Constraints on an atom for optimization calculations

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Just Got Here
Threads 1
Posts 4
Hello

I am trying to run a dft calculation with constraint to fix an atom at its position. But at the end of calculation its position changes. following is my input file

start H2
title "H2"
charge 0

geometry units angstrom print xyz autosym

H1 0 0 0
H2 0 0 0.74
end
constraints
fix atom 2
end
basis
H1 library 6-31g
H2 library 6-31g
end
dft
mult 1
xc b3ylp
maxiter 1000
print "final evals" "final vectors"
end
driver
maxiter 1000
xyz test
end
task dft optimize






kindly help me to solve this problem

thank you

regards
chirag

Gets Around
Threads 1
Posts 147
First, the input you posted will not run for two reason. One, you have a typo in your DFT block; it should be b3lyp not b3ylp. Two, you are trying to apply a cartesian constraint to an optimization in internal coordinates, and the code can't currently handle that. To fix that you need to add noautoz to your geometry line.

Second, even with those fixes, the absolute coordinates of all your atoms will change initially because you have specified autosym on the geometry line. This will rotate and translate your molecule before anything else is done or any constraints are considered. If you want to retain the coordinates that you specified in the input file, change autosym to noautosym.

Just Got Here
Threads 1
Posts 4
Hi ..thanks for reply ..I tried as u said ...that is using noautoz and noautosym ..but still coordinates are changing ...


start H2
title "H2"
charge 0

geometry noautoz noautosym

H1 0 0 0
H2 0 0 0.74
end

basis
H1 library 6-31g
H2 library 6-31g
end
dft
mult 1
xc b3ylp
maxiter 1000
print "final evals" "final vectors"
end

O/P is ....

          XYZ format geometry
-------------------
2
geometry
H1 0.00000000 0.00000000 -0.37000000
H2 0.00000000 0.00000000 0.37000000

Please guide ..
Thanks

Clicked A Few Times
Threads 3
Posts 5
Hello,

I previously used the following input file to constrain the Cartesian coordinates of some atoms, worked without any problems:

start geom_1
title "DP-Mes geometry relaxation"

