https://wiki.seas.harvard.edu/geos-chem/api.php?action=feedcontributions&user=Jeffrey+Pierce&feedformat=atomGeos-chem - User contributions [en]2024-03-29T14:44:19ZUser contributionsMediaWiki 1.24.2https://wiki.seas.harvard.edu/geos-chem/index.php?title=Aerosols_Working_Group&diff=20397Aerosols Working Group2015-04-07T21:37:34Z<p>Jeffrey Pierce: /* Current GEOS-Chem Aerosol Projects, alphabetized by institution (please add yours!) */</p>
<hr />
<div>All users interested in the GEOS-Chem aerosol simulations are encouraged to subscribe to the aerosols email list (click on the link in the [[#Contact information|contact information section]] below).<br />
<br />
Information on existing projects and future developments in aerosols will be posted here. We encourage user groups to keep their information up-to-date.<br />
<br />
== Contact information ==<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-<br />
|bgcolor="#CCCCCC"|'''Aerosols Working Group Co-Chairs'''<br />
|[http://web.mit.edu/heald/www/ Colette Heald], [http://pierce.atmos.colostate.edu/ Jeff Pierce]<br />
|-<br />
|bgcolor="#CCCCCC"|'''Aerosols Working Group email list'''<br />
|<tt>geos-chem-aerosols [at] seas.harvard.edu</tt><br />
|-<br />
|bgcolor="#CCCCCC"|'''To subscribe to email list'''<br />
|Send email to <tt>geos-chem-aerosols-join [at] seas.harvard.edu</tt><br />
|-<br />
|bgcolor="#CCCCCC"|'''To unsubscribe from email list'''<br />
|Send email to <tt>geos-chem-aerosols-leave [at] seas.harvard.edu</tt><br />
|}<br />
<br />
== Current GEOS-Chem Aerosol Projects, alphabetized by institution (please add yours!) ==<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!width="150px"|User Group <br />
!width="600px"|Description <br />
!width="150px"|Contact Person<br />
!width="100px"|Date Added<br />
|-<br />
|Beijing/SUNY<br />
|Representing GEOS-Chem in the AEROCOM intercomparisons<br />
|[mailto:mayfu@pku.edu.cn May Fu] <br>[mailto:yfq@asrc.cestm.albany.edu Fangqun Yu]<br />
|28 Jul 2010<br />
|-<br />
|CU Boulder<br />
|Inverse modeling of inorganic PM2.5 precursors. Direct aerosol radiative forcing. <br />
|[mailto:daven.henze@colorado.edu Daven Henze]<br />
|19 Apr 2009<br />
|-<br />
|CMU<br />
|Development of aerosol microphysics. Represented aerosols include size-resolved aerosol numbers and multi-component mass species, including sulfate, sea-salt, OM, EC, and dust. Evaluation against field campaign, e.g. ACE-Asia.<br />
|[mailto:petera@andrew.cmu.edu Peter Adams]<br>[mailto:dwesterv@andrew.cmu.edu Dan Westervelt]<br />
|23 Apr 2009<br />
|-<br />
|Colorado State University<br />
|Aerosol microphysics: effects of nucleation, emissions and SOA on aerosol size distribution<br />
|[mailto:jeffrey.robert.pierce@gmail.com Jeff Pierce]<br />
|03 Jan 2011<br />
|-<br />
|Colorado State University<br />
|Aerosol microphysics: Combustion aerosol microphysics, optical properties and radiative forcings<br />
|[mailto:jkodros@atmos.colostate.edu Jack Kodros]<br />
|03 Jan 2011<br />
|-<br />
|Dalhousie<br />
|Optimal estimation satellite retrieval of aerosols <br />
|[mailto:Aaron.van.Donkelaar@dal.ca Aaron van Donkelaar]<br />
|26 Sep 2012<br />
|-<br />
|Dalhousie<br />
|Global aerosol speciation<br />
|[mailto:philip.sajeev@gmail.com Sajeev Philip]<br />
|26 Sep 2012<br />
|-<br />
|Dalhousie/Tsinghua<br />
|Historical trends in Asian PM2.5 and emissions<br />
|[mailto:ggn220@gmail.com Guannan Geng]<br />
|26 Sep 2012<br />
|-<br />
|Dalhousie<br />
|Simulation of the absorbing aerosol index<br />
|[mailto:mhammer17@hotmail.com Melanie Hammer]<br />
|26 Sep 2012<br />
|-<br />
|Dalhousie<br />
|Diurnal variation in North American aerosol<br />
|[mailto:Andrew.Morrow@Dal.Ca Andrew Morrow]<br />
|26 Sep 2012<br />
|-<br />
|Dalhousie<br />
|Sensitivity of global PM2.5 to sources<br />
|[mailto:colin.lee@dal.ca Colin Lee]<br />
|26 Sep 2012<br />
|-<br />
|Dalhousie<br />
|Aerosol microphysics simulation of AOD and PM2.5<br />
|[mailto:AR731886@DAL.CA Arjya Sarkar]<br />
|26 Sep 2012<br />
|-<br />
|Dalhousie<br />
|Aerosol scavenging, nuclear accident simulation (137-CS, 133-XE)<br />
|[mailto:croft@mathstat.dal.ca Betty Croft]<br />
|03 Jan 2013<br />
|-<br />
|Dalhousie<br />
|Satellite-based estimates of Asian PM2.5<br />
|[mailto:jn231250@dal.ca Junwei Xu]<br />
|26 Sep 2012<br />
|-<br />
|Dalhousie<br />
|Historical trends in global satellite-derived estimates of PM2.5 <br />
|[mailto:briboys@gmail.com Brian Boys]<br />
|27 Apr 2011<br />
|-<br />
|Dalhousie<br />
|Historical (1980-) trends in aerosol speciation in North America <br />
|[mailto:nt662202@Dal.Ca Nathaniel Egan-Pimblett]<br />
|27 Apr 2011<br />
|-<br />
|Dalhousie<br />
|Assimilation of CALIOP vertical profiles<br />
|[mailto:colin.lee@dal.ca Colin Lee]<br />
|5 Dec 2013<br />
|-<br />
|Dalhousie<br />
|Simulation of heavy metals in PM<br />
|[mailto:fr526565@dal.ca Farhan Khan]<br />
|5 Dec 2013<br />
|-<br />
|Harvard<br />
|Aerosol scavenging in continental outflow; intercontinental transport and dissipation of pollution plumes<br />
|[mailto:kim68@fas.harvard.edu Sungshik Kim]<br />
|13 Jul 2010<br />
|-<br />
|Harvard<br />
|Irreversible uptake of isoprene SOA; estimate of organic aerosol yields with satellite observations<br />
|[mailto:emarais@seas.harvard.edu Eloise Marais]<br />
|27 April 2014<br />
|-<br />
|MIT<br />
|PM2.5 concentrations and health impacts, including future emissions trends<br />
|[mailto:selin@mit.edu Noelle Selin]<br />
|29 Jun 2010<br />
|-<br />
|MIT<br />
|Examining long term trends of dust in the tropics<br />
|[mailto:daridley@mit.edu Dave Ridley]<br />
|10 April 2012<br />
|-<br />
|MIT<br />
|Investigating sub-grid variability and scale invariance of dust emissions<br />
|[mailto:daridley@mit.edu Dave Ridley]<br />
|25 Sep 2012<br />
|-<br />
|MIT<br />
|Integrating RRTMG in GEOS-Chem (LW and SW, gases and aerosols), evaluating aerosol forcing<br />
|[mailto:daridley@mit.edu Dave Ridley]<br>[mailto:heald@mit.edu Colette Heald]<br />
|25 Sep 2012<br />
|-<br />
|MIT<br />
|Investigating impact of black carbon aging and mixing on radiative forcing<br />
|[mailto:xuanw12@mit.edu Xuan Wang]<br />
|25 Sep 2012<br />
|-<br />
|MIT<br />
|Investigating NHx system (GEOS-Chem compared to surface, CalNex and IASI observations) <br />
|[mailto:schiferl@mit.edu Luke Schiferl]<br />
|20 May 2010<br />
|-<br />
|MIT<br />
|Developing a scheme to describe the aging of organic aerosol<br />
|[mailto:qichen@mit.edu Qi Chen]<br />
|8 Apr 2013<br />
|-<br />
|MIT<br />
|Impact of 2000-2050 changes in climate, vegetation and land use on aerosols<br />
|[mailto:pkamostai@gmail.com Amos Tai]<br />
|9 May 2013<br />
|-<br />
|MIT/CU <br />
|Investigating transpacific transport of aerosol and gas-phase pollution.<br />
|[mailto:klapina@atmos.colostate.edu Kateryna Lapina]<br />
|13 Apr 2009<br />
|-<br />
|MIT/CSU <br />
|Investigating aerosols in the Southeastern US<br />
|[mailto:bonne@atmos.colostate.edu Bonne Ford]<br />
|01 Feb 2012<br />
|-<br />
|NASA LaRC<br />
|transpacific transport of dust and sulfate; composition of Asian upper tropopause aerosol layer (ATAL).<br />
|[mailto:t.d.fairlie@nasa.gov Duncan Fairlie]<br />
|10 Apr 2013<br />
|-<br />
|NIA / LaRC<br />
|Radiative effects of aerosols vs. clouds<br />
|[mailto:hyl@nianet.org Hongyu Liu]<br />
|05 Feb 2010<br />
|-<br />
|Peking University<br />
|Carbonaceous aerosols in China<br />
|[mailto:tmfu@pku.edu.cn May Fu]<br />
|01 Jul 2010<br />
|-<br />
|Peking University<br />
|Biomass burning aerosols in South and East Asia<br />
|[mailto:tmfu@pku.edu.cn May Fu]<br />
|01 Jul 2010<br />
|-<br />
|Peking University<br />
|Estimate of interdecadal variation in direct radiative effect of aerosols over global lands <br />
|[mailto:linjt@pku.edu.cn Jintai Lin]<br />
|01 Nov 2010<br />
|-<br />
|Peking University<br />
|Anthropogenic dust and impacts on global environment <br />
|[mailto:linjt@pku.edu.cn Jintai Lin]<br />
|01 May 2011<br />
|-<br />
|University of Athens-National Observatory of Athens (Greece)<br />
|Study of aerosols over Europe and Greece by coupling Geos-chem (v8-03-01) with Camx<br />
|[mailto:aprot@phys.uoa.gr Anna Protonotariou]<br />
|01 Jul 2010<br />
|-<br />
|UNL<br />
|aerosol retrieval from satellite, aerosol direct and indirect effect.<br />
|[mailto:jwang7@unl.edu Jun Wang]<br />
|22 Apr 2009<br />
|-<br />
|University of L'Aquila<br />
|Participation in organic aerosol AEROCOM intercomparison (v8.02.02 of GEOS-Chem)<br />
|[mailto:gabriele.curci@aquila.infn.it Gabriele Curci]<br />
|24 Jun 2009<br />
|-<br />
|University of L'Aquila<br />
|Development of a post-processing tool for aerosol optical properties computations<br />
|[mailto:gabriele.curci@aquila.infn.it Gabriele Curci]<br />
|20 Jan 2011<br />
|-<br />
|UW<br />
