Rename example
This commit is contained in:
Stan Moore
@ -1,9 +1,9 @@
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To run Baske's test, do
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lmp -in test.in
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lmp -in in.msmeam
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Then
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diff test.dump test.dump.bu
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diff dump.msmeam dump.msmeam.bu
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@ -1,5 +1,5 @@
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echo both
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log test.log
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log log.msmeam
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# Test of MEAM potential for HGa
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# ------------------------ INITIALIZATION ----------------------------
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@ -24,8 +24,8 @@ create_atoms 2 single 0.3 2.3 0 units box
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variable teng equal "c_eatoms"
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compute pot_energy all pe/atom
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compute stress all stress/atom NULL
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dump 1 all custom 1 test.dump id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
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dump 1 all custom 1 dump.msmeam id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
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run 1
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write_data test.data
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write_data data.msmeam
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print "All done!"
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107
examples/meam/msmeam/log.msmeam.bu
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107
examples/meam/msmeam/log.msmeam.bu
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@ -0,0 +1,107 @@
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# Test of MEAM potential for HGa
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# ------------------------ INITIALIZATION ----------------------------
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units metal
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dimension 3
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boundary p p p
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atom_style atomic
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variable latparam equal 4.646
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variable ncell equal 3
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# ----------------------- ATOM DEFINITION ----------------------------
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region box block -4 4 -4 4 -4 4
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create_box 2 box
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Created orthogonal box = (-4 -4 -4) to (4 4 4)
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1 by 1 by 1 MPI processor grid
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#
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include potential.mod
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# NOTE: This script can be modified for different pair styles
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# See in.elastic for more info.
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variable Pu string H
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print "potential chosen ${Pu}"
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potential chosen H
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# Choose potential
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pair_style MSmeam
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print "we just executed"
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we just executed
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pair_coeff * * library.MSmeam ${Pu} Ga4 HGaMS.meam ${Pu} Ga4
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pair_coeff * * library.MSmeam H Ga4 HGaMS.meam ${Pu} Ga4
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pair_coeff * * library.MSmeam H Ga4 HGaMS.meam H Ga4
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Reading potential file library.MSmeam with DATE: 2018-09-22
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# Setup neighbor style
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neighbor 1.0 nsq
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neigh_modify once no every 1 delay 0 check yes
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# Setup minimization style
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variable dmax equal 1.0e-2
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min_style cg
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min_modify dmax ${dmax} line quadratic
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min_modify dmax 0.01 line quadratic
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compute eng all pe/atom
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compute eatoms all reduce sum c_eng
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# Setup output
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thermo 100
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thermo_style custom step temp etotal press pxx pyy pzz pxy pxz pyz lx ly lz vol c_eatoms
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thermo_modify norm yes
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create_atoms 1 single 0 0 0 units box
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Created 1 atoms
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create_atoms 2 single 2.2 0 0 units box
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Created 1 atoms
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create_atoms 2 single 0.3 2.3 0 units box
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Created 1 atoms
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# ---------- Define Settings ---------------------
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variable teng equal "c_eatoms"
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compute pot_energy all pe/atom
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compute stress all stress/atom NULL
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dump 1 all custom 1 dump.msmeam id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
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run 1
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WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
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Neighbor list info ...
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2 neighbor list requests
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 6.9
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ghost atom cutoff = 6.9
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Memory usage per processor = 12.9295 Mbytes
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Step Temp TotEng Press Pxx Pyy Pzz Pxy Pxz Pyz Lx Ly Lz Volume eatoms
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0 0 15.433079 491354.68 838670.91 635393.13 0 80195.793 0 0 8 8 8 512 15.433079
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1 0 15.433079 491354.68 838670.91 635393.13 0 80195.793 0 0 8 8 8 512 15.433079
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Loop time of 0.000172138 on 1 procs for 1 steps with 3 atoms
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Performance: 501.922 ns/day, 0.048 hours/ns, 5809.285 timesteps/s
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81.3% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 6.6996e-05 | 6.6996e-05 | 6.6996e-05 | 0.0 | 38.92
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 1.9073e-06 | 1.9073e-06 | 1.9073e-06 | 0.0 | 1.11
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Output | 9.7036e-05 | 9.7036e-05 | 9.7036e-05 | 0.0 | 56.37
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 6.199e-06 | | | 3.60
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Nlocal: 3 ave 3 max 3 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 78 ave 78 max 78 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 7 ave 7 max 7 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 14 ave 14 max 14 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 14
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Ave neighs/atom = 4.66667
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Neighbor list builds = 0
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Dangerous builds = 0
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write_data data.msmeam
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print "All done!"
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All done!
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Total wall time: 0:00:00
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25
examples/meam/msmeam/msmeam.data
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25
examples/meam/msmeam/msmeam.data
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@ -0,0 +1,25 @@
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LAMMPS data file via write_data, version 22 Dec 2022, timestep = 1
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3 atoms
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2 atom types
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-4 4 xlo xhi
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-4 4 ylo yhi
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-4 4 zlo zhi
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Masses
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1 1.0079
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2 69.723
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Atoms # atomic/kk
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1 1 0 0 0 0 0 0
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2 2 2.2 0 0 0 0 0
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3 2 0.3 2.3 0 0 0 0
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Velocities
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1 0 0 0
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2 0 0 0
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3 0 0 0
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24
examples/meam/msmeam/msmeam.dump.bu
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24
examples/meam/msmeam/msmeam.dump.bu
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@ -0,0 +1,24 @@
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ITEM: TIMESTEP
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0
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ITEM: NUMBER OF ATOMS
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3
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ITEM: BOX BOUNDS pp pp pp
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-4 4
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-4 4
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-4 4
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ITEM: ATOMS id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
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1 0 0 0 -131.925 -88.3005 0 22.9153 -2.147e+08 -1.62661e+08 -0 -2.05301e+07 -0 -0
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2 2.2 0 0 120.809 -0.482171 0 14.7692 -2.12028e+08 -0 -0 403352 -0 -0
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3 0.3 2.3 0 11.1159 88.7827 0 8.61478 -2.67145e+06 -1.62661e+08 -0 -2.09335e+07 -0 -0
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ITEM: TIMESTEP
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1
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ITEM: NUMBER OF ATOMS
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3
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ITEM: BOX BOUNDS pp pp pp
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-4 4
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-4 4
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-4 4
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ITEM: ATOMS id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
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1 0 0 0 -131.925 -88.3005 0 22.9153 -2.147e+08 -1.62661e+08 -0 -2.05301e+07 -0 -0
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2 2.2 0 0 120.809 -0.482171 0 14.7692 -2.12028e+08 -0 -0 403352 -0 -0
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3 0.3 2.3 0 11.1159 88.7827 0 8.61478 -2.67145e+06 -1.62661e+08 -0 -2.09335e+07 -0 -0
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