2.2. Input of Coordinates¶
Coordinates can be either specified directly in the input file or read from an external file, and they can be in either Cartesian (“xyz”) or internal coordinate format (“Z-matrix”).
2.2.1. Reading coordinates from the input file¶
The easiest way to specify coordinates in the input file is by including a block like the following, enclosed by star symbols:
* CType Charge Multiplicity
...
coordinate specifications
...
*
Here CType can be one of xyz, int (or internal), or gzmt,
which correspond to Cartesian coordinates, internal coordinates, and
internal coordinates in Gaussian Z-matrix format.
The input of Cartesian coordinates in the “xyz” option is
straightforward. Each line consists of the label for a given atom type
and three numbers that specify the coordinates of the atom. The units
can be either Ångström (default) or Bohr.
This can be specified via the simple keywords !Angs or !Bohrs, respectively,
or via the variable Units in the %coords block described below.
* xyz Charge Multiplicity
Atom1 x1 y1 z1
Atom2 x2 y2 z2
...
*
For example for CO\(^+\) in a \(S=1/2\) state (multiplicity = \(2\times1/2+1=2\))
* xyz 1 2
C 0.0 0.0 0.0
O 0.0 0.0 1.1105
*
Internal coordinates are specified in the form of the familiar “Z-matrix”. A Z-matrix basically contains information about molecular connectivity, bond lengths, bond angles and dihedral angles. The program then constructs Cartesian coordinates from this information. Both sets of coordinates are printed in the output such that conversion between formats is facilitated. The input in that case looks like:
* int Charge Multiplicity
Atom1 0 0 0 0.0 0.0 0.0
Atom2 1 0 0 R1 0.0 0.0
Atom3 1 2 0 R2 A1 0.0
Atom4 1 2 3 R3 A2 D1
. . .
AtomN NA NB NC RN AN DN
*
The rules for connectivity in the “internal” mode are as follows:
NA: The atom that the actual atom has a distance (RN) with.NB: The actual atom has an angle (AN) with atomsNAandNB.NC: The actual atom has a dihedral angle (DN) with atomsNA,NBandNC. This is the angle between the actual atom and atomNCwhen looking down theNA-NBaxis.Note that - contrary to other parts in ORCA - atoms are counted starting from 1.
Angles are always given in degrees! The rules are compatible with those used in the well known MOPAC and ADF programs.
Finally, gzmt specifies internal coordinates in the format used by the
Gaussian program. This resembles the following:
* gzmt 0 1
C
O 1 4.454280
Si 2 1.612138 1 56.446186
O 3 1.652560 2 114.631525 1 -73.696925
C 4 1.367361 3 123.895399 2 -110.635060
...
*
An alternative way to specify coordinates in the input file is through
the use of the %coords block, which is organized as follows:
%coords
CTyp xyz # the type of coordinates = xyz or internal
Charge 0 # the total charge of the molecule
Mult 2 # the multiplicity = 2S+1
Units Angs # the unit of length = angs or bohrs
# the subblock coords is for the actual coordinates
# for CTyp=xyz
coords
Atom1 x1 y1 z1
Atom2 x2 y2 z2
end
# for CTyp=internal
coords
Atom1 0 0 0 0.0 0.0 0.0
Atom2 1 0 0 R1 0.0 0.0
Atom3 1 2 0 R2 A1 0.0
Atom4 1 2 3 R3 A2 D1
. . .
AtomN NA NB NC RN AN DN
end
end
Important
Since ORCA is a C++ based program its internal counting starts from zero. Therefore all electrons, atoms, frequencies, orbitals, excitation energies etc. are counted from zero. User-based counting such as the numeration of fragments is counted from one.
2.2.2. Reading coordinates from external files¶
It is also possible to read the coordinates from external files. The
most common format is a .xyz file, which can in principle contain more
than one structure (see section
Multiple XYZ File Scans for this multiple XYZ
feature):
* xyzfile Charge Multiplicity Filename
For example:
* xyzfile 1 2 mycoords.xyz
A lot of graphical tools like Gabedit, molden or Jmol can write Gaussian
Z-Matrices (.gzmt). ORCA can also read them from an external file with
the following
* gzmtfile 1 2 mycoords.gzmt
Note that if multiple jobs are specified in the same input file then new jobs can read the coordinates from previous jobs. If no filename is given as fourth argument then the name of the actual job is automatically used.
... specification for the first job
$new_job
! keywords
* xyzfile 1 2
In this way, optimization and single point jobs can be very conveniently combined in a single, simple input file. Examples are provided in the following sections.
