From 865b41e2014e489ce237a6fbfc0f3d516497bbda Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 23 Mar 2017 11:50:10 -0400
Subject: [PATCH] make pair style momb example follow LAMMPS conventions more
closely
---
.../USER/misc/momb/Ag_O1X5.5_O2X0.55.eam.fs | 0
.../USER/misc/momb/{system.in => in.system} | 16 +-
.../{log.momb => log.17Mar2017.system.g++.1} | 162 ++++----
.../USER/misc/momb/log.17Mar2017.system.g++.4 | 357 ++++++++++++++++++
4 files changed, 461 insertions(+), 74 deletions(-)
mode change 100755 => 100644 examples/USER/misc/momb/Ag_O1X5.5_O2X0.55.eam.fs
rename examples/USER/misc/momb/{system.in => in.system} (96%)
rename examples/USER/misc/momb/{log.momb => log.17Mar2017.system.g++.1} (76%)
create mode 100644 examples/USER/misc/momb/log.17Mar2017.system.g++.4
diff --git a/examples/USER/misc/momb/Ag_O1X5.5_O2X0.55.eam.fs b/examples/USER/misc/momb/Ag_O1X5.5_O2X0.55.eam.fs
old mode 100755
new mode 100644
diff --git a/examples/USER/misc/momb/system.in b/examples/USER/misc/momb/in.system
similarity index 96%
rename from examples/USER/misc/momb/system.in
rename to examples/USER/misc/momb/in.system
index df0931dd2f..d5e3e6b537 100644
--- a/examples/USER/misc/momb/system.in
+++ b/examples/USER/misc/momb/in.system
@@ -11,7 +11,7 @@ angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style hybrid/overlay eam/fs lj/charmm/coul/long 10.0 12.0 momb 12.0 0.75 20.0 morse 5.5
-kspace_style pppm 1e-4
+kspace_style pppm 1e-5
# ----------------- Atom Definition Section -----------------
@@ -166,15 +166,13 @@ special_bonds charmm
timestep 0.001
-restart 2000 NVT.restart.1_dup NVT.restart.1
-
-minimize 1.0e-3 1.0e-5 1000 10000
+minimize 1.0e-3 1.0e-5 1000 10000
+reset_timestep 0
velocity all create 413.0 12378 dist gaussian
-thermo 0
-thermo_style custom step pe ke etotal temp vol press lx lz pxx pyy pzz
-thermo_modify flush yes
+thermo 10
+thermo_style custom step pe ke etotal temp press pxx pyy pzz
variable STEP equal step
variable PE equal pe
@@ -190,8 +188,8 @@ variable PYY equal pyy
variable PZZ equal pzz
fix 1 all nvt temp 413.0 413.0 0.1 fixedpoint 0.0 0.0 0.0
-fix thermo_output all print 2000 "${STEP} ${PE} ${KE} ${ETOTAL} ${TEMP} ${VOL} ${PRESS} ${LX} ${LZ} ${PXX} ${PYY} ${PZZ}" file thermo.lammps title "# Step PotEng KinEng TotEng Temp Volume Press Lx Lz Pxx Pyy Pzz"
+#fix thermo_output all print 2000 "${STEP} ${PE} ${KE} ${ETOTAL} ${TEMP} ${VOL} ${PRESS} ${LX} ${LZ} ${PXX} ${PYY} ${PZZ}" file thermo.lammps title "# Step PotEng KinEng TotEng Temp Volume Press Lx Lz Pxx Pyy Pzz"
-dump 1 all custom 10 traj_npt.lammpstrj id mol type x y z ix iy iz
+#dump 1 all custom 10 traj_npt.lammpstrj id mol type x y z ix iy iz
run 100
diff --git a/examples/USER/misc/momb/log.momb b/examples/USER/misc/momb/log.17Mar2017.system.g++.1
similarity index 76%
rename from examples/USER/misc/momb/log.momb
rename to examples/USER/misc/momb/log.17Mar2017.system.g++.1
index 37e4b5c6a3..fc3ebd93ff 100644
--- a/examples/USER/misc/momb/log.momb
+++ b/examples/USER/misc/momb/log.17Mar2017.system.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (17 Nov 2016)
+LAMMPS (17 Mar 2017)
using 1 OpenMP thread(s) per MPI task
# ----------------- Settings Section -----------------
@@ -13,7 +13,7 @@ angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style hybrid/overlay eam/fs lj/charmm/coul/long 10.0 12.0 momb 12.0 0.75 20.0 morse 5.5
-kspace_style pppm 1e-4
+kspace_style pppm 1e-5
# ----------------- Atom Definition Section -----------------
@@ -192,73 +192,96 @@ special_bonds charmm
timestep 0.001
-restart 2000 NVT.restart.1_dup NVT.restart.1
-
-minimize 1.0e-3 1.0e-5 1000 10000
+minimize 1.0e-3 1.0e-5 1000 10000
PPPM initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:317)
- G vector (1/distance) = 0.187769
- grid = 16 16 40
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.224856
+ grid = 27 27 64
stencil order = 5
- estimated absolute RMS force accuracy = 0.00139106
- estimated relative force accuracy = 9.66035e-05
- using single precision FFTs
- 3d grid and FFT values/proc = 19845 10240
+ estimated absolute RMS force accuracy = 0.00015081
+ estimated relative force accuracy = 1.04732e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 79764 46656
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:218)
Neighbor list info ...
