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add reference outputs to temper/npt example

This commit is contained in:
Axel Kohlmeyer 2017-08-31 14:13:02 -04:00
parent f3dda30f8e
commit 4d2ed30b35
9 changed files with 1712 additions and 0 deletions
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LAMMPS (17 Aug 2017)
Running on 8 partitions of processors
Step T0 T1 T2 T3 T4 T5 T6 T7
500 0 1 2 3 4 5 6 7
600 0 1 2 3 5 4 7 6
700 0 2 1 4 6 3 7 5
800 0 2 1 4 6 3 7 5
900 0 2 1 3 6 4 7 5
1000 0 2 1 3 7 4 6 5
1100 0 1 2 3 7 4 6 5
1200 0 1 2 3 7 4 6 5
1300 0 1 2 4 7 3 5 6
1400 0 1 2 4 7 3 5 6
1500 0 2 1 4 7 3 5 6
1600 1 3 0 4 6 2 5 7
1700 1 3 0 4 5 2 6 7
1800 0 3 1 4 5 2 6 7
1900 0 3 2 4 5 1 6 7
2000 1 2 3 5 4 0 6 7
2100 2 1 3 5 4 0 6 7
2200 2 1 3 4 5 0 7 6
2300 1 2 4 3 5 0 7 6
2400 1 2 4 3 5 0 6 7
2500 2 1 3 4 5 0 6 7

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LAMMPS (17 Aug 2017)
Processor partition = 0
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
# Demonstrating temper/npt
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
thermo_style custom step temp epair emol etotal press density
thermo 50
variable temper_T world 275 280 285 290 295 300 305 310
variable rep world 0 1 2 3 4 5 6 7
fix myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000
fix myfix all npt temp 275 ${temper_T} 100.0 iso 1 1 1000
fix myfix all npt temp 275 275 100.0 iso 1 1 1000
run 500
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
Step Temp E_pair E_mol TotEng Press Density
0 190.0857 -6442.768 70.391457 -5237.4579 20361.998 0.98480122
50 221.73889 -7683.7524 1219.961 -5139.8856 -23756.591 0.996067
100 253.40719 -6992.3405 479.6715 -4999.6856 12620.614 1.0124851
150 273.60252 -6943.8714 474.24744 -4836.0631 6691.4146 1.0213937
200 265.37126 -7274.7854 1059.7586 -4630.6111 -17765.088 1.0221471
250 263.1769 -6503.9902 470.29014 -4462.3859 21936.742 1.0159924
300 274.03852 -7026.6057 1021.3683 -4369.0734 -14847.42 1.0095778
350 283.20032 -6715.3608 688.9769 -4335.5187 3430.7111 1.0045615
400 282.2987 -6645.6692 598.6786 -4361.5086 6318.9525 1.0001513
450 265.89091 -6977.5705 985.58718 -4404.465 -13261.32 0.99833097
500 270.30038 -6683.7902 650.5748 -4419.37 10014.277 1.000501
Loop time of 11.0158 on 2 procs for 500 steps with 2004 atoms
Performance: 7.843 ns/day, 3.060 hours/ns, 45.389 timesteps/s
99.4% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.6893 | 7.8012 | 7.9131 | 4.0 | 70.82
Bond | 0.085948 | 0.089635 | 0.093322 | 1.2 | 0.81
Kspace | 1.1113 | 1.2333 | 1.3552 | 11.0 | 11.20
Neigh | 1.2316 | 1.2336 | 1.2356 | 0.2 | 11.20
Comm | 0.24281 | 0.24305 | 0.2433 | 0.0 | 2.21
Output | 0.00052857 | 0.00053537 | 0.00054216 | 0.0 | 0.00
Modify | 0.35968 | 0.38071 | 0.40175 | 3.4 | 3.46
Other | | 0.03378 | | | 0.31
Nlocal: 1002 ave 1012 max 992 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8737.5 ave 8747 max 8728 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 359463 ave 359931 max 358995 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 718926
Ave neighs/atom = 358.746
Ave special neighs/atom = 2.34032
Neighbor list builds = 50
Dangerous builds = 0
temper/npt 2000 100 ${temper_T} myfix 0 58728 1
temper/npt 2000 100 275 myfix 0 58728 1
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.269166
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0224625
estimated relative force accuracy = 6.76451e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
Step Temp E_pair E_mol TotEng Press Density
500 270.30038 -6683.7883 650.5748 -4419.3682 10014.295 1.000501
550 270.02511 -6875.5939 861.97452 -4401.4176 -7136.4285 1.005266
600 278.94444 -6786.546 772.05516 -4349.0356 1262.4902 1.0110761
650 283.8929 -6763.9691 734.90211 -4334.0667 3664.1311 1.0138933
700 276.67406 -6889.5452 847.87041 -4389.775 -4754.9929 1.0145005
750 266.09032 -6720.4921 700.27463 -4431.5085 5654.8094 1.013756
800 277.69948 -6917.9358 860.12186 -4399.7918 -4729.7009 1.0124281
850 278.00722 -6808.1267 798.69768 -4349.5695 1468.5155 1.0139727
900 276.49266 -6784.5965 818.01248 -4315.7673 2510.6047 1.0158115
950 270.36225 -6847.6403 901.97122 -4331.4544 -3448.3968 1.0175668
1000 276.75533 -6809.4075 781.83481 -4375.1877 3379.8584 1.0173101
1050 271.67172 -6913.3268 847.97269 -4443.3211 -2045.5605 1.016761
1100 265.73149 -6867.7958 840.08439 -4441.1449 -323.23893 1.0170333
1150 274.51451 -6834.9841 792.48751 -4403.4906 2604.0644 1.0175885
1200 274.22914 -6919.9496 890.14423 -4392.5032 -3454.4418 1.0167016
1250 274.13019 -6817.7256 825.11317 -4355.901 2067.3849 1.0181714
1300 287.36094 -6906.5403 854.11016 -4336.7237 -438.01206 1.0180794
1350 275.51763 -6911.8172 855.25923 -4411.5627 -742.96412 1.0180086
1400 269.90457 -6919.4028 855.55485 -4452.3659 311.08918 1.0213368
1450 276.99478 -6980.8317 913.69108 -4413.326 -1810.1051 1.0265437
1500 282.20313 -6926.698 863.56525 -4378.2213 932.7594 1.0301769
1550 276.82056 -6917.141 910.22058 -4354.146 -899.64097 1.0361201
1600 278.2946 -6903.7351 893.14524 -4349.0145 1399.9679 1.0421849
1650 270.12097 -6863.0844 879.81355 -4370.4967 1132.9864 1.0410741
1700 274.02565 -6912.4818 893.37432 -4383.0202 -1359.393 1.0366624
1750 276.77322 -6866.3214 899.18224 -4314.6474 887.47588 1.0332821
1800 287.02945 -6961.9217 950.89476 -4297.2996 -1298.0904 1.0313542
1850 279.37232 -6930.51 898.78906 -4363.711 397.74804 1.0309206
1900 277.14727 -6978.8634 915.53145 -4408.6069 636.36898 1.0285813
1950 275.14272 -7010.256 927.28727 -4440.212 -2352.6961 1.0241747
2000 270.84972 -6967.52 913.42253 -4436.9722 1669.9637 1.0251906
2050 276.70108 -6992.4582 993.37473 -4347.0223 -500.38379 1.0325714
2100 278.49569 -6922.9266 939.43518 -4320.7155 700.24515 1.0385166
2150 279.69822 -6896.5008 923.58805 -4302.9571 702.22759 1.0415681
2200 284.136 -6951.6694 974.70903 -4280.5086 352.95043 1.0452009
2250 292.01941 -6960.5848 964.01635 -4253.0483 2680.7007 1.0430517
2300 277.58812 -6995.5006 1010.8176 -4327.3258 -1508.9961 1.0328658
2350 270.61616 -6978.93 966.12478 -4397.0745 -1636.7434 1.0267664
2400 279.36012 -6991.4739 957.43125 -4366.1056 432.00482 1.0260429
2450 286.38546 -7074.807 1004.3206 -4360.6042 160.9109 1.0251585
2500 269.98622 -6932.0456 957.35208 -4362.724 1748.1568 1.0186556
Loop time of 46.7361 on 2 procs for 2000 steps with 2004 atoms
Performance: 7.395 ns/day, 3.246 hours/ns, 42.793 timesteps/s
99.2% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 32.381 | 32.617 | 32.854 | 4.1 | 69.79
Bond | 0.3601 | 0.36578 | 0.37147 | 0.9 | 0.78
Kspace | 4.6658 | 4.933 | 5.2002 | 12.0 | 10.56
