{"action":"created","issue":{"url":"https://api.github.com/repos/tranqui/MDMAmazing/issues/3","repository_url":"https://api.github.com/repos/tranqui/MDMAmazing","labels_url":"https://api.github.com/repos/tranqui/MDMAmazing/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/tranqui/MDMAmazing/issues/3/comments","events_url":"https://api.github.com/repos/tranqui/MDMAmazing/issues/3/events","html_url":"https://github.com/tranqui/MDMAmazing/issues/3","id":371698303,"node_id":"MDU6SXNzdWUzNzE2OTgzMDM=","number":3,"title":"Opening lammps atom files fails","user":{"login":"merrygoat","id":13117069,"node_id":"MDQ6VXNlcjEzMTE3MDY5","avatar_url":"https://avatars2.githubusercontent.com/u/13117069?v=4","gravatar_id":"","url":"https://api.github.com/users/merrygoat","html_url":"https://github.com/merrygoat","followers_url":"https://api.github.com/users/merrygoat/followers","following_url":"https://api.github.com/users/merrygoat/following{/other_user}","gists_url":"https://api.github.com/users/merrygoat/gists{/gist_id}","starred_url":"https://api.github.com/users/merrygoat/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/merrygoat/subscriptions","organizations_url":"https://api.github.com/users/merrygoat/orgs","repos_url":"https://api.github.com/users/merrygoat/repos","events_url":"https://api.github.com/users/merrygoat/events{/privacy}","received_events_url":"https://api.github.com/users/merrygoat/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-10-18T20:26:09Z","updated_at":"2018-10-19T12:34:38Z","closed_at":null,"author_association":"NONE","body":"Opening an atom file with the snapshot reader fails in atom.py. \r\n\r\nAtom files store particle coordinates as a fraction of the box size, to convert the coordinates from fractional to real the code multiplies the coordinates by the box size. \r\n\r\nThe problem is that the code reads the box boundaires as -x, +x, etc. and then tries to multiply the coordinates by this tuple. The code should add the bounds to get the total box size and then multiply by this.\r\n\r\nPerhaps something like this?\r\n`\r\n\r\n                # Item containing the bounding box.\r\n                elif ' '.join(item[1:3]) == 'BOX BOUNDS':\r\n                    d = len(item[3:])\r\n                    self.x = numpy.empty((self.n, d))\r\n                    self.box = numpy.zeros(d, dtype=numpy.longdouble)\r\n\r\n                    for c in range(d):\r\n                        boundary = f.readline().split()\r\n                        for bound in boundary:\r\n                            self.box[c] += abs(float(bound))\r\n`"},"comment":{"url":"https://api.github.com/repos/tranqui/MDMAmazing/issues/comments/431347948","html_url":"https://github.com/tranqui/MDMAmazing/issues/3#issuecomment-431347948","issue_url":"https://api.github.com/repos/tranqui/MDMAmazing/issues/3","id":431347948,"node_id":"MDEyOklzc3VlQ29tbWVudDQzMTM0Nzk0OA==","user":{"login":"tranqui","id":14914477,"node_id":"MDQ6VXNlcjE0OTE0NDc3","avatar_url":"https://avatars1.githubusercontent.com/u/14914477?v=4","gravatar_id":"","url":"https://api.github.com/users/tranqui","html_url":"https://github.com/tranqui","followers_url":"https://api.github.com/users/tranqui/followers","following_url":"https://api.github.com/users/tranqui/following{/other_user}","gists_url":"https://api.github.com/users/tranqui/gists{/gist_id}","starred_url":"https://api.github.com/users/tranqui/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tranqui/subscriptions","organizations_url":"https://api.github.com/users/tranqui/orgs","repos_url":"https://api.github.com/users/tranqui/repos","events_url":"https://api.github.com/users/tranqui/events{/privacy}","received_events_url":"https://api.github.com/users/tranqui/received_events","type":"User","site_admin":false},"created_at":"2018-10-19T12:34:38Z","updated_at":"2018-10-19T12:34:38Z","author_association":"OWNER","body":"If this version works on your system, we can close it."}}
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