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Merge branch 'develop' into fix-mdi-qmmm

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This commit is contained in:
Steve Plimpton
2023-02-02 13:10:55 -07:00
parent b3262684af 11871ceb2e
commit 12079c32de
787 changed files with 21433 additions and 96776 deletions
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8
examples/COUPLE/library/irregular.cpp
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@ -119,7 +119,7 @@ void Irregular::pattern(int n, int *proclist)
for (int i = 0; i < nrecv; i++)
MPI_Irecv(&recvcount[i],1,MPI_INT,MPI_ANY_SOURCE,0,comm,&request[i]);
// barrier to insure receives are posted
// barrier to ensure receives are posted
MPI_Barrier(comm);
@ -128,7 +128,7 @@ void Irregular::pattern(int n, int *proclist)
for (int i = 0; i < nsend; i++)
MPI_Send(&sendcount[i],1,MPI_INT,sendproc[i],0,comm);
// insure all MPI_ANY_SOURCE messages are received
// ensure all MPI_ANY_SOURCE messages are received
// set recvproc
if (nrecv) MPI_Waitall(nrecv,request,status);
@ -270,7 +270,7 @@ void Irregular::exchange_same(char *sendbuf, char *recvbuf)
char *buf = (char *) memory->smalloc(nsendmax,"buf");
// barrier to insure receives are posted
// barrier to ensure receives are posted
MPI_Barrier(comm);
@ -325,7 +325,7 @@ void Irregular::exchange_varying(char *sendbuf, char *recvbuf)
char *buf = (char *) memory->smalloc(nsendmax,"buf");
// barrier to insure receives are posted
// barrier to ensure receives are posted
MPI_Barrier(comm);

2
examples/COUPLE/plugin/liblammpsplugin.h
View File

@ -169,7 +169,7 @@ struct _liblammpsplugin {
void (*scatter_subset)(void *, const char *, int, int, int, int *, void *);
/* lammps_create_atoms() takes tagint and imageint as args
* the ifdef insures they are compatible with rest of LAMMPS
* the ifdef ensures they are compatible with rest of LAMMPS
* caller must match to how LAMMPS library is built */
#ifndef LAMMPS_BIGBIG

11
examples/PACKAGES/mesont/README
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@ -4,16 +4,7 @@
The files in this folder provide examples of using the CNT
mesoscopic force field (MESONT).
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
"bundle" is an example with a single bundle composed of 7 nanotubes
using the mesont/tpm pair style
"film" is an example with a film composed of 396 200-nm-long
nanotubes (79596 nodes) using the mesont/tpm pair style
Contributing author: Philipp Kloza (U Cambridge), pak37@cam.ac.uk
"cnt" is an example showing CNT aerogel formation
"film_mesocnt" is an example showing CNT aerogel formation
using the mesocnt pair style

1
examples/PACKAGES/mesont/TABTP_10_10.mesont
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@ -1 +0,0 @@
../../../potentials/TABTP_10_10.mesont

93
examples/PACKAGES/mesont/data.bundle
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@ -1,93 +0,0 @@
77 atoms
1 atom types
-143.89 143.89 xlo xhi
-143.89 143.89 ylo yhi
0 220 zlo zhi
Masses
1 1.0
Atoms
1 1 1 11 2 5860.43 6.785 20 0 0 0 0 0 0 0
2 1 1 1 3 5860.43 6.785 20 0 0 0 20 0 0 0
3 1 1 2 4 5860.43 6.785 20 0 0 0 40 0 0 0
4 1 1 3 5 5860.43 6.785 20 0 0 0 60 0 0 0
5 1 1 4 6 5860.43 6.785 20 0 0 0 80 0 0 0
6 1 1 5 7 5860.43 6.785 20 0 0 0 100 0 0 0
7 1 1 6 8 5860.43 6.785 20 0 0 0 120 0 0 0
8 1 1 7 9 5860.43 6.785 20 0 0 0 140 0 0 0
9 1 1 8 10 5860.43 6.785 20 0 0 0 160 0 0 0
10 1 1 9 11 5860.43 6.785 20 0 0 0 180 0 0 0
11 1 1 10 1 5860.43 6.785 20 0 0 0 200 0 0 0
12 2 1 22 13 5860.43 6.785 20 0 16.6992 0 0 0 0 0
13 2 1 12 14 5860.43 6.785 20 0 16.6992 0 20 0 0 0
14 2 1 13 15 5860.43 6.785 20 0 16.6992 0 40 0 0 0
15 2 1 14 16 5860.43 6.785 20 0 16.6992 0 60 0 0 0
16 2 1 15 17 5860.43 6.785 20 0 16.6992 0 80 0 0 0
17 2 1 16 18 5860.43 6.785 20 0 16.6992 0 100 0 0 0
18 2 1 17 19 5860.43 6.785 20 0 16.6992 0 120 0 0 0
19 2 1 18 20 5860.43 6.785 20 0 16.6992 0 140 0 0 0
20 2 1 19 21 5860.43 6.785 20 0 16.6992 0 160 0 0 0
21 2 1 20 22 5860.43 6.785 20 0 16.6992 0 180 0 0 0
22 2 1 21 12 5860.43 6.785 20 0 16.6992 0 200 0 0 0
23 3 1 33 24 5860.43 6.785 20 0 8.3496 14.4619 0 0 0 0
24 3 1 23 25 5860.43 6.785 20 0 8.3496 14.4619 20 0 0 0
25 3 1 24 26 5860.43 6.785 20 0 8.3496 14.4619 40 0 0 0
26 3 1 25 27 5860.43 6.785 20 0 8.3496 14.4619 60 0 0 0
27 3 1 26 28 5860.43 6.785 20 0 8.3496 14.4619 80 0 0 0
28 3 1 27 29 5860.43 6.785 20 0 8.3496 14.4619 100 0 0 0
29 3 1 28 30 5860.43 6.785 20 0 8.3496 14.4619 120 0 0 0
30 3 1 29 31 5860.43 6.785 20 0 8.3496 14.4619 140 0 0 0
31 3 1 30 32 5860.43 6.785 20 0 8.3496 14.4619 160 0 0 0
32 3 1 31 33 5860.43 6.785 20 0 8.3496 14.4619 180 0 0 0
33 3 1 32 23 5860.43 6.785 20 0 8.3496 14.4619 200 0 0 0
34 4 1 44 35 5860.43 6.785 20 0 -8.3496 14.4619 0 0 0 0
35 4 1 34 36 5860.43 6.785 20 0 -8.3496 14.4619 20 0 0 0
36 4 1 35 37 5860.43 6.785 20 0 -8.3496 14.4619 40 0 0 0
37 4 1 36 38 5860.43 6.785 20 0 -8.3496 14.4619 60 0 0 0
38 4 1 37 39 5860.43 6.785 20 0 -8.3496 14.4619 80 0 0 0
39 4 1 38 40 5860.43 6.785 20 0 -8.3496 14.4619 100 0 0 0
40 4 1 39 41 5860.43 6.785 20 0 -8.3496 14.4619 120 0 0 0
41 4 1 40 42 5860.43 6.785 20 0 -8.3496 14.4619 140 0 0 0
42 4 1 41 43 5860.43 6.785 20 0 -8.3496 14.4619 160 0 0 0
43 4 1 42 44 5860.43 6.785 20 0 -8.3496 14.4619 180 0 0 0
44 4 1 43 34 5860.43 6.785 20 0 -8.3496 14.4619 200 0 0 0
45 5 1 55 46 5860.43 6.785 20 0 -16.6992 0 0 0 0 0
46 5 1 45 47 5860.43 6.785 20 0 -16.6992 0 20 0 0 0
47 5 1 46 48 5860.43 6.785 20 0 -16.6992 0 40 0 0 0
48 5 1 47 49 5860.43 6.785 20 0 -16.6992 0 60 0 0 0
49 5 1 48 50 5860.43 6.785 20 0 -16.6992 0 80 0 0 0
50 5 1 49 51 5860.43 6.785 20 0 -16.6992 0 100 0 0 0
51 5 1 50 52 5860.43 6.785 20 0 -16.6992 0 120 0 0 0
52 5 1 51 53 5860.43 6.785 20 0 -16.6992 0 140 0 0 0
53 5 1 52 54 5860.43 6.785 20 0 -16.6992 0 160 0 0 0
54 5 1 53 55 5860.43 6.785 20 0 -16.6992 0 180 0 0 0
55 5 1 54 45 5860.43 6.785 20 0 -16.6992 0 200 0 0 0
56 6 1 66 57 5860.43 6.785 20 0 -8.3496 -14.4619 0 0 0 0
57 6 1 56 58 5860.43 6.785 20 0 -8.3496 -14.4619 20 0 0 0
58 6 1 57 59 5860.43 6.785 20 0 -8.3496 -14.4619 40 0 0 0
59 6 1 58 60 5860.43 6.785 20 0 -8.3496 -14.4619 60 0 0 0
60 6 1 59 61 5860.43 6.785 20 0 -8.3496 -14.4619 80 0 0 0
61 6 1 60 62 5860.43 6.785 20 0 -8.3496 -14.4619 100 0 0 0
62 6 1 61 63 5860.43 6.785 20 0 -8.3496 -14.4619 120 0 0 0
63 6 1 62 64 5860.43 6.785 20 0 -8.3496 -14.4619 140 0 0 0
64 6 1 63 65 5860.43 6.785 20 0 -8.3496 -14.4619 160 0 0 0
65 6 1 64 66 5860.43 6.785 20 0 -8.3496 -14.4619 180 0 0 0
66 6 1 65 56 5860.43 6.785 20 0 -8.3496 -14.4619 200 0 0 0
67 7 1 77 68 5860.43 6.785 20 0 8.3496 -14.4619 0 0 0 0
68 7 1 67 69 5860.43 6.785 20 0 8.3496 -14.4619 20 0 0 0
69 7 1 68 70 5860.43 6.785 20 0 8.3496 -14.4619 40 0 0 0
70 7 1 69 71 5860.43 6.785 20 0 8.3496 -14.4619 60 0 0 0
71 7 1 70 72 5860.43 6.785 20 0 8.3496 -14.4619 80 0 0 0
72 7 1 71 73 5860.43 6.785 20 0 8.3496 -14.4619 100 0 0 0
73 7 1 72 74 5860.43 6.785 20 0 8.3496 -14.4619 120 0 0 0
74 7 1 73 75 5860.43 6.785 20 0 8.3496 -14.4619 140 0 0 0
75 7 1 74 76 5860.43 6.785 20 0 8.3496 -14.4619 160 0 0 0
76 7 1 75 77 5860.43 6.785 20 0 8.3496 -14.4619 180 0 0 0
77 7 1 76 67 5860.43 6.785 20 0 8.3496 -14.4619 200 0 0 0

