Example: FDE: H2O in water

Download FDE_H2O_128.run

#! /bin/sh

# This example demonstrates how to use FDE in combination with a large
# environment, that is modeled as a superposition of the densities of isolated
# molecules. Here, the excitation energies of a water molecule surrounded by an
# environment of 127 water molecules. For details, see also: C.R. Jacob, J.
# Neugebauer, L. Jensen and L. Visscher, Comparison of frozen-density embedding
# and discrete reaction field solvent models for molecular properties, Physical
# Chemistry Chemical Physics 8, 2349 (2006)

# This calculation consists of two steps:
# - First a prototype water molecule is calculated.
# - Next the embedding calculation of water in water is performed.

# To reduce the amount of output the next lines are included in the adf
# calculations:
#   EPRINT
#     SFO NOEIG NOOVL NOORBPOP
#     SCF NOPOP
#   END
#   NOPRINT BAS FUNCTIONS


# create atomic fragment files


$ADFBIN/adf -n 1 <<eor
create O file=$ADFRESOURCES/DZP/O 
eor
mv TAPE21 t21.DZP.O 
rm logfile

$ADFBIN/adf -n 1 <<eor
create H file=$ADFRESOURCES/DZP/H 
eor
mv TAPE21 t21.DZP.H 
rm logfile


# First, a prototype water molecule is calculated. The density of this isolated
# water molecules will afterwards be used to model the environment.


$ADFBIN/adf <<eor
Title Input generated by modco

EPRINT
  SFO NOEIG NOOVL NOORBPOP
  SCF NOPOP
END

NOPRINT BAS FUNCTIONS

UNITS
  length bohr
  angle degree
END

XC
LDA
END

SYMMETRY NOSYM

SCF
  iterations 50
  converge 1.0e-6 1.0e-6
  mixing 0.2
  lshift 0.0
  diis n=10 ok=0.5 cyc=5 cx=5.0 cxx=10.0
END
NumericalQuality good

FRAGMENTS
  O  t21.DZP.O 
  H  t21.DZP.H 
END

ATOMS
 O       -11.38048700000000    -11.81055300000000     -4.51522600000000    
 H       -13.10476265095705    -11.83766918322447     -3.96954531282721    
 H       -10.51089289290947    -12.85330720999229     -3.32020577897331    
END

eor

mv TAPE21 t21.mol_1
rm logfile


# Afterwards, the FDE calculation is performed. In this FDE calculation, there
# is one nonfrozen water molecule and the previously prepared water molecule is
# included as a frozen fragment that is duplicated 127 times. For this frozen
# fragment, the more efficient fitted density is used.



$ADFBIN/adf <<eor
Title Input generated by modco

EPRINT
  SFO NOEIG NOOVL NOORBPOP
  SCF NOPOP
END

NOPRINT BAS FUNCTIONS

UNITS
  length bohr
  angle degree
END

XC
MODEL SAOP
END

SYMMETRY NOSYM

NumericalQuality Good

SCF
  iterations 50
  converge 1.0e-6 1.0e-6
  mixing 0.2
  lshift 0.0
  diis n=10 ok=0.5 cyc=5 cx=5.0 cxx=10.0
END

EXCITATIONS
  ONLYSING
  LOWEST  5
END

FRAGMENTS
  O      t21.DZP.O 
  H      t21.DZP.H 
  frag1  t21.mol_1 type=fde &
    fdedenstype SCFfitted
  SubEnd
END

