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View Code? Open in Web Editor NEWVisual Interactive Analysis of Molecular Dynamics
License: MIT License
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corredd fanyini nityasagarjena lzenghui m-hakmi bc118 giantfurosemide genostack ferreira68 fakher77 bylehn sailfish009 genieus mathieulinares rgora rudrajoshi2481 icamps bkmgit dualword caiyingchun nkm-ml busugaacevedo pritampanda15 mfkiwl bit-part-young winnibobby wankiwi yongjiguan ecnuitaaviamd's Issues
Implement property export
Ability to export properties (over time and distributions) to some text-based format(s).
(xvg, csv).
For volumes, we should also support CUBE fileformat. Since there we can embed the structure as well as the volume.
Crash when clicking the windows on startup while it's not fully loaded
I get the following assert failure when I click on the window shortly after the program started, and before the imgui panels appear:
viamd/src/main.cpp:7451: void handle_camera_interaction(ApplicationData*): Assertion `data->picking.idx <= data->mold.mol.atom.count' failed.
Ramachandran plot
Implement atom element changer
Occasionally when loading datasets and the atom element information is not available (e.g. in .gro files), the element is 'guessed' from the atom label. This can lead to atoms being assigned incorrect elements.
My proposed solution for this is to expose a 'right-click' context menu option when clicking on an atom. This option named something like 'Change element' can either be applied to this single atom or to all atoms with the same label (default option).
Add desktop file
Linux desktop applications typically use a desktop file. Could one be added? Can also create a pull request to add one. Some references:
Implement Shape Space plot
This was present in a previous version as a prototype.
New version should:
Have a text-filter in which the user specifies an expression which should evaluate to a bitfield. Either by referencing bitfields defined in the script editor or providing self contained expressions.
This the expression evaluates into multiple bitfields, each bitfield should be assigned a *'unique'-color that is used to populate the shape-space.
- Unique up to a certain size.
Problem with the last release - Segmentation fault (core dumped)
Hi,
I 've downloaded the latest version and used the given instructions to compile it.
When I issue ./viamd in the bin directory I receive the following:
$ ./viamd
[08:58:22][debug]: Initializing GL... [/home/xxxx/sources/viamd/src/main.cpp:1443]
Failed to initialize OpenGL loader!
[08:58:23][debug]: Initializing framebuffer... [/home/xxxx/sources/viamd/src/main.cpp:1460]
[08:58:23][debug]: Initializing immediate draw... [/home/xxxx/sources/viamd/src/main.cpp:1469]
[08:58:23][debug]: Initializing ramachandran... [/home/xxxx/sources/viamd/src/main.cpp:1471]
[08:58:23][debug]: Initializing post processing... [/home/xxxx/sources/viamd/src/main.cpp:1473]
[08:58:23][debug]: Initializing volume... [/home/xxxx/sources/viamd/src/main.cpp:1475]
[08:58:23][debug]: Initializing task system... [/home/xxxx/sources/viamd/src/main.cpp:1477]
[08:58:23][error]: One or more shaders are invalid [link_program_transform_feedback]
[08:58:23][error]: Program link error: One or more shaders are invalid
[link_program]
Segmentation fault (core dumped)
I'm using Ubuntu 20.04
Thanks.
Saverio
md_benchmark Assertion "file" failed at line 436
Hiya! I am thrilled to be using VIAMD, I am hopeful this will spread widely. I installed VIAMD and I attached the cmake output. I tried to run the md_benchmark script that you provide, however I got the following error. Thanks for your help! Please let me know any additional info you need me to provide, such as GPU info (which I added below the error)
./md_benchmark
name min iter time (ms) min elem time (ns) throughput (MB/s)
Speed of light 1.18 0.37 14617.27
com_min_image_ref 65.07 20.68 264.04
com_trig_ref 71.02 22.58 241.90
com_min_image_sse 37.02 11.77 464.09
com_trig_sse 100.31 31.89 171.27
com_min_image_avx2 20.20 6.42 850.48
com_trig_avx2 48.43 15.39 354.75
com_min_image_avx512 8.29 2.63 2072.94
com_trig_avx512 21.73 6.91 790.77
[==========] Running 20 benchmarks.
[ RUN ] allocator.default
[ OK ] allocator.default (mean 0.137us, confidence interval +- 0.466282%)
[ RUN ] spatial_hash.init_regular
[ OK ] spatial_hash.init_regular (mean 32.125ms, confidence interval +- 0.248376%)
[ RUN ] spatial_hash.init_periodic
[ OK ] spatial_hash.init_periodic (mean 43.887ms, confidence interval +- 0.554247%)
[ RUN ] spatial_hash.query_regular
[ OK ] spatial_hash.query_regular (mean 176.643ms, confidence interval +- 0.283656%)
[ RUN ] spatial_hash.query_periodic
[ OK ] spatial_hash.query_periodic (mean 623.137ms, confidence interval +- 0.121939%)
[ RUN ] spatial_hash.query_regular_batch
[ OK ] spatial_hash.query_regular_batch (mean 23.075ms, confidence interval +- 0.220998%)
[ RUN ] spatial_hash.query_periodic_batch
[ OK ] spatial_hash.query_periodic_batch (mean 55.391ms, confidence interval +- 0.337296%)
[ RUN ] spatial_hash.query_bruteforce
[ OK ] spatial_hash.query_bruteforce (mean 429.741ms, confidence interval +- 0.083010%)
[ RUN ] xtc.load
[09:54:09][info]: XTC: Attempting to create new cache file...
[09:54:09][info]: XTC: Successfully created cache file for trajectory
[ OK ] xtc.load (mean 39.751ms, confidence interval +- 0.092922%)
[ RUN ] gro.load
[ OK ] gro.load (mean 27.231ms, confidence interval +- 1.384718%) (267.283 MB/s)
[ RUN ] pdb.dppc64
[ OK ] pdb.dppc64 (mean 3.129ms, confidence interval +- 0.069364%) (315.577 MB/s)
[ RUN ] pdb._100frames
Assertion "file" failed at line 436 in /home/ken/software/viamd/ext/mdlib/src/core/md_os.c:md_file_size
Illegal instruction (core dumped)
nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2023 NVIDIA Corporation
Built on Fri_Nov__3_17:16:49_PDT_2023
Cuda compilation tools, release 12.3, V12.3.103
Build cuda_12.3.r12.3/compiler.33492891_0
nvidia-smi
Fri Dec 1 10:01:02 2023
+---------------------------------------------------------------------------------------+
| NVIDIA-SMI 545.29.06 Driver Version: 545.29.06 CUDA Version: 12.3 |
|-----------------------------------------+----------------------+----------------------+
| GPU Name Persistence-M | Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
|=========================================+======================+======================|
| 0 NVIDIA GeForce RTX 4090 Off | 00000000:01:00.0 On | Off |
| 0% 50C P8 18W / 450W | 465MiB / 24564MiB | 4% Default |
| | | N/A |
+-----------------------------------------+----------------------+----------------------+
| 1 NVIDIA GeForce RTX 4090 Off | 00000000:03:00.0 Off | Off |
| 0% 47C P8 14W / 450W | 14MiB / 24564MiB | 0% Default |
| | | N/A |
+-----------------------------------------+----------------------+----------------------+
+---------------------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=======================================================================================|
| 0 N/A N/A 3286 G /usr/lib/xorg/Xorg 149MiB |
| 0 N/A N/A 3403 G /usr/bin/gnome-shell 53MiB |
| 0 N/A N/A 3858 G ...sion,SpareRendererForSitePerProcess 111MiB |
| 0 N/A N/A 13099 G ...RunOnOsLogin,WebAssemblyTrapHandler 132MiB |
| 1 N/A N/A 3286 G /usr/lib/xorg/Xorg 4MiB |
Install desktop and appdata files on linux
Modify CMakeLists.txt to install appdata and desktop files for linux.
