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rbbergerrbberger
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Merge branch 'master' of github.com:lammps/lammps-testing into master
2 parents 13a7377 + 2721d83 commit b3f8f4e

14 files changed

Lines changed: 1672 additions & 1632 deletions

tests/examples/USER/drude/swm4-ndp/log.11May20.linux.8.swm4-ndp.lang renamed to tests/examples/USER/drude/swm4-ndp/log.18Sep20.linux.8.swm4-ndp.lang

Lines changed: 44 additions & 38 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
LAMMPS (5 May 2020)
1+
LAMMPS (24 Aug 2020)
22
units real
33
boundary p p p
44

@@ -12,7 +12,8 @@ kspace_style pppm 1.0e-3
1212

1313
comm_modify vel yes
1414
read_data data.swm4-ndp
15-
orthogonal box = (-12 -12 -12) to (12 12 12)
15+
Reading data file ...
16+
orthogonal box = (-12.000000 -12.000000 -12.000000) to (12.000000 12.000000 12.000000)
1617
2 by 2 by 2 MPI processor grid
1718
reading atoms ...
1819
2500 atoms
@@ -24,12 +25,15 @@ read_data data.swm4-ndp
2425
2000 bonds
2526
reading angles ...
2627
500 angles
27-
4 = max # of 1-2 neighbors
28-
3 = max # of 1-3 neighbors
29-
3 = max # of 1-4 neighbors
30-
4 = max # of special neighbors
31-
special bonds CPU = 0.000549366 secs
32-
read_data CPU = 0.0160478 secs
28+
Finding 1-2 1-3 1-4 neighbors ...
29+
special bond factors lj: 0.0 0.0 0.5
30+
special bond factors coul: 0.0 0.0 0.5
31+
4 = max # of 1-2 neighbors
32+
3 = max # of 1-3 neighbors
33+
3 = max # of 1-4 neighbors
34+
4 = max # of special neighbors
35+
special bonds CPU = 0.001 seconds
36+
read_data CPU = 0.019 seconds
3337

3438
pair_coeff 1 1 0.210939 3.183950 # ODw ODw
3539
pair_coeff * 2* 0.000000 0.0
@@ -57,13 +61,14 @@ velocity DRUDES create ${TDK} 12345
5761
velocity DRUDES create 1 12345
5862

5963
delete_bonds ATOMS multi
64+
System init for delete_bonds ...
6065
PPPM initialization ...
61-
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
62-
G vector (1/distance) = 0.217457
66+
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
67+
G vector (1/distance) = 0.21745695
6368
grid = 10 10 10
6469
stencil order = 5
65-
estimated absolute RMS force accuracy = 0.197288
66-
estimated relative force accuracy = 0.000594128
70+
estimated absolute RMS force accuracy = 0.19728846
71+
estimated relative force accuracy = 0.00059412835
6772
using double precision FFTW3
6873
3d grid and FFT values/proc = 1000 200
6974
Rebuild special list taking Drude particles into account
@@ -81,6 +86,7 @@ Neighbor list info ...
8186
pair build: half/bin/newton
8287
stencil: half/bin/3d/newton
8388
bin: standard
89+
Deleting bonds ...
8490
2000 total bonds, 500 turned on, 1500 turned off
8591
500 total angles, 0 turned on, 500 turned off
8692
0 total dihedrals, 0 turned on, 0 turned off
@@ -92,9 +98,9 @@ fix TEMP all langevin/drude 300 100. 1256 1 20. 13977 zero yes
9298
fix NPH ATOMS rigid/nph/small molecule iso ${PBAR} ${PBAR} 500.
9399
fix NPH ATOMS rigid/nph/small molecule iso 1 ${PBAR} 500.
94100
fix NPH ATOMS rigid/nph/small molecule iso 1 1 500.
95-
create bodies CPU = 0.000285642 secs
96-
500 rigid bodies with 2000 atoms
97-
0.832099 = max distance from body owner to body atom
101+
create bodies CPU = 0.000 seconds
102+
500 rigid bodies with 2000 atoms
103+
0.83209864 = max distance from body owner to body atom
98104
fix NVE DRUDES nve
99105

