Hands-on: Data analysis and advanced scripting. Mario Orsi
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1 Hands-on: Data analysis and advanced scripting Mario Orsi LAMMPS workshop, ICTP Trieste, 25 March 2014
2 Learning objectives On-the-fly analysis: use LAMMPS to compute/accumulate/average properties of interest while the simulation is running Use variable commands to perform simple calculations Use compute and fix commands for more elaborate calculations Post-processing: use external tools (Python scripts) to perform additional analysis at the end of the simulation This hands-on activity was derived from actual research work (see paper in reference folder)
3 Bulk water basic simulation Enter directory simulation-bulk/1 Inspect input files: in.bulk, forcefield.tip3p, data.singletip3p Run: $ lammps < in.bulk Inspect output Visualize: Directly (.jpg,.mpg) With VMD (.lammpstrj) Pregenerated visuals available in viz subdirectory
4 Bulk water potential energy Work in directory 1/ Task: modify input script to compute and output the potential energy per molecule in units of kcal/mol Hints: Check out compute pe command Remember to normalize by the number of molecules Result should be ~ -9.9 kcal/mol When finished, compare your script and results with content of directory 2/
5 Bulk water mass density Work in directory 2/ Task: modify input script to compute and output the system density in units of g/cm 3 Hints: Use variable commands: To define useful constants (molecular mass, Avogadro s number, conversion factors, etc.) To perform the actual calculation Result should be ~ 1 g/cm 3 When finished, compare your script and results with content of directory 3/
6 Bulk water radial distribution function (RDF) Work in directory 3/ Task: modify input script to compute and output the oxygen-oxygen RDF Hints: Use compute rdf Obtain oxygen type from data file Use fix ave/time to generate output file When finished, compare your script and results with content of directory 4/
7 Bulk water radial distribution function (RDF) post-processing Work in directory 4/ Output goo.rdf contains comments, extra data, cannot be plot directly File goo.rdf needs to be post-processed Check out analysis-tools/rdf2data.py (open with text editor and see comments for usage instructions) Example: $ python../../analysis-tools/rdf2data.py goo.rdf > goo.dat goo.dat is now 2-column matrix (r goo) which can be plotted together with reference experimental data: $ xmgrace goo.dat../../reference/goo-exp.dat Compare results with 4-post
8 RDF: simulation vs. experiment Simulation curve is noisy because of short simulation time. For converged results, see paper in reference folder.
9 Bulk water mean squared Work in directory 4 displacement (MSD) Task: compute and output the MSD Hints: Use compute msd Assume oxygen MSD = water MSD Use fix ave/time to generate output file When finished, compare your script and results with content of directory 5
10 Bulk water Diffusion Work in directory 5 Diffusion coefficient defined as: D = MSD(t) / 6t with t sufficiently large to get convergence MSD data can be post-processed to obtain D: Check out analysis-tools/msd2diff.py (open with text editor and see comments for usage instructions) Example: $ python../../analysis-tools/msd2diff.py wat.msd 2 3 > wat.diff Compare with 5-post
11 MSD and diffusion Converged results from paper in reference folder
12 Water/vapor interface basic simulation Enter directory simulation-interface/1 Inspect input script Notice how the change_box command is used to increase z dimension and create water layers separated by vacuum layers Run: $ lammps < in.liquid-vapor Inspect output Visualize: Directly (.jpg,.mpg) With VMD (.lammpstrj) Pregenerated visuals available in viz subdirectory
13 Water surface tension Work in directory 1/ Task: modify input script to compute and output the surface tension of the water-vacuum system in units of mn/m (millinewton/meter) Surface tension = Lz * [ Pz - ( Px + Py ) / 2 ] / 2 Hints: Use equal-style variables Average with fix ave/time Define conversion factors between LAMMPS units and required output units When finished, compare your script and results with content of directory 2/
![Py ) / 2 ] / 2 Hints: Use equal-style variables Average with fix ave/time Define conversion factors between](/docs-images/41/12716284/images/page_13.jpg "LAMMPS units and required output units When finished, compare your script and results with content of")
14 Water number density profile Work in directory 2/ Task: modify input script to compute and output the number density profile across the water-vacuum interface Hints: Use fix ave/spatial with appropriate keywords Compute individual profiles for H and O When finished, compare your script and results with content of directory 3/
15 Water mass density profile Work in directory 3/ Task: post-process H and O number density profiles to obtain total H 2 O mass density profile Hints: Use../../analysis-tools/numDens2massDens.py (open file with text editor and see comments about usage) Compute individual profiles for H and O To get total profile, see../../analysistools/sumprofile.py When finished, compare your results with content of directory 3-post/
16 Mass density profile across watervapor interface for various models Converged results (see paper in reference folder)
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