{"action":"created","comment":{"url":"https://api.github.com/repos/paesanilab/potential_fitting/pulls/comments/216516897","pull_request_review_id":154015970,"id":216516897,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIxNjUxNjg5Nw==","diff_hunk":"@@ -11,64 +11,22 @@\n #\n # @author Ronak\n \n-import os\n-import sys\n-import shutil\n-\n-from configparser import ConfigParser\n-\n-from molecule import Molecule\n-import qcalc\n-\n-import gcn_runner\n-import config_loader\n-\n-import output_writer\n-\n-config = config_loader.load()\n-filenames, log_name = config_loader.process_files(config)\n-  \n-qcalc.init(config, log_name)\n-\n-with open(config['files']['input_geometry'], 'r') as input_file: \n-    molecule = Molecule(input_file.read())\n-\n-# Step 1\n-if config['config_generator'].getboolean('optimize'):  \n-    molecule, energy = qcalc.optimize(molecule, filenames, config)\n-        \n-    output_writer.write_optimized_geo(molecule, energy, filenames['optimized_geometry'])\n-\n-else:\n-    print(\"Optimized geometry already provided, skipping optimization.\\n\")\n-    \n-    try:\n-        shutil.copyfile(filenames['input_geometry'], filenames['optimized_geometry'])\n-    except:\n-        welp = \"it's the same file\"\n-\n-# Step 2\n-if 'input_normal_modes' not in config['files']:\n-    \n-    normal_modes, frequencies, red_masses = qcalc.frequencies(molecule, filenames, config)\n-    num_atoms = molecule.num_atoms\n-    dim_null = 3 * num_atoms - len(normal_modes)    \n-    \n-    output_writer.write_normal_modes(normal_modes, frequencies, red_masses, filenames['normal_modes'])\n-\n-else:\n-    print(\"Normal modes already provided, skipping frequency calculation.\\n\")\n-    \n-    try:\n-        shutil.copyfile(config['files']['input_normal_modes'], filenames['normal_modes'])\n-    except:\n-        welp = \"it's the same file\"\n-    \n-    with open(config['files']['input_normal_modes'], 'r') as input_file:\n-        contents = input_file.read()\n-        num_atoms = molecule.num_atoms\n-        dim_null = 3 * molecule.num_atoms - contents.count('normal mode')\n-\n-# Step 3\n-gcn_runner.generate(config, dim_null, num_atoms, filenames)\n-\n+import os, sys","path":"configuration_generator/src/nmcgen.py","position":65,"original_position":65,"commit_id":"d10aa2fec08ec8b4e2ceb628ed87d00a1b3af2d6","original_commit_id":"d10aa2fec08ec8b4e2ceb628ed87d00a1b3af2d6","user":{"login":"EthanBullVulpe","id":35387079,"node_id":"MDQ6VXNlcjM1Mzg3MDc5","avatar_url":"https://avatars1.githubusercontent.com/u/35387079?v=4","gravatar_id":"","url":"https://api.github.com/users/EthanBullVulpe","html_url":"https://github.com/EthanBullVulpe","followers_url":"https://api.github.com/users/EthanBullVulpe/followers","following_url":"https://api.github.com/users/EthanBullVulpe/following{/other_user}","gists_url":"https://api.github.com/users/EthanBullVulpe/gists{/gist_id}","starred_url":"https://api.github.com/users/EthanBullVulpe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/EthanBullVulpe/subscriptions","organizations_url":"https://api.github.com/users/EthanBullVulpe/orgs","repos_url":"https://api.github.com/users/EthanBullVulpe/repos","events_url":"https://api.github.com/users/EthanBullVulpe/events{/privacy}","received_events_url":"https://api.github.com/users/EthanBullVulpe/received_events","type":"User","site_admin":false},"body":"this file was reworked to use the new simplified 3-step process. Optimize geometry, then generate the normal modes, then generate the