Activity for cogli2
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cogli2 released /cogli2_2.3.0.tgz
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Lorenzo Rovigatti committed [r134] on Code
Update the CHANGELOG
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Make the code compile on some MacOsX computers
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Start working on a blender drawer
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Update the povray export for patchy particles
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Fix a bug whereby the particle indexes were not correctly set
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Fix a bug whereby the code would segfault on exit
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Update glfw to make the code work also on Wayland
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Remove an unused cmake option
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Add two ways of identifying the 3' and 5' ends of DNA and RNA strands. This can be done with the new `--end-handling, -e` option or by pressing the `e` key during the rendering
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Add the possibility of specifying group of shapes in an mgl file. Update the README accordingly
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Change NULL for nullptr to follow modern C++ guidelines
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Flavio committed [r123]
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Update the CHANGELOG for the new 2.1.0 release
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Update the README with a new option and start implementing back triangles
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Fix a bug that would prevent compilation with some compilers
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Add the --no-box option to hide the box from the command line
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Add spherical caps to the patches and fix a camera-related bug
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Remove a warning
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Make it so the colours of the axes' keys (whose appearance can be toggled with 'k') do not change with the world's lights.
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Fix a bug whereby the DNA parser would fail if the topology file didn't end with an empty line
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Add the option --drums-full to apply the DRUMS scheme to the whole nucleotide (as opposed to --drums, which colors only the bases).
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Rationalise the project structure
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Fix a bug whereby exporting scenes containing patch-less PatchyParticles to povray would segfault
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Make it possible to set custom colors for the different species with the PatchySwap parser
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Improve the performance by sorting only when transparent shapes are present
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Add a new action that can be used to hide/show particles
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Add a new parser to handle "patchy-swap" configurations.
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Prepare the code for the first cogli2 release
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Improve the opengl -> povray mapping by setting povray's assumed_gamma to 2.2
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Make small adjustments to the opengl-povray light mapping
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Bugfixing
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Improve (a bit) the labels, add a CHANGELOG file, fix the usage
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Use glText to render text
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Draw a background orange quad behind text strings
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Make it possible to show labels (= shape ids) by pressing 'l'
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Fix a bug whereby the camera would start misbehaving
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Handle shader source files as resources
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Add the cmake file for the previous commit
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Add a cmake resource compiler and use it to embed the ubuntu fonts
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Fix a bug that would sometimes result in a segfault
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Make it possible to compile without text rendering support
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Fix a bug that would result in a segfault when drawing cylinders
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Add a simple FPS counter
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Update the name and add back patchy particles and icosahedra
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Load the shaders' source code at compile time
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Make it possible to display axes' arrows (still buggy)
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Update the usage message
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Fix the axes' arrows
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Make the code compatible with Mac Os X
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Bring back picking
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Fix z-sorting
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Add back arrows and dipolar hard spheres
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Improve the mapping to the povray lights
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Remove the now-useless OGLEllipsoid class
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Add back support for oxDNA DNA/RNA configurations
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Instance data are now sent over to the GPU only when changes happen
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Draw cylinders with the new way (instancing)
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Improve the performance of the depth sorting algorithm
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Make the code compilable
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Fix a bug in the depth sorting + update lights only when they change
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Implement a basic mechanism for instancing spheres
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Add back cylinders
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Change the way the glm library is included
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Bring back the lights
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Draw spheres with modern opengl
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First commit
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Change a few names all around the code
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Remove old bits of code and upgrade some stuff to c++11
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Add more ways of specifying ids for the visibility and color files. Make the code compile with the c++11 standard
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Agnese Grison posted a comment on discussion General Discussion
I tried but I can't open any other GUIs. I thought it might be the CMake compilier that was not updated but after updating it still does not work. I get the same error in a MacBook. I will try from a computer at university. Thanks for the help for now, Agnese
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Do you have an X session attached to that shell? In other words, can you open other GUI software from that command line?
