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GiovanniBussiGiovanniBussi
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Merge branch 'v2.9' into v2.10
2 parents 9a880de + fc56f80 commit 910f109

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‎CHANGES/v2.9.md

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@@ -66,7 +66,7 @@ Changes from version 2.8 which are relevant for users:
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## Version 2.9.3 (Jan 15, 2025)
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- Patch for GROMACS 2024 was updated to fix a big issue preventing its use
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## Version 2.9.4 (in progress)
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## Version 2.9.4 (May 23, 2025)
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- Fixed an issue that might lead to a crash when using multicolvars implemented with linked cells and no PBCs, apparently
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only showing up with Intel Mac. See \issue{1181}.
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- Fixed compatibility with cython 3.11. See \issue{1256}.

‎regtest/basic/rt43/deriv.reference

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#! FIELDS time parameter stat.sqdevsum stat.corr stat.slope stat.intercept statn.sqdevsum statn.corr statn.slope statn.intercept
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0.000000 0 -0.0004 0.0002 0.1489 -0.4381 -0.0004 0.0002 0.1489 -0.4381
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0.000000 1 0.0003 -0.0003 0.1480 -0.4365 0.0003 -0.0003 0.1480 -0.4365
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0.000000 2 -0.0008 0.0005 0.3792 -0.8063 -0.0008 0.0005 0.3792 -0.8063
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0.000000 3 0.0004 -0.0004 0.3789 -0.8057 0.0004 -0.0004 0.3789 -0.8057
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0.000000 4 0.0001 0.0000 -1.0550 1.4867 0.0001 0.0000 -1.0550 1.4867
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0.050000 0 0.0128 0.0026 0.1559 -0.4518 0.0128 0.0026 0.1559 -0.4518
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0.050000 1 0.0136 0.0021 0.1548 -0.4501 0.0136 0.0021 0.1548 -0.4501
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0.050000 2 0.0206 -0.0015 0.3806 -0.8127 0.0206 -0.0015 0.3806 -0.8127
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0.050000 3 0.0219 -0.0024 0.3802 -0.8121 0.0219 -0.0024 0.3802 -0.8121
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0.050000 4 0.0059 -0.0007 -1.0715 1.5198 0.0059 -0.0007 -1.0715 1.5198
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0.100000 0 0.0149 0.0030 0.1602 -0.4609 0.0149 0.0030 0.1602 -0.4609
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0.100000 1 0.0157 0.0024 0.1590 -0.4591 0.0157 0.0024 0.1590 -0.4590
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0.100000 2 0.0270 -0.0018 0.3887 -0.8280 0.0270 -0.0018 0.3887 -0.8280
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0.100000 3 0.0283 -0.0027 0.3883 -0.8274 0.0283 -0.0027 0.3883 -0.8274
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0.100000 4 -0.0099 -0.0009 -1.0961 1.5571 -0.0099 -0.0009 -1.0961 1.5571
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0.150000 0 0.0115 0.0023 0.1640 -0.4699 0.0115 0.0023 0.1640 -0.4699
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0.150000 1 0.0122 0.0017 0.1628 -0.4680 0.0122 0.0017 0.1628 -0.4680
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0.150000 2 0.0269 -0.0012 0.4030 -0.8529 0.0269 -0.0012 0.4030 -0.8529
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0.150000 3 0.0282 -0.0022 0.4026 -0.8523 0.0282 -0.0022 0.4026 -0.8523
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0.150000 4 -0.0415 -0.0006 -1.1325 1.6078 -0.0415 -0.0006 -1.1325 1.6078
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0.200000 0 -0.0005 0.0006 0.1700 -0.4839 -0.0005 0.0006 0.1700 -0.4839
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0.200000 1 0.0002 0.0000 0.1687 -0.4818 0.0002 0.0000 0.1687 -0.4818
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0.200000 2 0.0196 0.0002 0.4300 -0.8978 0.0196 0.0002 0.4300 -0.8978
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0.200000 3 0.0209 -0.0008 0.4296 -0.8972 0.0209 -0.0008 0.4296 -0.8972
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0.200000 4 -0.1020 -0.0001 -1.1982 1.6952 -0.1020 -0.0001 -1.1982 1.6952
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#! FIELDS time parameter stat.sqdevsum stat.corr stat.slope stat.intercept
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0.000000 0 -0.0004 0.0002 0.1489 -0.4381
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0.000000 1 0.0003 -0.0003 0.1480 -0.4365
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0.000000 2 -0.0008 0.0005 0.3792 -0.8063
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0.000000 3 0.0004 -0.0004 0.3789 -0.8057
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0.000000 4 0.0001 0.0000 -1.0550 1.4867
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0.050000 0 0.0128 0.0026 0.1559 -0.4518
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0.050000 1 0.0136 0.0021 0.1548 -0.4501
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0.050000 2 0.0206 -0.0015 0.3806 -0.8127
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0.050000 3 0.0219 -0.0024 0.3802 -0.8121
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0.050000 4 0.0059 -0.0007 -1.0715 1.5198
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0.100000 0 0.0149 0.0030 0.1602 -0.4609
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0.100000 1 0.0157 0.0024 0.1590 -0.4591
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0.100000 2 0.0270 -0.0018 0.3887 -0.8280
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0.100000 3 0.0283 -0.0027 0.3883 -0.8274
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0.100000 4 -0.0099 -0.0009 -1.0961 1.5571
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0.150000 0 0.0115 0.0023 0.1640 -0.4699
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0.150000 1 0.0122 0.0017 0.1628 -0.4680
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0.150000 2 0.0269 -0.0012 0.4030 -0.8529
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0.150000 3 0.0282 -0.0022 0.4026 -0.8523
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0.150000 4 -0.0415 -0.0006 -1.1325 1.6078
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0.200000 0 -0.0005 0.0006 0.1700 -0.4839
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0.200000 1 0.0002 0.0000 0.1687 -0.4818
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0.200000 2 0.0196 0.0002 0.4300 -0.8978
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0.200000 3 0.0209 -0.0008 0.4296 -0.8972
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0.200000 4 -0.1020 -0.0001 -1.1982 1.6952

