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  1. #LAMMPS Input file generated by Avogadro
  2. # Mos2
  3.  
  4. # Intialization
  5. units real
  6. dimension 3
  7. boundary p p p
  8. atom_style full
  9. kspace_style ewald 1.0e-4
  10. neighbor 2.0 bin
  11.  
  12.  
  13. # Atom Definition
  14. read_data nmp_water_mos2_C_C2.data
  15.  
  16.  
  17. pair_style lj/cut/coul/long 10 15
  18. angle_style hybrid fourier harmonic
  19. bond_style harmonic
  20. improper_style fourier
  21. special_bonds lj 0 0 1 coul 1 1 1
  22.  
  23. improper_coeff 2 50 1 1 0
  24. improper_coeff 1 6 1 1 0
  25.  
  26. group MovingAtoms type 1 2 3 5 6
  27. group MoS2Atoms type 4 7
  28.  
  29.  
  30.  
  31. #pair c C_3 and C_3
  32. pair_coeff 1 1 0.420000 3.851000
  33. #pair c C_3 and C_2
  34. pair_coeff 1 2 0.420000 3.851000
  35. #pair c C_3 and H_
  36. pair_coeff 1 3 0.271882 3.368500
  37. #pair c C_3 and Mo6+6
  38. pair_coeff 1 4 0.306725 3.451500
  39. #pair c C_3 and N_2
  40. pair_coeff 1 5 0.340470 3.755500
  41. #pair c C_3 and O_2
  42. pair_coeff 1 6 0.317490 3.675500
  43. #pair c C_3 and S_2
  44. pair_coeff 1 7 0.678469 3.943000
  45. #pair c C_2 and C_2
  46. pair_coeff 1 1 0.420000 3.851000
  47. #pair c C_3 and C_2
  48. pair_coeff 1 2 0.420000 3.851000
  49. #pair c C_3 and H_
  50. pair_coeff 1 3 0.271882 3.368500
  51. #pair c C_3 and Mo6+6
  52. pair_coeff 1 4 0.306725 3.451500
  53. #pair c C_3 and N_2
  54. pair_coeff 1 5 0.340470 3.755500
  55. #pair c C_3 and O_2
  56. pair_coeff 1 6 0.317490 3.675500
  57. #pair c C_3 and S_2
  58. pair_coeff 1 7 0.678469 3.943000
  59. #pair c C_2 and C_2
  60. pair_coeff 2 2 0.420000 3.851000
  61. #pair c C_2 and H_
  62. pair_coeff 2 3 0.271882 3.368500
  63. #pair c C_2 and Mo6+6
  64. pair_coeff 2 4 0.306725 3.451500
  65. #pair c C_2 and N_2
  66. pair_coeff 2 5 0.340470 3.755500
  67. #pair c C_2 and O_2
  68. pair_coeff 2 6 0.317490 3.675500
  69. #pair c C_2 and S_2
  70. pair_coeff 2 7 0.678469 3.943000
  71. #pair c H_ and H_
  72. pair_coeff 3 3 0.176000 2.886000
  73. #pair c H_ and Mo6+6
  74. pair_coeff 3 4 0.198555 2.969000
  75. #pair c H_ and N_2
  76. pair_coeff 3 5 0.220400 3.273000
  77. #pair c H_ and O_2
  78. pair_coeff 3 6 0.205524 3.193000
  79. #pair c H_ and S_2
  80. pair_coeff 3 7 0.439199 3.460500
  81. #pair c Mo6+6 and Mo6+6
  82. pair_coeff 4 4 0.8382 2.5510
  83. #pair c Mo6+6 and N_2
  84. pair_coeff 4 5 0.248644 3.356000
  85. #pair c Mo6+6 and O_2
  86. pair_coeff 4 6 0.231862 3.276000
  87. #pair c Mo6+6 and S_2
  88. pair_coeff 4 7 0.0339 2.9318
  89. #pair c N_2 and N_2
  90. pair_coeff 5 5 0.276000 3.660000
  91. #pair c N_2 and O_2
  92. pair_coeff 5 6 0.257371 3.580000
  93. #pair c N_2 and S_2
  94. pair_coeff 5 7 0.549996 3.847500
  95. #pair c O_2 and O_2
  96. pair_coeff 6 6 0.240000 3.500000
  97. pair_coeff 6 6 0.240000 3.500000
  98. #pair c O_2 and S_2
  99. pair_coeff 6 7 0.512874 3.767500
  100. #pair c S_2 and S_2
  101. pair_coeff 7 7 0.0606 3.3695
  102.  
