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基于CP2K的大尺寸材料纳米锥分子动力学外加势场模拟
基于CP2K的大体系纳米锥分子动力学模拟与外加势场应用
近期发表在ACS Nano2024上的一篇文献《Strain-Engineered Ferroelectricity in 2H Bilayer MoS2》，详细介绍了实验制备的二硫化钼（MoS2）纳米锥，并用密度泛函理论（DFT）计算进行了模拟，如下图所示：
此文献所使用的计算软件是VASP。作为目前常用的第一性原理计算软件VASP在精确模拟小体系方面表现出色，但由于其计算尺度的限制，难以模拟大尺寸的材料。
那么，如果真的要模拟大尺度的材料，该如何做呢？首先推荐使用CP2K，CP2K的一个特点是其能够高效地处理大量原子的模拟，尤其适合进行高精度的材料模拟和大规模的分子动力学模拟。
本文将以二维半导体材料二硫化钼MoS2为例，详细介绍如何使用CP2K进行大尺寸材料纳米锥的分子动力学外加势场模拟。
步骤1：结构优化
目前，超算互联网提供编译好的CP2K，支持开箱即用。本次实操，我们使用cp2k 2023.1-intelmpi-2018版本，如下图所示：
首先，普通的结构优化我们只能得到基态的构型，如下图所示：
想要模拟纳米锥，我们需要加一个力场，模拟衬底对薄膜的作用，如下图所示：
要使得材料受到如图所示的力，可以考虑施加一个高斯势：
接下来，通过Multiwfn生成相关输入文件，准备扩胞后的cif文件，如下图所示：
然后依次输入：
cp2k-enter-enter—1-enter-4-enter-0-enter-q-enter
最终就会在当前文件夹生成结构优化的输入文件
当然，要外加势场，还需要对输入文件进行修改，这里先给出修改后的cp2k输入文件如下
shell
&GLOBAL
PROJECT 8-41
PRINT_LEVEL LOW
RUN_TYPE CELL_OPT
&END GLOBAL
&FORCE_EVAL
METHOD Quickstep
&SUBSYS
&CELL
A 25.45920000 0.00000000 0.00000000
B 0.00002347 22.04840100 0.00000000
C 0.00000000 0.00000000 40.00000000
PERIODIC XYZ #Direction(s) of applied PBC (geometry aspect)
&END CELL
&COORD
S 1.59015715 0.91743397 11.55700000
S 1.59016302 6.42953422 11.55700000
S 1.59016889 11.94163447 11.55700000
S 1.59017475 17.45373472 11.55700000
S 4.77255715 0.91743397 11.55700000
S 4.77256302 6.42953422 11.55700000
S 4.77256889 11.94163447 11.55700000
S 4.77257475 17.45373472 11.55700000
S 7.95495715 0.91743397 11.55700000
S 7.95496302 6.42953422 11.55700000
S 7.95496889 11.94163447 11.55700000
S 7.95497475 17.45373472 11.55700000
S 11.13735715 0.91743397 11.55700000
S 11.13736302 6.42953422 11.55700000
S 11.13736889 11.94163447 11.55700000
S 11.13737475 17.45373472 11.55700000
S 14.31975715 0.91743397 11.55700000
S 14.31976302 6.42953422 11.55700000
S 14.31976889 11.94163447 11.55700000
S 14.31977475 17.45373472 11.55700000
S 17.50215715 0.91743397 11.55700000
S 17.50216302 6.42953422 11.55700000
S 17.50216889 11.94163447 11.55700000
S 17.50217475 17.45373472 11.55700000
S 20.68455715 0.91743397 11.55700000
S 20.68456302 6.42953422 11.55700000
S 20.68456889 11.94163447 11.55700000
S 20.68457475 17.45373472 11.55700000
S 23.86695715 0.91743397 11.55700000
S 23.86696302 6.42953422 11.55700000
S 23.86696889 11.94163447 11.55700000
S 23.86697475 17.45373472 11.55700000
S 3.18136008 3.67348409 11.55700000
S 3.18136595 9.18558434 11.55700000
S 3.18137182 14.69768459 11.55700000
S 3.18137769 20.20978484 11.55700000
S 6.36376008 3.67348409 11.55700000
S 6.36376595 9.18558434 11.55700000
S 6.36377182 14.69768459 11.55700000
S 6.36377769 20.20978484 11.55700000
S 9.54616008 3.67348409 11.55700000
S 9.54616595 9.18558434 11.55700000
S 9.54617182 14.69768459 11.55700000
S 9.54617769 20.20978484 11.55700000
S 12.72856008 3.67348409 11.55700000
S 12.72856595 9.18558434 11.55700000
S 12.72857182 14.69768459 11.55700000
S 12.72857769 20.20978484 11.55700000
S 15.91096008 3.67348409 11.55700000
S 15.91096595 9.18558434 11.55700000
S 15.91097182 14.69768459 11.55700000
S 15.91097769 20.20978484 11.55700000
S 19.09336008 3.67348409 11.55700000
S 19.09336595 9.18558434 11.55700000
S 19.09337182 14.69768459 11.55700000
S 19.09337769 20.20978484 11.55700000
S 22.27576008 3.67348409 11.55700000
S 22.27576595 9.18558434 11.55700000
S 22.27577182 14.69768459 11.55700000
S 22.27577769 20.20978484 11.55700000
S 25.45816008 3.67348409 11.55700000
S 25.45816595 9.18558434 11.55700000
S 25.45817182 14.69768459 11.55700000
S 25.45817769 20.20978484 11.55700000
S 1.59015715 0.91743397 8.42952000
S 1.59016302 6.42953422 8.42952000
S 1.59016889 11.94163447 8.42952000
S 1.59017475 17.45373472 8.42952000
S 4.77255715 0.91743397 8.42952000
S 4.77256302 6.42953422 8.42952000
S 4.77256889 11.94163447 8.42952000
S 4.77257475 17.45373472 8.42952000
S 7.95495715 0.91743397 8.42952000
S 7.95496302 6.42953422 8.42952000
S 7.95496889 11.94163447 8.42952000
S 7.95497475 17.45373472 8.42952000
S 11.13735715 0.91743397 8.42952000
