From 17d5e1ded5cf51e54046fe343e82526bef6d4ed2 Mon Sep 17 00:00:00 2001 From: zyrd Date: Tue, 24 Sep 2019 13:32:27 -0700 Subject: [PATCH] Update docs --- docs/index.html | 22 +--------------------- docs/pymatgen.io.abinit.nodes.html | 24 ++++++++++++------------ docs/pymatgen.io.abinit.qjobs.html | 24 ++++++++++++------------ docs/searchindex.js | 2 +- 4 files changed, 26 insertions(+), 46 deletions(-) diff --git a/docs/index.html b/docs/index.html index 1d5af9afdef..6ffde4f40e3 100644 --- a/docs/index.html +++ b/docs/index.html @@ -191,24 +191,6 @@

Via conda (recommended)

Via pip

-
-

Note

-

Preparation

-

Before installing pymatgen, you may need to first install a few critical -dependencies manually.

-
    -

  1. It is highly recommended that you use Python>=2.7.9 or latest 3.x. In -fact, unless you are very sure you have dependencies that require Python -2, it is highly recommended that you use latest Python 3.x.

    2. -

  2. Installation has been tested to be most successful with gcc. Use gcc -where possible and do “export CC=gcc” prior to installation.

    3. -

  3. Numpy’s distutils is needed to compile the spglib and pyhull -dependencies. Numpy should be the first thing you install.

    4. -

  4. One of the best things you can do is to use conda to manage all this. -The instructions for Shared cluster installation pretty much -applies to any machine as well.

    5. -
-

The version at the Python Package Index (PyPI) is always the latest stable release that is relatively bug-free. The easiest way to install pymatgen on any system is to use pip:

@@ -274,9 +256,7 @@

Shared cluster installation
# Here, Python 3.6+ is assumed.
-# You can change the following to Miniconda2 if you prefer Python 2.7
-wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
 bash Miniconda3-latest-Linux-x86_64.sh -b
 
 # Reload bash profile.
diff --git a/docs/pymatgen.io.abinit.nodes.html b/docs/pymatgen.io.abinit.nodes.html
index ca83bb9087c..e97a7a3c7a9 100644
--- a/docs/pymatgen.io.abinit.nodes.html
+++ b/docs/pymatgen.io.abinit.nodes.html
@@ -309,7 +309,7 @@ 
Navigation

 
Nodes are hashable and can be tested for equality

 

 

-ALL_STATUS = [<Status: Initialized, at 120768604192>, <Status: Locked, at 120771305216>, <Status: Ready, at 120771302976>, <Status: Submitted, at 120771303776>, <Status: Running, at 120771301776>, <Status: Done, at 120771301616>, <Status: AbiCritical, at 120771304176>, <Status: QCritical, at 120771304256>, <Status: Unconverged, at 120771303456>, <Status: Error, at 120771305376>, <Status: Completed, at 120771304576>]

+ALL_STATUS = [<Status: Initialized, at 120815886576>, <Status: Locked, at 120815889856>, <Status: Ready, at 120815888016>, <Status: Submitted, at 120815889056>, <Status: Running, at 120815888336>, <Status: Done, at 120815888736>, <Status: AbiCritical, at 120815888816>, <Status: QCritical, at 120825309296>, <Status: Unconverged, at 120825308656>, <Status: Error, at 120816615248>, <Status: Completed, at 120816615168>]
 

 
 

@@ -326,57 +326,57 @@ 
Navigation

 
 

 

-S_ABICRITICAL = <Status: AbiCritical, at 120771304176>

+S_ABICRITICAL = <Status: AbiCritical, at 120815888816>
 

 
 

 

-S_DONE = <Status: Done, at 120771301616>

+S_DONE = <Status: Done, at 120815888736>
 

 
 

 

-S_ERROR = <Status: Error, at 120771305376>

+S_ERROR = <Status: Error, at 120816615248>
 

 
 

 

-S_INIT = <Status: Initialized, at 120768604192>

+S_INIT = <Status: Initialized, at 120815886576>
 

 
 

 

-S_LOCKED = <Status: Locked, at 120771305216>

+S_LOCKED = <Status: Locked, at 120815889856>
 

 
 

 

-S_OK = <Status: Completed, at 120771304576>

+S_OK = <Status: Completed, at 120816615168>
 

 
 

 

-S_QCRITICAL = <Status: QCritical, at 120771304256>

+S_QCRITICAL = <Status: QCritical, at 120825309296>
 

 
 

 

-S_READY = <Status: Ready, at 120771302976>

+S_READY = <Status: Ready, at 120815888016>
 

 
 

 

-S_RUN = <Status: Running, at 120771301776>

+S_RUN = <Status: Running, at 120815888336>
 

 
 

 

-S_SUB = <Status: Submitted, at 120771303776>

+S_SUB = <Status: Submitted, at 120815889056>
 

 
 

 

-S_UNCONVERGED = <Status: Unconverged, at 120771303456>

+S_UNCONVERGED = <Status: Unconverged, at 120825308656>
 

 
 

diff --git a/docs/pymatgen.io.abinit.qjobs.html b/docs/pymatgen.io.abinit.qjobs.html
index a752e812181..458f91137c2 100644
--- a/docs/pymatgen.io.abinit.qjobs.html
+++ b/docs/pymatgen.io.abinit.qjobs.html
@@ -141,7 +141,7 @@ 
Navigation

 

 

 

-PBSSTAT_TO_SLURM = {'E': <JobStatus: FAILED, at 120775450448>, 'F': <JobStatus: COMPLETED, at 120775449248>, 'Q': <JobStatus: PENDING, at 120775450704>, 'R': <JobStatus: RUNNING, at 120775447008>, 'S': <JobStatus: SUSPENDED, at 120775449648>}

+PBSSTAT_TO_SLURM = {'E': <JobStatus: FAILED, at 120822872496>, 'F': <JobStatus: COMPLETED, at 120822873936>, 'Q': <JobStatus: PENDING, at 120816575424>, 'R': <JobStatus: RUNNING, at 120816576544>, 'S': <JobStatus: SUSPENDED, at 120822873616>}
 

 
 

@@ -183,57 +183,57 @@ 
Navigation

 
 

 

-S_CANCELLED = <JobStatus: CANCELLED, at 120775449968>

+S_CANCELLED = <JobStatus: CANCELLED, at 120822871856>
 

 
 

 

-S_COMPLETED = <JobStatus: COMPLETED, at 120775449248>

+S_COMPLETED = <JobStatus: COMPLETED, at 120822873936>
 

 
 

 

-S_FAILED = <JobStatus: FAILED, at 120775450448>

+S_FAILED = <JobStatus: FAILED, at 120822872496>
 

 
 

 

-S_NODEFAIL = <JobStatus: NODEFAIL, at 120775448688>

+S_NODEFAIL = <JobStatus: NODEFAIL, at 120822872016>
 

 
 

 

-S_PENDING = <JobStatus: PENDING, at 120775450704>

+S_PENDING = <JobStatus: PENDING, at 120816575424>
 

 
 

 

-S_PREEMPTED = <JobStatus: PREEMPTED, at 120775450288>

+S_PREEMPTED = <JobStatus: PREEMPTED, at 120822870096>
 

 
 

 

-S_RESIZING = <JobStatus: RESIZING, at 120775450528>

+S_RESIZING = <JobStatus: RESIZING, at 120816574944>
 

 
 

 

-S_RUNNING = <JobStatus: RUNNING, at 120775447008>

+S_RUNNING = <JobStatus: RUNNING, at 120816576544>
 

 
 

 

-S_SUSPENDED = <JobStatus: SUSPENDED, at 120775449648>

+S_SUSPENDED = <JobStatus: SUSPENDED, at 120822873616>
 

 
 

 

-S_TIMEOUT = <JobStatus: TIMEOUT, at 120775450208>

+S_TIMEOUT = <JobStatus: TIMEOUT, at 120822873776>
 

 
 

 

-S_UNKNOWN = <JobStatus: UNKNOWN, at 120775452304>

+S_UNKNOWN = <JobStatus: UNKNOWN, at 120816577104>
 

 
 

