Crystal & volumetric visualization
Load structures, set views and measure distances, angles and isosurfaces.
20 project-authored proposals · taxonomy v1.1 · 0 new benchmark runs. Verifiers and partial-credit rules below are designs, not executed results.
- Typical applications
- VESTA · Mercury · OVITO
- Class GUI-need label
G2· GUI-essential
Task proposals · 20
Expand to inspect the complete original wording and proposed checks. Original proposal text remains English in both interfaces.
R08.02.01.03-T01 Build a 2×2×2 silicon supercell in VESTA and export it as POSCAR
Original instruction
Open input/Si.cif (diamond cubic, a = 5.431 Å) in VESTA. Use the unit-cell transformation dialog to build a 2×2×2 supercell as a new structure and export it in VASP format to output/Si_222.vasp.
- Platforms
mac· macOSwin· Windows- Applications
- VESTA
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & forms- Work product
WP04· 3D/spatial model- Conditions
- None declared
- Proposed difficulty
- 2 / 5
Proposed verifier
POSCAR must hold 64 Si atoms, cubic lattice 10.862±0.001 Å and fractional positions equal to the gold supercell set (tolerance 1e-4). The VESTA-written title/scale lines are checked; ASE/pymatgen are not installed in the image and python processes are logged.
Proposed partial credit
40% lattice vectors correct; 40% 64 atoms at correct positions; 20% valid VESTA POSCAR export.
R08.02.01.03-T02 Display the (104) lattice plane of corundum in VESTA and report its d-spacing
Original instruction
Open input/Al2O3.cif (corundum, hexagonal setting) in VESTA. Add the (1 0 4) lattice plane through the cell using the lattice-plane dialog, colour it semi-transparent orange, save output/corundum_104.vesta and write the d-spacing in Å to output/answer.json.
- Platforms
mac· macOSwin· Windows- Applications
- VESTA
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & formsvis· Visual judgment- Work product
WP12· Answer/decision- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
d-spacing must equal gold within 0.001 Å. The .vesta file must contain a PLANE entry with Miller indices 1 0 4 and an orange RGBA with alpha <255. pymatgen and ASE are not installed on the VM, and a file-system audit log flags a .vesta not written by VESTA.
Proposed partial credit
50% correct d-spacing; 35% (104) plane saved in .vesta; 15% colour/transparency set.
R08.02.01.03-T03 Render a charge-density isosurface from CHGCAR in VESTA at a specified level and view
Original instruction
Open input/CHGCAR (Li adsorbed on graphene, VASP) in VESTA. Set a single isosurface at level 0.05, yellow with 50% opacity, hide bonds to Li, view along [001] and export a 1600×1200 image with white background to output/rho.png. Save the session as output/rho.vesta.
- Platforms
mac· macOSwin· Windows- Applications
- VESTA
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgment- Work product
WP03· Visual layout- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
.vesta must list the CHGCAR with ISURF level 0.05, the stated colour/opacity and a view direction within 2° of [001]. rho.png must be 1600×1200 and reach SSIM ≥0.85 against the reference VESTA render. pymatgen and VESTA batch mode are not installed; the .vesta session must hold the isosurface settings, and a file-system audit log flags a .vesta or PNG not written by VESTA.
Proposed partial credit
35% isosurface level and colour; 25% view direction; 25% image matches reference; 15% session saved.
R08.02.01.03-T04 Measure the two distinct Ti–O bond lengths of rutile in Mercury
Original instruction
Open input/rutile.cif in Mercury, display the TiO6 octahedron around one Ti, measure the apical and equatorial Ti–O distances with the measurement tool and write both values (Å) to output/answer.json with keys apical and equatorial.
- Platforms
mac· macOSwin· Windows- Applications
- Mercury
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clickvis· Visual judgment- Work product
WP12· Answer/decision- Conditions
- None declared
- Proposed difficulty
- 2 / 5
Proposed verifier
Both values must match gold within 0.005 Å and be assigned to the correct key (apical is the longer bond). The CSD Python API and other crystallography toolkits are not installed in this image, so distances must be measured in Mercury.
