forked from lijiext/lammps
Add more examples
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@ -58,6 +58,13 @@ NOTE: The parameters presented in the parameter file (e.g. BNCH.ILP), are
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fitted with tapper function by setting the cutoff equal to 16.0 Angstrom.
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Using different cutoff or tapper function should be careful.
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NOTE: Two parameter files (BNCH.ILP and BNCH-old.ILP) are presented, BNCH-old.ILP
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contains the paramters published in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi, which
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is only suitable for long-range interaction. The paramters in BNCH.ILP provides
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a good description both for short- and long-range interaction. This is useful for
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simulations in the high pressure (small interlayer distances) regime. The comparison of
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two sets of paramters can be found in "(Ouyang)"_#Ouyang.
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This potential must be used in combination with hybrid/overlay.
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Other interactions can be set to zero using pair_style {none}.
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@ -104,3 +111,6 @@ coefficients listed in the appropriate units, if your simulation doesn’t use
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:link(Kolmogorov)
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[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
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:link(Ouyang)
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[(Ouyang)] W. Ouyang, D. Mandelli, O. Hod, M. Urbakh, In preparation.
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File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,61 @@
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# Initialization
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units metal
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boundary p p p
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atom_style full
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processors * * 1 # domain decomposition over x and y
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# System and atom definition
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# we use 2 atom types so that inter- and intra-layer
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# interactions can be specified separately
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# read lammps data file
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read_data Bi_gr_AB_stack_2L_noH_300K.data
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mass 1 12.0107 # carbon mass (g/mole) | membrane
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mass 2 12.0107 # carbon mass (g/mole) | adsorbate
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# Separate atom groups
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group membrane type 1
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group adsorbate type 2
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######################## Potential defition ########################
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pair_style hybrid/overlay rebo ILP/graphene/hBN 16.0
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####################################################################
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pair_coeff * * rebo CH.airebo NULL C # chemical
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pair_coeff * * ILP/graphene/hBN BNCH-old.ILP C C # long range
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####################################################################
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# Neighbor update settings
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neighbor 2.0 bin
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neigh_modify every 1
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neigh_modify delay 0
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neigh_modify check yes
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# calculate the COM
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variable adsxcom equal xcm(adsorbate,x)
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variable adsycom equal xcm(adsorbate,y)
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variable adszcom equal xcm(adsorbate,z)
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variable adsvxcom equal vcm(adsorbate,x)
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variable adsvycom equal vcm(adsorbate,y)
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variable adsvzcom equal vcm(adsorbate,z)
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#### Simulation settings ####
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timestep 0.001
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#velocity adsorbate create 300.0 12345
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fix subf membrane setforce 0.0 0.0 0.0
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fix thermostat all nve
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compute 0 all pair rebo
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compute 1 all pair ILP/graphene/hBN
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variable REBO equal c_0
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variable ILP equal c_1
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############################
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# Output
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thermo 100
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thermo_style custom step cpu etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
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thermo_modify line one format float %.16f
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thermo_modify flush yes norm no lost warn
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dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
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dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
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###### Run molecular dynamics ######
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run 10000
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@ -0,0 +1,228 @@
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LAMMPS (5 Feb 2018)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
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using 1 OpenMP thread(s) per MPI task
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# Initialization
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units metal
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boundary p p p
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atom_style full
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processors * * 1 # domain decomposition over x and y
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# System and atom definition
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# we use 2 atom types so that inter- and intra-layer
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# interactions can be specified separately
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# read lammps data file
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read_data Bi_gr_AB_stack_2L_noH_300K.data
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orthogonal box = (0 0 0) to (42.6 41.8117 100)
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2 by 2 by 1 MPI processor grid
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reading atoms ...
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1360 atoms
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reading velocities ...
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1360 velocities
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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mass 1 12.0107 # carbon mass (g/mole) | membrane
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mass 2 12.0107 # carbon mass (g/mole) | adsorbate
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# Separate atom groups
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group membrane type 1
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680 atoms in group membrane
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group adsorbate type 2
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680 atoms in group adsorbate
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######################## Potential defition ########################
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pair_style hybrid/overlay rebo ILP/graphene/hBN 16.0
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####################################################################
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pair_coeff * * rebo CH.airebo NULL C # chemical
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Reading potential file CH.airebo with DATE: 2011-10-25
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pair_coeff * * ILP/graphene/hBN BNCH-old.ILP C C # long range
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####################################################################
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# Neighbor update settings
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neighbor 2.0 bin
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neigh_modify every 1
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neigh_modify delay 0
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neigh_modify check yes
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# calculate the COM
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variable adsxcom equal xcm(adsorbate,x)
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variable adsycom equal xcm(adsorbate,y)
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variable adszcom equal xcm(adsorbate,z)
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variable adsvxcom equal vcm(adsorbate,x)
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variable adsvycom equal vcm(adsorbate,y)
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variable adsvzcom equal vcm(adsorbate,z)
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#### Simulation settings ####
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timestep 0.001
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#velocity adsorbate create 300.0 12345
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fix subf membrane setforce 0.0 0.0 0.0
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fix thermostat all nve
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compute 0 all pair rebo
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compute 1 all pair ILP/graphene/hBN
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variable REBO equal c_0
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variable ILP equal c_1
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############################
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# Output
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thermo 100
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thermo_style custom step cpu etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
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thermo_modify line one format float %.16f
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thermo_modify flush yes norm no lost warn
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dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
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dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
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###### Run molecular dynamics ######
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run 10000
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 18
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ghost atom cutoff = 18
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binsize = 9, bins = 5 5 12
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair rebo, perpetual, skip from (2)
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attributes: full, newton on, ghost
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pair build: skip/ghost
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stencil: none
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bin: none
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(2) pair ILP/graphene/hBN, perpetual
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attributes: full, newton on, ghost
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pair build: full/bin/ghost
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stencil: full/ghost/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 12.39 | 12.39 | 12.39 Mbytes
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Step CPU TotEng PotEng KinEng v_REBO v_ILP Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
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0 0.0000000000000000 -5029.3801131277232344 -5044.0700799791011377 14.6899668513774859 -5011.2636297758563160 -32.8064502032452268 83.6251135126841376 22.0155657205247799 20.2812150219063234 3.4623630944674200 0.0282287194990573 0.0535565744690331 0.2193320108238477
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100 1.2623029460082762 -5029.3895815657115236 -5045.3201249689691394 15.9305434032573761 -5012.4897058028163883 -32.8304191661527582 90.6873047362403781 22.0181751544732087 20.2867946176261533 3.4502536830854829 0.0239131348561319 0.0576557373214319 -0.4387830564309839
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200 2.5089902369654737 -5029.3874064118581373 -5045.8119502227937119 16.4245438109355142 -5012.7276250747399899 -33.0843251480532530 93.4994853616529298 22.0202931358059395 20.2926890775462887 3.3883512918454923 0.0180268638923536 0.0596894423424165 -0.6964675465005062
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300 3.7808456399943680 -5029.3851410393026526 -5044.9928147366936173 15.6076736973907035 -5012.1131531405408168 -32.8796615961530279 88.8493144891503590 22.0216852688933749 20.2985091182852351 3.3368274018412345 0.0093519892779965 0.0546775051020221 -0.2110676539008828
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400 5.0828477439936250 -5029.3900102081943260 -5045.6706717598035539 16.2806615516088193 -5012.7330095297320440 -32.9376622300724975 92.6804113371579206 22.0220931528717330 20.3035219615837050 3.3560233852136392 -0.0015365116268860 0.0454268926971423 0.5478139708774018
