mirror of https://github.com/lammps/lammps.git
fix elstop: Rename to fix electron/stopping
This commit is contained in:
Risto Toijala
parent
d1cb8970d5
commit
0d78c7b43d
|
|
@ -61,7 +61,7 @@ OPT.
|
|||
"edpd/source"_fix_dpd_source.html,
|
||||
"efield"_fix_efield.html,
|
||||
"ehex"_fix_ehex.html,
|
||||
"elstop"_fix_elstop.html,
|
||||
"electron/stopping"_fix_electron_stopping.html,
|
||||
"enforce2d (k)"_fix_enforce2d.html,
|
||||
"eos/cv"_fix_eos_cv.html,
|
||||
"eos/table"_fix_eos_table.html,
|
||||
|
|
|
|||
|
|
@ -199,7 +199,7 @@ accelerated styles exist.
|
|||
"edpd/source"_fix_dpd_source.html -
|
||||
"efield"_fix_efield.html - impose electric field on system
|
||||
"ehex"_fix_ehex.html - enhanced heat exchange algorithm
|
||||
"elstop"_fix_elstop.html - electronic stopping power as a friction force
|
||||
"electron/stopping"_fix_electron_stopping.html - electronic stopping power as a friction force
|
||||
"enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force
|
||||
"eos/cv"_fix_eos_cv.html -
|
||||
"eos/table"_fix_eos_table.html -
|
||||
|
|
|
|||
|
|
@ -6,14 +6,14 @@
|
|||
|
||||
:line
|
||||
|
||||
fix elstop command :h3
|
||||
fix electron/stopping command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID elstop Ecut file keyword value ... :pre
|
||||
fix ID group-ID electron/stopping Ecut file keyword value ... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
elstop = style name of this fix command :l
|
||||
electron/stopping = style name of this fix command :l
|
||||
Ecut = minimum kinetic energy for electronic stopping (energy units) :l
|
||||
file = name of the file containing the electronic stopping power table :l
|
||||
zero or more keyword/value pairs may be appended to args :l
|
||||
|
|
@ -21,14 +21,14 @@ keyword = {region} or {minneigh} :l
|
|||
{region} value = region-ID
|
||||
region-ID = region, whose atoms will be affected by this fix
|
||||
{minneigh} value = minneigh
|
||||
minneigh = minimum number of neighbors for atoms to have elstop applied :pre
|
||||
minneigh = minimum number of neighbors an atom to have stopping applied :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix el all elstop 10.0 elstop-table.txt
|
||||
fix el all elstop 10.0 elstop-table.txt minneigh 3
|
||||
fix el mygroup elstop 1.0 elstop-table.txt region bulk :pre
|
||||
fix el all electron/stopping 10.0 elstop-table.txt
|
||||
fix el all electron/stopping 10.0 elstop-table.txt minneigh 3
|
||||
fix el mygroup electron/stopping 1.0 elstop-table.txt region bulk :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
|
@ -48,9 +48,9 @@ to each atom as:
|
|||
\vec\{F\}_i = \vec\{F\}^0_i - \frac\{\vec\{v\}_i\}\{\|\vec\{v\}_i\|\} \cdot S_e
|
||||
\end\{equation\}
|
||||
|
||||
where \(\vec\{F\}_i\) is the resulting total force on the atom. \(\vec\{F\}^0_i\)
|
||||
is the original force applied to the atom, \(\vec\{v\}_i\) is its velocity and
|
||||
\(S_e\) is the stopping power of the ion.
|
||||
where \(\vec\{F\}_i\) is the resulting total force on the atom.
|
||||
\(\vec\{F\}^0_i\) is the original force applied to the atom, \(\vec\{v\}_i\) is
|
||||
its velocity and \(S_e\) is the stopping power of the ion.