- 5 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
- binsize = 7 -> bins = 8 8 23
-Memory usage per processor = 48.6138 Mbytes
+ binsize = 7, bins = 8 8 23
+ 5 neighbor lists, perpetual/occasional/extra = 5 0 0
+ (1) pair eam/fs, perpetual, skip from (5)
+ attributes: half, newton on
+ pair build: skip
+ stencil: none
+ bin: none
+ (2) pair lj/charmm/coul/long, perpetual, skip from (5)
+ attributes: half, newton on
+ pair build: skip
+ stencil: none
+ bin: none
+ (3) pair momb, perpetual, skip from (5)
+ attributes: half, newton on
+ pair build: skip
+ stencil: none
+ bin: none
+ (4) pair morse, perpetual, copy from (3)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+ (5) neighbor class addition, 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) = 99.82 | 99.82 | 99.82 Mbytes
Step Temp E_pair E_mol TotEng Press
- 0 0 -10041.86 218.18376 -9823.6761 -1155.6237
- 9 0 -10251.809 211.33378 -10040.475 -3384.1678
-Loop time of 2.01938 on 1 procs for 9 steps with 18146 atoms
+ 0 0 -10035.476 218.18376 -9817.2917 -1066.914
+ 9 0 -10244.892 211.35072 -10033.541 -3283.8636
+Loop time of 2.65996 on 1 procs for 9 steps with 18146 atoms
-99.7% CPU use with 1 MPI tasks x no OpenMP threads
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
- -9823.67611001 -10030.895598 -10040.4750172
- Force two-norm initial, final = 76.9199 27.3415
- Force max component initial, final = 11.8655 7.37992
- Final line search alpha, max atom move = 0.0472487 0.348692
+ -9817.29174185 -10023.887559 -10033.5413886
+ Force two-norm initial, final = 76.9233 27.3547
+ Force max component initial, final = 11.8658 7.37882
+ Final line search alpha, max atom move = 0.0472944 0.348977
Iterations, force evaluations = 9 11
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 1.6622 | 1.6622 | 1.6622 | 0.0 | 82.31
-Bond | 0.054745 | 0.054745 | 0.054745 | 0.0 | 2.71
-Kspace | 0.11761 | 0.11761 | 0.11761 | 0.0 | 5.82
-Neigh | 0.16836 | 0.16836 | 0.16836 | 0.0 | 8.34
-Comm | 0.0029683 | 0.0029683 | 0.0029683 | 0.0 | 0.15
+Pair | 2.2936 | 2.2936 | 2.2936 | 0.0 | 86.23
+Bond | 0.08754 | 0.08754 | 0.08754 | 0.0 | 3.29
+Kspace | 0.2664 | 0.2664 | 0.2664 | 0.0 | 10.02
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0041108 | 0.0041108 | 0.0041108 | 0.0 | 0.15
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 0.01347 | | | 0.67
+Other | | 0.008299 | | | 0.31
Nlocal: 18146 ave 18146 max 18146 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 29277 ave 29277 max 29277 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 5.49017e+06 ave 5.49017e+06 max 5.49017e+06 min
+Neighs: 439189 ave 439189 max 439189 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Total # of neighbors = 5490167
-Ave neighs/atom = 302.555
+Total # of neighbors = 439189
+Ave neighs/atom = 24.2031
Ave special neighs/atom = 5.92362
-Neighbor list builds = 1
+Neighbor list builds = 0
Dangerous builds = 0
+reset_timestep 0
velocity all create 413.0 12378 dist gaussian
-thermo 0
-thermo_style custom step pe ke etotal temp vol press lx lz pxx pyy pzz
-thermo_modify flush yes
+thermo 10
+thermo_style custom step pe ke etotal temp press pxx pyy pzz
variable STEP equal step
variable PE equal pe
@@ -274,52 +297,61 @@ variable PYY equal pyy
variable PZZ equal pzz
fix 1 all nvt temp 413.0 413.0 0.1 fixedpoint 0.0 0.0 0.0
-fix thermo_output all print 2000 "${STEP} ${PE} ${KE} ${ETOTAL} ${TEMP} ${VOL} ${PRESS} ${LX} ${LZ} ${PXX} ${PYY} ${PZZ}" file thermo.lammps title "# Step PotEng KinEng TotEng Temp Volume Press Lx Lz Pxx Pyy Pzz"
+#fix thermo_output all print 2000 "${STEP} ${PE} ${KE} ${ETOTAL} ${TEMP} ${VOL} ${PRESS} ${LX} ${LZ} ${PXX} ${PYY} ${PZZ}" file thermo.lammps title "# Step PotEng KinEng TotEng Temp Volume Press Lx Lz Pxx Pyy Pzz"
-dump 1 all custom 10 traj_npt.lammpstrj id mol type x y z ix iy iz
+#dump 1 all custom 10 traj_npt.lammpstrj id mol type x y z ix iy iz
run 100
PPPM initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:317)
- G vector (1/distance) = 0.187769
- grid = 16 16 40
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.224856
+ grid = 27 27 64
stencil order = 5
- estimated absolute RMS force accuracy = 0.00139106
- estimated relative force accuracy = 9.66035e-05
- using single precision FFTs
