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merge rst files and add omp style

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This commit is contained in:
Wengen Ouyang
2021-12-02 15:46:00 +02:00
parent 3bc36070a9
commit 30d3b2c209
12 changed files with 634 additions and 159 deletions
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0
examples/sw/in.mos2 → examples/sw/in.mos2.sw.mod
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examples/sw/in.mos2.sw.mod.omp Normal file
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# monolayer MoS2
units metal
boundary p p f
processors * * 1
atom_style full
read_data single_layer_MoS2.data
mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
########################## Define potentials ################################
pair_style sw/mod/omp
pair_coeff * * tmd.sw.mod Mo S S
#########################################################################
### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
############################
# Output
thermo 500
thermo_style custom step etotal pe ke temp
thermo_modify lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 5000

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examples/sw/log.27Oct21.mos2_sw_mod.g++.4 Normal file
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LAMMPS (27 Oct 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# monolayer MoS2
units metal
boundary p p f
processors * * 1
atom_style full
read_data single_layer_MoS2.data
Reading data file ...
triclinic box = (0.0000000 0.0000000 -100.00000) to (51.152320 44.299209 100.00000) with tilt (25.576160 0.0000000 0.0000000)
2 by 2 by 1 MPI processor grid
reading atoms ...
768 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.005 seconds
mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
########################## Define potentials ################################
pair_style sw/mod
pair_coeff * * tmd.sw.mod Mo S S
Reading sw potential file tmd.sw.mod with DATE: 2018-03-26
#########################################################################
### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
############################
# Output
thermo 500
thermo_style custom step etotal pe ke temp
thermo_modify lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 5000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.158796
ghost atom cutoff = 5.158796
binsize = 2.579398, bins = 30 18 78
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw/mod, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.360 | 6.360 | 6.360 Mbytes
Step TotEng PotEng KinEng Temp
0 -899.28605 -929.02881 29.742759 300
500 -899.28626 -922.45519 23.168929 233.69313
1000 -899.29247 -925.86547 26.573002 268.02828
1500 -899.27957 -916.95478 17.675214 178.28084
2000 -899.28171 -918.38728 19.105573 192.70814
2500 -899.28732 -922.50423 23.21691 234.17709
3000 -899.28195 -918.74112 19.459174 196.27473
3500 -899.27944 -918.03105 18.751604 189.13784
4000 -899.28397 -920.50737 21.223397 214.06955
4500 -899.28386 -919.79154 20.507685 206.85053
5000 -899.28077 -918.78947 19.508698 196.77425
Loop time of 0.741432 on 4 procs for 5000 steps with 768 atoms
Performance: 582.656 ns/day, 0.041 hours/ns, 6743.708 timesteps/s
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.64552 | 0.65764 | 0.66951 | 1.4 | 88.70
Bond | 0.00027894 | 0.00029732 | 0.00031402 | 0.0 | 0.04
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.054789 | 0.066165 | 0.078466 | 4.3 | 8.92
Output | 0.00010959 | 0.00011859 | 0.00013564 | 0.0 | 0.02
Modify | 0.0083096 | 0.0085094 | 0.0087577 | 0.2 | 1.15
Other | | 0.008697 | | | 1.17
Nlocal: 192.000 ave 194 max 190 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 194.000 ave 196 max 192 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 5120.00 ave 5170 max 5070 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Total # of neighbors = 20480
Ave neighs/atom = 26.666667
Ave special neighs/atom = 0.0000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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examples/sw/log.27Oct21.mos2_sw_mod_omp.g++.1 Normal file
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LAMMPS (27 Oct 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
package omp 0
using multi-threaded neighbor list subroutines
# monolayer MoS2
units metal
boundary p p f
processors * * 1
atom_style full
read_data single_layer_MoS2.data
Reading data file ...
triclinic box = (0.0000000 0.0000000 -100.00000) to (51.152320 44.299209 100.00000) with tilt (25.576160 0.0000000 0.0000000)
1 by 1 by 1 MPI processor grid
reading atoms ...
768 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.005 seconds
mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
########################## Define potentials ################################
pair_style sw/mod/omp
pair_coeff * * tmd.sw.mod Mo S S
Reading sw potential file tmd.sw.mod with DATE: 2018-03-26
#########################################################################
### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
############################
# Output
thermo 500
thermo_style custom step etotal pe ke temp
thermo_modify lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 5000
Last active /omp style is pair_style sw/mod/omp
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.158796
ghost atom cutoff = 5.158796
binsize = 2.579398, bins = 30 18 78
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw/mod/omp, perpetual
attributes: full, newton on, omp
pair build: full/bin/omp
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.539 | 6.539 | 6.539 Mbytes
Step TotEng PotEng KinEng Temp
0 -899.28605 -929.02881 29.742759 300
500 -899.28626 -922.45519 23.168929 233.69313
1000 -899.29247 -925.86547 26.573002 268.02828
1500 -899.27957 -916.95478 17.675214 178.28084
2000 -899.28171 -918.38728 19.105573 192.70814
2500 -899.28732 -922.50423 23.21691 234.17709
3000 -899.28195 -918.74112 19.459174 196.27473
3500 -899.27944 -918.03105 18.751604 189.13784
4000 -899.28397 -920.50737 21.223397 214.06955
4500 -899.28386 -919.79154 20.507685 206.85053
5000 -899.28077 -918.78947 19.508698 196.77425
Loop time of 2.43893 on 1 procs for 5000 steps with 768 atoms
Performance: 177.127 ns/day, 0.135 hours/ns, 2050.080 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.3796 | 2.3796 | 2.3796 | 0.0 | 97.57
Bond | 0.00021636 | 0.00021636 | 0.00021636 | 0.0 | 0.01
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0090182 | 0.0090182 | 0.0090182 | 0.0 | 0.37
Output | 0.00020341 | 0.00020341 | 0.00020341 | 0.0 | 0.01
Modify | 0.040174 | 0.040174 | 0.040174 | 0.0 | 1.65
Other | | 0.009731 | | | 0.40
Nlocal: 768.000 ave 768 max 768 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 354.000 ave 354 max 354 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 20480.0 ave 20480 max 20480 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 20480
Ave neighs/atom = 26.666667
Ave special neighs/atom = 0.0000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:02

