Add cgi script and documents for the website serving VR demos

parent 6abf213d
Subdirectories:
OpenVR: Demos for HTC vive.
webserver:
htdocs: Web pages containing the VR software and documentation.
cgi-bin: cgi scripts to create suitable config files from a material number.
More platforms will be added in the future.
#!/bin/bash
if ["$QUERY_STRING" eq ""]
then
#echo Location: /NOMAD/
echo Location:http://mrs-srv.srv.lrz.de/NOMAD/
echo ''
else
echo "Content-type: text-plain"
echo "Content-disposition: attachment; filename=${QUERY_STRING}.ncfg"
echo ''
echo \# Material $QUERY_STRING
echo baseurl \"http://enc-testing-nomad.esc.rzg.mpg.de/v1.0/materials/\"
echo jsonurl \"$QUERY_STRING\"
echo background 0 0 0
echo atomscaling 0.5
fi
# <- Introduces a comment, ignored
# Regular expression: * means 0 or more repetitions (additional constraints may apply), space or tab separated
# <X> denotes the type in non-comments (definition of lines)
# <Y> denotes the value of a parsed variable in comments (explanations)
#Number of timesteps T. Default value: 0, or that defined by xyzfile (see below) if it exists
timesteps <int>
#Number of isos I
#Default value: 0
isos <int>
#Values (after isos parameter): I strings. Default value: "" (empty string)
values <string>*
#Colours (after isos parameter): I*4 floats, rgba [0..1]. Default value: all 1 1 1 1 (white, opaque)
colours <float>*
#Translations(after isos parameter): I*3 floats, xyz displacements. Default value: all 0 0 0 (no translation)
translations <float>*
#User position, xyz displacement
userpos <float> <float> <float>
#path P of isosurface files, including file prefix. Needs to include the trailing slash as appropriate.
#Default value: "" (empty string)
path <string>
#xyz atom file AXYZF (extended xyz format) - For backwards compatibility, atomfile is an alias of xyzfile
#If timestep T does not match with the xyz file, the minimum of the two values is used
xyzfile <string>
#base vectors of unit cell. The unit cell is painted white
abc <float> <float> <float> <float> <float> <float> <float> <float> <float>
#Gaussian cube atom file ACUBEF. Only atoms (not volumetric data) are parsed at the moment. Implies timesteps T=1 for now.
cubefile <string>
#NOMAD integration. Baseurl gives the url where the material json can be downloaded
#by default, the value is "http://enc-testing-nomad.esc.rzg.mpg.de/v1.0/materials/"
baseurl <string>
#NOMAD integration. Jsonurl gives the material url (which is also the material code in the NOMAD encyclopaedia)
#This option downloads the materials from the NOMAD repository
jsonurl <string>
#NOMAD integration. For off-line use. Json provides the base string JSON for the desired, pre-downloaded material
#expected filenames: <JSON>_elements.json, and <JSON>_cells.json
json <string>
#scaling of atoms, default value: 1. This parameter scales the atom radius. Use 0.45 for compatibility with encyclopaedia.
atomscaling <float>
#This option indicates the simulation is non-periodic and that no replication of atoms at the cell borders should take place
nonperiodic
#This option indicates that the system is periodic and the number of repetitions of the grid and the atoms in the a b c base vector directions
#If this option is different from the default value 1 1 1, atoms in the unit cell border will not be replicated.
repetitions <int> <int> <int>
#In the case of simulation in which all atoms correspond in different timesteps, this is a list of atoms (starting in 1) which should have
#their full trajectory highlighted
#A single value of -1 means all atoms should have trajectories displayed.
showtrajectory <int>*
#image background rgb [0..1]. Default background: 0.95 0.95 0.95 (light grey)
background <float> <float> <float>
#Screenshot basename S. Default value: "C:\\temp\\frame"
screenshot <string>
#Expected filenames for isosurfaces: <P><timestep><value>.ply
#timesteps from 1 to T
#all values
#Expected filename for xyz file: <P><AXYZF>
#Expected filename for cube file: <P><ACUBEF>
#Screenshots saved to disk as bmp files with the following name: <S>[L|R]<screenshot number>.bmp
#Screenshot numbers are consecutive
#Fast access (SSD) disk strongly suggested to avoid tracking issues when recording.
