[LAMMPS] Visualizing log file

(About how to use Pizza.py, please refers to previous post of How to use Pizza.py for LAMMPS or the official Pizza.py Toolkit page.

Instead of asking pizza.py to get all the "Temp", "TotEng" .. by typing in each variable, and then do g.plot (a lot of repetitive keyboard work!), there's a much faster way to visualize the thermo-type data. It allows us to quickly view the trend of properties, and get an idea of the equilibrium status of the simulation.

This can be done directly on the shell or through pizza.py. Below is to do it in pizza.py:

$   python -i /home/pizza/src/pizza.py

First entering the pizza.py interactive interface. In the pizza.py interface, asking pizza to run the logview.py script:

Pizza.py (9 Feb 2012), a toolkit written in Python type ? for help, CTRL-D to quit Loading tools ... >@run logview.py gnu log* Executing file: /home/pizza/scripts/logview.py 200000 read 10001 log entries

Note that there's a "@" sign before run. When Pizza.py was installed, the path to where the scripts are stored was also established (/home/pizza/scripts/). The third argument gnu is to use Gnuplot to generate the graphs. Thus in this case, Gnuplot has to be installed in the machine as well. Last argument is the file name(s) where the thermo data are stored. It can be log* or can be multiple files, i.e. log.1 log.2 ..., etc.

After loading the data, a panel containing the output thermo data appears (left hand size panel below).
By toggling the display options, the corresponding property vs. step will show up. The graph can be saved by first switch on the select toggle next to the property (turning into red), and hit print as. We can also change the file name from "tmp" to a more informative one, such as "Press". The saved graph will be in .eps format and locate at where you activate pizza.py.

[LAMMPS] Read/Observe Log File

Although we could always write our own scripts to process LAMMPS output files, LAMMPS has this awesome package, Pizza.py , which already contains many powerful tools to allow quick observations on the simulation results.

At the beginning of a simulation, you might want to check how energies and temperature drift, get averages over blocks of trajectory, and visualize the fluctuation of the simulation box. All these information can be retrieved in the log file, and all we need is the Pizza.py toolkit. Since the whole package is a combination of Python scripts, we also need to have Python installed.

Download the Pizza.py toolkit from this page , and put it in your directory. After unzipping it, you could find the Python script pizza.py in the src folder. The Pizza.py toolkit can be used directly or interactively.

First set up an alias pointing to where you put the pizza.py file. For example:

$   alias pizza='python -i /home/pizza/src/pizza.py

Then run pizza.py by typing in

$   pizza

This will bring you into the pizza.py interactive interface:

Pizza.py (9 Feb 2012), a toolkit written in Python type ? for help, CTRL-D to quit Loading tools ... >

There might be some error messages after Loading tools if you don't have some of the modules required. Don't worry if you are missing some modules. Not every function uses all the modules.

Here I want to demonstrate how to use the interactive interface to observe the thermo output in LAMMPS log file.

>  l=log("*log") 180000000 182500000 185000000 187500000 190000000 192500000 read 6001 log entries

This function will read in the files that have names end with log. This command calls the log.py script in the src folder. It can take multiple files, single files, even incomplete files. Check the comments in log.py to get more information.

After reading in the thermo info stored in *log, we can get individual items. For example, to get timestep, pressure, temperature, energy:

s,t,p,E=l.get("Step","Temp","Press","TotEng")

Variables on the left hand side can just be any variables. The items inside the right hand parenthesis have to match with their names in the *log files.

The thermo information fluctuates a lot. A better way to look at them is to plot against time. In the Pizza.py toolkit, they incorporate Gnuplot (in gnu.py) so that we can directly use it in the interactive interface:

> g=gnu() > g.plot(s,t)

The first command calls Gnuplot and the second command will plot timesteps vs. temperature.

If you are like me, impatient of typing in those commands repetitively, don't worry. Pizza.py toolkit can also take scripts. There is a collection of scripts written by Pizza.py users. They come within the Pizza.py package. These scripts are handy to use and are very powerful. It allows me to do block averages in just one line.

Read more:
Block average
Visualizing log files

LAMMPS - A free open-source MD package

LAMMPS stands for "Large-scale Atomic/Molecular Massively Parallel Simulator", which is a molecular dynamics simulation package distributed by National Sandia Lab. LAMMPS incorporate MPI so it could run in parallel or on single processor.

The reason that I chose LAMMPS to simulate my ionomers for several reasons:

1. It could run coarse-grained/united-atom simulations - LAMMPS includes many widely used empirical potentials.
2. All codes are written in C++, so I am able to go into the code and do modification - the dihedral potential that I use for my ionomers are not included in the potentials LAMMPS provides. So I modified a similar potential in LAMMPS to describe the dihedral interactions.
3. Maintained and developed by experts - This is the most important. LAMMPS has a newer version almost every year. Many new useful functions/features are added and useful force fields are incorporated. It also has an very active mail-list.

To keep LAMMPS a simple and fast simulator, LAMMPS does not help you post-process data. This is very different from other MD package like Gromacs or NAMD, which performs analyses of your simulation. Because it doesn't have a GUI interface, so LAMMPS won't visualize your simulation either. There are a few tools that allow you to do some pre/post-process, but I found it is much easier to do analyses in my own C++ codes.

To know more specifics about LAMMPS, the official website has all you need to know, and is always up-to-date.