S 11.13736302 6.42953422 8.42952000
S 11.13736889 11.94163447 8.42952000
S 11.13737475 17.45373472 8.42952000
S 14.31975715 0.91743397 8.42952000
S 14.31976302 6.42953422 8.42952000
S 14.31976889 11.94163447 8.42952000
S 14.31977475 17.45373472 8.42952000
S 17.50215715 0.91743397 8.42952000
S 17.50216302 6.42953422 8.42952000
S 17.50216889 11.94163447 8.42952000
S 17.50217475 17.45373472 8.42952000
S 20.68455715 0.91743397 8.42952000
S 20.68456302 6.42953422 8.42952000
S 20.68456889 11.94163447 8.42952000
S 20.68457475 17.45373472 8.42952000
S 23.86695715 0.91743397 8.42952000
S 23.86696302 6.42953422 8.42952000
S 23.86696889 11.94163447 8.42952000
S 23.86697475 17.45373472 8.42952000
S 3.18136008 3.67348409 8.42952000
S 3.18136595 9.18558434 8.42952000
S 3.18137182 14.69768459 8.42952000
S 3.18137769 20.20978484 8.42952000
S 6.36376008 3.67348409 8.42952000
S 6.36376595 9.18558434 8.42952000
S 6.36377182 14.69768459 8.42952000
S 6.36377769 20.20978484 8.42952000
S 9.54616008 3.67348409 8.42952000
S 9.54616595 9.18558434 8.42952000
S 9.54617182 14.69768459 8.42952000
S 9.54617769 20.20978484 8.42952000
S 12.72856008 3.67348409 8.42952000
S 12.72856595 9.18558434 8.42952000
S 12.72857182 14.69768459 8.42952000
S 12.72857769 20.20978484 8.42952000
S 15.91096008 3.67348409 8.42952000
S 15.91096595 9.18558434 8.42952000
S 15.91097182 14.69768459 8.42952000
S 15.91097769 20.20978484 8.42952000
S 19.09336008 3.67348409 8.42952000
S 19.09336595 9.18558434 8.42952000
S 19.09337182 14.69768459 8.42952000
S 19.09337769 20.20978484 8.42952000
S 22.27576008 3.67348409 8.42952000
S 22.27576595 9.18558434 8.42952000
S 22.27577182 14.69768459 8.42952000
S 22.27577769 20.20978484 8.42952000
S 25.45816008 3.67348409 8.42952000
S 25.45816595 9.18558434 8.42952000
S 25.45817182 14.69768459 8.42952000
S 25.45817769 20.20978484 8.42952000
Mo 3.18135813 1.83614674 9.99324000
Mo 3.18136400 7.34824699 9.99324000
Mo 3.18136986 12.86034724 9.99324000
Mo 3.18137573 18.37244749 9.99324000
Mo 6.36375813 1.83614674 9.99324000
Mo 6.36376400 7.34824699 9.99324000
Mo 6.36376986 12.86034724 9.99324000
Mo 6.36377573 18.37244749 9.99324000
Mo 9.54615813 1.83614674 9.99324000
Mo 9.54616400 7.34824699 9.99324000
Mo 9.54616986 12.86034724 9.99324000
Mo 9.54617573 18.37244749 9.99324000
Mo 12.72855813 1.83614674 9.99324000
Mo 12.72856400 7.34824699 9.99324000
Mo 12.72856986 12.86034724 9.99324000
Mo 12.72857573 18.37244749 9.99324000
Mo 15.91095813 1.83614674 9.99324000
Mo 15.91096400 7.34824699 9.99324000
Mo 15.91096986 12.86034724 9.99324000
Mo 15.91097573 18.37244749 9.99324000
Mo 19.09335813 1.83614674 9.99324000
Mo 19.09336400 7.34824699 9.99324000
Mo 19.09336986 12.86034724 9.99324000
Mo 19.09337573 18.37244749 9.99324000
Mo 22.27575813 1.83614674 9.99324000
Mo 22.27576400 7.34824699 9.99324000
Mo 22.27576986 12.86034724 9.99324000
Mo 22.27577573 18.37244749 9.99324000
Mo 25.45815813 1.83614674 9.99324000
Mo 25.45816400 7.34824699 9.99324000
Mo 25.45816986 12.86034724 9.99324000
Mo 25.45817573 18.37244749 9.99324000
Mo 1.59016106 4.59219686 9.99324000
Mo 1.59016693 10.10429711 9.99324000
Mo 1.59017280 15.61639736 9.99324000
Mo 1.59017867 21.12849761 9.99324000
Mo 4.77256106 4.59219686 9.99324000
Mo 4.77256693 10.10429711 9.99324000
Mo 4.77257280 15.61639736 9.99324000
Mo 4.77257867 21.12849761 9.99324000
Mo 7.95496106 4.59219686 9.99324000
Mo 7.95496693 10.10429711 9.99324000
Mo 7.95497280 15.61639736 9.99324000
Mo 7.95497867 21.12849761 9.99324000
Mo 11.13736106 4.59219686 9.99324000
Mo 11.13736693 10.10429711 9.99324000
Mo 11.13737280 15.61639736 9.99324000
Mo 11.13737867 21.12849761 9.99324000
Mo 14.31976106 4.59219686 9.99324000
Mo 14.31976693 10.10429711 9.99324000
Mo 14.31977280 15.61639736 9.99324000
Mo 14.31977867 21.12849761 9.99324000
Mo 17.50216106 4.59219686 9.99324000
Mo 17.50216693 10.10429711 9.99324000
Mo 17.50217280 15.61639736 9.99324000
Mo 17.50217867 21.12849761 9.99324000
