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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11729 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-04-07 19:50:17 +00:00
parent 4f41258f5d
commit fe1d916552
5 changed files with 109 additions and 163 deletions
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examples/USER/cg-cmm/peg-verlet/data.pegc12e8.gz
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examples/USER/cg-cmm/peg-verlet/in.pegc12e8
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@ -9,8 +9,12 @@ atom_style angle
processors * * 1
# read topology and force field
read_data data.pegc12e8
include parm.pegc12e8
pair_style lj/sdk 15.0
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 1.0
read_data data.pegc12e8.gz
neighbor 3.0 bin
neigh_modify delay 5

12
examples/USER/cg-cmm/peg-verlet/in.pegc12e8-angle
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@ -9,10 +9,14 @@ atom_style angle
processors * * 1
# read topology and force field
read_data data.pegc12e8
include parm.pegc12e8-angle
pair_style lj/sdk 15.0
bond_style harmonic
angle_style sdk
special_bonds lj/coul 0.0 0.0 1.0
neighbor 2.0 bin
read_data data.pegc12e8.gz
neighbor 3.0 bin
neigh_modify delay 5
timestep 5.0
@ -28,5 +32,5 @@ fix 1 all nvt temp 303.0 303.0 100.0
thermo_style multi
thermo 200
run 1000
#write_restart pegc12e8-angle-1.restart
#write_restart pegc12e8-1.restart

121
examples/USER/cg-cmm/peg-verlet/log.pegc12e8
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@ -1,4 +1,5 @@
LAMMPS (21 Dec 2011-ICMS)
LAMMPS (20 Mar 2014-ICMS)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
@ -6,70 +7,35 @@ units real
dimension 3
atom_style angle
# enforce that in z-direction there is only one
# enforce that in z-direction there is only one
# processor (could be two) for optimal performance
processors * * 1
# read topology and force field
read_data data.pegc12e8
1 = max bonds/atom
1 = max angles/atom
orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
4 by 2 by 1 MPI processor grid
40140 atoms
13284 bonds
12177 angles
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
include parm.pegc12e8
# Solvated 5-mer peptide CG force field
pair_style lj/sdk 15.0
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 1.0
read_data data.pegc12e8.gz
orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
2 by 1 by 1 MPI processor grid
reading atoms ...
40140 atoms
reading velocities ...
40140 velocities
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
13284 bonds
reading angles ...
12177 angles
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of special neighbors
mass 1 31.035
mass 2 44.054
mass 3 42.081
mass 4 29.062
mass 5 54.000
pair_coeff 1 1 lj9_6 0.4491 3.7130
pair_coeff 1 2 lj9_6 0.4400 3.8900
pair_coeff 1 3 lj9_6 0.3650 3.9870
pair_coeff 1 4 lj9_6 0.3800 3.8400
pair_coeff 1 5 lj12_4 0.7000 3.9500
pair_coeff 2 2 lj9_6 0.4050 4.2500
pair_coeff 2 3 lj9_6 0.3770 4.2740
pair_coeff 2 4 lj9_6 0.3700 4.1400
pair_coeff 2 5 lj12_4 0.5700 4.3100
pair_coeff 3 3 lj9_6 0.4200 4.5060
pair_coeff 3 4 lj9_6 0.3620 4.3635
pair_coeff 3 5 lj12_4 0.3400 4.4385
pair_coeff 4 4 lj9_6 0.3120 4.2210
pair_coeff 4 5 lj12_4 0.2900 4.2960
pair_coeff 5 5 lj12_4 0.8950 4.3710
bond_coeff 1 15.00 2.79
bond_coeff 2 4.900 3.28
bond_coeff 3 7.100 3.56
bond_coeff 4 6.160 3.64
bond_coeff 5 9.000 3.13
angle_coeff 1 3.000 131.0
angle_coeff 2 3.400 132.0
angle_coeff 3 3.200 146.0
angle_coeff 4 1.500 172.0
