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add example for fix sgcmc

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This commit is contained in:
Axel Kohlmeyer
2022-12-13 16:35:49 -05:00
parent 88ac09a8c0
commit 49cccd7526
4 changed files with 9341 additions and 0 deletions
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examples/mc/FeCu.pasianot.eamfs Normal file
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# general variables
variable temperature equal 700
variable size equal 20
# variables for 'fix sgcmc'
variable nsteps_mc equal 100
variable swap_fraction equal 0.2
variable temperature_mc equal ${temperature}
variable deltamu equal -0.70
variable target_concentration equal 0.02
variable kappa equal 1e3
# general settings
units metal
atom_style atomic
# set up structure
boundary p p p
lattice bcc 2.88
region box block 0 ${size} 0 ${size} 0 ${size}
create_box 2 box
create_atoms 1 box
reset_timestep 0
timestep 0.0025
# set up interaction
pair_style eam/fs
pair_coeff * * FeCu.pasianot.eamfs Fe Cu
# initialize velocities
variable double_temp equal ${temperature}*2
velocity all create ${double_temp} 428459 dist gaussian
# what and how to run
fix integrate all npt &
temp ${temperature} ${temperature} 1.7 &
aniso 0.0 0.0 1.5
fix mc all sgcmc ${nsteps_mc} ${swap_fraction} ${temperature_mc} ${deltamu} &
randseed 324234 &
variance ${kappa} ${target_concentration}
# set up output
thermo 100
thermo_style custom step temp atoms pe press &
lx ly lz f_mc[1] f_mc[2] f_mc[3] f_mc[4]
#dump 1 all custom 200 mc.*.dump id type x y z
run 2000

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LAMMPS (3 Nov 2022)
using 1 OpenMP thread(s) per MPI task
# general variables
variable temperature equal 700
variable size equal 20
# variables for 'fix sgcmc'
variable nsteps_mc equal 100
variable swap_fraction equal 0.2
variable temperature_mc equal ${temperature}
variable temperature_mc equal 700
variable deltamu equal -0.70
variable target_concentration equal 0.02
variable kappa equal 1e3
# general settings
units metal
atom_style atomic
# set up structure
boundary p p p
lattice bcc 2.88
Lattice spacing in x,y,z = 2.88 2.88 2.88
region box block 0 ${size} 0 ${size} 0 ${size}
region box block 0 20 0 ${size} 0 ${size}
region box block 0 20 0 20 0 ${size}
region box block 0 20 0 20 0 20
create_box 2 box
Created orthogonal box = (0 0 0) to (57.6 57.6 57.6)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 16000 atoms
using lattice units in orthogonal box = (0 0 0) to (57.6 57.6 57.6)
create_atoms CPU = 0.001 seconds
reset_timestep 0
timestep 0.0025
# set up interaction
pair_style eam/fs
pair_coeff * * FeCu.pasianot.eamfs Fe Cu
# initialize velocities
variable double_temp equal ${temperature}*2
variable double_temp equal 700*2
velocity all create ${double_temp} 428459 dist gaussian
velocity all create 1400 428459 dist gaussian
# what and how to run
fix integrate all npt temp ${temperature} ${temperature} 1.7 aniso 0.0 0.0 1.5
fix integrate all npt temp 700 ${temperature} 1.7 aniso 0.0 0.0 1.5
fix integrate all npt temp 700 700 1.7 aniso 0.0 0.0 1.5
fix mc all sgcmc ${nsteps_mc} ${swap_fraction} ${temperature_mc} ${deltamu} randseed 324234 variance ${kappa} ${target_concentration}
fix mc all sgcmc 100 ${swap_fraction} ${temperature_mc} ${deltamu} randseed 324234 variance ${kappa} ${target_concentration}
