Basis sets and atomic fragments¶
STO basis sets¶
The basis functions used in ADF are commonly known as Slater Type Orbitals (STOs). The ADF package comes with a database of STO basis sets. The basis sets are simple ASCII files and they are located in the directory $AMSHOME/atomicdata/ADF
. A description of the basis set file format can be found in the appendix Basis set file format.
A basis set can roughly be characterized by its size (single, double, triplezeta; with or without polarization) and by the level of frozen core approximation. The standard basis sets available in ADF are:
 SZ Minimal basis sets: singlezeta without polarization. The exponents of the functions correspond to the standard STO3g basis sets used in programs that employ Gaussian type basis functions. TypeSZ files are provided only for the lighter elements, up to Kr.
 DZ Doublezeta basis sets without polarization functions. A triplezeta set is used for the 3d shells of the first row transition metals, the 4f shells of the Lanthanides, and the 5f shells of the Actinides. In all these cases a doublezeta set provides a rather poor expansion basis for the true (numerically computed) atomic orbital.
 DZP Double zeta polarized basis. The basis sets in DZP are derived from DZ, extended with a polarization function. This type of basis sets is thus far provided only for the elements up to Ar, and for the 4p series Ga through Kr.
 TZP Triplezeta basis sets. A polarization function is added for H through Ar and for Ga through Kr (from DZP)
 TZ2P Triplezeta with two polarization functions, for H through Ar and Ga through Kr (from DZP). Note that the TZ2P basis set files are provided only for the lighter elements, up to Kr. The ZORA/TZ2P basis set files are provided for all elements. Typically for all elements one polarization function is added compared to the corresponding TZP basis set. Note, however, that TZ2P will not always give you extra basis functions for most lanthanide and actinide frozen core basis sets.
In addition to the standard basis sets, the database contains directories with special basis sets:
 TZ2P+ For transition metals ScZn and lanthanides (ZORA) only: as TZ2P, but with extra dSTO (3d metals), and extra fSTO (lanthanides, ZORA)
 ZORA contains basis sets designed for ZORA relativistic calculations (relativistic calculation have special basis set requirements, especially in the core region). ZORA basis sets with frozen core should be used exclusively in relativistic calculations with the ZORA approach, while allelectron ZORA basis sets can be used for both relativistic and nonrelativistic calculations. The ZORA/QZ4P basis set can be loosely described as core triple zeta, valence quadruple zeta, with four sets of polarization functions.
 ET contains several even tempered basis sets which enables one to go to the basis set limit, such as ET/ETpVQZ, ET/ETQZ3P, ET/ETQZ3P1DIFFUSE, ET/ETQZ3P2DIFFUSE, ET/ETQZ3P3DIFFUSE. The accuracy of the smallest basis set in this directory can loosely be described as quadruple zeta in the valence with three polarization functions added. This directory also contains basis sets with extra diffuse functions. In Response calculations one should use such large basis sets. Very diffuse functions are absolutely necessary to get good results for excitation energies corresponding to high lying orbitals.
 AUG contains several augmented standard basis sets which enables one to get reasonable results for excitation energies with relatively small basis sets, such as AUG/ASZ, AUG/ADZ, AUG/ADZP, AUG/ATZP, AUG/ATZ2P.
Furthermore, in $AMSHOME/atomicdata/ADF
you will find:
 Special/AE contains nonrelativistic basis sets for allelectron calculations. However, these files cannot be used as such, because they don’t contain any fit sets. They serve as starting point for the development of (new) basis sets. For some of the allelectron sets appropriate fit sets have already been generated. The corresponding data base files can be found in the appropriate subdirectories SZ, DZ, DZP, et cetera.
 Special/Vdiff contains nonrelativistic basis sets that include very diffuse functions. These were recommended to be used for Response calculations. Very diffuse functions are absolutely necessary to get good results for excitation energies corresponding to high lying orbitals. Recommendation: use the even tempered basis sets in the ET directory, since these basis sets are better.