angle_coeff 5 1.190 173.0
angle_coeff 6 1.600 172.0
neighbor 3.0 bin
neigh_modify delay 5
@ -86,56 +52,59 @@ fix 1 all nvt temp 303.0 303.0 100.0
thermo_style multi
thermo 200
run 1000
Memory usage per processor = 10.0915 Mbytes
Memory usage per processor = 12.4188 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -217990.7972 KinEng = 36252.9606 Temp = 303.0000
PotEng = -254243.7577 E_bond = 4468.5931 E_angle = 3410.1642
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151
E_coul = 0.0000 E_long = 0.0000 Press = 105.8245
---------------- Step 200 ----- CPU = 2.8323 (sec) ----------------
---------------- Step 200 ----- CPU = 8.6552 (sec) ----------------
TotEng = -218203.1886 KinEng = 36162.5201 Temp = 302.2441
PotEng = -254365.7087 E_bond = 4568.6683 E_angle = 3409.8838
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262344.2608
E_coul = 0.0000 E_long = 0.0000 Press = 29.3660
---------------- Step 400 ----- CPU = 5.8481 (sec) ----------------
---------------- Step 400 ----- CPU = 17.5807 (sec) ----------------
TotEng = -217955.7366 KinEng = 36340.4946 Temp = 303.7316
PotEng = -254296.2312 E_bond = 4621.0208 E_angle = 3512.1547
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262429.4067
E_coul = 0.0000 E_long = 0.0000 Press = 16.4419
---------------- Step 600 ----- CPU = 8.8857 (sec) ----------------
---------------- Step 600 ----- CPU = 28.1043 (sec) ----------------
TotEng = -218291.9151 KinEng = 36079.2122 Temp = 301.5478
PotEng = -254371.1273 E_bond = 4626.3494 E_angle = 3476.1668
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262473.6435
E_coul = 0.0000 E_long = 0.0000 Press = 14.0304
---------------- Step 800 ----- CPU = 11.9061 (sec) ----------------
---------------- Step 800 ----- CPU = 40.5132 (sec) ----------------
TotEng = -218539.5667 KinEng = 36042.0419 Temp = 301.2372
PotEng = -254581.6086 E_bond = 4563.0010 E_angle = 3616.1814
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262760.7910
E_coul = 0.0000 E_long = 0.0000 Press = -6.8312
---------------- Step 1000 ----- CPU = 14.9738 (sec) ----------------
---------------- Step 1000 ----- CPU = 52.8166 (sec) ----------------
TotEng = -217783.9370 KinEng = 36453.9620 Temp = 304.6800
PotEng = -254237.8990 E_bond = 4693.8725 E_angle = 3528.1925
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262459.9639
E_coul = 0.0000 E_long = 0.0000 Press = 0.0980
Loop time of 14.9738 on 8 procs (8 MPI x 1 OpenMP) for 1000 steps with 40140 atoms
Performance: 28.850 ns/day 0.832 hours/ns 66.783 timesteps/s
Section | min time | avg time | max time |%total | #Thr
--------------------------------------------------------------
Pair | 11.92 | 12.15 | 12.39 | 81.13 | 1.0x
Bond | 0.2939 | 0.3141 | 0.3283 | 2.10 | 1.0x
Neigh | 1.068 | 1.09 | 1.119 | 7.28 | 1.0x
Comm | 0.8103 | 1.091 | 1.341 | 7.29 | 1.0x
Output | 0.0003598 | 0.0003798 | 0.0005069 | 0.00 | 1.0x
Modify | 0.1976 | 0.2041 | 0.2086 | 1.36 | 0.9x
Other | | 0.1261 | | 0.84 |
Loop time of 52.8166 on 2 procs for 1000 steps with 40140 atoms
99.6% CPU use with 2 MPI tasks x 1 OpenMP threads
Performance: 8.179 ns/day 2.934 hours/ns 18.933 timesteps/s
Nlocal: 5017.5 ave 5051 max 4982 min
Histogram: 1 2 0 0 1 0 1 1 0 2
Nghost: 11697.4 ave 11771 max 11645 min
Histogram: 3 0 0 0 2 1 0 1 0 1
Neighs: 711460 ave 720454 max 704238 min
Histogram: 2 1 1 0 0 1 1 1 0 1
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 45.657 | 45.84 | 46.022 | 2.7 | 86.79