|
||||
|
||||
NOTE: In addition to electronic stopping, atomic cascades and irradiation
|
||||
simulations require the use of an adaptive timestep (see
|
||||
|
|
@ -79,10 +79,10 @@ in bulk material. An alternative is to disable the check for neighbors by
|
|||
setting {minneigh} to zero and using the {region} keyword. This is necessary
|
||||
when running simulations of cluster bombardment.
|
||||
|
||||
If the {region} keyword is used, the atom must also be in the specified geometric
|
||||
"region"_region.html in order to have electronic stopping applied to it. This is
|
||||
useful if the position of the bulk material is fixed. By default the electronic
|
||||
stopping is applied everywhere in the simulation cell.
|
||||
If the {region} keyword is used, the atom must also be in the specified
|
||||
geometric "region"_region.html in order to have electronic stopping applied to
|
||||
it. This is useful if the position of the bulk material is fixed. By default
|
||||
the electronic stopping is applied everywhere in the simulation cell.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -40,7 +40,7 @@ Fixes :h1
|
|||
fix_dt_reset
|
||||
fix_efield
|
||||
fix_ehex
|
||||
fix_elstop
|
||||
fix_electron_stopping
|
||||
fix_enforce2d
|
||||
fix_eos_cv
|
||||
fix_eos_table
|
||||
|
|
|
|||
|
|
@ -264,7 +264,7 @@ fix_drude_transform.html
|
|||
fix_dt_reset.html
|
||||
fix_efield.html
|
||||
fix_ehex.html
|
||||
fix_elstop.html
|
||||
fix_electron_stopping.html
|
||||
fix_enforce2d.html
|
||||
fix_eos_cv.html
|
||||
fix_eos_table.html
|
||||
|
|
|
|||
|
|
@ -692,7 +692,6 @@ elong
|
|||
Elsevier
|
||||
Elsner
|
||||
Elstner
|
||||
elstop
|
||||
elt
|
||||
emacs
|
||||
emax
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
|
@ -45,7 +45,7 @@ dihedral_style table/cut, Mike Salerno, ksalerno@pha.jhu.edu, 11 May 18
|
|||
fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
|
||||
fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015
|
||||
fix bond/react, Jacob Gissinger (CU Boulder), info at disarmmd.org, 24 Feb 2018
|
||||
fix elstop, Konstantin Avchaciov, k.avchachov at gmail.com, 26 Feb 2019
|
||||
fix electron/stopping, Konstantin Avchaciov, k.avchachov at gmail.com, 26 Feb 2019
|
||||
fix ffl, David Wilkins (EPFL Lausanne), david.wilkins @ epfl.ch, 28 Sep 2018
|
||||
fix filter/corotate, Lukas Fath (KIT), lukas.fath at kit.edu, 15 Mar 2017
|
||||
fix flow/gauss, Joel Eaves (CU Boulder), Joel.Eaves@Colorado.edu, 23 Aug 2016
|
||||
|
|
|
|||
|
|
@ -19,7 +19,7 @@
|
|||
#include <cmath>
|
||||
#include <cstdio>
|
||||
#include <cstring>
|
||||
#include "fix_elstop.h"
|
||||
#include "fix_electron_stopping.h"
|
||||
#include "mpi.h"
|
||||
#include "atom.h"
|
||||
#include "update.h"
|
||||
|
|
@ -42,7 +42,7 @@ using namespace FixConst;
|
|||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixElstop::FixElstop(LAMMPS *lmp, int narg, char **arg) :
|
||||
FixElectronStopping::FixElectronStopping(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg)
|
||||
{
|
||||
scalar_flag = 1; // Has compute_scalar
|
||||
|
|
@ -51,16 +51,17 @@ FixElstop::FixElstop(LAMMPS *lmp, int narg, char **arg) :
|
|||
nevery = 1; // Run fix every step
|
||||
|
||||
|
||||
// args: 0 = fix ID, 1 = group ID, 2 = "elstop"
|
||||
// args: 0 = fix ID, 1 = group ID, 2 = "electron/stopping"
|
||||
// 3 = Ecut, 4 = file path
|
||||
