{"action":"created","comment":{"url":"https://api.github.com/repos/geodynamics/aspect/pulls/comments/199627969","pull_request_review_id":133781044,"id":199627969,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDE5OTYyNzk2OQ==","diff_hunk":"@@ -0,0 +1,206 @@\n+/*\n+  Copyright (C) 2011 - 2017 by the authors of the ASPECT code.\n+\n+  This file is part of ASPECT.\n+\n+  ASPECT is free software; you can redistribute it and/or modify\n+  it under the terms of the GNU General Public License as published by\n+  the Free Software Foundation; either version 2, or (at your option)\n+  any later version.\n+\n+  ASPECT is distributed in the hope that it will be useful,\n+  but WITHOUT ANY WARRANTY; without even the implied warranty of\n+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n+  GNU General Public License for more details.\n+\n+  You should have received a copy of the GNU General Public License\n+  along with ASPECT; see the file LICENSE.  If not see\n+  <http://www.gnu.org/licenses/>.\n+ */\n+\n+\n+#include <aspect/global.h>\n+#include <aspect/adiabatic_conditions/interface.h>\n+#include <aspect/initial_temperature/patch_on_S40RTS.h>\n+#include <aspect/utilities.h>\n+\n+namespace aspect\n+{\n+  namespace InitialTemperature\n+  {\n+    template <int dim>\n+    PatchOnS40RTS<dim>::PatchOnS40RTS ()\n+    {}\n+\n+\n+    template <int dim>\n+    void\n+    PatchOnS40RTS<dim>::initialize ()\n+    {\n+      Utilities::AsciiDataInitial<dim>::initialize(1);\n+      if (s40rts.vs_to_density_method == s40rts.file)\n+        {\n+          s40rts.profile.initialize(this->get_mpi_communicator());\n+          s40rts.vs_to_density_index = s40rts.profile.get_column_index_from_name(\"vs_to_density\");\n+        }","path":"source/initial_temperature/patch_on_S40RTS.cc","position":45,"original_position":45,"commit_id":"6148b40b594a5de3ea00aaec582ced7c2936c949","original_commit_id":"6148b40b594a5de3ea00aaec582ced7c2936c949","user":{"login":"gassmoeller","id":7582930,"node_id":"MDQ6VXNlcjc1ODI5MzA=","avatar_url":"https://avatars0.githubusercontent.com/u/7582930?v=4","gravatar_id":"","url":"https://api.github.com/users/gassmoeller","html_url":"https://github.com/gassmoeller","followers_url":"https://api.github.com/users/gassmoeller/followers","following_url":"https://api.github.com/users/gassmoeller/following{/other_user}","gists_url":"https://api.github.com/users/gassmoeller/gists{/gist_id}","starred_url":"https://api.github.com/users/gassmoeller/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gassmoeller/subscriptions","organizations_url":"https://api.github.com/users/gassmoeller/orgs","repos_url":"https://api.github.com/users/gassmoeller/repos","events_url":"https://api.github.com/users/gassmoeller/events{/privacy}","received_events_url":"https://api.github.com/users/gassmoeller/received_events","type":"User","site_admin":false},"body":"From what I see of S40RTS in the master branch, the code in the `if` statement above should have no effect. The same code is executed in `S40RTSPerturbation::initialize`, which is called by `S40RTSPerturbation::parse_parameters` (weird, but that is what it is at the moment), which is called by `PatchOnS40RTS::parse_parameters`, i.e. before we get to this particular line. In other words: Everything should be ready to go, we just repeat these lines here. ","created_at":"2018-07-02T21:34:48Z","updated_at":"2018-07-02T21:44:23Z","html_url":"https://github.com/geodynamics/aspect/pull/2509#discussion_r199627969","pull_request_url":"https://api.github.com/repos/geodynamics/aspect/pulls/2509","author_association":"CONTRIBUTOR","_links":{"self":{"href":"https://api.github.com/repos/geodynamics/aspect/pulls/comments/199627969"},"html":{"href":"https://github.com/geodynamics/aspect/pull/2509#discussion_r199627969"},"pull_request":{"href":"https://api.github.com/repos/geodynamics/aspect/pulls/2509"}}},"pull_request":{"url":"https://api.github.com/repos/geodynamics/aspect/pulls/2509","id":197815560,"node_id":"MDExOlB1bGxSZXF1ZXN0MTk3ODE1NTYw","html_url":"https://github.com/geodynamics/aspect/pull/2509","diff_url":"https://github.com/geodynamics/aspect/pull/2509.diff","patch_url":"https://github.com/geodynamics/aspect/pull/2509.patch","issue_url":"https://api.github.com/repos/geodynamics/aspect/issues/2509","number":2509,"state":"open","locked":false,"title":"Initial