make example input / output conform with LAMMPS conventions (no dump files, no... (7193fffe) · Commits · 郑智淋 / lammps

examples/USER/misc/ees/in.fix_wall

+1 −2

Original line number	Diff line number	Diff line
		log log_substrate
		units lj
		atom_style ellipsoid
		boundary p p f
		@@ -26,6 +25,6 @@ compute qj all property/atom quatj
		compute qk all property/atom quatk
		#------------------------------------#
		thermo 500
		dump 1 all custom 1000 dump_substrate id type x y z c_qw c_qi c_qj c_qk
		#dump 1 all custom 1000 dump_substrate id type x y z c_qw c_qi c_qj c_qk
		run 40000

examples/USER/misc/ees/in.fix_wall_region

+1 −2

Original line number	Diff line number	Diff line
		log log_region
		units lj
		atom_style ellipsoid
		boundary p p p
		@@ -25,6 +24,6 @@ compute qj all property/atom quatj
		compute qk all property/atom quatk
		#------------------------------------#
		thermo 500
		dump 1 all custom 1000 dump_region id type x y z c_qw c_qi c_qj c_qk
		#dump 1 all custom 1000 dump_region id type x y z c_qw c_qi c_qj c_qk
		run 50000

examples/USER/misc/ees/log.23Jun17.fix_wall.g++.1

0 → 100644

+162 −0

Original line number	Diff line number	Diff line
		LAMMPS (23 Jun 2017)
		using 1 OpenMP thread(s) per MPI task
		units lj
		atom_style ellipsoid
		boundary p p f
		read_data Data_wall
		orthogonal box = (0 0 0) to (60 60 60)
		1 by 1 by 1 MPI processor grid
		reading atoms ...
		1 atoms
		1 ellipsoids
		reading velocities ...
		1 velocities
		#------------------------------------#
		pair_style resquared 1
		pair_coeff 1 1 10.0 1.0 0.5 0.5 4 0.5 0.5 4 1
		#------------------------------------#
		timestep 0.0002
		#------------------------------------#

		compute temp all temp/asphere
		thermo_modify temp temp

		fix EES_substrate all wall/ees zhi EDGE 10 1 10 zlo EDGE 10 1 10
		#^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#

		thermo_style custom step temp press etotal f_EES_substrate f_EES_substrate[1]
		WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:705)

