From 37289f74766922155367bb88e3b9c7dcabdc74d2 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 28 Nov 2018 16:07:12 -0500
Subject: [PATCH] update log files for dipole and dreiding example inputs. add
running some MD steps for dreiding
---
....dipole.g++.1 => log.27Nov18.dipole.g++.1} | 35 ++--
....dipole.g++.4 => log.27Nov18.dipole.g++.4} | 33 +--
examples/dreiding/in.dreiding | 40 ++--
examples/dreiding/log.27Nov18.dreiding.g++.1 | 198 ++++++++++++++++++
examples/dreiding/log.27Nov18.dreiding.g++.4 | 198 ++++++++++++++++++
examples/dreiding/log.5Oct16.dreiding.g++.1 | 118 -----------
examples/dreiding/log.5Oct16.dreiding.g++.4 | 118 -----------
7 files changed, 459 insertions(+), 281 deletions(-)
rename examples/dipole/{log.5Oct16.dipole.g++.1 => log.27Nov18.dipole.g++.1} (76%)
rename examples/dipole/{log.5Oct16.dipole.g++.4 => log.27Nov18.dipole.g++.4} (77%)
create mode 100644 examples/dreiding/log.27Nov18.dreiding.g++.1
create mode 100644 examples/dreiding/log.27Nov18.dreiding.g++.4
delete mode 100644 examples/dreiding/log.5Oct16.dreiding.g++.1
delete mode 100644 examples/dreiding/log.5Oct16.dreiding.g++.4
diff --git a/examples/dipole/log.5Oct16.dipole.g++.1 b/examples/dipole/log.27Nov18.dipole.g++.1
similarity index 76%
rename from examples/dipole/log.5Oct16.dipole.g++.1
rename to examples/dipole/log.27Nov18.dipole.g++.1
index fc620f23fd..cc82422a9c 100644
--- a/examples/dipole/log.5Oct16.dipole.g++.1
+++ b/examples/dipole/log.27Nov18.dipole.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
@@ -13,6 +14,7 @@ Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 200 atoms
+ Time spent = 0.00140882 secs
# need both mass settings due to hybrid atom style
@@ -46,13 +48,18 @@ thermo 500
run 10000
Neighbor list info ...
- 1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 13 13 2
-Memory usage per processor = 4.47689 Mbytes
+ binsize = 1.4, bins = 13 13 2
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut/dipole/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/2d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.049 | 5.049 | 5.049 Mbytes
Step Temp E_pair c_erot TotEng Press
0 0 -2.1909822 0 -2.1909822 -2.5750971
500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899
@@ -75,20 +82,20 @@ Step Temp E_pair c_erot TotEng Press
9000 0.42532413 -2.748856 0.21378021 -2.3256584 0.015079949
9500 0.42237159 -2.7266142 0.20255034 -2.3063545 -0.15538561
10000 0.40758268 -2.778401 0.2746675 -2.3728562 -0.20811978
-Loop time of 1.05484 on 1 procs for 10000 steps with 200 atoms
+Loop time of 0.851938 on 1 procs for 10000 steps with 200 atoms
-Performance: 4095400.088 tau/day, 9480.093 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 5070791.481 tau/day, 11737.943 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.88325 | 0.88325 | 0.88325 | 0.0 | 83.73
-Neigh | 0.038596 | 0.038596 | 0.038596 | 0.0 | 3.66
-Comm | 0.034257 | 0.034257 | 0.034257 | 0.0 | 3.25
-Output | 0.00013828 | 0.00013828 | 0.00013828 | 0.0 | 0.01
-Modify | 0.083041 | 0.083041 | 0.083041 | 0.0 | 7.87
-Other | | 0.01556 | | | 1.48
+Pair | 0.64889 | 0.64889 | 0.64889 | 0.0 | 76.17
+Neigh | 0.04038 | 0.04038 | 0.04038 | 0.0 | 4.74
+Comm | 0.058003 | 0.058003 | 0.058003 | 0.0 | 6.81
+Output | 0.00021219 | 0.00021219 | 0.00021219 | 0.0 | 0.02
+Modify | 0.083454 | 0.083454 | 0.083454 | 0.0 | 9.80
+Other | | 0.021 | | | 2.47
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -101,4 +108,4 @@ Total # of neighbors = 1625
Ave neighs/atom = 8.125
Neighbor list builds = 673
Dangerous builds = 0
-Total wall time: 0:00:01
+Total wall time: 0:00:00
diff --git a/examples/dipole/log.5Oct16.dipole.g++.4 b/examples/dipole/log.27Nov18.dipole.g++.4
similarity index 77%
rename from examples/dipole/log.5Oct16.dipole.g++.4
rename to examples/dipole/log.27Nov18.dipole.g++.4
index b573253fbc..f33bfde451 100644
--- a/examples/dipole/log.5Oct16.dipole.g++.4
+++ b/examples/dipole/log.27Nov18.dipole.g++.4
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
@@ -13,6 +14,7 @@ Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 200 atoms
+ Time spent = 0.00139761 secs
# need both mass settings due to hybrid atom style
@@ -46,13 +48,18 @@ thermo 500
run 10000
Neighbor list info ...
