Add feature to print stress tensor components during MD

[d-rel82]

Summary

This pull request adds functionality to output the stress tensor alongside verbose output, enabling viscosity calculations using the Green-Kubo or Einstein relations.

Details

• Introduces a new keyword:

  • SAVE-STRESS controls whether the stress tensor is written during MD simulation.

• Writes components to the main output (.out) file as additional columns next to verbose out.

• Updates existing source files to integrate new functionality:

  • MOD_mdstuf.f includes new logical variable stresave.
  • mdinit.f checks if the SAVE-STRESS keyword is in the .key file.
  • pressure.f adds logic to calculate the stress tensor in NVT/NVE ensembles.
  • mdstat.f writes components to .out file.

Sample Output

Appears in the .out file:

SAVE-STRESS: The units of the stress tensor components are Atmospheres

 --- Tinker-HP: loading restart file for EtOH_rep01 system ---

 Molecular Dynamics Trajectory via Velocity Verlet Algorithm
     MD Step     E total   E Potential     E Kinetic       Temp       Pres     Stress(xx)     Stress(yy)     Stress(zz)     Stress(xy)     Stress(yz)     Stress(xz)
         1     4052.2025    -3911.2297     7963.4322     296.87     -65.05      -505.6220      -377.1029       687.5805      -271.1346         9.4270        49.8107
         2     4047.1898    -3968.8755     8016.0652     298.84    -141.67       -85.8715      -595.8872       256.7504      -161.0730       337.0726       280.8896
         3     4043.7029    -4012.5023     8056.2053     300.33    -257.10       159.3216      -777.0220      -153.5985      -102.2136       467.6862       362.6684
         4     4045.1988    -3993.1576     8038.3564     299.67    -319.47       241.5343      -834.2966      -365.6566       -84.6812       354.1359       260.8619
         5     4050.1036    -3937.8502     7987.9538     297.79    -335.75       205.0718      -809.6037      -402.7269       -77.7163        92.4782        65.1255

Performance

• Adds ~4% overhead.

Notes

Manuscript in preparation describing these modifications and a companion toolkit for viscosity calculations.

Happy to adjust anything to better align with project conventions. Thanks for your time and consideration.