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Merge branch 'master' into tgnh

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This commit is contained in:
Axel Kohlmeyer
2020-12-20 14:48:49 -05:00
parent 3d28f5d610 09028b27d4
commit 2e33887d0b
483 changed files with 19119 additions and 705896 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
examples/COUPLE/fortran2/Makefile
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@ -14,7 +14,7 @@ CXXLIB = -lstdc++ # replace with your C++ runtime libs
# Flags for Fortran compiler, C++ compiler, and C preprocessor, respectively
FFLAGS = -O2 -fPIC
CXXFLAGS = -O2 -fPIC
CPPFLAGS = -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX
CPPFLAGS = -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX -DLAMMPS_LIB_MPI
all : liblammps_fortran.a liblammps_fortran.so

2
examples/COUPLE/python/example.py
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@ -1,4 +1,4 @@
# this example requires the LAMMPS Python package (lammps.py) to be installed
# this example requires the LAMMPS Python package (python/lammps) to be installed
# and LAMMPS to be loadable as shared library in LD_LIBRARY_PATH
import lammps

2
examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
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@ -26,7 +26,7 @@ velocity all create 100 4928459 rot yes dist gaussian
#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
pair_coeff * * spin/exchange exchange 4.0 -0.3593 1.135028015e-05 1.064568567
pair_coeff * * spin/exchange exchange 4.0 -0.3593 1.135028015e-05 1.0645 offset yes
#pair_coeff * * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
neighbor 0.1 bin

2
examples/SPIN/iron/in.spin.iron
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@ -25,7 +25,7 @@ velocity all create 100 4928459 rot yes dist gaussian
pair_style hybrid/overlay eam/alloy spin/exchange 3.5
pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe
pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841
pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841 offset yes
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20

4
examples/SPIN/iron/in.spin.iron_cubic
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@ -21,9 +21,9 @@ mass 1 55.845
set group all spin 2.2 -1.0 0.0 0.0
velocity all create 100 4928459 rot yes dist gaussian
pair_style hybrid/overlay eam/alloy spin/exchange 3.5
pair_style hybrid/overlay eam/alloy spin/exchange/biquadratic 3.5
pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe
pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841
pair_coeff * * spin/exchange/biquadratic biquadratic 3.4 0.02726 0.2171 1.841 0.0 0.0 2.0 offset yes
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20

20
examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py
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@ -6,9 +6,17 @@ import matplotlib.pyplot as plt
import mpmath as mp
hbar=0.658212 # Planck's constant (eV.fs/rad)
J0=0.05 # per-neighbor exchange interaction (eV)
# J0=0.05 # per-neighbor exchange interaction (eV)
# exchange interaction parameters
J1 = 11.254 # in eV
J2 = 0.0 # adim
J3 = 1.0 # in Ang.
# initial spins
S1 = np.array([1.0, 0.0, 0.0])
S2 = np.array([0.0, 1.0, 0.0])
alpha=0.01 # damping coefficient
pi=math.pi
@ -30,6 +38,14 @@ def rotation_matrix(axis, theta):
[2 * (bc - ad), aa + cc - bb - dd, 2 * (cd + ab)],
[2 * (bd + ac), 2 * (cd - ab), aa + dd - bb - cc]])
#Definition of the Bethe-Slater function
def func_BS(x,a,b,c):
return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2)
#Definition of the derivative of the Bethe-Slater function
def func_dBS(x,a,b,c):
return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2)
# calculating precession field of spin Sr
def calc_rot_vector(Sr,Sf):
rot = (J0/hbar)*(Sf-alpha*np.cross(Sf,Sr))/(1.0+alpha**2)
@ -65,6 +81,6 @@ for t in range (0,N):
# calc. average magnetization
Sm = (S1+S2)*0.5
# calc. energy
en = -2.0*J0*(np.dot(S1,S2))
en = -J0*(np.dot(S1,S2))
# print res. in ps for comparison with LAMMPS
print(t*dt/1000.0,Sm[0],Sm[1],Sm[2],en)

4
examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh
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@ -13,7 +13,7 @@ en="$(echo "$en-$in" | bc -l)"
tail -n +$in log.lammps | head -n $en > res_lammps.dat
# compute Langevin
python3 -m llg_exchange.py > res_llg.dat
python3 llg_exchange.py > res_llg.dat
# plot results
python3 -m plot_precession.py res_lammps.dat res_llg.dat
python3 plot_precession.py res_lammps.dat res_llg.dat

23
examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in
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@ -5,22 +5,24 @@ atom_style spin
atom_modify map array
boundary f f f
read_data two_spins.data
atom_modify map array
lattice sc 3.0
region box block 0 2 0 1 0 1
create_box 1 box
create_atoms 1 box
mass 1 55.845
set atom 1 spin 2.0 1.0 0.0 0.0
set atom 2 spin 2.0 0.0 1.0 0.0
pair_style spin/exchange 3.1
pair_coeff * * exchange 3.1 11.254 0.0 1.0
group bead type 1
variable H equal 0.0
variable Kan equal 0.0
variable Temperature equal 0.0
variable RUN equal 30000
fix 1 all nve/spin lattice no
fix 2 all precession/spin zeeman ${H} 0.0 0.0 1.0 anisotropy ${Kan} 0.0 0.0 1.0
fix_modify 2 energy yes
fix 3 all langevin/spin ${Temperature} 0.01 12345
fix 1 all nve/spin lattice frozen
fix 2 all langevin/spin ${Temperature} 0.01 12345
compute out_mag all spin
compute out_pe all pe
@ -34,6 +36,9 @@ variable emag equal c_out_mag[5]
thermo_style custom step time v_magx v_magy v_magz v_emag pe etotal
thermo 10
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 1 all custom 10 dump.data type x y z c_outsp[1] c_outsp[2] c_outsp[3] fx fy fz
timestep 0.0001
run ${RUN}

22
examples/SPIN/test_problems/validation_damped_exchange/two_spins.data
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@ -1,22 +0,0 @@
LAMMPS data file via write_data, version 19 Sep 2019, timestep = 0
2 atoms
1 atom types
0.0 6.0 xlo xhi
0.0 3.0 ylo yhi
0.0 3.0 zlo zhi
Masses
1 1
Atoms # spin
1 1 2.0 0.0 0.0 0.0 1.0 0.0 0.0 0 0 0
2 1 2.0 3.0 0.0 0.0 0.0 1.0 0.0 0 0 0
Velocities
1 0.0 0.0 0.0
2 0.0 0.0 0.0

2
examples/SPIN/test_problems/validation_nve/run-test-nve.sh
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@ -13,4 +13,4 @@ en="$(echo "$en-$in" | bc -l)"
tail -n +$in log.lammps | head -n $en > res_lammps.dat
# plot results
python3 -m plot_nve.py res_lammps.dat res_llg.dat
python3 plot_nve.py res_lammps.dat res_llg.dat

2
examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice
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@ -30,7 +30,7 @@ neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
fix 2 all langevin 200.0 200.0 10.0 48279
fix 2 all langevin 200.0 200.0 1.0 48279
fix 3 all langevin/spin 0.0 0.00001 321
fix 4 all nve/spin lattice moving
timestep 0.001

2
examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin
View File

@ -29,7 +29,7 @@ neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
fix 2 all langevin/spin 200.0 0.1 321
fix 2 all langevin/spin 200.0 0.01 321
fix 3 all nve/spin lattice moving
timestep 0.001

2
examples/SPIN/test_problems/validation_nvt/plot_nvt.py
View File

@ -39,5 +39,5 @@ plt.xlabel('Time (in ps)')
plt.legend()
plt.show()
fig.savefig(os.path.join(os.getcwd(), "nve_spin_lattice.pdf"), bbox_inches="tight")
fig.savefig(os.path.join(os.getcwd(), "nvt_spin_lattice.pdf"), bbox_inches="tight")
plt.close(fig)

38
examples/USER/misc/electron_stopping/in.cascade_AlCu Normal file
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@ -0,0 +1,38 @@
# ***
# Example input for including electronic stopping effects using fix electron/stopping/fit
# Al lattice with a single incident Cu atom - multiple species simulation
# ***
units metal
boundary p p p
lattice fcc 4.0495
region box block -10 10 -10 10 -10 10
create_box 2 box
create_atoms 1 box
pair_style eam/alloy
pair_coeff * * ../../../../potentials/AlCu.eam.alloy Al Cu
mass 1 26.982
mass 2 63.546
velocity all create 300 42534 mom yes rot yes
set atom 1 type 2
group pka id 1
velocity pka set 1120 1620 400
fix 1 all nve
fix 2 all dt/reset 1 NULL 0.001 0.05 emax 10.0
fix 3 all electron/stopping/fit 3.49 1.8e-3 9.0e-8 7.57 4.2e-3 5.0e-8
thermo 5
thermo_style custom step dt time temp pe ke f_3
thermo_modify lost warn flush yes
#dump 0 all custom 10 dump.pka_* id type x y z vx vy vz fx fy fz
#dump_modify 0 first yes
run 100

36
examples/USER/misc/electron_stopping/in.cascade_SiSi Normal file
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@ -0,0 +1,36 @@
# ***
# Example input for including electronic stopping effects using fix electron/stopping/fit
# Si lattice with one primary knock-on atom (PKA) - single species simulation
# ***
units metal
boundary p p p
lattice diamond 5.431
region box block -10 10 -10 10 -10 10
create_box 1 box
create_atoms 1 box
pair_style tersoff/zbl
pair_coeff * * ../../../../potentials/SiC.tersoff.zbl Si
mass 1 28.0855
velocity all create 300 42534 mom yes rot yes
group pka id 1
velocity pka set 1120 1620 400
fix 1 all nve
fix 2 all dt/reset 1 NULL 0.001 0.05 emax 10.0
fix 3 all electron/stopping/fit 4.63 3.3e-3 4.0e-8
thermo 5
thermo_style custom step dt time temp pe ke f_3
thermo_modify lost warn flush yes
#dump 0 all custom 10 dump.pka_* id type x y z vx vy vz fx fy fz
#dump_modify 0 first yes
run 100

115
examples/USER/misc/electron_stopping/log.18Sep2020.cascade_AlCu.intel.1 Normal file
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@ -0,0 +1,115 @@
LAMMPS (18 Sep 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# ***
# Example input for including electronic stopping effects using fix electron/stopping/fit
# Al lattice with a single incident Cu atom - multiple species simulation
# ***
units metal
boundary p p p
lattice fcc 4.0495
Lattice spacing in x,y,z = 4.0495000 4.0495000 4.0495000
region box block -10 10 -10 10 -10 10
create_box 2 box
Created orthogonal box = (-40.495000 -40.495000 -40.495000) to (40.495000 40.495000 40.495000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.004 seconds
pair_style eam/alloy
pair_coeff * * ../../../../potentials/AlCu.eam.alloy Al Cu
Reading eam/alloy potential file ../../../../potentials/AlCu.eam.alloy with DATE: 2008-10-01
mass 1 26.982
mass 2 63.546
velocity all create 300 42534 mom yes rot yes
set atom 1 type 2
Setting atom values ...
1 settings made for type
group pka id 1
1 atoms in group pka
velocity pka set 1120 1620 400
fix 1 all nve
fix 2 all dt/reset 1 NULL 0.001 0.05 emax 10.0
fix 3 all electron/stopping/fit 3.49 1.8e-3 9.0e-8 7.57 4.2e-3 5.0e-8
thermo 5
thermo_style custom step dt time temp pe ke f_3
thermo_modify lost warn flush yes
#dump 0 all custom 10 dump.pka_* id type x y z vx vy vz fx fy fz
#dump_modify 0 first yes
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 = 8.6825
ghost atom cutoff = 8.6825
binsize = 4.34125, bins = 19 19 19
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam/alloy, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 23.27 | 23.27 | 23.27 Mbytes
Step Dt Time Temp PotEng KinEng f_3
0 2.4879625e-05 0 53029.167 -106186.96 219339 0
5 2.4881895e-05 0.00012440247 53019.542 -106184.2 219299.18 36.968257
10 1.0341799e-05 0.00021830163 53006.803 -106159.67 219246.49 64.866504
15 5.6753071e-06 0.0002583636 52996.09 -106127.26 219202.18 76.766363
20 4.0862476e-06 0.0002830119 52987.566 -106099.31 219166.93 84.086344
25 3.3677164e-06 0.00030179992 52980.99 -106077.67 219139.73 89.665096
30 3.0218093e-06 0.00031784053 52976.302 -106063.03 219120.34 94.427505
35 2.8935922e-06 0.00033262008 52973.489 -106055.77 219108.7 98.815168
40 2.9394209e-06 0.00034711037 52972.541 -106056.15 219104.78 103.11678
45 3.1822694e-06 0.00036220043 52973.425 -106064.3 219108.44 107.59642
50 3.743784e-06 0.00037905999 52976.072 -106080.26 219119.38 112.60152
55 5.0685177e-06 0.0003999287 52980.344 -106104.15 219137.05 118.79722
60 1.0189784e-05 0.00043198334 52985.861 -106136.52 219159.88 128.31484
65 1.8636384e-05 0.00052946777 52985.275 -106162.53 219157.45 157.2625
70 1.844772e-05 0.00061001061 52977.927 -106155.89 219127.06 181.17691
75 2.4893022e-05 0.00072690857 52972.391 -106168.08 219104.16 215.88136
80 7.390618e-06 0.00081149431 52959.379 -106139.89 219050.34 240.98969
85 4.1547853e-06 0.00084037647 52948.078 -106101.74 219003.59 249.56079
90 2.9763749e-06 0.00085843347 52938.03 -106065.54 218962.03 254.91825
95 2.3727508e-06 0.00087197081 52929.043 -106032.37 218924.86 258.93397
100 2.0138478e-06 0.00088304936 52921.103 -106002.81 218892.02 262.21977
Loop time of 9.53154 on 1 procs for 100 steps with 32000 atoms
Performance: 0.002 ns/day, 13147.213 hours/ns, 10.491 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 | 8.815 | 8.815 | 8.815 | 0.0 | 92.48
Neigh | 0.38408 | 0.38408 | 0.38408 | 0.0 | 4.03
Comm | 0.029049 | 0.029049 | 0.029049 | 0.0 | 0.30
Output | 0.0025912 | 0.0025912 | 0.0025912 | 0.0 | 0.03
Modify | 0.28624 | 0.28624 | 0.28624 | 0.0 | 3.00
Other | | 0.01456 | | | 0.15
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 26825.0 ave 26825 max 26825 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.81599e+06 ave 2.81599e+06 max 2.81599e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2815993
Ave neighs/atom = 87.999781
Neighbor list builds = 5
Dangerous builds = 3
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:09

