{"action":"created","issue":{"url":"https://api.github.com/repos/dthierry/kipet/issues/26","repository_url":"https://api.github.com/repos/dthierry/kipet","labels_url":"https://api.github.com/repos/dthierry/kipet/issues/26/labels{/name}","comments_url":"https://api.github.com/repos/dthierry/kipet/issues/26/comments","events_url":"https://api.github.com/repos/dthierry/kipet/issues/26/events","html_url":"https://github.com/dthierry/kipet/issues/26","id":318689560,"number":26,"title":"non absorbing species","user":{"login":"dthierry","id":16341267,"avatar_url":"https://avatars1.githubusercontent.com/u/16341267?v=4","gravatar_id":"","url":"https://api.github.com/users/dthierry","html_url":"https://github.com/dthierry","followers_url":"https://api.github.com/users/dthierry/followers","following_url":"https://api.github.com/users/dthierry/following{/other_user}","gists_url":"https://api.github.com/users/dthierry/gists{/gist_id}","starred_url":"https://api.github.com/users/dthierry/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dthierry/subscriptions","organizations_url":"https://api.github.com/users/dthierry/orgs","repos_url":"https://api.github.com/users/dthierry/repos","events_url":"https://api.github.com/users/dthierry/events{/privacy}","received_events_url":"https://api.github.com/users/dthierry/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":17,"created_at":"2018-04-29T04:44:05Z","updated_at":"2018-05-07T15:57:49Z","closed_at":null,"author_association":"OWNER","body":"A potential solution has been implemented in the branch `non_absorbing` the [file](https://github.com/dthierry/kipet/blob/non_absorbing/kipet/examples/Paper/replicate_example51a_non_absorbing.py) contains an example case study (lines 60 and 61). \r\n\r\nThe workflow is as follows:\r\ncreate *list* of strings of non-absorbing species. Pass it to the method `set_non_absorbing_species` referencing the model and the list. \r\nThe side effects of this method call are:\r\n- The creation of a new non_absorbing set.\r\n- Fixing the corresponding columns of the S matrix to 0.\r\n- Creating a constraint `C[time, fixed component] == Z[time, fixed component]`\r\n\r\nThe issues with `VarianceEstimation` were resolved for the most part although I can't verify that this strategy works out as expected.\r\nNo issues were found with `ParameterEstimation`.\r\n\r\nThe example will fail because the assertion would not be satisfied but other than that the model is constructed as expected.\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/dthierry/kipet/issues/comments/387112457","html_url":"https://github.com/dthierry/kipet/issues/26#issuecomment-387112457","issue_url":"https://api.github.com/repos/dthierry/kipet/issues/26","id":387112457,"user":{"login":"mchlshort","id":36671927,"avatar_url":"https://avatars3.githubusercontent.com/u/36671927?v=4","gravatar_id":"","url":"https://api.github.com/users/mchlshort","html_url":"https://github.com/mchlshort","followers_url":"https://api.github.com/users/mchlshort/followers","following_url":"https://api.github.com/users/mchlshort/following{/other_user}","gists_url":"https://api.github.com/users/mchlshort/gists{/gist_id}","starred_url":"https://api.github.com/users/mchlshort/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mchlshort/subscriptions","organizations_url":"https://api.github.com/users/mchlshort/orgs","repos_url":"https://api.github.com/users/mchlshort/repos","events_url":"https://api.github.com/users/mchlshort/events{/privacy}","received_events_url":"https://api.github.com/users/mchlshort/received_events","type":"User","site_admin":false},"created_at":"2018-05-07T15:57:49Z","updated_at":"2018-05-07T15:57:49Z","author_association":"COLLABORATOR","body":"I