add alternate log files with the latest version of LAMMPS (adbc75ca) · Commits · 郑智淋 / lammps

examples/gcmc/log.23Oct17.gcmc.co2.g++.1

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Original line number	Diff line number	Diff line
		LAMMPS (23 Oct 2017)
		using 1 OpenMP thread(s) per MPI task
		# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
		# Rigid CO2 TraPPE model
		# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
		# mixtures containing alkanes, carbon dioxide and
		# nitrogen AIChE J., 47,1676-1682 (2001)].

		# variables available on command line

		variable mu index -8.1
		variable disp index 0.5
		variable temp index 338.0
		variable lbox index 10.0
		variable spacing index 5.0

		# global model settings

		units real
		atom_style full
		boundary p p p
		pair_style lj/cut/coul/long 14
		pair_modify mix arithmetic tail yes
		kspace_style ewald 0.0001
		bond_style harmonic
		angle_style harmonic

		# box, start molecules on simple cubic lattice

		lattice sc ${spacing}
		lattice sc 5.0
		Lattice spacing in x,y,z = 5 5 5
		region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
		region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
		region box block 0 10.0 0 10.0 0 ${lbox} units box
		region box block 0 10.0 0 10.0 0 10.0 units box
		create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
		Created orthogonal box = (0 0 0) to (10 10 10)
		1 by 1 by 1 MPI processor grid
		molecule co2mol CO2.txt
		Read molecule co2mol:
		3 atoms with 2 types
		2 bonds with 1 types
		1 angles with 1 types
		0 dihedrals with 0 types
		0 impropers with 0 types
		create_atoms 0 box mol co2mol 464563 units box
		Created 24 atoms
		Time spent = 0.00196958 secs

		# rigid CO2 TraPPE model

		pair_coeff 1 1 0.053649 2.8
		pair_coeff 2 2 0.156973 3.05
		bond_coeff 1 0 1.16
		angle_coeff 1 0 180

		# masses

		mass 1 12.0107
		mass 2 15.9994

		# MD settings

		group co2 type 1 2
		24 atoms in group co2
		neighbor 2.0 bin
		neigh_modify every 1 delay 10 check yes
		velocity all create ${temp} 54654
		velocity all create 338.0 54654
		timestep 1.0

		# rigid constraints with thermostat

		fix myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
		fix myrigidnvt all rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
		fix myrigidnvt all rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol
		8 rigid bodies with 24 atoms
		1.16 = max distance from body owner to body atom
		fix_modify myrigidnvt dynamic/dof no

		# gcmc

		variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
		fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
		fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
		fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
		fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
		fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt

		# atom counts

		variable carbon atom "type==1"
		variable oxygen atom "type==2"
		group carbon dynamic all var carbon
		dynamic group carbon defined
		group oxygen dynamic all var oxygen
		dynamic group oxygen defined
		variable nC equal count(carbon)
		variable nO equal count(oxygen)

		# output

		variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
		variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
		variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
		variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
		compute_modify thermo_temp dynamic/dof yes
		thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
		thermo 1000