 Special/MDC contains nonrelativistic basis sets with optimized fit functions especially useful for accurate Multipole Derived Charges. These are available only for a limited number of basis sets.
The directory $AMSHOME/atomicdata/Dirac
contains the input files for the DIRAC auxiliary program (see the RELATIVITY keyword).
Frozen core
Multiple occurrences of one chemical element in the same basis set subdirectory correspond to different levels of the frozen core approximation. Manganese for instance may have a basis set for an atom with a frozen 2p shell and another one with a frozen 3p shell. The file names are selfexplanatory: Mn.2p stands for a data file for Manganese with frozen core shells up to the 2p level. An allelectron basis set would correspond to a file that has no frozencore suffix in its name.
Electronic configurations specific basis sets
Another type of multiple occurrence of one element in one basis set directory may be found when basis sets have been developed for different electronic configurations: the Slatertype basis sets are fitted then to numerical orbitals from runs with different occupation numbers. Currently this applies only for Ni (in $AMSHOME/atomicdata/ADF
DZ
, TZP
and TZ2P
), where basis sets are supplied for the d8s2 and the d9s1 configurations respectively. Since in earlier releases only the d8s2 variety was available, the names of the basis set files are Ni.2p (for d8s2) and Ni_d9.2p, and likewise Ni.3p and Ni_d9.3p.
References on basis sets
 E. van Lenthe and E.J. Baerends, Optimized Slatertype basis sets for the elements 1118. Journal of Computational Chemistry 24, 1142 (2003)
 D.P. Chong, E. van Lenthe, S.J.A. van Gisbergen and E.J. Baerends, Eventempered SlaterType orbitals revisited: From Hydrogen to Krypton. Journal of Computational Chemistry 25, 1030 (2004)
 D.P. Chong, Augmenting basis set for timedependent density functional theory calculation of excitation energies: Slatertype orbitals for hydrogen to krypton. Molecular Physics 103, 749 (2005)
Older references for STO basis sets are Refs. [1] [2] [3]. See also the paper by Raffennetti on design and optimization of eventempered STO basis sets [4]. The paper by Del Chong describes completeness profiles as a visual tool in estimating the completeness of a basis set [5]. Finally, Zeiss and coworkers [6] describe fieldinduced polarization functions for STOs. These are useful for defining basis sets with diffuse functions for (hyper)polarizability and other property calculations.
The procedure for the usage and optimization of fit functions is described by Baerends et al. [7].
For documentation on how to make custom eventempered basis/fit sets, see the old ADF 2014 documentation.
Available basis sets¶
ADF has optimized STO basis sets for the whole periodic table (Z=1120).
1  2  3  4  5  6  7  8  9  10  11  12  13  14  15  16  17  18  

1  1 H 
2 He 

2  3 Li 
4 Be 
5 B 
6 C 
7 N 
8 O 
9 F 
10 Ne 

3  11 Na 
12 Mg 
13 Al 
14 Si 
15 P 
16 S 
17 Cl 
18 Ar 

4  19 K 
20 Ca 
21 Sc 
22 Ti 
23 V 
24 Cr 
25 Mn 
26 Fe 
27 Co 
28 Ni 
29 Cu 
30 Zn 
31 Ga 
32 Ge 
33 As 
34 Se 
35 Br 
36 Kr 

5  37 Rb 
38 Sr 
39 Y 
40 Zr 
41 Nb 
42 Mo 
43 Tc 
44 Ru 
45 Rh 
46 Pd 
47 Ag 
48 Cd 
49 In 
50 Sn 
51 Sb 
52 Te 
53 I 
54 Xe 

6  55 Cs 
56 Ba 
La Yb 
71 Lu 
72 Hf 
73 Ta 
74 W 
75 Re 
76 Os 
77 Ir 
78 Pt 
79 Au 
80 Hg 
81 Tl 
82 Pb 
83 Bi 
84 Po 
85 At 
86 Rn 
7  87 Fr 
88 Ra 
Ac No 
103 Lr 
104 Rf 
105 Db 
106 Sg 
107 Bh 
108 Hs 
109 Mt 
110 Ds 
111 Rg 
112 Cn 
113 Nh 
114 Fl 
115 Mc 
116 Lv 
117 Ts 
118 Og 
8  119 Uue 
120 Ubn 

Lanthanide elements 
57 La 
58 Ce 
59 Pr 
60 Nd 
61 Pm 
62 Sm 
63 Eu 
64 Gd 
65 Tb 
66 Dy 
67 Ho 
68 Er 
69 Tm 
70 Yb 

Actinide elements 
89 Ac 
90 Th 
91 Pa 
92 U 
93 Np 
94 Pu 
95 Am 
96 Cm 
97 Bk 
98 Cf 
99 Es 
100 Fm 
101 Md 
102 No 
The next tables give an indication which all electron (ae) and frozen core (fc) standard basis sets are available for the different elements in ADF.
