{"action":"created","issue":{"url":"https://api.github.com/repos/rcooke-ast/ALIS/issues/14","repository_url":"https://api.github.com/repos/rcooke-ast/ALIS","labels_url":"https://api.github.com/repos/rcooke-ast/ALIS/issues/14/labels{/name}","comments_url":"https://api.github.com/repos/rcooke-ast/ALIS/issues/14/comments","events_url":"https://api.github.com/repos/rcooke-ast/ALIS/issues/14/events","html_url":"https://github.com/rcooke-ast/ALIS/issues/14","id":305809661,"number":14,"title":"Cannot give coverfactor","user":{"login":"lwymarie","id":20585911,"avatar_url":"https://avatars1.githubusercontent.com/u/20585911?v=4","gravatar_id":"","url":"https://api.github.com/users/lwymarie","html_url":"https://github.com/lwymarie","followers_url":"https://api.github.com/users/lwymarie/followers","following_url":"https://api.github.com/users/lwymarie/following{/other_user}","gists_url":"https://api.github.com/users/lwymarie/gists{/gist_id}","starred_url":"https://api.github.com/users/lwymarie/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lwymarie/subscriptions","organizations_url":"https://api.github.com/users/lwymarie/orgs","repos_url":"https://api.github.com/users/lwymarie/repos","events_url":"https://api.github.com/users/lwymarie/events{/privacy}","received_events_url":"https://api.github.com/users/lwymarie/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":7,"created_at":"2018-03-16T05:48:41Z","updated_at":"2018-03-21T11:40:02Z","closed_at":null,"author_association":"NONE","body":"Error messages are output when I give cover factors to my model. The error messages read\r\n\"14N_IV 765.1467 has no q-value. \"\r\neight times, as I have eight components. Then the program hangs. \r\n\r\nMy initial model is as follows. \r\n\r\n absorption\r\n  voigt   ion=14N_IV   14.1000000      1.1290800000RA      30.000000ba      0.0000000E4TA      0.0000000      0.0000000      1.0000        specid=0    \r\n  voigt   ion=14N_IV   14.0000000      1.1295200000RB      27.000000bb      0.0000000E4TA      0.0000000      0.0000000      1.0000        specid=0    \r\n  voigt   ion=14N_IV   13.4000000      1.1301700000RC      27.000000bc      0.0000000E4TA      0.0000000      0.0000000      1.0000        specid=0    \r\n  voigt   ion=14N_IV   14.1000000      1.1304500000RD      20.000000bd      0.0000000E4TA      0.0000000      0.0000000      1.0000        specid=0    \r\n  voigt   ion=14N_IV   13.6000000      1.1308900000RE      15.000000be      0.0000000E4TA      0.0000000      0.0000000      1.0000        specid=0    \r\n  voigt   ion=14N_IV   13.5000000      1.1312700000RF      18.000000bf      0.0000000E4TA      0.0000000      0.0000000      1.0000        specid=0    \r\n  voigt   ion=14N_IV   13.5000000      1.1314900000RG      25.000000bg      0.0000000E4TA      0.0000000      0.0000000      1.0000        specid=0    \r\n  voigt   ion=14N_IV   13.1000000      1.1329900000RH      10.000000bh      0.0000000E4TA      0.0000000      0.0000000      1.0000        specid=0    \r\n Convolution\r\n  lsf       life_position=1  name=COS  grating=G160M  cen_wave=1623\r\n\r\nA side note is that this NIV765 transition is manually added by me to an atomic_marie.xml file. However, I can do Voigt profile fitting as normal and convolve with COS's line spread function on this coverfactor branch. Did I not write my model in a correct format? \r\n\r\nThanks. "},"comment":{"url":"https://api.github.com/repos/rcooke-ast/ALIS/issues/comments/374909417","html_url":"https://github.com/rcooke-ast/ALIS/issues/14#issuecomment-374909417","issue_url":"https://api.github.com/repos/rcooke-ast/ALIS/issues/14","id":374909417,"user":{"login":"rcooke-ast","id":12585758,"avatar_url":"https://avatars2.githubusercontent.com/u/12585758?v=4","gravatar_id":"","url":"https://api.github.com/users/rcooke-ast","html_url":"https://github.com/rcooke-ast","followers_url":"https://api.github.com/users/rcooke-ast/followers","following_url":"https://api.github.com/users/rcooke-ast/following{/other_user}","gists_url":"https://api.github.com/users/rcooke-ast/gists{/gist_id}","starred_url":"https://api.github.com/users/rcooke-ast/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rcooke-ast/subscriptions","organizations_url":"https://api.github.com/users/rcooke-ast/orgs","repos_url":"https://api.github.com/users/rcooke-ast/repos","events_url":"https://api.github.com/users/rcooke-ast/events{/privacy}","received_events_url":"https://api.github.com/users/rcooke-ast/received_events","type":"User","site_admin":false},"created_at":"2018-03-21T11:40:02Z","updated_at":"2018-03-21T11:40:02Z","author_association":"OWNER","body":"Thanks for the update.\r\n\r\nYou're reading the code correctly. It is indeed:\r\n\r\n`continuum * (e^-tau + zerolevel*(1-e^-tau)/continuum)`\r\n\r\nTo see why I used this formulation, consider that `e^-tau` can take extreme values of 0 (the zerolevel) and 1 (the continuum). In the case `e^-tau=0`, we have `model=zerolevel`. When `e^-tau=1`, we have `model=continuum`.\r\n\r\nThe only problem with this formulation is when the continuum is not normalized, and you want to calculate the zerolevel as a _fraction_ of the continuum. I think the current version of the code trys to account for this, but I'll have to go back and decide if this is doing as I would expect. It should be no concern for you though, as your continuum is normalized."}}
{"actor":{"display_login":"rcooke-ast"}}