- 1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 13 13 2
-Memory usage per processor = 4.47621 Mbytes
+ binsize = 1.4, bins = 13 13 2
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut/dipole/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/2d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.047 | 5.047 | 5.047 Mbytes
Step Temp E_pair c_erot TotEng Press
0 0 -2.1909822 0 -2.1909822 -2.5750971
500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899
@@ -75,20 +82,20 @@ Step Temp E_pair c_erot TotEng Press
9000 0.42318631 -2.7600929 0.25229644 -2.3390225 0.36820391
9500 0.42857449 -2.6958592 0.18686752 -2.2694276 0.15379721
10000 0.43323126 -2.71981 0.22185737 -2.2887449 0.038354509
-Loop time of 0.406978 on 4 procs for 10000 steps with 200 atoms
+Loop time of 0.396069 on 4 procs for 10000 steps with 200 atoms
-Performance: 10614834.981 tau/day, 24571.377 timesteps/s
-99.5% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 10907185.759 tau/day, 25248.115 timesteps/s
+96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.18518 | 0.23558 | 0.25487 | 6.0 | 57.88
-Neigh | 0.0090437 | 0.011033 | 0.011971 | 1.1 | 2.71
-Comm | 0.086857 | 0.10807 | 0.16262 | 9.6 | 26.56
-Output | 0.00029182 | 0.00031263 | 0.00035739 | 0.1 | 0.08
-Modify | 0.022396 | 0.025649 | 0.026865 | 1.2 | 6.30
-Other | | 0.02633 | | | 6.47
+Pair | 0.13746 | 0.17338 | 0.19067 | 5.1 | 43.77
+Neigh | 0.0096052 | 0.011424 | 0.012275 | 1.0 | 2.88
+Comm | 0.12394 | 0.14718 | 0.1914 | 7.1 | 37.16
+Output | 0.00037861 | 0.00056618 | 0.0011225 | 0.0 | 0.14
+Modify | 0.021838 | 0.024665 | 0.026625 | 1.1 | 6.23
+Other | | 0.03886 | | | 9.81
Nlocal: 50 ave 53 max 41 min
Histogram: 1 0 0 0 0 0 0 0 0 3
diff --git a/examples/dreiding/in.dreiding b/examples/dreiding/in.dreiding
index 4b811248d4..db0738fd32 100644
--- a/examples/dreiding/in.dreiding
+++ b/examples/dreiding/in.dreiding
@@ -2,28 +2,28 @@ units real
atom_style full
boundary p p p
dielectric 1
-special_bonds lj/coul 0.0 0.0 1.0
+special_bonds lj/coul 0.0 0.0 1.0
pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
-bond_style harmonic
-angle_style harmonic
+bond_style harmonic
+angle_style harmonic
dihedral_style harmonic
improper_style none
-kspace_style pppm 0.001
+kspace_style pppm 0.001
read_data data.dreiding
-pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
-pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
-pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
-pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
-pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
-pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
-pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
-pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
-pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
-pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
-pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4
+pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
+pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
+pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
+pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
+pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
+pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
+pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
+pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
+pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
+pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
+pair_coeff 4 4 hbond/dreiding/lj 2 i 4.000 2.750000000000000 4
pair_modify mix arithmetic
neighbor 2.0 multi
neigh_modify every 2 delay 4 check yes
@@ -33,7 +33,11 @@ variable sname index ch3oh.box.dreiding
compute hb all pair hbond/dreiding/lj
variable C_hbond equal c_hb[1] #number hbonds
variable E_hbond equal c_hb[2] #hbond energy
-thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
-thermo_modify line multi format float %14.6f
+thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
+thermo_modify line multi format float %14.6f
-run 0
+fix 1 all nve
+
+thermo 10
+
+run 100
diff --git a/examples/dreiding/log.27Nov18.dreiding.g++.1 b/examples/dreiding/log.27Nov18.dreiding.g++.1
new file mode 100644
index 0000000000..bbc2105238
--- /dev/null
+++ b/examples/dreiding/log.27Nov18.dreiding.g++.1
@@ -0,0 +1,198 @@
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
+units real
+atom_style full
+boundary p p p
+dielectric 1
+special_bonds lj/coul 0.0 0.0 1.0
+
+pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
+bond_style harmonic
+angle_style harmonic
+dihedral_style harmonic
+improper_style none
+kspace_style pppm 0.001
+
+read_data data.dreiding
+ orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 384 atoms
+ scanning bonds ...
