Example: FDE: H2O in water¶
#! /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
AMS_JOBNAME=O $AMSBIN/ams <<eor
System
Atoms
O 0.0 0.0 0.0
End
End
Task SinglePoint
Engine ADF
create O file=$AMSRESOURCES/ADF/DZP/O
Relativity Level=None
EndEngine
eor
mv O.results/adf.rkf t21.DZP.O
AMS_JOBNAME=H $AMSBIN/ams <<eor
System
Atoms
H 0.0 0.0 0.0
End
End
Task SinglePoint
Engine ADF
create H file=$AMSRESOURCES/ADF/DZP/H
Relativity Level=None
EndEngine
eor
mv H.results/adf.rkf t21.DZP.H
# First, a prototype water molecule is calculated. The density of this isolated
# water molecules will afterwards be used to model the environment.
AMS_JOBNAME=H2O $AMSBIN/ams <<eor
System
atoms [bohr]
O -11.38048700000000 -11.81055300000000 -4.51522600000000
H -13.10476265095705 -11.83766918322447 -3.96954531282721
H -10.51089289290947 -12.85330720999229 -3.32020577897331
end
end
Task SinglePoint
Engine ADF
eprint
scf NOPOP
sfo NOEIG NOOVL NOORBPOP
end
fragments
O t21.DZP.O
H t21.DZP.H
end
noprint BAS FUNCTIONS
numericalquality good
scf
converge 1.0e-6 1.0e-6
diis
cx 5.0
cxx 10.0
cyc 5
n 10
ok 0.5
end
iterations 50
lshift 0.0
mixing 0.2
end
symmetry NOSYM
title Input generated by modco
xc
lda
end
Relativity Level=None
EndEngine
eor
mv H2O.results/adf.rkf t21.mol_1
# 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.
AMS_JOBNAME=FDE $AMSBIN/ams <<eor
System
atoms [Bohr]
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 adf.f=frag1|1
H -13.10476265095705 -11.83766918322447 -3.96954531282721 adf.f=frag1|1
H -10.51089289290947 -12.85330720999229 -3.32020577897331 adf.f=frag1|1
O -1.11635000000000 9.11918600000000 -3.23094800000000 adf.f=frag1|2
H -2.82271357869859 9.71703285239153 -3.18063201242303 adf.f=frag1|2
H -0.12378551814273 10.53819303003839 -2.70860866559857 adf.f=frag1|2
O -16.96901200000000 -3.65835300000000 -10.78571300000000 adf.f=frag1|3
H -15.70823656958949 -4.23996689198245 -9.62648920152293 adf.f=frag1|3
H -16.47814038897754 -4.36080868684451 -12.37857352487904 adf.f=frag1|3
O -10.76560800000000 -4.16357700000000 0.51803200000000 adf.f=frag1|4
H -9.16115845895954 -3.98623150326079 -0.29800688710696 adf.f=frag1|4
H -11.97483852095230 -3.79636551545084 -0.77600078745886 adf.f=frag1|4
O -6.55423300000000 -9.20297500000000 -11.23125400000000 adf.f=frag1|5
H -8.15301944239612 -9.65354271558258 -10.51536304076499 adf.f=frag1|5
H -6.90715220963067 -7.74998343249339 -12.24902957370683 adf.f=frag1|5
O -14.16713600000000 -6.55813200000000 -6.62957400000000 adf.f=frag1|6
H -13.74689800192609 -8.31204468643143 -6.76675830514850 adf.f=frag1|6
H -15.43294077464585 -6.49537593456625 -5.33906885435316 adf.f=frag1|6
O -1.01233800000000 -6.53737500000000 -20.63228300000000 adf.f=frag1|7
H 0.51358895613388 -7.01674081354516 -19.78766204266023 adf.f=frag1|7
H -2.25846754637793 -6.48721751306148 -19.32222614537351 adf.f=frag1|7
O -7.97372300000000 4.33381600000000 8.85869700000000 adf.f=frag1|8
H -7.39209897744333 2.71703281820261 9.42381190837837 adf.f=frag1|8
H -7.34133495205587 4.47772485325760 7.17021271491547 adf.f=frag1|8
O 1.68768000000000 -11.29316300000000 -2.87636700000000 adf.f=frag1|9
