计算化学公社

标题: 计算簇模型irc时，正常输出，但在gview中打开无法显示结构 [打印本页]

作者
Author: Jiangxue 时间: 2024-12-8 09:54
标题: 计算簇模型irc时，正常输出，但在gview中打开无法显示结构
本帖最后由 Jiangxue 于 2024-12-8 19:25 编辑

请教老师，我在用簇模型计算了过渡态后（振动趋势正确，虚频-1356.01），跑irc时，irc设定40步，只算了23步就正常输出结果了，且过渡态不在最高点，而且irc形状也很奇怪，最重要的是将irc的log文件用gview打开时无法显示每一步的结构。（在计算TS时，上一个文件能量很接近但一直没收敛，于是取了最后一帧的结构加了maxpoint=1来接着算TS）
以下是我算过渡态和irc的输入文件，恳请各位老师帮我看看，是什么原因。
irc图：
(, 下载次数 Times of downloads: 4)
过渡态输入文件：
%chk=clu-HAT-step1-2s-ts-1.chk
%nprocshared=48
%mem=50GB
# opt=(calcfc,ts,gdiis,maxstep=1,noeigen) freq ub3lyp scrf=(smd,solvent=chlorobenzene) nosymm def2svp em=gd3bj scf=xqc

Molecule Name

-3 2
C             -1 41.87098700 57.37900200 34.71700500
H             0 41.73923100 56.45285700 34.13148600
C             -1 41.49002500 57.07206600 36.16095200
H             0 40.40713800 56.83934300 36.21722100
H             0 42.01830300 56.13793500 36.43967400
O             -1 41.83197700 58.12296000 36.99804400
H             0 41.55131500 57.86462200 37.88811000
O             -1 39.93000500 58.15199000 33.57899700
C             -1 30.50800400 51.75296500 32.15500100
H             0 29.74168400 51.32062100 31.48574600
C             -1 29.85596900 52.72302500 33.13098200
H             0 30.56752600 52.86123000 33.96437000
H             0 29.81780100 53.72606900 32.66444600
C             -1 28.51300800 52.43798000 33.68900600
H             0 27.70544800 52.65760200 32.97248800
H             0 28.41814200 51.35928300 33.91944500
C             -1 28.17799700 53.19000200 34.95499900
O             -1 26.97300000 53.18900000 35.27099900
O             -1 28.94500000 53.96300000 35.55400000
O             -1 32.54903100 52.92692400 31.43102300
S             0 42.82952100 48.52424200 36.16491400
N             0 40.68980800 50.75616700 36.33365100
C             0 41.03148000 51.83039400 35.55306000
C             0 39.98047200 52.11561900 34.57829100
C             0 40.01983000 53.21353400 33.55163400
H             0 39.72675900 52.79711700 32.57389900
H             0 41.04714100 53.58819100 33.44453400
C             0 39.07114000 54.40055500 33.83228800
H             0 39.57298200 55.36226300 33.63241500
H             0 38.77506000 54.44216900 34.89216900
C             0 37.78850700 54.41100500 32.98902400
O             0 36.93075700 55.29717000 33.26105700
O             0 37.61744600 53.58177100 32.06542800
C             0 38.99149900 51.18831000 34.80575400
C             0 37.72646000 50.95552400 34.04702900
H             0 36.84779400 50.95717400 34.71067200
H             0 37.57971600 51.72166800 33.27457600
H             0 37.74582900 49.96668800 33.55438800
C             0 39.43818900 50.36937200 35.92345700
C             0 38.67897000 49.35564300 36.48278400
H             0 37.67496300 49.21615100 36.08565900
C             0 39.10180300 48.49829800 37.49741800
N             0 40.35083000 48.50404200 38.06259500
C             0 38.29490500 47.42916900 38.05310100
C             0 36.88473800 47.11654200 37.67266500
H             0 36.17843100 47.47247200 38.44097300
H             0 36.59872000 47.59215500 36.72443700
H             0 36.73543900 46.02998000 37.56516600
C             0 39.09820900 46.77904700 38.97662800
C             0 38.80529200 45.62533600 39.81445400
H             0 39.68082500 45.12472400 40.24196500
C             0 37.59871700 45.11189200 40.12186200
H             0 36.66086700 45.55275400 39.78072000
H             0 37.52341900 44.22718300 40.76068000
C             0 40.38247500 47.47453600 38.96087800
C             0 41.46337200 47.14031500 39.76696400
H             0 41.34954600 46.28320800 40.42861100
C             0 42.67559800 47.81736000 39.82549500
N             0 43.00781400 48.93763700 39.11176300
C             0 43.77080500 47.42947100 40.69114700
C             0 43.76480300 46.23986500 41.59595200
H             0 44.68182300 46.18456600 42.19917400
H             0 42.90735800 46.26349600 42.28895300
H             0 43.68870600 45.29837400 41.02529600