temperature condition - patch on S40RTS","user":{"login":"SophieCoulson","id":39568772,"node_id":"MDQ6VXNlcjM5NTY4Nzcy","avatar_url":"https://avatars0.githubusercontent.com/u/39568772?v=4","gravatar_id":"","url":"https://api.github.com/users/SophieCoulson","html_url":"https://github.com/SophieCoulson","followers_url":"https://api.github.com/users/SophieCoulson/followers","following_url":"https://api.github.com/users/SophieCoulson/following{/other_user}","gists_url":"https://api.github.com/users/SophieCoulson/gists{/gist_id}","starred_url":"https://api.github.com/users/SophieCoulson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SophieCoulson/subscriptions","organizations_url":"https://api.github.com/users/SophieCoulson/orgs","repos_url":"https://api.github.com/users/SophieCoulson/repos","events_url":"https://api.github.com/users/SophieCoulson/events{/privacy}","received_events_url":"https://api.github.com/users/SophieCoulson/received_events","type":"User","site_admin":false},"body":"Add initial temperature condition patch_on_S40RTS which combines S40RTS and an ascii grid containing an upper mantle tomography. Data is input in Vs and converted to temperature within the function (using the same method as S40RTS_perturbation). Includes an option to smooth by averaging between the two tomographies. Also added test for this function.\r\n\r\nChanges to S40RTS_perturbation.h allow calling all functions from S40RTS_perturbation.\r\nDefault data added into the data directory - upper_shell_3d.txt\r\n","created_at":"2018-06-27T18:26:31Z","updated_at":"2018-07-02T21:44:23Z","closed_at":null,"merged_at":null,"merge_commit_sha":"d2be0f507fdc1cc3d685ce142dfb19f3a38dcf5a","assignee":{"login":"anne-glerum","id":7631624,"node_id":"MDQ6VXNlcjc2MzE2MjQ=","avatar_url":"https://avatars1.githubusercontent.com/u/7631624?v=4","gravatar_id":"","url":"https://api.github.com/users/anne-glerum","html_url":"https://github.com/anne-glerum","followers_url":"https://api.github.com/users/anne-glerum/followers","following_url":"https://api.github.com/users/anne-glerum/following{/other_user}","gists_url":"https://api.github.com/users/anne-glerum/gists{/gist_id}","starred_url":"https://api.github.com/users/anne-glerum/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/anne-glerum/subscriptions","organizations_url":"https://api.github.com/users/anne-glerum/orgs","repos_url":"https://api.github.com/users/anne-glerum/repos","events_url":"https://api.github.com/users/anne-glerum/events{/privacy}","received_events_url":"https://api.github.com/users/anne-glerum/received_events","type":"User","site_admin":false},"assignees":[{"login":"anne-glerum","id":7631624,"node_id":"MDQ6VXNlcjc2MzE2MjQ=","avatar_url":"https://avatars1.githubusercontent.com/u/7631624?v=4","gravatar_id":"","url":"https://api.github.com/users/anne-glerum","html_url":"https://github.com/anne-glerum","followers_url":"https://api.github.com/users/anne-glerum/followers","following_url":"https://api.github.com/users/anne-glerum/following{/other_user}","gists_url":"https://api.github.com/users/anne-glerum/gists{/gist_id}","starred_url":"https://api.github.com/users/anne-glerum/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/anne-glerum/subscriptions","organizations_url":"https://api.github.com/users/anne-glerum/orgs","repos_url":"https://api.github.com/users/anne-glerum/repos","events_url":"https://api.github.com/users/anne-glerum/events{/privacy}","received_events_url":"https://api.github.com/users/anne-glerum/received_events","type":"User","site_admin":false}],"requested_reviewers":[],"requested_teams":[],"labels":[],"milestone":null,"commits_url":"https://api.github.com/repos/geodynamics/aspect/pulls/2509/commits","review_comments_url":"https://api.github.com/repos/geodynamics/aspect/pulls/2509/comments","review_comment_url":"https://api.github.com/repos/geodynamics/aspect/pulls/comments{/number}","comments_url":"https://api.github.com/repos/geodynamics/aspect/issues/2509/comments","statuses_url":"https://api.github.com/repos/geodynamics/aspect/statuses/6148b40b594a5de3ea00aaec582ced7c