energy in the comb potential

Hello,energyone. I am using the pair_style comb for si and oxygen mixed system. But the energy is not strictly conserved at NVE ensemble. I don’t know why.

#relax file
units metal
atom_style full
boundary p p p
read_data data
timestep 0.00001
pair_style comb
pair_coeff * * …/…/…/source/lammps-7May11/potentials/ffield.comb Si O

neighbor 2.0 bin
neigh_modify every 100 delay 0 check no

group si type 1
group o type 2
compute mke all ke/atom
compute mytemp all temp
compute mypress all pressure mytemp
compute mycoord all coord/atom 2.0
compute myrdf all rdf 300 1 2 2 1 1 1 2 2
fix my_charge all qeq/comb 100 1e-4 file charge.txt
fix 40 all ave/time 100 10 1000 c_myrdf file rdf.txt mode vector
fix 10 all nve
dump 1 all custom 100 dumpminimize.lammpstrj id type x y z vx vy vz c_mke c_mycoord
thermo_style custom step temp press pe ke etotal vol
thermo 100
thermo_modify lost warn
run 10000

Step Temp Press PotEng KinEng TotEng Volume
0 0 -30409.89 -8764.4647 0 -8764.4647 16710.449
100 3.2920439 -2831.3398 -9304.8349 0.57404007 -9304.2608 16710.449
200 8.8541363 -2753.4998 -9309.0456 1.5439129 -9307.5016 16710.449
300 17.064685 -2545.0014 -9310.7304 2.9756022 -9307.7548 16710.449
400 27.387098 -2589.5092 -9312.5881 4.7755414 -9307.8125 16710.449
500 39.206384 -2627.8077 -9314.737 6.836493 -9307.9005 16710.449
600 51.649505 -2656.7188 -9316.9205 9.0062242 -9307.9143 16710.449
700 64.062509 -2646.631 -9319.1331 11.170704 -9307.9624 16710.449
800 75.667136 -2606.8826 -9321.2449 13.194225 -9308.0506 16710.449
900 86.057877 -2514.7086 -9323.2116 15.006079 -9308.2055 16710.449
1000 94.787753 -2375.2974 -9324.6174 16.528324 -9308.0891 16710.449
1100 101.84296 -2153.8201 -9325.5275 17.758554 -9307.769 16710.449
1200 107.25102 -1906.3511 -9326.2126 18.701567 -9307.511 16710.449
1300 111.30853 -1665.2967 -9327.0939 19.409083 -9307.6848 16710.449
1400 114.50616 -1358.6667 -9327.0218 19.966661 -9307.0551 16710.449
1500 117.2052 -1052.1957 -9327.9975 20.437297 -9307.5602 16710.449
1600 120.43893 -488.41558 -9326.3032 21.001169 -9305.302 16710.449
1700 123.91806 -266.29832 -9328.6763 21.607832 -9307.0685 16710.449
1800 129.56759 419.06134 -9324.8052 22.592952 -9302.2123 16710.449
1900 135.66539 329.10572 -9329.7954 23.656237 -9306.1392 16710.449
2000 144.97429 820.37329 -9327.2936 25.279448 -9302.0142 16710.449
2100 154.63009 454.01447 -9333.0036 26.963148 -9306.0404 16710.449
2200 167.60253 651.50696 -9331.3669 29.225178 -9302.1417 16710.449
2300 180.1725 -74.435672 -9337.4451 31.417028 -9306.0281 16710.449
2400 195.49719 -279.93928 -9336.3616 34.089223 -9302.2723 16710.449
2500 209.25474 -1495.323 -9342.46 36.488153 -9305.9719 16710.449
2600 224.81402 -2259.2859 -9341.6736 39.201257 -9302.4724 16710.449
2700 237.57008 -4047.0341 -9347.3957 41.425554 -9305.9701 16710.449
2800 251.17445 -5325.7463 -9346.4827 43.797775 -9302.6849 16710.449
2900 261.09225 -7680.4216 -9351.4766 45.527162 -9305.9494 16710.449
3000 271.33599 -9288.4943 -9350.2005 47.313383 -9302.8871 16710.449
3100 277.78931 -11814.892 -9354.3692 48.438659 -9305.9306 16710.449
3200 284.52544 -13702.786 -9352.6776 49.613252 -9303.0643 16710.449
3300 287.64537 -16415.933 -9356.0656 50.15728 -9305.9083 16710.449
3400 291.28056 -18403.735 -9354.0117 50.791155 -9303.2205 16710.449
3500 291.7951 -21264.05 -9356.6685 50.880876 -9305.7877 16710.449
Regards,
Lisa