79612
examples/PACKAGES/mesont/data.film
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File diff suppressed because it is too large Load Diff

29
examples/PACKAGES/mesont/in.bundle
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@ -1,29 +0,0 @@
processors 1 1 *
newton on
units metal
lattice sc 1.0
boundary fs fs p
neighbor 1.0 bin
neigh_modify every 5 delay 0 check yes
atom_style mesont
# cut, path, BendingMode, TPMType
pair_style mesont/tpm 45.0 MESONT-TABTP_10_10.xrs 0 0
read_data data.bundle
pair_coeff * *
velocity all create 6000.0 2019
timestep 0.005
fix 1 all nve
thermo 10
reset_timestep 0
compute Es all mesont estretch
compute Eb all mesont ebend
compute Et all mesont etube
compute B all property/atom buckling
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
#dump out_dump all custom 50 dump.bundle id type x y z c_Es c_Eb c_Et c_B ix iy iz
run 100

28
examples/PACKAGES/mesont/in.film
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@ -1,28 +0,0 @@
newton on
units metal
lattice sc 1.0
boundary p p fs
neighbor 1.0 bin
neigh_modify every 5 delay 0 check yes
atom_style mesont
# cut, path, BendingMode, TPMType
pair_style mesont/tpm 30.0 MESONT-TABTP_10_10.xrs 1 0
read_data data.film
pair_coeff * *
velocity all create 600.0 2019
timestep 0.01
fix 1 all nve
thermo 10
reset_timestep 0
compute Es all mesont estretch
compute Eb all mesont ebend
compute Et all mesont etube
compute B all property/atom buckling
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
#dump out_dump all custom 10 dump.film id type x y z c_Es c_Eb c_Et c_B ix iy iz
run 20

90
examples/PACKAGES/mesont/log.2Jun2020.bundle.g++.1
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@ -1,90 +0,0 @@
LAMMPS (5 May 2020)
processors 1 1 *
newton on
units metal
lattice sc 1.0
Lattice spacing in x,y,z = 1 1 1
boundary fs fs p
neighbor 1.0 bin
neigh_modify every 5 delay 0 check yes
atom_style mesont
# cut, path, BendingMode, TPMType
pair_style mesont/tpm 45.0 MESONT-TABTP_10_10.xrs 0 0
read_data data.bundle
orthogonal box = (-143.89 -143.89 0) to (143.89 143.89 220)
1 by 1 by 1 MPI processor grid
reading atoms ...
77 atoms
read_data CPU = 0.000613213 secs
pair_coeff * *
velocity all create 6000.0 2019
timestep 0.005
fix 1 all nve
thermo 10
reset_timestep 0
compute Es all mesont estretch
compute Eb all mesont ebend
compute Et all mesont etube
compute B all property/atom buckling
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
#dump out_dump all custom 50 dump.bundle id type x y z c_Es c_Eb c_Et c_B ix iy iz
run 100
Neighbor list info ...
update every 5 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 46
ghost atom cutoff = 46
binsize = 23, bins = 7 7 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mesont/tpm, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.675 | 4.675 | 4.675 Mbytes
Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et
0 0 6000 -201.86935 58.942626 -260.81198 0 0 -260.81198
10 0.05 5114.1875 -201.86234 50.240607 -252.10295 4.8334861 2.3998206 -259.33626
20 0.1 3437.2958 -201.8522 33.767207 -235.61941 11.42384 8.3426957 -255.38594
30 0.15 2430.6571 -201.85242 23.878219 -225.73064 10.346152 14.72688 -250.80367
40 0.2 2154.4755 -201.85683 21.165074 -223.0219 6.8146112 18.325709 -248.16222
50 0.25 2021.7899 -201.85503 19.861601 -221.71663 9.2972022 17.644143 -248.65798
60 0.3 2234.553 -201.85193 21.951737 -223.80367 13.541921 13.673721 -251.01931
70 0.35 3099.6503 -201.85721 30.450255 -232.30747 11.833679 9.0583807 -253.19953
80 0.4 3849.9855 -201.8635 37.821376 -239.68487 7.9899173 6.4332848 -254.10807
90 0.45 3618.1311 -201.85967 35.543692 -237.40336 9.2616931 7.0452637 -253.71032
100 0.5 2866.2722 -201.85273 28.157602 -230.01033 12.204916 10.284525 -252.49977
Loop time of 0.419735 on 1 procs for 100 steps with 77 atoms
Performance: 102.922 ns/day, 0.233 hours/ns, 238.245 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.41922 | 0.41922 | 0.41922 | 0.0 | 99.88
Neigh | 5.8174e-05 | 5.8174e-05 | 5.8174e-05 | 0.0 | 0.01
Comm | 7.0333e-05 | 7.0333e-05 | 7.0333e-05 | 0.0 | 0.02
Output | 0.00017667 | 0.00017667 | 0.00017667 | 0.0 | 0.04
Modify | 0.00011945 | 0.00011945 | 0.00011945 | 0.0 | 0.03
Other | | 8.702e-05 | | | 0.02
Nlocal: 77 ave 77 max 77 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 35 ave 35 max 35 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 2222 ave 2222 max 2222 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2222
Ave neighs/atom = 28.8571
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:01

90
examples/PACKAGES/mesont/log.2Jun2020.bundle.g++.4
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@ -1,90 +0,0 @@
LAMMPS (5 May 2020)
processors 1 1 *
newton on
units metal
lattice sc 1.0
Lattice spacing in x,y,z = 1 1 1
boundary fs fs p
neighbor 1.0 bin
neigh_modify every 5 delay 0 check yes
atom_style mesont
# cut, path, BendingMode, TPMType
pair_style mesont/tpm 45.0 MESONT-TABTP_10_10.xrs 0 0
read_data data.bundle
orthogonal box = (-143.89 -143.89 0) to (143.89 143.89 220)
1 by 1 by 4 MPI processor grid
reading atoms ...
77 atoms
read_data CPU = 0.000590563 secs
pair_coeff * *
velocity all create 6000.0 2019
timestep 0.005
fix 1 all nve
thermo 10
reset_timestep 0
compute Es all mesont estretch
compute Eb all mesont ebend
compute Et all mesont etube
compute B all property/atom buckling
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
#dump out_dump all custom 50 dump.bundle id type x y z c_Es c_Eb c_Et c_B ix iy iz
run 100
Neighbor list info ...
update every 5 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 46
ghost atom cutoff = 46
binsize = 23, bins = 7 7 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mesont/tpm, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.671 | 4.671 | 4.671 Mbytes
Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et
0 0 6000 -201.86935 58.942626 -260.81198 0 0 -260.81198
10 0.05 5114.1875 -201.86234 50.240607 -252.10295 4.8334861 2.3998206 -259.33626
20 0.1 3437.2958 -201.8522 33.767207 -235.61941 11.42384 8.3426957 -255.38594
30 0.15 2430.6571 -201.85242 23.878219 -225.73064 10.346152 14.72688 -250.80367
40 0.2 2154.4755 -201.85683 21.165074 -223.0219 6.8146112 18.325709 -248.16222
50 0.25 2021.7899 -201.85503 19.861601 -221.71663 9.2972022 17.644143 -248.65798
60 0.3 2234.553 -201.85193 21.951737 -223.80367 13.541921 13.673721 -251.01931
70 0.35 3099.6503 -201.85721 30.450255 -232.30747 11.833679 9.0583807 -253.19953
80 0.4 3849.9855 -201.8635 37.821376 -239.68487 7.9899173 6.4332848 -254.10807
90 0.45 3618.1311 -201.85967 35.543692 -237.40336 9.2616931 7.0452637 -253.71032
100 0.5 2866.2722 -201.85273 28.157602 -230.01033 12.204916 10.284525 -252.49977
Loop time of 0.145545 on 4 procs for 100 steps with 77 atoms
Performance: 296.815 ns/day, 0.081 hours/ns, 687.071 timesteps/s
95.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.046723 | 0.097529 | 0.14388 | 11.0 | 67.01
Neigh | 2.5511e-05 | 2.8729e-05 | 3.171e-05 | 0.0 | 0.02
Comm | 0.00058556 | 0.045174 | 0.098462 | 16.5 | 31.04
Output | 0.0001483 | 0.0010182 | 0.002851 | 3.5 | 0.70
Modify | 3.8147e-05 | 4.065e-05 | 4.4107e-05 | 0.0 | 0.03
Other | | 0.001755 | | | 1.21
Nlocal: 19.25 ave 21 max 16 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 33.25 ave 40 max 28 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 555.5 ave 606 max 460 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 2222
Ave neighs/atom = 28.8571
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:01