2936c949","head":{"label":"SophieCoulson:combined-grid-smoothing","ref":"combined-grid-smoothing","sha":"6148b40b594a5de3ea00aaec582ced7c2936c949","user":{"login":"SophieCoulson","id":39568772,"node_id":"MDQ6VXNlcjM5NTY4Nzcy","avatar_url":"https://avatars0.githubusercontent.com/u/39568772?v=4","gravatar_id":"","url":"https://api.github.com/users/SophieCoulson","html_url":"https://github.com/SophieCoulson","followers_url":"https://api.github.com/users/SophieCoulson/followers","following_url":"https://api.github.com/users/SophieCoulson/following{/other_user}","gists_url":"https://api.github.com/users/SophieCoulson/gists{/gist_id}","starred_url":"https://api.github.com/users/SophieCoulson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SophieCoulson/subscriptions","organizations_url":"https://api.github.com/users/SophieCoulson/orgs","repos_url":"https://api.github.com/users/SophieCoulson/repos","events_url":"https://api.github.com/users/SophieCoulson/events{/privacy}","received_events_url":"https://api.github.com/users/SophieCoulson/received_events","type":"User","site_admin":false},"repo":{"id":134867981,"node_id":"MDEwOlJlcG9zaXRvcnkxMzQ4Njc5ODE=","name":"aspect","full_name":"SophieCoulson/aspect","owner":{"login":"SophieCoulson","id":39568772,"node_id":"MDQ6VXNlcjM5NTY4Nzcy","avatar_url":"https://avatars0.githubusercontent.com/u/39568772?v=4","gravatar_id":"","url":"https://api.github.com/users/SophieCoulson","html_url":"https://github.com/SophieCoulson","followers_url":"https://api.github.com/users/SophieCoulson/followers","following_url":"https://api.github.com/users/SophieCoulson/following{/other_user}","gists_url":"https://api.github.com/users/SophieCoulson/gists{/gist_id}","starred_url":"https://api.github.com/users/SophieCoulson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SophieCoulson/subscriptions","organizations_url":"https://api.github.com/users/SophieCoulson/orgs","repos_url":"https://api.github.com/users/SophieCoulson/repos","events_url":"https://api.github.com/users/SophieCoulson/events{/privacy}","received_events_url":"https://api.github.com/users/SophieCoulson/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/SophieCoulson/aspect","description":"A parallel, extensible finite element code to simulate convection in both 2D and 3D models.","fork":true,"url":"https://api.github.com/repos/SophieCoulson/aspect","forks_url":"https://api.github.com/repos/SophieCoulson/aspect/forks","keys_url":"https://api.github.com/repos/SophieCoulson/aspect/keys{/key_id}","collaborators_url":"https://api.github.com/repos/SophieCoulson/aspect/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/SophieCoulson/aspect/teams","hooks_url":"https://api.github.com/repos/SophieCoulson/aspect/hooks","issue_events_url":"https://api.github.com/repos/SophieCoulson/aspect/issues/events{/number}","events_url":"https://api.github.com/repos/SophieCoulson/aspect/events","assignees_url":"https://api.github.com/repos/SophieCoulson/aspect/assignees{/user}","branches_url":"https://api.github.com/repos/SophieCoulson/aspect/branches{/branch}","tags_url":"https://api.github.com/repos/SophieCoulson/aspect/tags","blobs_url":"https://api.github.com/repos/SophieCoulson/aspect/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/SophieCoulson/aspect/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/SophieCoulson/aspect/git/refs{/sha}","trees_url":"https://api.github.com/repos/SophieCoulson/aspect/git/trees{/sha}","statuses_url":"https://api.github.com/repos/SophieCoulson/aspect/statuses/{sha}","languages_url":"https://api.github.com/repos/SophieCoulson/aspect/languages","stargazers_url":"https://api.github.com/repos/SophieCoulson/aspect/stargazers","contributors_url":"https://api.github.com/repos/SophieCoulson/aspect/contributors","subscribers_url":"https://api.github.com/repos/SophieCoulson/aspect/subscribers","subscription_url":"https://api.github.com/repos/SophieCoulson/aspect/subscription","commits_url":"https://api.github.com/repos/SophieCoulson/aspect/commits{/sha}","git_commits_url":"https://api.github.com/repos/SophieCoulson/aspect/git/commits{/sha}","comments_url":"https://api.github.com/repos/SophieCoulson/aspect/comments{/number}","issue_comment_url":"https://api.github.com/repos/SophieCoulson/aspect/issues/comments{/number}","contents_url":"https://api.github.com/repos/SophieCoulson/aspect/contents/{+path}","compare_url":"https://api.github.com/repos/SophieCoulson/aspect/compare/{base}...