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fix elstop: Rename to fix electron/stopping

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This commit is contained in:
Risto Toijala
2019-04-04 09:57:15 +03:00
parent d1cb8970d5
commit 0d78c7b43d
17 changed files with 143 additions and 145 deletions
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0
examples/USER/misc/elstop/Si.Si.elstop → examples/USER/misc/electron_stopping/Si.Si.elstop
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0
examples/USER/misc/elstop/Si.sw → examples/USER/misc/electron_stopping/Si.sw
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4
examples/USER/misc/elstop/in.elstop → examples/USER/misc/electron_stopping/in.elstop
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@ -1,4 +1,4 @@
# Test case / example for the electronic stopping fix elstop
# Test case / example for fix electron/stopping
# Perfect Si lattice with one primary knock-on atom.
#
# Also uses fix dt/reset, as one should when energies are high
@ -26,7 +26,7 @@ pair_style sw
pair_coeff * * Si.sw Si
fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
fix fel all elstop 1.0 Si.Si.elstop
fix fel all electron/stopping 1.0 Si.Si.elstop
fix fnve all nve
thermo 10

6
examples/USER/misc/elstop/in.elstop.only → examples/USER/misc/electron_stopping/in.elstop.only
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@ -1,6 +1,6 @@
# Test case / example for the electronic stopping fix elstop
# Test case / example for fix electron/stopping
# One fast atom, no other interactions.
# Elstop only applied in a smaller box in the middle.
# Stopping only applied in a smaller box in the middle.
#
# Also uses fix dt/reset, as one should when energies are high
# enough to require electronic stopping.
@ -25,7 +25,7 @@ pair_style zero 1
pair_coeff * * 1
fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
fix fel all elstop 1.0 Si.Si.elstop minneigh 0 region rsmallbox
fix fel all electron/stopping 1.0 Si.Si.elstop minneigh 0 region rsmallbox
fix fnve all nve
compute ek all ke/atom

30
examples/USER/misc/elstop/log.20Mar19.elstop.g++.1 → examples/USER/misc/electron_stopping/log.20Mar19.elstop.g++.1
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@ -1,7 +1,7 @@
LAMMPS (28 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Test case / example for the electronic stopping fix elstop
# Test case / example for fix electron/stopping
# Perfect Si lattice with one primary knock-on atom.
#
# Also uses fix dt/reset, as one should when energies are high
@ -23,7 +23,7 @@ mass 1 28.0855
create_atoms 1 box
Created 32000 atoms
Time spent = 0.00365901 secs
create_atoms CPU = 0.00282311 secs
velocity all create 300 42534 mom yes rot yes
@ -36,7 +36,7 @@ pair_coeff * * Si.sw Si
Reading potential file Si.sw with DATE: 2007-06-11
fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
fix fel all elstop 1.0 Si.Si.elstop
fix fel all electron/stopping 1.0 Si.Si.elstop
fix fnve all nve
thermo 10
@ -58,7 +58,7 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) fix elstop, occasional, copy from (1)
(2) fix electron/stopping, occasional, copy from (1)
attributes: full, newton on
pair build: copy
stencil: none
@ -566,20 +566,20 @@ Step Time Dt f_fel
4980 0.014568876 3.9720495e-08 6777.8926
4990 0.014569265 3.7726941e-08 6778.0636
5000 0.014569634 3.5910753e-08 6778.2261
Loop time of 27.2739 on 1 procs for 5000 steps with 32000 atoms
Loop time of 24.155 on 1 procs for 5000 steps with 32000 atoms
Performance: 0.001 ns/day, 42193.880 hours/ns, 183.326 timesteps/s
96.6% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.001 ns/day, 37368.951 hours/ns, 206.996 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 | 17.626 | 17.626 | 17.626 | 0.0 | 64.62
Neigh | 1.5828 | 1.5828 | 1.5828 | 0.0 | 5.80
Comm | 0.78596 | 0.78596 | 0.78596 | 0.0 | 2.88
Output | 0.0082562 | 0.0082562 | 0.0082562 | 0.0 | 0.03
Modify | 6.414 | 6.414 | 6.414 | 0.0 | 23.52
Other | | 0.8573 | | | 3.14
Pair | 15.795 | 15.795 | 15.795 | 0.0 | 65.39
Neigh | 1.5182 | 1.5182 | 1.5182 | 0.0 | 6.29
Comm | 0.58555 | 0.58555 | 0.58555 | 0.0 | 2.42
Output | 0.0064323 | 0.0064323 | 0.0064323 | 0.0 | 0.03
Modify | 5.619 | 5.619 | 5.619 | 0.0 | 23.26
Other | | 0.6313 | | | 2.61
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -594,4 +594,4 @@ Total # of neighbors = 576016
Ave neighs/atom = 18.0005
Neighbor list builds = 68
Dangerous builds = 42
Total wall time: 0:00:27
Total wall time: 0:00:24

