Merge pull request #865 from athomps/fix_gcmc_temperature (7f9400ea) · Commits · 郑智淋 / lammps

examples/gcmc/in.gcmc.co2

+6 −1

Original line number	Diff line number	Diff line
		@@ -59,7 +59,9 @@ timestep 1.0
		# rigid constraints with thermostat

		fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
		fix_modify myrigidnvt dynamic/dof no

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

		# gcmc

		@@ -82,7 +84,10 @@ 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

examples/gcmc/in.gcmc.h2o

+10 −7

Original line number	Diff line number	Diff line
		@@ -30,8 +30,6 @@ create_box 2 box &
		extra/angle/per/atom 1 &
		extra/special/per/atom 2

		# we can load multiple molecule templates, but don't have to use them all
		molecule co2mol CO2.txt
		molecule h2omol H2O.txt
		create_atoms 0 box mol h2omol 464563 units box

		@@ -58,18 +56,24 @@ timestep 1.0

		minimize 0.0 0.0 100 1000
		reset_timestep 0

		# rigid constraints with thermostat

		fix mynvt all nvt temp ${temp} ${temp} 100
		fix wshake all shake 0.0001 50 0 b 1 a 1 mol h2omol
		# gcmc
		fix mynvt h2o nvt temp ${temp} ${temp} 100
		fix wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol

		# important to make temperature dofs dynamic

		compute_modify thermo_temp dynamic/dof yes
		compute_modify mynvt_temp dynamic/dof yes

		run 1000
		reset_timestep 0

		# 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 &
		fix mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
		h2omol tfac_insert ${tfac} group h2o shake wshake

		# atom counts
		@@ -87,7 +91,6 @@ 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_nO v_nH
		thermo 1000

examples/gcmc/log.23Oct17.gcmc.co2.g++.1→examples/gcmc/log.30Mar18.gcmc.co2.g++.1

+63 −59

Original line number	Diff line number	Diff line
		LAMMPS (23 Oct 2017)
		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
		@@ -39,14 +39,14 @@ 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
		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 = 0.00196958 secs
		Time spent = 0.00241756 secs

		# rigid CO2 TraPPE model

		@@ -72,29 +72,31 @@ 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
		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
		fix_modify myrigidnvt dynamic/dof no

		# 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 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
		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 all var carbon
		group carbon dynamic co2 var carbon
		dynamic group carbon defined
		group oxygen dynamic all var oxygen
		group oxygen dynamic co2 var oxygen
		dynamic group oxygen defined
		variable nC equal count(carbon)
		variable nO equal count(oxygen)
		@@ -105,7 +107,10 @@ 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

		@@ -113,13 +118,13 @@ thermo 1000

		run 20000
		Ewald initialization ...
		WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
		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)
		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
		WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
		@@ -138,55 +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
		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
		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

		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
		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
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 2310 ave 2310 max 2310 min
		Nghost: 2094 ave 2094 max 2094 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 7736 ave 7736 max 7736 min
		Neighs: 7664 ave 7664 max 7664 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 7736
		Ave neighs/atom = 257.867
		Total # of neighbors = 7664
		Ave neighs/atom = 255.467
		Ave special neighs/atom = 2
		Neighbor list builds = 20349
		Neighbor list builds = 20076
		Dangerous builds = 0

		Total wall time: 0:00:20
		Total wall time: 0:00:16

examples/gcmc/log.23Oct17.gcmc.co2.g++.4→examples/gcmc/log.30Mar18.gcmc.co2.g++.4

+131 −0

File changed and moved.

Preview size limit exceeded, changes collapsed.

examples/gcmc/log.23Oct17.gcmc.h2o.g++.1→examples/gcmc/log.30Mar18.gcmc.h2o.g++.1

+88 −91

File changed and moved.

Preview size limit exceeded, changes collapsed.

Admin message