求助:Lammps做变温循环采样时,RDF不输出

Yann-Lecun · 发表于 Post on 2024-10-23 10:08:03

在常温(298K)下做完了体系平衡, 得到数据文件sys_after_nvt4.data. 后续为节省时间和计算量, 想做变温循环采样, 设置了四个时间索引, 但在实际运行过程中, 发现只在第一个时间索引有RDF输出, 其余的时间索引下均无RDF输出(traj, msd, data文件均有正常输出)

input_up_v4.lammps (2.84 KB, 下载次数 Times of downloads: 2)

sys_after_nvt4.data (3.04 MB, 下载次数 Times of downloads: 1)

system.in.init (291 Bytes, 下载次数 Times of downloads: 1)

system.in.settings (4.04 KB, 下载次数 Times of downloads: 1)

附上脚本文件如下:
include "system.in.init"
read_data "sys_after_nvt4.data"
include "system.in.settings"

group          glion type 1
neigh_modify    delay 0 every 1 check yes
neigh_modify    one 5000

compute       md1 glion msd com yes
compute       myRDF2 all rdf 500 1 2 1 3 1 5 1 6 1 8 1 9 # need to modify the atom type

label          loop_start                # i: 1-5
variable       i loop 51                # 1-51

# Equilibration is 298K so we should start from 298K
variable       T equal 296+2*$i       #  298 300 302 304 ... 398 K 2K/1ns

timestep       2
thermo       5000                   # output thermodynamic data every 5000 steps(10ps)

# 采样10ns 2fs*5000000steps = 10ns  平衡1ns*2 2fs*500000steps*2 = 2ns
# total = (索引外 1ns*47 =  47ns) + (4*2ns) + (4*10ns) = 47ns + 8ns + 40ns = 95ns
if "(${T} == 298)" then &
"dump       1 all custom 50000 traj_nvt${T}.lammpstrj id mol type x y z ix iy iz" &
"dump       2 all custom 50000 dump.atom${T}.* id mol type x y z" &
"fix          fxnvt all nvt temp ${T} ${T} 200" &
"fix          msd1 glion ave/time 1 50000 50000 c_md1 file ${T}_msd.dat mode scalar" &
"fix          3 all ave/time 1 5000000 5000000 c_myRDF2 file ${T}_rdfK.dat mode vector" &
"run          5000000" &
"write_data str_nvt_${T}.data" &
"undump       1" &
"undump       2" &
"unfix       fxnvt" &
"unfix       msd1" &
"unfix       3" &
elif "(${T} == 338) || (${T} == 378) || (${T} == 398)"  &
"fix          fxnpt all npt temp ${T} ${T} 200.0 iso 1.0 1.0 1000" &
"run          500000" &
"unfix       fxnpt" &
"dump          eq all custom 5000 traj_nvt_equil${T}.lammpstrj id mol type x y z ix iy iz" &
"fix          fxnvt2 all nvt temp ${T} ${T} 200" &
"run          500000" &
"write_data    str_nvt_equil_${T}.data" &
"undump       eq" &
"unfix       fxnvt2" &
"dump       1 all custom 50000 traj_nvt${T}.lammpstrj id mol type x y z ix iy iz" &
"dump       2 all custom 50000 dump.atom${T}.* id mol type x y z" &
"fix          fxnvt3 all nvt temp ${T} ${T} 200" &
"fix          msd1 glion ave/time 1 50000 50000 c_md1 file ${T}_msd.dat mode scalar" &
"fix          3 all ave/time 1 5000000 5000000 c_myRDF2 file ${T}_rdfK.dat mode vector" &
"run          5000000" &
"write_data str_nvt_${T}.data" &
"undump       1" &
"undump       2" &
"unfix       fxnvt3" &
"unfix       msd1" &
"unfix       3" &
else    &
"fix          fxnpt2 all npt temp ${T} ${T} 200.0 iso 1.0 1.0 1000" &
"run          500000"  &
"unfix       fxnpt2" &

next i
jump SELF loop_start

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[Lammps] 求助:Lammps做变温循环采样时,RDF不输出