115
examples/USER/misc/electron_stopping/log.18Sep2020.cascade_AlCu.intel.4 Normal file
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@ -0,0 +1,115 @@
LAMMPS (18 Sep 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# ***
# Example input for including electronic stopping effects using fix electron/stopping/fit
# Al lattice with a single incident Cu atom - multiple species simulation
# ***
units metal
boundary p p p
lattice fcc 4.0495
Lattice spacing in x,y,z = 4.0495000 4.0495000 4.0495000
region box block -10 10 -10 10 -10 10
create_box 2 box
Created orthogonal box = (-40.495000 -40.495000 -40.495000) to (40.495000 40.495000 40.495000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.001 seconds
pair_style eam/alloy
pair_coeff * * ../../../../potentials/AlCu.eam.alloy Al Cu
Reading eam/alloy potential file ../../../../potentials/AlCu.eam.alloy with DATE: 2008-10-01
mass 1 26.982
mass 2 63.546
velocity all create 300 42534 mom yes rot yes
set atom 1 type 2
Setting atom values ...
1 settings made for type
group pka id 1
1 atoms in group pka
velocity pka set 1120 1620 400
fix 1 all nve
fix 2 all dt/reset 1 NULL 0.001 0.05 emax 10.0
fix 3 all electron/stopping/fit 3.49 1.8e-3 9.0e-8 7.57 4.2e-3 5.0e-8
thermo 5
thermo_style custom step dt time temp pe ke f_3
thermo_modify lost warn flush yes
#dump 0 all custom 10 dump.pka_* id type x y z vx vy vz fx fy fz
#dump_modify 0 first yes
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 = 8.6825
ghost atom cutoff = 8.6825
binsize = 4.34125, bins = 19 19 19
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam/alloy, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.014 | 9.014 | 9.014 Mbytes
Step Dt Time Temp PotEng KinEng f_3
0 2.4879625e-05 0 53029.167 -106186.96 219339 0
5 2.4881895e-05 0.00012440247 53019.542 -106184.2 219299.18 36.968257
10 1.0341742e-05 0.00021830123 53006.803 -106159.67 219246.49 64.866388
15 5.6752732e-06 0.00025836298 52996.09 -106127.26 219202.18 76.76618
20 4.0862174e-06 0.00028301112 52987.566 -106099.31 219166.93 84.086114
25 3.3676848e-06 0.00030179899 52980.99 -106077.67 219139.73 89.664821
30 3.021773e-06 0.00031783944 52976.302 -106063.02 219120.33 94.427181
35 2.8935472e-06 0.00033261879 52973.489 -106055.77 219108.7 98.814784
40 2.9393606e-06 0.00034710883 52972.541 -106056.15 219104.78 103.11632
45 3.1821803e-06 0.00036219854 52973.425 -106064.29 219108.43 107.59586
50 3.7436309e-06 0.00037905755 52976.071 -106080.26 219119.38 112.60079
55 5.0681667e-06 0.0003999252 52980.343 -106104.15 219137.05 118.79618
60 1.0187808e-05 0.00043197649 52985.861 -106136.51 219159.87 128.3128
65 1.8643099e-05 0.00052944037 52985.278 -106162.53 219157.46 157.25436
70 1.8445045e-05 0.00060999223 52977.928 -106155.89 219127.06 181.17146
75 2.4893021e-05 0.00072688076 52972.393 -106168.08 219104.17 215.8731
80 7.3916674e-06 0.0008114874 52959.382 -106139.9 219050.35 240.98764
85 4.1550998e-06 0.00084037284 52948.08 -106101.75 219003.6 249.55971
90 2.976545e-06 0.00085843108 52938.032 -106065.55 218962.04 254.91754
95 2.3728646e-06 0.00087196913 52929.045 -106032.38 218924.87 258.93348
100 2.0139362e-06 0.00088304819 52921.106 -106002.82 218892.03 262.21943
Loop time of 2.45676 on 4 procs for 100 steps with 32000 atoms
Performance: 0.007 ns/day, 3388.559 hours/ns, 40.704 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 | 2.2127 | 2.2257 | 2.2399 | 0.8 | 90.59
Neigh | 0.095856 | 0.097842 | 0.10197 | 0.8 | 3.98
Comm | 0.03626 | 0.054908 | 0.069787 | 6.3 | 2.23
Output | 0.00088538 | 0.0011005 | 0.0017236 | 1.1 | 0.04
Modify | 0.072449 | 0.072553 | 0.072611 | 0.0 | 2.95
Other | | 0.004684 | | | 0.19
Nlocal: 8000.00 ave 8033 max 7977 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Nghost: 12605.0 ave 12628 max 12572 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 703998.0 ave 706570 max 702282 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Total # of neighbors = 2815992
Ave neighs/atom = 87.999750
Neighbor list builds = 5
Dangerous builds = 3
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:02

113
examples/USER/misc/electron_stopping/log.18Sep2020.cascade_SiSi.intel.1 Normal file
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@ -0,0 +1,113 @@
LAMMPS (18 Sep 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# ***
# Example input for including electronic stopping effects using fix electron/stopping/fit
# Si lattice with one primary knock-on atom (PKA) - single species simulation
# ***
units metal
boundary p p p
lattice diamond 5.431
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
region box block -10 10 -10 10 -10 10
create_box 1 box
Created orthogonal box = (-54.310000 -54.310000 -54.310000) to (54.310000 54.310000 54.310000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 64000 atoms
create_atoms CPU = 0.008 seconds
pair_style tersoff/zbl
pair_coeff * * ../../../../potentials/SiC.tersoff.zbl Si
Reading tersoff/zbl potential file ../../../../potentials/SiC.tersoff.zbl with DATE: 2009-04-15
mass 1 28.0855
velocity all create 300 42534 mom yes rot yes
group pka id 1
1 atoms in group pka
velocity pka set 1120 1620 400
fix 1 all nve
fix 2 all dt/reset 1 NULL 0.001 0.05 emax 10.0
fix 3 all electron/stopping/fit 4.63 3.3e-3 4.0e-8
thermo 5
thermo_style custom step dt time temp pe ke f_3
thermo_modify lost warn flush yes
#dump 0 all custom 10 dump.pka_* id type x y z vx vy vz fx fy fz
#dump_modify 0 first yes
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 = 5
ghost atom cutoff = 5
binsize = 2.5, bins = 44 44 44
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/zbl, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 23.91 | 23.91 | 23.91 Mbytes
Step Dt Time Temp PotEng KinEng f_3
0 2.4879625e-05 0 21258.724 -296293.96 175863.22 0
5 9.2462185e-06 9.0354398e-05 21252.059 -296277.65 175808.08 38.834393
10 6.1558479e-06 0.00013003059 21246.736 -296250.63 175764.05 55.881868
15 4.9002335e-06 0.00015681379 21242.649 -296228.27 175730.24 67.386915
20 5.853687e-06 0.00018286317 21239.571 -296213.99 175704.78 78.574676
25 7.0182823e-06 0.00021483214 21237.286 -296208.81 175685.87 92.303028
30 8.2570048e-06 0.00025083646 21236.034 -296213.99 175675.52 107.76296
35 6.4734302e-06 0.00029194185 21233.473 -296210.33 175654.33 125.41212
40 7.3445302e-06 0.00032561085 21231.196 -296205.94 175635.5 139.86641
45 6.9480705e-06 0.00036268325 21230.21 -296213.68 175627.33 155.78046
50 7.2224188e-06 0.00039655436 21230.512 -296230.74 175629.84 170.32001
55 1.0773409e-05 0.00044221823 21230.023 -296246.37 175625.79 189.92217
60 5.7527075e-06 0.00048339879 21226.064 -296231.33 175593.04 207.5982
65 5.8568503e-06 0.0005110075 21222.544 -296213.97 175563.92 219.44643
70 6.7430644e-06 0.00054252027 21220.179 -296207.92 175544.35 232.96808
75 7.0523029e-06 0.00057648256 21219.781 -296219.19 175541.06 247.53974
80 1.784394e-05 0.00062210154 21221.276 -296251.35 175553.43 267.11364
85 2.1885193e-05 0.0007395532 21218.037 -296274.94 175526.64 317.50995
90 8.233509e-06 0.00081518257 21211.247 -296251.53 175470.47 349.95382
95 5.1490725e-06 0.00084789415 21205.33 -296216.55 175421.52 363.982
100 5.7628664e-06 0.0008764946 21200.168 -296186.27 175378.81 376.24357
Loop time of 20.4868 on 1 procs for 100 steps with 64000 atoms
Performance: 0.002 ns/day, 9874.909 hours/ns, 4.881 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 | 19.397 | 19.397 | 19.397 | 0.0 | 94.68
Neigh | 0.45332 | 0.45332 | 0.45332 | 0.0 | 2.21
Comm | 0.035144 | 0.035144 | 0.035144 | 0.0 | 0.17
Output | 0.0040397 | 0.0040397 | 0.0040397 | 0.0 | 0.02
Modify | 0.5739 | 0.5739 | 0.5739 | 0.0 | 2.80
Other | | 0.0229 | | | 0.11
Nlocal: 64000.0 ave 64000 max 64000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 18341.0 ave 18341 max 18341 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: 1.79199e+06 ave 1.79199e+06 max 1.79199e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1791990
Ave neighs/atom = 27.999844
Neighbor list builds = 7
Dangerous builds = 2
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:20