Add Hierarchy Info
Add a window (accessible via menu) that displays the structures present within the dataset in a hierarchical fashion.
Install instructions
Hi,
I copied your command from the install instructions,
git clone --recurse-submodules git://github.com/scanberg/viamd.git
however, I ran into an ssh problem and was refered to this blog entry: https://github.blog/2021-09-01-improving-git-protocol-security-github/
I managed to download with
git clone --recurse-submodules [email protected]:scanberg/viamd.git
Appdata file
Please add an appdata file. This is needed for linux GUI applications:
- https://www.freedesktop.org/software/appstream/docs/chap-Quickstart.html#sect-Quickstart-DesktopApps
- https://docs.fedoraproject.org/en-US/packaging-guidelines/AppData/
Can make a pull request if it would be considered
Viridis color scale not available for coloring a representation in function of a porperty
that's it
Basic math operators such as sqrt seems to crash the application
Tested on scalar values
Filtering in distribution
The filtering in the distribution is functioning for angle and dihedral but not distance
Selection Growth includes non visible atoms
A stored selction in the selection tool is not recognised by the script editor and cannot be used as a filter in Representations
importing .csv files
Dear authors,
First of all thank you for this project, this was really missing!
However, I'm not sure how to import external data. Specifically I ran a simulation with AMBER, converted the trajectory to .pdb and read out the total energy and saved it as .csv. The trajectory itself can be loaded, everything works fine. Now I want to have the corresponding energies beeing displayed in the timelines window.
I added the following to script editor "energy = import("/home/weasel/tolocal/energy.csv");" The path is found but I always get the error "number of columns in row 2 does not match the first row [parse]". This is how my .csv looks like:
time,energy
0.000,-181969.0759
0.100,-148270.2830
0.200,-140970.5800
0.300,-135127.0550
0.400,-130371.7956
0.500,-126459.5568
0.600,-123288.7108
0.700,-120653.1827
0.800,-118417.1584
0.900,-116522.2044
1.000,-115009.6799
1.100,-113757.2837
1.200,-112564.0433
...
Adding/removing the header or columns did not help. What am I missing?
Thank you in advance and best regards!
Density volumes window crash on Apple M1
When I want to open the density volumes window on my Macbook Pro 14 M1 ViaMD crashes immediately
Terminal output:
(base) Bastiaan@n154-p176 bin % ./viamd
[16:00:09][debug]: Initializing GL... [/Users/Bastiaan/Desktop/viamd/src/main.cpp:1337]
[16:00:10][debug]: Initializing framebuffer... [/Users/Bastiaan/Desktop/viamd/src/main.cpp:1393]
[16:00:10][debug]: Initializing immediate draw... [/Users/Bastiaan/Desktop/viamd/src/main.cpp:1402]
[16:00:10][debug]: Initializing ramachandran... [/Users/Bastiaan/Desktop/viamd/src/main.cpp:1404]
[16:00:10][debug]: Initializing post processing... [/Users/Bastiaan/Desktop/viamd/src/main.cpp:1406]
[16:00:10][debug]: Initializing volume... [/Users/Bastiaan/Desktop/viamd/src/main.cpp:1408]
[16:00:10][debug]: Initializing task system... [/Users/Bastiaan/Desktop/viamd/src/main.cpp:1410]
UNSUPPORTED (log once): gldCopyBufferSubData: NEEDS IMPLEMENTATION
[16:00:10][info]: File may also contain trajectory, attempting to load trajectory
[16:00:10][debug]: Initializing frame cache with 500 frames. [/Users/Bastiaan/Desktop/viamd/src/loader.cpp:281]
[16:00:10][debug]: Allocating 1.00 MB as frame cache.
zsh: segmentation fault ./viamd
(base) Bastiaan@n154-p176 bin %
And the problem report generated by MacOS:
-------------------------------------
Translated Report (Full Report Below)
-------------------------------------
Process: viamd [61132]
Path: /Users/USER/Desktop/*/viamd
Identifier: viamd
Version: ???
Code Type: X86-64 (Translated)
Parent Process: zsh [60073]
Responsible: Terminal [5601]
User ID: 502
Date/Time: 2023-12-08 15:48:31.5471 +0100
OS Version: macOS 14.1.1 (23B81)
Report Version: 12
Anonymous UUID: 4B287652-9F5E-AC36-679F-EBDAFE4B5F66
Sleep/Wake UUID: C89844FC-00B6-4235-A0BB-20009A284539
Time Awake Since Boot: 210000 seconds
Time Since Wake: 21981 seconds
System Integrity Protection: enabled
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000000
Exception Codes: 0x0000000000000001, 0x0000000000000000
Termination Reason: Namespace SIGNAL, Code 11 Segmentation fault: 11
Terminating Process: exc handler [61132]
VM Region Info: 0 is not in any region. Bytes before following region: 4335931392
REGION TYPE START - END [ VSIZE] PRT/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 102711000-102f11000 [ 8192K] r-x/r-x SM=COW ...sktop/*/viamd
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 ??? 0x0 ???
1 viamd 0x10279554f update_density_volume(ApplicationData*) + 575
2 viamd 0x1027511b0 draw_density_volume_window(ApplicationData*) + 4432
3 viamd 0x1027441c3 main + 2083
4 dyld 0x2033913a6 start + 1942
Thread 1:: com.apple.rosetta.exceptionserver
0 runtime 0x7ff7ffc26294 0x7ff7ffc22000 + 17044
Thread 2:
0 runtime 0x7ff7ffc4494c 0x7ff7ffc22000 + 141644
Thread 3:: com.apple.NSEventThread
0 ??? 0x7ff895c2aa78 ???
1 libsystem_kernel.dylib 0x7ff805735a6e mach_msg2_trap + 10
2 libsystem_kernel.dylib 0x7ff805743e7a mach_msg2_internal + 84
3 libsystem_kernel.dylib 0x7ff80573cb92 mach_msg_overwrite + 653
4 libsystem_kernel.dylib 0x7ff805735d5f mach_msg + 19
5 CoreFoundation 0x7ff80584fb49 __CFRunLoopServiceMachPort + 143
6 CoreFoundation 0x7ff80584e5bc __CFRunLoopRun + 1371
7 CoreFoundation 0x7ff80584da99 CFRunLoopRunSpecific + 557
8 AppKit 0x7ff808f1ca00 _NSEventThread + 122
9 libsystem_pthread.dylib 0x7ff805775202 _pthread_start + 99
10 libsystem_pthread.dylib 0x7ff805770bab thread_start + 15
Thread 4:
0 ??? 0x7ff895c2aa78 ???