100106
compute TEMP all temp/drude
@@ -104,45 +110,45 @@ thermo 20
104110

105111
run 20
106112
PPPM initialization ...
107-
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
108-
G vector (1/distance) = 0.217457
113+
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
114+
G vector (1/distance) = 0.21745695
109115
grid = 10 10 10
110116
stencil order = 5
111-
estimated absolute RMS force accuracy = 0.197288
112-
estimated relative force accuracy = 0.000594128
117+
estimated absolute RMS force accuracy = 0.19728846
118+
estimated relative force accuracy = 0.00059412835
113119
using double precision FFTW3
114120
3d grid and FFT values/proc = 1000 200
115121
Per MPI rank memory allocation (min/avg/max) = 15.82 | 16.13 | 16.21 Mbytes
116122
Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp c_TEMP[1] c_TEMP[2]
117123
0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785
118-
20 0.29049938 2934.9981 4591.7345 -1656.7364 566.94916 0 600.60029 155098.43 -157922.72 27115.32 14058.841 1027.6396 1460.0307 160.99411
119-
Loop time of 0.290551 on 8 procs for 20 steps with 2500 atoms
124+
20 0.26435679 2935.023 4591.6891 -1656.6661 566.95551 0 600.60316 155098.49 -157922.71 27116.247 14058.84 1027.6294 1460.0168 160.99145
125+
Loop time of 0.26448 on 8 procs for 20 steps with 2500 atoms
120126

121-
Performance: 5.947 ns/day, 4.035 hours/ns, 68.835 timesteps/s
122-
85.8% CPU use with 8 MPI tasks x no OpenMP threads
127+
Performance: 6.534 ns/day, 3.673 hours/ns, 75.620 timesteps/s
128+
95.6% CPU use with 8 MPI tasks x no OpenMP threads
123129

124130
MPI task timing breakdown:
125131
Section | min time | avg time | max time |%varavg| %total
126132
---------------------------------------------------------------
127-
Pair | 0.10654 | 0.16511 | 0.22003 | 12.1 | 56.83
128-
Bond | 7.3285e-05 | 9.6225e-05 | 0.0001239 | 0.0 | 0.03
129-
Kspace | 0.0092923 | 0.064953 | 0.12313 | 19.4 | 22.36
130-
Neigh | 0.015375 | 0.015427 | 0.015575 | 0.1 | 5.31
131-
Comm | 0.01326 | 0.014662 | 0.01552 | 0.7 | 5.05
132-
Output | 6.7354e-05 | 7.0232e-05 | 8.1708e-05 | 0.0 | 0.02
133-
Modify | 0.029008 | 0.029364 | 0.029568 | 0.1 | 10.11
134-
Other | | 0.0008661 | | | 0.30
135-
136-
Nlocal: 312.5 ave 326 max 289 min
133+
Pair | 0.12345 | 0.15325 | 0.17445 | 4.3 | 57.95
134+
Bond | 6.8771e-05 | 8.1467e-05 | 9.6492e-05 | 0.0 | 0.03
135+
Kspace | 0.030333 | 0.051559 | 0.080975 | 7.4 | 19.49
136+
Neigh | 0.010021 | 0.010029 | 0.010038 | 0.0 | 3.79
137+
Comm | 0.017455 | 0.018432 | 0.01908 | 0.4 | 6.97
138+
Output | 0.00012811 | 0.00013672 | 0.00017611 | 0.0 | 0.05
139+
Modify | 0.029661 | 0.029919 | 0.030354 | 0.2 | 11.31
140+
Other | | 0.001067 | | | 0.40
141+
142+
Nlocal: 312.500 ave 326 max 289 min
137143
Histogram: 1 0 1 0 0 1 0 2 1 2
138-
Nghost: 11329.8 ave 11442 max 11184 min
144+
Nghost: 11329.8 ave 11442 max 11184 min
139145
Histogram: 1 0 1 1 0 1 0 1 2 1
140-
Neighs: 321203 ave 343438 max 283647 min
146+
Neighs: 321203.0 ave 343439 max 283646 min
141147
Histogram: 1 0 0 0 1 2 0 2 0 2
142148

143-
Total # of neighbors = 2569621
144-
Ave neighs/atom = 1027.85
145-
Ave special neighs/atom = 4
149+
Total # of neighbors = 2569622
150+
Ave neighs/atom = 1027.8488
151+
Ave special neighs/atom = 4.0000000
146152
Neighbor list builds = 1
147153
Dangerous builds = 0
148154

tests/examples/USER/drude/swm4-ndp/log.06Jan19.linux.8.swm4-ndp.nh renamed to tests/examples/USER/drude/swm4-ndp/log.18Sep20.linux.8.swm4-ndp.nh

