Dec 13 2023

T69-2023 Notification regarding BIOVIA Materials Studio 2024

BIOVIA Materials Studio

Technical Note T69-2023

December 2023

 

Notification regarding BIOVIA Materials Studio 2024

Program

BIOVIA Materials Studio

Operating System

All supported operating systems

Description

We are providing this Technical Note to inform you about the release of BIOVIA Materials Studio 2024 which includes the following enhancements and fixed defects:

Enhancements

This release of BIOVIA Materials Studio includes the following enhancements.

User Story

Description

MS-31424

The CASTEP module now includes the DFT-D4 semi-empirical dispersion correction. This is faster than the many-body dispersion correction, MBD*, and produces accurate structures and energies for molecular crystals and other van der Waals systems.

MS-51686

Materials Studio includes updates to the COMPASS III forcefield charges, specifically the bond increments for the n4+ and h1+ forcefield types for ammonium (NH4+).

MS-54934

Materials Studio now allows you to apply exclusion rules to valence terms missing from forcefields. You can select No for the _Ignore exclusions for missing valence term_ option on the Forcefield Preferences dialog or specify IgnoreExclusionsForMissingTerms => "No" using MaterialsScript.

MS-55855

You can now use the Dipole Autocorrelation Function (DACF) analysis tool in Forcite and Mesocite to calculate the running average of static dielectric permittivity of the trajectory as well as the permittivity storage and loss spectrum. The Script menu now includes two new scripts to calculate an average DACF from analyses of multiple trajectories and to fit the DACF for permittivity spectrum calculation using a response function formalism with Debye relaxation time for long time-scales.

MS-57941

You can now choose the matching criteria for bonds in the Find Patterns tool.

MS-58624

A Pressure correction algorithm has been introduced into Boltzmann Inversion script for the determination of effective van der Waals interactions between beads. This change fixes the pressure and temperature for the dynamics at coarse grain level matching to that of the underlying input trajectory from atom-based simulations.

MS-59111

Forcite and Mesocite now have a new barostat, Anisotropic. This allows you to vary the three cell lengths independently (or to remain fixed) and to apply a different stress to each face of the cell.

MS-59551

You can now perform Anneal, Quench Dynamics, Confined Shear, Solvation Free Energy, Cohesive Energy Density, and Mechanical Properties calculations for mesostructures, using the Mesocite module.

MS-60108

The grand-canonical ensemble is now implemented in ONETEP for simulations of systems with a variable number of electrons and a fixed external potential. This functionality is particularly relevant for electrochemical studies of electrode-electrolyte interfaces.

MS-60182

The Velocity Autocorrelation Function (VACF) analysis tool in Forcite and Mesocite now also provides the diffusion coefficient generated using the Green-Kubo approach.

MS-60437

A PDF version of the introductory content of the Materials Studio online help is now available.

MS-60446

You can now use a new GULP ReaxFF library for modeling the surface-electrolyte interphase. This library, ReaxFF SEI2021, is based on the https://doi.org/10.1021/acs.jpclett.1c00279 publication.

MS-60508

You can now use all Forcite and Mesocite tasks in Materials Studio scripting through MaterialsScript. You can use the CopyScript feature for all tasks on both the Forcite Calculation and Mesocite Calculation dialogs.

MS-60654

Materials Studio integration with the CCDC tools now supports CSD 2023 installation.

MS-60674

You can now use the Effective Screening Medium (ESM) option in DMol3. The ESM option replaces the periodic boundary condition along the z direction, with a screening medium in the form of a vacuum or metal at the cell boundary. The metal boundary mirrors any charges in the system, allowing analysis of a charged system. DMol3 fixes the potential of the metal boundary at 0 eV. However, you can add an electric field for metal-metal systems to apply a bias between the metal surfaces. 

MS-60705

You can now use the new Granular Dynamics task in Mesocite to simulate the motion of spherical particles of micron size and negligible thermal velocity.

MS-60796

When using the Pipeline Pilot Connector to run protocols, you can now reliably download large results files to the Materials Studio Visualizer over limited bandwidth connections.

MS-60819

You can now run calculations that include electric fields on GPU compute resources.

MS-60918

Materials Studio now provides a scripting interface for the creation of bead types.