Bond | 0.98427 | 0.99283 | 1.0014 | 0.9 | 1.88
Neigh | 4.4454 | 4.4458 | 4.4462 | 0.0 | 8.42
Comm | 0.49872 | 0.6719 | 0.84508 | 21.1 | 1.27
Output | 0.00076818 | 0.00083113 | 0.00089407 | 0.2 | 0.00
Modify | 0.59218 | 0.59264 | 0.5931 | 0.1 | 1.12
Other | | 0.2731 | | | 0.52
Nlocal: 20070 ave 20109 max 20031 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 20234 ave 20281 max 20187 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 2.84584e+06 ave 2.85375e+06 max 2.83793e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 5691680
Ave neighs/atom = 141.796

131
examples/USER/cg-cmm/peg-verlet/log.pegc12e8-angle
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@ -1,4 +1,5 @@
LAMMPS (21 Dec 2011-ICMS)
LAMMPS (20 Mar 2014-ICMS)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
@ -6,71 +7,36 @@ units real
dimension 3
atom_style angle
# enforce that in z-direction there is only one
# enforce that in z-direction there is only one
# processor (could be two) for optimal performance
processors * * 1
# read topology and force field
read_data data.pegc12e8
1 = max bonds/atom
1 = max angles/atom
orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
4 by 2 by 1 MPI processor grid
40140 atoms
13284 bonds
12177 angles
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
include parm.pegc12e8-angle
# Solvated 5-mer peptide CG force field
pair_style lj/sdk 15.0
bond_style harmonic
angle_style sdk
special_bonds lj/coul 0.0 0.0 1.0
read_data data.pegc12e8.gz
orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
2 by 1 by 1 MPI processor grid
reading atoms ...
40140 atoms
reading velocities ...
40140 velocities
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
13284 bonds
reading angles ...
12177 angles
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of special neighbors
mass 1 31.035
mass 2 44.054
mass 3 42.081
mass 4 29.062
mass 5 54.000
pair_coeff 1 1 lj9_6 0.4491 3.7130
pair_coeff 1 2 lj9_6 0.4400 3.8900
pair_coeff 1 3 lj9_6 0.3650 3.9870
pair_coeff 1 4 lj9_6 0.3800 3.8400
pair_coeff 1 5 lj12_4 0.7000 3.9500
pair_coeff 2 2 lj9_6 0.4050 4.2500
pair_coeff 2 3 lj9_6 0.3770 4.2740
pair_coeff 2 4 lj9_6 0.3700 4.1400
pair_coeff 2 5 lj12_4 0.5700 4.3100
pair_coeff 3 3 lj9_6 0.4200 4.5060
pair_coeff 3 4 lj9_6 0.3620 4.3635
pair_coeff 3 5 lj12_4 0.3400 4.4385
pair_coeff 4 4 lj9_6 0.3120 4.2210
pair_coeff 4 5 lj12_4 0.2900 4.2960
pair_coeff 5 5 lj12_4 0.8950 4.3710
bond_coeff 1 15.00 2.79
bond_coeff 2 4.900 3.28
bond_coeff 3 7.100 3.56
bond_coeff 4 6.160 3.64
bond_coeff 5 9.000 3.13
angle_coeff 1 3.000 131.0
angle_coeff 2 3.400 132.0
angle_coeff 3 3.200 146.0
angle_coeff 4 1.500 172.0
angle_coeff 5 1.190 173.0
angle_coeff 6 1.600 172.0
neighbor 2.0 bin
neighbor 3.0 bin
neigh_modify delay 5
timestep 5.0
@ -86,61 +52,64 @@ fix 1 all nvt temp 303.0 303.0 100.0
thermo_style multi
thermo 200
run 1000
Memory usage per processor = 9.68794 Mbytes
Memory usage per processor = 12.4188 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -217835.8659 KinEng = 36252.9606 Temp = 303.0000
PotEng = -254088.8265 E_bond = 4468.5931 E_angle = 3565.0955
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151
E_coul = 0.0000 E_long = 0.0000 Press = 114.4952
---------------- Step 200 ----- CPU = 2.7456 (sec) ----------------
---------------- Step 200 ----- CPU = 8.7547 (sec) ----------------
TotEng = -217870.2208 KinEng = 36451.9852 Temp = 304.6634
PotEng = -254322.2060 E_bond = 4534.3652 E_angle = 3349.2174
