Hi,
I am trying to output the msd of a chain. However the output file contains only a header with no data:
c1.msd_
Time-averaged data for fix 3
TimeStep Number-of-rows
Row c_msd[1] c_msd[2] c_msd[3] c_msd[4]
with the following simplified input files. I would appreciate it if someone would point out how to correct my fix specification.
I am able to dump and monitor the atom positions and velocities.
Thanks,
RC
____________in.chain _____________
units lj
atom_style bond
special_bonds fene
read_data c1.dat
atom_modify sort 0 0.4
neighbor 0.4 bin
bond_style fene
bond_coeff 1 12.0 3.0 1.0 1.0
group chain molecule 1
fix 1 chain nve
fix 2 chain langevin 1.0 1.0 1.0 1
compute msd chain msd/molecule
timestep 0.01
fix 3 chain ave/time 1 1 1 c_msd mode vector file c1.msd
neigh_modify every 1 delay 0 check yes
minimize 1.e-8 1.0e-8 1000 100000
neigh_modify every 1 delay 1
run 100000
___c1.dat
LAMMPS FENE chain data file
10 atoms
9 bonds
1 atom types
1 bond types
-25.0 25.0 xlo xhi
-25.0 25.0 ylo yhi
-25.0 25.0 zlo zhi
Masses
1 1.0
Atoms
get
1 1 1 3.4200 2.7200 3.4800 0 0 0
2 1 1 3.4200 1.7200 3.4800 0 0 0
3 1 1 4.4200 1.7200 3.4800 0 0 0
4 1 1 4.4200 1.7200 4.4800 0 0 0
5 1 1 3.4200 1.7200 4.4800 0 0 0
6 1 1 2.4200 1.7200 4.4800 0 0 0
7 1 1 2.4200 2.7200 4.4800 0 0 0
8 1 1 2.4200 2.7200 3.4800 0 0 0
9 1 1 2.4200 2.7200 2.4800 0 0 0
10 1 1 3.4200 2.7200 2.4800 0 0 0
Bonds
1 1 1 2
2 1 2 3
3 1 3 4
4 1 4 5
5 1 5 6
6 1 6 7
7 1 7 8
8 1 8 9
9 1 9 10