Lines changed: 48 additions & 39 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
LAMMPS (4 Jan 2019)
1+
LAMMPS (24 Aug 2020)
22
units real
33
boundary p p p
44

@@ -11,7 +11,8 @@ pair_style lj/cut/coul/long 12.0 12.0
1111
kspace_style pppm 1.0e-3
1212

1313
read_data data.swm4-ndp
14-
orthogonal box = (-12 -12 -12) to (12 12 12)
14+
Reading data file ...
15+
orthogonal box = (-12.000000 -12.000000 -12.000000) to (12.000000 12.000000 12.000000)
1516
2 by 2 by 2 MPI processor grid
1617
reading atoms ...
1718
2500 atoms
@@ -23,10 +24,15 @@ read_data data.swm4-ndp
2324
2000 bonds
2425
reading angles ...
2526
500 angles
26-
4 = max # of 1-2 neighbors
27-
3 = max # of 1-3 neighbors
28-
3 = max # of 1-4 neighbors
29-
4 = max # of special neighbors
27+
Finding 1-2 1-3 1-4 neighbors ...
28+
special bond factors lj: 0.0 0.0 0.5
29+
special bond factors coul: 0.0 0.0 0.5
30+
4 = max # of 1-2 neighbors
31+
3 = max # of 1-3 neighbors
32+
3 = max # of 1-4 neighbors
33+
4 = max # of special neighbors
34+
special bonds CPU = 0.001 seconds
35+
read_data CPU = 0.018 seconds
3036

3137
pair_coeff 1 1 0.210939 3.183950 # ODw ODw
3238
pair_coeff * 2* 0.000000 0.0
@@ -54,14 +60,15 @@ velocity DRUDES create ${TDK} 12345
5460
velocity DRUDES create 1 12345
5561

5662
delete_bonds ATOMS multi
63+
System init for delete_bonds ...
5764
PPPM initialization ...
58-
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
59-
G vector (1/distance) = 0.217457
65+
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
66+
G vector (1/distance) = 0.21745695
6067
grid = 10 10 10
6168
stencil order = 5
62-
estimated absolute RMS force accuracy = 0.197288
63-
estimated relative force accuracy = 0.000594128
64-
using double precision FFTs
69+
estimated absolute RMS force accuracy = 0.19728846
70+
estimated relative force accuracy = 0.00059412835
71+
using double precision FFTW3
6572
3d grid and FFT values/proc = 1000 200
6673
Rebuild special list taking Drude particles into account
6774
Old max number of 1-2 to 1-4 neighbors: 4
@@ -78,6 +85,7 @@ Neighbor list info ...
7885
pair build: half/bin/newton
7986
stencil: half/bin/3d/newton
8087
bin: standard
88+
Deleting bonds ...
8189
2000 total bonds, 500 turned on, 1500 turned off
8290
500 total angles, 0 turned on, 500 turned off
8391
0 total dihedrals, 0 turned on, 0 turned off
@@ -93,10 +101,11 @@ fix RIGID ATOMS rigid/npt/small molecule temp 300 ${TK} 100 iso ${PBAR} ${PBAR}
93101
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso ${PBAR} ${PBAR} 500
94102
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 ${PBAR} 500
95103
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 1 500
96-
500 rigid bodies with 2000 atoms
97-
0.832099 = max distance from body owner to body atom
104+
create bodies CPU = 0.000 seconds
105+
500 rigid bodies with 2000 atoms
106+
0.83209864 = max distance from body owner to body atom
98107
fix_modify RIGID temp TATOM press thermo_press
99-
WARNING: Temperature for fix modify is not for group all (../fix_rigid_nh_small.cpp:1338)
108+
WARNING: Temperature for fix modify is not for group all (src/RIGID/fix_rigid_nh_small.cpp:1336)
100109
fix NVT DRUDES nvt temp ${TDK} ${TDK} 100.0
101110
fix NVT DRUDES nvt temp 1 ${TDK} 100.0
102111
fix NVT DRUDES nvt temp 1 1 100.0
@@ -107,45 +116,45 @@ thermo 20
107116

