Input Block 'String'

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Hello all,

I noticed in the QA/test directory there's h2o_zts and subdirectories with similar names (e.g. ch4_zts). By looking at those input files, I guess it's monitoring 'transition' and I have a couple of questions:

1. Can this be used to search transition state structure?

2. Where can I find more documentation about this String block? I didn't find much from the 'Documentation' link from this site.

Thank you!

Best,
Yue

  • Bert Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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String
1. Yes, it can be used to search for transition states, just like NEB.

2. This is a capability under development, and we are developing the documentation for this functionality. I'll have the person responsible for this develop provide more input.

Bert

  • Bylaska Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Which version of NWChem are you using? The input to the NEB and string codes has changed quite a bit in the last few months, so the input will be highly dependent on what version you're using.

  • Bylaska Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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The basic input for NEB looks like

echo
start ch4_neb_dat

permanent_dir ./permh
scratch_dir ./permh


basis
 * library 3-21G
end



scf
end


neb
  maxiter 200
nhist 15
xyz_path ./jjj.xyz
print_shift 1
end

task scf neb ignore

  • Bylaska Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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you can also enter extra geometries, i.e. middle and end geometries, to define the path. The labels of these geometries are "midgeom", "endgeom", e.g.

This run never really converges well because the two H's that are doing all the real work pop off to form H2 and do a little dance and then come back to the CH2 group they left behind. Optimizing the details of the little dance is about as likely has finding blinker fluid at the auto parts store

Note that this sends H1 right through the Carbon - atom avoidance code must work



echo

start ch4_string

permanent_dir ./permh
scratch_dir ./permh

geometry nocenter
 symmetry c1
C 0.000000 0.000000 0.000000
H 0.000000 0.000000 1.089000
H 1.026719 0.000000 -0.363000
H -0.513360 -0.889165 -0.363000
H -0.513360 0.889165 -0.363000
end

geometry endgeom nocenter
 symmetry c1
C 0.000000 0.000000 0.000000
H 0.000000 0.000000 -1.089000
H 1.026719 0.000000 0.363000
H -0.513360 -0.889165 0.363000
H -0.513360 0.889165 0.363000
end

basis
 * library STO-3G
end

scf
  maxiter 5001
end


string
  #tol  0.004d0
nhist 10
stepsize 1.00d0
nbeads 10
maxiter 100
interpol 1
freeze1 .true.
freezeN .true.
end
task scf string ignore
task scf string ignore

string
   nbeads 20
end
task scf string ignore
Edited On 2:33:35 PM PST - Wed, Jan 16th 2013 by Bert

  • Bylaska Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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You can also go back and forth between neb and string calculations, e.g.

This run never really converges well because the two H's that are doing all the real work pop off to form H2 and do a little dance and then come back to the CH2 group they left behind. Optimizing the details of the little dance is about as likely has finding blinker fluid at the auto parts store

Note that this sends H1 right through the Carbon - atom avoidance code must work


echo
start ch4_neb

permanent_dir ./permh
scratch_dir ./permh

geometry nocenter
 symmetry c1
C 0.000000 0.000000 0.000000
H 0.000000 0.000000 1.089000
H 1.026719 0.000000 -0.363000
H -0.513360 -0.889165 -0.363000
H -0.513360 0.889165 -0.363000
end

geometry endgeom nocenter
 symmetry c1
C 0.000000 0.000000 0.000000
H 0.000000 0.000000 -1.089000
H 1.026719 0.000000 0.363000
H -0.513360 -0.889165 0.363000
H -0.513360 0.889165 0.363000
end

basis
 * library STO-3G
end

scf
  thresh 1.0d-10
maxiter 5001
end

neb
  impose
nhist 10
nbeads 10
maxiter 100
stepsize 0.10d0
kbeads 0.1
end
task scf neb ignore

neb
  kbeads 1.0
nbeads 20
end
task scf neb ignore

string
 nbeads 20
nhist 10
maxiter 100
stepsize 1.0
freeze1 .true.
freezeN .true.
interpol 1
end

task scf string ignore
Edited On 2:32:42 PM PST - Wed, Jan 16th 2013 by Bert

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I'm running NWChem 6.1.


Quote:Bylaska Jan 16th 4:28 pm
Which version of NWChem are you using? The input to the NEB and string codes has changed quite a bit in the last few months, so the input will be highly dependent on what version you're using.

  • Bylaska Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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The input I posted is in the development tree and will part of the next release. You can download a development snapshot and use it, or you can use the input in the 6.1 QA. The older version of the string code doesn't converge very quickly, but it should work.

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can you explain a bit what those keywords in the string section mean? I guess 'nbeads' is the number of optimization points one wants, and maxiter is easy to understand. Beyond that, what is nhist? How to choose proper stepsize? What is interpol doing? What do freeze1 and freezeN do?

Thank you!


Quote:Bylaska Jan 16th 4:36 pm
you can also enter extra geometries, i.e. middle and end geometries, to define the path. The labels of these geometries are "midgeom", "endgeom", e.g.

This run never really converges well because the two H's that are doing all the real work pop off to form H2 and do a little dance and then come back to the CH2 group they left behind. Optimizing the details of the little dance is about as likely has finding blinker fluid at the auto parts store

Note that this sends H1 right through the Carbon - atom avoidance code must work



echo

start ch4_string

permanent_dir ./permh
scratch_dir ./permh

geometry nocenter
 symmetry c1
C 0.000000 0.000000 0.000000
H 0.000000 0.000000 1.089000
H 1.026719 0.000000 -0.363000
H -0.513360 -0.889165 -0.363000
H -0.513360 0.889165 -0.363000
end

geometry endgeom nocenter
 symmetry c1
C 0.000000 0.000000 0.000000
H 0.000000 0.000000 -1.089000
H 1.026719 0.000000 0.363000
H -0.513360 -0.889165 0.363000
H -0.513360 0.889165 0.363000
end

basis
 * library STO-3G
end

scf
  maxiter 5001
end


string
  #tol  0.004d0
nhist 10
stepsize 1.00d0
nbeads 10
maxiter 100
interpol 1
freeze1 .true.
freezeN .true.
end
task scf string ignore
task scf string ignore

string
   nbeads 20
end
task scf string ignore

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Are NEB function (for pure QM instead of QM/MM) and input also changed a lot from 6.1 to 6.2? Can you also explain a bit what 'impose', 'nhist', 'stepsize' and 'kbeads' do? Thank you!

Quote:Bylaska Jan 18th 5:00 pm
The input I posted is in the development tree and will part of the next release. You can download a development snapshot and use it, or you can use the input in the 6.1 QA. The older version of the string code doesn't converge very quickly, but it should work.

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Hi, Bylaska Jan.
How I can add extra geometries, i.e. middle and end geometries, to NEB task?
Can I add an initial MO vectors to geometries, in NEB or STRING tasks?
My version of NWCHEM is 6.1.1. Thank you!


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