Merge pull request #568 from akohlmey/fix_gcmc_parallel_workaround (e58bcd8b) · Commits · 郑智淋 / lammps

doc/src/fix_gcmc.txt

+3 −0

Original line number	Diff line number	Diff line
		@@ -383,6 +383,9 @@ called. Reneighboring is required.
		Can be run in parallel, but aspects of the GCMC part will not scale
		well in parallel. Only usable for 3D simulations.

		When using fix gcmc in combination with fix shake or fix rigid,
		only gcmc exchange moves are supported.

		Note that very lengthy simulations involving insertions/deletions of
		billions of gas molecules may run out of atom or molecule IDs and
		trigger an error, so it is better to run multiple shorter-duration

examples/gcmc/H2O.txt

0 → 100644

+62 −0

Original line number	Diff line number	Diff line
		# CO2 molecule file. TraPPE model.

		3 atoms
		2 bonds
		1 angles

		Coords

		1 1.12456 0.09298 1.27452
		2 1.53683 0.75606 1.89928
		3 0.49482 0.56390 0.65678

		Types

		1 1
		2 2
		3 2

		Charges

		1 -0.8472
		2 0.4236
		3 0.4236

		Bonds

		1 1 1 2
		2 1 1 3

		Angles

		1 1 2 1 3

		Shake Flags

		1 1
		2 1
		3 1

		Shake Atoms

		1 1 2 3
		2 1 2 3
		3 1 2 3

		Shake Bond Types

		1 1 1 1
		2 1 1 1
		3 1 1 1

		Special Bond Counts

		1 2 0 0
		2 1 1 0
		3 1 1 0

		Special Bonds

		1 2 3
		2 1 3
		3 1 2

examples/gcmc/in.gcmc.co2

+1 −1

Original line number	Diff line number	Diff line
		@@ -64,7 +64,7 @@ fix_modify myrigidnvt dynamic/dof no
		# gcmc

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

		# output

examples/gcmc/in.gcmc.h2o

0 → 100644

+88 −0

Original line number	Diff line number	Diff line
		# fix gcmc example with fix shake

		# 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}
		region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} 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

		# 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

		# rigid SPC/E water model

		pair_coeff 1 1 0.15535 3.166
		pair_coeff * 2 0.0000 0.0000

		bond_coeff 1 1000 1.0
		angle_coeff 1 100 109.47

		# masses

		mass 1 15.9994
		mass 2 1.0

		# MD settings

		group h2o type 1 2
		neighbor 2.0 bin
		neigh_modify every 1 delay 1 check yes
		velocity all create ${temp} 54654
		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



		run 1000

		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 &
		h2omol tfac_insert ${tfac} group h2o shake wshake

		# 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
		thermo 1000

		# run

		run 20000

examples/gcmc/log.24Mar17.gcmc.co2.g++.1→examples/gcmc/log.6Jul17.gcmc.co2.g++.1

+51 −48

Original line number	Diff line number	Diff line
		LAMMPS (17 Mar 2017)
		LAMMPS (6 Jul 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
		@@ -80,11 +81,11 @@ fix_modify myrigidnvt dynamic/dof no
		# gcmc

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

		# output

		@@ -106,7 +107,7 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
		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:439)
		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)
		@@ -122,56 +123,58 @@ Neighbor list info ...
		pair build: half/bin/newton
		stencil: half/bin/3d/newton
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 15.61 \| 15.61 \| 15.61 Mbytes
		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
		0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0
		1000 311.39835 -327.93481 -8.6795381 9.9010062 0.51155641 21 0.13302848 0.12331626 0.6894397 0.90997852
		WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
		2000 905.66812 319.43347 -0.50350961 6.2991241 0.14615898 6 0.20952183 0.20430213 0.71797992 0.92626683
		3000 275.57393 -719.89718 -26.534978 14.238181 0.80387436 33 0.21291069 0.20460696 0.72899202 0.9133259
		4000 254.70771 -245.01902 -20.981537 13.160079 0.80387436 33 0.17245726 0.16974613 0.70145764 0.90542759
		5000 96.073601 -517.98124 -34.019065 5.441166 0.87695385 36 0.14174575 0.13607057 0.6776754 0.90155771
		6000 397.57265 148.92645 -7.2012893 10.665797 0.43847693 18 0.12299956 0.1202471 0.66165464 0.90274793
		7000 455.4271 -347.44181 -5.9244703 12.217875 0.43847693 18 0.15182038 0.14791307 0.67904236 0.90560829
		8000 301.03124 -627.45324 -13.251012 11.066909 0.5846359 24 0.16687346 0.16315516 0.6936719 0.91129375
		9000 256.5747 -565.67983 -17.814128 11.981874 0.73079488 30 0.15458482 0.15131825 0.68966283 0.90993975
		10000 443.60076 89.586912 -6.077863 11.900606 0.43847693 18 0.16092552 0.16020353 0.69882461 0.91422145
		11000 436.43777 64.412921 -6.7128469 11.708443 0.43847693 18 0.17453966 0.17480683 0.70679243 0.91369445
		12000 594.42207 849.07743 -3.3708621 10.040536 0.29231795 12 0.17461606 0.17568622 0.71175869 0.91333367
		13000 426.85849 -1093.1334 -17.524618 17.813377 0.65771539 27 0.17742896 0.17792831 0.71363306 0.91450124
		14000 317.75995 336.31107 -10.46774 11.681912 0.5846359 24 0.18331181 0.18427921 0.71715557 0.91652256
		15000 272.65129 317.50536 -26.428336 14.087176 0.80387436 33 0.17449167 0.175957 0.71122398 0.91528038
		16000 344.28567 -577.91079 -18.177927 16.077919 0.73079488 30 0.1661682 0.16781514 0.70485136 0.91508882
		17000 134.55928 -193.5668 -30.297136 7.6208177 0.87695385 36 0.15965609 0.1605036 0.69658104 0.9140445
		18000 231.87302 -446.07671 -14.875027 9.6763722 0.65771539 27 0.15270985 0.15351831 0.69002918 0.91372795
		19000 328.6835 -280.22365 -20.001303 16.982214 0.80387436 33 0.15201017 0.15272181 0.69023195 0.91272534
		20000 0 -20.39554 -0.14872889 -0 0 0 0.15600204 0.15750795 0.69503275 0.9138765
		Loop time of 30.9008 on 1 procs for 20000 steps with 0 atoms

