{"action":"created","issue":{"url":"https://api.github.com/repos/StrikeNP/trac_test/issues/770","repository_url":"https://api.github.com/repos/StrikeNP/trac_test","labels_url":"https://api.github.com/repos/StrikeNP/trac_test/issues/770/labels{/name}","comments_url":"https://api.github.com/repos/StrikeNP/trac_test/issues/770/comments","events_url":"https://api.github.com/repos/StrikeNP/trac_test/issues/770/events","html_url":"https://github.com/StrikeNP/trac_test/issues/770","id":334664573,"node_id":"MDU6SXNzdWUzMzQ2NjQ1NzM=","number":770,"title":"Implement New PDf Closure Including Third-Order Moments of rt, thl (Trac #770)","user":{"login":"StrikeNP","id":2577059,"node_id":"MDQ6VXNlcjI1NzcwNTk=","avatar_url":"https://avatars0.githubusercontent.com/u/2577059?v=4","gravatar_id":"","url":"https://api.github.com/users/StrikeNP","html_url":"https://github.com/StrikeNP","followers_url":"https://api.github.com/users/StrikeNP/followers","following_url":"https://api.github.com/users/StrikeNP/following{/other_user}","gists_url":"https://api.github.com/users/StrikeNP/gists{/gist_id}","starred_url":"https://api.github.com/users/StrikeNP/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/StrikeNP/subscriptions","organizations_url":"https://api.github.com/users/StrikeNP/orgs","repos_url":"https://api.github.com/users/StrikeNP/repos","events_url":"https://api.github.com/users/StrikeNP/events{/privacy}","received_events_url":"https://api.github.com/users/StrikeNP/received_events","type":"User","site_admin":false},"labels":[{"id":971577014,"node_id":"MDU6TGFiZWw5NzE1NzcwMTQ=","url":"https://api.github.com/repos/StrikeNP/trac_test/labels/Migrated%20from%20Trac","name":"Migrated from Trac","color":"FFFFFF","default":false},{"id":971577865,"node_id":"MDU6TGFiZWw5NzE1Nzc4NjU=","url":"https://api.github.com/repos/StrikeNP/trac_test/labels/bmg2@uwm.edu","name":"bmg2@uwm.edu","color":"FFFFFF","default":false},{"id":971577274,"node_id":"MDU6TGFiZWw5NzE1NzcyNzQ=","url":"https://api.github.com/repos/StrikeNP/trac_test/labels/clubb_src","name":"clubb_src","color":"FFFFFF","default":false},{"id":971577020,"node_id":"MDU6TGFiZWw5NzE1NzcwMjA=","url":"https://api.github.com/repos/StrikeNP/trac_test/labels/defect","name":"defect","color":"FFFFFF","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":{"url":"https://api.github.com/repos/StrikeNP/trac_test/milestones/26","html_url":"https://github.com/StrikeNP/trac_test/milestone/26","labels_url":"https://api.github.com/repos/StrikeNP/trac_test/milestones/26/labels","id":3443175,"node_id":"MDk6TWlsZXN0b25lMzQ0MzE3NQ==","number":26,"title":"Create and implement a new trivariate analytic double Gaussian PDF in CLUBB","description":null,"creator":{"login":"StrikeNP","id":2577059,"node_id":"MDQ6VXNlcjI1NzcwNTk=","avatar_url":"https://avatars0.githubusercontent.com/u/2577059?v=4","gravatar_id":"","url":"https://api.github.com/users/StrikeNP","html_url":"https://github.com/StrikeNP","followers_url":"https://api.github.com/users/StrikeNP/followers","following_url":"https://api.github.com/users/StrikeNP/following{/other_user}","gists_url":"https://api.github.com/users/StrikeNP/gists{/gist_id}","starred_url":"https://api.github.com/users/StrikeNP/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/StrikeNP/subscriptions","organizations_url":"https://api.github.com/users/StrikeNP/orgs","repos_url":"https://api.github.com/users/StrikeNP/repos","events_url":"https://api.github.com/users/StrikeNP/events{/privacy}","received_events_url":"https://api.github.com/users/StrikeNP/received_events","type":"User","site_admin":false},"open_issues":5,"closed_issues":0,"state":"open","created_at":"2018-06-21T21:28:15Z","updated_at":"2018-06-21T21:32:00Z","due_on":null,"closed_at":null},"comments":115,"created_at":"2018-06-21T21:28:17Z","updated_at":"2018-06-24T10:34:48Z","closed_at":null,"author_association":"OWNER","body":"**Introduction**\nIn ticket:764, we've started implementing the Analytic Double Gaussian 2 PDF closure into CLUBB. In ADG2, the means and variances of each w component is diagnosed from Luhar et al. (1996). The means and variances of the theta-l and rt components are then diagnosed assuming there is no within-component correlation between w and rt and w and thl. \n\nWe think that we could improve the above strategy by diagnosing the means and variances of thl and rt similarly to finding the means and variances of the w components. We would like to use the w closure described in Luhar et al. (1996) but also for rt and thl (in addition to w). We would also need an equation for the skewness of thl and rt. We think in this way, we can more accurately parameterize the skewness of thl and rt which may be important for highly skewed cases.