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--- benzen_structure_optimization [2009/11/24 15:12]
jelen
+++ benzen_structure_optimization [2018/03/08 15:44]
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-Here we describe how to  perform structure optimization of a simple molecule using new version of Fireball.
-These are minimal steps required to optimize atomic structure using quenching optimization method:
- ===== atomic structure =====
-In this particular case, we are about to optimize atomic structure of  [[http://en.wikipedia.org/wiki/Benzene|benzene]] molecule.
-An initial configuration is written in a file with an arbitrary name (e.g. //initial.bas//, see text bellow)
-     -4.192725     -3.947918     -0.000885
-     -3.105518     -3.068150      0.003445
-     -3.324254     -1.686900      0.002294
-     -4.629983     -1.185844      0.001786
-     -5.717209     -2.065606     -0.001295
-     -5.498437     -3.446870     -0.005502
-     -6.367512     -4.151865     -0.010025
-     -4.018424     -5.053386     -0.000752
-     -2.061162     -3.470265      0.006507
-     -2.455303     -0.981710      0.003944
-     -4.804199     -0.080387      0.004380
-     -6.761568     -1.663453     -0.002176
-===== input file =====
-The **''fireball.in''** input file provides control over what sort of calculation will be done. If the file is not presented, fireball run default task with predefined parameters. Complete list of all choices can be found here.
-In our particular case, **''fireball.in''** file looks like:
-  &OPTION
-  basisfile = initial.bas
-  nstepf = 5000
-  iquench = -1
-  icluster = 1
-  iqout = 3
-  dt = 0.5
-  &END
-  &OUTPUT
-  iwrtxyz = 1
-  &END
-where\\
-keyword '''basisfile''' defines name of a file with an initial atomic configuration;\\
-keyword '''nstepf''' defines the maximal number of time steps; \\
-keyword '''iquench''' sets a type of structure optimization; \\
-keyword '''icluster''' defines type of boundary conditions (here no periodicity);  \\
-keyword '''dt''' is time step in femtoseconds;  \\
-keyword '''iwrtxyz''' allows to save history of atomic trajectories during optimization proces into xyz-format output file **''answer.xyz''**
-===== Fdata =====
-To initiate Fireball run, we need to create Fdata directory in working directory, which contains all electronic integrals
-to build up Hamiltonian for each geometry. These integrals has to be calculated in advance by create module.
-Once we have these data, usually we create **//Fdata//** dir via symbolic link
-   ln -s $CURRENT_DIR_Fdata Fdata
-===== run optimization process =====
-Initiate Fireball run we need to execute binary file **//fireball.x//**. Usually we do that via shell script e.g. named //run.bat//:
-   rm -fr CHARGES *.xv *.ac *.xyz
-   $DIR_FIR/fireball.x
-to run code we simply type in command line:
-   ./run.bat > out &
-this command run fireball on background.
-===== output =====
-Status of optimization process we can follow by simple command:
-   grep "+++" out
-You'll obtain on your screen comprehensive information how close optimization criteria are to used convergence tolerance:\\
-   ....
-   ++++ iter =       46 Etot=     -83.90303173 Fi_max=       0.074447
-    +++ Etot  RES =      0.00189182  TOL =       0.00010000   NOT CONVERGED
-    +++ Fmax  RES =      0.07444720  TOL =       0.05000000   NOT CONVERGED
-   ++++ iter =       47 Etot=     -83.90304323 Fi_max=       0.071943
-    +++ Etot  RES =      0.00013796  TOL =       0.00010000   NOT CONVERGED
-    +++ Fmax  RES =      0.07194256  TOL =       0.05000000   NOT CONVERGED
-   ++++ iter =       48 Etot=     -83.90307246 Fi_max=       0.065520
-    +++ Etot  RES =      0.00035078  TOL =       0.00010000   NOT CONVERGED
-    +++ Fmax  RES =      0.06552009  TOL =       0.05000000   NOT CONVERGED
-   ++++ iter =       49 Etot=     -83.90322186 Fi_max=       0.053999
-    +++ Etot  RES =      0.00179281  TOL =       0.00010000   NOT CONVERGED
-    +++ Fmax  RES =      0.05399895  TOL =       0.05000000   NOT CONVERGED
-   ++++ iter =       50 Etot=     -83.90327990 Fi_max=       0.040755
-    +++ Etot  RES =      0.00069654  TOL =       0.00010000   NOT CONVERGED
-    +++ Fmax  RES =      0.04075507  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  +++++
-History of the total energy during the optimization process can be easily plotted using [[http://www.gnuplot.info/|Gnuplot]] program as follows:
-  grep ETOT so_sp.out | cut -b22- > etot.dat
-  gnuplot
-  gnuplot> set xlabel "time step"
-  gnuplot> set xlabel "Etot [eV]"
-  gnuplot> set format y "%8.4f"
-  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 =====
-Current optimized structure is placed in **''answer.bas''** file and it can be directly used as input file for a next run.
-     -4.183507     -4.005641     -0.001142
-     -3.050800     -3.089167      0.003179
-     -3.278833     -1.650218      0.003065
-     -4.639215     -1.128095      0.001770
-     -5.771898     -2.044592     -0.001875
-     -5.543886     -3.483549     -0.004966
-     -6.427498     -4.200469     -0.008348
-     -4.006604     -5.129725     -0.002273
-     -1.988933     -3.498117      0.005219
-     -2.395194     -0.933283      0.005850
-     -4.815981     -0.004012      0.002952
-     -6.833808     -1.635777     -0.003761
-Each atomic configuration is recorded during the optimization procedure 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}}
-In addition, there is a file **''CHARGES''** which contains projected Lowdin charges onto individual shells.
-  initial0.bas                               3
-.99704005    3.10168254
-.99692942    3.10180981
-.99697651    3.10173483
-.99702943    3.10168959
-.99693536    3.10181070
-.99696818    3.10179334
-.89726521    0.00398424
-.89733723    0.00398285
-.89723911    0.00398370
-.89728961    0.00398349
-.89731948    0.00398339
-.89724802    0.00398392

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