diff --git a/docs/searchindex.js b/docs/searchindex.js
index 11475550591..26dd869d4d5 100644
--- a/docs/searchindex.js
+++ b/docs/searchindex.js
@@ -1 +1 @@
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,124,126,128,130,131,133,136,137,138,139,140,141,142,143,148,149,150,151,152,153,154,156,157,158,159,164,167,168,169,170,171,173,175,176,177,178,181,184,185,186,187,188,190,192,193,196,198,199,200,201,202,204,205,208,209,210,211,213,217,218,219,221,222,223,224,225,227,232,234,236,238,242,244,246,247,251,253,254,255,259,260,263,264,265],"enum":[0,3,63,71,124,134,137,152,168,221,244],"export":[2,3,158,175,204,226,256],"fe\u2082o\u2083":259,"final":[0,3,14,36,38,46,58,68,78,82,83,84,88,94,123,124,127,133,141,157,164,173,177,184,185,186,188,202,207,218,222,223,244,255,268],"float":[0,1,8,9,12,15,18,34,36,37,38,41,42,44,45,46,47,48,50,51,53,54,55,58,63,64,67,68,69,71,72,73,78,80,81,82,83,84,85,87,90,91,92,93,95,100,101,102,124,126,128,130,131,133,136,137,138,139,140,141,142,143,144,148,149,151,152,153,154,156,157,158,163,164,167,180,181,188,192,193,198,200,204,205,207,209,210,211,213,218,219,221,222,223,225,227,234,236,237,238,240,241,244,247,251,254,255,259,263,264,265],"function":[0,1,2,3,10,12,14,18,27,28,30,37,41,42,48,50,51,54,55,58,59,60,61,63,64,67,68,69,71,77,78,81,82,84,85,88,89,92,100,108,122,127,131,133,134,135,137,139,140,141,142,143,144,145,148,149,150,152,153,154,156,158,164,167,168,170,171,173,175,177,178,183,184,185,186,188,192,193,198,199,202,207,209,210,213,218,221,222,223,227,230,232,233,234,238,244,250,253,254,255,259,260,263,264,266,267,268],"gra\u017euli":161,"import":[0,1,2,3,55,60,61,64,69,133,140,149,158,169,173,177,178,179,181,184,220,221,226,244,256,268],"int":[0,10,12,18,36,37,42,44,47,48,50,54,55,58,60,61,63,64,67,69,71,80,81,84,85,87,91,92,94,107,127,128,131,133,136,137,138,140,141,142,143,148,149,151,153,154,161,163,164,173,175,177,178,180,188,192,198,199,200,204,205,206,207,208,209,210,217,219,221,222,223,236,238,242,244,246,247,255,259,265],"j\u00f3nsson":266,"jes\u00fa":150,"long":[0,1,37,75,137,218,222,268],"lua\u00f1a":124,"mart\u00edn":124,"n\u00f8rskov":145,"new":[0,1,3,9,10,36,41,44,47,48,54,55,59,60,63,64,67,76,77,85,88,89,90,101,103,124,133,140,141,142,144,150,152,154,164,167,168,169,173,175,177,178,180,184,185,186,187,188,202,209,215,217,221,222,223,234,247,255,256,268],"null":69,"okuli\u010d":161,"pend\u00e1":124,"public":[1,2,13,37,48,141,184,223,255,266],"quir\u00f3":161,"return":[0,1,2,6,8,9,10,12,13,14,15,18,19,21,23,24,28,31,34,36,37,38,39,41,42,44,45,46,47,48,50,51,52,53,54,55,58,60,61,63,64,67,68,69,71,72,73,74,76,77,78,80,81,82,83,84,85,87,88,89,90,91,92,94,95,100,101,102,103,104,106,107,123,124,126,127,128,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,148,149,150,151,152,153,154,156,157,158,159,161,162,164,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,190,191,192,193,194,196,198,199,200,201,202,204,206,207,208,209,210,211,212,213,218,219,221,222,223,224,225,226,227,230,232,233,234,236,237,238,240,241,242,244,245,246,247,248,250,251,252,253,254,255,256,258,259,260,263,264],"rodr\u00edguez":136,"short":[37,69,130,173,223,227],"static":[0,9,10,63,64,68,69,72,73,75,77,81,82,83,84,88,92,94,102,130,131,133,136,137,142,149,152,164,168,178,180,183,185,188,190,191,192,193,194,196,198,199,200,202,209,210,213,215,216,221,222,223,225,226,227,240,244,247,255,256,260,268],"super":[56,64,91,97,139,141,185],"switch":[0,1,154,173,184,244],"throw":[50,79,222,247],"transient":164,"true":[8,9,10,12,14,18,19,21,23,24,28,32,36,37,38,41,42,44,45,46,48,50,53,54,58,60,61,63,64,67,68,69,71,73,74,75,77,78,79,81,82,85,88,89,90,92,94,95,100,101,102,103,106,124,125,126,128,131,133,134,136,137,138,140,141,142,143,148,149,150,151,152,153,154,156,158,164,167,168,169,170,173,175,176,177,178,182,183,184,185,186,187,188,192,193,198,200,201,202,204,205,207,208,209,211,216,218,221,222,223,225,232,234,236,237,238,242,244,246,247,248,250,251,252,253,254,255,259,260,264,265],"try":[0,3,9,40,50,60,64,71,124,149,153,164,175,178,184,221,222,244,265],"var":[173,184],"void":[0,227],"while":[8,18,23,28,38,58,63,69,74,75,92,100,140,141,154,185,186,204,206,221,222,227,247,268],AND:[2,8,137,141,185,222,223],ASE:[0,3,54,190],Added:0,And:[1,69,222],Axes:[44,54,154,169,173,255],BNS:140,BUT:2,Being:58,Bus:180,But:[0,2,42,63,227,236,244,246,268],DLS:90,DOS:[0,111,139,149,150,153,154,164,186,209,233,234,263],Dos:[41,149,150,153,154,164,209,211,233,234,263,268],ECs:50,EOS:[0,54],EPS:[154,202,234,263],FMS:200,FOR:[2,141],For:[0,1,2,3,8,9,15,18,23,28,34,36,37,42,46,47,48,50,58,63,64,67,69,78,83,84,85,87,91,92,93,94,101,102,103,106,124,126,130,131,132,133,136,137,140,141,144,145,149,152,153,154,156,157,158,159,160,162,164,168,169,171,178,182,186,192,202,205,209,210,213,218,221,222,223,227,236,238,244,246,247,256,262,263,265,266,268],GBs:[63,141,244],Gus:[0,3,246],Has:[41,78,106,140,198,222,247],IDE:1,IDs:164,Ising:53,Its:[173,211],MOs:135,NOT:[2,34,36,42,64,78,204,222,223],Near:164,Not:[3,78,140,168,180,204,244],ONE:204,OPs:[0,69],OSes:3,One:[2,28,48,59,101,154,167,168,177,221,222,227,234,236,244],PBS:[180,183,184],PDs:[0,78,92],POS:208,PRs:0,Pls:0,QPS:184,RLS:90,RMS:[0,85],SQS:[127,244],Such:75,Sys:180,THE:[2,141],THe:153,That:[63,69,84,139],The:[0,1,2,3,6,8,9,10,12,13,15,18,19,21,23,24,28,35,38,39,40,41,42,44,45,46,47,48,50,53,54,55,56,58,60,61,63,64,66,67,68,69,74,75,77,78,79,81,82,83,84,85,87,88,89,91,92,93,94,95,97,101,102,103,104,105,106,107,123,124,127,130,131,132,133,135,136,137,138,139,140,141,143,144,145,146,148,149,150,151,152,153,154,156,157,161,162,163,164,167,168,172,173,175,176,177,178,179,180,181,183,184,185,186,188,190,192,193,198,199,200,201,202,204,205,206,207,208,209,210,211,213,215,218,221,222,223,227,229,230,232,233,234,235,236,237,238,242,243,244,246,247,249,253,254,255,256,260,262,263,265,266],Their:[74,130],Then:[1,3,72,236,260],There:[0,1,2,64,89,92,106,133,140,141,148,152,175,209,232,244,268],These:[2,19,48,50,55,64,78,94,162,164,193,202,209,222,223,268],USE:[2,247],Use:[0,1,2,44,45,46,47,50,55,64,69,94,131,134,136,138,140,141,152,156,158,162,164,167,168,173,175,177,178,186,192,221,223,244,246,247,256,265],Used:[47,53,78,81,92,123,143,149,152,173,200,202,222,240,247],Useful:[0,2,36,47,63,81,85,92,95,124,131,138,140,141,144,152,154,164,167,173,178,184,198,205,213,221,222,227,236,247,265],Uses:[10,37,54,69,92,94,107,167,168,192,213,221,222,223,236,254],Using:[67,140,145,156,162,164],WILL:141,WITH:[2,141,148,232,247],Will:[0,55,64,71,73,141,198,209,244,247,259],With:[0,1,2,3,69,193,236,250],XAS:[0,263],XES:200,Yes:185,__abinitflow__:173,__call__:67,__class__:[177,268],__eq__:260,__future__:1,__getitem__:131,__hash__:0,__init__:[10,50,51,52,56,63,76,79,80,97,139,140,141,142,161,172,173,215,223],__main__:0,__module__:268,__name__:[0,177,268],__new__:[50,51,52,76,79,80,142,144],__rmul__:0,__slots__:258,__str__:[198,202,215,221],_additional_condit:18,_angle_cutoff:18,_bp:222,_calculate_possible_shift:141,_cgraph:0,_continuous_symmetry_measure_cutoff:18,_defect_sit:3,_del:200,_den:[184,185],_distance_cutoff:18,_ev:222,_extrema_df:42,_get_nn_shell_info:69,_io:[169,173,177,178],_map:78,_materialsproject:[164,256],_matrix:55,_parse_bool:221,_parse_float:221,_parse_int:221,_parse_list:221,_parse_str:221,_path:168,_pickl:258,_proj_height:141,_reset:184,_set:223,_setup:186,_site:140,_sp:89,_threshold:89,a1604:50,a1826:50,a1fdb1089d0727f415416ec8082246ba:223,a1fit:188,a2b2:0,a2c9485ea86b2a7cf175077e6e5c7b3:223,a32:63,a35:69,a38:63,a395eb3aaf2fcab12fac3030a1146f61:223,a40:63,a45:63,a604ea3c6a9cc23c739b762f625cf449:223,a67:223,a6fd9a46aec185f4ad2acd0cbe4ae2fa:223,a74:223,a9182d436a13194b744640ac940ab9b0:223,a_1:[133,140,222],a_1a:222,a_1c:222,a_1p:222,a_2:[133,140],a_3:[133,140],a_i:46,a_pw:222,a_tot:222,a_vib:82,a_xb_1:13,a_xi:254,a_xx:254,a_xz:254,a_yi:254,a_yz:254,a_zz:254,aa_i:28,ab_shift:[63,67,244],abandon:0,abbrevi:[71,150,233],abc3:131,abc:[2,44,51,54,101,131,133,138,140,142,144,154,158,167,169,173,178,184,185,198,234,238,246,247,260],abcd:28,abcdefghijklmnopqrstuvwxyz0123456789:250,abcissa:202,abi_extens:185,abi_splitext:185,abicrit:[177,184],abiinput:172,abiinspect:[5,6,165,166],abil:[0,41],abinit:[0,2,5,6,133,145,164,165,267],abinit_build:184,abinitbuild:184,abinitcriticalwarn:172,abiniterror:172,abinitev:[172,177],abinitflow:185,abinithead:176,abinitinput:[173,184,186],abinitio:0,abinitixc_to_libxc:145,abinittask:[173,184,186],abinittim:169,abinittimerpars:[169,173,184,186],abinittimerparsererror:169,abinittimersect:169,abiobject:[5,6,165,166],abiopen:177,abipi:[170,173,175,184,186],abirun:[170,173],abitim:[5,6,165,166],abivalid:173,abivalidate_input:173,abivar:[63,133,140,168],abl:[3,41,58,63,74,137,167,244],abo3:[78,268],abo:[169,184],abo_:184,aborpt:199,abort:[172,180],about:[0,1,21,23,28,34,63,67,69,92,124,136,140,141,145,148,149,153,209,222,226,256],abov:[1,2,3,12,14,18,50,61,67,68,73,78,81,82,141,168,223,247,268],abs:[58,81,131,153,222,244,251,254],abs_cap:254,abs_tol:153,abscissa:202,absenc:193,absent:50,absent_sym:50,absolut:[1,2,28,36,44,45,46,71,78,101,131,136,141,142,144,153,173,175,177,184,185,186,187,199,222,223,236,237,251,254],absorb:[141,164,198,199,200,244],absorbing_atom:[198,199,200],absorbing_el:164,absorpt:[0,141,164,199,200,222,263],absorption_speci:97,abstractchemenvalgorithm:19,abstractchemenverror:27,abstractchemenvstrategi:18,abstractcompar:85,abstractdiffractionpatterncalcul:[44,45,46],abstractdron:[106,107],abstractelectrod:[101,102,103,104],abstracterror:183,abstracterrorpars:183,abstractfeffinputset:200,abstractgeometri:21,abstractmolatommapp:74,abstractratiofunct:30,abstractstructurefilt:[8,9],abstracttransform:[244,245,246,247,248],abstractvoltagepair:[101,102,103],abund:18,ac_:3,acc_err:149,acc_factor:[53,55],acc_thr:149,acceler:266,accept:[1,10,133,152,153,168,173,177,178,181,184,186,204,217,222,234,246,247,251,255],acceptor:37,access:[0,26,69,161,164,173,178,180,185,209,213,218,221,222,247,253],accommod:100,accomod:141,accord:[12,19,48,50,51,52,67,69,76,78,79,80,81,92,130,137,140,142,148,149,169,176,178,184,204,207,211,222,232,236,254],accordingli:[47,75,141],account:[0,1,19,36,41,42,46,69,71,92,133,135,140,141,148,149,150,173,186,222,232,236,251,252],accur:[0,63,64,71,149,164,222,223,244,246],accuraci:[0,55,149,170,178,223,227,246,247],acel:[133,168],acet:61,achiev:[142,149,173,219,247],acid:161,acknowledg:[2,75,222,266],aconvasp:[3,122],aconvasp_cal:[3,5,6,121],aconvasperror:122,acoust:[80,232],across:[58,69,78,101,102,103,131,200,223],acs:[21,41,71,81,162],act:[84,136],acta:[19,63,69,133],actanid:[131,137],actinoid:[131,137],action:[0,2,4,172,177,180],activ:[2,3,73,95,100,152,180,186,255],actual:[0,8,41,42,55,58,60,63,64,67,69,78,100,109,133,137,138,140,141,143,157,162,173,198,201,213,221,222,236,242,246,247,248,260,268],actual_kpoint:222,actual_kpoints_weight:222,adam:133,adap:37,adapt:[1,3,37,54,71,92,173,182,210,255],adaptor:[0,125,189,190,192,268],add:[0,1,3,9,10,12,15,21,23,28,44,50,51,54,55,60,63,64,67,73,78,92,104,131,139,140,141,143,150,151,154,158,164,167,169,173,175,177,185,186,188,192,211,215,217,221,223,227,234,244,246,255,258,263,265,268],add_adsorb:12,add_adsorbate_atom:141,add_bond:265,add_charges_from_oxi_state_guess:131,add_cohp:154,add_cohp_dict:154,add_com:175,add_config_var:116,add_coord_geom:23,add_dens:153,add_dep:177,add_do:[154,234],add_dos_dict:[154,234],add_edg:[64,265],add_electrod:104,add_emptylin:175,add_eq:50,add_error:184,add_fac:265,add_fig_kwarg:[154,255],add_filechild:177,add_flow:175,add_gg_gap:174,add_hydrogen:192,add_label_cycl:167,add_lin:[175,265],add_m_list:55,add_neighbors_set:23,add_opposit:19,add_opt:188,add_oxidation_st:55,add_oxidation_state_by_el:140,add_oxidation_state_by_guess:140,add_oxidation_state_by_sit:140,add_oxidation_state_by_site_fract:15,add_partial_spher:265,add_pick:265,add_picker_fix:265,add_polyhedron:265,add_sit:265,add_site_properti:140,add_sourc:23,add_spectra:263,add_spectrum:263,add_spin_by_el:140,add_spin_by_sit:140,add_strategy_visualization_to_subplot:18,add_subkei:188,add_tag:10,add_text:265,add_triangl:265,addadsorbatetransform:244,addditiona:186,added:[0,2,3,9,23,36,40,42,47,51,61,64,90,101,131,141,154,164,170,173,177,185,186,192,204,211,217,223,234,244,246,259,264,268],added_kpoint:223,adding:[12,61,140,141,184,217,223,244,268],addit:[0,2,3,9,10,18,21,23,29,36,42,54,60,63,64,67,83,91,126,131,132,136,139,140,141,144,157,164,173,176,193,202,204,210,211,223,227,232,244,256,259],addition:[14,223],additional_argu:2,additional_condit:[18,21,23,24,26],additional_info:[18,19],additionalcondit:[18,23,24,29],additionalconditionint:18,addon:92,address:[0,164,266],addsitepropertytransform:246,adengz:0,adf:[0,5,6,165],adf_run:188,adfinput:188,adfinputerror:188,adfkei:188,adfoutput:188,adfoutputerror:188,adftask:188,adjac:[48,58,101,102,103],adjacent_onli:[102,103],adjust:[58,67,69,92,149,156,164,200,207,222],administr:180,adn:3,adopt:[1,2,222],ads_coord:12,ads_entries_dict:92,ads_entry1:92,ads_entry2:92,adsorb:[12,92,141,244],adsorb_both_surfac:12,adsorbatesitefind:[0,12,244],adsorpt:[0,5,6,11,92,141],adsorption_sit:12,adsorptionsitefind:244,adv:223,advanc:[2,3,124,152,156,164,244,266,268],advanced_transform:[3,5,6,243],advantag:[0,2],advis:[37,244,267],aea79f322180fa6f0bfa74cb2a156dcf:223,aecar0:[123,124],aecar2:[123,124],aeccar0:[123,124],aeccar2:[123,124],aeccar:[123,124],affect:[0,140],affin:[136,140],affine_matrix:136,affine_transform:136,affine_transformation_matrix:136,afloat:259,aflow:[0,13,106],aflow_prototyp:[5,6,11],aflowlib:122,aflowprototypematch:13,afm:[71,72,168],afm_:72,afm_struct:72,afresh:69,after:[2,3,9,14,21,36,41,42,47,53,55,63,64,67,85,89,136,137,141,149,154,164,170,177,184,186,187,193,202,222,244,253],afterward:3,ag_sv_gw:223,again:[3,156,164,256],against:[0,37,47,92,130,156,164],agent:[0,164],aggreg:42,agka1:46,agka2:46,agka:46,agkb1:46,agr:95,agte3:81,aid:[1,260],aiida:[0,5,6,165],aiidastructureadaptor:189,aim:[60,73,192,244],aimd:47,ainput:184,ajjackson:0,aka:[60,133],al2o3:164,al3:244,al3sc:39,al_gw:223,al_structur:168,alan:[0,266,267],alarm:180,alat:208,albalu:0,albeit:185,alchemi:[0,2,5,6,246,247,248,260],alexand:253,algebra:41,algo:[0,21,23,55,64,90,133,168,192,223,246,247],algo_:[246,247],algo_best_first:[55,246,247],algo_complet:[55,246,247],algo_enumer:[246,247],algo_fast:[55,246,247],algo_time_limit:55,algorith:168,algorithm:[0,1,8,12,15,19,21,23,40,41,42,45,46,48,50,58,61,63,64,67,69,72,77,78,84,85,88,89,100,123,133,140,141,153,168,170,173,184,192,210,221,222,223,229,230,236,244,246,247,251,266],algorithm_typ:19,alia:[64,69,76,140,144,167,169,172,173,175,176,177,184,221,234],alias:[0,2,145],align:[12,21,28,37,67,76,133,154,198,221,227,259],align_x:67,aligned_lattic:133,aligned_matrix:133,alio_tol:244,alireza:0,alkali:[131,137,223],alkalin:[131,137],all:[0,1,2,3,8,9,10,12,14,15,18,19,21,23,28,29,31,36,37,38,41,42,44,45,46,47,48,50,54,55,56,58,60,61,63,64,67,68,69,71,74,77,78,81,83,85,89,90,91,92,94,95,97,99,100,101,102,103,104,106,124,125,130,131,133,137,138,139,140,141,142,143,144,148,149,150,151,152,153,154,156,157,158,159,161,163,164,167,168,169,173,175,176,177,178,180,182,183,184,185,186,188,192,193,200,201,202,2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