echo

memory total 4000 mb

constraints one
fix atom 9 13:14
fix atom 42 45:46
end

set constraints one

geometry noautoz
C -4.465439777516245989374965574825 2.840834064089797994512309742277 -4.277596737586850217383016570238
C -4.469463027071183702787493530195 1.405690204089798056585891572468 -4.303767315603653109690185374347
C -3.603117535504297919146665662993 0.724333783166223099669878138229 -3.518816749275908595251394217485
C -2.672756841327013077602714474779 1.426297923325316574505450262222 -2.647388105542451963714256635285
C -2.668645800244344723495260041091 2.878512189658765763056180730928 -2.621637843331020789605645404663
C -3.594627189061317729112943197833 3.550257074693953018851289016311 -3.467307704241954446899853792274
C -1.779917277508305639699415223731 3.570390475068639712930007590330 -1.778837319238987246805550057616
C -0.881427623433614804149272003997 2.908712662311789376445858579245 -0.924401862586118117093292312347
C -0.885964253905191512217243143823 1.448953270867075149297420466610 -0.950215377769993096990219783038
C -1.788827354867923435932652864722 0.761239242401741900145850650006 -1.828262547607430787977023101121
C -0.009548915881450740356095607808 3.631686369388908097732837632066 -0.050030221559949412946100011368
C 0.844491307483022923818793969986 2.933436936771573133597712512710 0.815888416497244084446549550194
C 0.841288988539175885961185485939 1.472414397910741135078183106089 0.791119779785639520852669193118
C -0.016587966741588730523737638123 0.750734229388908103075550570793 -0.098373622595290935444189983627
C 1.705479053408331946428688752349 3.622782634625814068840554682538 1.735475879844375013405510799203
C 2.528041196172119420282342616701 2.958328779730142521486868645297 2.617091939946968981445252211415
C 2.524421168144910243569256635965 1.505578816063591451879233318323 2.591177424374532911599544604542
C 1.698516051854086938988075417001 0.812475186376074520744339224620 1.686918605670558735099007208191
C 3.381215479799513978775848954683 3.660320895306047095374424316105 3.564820586286121528729609053698
C 4.170527898066596961257346265484 2.979299026521294191383049110300 4.427052836219217191171537706396
C 4.167152232789300470017224142794 1.544152986521293735577842198836 4.400745874230316267983198486036
C 3.373985691300728007036013877951 0.834618297139322784516934916610 3.513046743919065573180660067010
H -5.166380402530621473999872250715 3.363855109317531066892570379423 -4.912779532937987525542666844558
H -3.589261187978649569885192249785 4.643229815305044638762410613708 -3.445175874139360328030079472228
H -5.173379427362856830541204544716 0.860520570234169168699622787244 -4.958574502196554156796537426999
H -3.605150662086793023064501539920 -0.368462076222685064319506409447 -3.537260659072956503479190359940
H -1.778679640925810545581953192595 4.661473963235364337265309586655 -1.762686957469148829602545447415
H -1.795953001284387617886295629432 -0.329330724848344857935700247253 -1.851507562349713253979643923230
H 1.711722356324276050898447465443 4.714102306153543864297716936562 1.757355514975218691020586447848
H 1.701172626659806175197786615172 -0.278524466373838819333030869529 1.673108319095000906528980522125
H 3.382378767521177387322950380621 4.753234005000501305460147705162 3.583368360055266599317747022724
H 4.811769675496588405394504661672 3.524770381904652527538246431504 5.144639538423709801406857877737
H 3.368688807468146251267171464860 -0.258282723777314981994379650132 3.490789310761012842476702644490
H 4.805735707997454753126476134639 1.021283920682468648877261330199 5.098568201832042845467185543384
C 4.538471400029754576621598971542 -1.531558944671908450985142735590 -4.202283280244575536244155955501
C 4.545439200275331437239856313681 -2.966681254366362097130149777513 -4.175961318312173986555535520893
C 3.653456917187652308598444506060 -3.650471639232049980705596681219 -3.391992129181484738609242413077
C 2.695372952187151227576578094158 -2.951418474625814081235830599326 -2.572999500900527536373374459799
C 2.688769087135854274350776904612 -1.498804092792538789069567428669 -2.598711944888734581837752557476
C 3.640398070140517639003974181833 -0.824761470759779791173116336722 -3.443516797157898601255965331802
C 1.777454114991328548711635448853 -0.808330108574864203418997021799 -1.801879353668786709619098473922
C 0.861816010086484007857166034228 -1.470752044968281602166371158091 -0.941599595521640631012871835992
C 0.867344687804678771136934756214 -2.931510970162562124130545271328 -0.916276913755270649986073294713
C 1.788585280650248687805969893816 -3.618332862852507325612805288984 -1.753060780607623270199724174745
C -0.022617132573476816242985520944 -0.750801880611091876360774222121 -0.100048721761668568674963353260
C -0.878679835024781308305819038651 -1.450743056253902096841557067819 0.786525389672639962945766001212
C -0.872310031889775294722255694069 -2.910676690142983691345079932944 0.810297086550275325045333829621
C -0.010903205692372942847701011715 -3.631709429999999905191998550436 -0.053021382450071576075689705476
C -1.736089209731375593293023484875 -0.765431361730681714128365911165 1.687086451302963530096690192295
C -2.547775292698115201517339301063 -1.432941495985277313707229041029 2.600555445277296318096205141046
C -2.541900288646471217646194418194 -2.885218813235363999325500117266 2.625215738265850085042529826751
C -1.725011971794118581513544086192 -3.574702455925309330098116333829 1.733102826948009322904908913188
C -3.388561963499517659670345892664 -0.733863616490306958084488542227 3.536480138896520131197576120030
C -4.162795678721546543954445951385 -1.417778770744902772094064857811 4.437631381004124797584609041223
C -4.156604690697806248067536216695 -2.852897870439357053129469932173 4.462674250103596307326370151713
C -3.376958199979418928649010922527 -3.559724927101398872508752901922 3.585660643345898179745745437685
H 5.259676369816395968825872841990 -1.006570458946082657902820756135 -4.835915792427255333052471542032
H 3.634026264504644831987434372422 0.268074899240220265728140702777 -3.461775678648706833229198309709
