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missingwudi新蟲 (初入文壇)
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[求助]
用lammps做CH4的MSD均方位移過(guò)程中出現(xiàn)問(wèn)題 已有1人參與
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in文件是這樣的： units real boundary p p p atom_style full angle_style harmonic bond_style harmonic pair_style lj/cut 10.0 pair_modify mix arithmetic read_data data.final_0.3 replicate 1 1 1 group A_C type 3 group CH4 type 1 2 timestep 0.5 neighbor 2.0 bin neigh_modify delay 5 every 1 check yes velocity CH4 create 300.0 4928459 fix freeze A_C setforce 0.0 0.0 0.0 minimize 1.0e-4 1.0e-6 100 1000 fix 1 CH4 rigid single fix 2 CH4 nvt temp 300.0 300.0 0.01 compute methane_temp CH4 temp thermo_style custom step temp pe etotal press vol c_methane_temp thermo 1000 dump 1 all custom 1000 dump.lammpstrj id type x y z dump_modify 1 sort 1 first no log log.lammps run 1000000 undump 1 unfix 2 fix 3 CH4 nve fix 4 CH4 temp/rescale 100 1.0 1.1 0.02 0.5 dump 2 all custom 10000 nve.lammpstrj id type xu yu zu dump_modify 2 sort 1 dump 3 all xyz 10000 nve.xyz dump_modify 3 sort 1 compute msd_CH4 CH4 msd com yes fix 5 CH4 ave/time 1 1 10000 c_msd_CH4 file msd_CH4 start 1000000 mode vector run 1000000 問(wèn)題：導(dǎo)出來(lái)的文件出現(xiàn)了錯(cuò)誤 dump.lammpstrj文件： ITEM: TIMESTEP 1000 ITEM: NUMBER OF ATOMS 3310 ITEM: BOX BOUNDS pp pp pp 0 39.9 0 39.9 0 39.9 ITEM: ATOMS id type x y z 1 1 -nan -nan -nan 2 2 -nan -nan -nan 3 2 -nan -nan -nan 4 2 -nan -nan -nan 5 2 -nan -nan -nan 6 1 -nan -nan -nan 7 2 -nan -nan -nan 8 2 -nan -nan -nan 9 2 -nan -nan -nan 10 2 -nan -nan -nan 11 1 -nan -nan -nan 12 2 -nan -nan -nan 13 2 -nan -nan -nan 14 2 -nan -nan -nan 15 2 -nan -nan -nan 16 1 -nan -nan -nan 17 2 -nan -nan -nan 18 2 -nan -nan -nan 19 2 -nan -nan -nan 20 2 -nan -nan -nan 21 1 -nan -nan -nan 22 2 -nan -nan -nan 23 2 -nan -nan -nan 24 2 -nan -nan -nan 25 2 -nan -nan -nan 26 1 -nan -nan -nan 27 2 -nan -nan -nan 28 2 -nan -nan -nan 29 2 -nan -nan -nan 30 2 -nan -nan -nan 31 1 -nan -nan -nan 32 2 -nan -nan -nan 33 2 -nan -nan -nan 34 2 -nan -nan -nan 35 2 -nan -nan -nan 36 1 -nan -nan -nan 37 2 -nan -nan -nan 38 2 -nan -nan -nan 39 2 -nan -nan -nan 40 2 -nan -nan -nan 41 1 -nan -nan -nan 42 2 -nan -nan -nan 43 2 -nan -nan -nan 44 2 -nan -nan -nan 45 2 -nan -nan -nan 46 1 -nan -nan -nan 47 2 -nan -nan -nan 48 2 -nan -nan -nan 49 2 -nan -nan -nan 50 2 -nan -nan -nan 51 1 -nan -nan -nan 52 2 -nan -nan -nan 53 2 -nan -nan -nan 54 2 -nan -nan -nan 55 2 -nan -nan -nan 56 1 -nan -nan -nan 57 2 -nan -nan -nan 58 2 -nan -nan -nan 59 2 -nan -nan -nan 60 2 -nan -nan -nan 61 1 -nan -nan -nan 62 2 -nan -nan -nan 63 2 -nan -nan -nan 64 2 -nan -nan -nan 65 2 -nan -nan -nan 66 1 -nan -nan -nan 67 2 -nan -nan -nan 68 2 -nan -nan -nan 69 2 -nan -nan -nan 70 2 -nan -nan -nan 71 1 -nan -nan -nan 72 2 -nan -nan -nan 73 2 -nan -nan -nan 74 2 -nan -nan -nan 75 2 -nan -nan -nan 76 1 -nan -nan -nan 77 2 -nan -nan -nan 78 2 -nan -nan -nan 79 2 -nan -nan -nan 80 2 -nan -nan -nan 81 1 -nan -nan -nan 82 2 -nan -nan -nan 83 2 -nan -nan -nan log文件： WARNING: One or more atoms are time integrated more than once (../modify.cpp:245) WARNING: Inconsistent image flags (../domain.cpp:645) Memory usage per processor = 6.25594 Mbytes Step Temp PotEng TotEng Press Volume methane_ 32 0.10282812 3612.6324 3612.927 16623.972 63521.199 98.81782 1000 -nan -nan -nan -nan 63521.199 -nan 2000 -nan -nan -nan -nan 63521.199 -nan 3000 -nan -nan -nan -nan 63521.199 -nan 4000 -nan -nan -nan -nan 63521.199 -nan 5000 -nan -nan -nan -nan 63521.199 -nan 6000 -nan -nan -nan -nan 63521.199 -nan 7000 -nan -nan -nan -nan 63521.199 -nan 8000 -nan -nan -nan -nan 63521.199 -nan |
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lsloneil
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我不是很清楚，可以嘗試以下 1. 采用更小的timestep 2. 先把體系minimize之后再用nvt平衡 3. fix 1 CH4 rigid single fix 2 CH4 nvt temp 300.0 300.0 0.01 這個(gè)用法按照l(shuí)ammps手冊(cè)上的說(shuō)法有點(diǎn)可疑，或許可以把fix rigid去掉后試試看，或者把這兩個(gè)fix結(jié)合起來(lái)，直接用fix rigid/nvt. 4. 當(dāng)你體系的溫度變得無(wú)限大，可以把你lammpstrj 文件在VMD里顯示出來(lái)，看是否有很奇怪的構(gòu)型出現(xiàn)。 |
4樓2015-08-26 08:17:56
lsloneil
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【答案】應(yīng)助回帖
★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★
感謝參與，應(yīng)助指數(shù) +1
missingwudi: 金幣+50, ★★★★★最佳答案, 好像是可以的，程序還在跑，等結(jié)果出來(lái)了再向您討教 2015-08-25 15:00:13
感謝參與，應(yīng)助指數(shù) +1
missingwudi: 金幣+50, ★★★★★最佳答案, 好像是可以的，程序還在跑，等結(jié)果出來(lái)了再向您討教 2015-08-25 15:00:13
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minimize 1.0e-4 1.0e-6 100 1000 這個(gè)先去掉, minimize和fix nvt不能同時(shí)用。 |
2樓2015-08-25 11:24:33
missingwudi
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開始計(jì)算時(shí)好的，算著算著又出現(xiàn)問(wèn)題了，還是同樣的問(wèn)題 1100 2 -nan -nan -nan 1101 1 -nan -nan -nan 1102 2 -nan -nan -nan 1103 2 -nan -nan -nan 1104 2 -nan -nan -nan 1105 2 -nan -nan -nan 1106 1 -nan -nan -nan 1107 2 -nan -nan -nan 1108 2 -nan -nan -nan 1109 2 -nan -nan -nan 1110 2 -nan -nan -nan 1111 1 -nan -nan -nan 1112 2 -nan -nan -nan 1113 2 -nan -nan -nan 1114 2 -nan -nan -nan 1115 2 -nan -nan -nan 1116 1 -nan -nan -nan 1117 2 -nan -nan -nan 1118 2 -nan -nan -nan 1119 2 -nan -nan -nan 1120 2 -nan -nan -nan 1121 1 -nan -nan -nan 1122 2 -nan -nan -nan 1123 2 -nan -nan -nan 1124 2 -nan -nan -nan 1125 2 -nan -nan -nan 1126 1 -nan -nan -nan 1127 2 -nan -nan -nan 1128 2 -nan -nan -nan 1129 2 -nan -nan -nan 1130 2 -nan -nan -nan 1131 1 -nan -nan -nan 1132 2 -nan -nan -nan 1133 2 -nan -nan -nan 1134 2 -nan -nan -nan 1135 2 -nan -nan -nan 1136 1 -nan -nan -nan 1137 2 -nan -nan -nan 1138 2 -nan -nan -nan 1139 2 -nan -nan -nan 1140 2 -nan -nan -nan 1141 1 -nan -nan -nan 1142 2 -nan -nan -nan 1143 2 -nan -nan -nan 1144 2 -nan -nan -nan 1145 2 -nan -nan -nan 1146 1 -nan -nan -nan 1147 2 -nan -nan -nan 1148 2 -nan -nan -nan 1149 2 -nan -nan -nan 1150 2 -nan -nan -nan 1151 1 -nan -nan -nan 1152 2 -nan -nan -nan 1153 2 -nan -nan -nan 1154 2 -nan -nan -nan 1155 2 -nan -nan -nan 1156 1 -nan -nan -nan 1157 2 -nan -nan -nan 1158 2 -nan -nan -nan 1159 2 -nan -nan -nan 1160 2 -nan -nan -nan 1161 1 -nan -nan -nan |
3樓2015-08-25 15:32:53
missingwudi
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5樓2015-08-28 13:05:42
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