Upgrade cime in ACME to CIME5

cime/.github/PULL_REQUEST_TEMPLATE

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+[ Description of the changes in this Pull Request. It should be enough
+information for someone not following this development to understand.
+Lines should be wrapped at about 72 characters. ]
+
+Test suite: 
+Test baseline: 
+Test namelist changes: 
+Test status: [bit for bit, roundoff, climate changing]
+
+Fixes [CIME Github issue #]
+
+User interface changes?: 
+
+Code review: 

cime/.gitignore

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+# Ignore python bytecode files
+*.pyc
+
+# Ignore emacs backup files
+*~

cime/ChangeLog_template

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+======================================================================
+
+Originator: 
+Date: 
+Tag: cimeX.Y.Z
+Answer Changes: [None, Round Off, Climate Changing]
+Tests: 
+Dependencies:
+
+Brief Summary:
+
+User interface changes: 
+
+Modified files: git diff --name-status
+
+======================================================================
+

cime/LICENSE.TXT

@@ -1,34 +1,34 @@
 Copyright (c) 2015, University Corporation for Atmospheric Research (UCAR)
 All rights reserved.
 
-Developed by: 
+Developed by:
               University Corporation for Atmospheric Research - National Center for Atmospheric Research
               https://www2.cesm.ucar.edu/working-groups/sewg
 
-Permission is hereby granted, free of charge, to any person obtaining 
-a copy of this software and associated documentation files (the "Software"), 
-to deal with the Software without restriction, including without limitation 
-the rights to use, copy, modify, merge, publish, distribute, sublicense, 
-and/or sell copies of the Software, and to permit persons to whom 
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the "Software"),
+to deal with the Software without restriction, including without limitation
+the rights to use, copy, modify, merge, publish, distribute, sublicense,
+and/or sell copies of the Software, and to permit persons to whom
 the Software is furnished to do so, subject to the following conditions:
 
-    - Redistributions of source code must retain the above copyright notice, 
+    - Redistributions of source code must retain the above copyright notice,
       this list of conditions and the following disclaimers.
-    - Redistributions in binary form must reproduce the above copyright notice, 
-      this list of conditions and the following disclaimers in the documentation 
+    - Redistributions in binary form must reproduce the above copyright notice,
+      this list of conditions and the following disclaimers in the documentation
       and/or other materials provided with the distribution.
-    - Neither the names of [Name of Development Group, UCAR], 
-      nor the names of its contributors may be used to endorse or promote 
+    - Neither the names of [Name of Development Group, UCAR],
+      nor the names of its contributors may be used to endorse or promote
       products derived from this Software without specific prior written permission.
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
-ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE 
-LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
-CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
-SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
-INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
-CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
-ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
-POSSIBILITY OF SUCH DAMAGE.		
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.

cime/README.md

@@ -1,74 +1,45 @@
 # cime
 Common Infrastructure for Modeling the Earth
 
-cime (pronounced: seem) represents the infrastructure code for the 
+**cime** (pronounced: seem) represents the infrastructure code for the 
 <a href="http://www2.cesm.ucar.edu">Community Earth System Model </a>
-     (CESM) version 1.4
+     (CESM) and the Accelerated Climate Model for Energy (ACME).
+*cime* includes scripts for configuration, build, and testing of
+models, as well as data and stub models for climate components, 
+and a code for coupling different climate components together.
+
+# Developers
 
-See the CESM web site for documentation and information.
+*cime* was initially extracted from CESM as a stand-alone capability in 2015
+by members of the CSEG group at NCAR, the software engineering team of
+the CESM model. The CSEG group had been developing this infrastrucure within
+CESM for a number of years using NSF and DOE funding. After version 4 was released,
+a joint development partnership was started with the software engineering group of
+ACME, a DOE-funded project, which had branched from CESM in 2014. 
+Starting with development of version 5, *cime* is cooperative effort with contributions
+and ownership from members of both teams. 
 
-The cime directory structure (other than the externals/ directory)
-was generated from the following subversion trunk tags:
+The following table documents the developers who have contributed to *cime*,
+showing what versions of they contributed to, and with what source(s) of support.
 
-* cime/driver_cpl		  	        
-   https://svn-ccsm-models.cgd.ucar.edu/drv/seq_mct/trunk_tags/drvseq5_1_15
+Name     |     Institution  |  Versions  | Funding Source (for versions)
+---------|------------------|----------|----------------------
+Mariana Vertenstein | NCAR  |  1 - D   |   NSF, DOE
+Jim Edwards |         NCAR  |  1 - D   |   NSF (1-D), DOE(1-2)
+Jim Foucar  |         SNL   |  5 - D   |   DOE
+Rob Jacob |      ANL  |  5 - D   |   DOE
+Andreas Wilke |  ANL  | 5 - D | DOE
+Jason Sarich | ANL | 5 - D | DOE
+??Sean Santos |         NCAR  |  1 - 4   |   NSF
 