113
examples/USER/misc/electron_stopping/log.18Sep2020.cascade_SiSi.intel.4 Normal file
View File

@ -0,0 +1,113 @@
LAMMPS (18 Sep 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# ***
# Example input for including electronic stopping effects using fix electron/stopping/fit
# Si lattice with one primary knock-on atom (PKA) - single species simulation
# ***
units metal
boundary p p p
lattice diamond 5.431
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
region box block -10 10 -10 10 -10 10
create_box 1 box
Created orthogonal box = (-54.310000 -54.310000 -54.310000) to (54.310000 54.310000 54.310000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 64000 atoms
create_atoms CPU = 0.003 seconds
pair_style tersoff/zbl
pair_coeff * * ../../../../potentials/SiC.tersoff.zbl Si
Reading tersoff/zbl potential file ../../../../potentials/SiC.tersoff.zbl with DATE: 2009-04-15
mass 1 28.0855
velocity all create 300 42534 mom yes rot yes
group pka id 1
1 atoms in group pka
velocity pka set 1120 1620 400
fix 1 all nve
fix 2 all dt/reset 1 NULL 0.001 0.05 emax 10.0
fix 3 all electron/stopping/fit 4.63 3.3e-3 4.0e-8
thermo 5
thermo_style custom step dt time temp pe ke f_3
thermo_modify lost warn flush yes
#dump 0 all custom 10 dump.pka_* id type x y z vx vy vz fx fy fz
#dump_modify 0 first yes
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 = 5
ghost atom cutoff = 5
binsize = 2.5, bins = 44 44 44
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/zbl, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.777 | 7.777 | 7.777 Mbytes
Step Dt Time Temp PotEng KinEng f_3
0 2.4879625e-05 0 21258.724 -296293.96 175863.22 0
5 9.2462211e-06 9.0354422e-05 21252.059 -296277.66 175808.08 38.834403
10 6.1568847e-06 0.00013003069 21246.736 -296250.63 175764.05 55.881913
15 4.8997821e-06 0.00015681555 21242.649 -296228.27 175730.24 67.387669
20 5.8536714e-06 0.00018286203 21239.571 -296213.99 175704.78 78.574187
25 7.0160073e-06 0.00021483347 21237.285 -296208.8 175685.86 92.303599
30 8.2556386e-06 0.00025082046 21236.035 -296213.99 175675.53 107.75609
35 6.4735852e-06 0.00029193023 21233.474 -296210.34 175654.34 125.40713
40 7.3441556e-06 0.00032559783 21231.197 -296205.94 175635.5 139.86082
45 6.9483099e-06 0.00036267022 21230.21 -296213.68 175627.34 155.77487
50 7.2213562e-06 0.0003965413 21230.513 -296230.74 175629.84 170.31441
55 1.0776037e-05 0.00044219672 21230.024 -296246.38 175625.8 189.91293
60 5.7538246e-06 0.0004833796 21226.067 -296231.34 175593.06 207.58996
65 5.856213e-06 0.00051099409 21222.546 -296213.98 175563.94 219.44067
70 6.7431217e-06 0.00054250526 21220.18 -296207.92 175544.37 232.96164
75 7.0518411e-06 0.00057646788 21219.781 -296219.18 175541.07 247.53344
80 1.7829072e-05 0.00062207162 21221.276 -296251.34 175553.43 267.1008
85 2.1894958e-05 0.0007395084 21218.04 -296274.95 175526.66 317.49073
90 8.2365472e-06 0.00081516502 21211.25 -296251.55 175470.49 349.94629
95 5.1493496e-06 0.00084788428 21205.333 -296216.57 175421.54 363.97777
100 5.7652664e-06 0.00087648406 21200.171 -296186.3 175378.84 376.23905
Loop time of 5.23182 on 4 procs for 100 steps with 64000 atoms
Performance: 0.010 ns/day, 2520.759 hours/ns, 19.114 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 | 4.8069 | 4.8618 | 4.9229 | 2.0 | 92.93
Neigh | 0.11442 | 0.11856 | 0.12948 | 1.8 | 2.27
Comm | 0.040943 | 0.098988 | 0.15807 | 14.7 | 1.89
Output | 0.0013075 | 0.0014801 | 0.0019936 | 0.8 | 0.03
Modify | 0.14496 | 0.14502 | 0.1451 | 0.0 | 2.77
Other | | 0.005981 | | | 0.11
Nlocal: 16000.0 ave 16017 max 15987 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Nghost: 8044.00 ave 8058 max 8026 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 447998.0 ave 448471 max 447634 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 1791990
Ave neighs/atom = 27.999844
Neighbor list builds = 7
Dangerous builds = 2
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:05

2
examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_map
View File

@ -3,7 +3,7 @@ this is a nominal superimpose file
2 edgeIDs
18 equivalences
BondingIDs
InitiatorIDs
10
1

2
examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_map
View File

@ -3,7 +3,7 @@ this is a nominal superimpose file
2 edgeIDs
15 equivalences
BondingIDs
InitiatorIDs
4
12

2
examples/USER/reaction/tiny_epoxy/rxn1_stp1.map
View File

@ -3,7 +3,7 @@ this is a map file
1 edgeIDs
31 equivalences
BondingIDs
InitiatorIDs
15
1

2
examples/USER/reaction/tiny_epoxy/rxn1_stp2.map
View File

@ -3,7 +3,7 @@ this is a map file
1 edgeIDs
31 equivalences
BondingIDs
InitiatorIDs
4
25

2
examples/USER/reaction/tiny_epoxy/rxn2_stp1.map
View File

@ -3,7 +3,7 @@ this is a map file
2 edgeIDs
42 equivalences
BondingIDs
InitiatorIDs
15
32

2
examples/USER/reaction/tiny_epoxy/rxn2_stp2.map
View File

@ -3,7 +3,7 @@ this is a map file
2 edgeIDs
42 equivalences
BondingIDs
InitiatorIDs
35
24

2
examples/USER/reaction/tiny_nylon/rxn1_stp1_map
View File

@ -3,7 +3,7 @@ this is a nominal superimpose file
2 edgeIDs
18 equivalences
BondingIDs
InitiatorIDs
10
1

2
examples/USER/reaction/tiny_nylon/rxn1_stp2_map
View File

@ -3,7 +3,7 @@ this is a nominal superimpose file
2 edgeIDs
15 equivalences
BondingIDs
InitiatorIDs
4
12

2
examples/USER/reaction/tiny_polystyrene/2styrene_map
View File

@ -3,7 +3,7 @@ this is a map file
0 edgeIDs
32 equivalences
BondingIDs
InitiatorIDs
4
30