MS-60970

Performance is enhanced for the trajectory analysis methods: Rotational Time Correlation Function, Velocity Auto Correlation Function, Radial Distribution Function and Mean Square Displacement Function.

MS-61013

DFTB+ now uses version 22.2, which includes the ELPA eigensolver. This solver scales well for large systems and on massively parallel supercomputers, also exhibiting great efficiency for smaller systems. The ELPA solver supports the option of GPU acceleration, providing a significant additional performance gain for large systems. The GPU acceleration also supports the use of multiple GPUs. You can access the ELPA solver from the DFTB+ Calculation dialog, MaterialsScript, and through the DFTB+ components in the Pipeline Pilot Materials Studio Collection.

MS-61026

You can now use a Detail View of a structure from a study table as the Active Document on which to run Materials Studio scripts on a server. You can also use an edited, unsaved Detail View, indicated with asterisk in the title of the window. Both direct MaterialScript jobs and those launched from custom User Menu commands can work on a Detail View.

MS-61077

A new tutorial demonstrates the use of the new Mesocite Granular Dynamics task.

MS-61099

The ONETEP solver code is now upgraded to the academic version 6.1.45.

MS-61114

The GULP solver now uses academic version 6.2. This includes the addition of two new forcefield libraries (AA-CLP and Nitrates). ReaxFF calculations now include analytic second derivatives and phonons, so that you can evaluate full phonon dispersion and phonon density of states. You can calculate charges for s and p block elements using extended Huckel theory, in particular, to support the Gavezzotti AA-CLP forcefield. You can now calculate properties for variable charge models with charge derivatives including those for electric fields; enabling ReaxFF calculations with electric fields.

MS-60441

The version of Intel MPI has been updated to 2021.10

MS-60659

Materials Studio now includes Perl 5.36.0 on all platforms.

Fixed Defects

This release of BIOVIA Materials Studio includes the following fixed defects.

 

User Story

Description

MS-52235

The status text document in Forcite and Mesocite now reports the long-range correction to the van der Waals energy.

MS-60259

Charts created by ONETEP for local densities of states are no longer offset by half of the band gap.

MS-60370

There are no limitations now on file size for upload to Materials Studio gateways.

MS-60418

The scripting functions for computing SMILES and ChemicalName now automatically determine the formal charges, which fixes an issue with recognizing the wrong molecular species.

MS-60436

Fixed bug in "Statistics of Molecules" script to enable trajectories with predefined molecular hierarchies. Also changed script to run on server for performance reasons.

MS-60708

The MaterialsScript Fix and Unfix functions are now faster.

MS-60765

Some Forcite calculations were slower in Materials Studio 2023 compared to 2022 when run on GPU models with a small number double precision cores. Materials Studio 2024 has improved performance compared to both 2023 and 2022 on these GPU devices.

MS-60788

A missing correction term was added to the DMol3 total energy for dipole corrected surface calculations and its value is reported in the output file. The magnitude of the missing term scales with the magnitude of the dipole along the surface normal. 

MS-61466

Attempting to create an unrealistically large field during a Mesocite Density Field Analysis now reports an error.

MS-61663

We have corrected how the contact shift data is saved during the electron transport simulation. This resolves the occasional file-writing error that could occur when running in parallel on a Windows server.

MS-58791

Materials Studio Forcefield Editor now handles row deletion and updates the table accordingly.

MS-58825

An inversion term for n3-nitrogen in a nonaromatic 5-ring has been added to COMPASSIII to improve planarity of those compounds.

MS-59443

An issue with the calculation of fields (for example density fields) where the grid size was being estimated incorrectly  has been addressed.

MS-60260

Previously, Mesocite or Forcite GPU calculations were liable to fail when two particles were very close (in the order of 0.01 A), because the energy and force became very large. GPU calculations now have an identical behaviour to the CPU implementation, in which nonbond energies are limited for very close contacts. This avoids the problem.

MS-60300

Conversion issue for French locale resulting in error "Could not interpret ConQuest version" have been resolved.

MS-60391

Trajectory analysis can now analyse XYZ files with 3D periodic boundaries.

MS-60433

The Boltzmann Inversion script now constructs nonbond potentials which have an increasing value for small r (instead of a constant value). This is more realistic.