+ 4 = max bonds/atom
+ scanning angles ...
+ 6 = max angles/atom
+ scanning dihedrals ...
+ 3 = max dihedrals/atom
+ reading bonds ...
+ 320 bonds
+ reading angles ...
+ 448 angles
+ reading dihedrals ...
+ 192 dihedrals
+ 4 = max # of 1-2 neighbors
+ 3 = max # of 1-3 neighbors
+ 5 = max # of special neighbors
+
+pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
+pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
+pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
+pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
+pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
+pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
+pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
+pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
+pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
+pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
+pair_coeff 4 4 hbond/dreiding/lj 2 i 4.000 2.750000000000000 4
+pair_modify mix arithmetic
+neighbor 2.0 multi
+neigh_modify every 2 delay 4 check yes
+variable input index in.ch3oh.box.dreiding
+variable sname index ch3oh.box.dreiding
+
+compute hb all pair hbond/dreiding/lj
+variable C_hbond equal c_hb[1] #number hbonds
+variable E_hbond equal c_hb[2] #hbond energy
+thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
+thermo_modify line multi format float %14.6f
+
+fix 1 all nve
+
+thermo 10
+
+run 100
+PPPM initialization ...
+WARNING: System is not charge neutral, net charge = -0.00064 (src/kspace.cpp:302)
+ using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
+ G vector (1/distance) = 0.142073
+ grid = 3 3 3
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.154715
+ estimated relative force accuracy = 0.00046592
+ using double precision FFTs
+ 3d grid and FFT values/proc = 512 27
+Neighbor list info ...
+ update every 2 steps, delay 4 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 13.5
+ ghost atom cutoff = 13.5
+ binsize = 6.75, bins = 3 3 3
+ 3 neighbor lists, perpetual/occasional/extra = 3 0 0
+ (1) pair hbond/dreiding/lj, perpetual, skip from (3)
+ attributes: full, newton on
+ pair build: skip
+ stencil: none
+ bin: none
+ (2) pair lj/cut/coul/long, perpetual, half/full from (3)
+ attributes: half, newton on
+ pair build: halffull/newton
+ stencil: none
+ bin: none
+ (3) neighbor class addition, perpetual
+ attributes: full, newton on
+ pair build: full/multi
+ stencil: full/multi/3d
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.47 | 11.47 | 11.47 Mbytes
+---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
+TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000
+PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880
+E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
+E_coul = 597.219740 E_long = -361.164864 v_E_hbond = -69.322152
+v_C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335
+---------------- Step 10 ----- CPU = 0.0306 (sec) ----------------
+TotEng = 113.773202 KinEng = 1.537257 Temp = 1.346522
+PotEng = 112.235945 E_bond = 0.530880 E_angle = 1.407481
+E_dihed = 1.084172 E_impro = 0.000000 E_vdwl = -126.339883
+E_coul = 596.742306 E_long = -361.189011 v_E_hbond = -69.944278
+v_C_hbond = 240.000000 Press = -395.900496 Volume = 7447.236335
+---------------- Step 20 ----- CPU = 0.0597 (sec) ----------------
+TotEng = 113.879292 KinEng = 2.999580 Temp = 2.627407