2
examples/USER/reaction/tiny_polystyrene/chain_chain_map
View File

@ -8,7 +8,7 @@ EdgeIDs
17
34
BondingIDs
InitiatorIDs
14
38

2
examples/USER/reaction/tiny_polystyrene/chain_plus_styrene_map
View File

@ -7,7 +7,7 @@ EdgeIDs
30
BondingIDs
InitiatorIDs
14
34

111
examples/granular/in.pour.drum
View File

@ -2,99 +2,98 @@
# 'turn' cylinder by changing direction of gravity, then rotate it.
# This simulates a rotating drum powder characterization experiment.
variable name string rotating_drum_two_types
variable name string rotating_drum_two_types
atom_style sphere
units lj
atom_style sphere
units lj
###############################################
# Geometry-related parameters
###############################################
variable boxx equal 30
variable boxy equal 30
variable boxz equal 50
variable boxx equal 30
variable boxy equal 30
variable boxz equal 50
variable drum_rad equal ${boxx}*0.5
variable drum_height equal 20
variable drum_rad equal ${boxx}*0.5
variable drum_height equal 20
variable xc equal 0.5*${boxx}
variable yc equal 0.5*${boxx}
variable zc equal 0.5*${boxz}
variable xc equal 0.5*${boxx}
variable yc equal 0.5*${boxx}
variable zc equal 0.5*${boxz}
###############################################
# Particle-related parameters
###############################################
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dhi equal 2.0*${rhi}
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dhi equal 2.0*${rhi}
variable cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
variable cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
variable dens equal 1.0
variable dens equal 1.0
variable skin equal 0.4*${rhi}
#############
processors * * 1
region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
create_box 2 boxreg
change_box all boundary p p f
comm_modify vel yes
region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
create_box 2 boxreg
change_box all boundary p p f
variable theta equal 0
pair_style granular
pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
region curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
region bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
variable theta equal 0
region insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
region curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
region bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
fix 0 all balance 100 1.0 shift xy 5 1.1
fix 1 all nve/sphere
fix grav all gravity 10 vector 0 0 -1
fix ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
region insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
comm_modify vel yes
fix 0 all balance 100 1.0 shift xy 5 1.1
fix 1 all nve/sphere
fix grav all gravity 10 vector 0 0 -1
fix ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
neighbor ${skin} bin
neigh_modify delay 0 every 1 check yes
comm_modify vel yes
pair_style granular
pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
neighbor ${skin} bin
neigh_modify delay 0 every 1 check yes
fix 3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
fix 4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
fix 3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
fix 4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
thermo_style custom step atoms ke v_theta
thermo_modify lost warn
thermo 100
thermo_style custom step atoms ke v_theta
thermo_modify lost warn
thermo 100
timestep 0.001
timestep 0.001
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
#For removal later
compute 1 all property/atom radius
variable zmax atom z+c_1>0.5*${drum_height}
group delgroup dynamic all var zmax every 10000
compute 1 all property/atom radius
variable zmax atom z+c_1>0.5*${drum_height}
group delgroup dynamic all var zmax every 10000
run 2000
run 2000
#Remove any particles that are above z > 0.5*drum_height
delete_atoms group delgroup
delete_atoms group delgroup
#Add top lid
region top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
fix 5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
region top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
fix 5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
# 'Turn' drum by switching the direction of gravity
unfix grav
unfix ins1
unfix ins2
fix grav all gravity 10 vector 0 -1 0
unfix grav
unfix ins1
unfix ins2
fix grav all gravity 10 vector 0 -1 0
variable theta equal 2*PI*elapsed/20000.0
run 3000
variable theta equal 2*PI*elapsed/20000.0
run 3000

76
examples/granular/in.pour.flatwall
View File

@ -1,67 +1,65 @@
# pour two types of particles (cohesive and non-cohesive) on flat wall
variable name string pour_two_types
variable name string pour_two_types
atom_style sphere
units lj
atom_style sphere
units lj
###############################################
# Geometry-related parameters
###############################################
variable boxx equal 20
variable boxy equal 20
variable boxz equal 30
variable boxx equal 20
variable boxy equal 20
variable boxz equal 30
variable xc1 equal 0.3*${boxx}
variable xc2 equal 0.7*${boxx}
variable yc equal 0.5*${boxy}
variable xc1 equal 0.3*${boxx}
variable xc2 equal 0.7*${boxx}
variable yc equal 0.5*${boxy}
###############################################
# Particle-related parameters
###############################################
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dhi equal 2.0*${rhi}
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dhi equal 2.0*${rhi}
variable dens equal 1.0
variable dens equal 1.0
variable skin equal 0.3*${rhi}
#############
processors * * 1
region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
create_box 2 boxreg
change_box all boundary p p f
processors * * 1
region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
create_box 2 boxreg
change_box all boundary p p f
comm_modify vel yes
pair_style granular
pair_coeff 1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
region insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
region insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
comm_modify vel yes
fix 1 all nve/sphere
fix grav all gravity 10.0 vector 0 0 -1
fix ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
region insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
region insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
comm_modify vel yes
fix 1 all nve/sphere
fix grav all gravity 10.0 vector 0 0 -1
fix ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
neighbor ${skin} bin
neigh_modify delay 0 every 1 check yes
neighbor ${skin} bin
neigh_modify delay 0 every 1 check yes
pair_style granular
pair_coeff 1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
fix 3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
fix 3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
thermo_style custom step atoms ke
thermo_modify lost warn
thermo 100
thermo_style custom step cpu atoms ke
thermo_modify lost warn
thermo 100
timestep 0.001
timestep 0.001
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
run 5000
run 5000

150
examples/granular/log.29Mar19.pour.drum.g++.1 → examples/granular/log.29Oct20.pour.drum.g++.1
View File

