T40-2021 Notification regarding BIOVIA Materials Studio 2021

MS-31133

COMPASSIII has been extended to support boron compounds relevant to lithium-ion batteries, such as bis(oxalate)borate, difluoro(oxalate)borate, and pyridine boron trifluoride.

MS-38525

Calculation of the tensor of second harmonic generation coefficients is implemented in CASTEP to assist in development of nonlinear optical materials.

LPK-559

The License Pack now uses FlexLM 11.16. The License Pack on the license server must be the highest version installed on the network. Ensure that you update the License Pack on the license server to this version to enable the checkout of licenses on client machines.

MS-32947

Berry phase calculation of spontaneous polarization has been added to CASTEP.

MS-51910

New FlexTS functionality has been added to DFTB+ through the new Minimum Energy Path task. FlexTS provides tools for minimum energy path construction, including an implementation of the nudged elastic band method.

MS-52657

New FlexTS functionality has been added to DMol³ through the new Minimum Energy Path task. FlexTS provides tools for minimum energy path construction, including an implementation of the nudged elastic band method.

MS-54475

The spin-orbit coupling implementation in CASTEP has been extended to include:

¡  On the fly generated norm-conserving pseudopotentials

¡  Calculation of optical properties

¡  Calculations using nonlocal exchange-correlation functionals

A mechanism to set up non-collinear spin configurations in the Materials Visualizer.

MS-54487

Solvation energy calculations for isolated molecules have been implemented in CASTEP.

MS-54511

Support has been added for Urey-Bradley interactions and CHARMM inversions in Materials Studio forcefields.

MS-55386

A family of hybrid functionals has been implemented in ONETEP.

MS-55463

DMol³ molecular dynamics runs can now be initialized with the current velocities from an XSD file.

MS-55860

A new ReaxFF library, ReaxFF SEI, is now included in GULP. It is based on a Hossain et al. publication (J. Chem. Phys., 152, 184301 (2020)) and aims at the description of Li-battery electrolytes and of solid-electrolyte interphases.

MS-56712

The ONETEP module has been updated to use the academic release version 6.1.1 of the code.

MS-56713

GULP is upgraded to the version 6.0. Rigid molecules are now supported for geometry optimization and subsequent property and phonon calculations for bulk systems of any periodicity.

MS-56909

Cantera is upgraded to version 2.4.0 and Python is upgraded to version 3.8.1.

MS-56913

The fracture toughness estimate calculated using an empirical model of Niu et al. (2019) for brittle materials is now included in the results of elastic coefficients calculations in CASTEP and DMol³.

MS-56917

Support for a new van der Waals functional form LJ_12_6_14 has been added for Materials Studio forcefields. This allows you to specify different R0 and D0 values for 1-4 interactions.

MS-56977

A review of the Sorption module has prompted some changes to simplify the implementation, however this should not affect the operation of this module.

MS-57022

The COMPASS (2.8) and cvff_nocross_nomorse forcefields have been moved to the LEGACY_FORCEFIELD folder. Forcefields from this folder can be imported from the Forcite Forcefield Manager dialog. COMPASSII has been removed. Projects with COMPASS or COMPASSII selected will redirect to the current version COMPASSIII.

MS-57058

The Mozilla XPCOM software library has been removed from Materials Studio.

MS-57142

You can now request the use of GPU in Forcite and Mesocite calculations, including for jobs run on any supported queuing system.

MS-57168

A setting ReportAutomaticTerms has been added to all forcefield-based modules to turn on or off the reporting of details about the use of automatic terms, for forcefields that support those.

MS-57198

You can now transfer study tables and trajectories as a single compressed file from Materials Studio to Pipeline Pilot through the connector.

MS-57692

ONETEP implicit solvent calculations have been extended to include the Poisson-Boltzmann scheme. This allows you to include electrolyte ions as point charges that do not interact with each other but contribute to screening of solutes.

MS-57711

A new tutorial demonstrating the Grain Growth (Phasefield) protocol has been added to the Materials Studio documentation.

MS-57771

During the development of Materials Studio 2021 the security of the Gateway was examined in detail. As a consequence, an optional, more secure setting has been introduced for those users and organizations that have strict security requirements.