+PotEng = 110.879711 E_bond = 0.549156 E_angle = 1.323582
+E_dihed = 1.357398 E_impro = 0.000000 E_vdwl = -127.482103
+E_coul = 596.318729 E_long = -361.187051 v_E_hbond = -70.088343
+v_C_hbond = 237.000000 Press = -487.150418 Volume = 7447.236335
+---------------- Step 30 ----- CPU = 0.0889 (sec) ----------------
+TotEng = 113.587474 KinEng = 4.369566 Temp = 3.827412
+PotEng = 109.217908 E_bond = 0.416485 E_angle = 1.294630
+E_dihed = 1.710254 E_impro = 0.000000 E_vdwl = -128.565697
+E_coul = 595.560846 E_long = -361.198612 v_E_hbond = -69.848068
+v_C_hbond = 238.000000 Press = -423.966898 Volume = 7447.236335
+---------------- Step 40 ----- CPU = 0.1178 (sec) ----------------
+TotEng = 113.915503 KinEng = 6.466349 Temp = 5.664037
+PotEng = 107.449154 E_bond = 0.514530 E_angle = 1.342583
+E_dihed = 1.536929 E_impro = 0.000000 E_vdwl = -129.858713
+E_coul = 595.186400 E_long = -361.272576 v_E_hbond = -69.871393
+v_C_hbond = 237.000000 Press = -498.152652 Volume = 7447.236335
+---------------- Step 50 ----- CPU = 0.1467 (sec) ----------------
+TotEng = 113.787839 KinEng = 8.050614 Temp = 7.051734
+PotEng = 105.737226 E_bond = 0.652153 E_angle = 1.416041
+E_dihed = 1.363560 E_impro = 0.000000 E_vdwl = -130.513518
+E_coul = 594.139769 E_long = -361.320780 v_E_hbond = -69.593967
+v_C_hbond = 233.000000 Press = -557.299799 Volume = 7447.236335
+---------------- Step 60 ----- CPU = 0.1755 (sec) ----------------
+TotEng = 114.120941 KinEng = 10.318793 Temp = 9.038489
+PotEng = 103.802148 E_bond = 0.576578 E_angle = 1.285008
+E_dihed = 1.123936 E_impro = 0.000000 E_vdwl = -131.268312
+E_coul = 593.450009 E_long = -361.365070 v_E_hbond = -70.107165
+v_C_hbond = 238.000000 Press = -571.907188 Volume = 7447.236335
+---------------- Step 70 ----- CPU = 0.2044 (sec) ----------------
+TotEng = 113.836161 KinEng = 11.873184 Temp = 10.400019
+PotEng = 101.962977 E_bond = 0.633521 E_angle = 1.315999
+E_dihed = 1.055318 E_impro = 0.000000 E_vdwl = -131.673572
+E_coul = 592.039194 E_long = -361.407483 v_E_hbond = -70.518544
+v_C_hbond = 240.000000 Press = -576.731444 Volume = 7447.236335
+---------------- Step 80 ----- CPU = 0.2333 (sec) ----------------
+TotEng = 113.589436 KinEng = 13.546467 Temp = 11.865689
+PotEng = 100.042970 E_bond = 0.637759 E_angle = 1.439918
+E_dihed = 1.020307 E_impro = 0.000000 E_vdwl = -131.980346
+E_coul = 590.365879 E_long = -361.440548 v_E_hbond = -71.174370
+v_C_hbond = 245.000000 Press = -735.254308 Volume = 7447.236335
+---------------- Step 90 ----- CPU = 0.2622 (sec) ----------------
+TotEng = 114.100567 KinEng = 15.870735 Temp = 13.901574
+PotEng = 98.229832 E_bond = 0.724671 E_angle = 1.435914
+E_dihed = 1.028167 E_impro = 0.000000 E_vdwl = -132.680267
+E_coul = 589.225626 E_long = -361.504279 v_E_hbond = -72.653223
+v_C_hbond = 245.000000 Press = -820.598954 Volume = 7447.236335
+---------------- Step 100 ----- CPU = 0.2911 (sec) ----------------
+TotEng = 113.670041 KinEng = 17.406803 Temp = 15.247054
+PotEng = 96.263238 E_bond = 0.711253 E_angle = 1.338059
+E_dihed = 1.474770 E_impro = 0.000000 E_vdwl = -132.917719
+E_coul = 587.219020 E_long = -361.562145 v_E_hbond = -74.299795
+v_C_hbond = 246.000000 Press = -786.245946 Volume = 7447.236335
+Loop time of 0.291149 on 1 procs for 100 steps with 384 atoms
+
+Performance: 29.676 ns/day, 0.809 hours/ns, 343.467 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.255 | 0.255 | 0.255 | 0.0 | 87.59
