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liuchenhan新虫 (小有名气)
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[求助]
DNA模拟 已有1人参与
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本人最近做DNA的模拟，遇到如下问题，刚开始做，很多东西还不懂，希望大神指点一下。脚本文件与数据文件上传了。 LAMMPS (14 May 2013) Scanning data file ... 3 = max bonds/atom 6 = max angles/atom 14 = max dihedrals/atom 1 = max impropers/atom Reading data file ... orthogonal box = (-10.907 -10.699 -2.821) to (9.961 16.557 134.259) 1 by 1 by 1 MPI processor grid 2640 atoms 2839 bonds 5116 angles 8346 dihedrals 200 impropers Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-2 neighbors 7 = max # of 1-3 neighbors 18 = max # of 1-4 neighbors 20 = max # of special neighbors Finding SHAKE clusters ... 560 = # of size 2 clusters 120 = # of size 3 clusters 40 = # of size 4 clusters 0 = # of frozen angles PPPM initialization ... WARNING: System is not charge neutral, net charge = -80 (../pppm.cpp:267) G vector (1/distance)= 0.250095 grid = 12 15 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0239292 estimated relative force accuracy = 7.20622e-05 using double precision FFTs 3d grid and FFT values/proc = 20900 8100 Setting up run ... WARNING: Inconsistent image flags (../domain.cpp:594) WARNING: Bond/angle/dihedral extent > half of periodic box length (../domain.cpp:667) Memory usage per processor = 15.2446 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = 3810376070790533.0000 KinEng = 0.0000 Temp = 0.0000 PotEng = 3810376070790533.0000 E_bond = 46241.5899 E_angle = 8875.0528 E_dihed = 2838.1521 E_impro = 0.0019 E_vdwl = 3810376070730726.0000 E_coul = 29596.0619 E_long = -27743.5161 Press = 13404015013180646.0000 ERROR on proc 0: Out of range atoms - cannot compute PPPM (../pppm.cpp:1888) -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. |
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2014-03-19 10:47:03, 1.21 M
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liuchenhan
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脚本文件如下： # Created by charmm2lammps v1.8.1 on Wed Mar 19 10:44:19 CST 2014 units real neigh_modify delay 2 every 1 atom_style full bond_style harmonic angle_style charmm dihedral_style charmm improper_style harmonic pair_style lj/charmm/coul/long 8 10 pair_modify mix arithmetic kspace_style pppm 1e-4 read_data 1ac7.data special_bonds charmm fix 1 all nve fix 2 all shake 1e-6 500 0 m 1.0 velocity all create 0.0 12345678 dist uniform thermo 1 thermo_style multi timestep 0.5 restart 10 1ac7.restart1 1ac7.restart2 dump 1 all atom 10 1ac7.dump dump_modify 1 image yes scale yes run 20 |
2楼2014-03-19 10:48:13
liuchenhan
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用下面的脚本试了好像可以，但还是有warning;大神帮忙解释一下吧，头痛啊。 WARNING: Inconsistent image flags (../domain.cpp:594) WARNING: Bond/angle/dihedral extent > half of periodic box length (../domain.cpp:667) 脚本： # Created by charmm2lammps v1.8.1 on Wed Mar 19 10:44:19 CST 2014 units real neighbor 5.0 nsq neigh_modify delay 2 every 1 atom_style full bond_style harmonic angle_style charmm dihedral_style charmm improper_style harmonic pair_style lj/charmm/coul/long 8 10 pair_modify mix arithmetic kspace_style pppm 1e-4 read_data 1ac7.data special_bonds charmm min_style cg minimize 0.0 1.0e-7 10000 100000 fix 1 all nve fix 2 all shake 1e-6 500 0 m 1.0 velocity all create 0.0 12345678 dist uniform thermo 1 thermo_style multi timestep 0.5 restart 10 1ac7.restart1 1ac7.restart2 dump 1 all atom 10 1ac7.dump dump_modify 1 image yes scale yes run 20 |
3楼2014-03-19 10:57:09
liuasia
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4楼2014-04-04 14:51:11
5楼2014-04-04 15:59:32
liuchenhan
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7楼2016-11-30 21:12:26
wl2009071613
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你好，我最近也是在做lammps的DNA模拟，之前用lammps自带例子运行，出现如下错误提示： =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 139 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES =================================================================================== YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11) This typically refers to a problem with your application. Please see the FAQ page for debugging suggestions 后来采用你修改的in文件和data文件，多了两个warning： WARNING: Inconsistent image flags (../domain.cpp:678) WARNING: Bond/angle/dihedral extent > half of periodic box length (../domain.cpp:799) =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 139 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES =================================================================================== YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11) This typically refers to a problem with your application. Please see the FAQ page for debugging suggestions 求指教  |
8楼2018-04-09 16:43:28
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