// optional rest: "region" <region name>
|
||||
// "minneigh" <min number of neighbors>
|
||||
|
||||
if (narg < 5)
|
||||
error->all(FLERR, "Illegal fix elstop command: too few arguments");
|
||||
if (narg < 5) error->all(FLERR,
|
||||
"Illegal fix electron/stopping command: too few arguments");
|
||||
|
||||
Ecut = force->numeric(FLERR, arg[3]);
|
||||
if (Ecut <= 0.0) error->all(FLERR, "Illegal fix elstop command: Ecut <= 0");
|
||||
if (Ecut <= 0.0) error->all(FLERR,
|
||||
"Illegal fix electron/stopping command: Ecut <= 0");
|
||||
|
||||
int iarg = 5;
|
||||
iregion = -1;
|
||||
|
|
@ -69,27 +70,28 @@ FixElstop::FixElstop(LAMMPS *lmp, int narg, char **arg) :
|
|||
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg], "region") == 0) {
|
||||
if (iregion >= 0)
|
||||
error->all(FLERR, "Illegal fix elstop command: region given twice");
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR, "Illegal fix elstop command: region name missing");
|
||||
if (iregion >= 0) error->all(FLERR,
|
||||
"Illegal fix electron/stopping command: region given twice");
|
||||
if (iarg+2 > narg) error->all(FLERR,
|
||||
"Illegal fix electron/stopping command: region name missing");
|
||||
iregion = domain->find_region(arg[iarg+1]);
|
||||
if (iregion < 0)
|
||||
error->all(FLERR, "Region ID for fix elstop does not exist");
|
||||
if (iregion < 0) error->all(FLERR,
|
||||
"Region ID for fix electron/stopping does not exist");
|
||||
iarg += 2;
|
||||
}
|
||||
else if (strcmp(arg[iarg], "minneigh") == 0) {
|
||||
if (minneighflag)
|
||||
error->all(FLERR, "Illegal fix elstop command: minneigh given twice");
|
||||
if (minneighflag) error->all(FLERR,
|
||||
"Illegal fix electron/stopping command: minneigh given twice");
|
||||
minneighflag = true;
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR, "Illegal fix elstop command: minneigh number missing");
|
||||
if (iarg+2 > narg) error->all(FLERR,
|
||||
"Illegal fix electron/stopping command: minneigh number missing");
|
||||
minneigh = force->inumeric(FLERR, arg[iarg+1]);
|
||||
if (minneigh < 0)
|
||||
error->all(FLERR, "Illegal fix elstop command: minneigh < 0");
|
||||
if (minneigh < 0) error->all(FLERR,
|
||||
"Illegal fix electron/stopping command: minneigh < 0");
|
||||
iarg += 2;
|
||||
}
|
||||
else error->all(FLERR, "Illegal fix elstop command: unknown argument");
|
||||
else error->all(FLERR,
|
||||
"Illegal fix electron/stopping command: unknown argument");
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -98,7 +100,7 @@ FixElstop::FixElstop(LAMMPS *lmp, int narg, char **arg) :
|
|||
const int ncol = atom->ntypes + 1;
|
||||
if (comm->me == 0) {
|
||||
maxlines = 300;
|
||||
memory->create(elstop_ranges, ncol, maxlines, "elstop:tabs");
|
||||
memory->create(elstop_ranges, ncol, maxlines, "electron/stopping:table");
|
||||
read_table(arg[4]);
|
||||
}
|
||||
|
||||
|
|
@ -106,21 +108,21 @@ FixElstop::FixElstop(LAMMPS *lmp, int narg, char **arg) :
|
|||
MPI_Bcast(&table_entries, 1 , MPI_INT, 0, world);
|
||||
|
||||
if (comm->me != 0)
|
||||
memory->create(elstop_ranges, ncol, maxlines, "elstop:tabs");
|
||||
memory->create(elstop_ranges, ncol, maxlines, "electron/stopping:table");
|
||||
|
||||
MPI_Bcast(&elstop_ranges[0][0], ncol*maxlines, MPI_DOUBLE, 0, world);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixElstop::~FixElstop()
|
||||