|Investigating the chemistry of sulfate and nitrate aerosol formation utilizing observations and modeling of oxygen isotopes <br />
|[mailto:beckya@uw.edu Becky Alexander]<br />
|30 Jun 2010<br />
|-<br />
|UW<br />
|Developing a new parameterization of sea-salt emissions and dry deposition<br />
|[mailto:jaegle@uw.edu Lyatt Jaegl&eacute;]<br />
|01 Jul 2010<br />
|-<br />
|UW<br />
|Transport of aerosols to the Arctic using CALIOP observations<br />
|[mailto:dipierro@uw.edu Maurizio DiPierro]<br />
|01 Jul 2010<br />
|-<br />
|UW<br />
|Long-range transport of aerosols from Asia and N. America<br />
|[mailto:yrluan@uw.edu Yurong Luan]<br />
|01 Jul 2010<br />
|-<br />
|SNU<br />
|Evaluation of regional aerosol simulations with the nested G-C over East Asia<br />
|[mailto:rjpark@snu.ac.kr Rokjin Park]<br />
|15 Sep 2009<br />
|-<br />
|SNU<br />
|Implement the VBS method in GEOS-Chem for SOA <br />
|[mailto:rjpark@snu.ac.kr Rokjin Park]<br>[mailto:cdswk@snu.ac.kr Dusung Jo]<br />
|28 Sep 2012<br />
|-<br />
|SNU<br />
|Siberian forest fire aerosols and climatic effects <br />
|[mailto:rjpark@snu.ac.kr Rokjin Park]<br>[mailto:hb3099@hotmail.com Seungeun Lee]<br />
|28 Sep 2012<br />
|-<br />
|SUNY-Albany<br />
|Formation and evolution of particles in the troposphere <br />
|[mailto:yfq@asrc.cestm.albany.edu Fangqun Yu]<br />
|06 Mar 2010<br />
<br />
|-<br />
|}<br />
<br />
== Recent GEOS-Chem updates related to aerosols ==<br />
<br />
We have added the following updates pertaining to aerosols to recent GEOS-Chem versions: <br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|-bgcolor="#CCCCCC" valign="top"<br />
!width="75px"|Version<br />
!width="75px"|Released<br />
!width="600px"|Description<br />
!width="200px"|Contact<br />
|-valign="top"<br />
|[[GEOS-Chem v9-02|v9-02]]<br />
|Mar 2014<br />
|[[Secondary organic aerosols#SOA simulation with semi-volatile POA|Expansion of SOA option (SOA + nonvolatile POA)]]<br />
|Havala Pye (formerly Caltech, now EPA)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-02|v9-02]]<br />
|Mar 2014<br />
|[[Sulfate_aerosols#Cloud_water_pH_for_sulfate_formation|Cloud water pH for sulfate formation]]<br />
|Becky Alexander (U. Washington) <br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-02|v9-02]]<br />
|Mar 2014<br />
|[[Aerosol_optical_properties#Better_representation_of_OC_growth_with_RH_and_correction_to_sulfate_optics|Better representation of OC growth with RH and correction to sulfate optics]]<br />
|David Ridley (MIT)<br>Randall Martin (Dalhousie) <br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-02|v9-02]]<br />
|Mar 2014<br />
|[[Aerosol_optical_properties#Fix_to_jv_spec_aod.dat|Bug fix in jv_spec_aod.dat for dust species]]<br />
|Gabriele Curci (U. L'Aquila)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-02|v9-02]]<br />
|Mar 2014<br />
|[[Sea_salt_aerosols#Update_molecular_weight_of_sea_salt_tracers|Update molecular weight of sea salt tracers]]<br />
|Colette Heald (MIT) <br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-03|v9-01-03]]<br />
|Sep 2012<br />
|[[Mineral_dust_aerosols#Sub-micron_dust_mass_partitioning_change|Dust submicron size distribution for optics]]<br />
|Dave Ridley, CSU<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-03|v9-01-03]]<br />
|Sep 2012<br />
|Modifications to sea salt [[Sea_salt_aerosols#SST_dependent_sea_salt_emissions|emissions]] and [[Sea_salt_aerosols#Updates_to_sea_salt_dry_deposition|dry deposition]]<br />
|Lyatt Jaegle and Becky Alexander, U Washington<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-03|v9-01-03]]<br />
|Sep 2012<br />
|Various updates to wet deposition to impact aerosol simulation, see [http://wiki.seas.harvard.edu/geos-chem/index.php/Wet_deposition#Further_updates Wet Deposition Further Updates]<br />
|Qiaoqiao Wang, Harvard<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-02|v9-01-02]]<br />
|Nov 2011<br />
|Implementation of [[APM aerosol microphysics]] model<br />
|Fangqun Yu, SUNY Albany<br>Gan Luo, SUNY Albany<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-02|v9-01-02]]<br />
|Nov 2011<br />
|[[GEOS-Chem_v9-01-01#Inconsistencies_in_aerosol_diagnostics|Removing inconsistencies in aerosol diagnostics]]<br />
|Sungshik Patrick Kim, Harvard<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-02|v9-01-02]]<br />
|Nov 2011<br />
|[[Dry_deposition#Aerosol_dry_deposition_velocities_over_snow_and_ice_surfaces|Updated aerosol dry deposition velocities over snow and ice surfaces]]<br />
|Jenny Fisher, Harvard<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-02|v9-01-02]]<br />
|Nov 2011<br />
|[[Anthropogenic_emissions#Streets_2000|Added seasonality to Streets NH3 emissions over Asia]]<br />
|Jenny Fisher, Harvard<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-01|v9-01-01]]<br />
|Jun 2011<br />
|[[FlexAOD]] post-processing tool for the community<br />
|Gabriele Curci, University of l'Aquila<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v8-03-02|v8-03-02]]<br />
|Sep 2010<br />
|Using GEOS-5 liquid water content (LWC) and cloud fraction fields directly (rather than a parameterization) for aqueous sulfate chemistry<br />
|Jenny Fisher, Harvard<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v8-03-02|v8-03-02]]<br />
|Sep 2010<br />
|Implementation of new Bond et al. BC/OC emissions <br />
* NOTE: Aerosol comparisons have been added to the standard 1 year benchmark, including speciated IMPROVE and PM2.5 from North America and Europe. Others are welcome to contribute 2005 observations to this effort (Colette Heald, CSU)<br />
|E. Leibensperger, Harvard<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v8-03-01|v8-03-01]]<br />
|May 2010<br />
|[[Photolysis mechanism#Updated aerosol optical properties|Updating of GEOS-Chem aerosol optics]]<br />
|Colette Heald, CSU<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v8-03-01|v8-03-01]]<br />
|May 2010<br />
|[[ISORROPIA II]] in GEOS-Chem, implemented along with new isoprene chemistry from Caltech<br />
|Havala Pye, (formerly Caltech, now EPA)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v8-03-01|v8-03-01]]<br />
|May 2010<br />
|[[Secondary organic aerosols#Modification to SOA formulation|Recommendation to remove SOA condensation in inorganic aerosol from standard code]]<br />
|Colette Heald, CSU<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v8-03-01|v8-03-01]]<br />
|May 2010<br />
|Adding aromatic SOA to standard code, released with [[New isoprene scheme|Caltech isoprene chemistry]]<br />
|Daven Henze, CU Boulder<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v8-03-01|v8-03-01]]<br />
|May 2010<br />
|Implementation of [[TOMAS aerosol microphysics]] model<br />
|Peter Adams, CMU<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v8-02-04|v8-02-04]]<br />
|Feb 2010<br />
|Implementation of new [[Volcanic SO2 emissions from Aerocom|volcanic emissions of SO2 from AeroCom]]<br />
|Jenny Fisher, Harvard<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v8-02-04|v8-02-04]]<br />
|Feb 2010<br />
|[[Sea salt aerosols#Updates to sea salt emissions algorithm|Updates and fixes to sea salt routine]]<br />
|Lyatt Jaegle, UW<br>Becky Alexander, UW<br />
<br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 11:14, 17 January 2014 (EST)<br />
<br />
== On-going Aerosol Working Group Developments ==<br />
<br />
We plan to add these aerosol-related updates to GEOS-Chem in the next few releases:<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|-bgcolor="#CCCCCC" valign="top"<br />
!width="600px"|Update<br />
!width="200px"|Authors<br />
!width="200px"|Planned release<br />
|-valign="top"<br />
|[[Coupling GEOS-Chem with RRTMG|Integrating a radiative transfer model into GEOS-Chem]]<br />
|Colette Heald (MIT)<br>David Ridley (MIT)<br>Karen Cady-Pereira (AER)<br>Matt Alvarado (AER)<br />
|<br />
*Delivered to [[GEOS-Chem Support Team|GCST]]<br />
*Slated for inclusion into [[GEOS-Chem v10-01|v10-01]]<br />
|-valign="top"<br />
|[[Mineral dust aerosols#Surface chemistry on dust|Simplified description of uptake of SO2, nitric acid and sulfuric acid on mineral dust]]<br />
|Duncan Fairlie, Langley<br />
|<br />
*Delivered to [[GEOS-Chem Support Team|GCST]]<br />
*Slated for inclusion into [[GEOS-Chem v10-01|v10-01]]<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 15:05, 25 April 2014 (EDT)<br />
<br />
== Future Development Priorities ==<br />
<br />
These topics were raised at the IGC5 as future updates & development priorities for GEOS-Chem (with additions from the community in recent months): <br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|-bgcolor="#CCCCCC" valign="top"<br />
!width="600px"|Update<br />
!width="200px"|Authors<br />
!width="200px"|Priority<br />
<br />
|-valign="top"<br />
|Integrating online radiative forcing calculations into GEOS-Chem<br />
|Colette Heald (MIT)<br>David Ridley (MIT) <br />
|high<br />
