Transition State Calculations
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Transition State Calculations
Hi everyone,
I am not able to use the VASP code for Elastic Band Method calculations to
find the Transition states , Barrier. I would appreciate if any one tell me what the problems are.
I used the following just for two POSCARs which are written in two
subdirectories named 01 and 02
SYSTEM = Elastic Band Method
LSCALAPACK= .FALSE.
IBRION=3
POTIM=0.0
ISYM=0
ICHAIN=2
IMAGES=2
But it did not work
It instead says
hus no job control in this shell.
master mpi start node is dirac
nodes are:
dirac
langmuir
nodecount is 2
vasp.4.6.20 12Dec03 complex
ERROR: the following files does not exist POSCAR
Thank you.
<span class='smallblacktext'>[ Edited ]</span>
I am not able to use the VASP code for Elastic Band Method calculations to
find the Transition states , Barrier. I would appreciate if any one tell me what the problems are.
I used the following just for two POSCARs which are written in two
subdirectories named 01 and 02
SYSTEM = Elastic Band Method
LSCALAPACK= .FALSE.
IBRION=3
POTIM=0.0
ISYM=0
ICHAIN=2
IMAGES=2
But it did not work
It instead says
hus no job control in this shell.
master mpi start node is dirac
nodes are:
dirac
langmuir
nodecount is 2
vasp.4.6.20 12Dec03 complex
ERROR: the following files does not exist POSCAR
Thank you.
<span class='smallblacktext'>[ Edited ]</span>
Last edited by anagaw on Mon Jul 04, 2005 9:27 pm, edited 1 time in total.
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Transition State Calculations
1) the parameters to be set in INCAR to do an NEB cakculation are
SPRING = -5
IMAGES = # of intermediate geometries
ICHAIN is not a valid input parameter for vasp.4.6
2) by default, you need directories named 00 -- 0X:
00 and 0X contain the POSCARS of the initial and final state geometries, all other directories (01 -- 0(X-1) ) contain the POSCARS of the geometries interpolated between initial and final state.
the error message says that the POSCARS were not found where they had
been expected, probably because the NEB method was not started (SPRING
is missing in INCAR)
SPRING = -5
IMAGES = # of intermediate geometries
ICHAIN is not a valid input parameter for vasp.4.6
2) by default, you need directories named 00 -- 0X:
00 and 0X contain the POSCARS of the initial and final state geometries, all other directories (01 -- 0(X-1) ) contain the POSCARS of the geometries interpolated between initial and final state.
the error message says that the POSCARS were not found where they had
been expected, probably because the NEB method was not started (SPRING
is missing in INCAR)
Last edited by admin on Tue Jul 05, 2005 2:31 pm, edited 1 time in total.
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Transition State Calculations
The ICHAIN variable is used to control transition state methods which have not yet been incorporated into the main vasp distribution. The ICHAIN=2 is a setting to run the dimer saddle point finding method, for which only two images in the 01 and 02 directories are requried. The additional code required to run this method is available at http://theory.cm.utexas.edu/vtsttools/ . If you rebuild vasp with the additional code, your INCAR settings are appropriate for running the dimer method.
Vasp Masters: Would you considering incorporating these new methods into the main vasp distribution? The dimer method, and the climbing image NEB combined with an improved tangent are now mature methods which are used by folks in the vasp community. Also, it would be nice to have a version of the conjugate gradient optimizer which does not require the energy, to speed up convergence of the NEB. The combination of these changes will enable vasp to find transition states more efficiently.
Vasp Masters: Would you considering incorporating these new methods into the main vasp distribution? The dimer method, and the climbing image NEB combined with an improved tangent are now mature methods which are used by folks in the vasp community. Also, it would be nice to have a version of the conjugate gradient optimizer which does not require the energy, to speed up convergence of the NEB. The combination of these changes will enable vasp to find transition states more efficiently.
Last edited by graeme on Tue Jul 05, 2005 6:45 pm, edited 1 time in total.