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Hi, Thanks for the quick reply! I have tried deleting everything and I downloaded cogli1 again, but I still get the error. I have attached a picture of the error. (I am using Windows 10) Thanks, Agnese
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Hi, Thanks for the quick reply! I have tried deleting everything and I downloaded cogli1 again, but I still get the error. I have attached a picture of the error. Thanks, Agnese
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Hi there, I am not sure how to troubleshoot this. The code spits out that error when it doesn't manage to initialise GLFW (that is, when a call to glfwInit() fails). By the way, note that glfw, glm and glew are already included in the source. You shouldn't need to install them on your own. Maybe a conflict between the installed libraries and the ones that ship with the software is the cause of the issue. What OS are you using? cheers, Lorenzo
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Hello, I am trying to visualize the VMMC_MELTING_WD example using cogli1. I downloaded the software and all the libraries required (glfw, glew, glm, B Spline). The compilation seemed to have worked, as I got [100%] Built target cogli1. Then, I run this command in the folder $HOME/cogli1-code/build/bin/cogli1 --always-centre -I -v -m -t prova.top trajectory.dat to visualize the trajectory but I get this error: CRITICAL: Failed to initialize GLFW I am sure I have downloaded glfw and that it was succesfully...
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Hey Andy, sorry for the late answer. It's a known issue (either of libpng or cmake, I'm not sure). Delete the build folder and redo everything from scratch but using the -DNOPNG=ON when invoking cmake: mkdir build cd build cmake .. -DNOPNG=ON make Let me know if this solves your issue. cheers, Lorenzo
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Andrew Lee posted a comment on discussion General Discussion
I have tried to compile cogli1 on mac following the instructions but run into the following issue: alee90 ~/cogli1/build $ make [ 26%] Built target glfw [ 32%] Built target BSpline Scanning dependencies of target cogli1 [ 33%] Building CXX object CMakeFiles/cogli1.dir/OGL/OGLManager.cpp.o /Users/alee90/cogli1/OGL/OGLManager.cpp:17:10: fatal error: 'png.h' file not found #include <png.h> ^~~~~~~ 1 error generated. make[2]: *** [CMakeFiles/cogli1.dir/OGL/OGLManager.cpp.o] Error 1 make[1]: *** [CMakeFiles/cogli1.dir/all]...
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Add the --povray-shadows option that makes povray-generated objects cast shadows.
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Hey there! It's not possible at this moment, but it's something I might consider adding, as it shouldn't be too hard to implement. About the colour input file: you need to prepare a file that has two columns, like this: 0 1,1,1 10 1,0,0 5 0,1,0 Each line specifies the colour of a single nucleotide. On each line, the first number is the index of the nucleotide, while the second column stores the colour in RGB format. In the example above, the first nucleotide will be coloured white, the 11th red and...
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Joel Hochstetter posted a comment on discussion General Discussion
Is it possible to add additional shapes i.e. cylinders when visualising oxdna outputs? Also can you explain in more detail how to use a colour input file as I wasn't quite sure from reading the read me?
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The first header line of mgl files is now optional. If no header line is found, the dimensions of the bounding box of the configuration are used. The documentation has been updated accordingly.
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Fix compilation on old compilers
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Just use cogli1 -mt topology.dat conf.dat to display an oxDNA configuration. You can have the list of command-line options and keyboard/mouse bindings by using cogli1 --help. cheers, Lorenzo
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Reem Mokhtar posted a comment on discussion General Discussion
Can someone please post a simple example of using cogli1 for my benefit? Thanks!
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Ferdinando Randisi committed [r57]
Fixing a bug that would prevent compilation on some systems. Thanks to Emanuele for letting us now
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Adding the --drums option, that color-codes DNA bases depending on their chemical identity (i.e. A,C,G,T,U have differently color-coded ellipsoids).
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Hi, You can rotate more easily with the mouse. If you need to rotate by exactly 90 degrees, there are a couple options. First, you can use the new "action" feature. Create a new file (action.dat, for example) with the following content: r X Y Z 90 1 where X Y Z are the components of the axis you wish to rotate around. Now call cogli1 with the additional option cogli1 -a action.dat (for example cogli1 -a action.dat -vmt topology.dat last_conf.dat) and go to the next configuration (press +): you should...
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Sterling Baird modified a comment on discussion Feature requests
Hello, I have been impressed with the cogli1 visualization software and have been using it frequently. It has been taking me quite some time to do rotations by 90 degrees, and I was wondering if there was an easier option to do large rotations? I looked through the README and all I could find was using Ctrl+x or Ctrl+y for small rotations. If this is currently the only way, that is OK. Thank you, Sterling
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