Proposed partial credit
50% apical distance; 50% equatorial distance.
R08.02.01.03-T05 Identify the carboxylic-acid dimer motif in benzoic acid and report its H-bond geometry
Original instruction
Open input/benzoic_acid.cif in Mercury, display hydrogen bonds and expand contacts to reveal the centrosymmetric acid dimer. Report its graph-set descriptor, the O···O distance and the O–H···O angle in output/answer.json and save the view as output/dimer.mryx.
- Platforms
mac· macOSwin· Windows- Applications
- Mercury
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickvis· Visual judgment- Work product
WP12· Answer/decision- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
Graph set must equal R2,2(8) (normalized); O···O within 0.005 Å and angle within 0.5° of gold from the CIF. dimer.mryx must exist and show H-bond contacts enabled. The CSD Python API is not installed in this image, and a file-system audit log flags a dimer.mryx not written by Mercury.
Proposed partial credit
30% graph-set descriptor; 30% O···O distance; 25% angle; 15% session saved.
R08.02.01.03-T06 Match an experimental powder pattern to one of three polymorphs with Mercury
Original instruction
input/ has three polymorph CIFs (formA–C) of a drug and an experimental pattern exp_pxrd.xy (Cu Kα1, 5–40° 2θ). In Mercury calculate each powder pattern with FWHM 0.1°, compare against the experiment, write the matching form to output/answer.json, and export the matching calculated pattern to output/calc.xy.
- Platforms
mac· macOSwin· Windows- Applications
- Mercury
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clickvis· Visual judgment- Work product
WP12· Answer/decision- Conditions
- None declared
- Proposed difficulty
- 4 / 5
Proposed verifier
Polymorph choice must equal gold (decided by preferred-orientation-robust peak matching). calc.xy must cover 5–40° and correlate ≥0.99 with the reference Mercury pattern for that form at FWHM 0.1°. The CSD Python API is not installed; calc.xy must be a Mercury export, which a file-system audit log attributes to the Mercury process.
Proposed partial credit
50% correct polymorph; 30% calculated pattern settings correct; 20% exported file.
R08.02.01.03-T07 Draw TiO6 polyhedra for SrTiO3 viewed along [001] in VESTA
Original instruction
Open input/SrTiO3.cif in VESTA. Show 2×2×2 cells, draw TiO6 octahedra in blue with black edges, show Sr as spheres with radius 0.6 Å, hide Sr–O bonds, view along [001] with orthographic projection, then save output/sto.vesta and a 1200×1200 output/sto.png.
- Platforms
mac· macOSwin· Windows- Applications
- VESTA
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgment- Work product
WP03· Visual layout- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
Parse .vesta: BOUND 0 2 0 2 0 2, POLYS for Ti–O, SITET radius 0.6 for Sr, no Sr–O bond entry, orthographic flag, view direction within 2° of [001]. PNG SSIM ≥0.85 vs reference render. pymatgen and ASE are not installed; the .vesta must carry the polyhedra and view settings, and a file-system audit log flags a .vesta or PNG not written by VESTA.
Proposed partial credit
25% boundary range; 25% polyhedra style; 20% Sr spheres/bonds; 30% view and image match.
R08.02.01.03-T08 Isolate the major disorder component in Mercury and report its occupancy and torsion
Original instruction
input/disordered.cif contains a tert-butyl group disordered over two parts. In Mercury display only the major disorder component, report its occupancy and the torsion angle C3–C4–C5–C6 within that component in output/answer.json, and save the view as output/major.mryx.
- Platforms
mac· macOSwin· Windows- Applications
- Mercury
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickvis· Visual judgment- Work product
WP12· Answer/decision- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
Occupancy must equal the CIF value of the major part; torsion within 0.5° of gold computed with major-part atoms only (using a minor-part atom gives a distinct wrong value). Session must show disorder set to the major component. The CSD Python API is not installed in this image, and a file-system audit log flags a major.mryx not written by Mercury.
Proposed partial credit
35% correct component chosen; 35% torsion correct; 20% occupancy; 10% session saved.