-* cime/components/data_comps/datm	        
-   https://svn-ccsm-models.cgd.ucar.edu/datm7/trunk_tags/datm8_150310
-
-* cime/components/data_comps/dice	        
-   https://svn-ccsm-models.cgd.ucar.edu/dice7/trunk_tags/dice8_150310
-
-* cime/components/data_comps/dlnd	        
-   https://svn-ccsm-models.cgd.ucar.edu/dlnd7/trunk_tags/dlnd8_150310
-
-* cime/components/data_comps/docn       	
-   https://svn-ccsm-models.cgd.ucar.edu/docn7/trunk_tags/docn8_150310
-
-* cime/components/data_comps/drof  	
-   https://svn-ccsm-models.cgd.ucar.edu/drof/trunk_tags/drof_150310
-
-* cime/components/stub_comps		
-   https://svn-ccsm-models.cgd.ucar.edu/stubs/trunk_tags/stubs1_4_08
-
-* cime/components/xcpl_comps	
-   https://svn-ccsm-models.cgd.ucar.edu/dead7/trunk_tags/dead7_8_04
+_Key: D = Current development version (i.e. still active on project)_
 
-* cime/machines				
-   https://svn-ccsm-models.cgd.ucar.edu/Machines/trunk_tags/Machines_150309
+# Documentation
 
-* cime/scripts                            
-   https://svn-ccsm-models.cgd.ucar.edu/scripts/trunk_tags/scripts_150309
+Currently, this is a work in progress. 
 
-* cime/share/csm_share	  	        
-   https://svn-ccsm-models.cgd.ucar.edu/csm_share/trunk_tags/share3_150116
-
-* cime/share/esmf_wrf_timemgr	        
-   https://svn-ccsm-models.cgd.ucar.edu/esmf_wrf_timemgr/trunk_tags/esmf_wrf_timemgr_141217
-
-* cime/share/timing                       
-   https://svn-ccsm-models.cgd.ucar.edu/timing/trunk_tags/timing_150302
 
-* cime/utils/pythonlib    
-   https://svn-ccsm-models.cgd.ucar.edu/scripts/trunk_tags/scripts4_150204/scripts/ccsm_utils/Tools/pythonlib
-
-* cime/utils/perl5lib	                
-   https://svn-ccsm-models.cgd.ucar.edu/perl5lib/trunk_tags/perl5lib_150302
 
-* cime/tools/load_balancing_tool	
-   https://svn-ccsm-models.cgd.ucar.edu/tools/load_balancing_tool/trunk_tags/load_balancing_tool_141008
-
-* cime/tools/unit_testing                 
-   https://svn-ccsm-models.cgd.ucar.edu/unit_testing/trunk_tags/unit_testing_0_16
-
-* cime/tools/statistical_ensemble_test  
-   https://svn-ccsm-models.cgd.ucar.edu/validation_testing/trunk_tags/validation_20140708/run_CESM/
-
-* cime/tools/mapping                      
-   https://svn-ccsm-models.cgd.ucar.edu/tools/mapping/trunk_tags/mapping_141106
-
-* cime/tools/cprnc                        
-   https://svn-ccsm-models.cgd.ucar.edu/tools/cprnc/trunk_tags/cprnc_150301
 
 
 

