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[求助]
用lammps計算吸附時遇到bond missing
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請問一下,我在模擬異辛酸和Cu時,為什么我計算出來的結(jié)果,要么bond missing(調(diào)小時間步長的時候,溫度突然提升),要么cannot compute PPPM?(調(diào)大時間步長) in 文件: # # 1. 初始化與單位設(shè)置(固定為metal) units metal dimension 3 boundary p p f # x/y周期,z非周期(適配Cu表面吸附) atom_style full # 需包含鍵/角/二面角/電荷,匹配文檔2 neighbor 3.0 bin # 鄰居列表截斷3Å,bin算法高效 neigh_modify delay 0 every 1 check yes # 2. 勢函數(shù)類型設(shè)置(匹配文檔2的拓撲結(jié)構(gòu)) special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.5 # 明確LJ和庫侖的排除系數(shù),符合有機分子規(guī)則 bond_style harmonic angle_style harmonic dihedral_style hybrid fourier opls # 3. 混合勢函數(shù)(Cu用EAM,異辛酸用LJ/庫侖) pair_style hybrid lj/cut/coul/long 12.0 eam # 12Å截斷長程庫侖+EAM金屬勢 pair_modify mix geometric # 金屬-有機交叉參數(shù)用幾何平均,更合理 # 4. 體系盒子與原子生成(嚴格匹配文檔2拓撲) # 定義總模擬盒(z方向預(yù)留Cu基底+異辛酸空間) region total_box block -10.000 30 -10.000 30 -10.000 50.000 units box create_box 9 total_box bond/types 6 angle/types 13 dihedral/types 11 improper/types 0 extra/bond/per/atom 10 extra/angle/per/atom 10 extra/dihedral/per/atom 20 extra/improper/per/atom 0 # 讀入文檔2的異辛酸data文件(替換為你的實際文件路徑) read_data UNKm2.data add 0 0 # add 0 0 0:不額外偏移(后續(xù)手動調(diào)整位置) # 5. 體系分組與位置調(diào)整(避免初始碰撞) # 驗證總電荷:-0.6-0.6+0.4+0.1 = -0.7?需調(diào)整至-1e,確保平衡 group acid_group type 1 2 3 4 5 6 7 8 displace_atoms acid_group move 13.000 13.000 20 units box # x/y居中,z方向偏移20Å(原位置+20→25Å) # 6. Cu(111)基底構(gòu)建(metal單位適配) mass 9 63.546 # Cu原子量(amu,符合metal單位) lattice fcc 3.615 orient x 1 -1 0 orient y 1 1 -2 orient z 1 1 1 # Cu(111)晶格常數(shù)3.615Å(標準值) region cu_region block 0 30 0 30 0 10 units box # Cu在z=0-10Å(3層左右) create_atoms 9 region cu_region # 生成27號Cu原子 group cu_group type 9 # Cu原子分組 # 7. 相互作用參數(shù)(文檔2轉(zhuǎn)換后,完全適配metal單位) # C-C相關(guān)(類型1-4) pair_coeff 1 1 lj/cut/coul/long 0.002862 3.500 # 類型1-1(C-C) pair_coeff 1 2 lj/cut/coul/long 0.002862 3.500 # 類型1-2(C-C) pair_coeff 1 3 lj/cut/coul/long 0.002862 3.500 # 類型1-3(C-C) pair_coeff 1 4 lj/cut/coul/long 0.003615 3.625 # 類型1-4(C-C) pair_coeff 2 2 lj/cut/coul/long 0.002862 3.500 # 類型2-2(C-C) pair_coeff 2 3 lj/cut/coul/long 0.002862 3.500 # 類型2-3(C-C) pair_coeff 2 4 lj/cut/coul/long 0.003615 3.625 # 類型2-4(C-C) pair_coeff 3 3 lj/cut/coul/long 0.002862 3.500 # 類型3-3(C-C) pair_coeff 3 4 lj/cut/coul/long 0.003615 3.625 # 類型3-4(C-C) pair_coeff 4 4 lj/cut/coul/long 0.004553 3.750 # 類型4-4(C-C) # C-O相關(guān)(C=1-4;O=5-6) pair_coeff 1 5 lj/cut/coul/long 0.004617 3.250 # 類型1-5(C-O) pair_coeff 1 6 lj/cut/coul/long 0.005116 3.230 # 類型1-6(C-O) pair_coeff 2 5 lj/cut/coul/long 0.004617 3.250 # 類型2-5(C-O) pair_coeff 2 6 lj/cut/coul/long 0.005116 3.230 # 類型2-6(C-O) pair_coeff 3 5 lj/cut/coul/long 0.004617 3.250 # 類型3-5(C-O) pair_coeff 