{"action":"closed","issue":{"url":"https://api.github.com/repos/DrylandEcology/STEPWAT2/issues/111","repository_url":"https://api.github.com/repos/DrylandEcology/STEPWAT2","labels_url":"https://api.github.com/repos/DrylandEcology/STEPWAT2/issues/111/labels{/name}","comments_url":"https://api.github.com/repos/DrylandEcology/STEPWAT2/issues/111/comments","events_url":"https://api.github.com/repos/DrylandEcology/STEPWAT2/issues/111/events","html_url":"https://github.com/DrylandEcology/STEPWAT2/issues/111","id":325804354,"node_id":"MDU6SXNzdWUzMjU4MDQzNTQ=","number":111,"title":"Warning in logfile: NOTE: species relsize forced in Plot_Initialize","user":{"login":"kpalmqui","id":7769797,"node_id":"MDQ6VXNlcjc3Njk3OTc=","avatar_url":"https://avatars2.githubusercontent.com/u/7769797?v=4","gravatar_id":"","url":"https://api.github.com/users/kpalmqui","html_url":"https://github.com/kpalmqui","followers_url":"https://api.github.com/users/kpalmqui/followers","following_url":"https://api.github.com/users/kpalmqui/following{/other_user}","gists_url":"https://api.github.com/users/kpalmqui/gists{/gist_id}","starred_url":"https://api.github.com/users/kpalmqui/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kpalmqui/subscriptions","organizations_url":"https://api.github.com/users/kpalmqui/orgs","repos_url":"https://api.github.com/users/kpalmqui/repos","events_url":"https://api.github.com/users/kpalmqui/events{/privacy}","received_events_url":"https://api.github.com/users/kpalmqui/received_events","type":"User","site_admin":false},"labels":[{"id":82656362,"node_id":"MDU6TGFiZWw4MjY1NjM2Mg==","url":"https://api.github.com/repos/DrylandEcology/STEPWAT2/labels/bug","name":"bug","color":"fc2929","default":true}],"state":"closed","locked":false,"assignee":{"login":"chaukap","id":31867049,"node_id":"MDQ6VXNlcjMxODY3MDQ5","avatar_url":"https://avatars0.githubusercontent.com/u/31867049?v=4","gravatar_id":"","url":"https://api.github.com/users/chaukap","html_url":"https://github.com/chaukap","followers_url":"https://api.github.com/users/chaukap/followers","following_url":"https://api.github.com/users/chaukap/following{/other_user}","gists_url":"https://api.github.com/users/chaukap/gists{/gist_id}","starred_url":"https://api.github.com/users/chaukap/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chaukap/subscriptions","organizations_url":"https://api.github.com/users/chaukap/orgs","repos_url":"https://api.github.com/users/chaukap/repos","events_url":"https://api.github.com/users/chaukap/events{/privacy}","received_events_url":"https://api.github.com/users/chaukap/received_events","type":"User","site_admin":false},"assignees":[{"login":"chaukap","id":31867049,"node_id":"MDQ6VXNlcjMxODY3MDQ5","avatar_url":"https://avatars0.githubusercontent.com/u/31867049?v=4","gravatar_id":"","url":"https://api.github.com/users/chaukap","html_url":"https://github.com/chaukap","followers_url":"https://api.github.com/users/chaukap/followers","following_url":"https://api.github.com/users/chaukap/following{/other_user}","gists_url":"https://api.github.com/users/chaukap/gists{/gist_id}","starred_url":"https://api.github.com/users/chaukap/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chaukap/subscriptions","organizations_url":"https://api.github.com/users/chaukap/orgs","repos_url":"https://api.github.com/users/chaukap/repos","events_url":"https://api.github.com/users/chaukap/events{/privacy}","received_events_url":"https://api.github.com/users/chaukap/received_events","type":"User","site_admin":false}],"milestone":{"url":"https://api.github.com/repos/DrylandEcology/STEPWAT2/milestones/2","html_url":"https://github.com/DrylandEcology/STEPWAT2/milestone/2","labels_url":"https://api.github.com/repos/DrylandEcology/STEPWAT2/milestones/2/labels","id":2661580,"node_id":"MDk6TWlsZXN0b25lMjY2MTU4MA==","number":2,"title":"resource_partitioning_overhaul","description":"Changing how