{"action":"created","issue":{"url":"https://api.github.com/repos/colvars/colvars/issues/73","repository_url":"https://api.github.com/repos/colvars/colvars","labels_url":"https://api.github.com/repos/colvars/colvars/issues/73/labels{/name}","comments_url":"https://api.github.com/repos/colvars/colvars/issues/73/comments","events_url":"https://api.github.com/repos/colvars/colvars/issues/73/events","html_url":"https://github.com/colvars/colvars/issues/73","id":171728039,"number":73,"title":"Conflict with TclForces","user":{"login":"jhenin","id":4518166,"avatar_url":"https://avatars.githubusercontent.com/u/4518166?v=3","gravatar_id":"","url":"https://api.github.com/users/jhenin","html_url":"https://github.com/jhenin","followers_url":"https://api.github.com/users/jhenin/followers","following_url":"https://api.github.com/users/jhenin/following{/other_user}","gists_url":"https://api.github.com/users/jhenin/gists{/gist_id}","starred_url":"https://api.github.com/users/jhenin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jhenin/subscriptions","organizations_url":"https://api.github.com/users/jhenin/orgs","repos_url":"https://api.github.com/users/jhenin/repos","events_url":"https://api.github.com/users/jhenin/events{/privacy}","received_events_url":"https://api.github.com/users/jhenin/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/colvars/colvars/labels/bug","name":"bug","color":"fc2929"},{"url":"https://api.github.com/repos/colvars/colvars/labels/NAMD","name":"NAMD","color":"444444"}],"state":"closed","locked":false,"assignee":{"login":"giacomofiorin","id":4512089,"avatar_url":"https://avatars.githubusercontent.com/u/4512089?v=3","gravatar_id":"","url":"https://api.github.com/users/giacomofiorin","html_url":"https://github.com/giacomofiorin","followers_url":"https://api.github.com/users/giacomofiorin/followers","following_url":"https://api.github.com/users/giacomofiorin/following{/other_user}","gists_url":"https://api.github.com/users/giacomofiorin/gists{/gist_id}","starred_url":"https://api.github.com/users/giacomofiorin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/giacomofiorin/subscriptions","organizations_url":"https://api.github.com/users/giacomofiorin/orgs","repos_url":"https://api.github.com/users/giacomofiorin/repos","events_url":"https://api.github.com/users/giacomofiorin/events{/privacy}","received_events_url":"https://api.github.com/users/giacomofiorin/received_events","type":"User","site_admin":false},"assignees":[{"login":"giacomofiorin","id":4512089,"avatar_url":"https://avatars.githubusercontent.com/u/4512089?v=3","gravatar_id":"","url":"https://api.github.com/users/giacomofiorin","html_url":"https://github.com/giacomofiorin","followers_url":"https://api.github.com/users/giacomofiorin/followers","following_url":"https://api.github.com/users/giacomofiorin/following{/other_user}","gists_url":"https://api.github.com/users/giacomofiorin/gists{/gist_id}","starred_url":"https://api.github.com/users/giacomofiorin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/giacomofiorin/subscriptions","organizations_url":"https://api.github.com/users/giacomofiorin/orgs","repos_url":"https://api.github.com/users/giacomofiorin/repos","events_url":"https://api.github.com/users/giacomofiorin/events{/privacy}","received_events_url":"https://api.github.com/users/giacomofiorin/received_events","type":"User","site_admin":false}],"milestone":null,"comments":2,"created_at":"2016-08-17T18:30:22Z","updated_at":"2016-09-14T21:53:34Z","closed_at":"2016-09-14T21:53:34Z","body":"When scalable colvars are enabled and a TclForce script requests atoms, the NAMD proxy gives a segfault:\r\n```\r\n0x0000000000abca25 in colvarproxy_namd::calculate (this=0x14de520) at src/colvarproxy_namd.C:278\r\n278             atoms_total_forces[atoms_map[*a_i]] = cvm::rvector((*f_i).x, (*f_i).y, (*f_i).z);\r\n```\r\nIt tries to access the atom map, which is uninitialized because no atoms are used at the colvars level. Somehow the GlobalMaster iterators return the wrong atoms, apparently because of TclForces."},"comment":{"url":"https://api.github.com/repos/colvars/colvars/issues/comments/247167685","html_url":"https://github.com/colvars/colvars/issues/73#issuecomment-247167685","issue_url":"https://api.github.com/repos/colvars/colvars/issues/73","id":247167685,"user":{"login":"giacomofiorin","id":4512089,"avatar_url":"https://avatars.githubusercontent.com/u/4512089?v=3","gravatar_id":"","url":"https://api.github.com/users/giacomofiorin","html_url":"https://github.com/giacomofiorin","followers_url":"https://api.github.com/users/giacomofiorin/followers","following_url":"https://api.github.com/users/giacomofiorin/following{/other_user}","gists_url":"https://api.github.com/users/giacomofiorin/gists{/gist_id}","starred_url":"https://api.github.com/users/giacomofiorin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/giacomofiorin/subscriptions","organizations_url":"https://api.github.com/users/giacomofiorin/orgs","repos_url":"https://api.github.com/users/giacomofiorin/repos","events_url":"https://api.github.com/users/giacomofiorin/events{/privacy}","received_events_url":"https://api.github.com/users/giacomofiorin/received_events","type":"User","site_admin":false},"created_at":"2016-09-14T21:53:34Z","updated_at":"2016-09-14T21:53:34Z","body":"The issue was due to the tclForces script applying a force, but not requesting the corresponding position. The new version (commit a73f32f) adds to the inverse map both atoms whose positions were requested and atoms that had forces applied to them.\r\n\r\nThe check that updates the inverse map also takes care of the initialization issue #47."}}
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