- 3d grid and FFT values/proc = 19845 10240
+ estimated absolute RMS force accuracy = 0.00015081
+ estimated relative force accuracy = 1.04732e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 79764 46656
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:218)
-Memory usage per processor = 45.2388 Mbytes
-Step PotEng KinEng TotEng Temp Volume Press Lx Lz Pxx Pyy Pzz
- 9 -10040.475 968.66066 -9071.8144 413 460013.27 -1135.0076 53.6198 160 5128.2409 -4940.1319 -3593.1317
- 109 -9552.3639 560.57156 -8991.7924 239.00636 460013.27 -1193.1308 53.6198 160 1847.8619 -3035.3718 -2391.8825
-Loop time of 13.4379 on 1 procs for 100 steps with 18146 atoms
+Per MPI rank memory allocation (min/avg/max) = 96.44 | 96.44 | 96.44 Mbytes
+Step PotEng KinEng TotEng Temp Press Pxx Pyy Pzz
+ 0 -10033.541 968.66066 -9064.8807 413 -1034.7033 5221.7757 -4827.0742 -3498.8115
+ 10 -9717.5642 663.69058 -9053.8736 282.97238 -392.07182 5076.3825 -3643.5902 -2609.0078
+ 20 -9592.3732 550.97993 -9041.3932 234.91685 -737.21307 4729.9669 -4234.1008 -2707.5053
+ 30 -9689.9997 645.41353 -9044.5862 275.17974 -1095.6905 5368.8361 -5243.8524 -3412.0551
+ 40 -9721.5122 675.86683 -9045.6453 288.16387 -138.73949 6292.4674 -3623.6807 -3085.0052
+ 50 -9576.7583 544.96028 -9031.798 232.3503 -552.64225 4683.2668 -3286.1479 -3055.0457
+ 60 -9542.5531 522.39339 -9020.1597 222.72864 -1044.0254 3675.027 -3821.1015 -2986.0017
+ 70 -9572.4447 551.73535 -9020.7093 235.23893 132.77197 4550.5092 -2208.7446 -1943.4487
+ 80 -9684.4674 666.4064 -9018.061 284.1303 999.60397 3345.5104 -202.16376 -144.53477
+ 90 -9553.3377 550.82743 -9002.5103 234.85183 -1291.4189 1264.3148 -2496.9658 -2641.6058
+ 100 -9551.9716 560.31802 -8991.6536 238.89826 -1189.4791 1842.8208 -3025.5224 -2385.7357
+Loop time of 18.4128 on 1 procs for 100 steps with 18146 atoms
-Performance: 0.643 ns/day, 37.327 hours/ns, 7.442 timesteps/s
-99.8% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 0.469 ns/day, 51.147 hours/ns, 5.431 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 10.731 | 10.731 | 10.731 | 0.0 | 79.85
-Bond | 0.40862 | 0.40862 | 0.40862 | 0.0 | 3.04
-Kspace | 0.98401 | 0.98401 | 0.98401 | 0.0 | 7.32
-Neigh | 0.87771 | 0.87771 | 0.87771 | 0.0 | 6.53
-Comm | 0.022856 | 0.022856 | 0.022856 | 0.0 | 0.17
-Output | 0.36853 | 0.36853 | 0.36853 | 0.0 | 2.74
-Modify | 0.032646 | 0.032646 | 0.032646 | 0.0 | 0.24
-Other | | 0.01276 | | | 0.09
+Pair | 14.225 | 14.225 | 14.225 | 0.0 | 77.26
+Bond | 0.65464 | 0.65464 | 0.65464 | 0.0 | 3.56
+Kspace | 2.22 | 2.22 | 2.22 | 0.0 | 12.06
+Neigh | 1.1926 | 1.1926 | 1.1926 | 0.0 | 6.48
+Comm | 0.040519 | 0.040519 | 0.040519 | 0.0 | 0.22
+Output | 0.0023048 | 0.0023048 | 0.0023048 | 0.0 | 0.01
+Modify | 0.058326 | 0.058326 | 0.058326 | 0.0 | 0.32
+Other | | 0.01913 | | | 0.10
Nlocal: 18146 ave 18146 max 18146 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 29123 ave 29123 max 29123 min
+Nghost: 29127 ave 29127 max 29127 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 5.50412e+06 ave 5.50412e+06 max 5.50412e+06 min
+Neighs: 441898 ave 441898 max 441898 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Total # of neighbors = 5504118
-Ave neighs/atom = 303.324
+Total # of neighbors = 441898
+Ave neighs/atom = 24.3524
Ave special neighs/atom = 5.92362
Neighbor list builds = 5
Dangerous builds = 0
-Total wall time: 0:00:16
+Total wall time: 0:00:22
diff --git a/examples/USER/misc/momb/log.17Mar2017.system.g++.4 b/examples/USER/misc/momb/log.17Mar2017.system.g++.4
new file mode 100644
index 0000000000..b042feb953
--- /dev/null
+++ b/examples/USER/misc/momb/log.17Mar2017.system.g++.4
@@ -0,0 +1,357 @@
+LAMMPS (17 Mar 2017)
+ using 1 OpenMP thread(s) per MPI task
+
+# ----------------- Settings Section -----------------
+
+units metal
+boundary p p p
+neigh_modify delay 0 every 1 check yes
+
+atom_style full
+bond_style harmonic
+angle_style charmm
+dihedral_style charmm
+improper_style harmonic
+pair_style hybrid/overlay eam/fs lj/charmm/coul/long 10.0 12.0 momb 12.0 0.75 20.0 morse 5.5
+kspace_style pppm 1e-5
+
+# ----------------- Atom Definition Section -----------------
+
+read_data system.data
+ orthogonal box = (0 0 0) to (53.6198 53.6198 160)
+ 1 by 1 by 4 MPI processor grid
+ reading atoms ...
