Dear Lammps user,
I am trying to simulate a kerogen molecules with reax force field. However, the simulation stops before finishing. The input script is shown below:
ReaxFF potential for kerogen system
units real
atom_style full
dimension 3
boundary p p p
read_data Kerogen_all_types.data
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax 1 1 1 3 1 4 5 2 2
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
velocity all create 300.0 4928459 rot yes dist gaussian
neighbor 2.5 bin
neigh_modify every 10 delay 20 check yes
thermo_style custom step temp epair etotal press &
v_eb v_ea v_elp v_emol v_epen v_ecoa v_ehb &
v_et v_eco v_ew v_ep v_efi v_eqeq
thermo 2000
timestep 0.1
fix 1 all nvt temp 300.0 300.0 10.0
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
dump 1 all xyz 4000 kerogen_reax_nvt_300.xyz
dump 2 all image 40000 kerogen_reax_nvt_300.*.png type type
fix 1 all nvt temp 300.0 300.0 0.1
run 200000
write_restart kerogen_reax_nvt_300.restart
the log file only stop at timestep at 32000.
Working directory is /home/she8/heshuai/Kerogen_Reax
LAMMPS (9 Dec 2014)
Reading data file …
orthogonal box = (-30.2521 -56.0234 -2.2804) to (46.4637 13.2215 32.3103)
8 by 4 by 2 MPI processor grid
reading atoms …
1272 atoms
Finding 1-2 1-3 1-4 neighbors …
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
Setting up run …
Memory usage per processor = 11.5855 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol epen ecoa ehb et eco ew ep efi eqeq
0 300 -181229.84 -180093.26 32122.588 -243680 -2365.8896 2.1979658 0 184.82506 2.5577597e-11 -10.212182 1498.2505 -5085.287 65566.647 -2663.7653 0 1175.0794
2000 286.67841 -188949.85 -187863.73 356.52786 -243862.16 -2156.7883 56.292354 0 164.96268 8.959166e-11 -3.3245532 904.08541 -5176.849 58688.057 -2569.914 0 1088.2415
4000 299.54994 -189035.47 -187900.59 416.06742 -243934.87 -2228.4048 68.559834 0 163.27657 7.1295579e-11 -4.7748924 882.9766 -5175.387 58797.055 -2599.2197 0 1110.1247
6000 287.72074 -189090.37 -188000.31 -379.95504 -244094.27 -2171.9048 103.39324 0 165.44434 4.8539501e-11 -4.0159185 897.36408 -5173.8053 58789.435 -2635.6044 0 1139.5191
8000 298.01455 -189158.45 -188029.39 752.50269 -244401.55 -2136.3645 128.32376 0 167.62356 4.88234e-11 -6.5985255 869.04561 -5171.2917 59014.912 -2648.663 0 1156.0625
10000 296.2204 -189134.09 -188011.83 516.50878 -244236.24 -2110.145 119.10715 0 167.52562 9.0670668e-11 -7.6120035 900.41581 -5182.0204 58811.347 -2649.5746 0 1158.0686
12000 304.84436 -189216.41 -188061.47 386.4574 -244341.6 -2061.5708 89.076726 0 174.90782 1.0664177e-10 -7.5717835 883.69282 -5201.4379 58869.361 -2618.9704 0 1127.7036
14000 307.88731 -189138.03 -187971.57 -779.19199 -244206.55 -2175.9406 128.95918 0 163.61546 7.1725761e-11 -3.8473744 881.59257 -5177.0763 58839.471 -2679.1898 0 1171.59