configurations.","created_at":"2018-09-11T00:44:55Z","updated_at":"2018-09-11T00:44:55Z","html_url":"https://github.com/paesanilab/potential_fitting/pull/85#discussion_r216516897","pull_request_url":"https://api.github.com/repos/paesanilab/potential_fitting/pulls/85","author_association":"COLLABORATOR","_links":{"self":{"href":"https://api.github.com/repos/paesanilab/potential_fitting/pulls/comments/216516897"},"html":{"href":"https://github.com/paesanilab/potential_fitting/pull/85#discussion_r216516897"},"pull_request":{"href":"https://api.github.com/repos/paesanilab/potential_fitting/pulls/85"}}},"pull_request":{"url":"https://api.github.com/repos/paesanilab/potential_fitting/pulls/85","id":214044230,"node_id":"MDExOlB1bGxSZXF1ZXN0MjE0MDQ0MjMw","html_url":"https://github.com/paesanilab/potential_fitting/pull/85","diff_url":"https://github.com/paesanilab/potential_fitting/pull/85.diff","patch_url":"https://github.com/paesanilab/potential_fitting/pull/85.patch","issue_url":"https://api.github.com/repos/paesanilab/potential_fitting/issues/85","number":85,"state":"open","locked":false,"title":"Configuration generator cleanup","user":{"login":"EthanBullVulpe","id":35387079,"node_id":"MDQ6VXNlcjM1Mzg3MDc5","avatar_url":"https://avatars1.githubusercontent.com/u/35387079?v=4","gravatar_id":"","url":"https://api.github.com/users/EthanBullVulpe","html_url":"https://github.com/EthanBullVulpe","followers_url":"https://api.github.com/users/EthanBullVulpe/followers","following_url":"https://api.github.com/users/EthanBullVulpe/following{/other_user}","gists_url":"https://api.github.com/users/EthanBullVulpe/gists{/gist_id}","starred_url":"https://api.github.com/users/EthanBullVulpe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/EthanBullVulpe/subscriptions","organizations_url":"https://api.github.com/users/EthanBullVulpe/orgs","repos_url":"https://api.github.com/users/EthanBullVulpe/repos","events_url":"https://api.github.com/users/EthanBullVulpe/events{/privacy}","received_events_url":"https://api.github.com/users/EthanBullVulpe/received_events","type":"User","site_admin":false},"body":"I cleaned up a lot of the code in config_generator/src. It now uses the new molecule class. Also, nmcgen.py, and a lot of files are no longer useful. I also integrated the new error messages and added more logging print statements.","created_at":"2018-09-07T21:29:58Z","updated_at":"2018-09-11T00:44:55Z","closed_at":null,"merged_at":null,"merge_commit_sha":"222af820ff4ed0391b360d2f74bbc8548f191a1e","assignee":{"login":"EthanBullVulpe","id":35387079,"node_id":"MDQ6VXNlcjM1Mzg3MDc5","avatar_url":"https://avatars1.githubusercontent.com/u/35387079?v=4","gravatar_id":"","url":"https://api.github.com/users/EthanBullVulpe","html_url":"https://github.com/EthanBullVulpe","followers_url":"https://api.github.com/users/EthanBullVulpe/followers","following_url":"https://api.github.com/users/EthanBullVulpe/following{/other_user}","gists_url":"https://api.github.com/users/EthanBullVulpe/gists{/gist_id}","starred_url":"https://api.github.com/users/EthanBullVulpe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/EthanBullVulpe/subscriptions","organizations_url":"https://api.github.com/users/EthanBullVulpe/orgs","repos_url":"https://api.github.com/users/EthanBullVulpe/repos","events_url":"https://api.github.com/users/EthanBullVulpe/events{/privacy}","received_events_url":"https://api.github.com/users/EthanBullVulpe/received_events","type":"User","site_admin":false},"assignees":[{"login":"EthanBullVulpe","id":35387079,"node_id":"MDQ6VXNlcjM1Mzg3MDc5","avatar_url":"https://avatars1.githubusercontent.com/u/35387079?v=4","gravatar_id":"","url":"https://api.github.com/users/EthanBullVulpe","html_url":"https://github.com/EthanBullVulpe","followers_url":"https://api.github.com/users/EthanBullVulpe/followers","following_url":"https://api.github.com/users/EthanBullVulpe/following{/other_user}","gists_url":"https://api.github.com/users/EthanBullVulpe/gists{/gist_id}","starred_url":"https://api.github.com/users/EthanBullVulpe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/EthanBullVulpe/subscriptions","organizations_url":"https://api.github.com/users/EthanBullVulpe/orgs","repos_url":"https://api.github.com/users/EthanBullVulpe/repos","events_url":"https://api.github.com/users/EthanBullVulpe/events{/privacy}","received_events_url":"https://api.github.com/users/EthanBullVulpe/received_events","type":"User","site_admin":false}],"requested_reviewers":[{"login":"agoetz","id":1117673,"node_id":"MDQ6VXNlcjExMTc2NzM=","avatar_url":"https://avatars1.githubusercontent.com/u/1117673?v=4","gravatar_id":"","url":"https://api.github.com/users/agoetz","html_url":"https://github.com/agoetz","followers_url":"https://api.github.com/users/agoetz/followers","following_url":"https://api.github.com/users/agoetz/following{/other_user}","gists_url":"https://api.github.com/users/agoetz/gists{/gist_id}","starred_url":"https://api.github.com/users/agoetz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/agoetz/subscriptions","organizations_url":"https://api.github.com/users/agoetz/orgs","repos_url":"https://api.github.com/users/agoetz/repos","events_url":"https://api.github.com/users/agoetz/events{/privacy}","received_events_url":"https://api.github.com/users/agoetz/received_events","type":"User","site_admin":false}],"requested_teams":[],"labels":[],"milestone":null,"commits_url":"https://api.github.com/repos/paesanilab/potential_fitting/pulls/85/commits","review_comments_url":"https://api.github.com/repos/paesanilab/potential_fitting/pulls/85/comments","review_comment_url":"https://api.github.com/repos/paesanilab/potential_fitting/pulls/comments{/number}","comments_url":"https://api.github.com/repos/paesanilab/potential_fitting/issues/85/comments","statuses_url":"https://api.github.com/repos/paesanilab/potential_fitting/statuses/d10aa2fec08ec8b4e2ceb628ed87d00a1b3af2d6","head":{"label":"EthanBullVulpe:configuration_generator_cleanup","ref":"configuration_generator_cleanup","sha":"d10aa2fec08ec8b4e2ceb628ed87d00a1b3af2d6","user":{"login":"EthanBullVulpe","id":35387079,"node_id":"MDQ6VXNlcjM1Mzg3MDc5","avatar_url":"https://avatars1.githubusercontent.com/u/35387079?v=4","gravatar_id":"","url":"https://api.github.com/users/EthanBullVulpe","html_url":"https://github.com/EthanBullVulpe","followers_url":"https://api.github.com/users/EthanBullVulpe/followers","following_url":"https://api.github.com/users/EthanBullVulpe/following{/other_user}","gists_url":"https://api.github.com/users/EthanBullVulpe/gists{/gist_id}","starred_url":"https://api.github.com/users/EthanBullVulpe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/EthanBullVulpe/subscriptions","organizations_url":"https://api.github.com/users/EthanBullVulpe/orgs","repos_url":"https://api.github.com/users/EthanBullVulpe/repos","events_url":"https://api.github.com/users/EthanBullVulpe/events{/privacy}","received_events_url":"https://api.github.com/users/EthanBullVulpe/received_events","type":"User","site_admin":false},"repo":{"id":129985282,"node_id":"MDEwOlJlcG9zaXRvcnkxMjk5ODUyODI=","name":"potential_fitting","full_name":"EthanBullVulpe/potential_fitting","owner":{"login":"EthanBullVulpe","id":35387079,"node_id":"MDQ6VXNlcjM1Mzg3M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