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CP2K: Constrained MD

学习目标

  • CP2K Constrained MD 设置
  • Potential of Mean Force 方法计算反应自由能

学习资料

官网例子, NaCl解离能

Sun, JJ., Cheng, J. Solid-to-liquid phase transitions of sub-nanometer clusters enhance chemical transformation. Nature Communication, 10, 5400 (2019).

CP2K Constrained MD 设置

CP2K 提供了将施加 Constraint 过程中的拉格朗日乘子输出的能力,其统计平均即该反应坐标下的Potential of Mean Force (PMF)。 PMF对反应坐标积分即反应自由能。MLMD 可实现高精度长时间尺度模拟,因而适用于计算化学反应体系的自由能。 这里我们可结合 DeePMD 势进行 Constrained MD 模拟。

首先定义 Collective Variable (CV),这里我们选择两原子间距离进行控制:

&FORCE_EVAL
   ...
   &SUBSYS
      ...
      &COLVAR
         &DISTANCE
            ATOMS 225 226
         &END DISTANCE
      &END COLVAR
      ...
   &END SUBSYS
   ...
&END FORCE_EVAL

其中 225226 即为所需控制键长的原子序号。注意 CP2K 中原子序号从 1 开始。

然后定义所需控制的键长:

&MOTION
   &CONSTRAINT
      &COLLECTIVE
         COLVAR 1
         INTERMOLECULAR .TRUE.
         TARGET 3.4015070391941524 # (1)!
      &END COLLECTIVE
      &LAGRANGE_MULTIPLIERS ON
         COMMON_ITERATION_LEVELS 10000000 # (2)!
      &END LAGRANGE_MULTIPLIERS
   &END CONSTRAINT
   ...
&MOTION
  1. 设置两原子距离的目标值,注意这里的单位是 a.u.
  2. 缺省值为1,为防止输出过长的日志文件,请设置为一个大于总步数的值

注意这里 TARGET 的单位是 a.u.,请把常用的单位(如 Å)转换为原子单位。

附录:物理常数和单位换算

*** Fundamental physical constants (SI units) ***

 *** Literature: B. J. Mohr and B. N. Taylor,
 ***             CODATA recommended values of the fundamental physical
 ***             constants: 2006, Web Version 5.1
 ***             http://physics.nist.gov/constants

 Speed of light in vacuum [m/s]                             2.99792458000000E+08
 Magnetic constant or permeability of vacuum [N/A**2]       1.25663706143592E-06
 Electric constant or permittivity of vacuum [F/m]          8.85418781762039E-12
 Planck constant (h) [J*s]                                  6.62606896000000E-34
 Planck constant (h-bar) [J*s]                              1.05457162825177E-34
 Elementary charge [C]                                      1.60217648700000E-19
 Electron mass [kg]                                         9.10938215000000E-31
 Electron g factor [ ]                                     -2.00231930436220E+00
 Proton mass [kg]                                           1.67262163700000E-27
 Fine-structure constant                                    7.29735253760000E-03
 Rydberg constant [1/m]                                     1.09737315685270E+07
 Avogadro constant [1/mol]                                  6.02214179000000E+23
 Boltzmann constant [J/K]                                   1.38065040000000E-23
 Atomic mass unit [kg]                                      1.66053878200000E-27
 Bohr radius [m]                                            5.29177208590000E-11

 *** Conversion factors ***

 [u] -> [a.u.]                                              1.82288848426455E+03
 [Angstrom] -> [Bohr] = [a.u.]                              1.88972613288564E+00
 [a.u.] = [Bohr] -> [Angstrom]                              5.29177208590000E-01
 [a.u.] -> [s]                                              2.41888432650478E-17
 [a.u.] -> [fs]                                             2.41888432650478E-02
 [a.u.] -> [J]                                              4.35974393937059E-18
 [a.u.] -> [N]                                              8.23872205491840E-08
 [a.u.] -> [K]                                              3.15774647902944E+05
 [a.u.] -> [kJ/mol]                                         2.62549961709828E+03
 [a.u.] -> [kcal/mol]                                       6.27509468713739E+02
 [a.u.] -> [Pa]                                             2.94210107994716E+13
 [a.u.] -> [bar]                                            2.94210107994716E+08
 [a.u.] -> [atm]                                            2.90362800883016E+08
 [a.u.] -> [eV]                                             2.72113838565563E+01
 [a.u.] -> [Hz]                                             6.57968392072181E+15
 [a.u.] -> [1/cm] (wave numbers)                            2.19474631370540E+05
 [a.u./Bohr**2] -> [1/cm]                                   5.14048714338585E+03

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