		# run

		run 20000
		Ewald initialization ...
		WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
		G vector (1/distance) = 0.164636
		estimated absolute RMS force accuracy = 0.0332064
		estimated relative force accuracy = 0.0001
		KSpace vectors: actual max1d max3d = 16 2 62
		kxmax kymax kzmax = 2 2 2
		WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
		0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
		0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
		WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
		Neighbor list info ...
		update every 1 steps, delay 10 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 16
		ghost atom cutoff = 16
		binsize = 8, bins = 2 2 2
		1 neighbor lists, perpetual/occasional/extra = 1 0 0
		(1) pair lj/cut/coul/long, perpetual
		attributes: half, newton on
		pair build: half/bin/newton
		stencil: half/bin/3d/newton
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 15.62 \| 15.62 \| 15.62 Mbytes
		Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
		0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0 8 16
		WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
		1000 420.43475 1722.4052 -9.6956123 15.456579 0.5846359 24 0.20879341 0.20713005 0 0 8 16
		2000 302.29516 -547.83641 -22.017674 14.11699 0.73079488 30 0.1742478 0.1678018 0 0 10 20
		3000 316.6934 -1080.2672 -8.2218891 10.069364 0.51155641 21 0.13544917 0.13720634 0 0 7 14
		4000 246.81618 -679.83642 -14.577244 10.29997 0.65771539 27 0.1568939 0.15860229 0 0 9 18
		5000 260.22849 -896.29914 -16.097593 10.859684 0.65771539 27 0.13138744 0.13547049 0 0 9 18
		6000 291.70796 -1521.99 -22.303136 13.622574 0.73079488 30 0.12615476 0.12717694 0 0 10 20
		7000 236.02638 -599.92186 -27.580831 13.367447 0.87695385 36 0.119703 0.12145398 0 0 12 24
		8000 321.45341 688.10577 -10.09204 11.817696 0.5846359 24 0.10917411 0.11032646 0 0 8 16
		9000 502.85382 -302.31056 -0.22330142 0.99927447 0.073079488 3 0.1254105 0.12905828 0 0 1 2
		10000 249.98239 -510.0091 -32.815145 15.399767 0.95003334 39 0.1274504 0.12875623 0 0 13 26
		11000 247.59424 -1129.0274 -25.320205 12.792544 0.80387436 33 0.11739076 0.11916784 0 0 11 22
		12000 0 -20.39554 -0.14872889 -0 0 0 0.1254933 0.12920375 0 0 0 0
		13000 1272.2738 -474.79484 -0.29450485 8.8489483 0.14615898 6 0.13767133 0.14112496 0 0 2 4
		14000 516.54246 -36.296516 -5.0012009 11.291243 0.36539744 15 0.15632744 0.15955377 0 0 5 10
		15000 307.09233 1951.9301 -14.820362 12.815375 0.65771539 27 0.15393544 0.15716192 0 0 9 18
		16000 198.31989 -559.48443 -30.459487 11.231925 0.87695385 36 0.1482565 0.15025652 0 0 12 24
		17000 246.99311 657.85683 -18.579206 11.53442 0.73079488 30 0.14143958 0.14375423 0 0 10 20
		18000 467.13468 167.03738 -1.0945268 5.569759 0.21923846 9 0.13847359 0.14098533 0 0 3 6
		19000 359.54027 -1413.5407 -12.156233 13.217895 0.5846359 24 0.15169146 0.15294205 0 0 8 16
		20000 227.79597 -1204.5652 -23.24144 10.637925 0.73079488 30 0.14917199 0.15022946 0 0 10 20
		Loop time of 20.6928 on 1 procs for 20000 steps with 30 atoms

		Performance: 83.507 ns/day, 0.287 hours/ns, 966.519 timesteps/s
		99.2% CPU use with 1 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 2.5462 \| 2.5462 \| 2.5462 \| 0.0 \| 12.30
		Bond \| 0.029783 \| 0.029783 \| 0.029783 \| 0.0 \| 0.14
		Kspace \| 0.26167 \| 0.26167 \| 0.26167 \| 0.0 \| 1.26
		Neigh \| 0.10705 \| 0.10705 \| 0.10705 \| 0.0 \| 0.52
		Comm \| 0.23409 \| 0.23409 \| 0.23409 \| 0.0 \| 1.13
		Output \| 0.0013416 \| 0.0013416 \| 0.0013416 \| 0.0 \| 0.01
		Modify \| 17.458 \| 17.458 \| 17.458 \| 0.0 \| 84.37
		Other \| \| 0.05433 \| \| \| 0.26

		Nlocal: 30 ave 30 max 30 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 2310 ave 2310 max 2310 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 7736 ave 7736 max 7736 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 7736
		Ave neighs/atom = 257.867
		Ave special neighs/atom = 2
		Neighbor list builds = 20349
		Dangerous builds = 0

		Total wall time: 0:00:20

examples/gcmc/log.23Oct17.gcmc.co2.g++.4

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Original line number	Diff line number	Diff line
		LAMMPS (23 Oct 2017)
		using 1 OpenMP thread(s) per MPI task
		# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
		# Rigid CO2 TraPPE model
		# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
		# mixtures containing alkanes, carbon dioxide and
		# nitrogen AIChE J., 47,1676-1682 (2001)].