\n\n** Technical Spec **\nWe already have some code that uses ADG2 for the w plumes. Let's first modularize it into its own subroutine. We'll then need to find the skewness of thl, rt (already done for w). From the largest (in magnitude) skewness, we can compute the PDF parameters. \n\n** Tests **\nWe should enclose changes in a flag. Results should not change when the flag is set to `.false.`. However, after implementing, the results will change. In addition, CLUBB may need a retuning for this PDF closure since it would be a significant structural change.  \n\nAttachments:\n\n[plot_explicit_ta_configs.maff](https://github.com/larson-group/trac_attachment_archive/blob/master/trac_test/822/plot_explicit_ta_configs.maff)\n[plot_new_pdf_config_1_plot_2.maff](https://github.com/larson-group/trac_attachment_archive/blob/master/trac_test/822/plot_new_pdf_config_1_plot_2.maff)\n[plot_combo_pdf_run_3.maff](https://github.com/larson-group/trac_attachment_archive/blob/master/trac_test/822/plot_combo_pdf_run_3.maff)\n[plot_input_fields_rtp3_thlp3_1.maff](https://github.com/larson-group/trac_attachment_archive/blob/master/trac_test/822/plot_input_fields_rtp3_thlp3_1.maff)\n[plot_new_pdf_20180522_test_1.maff](https://github.com/larson-group/trac_attachment_archive/blob/master/trac_test/822/plot_new_pdf_20180522_test_1.maff)\n[plot_attempts_8_10.maff](https://github.com/larson-group/trac_attachment_archive/blob/master/trac_test/822/plot_attempts_8_10.maff)\n[plot_attempt_8_only.maff](https://github.com/larson-group/trac_attachment_archive/blob/master/trac_test/822/plot_attempt_8_only.maff)\n[plot_beta_1p3.maff](https://github.com/larson-group/trac_attachment_archive/blob/master/trac_test/822/plot_beta_1p3.maff)\n[plot_beta_1p3_all.maff](https://github.com/larson-group/trac_attachment_archive/blob/master/trac_test/822/plot_beta_1p3_all.maff)\n\nMigrated from http://carson.math.uwm.edu/trac/clubb/ticket/770\n```json\n{\n    \"status\": \"assigned\", \n    \"changetime\": \"2017-08-04T06:35:12\", \n    \"description\": \"'''Introduction'''\\nIn ticket:764, we've started implementing the Analytic Double Gaussian 2 PDF closure into CLUBB. In ADG2, the means and variances of each w component is diagnosed from Luhar et al. (1996). The means and variances of the theta-l and rt components are then diagnosed assuming there is no within-component correlation between w and rt and w and thl. \\n\\nWe think that we could improve the above strategy by diagnosing the means and variances of thl and rt similarly to finding the means and variances of the w components. We would like to use the w closure described in Luhar et al. (1996) but also for rt and thl (in addition to w). We would also need an equation for the skewness of thl and rt. We think in this way, we can more accurately parameterize the skewness of thl and rt which may be important for highly skewed cases.\\n\\n''' Technical Spec '''\\nWe already have some code that uses ADG2 for the w plumes. Let's first modularize it into its own subroutine. We'll then need to find the skewness of thl, rt (already done for w). From the largest (in magnitude) skewness, we can compute the PDF parameters. \\n\\n''' Tests '''\\nWe should enclose changes in a flag. Results should not change when the flag is set to `.false.`. However, after implementing, the results will change. In addition, CLUBB may need a retuning for this PDF closure since it would be a significant structural change.  \", \n    \"reporter\": \"weberjk@uwm.edu\", \n    \"cc\": \"vlarson@uwm.edu\", \n    \"resolution\": \"\", \n    \"_ts\": \"1501828512160353\", \n    \"component\": \"clubb_src\", \n    \"summary\": \"Implement New PDf Closure Including Third-Order Moments of rt, thl\", \n    \"priority\": \"major\", \n    \"keywords\": \"\", \n    \"time\": \"2015-06-01T12:39:45\", \n    \"milestone\": \"Create and implement a new trivariate analytic double Gaussian PDF in CLUBB\", \n    \"owner\": \"bmg2@uwm.edu\", \n    \"type\": \"defect\"\n}\n```\n"},"comment":{"url":"https://api.github.com/repos/StrikeNP/trac_test/issues/comments/399746369","html_url":"https://github.com/StrikeNP/trac_test/issues/770#issuecomment-399746369","issue_url":"https://api.github.com/repos/StrikeNP/trac_test/issues/770","id":399746369,"node_id":"MDEyOklzc3VlQ29tbWVudDM5OTc0NjM2OQ==","user":{"login":"StrikeNP","id":2577059,"node_id":"MDQ6VXNlcjI1NzcwNTk=","avatar_url":"https://avatars0.githubusercontent.com/u/2577059?v=4","gravatar_id":"","url":"https://api.github.com/users/StrikeNP","html_url":"https://github.com/StrikeNP","followers_url":"https://api.github.com/users/StrikeNP/followers","following_url":"https://api.github.com/users/StrikeNP/following{/other_user}","gists_url":"https://api.github.com/users/StrikeNP/gists{/gist_id}","starred_url":"https://api.github.com/users/StrikeNP/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/StrikeNP/subscriptions","organizations_url":"https://api.github.com/users/StrikeNP/orgs","repos_url":"https://api.github.com/users/StrikeNP/repos","events_url":"https://api.github.com/users/StrikeNP/events{/privacy}","received_events_url":"https://api.github.com/users/StrikeNP/received_events","type":"User","site_admin":false},"created_at":"2018-06-24T10:34:48Z","updated_at":"2018-06-24T10:34:48Z","author_association":"OWNER","body":"**Trac update on 2015/06/30 at 22:16**\n\n* bmg2@uwm.edu changed _comment0 from:\n\n> Replying to [comment:47 weberjk@…]:\n> > The saga continues. Theta-l remains a suspect of corruption. First, in the input_fields code, CLUBB reads in SAM's variable `TL2` as thlp2. One finds quickly (via ncdump) that TL2 is the variance of liquid water static energy, which, as the name implies, is not liquid water potential temperature. We were probably (semi-)saved by the fact that TL2 is in units of K^2^ (likely some division by cp, etc. and then written to disk) and that it is reasonable to think that TL2 and thlp2 could be similar. [http://anilol.com/sites/default/files/user_uploaded/nothing%20to%20be%20scared%20of.jpg We didn't notice]. That fix changes CLUBB's Skthl from  -1.8011 to -2.42129. Recall that SAM's value is -2.39469. Adding CLUBB's clipping to Matlab's SAM and CLUBB's calculation of skewness changes the values only slightly.\n> \n> On the same note, CLUBB input fields reads in covariance of l.w.s.e and (rv+rc+ri) for rtpthlp and covariance of w and l.w.s.e. for wpthlp.  CLUBB input fields also reads in the mean of (rv+rc+ri) as rtm.  It is supposed to read in a variable called \"QTFLUX\" as wprtp, but I don't even see \"QTFLUX\" listed in SAM's output anymore!\n> \n> All these variables are important in generating CLUBB's PDF.\n> \n> For me personally, here's the good news.  As part of the microphysics output from {{{MICRO_DRIZZLE}}} (just as a double check), I have included {{{THLM}}}, {{{RTM}}}, {{{WPRTP}}}, {{{WPTHLP}}}, {{{RTP2}}}, {{{THLP2}}}, and {{{RTPTHLP}}} as output.  So, I have everything I need to update input fields in CLUBB simulations run with {{{MICRO_DRIZZLE}}}.  However, that's just DYCOMS-II RF02 and RICO.\n> \n> I noticed that PNNL's {{{THEL2}}} was added recently to output correctly for thlp2.  I also noticed that PNNL stats correctly output {{{QT2}}} for rtp2.  However, I don't see any entries for a correct wpthlp, wprtp, rtpthlp, and even rtm.  So, it looks like these would have to be added to the SAM code and cases that don't use {{{MICRO_DRIZZLE}}} would have to be rerun.