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Merge pull request #133 from GEOS-ESM/develop
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GEOS-Chem and HEMCO exit the repo
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mmanyin authored May 17, 2021
2 parents 869541f + c85522c commit f33530b
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Showing 331 changed files with 421 additions and 479,785 deletions.
10 changes: 5 additions & 5 deletions .circleci/config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,8 @@ executors:
OMPI_ALLOW_RUN_AS_ROOT: 1
OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
OMPI_MCA_btl_vader_single_copy_mechanism: none
#XLARGE# resource_class: xlarge
resource_class: medium
resource_class: large
#MEDIUM# resource_class: medium

workflows:
version: 2.1
Expand Down Expand Up @@ -51,10 +51,10 @@ jobs:
cd ${CIRCLE_WORKING_DIRECTORY}/GEOSgcm
mkdir build
cd build
cmake .. -DBASEDIR=$BASEDIR/Linux -DCMAKE_Fortran_COMPILER=gfortran -DCMAKE_BUILD_TYPE=Debug
cmake .. -DBASEDIR=$BASEDIR/Linux -DCMAKE_Fortran_COMPILER=gfortran -DCMAKE_BUILD_TYPE=Debug -DUSE_F2PY=OFF
- run:
name: "Build"
command: |
cd ${CIRCLE_WORKING_DIRECTORY}/GEOSgcm/build
#XLARGE# make -j"$(nproc)" install
make -j4 install
make -j"$(nproc)" install
#MEDIUM# make -j4 install
2 changes: 2 additions & 0 deletions .gitignore
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@@ -1 +1,3 @@
Shared/HEMCO/@HEMCO
GEOSCHEMchem_GridComp/@geos-chem
/@GOCART/
133 changes: 133 additions & 0 deletions CODE_OF_CONDUCT.md
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@@ -0,0 +1,133 @@

# Contributor Covenant Code of Conduct

## Our Pledge

We as members, contributors, and leaders pledge to make participation in our
community a harassment-free experience for everyone, regardless of age, body
size, visible or invisible disability, ethnicity, sex characteristics, gender
identity and expression, level of experience, education, socio-economic status,
nationality, personal appearance, race, religion, or sexual identity
and orientation.

We pledge to act and interact in ways that contribute to an open, welcoming,
diverse, inclusive, and healthy community.

## Our Standards

Examples of behavior that contributes to a positive environment for our
community include:

* Demonstrating empathy and kindness toward other people
* Being respectful of differing opinions, viewpoints, and experiences
* Giving and gracefully accepting constructive feedback
* Accepting responsibility and apologizing to those affected by our mistakes,
and learning from the experience
* Focusing on what is best not just for us as individuals, but for the
overall community

Examples of unacceptable behavior include:

* The use of sexualized language or imagery, and sexual attention or
advances of any kind
* Trolling, insulting or derogatory comments, and personal or political attacks
* Public or private harassment
* Publishing others' private information, such as a physical or email
address, without their explicit permission
* Other conduct which could reasonably be considered inappropriate in a
professional setting

## Enforcement Responsibilities

Community leaders are responsible for clarifying and enforcing our standards of
acceptable behavior and will take appropriate and fair corrective action in
response to any behavior that they deem inappropriate, threatening, offensive,
or harmful.

Community leaders have the right and responsibility to remove, edit, or reject
comments, commits, code, wiki edits, issues, and other contributions that are
not aligned to this Code of Conduct, and will communicate reasons for moderation
decisions when appropriate.

## Scope

This Code of Conduct applies within all community spaces, and also applies when
an individual is officially representing the community in public spaces.
Examples of representing our community include using an official e-mail address,
posting via an official social media account, or acting as an appointed
representative at an online or offline event.

## Enforcement

Instances of abusive, harassing, or otherwise unacceptable behavior may be
reported to the community leaders responsible for enforcement at
[email protected].
All complaints will be reviewed and investigated promptly and fairly.

All community leaders are obligated to respect the privacy and security of the
reporter of any incident.

## Enforcement Guidelines

Community leaders will follow these Community Impact Guidelines in determining
the consequences for any action they deem in violation of this Code of Conduct:

### 1. Correction

**Community Impact**: Use of inappropriate language or other behavior deemed
unprofessional or unwelcome in the community.

**Consequence**: A private, written warning from community leaders, providing
clarity around the nature of the violation and an explanation of why the
behavior was inappropriate. A public apology may be requested.

### 2. Warning

**Community Impact**: A violation through a single incident or series
of actions.

**Consequence**: A warning with consequences for continued behavior. No
interaction with the people involved, including unsolicited interaction with
those enforcing the Code of Conduct, for a specified period of time. This
includes avoiding interactions in community spaces as well as external channels
like social media. Violating these terms may lead to a temporary or
permanent ban.

### 3. Temporary Ban

**Community Impact**: A serious violation of community standards, including
sustained inappropriate behavior.

**Consequence**: A temporary ban from any sort of interaction or public
communication with the community for a specified period of time. No public or
private interaction with the people involved, including unsolicited interaction
with those enforcing the Code of Conduct, is allowed during this period.
Violating these terms may lead to a permanent ban.

### 4. Permanent Ban

**Community Impact**: Demonstrating a pattern of violation of community
standards, including sustained inappropriate behavior, harassment of an
individual, or aggression toward or disparagement of classes of individuals.

**Consequence**: A permanent ban from any sort of public interaction within
the community.

## Attribution

This Code of Conduct is adapted from the [Contributor Covenant][homepage],
version 2.0, available at
[https://www.contributor-covenant.org/version/2/0/code_of_conduct.html][v2.0].

