Ensemble Optimization
An example on how te (re-)optimize ensembles with CREST.
Optimize along ensemble or trajectory files
Optimizations along ensemble or trajectory files are one of the core functions of the CREST code. For utility, the respective routines have been implemented as standalone applications and can be invoked by the --mdopt and --screen commands.
--mdopt <ensemble> simply performs the optimization of each point on a given file and writes the optimized structure to a new ensemble file crest_ensemble.xyz in the same order as the original. In the below example, the input input-esnemble.xyz contains n-butane structures optimized at the GFN-FF level, while the refined ensemble has the GFN2-xTB energies and geometries. Note, that for demonstration purposes the highest energy structure was placed as the first point in the input ensemble and --mdopt does not change this order.
crest --mdopt input-ensemble.xyz
14
-1.95476831
C -1.8280514558 0.1026283679 -0.3378109356
C -0.6096777513 -0.4807999039 0.3626338277
C 0.6096679585 0.4807861256 0.3626336492
C 1.8280554740 -0.1026120684 -0.3378127654
H -2.6737183814 -0.5895996214 -0.3384876099
H -1.6051787878 0.3482893729 -1.3783393521
H -2.1588537968 1.0236078559 0.1469845806
H -0.3239394543 -1.4268049722 -0.1182711212
H -0.8704029060 -0.7659987748 1.3922403082
H 0.8703773548 0.7659540027 1.3922522276
H 0.3239374558 1.4268002601 -0.1182574316
H 1.6052556663 -0.3480468876 -1.3784082402
H 2.1587507058 -1.0237028671 0.1468484919
H 2.6738409543 0.5894715887 -0.3381226983
14
-1.95933513
C -1.9450668421 0.1311167672 -0.0001772545
C -0.5674743975 -0.5132672899 0.0001933101
C 0.5674752787 0.5132638115 0.0001915171
C 1.9450638093 -0.1311175361 -0.0001779077
H -2.0853782627 0.7646639932 0.8782051254
H -2.7466842224 -0.6116573212 -0.0004139053
H -2.0848832626 0.7646834243 -0.8786240987
H -0.4586079390 -1.1740559621 -0.8706321703
H -0.4589068044 -1.1737556210 0.8712831745
H 0.4588981405 1.1737728909 0.8712658721
H 0.4586137126 1.1740687810 -0.8706234929
H 2.0850227749 -0.7644118141 -0.8787988057
H 2.0852599026 -0.7649044717 0.8780496213
H 2.7466915989 0.6116467123 -0.0000648118
14
-1.95861370
C -1.5634429064 0.0307829908 0.5671856584
C -0.6780400299 -0.3575310612 -0.6072767893
C 0.6780374832 0.3575328640 -0.6072807936
C 1.5634444854 -0.0307786855 0.5671868578
H -1.7381548026 1.1085042885 0.5904194743
H -1.1085086806 -0.2426226956 1.5210355320
H -2.5399702240 -0.4581336702 0.5235479812
H -1.2059135035 -0.1493891533 -1.5491742664
H -0.5130824651 -1.4435518231 -0.6080674515
H 0.5130888273 1.4435548434 -0.6080686466
H 1.2059008586 0.1493974488 -1.5491848268
H 1.1087081819 0.2429933207 1.5210259608
H 2.5401620514 0.4577301888 0.5232639016
H 1.7377812886 -1.1085555327 0.5906966592
14
-13.66103671
C -1.8189570311 0.1081182839 -0.3386195268
C -0.6003361267 -0.4812669222 0.3627086339
C 0.6003332769 0.4812333014 0.3627646448
C 1.8189747557 -0.1080993350 -0.3385718921
H -2.6452834880 -0.5996606573 -0.3297329893
H -1.5843571400 0.3472810277 -1.3737470764
H -2.1438184799 1.0191234683 0.1597802222
H -0.3205601634 -1.4095157615 -0.1393589481
H -0.8730158184 -0.7389888621 1.3877883008
H 0.8729817345 0.7388756115 1.3878727551
H 0.3205734286 1.4095212839 -0.1392393028
H 1.5844214615 -0.3471335953 -1.3737396356
H 2.1437868862 -1.0191720928 0.1597368360
H 2.6453197400 0.5996567278 -0.3295590909
14
-13.66512776
C -1.9378776420 0.1349368813 -0.0001081753
C -0.5610352612 -0.5177004414 0.0000506021
C 0.5610386129 0.5177070576 0.0001079710
C 1.9378809964 -0.1349302612 -0.0000855289
H -2.0638764712 0.7599162365 0.8815598623
H -2.7207589066 -0.6200754522 -0.0001652173
H -2.0636923965 0.7598567385 -0.8818443961
H -0.4615354382 -1.1553777317 -0.8815520107
H -0.4616978624 -1.1553045239 0.8817229081
H 0.4616847622 1.1552317536 0.8818361648
H 0.4615552388 1.1554637305 -0.8814387524
H 2.0637421337 -0.7597076170 -0.8819160206
H 2.0638334572 -0.7600520754 0.8814882103
H 2.7207622638 0.6200820692 0.0000205563
14
-13.66417742
C -1.5701818259 0.0341541241 0.5669980083
C -0.6722058440 -0.3642502197 -0.5984716668
C 0.6721959716 0.3642001521 -0.5985057684
C 1.5701916459 -0.0341317860 0.5669740172
H -1.7279994660 1.1107209346 0.5744336871
H -1.1293887314 -0.2561977056 1.5169777595
H -2.5388317596 -0.4533661830 0.4810842653
H -1.1899167863 -0.1401654483 -1.5344769575
H -0.4964239626 -1.4421497023 -0.5687647172
H 0.4964157705 1.4421015361 -0.5688640776
H 1.1898906010 0.1400553580 -1.5345056863
H 1.1294519108 0.2563472549 1.5169394335
H 2.5388668910 0.4533220799 0.4809723015
H 1.7279461492 -1.1107070713 0.5745186526
--screen <ensemble> does in principal the same as --mdopt. However, the final ensemble written to crest_ensemble.xyz is additionally sorted with the CREGEN routine. In the below example, the input input-esnemble.xyz again contains n-butane structures optimized at the GFN-FF level, while the refined ensemble has the GFN2-xTB energies and geometries. For demonstration purposes, the --ewin 1.0 command was added to this calculation. As can be seen, the output ensemble crest_ensemble.xyz contains only two structures due to the adjusted energy window.
