diff --git a/doc/src/Commands_fix.txt b/doc/src/Commands_fix.txt index 678cc9ba0d..ad884f7bd8 100644 --- a/doc/src/Commands_fix.txt +++ b/doc/src/Commands_fix.txt @@ -61,6 +61,7 @@ OPT. "edpd/source"_fix_dpd_source.html, "efield"_fix_efield.html, "ehex"_fix_ehex.html, +"elstop"_fix_elstop.html, "enforce2d (k)"_fix_enforce2d.html, "eos/cv"_fix_eos_cv.html, "eos/table"_fix_eos_table.html, diff --git a/doc/src/Eqs/fix_elstop.jpg b/doc/src/Eqs/fix_elstop.jpg new file mode 100644 index 0000000000..e862c938f0 Binary files /dev/null and b/doc/src/Eqs/fix_elstop.jpg differ diff --git a/doc/src/Eqs/fix_elstop.tex b/doc/src/Eqs/fix_elstop.tex new file mode 100644 index 0000000000..760ded00f1 --- /dev/null +++ b/doc/src/Eqs/fix_elstop.tex @@ -0,0 +1,13 @@ +\documentclass[12pt]{article} + +\begin{document} + +$$ + {\vec F}_i = {\vec F}^{0}_i - \frac{{\vec v}_i}{\|\vec{v}_i\|}\cdot S_e +$$ + +\end{document} + + + + diff --git a/doc/src/fix.txt b/doc/src/fix.txt index 395f2ad7a9..fa34dc17de 100644 --- a/doc/src/fix.txt +++ b/doc/src/fix.txt @@ -199,6 +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 "enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force "eos/cv"_fix_eos_cv.html - "eos/table"_fix_eos_table.html - diff --git a/doc/src/fix_elstop.txt b/doc/src/fix_elstop.txt new file mode 100644 index 0000000000..75bb2ef101 --- /dev/null +++ b/doc/src/fix_elstop.txt @@ -0,0 +1,163 @@ +"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 elstop command :h3 + +[Syntax:] + +fix ID group-ID elstop 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 +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 for atoms to have elstop 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 + +[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: + +:c,image(Eqs/fix_elstop.jpg) + +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 diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt index 3853bb77a9..7bbf269a2c 100644 --- a/doc/src/fixes.txt +++ b/doc/src/fixes.txt @@ -40,6 +40,7 @@ Fixes :h1 fix_dt_reset fix_efield fix_ehex + fix_elstop fix_enforce2d fix_eos_cv fix_eos_table diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 6b220ed241..692ffcd712 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -264,6 +264,7 @@ fix_drude_transform.html fix_dt_reset.html fix_efield.html fix_ehex.html +fix_elstop.html fix_enforce2d.html fix_eos_cv.html fix_eos_table.html diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 6eb158396f..6d376d7b1f 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -286,6 +286,7 @@ Cao Capolungo Caro cartesian +CasP Caswell Cates Cavium @@ -647,6 +648,7 @@ ec Ec ecoul ecp +Ecut edgeIDs edihed edim @@ -690,6 +692,7 @@ elong Elsevier Elsner Elstner +elstop elt emacs emax @@ -1272,6 +1275,7 @@ Keir Kelchner Kelkar Kemper +keV Keyes Khersonskii Khrapak @@ -1608,6 +1612,7 @@ minima minimizations minimizer minimizers +minneigh minorder minSteps mintcream @@ -2919,6 +2924,7 @@ Wi Wicaksono wih Wijk +Wikipedia wildcard Wildcard Wirnsberger diff --git a/examples/USER/misc/elstop/Si.Si.elstop b/examples/USER/misc/elstop/Si.Si.elstop new file mode 100644 index 0000000000..51618149ff --- /dev/null +++ b/examples/USER/misc/elstop/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 diff --git a/examples/USER/misc/elstop/Si.sw b/examples/USER/misc/elstop/Si.sw new file mode 120000 index 0000000000..e575921334 --- /dev/null +++ b/examples/USER/misc/elstop/Si.sw @@ -0,0 +1 @@ +../../../../potentials/Si.sw \ No newline at end of file diff --git a/examples/USER/misc/elstop/in.elstop b/examples/USER/misc/elstop/in.elstop new file mode 100644 index 0000000000..e31e6d8a65 --- /dev/null +++ b/examples/USER/misc/elstop/in.elstop @@ -0,0 +1,38 @@ +# Test case / example for the electronic stopping fix elstop +# 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 elstop 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 diff --git a/examples/USER/misc/elstop/in.elstop.only b/examples/USER/misc/elstop/in.elstop.only new file mode 100644 index 0000000000..1d09fa11f9 --- /dev/null +++ b/examples/USER/misc/elstop/in.elstop.only @@ -0,0 +1,39 @@ +# Test case / example for the electronic stopping fix elstop +# One fast atom, no other interactions. +# Elstop 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 elstop 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 diff --git a/examples/USER/misc/elstop/log.20Mar19.elstop.g++.1 