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500 6.3374099530046806 -5029.3985510532884291 -5046.0433160610555205 16.6447650077673792 -5013.0924334585288307 -32.9508826025281962 94.7531316611500074 22.0214795943650969 20.3074656871053847 3.4232399721971314 -0.0107212023950575 0.0332249365749148 0.6595923534430731
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600 7.5914500529761426 -5029.3929936745525993 -5045.4367231194828491 16.0437294449299230 -5012.7046931021195633 -32.7320300173640391 91.3316353653480064 22.0200027175784747 20.3101652564580348 3.4651727437862387 -0.0178110391142554 0.0210056001697192 0.1144372537107130
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700 8.8539019739837386 -5029.3934435811052026 -5045.6074608403341699 16.2140172592290135 -5012.7886962164220677 -32.8187646239108304 92.3010274643678201 22.0178838793005234 20.3116257076998501 3.4432436715031316 -0.0242636236518299 0.0078323423535019 -0.5162836954824445
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800 10.1049926480045542 -5029.3892931255340955 -5046.2270462379728997 16.8377531124386870 -5013.2383770824435487 -32.9886691555297418 95.8517489911287015 22.0151485190623291 20.3116305041057075 3.3780520461370140 -0.0302821177574879 -0.0083184718697242 -0.6710801514935791
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900 11.3630027609760873 -5029.3930414671476683 -5046.0272003817681252 16.6341589146203184 -5013.2317798383628542 -32.7954205434054487 94.6927546873744745 22.0119224939835121 20.3099187654038786 3.3350551183455268 -0.0341747588450106 -0.0256858065985706 -0.0799872839190919
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1000 12.6231660830089822 -5029.3908907830582393 -5045.6437703691590286 16.2528795861005300 -5012.6800867884940089 -32.9636835806647710 92.5222578135494871 22.0084902521404544 20.3065746721438387 3.3658243730415687 -0.0336536244697077 -0.0406018547138186 0.6191660973820151
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1100 13.8672335039591417 -5029.3936273537710804 -5045.9027321589628627 16.5091048051920097 -5012.9359164310717460 -32.9668157278903138 93.9808630812208889 22.0052717045119905 20.3019474054695905 3.4333328890827421 -0.0306983142305894 -0.0504731478622083 0.5931965879862887
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1200 15.1198259049560875 -5029.3940797064951767 -5045.6377384352035733 16.2436587287087058 -5012.8554686686165951 -32.7822697665871203 92.4697665279069270 22.0023306815922979 20.2966557735895385 3.4659529127677287 -0.0274706885173217 -0.0547501807332978 0.0091573603413281
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1300 16.3654009730089456 -5029.3984566732624444 -5045.6895616381252694 16.2911049648628570 -5012.7356994597503217 -32.9538621783744219 92.7398622282092333 21.9998860754741905 20.2910565803948018 3.4345399235545337 -0.0213260369994740 -0.0568287466574244 -0.5888067543760942
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1400 17.6155319709796458 -5029.3815168178471140 -5045.2912598742987029 15.9097430564518749 -5012.3239955600220128 -32.9672643142766546 90.5688952544279573 21.9981598497936552 20.2854554509222993 3.3672595338608167 -0.0132303590611009 -0.0543234153355907 -0.6236559250459623
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1500 18.8714692159555852 -5029.3921017874845347 -5045.6708613750924997 16.2787595876079862 -5012.8369791315399198 -32.8338822435533757 92.6695840863495306 21.9974041415691559 20.2802681532087163 3.3352413807666181 -0.0014089849714996 -0.0481849064168331 0.0587582898344604
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1600 20.1541873109526932 -5029.3874846931976208 -5045.7731643864972284 16.3856796932995650 -5012.8388777565696728 -32.9342866299264614 93.2782448182427402 21.9977706803512874 20.2759915865795222 3.3762928385876232 0.0085254010295789 -0.0376205539327122 0.6681442617907806
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1700 21.4234082509647124 -5029.3869010344951676 -5045.3169437830329116 15.9300427485373124 -5012.4635360220827351 -32.8534077609500770 90.6844546748195768 21.9990330035990027 20.2727720473957298 3.4424374239173727 0.0168149635384655 -0.0269413439785030 0.5265928985608515
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1800 22.6835704990080558 -5029.3860480733746954 -5045.4015510274330154 16.0155029540583165 -5012.6540263485476316 -32.7475246788853056 91.1709513061473160 22.0010236218414903 20.2706889597509488 3.4653364051690918 0.0229089788849714 -0.0142749791424698 -0.1062662269544749
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1900 23.9297129529877566 -5029.3992153438584864 -5046.0849535192628537 16.6857381754043104 -5013.1667872952384641 -32.9181662240248301 94.9863783273459319 22.0036010850046679 20.2699115012928246 3.4242520686326885 0.0283626891504371 -0.0012584790958115 -0.6446526361083699
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2000 25.1922093119937927 -5029.3947678008062212 -5046.0655253357617767 16.6707575349551895 -5013.1017054839030607 -32.9638198518594550 94.9010985053609772 22.0065845205626758 20.2704964280075011 3.3582948439944240 0.0313750540289036 0.0137999047920244 -0.5449451253646518
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2100 26.4518803840037435 -5029.3820643301123710 -5045.4331743009661295 16.0511099708533358 -5012.5538273606616713 -32.8793469403044938 91.3736502537662716 22.0097398064544976 20.2727372928018958 3.3379848824292826 0.0322718100086602 0.0304537099550799 0.1867563300323286
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2200 27.7058059349656105 -5029.3843727776211381 -5045.0848436909873271 15.7004709133658302 -5012.0668628677258312 -33.0179808232617233 89.3775782897492945 22.0127920131602473 20.2765354452670756 3.3881998421430568 0.0292294495100443 0.0449660178787396 0.7042838989885432
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2300 28.9594137629610486 -5029.3902199294761886 -5045.3993732492435811 16.0091533197674920 -5012.5253283328802354 -32.8740449163632320 91.1348049421897599 22.0155716600061417 20.2815245415556973 3.4510500976839618 0.0259484063993953 0.0538549628124416 0.4400016714913355
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2400 30.2447868830058724 -5029.3940355103695765 -5045.9434469962816365 16.5494114859119250 -5013.1710648528805905 -32.7723821434015932 94.2103156582501100 22.0179797175199319 20.2871333501902136 3.4632861236609225 0.0218917592723929 0.0581043349886307 -0.2124896915144417
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2500 31.5081150379846804 -5029.3842094590991110 -5045.4423687097469156 16.0581592506475950 -5012.4554219817418925 -32.9869467280046536 91.4137794677353384 22.0198491689972187 20.2929823072195745 3.4144243213892453 0.0156275666670157 0.0584945195169434 -0.6844296511643093
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2600 32.7705356059595942 -5029.3960582840263669 -5045.6469174766025390 16.2508591925761650 -5012.8198838898442773 -32.8270335867577927 92.5107563827072994 22.0210406125338700 20.2986562400797226 3.3502383230453026 0.0082866848267277 0.0535700449402662 -0.4533139815189942
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2700 34.0687214930076152 -5029.4005011063927668 -5046.1812481784818374 16.7807470720886371 -5013.3384539147527903 -32.8427942637283650 95.5272324933440444 22.0214074387511722 20.3035983394416988 3.3422072391285718 -0.0010968873414058 0.0448881856269352 0.3053226005544524
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2800 35.3371960269869305 -5029.3918450884730191 -5045.4663013118542949 16.0744562233815529 -5012.5518420452062855 -32.9144592666481230 91.5065527332286166 22.0208057886537567 20.3075286333744920 3.3990332666058265 -0.0107042888216099 0.0331308854628973 0.7104765178449446
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2900 36.5826528539764695 -5029.4007271172231412 -5046.3887404126471665 16.9880132954239791 -5013.5657268280101562 -32.8230135846359303 96.7071304215778440 22.0193692100171923 20.3101603808999265 3.4577797292506842 -0.0181908513743875 0.0197672476938271 0.3528489229883396
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3000 37.8225702039781027 -5029.3940496855184392 -5045.4382560043904959 16.0442063188722450 -5012.6853249922505711 -32.7529310121395909 91.3343500506812944 22.0171604936519856 20.3114668671039951 3.4591467250701471 -0.0250556884411515 0.0058380040945131 -0.3232243449560073
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3100 39.1152549439575523 -5029.3932299425177916 -5045.7076145083992742 16.3143845658812481 -5012.7273205114888697 -32.9802939969102908 92.8723852827122727 22.0144106189674247 20.3113170196305575 3.4036898869224110 -0.0295489605326196 -0.0093545138913292 -0.6945887338714194
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3200 40.3652645039837807 -5029.3999346652944951 -5046.2743567265588354 16.8744220612639957 -5013.3523379216176181 -32.9220188049421125 96.0604931659067063 22.0112657104147473 20.3096089828088715 3.3446022440995744 -0.0331585594875426 -0.0245083162220922 -0.3611700155337798
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3300 41.7497809809865430 -5029.3912545533439697 -5045.6188249698325308 16.2275704164882058 -5012.7210368537616887 -32.8977881160708634 92.3781810975735169 22.0079411449246116 20.3062958566965044 3.3478683972107479 -0.0330599183649122 -0.0412983807445889 0.4228102245782292
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3400 43.0772461489541456 -5029.3913786027551396 -5045.6933303802852606 16.3019517775300287 -5012.6836451483668498 -33.0096852319176293 92.8016095384462147 22.0046876041177768 20.3016343021786838 3.4103619804324348 -0.0302848635086505 -0.0508933045183329 0.6902755158347326
|
||||
3500 44.3340892840060405 -5029.3864373789210731 -5044.9075681866406740 15.5211308077191479 -5012.1156930534052663 -32.7918751332351519 88.3566544957194822 22.0018906600734354 20.2961922297910284 3.4617631548194869 -0.0260020821660879 -0.0574179239791507 0.2536077963142296
|
||||
3600 45.5714052729890682 -5029.3956106765108416 -5045.8281093106388653 16.4324986341276862 -5013.0062724883737246 -32.8218368222655954 93.5447695341190126 21.9995902792937201 20.2903196955397753 3.4528875370982139 -0.0198574899622142 -0.0590999812510351 -0.4161058838372516
|
||||
3700 46.8187310720095411 -5029.3999849462825296 -5045.8608125716009454 16.4608276253185934 -5012.9301564107845479 -32.9306561608159001 93.7060370936722506 21.9980000204408341 20.2845522706275894 3.3917483074441592 -0.0115465621905488 -0.0553944579545257 -0.6931324325703953
|
||||
3800 48.0849941459600814 -5029.3934499086271899 -5045.0668678198253474 15.6734179111983085 -5012.2357009255956655 -32.8311668942298382 89.2235745128853779 21.9973189064792436 20.2792712394156425 3.3397277035718815 -0.0020664024879512 -0.0492333401974764 -0.2331021270184729
|
||||
3900 49.3429405399947427 -5029.3995770528044886 -5046.0950053993201436 16.6954283465152358 -5013.2247015792199818 -32.8703038200997284 95.0415412604762082 21.9976186964129639 20.2749399452365466 3.3551882655200593 0.0084267344129547 -0.0373784583523626 0.5086238489046713
|
||||
4000 50.5998689539846964 -5029.3888468870900397 -5045.4588592431082361 16.0700123560180224 -5012.5056530215588282 -32.9532062215491379 91.4812552688796359 21.9989183465402434 20.2718151808636300 3.4207597363868252 0.0165850539989395 -0.0251757999596484 0.6640462831884847
|
||||
4100 51.8629528660094365 -5029.3910837396306306 -5045.2793764258776719 15.8882926862469578 -5012.4770743669359945 -32.8023020589422742 90.4467854047990585 22.0009590702850808 20.2699385934667973 3.4644847478947058 0.0233393143572127 -0.0117891349194484 0.1342112403658827
|
||||
4200 53.1236869489657693 -5029.3984010758495060 -5046.2448879520343326 16.8464868761852031 -5013.3818327446442709 -32.8630552073907438 95.9014674140553467 22.0035487123982918 20.2693875306188644 3.4447945125877593 0.0282346202644504 0.0006576204547461 -0.4934516926995214
|
||||
4300 54.3830584579845890 -5029.3974364654013698 -5045.8912824487397302 16.4938459833379767 -5012.8566186763018777 -33.0346637724379022 93.8939996646779349 22.0065160962032245 20.2702208441870937 3.3813367869591255 0.0318644587592501 0.0164543727145067 -0.6628252924648856
|
||||
4400 55.6534237450105138 -5029.3926368191096117 -5045.2218371804192429 15.8292003613099244 -5012.3457495788206870 -32.8760876015986199 90.1103923801868518 22.0096837224699016 20.2727742192121454 3.3372739454265710 0.0314356050658150 0.0335424174115672 -0.1161529061464756
|
||||
4500 56.9183939939830452 -5029.3940454417834189 -5045.9258580870837250 16.5318126453004588 -5012.9929638810244796 -32.9328942060604319 94.1101312903264073 22.0128271345169999 20.2768840530886756 3.3637778632090720 0.0302602474720397 0.0485668445849368 0.5881899043646754
|
||||
4600 58.1842329019564204 -5029.3897931061719646 -5045.3405006579350811 15.9507075517634878 -5012.4008178333297110 -32.9396828246052280 90.8020925519495847 22.0156613833127963 20.2821435957056515 3.4302716374285005 0.0260054978861435 0.0562442375978452 0.6083123358868219
|
||||
4700 59.4382298499695025 -5029.3969593583269670 -5045.7810386931287212 16.3840793348014095 -5013.0572476947481846 -32.7237909983807498 93.2691345076189435 22.0180314970645661 20.2879823773636403 3.4648846252063747 0.0214335018843589 0.0598518189522713 0.0304394820826928
|
||||
4800 60.6967262169928290 -5029.3856671230942084 -5045.3017305595958533 15.9160634365015543 -5012.4665014359597990 -32.8352291236367648 90.6048750836845613 22.0199625290182688 20.2941047508438963 3.4363593409545792 0.0167963433674092 0.0615833915650458 -0.5541548942758866
|
||||
4900 61.9512241869815625 -5029.3923848959475436 -5045.7384583560833562 16.3460734601355888 -5012.7852573671316350 -32.9532009889525597 93.0527796570441836 22.0212592278909085 20.3000537186652821 3.3718475316480969 0.0086391048459562 0.0563118558122456 -0.6148391029712286
|
||||
5000 63.2058322129887529 -5029.3915775167406537 -5045.1695079529654322 15.7779304362247856 -5012.3445352609178371 -32.8249726920481351 89.8185296858452773 22.0217142875197673 20.3052386826657560 3.3368855121137573 -0.0005848472434748 0.0469229219675754 -0.0025464403573191
|
||||
5100 64.4612582869594917 -5029.3892459301187046 -5045.4092843740309036 16.0200384439126253 -5012.4115638930270507 -32.9977204810038813 91.1967703469756117 22.0211363551768393 20.3092236811018836 3.3731385391734987 -0.0104558693316052 0.0318306688289283 0.6399924297249336
|
||||
5200 65.7134019279619679 -5029.4030454404182819 -5046.2627024036355579 16.8596569632174536 -5013.2682522266104570 -32.9944501770255414 95.9764403553959653 22.0196975554592207 20.3116344765031158 3.4385226880437783 -0.0183768904268109 0.0160982826367598 0.5345362236176538
|
||||
