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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7432 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2012-01-06 17:34:26 +00:00
parent 45d04dc45a
commit 0af770b923
5 changed files with 145 additions and 121 deletions
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14
examples/USER/cg-cmm/peg-verlet/in.pegc12e8
View File

@ -4,25 +4,29 @@ units real
dimension 3
atom_style angle
# 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
include parm.pegc12e8
neighbor 2.0 bin
neighbor 3.0 bin
neigh_modify delay 5
timestep 5.0
dump 1 all xtc 200 pegc12e8-1.xtc
dump_modify 1 unwrap yes
#dump 1 all xtc 200 pegc12e8-1.xtc
#dump_modify 1 unwrap yes
#dump 2 all dcd 200 pegc12e8-1.dcd unwrap
#dump_modify 2 unwrap yes
velocity all create 303.0 46659 mom yes rot yes dist gaussian
fix 1 all nvt 303.0 303.0 100.0
fix 1 all nvt temp 303.0 303.0 100.0
thermo_style multi
thermo 200
run 1000
write_restart pegc12e8-1.restart
#write_restart pegc12e8-1.restart

12
examples/USER/cg-cmm/peg-verlet/in.pegc12e8-angle
View File

@ -4,6 +4,10 @@ units real
dimension 3
atom_style angle
# 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
include parm.pegc12e8-angle
@ -12,17 +16,17 @@ neighbor 2.0 bin
neigh_modify delay 5
timestep 5.0
dump 1 all xtc 200 pegc12e8-1.xtc
dump_modify 1 unwrap yes
#dump 1 all xtc 200 pegc12e8-1.xtc
#dump_modify 1 unwrap yes
#dump 2 all dcd 200 pegc12e8-1.dcd unwrap
#dump_modify 2 unwrap yes
velocity all create 303.0 46659 mom yes rot yes dist gaussian
fix 1 all nvt 303.0 303.0 100.0
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-angle-1.restart

