{"action":"opened","issue":{"url":"https://api.github.com/repos/radical-cybertools/RepEx/issues/32","labels_url":"https://api.github.com/repos/radical-cybertools/RepEx/issues/32/labels{/name}","comments_url":"https://api.github.com/repos/radical-cybertools/RepEx/issues/32/comments","events_url":"https://api.github.com/repos/radical-cybertools/RepEx/issues/32/events","html_url":"https://github.com/radical-cybertools/RepEx/issues/32","id":89077694,"number":32,"title":"after adding math exp check, the exchange index seems not running right","user":{"login":"taisung","id":2932347,"avatar_url":"https://avatars.githubusercontent.com/u/2932347?v=3","gravatar_id":"","url":"https://api.github.com/users/taisung","html_url":"https://github.com/taisung","followers_url":"https://api.github.com/users/taisung/followers","following_url":"https://api.github.com/users/taisung/following{/other_user}","gists_url":"https://api.github.com/users/taisung/gists{/gist_id}","starred_url":"https://api.github.com/users/taisung/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/taisung/subscriptions","organizations_url":"https://api.github.com/users/taisung/orgs","repos_url":"https://api.github.com/users/taisung/repos","events_url":"https://api.github.com/users/taisung/events{/privacy}","received_events_url":"https://api.github.com/users/taisung/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-06-17T17:32:02Z","updated_at":"2015-06-17T17:32:02Z","closed_at":null,"body":"I added a check for overflow of exp() function in the file \"RepEx/src/radical/repex/md_kernels/md_kernel_3d_tuu.py\":\r\n\r\n            if item > math.log(sys.float_info.max) : new_item=sys.float_info.max\r\n            elif item < math.log(sys.float_info.min)  : new_item=0.0\r\n            else :\r\n               new_item = math.exp(item)\r\n\r\nNow the exchange step gives me the following error:\r\n\r\nTraceback (most recent call last):\r\n  File \"launch_simulation_pattern_b_3d_tuu.py\", line 53, in <module>\r\n    pilot_kernel.run_simulation( replicas, pilot_object, session, md_kernel )\r\n  File \"/usr/people/taisung/myenv/lib/python2.7/site-packages/pilot_kernels/pilot_kernel_pattern_b_multi_d.py\", line 356, in run_simulation\r\n    md_kernel.select_for_exchange(DIM, replicas, matrix_columns, current_cycle)\r\n  File \"/usr/people/taisung/myenv/lib/python2.7/site-packages/amber_kernels_3d_tuu/kernel_pattern_b_3d_tuu.py\", line 634, in select_for_exchange\r\n    self.do_exchange(dimension, current_group, swap_matrix)\r\n  File \"/usr/people/taisung/myenv/lib/python2.7/site-packages/amber_kernels_3d_tuu/kernel_pattern_b_3d_tuu.py\", line 552, in do_exchange\r\n    r_j = self.gibbs_exchange(r_i, replicas, swap_matrix)\r\n  File \"/usr/people/taisung/myenv/lib/python2.7/site-packages/md_kernels/md_kernel_3d_tuu.py\", line 158, in gibbs_exchange\r\n    r_j = replicas[j]\r\nTypeError: list indices must be integers, not NoneType\r\n"}}