Release Notes

Introduction

Here, in reverse order are the main features of ChemShell releases.

Version 3.7, July 2017

• Task-farming framework extended to support NWChem (Global Arrays).
• Revised ORCA interface including support for changes in ORCA v4.0.
• Updated interfaces to Dalton/LSDalton 2016.
• GULP interface now supports calling standalone GULP executables.
• Scripts for generating GULP forcefields for embedded cluster calculations.
• Revised tutorial.
• Compatible with Tcl version 8.6.

Version 3.6, October 2014

• Microiterative optimisation with DL-FIND, including:
  • Microiterative L-BFGS minimisation
  • Microiterative transition state search with P-RFO and dimer methods
  • Microiterative nudged elastic band
• Improved DALTON interface and new interface to LS-DALTON.
• Revised FHI-Aims interface.
• Support for direct linking to NWChem, DALTON, LS-DALTON and FHI-Aims.
• Improved solid state embedding models with GAMESS-UK, NWChem and FHI-Aims.
• Updated cluster preparation routines
• Analytic Hessian calculations in Gaussian interface

Version 3.5, May 2012

• Task-farming framework extended to support dl_poly calculations
• Charge-on-spring/drude oscillator and polarised-boundary RC(D) models for MM polarisation
• Rate calculations with DL-FIND (harmonic transition state theory, instanton rates)
• New interface to DALTON
• Revised interface to ORCA, including support for excited states calculations with CIS/TDDFT
• Enhanced NWChem interface with support for electrostatic embedding
• Default Tcl version changed to 8.5
• Improved tutorial

Version 3.4, April 2011

• Framework for task-farm parallel calculations. Currently supported methods:
  • Parallel Hessian evaluation (force module and in DL-FIND)
  • Parallel nudged elastic band optimisation in DL-FIND
  • Parallel minimisation (genetic algorithm, stochastic search) in DL-FIND
• The code for setting up QM/MM clusters from periodic structures has been rewritten to integrate more closely into ChemShell.
• Shell positions are now stored relative to the parent cores rather than as absolute coordinates, which makes optimisations using the shell model more efficient.
• Charmm EXT format in .psf file supported.
• Support for GULP without any modification needed (requires GULP version 3.5.3 or later).
• Module to automate QM/MM free energy perturbation calculations.
• Generalised solvent boundary potential (GSBP) and solvated macromolecule boundary potential (SMBP).
• QM/MM-based crystallographic refinement (with CNS).
• Interface to Q-Chem
• Improved Turbomole interface, including support for excited state calculations.

Version 3.3, August 2009

• Wider support for capabilities of the DL-FIND optimisation package, including NEB transition state location.
• Added new interfaces
  1. AIMS code from the Fritz Haber Institut
  2. GAMESS(US)
• Ability to load forcefield information from AMBER has been added
• Hybrid QM/MM module now supports multiple state calculations (including conical intersection optimisations with DL-FIND)
• A dispersion term can be added to DFT calculations using a variety of third-party codes
• MNDO Interface:
  • File-based MO tracking is supported for selecting the active space in GUGA-CI calculations
• Molpro Interface:
  • CASSCF and CASPT2 calculations (including multiple-state calculations) are now supported.
  • Suport for Molpro 2008
• Gaussian Interface:
  • CASSCF calculations (including multiple-state calculations) are now supported.
• GULP interface:
  • support for version 3.4, now including QM/MM with the Dreiding forcefield.
• Many minor changes to support builds on a variety of platforms including MPI builds on Opteron and Power5 clusters, Mac OSX port.

Version 3.2, July 2007

• Support for a large range of QM/MM models in GULP (e.g. Additive mechanical and electronic embedding). Adapt code for GULP 3.3 (latest release)
• Support for DMol3 Quantum Code.
• Support for trajectory files for Materials Studio
• Updated NWChem input
• Interface to DL-FIND optimisation package. Allows TS search by the dimer method and nudged-elastic band. It replaces the dimer module added in version 3.1b1.
• Restraint terms for difference between four bond lengths, spherical boundary conditions, and restraint of an atom towards a fixed position in space.
• Shell code FF handling in QM/MM embedding updated to maintain core-shell correspondences and to support a wider range of shell model forcefields for embedding.
• Support for excited state calculations in MNDO involving multiple PE surfaces. Conical intersections can be optimised using DL-FIND.
• Umbrella Sampling tutorial example
• Optimisation to the Gaussian interface for large QM regions.
• Default mass-table in the dynamics module was updated. Now it contains isotopically averaged atomic masses.

Version 3.1b1, October 2006

• SPME in the DL_POLY module
• microiterative QM/MM optimisation scheme in HDLCopt
• Improvements in periodic QM/MM treatment (even though only with cutoff)
• Dimer method for transition state search

a6 tag added May 24 2006

• fix for problems handling some crystalline inputs on linux
• bug fix - termination of space group strings
• reorganisation/rename of cluster cutting tools – added covalent surface script
• change to gamess-uk basis file handling ** not backwards compatible
• nwchem now working for polarised embedding (still developmental)
• documentation & tutorial updates
• change to # of degrees of freedom considered in dynamics w froz atoms.