81
examples/PACKAGES/mesont/log.2Jun2020.film.g++.1
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@ -1,81 +0,0 @@
LAMMPS (5 May 2020)
newton on
units metal
lattice sc 1.0
Lattice spacing in x,y,z = 1 1 1
boundary p p fs
neighbor 1.0 bin
neigh_modify every 5 delay 0 check yes
atom_style mesont
# cut, path, BendingMode, TPMType
pair_style mesont/tpm 30.0 MESONT-TABTP_10_10.xrs 1 0
read_data data.film
orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42)
1 by 1 by 1 MPI processor grid
reading atoms ...
79596 atoms
read_data CPU = 0.0860629 secs
pair_coeff * *
velocity all create 600.0 2019
timestep 0.01
fix 1 all nve
thermo 10
reset_timestep 0
compute Es all mesont estretch
compute Eb all mesont ebend
compute Et all mesont etube
compute B all property/atom buckling
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
#dump out_dump all custom 10 dump.film id type x y z c_Es c_Eb c_Et c_B ix iy iz
run 20
Neighbor list info ...
update every 5 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 31
ghost atom cutoff = 31
binsize = 15.5, bins = 323 323 26
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mesont/tpm, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 37.43 | 37.43 | 37.43 Mbytes
Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et
0 0 600 1347.2158 6173.0767 -4825.8609 28.669574 21.29406 -4875.8245
10 0.1 389.40755 1373.7864 4006.4045 -2632.6181 848.00267 1404.4323 -4885.053
20 0.2 313.65714 1399.9427 3227.0494 -1827.1067 1201.1732 1882.1342 -4910.4141
Loop time of 10.2438 on 1 procs for 20 steps with 79596 atoms
Performance: 1.687 ns/day, 14.228 hours/ns, 1.952 timesteps/s
99.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.226 | 10.226 | 10.226 | 0.0 | 99.82
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00081086 | 0.00081086 | 0.00081086 | 0.0 | 0.01
Output | 0.00046563 | 0.00046563 | 0.00046563 | 0.0 | 0.00
Modify | 0.015165 | 0.015165 | 0.015165 | 0.0 | 0.15
Other | | 0.001869 | | | 0.02
Nlocal: 79596 ave 79596 max 79596 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1879 ave 1879 max 1879 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 642270 ave 642270 max 642270 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 642270
Ave neighs/atom = 8.06912
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:11

81
examples/PACKAGES/mesont/log.2Jun2020.film.g++.4
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@ -1,81 +0,0 @@
LAMMPS (5 May 2020)
newton on
units metal
lattice sc 1.0
Lattice spacing in x,y,z = 1 1 1
boundary p p fs
neighbor 1.0 bin
neigh_modify every 5 delay 0 check yes
atom_style mesont
# cut, path, BendingMode, TPMType
pair_style mesont/tpm 30.0 MESONT-TABTP_10_10.xrs 1 0
read_data data.film
orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42)
2 by 2 by 1 MPI processor grid
reading atoms ...
79596 atoms
read_data CPU = 0.0704217 secs
pair_coeff * *
velocity all create 600.0 2019
timestep 0.01
fix 1 all nve
thermo 10
reset_timestep 0
compute Es all mesont estretch
compute Eb all mesont ebend
compute Et all mesont etube
compute B all property/atom buckling
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
#dump out_dump all custom 10 dump.film id type x y z c_Es c_Eb c_Et c_B ix iy iz
run 20
Neighbor list info ...
update every 5 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 31
ghost atom cutoff = 31
binsize = 15.5, bins = 323 323 26
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mesont/tpm, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.81 | 12.81 | 12.83 Mbytes
Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et
0 0 600 1347.2158 6173.0767 -4825.8609 28.669574 21.29406 -4875.8245
10 0.1 389.40755 1373.7864 4006.4045 -2632.6181 848.00267 1404.4323 -4885.053
20 0.2 313.65714 1399.9427 3227.0494 -1827.1067 1201.1732 1882.1342 -4910.4141
Loop time of 3.67186 on 4 procs for 20 steps with 79596 atoms
Performance: 4.706 ns/day, 5.100 hours/ns, 5.447 timesteps/s
95.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.7317 | 3.1286 | 3.6556 | 18.8 | 85.20
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0036943 | 0.53094 | 0.92822 | 45.8 | 14.46
Output | 0.00026512 | 0.00035298 | 0.00055647 | 0.0 | 0.01
Modify | 0.010463 | 0.010884 | 0.011153 | 0.3 | 0.30
Other | | 0.001109 | | | 0.03
Nlocal: 19899 ave 21951 max 18667 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost: 970.75 ave 1031 max 920 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 160568 ave 181723 max 147382 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 642270
Ave neighs/atom = 8.06912
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:04

17
examples/PACKAGES/pimd/para-h2/in.scp
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@ -1,5 +1,5 @@
variable ibead uloop 32 pad
variable out_freq string 1
variable out_freq string 100
variable job_name string H2
units real
@ -13,17 +13,18 @@ read_data H2.data
pair_coeff 1 * pair.table PAIR_H2
timestep 0.001
thermo_style custom step temp pe etotal pzz
thermo ${out_freq}
timestep 0.001
velocity all create 1.0 1985 rot yes dist gaussian
fix 1 all pimd method nmpimd fmass 1.0 temp 25.0 nhc 4
dump dcd all dcd ${out_freq} dcd/${job_name}_${ibead}.dcd
thermo_style custom step temp pe etotal pzz f_1[1] f_1[2] f_1[3]
thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
thermo ${out_freq}
restart ${out_freq} restart/${job_name}_${ibead}.restart1 restart/${job_name}_${ibead}.restart2
#dump dcd all dcd ${out_freq} ${job_name}_${ibead}.dcd
run 100000
#restart ${out_freq} ${job_name}_${ibead}.restart1 ${job_name}_${ibead}.restart2
run 10000

2
examples/PACKAGES/pimd/para-h2/run.sh
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@ -1 +1 @@
mpirun -np 64 lmp_mpi -partition 8x8 -in in.scp -log logfile/log.lammps -screen screen/screen
mpirun -np 64 lmp_mpi -partition 8x8 -in in.scp -log log.lammps -screen none

11
examples/PACKAGES/pimd/prot-hairpin/in.scp
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@ -14,18 +14,19 @@ pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data system.data
#read_restart restart/system_${ibead}.rest1
#read_restart system_${ibead}.rest1
special_bonds charmm
fix 1 all pimd method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0
thermo 10
thermo_style custom step temp pe etotal
thermo_style custom step temp pe etotal f_1[1] f_1[2] f_1[3]
thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
timestep 0.08
restart 100 restart/system_${ibead}.rest1 restart/system_${ibead}.rest2
# restart 100 system_${ibead}.rest1 system_${ibead}.rest2
group prot id <= 256
dump 1 prot dcd 100 dcd/prot_${ibead}.dcd
# dump 1 prot dcd 100 prot_${ibead}.dcd
run 2000000
run 200

2
examples/PACKAGES/pimd/prot-hairpin/run.sh
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@ -1 +1 @@
mpirun -np 8 lmp_mpi -partition 8x1 -in in.scp -log logfile/log.lammps -screen screen/screen
mpirun -np 8 lmp_mpi -partition 8x1 -in in.scp -log log.lammps -screen none

2
examples/QUANTUM/LATTE/README
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@ -79,7 +79,7 @@ Copy the LAMMPS executable (lmp_mpi or lmp) into this dir as lmp_mpi.
Copy the LATTE executable LATTE_DOUBLE into this dir.
The run commands below assume you have done this.
(5) Insure LD_LIBRARY_PATH includes the dir where MDI was built in (1)
(5) Ensure LD_LIBRARY_PATH includes the dir where MDI was built in (1)
with its libmdi.so file, e.g. mdi/build/MDI_Library. This is needed
so when LATTE_DOUBLE runs as an executable it will able to find
libmdi.so.

