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[求助] cannot zero langevin force of 0 atoms

你看這兩個(gè)group里明明有原子��？
為什么會(huì)出現(xiàn)這種情況？

未命名.jpg

未命名1.jpg

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【分享】嘗試lammps中, 分享中... 已經(jīng)有15人回復(fù)

1樓 2013-05-13 09:39:53

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2樓: Originally posted by ddll_slsl at 2013-05-13 09:44:29
把你的in文件貼出來(lái)。

dimension 3
units    real
boundary  p p f

atom_style full
neighbor    3.0 bin
neigh_modify  delay 5 every 1 check yes
read_data gufinal2-oh1.data
  #lattice diamond 3.5667
  #region box1 cylinder z 9 16.5 3 3 18 units box
  #create_atoms 1 region box1
  #group tip region box1

# force field
pair_style hybrid reax 6.0 1 0 1.0e-6 airebo 2.5 0 0 lj/cut 10.0
pair_coeff * * reax ffield.reax 1 1 1 1 3 2
pair_coeff * * airebo CH.airebo C C C C NULL NULL
pair_coeff 1 2*4 lj/cut 0.0654904 3.40
pair_coeff 2 3*4 lj/cut 0.0654904 3.40
pair_coeff 3 4 lj/cut 0.0654904 3.40
pair_coeff 2*4 5 lj/cut 0.101 3.283
pair_coeff 2*4 6 lj/cut 0.0475 3.025
pair_coeff 5 5 lj/cut 0.155402 3.166
pair_coeff 6 6 lj/cut 0.03459 2.65

# define region before define group
region rfix block INF INF INF INF INF -8 units box
region r1 block INF INF INF INF -8 -4.5 units box
region r2 block INF INF INF INF -4.5 -1 units box
region r3 block INF INF INF INF -1 INF units box
region th1 block INF INF INF 3.5 -8 INF units box
region th2 block INF INF 29.5 INF -8 INF units box

group gfix region rfix
group g1 region r1
group g2 region r2
group g3 region r3
group gth1 region th1
group gth2 region th2
group gth union gth1 gth2
group gthg12 subtract gth g3
group gthg3 subtract gth gthg12
group g12 union g1 g2
group gf12 union gfix g12

# compute and velocity
variable fg3x  equal fcm(g3,x)#x component of the total force on group g3
variable fg3y  equal fcm(g3,y)
variable fg3z  equal fcm(g3,z)
variable vg3x  equal vcm(g3,x)#x component of velocity of the center of mass of group g3
variable vg3y  equal vcm(g3,y)#y component of velocity of the center of mass of group g3
variable pg3x  equal xcm(g3,x)#x component of position of the center of mass of group g3
variable pg3y  equal xcm(g3,y)#y component of position of the center of mass of group g3
variable pg3z  equal xcm(g3,z)#z component of position of the center of mass of group g3
variable pg2x  equal xcm(g2,x)#x component of position of the center of mass of group g2
variable pg2y  equal xcm(g2,y)#y component of position of the center of mass of group g2
variable pg2z  equal xcm(g2,z)#z component of position of the center of mass of group g2
variable vg2x  equal vcm(g2,x)#x component of velocity of the center of mass of group g2
variable vg2y  equal vcm(g2,y)#y component of velocity of the center of mass of group g2

#displace_atoms g3 rotate 21.27 25.45 8.08 0.0 0.0 1.0 10.0 units box
#displace_atoms g3 move 0.0 0.0 0.5 units box
compute temp1 g3 temp
compute temp2 g3 temp/com
compute temp3 g12 temp
compute temp4 gthg12 temp
compute temp5 gthg3 temp
compute temp6 gthg3 temp/com
compute cf1 g3  group/group gf12
compute  ke1  g3  ke
compute  pe1  g3 pe/atom
compute  peg3 g3 reduce sum c_pe1
compute  pe2  g12 pe/atom
compute  peg12 g12 reduce sum c_pe2
velocity  gfix set 0.0 0.0 0.0 units box
#velocity  tip set 0.0 0.0 0.0 units box
velocity  g12 create 10 4928459 rot yes dist gaussian units box
velocity  g3 create 10 4928459 rot yes dist gaussian units box

