General
*******


Overview
========

An overview of the Amsterdam Modeling Suite (AMS) can be found in:
   E.J. Baerends, N.F. Aguirre, N.D. Austin, J. Autschbach, F.M.
   Bickelhaupt, R. Bulo, C. Cappelli, A.C.T. van Duin, F. Egidi, C.
   Fonseca Guerra, A. Förster, M. Franchini, T.P.M. Goumans, T. Heine,
   M. Hellström, C.R. Jacob, L. Jensen, M.V. Krykunov, E. van Lenthe,
   A. Michalak, M. Mitoraj, J. Neugebauer, V.P. Nicu, P.H.T.
   Philipsen, H. Ramanantoanina, R. Rüger, G. Schreckenbach, M.
   Stener, M. Swart, J.M. Thijssen, T. Trnka, L. Visscher, A.L.
   Yakovlev, S.J.A. van Gisbergen, *The Amsterdam Modeling Suite*,
   Journal of Chemical Physics 162, 162501 (2025)

The AMS driver handles all changes in the simulated system's geometry,
e.g. during a geometry optimization or molecular dynamics calculation,
using engines like ADF, BAND or DFTB to calculate energies and forces.

The AMS driver steers the engines across the potential energy surface.


What's new in the AMS driver?
=============================


New in AMS2026.1
----------------

* The PES scan task now has a faster, non-optimizing mode, where
  degrees of freedom other than the scanned ones are not optimized.

* Gibbs Free Energy calculations for periodic systems within the
  Harmonic Approximation, fully integrated into the PESExploration
  module for rapid thermodynamic profiling.

* MD simulations can now automatically stop if the temperature exceeds
  a threshold using the new CheckTemperature block. This helps detect
  and stop simulations where the system may have exploded.

* The Shake constraints in MD now support excluding atoms in a
  specific region from all constraints via the new "ExcludeRegion"
  keyword.

* MD Reflective walls now have a configurable "Thickness" parameter.
  This allows placing two walls back-to-back to create a two-sided
  wall that reflects in both directions.

* Engine result files are no longer written at every MD step during MD
  simulations (the default "EngineResultsFreq" is now 0). To re-enable
  writing them, set EngineResultsFreq to a nonzero value. Previously,
  "Checkpoint%Frequency" was sometimes used to suppress unwanted
  engine results files, but this also disabled checkpoints needed for
  restarts. The new defaults allow normal checkpoint frequencies while
  suppressing the engine files.

* AMS MD can now be used in path sampling simulations using the
  InfRETIS tool


New in AMS2025.1
----------------

* Dispersion add-on uses updated libraries for DFT-D3 (s-dftd3 1.2.1)
  and DFT-D4 (dftd4 3.7.0)

* Writing "MDStep" engine results files during MD can now be
  customized or completely disabled using EngineResultsFreq.

* When remapping atomic positions across periodic boundaries, the MD
  driver now uses intuitive and predictable coordinate ranges. This
  can be customized using the Remap Range setting and pre-AMS2025
  behavior can be restored using "Range=AroundCenter".

* MD Deformations can now automatically scale a box to a given
  "TargetDensity".


New in AMS2024.1
----------------

* Use image dependent pair potential (IDPP) to generate an initial
  path for NEB calculations

* Reaction boost (targeted MD) restraints for molecular dynamics

* Dipole moment added as an option to the BinLog output section for
  calculation of IR spectra from ab initio MD

* The dimer method for transition state search

* A new Reactions Discovery tool that can be used with any AMS engine.

* Use engine uncertainties.

* Stop MD trajectories early with exit conditions based on too short
  atom-atom distances or too high engine uncertainties.

* Store as part of the MD trajectory: temperature of individual
  thermostats, total BondBoost or Reactor restraint energy.


Removed in AMS2024.1
--------------------

* Old FCF program ($AMSBIN/oldfcf) is no longer supported

  * the new FCF program ($AMSBIN/fcf) has replaced the old FCF program
    in AMS2022.1

  * see documentation in the AMS2021.1 manual on the old FCF program


New in AMS2023.1
----------------

* A new Conformers tool tool allows conformer generation with any AMS
  engine.