30
examples/USER/misc/elstop/log.20Mar19.elstop.g++.4 → examples/USER/misc/electron_stopping/log.20Mar19.elstop.g++.4
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@ -1,7 +1,7 @@
LAMMPS (28 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Test case / example for the electronic stopping fix elstop
# Test case / example for fix electron/stopping
# Perfect Si lattice with one primary knock-on atom.
#
# Also uses fix dt/reset, as one should when energies are high
@ -23,7 +23,7 @@ mass 1 28.0855
create_atoms 1 box
Created 32000 atoms
Time spent = 0.000838995 secs
create_atoms CPU = 0.000856161 secs
velocity all create 300 42534 mom yes rot yes
@ -36,7 +36,7 @@ pair_coeff * * Si.sw Si
Reading potential file Si.sw with DATE: 2007-06-11
fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
fix fel all elstop 1.0 Si.Si.elstop
fix fel all electron/stopping 1.0 Si.Si.elstop
fix fnve all nve
thermo 10
@ -58,7 +58,7 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) fix elstop, occasional, copy from (1)
(2) fix electron/stopping, occasional, copy from (1)
attributes: full, newton on
pair build: copy
stencil: none
@ -566,20 +566,20 @@ Step Time Dt f_fel
4980 0.014615386 1.0814135e-07 6805.2899
4990 0.014616494 1.1414984e-07 6805.7869
5000 0.014617666 1.2114278e-07 6806.313
Loop time of 20.4871 on 4 procs for 5000 steps with 32000 atoms
Loop time of 9.26846 on 4 procs for 5000 steps with 32000 atoms
Performance: 0.003 ns/day, 9395.278 hours/ns, 244.056 timesteps/s
80.0% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 0.006 ns/day, 4250.474 hours/ns, 539.464 timesteps/s
96.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.3304 | 5.3747 | 5.4481 | 1.9 | 26.23
Neigh | 0.47764 | 0.49529 | 0.50484 | 1.5 | 2.42
Comm | 7.3264 | 7.6698 | 8.0174 | 11.5 | 37.44
Output | 0.020597 | 0.064879 | 0.11197 | 13.7 | 0.32
Modify | 4.3321 | 4.7499 | 5.1576 | 18.4 | 23.18
Other | | 2.132 | | | 10.41
Pair | 4.6281 | 4.7789 | 5.1937 | 11.0 | 51.56
Neigh | 0.40488 | 0.41576 | 0.43895 | 2.1 | 4.49
Comm | 0.8478 | 1.2799 | 1.4349 | 22.1 | 13.81
Output | 0.0048099 | 0.016429 | 0.050251 | 15.2 | 0.18
Modify | 2.1042 | 2.1347 | 2.1706 | 1.6 | 23.03
Other | | 0.6427 | | | 6.93
Nlocal: 8000 ave 8033 max 7977 min
Histogram: 1 0 1 1 0 0 0 0 0 1
@ -594,4 +594,4 @@ Total # of neighbors = 576008
Ave neighs/atom = 18.0003
Neighbor list builds = 67
Dangerous builds = 38
Total wall time: 0:00:20
Total wall time: 0:00:09

32
examples/USER/misc/elstop/log.20Mar19.elstop.only.g++.1 → examples/USER/misc/electron_stopping/log.20Mar19.elstop.only.g++.1
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@ -1,9 +1,9 @@
LAMMPS (28 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Test case / example for the electronic stopping fix elstop
# Test case / example for fix electron/stopping
# One fast atom, no other interactions.
# Elstop only applied in a smaller box in the middle.
# Stopping only applied in a smaller box in the middle.
#
# Also uses fix dt/reset, as one should when energies are high
# enough to require electronic stopping.
@ -26,14 +26,14 @@ mass 1 28.0855
create_atoms 1 single 0 0 0
Created 1 atoms
Time spent = 3.09944e-06 secs
create_atoms CPU = 4.05312e-06 secs
velocity all set 1120 1620 389
pair_style zero 1
pair_coeff * * 1
fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
fix fel all elstop 1.0 Si.Si.elstop minneigh 0 region rsmallbox
fix fel all electron/stopping 1.0 Si.Si.elstop minneigh 0 region rsmallbox
fix fnve all nve
compute ek all ke/atom
@ -45,8 +45,6 @@ thermo_style custom step time dt f_fel c_ektot
#dump mydump all custom 200 elstop.only.dump id x y z vx vy vz fx fy fz c_ek
run 10000
WARNING: More than one compute ke/atom (src/compute_ke_atom.cpp:55)
WARNING: More than one compute ke/atom (src/compute_ke_atom.cpp:55)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -59,7 +57,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix elstop, occasional
(2) fix electron/stopping, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
@ -167,20 +165,20 @@ Step Time Dt f_fel c_ektot
9800 0.57677384 6.0949329e-05 1947.6558 3917.8967
9900 0.58286878 6.0949329e-05 1947.6558 3917.8967
10000 0.58896371 6.0949329e-05 1947.6558 3917.8967
Loop time of 1.81749 on 1 procs for 10000 steps with 1 atoms
Loop time of 1.25184 on 1 procs for 10000 steps with 1 atoms
Performance: 28.974 ns/day, 0.828 hours/ns, 5502.087 timesteps/s
95.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 42.066 ns/day, 0.571 hours/ns, 7988.216 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 | 0.00068855 | 0.00068855 | 0.00068855 | 0.0 | 0.04
Neigh | 1.777 | 1.777 | 1.777 | 0.0 | 97.77
Comm | 0.028521 | 0.028521 | 0.028521 | 0.0 | 1.57
Output | 0.0020428 | 0.0020428 | 0.0020428 | 0.0 | 0.11
Modify | 0.0063827 | 0.0063827 | 0.0063827 | 0.0 | 0.35
Other | | 0.002891 | | | 0.16
Pair | 0.0005827 | 0.0005827 | 0.0005827 | 0.0 | 0.05
Neigh | 1.2134 | 1.2134 | 1.2134 | 0.0 | 96.93
Comm | 0.02822 | 0.02822 | 0.02822 | 0.0 | 2.25
Output | 0.0017159 | 0.0017159 | 0.0017159 | 0.0 | 0.14
Modify | 0.0052147 | 0.0052147 | 0.0052147 | 0.0 | 0.42
Other | | 0.002664 | | | 0.21
Nlocal: 1 ave 1 max 1 min
Histogram: 1 0 0 0 0 0 0 0 0 0

