Opis
TeraChem je računalni programski paket za kemijske simulacije. Omogućuje simuliranje svojstava molekula, kao što su geometrija, energija, spektroskopija i reaktivnost, koristeći metode kvantne kemije i molekularne mehanike.
GPU (Grafička procesorska jedinica) podrška omogućuje TeraChemu da koristi snagu grafičkih kartica kako bi ubrzao izvođenje računalnih simulacija.
Verzije
| Verzija | Modul | Red | Supek | Padobran |
|---|
| 1.96 | scientific/terachem/1.96 | gpu |  |  |
Službena dokumentacija
Primjer
Postavke simulacije, kao što su tip posla, DFT funkcional, osnovni skup, naboj molekule te ime datoteke u kojoj se nalaze koordinate, definirane su u .sp datoteci (start.sp). Primjer je dan niže:
# Job: minimize
# SCF method (rhf/blyp/b3lyp/etc...)
method b3lyp
# basis set
basis def2-svp
# coordinates file
coordinates molecule.xyz
# molecule charge
charge 0
# add dispersion correction (DFT-D)
dftd yes
# type of the job (energy/gradient/md/minimize/ts)
run minimize
end
Koordinate atoma molekule nalaze se u molecule.xyz datoteci. Primjer je dan niže:
80
N 11.6312087516194644 18.5712818987571495 5.4905821448133807
C 10.2318126720333478 18.5712818987571495 5.4905821448133807
C 9.5876915784923433 17.2153785305662126 5.5096080438463382
C 10.3945049832847349 16.0290934656690354 5.5275827408182341
C 11.8237433842737740 16.1265858360994869 5.5401985630719253
C 12.4934396107196726 17.4694910128286693 5.4859112144712032
C 8.1953385452329748 17.1123895696302668 5.4982449714725004
C 7.5731551972501006 15.8439889650339154 5.4833934715330539
C 8.3191491563154614 14.6490541494093289 5.4868301803081305
C 9.7632753843514219 14.7298407588396305 5.5245096420666417
C 12.6025620551488160 14.9670669009358601 5.5762435811528626
C 11.9906100294747997 13.6944701474983646 5.5876129589202179
C 10.5890961111393498 13.5441041624243290 5.5566713827362921
C 9.9395162537441148 12.2078154908889580 5.5483255717149973
C 8.4966881716416136 12.1270288814586600 5.4764407343974337
C 7.6708052491384873 13.3127654778739544 5.4459178139415396
C 10.6836248483065432 11.0128806752643680 5.6014405171404533
C 10.0621055533559343 9.7444800706680184 5.5690916135773136
C 8.6728963618024153 9.6414911097320672 5.4748901765206277
C 7.8670413778113790 10.8277761746292445 5.4316616597670127
C 6.2709775931689471 13.1623994927999188 5.3705442243524857
C 5.6616475719806676 11.8898027393624215 5.3128253387426447
C 6.4409579682478544 10.7302838041988000 5.3359136843287320
C 5.7773027661090275 9.3873786274696140 5.2310236247041679
N 6.6366993968075256 8.2855877415411356 5.3010329320783161
C 8.0320701241976700 8.2855877415411339 5.4070985754492860
O 8.6590004912903584 7.2322510850242878 5.4259269632705358
O 9.6052585890175397 19.6246185552739831 5.4618388946989072
O 4.5695409037684733 9.2322833057320963 5.0872737912405732
O 13.7086227113054200 17.6245863345661888 5.4341158208927993
H 6.2014363558304861 7.3741469483238262 5.1852346190386704
H 12.0739965639529583 19.4827226919744483 5.4081071947234935
H 11.7671541439977574 11.0423815130944032 5.6666644377234512
H 6.4877990920463340 15.8144881272038909 5.4663048983260172
H 5.6257379184858110 14.0359401282361578 5.3522758732650555
H 12.6353783061458671 12.8209295120621238 5.6183023680911717
H 10.6574037146316023 8.8341078658810623 5.6083660833147064
H 7.5987759905766037 18.0227617744172193 5.4922865175440041
H 4.5797007311464419 11.7927943609273118 5.2460693293634861
H 13.6864563803527304 15.0640752793709769 5.5916845322291255
N 8.8659732180638144 19.1329933820270597 2.1715591085968633
C 7.6539245673596898 18.4342294394891404 2.1629539226503933
C 7.7722533189872944 16.9391789922589950 2.0877413412880443
C 9.0609882708612428 16.3134829777864283 2.0950248443339134
C 10.2532239219725696 17.1110132112079967 2.1276269007059767
C 10.1635739546973305 18.6090403394207087 2.1676958207849815
C 6.6160474910636324 16.1562402133379166 2.0373739076437118
C 6.7070384430610464 14.7473867971010932 2.0062332662014004
C 7.9502184595082337 14.0827888826899432 2.0311658304243654
C 9.1598342755455651 14.8724924087487764 2.0778931774130296
C 11.5057020937517631 16.4940492044448384 2.1336815097270616
C 11.6076788257897778 15.0848829253070047 2.1287903788079010
C 10.4685597519058042 14.2563548391947457 2.1104339750785126
C 10.5693038958287318 12.7740807576083402 2.1305640990575299
C 9.3596258840762125 11.9843772315495141 2.0854755722826201
C 8.0521985536494185 12.6005148011035448 2.0187293990580901
C 11.8107976499100076 12.1094828431971973 2.1999286766856248
C 11.8991665974216900 10.7006294269603686 2.2378762986205061
C 10.7424690441058743 9.9176906480392955 2.2004655374710200
C 9.4568890836574564 10.5433866625118604 2.1100498812405668
C 6.9149648442683826 11.7719867149912876 1.9506947586783223
C 7.0162775232741179 10.3628204358534468 1.9633010313828514
C 8.2656118533474743 9.7458564290902956 2.0521940050867844
C 8.3519669646864525 8.2478293008775783 2.0989425851120753
N 9.6455423491239891 7.7238762582712237 2.2011449406711705
C 10.8547567714264090 8.4226402008091377 2.2844303643339732
O 11.9161965533588567 7.8245979328828970 2.4226270526982567
O 6.5850635471820524 19.0322717074153900 2.2203024613281013
O 7.3763092987375742 7.5062240280700010 2.0668794668575465
O 11.1388553365693230 19.3506456122282771 2.2096738013327286
H 9.7075677505769349 6.7142174100745713 2.3027783186373192
H 8.7964230452544268 20.1426522302237139 2.2681989937602474
H 12.7361162169278455 12.6775424180662917 2.2288264469560630
H 5.7821912740552737 14.1793272222319953 1.9649144378474368
H 5.9214795830075477 12.2059535019062881 1.8888881459078171
H 12.6029908965631527 14.6509161383920024 2.1424616442024469
H 12.8659045386542523 10.2046435511325360 2.3002599553483449
H 5.6473620654613850 16.6522260891657403 2.0263053092187722
H 6.1235353548242184 9.7422120668383112 1.9127381099903769
H 12.3997086555823675 17.1146575734599757 2.1509284153106378
U primjeru niže, aplikacija će se pokrenuti na jednom GPU čvoru, 2 GPU-a i 32 CPU jezgre.
#PBS -q gpu
#PBS -l select=1:ngpus=2:ncpus=32
module load scientific/terachem/1.96
cd $PBS_O_WORKDIR
terachem start.sp