30
examples/meam/msmeam/HGa.meam Normal file
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@ -0,0 +1,30 @@
bkgd_dyn = 1
emb_lin_neg = 1
augt1=0
ialloy=1
rc = 5.9
#H
attrac(1,1)=0.460
repuls(1,1)=0.460
Cmin(1,1,1)=1.3 # PuMS
Cmax(1,1,1)= 2.80
nn2(1,1)=1
#Ga
rho0(2) = 0.6
attrac(2,2)=0.097
repuls(2,2)=0.097
nn2(2,2)=1
#HGa
attrac(1,2)=0.300
repuls(1,2)=0.300
lattce(1,2)=l12
re(1,2)=3.19
delta(1,2)=-0.48
alpha(1,2)=6.6
Cmin(1,1,2)=2.0
Cmin(2,1,2)= 2.0
Cmin(1,2,1)=2.0
Cmin(2,2,1) = 1.4
Cmin(1,2,2) = 1.4
Cmin(1,1,2) = 1.4
nn2(1,2)=1

9
examples/meam/msmeam/README.md Normal file
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@ -0,0 +1,9 @@
To run Baske's test, do
lmp -in in.msmeam
Then
diff dump.msmeam dump.msmeam.bu

25
examples/meam/msmeam/data.msmeam.bu Normal file
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@ -0,0 +1,25 @@
LAMMPS data file via write_data, version 16 Feb 2016, timestep = 1
3 atoms
2 atom types
-4.0000000000000000e+00 4.0000000000000000e+00 xlo xhi
-4.0000000000000000e+00 4.0000000000000000e+00 ylo yhi
-4.0000000000000000e+00 4.0000000000000000e+00 zlo zhi
Masses
1 1.0079
2 69.723
Atoms # atomic
1 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
2 2 2.2000000000000002e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
3 2 2.9999999999999999e-01 2.2999999999999998e+00 0.0000000000000000e+00 0 0 0
Velocities
1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00

24
examples/meam/msmeam/dump.msmeam.bu Normal file
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@ -0,0 +1,24 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
3
ITEM: BOX BOUNDS pp pp pp
-4 4
-4 4
-4 4
ITEM: ATOMS id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
1 0 0 0 -131.925 -88.3005 0 22.9153 -2.147e+08 -1.62661e+08 -0 -2.05301e+07 -0 -0
2 2.2 0 0 120.809 -0.482171 0 14.7692 -2.12028e+08 -0 -0 403352 -0 -0
3 0.3 2.3 0 11.1159 88.7827 0 8.61478 -2.67145e+06 -1.62661e+08 -0 -2.09335e+07 -0 -0
ITEM: TIMESTEP
1
ITEM: NUMBER OF ATOMS
3
ITEM: BOX BOUNDS pp pp pp
-4 4
-4 4
-4 4
ITEM: ATOMS id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
1 0 0 0 -131.925 -88.3005 0 22.9153 -2.147e+08 -1.62661e+08 -0 -2.05301e+07 -0 -0
2 2.2 0 0 120.809 -0.482171 0 14.7692 -2.12028e+08 -0 -0 403352 -0 -0
3 0.3 2.3 0 11.1159 88.7827 0 8.61478 -2.67145e+06 -1.62661e+08 -0 -2.09335e+07 -0 -0

31
examples/meam/msmeam/in.msmeam Normal file
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@ -0,0 +1,31 @@
echo both
log log.msmeam
# Test of MEAM potential for HGa
# ------------------------ INITIALIZATION ----------------------------
units metal
dimension 3
boundary p p p
atom_style atomic
variable latparam equal 4.646
variable ncell equal 3
# ----------------------- ATOM DEFINITION ----------------------------
region box block -4 4 -4 4 -4 4
create_box 2 box
#
include potential.mod
create_atoms 1 single 0 0 0 units box
create_atoms 2 single 2.2 0 0 units box
create_atoms 2 single 0.3 2.3 0 units box
# ---------- Define Settings ---------------------
variable teng equal "c_eatoms"
compute pot_energy all pe/atom
compute stress all stress/atom NULL
dump 1 all custom 1 dump.msmeam id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
run 1
write_data data.msmeam
print "All done!"

14
examples/meam/msmeam/library.msmeam Normal file
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@ -0,0 +1,14 @@
# DATE: 2018-09-22 UNITS: metal CONTRIBUTOR: Steve Valone, smv@lanl.gov CITATION: Baskes, PRB 1992; smv, sr, mib, JNM 2010
# ms-meam data format May 2010
# elt lat z ielement atwt
# alpha b0 b1 b2 b3 b1m b2m b3m alat esub asub
# - t0 t1 t2 t3 t1m t2m t3m rozero ibar
# NOTE: leading character cannot be a space
'H' 'dim' 1.0 1 1.0079
2.960 2.960 3.0 1.0 1.0 1.0 3.0 1.0 0.741 2.235 2.50
1.0 0.44721 0.0 0.00 0.0 0.31623 0 6.70 0
'Ga4' 'fcc' 12.0 31 69.723
4.42 4.80 3.10 6.00 0.00 0.0 0.0 0.5 4.247 2.897 0.97
1.0 1.649 1.435 0.00 0.0 0.0 2.0 0.70 0

107
examples/meam/msmeam/log.msmeam.bu Normal file
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@ -0,0 +1,107 @@
# Test of MEAM potential for HGa
# ------------------------ INITIALIZATION ----------------------------
units metal
dimension 3
boundary p p p
atom_style atomic
variable latparam equal 4.646
variable ncell equal 3
# ----------------------- ATOM DEFINITION ----------------------------
region box block -4 4 -4 4 -4 4
create_box 2 box
Created orthogonal box = (-4 -4 -4) to (4 4 4)
1 by 1 by 1 MPI processor grid
#
include potential.mod
# NOTE: This script can be modified for different pair styles
# See in.elastic for more info.
variable Pu string H
print "potential chosen ${Pu}"
potential chosen H
# Choose potential
pair_style MSmeam
print "we just executed"
we just executed
pair_coeff * * library.MSmeam ${Pu} Ga4 HGaMS.meam ${Pu} Ga4
pair_coeff * * library.MSmeam H Ga4 HGaMS.meam ${Pu} Ga4
pair_coeff * * library.MSmeam H Ga4 HGaMS.meam H Ga4
Reading potential file library.MSmeam with DATE: 2018-09-22
# Setup neighbor style
neighbor 1.0 nsq
neigh_modify once no every 1 delay 0 check yes
# Setup minimization style
variable dmax equal 1.0e-2
min_style cg
min_modify dmax ${dmax} line quadratic
min_modify dmax 0.01 line quadratic
compute eng all pe/atom
compute eatoms all reduce sum c_eng
# Setup output
thermo 100
thermo_style custom step temp etotal press pxx pyy pzz pxy pxz pyz lx ly lz vol c_eatoms
thermo_modify norm yes
create_atoms 1 single 0 0 0 units box
Created 1 atoms
create_atoms 2 single 2.2 0 0 units box
Created 1 atoms
create_atoms 2 single 0.3 2.3 0 units box
Created 1 atoms
# ---------- Define Settings ---------------------
variable teng equal "c_eatoms"
compute pot_energy all pe/atom
compute stress all stress/atom NULL
dump 1 all custom 1 dump.msmeam id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
run 1
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.9
ghost atom cutoff = 6.9
Memory usage per processor = 12.9295 Mbytes
Step Temp TotEng Press Pxx Pyy Pzz Pxy Pxz Pyz Lx Ly Lz Volume eatoms
0 0 15.433079 491354.68 838670.91 635393.13 0 80195.793 0 0 8 8 8 512 15.433079
1 0 15.433079 491354.68 838670.91 635393.13 0 80195.793 0 0 8 8 8 512 15.433079
Loop time of 0.000172138 on 1 procs for 1 steps with 3 atoms
Performance: 501.922 ns/day, 0.048 hours/ns, 5809.285 timesteps/s
81.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.6996e-05 | 6.6996e-05 | 6.6996e-05 | 0.0 | 38.92
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.9073e-06 | 1.9073e-06 | 1.9073e-06 | 0.0 | 1.11
Output | 9.7036e-05 | 9.7036e-05 | 9.7036e-05 | 0.0 | 56.37
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 6.199e-06 | | | 3.60
Nlocal: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 78 ave 78 max 78 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7 ave 7 max 7 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 14 ave 14 max 14 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14
Ave neighs/atom = 4.66667
Neighbor list builds = 0
Dangerous builds = 0
write_data data.msmeam
print "All done!"
All done!
Total wall time: 0:00:00

