Explicit Solvation (SOLVATOR)#
显式溶剂化（SOLVATOR）

Implicit solvation models are an efficient way to model solvation effects. However, if the solute stronlgy interacts with the solvent or the solute acts as a reactant, an explicit treatment of solvent molecules in needed. The SOLVATOR is an algorithm for fully automatic inclusion of explicit solvent molecules and generation of solvation shells. It can be easily requested via the %solvator block:
隐式溶剂化模型是模拟溶剂化效应的有效方法。然而，若溶质与溶剂强烈相互作用或溶质作为反应物时，则需对溶剂分子进行显式处理。SOLVATOR 是一种全自动包含显式溶剂分子并生成溶剂化壳层的算法。它可通过 %solvator 块轻松请求：

! XTB ALPB(WATER)

%solvator
nsolv 30 
end

* XYZFILE 0 1 solute.xyz

Note 注释

Without any further input, the SOLVATOR can use all solvents available for ALPB. Nevertheless, custom solvents can be defined via the input.
无需额外输入，SOLVATOR 可利用所有适用于 ALPB 的溶剂。不过，用户仍可通过输入自定义溶剂。

If a large number of solvent molecules is to be added, the stochastic mode within the SOLVATOR may be used to massively speed up the procedure at the cost of accuracy.
如果要添加大量溶剂分子，可以在 SOLVATOR 中使用随机模式，以牺牲精度为代价大幅加快该过程。

! XTB ALPB(WATER)

%SOLVATOR 
    NSOLV       100 
    CLUSTERMODE STOCHASTIC
END
*XYZFILE 0 1 solute.xyz

Example 1: Explicit Solvation of Urea#
示例 1：尿素的显式溶剂化

As an example, we will solvate an urea molecule with 30 water molecules. To do so, we can use the input shown above and the corresponding output will look like:
作为一个示例，我们将用 30 个水分子溶剂化一个尿素分子。为此，我们可以使用上述输入，相应的输出将如下所示：

                       *****************
                       * ORCA Solvator *
                       *****************

Solvent chosen:                                WATER
Solvent radius:                                .... 1.69 Angs
Solvent max dimensions (x,y,z):                .... 2.73, 2.32, 1.52 Angs
Number of solvent molecules to be added:       .... 30 molecules
Method used to add the solvent:                .... docking
Number of atoms of solvent molecule:           .... 3 atoms
Coordinates of solvent in Angstroem:           

   O   -0.000006   0.397814  -0.000000
   H    0.763472  -0.198901   0.000000
   H   -0.763466  -0.198913   0.000000

Solute radius:                                 .... 2.93 Angs
Ellipsoid potential radii:                     .... 6.33, 5.88, 4.58 Angs
Adding solvent molecules to the solute         .... 


      Iter       Energy      Einter          dE          Time
                  (Eh)     (kcal/mol)    (kcal/mol)     (min)
      -------------------------------------------------------
         1    -19.210306    -4.659502     -4.659502      0.21
         2    -24.302552    -4.533387      0.126115      0.25
         3    -29.394688    -4.464434      0.068952      0.29
[...]
        24    -136.308378    -1.936280      4.656513      5.53
        25    -141.398670    -3.272224     -1.335945      6.09
        26    -146.487932    -2.627486      0.644738      6.47
Wall size increased by factor 1.05.
        27    -151.580491    -4.663392     -2.035905      7.87
        28    -156.682343    -4.840764     -0.177372      9.33
        29    -161.768524    -0.720711      4.120053      8.96
        30    -166.856255    -1.699958     -0.979247      10.30

Final radius after microsolvation:             .... 5.55 Angs
Time needed for microsolvation   :             .... 5511.52 s
Final structured saved to        :             basename.solvator.xyz

		****ORCA-SOLVATOR TERMINATED NORMALLY****

From this, we can see the iterative addition of water molecules, their respective interaction energies, and the overall energy change upon coordination. The structure of the solvated urea molecule is stored in the basename.solvator.xyz file and the cluster growth looks like:
由此，我们可以观察到水分子的迭代添加、各自相互作用能以及配位过程中整体能量的变化。溶剂化尿素分子的结构存储在 basename.solvator.xyz 文件中，而簇的生长过程如下：

../_images/urea-30water.gif

Structures Example 1# 结构示例 1

Urea 尿素
8

H     2.01822    0.20187   -0.06397
H     0.83499    1.40748   -0.41061
H    -1.39434    0.89498   -0.21940
H    -1.88388   -0.75647   -0.13275
O     0.40675   -1.67285    0.11342
C     0.11861   -0.48803   -0.06584
N     1.05605    0.49217   -0.06005
N    -1.15640   -0.07915   -0.28146