Community Impact Guidelines were inspired by
[Mozilla's code of conduct enforcement ladder][Mozilla CoC].

For answers to common questions about this code of conduct, see the FAQ at
[https://www.contributor-covenant.org/faq][FAQ]. Translations are available
at [https://www.contributor-covenant.org/translations][translations].

[homepage]: https://www.contributor-covenant.org
[v2.0]: https://www.contributor-covenant.org/version/2/0/code_of_conduct.html
[Mozilla CoC]: https://github.com/mozilla/diversity
[FAQ]: https://www.contributor-covenant.org/faq
[translations]: https://www.contributor-covenant.org/translations
16 changes: 16 additions & 0 deletions CONTRIBUTING.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
# Contributing to GEOSchem_GridComp

Contributing code to GEOSchem_GridComp should be done via a Pull Request to this repository.

## Contributor License Agreement (CLA)

All external developers contributing to GEOS-ESM projects must complete a [Contributor License
Agreement](https://github.com/GEOS-ESM/cla).

NOTE: Internal NASA contributors associated with GEOS, including contractors,
are covered by other agreements and do not need to sign a CLA.

## License

By contributing to GEOS-ESM projects, you agree your contributions will be
licensed under the [NASA Open Source Agreement (NOSA) License](LICENSE.md)
68 changes: 32 additions & 36 deletions GEOSCHEMchem_GridComp/CMakeLists.txt
Original file line number Diff line number Diff line change
Expand Up @@ -5,18 +5,18 @@ set (alldirs

set (src_directories
${CMAKE_CURRENT_SOURCE_DIR}
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/Headers
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/History
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/GeosUtil
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/NcdfUtil
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/ISOROPIA
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/KPP/Standard
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/GeosCore
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/GIGC
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/ObsPack
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/Headers
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/History
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/GeosUtil
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/NcdfUtil
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/ISORROPIA
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/KPP/fullchem
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/GeosCore
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/Interfaces/GCHP
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/ObsPack
)

include_directories (${CMAKE_CURRENT_SOURCE_DIR}/gc_column/Headers)
include_directories (${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/Headers)

set (srcs)
foreach (dir ${src_directories})
Expand All @@ -26,32 +26,28 @@ endforeach()

list (REMOVE_ITEM srcs
# this one is moved to HEMCO
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/GeosUtil/regrid_a2a_mod.F90
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/NcdfUtil/charpak_mod.F90
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/Headers/charpak_mod.F90
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/NcdfUtil/julday_mod.F
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/GeosUtil/julday_mod.F
#${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/GeosUtil/regrid_a2a_mod.F90
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/NcdfUtil/charpak_mod.F90
#${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/Headers/charpak_mod.F90
#${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/NcdfUtil/julday_mod.F90
#${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/GeosUtil/julday_mod.F90

# not sure about the rest
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/GeosCore/main.F
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/GeosCore/tpcore_fvdas_mod.F
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/GeosCore/tpcore_geos57_window_mod.F
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/GeosCore/tpcore_geos5_window_mod.F
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/GeosCore/transport_mod.F
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/GeosCore/rrtmg_rad_transfer_mod.F
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/GeosCore/tomas_mod.F
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/GeosCore/exchange_mod.F
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/GeosCore/get_met_mod.F90
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/GeosCore/flexgrid_read_mod.F90
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/GeosCore/aero_drydep.F
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/GeosCore/exchange_mod.F
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/GeosCore/YuIMN_Code.F
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/GIGC/gigc_manualexports_mod.F90
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/GIGC/GIGC_GridCompMod.F90
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/GIGC/Chem_GridCompMod.F90
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/GIGC/GEOS_ctmEnvGridComp.F90
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/GIGC/GEOSChem.F90
${CMAKE_CURRENT_SOURCE_DIR}/gc_column/Headers/inquireMod.F90
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/GeosCore/main.F90
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/GeosCore/tpcore_fvdas_mod.F90
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/GeosCore/tpcore_geos57_window_mod.F90
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/GeosCore/tpcore_geos5_window_mod.F90
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/GeosCore/transport_mod.F90
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/GeosCore/rrtmg_rad_transfer_mod.F90
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/GeosCore/tomas_mod.F90
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/GeosCore/exchange_mod.F90
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/GeosCore/get_met_mod.F90
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/GeosCore/flexgrid_read_mod.F90
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/GeosCore/aero_drydep.F90
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/GeosCore/exchange_mod.F90
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/GeosCore/YuIMN_Code.F90
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/GeosCore/apm_driv_mod.F90
${CMAKE_CURRENT_SOURCE_DIR}/@geos-chem/Interfaces/GCHP/Chem_GridCompMod.F90
)

if (CMAKE_Fortran_COMPILER_ID MATCHES Intel)
Expand All @@ -74,8 +70,8 @@ esma_add_library (${this}

target_include_directories (${this} PUBLIC ${INC_ESMF} ${INC_NETCDF})

target_compile_definitions(${this} PRIVATE ESMF_ DEVEL NO_BPCH UCX
EXTERNAL_GRID EXTERNAL_FORCING GEOS_FP USE_REAL8 USE_TEND NC_DIAG DISCOVER MODEL_GEOS)
target_compile_definitions(${this} PRIVATE
ESMF_ UCX EXTERNAL_GRID EXTERNAL_FORCING USE_REAL8 MODEL_GEOS)

if (CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
target_compile_definitions(${this} PRIVATE LINUX_IFORT)
Expand Down
1 change: 1 addition & 0 deletions GEOSCHEMchem_GridComp/Chem_GridCompMod.F90
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