<br />
|-valign="top"<br />
|Addition of effective wind speed to met fields for consistent resolution dust/sea salt emissions<br />
|Jeff Pierce (CSU)<br>David Ridley (MIT)<br>[[GEOS-Chem Support Team|GCST]]<br />
|medium<br />
<br />
|-valign="top"<br />
|Addition of deposition observations to aerosol benchmark<br />
|Colette Heald (MIT)<br />
|low<br />
<br />
|-valign="top"<br />
|dust simulation expansion (tagged simulation, oxalate, P, Fe chemistry)<br />
|Matthew Johnson (NC State)<br />
|low<br />
<br />
|-valign="top"<br />
|DMS oxidation scheme updating<br />
|TBD<br />
|low<br />
<br />
|-valign="top"<br />
|Investigation of how aerosol water is treated in PM comparisons (ISORROPIA vs. hygroscopic growth curves)<br />
|TBD<br />
|low<br />
<br />
|-valign="top"<br />
|APM capability for nested grid<br />
|Fangqun Yu (SUNY Albany)<br />
|<br />
<br />
|-valign="top"<br />
|TOMAS capability for nested grid<br />
|Jeff Pierce (Dalhousie)<br />
|<br />
<br />
|-valign="top"<br />
|Cloudwater pH for sulfate formation<br />
|Becky Alexander (U. Washington)<br />
|<br />
<br />
|-valign="top"<br />
|Tagged sulfate and nitrate simulation<br />
|Becky Alexander (U. Washington)<br />
|<br />
<br />
|-valign="top"<br />
|Improved dust simulation in nested-grid model<br />
|Rokjin Park (Seoul National University)<br />
|<br />
<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 15:04, 25 April 2014 (EDT)<br />
<br />
== Aerosol optical properties ==<br />
<br />
Please visit our new [[Aerosol optical properties|aerosol optical properties wiki page]] for more information about:<br />
<br />
# [http://www.atmos.colostate.edu/~heald/docs/GEOS_Chem_optics_description.pdf Description of GEOS-Chem aerosol optics] <br />
# [[Aerosol optical properties#Aerosol optical properties update for GEOS-Chem v8-03-01|Aerosol optical properties update for v8-03-01]]<br />
# [[Aerosol optical properties#Aerosol optical properties at high spectral resolution|Aerosol optical properties at high spectral resolution]]<br />
<br />
Here is a list of updates that were considered (2, 4 and 5 are included in the [[GEOS-Chem v8-03-01|v8-03-01]] update):<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!width="600px"|Proposed Update (include information on old values if known) <br />
!width="200px"|Reference <br />
!width="200px"|Contact<br />
|-<br />
|Account for absorption in the 300-500 nm range by OC, which may be greater than presently treated. Currently we have OC ss albedo in this range being > 0.95, though it may be lower than 0.85.<br />
|[http://www.atmos-chem-phys.net/8/6665/2008/acp-8-6665-2008.pdf Barnard et al, 2008]<br />
|[mailto:daven.henze@colorado.edu Daven Henze] <br />
|-<br />
|Expand Mie table to include more wavelengths. Most literature values compare at 500 or 550 nm. Current GC lookup table includes 400, then 600. A wider range is also necessary for integrating to get total SW flux; something greater than 1500 perhaps?<br />
|[http://www.atmos-chem-phys.net/4/183/2004/acp-4-183-2004.html Martin et al, 2004]<br />
|[mailto:daven.henze@colorado.edu Daven Henze] <br />
|-<br />
|Consider using the water content of the fine mode aerosol calculated in the aerosol thermodynamic module rather than hygroscopic growth curves to estimate wet particle effective radius.<br />
|N/A<br />
|[mailto:daven.henze@colorado.edu Daven Henze] <br />
|-<br />
|Consider changing the "default" AOD diagnostic wavelength from 400 nm to 550nm (for matching with MODIS & CALIPSO)<br />
|N/A<br />
|[mailto:heald@atmos.colostate.edu.edu Colette Heald] <br />
|-<br />
|Treat the radius of hydrophylic organic aerosol similar to that of sulfate. This is based on observations that organic aerosol and sulfate are often internally mixed. Should we consider something similar for black carbon? <br />
|[http://cat.inist.fr/?aModele=afficheN&cpsidt=17219054 Rupkheti et al., 2007]<br />
|[mailto:randall.martin@dal.ca Randall Martin] <br />
|}<br />
<br />
== Related Topics ==<br />
* [[Aerosol emissions]]<br />
* Aerosol microphysics simulations:<br />
** [[APM aerosol microphysics|with APM]]<br />
** [[TOMAS aerosol microphysics|with TOMAS]]<br />
* [[Aerosol-only simulation]]<br />
* [[Aerosol thermodynamical equilibrium]]<br />
* [[Carbonaceous aerosols]]<br />
* [[Mineral dust aerosols]]<br />
* [[Secondary organic aerosols]]<br />
* [[Sea salt aerosols]]<br />
* [[Sulfate aerosols]]<br />
* [[ISORROPIA II]]<br />
* [[Photolysis mechanism|Photolysis mechanisms in GEOS-Chem]]<br />
<br />
== Issues / Topics for Discussion ==</div>Jeffrey Piercehttps://wiki.seas.harvard.edu/geos-chem/index.php?title=GEOS-Chem_nested_grid_simulations&diff=5061GEOS-Chem nested grid simulations2010-08-12T13:39:23Z<p>Jeffrey Pierce: /* Transport fix */</p>
<hr />
<div>This page contains some basic information pertaining to the GEOS-Chem nested grid simulations. For more detailed information about met data availability for the various geographic regions, please see our [[Available met data for nested grid simulations]] wiki page. We also invite you to visit the [[Regional Air Quality Working Group|wiki page of the Regional Air Quality Working Group]], which is responsible for coordinating nested-grid simulations within the GEOS-Chem user community.<br />
<br />
Please also see our [http://acmg.seas.harvard.edu/geos/wiki_docs/nested_grids/geos_data_downloads.pdf protocol for downloading and processing nested grid met data], which outlines the responsibilities for user groups using GEOS-Chem nested grid simulations.<br />
<br />
== Nested Grid Frequently Asked Questions ==<br />
<br />
=== Can I perform a nested-grid simulation with GEOS-3 meteorology? ===<br />
<br />
Yes. You may perform a [http://acmg.seas.harvard.edu/geos/doc/man/appendix_4.html#A4.2 GEOS-3] nested-grid simulation for one of the following regions:<br />
<br />
* [http://acmg.seas.harvard.edu/geos/doc/man_test/appendix_2.html#A2.5.1 GEOS-3 1x1, China nested grid]<br />
* [http://acmg.seas.harvard.edu/geos/doc/man_test/appendix_2.html#A2.5.2 GEOS-3 1x1, North America nested grid]<br />
<br />
You should be aware that GEOS-3 is now considered to be obsolete. Also, there is only a limited amount of GEOS-3 met data (2000-2001) available for the nested grid simulations. <br />
<br />
=== Can I run a nested grid simulation with GEOS-5 meteorology? ===<br />
<br />
Yes! With [[GEOS-Chem v8-01-02]] and higher versions you may perform a nested grid simulation for the [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#A2.6.1 China/SE Asia region] at the native GEOS-5 resolution of 0.5&deg; x 0.666&deg;. Also, [[GEOS-Chem v8-03-01]] will contain several code updates for the [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#A2.6.2 North American] and European nested-grid regions.<br />
<br />
=== Boundary conditions ===<br />
<br />
'''''[mailto:dbm@umn.edu Dylan Millet] wrote:'''''<br />
<br />
:Do you know if the 0.5&deg; x 0.667&deg; nested simulation that's being developed uses a 4&deg; x 5&deg; or a 2&deg; x 2.5&deg; grid outside of the nested domain?"<br />
<br />
'''''[mailto:yxw@tsinghua.edu.cn Yuxuan Wang] replied:'''''<br />
:The nested simulation uses 4&deg; x 5&deg; simulation results only at the lateral boundaries of the nested domain. For example, the East Asia nested domain covers 10S to 55N and 70E to 150E, one needs to save 4x5 simulation results (tracer concentrations only) for each vertical layer, at a frequency of every 3 hours, at the following four boundaries:<br />
<br />
:lat = 10S, lon = 70E<br />
:lat = 10S, lon = 150E<br />
:lat = 55N, lon = 70E<br />
:lat = 55N, lon = 150E<br />
<br />
:One can easily change the code to have the nested-grid simulation use 2x2.5 simulation as boundary conditions, but the default has been to take 4x5 results since it's much faster to run a 4x5 simulation.<br />
<br />
'''''[mailto:srhb2@cam.ac.uk Steven Barrett] replied:'''''<br />
<br />
:Could you let me know the standard LL box and UR box of the 4x5 region used as boundary conditions for NA nested 1x1 GEOS-Chem simulations? I think it'll be LL = (9,26) and UR=(29,38), but the upper latitude extent of the NA region falls right on a grid cell boundary, so it's not clear to me which one would be the right one.<br />
<br />
'''''Philippe Le Sager replied:'''''<br />
<br />
:Those indices are correct. They are default Fortran (starting at one for 1st cell), and correspond to cell within the domain.<br />
<br />
--[[User:Bmy|Bob Y.]] 13:51, 3 March 2010 (EST)<br />
<br />
== Setting up a 0.5x0.667 nested-grid simulation for GEOS-5 ==<br />
<br />
=== Transport fix ===<br />
[mailto:linzhang@fas.harvard.edu Lin Zhang] reported a problem with the transport for nested simulations with GEOS-5 met fields.<br />
The problem was traced back to the fact that neither the latest pressure fixer nor the new advection have been set up to be used with nested grids. The problems in both were:<br />