Element  ae or fc  SZ, DZ  DZP  TZP, TZ2P  TZ2P+  QZ4P, ET  AUG 

HHe (Z=12)  ae  Yes  Yes  Yes  Yes  Yes  
LiNe (Z=310)  ae  Yes  Yes  Yes  Yes  Yes  
.1s  Yes  Yes  Yes  nonrel  
NaAr (Z=1118)  ae  Yes  Yes  Yes  Yes  Yes  
.1s .2p  Yes  Yes  Yes  nonrel  
KCa (Z=1920)  ae  Yes  Yes  Yes  Yes  Yes  
.2p .3p  Yes  Yes  Yes  nonrel  
ScZn (Z=2130)  ae  Yes  Yes  Yes  Yes  Yes  
.2p .3p  Yes  Yes  Yes  nonrel  
GaKr (Z=3136)  ae  Yes  Yes  Yes  Yes  Yes  
.3p .3d  Yes  Yes  Yes  nonrel 
Element  fc  DZ, TZP 

RbSr (Z=3738)  .3p .3d .4p  Yes 
YCd (Z=3948)  .3d .4p  Yes 
InBa (Z=4956)  .4p .4d  Yes 
LaLu (Z=5771)  .4d .5p  Yes 
HfHg (Z=7280)  .4d .4f  Yes 
TlRn (Z=8186)  .4d .4f .5p .5d  Yes 
FrRa (Z=8788)  .5p .5d  Yes 
AcCm (Z=8996)  .5d  Yes 
Element  ae or fc  DZ, TZP, TZ2P  TZ2P+  QZ4P 

RbSr (Z=3738)  ae  Yes  Yes  
.3p .3d .4p  Yes  
YCd (Z=3948)  ae  Yes  Yes  
.3d .4p  Yes  
InBa (Z=4956)  ae  Yes  Yes  
.4p .4d  Yes  
LaYb (Z=5770)  ae  Yes  Yes  Yes 
.4d .5p  Yes  Yes  
Lu (Z=71)  ae  Yes  Yes  
.4d .5p  Yes  
HfHg (Z=7280)  ae  Yes  Yes  
.4d .4f  Yes  
Tl (Z=81)  ae  Yes  Yes  
.4d .4f .5p  Yes  
PbRn (Z=8286)  ae  Yes  Yes  
.4d .4f .5p .5d  Yes  
FrRa (Z=8788)  ae  Yes  Yes  
.5p .5d  Yes  
AcLr (Z=89103)  ae  Yes  Yes  
.4f .5d  Yes  
RfCn (Z=104112)  ae  Yes  Yes  
.4f .5d .5f  Yes  
NhOg (Z=113118)  ae  Yes  Yes  
.5d .5f  Yes  
UueUbn (Z=119120)  ae  Yes  Yes  
.5f  Yes 
For heavier elements, from Rb on, the nonrelativistic all electron basis sets are missing. In the ZORA basis sets directory you will find allelectron basis sets for all elements (Z = 1120), which also could be used in nonrelativistic calculations. Note, however, that these basis sets were optimized for ZORA calculations, which means that nonrelativistic calculations will not always give you the expected accuracy. Nonrelativistically optimized basis sets for the heavier elements are provided in a separate directory AE, which contains basis sets of single, double and triplezeta quality indicated respectively by suffixes ‘sz’, ‘dz’, and ‘tz’. The files in Special/AE/ are not complete basis set files, because they don’t contain fit sets (the usage and relevance of fit functions is explained later).
