 tests/input_files/orientation-fitgroup_harmonic-ori-moving-enableFitGradients/AutoDiff/test_out_forces_0.dat create mode 100644 tests/input_files/orientation-fitgroup_harmonic-ori-moving-enableFitGradients/AutoDiff/test_out_forces_1.dat create mode 100644 tests/input_files/orientation-fitgroup_harmonic-ori-moving-enableFitGradients/AutoDiff/test_out_forces_2.dat create mode 100644 tests/input_files/orientation-fitgroup_harmonic-ori-moving-enableFitGradients/AutoDiff/test_out_forces_3.dat create mode 100644 tests/input_files/orientation-fitgroup_harmonic-ori-moving-enableFitGradients/AutoDiff/test_out_forces_4.dat create mode 100644 tests/input_files/orientation-fitgroup_harmonic-ori-moving-enableFitGradients/test.in create mode 100644 tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out.colvars.state create mode 100644 tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out.colvars.traj create mode 100644 tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out_forces_0.dat create mode 100644 tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out_forces_1.dat create mode 100644 tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out_forces_2.dat create mode 100644 tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out_forces_3.dat create mode 100644 tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out_forces_4.dat create mode 100644 tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/test.in create mode 100644 tests/input_files/orientationproj-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out.colvars.state create mode 100644 tests/input_files/orientationproj-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out.colvars.traj create mode 100644 tests/input_files/orientationproj-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out_forces_0.dat create mode 100644 tests/input_files/orientationproj-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out_forces_1.dat create mode 100644 tests/input_files/orientationproj-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out_forces_2.dat create mode 100644 tests/input_files/orientationproj-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out_forces_3.dat create mode 100644 tests/input_files/orientationproj-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out_forces_4.dat create mode 100644 tests/input_files/orientationproj-fitgroup_harmonic-fixed-enableFitGradients/test.in diff --git a/tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out.colvars.state b/tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out.colvars.state new file mode 100644 index 000000000..edb532d9d --- /dev/null +++ b/tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out.colvars.state @@ -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 + } +} + diff --git a/tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out.colvars.traj b/tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out.colvars.traj new file mode 100644 index 000000000..2b51c4e17 --- /dev/null +++ b/tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out.colvars.traj @@ -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 ) diff --git a/tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out_forces_0.dat b/tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out_forces_0.dat new file mode 100644 index 000000000..6ec483408 --- /dev/null +++ b/tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out_forces_0.dat @@ -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 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b/tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out_forces_1.dat new file mode 100644 index 000000000..562ed2f8c --- /dev/null +++ b/tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/AutoDiff/test_out_forces_1.dat @@ -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 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0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 diff --git a/tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/test.in b/tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/test.in new file mode 100644 index 000000000..f193c0ed1 --- /dev/null +++ b/tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed-enableFitGradients/test.in @@ -0,0 +1,41 @@ +colvarsTrajFrequency 1 +colvarsRestartFrequency 10 +indexFile index.ndx + +colvar { + + name one + + outputAppliedForce on + + width 0.5 + + distanceVec { + group1 { + indexGroup group1 + centerToReference yes + rotateToReference yes + enableFitGradients yes + fittingGroup { + indexGroup heavy_atoms + } + refPositionsFile heavy_atoms_refpos.xyz + } + group2 { + indexGroup group2 + centerToReference yes + rotateToReference yes + enableFitGradients yes + fittingGroup { + indexGroup heavy_atoms + } + refPositionsFile heavy_atoms_refpos.xyz + } + } +} + +harmonic { + colvars one + centers (0.0, 0.0, 0.0) + forceConstant 0.001 +} diff --git a/tests/input_files/orientation-fitgroup_harmonic-ori-fixed-enableFitGradients/AutoDiff/test_out.colvars.state b/tests/input_files/orientation-fitgroup_harmonic-ori-fixed-enableFitGradients/AutoDiff/test_out.colvars.state new file mode 100644 index 000000000..0a0680c8a --- /dev/null +++ b/tests/input_files/orientation-fitgroup_harmonic-ori-fixed-enableFitGradients/AutoDiff/test_out.colvars.state @@ -0,0 +1,19 @@ +configuration { + step 5 + dt 1.000000e+00 + version 2025-08-30 + units real +} + +colvar { + name one + x ( 0.70890274760359 , -0.27751793787123 , -0.051278376535469 , 0.64638318101547 ) +} + +restraint { + configuration { + step 5 + name harmonic1 + } +} + diff --git a/tests/input_files/orientation-fitgroup_harmonic-ori-fixed-enableFitGradients/AutoDiff/test_out.colvars.traj b/tests/input_files/orientation-fitgroup_harmonic-ori-fixed-enableFitGradients/AutoDiff/test_out.colvars.traj new file mode 100644 index 