crest --screen input-ensemble.xyz --ewin 1.0
14
-1.95476831
C -1.8280514558 0.1026283679 -0.3378109356
C -0.6096777513 -0.4807999039 0.3626338277
C 0.6096679585 0.4807861256 0.3626336492
C 1.8280554740 -0.1026120684 -0.3378127654
H -2.6737183814 -0.5895996214 -0.3384876099
H -1.6051787878 0.3482893729 -1.3783393521
H -2.1588537968 1.0236078559 0.1469845806
H -0.3239394543 -1.4268049722 -0.1182711212
H -0.8704029060 -0.7659987748 1.3922403082
H 0.8703773548 0.7659540027 1.3922522276
H 0.3239374558 1.4268002601 -0.1182574316
H 1.6052556663 -0.3480468876 -1.3784082402
H 2.1587507058 -1.0237028671 0.1468484919
H 2.6738409543 0.5894715887 -0.3381226983
14
-1.95933513
C -1.9450668421 0.1311167672 -0.0001772545
C -0.5674743975 -0.5132672899 0.0001933101
C 0.5674752787 0.5132638115 0.0001915171
C 1.9450638093 -0.1311175361 -0.0001779077
H -2.0853782627 0.7646639932 0.8782051254
H -2.7466842224 -0.6116573212 -0.0004139053
H -2.0848832626 0.7646834243 -0.8786240987
H -0.4586079390 -1.1740559621 -0.8706321703
H -0.4589068044 -1.1737556210 0.8712831745
H 0.4588981405 1.1737728909 0.8712658721
H 0.4586137126 1.1740687810 -0.8706234929
H 2.0850227749 -0.7644118141 -0.8787988057
H 2.0852599026 -0.7649044717 0.8780496213
H 2.7466915989 0.6116467123 -0.0000648118
14
-1.95861370
C -1.5634429064 0.0307829908 0.5671856584
C -0.6780400299 -0.3575310612 -0.6072767893
C 0.6780374832 0.3575328640 -0.6072807936
C 1.5634444854 -0.0307786855 0.5671868578
H -1.7381548026 1.1085042885 0.5904194743
H -1.1085086806 -0.2426226956 1.5210355320
H -2.5399702240 -0.4581336702 0.5235479812
H -1.2059135035 -0.1493891533 -1.5491742664
H -0.5130824651 -1.4435518231 -0.6080674515
H 0.5130888273 1.4435548434 -0.6080686466
H 1.2059008586 0.1493974488 -1.5491848268
H 1.1087081819 0.2429933207 1.5210259608
H 2.5401620514 0.4577301888 0.5232639016
H 1.7377812886 -1.1085555327 0.5906966592
14
-13.66512776
C -1.9379628968 0.1336606095 -0.0000667939
C -0.5607123276 -0.5180521254 0.0000722379
C 0.5607123347 0.5180521309 0.0000722067
C 1.9379628907 -0.1336606119 -0.0000667761
H -2.0643552047 0.7585953214 0.8815711926
H -2.7203681725 -0.6218367629 -0.0000713296
H -2.0642286761 0.7584728219 -0.8818100402
H -0.4608418122 -1.1557076807 -0.8815053991
H -0.4609576574 -1.1555856233 0.8817510478
H 0.4609572808 1.1555865342 0.8817503301
H 0.4608421800 1.1557067794 -0.8815061371
H 2.0642516918 -0.7584258880 -0.8818399157
H 2.0643321650 -0.7586422889 0.8815412836
H 2.7203681923 0.6218367498 -0.0000106228
14
-13.66417743
C -1.5703228906 0.0340785398 0.5636242134
C -0.6721073498 -0.3644271090 -0.6016224225
C 0.6721068847 0.3644268194 -0.6016224341
C 1.5703232540 -0.0340780913 0.5636242243
H -1.7286877225 1.1105826870 0.5706663561
H -1.1294494187 -0.2556853962 1.5137545190
H -2.5387370680 -0.4539555910 0.4778560132
H -1.1897350121 -0.1406378965 -1.5377481364
H -0.4960484199 -1.4422911637 -0.5717088872
H 0.4960487505 1.4422909540 -0.5717100530
H 1.1897337115 0.1406361009 -1.5377481357
H 1.1294779612 0.2557370494 1.5137520045
H 2.5387576375 0.4539102626 0.4778247298
H 1.7286407926 -1.1105888990 0.5707000338
Singlepoint energy calculations along ensemble files
While there is no dedicated function for singlepoint energy calculations in the same way as --mdopt or --screen, this still can be done via the --for command. The respective command call would be
crest -for input-ensemble.xyz --prop singlepoint
The output ensemble will be sorted with CREGEN, but also the unsorted ensemble just containing the singlepoint energies is available.