235,236,244,255,268],ethyl:61,etot:[167,184],etsf:176,etsf_read:176,eu2:[0,223],eu3:[0,223],eu_2:223,euler:51,ev_to_k:42,ev_to_kj_per_mol:68,eval:[2,222],evalu:[30,38,39,42,50,55,69,81,82,173,185,188,209,210,222],evaluate_rpn:185,evaluate_wavefunc:222,evan:128,even:[0,3,48,59,77,85,101,107,131,140,164,168,184,221,222,238,246,247,251,268],event:[2,5,6,165,166,173,177,180,184,255,256,265],event_class:172,event_handl:177,eventhandl:177,eventreport:172,eventspars:172,eventsparsererror:172,eventu:[14,141],everi:[2,9,41,47,84,124,133,149,175,177,183,185,186,205,209,222],everyth:[1,148,268],evolut:[78,167,173,184],ewald:[0,1,5,6,11,37,42,53,244,246,247,268],ewaldelectrostaticmodel:53,ewaldminim:55,ewaldpap:55,ewaldsum:53,ewaldsumm:[0,53,55],ex_mat:72,ex_param:[72,128],exact:[8,74,75,85,140,141,158,221,223,238],exactdens:188,exactli:[0,63,85,141,149,168,221,247],exaf:[139,198,199,200],exampl:[0,1,3,8,9,10,15,21,34,36,41,47,48,55,58,64,69,74,78,83,84,85,87,92,93,94,100,101,102,103,106,109,130,131,133,136,137,139,140,141,144,145,149,150,153,154,156,157,158,160,164,168,169,171,173,177,178,185,186,200,202,205,210,213,217,218,220,221,222,223,225,236,240,244,246,247,251,255,256,262,263,265],exc:172,exc_dft_opt:201,exc_info:177,exc_typ:168,exce:[85,244],exceed:[180,183],excel:[0,123,236,266],except:[0,1,27,42,51,54,64,69,77,78,83,85,89,122,125,126,131,136,137,140,144,149,153,156,164,167,169,172,175,177,180,185,186,188,193,198,210,213,218,221,222,223,236,250],exception:89,exception_on_bad_xml:222,excess:37,exchamiltonian:168,exchang:[0,64,71,72,128,134,145,168,170,188,200,210],exchange_const:64,excit:[5,6,11,165,199,201,202,210],excitationspectrum:[56,210],excitinginput:196,exclud:[8,21,37,42,78,80,140,141,156,173,178,183,207,265],exclude_dir:[173,178],exclude_ext:173,exclude_nod:[183,184],exclude_ok_task:173,exclude_wildard:186,exclude_wildcard:186,excluded_atom:21,excluded_bonding_el:265,exclus:[145,173,177],exe:3,exec_arg:184,execut:[3,8,123,124,126,128,150,161,172,173,175,180,184,187,208,253,260],execwrapp:187,exelf:200,exercis:222,exhf:222,exist:[0,2,3,8,19,21,23,37,38,41,42,47,50,54,64,71,75,77,78,81,85,89,130,140,141,151,152,154,173,177,178,184,185,186,188,200,205,208,221,250,255,268],existing_structur:8,exit:[77,173,175,180,184,185,222],exitcod:180,exp:[42,46,47,50,164,211,222],exp_cos_aa:69,exp_entri:[5,6,155],expand:[0,1,3,63,174,186,244],expand_tim:[63,244],expans:[50,137,142],expect:[1,3,8,28,39,47,63,69,73,94,126,137,144,152,153,179,223,236,237,244],expected_charg:14,expens:[0,55,222,247],expentri:[159,164],experi:[3,205],experiment:[15,21,69,78,93,154,159,164,173,233,244,247],exphp:0,expir:180,explain:[0,149,154,156],explan:[0,63,131,154,156,164,180,268],explicit:[18,21,167,168,177,186,192,221,222],explicit_indic:21,explicit_optimized_permut:19,explicit_path:168,explicit_permut:19,explicitli:[1,48,69,180],explicitpermutationsalgorithm:19,explictli:28,explor:[2,42,124,268],expnorm:42,expon:[69,149],exponenti:[42,250],export_envar:175,export_msdt:47,expr:50,express:[2,28,50,58,133,142,183,184,185,186,218,222],expression1:185,expression2:185,expressionn:185,exsit:188,ext:[0,5,6,169,173,177,178,185,186,268],extend:[9,10,12,34,42,50,52,76,77,131,136,139,140,143,153,157,159,173,176,184,200,217,233,244,260,268],extend_collect:10,extend_structur:64,extend_transform:[9,10],extens:[0,2,3,47,64,95,106,137,138,140,154,159,169,173,177,178,184,185,186,201,207,222,268],extern:[0,3,160,177,180,221,256,258],extra:[2,38,41,71,76,100,168,170,185,212,222,227,250,264],extra_abivar:170,extra_nn_info:69,extract:[0,3,9,63,64,67,71,72,140,141,149,167,169,172,184,211,222,234,244,268],extract_clust:140,extract_metadata:183,extracted_vasp_potcar:3,extrapol:[47,153],extrapolate_reciproc:250,extrapolate_simple_reciproc:250,extras_requir:2,extrem:[0,2,40,55,63,90,140,154,164,222,223,234,238,246,247,263,268],extrema:[42,94,149],extrema_coord:42,extrema_df:42,extremum_icohpvalu:151,extrins:[100,101],eye:[133,168],f1d01e845dccc52d448679911f301a73:223,f4ff16a495dd361ff5824ee61b418bb0:223,f_1:[152,154],f_2:[152,154],f_3:[152,154],f_constant:202,f_gw:223,f_h:223,f_j:46,f_lower:28,f_upper:28,f_x:153,f_xyz:153,f_xz:153,f_y:153,f_yz:153,f_z:153,fac_aa:69,face:[12,19,69,84,91,227,265],face_dist:69,faces_color_overrid:32,facet:[19,21,28,44,46,69,78,84,91,92,95,133,251],facili:181,facilit:[154,173,177,234],facmaxdl:42,fact:[2,69,148,232,268],factor:[0,15,21,31,36,42,45,46,47,63,69,81,83,91,95,131,133,140,141,142,144,149,150,154,208,211,222,223,234,247,265],factori:[51,167,170,183],faghaninia:0,fail:[0,1,3,8,38,60,64,82,137,153,173,180,183,184,221],failur:[0,180,183],fairli:[1,2,3,64,236,265],faith:240,fake:[150,169],fall:[78,133,140,244,265],fallback:21,fallback_to_sourc:18,fals:[0,8,9,10,12,14,18,19,21,23,28,31,32,37,38,40,41,42,44,45,46,47,48,50,51,54,55,58,60,61,63,64,67,68,69,71,73,77,78,81,82,84,85,87,88,89,90,91,92,94,95,101,102,106,123,124,125,126,128,131,133,135,136,138,140,141,142,143,148,149,150,151,153,154,156,158,164,167,168,169,172,173,17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188,192,193,198,200,201,204,206,207,208,209,210,211,212,213,218,221,222,223,232,234,236,238,244,245,246,247,248,250,251,254,255,259,265,266,268],generate_adsorption_structur:12,generate_all_slab:141,generate_defect_structur:36,generate_displac:211,generate_entry_label:81,generate_full_symmop:236,generate_interfac:67,generate_potcar:118,generate_pseudo:50,generate_r_and_g_vec:42,generate_reciprocal_vectors_squar:42,generate_sl_transformation_set:91,generate_substitution_structur:12,generate_surface_vector:91,genfmt:198,genom:[2,6,266],genrecip:42,geo_subkei:188,geoffroi:[0,2,21,237,267],geograph:66,geom:205,geom_opt_max_cycl:217,geometr:[69,74,77,100,266],geometri:[0,19,21,23,51,60,91,188,192,202,210,217,266],geometrically_equidist:18,geometry_info:18,geometry_opt:210,geometryoptim:188,geomstep:192,georg:[149,150],gerbrand:[2,77],germain:[0,154,267],get:[0,3,6,12,13,15,18,23,34,36,37,38,41,42,47,48,50,51,58,63,67,68,69,72,73,74,78,81,82,87,92,95,101,103,122,123,126,130,131,133,137,138,140,141,142,149,150,151,152,153,154,162,163,164,171,173,177,179,180,184,186,193,199,202,208,209,221,222,223,233,234,236,241,244,246,247,251,256,259,263,268],get_00t_magmom_with_xyz_saxi:152,get_13_bond:75,get_absorbing_atom_symbol_index:198,get_adjusted_fermi_level:222,get_all_anonymous_map:85,get_all_chempot:78,get_all_dist:133,get_all_entri:103,get_all_functional_group:61,get_all_neighbor:[0,140],get_all_neighbors_old:140,get_all_nn:69,get_all_nn_info:69,get_all_sit:69,get_all_statu:186,get_all_substr:164,get_all_voronoi_polyhedra:69,get_allowed_speci:89,get_alpha:222,get_analysi:73,get_analysis_and_structur:73,get_angl:[140,251],get_arrhenius_plot:47,get_asum_fcm:80,get_atom:190,get_atom_map:198,get_atomic_fract:[2,131],get_available_model:162,get_average_along_axi:222,get_average_eff_mass:149,get_average_voltag:101,get_ax3d_fig_plt:255,get_ax_fig_plt:255,get_axarray_fig_plt:255,get_axis_grid:222,get_band_gap:148,get_band_structur:[150,222],get_band_structure_from_vasp_multiple_branch:222,get_bandstructur:209,get_bandstructure_by_material_id:[164,268],get_basic_functional_group:61,get_bec_oper:80,get_best_electronegativity_anonymous_map:85,get_bibtex_str:193,get_bond_length:130,get_bond_ord:130,get_bonded_structur:[0,48,69,87],get_box_shift:204,get_boxed_structur:140,get_branch:[148,232],get_brillouin_zon:133,get_capacity_grav:101,get_capacity_vol:101,get_carrier_concentr:149,get_cart_coord:202,get_cartesian_coord:133,get_cbm:148,get_cbm_vbm:153,get_celldm:213,get_center_of_arc:31,get_centered_molecul:140,get_central_sit:19,get_charg:123,get_charge_transf:123,get_chempot_correct:68,get_chempot_range_map:[78,92],get_chempot_range_map_plot:78,get_chempot_range_stability_phas:78,get_chgint_plot:117,get_children:177,get_chunk:257,get_cluster_graph:185,get_cn:69,get_cn_dict:69,get_cod_id:161,get_coeff:83,get_cohesive_energi:164,get_cohp:151,get_cohp_by_label:151,get_cohp_dict:154,get_collect:[171,184],get_complete_do:149,get_complete_ph_do:211,get_complexity_factor:149,get_compliance_expans:50,get_composition_chempot:78,get_compound_pd:78,get_computed_entri:222,get_conduct:149,get_connect:84,get_connected_sit:64,get_consistent_set:152,get_consistent_set_and_saxi:152,get_contour_pd_plot:78,get_conv_struct:122,get_conventional_standard_structur:236,get_conventional_to_primitive_transformation_matrix:236,get_conversion_factor:[47,144],get_coordinating_elements_cn:42,get_coordination_environ:23,get_coordination_numb:19,get_coordination_of_sit:64,get_coordination_symmetry_measur:21,get_coordination_symmetry_measures_optim:21,get_correct:[36,37,156],get_corrections_dict:156,get_cost_per_kg:34,get_cost_per_mol:34,get_covalent_bond:140,get_critical_composit:78,get_critical_original_kink_ratio:68,get_critical_point_for_sit:124,get_crystal_field_spin:137,get_crystal_system:236,get_csm:23,get_csm_and_map:23,get_d:141,get_data:[107,164,268],get_datafram:169,get_decomp_and_e_above_hul:78,get_decomposit:78,get_decomposition_energi:81,get_default_basis_set:188,get_default_geo:188,get_default_scf:188,get_default_unit:188,get_default_xc:188,get_defectsite_multipl:42,get_deformation_matrix:51,get_delta_etim:175,get_dens:153,get_deriv:250,get_dict_for_mongodb_queri:173,get_diff_coeff:50,get_dihedr:140,get_dimension:0,get_dimensionality_cheon:48,get_dimensionality_gorai:48,get_dimensionality_larsen:48,get_direct_band_gap:148,get_direct_band_gap_dict:148,get_displaced_structur:211,get_dist:140,get_distance_and_imag:133,get_do:150,get_doc:[164,209],get_dop:153,get_dopability_limit:41,get_dopants_from_shannon_radii:87,get_dopants_from_substitution_prob:87,get_dos_by_material_id:[164,268],get_dos_dict:[154,234],get_dos_plot:117,get_drift_corrected_structur:47,get_e_above_hul:[0,78],get_effective_csm:18,get_effective_ec:50,get_el_amount:83,get_el_amt_dict:131,get_el_sp:137,get_element_do:[153,233,234],get_element_fract:81,get_element_profil:78,get_element_spd_do:153,get_elements_between_band:222,get_elt_projected_plot:154,get_elt_projected_plots_color:154,get_energi:[53,112,115,126,131],get_energy_buckingham:126,get_energy_dens:101,get_energy_relax_structure_buckingham:126,get_energy_tersoff:126,get_entri:[0,34,164],get_entries_in_chemsi:[0,164,268],get_entry_by_material_id:164,get_environ:[5,6,108],get_environments_figur:23,get_equilibrium_reaction_energi:78,get_equiv_transform:91,get_equivalent_atom:236,get_equivalent_kpoint:148,get_equivalent_qpoint:232,get_event_handler_class:172,get_exchang:72,get_exchange_group_info:71,get_excitation_spectrum:210,get_exp_entri:164,get_exp_thermo_data:164,get_explanation_dict:156,get_extended_surface_mesh:12,get_extrapolated_conduct:47,get_extrapolated_diffus:47,get_extrem:149,get_extrema:94,get_facet:78,get_factor:91,get_fcm_oper:80,get_fermi:153,get_fermi_interextrapol:[0,153],get_ferromagnetic_structur:71,get_filepaths_and_ext:177,get_film_indic:67,get_final_structur:184,get_form_energi:78,get_form_energy_per_atom:78,get_frac_coords_from_ll:133,get_fract:131,get_fractional_coord:133,get_framework_rms_plot:[0,47],get_free_sphere_param:227,get_from_hint:21,get_gap:153,get_gb_data:164,get_geometri:19,get_geometry_from_iucr_symbol:19,get_geometry_from_iupac_symbol:19,get_geometry_from_mp_symbol:19,get_geometry_from_nam:19,get_ggt:50,get_graphviz:173,get_graphviz_dirtre:177,get_grouped_indic:142,get_gruneisen_paramet:50,get_hal:236,get_hall_carrier_concentr:149,get_hash:85,get_heat_capac:50,get_heteroatom:61,get_high_accuracy_voronoi_nod:227,get_hull_energi:[78,81],get_icohp:151,get_icohp_by_label:151,get_icohp_dict_by_bondlength:151,get_icohp_dict_of_sit:151,get_ieee_rot:142,get_implemented_geometri:19,get_info:180,get_integer_formula_and_factor:131,get_integer_index:133,get_integrated_diff:222,get_interaction_graph:72,get_interface_react:164,get_interpolated_gap:153,get_interpolated_valu:[139,151,153,233],get_ir_mesh:0,get_ir_reciprocal_mesh:236,get_ist_oper:80,get_kink:68,get_kpoint:[163,223,237],get_kpoint_degeneraci:148,get_kpoint_weight:236,get_label:92,get_lattic:193,get_lattice_quanta:58,get_lattice_typ:236,get_lattvec:150,get_lin:198,get_line_in_facet:95,get_linear_interpolated_valu:251,get_linearly_independent_vector:31,get_lll_frac_coord:133,get_lll_reduced_lattic:133,get_local_extrema:42,get_local_order_paramet:69,get_locpot_along_slab_plot:92,get_low_energy_ord:72,get_lower_and_upper_f:28,get_lowest_decomposit:34,get_magnet:115,get_magnitude_of_effect_from_speci:73,get_magnitude_of_effect_from_spin_config:73,get_magsymop:193,get_map:85,get_mass:144,get_materials_id:164,get_materials_id_from_task_id:164,get_materials_id_refer:[0,164],get_max_bond_dist:69,get_max_bond_length:84,get_max_capgrav:100,get_max_capvol:100,get_max_inst:103,get_max_muo2:103,get_mdf_robot:186,get_messag:177,get_mft_temperatur:72,get_mi_vec:12,get_miller_index_from_coord:133,get_miller_index_from_site_index:140,get_min_inst:103,get_min_muo2:103,get_minkowski_r:122,get_molecule_hash:74,get_moment:152,get_moment_relative_to_crystal_ax:152,get_mongo_info:173,get_monolay:92,get_motif_typ:42,get_mp_structur:260,get_msd_plot:47,get_mu_bound:149,get_multipl:36,get_nac_eigendisplacements_along_dir:232,get_nac_frequencies_along_dir:232,get_nam:19,get_nearest_sit:58,get_neighb_voronoi_indic:23,get_neighbor:140,get_neighbors_in_shel:140,get_neighbors_of_site_with_index:69,get_neighbors_old:140,get_newnode_id:177,get_next_index:55,get_niggli_reduced_lattic:133,get_njobs_in_queu:[173,184],get_nmr_quadrupole_mo:137,get_nn:69,get_nn_data:69,get_nn_imag:69,get_nn_info:69,get_nn_shell_info:69,get_no_mixing_energi:68,get_nod:180,get_nonmagnetic_structur:71,get_noppmodel:168,get_not_implemented_geometri:19,get_num_division_kpoint:122,get_occup:222,get_okeeffe_distance_predict:69,get_okeeffe_param:69,get_op_valu:42,get_orbital_derivative_between_st:222,get_orbital_resolved_cohp:151,get_order_paramet:69,get_ordered_with_polici:184,get_oriented_slab:67,get_ortho_ax:67,get_orthogonal_c_slab:141,get_oxi_state_decorated_structur:15,get_oxidation_state_decorated_structur:123,get_par:177,get_paramet:69,get_parchg:222,get_pars:183,get_partial_dos:150,get_pattern:[44,45,46],get_pelecs_and_pion:58,get_percentage_bond_dist_chang:84,get_percentage_lattice_parameter_chang:84,get_percentage_volume_chang:84,get_perturbed_indic:51,get_ph_bs_symm_lin:211,get_ph_bs_symm_line_from_dict:211,get_ph_do:211,get_phonon_bandstructure_by_material_id:164,get_phonon_ddb_by_material_id:164,get_phonon_dos_by_material_id:164,get_phonon_frequ:222,get_phonopy_structur:211,get_piezo:80,get_plot:[44,78,94,95,104,154,234,263],get_plot_data:104,get_pmesh:19,get_pmg_structur:211,get_point_group_oper:236,get_point_group_symbol:236,get_pointgroup:236,get_points_in_spher:133,get_points_in_sphere_old:133,get_polarization_chang:58,get_polarization_change_norm:58,get_potcar:222,get_potcar_hash:221,get_potential_shift:37,get_pourbaix_domain:81,get_pourbaix_entri:164,get_pourbaix_plot:81,get_power_factor:149,get_predicted_structur:90,get_prim_struct:122,get_primitive_standard:0,get_primitive_standard_structur:[236,237],get_primitive_structur:140,get_product:68,get_projected_plots_dot:154,get_projected_plots_dots_patom_