5300 66.9578059059567750 -5029.3919597195299502 -5045.5335222071535100 16.1415624876236983 -5012.7301328351986740 -32.8033893719546015 91.8885664587487412 22.0175315555966975 20.3126154236309091 3.4630139347774884 -0.0242754059642420 0.0032173312250643 -0.0775763877645290
|
||||
5400 68.2489708719658665 -5029.3846231466677636 -5045.4515583416805384 16.0669351950124017 -5012.5148025922717352 -32.9367557494093148 91.4637380109446525 22.0148268891839543 20.3122214814806945 3.4262265154739362 -0.0300322552067342 -0.0114101644224351 -0.5957408015264980
|
||||
5500 69.5872814320027828 -5029.3976079434123676 -5046.2615016619420203 16.8638937185299866 -5013.2875337165860401 -32.9739679453564989 96.0005587994687488 22.0116064706776839 20.3102420050743042 3.3624439592830382 -0.0331793464510278 -0.0273205776972141 -0.5547024024481256
|
||||
5600 71.0810253079980612 -5029.3990311253737673 -5046.3786084092271267 16.9795772838533381 -5013.5810569834520720 -32.7975514257743583 96.6591070031231538 22.0082577080594533 20.3067263674726988 3.3382716477917813 -0.0327038891431524 -0.0431208290112252 0.1347255325181367
|
||||
5700 72.4856253899633884 -5029.3926984710069519 -5045.4056210227572592 16.0129225517498952 -5012.4766481517817738 -32.9289728709757838 91.1562619308659805 22.0050646686591129 20.3018397290024808 3.3836722937755463 -0.0302272076858413 -0.0535767293433688 0.6666043489739104
|
||||
5800 73.8634844649932347 -5029.3834029837780690 -5045.1129758304869029 15.7295728467090985 -5012.2694155058643446 -32.8435603246219827 89.5432459528482951 22.0022483685200818 20.2961021426530372 3.4452080928763542 -0.0254277345115299 -0.0599208650276596 0.4504328249672133
|
||||
5900 75.3915032909717411 -5029.3974484823693274 -5045.9428387883463074 16.5453903059766532 -5013.1858688276588509 -32.7569699606872575 94.1874244133654770 21.9999199731949346 20.2899812203382055 3.4600553052011818 -0.0206282083304644 -0.0609517769948545 -0.1746052875828525
|
||||
6000 76.6400258549838327 -5029.3913152258628543 -5045.4435744126367354 16.0522591867739663 -5012.4608078601768284 -32.9827665524597151 91.3801923591900334 21.9982238811128710 20.2840090111223468 3.4161665208076437 -0.0125595347519585 -0.0579440096045873 -0.6333327422350389
|
||||
6100 77.8959925099625252 -5029.3932757362208577 -5045.8790782711030261 16.4858025348824633 -5012.8969642404263141 -32.9821140306764420 93.8482109779551621 21.9973730537864682 20.2785476188032163 3.3549557462646411 -0.0042410493519084 -0.0506002459180393 -0.4680789345019807
|
||||
6200 79.1497183470055461 -5029.4088636981850868 -5046.6649961249258922 17.2561324267410470 -5013.7231617170655227 -32.9418344078599077 98.2334437902978976 21.9974997583151222 20.2740486557909172 3.3425028819702134 0.0059955322593470 -0.0383588614992616 0.2484046320153767
|
||||
6300 80.4047899909783155 -5029.3923725331251262 -5045.8449198462867571 16.4525473131614497 -5012.7774496031424860 -33.0674702431445411 93.6589000203849338 21.9985309965303522 20.2709033994038990 3.3945366047562309 0.0146161778945059 -0.0238717757127838 0.6755315511238056
|
||||
6400 81.6621199259534478 -5029.3873259574293115 -5045.4805995313954554 16.0932735739664388 -5012.6101575755155864 -32.8704419558798833 91.6136736746568658 22.0004178415001554 20.2692296192343555 3.4515126206720894 0.0224924238087105 -0.0095626954394393 0.3649317751543234
|
||||
6500 82.9068036190001294 -5029.3885153625169551 -5045.6513413124866929 16.2628259499700896 -5012.8502848348771295 -32.8010564776094071 92.5788791671608067 22.0028744822954785 20.2690295011692143 3.4565824273753738 0.0266893593346073 0.0051394765466491 -0.2690238272862540
|
||||
6600 84.1584947239607573 -5029.3921990608459964 -5045.6152780635047748 16.2230790026588494 -5012.6733651291715432 -32.9419129343335868 92.3526129669499198 22.0057446397104144 20.2703054065310688 3.4059684940340356 0.0301975147648949 0.0206588430605317 -0.6562141768091865
|
||||
6700 85.5309034659876488 -5029.3958221014900118 -5045.9855980438351253 16.5897759423451419 -5013.1614032626457629 -32.8241947811894832 94.4400971332701857 22.0088155297199890 20.2731431317838826 3.3483252260002931 0.0305868287843257 0.0360401338403821 -0.3706227597734457
|
||||
6800 86.7887097629718482 -5029.3989256161685262 -5046.1660314126675075 16.7671057964989494 -5013.3811893242827864 -32.7848420883840248 95.4495772316823547 22.0117933253442750 20.2774465117832499 3.3473285762193563 0.0293264534798696 0.0498605326239532 0.3567087933199659
|
||||
6900 88.0344084189855494 -5029.3894635412279968 -5045.3755615873205898 15.9860980460924917 -5012.4313435990561629 -32.9442179882648674 91.0035589089179382 22.0145527278245225 20.2830023561391073 3.4048481829747144 0.0261339472632872 0.0603043040288190 0.6629381496962342
|
||||
7000 89.2877694109920412 -5029.3931851776624171 -5046.2660855250323948 16.8729003473701340 -5013.4206101329300509 -32.8454753921025357 96.0518305529549394 22.0169018761537423 20.2892381473745935 3.4563764158029811 0.0215256303139502 0.0635714094149741 0.2735262616382870
|
||||
7100 90.5343435019603930 -5029.3943719418657565 -5045.8063859927260637 16.4120140508601793 -5012.9341376927177407 -32.8722483000083230 93.4281575894947309 22.0187504680106265 20.2956576132647477 3.4511897261914934 0.0151769557575876 0.0638586358909771 -0.3697827551013745
|
||||
7200 91.7890073219896294 -5029.3882574016588478 -5045.6074919269822203 16.2192345253231593 -5012.5576675194106429 -33.0498244075712222 92.3307276314112642 22.0199381323646897 20.3017542818957075 3.3949190800948910 0.0083746540157601 0.0572124597101438 -0.6554142442507734
|
||||
7300 93.0481603289954364 -5029.3919256510280320 -5045.3161120841996308 15.9241864331714869 -5012.3304308333417794 -32.9856812508580077 90.6511166120323679 22.0203434199504891 20.3069201065105531 3.3436661088988298 -0.0008082605025240 0.0457808438470512 -0.2589589418874469
|
||||
7400 94.2895189719856717 -5029.3973426785032643 -5045.6621408997361868 16.2647982212324713 -5012.7648025615653751 -32.8973383381705773 92.5901066539116755 22.0197952390567870 20.3107436357954469 3.3541554622638241 -0.0103306966484018 0.0301663424617996 0.4552583449586026
|
||||
7500 95.5377785899909213 -5029.3948467570653520 -5045.7331434291627374 16.3382966720969520 -5012.7514741351296834 -32.9816692940330185 93.0085089797121896 22.0182835442860032 20.3129031135621219 3.4158962237430512 -0.0195959596334220 0.0135047192390157 0.6456073746637249
|
||||
7600 96.8022272579837590 -5029.3931838808439352 -5045.4289963141181943 16.0358124332747032 -5012.6277589903447733 -32.8012373237726393 91.2865664414322850 22.0159526773315513 20.3134816232245754 3.4596215546593516 -0.0265035067457815 -0.0018448570141999 0.1605592216624496
|
||||
7700 98.0480918029788882 -5029.3927224394574296 -5045.5505410460209532 16.1578186065634384 -5012.7503911560907000 -32.8001498899307080 91.9811071571291450 22.0130792027109443 20.3125442860891496 3.4436146964093655 -0.0310809711922193 -0.0174733457478587 -0.4479487784855753
|
||||
7800 99.2981190299615264 -5029.4031547353506539 -5046.1752453778135532 16.7720906424625866 -5013.2528054902131771 -32.9224398875998361 95.4779543079392141 22.0098273587463140 20.3100791980582827 3.3840076444806408 -0.0342478030204245 -0.0319633867573659 -0.6355009600038708
|
||||
7900 100.5537567089777440 -5029.3944791921421711 -5044.9960502255426036 15.6015710334007611 -5012.1309422092845125 -32.8651080162585743 88.8145740452778938 22.0064004970442220 20.3061392621748453 3.3408200783635791 -0.0334515103138912 -0.0469088387662372 -0.1361992518732273
|
||||
8000 101.8002213349682279 -5029.3929935269861744 -5045.6154036718935458 16.2224101449071263 -5012.6903925591586813 -32.9250111127354685 92.3488053814068479 22.0031954529123475 20.3008903778718448 3.3630664386411944 -0.0303145741127793 -0.0573027579844121 0.5298234484194294
|
||||
8100 103.0604241339606233 -5029.3895181224415865 -5045.5242483757247101 16.1347302532831307 -5012.5130106423803227 -33.0112377333444016 91.8496728126257977 22.0004617169451784 20.2948581865125668 3.4259829025735637 -0.0235597360754076 -0.0625047587166574 0.5944988997279915
|
||||
8200 104.3003088539699093 -5029.3921128333386150 -5045.3442595710002934 15.9521467376618311 -5012.4679081513959318 -32.8763514196039210 90.8102853603699458 21.9984673460497753 20.2885772435489642 3.4606217876185612 -0.0159679066697783 -0.0624611171154739 0.0390314113354409
|
||||
8300 105.5484032649546862 -5029.3877455487827319 -5045.0575951302926114 15.6698495815094372 -5012.1517525987401314 -32.9058425315530698 89.2032611943938178 21.9972613261819880 20.2824755664924403 3.4344648587864106 -0.0085123036477869 -0.0597425423571583 -0.5144098325620685
|
||||
8400 106.7977103599696420 -5029.3940956297292360 -5045.7712194348414414 16.3771238051123973 -5012.7148337952312431 -33.0563856396105251 93.2295389819333309 21.9968254159544792 20.2768205630926097 3.3742357039982664 0.0005515507797924 -0.0525489103533247 -0.5831587742081521
|
||||
8500 108.0498831009608693 -5029.3966688220943979 -5045.9181006527742284 16.5214318306794148 -5013.1123929561299519 -32.8057076966441983 94.0510367525495781 21.9973649793415653 20.2722228282212278 3.3398553423288360 0.0104639615307145 -0.0388449586124005 -0.0141990665176662
|
||||
8600 109.3168672239989974 -5029.3901274034988091 -5045.9375078140647020 16.5473804105655624 -5012.9853021568969780 -32.9522056571671698 94.1987534193348921 21.9989049134571175 20.2690982462850933 3.3731313497904591 0.0192133927474549 -0.0232345679884083 0.5999078241684682
|
||||
8700 110.5636035219649784 -5029.3901389215689051 -5045.6376930378537509 16.2475541162848280 -5012.7481174817003193 -32.8895755561536873 92.4919416785743636 22.0011367928294845 20.2675706259688049 3.4350238082277742 0.0251426611885136 -0.0075450321086530 0.5206167046178872
|
||||
8800 111.8004809370031580 -5029.3924574370830669 -5045.1157123468474310 15.7232549097647301 -5012.3693783131229793 -32.7463340337239828 89.5072800313806596 22.0038756926631685 20.2674918694414608 3.4599837012727228 0.0287406400340964 0.0054631832109070 -0.0593929995926347
|
||||
8900 113.0429552759742364 -5029.3987474982423009 -5046.0489177048530109 16.6501702066103476 -5013.1575753877641546 -32.8913423170885579 94.7839016670577763 22.0068663666915683 20.2687690591312801 3.4257808041439497 0.0309099788432120 0.0202171302469460 -0.5672379170296111
|
||||
9000 114.3028285600012168 -5029.3950511511229706 -5045.5452299460939685 16.1501787949714100 -5012.5755502794254426 -32.9696796666691085 91.9376162413181817 22.0100025642331438 20.2715213988307390 3.3652959904269899 0.0310727498337748 0.0350587744467375 -0.5243423250951003
|
||||
9100 115.5504704579943791 -5029.4011682817399560 -5045.7686964972572241 16.3675282155176056 -5012.8956927574890869 -32.8730037397681514 93.1749144700332010 22.0129932323966244 20.2757847863275558 3.3416863642298322 0.0278865835662406 0.0500593574538005 0.1106488240215337
|
||||
9200 116.7946333579602651 -5029.4017720229812767 -5046.2095242659142968 16.8077522429334536 -5013.1790196502061008 -33.0305046157081676 95.6809639823375306 22.0155766145636562 20.2813847767229340 3.3837475995761923 0.0229459653959643 0.0606619684052993 0.6316843785669454
|
||||
9300 118.0373532379744574 -5029.3897983703673162 -5045.3852343116877819 15.9954359413206522 -5012.4098851963299239 -32.9753491153576448 91.0567164521802823 22.0176661603918404 20.2876093495490188 3.4433051081136128 0.0182119330164441 0.0630872424142740 0.4408646538230431
|
||||
9400 119.3096107059973292 -5029.3940044671780925 -5045.1494022809556554 15.7553978137776411 -5012.3373351985219415 -32.8120670824327760 89.6902589328241930 22.0191620625590261 20.2939150847352963 3.4576781527342213 0.0120237458614373 0.0624136446207651 -0.1706807559293053
|
||||
9500 120.5569760259822942 -5029.4028547635489304 -5046.4916138968292216 17.0887591332807105 -5013.5750575302763536 -32.9165563665534435 97.2806430926366943 22.0200362005428580 20.2999278998203252 3.4154427529782021 0.0047438742484681 0.0566484545204492 -0.6003708189460565
|
||||
9600 121.8032315599848516 -5029.3943080876824752 -5045.8625616630897639 16.4682535754077222 -5012.9435173518513693 -32.9190443112383448 93.7483105668138563 22.0201112440302111 20.3051306661589130 3.3573333481987917 -0.0034848828375071 0.0463786363566361 -0.4464499679272487
|
||||
9700 123.0481046040076762 -5029.3963743848999002 -5046.0931232530328998 16.6967488681334011 -5013.3188208671426764 -32.7743023858902305 95.0490585524709672 22.0192892506256435 20.3090481568511585 3.3449646688919508 -0.0126993251202254 0.0313153276927252 0.2347902151897416
|
||||
9800 124.3171976699959487 -5029.4041067798116273 -5046.2351730935588421 16.8310663137475451 -5013.3022700315450493 -32.9329030620125565 95.8136832619653376 22.0176816744773589 20.3113320548697089 3.3948762489105730 -0.0190003685475649 0.0145775023377736 0.6452872225841749
|
||||
9900 125.6034698109724559 -5029.3967328994849595 -5045.7044510326986710 16.3077181332140952 -5012.8792223601285514 -32.8252286725705744 92.8344354905748617 22.0154641674261171 20.3119427417383847 3.4494353673823004 -0.0251076944963040 -0.0022494305485361 0.3449321806936739
|
||||
10000 126.8703936609672382 -5029.3954046432463656 -5045.6299775343904912 16.2345728911443530 -5012.8287818160133611 -32.8011957183766398 92.4180438654010175 22.0127364302381388 20.3109725422284022 3.4537555828445510 -0.0290125415995836 -0.0167131954412302 -0.2644721653229455
|
||||
Loop time of 126.87 on 4 procs for 10000 steps with 1360 atoms
|
||||
|
||||
Performance: 6.810 ns/day, 3.524 hours/ns, 78.821 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 117.02 | 119.45 | 123.17 | 21.1 | 94.15
|
||||
Bond | 0.0041073 | 0.0042996 | 0.004639 | 0.3 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 3.4989 | 7.2187 | 9.6549 | 85.7 | 5.69
|
||||
Output | 0.013072 | 0.013851 | 0.016114 | 1.1 | 0.01
|
||||
Modify | 0.060992 | 0.063045 | 0.065171 | 0.8 | 0.05
|
||||
Other | | 0.1165 | | | 0.09
|
||||
|
||||
Nlocal: 340 ave 344 max 334 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 4628 ave 4634 max 4624 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 66301.5 ave 67860 max 63963 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
|
||||
Total # of neighbors = 265206
|
||||
Ave neighs/atom = 195.004
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:02:06
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,71 @@
|
|||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
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
|
||||
# interactions can be specified separately
|
||||
read_data gr_hBN_Cstack_2L_noH.data
|
||||
mass 1 10.8110 # boron mass (g/mole) | membrane
|
||||
mass 2 14.0067 # nitrogen mass (g/mole) | membrane
|
||||
mass 3 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
group membrane type 1 2
|
||||
group adsorbate type 3
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo tersoff ILP/graphene/hBN 16.0 coul/shield 16.0
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.airebo NULL NULL C # chemical
|
||||
pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
