update log files for gcmc example (41e24f6e) · Commits · 郑智淋 / lammps

examples/gcmc/log.30Mar18.gcmc.co2.g++.1→examples/gcmc/log.27Nov18.gcmc.co2.g++.1

+45 −45

Original line number	Diff line number	Diff line
		LAMMPS (30 Mar 2018)
		LAMMPS (27 Nov 2018)
		using 1 OpenMP thread(s) per MPI task
		# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
		# Rigid CO2 TraPPE model
		@@ -46,7 +46,7 @@ Read molecule co2mol:
		0 impropers with max type 0
		create_atoms 0 box mol co2mol 464563 units box
		Created 24 atoms
		Time spent = 0.00241756 secs
		Time spent = 0.00134993 secs

		# rigid CO2 TraPPE model

		@@ -118,16 +118,16 @@ thermo 1000

		run 20000
		Ewald initialization ...
		using 12-bit tables for long-range coulomb (../kspace.cpp:321)
		using 12-bit tables for long-range coulomb (src/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:485)
		WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:487)
		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)
		WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:471)
		Neighbor list info ...
		update every 1 steps, delay 10 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		@@ -143,54 +143,54 @@ Neighbor list info ...
		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
		1000 330.05964 -376.0111 -13.936335 13.773831 0.65771539 27 0.21142067 0.21453147 0 0 9 18
		2000 293.79769 -321.3209 -19.049256 13.720163 0.73079488 30 0.25170944 0.25426294 0 0 10 20
		3000 348.9085 259.04079 -0.23347965 2.4267366 0.14615898 6 0.22016906 0.23200597 0 0 2 4
		4000 360.54577 -329.12072 -16.584234 15.046059 0.65771539 27 0.19173099 0.19785362 0 0 9 18
		5000 275.58628 -58.283006 -12.520856 11.500585 0.65771539 27 0.16490585 0.17329884 0 0 9 18
		6000 338.59574 364.93514 -19.866569 17.494353 0.80387436 33 0.17971759 0.18331589 0 0 11 22
		7000 286.11586 -1252.5069 -19.588667 13.361427 0.73079488 30 0.15729895 0.16220459 0 0 10 20
		8000 454.86786 -642.89382 -20.818357 21.242037 0.73079488 30 0.15500235 0.15802382 0 0 10 20
		9000 326.36695 -364.71382 -31.376162 18.48392 0.87695385 36 0.14203985 0.14510714 0 0 12 24
		10000 348.46961 -387.75245 -21.068466 18.00451 0.80387436 33 0.14000907 0.14343389 0 0 11 22
		11000 409.74257 -15.843895 -20.648252 21.170323 0.80387436 33 0.14689306 0.15117074 0 0 11 22
		12000 523.93502 1003.0729 -6.0563102 14.055757 0.43847693 18 0.15337575 0.1580166 0 0 6 12
		13000 278.14441 -717.1097 -2.3488496 4.6982087 0.29231795 12 0.15952356 0.16422306 0 0 4 8
		14000 367.89375 1239.0841 -11.203323 13.524997 0.5846359 24 0.17002439 0.17460294 0 0 8 16
		15000 197.05319 -471.14343 -9.3890758 6.2653668 0.51155641 21 0.17702612 0.18155802 0 0 7 14
		16000 138.17147 -935.93437 -2.3846783 2.3338898 0.29231795 12 0.17884346 0.18268758 0 0 4 8
		17000 245.61833 -166.1694 -5.0970057 5.3690384 0.36539744 15 0.18909252 0.19317817 0 0 5 10
		18000 232.0142 -175.732 -14.320198 9.6822635 0.65771539 27 0.18977089 0.19280537 0 0 9 18
		19000 362.01189 864.87258 -6.4515321 9.7117982 0.43847693 18 0.19207244 0.19488984 0 0 6 12
		20000 441.19548 186.19779 -18.147268 20.603546 0.73079488 30 0.19713351 0.199073 0 0 10 20
		Loop time of 16.4949 on 1 procs for 20000 steps with 30 atoms