+ 18146 atoms
+ scanning bonds ...
+ 4 = max bonds/atom
+ scanning angles ...
+ 6 = max angles/atom
+ scanning dihedrals ...
+ 13 = max dihedrals/atom
+ scanning impropers ...
+ 1 = max impropers/atom
+ reading bonds ...
+ 12694 bonds
+ reading angles ...
+ 19786 angles
+ reading dihedrals ...
+ 29690 dihedrals
+ reading impropers ...
+ 5 impropers
+ 4 = max # of 1-2 neighbors
+ 8 = max # of 1-3 neighbors
+ 20 = max # of 1-4 neighbors
+ 23 = max # of special neighbors
+
+pair_coeff * * eam/fs Ag_O1X5.5_O2X0.55.eam.fs NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL O1 NULL NULL NULL O2 Ag
+pair_coeff 1*4 16 morse 0.00480 1.30 1.94 # HGA1, HGA2, HGA3
+pair_coeff 5 16 morse 0.00722 1.14 4.85 # CG2R53
+pair_coeff 6*8 16 morse 0.00244 1.01 4.92 # CG311, CG321, CG331
+pair_coeff 9 16 morse 0.00230 1.03 4.92 # CG3C52
+pair_coeff 10 16 morse 0.00492 1.76 3.26 # NG2R53
+pair_coeff 11 16 morse 0.00325 3.34 2.65 # OG2D1
+pair_coeff 12 16 morse 0.00480 1.30 1.94 # HCA2
+pair_coeff 13 16 morse 0.00448 1.06 2.13 # HCP1
+pair_coeff 14 16 morse 0.00216 1.26 4.99 # CC32A
+pair_coeff 15 16 morse 0.00217 2.09 3.43 # OC311
+pair_coeff 1*4 16 momb 0.0 1.0 1.0 10.2847 2.361 # H
+pair_coeff 5*9 16 momb 0.0 1.0 1.0 36.3619 2.812 # C
+pair_coeff 10 16 momb 0.0 1.0 1.0 30.4846 2.757 # N
+pair_coeff 11 16 momb 0.0 1.0 1.0 22.9973 2.702 # O
+pair_coeff 12 16 momb 0.0 1.0 1.0 10.2847 2.361 # HCA2
+pair_coeff 13 16 momb 0.0 1.0 1.0 10.2847 2.361 # HCP1
+pair_coeff 14 16 momb 0.0 1.0 1.0 36.3619 2.812 # CC32A
+pair_coeff 15 16 momb 0.0 1.0 1.0 22.9973 2.702 # OC311
+
+# arithmetic mixing for CHARMM pair coeffs
+pair_coeff 1 1 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HRA2 HRA2
+pair_coeff 1 2 lj/charmm/coul/long 0.001722 2.387609 0.001722 2.387609 #HRA2 HGA1
+pair_coeff 1 3 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HRA2 HGA2
+pair_coeff 1 4 lj/charmm/coul/long 0.001257 2.387609 0.001257 2.387609 #HRA2 HGA3
+pair_coeff 1 5 lj/charmm/coul/long 0.001150 3.153782 0.001150 3.153782 #HRA2 CG2R53
+pair_coeff 1 6 lj/charmm/coul/long 0.001454 2.975602 0.000808 2.886512 #HRA2 CG311
+pair_coeff 1 7 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #HRA2 CG321
+pair_coeff 1 8 lj/charmm/coul/long 0.002267 3.020147 0.000808 2.886512 #HRA2 CG331
+pair_coeff 1 9 lj/charmm/coul/long 0.001988 2.993420 0.000808 2.886512 #HRA2 CG3C52
+pair_coeff 1 10 lj/charmm/coul/long 0.003630 2.841967 0.003630 2.841967 #HRA2 NG2R53
+pair_coeff 1 11 lj/charmm/coul/long 0.002811 2.708333 0.002811 2.441063 #HRA2 OG2D1
+pair_coeff 1 12 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HRA2 HCA2
+pair_coeff 1 13 lj/charmm/coul/long 0.001739 1.393811 0.001739 1.393811 #HRA2 HCP1
+pair_coeff 1 14 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #HRA2 CC32A
+pair_coeff 1 15 lj/charmm/coul/long 0.003558 2.766240 0.003558 2.766240 #HRA2 OC311
+pair_coeff 2 2 lj/charmm/coul/long 0.001950 2.387609 0.001950 2.387609 #HGA1 HGA1
+pair_coeff 2 3 lj/charmm/coul/long 0.001722 2.387609 0.001722 2.387609 #HGA1 HGA2
+pair_coeff 2 4 lj/charmm/coul/long 0.001424 2.387609 0.001424 2.387609 #HGA1 HGA3
+pair_coeff 2 5 lj/charmm/coul/long 0.001302 3.153782 0.001302 3.153782 #HGA1 CG2R53
+pair_coeff 2 6 lj/charmm/coul/long 0.001646 2.975602 0.000916 2.886512 #HGA1 CG311
+pair_coeff 2 7 lj/charmm/coul/long 0.002177 2.984511 0.000916 2.886512 #HGA1 CG321
+pair_coeff 2 8 lj/charmm/coul/long 0.002567 3.020147 0.000916 2.886512 #HGA1 CG331
+pair_coeff 2 9 lj/charmm/coul/long 0.002252 2.993420 0.000916 2.886512 #HGA1 CG3C52
