Add support for trajectories of part of the system to new analysis framework - Redmine #1861
Currently the new analysis framework can only read trajectory files of
all atoms in the tpr. Convert could produce a tpr of a subgroup, but
that is messy (#1667).
Allowing reading of trajectories of part of the system should not be much work, since that just requires one extra selection with the xtc group and an index translation.
(from redmine: issue id 1861, created on 2015-11-25 by berkhess, closed on 2016-04-05)
- relates #1667 (closed)
- Revision 12c07b72 by Teemu Murtola on 2016-01-10T12:25:09Z:
Support arbitrary subset trajectories in poscalc.* - Make low-level selection code work with trajectories that contain an arbitrary subset of the topology atoms, instead of just the first N. - Add an entry to t_trxframe to represent such trajectories. - Add some basic tests. Negative cases crash with an assert, so not tested (should get caught higher up). This should cover all of selection evaluation, but various consistency checks need to be adjusted as well (will be done in a child change). Related to #1861. Change-Id: I727c79a38e39fb9142976875ab3311e7b1172a55
- Revision 4239f345 by Teemu Murtola on 2016-01-10T13:33:53Z:
Support frames with atom subsets in selections - Instead of just computing the highest atom index required for evaluating the selections, compute all the atom indices. - Use these to check that the input frame actually contains the necessary atoms. - Add basic tests for one positive and a few negative cases. Part of #1861. Change-Id: If4c2d031f638f56d81ca4c7844dffa242f863af8
- Revision 4ee73c88 by Teemu Murtola on 2016-01-10T16:19:44Z:
Support trajectory analysis with any atom subset Make tools written for the new C++ analysis framework support analyzing trajectories that contain an arbitrary subset of atoms. Part of #1861. Change-Id: I4a658e953f6f4e3d2ec1151c9c4d405c2e888780