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7 changes: 7 additions & 0 deletions
7
ipi_tests/regression_tests/tests/PLUMED/METAD.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 | ||
ref_HILLS numpy |
5 changes: 5 additions & 0 deletions
5
ipi_tests/regression_tests/tests/PLUMED/METAD.NOAUTO/init.xyz
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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/METAD.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
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ipi_tests/regression_tests/tests/PLUMED/METAD.NOAUTO/plumed.dat
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# default units are LENGTH=nm ENERGY=kJ/mol TIME=ps | ||
dhh: DISTANCE ATOMS=2,3 | ||
METAD ARG=dhh PACE=10 SIGMA=0.01 HEIGHT=20 FILE=HILLS BIASFACTOR=10 TEMP=300 LABEL=metad | ||
|
||
PRINT ARG=dhh,metad.* STRIDE=5 FILE=COLVAR | ||
FLUSH STRIDE=1 | ||
|
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ipi_tests/regression_tests/tests/PLUMED/METAD.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 |
13 changes: 13 additions & 0 deletions
13
ipi_tests/regression_tests/tests/PLUMED/METAD.NOAUTO/ref_HILLS
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#! FIELDS time dhh sigma_dhh height biasf | ||
#! SET multivariate false | ||
#! SET kerneltype stretched-gaussian | ||
0.00024188843 0.1549211771444685 0.01 22.22222222222222 10 | ||
0.00048377686 0.1394657546721228 0.01 16.98682245697788 10 | ||
0.0007256652899999999 0.1454511453378886 0.01 7.125139405924957 10 | ||
0.00096755372 0.1474917194020225 0.01 5.220447499489441 10 | ||
0.00120944215 0.1596346790688307 0.01 7.47862865628175 10 | ||
0.00145133058 0.1741707468887148 0.01 17.27051083233874 10 | ||
0.00169321901 0.1689106642077213 0.01 6.846063239044688 10 | ||
0.00193510744 0.1582870349379482 0.01 3.506897910172468 10 | ||
0.00217699587 0.1552386764037809 0.01 2.873548060189675 10 | ||
0.0024188843 0.1469124424133807 0.01 3.065518757280203 10 |
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30
ipi_tests/regression_tests/tests/PLUMED/METAD.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 2.04865e-02 1.00551e-02 5.68341e-02 | ||
H -1.43933e-02 -2.82911e-02 -7.13938e-02 | ||
H -6.09325e-03 1.82360e-02 1.45598e-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 -1.09557e-02 2.67334e-02 2.84741e-02 | ||
H -4.25606e-03 -9.31289e-03 -2.86912e-02 | ||
H 1.52117e-02 -1.74205e-02 2.17115e-04 | ||
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 1.12574e-02 -3.23849e-03 2.05735e-02 | ||
H -1.33301e-02 2.38665e-02 2.02790e-02 | ||
H 2.07268e-03 -2.06280e-02 -4.08526e-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 2.84007e-02 -2.16826e-02 -9.32255e-03 | ||
H -7.58183e-03 8.33039e-03 7.00661e-03 | ||
H -2.08188e-02 1.33522e-02 2.31594e-03 | ||
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 2.62025e-02 5.94171e-03 2.12597e-02 | ||
H -1.98991e-02 -1.35334e-02 -3.10173e-02 | ||
H -6.30340e-03 7.59173e-03 9.75759e-03 |
103 changes: 103 additions & 0 deletions
103
ipi_tests/regression_tests/tests/PLUMED/METAD.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 3.05942306e-02 | ||
2.00000000e+00 1.90266342e-02 | ||
3.00000000e+00 1.60349367e-02 | ||
4.00000000e+00 1.52102454e-02 | ||
5.00000000e+00 1.16190191e-02 | ||
6.00000000e+00 8.99753647e-03 | ||
7.00000000e+00 9.92540584e-03 | ||
8.00000000e+00 1.09996699e-02 | ||
9.00000000e+00 1.37685499e-02 | ||
1.00000000e+01 2.03824115e-02 | ||
1.10000000e+01 2.19904857e-02 | ||
1.20000000e+01 3.13668080e-02 | ||
1.30000000e+01 3.56232697e-02 | ||
1.40000000e+01 4.07015682e-02 | ||
1.50000000e+01 3.87624398e-02 | ||
1.60000000e+01 3.39657627e-02 | ||
1.70000000e+01 3.12618976e-02 | ||
1.80000000e+01 5.31161653e-02 | ||
1.90000000e+01 9.30897356e-02 | ||
2.00000000e+01 1.48443319e-01 | ||
2.10000000e+01 1.82447607e-01 | ||
2.20000000e+01 1.99778411e-01 | ||
2.30000000e+01 1.53434717e-01 | ||