fix mc all sgcmc 100 0.2 ${temperature_mc} ${deltamu} randseed 324234 variance ${kappa} ${target_concentration}
fix mc all sgcmc 100 0.2 700 ${deltamu} randseed 324234 variance ${kappa} ${target_concentration}
fix mc all sgcmc 100 0.2 700 -0.7 randseed 324234 variance ${kappa} ${target_concentration}
fix mc all sgcmc 100 0.2 700 -0.7 randseed 324234 variance 1000 ${target_concentration}
fix mc all sgcmc 100 0.2 700 -0.7 randseed 324234 variance 1000 0.02
SGC - Number of MD timesteps: 100
SGC - Fraction of swap atoms: 0.2
SGC - Temperature: %f
SGC - Chemical potential of species 2: -0.7
SGC - Random number seed: 324234
SGC - Kappa: 1000
SGC - Target concentration of species 2: 0.02
SGC - Target concentration of species 1: 0.98
# set up output
thermo 100
thermo_style custom step temp atoms pe press lx ly lz f_mc[1] f_mc[2] f_mc[3] f_mc[4]
#dump 1 all custom 200 mc.*.dump id type x y z
run 2000
SGC - Interaction radius: 5.50679
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.50679
ghost atom cutoff = 7.50679
binsize = 3.753395, bins = 16 16 16
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair eam/fs, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix sgcmc, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 25.06 | 25.06 | 25.06 Mbytes
Step Temp Atoms PotEng Press Lx Ly Lz f_mc[1] f_mc[2] f_mc[3] f_mc[4]
0 1400 16000 -65889.786 -28854.541 57.6 57.6 57.6 0 0 1 0
100 734.32713 16000 -64514.143 5439.4277 57.327173 57.322333 57.318848 12 3188 0.99925 0.00075
200 678.63428 16000 -64386.224 -920.7819 57.423954 57.409111 57.412727 22 3178 0.997875 0.002125
300 683.24749 16000 -64370.598 -1609.0429 57.427441 57.424568 57.426831 20 3180 0.996625 0.003375
400 689.28007 16000 -64359.115 2489.3933 57.376537 57.379856 57.372895 27 3173 0.9949375 0.0050625
500 693.85333 16000 -64337.222 -1935.9815 57.435754 57.43493 57.427453 18 3182 0.9938125 0.0061875
600 693.52855 16000 -64314.465 380.8264 57.410314 57.397604 57.408337 21 3179 0.9925 0.0075
700 690.62721 16000 -64284.369 208.21986 57.412407 57.407285 57.410684 31 3169 0.9905625 0.0094375
800 687.08129 16000 -64244.443 -936.31731 57.425765 57.438983 57.421321 31 3169 0.988625 0.011375
900 696.07347 16000 -64230.523 932.65537 57.414588 57.413865 57.402817 27 3173 0.9869375 0.0130625
1000 691.70667 16000 -64194.151 -690.02055 57.429033 57.420053 57.443245 23 3177 0.9855 0.0145
1100 691.21797 16000 -64169.016 -86.623524 57.42147 57.424262 57.436841 35 3165 0.9833125 0.0166875
1200 691.27155 16000 -64134.443 411.68129 57.425111 57.432481 57.4118 42 3158 0.9806875 0.0193125
1300 693.76194 16000 -64098.615 -943.9013 57.446704 57.448382 57.440727 64 3136 0.9800625 0.0199375
1400 691.16411 16000 -64080.423 1248.7921 57.417118 57.409651 57.435099 104 3096 0.9799375 0.0200625
1500 694.49681 16000 -64084.428 -179.5269 57.440533 57.432581 57.434409 68 3132 0.9799375 0.0200625
1600 697.58329 16000 -64089.682 -761.14401 57.450616 57.450654 57.422293 97 3103 0.98 0.02
1700 697.57549 16000 -64090.2 1370.3938 57.399319 57.423969 57.426788 85 3115 0.9801875 0.0198125
1800 694.18435 16000 -64083.812 -1381.5398 57.446114 57.438096 57.475109 84 3116 0.9799375 0.0200625
1900 702.82577 16000 -64096.005 918.83968 57.452789 57.404638 57.408161 70 3130 0.9799375 0.0200625
2000 696.02963 16000 -64080.059 276.99031 57.443085 57.452012 57.403928 81 3119 0.980125 0.019875
Loop time of 48.793 on 1 procs for 2000 steps with 16000 atoms