Neigh | 4.9833 | 4.9921 | 5.0009 | 0.4 | 10.68
Comm | 0.96477 | 0.96532 | 0.96587 | 0.1 | 2.07
Output | 0.0021896 | 0.0022331 | 0.0022767 | 0.1 | 0.00
Modify | 1.4424 | 1.5379 | 1.6334 | 7.7 | 3.29
Other | | 1.322 | | | 2.83
Nlocal: 1002 ave 1011 max 993 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8835 ave 8847 max 8823 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 366395 ave 367166 max 365624 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 732790
Ave neighs/atom = 365.664
Ave special neighs/atom = 2.34032
Neighbor list builds = 195
Dangerous builds = 0
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
group peptide type <= 12
84 atoms in group peptide
Total wall time: 0:00:58

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LAMMPS (17 Aug 2017)
Processor partition = 1
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
# Demonstrating temper/npt
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
thermo_style custom step temp epair emol etotal press density
thermo 50
variable temper_T world 275 280 285 290 295 300 305 310
variable rep world 0 1 2 3 4 5 6 7
fix myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000
fix myfix all npt temp 280 ${temper_T} 100.0 iso 1 1 1000
fix myfix all npt temp 280 280 100.0 iso 1 1 1000
run 500
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
Step Temp E_pair E_mol TotEng Press Density
0 190.0857 -6442.768 70.391457 -5237.4579 20361.998 0.98480122
50 222.19861 -7681.6246 1220.9355 -5134.0385 -23782.584 0.99586813
100 254.66243 -6984.8813 480.32613 -4984.0772 12653.925 1.0120499
150 275.28565 -6924.9875 473.42216 -4807.9551 6796.8759 1.0208676
200 266.52981 -7245.4283 1066.0809 -4588.0144 -17643.106 1.0213699
250 265.06051 -6458.7243 468.97999 -4407.1839 22476.585 1.0143215
300 276.91573 -6986.8723 1020.9402 -4312.5895 -14559.244 1.005554
350 284.26789 -6635.8191 681.27092 -4257.3089 2625.7849 0.99664411
400 284.48799 -6543.0099 637.61352 -4206.8431 7901.0269 0.99079237
450 271.30029 -6770.4441 1003.5624 -4147.0663 -13046.51 0.9856127
500 292.02418 -6514.8219 628.56367 -4142.7096 9871.7492 0.98625432
Loop time of 11.1841 on 2 procs for 500 steps with 2004 atoms
Performance: 7.725 ns/day, 3.107 hours/ns, 44.706 timesteps/s
98.4% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.8072 | 7.9267 | 8.0463 | 4.2 | 70.88
Bond | 0.08858 | 0.091102 | 0.093624 | 0.8 | 0.81
Kspace | 1.1403 | 1.2665 | 1.3927 | 11.2 | 11.32
Neigh | 1.2478 | 1.2496 | 1.2514 | 0.2 | 11.17
Comm | 0.21574 | 0.23191 | 0.24809 | 3.4 | 2.07
Output | 0.00054431 | 0.00054872 | 0.00055313 | 0.0 | 0.00
Modify | 0.36159 | 0.38512 | 0.40864 | 3.8 | 3.44
Other | | 0.03255 | | | 0.29
Nlocal: 1002 ave 1026 max 978 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8640.5 ave 8690 max 8591 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 354518 ave 367457 max 341580 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 709037
Ave neighs/atom = 353.811
Ave special neighs/atom = 2.34032
Neighbor list builds = 49
Dangerous builds = 0
temper/npt 2000 100 ${temper_T} myfix 0 58728 1
temper/npt 2000 100 280 myfix 0 58728 1
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268766
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0227872
estimated relative force accuracy = 6.8623e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
Step Temp E_pair E_mol TotEng Press Density
500 292.02418 -6514.8215 628.56367 -4142.7092 9871.7534 0.98625432
550 282.55729 -6813.6685 882.47773 -4244.1648 -5377.4053 0.98629839
600 274.41644 -6737.0424 793.45027 -4305.1716 -306.54594 0.98725369
650 274.38967 -6664.1973 722.25014 -4303.6865 4628.1283 0.99175575
700 282.07693 -6819.1345 897.72476 -4237.2518 -7210.1942 0.99693402
750 281.80476 -6580.3192 776.69527 -4121.091 5466.9616 1.0060075
800 288.76507 -6726.7205 885.07773 -4117.5529 -2623.0756 1.0132495
850 289.21519 -6755.4289 847.00353 -4181.648 776.75991 1.0160602
900 280.679 -6694.3766 777.91069 -4240.6544 2272.2098 1.0170439
950 280.93616 -6813.8865 910.52053 -4226.0191 -3872.8603 1.0202606
1000 289.91762 -6710.0317 786.39268 -4192.6678 4456.0575 1.0222223
1050 292.7318 -6830.313 882.85834 -4199.6812 -2434.3412 1.0214856
1100 280.61029 -6789.3828 846.07872 -4267.9028 580.25027 1.0202095
1150 277.27283 -6806.9599 852.2013 -4299.2838 18.428929 1.0180062
1200 284.68488 -6849.8644 877.54803 -4272.5875 -1041.3591 1.0171686
1250 290.47153 -6864.5918 827.15634 -4303.1571 2658.2245 1.0175104
1300 279.84219 -6892.8497 884.4759 -4337.5586 -1800.8783 1.0176916
1350 275.59818 -6848.0359 848.53171 -4354.028 1599.2311 1.0197901
1400 276.67929 -6893.565 900.40614 -4341.2278 295.46659 1.0221449
1450 281.18148 -6902.3901 931.40362 -4292.1748 -1585.1315 1.0243322
1500 282.82339 -6846.4364 887.9988 -4269.8228 2142.9076 1.0291373
1550 291.40537 -6898.3742 920.23257 -4238.2876 -355.99408 1.0308242
1600 279.9548 -6863.2068 923.64788 -4268.0713 233.83555 1.0259922
1650 282.90611 -6848.3952 903.97971 -4255.3069 369.65523 1.0200083
1700 292.24099 -6884.346 965.54265 -4173.9603 -971.39092 1.0155909
1750 285.95609 -6805.2486 955.25719 -4142.6727 646.23287 1.012031
1800 293.50173 -6823.8152 919.24584 -4152.199 530.19678 1.0078324
1850 300.737 -6918.3747 942.10944 -4180.6963 -949.67639 1.0061029
1900 284.98969 -6913.5357 956.78373 -4255.2032 -163.02524 1.0095568
1950 282.78589 -6905.1978 951.94384 -4264.8631 -891.31043 1.0177223
2000 289.82463 -6977.0203 1022.9525 -4223.6518 -540.73403 1.0269481
2050 292.13474 -6900.8375 924.54552 -4232.0833 2656.3028 1.0310097
2100 284.54116 -6958.82 968.35681 -4291.5924 -286.70605 1.0264636
2150 268.14376 -6966.2184 973.69354 -4391.5558 -1446.0052 1.0190957
2200 275.09872 -6957.02 982.37472 -4332.1512 -1449.1984 1.0199163
2250 285.69237 -7002.4814 1014.3438 -4282.3934 -1530.0347 1.0264012
2300 282.59746 -6922.8242 980.57612 -4254.9822 381.8231 1.0332785
2350 290.98138 -6993.8628 1022.527 -4234.0132 -559.9386 1.0396092
2400 281.29903 -6963.5226 967.13898 -4316.8702 1438.7922 1.0452404
2450 278.44605 -6968.5134 945.32295 -4360.7108 1102.9302 1.0498791
2500 278.65789 -7034.3651 1032.8711 -4337.7496 -923.32414 1.0527955
Loop time of 46.7418 on 2 procs for 2000 steps with 2004 atoms
Performance: 7.394 ns/day, 3.246 hours/ns, 42.788 timesteps/s
98.3% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 33.141 | 33.146 | 33.152 | 0.1 | 70.91
Bond | 0.36441 | 0.36647 | 0.36853 | 0.3 | 0.78
Kspace | 4.9269 | 4.9539 | 4.9808 | 1.2 | 10.60
Neigh | 5.2154 | 5.223 | 5.2306 | 0.3 | 11.17
Comm | 0.90923 | 0.97305 | 1.0369 | 6.5 | 2.08