108117
run 20
109118
PPPM initialization ...
110-
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
111-
G vector (1/distance) = 0.217457
119+
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
120+
G vector (1/distance) = 0.21745695
112121
grid = 10 10 10
113122
stencil order = 5
114-
estimated absolute RMS force accuracy = 0.197288
115-
estimated relative force accuracy = 0.000594128
116-
using double precision FFTs
123+
estimated absolute RMS force accuracy = 0.19728846
124+
estimated relative force accuracy = 0.00059412835
125+
using double precision FFTW3
117126
3d grid and FFT values/proc = 1000 200
118-
Per MPI rank memory allocation (min/avg/max) = 15.58 | 15.89 | 15.96 Mbytes
127+
Per MPI rank memory allocation (min/avg/max) = 15.82 | 16.13 | 16.21 Mbytes
119128
Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp c_TEMP[1] c_TEMP[2]
120129
0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785
121-
20 0.25570471 3742.8202 5338.828 -1596.0078 567.26788 0 662.20797 155098.52 -157924 31680.274 13979.575 1194.8407 1690.2355 201.6614
122-
Loop time of 0.255785 on 8 procs for 20 steps with 2500 atoms
130+
20 0.28928059 3742.8114 5338.8112 -1595.9999 567.27181 0 662.20936 155098.52 -157924 31679.868 13979.575 1194.8369 1690.2317 201.65774
131+
Loop time of 0.289343 on 8 procs for 20 steps with 2500 atoms
123132

124-
Performance: 6.756 ns/day, 3.553 hours/ns, 78.191 timesteps/s
125-
98.3% CPU use with 8 MPI tasks x no OpenMP threads
133+
Performance: 5.972 ns/day, 4.019 hours/ns, 69.122 timesteps/s
134+
93.3% CPU use with 8 MPI tasks x no OpenMP threads
126135

127136
MPI task timing breakdown:
128137
Section | min time | avg time | max time |%varavg| %total
129138
---------------------------------------------------------------
130-
Pair | 0.12109 | 0.13272 | 0.13908 | 1.8 | 51.89
131-
Bond | 5.4672e-05 | 5.9783e-05 | 6.5615e-05 | 0.0 | 0.02
132-
Kspace | 0.01205 | 0.018419 | 0.030091 | 4.8 | 7.20
133-
Neigh | 0.0098117 | 0.009816 | 0.0098189 | 0.0 | 3.84
134-
Comm | 0.013448 | 0.013578 | 0.013707 | 0.1 | 5.31
135-
Output | 5.9536e-05 | 6.7641e-05 | 0.00010464 | 0.0 | 0.03
136-
Modify | 0.080548 | 0.080682 | 0.080814 | 0.0 | 31.54
137-
Other | | 0.0004443 | | | 0.17
138-
139-
Nlocal: 312.5 ave 326 max 292 min
139+
Pair | 0.1288 | 0.14409 | 0.17346 | 3.3 | 49.80
140+
Bond | 7.6162e-05 | 8.3223e-05 | 9.4231e-05 | 0.0 | 0.03
141+
Kspace | 0.01032 | 0.039771 | 0.054956 | 6.3 | 13.75
142+
Neigh | 0.010001 | 0.010005 | 0.010013 | 0.0 | 3.46
143+
Comm | 0.012662 | 0.013401 | 0.01375 | 0.4 | 4.63
144+
Output | 7.2818e-05 | 0.00016643 | 0.0002415 | 0.0 | 0.06
145+
Modify | 0.080679 | 0.081196 | 0.082105 | 0.2 | 28.06
146+
Other | | 0.000631 | | | 0.22
147+
148+
Nlocal: 312.500 ave 326 max 292 min
140149
Histogram: 1 0 1 0 1 0 1 1 1 2
141-
Nghost: 11354.5 ave 11462 max 11209 min
150+
Nghost: 11354.5 ave 11462 max 11209 min
142151
Histogram: 1 0 0 2 1 0 0 1 1 2
143-
Neighs: 322375 ave 344480 max 285556 min
152+
Neighs: 322375.0 ave 344481 max 285557 min
144153
Histogram: 1 0 0 0 0 2 1 2 0 2
145154

146-
Total # of neighbors = 2579001
147-
Ave neighs/atom = 1031.6
148-
Ave special neighs/atom = 4
155+
Total # of neighbors = 2579003
156+
Ave neighs/atom = 1031.6012
157+
Ave special neighs/atom = 4.0000000
149158
Neighbor list builds = 1
150159
Dangerous builds = 0
151160

‎tests/examples/body/log.06Jan19.linux.8.body‎

Lines changed: 0 additions & 91 deletions
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