147 lines
6.3 KiB
Groff
147 lines
6.3 KiB
Groff
LAMMPS (8 Feb 2023)
|
|
Processor partition = 7
|
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
variable ibead uloop 8 pad
|
|
|
|
units real
|
|
neigh_modify delay 2 every 1
|
|
|
|
atom_style full
|
|
bond_style harmonic
|
|
angle_style charmm
|
|
dihedral_style charmm
|
|
improper_style harmonic
|
|
|
|
pair_style lj/charmm/coul/long 11 12
|
|
pair_modify mix arithmetic
|
|
kspace_style pppm 1e-4
|
|
|
|
read_data system.data
|
|
Reading data file ...
|
|
orthogonal box = (-23.109 -22.733 -23.141) to (22.853 22.912 22.8)
|
|
1 by 1 by 1 MPI processor grid
|
|
reading atoms ...
|
|
8674 atoms
|
|
reading velocities ...
|
|
8674 velocities
|
|
scanning bonds ...
|
|
4 = max bonds/atom
|
|
scanning angles ...
|
|
6 = max angles/atom
|
|
scanning dihedrals ...
|
|
18 = max dihedrals/atom
|
|
scanning impropers ...
|
|
1 = max impropers/atom
|
|
reading bonds ...
|
|
5869 bonds
|
|
reading angles ...
|
|
3264 angles
|
|
reading dihedrals ...
|
|
708 dihedrals
|
|
reading impropers ...
|
|
38 impropers
|
|
Finding 1-2 1-3 1-4 neighbors ...
|
|
special bond factors lj: 0 0 0
|
|
special bond factors coul: 0 0 0
|
|
4 = max # of 1-2 neighbors
|
|
9 = max # of 1-3 neighbors
|
|
17 = max # of 1-4 neighbors
|
|
21 = max # of special neighbors
|
|
special bonds CPU = 0.004 seconds
|
|
read_data CPU = 0.138 seconds
|
|
#read_restart system_${ibead}.rest1
|
|
special_bonds charmm
|
|
|
|
fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0
|
|
|
|
thermo 10
|
|
thermo_style custom step temp pe etotal f_1[1] f_1[2] f_1[3]
|
|
thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
|
|
timestep 0.08
|
|
|
|
# restart 100 system_${ibead}.rest1 system_${ibead}.rest2
|
|
|
|
group prot id <= 256
|
|
256 atoms in group prot
|
|
# dump 1 prot dcd 100 prot_${ibead}.dcd
|
|
|
|
run 200
|
|
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
|
PPPM initialization ...
|
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
|
G vector (1/distance) = 0.22071363
|
|
grid = 20 20 20
|
|
stencil order = 5
|
|
estimated absolute RMS force accuracy = 0.024910591
|
|
estimated relative force accuracy = 7.5017505e-05
|
|
using double precision KISS FFT
|
|
3d grid and FFT values/proc = 15625 8000
|
|
Generated 231 of 231 mixed pair_coeff terms from arithmetic mixing rule
|
|
Neighbor list info ...
|
|
update: every = 1 steps, delay = 2 steps, check = yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 14
|
|
ghost atom cutoff = 14
|
|
binsize = 7, bins = 7 7 7
|
|
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
|
|
bin: standard
|
|
WARNING: Inconsistent image flags (src/domain.cpp:815)
|
|
Per MPI rank memory allocation (min/avg/max) = 84.59 | 84.59 | 84.59 Mbytes
|
|
Step Temp PotEng TotEng espring T_ring virial
|
|
0 306.20099 -26166.171 -18250.089 0 0 -676.31071
|
|
10 11.858328 -24949.912 -24643.343 11.21746 379.42274 -589.42772
|
|
20 13.313433 -22332.782 -21988.595 25.891404 425.98075 -189.42618
|
|
30 14.492332 -18605.094 -18230.43 60.87232 463.70115 853.22726
|
|
40 10.100576 -15158.156 -14897.03 103.87947 323.18115 1870.5664
|
|
50 10.437976 -12976.762 -12706.913 161.50852 333.97672 2649.3283
|
|
60 10.544993 -11868.561 -11595.946 225.58416 337.40089 3264.9267
|
|
70 9.756396 -11851.23 -11599.002 303.66274 312.16868 3549.9084
|
|
80 10.642372 -12316.225 -12041.092 392.92619 340.51663 3853.3301
|
|
90 9.3834726 -12853.33 -12610.744 501.5373 300.2365 3943.7218
|
|
100 8.9858656 -13254.517 -13022.21 619.67563 287.51455 3852.5038
|
|
110 8.9674385 -13407.55 -13175.719 752.87088 286.92495 3047.0516
|
|
120 8.7200626 -13430.184 -13204.748 897.34682 279.00983 2614.6547
|
|
130 8.4404226 -13413.462 -13195.256 1051.1979 270.06239 2361.7563
|
|
140 8.1867868 -13405.663 -13194.013 1215.2723 261.94697 2042.4666
|
|
150 8.26024 -13427.11 -13213.561 1389.0864 264.29721 2179.5219
|
|
160 8.2139102 -13403.956 -13191.605 1573.9454 262.81482 2489.6486
|
|
170 8.2258918 -13367.291 -13154.631 1768.2198 263.19819 2793.6911
|
|
180 8.4548603 -13245.62 -13027.04 1968.4468 270.52434 3070.2942
|
|
190 8.4589955 -12920.954 -12702.268 2174.1321 270.65665 3360.4993
|
|
200 8.537811 -12448.973 -12228.248 2382.746 273.17846 3370.2077
|
|
Loop time of 35.3334 on 1 procs for 200 steps with 8674 atoms
|
|
|
|
Performance: 0.039 ns/day, 613.428 hours/ns, 5.660 timesteps/s, 49.098 katom-step/s
|
|
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 27.709 | 27.709 | 27.709 | 0.0 | 78.42
|
|
Bond | 0.13165 | 0.13165 | 0.13165 | 0.0 | 0.37
|
|
Kspace | 2.4416 | 2.4416 | 2.4416 | 0.0 | 6.91
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
Comm | 0.12826 | 0.12826 | 0.12826 | 0.0 | 0.36
|
|
Output | 0.002116 | 0.002116 | 0.002116 | 0.0 | 0.01
|
|
Modify | 4.863 | 4.863 | 4.863 | 0.0 | 13.76
|
|
Other | | 0.05754 | | | 0.16
|
|
|
|
Nlocal: 8674 ave 8674 max 8674 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 27366 ave 27366 max 27366 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 4.48585e+06 ave 4.48585e+06 max 4.48585e+06 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 4485849
|
|
Ave neighs/atom = 517.16036
|
|
Ave special neighs/atom = 2.2573207
|
|
Neighbor list builds = 0
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:35
|