cime/cime_config/acme/allactive/config_compsets.xml

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+<?xml version="1.0"?>
+
+<compsets>
+
+  <help>
+
+    =========================================
+    compset naming convention
+    =========================================
+    The compset longname below has the specified order
+    atm, lnd, ice, ocn, river, glc wave model-options
+
+    The notation for the compset longname is
+    TIME_ATM[%phys]_LND[%phys]_ICE[%phys]_OCN[%phys]_ROF[%phys]_GLC[%phys]_WAV[%phys][_ESP%phys][_BGC%phys]
+    Where for the CAM specific compsets below the following is supported
+    TIME = Time period (e.g. 2000, HIST, RCP8...)
+    ATM  = [CAM4, CAM5, SATM]
+    LND  = [CLM40, CLM45, CLM50, SLND]
+    ICE  = [MPASCICE, CICE, DICE, SICE]
+    OCN  = [MPASO, DOCN, ,AQUAP, SOCN]
+    ROF  = [RTM, MOSART, SROF]
+    GLC  = [MPASLISIA, MPASLIALB, CISM1, CISM2, SGLC]
+    WAV  = [WW3, DWAV, XWAV, SWAV]
+    ESP  = [SESP]
+    BGC  = optional BGC scenario
+
+    The OPTIONAL %phys attributes specify submodes of the given system
+    For example DOCN%DOM is the data ocean model for DOCN
+    ALL the possible %phys choices for each component are listed
+    with the -list command for create_newcase
+    ALL data models must have a %phys option that corresponds to the data  model mode
+
+    Each compset node is associated with the following elements
+    - lname
+    - alias
+    - support  (optional description of the support level for this compset)
+    Each compset node can also have the following attributes
+    - grid  (optional regular expression match for grid to work with the compset)
+
+  </help>
+
+<!-- ACME v1 science compsets -->
+
+<compset>
+  <alias>A_WCYCL2000</alias >
+  <lname>2000_CAM5%AV1C-L_CLM45%SPBC_MPASCICE_MPASO_MOSART_SGLC_SWAV</lname>
+</compset>
+
+<compset>
+  <alias>A_WCYCL2000S</alias >
+  <lname>2000_CAM5%AV1C-L_CLM45%SPBC_MPASCICE%SPUNUP_MPASO%SPUNUP_MOSART_SGLC_SWAV</lname>
+</compset>
+
+<compset>
+  <alias>A_WCYCL1850</alias>
+  <lname>1850_CAM5%AV1C-L_CLM45%SPBC_MPASCICE_MPASO_MOSART_SGLC_SWAV</lname>
+</compset>
+
+<compset>
+  <alias>A_WCYCL1850S</alias>
+  <lname>1850_CAM5%AV1C-L_CLM45%SPBC_MPASCICE%SPUNUP_MPASO%SPUNUP_MOSART_SGLC_SWAV</lname>
+</compset>
+
+<compset>
+  <alias>A_WCYCL20TR</alias>
+  <lname>20TR_CAM5%AV1C-L_CLM45%SPBC_MPASCICE_MPASO_MOSART_SGLC_SWAV</lname>
+</compset>
+
+<compset>
+  <alias>A_WCYCL20TRS</alias>
+  <lname>20TR_CAM5%AV1C-L_CLM45%SPBC_MPASCICE%SPUNUP_MPASO%SPUNUP_MOSART_SGLC_SWAV</lname>
+</compset>
+
+<compset>
+  <alias>A_CRYO</alias>
+  <lname>2000_CAM5%AV1C-L_CLM45%SPBC_MPASCICE_MPASO_RTM_MPASLIALB_SWAV</lname>
+</compset>
+
+<!-- ACME backup compsets -->
+<compset>
+ <alias>A_WCYCL1850_v0atm</alias> 
+ <lname>1850_CAM5_CLM45%SP_MPASCICE_MPASO_MOSART_SGLC_SWAV</lname>
+</compset>
+
+<compset>
+ <alias>A_WCYCL2000_v0atm</alias>
+ <lname>2000_CAM5_CLM45%SP_MPASCICE_MPASO_MOSART_SGLC_SWAVi</lname>
+</compset>
+
+<!-- ACME BG compsets -->
+
+<compset>
+  <alias>A_BG1850CN</alias>
+  <lname>1850_CAM5_CLM45%CN_MPASCICE_MPASO_RTM_MPASLI_SWAV</lname>
+</compset>
+
+<!-- OCN + CICE + GLC Only Compsets -->
+<compset>
+  <alias>MPAS_LISIO_TEST</alias>
+  <lname>2000_DATM%NYF_SLND_MPASCICE_MPASO_DROF%NYF_MPASLI_SWAV</lname>
+</compset>
+
+<compset>
+  <alias>ETEST</alias>
+  <lname>2000_CAM4_CLM40%SP_CICE_DOCN%SOM_RTM_SGLC_SWAV_TEST</lname>
+</compset>
+
+<compset>
+  <alias>E1850C5</alias>
+  <lname>1850_CAM5_CLM40%SP_CICE_DOCN%SOM_RTM_SGLC_SWAV</lname>
+</compset>
+
+<compset>
+  <alias>E1850C5TEST</alias>
+  <lname>1850_CAM5_CLM40%SP_CICE_DOCN%SOM_RTM_SGLC_SWAV_TEST</lname>
+</compset>
+
+<compset>
+  <alias>E1850CN</alias>
+  <lname>1850_CAM4_CLM40%CN_CICE_DOCN%SOM_RTM_SGLC_SWAV</lname>
+</compset>
+
+<compset>
+  <alias>E1850C5CN</alias>
+  <lname>1850_CAM5_CLM40%CN_CICE_DOCN%SOM_RTM_SGLC_SWAV</lname>
+</compset>
+
+<compset>
+  <alias>E1850C5CNTEST</alias>
+  <lname>1850_CAM5_CLM40%CN_CICE_DOCN%SOM_RTM_SGLC_SWAV_TEST </lname>
+</compset>
+
+<compset>
+  <alias>E1850C5CLM45</alias>
+  <lname>1850_CAM5_CLM45%SP_CICE_DOCN%SOM_RTM_SGLC_SWAV</lname>
+</compset>
+
+<compset>
+  <alias>E1850C5CLM45CN</alias>
+  <lname>1850_CAM5_CLM45%CN_CICE_DOCN%SOM_RTM_SGLC_SWAV</lname>
+</compset>
+
+<compset>
+  <alias>E1850C5CLM45BGC</alias>
+  <lname>1850_CAM5_CLM45%BGC_CICE_DOCN%SOM_RTM_SGLC_SWAV</lname>
+</compset>
+
+</compsets>