From 0e230c1fe3d7595a08dc9baf04dc6ad131b23e80 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Thu, 19 Dec 2024 18:07:51 +0000 Subject: [PATCH] Update documentation --- omega/develop/_sources/devGuide/TimeMgr.md.txt | 16 ++++++++++++---- omega/develop/devGuide/TimeMgr.html | 16 ++++++++++++---- omega/develop/searchindex.js | 2 +- 3 files changed, 25 insertions(+), 9 deletions(-) diff --git a/omega/develop/_sources/devGuide/TimeMgr.md.txt b/omega/develop/_sources/devGuide/TimeMgr.md.txt index 8adfe5329358..fb857d9e2950 100644 --- a/omega/develop/_sources/devGuide/TimeMgr.md.txt +++ b/omega/develop/_sources/devGuide/TimeMgr.md.txt @@ -159,16 +159,24 @@ is set as the new ring time: ```c++ SingleAlarm.reset(NewAlarmTime); ``` -If the Alarm is periodic, the new ring time will be set to the next interval -boundary after the input time: +If the Alarm is periodic, the ringing will be switched off as above and the +new ring time will be set to the next interval boundary after the input time. +The interval boundary is an integer number of intervals after the start time +provided on Alarm creation. ```c++ PeriodicAlarm.reset(CurrentTime); ``` -This Alarm will ring next at `CurrentTime + AlarmInterval`. An Alarm can be -permanently stopped using the `stop` method: +An Alarm can be permanently stopped using the `stop` method: ```c++ SingleAlarm.stop(); ``` +It is sometimes useful to retrieve other aspects of a periodic Alarm, namely +the Alarm interval and the last time the Alarm was ringing. Two retrieval +functions are provided that return const pointers to these values: +```c++ +const TimeInterval *AlarmInterval = PeriodicAlarm.getInterval(); +const TimeInstant *PriorRingTime = PeriodicAlarm.getRingTimePrev(); +``` ### 6. Clock diff --git a/omega/develop/devGuide/TimeMgr.html b/omega/develop/devGuide/TimeMgr.html index 90e5ba9b913f..0463b16ccc5d 100644 --- a/omega/develop/devGuide/TimeMgr.html +++ b/omega/develop/devGuide/TimeMgr.html @@ -327,16 +327,24 @@

5. Alarm
SingleAlarm.reset(NewAlarmTime);
-

If the Alarm is periodic, the new ring time will be set to the next interval -boundary after the input time:

+

If the Alarm is periodic, the ringing will be switched off as above and the +new ring time will be set to the next interval boundary after the input time. +The interval boundary is an integer number of intervals after the start time +provided on Alarm creation.

PeriodicAlarm.reset(CurrentTime);
-

This Alarm will ring next at CurrentTime + AlarmInterval. An Alarm can be -permanently stopped using the stop method:

+

An Alarm can be permanently stopped using the stop method:

SingleAlarm.stop();
+

It is sometimes useful to retrieve other aspects of a periodic Alarm, namely +the Alarm interval and the last time the Alarm was ringing. Two retrieval +functions are provided that return const pointers to these values:

+
const TimeInterval *AlarmInterval = PeriodicAlarm.getInterval();
+const TimeInstant *PriorRingTime = PeriodicAlarm.getRingTimePrev();
+
+

6. Clock

diff --git a/omega/develop/searchindex.js b/omega/develop/searchindex.js index b4e63f20dded..5c4bc577bf45 100644 --- a/omega/develop/searchindex.js +++ b/omega/develop/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["design/AuxiliaryState", "design/AuxiliaryVariables", "design/Broadcast", "design/Config", "design/DataTypes", "design/Decomp", "design/Driver", "design/Error", "design/Halo", "design/HorzMeshClass", "design/IO", "design/IOStreams", "design/Logging", "design/MachEnv", "design/Metadata", "design/OmegaV0ShallowWater", "design/Reductions", "design/State", "design/Template", "design/Tendencies", "design/Tendency", "design/TimeMgr", "design/TimeStepping", "design/Timers", "design/Tracers", "devGuide/AuxiliaryState", "devGuide/AuxiliaryVariables", "devGuide/Broadcast", "devGuide/BuildDocs", "devGuide/CMakeBuild", "devGuide/CondaEnv", "devGuide/Config", "devGuide/DataTypes", "devGuide/Decomp", "devGuide/Dimension", "devGuide/Docs", "devGuide/Driver", "devGuide/Field", 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[1, 3, 4, 5, 6, 7, 9, 11, 12, 14, 15, 16, 18, 20, 22, 23, 24, 27, 32, 33, 35, 37, 40, 42, 45, 50, 53, 54, 58, 63, 66, 67, 72, 76, 78], "arrai": [1, 3, 5, 6, 11, 13, 14, 15, 19, 21, 24, 26, 33, 34, 37, 38, 39, 40, 41, 42, 46, 48, 49, 50, 51, 54, 60, 63, 64, 67, 75, 76], "": [1, 3, 5, 11, 12, 15, 21, 22, 24, 26, 31, 35, 44, 47, 51, 56, 57, 58, 60, 63, 65, 68, 69, 70, 72, 74], "member": [1, 5, 8, 13, 14, 20, 23, 24, 33, 34, 37, 38, 39, 45, 46, 49, 50, 51, 52, 53, 54, 68, 76], "chunk": [1, 13, 20, 26, 38, 40, 50, 67], "vertic": [1, 8, 9, 15, 20, 24, 25, 26, 33, 34, 40, 46, 49, 50, 53, 56, 60, 65], "particular": [1, 2, 3, 8, 10, 11, 14, 15, 20, 24, 32, 33, 38, 41, 51, 65, 67, 76, 77], "mai": [1, 3, 4, 5, 6, 7, 8, 10, 11, 13, 14, 15, 16, 21, 22, 23, 24, 26, 30, 31, 32, 37, 47, 53, 56, 58, 63, 67, 68, 72, 78], "than": [1, 2, 3, 4, 5, 7, 8, 11, 12, 13, 14, 16, 21, 23, 26, 30, 31, 33, 37, 41, 47, 51, 67, 68], "one": [1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 24, 26, 29, 33, 37, 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8, 10, 15, 16, 20, 23, 33, 34, 37, 38, 41, 48, 60, 67], "devic": [1, 4, 13, 16, 17, 20, 24, 32, 33, 37, 39, 46, 48, 64], "constant": [1, 3, 15, 16, 18, 20, 22, 49, 50], "which": [1, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 29, 30, 31, 33, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 49, 50, 51, 60, 63, 65, 68, 72, 76, 77, 78], "simplifi": [1, 2, 20, 21, 24], "abil": [1, 3, 5, 7, 8, 16, 20, 21, 23, 47], "fuse": [1, 20], "separ": [1, 5, 7, 8, 9, 10, 12, 15, 20, 21, 23, 37, 38, 47, 50, 51, 52, 53, 58, 62, 66, 67, 68, 72], "specif": [1, 3, 7, 8, 9, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 27, 29, 31, 32, 33, 39, 40, 47, 49, 52, 53, 57, 58, 59, 65, 68, 72, 78], "inner": [1, 13, 20], "size": [1, 8, 9, 10, 11, 12, 16, 20, 33, 37, 41, 63], "set": [1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 20, 21, 22, 23, 24, 28, 29, 31, 35, 37, 39, 40, 41, 43, 44, 45, 51, 52, 53, 54, 60, 62, 64, 67, 68, 69, 70, 72, 76, 78], "length": [1, 13, 15, 16, 20, 21, 24, 29, 33, 34, 41, 45, 48, 51, 53, 65, 70], "machin": [1, 2, 5, 10, 15, 16, 20, 21, 22, 23, 29, 33, 34, 38, 43, 47, 54, 57, 64, 72], "gpu": [1, 8, 13, 20, 22, 26, 33, 45, 47, 70, 72], "possibl": [1, 4, 6, 7, 8, 11, 12, 13, 14, 16, 20, 22, 24, 25, 49], "base": [1, 2, 5, 6, 8, 10, 12, 13, 14, 15, 21, 23, 24, 27, 29, 30, 31, 33, 34, 37, 38, 41, 42, 47, 51, 53, 54, 58, 67, 70, 79], "retriev": [1, 6, 21, 24, 25, 26, 27, 31, 33, 34, 36, 37, 38, 39, 41, 45, 46, 49, 51, 52, 53, 60, 63, 70], "config": [1, 5, 14, 19, 20, 29, 33, 35, 36, 50, 54, 60, 62, 68, 78, 79], "enum": [1, 3, 5, 8, 10, 16, 21, 37, 38, 41, 51, 52, 54], "do": [1, 3, 5, 7, 13, 14, 15, 23, 24, 25, 30, 37, 47, 49], "thing": [1, 7, 35], "regist": [1, 9, 24, 25, 26, 37, 46, 55, 63, 71], "iostream": [1, 25, 34, 37, 41, 54, 63, 67], "anoth": [1, 3, 5, 7, 14, 15, 21, 35], "afterward": [1, 3, 72], "find": [1, 16, 72], "manag": [1, 4, 7, 8, 10, 11, 12, 13, 14, 16, 21, 23, 25, 36, 41, 42, 49, 53, 54, 62, 72, 78, 79], "strategi": [1, 9], "would": [1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 18, 22, 23, 24, 31, 41, 43, 45, 47, 57, 67, 77], "minim": [1, 6, 7, 10, 15, 58], "amount": [1, 15, 51], "persist": [1, 8, 14], "found": [1, 3, 15, 20, 27, 31, 34, 51, 53, 58, 60, 63, 65], "document": [1, 5, 7, 10, 15, 20, 21, 22, 24, 30, 32, 47, 67, 69], "exampl": [1, 3, 5, 7, 10, 11, 12, 13, 14, 15, 16, 21, 22, 24, 26, 31, 32, 34, 35, 37, 40, 41, 42, 46, 51, 53, 56, 57, 58, 67, 68, 69, 72, 79], "fluxthicktyp": 1, "center": [1, 15, 26, 56, 65, 76], "upwind": [1, 15, 26, 56], "These": [1, 3, 5, 6, 7, 8, 10, 12, 13, 15, 16, 21, 24, 27, 34, 37, 39, 44, 45, 47, 48, 51, 52, 53, 57, 60, 67, 68, 70, 76], "read": [1, 5, 13, 14, 24, 31, 33, 36, 39, 41, 42, 58, 60, 65, 67, 68, 72], "input": [1, 6, 7, 8, 9, 11, 13, 14, 15, 17, 21, 24, 26, 31, 36, 40, 41, 42, 50, 51, 54, 56, 58, 60, 63, 67, 68, 72], "file": [1, 4, 5, 6, 7, 8, 9, 14, 15, 18, 23, 24, 26, 27, 29, 30, 31, 35, 36, 37, 38, 41, 42, 43, 44, 47, 51, 53, 54, 56, 57, 58, 60, 63, 67, 68, 69, 72, 76, 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72, 77], "break": 1, "defineiofield": [1, 26], "horizont": [1, 3, 15, 20, 25, 31, 33, 46, 49, 52, 54, 56, 60, 76], "indic": [1, 5, 8, 12, 15, 16, 22, 24, 32, 33, 38, 40, 46, 69, 72], "handl": [1, 8, 38, 41, 46, 51, 53, 67], "enabl": [1, 3, 5, 10, 12, 13, 14, 20, 24, 29, 34, 44, 52, 54, 57, 72, 76], "layerthickcel": [1, 26], "normalveledg": [1, 26], "kstart": 1, "veclength": [1, 20, 40, 45], "jcell0": 1, "0": [1, 3, 6, 7, 8, 12, 13, 14, 16, 20, 21, 22, 24, 29, 33, 34, 41, 45, 46, 47, 48, 51, 53, 57, 58, 72, 79], "jcell1": 1, "kvec": 1, "k": [1, 5, 15, 20, 41], "5_real": 1, "fluxthickedgechoic": 1, "els": [1, 4, 6, 8, 34], "kokko": [1, 5, 6, 9, 11, 15, 16, 17, 19, 23, 29, 33, 34, 39, 46, 49, 50, 54, 69, 76], "max": [1, 14, 15, 23, 24, 33, 37, 48, 53, 74, 79], "ctest": [1, 3, 6, 7, 20, 72], "compar": [1, 4, 5, 11, 13, 14, 16, 20, 21, 22, 51], "result": [1, 2, 5, 7, 13, 15, 16, 20, 21, 23, 26, 33, 40, 47, 48, 58, 66, 67], "against": [1, 11, 14, 15, 16, 20, 22, 35, 42], "refer": [1, 3, 7, 9, 14, 16, 18, 20, 21, 23, 24, 31, 32, 35, 37, 40, 44, 47, 51, 53, 58, 66, 71, 73, 77, 78, 79], "valu": [1, 2, 4, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 27, 29, 31, 32, 34, 36, 37, 38, 40, 41, 42, 45, 48, 50, 51, 52, 53, 56, 58, 63, 65, 68, 69, 72, 74, 79], "shallow": [1, 20, 22, 40, 50, 54], "water": [1, 20, 22, 23, 50, 54], "equat": [1, 9, 20, 22, 24, 49, 50, 78], "exist": [1, 2, 5, 7, 9, 13, 20, 21, 23, 24, 31, 32, 35, 37, 41, 45, 51, 52, 53, 68], "polari": [1, 6, 14, 20, 35], "verifi": [1, 2, 3, 4, 5, 7, 8, 9, 12, 13, 20, 21, 29, 35, 42, 43], "produc": [1, 15, 20, 51], "correct": [1, 9, 17, 20, 21, 24, 58], "rate": [1, 20, 56], "In": [2, 3, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 21, 23, 24, 26, 29, 30, 31, 32, 33, 35, 36, 37, 38, 40, 41, 47, 50, 51, 52, 58, 60, 65, 67, 72, 77, 79], "parallel": [2, 5, 7, 8, 13, 15, 16, 22, 23, 24, 27, 33, 34, 37, 38, 39, 40, 42, 45, 50, 54, 60, 64, 65, 72, 76], "mpi": [2, 3, 5, 6, 7, 8, 10, 12, 15, 16, 29, 33, 36, 37, 38, 41, 45, 47, 48, 54, 57, 64, 67, 70, 72], "current": [2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 21, 23, 24, 26, 27, 33, 36, 37, 38, 40, 41, 43, 44, 46, 47, 50, 51, 52, 53, 56, 57, 58, 60, 62, 64, 65, 66, 67, 68, 72, 76, 77, 78], "configur": [2, 5, 6, 8, 10, 11, 12, 13, 14, 15, 18, 23, 29, 33, 35, 36, 37, 41, 42, 44, 47, 49, 53, 54, 55, 56, 59, 60, 61, 62, 63, 64, 66, 67, 68, 70, 72, 75, 76, 77, 78], "u": [2, 5, 7, 15, 22, 32], "mani": [2, 3, 5, 7, 8, 9, 10, 15, 16, 24, 41, 47, 60, 70, 72], "aspect": [2, 6, 15, 23, 27, 70], "we": [2, 3, 4, 5, 6, 7, 8, 10, 11, 13, 14, 15, 16, 21, 22, 23, 24, 30, 31, 32, 33, 35, 37, 41, 42, 47, 58, 59, 60, 61, 67, 73], "must": [2, 3, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 21, 23, 24, 31, 33, 34, 35, 37, 38, 41, 42, 44, 48, 51, 52, 57, 58, 60, 61, 63, 67, 68, 72], "abl": [2, 3, 5, 8, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 60], "i4": [2, 3, 4, 5, 8, 10, 14, 16, 23, 24, 31, 32, 33, 34, 37, 39, 41, 48, 51, 53, 57, 58, 79], "i8": [2, 3, 4, 10, 14, 16, 23, 31, 32, 37, 48, 57, 58], "r4": [2, 3, 4, 10, 14, 16, 31, 32, 37, 48, 57, 58], "r8": [2, 3, 4, 10, 14, 16, 23, 31, 32, 37, 48, 57, 58], "real": [2, 3, 8, 15, 16, 20, 21, 24, 31, 32, 41, 47, 51, 59, 68, 72], "boolean": [2, 3, 8, 14, 41], "gener": [2, 4, 5, 6, 8, 10, 11, 12, 13, 14, 15, 23, 24, 29, 31, 35, 37, 41, 51, 52, 58, 60, 65, 67, 68, 69, 72], "most": [2, 3, 5, 6, 7, 8, 11, 12, 13, 14, 17, 21, 22, 23, 31, 34, 37, 38, 41, 42, 51, 53, 58, 67, 69], "common": [2, 3, 4, 7, 11, 14, 21, 23, 52], "plan": [2, 3, 15, 43, 47, 54], "partit": [2, 6, 8, 9, 13, 15, 33, 38, 60], "domain": [2, 9, 17, 22, 38, 54, 64, 65], "sub": [2, 3, 12, 13, 31, 58, 65, 72], "so": [2, 3, 4, 5, 6, 7, 8, 10, 11, 13, 14, 15, 16, 21, 22, 23, 24, 25, 30, 31, 32, 33, 37, 38, 39, 41, 42, 45, 47, 49, 50, 53, 60, 67, 68, 73], "appropri": [2, 3, 9, 10, 11, 12, 13, 14, 16, 21, 23, 24, 37, 42, 47, 53, 67, 79], "commun": [2, 5, 6, 9, 10, 15, 16, 21, 27, 33, 36, 38, 41, 45, 48, 60, 67, 70], "overlap": [2, 10, 38], "comput": [2, 5, 6, 10, 15, 16, 20, 21, 22, 23, 24, 32, 33, 34, 37, 39, 40, 41, 46, 47, 48, 50, 51, 54, 56, 60, 64, 65, 67, 72, 76], "form": [2, 3, 5, 10, 11, 12, 13, 15, 16, 21, 23, 31, 32, 35, 37, 51, 58, 62], "beyond": [2, 13, 21, 75], "intern": [2, 6, 9, 10, 13, 14, 31, 34, 35, 36, 37, 40, 53, 58, 61, 63, 65, 76], "mostli": [2, 13, 21, 51, 67], "wrapper": [2, 3, 6, 10, 27, 31, 38, 41, 67], "around": [2, 3, 27, 31, 41, 67], "For": [2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 36, 37, 39, 41, 42, 44, 45, 46, 48, 49, 51, 52, 53, 56, 57, 58, 67, 69, 72, 73, 78], "alia": [2, 3, 30, 31, 32, 37], "mpi_request": [2, 8], "id": [2, 8, 10, 11, 13, 21, 34, 38, 41, 47], "broadcastid": 2, "four": [2, 15, 22, 29, 52, 68, 78], "integ": [2, 3, 5, 6, 7, 8, 13, 16, 21, 24, 32, 36, 41, 49, 51, 52, 53, 68], "note": [2, 3, 5, 7, 10, 11, 13, 14, 