{"action":"created","comment":{"url":"https://api.github.com/repos/simphony/simphony-lammps-md/pulls/comments/23308127","id":23308127,"diff_hunk":"@@ -58,6 +61,33 @@ def get_set(file_name):\n wrapper = LammpsWrapper()\n wrapper.CM[CUBA.NUMBEROF_TIME_STEPS] = 10000\n wrapper.CM[CUBA.TIME_STEP] = 0.003\n+wrapper.CM[CUBA.PAIR_POTENTIALS] = (\"lj:\\n\"","path":"examples/flow/flow_pois.py","position":39,"original_position":39,"commit_id":"91cf1da6772f92536471820395e80f8637b6528d","original_commit_id":"91cf1da6772f92536471820395e80f8637b6528d","user":{"login":"ahashibon","id":6462558,"avatar_url":"https://avatars.githubusercontent.com/u/6462558?v=3","gravatar_id":"","url":"https://api.github.com/users/ahashibon","html_url":"https://github.com/ahashibon","followers_url":"https://api.github.com/users/ahashibon/followers","following_url":"https://api.github.com/users/ahashibon/following{/other_user}","gists_url":"https://api.github.com/users/ahashibon/gists{/gist_id}","starred_url":"https://api.github.com/users/ahashibon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ahashibon/subscriptions","organizations_url":"https://api.github.com/users/ahashibon/orgs","repos_url":"https://api.github.com/users/ahashibon/repos","events_url":"https://api.github.com/users/ahashibon/events{/privacy}","received_events_url":"https://api.github.com/users/ahashibon/received_events","type":"User","site_admin":false},"body":"Thanks for your questions, the more examples we have, and the more we implement the clearer it will get. \r\n","created_at":"2015-01-21T15:46:51Z","updated_at":"2015-01-21T15:46:51Z","html_url":"https://github.com/simphony/simphony-lammps-md/pull/5#discussion_r23308127","pull_request_url":"https://api.github.com/repos/simphony/simphony-lammps-md/pulls/5","_links":{"self":{"href":"https://api.github.com/repos/simphony/simphony-lammps-md/pulls/comments/23308127"},"html":{"href":"https://github.com/simphony/simphony-lammps-md/pull/5#discussion_r23308127"},"pull_request":{"href":"https://api.github.com/repos/simphony/simphony-lammps-md/pulls/5"}}},"pull_request":{"url":"https://api.github.com/repos/simphony/simphony-lammps-md/pulls/5","id":27764111,"html_url":"https://github.com/simphony/simphony-lammps-md/pull/5","diff_url":"https://github.com/simphony/simphony-lammps-md/pull/5.diff","patch_url":"https://github.com/simphony/simphony-lammps-md/pull/5.patch","issue_url":"https://api.github.com/repos/simphony/simphony-lammps-md/issues/5","number":5,"state":"open","locked":false,"title":"WIP: Feature particles in Lammps","user":{"login":"nathanfranklin","id":8287580,"avatar_url":"https://avatars.githubusercontent.com/u/8287580?v=3","gravatar_id":"","url":"https://api.github.com/users/nathanfranklin","html_url":"https://github.com/nathanfranklin","followers_url":"https://api.github.com/users/nathanfranklin/followers","following_url":"https://api.github.com/users/nathanfranklin/following{/other_user}","gists_url":"https://api.github.com/users/nathanfranklin/gists{/gist_id}","starred_url":"https://api.github.com/users/nathanfranklin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nathanfranklin/subscriptions","organizations_url":"https://api.github.com/users/nathanfranklin/orgs","repos_url":"https://api.github.com/users/nathanfranklin/repos","events_url":"https://api.github.com/users/nathanfranklin/events{/privacy}","received_events_url":"https://api.github.com/users/nathanfranklin/received_events","type":"User","site_admin":false},"body":"This PR contains a working wrapper which focuses on running LAMMPS using FILE-IO (i.e. we are using input files to control LAMMPS). \r\n\r\nSpecifically in this PR, we are limiting **at first** the scope of how the user can use the LAMMPS wrapper.   Only some specific LAMMPS configuration will be supported at first.  Additionally, this PR adds only support for particles (i.e the lammps-related implementation of the ABCParticleContainer interface only has particles.  bonds will be added in a later PR).\r\n\r\nThis is work-in-progress.  