		fix NVE all nve/asphere
		#------------------------------------#
		compute qw all property/atom quatw
		compute qi all property/atom quati
		compute qj all property/atom quatj
		compute qk all property/atom quatk
		#------------------------------------#
		thermo 500
		#dump 1 all custom 1000 dump_substrate id type x y z c_qw c_qi c_qj c_qk
		run 40000
		Neighbor list info ...
		update every 1 steps, delay 10 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 1.3
		ghost atom cutoff = 1.3
		binsize = 0.65, bins = 93 93 93
		1 neighbor lists, perpetual/occasional/extra = 1 0 0
		(1) pair resquared, perpetual
		attributes: half, newton on
		pair build: half/bin/atomonly/newton
		stencil: half/bin/3d/newton
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 7.95 \| 7.95 \| 7.95 Mbytes
		Step Temp Press TotEng f_EES_substrate f_EES_substrate[1]
		0 0 0.00054301475 0 0 0
		500 0 0.00054301501 0 -0.002011167 -0.00089853601
		1000 0 0.0005430153 0 -0.0021039425 -0.00095953758
		1500 0 0.00054301561 0 -0.0022030914 -0.0010262478
		2000 0 0.00054301593 0 -0.002309218 -0.0010993652
		2500 0 0.00054301628 0 -0.0024230015 -0.0011796956
		3000 0 0.00054301666 0 -0.0025452078 -0.0012681725
		3500 0 0.00054301707 0 -0.0026767034 -0.0013658817
		4000 0 0.00054301751 0 -0.0028184722 -0.0014740918
		4500 0 0.00054301798 0 -0.0029716352 -0.0015942917
		5000 0 0.00054301849 0 -0.0031374752 -0.0017282378
		5500 0 0.00054301905 0 -0.0033174662 -0.0018780129
		6000 0 0.00054301965 0 -0.0035133093 -0.0020461007
		6500 0 0.00054302031 0 -0.0037269778 -0.0022354811
		7000 0 0.00054302103 0 -0.0039607721 -0.0024497521
		7500 0 0.00054302182 0 -0.0042173892 -0.0026932881
		8000 0 0.0005430227 0 -0.0045000102 -0.0029714471
		8500 0 0.00054302366 0 -0.0048124114 -0.003290844
		9000 0 0.00054302473 0 -0.0051591071 -0.0036597154
		9500 0 0.00054302592 0 -0.0055455349 -0.0040884113
		10000 0 0.00054302726 0 -0.0059782985 -0.0045900652
		10500 0 0.00054302876 0 -0.0064654891 -0.0051815166
		11000 0 0.00054303046 0 -0.0070171161 -0.0058845936
		11500 0 0.0005430324 0 -0.0076456899 -0.0067279075
		12000 0 0.00054303463 0 -0.0083670175 -0.0077493697
		12500 0 0.00054303721 0 -0.0092012967 -0.0089996821
		13000 0 0.00054304021 0 -0.010174616 -0.010546991
		13500 0 0.00054304375 0 -0.011320967 -0.012482357
		14000 0 0.00054304796 0 -0.012684757 -0.01492338
		14500 0 0.00054305301 0 -0.014323176 -0.01800425
		15000 0 0.00054305913 0 -0.016305242 -0.021804766
		15500 0 0.0005430665 0 -0.018693849 -0.026019991
		16000 0 0.00054307501 0 -0.021450982 -0.028460977
		16500 0 0.0005430828 0 -0.023974925 -0.017549988
		17000 0 0.00054307849 0 -0.022577692 0.07296284
		17500 0 0.00054298744 0 0.0069237358 0.72962844
		18000 0 0.00054212125 0 0.28756839 7.5171061
		18500 0 0.00052809177 0 4.8331004 159.56814
		19000 0 0.00019717774 0 112.04947 5692.3379
		19500 0 0.00051978321 0 7.5250598 262.38764
		20000 0 0.00054179603 0 0.39293697 10.289153
		20500 0 0.00054296932 0 0.01279406 0.89377639
		21000 0 0.00054308425 0 -0.02444466 0.081890707
		21500 0 0.0005430907 0 -0.026532401 -0.021386086
		22000 0 0.00054308271 0 -0.023944983 -0.032642459
		22500 0 0.00054307381 0 -0.02106205 -0.029524272
		23000 0 0.00054306612 0 -0.018569361 -0.024753431
		23500 0 0.00054305976 0 -0.01650866 -0.020566675
		24000 0 0.00054305452 0 -0.014811253 -0.017216347
		24500 0 0.00054305017 0 -0.013402896 -0.014581066
		25000 0 0.00054304653 0 -0.012222687 -0.01250069
		25500 0 0.00054304345 0 -0.011223677 -0.0108418
		26000 0 0.00054304081 0 -0.010370111 -0.0095034766
		26500 0 0.00054303854 0 -0.0096346546 -0.0084112161
		27000 0 0.00054303657 0 -0.0089962072 -0.0075100751
		27500 0 0.00054303485 0 -0.0084382935 -0.0067592209
		28000 0 0.00054303334 0 -0.0079478992 -0.0061279726
		28500 0 0.000543032 0 -0.0075146283 -0.0055930001
		29000 0 0.00054303081 0 -0.0071300893 -0.0051363504
		29500 0 0.00054302976 0 -0.0067874426 -0.00474405
		30000 0 0.00054302881 0 -0.0064810641 -0.0044051051
		30500 0 0.00054302796 0 -0.0062062911 -0.0041107799
		31000 0 0.0005430272 0 -0.0059592289 -0.0038540677
		31500 0 0.00054302651 0 -0.0057366023 -0.0036293011
		32000 0 0.00054302589 0 -0.0055356393 -0.0034318592
		32500 0 0.00054302533 0 -0.0053539804 -0.0032579475
		33000 0 0.00054302482 0 -0.0051896066 -0.0031044289
		33500 0 0.00054302436 0 -0.0050407818 -0.0029686945
		34000 0 0.00054302395 0 -0.0049060063 -0.002848562
		34500 0 0.00054302357 0 -0.0047839795 -0.002742197
		35000 0 0.00054302323 0 -0.0046735688 -0.0026480503
		35500 0 0.00054302292 0 -0.0045737849 -0.0025648085
		36000 0 0.00054302264 0 -0.0044837605 -0.0024913535
		36500 0 0.00054302239 0 -0.0044027327 -0.0024267309
		37000 0 0.00054302217 0 -0.0043300292 -0.0023701236
		37500 0 0.00054302197 0 -0.0042650554 -0.0023208304
		38000 0 0.00054302179 0 -0.0042072838 -0.0022782486
		38500 0 0.00054302163 0 -0.0041562461 -0.0022418592
		39000 0 0.0005430215 0 -0.0041115244 -0.0022112152
		39500 0 0.00054302138 0 -0.0040727453 -0.0021859312
		40000 0 0.00054302127 0 -0.0040395743 -0.0021656748
		Loop time of 0.111517 on 1 procs for 40000 steps with 1 atoms