  103.  
  104. #angle 1 C_3 - C_3 -C_3
  105. angle_coeff 1 fourier 214.211821 0.343737 0.374972 0.281246
  106. #angle 2 C_3 - C_3 -C_2
  107. angle_coeff 2 fourier 219.577892 0.343737 0.374972 0.281246
  108. #angle 3 C_3 - C_3 -H_
  109. angle_coeff 3 fourier 314.598624 0.343737 0.374972 0.281246
  110. #angle 4 C_3 - C_3 -N_2
  111. angle_coeff 4 fourier 229.993016 0.343737 0.374972 0.281246
  112. #angle 5 C_3 - C_2 -N_2
  113. angle_coeff 5 fourier 190.242283 0.500000 0.666667 0.333333
  114. #angle 6 C_3 - C_2 -O_2
  115. angle_coeff 6 fourier 260.559367 0.500000 0.666667 0.333333
  116. #angle 7 C_3 - N_2 -C_3
  117. angle_coeff 7 fourier 318.668043 0.362835 0.416030 0.287612
  118. #angle 8 C_3 - N_2 -C_2
  119. angle_coeff 8 fourier 327.104308 0.362835 0.416030 0.287612
  120. #angle 9 C_2 - C_3 -H_
  121. angle_coeff 9 fourier 325.237513 0.343737 0.374972 0.281246
  122. #angle 10 H_ - C_3 -H_
  123. angle_coeff 10 fourier 214.707737 0.343737 0.374972 0.281246
  124. #angle 11 H_ - C_3 -N_2
  125. angle_coeff 11 fourier 134.700632 0.343737 0.374972 0.281246
  126. #angle 12 H_ - O_2 -H_
  127. angle_coeff 12 fourier 296.916592 0.500000 0.666667 0.333333
  128. #angle 14 N_2 - C_2 -O_2
  129. angle_coeff 14 fourier 384.102629 0.500000 0.666667 0.333333
  130. #angle 13 Mo6+6 - S_2 -Mo6+6
  131. angle_coeff 13 harmonic 2.5163 82.0
  132. #angle 15 S_2 - Mo6+6 -S_2
  133. angle_coeff 15 harmonic 2.5163 82.0
  134.  
  135. #bond coeff C_3 and C_3
  136. bond_coeff 1 699.591799 1.514000
  137. #bond coeff C_3 and C_2
  138. bond_coeff 2 735.424751 1.489000
  139. #bond coeff C_3 and H_
  140. bond_coeff 3 748.039306 1.065197
  141. #bond coeff C_3 and N_2
  142. bond_coeff 4 1093.927607 1.434678
  143. #bond coeff C_2 and N_2
  144. bond_coeff 5 1152.837760 1.409812
  145. #bond coeff C_2 and O_2
  146. bond_coeff 6 2190.704010 1.100592
  147. #bond coeff H_ and O_2
  148. bond_coeff 7 1358.205818 0.928602
  149.  
  150.  
  151.  
  152. # Settings
  153. velocity MovingAtoms create 300 492459 rot yes mom yes dist gaussian
  154. fix NPT MovingAtoms npt temp 300 300 100 x 1.013 1.013 10 y 1.013 1.013 10 z 1.013 1.013 10 couple none drag 1
  155.  
  156.  
  157.  
  158. timestep .1
  159.  
  160. # Output
  161. dump dumpXYZ all xyz 50000 dump.mos2
  162. dump num1 all atom 50000 stationary_mos2_lj001.cray.phi.lammpstrj
  163.  
  164. thermo_style custom step etotal evdwl ecoul lx ly lz temp
  165. thermo 50000
  166.  
  167.  
  168. # Run the simulation
  169. variable numberOfRuns equal 1000000
  170. restart ${numberOfRuns} restartfile_*.restart
  171. run ${numberOfRuns}
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