Basis sets directories
Basis sets can be found in the directory $AMSHOME/atomicdata/ADF
, for nonrelativistic calculations in the subdirectories SZ, DZ, DZP, TZP, TZ2P, TZ2P+, for ZORA calculations in ZORA/SZ, ZORA/DZ, ZORA/DZP, ZORA/TZP, ZORA/TZ2P, ZORA/TZ2P+, ZORA/TZ2PJ, ZORA/QZ4P, ZORA/QZ4PJ, the augmented basis sets can be found in AUG/ASZ, AUG/ADZ, AUG/ADZP, AUG/ATZP, AUG/ATZ2P, and the even tempered basis sets in ET/ETpVQZ, ET/ETQZ3P, ET/ETQZ3P1DIFFUSE, ET/ETQZ3P2DIFFUSE, ET/ETQZ3P3DIFFUSE. All electron basis sets can be used in nonrelativistic and ZORA calculations.
Basis sets acronyms
 SZ: single zeta
 DZ: double zeta
 DZP: double zeta + 1 polarization function
 TZP: valence triple zeta + 1 polarization function
 TZ2P: valence triple zeta + 2 polarization function
 TZ2P+: = TZ2P + extra d (3d metals) or extra f (lanthanides)
 QZ4P: valence quadruple zeta + 4 polarization function, relativistically optimized
 ET: even tempered
 pVQZ, QZ3P: valence quadruple zeta + 3 polarization function, even tempered
 QZ3PnD: = QZ3P + n diffuse sets of s, p, d, and f functions, even tempered
 AUG: augmented
 ASZ, ADZ, ADZP, ATZP, ATZ2P: augmented for use in TDDFT
 TZ2PJ, QZ4PJ: for use in ESR hyperfine or NMR spinspin couplings
 TZ2P or QZ4P + extra tight (mainly 1s) functions
All electron or frozen core
 element name (without suffix): all electron
 .1s frozen: 1s
 .2p frozen: 1s 2s 2p
 .3p frozen: 1s 2s 2p 3s 3p
 .3d frozen: 1s 2s 2p 3s 3p 3d
 .4p frozen: 1s 2s 2p 3s 3p 3d 4s 4p
 .4d frozen: 1s 2s 2p 3s 3p 3d 4s 4p 4d
 .4f frozen: 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f
 .5p frozen: 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s 5p (LaLu)
 .5p frozen: 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p (other)
 .5d frozen: 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d
 .6p frozen: 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p (AcLr)
 .5f frozen: 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 6s 6p
The Basis Key¶
The basis set can be specified in the input via the Basis
key block.
The most important subkeys Type and Core.
Description of all subkeys:
Basis
Type [...]
Core [None  Small  Large]
End
Basis
Type: Block Description: Definition of the basis set Type
Type: Multiple Choice Default value: DZ Options: [SZ, DZ, DZP, TZP, TZ2P, QZ4P, TZ2PJ, QZ4PJ, AUG/ASZ, AUG/ADZ, AUG/ADZP, AUG/ATZP, AUG/ATZ2P, ET/ETpVQZ, ET/ETQZ3P, ET/ETQZ3P1DIFFUSE, ET/ETQZ3P2DIFFUSE, ET/ETQZ3P3DIFFUSE, POLTDDFT/DZ, POLTDDFT/DZP, POLTDDFT/TZP, POLTDDFT/TZ2P] GUI name: Basis set Description: Select the basis set to use. SZ: Single Z DZ: Double Z DZP: Double Z, 1 polarization function TZP: Triple Z, 1 polarization function TZ2P: Triple Z, 2 polarization functions QZ4P: Quad Z, 4 pol functions, allelectron AUG: Augmented (extra diffuse functions) ET: Even tempered all electron basis sets J: Extra tight functions These descriptions are meant to give an indication of the quality, but remember that ADF uses Slater type functions. For standard calculations (energies, geometries, etc.) the relative quality is: SZ < DZ < DZP < TZP < TZ2P < ETpVQZ < QZ4P The basis set chosen will apply to all atom types in your molecule. If no matching basis set is found, ADF will try to use a basis set of better quality. For TDDFT applications and small negatively charged atoms or molecules, use basis sets with extra diffuse functions. J: TZ2PJ, QZ4PJ: for use in ESR hyperfine or NMR spinspin couplings. Use the Basis panel to select a basis set per atom type, and to see what basis set actually will be used. Core
Type: Multiple Choice Default value: Large Options: [None, Small, Large] GUI name: Frozen core Description: Select the size of the frozen core you want to use. Small and Large will be interpreted within the basis sets available (of the selected quality), and might refer to the same core in some cases. If you specify ‘None’ you are guaranteed to have an allelectron basis set.