ATOMS
 O         0.00000000000000      0.00000000000000      0.00000000000000    
 H        -1.43014300000000      0.00000000000000      1.10739300000000    
 H         1.43014300000000      0.00000000000000      1.10739300000000    
 O       -11.38048700000000    -11.81055300000000     -4.51522600000000    f=frag1/1  
 H       -13.10476265095705    -11.83766918322447     -3.96954531282721    f=frag1/1  
 H       -10.51089289290947    -12.85330720999229     -3.32020577897331    f=frag1/1  
 O        -1.11635000000000      9.11918600000000     -3.23094800000000    f=frag1/2  
 H        -2.82271357869859      9.71703285239153     -3.18063201242303    f=frag1/2  
 H        -0.12378551814273     10.53819303003839     -2.70860866559857    f=frag1/2  
 O       -16.96901200000000     -3.65835300000000    -10.78571300000000    f=frag1/3  
 H       -15.70823656958949     -4.23996689198245     -9.62648920152293    f=frag1/3  
 H       -16.47814038897754     -4.36080868684451    -12.37857352487904    f=frag1/3  
 O       -10.76560800000000     -4.16357700000000      0.51803200000000    f=frag1/4  
 H        -9.16115845895954     -3.98623150326079     -0.29800688710696    f=frag1/4  
 H       -11.97483852095230     -3.79636551545084     -0.77600078745886    f=frag1/4  
 O        -6.55423300000000     -9.20297500000000    -11.23125400000000    f=frag1/5  
 H        -8.15301944239612     -9.65354271558258    -10.51536304076499    f=frag1/5  
 H        -6.90715220963067     -7.74998343249339    -12.24902957370683    f=frag1/5  
 O       -14.16713600000000     -6.55813200000000     -6.62957400000000    f=frag1/6  
 H       -13.74689800192609     -8.31204468643143     -6.76675830514850    f=frag1/6  
 H       -15.43294077464585     -6.49537593456625     -5.33906885435316    f=frag1/6  
 O        -1.01233800000000     -6.53737500000000    -20.63228300000000    f=frag1/7  
 H         0.51358895613388     -7.01674081354516    -19.78766204266023    f=frag1/7  
 H        -2.25846754637793     -6.48721751306148    -19.32222614537351    f=frag1/7  
 O        -7.97372300000000      4.33381600000000      8.85869700000000    f=frag1/8  
 H        -7.39209897744333      2.71703281820261      9.42381190837837    f=frag1/8  
 H        -7.34133495205587      4.47772485325760      7.17021271491547    f=frag1/8  
 O         1.68768000000000    -11.29316300000000     -2.87636700000000    f=frag1/9  
 H         1.52000307205134    -11.65999321781241     -4.63958827351129    f=frag1/9  
 H         0.92563970293820     -9.66478590395236     -2.67815953059656    f=frag1/9  
 O         1.09184600000000     -1.69811700000000    -18.81717100000000    f=frag1/10  
 H         2.07215988260319     -2.34326255514507    -20.19354345122146    f=frag1/10  
 H         0.13398919688371     -3.11903886392137    -18.23829710737747    f=frag1/10  
 O       -13.85258700000000     -1.51317200000000     -3.42847700000000    f=frag1/11  
 H       -13.34561409429037     -1.90947670800034     -5.11890601995987    f=frag1/11  
 H       -15.31887324674441     -2.53345289474331     -3.14451376182312    f=frag1/11  
 O         5.28960400000000     -6.81266800000000    -13.10585800000000    f=frag1/12  
 H         7.01709448187639     -6.62178372023976    -12.60488989024026    f=frag1/12  
 H         4.34671789396407     -5.97791594280375    -11.80749041866683    f=frag1/12  
 O       -11.47407200000000    -10.90708300000000     -9.44085000000000    f=frag1/13  
 H       -11.21611173248622    -12.45441460630369    -10.34132244308043    f=frag1/13  
 H       -11.17634020521638    -11.33593027595366     -7.70907363612158    f=frag1/13 
 O        -1.64592100000000    -11.43523300000000      1.48098000000000    f=frag1/14  
 H        -0.30557034252542    -10.47362907146570      0.73908565451392    f=frag1/14  
 H        -1.72993170289473    -12.94068698496448      0.48190338473989    f=frag1/14  
 O        -7.32468400000000     -5.01818100000000      4.38774900000000    f=frag1/15  
 H        -8.81838077448469     -4.73028985072788      3.40916949260461    f=frag1/15  
 H        -7.75923926090726     -6.38911120628163      5.48470646359115    f=frag1/15  