Output | 0.0021682 | 0.0027286 | 0.003289 | 1.1 | 0.01
Modify | 1.454 | 1.5534 | 1.6528 | 8.0 | 3.32
Other | | 0.5229 | | | 1.12
Nlocal: 1002 ave 1005 max 999 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 9059.5 ave 9084 max 9035 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 378277 ave 380641 max 375913 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 756554
Ave neighs/atom = 377.522
Ave special neighs/atom = 2.34032
Neighbor list builds = 197
Dangerous builds = 0
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
group peptide type <= 12
84 atoms in group peptide
Total wall time: 0:00:58

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LAMMPS (17 Aug 2017)
Processor partition = 2
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
# Demonstrating temper/npt
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
thermo_style custom step temp epair emol etotal press density
thermo 50
variable temper_T world 275 280 285 290 295 300 305 310
variable rep world 0 1 2 3 4 5 6 7
fix myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000
fix myfix all npt temp 285 ${temper_T} 100.0 iso 1 1 1000
fix myfix all npt temp 285 285 100.0 iso 1 1 1000
run 500
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
Step Temp E_pair E_mol TotEng Press Density
0 190.0857 -6442.768 70.391457 -5237.4579 20361.998 0.98480122
50 222.63643 -7679.59 1221.8685 -5128.4568 -23807.78 0.99567623
100 255.85049 -6977.7653 480.95894 -4969.235 12685.571 1.0116281
150 276.83083 -6906.8603 472.9485 -4781.076 6899.3786 1.0203576
200 267.19755 -7210.264 1068.2756 -4546.6687 -17521.505 1.0207097
250 263.8837 -6392.2545 463.0506 -4353.6698 22886.964 1.0130132
300 280.88953 -6919.81 1005.9833 -4236.7581 -14774.964 1.0024942
350 289.59472 -6621.8351 734.60058 -4158.1911 2409.0738 0.99451628
400 288.29076 -6495.283 634.61137 -4139.4136 6594.965 0.98796525
450 281.92055 -6838.8449 1025.3043 -4130.3164 -12795.112 0.98591519
500 298.25519 -6578.7232 652.75467 -4145.2172 10282.835 0.98902709
Loop time of 11.0965 on 2 procs for 500 steps with 2004 atoms
Performance: 7.786 ns/day, 3.082 hours/ns, 45.059 timesteps/s
99.1% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.9379 | 7.9449 | 7.952 | 0.2 | 71.60
Bond | 0.090588 | 0.090927 | 0.091265 | 0.1 | 0.82
Kspace | 1.1684 | 1.176 | 1.1837 | 0.7 | 10.60
Neigh | 1.2553 | 1.2556 | 1.256 | 0.0 | 11.32
Comm | 0.20599 | 0.21536 | 0.22474 | 2.0 | 1.94
Output | 0.00049877 | 0.00050557 | 0.00051236 | 0.0 | 0.00
Modify | 0.35224 | 0.37667 | 0.40111 | 4.0 | 3.39
Other | | 0.03635 | | | 0.33
Nlocal: 1002 ave 1007 max 997 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8699.5 ave 8735 max 8664 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 355600 ave 363554 max 347647 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 711201
Ave neighs/atom = 354.891
Ave special neighs/atom = 2.34032
Neighbor list builds = 50
Dangerous builds = 0
temper/npt 2000 100 ${temper_T} myfix 0 58728 1
temper/npt 2000 100 285 myfix 0 58728 1
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268844
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0227233
estimated relative force accuracy = 6.84305e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
Step Temp E_pair E_mol TotEng Press Density
500 298.25519 -6578.7239 652.75467 -4145.218 10282.81 0.98902709
550 280.55812 -6800.9339 904.37474 -4221.4693 -6284.3677 0.99138729
600 282.54117 -6736.9067 793.64464 -4256.3323 379.51956 0.99544144
650 289.246 -6695.3988 727.43292 -4241.0045 3741.9292 1.0004679
700 298.37935 -6898.8951 912.35329 -4205.0492 -5179.2622 1.0029455
750 276.21453 -6657.3814 738.83164 -4269.3936 6422.8684 1.003042
800 273.34049 -6770.7481 842.34057 -4296.411 -2699.1945 1.0011122
850 279.30106 -6766.7842 807.51048 -4291.6893 -583.46522 1.0039015
900 286.09076 -6808.4366 807.15205 -4293.1617 1405.0223 1.0062162
950 283.04021 -6838.8107 869.45604 -4279.4454 -2826.6403 1.008228
1000 278.36762 -6776.1595 827.04427 -4287.104 2510.6216 1.0123638
1050 276.46194 -6858.6173 893.69758 -4314.2864 -1818.0617 1.0153108
1100 270.91883 -6818.5634 864.2518 -4336.7738 1021.1432 1.0153455
1150 274.70844 -6747.0957 849.98378 -4256.948 1453.2165 1.0141005
1200 292.66211 -6864.4907 917.17522 -4199.958 -2889.5663 1.0130738
1250 288.1024 -6814.0744 887.46443 -4206.4766 2384.4467 1.0139599
1300 286.54446 -6864.9998 900.886 -4253.2821 -2397.0043 1.0140796
1350 274.86169 -6804.6738 866.75191 -4296.843 1112.3802 1.0143892
1400 275.30771 -6837.4182 904.04812 -4289.6282 136.99961 1.0170328
1450 296.09129 -6868.8691 910.61078 -4190.4268 -1076.0085 1.0204782
1500 292.50596 -6812.8248 889.10378 -4177.2959 1069.9919 1.0198406
1550 284.3886 -6876.901 909.58572 -4269.3554 -1153.6899 1.0177539
1600 276.41187 -6876.8574 907.69862 -4318.8244 114.8894 1.0158964
1650 275.68967 -6919.4356 902.04604 -4371.3672 -1493.2092 1.0141832
1700 271.20923 -6893.2373 912.27766 -4361.688 -563.23529 1.0157743
1750 279.40649 -6842.0743 892.63677 -4281.2237 944.83039 1.0207184
1800 282.84659 -6889.8537 934.73963 -4266.3608 -895.12942 1.0238833
1850 279.58052 -6900.6624 951.17313 -4280.2364 648.68857 1.024366
1900 276.44092 -6841.9805 881.15423 -4310.3185 1052.7352 1.0229576
1950 289.89625 -6960.295 949.2514 -4280.2 -2500.9996 1.0210089
2000 283.75058 -6908.6985 930.56698 -4283.9809 1529.221 1.0211902
2050 284.00141 -6837.2348 943.57188 -4198.0147 -710.45695 1.0190262
2100 294.53504 -6879.4583 983.431 -4137.4874 -496.16699 1.0172736
2150 296.46029 -6854.8307 926.58211 -4158.2139 757.20038 1.017548
2200 284.26196 -6896.5957 989.5222 -4209.8697 -1953.1733 1.0187998
2250 284.51713 -6852.3924 938.51853 -4215.1465 210.72971 1.0208918
2300 289.88921 -6867.2253 969.05163 -4167.372 -80.492209 1.0240397
2350 296.17997 -6836.2421 954.2497 -4113.6314 -389.76698 1.0272081
2400 309.56546 -6833.5714 970.44217 -4014.8493 610.57346 1.0294586
2450 300.61402 -6827.9964 1025.4417 -4007.7199 1121.4824 1.0284326
2500 298.82336 -6815.7862 945.53298 -4086.1097 -726.1131 1.0224541
Loop time of 46.7423 on 2 procs for 2000 steps with 2004 atoms
Performance: 7.394 ns/day, 3.246 hours/ns, 42.788 timesteps/s
99.3% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 32.492 | 32.625 | 32.758 | 2.3 | 69.80
Bond | 0.3584 | 0.36552 | 0.37265 | 1.2 | 0.78
Kspace | 4.7476 | 4.8898 | 5.0319 | 6.4 | 10.46
Neigh | 5.1461 | 5.1463 | 5.1464 | 0.0 | 11.01
Comm | 0.86246 | 0.89403 | 0.92559 | 3.3 | 1.91
Output | 0.0020437 | 0.0020902 | 0.0021367 | 0.1 | 0.00
Modify | 1.4279 | 1.5187 | 1.6095 | 7.4 | 3.25
Other | | 1.301 | | | 2.78