C             0 44.78722400 48.34089700 40.47053400
C             0 46.10484400 48.31327900 41.09927700
H             0 46.12558300 47.85119100 42.09393300
C             0 47.27575300 48.74232800 40.59512000
H             0 47.36710400 49.16190300 39.59040000
H             0 48.19576800 48.65564100 41.18059100
C             0 44.26813100 49.29665500 39.49313700
C             0 44.93054800 50.44177300 39.06307400
H             0 45.89743200 50.66076400 39.50928400
C             0 44.45740600 51.33345700 38.11151000
N             0 43.27515500 51.23083000 37.43144700
C             0 45.20650700 52.49750200 37.65156000
C             0 46.54930900 52.90407300 38.16894900
H             0 46.52611400 53.10280000 39.25389000
H             0 47.30411300 52.11609400 38.00388000
H             0 46.90784100 53.81564600 37.66954400
C             0 44.44729000 53.08320800 36.67101500
C             0 43.23467500 52.27830800 36.55204400
C             0 42.20802000 52.56148100 35.66172300
H             0 42.34497800 53.40465700 34.98029200
C             0 44.73791000 54.27790400 35.82121500
H             0 45.59909800 54.82540500 36.23202600
H             0 43.88329600 54.97117500 35.88468000
C             0 44.98904200 53.93973800 34.32202100
H             0 44.60496600 52.93295100 34.09951700
H             0 46.06950600 53.95294700 34.11047400
C             0 44.24801500 54.97829100 33.45275100
O             0 43.01370700 54.78089300 33.30214600
O             0 44.90988200 55.97155800 33.06569200
O             0 41.16887000 50.90005000 39.02209900
C             0 38.89775700 54.99839000 38.83339200
C             0 40.18181300 54.34044900 38.87923300
C             0 41.33371100 55.03439000 39.27285800
C             0 41.21051600 56.38216600 39.62830100
C             0 39.96109800 57.04150100 39.56991700
C             0 38.80748100 56.36214300 39.16809400
C             0 37.96134400 53.98704400 38.42754000
H             0 42.30047800 54.52659200 39.30949600
H             0 42.09614400 56.93130100 39.96121600
H             0 39.89580600 58.09720600 39.84778000
H             0 37.84799200 56.88554400 39.12572600
H             0 40.75326100 51.94097900 38.73588600
N             0 40.03532000 53.02633600 38.50918800
C             0 38.71905200 52.82681400 38.25143900
H             0 38.36051800 51.84368400 37.95395000
C             0 36.47207800 54.10099100 38.30215800
H             0 36.02969600 54.40373400 39.26892700
H             0 36.17859500 54.88088200 37.58259100
N             0 35.84511500 52.84126600 37.91478800
H             0 35.89975200 52.07633800 38.59515100
C             0 35.38590800 52.49898600 36.70319700
S             0 34.68944700 50.98082600 36.41392500
S             0 35.62185600 53.72742500 35.45709900
C             0 34.66247900 53.11768800 34.04811500
H             0 33.58778000 53.13830000 34.26964000
H             0 34.91031700 53.82488900 33.24581900
H             0 34.97456600 52.10593200 33.76599700
O             -1 36.31991900 50.08718300 39.07157100
H             0 37.23681000 49.91104400 38.80936100
H             0 35.82640500 50.07840000 38.22231000
Fe             0 41.80300100 49.90289100 37.77973400
C             0 41.51819000 47.87876500 35.07976400
H             0 40.99754300 48.68476800 34.54008600
H             0 41.98686900 47.21344300 34.33569100
H             0 40.77141800 47.29580300 35.64056200
N             -1 31.17663500 50.65721500 32.87130200
H             0 31.65053100 50.04767000 32.20192000
H             0 31.91807900 51.04778200 33.45854000
N             -1 43.28457400 57.78055300 34.75533600
H             0 43.67533600 57.63096000 35.68080700
H             0 43.83915600 57.25295000 34.07092900
C             0 40.98555100 58.42293000 34.10130800
H             0 41.37369500 59.47580800 34.14207500
C             0 31.38203000 52.65387800 31.27181800
H             0 30.79729900 53.14582900 30.44608800
IRC输入文件：