Performance: 8.854 ns/day, 2.711 hours/ns, 40.989 timesteps/s, 655.831 katom-step/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 | 47.46 | 47.46 | 47.46 | 0.0 | 97.27
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.13269 | 0.13269 | 0.13269 | 0.0 | 0.27
Output | 0.0011432 | 0.0011432 | 0.0011432 | 0.0 | 0.00
Modify | 1.0996 | 1.0996 | 1.0996 | 0.0 | 2.25
Other | | 0.0993 | | | 0.20
Nlocal: 16000 ave 16000 max 16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 17201 ave 17201 max 17201 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.344e+06 ave 1.344e+06 max 1.344e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 2.688e+06 ave 2.688e+06 max 2.688e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2688000
Ave neighs/atom = 168
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:48

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LAMMPS (3 Nov 2022)
using 1 OpenMP thread(s) per MPI task
# general variables
variable temperature equal 700
variable size equal 20
# variables for 'fix sgcmc'
variable nsteps_mc equal 100
variable swap_fraction equal 0.2
variable temperature_mc equal ${temperature}
variable temperature_mc equal 700
variable deltamu equal -0.70
variable target_concentration equal 0.02
variable kappa equal 1e3
# general settings
units metal
atom_style atomic
# set up structure
boundary p p p
lattice bcc 2.88
Lattice spacing in x,y,z = 2.88 2.88 2.88
region box block 0 ${size} 0 ${size} 0 ${size}
region box block 0 20 0 ${size} 0 ${size}
region box block 0 20 0 20 0 ${size}
region box block 0 20 0 20 0 20
create_box 2 box
Created orthogonal box = (0 0 0) to (57.6 57.6 57.6)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 16000 atoms
using lattice units in orthogonal box = (0 0 0) to (57.6 57.6 57.6)
create_atoms CPU = 0.001 seconds
reset_timestep 0
timestep 0.0025
# set up interaction
pair_style eam/fs
pair_coeff * * FeCu.pasianot.eamfs Fe Cu
# initialize velocities
variable double_temp equal ${temperature}*2
variable double_temp equal 700*2
velocity all create ${double_temp} 428459 dist gaussian
velocity all create 1400 428459 dist gaussian
# what and how to run
fix integrate all npt temp ${temperature} ${temperature} 1.7 aniso 0.0 0.0 1.5
fix integrate all npt temp 700 ${temperature} 1.7 aniso 0.0 0.0 1.5
fix integrate all npt temp 700 700 1.7 aniso 0.0 0.0 1.5
fix mc all sgcmc ${nsteps_mc} ${swap_fraction} ${temperature_mc} ${deltamu} randseed 324234 variance ${kappa} ${target_concentration}
fix mc all sgcmc 100 ${swap_fraction} ${temperature_mc} ${deltamu} randseed 324234 variance ${kappa} ${target_concentration}
fix mc all sgcmc 100 0.2 ${temperature_mc} ${deltamu} randseed 324234 variance ${kappa} ${target_concentration}
fix mc all sgcmc 100 0.2 700 ${deltamu} randseed 324234 variance ${kappa} ${target_concentration}
fix mc all sgcmc 100 0.2 700 -0.7 randseed 324234 variance ${kappa} ${target_concentration}
fix mc all sgcmc 100 0.2 700 -0.7 randseed 324234 variance 1000 ${target_concentration}
fix mc all sgcmc 100 0.2 700 -0.7 randseed 324234 variance 1000 0.02
SGC - Number of MD timesteps: 100
SGC - Fraction of swap atoms: 0.2
SGC - Temperature: %f
SGC - Chemical potential of species 2: -0.7
SGC - Random number seed: 324234
SGC - Kappa: 1000
SGC - Target concentration of species 2: 0.02
SGC - Target concentration of species 1: 0.98
# set up output
thermo 100
thermo_style custom step temp atoms pe press lx ly lz f_mc[1] f_mc[2] f_mc[3] f_mc[4]