The following is the goal of this PR:\r\n- [x] wrapper : basic sd-related methods for just ParticleContainer (e.g. get_particle_container, iter_particle_containers)\r\n- [ ] wrapper:  subset of basic cm/sp/bc-related configuration\r\n- [x] particle container (only particles)\r\n- [ ] documentation\r\n\r\nNot included in this PR (but to be done in subsequent PRs) are:\r\n- More advanced cm/sp/bc-related configuration\r\n- Support of bonds in ParticleContainer\r\n- Support of Mesh (i.e.for walls in lammps)","created_at":"2015-01-21T14:43:43Z","updated_at":"2015-01-21T15:46:51Z","closed_at":null,"merged_at":null,"merge_commit_sha":null,"assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/simphony/simphony-lammps-md/pulls/5/commits","review_comments_url":"https://api.github.com/repos/simphony/simphony-lammps-md/pulls/5/comments","review_comment_url":"https://api.github.com/repos/simphony/simphony-lammps-md/pulls/comments/{number}","comments_url":"https://api.github.com/repos/simphony/simphony-lammps-md/issues/5/comments","statuses_url":"https://api.github.com/repos/simphony/simphony-lammps-md/statuses/91cf1da6772f92536471820395e80f8637b6528d","head":{"label":"simphony:feature_particles","ref":"feature_particles","sha":"91cf1da6772f92536471820395e80f8637b6528d","user":{"login":"simphony","id":8048249,"avatar_url":"https://avatars.githubusercontent.com/u/8048249?v=3","gravatar_id":"","url":"https://api.github.com/users/simphony","html_url":"https://github.com/simphony","followers_url":"https://api.github.com/users/simphony/followers","following_url":"https://api.github.com/users/simphony/following{/other_user}","gists_url":"https://api.github.com/users/simphony/gists{/gist_id}","starred_url":"https://api.github.com/users/simphony/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/simphony/subscriptions","organizations_url":"https://api.github.com/users/simphony/orgs","repos_url":"https://api.github.com/users/simphony/repos","events_url":"https://api.github.com/users/simphony/events{/privacy}","received_events_url":"https://api.github.com/users/simphony/received_events","type":"Organization","site_admin":false},"repo":{"id":23785654,"name":"simphony-lammps-md","full_name":"simphony/simphony-lammps-md","owner":{"login":"simphony","id":8048249,"avatar_url":"https://avatars.githubusercontent.com/u/8048249?v=3","gravatar_id":"","url":"https://api.github.com/users/simphony","html_url":"https://github.com/simphony","followers_url":"https://api.github.com/users/simphony/followers","following_url":"https://api.github.com/users/simphony/following{/other_user}","gists_url":"https://api.github.com/users/simphony/gists{/gist_id}","starred_url":"https://api.github.com/users/simphony/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/simphony/subscriptions","organizations_url":"https://api.github.com/users/simphony/orgs","repos_url":"https://api.github.com/users/simphony/repos","events_url":"https://api.github.com/users/simphony/events{/privacy}","received_events_url":"https://api.github.com/users/simphony/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/simphony/simphony-lammps-md","description":"The lammps md wrapper to the simphony framework ","fork":false,"url":"https://api.github.com/repos/simphony/simphony-lammps-md","forks_url":"https://api.github.com/repos/simphony/simphony-lammps-md/forks","keys_url":"https://api.github.com/repos/simphony/simphony-lammps-md/keys{/key_id}","collaborators_url":"https://api.github.com/repos/simphony/simphony-lammps-md/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/simphony/simphony-lammps-md/teams","hooks_url":"https://api.github.com/repos/simphony/simphony-lammps-md/hooks","issue_events_url":"https://api.github.com/repos/simphony/simphony-lammps-md/issues/events{/number}","events_url":"https://api.github.com/repos/simphony/simphony-lammps-md/events","assignees_url":"https://api.github.com/repos/simphony/simphony-lammps-md/assignees{/user}","branches_url":"https://api.github.com/repos/simphony/simphony-lammps-md/branches{/branch}","tags_url":"https://api.github.com/repos/simphony/simphony-lammps-md/tags","blobs_url":"https://api.github.com/repos/simphony/simphony-lammps-md/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/simphony/simphony-lammps-md/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/simphony/simphony-lammps-md/git/refs{/sha}","trees_url":"https://api.github.com/repos/simphony/simphony-lammps-md/git/trees{/sha}","statuses_url":"https://api.github.com/repos/simphony/simphony-lammps-md/statuses/{sha}","languages_url":"https://api.github.com/repos/simphony/simphony-lammps-md/languages","stargazers_url":"https://api.github.com/repos/simphony/simphony-lammps-