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新虫 (小有名气)

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虫号: 2782558
注册: 2013-11-06
专业: 理论和计算化学

[求助] 刚做分子模拟的研究，求大神帮忙下！

下面是我做的计算乙炔在AL2O3孔道中的扩散系数的源文件，但是用LAMMPS运行的时候老是出现LOST ATOMS，能帮忙看看是哪里出问题了么

# description c2h2 diffusion in AL2O3
# used as template for the single atom molecules diffusion in AL2O3.

variable temperature equal 298.0
variable dumpstep equal 10000
variable thermostep equal 10000
variable comstep equal 10000
variable restartstep equal 10000000
variable runrelaxstep equal 1000000
variable runstep equal 20000000

units real
atom_style atomic

read_data AL2O3.c2h2.data.lammps05

pair_style lj/cut 17.0

#pair_coeff * * none

# parameter from Dreiding for materials: generally the type equals to the atom number. 4-Zinc
# 2-He from Peng X, 3-Li from UFF.
pair_coeff 1 1  0.5050 2.2495
pair_coeff 2 2  0.2104 1.7210
#parameter from Peng Xuan for species: 9-Methane, 10-Hydrogen2, 11-Nitrogen2, 12-Oxygen2
pair_coeff 3 3 0.1588 3.5742

pair_modify shift yes  mix arithmetic

label loop
variable a loop 2

group fluid type 3
group AL2O3 subtract all fluid

# fix freeze AL2O3 setforce 0.0 0.0 0.0

velocity fluid create ${temperature} 3654321 dist gaussian

neighbor 2.0 bin
neigh_modify exclude group AL2O3 AL2O3

timestep  0.1
# attention: for the new lammps exe, the fix nvt changed as
fix 1 fluid nvt temp 298.0 298.0 100.0
#fix 1 fluid nvt temp ${temperature} ${temperature} 100.0
#fix 1 fluid nvt ${temperature} ${temperature} 100.0
run ${runrelaxstep}
reset_timestep 0

# in the new lammps exe file, this two fix have been discarded.
fix 2 fluid msd 10000 AL2O3.c2h2.diff.out
#fix 3 fluid com 10000 AL2O3.c2h2.com

compute fluidtem fluid temp
#compute fluidpress all pressure fluidtem

#compute peratom fluid pe/atom
#compute pe fluid reduce sum c_peratom

#dump 1 fluid custom 100 dump.AL2O3.c2h2.fluid.wrap.$t id type x y z ix iy iz
dump 2 fluid custom 1000  dump.AL2O3.c2h2.fluid.unwrap.$a id type xu yu zu
#dump 3 all custom 1000 dump.AL2O3.c2h2.all id type x y z ix iy iz
#dump 4 fluid custom 100 dump.AL2O3.c2h2.fluid.v.$t id type vx vy vz
# dump_modify id scale no image yes

thermo ${thermostep}
thermo_style custom step temp c_fluidtem press  pe etotal
#thermo_style       custom step temp etotal press pe c_pe
# thermo_modify       temp fluidtem press fluidpress

restart ${restartstep} AL2O3.c2h2.restart.$a

run ${runstep}

clear
# use the restart file as the initial configuration of the md every loop
# because in the velocity command, the system has been set a new velocity
# so it may be independent with the former configuration run, i think.
read_restart AL2O3.c2h2.restart.$a.${runstep}
next a
jump in.lammps loop

这个程序是别人拿来做另外一种研究的，跟我的差不多，它的就能运行，怎么我的不行呢

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