pmorb:154,get_projection_on_el:[148,222],get_projections_on_elements_and_orbit:148,get_prototyp:13,get_pseudos_for_structur:178,get_q2:69,get_q4:69,get_q6:69,get_rand_bec:80,get_rand_fcm:80,get_rand_ist:80,get_ratio:63,get_rdf_figur:24,get_react:164,get_real_summ:37,get_reasonable_repetit:232,get_recip_summ:37,get_reconstructed_band_structur:148,get_recp_symmetry_oper:133,get_reduced_composition_and_factor:131,get_reduced_formula_and_factor:131,get_reduced_structur:140,get_refined_structur:236,get_relaxed_structur:126,get_removals_int_oxid:100,get_result:[173,177,184],get_rms_anonym:85,get_rms_dist:85,get_rmsd:74,get_rot:12,get_rotation_angle_from_sigma:[63,244],get_s2_like_s1:85,get_sadf_figur:24,get_same_branch_polarization_data:58,get_scal:142,get_scan_plot:202,get_scissors_build:184,get_script_str:175,get_sect:169,get_seebeck:149,get_seebeck_eff_mass:149,get_self_interact:37,get_set:0,get_shannon_radiu:137,get_shared_symmetry_oper:241,get_shear_reduced_slab:67,get_site_ce_fractions_and_neighbor:18,get_site_coordination_environ:18,get_site_coordination_environments_fract:18,get_site_do:[153,233],get_site_energi:55,get_site_info_for_specie_allc:23,get_site_info_for_specie_c:23,get_site_neighbor:18,get_site_orbital_do:153,get_site_spd_do:153,get_site_symmetri:241,get_site_t2g_eg_resolved_do:153,get_sitej:84,get_sites_in_spher:140,get_slab:141,get_slab_region:141,get_smeared_dens:[153,233],get_sorted_structur:[0,63,67,140,141],get_space_group_info:140,get_space_group_numb:236,get_space_group_oper:236,get_space_group_symbol:236,get_spacegroup_symbol:2,get_spd:[154,263],get_spd_do:[153,154],get_special_carbon:61,get_specific_energi:101,get_spectre_plot:202,get_stability_criteria:50,get_stabl:[0,164],get_stable_entri:[81,103],get_stable_entry_at_u:92,get_stable_fcm:80,get_stat:[180,185],get_statist:23,get_str:[143,198,204,208,221,222],get_strain_from_stress:50,get_strain_state_dict:50,get_structur:[0,21,143,164,190,193,260,268],get_structure_by_formula:161,get_structure_by_id:161,get_structure_by_material_id:[164,268],get_structure_compon:48,get_structure_from_dict:211,get_structure_from_mp:[0,2,6],get_structure_from_prev_run:223,get_structure_property_dict:50,get_structure_with_charg:209,get_structure_with_nod:42,get_structure_with_only_magnetic_atom:71,get_structure_with_spin:71,get_sub_electrod:[102,103],get_subgraphs_as_molecul:64,get_subset_in_chemsi:158,get_substr:164,get_suggested_saxi:152,get_summary_dict:[47,67,82,102],get_summed_cohp_by_label_and_orbital_list:151,get_summed_cohp_by_label_list:151,get_summed_icohp_by_label_list:151,get_supercell_matrix:85,get_surface_data:164,get_surface_equilibrium:92,get_surface_sit:141,get_sym_eq_kpoint:148,get_symbol_cn_map:19,get_symbol_dict:142,get_symbol_list:50,get_symbol_name_map:19,get_symm_band:149,get_symmetric_sit:141,get_symmetric_wallace_tensor:50,get_symmetrically_distinct_miller_indic:141,get_symmetrically_equivalent_miller_indic:141,get_symmetrized_fcm:80,get_symmetrized_structur:[236,242],get_symmetry_dataset:236,get_symmetry_oper:[0,236],get_symop:193,get_task_data:164,get_task_scfcycl:173,get_tasker2_slab:141,get_tgt:50,get_thermal_conduct:149,get_tick:[154,234],get_total_ionic_dipol:58,get_trans_mat:63,get_transform:85,get_transition_chempot:78,get_tri_area:95,get_typ:69,get_unique_famili:44,get_unit_primitive_area:92,get_unreconstructed_slab:141,get_unstable_entri:103,get_unstable_fcm:80,get_uvec:142,get_v:77,get_val:15,get_valid_path:106,get_valu:169,get_vars_datafram:177,get_vasp_input:[0,9,223],get_vasp_kpoint_file_sym:122,get_vasprun_outcar:223,get_vbm:148,get_vector_along_lattice_direct:[0,133],get_void_volume_surfarea:227,get_voigt_dict:142,get_volum:150,get_voronoi_nod:227,get_voronoi_polyhedra:69,get_wallace_tensor:50,get_weight:250,get_weights_of_nn_sit:69,get_wigner_seitz_cel:133,get_wt_fract:131,get_wulff_shap:164,get_xas_data:164,get_xrd_plot:[0,117],get_xyz_magmom_with_001_saxi:152,get_yield_stress:50,get_z_ordered_elmap:15,get_zmatrix:202,get_zt:149,getmessag:177,getmu_vertices_stability_phas:78,getsiz:185,gfactor:219,gflop:169,gfortran:[3,116],gfortranbinari:3,gga:[0,2,15,21,37,41,77,134,145,156,164,221,222,223,247,266],gga_c_am05:[134,145],gga_c_apb:134,gga_c_bgcp:134,gga_c_ft97:134,gga_c_gam:134,gga_c_hcth_a:134,gga_c_lm:134,gga_c_lyp:[134,145],gga_c_n12:134,gga_c_n12_sx:134,gga_c_op_b88:134,gga_c_op_g96:134,gga_c_op_pb:134,gga_c_op_pw91:134,gga_c_op_xalpha:134,gga_c_optc:134,gga_c_p86:134,gga_c_pb:[134,145],gga_c_pbe_jrgx:134,gga_c_pbe_sol:[134,145],gga_c_pbef:134,gga_c_pbeint:134,gga_c_pbeloc:134,gga_c_pw91:[134,145],gga_c_q2d:134,gga_c_regtpss:134,gga_c_revtca:134,gga_c_rge2:134,gga_c_sogga11:134,gga_c_sogga11_x:134,gga_c_spb:134,gga_c_tca:134,gga_c_wi0:134,gga_c_wi:134,gga_c_wl:134,gga_c_xpb:134,gga_c_zpbeint:134,gga_c_zpbesol:134,gga_k_absp1:134,gga_k_absp2:134,gga_k_apb:134,gga_k_apbeint:134,gga_k_baltin:134,gga_k_dk:134,gga_k_ernzerhof:134,gga_k_fr_b88:134,gga_k_fr_pw86:134,gga_k_ge2:134,gga_k_golden:134,gga_k_gp85:134,gga_k_gr:134,gga_k_lc94:134,gga_k_lieb:134,gga_k_llp:134,gga_k_ludena:134,gga_k_mey:134,gga_k_ol1:134,gga_k_ol2:134,gga_k_pearson:134,gga_k_perdew:134,gga_k_revapb:134,gga_k_revapbeint:134,gga_k_tfvw:134,gga_k_thakkar:134,gga_k_tw1:134,gga_k_tw2:134,gga_k_tw3:134,gga_k_tw4:134,gga_k_vjk:134,gga_k_vsk:134,gga_k_vw:134,gga_k_yt65:134,gga_relax:21,gga_x_2d_b86:134,gga_x_2d_b86_mgc:134,gga_x_2d_b88:134,gga_x_2d_pb:134,gga_x_airi:134,gga_x_ak13:134,gga_x_am05:[134,145],gga_x_apb:134,gga_x_b86:134,gga_x_b86_mgc:134,gga_x_b86_r:134,gga_x_b88:[134,145],gga_x_bayesian:134,gga_x_bgcp:134,gga_x_bpccac:134,gga_x_c09x:134,gga_x_cap:134,gga_x_dk87_r1:134,gga_x_dk87_r2:134,gga_x_ev93:134,gga_x_ft97_a:134,gga_x_ft97_b:134,gga_x_g96:134,gga_x_gam:134,gga_x_hcth_a:134,gga_x_herman:134,gga_x_hjs_b88:134,gga_x_hjs_b88_v2:134,gga_x_hjs_b97x:134,gga_x_hjs_pb:134,gga_x_hjs_pbe_sol:134,gga_x_htb:134,gga_x_ityh:134,gga_x_kt1:134,gga_x_lag:134,gga_x_lambda_ch_n:134,gga_x_lambda_lo_n:134,gga_x_lambda_oc2_n:134,gga_x_lb:134,gga_x_lbm:134,gga_x_lg93:134,gga_x_lv_rpw86:134,gga_x_mb88:134,gga_x_mpb:134,gga_x_mpw91:134,gga_x_n12:134,gga_x_ol2:134,gga_x_optb88_vdw:134,gga_x_optpbe_vdw:134,gga_x_optx:134,gga_x_pb:[134,145],gga_x_pbe_jsjr:134,gga_x_pbe_mol:134,gga_x_pbe_r:[134,145],gga_x_pbe_sol:[134,145],gga_x_pbe_tca:134,gga_x_pbea:134,gga_x_pbef:134,gga_x_pbeint:134,gga_x_pbek1_vdw:134,gga_x_pw86:134,gga_x_pw91:[134,145],gga_x_q2d:134,gga_x_rge2:134,gga_x_rpb:[134,145],gga_x_rpw86:134,gga_x_sfat:134,gga_x_sogga11:134,gga_x_sogga:134,gga_x_ssb:134,gga_x_ssb_d:134,gga_x_ssb_sw:134,gga_x_vmt84_g:134,gga_x_vmt84_pb:134,gga_x_vmt_g:134,gga_x_vmt_pb:134,gga_x_wc:134,gga_x_wpbeh:134,gga_x_xpb:134,gga_xc_b97_d:134,gga_xc_b97_gga1:134,gga_xc_edf1:134,gga_xc_hcth_120:134,gga_xc_hcth_147:134,gga_xc_hcth_407:134,gga_xc_hcth_407p:134,gga_xc_hcth_93:134,gga_xc_hcth_p14:134,gga_xc_hcth_p76:134,gga_xc_kt2:134,gga_xc_mohlyp2:134,gga_xc_mohlyp:134,gga_xc_mpwlyp1w:134,gga_xc_oblyp_d:134,gga_xc_opbe_d:134,gga_xc_opwlyp_d:134,gga_xc_pbe1w:134,gga_xc_pbelyp1w:134,gga_xc_th1:134,gga_xc_th2:134,gga_xc_th3:134,gga_xc_th4:134,gga_xc_th_fc:134,gga_xc_th_fcfo:134,gga_xc_th_fco:134,gga_xc_th_fl:134,gga_xc_vv10:134,gga_xc_xlyp:134,ggk:187,ggt:50,ghemic:192,ghost_sit:141,gian:21,giantomassi:[0,267],gibb:[0,78,81,82,92,149,154,202],gibbs_binding_energi:92,gin:126,git:[0,1,3],github:[0,2,4,95,124,162,164,180,232],gitlab:150,give:[0,2,13,28,34,36,41,55,58,63,64,69,71,73,77,78,85,90,91,92,100,122,124,126,131,149,150,152,153,154,164,172,173,185,208,209,222,236,244,251,252,268],give_only_index:236,given:[0,1,2,3,8,12,13,14,15,18,19,21,23,24,28,31,34,36,37,38,41,42,45,46,47,48,50,53,55,58,60,63,64,67,68,69,71,73,77,78,81,82,83,84,85,87,88,89,90,91,92,94,95,100,101,103,122,123,124,130,131,133,136,137,138,140,141,142,143,148,149,150,151,152,153,154,156,158,162,164,168,169,170,171,172,173,178,181,184,185,186,188,198,202,205,209,217,221,222,223,227,229,230,232,234,236,237,240,244,246,247,251,254,258,259,263,266,268],gjf:[2,140,268],gkk:[184,187],gkk_file:187,gkk_filepath:184,gkk_node:184,gkkpwork:186,glaum:21,global:[0,2,152,192,244],global_mo:152,gmail:[164,256],gmatteo:[0,54],gmolecul:188,gnu:3,gnuplot:[39,250],goal:[141,180],godbi:[168,170],goe:[46,198,200,253],goebel:21,going:[2,3,19,89,140,164,268],golden:[54,255],gonz:[21,149],good:[3,47,60,64,77,85,89,136,141,169,223,268],good_sect:169,googl:2,googlecod:176,gorai:48,gout:126,gov:[3,137,227],govern:184,gowoon:48,gpa:[54,82],gpa_to_ev_a3:50,gpaw:145,gpoint:222,gpretto:0,grab:[0,2],grad:124,gradep:124,gradient:[51,52,76,77,124,168,188,192,210,222,223,247],gradual:13,graef:[45,46,238],grain:[0,5,6,11,62,164,223,244,268],grain_label:63,grainboundari:63,grainboundarygener:63,grainboundarytransform:[0,244],gramschmidt:69,grand:[0,68,78,92,266],grandpotentialphasediagram:[0,68,78],grandpotpdentri:78,grant:2,granular:47,graph:[0,3,5,6,11,47,48,60,61,69,72,87,124,128,154,162,173,177,185,234],graph_attr:[173,185],graph_data:64,graph_dict:64,graphic:[2,78,154],graphit:260,graphviz:[3,64,173,177,185],graphviz_imshow:173,grav:100,gravimetr:101,grazuli:161,great:95,greater:[0,2,38,69,107,131,140,164,175,185,233],greatest:[31,131],greatli:[2,158],greedi:153,green:[50,51,64,154,168,259],green_kristoffel:50,green_lagrange_strain:51,grei:[255,265],grep:[0,213,218,222,223],grid:[0,18,23,37,42,44,54,77,124,149,153,154,167,168,169,173,178,185,201,209,213,219,221,222,223,234,236],grid_off:95,gridf:177,gridfs_fil:177,gridfsfil:177,gridspec_kw:255,grip:2,gross:133,grosspop:[0,209],ground:[0,68,72,91,128,137,158,164,167,184,186,187],ground_state_energi:91,ground_state_term_symbol:137,groundstatescfcycl:167,group:[0,2,3,5,6,10,13,19,21,28,36,42,47,48,58,61,64,71,74,85,94,124,131,133,137,140,141,142,158,164,169,173,176,193,198,204,208,218,222,223,235,236,239,240,241,247,266,268],group_array_indic:142,group_by_typ:140,group_entries_by_structur:158,group_molecul:74,group_structur:[0,85],groupby_statu:173,groupby_task_class:173,grow:2,growth:91,gruneisen:[50,82],gruneisen_paramet:82,gsr:[177,184,186],gstask:184,gswfk_file:187,guarante:[0,2,56,64,71,97,139,141,219,236,246,247,268],guard:164,guess:[0,3,47,58,60,71,90,131,140,204,247,250,268],guess_el:204,guesstim:73,guesstimate_spin:73,gui:173,guid:[0,3,58,268],guidanc:164,guidelin:[0,2,3],guido:[0,185],gulp:[0,3,53,55,126,225,227],gulp_cal:[0,3,5,6,121],gulp_cmd:126,gulpcal:126,gulpconvergenceerror:126,gulperror:126,gulpio:126,gunter:[2,266,267],gvallver:154,gvallverdu:0,gw_fiesta:201,gw_option:201,gw_qprang:168,gwcalctyp:168,gweight:18,gwpara:168,gzip:[0,107,123,124,193],h2o2:131,h2o:[81,156],h_gw:223,h_node:256,habit:184,had:[0,36,55,149],haeberlen:76,haeberlen_valu:76,haeberlennot:76,hafner:39,half:[0,85,141,202],halfspac:41,halfspaceinterect:41,halfspaceintersect:81,halit:141,halite_111_octopolar_2x2:141,hall:[149,150,154,161,236],hall_carrier_conc_trac:150,hall_carrier_conc_trace_mu:150,hall_dop:149,hallten:149,halogen:[131,137],halogen_list:75,hamilton:[0,151,154],hamiltonian:[71,72,168],hammer:145,hand:[3,106],handi:167,handl:[0,1,2,48,92,150,151,152,172,175,191,205,209,215,236],handle_input_ev:172,handle_task_ev:172,handler:[172,177,180,182],hangup:180,hanmei:0,hanmeitang:0,hansen:145,hanson:13,happen:[36,42,69],haranczyk:[40,42,266],hard:[73,137,173,204,246,247],hardwar:[180,183],harmon:82,harri:76,hart:[0,3,13,246],hartre:[167,168,178,186,210,222],hartree_paramet:174,has:[0,1,2,3,9,21,23,24,38,41,47,50,54,55,58,60,63,67,69,71,78,80,81,83,92,101,106,124,133,136,137,140,141,142,145,149,150,152,154,164,172,173,175,177,178,180,184,186,188,198,202,205,210,212,221,222,223,230,232,236,244,258,268],has_abiext:185,has_antibnd_states_below_efermi:151,has_chroot:173,has_db:[173,184],has_dojo_report:178,has_eigendisplac:232,has_error:193,has_good_quality_check_occupied_band:209,has_good_quality_maxdevi:209,has_hint:178,has_imaginary_freq:232,has_intersect:18,has_materials_project_access:26,has_mpi:184,has_mpiio:184,has_nac:[211,232],has_netcdf:184,has_node_failur:180,has_omp:184,has_opt:188,has_queu:184,has_schedul:173,has_subkei:188,hash:[0,74,85,137,142,156,178,221,222,223],hashabl:[74,85,131,138,140,145,177],hasn:221,hautier:[0,2,21,78,88,89,149,223,266,267],have:[0,1,2,3,8,12,14,15,21,23,36,38,41,47,48,51,53,55,58,59,60,61,63,64,67,69,71,73,75,77,78,84,85,87,91,92,94,95,100,101,102,103,106,107,121,122,126,131,135,137,138,140,141,142,143,144,148,149,152,153,154,156,157,164,167,169,173,176,177,178,180,183,184,185,186,188,192,204,209,211,219,221,222,223,227,234,236,242,244,245,246,247,248,251,253,259,260,266,268],have_consistent_saxi:152,have_equivalent_surfac:141,haven:[0,55,173],haydock:168,hbar:[42,50],hcp:[69,95,247],hdf5:[0,222],he_bcc:260,he_gw:223,head:207,headach:223,header:[0,3,163,176,193,198,199,200,208,212,218,222,225,259],header_pattern:[218,222],header_str:198,header_string_from_fil:198,heat:[50,233,234,255],heatmap:255,heavi:[0,164,268],heavier:157,heavili:268,hedin:221,height:[12,54,69,104,154,244,255],heisenberg:[0,5,6,11,64,70],heisenbergmapp:[72,128],heisenbergscreen:72,hello:171,helmholtz:[82,233],helmholtz_free_energi:233,helmoltz:234,help:[0,2,12,19,38,58,63,64,71,78,92,133,141,153,154,164,209,265],helper:[0,5,6,10,12,28,42,50,64,69,84,92,95,107,122,127,131,141,142,164,165,166,171,184,185,196,198,213,221,255],hematit:93,henc:[179,184,221,247,253],henchforth:0,heng:0,henkelman:[94,123,222,266],henkelmann:[0,3,123,266],henriquemiranda:232,here:[1,2,3,48,69,71,85,92,141,145,173,178,184,185,211,219,222,253,258,268],herebi:2,herfindahl:66,hermann:238,hessian:[0,124,154,202,210],heteroatom:61,heterostructur:[48,59,91],heurist:[71,73],hex:[0,63,177,237],hex_angle_tol:133,hex_bipyr:69,hex_length_tol:133,hex_pyr:69,hex_triplet:177,hexagon:[0,63,69,95,133,141,168,221,223,236,237,238,240,244],hf_pv:223,hf_sv_gw:223,hfscreen:223,hg_sv_gw:223,hhi:[0,5,6,11],hick:13,hide:64,hide_image_edg:64,hide_unconnected_nod:64,hierarchi:268,high:[0,2,10,42,71,73,92,137,149,150,162,170,178,192,210,223,227,236,237,265,266],highcharg:39,highchart:39,higher:[41,42,50,53,69,89,92,149,154,222,223,247],highest:[12,42,48,50,78,84,101,135,149,184,246,268],highest_protocol:260,highli:[0,1,2,3,168,221,222,246,268],highlight:268,highsymmkpath:[150,154,221,237],hight:221,hilber:168,hilbert:168,hilberttransform:168,hill:[50,131],hill_formula:131,hillari:0,hint:[0,19,21,23,71,178,184],hint_for_accuraci:178,hints_info:19,hints_typ:19,hirerachi:268,hirschman:66,hirshfeld:223,his:238,hist:[167,184,186],histfil:186,histo:149,histogram:[149,169,185],histori:[9,10,164,167,173,177,186,246,247,248,256],historynod:256,historyrecord:177,hit:250,hive:[5,6,98,105,107,268],hkil:[95,141],hkill:95,hkl:[44,46,48,95,133,141],hkl_list:95,hkl_transform:141,hkl_tuple_to_str:95,ho3:223,ho_3:223,hold:[63,141,227],holder:2,hole:[37,38,41,149,153],hollow:12,home:[2,185],homebrew:124,homo:135,homogen:50,homogeneous_poisson:50,hook:[0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221,222,223],incar_input:209,incar_output:209,incar_paramet:0,inch:[54,154,255],inchi:74,inchimolatommapp:74,incid:200,includ:[0,1,2,3,9,10,12,21,23,34,36,37,38,42,46,47,48,50,51,55,58,60,63,64,67,68,69,78,81,89,91,92,99,103,106,131,133,136,138,139,140,141,142,143,144