		Performance: 6198147.516 tau/day, 358689.092 timesteps/s
		98.6% CPU use with 1 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 0.0082421 \| 0.0082421 \| 0.0082421 \| 0.0 \| 7.39
		Neigh \| 0.021163 \| 0.021163 \| 0.021163 \| 0.0 \| 18.98
		Comm \| 0.045411 \| 0.045411 \| 0.045411 \| 0.0 \| 40.72
		Output \| 0.0012326 \| 0.0012326 \| 0.0012326 \| 0.0 \| 1.11
		Modify \| 0.022813 \| 0.022813 \| 0.022813 \| 0.0 \| 20.46
		Other \| \| 0.01265 \| \| \| 11.35

		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

		Total # of neighbors = 0
		Ave neighs/atom = 0
		Neighbor list builds = 33
		Dangerous builds = 0

		Total wall time: 0:00:00

examples/USER/misc/ees/log.23Jun17.fix_wall.g++.4

0 → 100644

+162 −0

Original line number	Diff line number	Diff line
		LAMMPS (23 Jun 2017)
		using 1 OpenMP thread(s) per MPI task
		units lj
		atom_style ellipsoid
		boundary p p f
		read_data Data_wall
		orthogonal box = (0 0 0) to (60 60 60)
		1 by 2 by 2 MPI processor grid
		reading atoms ...
		1 atoms
		1 ellipsoids
		reading velocities ...
		1 velocities
		#------------------------------------#
		pair_style resquared 1
		pair_coeff 1 1 10.0 1.0 0.5 0.5 4 0.5 0.5 4 1
		#------------------------------------#
		timestep 0.0002
		#------------------------------------#

		compute temp all temp/asphere
		thermo_modify temp temp

		fix EES_substrate all wall/ees zhi EDGE 10 1 10 zlo EDGE 10 1 10
		#^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#

		thermo_style custom step temp press etotal f_EES_substrate f_EES_substrate[1]
		WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:705)