R08.02.01.03-T09 Run dislocation analysis on a copper tensile MD trajectory in OVITO
Original instruction
Open input/cu_tension.dump (200 frames) in OVITO. Add adaptive Common Neighbor Analysis and Dislocation Analysis (fcc lattice). Report total dislocation line length (Å) and Shockley partial segment count at frames 50, 100 and 150 in output/dxa.csv, export frame 100 dislocation lines in CA format, and save output/session.ovito.
- Platforms
mac· macOSwin· Windows- Applications
- OVITO
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicknav· Pan/zoom/scrollvis· Visual judgment- Work product
WP07· Simulation result- Conditions
long· Long-horizon- Proposed difficulty
- 5 / 5
Proposed verifier
Per frame, line length within 5% and Shockley count within ±2 of the reference DXA run. session.ovito pipeline must contain CNA then DXA with fcc lattice; the CA file must parse with segments at frame 100. OVITO Basic is used: the ovito Python module, ovitos and the Python script modifier are not installed.
Proposed partial credit
20% pipeline configured; 45% three frames reported correctly (15 pts each); 20% CA export; 15% session saved.
R08.02.01.03-T10 Colour a metallic glass by coordination and render a mid-slab slice in OVITO
Original instruction
Open input/cuzr_glass.xyz in OVITO. Add Coordination Analysis (cutoff 3.2 Å), Color Coding on coordination 10–16 with the Viridis map, and a Slice through the box centre normal to z with 5 Å width. Render 1600×1200 output/slice.png from the +z view and save output/glass.ovito.
- Platforms
mac· macOSwin· Windows- Applications
- OVITO
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & formsvis· Visual judgment- Work product
WP03· Visual layout- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
Session pipeline parsed: Coordination cutoff 3.2, Color Coding range 10–16 Viridis, Slice normal (0,0,1) at box centre, width 5. Render must be 1600×1200 with SSIM ≥0.85 against the reference render. OVITO Basic is used: the ovito Python module, ovitos and the Python script modifier are not installed.
Proposed partial credit
25% coordination modifier; 25% color coding; 25% slice; 25% render matches.
R08.02.01.03-T11 Compute and slice a charge-density difference map in VESTA
Original instruction
input/ holds CHGCAR_AB, CHGCAR_A and CHGCAR_B on identical grids for a molecule on a surface. In VESTA build Δρ = ρAB − ρA − ρB with the volumetric-data arithmetic, show isosurfaces ±0.002 (yellow/cyan), export the (001) slice at z = 0.42 from 2D Data Display to output/slice.txt, and save output/diff.vesta.
- Platforms
mac· macOSwin· Windows- Applications
- VESTA
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & formsvis· Visual judgment- Work product
WP07· Simulation result- Conditions
- None declared
- Proposed difficulty
- 4 / 5
Proposed verifier
diff.vesta must reference all three files with subtract operations and isosurfaces at ±0.002. slice.txt values must match the reference Δρ slice (max abs error 1e-4 after grid alignment); report of max/min in slice within 1%. VESTA batch tools and pymatgen are not installed; slice.txt must be a 2D Data Display export, and a file-system audit log flags a slice.txt or .vesta not written by VESTA.
Proposed partial credit
35% difference density built; 20% isosurfaces set; 35% slice exported correctly; 10% session saved.
R08.02.01.03-T12 Calculate solvent-accessible voids in a MOF cell with Mercury
Original instruction
Open input/mof_cell.cif in Mercury and run the voids calculation with a 1.2 Šprobe, 0.7 Šgrid spacing, contact surface. Report total void volume (ų) and percentage of the unit cell in output/answer.json and save a void-surface view as output/voids.png.
- Platforms
mac· macOSwin· Windows- Applications
- Mercury
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clicktype· Text & forms- Work product
WP12· Answer/decision- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
Void volume and percentage must be within 1% of the reference Mercury calculation at the same settings (a different probe or surface type misses the band). voids.png must show the void surface (non-empty coloured pixels in the cell region). The CSD Python API is not installed in the image, so the calculation must run in Mercury.
Proposed partial credit
30% settings correct (probe/grid/surface); 50% void volume and percent; 20% image saved.
