Restart file collection + POD training

[siuwuncheung]

This PR implements the restart file collection for libROM snapshot/POD matrix generation. This PR also includes some groundworks for overall ROM workflow.

libROM snapshot generation at FOM simulation

If ROM.offline.save_librom_snapshot is set true, then the offline FOM simulation will generate libROM snapshot matrix files with ct.md_print_filename + "_mdstep" + std::to_string(mdstep) + "_orbital" + "." + std::to_string(rank), e.g.,
MD_mdstep1_snapshot.000000.

The libROM snapshot files will be generated at (md_iteration_ % ct.checkpoint) == 0.

ROM workflow main driver rom_main.cc and ROM workflow routines

• rom_main.cc will handle the entire workflow of ROM. Currently, only the restart file collection + POD training is implemented.
• The ROM workflow routines will be implemented in src/rom_workflows.h and src/rom_workflows.cc.
  • The restart file collection + POD training is implemented as readRestartFiles.
  • This does not require saving libROM snapshot file at offline FOM simulation. The standard mgmol restart files can be used for POD basis generation.

MGmol<OrbitalsType>::loadOrbitalFromRestartFile

MGmol<OrbitalsType>::loadOrbitalFromRestartFile reads the data from a restart file and generates a new OrbitalsType class.

• Currently in the main workflow, the loading process of a restart file is spread out throughout the entire workflow, not in a single routine.
• While OrbitalsType::read_func_hdf5 reads the wavefunction from the restart file, further manipulation is required with additional routines, at least the extrapolation if used.
• For the sake of safety, loadOrbitalFromRestartFile used most routines that are used if (ct.restart_info > 2).

Option description separated

• all the options described in src/main.cc are now moved into a separate header tools/OptionDescription.h. The ROM driver src/rom_main.cc shares the same option parsing routines.

ROM-related options/controls

• Control class has the ROM-related options all packed into one member variable ROMPrivateOption rom_pri_options. This member variable is private in order to prevent changes from outside.
• src/rom_Control.h will contain all enumeration/options related to ROM workflow.

Pointer initialization

• MGmol<OrbitalsType>::orbitals_extrapol_ and OrbitalsExtrapolation::orbitals_minus1_ are initialized as nullptr at class declaration. This is a change reflecting the issue nullptr initialization of pointer member variables in class definition #223 .

Minor changes

• Carbyne example is added.
• potential file is cherry-picked from the PR Add pseudo.C_ONCV_PBE_SG15 #222 .
• src/mgmol_config.h.in generates a compile-time header file, which has the libROM flag MGMOL_HAS_LIBROM. mgmol can be installed with/without libROM.
• src/tools/Signal_mgmol.h -> src/tools/mgmol_Signal.h

[dreamer2368]

@jeanlucf22 , this PR is still work-in-progress, but I'd like to ask you to review one function I drafted: MGmol<OrbitalsType>::loadOrbitalFromRestartFile. The function is defined in line 689 of src/md.cc.

The main intention with this function is to load wavefunctions from an existing restart file. Once the wavefunction data is loaded, we could convert/store the data into libROM matrix. This function will be called at least after MGmol<OrbitalsType>::setup.

Although, I'm not confident whether I put all the necessary routines in this function. Ultimately I should set up a unit test for this, but I just wanted to check with you if I missed something important or did not use some routines properly.

[jeanlucf22]

@jeanlucf22 , this PR is still work-in-progress, but I'd like to ask you to review one function I drafted: MGmol<OrbitalsType>::loadOrbitalFromRestartFile. The function is defined in line 689 of src/md.cc.

The main intention with this function is to load wavefunctions from an existing restart file. Once the wavefunction data is loaded, we could convert/store the data into libROM matrix. This function will be called at least after MGmol<OrbitalsType>::setup.

Although, I'm not confident whether I put all the necessary routines in this function. Ultimately I should set up a unit test for this, but I just wanted to check with you if I missed something important or did not use some routines properly.

Look at
https://github.com/LLNL/mgmol/blob/6dc6067436a51a6dd40ca145b1153bdacb0073a4/src/ExtendedGridOrbitals.cc#L781

This function loads the wavefunctions from an HDF5 file for the case OrbitalsType=ExtendedGridOrbitals. Would that fill your needs?

[dreamer2368]

This PR is rebased and replaced by a series of PRs #226, #228, #229 and #230.