		Performance: 55.921 ns/day, 0.429 hours/ns, 647.233 timesteps/s
		99.8% CPU use with 1 MPI tasks x no OpenMP threads
		1000 420.43475 1722.4052 -9.6956123 15.456579 0.5846359 24 0.20879341 0.20713005 0 0
		2000 302.29516 -547.83641 -22.017674 14.11699 0.73079488 30 0.1742478 0.1678018 0 0
		3000 316.6934 -1080.2672 -8.2218891 10.069364 0.51155641 21 0.13544917 0.13720634 0 0
		4000 246.81618 -679.83642 -14.577244 10.29997 0.65771539 27 0.1568939 0.15860229 0 0
		5000 260.22849 -896.29914 -16.097593 10.859684 0.65771539 27 0.13138744 0.13547049 0 0
		6000 291.70796 -1521.99 -22.303136 13.622574 0.73079488 30 0.12615476 0.12717694 0 0
		7000 236.02638 -599.92186 -27.580831 13.367447 0.87695385 36 0.119703 0.12145398 0 0
		8000 321.45341 688.10577 -10.09204 11.817696 0.5846359 24 0.10917411 0.11032646 0 0
		9000 502.85382 -302.31056 -0.22330142 0.99927447 0.073079488 3 0.1254105 0.12905828 0 0
		10000 249.98239 -510.0091 -32.815145 15.399767 0.95003334 39 0.1274504 0.12875623 0 0
		11000 247.59424 -1129.0274 -25.320205 12.792544 0.80387436 33 0.11739076 0.11916784 0 0
		12000 0 -20.39554 -0.14872889 -0 0 0 0.1254933 0.12920375 0 0
		13000 1272.2738 -474.79484 -0.29450485 8.8489483 0.14615898 6 0.13767133 0.14112496 0 0
		14000 516.54246 -36.296516 -5.0012009 11.291243 0.36539744 15 0.15632744 0.15955377 0 0
		15000 307.09233 1951.9301 -14.820362 12.815375 0.65771539 27 0.15393544 0.15716192 0 0
		16000 198.31989 -559.48443 -30.459487 11.231925 0.87695385 36 0.1482565 0.15025652 0 0
		17000 246.99311 657.85683 -18.579206 11.53442 0.73079488 30 0.14143958 0.14375423 0 0
		18000 467.13468 167.03738 -1.0945268 5.569759 0.21923846 9 0.13847359 0.14098533 0 0
		19000 359.54027 -1413.5407 -12.156233 13.217895 0.5846359 24 0.15169146 0.15294205 0 0
		20000 227.79597 -1204.5652 -23.24144 10.637925 0.73079488 30 0.14917199 0.15022946 0 0
		Loop time of 20.153 on 1 procs for 20000 steps with 30 atoms

		Performance: 85.744 ns/day, 0.280 hours/ns, 992.408 timesteps/s
		99.3% CPU use with 1 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 2.1985 \| 2.1985 \| 2.1985 \| 0.0 \| 7.11
		Bond \| 0.029596 \| 0.029596 \| 0.029596 \| 0.0 \| 0.10
		Kspace \| 0.23123 \| 0.23123 \| 0.23123 \| 0.0 \| 0.75
		Neigh \| 0.16141 \| 0.16141 \| 0.16141 \| 0.0 \| 0.52
		Comm \| 0.20628 \| 0.20628 \| 0.20628 \| 0.0 \| 0.67
		Output \| 0.00068831 \| 0.00068831 \| 0.00068831 \| 0.0 \| 0.00
		Modify \| 28.022 \| 28.022 \| 28.022 \| 0.0 \| 90.69
		Other \| \| 0.05058 \| \| \| 0.16

		Nlocal: 0 ave 0 max 0 min
		Pair \| 2.5352 \| 2.5352 \| 2.5352 \| 0.0 \| 12.58
		Bond \| 0.026112 \| 0.026112 \| 0.026112 \| 0.0 \| 0.13
		Kspace \| 0.25 \| 0.25 \| 0.25 \| 0.0 \| 1.24
		Neigh \| 0.10364 \| 0.10364 \| 0.10364 \| 0.0 \| 0.51
		Comm \| 0.22907 \| 0.22907 \| 0.22907 \| 0.0 \| 1.14
		Output \| 0.0013065 \| 0.0013065 \| 0.0013065 \| 0.0 \| 0.01
		Modify \| 16.957 \| 16.957 \| 16.957 \| 0.0 \| 84.14
		Other \| \| 0.05061 \| \| \| 0.25

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

		Total # of neighbors = 0
		Neighbor list builds = 40367
		Dangerous builds = 118
		Total # of neighbors = 7736
		Ave neighs/atom = 257.867
		Ave special neighs/atom = 2
		Neighbor list builds = 20349
		Dangerous builds = 0

		Total wall time: 0:00:30
		Total wall time: 0:00:20

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