{head}","merges_url":"https://api.github.com/repos/SophieCoulson/aspect/merges","archive_url":"https://api.github.com/repos/SophieCoulson/aspect/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/SophieCoulson/aspect/downloads","issues_url":"https://api.github.com/repos/SophieCoulson/aspect/issues{/number}","pulls_url":"https://api.github.com/repos/SophieCoulson/aspect/pulls{/number}","milestones_url":"https://api.github.com/repos/SophieCoulson/aspect/milestones{/number}","notifications_url":"https://api.github.com/repos/SophieCoulson/aspect/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/SophieCoulson/aspect/labels{/name}","releases_url":"https://api.github.com/repos/SophieCoulson/aspect/releases{/id}","deployments_url":"https://api.github.com/repos/SophieCoulson/aspect/deployments","created_at":"2018-05-25T14:38:04Z","updated_at":"2018-06-19T18:15:28Z","pushed_at":"2018-07-02T20:01:44Z","git_url":"git://github.com/SophieCoulson/aspect.git","ssh_url":"git@github.com:SophieCoulson/aspect.git","clone_url":"https://github.com/SophieCoulson/aspect.git","svn_url":"https://github.com/SophieCoulson/aspect","homepage":"https://aspect.geodynamics.org/","size":198634,"stargazers_count":0,"watchers_count":0,"language":"Gnuplot","has_issues":false,"has_projects":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":0,"mirror_url":null,"archived":false,"open_issues_count":0,"license":{"key":"other","name":"Other","spdx_id":null,"url":null,"node_id":"MDc6TGljZW5zZTA="},"forks":0,"open_issues":0,"watchers":0,"default_branch":"master"}},"base":{"label":"geodynamics:master","ref":"master","sha":"f5e6a41d5328ed9b61b72aae019701bddcf04714","user":{"login":"geodynamics","id":4052461,"node_id":"MDEyOk9yZ2FuaXphdGlvbjQwNTI0NjE=","avatar_url":"https://avatars1.githubusercontent.com/u/4052461?v=4","gravatar_id":"","url":"https://api.github.com/users/geodynamics","html_url":"https://github.com/geodynamics","followers_url":"https://api.github.com/users/geodynamics/followers","following_url":"https://api.github.com/users/geodynamics/following{/other_user}","gists_url":"https://api.github.com/users/geodynamics/gists{/gist_id}","starred_url":"https://api.github.com/users/geodynamics/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/geodynamics/subscriptions","organizations_url":"https://api.github.com/users/geodynamics/orgs","repos_url":"https://api.github.com/users/geodynamics/repos","events_url":"https://api.github.com/users/geodynamics/events{/privacy}","received_events_url":"https://api.github.com/users/geodynamics/received_events","type":"Organization","site_admin":false},"repo":{"id":19502452,"node_id":"MDEwOlJlcG9zaXRvcnkxOTUwMjQ1Mg==","name":"aspect","full_name":"geodynamics/aspect","owner":{"login":"geodynamics","id":4052461,"node_id":"MDEyOk9yZ2FuaXphdGlvbjQwNTI0NjE=","avatar_url":"https://avatars1.githubusercontent.com/u/4052461?v=4","gravatar_id":"","url":"https://api.github.com/users/geodynamics","html_url":"https://github.com/geodynamics","followers_url":"https://api.github.com/users/geodynamics/followers","following_url":"https://api.github.com/users/geodynamics/following{/other_user}","gists_url":"https://api.github.com/users/geodynamics/gists{/gist_id}","starred_url":"https://api.github.com/users/geodynamics/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/geodynamics/subscriptions","organizations_url":"https://api.github.com/users/geodynamics/orgs","repos_url":"https://api.github.com/users/geodynamics/repos","events_url":"https://api.github.com/users/geodynamics/events{/privacy}","received_events_url":"https://api.github.com/users/geodynamics/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/geodynamics/aspect","description":"A parallel, extensible finite element code to simulate convection in both 2D and 3D