{"action":"created","comment":{"url":"https://api.github.com/repos/ufz/ogs/pulls/comments/54533440","id":54533440,"diff_hunk":"@@ -0,0 +1,365 @@\n+/**\n+ * \\copyright\n+ * Copyright (c) 2012-2016, OpenGeoSys Community (http://www.opengeosys.org)\n+ *            Distributed under a Modified BSD License.\n+ *              See accompanying file LICENSE.txt or\n+ *              http://www.opengeosys.org/project/license\n+ *\n+ */\n+\n+#ifndef APPLICATIONSLIB_UNCOUPLED_PROCESSES_TIMElOOP\n+#define APPLICATIONSLIB_UNCOUPLED_PROCESSES_TIMElOOP\n+\n+#include <memory>\n+\n+#include <logog/include/logog.hpp>\n+\n+#include \"BaseLib/ConfigTree.h\"\n+#include \"NumLib/ODESolver/TimeDiscretizedODESystem.h\"\n+#include \"NumLib/ODESolver/NonlinearSolver.h\"\n+\n+#include \"ProjectData.h\"\n+\n+\n+namespace ApplicationsLib\n+{\n+\n+//! Time loop capable of time-integrating several uncoupled processes at once.\n+template<typename Matrix, typename Vector>\n+class UncoupledProcessesTimeLoop\n+{\n+public:\n+    bool loop(ProjectData& project, std::string const& outdir);\n+\n+private:\n+    //! An abstract nonlinear solver\n+    using NLSolver       = NumLib::NonlinearSolverBase<Matrix, Vector>;\n+    //! An abstract equations system\n+    using EquationSystem = NumLib::EquationSystem;\n+    //! An abstract process\n+    using Process        = ProcessLib::Process<GlobalSetupType>;\n+    //! An abstract time discretization\n+    using TimeDisc       = NumLib::TimeDiscretization<Vector>;\n+\n+    struct PerProcessData\n+    {\n+        template<NumLib::ODESystemTag ODETag, NumLib::NonlinearSolverTag NLTag>\n+        PerProcessData(NumLib::NonlinearSolver<Matrix, Vector, NLTag>& nl_slv,\n+                       TimeDisc& time_disc,\n+                       NumLib::ODESystem<Matrix, Vector, ODETag, NLTag>& ode_sys\n+                       )\n+            : nonlinear_solver_tag(NLTag)\n+            , nonlinear_solver(nl_slv)","path":"Applications/ApplicationsLib/UncoupledProcessesTimeLoop.h","position":52,"original_position":52,"commit_id":"9fa946998db54d70732331d5a12b0af6e6097ff8","original_commit_id":"710a6357f974836499555ef51a515ad4ae1afe32","user":{"login":"chleh","id":10530151,"avatar_url":"https://avatars.githubusercontent.com/u/10530151?v=3","gravatar_id":"","url":"https://api.github.com/users/chleh","html_url":"https://github.com/chleh","followers_url":"https://api.github.com/users/chleh/followers","following_url":"https://api.github.com/users/chleh/following{/other_user}","gists_url":"https://api.github.com/users/chleh/gists{/gist_id}","starred_url":"https://api.github.com/users/chleh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chleh/subscriptions","organizations_url":"https://api.github.com/users/chleh/orgs","repos_url":"https://api.github.com/users/chleh/repos","events_url":"https://api.github.com/users/chleh/events{/privacy}","received_events_url":"https://api.github.com/users/chleh/received_events","type":"User","site_admin":false},"body":"I always align initializer lists like this and method argument lists at word boundaries. So it's consistent. ^^\r\nI don't want to change my style here.","created_at":"2016-03-01T08:06:51Z","updated_at":"2016-03-01T08:06:51Z","html_url":"https://github.com/ufz/ogs/pull/1050#discussion_r54533440","pull_request_url":"https://api.github.com/repos/ufz/ogs/pulls/1050","_links":{"self":{"href":"https://api.github.com/repos/ufz/ogs/pulls/comments/54533440"},"html":{"href":"https://github.com/ufz/ogs/pull/1050#discussion_r54533440"},"pull_request":{"href":"https://api.github.com/repos/ufz/ogs/pulls/1050"}}},"pull_request":{"url":"https://api.github.com/repos/ufz/ogs/pulls/1050","id":60148690,"html_url":"https://github.com/ufz/ogs/pull/1050","diff_url":"https://github.com/ufz/ogs/pull/1050.diff","patch_url":"https://github.com/ufz/ogs/pull/1050.patch","issue_url":"https://api.github.com/repos/ufz/ogs/issues/1050","number":1050,"state":"open","locked":false,"title":"ODE Solver for transient and nonlinear processes – organ transplantation","user":{"login":"chleh","id":10530151,"avatar_url":"https://avatars.githubusercontent.com/u/10530151?v=3","gravatar_id":"","url":"https://api.github.com/users/chleh","html_url":"https://github.com/chleh","followers_url":"https://api.github.com/users/chleh/followers","following_url":"https://api.github.com/users/chleh/following{/other_user}","gists_url":"https://api.github.com/users/chleh/gists{/gist_id}","starred_url":"https://api.github.com/users/chleh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chleh/subscriptions","organizations_url":"https://api.github.com/users/chleh/orgs","repos_url":"https://api.github.com/users/chleh/repos","events_url":"https://api.github.com/users/chleh/events{/privacy}","received_events_url":"https://api.github.com/users/chleh/received_events","type":"User","site_admin":false},"body":"TODO\r\n* [x] cleanup\r\n* [x] docs\r\n* [x] adapt input files\r\n\r\nFuture work:\r\n* save some matrices (i.e. save space)\r\n* adaptive time stepping\r\n* different error norms\r\n* numerical Jacobians\r\n* process coupling\r\n* ...","created_at":"2016-02-22T09:59:19Z","updated_at":"2016-03-01T08:06:51Z","closed_at":null,"merged_at":null,"merge_commit_sha":"0098de2ccdc930745153b2a3f19e2cde81c9180c","assignee":null,"milestone":{"url":"https://api.github.com/repos/ufz/ogs/milestones/15","html_url":"https://github.com/ufz/ogs/milestones/TES%20Process","labels_url":"https://api.github.com/repos/ufz/ogs/milestones/15/labels","id":1459510,"number":15,"title":"TES Process","description":"","creator":{"login":"chleh","id":10530151,"avatar_url":"https://avatars.githubusercontent.com/u/10530151?v=3","gravatar_id":"","url":"https://api.github.com/users/chleh","html_url":"https://github.com/chleh","followers_url":"https://api.github.com/users/chleh/followers","following_url":"https://api.github.com/users/chleh/following{/other_user}","gists_url":"https://api.github.com/users/chleh/gists{/gist_id}","starred_url":"https://api.github.com/users/chleh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chleh/subscriptions","organizations_url":"https://api.github.com/users/chleh/orgs","repos_url":"https://api.github.com/users/chleh/repos","events_url":"https://api.github.com/users/chleh/events{/privacy}","received_events_url":"https://api.github.com/users/chleh/received_events","type":"User","site_admin":false},"open_issues":9,"closed_issues":8,"state":"open","created_at":"2015-12-14T15:47:32Z","updated_at":"2016-02-29T17:37:59Z","due_on":"2016-03-30T22:00:00Z","closed_at":null},"commits_url":"https://api.github.com/repos/ufz/ogs/pulls/1050/commits","review_comments_url":"https://api.github.com/repos/ufz/ogs/pulls/1050/comments","review_comment_url":"https://api.github.com/repos/ufz/ogs/pulls/comments{/number}","comments_url":"https://api.github.com/repos/ufz/ogs/issues/1050/comments","statuses_url":"https://api.github.com/repos/ufz/ogs/statuses/9fa946998db54d70732331d5a12b0af6e6097ff8","head":{"label":"chleh:t-int-ogs6","ref":"t-int-ogs6","sha":"9fa946998db54d70732331d5a12b0af6e6097ff8","user":{"login":"chleh","id":10530151,"avatar_url":"https://avatars.githubusercontent.com/u/10530151?v=3","gravatar_id":"","url":"https://api.github.com/users/chleh","html_url":"https://github.com/chleh","followers_url":"https://api.github.com/users/chleh/followers","following_url":"https://api.github.com/users/chleh/following{/other_user}","gists_url":"https://api.github.com/users/chleh/gists{/gist_id}","starred_url":"https://api.github.com/users/chleh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chleh/subscriptions","organizations_url":"https://api.github.com/users/chleh/orgs","repos_url":"https://api.github.com/users/chleh/repos","events_url":"https://api.github.com/users/chleh/events{/privacy}","received_events_url":"https://api.github.com/users/chleh/received_events","type":"User","site_admin":false},"repo":{"id":40347084,"name":"ogs6","full_name":"chleh/ogs6","owner":{"login":"chleh","id":10530151,"avatar_url":"https://avatars.githubusercontent.com/u/10530151?v=3","gravatar_id":"","url":"https://api.github.com/users/chleh","html_url":"https://github.com/chleh","followers_url":"https://api.github.com/users/chleh/followers","following_url":"https://api.github.com/users/chleh/following{/other_user}","gists_url":"https://api.github.com/users/chleh/gists{/gist_id}","starred_url":"https://api.github.com/users/chleh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chleh/subscriptions","organizations_url":"https://api.github.com/users/chleh/orgs","repos_url":"https://api.github.com/users/chleh/repos","events_url":"https://api.github.com/users/chleh/events{/privacy}","received_events_url":"https://api.github.com/users/chleh/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/chleh/ogs6","description":"Experimental