<br />
* the use of polar caps for the first and last latitude bands of the nested domain, although there is no pole in the domain.<br />
* the use of periodicity both in longitude and latitude.<br />
<br />
To solve the problems we modified both modules so that variables are updated only for an inner window of the domain, so that we do not need periodicity. The buffer zone for the pressure fixer is equal to 3 grid cells in all directions (defined in INIT_PJC_PFIX in GeosCore/pjc_pfix_geos5_window_mod.f). The buffer zone for the transport is the zone where the Boundary Conditions are fixed (as defined at the end of the NESTED MENU in input.geos). Note that the buffer zone for the advection must be larger than the buffer zone for the pressure-fixer.<br />
<br />
The fix will be available in [[GEOS-Chem v8-03-02]].<br />
<br />
--[[User:Ccarouge|Ccarouge]] 16:35, 4 August 2010 (EDT)<br />
<br />
'''''[mailto:jeffrey.pierce@dal.ca Jeff Pierce] replied:'''''<br />
<br />
I applied this fix, and the RAM requirements were increased. It went from 11 GB to 14 GB. I am using 148 tracers, which is why the RAM requirement is already high. However, I'm guessing this will affect everyone to some degree.<br />
<br />
=== 0.5x0.66 China nested grid simulation ===<br />
<br />
* [[Regional Air Quality Working Group#How to run the 0.5x0.667 nested-grid for GEOS-5|How to Run GEOS-5 0.5x0.667 China nested grid]]<br />
<br />
=== 0.5x0.66 NA nested grid simulation ===<br />
<br />
* [[Regional Air Quality Working Group#How to run the 0.5x0.667 nested-grid for GEOS-5|How to Run GEOS-5 0.5x0.667 NA nested grid]]<br />
<br />
== Setting up a 1x1 China nested-grid simulation for GEOS-3 ==<br />
<br />
'''''NOTE: With the advent of the GEOS-5 meteorology, the GEOS-3 1x1 nested-grid simulation described below is now obsolete. We strongly recommend to use the GEOS-5 meteorology for your nested grid simulation.'''''<br />
<br />
--[[User:Bmy|Bob Y.]] 14:00, 3 March 2010 (EST)<br />
<br />
Here is a check list and input.geos file that you need to run the nested-grid China simulation (supplied by Yuxuan Wang):<br />
<br />
=== define.h ===<br />
<br />
These are the settings you need to make in the GEOS-Chem <tt>define.h</tt> file:<br />
<br />
#define GEOS_3 'GEOS_3'<br />
#define GRID1x1 'GRID1x1'<br />
#define NESTED_CH 'NESTED_CH'<br />
#define GRID30LEV 'GRID30LEV'<br />
<br />
=== input.geos ===<br />
<br />
These are the settings you need to make in the GEOS-Chem <tt>input.geos</tt> file:<br />
<br />
==== Saving out 4 x 5 boundary conditions ====<br />
<br />
You will have to run the global model at 4 x 5 resolution to save out the transport boundary conditions. Here are the relevant settings in input.geos:<br />
<br />
%%% SIMULATION MENU %%% :<br />
Start YYYYMMDD, HHMMSS : 20010101 000000<br />
End YYYYMMDD, HHMMSS : 20020101 000000<br />
Run directory : ./<br />
Input restart file : restart.YYYYMMDDhh<br />
Make new restart file? : F<br />
Output restart file(s) : restart.YYYYMMDDhh<br />
Root data directory : /data/ctm/GEOS_4x5/<br />
=> GCAP subdir : AGRID/YYYY/MM/<br />
=> GEOS-3 subdir : GEOS_3/YYYY/MM/<br />
=> GEOS-4 subdir : GEOS_4_v4/YYYY/MM/<br />
=> GEOS-5 subdir : GEOS_5/YYYY/MM/<br />
Dir w/ 1x1 emissions etc: /data/ctm/GEOS_1x1/<br />
Temporary directory : TEMP/<br />
Unzip met fields? : T<br />
Wait for met fields? : T<br />
Use variable tropopause : N<br />
Global offsets I0, J0 : 0 0<br />
<br />
... <br />
<br />
%%% TRANSPORT MENU %%% :<br />
Turn on Transport : T<br />
=> Use Flux Correction?: F<br />
=> Fill Negative Values: T <br />
=> IORD, JORD, KORD : 3 3 7<br />
Transport Timestep [min]: 30 <br />
Use strat O3/NOy BC's : T<br />
<br />
...<br />
<br />
%%% CONVECTION MENU %%% :<br />
Turn on Cloud Conv? : T<br />
Turn on PBL Mixing? : T<br />
Convect Timestep (min) : 30<br />
<br />
...<br />
<br />
%%% NESTED GRID MENU %%%: <br />
Save TPCORE 4x5 BC's : T<br />
TPCORE 4x5 BC directory : /as/home/ctm/yxw/bc/bc_ozone_std/<br />
4x5 BC timestep [min] : 180<br />
LL box of 4x5 BC region : 51 21<br />
UR box of 4x5 BC region : 67 37<br />
1x1 offsets I0_W, J0_W : 3 3<br />
<br />
==== 1x1 nested grid simulation ====<br />
<br />
Then once you have saved out the 4 x 5 boundary conditions you can do the 1 x 1 nested grid simulation. Here are the appropriate settings in input.geos:<br />
<br />
%%% SIMULATION MENU %%% :<br />
Start YYYYMMDD, HHMMSS : 20010301 000000<br />
End YYYYMMDD, HHMMSS : 20010302 000000<br />
Run directory : ./<br />
Input restart file : restart.YYYYMMDDhh<br />
Make new restart file? : F<br />
Output restart file(s) : restart.YYYYMMDDhh<br />
Root data directory : /data/geos/GEOS_1x1_CH/<br />
=> GCAP subdir : AGRID/YYYY/MM/<br />
=> GEOS-3 subdir : GEOS_3/YYYY/MM/<br />
=> GEOS-4 subdir : GEOS_4_v4/YYYY/MM/<br />
=> GEOS-5 subdir : GEOS_5/YYYY/MM/<br />
Dir w/ 1x1 emissions etc: /data/ctm/GEOS_1x1/<br />
Temporary directory : TEMP/<br />
Unzip met fields? : T<br />
Wait for met fields? : T<br />
Use variable tropopause : F<br />
Global offsets I0, J0 : 250 79 # need to be changed for NA; index refer to 1x1 resolution<br />
<br />
...<br />
<br />
%%% TRANSPORT MENU %%% :<br />
Turn on Transport : T<br />
=> Use Flux Correction?: F<br />
=> Fill Negative Values: T <br />
=> IORD, JORD, KORD : 3 3 7<br />
Transport Timestep [min]: 10 <br />
Use strat O3/NOy BC's : T<br />
<br />
...<br />
<br />
%%% CONVECTION MENU %%% :<br />
Turn on Cloud Conv? : T<br />
Turn on PBL Mixing? : T<br />
Convect Timestep (min) : 10<br />
<br />
... <br />
<br />
%%% NESTED GRID MENU %%% <br />
Save TPCORE 4x5 BC's : T<br />
TPCORE 4x5 BC directory : /as/home/strat/yxw/bc/ # change to be your own directory<br />
4x5 BC timestep [min] : 180<br />
LL box of 4x5 BC region : 51 21 # need to be changed for NA; index refer to 4x5 resolution<br />
UR box of 4x5 BC region : 67 37 # need to be changed for NA; index refer to 4x5 resolution<br />
1x1 offsets I0_W, J0_W : 3 3 # do not change for NA<br />
<br />
=== NOTES to 1x1 nested-grid simulation for GEOS-3 ===<br />
<br />
==== General ====<br />
<br />
# If not NESTED_CH (East Asia window) or NESTED_NA (north America window), need to first obtain <br />
#* The 1x1 meteorological field for the nested domain; <br />
#* Tll the input files (mostly emissions) at 1x1 resolution for the nested domain. <br />
# There needs to be two run directories: one for the 4x5 global run and one for the 1x1 nested run<br />
# Only one code directory is necessary. Code version v7-01-02 and higher can be compiled for both the global run and the nested run<br />
# Run the 4x5 global simulation first. With correct switches in the 4x5 input.geos file, boundary conditions will <br />
#* be saved out automatically into the designated directory and will be read later by the nested run. <br />
#* The code automatically takes care of formatting. <br />
<br />
==== Code ====<br />
# Change grid size in define.h <br />
# Change scaling factor in lightning_nox_mod.f (if not Chinese window)<br />
#* search for 1x1 in the file to locate the lines of code where changes should be made<br />
# Change IGLOB, JGLOB in CMN_SIZE (if not Chinese window)<br />
#* IGLOB and JGLOB refers to the size of the nested window measured at 1x1 resolution<br />
# Change PARAMETER( NLAND=2681, NPULSE=3 ) in commsoil.h (if not Chinese window)<br />
#* changes are already made in the code; just uncomment the NA part<br />
# Change datadir for O3 column in toms_mod.f --- if not CHINA or NA windows<br />
#* need to create TOMS_O3col_2001.geos file at 1x1 resolution for the nested region <br />
#* use the IDL code: regrid_4to1_O3_column.pro (note that line 33 and 34 needs to be modified for NA)</div>Jeffrey Piercehttps://wiki.seas.harvard.edu/geos-chem/index.php?title=GEOS-Chem_nested_grid_simulations&diff=5033GEOS-Chem nested grid simulations2010-08-09T18:49:12Z<p>Jeffrey Pierce: /* Transport fix */</p>
<hr />
<div>This page contains some basic information pertaining to the GEOS-Chem nested grid simulations. For more detailed information about met data availability for the various geographic regions, please see our [[Available met data for nested grid simulations]] wiki page. We also invite you to visit the [[Regional Air Quality Working Group|wiki page of the Regional Air Quality Working Group]], which is responsible for coordinating nested-grid simulations within the GEOS-Chem user community.<br />
<br />
Please also see our [http://acmg.seas.harvard.edu/geos/wiki_docs/nested_grids/geos_data_downloads.pdf protocol for downloading and processing nested grid met data], which outlines the responsibilities for user groups using GEOS-Chem nested grid simulations.<br />
<br />
== Nested Grid Frequently Asked Questions ==<br />
<br />
