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Minimalistic and fast HTML5 visualization of chemical structures in CIF, POSCAR, and OPTIMADE formats

Home Page: http://nanoshow.mpds.io/

License: MIT License

HTML 1.36% TypeScript 98.55% CSS 0.10%

cif cifs crystal-structure crystallography optimade poscar symmetry threejs

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fossabot tobbyvic stan-donarise nik991

cifplayer's Issues

Cannot switch off WebGL if switched on for a not supported device

Only cookie cleaning, which is not a solution...

Cell translations in x, y, z according to a matrix

Periodic cell translations are normally done according to a matrix e.g. [[1, 0, 0], [0, 1, 0], [0, 0, 2]] expands a cell twice into vertical direction. Here a matrix determinant shows how much the volume is expanded.

(However this may expand the number of atoms drastically for bigger cells, so we have to define a reasonable limit, e.g. no more than 10x expansion, otherwise our rendering will burn out.)

Using matinfio in server environment

According to Dmitriy's message in our internal chat, seems to be easy, however still a concrete example would be very much appreciated.

Optional support of WebGL, where possible (?)

Choose file filepicker does not work

comparing an old and new versions

Could we avoid parsing the incoming data without the real need?

cifplayer/src/js/app/main.js

Line 558 in dac4ed2

    
           target_data = JSON.parse(event.data); // do we receive a JSON-object or a JSON-string?

Background color switcher

The minimum Optimade example does not work

{"attributes":{"immutable_id":"x","species":[{"chemical_symbols":["Au"]}],"cartesian_site_positions":[[0,0,0]],"lattice_vectors":[[0,2,2],[2,0,2],[2,2,0]]}}

flex: {direction: 'row' },

as well as

Body: {
  flex: { direction: 'column' },
}

and for https://github.com/tilde-lab/cifplayer/blob/master/app/app.view.tree#L15

body / <= Body $mol_view sub /

indeed prevent word-wraping, but the initial empty textarea becomes too short (cut).

Symmetry icon should only be displayed if symmetry info is present, otherwise not shown

Suggested code for https://github.com/tilde-lab/cifplayer/blob/master/player/player.view.web.ts#L469 does not work, symmetry icon is never shown, even for those structures which actually do contain symmetry.

if( !this.structure_3d_data().cell_matrix ) return []

return [
  this.Info(), 
  ... this.symlabel() ? [ this.Symlabel() ] : [],
  this.Center(),
]

CIF tag _atom_site_occupancy not supported

Orbiting directions are wrong

The rotation of the structure (orbiting) works strangely:

left-right correctly rotates the axis and atom positions, though the spheres representing atoms turn the other way
up-down rotation is flipped
rotation around z axis is flipped

Cell angles issue

As the structure below is rendered, all the cell angles are shown as 90, however it is seen to be wrong 🤔

{"data":[{"id":"data/gnome_data/by_id.zip/data/gnome_data/by_id/f88009011b.CIF","type":"structures","attributes":{"immutable_id":null,"last_modified":null,"elements":["Ag","K","P","Se"],"nelements":4,"elements_ratios":[0.1111111111111111,0.1111111111111111,0.2222222222222222,0.5555555555555556],"chemical_formula_descriptive":"Ag4K4P8Se20","chemical_formula_reduced":"AgKP2Se5","chemical_formula_hill":null,"chemical_formula_anonymous":"A5B2CD","dimension_types":[1,1,1],"nperiodic_dimensions":3,"lattice_vectors":[[8.359451,0.0,0.0],[0.0,10.84409822,0.0],[0.0,7.048636471698659,11.832816778560865]],"cartesian_site_positions":[[5.300351703805,12.202652545688954,9.255510956022524],[3.0590992961950008,5.690082146009705,2.577305822538342],[7.238824796195,8.678334309839624,3.3391025667420906],[1.120626203805,9.214400381859035,8.493714211818773],[2.8355508575529997,11.536835616154002,3.9261167743097167],[7.0152763575530015,2.831580839695326,1.990291614970716],[1.344174642447,15.061153852003335,9.842525163590148],[5.523900142446999,6.355899075544656,7.906700004251149],[5.382976517489,8.624899935989834,10.87440595076455],[7.8521326377120015,12.169026194562672,5.456253810395758],[0.507318362288,5.723708497135987,6.376562968165108],[7.156199982511,5.100581700140505,4.957997561484117],[2.976474482511,9.267834755708822,0.9584108277963158],[1.203251017489,12.792152991558154,6.874819217076748],[4.687043862287999,15.693344430412001,11.37266219967619],[3.672407137712,2.1993902612866574,0.4601545788846749],[5.755774594285,7.009337237489533,0.4433401462423399],[4.585418016481001,8.67154886470268,8.856898857203143],[1.187635563021,8.04890301785488,0.6345347997503263],[3.9634497837280005,15.44456444105876,9.310640049393838],[1.576049094285,7.359079218359796,5.473068243038093],[2.9920899369790006,11.57322125370421,6.550943189030759],[2.603676405715,10.883397454209124,11.389476632318525],[8.143175283728,5.9724884864892305,8.43858511844746],[6.161885083316,17.439125340978038,11.67622128131339],[1.982159583316,3.9779275865699493,6.073003886527906],[7.171815436979,9.843831673843777,11.198281978810538],[6.377291416684,13.914807105128709,5.759812892032958],[0.40569251648099997,12.745504062845308,8.892326310638154],[0.21627571627199998,11.920246205209429,3.3942316601134057],[5.367361063021,6.319513437994448,5.2818735895301065],[3.774032983519,9.221185826995976,2.975917921357722],[7.953758483519,5.147230628853352,2.940490467922711],[4.396001216272,2.448170250639901,2.522176729167027],[2.1975659166840007,0.4536093507206201,0.15659549724747449],[6.783401905715001,10.533655473338863,6.3597485355227725]],"nsites":36,"species":[{"name":"Se","chemical_symbols":["Se"],"concentration":[1.0],"mass":null,"original_name":null,"attached":null,"nattached":null},{"name":"P","chemical_symbols":["P"],"concentration":[1.0],"mass":null,"original_name":null,"attached":null,"nattached":null},{"name":"K","chemical_symbols":["K"],"concentration":[1.0],"mass":null,"original_name":null,"attached":null,"nattached":null},{"name":"Ag","chemical_symbols":["Ag"],"concentration":[1.0],"mass":null,"original_name":null,"attached":null,"nattached":null}],"species_at_sites":["K","K","K","K","Ag","Ag","Ag","Ag","P","P","P","P","P","P","P","P","Se","Se","Se","Se","Se","Se","Se","Se","Se","Se","Se","Se","Se","Se","Se","Se","Se","Se","Se","Se"],"assemblies":null,"structure_features":[],"_gnome_decomposition_energy_per_atom":-0.0132,"_gnome_material_id":"f88009011b","_gnome_formation_energy_per_atom":-0.6173}}],"meta":{"query":{"representation":"/structures?filter=chemical_formula_reduced=%22AgKP2Se5%22"},"api_version":"1.1.0","more_data_available":false,"schema":"https://schemas.optimade.org/openapi/v1.1.0/optimade.json","time_stamp":"2024-06-14T13:54:35Z","data_returned":1,"provider":{"name":"Gnome","description":"An unoffiical OPTIMADE API for the Gnome dataset from Google Deepmind (CC-BY NC). Full terms of use can be found on the project homepage.","prefix":"gnome","homepage":"https://github.com/google-deepmind/materials_discovery"},"data_available":384938,"implementation":{"name":"optimade-python-tools (modified for odbx.science)","version":"0.1","source_url":"https://github.com/ml-evs/odbx.science","maintainer":{"email":"[email protected]"},"issue_tracker":"https://github.com/ml-evs/odbx.science/issues"}},"included":[],"links":{"next":null}}