2.40000000e+01 1.11334565e-01 | ||
2.50000000e+01 9.44743014e-02 | ||
2.60000000e+01 8.63339633e-02 | ||
2.70000000e+01 9.89848969e-02 | ||
2.80000000e+01 1.15389799e-01 | ||
2.90000000e+01 1.33264521e-01 | ||
3.00000000e+01 1.53550763e-01 | ||
3.10000000e+01 1.58555449e-01 | ||
3.20000000e+01 1.45407875e-01 | ||
3.30000000e+01 1.11832557e-01 | ||
3.40000000e+01 6.96386353e-02 | ||
3.50000000e+01 4.98040694e-02 | ||
3.60000000e+01 4.46158799e-02 | ||
3.70000000e+01 4.14674186e-02 | ||
3.80000000e+01 5.13758622e-02 | ||
3.90000000e+01 5.02454311e-02 | ||
4.00000000e+01 4.42007214e-02 | ||
4.10000000e+01 3.03349953e-02 | ||
4.20000000e+01 2.22119743e-02 | ||
4.30000000e+01 1.96984157e-02 | ||
4.40000000e+01 1.53411228e-02 | ||
4.50000000e+01 6.76754736e-03 | ||
4.60000000e+01 2.05692781e-03 | ||
4.70000000e+01 9.49065538e-03 | ||
4.80000000e+01 2.57424651e-02 | ||
4.90000000e+01 4.63702011e-02 | ||
5.00000000e+01 8.56131263e-02 | ||
5.10000000e+01 1.33869652e-01 | ||
5.20000000e+01 1.73296390e-01 | ||
5.30000000e+01 2.16419862e-01 | ||
5.40000000e+01 2.66309619e-01 | ||
5.50000000e+01 3.12196361e-01 | ||
5.60000000e+01 3.56906979e-01 | ||
5.70000000e+01 3.73472078e-01 | ||
5.80000000e+01 3.74903373e-01 | ||
5.90000000e+01 3.45201037e-01 | ||
6.00000000e+01 3.01063563e-01 | ||
6.10000000e+01 2.62155829e-01 | ||
6.20000000e+01 2.52925857e-01 | ||
6.30000000e+01 2.62247359e-01 | ||
6.40000000e+01 2.72768890e-01 | ||
6.50000000e+01 2.43283647e-01 | ||
6.60000000e+01 2.03077954e-01 | ||
6.70000000e+01 1.73664217e-01 | ||
6.80000000e+01 1.60316301e-01 | ||
6.90000000e+01 1.74235312e-01 | ||
7.00000000e+01 1.81924340e-01 | ||
7.10000000e+01 1.88066099e-01 | ||
7.20000000e+01 1.77388023e-01 | ||
7.30000000e+01 1.61295958e-01 | ||
7.40000000e+01 1.23943021e-01 | ||
7.50000000e+01 9.52850083e-02 | ||
7.60000000e+01 7.26735367e-02 | ||
7.70000000e+01 5.56024676e-02 | ||
7.80000000e+01 5.61907770e-02 | ||
7.90000000e+01 6.29617648e-02 | ||
8.00000000e+01 6.10287178e-02 | ||
8.10000000e+01 4.77398529e-02 | ||
8.20000000e+01 4.18901067e-02 | ||
8.30000000e+01 3.88649041e-02 | ||
8.40000000e+01 3.53958012e-02 | ||
8.50000000e+01 3.27962946e-02 | ||
8.60000000e+01 2.61455439e-02 | ||
8.70000000e+01 1.87766372e-02 | ||
8.80000000e+01 1.63194487e-02 | ||
8.90000000e+01 1.59238243e-02 | ||
9.00000000e+01 1.75766792e-02 | ||
9.10000000e+01 1.53648955e-02 | ||
9.20000000e+01 1.18353549e-02 | ||
9.30000000e+01 1.11498261e-02 | ||
9.40000000e+01 9.14632639e-03 | ||
9.50000000e+01 7.65257671e-03 | ||
9.60000000e+01 3.14646759e-03 | ||
9.70000000e+01 7.82098849e-05 | ||
9.80000000e+01 6.72651225e-03 | ||
9.90000000e+01 2.59993981e-02 | ||
1.00000000e+02 3.79665209e-02 |
30 changes: 30 additions & 0 deletions
30
ipi_tests/regression_tests/tests/PLUMED/METAD.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 1.01254e+00 -1.85116e+00 -3.91895e-01 | ||
H 5.16678e-01 -2.23293e+00 -1.97266e+00 | ||
H 4.98084e-02 -3.70389e-01 -1.67402e-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 1.01837e+00 -1.85650e+00 -3.99305e-01 | ||
H 5.23818e-01 -2.11575e+00 -2.07253e+00 | ||
H -4.98662e-02 -4.02909e-01 5.00906e-02 | ||
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 9.96930e-01 -1.84402e+00 -4.25966e-01 | ||
H 6.26121e-01 -2.22185e+00 -2.18335e+00 | ||
H 1.88189e-01 -4.94871e-01 5.84100e-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 1.02806e+00 -1.82535e+00 -4.31273e-01 | ||
H 2.98306e-01 -2.29676e+00 -2.01974e+00 | ||
H 2.18604e-02 -7.16337e-01 5.04750e-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 1.05015e+00 -1.81115e+00 -4.51024e-01 | ||
H 5.14127e-02 -2.35120e+00 -1.77831e+00 | ||
H -8.18111e-02 -8.87253e-01 5.76822e-01 |
4 changes: 4 additions & 0 deletions
4
ipi_tests/regression_tests/tests/PLUMED/METAD.NOAUTO/test_settings.dat
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@@ -0,0 +1,4 @@ | ||
driver_model pswater | ||
address localhost | ||
port 32342 | ||
socket_mode unix |