		fix NVE all nve/asphere
		#------------------------------------#
		compute qw all property/atom quatw
		compute qi all property/atom quati
		compute qj all property/atom quatj
		compute qk all property/atom quatk
		#------------------------------------#
		thermo 500
		#dump 1 all custom 1000 dump_substrate id type x y z c_qw c_qi c_qj c_qk
		run 40000
		Neighbor list info ...
		update every 1 steps, delay 10 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 1.3
		ghost atom cutoff = 1.3
		binsize = 0.65, bins = 93 93 93
		1 neighbor lists, perpetual/occasional/extra = 1 0 0
		(1) pair resquared, perpetual
		attributes: half, newton on
		pair build: half/bin/atomonly/newton
		stencil: half/bin/3d/newton
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 5.128 \| 5.41 \| 5.753 Mbytes
		Step Temp Press TotEng f_EES_substrate f_EES_substrate[1]
		0 0 0.00054301475 0 0 0
		500 0 0.00054301501 0 -0.002011167 -0.00089853601
		1000 0 0.0005430153 0 -0.0021039425 -0.00095953758
		1500 0 0.00054301561 0 -0.0022030914 -0.0010262478
		2000 0 0.00054301593 0 -0.002309218 -0.0010993652
		2500 0 0.00054301628 0 -0.0024230015 -0.0011796956
		3000 0 0.00054301666 0 -0.0025452078 -0.0012681725
		3500 0 0.00054301707 0 -0.0026767034 -0.0013658817
		4000 0 0.00054301751 0 -0.0028184722 -0.0014740918
		4500 0 0.00054301798 0 -0.0029716352 -0.0015942917
		5000 0 0.00054301849 0 -0.0031374752 -0.0017282378
		5500 0 0.00054301905 0 -0.0033174662 -0.0018780129
		6000 0 0.00054301965 0 -0.0035133093 -0.0020461007
		6500 0 0.00054302031 0 -0.0037269778 -0.0022354811
		7000 0 0.00054302103 0 -0.0039607721 -0.0024497521
		7500 0 0.00054302182 0 -0.0042173892 -0.0026932881
		8000 0 0.0005430227 0 -0.0045000102 -0.0029714471
		8500 0 0.00054302366 0 -0.0048124114 -0.003290844
		9000 0 0.00054302473 0 -0.0051591071 -0.0036597154
		9500 0 0.00054302592 0 -0.0055455349 -0.0040884113
		10000 0 0.00054302726 0 -0.0059782985 -0.0045900652
		10500 0 0.00054302876 0 -0.0064654891 -0.0051815166
		11000 0 0.00054303046 0 -0.0070171161 -0.0058845936
		11500 0 0.0005430324 0 -0.0076456899 -0.0067279075
		12000 0 0.00054303463 0 -0.0083670175 -0.0077493697
		12500 0 0.00054303721 0 -0.0092012967 -0.0089996821
		13000 0 0.00054304021 0 -0.010174616 -0.010546991
		13500 0 0.00054304375 0 -0.011320967 -0.012482357
		14000 0 0.00054304796 0 -0.012684757 -0.01492338
		14500 0 0.00054305301 0 -0.014323176 -0.01800425
		15000 0 0.00054305913 0 -0.016305242 -0.021804766
		15500 0 0.0005430665 0 -0.018693849 -0.026019991
		16000 0 0.00054307501 0 -0.021450982 -0.028460977
		16500 0 0.0005430828 0 -0.023974925 -0.017549988
		17000 0 0.00054307849 0 -0.022577692 0.07296284
		17500 0 0.00054298744 0 0.0069237358 0.72962844
		18000 0 0.00054212125 0 0.28756839 7.5171061
		18500 0 0.00052809177 0 4.8331004 159.56814
		19000 0 0.00019717774 0 112.04947 5692.3379
		19500 0 0.00051978321 0 7.5250598 262.38764
		20000 0 0.00054179603 0 0.39293697 10.289153
		20500 0 0.00054296932 0 0.01279406 0.89377639