# fixes
fix 1 all nve
fix          2 gthg12 langevin 10 10 300 699483 zero yes
fix          3 gthg3 langevin 10 10 100 699483 zero yes
fix_modify    3 temp temp6
#fix          fnvt1 g12 nvt temp 10 10 0.1 drag 2.0
#fix          fnvt2 g3 nvt temp 10 10 0.1 drag 2.0
#fix_modify    fnvt2 temp temp2
#fix          2 g12 temp/berendsen 10 10 0.3
#fix          3 g3 temp/berendsen 10 10 0.3
#fix_modify    3 temp temp2
fix          4 gfix setforce 0.0 0.0 0.0
#fix          ftip tip setforce 0.0 0.0 0.0
#fix          ftip1 tip rigid single

#relax
#min_modify dmax 0.01
#minimize 1.0e-6 2.306e-7 1000 100000
#neigh_modify exclude group gfix gfix
#neigh_modify exclude group tip tip
timestep       1
thermo       100
thermo_style custom step temp pe ke etotal press pzz c_ke1 c_peg3 c_peg12 c_temp1 c_temp3 c_temp4 c_temp6 v_fg3x v_fg3y v_fg3z &
v_pg3x v_pg3y v_pg3z v_vg3x v_vg3y c_cf1 c_cf1[1] c_cf1[2] c_cf1[3] v_pg2x v_pg2y v_pg2z v_vg2x v_vg2y
thermo_modify temp temp2
dump 1 all xyz 200 gufinal2-oh.xyz
dump 2 all atom 200 gufinal2-oh.lammpstrj
run    50000

#Run
#variable dz1 equal ramp(17,15.6)
#fix       fw1 all wall/harmonic zhi v_dz1 0.1 1.0 2.5 units box
#fix_modify fw1 energy yes
#run 30000
#fix       fw1 all wall/harmonic zhi 15.6 0.1 1.0 2.5 units box
#fix_modify fw1 energy yes
#min_modify dmax 0.01
#minimize 1.0e-6 1.0e-8 1000 100000
#run 40000

velocity  g3 set 0.001 NULL NULL sum yes units box
run  100000

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3樓2013-05-13 10:45:13

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ddll_slsl

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【答案】應(yīng)助回帖

感謝參與，應(yīng)助指數(shù) +1

把你的in文件貼出來(lái)。

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2樓2013-05-13 09:44:29

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ddll_slsl

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【答案】應(yīng)助回帖

region rfix block INF INF INF INF INF -8 units box
region r1 block INF INF INF INF -8 -4.5 units box
你是否有－z坐標(biāo)正好是－8的原子？如果是這樣，這個(gè)原子同時(shí)屬于2個(gè)group，
fix 4 gfix setforce 0.0 0.0 0.0
這樣的原子被固定了，就不能用langevin了。

最好把你的log文件也貼出來(lái)，就能看個(gè)全面。

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4樓2013-05-13 10:56:46

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劍雪封侯

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引用回帖:

4樓: Originally posted by ddll_slsl at 2013-05-13 10:56:46
region rfix block INF INF INF INF INF -8 units box
region r1 block INF INF INF INF -8 -4.5 units box
你是否有－z坐標(biāo)正好是－8的原子？如果是這樣，這個(gè)原子同時(shí)屬于2個(gè)group，
fix 4 gfix ...

我沒(méi)有坐標(biāo)為-8的原子，我測(cè)試出來(lái)了，問(wèn)題出在那個(gè)勢(shì)函數(shù)reax那，如果把那個(gè)勢(shì)函數(shù)刪掉，就不會(huì)出現(xiàn)那種問(wèn)題，你用過(guò)reax么？我不知道我的參數(shù)設(shè)置對(duì)不對(duì)？

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5樓2013-05-13 11:10:32

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