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benzen_structure_optimization [2009/11/24 14:34] 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 37: | Line 35: | ||
iquench = -1 | iquench = -1 | ||
icluster = 1 | icluster = 1 | ||
+ | iqout = 3 | ||
dt = 0.5 | dt = 0.5 | ||
&END | &END | ||
Line 63: | 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 87: | Line 101: | ||
You'll obtain on your screen comprehensive information how close optimization criteria are to used convergence tolerance:\\ | You'll obtain on your screen comprehensive information how close optimization criteria are to used convergence tolerance:\\ | ||
+ | |||
- | ++++ iter = 31 Etot= -83.90490326 Fi_max= 0.049773 | + | .... |
- | +++ Etot RES = 0.00044855 TOL = 0.00010000 NOT CONVERGED | + | |
- | +++ Fmax RES = 0.04977333 TOL = 0.05000000 CONVERGED | + | ++++ iter = 46 Etot= -83.90303173 Fi_max= 0.074447 |
- | ++++ iter = 32 Etot= -83.90475702 Fi_max= 0.037080 | + | +++ Etot RES = 0.00189182 TOL = 0.00010000 NOT CONVERGED |
- | +++ Etot RES = 0.00175489 TOL = 0.00010000 NOT CONVERGED | + | +++ Fmax RES = 0.07444720 TOL = 0.05000000 NOT CONVERGED |
- | +++ Fmax RES = 0.03707963 TOL = 0.05000000 CONVERGED | + | ++++ iter = 47 Etot= -83.90304323 Fi_max= 0.071943 |
- | ++++ iter = 33 Etot= -83.90472022 Fi_max= 0.025251 | + | +++ Etot RES = 0.00013796 TOL = 0.00010000 NOT CONVERGED |
- | +++ Etot RES = 0.00044161 TOL = 0.00010000 NOT CONVERGED | + | +++ Fmax RES = 0.07194256 TOL = 0.05000000 NOT CONVERGED |
- | +++ Fmax RES = 0.02525064 TOL = 0.05000000 CONVERGED | + | ++++ iter = 48 Etot= -83.90307246 Fi_max= 0.065520 |
- | ++++ iter = 34 Etot= -83.90468896 Fi_max= 0.025764 | + | +++ Etot RES = 0.00035078 TOL = 0.00010000 NOT CONVERGED |
- | +++ Etot RES = 0.00037510 TOL = 0.00010000 NOT CONVERGED | + | +++ Fmax RES = 0.06552009 TOL = 0.05000000 NOT CONVERGED |
- | +++ Fmax RES = 0.02576449 TOL = 0.05000000 CONVERGED | + | ++++ iter = 49 Etot= -83.90322186 Fi_max= 0.053999 |
- | ++++ iter = 35 Etot= -83.90457769 Fi_max= 0.031889 | + | +++ Etot RES = 0.00179281 TOL = 0.00010000 NOT CONVERGED |
- | +++ Etot RES = 0.00133533 TOL = 0.00010000 NOT CONVERGED | + | +++ Fmax RES = 0.05399895 TOL = 0.05000000 NOT CONVERGED |
- | +++ Fmax RES = 0.03188856 TOL = 0.05000000 CONVERGED | + | ++++ iter = 50 Etot= -83.90327990 Fi_max= 0.040755 |
- | ++++ iter = 36 Etot= -83.90458419 Fi_max= 0.030593 | + | +++ Etot RES = 0.00069654 TOL = 0.00010000 NOT CONVERGED |
- | +++ Etot RES = 0.00007808 TOL = 0.00010000 CONVERGED | + | +++ Fmax RES = 0.04075507 TOL = 0.05000000 CONVERGED |
- | +++ Fmax RES = 0.03059333 TOL = 0.05000000 CONVERGED | + | ++++ iter = 51 Etot= -83.90347863 Fi_max= 0.024827 |
+ | +++ Etot RES = 0.00238468 TOL = 0.00010000 NOT CONVERGED | ||
+ | +++ Fmax RES = 0.02482667 TOL = 0.05000000 CONVERGED | ||
+ | ++++ iter = 52 Etot= -83.90359903 Fi_max= 0.011633 | ||
+ | +++ Etot RES = 0.00144488 TOL = 0.00010000 NOT CONVERGED | ||
+ | +++ Fmax RES = 0.01163264 TOL = 0.05000000 CONVERGED | ||
+ | ++++ iter = 53 Etot= -83.90365698 Fi_max= 0.022778 | ||
+ | +++ Etot RES = 0.00069536 TOL = 0.00010000 NOT CONVERGED | ||
+ | +++ Fmax RES = 0.02277786 TOL = 0.05000000 CONVERGED | ||
+ | ++++ iter = 54 Etot= -83.90365157 Fi_max= 0.021744 | ||
+ | +++ Etot RES = 0.00006491 TOL = 0.00010000 CONVERGED | ||
+ | +++ Fmax RES = 0.02174432 TOL = 0.05000000 CONVERGED | ||
+++++ Quenching process converged +++++ | +++++ Quenching process converged +++++ | ||
+ | |||
History of the total energy during the optimization process can be easily plotted using [[http://www.gnuplot.info/|Gnuplot]] program as follows: | History of the total energy during the optimization process can be easily plotted using [[http://www.gnuplot.info/|Gnuplot]] program as follows: | ||
Line 116: | Line 143: | ||
gnuplot> set format y "%8.4f" | gnuplot> set format y "%8.4f" | ||
gnuplot> plot "etot.dat" with linespoints | gnuplot> plot "etot.dat" with linespoints | ||
- | | + | |
+ | optionally, we save the output into png figure format doing | ||
+ | |||
+ | gnuplot> set term png | ||
+ | gnuplot> set output "etot.png" | ||
+ | |||
+ | |||
+ | {{:benzen:etot_benzen.png?700|}} | ||
+ | | ||
===== final optimized structure & charge analysis ===== | ===== final optimized structure & charge analysis ===== | ||
Line 122: | 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 |