|
||||
pair_coeff * * ILP/graphene/hBN BNCH-old.ILP B N C # long range
|
||||
pair_coeff 1 1 coul/shield 0.70
|
||||
pair_coeff 1 2 coul/shield 0.69498201415576216335
|
||||
pair_coeff 2 2 coul/shield 0.69
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
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
|
||||
velocity all create 300.0 12345
|
||||
fix thermostat all nve
|
||||
|
||||
compute 0 all pair rebo
|
||||
compute 1 all pair tersoff
|
||||
compute 2 all pair ILP/graphene/hBN
|
||||
compute 3 all pair coul/shield
|
||||
variable REBO equal c_0
|
||||
variable Tersoff equal c_1
|
||||
variable EILP equal c_2
|
||||
variable Ecoul equal c_3
|
||||
|
||||
# Calculate the pair potential between the substrate and slider
|
||||
compute sldsub adsorbate group/group membrane
|
||||
variable Evdw equal c_sldsub
|
||||
|
||||
############################
|
||||
|
||||
# Output
|
||||
thermo 100
|
||||
thermo_style custom step cpu etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
|
||||
thermo_modify line one format float %.16f
|
||||
|
||||
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
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 100000
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,60 @@
|
|||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
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
|
||||
# interactions can be specified separately
|
||||
# read lammps data file
|
||||
read_data Bi_gr_AB_stack_2L_noH_300K.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
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.airebo NULL C # chemical
|
||||
pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
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
|
||||
|
||||
compute 0 all pair rebo
|
||||
compute 1 all pair kolmogorov/crespi/full
|
||||
variable REBO equal c_0
|
||||
variable KC equal c_1
|
||||
|
||||
############################
|
||||
|
||||
# Output
|
||||
thermo 100
|
||||
thermo_style custom step cpu 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 %.16f
|
||||
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
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 10000
|
||||
|
|
@ -0,0 +1,227 @@
|
|||
LAMMPS (5 Feb 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
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 2 atom types 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
|
||||
orthogonal box = (0 0 0) to (42.6 41.8117 100)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1360 atoms
|
||||
reading velocities ...
|
||||
1360 velocities
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
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
|
||||
680 atoms in group membrane
|
||||
group adsorbate type 2
|
||||
680 atoms in group adsorbate
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.airebo NULL C # chemical
|
||||
Reading potential file CH.airebo with DATE: 2011-10-25
|
||||
pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
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
|
||||
|
||||
compute 0 all pair rebo
|
||||
compute 1 all pair kolmogorov/crespi/full
|
||||
variable REBO equal c_0
|
||||
variable KC equal c_1
|
||||
|
||||
############################
|
||||
|
||||
# Output
|
||||
thermo 100
|
||||
thermo_style custom step cpu 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 %.16f
|
||||
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
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 10000
|
||||
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, skip from (2)
|
||||
attributes: full, newton on, ghost
|
||||
pair build: skip/ghost
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair kolmogorov/crespi/full, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 12.39 | 12.39 | 12.39 Mbytes
|
||||
Step CPU TotEng PotEng KinEng v_REBO v_KC Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
|
||||
0 0.0000000000000000 -5025.3867722724935447 -5040.0767391238714481 14.6899668513774859 -5011.2636297758563160 -28.8131093480147769 83.6251135126841376 22.0155657205247799 20.2812150219063234 3.4623630944674200 0.0282287194990573 0.0535565744690331 0.2193320108238477
|
||||
100 1.2090328890481032 -5025.3962433292772403 -5041.3829775585218158 15.9867342292441723 -5012.5109377233984560 -28.8720398351239709 91.0071804887902687 22.0181858077562040 20.2867731676403515 3.4456714401609116 0.0241525932155392 0.0573807336146946 -0.5235069014277836
|
||||
200 2.4036352250259370 -5025.3942568861339169 -5041.9638220670003648 16.5695651808668281 -5012.7804299194813211 -29.1833921475196121 94.3250439653562438 22.0203529514796585 20.2926376510830444 3.3740502908038388 0.0186420747870426 0.0595018114242881 -0.7867265577251443
|
||||
300 3.5707715520402417 -5025.3919463074435043 -5040.9705419367464856 15.5785956293027752 -5012.0510295102558302 -28.9195124264904493 88.6837826830418550 22.0218424094691478 20.2984380399648714 3.3199036612722175 0.0106250874216957 0.0544668351685384 -0.1513745907556251
|
||||
400 4.7711801230325364 -5025.3965376948390258 -5041.6929964127411949 16.2964587179024178 -5012.6418090677252621 -29.0511873450172544 92.7703393702056616 22.0224243956700647 20.3034636121897307 3.3515794171886442 0.0006844934965578 0.0458598502111477 0.6967704496022608
|
||||
500 5.9397808950161561 -5025.4050172900369944 -5042.1712310052898829 16.7662137152530981 -5013.1850218644503911 -28.9862091408392573 95.4444989087561169 22.0220673443415116 20.3074634961872427 3.4286173277703296 -0.0078273438530378 0.0340764531684523 0.6845095066136071
|
||||
600 7.1201584940426983 -5025.3985715733606412 -5041.2158947892512515 15.8173232158908945 -5012.4875319344801028 -28.7283628547711061 90.0427797270119470 22.0209262700263473 20.3103065099326834 3.4653840647843963 -0.0141442607886095 0.0229602847458309 0.0009001092688723
|
||||
700 8.2871374670066871 -5025.3997561571868573 -5041.6276721305875981 16.2279159734002967 -5012.7093581188073586 -28.9183140117799340 92.3801482385678554 22.0191651506397577 20.3120184839872451 3.4291788223636952 -0.0208485646050276 0.0104216414448085 -0.6668311563864557
|
||||
800 9.4509126310003921 -5025.3967603736264209 -5042.3401685986937082 16.9434082250674400 -5013.3044877099318910 -29.0356808887622364 96.4532085366923582 22.0167259920093024 20.3122737442838215 3.3535033285498610 -0.0279747378394777 -0.0060833621062162 -0.7003492925383377
|
||||
900 10.6212659500306472 -5025.3984542800671989 -5042.2820667480700649 16.8836124680024433 -5013.4066841441726865 -28.8753826038976342 96.1128111060699695 22.0136711877076685 20.3107854822651177 3.3206430872229769 -0.0331979093628198 -0.0237440546972741 0.1335648638118817
|
||||
1000 11.7926044440246187 -5025.3988185617581621 -5041.9160822432759232 16.5172636815174414 -5012.8147737982535546 -29.1013084450222337 94.0273088605581080 22.0102627031673421 20.3075977017766007 3.3736867454007284 -0.0340065996333862 -0.0390649990984092 0.7872380118801856
|
||||
1100 13.0851637730374932 -5025.3989801127108876 -5041.7965283026751422 16.3975481899639917 -5012.8897602518782151 -28.9067680507963090 93.3458082369236024 22.0069241283902350 20.3031837024214354 3.4457666497828261 -0.0326106583004187 -0.0483645330358782 0.5228983819640343
|
||||
1200 14.2550687200273387 -5025.3992874004115947 -5041.7405216174720408 16.3412342170605562 -5012.8949220795147994 -28.8455995379571313 93.0252314497841297 22.0037928169574570 20.2980678584679524 3.4626948696122506 -0.0293478313470026 -0.0532412883321035 -0.2153480166167848
|
||||
1300 15.4206955539993942 -5025.4035659930168549 -5042.0283937223284738 16.6248277293119138 -5012.9218999373606493 -29.1064937849681300 94.6396353414618403 22.0010832216368293 20.2926192132286474 3.4089856465370070 -0.0244719444214278 -0.0557588495572362 -0.7710768515422161
|
||||
1400 16.5889568240381777 -5025.3837503472668686 -5041.1619872695664526 15.7782369222997669 -5012.1909520967401477 -28.9710351728264470 89.8202744095107306 21.9990363808598559 20.2870007320342864 3.3360138095172736 -0.0163606191510480 -0.0559299166221425 -0.5188880833578199
|
||||
1500 17.7671085790498182 -5025.3966017230777652 -5041.6813785354088395 16.2847768123309180 -5012.8020874008770988 -28.8792911345319823 92.7038381527866733 21.9979871457204972 20.2816848686464866 3.3282924364660564 -0.0045298722152426 -0.0496966023999349 0.3926011238047987
|
||||
1600 18.9589943360188045 -5025.3937345699878279 -5041.6141058440125562 16.2203712740251653 -5012.5931977854761499 -29.0209080585362997 92.3371987650906334 21.9979960708595854 20.2771303069271234 3.3957510840195448 0.0049490795871075 -0.0412397066201281 0.7981352140616215
|
||||
1700 20.1920844370033592 -5025.3920349717982390 -5041.3474422788585798 15.9554073070600726 -5012.5499564532892691 -28.7974858255688844 90.8288467015085956 21.9988824248280963 20.2734683062635952 3.4575828640693675 0.0127762700599154 -0.0313494515473505 0.3326934046758493
|
||||
1800 21.3635783740319312 -5025.3865162596666778 -5041.4209078040967142 16.0343915444297949 -5012.6149552063980082 -28.8059525976986919 91.2784777920740851 22.0004637748842455 20.2708693578177872 3.4521283623881351 0.0187721532950161 -0.0208398096893947 -0.4319057546214770
|
||||
1900 22.5351911650504917 -5025.4030154876936649 -5041.9703720842626353 16.5673565965688070 -5012.8736344691242266 -29.0967376151382418 94.3124712267998717 22.0026572989276374 20.2694060650691874 3.3853702468064513 0.0252934937455946 -0.0077824913573627 -0.7917373730797634
|
||||
2000 23.7021600700099953 -5025.4025246012934076 -5041.9864750467668273 16.5839504454735511 -5013.0748380269278641 -28.9116370198385084 94.4069345099584183 22.0054314642639071 20.2693585608976896 3.3237746010657330 0.0301055920092041 0.0074208853595260 -0.2863224338408705
|
||||
2100 24.8830241240211762 -5025.3870581274150027 -5040.9121729675962342 15.5251148401812902 -5011.8761736947853933 -29.0359992728101197 88.3793342723490412 22.0085483371208817 20.2709445247397930 3.3427033439317140 0.0311372848806408 0.0239761890014525 0.6114295821968323
|
||||
2200 26.0501821730285883 -5025.3918833881934916 -5041.6799723765943781 16.2880889884009576 -5012.5688853419105726 -29.1110870346840080 92.7226932736071063 22.0116684513606060 20.2740990090120867 3.4181627583397507 0.0308945173353687 0.0379066772496769 0.7271861390898796
|
||||
2300 27.2176894500153139 -5025.3949346032641188 -5041.7254573272766720 16.3305227240123081 -5012.8849770830092893 -28.8404802442676917 92.9642544692971882 22.0146384176519128 20.2783501662495809 3.4635799761850632 0.0286285885663440 0.0469492067266735 0.1073585873889057
|
||||
2400 28.3860884510213509 -5025.3963000158337309 -5041.6826909876272111 16.2863909717937148 -5012.7104483483453805 -28.9722426392815322 92.7130270277289696 22.0173575918610567 20.2833719117073876 3.4365406534706939 0.0248751997236569 0.0535646666600052 -0.6066967516565630
|
||||
2500 29.5582998979953118 -5025.3891173410784177 -5041.5906279381069908 16.2015105970288857 -5012.5517909903483087 -29.0388369477585861 92.2298311807592910 22.0196031753242529 20.2888529413860539 3.3617525635386030 0.0196652006111998 0.0549267012871614 -0.7369084634354620
|
||||
2600 30.7501633380306885 -5025.4052931473715944 -5041.7099788940795406 16.3046857467076656 -5012.9253328497143229 -28.7846460443654308 92.8171731190269753 22.0211867983163572 20.2943920370994455 3.3195676660631070 0.0117061903077485 0.0544890610455483 0.0041300364361864
|
||||
2700 31.9312072400352918 -5025.4054780236301667 -5041.8854982632174142 16.4800202395873789 -5012.8990747848783940 -28.9864234783388426 93.8152942869028550 22.0219652421667966 20.2994898926302128 3.3637955536480932 0.0042193082641918 0.0477783851053640 0.7622879364636829
|
||||
2800 33.0991695010452531 -5025.3912584140180115 -5041.7117266611994637 16.3204682471812355 -5012.7809950679111353 -28.9307315932885345 92.9070176644210619 22.0220139187549897 20.3038960471470880 3.4391227846691574 -0.0034173757467748 0.0402487406699638 0.5907117446321344
|
||||
2900 34.2735084790037945 -5025.3938120791799520 -5041.5807500998762407 16.1869380206962177 -5012.8426992339791468 -28.7380508658970015 92.1468743325702633 22.0213079578234847 20.3074511077868003 3.4637467480717130 -0.0104174548640656 0.0300542700286960 -0.1297243821532769
|
||||
3000 35.5088631500257179 -5025.4088836623213865 -5042.5790840858535375 17.1702004235320587 -5013.5654819329674865 -29.0136021528856887 97.7442613710707207 22.0199440197456582 20.3098582709772657 3.4167983757244911 -0.0169840323929214 0.0170240377769569 -0.7374145319073314
|
||||
3100 36.7295854010153562 -5025.4086406925371193 -5042.2697560277538287 16.8611153352168692 -5013.2134239426923159 -29.0563320850622908 95.9847423839321010 22.0178853132279109 20.3108565386005218 3.3420019405042907 -0.0242673913632101 0.0021711631697942 -0.6022358266725114
|
||||
3200 37.9420561690349132 -5025.3926910219461206 -5041.8149473963876517 16.4222563744419219 -5012.8374685859962483 -28.9774788103915029 93.4864637436761967 22.0151252427317345 20.3101374038003684 3.3241188409229054 -0.0303691045142071 -0.0154526688841053 0.2951232739354271
|
||||
3300 39.1072654760209844 -5025.4019168838058249 -5041.8245525223237564 16.4226356385176793 -5012.7438638561252446 -29.0806886661991690 93.4886227683838342 22.0118678336381457 20.3077932400083974 3.3868622776182424 -0.0338044438894221 -0.0313263193531266 0.8095221886528264
|
||||
3400 40.2726593170082197 -5025.3991199704587416 -5041.5436503483433626 16.1445303778847453 -5012.6447438628329110 -28.8989064855106470 91.9054616745435879 22.0084209536016466 20.3040661062772116 3.4539274247624481 -0.0348969431077094 -0.0420734210995361 0.4101686776950041
|
||||
3500 41.4296097320038825 -5025.3940844427597767 -5041.3374211652380836 15.9433367224780884 -5012.5810922125028810 -28.7563289527353803 90.7601328632783719 22.0050492911385724 20.2995122872307334 3.4573439358500311 -0.0322607562513154 -0.0487762186067769 -0.3358722426493447
|
||||
3600 42.6008598420303315 -5025.4043544972746531 -5042.0723763739933929 16.6680218767186084 -5013.0391944920975220 -29.0331818818965530 94.8855253095273525 22.0020786089923739 20.2943998710379638 3.3961228997702317 -0.0269433628563045 -0.0533133666136933 -0.7879587681174278
|
||||
3700 43.8028116130153649 -5025.4021846582545550 -5041.8106354045849002 16.4084507463306011 -5012.9859875236998050 -28.8246478808859727 93.4078728775698579 21.9996551299436334 20.2889571349277595 3.3287838075858094 -0.0198828701363438 -0.0541461234927997 -0.3953793498641726
|
||||
3800 44.9688759930431843 -5025.4009027180181874 -5041.4796132183219015 16.0787105003034405 -5012.5747426977468422 -28.9048705205747503 91.5307709220173820 21.9980988156843189 20.2836609669102153 3.3361624936284979 -0.0114502161673620 -0.0510195644013287 0.5193551642883544
|
||||
3900 46.1358508010162041 -5025.4044270906215388 -5042.0985642713785637 16.6941371807572700 -5013.0541027932831639 -29.0444614780964656 95.0341910816660089 21.9973956364988794 20.2788219343977296 3.4086752988334950 -0.0026647342074451 -0.0448873050508345 0.7645000369511740