Mo 20.68456106 4.59219686 9.99324000
Mo 20.68456693 10.10429711 9.99324000
Mo 20.68457280 15.61639736 9.99324000
Mo 20.68457867 21.12849761 9.99324000
Mo 23.86696106 4.59219686 9.99324000
Mo 23.86696693 10.10429711 9.99324000
Mo 23.86697280 15.61639736 9.99324000
Mo 23.86697867 21.12849761 9.99324000
&END COORD
&KIND S
ELEMENT S
BASIS_SET DZVP-MOLOPT-SR-GTH-q6
POTENTIAL GTH-PBE
&END KIND
&KIND Mo
ELEMENT Mo
BASIS_SET DZVP-MOLOPT-SR-GTH-q14
POTENTIAL GTH-PBE
&END KIND
&END SUBSYS
&DFT
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME POTENTIAL
# WFN_RESTART_FILE_NAME 8-41-RESTART.wfn
CHARGE 0 #Net charge
MULTIPLICITY 1 #Spin multiplicity
&QS
EPS_DEFAULT 1.0E-12 #Set all EPS_xxx to values such that the energy will be correct up to this value
&END QS
&POISSON
PERIODIC XYZ #Direction(s) of PBC for calculating electrostatics
PSOLVER PERIODIC #The way to solve Poisson equation
&END POISSON
&XC
&XC_FUNCTIONAL PBE
&END XC_FUNCTIONAL
&END XC
&MGRID
CUTOFF 400
REL_CUTOFF 55
&END MGRID
&SCF
MAX_SCF 128
EPS_SCF 1.0E-06 #Convergence threshold of density matrix of inner SCF
# SCF_GUESS RESTART #Use wavefunction from WFN_RESTART_FILE_NAME file as initial guess
# IGNORE_CONVERGENCE_FAILURE #Continue calculation even if SCF not converged, works for version >= 2024.1
&DIAGONALIZATION
ALGORITHM STANDARD #Algorithm for diagonalization
&END DIAGONALIZATION
&MIXING #How to mix old and new density matrices
METHOD BROYDEN_MIXING #PULAY_MIXING is also a good alternative
ALPHA 0.4 #Default. Mixing 40% of new density matrix with the old one
NBROYDEN 8 #Default is 4. Number of previous steps stored for the actual mixing scheme
&END MIXING
&PRINT
&RESTART #Note: Use "&RESTART OFF" can prevent generating .wfn file
BACKUP_COPIES 0 #Maximum number of backup copies of wfn file. 0 means never
&END RESTART
&END PRINT
&END SCF
&END DFT
&PRINT
&STRESS_TENSOR ON #Print stress tensor
&END STRESS_TENSOR
&END PRINT
STRESS_TENSOR ANALYTICAL #Compute full stress tensor analytically
&EXTERNAL_POTENTIAL
FUNCTION "-A * exp(- ( (X-25.45920000)^2 + (Y-22.04840100)^2 ) / (2 * sigma^2) ) * Z"
PARAMETERS A sigma
VALUES 0.01 10
ATOMS_LIST 15 19 46 79 83 110 143 174 178
&END EXTERNAL_POTENTIAL
&END FORCE_EVAL
&MOTION
&CELL_OPT
MAX_ITER 400 #Maximum number of geometry optimization
EXTERNAL_PRESSURE 1.01325E+00 #External pressure for cell optimization (bar)
CONSTRAINT Z #Constraint of cell length, can be: NONE, X, Y, Z, XY, XZ, YZ
KEEP_ANGLES F #If T, then cell angles will be kepted
KEEP_SYMMETRY F #If T, then cell symmetry specified by &CELL / SYMMETRY will be kepted
KEEP_SPACE_GROUP F #If T, then space group will be detected and preserved
TYPE DIRECT_CELL_OPT #Geometry and cell are optimized at the same time. Can also be GEO_OPT, MD
#The following thresholds of optimization convergence are the default ones
MAX_DR 3E-3 #Maximum geometry change
RMS_DR 1.5E-3 #RMS geometry change
MAX_FORCE 4.5E-4 #Maximum force
RMS_FORCE 3E-4 #RMS force
PRESSURE_TOLERANCE 100 #Pressure tolerance (w.r.t EXTERNAL_PRESSURE)
OPTIMIZER BFGS #Can also be CG (more robust for difficult cases) or LBFGS
&BFGS
TRUST_RADIUS 0.2 #Trust radius (maximum stepsize) in Angstrom
# RESTART_HESSIAN T #If read initial Hessian, uncomment this line and specify the file in the next line
# RESTART_FILE_NAME to_be_specified
&END BFGS
&END CELL_OPT
&PRINT
&TRAJECTORY
FORMAT pdb
&END TRAJECTORY
&RESTART
BACKUP_COPIES 0 #Maximum number of backing up restart file, 0 means never
&END RESTART
&RESTART_HISTORY OFF
&END RESTART_HISTORY
&END PRINT
&CONSTRAINT
&FIXED_ATOMS
LIST 157 158 159 160 129 133 137 141 145 149 153 157 # 固定这些原子（假设是边缘原子的索引）
COMPONENTS_TO_FIX Z # 只在 z 方向固定（如果二维材料在 x-y 平面）
&END FIXED_ATOMS
&END CONSTRAINT
&END MOTION大家可能会觉得输入文件比较长，需要重点关注的有以下几点：
（1）GLOBAL 模块，RUN_TYPE: 定义计算的类型，这里为CELL_OPT，表示优化晶胞和几何结构。
（2）FORCE_EVAL模块中的SUBSYS子模块，CELL: 定义晶胞参数。PERIODIC XYZ表示体系在x，y，z方向都施加周期性边界条件 (PBC)。
（3）FORCE_EVAL模块中EXTERNAL_POTENTIAL子模块，主要用来定义外部势函数。