b/examples/USER/misc/elstop/log.20Mar19.elstop.g++.1 new file mode 100644 index 0000000000..3547ced959 --- /dev/null +++ b/examples/USER/misc/elstop/log.20Mar19.elstop.g++.1 @@ -0,0 +1,597 @@ +LAMMPS (28 Feb 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Test case / example for the electronic stopping fix elstop +# 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 +Lattice spacing in x,y,z = 5.431 5.431 5.431 + +region rbox block -10 10 -10 10 -10 10 +create_box 1 rbox +Created orthogonal box = (-54.31 -54.31 -54.31) to (54.31 54.31 54.31) + 1 by 1 by 1 MPI processor grid + +mass 1 28.0855 + +create_atoms 1 box +Created 32000 atoms + Time spent = 0.00365901 secs + +velocity all create 300 42534 mom yes rot yes + +group gPKA id 1 +1 atoms in group gPKA +velocity gPKA set 1120 1620 389 + +pair_style sw +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 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 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.77118 + ghost atom cutoff = 5.77118 + binsize = 2.88559, bins = 38 38 38 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair sw, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) fix elstop, occasional, copy from (1) + attributes: full, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 10.89 | 10.89 | 10.89 Mbytes +Step Time Dt f_fel + 0 0 4.98128e-05 0 + 10 0.00030141297 7.4132113e-06 143.83504 + 20 0.00035951427 6.0316944e-06 171.53673 + 30 0.00057458971 3.5117251e-05 274.07596 + 40 0.00086591312 5.8243334e-06 412.87446 + 50 0.00090045701 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0.01361833 1.6441528e-06 6346.3866 + 4650 0.013632159 1.1592769e-06 6352.6667 + 4660 0.013642828 9.8623051e-07 6357.5101 + 4670 0.013652418 9.4451692e-07 6361.8626 + 4680 0.013662041 1.0034733e-06 6366.2295 + 4690 0.013672824 1.2061779e-06 6371.1243 + 4700 0.013686941 1.780995e-06 6377.5343 + 4710 0.013713088 4.7634009e-06 6389.4131 + 4720 0.013968014 3.9765415e-05 6505.2802 + 4730 0.014228787 6.2632217e-06 6623.7185 + 4740 0.014278333 4.7934169e-06 6646.2018 + 4750 0.014382212 5.1069055e-05 6693.3424 + 4760 0.014525205 2.0381123e-06 6758.2178 + 4770 0.014538504 8.2250651e-07 6764.2412 + 4780 0.014544984 4.9114353e-07 6767.1723 + 4790 0.014549144 3.4212232e-07 6769.0518 + 4800 0.014552156 2.589287e-07 6770.4109 + 4810 0.014554491 2.0641662e-07 6771.4633 + 4820 0.014556384 1.7052382e-07 6772.315 + 4830 0.014557966 1.4457875e-07 6773.0262 + 4840 0.014559319 1.250293e-07 6773.6339 + 4850 0.014560498 1.09819e-07 6774.1626 + 4860 0.014561539 9.7678962e-08 6774.629 + 4870 0.01456247 8.7785899e-08 6775.0453 + 4880 0.01456331 7.9583482e-08 6775.4205 + 4890 0.014564074 7.2682934e-08 6775.7613 + 4900 0.014564773 6.6804784e-08 6776.0732 + 4910 0.014565418 6.1743238e-08 6776.3601 + 4920 0.014566015 5.7343571e-08 6776.6256 + 4930 0.014566571 5.3487327e-08 6776.8723 + 4940 0.01456709 5.0082359e-08 6777.1026 + 4950 0.014567577 4.7055963e-08 6777.3183 + 4960 0.014568035 4.4350048e-08 6777.521 + 4970 0.014568467 4.1917669e-08 6777.712 + 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 + +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 + +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 + +Nlocal: 32000 ave 32000 max 32000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 13556 ave 13556 max 13556 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 576016 ave 576016 max 576016 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 576016 +Ave neighs/atom = 18.0005 +Neighbor list builds = 68 +Dangerous builds = 42 +Total wall time: 0:00:27 diff --git a/examples/USER/misc/elstop/log.20Mar19.elstop.g++.4 b/examples/USER/misc/elstop/log.20Mar19.elstop.g++.4 new file mode 100644 index 0000000000..4b06000522 --- /dev/null +++ b/examples/USER/misc/elstop/log.20Mar19.elstop.g++.4 @@ -0,0 +1,597 @@ +LAMMPS (28 Feb 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Test case / example for the electronic stopping fix elstop +# 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 +Lattice spacing in x,y,z = 5.431 5.431 5.431 + +region rbox block -10 10 -10 10 -10 10 +create_box 1 rbox +Created orthogonal box = (-54.31 -54.31 -54.31) to (54.31 54.31 54.31) + 1 by 2 by 2 MPI processor grid + +mass 1 28.0855 + +create_atoms 1 box +Created 32000 atoms + Time spent = 0.000838995 secs + +velocity all create 300 42534 mom yes rot