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Transition State Calculations
I have still problem in running the job. I have created four subdirectories
from 00 ..03 in the main directory in which vasp is started. Each
subdirectories has one POSCAR file. But when I execute the program with the following
INCAR files
SYSTEM = Elastic Band Method
SPRING= -5
IMAGES= 2
IBRION=3
POTIM=0.0
It syays vasp.4.6.20 12Dec03 complex
ERROR: the following files does not exist POSCAR
<span class='smallblacktext'>[ Edited Tue Jul 05 2005, 11:46PM ]</span>
from 00 ..03 in the main directory in which vasp is started. Each
subdirectories has one POSCAR file. But when I execute the program with the following
INCAR files
SYSTEM = Elastic Band Method
SPRING= -5
IMAGES= 2
IBRION=3
POTIM=0.0
It syays vasp.4.6.20 12Dec03 complex
ERROR: the following files does not exist POSCAR
<span class='smallblacktext'>[ Edited Tue Jul 05 2005, 11:46PM ]</span>
Last edited by anagaw on Tue Jul 05, 2005 9:44 pm, edited 1 time in total.
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Transition State Calculations
apart from the choice of POTIM (it is not reasonable to set it to 0) your input
should work.
please check the following
1) did you really use the parallel executable of VASP ( this is required for the
implemented version of the NEB method)
2) did your jobfile generate all subdirectories and copy the POSCARs
without errors ?
should work.
please check the following
1) did you really use the parallel executable of VASP ( this is required for the
implemented version of the NEB method)
2) did your jobfile generate all subdirectories and copy the POSCARs
without errors ?
Last edited by admin on Fri Jul 08, 2005 9:23 am, edited 1 time in total.
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Transition State Calculations
[quote author= Elastic Band Method
LSCALAPACK= .FALSE.
IBRION=3
POTIM=0.0
ISYM=0
ICHAIN=2
IMAGES=2
But it did not work
It instead says
hus no job control in this shell.
master mpi start node is dirac
nodes are:
dirac
langmuir
nodecount is 2
vasp.4.6.20 12Dec03 complex
ERROR: the following files does not exist POSCAR
Thank you.
[/quote]
LSCALAPACK= .FALSE.
IBRION=3
POTIM=0.0
ISYM=0
ICHAIN=2
IMAGES=2
But it did not work
It instead says
hus no job control in this shell.
master mpi start node is dirac
nodes are:
dirac
langmuir
nodecount is 2
vasp.4.6.20 12Dec03 complex
ERROR: the following files does not exist POSCAR
Thank you.
[/quote]
Last edited by wsyjsrrp on Tue Nov 14, 2006 7:48 am, edited 1 time in total.
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Transition State Calculations
I think that your POTIM=0.0 is error, POTIM should not 0.0,if that, structure will not change.so you can't find transition states
Last edited by wsyjsrrp on Tue Nov 14, 2006 7:53 am, edited 1 time in total.
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Transition State Calculations
you forgot to set SPRING=-5
[ Edited Tue Nov 14 2006, 09:43AM ]
[ Edited Tue Nov 14 2006, 09:43AM ]
Last edited by admin on Tue Nov 14, 2006 8:43 am, edited 1 time in total.
Transition State Calculations
The implementation of the nudged elastic band(NEB) method in VASP is based on parallel machine, it does not work on serial machines.
Last edited by Haley on Thu Jul 03, 2008 7:53 am, edited 1 time in total.
Transition State Calculations
Hi
I have an additional question. I have initial and final POSCARS but i have not been able to figure out how to use interpolatePOS. I guess i have to use it because my system is strictly two dimensional.
thanks
I have an additional question. I have initial and final POSCARS but i have not been able to figure out how to use interpolatePOS. I guess i have to use it because my system is strictly two dimensional.
thanks
Last edited by safak on Wed Feb 25, 2009 2:00 pm, edited 1 time in total.
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Transition State Calculations
interpolatePOS should work for any system, not just a 2D-one, all it does is to calculate the positions by interpolation between initial and final state. Please note that
1) the unit cells (Bravais matrices) for initial and final states have to be the same
2) take care whether all atoms are 'on the same side' of the cell (ie, none of the atoms re-enters the cell from the opposite side, due to the periodic boundary conditions)
1) the unit cells (Bravais matrices) for initial and final states have to be the same
2) take care whether all atoms are 'on the same side' of the cell (ie, none of the atoms re-enters the cell from the opposite side, due to the periodic boundary conditions)
Last edited by admin on Tue Mar 17, 2009 12:07 pm, edited 1 time in total.