FixElectronStopping::~FixElectronStopping()
|
||||
{
|
||||
memory->destroy(elstop_ranges);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixElstop::setmask()
|
||||
int FixElectronStopping::setmask()
|
||||
{
|
||||
int mask = 0;
|
||||
mask |= POST_FORCE;
|
||||
|
|
@ -129,7 +131,7 @@ int FixElstop::setmask()
|
|||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixElstop::init()
|
||||
void FixElectronStopping::init()
|
||||
{
|
||||
SeLoss_sync_flag = 0;
|
||||
SeLoss = 0.0;
|
||||
|
|
@ -145,14 +147,14 @@ void FixElstop::init()
|
|||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixElstop::init_list(int /*id*/, NeighList *ptr)
|
||||
void FixElectronStopping::init_list(int /*id*/, NeighList *ptr)
|
||||
{
|
||||
list = ptr;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixElstop::post_force(int /*vflag*/)
|
||||
void FixElectronStopping::post_force(int /*vflag*/)
|
||||
{
|
||||
SeLoss_sync_flag = 0;
|
||||
|
||||
|
|
@ -183,8 +185,8 @@ void FixElstop::post_force(int /*vflag*/)
|
|||
|
||||
if (energy < Ecut) continue;
|
||||
if (energy < elstop_ranges[0][0]) continue;
|
||||
if (energy > elstop_ranges[0][table_entries - 1])
|
||||
error->one(FLERR, "Atom kinetic energy too high for fix elstop");
|
||||
if (energy > elstop_ranges[0][table_entries - 1]) error->one(FLERR,
|
||||
"Atom kinetic energy too high for fix electron/stopping");
|
||||
|
||||
if (iregion >= 0) {
|
||||
// Only apply in the given region
|
||||
|
|
@ -207,7 +209,7 @@ void FixElstop::post_force(int /*vflag*/)
|
|||
double E_lo = elstop_ranges[0][idown];
|
||||
double E_hi = elstop_ranges[0][iup];
|
||||
|
||||
// Get elstop with a simple linear interpolation
|
||||
// Get electronic stopping with a simple linear interpolation
|
||||
double Se = (Se_hi - Se_lo) / (E_hi - E_lo) * (energy - E_lo) + Se_lo;
|
||||
|
||||
double vabs = sqrt(v2);
|
||||
|
|
@ -223,7 +225,7 @@ void FixElstop::post_force(int /*vflag*/)
|
|||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double FixElstop::compute_scalar()
|
||||
double FixElectronStopping::compute_scalar()
|
||||
{
|
||||
// only sum across procs when changed since last call
|
||||
|
||||
|
|
@ -236,7 +238,7 @@ double FixElstop::compute_scalar()
|
|||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixElstop::read_table(const char *file)
|
||||
void FixElectronStopping::read_table(const char *file)
|
||||
{
|
||||
char line[MAXLINE];
|
||||
|
||||
|
|
@ -266,30 +268,31 @@ void FixElstop::read_table(const char *file)
|
|||
}
|
||||
|
||||
if (i != ncol || pch != NULL) // too short or too long
|
||||
error->one(FLERR, "fix elstop: Invalid table line");
|
||||
error->one(FLERR, "fix electron/stopping: Invalid table line");
|
||||
|
||||
if (l >= 1 && elstop_ranges[0][l] <= elstop_ranges[0][l-1])
|
||||
error->one(FLERR, "fix elstop: Energies must be in ascending order");
|
||||
error->one(FLERR,
|
||||
"fix electron/stopping: Energies must be in ascending order");
|
||||
|
||||
l++;
|
||||
}
|
||||
table_entries = l;
|
||||
|
||||
if (table_entries == 0)
|
||||
error->one(FLERR, "Did not find any data in elstop table file");
|
||||
error->one(FLERR, "Did not find any data in electron/stopping table file");
|
||||
|
||||
fclose(fp);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixElstop::grow_table()
|
||||
void FixElectronStopping::grow_table()
|
||||
{
|
||||