Warning: Do not include the Corepotentials keys when using the Basis key. Typically one should not include both the the Basis key and the Fragments key.
Description of the other Basis subkeys:
Basis
CreateOutput Yes/No
Path string
PerAtomType
Core [None  Small  Large]
File string
Symbol string
Type [...]
End
PerRegion
Core [None  Small  Large]
Region string
Type [...]
End
FitType [...]
End
Basis
CreateOutput
Type: Bool Default value: No Description: If true, the output of the atomic create runs will be printed to standard output. If false, it will be saved to the file CreateAtoms.out in the AMS results folder. Path
Type: String Description: The name of an alternative directory with basis sets to use. ADF looks for appropriate basis sets only within this directory. Default $AMSRESOURCES/ADF. PerAtomType
Type: Block Recurring: True Description: Defines the basis set for all atoms of a particular type. Core
Type: Multiple Choice Options: [None, Small, Large] Description: Size of the frozen core. File
Type: String Description: The path of the basis set file (the path can either absolute or relative to $AMSRESOURCES/ADF). Note that one should include ZORA in the path for relativistic calculations, for example ‘ZORA/QZ4P/Au’. Specifying the path to the basis file explicitly overrides the automatic basis file selection via the Type and Core subkeys. Symbol
Type: String Description: The symbol for which to define the basis set. Type
Type: Multiple Choice Options: [SZ, DZ, DZP, TZP, TZ2P, QZ4P, TZ2PJ, QZ4PJ, AUG/ASZ, AUG/ADZ, AUG/ADZP, AUG/ATZP, AUG/ATZ2P, ET/ETpVQZ, ET/ETQZ3P, ET/ETQZ3P1DIFFUSE, ET/ETQZ3P2DIFFUSE, ET/ETQZ3P3DIFFUSE, POLTDDFT/DZ, POLTDDFT/DZP, POLTDDFT/TZP, POLTDDFT/TZ2P] Description: The basis sets to be used.
PerRegion
Type: Block Recurring: True Description: Defines the basis set for all atoms in a region. If specified, this overwrites the values set with the Basis%Type and Basis%PerAtomType keywords for atoms in that region. Note that if this keyword is used multiple times, the chosen regions may not overlap. Core
Type: Multiple Choice Default value: Large Options: [None, Small, Large] Description: Size of the frozen core. Region
Type: String Description: The identifier of the region for which to define the basis set. Note that this may also be a region expression, e.g. ‘myregion+myotherregion’ (the union of two regions). Type
Type: Multiple Choice Default value: DZ Options: [SZ, DZ, DZP, TZP, TZ2P, QZ4P, TZ2PJ, QZ4PJ, AUG/ASZ, AUG/ADZ, AUG/ADZP, AUG/ATZP, AUG/ATZ2P, ET/ETpVQZ, ET/ETQZ3P, ET/ETQZ3P1DIFFUSE, ET/ETQZ3P2DIFFUSE, ET/ETQZ3P3DIFFUSE, POLTDDFT/DZ, POLTDDFT/DZP, POLTDDFT/TZP, POLTDDFT/TZ2P] Description: The basis sets to be used.