（4）MOTION模块中的子模块CONSTRAINT模块，设置对原子位置的约束。
下面是每个模块详解：
GLOBAL 模块
PROJECT: 指定计算项目的名称。
PRINT_LEVEL: 设置输出的详细程度，这里为 LOW，即简化输出。
RUN_TYPE: 定义计算的类型，这里为 CELL_OPT，表示优化晶胞和几何结构。FORCE_EVAL 模块
定义如何计算体系的能量和力。
2.1 METHOD
使用 Quickstep 方法，基于 DFT 的快速计算方法。
2.2 SUBSYS 模块
定义体系的几何结构和物质属性。
CELL: 定义晶胞参数。
COORD: 列出了所有原子的位置坐标，格式为：元素符号 x y z。
KIND: 定义原子类型及其相关的基组和赝势。
S: 硫原子，使用 DZVP-MOLOPT-SR-GTH-q6 基组和 GTH-PBE 赝势。
Mo: 钼原子，使用 DZVP-MOLOPT-SR-GTH-q14 基组和 GTH-PBE 赝势。
2.3 DFT 模块
设置 DFT 相关的参数。
BASIS_SET_FILE_NAME 和 POTENTIAL_FILE_NAME: 提供基组和赝势文件路径。
CHARGE: 设置体系的总电荷，这里为中性体系（0）。
XC 模块:
使用 PBE 交换-相关泛函。
MGRID 模块:
CUTOFF 400: 定义计算网格的能量截止值（单位：Ry）。
REL_CUTOFF 55: 定义相对截止值。
SCF 模块: 设置自洽场 (SCF) 计算的相关参数。
EPS_SCF 1E-06: SCF 密度矩阵的收敛阈值。
DIAGONALIZATION: 使用标准对角化算法。
MIXING: 使用布罗伊登混合方法（BROYDEN_MIXING），α=0.4。
RESTART: 生成和保存波函数的中间文件。
2.4 PRINT 模块
输出应力张量（STRESS_TENSOR ON）。
STRESS_TENSOR ANALYTICAL: 采用解析方法计算应力张量。
2.5 EXTERNAL_POTENTIAL
定义外部势函数
- MOTION 模块
设置几何和晶胞优化的相关参数。
3.1 CELL_OPT 模块
MAX_ITER 400: 最大优化迭代步数。
EXTERNAL_PRESSURE 1.01325: 外部施加的压力，单位为 bar。
收敛标准:
MAX_DR 3E-3: 最大原子位移为 0.003 Å。
MAX_FORCE 4.5E-4: 最大力收敛阈值为 0.00045 eV/Å。
PRESSURE_TOLERANCE 100: 对压力的容忍范围。
OPTIMIZER: 使用 BFGS 优化器。
TRUST_RADIUS 0.2: 优化步长的最大信任半径。
3.2 PRINT 模块
输出轨迹文件（格式为 PDB）。
保存中间重启文件（RESTART）。
3.3 CONSTRAINT 模块
设置对原子位置的约束。
FIXED_ATOMS: 固定指定的原子（通过索引列表），并且只固定其Z坐标。
运行结束后会得到优化好的pdb文件，打开文件可以看到以下内容： 
Step代表优化的步数，CRYST1代表晶格常数，后面的六个参数分别是三个坐标轴的长度以及角度。继续往下是每个原子的笛卡尔坐标信息。为了直观地展示这些结构数据，第一种方法可以手动改写为POSCAR格式以实现可视化，这种方式较为繁琐；这里我们推荐使用超算互联网可视化软件ovito展示结构文件。 
在超算互联网搜索栏搜索OVITO，购买即用。我们使用图形的方式运行OVITO，并加载pdb文件，如下图所示： 
步骤2：分子动力学模拟
经过上一步的结构优化计算，我们会得到一个restart文件，接下来修改restart文件，进行分子动力学模拟，输入文件如下：
shell
&GLOBAL
PROJECT MoS2
PRINT_LEVEL MEDIUM
RUN_TYPE MD
EXTENDED_FFT_LENGTHS T
&END GLOBAL
&FORCE_EVAL
METHOD Quickstep
&SUBSYS
&CELL
A 2.5459410302705308E+01 0.0000000000000000E+00 0.0000000000000000E+00
B -1.4123355796776552E-04 2.2050289489867659E+01 0.0000000000000000E+00
C 0.0000000000000000E+00 0.0000000000000000E+00 4.0000000000000007E+01
PERIODIC XYZ
MULTIPLE_UNIT_CELL 1 1 1
&END CELL
&COORD
S 2.3371909369130224E+00 1.5602583020398935E+00 1.1549809845925406E+01
S 2.2854318022479907E+00 7.0471321727496612E+00 1.1601630681281591E+01
S 2.2550033361926962E+00 1.2588256561127332E+01 1.1657736296891240E+01
S 2.3033104760493028E+00 1.8127360929933879E+01 1.1606921172799041E+01
S 5.5168989001383615E+00 1.5779598678228586E+00 1.1560601460811831E+01
S 5.4059424958248110E+00 6.9871443320088247E+00 1.1786621509887194E+01
S 5.3409829832461195E+00 1.2585018390735581E+01 1.1990690992983090E+01
S 5.4422974643221007E+00 1.8185275681472596E+01 1.1781019113005506E+01
S 8.7010676899127635E+00 1.5993008368996566E+00 1.1571129076435762E+01
S 8.5709316854388700E+00 6.8960626661870812E+00 1.2039506386766972E+01
S 8.4830257307995183E+00 1.2587623122570383E+01 1.2460459231822888E+01
S 8.6180244344271966E+00 1.8266950876524554E+01 1.2015666940197349E+01
S 1.1887575152323528E+01 1.6131532676543687E+00 1.1576826483048603E+01
S 1.1817178245650188E+01 6.8234510578316270E+00 1.2253343130638473E+01
S 1.1804129402580047E+01 1.2595774175199173E+01 1.2959553349530786E+01
S 1.1847453785373917E+01 1.8338992372648352E+01 1.2193737485887398E+01
S 1.5075048017570156E+01 1.6130766203812570E+00 1.1577075438422698E+01
S 1.5137925283356013E+01 6.8237920744090239E+00 1.2254273379898169E+01
S 1.5147546131325164E+01 1.2595534682338602E+01 1.2960307360788121E+01
S 1.5111743630309400E+01 1.8338074804701819E+01 1.2193138625714973E+01
S 1.8260794753781607E+01 1.5988545999432313E+00 1.1570998332836851E+01
S 1.8385150345554958E+01 6.8972777828367215E+00 1.2042079174176356E+01
S 1.8470938408885825E+01 1.2587959836175903E+01 1.2462626651212169E+01
S 1.8340056610478687E+01 1.8264843391070833E+01 1.2015180473868343E+01
S 2.1442907140137837E+01 1.5779066236509158E+00 1.1560752341155149E+01
S 2.1551175275886081E+01 6.9885378724867424E+00 1.1789387406607029E+01
S 2.1615493425917869E+01 1.2585372102892798E+01 1.1993050281146399E+01