Nlocal: 1002 ave 1010 max 994 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8922 ave 9009 max 8835 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 367689 ave 371637 max 363741 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 735378
Ave neighs/atom = 366.955
Ave special neighs/atom = 2.34032
Neighbor list builds = 200
Dangerous builds = 0
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
group peptide type <= 12
84 atoms in group peptide
Total wall time: 0:00:58

211
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LAMMPS (17 Aug 2017)
Processor partition = 3
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
# Demonstrating temper/npt
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
thermo_style custom step temp epair emol etotal press density
thermo 50
variable temper_T world 275 280 285 290 295 300 305 310
variable rep world 0 1 2 3 4 5 6 7
fix myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000
fix myfix all npt temp 290 ${temper_T} 100.0 iso 1 1 1000
fix myfix all npt temp 290 290 100.0 iso 1 1 1000
run 500
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
Step Temp E_pair E_mol TotEng Press Density
0 190.0857 -6442.768 70.391457 -5237.4579 20361.998 0.98480122
50 223.053 -7677.6519 1222.7567 -5123.1433 -23832.135 0.99549097
100 256.97829 -6970.9352 481.56411 -4955.0662 12716.194 1.0112202
150 278.44824 -6890.5623 472.60764 -4755.4621 6994.6533 1.0198648
200 271.15638 -7198.8095 1073.0275 -4506.826 -17647.735 1.020128
250 271.19291 -6398.4699 477.07511 -4302.2206 23076.406 1.0123626
300 295.5039 -6953.4923 1007.5309 -4181.6369 -15039.211 1.0007168
350 297.29537 -6594.1646 707.50773 -4111.6362 1990.9893 0.99116796
400 294.93533 -6450.921 630.83559 -4059.1555 6431.7427 0.98805162
450 295.23265 -6781.3296 1002.9096 -4015.715 -12070.145 0.98722232
500 284.70036 -6389.6524 668.83647 -4020.9946 10958.208 0.98502274
Loop time of 11.0942 on 2 procs for 500 steps with 2004 atoms
Performance: 7.788 ns/day, 3.082 hours/ns, 45.069 timesteps/s
99.3% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.7626 | 7.8378 | 7.913 | 2.7 | 70.65
Bond | 0.086271 | 0.08859 | 0.090909 | 0.8 | 0.80
Kspace | 1.1309 | 1.2146 | 1.2982 | 7.6 | 10.95
Neigh | 1.2958 | 1.2978 | 1.2999 | 0.2 | 11.70
Comm | 0.24052 | 0.24249 | 0.24445 | 0.4 | 2.19
Output | 0.00055242 | 0.00056267 | 0.00057292 | 0.0 | 0.01
Modify | 0.35597 | 0.3786 | 0.40124 | 3.7 | 3.41
Other | | 0.03375 | | | 0.30
Nlocal: 1002 ave 1015 max 989 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8686.5 ave 8717 max 8656 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 354166 ave 365049 max 343283 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 708332
Ave neighs/atom = 353.459
Ave special neighs/atom = 2.34032
Neighbor list builds = 52
Dangerous builds = 0
temper/npt 2000 100 ${temper_T} myfix 0 58728 1
temper/npt 2000 100 290 myfix 0 58728 1
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268731
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228157
estimated relative force accuracy = 6.87089e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
Step Temp E_pair E_mol TotEng Press Density
500 284.70036 -6389.6523 668.83647 -4020.9946 10958.208 0.98502274
550 290.90514 -6715.0579 911.30009 -4066.8904 -6474.803 0.98383517
600 283.07652 -6555.4875 766.62589 -4098.7355 261.44315 0.98334866
650 293.39943 -6543.5525 727.38701 -4064.4058 5298.0746 0.98688936
700 295.77284 -6702.0803 912.68434 -4023.4658 -6806.6079 0.98957885
750 302.19503 -6545.9025 745.53299 -3996.0952 4624.9549 0.9931176
800 292.89947 -6664.6734 861.73293 -4054.1658 -1569.2753 0.99667377
850 288.96376 -6637.9753 841.33585 -4071.3632 -864.6336 1.0003373
900 291.22538 -6602.7272 806.80566 -4057.1422 2231.0477 1.0028411
950 290.78982 -6720.7893 893.26995 -4091.3406 -3898.6743 1.0021058
1000 285.74827 -6640.6252 810.15614 -4124.3911 558.53066 1.0051325
1050 288.3183 -6717.0357 867.9383 -4127.675 355.99916 1.0122228
1100 291.39421 -6746.7014 879.64717 -4127.2669 -736.99584 1.011619
1150 290.47863 -6710.1637 836.85441 -4138.9885 1105.9666 1.0069336
1200 288.94451 -6726.3595 867.56238 -4133.6359 -901.95525 1.0026837
1250 290.75557 -6716.8398 867.19843 -4113.6671 1376.8368 1.0000807
1300 289.52654 -6715.6758 904.46364 -4082.5758 -1400.2433 0.99935875
1350 292.30663 -6661.0526 904.32661 -4011.491 196.73374 0.99704618
1400 301.41479 -6661.807 880.88881 -3981.3023 1079.6673 0.99635503
1450 301.10415 -6704.7089 950.31941 -3956.6283 -1083.4574 0.99740883
1500 303.52341 -6687.1744 886.70817 -3988.2608 901.20455 0.99756877
1550 290.70908 -6738.4941 931.37971 -4071.4177 -56.269366 0.99843015
1600 289.8778 -6709.348 888.89193 -4089.7225 506.51952 1.0003118
1650 288.12183 -6724.4008 896.24971 -4107.9017 -1229.6117 1.004563
1700 297.81604 -6743.9356 906.62851 -4059.1778 1032.1913 1.0116813
1750 304.22415 -6761.8681 932.14203 -4013.3368 1825.359 1.015764
1800 286.62853 -6698.3527 911.17615 -4075.843 -1160.6136 1.0169905
1850 292.7719 -6787.8009 918.61838 -4121.1696 1455.4151 1.0203418
1900 290.87293 -6806.1448 960.43892 -4109.0309 -829.39096 1.022593
1950 304.5232 -6848.8518 954.93165 -4075.7453 915.93096 1.0221703
2000 286.15289 -6721.328 941.83273 -4071.0015 194.2717 1.0167052
2050 305.2696 -6720.8244 968.69939 -3929.4938 -1154.2389 1.0114409
2100 298.14935 -6678.8136 975.17824 -3923.516 794.1643 1.0070072
2150 301.51333 -6734.6863 950.33572 -3984.1464 -537.44292 1.0048337
2200 298.25074 -6736.277 945.4083 -4010.144 211.60185 1.0060101
2250 297.20864 -6820.7924 941.75394 -4104.5356 772.05119 1.0087884
2300 286.08552 -6853.0967 990.41746 -4154.5877 -760.47968 1.0110651
2350 295.49972 -6888.1433 937.27703 -4186.5667 966.37988 1.0150101
2400 289.60528 -6888.0768 967.74071 -4191.2297 1140.8847 1.0176507
2450 290.7003 -6906.443 998.89141 -4171.9073 -363.47638 1.0151765
2500 291.05855 -6817.2894 972.06896 -4107.4372 415.89846 1.0117849
Loop time of 46.7412 on 2 procs for 2000 steps with 2004 atoms
Performance: 7.394 ns/day, 3.246 hours/ns, 42.789 timesteps/s
99.3% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 31.884 | 32.272 | 32.659 | 6.8 | 69.04
Bond | 0.34239 | 0.35991 | 0.37742 | 2.9 | 0.77
Kspace | 4.6486 | 5.0781 | 5.5076 | 19.1 | 10.86
Neigh | 5.1657 | 5.1742 | 5.1828 | 0.4 | 11.07
Comm | 0.96743 | 0.96831 | 0.96918 | 0.1 | 2.07
Output | 0.0021966 | 0.0022568 | 0.002317 | 0.1 | 0.00
Modify | 1.4428 | 1.5251 | 1.6074 | 6.7 | 3.26
Other | | 1.362 | | | 2.91
Nlocal: 1002 ave 1004 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8824 ave 8848 max 8800 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 363564 ave 364653 max 362474 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 727127