15, 16, 22, 24, 26, 29, 32, 33, 37, 41, 45, 57, 67, 68, 72, 79], "interfac": [2, 3, 4, 7, 8, 10, 11, 12, 14, 16, 18, 23, 24, 31, 33, 36, 37, 38, 41, 42, 45, 48, 51, 52, 54, 58, 60, 64, 67, 68, 74], "below": [2, 5, 6, 7, 8, 10, 11, 13, 14, 15, 16, 21, 23, 24, 31, 33, 37, 41, 43, 47, 53, 57, 68, 72, 79], "could": [2, 3, 6, 8, 9, 12, 13, 15, 21, 22, 23, 31, 40, 41, 67, 69], "templat": [2, 3, 11, 23, 31, 32, 37, 38, 54, 68], "prefer": [2, 7, 10, 24, 31, 41, 67, 68, 72], "overload": [2, 3, 12, 13, 14, 20, 27, 38, 45], "keep": [2, 3, 5, 13, 21, 23, 24, 31, 68], "cleaner": [2, 3, 31], "first": [2, 3, 5, 7, 10, 11, 13, 14, 15, 21, 22, 26, 30, 31, 33, 34, 37, 38, 40, 43, 44, 45, 47, 48, 50, 51, 52, 53, 54, 72], "simplest": [2, 21], "where": [2, 3, 4, 7, 8, 9, 11, 12, 14, 15, 16, 21, 22, 23, 24, 29, 30, 31, 32, 37, 38, 41, 42, 47, 48, 52, 58, 67, 68, 72], "actual": [2, 3, 6, 7, 10, 14, 15, 18, 27, 33, 35, 37, 58, 62, 68], "look": [2, 3, 5, 6, 7, 13, 15, 24, 31, 33, 35, 47, 53, 58], "like": [2, 3, 5, 6, 10, 11, 13, 14, 15, 16, 18, 21, 22, 23, 24, 30, 31, 33, 37, 41, 45, 47, 50, 53, 58, 63, 67, 68, 70, 76], "err": [2, 3, 6, 7, 24, 31, 37, 39, 41, 42, 46, 51, 53], "myintvalu": 2, "myrealvalu": 2, "etc": [2, 5, 6, 9, 11, 14, 21, 22, 23, 30, 32, 34, 36, 37, 46], "On": [2, 6, 8, 10, 13, 45, 72], "remain": [2, 3, 14, 15, 20, 22, 23, 31, 33, 39], "unchang": 2, "receiv": [2, 38, 57, 64], "similar": [2, 3, 5, 6, 7, 8, 12, 13, 15, 16, 21, 24, 26, 31, 32, 41, 48, 58], "abov": [2, 3, 6, 7, 10, 11, 13, 14, 15, 16, 21, 22, 23, 30, 31, 32, 33, 37, 38, 41, 42, 45, 47, 51, 52, 57, 58, 60, 65, 68, 79], "add": [2, 3, 6, 7, 13, 15, 16, 21, 30, 31, 35, 41, 47, 53, 72, 79], "addit": [2, 3, 5, 6, 7, 9, 11, 12, 13, 14, 15, 16, 21, 23, 31, 32, 37, 38, 41, 45, 49, 52, 57, 60, 63, 65, 67, 72, 77, 78], "sourc": [2, 3, 24, 29, 30, 35, 57, 72], "srcrank": 2, "As": [2, 4, 5, 7, 9, 10, 12, 14, 15, 16, 21, 26, 28, 30, 32, 34, 36, 37, 38, 41, 42, 44, 45, 52, 60, 68, 69], "machenv": [2, 8, 10, 13, 16, 23, 31, 33, 38, 41, 54, 57, 60, 64], "subenv": 2, "ident": [2, 3, 5, 7, 14, 15, 16, 22, 31], "replac": [2, 11, 15, 37, 41, 68, 69], "option": [2, 6, 8, 10, 12, 15, 16, 19, 20, 23, 24, 26, 29, 31, 35, 36, 37, 45, 47, 48, 49, 50, 53, 55, 57, 58, 59, 60, 61, 62, 63, 65, 66, 67, 68, 72, 75, 77, 78, 79], "request": [2, 8, 11, 14, 16, 21, 24, 31, 35, 43, 68], "follow": [2, 3, 5, 7, 9, 12, 15, 18, 21, 22, 24, 26, 28, 29, 30, 32, 36, 38, 40, 43, 47, 50, 51, 52, 53, 56, 57, 65, 66, 69, 72, 76, 78], "standard": [2, 4, 5, 7, 8, 9, 11, 12, 13, 14, 15, 21, 22, 23, 24, 27, 32, 37, 41, 51, 53, 58, 59, 60, 64, 68, 72, 79], "ibroadcast": [2, 54], "ibroadcastwait": 2, "includ": [2, 3, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 29, 30, 31, 35, 37, 41, 42, 43, 44, 45, 47, 52, 60, 63, 65, 68, 69, 70, 72, 77, 79], "wait": 2, "complet": [2, 3, 5, 6, 8, 11, 12, 15, 23, 37, 60, 68, 72], "A": [2, 3, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 21, 23, 24, 25, 33, 34, 37, 38, 39, 42, 46, 47, 49, 51, 52, 53, 54, 58, 67, 68, 70, 77], "sequenc": [2, 7, 11, 21, 31, 58], "myreqid": 2, "myvar": [2, 7, 14], "perform": [2, 3, 5, 7, 8, 9, 10, 12, 13, 14, 16, 17, 21, 23, 24, 26, 32, 34, 37, 38, 39, 40, 43, 46, 48, 52, 53, 54, 59, 60, 61, 64, 67], "multi": [2, 5, 6, 7, 10, 14, 32, 33, 34, 51, 54], "processor": [2, 5, 10, 16, 23, 48, 60], "driver": [2, 3, 11, 13, 24, 54], "initi": [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 15, 17, 20, 21, 22, 24, 31, 33, 36, 37, 38, 39, 41, 42, 45, 46, 50, 51, 54, 60, 70, 75, 78], "zero": [2, 3, 6, 7, 14, 15, 16, 22, 24, 31, 34, 37, 41, 77], "empti": [2, 3, 14, 21, 23, 31, 37, 42, 78], "expect": [2, 3, 4, 5, 7, 8, 13, 14, 15, 21, 34, 41, 70], "repeat": [2, 5, 11, 15, 23, 41], "two": [2, 5, 6, 7, 8, 11, 13, 14, 15, 16, 21, 22, 24, 27, 29, 37, 38, 41, 42, 46, 49, 51, 52, 53, 56, 57, 63, 67, 72, 78, 79], "except": [2, 7, 8, 12, 14, 15, 24, 41, 65, 68], "tandem": [2, 15], "after": [2, 3, 5, 7, 8, 11, 13, 15, 21, 23, 31, 33, 38, 39, 42, 43, 46, 51, 52, 63, 68, 72], "issu": [2, 4, 12, 21, 31, 69], "extra": [2, 16, 33], "corrupt": [2, 12], "overwritten": 2, "necessari": [3, 8, 9, 11, 12, 16, 30, 31, 32, 33, 36, 37, 38, 39, 46, 58, 64, 67, 68, 72], "run": [3, 5, 7, 8, 10, 11, 13, 16, 23, 28, 30, 31, 33, 35, 36, 38, 43, 45, 51, 52, 58, 60, 62, 64, 70, 72], "physic": [3, 15, 31, 32, 38, 58], "coeffici": [3, 15, 31, 52, 58, 76], "parameter": [3, 15, 20, 31, 58], "variou": [3, 4, 6, 9, 10, 12, 13, 21, 23, 27, 31, 37, 40, 41, 44, 45, 51, 52, 58, 65, 67, 74, 77], "typic": [3, 5, 6, 7, 10, 11, 12, 13, 14, 15, 16, 18, 21, 23, 24, 30, 31, 33, 34, 37, 40, 41, 51, 53, 58, 68, 69, 77], "serv": [3, 8, 27, 31, 35, 36, 44, 58], "descript": [3, 7, 12, 14, 15, 24, 31, 37, 53, 54, 56, 58, 60, 65, 76, 79], "well": [3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 21, 23, 24, 31, 34, 36, 38, 51, 52, 58, 66, 72], "easili": [3, 24, 32, 65], "understood": [3, 15], "modifi": [3, 6, 11, 13, 21, 30, 31, 35, 40, 43, 51, 53, 57, 58, 62, 72, 77, 78], "expert": 3, "user": [3, 7, 8, 10, 11, 12, 14, 15, 21, 23, 24, 26, 29, 31, 32, 35, 41, 42, 44, 49, 51, 53, 55, 56, 58, 59, 60, 61, 62, 63, 66, 67, 68, 70, 72, 75, 76, 77, 78, 79], "markup": 3, "interfer": 3, "conform": [3, 14, 51], "eas": [3, 7, 15], "pars": 3, "potenti": [3, 5, 8, 12, 21, 24, 40, 51, 53, 69, 76, 79], "interoper": [3, 12, 15], "yaml": [3, 11, 24, 31, 35, 36, 53, 54, 58, 63, 68], "json": [3, 12], "xml": [3, 29, 47, 70, 72], "entir": [3, 8, 16, 24, 37, 77], "save": [3, 7, 8, 11, 31, 38, 44, 72], "act": 3, "although": [3, 9, 32, 41, 72], "relev": [3, 5, 6, 12, 15, 16, 20, 23, 37, 42, 51], "modul": [3, 6, 7, 10, 11, 14, 21, 24, 31, 36, 37, 38, 41, 42, 51, 52, 58, 60, 63, 68, 72], "inevit": 3, "depend": [3, 4, 5, 8, 9, 10, 13, 15, 21, 22, 24, 25, 37, 38, 39, 41, 49, 51, 64, 65], "other": [3, 4, 5, 6, 8, 9, 11, 12, 14, 15, 21, 24, 26, 31, 34, 35, 37, 39, 41, 42, 45, 47, 51, 52, 58, 62, 63, 66, 67, 68, 77, 78, 79], "therefor": [3, 35, 72], "float": [3, 8, 10, 11, 16, 21, 32, 51, 58, 59, 68, 69], "doubl": [3, 4, 8, 10, 11, 15, 16, 21, 32, 59, 68], "limit": [3, 8, 10, 69], "vector": [3, 5, 8, 10, 11, 14, 16, 21, 23, 24, 31, 37, 41, 45, 48, 51, 53, 57, 58, 70], "should": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 29, 31, 32, 34, 35, 37, 41, 42, 45, 47, 52, 53, 60, 62, 67, 68, 69, 72, 78], "never": [3, 15, 68], "consum": 3, "signific": 3, "resourc": [3, 38], "either": [3, 6, 7, 8, 11, 12, 15, 16, 21, 23, 24, 36, 37, 38, 41, 42, 47, 48, 50, 51, 53, 57, 62, 68, 70, 72, 74, 78, 79], "storag": [3, 4, 10, 17, 24, 41], "execut": [3, 5, 7, 12, 15, 29, 36, 38, 58, 62, 64, 72], "replic": [3, 5, 9, 10, 37, 39], "rank": [3, 5, 8, 10, 12, 13, 16, 24, 32, 53], "though": [3, 4, 11, 13, 14, 21, 23, 32, 35, 51, 67, 68], "manipul": [3, 24, 51], "eg": [3, 4, 5, 6, 7, 10, 11, 13, 14, 16, 21, 23, 31, 32, 33, 34, 37, 41, 42, 45, 51, 58, 68, 70, 77, 78], "describ": [3, 5, 6, 7, 8, 11, 14, 15, 16, 18, 21, 23, 24, 31, 32, 33, 34, 35, 37, 41, 42, 47, 58, 60, 63, 66, 67, 70, 74, 77, 78], "convert": [3, 9, 10, 16, 21, 32, 41, 51, 58, 67], "happen": [3, 7], "befor": [3, 5, 14, 16, 21, 23, 25, 32, 33, 34, 35, 37, 39, 41, 42, 43, 46, 48, 49, 51, 68], "simplic": [3, 57], "detail": [3, 6, 7, 12, 15, 16, 18, 23, 29, 32, 35, 58, 60, 61, 63, 67, 69, 72, 74], "maintain": [3, 5, 9, 11, 13, 14, 24, 37, 45, 57, 72], "If": [3, 7, 8, 10, 11, 12, 13, 15, 21, 22, 23, 24, 28, 30, 31, 37, 42, 43, 45, 47, 51, 53, 62, 68, 72, 78], "multipl": [3, 7, 12, 14, 21, 22, 24, 25, 27, 31, 33, 37, 45, 48, 49, 52, 53, 60, 68, 70, 72, 78], "obviou": 3, "link": [3, 21, 23, 32, 35, 47, 58, 59, 72], "main": [3, 4, 5, 11, 29, 36, 38, 44, 52, 58, 78], "easier": [3, 14, 21], "encapsul": [3, 41], "organ": [3, 8, 9, 22, 27, 38, 39], "wai": [3, 4, 5, 15, 22, 23, 24, 30, 35, 37, 40, 47, 56, 58, 60], "primarili": [3, 7, 10, 13, 14, 21, 34, 37, 54, 58], "those": [3, 5, 7, 8, 10, 15, 21, 22, 23, 31, 38, 42, 64, 65, 67, 75, 77], "becaus": [3, 4, 5, 7, 8, 10, 11, 14, 15, 16, 21, 22, 23, 26, 32, 37, 45, 58], "outsid": [3, 8, 23, 40, 42, 73], "c": [3, 4, 7, 12, 14, 15, 21, 23, 25, 26, 29, 32, 40, 45, 47, 49, 53, 54, 58, 66, 69, 79], "python": [3, 29, 47, 54, 72], "suppli": [3, 5, 6, 11, 13, 14, 21, 31, 37, 38, 41, 45, 51, 58, 72, 77], "throw": 3, "exit": [3, 6, 7, 10, 11, 32, 34, 37, 68], "becom": [3, 32, 59, 67], "part": [3, 4, 5, 6, 7, 10, 12, 13, 14, 15, 16, 21, 22, 29, 31, 32, 37, 43, 44, 52, 58, 65, 67], "unexpect": 3, "encount": [3, 6, 7, 24, 44], "ignor": [3, 10, 15, 37], "mean": [3, 4, 7, 14, 15, 16, 21, 22, 23, 52, 69, 78], "extract": [3, 14, 16, 24, 31, 36, 37, 38, 41, 42, 58], "what": [3, 5, 13, 15, 30, 35, 43], "extern": [3, 23, 29, 47, 72], "rang": [3, 12, 24, 31, 37, 48, 50, 51, 53, 67], "assign": [3, 5, 7, 13, 14, 21, 24, 37, 41, 53, 67], "anticip": [3, 14, 21, 23, 35], "packag": [3, 5, 24, 28, 30, 35, 43, 53, 79], "chosen": [3, 12, 15, 21, 22], "select": [3, 5, 10, 11, 21, 23, 29, 45, 54, 63, 78], "meet": [3, 15, 16, 33], "improv": [3, 4, 7, 9, 12, 13, 15, 16, 24], "over": [3, 4, 5, 8, 11, 12, 15, 16, 21, 24, 34, 36, 40, 51], "cpp": [3, 4, 7, 13, 27, 31, 44], "librari": [3, 5, 7, 8, 10, 11, 12, 13, 15, 21, 29, 31, 32, 33, 41, 60, 67, 72], "third": [3, 13, 15], "parti": [3, 4], "inform": [3, 6, 7, 8, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 33, 34, 35, 37, 38, 39, 44, 45, 49, 51, 60, 63, 64, 65, 69, 70], "node": [3, 10, 13, 22, 23, 31, 33, 41, 45, 47, 58, 60, 64, 67, 70, 72], "featur": [3, 12, 18, 21, 35, 47, 57], "syntax": [3, 4, 15, 31, 32, 57, 69], "larg": [3, 5, 8, 15, 21, 23, 37, 41, 60], "complex": [3, 21], "structur": [3, 5, 6, 12, 54], "less": [3, 7, 11, 15, 21, 67, 68], "full": [3, 8, 11, 12, 14, 16, 21, 24, 31, 37, 41, 43, 58, 60, 67, 68, 76], "routin": [3, 5, 6, 7, 8, 10, 11, 13, 16, 21, 23, 24, 32, 33, 37, 39, 41, 42, 45, 46, 52, 65], "later": [3, 5, 6, 7, 10, 13, 14, 15, 16, 21, 22, 23, 24, 29, 31, 37, 43, 47, 52, 67, 68], "forward": [3, 20, 21, 38, 51, 52, 78], "integr": [3, 6, 21, 22, 24, 29, 36, 44, 47, 51, 52, 54, 72], "broadcast": [3, 54], "believ": 3, "global": [3, 8, 12, 15, 22, 24, 33, 34, 37, 41, 42, 47, 53, 54, 63], "share": [3, 6, 7, 15, 33, 37, 47, 52], "fulli": [3, 33], "accur": [3, 21], "our": [3, 11, 15, 30], "nest": [3, 31, 38, 40, 58], "simpli": [3, 4, 5, 7, 11, 13, 14, 15, 18, 21, 22, 34, 37, 47, 53, 77, 79], "keyword": 3, "pair": [3, 5, 14, 15, 21, 24, 37, 42, 45, 53, 58], "lowest": 3, "simpl": [3, 7, 13, 14, 15, 21, 23, 24, 37, 45, 67, 68], "next": [3, 15, 17, 21, 42, 51, 68], "up": [3, 4, 5, 6, 7, 10, 13, 15, 21, 24, 28, 30, 31, 35, 36, 37, 40, 43, 45, 51, 54, 58], "collect": [3, 8, 14, 16, 24, 29, 37, 48, 74], "root": [3, 12, 28, 29, 30, 57, 67], "correspond": [3, 6, 10, 12, 15, 24, 32, 35, 42, 53], "stream": [3, 9, 14, 24, 31, 54, 58, 61, 63], "tbd": 3, "under": [3, 15, 16, 23, 27, 31, 47, 57, 72], "timemanag": [3, 54, 58, 62], "dorestart": 3, "fals": [3, 7, 8, 20, 21, 37, 51, 58, 68], "restarttimestampnam": [3, 58], "restarttimestamp": [3, 58], "starttim": [3, 6, 11, 21, 23, 36, 51, 52, 58, 62, 68, 78], "0001": [3, 58, 62, 68, 78], "01": [3, 47, 58, 62, 78], "01_00": [3, 58, 62, 68, 78], "00": [3, 58, 62, 68, 78], "stoptim": [3, 51, 52, 58, 62, 78], "none": [3, 15, 21, 23, 24, 51, 53, 58, 62, 78, 79], "rundur": [3, 58, 62, 78], "0010_00": [3, 58], "calendartyp": [3, 58, 62, 78], "noleap": [3, 58], "hmix": [3, 31, 58], "hmixscalewithmesh": [3, 31, 58], "maxmeshdens": [3, 31, 58], "hmixuserefwidth": [3, 31, 58], "hmixrefwidth": [3, 31, 58], "30": [3, 21, 51, 58, 62, 77], "0e3": [3, 58], "filenametempl": [3, 58], "nc": [3, 5, 11, 47, 58, 60, 68], "inputinterv": [3, 58], "initial_onli": [3, 58], "y": [3, 11, 30, 51, 58, 68], "m": [3, 4, 11, 15, 30, 51, 58, 65, 68], "d_": [3, 11, 15, 58, 68], "h": [3, 4, 11, 15, 21, 22, 27, 33, 39, 42, 44, 46, 51, 57, 58, 68, 69], "filenameinterv": [3, 58], "00_00": [3, 58], "referencetim": [3, 58], "clobbermod": 3, "truncat": 3, "precis": [3, 4, 6, 8, 10, 15, 16, 21, 22, 41, 54, 58, 68], "outputinterv": [3, 58], "0001_00": [3, 58], "content": [3, 10, 14, 15, 18, 22, 24, 30, 37, 42, 58, 68, 72], "tracer": [3, 8, 22, 25, 37, 46, 49, 52, 54, 56, 58, 60, 63, 68, 71, 76, 78], "ssh": [3, 15, 47, 58], "kineticenergycel": [3, 15, 26, 56, 58], "relativevorticitycel": [3, 58], "obvious": [3, 6], "wrap": 3, "context": [3, 17, 37, 70], "omegaconfig": [3, 31], "configread": 3, "yml": [3, 31, 36, 53, 58, 79], "retain": [3, 6, 11, 23, 65, 68], "throughout": [3, 4, 11, 13, 15, 24, 38], "onc": [3, 5, 6, 11, 16, 21, 24, 33, 37, 38, 39, 41, 42, 43, 45, 48, 60, 64, 68, 72], "ha": [3, 5, 6, 7, 8, 9, 12, 13, 14, 15, 16, 21, 22, 24, 25, 26, 31, 33, 36, 37, 39, 42, 45, 47, 49, 51, 52, 53, 57, 67, 68, 72], "been": [3, 5, 6, 8, 9, 12, 13, 14, 15, 16, 21, 24, 33, 37, 38, 39, 41, 42, 44, 45, 46, 51, 52, 57, 65, 68], "realli": [3, 5], "top": [3, 6, 10, 23, 24, 29, 31, 35, 36, 42], "local": [3, 8, 9, 13, 16, 17, 24, 30, 32, 33, 34, 38, 39, 41, 47, 48, 65], "sampl": [3, 5, 9, 11, 14, 17, 23, 24, 31, 68], "hmixconfig": [3, 31], "configget": 3, "ierr": 3, "refwidth": 3, "bool": [3, 8, 11, 13, 14, 20, 21, 23, 24, 