+Bond | 0.0042725 | 0.0042725 | 0.0042725 | 0.0 | 1.47
+Kspace | 0.027151 | 0.027151 | 0.027151 | 0.0 | 9.33
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0034399 | 0.0034399 | 0.0034399 | 0.0 | 1.18
+Output | 0.00025988 | 0.00025988 | 0.00025988 | 0.0 | 0.09
+Modify | 0.00059223 | 0.00059223 | 0.00059223 | 0.0 | 0.20
+Other | | 0.0004294 | | | 0.15
+
+Nlocal: 384 ave 384 max 384 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 4637 ave 4637 max 4637 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 101854 ave 101854 max 101854 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 5624 ave 5624 max 5624 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 101854
+Ave neighs/atom = 265.245
+Ave special neighs/atom = 4
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/dreiding/log.27Nov18.dreiding.g++.4 b/examples/dreiding/log.27Nov18.dreiding.g++.4
new file mode 100644
index 0000000000..f765d71fbe
--- /dev/null
+++ b/examples/dreiding/log.27Nov18.dreiding.g++.4
@@ -0,0 +1,198 @@
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
+units real
+atom_style full
+boundary p p p
+dielectric 1
+special_bonds lj/coul 0.0 0.0 1.0
+
+pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
+bond_style harmonic
+angle_style harmonic
+dihedral_style harmonic
+improper_style none
+kspace_style pppm 0.001
+
+read_data data.dreiding
+ orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
+ 2 by 1 by 2 MPI processor grid
+ reading atoms ...
+ 384 atoms
+ scanning bonds ...
+ 4 = max bonds/atom
+ scanning angles ...
+ 6 = max angles/atom
+ scanning dihedrals ...
+ 3 = max dihedrals/atom
+ reading bonds ...
+ 320 bonds
+ reading angles ...
+ 448 angles
+ reading dihedrals ...
+ 192 dihedrals
+ 4 = max # of 1-2 neighbors
+ 3 = max # of 1-3 neighbors
+ 5 = max # of special neighbors
+
+pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
+pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
+pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
+pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
+pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
+pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
+pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
+pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
+pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
+pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
+pair_coeff 4 4 hbond/dreiding/lj 2 i 4.000 2.750000000000000 4
+pair_modify mix arithmetic
+neighbor 2.0 multi
+neigh_modify every 2 delay 4 check yes
+variable input index in.ch3oh.box.dreiding
+variable sname index ch3oh.box.dreiding
+
+compute hb all pair hbond/dreiding/lj
+variable C_hbond equal c_hb[1] #number hbonds
+variable E_hbond equal c_hb[2] #hbond energy
+thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
+thermo_modify line multi format float %14.6f
+
+fix 1 all nve
+
+thermo 10
+
+run 100
+PPPM initialization ...
+WARNING: System is not charge neutral, net charge = -0.00064 (src/kspace.cpp:302)
+ using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
+ G vector (1/distance) = 0.142073
+ grid = 3 3 3
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.154715
+ estimated relative force accuracy = 0.00046592
+ using double precision FFTs
+ 3d grid and FFT values/proc = 392 12
+Neighbor list info ...