* Molecular orbitals energies and occupations can now be requested
  from the "Properties" block in the driver input and are printed in
  an engine independent manner.

* The AMSbatch utility program allows executing the same AMS job for
  multiple systems.

* A Martinez style Nanoreactor was added to the MD driver.

* The PES scan task can now use all geometry optimizers. Previously it
  was limited to using the Quasi-Newton optimizer. This will make pure
  lattice PES scans (e.g. energy-volume scans) with fast engines and
  large cells much faster.

* The "GeometryOptimization%Convergence%Quality" keyword can now be
  used to easily tighten or relax all convergence thresholds for
  geometry optimizations at once.

* The calculation of normal modes now also calculates and prints the
  reduced masses and force constants of the individual modes.

* The PES point characterization now uses the force constants instead
  of the vibrational frequencies to identify transition states, making
  it more reliable in the presence of numerical noise.

* Environment variables in the input will now be expanded.

* The default value of "VibrationalAnalysis%Displacement" has been
  changed to 0.005 Bohr, related to precision issues with derivatives
  of polarizability.

* The calculation of the vibronic density of states for transfer
  phenomena using the Adiabatic-Hessian Franck-Condon formalism has
  been added.

* Calculation of vibrational polarizabilities under the harmonic
  approximation.

* For the PES exploration task, it is now possible to read an energy
  landscape and/or add states from the input file. The algorithm for
  detecting and labeling binding sites was enhanced. Importantly, the
  Landscape Refinement job can now be run in parallel.


New in AMS2022.1
----------------

* The MD driver now supports Rattle/Shake methods for constrained
  molecular dynamics simulations. The FIRE optimizer now supports
  distance constraints.

* The PES scan task now allows the scanning of lattice degrees of
  freedom.

* The molecule gun now supports the generation of molecule mixtures
  through the "MoleFraction" keyword.

* The Replay task for recomputing properties for trajectory frames
  with a different engine.

* The PES exploration can now include fragmented states in the energy
  landscape when studying adsorption processes.

* A new option allows Geometry optimizations with PES point
  characterization and no symmetry to converge more reliably to minima
  instead of transition states or higher order saddle points: in case
  a geometry optimization converges to a TS, it will now automatically
  restart after displacing all atoms along the imaginary mode.

* The calculation of Franck-Condon factors with the FCF program has
  been improved regarding precision, speed, and memory requirements.


New in AMS2021.1
----------------

* PES exploration tasks for the automated discovery of stationary
  points on the potential energy surface.

  1. Process Search: a composite method for finding escape mechanisms
     from a state. This will find both local minima and their
     connecting saddle points.

  2. Basin Hopping: a Monte Carlo method for finding local minima.

  3. Saddle Search: a single-ended method for finding nearby saddle
     points.

* Force bias Monte Carlo is now available in AMS, enabling pure MC or
  mixed MD/MC simulations with any engine.

* The molecule gun can now generate random shooting directions in a
  given cone.

* A new wall potential engine add-on can be used to simulate spherical
  nanoreactors.

* The D4 dispersion add-on can now also be used for calculations on
  periodic systems.

* Graceful interactive termination of running jobs through the
  interactive input file.

* Geometry optimizations write the optimized geometry to the results
  directory as an extended XYZ file.


New in AMS2020.1
----------------

* ADF has been fully integrated as an AMS engine.

* New engines: MLPotential implementing several different types of
  machine learning (ML) potentials. A Hybrid engine for combining
  other engines in QM/MM calculations. Enhanced ForceField engine
  (formerly UFF).

* Improvements to the Quasi-Newton geometry optimizer: Periodic
  systems can now be optimized in delocalized coordinates. Better
  performance for systems made up of disconnected fragments.

* Geometry optimization can now be performed with frozen and equal
  strain constraints for the lattice degrees of freedom. This option
  is currently only available with the FIRE optimizer.