16000 295.80175 -189222.79 -188102.11 7.2030537 -244223.25 -2116.0606 109.53121 0 165.43988 8.1966638e-11 -5.3458455 930.62944 -5173.6076 58751.179 -2653.4255 0 1150.8208
18000 300.80633 -189134.7 -187995.06 360.05664 -244274.11 -2065.1255 113.74046 0 166.86256 5.8863147e-11 -3.8891549 954.81631 -5179.7616 58774.425 -2658.5246 0 1155.6241
20000 288.97774 -189195.48 -188100.66 604.73976 -244206.13 -2114.0619 121.40347 0 169.58035 5.0388421e-11 -6.7169659 923.14055 -5188.2738 58740.733 -2666.648 0 1161.693
22000 293.27909 -189191.93 -188080.81 71.562863 -244282.19 -2058.0083 84.326903 0 169.69207 3.7907976e-11 -5.3607125 927.86398 -5193.1068 58817.124 -2677.379 0 1166.5926
24000 296.72032 -189185.64 -188061.48 249.55833 -244290.79 -2109.2467 113.14052 0 167.80104 6.3749353e-11 -3.396529 941.26156 -5183.3926 58867.08 -2664.2813 0 1161.3865
26000 310.79374 -189235.37 -188057.89 -1354.2312 -244242.77 -2123.6401 122.42294 0 168.22481 8.8778034e-11 -4.549328 901.5706 -5193.6625 58783.591 -2665.4066 0 1161.2559
28000 310.08212 -189194.63 -188019.85 -480.68235 -244477.07 -1954.7772 107.57739 0 170.80374 8.531817e-11 -8.0591895 921.80106 -5198.207 58868.248 -2670.4034 0 1166.4056
30000 298.69168 -189203.39 -188071.76 519.52753 -244440.6 -2064.477 120.59149 0 167.6916 3.9003067e-11 -11.278444 910.85196 -5189.0075 58918.659 -2679.1912 0 1173.91
32000 300.2762 -189226.3 -188088.68 -1805.8711 -244437.21 -2013.2508 133.59586 0 167.04812 4.0642989e-11 -9.6356189 888.87112 -5190.4641 58850.548 -2683.172 0 1179.8703
Could someone give me some advice? Thanks.
Regards,
Shuai
Dear Lammps user,
I am trying to simulate a kerogen molecules with reax force field.
However, the simulation stops before finishing. The input script is shown
below:
# ReaxFF potential for kerogen system
units real
atom_style full
dimension 3
boundary p p p
read_data Kerogen_all_types.data
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax 1 1 1 3 1 4 5 2 2
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
velocity all create 300.0 4928459 rot yes dist gaussian
neighbor 2.5 bin
neigh_modify every 10 delay 20 check yes
thermo_style custom step temp epair etotal press &
v_eb v_ea v_elp v_emol v_epen v_ecoa v_ehb &
v_et v_eco v_ew v_ep v_efi v_eqeq
thermo 2000
timestep 0.1
fix 1 all nvt temp 300.0 300.0 10.0
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
dump 1 all xyz 4000 kerogen_reax_nvt_300.xyz
dump 2 all image 40000 kerogen_reax_nvt_300.*.png type type
# fix 1 all nvt temp 300.0 300.0 0.1
run 200000
# write_restart kerogen_reax_nvt_300.restart
the log file only stop at timestep at 32000.
Working directory is /home/she8/heshuai/Kerogen_Reax
LAMMPS (9 Dec 2014)
Reading data file ...
orthogonal box = (-30.2521 -56.0234 -2.2804) to (46.4637 13.2215 32.3103)
8 by 4 by 2 MPI processor grid
reading atoms ...
1272 atoms
Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
Setting up run ...