#L=Left Eye, R=Right Eye. Only left eye saved at the moment
#User is expected to modify background, screenshot, possibly userpos, possibly colours, possibly atomscaling
#Possibly showtrajectory
#NOMAD integration: Change baseurl to point to a different NOMAD clone, and jsonurl to choose the material
#Other parameters probably will not be changed by final user.
#Glucose, atomistic, 1 timestep
timesteps 1
path ""
background 0 0 0
atomfile "glucose.xyz"
atomscaling 0.5
24
GLUCOSE, FINAL HEAT OF FORMATION = -299.233668
C -1.214122 -0.553885 -1.079978
C -1.214122 -0.553885 0.470022
C 0.261483 -0.553885 0.944461
C 0.948273 0.718098 0.385103
O 0.854770 0.740335 -1.030988
C 2.462498 0.739859 0.715480
C -0.465364 0.707198 -1.566796
O -0.2749 0.699248 -2.940175
H -1.045899 1.640518 -1.335925
H -0.719391 -1.483302 -1.470474
O -2.534332 -0.467204 -1.574750
H -3.052275 -1.126786 -1.090802
H -1.761364 0.352337 0.851823
O -1.951234 -1.649617 0.963387
H -1.385128 -2.430797 0.919657
H 0.790607 -1.476921 0.577810
O 0.363577 -0.619816 2.348789
H -0.167836 0.098453 2.716805
H 0.454764 1.631579 0.815724
H 0.565016 0.140188 -3.105504
H 2.961679 1.563181 0.140094
H 2.920990 -0.246791 0.449076
O 2.658488 1.048668 274697
H 2.322793 0.304418 2.5942
\ No newline at end of file
<html>
<head>
<title>
NOMAD Virtual Reality demos, preview
</title>
</head>
<body>
<h1>
NOMAD Virtual Reality (preview, early prototype)
</h1>
<h2>
NOMAD Virtual Reality demo for <a href="https://www.vive.com">HTC Vive</a>
</h2>
<h3>Software</h3>
<p>
<a href="NOMADViveT-Setup.exe">NOMAD HTC Vive for time-dependant data,
64 bit Installer</a>, 20 MB
</p>
<p>
For <a href="https://nomad-coe.eu/">NOMAD</a> Encyclopaedia integration,
http is supported directly.
Other protocols (https, ftp) use an external wget program.
Wget.exe should be in the PATH to enable https and ftp support.
Download it <a href="https://eternallybored.org/misc/wget/">here</a>.
</p>
<h3>
Dataset corresponding to the reaction of gaseous CO<sub>2</sub> to CaO(001) surface.