,149,151,153,157,158,159,163,164,168,170,173,175,177,185,188,200,204,209,222,223,242,244,267,268],include_base_prop:50,include_bv_charg:40,include_central_site_in_centroid:21,include_cif:[10,223],include_deactiv:19,include_dist:85,include_gamma:163,include_ignored_speci:85,include_imag:140,include_improp:142,include_index:140,include_mscd_t:47,include_msd_t:47,include_myself:103,include_no_mixing_energi:68,include_reconstruct:141,include_strain:91,include_unprocessed_entri:81,include_user_ag:164,include_work_of_separ:164,inclus:131,inclusionari:244,inclvkb:[168,170],incompat:[0,3,41,156,193],incomplet:[21,206],inconsist:[47,142,152,173],incorpor:[64,164,222],incorport:135,incorrect:0,incorrectli:0,incr:92,increas:[0,2,23,28,42,55,63,84,90,131,140,164,172,183,184,221,223,244,254,265],increase_cpu:183,increase_mem:[183,184],increase_ncpu:184,increase_resourc:184,increase_tim:[183,184],incred:141,increment:[92,149,222],incres:183,ind1:140,ind2:140,ind:[133,222],ind_zero_freq:233,indata:186,inde:[173,180,185],indent:196,indentifi:182,independ:[0,50,51,78,91,92,148,150,168,173,188,202,210],index1:84,index2:84,index:[0,1,2,12,21,23,28,37,38,39,42,48,50,51,55,58,59,60,63,64,66,68,69,74,75,80,84,91,92,95,123,124,128,133,137,138,140,141,142,143,148,149,152,154,164,168,176,185,186,188,192,198,199,200,201,202,204,207,213,222,223,232,233,241,244,251,252,254,265,268],index_non:63,index_of_sit:141,indexerror:[9,10],indic:[0,9,10,12,19,21,24,28,37,42,44,48,50,51,55,61,63,64,67,69,74,77,84,85,91,92,95,124,130,131,133,136,138,140,141,142,148,149,151,152,153,154,168,173,198,202,204,209,221,222,223,232,236,244,246,248,251,252,254,256,263],indices_from_symbol:140,indices_left:55,indices_neigh:69,indices_separ:28,indices_species_map:246,indices_to_mov:246,indices_to_remov:246,indici:91,individidu:178,individu:[2,47,81,92,94,151,154,222],induc:64,inequival:[71,211],inertia:236,inext:185,inf:[23,150,168,186,244],infer:204,infin:[0,18,92],infinit:[24,69,74,133,149,175,268],infit:[40,42],influenc:[55,149],info:[0,2,21,23,69,82,124,164,169,172,173,177,180,184,199,201,204,209,222,223,227,265],info_dict:[23,134],inform:[0,2,3,14,18,21,23,28,36,38,42,44,47,48,63,64,67,68,69,71,83,84,85,124,126,128,132,135,140,141,142,143,144,145,148,149,151,152,155,157,164,167,173,177,184,192,193,198,209,222,223,225,226,227,232,244,246,247,248,266,268],inforn:177,infos_on_basis_set:201,infos_on_system:201,infrastructur:[223,266],inher:[141,244],inherit:[50,58,177,223,246,247],init:[0,42,63,69,91,131,134,141,172,173,222,223],init_3point:28,init_cel:63,init_count:177,init_inplane_shift:67,init_neighbors_set:23,init_slab:141,initi:[0,3,9,10,14,15,19,21,23,24,28,36,37,38,40,42,45,46,47,50,53,54,55,60,63,67,69,71,75,78,81,84,90,91,92,94,100,102,123,126,130,131,136,137,140,141,142,144,151,152,153,154,157,164,167,173,175,177,179,180,184,185,186,188,192,201,209,213,221,223,224,234,236,240,247,251,263,268],initial_angle_tol:13,initial_comp:102,initial_defect_structur:[37,38],initial_disp:47,initial_entri:14,initial_fit:142,initial_ltol:13,initial_molecul:14,initial_norm:23,initial_r:23,initial_stol:13,initial_structur:[47,63,84,141],initial_structure_environ:21,initialis:69,initialization_opt:18,initializationchemenverror:27,initio:[149,154,175],inner:[133,140],innov:266,inorgan:[88,89,131,137,223,255],inp:[140,184,186,198,199,200,207,268],inpfil:188,input:[0,2,3,5,6,9,10,12,13,19,36,42,44,45,46,47,48,50,54,55,58,61,63,64,67,69,71,72,73,76,78,81,84,85,88,89,90,95,103,106,109,126,127,128,131,133,135,137,140,141,142,143,148,149,150,151,154,156,157,158,159,164,165,168,172,173,174,175,177,178,180,184,185,186,188,191,192,193,194,195,197,199,200,201,202,203,204,206,207,208,209,210,212,213,214,217,218,219,220,222,223,225,226,227,236,237,242,244,246,247,248,251,254,259,260,268],input_arrai:[50,142],input_dir:[200,221],input_fil:[173,184,207,217],input_filenam:[2,207],input_grid:209,input_matrix:[50,79,80],input_mil:95,input_paramet:202,input_set:156,input_str:[140,224],input_vasp_arrai:79,inputset:156,inscrib:244,insensit:177,insert:[0,42,63,64,100,101,103,140,164,173,185,209,244,246,268],insert_nod:64,insertion_batteri:[5,6,98,99],insertionelectrod:[99,103],insertionvoltagepair:103,insertsitestransform:246,insid:[12,149,154,167,173,184,187,193,201,244],inspect:[167,173,184,185,205,244],inspir:[122,145,156],instabl:[78,103],instal:[0,1,5,6,69,124,126,140,165,177,204,246,268],install_event_handl:177,install_softwar:116,installzeo:3,instanc:[0,8,9,19,34,61,64,69,76,78,81,89,90,133,137,138,140,144,145,149,154,168,170,173,176,177,178,180,184,186,192,204,205,221,223,234,236,247,256,258,260,268],instanci:[168,176],instanti:[37,61,140,154,167,168,173,178,186,190,219],instead:[0,1,2,3,8,45,47,48,54,60,68,69,71,78,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module","pymatgen.io.zeopp module","pymatgen.optimization package","pymatgen.optimization.linear_assignment module","pymatgen.optimization.linear_assignment_numpy module","pymatgen.phonon package","pymatgen.phonon.bandstructure module","pymatgen.phonon.dos module","pymatgen.phonon.plotter module","pymatgen.symmetry package","pymatgen.symmetry.analyzer module","pymatgen.symmetry.bandstructure module","pymatgen.symmetry.groups module","pymatgen.symmetry.maggroups module","pymatgen.symmetry.settings module","pymatgen.symmetry.site_symmetries module","pymatgen.symmetry.structure module","pymatgen.transformations package","pymatgen.transformations.advanced_transformations module","pymatgen.transformations.defect_transformations module","pymatgen.transformations.site_transformations module","pymatgen.transformations.standard_transformations module","pymatgen.transformations.transformation_abc module","pymatgen.util package","pymatgen.util.convergence module","pymatgen.util.coord module","pymatgen.util.coord_cython module","pymatgen.util.io_utils module","pymatgen.util.num module","pymatgen.util.plotting module","pymatgen.util.provenance module","pymatgen.util.sequence module","pymatgen.util.serialization module","pymatgen.util.string module","pymatgen.util.testing module","pymatgen.util.typing module","pymatgen.vis package","pymatgen.vis.plotters module","pymatgen.vis.structure_chemview module","pymatgen.vis.structure_vtk module","References","Active Core Team","Overview"],titleterms:{"new":2,The:268,abiinspect:167,abinit:[166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187],abiobject:168,abitim:169,about:2,aconvasp_cal:122,activ:267,add:2,adf:188,adsorpt:12,advanced_transform:244,aflow_prototyp:13,aiida:189,alchemi:[7,8,9,10,268],alumni:267,analysi:[11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,266,268],analyz:[71,100,236],anoth:268,api:[2,268],app:[98,99,100,101,102,103,104,105,106,107],as_dict:268,ase:190,assimil:268,atat:191,babel:192,bader:3,bader_cal:[123,266],bandstructur:[148,232,237],base:3,basic:268,batteri:[99,100,101,102,103,104],battery_abc:101,boltztrap2:150,boltztrap:149,bond:130,bond_dissoci:14,bond_val:15,borg:[105,106,107,268],calcul:[170,268],can:268,chang:[0,2,4],check:227,chemenv:[16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32],chemenv_config:26,chemenv_error:27,chemenv_strategi:18,cif:193,cite:2,cli:[108,109,110,111,112,113,114,115,116,117,118,119,120],cluster:2,cod:161,code:1,cohp:151,collabor:1,command:2,command_lin:[121,122,123,124,125,126,127,128,266],compat:[1,156,266,268],composit:131,computed_entri:157,conda:[2,3],config:268,content:[6,7,11,16,17,20,22,25,33,35,43,49,57,62,65,70,86,96,98,99,105,108,121,129,147,155,160,165,166,195,197,203,214,220,228,231,235,243,249,262],contribut:2,contributor:267,converg:250,conversion_batteri:102,coord:251,coord_cython:252,coordination_environ:[17,18,19,20,21,22,23,24],coordination_geometri:19,coordination_geometries_fil:20,coordination_geometry_find:21,coordination_geometry_util:28,copyright:2,core:[36,44,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,152,266,267],correct:37,cost:[33,34],creat:[3,268],critic2_cal:124,crystalsai:162,cssr:194,dao:146,data:[204,268],decod:268,defect:[35,36,37,38,39,40,41,42],defect_compat:38,defect_transform:245,defs_util:29,depend:3,develop:[2,3],development:3,diagram:268,diffract:[43,44,45,46],diffusion_analyz:47,dilute_solution_model:39,dimension:48,doc:2,document:2,dopant_predictor:87,dos:[153,233],effect:2,elast:[49,50,51,52],electronic_structur:[147,148,149,150,151,152,153,154],energi:268,energy_model:53,entri:[155,156,157,158,159,266,268],entry_tool:158,enumlib:3,enumlib_cal:125,environ:3,eos:54,event:172,ewald:55,exampl:[2,268],excit:[56,195,196],exp_entri:159,ext:[160,161,162,163,164],extern:267,feff:[197,198,199,200,266],feff_input_gener:109,feff_plot_cross_sect:110,feff_plot_do:111,ferroelectr:[57,58],fiesta:201,file:268,filter:8,find_dimens:59,flow:173,fragment:60,from:2,from_dict:268,func_util:30,functional_group:61,gaussian:202,gaussian_analyz:112,gener:40,get:2,get_environ:113,gga:268,github:[1,3],grain:63,graph:64,group:238,guidelin:1,gulp_cal:126,heisenberg:72,helper:174,hhi:[65,66],high:268,hive:106,how:2,indic:2,input:[196,198,205,215,221],insertion_batteri:103,instal:[2,3,227],integr:268,interfac:67,interface_react:68,introduct:2,io_util:253,ion:132,jahntel:73,jhu:163,lammp:[203,204,205,206,207],lattic:133,launcher:175,librari:3,libxcfunc:134,licens:2,line:2,linear_assign:229,linear_assignment_numpi:230,linux:3,lmto:208,lobster:209,local_env:69,log:[0,2,4],mac:3,maggroup:239,magnet:[70,71,72,73],make:268,manual:268,materi:[9,268],matgeni:2,math_util:31,matproj:[164,266,268],mcsqs_caller:127,method:268,mix:268,mode:3,modifi:268,modul:[6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265],molecul:268,molecular_orbit:135,molecule_match:74,molecule_structure_compar:75,montyencod:268,more:2,netcdf:176,neutron:45,nmr:76,node:177,non:3,note:268,num:254,nwchem:210,offlin:2,onli:[2,3],ons:2,openbabel:3,oper:136,optim:[228,229,230],option:3,osx:3,output:[199,206,216,222],overview:268,packag:[6,7,11,16,17,20,22,25,33,35,43,49,57,62,65,70,86,96,98,99,105,108,121,129,147,155,160,165,166,195,197,203,214,220,228,231,235,243,249,262],path_find:[77,266],periodic_t:137,phase:268,phase_diagram:78,phasediagram:266,phonon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\ No newline at end of file
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,124,126,128,130,131,133,136,137,138,139,140,141,142,143,148,149,150,151,152,153,154,156,157,158,159,164,167,168,169,170,171,173,175,176,177,178,181,184,185,186,187,188,190,192,193,196,198,199,200,201,202,204,205,208,209,210,211,213,217,218,219,221,222,223,224,225,227,232,234,236,238,242,244,246,247,251,253,254,255,259,260,263,264,265],"enum":[0,3,63,71,124,134,137,152,168,221,244],"export":[3,158,175,204,226,256],"fe\u2082o\u2083":259,"final":[0,3,14,36,38,46,58,68,78,82,83,84,88,94,123,124,127,133,141,157,164,173,177,184,185,186,188,202,207,218,222,223,244,255,268],"float":[0,1,8,9,12,15,18,34,36,37,38,41,42,44,45,46,47,48,50,51,53,54,55,58,63,64,67,68,69,71,72,73,78,80,81,82,83,84,85,87,90,91,92,93,95,100,101,102,124,126,128,130,131,133,136,137,138,139,140,141,142,143,144,148,149,151,152,153,154,156,157,158,163,164,167,180,181,188,192,193,198,200,204,205,207,209,210,211,213,218,219,221,222,223,225,227,234,236,237,238,240,241,244,247,251,254,255,259,263,264,265],"function":[0,1,2,3,10,12,14,18,27,28,30,37,41,42,48,50,51,54,55,58,59,60,61,63,64,67,68,69,71,77,78,81,82,84,85,88,89,92,100,108,122,127,131,133,134,135,137,139,140,141,142,143,144,145,148,149,150,152,153,154,156,158,164,167,168,170,171,173,175,177,178,183,184,185,186,188,192,193,198,199,202,207,209,210,213,218,221,222,223,227,230,232,233,234,238,244,250,253,254,255,259,260,263,264,266,267,268],"gra\u017euli":161,"import":[0,1,2,3,55,60,61,64,69,133,140,149,158,169,173,177,178,179,181,184,220,221,226,244,256,268],"int":[0,10,12,18,36,37,42,44,47,48,50,54,55,58,60,61,63,64,67,69,71,80,81,84,85,87,91,92,94,107,127,128,131,133,136,137,138,140,141,142,143,148,149,151,153,154,161,163,164,173,175,177,178,180,188,192,198,199,200,204,205,206,207,208,209,210,217,219,221,222,223,236,238,242,244,246,247,255,259,265],"j\u00f3nsson":266,"jes\u00fa":150,"long":[0,1,37,75,137,218,222,268],"lua\u00f1a":124,"mart\u00edn":124,"n\u00f8rskov":145,"new":[0,1,3,9,10,36,41,44,47,48,54,55,59,60,63,64,67,76,77,85,88,89,90,101,103,124,133,140,141,142,144,150,152,154,164,167,168,169,173,175,177,178,180,184,185,186,187,188,202,209,215,217,221,222,223,234,247,255,256,268],"null":69,"okuli\u010d":161,"pend\u00e1":124,"public":[1,2,13,37,48,141,184,223,255,266],"quir\u00f3":161,"return":[0,1,2,6,8,9,10,12,13,14,15,18,19,21,23,24,28,31,34,36,37,38,39,41,42,44,45,46,47,48,50,51,52,53,54,55,58,60,61,63,64,67,68,69,71,72,73,74,76,77,78,80,81,82,83,84,85,87,88,89,90,91,92,94,95,100,101,102,103,104,106,107,123,124,126,127,128,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,148,149,150,151,152,153,154,156,157,158,159,161,162,164,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,190,191,192,193,194,196,198,199,200,201,202,204,206,207,208,209,210,211,212,213,218,219,221,222,223,224,225,226,227,230,232,233,234,236,237,238,240,241,242,244,245,246,247,248,250,251,252,253,254,255,256,258,259,260,263,264],"rodr\u00edguez":136,"short":[37,69,130,173,223,227],"static":[0,9,10,63,64,68,69,72,73,75,77,81,82,83,84,88,92,94,102,130,131,133,136,137,142,149,152,164,168,178,180,183,185,188,190,191,192,193,194,196,198,199,200,202,209,210,213,215,216,221,222,223,225,226,227,240,244,247,255,256,260,268],"super":[56,64,91,97,139,141,185],"switch":[0,1,154,173,184,244],"throw":[50,79,222,247],"transient":164,"true":[8,9,10,12,14,18,19,21,23,24,28,32,36,37,38,41,42,44,45,46,48,50,53,54,58,60,61,63,64,67,68,69,71,73,74,75,77,78,79,81,82,85,88,89,90,92,94,95,100,101,102,103,106,124,125,126,128,131,133,134,136,137,138,140,141,142,143,148,149,150,151,152,153,154,156,158,164,167,168,169,170,173,175,176,177,178,182,183,184,185,186,187,188,192,193,198,200,201,202,204,205,207,208,209,211,216,218,221,222,223,225,232,234,236,237,238,242,244,246,247,248,250,251,252,253,254,255,259,260,264,265],"try":[0,3,9,40,50,60,64,71,124,149,153,164,175,178,184,221,222,244,265],"var":[173,184],"void":[0,227],"while":[8,18,23,28,38,58,63,69,74,75,92,100,140,141,154,185,186,204,206,221,222,227,247,268],AND:[2,8,137,141,185,222,223],ASE:[0,3,54,190],Added:0,And:[1,69,222],Axes:[44,54,154,169,173,255],BNS:140,BUT:2,Being:58,Bus:180,But:[0,2,42,63,227,236,244,246,268],DLS:90,DOS:[0,111,139,149,150,153,154,164,186,209,233,234,263],Dos:[41,149,150,153,154,164,209,211,233,234,263,268],ECs:50,EOS:[0,54],EPS:[154,202,234,263],FMS:200,FOR:[2,141],For:[0,1,2,3,8,9,15,18,23,28,34,36,37,42,46,47,48,50,58,63,64,67,69,78,83,84,85,87,91,92,93,94,101,102,103,106,124,126,130,131,132,133,136,137,140,141,144,145,149,152,153,154,156,157,158,159,160,162,164,168,169,171,178,182,186,192,202,205,209,210,213,218,221,222,223,227,236,238,244,246,247,256,262,263,265,266,268],GBs:[63,141,244],Gus:[0,3,246],Has:[41,78,106,140,198,222,247],IDE:1,IDs:164,Ising:53,Its:[173,211],MOs:135,NOT:[2,34,36,42,64,78,204,222,223],Near:164,Not:[3,78,140,168,180,204,244],ONE:204,OPs:[0,69],OSes:3,One:[2,28,48,59,101,154,167,168,177,221,222,227,234,236,244],PBS:[180,183,184],PDs:[0,78,92],POS:208