Memory usage per processor = 11.5855 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol epen ecoa ehb et eco ew ep
efi eqeq
0 300 -181229.84 -180093.26 32122.588 -243680
-2365.8896 2.1979658 0 184.82506 2.5577597e-11
-10.212182 1498.2505 -5085.287 65566.647 -2663.7653 0
1175.0794
2000 286.67841 -188949.85 -187863.73 356.52786 -243862.16
-2156.7883 56.292354 0 164.96268 8.959166e-11
-3.3245532 904.08541 -5176.849 58688.057 -2569.914 0
1088.2415
4000 299.54994 -189035.47 -187900.59 416.06742 -243934.87
-2228.4048 68.559834 0 163.27657 7.1295579e-11
-4.7748924 882.9766 -5175.387 58797.055 -2599.2197 0
1110.1247
6000 287.72074 -189090.37 -188000.31 -379.95504 -244094.27
-2171.9048 103.39324 0 165.44434 4.8539501e-11
-4.0159185 897.36408 -5173.8053 58789.435 -2635.6044 0
1139.5191
8000 298.01455 -189158.45 -188029.39 752.50269 -244401.55
-2136.3645 128.32376 0 167.62356 4.88234e-11
-6.5985255 869.04561 -5171.2917 59014.912 -2648.663 0
1156.0625
10000 296.2204 -189134.09 -188011.83 516.50878 -244236.24
-2110.145 119.10715 0 167.52562 9.0670668e-11
-7.6120035 900.41581 -5182.0204 58811.347 -2649.5746 0
1158.0686
12000 304.84436 -189216.41 -188061.47 386.4574 -244341.6
-2061.5708 89.076726 0 174.90782 1.0664177e-10
-7.5717835 883.69282 -5201.4379 58869.361 -2618.9704 0
1127.7036
14000 307.88731 -189138.03 -187971.57 -779.19199 -244206.55
-2175.9406 128.95918 0 163.61546 7.1725761e-11
-3.8473744 881.59257 -5177.0763 58839.471 -2679.1898 0
1171.59
16000 295.80175 -189222.79 -188102.11 7.2030537 -244223.25
-2116.0606 109.53121 0 165.43988 8.1966638e-11
-5.3458455 930.62944 -5173.6076 58751.179 -2653.4255 0
1150.8208
18000 300.80633 -189134.7 -187995.06 360.05664 -244274.11
-2065.1255 113.74046 0 166.86256 5.8863147e-11
-3.8891549 954.81631 -5179.7616 58774.425 -2658.5246 0
1155.6241
20000 288.97774 -189195.48 -188100.66 604.73976 -244206.13
-2114.0619 121.40347 0 169.58035 5.0388421e-11
-6.7169659 923.14055 -5188.2738 58740.733 -2666.648 0
1161.693
22000 293.27909 -189191.93 -188080.81 71.562863 -244282.19
-2058.0083 84.326903 0 169.69207 3.7907976e-11
-5.3607125 927.86398 -5193.1068 58817.124 -2677.379 0
1166.5926
24000 296.72032 -189185.64 -188061.48 249.55833 -244290.79
-2109.2467 113.14052 0 167.80104 6.3749353e-11
-3.396529 941.26156 -5183.3926 58867.08 -2664.2813 0
1161.3865
26000 310.79374 -189235.37 -188057.89 -1354.2312 -244242.77
-2123.6401 122.42294 0 168.22481 8.8778034e-11
-4.549328 901.5706 -5193.6625 58783.591 -2665.4066 0
1161.2559
28000 310.08212 -189194.63 -188019.85 -480.68235 -244477.07
-1954.7772 107.57739 0 170.80374 8.531817e-11
-8.0591895 921.80106 -5198.207 58868.248 -2670.4034 0
1166.4056
30000 298.69168 -189203.39 -188071.76 519.52753 -244440.6
-2064.477 120.59149 0 167.6916 3.9003067e-11
-11.278444 910.85196 -5189.0075 58918.659 -2679.1912 0
1173.91
32000 300.2762 -189226.3 -188088.68 -1805.8711 -244437.21
-2013.2508 133.59586 0 167.04812 4.0642989e-11
-9.6356189 888.87112 -5190.4641 58850.548 -2683.172 0
1179.8703
Could someone give me some advice? Thanks.
No, not with this limited information. Also your input and output don't
add up. The pair_coeff command of the 9 Dec 2014 version already reads
element names not numbers. Double check the version of LAMMPS you are
using.
Ray