radical.repex 1.103.0

RADICAL-Cybertools Replica Exchange Framework

ReplicaExchange

Replica-Exchange (RE) is a family of simulation techniques used to enhance sampling and more thoroughly explore phase space of simulations. RE simulations involve the concurrent execution of independent simulations which interact and exchange information. Replica Exchange (RE), a method devised as early as 1986 by Swendsen et. al., is a popular technique to enhance sampling in molecular simulations. Replica Exchange Molecular Dynamics (REMD) was first formulated in 1999 by Sugita and Okamoto. Initially REMD was used to perform exchanges of temperatures, but was later extended to perform other exchange types. Over the years, REMD has been adopted by many scientific disciplines including chemistry, physics, biology and materials science.

Most RE implementations however are confined within their parent molecular dynamics (MD) packages. This is limiting because it becomes difficult to implement new RE methods, or apply exchange methods across MD packages.

RepEx is designed to be scalable, flexible, and above all, extensible. New developments in replica exchange (RE) should not only be limited to specific MD packages in which they were developed. RepEx aims to decouple the development of new advanced sampling algorithms from specific MD engines, and allows users to easily implement their cumstom RE algorithms and plug them into RepEx. RepEx also supports multiple MD engines including AMBER and GROMACS.

RepEx is available under the MIT License.

Documentation

RepEx replica exchange package implemented via the Ensemble Toolkit 0.7 API. Documentation can be found at: https://repex-30.readthedocs.io/en/latest/

Run the base example as follows:

bin/radical-repex examples/workload_test.json examples/resource_local.json

While that example is running, a number of state update messages will be printed on screen. One can also follow the overall progress of the run by watching the created dump.log file:

$ tail -F dump.log
 |    1.30 |++++++++++++++++++++++++++++++++| startup
 |   78.45 |||||||||||||||||||||||||||||-||||
 |   78.49 ||||||||||||-||||||||||||||||-||||
 |   78.51 ||||||||||||-||||-|||||||||||-||||
 |   78.55 ||||||||||||-||||-|||||||||||-|-||
 |   78.59 ||||||||||||-||||-||||||||-||-|-||
 |   78.62 ||||||-|||||-||||-||||||||-||-|-||
 |   78.64 ||||||-||||--||||-||||||||-||-|-||
 |   78.67 ||||||v||||vv|||vv||||||||v||v|v||  > rep.0015: ['rep.0005', 'rep.0011', 'rep.0016', 'rep.0025', 'rep.0028', 'rep.0010', 'rep.0015', 'rep.0030']
 |   78.71 ||||||-||||--||||-|||-||||-||-|-||
 |   78.76 |-||||-||||--||||-|||-||||-||-|-||
 |   78.77 |-||||-||||--||||-|||-||||-||---||
 |   78.80 |-|||--||||--||||-|||-||||-||---||
 |   78.83 |-|||--||||--||||-|||-|||--||---||
 |   78.86 |-|||--|||---||||-|||-|||--||---||
 |   78.88 |-|||--|||---||-|-|||-|||--||---||
 |   78.90 |v|||v-|||v--||v|-||vv|||v-||-v-||  > rep.0019: ['rep.0020', 'rep.0014', 'rep.0019', 'rep.0029', 'rep.0024', 'rep.0000', 'rep.0009', 'rep.0004']
 |   79.03 |-||---|||---||-|-|||-|||--||---||
 |   79.07 |-||---|||---||-|-|||-||---||---||
 |   79.13 |-||---|||---|--|-|||-||---||---||
 |   79.15 |-||---||----|--|-|||-||---||---||
 |   79.17 |-|----||----|--|-|||-||---||---||
 |   79.20 |-|----||----|--|-|-|-||---||---||
 |   79.23 |-|----||----|--|-|-|-||---|----||
 |   79.26 |-|vv--||v---|v-|-|v|-|vv--|v---||  > rep.0022: ['rep.0003', 'rep.0018', 'rep.0023', 'rep.0022', 'rep.0008', 'rep.0002', 'rep.0027', 'rep.0013']
 |   79.30 |-|----||----|--|-|-|-||---|----||
 |   79.30 |-|---^||--^^|--^^|-|-||--^|-^-^||  < rep.0015: ['rep.0005', 'rep.0011', 'rep.0016', 'rep.0025', 'rep.0028', 'rep.0010', 'rep.0015', 'rep.0030']
 |   79.34 |-|---||---|||--|||-|-||--||-|-|||
 |   79.37 |-|---||---||---|||-|-||--||-|-|||
 |   79.39 |-|---||---||---|||-|-||--||-|-|||
 |   79.39 |^|--^||--^||--^|||-^^||-^||-|^|||  < rep.0019: ['rep.0020', 'rep.0014', 'rep.0019', 'rep.0029', 'rep.0024', 'rep.0000', 'rep.0009', 'rep.0004']
 |   79.56 |||--|||--|||--|||--||||-|||-|||||
 |   79.72 |||--|||--|||--|||--||||-|||-|||-|
 |   79.76 ||---|||--|||--|||--||||-|||-|||-|
 |   79.81 ||---|||--|||--|||--||||-|||-|||-|
 |   79.81 ||-^^|||-^|||-^|||-^|||^^|||^|||-|  < rep.0022: ['rep.0003', 'rep.0018', 'rep.0023', 'rep.0022', 'rep.0008', 'rep.0002', 'rep.0027', 'rep.0013']
 |   79.96 ||-|||||-||||-||||-|||-|||||||||-|
 |   80.04 ||-|||||-||||-||||-|||-||||-||||-|
 |   80.12 ||v||||vv||||v||||v|||v||||v||||v|  > rep.0006: ['rep.0012', 'rep.0001', 'rep.0006', 'rep.0017', 'rep.0007', 'rep.0026', 'rep.0021', 'rep.0031']
 |   80.66 ||-|||||-||||-||||-|||-||||-||||-|
 |   80.66 ||^||||^^||||^||||^|||^||||^||||^|  < rep.0006: ['rep.0012', 'rep.0001', 'rep.0006', 'rep.0017', 'rep.0007', 'rep.0026', 'rep.0021', 'rep.0031']
 |  126.39 |-||||||||||||||||||||||||||||||||
 |  126.45 |-|||||||||||||||||||-||||||||||||

More detailed log traces can be found in radical.repex.log.