Merge pull request #1096 from ProfessorMiller/master
Changes to the NH fix enabling Cauchy stress control (Cauhchystat) du…
This commit is contained in:
Axel Kohlmeyer
1
examples/USER/misc/cauchy/NiAlH_jea.eam.alloy
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examples/USER/misc/cauchy/NiAlH_jea.eam.alloy
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../../../../potentials/NiAlH_jea.eam.alloy
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10
examples/USER/misc/cauchy/README
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10
examples/USER/misc/cauchy/README
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Run this example by executing:
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% lmp -in in.cauchystat
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Note that this example use an EAM potential, and therefore must be
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run with a LAMMPS executable built with the MANYBODY package.
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The first cauchystat fix equilibrates the temperature at zero stress,
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the second fix applies a shear stress. Output in avg.txt shows
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convergence to correct values.
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68
examples/USER/misc/cauchy/in.cauchystat
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68
examples/USER/misc/cauchy/in.cauchystat
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units metal
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atom_style atomic
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atom_modify map array
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# Box and atom positions:
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boundary p p p
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# Defining lattice and creating simulation
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# box with atoms inside
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lattice fcc 4.05
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region simbox prism 0 5 0 5 0 5 0 0 0 units lattice
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create_box 2 simbox
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create_atoms 2 box
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# Atomic mass:
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mass 1 58.69
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mass 2 26.98154
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# Potential, Al fcc crystal
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pair_style eam/alloy
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pair_coeff * * NiAlH_jea.eam.alloy Ni Al
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neigh_modify delay 5
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thermo 100
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thermo_style custom step temp pxx pyy pzz pxy pxz pyz
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compute cna all cna/atom 2.8
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fix 1 all npt/cauchy temp 600.0 600.0 1.0 &
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x 0.0 0.0 0.1 &
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y 0.0 0.0 0.1 &
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z 0.0 0.0 0.1 &
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couple none alpha 0.001 continue no
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# dump 1 all cfg 1000 test*.cfg mass type xs ys zs type c_cna
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timestep 0.002
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variable px equal pxx
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variable py equal pyy
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variable pz equal pzz
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variable sxy equal pxy
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variable sxz equal pxz
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variable syz equal pyz
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variable t equal temp
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fix avg all ave/time 1 100 100 v_t v_px v_py v_pz v_sxy v_sxz v_syz file avg.txt
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variable lx equal lx
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variable ly equal ly
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variable lz equal ly
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variable xy equal xy
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variable xz equal xz
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variable yz equal yz
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fix box all ave/time 1 100 100 v_lx v_ly v_lz v_xy v_xz v_yz file box.txt
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velocity all create 1200 4928459 rot yes dist gaussian
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run 1000
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fix 1 all npt/cauchy temp 600.0 600.0 1.0 &
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x 0.0 0.0 0.1 &
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y 0.0 0.0 0.1 &
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z 0.0 0.0 0.1 &
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xy -10000.0 -10000.0 0.1 &
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couple none alpha 0.001 continue yes
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run 1000
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172
examples/USER/misc/cauchy/log.9Jan2020.cauchystat.g++.1
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172
examples/USER/misc/cauchy/log.9Jan2020.cauchystat.g++.1
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LAMMPS (09 Jan 2020)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
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using 1 OpenMP thread(s) per MPI task
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units metal
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atom_style atomic
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atom_modify map array
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# Box and atom positions:
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boundary p p p
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# Defining lattice and creating simulation
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# box with atoms inside
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lattice fcc 4.05
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Lattice spacing in x,y,z = 4.05 4.05 4.05
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region simbox prism 0 5 0 5 0 5 0 0 0 units lattice
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create_box 2 simbox
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Created triclinic box = (0 0 0) to (20.25 20.25 20.25) with tilt (0 0 0)
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1 by 1 by 1 MPI processor grid
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create_atoms 2 box
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Created 500 atoms
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create_atoms CPU = 0.000987053 secs
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# Atomic mass:
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mass 1 58.69
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mass 2 26.98154
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# Potential, Al fcc crystal
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pair_style eam/alloy
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pair_coeff * * NiAlH_jea.eam.alloy Ni Al
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Reading potential file NiAlH_jea.eam.alloy with DATE: 2007-11-30
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neigh_modify delay 5
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thermo 100
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thermo_style custom step temp pxx pyy pzz pxy pxz pyz
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compute cna all cna/atom 2.8
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fix 1 all npt/cauchy temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 couple none alpha 0.001 continue no
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Using fix npt/cauchy with alpha=0.001000
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this is NOT a continuation run
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# dump 1 all cfg 1000 test*.cfg mass type xs ys zs type c_cna
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timestep 0.002
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variable px equal pxx
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variable py equal pyy
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variable pz equal pzz
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variable sxy equal pxy
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variable sxz equal pxz
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variable syz equal pyz
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variable t equal temp
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fix avg all ave/time 1 100 100 v_t v_px v_py v_pz v_sxy v_sxz v_syz file avg.txt
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variable lx equal lx
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variable ly equal ly
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variable lz equal ly
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variable xy equal xy
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variable xz equal xz
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variable yz equal yz
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fix box all ave/time 1 100 100 v_lx v_ly v_lz v_xy v_xz v_yz file box.txt
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velocity all create 1200 4928459 rot yes dist gaussian
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run 1000
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Neighbor list info ...