Example 2: Custom Solvents - Helium Droplet#
示例 2：定制溶剂——氦滴

SOLVATOR is not restricted to predefined solvents. You can easily define any custom solvent via the %SOLVATOR block. In this example, we will use the STOCHASTIC and DROPLET modes to spherically solvate a sesqui-siloxane with 2000 Helium atoms. In this case our custom solvent is a neutral singlet Helium atom that we define in a he.xyz file. Charge and multiplicity are given via the second line in the .xyz file.
SOLVATOR 不受限于预定义溶剂。您可以通过 %SOLVATOR 块轻松定义任何自定义溶剂。在此示例中，我们将使用 STOCHASTIC 和 DROPLET 模式，以 2000 个氦原子球形溶剂化一个倍半硅氧烷。在这种情况下，我们的自定义溶剂是我们在 he.xyz 文件中定义的中性单重态氦原子。电荷和多重性通过 .xyz 文件中的第二行给出。

2
0 1
He 0 0 0

We now run the SOLVATOR and obtain a spherical Helium droplet around our sesqui-siloxane molecule.
我们现在运行 SOLVATOR，并在我们的倍半硅氧烷分子周围获得一个球形氦滴。

!XTB

%SOLVATOR
    SOLVENTFILE "he.xyz"
    NSOLV       2000
    CLUSTERMODE STOCHASTIC
    DROPLET     true
END

* XYZFILE 0 1 solute.xyz
../_images/helium-droplet.png

Figure: Spherical Helium droplet of 2000 He atoms around a sesqui-siloxane molecule.
图：围绕一个倍半硅氧烷分子的 2000 个氦原子组成的球形液滴。#