2.2.3. Special definitions¶
Dummy atoms are defined in exactly the same way as any other atom, by using “DA”, “X”, or “Xx” as the atomic symbol.
Ghost atoms are specified by adding “:” right after the symbol of the element (see Counterpoise Corrections).
Point charges are specified with the symbol “Q”, followed by the charge (see Inclusion of Point Charges).
Embedding potentials are specified by adding a “>” right after the symbol of the element (see ECP Embedding).
Non-standard isotopes or nuclear charges are specified with the statements “
M =…” and “Z =…”, respectively, after the atomic coordinate definition.Note
The nuclear charge can adopt non-integer values
When the nuclear charge is modified throughca “
Z =…” statement, the total charge of the system should still be calculated based on the unmodified charge. For example, for a calculation of a single hydrogen atom whoseZis set to 1.5, a charge of 0 and a spin multiplicity of 2 should be entered into the charge and multiplicity sections of the input file, despite that the actual total charge is 0.5.
Fragments can be conveniently defined by declaring the fragment number a given atom belongs to in parentheses “
(n)” following the element symbol (see Fragment Specification).
2.2.4. Defining Geometry Parameters and Scanning Potential Energy Surfaces¶
ORCA lets you define the coordinates of all atoms as functions of user
defined geometry parameters. By giving not only a value but a range of
values (or a list of values) to this parameters potential energy
surfaces can be scanned. In this case the variable RunTyp is
automatically changed to Scan. The format for the parameter
specification is straightforward:
%coords
CTyp internal
Charge 0
Mult 1
pardef
rCH = 1.09; # a C-H distance
ACOH = 120.0; # a C-O-H angle
rCO = 1.35, 1.10, 26; # a C-O distance that will be scanned
end
coords
C 0 0 0 0 0 0
O 1 0 0 {rCO} 0 0
H 1 2 0 {rCH} {ACOH} 0
H 1 2 3 {rCH} {ACOH} 180
end
end
In the example above the geometry of formaldehyde is defined in internal
coordinates (the geometry functions work exactly the same way with
Cartesian coordinates). Each geometric parameter can be assigned as a
function of by enclosing an expression within function braces, “{} “.
For example, a function may look like *cos(Theta)*rML+R. Note that all
trigonometric functions expect their arguments to be in degrees and not
radians. The geometry parameters are expected to be defined such that
the lengths come out in Ångströms and the angles in degrees. After
evaluating the functions, the coordinates will be converted to atomic
units. In the example above, the variable rCO was defined as a “Scan
parameter”. Its value will be changed in 26 steps from 1.3 Å down to 1.1
Å and at each point a single point calculation will be done. At the end
of the run the program will summarize the total energy at each point.
This information can then be copied into the spreadsheet of a graphics
program and the potential energy surface can be plotted. Up to three
parameters can be scan parameters. In this way grids or cubes of energy
(or property) values as a function of geometry can be constructed.
If you want to define a parameter at a series of values rather than evenly spaced intervals, the following syntax is to be used:
%coords
CTyp internal
Charge 0
Mult 1
pardef
rCH = 1.09; # a C-H distance
ACOH= 120.0; # a C-O-H angle
rCO [1.3 1.25 1.22 1.20 1.18 1.15 1.10]; # a C-O distance that will be scanned
end
coords
C 0 0 0 0 0 0
O 1 0 0 {rCO} 0 0
H 1 2 0 {rCH} {ACOH} 0
H 1 2 3 {rCH} {ACOH} 180
end
end
In this example the C-O distance is changed in seven non-equidistant steps. This can be used in order to provide more points close to a minimum or maximum and fewer points at less interesting parts of the surface.
A special feature has also been implemented into ORCA - the parameters themselves can be made functions of the other parameters as in the following (nonsense) example:
%coords
CTyp internal
Charge 0
Mult 1
pardef
rCOHalf= 0.6;
rCO = { 2.0*rCOHalf };
end
coords
C 0 0 0 0 0 0
O 1 0 0 {rCO} 0 0
O 1 0 0 {rCO} 180 0
end
end
In this example the parameter rCO is computed from the parameter
rCOHalf. In general the geometry is computed (assuming a Scan
calculation) by:
(a) incrementing the value of the parameter to be
scanned
(b) evaluating the functions that assign values to parameters,
and
(c) evaluating functions that assign values to geometrical
variables.
Although it is not mandatory, it is good practice to first define the static or scan-parameters and then define the parameters that are functions of these parameters.
