Add fix electron/stopping to USER-MISC

doc/src/Commands_fix.txt

@@ -61,6 +61,7 @@ OPT.
 "edpd/source"_fix_dpd_source.html,
 "efield"_fix_efield.html,
 "ehex"_fix_ehex.html,
+"electron/stopping"_fix_electron_stopping.html,
 "enforce2d (k)"_fix_enforce2d.html,
 "eos/cv"_fix_eos_cv.html,
 "eos/table"_fix_eos_table.html,

doc/src/fix.txt

@@ -201,6 +201,7 @@ 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
+"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 -

doc/src/fix_electron_stopping.txt

@@ -0,0 +1,165 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+fix electron/stopping command :h3
+
+[Syntax:]
+
+fix ID group-ID electron/stopping Ecut file keyword value ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,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
+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 an atom to have stopping applied :pre
+:ule
+
+[Examples:]
+
+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:]
+
+This fix implements inelastic energy loss for fast projectiles in solids. It
+applies a friction force to fast moving atoms to slow them down due to
+"electronic stopping"_#elstopping (energy lost via electronic collisions per
+unit of distance). This fix should be used for simulation of irradiation
+damage or ion implantation, where the ions can lose noticeable amounts of
+energy from electron excitations. If the electronic stopping power is not
+considered, the simulated range of the ions can be severely overestimated
+("Nordlund98"_#Nordlund98, "Nordlund95"_#Nordlund95).
+
+The electronic stopping is implemented by applying a friction force
+to each atom as:
+
+\begin\{equation\}
+\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.
+
+NOTE: In addition to electronic stopping, atomic cascades and irradiation
+simulations require the use of an adaptive timestep (see
+"fix dt/reset"_fix_dt_reset.html) and the repulsive ZBL potential (see
+"ZBL"_pair_zbl.html potential) or similar. Without these settings the
+interaction between the ion and the target atoms will be faulty. It is also
+common to use in such simulations a thermostat ("fix_nvt"_fix_nh.html) in
+the borders of the simulation cell.
+
+NOTE: This fix removes energy from fast projectiles without depositing it as a
+heat to the simulation cell. Such implementation might lead to the unphysical
+results when the amount of energy deposited to the electronic system is large,
+e.g. simulations of Swift Heavy Ions (energy per nucleon of 100 keV/amu or
+higher) or multiple projectiles. You could compensate energy loss by coupling
+bulk atoms with some thermostat or control heat transfer between electronic and
+atomic subsystems with the two-temperature model ("fix_ttm"_fix_ttm.html).
+
+At low velocities the electronic stopping is negligible. The electronic
+friction is not applied to atoms whose kinetic energy is smaller than {Ecut},
+or smaller than the lowest energy value given in the table in {file}.
+Electronic stopping should be applied only when a projectile reaches bulk
+material. This fix scans neighbor list and excludes atoms with fewer than
+{minneigh} neighbors (by default one). If the pair potential cutoff is large,
+minneigh should be increased, though not above the number of nearest neighbors
+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.
+
+:line
+
+The energy ranges and stopping powers are read from the file {file}.
+Lines starting with {#} and empty lines are ignored. Otherwise each
+line must contain exactly [N+1] numbers, where [N] is the number of atom
+types in the simulation.
+
+The first column is the energy for which the stopping powers on that
+line apply. The energies must be sorted from the smallest to the largest.
+The other columns are the stopping powers \(S_e\) for each atom type,
+in ascending order, in force "units"_units.html. The stopping powers for
+intermediate energy values are calculated with linear interpolation between
+2 nearest points.
+
+For example:
+
+# This is a comment
+#       atom-1    atom-2
+# eV    eV/Ang    eV/Ang  # units metal
+ 10        0        0
+250       60       80
+750      100      150 :pre
+
+
+If an atom which would have electronic stopping applied to it has a
+kinetic energy higher than the largest energy given in {file}, LAMMPS
+will exit with an error message.
+
+The stopping power depends on the energy of the ion and the target
+material. The electronic stopping table can be obtained from
+scientific publications, experimental databases or by using
+"SRIM"_#SRIM software. Other programs such as "CasP"_#CasP or
+"PASS"_#PASS can calculate the energy deposited as a function
+of the impact parameter of the ion; these results can be used
+to derive the stopping power.
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.
+
+The "fix_modify"_fix_modify.html options are not supported.
+
+This fix computes a global scalar, which can be accessed by various
+"output commands"_Howto_output.html. The scalar is the total energy
+loss from electronic stopping applied by this fix since the start of
+the latest run. It is considered "intensive".
+
+The {start/stop} keywords of the "run"_run.html command have no effect
+on this fix.
+
+[Restrictions:]
+
+This pair style is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Build package"_Build_package.html
+doc page for more info.
+
+[Default:]
+
+The default is no limitation by region, and minneigh = 1.
+
+:line
+:link(elstopping)
+[(electronic stopping)] Wikipedia - Electronic Stopping Power: https://en.wikipedia.org/wiki/Stopping_power_%28particle_radiation%29
+
+:link(Nordlund98)
+[(Nordlund98)] Nordlund, Kai, et al.  Physical Review B 57.13 (1998): 7556.
+
+:link(Nordlund95)
+[(Nordlund95)] Nordlund, Kai. Computational materials science 3.4 (1995): 448-456.
+
+:link(SRIM)
+[(SRIM)] SRIM webpage: http://www.srim.org/
+
+:link(CasP)
+[(CasP)] CasP webpage: https://www.helmholtz-berlin.de/people/gregor-schiwietz/casp_en.html
+
+:link(PASS)
+[(PASS)] PASS webpage: https://www.sdu.dk/en/DPASS

