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LAMMPS入門(mén)報(bào)錯(cuò)求指導(dǎo)！急�。�
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各位大佬： LAMMPS in文件設(shè)置如下圖所示，報(bào)錯(cuò)ERROR: All pair coeffs are not set (../pair.cpp:254)。 想用兩種reaxff力場(chǎng)描述混合體系。其中 reaxff_JPCL力場(chǎng)描述mass 1-6，即S O C F Li H。用ffield.reax.ZnOH力場(chǎng)描述mass 7-9 Zn H O。請(qǐng)大佬指正如何設(shè)置好in文件？感謝感謝。 in 文件： ------------------------------------------ # LAMMPS input script for MD simulation # Initialization units real dimension 3 boundary p p p atom_style charge # Atom definition read_data LiFBS_3mol_MD.data # Mass and atom types mass 1 32.065 # S mass 2 15.9994 # O mass 3 12.0107 # C mass 4 18.9984032 # F mass 5 6.941 # Li mass 6 1.00794 # H mass 7 65.409 # Zn mass 8 1.00794 # H mass 9 15.9994 # O # Define other masses and atom types as needed set type 1 charge 0 set type 2 charge 0 set type 3 charge 0 set type 4 charge 0 set type 5 charge 0 set type 6 charge 0 set type 7 charge 0 set type 8 charge 0.4238 set type 9 charge -0.8476 # Force field settings pair_style reaxff NULL # Force field parameters for molecule pair_coeff * * reaxff_JPCL S O C F Li H NULL NULL NULL pair_coeff * * ffield.reax.ZnOH NULL NULL NULL NULL NULL NULL Zn H O fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff #pair_coeff 7 7 lj/cut/coul/long 0.222 2.68 # Settings for simulation neighbor 2 bin neigh_modify every 1 delay 0 check yes # Minimization settings thermo_style custom step temp pe ke etotal press lx ly lz pxx pyy pzz thermo 100 dump 1 all custom 200 oxy.xyz id type x y z vx vy vz min_style cg minimize 1e-6 1e-8 1000 100000 # Equilibration timestep 1.0 unfix 1 fix 2 all npt temp 298.15 298.15 100 aniso 1.0 1.0 1000 run 5000 # 100 ps equilibration # Production MD #timestep 1.0 #unfix 2 #fix 3 all nvt temp 298.15 298.15 100 #run 5000 # 1 ns MD run ------------------------------------------ data文件在網(wǎng)盤(pán)： 鏈接: https://pan.baidu.com/s/1sVyUcJBCeSousqCaJtOBLQ 提取碼: pdjh 報(bào)錯(cuò)信息： LAMMPS (20 Sep 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98) using 1 OpenMP thread(s) per MPI task # LAMMPS input script for MD simulation # Initialization units real dimension 3 boundary p p p atom_style charge # Atom definition read_data LiFBS_3mol_MD.data Reading data file ... orthogonal box = (0.0000000 0.0000000 0.0000000) to (18.000000 18.000000 18.000000) 4 by 4 by 4 MPI processor grid reading atoms ... 653 atoms read_data CPU = 0.047 seconds # Mass and atom types mass 1 32.065 # S mass 2 15.9994 # O mass 3 12.0107 # C mass 4 18.9984032 # F mass 5 6.941 # Li mass 6 1.00794 # H mass 7 65.409 # Zn mass 8 1.00794 # H mass 9 15.9994 # O # Define other masses and atom types as needed set type 1 charge 0 Setting atom values ... 21 settings made for charge set type 2 charge 0 Setting atom values ... 63 settings made for charge set type 3 charge 0 Setting atom values ... 42 settings made for charge set type 4 charge 0 Setting atom values ... 63 settings made for charge set type 5 charge 0 Setting atom values ... 7 settings made for charge set type 6 charge 0 Setting atom values ... 42 settings made for charge set type 7 charge 0 Setting atom values ... 7 settings made for charge set type 8 charge 0.4238 Setting atom values ... 272 settings made for charge set type 9 charge -0.8476 Setting atom values ... 136 settings made for charge # Force field settings pair_style reaxff NULL # Force field parameters for molecule pair_coeff * * reaxff_JPCL S O C F Li H NULL NULL NULL WARNING: Van der Waals parameters for element MO indicate shielding without inner wall, but earlier elements indicate a different van der Waals method. This may cause division-by-zero errors. Keeping van der Waals setting for earlier atoms. (../reaxff_ffield.cpp:279) WARNING: Van der Waals parameters for element NI indicate shielding without inner wall, but earlier elements indicate a different van der Waals method. This may cause division-by-zero errors. Keeping van der Waals setting for earlier atoms. (../reaxff_ffield.cpp:279) WARNING: Van der Waals parameters for element B indicate shielding without inner wall, but earlier elements indicate a different van der Waals method. This may cause division-by-zero errors. Keeping van der Waals setting for earlier atoms. (../reaxff_ffield.cpp:279) WARNING: Van der Waals parameters for element F indicate shielding without inner wall, but earlier elements indicate a different van der Waals method. This may cause division-by-zero errors. Keeping van der Waals setting for earlier atoms. (../reaxff_ffield.cpp:279) WARNING: Van der Waals parameters for element P indicate shielding without inner wall, but earlier elements indicate a different van der Waals method. This may cause division-by-zero errors. Keeping van der Waals setting for earlier atoms. (../reaxff_ffield.cpp:279) WARNING: Changed valency_val to valency_boc for F (../reaxff_ffield.cpp:296) pair_coeff * * ffield.reax.ZnOH NULL NULL NULL NULL NULL NULL Zn H O Reading potential file ffield.reax.ZnOH with DATE: 2011-02-18 WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296) fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff #pair_coeff 7 7 lj/cut/coul/long 0.222 2.68 # Settings for simulation neighbor 2 bin neigh_modify every 1 delay 0 check yes # Minimization settings thermo_style custom step temp pe ke etotal press lx ly lz pxx pyy pzz thermo 100 dump 1 all custom 200 oxy.xyz id type x y z vx vy vz min_style cg minimize 1e-6 1e-8 1000 100000 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - pair reaxff command: @Article{Aktulga12, author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama}, title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques}, journal = {Parallel Computing}, year = 2012, volume = 38, pages = {245--259} } - fix qeq/reaxff command: @Article{Aktulga12, author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama}, title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques}, journal = {Parallel Computing}, year = 2012, volume = 38, pages = {245--259} } CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE ERROR: All pair coeffs are not set (../pair.cpp:254) Last command: minimize 1e-6 1e-8 1000 100000 |
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