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## Calculating Harmonic Frequencies By Finite Differences In ParallelThe following gives a general overview for how to run harmonic frequency calculations in an efficient manner, if one is using finite differences of analytic gradients for the force constant evaluation. A typical input file for such a calculation might look like this: water The two keywords on the bottom line are the directives for the harmonic frequency calculation; the latter is the ``usual" one, and the former is that which needs to be used for this (coarse-grained) parallel approach. The procedure: 1. With a GENBAS file in place (and the ZMAT like that above), do the following. xjoda After doing this, you will find a number of files labeled zmat001, zmat002 ... zmatxxx (for this example, xxx=005) in the directory. Each of these is the input file appropriate to calculate one of the required gradients at a displaced geometry. For example, here is zmat005: Perturbed geometry 5 for parallel findif calculation 2. Run a separate job, using each of the zmatxxx files as input. The specifics of doing this, of course, depend on your local machine configuation and your predilections. The important thing, however, is to invoke the executable xja2fja after the xcfour run. This extracts the relevant parts from the JOBARC file and writes them to a formatted file called FJOBARC. Keep this file. For bookkeeping purposes, it is a good idea to name this file something like fja.xxx, where this is the relevant contents of the JOBARC file for the job associated with the input file zmatxxx. In short, something like this: cp /whatever/directory/you/areusing/zmat005 ZMAT 3. At the end, you will have fja.001, fja.002 ... fja.xxx. 4. Place the original ZMAT file, together with the fja.xxx files in a clean directory, together with an appropriate GENBAS file. Then invoke the following script: #!/bin/csh Vibrational frequencies (cm-1) : 1 1659.61804 73.02578 2 3834.88901 6.37419 Vibrational frequencies (cm-1) : 1 3958.09739 42.64690 @CHECKOUT-I, Total execution time : 0.0000 seconds. and the first part of the xjoda output is Normal Coordinate Analysis ---------------------------------------------------------------- Irreducible Harmonic Infrared Type Representation Frequency Intensity ---------------------------------------------------------------- (cm-1) (km/mol) ---------------------------------------------------------------- ---- 0.0000i 0.0000 --------- ---- 0.0000i 0.0000 --------- ---- 0.0000i 0.0000 --------- ---- 0.0000 0.0000 --------- ---- 0.0000 0.0000 --------- ---- 0.0000 0.0000 --------- A1 1659.6203 73.0258 VIBRATION A1 3834.8942 6.3742 VIBRATION B2 3958.1028 42.6469 VIBRATION ---------------------------------------------------------------- 6. If one is doing this as part of an anharmonic calculation - FD_PROJECT=OFF is necessary (and is the defaut) which disables the projection of the rotational coordinates from the displacements used. This will require that more gradients are evaluated to get the harmonic frequencies, but it is absolutely necessary to do this at a non-stationary geometry. All will proceed as above, except that the number of displaced points goes from five to eight in the present example. At the end, the xsymcor and xjoda outputs are: Vibrational frequencies (cm-1) : 1 1659.61769 73.02580 2 3834.88868 6.37419 Vibrational frequencies (cm-1) : 1 0.75341 0.00000 Vibrational frequencies (cm-1) : 1 0.65364 251.04696 Vibrational frequencies (cm-1) : 1 1.60022i 89.07105 2 3958.09722 42.64684 @CHECKOUT-I, Total execution time : 0.0000 seconds. and Normal Coordinate Analysis ---------------------------------------------------------------- Irreducible Harmonic Infrared Type Representation Frequency Intensity ---------------------------------------------------------------- (cm-1) (km/mol) ---------------------------------------------------------------- ---- 1.6002i 89.0711 ROTATION ---- 0.0000i 0.0000 TRANSLATION ---- 0.0000 0.0000 TRANSLATION ---- 0.0937 0.8736 TRANSLATION ---- 0.6881 0.0000 ROTATION ---- 0.7159 250.1733 ROTATION A1 1659.6200 73.0258 VIBRATION A1 3834.8939 6.3742 VIBRATION B2 3958.1026 42.6468 VIBRATION ---------------------------------------------------------------- respectively. The rotational frequencies are (effectively) zero, and the harmonic frequencies are (effectively) unchanged, because the geometry used in this example is the real minimum at the CCSD(T)/ANO0 (Taylor-AlmlĂ¶f valence double-zeta) level of theory. Finally, if gradients are unavailable at the desired level of theory, the procedures here can be used together with FD_CALCTYPE=ENERONLY, the only difference being that there will be (perhaps many) more displaced points, and an additional (unperturbed) point with its corresponding input file, zmat000. |

Page last modified on February 28, 2016, at 06:54 PM

CFOUR is partially supported by the U.S. National Science Foundation.