H 1.52000307205134 -11.65999321781241 -4.63958827351129 adf.f=frag1|9
H 0.92563970293820 -9.66478590395236 -2.67815953059656 adf.f=frag1|9
O 1.09184600000000 -1.69811700000000 -18.81717100000000 adf.f=frag1|10
H 2.07215988260319 -2.34326255514507 -20.19354345122146 adf.f=frag1|10
H 0.13398919688371 -3.11903886392137 -18.23829710737747 adf.f=frag1|10
O -13.85258700000000 -1.51317200000000 -3.42847700000000 adf.f=frag1|11
H -13.34561409429037 -1.90947670800034 -5.11890601995987 adf.f=frag1|11
H -15.31887324674441 -2.53345289474331 -3.14451376182312 adf.f=frag1|11
O 5.28960400000000 -6.81266800000000 -13.10585800000000 adf.f=frag1|12
H 7.01709448187639 -6.62178372023976 -12.60488989024026 adf.f=frag1|12
H 4.34671789396407 -5.97791594280375 -11.80749041866683 adf.f=frag1|12
O -11.47407200000000 -10.90708300000000 -9.44085000000000 adf.f=frag1|13
H -11.21611173248622 -12.45441460630369 -10.34132244308043 adf.f=frag1|13
H -11.17634020521638 -11.33593027595366 -7.70907363612158 adf.f=frag1|13
O -1.64592100000000 -11.43523300000000 1.48098000000000 adf.f=frag1|14
H -0.30557034252542 -10.47362907146570 0.73908565451392 adf.f=frag1|14
H -1.72993170289473 -12.94068698496448 0.48190338473989 adf.f=frag1|14
O -7.32468400000000 -5.01818100000000 4.38774900000000 adf.f=frag1|15
H -8.81838077448469 -4.73028985072788 3.40916949260461 adf.f=frag1|15
H -7.75923926090726 -6.38911120628163 5.48470646359115 adf.f=frag1|15
O 5.20879700000000 -6.83850600000000 3.69146100000000 adf.f=frag1|16
H 5.26579130261858 -6.68511818556767 1.89011343551333 adf.f=frag1|16
H 6.39162739624924 -5.60718291987245 4.28841938067655 adf.f=frag1|16
O 6.73749100000000 -0.26065600000000 -6.58850100000000 adf.f=frag1|17
H 6.56301678911955 -2.04681439624047 -6.81394756463717 adf.f=frag1|17
H 8.29925639010887 0.14828805200118 -7.40413401232653 adf.f=frag1|17
O 5.30624300000000 -5.54309500000000 -6.43599300000000 adf.f=frag1|18
H 3.81279050995479 -6.09072594663625 -7.29699777727678 adf.f=frag1|18
H 6.65189674819999 -6.43527789528092 -7.25136362341575 adf.f=frag1|18
O -5.72214300000000 -7.59376400000000 -5.60989200000000 adf.f=frag1|19
H -5.63766272358672 -7.49959469188493 -7.41422690365166 adf.f=frag1|19
H -3.99734274429106 -7.51425600722341 -5.07105423295232 adf.f=frag1|19
O -4.96412100000000 4.32334900000000 -3.25899700000000 adf.f=frag1|20
H -6.26920382212011 5.55951483151335 -3.05829302735551 adf.f=frag1|20
H -3.43114054713299 5.22630232648312 -2.93303718111639 adf.f=frag1|20
O -10.94232600000000 0.55437900000000 -13.18244900000000 adf.f=frag1|21
H -9.99364526446256 2.08335246724114 -13.36649850073860 adf.f=frag1|21
H -12.25798450895047 0.68645755108753 -14.41662950801929 adf.f=frag1|21
O -9.29636700000000 5.39923600000000 -12.62463400000000 adf.f=frag1|22
H -7.78716246923940 5.39969899801535 -11.62767327349474 adf.f=frag1|22
H -8.71366631604628 5.57073538127912 -14.32835095341294 adf.f=frag1|22
O 2.97641300000000 -12.44506100000000 3.62605000000000 adf.f=frag1|23
H 3.66110125710447 -10.77090992621746 3.63307801290360 adf.f=frag1|23
H 1.22148596207982 -12.21500271544869 3.25334655288432 adf.f=frag1|23
