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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 
    
benzen_structure_optimization.1259069660.txt.gz · Last modified: 2011/02/18 13:14 (external edit)

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