H 5.271948035169771173968911170959 -3.509965668946082750778714398621 -4.789803843281688955357822123915
H 3.656585999851082124934009698336 -4.743333988315412419467520521721 -3.369854724635217291250910420786
H 1.777102251105715513546101647080 0.282557202952865349487865387346 -1.825069943160288810091174127592
H 1.795372679564111617622756966739 -4.709638084074691199987228173995 -1.737212928671753919829257029050
H -1.745761188117161744060013006674 0.325223936436042804221102642259 1.673787557005742110405321909639
H -1.724584162657724961675853592169 -4.665797894397579526071240252350 1.753432069106409141312497013132
H -3.390659660274558895309837680543 0.358924692898601238599809448715 3.515481526877635154448853427311
H -4.793438595796429169126895430963 -0.874604175248544724041721565300 5.147271681654372876835168426624
H -3.370691186176820952624666460906 -4.652657227101398618174243893009 3.603129848420242087314591117320
H -4.782716302136815755829957197420 -3.377889473720815161073005583603 5.191176928800633305627343361266
C 0.002910628336223801577997694068 5.133428579083362031099113664823 -0.026321398986472593906071892889
C -0.851742440641075959639749726193 5.837988357280070594867993349908 0.853383192839865856171854829881
C -0.807361735679731684633964050590 7.238201198502254740674288768787 0.873384794519751928021378262201
C 0.058000371619917757970430471914 7.965494069694454282171136583202 0.045614181400855782766434742825
C 0.892918453460130434606867311231 7.249329892414383635923513793387 -0.818518326034840093541333772009
C 0.881338127276602323334486754902 5.847121772108836879056070756633 -0.871176099242455870275136931014
H -1.468092200850965367564526786737 7.776085543809534428305596520659 1.560401374874860414010413478536
H 1.579751944150769027430669666501 7.795343400773653286250919336453 -1.472408409512313554046158969868
C -0.015687434636220024680719475896 -5.133474889999999568601651844801 -0.034573023486646023427759644164
C -0.885509737299649435371406980266 -5.831008867864647449152926128590 -0.887085079159440459406482659688
C 0.843285061448182826637776088319 -5.854087142135353083460813650163 0.841858202398273247624160831037
C 0.811860079731375416933758515370 -7.253418069690985348074718785938 0.849734704692719833296621345653
C -0.045880967458742996645248979348 -7.965410870000000365109826816479 0.014056004768798046472566554144
C -0.884204298405364852442289702594 -7.233972800003468428542419133009 -0.846402456864994046092931512248
H 1.477916689399313865393992273312 -7.803630616771572547918367490638 1.531712285300343090455044148257
H -1.562203282513508595386042543396 -7.767777292922880327807888534153 -1.508619032786834512904761140817
C -0.055628884618877189049968023937 -9.475746410916636719434791302774 0.047712309006051063786646437848
H -0.808311196860292513477475040418 -9.877265472225305487086188804824 -0.640478302615099637229434392793
H 0.954032966762400125304566245177 -9.895992946768105369415025052149 -0.211447062777661787258409731294
H -0.306057670198250586501842462894 -9.859983197117509590157169441227 1.033404047123212876613251864910
C -1.813768296273480462588167938520 -5.090032806257370090463609813014 -1.835919315515936567351218400290
H -2.414506983105022097646497059031 -5.791715168343160691222237801412 -2.419461977326164969781530089676
H -2.506416599524954769151463551680 -4.423083622624272237544573727064 -1.295186640872779459954244885012
H -1.253927494025128153154469146102 -4.455657624918718084927604650147 -2.543729766595136609907967795152
C 1.786429307944193967117030297231 -5.133808183742630149026808794588 1.764203620266389105353255217778
H 2.371762139973484284638516328414 -5.848527939823563670529438240919 2.374214459900874540920767685748
H 2.497337544274174536695909409900 -4.504962641985431837099440599559 1.203789074075923615225747198565
H 1.236191023776082031915279912937 -4.463952152915944715516616270179 2.443000788078004692494005212211
C 0.069470405106563798414143207083 9.474752578083709408929280471057 0.075605348716615061732682079310
H 0.988214996457856931222352159239 9.901196169661000467954181658570 -0.392903440958260574689120403491
H -0.816572371362931703764331814455 9.822992704710062028539141465444 -0.451620749124985010336530422137
H 0.025127220825452316332881963490 9.904518982463946130678777990397 1.092000769052144937276693781314
C 1.807210378671753936430377507349 5.122949932772960401905493199592 -1.821588969873126240273109033296
H 2.416402377223570763220550361439 5.835417975021313097272468439769 -2.397312141128762341679703240516
H 2.487012427566038130777315018349 4.492578882373993387489008455304 -1.278126443034647730101482920873
H 1.249471260202952072049242815410 4.454063532949396275739673001226 -2.541430105671561801017332982155
C -1.801834235330327160795604868326 5.101078398449223172406163939741 1.769604385819246727962195109285
H -2.386860099445407890073056478286 5.805388318950783776983826101059 2.379138310980074333400580144371
H -2.510537328936909950982681039022 4.431931003819940428911650087684 1.201688846852352776650718624296
H -1.259652211132231247603385781986 4.469197802384399231812039943179 2.451393615686668692177363482188
end

basis spherical
  • library cc-pvdz
end

dft
iterations 200
xc b3lyp
direct
grid nodisk
end

driver
loose
maxiter 500
end

task dft optimize

Just Got Here
Threads 1
Posts 4
Thanks for reply Alvert ...I tried this !!

echo
start H2
title "H2"

charge 0

constraints one
fix atom 2
end

set constraints one

geometry noautoz

H1 0 0 0
H2 0 0 0.74
end

basis
H1 library 6-31g
H2 library 6-31g
end

dft
mult 1
xc b3lyp
maxiter 1000
print "final evals" "final vectors"
end


Its still not working for me...O/P coordinates are changing ! I tried this on other systems too..but not working !Am I still missing some thing !
Please guide !!!

Gets Around
Threads 1
Posts 147
My bad. You also need nocenter on the geometry line to avoid changes from the input coordinates.

Just Got Here
Threads 1
Posts 4
Thnx Sean.... finally its working !!!!


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