|
||||
4000 47.3026360210496932 -5025.3954718507548023 -5041.3262379385632812 15.9307660878089106 -5012.5576639138616883 -28.7685740247013015 90.6885724056019171 21.9975429003444383 20.2747072410190867 3.4617517103044699 0.0048995201173917 -0.0374323746582634 0.2116010371043403
|
||||
4100 48.4589538380387239 -5025.4047534487826852 -5041.8008682831587066 16.3961148343756129 -5012.8773139083332353 -28.9235543748263382 93.3376486185259040 21.9983947399693136 20.2714890086889667 3.4455669507407385 0.0116215188606004 -0.0267084491147554 -0.5160314869363558
|
||||
4200 49.6870953830075450 -5025.4040425363737086 -5041.8879901694490400 16.4839476330749370 -5012.7598335304282955 -29.1281566390214763 93.8376516366184035 21.9998528364627610 20.2693730209178362 3.3741713364804116 0.0178705348058012 -0.0145748652370947 -0.7806350357809819
|
||||
4300 50.8562145699979737 -5025.4044242163436138 -5041.6563978781996411 16.2519736618556401 -5012.7627558388539910 -28.8936420393467870 92.5171006870168497 22.0018951506242608 20.2686014427215824 3.3212120228517752 0.0234319429320006 0.0004943293969114 -0.1426370973565776
|
||||
4400 52.0283764940104447 -5025.3927134732630293 -5041.2695045736281827 15.8767911003648230 -5012.2183847211681496 -29.0511198524600545 90.3813106876196031 22.0044857492060721 20.2695565815015009 3.3528429881520223 0.0279186879430288 0.0172965694804035 0.6854511544787831
|
||||
4500 53.1905290260328911 -5025.3985627613592442 -5041.8741225357753137 16.4755597744162223 -5012.8837212407361221 -28.9904012950389784 93.7899023367350253 22.0073726592588379 20.2720211826135674 3.4281218168340750 0.0293916215690875 0.0308967742220515 0.6658600870219290
|
||||
4600 54.3571357890032232 -5025.4030459055366009 -5041.6564824541692360 16.2534365486328944 -5012.9056573639236376 -28.7508250902455202 92.5254284166871628 22.0103511916306367 20.2756370304082481 3.4637820951474532 0.0294307649769785 0.0417680653709620 -0.0058132312600395
|
||||
4700 55.5370646170340478 -5025.4001910298129587 -5041.7414930717031893 16.3413020418903656 -5012.7996878950380051 -28.9418051766647757 93.0256175540653061 22.0131565411710390 20.2800753547754908 3.4273163365998669 0.0270124802631130 0.0473687758079074 -0.6670593953609443
|
||||
4800 56.7563687619986013 -5025.3970095918302832 -5041.7422910469977069 16.3452814551670258 -5012.7216399349827043 -29.0206511120158481 93.0482710352025606 22.0156808325349225 20.2851061286242143 3.3523725032197911 0.0234068222788119 0.0525631509064944 -0.6782133515097872
|
||||
4900 57.9812595020048320 -5025.4045337102616031 -5041.9408737919047780 16.5363400816427699 -5013.0636880874308190 -28.8771857044747691 94.1359044851795801 22.0177398691825310 20.2905584995200492 3.3213846154694506 0.0174077061305399 0.0550412996935653 0.1444813620920061
|
||||
5000 59.3218032810254954 -5025.3962333034423864 -5041.5309003858565120 16.1346670824138947 -5012.4020743451865201 -29.1288260406696793 91.8493132017999869 22.0190805858925351 20.2959422932664175 3.3744572644527548 0.0092139201306282 0.0519348392700130 0.7753071899805003
|
||||
5100 60.5568367950036190 -5025.3986897876229705 -5041.7565575138560234 16.3578677262329677 -5012.8062332908430108 -28.9503242230128492 93.1199205057043997 22.0196598900432008 20.3008510568789688 3.4451873132307109 0.0022328021009227 0.0455289361760877 0.5086920041557489
|
||||
5200 61.7441689710249193 -5025.4086477484779607 -5042.1891559391060582 16.7805081906281437 -5013.3313045021295693 -28.8578514369759453 95.5258726203469166 22.0195729062207910 20.3049844118216853 3.4599894169738934 -0.0043702498962095 0.0368958159104244 -0.2306537658669780
|
||||
5300 62.9076888910494745 -5025.4047630119666792 -5042.2497651384219353 16.8450021264550287 -5013.1662090122745212 -29.0835561261479043 95.8930152258387380 22.0188694550064135 20.3081712448169753 3.4059695294096115 -0.0097372015534203 0.0264821769201272 -0.7581161217469209
|
||||
5400 64.0683258480275981 -5025.3933251833759641 -5041.3747031343818890 15.9813779510059568 -5012.3052544367146766 -29.0694486976670419 90.9766889716746761 22.0175055937439126 20.3100926022901866 3.3355679509867397 -0.0177201631774805 0.0117950823628956 -0.4946380030647148
|
||||
5500 65.2179911470157094 -5025.3935708413573593 -5041.8358929495343546 16.4423221081772937 -5012.8774868877389963 -28.9584060617955998 93.6006913167069996 22.0154086611623541 20.3103936048593425 3.3298144426076877 -0.0243002986248679 -0.0066858929837734 0.4051029626040160
|
||||
5600 66.3825001540244557 -5025.4033630998110311 -5041.9944576209154548 16.5910945211040293 -5012.9336477538354302 -29.0608098670803940 94.4476033652108811 22.0127064018791891 20.3088828802371886 3.3973974994341418 -0.0296421428435360 -0.0234023677146545 0.7924374772807079
|
||||
5700 67.5387458290206268 -5025.4064170374704190 -5042.3089591155567177 16.9025420780860394 -5013.4709838355611282 -28.8379752799952662 96.2205711036252467 22.0096596368001904 20.3059642066740196 3.4573305989946799 -0.0307452903816626 -0.0342930346706216 0.3019228865322697
|
||||
5800 68.6898558190441690 -5025.4061379335107631 -5041.8074986877008996 16.4013607541903390 -5012.9602210852863209 -28.8472776024147421 93.3675119017057114 22.0065887294783344 20.3020529443920665 3.4497605237377127 -0.0307408713729807 -0.0429246008353057 -0.4408374456500690
|
||||
5900 70.0917209680192173 -5025.3977138810505494 -5041.5243953933731973 16.1266815123228398 -5012.4530953037283325 -29.0713000896457601 91.8038539974270691 22.0036093293714039 20.2974427818030136 3.3830406669234994 -0.0276754433884746 -0.0487340588861634 -0.7731644790859656
|
||||
6000 71.2613310019951314 -5025.4061897320334538 -5042.4973921892833459 17.0912024572499490 -5013.5346207663915266 -28.9627714228926898 97.2945521263563080 22.0010725656439803 20.2924349365514125 3.3248475534562418 -0.0226297068438173 -0.0517943560203192 -0.2513566834436860
|
||||
6100 72.4216459180461243 -5025.4111943337366029 -5042.4304955357329163 17.0193012019962850 -5013.4446926488462850 -28.9858028868861908 96.8852421059100521 21.9992326732656416 20.2872743822956600 3.3454905118317124 -0.0138160202955120 -0.0501527604556697 0.6139595522353440
|
||||
6200 73.5876242220401764 -5025.3998619486119424 -5041.8009544770320645 16.4010925284199089 -5012.7254287269834094 -29.0755257500489890 93.3659849812758722 21.9982551894938574 20.2823559183307758 3.4200524172167195 -0.0058682357664527 -0.0477653950326091 0.7072791948884631
|
||||
6300 74.7366292540100403 -5025.3991024532933807 -5041.6578117585850123 16.2587093052920402 -5012.8397513602722029 -28.8180603983131718 92.5554444731294268 21.9980348192884492 20.2778618173320844 3.4621508509649850 0.0012759918628081 -0.0415391303210138 0.0719391735259730
|
||||
6400 75.8949150920379907 -5025.3985438479558070 -5041.8926157501973648 16.4940719022415543 -5012.9343359646609315 -28.9582797855367176 93.8952857461339079 21.9984608992216870 20.2740639069954121 3.4333413348240081 0.0071673667795489 -0.0342923190921417 -0.6024624741325313
|
||||
6500 77.0539659400237724 -5025.3999600806355375 -5041.8653986061344767 16.4654385254990245 -5012.7464610083952721 -29.1189375977399578 93.7322854204986555 21.9994997416619711 20.2710982777120954 3.3610062476568374 0.0142487960766090 -0.0238185878593028 -0.7047715901527828
|
||||
6600 78.5999028970254585 -5025.4057704511451448 -5042.3215944746934838 16.9158240235481756 -5013.4556086412558216 -28.8659858334370156 96.2961808179409928 22.0012244339992940 20.2694975559910091 3.3221119559272521 0.0206236059170565 -0.0086820184699541 0.0358687376074831
|
||||
6700 79.8250733939930797 -5025.4042369629851237 -5042.2991847843286450 16.8949478213436102 -5013.2745186145393745 -29.0246661697894055 96.1773395164776872 22.0035228933514233 20.2694298883667052 3.3665382079959651 0.0251929228865793 0.0064452615862544 0.7398164418248552
|
||||
6800 80.9874257780029438 -5025.4149541181532186 -5042.7962990017040283 17.3813448835506001 -5013.8631914424222487 -28.9331075592822771 98.9462368156217877 22.0061969306599998 20.2708479540842212 3.4383567097341898 0.0277090864588332 0.0208924976028228 0.5485097024541594
|
||||
6900 82.2781793380272575 -5025.3945564155828833 -5041.2566713058931782 15.8621148903101510 -5012.4623560467261996 -28.7943152591673730 90.2977638869920156 22.0089986714469674 20.2734300773294862 3.4600092984345316 0.0280593910782676 0.0310896707675793 -0.1463209852219078
|
||||
7000 83.4404686560155824 -5025.3952994606634093 -5041.6543672051639078 16.2590677445006015 -5012.6069843852856138 -29.0473828198785782 92.5574849487687885 22.0117925249332593 20.2770676863368315 3.4134107292366291 0.0269363686714677 0.0411713877401656 -0.7112212465178037
|
||||
7100 84.5968778430251405 -5025.4007603676855069 -5042.2329345346870468 16.8321741670019307 -5013.2275493052911770 -29.0053852293960759 95.8199899034363938 22.0143610431743149 20.2816289673576087 3.3427075272995799 0.0237872415502196 0.0490441626858190 -0.5472896336687677
|
||||
7200 85.7572498430381529 -5025.3974915436865558 -5041.7945955363265966 16.3971039926398028 -5012.8313575860174751 -28.9632379503097042 93.3432795687493808 22.0163859033172216 20.2867748265654058 3.3285600536621693 0.0165298576203055 0.0538311426566842 0.2938370338019134
|
||||
7300 86.9434509190032259 -5025.4100572623510743 -5042.0883477745555865 16.6782905122044660 -5012.9702743899733832 -29.1180733845828428 94.9439812486600232 22.0177218159220800 20.2920813914563816 3.3889711610256499 0.0099257716002105 0.0524971881967137 0.7654243328780935
|
||||
7400 88.1003905290272087 -5025.4008152901669746 -5041.6485797847517460 16.2477644945846578 -5012.7509075535590455 -28.8976722311927219 92.4931392925228550 22.0184429996648170 20.2972136001887762 3.4511166990362638 0.0044130292334549 0.0493609850661665 0.3682517730369118
|
||||
7500 89.2996820280095562 -5025.4020754014563863 -5041.9550073109521691 16.5529319094957543 -5013.1017666545494649 -28.8532406564024804 94.2303562631601892 22.0186059673764127 20.3019306435107829 3.4515445354063168 -0.0010697714965434 0.0436146952934956 -0.3551397060837367
|
||||
7600 90.5618456410011277 -5025.3929519484890989 -5041.5352890260082859 16.1423370775190982 -5012.5185731109741027 -29.0167159150341760 91.8929759423496080 22.0181918732783508 20.3058093897626541 3.3907072098692783 -0.0077906403123609 0.0344875434248021 -0.7510478289850223
|
||||
7700 91.7723228640388697 -5025.4083899039087555 -5042.3085035279354997 16.9001136240271137 -5013.3862163999392578 -28.9222871279962845 96.2067467193776338 22.0171116461022791 20.3085395281403258 3.3294602057393976 -0.0140242417133003 0.0194488897998306 -0.3291988824677945
|
||||
7800 92.9413640320417471 -5025.4088205050420584 -5041.6937795006360830 16.2849589955940068 -5012.7518738556918834 -28.9419056449434464 92.7048752617338891 22.0153699245972980 20.3096402131253626 3.3405377445245996 -0.0206874492959494 0.0024020372787611 0.5268251462470672
|
||||
7900 94.4233713660505600 -5025.4086877788031416 -5042.0898070334278600 16.6811192546242708 -5013.0557892763890777 -29.0340177570384341 94.9600843419037091 22.0130135165568248 20.3092263402688644 3.4109056375926126 -0.0253561229093074 -0.0114521930970601 0.7247193201128768
|
||||
8000 95.6260597730288282 -5025.4005274389073747 -5041.5154853271778848 16.1149578882706237 -5012.7120503802434541 -28.8034349469349920 91.7371152905215013 22.0103036454440684 20.3073931276852804 3.4590979710673522 -0.0281528841740650 -0.0237682605693130 0.1613878328187369
|
||||
8100 96.7842931560007855 -5025.4053665421533879 -5042.1894447903450782 16.7840782481914665 -5013.2333102392240107 -28.9561345511206838 95.5461957750551818 22.0074529851401053 20.3045049731579077 3.4391653754846176 -0.0285053466321131 -0.0335616960987157 -0.5315168066124235
|
||||
8200 97.9501550050335936 -5025.4056941639546494 -5041.9921704239559404 16.5864762600012661 -5012.8905319814539325 -29.1016384425013328 94.4213131350927881 22.0046033201667974 20.3006386231954856 3.3697166434334109 -0.0279171913030586 -0.0440297345634183 -0.7233209623948276
|
||||
8300 99.1202951990417205 -5025.3993864105968896 -5041.6550396005832226 16.2556531899865853 -5012.7354100842831031 -28.9196295163002119 92.5380470213916482 22.0020282884824283 20.2959383079965683 3.3236096037486442 -0.0234814295194575 -0.0495757237271515 -0.0781852877134260
|
||||
8400 100.2907066670013592 -5025.4050168007570392 -5042.4116164615488742 17.0065996607914265 -5013.3253826950494840 -29.0862337664993156 96.8129364407040924 21.9999747851567946 20.2907043369736293 3.3580457506538419 -0.0172292815521034 -0.0540194901749135 0.6743678827760200
|
||||
8500 101.4595158430165611 -5025.3896509324949875 -5041.2159279476472875 15.8262770151526624 -5012.2067880886852436 -29.0091398589626195 90.0937507392143999 21.9985684955843546 20.2853297444598226 3.4300279660165618 -0.0111633348131576 -0.0523517871524280 0.6129192799521199
|
||||
8600 102.6223388280486688 -5025.4018476745841326 -5041.4510907574731391 16.0492430828888608 -5012.6451181237571291 -28.8059726337163227 91.3630226792098199 21.9977945492323492 20.2802923055429680 3.4601353788922511 -0.0045089085677838 -0.0490401321065509 -0.0560793211441527
|
||||
8700 103.7857662939932197 -5025.3942518544345148 -5041.2184273163638863 15.8241754619297001 -5012.2565174217952517 -28.9619098945681799 90.0817872931017405 21.9976866638961610 20.2757523819081804 3.4211478907276227 0.0020659146206532 -0.0414436983596942 -0.6562444939603165
|
||||
8800 104.9577097550500184 -5025.4022671237153190 -5041.8626441679734853 16.4603770442582658 -5012.8426762097215033 -29.0199679582518151 93.7034720850035541 21.9982205093549688 20.2721004487751912 3.3509491647330680 0.0085057984890194 -0.0308961138564155 -0.6069595457833823
|
||||
8900 106.1287890840321779 -5025.4052507845035507 -5042.2508636213824502 16.8456128368789493 -5013.3629703916931248 -28.8878932296881956 95.8964917979127449 21.9994405230768102 20.2696708412316546 3.3265804933545531 0.0155084216130566 -0.0167964958841456 0.1826414328899625
|
||||
9000 107.3016250670189038 -5025.4004751143402245 -5041.6628696531170135 16.2623945387763733 -5012.6074414951381186 -29.0554281579796871 92.5764232861904759 22.0012198615606422 20.2687838521467185 3.3793520753014836 0.0199734843735534 -0.0019939871679624 0.7393704825316162
|
||||
9100 108.4706182610243559 -5025.4021047075621027 -5041.8073065771823167 16.4052018696199333 -5012.8640984802987077 -28.9432080968828522 93.3893780990269988 22.0034855215300205 20.2692639615896404 3.4450793491809684 0.0240871130007129 0.0114742738717532 0.4476821128123131
|
||||
9200 109.6369604960200377 -5025.4031454767773539 -5042.1816796811663153 16.7785342043892634 -5013.3058475082143559 -28.8758321729517640 95.5146353708031342 22.0059499464219179 20.2710026662379228 3.4543741700290989 0.0250098145089318 0.0232231191592319 -0.2737178351814341
|
||||