1 libsystem_kernel.dylib 0x7ff8057359ea semaphore_wait_trap + 10
2 libdispatch.dylib 0x7ff8055cda6a _dispatch_sema4_wait + 16
3 libdispatch.dylib 0x7ff8055cdf5f _dispatch_semaphore_wait_slow + 98
4 viamd 0x102a09d8f enki::SemaphoreWait(enki::semaphoreid_t&) + 31
5 viamd 0x102a07fc4 enki::TaskScheduler::WaitForNewTasks(unsigned int) + 228
6 viamd 0x102a07d84 enki::TaskScheduler::TaskingThreadFunction(enki::ThreadArgs const&) + 196
7 viamd 0x102a0cf6d decltype(std::declval<void (*)(enki::ThreadArgs const&)>()(std::declval<enki::ThreadArgs>())) std::__1::__invoke[abi:v160006]<void (*)(enki::ThreadArgs const&), enki::ThreadArgs>(void (*&&)(enki::ThreadArgs const&), enki::ThreadArgs&&) + 29
8 viamd 0x102a0cefe void std::__1::__thread_execute[abi:v160006]<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct>>, void (*)(enki::ThreadArgs const&), enki::ThreadArgs, 2ul>(std::__1::tuple<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct>>, void (*)(enki::ThreadArgs const&), enki::ThreadArgs>&, std::__1::__tuple_indices<2ul>) + 46
9 viamd 0x102a0c892 void* std::__1::__thread_proxy[abi:v160006]<std::__1::tuple<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct>>, void (*)(enki::ThreadArgs const&), enki::ThreadArgs>>(void*) + 98
10 libsystem_pthread.dylib 0x7ff805775202 _pthread_start + 99
11 libsystem_pthread.dylib 0x7ff805770bab thread_start + 15
Thread 5:
0 ??? 0x7ff895c2aa78 ???
1 libsystem_kernel.dylib 0x7ff8057359ea semaphore_wait_trap + 10
2 libdispatch.dylib 0x7ff8055cda6a _dispatch_sema4_wait + 16
3 libdispatch.dylib 0x7ff8055cdf5f _dispatch_semaphore_wait_slow + 98
4 viamd 0x102a09d8f enki::SemaphoreWait(enki::semaphoreid_t&) + 31
5 viamd 0x102a07fc4 enki::TaskScheduler::WaitForNewTasks(unsigned int) + 228
6 viamd 0x102a07d84 enki::TaskScheduler::TaskingThreadFunction(enki::ThreadArgs const&) + 196
7 viamd 0x102a0cf6d decltype(std::declval<void (*)(enki::ThreadArgs const&)>()(std::declval<enki::ThreadArgs>())) std::__1::__invoke[abi:v160006]<void (*)(enki::ThreadArgs const&), enki::ThreadArgs>(void (*&&)(enki::ThreadArgs const&), enki::ThreadArgs&&) + 29
8 viamd 0x102a0cefe void std::__1::__thread_execute[abi:v160006]<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct>>, void (*)(enki::ThreadArgs const&), enki::ThreadArgs, 2ul>(std::__1::tuple<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct>>, void (*)(enki::ThreadArgs const&), enki::ThreadArgs>&, std::__1::__tuple_indices<2ul>) + 46
9 viamd 0x102a0c892 void* std::__1::__thread_proxy[abi:v160006]<std::__1::tuple<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct>>, void (*)(enki::ThreadArgs const&), enki::ThreadArgs>>(void*) + 98
10 libsystem_pthread.dylib 0x7ff805775202 _pthread_start + 99
11 libsystem_pthread.dylib 0x7ff805770bab thread_start + 15
Thread 6:
0 ??? 0x7ff895c2aa78 ???
1 libsystem_kernel.dylib 0x7ff8057359ea semaphore_wait_trap + 10
2 libdispatch.dylib 0x7ff8055cda6a _dispatch_sema4_wait + 16
3 libdispatch.dylib 0x7ff8055cdf5f _dispatch_semaphore_wait_slow + 98
4 viamd 0x102a09d8f enki::SemaphoreWait(enki::semaphoreid_t&) + 31
5 viamd 0x102a07fc4 enki::TaskScheduler::WaitForNewTasks(unsigned int) + 228
6 viamd 0x102a07d84 enki::TaskScheduler::TaskingThreadFunction(enki::ThreadArgs const&) + 196
7 viamd 0x102a0cf6d decltype(std::declval<void (*)(enki::ThreadArgs const&)>()(std::declval<enki::ThreadArgs>())) std::__1::__invoke[abi:v160006]<void (*)(enki::ThreadArgs const&), enki::ThreadArgs>(void (*&&)(enki::ThreadArgs const&), enki::ThreadArgs&&) + 29
8 viamd 0x102a0cefe void std::__1::__thread_execute[abi:v160006]<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct>>, void (*)(enki::ThreadArgs const&), enki::ThreadArgs, 2ul>(std::__1::tuple<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct>>, void (*)(enki::ThreadArgs const&), enki::ThreadArgs>&, std::__1::__tuple_indices<2ul>) + 46
9 viamd 0x102a0c892 void* std::__1::__thread_proxy[abi:v160006]<std::__1::tuple<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct>>, void (*)(enki::ThreadArgs const&), enki::ThreadArgs>>(void*) + 98
10 libsystem_pthread.dylib 0x7ff805775202 _pthread_start + 99
11 libsystem_pthread.dylib 0x7ff805770bab thread_start + 15
Thread 7:
0 ??? 0x7ff895c2aa78 ???
1 libsystem_kernel.dylib 0x7ff8057359ea semaphore_wait_trap + 10
2 libdispatch.dylib 0x7ff8055cda6a _dispatch_sema4_wait + 16
3 libdispatch.dylib 0x7ff8055cdf5f _dispatch_semaphore_wait_slow + 98
4 viamd 0x102a09d8f enki::SemaphoreWait(enki::semaphoreid_t&) + 31
5 viamd 0x102a07fc4 enki::TaskScheduler::WaitForNewTasks(unsigned int) + 228
6 viamd 0x102a07d84 enki::TaskScheduler::TaskingThreadFunction(enki::ThreadArgs const&) + 196
7 viamd 0x102a0cf6d decltype(std::declval<void (*)(enki::ThreadArgs const&)>()(std::declval<enki::ThreadArgs>())) std::__1::__invoke[abi:v160006]<void (*)(enki::ThreadArgs const&), enki::ThreadArgs>(void (*&&)(enki::ThreadArgs const&), enki::ThreadArgs&&) + 29
8 viamd 0x102a0cefe void std::__1::__thread_execute[abi:v160006]<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct>>, void (*)(enki::ThreadArgs const&), enki::ThreadArgs, 2ul>(std::__1::tuple<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct>>, void (*)(enki::ThreadArgs const&), enki::ThreadArgs>&, std::__1::__tuple_indices<2ul>) + 46
9 viamd 0x102a0c892 void* std::__1::__thread_proxy[abi:v160006]<std::__1::tuple<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct>>, void (*)(enki::ThreadArgs const&), enki::ThreadArgs>>(void*) + 98
10 libsystem_pthread.dylib 0x7ff805775202 _pthread_start + 99
11 libsystem_pthread.dylib 0x7ff805770bab thread_start + 15
Thread 8:
0 ??? 0x7ff895c2aa78 ???
