Monitor the Output

1.

Now try again:

• Make sure you are in the directory with your input files
• Run it:

  
  

  alpha:~/tutorial/h2co> paw_run -c h2co.cntl

• Observe the run output to the stdout (screen)
• It should be okay. You can run it in the background by hitting control-Z to suspend the program and then typing ``bg''. If you want to put it in the foreground again, just type ``fg'' (if you have no other jobs running). Always make sure that a previous run is completely done before you start a new one for the same system in the same working directory. Otherwise, you may have two programs writing to the same output files.

2.

Check the output:

• The protocol (PROT) file has the info you want to check. This file should be created when the program runs. In true lab notebook style, its contents are not overwritten when you restart a run, but just appended to the previously created file.
• Monitor it as the calculation runs with the ``tail'' program (which can be killed with control-C):

  
  

  alpha:~/tutorial/h2co> tail -f h2co.prot

  
  

  
  

    

  Figure: Excerpt from h2co.prot (1)

  
  
  

• The PROT file starts with some information about your setup, then starts to print out the one-particle energies in the manner shown in Figure 5:

  
  

• The headings we are interested in mean:

  
  

  NFI	Number of iterations
  T[K]	Temperature in Kelvins
  EKIN(PSI)	Wavefunction Kinetic Energy
  E(RHO)	Energy of the System
  ANNEE	The friction applied

3.

Watch the energy of the system:

• This energy should be going down.
• The friction should go down as the energy does.
• If the energy goes up, it should switch to the higher friction
• If the friction continually switches back and forth between low and high friction, we are in trouble. We may think we converge when we are actually not. I seem to have had this problem, so let's try to fix it. . .

4.

Fixing an oscillation: Edit the file to make sure it has a constant and low friction: Friction values (f) are from 0 <= f <= 1.

• set !PSIDYN FRIC=0.01 in the .cntl file
• change the previous friction keyword from !AUTO to !AUTO_OFF. This makes that particular block invisible, but we can still keep it for future reference or if we want to turn the variable friction back on later. Note that the _OFF option can be used for any block!
• You can prematurely stop the program in a nice way by creating a .exit file. PAW will then exit after completion of the next iteration.

  
  

  alpha:~/tutorial/h2co> touch h2co.exit