34
examples/USER/misc/elstop/log.20Mar19.elstop.only.g++.4 → examples/USER/misc/electron_stopping/log.20Mar19.elstop.only.g++.4
View File

@ -1,9 +1,9 @@
LAMMPS (28 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Test case / example for the electronic stopping fix elstop
# Test case / example for fix electron/stopping
# One fast atom, no other interactions.
# Elstop only applied in a smaller box in the middle.
# Stopping only applied in a smaller box in the middle.
#
# Also uses fix dt/reset, as one should when energies are high
# enough to require electronic stopping.
@ -26,14 +26,14 @@ mass 1 28.0855
create_atoms 1 single 0 0 0
Created 1 atoms
Time spent = 2.00272e-05 secs
create_atoms CPU = 1.19209e-05 secs
velocity all set 1120 1620 389
pair_style zero 1
pair_coeff * * 1
fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
fix fel all elstop 1.0 Si.Si.elstop minneigh 0 region rsmallbox
fix fel all electron/stopping 1.0 Si.Si.elstop minneigh 0 region rsmallbox
fix fnve all nve
compute ek all ke/atom
@ -45,8 +45,6 @@ thermo_style custom step time dt f_fel c_ektot
#dump mydump all custom 200 elstop.only.dump id x y z vx vy vz fx fy fz c_ek
run 10000
WARNING: More than one compute ke/atom (src/compute_ke_atom.cpp:55)
WARNING: More than one compute ke/atom (src/compute_ke_atom.cpp:55)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -59,7 +57,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix elstop, occasional
(2) fix electron/stopping, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
@ -167,20 +165,20 @@ Step Time Dt f_fel c_ektot
9800 0.57677384 6.0949329e-05 1947.6558 3917.8967
9900 0.58286878 6.0949329e-05 1947.6558 3917.8967
10000 0.58896371 6.0949329e-05 1947.6558 3917.8967
Loop time of 3.82192 on 4 procs for 10000 steps with 1 atoms
Loop time of 1.38891 on 4 procs for 10000 steps with 1 atoms
Performance: 13.778 ns/day, 1.742 hours/ns, 2616.487 timesteps/s
76.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 37.915 ns/day, 0.633 hours/ns, 7199.876 timesteps/s
94.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0006454 | 0.00077975 | 0.001003 | 0.0 | 0.02
Neigh | 1.3094 | 1.3771 | 1.441 | 4.0 | 36.03
Comm | 0.13665 | 0.16207 | 0.20281 | 6.1 | 4.24
Output | 0.036584 | 0.046189 | 0.060792 | 4.2 | 1.21
Modify | 2.1326 | 2.212 | 2.3096 | 4.3 | 57.88
Other | | 0.02382 | | | 0.62
Pair | 0.0004971 | 0.00060463 | 0.00069618 | 0.0 | 0.04
Neigh | 1.1005 | 1.1507 | 1.2839 | 7.2 | 82.85
Comm | 0.025918 | 0.026382 | 0.027041 | 0.3 | 1.90
Output | 0.0016336 | 0.005001 | 0.01507 | 8.2 | 0.36
Modify | 0.059378 | 0.20196 | 0.25453 | 18.3 | 14.54
Other | | 0.00422 | | | 0.30
Nlocal: 0.25 ave 1 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
@ -195,4 +193,4 @@ Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 960
Dangerous builds = 568
Total wall time: 0:00:03
Total wall time: 0:00:01