ECCE 9.3.0

ECCE 9.3.0. Please report problems as issues.

Platforms. Linux (Debian 13; Ubuntu 24.04, RHEL/Rocky 9 and Fedora packages are built on those systems but not tested). Windows 10 and 11. macOS, Apple silicon and Intel: experimental.

GROMACS (#262, #334, #336, #363, #375)

• Prepare task: a task that builds the system for the MD tasks that follow. Sources: a PDB file (pdb2gmx), a mineral or clay (MINFF, or ClayFF as the force field), or a structure from the Builder. Verify shows a labelled summary, the real file names with sizes and the commands that will run; a force field can be imported (folder or zip) into a per-user library and is staged with the job.
• Minerals (MINFF, ClayFF): the MINFF unit cells, atomipy and min.ff are bundled, so this route needs no download. The editor sets layer repeats (one field per axis), ions (genion -rmin, a neutralise tick box, ion parameter set) and a gap for a cell that bonds to its own image along c; min.itp carries position restraints on heavy atoms. ClayFF parameters follow the published ClayFF set. The Layer Builder (Tools > Layer Builder) stacks a layer with ions and water, undoably. For a crystal that is not layered along c the editor says what to do instead (no water layer for the bulk, or a slab cell).
• Launch check: stopping warnings and grompp errors are shown in a dialog with Cancel and Launch anyway; harmless warnings are not shown. Launch without a structure says what each source needs; Build topology is framed in red until the topology is built (#399).
• Results: one MD Summary panel with final values and run averages with their standard deviations; minimisation shows the energy and the maximum force (#334). The trajectory is kept as a geometry trace that the Builder animates (at most 100 frames). The Viewer draws the true box, including the rhombic dodecahedron and the truncated octahedron, with the molecules wrapped into it.
• Run importer: File > Import GROMACS Run... turns a finished run into a GROMACS MD study (#375). A protein example (the 1L2Y Trp-cage) made from a real run is imported at first start, with a first-calculation tutorial in the help.
• MD editor: defines, restraints, groups, barostat type and extra .mdp lines. A Dynamics task after Equilibrate or Dynamics opens with Continue ticked (#374).
• Fixes: a Prepare placed after other tasks no longer inherits their structure and topology (#397); the box is drawn around the atoms (#398); the Inputs and Run settings pages scroll instead of being cut off.

CP2K (#329)

A new code: registration, Theory Details and Runtype Details, input generation and checking, output parsing with Progress, and reasons for failure.

Quantum ESPRESSO

• Verify checks the sections and marks the deck lines it examined.
• On a cluster, the code's ESPRESSO_PSEUDO setting replaces the client's folder in pseudo_dir when the job runs.

Gaussian 16: relaxed scan (#393, #396)

A scan option in the Geometry Constraints window (Scan... and Save, the scan shown in its row). The step count and step go to the ModRedundant line as S n step; the step is always written as a number with a decimal point. The Viewer has a Relaxed Scan panel with CSV export, read from the Summary of Optimized Potential Surface Scan. Verify no longer counts ModRedundant lines as atoms.

Duplicate with Final Orbitals, ORCA (#75)

Duplicate with Final Orbitals starts the copy from the source calculation's MOs. The Calculation Editor's initial-guess line says when the orbital file is missing or older than the input file, and follows changes of property.

Vibrational Frequencies (#367, #392, #369)

• The table gives each mode's symmetry and a description; frequency and description are on their own lines, and the detail line breaks at its separators.
• Export .csv writes the spectrum for a spreadsheet (#392).
• The panel opens on the first vibration with a 0-3400 spectrum.
• MOPAC FORCE normal modes are rotated into the stored geometry's frame (#369).

Register Machines

• A Modules line on the Codes tab, with Find loading modules; one box per setting.
• The Machine tab has per-user fields: run directory and account. A job that runs on this computer shows no remote login in the Launcher.
• First start registers every code found on the PATH (#377); on macOS the login shell's PATH and the Homebrew and MacPorts folders are searched too.

Calculation menu and Organizer

• Gaussian 09 is no longer offered under New Calculation; existing calculations still open.
• The right-click menu offers Import Calculation from Output File.
• The Organizer detail pane shows no Basis Set button for a code whose theories need no basis set; ECCE-QM keeps it.

