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john1990

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应助: 0 (幼儿园)
金币: 373.9
红花: 1
帖子: 44
在线: 58.2小时
虫号: 2228668
注册: 2013-01-08
性别: GG
专业: 机械摩擦学与表面技术

[求助] 請問C原子與H原子間不正常的鍵結

?????????????(Diamond Like Carbon)?????????????(DLC?????c??????????????x?_)??????????????S?C????1000?wH???(???^?_??????????w?? ??Щ???????????)??
????????????? tersoff (tersoff1994)?????????? REBO2??  (??????????? AIREBO ?P?? LJ_flag ?? torsion_flag)

??????rebo2????? ?????DLC???Щ??????????h???H?????F?Щ?????????I?Y?????vmd??????????Щ?????O???box???????I?Y(??????L)

???????λ?????????????}??????F?@?N?????????I?Y???
??????D ??????DLC ?????????
?@?e????????
-------------------------------------------------------
units metal
boundary p p s
dimension 3
atom_style atomic
neighbor 2.0 bin
neigh_modify every 5 delay 0 check yes

read_data R25-diamond.txt
region workpiece block -44.5 44.5 -44.5 44.5 -70 160 units box
group workpiece region workpiece

#region 1 block -3.0 5.0 INF 10.0 INF INF

region diabound block INF INF INF INF INF -55.01
region diathermal block INF INF INF INF -55 -50.01
region dianewdun block INF INF INF INF -50 1
region dlcnewdun block INF INF INF INF 125 142
region dlcthermal block INF INF INF INF 142.01 146
region dlcbound block INF INF INF INF 146.01 INF

group       diabound region diabound
group diathermal region diathermal
group dianewdun region dianewdun
group dlcnewdun region dlcnewdun
group dlcthermal region dlcthermal
group       dlcbound region dlcbound

set group diabound  type 1
set group diathermal  type 2
set group dianewdun  type 3
set group dlcnewdun  type 4
set group dlcthermal  type 5
set group dlcbound  type 6

group dia union diabound diathermal dianewdun
group dlc union dlcnewdun dlcthermal dlcbound

mass * 12.0107

region hydrogen block -44.5 44.5 -44.5 44.5 1.1 2.0
create_atoms 7 random 1000 568991 hydrogen
mass 7 1

group hydro region hydrogen
set group hydro type 7
group mobile union diathermal dianewdun dlcnewdun dlcthermal hydro
group work union diabound diathermal dianewdun dlcnewdun dlcthermal dlcbound hydro
group therm union dlcthermal diathermal

pair_style rebo
pair_coeff * * CH.airebo C C C C C C H

compute 1 all coord/atom 1.75
compute dlcRDF dlcnewdun rdf 100

fix dlcrdf dlcnewdun ave/time 100 1 100 c_dlcRDF file dlc-tmp.rdf mode vector

compute k all ke/atom
compute p all pe/atom
variable b atom c_k*1.602e-19/(1.5*1.3806505e-23)

#temp controllers
compute new3d mobile temp

# Compute stress information for Atomeye visualization
compute stressall all stress/atom NULL
compute stress1 all reduce sum c_stressall[1]
compute stress2 all reduce sum c_stressall[2]
compute stress3 all reduce sum c_stressall[3]
compute stress4 all reduce sum c_stressall[4]
compute stress5 all reduce sum c_stressall[5]
compute stress6 all reduce sum c_stressall[6]

#equilibrate
velocity mobile create 300 699845 temp new3d loop local#
thermo 1000

minimize 1.0e-9 1.0e-9 1000000 1000000

fix 1 work nve
fix 2 diabound setforce 0 0 0
fix 3 mobile langevin 300 300 0.01 699483
fix_modify 3 temp new3d
fix 4 dlcbound setforce 0 0 0

dump 1 all atom 2000 dump.relax.lammpstrj#
dump_modify 1 sort id

thermo_style custom step temp c_new3d epair emol pe ke etotal ebond press vol c_stress1 c_stress2 c_stress3 c_stress4 c_stress5 c_stress6
thermo 1000
timestep 0.001
run 50000
undump 1

#120528modify
displace_atoms dlc move 0 0 -120 units box
compute 10 dlcbound reduce sum fx fy fz
compute 13 diabound reduce sum fx fy fz

# Setup file output (time in ps, pressure in GPa)
#variable p1 equal "(ly-v_ly0)/v_ly0"
variable p2 equal "-pxx/10000"
variable p3 equal "-pyy/10000"
variable p4 equal "-pzz/10000"
variable p5 equal "-pxy/10000"
variable p6 equal "-pxz/10000"
variable p7 equal "-pyz/10000"
variable p8 equal "pe"
# Output stress and strain information to datafile for Matlab post-processing
fix equil1 dlcnewdun print 1000 " ${p2} ${p3} ${p4} ${p5} ${p6} ${p7} ${p8}" file dlcnewdun.stress.txt screen no# ${p1}
fix equil2 dianewdun print 1000 " ${p2} ${p3} ${p4} ${p5} ${p6} ${p7} ${p8}" file dianewdun.stress.txt screen no# ${p1}

unfix 3
#fix 3 therm langevin 300 300 0.01 699483
#fix 3 dlcthermal  langevin 300 300 0.01 699483
fix 3 diathermal langevin 300 300 0.01 699483

velocity dlcbound set 0 0 -0.1 units box
fix 10 all ave/time 10 10 100  f_4[1] f_4[2] f_4[3] file force-dlcbound100.txt
fix 11 all ave/time 50 10 500  f_4[1] f_4[2] f_4[3] file force-dlcbound500.txt
fix 12 all ave/time 100 10 1000  f_4[1] f_4[2] f_4[3] file force-dlcbound1000.txt
fix 13 all ave/time 500 10 5000  f_4[1] f_4[2] f_4[3] file force-dlcbound5000.txt
fix 14 all ave/time 10 10 100  f_2[1] f_2[2] f_2[3] file force-diabound100.txt
fix 15 all ave/time 50 10 500  f_2[1] f_2[2] f_2[3] file force-diabound500.txt
fix 16 all ave/time 100 10 1000  f_2[1] f_2[2] f_2[3] file force-diabound1000.txt
fix 17 all ave/time 500 10 5000  f_2[1] f_2[2] f_2[3] file force-diabound5000.txt
fix 18 all ave/time 10 10 100  c_10[1] c_10[2] c_10[3] file force-dlcbound-sum.txt
fix 19 all ave/time 10 10 100  c_13[1] c_13[2] c_13[3] file force-diabound-sum.txt

dump 1 all custom 1000 dump.lammpstrj id type x y z c_1 c_k c_p v_b
dump_modify 1 sort id

dump 4 all custom 1000 dump4.lammpstrj id type x y z ix iy iz fx fy fz  c_stressall[1] c_stressall[2] c_stressall[3] c_stressall[4] c_stressall[5] c_stressall[6]
dump_modify 4 sort id

run 100000

velocity dlcbound set 0 0 0 units box

run                            100000

#unload
velocity dlcbound set 0 0 0.1 units box

run 200000
---------------------------------------------------

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