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DL-FIND: A Geometry Optimizer for Atomistic Simulation Codes

A geometry optimization library for quantum chemical and QM/MM calculations to be included into electronic structure codes.

DL-FIND can be used to search for minima, transition states (the main strength of the code), and conical intersections.

 Reference

All work totally or partially based on DL-FIND should cite [16] as well as the original references of the optimization algorithms used (references given in [16]).

Description

A light-weighted description of geometry optimization in general and DL-FIND in particular can be found in Frontiers 2007.

Functionality

Coordinate systems:

  • Cartesian coordinates (including frozen atoms and components), mass-weighted Cartesian coordinates
  • Internal coordinates (including all constraints):
    • DLC (delocalized internal coordinates, i.e. redundant internal coordinates)
    • DLC-TC (total connection)
    • HDLC (hybrid delocalized internal coordinates, see Phys. Chem. Chem. Phys. 2, 2177 (2000))
    • HDLC-TC

Combinations of coordinates (images):

  • Dimer method [11]
  • NEB (nudged elastic band) [12]

All of the combinations work with all versions of coordinate systems.

Optimizers:

  • steepest descent
  • conjugate gradient
  • L-BFGS
  • P-RFO, Hessian update mechanisms: Powell and Bofill. Hessian either by input or by finite-difference. In the latter case either in Cartesians (then the update also in Cartesians, and one can output frequencies), or in internals.
  • Damped dynamics
  • Algorithms for Conical intersection search:
    • Penalty function
    • Gradient projection method
    • Lagrange-Newton method
  • Stochastic search methods (including a genetic algorithm) for global and local minimization. These methods optimize by calculating may energies in parallel and are thus well-suited for massively parallel computation.

Line search algorithms:

  • Simple scaling of the proposed step (covering the maximum step length)
  • Trust radius based on energy decrease
  • Trust radius based on the projection of the gradient on the step

The design allows new methods to be easily implemented.

Reaction rate calculations with or without tunneling contributions

  • Instanton theory (aka imaginary-F theory or harmonic quantum transition state theory) to calculate tunneling rates.
  • Instanton optimizations with a quadratically-converging optimizer [20]
  • Instanton rate calculations (parallelized)
  • Adaptive step size in instanton calculations [22]
  • Reaction rates without tunneling

Other functionality:

  • The optimizer is fully restartable.
  • DL-FIND can be included in ChemShell and GAMESS-UK and was used in conjuction with a nuber of other codes

Authors

  • Johannes Kästner, main author
  • Tom W. Keal contributed conical intersection search algorithms, parallelization of NEB and finite-difference Hessian calculations and fixed many bugs.
  • Joanne M. Carr is adding parallel search algorithms
  • Judith B. Rommel contributed to the implementation of instanton theory
  • Salomon Billeter and Alexander Turner: parts of their HDLCopt routines have been used in the coordinate transformation, by courtesy of the Max-Planck-Institute for coal research.
  • The L-BFGS code by Jorge Nocedal was used

Download

DL-FIND is distributed at http://ccpforge.cse.rl.ac.uk/gf/project/dl-find/ under the L-GPL license. It can be checked out (svn) after registering at CCPForge. It is written in Fortran 95. The interface to the calling program is kept slim and well-defined, which should facilitate to interface DL-FIND to various programs. Up to now, DL-FIND is included in ChemShell, GAMESS-UK, TeraChem, and a few other codes.

 

Trajectories of two transition-state searches using the dimer method in DL-FIND. The dimer midpoint converges to the transition state (blue sphere).

The dimer method applied to a biological system (the enzyme PHBH) in HDLC coordinates.

Converged nudged-elastic band path on an example surface (Müller-Brown potential). The green spheres indicate minima, the blue sphere indicates the climbing image which converged to the transition state.

Energy and geometries of a nudged-elastic band path of a simple chemical system, optimized with DL-FIND.