{"action":"created","issue":{"url":"https://api.github.com/repos/atztogo/phonopy/issues/71","repository_url":"https://api.github.com/repos/atztogo/phonopy","labels_url":"https://api.github.com/repos/atztogo/phonopy/issues/71/labels{/name}","comments_url":"https://api.github.com/repos/atztogo/phonopy/issues/71/comments","events_url":"https://api.github.com/repos/atztogo/phonopy/issues/71/events","html_url":"https://github.com/atztogo/phonopy/issues/71","id":332409742,"node_id":"MDU6SXNzdWUzMzI0MDk3NDI=","number":71,"title":"Siesta reading discards LatticeVector units for non-Bohr unit","user":{"login":"zerothi","id":4789793,"node_id":"MDQ6VXNlcjQ3ODk3OTM=","avatar_url":"https://avatars1.githubusercontent.com/u/4789793?v=4","gravatar_id":"","url":"https://api.github.com/users/zerothi","html_url":"https://github.com/zerothi","followers_url":"https://api.github.com/users/zerothi/followers","following_url":"https://api.github.com/users/zerothi/following{/other_user}","gists_url":"https://api.github.com/users/zerothi/gists{/gist_id}","starred_url":"https://api.github.com/users/zerothi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zerothi/subscriptions","organizations_url":"https://api.github.com/users/zerothi/orgs","repos_url":"https://api.github.com/users/zerothi/repos","events_url":"https://api.github.com/users/zerothi/events{/privacy}","received_events_url":"https://api.github.com/users/zerothi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-06-14T13:44:52Z","updated_at":"2018-06-15T06:52:50Z","closed_at":null,"author_association":"NONE","body":"When using phonopy to create the displacement table for Siesta I find that it only corrects the positions depending on the LatticeConstant, and not the LatticeVectors.\r\n\r\nI.e. when it writes out the supercell afterwards the fractional coordinates are *correct* while the supercell becomes too small.\r\n\r\nThanks for this great software!"},"comment":{"url":"https://api.github.com/repos/atztogo/phonopy/issues/comments/397530645","html_url":"https://github.com/atztogo/phonopy/issues/71#issuecomment-397530645","issue_url":"https://api.github.com/repos/atztogo/phonopy/issues/71","id":397530645,"node_id":"MDEyOklzc3VlQ29tbWVudDM5NzUzMDY0NQ==","user":{"login":"zerothi","id":4789793,"node_id":"MDQ6VXNlcjQ3ODk3OTM=","avatar_url":"https://avatars1.githubusercontent.com/u/4789793?v=4","gravatar_id":"","url":"https://api.github.com/users/zerothi","html_url":"https://github.com/zerothi","followers_url":"https://api.github.com/users/zerothi/followers","following_url":"https://api.github.com/users/zerothi/following{/other_user}","gists_url":"https://api.github.com/users/zerothi/gists{/gist_id}","starred_url":"https://api.github.com/users/zerothi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zerothi/subscriptions","organizations_url":"https://api.github.com/users/zerothi/orgs","repos_url":"https://api.github.com/users/zerothi/repos","events_url":"https://api.github.com/users/zerothi/events{/privacy}","received_events_url":"https://api.github.com/users/zerothi/received_events","type":"User","site_admin":false},"created_at":"2018-06-15T06:52:50Z","updated_at":"2018-06-15T06:52:50Z","author_association":"NONE","body":"Dear @atztogo and @henriquemiranda \r\n\r\nI have found the bug.\r\n\r\nThe errors come up with these files:\r\n\r\n`Ang.fdf`:\r\n```bash\r\nLatticeConstant 1. Ang\r\n%block LatticeVectors\r\n 1.00000000 0.00000000 0.00000000\r\n 0.00000000 10.00000000 0.00000000\r\n 0.00000000 0.00000000 10.00000000\r\n%endblock LatticeVectors\r\n\r\nNumberOfAtoms 1\r\nAtomicCoordinatesFormat Ang\r\n%block AtomicCoordinatesAndAtomicSpecies\r\n 0.50000000 0.50000000 0.50000000 1 # 1\r\n%endblock AtomicCoordinatesAndAtomicSpecies\r\n```\r\n\r\n`Bohr.fdf`\r\n```bash\r\nLatticeConstant 1. Bohr\r\n%block LatticeVectors\r\n 1.88972688 0.00000000 0.00000000\r\n 0.00000000 18.89726878 0.00000000\r\n 0.00000000 0.00000000 18.89726878\r\n%endblock LatticeVectors\r\n\r\nNumberOfAtoms 1\r\nAtomicCoordinatesFormat Bohr\r\n%block AtomicCoordinatesAndAtomicSpecies\r\n 0.94486344 0.94486344 0.94486344 1 # 1\r\n%endblock AtomicCoordinatesAndAtomicSpecies\r\n```\r\n\r\n\r\n`Fractional.fdf`:\r\nLatticeConstant 1. Ang\r\n%block LatticeVectors\r\n 1.00000000 0.00000000 0.00000000\r\n 0.00000000 10.00000000 0.00000000\r\n 0.00000000 0.00000000 10.00000000\r\n%endblock LatticeVectors\r\n\r\nNumberOfAtoms 1\r\nAtomicCoordinatesFormat Fractional\r\n%block AtomicCoordinatesAndAtomicSpecies\r\n 0.50000000 0.05000000 0.05000000 1 # 1\r\n%endblock AtomicCoordinatesAndAtomicSpecies\r\n```\r\n\r\nin which case only `Bohr.fdf` produces the correct `supercell.fdf`.\r\nThey were converted using:\r\n\r\n    phonopy --siesta -d --dim=\"2 1 1\" -c ../<>.fdf\r\n\r\nand each checked.\r\n\r\nI have a fix that I will submit. But perhaps you may want to add these as tests?"}}
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