Basic Improvements

The following improvements were made:

1. The random number generator is appended to the end of the coord.d file. This ensures that after a restart, the same results are obtained as if the code would not have been stopped.
2. I gave control of flushing I/O back to the operating system.
3. I set the third Nordsieck parameter from the forces if it is undefined (i.e. all zero). This should reduce startup-transients.
4. I write output for the initial state too, as you would normally like. The program only did output after a step was taken.
5. I added a, currently trivial, subroutine step_end_hook, which can be used to perform desired custom output after each time step, or whatever.
6. I also wrote the potential energy per atom out to output.d.
7. I reduced the screen output frequency, but increased the amount of info written to the screen.
8. I put in smoothing of the cut-off in the rotational potential.
9. I put in removal of the jump in the Lennard-Jones potential.
10. The files are ready to run.

Files

Unzipping mdmod.zip will create a directory mdexe with the following modified or new files:

check_box.f

• Checks the box size to verify that atoms do not interact with more than one periodic image of another atom. This would make the code misbehave.

close.inc

• Added comments.
• Cleaned up.

common_files.inc

• Ready to run, set directories appropriately.
• Added common_leon.inc. (See below.)

common_leon.inc

• Common block for the random number generator data.

coord_read_hook.f

• Restores the random number generator from the data written to coord.d by coord_write_hook. (See below.)

coord_write_hook.f

• Writes out the random number generator state at the end of the coord.d file. This allows us to resume operation exactly where we left off.

flush.f

• Created a trivial subroutine flush. Let the operating system do it.

input.d

• Ready to run.
• Changed the comments a bit.

main.f

• Added two parameter modification subroutines.
• Checked the periodic box size.
• Initialized Nordsieck parameter R2 from the forces if it was zero.
• Write out initial state too.
• Added a subroutine step_end_hook, which is currently trivial but can be used to perform desired output after each time step.

open.inc

• Added comments.
• Cleaned up.

param_mod.f

• Change some key parameters more easily.

parameters.inc

• No changes. It is just a file you want to have available for changing.

random_numbers.f

• Added a link to setran_hook.f

read_write.f

• Added a link to coord_read_hook to read_data.
• Wrote also the potential energy per atom out to output.d in write_data2.
• Reduced screen output frequency, increased info in write_data2.
• Added a link to coord_write_hook to write_data3.

setin.f

• Changed the header printed in setmd to include potential energy.

setr2.f

• In order to reduce startup transients, sets Nordsieck parameter R2 from the forces if it is zero (which is what make_tube and chiral set it to.)

setran_hook.f

• Restore random number generator from coord.d. This allows you to break execution without affecting results.

step_end-hook.f

• Currently blank subroutine. Use it to do custom output at the end of time steps. Uncomment the include statement.

subroutines.inc

• Ready to run: commented out stuff that was not used and set directories.
• Added new subroutines to the list.

Note: I initially wanted to create a version of main.f without energy minimization and tight-binding, by making special crashing subroutines minimize_bo.f and tight_bind_bo.f. But since the executable was only 70 kb smaller, I concluded it was not worth it.