Atoms are neither translated nor recreated by symmetry

CIF without the cell translation block is not accepted

data_image0
_chemical_formula_structural       Cu13C2H3SiCH3CH3CH3
_chemical_formula_sum              "Cu13 C5 H12 Si1"
loop_
  _atom_site_type_symbol
  _atom_site_label
  _atom_site_symmetry_multiplicity
  _atom_site_Cartn_x
  _atom_site_Cartn_y
  _atom_site_Cartn_z
  _atom_site_occupancy
  Cu  Cu1       1.0  -2.94433  -0.80816  -13.10687  1.0000
  Cu  Cu2       1.0  -1.44585  -0.86013  -11.15329  1.0000
  Cu  Cu3       1.0  -2.82502  1.18948  -11.51586  1.0000
  Cu  Cu4       1.0  -1.29643  1.15248  -9.59309  1.0000
  Cu  Cu5       1.0  -2.70266  3.18792  -9.92604  1.0000
  Cu  Cu6       1.0  -0.41576  -0.67646  -13.46114  1.0000
  Cu  Cu7       1.0  1.11555  -0.65642  -11.55574  1.0000
  Cu  Cu8       1.0  -0.29502  1.31977  -11.87099  1.0000
  Cu  Cu9       1.0  1.24215  1.33229  -9.98270  1.0000
  Cu  Cu10      1.0  -0.17432  3.31683  -10.28173  1.0000
  Cu  Cu11      1.0  2.11309  -0.54894  -13.81632  1.0000
  Cu  Cu12      1.0  2.23512  1.44929  -12.22534  1.0000
  Cu  Cu13      1.0  2.35416  3.44726  -10.63467  1.0000
  C   C1        1.0  -1.13470  -1.91411  -9.15128  1.0000
  C   C2        1.0  -0.39000  -1.09033  -8.38364  1.0000
  H   H1        1.0  -0.92703  -0.35334  -7.79134  1.0000
  H   H2        1.0  -2.21677  -1.87006  -9.15870  1.0000
  H   H3        1.0  -0.69429  -2.72110  -9.72433  1.0000
  Si  Si1       1.0  1.48876  -1.19305  -8.11693  1.0000
  C   C3        1.0  2.36171  -2.20822  -9.45311  1.0000
  H   H4        1.0  2.11571  -1.83431  -10.45254  1.0000
  H   H5        1.0  3.44482  -2.14003  -9.36290  1.0000
  H   H6        1.0  2.08574  -3.26142  -9.42279  1.0000
  C   C4        1.0  2.31094  0.41998  -7.57307  1.0000
  H   H7        1.0  1.98398  0.73113  -6.58209  1.0000
  H   H8        1.0  3.39758  0.36529  -7.57785  1.0000
  H   H9        1.0  2.04820  1.23875  -8.25357  1.0000
  C   C5        1.0  1.70533  -2.20156  -6.53333  1.0000
  H   H10       1.0  1.30571  -3.20785  -6.65254  1.0000
  H   H11       1.0  2.75993  -2.28755  -6.27143  1.0000
  H   H12       1.0  1.19003  -1.73457  -5.69466  1.0000

Multi-touch bug in Three.js r72

unvibrate() causes uncaught promise

calling web_component.unvibrate() results in an error warning in a console:

Uncaught Promise { <state>: "pending" }

However the phonon movement is stopped correctly.