Ave neighs/atom = 362.838
Ave special neighs/atom = 2.34032
Neighbor list builds = 201
Dangerous builds = 0
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
group peptide type <= 12
84 atoms in group peptide
Total wall time: 0:00:58

211
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LAMMPS (17 Aug 2017)
Processor partition = 4
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
# Demonstrating temper/npt
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
thermo_style custom step temp epair emol etotal press density
thermo 50
variable temper_T world 275 280 285 290 295 300 305 310
variable rep world 0 1 2 3 4 5 6 7
fix myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000
fix myfix all npt temp 295 ${temper_T} 100.0 iso 1 1 1000
fix myfix all npt temp 295 295 100.0 iso 1 1 1000
run 500
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
Step Temp E_pair E_mol TotEng Press Density
0 190.0857 -6442.768 70.391457 -5237.4579 20361.998 0.98480122
50 223.44965 -7675.7636 1223.6082 -5118.0353 -23854.901 0.99531214
100 258.05368 -6964.3986 482.14839 -4941.5246 12745.624 1.010825
150 279.95689 -6874.6176 472.25664 -4730.8609 7091.9355 1.0193879
200 275.57578 -7193.9232 1079.6288 -4468.952 -17877.542 1.0195441
250 279.43717 -6402.2754 479.97988 -4253.8984 23273.809 1.0116181
300 292.20824 -6863.5426 998.78846 -4120.1066 -14524.477 0.99985013
350 297.83477 -6520.8204 705.46814 -4037.1112 1640.5321 0.99100268
400 300.71476 -6441.8834 652.50284 -3993.9443 7052.2304 0.98787311
450 298.04546 -6757.2898 986.07239 -3991.7184 -11211.612 0.98470906
500 290.54704 -6432.0836 676.82263 -4020.5317 9503.0303 0.98022653
Loop time of 11.0411 on 2 procs for 500 steps with 2004 atoms
Performance: 7.825 ns/day, 3.067 hours/ns, 45.286 timesteps/s
99.2% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.7513 | 7.8142 | 7.8771 | 2.3 | 70.77
Bond | 0.087844 | 0.089858 | 0.091872 | 0.7 | 0.81
Kspace | 1.1507 | 1.2078 | 1.2649 | 5.2 | 10.94
Neigh | 1.2777 | 1.2798 | 1.282 | 0.2 | 11.59
Comm | 0.21883 | 0.2369 | 0.25497 | 3.7 | 2.15
Output | 0.00052476 | 0.00053084 | 0.00053692 | 0.0 | 0.00
Modify | 0.35187 | 0.38007 | 0.40828 | 4.6 | 3.44
Other | | 0.03188 | | | 0.29
Nlocal: 1002 ave 1018 max 986 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8685.5 ave 8713 max 8658 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 352674 ave 363841 max 341507 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 705348
Ave neighs/atom = 351.97
Ave special neighs/atom = 2.34032
Neighbor list builds = 51
Dangerous builds = 0
temper/npt 2000 100 ${temper_T} myfix 0 58728 1
temper/npt 2000 100 295 myfix 0 58728 1
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268595
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0229274
estimated relative force accuracy = 6.90452e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
Step Temp E_pair E_mol TotEng Press Density
500 290.54704 -6432.0826 676.82263 -4020.5307 9503.0509 0.98022653
550 299.80307 -6732.1631 858.08424 -4084.0858 -5804.5234 0.97922483
600 282.09517 -6605.4814 819.96587 -4101.2486 -819.40251 0.98081741
650 294.53657 -6522.7525 767.04478 -3997.1588 4596.0585 0.98382352
700 305.841 -6619.4153 905.5064 -3887.8662 -5973.5686 0.98622017
750 307.23206 -6438.653 789.70387 -3814.6009 6681.8219 0.98950206
800 307.87505 -6564.5918 887.75178 -3838.6527 -1917.6181 0.98688326
850 298.61627 -6528.5749 847.91654 -3897.7513 -3785.6609 0.9806677
900 300.37107 -6492.7964 828.13288 -3871.2792 3123.0873 0.97992098
950 313.50832 -6648.6955 936.69562 -3840.1788 -3465.5075 0.97832705
1000 300.79594 -6452.6853 828.10459 -3828.6598 2639.7489 0.9724972
1050 316.04685 -6570.6422 935.04399 -3748.6208 -2434.9525 0.96835974
1100 311.0203 -6489.14 897.50532 -3734.6686 -1557.8625 0.97044387
1150 311.75575 -6489.2845 888.02191 -3739.9054 1954.7864 0.97411485
1200 304.34674 -6521.7138 905.22814 -3799.3644 -1699.1298 0.98025305
1250 305.82 -6594.6645 927.05285 -3841.6942 1061.9124 0.98818343
1300 300.78043 -6566.1931 942.90743 -3827.4574 -864.10057 0.99107957
1350 314.72676 -6545.9508 912.22446 -3754.6305 606.75529 0.9929135
1400 315.913 -6551.4197 960.628 -3704.6134 1064.6728 0.99029667
1450 309.18966 -6497.0696 918.08358 -3732.9498 -1325.2759 0.98343775
1500 312.58526 -6494.4875 891.16465 -3737.013 1380.3782 0.98291945
1550 317.55684 -6590.3216 970.14576 -3724.1828 -1866.6608 0.9847875
1600 307.38151 -6552.4153 940.826 -3776.3487 -390.22458 0.98596757
1650 295.78641 -6508.499 880.69089 -3861.7969 -1368.3717 0.98931642
1700 306.06415 -6655.9157 976.17248 -3852.3681 -1599.4137 0.99512042
1750 303.02767 -6625.01 920.50823 -3895.2561 2274.9319 1.0015941
1800 295.63701 -6674.2337 928.57382 -3980.5406 -290.52041 1.0049878
1850 302.04323 -6768.1711 959.29198 -4005.5112 -688.59334 1.0096755
1900 299.41653 -6746.3896 940.56717 -4018.1373 1011.075 1.0170047
1950 298.83395 -6766.5655 950.11421 -4032.2445 -187.97792 1.0202189
2000 299.45823 -6824.2159 958.18625 -4078.0956 -715.67202 1.0223031
2050 290.49349 -6835.2073 950.68063 -4150.1172 -345.43177 1.0232367
2100 283.23103 -6798.203 936.42547 -4170.729 300.36081 1.0201704
2150 295.58133 -6797.5304 933.21906 -4099.5245 -293.26979 1.0191458
2200 287.12783 -6693.6112 942.32795 -4036.9686 -1430.1972 1.0191149
2250 301.19592 -6762.0204 998.15337 -3965.5579 -956.39215 1.0207659
2300 303.62433 -6716.6297 960.83467 -3942.987 77.237938 1.0202529
2350 292.95455 -6741.789 993.45295 -3999.2326 1009.5683 1.0189011
2400 295.01475 -6781.545 966.72586 -4053.4151 109.26284 1.0174852
2450 300.36482 -6827.3015 978.76759 -4055.187 -395.9959 1.0168907
2500 303.77029 -6833.9094 987.05071 -4033.1791 259.58796 1.0139892
Loop time of 46.7422 on 2 procs for 2000 steps with 2004 atoms
Performance: 7.394 ns/day, 3.246 hours/ns, 42.788 timesteps/s
99.3% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 31.75 | 32.061 | 32.372 | 5.5 | 68.59
Bond | 0.36191 | 0.36261 | 0.36331 | 0.1 | 0.78
Kspace | 4.6321 | 4.925 | 5.2179 | 13.2 | 10.54
Neigh | 5.3267 | 5.3348 | 5.3429 | 0.3 | 11.41
Comm | 0.88959 | 0.96174 | 1.0339 | 7.4 | 2.06
Output | 0.0022326 | 0.0022967 | 0.0023608 | 0.1 | 0.00
Modify | 1.4187 | 1.5349 | 1.6512 | 9.4 | 3.28
Other | | 1.56 | | | 3.34
Nlocal: 1002 ave 1009 max 995 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8864 ave 8880 max 8848 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 364886 ave 365536 max 364236 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 729772