The first point where the new optional security setting is encountered on Windows is during installation. The default installation does not allow access to the installed gateway, except from the locally installed Materials Studio Visualizer client. You can change this later if required. Other changes that users might notice are:

¡  Passwords are now more securely encrypted and must be not less than 8 characters, contain at least one alphabetical character, one numerical character, and one special character.

¡  You can activate a secure mode, which limits the Materials Studio scripting API to a secure subset (that is, no system calls can be executed and there is no access to any files outside the current job directory). QMERA and Cantera are not available in this mode since they have embedded scripting layers.

¡  All access to a password protected Gateway is blocked, except from authenticated clients.

¡  The possibility of JavaScript injection attack has been greatly reduced.

¡  Gateway components that were out of date, namely Apache, PERL and mod_perl, have been updated to more secure versions.

¡  The SSL/TLS configuration now follows security best practice.

The Material Studio Gateway no longer discloses technical information which could be used by an attacker to perform tailored attacks against identified components.

MS-57779

An augmented version of the cvff forcefield, cvff_aug, can be now imported from the Forcite Forcefield Manager and used in calculations.

MS-57872

All examples structures in .msi format have been converted to .xsd.

MS-57968

A tutorial has been added for both DMol³ and DFTB+ modules to explain the use of the new FlexTS feature for a complex molecular switch energy landscape.  

LPK-562

Security vulnerabilities in FlexNet License Server libraries used in the BIOVIA License Pack have been addressed by upgrading them to FlexNet 11.16.6.

MS-56785

Imposing a found crystal symmetry is no longer at risk of instability, even in the rare cases previously observed.

MS-56791

For certain structures containing either empty space or fixed atoms, parallel Forcite PPPM calculations no longer fail.

MS-56793

DMol³ calculations of very small symmetric molecules on highly parallel computers is now more stable, use of a small number of cores is enforced.

MS-56853

Mol2 files produced by Discovery Studio, containing @<SCITEGIC>ROOT_PROPERTY records, can now be imported.

MS-56864

Forcite cannot modify .mol2 trajectories. An improved, more clear error message now reports this.

MS-56939

The description of block averaging in Forcite and Mesocite Analysis has been corrected.

MS-57279

COMPASS III torsions were restored to those in COMPASS 2.8.

MS-57523

The documentation on importing PDB files has been extended with a note on how to obtain the correct bond orders.

MS-57796

The use of cutoff Coulomb scheme in ONETEP is improved: only molecule in a box systems are accepted, and the molecule is automatically translated to the center of the cell.

MS-57892

The version of Apache deployed in the Materials Studio Gateway has been upgraded to 2.4.46 on all supported platforms.

MS-57936

VAMP frequency calculation takes isotopes into account.

LPK-493

The diagnositic lp_profile command no longer generates repeated output.

MS-53148

For a cell file with a hexagonal unit cell, %BLOCK POSITIONS_NOISE no longer discards the actual cell vectors.

MS-54778

The exocyclic scale factor now applies to the Scaled Dihedral functional form. This affects only custom forcefields that use both the Scaled Dihedral form and have a non-unity exocyclic scale factor. The standard forcefields are unaffected.

MS-56652

In the Reaction Preview dialog, any molecular hierarchy in input documents is now removed before generating the preview, which makes using it significantly more stable. 

The Superpose Structures checkbox is now checked by default, reflecting updated best practices for working with reaction previews.

MS-56670

The .elec file produced by a DFTB+ parameterization is no longer hidden. The DFTB+ tutorial has been modified to reflect this.

MS-56702

The Forcite multiple time step algorithm now performs an electrostatic k-space calculation every fourth time step (by default), using a one-based count of the time steps (previously a zero-based count was used). This is now in synchronization with the writing of energies to the trajectory file (which is also done according to a one-based count). This ensures that the trajectory energies are accurate when multiple time-stepping is used.

MS-56790

The GULP input file reader now properly ignores empty lines at the end of the spline potential specification.

MS-56797

Context-sensitive access to the online help has been added for workfunction-related results in DMol³ and CASTEP scripting. The units for the DMol³ workfunction results have been corrected in the scripting documentation.

MS-56818

The Fragment Browser dialog now displays correctly when it is opened.