31, 34, 37, 42, 57, 58, 76], "userefwidth": 3, "confignam": 3, "varnam": [3, 41], "report": [3, 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[7, "requirements"], [8, "requirements"], [9, "requirements"], [10, "requirements"], [11, "requirements"], [12, "requirements"], [13, "requirements"], [14, "requirements"], [15, "requirements"], [16, "requirements"], [17, "requirements"], [18, "requirements"], [19, "requirements"], [20, "requirements"], [21, "requirements"], [22, "requirements"], [23, "requirements"], [24, "requirements"]], "2.1 Requirement: Auxiliary state should register auxiliary variables with IOStreams": [[0, "requirement-auxiliary-state-should-register-auxiliary-variables-with-iostreams"]], "2.2 Requirement: Computation of auxiliary variables": [[0, "requirement-computation-of-auxiliary-variables"]], "2.3 Requirement: Multiple auxiliary states can be present": [[0, "requirement-multiple-auxiliary-states-can-be-present"]], "3 Algorithmic Formulation": [[0, "algorithmic-formulation"], [1, "algorithmic-formulation"], [2, "algorithmic-formulation"], [3, "algorithmic-formulation"], [4, "algorithmic-formulation"], [5, "algorithmic-formulation"], [6, "algorithmic-formulation"], [7, "algorithmic-formulation"], [8, "algorithmic-formulation"], [9, "algorithmic-formulation"], [10, "algorithmic-formulation"], [11, "algorithmic-formulation"], [12, "algorithmic-formulation"], [13, "algorithmic-formulation"], [14, "algorithmic-formulation"], [15, "algorithmic-formulation"], [16, "algorithmic-formulation"], [17, "algorithmic-formulation"], [18, "algorithmic-formulation"], [19, "algorithmic-formulation"], [20, "algorithmic-formulation"], [21, "algorithmic-formulation"], [22, "algorithmic-formulation"], [23, "algorithmic-formulation"], [24, "algorithmic-formulation"]], "4 Design": [[0, "design"], [1, "design"], [2, "design"], [3, "design"], [4, "design"], [5, "design"], [6, "design"], [7, "design"], [8, "design"], [9, "design"], [10, "design"], [11, "design"], [12, "design"], [13, "design"], [14, "design"], [15, "design"], [16, "design"], [17, "design"], [18, "design"], [19, "design"], [20, "design"], [21, "design"], [22, "design"], [23, "design"], [24, "design"]], "4.1 Data types and parameters": [[0, "data-types-and-parameters"], [1, "data-types-and-parameters"], [2, "data-types-and-parameters"], [3, "data-types-and-parameters"], [4, "data-types-and-parameters"], [5, "data-types-and-parameters"], [6, "data-types-and-parameters"], [7, "data-types-and-parameters"], [8, "data-types-and-parameters"], [9, "data-types-and-parameters"], [10, "data-types-and-parameters"], [11, "data-types-and-parameters"], [12, "data-types-and-parameters"], [13, "data-types-and-parameters"], [14, "data-types-and-parameters"], [16, "data-types-and-parameters"], [17, "data-types-and-parameters"], [18, "data-types-and-parameters"], [19, "data-types-and-parameters"], [20, "data-types-and-parameters"], [21, "data-types-and-parameters"], [23, "data-types-and-parameters"]], "4.1.1 Parameters": [[0, "parameters"], [1, "parameters"], [3, "parameters"], [4, "parameters"], [5, "parameters"], [6, "parameters"], [7, "parameters"], [8, "parameters"], [9, "parameters"], [10, "parameters"], [11, "parameters"], [12, "parameters"], [13, "parameters"], [14, "parameters"], [16, "parameters"], [17, "parameters"], [18, "parameters"], [19, "parameters"], [20, "parameters"], [21, "parameters"], [23, "parameters"]], "4.1.2 Class/structs/data types": [[0, "class-structs-data-types"], [1, "class-structs-data-types"], [3, "class-structs-data-types"], [4, "class-structs-data-types"], [5, "class-structs-data-types"], [6, "class-structs-data-types"], [7, "class-structs-data-types"], [8, "class-structs-data-types"], [9, "class-structs-data-types"], [10, "class-structs-data-types"], [11, "class-structs-data-types"], [12, "class-structs-data-types"], [13, "class-structs-data-types"], [14, "class-structs-data-types"], [16, "class-structs-data-types"], [17, "class-structs-data-types"], [18, "class-structs-data-types"], [19, "class-structs-data-types"], [20, "class-structs-data-types"], [21, "class-structs-data-types"], [23, "class-structs-data-types"]], "4.2 Methods": [[0, "methods"], [1, "methods"], [2, "methods"], [3, "methods"], [4, "methods"], [5, "methods"], [6, "methods"], [7, "methods"], [8, "methods"], [9, "methods"], [10, "methods"], [11, "methods"], [12, "methods"], [13, "methods"], [14, "methods"], [16, "methods"], [17, "methods"], [18, "methods"], [19, "methods"], [20, "methods"], [21, "methods"], [23, "methods"], [24, "methods"]], "4.2.1 Creation": [[0, "creation"], [19, "creation"]], "4.2.2 Initialization": [[0, "initialization"], [19, "initialization"]], "4.2.3 Retrieval": [[0, "retrieval"], [19, "retrieval"]], "4.2.4 Computation": [[0, "computation"], [19, "computation"]], "4.2.5 Destruction and removal": [[0, "destruction-and-removal"], [19, "destruction-and-removal"]], "5 Verification and Testing": [[0, "verification-and-testing"], [1, "verification-and-testing"], [2, "verification-and-testing"], [3, "verification-and-testing"], [4, "verification-and-testing"], [5, "verification-and-testing"], [6, "verification-and-testing"], [7, "verification-and-testing"], [8, "verification-and-testing"], [9, "verification-and-testing"], [10, "verification-and-testing"], [11, "verification-and-testing"], [12, "verification-and-testing"], [13, "verification-and-testing"], [14, "verification-and-testing"], [15, "verification-and-testing"], [16, "verification-and-testing"], [17, "verification-and-testing"], [18, "verification-and-testing"], [19, "verification-and-testing"], [20, "verification-and-testing"], [21, "verification-and-testing"], [22, "verification-and-testing"], [23, "verification-and-testing"], [24, "verification-and-testing"]], "5.1 Test multiple auxiliary states": [[0, "test-multiple-auxiliary-states"]], "5.2 Test computation": [[0, "test-computation"], [19, "test-computation"]], "Auxiliary variables": [[1, "auxiliary-variables"]], "2.1 Requirement: Functions that compute auxiliary variables should have simple, intuitive calling arguments": [[1, "requirement-functions-that-compute-auxiliary-variables-should-have-simple-intuitive-calling-arguments"]], "2.2 Requirement: Auxiliary variables computations should be able to be grouped under different outer loops over mesh locations": [[1, "requirement-auxiliary-variables-computations-should-be-able-to-be-grouped-under-different-outer-loops-over-mesh-locations"]], "2.3 Requirement: Vectorization on CPU architectures": [[1, "requirement-vectorization-on-cpu-architectures"]], "2.4 Requirement: Configuration options": [[1, "requirement-configuration-options"]], "2.5 Requirement: Output": [[1, "requirement-output"]], "2.6 Desired: Small memory footprint": [[1, "desired-small-memory-footprint"]], "4.2.1 Constructor": [[1, "constructor"], [5, "constructor"], [9, "constructor"], [17, "constructor"], [20, "constructor"]], "4.2.2 Compute methods": [[1, "compute-methods"]], "5.1 Unit testing": [[1, "unit-testing"], [20, "unit-testing"]], "5.2 Convergence testing": [[1, "convergence-testing"], [20, "convergence-testing"]], "Broadcast": [[2, "broadcast"]], "2.1 Requirement: Broadcast all supported data types": [[2, "requirement-broadcast-all-supported-data-types"]], "2.2 Requirement: Broadcast scalars and vectors": [[2, "requirement-broadcast-scalars-and-vectors"]], "2.3 Requirement: Broadcast from any rank": [[2, "requirement-broadcast-from-any-rank"]], "2.4 Desired: Broadcast within alternative environments": [[2, "desired-broadcast-within-alternative-environments"]], "2.5 Desired: Non-blocking broadcast": [[2, "desired-non-blocking-broadcast"]], "4.2.1 Broadcast from master task in default environment": [[2, "broadcast-from-master-task-in-default-environment"]], "4.2.2 Broadcast from another rank within default environment": [[2, "broadcast-from-another-rank-within-default-environment"]], "4.2.3 Broadcast from master rank within a different environment": [[2, "broadcast-from-master-rank-within-a-different-environment"]], "4.2.4 Broadcast from another rank within a different environment": [[2, "broadcast-from-another-rank-within-a-different-environment"]], "4.2.5 Broadcast of vector variables": [[2, "broadcast-of-vector-variables"]], "4.2.6 Non-blocking broadcasts": [[2, "non-blocking-broadcasts"]], "5.1 Test scalars of all data types": [[2, "test-scalars-of-all-data-types"]], "5.2 Test vectors of all types": [[2, "test-vectors-of-all-types"]], "5.3 Test broadcast from other ranks": [[2, "test-broadcast-from-other-ranks"]], "5.4 Test non-blocking broadcasts": [[2, "test-non-blocking-broadcasts"]], "5.5 Test within a subset environment": [[2, "test-within-a-subset-environment"]], "Config": [[3, "config"]], "2.1 Requirement: Human readability": [[3, "requirement-human-readability"]], "2.2 Requirement: Standard format": [[3, "requirement-standard-format"]], "2.3 Requirement: Archiving and provenance": [[3, "requirement-archiving-and-provenance"]], "2.4 Requirement: Internal accessibility": [[3, "requirement-internal-accessibility"]], "2.5 Requirement: Support of data types": [[3, "requirement-support-of-data-types"]], "2.6 Requirement: Efficiency and parallelism": [[3, "requirement-efficiency-and-parallelism"]], "2.8 Desired: Single configuration input": [[3, "desired-single-configuration-input"]], "2.9 Required: Hierarchy or grouping": [[3, "required-hierarchy-or-grouping"]], "2.10 Requirement: Language support": [[3, "requirement-language-support"]], "2.11 Requirement: Optional or missing values": [[3, "requirement-optional-or-missing-values"]], "2.12 Requirement: Extra values": [[3, "requirement-extra-values"]], "2.13 Desired: Automated generation of default input and error checking": [[3, "desired-automated-generation-of-default-input-and-error-checking"]], "2.14 Desired: Acceptable values": [[3, "desired-acceptable-values"]], "4.2.1 File read and master config": [[3, "file-read-and-master-config"]], "4.2.2 Get/Retrieval": [[3, "get-retrieval"], [13, "get-retrieval"]], "4.2.3 Change an existing value": [[3, "change-an-existing-value"]], "4.2.3 Adding new entries": [[3, "adding-new-entries"]], "4.2.4 Existence": [[3, "existence"]], "4.2.5 File write": [[3, "file-write"]], "4.2.6 Constructor/destructor": [[3, "constructor-destructor"]], "4.3 Documentation and Auto-generation of Default Inputs": [[3, "documentation-and-auto-generation-of-default-inputs"]], "5.1 Test default constructor": [[3, "test-default-constructor"]], "5.2 Test Set function": [[3, "test-set-function"]], "5.3 Test Get function": [[3, "test-get-function"]], "5.4 Test for missing variables": [[3, "test-for-missing-variables"]], "5.5 Test write and re-read": [[3, "test-write-and-re-read"]], "DataTypes": [[4, "datatypes"]], "2.1 Requirement: Both flexible and fixed floating point": [[4, "requirement-both-flexible-and-fixed-floating-point"]], "2.2 Desired: Readability for array types": [[4, "desired-readability-for-array-types"]], "2.3 Desired: Fixed width integer types": [[4, "desired-fixed-width-integer-types"]], "2.4 Desired: Interoperability": [[4, "desired-interoperability"]], "2.5 Future: Floating point conversion": [[4, "future-floating-point-conversion"]], "5.1 Test explicit types": [[4, "test-explicit-types"]], "5.2 Test global switch for default real size": [[4, "test-global-switch-for-default-real-size"]], "5.3 Kokkos array test": [[4, "kokkos-array-test"]], "Decomp": [[5, "decomp"]], "2.1 Requirement: Mesh partition": [[5, "requirement-mesh-partition"]], "2.2 Requirement: Metis option": [[5, "requirement-metis-option"]], "2.3 Required: Online partitioning": [[5, "required-online-partitioning"]], "2.4 Required: Input mesh information": [[5, "required-input-mesh-information"]], "2.5 Required: All mesh locations": [[5, "required-all-mesh-locations"]], "2.6 Required: Halo": [[5, "required-halo"]], "2.7 Required: Local to global index mapping": [[5, "required-local-to-global-index-mapping"]], "2.8 Required: Local sorting": [[5, "required-local-sorting"]], "2.9 Required: Release memory": [[5, "required-release-memory"]], "2.10 Desired: Weighted partitioning option": [[5, "desired-weighted-partitioning-option"]], "2.11 Desired: Multiple partitions of same mesh": [[5, "desired-multiple-partitions-of-same-mesh"]], "2.12 Desired: Multiple domains, sub-blocking or coloring": [[5, "desired-multiple-domains-sub-blocking-or-coloring"]], "4.2.2 Destructor": [[5, "destructor"], [9, "destructor"], [17, "destructor"]], "5.1 Test Metis": [[5, "test-metis"]], "5.2 Back compatibility": [[5, "back-compatibility"]], "5.3 Check global IDs": [[5, "check-global-ids"]], "Driver and Component Layer": [[6, "driver-and-component-layer"]], "2.1 Requirement: Component interfaces": [[6, "requirement-component-interfaces"]], "2.2 Requirement: Standalone driver": [[6, "requirement-standalone-driver"]], "2.3 Requirement: Encapsulation and persistent model state": [[6, "requirement-encapsulation-and-persistent-model-state"]], "2.4 Requirement: Managing