000000000..b04148377 --- /dev/null +++ b/tests/input_files/orientation-fitgroup_harmonic-ori-fixed-enableFitGradients/AutoDiff/test_out.colvars.traj @@ -0,0 +1,6 @@ +# step one fa_one + 0 ( 5.62753692138853e-01 , -2.45779603872334e-01 , -3.76057696410047e-01 , -6.93888519342420e-01 ) ( 3.21749764191866e-03 , 6.51277006619137e-04 , 9.96493309352232e-04 , 1.83869463000459e-03 ) + 1 ( 6.66769687979787e-01 , -1.94254951740896e-01 , 5.92235109074314e-02 , 7.17060508375184e-01 ) ( 2.50686019064759e-03 , 5.84598863257766e-04 , -1.78229676228786e-04 , -2.15795146700972e-03 ) + 2 ( 7.28868646404118e-01 , -2.27035546742512e-01 , -1.95077871642104e-02 , 6.45619704659263e-01 ) ( 2.06526644368611e-03 , 7.29083846952732e-04 , 6.26457518009203e-05 , -2.07329162633422e-03 ) + 3 ( 6.91625477259386e-01 , -2.43051229141854e-01 , 1.40285145088620e-03 , 6.80131113261383e-01 ) ( 2.33161426725403e-03 , 7.51350882803453e-04 , -4.33667288903227e-06 , -2.10250783003770e-03 ) + 4 ( 7.08902747603586e-01 , -2.77517937871227e-01 , -5.12783765354689e-02 , 6.46383181015467e-01 ) ( 2.20861020330953e-03 , 8.73456617082862e-04 , 1.61392945053357e-04 , -2.03441864320499e-03 ) diff --git a/tests/input_files/orientation-fitgroup_harmonic-ori-fixed-enableFitGradients/AutoDiff/test_out_forces_0.dat b/tests/input_files/orientation-fitgroup_harmonic-ori-fixed-enableFitGradients/AutoDiff/test_out_forces_0.dat new file mode 100644 index 000000000..2ef3410fe --- /dev/null +++ b/tests/input_files/orientation-fitgroup_harmonic-ori-fixed-enableFitGradients/AutoDiff/test_out_forces_0.dat @@ -0,0 +1,104 @@ + 2.867381584177e-04 -1.300461222056e-04 8.213035253358e-05 + 1.919057477390e-04 -1.283415270380e-04 4.787155953501e-05 + 1.652129922744e-04 4.115283034587e-05 6.662847560414e-05 + 1.092795472047e-04 7.722033905544e-05 5.231741711388e-05 + 3.212019118626e-05 -6.365946060365e-05 9.162611106759e-07 + -5.130784331154e-05 -5.984676930888e-05 -2.895927716980e-05 + -8.164505304701e-05 1.034144588714e-04 -1.261673271801e-05 + -1.415386176383e-04 1.066703621735e-04 -3.370391405462e-05 + -2.269755120527e-04 -2.182478129197e-05 -8.615410058703e-05 + -2.825294266295e-04 5.233248530278e-05 -9.399670625825e-05 + 6.567181548699e-06 -3.363238770284e-05 -6.604268995742e-06 + 1.506369224267e-05 -3.549388281046e-05 -4.278879588889e-06 + 4.562504237581e-06 -3.007251149823e-05 -6.338516071399e-06 + 4.147358381436e-06 -2.423719290155e-05 -4.953018041839e-06 + 2.271570331578e-06 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0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 diff --git a/tests/input_files/orientation-fitgroup_harmonic-ori-fixed-enableFitGradients/test.in b/tests/input_files/orientation-fitgroup_harmonic-ori-fixed-enableFitGradients/test.in new file mode 100644 index 000000000..2a8912a41 --- /dev/null +++ b/tests/input_files/orientation-fitgroup_harmonic-ori-fixed-enableFitGradients/test.in @@ -0,0 +1,32 @@ +colvarsTrajFrequency 1 +colvarsRestartFrequency 10 +indexFile index.ndx + +colvar { + + name one + + outputAppliedForce on + + width 0.5 + + orientation { + atoms { + indexGroup RMSD_atoms + centerToReference yes + rotateToReference yes + enableFitGradients yes + fittingGroup { + indexGroup heavy_atoms + } + refPositionsFile heavy_atoms_refpos.xyz + } + refPositionsFile rmsd_atoms_refpos.xyz + } +} + +harmonic { + colvars one + centers (1.0, 0.0, 0.0, 0.0) + forceConstant 0.001 +} diff --git a/tests/input_files/orientation-fitgroup_harmonic-ori-moving-enableFitGradients/AutoDiff/test_out.colvars.state b/tests/input_files/orientation-fitgroup_harmonic-ori-moving-enableFitGradients/AutoDiff/test_out.colvars.state new file mode 100644 index 000000000..c3ed6daa6 --- /dev/null +++ b/tests/input_files/orientation-fitgroup_harmonic-ori-moving-enableFitGradients/AutoDiff/test_out.colvars.state @@ -0,0 +1,22 @@ +configuration { + step 5 + dt 1.000000e+00 + version 2025-08-30 + units real +} + +colvar { + name one + x ( 0.70890274760359 , -0.27751793787123 , -0.051278376535469 , 0.64638318101547 ) +} + +restraint { + configuration { + step 5 + name harmonic1 +firstStep 0 +centers ( 1.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) +accumulatedWork 0.00000000000000e+00 + } +} + diff --git a/tests/input_files/orientation-fitgroup_harmonic-ori-moving-enableFitGradients/AutoDiff/test_out.colvars.traj b/tests/input_files/orientation-fitgroup_harmonic-ori-moving-enableFitGradients/AutoDiff/test_out.colvars.traj new file mode 100644 index 000000000..350df72ec --- /dev/null +++ b/tests/input_files/orientation-fitgroup_harmonic-ori-moving-enableFitGradients/AutoDiff/test_out.colvars.traj @@ -0,0 +1,6 @@ +# step one fa_one E_harmonic1 x0_one W_harmonic1 + 0 ( 5.62753692138853e-01 , -2.45779603872334e-01 , -3.76057696410047e-01 , -6.93888519342420e-01 ) ( 3.21749764191866e-03 , 6.51277006619137e-04 , 9.96493309352232e-04 , 1.83869463000459e-03 ) 1.89378120913680e-03 ( 1.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 0.00000000000000e+00 + 1 ( 6.66769687979787e-01 , -1.94254951740896e-01 , 5.92235109074314e-02 , 7.17060508375184e-01 ) ( 2.50686019064759e-03 , 5.84598863257766e-04 , -1.78229676228786e-04 , -2.15795146700972e-03 ) 1.41432802472925e-03 ( 1.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 0.00000000000000e+00 + 2 ( 7.28868646404118e-01 , -2.27035546742512e-01 , -1.95077871642104e-02 , 6.45619704659263e-01 ) ( 2.06526644368611e-03 , 7.29083846952732e-04 , 6.26457518009203e-05 , -2.07329162633422e-03 ) 1.13741892466870e-03 ( 1.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 0.00000000000000e+00 + 3 ( 6.91625477259386e-01 , -2.43051229141854e-01 , 1.40285145088620e-03 , 6.80131113261383e-01 ) ( 2.33161426725403e-03 , 7.51350882803453e-04 , -4.33667288903227e-06 , -2.10250783003770e-03 ) 1.30268890280671e-03 ( 1.