 O         5.20879700000000     -6.83850600000000      3.69146100000000    f=frag1/16  
 H         5.26579130261858     -6.68511818556767      1.89011343551333    f=frag1/16  
 H         6.39162739624924     -5.60718291987245      4.28841938067655    f=frag1/16  
 O         6.73749100000000     -0.26065600000000     -6.58850100000000    f=frag1/17  
 H         6.56301678911955     -2.04681439624047     -6.81394756463717    f=frag1/17  
 H         8.29925639010887      0.14828805200118     -7.40413401232653    f=frag1/17  
 O         5.30624300000000     -5.54309500000000     -6.43599300000000    f=frag1/18  
 H         3.81279050995479     -6.09072594663625     -7.29699777727678    f=frag1/18  
 H         6.65189674819999     -6.43527789528092     -7.25136362341575    f=frag1/18  
 O        -5.72214300000000     -7.59376400000000     -5.60989200000000    f=frag1/19  
 H        -5.63766272358672     -7.49959469188493     -7.41422690365166    f=frag1/19  
 H        -3.99734274429106     -7.51425600722341     -5.07105423295232    f=frag1/19  
 O        -4.96412100000000      4.32334900000000     -3.25899700000000    f=frag1/20  
 H        -6.26920382212011      5.55951483151335     -3.05829302735551    f=frag1/20  
 H        -3.43114054713299      5.22630232648312     -2.93303718111639    f=frag1/20  
 O       -10.94232600000000      0.55437900000000    -13.18244900000000    f=frag1/21  
 H        -9.99364526446256      2.08335246724114    -13.36649850073860    f=frag1/21  
 H       -12.25798450895047      0.68645755108753    -14.41662950801929    f=frag1/21  
 O        -9.29636700000000      5.39923600000000    -12.62463400000000    f=frag1/22  
 H        -7.78716246923940      5.39969899801535    -11.62767327349474    f=frag1/22  
 H        -8.71366631604628      5.57073538127912    -14.32835095341294    f=frag1/22  
 O         2.97641300000000    -12.44506100000000      3.62605000000000    f=frag1/23  
 H         3.66110125710447    -10.77090992621746      3.63307801290360    f=frag1/23  
 H         1.22148596207982    -12.21500271544869      3.25334655288432    f=frag1/23  
 O        -7.52033800000000     -2.70960600000000    -16.43185500000000    f=frag1/24  
 H        -8.54144292463491     -2.01657808726233    -15.10947598274278    f=frag1/24  
 H        -8.12619297191493     -1.91113986970532    -17.93750940057940    f=frag1/24  
 O        -1.69701700000000     -2.04382200000000     -8.20675700000000    f=frag1/25  
 H        -1.16935910005967     -0.43265303835196     -8.83710685355905    f=frag1/25  
 H        -0.63663168422293     -2.33781858979711     -6.77122484449879    f=frag1/25 
 O         5.30132200000000     -9.56047300000000      8.45223600000000    f=frag1/26  
 H         5.27386189469879     -8.61762538446407      6.90889108173823    f=frag1/26  
 H         4.55017557362690     -8.45544294990206      9.67137143822390    f=frag1/26  
 O         5.99489300000000     -5.84398700000000     -1.27866800000000    f=frag1/27  
 H         6.10499825242707     -5.94881824033588     -3.08103213209623    f=frag1/27  
 H         7.02298278120587     -4.42064928461433     -0.84422038296580    f=frag1/27  
 O        -8.49933400000000      6.30730300000000      1.26206900000000    f=frag1/28  
 H        -9.26414421853983      5.21634012956926      0.03875605345364    f=frag1/28  
 H        -9.84131776823032      6.72028388514297      2.40230140460829    f=frag1/28  
 O         1.42265800000000      7.15100500000000     -6.70245700000000    f=frag1/29  
 H         0.49123529007929      7.74531228135872     -5.27036768330312    f=frag1/29  
 H         2.87243479479048      6.33486591183760     -5.99276142000362    f=frag1/29  
 O         1.16572300000000    -15.86327300000000     -8.03011700000000    f=frag1/30  
 H        -0.43980652899404    -16.56646285956896     -8.47669081602252    f=frag1/30  
 H         1.27023658519214    -14.33069688850776     -8.98504681689730    f=frag1/30  
 O        -1.89194800000000    -10.63552100000000     -8.58469800000000    f=frag1/31  
 H        -2.78816305171149    -10.71751973024788    -10.15367983850320    f=frag1/31  