FitType
Type: Multiple Choice Default value: Auto Options: [Auto, SZ, DZ, DZP, TZP, TZ2P, QZ4P, TZ2PJ, QZ4PJ, AUG/ASZ, AUG/ADZ, AUG/ADZP, AUG/ATZP, AUG/ATZ2P, ET/ETpVQZ, ET/ETQZ3P, ET/ETQZ3P1DIFFUSE, ET/ETQZ3P2DIFFUSE, ET/ETQZ3P3DIFFUSE] GUI name: STO fit set Description: Expert option. Select the auxiliary fit to be used for STOfit or old HartreeFock RI scheme. The fit set for a given atom is taken from the allelectron basis set file for the specified choice, for the same element as the atom. By default (Auto) the fit set is taken from the original basis set file.
An example where you can use regions to define basis sets for parts of your system, see Example: Multiresolution.
Automatic mode¶
The following input will run a geometry optimization on water, using a (almost) minimal input:
"$AMSBIN/ams" <<eor
Task GeometryOptimization
System
Atoms
O 0 0 0
H 1 1 0
H 1 1 0
End
Symmetrize Yes
End
Engine ADF
Basis
Type TZP
End
EndEngine
eor
 The
ATOMS
subblock key in theSystem
block key specifies the geometry of the system;  the
Task GeometryOptimization
key instructs AMS to perform a geometry optimization;  the
Basis
block key instructs ADF to run the create runs automatically, using a TZP basis sets.
The automatic mode will be used when the Basis
key is present in the input, or if no Fragments
block key is present.
In automatic mode ADF will first create fragment files for all the basic atom fragments found in the Atoms
block. Normally this means that for each atom type in your molecule a fragment file will be created.
You may have different fragments with the same atom: add a dot and a name (without spaces) after the name of the element. For example: H.1
and H.2
. In this example two fragment files will be created: one for the H.1
fragment and one for the H.2
fragment. Using the PerAtomType
subkey you may assign different basis sets to these fragments. Another consequence is that the H.1
and H.2
atoms will never be symmetry equivalent to each other.
In case of a relativistic calculation, the DIRAC program will also be run automatically, and the create runs will include the correct relativistic key and corresponding basis sets. For ZORA calculations, ADF first tries to locate a special ZORA basis set. If this does not succeed it will use a normal basis set if the required basis set does not use a frozen core.
Create mode¶
Expert option. In Create mode the input file is relatively simple. First, the geometry is trivial: one atom at the origin.
Second, the problem is computationally so simple that default settings for precision aspects, such as convergence criteria and levels of numerical integration accuracy, are internally defined to be much more stringent than in normal calculations. These aspects don’t have to be looked after. Also one should specify the wanted XC functional. If you use the Basis key all this will be handled automatically.
In Create mode you need an input file of the following form:
System
Atoms
Atomtype 0 0 0
End
end
Task SinglePoint
Engine ADF
CREATE Atomtype Datafile
EndEngine
Create
 is the keyword. The remainder of the record (atomtype datafile) is the argument.
Atomtype
 is a name for the basic atom that you want to create. The program reads and interprets this name. Therefore, the name must begin with the standard chemical symbol (H, He, Li, …) of the element to be created. Optionally the name may have an suffix of the form .text. The suffix begins with a period (.); the part after the period (text) is at your discretion as long as it does not contain a delimiter. A few examples:
appropriate names  inappropriate names 
K  Siwithcore (no period after the chemical symbol) 
Li.newbasis  $HOME/atomicdata/ADF/C.dzp (not beginning with the chemical symbol) 
P.1992_Feb.30  Ga.nocore,smallbasis (contains a comma (a delimiter)) 
Sodium.2s (Sodium is not the symbol for this element (Na)) 
Datafile
 specifies the data file that contains the basis set and related items. It may contain a full path if the file does not reside in the working directory of the job. The datafile part is optional. If you omit it, ADF assumes that the file name is identical to the atom type name, i.e. Create Atomtype is equivalent to and interpreted as Create Atomtype Atomtype In view of the restrictions that apply to the atom type name, the option to use the short form can only be used if the file name has the appropriate format. To make the input file easier to understand for a human reader you may, for Datafile, also type file=Datafile, where file= must be typed as such, and datafile is the name of the file.