MS-56832

DMol³ COOP analysis now displays the correct energy range.

MS-56842

Atom constraints are now applied correctly in CASTEP parallel molecular dynamics calculations.

MS-56851

When using AppendFramesFrom in the MaterialsScript API, the ValenceDiagonalEnergy property is now updated.

MS-56874

Execution time information in the CASTEP NMR tutorial has been revised.

MS-56957

The documentation for running standalone band structure and density of states calculations in DMol³ have been clarified.

MS-56965

You can now remove filters applied to the QSAR Models dialog even when no models are displayed by the current filters.

MS-56992

Forcite Analysis of the spatial orientation correlation function when applied to trajectories containing a structure with a non-zero lattice origin is now more reliable.

MS-57026

CASTEP's linear response calculation of phonons is now more robust. Previously, under extremely rare circumstances it produced unphysical large imaginary phonon frequencies resulting in an error, when:

¡  There is a non-symmorphic symmetry operation in the group of phonon wave -vector q.

¡  One of the perturbations does not reduce the symmetry further.

The non-symmorphic symmetry maps an ion i onto itself. Considering the displacement, this can only occur if the ion is mapped onto a periodic image.

MS-57029

CASTEP preconditioned geometry optimizations are now more robust.

MS-57036

At the end of a Forcite energy calculation using the Ewald sum for the van der Waals interaction, the "Ewald Self correction" and "Ewald Excluded correction" values are no longer incorrectly transposed. The value of the total van der Waals interaction was always correctly calculated.

MS-57039

Scaled 1-4 interactions in 5-membered rings in Forcite are now handled consistently.

MS-57069

Finite displacement phonon calculations that use the Several small supercells option are faster because they use a better-tuned set of k-points.

MS-57138

The Adsorption Locator documentation on preparing the adsorbate structures using Forcite has been extended with a recommendation on which summation methods to use.

MS-57153

MOL2 format files with large SET records can now be read successfully. This fault could previously occur in cases such as proteins, having larger backbone or side-chain groups, and resulted in an empty or incomplete structure.

MS-57269

COOP charts use significantly less memory by no longer charting zero-valued results.

MS-57339

The CopyScript content for the Mesocite Shear task now includes the energy settings.

MS-57438

The functional form LJ_12_10 can now be selected for van der Waals Form of types in the forcefield viewer.

MS-57448

CASTEP population analysis is no longer performed during properties calculations, Mulliken and Hirshfeld analysis is only reported in the output of the  main calculation.

MS-57559

A Forcite Mechanical Properties calculation using the Stress fluctuation or Static method on a very large structure can fail because a large Hessian matrix must be calculated and that can exceed the available memory. In the case of a Forcite Energy Hessian calculation, a warning message is already given before the job is started. An identical warning is now given when required before a Forcite Mechanical Properties calculation.

MS-57650

The message that appears on opening a view on an encrypted forcefield has been improved.

MS-57684

Description of constraints support in GULP module is corrected in the Visualizer Tools documentation.

MS-57785

Enablement of DMol³ user interface controls for metallic systems and smearing value is corrected.

MS-57792

Centroids are now excluded from the radius of gyration analysis in Forcite.

MS-57849

The parameters and units of the Cosine Periodic angle bend potential have been corrected in documentation and in the forcefield viewer.

MS-57935

GULP implementation of the Tersoff potential for mixed systems was found to be inconsistent with other implementations in the case where a three-body contribution is present. The convention has been changed to be consistent with other codes, and additional functionality has been added to support further terms in the Tersoff expressions that were 1 in the original paper, but have been subsequently used in other parameterisations.

MS-58023

Documentation in configuration files for supported queruing systems has been improved; it is now more specific on the syntax for specifying various parameters.

MS-58025

For Materials Studio installations using the SLURM queueing system, you can now request that SLURM provides hostname addresses instead of machine names in the list of available nodes on which to run jobs.

MS-58064

You can now use the RSCAN functional in CASTEP with any type of runtime optimization.

MS-58115

The tutorial Coarse graining atoms to beads has been modified to improve the bead representation of a nanotube.

MS-56699

The instructions in the Polymorph tutorial "Predicting the crystal structure of 3-oxabicyclo(3.2.0)hepta-1,4-diene" now include generation of a density chart.

