Increase use of SafeFilePtr class

[akohlmey]

Summary

The SafeFilePtr class will automatically close files when their file pointer goes out of scope.
This helps to simplify code. This pull request expands the usage and adds to the documentation.

Author(s)

Axel Kohlmeyer, Temple U

Licensing

By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).

Artificial Intelligence (AI) Tools Usage

A first draft of some of the additional uses was generated by Claude Opus 4.6.
The more complex changes were done manually.

Backward Compatibility

No known issues.

Implementation Notes

This extends the existing class to include a flag if a FILE * needs to be closed with pclose() instead of fclose() to avoid file descriptor leaks.

Post Submission Checklist

• The feature or features in this pull request is complete
• Licensing information is complete
• Corresponding author information is complete
• The source code follows the LAMMPS formatting guidelines
• Suitable new documentation files and/or updates to the existing docs are included
• The added/updated documentation is integrated and tested with the documentation build system
• The feature has been verified to work with the conventional build system
• The feature has been verified to work with the CMake based build system

[Copilot]

Pull request overview

This PR expands adoption of the SafeFilePtr RAII wrapper across LAMMPS to simplify FILE* lifetime management and reduce file descriptor leaks, and extends the wrapper to support pclose() for streams opened via popen() (e.g., on-the-fly compression).

Changes:

• Extend SafeFilePtr with a pclose() option and move destructor/assignment logic into a new safe_pointers.cpp.
• Replace many FILE* members/locals with SafeFilePtr and remove corresponding manual fclose()/pclose() calls.
• Add developer documentation and Doxygen input integration for SafeFilePtr.

