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example:structure_optimization [2009/11/23 21:44]
jelen
example:structure_optimization [2011/02/18 13:13] (current)
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 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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 ===== input file ===== ===== 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. +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:+In our particular case, //fireball.in// file looks like:
  
  
-&OPTION\\ +  ​&​OPTION 
-basisfile = initial.bas\\ +  basisfile = initial.bas 
-nstepf = 5000\\ +  nstepf = 5000 
-iquench = -1\\ +  iquench = -1 
-icluster = 1\\ +  icluster = 1 
-dt = 0.5\\ +  dt = 0.5 
-&END\\ +  &END 
-&OUTPUT\\ +  &​OUTPUT 
-iwrtxyz = 1\\ +  iwrtxyz = 1 
-&END\\+  &END
  
  
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 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//:
  
  
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-to run code we simply type in command line:\\ +to run code we simply type in command line:
  
    ​./​run.bat > out &    ​./​run.bat > out &
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 ===== 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
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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.1259009056.txt.gz · Last modified: 2011/02/18 13:14 (external edit)