Table of Contents
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 going to optimize atomic structure of [http://en.wikipedia.org/wiki/Diarylethene Dithienylethene] molecule. Initial configuration is written in a file with an arbitrary name e.g. initial.bas
22 1 -4.9733425385 -1.5889446414 -0.6324262614 1 -3.5407118660 1.9647924939 0.0295048409 1 -1.2425048935 3.4347884406 0.1880405389 1 -0.4883657050 -0.0307476937 -1.4365138827 1 0.4883442161 -0.0307175904 1.4365127074 1 1.2424716028 3.4348261025 -0.1879964427 1 3.5407067601 1.9648329703 -0.0295429145 1 4.9733510894 -1.5889481906 0.6324807825 6 -3.2259570193 -0.1187553365 0.1227953048 6 -2.8463998459 1.1491909656 0.0196177528 6 -1.4086936247 1.3589710806 -0.0822094116 6 -0.7300575245 2.5041053928 0.0366849646 6 -0.6563976212 0.0654235722 -0.3703685714 6 0.6563995457 0.0654301045 0.3703705700 6 0.7300443321 2.5041165409 -0.0366782638 6 1.4086854525 1.3589852923 0.0821935312 6 2.8464056724 1.1492164454 -0.0196277792 6 3.2259671922 -0.1187335668 -0.1227750796 16 -1.8486925311 -1.3226946514 0.1183120883 16 1.8486919128 -1.3226609144 -0.1182720601 16 -4.9269798064 -0.6874300708 0.3778441339 16 4.9269717770 -0.6874703584 -0.3778194289
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 dt = 0.5 &END &OUTPUT iwrtxyz = 1 &END
where
keyword 'basisfile' defines name of file with an initial atomic configuration;
keyword 'nstepf' sets maximal number of time steps;
keyword 'iquench' type of structure optimization;
keyword 'icluster' defines type of boundary conditions (here no periodicity);
keyword 'dt' is time step in femtoseconds;
keyword 'iwrtxyz' allows 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 = 244 Etot= -125.75780733 Fi_max= 0.051624 +++ Etot RES = 0.00006208 TOL = 0.00010000 CONVERGED +++ Fmax RES = 0.05162403 TOL = 0.05000000 NOT CONVERGED ++++ iter = 245 Etot= -125.75783474 Fi_max= 0.050696 +++ Etot RES = 0.00060299 TOL = 0.00010000 NOT CONVERGED +++ Fmax RES = 0.05069560 TOL = 0.05000000 NOT CONVERGED ++++ iter = 246 Etot= -125.75780865 Fi_max= 0.049891 +++ Etot RES = 0.00057405 TOL = 0.00010000 NOT CONVERGED +++ Fmax RES = 0.04989075 TOL = 0.05000000 CONVERGED ++++ iter = 247 Etot= -125.75780503 Fi_max= 0.049054 +++ Etot RES = 0.00007959 TOL = 0.00010000 CONVERGED +++ Fmax RES = 0.04905359 TOL = 0.05000000 CONVERGED +++++ Quenching process converged +++++
final optimized structure
Current optimized structure is placed in answer.bas file and it can be directly used as input file for a next run.
22 1 -4.725762 -2.015808 -0.087119 1 -3.609256 1.985578 0.023008 1 -1.250107 3.495166 0.140739 1 -0.483272 -0.086442 -1.465570 1 0.482065 -0.087248 1.464818 1 1.250232 3.495031 -0.140569 1 3.608862 1.985817 -0.022156 1 4.726247 -2.015096 0.089315 6 -3.250443 -0.108624 0.117464 6 -2.866935 1.174479 -0.002012 6 -1.446633 1.401806 -0.116652 6 -0.725770 2.542664 0.011912 6 -0.661669 0.090882 -0.382848 6 0.661445 0.090614 0.382310 6 0.725933 2.542528 -0.011857 6 1.446565 1.401528 0.116997 6 2.866829 1.174498 0.002597 6 3.250469 -0.108498 -0.117342 16 -1.881528 -1.338913 0.093151 16 1.881703 -1.339239 -0.092984 16 -4.948018 -0.711555 0.385735 16 4.947941 -0.711661 -0.386126
