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43 Commits

Author SHA1 Message Date
Richard Berger e1b2235d36
Update py_nve.py 2021-05-10 18:42:27 -04:00
Richard Berger 147e561dca
Update in.fix_python_invoke_neighlist example 2021-05-07 12:51:58 -04:00
Richard Berger 02b10380bc
Create ctypes only neighbor list API variant 
This moves the lammps.get_neighlist() method to lammps.numpy.get_neighlist().
lammps.get_neighlist() now returns a NeighList object, while the NumPy variants
returns a NumPyNeighList object. The main difference between the two is that while
the ctypes variant returns neighlist elements as

atom idx (int), numneighs (int), neighbors (POINTER(c_int))

the NumPy variant returns

atom idx (int), neighbors (numpy.array)
 2020-10-05 16:21:37 -04:00
Richard Berger b4a1c9c24c
Update examples 2020-09-17 17:08:13 -04:00
Richard Berger be72ce2534
Simplify Python examples to use numpy.extract_atom 2020-09-17 16:51:46 -04:00
Richard Berger e6703019bc
Update examples to use Python API constants 2020-09-16 16:10:43 -04:00
Richard Berger 34dbcf4f20 Update example 2019-09-12 13:53:29 -04:00
Richard Berger 69854eab42 Expose Neighbor lists via library interface 2019-09-12 13:46:05 -04:00
Axel Kohlmeyer 46bf4b7efb update log files for peptide, peri, pour and python examples 2018-11-29 14:51:25 -05:00
Steve Plimpton 1bd9e175e9
Merge pull request #749 from akohlmey/collected-bugfixes-and-updates 
Collected bugfixes and updates for the next patch release
 2018-01-08 09:20:18 -07:00
Axel Kohlmeyer 46217db8a5 make python functions examples more complete by adding exception handling and initializing variables 2018-01-06 12:56:42 -05:00
Richard Berger bcc5f49d0b Rename fix python to fix python/invoke 2017-12-15 13:53:04 -05:00
Richard Berger 950bfb84a9 Clean up after renaming back to fix python/move 2017-12-15 13:27:27 -05:00
Richard Berger 4d725c3153 Revert "Rename fix python/move to move/python" 
This reverts commit 4d915dba08.
 2017-12-15 13:17:12 -05:00
Richard Berger 4d915dba08 Rename fix python/move to move/python 2017-12-05 23:42:57 -05:00
Richard Berger f8891a4451 Rename fix python/integrate to python/move 
This is to avoid confusion to what LAMMPS considers to be an
integrator like Verlet and RESPA.
 2017-12-02 01:04:46 -05:00
Giacomo Fiorin 51688b2504 Improve performance of Python integrator (NVE_Opt version) 
Removing the loop over atoms by using NumPy array indexing allows to recover
performance close to that of plain fix nve.
 2017-12-02 00:40:21 -05:00
Richard Berger 93be2d264e Detect correct integer type in lammps python interface 2017-12-02 00:39:15 -05:00
Richard Berger b9fd1156b2 Completed first version of fix python/integrate 
This includes an example of how to implement fix NVE in Python.

The library interface was extended to provide direct access to atom data using
numpy arrays. No data copies are made and numpy operations directly manipulate
memory of the native code.

To keep this numpy dependency optional, all functions are wrapped into the
lammps.numpy sub-object which is only loaded when accessed.
 2017-12-02 00:39:15 -05:00
Axel Kohlmeyer 0208fe9996 update example outputs 2017-05-18 00:46:49 -04:00
Axel Kohlmeyer 8d46aa6056 add readme file to discuss various python pair style usage examples 2017-05-18 00:31:54 -04:00
Axel Kohlmeyer 09f3b687f7 new long-rance example with using hybrid/overlay and table only for lj part 2017-05-18 00:31:15 -04:00
Axel Kohlmeyer 436d3fd761 make hybrid example use half the atoms with python, half with lj/cut 2017-05-18 00:30:41 -04:00
Axel Kohlmeyer 9833f38499 change coulomb example to use cutoff coulomb 2017-05-18 00:30:19 -04:00
Axel Kohlmeyer 67962b15fc a bunch refactoring changes in the python pair style and the examples 
- make all python potential classes derived from LAMMPSPairPotential
  which contains shared functionality. We currently don't check
  for supported atom types. may want to add that again later.
- keep track of skipped atom types in the C++ code.
- add test against units setting. must set self.units='...' in constructor
- make compute_force method consistent with Pair::single() in LAMMPS and return force/r instead of force.
- rename potentials.py to py_pot.py
- update test runs. some small tweaks.
 2017-05-17 20:55:48 -04:00
Axel Kohlmeyer 1d48f287f0 add partial documentation for pair style python 2017-05-17 19:05:18 -04:00
Axel Kohlmeyer 43efe9e417 adding Pair::single() support to python pair style and examples 
with the single function, python pair styles can be massively
sped up and made compatible to accelerators, as one can translate
the analytic force and energy functions through LAMMPS into suitable
tables and then simply use the on-the-fly tables for production runs
 2017-05-17 17:20:56 -04:00
Axel Kohlmeyer a34c935e20 update log files in python pair style example 2017-05-17 08:00:21 -04:00
Axel Kohlmeyer 13e16dc3f1 update log files for pair style python examples 2017-05-17 07:52:13 -04:00
Axel Kohlmeyer 96f0a82aa5 simplify class names in pair style python examples. add SPC/E water example 2017-05-17 07:48:15 -04:00
Richard Berger 7caf6cf459 Change how a Python pair style is loaded 
Implements a class loader which takes a fully qualified Python class
name, loads the module and creates an object instance.

To add flexibility, the current working directory and the
directory specified by the LAMMPS_POTENTIALS environment variable are
added to the module search path.
 2017-05-16 23:29:48 -04:00
Richard Berger 14f3deed6b Minor coefficient lookup improvement 2017-05-15 18:43:46 -04:00
Richard Berger 93cc6f4a5d Use in syntax for key lookup for Python 3 compatibility 2017-05-15 17:34:48 -04:00
Axel Kohlmeyer 6a1f7e61f2 provide reference output for python pair style inputs 2017-05-15 00:25:11 -04:00
Axel Kohlmeyer df55a90ef6 some example input file tweaks 2017-05-15 00:22:03 -04:00
Axel Kohlmeyer f484ab6dfb completed lj parameter set and compute functions for melt example 2017-05-15 00:14:36 -04:00
Axel Kohlmeyer 86283c6309 make melt input consistent with melt example again 2017-05-15 00:13:32 -04:00
Axel Kohlmeyer 34cc3946b8 first few pieces of pair style python 2017-05-14 18:29:06 -04:00
Richard Berger c4d0f07093 Allow fix python to only execute every N steps 2017-05-12 00:29:58 -04:00
Richard Berger 110bb79b14 Implement fix python mentioned in issue #454 
Allows to call a python function at defined points in the integration loop
 2017-05-11 23:50:30 -04:00
Richard Berger 9a027a01da Add Python 3 compatibility to PYTHON package 2017-04-11 20:24:42 -04:00
Steve Plimpton 493873fb93 clean up doc src 2016-10-06 13:00:46 -06:00
sjplimp 03662ee700 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13238 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-03-17 16:06:01 +00:00