24
examples/meam/msmeam/msmeam.dump.bu Normal file
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@ -0,0 +1,24 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
3
ITEM: BOX BOUNDS pp pp pp
-4 4
-4 4
-4 4
ITEM: ATOMS id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
1 0 0 0 -131.925 -88.3005 0 22.9153 -2.147e+08 -1.62661e+08 -0 -2.05301e+07 -0 -0
2 2.2 0 0 120.809 -0.482171 0 14.7692 -2.12028e+08 -0 -0 403352 -0 -0
3 0.3 2.3 0 11.1159 88.7827 0 8.61478 -2.67145e+06 -1.62661e+08 -0 -2.09335e+07 -0 -0
ITEM: TIMESTEP
1
ITEM: NUMBER OF ATOMS
3
ITEM: BOX BOUNDS pp pp pp
-4 4
-4 4
-4 4
ITEM: ATOMS id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
1 0 0 0 -131.925 -88.3005 0 22.9153 -2.147e+08 -1.62661e+08 -0 -2.05301e+07 -0 -0
2 2.2 0 0 120.809 -0.482171 0 14.7692 -2.12028e+08 -0 -0 403352 -0 -0
3 0.3 2.3 0 11.1159 88.7827 0 8.61478 -2.67145e+06 -1.62661e+08 -0 -2.09335e+07 -0 -0

25
examples/meam/msmeam/potential.mod Normal file
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@ -0,0 +1,25 @@
# NOTE: This script can be modified for different pair styles
# See in.elastic for more info.
variable Pu string H
print "potential chosen ${Pu}"
# Choose potential
pair_style meam/ms
print "we just executed"
pair_coeff * * library.msmeam ${Pu} Ga4 HGa.meam ${Pu} Ga4
# Setup neighbor style
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# Setup minimization style
variable dmax equal 1.0e-2
min_style cg
min_modify dmax ${dmax} line quadratic
compute eng all pe/atom
compute eatoms all reduce sum c_eng
# Setup output
thermo 100
thermo_style custom step temp etotal press pxx pyy pzz pxy pxz pyz lx ly lz vol c_eatoms
thermo_modify norm yes

11
examples/neb/log.14Jan23.neb.hop1.end.g++.4 Normal file
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@ -0,0 +1,11 @@
LAMMPS (22 Dec 2022)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4
0 229.26196 21515.76 2.9774577 4.4127369 233.11559 0.023301843 0.0224626 1.4763579 0 -3.048332 0.33333333 -3.0250302 0.66666667 -3.0291888 1 -3.0474928
100 0.11027532 0.0072949206 3.0967938 0.024201563 0.38551033 0.0017583261 0.0021866943 1.7710358 0 -3.0483469 0.31192818 -3.0465886 0.61093022 -3.0466143 1 -3.0487752
130 0.09954083 0.0056973977 3.0927626 0.015664388 0.37491833 0.0017573704 0.0021913201 1.7713726 0 -3.048342 0.31428487 -3.0465846 0.61762817 -3.0466296 1 -3.048776
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4
130 0.37838747 0.12267051 3.0927626 0.015664388 0.37491833 0.0017573704 0.0021913201 1.7713726 0 -3.048342 0.31428487 -3.0465846 0.61762817 -3.0466296 1 -3.048776
230 0.14827532 0.015635771 3.1230352 0.0083310795 0.14070676 0.0018353858 0.0022776729 1.769345 0 -3.0483349 0.39530832 -3.0464995 0.64330942 -3.046694 1 -3.0487772
279 0.099842536 0.0074295981 3.1400424 0.0068603912 0.095180758 0.0018424455 0.0022860594 1.7685036 0 -3.0483338 0.41228692 -3.0464914 0.65522525 -3.0467282 1 -3.0487775

10
examples/neb/log.14Jan23.neb.hop1.end.g++.8 Normal file
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@ -0,0 +1,10 @@
LAMMPS (22 Dec 2022)
Running on 8 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4 RD5 PE5 RD6 PE6 RD7 PE7 RD8 PE8
0 353.31221 52709.758 2.9774577 4.4127369 354.16808 0.035499368 0.034660125 1.4763579 0 -3.048332 0.14285714 -3.0450092 0.28571429 -3.0318848 0.42857143 -3.0128327 0.57142857 -3.0157894 0.71428571 -3.0354827 0.85714286 -3.0458819 1 -3.0474928
100 0.18371802 0.016897952 3.0181603 0.026618267 0.11111596 0.0018567895 0.0022827846 1.8009397 0 -3.0483491 0.13062498 -3.0471842 0.26462893 -3.0466755 0.40763124 -3.0464923 0.53986455 -3.0465208 0.68351825 -3.0468184 0.81489539 -3.0476023 1 -3.0487751
182 0.099603091 0.0039050116 3.0068142 0.010832038 0.074630455 0.001848721 0.0022882994 1.8108868 0 -3.0483371 0.13698322 -3.0471393 0.27599082 -3.0466464 0.41841798 -3.0464884 0.55670019 -3.046546 0.69926219 -3.0469046 0.83686246 -3.0478727 1 -3.0487767
Climbing replica = 4
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4 RD5 PE5 RD6 PE6 RD7 PE7 RD8 PE8
182 0.093479786 0.0046539741 3.0068142 0.010832038 0.074630455 0.001848721 0.0022882994 1.8108868 0 -3.0483371 0.13698322 -3.0471393 0.27599082 -3.0466464 0.41841798 -3.0464884 0.55670019 -3.046546 0.69926219 -3.0469046 0.83686246 -3.0478727 1 -3.0487767
183 0.093479786 0.0046539741 3.0068142 0.010832038 0.074630455 0.001848721 0.0022882994 1.8108868 0 -3.0483371 0.13698322 -3.0471393 0.27599082 -3.0466464 0.41841798 -3.0464884 0.55670019 -3.046546 0.69926219 -3.0469046 0.83686246 -3.0478727 1 -3.0487767

9
examples/neb/log.14Jan23.neb.hop1.g++.4 Normal file
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@ -0,0 +1,9 @@
LAMMPS (22 Dec 2022)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4
0 4327.2753 7542371.4 0.082169072 4.9967651 4514.5424 0.42933428 0.42323635 1.8941131 0 -3.0535948 0.33333333 -2.6242605 0.66666667 -2.7623811 1 -3.0474969
87 0.095951502 0.0027794936 0.005588927 0.065110105 0.12467831 0.0071014928 0.0022798007 2.3003372 0 -3.0535967 0.32435271 -3.0473127 0.62805027 -3.0464952 1 -3.048775
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4
87 0.14137277 0.012340886 0.005588927 0.065110105 0.12467831 0.0071014928 0.0022798007 2.3003372 0 -3.0535967 0.32435271 -3.0473127 0.62805027 -3.0464952 1 -3.048775
124 0.099583263 0.0073851506 0.0044220372 0.023873795 0.091308308 0.0071061754 0.0022863931 2.308121 0 -3.0535968 0.32223905 -3.0473329 0.61673898 -3.0464906 1 -3.048777

10
examples/neb/log.14Jan23.neb.hop1.g++.8 Normal file
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@ -0,0 +1,10 @@
LAMMPS (22 Dec 2022)
Running on 8 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4 RD5 PE5 RD6 PE6 RD7 PE7 RD8 PE8
0 12172.47 48315818 0.082169072 4.9967651 12254.987 1.1034547 1.0973568 1.8941131 0 -3.0535948 0.14285714 -3.0398884 0.28571429 -2.8426874 0.42857143 -1.9501401 0.57142857 -2.1439119 0.71428571 -2.9187789 0.85714286 -3.0422538 1 -3.0474969
100 0.14433533 0.0056834028 0.0051714625 0.047051976 0.11774619 0.0071018066 0.002280994 2.3772214 0 -3.0535967 0.12651739 -3.0512933 0.26516133 -3.0480936 0.41814034 -3.0467867 0.55534109 -3.0464949 0.69779433 -3.0465932 0.83399724 -3.0472934 1 -3.0487759
147 0.098667494 0.0031400895 0.0040851637 0.017209593 0.096695061 0.007103925 0.002284434 2.3892288 0 -3.0535968 0.13266908 -3.051146 0.27206276 -3.0479976 0.42113052 -3.046774 0.55968697 -3.0464929 0.7017833 -3.0466074 0.8397451 -3.0473745 1 -3.0487774
Climbing replica = 5
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4 RD5 PE5 RD6 PE6 RD7 PE7 RD8 PE8
147 0.10065405 0.0077673218 0.0040851637 0.017209593 0.096695061 0.007103925 0.002284434 2.3892288 0 -3.0535968 0.13266908 -3.051146 0.27206276 -3.0479976 0.42113052 -3.046774 0.55968697 -3.0464929 0.7017833 -3.0466074 0.8397451 -3.0473745 1 -3.0487774
150 0.099859382 0.0075603521 0.0040615957 0.016809825 0.096007238 0.0071040699 0.0022845963 2.3894645 0 -3.0535969 0.13277764 -3.0511437 0.27216411 -3.0479964 0.42112067 -3.0467741 0.55997348 -3.0464928 0.70181216 -3.0466076 0.83985415 -3.0473761 1 -3.0487774

