标题: CP2K跑AIMD求助，目的：计算溶液体系Z轴方向的氢键数目分布 [打印本页] 作者Author: 1285050231 时间: 2024-9-10 20:03 标题: CP2K跑AIMD求助，目的：计算溶液体系Z轴方向的氢键数目分布 各位同学、老师：
我想使用CP2K做固-液界面的AIMD模拟，整体思路如下：
1.使用MS做晶胞切面，例如（111）面，使用redefine将其改成正交构型，添加真空层（厚度大概25A），使用supercell进行扩胞，使其XY平面满足25A*25A的最小尺寸要求。
2.利用MS自带的AC模块构建溶液体系（溶液组成为：KOH、正丙醇、水分子）。PS：最开始溶液相只画了K+、正丙醇、水分子。今天请教了sob老师，要添加平衡的OH-根离子，后续会加入，使其溶液相电荷总量为0，即charge=0.
3.使用MS的build layer模块组合固-液两相，保证XY平面尺寸满足25A*25A的最低要求。
3.利用MS直接导出cif文件，放入Multiwfn进行CP2K输入文件的编写。目前是直接使用NPT系综进行计算，发现.out文件跑一半任务就中断了。使用.restart文件续算，也是一样的报错结果。
NPT系综参数如下：
&MD
ENSEMBLE NPT_F
STEPS 10000 #Number of steps to run
TIMESTEP 1.0 #Step size in fs. Decrease it properly for high temperature simulation
TEMPERATURE 298.15 #Initial and maintained temperature (K)
# COMVEL_TOL 0 #Uncomment this can remove translation motion of center-of-mass every step
&THERMOSTAT
TYPE CSVR
&CSVR
TIMECON 100 #Time constant in fs. Smaller/larger results in stronger/weaker temperature coupling
&END CSVR
&END THERMOSTAT
&BAROSTAT
PRESSURE 1.01325 #Initial and maintained pressure (bar)
TIMECON 250 #Barostat time constant (fs)
VIRIAL Z #Relax the cell along which cartesian axes
&END BAROSTAT
&PRINT
&PROGRAM_RUN_INFO
&EACH
MD 1 #Output frequency of MD information, 0 means never
&END EACH
&END PROGRAM_RUN_INFO
&END PRINT
&END MD
1.“发现.out文件跑一半任务就中断了”，.out文件写到一半就不写了。这是.out文件最后那一部分，突然就中断了。
----------------------------------- OT ---------------------------------------
Minimizer : DIIS : direct inversion
in the iterative subspace
using 7 DIIS vectors
safer DIIS on
Preconditioner : FULL_KINETIC : inversion of T + eS
Precond_solver : DEFAULT
stepsize : 0.15000000 energy_gap : 0.20000000
eps_taylor : 0.10000E-15 max_taylor : 4
----------------------------------- OT ---------------------------------------
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
1 OT DIIS 0.15E+00 43.9 0.00002402 -74203.5090124383 4.80E-01
2 OT SD 0.15E+00 15.0 0.00084341 -74243.4686953126 -4.00E+01
3 OT SD 0.15E+00 17.0 0.00032434 -74250.4201344706 -6.95E+00
4 OT SD 0.15E+00 16.8 0.00028082 -74251.7556910641 -1.34E+00
5 OT SD 0.15E+00 16.8 0.00041374 -74252.4957362250 -7.40E-01
6 OT DIIS 0.15E+00 15.1 0.00086388 -74251.8863354406 6.09E-01
7 OT DIIS 0.15E+00 14.8 0.00085655 -74243.1139618725 8.77E+00
8 OT DIIS 0.15E+00 16.4 0.00084633 -74243.3455312088 -2.32E-01
9 OT DIIS 0.15E+00 16.8 0.00023922 -74253.0525640467 -9.71E+00
10 OT SD 0.15E+00 16.7 0.00049087 -74254.1101209751 -1.06E+00
11 OT DIIS 0.15E+00 16.7 0.00053035 -74255.4415508160 -1.33E+00
12 OT SD 0.15E+00 16.8 0.00029771 -74252.9173701697 2.52E+00
13 OT SD 0.15E+00 16.8 0.00031419 -74253.4693215293 -5.52E-01
14 OT DIIS 0.15E+00 16.8 0.00056504 -74253.6472361066 -1.78E-01
15 OT SD 0.15E+00 16.8 0.00088073 -74248.5703772239 5.08E+00
16 OT DIIS 0.15E+00 16.8 0.00049381 -74251.9277156837 -3.36E+00
17 OT DIIS 0.15E+00 16.8 0.00035888 -74252.7865259087 -8.59E-01
18 OT SD 0.15E+00 16.7 0.00026900 -74256.6042538035 -3.82E+00
19 OT SD 0.15E+00 16.7 0.00039414 -74254.0591334464 2.55E+00
20 OT SD 0.15E+00 16.8 0.00118470 -74240.3496510453 1.37E+01
21 OT DIIS 0.15E+00 16.7 0.00130744 -74246.9227949049 -6.57E+00
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 0 PID 302852 RUNNING AT m3co1706
= KILLED BY SIGNAL: 9 (Killed)
===================================================================================
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 1 PID 302853 RUNNING AT m3co1706
= KILLED BY SIGNAL: 9 (Killed)
===================================================================================
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 2 PID 302854 RUNNING AT m3co1706
= KILLED BY SIGNAL: 9 (Killed)
===================================================================================
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 3 PID 302855 RUNNING AT m3co1706
= KILLED BY SIGNAL: 9 (Killed)
===================================================================================
…………
2.关于25A*25A的最小要求，这个是从B站学习MS建模构建液相盒子时学到的知识，就是盒子尺寸要满足“大于常用的范德华力截断半径（12.5A）的两倍，即25A”。不确定这句话是否我的体系也需要考虑？
体系是固相-Ni(111)单晶与液相-KOH、丙醇、水构建的溶液盒子模型。不知道sob老师说的体系特征是不是这个？
3.“MD只要跑起来不崩”这句话的含义是：只要收敛不报错就可以不进行结构优化，我理解的对吗？
4.做NPT条件盒子让密度自发变得合理：关于这个具体的参数设计，请教一下sob老师，我应该采用NPT_F还是NPT_I？参考《TiO2与水界面的模拟》案例倾向于使用NPT_F模型，即各项异性。且同时仿照案例参数将VIRIAL设为Z使得模拟过程中只有盒子Z方向运行改变（液相在Z轴上方/固相在Z轴下方），这样是否可行？