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202 Commits

Author SHA1 Message Date
Jaron Krogel 161515a188 nexus: preliminary testing framework 2018-03-02 09:22:21 -05:00
Jaron Krogel 40f43fab9f nexus: fix qfit for variable length input data 2017-12-21 14:09:13 -05:00
Jaron Krogel 7b224c6512 nexus: modify qmca to print output in same order as inputted files 2017-12-20 15:41:28 -05:00
Jaron Krogel d05689f91a nexus: fix qmcpack analyzer to handle stat.h5 data with or without value_squared 2017-12-14 09:58:32 -05:00
Jaron Krogel abc803952a nexus: fix bad default for pw2qmcpack input 2017-12-08 13:35:36 -05:00
Mark Dewing 37c8794310 Skip Nexus example tests if numpy is not present 
Fixes #484
 2017-11-10 10:21:34 -06:00
Jaron Krogel 9242a84cfa nexus: fix k-point add for tiling corner case 2017-11-08 09:24:29 -05:00
Jaron Krogel 9c36dff459 nexus: guard against save fail on analysis step of workflows 2017-11-07 10:33:42 -05:00
Jaron Krogel c57a843db4 nexus: include changes in pwscf_postprocessors 2017-11-06 13:19:57 -05:00
Jaron Krogel edb0733130 nexus: add QE postproc support in qmcpack_workflows 2017-11-06 13:05:39 -05:00
Jaron Krogel 9c7d20abb8 nexus: fix failing LiH test 2017-11-03 14:13:39 -04:00
Jaron Krogel 4bcf313158 nexus: tiling fix when net_spin="low", ability to plot gaussian primitive widths 2017-11-03 10:10:31 -04:00
Mark Dewing 0e742caf25 Add tests for Nexus examples. 
Nexus scripts are run with 'generate_only' set to True.
This will at least test the Nexus API and catch breaking changes.
 2017-09-28 13:31:43 -05:00
Jaron Krogel fb65b4e84f clean up nofk input block, add nexus support 2017-09-08 14:22:56 -04:00
Jaron Krogel c48aeb41f4 QMCPACK manual entry for timestep fitting tool 2017-08-29 12:17:52 -04:00
Jaron Krogel 92cf871e29 nexus: add makov payne correction, make plotting robust 2017-08-08 10:31:27 -04:00
Jaron Krogel 53a6bbb492 nexus: better support for density file postprocessing, support for QE angle keywords 2017-08-02 14:33:50 -04:00
Duy Le 1f684f8086 Update machines.py 2017-07-26 16:39:54 -04:00
Duy Le ad604dde7a Change name of local machine file 2017-07-26 16:17:30 -04:00
Duy Le 83dc03e6aa Add local machine to Nexus 
This change will allows local clusters, which is not available for vast users, survive after version update.
 2017-07-26 15:36:22 -04:00
Duy Le 8d783fb184 exit_call = sys.exit to work with ipython 
exit_call = exit: ipython does not recognize exit (NameError: name 'exit' is not defined). sys.exit should work for all environments.
 2017-07-24 15:15:58 -04:00
Jaron Krogel 9da70c89ae nexus: add Cori at NERSC 2017-06-19 16:38:21 -04:00
Jaron Krogel db77f3dd5b nexus: better guard for structure file and internal consistency 2017-06-12 14:25:04 -04:00
Jaron Krogel 828a88fae1 nexus: forbid bundling sims that depend on each other 2017-06-01 16:30:34 -04:00
Jaron Krogel 5da1c1be6f nexus: fix for net_spin="low" in generate_physical_system 2017-06-01 13:27:34 -04:00
Jaron Krogel 6d574eff85 add bundled job fix 2017-05-25 16:03:06 -04:00
Jaron Krogel 4c31e176ff fix for parallel pw2qmcpack workflow, small updates to pwscf and qmcpack inputs, add basic ability to serialize objects 2017-05-25 14:32:29 -04:00
Jaron Krogel 02ef45e364 nexus: fix __main__ in structure.py 2017-03-22 13:20:42 -04:00
Jaron Krogel c1a6616cf2 nexus: remove spurious line 2017-03-22 12:22:23 -04:00
Jaron Krogel adb2b30527 nexus: improve optimal_tilematrix routine 
optimal_tilematrix (structure.py) is improved in the following ways:
1) Accelerated computation of candidate tilematrix determinants for target volume matching.