+pair_coeff 2 10 lj/charmm/coul/long 0.004112 2.841967 0.004112 2.841967 #HGA1 NG2R53
+pair_coeff 2 11 lj/charmm/coul/long 0.003184 2.708333 0.003184 2.441063 #HGA1 OG2D1
+pair_coeff 2 12 lj/charmm/coul/long 0.001722 2.387609 0.001722 2.387609 #HGA1 HCA2
+pair_coeff 2 13 lj/charmm/coul/long 0.001970 1.393811 0.001970 1.393811 #HGA1 HCP1
+pair_coeff 2 14 lj/charmm/coul/long 0.002177 2.984511 0.000916 2.886512 #HGA1 CC32A
+pair_coeff 2 15 lj/charmm/coul/long 0.004030 2.766240 0.004030 2.766240 #HGA1 OC311
+pair_coeff 3 3 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HGA2 HGA2
+pair_coeff 3 4 lj/charmm/coul/long 0.001257 2.387609 0.001257 2.387609 #HGA2 HGA3
+pair_coeff 3 5 lj/charmm/coul/long 0.001150 3.153782 0.001150 3.153782 #HGA2 CG2R53
+pair_coeff 3 6 lj/charmm/coul/long 0.001454 2.975602 0.000808 2.886512 #HGA2 CG311
+pair_coeff 3 7 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #HGA2 CG321
+pair_coeff 3 8 lj/charmm/coul/long 0.002267 3.020147 0.000808 2.886512 #HGA2 CG331
+pair_coeff 3 9 lj/charmm/coul/long 0.001988 2.993420 0.000808 2.886512 #HGA2 CG3C52
+pair_coeff 3 10 lj/charmm/coul/long 0.003630 2.841967 0.003630 2.841967 #HGA2 NG2R53
+pair_coeff 3 11 lj/charmm/coul/long 0.002811 2.708333 0.002811 2.441063 #HGA2 OG2D1
+pair_coeff 3 12 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HGA2 HCA2
+pair_coeff 3 13 lj/charmm/coul/long 0.001739 1.393811 0.001739 1.393811 #HGA2 HCP1
+pair_coeff 3 14 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #HGA2 CC32A
+pair_coeff 3 15 lj/charmm/coul/long 0.003558 2.766240 0.003558 2.766240 #HGA2 OC311
+pair_coeff 4 4 lj/charmm/coul/long 0.001040 2.387609 0.001040 2.387609 #HGA3 HGA3
+pair_coeff 4 5 lj/charmm/coul/long 0.000951 3.153782 0.000951 3.153782 #HGA3 CG2R53
+pair_coeff 4 6 lj/charmm/coul/long 0.001202 2.975602 0.000669 2.886512 #HGA3 CG311
+pair_coeff 4 7 lj/charmm/coul/long 0.001590 2.984511 0.000669 2.886512 #HGA3 CG321
+pair_coeff 4 8 lj/charmm/coul/long 0.001875 3.020147 0.000669 2.886512 #HGA3 CG331
+pair_coeff 4 9 lj/charmm/coul/long 0.001644 2.993420 0.000669 2.886512 #HGA3 CG3C52
+pair_coeff 4 10 lj/charmm/coul/long 0.003003 2.841967 0.003003 2.841967 #HGA3 NG2R53
+pair_coeff 4 11 lj/charmm/coul/long 0.002326 2.708333 0.002326 2.441063 #HGA3 OG2D1
+pair_coeff 4 12 lj/charmm/coul/long 0.001257 2.387609 0.001257 2.387609 #HGA3 HCA2
+pair_coeff 4 13 lj/charmm/coul/long 0.001439 1.393811 0.001439 1.393811 #HGA3 HCP1
+pair_coeff 4 14 lj/charmm/coul/long 0.001590 2.984511 0.000669 2.886512 #HGA3 CC32A
+pair_coeff 4 15 lj/charmm/coul/long 0.002943 2.766240 0.002943 2.766240 #HGA3 OC311
+pair_coeff 5 5 lj/charmm/coul/long 0.000870 3.919954 0.000870 3.919954 #CG2R53CG2R53
+pair_coeff 5 6 lj/charmm/coul/long 0.001100 3.741775 0.000612 3.652685 #CG2R53CG311
+pair_coeff 5 7 lj/charmm/coul/long 0.001454 3.750684 0.000612 3.652685 #CG2R53CG321
+pair_coeff 5 8 lj/charmm/coul/long 0.001715 3.786320 0.000612 3.652685 #CG2R53CG331
+pair_coeff 5 9 lj/charmm/coul/long 0.001504 3.759593 0.000612 3.652685 #CG2R53CG3C52
+pair_coeff 5 10 lj/charmm/coul/long 0.002746 3.608140 0.002746 3.608140 #CG2R53NG2R53
+pair_coeff 5 11 lj/charmm/coul/long 0.002127 3.474505 0.002127 3.207235 #CG2R53OG2D1
+pair_coeff 5 12 lj/charmm/coul/long 0.001150 3.153782 0.001150 3.153782 #CG2R53HCA2
+pair_coeff 5 13 lj/charmm/coul/long 0.001316 2.159984 0.001316 2.159984 #CG2R53HCP1
+pair_coeff 5 14 lj/charmm/coul/long 0.001454 3.750684 0.000612 3.652685 #CG2R53CC32A
+pair_coeff 5 15 lj/charmm/coul/long 0.002692 3.532413 0.002692 3.532413 #CG2R53OC311