So you could have a simple calculation as follows (the ‘creation’ of a Carbon atom);
$AMSBIN/ams << eor
System
Atoms
C 0 0 0
End
end
Task SinglePoint
Engine ADF
Create C $AMSHOME/atomicdata/ADF/DZ/C.1s
EndEngine
eor
The presence of the keyword create
sets the computational mode of ADF to: create a basic atom.
Here a basis set file is located in $AMSHOME/atomicdata/ADF
, where
the file ‘C.1s’ in the subdirectory DZ/ (this contains basis sets of doublezeta quality).
Examine logfile and out to check that everything has gone well.
A considerable number of basis set files are included in the ADF. You can also create basic atoms corresponding to socalled Alternative Elements, with for instance a noninteger nuclear charge or a different mass. See the next section.
Ghost Atoms, Nonstandard Chemical Elements¶
The atom type names used under atoms (and in the create record) must begin with the standard chemical element symbol (H, He, Li…). The program uses this to deduce the nuclear charge and other elemental properties.
For the standard elements one can redefine the atomic mass (for instance to define a suitable isotope). Masses are specified by adding the desired mass (in Dalton) at the end of the atom’s line (mass=).
It is also possible to define an artificial chemical element with userspecified properties. Such new elements are denoted Alternative Elements; and may for instance have a noninteger nuclear charge.
The chemical symbol of for a (ghost) atom that has zero nuclear charge is Gh.
The BASIS
key recognizes elements denoted with Gh.atom in the ATOMS key as being ghost atoms. If one does not specifically select a basis set for this ghost atom, the all electron basis set for the atom is selected in the creation of the ghost atom using the type of basis set chosen with the BASIS key. The atom name must begin with the standard one or twocharacter symbol for the chemical element: Gh.H, Gh.He, Gh.Li, and so on. Optionally it may be appended by .text, where text is any string (not containing delimiters). Examples: Gh.H, Gh.Mn.3, Gh.Cu.dznew.
See also the Basis set superposition error (BSSE) tutorial.
For other alternative elements, for instance that have a noninteger nuclear charge, one should use one of the standard chemical symbols.
The BASIS
key will use this chemical symbol for selecting the basis set for this alternative element.
Nuclear charges are specified by adding the nuclear charge at the end of the atom’s line (adf.nuclear_charge=).
You can create Ghtype basic atoms and other alternative elements and use them subsequently as fragments in a molecule.
Automatic mode¶
AMS allows to set userdefined masses for particular atoms. This can be used to simulate isotopes of different atoms. Masses are specified by adding the desired mass (in Dalton) at the end of the atom’s line.
Example: three different hydrogen isotopes:
System
Atoms
N 0.000000 0.000000 0.010272
H 0.471582 0.816803 0.407861
H 0.943163 0.000000 0.407861 mass=2.014101778
H 0.471582 0.816803 0.407861 mass=3.01604927
End
End
Use as fragment
Alternative basic atoms can be used like any other basic atoms to build up larger fragments and molecules. Gh can be considered just one more chemical symbol along with the other traditional ones. For other alternative elements one should define the nuclear charge, and possibly the nuclear mass.
You may have different alternative elements in a molecule, with different nuclear charges for instance.
