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[WIP] merge in NMR workflow stuff#21

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dwinston wants to merge 216 commits intomaterialsproject:masterfrom

xhqu1981:mb_nmr_wf

Commits on Jun 1, 2016

Commits on Jun 2, 2016

Commits on Jun 4, 2016

use prec=accurate throught the triple jump relaxation
Xiaohui Qu
committed

Commits on Jun 5, 2016

Shyue Ping removed name parameter from DictSet, refactor to adapt this change
Xiaohui Qu
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change the default input set to the ongoing one in the task
Xiaohui Qu
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fix bugs in setting default custodian input set
Xiaohui Qu
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fix INCAR keyword
Xiaohui Qu
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use LREAL=Auto for all steps
Xiaohui Qu
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Commits on Jun 6, 2016

Commits on Jun 7, 2016

also use symprec in EFG calculations
Xiaohui Qu
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Commits on Jun 12, 2016

update chemical shift parsing
Xiaohui Qu
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setup MOVE_TO_GARDEN for nmr workflows
Xiaohui Qu
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add support for job packing
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prefix GARDEN variables with module name
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fix nprocs per node
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refactor GARDEN variable to singleton to unable dynamic adjustment
Xiaohui Qu
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fix typos in accessing WFSettings
Xiaohui Qu
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Commits on Jun 13, 2016

add TripleJumpRelaxVaspToDBTask to setup NMR only Garden locations
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fix return value bug
Xiaohui Qu
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fix parameter typo
Xiaohui Qu
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Commits on Jun 22, 2016

fix mpirun name
xhqu1981
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Commits on Jul 1, 2016

Commits on Jul 8, 2016

Commits on Jul 18, 2016

use ISYM=0 instead of SYMPREC
Xiaohui Qu
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use tighter tolerance in SNLGroup search for NMR
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use the same settings in NMR tensor calculations
Xiaohui Qu
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Commits on Jul 20, 2016

don't use default input set in NMR VaspJob setup
xhqu1981
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Commits on Jul 23, 2016

Merge branch 'master' into nmr_wf
Xiaohui Qu
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Commits on Jul 26, 2016

make iterate dict items Python3 compatible
Xiaohui Qu
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Commits on Jul 27, 2016

explicity using text mode for zopen to be compatible with Python3 for the error of "TypeError: the JSON object must be str, not 'bytes'"
xhqu1981
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Commits on Aug 26, 2016

Commits on Jan 20, 2017

Merge branch 'master' into nmr_wf
xhqu1981
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Commits on Jan 21, 2017

use NCORE instead of NPAR/KPAR since it works for both geometry optimization and NMR
xhqu1981
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Commits on Jan 23, 2017

Commits on Jan 24, 2017

Commits on Jan 25, 2017

use explicit integer division operator to be py3 compatible
xhqu1981
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Commits on Jan 26, 2017

ensure srun is running with -v option
Xiaohui Qu
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fix multiple binary logic, propogate CustodianError exception
Xiaohui Qu
committed

Commits on Jan 27, 2017

Commits on Feb 3, 2017

Commits on Mar 24, 2017

handle run location in the period of CSCRATCH transition, in which the scratch file path has ".new" in it.
Xiaohui Qu
committed

Commits on Mar 25, 2017

change K-points in NMR workflow to full automatic
Xiaohui Qu
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reduce number of K-points
Xiaohui Qu
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Commits on Mar 26, 2017

tighten structure compare by 10 times for NMR calculation
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add mechanism to avoid infinite loop in spawning dynamic FW
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if the structure is relaxed for more than 3 step while StructureMatcher categories to the same snlgroup, issue a warning
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fix input rewind logic
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always update geometry
Xiaohui Qu
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add missing target file
Xiaohui Qu
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Commits on Mar 27, 2017

Commits on Mar 28, 2017

Commits on Mar 29, 2017

fix fw_name
Xiaohui Qu
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remove old file before starting new calculations to avoid confuse custodian
Xiaohui Qu
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fix "TypeError: a bytes-like object is required, not 'int'" in VaspCopyTask
Xiaohui Qu
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Commits on Mar 30, 2017

Commits on Apr 1, 2017

Put the larger ENMAX specie first, fix the "PSMAXN for non-local potential too small" warning
Xiaohui Qu
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don't sort structure again by DictSet
Xiaohui Qu
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update FIRE optimizer parameters
Xiaohui Qu
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Commits on Apr 3, 2017

Commits on Apr 4, 2017

remove unnecessary keywords for EFG
Xiaohui Qu
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also consider ENMIN
xhqu1981
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Commits on Apr 5, 2017

further tighten NMR structure matcher threshold
xhqu1981
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Commits on Apr 10, 2017

update NMR calculation parameters
xhqu1981
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Commits on Apr 12, 2017

Merge branch 'mb_nmr_wf' of github.com:xhqu1981/MPWorks into mb_nmr_wf
Xiaohui Qu
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remove uneccessary keywords in EFG INCAR
Xiaohui Qu
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Commits on Apr 16, 2017

also delete custodian.json
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use 50 atoms as threshold to define as large cell in NMR workflow
Xiaohui Qu
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Commits on Apr 23, 2017

use fresh error handlers to reset error_count for every custodian run
Xiaohui Qu
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make a deep copy to make sure the new instance is independent
Xiaohui Qu
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Commits on Apr 24, 2017

Commits on Apr 25, 2017

large molecules use large NPAR since it will be run with more CPU cores
xhqu1981
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Commits on Apr 27, 2017

update NPAR/KPAR setting
xhqu1981
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Commits on Apr 28, 2017

also backup OUTCAR and vasp.out to binary run file
xhqu1981
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Commits on Apr 29, 2017

also back up INCAR POSCAR and KPOINTS to binary.#.tar.gz
Xiaohui Qu
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Commits on May 3, 2017

Commits on May 4, 2017

Commits on May 5, 2017

Commits on May 18, 2017

file NMR SCF job file path
Xiaohui Qu
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fix typo
Xiaohui Qu
committed

Commits on May 19, 2017

add option to use environment variable GARDEN_LOC to customize the location of GARDEN
xhqu1981
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Commits on May 22, 2017

merge run_tags to query in DupeFinder to be consistent with Kiran's change to FireWorks
xhqu1981
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Commits on May 29, 2017

fix type error
Xiaohui Qu
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fix DB insertion
Xiaohui Qu
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fix file name
Xiaohui Qu
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fix tweak of fw_spec
Xiaohui Qu
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fix data formating
Xiaohui Qu
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fix data type
Xiaohui Qu
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Commits on Jul 4, 2017

reder nuclear quadruplar moments after the atoms were reordered
Xiaohui Qu
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make a private method
Xiaohui Qu
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fix a bug of copied instance
Xiaohui Qu
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Commits on Aug 30, 2017

Commits on Oct 20, 2017

add pawpot for B, In, Pb
Xiaohui Qu
committed