1 libsystem_kernel.dylib 0x7ff8057359ea semaphore_wait_trap + 10
2 libdispatch.dylib 0x7ff8055cda6a _dispatch_sema4_wait + 16
3 libdispatch.dylib 0x7ff8055cdf5f _dispatch_semaphore_wait_slow + 98
4 viamd 0x102a09d8f enki::SemaphoreWait(enki::semaphoreid_t&) + 31
5 viamd 0x102a07fc4 enki::TaskScheduler::WaitForNewTasks(unsigned int) + 228
6 viamd 0x102a07d84 enki::TaskScheduler::TaskingThreadFunction(enki::ThreadArgs const&) + 196
7 viamd 0x102a0cf6d decltype(std::declval<void (*)(enki::ThreadArgs const&)>()(std::declval<enki::ThreadArgs>())) std::__1::__invoke[abi:v160006]<void (*)(enki::ThreadArgs const&), enki::ThreadArgs>(void (*&&)(enki::ThreadArgs const&), enki::ThreadArgs&&) + 29
8 viamd 0x102a0cefe void std::__1::__thread_execute[abi:v160006]<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct>>, void (*)(enki::ThreadArgs const&), enki::ThreadArgs, 2ul>(std::__1::tuple<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct>>, void (*)(enki::ThreadArgs const&), enki::ThreadArgs>&, std::__1::__tuple_indices<2ul>) + 46
9 viamd 0x102a0c892 void* std::__1::__thread_proxy[abi:v160006]<std::__1::tuple<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct>>, void (*)(enki::ThreadArgs const&), enki::ThreadArgs>>(void*) + 98
10 libsystem_pthread.dylib 0x7ff805775202 _pthread_start + 99
11 libsystem_pthread.dylib 0x7ff805770bab thread_start + 15
Thread 9:
0 ??? 0x7ff895c2aa78 ???
1 libsystem_kernel.dylib 0x7ff8057359ea semaphore_wait_trap + 10
2 libdispatch.dylib 0x7ff8055cda6a _dispatch_sema4_wait + 16
3 libdispatch.dylib 0x7ff8055cdf5f _dispatch_semaphore_wait_slow + 98
4 viamd 0x102a09d8f enki::SemaphoreWait(enki::semaphoreid_t&) + 31
5 viamd 0x102a07fc4 enki::TaskScheduler::WaitForNewTasks(unsigned int) + 228
6 viamd 0x102a07d84 enki::TaskScheduler::TaskingThreadFunction(enki::ThreadArgs const&) + 196
7 viamd 0x102a0cf6d decltype(std::declval<void (*)(enki::ThreadArgs const&)>()(std::declval<enki::ThreadArgs>())) std::__1::__invoke[abi:v160006]<void (*)(enki::ThreadArgs const&), enki::ThreadArgs>(void (*&&)(enki::ThreadArgs const&), enki::ThreadArgs&&) + 29
8 viamd 0x102a0cefe void std::__1::__thread_execute[abi:v160006]<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct>>, void (*)(enki::ThreadArgs const&), enki::ThreadArgs, 2ul>(std::__1::tuple<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct>>, void (*)(enki::ThreadArgs const&), enki::ThreadArgs>&, std::__1::__tuple_indices<2ul>) + 46
9 viamd 0x102a0c892 void* std::__1::__thread_proxy[abi:v160006]<std::__1::tuple<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct>>, void (*)(enki::ThreadArgs const&), enki::ThreadArgs>>(void*) + 98
10 libsystem_pthread.dylib 0x7ff805775202 _pthread_start + 99
11 libsystem_pthread.dylib 0x7ff805770bab thread_start + 15
Thread 10:
0 ??? 0x7ff895c2aa78 ???
1 libsystem_kernel.dylib 0x7ff8057359ea semaphore_wait_trap + 10
2 libdispatch.dylib 0x7ff8055cda6a _dispatch_sema4_wait + 16
3 libdispatch.dylib 0x7ff8055cdf5f _dispatch_semaphore_wait_slow + 98
4 viamd 0x102a09d8f enki::SemaphoreWait(enki::semaphoreid_t&) + 31
5 viamd 0x102a07fc4 enki::TaskScheduler::WaitForNewTasks(unsigned int) + 228
6 viamd 0x102a07d84 enki::TaskScheduler::TaskingThreadFunction(enki::ThreadArgs const&) + 196
7 viamd 0x102a0cf6d decltype(std::declval<void (*)(enki::ThreadArgs const&)>()(std::declval<enki::ThreadArgs>())) std::__1::__invoke[abi:v160006]<void (*)(enki::ThreadArgs const&), enki::ThreadArgs>(void (*&&)(enki::ThreadArgs const&), enki::ThreadArgs&&) + 29
8 viamd 0x102a0cefe void std::__1::__thread_execute[abi:v160006]<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct>>, void (*)(enki::ThreadArgs const&), enki::ThreadArgs, 2ul>(std::__1::tuple<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct>>, void (*)(enki::ThreadArgs const&), enki::ThreadArgs>&, std::__1::__tuple_indices<2ul>) + 46
9 viamd 0x102a0c892 void* std::__1::__thread_proxy[abi:v160006]<std::__1::tuple<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct>>, void (*)(enki::ThreadArgs const&), enki::ThreadArgs>>(void*) + 98
10 libsystem_pthread.dylib 0x7ff805775202 _pthread_start + 99
11 libsystem_pthread.dylib 0x7ff805770bab thread_start + 15
Thread 11:
0 runtime 0x7ff7ffc4494c 0x7ff7ffc22000 + 141644
Thread 12:
0 runtime 0x7ff7ffc4494c 0x7ff7ffc22000 + 141644
Thread 13:
0 runtime 0x7ff7ffc4494c 0x7ff7ffc22000 + 141644
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000000010c501bd0 rcx: 0x0000000000000000 rdx: 0x0000000309ba2c28
rdi: 0x0000000000000de1 rsi: 0x0000000000000001 rbp: 0x0000000309b9d0c0 rsp: 0x0000000309b9d088
r8: 0x0000000000000000 r9: 0x0000000102ed433a r10: 0x0000000102ed433e r11: 0x00007f81b9b56100
r12: 0x0000000309ba3580 r13: 0x0000000000000000 r14: 0x00000001027439a0 r15: 0x0000000309ba3700
rip: 0x0000000000000000 rfl: 0x0000000000000246
tmp0: 0x0000000000000000 tmp1: 0x00000001027b57ee tmp2: 0x00000001031ed318
Binary Images:
0x20338b000 - 0x20342afff dyld (*) <d5406f23-6967-39c4-beb5-6ae3293c7753> /usr/lib/dyld
0x115e2d000 - 0x115e9cfff com.apple.AppleMetalOpenGLRenderer (1.0) <e8731326-3e64-3623-8b4f-7b010926a559> /System/Library/Extensions/AppleMetalOpenGLRenderer.bundle/Contents/MacOS/AppleMetalOpenGLRenderer
0x10c3c0000 - 0x10c3cffff libobjc-trampolines.dylib (*) <7e101877-a6ff-3331-99a3-4222cb254447> /usr/lib/libobjc-trampolines.dylib
0x7ff7ffc22000 - 0x7ff7ffc51fff runtime (*) <2c5acb8c-fbaf-31ab-aeb3-90905c3fa905> /usr/libexec/rosetta/runtime
0x10bb24000 - 0x10bb77fff libRosettaRuntime (*) <a61ec9e9-1174-3dc6-9cdb-0d31811f4850> /Library/Apple/*/libRosettaRuntime
0x102711000 - 0x102f10fff viamd (*) <dcde2758-7d5d-392a-a9db-d745c6111f4e> /Users/USER/Desktop/*/viamd
0x0 - 0xffffffffffffffff ??? (*) <00000000-0000-0000-0000-000000000000> ???