Look (#210)

• Builder and Viewer toolbar: the Classic ECCE icons redrawn as scalable images, one family, the toolbars side by side from the left.
• Calculation Editor: the code buttons are grouped (DFT, Semi-empirical, Periodic) with new icons for ORCA, ECCE-QM, Quantum ESPRESSO, CP2K and MOPAC.
• Plots: every plot (step plots, geometry trace, relaxed scan, MO levels, reaction plots) is drawn like the vibrational spectrum: hover readout, drag or wheel to zoom, double-click to fit.
• Properties list (list and detail layout): as tall as its entries, so the panel below gets the rest; no header above it.
• About: one window, left-aligned.

MO diagram (experimental, #301, #368)

Rebuilt as a model-first fragment-orbital diagram: choose it by picking one atom or one bond, with a verdict, an About dialog and a Ligand-field view. It remains experimental and can be incomplete for larger molecules.

Other changes

• Copy values (#408): in Energies and the other panels that list values, a right-click copies a value, a value with its unit, or all rows as tab-separated lines for a spreadsheet.
• Launcher: a machine with queues shows its full form again; wider fields; a small message area.
• Periodic Builder: space groups listed with their number and crystal system; a click in a cell field selects its value; the crystal system of the chosen group fixes the dependent cell parameters.
• Builder: clicking an atom with the same element and shape builds on its first open site (two O atoms now bond); the second click of a double-click no longer adds an atom.
• MOPAC: the bundled example has its orbital file, so its MOs show a composition; an imported run's .mgf beside the output is read.
• ECCE-QM lists the spin expectation value S^2 only for an unrestricted reference, and for restricted open-shell runs (#390).
• Builder: an editable calculation opens with the Build tool shown; units appear as kJ/mol, kcal/mol and K; elements 110-118 use the IUPAC symbols.
• ECCE-QM basis menu grouped (minimal, Pople, Dunning, Karlsruhe), with def2-TZVP added.
• NWChem MD: the force-field defaults no longer depend on the DataServers file, and the solvent boxes are found from the job script (#380).
• Windows that fit small screens: the Basis Set Tool, the Geometry Step Plots, the Properties list and the panel decoration (#337, #335, #351, #379).
• About names the commit of a development build.

Fixed from the 9.3 test round

• Lattices from cell parameters were transposed for cells without right angles (#398).
• Relaxed scan input: a scanned coordinate carried a value on its ModRedundant line (#396).
• Prepare after other tasks inherited their structure and topology (#397).
• Progress plot: a plot is drawn again from two points (#400); a time estimate needs two finished steps.
• Relaxed scan plot: the scanned coordinate was taken from a bond that hardly moved, and a dihedral scan through 180 degrees was unwrapped wrongly (#396).
• Help pages: the walkthroughs use the Organizer's tool buttons and are reworded to match the windows.

Bundled for GROMACS minerals

• atomipy 0.98 and min.ff at commit d12b895 (the newest min.ff renames its parameter files, which ECCE does not follow yet), tested with the MINFF and ClayFF suites.

Known issues

• GROMACS, CP2K and Quantum ESPRESSO remain experimental.
• The MO diagram is experimental.

Packages

System	Files
Debian 13	ecce-client_9.3.0_amd64.deb, ecce-server_9.3.0_amd64.deb
Ubuntu 24.04	ecce-client_9.3.0_ubuntu24.04_amd64.deb, ecce-server_9.3.0_ubuntu24.04_amd64.deb
RHEL/Rocky 9	ecce-client-9.3.0-1.el9.x86_64.rpm, ecce-server-9.3.0-1.el9.x86_64.rpm
Fedora	ecce-client-9.3.0-1.fedora.x86_64.rpm, ecce-server-9.3.0-1.fedora.x86_64.rpm
macOS 11 or newer (experimental)	ECCE-9.3.0-arm64.dmg (Apple silicon), ECCE-9.3.0-x86_64.dmg (Intel)
Windows 10/11	ECCE-windows-9.3.0.msi (installer) or ECCE-windows-9.3.0.zip

Installation: Installing ECCE. Videos: chem4eva on YouTube.