New bonds created with fix bond/create not written out to data file

Hello,

I`ve been running simulations in which I use the fix bond/create and fix bond/delete commands on a particular type of atom pairs. To monitor the process of bond formation, I write down the output from the fixes to my output file and the cumulative number of bonds corresponds to more than 500 at the end of the simulation (as per the output of the fixbondc[2]). However, when I write the data file at the end of the simulation, it only lists the initial number of bonds. I use the 22-Aug-18 mpi build of lammps.

The link to the final data file written by lammps is : https://www.dropbox.com/s/37o205ky1b5ly0b/sh3_prm_equi.data?dl=0

The initial data file can be found here:
https://www.dropbox.com/s/l1kuf1xyhze4vlb/SH3_PRM_100uM.data?dl=0

"Step E_bond TotEng Temp f_bondc[1] f_bondc[2]
2131 11.603684 3631.5974 0 0 0
10000 18103.01 103702.77 310.34538 0 50
20000 18029.493 103746.31 310.38238 0 58
30000 18036.495 103934.5 312.74961 0 62
40000 17879.702 102806.43 308.90296 0 70
.
.
.
.4950000 18051.107 81304.221 310.75834 0 590
4960000 17853.917 81353.685 310.10719 0 591
4970000 17929.782 81108.554 309.73474 0 592
4980000 17953.642 81357.482 309.77574 0 592
4990000 18096.472 80915.232 308.14161 0 592
5000000 17802.297 80452.017 309.08577 0 592
5002131 17829.428 81120.475 309.2107 0 592
"

Regards

Srivastav Ranganathan
Postdoctoral Student
Department of Chemistry and Chemical Biology
Harvard University

testsim.in (1.43 KB)

out.log (41.9 KB)

Hello,

I`ve been running simulations in which I use the fix bond/create and fix bond/delete commands on a particular type of atom pairs. To monitor the process of bond formation, I write down the output from the fixes to my output file and the cumulative number of bonds corresponds to more than 500 at the end of the simulation (as per the output of the fixbondc[2]). However, when I write the data file at the end of the simulation, it only lists the initial number of bonds. I use the 22-Aug-18 mpi build of lammps.

that is because you are discounting the bonds that are broken. if you make the following changes:

variable netbond equal f_bondc[2]-f_bondbr[2]
thermo_style custom step ebond etotal temp f_bondc[2] f_bondbr[2] v_netbond

you will see, that LAMMPS is doing exactly what you ask it to do and that the total number of bonds at the end is what it should be.

axel.