		Performance: 104.760 ns/day, 0.229 hours/ns, 1212.498 timesteps/s
		99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
		1000 267.9799 -73.919548 -3.6735999 5.8578459 0.36539744 15 0.23663972 0.2494423 0 0 5 10
		2000 409.06596 -98.033864 -6.7570039 10.974131 0.43847693 18 0.29379544 0.29816284 0 0 6 12
		3000 279.3225 -836.47758 -26.434976 15.819539 0.87695385 36 0.23798567 0.24203908 0 0 12 24
		4000 333.6181 606.63478 -30.35312 18.894592 0.87695385 36 0.19121778 0.19481508 0 0 12 24
		5000 405.98741 -103.97582 -14.180277 16.942399 0.65771539 27 0.15272841 0.15982952 0 0 9 18
		6000 283.5835 -240.01076 -6.7198093 7.607777 0.43847693 18 0.1606796 0.16536735 0 0 6 12
		7000 142.00717 154.95914 -0.74192319 0.98769159 0.14615898 6 0.19501993 0.20103405 0 0 2 4
		8000 376.67702 -118.12474 -10.774631 13.847899 0.5846359 24 0.20133396 0.20468352 0 0 8 16
		9000 305.43166 -1095.8633 -10.388279 9.7112935 0.51155641 21 0.19445239 0.19869334 0 0 7 14
		10000 244.08225 -179.31274 -12.974988 8.9732748 0.5846359 24 0.19098971 0.19586397 0 0 8 16
		11000 305.03389 -568.94714 -21.745425 14.244887 0.73079488 30 0.18517522 0.18978828 0 0 10 20
		12000 318.29735 767.76579 -37.184231 21.189508 1.0231128 42 0.17256426 0.17580267 0 0 14 28
		13000 411.21707 433.01125 -4.5149215 8.9889065 0.36539744 15 0.16329385 0.16767604 0 0 5 10
		14000 304.29535 148.28607 -2.3505844 6.6516754 0.36539744 15 0.17435868 0.17897674 0 0 5 10
		15000 338.00555 2384.1424 -21.438264 17.463859 0.80387436 33 0.17237066 0.17634112 0 0 11 22
		16000 613.56062 610.93867 -0.057364228 1.2192718 0.073079488 3 0.17128158 0.1758886 0 0 1 2
		17000 432.63323 -980.52384 -15.79844 18.054365 0.65771539 27 0.17145651 0.17504846 0 0 9 18
		18000 181.74572 -352.81765 -1.8617959 2.1669979 0.21923846 9 0.17292463 0.17654774 0 0 3 6
		19000 208.55292 -248.38735 -4.2287767 4.5588154 0.36539744 15 0.18168324 0.18454331 0 0 5 10
		20000 304.73317 -649.9896 -16.532405 12.716924 0.65771539 27 0.18085983 0.18345574 0 0 9 18
		Loop time of 21.0434 on 1 procs for 20000 steps with 27 atoms

		Performance: 82.116 ns/day, 0.292 hours/ns, 950.415 timesteps/s
		98.5% CPU use with 1 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 1.8955 \| 1.8955 \| 1.8955 \| 0.0 \| 11.49
		Bond \| 0.026564 \| 0.026564 \| 0.026564 \| 0.0 \| 0.16
		Kspace \| 0.21215 \| 0.21215 \| 0.21215 \| 0.0 \| 1.29
		Neigh \| 0.088336 \| 0.088336 \| 0.088336 \| 0.0 \| 0.54
		Comm \| 0.19828 \| 0.19828 \| 0.19828 \| 0.0 \| 1.20
		Output \| 0.001025 \| 0.001025 \| 0.001025 \| 0.0 \| 0.01
		Modify \| 14.024 \| 14.024 \| 14.024 \| 0.0 \| 85.02
		Other \| \| 0.0491 \| \| \| 0.30