Example: ghost atoms:
System
atoms
Gh.O 0.525330 0.050971 0.314517
Gh.H 0.942007 0.747902 0.011253
Gh.H 0.403697 0.059786 0.073568
O 2.316633 0.045501 0.071858
H 2.684616 0.526577 0.749387
C 2.781638 0.426129 1.190301
H 2.350821 0.224965 1.943415
H 3.867602 0.375336 1.264613
H 2.453296 1.445999 1.389381
end
end
Example: alternative elements:
System
Atoms
Mg 0.0 0.0 0.0
F 1.0 1.0 1.0 adf.nuclear_charge=9.5
F 1.0 1.0 1.0 adf.nuclear_charge=9.5
F 1.0 1.0 1.0 adf.nuclear_charge=9.5
F 1.0 1.0 1.0 adf.nuclear_charge=9.5
End
End
Nuclear Model¶
By default in ADF a point charge model is used for the nuclear charge distribution. Alternatively, one can use a spherical Gaussian nuclear charge distribution model, see Ref. [8]. Nuclear finite size effects can have large effects on hyperfine interactions (ESR Atensor, NMR spinspin coupling) if heavy atoms like, for example, Mercury (Hg), are involved. In Ref. [8] it was asserted that the isotropic Jcouplings (parameters in NMR spinspin coupling) are typically reduced in magnitude by about 10 to 15 % for couplings between one of the heaviest NMR nuclei and a light atomic ligand, and even more so for couplings between two heavy atoms. This Ref. [8] gives more details on the parameters used in the Gaussian nuclear charge distribution model. Note that one needs basis sets with very tight functions to see any effect of using a finite size of the nucleus instead of a point nucleus. Such basis sets can be found for all elements in $AMSRESOURCES/ZORA/TZ2PJ
and $AMSRESOURCES/ZORA/QZ4PJ
, and for some elements in $AMSRESOURCES/ZORA/jcpl
, which are basis sets especially designed for ESR hyperfine and NMR spinspin coupling calculations.
NuclearModel [PointCharge  Gaussian]
NuclearModel
Type: Multiple Choice Default value: PointCharge Options: [PointCharge, Gaussian] Description: Model for the nuclear charge distribution. To see effects from your choice you will need to use a basis set with extra steep functions. For example you can find these in the ZORA/TZ2PJ basis directory.
In the ADF output parameters will be shown for the Gaussian nuclear charge distribution if one includes in the input for ADF:
PRINT Nuclei
Starting from ADF2013 ADF also uses a finite distribution of the nuclear magnetic dipole moment for the calculation of the Atensor.
References
[1]  E. Clementi, C. Roetti, RoothaanHartreeFock atomic wavefunctions: Basis functions and their coefficients for ground and certain excited states of neutral and ionized atoms, Z \(\leq\) 54, Atomic Data and Nuclear Data Tables 14, 177 (1974) 
[2]  A.D. McLean, R.S. McLean, RoothaanHartreeFock atomic wave functions Slater basisset expansions for Z = 5592, Atomic Data and Nuclear Data Tables 26, 197 (1981) 
[3]  J.G. Snijders, P. Vernooijs, E.J. Baerends, RoothaanHartreeFockSlater atomic wave functions: Singlezeta, doublezeta, and extended Slatertype basis sets for _{87} Fr_{103} Lr, Atomic Data and Nuclear Data Tables 26, 483 (1981) 
[4]  R.C. Raffenetti, Eventempered atomic orbitals. II. Atomic SCF wavefunctions in terms of eventempered exponential bases, Journal of Chemical Physics 59, 5936 (1973) 
[5]  D.P. Chong, Completeness profiles of oneelectron basis sets, Canadian Journal of Chemistry 73, 79 (1995) 
[6]  G.D. Zeiss, W.R. Scott, N. Suzuki, D.P. Chong, S.R. Langhoff, Finitefield calculations of molecular polarizabilities using fieldinduced polarization functions: second and thirdorder perturbation correlation corrections to the coupled HartreeFock polarizability of H_{2} O, Molecular Physics 37, 1543 (1979) 
[7]  E.J. Baerends, D.E. Ellis and P. Ros, Selfconsistent molecular HartreeFockSlater calculations I. The computational procedure, Chemical Physics 2, 41 (1973) 
[8]  (1, 2, 3) J. Autschbach, Magnitude of FiniteNucleusSize Effects in Relativistic Density Functional Computations of Indirect NMR Nuclear SpinSpin Coupling Constants, ChemPhysChem 10, 2274 (2009) 