MS-56704

The new Morse potential option is now recorded correctly in the GULP restart file.

MS-56711

The crystal structures of ethanol and toluene have been updated to show the correct number of molecules in the unit cell. Hydrogen atoms have been added to molecular crystals where they were missing.

MS-56796

During vibration property calculations in DMol³, the potential and density files are only kept in memory and not written to disk, leading to significant performance improvements for restarted vibrations runs.

MS-56814

The MaterialsScript filter documentation topics now offer more assistance on working with symmetric and periodic systems.

MS-56826

Gradient (.grad) files created by DMol³ are now hidden in the Materials Studio Visualizer.

MS-56865

Aromatic bonds are now correctly exported as 'ar' in mol2 format.

MS-56899

In rare cases of constrained geometry optimizations for DMol³, convergence can only be achieved with taking very small steps. An error message has been clarified to reflect this.

MS-56911

Issues when opening a file in Materials Studio from outside of Materials Studio have been resolved. For example, from Windows Explorer or a browser's downloads list.

MS-56927

When scripts jobs are run client-side with the Polymer Builder dialog open, the dialog now correctly resets itself on job completion.

MS-56958

The format of band files created with EDFT calculations in ONETEP has been standardized, leading to an improved user experience when analysing calculations.

MS-56959

You can now import .xyz files where element lines start with a space.

MS-56976

The mass density profile (obtained using the Forcite Analysis Concentration profile method with Property set to "Mass density") now gives the correct result when "Frames to average" is selected.

MS-56988

The VAMP documentation now includes a list of conditions that must be satisfied for the calculation of 13C NMR chemical shifts.

MS-57019

Editing gateway settings no longer appends spurious errors to the log.

MS-57041

The solvent lists in all Materials Studio modules are now the same.

MS-57150

The online help now includes a note linking to an external cif file syntax checker. 

MS-57152

An angle potential for (p4= n2= c3n) was introduced to COMPASSIII resolving an issue in PoLyInfo structure P180043.

MS-57154

The message regarding scf_direct in DMol³ outmol files has been clarified to match the documented keyword syntax. 

MS-57166

Explicit bond and angle potentials for sulfur hexafluoride were added to COMPASS III.

MS-57171

The DMol³ and CASTEP documentation on running standalone jobs now states the correct location of the ms_vars.sbd gateway file.

MS-57255

The cvff_nocross_nomorse forcefield has been moved to the FORCEFIELD-LEGACY folder, and can be imported in the project via the Forcite Forcefield Manager dialog.

MS-57288

The COMPASSIII bond increments for fluorine-carbon in perfluoroalkanes have been refitted to ESP charges from DMol³, averaged over large number of substituted alkanes.

MS-57291

The number of significant figures printed in the outmol for the atomic population analysis for Mulliken, Hirshfeld, and ESP charges has been increased to six throughout.

MS-57293

Polymorph no longer generates a spurious and confusing error message when no solution is found.

MS-57377

The TrajectoryRestart and AppendTrajectory settings are now included in the Copy Script for the Mesocite DPD tasks, and are documented in MaterialsScript.

MS-57401

Saving the settings for Forcite or Mesocite with an unsaved custom forcefield selected on the dialog no longer reports an error.

MS-57567

The Confined Shear output report now contains the wall velocity, and no longer contains the unused ensemble, thermostat, and barostat settings.

MS-57592

The CASTEP documentation now explains the difference between the charge spilling parameter and the all bands spilling parameter in population analysis.

MS-57606

Temporary folders created during the copying of Documents into Study Table cells are no longer left behind.

MS-57621

The link to the Materials Studio Home Page from the Help menu has been updated.

MS-57725

The DMol³ Materials Studio logic will no longer attempt to calculate orbitals for periodic lattices in situations when they had been previously selected to run for another system.

MS-57772

The documentation on cvff_aug has been updated.

MS-57820

Fixed atom constraints are now removed immediately when requested.

MS-57822

The status report for CASTEP properties runs now includes the exchange-correlation functional when it's different from that used in the SCF calculation.

MS-58090

Protocol Completed dialog instead of reporting process-failure  as the status  will report now unknown-completed if it was not able to find the actual  status the protocol