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Unformatted (binary) checkpointing #558

Merged
merged 63 commits into from
Sep 25, 2023
Merged

Unformatted (binary) checkpointing #558

merged 63 commits into from
Sep 25, 2023

Commits on Sep 25, 2023

  1. Simplify formatted state writing

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  2. Remove trivial derivations of base-class functions

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  3. Initial implementation of memory_stream class

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  4. Add missing const accessors

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  5. Abstract the stream operators for colvarvalue

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  6. Formatting tweaks

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  7. Add unit test for memory stream

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  8. Work around incomplete C++11 compliance for old GCC

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  9. Refine compiler selection to address overlap between Clang and GCC ma… 

    …cros

1. Clang defines __GNUC__

2. Older Clang versions do not support std::trivially_copyable yet, but
   the most recent ones deprecate __has_trivial_copy
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  10. MSVC fixes

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  11. Add template specializations to ignore formatting operators

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  12. Do not specify the starting point if not needed

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  13. Move specializations to source file

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  14. Make memory_stream compatible with STL streams in templates

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  15. Unformatted I/O for colvar objects

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  16. Implement read_block() for unformatted input streams

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  17. Separate checking the name of the colvar from reading its state data

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  18. Unformatted I/O for grid objects

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  19. Remove duplicate specialization specific to Visual Studio and Sun com… 

    …piler
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  20. Unformatted I/O for colvarbias base class

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  21. Unformatted I/O for colvarbias_abf and colvarbias_histogram

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  22. More formatting functions being ignored

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  23. Unformatted I/O for colvarbias_ti

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  24. Remove obsolete code block

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  25. Forward declare STL streams in colvargrid template

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  26. Small fixes

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  27. Remove declarations of functions that were never defined

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  28. Simplify and improve error handling

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  29. More forward declarations of STL streams

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  30. Unformatted I/O for reweightAMD

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  31. Condense and simplify metadynamics state reading

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  32. Refactor formatted I/O for metadynamics before adding unformatted ver… 

    …sion
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  33. Unformatted state I/O for metadynamics

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  34. Ensure that a string object is written

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  35. Unformatted I/O for colvarmodule

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  36. Always allow seeking in a memory buffer

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  37. Stop using preprocessor macros for return codes

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  38. Open text files in binary mode (we are not using EOL conversion anyway)

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  39. Remove check no longer needed after #537

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  40. Enable binary restarts from environment variable

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  41. Fix forgotten renaming of functions

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  42. Remove non-essential debug call to avoid segfault

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  43. Embed unformatted state in LAMMPS restart file

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  44. Remove now unneeded LAMMPS proxy wrappers

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  45. Auto-detect unformatted vs. formatted input

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  46. Cosmetic changes

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  47. Add warning about mismatched binary state versions

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  48. Ignore unformatted input state buffer (e.g. LAMMPS restart) if explic… 

    …it input state is defined
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  49. Only write output state if the prefix is not null

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  50. Clarify that an empty output prefix is allowed in LAMMPS

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  51. Document binary vs. formatted state file format

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  52. Remove last instance of #include <iostream> in widely included header

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  53. Move include to where it is required

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  54. More consistent naming of stream I/O template functions

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  55. Silence redundant Clang analyzer warning

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  56. Support external output buffer in memory_stream

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  57. Silence compiler warning

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  58. Add wrapper code to serialize/deserialize to std::vector<unsigned char>

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  59. Simplify test

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  60. Expand doc on binary restart 

    in addition, a general round of spelling fixes
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  61. Further improve doc

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  62. Fix incomplete sections

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  63. Mini-edit in doc

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