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update every 1 steps, delay 5 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 7.65
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ghost atom cutoff = 7.65
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binsize = 3.825, bins = 6 6 6
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2 neighbor lists, perpetual/occasional/extra = 1 1 0
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(1) pair eam/alloy, perpetual
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attributes: half, newton on
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pair build: half/bin/newton/tri
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stencil: half/bin/3d/newton/tri
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bin: standard
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(2) compute cna/atom, occasional
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.04 | 4.04 | 4.04 Mbytes
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Step Temp Pxx Pyy Pzz Pxy Pxz Pyz
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0 1200 9859.2374 9729.7389 10279.526 -110.10907 -391.60768 295.10918
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100 461.95579 11262.405 9918.4702 7373.1896 1389.9833 -165.54737 -128.04989
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200 452.7497 4758.0631 6285.2022 9593.9725 389.15901 835.71435 -1853.9679
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300 451.50974 7980.6036 7524.3514 9584.5276 297.33672 -154.88768 -1927.573
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400 461.52812 5074.9544 4877.0864 2689.9029 389.66084 224.44814 563.12739
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500 458.17416 7672.6668 5358.5073 4670.0236 -1251.047 1175.8268 -373.96822
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600 461.28593 3629.8562 7265.1611 6970.1746 523.3139 1295.8252 -121.17116
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700 466.86592 5224.2421 4121.434 4368.4226 230.85768 -65.765274 -1271.8354
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800 491.38828 -233.79818 2799.6028 5023.998 919.08469 -411.66796 422.33219
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900 473.16465 6486.5426 4028.6955 2503.9771 451.96928 1309.8322 -557.83472
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1000 472.85932 4303.6923 4674.969 5268.2263 94.551286 1425.2222 -1352.0883
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Loop time of 1.24705 on 1 procs for 1000 steps with 500 atoms
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Performance: 138.567 ns/day, 0.173 hours/ns, 801.892 timesteps/s
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94.0% CPU use with 1 MPI tasks x 1 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 | 1.112 | 1.112 | 1.112 | 0.0 | 89.17
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Neigh | 0.063329 | 0.063329 | 0.063329 | 0.0 | 5.08
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Comm | 0.01994 | 0.01994 | 0.01994 | 0.0 | 1.60
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Output | 0.0014246 | 0.0014246 | 0.0014246 | 0.0 | 0.11
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Modify | 0.045429 | 0.045429 | 0.045429 | 0.0 | 3.64
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Other | | 0.004881 | | | 0.39
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Nlocal: 500 ave 500 max 500 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 2017 ave 2017 max 2017 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 24689 ave 24689 max 24689 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 24689
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Ave neighs/atom = 49.378
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Neighbor list builds = 34
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Dangerous builds = 0
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fix 1 all npt/cauchy temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 xy -10000.0 -10000.0 0.1 couple none alpha 0.001 continue yes
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Using fix npt/cauchy with alpha=0.001000
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this is a continuation run
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run 1000
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Per MPI rank memory allocation (min/avg/max) = 4.056 | 4.056 | 4.056 Mbytes
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Step Temp Pxx Pyy Pzz Pxy Pxz Pyz
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1000 472.85932 4303.6923 4674.969 5268.2263 94.551286 1425.2222 -1352.0883
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1100 471.04772 5593.1614 5874.9867 3608.9922 -1861.938 459.86813 -813.36882
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1200 473.34727 2337.4765 2050.4694 4330.2198 -3590.2198 -1285.2197 748.05137
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1300 465.46145 4909.5722 2880.9183 4995.0091 -2860.6934 -895.40937 -382.07531
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1400 508.53262 92.57534 3722.1136 557.50974 -3121.7615 349.6147 194.5089
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1500 498.34579 -5755.2352 -3798.1466 -1445.2047 -3218.0887 1733.9103 -555.96371
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1600 546.45882 -257.80132 407.73403 -39.803803 -3578.1137 1438.3526 -1710.3139
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1700 570.72785 -2951.9658 -622.89945 1138.4113 -4573.7982 -984.65235 2906.3144
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1800 650.75622 6086.1524 1111.2919 1726.5115 -3504.716 1140.9767 414.81284
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1900 690.32264 2763.2044 -609.41535 289.85307 -3788.8761 -1306.8569 760.00116
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2000 724.01451 -675.72484 522.04263 -468.58167 -6603.3906 -1712.7317 47.61212
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Loop time of 1.27211 on 1 procs for 1000 steps with 500 atoms
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Performance: 135.837 ns/day, 0.177 hours/ns, 786.093 timesteps/s
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93.9% CPU use with 1 MPI tasks x 1 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 | 1.0529 | 1.0529 | 1.0529 | 0.0 | 82.77
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Neigh | 0.13671 | 0.13671 | 0.13671 | 0.0 | 10.75
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Comm | 0.018747 | 0.018747 | 0.018747 | 0.0 | 1.47
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Output | 0.00075722 | 0.00075722 | 0.00075722 | 0.0 | 0.06
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Modify | 0.057984 | 0.057984 | 0.057984 | 0.0 | 4.56
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Other | | 0.00499 | | | 0.39
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Nlocal: 500 ave 500 max 500 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 2040 ave 2040 max 2040 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 23757 ave 23757 max 23757 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 23757
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Ave neighs/atom = 47.514
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Neighbor list builds = 78
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Dangerous builds = 0
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Total wall time: 0:00:02
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