S 2.1515012191556416E+01 1.8183445015330321E+01 1.1780743744206163E+01
S 2.4621241562197476E+01 1.5603580765383178E+00 1.1549739742520416E+01
S 2.4673078292597307E+01 7.0475463029469516E+00 1.1602551149156023E+01
S 2.4703629763479178E+01 1.2588601161815234E+01 1.1658496874507771E+01
S 2.4653435572655475E+01 1.8126878449474670E+01 1.1606660069143864E+01
S 3.8901273044334208E+00 4.2882134471801647E+00 1.1592359285748172E+01
S 3.8051969263694017E+00 9.7896972141165630E+00 1.1774853522588877E+01
S 3.8262089582908576E+00 1.5374815524177992E+01 1.1768068131964393E+01
S 3.9083718815887942E+00 2.0898448719637589E+01 1.1588580215333085E+01
S 7.0584041418765819E+00 4.2334903966737549E+00 1.1667029905357596E+01
S 6.9138226852875526E+00 9.7337539214214104E+00 1.2133922098848599E+01
S 6.9529948234265690E+00 1.5433711470598260E+01 1.2111703655737655E+01
S 7.0841217662597504E+00 2.0955857985648642E+01 1.1682648493281389E+01
S 1.0253546467732511E+01 4.1793586710262733E+00 1.1745232264158348E+01
S 1.0098397378779644E+01 9.6558193968351027E+00 1.2564184198127423E+01
S 1.0160710132576158E+01 1.5518689474253105E+01 1.2492669834074036E+01
S 1.0275207408990459E+01 2.1011861625224672E+01 1.1774839495855936E+01
S 1.3480109260534674E+01 4.1549782704096385E+00 1.1782279642330995E+01
S 1.3475824370238612E+01 9.6747850037314898E+00 1.2865678070048757E+01
S 1.3477477031066396E+01 1.5583371813911777E+01 1.2678776824678284E+01
S 1.3481140177838608E+01 2.1035474170434380E+01 1.1814023896582135E+01
S 1.6706524945456874E+01 4.1792012657250535E+00 1.1745881131564181E+01
S 1.6854623444810915E+01 9.6572177077148673E+00 1.2566174076149254E+01
S 1.6794310569851735E+01 1.5517773803465102E+01 1.2492661890962053E+01
S 1.6687154196334379E+01 2.1011324926437272E+01 1.1774591123236773E+01
S 1.9900445801314554E+01 4.2341185340823939E+00 1.1668318756593981E+01
S 2.0041414614364854E+01 9.7351808426001778E+00 1.2137334827821002E+01
S 2.0002307975641493E+01 1.5432460348905568E+01 1.2112484149714509E+01
S 1.9875966147026009E+01 2.0954124048270074E+01 1.1681967091424241E+01
S 2.3068196137724481E+01 4.2891671855832385E+00 1.1593070754361829E+01
S 2.3152875217648685E+01 9.7905745854219095E+00 1.1777373239835569E+01
S 2.3130765711195405E+01 1.5374115731664705E+01 1.1768755394037894E+01
S 2.3049689867552317E+01 2.0897132995099035E+01 1.1588108169138742E+01
S 2.6208672274587343E+01 4.3124691884362392E+00 1.1560768427398884E+01
S 2.6209470835654923E+01 9.7972511351457268E+00 1.1615666482815026E+01
S 2.6208371817826059E+01 1.5327622323380332E+01 1.1598169038724153E+01
S 2.6208314729887373E+01 2.0868891005126528E+01 1.1542582949211805E+01
S 2.3472274234606911E+00 1.5713005617160107E+00 8.4175996506606552E+00
S 2.4084565398912821E+00 7.1252988517066411E+00 8.4761061817303016E+00
S 2.4466588439263219E+00 1.2601464195404303E+01 8.5349620470111383E+00
S 2.3876599820435440E+00 1.8074238277751217E+01 8.4766527845903958E+00
S 5.5399938935675701E+00 1.5539915783523879E+00 8.4294490506762649E+00
S 5.6617745818699552E+00 7.1828615489516734E+00 8.6737028275654318E+00
S 5.7219864673386347E+00 1.2602593372107641E+01 8.8834285059495848E+00
S 5.6228985290312270E+00 1.8016789500038996E+01 8.6587342804970380E+00
S 8.7243638806831108E+00 1.5314357795686169E+00 8.4459686599719443E+00
S 8.8554686505014786E+00 7.2662191909053924E+00 8.9445652032580085E+00
S 8.9183218620786384E+00 1.2595008561484617E+01 9.3706516401423610E+00
S 8.8032083407100536E+00 1.7932030074487137E+01 8.9091535514160665E+00
S 1.1897636707933337E+01 1.5140563105228095E+00 8.4586678725579922E+00
S 1.1966965022595202E+01 7.3332812881168259E+00 9.1717333116336714E+00
S 1.2006324861441490E+01 1.2551770064117447E+01 9.8459238852100555E+00
S 1.1929078817152009E+01 1.7862548646231065E+01 9.1021116047783650E+00
S 1.5065013241208772E+01 1.5137812530233343E+00 8.4586228149644480E+00
S 1.4989986866093449E+01 7.3339478953068982E+00 9.1728215078886102E+00
