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using 8 OpenMP thread(s) per MPI task
using multi-threaded neighbor list subroutines
Reading restart file ...
restart file = 29 Aug 2024, LAMMPS = 29 Aug 2024
restoring atom style full from restart
orthogonal box = (-22.256144 -11.128072 -11.128072) to (22.256144 11.128072 11.128072)
1 by 1 by 1 MPI processor grid
restoring pair style lj/cut/coul/long/omp from restart
restoring bond style harmonic/omp from restart
restoring angle style harmonic/omp from restart
restoring dihedral style harmonic/omp from restart
2100 atoms
1400 bonds
700 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 1
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
15 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_restart CPU = 0.005 seconds
Read molecule template pegmol:
PEG molecule
1 molecules
0 fragments
59 atoms with max type 6
58 bonds with max type 6
104 angles with max type 7
116 dihedrals with max type 4
0 impropers with max type 0
Created 59 atoms
using lattice units in orthogonal box = (-22.256144 -11.128072 -11.128072) to (22.256144 11.128072 11.128072)
create_atoms CPU = 0.000 seconds
59 atoms in group PEG
System init for delete_atoms ...
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.30147332
grid = 32 20 20
stencil order = 5
estimated absolute RMS force accuracy = 0.0034375004
estimated relative force accuracy = 1.035193e-05
using double precision KISS FFT
3d grid and FFT values/proc = 28431 12800
Generated 28 of 28 mixed pair_coeff terms from geometric mixing rule
Unused restart file global fix info:
fix style: npt, fix ID: mynpt
Last active /omp style is kspace_style pppm/omp
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 8 4 4
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on, omp
pair build: full/bin/omp
stencil: full/bin/3d
bin: standard
(2) pair lj/cut/coul/long/omp, perpetual
attributes: half, newton on, omp
pair build: half/bin/newton/omp
stencil: half/bin/3d
bin: standard
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:141)
Deleted 96 atoms, new total = 2063
Deleted 64 bonds, new total = 1394
Deleted 32 angles, new total = 772
Deleted 0 dihedrals, new total = 116
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
The log file lists these citations in BibTeX format.
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.30147173
grid = 32 20 20
stencil order = 5
estimated absolute RMS force accuracy = 0.0033561701
estimated relative force accuracy = 1.0107007e-05
using double precision KISS FFT
3d grid and FFT values/proc = 28431 12800
Generated 28 of 28 mixed pair_coeff terms from geometric mixing rule
Last active /omp style is kspace_style pppm/omp
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 8 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long/omp, perpetual
attributes: half, newton on, omp
pair build: half/bin/newton/omp
stencil: half/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 15000
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 21.57 | 21.57 | 21.57 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
15000 293.96336 -6937.5692 809.92925 -4320.8147 -324.16098 22048.535
15500 303.55223 -7052.6966 800.95294 -4385.981 159.56378 22126.265
16000 299.6112 -7008.7809 788.22037 -4379.0211 -521.48094 22225.118
16500 297.84365 -7024.1933 799.14999 -4394.368 -549.95427 22078.839
17000 304.4771 -7151.7783 828.86978 -4451.4613 -1196.0884 21797.644
17500 297.2736 -7140.0735 799.15477 -4513.7472 -64.748238 21483.268
18000 290.38437 -7125.4702 772.583 -4568.0599 -147.3855 21603.548
18500 300.21995 -7069.3954 797.33657 -4426.7778 -858.54751 21744.808
19000 304.5521 -7222.3234 892.996 -4457.4191 -299.2864 21693.475
19500 300.26279 -7212.0992 892.97173 -4473.5832 317.78627 21838.822
20000 296.16369 -7088.4563 790.03404 -4478.0727 -324.19543 21847.186
20500 294.2846 -7173.3437 862.60611 -4501.9378 -10.865505 21688.816
21000 307.82989 -7129.0355 839.23064 -4397.7499 483.90536 21507.857
21500 298.67151 -7128.1414 811.38427 -4480.9935 508.12832 21488.203
22000 293.33114 -7103.4785 840.9377 -4459.6014 1534.3863 21399.357
22500 300.04254 -7088.2347 811.98583 -4432.0583 13.37241 21477.914
23000 297.09602 -7052.5148 855.06239 -4371.3725 -99.140411 21868.119
23500 304.62568 -7119.4796 835.07566 -4412.0435 -66.958474 21978.769
24000 301.80283 -7134.5524 806.69856 -4472.8438 399.88923 21660.515
24500 296.45896 -7156.1096 838.01791 -4495.9273 456.62139 21628.227
25000 297.98494 -7041.5008 828.93835 -4381.0188 146.83299 21852.916
Loop time of 68.6241 on 8 procs for 10000 steps with 2063 atoms
Performance: 12.590 ns/day, 1.906 hours/ns, 145.721 timesteps/s, 300.623 katom-step/s
713.6% CPU use with 1 MPI tasks x 8 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 21.648 | 21.648 | 21.648 | 0.0 | 31.55
Bond | 0.39399 | 0.39399 | 0.39399 | 0.0 | 0.57
Kspace | 25.793 | 25.793 | 25.793 | 0.0 | 37.59
Neigh | 2.7759 | 2.7759 | 2.7759 | 0.0 | 4.05
Comm | 0.82742 | 0.82742 | 0.82742 | 0.0 | 1.21
Output | 10.283 | 10.283 | 10.283 | 0.0 | 14.98
Modify | 6.8375 | 6.8375 | 6.8375 | 0.0 | 9.96
Other | | 0.06478 | | | 0.09
Nlocal: 2063 ave 2063 max 2063 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11827 ave 11827 max 11827 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 703928 ave 703928 max 703928 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 703928
Ave neighs/atom = 341.21571
Ave special neighs/atom = 2.2171595
Neighbor list builds = 542
Dangerous builds = 0
System init for write_restart ...
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.30178312
grid = 32 20 20
stencil order = 5
estimated absolute RMS force accuracy = 0.0033082643
estimated relative force accuracy = 9.9627396e-06
using double precision KISS FFT
3d grid and FFT values/proc = 28431 12800
Generated 28 of 28 mixed pair_coeff terms from geometric mixing rule
Last active /omp style is kspace_style pppm/omp