models.","fork":false,"url":"https://api.github.com/repos/geodynamics/aspect","forks_url":"https://api.github.com/repos/geodynamics/aspect/forks","keys_url":"https://api.github.com/repos/geodynamics/aspect/keys{/key_id}","collaborators_url":"https://api.github.com/repos/geodynamics/aspect/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/geodynamics/aspect/teams","hooks_url":"https://api.github.com/repos/geodynamics/aspect/hooks","issue_events_url":"https://api.github.com/repos/geodynamics/aspect/issues/events{/number}","events_url":"https://api.github.com/repos/geodynamics/aspect/events","assignees_url":"https://api.github.com/repos/geodynamics/aspect/assignees{/user}","branches_url":"https://api.github.com/repos/geodynamics/aspect/branches{/branch}","tags_url":"https://api.github.com/repos/geodynamics/aspect/tags","blobs_url":"https://api.github.com/repos/geodynamics/aspect/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/geodynamics/aspect/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/geodynamics/aspect/git/refs{/sha}","trees_url":"https://api.github.com/repos/geodynamics/aspect/git/trees{/sha}","statuses_url":"https://api.github.com/repos/geodynamics/aspect/statuses/{sha}","languages_url":"https://api.github.com/repos/geodynamics/aspect/languages","stargazers_url":"https://api.github.com/repos/geodynamics/aspect/stargazers","contributors_url":"https://api.github.com/repos/geodynamics/aspect/contributors","subscribers_url":"https://api.github.com/repos/geodynamics/aspect/subscribers","subscription_url":"https://api.github.com/repos/geodynamics/aspect/subscription","commits_url":"https://api.github.com/repos/geodynamics/aspect/commits{/sha}","git_commits_url":"https://api.github.com/repos/geodynamics/aspect/git/commits{/sha}","comments_url":"https://api.github.com/repos/geodynamics/aspect/comments{/number}","issue_comment_url":"https://api.github.com/repos/geodynamics/aspect/issues/comments{/number}","contents_url":"https://api.github.com/repos/geodynamics/aspect/contents/{+path}","compare_url":"https://api.github.com/repos/geodynamics/aspect/compare/{base}...{head}","merges_url":"https://api.github.com/repos/geodynamics/aspect/merges","archive_url":"https://api.github.com/repos/geodynamics/aspect/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/geodynamics/aspect/downloads","issues_url":"https://api.github.com/repos/geodynamics/aspect/issues{/number}","pulls_url":"https://api.github.com/repos/geodynamics/aspect/pulls{/number}","milestones_url":"https://api.github.com/repos/geodynamics/aspect/milestones{/number}","notifications_url":"https://api.github.com/repos/geodynamics/aspect/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/geodynamics/aspect/labels{/name}","releases_url":"https://api.github.com/repos/geodynamics/aspect/releases{/id}","deployments_url":"https://api.github.com/repos/geodynamics/aspect/deployments","created_at":"2014-05-06T16:47:18Z","updated_at":"2018-07-02T20:53:48Z","pushed_at":"2018-07-02T21:18:21Z","git_url":"git://github.com/geodynamics/aspect.git","ssh_url":"git@github.com:geodynamics/aspect.git","clone_url":"https://github.com/geodynamics/aspect.git","svn_url":"https://github.com/geodynamics/aspect","homepage":"https://aspect.geodynamics.org/","size":177274,"stargazers_count":54,"watchers_count":54,"language":"Gnuplot","has_issues":true,"has_projects":true,"has_downloads":true,"has_wiki":true,"has_pages":true,"forks_count":98,"mirror_url":null,"archived":false,"open_issues_count":207,"license":{"key":"other","name":"Other","spdx_id":null,"url":null,"node_id":"MDc6TGljZW5zZTA="},"forks":98,"open_issues":207,"watchers":54,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/geodynamics/aspect/pulls/2509"},"html":{"href":"https://github.com/geodynamics/aspect/pull/2509"},"issue":{"href":"https://api.github.com/repos/geodynamics/aspect/issues/2509"},"comments":{"href":"https://api.github.com/repos/geodynamics/aspect/issues/2509/comments"},"review_comments":{"href":"https://api.github.com/repos/geodynamics/aspect/pulls/2509/comments"},"review_comment":{"href":"https://api.github.com/repos/geodynamics/aspect/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/geodynamics/aspect/pulls/2509/commits"},"statuses":{"href":"https://api.github.com/repos/geodynamics/aspect/statuses/6148b40b594a5de3ea00aaec582ced7c2936c949"}},"author_association":"CONTRIBUTOR"}}
{"actor":{"display_login":"gassmoeller"}}