update reference examples with versions that do not vary by MPI rank count (44fcdc40) · Commits · 郑智淋 / lammps

examples/USER/misc/mop/data.mop

0 → 100644

+2467 −0

File added.

Preview size limit exceeded, changes collapsed.

examples/USER/misc/mop/in.compute_stress_mop

+11 −33

Original line number	Diff line number	Diff line
		variable T equal 0.8
		variable p_solid equal 0.05

		lattice fcc 1.0
		region box block 0.0 6.0 0.0 6.0 -2.0 12.0
		create_box 2 box
		read_data data.mop

		mass * 1.0
		pair_style lj/cut 2.5
		pair_coeff * * 1.0 1.0
		pair_coeff 1 2 0.5 1.0
		pair_coeff 2 2 0.0 0.0
		neigh_modify delay 0

		region solid_bottom block INF INF INF INF -1.1 0.1
		region liquid block INF INF INF INF 1.1 8.9
		region solid_up block INF INF INF INF 9.9 11.1

		create_atoms 1 region liquid
		delete_atoms porosity liquid 0.26 88765
		group liquid region liquid

		create_atoms 2 region solid_bottom
		group solid_bottom region solid_bottom
		create_atoms 2 region solid_up
		group solid_up region solid_up
		group solid union solid_bottom solid_up
		group liquid type 1
		group solid type 2
		region bottom block INF INF INF INF INF 7.0
		group bottom region bottom
		group solid_bottom intersect solid bottom
		group solid_up subtract solid solid_bottom

		variable faSolid equal ${p_solid}lxly/count(solid_up)
		fix piston_up solid_up aveforce NULL NULL -${faSolid}
		@@ -35,28 +25,16 @@ compute Tliq liquid temp
		fix nvtliq liquid nvt temp $T $T 0.5
		fix_modify nvtliq temp Tliq

		thermo 10000
		thermo 1000
		thermo_modify flush yes temp Tliq

		dump 1 all atom 10000 dump.lammpstrj

		fix fxbal all balance 1000 1.05 shift z 10 1.05
		velocity liquid create $T 47298 dist gaussian rot yes
		run 50000
		undump 1
		reset_timestep 0

		compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box

		compute liquidStress_ke liquid stress/atom NULL ke
		compute liquidStress_vir liquid stress/atom NULL virial
		fix profile_z liquid ave/chunk 10 1000 10000 bin_z density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6] ave running overwrite file profile.z

		compute mopz0 all stress/mop z center kin conf
		fix mopz0t all ave/time 10 1000 10000 c_mopz0[*] file mopz0.time
		fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time

		compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf
		fix moppzt all ave/time 100 100 10000 c_moppz[*] ave running overwrite file moppz.time mode vector
		fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector

		run 40000
		run 0

examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.1

0 → 100644

+111 −0

Original line number	Diff line number	Diff line
		LAMMPS (5 Sep 2018)
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
		using 1 OpenMP thread(s) per MPI task
		variable T equal 0.8
		variable p_solid equal 0.05

		read_data data.mop
		orthogonal box = (0 0 -2) to (9.52441 9.52441 16)
		1 by 1 by 1 MPI processor grid
		reading atoms ...
		1224 atoms
		reading velocities ...
		1224 velocities

		pair_style lj/cut 2.5
		pair_coeff * * 1.0 1.0
		pair_coeff 1 2 0.5 1.0
		pair_coeff 2 2 0.0 0.0
		neigh_modify delay 0

		group liquid type 1
		792 atoms in group liquid
		group solid type 2
		432 atoms in group solid
		region bottom block INF INF INF INF INF 7.0
		group bottom region bottom
		630 atoms in group bottom
		group solid_bottom intersect solid bottom
		216 atoms in group solid_bottom
		group solid_up subtract solid solid_bottom
		216 atoms in group solid_up

		variable faSolid equal ${p_solid}lxly/count(solid_up)
		variable faSolid equal 0.05lxly/count(solid_up)
		fix piston_up solid_up aveforce NULL NULL -${faSolid}
		fix piston_up solid_up aveforce NULL NULL -0.0209986841649146
		fix freeze_up solid_up setforce 0.0 0.0 NULL
		fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
		fix nvesol solid nve
		compute Tliq liquid temp
		fix nvtliq liquid nvt temp $T $T 0.5
		fix nvtliq liquid nvt temp 0.8 $T 0.5
		fix nvtliq liquid nvt temp 0.8 0.8 0.5
		fix_modify nvtliq temp Tliq
		WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404)

		thermo 1000
		thermo_modify flush yes temp Tliq
		WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)

		fix fxbal all balance 1000 1.05 shift z 10 1.05

		compute mopz0 all stress/mop z center kin conf
		fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time

		compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf
		fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector

		run 0
		Neighbor list info ...
		update every 1 steps, delay 0 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 2.8
		ghost atom cutoff = 2.8
		binsize = 1.4, bins = 7 7 13
		3 neighbor lists, perpetual/occasional/extra = 1 2 0
		(1) pair lj/cut, perpetual
		attributes: half, newton on
		pair build: half/bin/atomonly/newton
		stencil: half/bin/3d/newton
		bin: standard
		(2) compute stress/mop, occasional, copy from (1)
		attributes: half, newton on
		pair build: copy
		stencil: none
		bin: none
		(3) compute stress/mop/profile, occasional, copy from (1)
		attributes: half, newton on
		pair build: copy
		stencil: none
		bin: none
		Per MPI rank memory allocation (min/avg/max) = 3.596 \| 3.596 \| 3.596 Mbytes
		Step Temp E_pair E_mol TotEng Press Volume
		0 0.82011245 -3.0642111 0 -2.2692246 0.16906107 1632.8577
		Loop time of 1.19209e-06 on 1 procs for 0 steps with 1224 atoms