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 0.00000000000000e+00 + 4 ( 7.08902747603586e-01 , -2.77517937871227e-01 , -5.12783765354689e-02 , 6.46383181015467e-01 ) ( 2.20861020330953e-03 , 8.73456617082862e-04 , 1.61392945053357e-04 , -2.03441864320499e-03 ) 1.22572404882773e-03 ( 1.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 0.00000000000000e+00 diff --git a/tests/input_files/orientation-fitgroup_harmonic-ori-moving-enableFitGradients/AutoDiff/test_out_forces_0.dat b/tests/input_files/orientation-fitgroup_harmonic-ori-moving-enableFitGradients/AutoDiff/test_out_forces_0.dat new file mode 100644 index 000000000..2ef3410fe --- /dev/null +++ b/tests/input_files/orientation-fitgroup_harmonic-ori-moving-enableFitGradients/AutoDiff/test_out_forces_0.dat @@ -0,0 +1,104 @@ + 2.867381584177e-04 -1.300461222056e-04 8.213035253358e-05 + 1.919057477390e-04 -1.283415270380e-04 4.787155953501e-05 + 1.652129922744e-04 4.115283034587e-05 6.662847560414e-05 + 1.092795472047e-04 7.722033905544e-05 5.231741711388e-05 + 3.212019118626e-05 -6.365946060365e-05 9.162611106759e-07 + -5.130784331154e-05 -5.984676930888e-05 -2.895927716980e-05 + -8.164505304701e-05 1.034144588714e-04 -1.261673271801e-05 + -1.415386176383e-04 1.066703621735e-04 -3.370391405462e-05 + -2.269755120527e-04 -2.182478129197e-05 -8.615410058703e-05 + -2.825294266295e-04 5.233248530278e-05 -9.399670625825e-05 + 6.567181548699e-06 -3.363238770284e-05 -6.604268995742e-06 + 1.506369224267e-05 -3.549388281046e-05 -4.278879588889e-06 + 4.562504237581e-06 -3.007251149823e-05 -6.338516071399e-06 + 4.147358381436e-06 -2.423719290155e-05 -4.953018041839e-06 + 2.271570331578e-06 -3.240310793102e-05 -7.704723491343e-06 + -3.103874593189e-06 -3.303526109480e-05 -9.648237702516e-06 + 1.551881309017e-06 -2.264141649694e-05 -5.395314397863e-06 + -1.462579714674e-06 -1.733061990527e-05 -5.006721122040e-06 + 7.713971445580e-06 -2.335259766022e-05 -3.542100434073e-06 + 1.789198343055e-05 -2.084006522800e-05 4.811355218605e-07 + 1.198947874090e-05 -1.281803785351e-05 6.217351146313e-07 + 1.150819290439e-05 -7.037972197755e-06 1.970930351025e-06 + 1.295527107369e-05 -1.475740977931e-05 4.351590351976e-07 + 1.598613559669e-05 -1.419619808589e-05 1.584422814010e-06 + 7.029456677570e-06 -6.699385240887e-06 5.774405425353e-07 + 6.595599611051e-06 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b/tests/input_files/orientation-fitgroup_harmonic-ori-moving-enableFitGradients/AutoDiff/test_out_forces_4.dat new file mode 100644 index 000000000..e6a2ed5ac --- /dev/null +++ b/tests/input_files/orientation-fitgroup_harmonic-ori-moving-enableFitGradients/AutoDiff/test_out_forces_4.dat @@ -0,0 +1,104 @@ + 1.603671228341e-04 -1.264659142845e-04 -7.232684588460e-05 + 2.030933435038e-04 -1.277056983250e-04 2.550101425028e-04 + -1.122483637842e-04 1.245928417837e-04 3.227300402030e-04 + -1.984161639046e-04 1.393871341073e-04 -8.912159034870e-05 + 9.299957369011e-05 -9.155016511389e-05 -1.776269796858e-04 + 1.393374971921e-04 -7.948777614413e-05 1.297190848431e-04 + -1.682485871492e-04 1.371256398740e-04 8.560475017260e-05 + -1.989926345817e-04 1.047085061754e-04 -3.112853713135e-04 + 8.593029342786e-05 -9.250388508230e-05 -2.142771119529e-04 + -9.568499818605e-06 1.903431599075e-05 9.698593390269e-05 + 4.992758315080e-07 -4.431460817063e-05 1.358030285728e-05 + 3.285071095886e-06 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0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 diff --git a/tests/input_files/orientation-fitgroup_harmonic-ori-moving-enableFitGradients/test.in b/tests/input_files/orientation-fitgroup_harmonic-ori-moving-enableFitGradients/test.in new file mode 100644 index 000000000..04a69f15f --- /dev/null +++ b/tests/input_files/orientation-fitgroup_harmonic-ori-moving-enableFitGradients/test.in @@ -0,0 +1,40 @@ +colvarsTrajFrequency 1 +colvarsRestartFrequency 10 +indexFile index.ndx + +colvar { + + name one + + outputAppliedForce on + + width 0.5 + + orientation { + atoms { + indexGroup RMSD_atoms + centerToReference yes + rotateToReference yes + enableFitGradients yes + fittingGroup { + indexGroup heavy_atoms + } + refPositionsFile heavy_atoms_refpos.xyz + } + refPositionsFile rmsd_atoms_refpos.xyz + } +} + +harmonic { + colvars one + centers (1.0, 0.0, 0.0, 0.0) + forceConstant 0.001 + + + targetCenters (0.0, 0.0, 1.0, 0.0) + targetNumSteps 10 + + outputEnergy yes + outputCenters yes + outputAccumulatedWork yes +} diff --git a/tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out.colvars.state b/tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out.colvars.state new file mode 100644 index 000000000..84a3182d2 --- /dev/null +++ b/tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out.colvars.state @@ -0,0 +1,19 @@ +configuration { + step 5 + dt 1.000000e+00 + version 2025-08-30 + units real +} + +colvar { + name one + x 89.70858031263 +} + +restraint { + configuration { + step 5 + name harmonic1 + } +} + diff --git a/tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out.colvars.traj b/tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out.colvars.traj new file mode 100644 index 000000000..194532684 --- /dev/null +++ b/tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out.colvars.traj @@ -0,0 +1,6 @@ +# step one fa_one + 0 1.11507102723434e+02 -4.45628410893735e-01 + 1 9.63635306594849e+01 -3.85054122637940e-01 + 2 8.64167352834615e+01 -3.45266941133846e-01 + 3 9.24821647910958e+01 -3.69528659164383e-01 + 4 8.97085803126298e+01 -3.58434321250519e-01 diff --git a/tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out_forces_0.dat b/tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out_forces_0.dat new file mode 100644 index 000000000..6c6fd32d1 --- /dev/null +++ b/tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out_forces_0.dat @@ -0,0 +1,104 @@ + 3.761846722113e+00 -1.706133502573e+00 1.077504993299e+00 + 2.517697721400e+00 -1.683770152753e+00 6.280484966249e-01 + 2.167503470301e+00 5.399024698930e-01 8.741289053886e-01 + 1.433687475411e+00 1.013088320575e+00 6.863756995767e-01 + 4.213992186965e-01 -8.351770637185e-01 1.202084115632e-02 + -6.731306472961e-01 -7.851566537081e-01 -3.799297676219e-01 + -1.071138131306e+00 1.356740746580e+00 -1.655245848022e-01 + -1.856908713347e+00 1.399456404768e+00 -4.421767905200e-01 + -2.977793715100e+00 -2.863291109111e-01 -1.130294351747e+00 + -3.706630478941e+00 6.865733859165e-01 -1.233185018967e+00 + 8.615780515165e-02 -4.412384041766e-01 -8.664437203154e-02 + 1.976273461429e-01 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0.000000000000e+00 diff --git a/tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out_forces_3.dat b/tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out_forces_3.dat new file mode 100644 index 000000000..540317bbe --- /dev/null +++ b/tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out_forces_3.dat @@ -0,0 +1,104 @@ + 2.069210175435e+00 -1.177504346976e+00 -1.409000263703e+00 + 3.525852321865e+00 -1.675054052583e+00 2.956958656445e+00 + -1.016630213462e+00 9.807576986597e-01 5.061680741667e+00 + -3.243764917835e+00 1.650598927648e+00 -4.547217654438e-01 + 9.369931033007e-01 -7.615814730532e-01 -2.813623414510e+00 + 2.414554738100e+00 -1.003764038411e+00 1.305670542174e+00 + -2.246937283163e+00 1.358994360396e+00 1.759052058767e+00 + -3.637375225796e+00 1.454645182226e+00 -3.762080547192e+00 + 8.898594754589e-01 -8.074107975976e-01 -3.478076562538e+00 + 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/dev/null +++ b/tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out_forces_4.dat @@ -0,0 +1,104 @@ + 2.103469439343e+00 -1.658801262470e+00 -9.486814209396e-01 + 2.663891662109e+00 -1.675062998632e+00 3.344862912030e+00 + -1.472315513701e+00 1.634232942646e+00 4.233116892837e+00 + -2.602543025459e+00 1.828283576151e+00 -1.168971160491e+00 + 1.219837069293e+00 -1.200825774514e+00 -2.329859866340e+00 + 1.827632509198e+00 -1.042608391081e+00 1.701471759578e+00 + -2.206847357653e+00 1.798620488587e+00 1.122842217708e+00 + -2.610104353681e+00 1.373418309730e+00 -4.083001889044e+00 + 1.127112234383e+00 -1.213335326171e+00 -2.810584542379e+00 + -1.255060675348e-01 2.496652760100e-01 1.272124512837e+00 + 6.548795256903e-03 -5.812564468078e-01 1.781272341392e-01 + 4.308892330388e-02 -8.546967986251e-02 -1.789983971133e-01 + -5.347824553334e-02 -3.423077182138e-02 2.728550126139e-01 + -2.679387725888e-02 -1.486385518679e-01 1.842175361969e-01 + 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+ 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 diff --git a/tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/test.in b/tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/test.in new file mode 100644 index 000000000..f2ce18147 --- /dev/null +++ b/tests/input_files/orientationangle-fitgroup_harmonic-fixed-enableFitGradients/test.in @@ -0,0 +1,33 @@ +colvarsTrajFrequency 1 +colvarsRestartFrequency 10 +indexFile index.ndx + +colvar { + + name one + + outputAppliedForce on + + width 0.5 + + orientationAngle { + debugGradients on + atoms { + indexGroup RMSD_atoms + centerToReference yes + rotateToReference yes + enableFitGradients yes + fittingGroup { + indexGroup heavy_atoms + } + refPositionsFile heavy_atoms_refpos.xyz + } + refPositionsFile rmsd_atoms_refpos.xyz + } +} + +harmonic { + colvars one + centers 0.1 + forceConstant 0.001 +} diff --git a/tests/input_files/orientationproj-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out.colvars.state b/tests/input_files/orientationproj-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out.colvars.state new file mode 100644 index 000000000..1b043c412 --- /dev/null +++ b/tests/input_files/orientationproj-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out.colvars.state @@ -0,0 +1,19 @@ +configuration { + step 5 + dt 1.000000e+00 + version 2025-08-30 + units real +} + +colvar { + name one + x 0.0050862111198275 +} + +restraint { + configuration { + step 5 + name harmonic1 + } +} + diff --git a/tests/input_files/orientationproj-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out.colvars.traj b/tests/input_files/orientationproj-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out.colvars.traj new file mode 100644 index 000000000..d779c0053 --- /dev/null +++ b/tests/input_files/orientationproj-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out.colvars.traj @@ -0,0 +1,6 @@ +# step one fa_one + 0 -3.66616563968177e-01 1.86646625587271e-03 + 1 -1.10836366382674e-01 8.43345465530697e-04 + 2 6.24990074219429e-02 1.50003970312228e-04 + 3 -4.33083984114542e-02 5.73233593645817e-04 + 4 5.08621111982754e-03 3.79655155520690e-04 diff --git a/tests/input_files/orientationproj-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out_forces_0.dat b/tests/input_files/orientationproj-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out_forces_0.dat new file mode 100644 index 000000000..7e4feba54 --- /dev/null +++ b/tests/input_files/orientationproj-fitgroup_harmonic-fixed-enableFitGradients/AutoDiff/test_out_forces_0.dat @@ -0,0 +1,104 @@ + 2.558482353938e-04 -1.160364252519e-04 7.328255814972e-05 + 1.712319950435e-04 -1.145154638700e-04 4.271441966486e-05 + 1.474148148638e-04 3.671949029579e-05 5.945067794384e-05 + 9.750700594312e-05 6.890149393743e-05 4.668133087976e-05 + 2.865992542069e-05 -5.680151100727e-05 8.175535116080e-07 + -4.578051712949e-05 -5.339955590910e-05 -2.583953249564e-05 + -7.284953933575e-05 9.227375582820e-05 -1.125754876907e-05 + -1.262908493333e-04 9.517890496861e-05 -3.007303591655e-05 + -2.025237399750e-04 -1.947362643402e-05 -7.687283314076e-05 + -2.520929047214e-04 4.669477579257e-05 -8.387056526314e-05 + 5.859707755735e-06 -3.000921500415e-05 -5.892799821101e-06 + 1.344090057657e-05 -3.167017370287e-05 -3.817921543198e-06 + 4.070991683156e-06 -2.683283956045e-05 -5.655676108237e-06 + 3.700568941683e-06 -2.162615212771e-05 -4.419435951152e-06 + 2.026857060512e-06 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0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 diff --git a/tests/input_files/orientationproj-fitgroup_harmonic-fixed-enableFitGradients/test.in b/tests/input_files/orientationproj-fitgroup_harmonic-fixed-enableFitGradients/test.in new file mode 100644 index 000000000..2a32a0f40 --- /dev/null +++ b/tests/input_files/orientationproj-fitgroup_harmonic-fixed-enableFitGradients/test.in @@ -0,0 +1,32 @@ +colvarsTrajFrequency 1 +colvarsRestartFrequency 10 +indexFile index.ndx + +colvar { + + name one + + outputAppliedForce on + + width 0.5 + + orientationProj { + atoms { + indexGroup RMSD_atoms + centerToReference yes + rotateToReference yes + enableFitGradients yes + fittingGroup { + indexGroup heavy_atoms + } + refPositionsFile heavy_atoms_refpos.xyz + } + refPositionsFile rmsd_atoms_refpos.xyz + } +} + +harmonic { + colvars one + centers 0.1 + forceConstant 0.001 +} From f2af1d881f2d7ecc2905bcbbe93f50cad3c7feff Mon Sep 17 00:00:00 2001 From: HanatoK Date: Fri, 17 Oct 2025 11:33:54 -0500 Subject: [PATCH 2/5] fix: add a warning when fit gradients are disabled when it should not --- doc/colvars-refman-main.tex | 2 +- src/colvaratoms.cpp | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/doc/colvars-refman-main.tex b/doc/colvars-refman-main.tex index ae482759b..405055ea7 100644 --- a/doc/colvars-refman-main.tex +++ b/doc/colvars-refman-main.tex @@ -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} diff --git a/src/colvaratoms.cpp b/src/colvaratoms.cpp index 56d750fed..65a52f0dc 100644 --- a/src/colvaratoms.cpp +++ b/src/colvaratoms.cpp @@ -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; From f5bd1e71e3a628be6ffcbc848957902e60649bcc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Thu, 2 Apr 2026 23:07:19 +0200 Subject: [PATCH 3/5] doc: Update fit gradient documentation - remove enableFitGradients keyword - keep its documentation as an information subsection on fit gradients - remove performance warning in fittingGroup, because linear scaling! --- doc/colvars-refman-main.tex | 33 ++++++++++----------------------- 1 file changed, 10 insertions(+), 23 deletions(-) diff --git a/doc/colvars-refman-main.tex b/doc/colvars-refman-main.tex index 405055ea7..7d3087a18 100644 --- a/doc/colvars-refman-main.tex +++ b/doc/colvars-refman-main.tex @@ -5219,7 +5219,6 @@ This atom group itself}{% If either \texttt{centerToReference} or \texttt{rotateToReference} is defined, this keyword defines an alternate atom group to calculate the optimal roto-translation. Use this option to define a continuous rotation if the structure of the group involved changes significantly (a typical symptom would be the message ``Warning: discontinuous rotation!''). - \textbf{Performance considerations:} note that enabling this option will result in projecting each of the atomic gradients of the colvar (e.g.{} the RMSD) onto each the gradients of the roto-translation, which may be a computationally expensive operation: see the closely related \refkey{enableFitGradients}{atom-group|enableFitGradients} for details.% } \end{itemize} @@ -5253,34 +5252,22 @@ \end{cvexampleinput} } -The following options have default values appropriate for the vast majority of applications, and are only provided to support rare, special cases. -\begin{itemize} -\item % - \labelkey{atom-group|enableFitGradients} % - \keydef% - {enableFitGradients}{% - atom group}{% - Include the roto-translational contribution to colvar gradients}{% - boolean}{% - \texttt{on}}{% - When either \texttt{centerToReference} or \texttt{rotateToReference} is on, - the gradients of some colvars include terms proportional to - $\partial{}R/\partial\mathbf{x}_{i}$ (rotational gradients) and - $\partial\mathbf{x}^{\mathrm{C}}/\partial\mathbf{x}_{i}$ (translational gradients). - In practice, these terms are calculated as follows,\newline - $\begin{aligned} +\cvsubsubsec{Note on fit gradients}{sec:fit_gradients} + +When either \texttt{centerToReference} or \texttt{rotateToReference} is on, +the gradients of some colvars include terms proportional to +$\partial{}R/\partial\mathbf{x}_{i}$ (rotational gradients) and +$\partial\mathbf{x}^{\mathrm{C}}/\partial\mathbf{x}_{i}$ (translational gradients). +In practice, these terms are calculated as follows,\newline +$\begin{aligned} \nabla_k \zeta(\mathbf{X})&=\sum_{l,\rm main}\left[\nabla_l f \cdot \nabla_k R\left(\mathbf{x}_l-\mathbf{\bar{x}}^{\rm (fit)}\right) - \frac{1}{n^{\rm (fit)}} \nabla_l f \cdot R \mathbbm{1}\right] \\ &=\left(\sum_{l,\rm main}\nabla_l f \cdot\frac{\partial R}{\partial q_0}\left(\mathbf{x}_l-\mathbf{\bar{x}}^{\rm (fit)}\right), \sum_{l,\rm main}\nabla_l f \cdot\frac{\partial R}{\partial q_1}\left(\mathbf{x}_l-\mathbf{\bar{x}}^{\rm (fit)}\right), \sum_{l,\rm main}\nabla_l f \cdot\frac{\partial R}{\partial q_2}\left(\mathbf{x}_l-\mathbf{\bar{x}}^{\rm (fit)}\right), \right.\\ &\left.\sum_{l,\rm main}\nabla_l f \cdot\frac{\partial R}{\partial q_3}\left(\mathbf{x}_l-\mathbf{\bar{x}}^{\rm (fit)}\right)\right) \cdot \left(\nabla_k q_0, \nabla_k q_1, \nabla_k q_2, \nabla_k q_3\right)-\frac{1}{n^{\rm (fit)}} R^{\intercal}\sum_{l,\rm main}{\nabla_l f} \end{aligned}$\newline - 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. \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} +In the case of a minimum RMSD component, the contributions of those derivatives to the gradients cancel out, so this term is not computed. Other types of variable 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 -- that is, linear in both atom group sizes, for all variables including RMSDs. \cvsubsec{Treatment of periodic boundary conditions.