9
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LAMMPS (22 Dec 2022)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4
0 14.104748 108.56876 0.1227071 4.999238 8.2087606 0.0018276223 0.00064050211 0.98401186 0 -3.0514921 0.33333333 -3.0496673 0.66666667 -3.0496645 1 -3.050305
46 0.049691778 0.001449144 0.0041836599 0.0070455894 0.94610709 0.0014279446 0.0014276971 1.1698782 0 -3.0514942 0.3026746 -3.0502925 0.63457326 -3.0500662 1 -3.0514939
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4
46 0.94646532 0.8692782 0.0041836599 0.0070455894 0.94610709 0.0014279446 0.0014276971 1.1698782 0 -3.0514942 0.3026746 -3.0502925 0.63457326 -3.0500662 1 -3.0514939
88 0.042941386 0.00046017358 0.0021155242 0.0031463438 0.0095074767 0.0016016953 0.0016016258 1.1725045 0 -3.0514943 0.26292929 -3.0504854 0.50610293 -3.0498926 1 -3.0514943

9
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LAMMPS (22 Dec 2022)
Running on 8 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4 RD5 PE5 RD6 PE6 RD7 PE7 RD8 PE8
0 15.805883 137.15721 0.1227071 4.999238 15.828539 0.0021830032 0.00099588309 0.98401186 0 -3.0514921 0.14285714 -3.0509383 0.28571429 -3.049949 0.42857143 -3.0493091 0.57142857 -3.0493602 0.71428571 -3.0498345 0.85714286 -3.0502192 1 -3.050305
73 0.049714315 0.0011853232 0.0036385263 0.0057874304 0.079285231 0.0016005788 0.001600399 1.2115403 0 -3.0514942 0.13043211 -3.0512538 0.25481496 -3.0505642 0.37535798 -3.0500676 0.49844851 -3.0498936 0.63571599 -3.0500698 0.80272589 -3.0508376 1 -3.051494
Climbing replica = 5
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4 RD5 PE5 RD6 PE6 RD7 PE7 RD8 PE8
73 0.079737673 0.0060506501 0.0036385263 0.0057874304 0.079285231 0.0016005788 0.001600399 1.2115403 0 -3.0514942 0.13043211 -3.0512538 0.25481496 -3.0505642 0.37535798 -3.0500676 0.49844851 -3.0498936 0.63571599 -3.0500698 0.80272589 -3.0508376 1 -3.051494
82 0.046923812 0.00207513 0.0033938491 0.0054082765 0.046102157 0.0016015266 0.0016013694 1.2125153 0 -3.0514942 0.13012408 -3.0512565 0.25462869 -3.0505663 0.37576663 -3.0500667 0.50363184 -3.0498927 0.63838032 -3.0500776 0.80516707 -3.0508541 1 -3.0514941

18
examples/neb/log.14Jan23.neb.sivac.g++.4 Normal file
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LAMMPS (22 Dec 2022)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4
0 7.5525391 2.671788 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.33333333 -2212.7428 0.66666667 -2212.2247 1 -2211.7959
10 0.24005275 0.0013324036 0.036483049 0.24005275 0.68351722 0.42916118 0.41794425 1.6989349 0 -2213.3365 0.32909183 -2212.9587 0.65386736 -2212.9073 1 -2213.3253
20 0.07940898 0.00026889621 0.024706844 0.07940898 0.71637784 0.41387872 0.41157886 1.7343662 0 -2213.3369 0.32478734 -2212.9621 0.65348766 -2212.923 1 -2213.3346
30 0.094973706 6.994258e-05 0.015145947 0.035267404 0.7535772 0.40072717 0.40024605 1.7504612 0 -2213.3372 0.32705584 -2212.9584 0.65894506 -2212.9365 1 -2213.3367
40 0.027727472 1.9827557e-05 0.011618173 0.022562656 0.76133752 0.39614635 0.39591731 1.7547519 0 -2213.3373 0.32873163 -2212.9562 0.66124255 -2212.9411 1 -2213.337
50 0.019429351 9.0662903e-06 0.0087135562 0.015391975 0.76952681 0.39274846 0.3926388 1.7578616 0 -2213.3373 0.33022595 -2212.9543 0.66307279 -2212.9446 1 -2213.3372
60 0.018992557 2.6317454e-06 0.005342608 0.0086165759 0.777596 0.38936859 0.38933361 1.7610433 0 -2213.3374 0.33187549 -2212.9523 0.66497619 -2212.948 1 -2213.3373
63 0.0097571737 1.6189866e-06 0.0047788465 0.0076143824 0.77864965 0.38888882 0.3888615 1.7615283 0 -2213.3374 0.33212054 -2212.952 0.66525325 -2212.9485 1 -2213.3373
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4
63 0.77864965 0.096633568 0.0047788465 0.0076143824 0.77864965 0.38888882 0.3888615 1.7615283 0 -2213.3374 0.33212054 -2212.952 0.66525325 -2212.9485 1 -2213.3373
73 0.098863403 0.0011310488 0.0027890076 0.0042744972 0.036283915 0.5102483 0.51023975 1.76072 0 -2213.3374 0.2757098 -2213.0417 0.50430234 -2212.8271 1 -2213.3374
83 0.031748825 0.00015683838 0.0020809514 0.0031533485 0.0099572603 0.51014575 0.51014111 1.7602531 0 -2213.3374 0.26034606 -2213.0674 0.50354802 -2212.8272 1 -2213.3374
93 0.011560904 6.778749e-06 0.0013983005 0.0020949841 0.0052524482 0.51011026 0.51010823 1.7601164 0 -2213.3374 0.2537964 -2213.0786 0.50388122 -2212.8273 1 -2213.3374
96 0.0080547159 4.4226058e-06 0.001318412 0.0019726613 0.0048040798 0.510108 0.5101062 1.7601158 0 -2213.3374 0.25347618 -2213.0792 0.50393582 -2212.8273 1 -2213.3374

20
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LAMMPS (22 Dec 2022)
Running on 8 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4 RD5 PE5 RD6 PE6 RD7 PE7 RD8 PE8
0 7.5525391 2.671788 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.14285714 -2213.1848 0.28571429 -2212.8577 0.42857143 -2212.5353 0.57142857 -2212.3131 0.71428571 -2212.192 0.85714286 -2212.0797 1 -2211.7959
10 0.45237221 0.0038899054 0.043713415 0.45237221 0.33984237 0.50434364 0.47974444 1.681593 0 -2213.3362 0.145972 -2213.2393 0.28963267 -2213.0224 0.43234899 -2212.8512 0.57436617 -2212.8319 0.71564291 -2212.9699 0.85294239 -2213.1766 1 -2213.3116
20 0.17466055 0.00038449492 0.027733064 0.16054263 0.29142661 0.49877454 0.49547267 1.7524163 0 -2213.3369 0.14387205 -2213.2456 0.28439667 -2213.0291 0.42233932 -2212.8573 0.5588361 -2212.8381 0.69513708 -2212.9781 0.83702043 -2213.2011 1 -2213.3336
30 0.045422642 0.00010721083 0.01818213 0.045422642 0.28112975 0.49759387 0.49675173 1.7746784 0 -2213.3371 0.14290957 -2213.2488 0.28281709 -2213.0326 0.41989281 -2212.859 0.55582211 -2212.8395 0.69368801 -2212.9853 0.83973606 -2213.2161 1 -2213.3363
40 0.038021578 6.0627173e-05 0.013142053 0.027303941 0.28657705 0.49667648 0.49635337 1.7848045 0 -2213.3372 0.1420496 -2213.2509 0.28169834 -2213.0351 0.41895631 -2212.8598 0.55576002 -2212.8406 0.69554601 -2212.9918 0.84293215 -2213.2247 1 -2213.3369
50 0.023478387 2.5440651e-05 0.0094370881 0.017117841 0.2948129 0.4956627 0.49552819 1.7913648 0 -2213.3373 0.14130551 -2213.2524 0.28080367 -2213.0371 0.41862494 -2212.8601 0.55666336 -2212.8417 0.69796419 -2212.9977 0.84561062 -2213.2308 1 -2213.3372
60 0.015568348 1.3385057e-05 0.0065356733 0.010880239 0.30476692 0.49454143 0.49448589 1.7961707 0 -2213.3374 0.14069048 -2213.2537 0.28018046 -2213.0385 0.41875119 -2212.86 0.55806463 -2212.8428 0.70047903 -2213.0032 0.84789117 -2213.2356 1 -2213.3373
70 0.011117036 8.589416e-06 0.0046665959 0.0074340441 0.31343723 0.4935777 0.49355166 1.7991441 0 -2213.3374 0.14033265 -2213.2544 0.27992696 -2213.0392 0.41915513 -2212.8596 0.55940642 -2212.8438 0.7024513 -2213.0073 0.8494878 -2213.2387 1 -2213.3373
77 0.0095032996 6.4872648e-06 0.003778822 0.0059131255 0.31843187 0.49301961 0.49300316 1.8005356 0 -2213.3374 0.14019726 -2213.2547 0.27989276 -2213.0394 0.41949002 -2212.8594 0.56021116 -2212.8444 0.70351827 -2213.0094 0.85030233 -2213.2402 1 -2213.3374
Climbing replica = 5
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4 RD5 PE5 RD6 PE6 RD7 PE7 RD8 PE8
77 0.31843187 0.016533023 0.003778822 0.0059131255 0.31843187 0.49301961 0.49300316 1.8005356 0 -2213.3374 0.14019726 -2213.2547 0.27989276 -2213.0394 0.41949002 -2212.8594 0.56021116 -2212.8444 0.70351827 -2213.0094 0.85030233 -2213.2402 1 -2213.3374
87 0.068521294 0.00041696849 0.002590902 0.0039658354 0.024993269 0.51001428 0.51000692 1.8017659 0 -2213.3374 0.13988527 -2213.2554 0.27815879 -2213.0427 0.4060317 -2212.8709 0.50551576 -2212.8274 0.69112296 -2212.99 0.84991798 -2213.2398 1 -2213.3374
97 0.031487615 0.00015286198 0.0020335677 0.0030841188 0.0070128682 0.51009653 0.51009209 1.8020354 0 -2213.3374 0.13898618 -2213.2569 0.27382107 -2213.0504 0.39686059 -2212.8798 0.50256203 -2212.8273 0.68247072 -2212.9764 0.84621774 -2213.2346 1 -2213.3374
107 0.016814587 4.4986184e-05 0.0013659976 0.0020482331 0.0024996635 0.51009833 0.51009639 1.8028763 0 -2213.3374 0.13616152 -2213.2608 0.26706798 -2213.0624 0.38875801 -2212.8885 0.50194006 -2212.8273 0.67498881 -2212.9648 0.84072701 -2213.2269 1 -2213.3374
117 0.013420011 2.244148e-05 0.00091637825 0.0013624439 0.0016781664 0.51009641 0.51009556 1.8036672 0 -2213.3374 0.13322116 -2213.2647 0.26208966 -2213.0712 0.38454183 -2212.8933 0.50207828 -2212.8273 0.67150999 -2212.9596 0.83745606 -2213.2222 1 -2213.3374
127 0.0091080864 1.3208992e-05 0.00070311367 0.0010407514 0.0013146017 0.5100957 0.5100952 1.804094 0 -2213.3374 0.13160053 -2213.2667 0.25966338 -2213.0755 0.38274006 -2212.8954 0.50217662 -2212.8273 0.6702885 -2212.9577 0.83622287 -2213.2204 1 -2213.3374