yes + +group gPKA id 1 +1 atoms in group gPKA +velocity gPKA set 1120 1620 389 + +pair_style sw +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 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 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.77118 + ghost atom cutoff = 5.77118 + binsize = 2.88559, bins = 38 38 38 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair sw, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) fix elstop, occasional, copy from (1) + attributes: full, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.825 | 3.825 | 3.825 Mbytes +Step Time Dt f_fel + 0 0 4.98128e-05 0 + 10 0.00030141235 7.4131221e-06 143.83474 + 20 0.00035951242 6.0314282e-06 171.53584 + 30 0.00057457861 3.511731e-05 274.07067 + 40 0.00086591115 5.8248574e-06 412.87352 + 50 0.00090045749 2.102773e-06 429.31482 + 60 0.00091828633 1.5369556e-06 437.79502 + 70 0.00093306208 1.4645168e-06 444.82135 + 80 0.00094861336 1.7491631e-06 452.21657 + 90 0.00097033523 3.0804023e-06 462.54893 + 100 0.0010792154 4.9075683e-05 514.37014 + 110 0.0012080866 2.3201427e-06 575.68827 + 120 0.0012239719 1.0507964e-06 583.23648 + 130 0.0012325518 6.8263389e-07 587.30975 + 140 0.0012385211 5.1201217e-07 590.14147 + 150 0.0012431661 4.1521773e-07 592.34347 + 160 0.001247021 3.5379338e-07 594.16984 + 170 0.0012503586 3.1202939e-07 595.75031 + 180 0.0012533374 2.8236002e-07 597.16021 + 190 0.0012560582 2.6071816e-07 598.44745 + 200 0.0012585895 2.4474279e-07 599.64465 + 210 0.001260981 2.3298831e-07 600.7754 + 220 0.0012632704 2.2454021e-07 601.85763 + 230 0.001265488 2.1881458e-07 602.90571 + 240 0.0012676591 2.154488e-07 603.93173 + 250 0.0012698064 2.1424147e-07 604.94641 + 260 0.0012719511 2.1512161e-07 605.9598 + 270 0.0012741141 2.1813836e-07 606.98189 + 280 0.0012763174 2.2346783e-07 608.02314 + 290 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6800.9557 + 4880 0.014606464 7.6929481e-08 6801.2958 + 4890 0.014607241 7.8625665e-08 6801.643 + 4900 0.014608036 8.0537626e-08 6801.9983 + 4910 0.01460885 8.2690811e-08 6802.3627 + 4920 0.014609688 8.5115787e-08 6802.7374 + 4930 0.014610551 8.7849474e-08 6803.1237 + 4940 0.014611443 9.0936752e-08 6803.5231 + 4950 0.014612368 9.4432608e-08 6803.9372 + 4960 0.01461333 9.8405013e-08 6804.3681 + 4970 0.014614334 1.0293885e-07 6804.8181 + 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 + +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 + +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 + +Nlocal: 8000 ave 8033 max 7977 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Nghost: 6061.25 ave 6085 max 6028 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 144002 ave 144601 max 143596 min +Histogram: 1 0 1 1 0 0 0 0 0 1 + +Total # of neighbors = 576008 +Ave neighs/atom = 18.0003 +Neighbor list builds = 67 +Dangerous builds = 38 +Total wall time: 0:00:20 diff --git a/examples/USER/misc/elstop/log.20Mar19.elstop.only.g++.1 b/examples/USER/misc/elstop/log.20Mar19.elstop.only.g++.1 new file mode 100644 index 0000000000..e586fb5afb --- /dev/null +++ b/examples/USER/misc/elstop/log.20Mar19.elstop.only.g++.1 @@ -0,0 +1,198 @@ +LAMMPS (28 Feb 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Test case / example for the electronic stopping fix elstop +# One fast atom, no other interactions. +# Elstop 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 +Lattice spacing in x,y,z = 1 1 1 + +region rbox block -100 100 -100 100 -100 100 +region rsmallbox block -90 90 -90 90 -90 90 + +create_box 1 rbox +Created orthogonal box = (-100 -100 -100) to (100 100 100) + 1 by 1 by 1 MPI processor grid + +mass 1 28.0855 + +create_atoms 1 single 0 0 0 +Created 1 atoms + Time spent = 3.09944e-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 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 +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 + master list distance cutoff = 3 + ghost atom cutoff = 3 + binsize = 1.5, bins = 134 134 134 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix elstop, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 13.31 | 13.31 | 13.31 Mbytes +Step Time Dt f_fel c_ektot + 0 0 4.98128e-05 0 5865.5525 + 100 0.0049972222 5.0137252e-05 76.048699 5789.883 + 200 0.010027278 5.0467945e-05 151.67477 5714.2548 + 300 0.015090636 5.0803375e-05 226.8806 5639.0469 + 400 0.020187777 5.1143663e-05 301.6685 5564.2569 + 500 0.025319192 