 H        -2.90779524204234    -11.59056143861734     -7.43250195607063    f=frag1/31  
 O         1.30322100000000     -6.54666700000000     -9.29066800000000    f=frag1/32  
 H         0.04144584195376     -7.80383112457906     -8.97588071525340    f=frag1/32  
 H         0.43997569188912     -4.97291783823648     -9.06767765025571    f=frag1/32  
 O        -4.10800400000000     -6.59387200000000    -16.43397700000000    f=frag1/33  
 H        -4.90090013771901     -8.11414568563407    -17.00992218470793    f=frag1/33  
 H        -5.44796070593591     -5.38061594011036    -16.36971704696261    f=frag1/33  
 O        -5.19983400000000    -12.82687600000000     -4.96878500000000    f=frag1/34  
 H        -6.70471369416354    -13.43327229448220     -5.76831602526536    f=frag1/34  
 H        -5.42955949756766    -11.03545071340780     -4.87067679172327    f=frag1/34  
 O        -4.89786700000000      5.50178800000000    -16.51771100000000    f=frag1/35  
 H        -4.96675000682788      7.30587317882606    -16.40743398906903    f=frag1/35  
 H        -3.22762417250174      5.07795982200470    -15.96792726530632    f=frag1/35  
 O       -17.57898700000000     -4.99346700000000     -2.97681500000000    f=frag1/36  
 H       -18.76387465651032     -3.84193458717524     -2.24085062321750    f=frag1/36  
 H       -17.39866900954461     -6.30611916234463     -1.74554195748830    f=frag1/36  
 O        -3.50776800000000    -17.32380200000000    -10.10442500000000    f=frag1/37  
 H        -4.40193812130934    -18.63309464188228    -10.97496609167801    f=frag1/37  
 H        -4.53952158473348    -16.94953791159138     -8.66671344522861    f=frag1/37  
 O       -10.81911600000000     -4.66640800000000    -11.14487100000000    f=frag1/38  
 H       -11.62185710527301     -4.88296610749300     -9.53852778505075    f=frag1/38  
 H       -10.60915967583231     -2.87735761828481    -11.30864113107593    f=frag1/38  
 O        -6.39205500000000      0.01793500000000     -6.73248500000000    f=frag1/39  
 H        -5.82125006722311      1.22625909145182     -5.51356587267281    f=frag1/39  
 H        -4.87489255123650     -0.72801711445480     -7.37542911048570    f=frag1/39  
 O       -11.30505500000000      0.46379700000000     -8.25065700000000    f=frag1/40  
 H        -9.64226007733910      0.80674572776125     -7.62685540050746    f=frag1/40  
 H       -11.19896085378185      0.79109534466454    -10.02638879504226    f=frag1/40  
 O         9.00392400000000      1.26046800000000    -13.97805200000000    f=frag1/41  
 H         8.87294935217592      1.02947962110145    -12.18888481086687    f=frag1/41  
 H         7.29424845398649      1.45338312957695    -14.53608144577292    f=frag1/41  
 O       -10.89041700000000      3.43422700000000     -2.58901500000000    f=frag1/42  
 H       -11.04828427051772      1.96350979597573     -3.63002318964871    f=frag1/42  
 H       -12.48348293054753      3.56267021936991     -1.74211071819919    f=frag1/42  
 O        -5.77532000000000     11.85364600000000     -3.10184700000000    f=frag1/43  
 H        -7.42098370181530     11.26896732951829     -2.63113365512790    f=frag1/43  
 H        -5.59494422717391     13.43644886209393     -2.24522382582680    f=frag1/43  
 O        -1.56797700000000      3.41013100000000     -9.46461500000000    f=frag1/44  
 H        -0.62647981010343      4.69229425860768     -8.60364482634544    f=frag1/44  
 H        -1.22975840621731      3.70013224540235    -11.21764410491830    f=frag1/44  
 O        -5.85114500000000      5.94789900000000     -8.75297600000000    f=frag1/45  
 H        -4.36435430864595      4.93739949116572     -8.95290949638818    f=frag1/45  
 H        -5.23356351746774      7.64390869587085     -8.63572496098009    f=frag1/45  
 O        -5.55413300000000     -7.92360000000000      0.25554800000000    f=frag1/46  
 H        -4.38326585687764     -9.28844448621082      0.45022435153192    f=frag1/46  
 H        -6.01769107687214     -7.47995835111906      1.94667176216252    f=frag1/46  
 O       -10.80147900000000      4.92460700000000    -18.42825600000000    f=frag1/47  