		# variables available on command line

		variable mu index -8.1
		variable disp index 0.5
		variable temp index 338.0
		variable lbox index 10.0
		variable spacing index 5.0

		# global model settings

		units real
		atom_style full
		boundary p p p
		pair_style lj/cut/coul/long 14
		pair_modify mix arithmetic tail yes
		kspace_style ewald 0.0001
		bond_style harmonic
		angle_style harmonic

		# box, start molecules on simple cubic lattice

		lattice sc ${spacing}
		lattice sc 5.0
		Lattice spacing in x,y,z = 5 5 5
		region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
		region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
		region box block 0 10.0 0 10.0 0 ${lbox} units box
		region box block 0 10.0 0 10.0 0 10.0 units box
		create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
		Created orthogonal box = (0 0 0) to (10 10 10)
		1 by 2 by 2 MPI processor grid
		molecule co2mol CO2.txt
		Read molecule co2mol:
		3 atoms with 2 types
		2 bonds with 1 types
		1 angles with 1 types
		0 dihedrals with 0 types
		0 impropers with 0 types
		create_atoms 0 box mol co2mol 464563 units box
		Created 24 atoms
		Time spent = 0.00261331 secs

		# rigid CO2 TraPPE model

		pair_coeff 1 1 0.053649 2.8
		pair_coeff 2 2 0.156973 3.05
		bond_coeff 1 0 1.16
		angle_coeff 1 0 180

		# masses

		mass 1 12.0107
		mass 2 15.9994

		# MD settings

		group co2 type 1 2
		24 atoms in group co2
		neighbor 2.0 bin
		neigh_modify every 1 delay 10 check yes
		velocity all create ${temp} 54654
		velocity all create 338.0 54654
		timestep 1.0

		# rigid constraints with thermostat

		fix myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
		fix myrigidnvt all rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
		fix myrigidnvt all rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol
		8 rigid bodies with 24 atoms
		1.16 = max distance from body owner to body atom
		fix_modify myrigidnvt dynamic/dof no

		# gcmc

		variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
		fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
		fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
		fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
		fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
		fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt

		# atom counts

		variable carbon atom "type==1"
		variable oxygen atom "type==2"
		group carbon dynamic all var carbon
		dynamic group carbon defined
		group oxygen dynamic all var oxygen
		dynamic group oxygen defined
		variable nC equal count(carbon)
		variable nO equal count(oxygen)

		# output

		variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
		variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
		variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
		variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
		compute_modify thermo_temp dynamic/dof yes
		thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
		thermo 1000