9300 110.8078396720229648 -5025.3992883854634783 -5041.5310269301671724 16.1317385447035591 -5012.5173159573560042 -29.0137109728104114 91.8326420070361849 22.0084617214542924 20.2738402346505993 3.3995496325670125 0.0252037567343996 0.0335240097442505 -0.7200850104543423
|
||||
9400 111.9826453819987364 -5025.3988527094979872 -5041.7418936811573076 16.3430409716589438 -5012.7308085838158149 -29.0110850973410592 93.0355167050136629 22.0109364415103386 20.2777564631153098 3.3357718843630857 0.0237501814778520 0.0444235846615718 -0.4158703702081880
|
||||
9500 113.1567846690304577 -5025.4051255531121569 -5042.2489687624847647 16.8438432093728032 -5013.3397718220858224 -28.9091969403984521 95.8864178949166615 22.0131903134697460 20.2825381608416215 3.3351665472353877 0.0203457038293413 0.0508047188326974 0.4211121614393614
|
||||
9600 114.3233812840189785 -5025.4041532078053933 -5042.0758767508377787 16.6717235430326198 -5012.9894578671246563 -29.0864188837131117 94.9065976692424584 22.0149721140890797 20.2878771553206860 3.4007300130942268 0.0158541211761416 0.0552359416684117 0.7315105552398365
|
||||
9700 115.4929532760288566 -5025.3998314232658231 -5041.4491160600928197 16.0492846368267905 -5012.5665063170945359 -28.8826097429975661 91.3632592320088435 22.0163104129693679 20.2933608101085134 3.4538398927567129 0.0107475116378220 0.0533745483954881 0.2423720374586358
|
||||
9800 116.6568448590114713 -5025.4060328077384838 -5041.9441021408847519 16.5380693331462645 -5013.0600606356529170 -28.8840415052319699 94.1457485409718657 22.0171383538163319 20.2984615200070699 3.4418436654918718 0.0055691607030332 0.0484221019754039 -0.4555881967899209
|
||||
9900 117.8205927780363709 -5025.4059535467131354 -5042.1049269188570179 16.6989733721435982 -5013.0326878900941665 -29.0722390287624570 95.0617219166735055 22.0173811382230866 20.3029333126575224 3.3777971259251927 -0.0004208957689860 0.0399240614860051 -0.7066946321892024
|
||||
10000 118.9876703190384433 -5025.4003336218293043 -5041.6049734892676497 16.2046398674379049 -5012.5657855383178685 -29.0391879509508577 92.2476450802604688 22.0169880599834578 20.3062835677433853 3.3276491770664203 -0.0079109840550239 0.0265739864961977 -0.1844514587639604
|
||||
Loop time of 118.988 on 4 procs for 10000 steps with 1360 atoms
|
||||
|
||||
Performance: 7.261 ns/day, 3.305 hours/ns, 84.042 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 110.45 | 112 | 113.28 | 9.6 | 94.13
|
||||
Bond | 0.0044251 | 0.0047127 | 0.0049699 | 0.3 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 5.5177 | 6.7957 | 8.3394 | 39.1 | 5.71
|
||||
Output | 0.012448 | 0.013192 | 0.015358 | 1.1 | 0.01
|
||||
Modify | 0.060352 | 0.062195 | 0.063596 | 0.5 | 0.05
|
||||
Other | | 0.114 | | | 0.10
|
||||
|
||||
Nlocal: 340 ave 344 max 334 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 4628 ave 4634 max 4624 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 66301.5 ave 67860 max 63963 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
|
||||
Total # of neighbors = 265206
|
||||
Ave neighs/atom = 195.004
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:59
|
||||
|
|
@ -0,0 +1,266 @@
|
|||
info: xyz2data 18:31, Mon 27-02-2017
|
||||
256 atoms
|
||||
2 atom types
|
||||
|
||||
0.00000000 17.04000000 xlo xhi
|
||||
0.00000000 19.67609717 ylo yhi
|
||||
-20.00000000 40.00000000 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 0.00000000 0.00000000 0.00000000
|
||||
2 1 1.42000000 0.00000000 0.00000000
|
||||
3 2 1.42000000 0.00000000 3.30000000
|
||||
4 2 2.84000000 0.00000000 3.30000000
|
||||
5 1 2.13000000 1.22975607 0.00000000
|
||||
6 1 3.55000000 1.22975607 0.00000000
|
||||
7 2 3.55000000 1.22975607 3.30000000
|
||||
8 2 4.97000000 1.22975607 3.30000000
|
||||
9 1 0.00000000 2.45951215 0.00000000
|
||||
10 1 1.42000000 2.45951215 0.00000000
|
||||
11 2 1.42000000 2.45951215 3.30000000
|
||||
12 2 2.84000000 2.45951215 3.30000000
|
||||
13 1 2.13000000 3.68926822 0.00000000
|
||||
14 1 3.55000000 3.68926822 0.00000000
|
||||
15 2 3.55000000 3.68926822 3.30000000
|
||||
16 2 4.97000000 3.68926822 3.30000000
|
||||
17 1 0.00000000 4.91902429 0.00000000
|
||||
18 1 1.42000000 4.91902429 0.00000000
|
||||
19 2 1.42000000 4.91902429 3.30000000
|
||||
20 2 2.84000000 4.91902429 3.30000000
|
||||
21 1 2.13000000 6.14878037 0.00000000
|
||||
22 1 3.55000000 6.14878037 0.00000000
|
||||
23 2 3.55000000 6.14878037 3.30000000
|
||||
24 2 4.97000000 6.14878037 3.30000000
|
||||
25 1 0.00000000 7.37853644 0.00000000
|
||||
26 1 1.42000000 7.37853644 0.00000000
|
||||
27 2 1.42000000 7.37853644 3.30000000
|
||||
28 2 2.84000000 7.37853644 3.30000000
|
||||
29 1 2.13000000 8.60829251 0.00000000
|
||||
30 1 3.55000000 8.60829251 0.00000000
|
||||
31 2 3.55000000 8.60829251 3.30000000
|
||||
32 2 4.97000000 8.60829251 3.30000000
|
||||
33 1 0.00000000 9.83804859 0.00000000
|
||||
34 1 1.42000000 9.83804859 0.00000000
|
||||
35 2 1.42000000 9.83804859 3.30000000
|
||||
36 2 2.84000000 9.83804859 3.30000000
|
||||
37 1 2.13000000 11.06780466 0.00000000
|
||||
38 1 3.55000000 11.06780466 0.00000000
|
||||
39 2 3.55000000 11.06780466 3.30000000
|
||||
40 2 4.97000000 11.06780466 3.30000000
|
||||
41 1 0.00000000 12.29756073 0.00000000
|
||||
42 1 1.42000000 12.29756073 0.00000000
|
||||
43 2 1.42000000 12.29756073 3.30000000
|
||||
44 2 2.84000000 12.29756073 3.30000000
|
||||
45 1 2.13000000 13.52731681 0.00000000
|
||||
46 1 3.55000000 13.52731681 0.00000000
|
||||
47 2 3.55000000 13.52731681 3.30000000
|
||||
48 2 4.97000000 13.52731681 3.30000000
|
||||
49 1 0.00000000 14.75707288 0.00000000
|
||||
50 1 1.42000000 14.75707288 0.00000000
|
||||
51 2 1.42000000 14.75707288 3.30000000
|
||||
52 2 2.84000000 14.75707288 3.30000000
|
||||
53 1 2.13000000 15.98682895 0.00000000
|
||||
54 1 3.55000000 15.98682895 0.00000000
|
||||
55 2 3.55000000 15.98682895 3.30000000
|
||||
56 2 4.97000000 15.98682895 3.30000000
|
||||
57 1 0.00000000 17.21658503 0.00000000
|
||||
58 1 1.42000000 17.21658503 0.00000000
|
||||
59 2 1.42000000 17.21658503 3.30000000
|
||||
60 2 2.84000000 17.21658503 3.30000000
|
||||
61 1 2.13000000 18.44634110 0.00000000
|
||||
62 1 3.55000000 18.44634110 0.00000000
|
||||
63 2 3.55000000 18.44634110 3.30000000
|
||||
64 2 4.97000000 18.44634110 3.30000000
|
||||
65 1 4.26000000 0.00000000 0.00000000
|
||||
66 1 5.68000000 0.00000000 0.00000000
|
||||
67 2 5.68000000 0.00000000 3.30000000
|
||||
68 2 7.10000000 0.00000000 3.30000000
|
||||
69 1 6.39000000 1.22975607 0.00000000
|
||||
70 1 7.81000000 1.22975607 0.00000000
|
||||
71 2 7.81000000 1.22975607 3.30000000
|
||||
72 2 9.23000000 1.22975607 3.30000000
|
||||
73 1 4.26000000 2.45951215 0.00000000
|
||||
74 1 5.68000000 2.45951215 0.00000000
|
||||
75 2 5.68000000 2.45951215 3.30000000
|
||||
76 2 7.10000000 2.45951215 3.30000000
|
||||
77 1 6.39000000 3.68926822 0.00000000
|
||||
78 1 7.81000000 3.68926822 0.00000000
|
||||
79 2 7.81000000 3.68926822 3.30000000
|
||||
80 2 9.23000000 3.68926822 3.30000000
|
||||
81 1 4.26000000 4.91902429 0.00000000
|
||||
82 1 5.68000000 4.91902429 0.00000000
|
||||
83 2 5.68000000 4.91902429 3.30000000
|
||||
84 2 7.10000000 4.91902429 3.30000000
|
||||
85 1 6.39000000 6.14878037 0.00000000
|
||||
86 1 7.81000000 6.14878037 0.00000000
|
||||
87 2 7.81000000 6.14878037 3.30000000
|
||||
88 2 9.23000000 6.14878037 3.30000000
|
||||
89 1 4.26000000 7.37853644 0.00000000
|
||||
90 1 5.68000000 7.37853644 0.00000000
|
||||
91 2 5.68000000 7.37853644 3.30000000
|
||||
92 2 7.10000000 7.37853644 3.30000000
|
||||
93 1 6.39000000 8.60829251 0.00000000
|
||||
94 1 7.81000000 8.60829251 0.00000000
|
||||
95 2 7.81000000 8.60829251 3.30000000
|
||||
96 2 9.23000000 8.60829251 3.30000000
|
||||
97 1 4.26000000 9.83804859 0.00000000
|
||||
98 1 5.68000000 9.83804859 0.00000000
|
||||
99 2 5.68000000 9.83804859 3.30000000
|
||||
100 2 7.10000000 9.83804859 3.30000000
|
||||
101 1 6.39000000 11.06780466 0.00000000
|
||||
102 1 7.81000000 11.06780466 0.00000000
|
||||
103 2 7.81000000 11.06780466 3.30000000
|
||||
104 2 9.23000000 11.06780466 3.30000000
|
||||
105 1 4.26000000 12.29756073 0.00000000
|
||||
106 1 5.68000000 12.29756073 0.00000000
|
||||
107 2 5.68000000 12.29756073 3.30000000
|
||||
108 2 7.10000000 12.29756073 3.30000000
|
||||
109 1 6.39000000 13.52731681 0.00000000
|
||||
110 1 7.81000000 13.52731681 0.00000000
|
||||
111 2 7.81000000 13.52731681 3.30000000
|
||||
112 2 9.23000000 13.52731681 3.30000000
|
||||
113 1 4.26000000 14.75707288 0.00000000
|
||||
114 1 5.68000000 14.75707288 0.00000000
|
||||
115 2 5.68000000 14.75707288 3.30000000
|
||||
116 2 7.10000000 14.75707288 3.30000000
|
||||
117 1 6.39000000 15.98682895 0.00000000
|
||||
118 1 7.81000000 15.98682895 0.00000000
|
||||
119 2 7.81000000 15.98682895 3.30000000
|
||||
120 2 9.23000000 15.98682895 3.30000000
|
||||
121 1 4.26000000 17.21658503 0.00000000
|
||||
122 1 5.68000000 17.21658503 0.00000000
|
||||
123 2 5.68000000 17.21658503 3.30000000
|
||||
124 2 7.10000000 17.21658503 3.30000000
|
||||
125 1 6.39000000 18.44634110 0.00000000
|
||||
126 1 7.81000000 18.44634110 0.00000000
|
||||
127 2 7.81000000 18.44634110 3.30000000
|
||||
128 2 9.23000000 18.44634110 3.30000000
|
||||
129 1 8.52000000 0.00000000 0.00000000
|
||||
130 1 9.94000000 0.00000000 0.00000000
|
||||
131 2 9.94000000 0.00000000 3.30000000
|
||||
132 2 11.36000000 0.00000000 3.30000000
|
||||
133 1 10.65000000 1.22975607 0.00000000
|
||||
134 1 12.07000000 1.22975607 0.00000000
|
||||
135 2 12.07000000 1.22975607 3.30000000
|
||||
136 2 13.49000000 1.22975607 3.30000000
|
||||
137 1 8.52000000 2.45951215 0.00000000
|
||||
138 1 9.94000000 2.45951215 0.00000000
|
||||
139 2 9.94000000 2.45951215 3.30000000
|
||||
140 2 11.36000000 2.45951215 3.30000000
|
||||
141 1 10.65000000 3.68926822 0.00000000
|
||||
142 1 12.07000000 3.68926822 0.00000000
|
||||
143 2 12.07000000 3.68926822 3.30000000
|
||||
144 2 13.49000000 3.68926822 3.30000000
|
||||
145 1 8.52000000 4.91902429 0.00000000
|
||||
146 1 9.94000000 4.91902429 0.00000000
|
||||
147 2 9.94000000 4.91902429 3.30000000
|
||||
148 2 11.36000000 4.91902429 3.30000000
|
||||
149 1 10.65000000 6.14878037 0.00000000
|
||||
150 1 12.07000000 6.14878037 0.00000000
|
||||
151 2 12.07000000 6.14878037 3.30000000
|
||||
152 2 13.49000000 6.14878037 3.30000000
|
||||
153 1 8.52000000 7.37853644 0.00000000
|
||||
154 1 9.94000000 7.37853644 0.00000000
|
||||
155 2 9.94000000 7.37853644 3.30000000
|
||||
156 2 11.36000000 7.37853644 3.30000000
|
||||
157 1 10.65000000 8.60829251 0.00000000
|
||||
158 1 12.07000000 8.60829251 0.00000000
|
||||
159 2 12.07000000 8.60829251 3.30000000
|
||||
160 2 13.49000000 8.60829251 3.30000000
|
||||
161 1 8.52000000 9.83804859 0.00000000
|
||||
162 1 9.94000000 9.83804859 0.00000000
|
||||
163 2 9.94000000 9.83804859 3.30000000
|
||||
164 2 11.36000000 9.83804859 3.30000000
|
||||
165 1 10.65000000 11.06780466 0.00000000
|
||||
166 1 12.07000000 11.06780466 0.00000000
|
||||
167 2 12.07000000 11.06780466 3.30000000
|
||||
168 2 13.49000000 11.06780466 3.30000000
|
||||
169 1 8.52000000 12.29756073 0.00000000
|
||||
170 1 9.94000000 12.29756073 0.00000000
|
||||
171 2 9.94000000 12.29756073 3.30000000
|
||||
172 2 11.36000000 12.29756073 3.30000000
|
||||
173 1 10.65000000 13.52731681 0.00000000
|
||||
174 1 12.07000000 13.52731681 0.00000000
|
||||
175 2 12.07000000 13.52731681 3.30000000
|
||||
176 2 13.49000000 13.52731681 3.30000000
|
||||
177 1 8.52000000 14.75707288 0.00000000
|
||||
178 1 9.94000000 14.75707288 0.00000000
|
||||
179 2 9.94000000 14.75707288 3.30000000
|
||||
180 2 11.36000000 14.75707288 3.30000000
|
||||
181 1 10.65000000 15.98682895 0.00000000
|
||||
182 1 12.07000000 15.98682895 0.00000000
|
||||
183 2 12.07000000 15.98682895 3.30000000
|
||||
184 2 13.49000000 15.98682895 3.30000000
|
||||
185 1 8.52000000 17.21658503 0.00000000
|
||||
186 1 9.94000000 17.21658503 0.00000000
|
||||
187 2 9.94000000 17.21658503 3.30000000
|
||||
188 2 11.36000000 17.21658503 3.30000000
|
||||
189 1 10.65000000 18.44634110 0.00000000
|
||||
190 1 12.07000000 18.44634110 0.00000000
|
||||
191 2 12.07000000 18.44634110 3.30000000
|
||||
192 2 13.49000000 18.44634110 3.30000000
|
||||
193 1 12.78000000 0.00000000 0.00000000
|
||||
194 1 14.20000000 0.00000000 0.00000000
|
||||
195 2 14.20000000 0.00000000 3.30000000
|
||||
196 2 15.62000000 0.00000000 3.30000000
|
||||
197 1 14.91000000 1.22975607 0.00000000
|
||||
198 1 16.33000000 1.22975607 0.00000000
|
||||
199 2 16.33000000 1.22975607 3.30000000
|
||||
200 2 17.75000000 1.22975607 3.30000000
|
||||
201 1 12.78000000 2.45951215 0.00000000
|
||||
202 1 14.20000000 2.45951215 0.00000000
|
||||
203 2 14.20000000 2.45951215 3.30000000
|
||||
204 2 15.62000000 2.45951215 3.30000000
|
||||
205 1 14.91000000 3.68926822 0.00000000
|
||||
206 1 16.33000000 3.68926822 0.00000000
|
||||
207 2 16.33000000 3.68926822 3.30000000
|
||||
208 2 17.75000000 3.68926822 3.30000000
|
||||
209 1 12.78000000 4.91902429 0.00000000
|
||||
210 1 14.20000000 4.91902429 0.00000000
|
||||
211 2 14.20000000 4.91902429 3.30000000
|
||||
212 2 15.62000000 4.91902429 3.30000000
|
||||
213 1 14.91000000 6.14878037 0.00000000
|
||||
214 1 16.33000000 6.14878037 0.00000000
|
||||
215 2 16.33000000 6.14878037 3.30000000
|
||||
216 2 17.75000000 6.14878037 3.30000000
|
||||
217 1 12.78000000 7.37853644 0.00000000
|
||||
218 1 14.20000000 7.37853644 0.00000000
|
||||
219 2 14.20000000 7.37853644 3.30000000
|
||||
220 2 15.62000000 7.37853644 3.30000000
|
||||
221 1 14.91000000 8.60829251 0.00000000
|
||||
222 1 16.33000000 8.60829251 0.00000000
|
||||
223 2 16.33000000 8.60829251 3.30000000
|
||||
224 2 17.75000000 8.60829251 3.30000000
|
||||
225 1 12.78000000 9.83804859 0.00000000
|
||||
226 1 14.20000000 9.83804859 0.00000000
|
||||
227 2 14.20000000 9.83804859 3.30000000
|
||||
228 2 15.62000000 9.83804859 3.30000000
|
||||
229 1 14.91000000 11.06780466 0.00000000
|
||||
230 1 16.33000000 11.06780466 0.00000000
|
||||
231 2 16.33000000 11.06780466 3.30000000
|
||||
232 2 17.75000000 11.06780466 3.30000000
|
||||
233 1 12.78000000 12.29756073 0.00000000
|
||||
234 1 14.20000000 12.29756073 0.00000000
|
||||
235 2 14.20000000 12.29756073 3.30000000
|
||||
236 2 15.62000000 12.29756073 3.30000000
|
||||
237 1 14.91000000 13.52731681 0.00000000
|
||||
238 1 16.33000000 13.52731681 0.00000000
|
||||
239 2 16.33000000 13.52731681 3.30000000
|
||||
240 2 17.75000000 13.52731681 3.30000000
|
||||
241 1 12.78000000 14.75707288 0.00000000
|
||||
242 1 14.20000000 14.75707288 0.00000000
|
||||
243 2 14.20000000 14.75707288 3.30000000
|
||||
244 2 15.62000000 14.75707288 3.30000000
|
||||
245 1 14.91000000 15.98682895 0.00000000
|
||||
246 1 16.33000000 15.98682895 0.00000000
|
||||
247 2 16.33000000 15.98682895 3.30000000
|
||||
248 2 17.75000000 15.98682895 3.30000000
|
||||
249 1 12.78000000 17.21658503 0.00000000
|
||||
250 1 14.20000000 17.21658503 0.00000000
|
||||
251 2 14.20000000 17.21658503 3.30000000
|
||||
252 2 15.62000000 17.21658503 3.30000000
|
||||
253 1 14.91000000 18.44634110 0.00000000