2) Ability to use a mask array to restrict form of tilematrix search, e.g. only look for tilings of the form:
  x x 0
  x x 0
  0 0 x
3) Use of wigner radius to select among cells w/ equivalent inscribing radius.
4) Use of devation of cubic shape (as judged by face diagonals) to select among cells w/ equivalent wigner radius.
5) Prioritization of certain tile matrix aesthetics (diagonal, symmetric, etc) to select among cells w/ equivalent cubicity

Changes result in speedup of ~5x and superior cell selection for typical problem sets over the original algorithm.
 2017-03-22 11:53:53 -04:00
Jaron Krogel 2440d88744 nexus: add comment about +1 added to tiling vector 2017-02-22 09:40:41 -05:00
Jaron Krogel 1287ba335c nexus: fix non-integer diagonal tiling case and greatly increase its speed 2017-02-21 16:19:54 -05:00
Jaron Krogel fa9a49b4be nexus: fix if statement in machines.py 2017-02-01 12:09:13 -05:00
Jaron Krogel f1e7c52018 nexus: add machine supermuc at LRZ 2017-01-31 14:42:59 -05:00
Jaron Krogel 59b307f55f qmca: keep weight correct 2017-01-27 16:31:36 -05:00
Jaron Krogel e65ba41ac5 qmca: make TotalTime, TotalSamples, Efficiency compatible with provided equilibration time 2017-01-27 16:27:24 -05:00
Jaron Krogel c4bc77f2a4 nexus: bugfix for case sensitivity issues in pwscf input 2017-01-27 10:05:36 -05:00
Jaron Krogel 169b85f258 nexus: add functionality to average (relaxed) bulk positions into a subcell related by tiling 2017-01-25 14:02:17 -05:00
Jaron Krogel 2f2590159f nexus: small fix for pwscf restarts 2017-01-20 11:27:42 -05:00
Jaron Krogel 1cb8131217 nexus: enable automatic pwscf restarts 
use restartable=True in generate_pwscf to enable\nwill automatically restart if prior run has finished and either a time limit is reached or non-convergence is evident
 2017-01-19 16:53:57 -05:00
Mark Dewing 04f55519b5 Nexus: Display memory of child processes 
Currently the polling output only shows the memory of the python process
running Nexus.  Show the memory used by all the child processes as well.
 2017-01-19 14:40:56 -06:00
Jaron Krogel c4ab3a2f4f test commit 2, remove a space from nexus.py 2017-01-18 17:06:37 -05:00
Jaron Krogel 10183b59fa test commit, add a space to nexus readme 2017-01-18 15:43:23 -05:00
Jaron Krogel a84adc6e3f nexus: fix for structure dependency resolution 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7384 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-12-28 21:58:18 +00:00
Jaron Krogel 165ebe2c18 nexus: enable bypass of orbital dependency via user defined orbital file 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7382 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-12-27 21:10:01 +00:00
Raymond Clay db62146644 add return_system() to VASP input file class 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7366 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-12-20 23:04:02 +00:00
Yubo “Paul” 848bc4cdb5 nexus: addionion flag to force estimator 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7365 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-12-20 22:51:19 +00:00
Jaron Krogel b7e9bf54e4 nexus: small changes to jastrow opt workflow 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7347 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-12-15 15:03:57 +00:00
Yubo “Paul” cf2c8fdcbe nexus: allow manual nbnd input 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7345 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-12-13 16:58:54 +00:00
Jaron Krogel f2a97e44f0 nexus: small fixes 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7338 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-12-09 17:34:55 +00:00