environments": [[6, "requirement-managing-environments"]], "2.5 Requirement: Run method": [[6, "requirement-run-method"]], "2.6 Requirement: Finalize method": [[6, "requirement-finalize-method"]], "2.7 Requirement: Init method": [[6, "requirement-init-method"]], "4.2.1 Init": [[6, "init"]], "4.2.2 Run": [[6, "run"]], "4.2.3 Finalize": [[6, "finalize"]], "4.2.4 Standalone driver (main)": [[6, "standalone-driver-main"]], "4.2.5 Coupler-component interfaces": [[6, "coupler-component-interfaces"]], "5.1 Test forward model": [[6, "test-forward-model"]], "5.2 Coupled model testing": [[6, "coupled-model-testing"]], "ErrorHandler (Error)": [[7, "errorhandler-error"]], "2.1 Requirement: Logging errors": [[7, "requirement-logging-errors"]], "2.2 Requirement: Levels of error severity": [[7, "requirement-levels-of-error-severity"]], "2.3 Requirement: Abort on error": [[7, "requirement-abort-on-error"]], "2.4 Requirement: Generate stack trace": [[7, "requirement-generate-stack-trace"]], "2.5 Requirement: Identify task id": [[7, "requirement-identify-task-id"]], "2.6 Requirement: Output location": [[7, "requirement-output-location"]], "2.7 Requirement: Success/fail error codes": [[7, "requirement-success-fail-error-codes"]], "2.8 Requirement: Error messages and formatting": [[7, "requirement-error-messages-and-formatting"]], "2.9 Requirement: Accumulated error": [[7, "requirement-accumulated-error"]], "2.10 Desired: Compact error checking": [[7, "desired-compact-error-checking"]], "2.11 Desired: Registering error codes and messages": [[7, "desired-registering-error-codes-and-messages"]], "4.2.1 Macros": [[7, "macros"]], "4.2.2 Other Error methods": [[7, "other-error-methods"]], "5.1 Test all failure modes": [[7, "test-all-failure-modes"]], "Halo": [[8, "halo"]], "2.1 Requirement: Compatible with all types of arrays": [[8, "requirement-compatible-with-all-types-of-arrays"]], "2.2 Requirement: Exchange at all types of mesh elements": [[8, "requirement-exchange-at-all-types-of-mesh-elements"]], "2.3 Requirement: Variable halo depth": [[8, "requirement-variable-halo-depth"]], "2.4 Requirement: Exchange lists": [[8, "requirement-exchange-lists"]], "2.5 Requirement: Send and receive buffers": [[8, "requirement-send-and-receive-buffers"]], "2.6 Requirement: Non-blocking communication": [[8, "requirement-non-blocking-communication"]], "2.7 Requirement: Compatible with device-resident arrays": [[8, "requirement-compatible-with-device-resident-arrays"]], "2.8 Desired: Communicate subset of halo layers": [[8, "desired-communicate-subset-of-halo-layers"]], "2.9 Desired: Exchange multiple arrays simultaneously": [[8, "desired-exchange-multiple-arrays-simultaneously"]], "2.10 Desired: Multiple environments/decompositions": [[8, "desired-multiple-environments-decompositions"]], "2.11 Desired: OpenMP threading": [[8, "desired-openmp-threading"]], "2.12 Desired: Minimize buffer memory allocation/deallocation": [[8, "desired-minimize-buffer-memory-allocation-deallocation"]], "4.2.1 Constructors": [[8, "constructors"]], "4.2.2 Array halo exchange": [[8, "array-halo-exchange"]], "4.2.3 Start receive/send": [[8, "start-receive-send"]], "4.2.4 Buffer pack/unpack": [[8, "buffer-pack-unpack"]], "5.1 Halo exchange tests": [[8, "halo-exchange-tests"]], "Horizontal Mesh": [[9, "horizontal-mesh"], [39, "horizontal-mesh"], [65, "horizontal-mesh"]], "2.1 Requirement: OMEGA will use the previously established MPAS Mesh Spec": [[9, "requirement-omega-will-use-the-previously-established-mpas-mesh-spec"]], "2.2 Requirement: Functionality is needed to read the mesh on the host and transfer relevant data to the device for computation": [[9, "requirement-functionality-is-needed-to-read-the-mesh-on-the-host-and-transfer-relevant-data-to-the-device-for-computation"]], "2.3 Requirement: Zero-based cell, edge, and vertex numbering": [[9, "requirement-zero-based-cell-edge-and-vertex-numbering"]], "2.4 Requirement: Work with Decomp class to decompose mesh": [[9, "requirement-work-with-decomp-class-to-decompose-mesh"]], "2.5 Requirement: Mesh variables will be associated with metadata to describe data": [[9, "requirement-mesh-variables-will-be-associated-with-metadata-to-describe-data"]], "2.6 Requirement: I/O to obtain mesh data": [[9, "requirement-i-o-to-obtain-mesh-data"]], "2.7 Desired: Ability to support multiple independent mesh objects": [[9, "desired-ability-to-support-multiple-independent-mesh-objects"]], "2.8 Desired: OMEGA can read in a reduced number of mesh variables and compute the remaining array information online.": [[9, "desired-omega-can-read-in-a-reduced-number-of-mesh-variables-and-compute-the-remaining-array-information-online"]], "4.2.2 Read": [[9, "read"]], "4.2.3 Compute": [[9, "compute"]], "4.2.4 Device copy creation": [[9, "device-copy-creation"]], "4.2.5 Metadata registration": [[9, "metadata-registration"]], "5.1 Test mesh compute routines": [[9, "test-mesh-compute-routines"]], "Input/Output (IO)": [[10, "input-output-io"]], "2.1 Requirement: Read fields and metadata": [[10, "requirement-read-fields-and-metadata"]], "2.2 Requirement: Write fields and metadata": [[10, "requirement-write-fields-and-metadata"]], "2.3 Requirement: Self-describing formats": [[10, "requirement-self-describing-formats"]], "2.4 Requirement: multiple files/streams": [[10, "requirement-multiple-files-streams"]], "2.5 Requirement: parallel I/O": [[10, "requirement-parallel-i-o"]], "2.6 Requirement: parallel I/O tuning": [[10, "requirement-parallel-i-o-tuning"]], "2.7 Requirement: Data types and type conversion": [[10, "requirement-data-types-and-type-conversion"]], "2.8 Requirement: Kokkos arrays and host/device support": [[10, "requirement-kokkos-arrays-and-host-device-support"]], "2.9 Requirement: Modes on file existence": [[10, "requirement-modes-on-file-existence"]], "2.10 Desired: Asynchronous I/O": [[10, "desired-asynchronous-i-o"]], "2.11 Desired: File compression": [[10, "desired-file-compression"]], "4.2.1 Environment constructor": [[10, "environment-constructor"]], "4.2.2 File open/close": [[10, "file-open-close"]], "4.2.3 Write operations": [[10, "write-operations"]], "4.2.4 Read operations": [[10, "read-operations"]], "4.2.5 Defining IO fields": [[10, "defining-io-fields"]], "5.1 Test via IOStreams": [[10, "test-via-iostreams"]], "IOStreams": [[11, "iostreams"]], "2.1 Requirement: Multiple streams": [[11, "requirement-multiple-streams"]], "2.2 Requirement: Reduced precision": [[11, "requirement-reduced-precision"]], "2.3 Requirement: Contents for each stream": [[11, "requirement-contents-for-each-stream"]], "2.4 Requirement: Exact restart": [[11, "requirement-exact-restart"]], "2.5 Requirement: Restart pointer": [[11, "requirement-restart-pointer"]], "2.6 Requirement: Time intervals": [[11, "requirement-time-intervals"]], "2.7 Requirement: Optional start/stop times": [[11, "requirement-optional-start-stop-times"]], "2.8 Requirement: Filenames": [[11, "requirement-filenames"]], "2.9 Requirement: Multiple time slices per file": [[11, "requirement-multiple-time-slices-per-file"]], "2.10 Requirement: Behavior on file existence": [[11, "requirement-behavior-on-file-existence"]], "2.11 Desired: Time averaging": [[11, "desired-time-averaging"]], "2.12 Desired: Data compression": [[11, "desired-data-compression"]], "4.2.1 Create/Destroy": [[11, "create-destroy"]], "4.2.2 Add fields": [[11, "add-fields"]], "4.2.3 Write streams": [[11, "write-streams"]], "4.2.3 Read streams": [[11, "read-streams"]], "5.1 Test All": [[11, "test-all"], [24, "test-all"]], "Logging": [[12, "logging"]], "2.1 Requirement: Basic logging": [[12, "requirement-basic-logging"]], "2.2 Requirement: Inter-operability with E3SM": [[12, "requirement-inter-operability-with-e3sm"]], "2.3 Requirement: Multi-processing": [[12, "requirement-multi-processing"]], "2.4 Requirement: Multi-threading": [[12, "requirement-multi-threading"]], "2.5 Requirement: Omega data types": [[12, "requirement-omega-data-types"]], "2.6 Requirement: Buffered file input/output": [[12, "requirement-buffered-file-input-output"]], "2.7 Desired: Formatter": [[12, "desired-formatter"]], "2.8 Desired: Output sinks": [[12, "desired-output-sinks"]], "2.9 Desired: Local logging": [[12, "desired-local-logging"]], "4.2.1 Log write": [[12, "log-write"]], "5.1 Test OMEGA logging capabilities": [[12, "test-omega-logging-capabilities"]], "5.2 Test OMEGA data type support": [[12, "test-omega-data-type-support"]], "5.3 Test E3SM inter-operability": [[12, "test-e3sm-inter-operability"]], "MachineEnv": [[13, "machineenv"]], "2.1 Requirement: Initialize MPI in Standalone": [[13, "requirement-initialize-mpi-in-standalone"]], "2.2 Requirement: Create MPI communicator in coupled mode": [[13, "requirement-create-mpi-communicator-in-coupled-mode"]], "2.3 Requirement: Define MPI layouts": [[13, "requirement-define-mpi-layouts"]], "2.4 Requirement: Kokkos initialization": [[13, "requirement-kokkos-initialization"]], "2.5 Requirement: Vector blocking size defined at compile time": [[13, "requirement-vector-blocking-size-defined-at-compile-time"]], "2.6 Desired: Set alternative master task": [[13, "desired-set-alternative-master-task"]], "2.7 Desired: Multiple environments": [[13, "desired-multiple-environments"]], "2.8 Desired: Define threading parameters": [[13, "desired-define-threading-parameters"]], "2.9 Desired: Define other machine parameters": [[13, "desired-define-other-machine-parameters"]], "4.1.3 Default environment": [[13, "default-environment"]], "4.2.1 Initialization": [[13, "initialization"]], "4.2.2 Constructors": [[13, "constructors"]], "4.2.3 Change master task": [[13, "change-master-task"]], "5.1 Test standalone initialization": [[13, "test-standalone-initialization"]], "5.2 Test changing master task": [[13, "test-changing-master-task"]], "5.3 Test multiple environments": [[13, "test-multiple-environments"]], "5.4 Initialization in coupled mode": [[13, "initialization-in-coupled-mode"]], "5.5 Test vector blocking factor": [[13, "test-vector-blocking-factor"]], "Metadata": [[14, "metadata"]], "2.1 Requirement: Data types": [[14, "requirement-data-types"]], "2.2 Requirement: Global and variable metadata": [[14, "requirement-global-and-variable-metadata"]], "2.3 Requirement: Metadata conventions": [[14, "requirement-metadata-conventions"]], "2.4 Requirement: Required metadata": [[14, "requirement-required-metadata"]], "2.5 Requirement: Dimensions": [[14, "requirement-dimensions"]], "2.6 Requirement: Available fields": [[14, "requirement-available-fields"]], "2.7 Desired: Metadata groups": [[14, "desired-metadata-groups"]], "4.2.1 Metadata container creation": [[14, "metadata-container-creation"]], "4.2.2 Add/remove metadata": [[14, "add-remove-metadata"]], "4.2.3 Retrieve metadata": [[14, "retrieve-metadata"]], "4.2.4 Create dimension": [[14, "create-dimension"]], "4.2.5 Retrieve dim length": [[14, "retrieve-dim-length"]], "4.2.6 Existence inquiry": [[14, "existence-inquiry"]], "4.2.6.1 Existence inquiry for metadata container and metadim container": [[14, "existence-inquiry-for-metadata-container-and-metadim-container"]], "4.2.6.2 Existence inquiry for metadata": [[14, "existence-inquiry-for-metadata"]], "4.2.7 Metadata groups": [[14, "metadata-groups"]], "5.1 Test creation/retrieval": [[14, "test-creation-retrieval"]], "5.2 Test global metadata": [[14, "test-global-metadata"]], "5.3 Test inquiry functions": [[14, "test-inquiry-functions"]], "5.4 Test metadata groups": [[14, "test-metadata-groups"]], "5.5 Test CF compliance": [[14, "test-cf-compliance"]], "Omega V0: Shallow Water": [[15, "omega-v0-shallow-water"]], "2.1 Omega-0 will solve the nonlinear shallow water equations, plus inactive tracers": [[15, "omega-0-will-solve-the-nonlinear-shallow-water-equations-plus-inactive-tracers"]], "2.2 Numerical method will be the TRiSK formulation": [[15, "numerical-method-will-be-the-trisk-formulation"]], "2.3 Omega-0 will use MPAS format unstructured-mesh domains": [[15, "omega-0-will-use-mpas-format-unstructured-mesh-domains"]], "2.4 Omega-0 will interface with polaris for preprocessing and postprocessing": [[15, "omega-0-will-interface-with-polaris-for-preprocessing-and-postprocessing"]], "2.5 Omega-0 will run portably on various DOE architectures (CPU and GPU nodes)": [[15, "omega-0-will-run-portably-on-various-doe-architectures-cpu-and-gpu-nodes"]], "2.6 Omega-0 will run on multi-node with domain decomposition": [[15, "omega-0-will-run-on-multi-node-with-domain-decomposition"]], "2.7 Correct convergence rates of operators and exact solutions": [[15, "correct-convergence-rates-of-operators-and-exact-solutions"]], "2.8 Conservation of volume and tracer": [[15, "conservation-of-volume-and-tracer"]], "2.9 Performance will be at least as good or better than MPAS-Ocean": [[15, "performance-will-be-at-least-as-good-or-better-than-mpas-ocean"]], "2.10 Full-node GPU throughput will be comparable or better than full-node CPU throughput": [[15, "full-node-gpu-throughput-will-be-comparable-or-better-than-full-node-cpu-throughput"]], "3.1 Governing