+pair_coeff 6 6 lj/charmm/coul/long 0.001390 3.563595 0.000430 3.385415 #CG311 CG311
+pair_coeff 6 7 lj/charmm/coul/long 0.001838 3.572504 0.000430 3.385415 #CG311 CG321
+pair_coeff 6 8 lj/charmm/coul/long 0.002168 3.608140 0.000430 3.385415 #CG311 CG331
+pair_coeff 6 9 lj/charmm/coul/long 0.001901 3.581413 0.000430 3.385415 #CG311 CG3C52
+pair_coeff 6 10 lj/charmm/coul/long 0.003471 3.429960 0.001931 3.340870 #CG311 NG2R53
+pair_coeff 6 11 lj/charmm/coul/long 0.002688 3.296326 0.001495 2.939966 #CG311 OG2D1
+pair_coeff 6 12 lj/charmm/coul/long 0.001454 2.975602 0.000808 2.886512 #CG311 HCA2
+pair_coeff 6 13 lj/charmm/coul/long 0.001663 1.981804 0.000925 1.892714 #CG311 HCP1
+pair_coeff 6 14 lj/charmm/coul/long 0.001838 3.572504 0.000430 3.385415 #CG311 CC32A
+pair_coeff 6 15 lj/charmm/coul/long 0.003403 3.354233 0.001893 3.265143 #CG311 OC311
+pair_coeff 7 7 lj/charmm/coul/long 0.002430 3.581413 0.000430 3.385415 #CG321 CG321
+pair_coeff 7 8 lj/charmm/coul/long 0.002866 3.617049 0.000430 3.385415 #CG321 CG331
+pair_coeff 7 9 lj/charmm/coul/long 0.002514 3.590322 0.000430 3.385415 #CG321 CG3C52
+pair_coeff 7 10 lj/charmm/coul/long 0.004590 3.438869 0.001931 3.340870 #CG321 NG2R53
+pair_coeff 7 11 lj/charmm/coul/long 0.003555 3.305235 0.001495 2.939966 #CG321 OG2D1
+pair_coeff 7 12 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #CG321 HCA2
+pair_coeff 7 13 lj/charmm/coul/long 0.002199 1.990713 0.000925 1.892714 #CG321 HCP1
+pair_coeff 7 14 lj/charmm/coul/long 0.002430 3.581413 0.000430 3.385415 #CG321 CC32A
+pair_coeff 7 15 lj/charmm/coul/long 0.004499 3.363142 0.001893 3.265143 #CG321 OC311
+pair_coeff 8 8 lj/charmm/coul/long 0.003380 3.652685 0.000430 3.385415 #CG331 CG331
+pair_coeff 8 9 lj/charmm/coul/long 0.002964 3.625958 0.000430 3.385415 #CG331 CG3C52
+pair_coeff 8 10 lj/charmm/coul/long 0.005413 3.474505 0.001931 3.340870 #CG331 NG2R53
+pair_coeff 8 11 lj/charmm/coul/long 0.004192 3.340871 0.001495 2.939966 #CG331 OG2D1
+pair_coeff 8 12 lj/charmm/coul/long 0.002267 3.020147 0.000808 2.886512 #CG331 HCA2
+pair_coeff 8 13 lj/charmm/coul/long 0.002593 2.026349 0.000925 1.892714 #CG331 HCP1
+pair_coeff 8 14 lj/charmm/coul/long 0.002866 3.617049 0.000430 3.385415 #CG331 CC32A
+pair_coeff 8 15 lj/charmm/coul/long 0.005306 3.398778 0.001893 3.265143 #CG331 OC311
+pair_coeff 9 9 lj/charmm/coul/long 0.002600 3.599231 0.000430 3.385415 #CG3C52CG3C52
+pair_coeff 9 10 lj/charmm/coul/long 0.004748 3.447778 0.001931 3.340870 #CG3C52NG2R53
+pair_coeff 9 11 lj/charmm/coul/long 0.003677 3.314144 0.001495 2.939966 #CG3C52OG2D1
+pair_coeff 9 12 lj/charmm/coul/long 0.001988 2.993420 0.000808 2.886512 #CG3C52HCA2
+pair_coeff 9 13 lj/charmm/coul/long 0.002275 1.999622 0.000925 1.892714 #CG3C52HCP1
+pair_coeff 9 14 lj/charmm/coul/long 0.002514 3.590322 0.000430 3.385415 #CG3C52CC32A
+pair_coeff 9 15 lj/charmm/coul/long 0.004654 3.372051 0.001893 3.265143 #CG3C52OC311
+pair_coeff 10 10 lj/charmm/coul/long 0.008670 3.296325 0.008670 3.296325 #NG2R53NG2R53
+pair_coeff 10 11 lj/charmm/coul/long 0.006714 3.162691 0.006714 2.895421 #NG2R53OG2D1
+pair_coeff 10 12 lj/charmm/coul/long 0.003630 2.841967 0.003630 2.841967 #NG2R53HCA2
+pair_coeff 10 13 lj/charmm/coul/long 0.004154 1.848169 0.004154 1.848169 #NG2R53HCP1
+pair_coeff 10 14 lj/charmm/coul/long 0.004590 3.438869 0.001931 3.340870 #NG2R53CC32A
+pair_coeff 10 15 lj/charmm/coul/long 0.008498 3.220598 0.008498 3.220598 #NG2R53OC311
+pair_coeff 11 11 lj/charmm/coul/long 0.005200 3.029056 0.005200 2.494516 #OG2D1 OG2D1
