(sec:essentialelements.coordinates)= # 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"). ## 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: ```orca * 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. ```orca * xyz Charge Multiplicity Atom1 x1 y1 z1 Atom2 x2 y2 z2 ... * ``` For example for CO$^+$ in a $S=1/2$ state (multiplicity = $2\times1/2+1=2$) ```orca * 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: ```orca * 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 atoms `NA` and `NB`. - `NC`: The actual atom has a dihedral angle (`DN`) with atoms `NA`, `NB` and `NC`. This is the angle between the actual atom and atom `NC` when looking down the `NA-NB` axis. - 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: ```orca * 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: ```orca %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. ::: ## 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 {ref}`sec:structurereactivity.optimization.multiplexyz` for this multiple XYZ feature): ```orca * xyzfile Charge Multiplicity Filename ``` For example: ```orca * 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 ```orca * 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. ```orca ... 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. (sec:essentialelements.coordinates.special)= ## 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 {ref}`sec:essentialelements.counterpoise`). - **Point charges** are specified with the symbol "Q", followed by the charge (see {ref}`sec:essentialelements.coordinates.pointcharges`). - **Embedding potentials** are specified by adding a "\>" right after the symbol of the element (see {ref}`sec:essentialelements.basisset.embeddingpotentials`). - **Non-standard** isotopes or nuclear charges are specified with the statements "`M = `..." and "`Z = `...", respectively, after the atomic coordinate definition. :::{NOTE} 1. The nuclear charge can adopt non-integer values 2. 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 whose `Z` is 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 {ref}`sec:essentialelements.fragmentation`). (sec:essentialelements.coordinates.parascan)= ## 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: ```orca %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: ```orca %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: ```orca %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: ```orca %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 `NMScan` feature as described in section {ref}`sec:spectroscopyproperties.tddft.scan.normalModeScan`. - The surface scan options are also supported in conjunction with TD-DFT/CIS or MR-CI calculations (see section {ref}`sec:spectroscopyproperties.tddft.scan`). ::: (sec:essentialelements.coordinates.mixed)= ## 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 {ref}`sec:structurereactivity.optimization.relaxedsurface`, where the methyl group is given first in an arbitrary Cartesian reference frame and then the water molecule is specified in internal coordinates: ```{literalinclude} ../../orca_working_input/mixed_coords.inp :language: orca ``` 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. (sec:essentialelements.coordinates.pointcharges)= ## 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: ```{literalinclude} ../../orca_working_input/C06S01_248.inp :language: orca ``` 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: ```{literalinclude} ../../orca_working_input/C06S01_249.inp :language: orca ``` 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: ```orca 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. ```orca # 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)! :::