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example:structure_optimization [2009/11/07 10:15]
jelen
example:structure_optimization [2011/02/18 13:13] (current)
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 These are minimal steps required to optimize atomic structure using quenching optimization method: These are minimal steps required to optimize atomic structure using quenching optimization method:
  
----- 
  
- ===== define ​atomic structure =====+ 
 + ===== atomic structure =====
  
 In this particular case, we are going to optimize atomic structure of [http://​en.wikipedia.org/​wiki/​Diarylethene Dithienylethene] molecule. ​ 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'''​+Initial configuration is written in a file with an arbitrary name e.g. //initial.bas//
  
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----- 
  
-===== edit input file //​fireball.in//​ ===== 
  
-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. +===== input file =====
-In our particular case, '''​fireball.in'''​ file looks like:+
  
 +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\\ 
  
 +  &OPTION
 +  basisfile = initial.bas
 +  nstepf = 5000
 +  iquench = -1
 +  icluster = 1
 +  dt = 0.5
 +  &END
 +  &OUTPUT
 +  iwrtxyz = 1
 +  &END
  
-where  <​br ​\> + 
-keyword '''​basisfile'''​ defines name of file with an initial atomic configuration; ​<​br ​\> +where\\ 
-keyword '''​nstepf'''​ sets maximal number of time steps; ​ <​br ​\> +keyword '''​basisfile'''​ defines name of file with an initial atomic configuration;​\\ 
-keyword '''​iquench'''​ type of structure optimization; ​ <​br ​\> +keyword '''​nstepf'''​ sets maximal number of time steps; \\ 
-keyword '''​icluster'''​ defines type of boundary conditions (here no periodicity);  ​<​br ​\> +keyword '''​iquench'''​ type of structure optimization;​ \\ 
-keyword '''​dt'''​ is time step in femtoseconds;  ​<​br ​\>+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'''​ keyword '''​iwrtxyz'''​ allows save history of atomic trajectories during optimization proces into xyz-format output file '''​ answer.xyz'''​
  
  
----- 
  
-* link to tabulated electronic integral ​Fdata+ 
 +===== Fdata ===== 
 To initiate Fireball run, we need to create Fdata directory in working directory, which contains all electronic integrals 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. 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'' ​+Once we have these data, usually we create ​//Fdata// dir via symbolic link  
 + 
 +   ln -s $CURRENT_DIR_Fdata Fdata
  
----- 
  
 ===== run optimization process ===== ===== 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''​:+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\\+   rm -fr CHARGES *.xv *.ac *.xyz
    ​$DIR_FIR/​fireball.x    ​$DIR_FIR/​fireball.x
    
  
-to run code we simply type in command line:\\  +to run code we simply type in command line: 
-'' ​./run.bat > out &'';​\\+ 
 +   ./run.bat > out & 
 this command run fireball on background. this command run fireball on background.
  
-----+
  
 ===== output ===== ===== output =====
  
-Status of optimization process we can follow by simple command:\\  +Status of optimization process we can follow by simple command: 
-'' ​grep "​+++"​ out''​\\ ​+ 
 +   grep "​+++"​ out
  
 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:​\\
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-----+
  
 =====  final optimized structure ===== =====  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.+Current optimized structure is placed in //answer.bas// file and it can be directly used as input file for a next run.
  
  
example/structure_optimization.1257585301.txt.gz · Last modified: 2011/02/18 13:14 (external edit)