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Functionalities to incorporate rotational averaging in i-PI (i-pi#372)
* Added functions to manipulate rotations * Added some utilities for rotational averaging * GenericCell object handling non-triangular cells This in no way allows using generic cells in i-PI, but allows us to handle arbitrary rotations from the forcefield to the socket * Added an example, and options, to use lebedev grids in o3-averaging * Implement defining and storing a separate PRNG for the random rotations * smaller box size for geop examples these make the tests run much faster
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| O3 rotational averaging. | ||
| ======================== | ||
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| Examples of the averaging module to handle non-equivariant potentials. | ||
| The `<ffrotations>` socket allows to evaluate a potential multiple times, | ||
| using random rotations or a grid of rotations, to reduce the impact of the | ||
| lack of rotational equivariance on the quality of the dynamics. | ||
| The examples use the `noo3_h2o` potential, that assumes the structure is | ||
| a sequence of H2O molecules and adds a orientation-dependent potential to each | ||
| water molecule. | ||
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| `noo3`: no correction is applied. The structure of the liquid will be badly | ||
| disrupted. | ||
| `random`: the structure is randomly oriented at each evaluation. | ||
| This effectively introduces a noise in the forces, that must be contrasted | ||
| by an aggressive thermostat. There is a large drift in the conserved quantity | ||
| but the mean potential is OK and water molecules do not orient artificially | ||
| `grid`: the potential is averaged over a grid of rotations. | ||
| This reduces the orientational error, but comes at the cost of many additional | ||
| energy evaluations per step. |
42 changes: 42 additions & 0 deletions
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examples/features/o3_averaging/direct_liquid_water/input.xml
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| <simulation verbosity='medium'> | ||
| <output prefix='simulation'> | ||
| <properties stride='1' filename='out'> [ step, time{picosecond}, conserved{electronvolt}, temperature{kelvin}, kinetic_md{electronvolt}, potential{electronvolt}, pressure_md{megapascal}, stress_md{megapascal} ] </properties> | ||
| <trajectory filename='noo3_pots' stride='2' cell_units='angstrom' extra_type="o3grid_pots"> extras_component_raw(1) </trajectory> | ||
| <trajectory filename='pos' stride='20' cell_units='angstrom'> positions{angstrom} </trajectory> | ||
| <checkpoint stride='200'/> | ||
| </output> | ||
| <total_steps>1000</total_steps> | ||
| <prng> | ||
| <seed>31415</seed> | ||
| </prng> | ||
| <ffsocket name='driver-qtip4pf' mode='unix' pbc='false'> | ||
| <address>h2o-base</address> | ||
| </ffsocket> | ||
| <ffrotations name='driver-noo3' pbc='false'> | ||
| <ffdirect name='base-noo3'> | ||
| <pes> dummy </pes> <!-- This is just a dummy ff --> | ||
| </ffdirect> | ||
| <random> True </random> | ||
| </ffrotations> | ||
| <system> | ||
| <initialize nbeads='1'> | ||
| <file mode='xyz'> water_216.xyz </file> | ||
| <velocities mode='thermal' units='kelvin'> 300 </velocities> | ||
| </initialize> | ||
| <forces> | ||
| <force forcefield='driver-qtip4pf'/> | ||
| <force forcefield='driver-noo3' weight="1"/> | ||
| </forces> | ||
| <motion mode='dynamics'> | ||
| <dynamics mode='nvt'> | ||
| <timestep units='femtosecond'> 0.5 </timestep> | ||
| <thermostat mode='langevin'> | ||
| <tau units='femtosecond'> 10 </tau> | ||
| </thermostat> | ||
| </dynamics> | ||
| </motion> | ||
| <ensemble> | ||
| <temperature units='kelvin'> 300 </temperature> | ||
| </ensemble> | ||
| </system> | ||
| </simulation> |