%chk=clu-HAT-step1-2s-ts-1.chk
%nprocshared=48
%mem=50GB
# irc=(calcfc,maxpoints=20,stepsize=40,lqa) ub3lyp guess=read
scrf=(smd,solvent=chlorobenzene) nosymm def2svp em=gd3bj

Molecule Name

-3 2
C             -1 41.87098700 57.37900200 34.71700500
H             0 41.73921600 56.45286200 34.13147600
C             -1 41.49002500 57.07206600 36.16095200
H             0 40.40713900 56.83934200 36.21721600
H             0 42.01830700 56.13793700 36.43967400
O             -1 41.83197700 58.12296000 36.99804400
H             0 41.55129000 57.86464600 37.88810700
O             -1 39.93000500 58.15199000 33.57899700
C             -1 30.50800400 51.75296500 32.15500100
H             0 29.74163100 51.32064000 31.48579600
C             -1 29.85596900 52.72302500 33.13098200
H             0 30.56759400 52.86125800 33.96433300
H             0 29.81776800 53.72606000 32.66443200
C             -1 28.51300800 52.43798000 33.68900600
H             0 27.70545800 52.65757900 32.97247200
H             0 28.41813800 51.35928500 33.91944800
C             -1 28.17799700 53.19000200 34.95499900
O             -1 26.97300000 53.18900000 35.27099900
O             -1 28.94500000 53.96300000 35.55400000
O             -1 32.54903100 52.92692400 31.43102300
S             0 42.82949500 48.52437300 36.16498600
N             0 40.68963500 50.75617100 36.33362300
C             0 41.03123100 51.83039900 35.55299500
C             0 39.98020100 52.11550000 34.57820500
C             0 40.01946800 53.21337800 33.55150600
H             0 39.72635700 52.79690800 32.57381000
H             0 41.04676100 53.58806700 33.44434900
C             0 39.07075800 54.40040900 33.83213600
H             0 39.57262600 55.36210700 33.63226800
H             0 38.77467800 54.44202100 34.89202100
C             0 37.78809700 54.41083800 32.98886000
O             0 36.93052400 55.29722400 33.26069200
O             0 37.61695000 53.58137200 32.06548600
C             0 38.99130500 51.18811800 34.80569500
C             0 37.72628600 50.95520400 34.04697200
H             0 36.84761400 50.95690500 34.71060400
H             0 37.57954100 51.72127400 33.27444000
H             0 37.74569300 49.96631600 33.55443600
C             0 39.43804500 50.36926700 35.92343700
C             0 38.67889400 49.35551000 36.48281400
H             0 37.67489900 49.21592700 36.08569000
C             0 39.10177700 48.49825500 37.49750300
N             0 40.35080200 48.50411500 38.06268600
C             0 38.29494500 47.42910600 38.05325100
C             0 36.88481000 47.11634000 37.67280500
H             0 36.17840900 47.47285200 38.44075800
H             0 36.59899100 47.59134000 36.72420700
H             0 36.73543900 46.02971900 37.56602900
C             0 39.09828600 46.77910700 38.97682700
C             0 38.80540800 45.62543500 39.81473100
H             0 39.68097800 45.12449700 40.24179300
C             0 37.59879200 45.11242000 40.12267600
H             0 36.66095200 45.55369000 39.78201900
H             0 37.52344900 44.22768700 40.76145800
C             0 40.38251100 47.47466300 38.96102700
C             0 41.46342400 47.14054600 39.76713400
H             0 41.34963100 46.28347600 40.42883800
C             0 42.67562000 47.81764700 39.82560900
N             0 43.00776600 48.93791200 39.11181800
C             0 43.77086700 47.42984500 40.69124500
C             0 43.76494300 46.24028200 41.59610800
H             0 44.68201400 46.18501100 42.19925600
H             0 42.90755600 46.26394700 42.28918100
H             0 43.68879600 45.29876200 41.02550600
C             0 44.78724000 48.34130800 40.47056100
C             0 46.10488700 48.31377100 41.09925100
H             0 46.12568700 47.85173800 42.09393100
C             0 47.27575700 48.74283500 40.59501600