resources are determined each year and then partitioned to functional groups and then individuals. \r\n\r\nWe need to overhaul how resource availability is calculated each year. Currently, it is based on monthly transpiration in each soil layer. This is problematic because of a positive feedback loop between biomass and transpiration that occurs. Biomass influences transpiration and in turn transpiration (resources) influences biomass through plant growth and mortality. Thus, if biomass is low, transpiration will be low, resources will be low, and biomass will not increase. This positive feedback loop means it can take a good deal of time for functional groups to respond to higher resource availability. This is very apparent when sagebrush biomass goes to 0 - because resource availability is based on biomass of established plant functional groups - there is not an increase in resources after sagebrush dies (while conceptually there should be). Therefore, we do not see a response from the annual and perennial grasses to increased resource availability when sagebrush dies.","creator":{"login":"kpalmqui","id":7769797,"node_id":"MDQ6VXNlcjc3Njk3OTc=","avatar_url":"https://avatars2.githubusercontent.com/u/7769797?v=4","gravatar_id":"","url":"https://api.github.com/users/kpalmqui","html_url":"https://github.com/kpalmqui","followers_url":"https://api.github.com/users/kpalmqui/followers","following_url":"https://api.github.com/users/kpalmqui/following{/other_user}","gists_url":"https://api.github.com/users/kpalmqui/gists{/gist_id}","starred_url":"https://api.github.com/users/kpalmqui/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kpalmqui/subscriptions","organizations_url":"https://api.github.com/users/kpalmqui/orgs","repos_url":"https://api.github.com/users/kpalmqui/repos","events_url":"https://api.github.com/users/kpalmqui/events{/privacy}","received_events_url":"https://api.github.com/users/kpalmqui/received_events","type":"User","site_admin":false},"open_issues":4,"closed_issues":45,"state":"open","created_at":"2017-07-25T19:50:15Z","updated_at":"2018-09-03T19:01:23Z","due_on":"2018-04-15T07:00:00Z","closed_at":null},"comments":10,"created_at":"2018-05-23T17:32:15Z","updated_at":"2018-09-03T19:01:23Z","closed_at":"2018-09-03T19:01:23Z","author_association":"MEMBER","body":"With _extra_growth and _kill_extra_growth now functional, there is a new warning in the logfile.\r\nExample:\r\nNOTE: phho relsize (0.803718) forced in Plot_Initialize\r\nNOTE: arfr relsize (0.362966) forced in Plot_Initialize\r\nNOTE: pssp relsize (1.817489) forced in Plot_Initialize\r\nNOTE: spcr relsize (2.308077) forced in Plot_Initialize\r\nNOTE: chvi relsize (4.142667) forced in Plot_Initialize\r\n\r\nThis warning is throw at the beginning of each iteration in Year 1 when Species relsizes are cleared and set to 0. See Line 297 in ST_main.c. Need to figure out what is going wrong here. Note, this problem disappears if _extra_growth is turned off and does not occur in the first iteration.\r\n\r\nUPDATE: I think something is going wrong with removal (i.e killing) of Species[sp]->relsize and Rgroup[rg]->relsize. In some cases, Species[sp]->relsize is positive, but there are no established individuals of that species (see attached spreadsheet and yellow cells for a few examples of those cases).\r\n\r\n[bmassavg_biomass0_relsize_non-zero.xlsx](https://github.com/DrylandEcology/STEPWAT2/files/2037395/bmassavg_biomass0_relsize_non-zero.xlsx)\r\n\r\n I believe the problem exists in Species_Update_Newsize. An issue in this code would explain why the above warning is throw as well, because it calls Species_Update_Newsize (ST_species.c).\r\n\r\nSee the long note at the top of Species_Update_Newsize (written quite some time ago) that describes why values that should be 0.0 are sometime non-zero in this function. \r\n"}}
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