11
examples/neb/log.19Jun17.neb.hop1.end.g++.4
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LAMMPS (19 May 2017)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 229.26196 146.68251 2.9774577 4.4127369 233.11559 0.023301843 0.0224626 1.4763579 0 -3.048332 0.33333333 -3.0250302 0.66666667 -3.0291888 1 -3.0474928
100 0.11027532 0.085410308 3.0967938 0.024201563 0.38551033 0.0017583261 0.0021866943 1.7710358 0 -3.0483469 0.31192818 -3.0465886 0.61093022 -3.0466143 1 -3.0487752
130 0.09954083 0.075481108 3.0927626 0.015664388 0.37491833 0.0017573704 0.0021913201 1.7713726 0 -3.048342 0.31428487 -3.0465846 0.61762817 -3.0466296 1 -3.048776
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
130 0.37838747 0.3502435 3.0927626 0.015664388 0.37491833 0.0017573704 0.0021913201 1.7713726 0 -3.048342 0.31428487 -3.0465846 0.61762817 -3.0466296 1 -3.048776
230 0.22757286 0.12027481 3.1250243 0.0081260569 0.14019507 0.0018364585 0.002278918 1.76926 0 -3.0483347 0.39730698 -3.0464983 0.64450769 -3.0466973 1 -3.0487772
278 0.096184498 0.085088496 3.1405655 0.0068164307 0.093861113 0.0018426056 0.002286256 1.7684765 0 -3.0483338 0.41277997 -3.0464912 0.65562984 -3.0467294 1 -3.0487775

11
examples/neb/log.19Jun17.neb.hop1.end.g++.8
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LAMMPS (19 May 2017)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 229.26196 146.68251 2.9774577 4.4127369 233.11559 0.023301843 0.0224626 1.4763579 0 -3.048332 0.33333333 -3.0250302 0.66666667 -3.0291888 1 -3.0474928
100 0.11375359 0.085350745 3.0966418 0.0236765 0.38531777 0.0017582606 0.0021868783 1.7710738 0 -3.0483467 0.31201141 -3.0465884 0.61117406 -3.0466149 1 -3.0487753
119 0.09996986 0.078639268 3.0937691 0.017444108 0.3780308 0.0017574935 0.0021899317 1.7713574 0 -3.0483433 0.31354192 -3.0465858 0.61555533 -3.0466249 1 -3.0487758
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
119 0.3793192 0.35281863 3.0937691 0.017444108 0.3780308 0.0017574935 0.0021899317 1.7713574 0 -3.0483433 0.31354192 -3.0465858 0.61555533 -3.0466249 1 -3.0487758
219 0.20159133 0.12247026 3.1244061 0.0085896057 0.13938632 0.0018362816 0.0022783681 1.7693295 0 -3.048335 0.39646633 -3.0464988 0.64277703 -3.0466925 1 -3.0487771
266 0.099868725 0.086180598 3.1401661 0.0070922949 0.095128081 0.001842608 0.002286044 1.7685191 0 -3.048334 0.41231024 -3.0464914 0.65425179 -3.0467252 1 -3.0487774

9
examples/neb/log.19Jun17.neb.hop1.g++.4
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LAMMPS (19 May 2017)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 4327.2753 2746.3378 0.082169072 4.9967651 4514.5424 0.42933428 0.42323635 1.8941131 0 -3.0535948 0.33333333 -2.6242605 0.66666667 -2.7623811 1 -3.0474969
87 0.095951502 0.052720903 0.005588927 0.065110105 0.12467831 0.0071014928 0.0022798007 2.3003372 0 -3.0535967 0.32435271 -3.0473127 0.62805027 -3.0464952 1 -3.048775
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
87 0.14137277 0.11108954 0.005588927 0.065110105 0.12467831 0.0071014928 0.0022798007 2.3003372 0 -3.0535967 0.32435271 -3.0473127 0.62805027 -3.0464952 1 -3.048775
124 0.099583263 0.085936899 0.0044220372 0.023873795 0.091308308 0.0071061754 0.0022863931 2.308121 0 -3.0535968 0.32223905 -3.0473329 0.61673898 -3.0464906 1 -3.048777

9
examples/neb/log.19Jun17.neb.hop1.g++.8
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LAMMPS (19 May 2017)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 4327.2753 2746.3378 0.082169072 4.9967651 4514.5424 0.42933428 0.42323635 1.8941131 0 -3.0535948 0.33333333 -2.6242605 0.66666667 -2.7623811 1 -3.0474969
87 0.095951792 0.052720902 0.0055889267 0.065110091 0.12467831 0.0071014928 0.0022798007 2.3003372 0 -3.0535967 0.32435271 -3.0473127 0.62805027 -3.0464952 1 -3.048775
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
87 0.14137297 0.11108954 0.0055889267 0.065110091 0.12467831 0.0071014928 0.0022798007 2.3003372 0 -3.0535967 0.32435271 -3.0473127 0.62805027 -3.0464952 1 -3.048775
124 0.099582186 0.08593683 0.0044220345 0.023873731 0.091308197 0.0071061754 0.0022863931 2.3081211 0 -3.0535968 0.32223904 -3.0473329 0.61673896 -3.0464906 1 -3.048777

12
examples/neb/log.19Jun17.neb.hop2.g++.4
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LAMMPS (19 May 2017)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 14.104748 10.419633 0.1227071 4.999238 8.2087606 0.0018276223 0.00064050211 0.98401186 0 -3.0514921 0.33333333 -3.0496673 0.66666667 -3.0496645 1 -3.050305
100 0.24646695 0.10792196 0.0077146918 0.058733261 0.63504706 0.001516756 0.0015151635 1.165391 0 -3.0514939 0.2890334 -3.0503533 0.59718494 -3.0499771 1 -3.0514923
200 0.061777741 0.050288749 0.0047486883 0.0095236035 0.88698597 0.0014465772 0.0014462528 1.1692938 0 -3.0514941 0.29975094 -3.0503052 0.62768286 -3.0500476 1 -3.0514938
261 0.048699591 0.038138604 0.0040083594 0.0074854409 0.95722712 0.0014243579 0.0014241377 1.1696848 0 -3.0514942 0.30525481 -3.0502812 0.6357998 -3.0500698 1 -3.051494
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
261 0.95753855 0.94297239 0.0040083594 0.0074854409 0.95722712 0.0014243579 0.0014241377 1.1696848 0 -3.0514942 0.30525481 -3.0502812 0.6357998 -3.0500698 1 -3.051494
361 0.072509627 0.06580631 0.0027545765 0.0044749366 0.016746483 0.0016018879 0.0016017805 1.1704611 0 -3.0514943 0.28176307 -3.0503855 0.50355454 -3.0498924 1 -3.0514942
381 0.04884836 0.040787876 0.0023445904 0.0035162935 0.017959209 0.0016017716 0.0016016898 1.1713862 0 -3.0514943 0.27120138 -3.0504399 0.50428218 -3.0498925 1 -3.0514942

