benzen_structure_optimization
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benzen_structure_optimization [2009/11/24 15:00] jelen |
benzen_structure_optimization [2018/03/08 15:44] (current) |
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| - | Here we describe how to perform structure optimization of a simple molecule using new version of Fireball. | + | Here we describe how to perform structure optimization of a simple molecule using the new version of the Fireball code. |
| - | These are minimal steps required to optimize atomic structure using quenching optimization method: | + | There are minimal steps required to optimize atomic structure using quenching optimization method: |
| Line 9: | Line 9: | ||
| An initial configuration is written in a file with an arbitrary name (e.g. //initial.bas//, see text bellow) | An initial configuration is written in a file with an arbitrary name (e.g. //initial.bas//, see text bellow) | ||
| - | 12 | + | 12 |
| - | 6 -4.183081 -4.008593 -0.000092 | + | 6 -4.192725 -3.947918 -0.000885 |
| - | 6 -3.047805 -3.090020 0.004490 | + | 6 -3.105518 -3.068150 0.003445 |
| - | 6 -3.275844 -1.647830 0.001899 | + | 6 -3.324254 -1.686900 0.002294 |
| - | 6 -4.639523 -1.125588 0.002371 | + | 6 -4.629983 -1.185844 0.001786 |
| - | 6 -5.775305 -2.043508 0.000193 | + | 6 -5.717209 -2.065606 -0.001295 |
| - | 6 -5.546619 -3.485699 -0.007522 | + | 6 -5.498437 -3.446870 -0.005502 |
| - | 1 -6.432266 -4.204789 -0.015592 | + | 1 -6.367512 -4.151865 -0.010025 |
| - | 1 -4.005535 -5.135519 -0.000976 | + | 1 -4.018424 -5.053386 -0.000752 |
| - | 1 -1.983459 -3.500264 0.005183 | + | 1 -2.061162 -3.470265 0.006507 |
| - | 1 -2.389446 -0.929457 -0.002861 | + | 1 -2.455303 -0.981710 0.003944 |
| - | 1 -4.816925 0.001517 -0.000293 | + | 1 -4.804199 -0.080387 0.004380 |
| - | 1 -6.839935 -1.633156 -0.001403 | + | 1 -6.761568 -1.663453 -0.002176 |
| - | + | ||
| Line 64: | Line 62: | ||
| ln -s $CURRENT_DIR_Fdata Fdata | ln -s $CURRENT_DIR_Fdata Fdata | ||
| + | or we add the path in fireball.in file: | ||
| + | |||
| + | |||
| + | &OPTION | ||
| + | basisfile = initial.bas | ||
| + | nstepf = 5000 | ||
| + | iquench = -1 | ||
| + | icluster = 1 | ||
| + | iqout = 3 | ||
| + | dt = 0.5 | ||
| + | fdataLocation = '$CURRENT_DIR_Fdata' | ||
| + | &END | ||
| + | &OUTPUT | ||
| + | iwrtxyz = 1 | ||
| + | &END | ||
| ===== run optimization process ===== | ===== run optimization process ===== | ||
| Line 137: | Line 150: | ||
| - | {{:benzen:etot_benzen.png|}} | + | {{:benzen:etot_benzen.png?700|}} |
| Line 144: | Line 157: | ||
| Current optimized structure is placed in **''answer.bas''** file and it can be directly used as input file for a next run. | Current optimized structure is placed in **''answer.bas''** file and it can be directly used as input file for a next run. | ||
| + | 12 | ||
| + | 6 -4.183507 -4.005641 -0.001142 | ||
| + | 6 -3.050800 -3.089167 0.003179 | ||
| + | 6 -3.278833 -1.650218 0.003065 | ||
| + | 6 -4.639215 -1.128095 0.001770 | ||
| + | 6 -5.771898 -2.044592 -0.001875 | ||
| + | 6 -5.543886 -3.483549 -0.004966 | ||
| + | 1 -6.427498 -4.200469 -0.008348 | ||
| + | 1 -4.006604 -5.129725 -0.002273 | ||
| + | 1 -1.988933 -3.498117 0.005219 | ||
| + | 1 -2.395194 -0.933283 0.005850 | ||
| + | 1 -4.815981 -0.004012 0.002952 | ||
| + | 1 -6.833808 -1.635777 -0.003761 | ||
| + | |||
| + | Each atomic configuration achieved during the optimization procedure is recorded into the **''answer.xyz''** file. The history can be visualized by e.g. [[http://jmol.sourceforge.net/|Jmol]] program. | ||
| + | |||
| + | {{:benzen:benzen_opt.png?700|benzene}} | ||
| - | 12 | ||
| - | 6 -4.183421 -4.006572 -0.000382 | ||
| - | 6 -3.049741 -3.089443 0.004202 | ||
| - | 6 -3.277656 -1.649257 0.001957 | ||
| - | 6 -4.639330 -1.127297 0.002109 | ||
| - | 6 -5.773138 -2.044253 -0.000364 | ||
| - | 6 -5.544980 -3.484420 -0.006813 | ||
| - | 1 -6.429495 -4.202168 -0.013594 | ||
| - | 1 -4.005512 -5.131722 -0.001362 | ||
| - | 1 -1.986751 -3.498702 0.006074 | ||
| - | 1 -2.392519 -0.932155 -0.000013 | ||
| - | 1 -4.815967 -0.001880 0.002503 | ||
| - | 1 -6.836271 -1.634989 -0.002052 | ||
| In addition, there is a file **''CHARGES''** which contains projected Lowdin charges onto individual shells. | In addition, there is a file **''CHARGES''** which contains projected Lowdin charges onto individual shells. | ||
| - | 12 c6h6.bas 1 | + | 12 initial0.bas 3 |
| - | 0.99538890 3.10407153 | + | 0.99704005 3.10168254 |
| - | 0.99534701 3.10417360 | + | 0.99692942 3.10180981 |
| - | 0.99539011 3.10410887 | + | 0.99697651 3.10173483 |
| - | 0.99538154 3.10398977 | + | 0.99702943 3.10168959 |
| - | 0.99535394 3.10408536 | + | 0.99693536 3.10181070 |
| - | 0.99536810 3.10408846 | + | 0.99696818 3.10179334 |
| - | 0.88948727 0.01101221 | + | 0.89726521 0.00398424 |
| - | 0.88959544 0.01102157 | + | 0.89733723 0.00398285 |
| - | 0.88948600 0.01101498 | + | 0.89723911 0.00398370 |
| - | 0.88949241 0.01100765 | + | 0.89728961 0.00398349 |
| - | 0.88961717 0.01102288 | + | 0.89731948 0.00398339 |
| - | 0.88948823 0.01100698 | + | 0.89724802 0.00398392 |
benzen_structure_optimization.1259071256.txt.gz · Last modified: 2011/02/18 13:14 (external edit)
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