know I am a bit late on this one, but are you guys getting any errors running problems with the with_d_vars option on? I get the following:\r\n\r\nERROR: Rule failed when generating expression for constraint D_bar_constraint\r\n    with index (0.9, 1.0): AttributeError: 'ConcreteModel' object has no\r\n    attribute '_sublist_components'\r\nERROR: Constructing component 'D_bar_constraint' from data=None failed:\r\n    AttributeError: 'ConcreteModel' object has no attribute\r\n    '_sublist_components'\r\nTraceback (most recent call last):\r\n\r\n  File \"<ipython-input-2-d036e95f6da1>\", line 1, in <module>\r\n    runfile('/home/shortm/anaconda2/lib/python2.7/site-packages/kipet-0.0.0-py2.7.egg/kipet/examples/Paper/replicate_example52a.py', wdir='/home/shortm/anaconda2/lib/python2.7/site-packages/kipet-0.0.0-py2.7.egg/kipet/examples/Paper')\r\n\r\n  File \"/home/shortm/anaconda2/lib/python2.7/site-packages/spyder/utils/site/sitecustomize.py\", line 705, in runfile\r\n    execfile(filename, namespace)\r\n\r\n  File \"/home/shortm/anaconda2/lib/python2.7/site-packages/spyder/utils/site/sitecustomize.py\", line 94, in execfile\r\n    builtins.execfile(filename, *where)\r\n\r\n  File \"/home/shortm/anaconda2/lib/python2.7/site-packages/kipet-0.0.0-py2.7.egg/kipet/examples/Paper/replicate_example52a.py\", line 119, in <module>\r\n    with_d_vars=True)\r\n\r\n  File \"/home/shortm/anaconda2/lib/python2.7/site-packages/kipet-0.0.0-py2.7.egg/kipet/opt/ParameterEstimator.py\", line 411, in run_opt\r\n    **kwds)\r\n\r\n  File \"/home/shortm/anaconda2/lib/python2.7/site-packages/kipet-0.0.0-py2.7.egg/kipet/opt/ParameterEstimator.py\", line 106, in _solve_extended_model\r\n    rule=rule_D_bar)\r\n\r\n  File \"/home/shortm/anaconda2/lib/python2.7/site-packages/Pyomo-5.4.3-py2.7.egg/pyomo/core/base/block.py\", line 540, in __setattr__\r\n    self.add_component(name, val)\r\n\r\n  File \"/home/shortm/anaconda2/lib/python2.7/site-packages/Pyomo-5.4.3-py2.7.egg/pyomo/core/base/block.py\", line 980, in add_component\r\n    val.construct(data)\r\n\r\n  File \"/home/shortm/anaconda2/lib/python2.7/site-packages/Pyomo-5.4.3-py2.7.egg/pyomo/core/base/constraint.py\", line 793, in construct\r\n    ndx)\r\n\r\n  File \"/home/shortm/anaconda2/lib/python2.7/site-packages/Pyomo-5.4.3-py2.7.egg/pyomo/core/base/misc.py\", line 57, in apply_indexed_rule\r\n    return rule(model, *index)\r\n\r\n  File \"/home/shortm/anaconda2/lib/python2.7/site-packages/kipet-0.0.0-py2.7.egg/kipet/opt/ParameterEstimator.py\", line 102, in rule_D_bar\r\n    return m.D_bar[t, l] == sum(m.C[t, k] * m.S[l, k] for k in m._sublist_components)\r\n\r\n  File \"/home/shortm/anaconda2/lib/python2.7/site-packages/Pyomo-5.4.3-py2.7.egg/pyomo/core/base/block.py\", line 521, in __getattr__\r\n    % (self.__class__.__name__, val))\r\n\r\nAttributeError: 'ConcreteModel' object has no attribute '_sublist_components'\r\n\r\nAlso, @dthierry , is it possible for you to please turn off the generation of whatevs.nl, whatevs.row, whatevs.col, _reconcilied.col, _reconcilied.row, and iterations.log when you next merge. Otherwise, I think we can close this issue when these have been implemented and tested."}}
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