0x7ff805734000 - 0x7ff80576eff7 libsystem_kernel.dylib (*) <4df0d732-7fc4-3200-8176-f1804c63f2c8> /usr/lib/system/libsystem_kernel.dylib
0x7ff8057d4000 - 0x7ff805c6cffc com.apple.CoreFoundation (6.9) <4d842118-bb65-3f01-9087-ff1a2e3ab0d5> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
0x7ff808d81000 - 0x7ff80a186ffb com.apple.AppKit (6.9) <27fed5dd-d148-3238-bc95-1dac5dd57fa1> /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit
0x7ff80576f000 - 0x7ff80577afff libsystem_pthread.dylib (*) <c64722b0-e96a-3fa5-96c3-b4beaf0c494a> /usr/lib/system/libsystem_pthread.dylib
0x7ff8055ca000 - 0x7ff805610ffd libdispatch.dylib (*) <4472f1a5-1d47-3665-ac8d-7adb0e9d2d87> /usr/lib/system/libdispatch.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by all processes on this machine:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=654.5M resident=0K(0%) swapped_out_or_unallocated=654.5M(100%)
Writable regions: Total=8.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=8.9G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 128K 1
Activity Tracing 256K 1
CG image 128K 26
ColorSync 236K 29
CoreAnimation 320K 55
CoreGraphics 20K 4
CoreUI image data 1372K 16
Foundation 32K 2
Kernel Alloc Once 8K 1
MALLOC 8.6G 113
MALLOC guard page 192K 12
MALLOC_LARGE (reserved) 128.0M 1 reserved VM address space (unallocated)
OpenGL GLSL 256K 3
Rosetta Arena 4096K 2
Rosetta Generic 1028K 254
Rosetta IndirectBranch 1024K 1
Rosetta JIT 128.0M 1
Rosetta Return Stack 240K 24
Rosetta Thread Context 240K 24
STACK GUARD 16K 4
Stack 14.1M 13
Stack Guard 56.0M 9
VM_ALLOCATE 11.3M 97
VM_ALLOCATE (reserved) 4K 1 reserved VM address space (unallocated)
__CTF 824 1
__DATA 25.4M 513
__DATA_CONST 32.2M 331
__DATA_DIRTY 1400K 168
__FONT_DATA 2352 1
__GLSLBUILTINS 5174K 1
__INFO_FILTER 8 1
__LINKEDIT 145.1M 10
__OBJC_RO 70.7M 1
__OBJC_RW 2154K 2
__TEXT 509.4M 534
dyld private memory 260K 2
mapped file 7.1G 845
shared memory 804K 15
unshared pmap 16.2M 11
=========== ======= =======
TOTAL 16.8G 3130
TOTAL, minus reserved VM space 16.7G 3130
-----------
Full Report
-----------
{"app_name":"viamd","timestamp":"2023-12-08 15:49:02.00 +0100","app_version":"","slice_uuid":"dcde2758-7d5d-392a-a9db-d745c6111f4e","build_version":"","platform":1,"share_with_app_devs":0,"is_first_party":1,"bug_type":"309","os_version":"macOS 14.1.1 (23B81)","roots_installed":0,"incident_id":"B6215C84-5AC1-49B0-AAF4-40F7E4C46C69","name":"viamd"}
{
"uptime" : 210000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 4360,
"osVersion" : {
"train" : "macOS 14.1.1",
"build" : "23B81",
"releaseType" : "User"
},
"captureTime" : "2023-12-08 15:48:31.5471 +0100",
"codeSigningMonitor" : 1,
"incident" : "B6215C84-5AC1-49B0-AAF4-40F7E4C46C69",
"pid" : 61132,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-12-08 15:02:02.3613 +0100",
"procStartAbsTime" : 4978213809453,
"procExitAbsTime" : 5045154701028,
"procName" : "viamd",
"procPath" : "\/Users\/USER\/Desktop\/*\/viamd",
"parentProc" : "zsh",
"parentPid" : 60073,
"coalitionName" : "com.apple.Terminal",
"crashReporterKey" : "4B287652-9F5E-AC36-679F-EBDAFE4B5F66",
"responsiblePid" : 5601,
"responsibleProc" : "Terminal",
"codeSigningID" : "",
"codeSigningTeamID" : "",
"codeSigningValidationCategory" : 0,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 21981,
"sleepWakeUUID" : "C89844FC-00B6-4235-A0BB-20009A284539",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4335931392\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102711000-102f11000 [ 8192K] r-x\/r-x SM=COW ...sktop\/*\/viamd",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"exc handler","byPid":61132},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4335931392\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102711000-102f11000 [ 8192K] r-x\/r-x SM=COW ...sktop\/*\/viamd",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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Helix and sheet scale labels are swapped in cartoon representation
In the representations window when viewing a protein in cartoon style, the labels for the helix scale and sheet scale sliders are swapped.
when active selection in the spatial view, the lines from the visual feedback is occluded
Selections tools + Spatial query
Growing operation through space and bonds.
Saving the selection to be used as a subset for property or representations.
md-unittest [ FAILED ] spatial_hash.test_correctness_periodic_centered
Hiya again! I ran the md_unittest file and I have attached the piped output file along with the information that was not piped to the file below. Thanks for your help. Please let me know any additional info I can provide to help. ~Ken
./md_unittest > viam-md-unittest.txt
[10:03:35][info]: Estimated serialization bytes for a: 332, actual bytes: 71
[10:03:35][info]: Deserialization of b: true
[10:03:35][info]: Serialized bytes bytes for c: 332
[10:03:35][info]: Opened '/home/ken/software/viamd/ext/mdlib/unittest/../test_data/inside-md-pullout.edr' as single precision energy file
[10:03:35][info]: Opened '/home/ken/software/viamd/ext/mdlib/unittest/../test_data/orires.edr' as single precision energy file
[10:03:35][info]: Failed to match supplied unit 'obs'
[10:03:35][info]: Opened '/home/ken/software/viamd/ext/mdlib/unittest/../test_data/ener.edr' as single precision energy file
[10:03:35][info]: Opened '/home/ken/software/viamd/ext/mdlib/unittest/../test_data/dhdl.edr' as double precision energy file
[10:03:38][debug]: No atom type or atom resname were given, will default to covalent order of 1 for all bonds. [/home/ken/software/viamd/ext/mdlib/src/md_util.c:1103]
[10:03:45][debug]: Allocating 0.96 MB as frame cache.
[10:03:49][error]: Base64: Failed to read and decode 4 consecutive bytes in input [md_base64_decode]
[10:03:49][error]: Base64: Encountered invalid character in sequence. [md_base64_decode]
viam-md-unittest.txt
[ FAILED ] 1 tests, listed [below:]
[ FAILED ] spatial_hash.test_correctness_periodic_centered
Grow radial selection does not work - Windows v0.1.32
Hi,
Unfortunately, after I selected the ligand with shift + left click and did the radial grow it did not expand my selection. I don't know if this is a bug. I used the version v0.1.32.
I noticed that this is system dependent. So for one system with 2 ligands and 2 protein chains it did not work while for another system it did work.
Best
Eddie
Cache histograms for visualization
When computing histograms for display in the distribution window, these are currently computed on the fly.
This works fine for smaller datasets but becomes a bottleneck when dealing with long trajectories or properties that represent absurdly large aggregates (e.g. angle(1,2,3) in water).
This could and should be moved into a cached histogram that resides within the VIAMD property representation.
Loading LAMMPS data file with nb_angles > nb_dihedrals
Hi Robin !
I noticed an issue when trying to load LAMMPS data file in specific cases where the number of angles in the topology is higher than the number of dihedrals.
In that case, VIAMD fails to parse angles with the following error : [error]: Failed to parse angle line, expected 5 tokens, got 0 [parse_angles]
I suspect that there is a small bug in mdlib/src
/md_lammps.c
I think that when parsing the dihedrals (from line 570), functions corresponding to angles parsing are called instead of dihedrals ones.