@ -1,5 +1,4 @@
LAMMPS (29 Mar 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
LAMMPS (29 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# pour two types of particles (cohesive and non-cohesive) into cylinder
# 'turn' cylinder by changing direction of gravity, then rotate it.
@ -55,10 +54,14 @@ region boxreg block 0 30 0 ${boxy} 0 ${boxz}
region boxreg block 0 30 0 30 0 ${boxz}
region boxreg block 0 30 0 30 0 50
create_box 2 boxreg
Created orthogonal box = (0 0 0) to (30 30 50)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (30.000000 30.000000 50.000000)
1 by 1 by 1 MPI processor grid
change_box all boundary p p f
comm_modify vel yes
Changing box ...
pair_style granular
pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
variable theta equal 0
@ -104,10 +107,6 @@ neighbor ${skin} bin
neighbor 0.2 bin
neigh_modify delay 0 every 1 check yes
pair_style granular
pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
fix 3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
fix 4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
@ -117,8 +116,7 @@ thermo 100
timestep 0.001
dump 1 all custom 100 ${name}.dump id type radius mass x y z
dump 1 all custom 100 rotating_drum_two_types.dump id type radius mass x y z
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
#For removal later
compute 1 all property/atom radius
@ -140,7 +138,7 @@ Neighbor list info ...
pair build: half/size/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 13.02 | 13.02 | 13.02 Mbytes
Per MPI rank memory allocation (min/avg/max) = 13.03 | 13.03 | 13.03 Mbytes
Step Atoms KinEng v_theta
0 0 -0 0
100 4000 -0 0
@ -163,32 +161,32 @@ Step Atoms KinEng v_theta
1800 4000 -0 0
1900 4000 -0 0
2000 4000 -0 0
Loop time of 3.54461 on 1 procs for 2000 steps with 4000 atoms
Loop time of 10.5178 on 1 procs for 2000 steps with 4000 atoms
Performance: 48750.057 tau/day, 564.237 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 16429.309 tau/day, 190.154 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.61949 | 0.61949 | 0.61949 | 0.0 | 17.48
Neigh | 1.2492 | 1.2492 | 1.2492 | 0.0 | 35.24
Comm | 0.046404 | 0.046404 | 0.046404 | 0.0 | 1.31
Output | 0.15901 | 0.15901 | 0.15901 | 0.0 | 4.49
Modify | 1.4165 | 1.4165 | 1.4165 | 0.0 | 39.96
Other | | 0.05391 | | | 1.52
Pair | 1.0701 | 1.0701 | 1.0701 | 0.0 | 10.17
Neigh | 4.2135 | 4.2135 | 4.2135 | 0.0 | 40.06
Comm | 0.38276 | 0.38276 | 0.38276 | 0.0 | 3.64
Output | 0.0013647 | 0.0013647 | 0.0013647 | 0.0 | 0.01
Modify | 4.7076 | 4.7076 | 4.7076 | 0.0 | 44.76
Other | | 0.1424 | | | 1.35
Nlocal: 4000 ave 4000 max 4000 min
Nlocal: 4000.00 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 166 ave 166 max 166 min
Nghost: 171.000 ave 171 max 171 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8195 ave 8195 max 8195 min
Neighs: 8093.00 ave 8093 max 8093 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8195
Ave neighs/atom = 2.04875
Total # of neighbors = 8093
Ave neighs/atom = 2.0232500
Neighbor list builds = 1004
Dangerous builds = 3
Dangerous builds = 4
#Remove any particles that are above z > 0.5*drum_height
delete_atoms group delgroup
@ -205,67 +203,69 @@ fix 5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindl
# 'Turn' drum by switching the direction of gravity
unfix grav
unfix ins1
unfix ins2
fix grav all gravity 10 vector 0 -1 0
variable theta equal 2*PI*elapsed/20000.0
run 3000
Per MPI rank memory allocation (min/avg/max) = 24.81 | 24.81 | 24.81 Mbytes
Per MPI rank memory allocation (min/avg/max) = 19.37 | 19.37 | 19.37 Mbytes
Step Atoms KinEng v_theta
2000 4000 64.333531 0
2100 4000 106.69182 0.031415927
2200 4000 121.8461 0.062831853
2300 4000 88.767952 0.09424778
2400 4000 82.850721 0.12566371
2500 4000 91.683284 0.15707963
2600 4000 31.56344 0.18849556
2700 4000 4.5697672 0.21991149
2800 4000 3.9879051 0.25132741
2900 4000 4.4394235 0.28274334
3000 4000 5.1212931 0.31415927
3100 4000 5.8608892 0.34557519
3200 4000 6.600714 0.37699112
3300 4000 7.3497851 0.40840704
3400 4000 8.0490988 0.43982297
3500 4000 8.6712396 0.4712389
3600 4000 9.1328667 0.50265482
3700 4000 9.4683561 0.53407075
3800 4000 9.5878145 0.56548668
3900 4000 9.387745 0.5969026
4000 4000 8.9117631 0.62831853
4100 4000 8.2344368 0.65973446
4200 4000 7.5335088 0.69115038
4300 4000 6.8426179 0.72256631
4400 4000 6.0567247 0.75398224
4500 4000 5.4166132 0.78539816
4600 4000 4.6012409 0.81681409
4700 4000 3.8314982 0.84823002
4800 4000 3.1916415 0.87964594
4900 4000 2.7833964 0.91106187
5000 4000 2.5051362 0.9424778
Loop time of 11.9545 on 1 procs for 3000 steps with 4000 atoms
2000 4000 65.647582 0
2100 4000 105.60001 0.031415927
2200 4000 112.27573 0.062831853
2300 4000 92.758671 0.09424778
2400 4000 88.925835 0.12566371
2500 4000 81.369163 0.15707963
2600 4000 32.046943 0.18849556
2700 4000 4.1926368 0.21991149
2800 4000 3.9933453 0.25132741
2900 4000 4.5062193 0.28274334
3000 4000 5.3409521 0.31415927
3100 4000 6.0165991 0.34557519
3200 4000 6.606767 0.37699112
3300 4000 7.3997751 0.40840704
3400 4000 8.1098807 0.43982297
3500 4000 8.6552424 0.4712389
3600 4000 9.8445204 0.50265482
3700 4000 10.098753 0.53407075
3800 4000 10.039489 0.56548668
3900 4000 9.6376278 0.5969026
4000 4000 9.2598836 0.62831853
4100 4000 8.7116037 0.65973446
4200 4000 8.1274117 0.69115038
4300 4000 7.1487627 0.72256631
4400 4000 6.2253778 0.75398224
4500 4000 5.3061398 0.78539816
4600 4000 4.4319316 0.81681409
4700 4000 4.205607 0.84823002
4800 4000 3.2112987 0.87964594
4900 4000 2.6449777 0.91106187
5000 4000 2.3475497 0.9424778
Loop time of 32.4926 on 1 procs for 3000 steps with 4000 atoms
Performance: 21682.142 tau/day, 250.951 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 7977.205 tau/day, 92.329 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.8291 | 4.8291 | 4.8291 | 0.0 | 40.40
Neigh | 2.7489 | 2.7489 | 2.7489 | 0.0 | 22.99
Comm | 0.071249 | 0.071249 | 0.071249 | 0.0 | 0.60
Output | 0.20547 | 0.20547 | 0.20547 | 0.0 | 1.72
Modify | 4.0179 | 4.0179 | 4.0179 | 0.0 | 33.61
Other | | 0.0819 | | | 0.69
Pair | 8.0124 | 8.0124 | 8.0124 | 0.0 | 24.66
Neigh | 10.993 | 10.993 | 10.993 | 0.0 | 33.83
Comm | 0.86697 | 0.86697 | 0.86697 | 0.0 | 2.67
Output | 0.0021827 | 0.0021827 | 0.0021827 | 0.0 | 0.01
Modify | 12.367 | 12.367 | 12.367 | 0.0 | 38.06
Other | | 0.2515 | | | 0.77
Nlocal: 4000 ave 4000 max 4000 min
Nlocal: 4000.00 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 322 ave 322 max 322 min
Nghost: 318.000 ave 318 max 318 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 14849 ave 14849 max 14849 min
Neighs: 14807.0 ave 14807 max 14807 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14849
Ave neighs/atom = 3.71225
Neighbor list builds = 1290
Dangerous builds = 672
Total wall time: 0:00:15
Total # of neighbors = 14807
Ave neighs/atom = 3.7017500
Neighbor list builds = 2189
Dangerous builds = 1536
Total wall time: 0:00:43

156
examples/granular/log.29Mar19.pour.drum.g++.4 → examples/granular/log.29Oct20.pour.drum.g++.4
View File