5.1488933e-05 376.04082 5489.8825 + 600 0.030485386 5.1839314e-05 449.99984 5415.9215 + 700 0.035686876 5.2194938e-05 523.54788 5342.3714 + 800 0.040924195 5.2555944e-05 596.68721 5269.23 + 900 0.046197886 5.2922477e-05 669.42011 5196.4951 + 1000 0.05150851 5.3294685e-05 741.74883 5124.1643 + 1100 0.056856642 5.3672723e-05 813.67563 5052.2355 + 1200 0.062229338 5.3731851e-05 824.43012 5041.1224 + 1300 0.067602524 5.3731851e-05 824.43012 5041.1224 + 1400 0.072978188 5.387166e-05 850.91948 5014.9907 + 1500 0.07838447 5.425887e-05 922.23961 4943.6685 + 1600 0.08382978 5.4652329e-05 993.16341 4872.7428 + 1700 0.089299984 5.4705935e-05 1002.3545 4863.198 + 1800 0.094770578 5.4705935e-05 1002.3545 4863.198 + 1900 0.10024117 5.4705935e-05 1002.3545 4863.198 + 2000 0.10571333 5.4819488e-05 1022.8338 4843.0716 + 2100 0.11121515 5.5222127e-05 1093.1986 4772.7048 + 2200 0.11675757 5.5631458e-05 1163.1724 4702.7291 + 2300 0.12234126 5.6047675e-05 1232.7573 4633.1422 + 2400 0.12796692 5.6470985e-05 1301.9555 4563.942 + 2500 0.13363527 5.6901598e-05 1370.7692 4495.1264 + 2600 0.13934706 5.7339739e-05 1439.2006 4426.6932 + 2700 0.14510304 5.7785637e-05 1507.2516 4358.6403 + 2800 0.150904 5.8239536e-05 1574.9245 4290.9655 + 2900 0.15675076 5.8701688e-05 1642.2213 4223.6668 + 3000 0.16264416 5.9172358e-05 1709.1441 4156.7422 + 3100 0.16858505 5.9651822e-05 1775.695 4090.1894 + 3200 0.17457434 6.0140369e-05 1841.8761 4024.0064 + 3300 0.18061294 6.0638302e-05 1907.6894 3958.1913 + 3400 0.18669814 6.0949329e-05 1947.6558 3917.8967 + 3500 0.19279307 6.0949329e-05 1947.6558 3917.8967 + 3600 0.198888 6.0949329e-05 1947.6558 3917.8967 + 3700 0.20498294 6.0949329e-05 1947.6558 3917.8967 + 3800 0.21107787 6.0949329e-05 1947.6558 3917.8967 + 3900 0.2171728 6.0949329e-05 1947.6558 3917.8967 + 4000 0.22326773 6.0949329e-05 1947.6558 3917.8967 + 4100 0.22936267 6.0949329e-05 1947.6558 3917.8967 + 4200 0.2354576 6.0949329e-05 1947.6558 3917.8967 + 4300 0.24155253 6.0949329e-05 1947.6558 3917.8967 + 4400 0.24764747 6.0949329e-05 1947.6558 3917.8967 + 4500 0.2537424 6.0949329e-05 1947.6558 3917.8967 + 4600 0.25983733 6.0949329e-05 1947.6558 3917.8967 + 4700 0.26593227 6.0949329e-05 1947.6558 3917.8967 + 4800 0.2720272 6.0949329e-05 1947.6558 3917.8967 + 4900 0.27812213 6.0949329e-05 1947.6558 3917.8967 + 5000 0.28421706 6.0949329e-05 1947.6558 3917.8967 + 5100 0.290312 6.0949329e-05 1947.6558 3917.8967 + 5200 0.29640693 6.0949329e-05 1947.6558 3917.8967 + 5300 0.30250186 6.0949329e-05 1947.6558 3917.8967 + 5400 0.3085968 6.0949329e-05 1947.6558 3917.8967 + 5500 0.31469173 6.0949329e-05 1947.6558 3917.8967 + 5600 0.32078666 6.0949329e-05 1947.6558 3917.8967 + 5700 0.32688159 6.0949329e-05 1947.6558 3917.8967 + 5800 0.33297653 6.0949329e-05 1947.6558 3917.8967 + 5900 0.33907146 6.0949329e-05 1947.6558 3917.8967 + 6000 0.34516639 6.0949329e-05 1947.6558 3917.8967 + 6100 0.35126133 6.0949329e-05 1947.6558 3917.8967 + 6200 0.35735626 6.0949329e-05 1947.6558 3917.8967 + 6300 0.36345119 6.0949329e-05 1947.6558 3917.8967 + 6400 0.36954612 6.0949329e-05 1947.6558 3917.8967 + 6500 0.37564106 6.0949329e-05 1947.6558 3917.8967 + 6600 0.38173599 6.0949329e-05 1947.6558 3917.8967 + 6700 0.38783092 6.0949329e-05 1947.6558 3917.8967 + 6800 0.39392586 6.0949329e-05 1947.6558 3917.8967 + 6900 0.40002079 6.0949329e-05 1947.6558 3917.8967 + 7000 0.40611572 6.0949329e-05 1947.6558 3917.8967 + 7100 0.41221066 6.0949329e-05 1947.6558 3917.8967 + 7200 0.41830559 6.0949329e-05 1947.6558 3917.8967 + 7300 0.42440052 6.0949329e-05 1947.6558 3917.8967 + 7400 0.43049545 6.0949329e-05 1947.6558 3917.8967 + 7500 0.43659039 6.0949329e-05 1947.6558 3917.8967 + 7600 0.44268532 6.0949329e-05 1947.6558 3917.8967 + 7700 0.44878025 6.0949329e-05 1947.6558 3917.8967 + 7800 0.45487519 6.0949329e-05 1947.6558 3917.8967 + 7900 0.46097012 6.0949329e-05 1947.6558 3917.8967 + 8000 0.46706505 6.0949329e-05 1947.6558 3917.8967 + 8100 0.47315998 6.0949329e-05 1947.6558 3917.8967 + 8200 0.47925492 6.0949329e-05 1947.6558 3917.8967 + 8300 0.48534985 6.0949329e-05 1947.6558 3917.8967 + 8400 0.49144478 6.0949329e-05 1947.6558 3917.8967 + 8500 0.49753972 6.0949329e-05 1947.6558 3917.8967 + 8600 0.50363465 6.0949329e-05 1947.6558 3917.8967 + 8700 0.50972958 6.0949329e-05 1947.6558 3917.8967 + 8800 0.51582452 6.0949329e-05 1947.6558 3917.8967 + 8900 0.52191945 6.0949329e-05 1947.6558 3917.8967 + 9000 