}{sec:colvar_atom_groups_wrapping} From fb7c29e1bd3616a2eed4fbecb3b1429bfef52384 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Thu, 2 Apr 2026 23:35:41 +0200 Subject: [PATCH 4/5] test: remove enablefitgradients no from unit tests --- tests/distancedir-fitgroup.in | 2 - tests/distancevec-PDBflags.in | 4 - tests/distancevec-fitgroup.in | 2 - tests/distancevec-refposgroup.in | 2 - .../AutoDiff/test_out.colvars.state | 2 +- .../AutoDiff/test_out_forces_0.dat | 102 +++++++++--------- .../AutoDiff/test_out_forces_1.dat | 102 +++++++++--------- .../AutoDiff/test_out_forces_2.dat | 102 +++++++++--------- .../AutoDiff/test_out_forces_3.dat | 102 +++++++++--------- .../AutoDiff/test_out_forces_4.dat | 102 +++++++++--------- .../test.in | 2 - .../test.in | 2 - tests/input_files/generate_ref.sh | 14 +++ .../AutoDiff/test_out.colvars.state | 2 +- .../AutoDiff/test_out_forces_0.dat | 102 +++++++++--------- .../AutoDiff/test_out_forces_1.dat | 102 +++++++++--------- .../AutoDiff/test_out_forces_2.dat | 102 +++++++++--------- .../AutoDiff/test_out_forces_3.dat | 102 +++++++++--------- .../AutoDiff/test_out_forces_4.dat | 102 +++++++++--------- .../test.in | 1 - .../AutoDiff/test_out.colvars.state | 2 +- .../AutoDiff/test_out_forces_0.dat | 102 +++++++++--------- .../AutoDiff/test_out_forces_1.dat | 102 +++++++++--------- .../AutoDiff/test_out_forces_2.dat | 102 +++++++++--------- .../AutoDiff/test_out_forces_3.dat | 102 +++++++++--------- .../AutoDiff/test_out_forces_4.dat | 102 +++++++++--------- .../test.in | 1 - .../AutoDiff/test_out.colvars.state | 2 +- .../AutoDiff/test_out_forces_0.dat | 102 +++++++++--------- .../AutoDiff/test_out_forces_1.dat | 102 +++++++++--------- .../AutoDiff/test_out_forces_2.dat | 102 +++++++++--------- .../AutoDiff/test_out_forces_3.dat | 102 +++++++++--------- .../AutoDiff/test_out_forces_4.dat | 102 +++++++++--------- .../test.in | 1 - .../AutoDiff/test_out.colvars.state | 2 +- .../AutoDiff/test_out_forces_0.dat | 102 +++++++++--------- .../AutoDiff/test_out_forces_1.dat | 102 +++++++++--------- .../AutoDiff/test_out_forces_2.dat | 102 +++++++++--------- .../AutoDiff/test_out_forces_3.dat | 102 +++++++++--------- .../AutoDiff/test_out_forces_4.dat | 102 +++++++++--------- .../test.in | 1 - tests/orientation-fitgroup.in | 1 - tests/orientation-refposgroup.in | 1 - tests/orientationangle-fitgroup.in | 1 - tests/orientationangle-refposgroup.in | 1 - tests/orientationproj-fitgroup.in | 1 - tests/orientationproj-refposgroup.in | 1 - tests/unittests/CMakeLists.txt | 2 +- 48 files changed, 1295 insertions(+), 1305 deletions(-) create mode 100755 tests/input_files/generate_ref.sh diff --git a/tests/distancedir-fitgroup.in b/tests/distancedir-fitgroup.in index b5baa842d..011e5fe6a 100644 --- a/tests/distancedir-fitgroup.in +++ b/tests/distancedir-fitgroup.in @@ -11,7 +11,6 @@ colvar { indexGroup group1 centerToReference yes rotateToReference yes - enableFitGradients no # Not available because gradients are implicit fittingGroup { indexGroup heavy_atoms } @@ -21,7 +20,6 @@ colvar { indexGroup group2 centerToReference yes rotateToReference yes - enableFitGradients no # Not available because gradients are implicit fittingGroup { indexGroup heavy_atoms } diff --git a/tests/distancevec-PDBflags.in b/tests/distancevec-PDBflags.in index 1408e93ac..f6795156d 100644 --- a/tests/distancevec-PDBflags.in +++ b/tests/distancevec-PDBflags.in @@ -17,7 +17,6 @@ colvar { centerToReference yes rotateToReference yes - enableFitGradients no # Not available because gradients are implicit refPositionsFile ../Common/da-flags.pdb refPositionsCol B refPositionsColValue 1 @@ -29,7 +28,6 @@ colvar { centerToReference yes rotateToReference yes - enableFitGradients no # Not available because gradients are implicit refPositionsFile ../Common/da-flags.pdb refPositionsCol B refPositionsColValue 2 @@ -53,7 +51,6 @@ colvar { centerToReference yes rotateToReference yes - enableFitGradients no # Not available because gradients are implicit refPositionsFile ../Common/da-partial.pdb } group2 { @@ -63,7 +60,6 @@ colvar { centerToReference yes rotateToReference yes - enableFitGradients no # Not available because gradients are implicit refPositionsFile ../Common/da-flags.pdb refPositionsCol B refPositionsColValue 2 diff --git a/tests/distancevec-fitgroup.in b/tests/distancevec-fitgroup.in index 767d15320..54fea4d28 100644 --- a/tests/distancevec-fitgroup.in +++ b/tests/distancevec-fitgroup.in @@ -11,7 +11,6 @@ colvar { indexGroup group1 centerToReference yes rotateToReference yes - enableFitGradients no # Not available because gradients are implicit fittingGroup { indexGroup heavy_atoms } @@ -21,7 +20,6 @@ colvar { indexGroup group2 centerToReference yes rotateToReference yes - enableFitGradients no # Not available because gradients are implicit fittingGroup { indexGroup heavy_atoms } diff --git a/tests/distancevec-refposgroup.in b/tests/distancevec-refposgroup.in index 842c91384..09f4b150f 100644 --- a/tests/distancevec-refposgroup.in +++ b/tests/distancevec-refposgroup.in @@ -11,7 +11,6 @@ colvar { indexGroup group1 centerToReference yes rotateToReference yes - enableFitGradients no # Not available because gradients are implicit refPositionsGroup { indexGroup heavy_atoms } @@ -21,7 +20,6 @@ colvar { indexGroup group2 centerToReference yes rotateToReference yes - enableFitGradients no # Not available because gradients are implicit refPositionsGroup { indexGroup heavy_atoms } diff --git a/tests/input_files/distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test_out.colvars.state b/tests/input_files/distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test_out.colvars.state index 9993de740..ab6c056b4 