Fix communication bug of ILP (76bac4ce) · Commits · 郑智淋 / lammps

examples/USER/misc/kolmogorov_crespi_full/Bi_gr_AB_stack_2L_noH.data

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File added.

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examples/USER/misc/kolmogorov_crespi_full/CH.KC

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		../../../../potentials/CH.KC
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examples/USER/misc/kolmogorov_crespi_full/CH_taper.KC

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		../../../../potentials/CH_taper.KC
		No newline at end of file

examples/USER/misc/kolmogorov_crespi_full/in.bilayer-graphene

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		@@ -5,21 +5,22 @@ atom_style full
		processors * * 1 # domain decomposition over x and y

		# System and atom definition
		# we use 2 atom types so that inter- and intra-layer
		# we use different molecule ids for each layer of hBN
		# so that inter- and intra-layer
		# interactions can be specified separately
		# read lammps data file
		read_data Bi_gr_AB_stack_2L_noH_300K.data

		read_data Bi_gr_AB_stack_2L_noH.data
		mass 1 12.0107 # carbon mass (g/mole) \| membrane
		mass 2 12.0107 # carbon mass (g/mole) \| adsorbate
		# Separate atom groups
		group membrane type 1
		group adsorbate type 2
		group layer1 molecule 1
		group layer2 molecule 2

		######################## Potential defition ########################
		pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
		pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1
		####################################################################
		pair_coeff * * rebo CH.rebo NULL C # chemical
		pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range
		pair_coeff * * rebo CH.rebo C C # chemical
		pair_coeff * * kolmogorov/crespi/full CH_taper.KC C C # long range
		####################################################################
		# Neighbor update settings
		neighbor 2.0 bin
		@@ -27,34 +28,25 @@ neigh_modify every 1
		neigh_modify delay 0
		neigh_modify check yes

		# calculate the COM
		variable adsxcom equal xcm(adsorbate,x)
		variable adsycom equal xcm(adsorbate,y)
		variable adszcom equal xcm(adsorbate,z)
		variable adsvxcom equal vcm(adsorbate,x)
		variable adsvycom equal vcm(adsorbate,y)
		variable adsvzcom equal vcm(adsorbate,z)

		#### Simulation settings ####
		timestep 0.001
		fix subf membrane setforce 0.0 0.0 0.0
		fix thermostat all nve
		velocity all create 300.0 12345

		compute 0 all pair rebo
		compute 1 all pair kolmogorov/crespi/full
		variable REBO equal c_0
		variable KC equal c_1
		variable REBO equal c_0 # REBO energy
		variable KC equal c_1 # total interlayer energy
		variable Evdw equal c_1[1] # attractive energy
		variable Erep equal c_1[2] # repulsive energy

		############################

		# Output
		thermo 100
		thermo_style custom step etotal pe ke v_REBO v_KC temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
		thermo_modify line one format float %.10f
		thermo_modify flush yes norm no lost warn #ignore

		#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
		#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
		thermo_style custom step cpu etotal pe ke v_REBO v_KC v_Erep v_Evdw temp
		thermo_modify line one format float %.16f
		thermo_modify flush yes norm no lost warn

		###### Run molecular dynamics ######
		fix thermostat all nve
		run 1000

examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.icc.1

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Original line number	Diff line number	Diff line
		LAMMPS (5 Jun 2019)
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
		using 1 OpenMP thread(s) per MPI task
		# Initialization
		units metal
		boundary p p p
		atom_style full
		processors * * 1 # domain decomposition over x and y

		# System and atom definition
		# we use different molecule ids for each layer of hBN
		# so that inter- and intra-layer
		# interactions can be specified separately

		read_data Bi_gr_AB_stack_2L_noH.data
		orthogonal box = (0 0 0) to (42.6 41.8117 100)
		1 by 1 by 1 MPI processor grid
		reading atoms ...
		1360 atoms
		0 = max # of 1-2 neighbors
		0 = max # of 1-3 neighbors
		0 = max # of 1-4 neighbors
		1 = max # of special neighbors
		special bonds CPU = 0.000143357 secs
		read_data CPU = 0.00128686 secs
		mass 1 12.0107 # carbon mass (g/mole) \| membrane
		mass 2 12.0107 # carbon mass (g/mole) \| adsorbate
		# Separate atom groups
		group layer1 molecule 1
		680 atoms in group layer1
		group layer2 molecule 2
		680 atoms in group layer2

		######################## Potential defition ########################
		pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1
		####################################################################
		pair_coeff * * rebo CH.rebo C C # chemical
		Reading potential file CH.rebo with DATE: 2018-7-3
		pair_coeff * * kolmogorov/crespi/full CH_taper.KC C C # long range
		####################################################################
		# Neighbor update settings
		neighbor 2.0 bin
		neigh_modify every 1
		neigh_modify delay 0
		neigh_modify check yes

		#### Simulation settings ####
		timestep 0.001
		velocity all create 300.0 12345

		compute 0 all pair rebo
		compute 1 all pair kolmogorov/crespi/full
		variable REBO equal c_0 # REBO energy
		variable KC equal c_1 # total interlayer energy
		variable Evdw equal c_1[1] # attractive energy
		variable Erep equal c_1[2] # repulsive energy