Hello,energyone. I am using the pair_style comb for si and oxygen mixed
system. But the energy is not strictly conserved at NVE ensemble. I don't
know why.

lisa,

your system is not equilibrated. note how the temperature is
rising. that will change the average potential energy for any
interaction model with a cutoff.

cheers,
    axel.

Yes, the system is a perfect crysal structure and it is not equilibrated. It is normal that the potential energy
changes, but it is strange that the total energy also change, right?

Lisa

2011/7/30 Axel Kohlmeyer <[email protected]>

no, it is not strange.

axel.

The energy still not conserved under NVE ensemble after relax the sample.

Reading restart file …
orthogonal box = (0.112875 0.265733 -0.178695) to (24.7611 23.9103 26.5607)
1 by 1 by 1 processor grid
1350 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
Pair COMB:
generating Coulomb integral lookup table …
will not apply over-coordination correction …
450 atoms in group si
900 atoms in group o
Setting up run …
Memory usage per processor = 13.2162 Mbytes
Step Temp Press PotEng KinEng TotEng Volume
40030 299.50632 -3399.0848 -9380.0501 52.225496 -9327.8246 15583.62
40100 301.40278 -3627.9597 -9380.3944 52.556187 -9327.8382 15583.62
40200 299.49369 -3058.3614 -9380.4338 52.223294 -9328.2105 15583.62
40300 297.73704 -3008.8485 -9380.3931 51.916985 -9328.4761 15583.62
40400 298.4974 -3815.1401 -9380.7934 52.04957 -9328.7438 15583.62
40500 296.93445 -2871.7237 -9380.6623 51.777034 -9328.8852 15583.62
40600 296.22056 -2385.6761 -9380.6744 51.652553 -9329.0218 15583.62
40700 295.5413 -2485.1103 -9380.7871 51.534109 -9329.253 15583.62
40800 294.40453 -2800.4769 -9380.757 51.335887 -9329.4211 15583.62
40900 294.91109 -4029.2684 -9380.9951 51.424217 -9329.5709 15583.62
41000 294.8136 -4550.1485 -9381.1722 51.407218 -9329.7649 15583.62
41100 294.52002 -4692.1473 -9381.294 51.356026 -9329.938 15583.62
41200 293.74085 -4299.1427 -9381.3302 51.220161 -9330.11 15583.62
41300 292.84458 -4166.7008 -9381.3051 51.063876 -9330.2412 15583.62
41400 291.9875 -3818.1368 -9381.288 50.914425 -9330.3736 15583.62
41500 292.22486 -4139.7661 -9381.3909 50.955814 -9330.4351 15583.62
41600 291.44179 -4357.3229 -9381.3123 50.819268 -9330.4931 15583.62
41700 292.04081 -5231.8378 -9381.5747 50.923721 -9330.651 15583.62
41800 291.30429 -4315.847 -9381.6166 50.795293 -9330.8213 15583.62
41900 291.43694 -3820.0453 -9381.8236 50.818423 -9331.0052 15583.62
42000 291.54592 -3465.1579 -9382.0039 50.837427 -9331.1665 15583.62
42100 291.18235 -3581.6862 -9382.0957 50.77403 -9331.3217 15583.62
42200 290.8084 -4693.1224 -9382.078 50.708823 -9331.3692 15583.62
42300 290.46741 -5741.197 -9382.1064 50.649364 -9331.457 15583.62
