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小木虫论坛-学术科研互动平台 » 计算模拟区 » 分子模拟 » LAMMPS/DL_POLY » 计算W-Mo合金的熔点，程序lost atoms，请教能人解答
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ytudou

银虫 (小有名气)

[求助] 计算W-Mo合金的熔点，程序lost atoms，请教能人解答 已有1人参与

参照上海交大那个求Cu或Al熔点的例子，把lattice部分换成了我Mo-0.25W成分合金的原子分布，in文件如下：

++++++++++++++++++++++++++++++++++++++++++++++++++++++
  in.melt_temp
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

                   # LAMMPS Melt_Mo-W_temp
units metal
boundary p p p
atom_style atomic
variable x index 10 500 1000 1800 2000

variable y equal 3.1466/15.733
variable z universe 15.733
lattice custom $z a1 0.4 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 $y basis 0.0 0.0 0.0 basis 0.25 0.1 0.5 basis 0.0 0.2 0.0 basis 0.0 0.4 0.0 basis 0.0 0.6 0.0 basis 0.0 0.8 0.0 basis 0.25 0.9 0.5 basis 0.5 0.0 0.0 basis 0.75 0.1 0.5 basis 0.75 0.5 0.5 basis 0.5 0.8 0.0 basis 0.75 0.9 0.5 basis 0.5 0.4 0.0 basis 0.5 0.6 0.0 basis 0.5 0.2 0.0 basis 0.25 0.5 0.5 basis 0.25 0.3 0.5 basis 0.25 0.7 0.5 basis 0.75 0.7 0.5 basis 0.75 0.3 0.5
lattice custom 15.733 a1 0.4 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 $y basis 0.0 0.0 0.0 basis 0.25 0.1 0.5 basis 0.0 0.2 0.0 basis 0.0 0.4 0.0 basis 0.0 0.6 0.0 basis 0.0 0.8 0.0 basis 0.25 0.9 0.5 basis 0.5 0.0 0.0 basis 0.75 0.1 0.5 basis 0.75 0.5 0.5 basis 0.5 0.8 0.0 basis 0.75 0.9 0.5 basis 0.5 0.4 0.0 basis 0.5 0.6 0.0 basis 0.5 0.2 0.0 basis 0.25 0.5 0.5 basis 0.25 0.3 0.5 basis 0.25 0.7 0.5 basis 0.75 0.7 0.5 basis 0.75 0.3 0.5
lattice custom 15.733 a1 0.4 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.2 basis 0.0 0.0 0.0 basis 0.25 0.1 0.5 basis 0.0 0.2 0.0 basis 0.0 0.4 0.0 basis 0.0 0.6 0.0 basis 0.0 0.8 0.0 basis 0.25 0.9 0.5 basis 0.5 0.0 0.0 basis 0.75 0.1 0.5 basis 0.75 0.5 0.5 basis 0.5 0.8 0.0 basis 0.75 0.9 0.5 basis 0.5 0.4 0.0 basis 0.5 0.6 0.0 basis 0.5 0.2 0.0 basis 0.25 0.5 0.5 basis 0.25 0.3 0.5 basis 0.25 0.7 0.5 basis 0.75 0.7 0.5 basis 0.75 0.3 0.5

region box block -4.0 4.0 -3.0 3.0 0.1 45.0
create_box 2 box

region Mo-0.25W block -4.0 4.0 -3.0 3.0 0.1 45.0
create_atoms 2 region Mo-0.25W basis 1 1 basis 2 1 basis 3 1 basis 4 1 basis 5 1 basis 6 1 basis 7 1 basis 8 1 basis 9 1 basis 10 1 basis 11 1 basis 12 1 basis 13 1 basis 14 1 basis 15 1 basis 16 2 basis 17 2 basis 18 2 basis 19 2 basis 20 2                       
group Mo-0.25W region Mo-0.25W

region Mo-0.25W11 block -4.0 4.0 -3.0 3.0 43.0 45.0
region Mo-0.25W22 block -4.0 4.0 -3.0 3.0 0.1 3.0
group Mo-0.25W11 region Mo-0.25W11
group Mo-0.25W22 region Mo-0.25W22
fix  region Mo-0.25W11 setforce 0 0 0
fix  region Mo-0.25W22 setforce 0 0 0

mass           1 95.941
mass           2 183.841
#fix            wall all wall/reflect zlo zhi   

timestep 0.01
thermo 100


pair_style      hybrid morse 10.0
pair_coeff      1 1 morse    0.77019   1.434  3.012
pair_coeff      1 2 morse    13.68932  1.82699   2.30154
pair_coeff      2 2 morse    0.969483  1.385  3.053

neighbor 0.6 bin
neigh_modify every 5 delay 0 check yes
velocity all create $x 825577 dist gaussian
fix 1 all npt $x $x 2.0 xyz 0.0 0.0 45.0 drag 0.2 #在x温度下保持外压为零弛豫
compute 3 all pe/atom
compute 4 all ke/atom
compute 5 all coord/atom 3.0
run 10000
unfix 1
fix 1 all nvt $x $x 2.0 drag 0.2 #NVT控温
dump 1 all custom 50 dump_$x.atom id xs ys zs c_3 c_4 c_5
fix 2 all msd 1 msd_Mo-W_$x.dat #输出MSD文件
run 10000
clear
next x
jump in.melt_Mo-W_temp

