Dear lamms user,
I am having an issue in simulation using lammps. It is showing an error as “ERROR: Invalid mass line in data file (…/read_data.cpp:1715)”. I am very confused how to solve the issue. In data file I have provided the mass for all type of atom. I have 10 atom types and for each type I have provided the mass. My data file is as following
Try this:
I could not see any obvious errors looking at the excerpt you posted
in your message. Sometimes LAMMPS error messages are cryptic. You
can try running your data file into another program which can read
LAMMPS data files (such as VMD/topotools, or MOLTEMPLATE/ltemplify.py,
or pizza.py, or perhaps VIPSTER) to see what kinds of error messages
those programs generate. Sometimes that helps. Alternatively, if the
file is not very large (less than 200kb), you can post it here, and
someone might look at it.
In VMD select the Extensions-Tk Console menu option and type:
topo readlammpsdata YOUR_FILE full
If you have moltemplate, try:
ltemplify.py YOUR_FILE
other software I am aware of:
https://pizza.sandia.gov
https://github.com/sgsaenger/vipster
good luck.
Andrew
Oops. The message from Thomas Leps was correct.
He suggested you should get rid of the "mass" at the beginning of
every line of the "Masses" section. His advice is correct.
(But you don't need to put a blank space between each line.)
Please disregard my previous message on this thread.
Cheers
Andrew
Thank you Evangelos, Thomas and Andrew for your valuable suggestion. I have checked by removing “mass” from each line but it is not working and in the later case the log.lammps file remains empty. I am attaching my input files. Can you please check if I did it correctly? Thank you for your kind help. I am using LAMMPS (16 Mar 2018) version of lammps.
rameswar
watermolecule.txt (328 Bytes)
zeolite-2-mod.in (11.1 KB)
zeolite-glu.txt (37 KB)
Your zeolite-glu.txt file still has “mass” on each line before the particle type.
Thank you very much. But as I told if I remove mass then lammps does not print anything in the output file. So I wrote it back.
Rameswar
Thank you very much. But as I told if I remove mass then lammps does not print anything in the output file. So I wrote it back.
well, if you prefer to have a known error due to incorrect syntax in your input deck rather than systematically looking for some other problem, then nobody can help you.
axel.
also, why do you say, that there is no output? if i change your molecule files to have the correct syntax, i do get an error before the simulation stops:
ERROR: Numeric index is out of bounds (src/MOLECULE/bond_harmonic.cpp:126)
Last command: bond_coeff 9 320.00 1.4243 #C8-O10
and that is deserved because at this point you have only 8 bond types (7 in the data file and one extra).
axel.
Thank you Axel for you extreme help. I have corrected the bond type and ran the job again but it is again not printing any output for me. Is this can be a problem of the lammps version (LAMMPS (16 Mar 2018))? I have attached my input files again. It would be very kind of you if you please check this inputs again. Thank you very much.
Rameswar
watermolecule.txt (328 Bytes)
zeolite-glu.txt (36.9 KB)
zeolite-2-mod.in (11.1 KB)
What platform are you running on?
And what is your command line to run LAMMPS?
Axel
Thank you Axel, I use a script to run lammps. The cluster I am using to run this is a CentOS. I have pasted the important part of the script file here. I can also attach the whole script if you would like to see it. Thank you.
There are blatantly obvious errors in the bonds section of your data file. It is a mystery to me how you can even expect this is to work. There must be output. You are probably not looking in the right spot for it.
Run the input with just one processor interactively on a local machine or compile a serial version and use that for debugging and testing. The latter one will definitely print error messages on such gross errors. The errors you had in your input so far are so fundamental, it doesn’t matter that you have an older version of LAMMPS.
At any rate. This is the end of the line as far as I am concerned. I will disregard future e-mails from you. I have no time to spend on doing debugging for someone who disregards documentation left and right, makes decisions that make no sense (to me), and has no meaningful strategy of debugging.
Good luck,
Axel.
why on earth do you run this on a cluster and not your desktop? you are just making your life miserable and wasting a lot of time.
If you want us to get to the bottom of the problem we need the script in its entirety. If the script you show here is all there is, then there is no output because the script does not actually run Lammps.