#dump 1 all custom 200 mc.*.dump id type x y z
run 2000
SGC - Interaction radius: 5.50679
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.50679
ghost atom cutoff = 7.50679
binsize = 3.753395, bins = 16 16 16
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair eam/fs, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix sgcmc, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.809 | 7.809 | 7.809 Mbytes
Step Temp Atoms PotEng Press Lx Ly Lz f_mc[1] f_mc[2] f_mc[3] f_mc[4]
0 1400 16000 -65889.786 -28854.541 57.6 57.6 57.6 0 0 1 0
100 741.39222 16000 -64528.923 5317.2919 57.324639 57.32318 57.314928 19 3181 0.9988125 0.0011875
200 691.21024 16000 -64405.429 -1238.5107 57.421346 57.415516 57.412006 16 3184 0.9978125 0.0021875
300 686.85178 16000 -64377.312 -1816.799 57.424469 57.424335 57.425065 25 3175 0.996375 0.003625
400 690.93203 16000 -64358.609 2211.7763 57.376246 57.38185 57.381742 16 3184 0.995375 0.004625
500 696.77972 16000 -64350.3 -1583.8383 57.432929 57.426928 57.425935 22 3178 0.994125 0.005875
600 694.13567 16000 -64320.831 144.2514 57.420097 57.403531 57.401394 19 3181 0.9930625 0.0069375
700 691.79625 16000 -64295.155 384.47869 57.410637 57.412957 57.40707 25 3175 0.991625 0.008375
800 692.12887 16000 -64270.053 -764.91901 57.415576 57.43037 57.428708 21 3179 0.9903125 0.0096875
900 693.26555 16000 -64249.904 666.65335 57.408245 57.407059 57.417437 34 3166 0.9885625 0.0114375
1000 697.97016 16000 -64230.234 -562.91022 57.432317 57.424316 57.423668 28 3172 0.9868125 0.0131875
1100 686.52149 16000 -64177.536 -267.21801 57.429 57.434594 57.419878 35 3165 0.984875 0.015125
1200 691.55047 16000 -64156.268 810.17844 57.422282 57.413529 57.422883 37 3163 0.9828125 0.0171875
1300 691.91944 16000 -64124.602 -1012.7184 57.441793 57.433848 57.446947 32 3168 0.9810625 0.0189375
1400 701.78807 16000 -64116.475 180.93518 57.425156 57.438679 57.419575 76 3124 0.9799375 0.0200625
1500 692.75501 16000 -64080.481 176.96902 57.429275 57.442405 57.426519 81 3119 0.980125 0.019875
1600 694.11818 16000 -64083.435 -785.49617 57.442143 57.432114 57.458304 86 3114 0.98 0.02
1700 697.72576 16000 -64088.874 1227.5194 57.423225 57.408678 57.427056 75 3125 0.9800625 0.0199375
1800 697.24171 16000 -64086.742 -1166.4832 57.447168 57.47416 57.425229 67 3133 0.98025 0.01975
1900 699.53558 16000 -64092.97 214.99908 57.425459 57.437864 57.431139 86 3114 0.98025 0.01975
2000 699.00277 16000 -64089.117 978.69672 57.429266 57.39107 57.448289 81 3119 0.9798125 0.0201875
Loop time of 15.2907 on 4 procs for 2000 steps with 16000 atoms
Performance: 28.252 ns/day, 0.849 hours/ns, 130.798 timesteps/s, 2.093 Matom-step/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 14.31 | 14.404 | 14.479 | 1.6 | 94.20
Neigh | 0.090756 | 0.091006 | 0.091258 | 0.1 | 0.60
Comm | 0.27623 | 0.35113 | 0.44457 | 10.4 | 2.30
Output | 0.0006002 | 0.0013338 | 0.0035331 | 3.5 | 0.01
Modify | 0.38023 | 0.38128 | 0.38228 | 0.2 | 2.49
Other | | 0.06148 | | | 0.40
Nlocal: 4000 ave 4017 max 3970 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 8274.75 ave 8305 max 8257 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Neighs: 311257 ave 313506 max 308273 min
Histogram: 1 0 0 0 0 1 0 1 0 1
FullNghs: 622514 ave 626251 max 616896 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 2490056
Ave neighs/atom = 155.6285
Neighbor list builds = 6
Dangerous builds = 0
Total wall time: 0:00:15