+ update every 2 steps, delay 4 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 13.5
+ ghost atom cutoff = 13.5
+ binsize = 6.75, bins = 3 3 3
+ 3 neighbor lists, perpetual/occasional/extra = 3 0 0
+ (1) pair hbond/dreiding/lj, perpetual, skip from (3)
+ attributes: full, newton on
+ pair build: skip
+ stencil: none
+ bin: none
+ (2) pair lj/cut/coul/long, perpetual, half/full from (3)
+ attributes: half, newton on
+ pair build: halffull/newton
+ stencil: none
+ bin: none
+ (3) neighbor class addition, perpetual
+ attributes: full, newton on
+ pair build: full/multi
+ stencil: full/multi/3d
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 10.17 | 10.17 | 10.17 Mbytes
+---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
+TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000
+PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880
+E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
+E_coul = 597.219740 E_long = -361.164864 v_E_hbond = -69.322152
+v_C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335
+---------------- Step 10 ----- CPU = 0.0112 (sec) ----------------
+TotEng = 113.773202 KinEng = 1.537257 Temp = 1.346522
+PotEng = 112.235945 E_bond = 0.530880 E_angle = 1.407481
+E_dihed = 1.084172 E_impro = 0.000000 E_vdwl = -126.339883
+E_coul = 596.742306 E_long = -361.189011 v_E_hbond = -69.944278
+v_C_hbond = 240.000000 Press = -395.900496 Volume = 7447.236335
+---------------- Step 20 ----- CPU = 0.0206 (sec) ----------------
+TotEng = 113.879292 KinEng = 2.999580 Temp = 2.627407
+PotEng = 110.879711 E_bond = 0.549156 E_angle = 1.323582
+E_dihed = 1.357398 E_impro = 0.000000 E_vdwl = -127.482103
+E_coul = 596.318729 E_long = -361.187051 v_E_hbond = -70.088343
+v_C_hbond = 237.000000 Press = -487.150418 Volume = 7447.236335
+---------------- Step 30 ----- CPU = 0.0299 (sec) ----------------
+TotEng = 113.587474 KinEng = 4.369566 Temp = 3.827412
+PotEng = 109.217908 E_bond = 0.416485 E_angle = 1.294630
+E_dihed = 1.710254 E_impro = 0.000000 E_vdwl = -128.565697
+E_coul = 595.560846 E_long = -361.198612 v_E_hbond = -69.848068
+v_C_hbond = 238.000000 Press = -423.966898 Volume = 7447.236335
+---------------- Step 40 ----- CPU = 0.0403 (sec) ----------------
+TotEng = 113.915503 KinEng = 6.466349 Temp = 5.664037
+PotEng = 107.449154 E_bond = 0.514530 E_angle = 1.342583
+E_dihed = 1.536929 E_impro = 0.000000 E_vdwl = -129.858713
+E_coul = 595.186400 E_long = -361.272576 v_E_hbond = -69.871393
+v_C_hbond = 237.000000 Press = -498.152652 Volume = 7447.236335
+---------------- Step 50 ----- CPU = 0.0494 (sec) ----------------
+TotEng = 113.787839 KinEng = 8.050614 Temp = 7.051734
+PotEng = 105.737226 E_bond = 0.652153 E_angle = 1.416041
+E_dihed = 1.363560 E_impro = 0.000000 E_vdwl = -130.513518
+E_coul = 594.139769 E_long = -361.320780 v_E_hbond = -69.593967
+v_C_hbond = 233.000000 Press = -557.299799 Volume = 7447.236335
+---------------- Step 60 ----- CPU = 0.0588 (sec) ----------------
+TotEng = 114.120941 KinEng = 10.318793 Temp = 9.038489
+PotEng = 103.802148 E_bond = 0.576578 E_angle = 1.285008
+E_dihed = 1.123936 E_impro = 0.000000 E_vdwl = -131.268312
+E_coul = 593.450009 E_long = -361.365070 v_E_hbond = -70.107165
+v_C_hbond = 238.000000 Press = -571.907188 Volume = 7447.236335
+---------------- Step 70 ----- CPU = 0.0680 (sec) ----------------
+TotEng = 113.836161 KinEng = 11.873184 Temp = 10.400019
+PotEng = 101.962977 E_bond = 0.633521 E_angle = 1.315999
+E_dihed = 1.055318 E_impro = 0.000000 E_vdwl = -131.673572
+E_coul = 592.039194 E_long = -361.407483 v_E_hbond = -70.518544
+v_C_hbond = 240.000000 Press = -576.731444 Volume = 7447.236335
+---------------- Step 80 ----- CPU = 0.0790 (sec) ----------------
+TotEng = 113.589436 KinEng = 13.546467 Temp = 11.865689
+PotEng = 100.042970 E_bond = 0.637759 E_angle = 1.439918
+E_dihed = 1.020307 E_impro = 0.000000 E_vdwl = -131.980346
+E_coul = 590.365879 E_long = -361.440548 v_E_hbond = -71.174370
+v_C_hbond = 245.000000 Press = -735.254308 Volume = 7447.236335
+---------------- Step 90 ----- CPU = 0.0883 (sec) ----------------
+TotEng = 114.100567 KinEng = 15.870735 Temp = 13.901574