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H -8.54144292463491 -2.01657808726233 -15.10947598274278 adf.f=frag1|24
H -8.12619297191493 -1.91113986970532 -17.93750940057940 adf.f=frag1|24
O -1.69701700000000 -2.04382200000000 -8.20675700000000 adf.f=frag1|25
H -1.16935910005967 -0.43265303835196 -8.83710685355905 adf.f=frag1|25
H -0.63663168422293 -2.33781858979711 -6.77122484449879 adf.f=frag1|25
O 5.30132200000000 -9.56047300000000 8.45223600000000 adf.f=frag1|26
H 5.27386189469879 -8.61762538446407 6.90889108173823 adf.f=frag1|26
H 4.55017557362690 -8.45544294990206 9.67137143822390 adf.f=frag1|26
O 5.99489300000000 -5.84398700000000 -1.27866800000000 adf.f=frag1|27
H 6.10499825242707 -5.94881824033588 -3.08103213209623 adf.f=frag1|27
H 7.02298278120587 -4.42064928461433 -0.84422038296580 adf.f=frag1|27
O -8.49933400000000 6.30730300000000 1.26206900000000 adf.f=frag1|28
H -9.26414421853983 5.21634012956926 0.03875605345364 adf.f=frag1|28
H -9.84131776823032 6.72028388514297 2.40230140460829 adf.f=frag1|28
O 1.42265800000000 7.15100500000000 -6.70245700000000 adf.f=frag1|29
H 0.49123529007929 7.74531228135872 -5.27036768330312 adf.f=frag1|29
H 2.87243479479048 6.33486591183760 -5.99276142000362 adf.f=frag1|29
O 1.16572300000000 -15.86327300000000 -8.03011700000000 adf.f=frag1|30
H -0.43980652899404 -16.56646285956896 -8.47669081602252 adf.f=frag1|30
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H 0.04144584195376 -7.80383112457906 -8.97588071525340 adf.f=frag1|32
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H 8.87294935217592 1.02947962110145 -12.18888481086687 adf.f=frag1|41
H 7.29424845398649 1.45338312957695 -14.53608144577292 adf.f=frag1|41
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H -9.46772203676955 4.11444445205056 -19.34278223208070 adf.f=frag1|47
H -12.08285494971162 3.65684979597704 -18.27835293347214 adf.f=frag1|47
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H 12.23822731048506 7.54282902057004 -4.66519785219186 adf.f=frag1|48
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H 4.56888064677390 17.00621625499974 -6.03687769799284 adf.f=frag1|59
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H 14.68468379195669 0.44423157042895 0.88898485624517 adf.f=frag1|64
H 13.43262120167169 1.60465761841764 -1.40602569068362 adf.f=frag1|64
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H 7.80239299356986 -6.14232206320171 -18.05104612139325 adf.f=frag1|66
O 3.76793000000000 -11.87319400000000 -12.00003600000000 adf.f=frag1|67
H 5.53017998300823 -12.15041382890993 -12.29878904864723 adf.f=frag1|67
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end
end
Task SinglePoint
Engine ADF
eprint
scf NOPOP
sfo NOEIG NOOVL NOORBPOP
end
excitations
lowest 5
onlysing
end
fde
pw91k
end
fragments
O t21.DZP.O
H t21.DZP.H
frag1 t21.mol_1 type=fde &
fdedenstype SCFfitted
SubEnd
end
noprint BAS FUNCTIONS
numericalquality Good
scf
converge 1.0e-6 1.0e-6
diis
cx 5.0
cxx 10.0
cyc 5
n 10
ok 0.5
end
iterations 50
lshift 0.0
mixing 0.2
end
symmetry NOSYM
title Input generated by modco
xc
model SAOP
end
Relativity Level=None
EndEngine
eor