Add cgi script and documents for the website serving VR demos

README.md

+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.
+

webserver/cgi-bin/NOMAD/material

+#!/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

webserver/htdocs/NOMAD/Format.txt

+# <- 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.
+

webserver/htdocs/NOMAD/Glucose.ncfg

+#Glucose, atomistic, 1 timestep
+
+timesteps 1
+
+path ""
+background 0 0 0
+
+atomfile "glucose.xyz"
+atomscaling 0.5
+
+

webserver/htdocs/NOMAD/glucose.xyz

+   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

webserver/htdocs/NOMAD/index.html

+<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>