Cheers !
Nicolas
Loading on Ubuntu 22.04 fails
Hello developers,
I have installed viamd by following the instructions on GitHub.
Loading it fails with the following error:
[11:00:12][debug]: Initializing GL... [/home/ali/Downloads/viamd/src/main.cpp:1184]
[11:00:13][debug]: Creating framebuffer... [/home/ali/Downloads/viamd/src/main.cpp:1191]
[11:00:13][debug]: Initializing immediate draw... [/home/ali/Downloads/viamd/src/main.cpp:1200]
[11:00:13][debug]: Initializing ramachandran... [/home/ali/Downloads/viamd/src/main.cpp:1202]
[11:00:13][debug]: Initializing post processing... [/home/ali/Downloads/viamd/src/main.cpp:1204]
[11:00:13][error]: Failed to open source file for shader '' [compile_shader_from_file]
[11:00:13][error]: A SEVERE GL ERROR HAS OCCURED: GL_INVALID_VALUE error generated. Program handle does not refer to an object generated by OpenGL. [gl_callback]
Assertion "false" failed at line 51 in /home/ali/Downloads/viamd/src/application/application.cpp:gl_callback
Illegal instruction (core dumped)
I am using Ubuntu 22.04, output of uname -a:
Linux boltzmann 5.19.0-35-generic #36~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Feb 17 15:17:25 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
I am using Nvidia display driver: 515.86.01
And Nvidia cuda version: 11.7
I have attached the output of cmake and make commands:
viamd_cmake_output.txt
viamd_make_output.txt
Let me know if you need any additional details.
Cannot build on Mac M2
Hi,
I tried to build VIAMD on my Mac M2 but it fails, is it only available on intel Macs ?
cretin@cronos: ~/Documents/PROJETS/viamd/build $ cmake ..
-- The CXX compiler identification is AppleClang 15.0.0.15000040
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenGL: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/System/Library/Frameworks/OpenGL.framework
-- The C compiler identification is AppleClang 15.0.0.15000040
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Performing Test HAVE_AVX512_EXTENSIONS
-- Performing Test HAVE_AVX512_EXTENSIONS - Failed
-- Performing Test HAVE_AVX2_EXTENSIONS
-- Performing Test HAVE_AVX2_EXTENSIONS - Failed
-- Performing Test HAVE_FMA_EXTENSIONS
-- Performing Test HAVE_FMA_EXTENSIONS - Failed
-- Performing Test HAVE_AVX_EXTENSIONS
-- Performing Test HAVE_AVX_EXTENSIONS - Failed
-- Writing resources to gen/gl_shaders.inl
-- mdlib: AppleClang configuration was used
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Using Cocoa for window creation
CMake Deprecation Warning at ext/enkiTS/CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
-- Writing resources to gen/shaders.inl
-- Configuring done (3.9s)
-- Generating done (0.1s)
-- Build files have been written to: /Users/cretin/Documents/PROJETS/viamd/build
cretin@cronos: ~/Documents/PROJETS/viamd/build $ cmake --build .
[ 0%] Built target imgui_notify
[ 1%] Generating bin/datasets/1ALA-500.pdb
[ 1%] Built target viamd_copy_datasets
[ 2%] Building C object ext/mdlib/CMakeFiles/mdlib.dir/src/core/md_allocator.c.o
In file included from /Users/cretin/Documents/PROJETS/viamd/ext/mdlib/src/core/md_allocator.c:1:
/Users/cretin/Documents/PROJETS/viamd/ext/mdlib/src/core/md_allocator.h:49:47: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
uint64_t md_temp_allocator_max_allocation_size();
^
void
/Users/cretin/Documents/PROJETS/viamd/ext/mdlib/src/core/md_allocator.h:58:53: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
struct md_ring_allocator_t* md_thread_ring_allocator();
^
void
In file included from /Users/cretin/Documents/PROJETS/viamd/ext/mdlib/src/core/md_allocator.c:5:
/Users/cretin/Documents/PROJETS/viamd/ext/mdlib/src/core/md_os.h:17:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
uint64_t md_os_physical_ram();
^
void
/Users/cretin/Documents/PROJETS/viamd/ext/mdlib/src/core/md_os.h:19:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
uint64_t md_os_num_processors();
^
void
/Users/cretin/Documents/PROJETS/viamd/ext/mdlib/src/core/md_allocator.c:16:47: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
uint64_t md_temp_allocator_max_allocation_size() {
^
void
/Users/cretin/Documents/PROJETS/viamd/ext/mdlib/src/core/md_allocator.c:55:53: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
struct md_ring_allocator_t* md_thread_ring_allocator() {
^
void
6 warnings generated.
[ 3%] Building C object ext/mdlib/CMakeFiles/mdlib.dir/src/core/md_arena_allocator.c.o
In file included from /Users/cretin/Documents/PROJETS/viamd/ext/mdlib/src/core/md_arena_allocator.c:3:
/Users/cretin/Documents/PROJETS/viamd/ext/mdlib/src/core/md_allocator.h:49:47: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
uint64_t md_temp_allocator_max_allocation_size();
^
void
/Users/cretin/Documents/PROJETS/viamd/ext/mdlib/src/core/md_allocator.h:58:53: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
struct md_ring_allocator_t* md_thread_ring_allocator();
^
void
In file included from /Users/cretin/Documents/PROJETS/viamd/ext/mdlib/src/core/md_arena_allocator.c:5:
/Users/cretin/Documents/PROJETS/viamd/ext/mdlib/src/core/md_os.h:17:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
uint64_t md_os_physical_ram();
^
void
/Users/cretin/Documents/PROJETS/viamd/ext/mdlib/src/core/md_os.h:19:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
uint64_t md_os_num_processors();
^
void
4 warnings generated.
[ 3%] Building C object ext/mdlib/CMakeFiles/mdlib.dir/src/core/md_base64.c.o
[ 4%] Building C object ext/mdlib/CMakeFiles/mdlib.dir/src/core/md_bitfield.c.o
In file included from /Users/cretin/Documents/PROJETS/viamd/ext/mdlib/src/core/md_bitfield.c:3:
/Users/cretin/Documents/PROJETS/viamd/ext/mdlib/src/core/md_allocator.h:49:47: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
uint64_t md_temp_allocator_max_allocation_size();
^
void
/Users/cretin/Documents/PROJETS/viamd/ext/mdlib/src/core/md_allocator.h:58:53: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
struct md_ring_allocator_t* md_thread_ring_allocator();
^
void
In file included from /Users/cretin/Documents/PROJETS/viamd/ext/mdlib/src/core/md_bitfield.c:7:
In file included from /Users/cretin/Documents/PROJETS/viamd/ext/mdlib/src/core/md_intrinsics.h:8:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/x86intrin.h:15:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/immintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
#error "This header is only meant to be used on x86 and x64 architecture"
^
In file included from /Users/cretin/Documents/PROJETS/viamd/ext/mdlib/src/core/md_bitfield.c:7:
In file included from /Users/cretin/Documents/PROJETS/viamd/ext/mdlib/src/core/md_intrinsics.h:8:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/x86intrin.h:15:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/immintrin.h:17:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/x86gprintrin.h:15:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/hresetintrin.h:42:27: error: invalid input constraint 'a' in asm
__asm__ ("hreset $0" :: "a"(__eax));
^
In file included from /Users/cretin/Documents/PROJETS/viamd/ext/mdlib/src/core/md_bitfield.c:7:
In file included from /Users/cretin/Documents/PROJETS/viamd/ext/mdlib/src/core/md_intrinsics.h:8:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/x86intrin.h:15:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/immintrin.h:21:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
#error "This header is only meant to be used on x86 and x64 architecture"
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:54:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:133:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_packsswb((__v4hi)__m1, (__v4hi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:163:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_packssdw((__v2si)__m1, (__v2si)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:193:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_packuswb((__v4hi)__m1, (__v4hi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:220:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:243:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpckhwd((__v4hi)__m1, (__v4hi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:264:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpckhdq((__v2si)__m1, (__v2si)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:291:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpcklbw((__v8qi)__m1, (__v8qi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:314:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpcklwd((__v4hi)__m1, (__v4hi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:335:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpckldq((__v2si)__m1, (__v2si)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:356:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_paddb((__v8qi)__m1, (__v8qi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:377:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_paddw((__v4hi)__m1, (__v4hi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:398:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_paddd((__v2si)__m1, (__v2si)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:420:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_paddsb((__v8qi)__m1, (__v8qi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:443:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_paddsw((__v4hi)__m1, (__v4hi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:465:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_paddusb((__v8qi)__m1, (__v8qi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
2 warnings and 20 errors generated.