S 1.4947045941306653E+01 1.2551393290680611E+01 9.8467966359162649E+00
S 1.5029285312337265E+01 1.7862052411221679E+01 9.1017470409644794E+00
S 1.8237684410876845E+01 1.5317427092010092E+00 8.4455137527192328E+00
S 1.8101364573874257E+01 7.2679332286853011E+00 8.9471000616990803E+00
S 1.8036516946177862E+01 1.2593923497729778E+01 9.3719759754527914E+00
S 1.8154775092749841E+01 1.7930070612872445E+01 8.9082580838773424E+00
S 2.1419879302192051E+01 1.5546416751843886E+00 8.4289822283530160E+00
S 2.1294422351948405E+01 7.1852426182044180E+00 8.6763534251318362E+00
S 2.1234395168445413E+01 1.2601523421953560E+01 8.8854881132722703E+00
S 2.1334126619273583E+01 1.8014098224289157E+01 8.6577772018149677E+00
S 2.4611162543148247E+01 1.5716228736689841E+00 8.4174884296666370E+00
S 2.4548115864626549E+01 7.1267075907048083E+00 8.4774111174592210E+00
S 2.4511147388408318E+01 1.2600995609292760E+01 8.5363247099412352E+00
S 2.4569496557547129E+01 1.8073222237681193E+01 8.4764366808300533E+00
S 3.9832791858314369E+00 4.3645102281607713E+00 8.4638832055549980E+00
S 4.0819607156175177E+00 9.8930193072593031E+00 8.6585309645991781E+00
S 4.0586939730621872E+00 1.5321025940195602E+01 8.6456901609021770E+00
S 3.9670957415197048E+00 2.0815427977635423E+01 8.4581648433026118E+00
S 7.1874441829151703E+00 4.4258777852119957E+00 8.5472009740069605E+00
S 7.3238924055606827E+00 9.9378350983881028E+00 9.0396858658055699E+00
S 7.2822185275424536E+00 1.5262080291007228E+01 9.0032373724070531E+00
S 7.1624116201949617E+00 2.0753584218178190E+01 8.5588802272621010E+00
S 1.0356430484308419E+01 4.4952836857513114E+00 8.6367054740874583E+00
S 1.0483395150395312E+01 9.9898621714135611E+00 9.4951382375924869E+00
S 1.0420608828669526E+01 1.5181902103577539E+01 9.4005453467458207E+00
S 1.0331821997850826E+01 2.0684280683921369E+01 8.6615012152996051E+00
S 1.3480560337227987E+01 4.5260673466243579E+00 8.6771435498243488E+00
S 1.3476979510967348E+01 1.0023697049985952E+01 9.7615047171397666E+00
S 1.3477208360851119E+01 1.5133545214817497E+01 9.6018368093574686E+00
S 1.3481053402769829E+01 2.0652273254086605E+01 8.7071727939194261E+00
S 1.6604234528534199E+01 4.4959069575465884E+00 8.6372383360167131E+00
S 1.6471008368021117E+01 9.9907315354489850E+00 9.4971049030618175E+00
S 1.6534386916783610E+01 1.5179981251761172E+01 9.4002442827577983E+00
S 1.6629629659872045E+01 2.0684288958636600E+01 8.6606733696595946E+00
S 1.9771449835286408E+01 4.4279373216890789E+00 8.5478009966158588E+00
S 1.9631958228200265E+01 9.9387479303708890E+00 9.0427922990813503E+00
S 1.9673911981293639E+01 1.5259467515525648E+01 9.0036204948472278E+00
S 1.9797775409553399E+01 2.0752151859956872E+01 8.5576596393319289E+00
S 2.2973972600165183E+01 4.3662719516814246E+00 8.4647928635798522E+00
S 2.2875041021523788E+01 9.8936531666282317E+00 8.6612862214472806E+00
S 2.2898050351459318E+01 1.5318937995028177E+01 8.6461178012717461E+00
S 2.2991285005176529E+01 2.0814591282628346E+01 8.4574151983309669E+00
S 2.6208402087870013E+01 4.3417372723077676E+00 8.4287631988719198E+00
S 2.6208406745734049E+01 9.8852437087624931E+00 8.4888503999764193E+00
S 2.6208219918918090E+01 1.5362980478108408E+01 8.4696117226564738E+00
S 2.6208636302107621E+01 2.0844267120604897E+01 8.4096097266782728E+00
Mo 3.9353323311283432E+00 2.4858790114267517E+00 9.9932400000000001E+00
Mo 3.9420335076836994E+00 8.0043226467339981E+00 1.0149582256911964E+01
Mo 3.9445973360952231E+00 1.3511565456554122E+01 1.0236330323158743E+01
Mo 3.9401290325352099E+00 1.9018525853051468E+01 1.0082858065208333E+01
Mo 7.1201390771281927E+00 2.4885789082940621E+00 9.9932400000000001E+00
Mo 7.1206567178115572E+00 7.9995595966900428E+00 1.0441035291694153E+01
Mo 7.1145683400806741E+00 1.3511435226163062E+01 1.0654792354337065E+01
Mo 7.1239323238220180E+00 1.9017836102428163E+01 1.0261807513414736E+01
Mo 1.0302539240819931E+01 2.4949793032705618E+00 9.9932400000000001E+00