,PRs:0,Pls:0,QPS:184,RLS:90,RMS:[0,85],SQS:[127,244],Such:75,Sys:180,THE:[2,141],THe:153,That:[63,69,84,139],The:[0,1,2,3,6,8,9,10,12,13,15,18,19,21,23,24,28,35,38,39,40,41,42,44,45,46,47,48,50,53,54,55,56,58,60,61,63,64,66,67,68,69,74,75,77,78,79,81,82,83,84,85,87,88,89,91,92,93,94,95,97,101,102,103,104,105,106,107,123,124,127,130,131,132,133,135,136,137,138,139,140,141,143,144,145,146,148,149,150,151,152,153,154,156,157,161,162,163,164,167,168,172,173,175,176,177,178,179,180,181,183,184,185,186,188,190,192,193,198,199,200,201,202,204,205,206,207,208,209,210,211,213,215,218,221,222,223,227,229,230,232,233,234,235,236,237,238,242,243,244,246,247,249,253,254,255,256,260,262,263,265,266],Their:[74,130],Then:[1,3,72,236,260],There:[0,1,2,64,89,92,106,133,140,141,148,152,175,209,232,244,268],These:[2,19,48,50,55,64,78,94,162,164,193,202,209,222,223,268],USE:[2,247],Use:[0,1,44,45,46,47,50,55,64,69,94,131,134,136,138,140,141,152,156,158,162,164,167,168,173,175,177,178,186,192,221,223,244,246,247,256,265],Used:[47,53,78,81,92,123,143,149,152,173,200,202,222,240,247],Useful:[0,2,36,47,63,81,85,92,95,124,131,138,140,141,144,152,154,164,167,173,178,184,198,205,213,221,222,227,236,247,265],Uses:[10,37,54,69,92,94,107,167,168,192,213,221,222,223,236,254],Using:[67,140,145,156,162,164],WILL:141,WITH:[2,141,148,232,247],Will:[0,55,64,71,73,141,198,209,244,247,259],With:[0,1,2,3,69,193,236,250],XAS:[0,263],XES:200,Yes:185,__abinitflow__:173,__call__:67,__class__:[177,268],__eq__:260,__future__:1,__getitem__:131,__hash__:0,__init__:[10,50,51,52,56,63,76,79,80,97,139,140,141,142,161,172,173,215,223],__main__:0,__module__:268,__name__:[0,177,268],__new__:[50,51,52,76,79,80,142,144],__rmul__:0,__slots__:258,__str__:[198,202,215,221],_additional_condit:18,_angle_cutoff:18,_bp:222,_calculate_possible_shift:141,_cgraph:0,_continuous_symmetry_measure_cutoff:18,_defect_sit:3,_del:200,_den:[184,185],_distance_cutoff:18,_ev:222,_extrema_df:42,_get_nn_shell_info:69,_io:[169,173,177,178],_map:78,_materialsproject:[164,256],_matrix:55,_parse_bool:221,_parse_float:221,_parse_int:221,_parse_list:221,_parse_str:221,_path:168,_pickl:258,_proj_height:141,_reset:184,_set:223,_setup:186,_site:140,_sp:89,_threshold:89,a1604:50,a1826:50,a1fdb1089d0727f415416ec8082246ba:223,a1fit:188,a2b2:0,a2c9485ea86b2a7cf175077e6e5c7b3:223,a32:63,a35:69,a38:63,a395eb3aaf2fcab12fac3030a1146f61:223,a40:63,a45:63,a604ea3c6a9cc23c739b762f625cf449:223,a67:223,a6fd9a46aec185f4ad2acd0cbe4ae2fa:223,a74:223,a9182d436a13194b744640ac940ab9b0:223,a_1:[133,140,222],a_1a:222,a_1c:222,a_1p:222,a_2:[133,140],a_3:[133,140],a_i:46,a_pw:222,a_tot:222,a_vib:82,a_xb_1:13,a_xi:254,a_xx:254,a_xz:254,a_yi:254,a_yz:254,a_zz:254,aa_i:28,ab_shift:[63,67,244],abandon:0,abbrevi:[71,150,233],abc3:131,abc:[2,44,51,54,101,131,133,138,140,142,144,154,158,167,169,173,178,184,185,198,234,238,246,247,260],abcd:28,abcdefghijklmnopqrstuvwxyz0123456789:250,abcissa:202,abi_extens:185,abi_splitext:185,abicrit:[177,184],abiinput:172,abiinspect:[5,6,165,166],abil:[0,41],abinit:[0,2,5,6,133,145,164,165,267],abinit_build:184,abinitbuild:184,abinitcriticalwarn:172,abiniterror:172,abinitev:[172,177],abinitflow:185,abinithead:176,abinitinput:[173,184,186],abinitio:0,abinitixc_to_libxc:145,abinittask:[173,184,186],abinittim:169,abinittimerpars:[169,173,184,186],abinittimerparsererror:169,abinittimersect:169,abiobject:[5,6,165,166],abiopen:177,abipi:[170,173,175,184,186],abirun:[170,173],abitim:[5,6,165,166],abivalid:173,abivalidate_input:173,abivar:[63,133,140,168],abl:[3,41,58,63,74,137,167,244],abo3:[78,268],abo:[169,184],abo_:184,aborpt:199,abort:[172,180],about:[0,1,21,23,28,34,63,67,69,92,124,136,140,141,145,148,149,153,209,222,226,256],abov:[1,2,3,12,14,18,50,61,67,68,73,78,81,82,141,168,223,247,268],abs:[58,81,131,153,222,244,251,254],abs_cap:254,abs_tol:153,abscissa:202,absenc:193,absent:50,absent_sym:50,absolut:[1,2,28,36,44,45,46,71,78,101,131,136,141,142,144,153,173,175,177,184,185,186,187,199,222,223,236,237,251,254],absorb:[141,164,198,199,200,244],absorbing_atom:[198,199,200],absorbing_el:164,absorpt:[0,141,164,199,200,222,263],absorption_speci:97,abstractchemenvalgorithm:19,abstractchemenverror:27,abstractchemenvstrategi:18,abstractcompar:85,abstractdiffractionpatterncalcul:[44,45,46],abstractdron:[106,107],abstractelectrod:[101,102,103,104],abstracterror:183,abstracterrorpars:183,abstractfeffinputset:200,abstractgeometri:21,abstractmolatommapp:74,abstractratiofunct:30,abstractstructurefilt:[8,9],abstracttransform:[244,245,246,247,248],abstractvoltagepair:[101,102,103],abund:18,ac_:3,acc_err:149,acc_factor:[53,55],acc_thr:149,acceler:266,accept:[1,10,133,152,153,168,173,177,178,181,184,186,204,217,222,234,246,247,251,255],acceptor:37,access:[0,26,69,161,164,173,178,180,185,209,213,218,221,222,247,253],accommod:100,accomod:141,accord:[12,19,48,50,51,52,67,69,76,78,79,80,81,92,130,137,140,142,148,149,169,176,178,184,204,207,211,222,232,236,254],accordingli:[47,75,141],account:[0,1,19,36,41,42,46,69,71,92,133,135,140,141,148,149,150,173,186,222,232,236,251,252],accur:[0,63,64,71,149,164,222,223,244,246],accuraci:[0,55,149,170,178,223,227,246,247],acel:[133,168],acet:61,achiev:[142,149,173,219,247],acid:161,acknowledg:[2,75,222,266],aconvasp:[3,122],aconvasp_cal:[3,5,6,121],aconvasperror:122,acoust:[80,232],across:[58,69,78,101,102,103,131,200,223],acs:[21,41,71,81,162],act:[84,136],acta:[19,63,69,133],actanid:[131,137],actinoid:[131,137],action:[0,2,4,172,177,180],activ:[2,3,73,95,100,152,180,186,255],actual:[0,8,41,42,55,58,60,63,64,67,69,78,100,109,133,137,138,140,141,143,157,162,173,198,201,213,221,222,236,242,246,247,248,260,268],actual_kpoint:222,actual_kpoints_weight:222,adam:133,adap:37,adapt:[1,3,37,54,71,92,173,182,210,255],adaptor:[0,125,189,190,192,268],add:[0,1,3,9,10,12,15,21,23,28,44,50,51,54,55,60,63,64,67,73,78,92,104,131,139,140,141,143,150,151,154,158,164,167,169,173,175,177,185,186,188,192,211,215,217,221,223,227,234,244,246,255,258,263,265,268],add_adsorb:12,add_adsorbate_atom:141,add_bond:265,add_charges_from_oxi_state_guess:131,add_cohp:154,add_cohp_dict:154,add_com:175,add_config_var:116,add_coord_geom:23,add_dens:153,add_dep:177,add_do:[154,234],add_dos_dict:[154,234],add_edg:[64,265],add_electrod:104,add_emptylin:175,add_eq:50,add_error:184,add_fac:265,add_fig_kwarg:[154,255],add_filechild:177,add_flow:175,add_gg_gap:174,add_hydrogen:192,add_label_cycl:167,add_lin:[175,265],add_m_list:55,add_neighbors_set:23,add_opposit:19,add_opt:188,add_oxidation_st:55,add_oxidation_state_by_el:140,add_oxidation_state_by_guess:140,add_oxidation_state_by_sit:140,add_oxidation_state_by_site_fract:15,add_partial_spher:265,add_pick:265,add_picker_fix:265,add_polyhedron:265,add_sit:265,add_site_properti:140,add_sourc:23,add_spectra:263,add_spectrum:263,add_spin_by_el:140,add_spin_by_sit:140,add_strategy_visualization_to_subplot:18,add_subkei:188,add_tag:10,add_text:265,add_triangl:265,addadsorbatetransform:244,addditiona:186,added:[0,2,3,9,23,36,40,42,47,51,61,64,90,101,131,141,154,164,170,173,177,185,186,192,204,211,217,223,234,244,246,259,264,268],added_kpoint:223,adding:[12,61,140,141,184,217,223,244,268],addit:[0,2,3,9,10,18,21,23,29,36,42,54,60,63,64,67,83,91,126,131,132,136,139,140,141,144,157,164,173,176,193,202,204,210,211,223,227,232,244,256,259],addition:[14,223],additional_argu:2,additional_condit:[18,21,23,24,26],additional_info:[18,19],additionalcondit:[18,23,24,29],additionalconditionint:18,addon:92,address:[0,164,266],addsitepropertytransform:246,adengz:0,adf:[0,5,6,165],adf_run:188,adfinput:188,adfinputerror:188,adfkei:188,adfoutput:188,adfoutputerror:188,adftask:188,adjac:[48,58,101,102,103],adjacent_onli:[102,103],adjust:[58,67,69,92,149,156,164,200,207,222],administr:180,adn:3,adopt:[1,2,222],ads_coord:12,ads_entries_dict:92,ads_entry1:92,ads_entry2:92,adsorb:[12,92,141,244],adsorb_both_surfac:12,adsorbatesitefind:[0,12,244],adsorpt:[0,5,6,11,92,141],adsorption_sit:12,adsorptionsitefind:244,adv:223,advanc:[2,3,124,152,156,164,244,266,268],advanced_transform:[3,5,6,243],advantag:[0,2],advis:[37,244,267],aea79f322180fa6f0bfa74cb2a156dcf:223,aecar0:[123,124],aecar2:[123,124],aeccar0:[123,124],aeccar2:[123,124],aeccar:[123,124],affect:[0,140],affin:[136,140],affine_matrix:136,affine_transform:136,affine_transformation_matrix:136,afloat:259,aflow:[0,13,106],aflow_prototyp:[5,6,11],aflowlib:122,aflowprototypematch:13,afm:[71,72,168],afm_:72,afm_struct:72,afresh:69,after:[2,3,9,14,21,36,41,42,47,53,55,63,64,67,85,89,136,137,141,149,154,164,170,177,184,186,187,193,202,222,244,253],afterward:3,ag_sv_gw:223,again:[3,156,164,256],against:[0,37,47,92,130,156,164],agent:[0,164],aggreg:42,agka1:46,agka2:46,agka:46,agkb1:46,agr:95,agte3:81,aid:[1,260],aiida:[0,5,6,165],aiidastructureadaptor:189,aim:[60,73,192,244],aimd:47,ainput:184,ajjackson:0,aka:[60,133],al2o3:164,al3:244,al3sc:39,al_gw:223,al_structur:168,alan:[0,266,267],alarm:180,alat:208,albalu:0,albeit:185,alchemi:[0,2,5,6,246,247,248,260],alexand:253,algebra:41,algo:[0,21,23,55,64,90,133,168,192,223,246,247],algo_:[246,247],algo_best_first:[55,246,247],algo_complet:[55,246,247],algo_enumer:[246,247],algo_fast:[55,246,247],algo_time_limit:55,algorith:168,algorithm:[0,1,8,12,15,19,21,23,40,41,42,45,46,48,50,58,61,63,64,67,69,72,77,78,84,85,88,89,100,123,133,140,141,153,168,170,173,184,192,210,221,222,223,229,230,236,244,246,247,251,266],algorithm_typ:19,alia:[64,69,76,140,144,167,169,172,173,175,176,177,184,221,234],alias:[0,2,145],align:[12,21,28,37,67,76,133,154,198,221,227,259],align_x:67,aligned_lattic:133,aligned_matrix:133,alio_tol:244,alireza:0,alkali:[131,137,223],alkalin:[131,137],all:[0,1,2,3,8,9,10,12,14,15,18,19,21,23,28,29,31,36,37,38,41,42,44,45,46,47,48,50,54,55,56,58,60,61,63,64,67,68,69,71,74,77,78,81,83,85,89,90,91,92,94,95,97,99,100,101,102,103,104,106,124,125,130,131,133,137,138,139,140,141,142,143,144,148,149,150,151,152,153,154,156,157,158,159,161,163,164,167,168,169,173,175,176,177,178,180,182,183,184,185,186,188,192,193,200,201,202,204,2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hyl:61,etot:[167,184],etsf:176,etsf_read:176,eu2:[0,223],eu3:[0,223],eu_2:223,euler:51,ev_to_k:42,ev_to_kj_per_mol:68,eval:[2,222],evalu:[30,38,39,42,50,55,69,81,82,173,185,188,209,210,222],evaluate_rpn:185,evaluate_wavefunc:222,evan:128,even:[0,3,48,59,77,85,101,107,131,140,164,168,184,221,222,238,246,247,251,268],event:[2,5,6,165,166,173,177,180,184,255,256,265],event_class:172,event_handl:177,eventhandl:177,eventreport:172,eventspars:172,eventsparsererror:172,eventu:[14,141],everi:[2,9,41,47,84,124,133,149,175,177,183,185,186,205,209,222],everyth:[1,148,268],evolut:[78,167,173,184],ewald:[0,1,5,6,11,37,42,53,244,246,247,268],ewaldelectrostaticmodel:53,ewaldminim:55,ewaldpap:55,ewaldsum:53,ewaldsumm:[0,53,55],ex_mat:72,ex_param:[72,128],exact:[8,74,75,85,140,141,158,221,223,238],exactdens:188,exactli:[0,63,85,141,149,168,221,247],exaf:[139,198,199,200],exampl:[0,1,3,8,9,10,15,21,34,36,41,47,48,55,58,64,69,74,78,83,84,85,87,92,93,94,100,101,102,103,106,109,130,131,133,136,137,139,140,141,144,145,149,150,153,154,156,157,158,160,164,168,169,171,173,177,178,185,186,200,202,205,210,213,217,218,220,221,222,223,225,236,240,244,246,247,251,255,256,262,263,265],exc:172,exc_dft_opt:201,exc_info:177,exc_typ:168,exce:[85,244],exceed:[180,183],excel:[0,123,236,266],except:[0,1,27,42,51,54,64,69,77,78,83,85,89,122,125,126,131,136,137,140,144,149,153,156,164,167,169,172,175,177,180,185,186,188,193,198,210,213,218,221,222,223,236,250],exception:89,exception_on_bad_xml:222,excess:37,exchamiltonian:168,exchang:[0,64,71,72,128,134,145,168,170,188,200,210],exchange_const:64,excit:[5,6,11,165,199,201,202,210],excitationspectrum:[56,210],excitinginput:196,exclud:[8,21,37,42,78,80,140,141,156,173,178,183,207,265],exclude_dir:[173,178],exclude_ext:173,exclude_nod:[183,184],exclude_ok_task:173,exclude_wildard:186,exclude_wildcard:186,excluded_atom:21,excluded_bonding_el:265,exclus:[145,173,177],exe:3,exec_arg:184,execut:[3,8,123,124,126,128,150,161,172,173,175,180,184,187,208,253,260],execwrapp:187,exelf:200,exercis:222,exhf:222,exist:[0,2,3,8,19,21,23,37,38,41,42,47,50,54,64,71,75,77,78,81,85,89,130,140,141,151,152,154,173,177,178,184,185,186,188,200,205,208,221,250,255,268],existing_structur:8,exit:[77,173,175,180,184,185,222],exitcod:180,exp:[42,46,47,50,164,211,222],exp_cos_aa:69,exp_entri:[5,6,155],expand:[0,1,3,63,174,186,244],expand_tim:[63,244],expans:[50,137,142],expect:[1,3,8,28,39,47,63,69,73,94,126,137,144,152,153,179,223,236,237,244],expected_charg:14,expens:[0,55,222,247],expentri:[159,164],experi:[3,205],experiment:[15,21,69,78,93,154,159,164,173,233,244,247],exphp:0,expir:180,explain:[0,149,154,156],explan:[0,63,131,154,156,164,180,268],explicit:[18,21,167,168,177,186,192,221,222],explicit_indic:21,explicit_optimized_permut:19,explicit_path:168,explicit_permut:19,explicitli:[1,48,69,180],explicitpermutationsalgorithm:19,explictli:28,explor:[2,42,124,268],expnorm:42,expon:[69,149],exponenti:[42,250],export_envar:175,export_msdt:47,expr:50,express:[2,28,50,58,133,142,183,184,185,186,218,222],expression1:185,expression2:185,expressionn:185,exsit:188,ext:[0,5,6,169,173,177,178,185,186,268],extend:[9,10,12,34,42,50,52,76,77,131,136,139,140,143,153,157,159,173,176,184,200,217,233,244,260,268],extend_collect:10,extend_structur:64,extend_transform:[9,10],extens:[0,2,3,47,64,95,106,137,138,140,154,159,169,173,177,178,184,185,186,201,207,222,268],extern:[0,3,160,177,180,221,256,258],extra:[2,38,41,71,76,100,168,170,185,212,222,227,250,264],extra_abivar:170,extra_nn_info:69,extract:[0,3,9,63,64,67,71,72,140,141,149,167,169,172,184,211,222,234,244,268],extract_clust:140,extract_metadata:183,extracted_vasp_potcar:3,extrapol:[47,153],extrapolate_reciproc:250,extrapolate_simple_reciproc:250,extras_requir:2,extrem:[0,2,40,55,63,90,140,154,164,222,223,234,238,246,247,263,268],extrema:[42,94,149],extrema_coord:42,extrema_df:42,extremum_icohpvalu:151,extrins:[100,101],eye:[133,168],f1d01e845dccc52d448679911f301a73:223,f4ff16a495dd361ff5824ee61b418bb0:223,f_1:[152,154],f_2:[152,154],f_3:[152,154],f_constant:202,f_gw:223,f_h:223,f_j:46,f_lower:28,f_upper:28,f_x:153,f_xyz:153,f_xz:153,f_y:153,f_yz:153,f_z:153,fac_aa:69,face:[12,19,69,84,91,227,265],face_dist:69,faces_color_overrid:32,facet:[19,21,28,44,46,69,78,84,91,92,95,133,251],facili:181,facilit:[154,173,177,234],facmaxdl:42,fact:[2,69,148,232,268],factor:[0,15,21,31,36,42,45,46,47,63,69,81,83,91,95,131,133,140,141,142,144,149,150,154,208,211,222,223,234,247,265],factori:[51,167,170,183],faghaninia:0,fail:[0,1,3,8,38,60,64,82,137,153,173,180,183,184,221],failur:[0,180,183],fairli:[1,2,3,64,236,265],faith:240,fake:[150,169],fall:[78,133,140,244,265],fallback:21,fallback_to_sourc:18,fals:[0,8,9,10,12,14,18,19,21,23,28,31,32,37,38,40,41,42,44,45,46,47,48,50,51,54,55,58,60,61,63,64,67,68,69,71,73,77,78,81,82,84,85,87,88,89,90,91,92,94,95,101,102,106,123,124,125,126,128,131,133,135,136,138,140,141,142,143,148,149,150,151,153,154,156,158,164,167,168,169,172,173,174,177,178,182,183,184,1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,206,207,208,209,210,211,212,213,218,221,222,223,232,234,236