{"action":"created","issue":{"url":"https://api.github.com/repos/pekkosk/hotbit/issues/20","repository_url":"https://api.github.com/repos/pekkosk/hotbit","labels_url":"https://api.github.com/repos/pekkosk/hotbit/issues/20/labels{/name}","comments_url":"https://api.github.com/repos/pekkosk/hotbit/issues/20/comments","events_url":"https://api.github.com/repos/pekkosk/hotbit/issues/20/events","html_url":"https://github.com/pekkosk/hotbit/issues/20","id":313626133,"number":20,"title":"Repulsion Fitting in hotbit  ","user":{"login":"sh-pan","id":38124087,"avatar_url":"https://avatars2.githubusercontent.com/u/38124087?v=4","gravatar_id":"","url":"https://api.github.com/users/sh-pan","html_url":"https://github.com/sh-pan","followers_url":"https://api.github.com/users/sh-pan/followers","following_url":"https://api.github.com/users/sh-pan/following{/other_user}","gists_url":"https://api.github.com/users/sh-pan/gists{/gist_id}","starred_url":"https://api.github.com/users/sh-pan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sh-pan/subscriptions","organizations_url":"https://api.github.com/users/sh-pan/orgs","repos_url":"https://api.github.com/users/sh-pan/repos","events_url":"https://api.github.com/users/sh-pan/events{/privacy}","received_events_url":"https://api.github.com/users/sh-pan/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-04-12T08:30:24Z","updated_at":"2018-04-12T12:47:04Z","closed_at":null,"author_association":"NONE","body":"Hi there, \r\nI am using hotbit for parametrization of Cu-M (where M is another transition metal). \r\nI am able to get  the .elm and Slako tables with no repulsion. \r\nHowever, when I try the fourth step of repulsion fitting, I end up with the following error.\r\n\r\n\"\r\nFitting repulsion curve between Cu and Cu\r\n\r\nAdding a scalable system ['Cu', 'Cu'] with 1 bonds at R=2.4900.\r\n\r\nAppending energy curve data from dimer_curve.traj...\r\nTraceback (most recent call last):\r\n  File \"CuCu-repfit.py\", line 37, in <module>\r\n    rep.append_energy_curve(weight=1.0,calc=calc0,traj='dimer_curve.traj',comment='dimer curve')\r\n  File \"/home/sha/hotbit/hotbit/parametrization/fitting.py\", line 554, in append_energy_curve\r\n    traj = Trajectory(traj)\r\n  File \"/home/sha/ase/ase/io/trajectory.py\", line 48, in Trajectory\r\n    return TrajectoryReader(filename)\r\n  File \"/home/sha/ase/ase/io/trajectory.py\", line 217, in __init__\r\n    self._open(filename)\r\n  File \"/home/sha/ase/ase/io/trajectory.py\", line 222, in _open\r\n    self.backend = ulm.open(filename, 'r')\r\n  File \"/home/sha/ase/ase/io/ulm.py\", line 78, in open\r\n    return Reader(filename, index or 0)\r\n  File \"/home/sha/ase/ase/io/ulm.py\", line 346, in __init__\r\n    fd = builtins.open(fd, 'rb')\r\nIOError: [Errno 2] No such file or directory: 'dimer_curve.traj'\r\n\r\n\"\r\nI am not sure what is going wrong. Could someone help me solve this error? \r\n\r\nThanks\r\nSha"},"comment":{"url":"https://api.github.com/repos/pekkosk/hotbit/issues/comments/380792658","html_url":"https://github.com/pekkosk/hotbit/issues/20#issuecomment-380792658","issue_url":"https://api.github.com/repos/pekkosk/hotbit/issues/20","id":380792658,"user":{"login":"sh-pan","id":38124087,"avatar_url":"https://avatars2.githubusercontent.com/u/38124087?v=4","gravatar_id":"","url":"https://api.github.com/users/sh-pan","html_url":"https://github.com/sh-pan","followers_url":"https://api.github.com/users/sh-pan/followers","following_url":"https://api.github.com/users/sh-pan/following{/other_user}","gists_url":"https://api.github.com/users/sh-pan/gists{/gist_id}","starred_url":"https://api.github.com/users/sh-pan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sh-pan/subscriptions","organizations_url":"https://api.github.com/users/sh-pan/orgs","repos_url":"https://api.github.com/users/sh-pan/repos","events_url":"https://api.github.com/users/sh-pan/events{/privacy}","received_events_url":"https://api.github.com/users/sh-pan/received_events","type":"User","site_admin":false},"created_at":"2018-04-12T12:47:04Z","updated_at":"2018-04-12T12:47:04Z","author_association":"NONE","body":"Hi Pekkosk, Thanks for theimmediate reply. \r\nThe dimer_curve.traj file was in a different folder, which was then changed to the present folder.\r\nNow, when I try the next steps of appending energy curve data (homogeneous cluster-similar to Au12, as Au is 5d10 6s1 and Cu is 3d10 4s1), I end up with the following:\r\n\r\n\">>> rep.append_homogeneous_cluster(weight=1.0,calc=calc2,atoms='Cu12-.xyz')\r\n    No forces (equilibrium cluster)\r\n/home/sha/hotbit/hotbit/containers/bravais.py:28: RuntimeWarning: invalid value encountered in double_scalars\r\n  a12 = np.dot(cell[0],cell[1])/(d[0]*d[1])\r\n/home/sha/hotbit/hotbit/containers/bravais.py:29: RuntimeWarning: invalid value encountered in double_scalars\r\n  a13 = np.dot(cell[0],cell[2])/(d[0]*d[2])\r\n/home/sha/hotbit/hotbit/containers/bravais.py:30: RuntimeWarning: invalid value encountered in double_scalars\r\n  a23 = np.dot(cell[1],cell[2])/(d[1]*d[2])\r\nTraceback (most recent call last):\r\n  File \"<stdin>\", line 1, in <module>\r\n  File \"/home/sha/hotbit/hotbit/parametrization/fitting.py\", line 638, in append_homogeneous_cluster\r\n    print(\"\\nAppending homogeneous cluster %s...\" % atoms.get_name(), file=self.txt)\r\nAttributeError: 'Atoms' object has no attribute 'get_name'\r\n\"\r\n\r\nI guess this is to do with ase. Not sure exactly.\r\n\r\n"}}
{"actor":{"display_login":"sh-pan"}}