		Nlocal: 30 ave 30 max 30 min
		Pair \| 2.2373 \| 2.2373 \| 2.2373 \| 0.0 \| 10.63
		Bond \| 0.022895 \| 0.022895 \| 0.022895 \| 0.0 \| 0.11
		Kspace \| 0.16756 \| 0.16756 \| 0.16756 \| 0.0 \| 0.80
		Neigh \| 0.11436 \| 0.11436 \| 0.11436 \| 0.0 \| 0.54
		Comm \| 0.26988 \| 0.26988 \| 0.26988 \| 0.0 \| 1.28
		Output \| 0.0014684 \| 0.0014684 \| 0.0014684 \| 0.0 \| 0.01
		Modify \| 18.193 \| 18.193 \| 18.193 \| 0.0 \| 86.45
		Other \| \| 0.03692 \| \| \| 0.18

		Nlocal: 27 ave 27 max 27 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 2094 ave 2094 max 2094 min
		Nghost: 2081 ave 2081 max 2081 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 7664 ave 7664 max 7664 min
		Neighs: 6264 ave 6264 max 6264 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 7664
		Ave neighs/atom = 255.467
		Total # of neighbors = 6264
		Ave neighs/atom = 232
		Ave special neighs/atom = 2
		Neighbor list builds = 20076
		Neighbor list builds = 20177
		Dangerous builds = 0

		Total wall time: 0:00:16
		Total wall time: 0:00:21

examples/gcmc/log.30Mar18.gcmc.h2o.g++.1→examples/gcmc/log.27Nov18.gcmc.h2o.g++.1

+86 −86

File changed and moved.

Preview size limit exceeded, changes collapsed.

examples/gcmc/log.30Mar18.gcmc.lj.g++.1→examples/gcmc/log.27Nov18.gcmc.lj.g++.1

+11 −11

Original line number	Diff line number	Diff line
		LAMMPS (30 Mar 2018)
		LAMMPS (27 Nov 2018)
		using 1 OpenMP thread(s) per MPI task
		# GCMC for LJ simple fluid, no dynamics
		# T = 2.0
		@@ -112,20 +112,20 @@ Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v
		8000 2.2135488 2.0878792 -3.0471089 3.2707661 0.536 67 0.067926473 0.067738312 0.1135594 0.52736 1.4348314 0.034380623 62.43
		9000 1.8904287 0.52639383 -3.3548657 2.7920177 0.52 65 0.06818197 0.068003094 0.11356319 0.53072 1.4528143 0.021683615 63.23
		10000 2.2353281 0.73275312 -3.2197702 3.3006016 0.512 64 0.068465059 0.068208485 0.11414748 0.52712 1.4143492 0.03497858 62.44
		Loop time of 21.2409 on 1 procs for 10000 steps with 64 atoms
		Loop time of 27.8547 on 1 procs for 10000 steps with 64 atoms

		Performance: 203381.368 tau/day, 470.790 timesteps/s
		99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
		Performance: 155090.656 tau/day, 359.006 timesteps/s
		99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 0.45931 \| 0.45931 \| 0.45931 \| 0.0 \| 2.16
		Neigh \| 1.1637 \| 1.1637 \| 1.1637 \| 0.0 \| 5.48
		Comm \| 0.17294 \| 0.17294 \| 0.17294 \| 0.0 \| 0.81
		Output \| 0.00027394 \| 0.00027394 \| 0.00027394 \| 0.0 \| 0.00
		Modify \| 19.416 \| 19.416 \| 19.416 \| 0.0 \| 91.41
		Other \| \| 0.02919 \| \| \| 0.14
		Pair \| 0.43892 \| 0.43892 \| 0.43892 \| 0.0 \| 1.58
		Neigh \| 1.278 \| 1.278 \| 1.278 \| 0.0 \| 4.59
		Comm \| 0.24105 \| 0.24105 \| 0.24105 \| 0.0 \| 0.87
		Output \| 0.00032067 \| 0.00032067 \| 0.00032067 \| 0.0 \| 0.00
		Modify \| 25.88 \| 25.88 \| 25.88 \| 0.0 \| 92.91
		Other \| \| 0.01693 \| \| \| 0.06