Equations": [[15, "governing-equations"]], "3.1.1 Continuous Equations": [[15, "continuous-equations"]], "3.1.2 Discrete Equations": [[15, "discrete-equations"]], "3.2 Variable Definitions": [[15, "variable-definitions"]], "3.2 Operator Formulation": [[15, "operator-formulation"]], "3.2.1. Divergence": [[15, "divergence"]], "3.2.2. Gradient": [[15, "gradient"]], "3.2.3. Curl": [[15, "curl"]], "3.2.4. Perpendicular vector component": [[15, "perpendicular-vector-component"]], "3.2.5. Perpendicular Gradient": [[15, "perpendicular-gradient"]], "3.2.6. Cell to Edge Interpolation": [[15, "cell-to-edge-interpolation"]], "3.2.7. Vertex to Edge Interpolation": [[15, "vertex-to-edge-interpolation"]], "3.2.8. Cell to Vertex Interpolation": [[15, "cell-to-vertex-interpolation"]], "3.2.9. Vertex to Cell Interpolation": [[15, "vertex-to-cell-interpolation"]], "3.2.10. Vector from Edge to Cell": [[15, "vector-from-edge-to-cell"]], "3.3 Momentum Terms": [[15, "momentum-terms"]], "3.3.1. Kinetic energy gradient": [[15, "kinetic-energy-gradient"]], "3.3.2. Potential vorticity term": [[15, "potential-vorticity-term"]], "3.3.3. Sea surface height gradient": [[15, "sea-surface-height-gradient"]], "3.3.4. Del2 momentum dissipation": [[15, "del2-momentum-dissipation"]], "3.3.5. Del4 momentum dissipation": [[15, "del4-momentum-dissipation"]], "3.3.6. Rayleigh Drag": [[15, "rayleigh-drag"]], "3.3.7. Bottom drag": [[15, "bottom-drag"]], "3.3.8. Wind forcing": [[15, "wind-forcing"]], "3.4 Thickness and Tracer Terms": [[15, "thickness-and-tracer-terms"]], "3.4.1. Tracer advection": [[15, "tracer-advection"]], "3.4.2. Del2 tracer diffusion": [[15, "del2-tracer-diffusion"]], "3.4.3. Del4 tracer diffusion": [[15, "del4-tracer-diffusion"]], "5.1 Convergence of individual terms": [[15, "convergence-of-individual-terms"]], "5.2 Inertia Gravity Wave: linearized shallow water, no tracers": [[15, "inertia-gravity-wave-linearized-shallow-water-no-tracers"]], "5.3 Manufactured Solution: full nonlinear shallow water, no tracers": [[15, "manufactured-solution-full-nonlinear-shallow-water-no-tracers"]], "5.4 Tracer transport on a sphere": [[15, "tracer-transport-on-a-sphere"]], "5.5 Performance testing": [[15, "performance-testing"]], "5.6 Shallow water tests on spherical domains and with realistic coastlines": [[15, "shallow-water-tests-on-spherical-domains-and-with-realistic-coastlines"]], "5.7 Further tests for Omega-0": [[15, "further-tests-for-omega-0"]], "References": [[15, "references"]], "Global Reductions": [[16, "global-reductions"], [48, "global-reductions"], [74, "global-reductions"]], "2.1 Requirement: Global sums": [[16, "requirement-global-sums"]], "2.2 Requirement: Global min/max": [[16, "requirement-global-min-max"]], "2.3 Requirement: Data types": [[16, "requirement-data-types"]], "2.4 Requirement: Sums with product": [[16, "requirement-sums-with-product"]], "2.5 Requirement: Restricted address space": [[16, "requirement-restricted-address-space"]], "2.6 Requirement: Multiple fields/arrays": [[16, "requirement-multiple-fields-arrays"]], "2.7 Requirement: Other environments/decompositions": [[16, "requirement-other-environments-decompositions"]], "2.8 Requirement: Reproducibility": [[16, "requirement-reproducibility"]], "2.9 Requirement: Accelerators and location": [[16, "requirement-accelerators-and-location"]], "2.10 Requirement: CPU threading": [[16, "requirement-cpu-threading"]], "2.11 Desired: Other reduction operations": [[16, "desired-other-reduction-operations"]], "4.2.1 Global sum": [[16, "global-sum"]], "4.2.2 Global sum with product": [[16, "global-sum-with-product"]], "4.2.3 Global sum multi-field": [[16, "global-sum-multi-field"]], "4.2.4 Global sum multi-field with product": [[16, "global-sum-multi-field-with-product"]], "4.2.5 Global minval": [[16, "global-minval"]], "4.2.6 Global maxval": [[16, "global-maxval"]], "5.1 Test basics": [[16, "test-basics"]], "5.2 Reproducibility": [[16, "reproducibility"]], "5.3 Restricted index range": [[16, "restricted-index-range"]], "5.4 Sum with product": [[16, "sum-with-product"]], "5.5 Multi-field sums": [[16, "multi-field-sums"]], "5.6 Min/Max": [[16, "min-max"]], "State": [[17, "state"]], "2.1 Requirement: State should register prognostic variables with IOStreams": [[17, "requirement-state-should-register-prognostic-variables-with-iostreams"]], "2.2 Requirement: Update timestep": [[17, "requirement-update-timestep"]], "2.3 Requirement: Can be used as a common data type for tendency and provis variables": [[17, "requirement-can-be-used-as-a-common-data-type-for-tendency-and-provis-variables"]], "4.2.3 Time level update": [[17, "time-level-update"]], "5.1 Test read": [[17, "test-read"]], "5.2 Test time level update": [[17, "test-time-level-update"]], "Template": [[18, "template"]], "2.1 Requirement: xxx": [[18, "requirement-xxx"]], "2.2 Requirement: yyy": [[18, "requirement-yyy"]], "2.3 Desired: zzz": [[18, "desired-zzz"]], "5.1 Test xxx": [[18, "test-xxx"]], "5.2 Test yyy": [[18, "test-yyy"]], "Tendencies": [[19, "tendencies"], [49, "tendencies"], [75, "tendencies"]], "2.1 Requirement: Computation of tendency terms": [[19, "requirement-computation-of-tendency-terms"]], "2.2 Requirement: Multiple tendencies can be present": [[19, "requirement-multiple-tendencies-can-be-present"]], "5.1 Test multiple tendencies instances": [[19, "test-multiple-tendencies-instances"]], "Tendency": [[20, "tendency"]], "2.1 Requirement: Tendencies should be able to be grouped under different outer loops over mesh locations.": [[20, 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47, 69, 72], "cmake": [29, 72], "setup": 29, "develop": [30, 44, 47, 54], "conda": [30, 47], "instal": 30, "miniforge3": 30, "ocninit": 36, "ocnrun": 36, "ocnfin": 36, "lint": 43, "enabl": 43, "bypass": 43, "c": 43, "python": 43, "pacakg": 43, "logger": 44, "custom": 44, "machenv": [45, 70], "quick": [47, 73], "up": 47, "fork": 47, "out": 47, "ctest": 47, "util": [47, 48, 52], "debug": 47, "tip": 47, "parmeti": 47, "style": 47, "v": 47, "globalmin": 48, "globalmax": 48, "timemgr": [51, 77], "descript": 51, "stepper": 52, "timestepp": 52, "do": 52, "getter": 52, "concept": 53, "kei": 53, "api": 53, "getallhost": 53, "gethostbyindex": 53, "getfieldbyindex": 53, "updatetimelevel": 53, "user": [54, 73], "": 54, "guid": 54, "includ": 57, "your": 57, "specifi": 57, "manual": 72, "prepar": 72, "come": 73, "soon": 73, "defint": 79, "tracerdef": 79, "inc": 79, "yaml": 79}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 8, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1, "sphinx": 57}, "alltitles": {"AuxiliaryState": [[0, "auxiliarystate"]], "1 Overview": [[0, "overview"], [1, "overview"], [2, "overview"], [3, "overview"], [4, "overview"], [5, "overview"], [6, "overview"], [7, "overview"], [8, "overview"], [9, "overview"], [10, "overview"], [11, "overview"], [12, "overview"], [13, "overview"], [14, "overview"], [15, "overview"], [16, "overview"], [17, "overview"], [18, "overview"], [19, "overview"], [20, "overview"], [21, "overview"], [22, "overview"], [23, "overview"], [24, "overview"]], "2 Requirements": [[0, "requirements"], [1, "requirements"], [2, "requirements"], [3, "requirements"], [4, "requirements"], [5, "requirements"], [6, "requirements"], [7, "requirements"], [8, "requirements"], [9, "requirements"], [10, "requirements"], [11, "requirements"], [12, "requirements"], [13, "requirements"], [14, "requirements"], [15, "requirements"], [16, "requirements"], [17, "requirements"], [18, "requirements"], [19, "requirements"], [20, "requirements"], [21, "requirements"], [22, "requirements"], [23, "requirements"], [24, "requirements"]], "2.1 Requirement: Auxiliary state should register auxiliary variables with IOStreams": [[0, "requirement-auxiliary-state-should-register-auxiliary-variables-with-iostreams"]], "2.2 Requirement: Computation of auxiliary variables": [[0, "requirement-computation-of-auxiliary-variables"]], "2.3 Requirement: Multiple auxiliary states can be present": [[0, "requirement-multiple-auxiliary-states-can-be-present"]], "3 Algorithmic Formulation": [[0, "algorithmic-formulation"], [1, "algorithmic-formulation"], [2, "algorithmic-formulation"], [3, "algorithmic-formulation"], [4, "algorithmic-formulation"], [5, "algorithmic-formulation"], [6, "algorithmic-formulation"], [7, "algorithmic-formulation"], [8, "algorithmic-formulation"], [9, "algorithmic-formulation"], [10, "algorithmic-formulation"], [11, "algorithmic-formulation"], [12, "algorithmic-formulation"], [13, "algorithmic-formulation"], [14, "algorithmic-formulation"], [15, "algorithmic-formulation"], [16, "algorithmic-formulation"], [17, "algorithmic-formulation"], [18, "algorithmic-formulation"], [19, "algorithmic-formulation"], [20, "algorithmic-formulation"], [21, "algorithmic-formulation"], [22, "algorithmic-formulation"], [23, "algorithmic-formulation"], [24, "algorithmic-formulation"]], "4 Design": [[0, "design"], [1, "design"], [2, "design"], [3, "design"], [4, "design"], [5, "design"], [6, "design"], [7, "design"], [8, "design"], [9, "design"], [10, "design"], [11, "design"], [12, "design"], [13, "design"], [14, "design"], [15, "design"], [16, "design"], [17, "design"], [18, "design"], [19, "design"], [20, "design"], [21, "design"], [22, "design"], [23, "design"], [24, "design"]], "4.1 Data types and parameters": [[0, "data-types-and-parameters"], [1, "data-types-and-parameters"], [2, "data-types-and-parameters"], [3, "data-types-and-parameters"], [4, "data-types-and-parameters"], [5, "data-types-and-parameters"], [6, "data-types-and-parameters"], [7, "data-types-and-parameters"], [8, "data-types-and-parameters"], [9, "data-types-and-parameters"], [10, "data-types-and-parameters"], [11, "data-types-and-parameters"], [12, "data-types-and-parameters"], [13, "data-types-and-parameters"], [14, "data-types-and-parameters"], [16, "data-types-and-parameters"], [17, "data-types-and-parameters"], [18, "data-types-and-parameters"], [19, "data-types-and-parameters"], [20, "data-types-and-parameters"], [21, "data-types-and-parameters"], [23, "data-types-and-parameters"]], "4.1.1 Parameters": [[0, "parameters"], [1, "parameters"], [3, "parameters"], [4, "parameters"], [5, "parameters"], [6, "parameters"], [7, "parameters"], [8, "parameters"], [9, "parameters"], [10, "parameters"], [11, "parameters"], [12, "parameters"], [13, "parameters"], [14, "parameters"], [16, "parameters"], [17, "parameters"], [18, "parameters"], [19, "parameters"], [20, "parameters"], [21, "parameters"], [23, "parameters"]], "4.1.2 Class/structs/data types": [[0, "class-structs-data-types"], [1, "class-structs-data-types"], [3, "class-structs-data-types"], [4, "class-structs-data-types"], [5, "class-structs-data-types"], [6, "class-structs-data-types"], [7, "class-structs-data-types"], [8, "class-structs-data-types"], [9, "class-structs-data-types"], [10, "class-structs-data-types"], [11, "class-structs-data-types"], [12, "class-structs-data-types"], [13, "class-structs-data-types"], [14, "class-structs-data-types"], [16, "class-structs-data-types"], [17, "class-structs-data-types"], [18, "class-structs-data-types"], [19, "class-structs-data-types"], [20, "class-structs-data-types"], [21, "class-structs-data-types"], [23, "class-structs-data-types"]], "4.2 Methods": [[0, "methods"], [1, "methods"], [2, "methods"], [3, "methods"], [4, "methods"], [5, "methods"], [6, "methods"], [7, "methods"], [8, "methods"], [9, "methods"], [10, "methods"], [11, "methods"], [12, "methods"], [13, "methods"], [14, "methods"], [16, "methods"], [17, "methods"], [18, "methods"], [19, "methods"], [20, "methods"], [21, "methods"], [23, "methods"], [24, "methods"]], "4.2.1 Creation": [[0, "creation"], [19, "creation"]], "4.2.2 Initialization": [[0, "initialization"], [19, "initialization"]], "4.2.3 Retrieval": [[0, "retrieval"], [19, "retrieval"]], "4.2.4 Computation": [[0, "computation"], [19, "computation"]], "4.2.5 Destruction and removal": [[0, "destruction-and-removal"], [19, "destruction-and-removal"]], "5 Verification and Testing": [[0, "verification-and-testing"], [1, "verification-and-testing"], [2, "verification-and-testing"], [3, "verification-and-testing"], [4, "verification-and-testing"], [5, "verification-and-testing"], [6, "verification-and-testing"], [7, "verification-and-testing"], [8, "verification-and-testing"], [9, "verification-and-testing"], [10, "verification-and-testing"], [11, "verification-and-testing"], [12, "verification-and-testing"], [13, "verification-and-testing"], [14, "verification-and-testing"], [15, "verification-and-testing"], [16, "verification-and-testing"], [17, "verification-and-testing"], [18, "verification-and-testing"], [19, "verification-and-testing"], [20, "verification-and-testing"], [21, "verification-and-testing"], [22, "verification-and-testing"], [23, "verification-and-testing"], [24, "verification-and-testing"]], "5.1 Test multiple auxiliary states": [[0, "test-multiple-auxiliary-states"]], "5.2 Test computation": [[0, "test-computation"], [19, "test-computation"]], "Auxiliary