const int ncol = atom->ntypes + 1;
|
||||
int new_maxlines = 2 * maxlines;
|
||||
|
||||
double **new_array;
|
||||
memory->create(new_array, ncol, new_maxlines, "elstop:tabscopy");
|
||||
memory->create(new_array, ncol, new_maxlines, "electron/stopping:table");
|
||||
|
||||
for (int i = 0; i < ncol; i++)
|
||||
memcpy(new_array[i], elstop_ranges[i], maxlines*sizeof(double));
|
||||
|
|
@ -18,22 +18,22 @@
|
|||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(elstop,FixElstop)
|
||||
FixStyle(electron/stopping,FixElectronStopping)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_ELSTOP_H
|
||||
#define LMP_FIX_ELSTOP_H
|
||||
#ifndef LMP_FIX_ELECTRON_STOPPING_H
|
||||
#define LMP_FIX_ELECTRON_STOPPING_H
|
||||
|
||||
#include "fix.h"
|
||||
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixElstop : public Fix {
|
||||
class FixElectronStopping : public Fix {
|
||||
public:
|
||||
FixElstop(class LAMMPS *, int, char **);
|
||||
~FixElstop();
|
||||
FixElectronStopping(class LAMMPS *, int, char **);
|
||||
~FixElectronStopping();
|
||||
int setmask();
|
||||
void init();
|
||||
void post_force(int);
|
||||
|
|
@ -72,33 +72,33 @@ Self-explanatory. Check the input script syntax and compare to the
|
|||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Region ID for fix elstop does not exist
|
||||
E: Region ID for fix electron/stopping does not exist
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Atom kinetic energy too high for fix elstop
|
||||
E: Atom kinetic energy too high for fix electron/stopping
|
||||
|
||||
The group given in the fix elstop command includes an atom that has
|
||||
a kinetic energy higher than the largest energy in the elstop table.
|
||||
Reconsider whether the table is physically applicable to your system.
|
||||
The group given in the fix electron/stopping command includes an atom
|
||||
that has a kinetic energy higher than the largest energy in the stopping
|
||||
table. Reconsider whether the table is physically applicable to your system.
|
||||
|
||||
E: Cannot open stopping range table ...
|
||||
|
||||
The file containing the elstop table could not be opened. Chck the
|
||||
given path and the file's permissions.
|
||||
The file containing the electronic stopping table could not be opened.
|
||||
Check the given path and the file's permissions.
|
||||
|
||||
E: fix elstop: Invalid table line
|
||||
E: fix electron/stopping: Invalid table line
|
||||
|
||||
A line in the elstop table file contained too many or too few columns.
|
||||
A line in the stopping table file contained too many or too few columns.
|
||||
|
||||
E: fix elstop: Energies must be in ascending order
|
||||
E: fix electron/stopping: Energies must be in ascending order
|
||||
|
||||
The first column in the elstop table must be sorted from the smallest
|
||||
The first column in the stopping table must be sorted from the smallest
|
||||
energy to the largest.
|
||||
|
||||
E: Did not find any data in elstop table file
|
||||
E: Did not find any data in electronic stopping table file
|
||||
|
||||
Parsing the elstop table file produced no lines that were identifiable
|
||||
Parsing the stopping table file produced no lines that were identifiable
|
||||
as energies/stopping powers. Most likely the file is empty or contains
|
||||
only comments.
|
||||
|
||||
Loading…
Reference in New Issue