		167.8% 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 \| 0 \| 0 \| 0.0 \| 0.00
		Neigh \| 0 \| 0 \| 0 \| 0.0 \| 0.00
		Comm \| 0 \| 0 \| 0 \| 0.0 \| 0.00
		Output \| 0 \| 0 \| 0 \| 0.0 \| 0.00
		Modify \| 0 \| 0 \| 0 \| 0.0 \| 0.00
		Other \| \| 1.192e-06 \| \| \|100.00

		Nlocal: 1224 ave 1224 max 1224 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 2975 ave 2975 max 2975 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 40241 ave 40241 max 40241 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 40241
		Ave neighs/atom = 32.8766
		Neighbor list builds = 0
		Dangerous builds = 0

		Total wall time: 0:00:00

examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.4

0 → 100644

+111 −0

Original line number	Diff line number	Diff line
		LAMMPS (5 Sep 2018)
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
		using 1 OpenMP thread(s) per MPI task
		variable T equal 0.8
		variable p_solid equal 0.05

		read_data data.mop
		orthogonal box = (0 0 -2) to (9.52441 9.52441 16)
		1 by 2 by 2 MPI processor grid
		reading atoms ...
		1224 atoms
		reading velocities ...
		1224 velocities

		pair_style lj/cut 2.5
		pair_coeff * * 1.0 1.0
		pair_coeff 1 2 0.5 1.0
		pair_coeff 2 2 0.0 0.0
		neigh_modify delay 0

		group liquid type 1
		792 atoms in group liquid
		group solid type 2
		432 atoms in group solid
		region bottom block INF INF INF INF INF 7.0
		group bottom region bottom
		630 atoms in group bottom
		group solid_bottom intersect solid bottom
		216 atoms in group solid_bottom
		group solid_up subtract solid solid_bottom
		216 atoms in group solid_up

		variable faSolid equal ${p_solid}lxly/count(solid_up)
		variable faSolid equal 0.05lxly/count(solid_up)
		fix piston_up solid_up aveforce NULL NULL -${faSolid}
		fix piston_up solid_up aveforce NULL NULL -0.0209986841649146
		fix freeze_up solid_up setforce 0.0 0.0 NULL
		fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
		fix nvesol solid nve
		compute Tliq liquid temp
		fix nvtliq liquid nvt temp $T $T 0.5
		fix nvtliq liquid nvt temp 0.8 $T 0.5
		fix nvtliq liquid nvt temp 0.8 0.8 0.5
		fix_modify nvtliq temp Tliq
		WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404)

		thermo 1000
		thermo_modify flush yes temp Tliq
		WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)

		fix fxbal all balance 1000 1.05 shift z 10 1.05

		compute mopz0 all stress/mop z center kin conf
		fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time

		compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf
		fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector

		run 0
		Neighbor list info ...
		update every 1 steps, delay 0 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 2.8
		ghost atom cutoff = 2.8
		binsize = 1.4, bins = 7 7 13
		3 neighbor lists, perpetual/occasional/extra = 1 2 0
		(1) pair lj/cut, perpetual
		attributes: half, newton on
		pair build: half/bin/atomonly/newton
		stencil: half/bin/3d/newton
		bin: standard
		(2) compute stress/mop, occasional, copy from (1)
		attributes: half, newton on
		pair build: copy
		stencil: none
		bin: none
		(3) compute stress/mop/profile, occasional, copy from (1)
		attributes: half, newton on
		pair build: copy
		stencil: none
		bin: none
		Per MPI rank memory allocation (min/avg/max) = 3.509 \| 3.51 \| 3.511 Mbytes
		Step Temp E_pair E_mol TotEng Press Volume
		0 0.82011245 -3.0642111 0 -2.2692246 0.16906107 1632.8577
		Loop time of 4.06504e-05 on 4 procs for 0 steps with 1224 atoms

		65.2% 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 \| 0 \| 0 \| 0.0 \| 0.00
		Neigh \| 0 \| 0 \| 0 \| 0.0 \| 0.00
		Comm \| 0 \| 0 \| 0 \| 0.0 \| 0.00
		Output \| 0 \| 0 \| 0 \| 0.0 \| 0.00
		Modify \| 0 \| 0 \| 0 \| 0.0 \| 0.00
		Other \| \| 4.065e-05 \| \| \|100.00

		Nlocal: 306 ave 320 max 295 min
		Histogram: 1 1 0 0 0 0 1 0 0 1
		Nghost: 1450.25 ave 1485 max 1422 min
		Histogram: 2 0 0 0 0 0 0 1 0 1
		Neighs: 10060.2 ave 10866 max 9507 min
		Histogram: 2 0 0 0 0 1 0 0 0 1

		Total # of neighbors = 40241
		Ave neighs/atom = 32.8766
		Neighbor list builds = 0
		Dangerous builds = 0

		Total wall time: 0:00:00

examples/USER/misc/mop/moppz.time.reference

+182 −223

File changed.

Preview size limit exceeded, changes collapsed.

Admin message