+++++++++++++++++++++++++++++++++++++++++++++++++++=
以下是log文件
+++++++++++++++++++++++++++++++++++++++++++++++++++++

                   LAMMPS (7 Jul 2009)
jump in.melt_temp
# LAMMPS Melt_Mo-W_temp
units metal
boundary p p p
atom_style atomic
variable x index 10 500 1000 1800 2000

variable y equal 3.1466/15.733
variable z universe 15.733
Initial ${z} setting: value 1 on partition 0
lattice custom $z a1 0.4 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 $y basis 0.0 0.0 0.0 basis 0.25 0.1 0.5 basis 0.0 0.2 0.0 basis 0.0 0.4 0.0 basis 0.0 0.6 0.0 basis 0.0 0.8 0.0 basis 0.25 0.9 0.5 basis 0.5 0.0 0.0 basis 0.75 0.1 0.5 basis 0.75 0.5 0.5 basis 0.5 0.8 0.0 basis 0.75 0.9 0.5 basis 0.5 0.4 0.0 basis 0.5 0.6 0.0 basis 0.5 0.2 0.0 basis 0.25 0.5 0.5 basis 0.25 0.3 0.5 basis 0.25 0.7 0.5 basis 0.75 0.7 0.5 basis 0.75 0.3 0.5
lattice custom 15.733 a1 0.4 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 $y basis 0.0 0.0 0.0 basis 0.25 0.1 0.5 basis 0.0 0.2 0.0 basis 0.0 0.4 0.0 basis 0.0 0.6 0.0 basis 0.0 0.8 0.0 basis 0.25 0.9 0.5 basis 0.5 0.0 0.0 basis 0.75 0.1 0.5 basis 0.75 0.5 0.5 basis 0.5 0.8 0.0 basis 0.75 0.9 0.5 basis 0.5 0.4 0.0 basis 0.5 0.6 0.0 basis 0.5 0.2 0.0 basis 0.25 0.5 0.5 basis 0.25 0.3 0.5 basis 0.25 0.7 0.5 basis 0.75 0.7 0.5 basis 0.75 0.3 0.5
lattice custom 15.733 a1 0.4 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.2 basis 0.0 0.0 0.0 basis 0.25 0.1 0.5 basis 0.0 0.2 0.0 basis 0.0 0.4 0.0 basis 0.0 0.6 0.0 basis 0.0 0.8 0.0 basis 0.25 0.9 0.5 basis 0.5 0.0 0.0 basis 0.75 0.1 0.5 basis 0.75 0.5 0.5 basis 0.5 0.8 0.0 basis 0.75 0.9 0.5 basis 0.5 0.4 0.0 basis 0.5 0.6 0.0 basis 0.5 0.2 0.0 basis 0.25 0.5 0.5 basis 0.25 0.3 0.5 basis 0.25 0.7 0.5 basis 0.75 0.7 0.5 basis 0.75 0.3 0.5
Lattice spacing in x,y,z = 6.2932 15.733 3.1466
lattice custom 15.733 a1 0.4 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 $y basis 0.0 0.0 0.0 basis 0.25 0.1 0.5 basis 0.0 0.2 0.0 basis 0.0 0.4 0.0 basis 0.0 0.6 0.0 basis 0.0 0.8 0.0 basis 0.25 0.9 0.5 basis 0.5 0.0 0.0 basis 0.75 0.1 0.5 basis 0.75 0.5 0.5 basis 0.5 0.8 0.0 basis 0.75 0.9 0.5 basis 0.5 0.4 0.0 basis 0.5 0.6 0.0 basis 0.5 0.2 0.0 basis 0.25 0.5 0.5 basis 0.25 0.3 0.5 basis 0.25 0.7 0.5 basis 0.75 0.7 0.5 basis 0.75 0.3 0.5
lattice custom 15.733 a1 0.4 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.2 basis 0.0 0.0 0.0 basis 0.25 0.1 0.5 basis 0.0 0.2 0.0 basis 0.0 0.4 0.0 basis 0.0 0.6 0.0 basis 0.0 0.8 0.0 basis 0.25 0.9 0.5 basis 0.5 0.0 0.0 basis 0.75 0.1 0.5 basis 0.75 0.5 0.5 basis 0.5 0.8 0.0 basis 0.75 0.9 0.5 basis 0.5 0.4 0.0 basis 0.5 0.6 0.0 basis 0.5 0.2 0.0 basis 0.25 0.5 0.5 basis 0.25 0.3 0.5 basis 0.25 0.7 0.5 basis 0.75 0.7 0.5 basis 0.75 0.3 0.5
Lattice spacing in x,y,z = 6.2932 15.733 3.1466
lattice custom 15.733 a1 0.4 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.2 basis 0.0 0.0 0.0 basis 0.25 0.1 0.5 basis 0.0 0.2 0.0 basis 0.0 0.4 0.0 basis 0.0 0.6 0.0 basis 0.0 0.8 0.0 basis 0.25 0.9 0.5 basis 0.5 0.0 0.0 basis 0.75 0.1 0.5 basis 0.75 0.5 0.5 basis 0.5 0.8 0.0 basis 0.75 0.9 0.5 basis 0.5 0.4 0.0 basis 0.5 0.6 0.0 basis 0.5 0.2 0.0 basis 0.25 0.5 0.5 basis 0.25 0.3 0.5 basis 0.25 0.7 0.5 basis 0.75 0.7 0.5 basis 0.75 0.3 0.5
Lattice spacing in x,y,z = 6.2932 15.733 3.1466