,238,244,245,246,247,248,250,251,254,255,259,265,266,268],generate_adsorption_structur:12,generate_all_slab:141,generate_defect_structur:36,generate_displac:211,generate_entry_label:81,generate_full_symmop:236,generate_interfac:67,generate_potcar:118,generate_pseudo:50,generate_r_and_g_vec:42,generate_reciprocal_vectors_squar:42,generate_sl_transformation_set:91,generate_substitution_structur:12,generate_surface_vector:91,genfmt:198,genom:[2,6,266],genrecip:42,geo_subkei:188,geoffroi:[0,2,21,237,267],geograph:66,geom:205,geom_opt_max_cycl:217,geometr:[69,74,77,100,266],geometri:[0,19,21,23,51,60,91,188,192,202,210,217,266],geometrically_equidist:18,geometry_info:18,geometry_opt:210,geometryoptim:188,geomstep:192,georg:[149,150],gerbrand:[2,77],germain:[0,154,267],get:[0,3,6,12,13,15,18,23,34,36,37,38,41,42,47,48,50,51,58,63,67,68,69,72,73,74,78,81,82,87,92,95,101,103,122,123,126,130,131,133,137,138,140,141,142,149,150,151,152,153,154,162,163,164,171,173,177,179,180,184,186,193,199,202,208,209,221,222,223,233,234,236,241,244,246,247,251,256,259,263,268],get_00t_magmom_with_xyz_saxi:152,get_13_bond:75,get_absorbing_atom_symbol_index:198,get_adjusted_fermi_level:222,get_all_anonymous_map:85,get_all_chempot:78,get_all_dist:133,get_all_entri:103,get_all_functional_group:61,get_all_neighbor:[0,140],get_all_neighbors_old:140,get_all_nn:69,get_all_nn_info:69,get_all_sit:69,get_all_statu:186,get_all_substr:164,get_all_voronoi_polyhedra:69,get_allowed_speci:89,get_alpha:222,get_analysi:73,get_analysis_and_structur:73,get_angl:[140,251],get_arrhenius_plot:47,get_asum_fcm:80,get_atom:190,get_atom_map:198,get_atomic_fract:[2,131],get_available_model:162,get_average_along_axi:222,get_average_eff_mass:149,get_average_voltag:101,get_ax3d_fig_plt:255,get_ax_fig_plt:255,get_axarray_fig_plt:255,get_axis_grid:222,get_band_gap:148,get_band_structur:[150,222],get_band_structure_from_vasp_multiple_branch:222,get_bandstructur:209,get_bandstructure_by_material_id:[164,268],get_basic_functional_group:61,get_bec_oper:80,get_best_electronegativity_anonymous_map:85,get_bibtex_str:193,get_bond_length:130,get_bond_ord:130,get_bonded_structur:[0,48,69,87],get_box_shift:204,get_boxed_structur:140,get_branch:[148,232],get_brillouin_zon:133,get_capacity_grav:101,get_capacity_vol:101,get_carrier_concentr:149,get_cart_coord:202,get_cartesian_coord:133,get_cbm:148,get_cbm_vbm:153,get_celldm:213,get_center_of_arc:31,get_centered_molecul:140,get_central_sit:19,get_charg:123,get_charge_transf:123,get_chempot_correct:68,get_chempot_range_map:[78,92],get_chempot_range_map_plot:78,get_chempot_range_stability_phas:78,get_chgint_plot:117,get_children:177,get_chunk:257,get_cluster_graph:185,get_cn:69,get_cn_dict:69,get_cod_id:161,get_coeff:83,get_cohesive_energi:164,get_cohp:151,get_cohp_by_label:151,get_cohp_dict:154,get_collect:[171,184],get_complete_do:149,get_complete_ph_do:211,get_complexity_factor:149,get_compliance_expans:50,get_composition_chempot:78,get_compound_pd:78,get_computed_entri:222,get_conduct:149,get_connect:84,get_connected_sit:64,get_consistent_set:152,get_consistent_set_and_saxi:152,get_contour_pd_plot:78,get_conv_struct:122,get_conventional_standard_structur:236,get_conventional_to_primitive_transformation_matrix:236,get_conversion_factor:[47,144],get_coordinating_elements_cn:42,get_coordination_environ:23,get_coordination_numb:19,get_coordination_of_sit:64,get_coordination_symmetry_measur:21,get_coordination_symmetry_measures_optim:21,get_correct:[36,37,156],get_corrections_dict:156,get_cost_per_kg:34,get_cost_per_mol:34,get_covalent_bond:140,get_critical_composit:78,get_critical_original_kink_ratio:68,get_critical_point_for_sit:124,get_crystal_field_spin:137,get_crystal_system:236,get_csm:23,get_csm_and_map:23,get_d:141,get_data:[107,164,268],get_datafram:169,get_decomp_and_e_above_hul:78,get_decomposit:78,get_decomposition_energi:81,get_default_basis_set:188,get_default_geo:188,get_default_scf:188,get_default_unit:188,get_default_xc:188,get_defectsite_multipl:42,get_deformation_matrix:51,get_delta_etim:175,get_dens:153,get_deriv:250,get_dict_for_mongodb_queri:173,get_diff_coeff:50,get_dihedr:140,get_dimension:0,get_dimensionality_cheon:48,get_dimensionality_gorai:48,get_dimensionality_larsen:48,get_direct_band_gap:148,get_direct_band_gap_dict:148,get_displaced_structur:211,get_dist:140,get_distance_and_imag:133,get_do:150,get_doc:[164,209],get_dop:153,get_dopability_limit:41,get_dopants_from_shannon_radii:87,get_dopants_from_substitution_prob:87,get_dos_by_material_id:[164,268],get_dos_dict:[154,234],get_dos_plot:117,get_drift_corrected_structur:47,get_e_above_hul:[0,78],get_effective_csm:18,get_effective_ec:50,get_el_amount:83,get_el_amt_dict:131,get_el_sp:137,get_element_do:[153,233,234],get_element_fract:81,get_element_profil:78,get_element_spd_do:153,get_elements_between_band:222,get_elt_projected_plot:154,get_elt_projected_plots_color:154,get_energi:[53,112,115,126,131],get_energy_buckingham:126,get_energy_dens:101,get_energy_relax_structure_buckingham:126,get_energy_tersoff:126,get_entri:[0,34,164],get_entries_in_chemsi:[0,164,268],get_entry_by_material_id:164,get_environ:[5,6,108],get_environments_figur:23,get_equilibrium_reaction_energi:78,get_equiv_transform:91,get_equivalent_atom:236,get_equivalent_kpoint:148,get_equivalent_qpoint:232,get_event_handler_class:172,get_exchang:72,get_exchange_group_info:71,get_excitation_spectrum:210,get_exp_entri:164,get_exp_thermo_data:164,get_explanation_dict:156,get_extended_surface_mesh:12,get_extrapolated_conduct:47,get_extrapolated_diffus:47,get_extrem:149,get_extrema:94,get_facet:78,get_factor:91,get_fcm_oper:80,get_fermi:153,get_fermi_interextrapol:[0,153],get_ferromagnetic_structur:71,get_filepaths_and_ext:177,get_film_indic:67,get_final_structur:184,get_form_energi:78,get_form_energy_per_atom:78,get_frac_coords_from_ll:133,get_fract:131,get_fractional_coord:133,get_framework_rms_plot:[0,47],get_free_sphere_param:227,get_from_hint:21,get_gap:153,get_gb_data:164,get_geometri:19,get_geometry_from_iucr_symbol:19,get_geometry_from_iupac_symbol:19,get_geometry_from_mp_symbol:19,get_geometry_from_nam:19,get_ggt:50,get_graphviz:173,get_graphviz_dirtre:177,get_grouped_indic:142,get_gruneisen_paramet:50,get_hal:236,get_hall_carrier_concentr:149,get_hash:85,get_heat_capac:50,get_heteroatom:61,get_high_accuracy_voronoi_nod:227,get_hull_energi:[78,81],get_icohp:151,get_icohp_by_label:151,get_icohp_dict_by_bondlength:151,get_icohp_dict_of_sit:151,get_ieee_rot:142,get_implemented_geometri:19,get_info:180,get_integer_formula_and_factor:131,get_integer_index:133,get_integrated_diff:222,get_interaction_graph:72,get_interface_react:164,get_interpolated_gap:153,get_interpolated_valu:[139,151,153,233],get_ir_mesh:0,get_ir_reciprocal_mesh:236,get_ist_oper:80,get_kink:68,get_kpoint:[163,223,237],get_kpoint_degeneraci:148,get_kpoint_weight:236,get_label:92,get_lattic:193,get_lattice_quanta:58,get_lattice_typ:236,get_lattvec:150,get_lin:198,get_line_in_facet:95,get_linear_interpolated_valu:251,get_linearly_independent_vector:31,get_lll_frac_coord:133,get_lll_reduced_lattic:133,get_local_extrema:42,get_local_order_paramet:69,get_locpot_along_slab_plot:92,get_low_energy_ord:72,get_lower_and_upper_f:28,get_lowest_decomposit:34,get_magnet:115,get_magnitude_of_effect_from_speci:73,get_magnitude_of_effect_from_spin_config:73,get_magsymop:193,get_map:85,get_mass:144,get_materials_id:164,get_materials_id_from_task_id:164,get_materials_id_refer:[0,164],get_max_bond_dist:69,get_max_bond_length:84,get_max_capgrav:100,get_max_capvol:100,get_max_inst:103,get_max_muo2:103,get_mdf_robot:186,get_messag:177,get_mft_temperatur:72,get_mi_vec:12,get_miller_index_from_coord:133,get_miller_index_from_site_index:140,get_min_inst:103,get_min_muo2:103,get_minkowski_r:122,get_molecule_hash:74,get_moment:152,get_moment_relative_to_crystal_ax:152,get_mongo_info:173,get_monolay:92,get_motif_typ:42,get_mp_structur:260,get_msd_plot:47,get_mu_bound:149,get_multipl:36,get_nac_eigendisplacements_along_dir:232,get_nac_frequencies_along_dir:232,get_nam:19,get_nearest_sit:58,get_neighb_voronoi_indic:23,get_neighbor:140,get_neighbors_in_shel:140,get_neighbors_of_site_with_index:69,get_neighbors_old:140,get_newnode_id:177,get_next_index:55,get_niggli_reduced_lattic:133,get_njobs_in_queu:[173,184],get_nmr_quadrupole_mo:137,get_nn:69,get_nn_data:69,get_nn_imag:69,get_nn_info:69,get_nn_shell_info:69,get_no_mixing_energi:68,get_nod:180,get_nonmagnetic_structur:71,get_noppmodel:168,get_not_implemented_geometri:19,get_num_division_kpoint:122,get_occup:222,get_okeeffe_distance_predict:69,get_okeeffe_param:69,get_op_valu:42,get_orbital_derivative_between_st:222,get_orbital_resolved_cohp:151,get_order_paramet:69,get_ordered_with_polici:184,get_oriented_slab:67,get_ortho_ax:67,get_orthogonal_c_slab:141,get_oxi_state_decorated_structur:15,get_oxidation_state_decorated_structur:123,get_par:177,get_paramet:69,get_parchg:222,get_pars:183,get_partial_dos:150,get_pattern:[44,45,46],get_pelecs_and_pion:58,get_percentage_bond_dist_chang:84,get_percentage_lattice_parameter_chang:84,get_percentage_volume_chang:84,get_perturbed_indic:51,get_ph_bs_symm_lin:211,get_ph_bs_symm_line_from_dict:211,get_ph_do:211,get_phonon_bandstructure_by_material_id:164,get_phonon_ddb_by_material_id:164,get_phonon_dos_by_material_id:164,get_phonon_frequ:222,get_phonopy_structur:211,get_piezo:80,get_plot:[44,78,94,95,104,154,234,263],get_plot_data:104,get_pmesh:19,get_pmg_structur:211,get_point_group_oper:236,get_point_group_symbol:236,get_pointgroup:236,get_points_in_spher:133,get_points_in_sphere_old:133,get_polarization_chang:58,get_polarization_change_norm:58,get_potcar:222,get_potcar_hash:221,get_potential_shift:37,get_pourbaix_domain:81,get_pourbaix_entri:164,get_pourbaix_plot:81,get_power_factor:149,get_predicted_structur:90,get_prim_struct:122,get_primitive_standard:0,get_primitive_standard_structur:[236,237],get_primitive_structur:140,get_product:68,get_projected_plots_dot:154,get_projected_plots_dots_patom_pmorb:154,get_projection_on_el:[148,222],get_projections_on_elements_and_orbit:148,get_prototyp:13,get_pseudos_for_structur:178,get_q2:69,get_q4:69,get_q6:69,get_rand_bec:80,get_rand_fcm:80,get_rand_ist:80,get_ratio:63,get_rdf_figur:24,get_react:164,get_real_summ:37,get_reasonable_repetit:232,get_recip_summ:37,get_reconstructed_band_structur:148,get_recp_symmetry_oper:133,get_reduced_composition_and_factor:131,get_reduced_formula_and_factor:131,get_reduced_structur:140,get_refined_structur:236,get_relaxed_structur:126,get_removals_int_oxid:100,get_result:[173,177,184],get_rms_anonym:85,get_rms_dist:85,get_rmsd:74,get_rot:12,get_rotation_angle_from_sigma:[63,244],get_s2_like_s1:85,get_sadf_figur:24,get_same_branch_polarization_data:58,get_scal:142,get_scan_plot:202,get_scissors_build:184,get_script_str:175,get_sect:169,get_seebeck:149,get_seebeck_eff_mass:149,get_self_interact:37,get_set:0,get_shannon_radiu:137,get_shared_symmetry_oper:241,get_shear_reduced_slab:67,get_site_ce_fractions_and_neighbor:18,get_site_coordination_environ:18,get_site_coordination_environments_fract:18,get_site_do:[153,233],get_site_energi:55,get_site_info_for_specie_allc:23,get_site_info_for_specie_c:23,get_site_neighbor:18,get_site_orbital_do:153,get_site_spd_do:153,get_site_symmetri:241,get_site_t2g_eg_resolved_do:153,get_sitej:84,get_sites_in_spher:140,get_slab:141,get_slab_region:141,get_smeared_dens:[153,233],get_sorted_structur:[0,63,67,140,141],get_space_group_info:140,get_space_group_numb:236,get_space_group_oper:236,get_space_group_symbol:236,get_spacegroup_symbol:2,get_spd:[154,263],get_spd_do:[153,154],get_special_carbon:61,get_specific_energi:101,get_spectre_plot:202,get_stability_criteria:50,get_stabl:[0,164],get_stable_entri:[81,103],get_stable_entry_at_u:92,get_stable_fcm:80,get_stat:[180,185],get_statist:23,get_str:[143,198,204,208,221,222],get_strain_from_stress:50,get_strain_state_dict:50,get_structur:[0,21,143,164,190,193,260,268],get_structure_by_formula:161,get_structure_by_id:161,get_structure_by_material_id:[164,268],get_structure_compon:48,get_structure_from_dict:211,get_structure_from_mp:[0,2,6],get_structure_from_prev_run:223,get_structure_property_dict:50,get_structure_with_charg:209,get_structure_with_nod:42,get_structure_with_only_magnetic_atom:71,get_structure_with_spin:71,get_sub_electrod:[102,103],get_subgraphs_as_molecul:64,get_subset_in_chemsi:158,get_substr:164,get_suggested_saxi:152,get_summary_dict:[47,67,82,102],get_summed_cohp_by_label_and_orbital_list:151,get_summed_cohp_by_label_list:151,get_summed_icohp_by_label_list:151,get_supercell_matrix:85,get_surface_data:164,get_surface_equilibrium:92,get_surface_sit:141,get_sym_eq_kpoint:148,get_symbol_cn_map:19,get_symbol_dict:142,get_symbol_list:50,get_symbol_name_map:19,get_symm_band:149,get_symmetric_sit:141,get_symmetric_wallace_tensor:50,get_symmetrically_distinct_miller_indic:141,get_symmetrically_equivalent_miller_indic:141,get_symmetrized_fcm:80,get_symmetrized_structur:[236,242],get_symmetry_dataset:236,get_symmetry_oper:[0,236],get_symop:193,get_task_data:164,get_task_scfcycl:173,get_tasker2_slab:141,get_tgt:50,get_thermal_conduct:149,get_tick:[154,234],get_total_ionic_dipol:58,get_trans_mat:63,get_transform:85,get_transition_chempot:78,get_tri_area:95,get_typ:69,get_unique_famili:44,get_unit_primitive_area:92,get_unreconstructed_slab:141,get_unstable_entri:103,get_unstable_fcm:80,get_uvec:142,get_v:77,get_val:15,get_valid_path:106,get_valu:169,get_vars_datafram:177,get_vasp_input:[0,9,223],get_vasp_kpoint_file_sym:122,get_vasprun_outcar:223,get_vbm:148,get_vector_along_lattice_direct:[0,133],get_void_volume_surfarea:227,get_voigt_dict:142,get_volum:150,get_voronoi_nod:227,get_voronoi_polyhedra:69,get_wallace_tensor:50,get_weight:250,get_weights_of_nn_sit:69,get_wigner_seitz_cel:133,get_wt_fract:131,get_wulff_shap:164,get_xas_data:164,get_xrd_plot:[0,117],get_xyz_magmom_with_001_saxi:152,get_yield_stress:50,get_z_ordered_elmap:15,get_zmatrix:202,get_zt:149,getmessag:177,getmu_vertices_stability_phas:78,getsiz:185,gfactor:219,gflop:169,gfortran:[3,116],gfortranbinari:3,gga:[0,2,15,21,37,41,77,134,145,156,164,221,222,223,247,266],gga_c_am05:[134,145],gga_c_apb:134,gga_c_bgcp:134,gga_c_ft97:134,gga_c_gam:134,gga_c_hcth_a:134,gga_c_lm:134,gga_c_lyp:[134,145],gga_c_n12:134,gga_c_n12_sx:134,gga_c_op_b88:134,gga_c_op_g96:134,gga_c_op_pb:134,gga_c_op_pw91:134,gga_c_op_xalpha:134,gga_c_optc:134,gga_c_p86:134,gga_c_pb:[134,145],gga_c_pbe_jrgx:134,gga_c_pbe_sol:[134,145],gga_c_pbef:134,gga_c_pbeint:134,gga_c_pbeloc:134,gga_c_pw91:[134,145],gga_c_q2d:134,gga_c_regtpss:134,gga_c_revtca:134,gga_c_rge2:134,gga_c_sogga11:134,gga_c_sogga11_x:134,gga_c_spb:134,gga_c_tca:134,gga_c_wi0:134,gga_c_wi:134,gga_c_wl:134,gga_c_xpb:134,gga_c_zpbeint:134,gga_c_zpbesol:134,gga_k_absp1:134,gga_k_absp2:134,gga_k_apb:134,gga_k_apbeint:134,gga_k_baltin:134,gga_k_dk:134,gga_k_ernzerhof:134,gga_k_fr_b88:134,gga_k_fr_pw86:134,gga_k_ge2:134,gga_k_golden:134,gga_k_gp85:134,gga_k_gr:134,gga_k_lc94:134,gga_k_lieb:134,gga_k_llp:134,gga_k_ludena:134,gga_k_mey:134,gga_k_ol1:134,gga_k_ol2:134,gga_k_pearson:134,gga_k_perdew:134,gga_k_revapb:134