=== Can I perform a nested-grid simulation with GEOS-3 meteorology? ===<br />
<br />
Yes. You may perform a [http://acmg.seas.harvard.edu/geos/doc/man/appendix_4.html#A4.2 GEOS-3] nested-grid simulation for one of the following regions:<br />
<br />
* [http://acmg.seas.harvard.edu/geos/doc/man_test/appendix_2.html#A2.5.1 GEOS-3 1x1, China nested grid]<br />
* [http://acmg.seas.harvard.edu/geos/doc/man_test/appendix_2.html#A2.5.2 GEOS-3 1x1, North America nested grid]<br />
<br />
You should be aware that GEOS-3 is now considered to be obsolete. Also, there is only a limited amount of GEOS-3 met data (2000-2001) available for the nested grid simulations. <br />
<br />
=== Can I run a nested grid simulation with GEOS-5 meteorology? ===<br />
<br />
Yes! With [[GEOS-Chem v8-01-02]] and higher versions you may perform a nested grid simulation for the [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#A2.6.1 China/SE Asia region] at the native GEOS-5 resolution of 0.5&deg; x 0.666&deg;. Also, [[GEOS-Chem v8-03-01]] will contain several code updates for the [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#A2.6.2 North American] and European nested-grid regions.<br />
<br />
=== Boundary conditions ===<br />
<br />
'''''[mailto:dbm@umn.edu Dylan Millet] wrote:'''''<br />
<br />
:Do you know if the 0.5&deg; x 0.667&deg; nested simulation that's being developed uses a 4&deg; x 5&deg; or a 2&deg; x 2.5&deg; grid outside of the nested domain?"<br />
<br />
'''''[mailto:yxw@tsinghua.edu.cn Yuxuan Wang] replied:'''''<br />
:The nested simulation uses 4&deg; x 5&deg; simulation results only at the lateral boundaries of the nested domain. For example, the East Asia nested domain covers 10S to 55N and 70E to 150E, one needs to save 4x5 simulation results (tracer concentrations only) for each vertical layer, at a frequency of every 3 hours, at the following four boundaries:<br />
<br />
:lat = 10S, lon = 70E<br />
:lat = 10S, lon = 150E<br />
:lat = 55N, lon = 70E<br />
:lat = 55N, lon = 150E<br />
<br />
:One can easily change the code to have the nested-grid simulation use 2x2.5 simulation as boundary conditions, but the default has been to take 4x5 results since it's much faster to run a 4x5 simulation.<br />
<br />
'''''[mailto:srhb2@cam.ac.uk Steven Barrett] replied:'''''<br />
<br />
:Could you let me know the standard LL box and UR box of the 4x5 region used as boundary conditions for NA nested 1x1 GEOS-Chem simulations? I think it'll be LL = (9,26) and UR=(29,38), but the upper latitude extent of the NA region falls right on a grid cell boundary, so it's not clear to me which one would be the right one.<br />
<br />
'''''Philippe Le Sager replied:'''''<br />
<br />
:Those indices are correct. They are default Fortran (starting at one for 1st cell), and correspond to cell within the domain.<br />
<br />
--[[User:Bmy|Bob Y.]] 13:51, 3 March 2010 (EST)<br />
<br />
== Setting up a 0.5x0.667 nested-grid simulation for GEOS-5 ==<br />
<br />
=== Transport fix ===<br />
[mailto:linzhang@fas.harvard.edu Lin Zhang] reported a problem with the transport for nested simulations with GEOS-5 met fields.<br />
The problem was traced back to the fact that neither the latest pressure fixer nor the new advection have been set up to be used with nested grids. The problems in both were:<br />
<br />
* the use of polar caps for the first and last latitude bands of the nested domain, although there is no pole in the domain.<br />
* the use of periodicity both in longitude and latitude.<br />
<br />
To solve the problems we modified both modules so that variables are updated only for an inner window of the domain, so that we do not need periodicity. The buffer zone for the pressure fixer is equal to 3 grid cells in all directions (defined in INIT_PJC_PFIX in GeosCore/pjc_pfix_geos5_window_mod.f). The buffer zone for the transport is the zone where the Boundary Conditions are fixed (as defined at the end of the NESTED MENU in input.geos). Note that the buffer zone for the advection must be larger than the buffer zone for the pressure-fixer.<br />
<br />
The fix will be available in [[GEOS-Chem v8-03-02]].<br />
<br />
--[[User:Ccarouge|Ccarouge]] 16:35, 4 August 2010 (EDT)<br />
<br />
'''''[mailto:jeffrey.pierce@dal.ca Jeff Pierce] replied:'''''<br />
<br />
I applied this fix, and the RAM requirements were increased. This is problematic since I was operating near the maximum RAM of the node for nested sims before the fix. It went from 11 GB to over 16 GB (the maximum RAM). I am using 148 tracers, which is why the RAM requirement is already high. Is there a way to fix the transport issue without increasing the RAM?<br />
<br />
=== 0.5x0.66 China nested grid simulation ===<br />
<br />
* [[Regional Air Quality Working Group#How to run the 0.5x0.667 nested-grid for GEOS-5|How to Run GEOS-5 0.5x0.667 China nested grid]]<br />
<br />
=== 0.5x0.66 NA nested grid simulation ===<br />
<br />
* [[Regional Air Quality Working Group#How to run the 0.5x0.667 nested-grid for GEOS-5|How to Run GEOS-5 0.5x0.667 NA nested grid]]<br />
<br />
== Setting up a 1x1 China nested-grid simulation for GEOS-3 ==<br />
<br />
'''''NOTE: With the advent of the GEOS-5 meteorology, the GEOS-3 1x1 nested-grid simulation described below is now obsolete. We strongly recommend to use the GEOS-5 meteorology for your nested grid simulation.'''''<br />
<br />
--[[User:Bmy|Bob Y.]] 14:00, 3 March 2010 (EST)<br />
<br />
Here is a check list and input.geos file that you need to run the nested-grid China simulation (supplied by Yuxuan Wang):<br />
<br />
=== define.h ===<br />
<br />
These are the settings you need to make in the GEOS-Chem <tt>define.h</tt> file:<br />
<br />
#define GEOS_3 'GEOS_3'<br />
#define GRID1x1 'GRID1x1'<br />
#define NESTED_CH 'NESTED_CH'<br />
#define GRID30LEV 'GRID30LEV'<br />
<br />
=== input.geos ===<br />
<br />
These are the settings you need to make in the GEOS-Chem <tt>input.geos</tt> file:<br />
<br />
==== Saving out 4 x 5 boundary conditions ====<br />
<br />
You will have to run the global model at 4 x 5 resolution to save out the transport boundary conditions. Here are the relevant settings in input.geos:<br />
<br />
%%% SIMULATION MENU %%% :<br />
Start YYYYMMDD, HHMMSS : 20010101 000000<br />
End YYYYMMDD, HHMMSS : 20020101 000000<br />
Run directory : ./<br />
Input restart file : restart.YYYYMMDDhh<br />
Make new restart file? : F<br />
Output restart file(s) : restart.YYYYMMDDhh<br />
Root data directory : /data/ctm/GEOS_4x5/<br />
=> GCAP subdir : AGRID/YYYY/MM/<br />
=> GEOS-3 subdir : GEOS_3/YYYY/MM/<br />
=> GEOS-4 subdir : GEOS_4_v4/YYYY/MM/<br />
=> GEOS-5 subdir : GEOS_5/YYYY/MM/<br />
Dir w/ 1x1 emissions etc: /data/ctm/GEOS_1x1/<br />
Temporary directory : TEMP/<br />
Unzip met fields? : T<br />
Wait for met fields? : T<br />
Use variable tropopause : N<br />
Global offsets I0, J0 : 0 0<br />
<br />
... <br />
<br />
%%% TRANSPORT MENU %%% :<br />
Turn on Transport : T<br />
=> Use Flux Correction?: F<br />
=> Fill Negative Values: T <br />
=> IORD, JORD, KORD : 3 3 7<br />
Transport Timestep [min]: 30 <br />
Use strat O3/NOy BC's : T<br />
<br />
...<br />
<br />
%%% CONVECTION MENU %%% :<br />
Turn on Cloud Conv? : T<br />
Turn on PBL Mixing? : T<br />
Convect Timestep (min) : 30<br />
<br />
...<br />
<br />
%%% NESTED GRID MENU %%%: <br />
Save TPCORE 4x5 BC's : T<br />
TPCORE 4x5 BC directory : /as/home/ctm/yxw/bc/bc_ozone_std/<br />
4x5 BC timestep [min] : 180<br />
LL box of 4x5 BC region : 51 21<br />
UR box of 4x5 BC region : 67 37<br />
1x1 offsets I0_W, J0_W : 3 3<br />
<br />
==== 1x1 nested grid simulation ====<br />
<br />
Then once you have saved out the 4 x 5 boundary conditions you can do the 1 x 1 nested grid simulation. Here are the appropriate settings in input.geos:<br />
<br />
%%% SIMULATION MENU %%% :<br />
Start YYYYMMDD, HHMMSS : 20010301 000000<br />
End YYYYMMDD, HHMMSS : 20010302 000000<br />
Run directory : ./<br />
Input restart file : restart.YYYYMMDDhh<br />
Make new restart file? : F<br />
Output restart file(s) : restart.YYYYMMDDhh<br />
Root data directory : /data/geos/GEOS_1x1_CH/<br />
=> GCAP subdir : AGRID/YYYY/MM/<br />
=> GEOS-3 subdir : GEOS_3/YYYY/MM/<br />
=> GEOS-4 subdir : GEOS_4_v4/YYYY/MM/<br />
=> GEOS-5 subdir : GEOS_5/YYYY/MM/<br />
Dir w/ 1x1 emissions etc: /data/ctm/GEOS_1x1/<br />
Temporary directory : TEMP/<br />
Unzip met fields? : T<br />
Wait for met fields? : T<br />
Use variable tropopause : F<br />
Global offsets I0, J0 : 250 79 # need to be changed for NA; index refer to 1x1 resolution<br />
<br />
...<br />
<br />
%%% TRANSPORT MENU %%% :<br />
Turn on Transport : T<br />
=> Use Flux Correction?: F<br />
=> Fill Negative Values: T <br />
=> IORD, JORD, KORD : 3 3 7<br />
Transport Timestep [min]: 10 <br />
Use strat O3/NOy BC's : T<br />
<br />
...<br />
<br />
%%% CONVECTION MENU %%% :<br />
