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remove obsolete inputs and logs

This commit is contained in:
Axel Kohlmeyer 2020-06-14 11:03:40 -04:00
parent d2404cc88e
commit 3083306dbc
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24
bench/POTENTIALS/in.meam
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# bulk Ni in MEAM
units metal
atom_style atomic
lattice fcc 3.52
region box block 0 20 0 20 0 20
create_box 1 box
create_atoms 1 box
pair_style meam
pair_coeff * * library.meam Ni4 Ni.meam Ni4
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.005
thermo 50
run 100

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bench/POTENTIALS/in.reax
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# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
units real
atom_style charge
read_data data.reax
#replicate 7 8 10
replicate 7 8 5
velocity all create 300.0 9999
pair_style reax
pair_coeff * * ffield.reax 1 2 3 4
timestep 0.1
fix 2 all nve
thermo 10
thermo_style custom step temp ke pe pxx pyy pzz etotal
run 100

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bench/POTENTIALS/log.16Mar18.meam.1
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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# bulk Ni in MEAM
units metal
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.00186539 secs
pair_style meam
WARNING: The pair_style meam command is unsupported. Please use pair_style meam/c instead (../pair_meam.cpp:51)
pair_coeff * * library.meam Ni4 Ni.meam Ni4
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.005
thermo 50
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5
ghost atom cutoff = 5
binsize = 2.5, bins = 29 29 29
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 55.91 | 55.91 | 55.91 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -142400 0 -135782.09 20259.18
50 885.10702 -139411.51 0 -135750.54 32425.433
100 895.5097 -139454.3 0 -135750.3 31804.187
Loop time of 30.6278 on 1 procs for 100 steps with 32000 atoms
Performance: 1.410 ns/day, 17.015 hours/ns, 3.265 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 | 30.088 | 30.088 | 30.088 | 0.0 | 98.24
Neigh | 0.48914 | 0.48914 | 0.48914 | 0.0 | 1.60
Comm | 0.015916 | 0.015916 | 0.015916 | 0.0 | 0.05
Output | 0.00022554 | 0.00022554 | 0.00022554 | 0.0 | 0.00
Modify | 0.025481 | 0.025481 | 0.025481 | 0.0 | 0.08
Other | | 0.009055 | | | 0.03
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 13576 ave 13576 max 13576 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 780360 ave 780360 max 780360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.56072e+06 ave 1.56072e+06 max 1.56072e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1560720
Ave neighs/atom = 48.7725
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:30

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bench/POTENTIALS/log.16Mar18.meam.4
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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# bulk Ni in MEAM
units metal
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.000587463 secs
pair_style meam
WARNING: The pair_style meam command is unsupported. Please use pair_style meam/c instead (../pair_meam.cpp:51)
pair_coeff * * library.meam Ni4 Ni.meam Ni4
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.005
thermo 50
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5
ghost atom cutoff = 5
binsize = 2.5, bins = 29 29 29
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 17.41 | 17.41 | 17.41 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -142400 0 -135782.09 20259.18
50 885.10702 -139411.51 0 -135750.54 32425.433
100 895.5097 -139454.3 0 -135750.3 31804.187
Loop time of 8.21941 on 4 procs for 100 steps with 32000 atoms
Performance: 5.256 ns/day, 4.566 hours/ns, 12.166 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.0277 | 8.0384 | 8.0504 | 0.3 | 97.80
Neigh | 0.12555 | 0.12645 | 0.12713 | 0.2 | 1.54
Comm | 0.024279 | 0.036776 | 0.048389 | 4.5 | 0.45
Output | 9.4414e-05 | 0.00011903 | 0.00018597 | 0.0 | 0.00
Modify | 0.01252 | 0.012608 | 0.012795 | 0.1 | 0.15
Other | | 0.005028 | | | 0.06
Nlocal: 8000 ave 8045 max 7947 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 6066.75 ave 6120 max 6021 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 195090 ave 196403 max 193697 min
Histogram: 1 0 0 1 0 0 0 1 0 1
FullNghs: 390180 ave 392616 max 387490 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 1560720
Ave neighs/atom = 48.7725
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:08

