KJM5610 exercises week 8

The purpose of this exercise is to get introduced to the quantum chemistry package DALTON, and get acquainted with some useful commands in UNIX. To learn more about the intrinsic UNIX-commands mentined below, you may use the man command, by typing man command. 1. For chemical systems the potential energy surface (PES) describes the energy as a function of the geometrical coordinates describing the system. For a diatomic system the PES depends solely on the interatomic distance between the two atoms. In this exercise we will plot the PES of H2 , and nd the equilibrium bond length. (a) Start by downloading the two les energy.dal and H2.mol from the course homepages, and move the les into a directory of your choice. In that directory you can run a calculation by typing: > dalton energy H2 and you will create an output-le with the name energy H2.out. Run dalton dalton daltonle moleculele Have a look at the output-le in a text editor. By searching for Total energy CCSD(T) you should nd the value -1.0204550049 a.u., which is the single point energy of this particular calculation. (b) Now have a look at the moleculele H2.mol : BASIS cc-pVTZ H2-molecule. Task: determine the bond-distance by plotting the potential energy surface. 1 0 A 1.0 2 H 0.000000000 0.000000000 0.000000000 H 2.000000000 0.000000000 0.000000000 The rst line BASIS species that we will read a (predined)basis from a le, and the second line species the name of this basis. The third and fourth lines are simply comment-lines which are not used by the progam. The fth line species that we have only one atomic type, that we will not use symmertry (the zero) and that we type our coordinates in Angstrom. The sixth line species that our atomtype has a nuclear charge of one, and that we have two such atoms. The 1

last two lines species the cartesian coordinates of the H2 molecule. NOTE: DALTON is extremly sensitive to the positioning of the different speciers. For example the specier indicating that we have one atomic type must be the fth character on the fth line! You should now create moleculeles with dierent interatomic distances; in the range 0.4 to 3.0 Angstrom. You may do this by manually changing the rst coordinate of the second hydrogen atom from 2 to say 0.4 in the text editor, and then save the le as for example H2 04.mol. However, in order to make many such les in the whole range, it is much easier to use a UNIX-command named sed. Type the following: > sed -e s/2\.0/0\.4/g H2.mol > H2_04.mol to create a le H2 04.mol which is equal to H2.mol except that all instances of 2.0 has been exchanged with 0.4. Check that this is indeed the case, and create multiple les to cover the PES in the range from 0.4 to 3.0 Angstrom. SED (search and replace) sed -e s/old/new/g oldle > newle NOTE: some characters, like ., *, and , have special meaning and to search for them specically you must use backslash in front, \., \* and \. (c) Run DALTON for all the dierent moleculeles, and plot the energy as a function of the interatomic distance. What is the equlibrium bonddistance? Here you may wish to search for the Total energy CCSD(T) in multiple output-les at once. The UNIX-command grep is useful when searching for text-strings in one or more les. If you type the following: > grep -i total energy ccsd(t) energy_H2_04.out youll nd both matches of Total energy CCSD(T), in the le energy H2 04.out. To do the same for all les starting with energy H2 and ending with .out type: > grep -i total energy ccsd(t) energy_H2_*.out GREP grep -options text les(s) NOTE: also here some characters have special meaning. 2

(d) Download the dalton-le optimize.dal from the web pages of this course, and run any one of the H2 molecule-les of your choice. The optimize.dal species that DALTON should search for minima on the PES. For diatomic systems, there is only one minima. What is the energy of this minima, and what is the equlibrium bond-distance? 2. In this exercise we will nd both a minima and a saddelpoint on the PES of water. (a) Create a molecule input-le for water (make sure that it is not linear), and run a geometry-optimization on it. This takes about 15 minutes. What is the bond-distances, the bond angle and the energy? (b) If you start out with a linear water-molecule the molecule will remain linear throughout the calculation, and you will end up at a saddlepoint. Create a linear water-molecule, and run an optimization with the optimize linear.dal. What is the bond angle and energy? (c) How much energy does it take to invert water? 3. In this exercise the purpose it to get introduced to the dalton-input le. When we run our geometry optimization the le (optimize.dal ) looks like this: **DALTON INPUT .OPTIMIZE **INTEGRAL .DIPLEN .DEROVL .DERHAM **WAVEFUNCTION .CC *CC INPUT .MP2 .CCSD .CC(T) **END OF DALTON INPUT The .OPTIMIZE keyword species that we will run a geometry optimization, and it has to be put under the **DALTON INPUT section. Under the **INTEGRALS section we specify some integrals needed to calculate an optimized Coupled Cluster (CC) geometry. Under the **WAVEFUNTION section we specify that we will run with a Coupled Cluster wavefuntion with single and double amplitudes, and with the tripples included in a perturbative manner, i.e. a CCSD(T) calculation. 3

If you are not acquainted with DALTON or quantum chemical methods this probably does not make much sense. We will not go into the dierent quantum chemical method in this exercise, and will continue to use CCSD(T) (which is considered an accurate method). In order to nd out how to run dierent types of calculations one should consult the DALTON manual. From the DALTON web-pages: http://www.kjemi.uio.no/software/dalton

you can download the DALTON manual (for DALTON 2.0). (a) Download the DALTON manual, and nd out how to calculate the dipole moment. Calculate the dipole moment for H2 and water at their optimized geometry at CCSD(T) level of theory. Are the results as expected? (b) Calculate the rst excited state energy of H2 . What wavelenght would a de-exitation from the rst excited state to the ground state correspond to? (c) Calculate the vibrational frequencies for H2 .