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Implement Mdtraj-hdf5 format #108

Merged
merged 33 commits into from
Jul 21, 2023
Merged

Implement Mdtraj-hdf5 format #108

merged 33 commits into from
Jul 21, 2023

Commits on Jun 21, 2023

  1. added highfive as dependency

    @agrossfield
    agrossfield committed Jun 21, 2023
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Commits on Jun 22, 2023

  1. add test prog to build list

    @agrossfield
    agrossfield committed Jun 22, 2023
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Commits on Jun 23, 2023

  1. totally non-functional

    @agrossfield
    agrossfield committed Jun 23, 2023
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  2. going to give up on HighFive, storing

    @agrossfield
    agrossfield committed Jun 23, 2023
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  3. build broken

    @agrossfield
    agrossfield committed Jun 23, 2023
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Commits on Jun 24, 2023

  1. Builds under ubuntu...

    @tromo
    tromo committed Jun 24, 2023
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Commits on Jun 26, 2023

  1. link against boost::json

    @agrossfield
    agrossfield committed Jun 26, 2023
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  2. find_package boost json

    @agrossfield
    agrossfield committed Jun 26, 2023
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  3. parsing works, converting to string sorta

    @agrossfield
    agrossfield committed Jun 26, 2023
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Commits on Jun 27, 2023

  1. successfully read the topology

    @agrossfield
    agrossfield committed Jun 27, 2023
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  2. successfully reads topology!

    @agrossfield
    agrossfield committed Jun 27, 2023
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  3. removed comments

    @agrossfield
    agrossfield committed Jun 27, 2023
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  4. preliminary reading box dimensions

    @agrossfield
    agrossfield committed Jun 27, 2023
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  5. can read box size for arbitrary frame

    @agrossfield
    agrossfield committed Jun 27, 2023
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  6. can read individual coordinate frames

    @agrossfield
    agrossfield committed Jun 27, 2023
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Commits on Jun 28, 2023

  1. preliminary setup for MDTraj class

    @agrossfield
    agrossfield committed Jun 28, 2023
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  2. added mdtraj.* to build dependencies

    @agrossfield
    agrossfield committed Jun 28, 2023
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  3. compiles, so it must be right, all pieces present

    @agrossfield
    agrossfield committed Jun 28, 2023
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  4. add a missing exception

    @agrossfield
    agrossfield committed Jun 28, 2023
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  5. mdtraj.i breaks swig, temporarily removed

    @agrossfield
    agrossfield committed Jun 28, 2023
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  6. builds, get H5::FileIException on read

    @agrossfield
    agrossfield committed Jun 28, 2023
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Commits on Jun 29, 2023

  1. success reading topology and bonds

    @agrossfield
    agrossfield committed Jun 29, 2023
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  2. compiles, so it must be right

    @agrossfield
    agrossfield committed Jun 29, 2023
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  3. interim commit, reading crashes

    @agrossfield
    agrossfield committed Jun 29, 2023
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Commits on Jun 30, 2023

  1. trajectory reading works

    @agrossfield
    agrossfield committed Jun 30, 2023
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  2. MDTraj reads first coords on read

    @agrossfield
    agrossfield committed Jun 30, 2023
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  3. updated createTrajectory

    @agrossfield
    agrossfield committed Jun 30, 2023
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  4. check if system is periodic

    @agrossfield
    agrossfield committed Jun 30, 2023
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  5. fixed logic to recognize end of file

    @agrossfield
    agrossfield committed Jun 30, 2023
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  6. forgot to take out highfive dependency

    @agrossfield
    agrossfield committed Jun 30, 2023
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Commits on Jul 10, 2023

  1. add hdf5 to conda_build script

    @agrossfield
    agrossfield committed Jul 10, 2023
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Commits on Jul 12, 2023

  1. replaced alloc on frame read with single alloc

    @agrossfield
    agrossfield committed Jul 12, 2023
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Commits on Jul 20, 2023

  1. final cleanup before merge -- remove tests

    @agrossfield
    agrossfield committed Jul 20, 2023
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