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| ipi=i-pi | ||
| driver1="i-pi-driver -m qtip4pf -u -a h2o-base" | ||
| sleep_time=4 | ||
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| ${ipi} input.xml > log.i-pi & | ||
| echo "# i-PI is running" | ||
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| echo "# Waiting for ${sleep_time} (s) before executing driver" | ||
| sleep ${sleep_time} | ||
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| ${driver1} > /dev/null & | ||
| echo "# Driver is running" | ||
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| wait | ||
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| echo "# Simulation complete" |
3 changes: 3 additions & 0 deletions
3
examples/features/o3_averaging/direct_liquid_water/test_settings.dat
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| #Settings file for automatic test | ||
| driver_model qtip4pf | ||
| nsteps 10 |
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examples/features/o3_averaging/direct_liquid_water/water_216.xyz
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| ../../../init_files/water_216.xyz |
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examples/features/o3_averaging/grid_liquid_water/input.xml
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| <simulation verbosity='medium'> | ||
| <output prefix='simulation'> | ||
| <properties stride='1' filename='out'> [ step, time{picosecond}, conserved{electronvolt}, temperature{kelvin}, kinetic_md{electronvolt}, potential{electronvolt}, pressure_md{megapascal}, stress_md{megapascal} ] </properties> | ||
| <trajectory filename='noo3_pots' stride='2' cell_units='angstrom' extra_type="o3grid_pots"> extras_component_raw(1) </trajectory> | ||
| <trajectory filename='pos' stride='20' cell_units='angstrom'> positions{angstrom} </trajectory> | ||
| <checkpoint stride='200'/> | ||
| </output> | ||
| <total_steps>1000</total_steps> | ||
| <prng> | ||
| <seed>31415</seed> | ||
| </prng> | ||
| <ffsocket name='driver-qtip4pf' mode='unix' pbc='false'> | ||
| <address>h2o-base</address> | ||
| </ffsocket> | ||
| <ffrotations name='driver-noo3' pbc='false'> | ||
| <ffsocket name='base-noo3' mode='unix' pbc='false'> | ||
| <address>h2o-noo3</address> | ||
| </ffsocket> | ||
| <grid_order> 2 </grid_order> | ||
| <grid_mode> legendre </grid_mode> | ||
| <inversion> True </inversion> | ||
| </ffrotations> | ||
| <system> | ||
| <initialize nbeads='1'> | ||
| <file mode='xyz'> water_216.xyz </file> | ||
| <velocities mode='thermal' units='kelvin'> 300 </velocities> | ||
| </initialize> | ||
| <forces> | ||
| <force forcefield='driver-qtip4pf'/> | ||
| <force forcefield='driver-noo3' weight="1.0"/> | ||
| </forces> | ||
| <motion mode='dynamics'> | ||
| <dynamics mode='nvt'> | ||
| <timestep units='femtosecond'> 0.5 </timestep> | ||
| <thermostat mode='langevin'> | ||
| <tau units='femtosecond'> 100 </tau> | ||
| </thermostat> | ||
| </dynamics> | ||
| </motion> | ||
| <ensemble> | ||
| <temperature units='kelvin'> 300 </temperature> | ||
| </ensemble> | ||
| </system> | ||
| </simulation> |
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| @@ -0,0 +1,18 @@ | ||
| ipi=i-pi | ||
| driver1="i-pi-driver -m noo3-h2o -u -a h2o-noo3" | ||
| driver2="i-pi-driver -m qtip4pf -u -a h2o-base" | ||
| sleep_time=4 | ||
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| ${ipi} input.xml > log.i-pi & | ||
| echo "# i-PI is running" | ||
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| echo "# Waiting for ${sleep_time} (s) before executing driver" | ||
| sleep ${sleep_time} | ||
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| ${driver1} > /dev/null & | ||
| ${driver2} > /dev/null & | ||
| echo "# Driver is running" | ||
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| wait | ||
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| echo "# Simulation complete" |