Turn on Cloud Conv? : T<br />
Turn on PBL Mixing? : T<br />
Convect Timestep (min) : 10<br />
<br />
... <br />
<br />
%%% NESTED GRID MENU %%% <br />
Save TPCORE 4x5 BC's : T<br />
TPCORE 4x5 BC directory : /as/home/strat/yxw/bc/ # change to be your own directory<br />
4x5 BC timestep [min] : 180<br />
LL box of 4x5 BC region : 51 21 # need to be changed for NA; index refer to 4x5 resolution<br />
UR box of 4x5 BC region : 67 37 # need to be changed for NA; index refer to 4x5 resolution<br />
1x1 offsets I0_W, J0_W : 3 3 # do not change for NA<br />
<br />
=== NOTES to 1x1 nested-grid simulation for GEOS-3 ===<br />
<br />
==== General ====<br />
<br />
# If not NESTED_CH (East Asia window) or NESTED_NA (north America window), need to first obtain <br />
#* The 1x1 meteorological field for the nested domain; <br />
#* Tll the input files (mostly emissions) at 1x1 resolution for the nested domain. <br />
# There needs to be two run directories: one for the 4x5 global run and one for the 1x1 nested run<br />
# Only one code directory is necessary. Code version v7-01-02 and higher can be compiled for both the global run and the nested run<br />
# Run the 4x5 global simulation first. With correct switches in the 4x5 input.geos file, boundary conditions will <br />
#* be saved out automatically into the designated directory and will be read later by the nested run. <br />
#* The code automatically takes care of formatting. <br />
<br />
==== Code ====<br />
# Change grid size in define.h <br />
# Change scaling factor in lightning_nox_mod.f (if not Chinese window)<br />
#* search for 1x1 in the file to locate the lines of code where changes should be made<br />
# Change IGLOB, JGLOB in CMN_SIZE (if not Chinese window)<br />
#* IGLOB and JGLOB refers to the size of the nested window measured at 1x1 resolution<br />
# Change PARAMETER( NLAND=2681, NPULSE=3 ) in commsoil.h (if not Chinese window)<br />
#* changes are already made in the code; just uncomment the NA part<br />
# Change datadir for O3 column in toms_mod.f --- if not CHINA or NA windows<br />
#* need to create TOMS_O3col_2001.geos file at 1x1 resolution for the nested region <br />
#* use the IDL code: regrid_4to1_O3_column.pro (note that line 33 and 34 needs to be modified for NA)</div>Jeffrey Piercehttps://wiki.seas.harvard.edu/geos-chem/index.php?title=GEOS-Chem_nested_grid_simulations&diff=5032GEOS-Chem nested grid simulations2010-08-09T18:48:05Z<p>Jeffrey Pierce: /* Transport fix */</p>
<hr />
<div>This page contains some basic information pertaining to the GEOS-Chem nested grid simulations. For more detailed information about met data availability for the various geographic regions, please see our [[Available met data for nested grid simulations]] wiki page. We also invite you to visit the [[Regional Air Quality Working Group|wiki page of the Regional Air Quality Working Group]], which is responsible for coordinating nested-grid simulations within the GEOS-Chem user community.<br />
<br />
Please also see our [http://acmg.seas.harvard.edu/geos/wiki_docs/nested_grids/geos_data_downloads.pdf protocol for downloading and processing nested grid met data], which outlines the responsibilities for user groups using GEOS-Chem nested grid simulations.<br />
<br />
== Nested Grid Frequently Asked Questions ==<br />
<br />
=== Can I perform a nested-grid simulation with GEOS-3 meteorology? ===<br />
<br />
Yes. You may perform a [http://acmg.seas.harvard.edu/geos/doc/man/appendix_4.html#A4.2 GEOS-3] nested-grid simulation for one of the following regions:<br />
<br />
* [http://acmg.seas.harvard.edu/geos/doc/man_test/appendix_2.html#A2.5.1 GEOS-3 1x1, China nested grid]<br />
* [http://acmg.seas.harvard.edu/geos/doc/man_test/appendix_2.html#A2.5.2 GEOS-3 1x1, North America nested grid]<br />
<br />
You should be aware that GEOS-3 is now considered to be obsolete. Also, there is only a limited amount of GEOS-3 met data (2000-2001) available for the nested grid simulations. <br />
<br />
=== Can I run a nested grid simulation with GEOS-5 meteorology? ===<br />
<br />
Yes! With [[GEOS-Chem v8-01-02]] and higher versions you may perform a nested grid simulation for the [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#A2.6.1 China/SE Asia region] at the native GEOS-5 resolution of 0.5&deg; x 0.666&deg;. Also, [[GEOS-Chem v8-03-01]] will contain several code updates for the [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#A2.6.2 North American] and European nested-grid regions.<br />
<br />
=== Boundary conditions ===<br />
<br />
'''''[mailto:dbm@umn.edu Dylan Millet] wrote:'''''<br />
<br />
:Do you know if the 0.5&deg; x 0.667&deg; nested simulation that's being developed uses a 4&deg; x 5&deg; or a 2&deg; x 2.5&deg; grid outside of the nested domain?"<br />
<br />
'''''[mailto:yxw@tsinghua.edu.cn Yuxuan Wang] replied:'''''<br />
:The nested simulation uses 4&deg; x 5&deg; simulation results only at the lateral boundaries of the nested domain. For example, the East Asia nested domain covers 10S to 55N and 70E to 150E, one needs to save 4x5 simulation results (tracer concentrations only) for each vertical layer, at a frequency of every 3 hours, at the following four boundaries:<br />
<br />
:lat = 10S, lon = 70E<br />
:lat = 10S, lon = 150E<br />
:lat = 55N, lon = 70E<br />
:lat = 55N, lon = 150E<br />
<br />
:One can easily change the code to have the nested-grid simulation use 2x2.5 simulation as boundary conditions, but the default has been to take 4x5 results since it's much faster to run a 4x5 simulation.<br />
<br />
'''''[mailto:srhb2@cam.ac.uk Steven Barrett] replied:'''''<br />
<br />
:Could you let me know the standard LL box and UR box of the 4x5 region used as boundary conditions for NA nested 1x1 GEOS-Chem simulations? I think it'll be LL = (9,26) and UR=(29,38), but the upper latitude extent of the NA region falls right on a grid cell boundary, so it's not clear to me which one would be the right one.<br />
<br />
'''''Philippe Le Sager replied:'''''<br />
<br />
:Those indices are correct. They are default Fortran (starting at one for 1st cell), and correspond to cell within the domain.<br />
<br />
--[[User:Bmy|Bob Y.]] 13:51, 3 March 2010 (EST)<br />
<br />
== Setting up a 0.5x0.667 nested-grid simulation for GEOS-5 ==<br />
<br />
=== Transport fix ===<br />
[mailto:linzhang@fas.harvard.edu Lin Zhang] reported a problem with the transport for nested simulations with GEOS-5 met fields.<br />
The problem was traced back to the fact that neither the latest pressure fixer nor the new advection have been set up to be used with nested grids. The problems in both were:<br />
<br />
* the use of polar caps for the first and last latitude bands of the nested domain, although there is no pole in the domain.<br />
* the use of periodicity both in longitude and latitude.<br />
<br />
To solve the problems we modified both modules so that variables are updated only for an inner window of the domain, so that we do not need periodicity. The buffer zone for the pressure fixer is equal to 3 grid cells in all directions (defined in INIT_PJC_PFIX in GeosCore/pjc_pfix_geos5_window_mod.f). The buffer zone for the transport is the zone where the Boundary Conditions are fixed (as defined at the end of the NESTED MENU in input.geos). Note that the buffer zone for the advection must be larger than the buffer zone for the pressure-fixer.<br />
<br />
The fix will be available in [[GEOS-Chem v8-03-02]].<br />
<br />
--[[User:Ccarouge|Ccarouge]] 16:35, 4 August 2010 (EDT)<br />
<br />
I applied this fix, and the RAM requirements were increased. This is problematic since I was operating near the maximum RAM of the node for nested sims before the fix. It went from 11 GB to over 16 GB (the maximum RAM). I am using 148 tracers, which is why the RAM requirement is already high. Is there a way to fix the transport issue without increasing the RAM?<br />
<br />
--[[User:Jeff Pierce]] 02:38, 9 August 2010 (EDT)<br />
<br />
=== 0.5x0.66 China nested grid simulation ===<br />
<br />
* [[Regional Air Quality Working Group#How to run the 0.5x0.667 nested-grid for GEOS-5|How to Run GEOS-5 0.5x0.667 China nested grid]]<br />
<br />
=== 0.5x0.66 NA nested grid simulation ===<br />
<br />
* [[Regional Air Quality Working Group#How to run the 0.5x0.667 nested-grid for GEOS-5|How to Run GEOS-5 0.5x0.667 NA nested grid]]<br />
<br />
== Setting up a 1x1 China nested-grid simulation for GEOS-3 ==<br />
<br />
'''''NOTE: With the advent of the GEOS-5 meteorology, the GEOS-3 1x1 nested-grid simulation described below is now obsolete. We strongly recommend to use the GEOS-5 meteorology for your nested grid simulation.'''''<br />
<br />
--[[User:Bmy|Bob Y.]] 14:00, 3 March 2010 (EST)<br />
<br />
Here is a check list and input.geos file that you need to run the nested-grid China simulation (supplied by Yuxuan Wang):<br />
