From 8d46aa605606a5ac047077c4827fc87ea4da98f0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 18 May 2017 00:31:54 -0400 Subject: [PATCH] add readme file to discuss various python pair style usage examples --- examples/python/README.pair_python | 41 ++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 examples/python/README.pair_python diff --git a/examples/python/README.pair_python b/examples/python/README.pair_python new file mode 100644 index 0000000000..3844a2676e --- /dev/null +++ b/examples/python/README.pair_python @@ -0,0 +1,41 @@ +This folder contains several LAMMPS input scripts and a python module +file py_pot.py to demonstrate the use of the pair style python. + +in.pair_python_melt: +This is a version of the melt example using the python pair style. The first +part of the output should have identical energies, temperature and pressure +than the melt example. The following two sections then demonstrate how to +restart with pair style python from a restart file and a data file. + +in.pair_python_hybrid: +This versions shows how to mix regular pair styles with a python pair style. +However, in this case both potentials are the same, so the energies and +pressure in the output should be identical to that of the previous example. + +in.pair_python_spce: +This input shows a simulation of small bulk water system with the SPC/E +water potential. Since the python pair style does not support computing +coulomb contributions, pair style hybrid/overload is used to combine +the python style containing the Lennard-Jones part with the long-range coulomb. +Same as for the previous example, it also showcases restarting. + +in.pair_python_table: +This input demonstrates the use of using the python pair style to build +a table file for use with pair style table. This will run much faster +than the python pair style. This example tabulates the melt example from +above. Note that tabulation is approximative, so the output will only +agree with the melt result to some degree. + +in.pair_python_coulomb: +This is another tabulation example, this time for the SPC/E water example +with cutoff coulomb interactions. +Please note, that tabulating long-range coulomb has a systematic error in +forces and energies for all systems with bonds, angle and dihedrals. +In this case, this will only affect the energies, since the water molecules +are held rigid with fix shake. To enable long-range coulomb the coul/cut +style needs to be replaced with coul/long, a suitable kspace style added +and the pppm keyword added to the table pair style definition. + +in.pair_python_long: +The final example shows how to combine long-range coulomb with tabulation +for only the short range interactions via pair style hybrid/overlay.