+PotEng = 98.229832 E_bond = 0.724671 E_angle = 1.435914
+E_dihed = 1.028167 E_impro = 0.000000 E_vdwl = -132.680267
+E_coul = 589.225626 E_long = -361.504279 v_E_hbond = -72.653223
+v_C_hbond = 245.000000 Press = -820.598954 Volume = 7447.236335
+---------------- Step 100 ----- CPU = 0.0976 (sec) ----------------
+TotEng = 113.670041 KinEng = 17.406803 Temp = 15.247054
+PotEng = 96.263238 E_bond = 0.711253 E_angle = 1.338059
+E_dihed = 1.474770 E_impro = 0.000000 E_vdwl = -132.917719
+E_coul = 587.219020 E_long = -361.562145 v_E_hbond = -74.299795
+v_C_hbond = 246.000000 Press = -786.245946 Volume = 7447.236335
+Loop time of 0.0976357 on 4 procs for 100 steps with 384 atoms
+
+Performance: 88.492 ns/day, 0.271 hours/ns, 1024.215 timesteps/s
+96.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.055383 | 0.065178 | 0.07438 | 2.7 | 66.76
+Bond | 0.00099874 | 0.0011503 | 0.001229 | 0.3 | 1.18
+Kspace | 0.013823 | 0.022918 | 0.032308 | 4.4 | 23.47
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0064669 | 0.0072899 | 0.0078194 | 0.6 | 7.47
+Output | 0.00039268 | 0.00043893 | 0.00056481 | 0.0 | 0.45
+Modify | 0.000175 | 0.00019002 | 0.00020623 | 0.0 | 0.19
+Other | | 0.0004706 | | | 0.48
+
+Nlocal: 96 ave 104 max 87 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost: 3063.25 ave 3108 max 3024 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Neighs: 25463.5 ave 28799 max 22471 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+FullNghs: 1406 ave 1664 max 1237 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+
+Total # of neighbors = 101854
+Ave neighs/atom = 265.245
+Ave special neighs/atom = 4
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/dreiding/log.5Oct16.dreiding.g++.1 b/examples/dreiding/log.5Oct16.dreiding.g++.1
deleted file mode 100644
index 5208fe7d1c..0000000000
--- a/examples/dreiding/log.5Oct16.dreiding.g++.1
+++ /dev/null
@@ -1,118 +0,0 @@
-LAMMPS (5 Oct 2016)
-units real
-atom_style full
-boundary p p p
-dielectric 1
-special_bonds lj/coul 0.0 0.0 1.0
-
-pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
-bond_style harmonic
-angle_style harmonic
-dihedral_style harmonic
-improper_style none
-kspace_style pppm 0.001
-
-read_data data.dreiding
- orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 384 atoms
- scanning bonds ...
- 4 = max bonds/atom
- scanning angles ...
- 6 = max angles/atom
- scanning dihedrals ...
- 3 = max dihedrals/atom
- reading bonds ...
- 320 bonds
- reading angles ...
- 448 angles
- reading dihedrals ...
- 192 dihedrals
- 4 = max # of 1-2 neighbors
- 3 = max # of 1-3 neighbors
- 5 = max # of special neighbors
-
-pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
-pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
-pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
-pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
-pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
-pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
-pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
-pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
-pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
-pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
-pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4
-pair_modify mix arithmetic
-neighbor 2.0 multi
-neigh_modify every 2 delay 4 check yes
-variable input index in.ch3oh.box.dreiding
-variable sname index ch3oh.box.dreiding
-
-compute hb all pair hbond/dreiding/lj
-variable C_hbond equal c_hb[1] #number hbonds
-variable E_hbond equal c_hb[2] #hbond energy
-thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
-thermo_modify line multi format float %14.6f
-
-run 0
-WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
-PPPM initialization ...
-WARNING: System is not charge neutral, net charge = -0.00064 (../kspace.cpp:297)
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
- G vector (1/distance) = 0.142073
- grid = 3 3 3
- stencil order = 5
- estimated absolute RMS force accuracy = 0.154715
- estimated relative force accuracy = 0.00046592
- using double precision FFTs
- 3d grid and FFT values/proc = 512 27
-Neighbor list info ...