* Support for external electric fields: Homogeneous as well as
  multipole charges.

* Enhanced support for vibrational spectroscopy: (resonance) Raman,
  (resonance) vibrational Raman optical activity, vibrational circular
  dichroism.

* The MD driver now supports time-dependent lattice deformations as
  well as a method for accelerating bonding reactions (Bond Boost
  method).

* Reactive MD calculations with the AMS driver can now be analyzed
  with ChemTraYzer.

* It is now possible to selectively disable writing some parts of a MD
  trajectory to save space.

* More trajectory analysis options: autocorrelation functions and
  diffusion coefficient

* The molecular composition analysis can now be done with respect to
  an adsorption support region.

* The transition state search task now allows users to specify an
  approximate reaction coordinate (TSRC).

* For the calculation of normal modes, the Mobile Block Hessian method
  now allows to treat parts of the system as rigid blocks.

* New coordinates for constrained geometry optimizations and PES
  scans: Sum of distances and difference of distances.

* Added the ability to include additional potential terms (i.e.
  springs) through the Restraints engine add-on.

* A running AMS driver process can be used from Python through the new
  AMSWorker class in the PLAMS library. The communication between
  PLAMS and the AMS driver happens via the new Pipe interface
  protocol.

* Introduced Regions to simplify the input syntax for options that
  apply to a subset of atoms only.

* Symmetrization of systems from the input and the option to input a
  Z-matrix.

* Low-frequency contributions to thermodynamics properties can be
  corrected using a free rotor interpolation method.


New in AMS2019.3
----------------

* The Nudged elastic band method (NEB) for finding minimum energy
  paths of transitions has been added.

* The new PES point character property can be used to quickly
  calculate a few of the lowest vibrational modes of a system and to
  verify the success of a geometry optimization or transitions state
  search.

* Driver level parallelism is now enabled and managed automatically,
  improving the performance and scalability of many applications.

* A Mode Scanning calculation can now be started automatically for all
  modes within a specific frequency range.

* Methods for the quick calculation of the vibrationally resolved
  electronic spectra: Vibronic-Structure Refinement and Vibronic-
  Structure Tracking.

* New geometry optimizer available: Limited-memory BFGS

* Input keywords that expect lists of numbers can now be specified as
  ranges using a Python slice-like notation. Input keywords that
  expect a single real number now also accept fractions (of integers).

* New option to include a non-isotropic external stress for 1D, 2D,
  and 3D periodic systems. This can be used to study structural
  deformation and mechanical properties of materials under non-
  isotropic stress.

* New add-on system for manipulating and augmenting the results
  returned from the engines:

  1. Grimme's D4 and D3 dispersion corrections can be used with any
     engine through the D4Dispersion and D3Dispersion add-ons.


New in AMS2019.1
----------------

* Intrinsic Reaction Coordinate (IRC) Scan is now available in the AMS
  driver for molecular and periodic systems.

* Support for the Grand Canonical Monte Carlo (GCMC) method has been
  added in the AMS driver.

* Molecular composition analysis for molecular dynamics simulations
  (see tutorial)

* Collective Variable-driven Hyperdynamics (CVHD)

* Molecule gun and molecule sink  for molecular dynamics

* PLUMED library support for MD analysis and a wide variety of free
  energy methods

* The initial symmetry of a system is enforced during geometry
  optimizations with the Quasi-Newton optimizer.

* Thermodynamic properties (assuming an ideal gas) are automatically
  computed after normal modes calculations.

* Partial vibrational density of states (PVDOS) for normal modes.

* The system's symmetry is used to accelerate numerical nuclear
  derivatives and to provide symmetry labels for normal modes.

* The AMS driver starts up much faster, significantly speeding up
  scripting applications that launch AMS many times.

* New tools for mode selective vibrational analysis:

  1. Mode Scanning (aka ADF's ScanFreq)

  2. Mode Refinement (aka "Frequency range selection")

  3. Mode Tracking