0.52801438 6.0949329e-05 1947.6558 3917.8967 + 9100 0.53410931 6.0949329e-05 1947.6558 3917.8967 + 9200 0.54020425 6.0949329e-05 1947.6558 3917.8967 + 9300 0.54629918 6.0949329e-05 1947.6558 3917.8967 + 9400 0.55239411 6.0949329e-05 1947.6558 3917.8967 + 9500 0.55848905 6.0949329e-05 1947.6558 3917.8967 + 9600 0.56458398 6.0949329e-05 1947.6558 3917.8967 + 9700 0.57067891 6.0949329e-05 1947.6558 3917.8967 + 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 + +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 + +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 + +Nlocal: 1 ave 1 max 1 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 960 +Dangerous builds = 568 +Total wall time: 0:00:01 diff --git a/examples/USER/misc/elstop/log.20Mar19.elstop.only.g++.4 b/examples/USER/misc/elstop/log.20Mar19.elstop.only.g++.4 new file mode 100644 index 0000000000..5ed0d86f1c --- /dev/null +++ b/examples/USER/misc/elstop/log.20Mar19.elstop.only.g++.4 @@ -0,0 +1,198 @@ +LAMMPS (28 Feb 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Test case / example for the electronic stopping fix elstop +# One fast atom, no other interactions. +# Elstop 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 +Lattice spacing in x,y,z = 1 1 1 + +region rbox block -100 100 -100 100 -100 100 +region rsmallbox block -90 90 -90 90 -90 90 + +create_box 1 rbox +Created orthogonal box = (-100 -100 -100) to (100 100 100) + 1 by 2 by 2 MPI processor grid + +mass 1 28.0855 + +create_atoms 1 single 0 0 0 +Created 1 atoms + Time spent = 2.00272e-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 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 +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 + master list distance cutoff = 3 + ghost atom cutoff = 3 + binsize = 1.5, bins = 134 134 134 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix elstop, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.637 | 4.2 | 5.887 Mbytes +Step Time Dt f_fel c_ektot + 0 0 4.98128e-05 0 5865.5525 + 100 0.0049972222 5.0137252e-05 76.048699 5789.883 + 200 0.010027278 5.0467945e-05 151.67477 5714.2548 + 300 0.015090636 5.0803375e-05 226.8806 5639.0469 + 400 0.020187777 5.1143663e-05 301.6685 5564.2569 + 500 0.025319192 5.1488933e-05 376.04082 5489.8825 + 600 0.030485386 5.1839314e-05 449.99984 5415.9215 + 700 0.035686876 5.2194938e-05 523.54788 5342.3714 + 800 0.040924195 5.2555944e-05 596.68721 5269.23 + 900 0.046197886 5.2922477e-05 669.42011 5196.4951 + 1000 0.05150851 5.3294685e-05 741.74883 5124.1643 + 1100 0.056856642 5.3672723e-05 813.67563 5052.2355 + 1200 0.062229338 5.3731851e-05 824.43012 5041.1224 + 1300 0.067602524 5.3731851e-05 824.43012 5041.1224 + 1400 0.072978188 5.387166e-05 850.91948 5014.9907 + 1500 0.07838447 5.425887e-05 922.23961 4943.6685 + 1600 0.08382978 5.4652329e-05 993.16341 4872.7428 + 1700 0.089299984 5.4705935e-05 1002.3545 4863.198 + 1800 0.094770578 5.4705935e-05 1002.3545 4863.198 + 1900 0.10024117 5.4705935e-05 1002.3545 4863.198 + 2000 0.10571333 5.4819488e-05 1022.8338 4843.0716 + 2100 0.11121515 5.5222127e-05 1093.1986 4772.7048 + 2200 0.11675757 5.5631458e-05 1163.1724 4702.7291 + 2300 0.12234126 5.6047675e-05 1232.7573 4633.1422 + 2400 0.12796692 5.6470985e-05 1301.9555 4563.942 + 2500 0.13363527 5.6901598e-05 1370.7692 4495.1264 + 2600 0.13934706 5.7339739e-05 1439.2006 4426.6932 + 2700 0.14510304 5.7785637e-05 1507.2516 4358.6403 + 2800 0.150904 5.8239536e-05 1574.9245 4290.9655 + 2900 0.15675076 5.8701688e-05 1642.2213 4223.6668 + 3000 0.16264416 5.9172358e-05 1709.1441 4156.7422 + 3100 0.16858505 5.9651822e-05 1775.695 4090.1894 + 3200 0.17457434 6.0140369e-05 1841.8761 4024.0064 + 3300 0.18061294 6.0638302e-05 1907.6894 3958.1913 + 3400 0.18669814 6.0949329e-05 1947.6558 3917.8967 + 3500 0.19279307 6.0949329e-05 1947.6558 3917.8967 + 3600 0.198888 6.0949329e-05 1947.6558 3917.8967 + 3700 0.20498294 6.0949329e-05 1947.6558 3917.8967 + 3800 0.21107787 6.0949329e-05 1947.6558 3917.8967 + 3900 0.2171728 6.0949329e-05 1947.6558 3917.8967 + 4000 0.22326773 6.0949329e-05 1947.6558 3917.8967 + 4100 0.22936267 6.0949329e-05 1947.6558 3917.8967 + 4200 0.2354576 6.0949329e-05 1947.6558 3917.8967 + 4300 0.24155253 6.0949329e-05 1947.6558 3917.8967 + 4400 0.24764747 6.0949329e-05 1947.6558 3917.8967 + 4500 0.2537424 6.0949329e-05 1947.6558 3917.8967 + 4600 0.25983733 6.0949329e-05 1947.6558 3917.8967 + 