42400 289.90072 -6021.0294 -9382.0765 50.55055 -9331.5259 15583.62
42500 289.74831 -5817.0606 -9382.2663 50.523973 -9331.7423 15583.62
42600 289.0337 -4688.3145 -9382.2746 50.399366 -9331.8752 15583.62
42700 288.82344 -4578.9096 -9382.3418 50.362702 -9331.9791 15583.62
42800 288.13419 -5038.9561 -9382.2868 50.242516 -9332.0443 15583.62
42900 287.66444 -5893.5646 -9382.2405 50.160605 -9332.0799 15583.62
43000 287.69965 -5804.7759 -9382.2847 50.166745 -9332.118 15583.62
43100 287.53874 -4900.548 -9382.3959 50.138687 -9332.2572 15583.62
43200 287.22545 -4039.2704 -9382.5019 50.084058 -9332.4178 15583.62
43300 287.62307 -4079.8858 -9382.7013 50.153391 -9332.5479 15583.62
43400 287.34961 -4954.6279 -9382.7308 50.105708 -9332.6251 15583.62
43500 287.25614 -6208.2754 -9382.7393 50.089409 -9332.6499 15583.62
43600 286.82393 -6446.6266 -9382.7605 50.014044 -9332.7464 15583.62
43700 286.65502 -6880.4882 -9382.8722 49.984592 -9332.8876 15583.62
43800 286.19159 -6486.8399 -9382.8148 49.903782 -9332.9111 15583.62
43900 285.58009 -5994.9374 -9382.8162 49.797153 -9333.0191 15583.62
44000 284.92103 -5880.9965 -9382.7376 49.682232 -9333.0554 15583.62
44100 284.77501 -6123.1108 -9382.6799 49.656771 -9333.0232 15583.62
44200 284.47699 -6025.0264 -9382.773 49.604803 -9333.1682 15583.62
44300 284.78004 -5654.9529 -9382.9334 49.657646 -9333.2757 15583.62
44400 284.34099 -4908.5595 -9383.0142 49.581089 -9333.4331 15583.62
44500 284.43275 -4750.5852 -9383.0428 49.59709 -9333.4457 15583.62
44600 284.5622 -5307.7774 -9383.1382 49.619661 -9333.5186 15583.62
44700 283.92551 -6206.3685 -9383.0019 49.508641 -9333.4933 15583.62
44800 283.94064 -6840.4254 -9383.0952 49.51128 -9333.5839 15583.62
44900 283.46357 -7082.4866 -9383.0817 49.428092 -9333.6536 15583.62
45000 283.42072 -7100.1237 -9383.1389 49.420619 -9333.7182 15583.62
45100 283.61109 -6785.3698 -9383.2587 49.453814 -9333.8049 15583.62
45200 283.22409 -6238.2096 -9383.2362 49.386333 -9333.8499 15583.62
45300 283.10302 -6235.7409 -9383.1356 49.365222 -9333.7703 15583.62
45400 283.44208 -6335.29 -9383.3281 49.424344 -9333.9038 15583.62
45500 283.19765 -6543.2803 -9383.2491 49.381722 -9333.8673 15583.62
45600 283.08831 -6186.3419 -9383.3248 49.362657 -9333.9621 15583.62
45700 282.81775 -6000.5188 -9383.4641 49.315478 -9334.1487 15583.62

Lisa

2011/7/30 Axel Kohlmeyer <[email protected]>

The energy still not conserved under NVE ensemble after relax the sample.

your kinetic energy is decreasing, so you are not in equilibrium.

axel.

Send an email to the COMB author (Ray Shan, see the
top of src/pair_comb.cpp for his email) with your script
and see if he has any concerns - e.g. if
your timestep is too big.

Steve