Ave neighs/atom = 364.158
Ave special neighs/atom = 2.34032
Neighbor list builds = 206
Dangerous builds = 0
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
group peptide type <= 12
84 atoms in group peptide
Total wall time: 0:00:58

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LAMMPS (17 Aug 2017)
Processor partition = 5
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
# Demonstrating temper/npt
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
thermo_style custom step temp epair emol etotal press density
thermo 50
variable temper_T world 275 280 285 290 295 300 305 310
variable rep world 0 1 2 3 4 5 6 7
fix myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000
fix myfix all npt temp 300 ${temper_T} 100.0 iso 1 1 1000
fix myfix all npt temp 300 300 100.0 iso 1 1 1000
run 500
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
Step Temp E_pair E_mol TotEng Press Density
0 190.0857 -6442.768 70.391457 -5237.4579 20361.998 0.98480122
50 223.82864 -7673.9648 1224.4256 -5113.1564 -23877.062 0.99513919
100 259.08234 -6958.1555 482.71038 -4928.5779 12773.331 1.010442
150 281.33296 -6859.1832 472.14676 -4707.3204 7185.467 1.0189247
200 278.97145 -7183.3765 1085.5768 -4432.1832 -18068.845 1.0189951
250 279.03591 -6351.7829 479.41881 -4206.3627 23082.567 1.0112758
300 300.6326 -6884.9027 1026.5309 -4063.426 -13809.886 0.99975981
350 305.9627 -6542.2739 749.87415 -3965.6303 1365.919 0.98893682
400 300.95813 -6356.16 664.78738 -3894.4833 7945.2634 0.98104761
450 305.74067 -6698.3004 1016.1128 -3856.7437 -11928.509 0.97692928
500 295.19123 -6343.4664 707.06763 -3873.9411 9895.6164 0.97622451
Loop time of 11.1232 on 2 procs for 500 steps with 2004 atoms
Performance: 7.768 ns/day, 3.090 hours/ns, 44.951 timesteps/s
99.0% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.8133 | 7.8368 | 7.8603 | 0.8 | 70.45
Bond | 0.088746 | 0.089125 | 0.089505 | 0.1 | 0.80
Kspace | 1.2047 | 1.2319 | 1.2591 | 2.5 | 11.07
Neigh | 1.3081 | 1.31 | 1.3119 | 0.2 | 11.78
Comm | 0.21978 | 0.23832 | 0.25687 | 3.8 | 2.14
Output | 0.00053644 | 0.00054514 | 0.00055385 | 0.0 | 0.00
Modify | 0.35216 | 0.38209 | 0.41202 | 4.8 | 3.44
Other | | 0.03448 | | | 0.31
Nlocal: 1002 ave 1003 max 1001 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8664.5 ave 8679 max 8650 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 350634 ave 352508 max 348761 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 701269
Ave neighs/atom = 349.935
Ave special neighs/atom = 2.34032
Neighbor list builds = 52
Dangerous builds = 0
temper/npt 2000 100 ${temper_T} myfix 0 58728 1
temper/npt 2000 100 300 myfix 0 58728 1
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.26848
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0230214
estimated relative force accuracy = 6.93284e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
Step Temp E_pair E_mol TotEng Press Density
500 295.19123 -6343.4702 707.06763 -3873.9449 9895.5638 0.97622451
550 302.94979 -6642.4394 911.36179 -3922.2969 -5410.8109 0.97461641
600 297.33068 -6551.2919 805.26047 -3970.8 -646.78096 0.97348192
650 294.80947 -6578.9544 780.59748 -4038.1786 3293.0695 0.97423526
700 286.5511 -6718.4475 944.64841 -4062.9279 -5230.2518 0.97771554
750 294.49463 -6602.2482 777.88337 -4066.0662 4142.887 0.9831379
800 291.06018 -6664.3537 858.09465 -4068.466 -2624.3753 0.98991103
850 293.82285 -6689.8325 860.75951 -4074.7853 -435.3378 0.99623629
900 287.38111 -6671.9376 837.28605 -4118.8247 2185.0063 0.99906496
950 288.54911 -6783.7293 916.92837 -4144.0005 -2644.9104 0.99578685
1000 293.00277 -6687.2173 803.00518 -4134.8207 2220.968 0.98936787
1050 301.16902 -6760.9066 892.18697 -4070.5711 -2974.6886 0.98583275
1100 309.08554 -6738.1202 875.08899 -4017.6166 921.61791 0.98892607
1150 298.58252 -6674.1083 871.86516 -4019.5376 944.64401 0.98978942
1200 298.47184 -6760.3869 925.22004 -4053.1221 -798.3384 0.98947798
1250 291.12935 -6703.3237 856.27457 -4108.8431 544.44438 0.98937896
1300 293.02206 -6830.1194 917.90705 -4162.7058 432.93648 0.98837688
1350 282.12152 -6775.1505 898.35169 -4192.3746 -968.85129 0.98738197
1400 284.13008 -6684.782 848.15892 -4140.2066 -909.72792 0.98855422
1450 283.07781 -6640.5698 889.19504 -4061.241 120.67624 0.99460963
1500 299.32129 -6744.9956 896.07755 -4061.8016 -500.39827 1.002166
1550 290.06547 -6763.7114 921.50981 -4110.3475 1970.1344 1.0045278
1600 294.31127 -6824.5224 885.60385 -4181.7147 -1450.5522 1.0021664
1650 289.14351 -6837.8321 902.7679 -4208.7148 -36.719886 1.0010127
1700 284.10327 -6855.1076 903.75736 -4255.0939 984.04625 1.0006878
1750 280.04385 -6904.9119 918.67229 -4314.2203 -1431.4015 1.0004286
1800 281.68654 -6818.1122 846.72598 -4289.5591 520.17793 1.0021784
1850 286.93593 -6902.5226 934.50057 -4254.8531 -793.77873 1.0057534
1900 292.37295 -6876.9829 886.20947 -4245.1425 1563.8149 1.0119959
1950 278.61219 -6897.2099 935.36125 -4298.3772 -498.09374 1.0139668
2000 278.03754 -6936.4809 912.07762 -4364.3628 -475.0812 1.0140553
2050 280.17142 -6999.6889 907.21584 -4419.692 -483.15119 1.0159549
2100 275.01317 -7045.1909 966.49463 -4436.7129 516.29126 1.0192102
2150 275.36286 -6985.3989 879.47784 -4461.8499 -33.602001 1.0183533
2200 276.11062 -7026.4293 936.6898 -4441.2038 -1270.9384 1.0213402
2250 283.79417 -7011.4884 977.04948 -4340.0281 -178.52826 1.0266779
2300 276.26548 -6911.7259 909.12359 -4353.142 1380.5761 1.0284968
2350 279.5692 -7056.2521 960.48747 -4426.5792 202.29669 1.0282733
2400 270.18994 -6995.9308 932.57134 -4450.1735 -1921.755 1.0261097
2450 273.41894 -6999.2367 955.71826 -4411.0536 -376.50236 1.0265598
2500 279.53567 -6995.6096 941.2382 -4385.3862 300.84721 1.0300527
Loop time of 46.7426 on 2 procs for 2000 steps with 2004 atoms
Performance: 7.394 ns/day, 3.246 hours/ns, 42.788 timesteps/s
98.6% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 32.111 | 32.533 | 32.954 | 7.4 | 69.60
Bond | 0.36551 | 0.36836 | 0.3712 | 0.5 | 0.79
Kspace | 4.9203 | 5.3226 | 5.7249 | 17.4 | 11.39
Neigh | 5.2618 | 5.2695 | 5.2772 | 0.3 | 11.27
Comm | 0.89292 | 0.96319 | 1.0335 | 7.2 | 2.06
Output | 0.0021534 | 0.0022 | 0.0022466 | 0.1 | 0.00
Modify | 1.4108 | 1.5304 | 1.65 | 9.7 | 3.27
Other | | 0.7537 | | | 1.61
Nlocal: 1002 ave 1023 max 981 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8955 ave 9060 max 8850 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 370398 ave 378514 max 362281 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 740795
Ave neighs/atom = 369.658
Ave special neighs/atom = 2.34032
Neighbor list builds = 200