@ -1,5 +1,4 @@
LAMMPS (29 Mar 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
LAMMPS (29 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# pour two types of particles (cohesive and non-cohesive) into cylinder
# 'turn' cylinder by changing direction of gravity, then rotate it.
@ -55,10 +54,14 @@ region boxreg block 0 30 0 ${boxy} 0 ${boxz}
region boxreg block 0 30 0 30 0 ${boxz}
region boxreg block 0 30 0 30 0 50
create_box 2 boxreg
Created orthogonal box = (0 0 0) to (30 30 50)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (30.000000 30.000000 50.000000)
2 by 2 by 1 MPI processor grid
change_box all boundary p p f
comm_modify vel yes
Changing box ...
pair_style granular
pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
variable theta equal 0
@ -104,10 +107,6 @@ neighbor ${skin} bin
neighbor 0.2 bin
neigh_modify delay 0 every 1 check yes
pair_style granular
pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
fix 3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
fix 4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
@ -117,8 +116,7 @@ thermo 100
timestep 0.001
dump 1 all custom 100 ${name}.dump id type radius mass x y z
dump 1 all custom 100 rotating_drum_two_types.dump id type radius mass x y z
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
#For removal later
compute 1 all property/atom radius
@ -163,32 +161,32 @@ Step Atoms KinEng v_theta
1800 4000 -0 0
1900 4000 -0 0
2000 4000 -0 0
Loop time of 2.0709 on 4 procs for 2000 steps with 4000 atoms
Loop time of 3.86825 on 4 procs for 2000 steps with 4000 atoms
Performance: 83442.024 tau/day, 965.764 timesteps/s
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 44671.398 tau/day, 517.030 timesteps/s
96.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.24679 | 0.26336 | 0.28853 | 3.0 | 12.72
Neigh | 0.52279 | 0.5332 | 0.53858 | 0.9 | 25.75
Comm | 0.17418 | 0.20253 | 0.23266 | 4.7 | 9.78
Output | 0.092897 | 0.093531 | 0.09515 | 0.3 | 4.52
Modify | 0.88151 | 0.89571 | 0.90582 | 0.9 | 43.25
Other | | 0.08257 | | | 3.99
Pair | 0.26114 | 0.27918 | 0.28728 | 2.0 | 7.22
Neigh | 1.2044 | 1.2414 | 1.3105 | 3.7 | 32.09
Comm | 0.38592 | 0.47065 | 0.51052 | 7.4 | 12.17
Output | 0.0007236 | 0.0013456 | 0.0024846 | 1.8 | 0.03
Modify | 1.6217 | 1.6723 | 1.7801 | 5.0 | 43.23
Other | | 0.2034 | | | 5.26
Nlocal: 1000 ave 1001 max 999 min
Nlocal: 1000.00 ave 1012 max 988 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 267.75 ave 276 max 262 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Neighs: 2031.5 ave 2091 max 1958 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Nghost: 269.250 ave 278 max 256 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 2060.50 ave 2156 max 1921 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 8126
Ave neighs/atom = 2.0315
Total # of neighbors = 8242
Ave neighs/atom = 2.0605000
Neighbor list builds = 1004
Dangerous builds = 3
Dangerous builds = 4
#Remove any particles that are above z > 0.5*drum_height
delete_atoms group delgroup
@ -205,67 +203,69 @@ fix 5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindl
# 'Turn' drum by switching the direction of gravity
unfix grav
unfix ins1
unfix ins2
fix grav all gravity 10 vector 0 -1 0
variable theta equal 2*PI*elapsed/20000.0
run 3000
Per MPI rank memory allocation (min/avg/max) = 21.6 | 22.6 | 23.82 Mbytes
Per MPI rank memory allocation (min/avg/max) = 18.55 | 18.55 | 18.55 Mbytes
Step Atoms KinEng v_theta
2000 4000 64.255821 0
2100 4000 106.47082 0.031415927
2200 4000 121.52634 0.062831853
2300 4000 87.748818 0.09424778
2400 4000 82.712784 0.12566371
2500 4000 90.618713 0.15707963
2600 4000 30.096031 0.18849556
2700 4000 4.0838611 0.21991149
2800 4000 3.7485959 0.25132741
2900 4000 4.2159774 0.28274334
3000 4000 4.8730048 0.31415927
3100 4000 5.6109465 0.34557519
3200 4000 6.4290528 0.37699112
3300 4000 7.2699677 0.40840704
3400 4000 8.0895944 0.43982297
3500 4000 8.7222781 0.4712389
3600 4000 9.133205 0.50265482
3700 4000 9.3404584 0.53407075
3800 4000 9.3359844 0.56548668
3900 4000 9.0916854 0.5969026
4000 4000 8.5596424 0.62831853
4100 4000 7.9734883 0.65973446
4200 4000 7.2154383 0.69115038
4300 4000 6.7039232 0.72256631
4400 4000 6.1542738 0.75398224
4500 4000 5.4049454 0.78539816
4600 4000 4.4603192 0.81681409
4700 4000 3.6197985 0.84823002
4800 4000 2.9895571 0.87964594
4900 4000 2.5314553 0.91106187
5000 4000 2.2645533 0.9424778
Loop time of 6.64209 on 4 procs for 3000 steps with 4000 atoms
2000 4000 65.819213 0
2100 4000 105.02389 0.031415927
2200 4000 112.02469 0.062831853
2300 4000 92.271262 0.09424778
2400 4000 89.369506 0.12566371
2500 4000 80.910925 0.15707963
2600 4000 31.620722 0.18849556
2700 4000 4.3019937 0.21991149
2800 4000 3.9913967 0.25132741
2900 4000 4.5203726 0.28274334
3000 4000 5.484886 0.31415927
3100 4000 6.1085958 0.34557519
3200 4000 6.7085635 0.37699112
3300 4000 7.4787777 0.40840704
3400 4000 8.2116413 0.43982297
3500 4000 8.7979302 0.4712389
3600 4000 9.871649 0.50265482
3700 4000 10.012426 0.53407075
3800 4000 9.9067754 0.56548668
3900 4000 9.725458 0.5969026
4000 4000 9.3350056 0.62831853
4100 4000 8.8337295 0.65973446
4200 4000 8.2712493 0.69115038
4300 4000 6.9609934 0.72256631
4400 4000 6.0120294 0.75398224
4500 4000 5.0490036 0.78539816
4600 4000 4.2796544 0.81681409
4700 4000 4.1736483 0.84823002
4800 4000 3.0860106 0.87964594
4900 4000 2.6670909 0.91106187
5000 4000 2.2901814 0.9424778
Loop time of 10.7627 on 4 procs for 3000 steps with 4000 atoms
Performance: 39023.861 tau/day, 451.665 timesteps/s
96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 24083.252 tau/day, 278.741 timesteps/s
97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.8376 | 2.126 | 2.3131 | 12.6 | 32.01
Neigh | 0.97762 | 1.0518 | 1.1337 | 5.4 | 15.84
Comm | 0.53699 | 0.84265 | 1.2325 | 27.6 | 12.69
Output | 0.13922 | 0.14159 | 0.14388 | 0.4 | 2.13
Modify | 1.8815 | 2.1026 | 2.3368 | 11.2 | 31.66
Other | | 0.3774 | | | 5.68
Pair | 1.6731 | 2.0701 | 2.3327 | 18.9 | 19.23
Neigh | 2.7389 | 3.1706 | 3.5146 | 15.7 | 29.46
Comm | 0.93507 | 1.5441 | 2.1182 | 39.1 | 14.35
Output | 0.0021682 | 0.0044412 | 0.006026 | 2.2 | 0.04
Modify | 3.0031 | 3.4223 | 3.9262 | 18.3 | 31.80
Other | | 0.5511 | | | 5.12
Nlocal: 1000 ave 1256 max 744 min
Nlocal: 1000.00 ave 1277 max 723 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 579.5 ave 789 max 498 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Neighs: 3696.25 ave 4853 max 2590 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 569.750 ave 809 max 454 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Neighs: 3690.50 ave 4937 max 2426 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 14785
Ave neighs/atom = 3.69625
Neighbor list builds = 1230
Dangerous builds = 676
Total wall time: 0:00:08
Total # of neighbors = 14762
Ave neighs/atom = 3.6905000
Neighbor list builds = 2187
Dangerous builds = 1610
Total wall time: 0:00:14

120
examples/granular/log.29Mar19.pour.flatwall.g++.1 → examples/granular/log.29Oct20.pour.flatwall.g++.1
View File

@ -1,5 +1,4 @@
LAMMPS (29 Mar 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
LAMMPS (29 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# pour two types of particles (cohesive and non-cohesive) on flat wall
@ -45,9 +44,14 @@ region boxreg block 0 20 0 ${boxy} 0 ${boxz}
region boxreg block 0 20 0 20 0 ${boxz}
region boxreg block 0 20 0 20 0 30
create_box 2 boxreg
Created orthogonal box = (0 0 0) to (20 20 30)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (20.000000 20.000000 30.000000)
1 by 1 by 1 MPI processor grid
change_box all boundary p p f
Changing box ...
pair_style granular
pair_coeff 1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
comm_modify vel yes
@ -75,19 +79,13 @@ fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1
Particle insertion: 562 every 346 steps, 1500 by step 693
comm_modify vel yes
neighbor ${skin} bin
neighbor 0.15 bin
neigh_modify delay 0 every 1 check yes
pair_style granular
pair_coeff 1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
fix 3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
thermo_style custom step cpu atoms ke
thermo_style custom step atoms ke
thermo_modify lost warn
thermo 100
@ -109,26 +107,82 @@ Neighbor list info ...
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.22 | 12.22 | 12.22 Mbytes
Step CPU Atoms KinEng
0 0 0 -0
100 3.8153191 855 -0
200 4.195287 855 -0
300 4.5890362 855 -0
400 10.636087 1500 -0
500 11.306909 1500 -0
600 11.968198 1500 -0
700 22.631892 2288 -0
800 23.711387 2288 -0
900 24.754344 2288 -0
1000 25.811778 2288 -0
1100 35.368869 2845 -0
1200 37.149843 2845 -0
1300 39.026458 2845 -0
1400 41.757583 3000 -0
1500 45.155503 3000 -0
1600 48.570241 3000 -0
1700 52.839322 3000 -0
1800 59.772697 3000 -0
1900 69.493305 3000 -0
2000 114.61886 3000 -0
2100 152.89232 3000 -0
Step Atoms KinEng
0 0 -0
100 926 -0
200 926 -0
300 926 -0
400 1498 -0
500 1498 -0
600 1498 -0
700 2275 -0
800 2275 -0
900 2275 -0
1000 2275 -0
1100 2954 -0
1200 2954 -0
1300 2954 -0
1400 3000 -0
1500 3000 -0
1600 3000 -0
1700 3000 -0
1800 3000 -0
1900 3000 -0
2000 3000 -0
2100 3000 -0
2200 3000 -0
2300 3000 -0
2400 3000 -0
2500 3000 -0
2600 3000 -0
2700 3000 -0
2800 3000 -0
2900 3000 -0
3000 3000 -0
3100 3000 -0
3200 3000 -0
3300 3000 -0
3400 3000 -0
3500 3000 -0
3600 3000 -0
3700 3000 -0
3800 3000 -0
3900 3000 -0
4000 3000 -0
4100 3000 -0
4200 3000 -0
4300 3000 -0
4400 3000 -0
4500 3000 -0
4600 3000 -0
4700 3000 -0
4800 3000 -0
4900 3000 -0
5000 3000 -0
Loop time of 24.3889 on 1 procs for 5000 steps with 3000 atoms
Performance: 17713.003 tau/day, 205.012 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 14.362 | 14.362 | 14.362 | 0.0 | 58.89
Neigh | 3.3483 | 3.3483 | 3.3483 | 0.0 | 13.73
Comm | 0.42893 | 0.42893 | 0.42893 | 0.0 | 1.76
Output | 0.0025065 | 0.0025065 | 0.0025065 | 0.0 | 0.01
Modify | 6.059 | 6.059 | 6.059 | 0.0 | 24.84
Other | | 0.1876 | | | 0.77
Nlocal: 3000.00 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 462.000 ave 462 max 462 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 17694.0 ave 17694 max 17694 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 17694
Ave neighs/atom = 5.8980000
Neighbor list builds = 1133
Dangerous builds = 0
Total wall time: 0:00:24