\n> \n> \n\nto:\n\n> 1435703396193124\n\n\n* bmg2@uwm.edu changed _comment1 from:\n\n> Replying to [comment:47 weberjk@…]:\n> > The saga continues. Theta-l remains a suspect of corruption. First, in the input_fields code, CLUBB reads in SAM's variable `TL2` as thlp2. One finds quickly (via ncdump) that TL2 is the variance of liquid water static energy, which, as the name implies, is not liquid water potential temperature. We were probably (semi-)saved by the fact that TL2 is in units of K^2^ (likely some division by cp, etc. and then written to disk) and that it is reasonable to think that TL2 and thlp2 could be similar. [http://anilol.com/sites/default/files/user_uploaded/nothing%20to%20be%20scared%20of.jpg We didn't notice]. That fix changes CLUBB's Skthl from  -1.8011 to -2.42129. Recall that SAM's value is -2.39469. Adding CLUBB's clipping to Matlab's SAM and CLUBB's calculation of skewness changes the values only slightly.\n> \n> On the same note, CLUBB input fields reads in covariance of l.w.s.e and (rv+rc+ri) for rtpthlp and covariance of w and l.w.s.e. for wpthlp.  CLUBB input fields also reads in the mean of (rv+rc+ri) as rtm.  It is supposed to read in a variable called \"QTFLUX\" as wprtp, but I don't even see \"QTFLUX\" listed in SAM's output anymore! (edit:  I found \"QTFLUX\", and it is the flux of (rv+rc+ri)).\n> \n> All these variables are important in generating CLUBB's PDF.\n> \n> For me personally, here's the good news.  As part of the microphysics output from {{{MICRO_DRIZZLE}}} (just as a double check), I have included {{{THLM}}}, {{{RTM}}}, {{{WPRTP}}}, {{{WPTHLP}}}, {{{RTP2}}}, {{{THLP2}}}, and {{{RTPTHLP}}} as output.  So, I have everything I need to update input fields in CLUBB simulations run with {{{MICRO_DRIZZLE}}}.  However, that's just DYCOMS-II RF02 and RICO.\n> \n> I noticed that PNNL's {{{THEL2}}} was added recently to output correctly for thlp2.  I also noticed that PNNL stats correctly output {{{QT2}}} for rtp2.  However, I don't see any entries for a correct wpthlp, wprtp, rtpthlp, and even rtm.  So, it looks like these would have to be added to the SAM code and cases that don't use {{{MICRO_DRIZZLE}}} would have to be rerun.\n> \n> \n\nto:\n\n> 1435703487698581\n\n\n* **bmg2@uwm.edu commented:**\n\nReplying to [comment:47 weberjk@…]:\n> The saga continues. Theta-l remains a suspect of corruption. First, in the input_fields code, CLUBB reads in SAM's variable `TL2` as thlp2. One finds quickly (via ncdump) that TL2 is the variance of liquid water static energy, which, as the name implies, is not liquid water potential temperature. We were probably (semi-)saved by the fact that TL2 is in units of K^2^ (likely some division by cp, etc. and then written to disk) and that it is reasonable to think that TL2 and thlp2 could be similar. [http://anilol.com/sites/default/files/user_uploaded/nothing%20to%20be%20scared%20of.jpg We didn't notice]. That fix changes CLUBB's Skthl from  -1.8011 to -2.42129. Recall that SAM's value is -2.39469. Adding CLUBB's clipping to Matlab's SAM and CLUBB's calculation of skewness changes the values only slightly.\n\n\nOn the same note, CLUBB input fields reads in covariance of l.w.s.e and (rv+rc+ri) for rtpthlp and the flux of l.w.s.e. for wpthlp.  CLUBB input fields also reads in the mean of (rv+rc+ri) as rtm.  It is supposed to read in a variable called \"QTFLUX\" as wprtp, but I don't even see \"QTFLUX\" listed in SAM's output anymore! (edit:  I found \"QTFLUX\", and it is the flux of (rv+rc+ri)).\n\nAll these variables are important in generating CLUBB's PDF.\n\nFor me personally, here's the good news.  As part of the microphysics output from ```MICRO_DRIZZLE``` (just as a double check), I have included ```THLM```, ```RTM```, ```WPRTP```, ```WPTHLP```, ```RTP2```, ```THLP2```, and ```RTPTHLP``` as output.  So, I have everything I need to update input fields in CLUBB simulations run with ```MICRO_DRIZZLE```.  However, that's just DYCOMS-II RF02 and RICO.\n\nI noticed that PNNL's ```THEL2``` was added recently to output correctly for thlp2.  I also noticed that PNNL stats correctly output ```QT2``` for rtp2.  However, I don't see any entries for a correct wpthlp, wprtp, rtpthlp, and even rtm.  So, it looks like these would have to be added to the SAM code and cases that don't use ```MICRO_DRIZZLE``` would have to be rerun.\n\n\n\n"}}
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