<br />
=== define.h ===<br />
<br />
These are the settings you need to make in the GEOS-Chem <tt>define.h</tt> file:<br />
<br />
#define GEOS_3 'GEOS_3'<br />
#define GRID1x1 'GRID1x1'<br />
#define NESTED_CH 'NESTED_CH'<br />
#define GRID30LEV 'GRID30LEV'<br />
<br />
=== input.geos ===<br />
<br />
These are the settings you need to make in the GEOS-Chem <tt>input.geos</tt> file:<br />
<br />
==== Saving out 4 x 5 boundary conditions ====<br />
<br />
You will have to run the global model at 4 x 5 resolution to save out the transport boundary conditions. Here are the relevant settings in input.geos:<br />
<br />
%%% SIMULATION MENU %%% :<br />
Start YYYYMMDD, HHMMSS : 20010101 000000<br />
End YYYYMMDD, HHMMSS : 20020101 000000<br />
Run directory : ./<br />
Input restart file : restart.YYYYMMDDhh<br />
Make new restart file? : F<br />
Output restart file(s) : restart.YYYYMMDDhh<br />
Root data directory : /data/ctm/GEOS_4x5/<br />
=> GCAP subdir : AGRID/YYYY/MM/<br />
=> GEOS-3 subdir : GEOS_3/YYYY/MM/<br />
=> GEOS-4 subdir : GEOS_4_v4/YYYY/MM/<br />
=> GEOS-5 subdir : GEOS_5/YYYY/MM/<br />
Dir w/ 1x1 emissions etc: /data/ctm/GEOS_1x1/<br />
Temporary directory : TEMP/<br />
Unzip met fields? : T<br />
Wait for met fields? : T<br />
Use variable tropopause : N<br />
Global offsets I0, J0 : 0 0<br />
<br />
... <br />
<br />
%%% TRANSPORT MENU %%% :<br />
Turn on Transport : T<br />
=> Use Flux Correction?: F<br />
=> Fill Negative Values: T <br />
=> IORD, JORD, KORD : 3 3 7<br />
Transport Timestep [min]: 30 <br />
Use strat O3/NOy BC's : T<br />
<br />
...<br />
<br />
%%% CONVECTION MENU %%% :<br />
Turn on Cloud Conv? : T<br />
Turn on PBL Mixing? : T<br />
Convect Timestep (min) : 30<br />
<br />
...<br />
<br />
%%% NESTED GRID MENU %%%: <br />
Save TPCORE 4x5 BC's : T<br />
TPCORE 4x5 BC directory : /as/home/ctm/yxw/bc/bc_ozone_std/<br />
4x5 BC timestep [min] : 180<br />
LL box of 4x5 BC region : 51 21<br />
UR box of 4x5 BC region : 67 37<br />
1x1 offsets I0_W, J0_W : 3 3<br />
<br />
==== 1x1 nested grid simulation ====<br />
<br />
Then once you have saved out the 4 x 5 boundary conditions you can do the 1 x 1 nested grid simulation. Here are the appropriate settings in input.geos:<br />
<br />
%%% SIMULATION MENU %%% :<br />
Start YYYYMMDD, HHMMSS : 20010301 000000<br />
End YYYYMMDD, HHMMSS : 20010302 000000<br />
Run directory : ./<br />
Input restart file : restart.YYYYMMDDhh<br />
Make new restart file? : F<br />
Output restart file(s) : restart.YYYYMMDDhh<br />
Root data directory : /data/geos/GEOS_1x1_CH/<br />
=> GCAP subdir : AGRID/YYYY/MM/<br />
=> GEOS-3 subdir : GEOS_3/YYYY/MM/<br />
=> GEOS-4 subdir : GEOS_4_v4/YYYY/MM/<br />
=> GEOS-5 subdir : GEOS_5/YYYY/MM/<br />
Dir w/ 1x1 emissions etc: /data/ctm/GEOS_1x1/<br />
Temporary directory : TEMP/<br />
Unzip met fields? : T<br />
Wait for met fields? : T<br />
Use variable tropopause : F<br />
Global offsets I0, J0 : 250 79 # need to be changed for NA; index refer to 1x1 resolution<br />
<br />
...<br />
<br />
%%% TRANSPORT MENU %%% :<br />
Turn on Transport : T<br />
=> Use Flux Correction?: F<br />
=> Fill Negative Values: T <br />
=> IORD, JORD, KORD : 3 3 7<br />
Transport Timestep [min]: 10 <br />
Use strat O3/NOy BC's : T<br />
<br />
...<br />
<br />
%%% CONVECTION MENU %%% :<br />
Turn on Cloud Conv? : T<br />
Turn on PBL Mixing? : T<br />
Convect Timestep (min) : 10<br />
<br />
... <br />
<br />
%%% NESTED GRID MENU %%% <br />
Save TPCORE 4x5 BC's : T<br />
TPCORE 4x5 BC directory : /as/home/strat/yxw/bc/ # change to be your own directory<br />
4x5 BC timestep [min] : 180<br />
LL box of 4x5 BC region : 51 21 # need to be changed for NA; index refer to 4x5 resolution<br />
UR box of 4x5 BC region : 67 37 # need to be changed for NA; index refer to 4x5 resolution<br />
1x1 offsets I0_W, J0_W : 3 3 # do not change for NA<br />
<br />
=== NOTES to 1x1 nested-grid simulation for GEOS-3 ===<br />
<br />
==== General ====<br />
<br />
# If not NESTED_CH (East Asia window) or NESTED_NA (north America window), need to first obtain <br />
#* The 1x1 meteorological field for the nested domain; <br />
#* Tll the input files (mostly emissions) at 1x1 resolution for the nested domain. <br />
# There needs to be two run directories: one for the 4x5 global run and one for the 1x1 nested run<br />
# Only one code directory is necessary. Code version v7-01-02 and higher can be compiled for both the global run and the nested run<br />
# Run the 4x5 global simulation first. With correct switches in the 4x5 input.geos file, boundary conditions will <br />
#* be saved out automatically into the designated directory and will be read later by the nested run. <br />
#* The code automatically takes care of formatting. <br />
<br />
==== Code ====<br />
# Change grid size in define.h <br />
# Change scaling factor in lightning_nox_mod.f (if not Chinese window)<br />
#* search for 1x1 in the file to locate the lines of code where changes should be made<br />
# Change IGLOB, JGLOB in CMN_SIZE (if not Chinese window)<br />
#* IGLOB and JGLOB refers to the size of the nested window measured at 1x1 resolution<br />
# Change PARAMETER( NLAND=2681, NPULSE=3 ) in commsoil.h (if not Chinese window)<br />
#* changes are already made in the code; just uncomment the NA part<br />
# Change datadir for O3 column in toms_mod.f --- if not CHINA or NA windows<br />
#* need to create TOMS_O3col_2001.geos file at 1x1 resolution for the nested region <br />
#* use the IDL code: regrid_4to1_O3_column.pro (note that line 33 and 34 needs to be modified for NA)</div>Jeffrey Piercehttps://wiki.seas.harvard.edu/geos-chem/index.php?title=GEOS-Chem_nested_grid_simulations&diff=5031GEOS-Chem nested grid simulations2010-08-09T18:40:13Z<p>Jeffrey Pierce: /* Transport fix */</p>
<hr />
<div>This page contains some basic information pertaining to the GEOS-Chem nested grid simulations. For more detailed information about met data availability for the various geographic regions, please see our [[Available met data for nested grid simulations]] wiki page. We also invite you to visit the [[Regional Air Quality Working Group|wiki page of the Regional Air Quality Working Group]], which is responsible for coordinating nested-grid simulations within the GEOS-Chem user community.<br />
<br />
Please also see our [http://acmg.seas.harvard.edu/geos/wiki_docs/nested_grids/geos_data_downloads.pdf protocol for downloading and processing nested grid met data], which outlines the responsibilities for user groups using GEOS-Chem nested grid simulations.<br />
<br />
== Nested Grid Frequently Asked Questions ==<br />
<br />
=== Can I perform a nested-grid simulation with GEOS-3 meteorology? ===<br />
<br />
Yes. You may perform a [http://acmg.seas.harvard.edu/geos/doc/man/appendix_4.html#A4.2 GEOS-3] nested-grid simulation for one of the following regions:<br />
<br />
* [http://acmg.seas.harvard.edu/geos/doc/man_test/appendix_2.html#A2.5.1 GEOS-3 1x1, China nested grid]<br />
* [http://acmg.seas.harvard.edu/geos/doc/man_test/appendix_2.html#A2.5.2 GEOS-3 1x1, North America nested grid]<br />
<br />
You should be aware that GEOS-3 is now considered to be obsolete. Also, there is only a limited amount of GEOS-3 met data (2000-2001) available for the nested grid simulations. <br />
<br />
=== Can I run a nested grid simulation with GEOS-5 meteorology? ===<br />
<br />
Yes! With [[GEOS-Chem v8-01-02]] and higher versions you may perform a nested grid simulation for the [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#A2.6.1 China/SE Asia region] at the native GEOS-5 resolution of 0.5&deg; x 0.666&deg;. Also, [[GEOS-Chem v8-03-01]] will contain several code updates for the [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#A2.6.2 North American] and European nested-grid regions.<br />
<br />
=== Boundary conditions ===<br />
<br />
'''''[mailto:dbm@umn.edu Dylan Millet] wrote:'''''<br />
<br />
:Do you know if the 0.5&deg; x 0.667&deg; nested simulation that's being developed uses a 4&deg; x 5&deg; or a 2&deg; x 2.5&deg; grid outside of the nested domain?"<br />
<br />
'''''[mailto:yxw@tsinghua.edu.cn Yuxuan Wang] replied:'''''<br />
:The nested simulation uses 4&deg; x 5&deg; simulation results only at the lateral boundaries of the nested domain. For example, the East Asia nested domain covers 10S to 55N and 70E to 150E, one needs to save 4x5 simulation results (tracer concentrations only) for each vertical layer, at a frequency of every 3 hours, at the following four boundaries:<br />
<br />
:lat = 10S, lon = 70E<br />
:lat = 10S, lon = 150E<br />
:lat = 55N, lon = 70E<br />
:lat = 55N, lon = 150E<br />
<br />
:One can easily change the code to have the nested-grid simulation use 2x2.5 simulation as boundary conditions, but the default has been to take 4x5 results since it's much faster to run a 4x5 simulation.<br />