100644 --- a/tests/input_files/distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test_out.colvars.state +++ b/tests/input_files/distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test_out.colvars.state @@ -1,7 +1,7 @@ configuration { step 5 dt 1.000000e+00 - version 2025-08-30 + version 2026-01-22 units real } diff --git a/tests/input_files/distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test_out_forces_0.dat b/tests/input_files/distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test_out_forces_0.dat index b825ce44a..f6fce2603 100644 --- a/tests/input_files/distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test_out_forces_0.dat +++ b/tests/input_files/distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test_out_forces_0.dat @@ -1,54 +1,54 @@ - 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enableFitGradients no # Not available because gradients are implicit fittingGroup { indexGroup heavy_atoms } @@ -25,7 +24,6 @@ colvar { indexGroup group2 centerToReference yes rotateToReference yes - enableFitGradients no # Not available because gradients are implicit fittingGroup { indexGroup heavy_atoms } diff --git a/tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed/test.in b/tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed/test.in index e5a6ed041..ee9258064 100644 --- a/tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed/test.in +++ b/tests/input_files/distancevec-fitgroup_harmonic-dvec-fixed/test.in @@ -15,7 +15,6 @@ colvar { indexGroup group1 centerToReference yes rotateToReference yes - enableFitGradients no # Not available because gradients are implicit fittingGroup { indexGroup heavy_atoms } @@ -25,7 +24,6 @@ colvar { indexGroup group2 centerToReference yes rotateToReference yes - enableFitGradients no # Not available because gradients are implicit fittingGroup { indexGroup heavy_atoms } diff --git a/tests/input_files/generate_ref.sh b/tests/input_files/generate_ref.sh new file mode 100755 index 000000000..55991336b --- /dev/null +++ b/tests/input_files/generate_ref.sh @@ -0,0 +1,14 @@ +#!/bin/bash +# This script generates reference output for the AutoDiff tests. +# Run from the tests/input_files directory, with the test names as arguments, e.g.: +# ./generate_ref.sh test1 test2 test3 + +RUN=~/Projects/colvars/build/tests/functional/run_colvars_test +TESTS=$* + +for TEST in $TESTS +do + # remove trailing _spiff if present (output from ctest) + TEST=${TEST%_spiff} + $RUN -c $TEST/test.in -t trajectory.xyz --force -o $TEST/AutoDiff/test_out +done diff --git a/tests/input_files/orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test_out.colvars.state b/tests/input_files/orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test_out.colvars.state index 0a0680c8a..d262ca5cc 100644 --- a/tests/input_files/orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test_out.colvars.state +++ b/tests/input_files/orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test_out.colvars.state @@ -1,7 +1,7 @@ configuration { step 5 dt 1.000000e+00 - version 2025-08-30 + version 2026-01-22 units real } diff --git a/tests/input_files/orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test_out_forces_0.dat b/tests/input_files/orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test_out_forces_0.dat index d331c4f93..2ef3410fe 100644 --- a/tests/input_files/orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test_out_forces_0.dat +++ b/tests/input_files/orientation-fitgroup_harmonic-ori-fixed/AutoDiff/test_out_forces_0.dat @@ -1,54 +1,54 @@ - 2.789477607907e-04 -9.505253642879e-05 8.868513823455e-05 - 1.933852721459e-04 -9.975158315217e-05 5.582225531068e-05 - 1.539342332992e-04 5.920929878818e-05 6.760897560002e-05 - 9.586692838729e-05 8.757695708711e-05 5.058245487037e-05 - 3.673158837534e-05 -5.635187772277e-05 4.349079839677e-06 - -4.515428532051e-05 -5.996229351175e-05 -2.695343639705e-05 - -8.911443108311e-05 9.242287977029e-05 -1.795657359771e-05 - -1.419449048014e-04 9.022517818857e-05 -3.813007226717e-05 - -2.107565285773e-04 -4.180091202731e-05 -8.600103741615e-05 - 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enableFitGradients no # Not available because gradients are implicit fittingGroup { indexGroup heavy_atoms } diff --git a/tests/input_files/orientation-fitgroup_harmonic-ori-moving/AutoDiff/test_out.colvars.state b/tests/input_files/orientation-fitgroup_harmonic-ori-moving/AutoDiff/test_out.colvars.state index c3ed6daa6..566e1a18f 100644 --- a/tests/input_files/orientation-fitgroup_harmonic-ori-moving/AutoDiff/test_out.colvars.state +++ b/tests/input_files/orientation-fitgroup_harmonic-ori-moving/AutoDiff/test_out.colvars.state @@ -1,7 +1,7 @@ configuration { step 5 dt 1.000000e+00 - version 2025-08-30 + version 2026-01-22 units real } diff --git a/tests/input_files/orientation-fitgroup_harmonic-ori-moving/AutoDiff/test_out_forces_0.dat b/tests/input_files/orientation-fitgroup_harmonic-ori-moving/AutoDiff/test_out_forces_0.dat index d331c4f93..2ef3410fe 100644 --- a/tests/input_files/orientation-fitgroup_harmonic-ori-moving/AutoDiff/test_out_forces_0.dat +++ b/tests/input_files/orientation-fitgroup_harmonic-ori-moving/AutoDiff/test_out_forces_0.dat @@ -1,54 +1,54 @@ - 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enableFitGradients no # Not available because gradients are implicit fittingGroup { indexGroup heavy_atoms } diff --git a/tests/input_files/orientationangle-fitgroup_harmonic-fixed/AutoDiff/test_out.colvars.state b/tests/input_files/orientationangle-fitgroup_harmonic-fixed/AutoDiff/test_out.colvars.state index 84a3182d2..4da12c2d0 100644 --- a/tests/input_files/orientationangle-fitgroup_harmonic-fixed/AutoDiff/test_out.colvars.state +++ b/tests/input_files/orientationangle-fitgroup_harmonic-fixed/AutoDiff/test_out.colvars.state @@ -1,7 +1,7 @@ configuration { step 5 dt 1.000000e+00 - version 2025-08-30 + version 2026-01-22 units real } diff --git a/tests/input_files/orientationangle-fitgroup_harmonic-fixed/AutoDiff/test_out_forces_0.dat b/tests/input_files/orientationangle-fitgroup_harmonic-fixed/AutoDiff/test_out_forces_0.dat index 71da653b1..6c6fd32d1 100644 --- a/tests/input_files/orientationangle-fitgroup_harmonic-fixed/AutoDiff/test_out_forces_0.dat +++ b/tests/input_files/orientationangle-fitgroup_harmonic-fixed/AutoDiff/test_out_forces_0.dat @@ -1,54 +1,54 @@ - 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enableFitGradients no # Not available because gradients are implicit fittingGroup { indexGroup heavy_atoms } diff --git a/tests/input_files/orientationproj-fitgroup_harmonic-fixed/AutoDiff/test_out.colvars.state b/tests/input_files/orientationproj-fitgroup_harmonic-fixed/AutoDiff/test_out.colvars.state index 1b043c412..f86c2e009 100644 --- a/tests/input_files/orientationproj-fitgroup_harmonic-fixed/AutoDiff/test_out.colvars.state +++ b/tests/input_files/orientationproj-fitgroup_harmonic-fixed/AutoDiff/test_out.colvars.state @@ -1,7 +1,7 @@ configuration { step 5 dt 1.000000e+00 - version 2025-08-30 + version 2026-01-22 units real } diff --git a/tests/input_files/orientationproj-fitgroup_harmonic-fixed/AutoDiff/test_out_forces_0.dat b/tests/input_files/orientationproj-fitgroup_harmonic-fixed/AutoDiff/test_out_forces_0.dat index 007b9f431..7e4feba54 100644 --- a/tests/input_files/orientationproj-fitgroup_harmonic-fixed/AutoDiff/test_out_forces_0.dat +++ b/tests/input_files/orientationproj-fitgroup_harmonic-fixed/AutoDiff/test_out_forces_0.dat @@ -1,54 +1,54 @@ - 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enableFitGradients no # Not available because gradients are implicit fittingGroup { indexGroup heavy_atoms } diff --git a/tests/orientation-fitgroup.in b/tests/orientation-fitgroup.in index 8db516a04..3c2f9fd66 100644 --- a/tests/orientation-fitgroup.in +++ b/tests/orientation-fitgroup.in @@ -11,7 +11,6 @@ colvar { indexGroup RMSD_atoms centerToReference yes rotateToReference yes - enableFitGradients no # Not available because gradients are implicit fittingGroup { indexGroup heavy_atoms } diff --git a/tests/orientation-refposgroup.in b/tests/orientation-refposgroup.in index 58cb9561d..9979fe6aa 100644 --- a/tests/orientation-refposgroup.in +++ b/tests/orientation-refposgroup.in @@ -11,7 +11,6 @@ colvar { indexGroup RMSD_atoms centerToReference yes rotateToReference yes - enableFitGradients no # Not available because gradients are implicit refPositionsGroup { indexGroup heavy_atoms } diff --git a/tests/orientationangle-fitgroup.in b/tests/orientationangle-fitgroup.in index 239f92837..42922befb 100644 --- a/tests/orientationangle-fitgroup.in +++ b/tests/orientationangle-fitgroup.in @@ -12,7 +12,6 @@ colvar { indexGroup RMSD_atoms centerToReference yes rotateToReference yes - enableFitGradients no # Not available because gradients are implicit fittingGroup { indexGroup heavy_atoms } diff --git a/tests/orientationangle-refposgroup.in b/tests/orientationangle-refposgroup.in index 092e70e34..632c52b25 100644 --- a/tests/orientationangle-refposgroup.in +++ b/tests/orientationangle-refposgroup.in @@ -12,7 +12,6 @@ colvar { indexGroup RMSD_atoms centerToReference yes rotateToReference yes - enableFitGradients no # Not available because gradients are implicit refPositionsGroup { indexGroup heavy_atoms } diff --git a/tests/orientationproj-fitgroup.in b/tests/orientationproj-fitgroup.in index 3b5819128..8d3eb4fb3 100644 --- a/tests/orientationproj-fitgroup.in +++ b/tests/orientationproj-fitgroup.in @@ -11,7 +11,6 @@ colvar { indexGroup RMSD_atoms centerToReference yes rotateToReference yes - enableFitGradients no # Not available because gradients are implicit fittingGroup { indexGroup heavy_atoms } diff --git a/tests/orientationproj-refposgroup.in b/tests/orientationproj-refposgroup.in index a9c5168f4..76dddbed3 100644 --- a/tests/orientationproj-refposgroup.in +++ b/tests/orientationproj-refposgroup.in @@ -11,7 +11,6 @@ colvar { indexGroup RMSD_atoms centerToReference yes rotateToReference yes - enableFitGradients no # Not available because gradients are implicit refPositionsGroup { indexGroup heavy_atoms } diff --git a/tests/unittests/CMakeLists.txt b/tests/unittests/CMakeLists.txt index 6847ffc60..a6a6511f2 100644 --- a/tests/unittests/CMakeLists.txt +++ b/tests/unittests/CMakeLists.txt @@ -26,7 +26,7 @@ if(COLVARS_TCL) endif() add_custom_command( - TARGET link_files + TARGET link_files POST_BUILD COMMAND ${CMAKE_COMMAND} -E create_symlink ${CMAKE_CURRENT_SOURCE_DIR}/index.ndx ${CMAKE_CURRENT_BINARY_DIR}/index.ndx From 69f90362978e0af314703222a9eb66796f9c7272 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Thu, 2 Apr 2026 23:38:20 +0200 Subject: [PATCH 5/5] fix: cvmodule pointer And silence CMake warning --- cmake/buildColvarsTests.cmake | 2 +- src/colvaratoms.cpp | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cmake/buildColvarsTests.cmake b/cmake/buildColvarsTests.cmake index 5fef0626c..86da1347d 100644 --- a/cmake/buildColvarsTests.cmake +++ b/cmake/buildColvarsTests.cmake @@ -40,7 +40,7 @@ if(BUILD_TESTS) endforeach() # Copy input files (coordinates, index files, etc) - add_custom_command(TARGET copy_test_files + add_custom_command(TARGET copy_test_files POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy_directory ${COLVARS_SOURCE_DIR}/tests/input_files ${CMAKE_BINARY_DIR}/tests/functional diff --git a/src/colvaratoms.cpp b/src/colvaratoms.cpp index 65a52f0dc..3be1f428a 100644 --- a/src/colvaratoms.cpp +++ b/src/colvaratoms.cpp @@ -930,7 +930,7 @@ 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))) { - cvm::log( + cvmodule->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"); }