Structures Example 2# 结构示例 2

Sesqui-siloxane 倍半硅氧烷
100

Si 2.30883927191187021677 -1.51404107261898013270 -0.06479458802821000396
Si 0.69844495028425856997 2.53054881818156962581 -0.57025875838537964935
Si 1.76968132551996903956 0.88645731306134989413 1.81815072089804852240
Si 1.24023679693334010210 0.12887051433739010742 -2.45462644723449940898
O  1.47797606920943969122 2.09710588445933909796 0.78327428664550924342
O  2.47037162112476949005 -0.36267740860083069743 1.06318958760345028125
O  2.14724279926403971430 -0.84019824205737059231 -1.52811718998416923299
O  1.17449611044826007777 1.61711183569708993879 -1.81868142591142012421
O  0.39950516912156014415 0.41014517960417962161 2.53909316241434979133
O  1.03577796006599931466 -2.45939073017393816656 0.26658822054469016871
C  3.86064736032040034530 -2.60084865441333024094 -0.09415481382276005839
C  1.14364000674242949351 4.33130288798302132136 -0.95831926241946008282
C  2.95427276296586960314 1.52116262557503967301 3.14908160016116855928
C  2.06043263801967002635 0.24730786165735027526 -4.15902291357893094670
C  3.90575117563901885731 -3.65841588533059125510 1.01113071648778030109
C  1.03633523105185809676 4.69271580225670970066 -2.44175622400742931006
C  2.42612388212526886022 2.75762877421782803822 3.87739875337951023226
C  2.76895479629271035193 -1.03630441656062011191 -4.59817790597404041364
C  3.99617575306170946803 -3.03554304523522056058 2.39737038341486030646
C  -0.38978418583185003854 4.56868838311114000561 -2.95899800040501936849
C  3.40223083440897999807 3.25170654911326062475 4.93973454914741871846
C  1.79904320713196952397 -2.19849925304276050397 -4.75739565686958876256
Si -2.16923648489345977097 1.45426783117045044236 -0.01870960599793020790
Si -0.56318192368503949830 -2.58406051784629031687 0.49418191599628003008
Si -1.63152308951002988913 -0.93828528229811991590 -1.90091815923119988874
Si -1.09893107745471896308 -0.18602740921880953073 2.37739116950383966298
O  -1.34685273353240986260 -2.13973745660979997041 -0.85332000914464001262
O  -2.33456025887852014478 0.32000944971483041845 -1.16296686079512978651
O  -2.00281184230103015409 0.77767883065566023593 1.44192675840557971156
O  -1.03318807002326851219 -1.67816481400793904299 1.75111237908015970888
O  -0.25591078342145984204 -0.47104763472030986016 -2.61742643815765951842
O  -0.90165733572753015146 2.40762179951717092408 -0.34545383340373003733
C  -3.73428050087115925848 2.51603829101419851355 -0.01815659898138005657
C  -1.01235827566696867663 -4.38784603836863862369 0.86651868482533955795
C  -2.80604844640132977673 -1.59380669992410939351 -3.23072457802342949407
C  -1.92219349146365003911 -0.29101512884843022677 4.08107501501395031340
C  -4.01896736325925019173 3.15358491116559047640 -1.37854494362718993372
C  -0.96828017732090965186 -4.75078626933027869939 2.35290323022157021882
C  -2.28944557534834869372 -2.86499709299084015512 -3.90555810015316007267
C  -2.63016186476952018580 0.99701470478872022962 4.50870889568977872841
C  -5.29465505813576875482 3.98863268133149162509 -1.36009570325191009310
C  0.43400029910372006636 -4.62639632611979045862 2.93113716048616979037
C  -3.26303206554563995923 -3.38698577510639875499 -4.95678581013346875039
C  -1.65879639885883878314 2.15844255245909044660 4.66558459805101932716
H  3.91951010594626980676 -3.10369193013083144450 -1.05973816979330970334
H  4.75013834211284891040 -1.97537461313113049677 -0.01669722396988995369
H  0.50054673213437972379 5.00161909257629133663 -0.38768802597859025605
H  2.16371909638209958260 4.52455437533658066940 -0.62639764452651036652
H  3.14542544271343915696 0.73649492147874962011 3.88167628963121913444
H  3.91736932797826975516 1.76343870330954977099 2.69946537333993008545
H  1.31470770815672022280 0.50997254094894017840 -4.90954460832408035031
H  2.78771120244437087266 1.05905880843276056780 -4.14858700990401718656
H  3.00534986598125808399 -4.26938181753094614379 0.94907211175572059325
H  4.76954135253091848767 -4.30990703001076802536 0.85218243687316996837
H  1.38666197667096047219 5.71820642646272947474 -2.58893781604851058731
H  1.68322554092942966442 4.02803417397333074490 -3.01448664696216894754
H  2.24529627004391851841 3.54810008489985984070 3.14851734744065980820
H  1.47103305153703978192 2.51523697374575938568 4.34312230329484982860
H  3.28025904039187032879 -0.85902566957414994153 -5.54847977452326901471
H  3.52024789644420854628 -1.29657705457920746639 -3.85253639854650931085
H  3.14668902674270967168 -2.38151877517681098695 2.56756735695418880638
H  4.00711771561967999844 -3.80743850933508198864 3.16405351573453952341
H  4.90391151558519844400 -2.44338553454369744600 2.48795323727609973830
H  -1.05324373529086856571 5.22214434287834716741 -2.39667419157567884724
H  -0.44200202603668981016 4.84521860375389046283 -4.01000508779899966783
H  -0.73701094612906004055 3.54566058125262006939 -2.84625863873755013955
H  4.35534625093372707028 3.51721477088752942919 4.48791970564398479127
H  3.00657477635410019801 4.12858427786754766942 5.44703648328616019114
H  3.58131708538499937688 2.47712734176321003332 5.68211170546796928704
H  1.03844542603209943898 -1.95635206821307017222 -5.49622938457011755986
H  2.32358818936812072664 -3.09454422193371092575 -5.08274073080039912043
H  1.30688236711312022464 -2.40240917758488015110 -3.81083588856759947205
H  -4.59223453559549987801 1.90833280028286011998 0.27062566445760011247
H  -3.64938883216220988359 3.30502599627088056167 0.72956950004708975843
H  -2.01598654557988021807 -4.58643944548276127904 0.49028182462367042582
H  -0.34183817421683959648 -5.05453229314074103939 0.32361826110324021233
H  -3.78165341186373016313 -1.80188256932753954054 -2.79109577346592052649
H  -2.96783654511175898350 -0.83203933706014954197 -3.99365066659321898968
H  -2.65051356366059964742 -1.10204911215061041041 4.07548184529990020764
H  -1.17845880359745991406 -0.54880046191694031865 4.83545608005379978778
H  -3.17425636671041999648 3.78197656898877099252 -1.66011213965578030560
H  -4.10692092972908895376 2.36599151951094821555 -2.12723450018604065548
H  -1.63934897095727949434 -4.08680248081823105366 2.89789727201267988121
H  -1.32445903563647049417 -5.77641257499842097900 2.48397765013837013015
H  -1.32689939382206967267 -2.65448661718140055399 -4.37123161520532033109
H  -2.12644275071908905872 -3.62858778509852974992 -3.14480528099144907017
H  -3.37716247278667047738 1.25474422738565971613 3.75776950622156791226
H  -3.14626184984560808289 0.82641495329852054930 5.45761245326638899655
H  -5.21798740459044019246 4.78539784652138067145 -0.62389997330403046405
H  -5.47423288763323778738 4.43751329567928198827 -2.33428761593805722541
H  -6.15154417304282752355 3.36977611319346692653 -1.10419104363117792644
H  0.78936333102788935889 -3.60641984220516942372 2.82136714407547994909
H  0.43857927461324219820 -4.88989719753061091723 3.98666481754406865079
H  1.12048236632775966015 -5.28809174614212196275 2.40800635183417766072
H  -3.42531384075182909754 -2.64005312060207009139 -5.73034451244428932881
H  -2.87535577178886736505 -4.28811600615014931748 -5.42588319013786701817
H  -4.22334594297450838241 -3.62187340364976950724 -4.50377181308966800799
H  -1.16165677135020972699 2.35565262654516871521 3.72022806433342889676
H  -2.18360718306651824250 3.05749725542114125787 4.98250872245835818575
H  -0.90240043070232012212 1.92008284489281999541 5.41019438066246038943