,gga_k_revapbeint:134,gga_k_tfvw:134,gga_k_thakkar:134,gga_k_tw1:134,gga_k_tw2:134,gga_k_tw3:134,gga_k_tw4:134,gga_k_vjk:134,gga_k_vsk:134,gga_k_vw:134,gga_k_yt65:134,gga_relax:21,gga_x_2d_b86:134,gga_x_2d_b86_mgc:134,gga_x_2d_b88:134,gga_x_2d_pb:134,gga_x_airi:134,gga_x_ak13:134,gga_x_am05:[134,145],gga_x_apb:134,gga_x_b86:134,gga_x_b86_mgc:134,gga_x_b86_r:134,gga_x_b88:[134,145],gga_x_bayesian:134,gga_x_bgcp:134,gga_x_bpccac:134,gga_x_c09x:134,gga_x_cap:134,gga_x_dk87_r1:134,gga_x_dk87_r2:134,gga_x_ev93:134,gga_x_ft97_a:134,gga_x_ft97_b:134,gga_x_g96:134,gga_x_gam:134,gga_x_hcth_a:134,gga_x_herman:134,gga_x_hjs_b88:134,gga_x_hjs_b88_v2:134,gga_x_hjs_b97x:134,gga_x_hjs_pb:134,gga_x_hjs_pbe_sol:134,gga_x_htb:134,gga_x_ityh:134,gga_x_kt1:134,gga_x_lag:134,gga_x_lambda_ch_n:134,gga_x_lambda_lo_n:134,gga_x_lambda_oc2_n:134,gga_x_lb:134,gga_x_lbm:134,gga_x_lg93:134,gga_x_lv_rpw86:134,gga_x_mb88:134,gga_x_mpb:134,gga_x_mpw91:134,gga_x_n12:134,gga_x_ol2:134,gga_x_optb88_vdw:134,gga_x_optpbe_vdw:134,gga_x_optx:134,gga_x_pb:[134,145],gga_x_pbe_jsjr:134,gga_x_pbe_mol:134,gga_x_pbe_r:[134,145],gga_x_pbe_sol:[134,145],gga_x_pbe_tca:134,gga_x_pbea:134,gga_x_pbef:134,gga_x_pbeint:134,gga_x_pbek1_vdw:134,gga_x_pw86:134,gga_x_pw91:[134,145],gga_x_q2d:134,gga_x_rge2:134,gga_x_rpb:[134,145],gga_x_rpw86:134,gga_x_sfat:134,gga_x_sogga11:134,gga_x_sogga:134,gga_x_ssb:134,gga_x_ssb_d:134,gga_x_ssb_sw:134,gga_x_vmt84_g:134,gga_x_vmt84_pb:134,gga_x_vmt_g:134,gga_x_vmt_pb:134,gga_x_wc:134,gga_x_wpbeh:134,gga_x_xpb:134,gga_xc_b97_d:134,gga_xc_b97_gga1:134,gga_xc_edf1:134,gga_xc_hcth_120:134,gga_xc_hcth_147:134,gga_xc_hcth_407:134,gga_xc_hcth_407p:134,gga_xc_hcth_93:134,gga_xc_hcth_p14:134,gga_xc_hcth_p76:134,gga_xc_kt2:134,gga_xc_mohlyp2:134,gga_xc_mohlyp:134,gga_xc_mpwlyp1w:134,gga_xc_oblyp_d:134,gga_xc_opbe_d:134,gga_xc_opwlyp_d:134,gga_xc_pbe1w:134,gga_xc_pbelyp1w:134,gga_xc_th1:134,gga_xc_th2:134,gga_xc_th3:134,gga_xc_th4:134,gga_xc_th_fc:134,gga_xc_th_fcfo:134,gga_xc_th_fco:134,gga_xc_th_fl:134,gga_xc_vv10:134,gga_xc_xlyp:134,ggk:187,ggt:50,ghemic:192,ghost_sit:141,gian:21,giantomassi:[0,267],gibb:[0,78,81,82,92,149,154,202],gibbs_binding_energi:92,gin:126,git:[0,1,3],github:[0,2,4,95,124,162,164,180,232],gitlab:150,give:[0,2,13,28,34,36,41,55,58,63,64,69,71,73,77,78,85,90,91,92,100,122,124,126,131,149,150,152,153,154,164,172,173,185,208,209,222,236,244,251,252,268],give_only_index:236,given:[0,1,2,3,8,12,13,14,15,18,19,21,23,24,28,31,34,36,37,38,41,42,45,46,47,48,50,53,55,58,60,63,64,67,68,69,71,73,77,78,81,82,83,84,85,87,88,89,90,91,92,94,95,100,101,103,122,123,124,130,131,133,136,137,138,140,141,142,143,148,149,150,151,152,153,154,156,158,162,164,168,169,170,171,172,173,178,181,184,185,186,188,198,202,205,209,217,221,222,223,227,229,230,232,234,236,237,240,244,246,247,251,254,258,259,263,266,268],gjf:[2,140,268],gkk:[184,187],gkk_file:187,gkk_filepath:184,gkk_node:184,gkkpwork:186,glaum:21,global:[0,2,152,192,244],global_mo:152,gmail:[164,256],gmatteo:[0,54],gmolecul:188,gnu:3,gnuplot:[39,250],goal:[141,180],godbi:[168,170],goe:[46,198,200,253],goebel:21,going:[2,3,19,89,140,164,268],golden:[54,255],gonz:[21,149],good:[3,47,60,64,77,85,89,136,141,169,223,268],good_sect:169,googl:2,googlecod:176,gorai:48,gout:126,gov:[3,137,227],govern:184,gowoon:48,gpa:[54,82],gpa_to_ev_a3:50,gpaw:145,gpoint:222,gpretto:0,grab:[0,2],grad:124,gradep:124,gradient:[51,52,76,77,124,168,188,192,210,222,223,247],gradual:13,graef:[45,46,238],grain:[0,5,6,11,62,164,223,244,268],grain_label:63,grainboundari:63,grainboundarygener:63,grainboundarytransform:[0,244],gramschmidt:69,grand:[0,68,78,92,266],grandpotentialphasediagram:[0,68,78],grandpotpdentri:78,grant:2,granular:47,graph:[0,3,5,6,11,47,48,60,61,69,72,87,124,128,154,162,173,177,185,234],graph_attr:[173,185],graph_data:64,graph_dict:64,graphic:[2,78,154],graphit:260,graphviz:[3,64,173,177,185],graphviz_imshow:173,grav:100,gravimetr:101,grazuli:161,great:95,greater:[0,2,38,69,107,131,140,164,175,185,233],greatest:[31,131],greatli:[2,158],greedi:153,green:[50,51,64,154,168,259],green_kristoffel:50,green_lagrange_strain:51,grei:[255,265],grep:[0,213,218,222,223],grid:[0,18,23,37,42,44,54,77,124,149,153,154,167,168,169,173,178,185,201,209,213,219,221,222,223,234,236],grid_off:95,gridf:177,gridfs_fil:177,gridfsfil:177,gridspec_kw:255,grip:2,gross:133,grosspop:[0,209],ground:[0,68,72,91,128,137,158,164,167,184,186,187],ground_state_energi:91,ground_state_term_symbol:137,groundstatescfcycl:167,group:[0,2,3,5,6,10,13,19,21,28,36,42,47,48,58,61,64,71,74,85,94,124,131,133,137,140,141,142,158,164,169,173,176,193,198,204,208,218,222,223,235,236,239,240,241,247,266,268],group_array_indic:142,group_by_typ:140,group_entries_by_structur:158,group_molecul:74,group_structur:[0,85],groupby_statu:173,groupby_task_class:173,grow:2,growth:91,gruneisen:[50,82],gruneisen_paramet:82,gsr:[177,184,186],gstask:184,gswfk_file:187,guarante:[0,2,56,64,71,97,139,141,219,236,246,247,268],guard:164,guess:[0,3,47,58,60,71,90,131,140,204,247,250,268],guess_el:204,guesstim:73,guesstimate_spin:73,gui:173,guid:[0,3,58,268],guidanc:164,guidelin:[0,2,3],guido:[0,185],gulp:[0,3,53,55,126,225,227],gulp_cal:[0,3,5,6,121],gulp_cmd:126,gulpcal:126,gulpconvergenceerror:126,gulperror:126,gulpio:126,gunter:[2,266,267],gvallver:154,gvallverdu:0,gw_fiesta:201,gw_option:201,gw_qprang:168,gwcalctyp:168,gweight:18,gwpara:168,gzip:[0,107,123,124,193],h2o2:131,h2o:[81,156],h_gw:223,h_node:256,habit:184,had:[0,36,55,149],haeberlen:76,haeberlen_valu:76,haeberlennot:76,hafner:39,half:[0,85,141,202],halfspac:41,halfspaceinterect:41,halfspaceintersect:81,halit:141,halite_111_octopolar_2x2:141,hall:[149,150,154,161,236],hall_carrier_conc_trac:150,hall_carrier_conc_trace_mu:150,hall_dop:149,hallten:149,halogen:[131,137],halogen_list:75,hamilton:[0,151,154],hamiltonian:[71,72,168],hammer:145,hand:[3,106],handi:167,handl:[0,1,2,48,92,150,151,152,172,175,191,205,209,215,236],handle_input_ev:172,handle_task_ev:172,handler:[172,177,180,182],hangup:180,hanmei:0,hanmeitang:0,hansen:145,hanson:13,happen:[36,42,69],haranczyk:[40,42,266],hard:[73,137,173,204,246,247],hardwar:[180,183],harmon:82,harri:76,hart:[0,3,13,246],hartre:[167,168,178,186,210,222],hartree_paramet:174,has:[0,1,2,3,9,21,23,24,38,41,47,50,54,55,58,60,63,67,69,71,78,80,81,83,92,101,106,124,133,136,137,140,141,142,145,149,150,152,154,164,172,173,175,177,178,180,184,186,188,198,202,205,210,212,221,222,223,230,232,236,244,258,268],has_abiext:185,has_antibnd_states_below_efermi:151,has_chroot:173,has_db:[173,184],has_dojo_report:178,has_eigendisplac:232,has_error:193,has_good_quality_check_occupied_band:209,has_good_quality_maxdevi:209,has_hint:178,has_imaginary_freq:232,has_intersect:18,has_materials_project_access:26,has_mpi:184,has_mpiio:184,has_nac:[211,232],has_netcdf:184,has_node_failur:180,has_omp:184,has_opt:188,has_queu:184,has_schedul:173,has_subkei:188,hash:[0,74,85,137,142,156,178,221,222,223],hashabl:[74,85,131,138,140,145,177],hasn:221,hautier:[0,2,21,78,88,89,149,223,266,267],have:[0,1,2,3,8,12,14,15,21,23,36,38,41,47,48,51,53,55,58,59,60,61,63,64,67,69,71,73,75,77,78,84,85,87,91,92,94,95,100,101,102,103,106,107,121,122,126,131,135,137,138,140,141,142,143,144,148,149,152,153,154,156,157,164,167,169,173,176,177,178,180,183,184,185,186,188,192,204,209,211,219,221,222,223,227,234,236,242,244,245,246,247,248,251,253,259,260,266,268],have_consistent_saxi:152,have_equivalent_surfac:141,haven:[0,55,173],haydock:168,hbar:[42,50],hcp:[69,95,247],hdf5:[0,222],he_bcc:260,he_gw:223,head:207,headach:223,header:[0,3,163,176,193,198,199,200,208,212,218,222,225,259],header_pattern:[218,222],header_str:198,header_string_from_fil:198,heat:[50,233,234,255],heatmap:255,heavi:[0,164,268],heavier:157,heavili:268,hedin:221,height:[12,54,69,104,154,244,255],heisenberg:[0,5,6,11,64,70],heisenbergmapp:[72,128],heisenbergscreen:72,hello:171,helmholtz:[82,233],helmholtz_free_energi:233,helmoltz:234,help:[0,2,12,19,38,58,63,64,71,78,92,133,141,153,154,164,209,265],helper:[0,5,6,10,12,28,42,50,64,69,84,92,95,107,122,127,131,141,142,164,165,166,171,184,185,196,198,213,221,255],hematit:93,henc:[179,184,221,247,253],henchforth:0,heng:0,henkelman:[94,123,222,266],henkelmann:[0,3,123,266],henriquemiranda:232,here:[1,2,3,48,69,71,85,92,141,145,173,178,184,185,211,219,222,253,258,268],herebi:2,herfindahl:66,hermann:238,hessian:[0,124,154,202,210],heteroatom:61,heterostructur:[48,59,91],heurist:[71,73],hex:[0,63,177,237],hex_angle_tol:133,hex_bipyr:69,hex_length_tol:133,hex_pyr:69,hex_triplet:177,hexagon:[0,63,69,95,133,141,168,221,223,236,237,238,240,244],hf_pv:223,hf_sv_gw:223,hfscreen:223,hg_sv_gw:223,hhi:[0,5,6,11],hick:13,hide:64,hide_image_edg:64,hide_unconnected_nod:64,hierarchi:268,high:[0,2,10,42,71,73,92,137,149,150,162,170,178,192,210,223,227,236,237,265,266],highcharg:39,highchart:39,higher:[41,42,50,53,69,89,92,149,154,222,223,247],highest:[12,42,48,50,78,84,101,135,149,184,246,268],highest_protocol:260,highli:[0,1,2,3,168,221,222,246,268],highlight:268,highsymmkpath:[150,154,221,237],hight:221,hilber:168,hilbert:168,hilberttransform:168,hill:[50,131],hill_formula:131,hillari:0,hint:[0,19,21,23,71,178,184],hint_for_accuraci:178,hints_info:19,hints_typ:19,hirerachi:268,hirschman:66,hirshfeld:223,his:238,hist:[167,184,186],histfil:186,histo:149,histogram:[149,169,185],histori:[9,10,164,167,173,177,186,246,247,248,256],historynod:256,historyrecord:177,hit:250,hive:[5,6,98,105,107,268],hkil:[95,141],hkill:95,hkl:[44,46,48,95,133,141],hkl_list:95,hkl_transform:141,hkl_tuple_to_str:95,ho3:223,ho_3:223,hold:[63,141,227],holder:2,hole:[37,38,41,149,153],hollow:12,home:[2,185],homebrew:124,homo:135,homogen:50,homogeneous_poisson:50,hook:[0,1],hop:69,hopkin:0,hopp:69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module","pymatgen.io.zeopp module","pymatgen.optimization package","pymatgen.optimization.linear_assignment module","pymatgen.optimization.linear_assignment_numpy module","pymatgen.phonon package","pymatgen.phonon.bandstructure module","pymatgen.phonon.dos module","pymatgen.phonon.plotter module","pymatgen.symmetry package","pymatgen.symmetry.analyzer module","pymatgen.symmetry.bandstructure module","pymatgen.symmetry.groups module","pymatgen.symmetry.maggroups module","pymatgen.symmetry.settings module","pymatgen.symmetry.site_symmetries module","pymatgen.symmetry.structure module","pymatgen.transformations package","pymatgen.transformations.advanced_transformations module","pymatgen.transformations.defect_transformations module","pymatgen.transformations.site_transformations module","pymatgen.transformations.standard_transformations module","pymatgen.transformations.transformation_abc module","pymatgen.util package","pymatgen.util.convergence module","pymatgen.util.coord module","pymatgen.util.coord_cython module","pymatgen.util.io_utils module","pymatgen.util.num module","pymatgen.util.plotting module","pymatgen.util.provenance module","pymatgen.util.sequence module","pymatgen.util.serialization module","pymatgen.util.string module","pymatgen.util.testing module","pymatgen.util.typing module","pymatgen.vis package","pymatgen.vis.plotters module","pymatgen.vis.structure_chemview module","pymatgen.vis.structure_vtk module","References","Active Core Team","Overview"],titleterms:{"new":2,The:268,abiinspect:167,abinit:[166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187],abiobject:168,abitim:169,about:2,aconvasp_cal:122,activ:267,add:2,adf:188,adsorpt:12,advanced_transform:244,aflow_prototyp:13,aiida:189,alchemi:[7,8,9,10,268],alumni:267,analysi:[11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,266,268],analyz:[71,100,236],anoth:268,api:[2,268],app:[98,99,100,101,102,103,104,105,106,107],as_dict:268,ase:190,assimil:268,atat:191,babel:192,bader:3,bader_cal:[123,266],bandstructur:[148,232,237],base:3,basic:268,batteri:[99,100,101,102,103,104],battery_abc:101,boltztrap2:150,boltztrap:149,bond:130,bond_dissoci:14,bond_val:15,borg:[105,106,107,268],calcul:[170,268],can:268,chang:[0,2,4],check:227,chemenv:[16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32],chemenv_config:26,chemenv_error:27,chemenv_strategi:18,cif:193,cite:2,cli:[108,109,110,111,112,113,114,115,116,117,118,119,120],cluster:2,cod:161,code:1,cohp:151,collabor:1,command:2,command_lin:[121,122,123,124,125,126,127,128,266],compat:[1,156,266,268],composit:131,computed_entri:157,conda:[2,3],config:268,content:[6,7,11,16,17,20,22,25,33,35,43,49,57,62,65,70,86,96,98,99,105,108,121,129,147,155,160,165,166,195,197,203,214,220,228,231,235,243,249,262],contribut:2,contributor:267,converg:250,conversion_batteri:102,coord:251,coord_cython:252,coordination_environ:[17,18,19,20,21,22,23,24],coordination_geometri:19,coordination_geometries_fil:20,coordination_geometry_find:21,coordination_geometry_util:28,copyright:2,core:[36,44,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,152,266,267],correct:37,cost:[33,34],creat:[3,268],critic2_cal:124,crystalsai:162,cssr:194,dao:146,data:[204,268],decod:268,defect:[35,36,37,38,39,40,41,42],defect_compat:38,defect_transform:245,defs_util:29,depend:3,develop:[2,3],development:3,diagram:268,diffract:[43,44,45,46],diffusion_analyz:47,dilute_solution_model:39,dimension:48,doc:2,document:2,dopant_predictor:87,dos:[153,233],effect:2,elast:[49,50,51,52],electronic_structur:[147,148,149,150,151,152,153,154],energi:268,energy_model:53,entri:[155,156,157,158,159,266,268],entry_tool:158,enumlib:3,enumlib_cal:125,environ:3,eos:54,event:172,ewald:55,exampl:[2,268],excit:[56,195,196],exp_entri:159,ext:[160,161,162,163,164],extern:267,feff:[197,198,199,200,266],feff_input_gener:109,feff_plot_cross_sect:110,feff_plot_do:111,ferroelectr:[57,58],fiesta:201,file:268,filter:8,find_dimens:59,flow:173,fragment:60,from:2,from_dict:268,func_util:30,functional_group:61,gaussian:202,gaussian_analyz:112,gener:40,get:2,get_environ:113,gga:268,github:[1,3],grain:63,graph:64,group:238,guidelin:1,gulp_cal:126,heisenberg:72,helper:174,hhi:[65,66],high:268,hive:106,how:2,indic:2,input:[196,198,205,215,221],insertion_batteri:103,instal:[2,3,227],integr:268,interfac:67,interface_react:68,introduct:2,io_util:253,ion:132,jahntel:73,jhu:163,lammp:[203,204,205,206,207],lattic:133,launcher:175,librari:3,libxcfunc:134,licens:2,line:2,linear_assign:229,linear_assignment_numpi:230,linux:3,lmto:208,lobster:209,local_env:69,log:[0,2,4],mac:3,maggroup:239,magnet:[70,71,72,73],make:268,manual:268,materi:[9,268],matgeni:2,math_util:31,matproj:[164,266,268],mcsqs_caller:127,method:268,mix:268,mode:3,modifi:268,modul:[6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265],molecul:268,molecular_orbit:135,molecule_match:74,molecule_structure_compar:75,montyencod:268,more:2,netcdf:176,neutron:45,nmr:76,node:177,non:3,note:268,num:254,nwchem:210,offlin:2,onli:[2,3],ons:2,openbabel:3,oper:136,optim:[228,229,230],option:3,osx:3,output:[199,206,216,222],overview:268,packag:[6,7,11,16,17,20,22,25,33,35,43,49,57,62,65,70,86,96,98,99,105,108,121,129,147,155,160,165,166,195,197,203,214,220,228,231,235,243,249,262],path_find:[77,266],periodic_t:137,phase:268,phase_diagram:78,phasediagram:266,phonon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