md/stargazers","contributors_url":"https://api.github.com/repos/simphony/simphony-lammps-md/contributors","subscribers_url":"https://api.github.com/repos/simphony/simphony-lammps-md/subscribers","subscription_url":"https://api.github.com/repos/simphony/simphony-lammps-md/subscription","commits_url":"https://api.github.com/repos/simphony/simphony-lammps-md/commits{/sha}","git_commits_url":"https://api.github.com/repos/simphony/simphony-lammps-md/git/commits{/sha}","comments_url":"https://api.github.com/repos/simphony/simphony-lammps-md/comments{/number}","issue_comment_url":"https://api.github.com/repos/simphony/simphony-lammps-md/issues/comments/{number}","contents_url":"https://api.github.com/repos/simphony/simphony-lammps-md/contents/{+path}","compare_url":"https://api.github.com/repos/simphony/simphony-lammps-md/compare/{base}...{head}","merges_url":"https://api.github.com/repos/simphony/simphony-lammps-md/merges","archive_url":"https://api.github.com/repos/simphony/simphony-lammps-md/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/simphony/simphony-lammps-md/downloads","issues_url":"https://api.github.com/repos/simphony/simphony-lammps-md/issues{/number}","pulls_url":"https://api.github.com/repos/simphony/simphony-lammps-md/pulls{/number}","milestones_url":"https://api.github.com/repos/simphony/simphony-lammps-md/milestones{/number}","notifications_url":"https://api.github.com/repos/simphony/simphony-lammps-md/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/simphony/simphony-lammps-md/labels{/name}","releases_url":"https://api.github.com/repos/simphony/simphony-lammps-md/releases{/id}","created_at":"2014-09-08T09:43:18Z","updated_at":"2015-01-12T15:24:22Z","pushed_at":"2015-01-21T14:31:44Z","git_url":"git://github.com/simphony/simphony-lammps-md.git","ssh_url":"git@github.com:simphony/simphony-lammps-md.git","clone_url":"https://github.com/simphony/simphony-lammps-md.git","svn_url":"https://github.com/simphony/simphony-lammps-md","homepage":null,"size":388,"stargazers_count":1,"watchers_count":1,"language":null,"has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":0,"mirror_url":null,"open_issues_count":3,"forks":0,"open_issues":3,"watchers":1,"default_branch":"master"}},"base":{"label":"simphony:master","ref":"master","sha":"aea50d513b5203c7f317650f766d2360f60e5a83","user":{"login":"simphony","id":8048249,"avatar_url":"https://avatars.githubusercontent.com/u/8048249?v=3","gravatar_id":"","url":"https://api.github.com/users/simphony","html_url":"https://github.com/simphony","followers_url":"https://api.github.com/users/simphony/followers","following_url":"https://api.github.com/users/simphony/following{/other_user}","gists_url":"https://api.github.com/users/simphony/gists{/gist_id}","starred_url":"https://api.github.com/users/simphony/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/simphony/subscriptions","organizations_url":"https://api.github.com/users/simphony/orgs","repos_url":"https://api.github.com/users/simphony/repos","events_url":"https://api.github.com/users/simphony/events{/privacy}","received_events_url":"https://api.github.com/users/simphony/received_events","type":"Organization","site_admin":false},"repo":{"id":23785654,"name":"simphony-lammps-md","full_name":"simphony/simphony-lammps-md","owner":{"login":"simphony","id":8048249,"avatar_url":"https://avatars.githubusercontent.com/u/8048249?v=3","gravatar_id":"","url":"https://api.github.com/users/simphony","html_url":"https://github.com/simphony","followers_url":"https://api.github.com/users/simphony/followers","following_url":"https://api.github.com/users/simphony/following{/other_user}","gists_url":"https://api.github.com/users/simphony/gists{/gist_id}","starred_url":"https://api.github.com/users/simphony/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/simphony/subscriptions","organizations_url":"https://api.github.com/users/simphony/orgs","repos_url":"https://api.github.com/users/simphony/repos","events_url":"https://api.github.com/users/simphony/events{/privacy}","received_events_url":"https://api.github.com/users/simphony/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/simphony/simphony-lammps-md","description":"The lammps md wrapper to the simphony framework ","fork":false,"url":"https://api.github.com/repos/simphony/simphony-lammps-md","forks_url":"https://api.github.com/repos/simphony/simphony-lammps-md/forks","keys_url":"https://api.github.com/repos/simphony/simphony-lammps-md/keys{/key_id}","collaborators_url":"https://api.github.com/repos/simphony/simphony-lammps-md/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/simphony/simphony-lammps-md/teams","hooks_url":"https://api.github.com/repos/simphony/simphony-lammps-md/hooks","issue_events_url":"https://api.github.com/repos/simphony/simphony-lammps-md/issues/events{/number}","events_url":"https://api.github.com/repos/simphony/simphony-lammps-md/events","assignees_url":"https://api.github.com/repos/simphony/simphony-lammps-md/assignees{/user}","branches_url":"https://api.github.com/repos/simphony/simphony-lammps-md/branches{/branch}","tags_url":"https://api.github.com/repos/simphony/simphony-lammps-md/tags","blobs_url":"https://api.github.com/repos/simphony/simphony-lammps-md/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/simphony/simphony-lammps-md/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/simphony/simphony-lammps-md/git/refs{/sha}","trees_url":"https://api.github.com/repos/simphony/simphony-lammps-md/git/trees{/sha}","statuses_url":"https://api.github.com/repos/simphony/simphony-lammps-md/statuses/{sha}","languages_url":"https://api.github.com/repos/simphony/simphony-lammps-md/languages","stargazers_url":"https://api.github.com/repos/simphony/simphony-lammps-md/stargazers","contributors_url":"https://api.github.com/repos/simphony/simphony-lammps-md/contributors","subscribers_url":"https://api.github.com/repos/simphony/simphony-lammps-md/subscribers","subscription_url":"https://api.github.com/repos/simphony/simphony-lammps-md/subscription","commits_url":"https://api.github.com/repos/simphony/simphony-lammps-md/commits{/sha}","git_commits_url":"https://api.github.com/repos/simphony/simphony-lammps-md/git/commits{/sha}","comments_url":"https://api.github.com/repos/simphony/simphony-lammps-md/comments{/number}","issue_comment_url":"https://api.github.com/repos/simphony/simphony-lammps-md/issues/comments/{number}","contents_url":"https://api.github.com/repos/simphony/simphony-lammps-md/contents/{+path}","compare_url":"https://api.github.com/repos/simphony/simphony-lammps-md/compare/{base}...{head}","merges_url":"https://api.github.com/repos/simphony/simphony-lammps-md/merges","archive_url":"https://api.github.com/repos/simphony/simphony-lammps-md/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/simphony/simphony-lammps-md/downloads","issues_url":"https://api.github.com/repos/simphony/simphony-lammps-md/issues{/number}","pulls_url":"https://api.github.com/repos/simphony/simphony-lammps-md/pulls{/number}","milestones_url":"https://api.github.com/repos/simphony/simphony-lammps-md/milestones{/number}","notifications_url":"https://api.github.com/repos/simphony/simphony-lammps-md/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/simphony/simphony-lammps-md/labels{/name}","releases_url":"https://api.github.com/repos/simphony/simphony-lammps-md/releases{/id}","created_at":"2014-09-08T09:43:18Z","updated_at":"2015-01-12T15:24:22Z","pushed_at":"2015-01-21T14:31:44Z","git_url":"git://github.com/simphony/simphony-lammps-md.git","ssh_url":"git@github.com:simphony/simphony-lammps-md.git","clone_url":"https://github.com/simphony/simphony-lammps-md.git","svn_url":"https://github.com/simphony/simphony-lammps-md","homepage":null,"size":388,"stargazers_count":1,"watchers_count":1,"language":null,"has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":0,"mirror_url":null,"open_issues_count":3,"forks":0,"open_issues":3,"watchers":1,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/simphony/simphony-lammps-md/pulls/5"},"html":{"href":"https://github.com/simphony/simphony-lammps-md/pull/5"},"issue":{"href":"https://api.github.com/repos/simphony/simphony-lammps-md/issues/5"},"comments":{"href":"https://api.github.com/repos/simphony/simphony-lammps-md/issues/5/comments"},"review_comments":{"href":"https://api.github.com/repos/simphony/simphony-lammps-md/pulls/5/comments"},"review_comment":{"href":"https://api.github.com/repos/simphony/simphony-lammps-md/pulls/comments/{number}"},"commits":{"href":"https://api.github.com/repos/simphony/simphony-lammps-md/pulls/5/commits"},"statuses":{"href":"https://api.github.com/repos/simphony/simphony-lammps-md/statuses/91cf1da6772f92536471820395e80f8637b6528d"}}}}