variables": [[1, "auxiliary-variables"]], "2.1 Requirement: Functions that compute auxiliary variables should have simple, intuitive calling arguments": [[1, "requirement-functions-that-compute-auxiliary-variables-should-have-simple-intuitive-calling-arguments"]], "2.2 Requirement: Auxiliary variables computations should be able to be grouped under different outer loops over mesh locations": [[1, "requirement-auxiliary-variables-computations-should-be-able-to-be-grouped-under-different-outer-loops-over-mesh-locations"]], "2.3 Requirement: Vectorization on CPU architectures": [[1, "requirement-vectorization-on-cpu-architectures"]], "2.4 Requirement: Configuration options": [[1, "requirement-configuration-options"]], "2.5 Requirement: Output": [[1, "requirement-output"]], "2.6 Desired: Small memory footprint": [[1, "desired-small-memory-footprint"]], "4.2.1 Constructor": [[1, "constructor"], [5, "constructor"], [9, "constructor"], [17, "constructor"], [20, "constructor"]], "4.2.2 Compute methods": [[1, "compute-methods"]], "5.1 Unit testing": [[1, "unit-testing"], [20, "unit-testing"]], "5.2 Convergence testing": [[1, "convergence-testing"], [20, "convergence-testing"]], "Broadcast": [[2, "broadcast"]], "2.1 Requirement: Broadcast all supported data types": [[2, "requirement-broadcast-all-supported-data-types"]], "2.2 Requirement: Broadcast scalars and vectors": [[2, "requirement-broadcast-scalars-and-vectors"]], "2.3 Requirement: Broadcast from any rank": [[2, "requirement-broadcast-from-any-rank"]], "2.4 Desired: Broadcast within alternative environments": [[2, "desired-broadcast-within-alternative-environments"]], "2.5 Desired: Non-blocking broadcast": [[2, "desired-non-blocking-broadcast"]], "4.2.1 Broadcast from master task in default environment": [[2, "broadcast-from-master-task-in-default-environment"]], "4.2.2 Broadcast from another rank within default environment": [[2, "broadcast-from-another-rank-within-default-environment"]], "4.2.3 Broadcast from master rank within a different environment": [[2, "broadcast-from-master-rank-within-a-different-environment"]], "4.2.4 Broadcast from another rank within a different environment": [[2, "broadcast-from-another-rank-within-a-different-environment"]], "4.2.5 Broadcast of vector variables": [[2, "broadcast-of-vector-variables"]], "4.2.6 Non-blocking broadcasts": [[2, "non-blocking-broadcasts"]], "5.1 Test scalars of all data types": [[2, "test-scalars-of-all-data-types"]], "5.2 Test vectors of all types": [[2, "test-vectors-of-all-types"]], "5.3 Test broadcast from other ranks": [[2, "test-broadcast-from-other-ranks"]], "5.4 Test non-blocking broadcasts": [[2, "test-non-blocking-broadcasts"]], "5.5 Test within a subset environment": [[2, "test-within-a-subset-environment"]], "Config": [[3, "config"]], "2.1 Requirement: Human readability": [[3, "requirement-human-readability"]], "2.2 Requirement: Standard format": [[3, "requirement-standard-format"]], "2.3 Requirement: Archiving and provenance": [[3, "requirement-archiving-and-provenance"]], "2.4 Requirement: Internal accessibility": [[3, "requirement-internal-accessibility"]], "2.5 Requirement: Support of data types": [[3, "requirement-support-of-data-types"]], "2.6 Requirement: Efficiency and parallelism": [[3, "requirement-efficiency-and-parallelism"]], "2.8 Desired: Single configuration input": [[3, "desired-single-configuration-input"]], "2.9 Required: Hierarchy or grouping": [[3, "required-hierarchy-or-grouping"]], "2.10 Requirement: Language support": [[3, "requirement-language-support"]], "2.11 Requirement: Optional or missing values": [[3, "requirement-optional-or-missing-values"]], "2.12 Requirement: Extra values": [[3, "requirement-extra-values"]], "2.13 Desired: Automated generation of default input and error checking": [[3, "desired-automated-generation-of-default-input-and-error-checking"]], "2.14 Desired: Acceptable values": [[3, "desired-acceptable-values"]], "4.2.1 File read and master config": [[3, "file-read-and-master-config"]], "4.2.2 Get/Retrieval": [[3, "get-retrieval"], [13, "get-retrieval"]], "4.2.3 Change an existing value": [[3, "change-an-existing-value"]], "4.2.3 Adding new entries": [[3, "adding-new-entries"]], "4.2.4 Existence": [[3, "existence"]], "4.2.5 File write": [[3, "file-write"]], "4.2.6 Constructor/destructor": [[3, "constructor-destructor"]], "4.3 Documentation and Auto-generation of Default Inputs": [[3, "documentation-and-auto-generation-of-default-inputs"]], "5.1 Test default constructor": [[3, "test-default-constructor"]], "5.2 Test Set function": [[3, "test-set-function"]], "5.3 Test Get function": [[3, "test-get-function"]], "5.4 Test for missing variables": [[3, "test-for-missing-variables"]], "5.5 Test write and re-read": [[3, "test-write-and-re-read"]], "DataTypes": [[4, "datatypes"]], "2.1 Requirement: Both flexible and fixed floating point": [[4, "requirement-both-flexible-and-fixed-floating-point"]], "2.2 Desired: Readability for array types": [[4, "desired-readability-for-array-types"]], "2.3 Desired: Fixed width integer types": [[4, "desired-fixed-width-integer-types"]], "2.4 Desired: Interoperability": [[4, "desired-interoperability"]], "2.5 Future: Floating point conversion": [[4, "future-floating-point-conversion"]], "5.1 Test explicit types": [[4, "test-explicit-types"]], "5.2 Test global switch for default real size": [[4, "test-global-switch-for-default-real-size"]], "5.3 Kokkos array test": [[4, "kokkos-array-test"]], "Decomp": [[5, "decomp"]], "2.1 Requirement: Mesh partition": [[5, "requirement-mesh-partition"]], "2.2 Requirement: Metis option": [[5, "requirement-metis-option"]], "2.3 Required: Online partitioning": [[5, "required-online-partitioning"]], "2.4 Required: Input mesh information": [[5, "required-input-mesh-information"]], "2.5 Required: All mesh locations": [[5, "required-all-mesh-locations"]], "2.6 Required: Halo": [[5, "required-halo"]], "2.7 Required: Local to global index mapping": [[5, "required-local-to-global-index-mapping"]], "2.8 Required: Local sorting": [[5, "required-local-sorting"]], "2.9 Required: Release memory": [[5, "required-release-memory"]], "2.10 Desired: Weighted partitioning option": [[5, "desired-weighted-partitioning-option"]], "2.11 Desired: Multiple partitions of same mesh": [[5, "desired-multiple-partitions-of-same-mesh"]], "2.12 Desired: Multiple domains, sub-blocking or coloring": [[5, "desired-multiple-domains-sub-blocking-or-coloring"]], "4.2.2 Destructor": [[5, "destructor"], [9, "destructor"], [17, "destructor"]], "5.1 Test Metis": [[5, "test-metis"]], "5.2 Back compatibility": [[5, "back-compatibility"]], "5.3 Check global IDs": [[5, "check-global-ids"]], "Driver and Component Layer": [[6, "driver-and-component-layer"]], "2.1 Requirement: Component interfaces": [[6, "requirement-component-interfaces"]], "2.2 Requirement: Standalone driver": [[6, "requirement-standalone-driver"]], "2.3 Requirement: Encapsulation and persistent model state": [[6, "requirement-encapsulation-and-persistent-model-state"]], "2.4 Requirement: Managing environments": [[6, "requirement-managing-environments"]], "2.5 Requirement: Run method": [[6, "requirement-run-method"]], "2.6 Requirement: Finalize method": [[6, "requirement-finalize-method"]], "2.7 Requirement: Init method": [[6, "requirement-init-method"]], "4.2.1 Init": [[6, "init"]], "4.2.2 Run": [[6, "run"]], "4.2.3 Finalize": [[6, "finalize"]], "4.2.4 Standalone driver (main)": [[6, "standalone-driver-main"]], "4.2.5 Coupler-component interfaces": [[6, "coupler-component-interfaces"]], "5.1 Test forward model": [[6, "test-forward-model"]], "5.2 Coupled model testing": [[6, "coupled-model-testing"]], "ErrorHandler (Error)": [[7, "errorhandler-error"]], "2.1 Requirement: Logging errors": [[7, "requirement-logging-errors"]], "2.2 Requirement: Levels of error severity": [[7, "requirement-levels-of-error-severity"]], "2.3 Requirement: Abort on error": [[7, "requirement-abort-on-error"]], "2.4 Requirement: Generate stack trace": [[7, "requirement-generate-stack-trace"]], "2.5 Requirement: Identify task id": [[7, "requirement-identify-task-id"]], "2.6 Requirement: Output location": [[7, "requirement-output-location"]], "2.7 Requirement: Success/fail error codes": [[7, "requirement-success-fail-error-codes"]], "2.8 Requirement: Error messages and formatting": [[7, "requirement-error-messages-and-formatting"]], "2.9 Requirement: Accumulated error": [[7, "requirement-accumulated-error"]], "2.10 Desired: Compact error checking": [[7, "desired-compact-error-checking"]], "2.11 Desired: Registering error codes and messages": [[7, "desired-registering-error-codes-and-messages"]], "4.2.1 Macros": [[7, "macros"]], "4.2.2 Other Error methods": [[7, "other-error-methods"]], "5.1 Test all failure modes": [[7, "test-all-failure-modes"]], "Halo": [[8, "halo"]], "2.1 Requirement: Compatible with all types of arrays": [[8, "requirement-compatible-with-all-types-of-arrays"]], "2.2 Requirement: Exchange at all types of mesh elements": [[8, "requirement-exchange-at-all-types-of-mesh-elements"]], "2.3 Requirement: Variable halo depth": [[8, "requirement-variable-halo-depth"]], "2.4 Requirement: Exchange lists": [[8, "requirement-exchange-lists"]], "2.5 Requirement: Send and receive buffers": [[8, "requirement-send-and-receive-buffers"]], "2.6 Requirement: Non-blocking communication": [[8, "requirement-non-blocking-communication"]], "2.7 Requirement: Compatible with device-resident arrays": [[8, "requirement-compatible-with-device-resident-arrays"]], "2.8 Desired: Communicate subset of halo layers": [[8, "desired-communicate-subset-of-halo-layers"]], "2.9 Desired: Exchange multiple arrays simultaneously": [[8, "desired-exchange-multiple-arrays-simultaneously"]], "2.10 Desired: Multiple environments/decompositions": [[8, "desired-multiple-environments-decompositions"]], "2.11 Desired: OpenMP threading": [[8, "desired-openmp-threading"]], "2.12 Desired: Minimize buffer memory allocation/deallocation": [[8, "desired-minimize-buffer-memory-allocation-deallocation"]], "4.2.1 Constructors": [[8, "constructors"]], "4.2.2 Array halo exchange": [[8, "array-halo-exchange"]], "4.2.3 Start receive/send": [[8, "start-receive-send"]], "4.2.4 Buffer pack/unpack": [[8, "buffer-pack-unpack"]], "5.1 Halo exchange tests": [[8, "halo-exchange-tests"]], "Horizontal Mesh": [[9, "horizontal-mesh"], [39, "horizontal-mesh"], [65, "horizontal-mesh"]], "2.1 Requirement: OMEGA will use the previously established MPAS Mesh Spec": [[9, "requirement-omega-will-use-the-previously-established-mpas-mesh-spec"]], "2.2 Requirement: Functionality is needed to read the mesh on the host and transfer relevant data to the device for computation": [[9, "requirement-functionality-is-needed-to-read-the-mesh-on-the-host-and-transfer-relevant-data-to-the-device-for-computation"]], "2.3 Requirement: Zero-based cell, edge, and vertex numbering": [[9, "requirement-zero-based-cell-edge-and-vertex-numbering"]], "2.4 Requirement: Work with Decomp class to decompose mesh": [[9, "requirement-work-with-decomp-class-to-decompose-mesh"]], "2.5 Requirement: Mesh variables will be associated with metadata to describe data": [[9, "requirement-mesh-variables-will-be-associated-with-metadata-to-describe-data"]], "2.6 Requirement: I/O to obtain mesh data": [[9, "requirement-i-o-to-obtain-mesh-data"]], "2.7 Desired: Ability to support multiple independent mesh objects": [[9, "desired-ability-to-support-multiple-independent-mesh-objects"]], "2.8 Desired: OMEGA can read in a reduced number of mesh variables and compute the remaining array information online.": [[9, "desired-omega-can-read-in-a-reduced-number-of-mesh-variables-and-compute-the-remaining-array-information-online"]], "4.2.2 Read": [[9, "read"]], "4.2.3 Compute": [[9, "compute"]], "4.2.4 Device copy creation": [[9, "device-copy-creation"]], "4.2.5 Metadata registration": [[9, "metadata-registration"]], "5.1 Test mesh compute routines": [[9, "test-mesh-compute-routines"]], "Input/Output (IO)": [[10, "input-output-io"]], "2.1 Requirement: Read fields and metadata": [[10, "requirement-read-fields-and-metadata"]], "2.2 Requirement: Write fields and metadata": [[10, "requirement-write-fields-and-metadata"]], "2.3 Requirement: Self-describing formats": [[10, "requirement-self-describing-formats"]], "2.4 Requirement: multiple files/streams": [[10, "requirement-multiple-files-streams"]], "2.5 Requirement: parallel I/O": [[10, "requirement-parallel-i-o"]], "2.6 Requirement: parallel I/O tuning": [[10, "requirement-parallel-i-o-tuning"]], "2.7 Requirement: Data types and type conversion": [[10, "requirement-data-types-and-type-conversion"]], "2.8 Requirement: Kokkos arrays and host/device support": [[10, "requirement-kokkos-arrays-and-host-device-support"]], "2.9 Requirement: Modes on file existence": [[10, "requirement-modes-on-file-existence"]], "2.10 Desired: Asynchronous I/O": [[10, "desired-asynchronous-i-o"]], "2.11 Desired: File compression": [[10, "desired-file-compression"]], "4.2.1 