Finally, ORCA has some special features that may help to reduce the computational effort for surface scans:
%method
SwitchToSOSCF true # switches the converger to SOSCF
# after the first point. SOSCF may
# converge better than DIIS if the
# starting orbitals are good.
# default = false
ReducePrint true # reduce printout after the first point
# default=true
# The initial guess can be changed after the first point.
# The default is MORead. The MOs of the previous point will,
# in many cases, be a very good guess for the next point.
# However, in some cases you may want to be more conservative
# and use a general guess.
ScanGuess OneElec # the one-electron matrix
Hueckel # the extended Hueckel guess
PAtom # the PAtom guess
PModel # the PModel guess
MORead # MOs of the previous point
end
Note
You can scan along normal modes of a Hessian using the
NMScanfeature as described in section Normal Mode Scan Calculations Between Different Structures.The surface scan options are also supported in conjunction with TD-DFT/CIS or MR-CI calculations (see section Potential Energy Surface Scans).
2.2.5. Mixing internal and Cartesian coordinates¶
In some cases it may be practical to define some atomic positions in
Cartesian and some in internal coordinates. This can be achieved by
specifying all coordinates in the *int block: using “0 0 0” as
reference atoms indicates Cartesian coordinates. Note that for the first
atom the flags are “1 1 1”, as “0 0 0” would be the normal values for
internal coordinates. Consider, for example, the relaxed surface scan
from section
Theory, where the methyl
group is given first in an arbitrary Cartesian reference frame and then
the water molecule is specified in internal coordinates:
! UKS B3LYP SV(P) TightSCF Opt SlowConv
%geom scan B 4 0 = 2.0, 1.0, 15 end end
* int 0 2
# First atom - reference atoms 1,1,1 mean Cartesian coordinates
C 1 1 1 -0.865590 1.240463 -2.026957
# Next atoms - reference atoms 0,0,0 mean Cartesian coordinates
H 0 0 0 -1.141534 2.296757 -1.931942
H 0 0 0 -1.135059 0.703085 -2.943344
H 0 0 0 -0.607842 0.670110 -1.127819
# Actual internal coordinates
H 1 2 3 1.999962 100.445 96.050
O 5 1 2 0.984205 164.404 27.073
H 6 5 1 0.972562 103.807 10.843
*
Internal and Cartesian coordinates can thus be mixed in any order but it is recommended that the first 3 atoms are specified in Cartesian coordinates in order to define a unique reference frame.
2.2.6. Inclusion of Point Charges¶
In some situations it is desirable to add point charges to the system. In ORCA there are two mechanisms to add point-charges. If you only want to add a few point charges you can “mask” them as atoms as in the following (nonsense) input:
# A water dimer
! BP86 def2-SVP
* xyz 0 1
O 1.4190 0.0000 0.0597
H 1.6119 0.0000 -0.8763
H 0.4450 0.0000 0.0898
Q -0.834 -1.3130 0.0000 -0.0310
Q 0.417 -1.8700 0.7570 0.1651
Q 0.417 -1.8700 -0.7570 0.1651
*
Here the “Q“‘s define the atoms as point charges. The next four numbers are the magnitude of the point charge and its position. The program will then treat the point charges as atoms with no basis functions and nuclear charges equal to the “Q” values.
If you have thousands of point charges to treat, as in a QM/MM calculation, it is more convenient, and actually necessary, to read the point charges from an external file as in the following example:
# A water dimer
! BP86 def2-SVP
% pointcharges "pointcharges.pc"
* xyz 0 1
O 1.4190 0.0000 0.0597
H 1.6119 0.0000 -0.8763
H 0.4450 0.0000 0.0898
*
The program will now read the file “pointcharges.pc” that contains the
point-charge information and then call the module orca_pc which adds
the point charge contribution to the one-electron matrix and the nuclear
repulsion. The file “pointcharges.pc” is a simple ASCII file in the
following format:
3
-0.834 -1.3130 0.0000 -0.0310
0.417 -1.8700 0.7570 0.1651
0.417 -1.8700 -0.7570 0.1651
The first line gives the number of point charges. Each consecutive line
gives the magnitude of the point charge (in atomic units) and its
position (in Ångström units!). However, it should be noted that ORCA
treats point charges from an external file differently than “Q” atoms.
When using an external point charge file, the interaction between the
point charges is not included in the nuclear energy. This behavior
originates from QM/MM, where the interactions among the point charges is
done by the MM program. These programs typically use an external point
charge file when generating the ORCA input. To add the interaction of
the point charges to the nuclear energy, the DoEQ keyword is used
either in the simple input or the %method block as shown below.
# A non QM/MM pointcharge calculation
! DoEQ
%pointcharges "pointcharges.pc"
%method
DoEQ true
end
Warning
The DoEQ keyword has no effect for semi-empirical calculations (e.g., AM1)!