12
examples/neb/log.19Jun17.neb.hop2.g++.8
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@ -1,12 +0,0 @@
LAMMPS (19 May 2017)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 14.104748 10.419633 0.1227071 4.999238 8.2087606 0.0018276223 0.00064050211 0.98401186 0 -3.0514921 0.33333333 -3.0496673 0.66666667 -3.0496645 1 -3.050305
100 0.24646695 0.10792196 0.0077146918 0.058733261 0.63504706 0.001516756 0.0015151635 1.165391 0 -3.0514939 0.2890334 -3.0503533 0.59718494 -3.0499771 1 -3.0514923
200 0.061777741 0.050288749 0.0047486883 0.0095236035 0.88698597 0.0014465772 0.0014462528 1.1692938 0 -3.0514941 0.29975094 -3.0503052 0.62768286 -3.0500476 1 -3.0514938
261 0.048699591 0.038138604 0.0040083594 0.0074854409 0.95722712 0.0014243579 0.0014241377 1.1696848 0 -3.0514942 0.30525481 -3.0502812 0.6357998 -3.0500698 1 -3.051494
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
261 0.95753855 0.94297239 0.0040083594 0.0074854409 0.95722712 0.0014243579 0.0014241377 1.1696848 0 -3.0514942 0.30525481 -3.0502812 0.6357998 -3.0500698 1 -3.051494
361 0.072509627 0.06580631 0.0027545765 0.0044749366 0.016746483 0.0016018879 0.0016017805 1.1704611 0 -3.0514943 0.28176307 -3.0503855 0.50355454 -3.0498924 1 -3.0514942
381 0.04884836 0.040787876 0.0023445904 0.0035162935 0.017959209 0.0016017716 0.0016016898 1.1713862 0 -3.0514943 0.27120138 -3.0504399 0.50428218 -3.0498925 1 -3.0514942

17
examples/neb/log.19Jun17.neb.sivac.g++.4
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@ -1,17 +0,0 @@
LAMMPS (19 May 2017)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.33333333 -2212.7428 0.66666667 -2212.2247 1 -2211.7959
10 0.24005275 0.036502104 0.036483049 0.24005275 0.68351722 0.42916118 0.41794425 1.6989349 0 -2213.3365 0.32909183 -2212.9587 0.65386736 -2212.9073 1 -2213.3253
20 0.07940898 0.016398055 0.024706844 0.07940898 0.71637784 0.41387872 0.41157886 1.7343662 0 -2213.3369 0.32478734 -2212.9621 0.65348766 -2212.923 1 -2213.3346
30 0.094973707 0.0083631681 0.015145947 0.035267404 0.7535772 0.40072717 0.40024605 1.7504612 0 -2213.3372 0.32705584 -2212.9584 0.65894506 -2212.9365 1 -2213.3367
40 0.027727472 0.0044528145 0.011618173 0.022562656 0.76133752 0.39614635 0.39591731 1.7547519 0 -2213.3373 0.32873163 -2212.9562 0.66124255 -2212.9411 1 -2213.337
50 0.019429348 0.0030110281 0.0087135563 0.015391975 0.76952681 0.39274846 0.3926388 1.7578616 0 -2213.3373 0.33022595 -2212.9543 0.66307279 -2212.9446 1 -2213.3372
60 0.019009471 0.0016234562 0.0053426307 0.0086166186 0.77759617 0.38936861 0.38933364 1.7610433 0 -2213.3374 0.33187548 -2212.9523 0.66497617 -2212.948 1 -2213.3373
63 0.0097365134 0.0012734598 0.004777604 0.0076121987 0.77865149 0.38888778 0.38886047 1.7615294 0 -2213.3374 0.33212107 -2212.952 0.66525385 -2212.9485 1 -2213.3373
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
63 0.77865149 0.31085821 0.004777604 0.0076121987 0.77865149 0.38888778 0.38886047 1.7615294 0 -2213.3374 0.33212107 -2212.952 0.66525385 -2212.9485 1 -2213.3373
73 0.098175496 0.033609035 0.0027886955 0.0042742148 0.036594003 0.51024838 0.51023983 1.7607181 0 -2213.3374 0.27574151 -2213.0416 0.50432348 -2212.8271 1 -2213.3374
83 0.03341862 0.012760857 0.0020868177 0.0031625649 0.010189924 0.51014634 0.51014168 1.7602562 0 -2213.3374 0.26045338 -2213.0672 0.50355193 -2212.8272 1 -2213.3374
93 0.0097374358 0.0028416114 0.0014003718 0.0020986584 0.0053485291 0.51011052 0.51010848 1.7601202 0 -2213.3374 0.25397887 -2213.0783 0.50388111 -2212.8273 1 -2213.3374

18
examples/neb/log.19Jun17.neb.sivac.g++.8
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@ -1,18 +0,0 @@
LAMMPS (19 May 2017)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.33333333 -2212.7428 0.66666667 -2212.2247 1 -2211.7959
10 0.24005275 0.036502104 0.036483049 0.24005275 0.68351722 0.42916118 0.41794425 1.6989349 0 -2213.3365 0.32909183 -2212.9587 0.65386736 -2212.9073 1 -2213.3253
20 0.07940898 0.016398055 0.024706844 0.07940898 0.71637784 0.41387872 0.41157886 1.7343662 0 -2213.3369 0.32478734 -2212.9621 0.65348766 -2212.923 1 -2213.3346
30 0.094973708 0.0083631681 0.015145947 0.035267404 0.7535772 0.40072717 0.40024605 1.7504612 0 -2213.3372 0.32705584 -2212.9584 0.65894506 -2212.9365 1 -2213.3367
40 0.027727472 0.0044528144 0.011618173 0.022562656 0.76133752 0.39614635 0.39591731 1.7547519 0 -2213.3373 0.32873163 -2212.9562 0.66124255 -2212.9411 1 -2213.337
50 0.019429341 0.0030110281 0.0087135565 0.015391975 0.7695268 0.39274846 0.3926388 1.7578616 0 -2213.3373 0.33022595 -2212.9543 0.66307279 -2212.9446 1 -2213.3372
60 0.019048963 0.0016262345 0.0053426844 0.0086167196 0.77759655 0.38936867 0.3893337 1.7610433 0 -2213.3374 0.33187545 -2212.9523 0.66497615 -2212.948 1 -2213.3373
63 0.0097037048 0.0012761841 0.0047749367 0.0076075138 0.77865545 0.38888554 0.38885827 1.7615318 0 -2213.3374 0.33212221 -2212.952 0.66525512 -2212.9485 1 -2213.3373
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
63 0.77865545 0.3108551 0.0047749367 0.0076075138 0.77865545 0.38888554 0.38885827 1.7615318 0 -2213.3374 0.33212221 -2212.952 0.66525512 -2212.9485 1 -2213.3373
73 0.098595989 0.033659485 0.0027927196 0.0042813387 0.038224344 0.51024759 0.51023901 1.7607156 0 -2213.3374 0.27595612 -2213.0413 0.50453988 -2212.8271 1 -2213.3374
83 0.033344977 0.012868685 0.0020880608 0.0031645847 0.010250413 0.51014677 0.5101421 1.7602601 0 -2213.3374 0.26053624 -2213.067 0.50358775 -2212.8272 1 -2213.3374
93 0.013254873 0.0038176141 0.0014928226 0.0022407967 0.0058577818 0.51011371 0.51011138 1.7601272 0 -2213.3374 0.25452741 -2213.0774 0.50382161 -2212.8273 1 -2213.3374
95 0.0099964951 0.0031053214 0.0014131665 0.0021184362 0.0053683638 0.51011105 0.51010897 1.7601232 0 -2213.3374 0.2540975 -2213.0781 0.50387313 -2212.8273 1 -2213.3374

2
examples/pour/in.pour.2d.molecule
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@ -34,7 +34,7 @@ fix ywalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 &
molecule object molecule.vshape
fix 3 all rigid/small molecule mol object
# insure region size + molecule size does not overlap wall
# ensure region size + molecule size does not overlap wall
region slab block 3.0 97.0 30 34.5 -0.5 0.5 units box
fix ins all pour 500 0 4767548 vol 0.8 10 &

2
examples/pour/log.27Nov18.pour.2d.molecule.g++.1
View File

@ -44,7 +44,7 @@ fix 3 all rigid/small molecule mol object
0 rigid bodies with 0 atoms
2.23607 = max distance from body owner to body atom
# insure region size + molecule size does not overlap wall
# ensure region size + molecule size does not overlap wall
region slab block 3.0 97.0 30 34.5 -0.5 0.5 units box
fix ins all pour 500 0 4767548 vol 0.8 10 region slab mol object rigid 3

2
examples/pour/log.27Nov18.pour.2d.molecule.g++.4
View File

@ -44,7 +44,7 @@ fix 3 all rigid/small molecule mol object
0 rigid bodies with 0 atoms
2.23607 = max distance from body owner to body atom
# insure region size + molecule size does not overlap wall
# ensure region size + molecule size does not overlap wall
region slab block 3.0 97.0 30 34.5 -0.5 0.5 units box
fix ins all pour 500 0 4767548 vol 0.8 10 region slab mol object rigid 3