H             0 47.36704200 49.16236200 39.59026900
H             0 48.19580400 48.65621400 41.18044800
C             0 44.26807300 49.29700100 39.49314200
C             0 44.93041800 50.44214600 39.06302900
H             0 45.89729800 50.66120500 39.50921500
C             0 44.45720500 51.33377800 38.11145800
N             0 43.27495200 51.23105400 37.43140400
C             0 45.20621300 52.49787100 37.65148200
C             0 46.54899900 52.90454200 38.16883500
H             0 46.52587800 53.10302200 39.25382100
H             0 47.30391300 52.11671900 38.00351500
H             0 46.90734100 53.81628100 37.66959600
C             0 44.44694100 53.08350700 36.67093700
C             0 43.23438800 52.27850800 36.55198100
C             0 42.20771200 52.56157700 35.66164200
H             0 42.34463500 53.40472600 34.98016500
C             0 44.73747300 54.27821100 35.82112100
H             0 45.59853200 54.82586000 36.23200900
H             0 43.88274700 54.97135000 35.88445600
C             0 44.98882500 53.94002700 34.32196800
H             0 44.60502000 52.93312600 34.09950000
H             0 46.06930300 53.95349100 34.11050800
C             0 44.24760900 54.97830100 33.45251500
O             0 43.01328600 54.78077200 33.30218000
O             0 44.90934800 55.97147600 33.06501100
O             0 41.16869600 50.90023400 39.02204800
C             0 38.89744500 54.99839000 38.83339700
C             0 40.18153900 54.34053800 38.87912800
C             0 41.33341300 55.03450900 39.27272900
C             0 41.21015100 56.38226300 39.62825400
C             0 39.96069700 57.04152300 39.56997300
C             0 38.80709300 56.36211300 39.16819200
C             0 37.96106300 53.98700100 38.42756800
H             0 42.30021000 54.52676500 39.30929900
H             0 42.09576100 56.93142800 39.96116600
H             0 39.89535900 58.09721100 39.84788900
H             0 37.84756600 56.88544900 39.12592000
H             0 40.75303400 51.94122400 38.73572700
N             0 40.03509400 53.02641700 38.50902900
C             0 38.71884500 52.82681100 38.25136900
H             0 38.36035600 51.84366300 37.95388900
C             0 36.47174300 54.10070900 38.30260800
H             0 36.02960200 54.40309100 39.26959900
H             0 36.17785600 54.88071900 37.58333300
N             0 35.84492200 52.84093800 37.91519200
H             0 35.89967800 52.07595900 38.59550100
C             0 35.38587000 52.49865200 36.70354700
S             0 34.68951500 50.98048800 36.41409600
S             0 35.62192500 53.72708000 35.45744600
C             0 34.66183300 53.11758600 34.04886000
H             0 33.58735600 53.13650800 34.27165000
H             0 34.90795800 53.82582400 33.24696500
H             0 34.97487200 52.10650500 33.76540600
O             -1 36.31991900 50.08718300 39.07157100
H             0 37.23680400 49.91093000 38.80941100
H             0 35.82640300 50.07823900 38.22230800
Fe             0 41.80288400 49.90304200 37.77975400
C             0 41.51821700 47.87879700 35.07982700
H             0 40.99752800 48.68475300 34.54012000
H             0 41.98695000 47.21349000 34.33577300
H             0 40.77147300 47.29579800 35.64062400
N             -1 31.17663500 50.65721500 32.87130200
H             0 31.65008100 50.04740000 32.20184700
H             0 31.91852500 51.04780200 33.45798700
N             -1 43.28457400 57.78055300 34.75533600
H             0 43.67532800 57.63103100 35.68082000
H             0 43.83914700 57.25294200 34.07093900
C             0 40.98555600 58.42293000 34.10129700
H             0 41.37371600 59.47580400 34.14203100
C             0 31.38200700 52.65392900 31.27184700
H             0 30.79723100 53.14603100 30.44623900