Mo 1.0295151486496332E+01 7.9860073034349908E+00 1.0770342164128904E+01
Mo 1.0287372631597485E+01 1.3511554500009716E+01 1.1150091614723417E+01
Mo 1.0301817106815044E+01 1.9017376806901353E+01 1.0444157865936806E+01
Mo 1.3481162181403644E+01 2.4982678971306465E+00 9.9932400000000001E+00
Mo 1.3477545757947901E+01 7.9900430128317064E+00 1.0960477749587421E+01
Mo 1.3476582769954543E+01 1.3509803596404620E+01 1.1434058804037120E+01
Mo 1.3479816182385568E+01 1.9017101036309594E+01 1.0523880822121990E+01
Mo 1.6659397573165165E+01 2.4950422488067865E+00 9.9932400000000001E+00
Mo 1.6660366545135439E+01 7.9870404739839644E+00 1.0772636161982307E+01
Mo 1.6666073936409550E+01 1.3510332600514817E+01 1.1151010485351845E+01
Mo 1.6657524102411610E+01 1.9016578230151332E+01 1.0443417100650008E+01
Mo 1.9840386619868429E+01 2.4895355220681989E+00 9.9932400000000001E+00
Mo 1.9835753873818614E+01 8.0009964122906680E+00 1.0444290540240818E+01
Mo 1.9840987356806970E+01 1.3510341334067117E+01 1.0656298735230415E+01
Mo 1.9834324842463232E+01 1.9015933410320159E+01 1.0261012840010300E+01
Mo 2.3023418470961648E+01 2.4866731393678987E+00 9.9932400000000001E+00
Mo 2.3015077874213844E+01 8.0053043109692030E+00 1.0152036761725979E+01
Mo 2.3012450478679284E+01 1.3510656775397699E+01 1.0237841656697933E+01
Mo 2.3016833805946451E+01 1.9017164131593727E+01 1.0082293179140681E+01
Mo 2.6208856445036609E+01 2.4865353595284496E+00 9.9932400000000001E+00
Mo 2.6208721301169319E+01 8.0040298530257985E+00 9.9932400000000001E+00
Mo 2.6208833172881505E+01 1.3508768227756043E+01 9.9932400000000001E+00
Mo 2.6208184483689664E+01 1.9018119568457717E+01 9.9932400000000001E+00
Mo 2.3438876506485826E+00 5.2459580706414997E+00 1.0004471053540254E+01
Mo 2.3495255940974760E+00 1.0757806609027577E+01 1.0101353098956215E+01
Mo 2.3478532835554495E+00 1.6263740273472688E+01 1.0077056319262075E+01
Mo 2.3430228131749042E+00 2.1775973996452706E+01 9.9805642527539966E+00
Mo 5.5301477903240412E+00 5.2474950115448706E+00 1.0108083392320397E+01
Mo 5.5306169848228057E+00 1.0756241486398851E+01 1.0415158757716529E+01
Mo 5.5328738984443682E+00 1.6264860715435745E+01 1.0325963714411825E+01
Mo 5.5304539641845443E+00 2.1775208589454568E+01 1.0029855435727416E+01
Mo 8.7123525614024100E+00 5.2522964950866831E+00 1.0250914496888560E+01
Mo 8.6942370937577458E+00 1.0748925026569047E+01 1.0878819158163939E+01
Mo 8.7053254811344551E+00 1.6267756842500958E+01 1.0674272475283551E+01
Mo 8.7144790717486451E+00 2.1770699402650092E+01 1.0094553102810778E+01
Mo 1.1892719563253296E+01 5.2576769619478361E+00 1.0369176563117659E+01
Mo 1.1884164881243695E+01 1.0741797707186363E+01 1.1361386136599835E+01
Mo 1.1880790322540028E+01 1.6279669982352679E+01 1.0950013929030284E+01
Mo 1.1892934626788593E+01 2.1764407798365127E+01 1.0141346088985216E+01
Mo 1.5066911172557177E+01 5.2578335937419487E+00 1.0369709332954328E+01
Mo 1.5068888844451802E+01 1.0741859238856698E+01 1.1362409822164730E+01
Mo 1.5075191133192027E+01 1.6279238337165797E+01 1.0949189847299907E+01
Mo 1.5069369973026447E+01 2.1764263505416562E+01 1.0141479212121480E+01
Mo 1.8246489073128654E+01 5.2534588553798063E+00 1.0252560606199197E+01
Mo 1.8260647749778222E+01 1.0749247246401708E+01 1.0881069680050510E+01
Mo 1.8250760303889091E+01 1.6265708137784998E+01 1.0673723725983727E+01
Mo 1.8246901814044715E+01 2.1770274311796587E+01 1.0093860125037351E+01
Mo 2.1427656010532196E+01 5.2492698286411770E+00 1.0109809439566904E+01
Mo 2.1425876388693268E+01 1.0756525961940500E+01 1.0418356263649661E+01
Mo 2.1423466059972053E+01 1.6262908902638380E+01 1.0326227633955657E+01
Mo 2.1428707830006367E+01 2.1774886858186413E+01 1.0029503128687182E+01
Mo 2.4613950901676127E+01 5.2466956579050139E+00 1.0004921373698510E+01
Mo 2.4608655658810179E+01 1.0757784951514505E+01 1.0102810104581421E+01
Mo 2.4608933505561865E+01 1.6262913818733789E+01 1.0077221894885581E+01
Mo 2.4614719635523141E+01 2.1775784751728050E+01 9.9805045736922136E+00