Dangerous builds = 0
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
group peptide type <= 12
84 atoms in group peptide
Total wall time: 0:00:58

211
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LAMMPS (17 Aug 2017)
Processor partition = 6
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
# Demonstrating temper/npt
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
thermo_style custom step temp epair emol etotal press density
thermo 50
variable temper_T world 275 280 285 290 295 300 305 310
variable rep world 0 1 2 3 4 5 6 7
fix myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000
fix myfix all npt temp 305 ${temper_T} 100.0 iso 1 1 1000
fix myfix all npt temp 305 305 100.0 iso 1 1 1000
run 500
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
Step Temp E_pair E_mol TotEng Press Density
0 190.0857 -6442.768 70.391457 -5237.4579 20361.998 0.98480122
50 224.19041 -7672.2342 1225.2069 -5108.4844 -23898.427 0.9949719
100 260.06304 -6952.1103 483.25334 -4916.1343 12800.907 1.01007
150 282.69922 -6844.8106 472.2939 -4684.6433 7274.1665 1.0184736
200 283.07925 -7183.2915 1096.3999 -4396.7493 -18428.465 1.0184431
250 283.61722 -6327.2943 475.82271 -4158.1172 23020.286 1.0107938
300 301.71789 -6811.4188 1004.2807 -4005.7126 -14017.258 0.99889097
350 311.03337 -6506.7477 765.85039 -3883.8531 763.04925 0.98860598
400 317.775 -6392.1118 666.55754 -3828.2587 7828.8386 0.98148763
450 303.51186 -6657.5211 1017.7742 -3827.6103 -12704.511 0.97662555
500 296.45297 -6312.4144 719.53961 -3822.8838 8469.2935 0.97646495
Loop time of 10.8893 on 2 procs for 500 steps with 2004 atoms
Performance: 7.934 ns/day, 3.025 hours/ns, 45.917 timesteps/s
99.4% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.7295 | 7.7574 | 7.7852 | 1.0 | 71.24
Bond | 0.088436 | 0.089395 | 0.090353 | 0.3 | 0.82
Kspace | 1.1269 | 1.16 | 1.1931 | 3.1 | 10.65
Neigh | 1.2353 | 1.2377 | 1.2402 | 0.2 | 11.37
Comm | 0.21436 | 0.23339 | 0.25242 | 3.9 | 2.14
Output | 0.00055766 | 0.00056684 | 0.00057602 | 0.0 | 0.01
Modify | 0.34907 | 0.37832 | 0.40758 | 4.8 | 3.47
Other | | 0.03245 | | | 0.30
Nlocal: 1002 ave 1007 max 997 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8685.5 ave 8750 max 8621 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 350698 ave 351936 max 349459 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 701395
Ave neighs/atom = 349.998
Ave special neighs/atom = 2.34032
Neighbor list builds = 50
Dangerous builds = 0
temper/npt 2000 100 ${temper_T} myfix 0 58728 1
temper/npt 2000 100 305 myfix 0 58728 1
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268487
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0230158
estimated relative force accuracy = 6.93113e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
Step Temp E_pair E_mol TotEng Press Density
500 296.45297 -6312.4159 719.53961 -3822.8853 8469.2763 0.97646495
550 303.89646 -6501.1353 863.14038 -3823.5621 -2928.2904 0.98030197
600 309.76597 -6524.1714 843.08835 -3831.606 -871.10399 0.98376234
650 299.00298 -6442.6354 805.96883 -3851.4506 3266.5866 0.98567102
700 309.92953 -6599.5125 902.18135 -3846.8775 -4895.7743 0.9877618
750 310.03453 -6432.9154 800.77648 -3781.0583 4312.9432 0.98939465
800 313.79353 -6482.8645 876.10518 -3733.2354 459.73904 0.9883653
850 308.0727 -6473.4666 891.51665 -3742.5826 -1645.1499 0.9829221
900 312.68166 -6456.773 820.7786 -3769.109 2194.8957 0.97822936
950 305.94065 -6546.0017 902.97469 -3816.3892 -2693.7918 0.97584317
1000 298.40902 -6464.4155 886.05639 -3796.6893 592.46618 0.9764313
1050 308.71394 -6480.6485 854.83864 -3782.6139 843.67793 0.97834087
1100 309.34645 -6526.4283 897.66923 -3781.7868 -297.6956 0.98046791
1150 303.65216 -6540.534 858.53216 -3869.0276 623.45838 0.98196819
1200 298.33689 -6610.5403 897.10898 -3932.1923 -1107.1097 0.98263413
1250 302.10596 -6587.4254 875.62056 -3908.0623 1244.7382 0.98273784
1300 316.19456 -6618.7414 894.33747 -3836.5445 -1399.1921 0.98252654
1350 302.28789 -6625.1555 938.19878 -3882.1279 -57.818071 0.98275084
1400 301.42717 -6602.0706 858.72022 -3943.6606 1462.1175 0.97898596
1450 299.43442 -6655.6584 893.68574 -3974.1807 383.13882 0.97462948
1500 301.76848 -6653.4568 896.33172 -3955.3975 -756.22375 0.96978565
1550 310.10887 -6664.8547 953.35222 -3859.9781 -1305.0786 0.96689812
1600 297.16621 -6510.7805 907.3012 -3829.2299 992.41943 0.96413868
1650 295.71413 -6598.1621 990.18935 -3842.3931 -2049.7934 0.96131396
1700 303.88264 -6629.5417 931.13321 -3884.0582 -630.7683 0.96321179
1750 300.85941 -6666.8007 941.42895 -3929.0719 357.85887 0.96822524
1800 299.34518 -6674.9694 932.15075 -3955.5595 -914.97614 0.97074982
1850 298.12166 -6610.2338 910.63353 -3919.6462 1390.5062 0.97402953
1900 307.86527 -6647.8711 931.49082 -3878.2514 -1629.6931 0.97542316
1950 305.04604 -6616.6069 937.35845 -3857.952 858.37861 0.97770539
2000 305.41215 -6597.2293 916.75863 -3856.9883 763.6265 0.98001111
2050 294.66502 -6632.9068 1035.729 -3837.8618 -2248.1496 0.98430681
2100 300.5948 -6569.1213 956.22884 -3818.1724 291.3677 0.99188971
2150 305.73836 -6623.7387 1021.1569 -3777.1519 -603.41468 1.0003649
2200 316.63308 -6681.0402 972.23429 -3818.3283 948.97143 1.0073383
2250 306.36381 -6653.5361 947.42424 -3876.9476 900.19264 1.010245
2300 301.9961 -6699.2583 1022.4799 -3873.6918 -499.39887 1.0119712
2350 307.25098 -6642.8345 970.32723 -3838.0461 366.40507 1.0118686
2400 311.79941 -6675.2645 1030.8811 -3782.7656 -1083.5459 1.0113601
2450 309.31064 -6630.1585 958.35981 -3825.0401 471.39091 1.0099697
2500 301.87691 -6689.2603 967.59935 -3919.2859 -854.45149 1.0097679
Loop time of 46.7431 on 2 procs for 2000 steps with 2004 atoms
Performance: 7.394 ns/day, 3.246 hours/ns, 42.787 timesteps/s
99.4% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 31.029 | 31.472 | 31.916 | 7.9 | 67.33
Bond | 0.36154 | 0.36249 | 0.36343 | 0.2 | 0.78
Kspace | 4.7001 | 5.1269 | 5.5536 | 18.8 | 10.97
Neigh | 5.311 | 5.3205 | 5.33 | 0.4 | 11.38
Comm | 0.86766 | 0.94238 | 1.0171 | 7.7 | 2.02
Output | 0.0022194 | 0.0022837 | 0.0023479 | 0.1 | 0.00
Modify | 1.4059 | 1.5219 | 1.638 | 9.4 | 3.26
Other | | 1.994 | | | 4.27
Nlocal: 1002 ave 1012 max 992 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8807.5 ave 8818 max 8797 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 363096 ave 369482 max 356711 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 726193
Ave neighs/atom = 362.372
Ave special neighs/atom = 2.34032
Neighbor list builds = 207
Dangerous builds = 0
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
