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Did is so that it does not run in the CI as we don't have PLUMED there
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6 changes: 6 additions & 0 deletions
6
ipi_tests/regression_tests/tests/PLUMED/BIAS.NOAUTO/files_to_check.txt
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filename format | ||
---------------------------------------------------------- | ||
ref_simulation.frc_c.xyz xyz | ||
ref_simulation.pos_c.xyz xyz | ||
ref_simulation.out numpy | ||
ref_COLVAR numpy |
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3 | ||
# | ||
O 0.54044984 -0.97485007 -0.21657970 | ||
H 0.18385954 -1.25804198 -1.07875142 | ||
H 0.04233158 -0.19485993 0.09228101 |
41 changes: 41 additions & 0 deletions
41
ipi_tests/regression_tests/tests/PLUMED/BIAS.NOAUTO/input.xml
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<simulation mode="static" verbosity="medium"> | ||
<output prefix='simulation'> | ||
<properties stride='1' filename='out'> [ step, potential{electronvolt}] </properties> | ||
<trajectory stride="20" filename="pos_c" format="xyz"> x_centroid </trajectory> | ||
<trajectory stride="20" filename="frc_c" format="xyz"> f_centroid </trajectory> | ||
</output> | ||
<total_steps> 100 </total_steps> | ||
<ffsocket name="pswater" mode="unix"> | ||
<address> localhost </address> | ||
</ffsocket> | ||
<ffplumed name="plumed"> | ||
<file mode="xyz">./init.xyz</file> | ||
<plumeddat> plumed.dat </plumeddat> | ||
</ffplumed> | ||
<system > | ||
<initialize nbeads='1'> | ||
<file mode='xyz' units='angstrom'>init.xyz</file> | ||
<cell> [ 25.29166, 0, 0, 0, 25.29166, 0, 0, 0, 25.29166 ] </cell> | ||
</initialize> | ||
<forces> | ||
<force forcefield="pswater"> </force> | ||
</forces> | ||
<ensemble> | ||
<temperature units="kelvin"> 300.0 </temperature> | ||
<bias> | ||
<force forcefield="plumed" nbeads="1"></force> | ||
</bias> | ||
</ensemble> | ||
<motion mode="dynamics"> | ||
<dynamics mode="nvt"> | ||
<timestep units="femtosecond"> 0.5 </timestep> | ||
<thermostat mode="langevin"> | ||
<tau units="femtosecond"> 5 </tau> | ||
</thermostat> | ||
</dynamics> | ||
</motion> | ||
</system> | ||
<smotion mode="metad"> | ||
<metad> <metaff> [ plumed ] </metaff> </metad> | ||
</smotion> | ||
</simulation> |
7 changes: 7 additions & 0 deletions
7
ipi_tests/regression_tests/tests/PLUMED/BIAS.NOAUTO/plumed.dat
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# default units are LENGTH=nm ENERGY=kJ/mol TIME=ps | ||
dhh: DISTANCE ATOMS=2,3 | ||
RESTRAINT ARG=dhh AT=0.25 KAPPA=1e5 LABEL=rest | ||
|
||
PRINT ARG=dhh,rest.* STRIDE=4 FILE=COLVAR | ||
FLUSH STRIDE=1 | ||
|
26 changes: 26 additions & 0 deletions
26
ipi_tests/regression_tests/tests/PLUMED/BIAS.NOAUTO/ref_COLVAR
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#! FIELDS time dhh rest.bias rest.force2 | ||
0.000097 0.184331 215.623573 43124714.631938 | ||
0.000194 0.220153 44.540998 8908199.552153 | ||
