Bug #1510
gmx check and gmx dump do not work for tng files
Description
gmx dump -f traj2.tng shows only the molecule definition but no coordinates, etc.
Command line:
gmx dump -f traj2.tng
Molecule: trichloromethane, count: 1000
Chain:
Residue: MOL
Atom: C1 (c3)
Atom: H1 (h3)
Atom: Cl1 (cl)
Atom: Cl2 (cl)
Atom: Cl3 (cl)
gcq#22: "I Had So Many Problem, and Then I Got Me a Walkman" (F. Black)
Associated revisions
Fix bug writing TNG output from dump.
The output was incorrectly located in an if statement.
Partial fix of #1510
Change-Id: I85823d9369f208f21f4bafe19705e9e4dd2da027
History
#1 Updated by Erik Lindahl about 5 years ago
- Target version changed from 5.0 to 5.x
#2 Updated by David van der Spoel about 5 years ago
Ok this one is not a show stopper, but #1502 is IMHO. Working on it now.
#3 Updated by David van der Spoel about 5 years ago
The example file in
gromacs/src/external/tng_io/example_files/tng_example.tng
can not be read by gromacs tng tools:
Checking file gromacs/src/external/tng_io/example_files/tng_example.tng
Reading frame 0 time 0.000
- Atoms 15
TNG library: Cannot read header size. /Users/spoel/GG/correl/gromacs/src/external/tng_io/src/lib/tng_io.c: 820
TNG library: Cannot read block header at pos 2531. /Users/spoel/GG/correl/gromacs/src/external/tng_io/src/lib/tng_io.c: 18347
-------------------------------------------------------
Program gmx check, VERSION 5.1-dev-20140523-89c1dac-dirty
Source code file: gromacs/src/gromacs/fileio/tngio_for_tools.cpp, line: 743
File input/output error:
Cannot read TNG file. Cannot find data blocks of next frame.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
#4 Updated by David van der Spoel about 5 years ago
- Subject changed from gmx dump does not work for tng files to gmx check and gmx dump do not work for tng files
#5 Updated by Gerrit Code Review Bot about 5 years ago
Gerrit received a related patchset '1' for Issue #1510.
Uploader: Magnus Lundborg (magnus.lundborg@scilifelab.se)
Change-Id: I85823d9369f208f21f4bafe19705e9e4dd2da027
Gerrit URL: https://gerrit.gromacs.org/3517
#6 Updated by Magnus Lundborg about 5 years ago
- Status changed from New to Resolved
With these two associated revisions this should work now.
#7 Updated by Rossen Apostolov about 5 years ago
- Status changed from Resolved to Closed
#8 Updated by Teemu Murtola about 5 years ago
- Target version changed from 5.x to 5.0
Bug fix in the TNG library to improve reading.
Reading single frame frame sets did not work properly.
Fixes #1502 and partial fix of #1510.
Reread frame set after getting stride length.
Extra check to avoid reading past end of file when
checking what data blocks are present.
Change-Id: I5275382bd49b5b46ebfdebe535c53d2f09015bc0