doc/src/fixes.txt

@@ -40,6 +40,7 @@ Fixes :h1
    fix_dt_reset
    fix_efield
    fix_ehex
+   fix_electron_stopping
    fix_enforce2d
    fix_eos_cv
    fix_eos_table

doc/src/lammps.book

@@ -265,6 +265,7 @@ fix_drude_transform.html
 fix_dt_reset.html
 fix_efield.html
 fix_ehex.html
+fix_electron_stopping.html
 fix_enforce2d.html
 fix_eos_cv.html
 fix_eos_table.html

doc/utils/sphinx-config/false_positives.txt

@@ -289,6 +289,7 @@ Cao
 Capolungo
 Caro
 cartesian
+CasP
 Caswell
 Cates
 Cavium
@@ -656,6 +657,7 @@ ec
 Ec
 ecoul
 ecp
+Ecut
 edgeIDs
 edihed
 edim
@@ -1255,6 +1257,7 @@ Jy
 Jz
 jzimmer
 Kadiri
+Kai
 Kalia
 Kamberaj
 Kapfer
@@ -1285,6 +1288,7 @@ Keir
 Kelchner
 Kelkar
 Kemper
+keV
 Keyes
 Khersonskii
 Khrapak
@@ -1627,6 +1631,7 @@ minima
 minimizations
 minimizer
 minimizers
+minneigh
 minorder
 minSteps
 mintcream
@@ -2944,6 +2949,7 @@ Wi
 Wicaksono
 wih
 Wijk
+Wikipedia
 wildcard
 Wildcard
 Wirnsberger

examples/USER/misc/electron_stopping/Si.Si.elstop

@@ -0,0 +1,14 @@
+# Electronic stopping for Si in Si
+# Uses metal units
+# Kinetic energy in eV, stopping power in eV/A
+# For other atom types, add columns.
+
+# energy    Si in Si
+  3918.2      6.541
+ 15672.9     13.091
+ 35263.9     19.660
+ 62691.5     26.257
+ 97955.4     32.889
+141055.9     39.566
+191992.0     46.292
+250766.1     53.074

examples/USER/misc/electron_stopping/Si.sw

@@ -0,0 +1 @@
+../../../../potentials/Si.sw

examples/USER/misc/electron_stopping/in.elstop

@@ -0,0 +1,38 @@
+# 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
+# enough to require electronic stopping.
+
+units metal
+boundary p p p
+timestep 0.0001
+
+lattice fcc 5.431
+
+region rbox block -10 10 -10 10 -10 10
+create_box 1 rbox
+
+mass 1 28.0855
+
+create_atoms 1 box
+
+velocity all create 300 42534 mom yes rot yes
+
+group gPKA id 1
+velocity gPKA set 1120 1620 389
+
+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 electron/stopping 1.0 Si.Si.elstop
+fix fnve all nve
+
+thermo 10
+thermo_style custom step time dt f_fel
+
+#compute ek all ke/atom
+#dump mydump all custom 200 elstop.dump id x y z vx vy vz fx fy fz c_ek
+
+run 5000

examples/USER/misc/electron_stopping/in.elstop.only

@@ -0,0 +1,39 @@
+# Test case / example for fix electron/stopping
+# One fast atom, no other interactions.
+# 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.
+
+units metal
+boundary p p p
+timestep 0.0001
+
+lattice fcc 1
+
+region rbox block -100 100 -100 100 -100 100
+region rsmallbox block -90 90 -90 90 -90 90
+
+create_box 1 rbox
+
+mass 1 28.0855
+
+create_atoms 1 single 0 0 0
+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 electron/stopping 1.0 Si.Si.elstop minneigh 0 region rsmallbox
+fix fnve all nve
+
+compute ek all ke/atom
+compute ektot all reduce sum c_ek
+
+thermo 100
+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