		21000 0 0.00054308425 0 -0.02444466 0.081890707
		21500 0 0.0005430907 0 -0.026532401 -0.021386086
		22000 0 0.00054308271 0 -0.023944983 -0.032642459
		22500 0 0.00054307381 0 -0.02106205 -0.029524272
		23000 0 0.00054306612 0 -0.018569361 -0.024753431
		23500 0 0.00054305976 0 -0.01650866 -0.020566675
		24000 0 0.00054305452 0 -0.014811253 -0.017216347
		24500 0 0.00054305017 0 -0.013402896 -0.014581066
		25000 0 0.00054304653 0 -0.012222687 -0.01250069
		25500 0 0.00054304345 0 -0.011223677 -0.0108418
		26000 0 0.00054304081 0 -0.010370111 -0.0095034766
		26500 0 0.00054303854 0 -0.0096346546 -0.0084112161
		27000 0 0.00054303657 0 -0.0089962072 -0.0075100751
		27500 0 0.00054303485 0 -0.0084382935 -0.0067592209
		28000 0 0.00054303334 0 -0.0079478992 -0.0061279726
		28500 0 0.000543032 0 -0.0075146283 -0.0055930001
		29000 0 0.00054303081 0 -0.0071300893 -0.0051363504
		29500 0 0.00054302976 0 -0.0067874426 -0.00474405
		30000 0 0.00054302881 0 -0.0064810641 -0.0044051051
		30500 0 0.00054302796 0 -0.0062062911 -0.0041107799
		31000 0 0.0005430272 0 -0.0059592289 -0.0038540677
		31500 0 0.00054302651 0 -0.0057366023 -0.0036293011
		32000 0 0.00054302589 0 -0.0055356393 -0.0034318592
		32500 0 0.00054302533 0 -0.0053539804 -0.0032579475
		33000 0 0.00054302482 0 -0.0051896066 -0.0031044289
		33500 0 0.00054302436 0 -0.0050407818 -0.0029686945
		34000 0 0.00054302395 0 -0.0049060063 -0.002848562
		34500 0 0.00054302357 0 -0.0047839795 -0.002742197
		35000 0 0.00054302323 0 -0.0046735688 -0.0026480503
		35500 0 0.00054302292 0 -0.0045737849 -0.0025648085
		36000 0 0.00054302264 0 -0.0044837605 -0.0024913535
		36500 0 0.00054302239 0 -0.0044027327 -0.0024267309
		37000 0 0.00054302217 0 -0.0043300292 -0.0023701236
		37500 0 0.00054302197 0 -0.0042650554 -0.0023208304
		38000 0 0.00054302179 0 -0.0042072838 -0.0022782486
		38500 0 0.00054302163 0 -0.0041562461 -0.0022418592
		39000 0 0.0005430215 0 -0.0041115244 -0.0022112152
		39500 0 0.00054302138 0 -0.0040727453 -0.0021859312
		40000 0 0.00054302127 0 -0.0040395743 -0.0021656748
		Loop time of 0.216115 on 4 procs for 40000 steps with 1 atoms

		Performance: 3198303.409 tau/day, 185087.003 timesteps/s
		98.5% CPU use with 4 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 0.0020442 \| 0.0047204 \| 0.012008 \| 6.1 \| 2.18
		Neigh \| 0.0069654 \| 0.0072649 \| 0.0074701 \| 0.2 \| 3.36
		Comm \| 0.024762 \| 0.039833 \| 0.056166 \| 7.4 \| 18.43
		Output \| 0.0020285 \| 0.0023268 \| 0.0026891 \| 0.5 \| 1.08
		Modify \| 0.0081856 \| 0.013537 \| 0.029052 \| 7.7 \| 6.26
		Other \| \| 0.1484 \| \| \| 68.68

		Nlocal: 0.25 ave 1 max 0 min
		Histogram: 3 0 0 0 0 0 0 0 0 1
		Nghost: 0.25 ave 1 max 0 min
		Histogram: 3 0 0 0 0 0 0 0 0 1
		Neighs: 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 = 33
		Dangerous builds = 0

		Total wall time: 0:00:00

examples/USER/misc/ees/log.23Jun17.fix_wall_region.g++.1

0 → 100644

+180 −0

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