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bench/POTENTIALS/log.16Mar18.reax.1
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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
units real
atom_style charge
read_data data.reax
orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
1 by 1 by 1 MPI processor grid
reading atoms ...
58 atoms
#replicate 7 8 10
replicate 7 8 5
orthogonal box = (0 0 0) to (66.4375 75.9285 34.9562)
1 by 1 by 1 MPI processor grid
16240 atoms
Time spent = 0.000834942 secs
velocity all create 300.0 9999
pair_style reax
WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
pair_coeff * * ffield.reax 1 2 3 4
timestep 0.1
fix 2 all nve
thermo 10
thermo_style custom step temp ke pe pxx pyy pzz etotal
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 12 13 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair reax, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 115.8 | 115.8 | 115.8 Mbytes
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
0 300 14521.612 -1616144.2 22296.712 -29858.677 5721.0921 -1601622.5
10 298.98728 14472.591 -1616093.9 21955.847 -24067.096 7389.148 -1601621.3
20 294.76158 14268.045 -1615890.1 19179.258 -10513.494 10789.925 -1601622
30 288.56967 13968.323 -1615591.2 13854.377 5833.02 13949.731 -1601622.9
40 282.06725 13653.571 -1615278.2 6259.9845 19406.33 14947.939 -1601624.6
50 274.84112 13303.787 -1614931.9 -2009.6832 26964.336 13346.855 -1601628.2
60 266.20153 12885.585 -1614519.7 -8441.1641 28485.532 10195.429 -1601634.1
70 259.17085 12545.262 -1614184.2 -11426.993 24941.516 6572.2953 -1601638.9
80 259.73004 12572.33 -1614216.7 -10867.598 16928.461 3033.9021 -1601644.3
90 269.2352 13032.431 -1614679 -7962.3129 4931.5317 -280.22164 -1601646.6
100 280.67181 13586.024 -1615234.3 -3606.1519 -8769.8482 -2527.5887 -1601648.3
Loop time of 358.104 on 1 procs for 100 steps with 16240 atoms
Performance: 0.002 ns/day, 9947.338 hours/ns, 0.279 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 | 358.07 | 358.07 | 358.07 | 0.0 | 99.99
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.01623 | 0.01623 | 0.01623 | 0.0 | 0.00
Output | 0.0013328 | 0.0013328 | 0.0013328 | 0.0 | 0.00
Modify | 0.012679 | 0.012679 | 0.012679 | 0.0 | 0.00
Other | | 0.006895 | | | 0.00
Nlocal: 16240 ave 16240 max 16240 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 32428 ave 32428 max 32428 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6.69975e+06 ave 6.69975e+06 max 6.69975e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6699752
Ave neighs/atom = 412.546
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:06:02

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bench/POTENTIALS/log.16Mar18.reax.4
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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
units real
atom_style charge
read_data data.reax
orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
2 by 2 by 1 MPI processor grid
reading atoms ...
58 atoms
#replicate 7 8 10
replicate 7 8 5
orthogonal box = (0 0 0) to (66.4375 75.9285 34.9562)
2 by 2 by 1 MPI processor grid
16240 atoms
Time spent = 0.000491619 secs
velocity all create 300.0 9999
pair_style reax
WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
pair_coeff * * ffield.reax 1 2 3 4
timestep 0.1
fix 2 all nve
thermo 10
thermo_style custom step temp ke pe pxx pyy pzz etotal
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 12 13 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair reax, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 35.58 | 35.68 | 35.77 Mbytes
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
0 300 14521.612 -1616144.1 22296.712 -29858.677 5721.0922 -1601622.5
10 298.98728 14472.591 -1616093.8 21955.847 -24067.094 7389.149 -1601621.3
20 294.76158 14268.044 -1615890 19179.258 -10513.494 10789.925 -1601622
30 288.56967 13968.323 -1615591.2 13854.38 5833.0219 13949.731 -1601622.9
40 282.06725 13653.571 -1615278.2 6259.981 19406.327 14947.938 -1601624.7
50 274.84112 13303.787 -1614931.9 -2009.6844 26964.334 13346.855 -1601628.1
60 266.20153 12885.585 -1614519.8 -8441.1628 28485.533 10195.428 -1601634.2
70 259.17085 12545.262 -1614184.2 -11426.992 24941.517 6572.295 -1601639
80 259.73004 12572.33 -1614216.8 -10867.596 16928.464 3033.9024 -1601644.5
90 269.2352 13032.431 -1614679 -7962.3097 4931.5336 -280.21988 -1601646.5
100 280.67181 13586.024 -1615234.3 -3606.1482 -8769.8463 -2527.5874 -1601648.3
Loop time of 97.054 on 4 procs for 100 steps with 16240 atoms
Performance: 0.009 ns/day, 2695.944 hours/ns, 1.030 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 94.83 | 95.764 | 96.883 | 9.2 | 98.67
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.16123 | 1.2801 | 2.2132 | 79.9 | 1.32
Output | 0.00056076 | 0.00066662 | 0.00095987 | 0.0 | 0.00
Modify | 0.0048354 | 0.0049006 | 0.0049515 | 0.1 | 0.01
Other | | 0.004639 | | | 0.00
Nlocal: 4060 ave 4080 max 4040 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 14972 ave 14992 max 14952 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1.8135e+06 ave 1.82186e+06 max 1.80514e+06 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 7253988
Ave neighs/atom = 446.674
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:01:38