+pair_coeff 11 12 lj/charmm/coul/long 0.002811 2.708333 0.002811 2.441063 #OG2D1 HCA2
+pair_coeff 11 13 lj/charmm/coul/long 0.003217 1.714535 0.003217 1.447265 #OG2D1 HCP1
+pair_coeff 11 14 lj/charmm/coul/long 0.003555 3.305235 0.001495 2.939966 #OG2D1 CC32A
+pair_coeff 11 15 lj/charmm/coul/long 0.006581 3.086964 0.006581 2.819694 #OG2D1 OC311
+pair_coeff 12 12 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HCA2 HCA2
+pair_coeff 12 13 lj/charmm/coul/long 0.001739 1.393811 0.001739 1.393811 #HCA2 HCP1
+pair_coeff 12 14 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #HCA2 CC32A
+pair_coeff 12 15 lj/charmm/coul/long 0.003558 2.766240 0.003558 2.766240 #HCA2 OC311
+pair_coeff 13 13 lj/charmm/coul/long 0.001990 0.400014 0.001990 0.400014 #HCP1 HCP1
+pair_coeff 13 14 lj/charmm/coul/long 0.002199 1.990713 0.000925 1.892714 #HCP1 CC32A
+pair_coeff 13 15 lj/charmm/coul/long 0.004071 1.772443 0.004071 1.772443 #HCP1 OC311
+pair_coeff 14 14 lj/charmm/coul/long 0.002430 3.581413 0.000430 3.385415 #CC32A CC32A
+pair_coeff 14 15 lj/charmm/coul/long 0.004499 3.363142 0.001893 3.265143 #CC32A OC311
+pair_coeff 15 15 lj/charmm/coul/long 0.008330 3.144872 0.008330 3.144872 #OC311 OC311
+
+
+special_bonds charmm
+
+# ----------------- Run Section -----------------
+
+timestep 0.001
+
+minimize 1.0e-3 1.0e-5 1000 10000
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.224856
+ grid = 27 27 64
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.00015081
+ estimated relative force accuracy = 1.04732e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 24276 11664
+WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:218)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 14
+ ghost atom cutoff = 14
+ binsize = 7, bins = 8 8 23
+ 5 neighbor lists, perpetual/occasional/extra = 5 0 0
+ (1) pair eam/fs, perpetual, skip from (5)
+ attributes: half, newton on
+ pair build: skip
+ stencil: none
+ bin: none
+ (2) pair lj/charmm/coul/long, perpetual, skip from (5)
+ attributes: half, newton on
+ pair build: skip
+ stencil: none
+ bin: none
+ (3) pair momb, perpetual, skip from (5)
+ attributes: half, newton on
+ pair build: skip
+ stencil: none
+ bin: none
+ (4) pair morse, perpetual, copy from (3)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+ (5) neighbor class addition, 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) = 21.64 | 38.62 | 61.37 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0 -10035.476 218.18376 -9817.2917 -1066.914
+ 9 0 -10244.892 211.35072 -10033.541 -3283.8636
+Loop time of 1.5282 on 4 procs for 9 steps with 18146 atoms
+
+98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+ Stopping criterion = energy tolerance
+ Energy initial, next-to-last, final =
+ -9817.29174185 -10023.887559 -10033.5413886
+ Force two-norm initial, final = 76.9233 27.3547
+ Force max component initial, final = 11.8658 7.37882
+ Final line search alpha, max atom move = 0.0472944 0.348977
+ Iterations, force evaluations = 9 11
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.13991 | 0.61651 | 1.354 | 63.8 | 40.34
+Bond | 0.00096774 | 0.021362 | 0.048298 | 13.1 | 1.40
+Kspace | 0.11483 | 0.87954 | 1.3772 | 55.5 | 57.55
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0038254 | 0.0055712 | 0.0068097 | 1.6 | 0.36
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.005224 | | | 0.34
+