region box block -4.0 4.0 -3.0 3.0 0.1 45.0
create_box 2 box
Created orthogonal box = (-25.1728 -47.199 0.31466) to (25.1728 47.199 141.597)
  1 by 1 by 1 processor grid

region Mo-0.25W block -4.0 4.0 -3.0 3.0 0.1 45.0
create_atoms 2 region Mo-0.25W basis 1 1 basis 2 1 basis 3 1 basis 4 1 basis 5 1 basis 6 1 basis 7 1 basis 8 1 basis 9 1 basis 10 1 basis 11 1 basis 12 1 basis 13 1 basis 14 1 basis 15 1 basis 16 2 basis 17 2 basis 18 2 basis 19 2 basis 20 2                       
Created 42720 atoms
group Mo-0.25W region Mo-0.25W
42720 atoms in group Mo-0.25W

region Mo-0.25W11 block -4.0 4.0 -3.0 3.0 43.0 45.0
region Mo-0.25W22 block -4.0 4.0 -3.0 3.0 0.1 3.0
group Mo-0.25W11 region Mo-0.25W11
1920 atoms in group Mo-0.25W11
group Mo-0.25W22 region Mo-0.25W22
2880 atoms in group Mo-0.25W22
fix  region Mo-0.25W11 setforce 0 0 0
fix  region Mo-0.25W22 setforce 0 0 0

mass           1 95.941
mass           2 183.841
#fix            wall all wall/reflect zlo zhi   

timestep 0.01
thermo 100


pair_style      hybrid morse 10.0
pair_coeff      1 1 morse    0.77019   1.434  3.012
pair_coeff      1 2 morse    13.68932  1.82699   2.30154
pair_coeff      2 2 morse    0.969483  1.385  3.053

neighbor 0.6 bin
neigh_modify every 5 delay 0 check yes
velocity all create $x 825577 dist gaussian
velocity all create 10 825577 dist gaussian
fix 1 all npt $x $x 2.0 xyz 0.0 0.0 45.0 drag 0.2 #在x温度下保持外压为零弛豫
fix 1 all npt 10 $x 2.0 xyz 0.0 0.0 45.0 drag 0.2 fix 1 all npt 10 10 2.0 xyz 0.0 0.0 45.0 drag 0.2 compute 3 all pe/atom
compute 4 all ke/atom
compute 5 all coord/atom 3.0
run 10000
Memory usage per processor = 40.9131 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
       0           10   -1187595.7            0   -1187540.5   -3305841.1     671447.7
ERROR: Lost atoms: original 42720 current 41050

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

请教一下大神们，这个问题要怎么解决啊？我试图加一段能量最小化的代码，可是运行后是各种数据都输出为0……同样不知道怎么解决~
请教大神，望各位能积极援助，不胜感激~~~

@老虎大王        @月只蓝
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1楼 2014-09-27 10:55:48
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《一厶

新虫 (小有名气)
你好，我现在也出现了同样的问题，我想问问是什么原因呢，你解决了吗

发自小木虫Android客户端
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3楼2018-10-25 10:33:05
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老虎大王

木虫 (著名写手)

【答案】应助回帖

★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★
感谢参与，应助指数 +1
ytudou: 金币+20, ★★★很有帮助, 原程序计算Cu的熔点运行没问题，又因为有Mo-0.25W的构型和熔点信息，就计算了这个成分的，但是出错~其实这个成分的合金的构型我也不确定对不对，大王能受累帮忙指正下吗？拜托~ 2014-09-28 10:40:55
丢失原子了。主要检查势函数和初始构型。先做一个简单的合金构型，比如B2，L12之类的，看看能不能正常运算，能量是否正确。
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2楼2014-09-27 19:40:33
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