作者
Author: sobereva 时间: 2024-12-8 16:52
maxpoint=1莫名其妙，找过渡态那是maxstep

问这种事一律自觉上传压缩后的输出文件

作者
Author: Jiangxue 时间: 2024-12-8 19:27

sobereva 发表于 2024-12-8 16:52
maxpoint=1莫名其妙，找过渡态那是maxstep

问这种事一律自觉上传压缩后的输出文件

不好意思写错了，过渡态和irc输出文件已上传，麻烦老师帮我看看是什么问题

作者
Author: sobereva 时间: 2024-12-9 03:57
是gview的bug或版本兼容性问题（连Chemcraft都能看到各帧的结构）。用gview打开chk/fch文件看看能否看到各帧结构

作者
Author: Jiangxue 时间: 2024-12-9 08:59

sobereva 发表于 2024-12-9 03:57
是gview的bug或版本兼容性问题（连Chemcraft都能看到各帧的结构）。用gview打开chk/fch文件看看能否看到各 ...

用fchk打开能看到每一帧的结构。我跑irc的目的是想得查看这个过渡态是否准确，并得到反应物和产物的结构，请问这个irc能用吗，虽然形状很怪异，但两端有反应物和产物的结构

作者
Author: sobereva 时间: 2024-12-9 10:20

Jiangxue 发表于 2024-12-9 08:59
用fchk打开能看到每一帧的结构。我跑irc的目的是想得查看这个过渡态是否准确，并得到反应物和产物的结构 ...

如果IRC轨迹连续，可以说明

作者
Author: QJW 时间: 2025-9-23 21:10

sobereva 发表于 2024-12-9 10:20
如果IRC轨迹连续，可以说明

老师，请问这个bug如何解决

作者
Author: sobereva 时间: 2025-9-24 03:50

QJW 发表于 2025-9-23 21:10
老师，请问这个bug如何解决

尝试其它版本或者换其它程序

作者
Author: QJW 时间: 2025-9-29 17:58

sobereva 发表于 2025-9-24 03:50
尝试其它版本或者换其它程序

辛苦老师！请问老师，我还有个问题，有没有比DFT精度更高的算法可以矫正DFT计算的基组泛函的呢？辛苦老师！

作者
Author: sobereva 时间: 2025-9-30 05:55

QJW 发表于 2025-9-29 17:58
辛苦老师！请问老师，我还有个问题，有没有比DFT精度更高的算法可以矫正DFT计算的基组泛函的呢？辛苦老师 ...

“矫正DFT计算的基组泛函” 完全语义不明
理论方法和基组是两码事，仔细看
辨析计算化学中的任务类型和理论方法
http://sobereva.com/680（http://bbs.keinsci.com/thread-38982-1-1.html）

并且看此文
简谈量子化学计算中DFT泛函的选择
http://sobereva.com/272（http://bbs.keinsci.com/thread-536-1-1.html）

欢迎光临计算化学公社 (http://bbs.keinsci.com/)