		# run

		run 20000
		Ewald initialization ...
		WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
		G vector (1/distance) = 0.164636
		estimated absolute RMS force accuracy = 0.0332064
		estimated relative force accuracy = 0.0001
		KSpace vectors: actual max1d max3d = 16 2 62
		kxmax kymax kzmax = 2 2 2
		WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
		0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
		0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
		WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
		Neighbor list info ...
		update every 1 steps, delay 10 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 16
		ghost atom cutoff = 16
		binsize = 8, bins = 2 2 2
		1 neighbor lists, perpetual/occasional/extra = 1 0 0
		(1) pair lj/cut/coul/long, perpetual
		attributes: half, newton on
		pair build: half/bin/newton
		stencil: half/bin/3d/newton
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 15.41 \| 15.41 \| 15.41 Mbytes
		Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
		0 386.52184 23582.465 -3.2433417 14.209828 0.5846359 24 0 0 0 0 8 16
		WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
		1000 335.66829 -3.7743052 -4.6268612 7.3374649 0.36539744 15 0.20601899 0.20787963 0 0 5 10
		2000 459.73529 238.91592 -0.42937831 5.4815343 0.21923846 9 0.30392058 0.30105616 0 0 3 6
		3000 255.47773 -479.67802 -36.850434 15.738299 0.95003334 39 0.22220744 0.2197582 0 0 13 26
		4000 182.70803 -1059.2262 -43.044833 12.163134 1.0231128 42 0.16781689 0.16716177 0 0 14 28
		5000 234.00907 -1821.0444 -46.04795 15.578317 1.0231128 42 0.13498091 0.13704201 0 0 14 28
		6000 163.42759 -774.67294 -49.686261 11.691518 1.0961923 45 0.11401677 0.11296973 0 0 15 30
		7000 171.64616 -355.23516 -49.323434 12.27947 1.0961923 45 0.098302308 0.098552065 0 0 15 30
		8000 251.29791 -905.47863 -37.841209 15.480807 0.95003334 39 0.086856972 0.08638658 0 0 13 26
		9000 143.69498 -849.95393 -49.073188 10.279858 1.0961923 45 0.078261061 0.077955243 0 0 15 30
		10000 239.35727 -1158.1879 -43.562047 15.934355 1.0231128 42 0.070789792 0.070807529 0 0 14 28
		11000 169.51213 -1574.7885 -51.125228 12.126803 1.0961923 45 0.065008734 0.06498871 0 0 15 30
		12000 181.39739 160.11631 -46.850937 12.977068 1.0961923 45 0.059648717 0.059514803 0 0 15 30
		13000 164.14601 -1107.7629 -50.726722 11.742914 1.0961923 45 0.055207333 0.055097701 0 0 15 30
		14000 287.26285 418.51463 -41.664766 19.123497 1.0231128 42 0.051346789 0.051222285 0 0 14 28
		15000 256.94593 -532.36615 -41.651618 17.105257 1.0231128 42 0.047870301 0.047861685 0 0 14 28
		16000 166.92132 151.15933 -39.957018 11.11219 1.0231128 42 0.045205599 0.045042211 0 0 14 28
		17000 163.22452 -1299.8119 -42.677558 10.866089 1.0231128 42 0.043122086 0.042993687 0 0 14 28
		18000 158.01154 475.77329 -48.803162 11.304057 1.0961923 45 0.041016683 0.040647229 0 0 15 30
		19000 138.49297 -1585.1508 -47.517099 9.9077098 1.0961923 45 0.038929287 0.038436764 0 0 15 30
		20000 173.84439 -1362.6301 -53.002743 12.436731 1.0961923 45 0.036973919 0.036523816 0 0 15 30
		Loop time of 32.4481 on 4 procs for 20000 steps with 45 atoms

		Performance: 53.254 ns/day, 0.451 hours/ns, 616.369 timesteps/s
		98.4% CPU use with 4 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 1.1687 \| 1.6702 \| 2.1864 \| 30.8 \| 5.15
		Bond \| 0.018828 \| 0.020035 \| 0.020975 \| 0.6 \| 0.06
		Kspace \| 0.57506 \| 1.0931 \| 1.5898 \| 37.7 \| 3.37
		Neigh \| 0.068863 \| 0.069524 \| 0.070128 \| 0.2 \| 0.21
		Comm \| 2.0735 \| 2.0865 \| 2.0979 \| 0.7 \| 6.43
		Output \| 0.0025017 \| 0.0025966 \| 0.0027781 \| 0.2 \| 0.01
		Modify \| 27.335 \| 27.344 \| 27.363 \| 0.2 \| 84.27
		Other \| \| 0.1621 \| \| \| 0.50

		Nlocal: 11.25 ave 14 max 8 min
		Histogram: 1 0 0 0 0 1 1 0 0 1
		Nghost: 2639.75 ave 2656 max 2617 min
		Histogram: 1 0 0 0 0 0 2 0 0 1
		Neighs: 4320 ave 5824 max 2201 min
		Histogram: 1 0 0 0 0 0 1 1 0 1

		Total # of neighbors = 17280
		Ave neighs/atom = 384
		Ave special neighs/atom = 2
		Neighbor list builds = 20394
		Dangerous builds = 0

		Total wall time: 0:00:32

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