4700 0.26593227 6.0949329e-05 1947.6558 3917.8967 + 4800 0.2720272 6.0949329e-05 1947.6558 3917.8967 + 4900 0.27812213 6.0949329e-05 1947.6558 3917.8967 + 5000 0.28421706 6.0949329e-05 1947.6558 3917.8967 + 5100 0.290312 6.0949329e-05 1947.6558 3917.8967 + 5200 0.29640693 6.0949329e-05 1947.6558 3917.8967 + 5300 0.30250186 6.0949329e-05 1947.6558 3917.8967 + 5400 0.3085968 6.0949329e-05 1947.6558 3917.8967 + 5500 0.31469173 6.0949329e-05 1947.6558 3917.8967 + 5600 0.32078666 6.0949329e-05 1947.6558 3917.8967 + 5700 0.32688159 6.0949329e-05 1947.6558 3917.8967 + 5800 0.33297653 6.0949329e-05 1947.6558 3917.8967 + 5900 0.33907146 6.0949329e-05 1947.6558 3917.8967 + 6000 0.34516639 6.0949329e-05 1947.6558 3917.8967 + 6100 0.35126133 6.0949329e-05 1947.6558 3917.8967 + 6200 0.35735626 6.0949329e-05 1947.6558 3917.8967 + 6300 0.36345119 6.0949329e-05 1947.6558 3917.8967 + 6400 0.36954612 6.0949329e-05 1947.6558 3917.8967 + 6500 0.37564106 6.0949329e-05 1947.6558 3917.8967 + 6600 0.38173599 6.0949329e-05 1947.6558 3917.8967 + 6700 0.38783092 6.0949329e-05 1947.6558 3917.8967 + 6800 0.39392586 6.0949329e-05 1947.6558 3917.8967 + 6900 0.40002079 6.0949329e-05 1947.6558 3917.8967 + 7000 0.40611572 6.0949329e-05 1947.6558 3917.8967 + 7100 0.41221066 6.0949329e-05 1947.6558 3917.8967 + 7200 0.41830559 6.0949329e-05 1947.6558 3917.8967 + 7300 0.42440052 6.0949329e-05 1947.6558 3917.8967 + 7400 0.43049545 6.0949329e-05 1947.6558 3917.8967 + 7500 0.43659039 6.0949329e-05 1947.6558 3917.8967 + 7600 0.44268532 6.0949329e-05 1947.6558 3917.8967 + 7700 0.44878025 6.0949329e-05 1947.6558 3917.8967 + 7800 0.45487519 6.0949329e-05 1947.6558 3917.8967 + 7900 0.46097012 6.0949329e-05 1947.6558 3917.8967 + 8000 0.46706505 6.0949329e-05 1947.6558 3917.8967 + 8100 0.47315998 6.0949329e-05 1947.6558 3917.8967 + 8200 0.47925492 6.0949329e-05 1947.6558 3917.8967 + 8300 0.48534985 6.0949329e-05 1947.6558 3917.8967 + 8400 0.49144478 6.0949329e-05 1947.6558 3917.8967 + 8500 0.49753972 6.0949329e-05 1947.6558 3917.8967 + 8600 0.50363465 6.0949329e-05 1947.6558 3917.8967 + 8700 0.50972958 6.0949329e-05 1947.6558 3917.8967 + 8800 0.51582452 6.0949329e-05 1947.6558 3917.8967 + 8900 0.52191945 6.0949329e-05 1947.6558 3917.8967 + 9000 0.52801438 6.0949329e-05 1947.6558 3917.8967 + 9100 0.53410931 6.0949329e-05 1947.6558 3917.8967 + 9200 0.54020425 6.0949329e-05 1947.6558 3917.8967 + 9300 0.54629918 6.0949329e-05 1947.6558 3917.8967 + 9400 0.55239411 6.0949329e-05 1947.6558 3917.8967 + 9500 0.55848905 6.0949329e-05 1947.6558 3917.8967 + 9600 0.56458398 6.0949329e-05 1947.6558 3917.8967 + 9700 0.57067891 6.0949329e-05 1947.6558 3917.8967 + 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 + +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 + +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 + +Nlocal: 0.25 ave 1 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 960 +Dangerous builds = 568 +Total wall time: 0:00:03 diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 13e406d42f..43deda0bdb 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -45,6 +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 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 diff --git a/src/USER-MISC/fix_elstop.cpp b/src/USER-MISC/fix_elstop.cpp new file mode 100644 index 0000000000..def576cfca --- /dev/null +++ b/src/USER-MISC/fix_elstop.cpp @@ -0,0 +1,326 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Electronic stopping power + Contributing authors: K. Avchaciov and T. Metspalu + Information: k.avchachov@gmail.com +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "fix_elstop.h" +#include "mpi.h" +#include "atom.h" +#include "update.h" +#include "domain.h" +#include "region.h" +#include "group.h" +#include "force.h" +#include "pair.h" +#include "fix.h" +#include "compute.h" +#include "modify.h" +#include "memory.h" +#include "comm.h" +#include "error.