OGS-6 source code","fork":true,"url":"https://api.github.com/repos/chleh/ogs6","forks_url":"https://api.github.com/repos/chleh/ogs6/forks","keys_url":"https://api.github.com/repos/chleh/ogs6/keys{/key_id}","collaborators_url":"https://api.github.com/repos/chleh/ogs6/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/chleh/ogs6/teams","hooks_url":"https://api.github.com/repos/chleh/ogs6/hooks","issue_events_url":"https://api.github.com/repos/chleh/ogs6/issues/events{/number}","events_url":"https://api.github.com/repos/chleh/ogs6/events","assignees_url":"https://api.github.com/repos/chleh/ogs6/assignees{/user}","branches_url":"https://api.github.com/repos/chleh/ogs6/branches{/branch}","tags_url":"https://api.github.com/repos/chleh/ogs6/tags","blobs_url":"https://api.github.com/repos/chleh/ogs6/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/chleh/ogs6/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/chleh/ogs6/git/refs{/sha}","trees_url":"https://api.github.com/repos/chleh/ogs6/git/trees{/sha}","statuses_url":"https://api.github.com/repos/chleh/ogs6/statuses/{sha}","languages_url":"https://api.github.com/repos/chleh/ogs6/languages","stargazers_url":"https://api.github.com/repos/chleh/ogs6/stargazers","contributors_url":"https://api.github.com/repos/chleh/ogs6/contributors","subscribers_url":"https://api.github.com/repos/chleh/ogs6/subscribers","subscription_url":"https://api.github.com/repos/chleh/ogs6/subscription","commits_url":"https://api.github.com/repos/chleh/ogs6/commits{/sha}","git_commits_url":"https://api.github.com/repos/chleh/ogs6/git/commits{/sha}","comments_url":"https://api.github.com/repos/chleh/ogs6/comments{/number}","issue_comment_url":"https://api.github.com/repos/chleh/ogs6/issues/comments{/number}","contents_url":"https://api.github.com/repos/chleh/ogs6/contents/{+path}","compare_url":"https://api.github.com/repos/chleh/ogs6/compare/{base}...{head}","merges_url":"https://api.github.com/repos/chleh/ogs6/merges","archive_url":"https://api.github.com/repos/chleh/ogs6/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/chleh/ogs6/downloads","issues_url":"https://api.github.com/repos/chleh/ogs6/issues{/number}","pulls_url":"https://api.github.com/repos/chleh/ogs6/pulls{/number}","milestones_url":"https://api.github.com/repos/chleh/ogs6/milestones{/number}","notifications_url":"https://api.github.com/repos/chleh/ogs6/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/chleh/ogs6/labels{/name}","releases_url":"https://api.github.com/repos/chleh/ogs6/releases{/id}","deployments_url":"https://api.github.com/repos/chleh/ogs6/deployments","created_at":"2015-08-07T07:24:24Z","updated_at":"2016-01-14T16:07:04Z","pushed_at":"2016-03-01T07:52:23Z","git_url":"git://github.com/chleh/ogs6.git","ssh_url":"git@github.com:chleh/ogs6.git","clone_url":"https://github.com/chleh/ogs6.git","svn_url":"https://github.com/chleh/ogs6","homepage":"www.opengeosys.org","size":12169,"stargazers_count":0,"watchers_count":0,"language":"C++","has_issues":false,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":1,"mirror_url":null,"open_issues_count":0,"forks":1,"open_issues":0,"watchers":0,"default_branch":"master"}},"base":{"label":"ufz:master","ref":"master","sha":"b7dd83bfd6c6a5f1729e0dcd358fe106fed3435e","user":{"login":"ufz","id":767517,"avatar_url":"https://avatars.githubusercontent.com/u/767517?v=3","gravatar_id":"","url":"https://api.github.com/users/ufz","html_url":"https://github.com/ufz","followers_url":"https://api.github.com/users/ufz/followers","following_url":"https://api.github.com/users/ufz/following{/other_user}","gists_url":"https://api.github.com/users/ufz/gists{/gist_id}","starred_url":"https://api.github.com/users/ufz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ufz/subscriptions","organizations_url":"https://api.github.com/users/ufz/orgs","repos_url":"https://api.github.com/users/ufz/repos","events_url":"https://api.github.com/users/ufz/events{/privacy}","received_events_url":"https://api.github.com/users/ufz/received_events","type":"Organization","site_admin":false},"repo":{"id":1701384,"name":"ogs","full_name":"ufz/ogs","owner":{"login":"ufz","id":767517,"avatar_url":"https://avatars.githubusercontent.com/u/767517?v=3","gravatar_id":"