R08.02.01.03-T13 Build a Pt(111) four-layer slab with vacuum from a bulk CIF
Original instruction
Starting from input/Pt.cif, build a Pt(111) slab with a 3×3 surface cell, four atomic layers and 15 Å vacuum along c, with the surface normal parallel to c. Use VESTA's lattice transformation and any scripting you need, and write output/POSCAR plus a VESTA view output/slab.png along [100].
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- VESTA · ASE
- Interfaces
desk· Desktop GUIterm· Terminal- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickcode· Code & commandsvis· Visual judgment- Work product
WP04· 3D/spatial model- Conditions
multiapp· Multi-app- Proposed difficulty
- 4 / 5
Proposed verifier
POSCAR: 36 Pt atoms in 4 layers spaced 2.26±0.02 Å, in-plane hexagonal a = 8.32±0.02 Å, c ⟂ surface, vacuum gap ≥15 Å, fcc ABCA stacking. slab.png must show four layers (layer count by intensity profile).
Proposed partial credit
25% surface cell correct; 25% four layers with correct stacking; 25% vacuum; 25% view image.
R08.02.01.03-T14 Measure π–π stacking between pyrene molecules in Mercury
Original instruction
Open input/pyrene.cif in Mercury. Define centroids on the aromatic rings, find the shortest centroid–centroid contact between parallel rings of adjacent molecules, and report that distance and the interplanar angle in output/answer.json. Save output/stack.mryx with the centroids and measurement shown.
- Platforms
mac· macOSwin· Windows- Applications
- Mercury
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickvis· Visual judgmentnav· Pan/zoom/scroll- Work product
WP12· Answer/decision- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
Distance within 0.01 Å and angle within 0.5° of gold (gold excludes intramolecular and non-parallel ring pairs). Session must contain centroid objects and the measurement. The CSD Python API is not installed in this image, and a file-system audit log flags a stack.mryx not written by Mercury.
Proposed partial credit
50% correct ring pair and distance; 30% interplanar angle; 20% session saved.
R08.02.01.03-T15 Read formula units, density and symmetry-operation count for a garnet in VESTA
Original instruction
Open input/garnet.cif (Ia-3d) in VESTA. From VESTA's structure information output, report Z, the calculated density (g/cm³, 3 decimals) and the number of symmetry operations in output/answer.json.
- Platforms
mac· macOSwin· Windows- Applications
- VESTA
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicknav· Pan/zoom/scroll- Work product
WP12· Answer/decision- Conditions
- None declared
- Proposed difficulty
- 2 / 5
Proposed verifier
Z and symmetry-operation count must equal gold exactly; density within 0.001 g/cm³. pymatgen, ASE and spglib are not installed on the VM, so the values must be read from VESTA's structure-information output.
Proposed partial credit
35% Z; 35% density; 30% symmetry operations.
R08.02.01.03-T16 Segment grains in an aluminium polycrystal in OVITO and export a grain table
Original instruction
Open input/al_poly.data in OVITO. Add Polyhedral Template Matching with orientation output, then Grain Segmentation; tune the merge threshold until the 8 grains are recovered. Export a grain table (ID, atom count, orientation quaternion) to output/grains.txt, render grains coloured by ID to output/grains.png, and save output/poly.ovito.
- Platforms
mac· macOSwin· Windows- Applications
- OVITO
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & formsvis· Visual judgment- Work product
WP07· Simulation result- Conditions
- None declared
- Proposed difficulty
- 5 / 5
Proposed verifier
Exactly 8 grains; per-grain atom counts within 3% and orientations within 2° misorientation of gold after best matching. poly.ovito pipeline must contain PTM (orientations on) then Grain Segmentation. The ovito Python module, ovitos and the Python script modifier are not installed (OVITO Basic), so the pipeline must be built in the OVITO GUI.
Proposed partial credit
20% PTM configured; 35% eight grains found; 30% counts and orientations match; 15% render and session.
