(sec:coords.detailed)= # More on Coordinate Input We will now enter the detailed discussion of the features of ORCA. Note that some examples are still written in the "old syntax" but there is no need for the user to adopt that old syntax. The new syntax works as well. (sec:coords.fragment.detailed)= ## Fragment Specification The atoms in the molecule can be assigned to certain *fragments*. This helps to organize the output in the population analysis section, is used for the fragment optimization feature, for the local energy decomposition and for multi-level calculations. There are two options to assign atoms to fragments. The first option is to assign a given atom to a given fragment by putting a `(n) ` directly after the atomic symbol. Fragment enumeration starts with fragment 1! ```orca %coords CTyp xyz # the type of coordinates xyz or internal Charge -2 # the total charge of the molecule Mult 2 # the multiplicity = 2S+1 coords Cu(1) 0 0 0 Cl(2) 2.25 0 0 Cl(2) -2.25 0 0 Cl(2) 0 2.25 0 Cl(2) 0 -2.25 0 end end ``` In this example the fragment feature is used to divide the molecule into a "metal" and a "ligand" fragment and consequently the program will print the metal and ligand characters contained in each MO in the population analysis section. Alternatively you can assign atoms to fragments in the geom block: ```orca *xyz -2 2 Cu 0 0 0 Cl 2.25 0 0 Cl -2.25 0 0 Cl 0 2.25 0 Cl 0 -2.25 0 * %geom Fragments 1 {0} end # atom 0 for fragment 1 2 {1:4} end # atoms 1 to 4 for fragment 2 end end ``` :::{Note} - With the second option (geom-fragments) the %geom block has to be written after the coordinate section. - geom-fragments also works with coordinates that are defined via an external file. - For the geom-fragments option the atoms are assigned to fragment 1 if no assignment is given. ::: (sec:coords.geom.para.detailed)= ## 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:tddft.compute.normalModeScan.detailed`. - The surface scan options are also supported in conjunction with TD-DFT/CIS or MR-CI calculations (see section {ref}`sec:tddft.compute.surfaceScan.detailed`). ::: (sec:coords.mixed.detailed)= ## 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:optimization.relaxedsurface.typical`, 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:coords.pointcharges.detailed)= ## 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 ```