0.000290 0.228350 23.437102 4687420.313194 | ||
0.000387 0.208506 86.087415 17217483.027251 | ||
0.000484 0.186316 202.783446 40556689.120482 | ||
0.000581 0.195882 146.437129 29287425.761376 | ||
0.000677 0.214331 63.613732 12722746.423567 | ||
0.000774 0.219615 46.161372 9232274.453717 | ||
0.000871 0.209151 83.431772 16686354.439035 | ||
0.000968 0.193753 158.186674 31637334.717337 | ||
0.001064 0.189815 181.114349 36222869.853859 | ||
0.001161 0.201878 115.787834 23157566.814556 | ||
0.001258 0.213007 68.424614 13684922.701663 | ||
0.001355 0.213897 65.169567 13033913.399078 | ||
0.001451 0.206660 93.918793 18783758.690671 | ||
0.001548 0.194784 152.440133 30488026.631448 | ||
0.001645 0.199688 126.563246 25312649.262310 | ||
0.001742 0.205663 98.287587 19657517.347279 | ||
0.001838 0.206943 92.697079 18539415.792061 | ||
0.001935 0.203886 106.323087 21264617.450864 | ||
0.002032 0.200653 121.758531 24351706.255268 | ||
0.002129 0.197283 138.953307 27790661.446668 | ||
0.002225 0.200037 124.813581 24962716.130805 | ||
0.002322 0.205228 100.224485 20044897.099738 | ||
0.002419 0.202661 112.047234 22409446.836354 |
30 changes: 30 additions & 0 deletions
30
ipi_tests/regression_tests/tests/PLUMED/BIAS.NOAUTO/ref_simulation.frc_c.xyz
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3 | ||
# CELL(abcABC): 25.29166 25.29166 25.29166 90.00000 90.00000 90.00000 Step: 0 Bead: 0 f_centroid{atomic_unit} cell{atomic_unit} | ||
O -7.34145e-03 4.55046e-03 -4.38801e-03 | ||
H 1.78151e-03 1.10616e-02 1.67248e-02 | ||
H 5.55994e-03 -1.56120e-02 -1.23368e-02 | ||
3 | ||
# CELL(abcABC): 25.29166 25.29166 25.29166 90.00000 90.00000 90.00000 Step: 20 Bead: 0 f_centroid{atomic_unit} cell{atomic_unit} | ||
O 3.00660e-02 -6.51393e-02 -2.11490e-02 | ||
H -1.36193e-02 5.76692e-02 5.16106e-02 | ||
H -1.64467e-02 7.47005e-03 -3.04616e-02 | ||
3 | ||
# CELL(abcABC): 25.29166 25.29166 25.29166 90.00000 90.00000 90.00000 Step: 40 Bead: 0 f_centroid{atomic_unit} cell{atomic_unit} | ||
O -8.54149e-03 6.99613e-03 -1.05965e-02 | ||
H -8.06995e-03 5.15873e-02 7.46366e-02 | ||
H 1.66114e-02 -5.85834e-02 -6.40401e-02 | ||
3 | ||
# CELL(abcABC): 25.29166 25.29166 25.29166 90.00000 90.00000 90.00000 Step: 60 Bead: 0 f_centroid{atomic_unit} cell{atomic_unit} | ||
O 2.25533e-03 1.23581e-02 3.15938e-02 | ||
H -1.72452e-02 5.30545e-02 6.25606e-02 | ||
H 1.49899e-02 -6.54126e-02 -9.41544e-02 | ||
3 | ||
# CELL(abcABC): 25.29166 25.29166 25.29166 90.00000 90.00000 90.00000 Step: 80 Bead: 0 f_centroid{atomic_unit} cell{atomic_unit} | ||
O 5.90243e-03 -1.75604e-03 1.37665e-03 | ||
H -1.36026e-02 5.64416e-02 8.00102e-02 | ||
H 7.70016e-03 -5.46855e-02 -8.13869e-02 | ||
3 | ||
# CELL(abcABC): 25.29166 25.29166 25.29166 90.00000 90.00000 90.00000 Step: 100 Bead: 0 f_centroid{atomic_unit} cell{atomic_unit} | ||
O -3.77567e-03 -2.01726e-03 -2.78397e-03 | ||
H -2.26877e-03 5.64479e-02 8.41792e-02 | ||
H 6.04444e-03 -5.44307e-02 -8.13952e-02 |
103 changes: 103 additions & 0 deletions