Corresponding material:
<a href="http://enc-production-nomad.esc.rzg.mpg.de/gui/#/material/131424">
CaO - space group 225</a> (NOMAD encyclopaedia)
</h3>
<h4> Simulation parameters</h4>
-From <a href="https://gitlab.rzg.mpg.de/nomad-lab/public-wiki/wikis/remoteviz/UseCase1">
NOMAD Usecase 1</a><br/>
-Molecular Dynamics (MD) simulation<br/>
-35 atoms (1 CO<sub>2</sub> molecule, two layer 4x4 CaO solid)<br/>
-Fixed bottom layer<br/>
-423 timesteps<br/>
<img width=10% src="CO2-CaO.png"/>
<h4>Datasets</h4>
<p>
<a href="CO2-CaO-Rel.rar">CO<sub>2</sub>-CaO, relative electron densities</a>, 137 MB
</p>
<p>
<a href="CO2-CaO.rar">CO<sub>2</sub>-CaO, full electron densities</a>, 1.8 GB
</p>
<h3>Dataset corresponding to an Ag Fermi surface</h3>
<p>
<img src="AgAll_bands.png" width=10% /><br/>
<a href="AgFermi.rar">Ag Fermi surface</a>, 374 KB
</p>
<h3>Dataset for molecular dynamics using extended xyz file</h3>
<p>
Atomistic viewer: Glucose (from <a href="http://wetche.cmbi.ru.nl/organic/methods/xyzf.html">this example</a>)<br/>
<a href="Glucose.ncfg">Glucose.ncfg</a><br/>
<a href="glucose.xyz">Glucose.xyz</a><br/>
</p>
<h3>Instructions</h3>
<p>
-Download the installer, and install.<br/>
-Download the rar file, and decompress.<br/>
-Double click on the .ncfg file and assign to the installed program NOMADViveT.exe
</p>
<h4>
Control:</h4>
-Trigger of controller 1 moves the user in the gaze direction<br/>
-Trigger of controller 2 moves the time forward (continuous)<br/>
-Side button of controller 1 moves the time backwards (discrete)<br/>
-Side button of controller 2 shows isosurfaces one-by-one, then atoms, then
everything with transparency (caveat: ).<br/>
-Menu (3 lines) button of controller 2 starts/stops recording in c:/temp.
</p>
<h4>
Caveats:</h4>
-At the beginning of the CO<sub>2</sub>+CaO reaction, the relative densities are zero, so nothing
is shown if you press the isosurfaces button too early; if you press it by
mistake, press it again until you see the atoms, then once more for the full
system<br/>
-Recording: SSD advised, affects tracking negativelly<br/>
-A high-end graphics card is required.
See also <a href="https://github.com/ValveSoftware/openvr/issues/258">here</a>
regarding slow framerates for 60Hz monitors in Geforce GTX 980 and workarounds
for the issue.<br/>
-The Fermi surface is static; the time controls are disabled for this example.
</p>
<p>
<a href="Format.txt">Format</a> of the NOMADViveT configuration file.
</p>
<p>
---------------------------------------------------------------------------
</p>
<h1>From here on, experimental demos, do not copy to the NOMAD wp3 website yet!
</h1>
<h2>
NOMAD Virtual Reality demo for <a href="http://www.samsung.com/de/wearables/gear-vr-r322/">Samsung GearVR</a>
</h2>
<h3>
Reaction of gaseous CO<sub>2</sub> to CaO(001) surface, like above
</h3>
<p>
<a href="CO2-CaO-Rel.apk">Android Installer (apk), Relative densities</a>, 2 MB
</p>
<p>
<a href="CO2-CaO.apk">Android Installer (apk), Full densities, 200 timesteps (1,3,...)</a>, 2 MB
</p>
<p>
Install instructions:<br/>
-Allow unsigned software in oculus
(see <a href="https://support.oculus.com/878170922281071">here</a>).<br/>
-Install desired apk(s)<br/>
-Relative densities: download <a href="CO2-CaO-Rel.rar">CO2-CaO-Rel.rar</a> (same file as above) and decompress content in sdcard/Oculus. Rename the folder data to NOMAD and inside that,
the to CO2CaOrel to CO2-CaO-rel.<br/>
-Full densities: download <a href="CO2-CaO.rar">CO2-CaO.rar</a> (same file as above) and
decompress content in sdcard/Oculus.
Rename the folder data to NOMAD and inside that,
the to CO2-CaO-B to CO2-CaO (if the NOMAD folder already exists, you should just move
CO2-CaO-B inside the NOMAD folder before renaming).<br/>
-You may remove the .ncfg files, they are unused.<br/>
-The procedure will be simplified in the next version!
</p>
<p>
Control:<br/>
-Swipe forward to fly in the direction of gaze<br/>
-Swipe backwards to stop the movement<br/>
-Swipe up/down to go forward/backward in time<br/>
-Press back to show isosurfaces one by one (same caveat as above).
</p>
</body>
</html>
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