Environment constructor": [[10, "environment-constructor"]], "4.2.2 File open/close": [[10, "file-open-close"]], "4.2.3 Write operations": [[10, "write-operations"]], "4.2.4 Read operations": [[10, "read-operations"]], "4.2.5 Defining IO fields": [[10, "defining-io-fields"]], "5.1 Test via IOStreams": [[10, "test-via-iostreams"]], "IOStreams": [[11, "iostreams"]], "2.1 Requirement: Multiple streams": [[11, "requirement-multiple-streams"]], "2.2 Requirement: Reduced precision": [[11, "requirement-reduced-precision"]], "2.3 Requirement: Contents for each stream": [[11, "requirement-contents-for-each-stream"]], "2.4 Requirement: Exact restart": [[11, "requirement-exact-restart"]], "2.5 Requirement: Restart pointer": [[11, "requirement-restart-pointer"]], "2.6 Requirement: Time intervals": [[11, "requirement-time-intervals"]], "2.7 Requirement: Optional start/stop times": [[11, "requirement-optional-start-stop-times"]], "2.8 Requirement: Filenames": [[11, "requirement-filenames"]], "2.9 Requirement: Multiple time slices per file": [[11, "requirement-multiple-time-slices-per-file"]], "2.10 Requirement: Behavior on file existence": [[11, "requirement-behavior-on-file-existence"]], "2.11 Desired: Time averaging": [[11, "desired-time-averaging"]], "2.12 Desired: Data compression": [[11, "desired-data-compression"]], "4.2.1 Create/Destroy": [[11, "create-destroy"]], "4.2.2 Add fields": [[11, "add-fields"]], "4.2.3 Write streams": [[11, "write-streams"]], "4.2.3 Read streams": [[11, "read-streams"]], "5.1 Test All": [[11, "test-all"], [24, "test-all"]], "Logging": [[12, "logging"]], "2.1 Requirement: Basic logging": [[12, "requirement-basic-logging"]], "2.2 Requirement: Inter-operability with E3SM": [[12, "requirement-inter-operability-with-e3sm"]], "2.3 Requirement: Multi-processing": [[12, "requirement-multi-processing"]], "2.4 Requirement: Multi-threading": [[12, "requirement-multi-threading"]], "2.5 Requirement: Omega data types": [[12, "requirement-omega-data-types"]], "2.6 Requirement: Buffered file input/output": [[12, "requirement-buffered-file-input-output"]], "2.7 Desired: Formatter": [[12, "desired-formatter"]], "2.8 Desired: Output sinks": [[12, "desired-output-sinks"]], "2.9 Desired: Local logging": [[12, "desired-local-logging"]], "4.2.1 Log write": [[12, "log-write"]], "5.1 Test OMEGA logging capabilities": [[12, "test-omega-logging-capabilities"]], "5.2 Test OMEGA data type support": [[12, "test-omega-data-type-support"]], "5.3 Test E3SM inter-operability": [[12, "test-e3sm-inter-operability"]], "MachineEnv": [[13, "machineenv"]], "2.1 Requirement: Initialize MPI in Standalone": [[13, "requirement-initialize-mpi-in-standalone"]], "2.2 Requirement: Create MPI communicator in coupled mode": [[13, "requirement-create-mpi-communicator-in-coupled-mode"]], "2.3 Requirement: Define MPI layouts": [[13, "requirement-define-mpi-layouts"]], "2.4 Requirement: Kokkos initialization": [[13, "requirement-kokkos-initialization"]], "2.5 Requirement: Vector blocking size defined at compile time": [[13, "requirement-vector-blocking-size-defined-at-compile-time"]], "2.6 Desired: Set alternative master task": [[13, "desired-set-alternative-master-task"]], "2.7 Desired: Multiple environments": [[13, "desired-multiple-environments"]], "2.8 Desired: Define threading parameters": [[13, "desired-define-threading-parameters"]], "2.9 Desired: Define other machine parameters": [[13, "desired-define-other-machine-parameters"]], "4.1.3 Default environment": [[13, "default-environment"]], "4.2.1 Initialization": [[13, "initialization"]], "4.2.2 Constructors": [[13, "constructors"]], "4.2.3 Change master task": [[13, "change-master-task"]], "5.1 Test standalone initialization": [[13, "test-standalone-initialization"]], "5.2 Test changing master task": [[13, "test-changing-master-task"]], "5.3 Test multiple environments": [[13, "test-multiple-environments"]], "5.4 Initialization in coupled mode": [[13, "initialization-in-coupled-mode"]], "5.5 Test vector blocking factor": [[13, "test-vector-blocking-factor"]], "Metadata": [[14, "metadata"]], "2.1 Requirement: Data types": [[14, "requirement-data-types"]], "2.2 Requirement: Global and variable metadata": [[14, "requirement-global-and-variable-metadata"]], "2.3 Requirement: Metadata conventions": [[14, "requirement-metadata-conventions"]], "2.4 Requirement: Required metadata": [[14, "requirement-required-metadata"]], "2.5 Requirement: Dimensions": [[14, "requirement-dimensions"]], "2.6 Requirement: Available fields": [[14, "requirement-available-fields"]], "2.7 Desired: Metadata groups": [[14, "desired-metadata-groups"]], "4.2.1 Metadata container creation": [[14, "metadata-container-creation"]], "4.2.2 Add/remove metadata": [[14, "add-remove-metadata"]], "4.2.3 Retrieve metadata": [[14, "retrieve-metadata"]], "4.2.4 Create dimension": [[14, "create-dimension"]], "4.2.5 Retrieve dim length": [[14, "retrieve-dim-length"]], "4.2.6 Existence inquiry": [[14, "existence-inquiry"]], "4.2.6.1 Existence inquiry for metadata container and metadim container": [[14, "existence-inquiry-for-metadata-container-and-metadim-container"]], "4.2.6.2 Existence inquiry for metadata": [[14, "existence-inquiry-for-metadata"]], "4.2.7 Metadata groups": [[14, "metadata-groups"]], "5.1 Test creation/retrieval": [[14, "test-creation-retrieval"]], "5.2 Test global metadata": [[14, "test-global-metadata"]], "5.3 Test inquiry functions": [[14, "test-inquiry-functions"]], "5.4 Test metadata groups": [[14, "test-metadata-groups"]], "5.5 Test CF compliance": [[14, "test-cf-compliance"]], "Omega V0: Shallow Water": [[15, "omega-v0-shallow-water"]], "2.1 Omega-0 will solve the nonlinear shallow water equations, plus inactive tracers": [[15, "omega-0-will-solve-the-nonlinear-shallow-water-equations-plus-inactive-tracers"]], "2.2 Numerical method will be the TRiSK formulation": [[15, "numerical-method-will-be-the-trisk-formulation"]], "2.3 Omega-0 will use MPAS format unstructured-mesh domains": [[15, "omega-0-will-use-mpas-format-unstructured-mesh-domains"]], "2.4 Omega-0 will interface with polaris for preprocessing and postprocessing": [[15, "omega-0-will-interface-with-polaris-for-preprocessing-and-postprocessing"]], "2.5 Omega-0 will run portably on various DOE architectures (CPU and GPU nodes)": [[15, "omega-0-will-run-portably-on-various-doe-architectures-cpu-and-gpu-nodes"]], "2.6 Omega-0 will run on multi-node with domain decomposition": [[15, "omega-0-will-run-on-multi-node-with-domain-decomposition"]], "2.7 Correct convergence rates of operators and exact solutions": [[15, "correct-convergence-rates-of-operators-and-exact-solutions"]], "2.8 Conservation of volume and tracer": [[15, "conservation-of-volume-and-tracer"]], "2.9 Performance will be at least as good or better than MPAS-Ocean": [[15, "performance-will-be-at-least-as-good-or-better-than-mpas-ocean"]], "2.10 Full-node GPU throughput will be comparable or better than full-node CPU throughput": [[15, "full-node-gpu-throughput-will-be-comparable-or-better-than-full-node-cpu-throughput"]], "3.1 Governing Equations": [[15, "governing-equations"]], "3.1.1 Continuous Equations": [[15, "continuous-equations"]], "3.1.2 Discrete Equations": [[15, "discrete-equations"]], "3.2 Variable Definitions": [[15, "variable-definitions"]], "3.2 Operator Formulation": [[15, "operator-formulation"]], "3.2.1. Divergence": [[15, "divergence"]], "3.2.2. Gradient": [[15, "gradient"]], "3.2.3. Curl": [[15, "curl"]], "3.2.4. Perpendicular vector component": [[15, "perpendicular-vector-component"]], "3.2.5. Perpendicular Gradient": [[15, "perpendicular-gradient"]], "3.2.6. Cell to Edge Interpolation": [[15, "cell-to-edge-interpolation"]], "3.2.7. Vertex to Edge Interpolation": [[15, "vertex-to-edge-interpolation"]], "3.2.8. Cell to Vertex Interpolation": [[15, "cell-to-vertex-interpolation"]], "3.2.9. Vertex to Cell Interpolation": [[15, "vertex-to-cell-interpolation"]], "3.2.10. Vector from Edge to Cell": [[15, "vector-from-edge-to-cell"]], "3.3 Momentum Terms": [[15, "momentum-terms"]], "3.3.1. Kinetic energy gradient": [[15, "kinetic-energy-gradient"]], "3.3.2. Potential vorticity term": [[15, "potential-vorticity-term"]], "3.3.3. Sea surface height gradient": [[15, "sea-surface-height-gradient"]], "3.3.4. Del2 momentum dissipation": [[15, "del2-momentum-dissipation"]], "3.3.5. Del4 momentum dissipation": [[15, "del4-momentum-dissipation"]], "3.3.6. Rayleigh Drag": [[15, "rayleigh-drag"]], "3.3.7. Bottom drag": [[15, "bottom-drag"]], "3.3.8. Wind forcing": [[15, "wind-forcing"]], "3.4 Thickness and Tracer Terms": [[15, "thickness-and-tracer-terms"]], "3.4.1. Tracer advection": [[15, "tracer-advection"]], "3.4.2. Del2 tracer diffusion": [[15, "del2-tracer-diffusion"]], "3.4.3. Del4 tracer diffusion": [[15, "del4-tracer-diffusion"]], "5.1 Convergence of individual terms": [[15, "convergence-of-individual-terms"]], "5.2 Inertia Gravity Wave: linearized shallow water, no tracers": [[15, "inertia-gravity-wave-linearized-shallow-water-no-tracers"]], "5.3 Manufactured Solution: full nonlinear shallow water, no tracers": [[15, "manufactured-solution-full-nonlinear-shallow-water-no-tracers"]], "5.4 Tracer transport on a sphere": [[15, "tracer-transport-on-a-sphere"]], "5.5 Performance testing": [[15, "performance-testing"]], "5.6 Shallow water tests on spherical domains and with realistic coastlines": [[15, "shallow-water-tests-on-spherical-domains-and-with-realistic-coastlines"]], "5.7 Further tests for Omega-0": [[15, "further-tests-for-omega-0"]], "References": [[15, "references"]], "Global Reductions": [[16, "global-reductions"], [48, "global-reductions"], [74, "global-reductions"]], "2.1 Requirement: Global sums": [[16, "requirement-global-sums"]], "2.2 Requirement: Global min/max": [[16, "requirement-global-min-max"]], "2.3 Requirement: Data types": [[16, "requirement-data-types"]], "2.4 Requirement: Sums with product": [[16, "requirement-sums-with-product"]], "2.5 Requirement: Restricted address space": [[16, "requirement-restricted-address-space"]], "2.6 Requirement: Multiple fields/arrays": [[16, "requirement-multiple-fields-arrays"]], "2.7 Requirement: Other environments/decompositions": [[16, "requirement-other-environments-decompositions"]], "2.8 Requirement: Reproducibility": [[16, "requirement-reproducibility"]], "2.9 Requirement: Accelerators and location": [[16, "requirement-accelerators-and-location"]], "2.10 Requirement: CPU threading": [[16, "requirement-cpu-threading"]], "2.11 Desired: Other reduction operations": [[16, "desired-other-reduction-operations"]], "4.2.1 Global sum": [[16, "global-sum"]], "4.2.2 Global sum with product": [[16, "global-sum-with-product"]], "4.2.3 Global sum multi-field": [[16, "global-sum-multi-field"]], "4.2.4 Global sum multi-field with product": [[16, "global-sum-multi-field-with-product"]], "4.2.5 Global minval": [[16, "global-minval"]], "4.2.6 Global maxval": [[16, "global-maxval"]], "5.1 Test basics": [[16, "test-basics"]], "5.2 Reproducibility": [[16, "reproducibility"]], "5.3 Restricted index range": [[16, "restricted-index-range"]], "5.4 Sum with product": [[16, "sum-with-product"]], "5.5 Multi-field sums": [[16, "multi-field-sums"]], "5.6 Min/Max": [[16, "min-max"]], "State": [[17, "state"]], "2.1 Requirement: State should register prognostic variables with IOStreams": [[17, "requirement-state-should-register-prognostic-variables-with-iostreams"]], "2.2 Requirement: Update timestep": [[17, "requirement-update-timestep"]], "2.3 Requirement: Can be used as a common data type for tendency and provis variables": [[17, "requirement-can-be-used-as-a-common-data-type-for-tendency-and-provis-variables"]], "4.2.3 Time level update": [[17, "time-level-update"]], "5.1 Test read": [[17, "test-read"]], "5.2 Test time level update": [[17, "test-time-level-update"]], "Template": [[18, "template"]], "2.1 Requirement: xxx": [[18, "requirement-xxx"]], "2.2 Requirement: yyy": [[18, "requirement-yyy"]], "2.3 Desired: zzz": [[18, "desired-zzz"]], "5.1 Test xxx": [[18, "test-xxx"]], "5.2 Test yyy": [[18, "test-yyy"]], "Tendencies": [[19, "tendencies"], [49, "tendencies"], [75, "tendencies"]], "2.1 Requirement: Computation of tendency terms": [[19, "requirement-computation-of-tendency-terms"]], "2.2 Requirement: Multiple tendencies can be present": [[19, "requirement-multiple-tendencies-can-be-present"]], "5.1 Test multiple tendencies instances": [[19, "test-multiple-tendencies-instances"]], "Tendency": [[20, "tendency"]], "2.1 Requirement: Tendencies should be able to be grouped under different outer loops over mesh locations.": [[20, "requirement-tendencies-should-be-able-to-be-grouped-under-different-outer-loops-over-mesh-locations"]], "2.2 Requirement: Tendency operator calls should have simple, intuitive calling arguments.": [[20, "requirement-tendency-operator-calls-should-have-simple-intuitive-calling-arguments"]], "2.3 Requirement: Tendencies must allow for vectorization on CPU architectures.": [[20, "requirement-tendencies-must-allow-for-vectorization-on-cpu-architectures"]], "4.2.2 