group peptide type <= 12
84 atoms in group peptide
Total wall time: 0:00:58

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LAMMPS (17 Aug 2017)
Processor partition = 7
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
# Demonstrating temper/npt
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
thermo_style custom step temp epair emol etotal press density
thermo 50
variable temper_T world 275 280 285 290 295 300 305 310
variable rep world 0 1 2 3 4 5 6 7
fix myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000
fix myfix all npt temp 310 ${temper_T} 100.0 iso 1 1 1000
fix myfix all npt temp 310 310 100.0 iso 1 1 1000
run 500
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
Step Temp E_pair E_mol TotEng Press Density
0 190.0857 -6442.768 70.391457 -5237.4579 20361.998 0.98480122
50 224.5362 -7670.5503 1225.9519 -5103.9909 -23918.514 0.99480995
100 261.00419 -6946.2961 483.78483 -4904.1694 12827.309 1.0097087
150 284.14624 -6832.0094 472.66187 -4662.8346 7354.8252 1.0180355
200 284.05862 -7160.8537 1102.3553 -4362.5087 -18524.276 1.0178951
250 290.82577 -6319.5357 471.77841 -4111.3638 22989.86 1.0099523
300 306.50487 -6809.5465 1015.3715 -3964.1684 -13215.763 0.99625687
350 319.20654 -6502.4307 761.98704 -3834.601 -965.94424 0.98284646
400 316.81299 -6295.1539 646.79195 -3756.8102 8469.8917 0.97675631
450 312.90373 -6639.6427 1048.7063 -3722.7251 -13014.646 0.97486033
500 319.55848 -6335.5865 712.00927 -3715.6334 9980.2286 0.97468964
Loop time of 10.7877 on 2 procs for 500 steps with 2004 atoms
Performance: 8.009 ns/day, 2.997 hours/ns, 46.349 timesteps/s
99.1% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.6698 | 7.7211 | 7.7724 | 1.8 | 71.57
Bond | 0.085352 | 0.086755 | 0.088159 | 0.5 | 0.80
Kspace | 1.089 | 1.1417 | 1.1944 | 4.9 | 10.58
Neigh | 1.2554 | 1.2554 | 1.2554 | 0.0 | 11.64
Comm | 0.16438 | 0.17539 | 0.1864 | 2.6 | 1.63
Output | 0.00045967 | 0.0004642 | 0.00046873 | 0.0 | 0.00
Modify | 0.35006 | 0.37517 | 0.40028 | 4.1 | 3.48
Other | | 0.0317 | | | 0.29
Nlocal: 1002 ave 1004 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8709.5 ave 8714 max 8705 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 350398 ave 352725 max 348070 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 700795
Ave neighs/atom = 349.698
Ave special neighs/atom = 2.34032
Neighbor list builds = 51
Dangerous builds = 0
temper/npt 2000 100 ${temper_T} myfix 0 58728 1
temper/npt 2000 100 310 myfix 0 58728 1
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268436
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0230577
estimated relative force accuracy = 6.94376e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
Step Temp E_pair E_mol TotEng Press Density
500 319.55848 -6335.5878 712.00927 -3715.6347 9980.2224 0.97468964
550 312.3068 -6517.9692 882.51888 -3770.8031 -4737.1103 0.97368346
600 306.74828 -6500.9408 860.97959 -3808.5014 -1687.6369 0.97333001
650 309.25363 -6453.3615 753.23233 -3853.711 4484.0534 0.97330212
700 305.22336 -6644.7434 922.38867 -3899.9996 -5823.8028 0.97262421
750 297.24363 -6480.4086 771.41874 -3934.2782 5025.8889 0.97337406
800 300.89643 -6587.4079 835.06282 -3955.8242 -1517.9426 0.97460241
850 305.43206 -6685.1173 846.71999 -4014.7961 -1788.398 0.97836973
900 289.95008 -6574.8681 806.12799 -4037.575 2604.847 0.98232784
950 299.22424 -6671.7556 898.72395 -3986.4946 -2702.719 0.98919804
1000 305.3932 -6576.089 826.21317 -3926.5066 2254.7456 0.99471125
1050 304.62574 -6619.698 893.18161 -3907.7293 -1010.7916 0.99551385
1100 304.13778 -6603.0961 846.91376 -3940.3087 -211.63132 0.99359493
1150 285.80722 -6557.1116 859.12907 -3991.5526 1777.6534 0.99165538
1200 295.20871 -6612.8101 855.05738 -3995.1906 -389.55216 0.98957199
1250 301.4547 -6623.3355 907.78288 -3915.6984 1193.6428 0.98887879
1300 302.29836 -6545.5769 862.86619 -3877.8194 443.76145 0.9853829
1350 309.29624 -6539.3158 878.22476 -3814.4185 -769.46378 0.98002173
1400 311.28962 -6582.4295 939.53596 -3784.3195 -239.11773 0.97952655
1450 307.46833 -6597.7591 922.88062 -3839.1196 453.60414 0.98288752
1500 308.8234 -6660.3138 910.39719 -3906.0672 356.0472 0.98507945
1550 297.42322 -6596.3955 938.61921 -3881.9924 -883.10576 0.98730686
1600 309.492 -6649.4174 963.57197 -3838.0041 470.91335 0.99194955
1650 309.46921 -6602.6445 958.19972 -3796.7395 1417.6814 0.99437216
1700 308.27043 -6575.0156 941.02926 -3793.4384 -445.78985 0.99171728
1750 306.31262 -6515.703 929.60371 -3757.2406 944.20045 0.98661702
1800 308.63008 -6484.7465 959.53268 -3682.5186 333.02755 0.98504191
1850 316.69569 -6520.4677 975.02618 -3654.5901 -835.64735 0.98329409
1900 316.03266 -6531.6456 948.03331 -3696.7196 -745.03047 0.98236945
1950 308.97313 -6562.2733 955.48033 -3762.0496 -1147.5825 0.983921
2000 305.67836 -6611.4675 991.3364 -3795.0594 -2361.1127 0.98852677
2050 312.66709 -6687.3067 980.96042 -3839.5479 -244.80211 0.99714887
2100 307.23751 -6664.4853 963.74125 -3866.3633 268.84485 1.0050595
2150 296.36081 -6633.5455 966.74219 -3897.3626 -741.15958 1.0135557
2200 306.79331 -6709.7668 989.09713 -3888.9411 -108.31295 1.0211476
2250 310.62715 -6713.5021 973.14019 -3885.7431 1576.0539 1.0235204
2300 304.34901 -6675.1811 1001.4509 -3856.5955 -481.96378 1.0180933
2350 300.55584 -6592.7909 993.96783 -3804.3356 114.74351 1.0116595
2400 307.16641 -6626.7049 984.70783 -3808.0408 620.2875 1.0087872
2450 301.62279 -6643.7063 978.76012 -3864.0884 72.614095 1.0085247
2500 307.17634 -6691.4794 975.63125 -3881.8326 495.45555 1.0099428
Loop time of 46.7465 on 2 procs for 2000 steps with 2004 atoms
Performance: 7.393 ns/day, 3.246 hours/ns, 42.784 timesteps/s
99.1% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 31.19 | 31.703 | 32.216 | 9.1 | 67.82
Bond | 0.35397 | 0.35463 | 0.35528 | 0.1 | 0.76
Kspace | 4.3783 | 4.8922 | 5.4062 | 23.2 | 10.47
Neigh | 5.2885 | 5.2889 | 5.2893 | 0.0 | 11.31
Comm | 0.67571 | 0.71687 | 0.75803 | 4.9 | 1.53
Output | 0.0019109 | 0.0019529 | 0.0019948 | 0.1 | 0.00
Modify | 1.4216 | 1.5185 | 1.6154 | 7.9 | 3.25
Other | | 2.271 | | | 4.86
Nlocal: 1002 ave 1010 max 994 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8811.5 ave 8832 max 8791 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 363080 ave 367967 max 358193 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 726160
Ave neighs/atom = 362.355
Ave special neighs/atom = 2.34032
Neighbor list builds = 207
Dangerous builds = 0
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
group peptide type <= 12
84 atoms in group peptide
Total wall time: 0:00:58