112
examples/USER/cg-cmm/peg-verlet/log.pegc12e8
View File

@ -1,16 +1,21 @@
LAMMPS (22 Jan 2008 / Patchlevel 25 Jan 2008 / CMM-CG v0.97)
LAMMPS (21 Dec 2011-ICMS)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
dimension 3
atom_style angle
# 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)
1 by 1 by 4 processor grid
4 by 2 by 1 MPI processor grid
40140 atoms
13284 bonds
12177 angles
@ -21,10 +26,10 @@ read_data data.pegc12e8
include parm.pegc12e8
# Solvated 5-mer peptide CG force field
pair_style cg/cmm 15.0
pair_style lj/sdk 15.0
bond_style harmonic
angle_style harmonic
special_bonds 0.0 0.0 1.0
special_bonds lj/coul 0.0 0.0 1.0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of special neighbors
@ -65,74 +70,77 @@ 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
dump 1 all xtc 200 pegc12e8-1.xtc
dump_modify 1 unwrap yes
#dump 1 all xtc 200 pegc12e8-1.xtc
#dump_modify 1 unwrap yes
#dump 2 all dcd 200 pegc12e8-1.dcd unwrap
#dump_modify 2 unwrap yes
velocity all create 303.0 46659 mom yes rot yes dist gaussian
fix 1 all nvt 303.0 303.0 100.0
fix 1 all nvt temp 303.0 303.0 100.0
thermo_style multi
thermo 200
run 1000
Memory usage per processor = 4.43925 Mbytes
Memory usage per processor = 10.0915 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 = 27.1134 (sec) ----------------
TotEng = -217991.2189 KinEng = 36188.3877 Temp = 302.4603
PotEng = -254179.6067 E_bond = 4590.3067 E_angle = 3421.2609
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262191.1742
E_coul = 0.0000 E_long = 0.0000 Press = 37.0652
---------------- Step 400 ----- CPU = 55.8229 (sec) ----------------
TotEng = -217934.5954 KinEng = 36330.2463 Temp = 303.6459
PotEng = -254264.8418 E_bond = 4626.8916 E_angle = 3512.1639
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262403.8973
E_coul = 0.0000 E_long = 0.0000 Press = 17.4311
---------------- Step 600 ----- CPU = 83.0111 (sec) ----------------
TotEng = -218281.8191 KinEng = 36141.0168 Temp = 302.0644
PotEng = -254422.8358 E_bond = 4628.2093 E_angle = 3492.7509
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262543.7960
E_coul = 0.0000 E_long = 0.0000 Press = 9.5773
---------------- Step 800 ----- CPU = 110.5361 (sec) ----------------
TotEng = -218232.9755 KinEng = 36343.0623 Temp = 303.7531
PotEng = -254576.0378 E_bond = 4659.4462 E_angle = 3567.9426
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262803.4265
E_coul = 0.0000 E_long = 0.0000 Press = -9.6008
---------------- Step 1000 ----- CPU = 137.3658 (sec) ----------------
TotEng = -218073.8055 KinEng = 36426.1635 Temp = 304.4476
PotEng = -254499.9689 E_bond = 4602.2406 E_angle = 3636.2557
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262738.4653
E_coul = 0.0000 E_long = 0.0000 Press = -11.9067
Loop time of 137.366 on 4 procs for 1000 steps with 40140 atoms
Performance: 3.145 ns/day 7.631 hours/ns
---------------- Step 200 ----- CPU = 2.8323 (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) ----------------
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) ----------------
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) ----------------
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) ----------------
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
Pair time (%) = 59.0174 (42.9636)
Bond time (%) = 0.932444 (0.678802)
Neigh time (%) = 6.30874 (4.59265)
Comm time (%) = 69.5999 (50.6674)
Outpt time (%) = 0.0389841 (0.0283797)
Other time (%) = 1.46867 (1.06916)
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 |
Nlocal: 10035 ave 19552 max 532 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 11779.5 ave 18122 max 5457 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1.19488e+06 ave 2.39205e+06 max 12991 min
Histogram: 2 0 0 0 0 0 0 0 0 2
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
Total # of neighbors = 4779515
Ave neighs/atom = 119.071
Total # of neighbors = 5691680
Ave neighs/atom = 141.796
Ave special neighs/atom = 1.26861
Neighbor list builds = 61
Neighbor list builds = 38
Dangerous builds = 0
write_restart pegc12e8-1.restart
#write_restart pegc12e8-1.restart

