Dear,
In a simulation I generate dump every 100 time steps from step 3002000. All good with this, snapshoot generated are :
3002000
3002100
3002200
.
.
.
6002000
total: 30000 snapshot. Now I intend to calculate the rdf from the rerun command. However, when I create the dump does not take account Nevery parameter of fix ave/time: “The final averaged quantities are generated on timesteps that are a multiple of Nfreq”.
Therefore I can not use the option “ave one” of fix ave/time to average 30000 snapshot, because of missing 20 snapshot to get the average to step 6000000. I can only averaging 20,000 maximum snapshot , wasting 10000.
This I can solve simulation running again , however, it involves a long wait. Change the steps manually see it complex, the file size approx 100GB. I was thinking of something like reset to flight time steps the dump file , to 0,1,2,3 , … 30000. However, with the rerun command I do not see how to do this. Also probe the start option start of ave/time but got no results.
The ave running option could partially solve the problem, Nfreq=100, but my intention is to average with ave one
Any recommendation?
Thanks
Regards
Dear,
In a simulation I generate dump every 100 time steps from step 3002000. All
good with this, snapshoot generated are :
3002000
3002100
3002200
.
.
.
6002000
total: 30000 snapshot. Now I intend to calculate the rdf from the rerun
command. However, when I create the dump does not take account Nevery
parameter of fix ave/time: "The final averaged quantities are generated on
timesteps that are a multiple of Nfreq".
Therefore I can not use the option "ave one" of fix ave/time to average
30000 snapshot, because of missing 20 snapshot to get the average to step
6000000. I can only averaging 20,000 maximum snapshot , wasting 10000.
This I can solve simulation running again , however, it involves a long
wait. Change the steps manually see it complex, the file size approx 100GB.
I was thinking of something like reset to flight time steps the dump file ,
to 0,1,2,3 , ..... 30000. However, with the rerun command I do not see how
to do this. Also probe the start option start of ave/time but got no
results.
The ave running option could partially solve the problem, Nfreq=100, but my
intention is to average with ave one
Any recommendation?
if you read the trajectory via the vmd molfile plugin for LAMMPS
instead of the native reader (requires installing the USER-MOLFILE
package) and the corresponding molfile plugin binary from a compatible
VMD installation), the timestep field should be ignored (i think) and
then the desired renumbering would happen.
axel.
Mr. Axel thanks for the suggestion. I will review the package you mentioned.