161
examples/granular/log.29Mar19.pour.flatwall.g++.4 → examples/granular/log.29Oct20.pour.flatwall.g++.4
View File

@ -1,5 +1,4 @@
LAMMPS (29 Mar 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
LAMMPS (29 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# pour two types of particles (cohesive and non-cohesive) on flat wall
@ -45,9 +44,14 @@ region boxreg block 0 20 0 ${boxy} 0 ${boxz}
region boxreg block 0 20 0 20 0 ${boxz}
region boxreg block 0 20 0 20 0 30
create_box 2 boxreg
Created orthogonal box = (0 0 0) to (20 20 30)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (20.000000 20.000000 30.000000)
2 by 2 by 1 MPI processor grid
change_box all boundary p p f
Changing box ...
pair_style granular
pair_coeff 1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
comm_modify vel yes
@ -75,26 +79,19 @@ fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1
Particle insertion: 562 every 346 steps, 1500 by step 693
comm_modify vel yes
neighbor ${skin} bin
neighbor 0.15 bin
neigh_modify delay 0 every 1 check yes
pair_style granular
pair_coeff 1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
fix 3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
thermo_style custom step cpu atoms ke
thermo_style custom step atoms ke
thermo_modify lost warn
thermo 100
timestep 0.001
dump 1 all custom 100 ${name}.dump id type radius mass x y z
dump 1 all custom 100 pour_two_types.dump id type radius mass x y z
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
run 5000
Neighbor list info ...
@ -110,82 +107,82 @@ Neighbor list info ...
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.98 | 11.98 | 11.98 Mbytes
Step CPU Atoms KinEng
0 0 0 -0
100 0.11584234 855 -0
200 0.12743592 855 -0
300 0.13925815 855 -0
400 0.35203671 1500 -0
500 0.37055922 1500 -0
600 0.38671875 1500 -0
700 0.71736908 2288 -0
800 0.74506783 2288 -0
900 0.77112222 2288 -0
1000 0.79632139 2288 -0
1100 1.0384252 2845 -0
1200 1.08093 2845 -0
1300 1.1224561 2845 -0
1400 1.1811485 3000 -0
1500 1.2414908 3000 -0
1600 1.3105879 3000 -0
1700 1.390928 3000 -0
1800 1.4869275 3000 -0
1900 1.5958266 3000 -0
2000 1.7172487 3000 -0
2100 1.851155 3000 -0
2200 1.9957182 3000 -0
2300 2.1593764 3000 -0
2400 2.3433132 3000 -0
2500 2.532742 3000 -0
2600 2.7376895 3000 -0
2700 2.9463468 3000 -0
2800 3.1645725 3000 -0
2900 3.3879526 3000 -0
3000 3.6152103 3000 -0
3100 3.8467371 3000 -0
3200 4.0787683 3000 -0
3300 4.3097105 3000 -0
3400 4.5423617 3000 -0
3500 4.7773693 3000 -0
3600 5.0127218 3000 -0
3700 5.2519271 3000 -0
3800 5.4951298 3000 -0
3900 5.7210469 3000 -0
4000 5.9432652 3000 -0
4100 6.1687591 3000 -0
4200 6.3942792 3000 -0
4300 6.6331475 3000 -0
4400 6.8632154 3000 -0
4500 7.0979366 3000 -0
4600 7.3305347 3000 -0
4700 7.5670528 3000 -0
4800 7.8086057 3000 -0
4900 8.0407174 3000 -0
5000 8.2765219 3000 -0
Loop time of 8.27669 on 4 procs for 5000 steps with 3000 atoms
Step Atoms KinEng
0 0 -0
100 926 -0
200 926 -0
300 926 -0
400 1498 -0
500 1498 -0
600 1498 -0
700 2275 -0
800 2275 -0
900 2275 -0
1000 2275 -0
1100 2954 -0
1200 2954 -0
1300 2954 -0
1400 3000 -0
1500 3000 -0
1600 3000 -0
1700 3000 -0
1800 3000 -0
1900 3000 -0
2000 3000 -0
2100 3000 -0
2200 3000 -0
2300 3000 -0
2400 3000 -0
2500 3000 -0
2600 3000 -0
2700 3000 -0
2800 3000 -0
2900 3000 -0
3000 3000 -0
3100 3000 -0
3200 3000 -0
3300 3000 -0
3400 3000 -0
3500 3000 -0
3600 3000 -0
3700 3000 -0
3800 3000 -0
3900 3000 -0
4000 3000 -0
4100 3000 -0
4200 3000 -0
4300 3000 -0
4400 3000 -0
4500 3000 -0
4600 3000 -0
4700 3000 -0
4800 3000 -0
4900 3000 -0
5000 3000 -0
Loop time of 12.1982 on 4 procs for 5000 steps with 3000 atoms
Performance: 52194.788 tau/day, 604.106 timesteps/s
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 35414.923 tau/day, 409.895 timesteps/s
97.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.6106 | 3.4073 | 5.4191 | 95.7 | 41.17
Neigh | 0.51456 | 0.64572 | 0.81542 | 16.6 | 7.80
Comm | 0.2808 | 2.5222 | 4.4998 | 121.9 | 30.47
Output | 0.15695 | 0.15919 | 0.16502 | 0.8 | 1.92
Modify | 1.3517 | 1.4192 | 1.4904 | 4.9 | 17.15
Other | | 0.123 | | | 1.49
Pair | 1.7141 | 3.8131 | 6.2143 | 107.3 | 31.26
Neigh | 0.77648 | 0.96585 | 1.1892 | 18.3 | 7.92
Comm | 0.7427 | 3.5566 | 5.9731 | 128.4 | 29.16
Output | 0.0067544 | 0.0086352 | 0.011408 | 1.8 | 0.07
Modify | 3.3476 | 3.5826 | 3.8235 | 11.5 | 29.37
Other | | 0.2715 | | | 2.23
Nlocal: 750 ave 1036 max 482 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 429.75 ave 475 max 386 min
Nlocal: 750.000 ave 1033 max 463 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 435.000 ave 492 max 378 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 4434.50 ave 7028 max 1967 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 4051.75 ave 6274 max 2057 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 16207
Ave neighs/atom = 5.40233
Neighbor list builds = 1165
Total # of neighbors = 17738
Ave neighs/atom = 5.9126667
Neighbor list builds = 1139
Dangerous builds = 0
Total wall time: 0:00:08
Total wall time: 0:00:12