+Nlocal: 4536.5 ave 8000 max 700 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Nghost: 11329.2 ave 16795 max 5072 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Neighs: 109797 ave 237808 max 8314 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+
+Total # of neighbors = 439189
+Ave neighs/atom = 24.2031
+Ave special neighs/atom = 5.92362
+Neighbor list builds = 0
+Dangerous builds = 0
+reset_timestep 0
+
+velocity all create 413.0 12378 dist gaussian
+
+thermo 10
+thermo_style custom step pe ke etotal temp press pxx pyy pzz
+
+variable STEP equal step
+variable PE equal pe
+variable KE equal ke
+variable ETOTAL equal etotal
+variable TEMP equal temp
+variable VOL equal vol
+variable PRESS equal press
+variable LX equal lx
+variable LZ equal lz
+variable PXX equal pxx
+variable PYY equal pyy
+variable PZZ equal pzz
+
+fix 1 all nvt temp 413.0 413.0 0.1 fixedpoint 0.0 0.0 0.0
+#fix thermo_output all print 2000 "${STEP} ${PE} ${KE} ${ETOTAL} ${TEMP} ${VOL} ${PRESS} ${LX} ${LZ} ${PXX} ${PYY} ${PZZ}" file thermo.lammps title "# Step PotEng KinEng TotEng Temp Volume Press Lx Lz Pxx Pyy Pzz"
+
+#dump 1 all custom 10 traj_npt.lammpstrj id mol type x y z ix iy iz
+
+run 100
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.224856
+ grid = 27 27 64
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.00015081
+ estimated relative force accuracy = 1.04732e-05
+ using double precision FFTs
+ 3d grid and FFT values/proc = 24276 11664
+WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:218)
+Per MPI rank memory allocation (min/avg/max) = 20.51 | 36.93 | 59.12 Mbytes
+Step PotEng KinEng TotEng Temp Press Pxx Pyy Pzz
+ 0 -10033.541 968.66066 -9064.8807 413 -1034.7033 5221.7757 -4827.0742 -3498.8115
+ 10 -9717.5642 663.69058 -9053.8736 282.97238 -392.07182 5076.3825 -3643.5902 -2609.0078
+ 20 -9592.3732 550.97993 -9041.3932 234.91685 -737.21307 4729.9669 -4234.1008 -2707.5053
+ 30 -9689.9997 645.41353 -9044.5862 275.17974 -1095.6905 5368.8361 -5243.8524 -3412.0551
+ 40 -9721.5122 675.86683 -9045.6453 288.16387 -138.73949 6292.4674 -3623.6807 -3085.0052
+ 50 -9576.7583 544.96028 -9031.798 232.3503 -552.64225 4683.2668 -3286.1479 -3055.0457
+ 60 -9542.5531 522.39339 -9020.1597 222.72864 -1044.0254 3675.027 -3821.1015 -2986.0017
+ 70 -9572.4447 551.73535 -9020.7093 235.23893 132.77197 4550.5092 -2208.7446 -1943.4487
+ 80 -9684.4674 666.4064 -9018.061 284.1303 999.60397 3345.5104 -202.16376 -144.53477
+ 90 -9553.3377 550.82743 -9002.5103 234.85183 -1291.4189 1264.3148 -2496.9658 -2641.6058
+ 100 -9551.9716 560.31802 -8991.6536 238.89826 -1189.4791 1842.8208 -3025.5224 -2385.7357
+Loop time of 10.6429 on 4 procs for 100 steps with 18146 atoms
+
+Performance: 0.812 ns/day, 29.564 hours/ns, 9.396 timesteps/s
+98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.1093 | 3.9562 | 8.5073 | 153.7 | 37.17
+Bond | 0.0072014 | 0.1612 | 0.36361 | 36.2 | 1.51
+Kspace | 0.96559 | 5.5587 | 8.4333 | 131.1 | 52.23
+Neigh | 0.70939 | 0.70989 | 0.7104 | 0.0 | 6.67
+Comm | 0.057808 | 0.21244 | 0.39607 | 26.3 | 2.00
+Output | 0.0013831 | 0.0014417 | 0.001529 | 0.1 | 0.01
+Modify | 0.023245 | 0.028182 | 0.038124 | 3.5 | 0.26
+Other | | 0.0148 | | | 0.14
+
+Nlocal: 4536.5 ave 8016 max 572 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Nghost: 11368.2 ave 16706 max 5173 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Neighs: 110474 ave 236783 max 9217 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+
+Total # of neighbors = 441898
+Ave neighs/atom = 24.3524
+Ave special neighs/atom = 5.92362
+Neighbor list builds = 5
+Dangerous builds = 0
+Total wall time: 0:00:12
--
GitLab