MS-60470

Tools | Materials Studio Scripts | Utilities | Select Same Molecules has improved behaviour for radicals.

MS-60478

The links to the external website with PAW datasets for ONETEP calculations now use their updated locations.

MS-60597

The two tutorials Polymer Coarse Graining with Martini 3 Tools and Polymer Coarse Graining with Martini 3 Protocols now include links between them. You can use either of the two versions of the tutorial to achieve the same results using different tools; Materials Studio scripts or  Pipeline Pilot protocols.

MS-60638

We substantially decreased the number of ssh sessions created by Materials Studio to monitor job status which should improve the performance of the ssh gateway front-end machine.

MS-60657

The close contact calculation tool now allows exclusion of contacts within sets of beads, as well as atom sets.

MS-60658

CASTEP reporting of the band gap is made more robust to exclude the false diagnostic of an insulator when the Fermi level is within a narrow electronic band (e.g., f-states band).

MS-60733

On Linux at the end of any CASTEP run VmHWM (Virtual memory High Water Mark consumption for the main thread will be printed at the end of the CASTEP file

MS-60763

CASTEP nonlinear optics calculations now can be requested as part of the property run

MS-60826

Density field analysis of trajectory with 'exclude analyzed objects' now only excludes matter objects.

MS-60844

FlexTS with DMol3 properly accounts for unit cell alignments with dipole and ESM calculations and explicitly checks whether constrained atoms line up in reactant, product, and TS calculations where applicable. It also hides all but the last iteration of the nudged elastic band chart to make the correspondence between chart and trajectory more obvious. 

MS-61020

The field average produced when asking for Electrostatics and Work function have been corrected. The average for the point at the fractional position 1 was incorrectly averaged. This issue is only noticeable if the slab has atoms in this region.  

MS-61024

Explained that DMol3 MinimumEnergyPath tasks cannot be run in standalone mode. 

MS-61036

For connection to Pipeline Pilot server, Materials Studio is now using a more secure windows native widget

MS-61042

Forcite and Mesocite Dipole Autocorreleation Function now supports trajectories to be calculated with periodic cells having non-zero origin.

MS-61092

Starting a Pipeline Pilot protocol with an active document being a cell of a study table will now create the result folder as a subfolder of the Study Table folder

MS-61436

The version of the COMPASSIII forcefield has been changed to 1.3.

MS-61503

Added a blocking check for use of Optical and Frequency property  in the same task.

MS-61523

The Forcite Solvation Free Energy task now handles solute atoms with ignored van der Waals interactions correctly.

MS-61579

SumOfMasses option of Bead_Mass_Assignment parameter in MS Martini 3 Coarse Grainer now assigns sum of the underlying atoms masses instead of Martini 3 bead type masses if selected.

MS-61640

The requirement for atom/bead velocities for Forcite/Mesocite temperature profile analysis is made clear.

MS-59612

The COMPASSIII torsion parameters for fluoroalkanes (Teflon, PVDF, PVF) have been optimized to improve the density prediction.

MS-60681

Documentation of the steps for displaying electrostatic potential from ONETEP calculations is now correct.

MS-60718

Mean square displacement analysis is not recommended for trajectories with variable cell lengths (NPT ensemble), since results will depend on which periodic images are chosen. A note has been added to documentation discussing this issue.

MS-60964

If you attempt to start the Materials Studio gateway from the 32-bit folder, you now receive a message instructing you to use the 64-bit gateway.

MS-61008

A bug in CASTEP that led to unphysical band structure results with nonlocal functionals B3LYP and PBE0 is fixed.

MS-61057

Forcite and Mesocite now correctly analyze trajectories in which property values are all close to 0.

MS-61657

MS Martini 3 Coarse Grainer script at Materials Studio Scripts menu now supports running with multiple CPUs on remote Windows server.

Resolution                                                                         

BIOVIA Materials Studio 2024 was released in December 2023 and is available for download at https://software.3ds.com under BIOVIA products and can be found under:

Product line: Lab, Scientific and Content Solutions

Release: 2024

Level: BIOVIA 2024 GOLDEN

How to contact BIOVIA Support

If you have any questions, please contact BIOVIA Support.