		Nlocal: 64 ave 64 max 64 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		@@ -138,4 +138,4 @@ Total # of neighbors = 2423
		Ave neighs/atom = 37.8594
		Neighbor list builds = 10000
		Dangerous builds = 0
		Total wall time: 0:00:21
		Total wall time: 0:00:27

examples/gcmc/log.30Mar18.gcmc.lj.g++.4→examples/gcmc/log.27Nov18.gcmc.lj.g++.4

+11 −11

Original line number	Diff line number	Diff line
		LAMMPS (30 Mar 2018)
		LAMMPS (27 Nov 2018)
		using 1 OpenMP thread(s) per MPI task
		# GCMC for LJ simple fluid, no dynamics
		# T = 2.0
		@@ -112,20 +112,20 @@ Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v
		8000 1.947817 0.74570466 -3.0935809 2.8753489 0.504 63 0.068034071 0.067855883 0.11217045 0.53304 1.4924302 0.012298733 63.45
		9000 1.8942389 1.3367401 -2.8925016 2.7962574 0.504 63 0.068117479 0.067943081 0.11236152 0.536 1.4091106 0.0011494886 63.73
		10000 2.2092799 0.95517153 -2.9117781 3.2586879 0.48 60 0.068264792 0.068016591 0.11310789 0.52272 1.4774174 0.051284873 62.04
		Loop time of 29.2417 on 4 procs for 10000 steps with 60 atoms
		Loop time of 26.0069 on 4 procs for 10000 steps with 60 atoms

		Performance: 147733.999 tau/day, 341.977 timesteps/s
		96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
		Performance: 166109.741 tau/day, 384.513 timesteps/s
		95.9% CPU use with 4 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 0.11648 \| 0.1221 \| 0.13001 \| 1.5 \| 0.42
		Neigh \| 0.34452 \| 0.35618 \| 0.36328 \| 1.2 \| 1.22
		Comm \| 0.63561 \| 0.65617 \| 0.67542 \| 1.8 \| 2.24
		Output \| 0.00056601 \| 0.00069755 \| 0.00074744 \| 0.0 \| 0.00
		Modify \| 28.069 \| 28.076 \| 28.082 \| 0.1 \| 96.01
		Other \| \| 0.03094 \| \| \| 0.11
		Pair \| 0.10309 \| 0.115 \| 0.1225 \| 2.2 \| 0.44
		Neigh \| 0.3907 \| 0.40447 \| 0.41957 \| 1.7 \| 1.56
		Comm \| 0.44236 \| 0.46678 \| 0.49472 \| 2.8 \| 1.79
		Output \| 0.0011411 \| 0.0062903 \| 0.0080109 \| 3.7 \| 0.02
		Modify \| 25 \| 25.002 \| 25.005 \| 0.0 \| 96.14
		Other \| \| 0.01231 \| \| \| 0.05

		Nlocal: 15 ave 16 max 14 min
		Histogram: 2 0 0 0 0 0 0 0 0 2
		@@ -138,4 +138,4 @@ Total # of neighbors = 2116
		Ave neighs/atom = 35.2667
		Neighbor list builds = 10000
		Dangerous builds = 0
		Total wall time: 0:00:29
		Total wall time: 0:00:26

examples/gcmc/log.30Mar18.gcmc.co2.g++.4

deleted100644 → 0

+0 −131

Original line number	Diff line number	Diff line
		LAMMPS (30 Mar 2018)
		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 max type 2
		2 bonds with max type 1
		1 angles with max type 1
		0 dihedrals with max type 0
		0 impropers with max type 0
		create_atoms 0 box mol co2mol 464563 units box
		Created 24 atoms
		Time spent = 0.00257635 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 co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
		fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
		fix myrigidnvt co2 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

		# dynamically update fix rigid/nvt/small temperature ndof
		fix_modify myrigidnvt dynamic/dof yes

		# gcmc

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

		# dynamically update default temperature ndof
		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 ...
		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:485)
		0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
		0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
		ERROR: fix gcmc does currently not support full_energy option with molecules on more than 1 MPI process. (../fix_gcmc.cpp:721)
		Last command: run 20000

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