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沙发

楼主 |
发表于 2018-12-6 17:29:05
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#########################################################
# Equilibration #
#########################################################
# STAGE1 NVT from 1000 to 300 K
reset_timestep 0
timestep ${timestep}
#velocity all create ${temperature} 1231
fix 1 all nvt temp 1000 300 100 drag 0.1
run 5000
unfix 1
# STAGE2 NPT from 300K to 300K
fix 1 all npt temp 300 300 100 iso 0 0 1000 drag 0.1
run 5000
unfix 1
# Output file
fix def1 all print 1000 "${p1} ${p2} ${p3} ${p4} ${p5} ${p6} ${p7}" file equilibration.txt screen no
dump 1 all cfg ${dtdump} equi.dump.* mass type xs ys zs id mol q x y z mol
#dump_modify 1 element o_2 ho2 oh c hc c1 c_1 o_1 cp c_0 ho
###############################################
###############################################
variable simname equal PETG
variable equisteps equal 50000
variable thermosteps equal 100
variable strain_rate equal 1e-5
###############################################
# Deformation
reset_timestep 0
thermo ${thermosteps}
timestep 0.5
fix 1 all npt temp 300 300 25 y 0.0 0.0 500 z 0.0 0.0 500 nreset 1000
fix 2 all deform 1 x erate ${strain_rate} units box remap x
variable tmp equal "lx"
variable L0 equal ${tmp}
variable strain equal "(lx - v_L0)/v_L0"
variable p1 equal "step"
variable p2 equal "dt"
variable p3 equal "pe"
variable p4 equal "ke"
variable p5 equal "etotal"
variable p6 equal "v_strain"
variable p7 equal "-pxx/10000*1.01325"
variable p8 equal "-pyy/10000*1.01325"
variable p9 equal "-pzz/10000*1.01325"
variable p10 equal "lx"
variable p11 equal "ly"
variable p12 equal "lz"
variable p13 equal "press"
variable p14 equal "pxy"
variable p15 equal "pxz"
variable p16 equal "pyz"
variable p17 equal "temp"
variable t2 equal "epair"
variable t3 equal "ebond"
variable t4 equal "eangle"
variable t5 equal "edihed"
fix def1 all print 100 "${p1} ${p6} ${p7} ${p8} ${p9} ${p10} ${p11} ${p12} ${p13} ${p14} ${p15} ${p16} ${p17}" file PETG_npt.def1.txt screen no title "step v_strain pxx pyy pzz lx ly lz press pxy pxz pyz temp"
fix def2 all print 100 "${p1} ${t2} ${t3} ${t4} ${t5}" file PETG_npt.def2.txt screen no
fix myprint all print 100 "${p1} ${p2} ${p3} ${p4} ${p5}" file PETG_npt.engergy.txt screen no title "step dt pe ke etotal"
dump 2 all custom 10000 dump_npt.mole.* id type mol fx fy fy mass x y z
thermo_style custom step dt pe ke etotal pxx pyy pzz lx ly lz epair ebond eangle edihed
run 20000
write_restart ${project}.restart2
write_data data.*
print "All Done!"
我问过我的导师,他说可以用一下fix bond/react来试一下,可是我发现那个指令需要拓扑结构(molecule指令)。
(语句表达比较混乱,望见谅) |
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