OptBench

Transition State Optimization

Lennard-Jones 38

This benchmark tests the performance of algorithms for finding the nearest transition state. The starting point are structures taken from the highest energy image in a DNEB run. Idealy they should all be reasonably close to a transition state (Although there are a few structures which converge to states with positive lowest eigenvalue. Should we delete these from the starting structure database?) A tar file containing the random and minimized structures is (will be) here lj38.tar.gz.

The benchmark requires that each provided Lennard-Jones starting structures be optimized until the norm of the gradient is less that 0.001. Runs that don't reach the required tolerance or those with positive zero eigenvalue are considered failures. If a run was successful, the number of forcecalls necessary to reach the global minimum the first time is recorded.

Avg FCs: Average number of force calls needed to find global minimum (average over successful runs)

min(FCs): Minimum number of force calls needed to find global minimum (best successful run)

max(FCs): Maximum number of forcecalls needed to find the global minimum(worst successful run)

Algorithm <FCs> min(FCs) median(FCs) max(FCs) nfailed
sella

Date: 2019-12-10 Contributor: Eric D. Hermes, Khachik Sargsyan, Habib Najm, Judit Zádor Code: Sella-0.1.1.tar.gz Input files: sella.tgz

70 24 64 158 0
optim_ffd

Comments: This uses Rayleigh-Ritz minimization to find the lowest eigenvector and moves using the hybrid eigenvector following method. The Rayleigh-Ritz minimization uses a first order (forward finite differences) expansion.
Date: 06 Aug 2014 Contributor: Jacob Stevenson and Cheng Shang Code: wales-27058.tar.bz2 Input files: optim_ffd.tgz

145 57 119 565 0
pele_ffd

Comments: this uses Rayleigh-Ritz minimization to find the lowest eigenvector and moves using the hybrid eigenvector following method. The Rayleigh-Ritz minimization uses a first order (forward finite differences) expansion.
Date: 19 Sep 2014 Contributor: Jacob Stevenson Code: pele-a68ec5.tgz Input files: pele_ffd.tgz

192 59 150 1488 0
eon-lanczos-improved1

Date: 29 Aug 2013 Contributor: Sam Chill Input files: eon-lanczos-improved.tgz

237 65 181 1898 0
eon-lanczos1

Date: 29 Aug 2013 Contributor: Sam Chill Input files: eon-lanczos.tgz

321 83 220 8857 0
eon-dimer1

Date: 02 Jul 2013 Contributor: Sam Chill Input files: eon-dimer.tgz

528 92 388 3581 0
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Pt(111) Heptamer Island

This test is similar to that of the Lennard-Jones cluster above. Starting strucures are provided which are near to known transition states. The goal is to find those transition states. The termination condition is that the norm of the gradient is less than 0.001. The coordinates of a nearby minimum are also provided (reactant.con). The vector between the starting structrure and reactant.con can be used to provide an initial guess for the lowest eigenvector.
Algorithm <FCs> min(FCs) median(FCs) max(FCs) nfailed
sella

Date: 2019-12-11 Contributor: Eric D. Hermes, Khachik Sargsyan, Habib Najm, Judit Zádor Code: Sella-0.1.1.tar.gz Input files: sella.tgz

53 31 51 108 0
optim_ffd

Comments: The hybrid eigenvector following method. This uses Rayleigh-Ritz minimization to find the lowest eigenvector and moves using the hybrid eigenvector following method. The Rayleigh-Ritz minimization uses a first order (forward finite differences) expansion.
Date: 06 Aug 2014 Contributor: Jacob Stevenson and Cheng Shang Code: wales-27058.tar.bz2 Input files: optim_ffd.tgz

71 43 70 143 0
pele

Comments: This uses Rayleigh-Ritz minimization to find the lowest eigenvector and moves towards the transition state using the hybrid eigenvector following method. The Rayleigh-Ritz minimization uses a first order (forward finite differences) expansion.
Date: 06 Aug 2014 Contributor: Jacob Stevenson Code: pele-a68ec5.tgz Input files: pele.tgz

88 52 78 198 0
optim_cd

Comments: The hybrid eigenvector following method. This uses Rayleigh-Ritz minimization to find the lowest eigenvector and moves using the hybrid eigenvector following method. The Rayleigh-Ritz minimization uses a second order (central differences) expansion.
Date: 06 Aug 2014 Contributor: Jacob Stevenson and Cheng Shang Code: wales-27058.tar.bz2 Input files: optim_cd.tgz

90 52 86 199 0
eon-lanczos-improved1

Date: 19 Jun 2014 Contributor: Sam Chill Input files: eon-lanczos-improved.tgz

106 71 100 163 0
eon-dimer1

Date: 20 Jun 2014 Contributor: Sam Chill Input files: eon-dimer.tgz

116 83 114 160 0
eon-lanczos1

Date: 29 Aug 2013 Contributor: Sam Chill Input files: eon-lanczos.tgz

143 106 139 292 0
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