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +#define MAXLINE 1024 + +/* ---------------------------------------------------------------------- */ + +FixElstop::FixElstop(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + scalar_flag = 1; // Has compute_scalar + global_freq = 1; // SeLoss computed every step + extscalar = 0; // SeLoss compute_scalar is intensive + nevery = 1; // Run fix every step + + + // Make sure the id for the kinetic energy compute is unique + // by prepending the ID of this fix. + int n = strlen(id) + strlen("_ke_atom") + 1; + id_ke_atom = new char[n]; + strcpy(id_ke_atom, id); + strcat(id_ke_atom, "_ke_atom"); + + char *newarg[3]; + newarg[0] = id_ke_atom; + newarg[1] = group->names[igroup]; + newarg[2] = (char *) "ke/atom"; + modify->add_compute(3, newarg); + + + // args: 0 = fix ID, 1 = group ID, 2 = "elstop" + // 3 = Ecut, 4 = file path + // optional rest: "region" + // "minneigh" + + if (narg < 5) + error->all(FLERR, "Illegal fix elstop command: too few arguments"); + + Ecut = force->numeric(FLERR, arg[3]); + if (Ecut <= 0.0) error->all(FLERR, "Illegal fix elstop command: Ecut <= 0"); + + int iarg = 5; + iregion = -1; + minneigh = 1; + bool minneighflag = false; + + 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"); + iregion = domain->find_region(arg[iarg+1]); + if (iregion < 0) + error->all(FLERR, "Region ID for fix elstop does not exist"); + iarg += 2; + } + else if (strcmp(arg[iarg], "minneigh") == 0) { + if (minneighflag) + error->all(FLERR, "Illegal fix elstop command: minneigh given twice"); + minneighflag = true; + if (iarg+2 > narg) + error->all(FLERR, "Illegal fix elstop command: minneigh number missing"); + minneigh = force->inumeric(FLERR, arg[iarg+1]); + if (minneigh < 0) + error->all(FLERR, "Illegal fix elstop command: minneigh < 0"); + iarg += 2; + } + else error->all(FLERR, "Illegal fix elstop command: unknown argument"); + } + + + // Read the input file for energy ranges and stopping powers. + // First proc 0 reads the file, then bcast to others. + const int ncol = atom->ntypes + 1; + if (comm->me == 0) { + maxlines = 300; + memory->create(elstop_ranges, ncol, maxlines, "elstop:tabs"); + read_table(arg[4]); + } + + MPI_Bcast(&maxlines, 1 , MPI_INT, 0, world); + MPI_Bcast(&table_entries, 1 , MPI_INT, 0, world); + + if (comm->me != 0) + memory->create(elstop_ranges, ncol, maxlines, "elstop:tabs"); + + MPI_Bcast(&elstop_ranges[0][0], ncol*maxlines, MPI_DOUBLE, 0, world); +} + +/* ---------------------------------------------------------------------- */ + +FixElstop::~FixElstop() +{ + memory->destroy(elstop_ranges); + modify->delete_compute(id_ke_atom); + delete id_ke_atom; +} + +/* ---------------------------------------------------------------------- */ + +int FixElstop::setmask() +{ + int mask = 0; + mask |= POST_FORCE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixElstop::init() +{ + SeLoss_sync_flag = 0; + SeLoss = 0.0; + + int ikeatom = modify->find_compute(id_ke_atom); + if (ikeatom < 0) + error->all(FLERR, "KE compute ID for fix elstop does not exist"); + c_ke = modify->compute[ikeatom]; + + + // need an occasional full neighbor list + int irequest = neighbor->request(this, instance_me); + neighbor->requests[irequest]->pair = 0; + neighbor->requests[irequest]->fix = 1; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + neighbor->requests[irequest]->occasional = 1; +} + +/* ---------------------------------------------------------------------- */ + +void FixElstop::init_list(int /*id*/, NeighList *ptr) +{ + list = ptr; +} + +/* ---------------------------------------------------------------------- */ + +void FixElstop::post_force(int /*vflag*/) +{ + SeLoss_sync_flag = 0; + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + double dt = update->dt; + + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + neighbor->build_one(list); + int *numneigh = list->numneigh; + + c_ke->compute_peratom(); + double *ke = c_ke->vector_atom; + + for (int i = 0; i < nlocal; ++i) { + + // Do fast checks first, only then the region check + if (!(mask[i] & groupbit)) continue; + + // Avoid atoms outside bulk material + if (numneigh[i] < minneigh) continue; + + double energy = ke[i]; + 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 (iregion >= 0) { + // Only apply in the given region + if (domain->regions[iregion]->match(x[i][0], x[i][1], x[i][2]) != 1) + continue; + } + + // Binary search to find correct energy range + int iup = table_entries - 1; + int idown = 0; + while (true) { + int ihalf = idown + (iup - idown) / 2; + if (ihalf == idown) break; + if (elstop_ranges[0][ihalf] < energy) idown = ihalf; + else iup = ihalf; + } + + int itype = type[i]; + double Se_lo = elstop_ranges[itype][idown]; + double Se_hi = elstop_ranges[itype][iup]; + double E_lo = elstop_ranges[0][idown]; + double E_hi = elstop_ranges[0][iup]; + + // Get