make[2]: *** [ext/mdlib/CMakeFiles/mdlib.dir/src/core/md_bitfield.c.o] Error 1
make[1]: *** [ext/mdlib/CMakeFiles/mdlib.dir/all] Error 2
make: *** [all] Error 2
Implement 'hover' line in plots
Implement a line that follows the mouse cursor when hovering plots and displays the current value.
crash when opening the via file!
no error message
<< Loading PDB error >>
Hi.
I tried to load a PDB with multiple modes of a boron-nitride nanotube surrounded by water molecules and got the following error:
Assertion "cell_data[ci] < LENGTH_CAP && "Too many entities per cell"" failed at line 740 in /home/icamps/Downloads/viamd/ext/mdlib/src/core/md_spatial_hash.c:md_spatial_hash_create_soa
Illegal instruction (core dumped)
Any ideas about this?
Thanks in advance.
functions
Some functions needs to be checked and/or fixed: rdf, pair fcts...
scaling of ramachadran windown
Lock the ratio of ramachandran window to square
Property Export: Distribution axis and overall layout.
The axis for data exported example rdf is off.
Issue with the Density Volume window
On Ubuntu:
- The density volume window can be interacted with, only if in the viamd window and not outside.
- When using filtering, the density is not updated properly.
auto-update of a dynamic selection
This issue appear with coloring a representation in function of a property, or when using a dynamic selection (i.e. within).
In the .via file, no indication is saved about the fact that those representation should be auto-updated and therefore the box is not ticked when reopening the via file.
I understand that this is because the parameters has not been evaluated for property calculation, and it raise the question if the script editor should be evaluated upon loading of the via file.... but for dynamic selection it should be saved automatically and autoupdated on load
Implement recentering
When a user right-clicks on any structure, the user should be presented with a context menu option to 'recenter' the trajectory on (chain/residue/atom). An option to also apply a rotation could also be viable, given that the structure is a residue!
Implement MMCIF support (Topology)
There is no excuse! Just do it!
coloring in fct of parameters
- the auto-update button should be activated from begining.
- the dihedral scale is not available on my version
- The coloring in fct of the secondary structure is not working as it should. For example, in the first frame of the alanine dataset (linear), only two residues are colored as beta sheet.
Missing semantic check in static check
This expression evaluates into float[1]:
'resname("ALA") distance(1,2)'
This should not be a valid expression semantically.
Potential rendering glitch in i3
I don't think this is an actual issue, and is probably more related to my own setup, but the performance of the 3D visualization (~speed with which the image follows my mouse movement when I rotate, for example) is heavily dependent on the size of the window. Is this entirely expected because he needs to render more pixels?
Also, I got some weird behavior when resizing the window:
This could be super system-dependent, so if this is not worth looking into I'd totally understand.
inxi -Gxx:
Graphics:
Device-1: Intel TigerLake-LP GT2 [Iris Xe Graphics] vendor: Dell
driver: i915 v: kernel ports: active: DP-4 off: eDP-1
empty: DP-1, DP-2, DP-3, DP-5, HDMI-A-1, HDMI-A-2, HDMI-A-3
bus-ID: 0000:00:02.0 chip-ID: 8086:9a49
Device-2: NVIDIA GA102 [GeForce RTX 3080 Ti] vendor: ASUSTeK
driver: nvidia v: 545.29.02 ports: active: none
empty: DP-6, DP-7, DP-8, HDMI-A-4, HDMI-A-5 bus-ID: 0000:09:00.0
chip-ID: 10de:2208
Device-3: Sunplus Innovation Integrated_Webcam_FHD type: USB
driver: uvcvideo bus-ID: 3-6:3 chip-ID: 1bcf:2ba0
Display: x11 server: X.Org v: 1.21.1.4 driver: X: loaded: modesetting
unloaded: fbdev,nouveau,vesa failed: nvidia gpu: i915 display-ID: :1
screens: 1
Screen-1: 0 s-res: 3840x2160 s-dpi: 96
Monitor-1: DP-1-2 res: 3840x2160 dpi: 138 diag: 813mm (32")
OpenGL: renderer: Mesa Intel Xe Graphics (TGL GT2)
v: 4.6 Mesa 23.1.3-1pop0~1689084530~22.04~0618746 direct render: Yes
inxi -Sxx:
System:
Host: pop-os Kernel: 6.5.6-76060506-generic x86_64 bits: 64 compiler: N/A
Desktop: GNOME 42.5 tk: GTK 3.24.33 wm: i3 dm: GDM3
Distro: Pop!_OS 22.04 LTS base: Ubuntu 22.04 LTS Jammy
Support for AMBER and small issues
Hi. Thanks for the nice viewer 👍 Any chance to get support for AMBER files, particularly parm7 and netCDF formats? Right now one can do transformations with parmed, but that is not ideal.
I also had two issues until now while running the program (as compiled from a cloned repo yesterday, 29.11.2023):
- Got a core dumped while passing the mouse over a script with selections:
Assertion "get_identifier(ir, name) == NULL" failed at line 1059 in /viamd/ext/mdlib/src/md_script.c:create_identifier
Illegal instruction (core dumped)
- I defined a distance measurement, and ran the evaluation, but no plot was generated. The plot area had inf,inf as the min.max boundaries, but no data was displayed even when modifying the plot region. Exporting the data shows the expected values though.
Can it use ffmpeg to export trajectory movies like pymol?
The movie effect is fantastic!
Serialization and deserialization of stored selections seems broken
On MSVC it seems to corrupt the heap upon decompression of the bitfield.
Tested on amyloid dataset with PFTAA
Loading Structures
Improve loading of structures:
Dialog
- CG: Let user specify radii for beads
- Supply time between frames
- List of different residues and filtering of what to load
GRO
- Load Trajectory Button
Amber
- Support amber files
Sync X-Axis
when playing around with VIAMD: Unchecking the "Sync X-Axis per type" checkbox in Distributions>Settings crashes the application with "Seg fault"
failure to build with gcc 13.2.1 or llvm 17.0.4
trying to build with gcc 13.2.1 or llvm 17.0.4 results in in enkit not compiling and failing with this error.
