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161 Commits

Author SHA1 Message Date
Jaron Krogel 341e783022 nexus: move to sys.exit generically 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6687 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-01-20 16:34:29 +00:00
Jaron Krogel a27bbeed11 nexus: small fix for generic containers 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6685 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-01-14 22:07:33 +00:00
Jaron Krogel 71a54fa2a2 fix small bug in units for qmca, credit Mark Dewing 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6681 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-01-06 20:30:37 +00:00
Jaron Krogel 2ff7ebdf7a nexus: minor bugfix for job command 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6675 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-12-31 19:26:50 +00:00
Jaron Krogel 4399bd4ccc nexus: supporting structure functions 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6674 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-12-31 19:04:56 +00:00
Jaron Krogel 290c492f3c nexus: atomic ring detection based on voronoi graph topology 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6667 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-12-29 18:16:31 +00:00
Jaron Krogel 64a86127ee nexus: fix for job objects modified by user after instantiation 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6660 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-12-23 15:59:51 +00:00
Jaron Krogel f1d50d06ff nexus: small bugfix for bundled jobs 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6657 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-12-22 14:27:07 +00:00
Jaron Krogel df06ef7b0d nexus: support for CIF files and also spglib 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6656 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-12-22 00:08:02 +00:00
Jaron Krogel 5d80632aa3 nexus: fix obsolete call to add_attributes 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6621 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-11-23 22:11:00 +00:00
Jaron Krogel f045624e86 nexus: add missing basisset.py 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6620 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-11-20 16:55:48 +00:00
Jaron Krogel 461c3a63e9 Major updates to Nexus: see full text of message 
Changes made to render core of Nexus more robust, a couple of bug fixes, 
several additions to functionality, and several files relegated to "legacy".


=================
new functionality
=================
 -added support for templated input for qmcpack 
    generation is no longer required
    should also work for all supported codes now
    also allows driving of generic simulation codes lacking detailed nexus interface

 -added basic interfaces to drive CRYSTAL and properties
  
 -added support to convert to CASINO pseudopotential format for semilocal PPs
    can convert from GAMESS/CRYSTAL to QMCPACK/CASINO
    also convert between QMCPACK and CASINO
  
 -improved handling of gamma point calculations for pwscf
    better autodetection of gamma point
    explicit user override to forbid "KPOINTS gamma"

 -added support for head node/local job submission 
    useful for lightweight serial tools or scripts in workflows
  
 -added "execute" function to Simulation
    will later enable use generation/running of simulations directly within user script
    will allow for dynamic workflows, rather than dynamic execution of static workflows

 -added enum class to developer.py

 -added general formatted read to TextFile class in fileio.py


=========
bug fixes
=========
 -dependents of failed simulations now guaranteed not to run following interruption and restart of user script

 -run directory creation now guaranteed to occur prior to simulation dependency processing


================
added robustness
================
 -restructured global base class (obj) in generic.py
    remove dependence on abilities.py classes
    streamline and expand base class functions
    move to "new-style" Python classes (inherit from object)

 -added nexuscore "namespace" and NexusCore base class 
    better control of core vs. noncore information propagation
    less chance of downstream breakage (e.g. for derived Simulation classes)
    classes inheriting from NexusCore:
      Settings
      ProjectManager
      Machine
      Job
      Simulation
      SimulationImage
      SimulationInput
      SimulationAnalyzer
  
 -added separate SimulationImage class for save/load of Simulation state
    ensures only central information is saved/loaded
    prevents interaction with derived Simulation classes
  
 -improved organization for Settings class
  
 -removed debug log cruft from ProjectManager
  
 -improved definition of SimulationTemplateInput
    now uses string.Template rather than custom code

 -replaced dynamic type detection functionality from types module with inspect

 -simplified UnitConverter class
  
 -made periodic_table process symbols consistently
  

============
housekeeping
============
 -removed unused files
    converters.py  auxilliary.py
  
 -relegated several superseded/less used files to new legacy directory
    abilities.py         differences.py           qmcpack_pp_validation.py
    cascade.py           eos_fit.py               qmcpack_variations.py
    density_analyzer.py  generator.py             qmc.py
    dft.py               qmcpack_calculations.py
  
 -consolidated orbital converters for qmcpack into qmcpack_converters.py
    replaces convert4qmc.py, pw2qmcpack.py, wfconvert.py
  
 -consolidated numerical functionality into numerics.py
    extended_numpy.py is removed along with ill-advised "from numpy import *"
  
 -consolidated files associated with QmcpackAnalyzer
    plotter.py qaobject.py spacegrid.py
  
 -renamed project.py as nexus.py, removing vacuous nexus.py
    also renamed project_base.py as nexus_base.py 