&END COORD
&KIND S
ELEMENT S
BASIS_SET DZVP-MOLOPT-SR-GTH-q6
POTENTIAL GTH-PBE
&END KIND
&KIND Mo
ELEMENT Mo
BASIS_SET DZVP-MOLOPT-SR-GTH-q14
POTENTIAL GTH-PBE
&END KIND
&END SUBSYS
&DFT
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME POTENTIAL
# WFN_RESTART_FILE_NAME 33-RESTART.wfn
CHARGE 0 #Net charge
MULTIPLICITY 1 #Spin multiplicity
&QS
EPS_DEFAULT 1.0E-10 #Set all EPS_xxx to values such that the energy will be correct up to this value
EXTRAPOLATION ASPC #Extrapolation for wavefunction during e.g. MD. ASPC is default, PS can also be used
EXTRAPOLATION_ORDER 3 #Order for PS or ASPC extrapolation. 3 is default
&END QS
&POISSON
PERIODIC XYZ #Direction(s) of PBC for calculating electrostatics
PSOLVER PERIODIC #The way to solve Poisson equation
&END POISSON
&XC
&XC_FUNCTIONAL PBE
&END XC_FUNCTIONAL
&END XC
&MGRID
CUTOFF 300
REL_CUTOFF 40
&END MGRID
&SCF
MAX_SCF 25 #Maximum number of steps of inner SCF
EPS_SCF 1.0E-05 #Convergence threshold of density matrix of inner SCF
# SCF_GUESS RESTART #Use wavefunction from WFN_RESTART_FILE_NAME file as initial guess
# IGNORE_CONVERGENCE_FAILURE #Continue calculation even if SCF not converged, works for version >= 2024.1
&OT
PRECONDITIONER FULL_SINGLE_INVERSE #Usually best but expensive for large system. Cheaper: FULL_SINGLE_INVERSE and FULL_KINETIC
MINIMIZER CG #CG is worth to consider in difficult cases
LINESEARCH 2PNT #1D line search algorithm for CG. 2PNT is default, 3PNT is better but more costly. GOLD is best but very expensive
ALGORITHM STRICT #Algorithm of OT. Can be STRICT (default) or IRAC
&END OT
&OUTER_SCF
MAX_SCF 200 #Maximum number of steps of outer SCF
EPS_SCF 1.0E-05 #Convergence threshold of outer SCF
&END OUTER_SCF
&PRINT
&RESTART OFF #Do not generate wfn file to suppress meaningless I/O cost
&END RESTART
&END PRINT
&END SCF
&END DFT
&EXTERNAL_POTENTIAL
FUNCTION "-A * exp(- ( (X-25.45920000)^2 + (Y-22.04840100)^2 ) / (2 * sigma^2) ) * Z"
PARAMETERS A sigma
VALUES 0.01 10
ATOMS_LIST 15 19 46 79 83 110 143 174 178
&END EXTERNAL_POTENTIAL
#&EXTERNAL_POTENTIAL
# FUNCTION "A * X"
# PARAMETERS A
# VALUES 1.0
# ATOMS_LIST 1..5
#&END EXTERNAL_POTENTIAL
&END FORCE_EVAL
&MOTION
&MD
ENSEMBLE NVT
STEPS 5000 #Number of steps to run
TIMESTEP 1.0 #Step size in fs. Decrease it properly for high temperature simulation
TEMPERATURE 300 #Initial and maintained temperature (K)
&THERMOSTAT
TYPE NOSE
&NOSE
TIMECON 50 #默认值为1000，如果发现温度不能稳定在设置的温度附近的话，可以调小这个值
&END NOSE
&END THERMOSTAT
# COMVEL_TOL 0 #Uncomment this can remove translation motion of center-of-mass every step
&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
&PRINT
&TRAJECTORY
#&EACH
# MD 1 #Output frequency of coordinates, 0 means never
#&END EACH
#FORMAT xyz
FORMAT PDB
FILENAME trajectory
&EACH
MD 1
&END EACH
&END TRAJECTORY
&VELOCITIES
&EACH
MD 0 #Output frequency of velocities, 0 means never
&END EACH
&END VELOCITIES
###########################################
&FORCES SILENT
&EACH
MD 1
&END EACH
&END FORCES
###########################################
&RESTART
BACKUP_COPIES 0 #Maximum number of backing up restart file, 0 means never
&EACH
MD 0 #Frequency of updating last restart file, 0 means never
&END EACH
&END RESTART
&RESTART_HISTORY
&EACH
MD 1
&END EACH
&END RESTART_HISTORY
&END PRINT
&CONSTRAINT
&FIXED_ATOMS
LIST 157 158 159 160 129 133 137 141 145 149 153 157 # 固定这些原子（假设是边缘原子的索引）
COMPONENTS_TO_FIX Z # 只在 z 方向固定（如果二维材料在 x-y 平面）
&END FIXED_ATOMS
&END CONSTRAINT
&END MOTION相比于第一步的结构优化，最后只需要修改几个关键参数：
（1）GLOBAL模块中的RUN_TYPE，改为MD，进行分子动力学模拟
（2）MOTION中改为分子动力学相关的参数。
分子动力学详细参数解释如下：
MD 模块的主要设置
1 ENSEMBLE
NVT: 设置分子动力学的集合类型为 NVT（恒粒子数、恒体积、恒温），也就是在模拟中保持粒子数、体积和温度不变。
2 STEPS
5000: 定义分子动力学模拟的总步数。每一步模拟的时间间隔由 TIMESTEP 决定。
3 TIMESTEP
1.0 fs: 定义模拟中的时间步长，单位为飞秒 (fs)。
4 TEMPERATURE
300 K: 设置模拟的目标温度为 300 开尔文 (K)。初始温度和随后使用的恒温器都会以此为目标值。
运行结束后会得到pdb文件，同样可以用OVITO软件进行可视化呈现：
以上，我们就完成了二维半导体材料二硫化钼MoS2大尺寸材料纳米锥的分子动力学外加势场模拟的详细步骤。希望本篇最佳实践为您提供一些有价值的信息和实践技巧。