Table of Contents
Here we describe how to perform structure optimization of a simple molecule using the new version of the Fireball code. There 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 benzene molecule. An initial configuration is written in a file with an arbitrary name (e.g. initial.bas, see text bellow)
12 6 -4.192725 -3.947918 -0.000885 6 -3.105518 -3.068150 0.003445 6 -3.324254 -1.686900 0.002294 6 -4.629983 -1.185844 0.001786 6 -5.717209 -2.065606 -0.001295 6 -5.498437 -3.446870 -0.005502 1 -6.367512 -4.151865 -0.010025 1 -4.018424 -5.053386 -0.000752 1 -2.061162 -3.470265 0.006507 1 -2.455303 -0.981710 0.003944 1 -4.804199 -0.080387 0.004380 1 -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 $CURRENT_DIR_Fdata Fdata
or we add the path in fireball.in file:
&OPTION basisfile = initial.bas nstepf = 5000 iquench = -1 icluster = 1 iqout = 3 dt = 0.5 fdataLocation = '$CURRENT_DIR_Fdata' &END &OUTPUT iwrtxyz = 1 &END
run optimization process
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 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"
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.
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. Jmol program.
In addition, there is a file CHARGES which contains projected Lowdin charges onto individual shells.
12 initial0.bas 3
0.99704005 3.10168254
0.99692942 3.10180981
0.99697651 3.10173483
0.99702943 3.10168959
0.99693536 3.10181070
0.99696818 3.10179334
0.89726521 0.00398424
0.89733723 0.00398285
0.89723911 0.00398370
0.89728961 0.00398349
0.89731948 0.00398339
0.89724802 0.00398392