		############################

		# Output
		thermo 100
		thermo_style custom step cpu etotal pe ke v_REBO v_KC v_Erep v_Evdw temp
		thermo_modify line one format float %.16f
		thermo_modify flush yes norm no lost warn

		###### Run molecular dynamics ######
		fix thermostat all nve
		run 1000
		Neighbor list info ...
		update every 1 steps, delay 0 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 18
		ghost atom cutoff = 18
		binsize = 9, bins = 5 5 12
		2 neighbor lists, perpetual/occasional/extra = 2 0 0
		(1) pair rebo, perpetual
		attributes: full, newton on, ghost
		pair build: full/bin/ghost
		stencil: full/ghost/bin/3d
		bin: standard
		(2) pair kolmogorov/crespi/full, perpetual, copy from (1)
		attributes: full, newton on, ghost
		pair build: copy
		stencil: none
		bin: none
		Per MPI rank memory allocation (min/avg/max) = 17.21 \| 17.21 \| 17.21 Mbytes
		Step CPU TotEng PotEng KinEng v_REBO v_KC v_Erep v_Evdw Temp
		0 0.0000000000000000 -10037.7640583248121402 -10090.4634194413119985 52.6993611164999436 -10057.1894932863488066 -33.2739261549639664 35.9559834316876348 -69.2299095866357561 299.9999999999996589
		100 5.3877589240437374 -10037.5122858156355505 -10065.4637593850693520 27.9514735694345475 -10032.2132655062632693 -33.2504938788055995 25.2100699045900747 -58.4605637833913789 159.1184768311149185
		200 10.7755050340201706 -10037.4414086674350983 -10061.6271012692632212 24.1856926018286202 -10028.9093252939674130 -32.7177759752951403 18.5366534598604176 -51.2544294351563394 137.6811336385792970
		300 16.1665089030284435 -10037.4824653300311184 -10064.2845326005663082 26.8020672705344225 -10030.9195389405322203 -33.3649936600345924 26.3639208740001152 -59.7289145340284122 152.5752876469470891
		400 21.5454839280573651 -10037.5105626329259394 -10064.8769084956420556 27.3663458627154164 -10031.8478821022799821 -33.0290263933626349 36.6142885774199272 -69.6433149707719963 155.7875386888538571
		500 26.9370588400634006 -10037.5010433785082569 -10064.8363209936451312 27.3352776151367571 -10031.4417172103931080 -33.3946037832518243 26.2980262321670750 -59.6926300154142595 155.6106774503846850
		600 32.4204196080099791 -10037.4817772372425679 -10064.1925798287738871 26.7108025915316247 -10031.4376178099264507 -32.7549620188478201 18.5745873777024606 -51.3295493965519327 152.0557480714992380
		700 37.8001567909959704 -10037.4834430268438155 -10064.1291975032218033 26.6457544763788299 -10030.8722888097800023 -33.2569086934421492 25.2322818106646771 -58.4891905041015008 151.6854507067418467
		800 43.1622281169984490 -10037.5047888097760733 -10064.8671187128948077 27.3623299031188978 -10031.9815058608437539 -32.8856128520517217 36.5236695083771536 -69.4092823604148350 155.7646771616279011
		900 48.5261204120470211 -10037.5068323940176924 -10065.3998155271074211 27.8929831330889542 -10032.1734374829957233 -33.2263780441125931 27.7314849391008309 -60.9578629832065317 158.7855101588076820
		1000 53.8888844919856638 -10037.4811494880468672 -10064.0099109142265661 26.5287614261789670 -10031.3325267421259923 -32.6773841721003464 18.9005970229871600 -51.5779811950879434 151.0194480396057202
		Loop time of 53.8889 on 1 procs for 1000 steps with 1360 atoms

		Performance: 1.603 ns/day, 14.969 hours/ns, 18.557 timesteps/s
		100.0% CPU use with 1 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 53.836 \| 53.836 \| 53.836 \| 0.0 \| 99.90
		Bond \| 0.00043479 \| 0.00043479 \| 0.00043479 \| 0.0 \| 0.00
		Neigh \| 0 \| 0 \| 0 \| 0.0 \| 0.00
		Comm \| 0.032452 \| 0.032452 \| 0.032452 \| 0.0 \| 0.06
		Output \| 0.00058326 \| 0.00058326 \| 0.00058326 \| 0.0 \| 0.00
		Modify \| 0.0094135 \| 0.0094135 \| 0.0094135 \| 0.0 \| 0.02
		Other \| \| 0.009815 \| \| \| 0.02

		Nlocal: 1360 ave 1360 max 1360 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 7964 ave 7964 max 7964 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
		FullNghs: 1.037e+06 ave 1.037e+06 max 1.037e+06 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 1037000
		Ave neighs/atom = 762.5
		Ave special neighs/atom = 0
		Neighbor list builds = 0
		Dangerous builds = 0
		Total wall time: 0:00:54

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