 H        -9.46772203676955      4.11444445205056    -19.34278223208070    f=frag1/47  
 H       -12.08285494971162      3.65684979597704    -18.27835293347214    f=frag1/47  
 O        11.84765600000000      6.04652000000000     -5.60335700000000    f=frag1/48  
 H        12.23822731048506      7.54282902057004     -4.66519785219186    f=frag1/48  
 H        10.14515882225660      6.29374114330687     -6.16191644024222    f=frag1/48  
 O         9.40177200000000     -2.16451100000000      0.06593400000000    f=frag1/49  
 H         9.99192042697073     -0.60334687050214     -0.63128950443925    f=frag1/49  
 H        10.90850263662718     -3.09972302317630      0.42194641911128    f=frag1/49  
 O        -3.83766900000000     11.00009100000000     -8.55948700000000    f=frag1/50  
 H        -3.74373964993300     10.83305937748681     -6.76090229682198    f=frag1/50  
 H        -4.87440105609424     12.45821519867243     -8.82531410042130    f=frag1/50  
 O        -8.92277200000000      7.51515500000000     -5.13005000000000    f=frag1/51  
 H        -7.64240242456374      6.79630036125453     -6.18623699995818    f=frag1/51  
 H        -9.98750814060132      6.11915279273326     -4.69517258001857    f=frag1/51  
 O        -0.32879900000000      4.85643700000000    -14.28493900000000    f=frag1/52  
 H        -0.20121901190276      6.61816864447670    -13.89551098390984    f=frag1/52  
 H         1.10559652418602      4.51955612567933    -15.33404544784882    f=frag1/52  
 O        -2.88119200000000    -21.16143900000000    -13.73773700000000    f=frag1/53  
 H        -1.09646919425263    -20.88154858029820    -13.82748709656689    f=frag1/53  
 H        -3.12787937393977    -22.76872743498338    -14.52980568926457    f=frag1/53  
 O         4.08430100000000    -17.32350200000000      4.72137100000000    f=frag1/54  
 H         4.02413151632988    -15.51826748869058      4.62578223161330    f=frag1/54  
 H         2.36935484299032    -17.81891859379031      5.01313401917970    f=frag1/54  
 O       -12.71856600000000      7.20558900000000      4.46079500000000    f=frag1/55  
 H       -14.45999505747860      7.69416069947355      4.47955006523861    f=frag1/55  
 H       -11.90975612966972      8.36888327939108      5.58515108034031    f=frag1/55  
 O         3.64630900000000     -5.77729500000000     11.93616900000000    f=frag1/56  
 H         4.69770672445712     -5.28069451760816     13.32165808553043    f=frag1/56  
 H         1.98018929821852     -5.85215747794930     12.63620066423870    f=frag1/56  
 O       -11.58290200000000     -8.00977000000000    -14.71744100000000    f=frag1/57  
 H       -11.15452934215944     -6.96177583707747    -13.30682612671804    f=frag1/57  
 H       -13.31014912674778     -7.60719902330076    -15.07262764680259    f=frag1/57  
 O       -22.69131900000000     -4.60206700000000    -11.33851100000000    f=frag1/58  
 H       -22.22272486043639     -6.12263420792208    -12.19869942051499    f=frag1/58  
 H       -21.13544211851963     -3.70468130859725    -11.12508740068061    f=frag1/58  
 O         4.56872600000000     15.36672100000000     -5.27290200000000    f=frag1/59  
 H         6.23209824653603     14.72493681821289     -5.57775451137379    f=frag1/59  
 H         4.56888064677390     17.00621625499974     -6.03687769799284    f=frag1/59  
 O       -19.42024500000000      0.10101200000000    -13.92810800000000    f=frag1/60  
 H       -18.31405236374814     -1.07169409540655    -13.10790833801040    f=frag1/60  
 H       -20.71321177209865      0.43336205711680    -12.70770480925147    f=frag1/60  
 O         4.02837000000000     -8.18071600000000    -24.03669300000000    f=frag1/61  
 H         5.65512609076238     -8.96585900909256    -24.13073712086871    f=frag1/61  
 H         3.08016870759219     -9.23647651818391    -22.91513710771192    f=frag1/61  
 O       -16.59841600000000    -12.07983100000000     -3.02725000000000    f=frag1/62  
 H       -16.86792190502099    -10.47849662259938     -2.23055432463633    f=frag1/62  
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END

FDE
  PW91K
END

eor