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examples/sw/log.27Oct21.mos2_sw_mod_omp.g++.4 Normal file
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LAMMPS (27 Oct 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
package omp 0
using multi-threaded neighbor list subroutines
# monolayer MoS2
units metal
boundary p p f
processors * * 1
atom_style full
read_data single_layer_MoS2.data
Reading data file ...
triclinic box = (0.0000000 0.0000000 -100.00000) to (51.152320 44.299209 100.00000) with tilt (25.576160 0.0000000 0.0000000)
2 by 2 by 1 MPI processor grid
reading atoms ...
768 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.005 seconds
mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
########################## Define potentials ################################
pair_style sw/mod/omp
pair_coeff * * tmd.sw.mod Mo S S
Reading sw potential file tmd.sw.mod with DATE: 2018-03-26
#########################################################################
### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
############################
# Output
thermo 500
thermo_style custom step etotal pe ke temp
thermo_modify lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 5000
Last active /omp style is pair_style sw/mod/omp
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.158796
ghost atom cutoff = 5.158796
binsize = 2.579398, bins = 30 18 78
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw/mod/omp, perpetual
attributes: full, newton on, omp
pair build: full/bin/omp
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.361 | 6.361 | 6.361 Mbytes
Step TotEng PotEng KinEng Temp
0 -899.28605 -929.02881 29.742759 300
500 -899.28626 -922.45519 23.168929 233.69313
1000 -899.29247 -925.86547 26.573002 268.02828
1500 -899.27957 -916.95478 17.675214 178.28084
2000 -899.28171 -918.38728 19.105573 192.70814
2500 -899.28732 -922.50423 23.21691 234.17709
3000 -899.28195 -918.74112 19.459174 196.27473
3500 -899.27944 -918.03105 18.751604 189.13784
4000 -899.28397 -920.50737 21.223397 214.06955
4500 -899.28386 -919.79154 20.507685 206.85053
5000 -899.28077 -918.78947 19.508698 196.77425
Loop time of 0.703794 on 4 procs for 5000 steps with 768 atoms
Performance: 613.816 ns/day, 0.039 hours/ns, 7104.353 timesteps/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.60288 | 0.60616 | 0.60938 | 0.3 | 86.13
Bond | 0.00018681 | 0.00019351 | 0.00020187 | 0.0 | 0.03
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.070503 | 0.07298 | 0.077342 | 1.0 | 10.37
Output | 0.00011523 | 0.00012677 | 0.00014986 | 0.0 | 0.02
Modify | 0.014053 | 0.014315 | 0.014556 | 0.1 | 2.03
Other | | 0.01002 | | | 1.42
Nlocal: 192.000 ave 194 max 190 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 194.000 ave 196 max 192 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 5120.00 ave 5170 max 5070 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Total # of neighbors = 20480
Ave neighs/atom = 26.666667
Ave special neighs/atom = 0.0000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00