<br />
'''''[mailto:srhb2@cam.ac.uk Steven Barrett] replied:'''''<br />
<br />
:Could you let me know the standard LL box and UR box of the 4x5 region used as boundary conditions for NA nested 1x1 GEOS-Chem simulations? I think it'll be LL = (9,26) and UR=(29,38), but the upper latitude extent of the NA region falls right on a grid cell boundary, so it's not clear to me which one would be the right one.<br />
<br />
'''''Philippe Le Sager replied:'''''<br />
<br />
:Those indices are correct. They are default Fortran (starting at one for 1st cell), and correspond to cell within the domain.<br />
<br />
--[[User:Bmy|Bob Y.]] 13:51, 3 March 2010 (EST)<br />
<br />
== Setting up a 0.5x0.667 nested-grid simulation for GEOS-5 ==<br />
<br />
=== Transport fix ===<br />
[mailto:linzhang@fas.harvard.edu Lin Zhang] reported a problem with the transport for nested simulations with GEOS-5 met fields.<br />
The problem was traced back to the fact that neither the latest pressure fixer nor the new advection have been set up to be used with nested grids. The problems in both were:<br />
<br />
* the use of polar caps for the first and last latitude bands of the nested domain, although there is no pole in the domain.<br />
* the use of periodicity both in longitude and latitude.<br />
<br />
To solve the problems we modified both modules so that variables are updated only for an inner window of the domain, so that we do not need periodicity. The buffer zone for the pressure fixer is equal to 3 grid cells in all directions (defined in INIT_PJC_PFIX in GeosCore/pjc_pfix_geos5_window_mod.f). The buffer zone for the transport is the zone where the Boundary Conditions are fixed (as defined at the end of the NESTED MENU in input.geos). Note that the buffer zone for the advection must be larger than the buffer zone for the pressure-fixer.<br />
<br />
The fix will be available in [[GEOS-Chem v8-03-02]].<br />
<br />
--[[User:Ccarouge|Ccarouge]] 16:35, 4 August 2010 (EDT)<br />
<br />
I applied this fix, and the RAM requirements were increased. This is problematic since I was operating near the maximum RAM of the node for nested sims before the fix. Is there a way to fix the transport issue without increasing the RAM?<br />
<br />
--[[User:Jeff Pierce]] 02:38, 9 August 2010 (EDT)<br />
<br />
=== 0.5x0.66 China nested grid simulation ===<br />
<br />
* [[Regional Air Quality Working Group#How to run the 0.5x0.667 nested-grid for GEOS-5|How to Run GEOS-5 0.5x0.667 China nested grid]]<br />
<br />
=== 0.5x0.66 NA nested grid simulation ===<br />
<br />
* [[Regional Air Quality Working Group#How to run the 0.5x0.667 nested-grid for GEOS-5|How to Run GEOS-5 0.5x0.667 NA nested grid]]<br />
<br />
== Setting up a 1x1 China nested-grid simulation for GEOS-3 ==<br />
<br />
'''''NOTE: With the advent of the GEOS-5 meteorology, the GEOS-3 1x1 nested-grid simulation described below is now obsolete. We strongly recommend to use the GEOS-5 meteorology for your nested grid simulation.'''''<br />
<br />
--[[User:Bmy|Bob Y.]] 14:00, 3 March 2010 (EST)<br />
<br />
Here is a check list and input.geos file that you need to run the nested-grid China simulation (supplied by Yuxuan Wang):<br />
<br />
=== define.h ===<br />
<br />
These are the settings you need to make in the GEOS-Chem <tt>define.h</tt> file:<br />
<br />
#define GEOS_3 'GEOS_3'<br />
#define GRID1x1 'GRID1x1'<br />
#define NESTED_CH 'NESTED_CH'<br />
#define GRID30LEV 'GRID30LEV'<br />
<br />
=== input.geos ===<br />
<br />
These are the settings you need to make in the GEOS-Chem <tt>input.geos</tt> file:<br />
<br />
==== Saving out 4 x 5 boundary conditions ====<br />
<br />
You will have to run the global model at 4 x 5 resolution to save out the transport boundary conditions. Here are the relevant settings in input.geos:<br />
<br />
%%% SIMULATION MENU %%% :<br />
Start YYYYMMDD, HHMMSS : 20010101 000000<br />
End YYYYMMDD, HHMMSS : 20020101 000000<br />
Run directory : ./<br />
Input restart file : restart.YYYYMMDDhh<br />
Make new restart file? : F<br />
Output restart file(s) : restart.YYYYMMDDhh<br />
Root data directory : /data/ctm/GEOS_4x5/<br />
=> GCAP subdir : AGRID/YYYY/MM/<br />
=> GEOS-3 subdir : GEOS_3/YYYY/MM/<br />
=> GEOS-4 subdir : GEOS_4_v4/YYYY/MM/<br />
=> GEOS-5 subdir : GEOS_5/YYYY/MM/<br />
Dir w/ 1x1 emissions etc: /data/ctm/GEOS_1x1/<br />
Temporary directory : TEMP/<br />
Unzip met fields? : T<br />
Wait for met fields? : T<br />
Use variable tropopause : N<br />
Global offsets I0, J0 : 0 0<br />
<br />
... <br />
<br />
%%% TRANSPORT MENU %%% :<br />
Turn on Transport : T<br />
=> Use Flux Correction?: F<br />
=> Fill Negative Values: T <br />
=> IORD, JORD, KORD : 3 3 7<br />
Transport Timestep [min]: 30 <br />
Use strat O3/NOy BC's : T<br />
<br />
...<br />
<br />
%%% CONVECTION MENU %%% :<br />
Turn on Cloud Conv? : T<br />
Turn on PBL Mixing? : T<br />
Convect Timestep (min) : 30<br />
<br />
...<br />
<br />
%%% NESTED GRID MENU %%%: <br />
Save TPCORE 4x5 BC's : T<br />
TPCORE 4x5 BC directory : /as/home/ctm/yxw/bc/bc_ozone_std/<br />
4x5 BC timestep [min] : 180<br />
LL box of 4x5 BC region : 51 21<br />
UR box of 4x5 BC region : 67 37<br />
1x1 offsets I0_W, J0_W : 3 3<br />
<br />
==== 1x1 nested grid simulation ====<br />
<br />
Then once you have saved out the 4 x 5 boundary conditions you can do the 1 x 1 nested grid simulation. Here are the appropriate settings in input.geos:<br />
<br />
%%% SIMULATION MENU %%% :<br />
Start YYYYMMDD, HHMMSS : 20010301 000000<br />
End YYYYMMDD, HHMMSS : 20010302 000000<br />
Run directory : ./<br />
Input restart file : restart.YYYYMMDDhh<br />
Make new restart file? : F<br />
Output restart file(s) : restart.YYYYMMDDhh<br />
Root data directory : /data/geos/GEOS_1x1_CH/<br />
=> GCAP subdir : AGRID/YYYY/MM/<br />
=> GEOS-3 subdir : GEOS_3/YYYY/MM/<br />
=> GEOS-4 subdir : GEOS_4_v4/YYYY/MM/<br />
=> GEOS-5 subdir : GEOS_5/YYYY/MM/<br />
Dir w/ 1x1 emissions etc: /data/ctm/GEOS_1x1/<br />
Temporary directory : TEMP/<br />
Unzip met fields? : T<br />
Wait for met fields? : T<br />
Use variable tropopause : F<br />
Global offsets I0, J0 : 250 79 # need to be changed for NA; index refer to 1x1 resolution<br />
<br />
...<br />
<br />
%%% TRANSPORT MENU %%% :<br />
Turn on Transport : T<br />
=> Use Flux Correction?: F<br />
=> Fill Negative Values: T <br />
=> IORD, JORD, KORD : 3 3 7<br />
Transport Timestep [min]: 10 <br />
Use strat O3/NOy BC's : T<br />
<br />
...<br />
<br />
%%% CONVECTION MENU %%% :<br />
Turn on Cloud Conv? : T<br />
Turn on PBL Mixing? : T<br />
Convect Timestep (min) : 10<br />
<br />
... <br />
<br />
%%% NESTED GRID MENU %%% <br />
Save TPCORE 4x5 BC's : T<br />
TPCORE 4x5 BC directory : /as/home/strat/yxw/bc/ # change to be your own directory<br />
4x5 BC timestep [min] : 180<br />
LL box of 4x5 BC region : 51 21 # need to be changed for NA; index refer to 4x5 resolution<br />
UR box of 4x5 BC region : 67 37 # need to be changed for NA; index refer to 4x5 resolution<br />
1x1 offsets I0_W, J0_W : 3 3 # do not change for NA<br />
<br />
=== NOTES to 1x1 nested-grid simulation for GEOS-3 ===<br />
<br />
==== General ====<br />
<br />
# If not NESTED_CH (East Asia window) or NESTED_NA (north America window), need to first obtain <br />
#* The 1x1 meteorological field for the nested domain; <br />
#* Tll the input files (mostly emissions) at 1x1 resolution for the nested domain. <br />
# There needs to be two run directories: one for the 4x5 global run and one for the 1x1 nested run<br />
# Only one code directory is necessary. Code version v7-01-02 and higher can be compiled for both the global run and the nested run<br />
# Run the 4x5 global simulation first. With correct switches in the 4x5 input.geos file, boundary conditions will <br />
#* be saved out automatically into the designated directory and will be read later by the nested run. <br />
#* The code automatically takes care of formatting. <br />
<br />
==== Code ====<br />
# Change grid size in define.h <br />
# Change scaling factor in lightning_nox_mod.f (if not Chinese window)<br />
#* search for 1x1 in the file to locate the lines of code where changes should be made<br />
# Change IGLOB, JGLOB in CMN_SIZE (if not Chinese window)<br />
#* IGLOB and JGLOB refers to the size of the nested window measured at 1x1 resolution<br />
# Change PARAMETER( NLAND=2681, NPULSE=3 ) in commsoil.h (if not Chinese window)<br />
#* changes are already made in the code; just uncomment the NA part<br />
# Change datadir for O3 column in toms_mod.f --- if not CHINA or NA windows<br />
#* need to create TOMS_O3col_2001.geos file at 1x1 resolution for the nested region <br />
#* use the IDL code: regrid_4to1_O3_column.pro (note that line 33 and 34 needs to be modified for NA)</div>Jeffrey Pierce