3 6 lj/cut/coul/long 0.005116 3.230 # 類型3-6(C-O) pair_coeff 4 5 lj/cut/coul/long 0.005822 3.375 # 類型4-5(C-O) pair_coeff 4 6 lj/cut/coul/long 0.006487 3.355 # 類型4-6(C-O) # O-O相關(guān)(類型5-6) pair_coeff 5 5 lj/cut/coul/long 0.007372 3.000 # 類型5-5(O-O) pair_coeff 5 6 lj/cut/coul/long 0.008200 2.980 # 類型5-6(O-O) pair_coeff 6 6 lj/cut/coul/long 0.009106 2.960 # 類型6-6(O-O) # C-H相關(guān)(C=1-4;H=7-8) pair_coeff 1 7 lj/cut/coul/long 0.002000 3.000 # 類型1-7(C-H) pair_coeff 2 7 lj/cut/coul/long 0.002000 3.000 # 類型2-7(C-H) pair_coeff 2 8 lj/cut/coul/long 0.000000 1.750 # 類型2-8(C-H) pair_coeff 3 7 lj/cut/coul/long 0.002000 3.000 # 類型3-7(C-H) pair_coeff 3 8 lj/cut/coul/long 0.000000 1.750 # 類型3-8(C-H) pair_coeff 4 7 lj/cut/coul/long 0.002433 3.125 # 類型4-7(C-H) pair_coeff 4 8 lj/cut/coul/long 0.000000 1.875 # 類型4-8(C-H) # O-H相關(guān)(O=5-6;H=7-8) pair_coeff 5 7 lj/cut/coul/long 0.003085 2.750 # 類型5-7(O-H) pair_coeff 6 7 lj/cut/coul/long 0.003456 2.730 # 類型6-7(O-H) pair_coeff 6 8 lj/cut/coul/long 0.000000 1.480 # 類型6-8(O-H) pair_coeff 8 8 lj/cut/coul/long 0.001301 2.500 # 與類型7-7一致,避免無排斥力 # 修正C-H(類型1-8):ε=0.002000,σ=2.425(幾何平均C和H的σ) pair_coeff 1 8 lj/cut/coul/long 0.002000 2.425 # 修正O-H(類型5-8):ε=0.003085,σ=2.125(而非1.500) pair_coeff 5 8 lj/cut/coul/long 0.003085 2.125 # H-H相關(guān)(類型7-8) pair_coeff 7 7 lj/cut/coul/long 0.001301 2.500 # 類型7-7(H-H) pair_coeff 7 8 lj/cut/coul/long 0.000000 1.250 # 類型7-8(H-H) pair_coeff 8 8 lj/cut/coul/long 0.000000 0.000 pair_coeff 1 9 lj/cut/coul/long 0.021862 2.905 # C_aliphatic-Cu pair_coeff 2 9 lj/cut/coul/long 0.021862 2.905 # C_aliphatic-Cu pair_coeff 3 9 lj/cut/coul/long 0.021862 2.905 # C_aliphatic-Cu pair_coeff 4 9 lj/cut/coul/long 0.275745 3.030 # C_carboxyl-Cu pair_coeff 5 9 lj/cut/coul/long 0.027837 2.665 # O_carbonyl-Cu pair_coeff 6 9 lj/cut/coul/long 0.038996 2.635 # O_hydroxyl-Cu pair_coeff 7 9 lj/cut/coul/long 0.022420 2.405 # H_aliphatic-Cu pair_coeff 8 9 lj/cut/coul/long 0.000000 1.155 # H_hydroxyl-Cu # -------------------------- 異辛酸與Cu的相互作用(核心修正:Cu類型從2→9) -------------------------- pair_coeff 9 9 eam Cu_u6.eam # 8. 長程庫侖作用(metal單位適配,精度1e-6) kspace_style pppm 1e-4 # PPPM算法,能量精度1e-6 kspace_modify slab nozforce min_style cg # 共軛梯度算法(適合能量最小化) minimize 1e-6 1e-8 1000 10000 # 第一步:快速消除大應(yīng)力(收斂判據(jù)1e-6/1e-8) minimize 1e-8 1e-10 5000 50000 # 第二步:中等收斂(判據(jù)1e-8/1e-10) minimize 1e-15 1e-15 100000 1000000 # 第三步:高精度收斂(判據(jù)1e-10/1e-12) # 10. 