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Atom too close是检查到原子之间的距离比某个阈值(例如0.44埃)更小,不太合理,从而出现的一个报错提示:
<Sep28-2022> <16:32:08> AMS 2022.103 RunTime: Sep28-2022 16:32:08 ShM Nodes: 1 Procs: 1 <Sep28-2022> <16:32:08> Starting MD calculation: <Sep28-2022> <16:32:08> -------------------- <Sep28-2022> <16:32:08> Molecular Dynamics <Sep28-2022> <16:32:08> -------------------- <Sep28-2022> <16:32:08> Step Time Temp. E Pot Pressure Volume <Sep28-2022> <16:32:08> (fs) (K) (au) (MPa) (A^3) <Sep28-2022> <16:32:09> 0 0.00 100000. -39.24009 133821.625 3048.6 <Sep28-2022> <16:32:09> ERROR: Atoms are too close
应对方法可以选择: 减小步长 使用更强的原子核排斥力场 关闭原子距离合理性检查:在*.run文件中System关键词下添加一行AllowCloseAtoms 例如下面所示:
Task MolecularDynamics MolecularDynamics NSteps 10000 InitialVelocities Temperature 100000 End End System AllowCloseAtoms Atoms O -0.504773 5.284954 -2.548218 region=Auto_Generated H -0.328778 5.33505 -1.591707 region=Auto_Generated H 0.040776 6.00106 -2.919658 region=Auto_Generated O -3.843405 5.844568 -2.731233 region=Auto_Generated H -3.644653 5.433078 -3.591217 region=Auto_Generated H -2.964097 5.999452 -2.342355 region=Auto_Generated ……