forked from i-pi/i-pi
-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Weighted baseline example with JSON committee (i-pi#318)
* Added an example of weighted baseline that uses the new JSON committee * Delta-JSON qtip4p mode in f90 driver * Updated readme
- Loading branch information
Showing
7 changed files
with
94 additions
and
11 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
2 changes: 1 addition & 1 deletion
2
examples/features/committee_models/weighted_baseline/test_settings.dat
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| driver_model dummy | ||
| driver_model2 dummy | ||
| driver_model3 dummt | ||
| driver_model3 dummy | ||
| nsteps 10 |
59 changes: 59 additions & 0 deletions
59
examples/features/committee_models/weighted_baseline_extra/input.xml
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,59 @@ | ||
| <simulation verbosity='medium' threading='false'> | ||
| <output prefix='simulation'> | ||
| <properties stride='10' filename='out'> [ step, time{picosecond}, conserved{electronvolt}, temperature{kelvin}, kinetic_cv{electronvolt}, potential{electronvolt}, pressure_cv{megapascal} ] </properties> | ||
| <trajectory filename='pos' stride='10'> positions </trajectory> | ||
| <trajectory filename='committee_pot' stride='10' extra_type='committee_pot'> extras </trajectory> | ||
| <trajectory filename='committee_force' stride='10' extra_type='committee_force'> extras </trajectory> | ||
| <trajectory filename='committee_virial' stride='10' extra_type='committee_virial'> extras </trajectory> | ||
| <trajectory filename='baseline_pot' stride='10' extra_type='baseline_pot'> extras </trajectory> | ||
| <trajectory filename='baseline_force' stride='10' extra_type='baseline_force'> extras </trajectory> | ||
| <trajectory filename='baseline_virial' stride='10' extra_type='baseline_virial'> extras </trajectory> | ||
| <trajectory filename='weight' stride='10' extra_type='wb_mixing'> extras </trajectory> | ||
| <checkpoint stride='100'/> | ||
| </output> | ||
| <total_steps>100</total_steps> | ||
| <prng> | ||
| <seed>31415</seed> | ||
| </prng> | ||
| <ffcommittee name="committee"> | ||
| <!-- | ||
| This is just an example of the structure of a baselined-committee model. | ||
| The baseline is a QTIP4P/f water potential, while the corrections are | ||
| artificial LJ terms. | ||
| --> | ||
| <baseline_name> base </baseline_name> | ||
| <alpha> 1.5 </alpha> | ||
| <baseline_uncertainty units="electronvolt"> 0.1 </baseline_uncertainty> | ||
| <active_thresh> 0.05 </active_thresh> | ||
| <ffsocket name='base' mode='unix' matching="any" pbc="false"> | ||
| <address> base </address> <latency> 1e-3 </latency> | ||
| </ffsocket> | ||
| <ffsocket name='driver-combo' mode='unix' matching="any" pbc="false"> | ||
| <address>h2o-comm.json</address> <latency> 1e-3 </latency> | ||
| </ffsocket> | ||
| <parse_json> True </parse_json> | ||
| </ffcommittee> | ||
| <system> | ||
| <initialize nbeads='4'> | ||
| <file mode='xyz'> water_216.xyz </file> | ||
| <velocities mode='thermal' units='kelvin'> 300 </velocities> | ||
| </initialize> | ||
| <forces> | ||
| <force forcefield='committee' nbeads='1'> | ||
| <!-- adding these to force_extras will make the committee extras be treated properly with ring-polymer contraction, ect. --> | ||
| <force_extras> [committee_pot, committee_force, committee_virial, baseline_pot, baseline_force, baseline_virial, wb_mixing] </force_extras> | ||
| </force> | ||
| </forces> | ||
| <motion mode='dynamics'> | ||
| <dynamics mode='nvt'> | ||
| <timestep units='femtosecond'> 0.5 </timestep> | ||
| <thermostat mode='pile_g'> | ||
| <tau units='femtosecond'> 10 </tau> | ||
| </thermostat> | ||
| </dynamics> | ||
| </motion> | ||
| <ensemble> | ||
| <temperature units='kelvin'> 300 </temperature> | ||
| </ensemble> | ||
| </system> | ||
| </simulation> |
18 changes: 18 additions & 0 deletions
18
examples/features/committee_models/weighted_baseline_extra/run.sh
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,18 @@ | ||
| ipi=i-pi | ||
| driver=i-pi-driver | ||
| sleep_time=2 | ||
|
|
||
| ${ipi} input.xml > log.i-pi & | ||
| echo "# i-PI is running" | ||
|
|
||
| echo "# Waiting for ${sleep_time} (s) before executing driver" | ||
| sleep ${sleep_time} | ||
|
|
||
| ${driver} -u -a base -m qtip4pf & | ||
| ${driver} -u -a h2o-comm.json -m qtip4pf-c-json-delta & | ||
|
|
||
| echo "# All driver instances are running" | ||
|
|
||
| wait | ||
|
|
||
| echo "# Simulation complete" |
3 changes: 3 additions & 0 deletions
3
examples/features/committee_models/weighted_baseline_extra/test_settings.dat
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| driver_model dummy | ||
| driver_model2 dummy | ||
| nsteps 10 |
1 change: 1 addition & 0 deletions
1
examples/features/committee_models/weighted_baseline_extra/water_216.xyz
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| ../../../init_files/water_216.xyz |