分子動力學模擬(NVT系綜,控溫300K) # 10.1 初始速度與約束 thermo 100 # 每1000步輸出熱力學數(shù)據(jù) thermo_style custom step temp pe ke press vol density # 輸出步長、溫度、勢能、動能、壓力、體積、密度 dump 1 all atom 10 traj_adsorb1.lammpstrj # 每100步輸出軌跡(可視化用) dump find_out_of_bounds all atom 10 out_of_bounds.lammpstrj # 監(jiān)控原子逸出 fix 10 cu_group setforce 0 0 0 fix 2 all nve/limit 0.05 run 50000 unfix 2 fix 4 all nvt temp 100 300 10 # 第二階段:100-300K波動(增強采樣) timestep 0.001 #(metal單位:1 timestep=1 fs) run 1000000 # 第二階段:200萬步(1ns)run 2000000 # 第二階段:200萬步(1ns) data文件 # LAMMPS Atom File (metal units) - Converted from AuToFF OPLS file # 轉(zhuǎn)換說明:1 kcal/mol = 0.043364435 eV(力常數(shù)/能量參數(shù)統(tǒng)一乘此系數(shù)) 26 atoms 25 bonds 46 angles 62 dihedrals 0 impropers 8 atom types 6 bond types 13 angle types 11 dihedral types 0 improper types -12.00000 32.00000 xlo xhi # Å(metal單位與OPLS一致,直接保留) -12.00000 32.00000 ylo yhi -10.00000 50.00000 zlo zhi Masses # amu(兩種單位一致,直接保留) 1 12.0110 # oplsm_135 2 12.0110 # oplsm_136 3 12.0110 # oplsm_274 4 12.0110 # oplsm_267 5 15.9994 # oplsm_268 6 15.9994 # oplsm_269 7 1.0080 # oplsm_140 8 1.0080 # oplsm_270 Bond Coeffs # harmonic(k:kcal/mol·Å²→eV/Ų;r0:Å不變) 1 11.6216 1.530000 # 268.000000×0.043364435 2 19.5140 1.360000 # 450.000000×0.043364435 3 24.8304 1.230000 # 570.000000×0.043364435 4 14.7660 1.090000 # 340.000000×0.043364435 5 24.0045 0.950000 # 553.000000×0.043364435 6 104.6940 1.521819 # 2390.057361×0.043364435 Angle Coeffs # harmonic(k:kcal/mol·rad²→eV/rad²;θ0:度不變) 1 1.6262 110.700000 # 37.500000×0.043364435 2 1.4310 107.800000 # 32.999522×0.043364435 3 2.5305 112.700000 # 58.350860×0.043364435 4 3.4692 121.000000 # 80.000000×0.043364435 5 1.5177 113.000000 # 35.000000×0.043364435 6 10.4683 110.730259 # 239.005736×0.043364435 7 10.4683 112.973118 # 239.005736×0.043364435 8 10.4683 115.128063 # 239.005736×0.043364435 9 10.4683 110.480160 # 239.005736×0.043364435 10 10.4683 110.054924 # 239.005736×0.043364435 11 10.4683 106.758589 # 239.005736×0.043364435 12 10.4683 113.088339 # 239.005736×0.043364435 13 10.4683 124.892120 # 239.005736×0.043364435 Dihedral Coeffs # hybrid(所有系數(shù):kcal/mol→eV) 1 opls -0.000010 0.000000 0.012999 0.000000 # 原系數(shù)×0.043364435 2 opls 0.056479 -0.008675 0.008675 0.000000 3 opls -0.000005 0.000000 -0.009768 0.000000 4 opls 0.065047 0.238504 0.000000 0.000000 5 opls 0.000000 0.238504 0.000000 0.000000 6 fourier 1 0.000000 1 1.5933 # 36.7312×0.043364435 7 fourier 1 0.000000 1 -6.2634 # -144.4374×0.043364435 8 fourier 1 0.000000 1 6.5850 # 151.6206×0.043364435 9 fourier 1 0.000000 1 -3.4765 # -80.1437×0.043364435 10 fourier 1 0.000000 1 -1.2813 # -29.5480×0.043364435 11 fourier 1 0.000000 1 4.2806 # 98.6878×0.043364435 Atoms # 坐標:Å(不變);電荷:電子電荷(不變) # atom mol type charge X Y Z 1 1 1 -0.180000 0.925400 -0.258900 0.369800 2 1 2 -0.120000 2.441600 -0.138400 0.287900 3 1 2 -0.120000 2.941000 -0.519300 -1.108800 4 1 2 -0.120000 4.465500 -0.420600 -1.234700 5 1 3 -0.220000 4.982300 -0.822400 -2.634300 6 1 2 -0.120000 4.417200 0.005000 -3.801700 7 1 1 -0.180000 4.739700 1.495200 -3.759000 8 1 4 0.520000 