operator": [[20, "operator"]], "TimeManager": [[21, "timemanager"]], "2.1 Required: Simulation time": [[21, "required-simulation-time"]], "2.2 Required: No accumulation roundoff": [[21, "required-no-accumulation-roundoff"]], "2.3 Required: Calendar support": [[21, "required-calendar-support"]], "2.4 Required: Time intervals": [[21, "required-time-intervals"]], "2.5 Required: Events or alarms": [[21, "required-events-or-alarms"]], "2.6 Required: Long times": [[21, "required-long-times"]], "2.7 Required: Time string representation": [[21, "required-time-string-representation"]], "4.1.2.1 TimeFrac class": [[21, "timefrac-class"]], "4.1.2.2 Calendar class": [[21, "calendar-class"]], "4.1.2.3 TimeInstant class": [[21, "timeinstant-class"]], "4.1.2.4 TimeInterval class": [[21, "timeinterval-class"]], "4.1.2.5 Alarm class": [[21, "alarm-class"]], "4.1.2.6 Clock class": [[21, "clock-class"]], "4.2.1 TimeFrac class": [[21, "id1"]], "4.2.2 Calendar class": [[21, "id2"]], "4.2.3 TimeInstant class": [[21, "id3"]], "4.2.4 TimeInterval class": [[21, "id4"]], "4.2.5 Alarm Class": [[21, "id5"]], "4.2.6 Clock Class": [[21, "id6"]], "5.1 Test TimeFrac": [[21, "test-timefrac"]], "5.2 Test TimeInstant": [[21, "test-timeinstant"]], "5.3 Test Calendar": [[21, "test-calendar"]], "5.4 Test Time Intervals": [[21, "test-time-intervals"]], "5.5 Test Alarms": [[21, "test-alarms"]], "5.6 Test Clock": [[21, "test-clock"]], "Time Stepping": [[22, "time-stepping"]], "2.1 Requirement: Accurate discretization of time derivative": [[22, "requirement-accurate-discretization-of-time-derivative"]], "2.2 Requirement: Stability": [[22, "requirement-stability"]], "2.3 Requirement: Performance": [[22, "requirement-performance"]], "2.4 Requirement: Modularity": [[22, "requirement-modularity"]], "2.5 Requirement: Conservation": [[22, "requirement-conservation"]], "2.6 Requirement: The RHS must accept a time argument": [[22, "requirement-the-rhs-must-accept-a-time-argument"]], "3.1 Forward-Backward Scheme": [[22, "forward-backward-scheme"]], "3.2 Other Schemes": [[22, "other-schemes"]], "Timers": [[23, "timers"]], "2.1 Requirement: Timers": [[23, "requirement-timers"]], "2.2 Requirement: Timing statistics": [[23, "requirement-timing-statistics"]], "2.3 Requirement: Timing context": [[23, "requirement-timing-context"]], "2.4 Requirement: Call sequence": [[23, "requirement-call-sequence"]], "2.5 Requirement: Output and E3SM compatibility": [[23, "requirement-output-and-e3sm-compatibility"]], "2.6 Requirement: Full coverage": [[23, "requirement-full-coverage"]], "2.7 Requirement: MPI context": [[23, "requirement-mpi-context"]], "2.8 Desired: Support for multiple devices": [[23, "desired-support-for-multiple-devices"]], "2.9 Desired: Other hardware counters": [[23, "desired-other-hardware-counters"]], "2.10 Desired: Thread support": [[23, "desired-thread-support"]], "2.11 Desired: Memory profiling": [[23, "desired-memory-profiling"]], "2.12 Desired: Interaction with other profiling tools": [[23, "desired-interaction-with-other-profiling-tools"]], "4.2.1 Start": [[23, "start"]], "4.2.2 Stop": [[23, "stop"]], "4.2.3 Print": [[23, "print"]], "4.2.5 Initialize, Finalize": [[23, "initialize-finalize"]], "5.1 Test all internal timers": [[23, "test-all-internal-timers"]], "5.2 Test all timers with GPTL library": [[23, "test-all-timers-with-gptl-library"]], "Tracer Infrastructure": [[24, "tracer-infrastructure"]], "2.1 Requirement: Tracer definition and metadata": [[24, "requirement-tracer-definition-and-metadata"]], "2.2 Requirement: Tracer identification": [[24, "requirement-tracer-identification"]], "2.3 Requirement: Tracer groups": [[24, "requirement-tracer-groups"]], "2.4 Requirement: Tracer selection": [[24, "requirement-tracer-selection"]], "2.5 Requirement: Tracer restart and I/O": [[24, "requirement-tracer-restart-and-i-o"]], "2.6 Requirement: Time levels": [[24, "requirement-time-levels"]], "2.7 Requirement: Acceleration or supercycling": [[24, "requirement-acceleration-or-supercycling"]], "2.8 Desired: Per-tracer/group algorithmic requirements": [[24, "desired-per-tracer-group-algorithmic-requirements"]], "4.1 Data Types and Parameters": [[24, "data-types-and-parameters"]], "4.1.1 Definition": [[24, "definition"]], "4.1.2 Configuration": [[24, "configuration"]], "4.1.3 Classes/Structs/Data Types": [[24, "classes-structs-data-types"]], "4.2.1 init": [[24, "init"]], "4.2.2 define": [[24, "define"]], "4.2.3 getNumTracers": [[24, "getnumtracers"]], "4.2.4 getIndex": [[24, "getindex"]], "4.2.5 getAll": [[24, "getall"]], "4.2.6 getByIndex (Single Tracer)": [[24, "getbyindex-single-tracer"]], "4.2.7 getGroupRange": [[24, "getgrouprange"]], "4.2.8 isGroupMemberByIndex": [[24, "isgroupmemberbyindex"]], "4.2.9 Managing Time Levels": [[24, "managing-time-levels"]], "4.2.10 clear": [[24, "clear"]], "Auxiliary State": [[25, "auxiliary-state"], [55, "auxiliary-state"]], "Initialization": [[25, "initialization"], [49, "initialization"], [52, "initialization"]], "Creation of non-default auxiliary states": [[25, "creation-of-non-default-auxiliary-states"]], "Computation of auxiliary variables": [[25, "computation-of-auxiliary-variables"]], "Removal of auxiliary states": [[25, "removal-of-auxiliary-states"]], "Auxiliary Variables": [[26, "auxiliary-variables"], [56, "auxiliary-variables"]], "Basic class structure": [[26, "basic-class-structure"]], "Configuration enums": [[26, "configuration-enums"]], "Constructor": [[26, "constructor"]], "Compute member functions": [[26, "compute-member-functions"]], "Implemented groups": [[26, "implemented-groups"]], "Omega Broadcast": [[27, "omega-broadcast"], [57, "omega-broadcast"]], "Code Structure": [[27, "code-structure"]], "IBroadcast Interface": [[27, "ibroadcast-interface"]], "Integration with MPI": [[27, "integration-with-mpi"]], "Building the Documentation": [[28, "building-the-documentation"]], "Omega Build with CMake": [[29, "omega-build-with-cmake"]], "Step 1: Setup": [[29, "step-1-setup"]], "Step 2: Update": [[29, "step-2-update"]], "Step 3: Build": [[29, "step-3-build"]], "Step 4: Output": [[29, "step-4-output"]], "Development Conda Environment": [[30, "development-conda-environment"]], "Installing Miniforge3": [[30, "installing-miniforge3"]], "Creating the Conda Environment": [[30, "creating-the-conda-environment"]], "Updating the Conda Environment": [[30, "updating-the-conda-environment"]], "Model Configuration (Config)": [[31, "model-configuration-config"], [58, "model-configuration-config"]], "Data Types and Precision": [[32, "data-types-and-precision"], [59, "data-types-and-precision"]], "Arrays and Kokkos": [[32, "arrays-and-kokkos"]], "Domain Decomposition (Decomp)": [[33, "domain-decomposition-decomp"], [60, "domain-decomposition-decomp"]], "Dimension": [[34, "dimension"], [61, "dimension"]], "Documentation": [[35, "documentation"]], "Driver": [[36, "driver"], [62, "driver"]], "ocnInit": [[36, "ocninit"]], "ocnRun": [[36, "ocnrun"]], "ocnFinalize": [[36, "ocnfinalize"]], "Fields and Metadata (Field)": [[37, "fields-and-metadata-field"], [63, "fields-and-metadata-field"]], "Halo Exchanges (Halo)": [[38, "halo-exchanges-halo"], [64, "halo-exchanges-halo"]], "Horizontal Operators": [[40, "horizontal-operators"], [66, "horizontal-operators"]], "Parallel IO (IO)": [[41, "parallel-io-io"], [67, "parallel-io-io"]], "IO Streams (IOStream)": [[42, "io-streams-iostream"], [68, "io-streams-iostream"]], "Linting Code": [[43, "linting-code"]], "Enabling Lint Checks": [[43, "enabling-lint-checks"]], "Bypassing Linting": [[43, "bypassing-linting"]], "Linting C++ Code": [[43, "linting-c-code"]], "Linting Python Code": [[43, "linting-python-code"]], "Updating the linting pacakge": [[43, "updating-the-linting-pacakge"]], "Developing Omega Logging": [[44, "developing-omega-logging"]], "Initializing Omega Logger": [[44, "initializing-omega-logger"]], "Creating Logging Macros": [[44, "creating-logging-macros"]], "Customer formatter for Kokkos": [[44, "customer-formatter-for-kokkos"]], "Machine Environment (MachEnv)": [[45, "machine-environment-machenv"], [70, "machine-environment-machenv"]], "Ocean State": [[46, "ocean-state"], [71, "ocean-state"]], "Quick Start for Developers": [[47, "quick-start-for-developers"]], "Getting set up": [[47, "getting-set-up"]], "Creating an E3SM fork": [[47, "creating-an-e3sm-fork"]], "Check out the code": [[47, "check-out-the-code"]], "Create a conda environment": [[47, "create-a-conda-environment"]], "Building and testing Omega": [[47, "building-and-testing-omega"]], "Polaris CTest Utility": [[47, "polaris-ctest-utility"]], "Building Omega": [[47, "building-omega"]], "Getting test meshes": [[47, "getting-test-meshes"]], "Running CTests": [[47, "running-ctests"]], "Debugging tips": [[47, "debugging-tips"]], "Metis and Parmetis libraries": [[47, "metis-and-parmetis-libraries"]], "Code development": [[47, "code-development"]], "Code style": [[47, "code-style"]], "VS Code": [[47, "vs-code"]], "Global sum": [[48, "global-sum"]], "Global sum with product": [[48, "global-sum-with-product"]], "Global sum multi-field": [[48, "global-sum-multi-field"]], "Global sum multi-field with product": [[48, "global-sum-multi-field-with-product"]], "Global minval and maxval": [[48, "global-minval-and-maxval"]], "Utility functions globalMin globalMax": [[48, "utility-functions-globalmin-globalmax"]], "Creation of non-default tendencies": [[49, "creation-of-non-default-tendencies"]], "Computation of tendencies": [[49, "computation-of-tendencies"]], "Removal of tendencies": [[49, "removal-of-tendencies"]], "Tendency Terms": [[50, "tendency-terms"], [76, "tendency-terms"]], "Time Manager (TimeMgr)": [[51, "time-manager-timemgr"], [77, "time-manager-timemgr"]], "Class Descriptions": [[51, "class-descriptions"]], "1. TimeFrac": [[51, "timefrac"]], "2. Calendar": [[51, "calendar"]], "3. TimeInstant": [[51, "timeinstant"]], "4. TimeInterval": [[51, "timeinterval"]], "5. Alarm": [[51, "alarm"]], "6. Clock": [[51, "clock"]], "Implementation": [[51, "implementation"]], "Time stepping": [[52, "time-stepping"], [78, "time-stepping"]], "Time stepper type": [[52, "time-stepper-type"]], "TimeStepper base class": [[52, "timestepper-base-class"]], "Do step method": [[52, "do-step-method"]], "Time stepper management methods": [[52, "time-stepper-management-methods"]], "Creation of non-default time steppers": [[52, "creation-of-non-default-time-steppers"]], "Changing the time step": [[52, "changing-the-time-step"]], "Getters": [[52, "getters"]], "Removal of time steppers": [[52, "removal-of-time-steppers"]], "Utility methods": [[52, "utility-methods"]], "Implemented time steppers": [[52, "implemented-time-steppers"]], "Tracers": [[53, "tracers"], [79, "tracers"]], "Concepts": [[53, "concepts"]], "Arrays in Host and Device Memory": [[53, "arrays-in-host-and-device-memory"]], "Tracer Groups": [[53, "tracer-groups"]], "Time Levels": [[53, "time-levels"]], "Initialization and Finalization": [[53, "initialization-and-finalization"]], "Key APIs": [[53, "key-apis"]], "getAll and getAllHost": [[53, "getall-and-getallhost"]], "getGroupRange": [[53, "getgrouprange"]], "getByIndex and getHostByIndex": [[53, "getbyindex-and-gethostbyindex"]], "getIndex": [[53, "getindex"]], "getFieldByIndex": [[53, "getfieldbyindex"]], "updateTimeLevels": [[53, "updatetimelevels"]], "getNumTracers": [[53, "getnumtracers"]], "Omega": [[54, "omega"]], "User's guide": [[54, null]], "Developer's guide": [[54, null]], "Design documents": [[54, null]], "Broadcasting Functions": [[57, "broadcasting-functions"]], "Blocking Broadcasting Functions": [[57, "blocking-broadcasting-functions"]], "Including the Broadcasting Functions in Your Code": [[57, "including-the-broadcasting-functions-in-your-code"]], "Broadcasting Scalar or Array Values": [[57, "broadcasting-scalar-or-array-values"]], "Specifying broadcasting task and/or environment in Omega": [[57, "specifying-broadcasting-task-and-or-environment-in-omega"]], "Broadcasting Array Values": [[57, "broadcasting-array-values"]], "Supported Data Types for Broadcasting": [[57, "supported-data-types-for-broadcasting"]], "Non-blocking Broadcasting Functions": [[57, "non-blocking-broadcasting-functions"]], "Omega Logging": [[69, "omega-logging"]], "Logging in Standalone Build mode": [[69, "logging-in-standalone-build-mode"]], "E3SM Component Build": [[69, "e3sm-component-build"], [72, "e3sm-component-build"]], "CMake-based Omega Build": [[72, "cmake-based-omega-build"]], "Standalone Build": [[72, "standalone-build"]], "Manual Preparation for E3SM Component Build": [[72, "manual-preparation-for-e3sm-component-build"]], "Quick Start for Users": [[73, "quick-start-for-users"]], "Quick Start for Users is coming soon": [[73, null]], "Updating tracer defintions in TracerDefs.inc file": [[79, "updating-tracer-defintions-in-tracerdefs-inc-file"]], "Selecting tracers using YAML configuration file": [[79, "selecting-tracers-using-yaml-configuration-file"]]}, "indexentries": {}}) \ No newline at end of file