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262205.7887
E_coul = 0.0000 E_long = 0.0000 Press = 39.4030
---------------- Step 400 ----- CPU = 5.5655 (sec) ----------------
---------------- Step 400 ----- CPU = 17.7479 (sec) ----------------
TotEng = -218169.7022 KinEng = 36263.1022 Temp = 303.0848
PotEng = -254432.8045 E_bond = 4598.1819 E_angle = 3416.3763
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262447.3627
E_coul = 0.0000 E_long = 0.0000 Press = 9.8923
---------------- Step 600 ----- CPU = 8.3509 (sec) ----------------
---------------- Step 600 ----- CPU = 26.7299 (sec) ----------------
TotEng = -217912.9317 KinEng = 36465.5757 Temp = 304.7770
PotEng = -254378.5074 E_bond = 4648.1881 E_angle = 3412.8346
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262439.5301
E_coul = 0.0000 E_long = 0.0000 Press = 25.6392
---------------- Step 800 ----- CPU = 11.2052 (sec) ----------------
---------------- Step 800 ----- CPU = 35.8941 (sec) ----------------
TotEng = -218439.8078 KinEng = 36035.8518 Temp = 301.1854
PotEng = -254475.6596 E_bond = 4557.5842 E_angle = 3438.5605
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262471.8043
E_coul = 0.0000 E_long = 0.0000 Press = -1.6281
---------------- Step 1000 ----- CPU = 14.0956 (sec) ----------------
---------------- Step 1000 ----- CPU = 45.1542 (sec) ----------------
TotEng = -217925.0543 KinEng = 36271.3928 Temp = 303.1541
PotEng = -254196.4471 E_bond = 4624.7673 E_angle = 3487.7805
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262308.9949
E_coul = 0.0000 E_long = 0.0000 Press = -7.3081
Loop time of 14.0956 on 8 procs (8 MPI x 1 OpenMP) for 1000 steps with 40140 atoms
Performance: 30.648 ns/day 0.783 hours/ns 70.944 timesteps/s
Section | min time | avg time | max time |%total | #Thr
--------------------------------------------------------------
Pair | 10.92 | 11.06 | 11.22 | 78.46 | 1.0x
Bond | 0.3011 | 0.3112 | 0.3199 | 2.21 | 1.0x
Neigh | 1.522 | 1.543 | 1.567 | 10.94 | 1.0x
Comm | 0.696 | 0.8695 | 1.044 | 6.17 | 1.0x
Output | 0.0003402 | 0.000362 | 0.0004911 | 0.00 | 1.0x
Modify | 0.1941 | 0.2011 | 0.2144 | 1.43 | 1.0x
Other | | 0.1113 | | 0.79 |
Loop time of 45.1542 on 2 procs for 1000 steps with 40140 atoms
99.5% CPU use with 2 MPI tasks x 1 OpenMP threads
Performance: 9.567 ns/day 2.509 hours/ns 22.146 timesteps/s
Nlocal: 5017.5 ave 5041 max 4963 min
Histogram: 1 0 0 0 0 2 1 0 1 3
Nghost: 10895.1 ave 10955 max 10838 min
Histogram: 2 1 0 1 0 0 0 2 1 1
Neighs: 596997 ave 602732 max 590121 min
Histogram: 1 0 1 0 1 1 1 1 1 1
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 38.906 | 38.953 | 39.001 | 0.8 | 86.27
Bond | 0.90927 | 0.96844 | 1.0276 | 6.0 | 2.14
Neigh | 3.7623 | 3.7641 | 3.766 | 0.1 | 8.34
Comm | 0.56974 | 0.67309 | 0.77643 | 12.6 | 1.49
Output | 0.00067949 | 0.00072169 | 0.00076389 | 0.2 | 0.00
Modify | 0.52627 | 0.53756 | 0.54885 | 1.5 | 1.19
Other | | 0.2571 | | | 0.57
Total # of neighbors = 4775973
Ave neighs/atom = 118.983
Nlocal: 20070 ave 20100 max 20040 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 20230.5 ave 20241 max 20220 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 2.84338e+06 ave 2.85198e+06 max 2.83477e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 5686756
Ave neighs/atom = 141.673
Ave special neighs/atom = 1.26861
Neighbor list builds = 59
Neighbor list builds = 38
Dangerous builds = 0
#write_restart pegc12e8-angle-1.restart
#write_restart pegc12e8-1.restart