 -separated processing of basis sets to basissets.py

 -removed outdated BundledQmcpack class


git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6616 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-11-11 19:39:04 +00:00
Jaron Krogel 2ab07c0c7d nexus: more species querying support 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6575 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-09-16 20:45:02 +00:00
Jaron Krogel a209ce1b1b nexus: slice support for memory mapped files 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6573 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-09-15 15:47:24 +00:00
Jaron Krogel 08f1d5c844 nexus: ensure positions are always floats 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6569 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-09-10 18:00:28 +00:00
Jaron Krogel b50f918e46 nexus: Interface to Pitzer's ATOMSCF code. Often used in PP basis set development. 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6564 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-09-01 13:34:29 +00:00
Jaron Krogel 6fed27af80 gamess analyzer, trimer structure 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6562 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-08-24 13:54:43 +00:00
Jaron Krogel c4f480a9fa nexus: small bug fix in rename 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6558 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-08-17 20:18:45 +00:00
Jaron Krogel a797abadea nexus: gaussian basis set manipulation, interface smoothing 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6556 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-08-17 14:40:03 +00:00
Jaron Krogel 876c4fb70d nexus: revert support for poor qmcpack input design choices 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6546 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-08-10 14:29:42 +00:00
Jaron Krogel de86b8769a nexus: revised user manual 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6532 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-07-31 13:52:07 +00:00
Jaron Krogel 4954dc350c nexus: fix mangling of numerics file 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6530 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-07-29 17:45:43 +00:00
Jaron Krogel 6060f56705 nexus: descriptive headers for all files 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6529 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-07-29 17:41:20 +00:00
Jaron Krogel 8a3426f45c nexus: considering CRYSTAL interface 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6528 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-07-29 16:09:41 +00:00
Jaron Krogel fb68e4299a nexus: all known attrs/elements for qmcpack input 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6527 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-07-29 16:08:07 +00:00
Jaron Krogel a40b240370 nexus: GAUSSIAN/GAMESS/CRYSTAL basis set conversion 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6526 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-07-28 17:35:35 +00:00
Jaron Krogel 986ab4e171 nexus: small tiling fix 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6525 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-07-28 17:34:39 +00:00
Vinit Sharma a046146f37 JTK: fix read of old poscar files 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6523 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-07-27 18:49:30 +00:00
Jaron Krogel 09c2c8edc6 gamess update 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6520 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-07-22 18:32:40 +00:00
Jaron Krogel d4e8ca7476 update pwscf spin handling 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6506 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-07-09 14:06:41 +00:00
Jaron Krogel b376e831f7 small update for generic simulations 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6459 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-05-14 13:53:46 +00:00
Jaron Krogel 31a55a2727 get optimized jastrow or full wavefunction based on last cost used 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6458 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-05-14 13:19:24 +00:00
Jaron Krogel d4cfacc1c9 nexus vasp update: band structures 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6439 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-03-31 14:53:51 +00:00
Jaron Krogel 11ea36f407 gamess fixes: ci workflows, species input ordering, and efficient handling of large log files 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6438 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-03-31 14:41:57 +00:00
Jaron Krogel 855f1d8f93 update for connected graph mappings 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6433 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-03-12 18:39:12 +00:00
Jaron Krogel ee17dfc319 qdens support 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6432 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-02-26 15:43:53 +00:00
Jaron Krogel 0e582a0001 small pwscf update 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6431 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-02-11 17:00:29 +00:00
Jaron Krogel 3b9ecbc2b2 Add Nexus license, readme, and copyright headers 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6430 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-02-09 20:43:50 +00:00
Jaron Krogel 72d4e7defb nexus vasp update 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6429 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-02-03 23:23:58 +00:00
Jaron Krogel 7d0c8dae1e structure update 2 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6428 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-02-03 22:41:01 +00:00
Jaron Krogel e37274ffe8 structure update 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6427 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-02-03 20:41:28 +00:00
Jaron Krogel 6da0c00939 fix for negative (space removing) cleave 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6426 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-02-02 23:38:00 +00:00
Jaron Krogel 36c79bc3c6 layer finding/cleaving; connected graph locator for monomers, dimers, trimers, etc. 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6425 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-02-02 21:18:29 +00:00
Jaron Krogel 2e508baf2f xsf density file writing for QmcpackAnalyzer 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6424 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-01-22 18:03:30 +00:00
Jaron Krogel c15e411188 vasp relax+neb workflows 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6421 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-01-15 21:51:03 +00:00
Jaron Krogel b0e9da8630 restore mpc kecorr to qmcpack analyzer 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6419 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2015-01-02 18:15:17 +00:00
Jaron Krogel 8365ca42e4 allow pseudos to be None 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6417 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2014-12-10 23:00:29 +00:00
Jaron Krogel e9f507d07b finish mcscf + cusp correction workflow 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6416 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2014-12-09 13:49:14 +00:00
Jaron Krogel 0d736669ef update to generic pwscf 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6413 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2014-12-05 20:35:10 +00:00
Jaron Krogel 96d290d977 small fixes 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6412 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2014-12-05 14:23:29 +00:00
Jaron Krogel c83a8bd788 add fitting capabilities: morse + jackknife 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6411 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2014-12-04 14:15:07 +00:00
Jaron Krogel 3751252aa2 gamess update for mcscf workflows 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6410 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2014-12-04 14:13:43 +00:00
Jaron Krogel e7b93af71d fixed transmission of relaxed structures to qmcpack 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6409 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2014-12-01 15:49:38 +00:00
Jaron Krogel 77d9ea6a80 small fixes 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6408 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2014-11-26 18:24:36 +00:00
Jaron Krogel e1563ef7c4 vasp input fix 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6407 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2014-11-26 16:38:16 +00:00
Jaron Krogel ca5bd1e181 clean interface to generate nearly any pwscf input file 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6405 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2014-11-25 17:16:12 +00:00
Jaron Krogel 2828381b3c ability to alter environment per job 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6401 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2014-11-13 20:33:08 +00:00
Jaron Krogel 2e5d08eb34 fix syntax. ready for public release. 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6396 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2014-10-30 20:17:47 +00:00
Jaron Krogel 699a965b41 updated behavior for Amos supercomputer 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6395 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2014-10-30 16:35:09 +00:00
Jaron Krogel c55b0b8288 remove deprecated nexus source and tools directories 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6394 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2014-10-29 18:54:51 +00:00
Jaron Krogel 5b84a88c89 final nexus rebrand 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6393 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2014-10-29 18:52:03 +00:00