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bench/POTENTIALS/reax_defs.h
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#define PORTABLECOMMENTFLAG
#ifndef PORTABLECOMMENTFLAG
// This is just a way to have portable comments
// for both C++ and FORTRAN preprocessing.
/* ///:EOH~ */
/* */
/* This file contains array dimension parameters for all the main */
/* ReaxFF data structures, some of which need to be directly accessed */
/* by Grasp C++ functions. If they are set too small, the calculation */
/* will run out of allocated memory. If they are set too big, the machine */
/* will not be able to allocate enough memory. */
/* */
/* NNEIGHMAXDEF = Max number of neighbors / NATDEF */
/* NATDEF = Max number of atoms */
/* NATTOTDEF = Max number of global atoms */
/* NSORTDEF = Max number of atom types */
/* MBONDDEF = Max number of bonds connected to one atom */
/* NAVIBDEF = for 2nd derivatives */
/* NBOTYMDEF = Max number of bond types */
/* NVATYMDEF = Max number of valency angle types */
/* NTOTYMDEF = Max number of torsion angle types */
/* NHBTYMDEF = Max number of hydrogen bond types */
/* NODMTYMDEF = Max number of off-diagonal Morse types */
/* NBOALLMAXDEF = Max number of all bonds */
/* NBOMAXDEF = Max number of bonds */
/* NHBMAXDEF = Max number of hydrogen bonds */
/* NVAMAXDEF = Max number of valency angles */
/* NOPMAXDEF = Max number of out of plane angles */
/* NTOMAXDEF = Max number of torsion angles */
/* NPAMAXDEF = Max number of general parameters in force field */
/* NMOLMAXDEF = Max number of molecules in system */
/* NMOLSETDEF = Max number of molecules in training set */
/* MRESTRADEF = Max number of restraints */
/* MTREGDEF = Max number of temperature regimes */
/* MTZONEDEF = Max number of temperature zones */
/* MVREGDEF = Max number of volume regimes */
/* MVZONEDEF = Max number of volume zones */
/* MEREGDEF = Max number of electric field regimes */
/* MEZONEDEF = Max number of electric field zones */
#endif
#define NNEIGHMAXDEF 200
#define NATDEF 50000
#define NATTOTDEF 1
#define NSORTDEF 20
#define MBONDDEF 20
#define NAVIBDEF 50
#define NBOTYMDEF 200
#define NVATYMDEF 200
#define NTOTYMDEF 200
#define NHBTYMDEF 200
#define NODMTYMDEF 20
#define NBOALLMAXDEF 180000
#define NBOMAXDEF 90000
#define NHBMAXDEF 400000
#define NVAMAXDEF 300000
#define NOPMAXDEF 00010
#define NTOMAXDEF 200000
#define NPAMAXDEF 50
#define NMOLMAXDEF 2000
#define NMOLSETDEF 1500
#define MRESTRADEF 100
#define MTREGDEF 100
#define MTZONEDEF 5
#define MVREGDEF 100
#define MVZONEDEF 6
#define MEREGDEF 100
#define MEZONEDEF 3