[ 53%] Building CXX object ext/enkiTS/CMakeFiles/enkiTS.dir/src/TaskScheduler.cpp.o
In file included from /home/drFaustroll/lavello/viamd/ext/enkiTS/src/TaskScheduler.cpp:19:
/home/drFaustroll/lavello/viamd/ext/enkiTS/src/TaskScheduler.h:114:103: error: no template named 'initializer_list' in namespace 'std'
114 | template<typename D, typename T> void SetDependenciesArr( D& dependencyArray_, std::initializer_list<T*> taskpList_ );
| ~~~~~^
/home/drFaustroll/lavello/viamd/ext/enkiTS/src/TaskScheduler.h:116:110: error: no template named 'initializer_list' in namespace 'std'
116 | template<typename D, typename T, int SIZE> void SetDependenciesArr( D(&dependencyArray_)[SIZE], std::initializer_list<T*> taskpList_ );
| ~~~~~^
/home/drFaustroll/lavello/viamd/ext/enkiTS/src/TaskScheduler.h:118:101: error: no template named 'initializer_list' in namespace 'std'
118 | template<typename D, typename T> void SetDependenciesVec( D& dependencyVec_, std::initializer_list<T*> taskpList_ );
| ~~~~~^
/home/drFaustroll/lavello/viamd/ext/enkiTS/src/TaskScheduler.h:532:70: error: no template named 'initializer_list' in namespace 'std'
532 | void ICompletable::SetDependenciesArr( D& dependencyArray_, std::initializer_list<T*> taskpList_ ) {
| ~~~~~^
/home/drFaustroll/lavello/viamd/ext/enkiTS/src/TaskScheduler.h:548:24: warning: variable templates are a C++14 extension [-Wc++14-extensions]
548 | void ICompletable::SetDependenciesArr( D(&dependencyArray_)[SIZE], std::initializer_list<T*> taskpList_ ) {
| ^
/home/drFaustroll/lavello/viamd/ext/enkiTS/src/TaskScheduler.h:548:24: error: variable has incomplete type 'void'
/home/drFaustroll/lavello/viamd/ext/enkiTS/src/TaskScheduler.h:548:47: error: use of undeclared identifier 'dependencyArray_'
548 | void ICompletable::SetDependenciesArr( D(&dependencyArray_)[SIZE], std::initializer_list<T*> taskpList_ ) {
| ^
/home/drFaustroll/lavello/viamd/ext/enkiTS/src/TaskScheduler.h:548:77: error: no member named 'initializer_list' in namespace 'std'
548 | void ICompletable::SetDependenciesArr( D(&dependencyArray_)[SIZE], std::initializer_list<T*> taskpList_ ) {
| ~~~~~^
/home/drFaustroll/lavello/viamd/ext/enkiTS/src/TaskScheduler.h:548:94: error: 'T' does not refer to a value
548 | void ICompletable::SetDependenciesArr( D(&dependencyArray_)[SIZE], std::initializer_list<T*> taskpList_ ) {
| ^
/home/drFaustroll/lavello/viamd/ext/enkiTS/src/TaskScheduler.h:547:35: note: declared here
547 | template<typename D, typename T, int SIZE>
| ^
/home/drFaustroll/lavello/viamd/ext/enkiTS/src/TaskScheduler.h:548:96: error: expected expression
548 | void ICompletable::SetDependenciesArr( D(&dependencyArray_)[SIZE], std::initializer_list<T*> taskpList_ ) {
| ^
/home/drFaustroll/lavello/viamd/ext/enkiTS/src/TaskScheduler.h:548:98: error: use of undeclared identifier 'taskpList_'
548 | void ICompletable::SetDependenciesArr( D(&dependencyArray_)[SIZE], std::initializer_list<T*> taskpList_ ) {
| ^
/home/drFaustroll/lavello/viamd/ext/enkiTS/src/TaskScheduler.h:548:110: error: expected ';' at end of declaration
548 | void ICompletable::SetDependenciesArr( D(&dependencyArray_)[SIZE], std::initializer_list<T*> taskpList_ ) {
| ^
| ;
/home/drFaustroll/lavello/viamd/ext/enkiTS/src/TaskScheduler.h:548:111: error: expected unqualified-id
548 | void ICompletable::SetDependenciesArr( D(&dependencyArray_)[SIZE], std::initializer_list<T*> taskpList_ ) {
| ^
/home/drFaustroll/lavello/viamd/ext/enkiTS/src/TaskScheduler.h:566:68: error: no template named 'initializer_list' in namespace 'std'
566 | void ICompletable::SetDependenciesVec( D& dependencyVec_, std::initializer_list<T*> taskpList_ ) {
| ~~~~~^
1 warning and 13 errors generated.
gmake[2]: *** [ext/enkiTS/CMakeFiles/enkiTS.dir/build.make:76: ext/enkiTS/CMakeFiles/enkiTS.dir/src/TaskScheduler.cpp.o] Error 1
gmake[1]: *** [CMakeFiles/Makefile2:583: ext/enkiTS/CMakeFiles/enkiTS.dir/all] Error 2
gmake: *** [Makefile:91: all] Error 2
Crash when loading dataset without backbone when having active secondary structure visualization
receive erreor message
Discussed in #53
Originally posted by fakher77 December 17, 2023
I have try Viamd on windows 10 but the application dont started
by using unbutu i receive this message
[19:11:14][error]: A SEVERE GL ERROR HAS OCCURED: 0:2(10): error: GLSL 1.50 is not supported. Supported versions are: 1.10, 1.20, 1.30, 1.40, 1.00 ES, and 3.00 ES [gl_callback]
can you help me
Implement Coordinate System Widget
Implement a Coordinate System widget.
XYZ red, green, blue.
Small clickable area for each XY, XZ, YZ: When clicked aligns view with coordinate-system.
Illegal instruction when loading XYZs (Ubuntu 22.04, x86)
I get illegal instruction when trying to load any of my XYZ files;
[12:48:22][debug]: Initializing GL... [/home/sandervandenhaute/viamd/src/main.cpp:1336]
[12:48:22][debug]: Initializing framebuffer... [/home/sandervandenhaute/viamd/src/main.cpp:1392]
[12:48:22][debug]: Initializing immediate draw... [/home/sandervandenhaute/viamd/src/main.cpp:1401]
[12:48:22][debug]: Initializing ramachandran... [/home/sandervandenhaute/viamd/src/main.cpp:1403]
[12:48:22][debug]: Initializing post processing... [/home/sandervandenhaute/viamd/src/main.cpp:1405]
[12:48:22][debug]: Initializing volume... [/home/sandervandenhaute/viamd/src/main.cpp:1407]
[12:48:22][debug]: Initializing task system... [/home/sandervandenhaute/viamd/src/main.cpp:1409]
[12:48:22][error]: One or more arguments are missing [md_gl_molecule_set_atom_flags]
[12:48:45][debug]: No atom type or atom resname were given, will default to covalent order of 1 for all bonds. [/home/sandervandenhaute/viamd/ext/mdlib/src/md_util.c:1103]
[12:48:45][info]: File may also contain trajectory, attempting to load trajectory
[12:48:45][info]: The xyz file did not contain multiple entries and cannot be read as a trajectory
Assertion "mol->residue.atom_range" failed at line 927 in /home/sandervandenhaute/viamd/ext/mdlib/src/md_script_functions.inl:get_residue_indices_in_context
Illegal instruction (core dumped)
XYZ is ill-defined as a format, and many variations exist. However, I've tried a bunch of slightly different ones but all give the same result. The systems are both periodic and nonperiodic, but entirely inorganic, i.e. they're just a bunch of atomic elements with positions. There are no residues, no chains, no topology or any other piece of information you might normally include in e.g. a pdb file. They were generated either manually or saved with ASE.
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