103
ipi_tests/regression_tests/tests/PLUMED/BIAS.NOAUTO/ref_simulation.out
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# column 1 --> step : The current simulation time step. | ||
# column 2 --> potential{electronvolt} : The physical system potential energy. | ||
0.00000000e+00 3.25615492e-02 | ||
1.00000000e+00 5.76949314e-02 | ||
2.00000000e+00 1.41165251e-01 | ||
3.00000000e+00 3.66274711e-01 | ||
4.00000000e+00 7.39957788e-01 | ||
5.00000000e+00 1.18657709e+00 | ||
6.00000000e+00 1.64059978e+00 | ||
7.00000000e+00 2.11730348e+00 | ||
8.00000000e+00 2.51283801e+00 | ||
9.00000000e+00 2.80217377e+00 | ||
1.00000000e+01 2.98085379e+00 | ||
1.10000000e+01 3.02318306e+00 | ||
1.20000000e+01 2.90767615e+00 | ||
1.30000000e+01 2.71609007e+00 | ||
1.40000000e+01 2.45544674e+00 | ||
1.50000000e+01 2.13952149e+00 | ||
1.60000000e+01 1.78209900e+00 | ||
1.70000000e+01 1.45127851e+00 | ||
1.80000000e+01 1.18472483e+00 | ||
1.90000000e+01 9.72369496e-01 | ||
2.00000000e+01 8.25580153e-01 | ||
2.10000000e+01 7.68242936e-01 | ||
2.20000000e+01 7.84240488e-01 | ||
2.30000000e+01 9.09298701e-01 | ||
2.40000000e+01 1.13361847e+00 | ||
2.50000000e+01 1.38850907e+00 | ||
2.60000000e+01 1.64658535e+00 | ||
2.70000000e+01 1.88173226e+00 | ||
2.80000000e+01 2.05674122e+00 | ||
2.90000000e+01 2.19192921e+00 | ||
3.00000000e+01 2.28081628e+00 | ||
3.10000000e+01 2.34212600e+00 | ||
3.20000000e+01 2.34394085e+00 | ||
3.30000000e+01 2.30719281e+00 | ||
3.40000000e+01 2.13131605e+00 | ||
3.50000000e+01 1.96317480e+00 | ||
3.60000000e+01 1.74668285e+00 | ||
3.70000000e+01 1.50102140e+00 | ||
3.80000000e+01 1.30438679e+00 | ||
3.90000000e+01 1.12391496e+00 | ||
4.00000000e+01 9.69291798e-01 | ||
4.10000000e+01 8.66893892e-01 | ||
4.20000000e+01 7.85790720e-01 | ||
4.30000000e+01 7.61510117e-01 | ||
4.40000000e+01 7.99245224e-01 | ||
4.50000000e+01 8.98409910e-01 | ||
4.60000000e+01 1.04454649e+00 | ||
4.70000000e+01 1.22633875e+00 | ||
4.80000000e+01 1.40156356e+00 | ||
4.90000000e+01 1.56699046e+00 | ||
5.00000000e+01 1.74743959e+00 | ||
5.10000000e+01 1.89622664e+00 | ||
5.20000000e+01 1.99519129e+00 | ||
5.30000000e+01 2.04454885e+00 | ||
5.40000000e+01 2.05902285e+00 | ||
5.50000000e+01 2.05184435e+00 | ||
5.60000000e+01 2.03091989e+00 | ||
5.70000000e+01 1.96961817e+00 | ||
5.80000000e+01 1.89824694e+00 | ||
5.90000000e+01 1.78203375e+00 | ||
6.00000000e+01 1.62576266e+00 | ||
6.10000000e+01 1.43878440e+00 | ||
6.20000000e+01 1.27078130e+00 | ||
6.30000000e+01 1.12019035e+00 | ||
6.40000000e+01 1.05533955e+00 | ||
6.50000000e+01 1.08185462e+00 | ||
6.60000000e+01 1.14155728e+00 | ||
6.70000000e+01 1.20894642e+00 | ||
6.80000000e+01 1.25352795e+00 | ||
6.90000000e+01 1.33414251e+00 | ||
7.00000000e+01 1.39149390e+00 | ||
7.10000000e+01 1.47005568e+00 | ||
7.20000000e+01 1.53239691e+00 | ||
7.30000000e+01 1.58728429e+00 | ||
7.40000000e+01 1.59932992e+00 | ||
7.50000000e+01 1.60508486e+00 | ||
7.60000000e+01 1.59916236e+00 | ||