- 3 neighbor list requests
- update every 2 steps, delay 4 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 13.5
- ghost atom cutoff = 13.5
- binsize = 6.75 -> bins = 3 3 3
-Memory usage per processor = 9.19186 Mbytes
----------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
-TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000
-PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880
-E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
-E_coul = 597.219740 E_long = -361.164864 v_E_hbond = -69.322152
-v_C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335
-Loop time of 9.53674e-07 on 1 procs for 0 steps with 384 atoms
-
-0.0% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0 | 0 | 0 | 0.0 | 0.00
-Bond | 0 | 0 | 0 | 0.0 | 0.00
-Kspace | 0 | 0 | 0 | 0.0 | 0.00
-Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0 | 0 | 0 | 0.0 | 0.00
-Output | 0 | 0 | 0 | 0.0 | 0.00
-Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 9.537e-07 | | |100.00
-
-Nlocal: 384 ave 384 max 384 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 4637 ave 4637 max 4637 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 101854 ave 101854 max 101854 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs: 203708 ave 203708 max 203708 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 203708
-Ave neighs/atom = 530.49
-Ave special neighs/atom = 4
-Neighbor list builds = 0
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:00
diff --git a/examples/dreiding/log.5Oct16.dreiding.g++.4 b/examples/dreiding/log.5Oct16.dreiding.g++.4
deleted file mode 100644
index 551b8cbb1b..0000000000
--- a/examples/dreiding/log.5Oct16.dreiding.g++.4
+++ /dev/null
@@ -1,118 +0,0 @@
-LAMMPS (5 Oct 2016)
-units real
-atom_style full
-boundary p p p
-dielectric 1
-special_bonds lj/coul 0.0 0.0 1.0
-
-pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
-bond_style harmonic
-angle_style harmonic
-dihedral_style harmonic
-improper_style none
-kspace_style pppm 0.001
-
-read_data data.dreiding
- orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
- 2 by 1 by 2 MPI processor grid
- reading atoms ...
- 384 atoms
- scanning bonds ...
- 4 = max bonds/atom
- scanning angles ...
- 6 = max angles/atom
- scanning dihedrals ...
- 3 = max dihedrals/atom
- reading bonds ...
- 320 bonds
- reading angles ...
- 448 angles
- reading dihedrals ...
- 192 dihedrals
- 4 = max # of 1-2 neighbors
- 3 = max # of 1-3 neighbors
- 5 = max # of special neighbors
-
-pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
-pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
-pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
-pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
-pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
-pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
-pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
-pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
-pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
-pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
-pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4
-pair_modify mix arithmetic
-neighbor 2.0 multi
-neigh_modify every 2 delay 4 check yes
-variable input index in.ch3oh.box.dreiding
-variable sname index ch3oh.box.dreiding
-
-compute hb all pair hbond/dreiding/lj
-variable C_hbond equal c_hb[1] #number hbonds
-variable E_hbond equal c_hb[2] #hbond energy
-thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
-thermo_modify line multi format float %14.6f
-
-run 0
-WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
-PPPM initialization ...
-WARNING: System is not charge neutral, net charge = -0.00064 (../kspace.cpp:297)
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
- G vector (1/distance) = 0.142073
- grid = 3 3 3
- stencil order = 5
- estimated absolute RMS force accuracy = 0.154715
- estimated relative force accuracy = 0.00046592
- using double precision FFTs
- 3d grid and FFT values/proc = 392 12
-Neighbor list info ...
- 3 neighbor list requests
- update every 2 steps, delay 4 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 13.5
- ghost atom cutoff = 13.5
- binsize = 6.75 -> bins = 3 3 3
-Memory usage per processor = 9.05502 Mbytes
----------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
-TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000
-PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880
-E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
-E_coul = 597.219740 E_long = -361.164864 v_E_hbond = -69.322152
-v_C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335
-Loop time of 4.52995e-06 on 4 procs for 0 steps with 384 atoms
-
-0.0% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0 | 0 | 0 | 0.0 | 0.00
-Bond | 0 | 0 | 0 | 0.0 | 0.00
-Kspace | 0 | 0 | 0 | 0.0 | 0.00
-Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0 | 0 | 0 | 0.0 | 0.00
-Output | 0 | 0 | 0 | 0.0 | 0.00
-Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 4.53e-06 | | |100.00
-
-Nlocal: 96 ave 104 max 87 min
-Histogram: 1 1 0 0 0 0 0 0 0 2
-Nghost: 3063.25 ave 3108 max 3024 min
-Histogram: 1 0 1 0 0 0 1 0 0 1
-Neighs: 25463.5 ave 28799 max 22471 min
-Histogram: 1 0 0 1 0 1 0 0 0 1
-FullNghs: 50927 ave 55516 max 46073 min
-Histogram: 1 1 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 203708
-Ave neighs/atom = 530.49
-Ave special neighs/atom = 4
-Neighbor list builds = 0
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:00
--
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