|
||||
254 1 16.33000000 18.44634110 0.00000000
|
||||
255 2 16.33000000 18.44634110 3.30000000
|
||||
256 2 17.75000000 18.44634110 3.30000000
|
||||
|
|
@ -0,0 +1,139 @@
|
|||
info: xyz2data 11:52, Tue 28-02-2017
|
||||
129 atoms
|
||||
2 atom types
|
||||
|
||||
0.00000000 17.04000000 xlo xhi
|
||||
0.00000000 19.67609717 ylo yhi
|
||||
-10.00000000 40.00000000 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 0.00000000 0.00000000 0.00000000
|
||||
2 1 1.42000000 0.00000000 0.00000000
|
||||
3 1 2.13000000 1.22975607 0.00000000
|
||||
4 1 3.55000000 1.22975607 0.00000000
|
||||
5 1 0.00000000 2.45951215 0.00000000
|
||||
6 1 1.42000000 2.45951215 0.00000000
|
||||
7 1 2.13000000 3.68926822 0.00000000
|
||||
8 1 3.55000000 3.68926822 0.00000000
|
||||
9 1 0.00000000 4.91902429 0.00000000
|
||||
10 1 1.42000000 4.91902429 0.00000000
|
||||
11 1 2.13000000 6.14878037 0.00000000
|
||||
12 1 3.55000000 6.14878037 0.00000000
|
||||
13 1 0.00000000 7.37853644 0.00000000
|
||||
14 1 1.42000000 7.37853644 0.00000000
|
||||
15 1 2.13000000 8.60829251 0.00000000
|
||||
16 1 3.55000000 8.60829251 0.00000000
|
||||
17 1 0.00000000 9.83804859 0.00000000
|
||||
18 1 1.42000000 9.83804859 0.00000000
|
||||
19 1 2.13000000 11.06780466 0.00000000
|
||||
20 1 3.55000000 11.06780466 0.00000000
|
||||
21 1 0.00000000 12.29756073 0.00000000
|
||||
22 1 1.42000000 12.29756073 0.00000000
|
||||
23 1 2.13000000 13.52731681 0.00000000
|
||||
24 1 3.55000000 13.52731681 0.00000000
|
||||
25 1 0.00000000 14.75707288 0.00000000
|
||||
26 1 1.42000000 14.75707288 0.00000000
|
||||
27 1 2.13000000 15.98682895 0.00000000
|
||||
28 1 3.55000000 15.98682895 0.00000000
|
||||
29 1 0.00000000 17.21658503 0.00000000
|
||||
30 1 1.42000000 17.21658503 0.00000000
|
||||
31 1 2.13000000 18.44634110 0.00000000
|
||||
32 1 3.55000000 18.44634110 0.00000000
|
||||
33 1 4.26000000 0.00000000 0.00000000
|
||||
34 1 5.68000000 0.00000000 0.00000000
|
||||
35 1 6.39000000 1.22975607 0.00000000
|
||||
36 1 7.81000000 1.22975607 0.00000000
|
||||
37 1 4.26000000 2.45951215 0.00000000
|
||||
38 1 5.68000000 2.45951215 0.00000000
|
||||
39 1 6.39000000 3.68926822 0.00000000
|
||||
40 1 7.81000000 3.68926822 0.00000000
|
||||
41 1 4.26000000 4.91902429 0.00000000
|
||||
42 1 5.68000000 4.91902429 0.00000000
|
||||
43 1 6.39000000 6.14878037 0.00000000
|
||||
44 1 7.81000000 6.14878037 0.00000000
|
||||
45 1 4.26000000 7.37853644 0.00000000
|
||||
46 1 5.68000000 7.37853644 0.00000000
|
||||
47 1 6.39000000 8.60829251 0.00000000
|
||||
48 1 7.81000000 8.60829251 0.00000000
|
||||
49 1 4.26000000 9.83804859 0.00000000
|
||||
50 1 5.68000000 9.83804859 0.00000000
|
||||
51 1 6.39000000 11.06780466 0.00000000
|
||||
52 1 7.81000000 11.06780466 0.00000000
|
||||
53 1 4.26000000 12.29756073 0.00000000
|
||||
54 1 5.68000000 12.29756073 0.00000000
|
||||
55 1 6.39000000 13.52731681 0.00000000
|
||||
56 1 7.81000000 13.52731681 0.00000000
|
||||
57 1 4.26000000 14.75707288 0.00000000
|
||||
58 1 5.68000000 14.75707288 0.00000000
|
||||
59 1 6.39000000 15.98682895 0.00000000
|
||||
60 1 7.81000000 15.98682895 0.00000000
|
||||
61 1 4.26000000 17.21658503 0.00000000
|
||||
62 1 5.68000000 17.21658503 0.00000000
|
||||
63 1 6.39000000 18.44634110 0.00000000
|
||||
64 1 7.81000000 18.44634110 0.00000000
|
||||
65 1 8.52000000 0.00000000 0.00000000
|
||||
66 1 9.94000000 0.00000000 0.00000000
|
||||
67 1 10.65000000 1.22975607 0.00000000
|
||||
68 1 12.07000000 1.22975607 0.00000000
|
||||
69 1 8.52000000 2.45951215 0.00000000
|
||||
70 1 9.94000000 2.45951215 0.00000000
|
||||
71 1 10.65000000 3.68926822 0.00000000
|
||||
72 1 12.07000000 3.68926822 0.00000000
|
||||
73 1 8.52000000 4.91902429 0.00000000
|
||||
74 1 9.94000000 4.91902429 0.00000000
|
||||
75 1 10.65000000 6.14878037 0.00000000
|
||||
76 1 12.07000000 6.14878037 0.00000000
|
||||
77 1 8.52000000 7.37853644 0.00000000
|
||||
78 1 9.94000000 7.37853644 0.00000000
|
||||
79 1 10.65000000 8.60829251 0.00000000
|
||||
80 1 12.07000000 8.60829251 0.00000000
|
||||
81 1 8.52000000 9.83804859 0.00000000
|
||||
82 1 9.94000000 9.83804859 0.00000000
|
||||
83 1 10.65000000 11.06780466 0.00000000
|
||||
84 1 12.07000000 11.06780466 0.00000000
|
||||
85 1 8.52000000 12.29756073 0.00000000
|
||||
86 1 9.94000000 12.29756073 0.00000000
|
||||
87 1 10.65000000 13.52731681 0.00000000
|
||||
88 1 12.07000000 13.52731681 0.00000000
|
||||
89 1 8.52000000 14.75707288 0.00000000
|
||||
90 1 9.94000000 14.75707288 0.00000000
|
||||
91 1 10.65000000 15.98682895 0.00000000
|
||||
92 1 12.07000000 15.98682895 0.00000000
|
||||
93 1 8.52000000 17.21658503 0.00000000
|
||||
94 1 9.94000000 17.21658503 0.00000000
|
||||
95 1 10.65000000 18.44634110 0.00000000
|
||||
96 1 12.07000000 18.44634110 0.00000000
|
||||
97 1 12.78000000 0.00000000 0.00000000
|
||||
98 1 14.20000000 0.00000000 0.00000000
|
||||
99 1 14.91000000 1.22975607 0.00000000
|
||||
100 1 16.33000000 1.22975607 0.00000000
|
||||
101 1 12.78000000 2.45951215 0.00000000
|
||||
102 1 14.20000000 2.45951215 0.00000000
|
||||
103 1 14.91000000 3.68926822 0.00000000
|
||||
104 1 16.33000000 3.68926822 0.00000000
|
||||
105 1 12.78000000 4.91902429 0.00000000
|
||||
106 1 14.20000000 4.91902429 0.00000000
|
||||
107 1 14.91000000 6.14878037 0.00000000
|
||||
108 1 16.33000000 6.14878037 0.00000000
|
||||
109 1 12.78000000 7.37853644 0.00000000
|
||||
110 1 14.20000000 7.37853644 0.00000000
|
||||
111 1 14.91000000 8.60829251 0.00000000
|
||||
112 1 16.33000000 8.60829251 0.00000000
|
||||
113 1 12.78000000 9.83804859 0.00000000
|
||||
114 1 14.20000000 9.83804859 0.00000000
|
||||
115 1 14.91000000 11.06780466 0.00000000
|
||||
116 1 16.33000000 11.06780466 0.00000000
|
||||
117 1 12.78000000 12.29756073 0.00000000
|
||||
118 1 14.20000000 12.29756073 0.00000000
|
||||
119 1 14.91000000 13.52731681 0.00000000
|
||||
120 1 16.33000000 13.52731681 0.00000000
|
||||
121 1 12.78000000 14.75707288 0.00000000
|
||||
122 1 14.20000000 14.75707288 0.00000000
|
||||
123 1 14.91000000 15.98682895 0.00000000
|
||||
124 1 16.33000000 15.98682895 0.00000000
|
||||
125 1 12.78000000 17.21658503 0.00000000
|
||||
126 1 14.20000000 17.21658503 0.00000000
|
||||
127 1 14.91000000 18.44634110 0.00000000
|
||||
128 1 16.33000000 18.44634110 0.00000000
|
||||
129 2 10.00000000 10.00000000 3.30000000
|
||||
|
|
@ -0,0 +1,45 @@
|
|||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use 2 atom types so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data data.graphene-adsorbant # read lammps data file
|
||||
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
||||
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
# Separate atom groups
|
||||
group membrane type 1
|
||||
group adsorbant type 2
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay kolmogorov/crespi/z 14.0
|
||||
####################################################################
|
||||
pair_coeff * * none
|
||||
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
|
||||
####################################################################
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.0001
|
||||
fix thermostat adsorbant nve
|
||||
fix rigid_membrane membrane setforce 0 0 0
|
||||
compute COM1 membrane com
|
||||
compute COM2 adsorbant com
|
||||
############################
|
||||
|
||||
# Output
|
||||
#dump 1 all xyz 100 trajec.xyz
|
||||
#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
|
||||
thermo 100
|
||||
thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
|
||||
thermo_modify line one format float %14.8f
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 10000
|
||||
|
|
@ -0,0 +1,45 @@
|
|||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use 2 atom types so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data data.bilayer-graphene # read lammps data file
|
||||
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
||||
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
# Separate atom groups
|
||||
group membrane type 1
|
||||
group adsorbant type 2
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.airebo C C # chemical
|
||||
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
|
||||
####################################################################
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.0001
|
||||
velocity all create 300.0 12345
|
||||
fix thermostat all nve
|
||||
compute COM1 membrane com
|
||||
compute COM2 adsorbant com
|
||||
############################
|
||||
|
||||
# Output
|
||||
#dump 1 all xyz 100 trajec.xyz
|
||||
#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
|
||||
thermo 10
|
||||
thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
|
||||
thermo_modify line one format float %14.8f
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
|
|
@ -0,0 +1,189 @@
|
|||
LAMMPS (17 Nov 2016)
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use 2 atom types so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data data.graphene-adsorbant # read lammps data file
|
||||
orthogonal box = (0 0 -10) to (17.04 19.6761 40)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
129 atoms
|
||||
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
||||
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
# Separate atom groups
|
||||
group membrane type 1
|
||||
128 atoms in group membrane
|
||||
group adsorbant type 2
|
||||
1 atoms in group adsorbant
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay kolmogorov/crespi/z 14.0
|
||||
####################################################################
|
||||
pair_coeff * * none
|
||||
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
|
||||
####################################################################
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.0001
|
||||
fix thermostat adsorbant nve
|
||||
fix rigid_membrane membrane setforce 0 0 0
|
||||
compute COM1 membrane com
|
||||
compute COM2 adsorbant com
|
||||
############################
|
||||
|
||||
# Output
|
||||
#dump 1 all xyz 100 trajec.xyz
|
||||
#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
|
||||
thermo 100
|
||||
thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
|
||||
thermo_modify line one format float %14.8f
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
2 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 16
|
||||
ghost atom cutoff = 16
|
||||
binsize = 8 -> bins = 3 3 7
|
||||
Memory usage per processor = 2.48399 Mbytes
|
||||
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
|
||||
0 0.00000000 -0.02562011 -0.02562011 0.00000000 0.00000000 3.30000000
|
||||
100 0.01000000 -0.02562011 -0.02584808 0.01377831 0.00000000 3.30302413
|
||||
200 0.02000000 -0.02562011 -0.02650010 0.05318658 0.00000000 3.31198892
|
||||
300 0.03000000 -0.02562011 -0.02748822 0.11290898 0.00000000 3.32658305
|
||||
400 0.04000000 -0.02562011 -0.02868854 0.18545625 0.00000000 3.34632324
|
||||
500 0.05000000 -0.02562011 -0.02996656 0.26269978 0.00000000 3.37059992
|
||||
600 0.06000000 -0.02562011 -0.03120006 0.33725276 0.00000000 3.39872815
|
||||
700 0.07000000 -0.02562011 -0.03229421 0.40338328 0.00000000 3.42999603
|
||||
800 0.08000000 -0.02562011 -0.03318758 0.45737874 0.00000000 3.46370507
|
||||
900 0.09000000 -0.02562011 -0.03385069 0.49745690 0.00000000 3.49919977
|
||||
1000 0.10000000 -0.02562011 -0.03428002 0.52340564 0.00000000 3.53588638
|
||||
1100 0.11000000 -0.02562011 -0.03449041 0.53612164 0.00000000 3.57324216
|
||||
1200 0.12000000 -0.02562011 -0.03450775 0.53717016 0.00000000 3.61081749
|
||||
1300 0.13000000 -0.02562011 -0.03436312 0.52842859 0.00000000 3.64823296
|
||||
1400 0.14000000 -0.02562011 -0.03408851 0.51183115 0.00000000 3.68517357
|
||||
1500 0.15000000 -0.02562011 -0.03371417 0.48920613 0.00000000 3.72138134
|
||||
1600 0.16000000 -0.02562011 -0.03326714 0.46218758 0.00000000 3.75664759
|
||||
1700 0.17000000 -0.02562011 -0.03277063 0.43217815 0.00000000 3.79080541
|
||||
1800 0.18000000 -0.02562011 -0.03224395 0.40034589 0.00000000 3.82372274
|
||||
1900 0.19000000 -0.02562011 -0.03170282 0.36763982 0.00000000 3.85529629
|
||||
2000 0.20000000 -0.02562011 -0.03115972 0.33481494 0.00000000 3.88544626
|
||||
2100 0.21000000 -0.02562011 -0.03062440 0.30246010 0.00000000 3.91411185
|
||||
2200 0.22000000 -0.02562011 -0.03010433 0.27102702 0.00000000 3.94124749
|
||||
2300 0.23000000 -0.02562011 -0.02960514 0.24085558 0.00000000 3.96681976
|
||||
2400 0.24000000 -0.02562011 -0.02913096 0.21219623 0.00000000 3.99080483
|
||||
2500 0.25000000 -0.02562011 -0.02868478 0.18522907 0.00000000 4.01318637
|
||||
2600 0.26000000 -0.02562011 -0.02826867 0.16007955 0.00000000 4.03395384
|
||||
2700 0.27000000 -0.02562011 -0.02788403 0.13683143 0.00000000 4.05310113
|
||||
2800 0.28000000 -0.02562011 -0.02753171 0.11553708 0.00000000 4.07062542
|
||||
2900 0.29000000 -0.02562011 -0.02721220 0.09622581 0.00000000 4.08652629
|
||||
3000 0.30000000 -0.02562011 -0.02692571 0.07891041 0.00000000 4.10080498
|
||||
3100 0.31000000 -0.02562011 -0.02667226 0.06359229 0.00000000 4.11346382
|
||||
3200 0.32000000 -0.02562011 -0.02645177 0.05026555 0.00000000 4.12450573
|
||||
3300 0.33000000 -0.02562011 -0.02626406 0.03892009 0.00000000 4.13393390
|
||||
3400 0.34000000 -0.02562011 -0.02610893 0.02954399 0.00000000 4.14175142
|
||||
3500 0.35000000 -0.02562011 -0.02598618 0.02212545 0.00000000 4.14796110
|
||||
3600 0.36000000 -0.02562011 -0.02589566 0.01665409 0.00000000 4.15256529
|
||||
3700 0.37000000 -0.02562011 -0.02583722 0.01312208 0.00000000 4.15556569
|
||||
3800 0.38000000 -0.02562011 -0.02581079 0.01152492 0.00000000 4.15696329
|
||||
3900 0.39000000 -0.02562011 -0.02581636 0.01186148 0.00000000 4.15675830
|
||||
4000 0.40000000 -0.02562011 -0.02585398 0.01413478 0.00000000 4.15495012
|
||||
4100 0.41000000 -0.02562011 -0.02592375 0.01835185 0.00000000 4.15153731
|
||||
4200 0.42000000 -0.02562011 -0.02602587 0.02452390 0.00000000 4.14651764
|
||||
4300 0.43000000 -0.02562011 -0.02616057 0.03266513 0.00000000 4.13988811
|
||||
4400 0.44000000 -0.02562011 -0.02632813 0.04279292 0.00000000 4.13164506
|
||||
4500 0.45000000 -0.02562011 -0.02652889 0.05492664 0.00000000 4.12178432
|
||||
4600 0.46000000 -0.02562011 -0.02676317 0.06908643 0.00000000 4.11030130
|
||||
4700 0.47000000 -0.02562011 -0.02703129 0.08529164 0.00000000 4.09719124
|
||||
4800 0.48000000 -0.02562011 -0.02733352 0.10355859 0.00000000 4.08244950
|
||||
4900 0.49000000 -0.02562011 -0.02767004 0.12389788 0.00000000 4.06607186
|
||||
5000 0.50000000 -0.02562011 -0.02804086 0.14631034 0.00000000 4.04805502
|
||||
5100 0.51000000 -0.02562011 -0.02844575 0.17078211 0.00000000 4.02839708
|
||||
5200 0.52000000 -0.02562011 -0.02888415 0.19727899 0.00000000 4.00709829
|
||||
5300 0.53000000 -0.02562011 -0.02935502 0.22573844 0.00000000 3.98416189
|
||||
5400 0.54000000 -0.02562011 -0.02985670 0.25605986 0.00000000 3.95959511
|
||||
5500 0.55000000 -0.02562011 -0.03038669 0.28809268 0.00000000 3.93341053