","url":"https://api.github.com/users/ufz","html_url":"https://github.com/ufz","followers_url":"https://api.github.com/users/ufz/followers","following_url":"https://api.github.com/users/ufz/following{/other_user}","gists_url":"https://api.github.com/users/ufz/gists{/gist_id}","starred_url":"https://api.github.com/users/ufz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ufz/subscriptions","organizations_url":"https://api.github.com/users/ufz/orgs","repos_url":"https://api.github.com/users/ufz/repos","events_url":"https://api.github.com/users/ufz/events{/privacy}","received_events_url":"https://api.github.com/users/ufz/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/ufz/ogs","description":"Experimental OGS-6 source code","fork":false,"url":"https://api.github.com/repos/ufz/ogs","forks_url":"https://api.github.com/repos/ufz/ogs/forks","keys_url":"https://api.github.com/repos/ufz/ogs/keys{/key_id}","collaborators_url":"https://api.github.com/repos/ufz/ogs/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/ufz/ogs/teams","hooks_url":"https://api.github.com/repos/ufz/ogs/hooks","issue_events_url":"https://api.github.com/repos/ufz/ogs/issues/events{/number}","events_url":"https://api.github.com/repos/ufz/ogs/events","assignees_url":"https://api.github.com/repos/ufz/ogs/assignees{/user}","branches_url":"https://api.github.com/repos/ufz/ogs/branches{/branch}","tags_url":"https://api.github.com/repos/ufz/ogs/tags","blobs_url":"https://api.github.com/repos/ufz/ogs/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/ufz/ogs/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/ufz/ogs/git/refs{/sha}","trees_url":"https://api.github.com/repos/ufz/ogs/git/trees{/sha}","statuses_url":"https://api.github.com/repos/ufz/ogs/statuses/{sha}","languages_url":"https://api.github.com/repos/ufz/ogs/languages","stargazers_url":"https://api.github.com/repos/ufz/ogs/stargazers","contributors_url":"https://api.github.com/repos/ufz/ogs/contributors","subscribers_url":"https://api.github.com/repos/ufz/ogs/subscribers","subscription_url":"https://api.github.com/repos/ufz/ogs/subscription","commits_url":"https://api.github.com/repos/ufz/ogs/commits{/sha}","git_commits_url":"https://api.github.com/repos/ufz/ogs/git/commits{/sha}","comments_url":"https://api.github.com/repos/ufz/ogs/comments{/number}","issue_comment_url":"https://api.github.com/repos/ufz/ogs/issues/comments{/number}","contents_url":"https://api.github.com/repos/ufz/ogs/contents/{+path}","compare_url":"https://api.github.com/repos/ufz/ogs/compare/{base}...{head}","merges_url":"https://api.github.com/repos/ufz/ogs/merges","archive_url":"https://api.github.com/repos/ufz/ogs/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/ufz/ogs/downloads","issues_url":"https://api.github.com/repos/ufz/ogs/issues{/number}","pulls_url":"https://api.github.com/repos/ufz/ogs/pulls{/number}","milestones_url":"https://api.github.com/repos/ufz/ogs/milestones{/number}","notifications_url":"https://api.github.com/repos/ufz/ogs/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/ufz/ogs/labels{/name}","releases_url":"https://api.github.com/repos/ufz/ogs/releases{/id}","deployments_url":"https://api.github.com/repos/ufz/ogs/deployments","created_at":"2011-05-04T14:09:57Z","updated_at":"2015-10-23T03:43:52Z","pushed_at":"2016-03-01T07:52:23Z","git_url":"git://github.com/ufz/ogs.git","ssh_url":"git@github.com:ufz/ogs.git","clone_url":"https://github.com/ufz/ogs.git","svn_url":"https://github.com/ufz/ogs","homepage":"www.opengeosys.org","size":12966,"stargazers_count":18,"watchers_count":18,"language":"C++","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":40,"mirror_url":null,"open_issues_count":86,"forks":40,"open_issues":86,"watchers":18,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/ufz/ogs/pulls/1050"},"html":{"href":"https://github.com/ufz/ogs/pull/1050"},"issue":{"href":"https://api.github.com/repos/ufz/ogs/issues/1050"},"comments":{"href":"https://api.github.com/repos/ufz/ogs/issues/1050/comments"},"review_comments":{"href":"https://api.github.com/repos/ufz/ogs/pulls/1050/comments"},"review_comment":{"href":"https://api.github.com/repos/ufz/ogs/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/ufz/ogs/pulls/1050/commits"},"statuses":{"href":"https://api.github.com/repos/ufz/ogs/statuses/9fa946998db54d70732331d5a12b0af6e6097ff8"}}}}