6.503600 -0.799700 -2.666900 9 1 5 -0.530000 7.028800 -1.670200 -3.562100 10 1 6 -0.440000 7.204300 -0.070700 -1.987700 11 1 7 0.060000 0.569500 0.044700 1.358900 12 1 7 0.060000 0.606100 -1.291700 0.195600 13 1 7 0.060000 0.440200 0.379100 -0.376100 14 1 7 0.060000 2.732800 0.892700 0.518600 15 1 7 0.060000 2.898700 -0.784900 1.044100 16 1 7 0.060000 2.462100 0.144600 -1.834200 17 1 7 0.060000 2.623200 -1.542300 -1.341900 18 1 7 0.060000 4.927100 -1.080600 -0.488000 19 1 7 0.060000 4.794100 0.592700 -0.976400 20 1 7 0.060000 4.677400 -1.869100 -2.782400 21 1 7 0.060000 3.329200 -0.119300 -3.840800 22 1 7 0.060000 4.793100 -0.395500 -4.751700 23 1 7 0.060000 4.672800 1.914900 -2.753000 24 1 7 0.060000 4.036700 2.044500 -4.393300 25 1 7 0.060000 5.746300 1.684300 -4.144100 26 1 8 0.450000 6.364300 -2.192100 -4.051500 Bonds # 拓撲結(jié)構(gòu)不變(原子索引、鍵類型索引保留原始) # NO. Type atom_i atom_j 1 1 2 3 2 1 3 4 3 1 4 5 4 1 5 6 5 1 6 7 6 1 2 1 7 2 8 9 8 3 8 10 9 4 1 11 10 4 1 12 11 4 1 13 12 4 2 14 13 4 2 15 14 4 3 16 15 4 3 17 16 4 4 18 17 4 4 19 18 4 5 20 19 4 6 21 20 4 6 22 21 4 7 23 22 4 7 24 23 4 7 25 24 5 9 26 25 6 5 8 Angles # 拓撲結(jié)構(gòu)不變 # NO. Type atom_i atom_j atom_k 1 1 2 1 11 2 1 2 1 12 3 1 2 1 13 4 2 11 1 12 5 2 11 1 13 6 2 12 1 13 7 1 3 2 14 8 1 3 2 15 9 1 1 2 14 10 1 1 2 15 11 2 14 2 15 12 3 2 3 4 13 1 2 3 16 14 1 2 3 17 15 1 4 3 16 16 1 4 3 17 17 2 16 3 17 18 1 3 4 18 19 1 3 4 19 20 1 5 4 18 21 1 5 4 19 22 2 18 4 19 23 1 4 5 20 24 1 6 5 20 25 3 5 6 7 26 1 5 6 21 27 1 5 6 22 28 1 7 6 21 29 1 7 6 22 30 2 21 6 22 31 1 6 7 23 32 1 6 7 24 33 1 6 7 25 34 2 23 7 24 35 2 23 7 25 36 2 24 7 25 37 4 9 8 10 38 5 8 9 26 39 6 1 2 3 40 7 3 4 5 41 8 4 5 6 42 9 4 5 8 43 10 6 5 8 44 11 8 5 20 45 12 5 8 9 46 13 5 8 10 Dihedrals # 拓撲結(jié)構(gòu)不變 # NO. Type atom_i atom_j atom_k atom_l 1 1 11 1 2 3 2 1 12 1 2 3 3 1 13 1 2 3 4 1 14 2 3 4 5 1 14 2 1 11 6 1 14 2 1 12 7 1 14 2 1 13 8 1 15 2 3 4 9 1 15 2 1 11 10 1 15 2 1 12 11 1 15 2 1 13 12 2 4 3 2 1 13 2 16 3 2 1 14 1 16 3 2 14 15 1 16 3 2 15 16 2 16 3 4 5 17 2 17 3 2 1 18 1 17 3 2 14 19 1 17 3 2 15 20 2 17 3 4 5 21 2 5 4 3 2 22 1 18 4 3 2 23 1 18 4 3 16 24 1 18 4 3 17 25 3 18 4 5 6 26 3 18 4 5 8 27 1 19 4 3 2 28 1 19 4 3 16 29 1 19 4 3 17 30 3 19 4 5 6 31 3 19 4 5 8 32 3 6 5 4 3 33 3 8 5 4 3 34 3 8 5 6 7 35 1 20 5 4 3 36 1 20 5 4 18 37 1 20 5 4 19 38 1 20 5 6 7 39 3 7 6 5 4 40 3 21 6 5 4 41 3 21 6 5 8 42 1 21 6 5 20 43 3 22 6 5 4 44 3 22 6 5 8 45 1 22 6 5 20 46 1 23 7 6 5 47 1 23 7 6 21 48 1 23 7 6 22 49 1 24 7 6 5 50 1 24 7 6 21 51 1 24 7 6 22 52 1 25 7 6 5 53 1 25 7 6 21 54 1 25 7 6 22 55 4 26 9 8 5 56 5 26 9 8 10 57 6 20 5 8 9 58 7 20 5 8 10 59 8 9 8 5 4 60 9 9 8 5 6 61 10 10 8 5 4 62 11 10 8 5 6 |
銅蟲 (小有名氣)
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