7.70000000e+01 1.55469308e+00 | ||
7.80000000e+01 1.52514794e+00 | ||
7.90000000e+01 1.49101237e+00 | ||
8.00000000e+01 1.44091236e+00 | ||
8.10000000e+01 1.41637975e+00 | ||
8.20000000e+01 1.39748798e+00 | ||
8.30000000e+01 1.34828554e+00 | ||
8.40000000e+01 1.28372097e+00 | ||
8.50000000e+01 1.24049201e+00 | ||
8.60000000e+01 1.17313816e+00 | ||
8.70000000e+01 1.12352079e+00 | ||
8.80000000e+01 1.11917209e+00 | ||
8.90000000e+01 1.10723717e+00 | ||
9.00000000e+01 1.14348946e+00 | ||
9.10000000e+01 1.17896254e+00 | ||
9.20000000e+01 1.25654189e+00 | ||
9.30000000e+01 1.34171864e+00 | ||
9.40000000e+01 1.43036501e+00 | ||
9.50000000e+01 1.49167593e+00 | ||
9.60000000e+01 1.51978189e+00 | ||
9.70000000e+01 1.51103238e+00 | ||
9.80000000e+01 1.46516604e+00 | ||
9.90000000e+01 1.40203871e+00 | ||
1.00000000e+02 1.37586058e+00 |
30 changes: 30 additions & 0 deletions
30
ipi_tests/regression_tests/tests/PLUMED/BIAS.NOAUTO/ref_simulation.pos_c.xyz
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3 | ||
# CELL(abcABC): 25.29166 25.29166 25.29166 90.00000 90.00000 90.00000 Step: 0 Bead: 0 x_centroid{atomic_unit} cell{atomic_unit} | ||
O 1.02130e+00 -1.84220e+00 -4.09276e-01 | ||
H 3.47444e-01 -2.37735e+00 -2.03854e+00 | ||
H 7.99951e-02 -3.68232e-01 1.74386e-01 | ||
3 | ||
# CELL(abcABC): 25.29166 25.29166 25.29166 90.00000 90.00000 90.00000 Step: 20 Bead: 0 x_centroid{atomic_unit} cell{atomic_unit} | ||
O 9.69225e-01 -1.82197e+00 -4.19100e-01 | ||
H 8.30712e-01 -2.73182e+00 -2.12743e+00 | ||
H 4.23365e-01 -3.34913e-01 4.19203e-01 | ||
3 | ||
# CELL(abcABC): 25.29166 25.29166 25.29166 90.00000 90.00000 90.00000 Step: 40 Bead: 0 x_centroid{atomic_unit} cell{atomic_unit} | ||
O 9.86598e-01 -1.84319e+00 -4.13643e-01 | ||
H 7.48846e-01 -2.49957e+00 -2.31041e+00 | ||
H 2.29459e-01 -2.30219e-01 5.15560e-01 | ||
3 | ||
# CELL(abcABC): 25.29166 25.29166 25.29166 90.00000 90.00000 90.00000 Step: 60 Bead: 0 x_centroid{atomic_unit} cell{atomic_unit} | ||
O 9.76284e-01 -1.83587e+00 -4.39929e-01 | ||
H 8.20561e-01 -2.52441e+00 -2.28179e+00 | ||
H 3.21472e-01 -3.21702e-01 9.04183e-01 | ||
3 | ||
# CELL(abcABC): 25.29166 25.29166 25.29166 90.00000 90.00000 90.00000 Step: 80 Bead: 0 x_centroid{atomic_unit} cell{atomic_unit} | ||
O 9.99042e-01 -1.80673e+00 -4.46798e-01 | ||
H 6.00194e-01 -2.74082e+00 -2.21121e+00 | ||
H 1.80588e-01 -5.67817e-01 9.42645e-01 | ||
3 | ||
# CELL(abcABC): 25.29166 25.29166 25.29166 90.00000 90.00000 90.00000 Step: 100 Bead: 0 x_centroid{atomic_unit} cell{atomic_unit} | ||
O 1.01297e+00 -1.78473e+00 -4.65187e-01 | ||
H 3.71459e-01 -2.89285e+00 -2.07779e+00 | ||
H 1.88253e-01 -7.64974e-01 1.10112e+00 |
4 changes: 4 additions & 0 deletions
4
ipi_tests/regression_tests/tests/PLUMED/BIAS.NOAUTO/test_settings.dat
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driver_model pswater | ||
address localhost | ||
port 32342 | ||
socket_mode unix |
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