124
examples/USER/cg-cmm/peg-verlet/log.pegc12e8-angle
View File

@ -1,16 +1,21 @@
LAMMPS (22 Jan 2008 / Patchlevel 25 Jan 2008 / CMM-CG v0.97)
LAMMPS (21 Dec 2011-ICMS)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
dimension 3
atom_style angle
# 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)
1 by 1 by 4 processor grid
4 by 2 by 1 MPI processor grid
40140 atoms
13284 bonds
12177 angles
@ -21,10 +26,10 @@ read_data data.pegc12e8
include parm.pegc12e8-angle
# Solvated 5-mer peptide CG force field
pair_style cg/cmm 15.0
pair_style lj/sdk 15.0
bond_style harmonic
angle_style cg/cmm
special_bonds 0.0 0.0 1.0
angle_style sdk
special_bonds lj/coul 0.0 0.0 1.0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of special neighbors
@ -57,82 +62,85 @@ 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 lj9_6 0.4400 3.8900
angle_coeff 2 3.400 132.0 lj9_6 0.4050 4.2500
angle_coeff 3 3.200 146.0 lj9_6 0.3770 4.2740
angle_coeff 4 1.500 172.0 lj9_6 0.3770 4.2740
angle_coeff 5 1.190 173.0 lj9_6 0.4200 4.5060
angle_coeff 6 1.600 172.0 lj9_6 0.3620 4.3635
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
neigh_modify delay 5
timestep 5.0
dump 1 all xtc 200 pegc12e8-1.xtc
dump_modify 1 unwrap yes
#dump 1 all xtc 200 pegc12e8-1.xtc
#dump_modify 1 unwrap yes
#dump 2 all dcd 200 pegc12e8-1.dcd unwrap
#dump_modify 2 unwrap yes
velocity all create 303.0 46659 mom yes rot yes dist gaussian
fix 1 all nvt 303.0 303.0 100.0
fix 1 all nvt temp 303.0 303.0 100.0
thermo_style multi
thermo 200
run 1000
Memory usage per processor = 4.43925 Mbytes
Memory usage per processor = 9.68794 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 = 105.8245
---------------- Step 200 ----- CPU = 29.9183 (sec) ----------------
TotEng = -218051.4566 KinEng = 36272.3725 Temp = 303.1622
PotEng = -254323.8292 E_bond = 4530.3699 E_angle = 3351.7084
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262205.9074
E_coul = 0.0000 E_long = 0.0000 Press = 36.2458
---------------- Step 400 ----- CPU = 60.9372 (sec) ----------------
TotEng = -218054.5847 KinEng = 36253.0519 Temp = 303.0008
PotEng = -254307.6366 E_bond = 4620.3304 E_angle = 3417.4287
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262345.3957
E_coul = 0.0000 E_long = 0.0000 Press = 12.6545
---------------- Step 600 ----- CPU = 89.8983 (sec) ----------------
TotEng = -218042.2111 KinEng = 36394.6544 Temp = 304.1843
PotEng = -254436.8655 E_bond = 4623.6900 E_angle = 3419.7393
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262480.2949
E_coul = 0.0000 E_long = 0.0000 Press = 20.4952
---------------- Step 800 ----- CPU = 119.1245 (sec) ----------------
TotEng = -217865.4500 KinEng = 36565.4671 Temp = 305.6119
PotEng = -254430.9171 E_bond = 4590.5794 E_angle = 3466.0941
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262487.5906
E_coul = 0.0000 E_long = 0.0000 Press = 2.9466
---------------- Step 1000 ----- CPU = 147.8398 (sec) ----------------
TotEng = -218219.2310 KinEng = 36266.8018 Temp = 303.1157
PotEng = -254486.0328 E_bond = 4542.7739 E_angle = 3415.8267
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262444.6334
E_coul = 0.0000 E_long = 0.0000 Press = -8.6110
Loop time of 147.84 on 4 procs for 1000 steps with 40140 atoms
Performance: 2.922 ns/day 8.213 hours/ns
E_coul = 0.0000 E_long = 0.0000 Press = 114.4952
---------------- Step 200 ----- CPU = 2.7456 (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) ----------------
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) ----------------
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) ----------------
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) ----------------
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
Pair time (%) = 61.7803 (41.7886)
Bond time (%) = 1.17913 (0.797574)
Neigh time (%) = 6.23896 (4.22007)
Comm time (%) = 76.805 (51.9514)
Outpt time (%) = 0.0374529 (0.0253334)
Other time (%) = 1.79919 (1.21699)
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 |
Nlocal: 10035 ave 19571 max 538 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 11797.5 ave 18129 max 5484 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1.19407e+06 ave 2.388e+06 max 12690 min
Histogram: 2 0 0 0 0 0 0 0 0 2
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
Total # of neighbors = 4776294
Ave neighs/atom = 118.991
Total # of neighbors = 4775973
Ave neighs/atom = 118.983
Ave special neighs/atom = 1.26861
Neighbor list builds = 59
Dangerous builds = 0
write_restart pegc12e8-angle-1.restart
#write_restart pegc12e8-angle-1.restart

4
examples/USER/cg-cmm/peg-verlet/parm.pegc12e8
View File

@ -1,9 +1,9 @@
# Solvated 5-mer peptide CG force field
pair_style cg/cmm 15.0
pair_style lj/sdk 15.0
bond_style harmonic
angle_style harmonic
special_bonds 0.0 0.0 1.0
special_bonds lj/coul 0.0 0.0 1.0
mass 1 31.035
mass 2 44.054