{"action":"created","issue":{"url":"https://api.github.com/repos/alexvakimov/libra-gamess_interface/issues/9","repository_url":"https://api.github.com/repos/alexvakimov/libra-gamess_interface","labels_url":"https://api.github.com/repos/alexvakimov/libra-gamess_interface/issues/9/labels{/name}","comments_url":"https://api.github.com/repos/alexvakimov/libra-gamess_interface/issues/9/comments","events_url":"https://api.github.com/repos/alexvakimov/libra-gamess_interface/issues/9/events","html_url":"https://github.com/alexvakimov/libra-gamess_interface/pull/9","id":139414949,"number":9,"title":"Added some flags for debugging and a module for executing MD coupled to Nose-Hoover thermostat.","user":{"login":"kosukesato","id":16888714,"avatar_url":"https://avatars.githubusercontent.com/u/16888714?v=3","gravatar_id":"","url":"https://api.github.com/users/kosukesato","html_url":"https://github.com/kosukesato","followers_url":"https://api.github.com/users/kosukesato/followers","following_url":"https://api.github.com/users/kosukesato/following{/other_user}","gists_url":"https://api.github.com/users/kosukesato/gists{/gist_id}","starred_url":"https://api.github.com/users/kosukesato/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kosukesato/subscriptions","organizations_url":"https://api.github.com/users/kosukesato/orgs","repos_url":"https://api.github.com/users/kosukesato/repos","events_url":"https://api.github.com/users/kosukesato/events{/privacy}","received_events_url":"https://api.github.com/users/kosukesato/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-03-08T22:37:24Z","updated_at":"2016-03-09T15:01:56Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/alexvakimov/libra-gamess_interface/pulls/9","html_url":"https://github.com/alexvakimov/libra-gamess_interface/pull/9","diff_url":"https://github.com/alexvakimov/libra-gamess_interface/pull/9.diff","patch_url":"https://github.com/alexvakimov/libra-gamess_interface/pull/9.patch"},"body":"\\run.py\r\n\r\nAdded some flags for debugging and parameters for defining thermostat object.\r\n\r\n\\md1.py\r\n\r\nImplements a function which executes MD coupled to Nose-Hoover chain thermostat.\r\nThis is coded followed by the module Alexey coded.\r\nAlmost same as md.py except the lines related to thermostat object.\r\n\r\n\\ Functions in unpack_file module (detect.py, extract.py, etc...)\r\n\r\nAdded flags for debugging.\r\n\r\n\\run.manual\r\n\r\nAdded some flags and thermostat parameters."},"comment":{"url":"https://api.github.com/repos/alexvakimov/libra-gamess_interface/issues/comments/194334594","html_url":"https://github.com/alexvakimov/libra-gamess_interface/pull/9#issuecomment-194334594","issue_url":"https://api.github.com/repos/alexvakimov/libra-gamess_interface/issues/9","id":194334594,"user":{"login":"alexvakimov","id":8313721,"avatar_url":"https://avatars.githubusercontent.com/u/8313721?v=3","gravatar_id":"","url":"https://api.github.com/users/alexvakimov","html_url":"https://github.com/alexvakimov","followers_url":"https://api.github.com/users/alexvakimov/followers","following_url":"https://api.github.com/users/alexvakimov/following{/other_user}","gists_url":"https://api.github.com/users/alexvakimov/gists{/gist_id}","starred_url":"https://api.github.com/users/alexvakimov/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/alexvakimov/subscriptions","organizations_url":"https://api.github.com/users/alexvakimov/orgs","repos_url":"https://api.github.com/users/alexvakimov/repos","events_url":"https://api.github.com/users/alexvakimov/events{/privacy}","received_events_url":"https://api.github.com/users/alexvakimov/received_events","type":"User","site_admin":false},"created_at":"2016-03-09T15:01:56Z","updated_at":"2016-03-09T15:01:56Z","body":"Hi Kosuke,\r\n\r\nBefore I merge, please address the following:\r\n1) why do we need a separate file md1.py? please, move the new additions to the original file md.py \r\n2) in md.py - make the thermostat utilization optional (introduce options: NVE and NVT)\r\n3) when you set up the thermostat, look at the instructions: THERM.set_Nf_t(1); THERM.set_Nf_r(0); - here you should use the number of translational and rotational degrees of freedom in the molecular system\r\n4) when you rescale velocities, mol.p[0] = mol.p[0] * THERM.vel_scale(0.5*dt_nucl), you should rescale all of them (index in p[i] should run from 0 to 3N), not just 1 DOF (in my example i always considered 1D case, that is why i used only p[0])\r\n5) try running some reasonably long test (e.g. take several water molecules or some cluster) - see if you temperature really behaves as you expect, or at least reasonably close "}}