Reviewed changes

Copilot reviewed 77 out of 77 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
src/write_restart.h	Replace FILE* member with SafeFilePtr.
src/write_restart.cpp	Use RAII close (fp=nullptr) and add earlier I/O error reduction.
src/write_data.h	Replace FILE* member with SafeFilePtr.
src/write_data.cpp	Use SafeFilePtr and mark compressed output for pclose().
src/write_coeff.cpp	Use SafeFilePtr for temp/output coeff files.
src/variable.h	Replace FILE* member with SafeFilePtr for VarReader.
src/variable.cpp	Use SafeFilePtr for several temporary/utility file opens.
src/universe.cpp	Use SafeFilePtr in reorder file reading.
src/safe_pointers.h	Extend/document SafeFilePtr (including pclose() support).
src/safe_pointers.cpp	New: implementation of SafeFilePtr destructor/assignment with pclose() support.
src/reader.h	Replace FILE* with SafeFilePtr; remove explicit compressed member.
src/reader.cpp	Use SafeFilePtr for compressed/uncompressed open/close.
src/read_restart.h	Replace FILE* member with SafeFilePtr.
src/read_restart.cpp	Remove manual fclose() in favor of SafeFilePtr reset.
src/read_data.h	Replace FILE* member with SafeFilePtr; drop compressed flag.
src/read_data.cpp	Use SafeFilePtr and mark compressed reads for pclose().
src/procmap.cpp	Use SafeFilePtr and improve custom-grid error messages.
src/platform.cpp	Use SafeFilePtr in file readability/writability helpers.
src/pair.cpp	Use SafeFilePtr for pair-table writing.
src/molecule.h	Replace FILE* member with SafeFilePtr.
src/molecule.cpp	Remove manual fclose() calls; minor formatting and rename print() parameter.
src/min_hftn.h	Replace progress FILE* with SafeFilePtr; remove explicit close helper decl.
src/min_hftn.cpp	Remove explicit fclose() management for progress file.
src/label_map.cpp	Use SafeFilePtr for label map writing.
src/fix_print.h	Replace FILE* member with SafeFilePtr.
src/fix_print.cpp	Remove manual fclose() in destructor; rely on RAII.
src/fix_ave_time.h	Replace FILE* member with SafeFilePtr.
src/fix_ave_time.cpp	Rely on RAII close; keep YAML trailer write logic.
src/fix_ave_histo.h	Replace FILE* member with SafeFilePtr.
src/fix_ave_histo.cpp	Remove manual fclose() in destructor.
src/fix_ave_correlate.h	Replace FILE* member with SafeFilePtr.
src/fix_ave_correlate.cpp	Remove manual fclose() in destructor.
src/fix_ave_chunk.h	Replace FILE* member with SafeFilePtr.
src/fix_ave_chunk.cpp	Remove manual fclose() in destructor.
src/dump.h	Replace FILE* member with SafeFilePtr.
src/dump.cpp	Remove manual close logic; use RAII and fp=nullptr on multifile writes.
src/citeme.h	Replace FILE* member with SafeFilePtr.
src/citeme.cpp	Remove manual fclose() in destructor.
src/balance.h	Replace FILE* member with SafeFilePtr.
src/balance.cpp	Remove manual fclose() in destructor.
src/RIGID/fix_rigid.cpp	Use SafeFilePtr for rigid restart sidecar file write.
src/PYTHON/python_impl.cpp	Use SafeFilePtr for Python file execution.
src/PHONON/fix_phonon.cpp	Use SafeFilePtr for map/binary output files.
src/ORIENT/fix_orient_fcc.cpp	Use SafeFilePtr for reading orientation data files.
src/ORIENT/fix_orient_eco.cpp	Use SafeFilePtr for reading orientation data file.
src/ORIENT/fix_orient_bcc.cpp	Use SafeFilePtr for reading orientation data files.
src/ML-SNAP/pair_snap.cpp	Use SafeFilePtr for SNAP coeff/param reads.
src/ML-RANN/pair_rann.cpp	Use SafeFilePtr for RANN potential file reads.
src/ML-POD/pair_pod.cpp	Use SafeFilePtr for binary debug outputs.
src/ML-POD/fitpod_command.cpp	Use SafeFilePtr for POD training IO and binary outputs.
src/ML-POD/eapod.cpp	Use SafeFilePtr for POD model file reads.
src/ML-IAP/mliap_model_nn.cpp	Use SafeFilePtr for NN coeff reads.
src/ML-IAP/mliap_descriptor_snap.cpp	Use SafeFilePtr for SNAP param reads.
src/MBX/fix_mbx.cpp	Use SafeFilePtr for JSON existence check.
src/MANYBODY/pair_eim.cpp	Use SafeFilePtr for EIM potential read/parse.
src/MACHDYN/fix_smd_wall_surface.cpp	Use SafeFilePtr for triangle mesh file reads.
src/KOKKOS/pair_pod_kokkos.cpp	Use SafeFilePtr for POD Kokkos binary outputs.
src/KOKKOS/pair_exp6_rx_kokkos.cpp	Use SafeFilePtr for EXP6-RX file reads.
src/INTEL/pair_snap_intel.cpp	Use SafeFilePtr for SNAP Intel coeff/param reads.
src/GRAPHICS/fix_graphics_labels.cpp	Use SafeFilePtr for image file reads.
src/GRAPHICS/fix_graphics_isosurface.cpp	Use SafeFilePtr for isosurface output file writes (including compressed).
src/GRAPHICS/dump_image.cpp	Use RAII close via fp=nullptr for multifile outputs.
src/EXTRA-FIX/fix_ttm_mod.cpp	Use SafeFilePtr for electron temperature output.
src/EXTRA-FIX/fix_ttm_grid.cpp	Use SafeFilePtr for grid file reads.
src/EXTRA-FIX/fix_ttm.cpp	Use SafeFilePtr for electron temperature output.
src/EXTRA-DUMP/dump_xtc.cpp	Remove explicit fp=nullptr handling (XTC uses separate handle).
src/EXTRA-COMMAND/geturl.cpp	Use SafeFilePtr for output file in curl download.
src/DPD-REACT/pair_multi_lucy.cpp	Use SafeFilePtr for table file reads.
src/DPD-REACT/pair_exp6_rx.cpp	Use SafeFilePtr for EXP6-RX file reads.
src/DPD-REACT/fix_rx.cpp	Use SafeFilePtr for RX kinetics/parameter file reads.
src/DPD-REACT/fix_eos_table_rx.cpp	Use SafeFilePtr for EOS table reads.
src/BOCS/fix_bocs.cpp	Use SafeFilePtr for reading BOCS table file.
src/ADIOS/reader_adios.cpp	Use SafeFilePtr for adios2_config.xml existence/create.
src/ADIOS/dump_custom_adios.cpp	Use SafeFilePtr for adios2_config.xml existence/create.
src/ADIOS/dump_atom_adios.cpp	Use SafeFilePtr for adios2_config.xml existence/create.
doc/src/Developer_utils.rst	Add Safe pointer documentation section and navigation tweaks.
doc/doxygen/Doxyfile.in	Include safe_pointers.h in Doxygen input list.

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