UtilsΒΆ

Here, we report a list of the subroutines included in the directory utils/ along with a brief comment on what is their purpose.

Note

These programs are useful for cleaving pre/post processing calculations (e.g., extracting and averaging useful quantities). These small programs are given without warranty

  • TzerogatherEn.sh: Extract the value of \(\gamma\) as difference in energy for a zero temperature LJ crystal at different strains

  • Tzerogathermin.sh: Extract the value of \(\gamma\) from step3 for a zero temperature LJ crystal at different strains

  • allgatheresults.sh: Collect work in all the four steps, for different run of cleaving, at different temperature, with different crystal orientation and different cleaving potential in a LJ crystal

  • athenawork.sh: Collect work in all the four steps for a LJ crystal, version to be used in a queue system to run the postprocessing as a batch job

  • blockAv.py: Script to calculate block average and some statistics of a list of measurements

  • c3cryst.f90: Rewrite the file inters3.* obtained in step3 in a format similar to step1/2/4 to be read using the same subroutines used for these steps. Valid for zero temperature LJ crystals

  • c3cryst_wells.f90: Same as c3cryst.f90, to be used with wells cleaving potential

  • calcintegrals.f90: Trapezoidal rule to calculate work integrals

  • calcworkstep3.f90: Same as c3cryst.f90, valid for solid-liquid interfaces in a LJ crystal

  • calcworkstep3_nodupl.f90: Same as calcworkstep3.f90, do not consider the duplicate atoms in step3

  • check_sim.sh: Check if the simulation in a queue system are still running or if they have stopped before the end of the calculation completed

  • cleaving.sh: Automated script to run the entire cleaving model for a solid-liquid interface. It needs preparation.sh

  • compile.sh: Compile the fortran subroutines in the utils/ directory

  • dump2.data.sh: Convert dump configuration to data file. It needs dump2data.f90

  • dump2.data.sh: Convert dump configuration to data file. It is called by dump2data.f90

  • fixedlayer.f90: Create a block of FCC crystal with certain orientation

  • gatherwork.sh: Check if cleaving calculation is running, if not, it collects the work file at each step

  • multiple_sim.sh: Submit cleaving calculations in different condition to a queue system

  • new_step3IN.f90: Create input file for step3 in a LJ crystal

  • preparation.sh: Script called by cleaving.sh to initialize the different directories used for cleaving

  • pressureprofile.sh: Script to calculate the ensemble average of the pressure (stress) profile in a box

  • remove.sh: Clean directory

  • restartmann.sh: restart cleaving calculation on a queue system (written for mannitol system)

  • runcleav.sh: Submit a new cleaving calculation or restart it to a queue system

  • runcleavcry.sh: Same as cleaving.sh but for a solid-vacuum LJ crystal at finite temperature

  • runzerocleavcry.sh: Same as runcleavcry.sh but for a system at zero temperature

  • s3zeroinpljcry.sh: Set up step3 for solid-vacuum interface for a LJ crystal at zero temperature

  • s4inpljcry.sh: Set up step4 for solid-vacuum interface for a LJ crystal

  • selwall.sh: Calculate work separately for the two pairs of walls in step4

  • singleres.sh: Calculate work in all the steps for a single configuration of the inputs (e.g., orientation, temperature) for walls cleaving potential

  • singleres_wells.sh: Same as singleres.sh but for wells cleaving potential

  • step3IN.f90: Create input file for step3 in a LJ crystal

  • step4IN.f90: Create input file for step4 in a LJ crystal

  • submit.sh: Submit a range of cleaving calculation as batch jobs

  • work.sh: Calculate block average of the work at each step of cleaving for a LJ system

  • work_new_s4.sh: Same as work.sh but modified to give the work for each pairs of walls separately

  • work_s3.sh: Same as work, modified with to use a different convention for the fixes name identifying the cleaving work

  • workmannitol.sh: Same as work.sh but modified for mannitol system