‎regtest/basic/rt43/numerical_deriv.reference

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#! FIELDS time parameter statn.sqdevsum statn.corr statn.slope statn.intercept
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0.000000 0 -0.000 0.000 0.149 -0.438
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0.000000 1 0.000 -0.000 0.148 -0.437
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0.000000 2 -0.001 0.000 0.379 -0.806
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0.000000 3 0.000 -0.000 0.379 -0.806
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0.000000 4 0.000 0.000 -1.055 1.487
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0.050000 0 0.013 0.003 0.156 -0.452
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0.050000 1 0.014 0.002 0.155 -0.450
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0.050000 2 0.021 -0.002 0.381 -0.813
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0.050000 3 0.022 -0.002 0.380 -0.812
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0.050000 4 0.006 -0.001 -1.072 1.520
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0.100000 0 0.015 0.003 0.160 -0.461
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0.100000 1 0.016 0.002 0.159 -0.459
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0.100000 2 0.027 -0.002 0.389 -0.828
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0.100000 3 0.028 -0.003 0.388 -0.827
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0.100000 4 -0.010 -0.001 -1.096 1.557
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0.150000 0 0.012 0.002 0.164 -0.470
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0.150000 1 0.012 0.002 0.163 -0.468
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0.150000 2 0.027 -0.001 0.403 -0.853
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0.150000 3 0.028 -0.002 0.403 -0.852
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0.150000 4 -0.042 -0.001 -1.132 1.608
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0.200000 0 -0.000 0.001 0.170 -0.484
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0.200000 1 0.000 0.000 0.169 -0.482
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0.200000 2 0.020 0.000 0.430 -0.898
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0.200000 3 0.021 -0.001 0.430 -0.897
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0.200000 4 -0.102 -0.000 -1.198 1.695

‎regtest/basic/rt43/plumed.dat

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@@ -8,7 +8,8 @@ stat: STATS ARG=rmsd0,rmsd1,rmsd2,rmsd3,rmsd4 PARAMETERS=1.496,1.496,1.337,1.336
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statn: STATS ARG=rmsd0,rmsd1,rmsd2,rmsd3,rmsd4 PARAMETERS=1.496,1.496,1.337,1.336,2.329 NUMERICAL_DERIVATIVES
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statsq: STATS ARG=rmsd0,rmsd1,rmsd2,rmsd3,rmsd4 PARAMETERS=1.496,1.496,1.337,1.336,2.329 SQDEVSUM
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DUMPDERIVATIVES ARG=stat.*,statn.* STRIDE=1 FILE=deriv FMT=%8.4f
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DUMPDERIVATIVES ARG=stat.* STRIDE=1 FILE=deriv FMT=%8.4f
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DUMPDERIVATIVES ARG=statn.* STRIDE=1 FILE=numerical_deriv FMT=%8.3f
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PRINT ...
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STRIDE=1

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