R08.02.01.03-T17 Locate stereochemically active lone pairs from an ELF isosurface in VESTA
Original instruction
input/ holds Sb2O4.cif and its ELFCAR. In VESTA show the ELF isosurface at 0.80 and decide which Sb site (Sb1 or Sb2) is Sb(III) from the lone-pair lobe. Report that site and the fractional coordinates of its lone-pair ELF maximum in output/answer.json; save output/elf.vesta.
- Platforms
mac· macOSwin· Windows- Applications
- VESTA
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgment- Work product
WP12· Answer/decision- Conditions
- None declared
- Proposed difficulty
- 4 / 5
Proposed verifier
Site label must equal gold. Lone-pair maximum must lie within 0.3 Å of the gold ELF maximum (Cartesian, minimum image). elf.vesta must contain the ELFCAR with ISURF 0.80. pymatgen and ASE are not installed on the VM, and a file-system audit log flags an elf.vesta not written by VESTA.
Proposed partial credit
50% correct Sb(III) site; 35% lone-pair position; 15% session saved.
R08.02.01.03-T18 Control: build the silicon supercell POSCAR with a Python script
Original instruction
Control pair of T01. Without a GUI, use ASE or pymatgen from the terminal to build a 2×2×2 supercell of input/Si.cif and write it as output/Si_222.vasp in VASP format.
- Platforms
mac· macOSlin· Linux- Applications
- ASE · pymatgen
- Interfaces
term· Terminal- GUI need · task setting
CL· CLI-sufficient- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
code· Code & commands- Work product
WP04· 3D/spatial model- Conditions
- None declared
- Proposed difficulty
- 2 / 5
Proposed verifier
Same checker as T01 for lattice and atom positions (64 Si, a = 10.862±0.001 Å). Scored as the CLI control of T01.
Proposed partial credit
40% lattice; 40% atom positions; 20% valid POSCAR.
R08.02.01.03-T19 Compare two polymorph packings with Crystal Packing Similarity in Mercury
Original instruction
Open input/formI.cif and input/formII.cif in Mercury (CSD-Materials licence active). Run Crystal Packing Similarity with a 15-molecule cluster, 20% distance and 20° angle tolerances, ignoring H. Report the number of matched molecules and RMSD in output/answer.json and save the overlay image as output/overlay.png.
- Platforms
mac· macOSwin· Windows- Applications
- Mercury
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & formsvis· Visual judgment- Work product
WP12· Answer/decision- Conditions
licensed· Licensed pro apptutorial· Follow docs/tutorial- Proposed difficulty
- 5 / 5
Proposed verifier
Matched-molecule count must equal gold exactly and RMSD be within 0.01 Å of the reference run at the stated settings. overlay.png must show two coloured overlaid clusters (two dominant hues present). The CSD Python API is not installed, so the comparison must run in Mercury; a file-system audit log flags an overlay.png not written by Mercury.
Proposed partial credit
25% settings correct; 40% matched count; 25% RMSD; 10% overlay image.
R08.02.01.03-T20 Display antiferromagnetic NiO spin vectors in VESTA and identify the ferromagnetic planes
Original instruction
Open input/NiO_mag.mcif in VESTA, add vector objects on Ni for the magnetic moments (scale 1 Å per μB, red for one spin direction and blue for the other) in a 2×2×2 view, save output/nio.vesta, and report in output/answer.json the Miller index family of the ferromagnetically aligned Ni planes.
- Platforms
mac· macOSwin· Windows- Applications
- VESTA
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & formsvis· Visual judgment- Work product
WP04· 3D/spatial model- Conditions
- None declared
- Proposed difficulty
- 4 / 5
Proposed verifier
nio.vesta VECTR/VECTT entries must assign vectors to all Ni sites with directions matching the mcif moments (cosine >0.99), lengths scaled 1 Å/μB and two colours by sign. Answer must be the {111} family. pymatgen's magnetic tools are not installed; vectors must exist as VESTA objects, and a file-system audit log flags a nio.vesta not written by VESTA.
Proposed partial credit
40% vectors on all Ni with correct directions; 20% scale and colours; 40% correct plane family.
Mapped research references
Existing benchmark-to-class links from the research catalog. They are not record-level annotations, executions or product endorsements.