Dear all!
I would like to ask some questions about the dimer scripts.
1、I run a dimer job with the sample from henkelman websit! When the job has been done, I check the files,there are: INCAR, POSCAR, KPOINTS, POTCAR, MODECAR,NEWMODCAR,CENTCAR,DIMCAR,OUTCAR...! But I can't find the files out.dat and dimer.dat like dwyan said! So where are they??? I need them to plot the energy path!
I have used vfin.pl and there is no output. “usage:perl vfin.pl test1”! The error message like this:
gnuplot> plot "out.dat" u 1 w 1p 1t 1 1w 3 pt 7
can't read data file "out.dat"
"/home/langes/dimrun_complete/dimplot.gnu",line 10:util.c:No such file or directory!
So what I should do to avoid this error?Thanks!
2、I kown that new codes vtst 2.01b has been changed a lot than old codes.Espacially for the input parameters POSCAR,there are no need the directory 01 and 02. Is it right? And is the dimer scripts fit to 2.01b codes??
Any reply is appreciated!
langes
post-analysis of dimer job!
Moderator: moderators
You have pointed out some inconsistencies in the current scripts, that need to be fixed.
1. The latest dimer code does not generate the old dimer.dat or out.dat files. The data that was in out.dat is now in the file called DIMCAR. The data in the old dimer.dat can be obtained from the OUTCAR (grep Dimer OUTCAR).
In the current vtstscripts, the dimer data is not plotted. Updating your scripts will avoid the error you are getting. There is, however, a dimplot.pl script which still looks for the old out.dat. I'll update this script to use the DIMCAR data, and post back when it's done.
1. The latest dimer code does not generate the old dimer.dat or out.dat files. The data that was in out.dat is now in the file called DIMCAR. The data in the old dimer.dat can be obtained from the OUTCAR (grep Dimer OUTCAR).
In the current vtstscripts, the dimer data is not plotted. Updating your scripts will avoid the error you are getting. There is, however, a dimplot.pl script which still looks for the old out.dat. I'll update this script to use the DIMCAR data, and post back when it's done.
Dear graeme
I have another question about diffusion pathway!
I want to plot the pathway along which dimers search saddle points! And I notice that the DIMCAR contains the step, energy and force. In my caculation step is 6. The file DIMCAR is:
Step Force Torque Energy Curvature Angle
1 0.20555 0.21194 -36.83778 2.40597 85.76105
2 0.07773 0.08571 -36.81248 -0.91674 1.19925
3 0.04746 0.15236 -36.81237 -0.74968 2.24202
4 0.01022 0.10511 -36.81137 -0.86767 1.34327
5 0.00796 0.01097 -36.81138 -0.87557 0.13698
6 0.00521 0.04415 -36.81137 -0.88008 0.56339
But in OSZICAR, the ion relaxation step is 25!
So what is the relationship with step in DIMCAR and step in OSZICAR? Which one is correct?
Thank you !
I have another question about diffusion pathway!
I want to plot the pathway along which dimers search saddle points! And I notice that the DIMCAR contains the step, energy and force. In my caculation step is 6. The file DIMCAR is:
Step Force Torque Energy Curvature Angle
1 0.20555 0.21194 -36.83778 2.40597 85.76105
2 0.07773 0.08571 -36.81248 -0.91674 1.19925
3 0.04746 0.15236 -36.81237 -0.74968 2.24202
4 0.01022 0.10511 -36.81137 -0.86767 1.34327
5 0.00796 0.01097 -36.81138 -0.87557 0.13698
6 0.00521 0.04415 -36.81137 -0.88008 0.56339
But in OSZICAR, the ion relaxation step is 25!
So what is the relationship with step in DIMCAR and step in OSZICAR? Which one is correct?
Thank you !
The dimer requires more than one force call per step (it take 1 to start, plus 2 per rotation step). Also, if the optimizer uses a line minimization step, that requires an extra force call.
In your calculation, each dimer step took 3 force calls, and the optimizer takes one extra, bring the total to 4. There was one final force call at the end when it decided it was converged, bringing the total to (4x6+1) = 25.
If you plot the 25 steps in the xdatcar, there will be 6 significant moves.
In your calculation, each dimer step took 3 force calls, and the optimizer takes one extra, bring the total to 4. There was one final force call at the end when it decided it was converged, bringing the total to (4x6+1) = 25.
If you plot the 25 steps in the xdatcar, there will be 6 significant moves.