a5 tag added March 16 2006

• a bunch of checkins to contrib directory
• manual corrections (ongoing)

a4 tag added August 31, 2005

• removed NAG routines 15/3/2004
• analytic force for link atoms 16/12/2004
• added perturbation code from Johannes Kaestner 3/6/2005
• fix for symm check + active atoms specified 9/6/2005
• mndo core added 26/7/2005
• bug fix for monoclinic cells 31/8/2005
• code tested with g95 (cygwin)

a3 tag4/9/2003

• addition of symmetry code

a2 28/8/2003

• bug in urey bradley implementation fixed

Version 3.00, July 2003

• Extensions to Dynamics Module:
  • Friction Dynamics
  • Nose Hoover Thermostats
  • reaction path constraints based on linear-combination of distances.
• Subtractive QM/MM (and QM/QM) implementation (equivalent to QM-Pot) with DL_POLY, MNDO, GAMESS-UK.
• Support for the Universal Force Field
• Support for TURBOMOLE 5.5, GAMESS-UK 6.4
• Extended MNDO interface supporting GUGA CI
• A Python/VTK/Tk Open Source GUI (replacing the SDK GUI as the basis for future graphical developments.
• Minor fixes and enhancements
  • Support for the Urey Bradley term when using CHARMM parameterisation.
  • Inversion force-field terms
  • Autoconf build procedure

Version 2.05, Early 2001

non-compatibilities and significant changes

• By default, the non-graphical code will be started from the command chemsh, use chemsh -tk to get the graphics version.
• z_prepare_input (and c_prepare_input): results are now returned as a Tcl result, rather than being printed to stdout.
• hdlcopt: Fix to internal coordinate generation (some dihedrals were missing from previous coordinate set in earlier versions).
• dynamics: Shake constraints are now input in au for consistency with the rest of the code.
• hybrid: The electrostatics_option= argument still works but should be replaced by coupling=. Valid settings for coupling= are mechanical, shift, L0, L1, L2, and ACA (although not all are available for all choices of QM code). The shift option is equivalent to the polarised option in earlier versions.

Other Changes

• Availability of SDK GUI, which produces a ChemShell script for further development.
• More consistent handling of shells (for shell model forcefields).
• Charges are now carried as a part of the zmatrix and can be provided as part of the input to z_create.
• The GULP interface now supports parallel execution.
• Various charmm interface enhancements...
• Automatic features in hybrid
  • setting charges on QM region to zero
  • automatic reorganisation of MM charge groups when required
  • charge shift on qm/mm boundary ... only for zeolites with q(O) = -0.6
• Support for UFF (incomplete)
  • new data for the entire periodic table, electronegativity data from Rappe'
  • ability to provide bond orders and UFF types manually
• Dynamics Module:
  • Automatic shake option available
  • Tests for group fragmentation (e.g. dynamics)
• Periodic images are taken into account when computing bond lengths, angles and torsions.

Building

• ChemShell version 2.05 requires tcl/tk version 8.3 or higher.

Version 2.04

• Storage of fractional coordinates as part of fragment structure
• handling of structures and potentials for crystalline systems.
• Update of gulp to 1.3.
• Availability of L1 and ACA coupling schemes when using MNDO
• Internal basis set lib extended + inclusion of pseudopotentials.
• Fixes for CHARMM interface relating to large systems (> 9999 residues)
• Availability of link-cells pairlist algorithm

• Recoding of HDLCOpt to use LAPACK
• NWChem interface updated (includes coupling to parallel code).

Version 2.03, Feb 2000

• HDLCopt changes
  • Added function=pick sets={<residue_name> ...} to the inlist command: generate a residue list containing selected residues from another residue list
  • Added optional argument verb={on,off} to the inlist command to suppress irrelevant warnings
  • Added optional argument core=<residue_name_of_reaction_core> to the hdlcopt command
  • Removed an irrelevant warning connected with active_atoms
• Point charges are now visible in the wireframe drawing in ChemGui.
• Internal basis set library is enhanced, glob-style pattern matching is used and the molecule can use atom symbols to set up mixed basis sets.
• Fixes for output of energy components for parallel DL_POLY.
• Bug in serial NPT dynamics code fixed.
• Changes to handling of force constant evaluation for systems with frozen atoms.
• Some changes to parallel initialisation, so the MPI code will now build without GAMESS-UK present.
• write_pdb will now work without preceeding read_pdb

Version 2.02. Dec 1999

• Bug fix - relaxation of requirement that groups= specification indicates the QM group first, and handling of QM/MM electrostatic cutoffs corrected.
• Improvements to output of dynamics module.
• Addition of read_pdb and write_pdb functions

Version 2.0

• ChemShell version 2.0 requires tcl/tk version 8.0.3 or higher.

• A standardised set of arguments has been adopted (see docs/quasi2/quantum.html) and a simple basis set library has been added
• An interface to TURBOMOLE has been added.
• mndo module

• the name (as used in the theory= argument) is now dl_poly (formerly mm)
• support for simulation of the charmm forcefield is provided, provided the charmm interface is present.
• the definition of the input parameters for all energy terms of the type e = k (x-xo)**n is such that k is provided (in kcal/mol). formerly the force constant (2*k for a harmonic term) was used. ** With respect to recent versions of ChemShell this only affects ** the improper dihedral. Early versions used the E=1/2k(x-x0)**2 for all harmonic terms.
• multiple topologies can be maintained - the second instances accessed through theory=dl_poly2 etc.

• It is assumed that a recent version of GAMESS-UK is being used (6.2 or later). i.e. the energy of interaction between point charges will be deleted from the energy expression.
• "qm" replaces qc in all input arguments (e.g. qm_theory).
• The calculation type for hybrid_setup is given as "qm" for the qm code (not the code name, gamess, mopac etc as before).
• the hybrid module accepts the qm_region argument to automatically set up the qm/mm parameters and add dummy atoms
• the hybrid module accepts the cutoff= and groups= arguments so that only a subset of the mm atoms are included as point charges.
• some arguments have been lost (qc_coords etc), these values are now automatically generated.
• subtractive qm/mm schemes are supported the low level theory can be dl_poly or mopac only at present.