elstop with a simple linear interpolation + double Se = (Se_hi - Se_lo) / (E_hi - E_lo) * (energy - E_lo) + Se_lo; + + double v2 = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]; + double vabs = sqrt(v2); + double factor = -Se / vabs; + + f[i][0] += v[i][0] * factor; + f[i][1] += v[i][1] * factor; + f[i][2] += v[i][2] * factor; + + SeLoss += Se * vabs * dt; // very rough approx + } +} + +/* ---------------------------------------------------------------------- */ + +double FixElstop::compute_scalar() +{ + // only sum across procs when changed since last call + + if (SeLoss_sync_flag == 0) { + MPI_Allreduce(&SeLoss, &SeLoss_all, 1, MPI_DOUBLE, MPI_SUM, world); + SeLoss_sync_flag = 1; + } + return SeLoss_all; +} + +/* ---------------------------------------------------------------------- */ + +void FixElstop::read_table(const char *file) +{ + char line[MAXLINE]; + + FILE *fp = force->open_potential(file); + if (fp == NULL) { + char str[128]; + snprintf(str, 128, "Cannot open stopping range table %s", file); + error->one(FLERR, str); + } + + const int ncol = atom->ntypes + 1; + + int l = 0; + while (true) { + if (fgets(line, MAXLINE, fp) == NULL) break; // end of file + if (line[0] == '#') continue; // comment + + char *pch = strtok(line, " \t\n\r"); + if (pch == NULL) continue; // blank line + + if (l >= maxlines) grow_table(); + + int i = 0; + for ( ; i < ncol && pch != NULL; i++) { + elstop_ranges[i][l] = force->numeric(FLERR, pch); + pch = strtok(NULL, " \t\n\r"); + } + + if (i != ncol || pch != NULL) // too short or too long + error->one(FLERR, "fix elstop: 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"); + + l++; + } + table_entries = l; + + if (table_entries == 0) + error->one(FLERR, "Did not find any data in elstop table file"); + + fclose(fp); +} + +/* ---------------------------------------------------------------------- */ + +void FixElstop::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"); + + for (int i = 0; i < ncol; i++) + memcpy(new_array[i], elstop_ranges[i], maxlines*sizeof(double)); + + memory->destroy(elstop_ranges); + elstop_ranges = new_array; + maxlines = new_maxlines; +} diff --git a/src/USER-MISC/fix_elstop.h b/src/USER-MISC/fix_elstop.h new file mode 100644 index 0000000000..dc49825290 --- /dev/null +++ b/src/USER-MISC/fix_elstop.h @@ -0,0 +1,111 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Electronic stopping power + Contributing authors: K. Avchaciov and T. Metspalu + Information: k.avchachov@gmail.com +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(elstop,FixElstop) + +#else + +#ifndef LMP_FIX_ELSTOP_H +#define LMP_FIX_ELSTOP_H + +#include "fix.h" + + +namespace LAMMPS_NS { + +class FixElstop : public Fix { + public: + FixElstop(class LAMMPS *, int, char **); + ~FixElstop(); + int setmask(); + void init(); + void post_force(int); + void init_list(int, class NeighList *); + double compute_scalar(); + + private: + void read_table(const char *); + void grow_table(); + + double Ecut; // cutoff energy + double SeLoss, SeLoss_all; // electronic energy loss + int SeLoss_sync_flag; // sync done since last change? + + int maxlines; // max number of lines in table + int table_entries; // number of table entries actually read + double **elstop_ranges; // [ 0][i]: energies + // [>0][i]: stopping powers per type + + char *id_ke_atom; // name of kinetic energy compute + int iregion; // region index if used, else -1 + int minneigh; // minimum number of neighbors + + class NeighList *list; + class Compute *c_ke; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +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 + +Self-explanatory. + +E: KE compute ID for fix elstop does not exist + +Internal error. Should not happen. + +E: Atom kinetic energy too high for fix elstop + +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. + +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. + +E: fix elstop: Invalid table line + +A line in the elstop table file contained too many or too few columns. + +E: fix elstop: Energies must be in ascending order + +The first column in the elstop table must be sorted from the smallest +energy to the largest. + +E: Did not find any data in elstop table file + +Parsing the elstop table file produced no lines that were identifiable +as energies/stopping powers. Most likely the file is empty or contains +only comments. + +*/