4 changes: 4 additions & 0 deletions
4
examples/features/o3_averaging/grid_liquid_water/test_settings.dat
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| Original file line number | Diff line number | Diff line change |
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| #Settings file for automatic test | ||
| driver_model qtip4pf | ||
| driver_model2 noo3-h2o | ||
| nsteps 10 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| ../../../init_files/water_216.xyz |
43 changes: 43 additions & 0 deletions
43
examples/features/o3_averaging/lebedev_liquid_water/input.xml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
| <simulation verbosity='high'> | ||
| <output prefix='simulation'> | ||
| <properties stride='1' filename='out'> [ step, time{picosecond}, conserved{electronvolt}, temperature{kelvin}, kinetic_md{electronvolt}, potential{electronvolt}, pressure_md{megapascal}, stress_md{megapascal} ] </properties> | ||
| <trajectory filename='noo3_pots' stride='2' cell_units='angstrom' extra_type="o3grid_pots"> extras_component_raw(1) </trajectory> | ||
| <trajectory filename='pos' stride='20' cell_units='angstrom'> positions{angstrom} </trajectory> | ||
| <checkpoint stride='200'/> | ||
| </output> | ||
| <total_steps>1000</total_steps> | ||
| <prng> | ||
| <seed>31415</seed> | ||
| </prng> | ||
| <ffsocket name='driver-qtip4pf' mode='unix' pbc='false'> | ||
| <address>h2o-base</address> | ||
| </ffsocket> | ||
| <ffrotations name='driver-noo3' pbc='false'> | ||
| <ffsocket name='base-noo3' mode='unix' pbc='false'> | ||
| <address>h2o-noo3</address> | ||
| </ffsocket> | ||
| <grid_order> 3 </grid_order> <grid_mode> lebedev </grid_mode> | ||
| <inversion> True </inversion> | ||
| </ffrotations> | ||
| <system> | ||
| <initialize nbeads='1'> | ||
| <file mode='xyz'> water_216.xyz </file> | ||
| <velocities mode='thermal' units='kelvin'> 300 </velocities> | ||
| </initialize> | ||
| <forces> | ||
| <force forcefield='driver-qtip4pf'/> | ||
| <force forcefield='driver-noo3' weight="1.0"/> | ||
| </forces> | ||
| <motion mode='dynamics'> | ||
| <dynamics mode='nvt'> | ||
| <timestep units='femtosecond'> 0.5 </timestep> | ||
| <thermostat mode='langevin'> | ||
| <tau units='femtosecond'> 100 </tau> | ||
| </thermostat> | ||
| </dynamics> | ||
| </motion> | ||
| <ensemble> | ||
| <temperature units='kelvin'> 300 </temperature> | ||
| </ensemble> | ||
| </system> | ||
| </simulation> |
18 changes: 18 additions & 0 deletions
18
examples/features/o3_averaging/lebedev_liquid_water/run.sh
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,18 @@ | ||
| ipi=i-pi | ||
| driver1="i-pi-driver -m noo3-h2o -u -a h2o-noo3" | ||
| driver2="i-pi-driver -m qtip4pf -u -a h2o-base" | ||
| sleep_time=4 | ||
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| ${ipi} input.xml > log.i-pi & | ||
| echo "# i-PI is running" | ||
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| echo "# Waiting for ${sleep_time} (s) before executing driver" | ||
| sleep ${sleep_time} | ||
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| ${driver1} > /dev/null & | ||
| ${driver2} > /dev/null & | ||
| echo "# Driver is running" | ||
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| wait | ||
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| echo "# Simulation complete" |
4 changes: 4 additions & 0 deletions
4
examples/features/o3_averaging/lebedev_liquid_water/test_settings.dat
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| #Settings file for automatic test | ||
| driver_model qtip4pf | ||
| driver_model2 noo3-h2o | ||
| nsteps 10 |
1 change: 1 addition & 0 deletions
1
examples/features/o3_averaging/lebedev_liquid_water/water_216.xyz
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1 @@ | ||
| ../../../init_files/water_216.xyz |
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