|
||||
5600 0.56000000 -0.02562011 -0.03094143 0.32162137 0.00000000 3.90562766
|
||||
5700 0.57000000 -0.02562011 -0.03151597 0.35634628 0.00000000 3.87627492
|
||||
5800 0.58000000 -0.02562011 -0.03210361 0.39186361 0.00000000 3.84539210
|
||||
5900 0.59000000 -0.02562011 -0.03269556 0.42764084 0.00000000 3.81303330
|
||||
6000 0.60000000 -0.02562011 -0.03328042 0.46299030 0.00000000 3.77927044
|
||||
6100 0.61000000 -0.02562011 -0.03384380 0.49704060 0.00000000 3.74419758
|
||||
6200 0.62000000 -0.02562011 -0.03436783 0.52871353 0.00000000 3.70793588
|
||||
6300 0.63000000 -0.02562011 -0.03483104 0.55670974 0.00000000 3.67063945
|
||||
6400 0.64000000 -0.02562011 -0.03520832 0.57951248 0.00000000 3.63250187
|
||||
6500 0.65000000 -0.02562011 -0.03547159 0.59542438 0.00000000 3.59376331
|
||||
6600 0.66000000 -0.02562011 -0.03559125 0.60265655 0.00000000 3.55471782
|
||||
6700 0.67000000 -0.02562011 -0.03553879 0.59948637 0.00000000 3.51572023
|
||||
6800 0.68000000 -0.02562011 -0.03529110 0.58451568 0.00000000 3.47719153
|
||||
6900 0.69000000 -0.02562011 -0.03483635 0.55703035 0.00000000 3.43962129
|
||||
7000 0.70000000 -0.02562011 -0.03418150 0.51745146 0.00000000 3.40356509
|
||||
7100 0.71000000 -0.02562011 -0.03336032 0.46781889 0.00000000 3.36963482
|
||||
7200 0.72000000 -0.02562011 -0.03243997 0.41219328 0.00000000 3.33847933
|
||||
7300 0.73000000 -0.02562011 -0.03152342 0.35679665 0.00000000 3.31075400
|
||||
7400 0.74000000 -0.02562011 -0.03074422 0.30970201 0.00000000 3.28707906
|
||||
7500 0.75000000 -0.02562011 -0.03025182 0.27994115 0.00000000 3.26798907
|
||||
7600 0.76000000 -0.02562011 -0.03018799 0.27608346 0.00000000 3.25387900
|
||||
7700 0.77000000 -0.02562011 -0.03065928 0.30456818 0.00000000 3.24495492
|
||||
7800 0.78000000 -0.02562011 -0.03171321 0.36826788 0.00000000 3.24119821
|
||||
7900 0.79000000 -0.02562011 -0.03332635 0.46576624 0.00000000 3.24235091
|
||||
8000 0.80000000 -0.02562011 -0.03540847 0.59160963 0.00000000 3.24792582
|
||||
8100 0.81000000 -0.02562011 -0.03782107 0.73742737 0.00000000 3.25723999
|
||||
8200 0.82000000 -0.02562011 -0.04040358 0.89351498 0.00000000 3.26946524
|
||||
8300 0.83000000 -0.02562011 -0.04299943 1.05040805 0.00000000 3.28368734
|
||||
8400 0.84000000 -0.02562011 -0.04547588 1.20008497 0.00000000 3.29896495
|
||||
8500 0.85000000 -0.02562011 -0.04773539 1.33664998 0.00000000 3.31438148
|
||||
8600 0.86000000 -0.02562011 -0.04971913 1.45654768 0.00000000 3.32908572
|
||||
8700 0.87000000 -0.02562011 -0.05140498 1.55844058 0.00000000 3.34231951
|
||||
8800 0.88000000 -0.02562011 -0.05280154 1.64284923 0.00000000 3.35343297
|
||||
8900 0.89000000 -0.02562011 -0.05394019 1.71166905 0.00000000 3.36188901
|
||||
9000 0.90000000 -0.02562011 -0.05486563 1.76760281 0.00000000 3.36725955
|
||||
9100 0.91000000 -0.02562011 -0.05562624 1.81357448 0.00000000 3.36921674
|
||||
9200 0.92000000 -0.02562011 -0.05626439 1.85214388 0.00000000 3.36752214
|
||||
9300 0.93000000 -0.02562011 -0.05680723 1.88495335 0.00000000 3.36201704
|
||||
9400 0.94000000 -0.02562011 -0.05725852 1.91222952 0.00000000 3.35261669
|
||||
9500 0.95000000 -0.02562011 -0.05759110 1.93233038 0.00000000 3.33931122
|
||||
9600 0.96000000 -0.02562011 -0.05774152 1.94142215 0.00000000 3.32217490
|
||||
9700 0.97000000 -0.02562011 -0.05760814 1.93336063 0.00000000 3.30138553
|
||||
9800 0.98000000 -0.02562012 -0.05705439 1.89989139 0.00000000 3.27725394
|
||||
9900 0.99000000 -0.02562012 -0.05592079 1.83137685 0.00000000 3.25026233
|
||||
10000 1.00000000 -0.02562012 -0.05404919 1.71825669 0.00000000 3.22110695
|
||||
Loop time of 0.381846 on 1 procs for 10000 steps with 129 atoms
|
||||
|
||||
Performance: 226.269 ns/day, 0.106 hours/ns, 26188.568 timesteps/s
|
||||
131.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.30936 | 0.30936 | 0.30936 | 0.0 | 81.02
|
||||
Neigh | 0.000139 | 0.000139 | 0.000139 | 0.0 | 0.04
|
||||
Comm | 0.051287 | 0.051287 | 0.051287 | 0.0 | 13.43
|
||||
Output | 0.00181 | 0.00181 | 0.00181 | 0.0 | 0.47
|
||||
Modify | 0.005645 | 0.005645 | 0.005645 | 0.0 | 1.48
|
||||
Other | | 0.01361 | | | 3.56
|
||||
|
||||
Nlocal: 129 ave 129 max 129 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1867 ave 1867 max 1867 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 290 ave 290 max 290 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 290
|
||||
Ave neighs/atom = 2.24806
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,192 @@
|
|||
LAMMPS (17 Nov 2016)
|
||||
# Initialization
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
|
||||
# System and atom definition
|
||||
# we use 2 atom types so that inter- and intra-layer
|
||||
# interactions can be specified separately
|
||||
read_data data.bilayer-graphene # read lammps data file
|
||||
orthogonal box = (0 0 -20) to (17.04 19.6761 40)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
256 atoms
|
||||
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
||||
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Neighbor update settings
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1
|
||||
neigh_modify delay 0
|
||||
neigh_modify check yes
|
||||
# Separate atom groups
|
||||
group membrane type 1
|
||||
128 atoms in group membrane
|
||||
group adsorbant type 2
|
||||
128 atoms in group adsorbant
|
||||
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.airebo C C # chemical
|
||||
Reading potential file CH.airebo with DATE: 2011-10-25
|
||||
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
|
||||
####################################################################
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.0001
|
||||
velocity all create 300.0 12345
|
||||
fix thermostat all nve
|
||||
compute COM1 membrane com
|
||||
compute COM2 adsorbant com
|
||||
############################
|
||||
|
||||
# Output
|
||||
#dump 1 all xyz 100 trajec.xyz
|
||||
#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
|
||||
thermo 10
|
||||
thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
|
||||
thermo_modify line one format float %14.8f
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
3 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 16
|
||||
ghost atom cutoff = 16
|
||||
binsize = 8 -> bins = 3 3 8
|
||||
Memory usage per processor = 3.22197 Mbytes
|
||||
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
|
||||
0 0.00000000 -1888.67041214 -1898.55881323 300.00000000 0.00000000 3.30000000
|
||||
10 0.00100000 -1888.67037221 -1898.21029897 289.42778520 -0.00020126 3.30020126
|
||||
20 0.00200000 -1888.67021541 -1897.22943612 259.67456089 -0.00041357 3.30041357
|
||||
30 0.00300000 -1888.66999308 -1895.86681311 218.34126559 -0.00063673 3.30063673
|
||||
40 0.00400000 -1888.66978354 -1894.47163830 176.02000692 -0.00087055 3.30087055
|
||||
50 0.00500000 -1888.66966068 -1893.37123377 142.63902862 -0.00111486 3.30111486
|
||||
60 0.00600000 -1888.66966132 -1892.75822749 124.04127205 -0.00136952 3.30136952
|
||||
70 0.00700000 -1888.66976974 -1892.63445751 120.28297808 -0.00163441 3.30163441
|
||||
80 0.00800000 -1888.66992867 -1892.83467462 126.35245792 -0.00190946 3.30190946
|
||||
90 0.00900000 -1888.67006868 -1893.11387069 134.81862145 -0.00219458 3.30219458
|
||||
100 0.01000000 -1888.67013621 -1893.25481851 139.09272853 -0.00248973 3.30248973
|
||||
110 0.01100000 -1888.67011201 -1893.15155790 135.96068294 -0.00279489 3.30279489
|
||||
120 0.01200000 -1888.67001496 -1892.84002960 126.51230266 -0.00311004 3.30311004
|
||||
130 0.01300000 -1888.66988997 -1892.47004238 115.29120968 -0.00343519 3.30343519
|
||||
140 0.01400000 -1888.66979230 -1892.23503116 108.16426723 -0.00377038 3.30377038
|
||||
150 0.01500000 -1888.66976478 -1892.28630583 109.72070257 -0.00411562 3.30411562
|
||||
160 0.01600000 -1888.66982054 -1892.66640611 121.25071190 -0.00447099 3.30447099
|
||||
170 0.01700000 -1888.66993790 -1893.28862637 140.12442721 -0.00483654 3.30483654
|
||||
180 0.01800000 -1888.67007017 -1893.97029258 160.80119589 -0.00521235 3.30521235
|
||||
190 0.01900000 -1888.67016712 -1894.50458787 177.00801243 -0.00559851 3.30559851
|
||||
200 0.02000000 -1888.67019459 -1894.73890106 184.11590729 -0.00599512 3.30599512
|
||||
210 0.02100000 -1888.67014420 -1894.62906014 180.78501932 -0.00640230 3.30640230
|
||||
220 0.02200000 -1888.67003680 -1894.25249103 169.36370738 -0.00682016 3.30682016
|
||||
230 0.02300000 -1888.66991386 -1893.77601613 154.91186767 -0.00724883 3.30724883
|
||||
240 0.02400000 -1888.66982525 -1893.38995084 143.20188490 -0.00768845 3.30768845
|
||||
250 0.02500000 -1888.66980630 -1893.23138936 138.39193056 -0.00813913 3.30813913
|
||||
260 0.02600000 -1888.66986130 -1893.32993923 141.38012476 -0.00860097 3.30860097
|
||||
270 0.02700000 -1888.66996305 -1893.60070606 149.59171763 -0.00907408 3.30907408
|
||||
280 0.02800000 -1888.67006686 -1893.88587226 158.24010433 -0.00955849 3.30955849
|
||||
290 0.02900000 -1888.67012981 -1894.02402669 162.42960292 -0.01005424 3.31005424
|
||||
300 0.03000000 -1888.67012722 -1893.91715234 159.18726627 -0.01056129 3.31056129
|
||||
310 0.03100000 -1888.67005731 -1893.57037242 148.66857852 -0.01107957 3.31107957
|
||||
320 0.03200000 -1888.66994573 -1893.09358619 134.20694883 -0.01160898 3.31160898
|
||||
330 0.03300000 -1888.66983589 -1892.66132663 121.09614207 -0.01214935 3.31214935
|
||||
340 0.03400000 -1888.66977410 -1892.44446345 114.51869676 -0.01270046 3.31270046
|
||||
350 0.03500000 -1888.66978826 -1892.53901235 117.38674604 -0.01326207 3.31326207
|
||||
360 0.03600000 -1888.66987439 -1892.92337288 129.04508371 -0.01383390 3.31383390
|
||||
370 0.03700000 -1888.66999800 -1893.46445570 145.45701555 -0.01441561 3.31441561
|
||||
380 0.03800000 -1888.67010960 -1893.97065516 160.81100020 -0.01500688 3.31500688
|
||||
390 0.03900000 -1888.67016540 -1894.26835818 169.84119247 -0.01560734 3.31560734
|
||||
400 0.04000000 -1888.67014667 -1894.26967975 169.88185546 -0.01621664 3.31621664
|
||||
410 0.04100000 -1888.67006166 -1894.00321069 161.80014280 -0.01683442 3.31683442
|
||||
420 0.04200000 -1888.66994367 -1893.60086324 149.59707418 -0.01746033 3.31746033
|
||||
430 0.04300000 -1888.66984058 -1893.24559841 138.82197275 -0.01809405 3.31809405
|
||||
440 0.04400000 -1888.66979399 -1893.09727874 134.32357877 -0.01873527 3.31873527
|
||||
450 0.04500000 -1888.66982139 -1893.22837442 138.30000378 -0.01938373 3.31938373
|
||||
460 0.04600000 -1888.66990972 -1893.59670383 149.47191354 -0.02003918 3.32003918
|
||||
470 0.04700000 -1888.67002173 -1894.06542598 163.68887743 -0.02070143 3.32070143
|
||||
480 0.04800000 -1888.67011389 -1894.46010842 175.66018439 -0.02137030 3.32137030
|
||||
490 0.04900000 -1888.67015175 -1894.63688098 181.02206322 -0.02204565 3.32204565
|
||||
500 0.05000000 -1888.67012158 -1894.53632221 177.97216882 -0.02272740 3.32272740
|
||||
510 0.05100000 -1888.67003762 -1894.20444731 167.90610436 -0.02341547 3.32341547
|
||||
520 0.05200000 -1888.66993151 -1893.77231066 154.79891353 -0.02410981 3.32410981
|
||||
530 0.05300000 -1888.66984505 -1893.40525927 143.66572038 -0.02481040 3.32481040
|
||||
540 0.05400000 -1888.66981408 -1893.23762083 138.58074854 -0.02551724 3.32551724
|
||||
550 0.05500000 -1888.66985005 -1893.31793594 141.01630317 -0.02623032 3.32623032
|
||||
560 0.05600000 -1888.66993737 -1893.59069013 149.28862751 -0.02694963 3.32694963
|
||||
570 0.05700000 -1888.67003852 -1893.92089571 159.30352588 -0.02767517 3.32767517
|
||||
580 0.05800000 -1888.67011322 -1894.15124753 166.28980524 -0.02840691 3.32840691
|
||||
590 0.05900000 -1888.67013192 -1894.16548041 166.72104345 -0.02914478 3.32914478
|
||||
600 0.06000000 -1888.67008713 -1893.93443318 159.71275856 -0.02988871 3.32988871
|
||||
610 0.06100000 -1888.66999438 -1893.52841656 147.39760646 -0.03063856 3.33063856
|
||||
620 0.06200000 -1888.66988809 -1893.09235021 134.17119963 -0.03139416 3.33139416
|
||||
630 0.06300000 -1888.66980996 -1892.79172016 125.05288240 -0.03215531 3.33215531
|
||||
640 0.06400000 -1888.66979261 -1892.74755390 123.71346730 -0.03292176 3.33292176
|
||||
650 0.06500000 -1888.66984332 -1892.98665459 130.96590324 -0.03369323 3.33369323
|
||||
660 0.06600000 -1888.66994245 -1893.42999868 144.41332389 -0.03446937 3.33446937
|
||||
670 0.06700000 -1888.67005233 -1893.92310681 159.37018806 -0.03524986 3.33524986
|
||||
680 0.06800000 -1888.67013309 -1894.29451581 170.63575808 -0.03603430 3.33603430
|
||||
690 0.06900000 -1888.67015452 -1894.41878117 174.40514192 -0.03682229 3.33682229
|
||||
700 0.07000000 -1888.67010897 -1894.26288036 169.67671530 -0.03761343 3.33761343
|
||||
710 0.07100000 -1888.67001367 -1893.89812904 158.61357114 -0.03840729 3.33840729
|
||||
720 0.07200000 -1888.66990378 -1893.47348746 145.73388454 -0.03920344 3.33920344
|
||||
730 0.07300000 -1888.66982212 -1893.15984839 136.22099960 -0.04000148 3.34000148
|
||||
740 0.07400000 -1888.66980109 -1893.08373746 133.91254029 -0.04080098 3.34080098
|
||||
750 0.07500000 -1888.66984794 -1893.27755511 139.79127024 -0.04160156 3.34160156
|
||||
760 0.07600000 -1888.66994215 -1893.66837365 151.64528967 -0.04240282 3.34240282
|
||||
770 0.07700000 -1888.67004554 -1894.10941206 165.02263027 -0.04320441 3.34320441
|
||||
780 0.07800000 -1888.67011702 -1894.43947545 175.03411436 -0.04400599 3.34400599
|
||||
790 0.07900000 -1888.67013297 -1894.54590471 178.26254255 -0.04480726 3.34480726
|
||||
800 0.08000000 -1888.67008751 -1894.40384142 173.95392406 -0.04560792 3.34560792
|
||||
810 0.08100000 -1888.66999923 -1894.08389003 164.24973321 -0.04640773 3.34640773
|
||||
820 0.08200000 -1888.66990447 -1893.72313979 153.30795965 -0.04720647 3.34720647
|
||||
830 0.08300000 -1888.66984367 -1893.46839190 145.58111626 -0.04800393 3.34800393
|
||||
840 0.08400000 -1888.66984156 -1893.41412536 143.93481093 -0.04879995 3.34879995
|
||||
850 0.08500000 -1888.66989670 -1893.56426154 148.48805553 -0.04959439 3.34959439
|
||||
860 0.08600000 -1888.66998222 -1893.83463719 156.68827294 -0.05038713 3.35038713
|
||||
870 0.08700000 -1888.67006171 -1894.09325045 164.53181920 -0.05117805 3.35117805
|
||||
880 0.08800000 -1888.67010273 -1894.21712661 168.28880100 -0.05196706 3.35196706
|
||||
890 0.08900000 -1888.67008993 -1894.14263950 166.02935656 -0.05275408 3.35275408
|
||||
900 0.09000000 -1888.67002891 -1893.89014571 158.37090587 -0.05353904 3.35353904
|
||||
910 0.09100000 -1888.66994326 -1893.55535709 148.21649469 -0.05432186 3.35432186
|
||||
920 0.09200000 -1888.66986526 -1893.27257949 139.63979178 -0.05510247 3.35510247
|
||||
930 0.09300000 -1888.66982730 -1893.16330891 136.32582949 -0.05588078 3.35588078
|
||||
940 0.09400000 -1888.66984631 -1893.28643285 140.06065785 -0.05665670 3.35665670
|
||||
950 0.09500000 -1888.66991503 -1893.61245342 149.94957268 -0.05743015 3.35743015
|
||||
960 0.09600000 -1888.67000691 -1894.03423922 162.74316516 -0.05820101 3.35820101
|
||||
970 0.09700000 -1888.67008649 -1894.40848025 174.09469037 -0.05896915 3.35896915
|
||||
980 0.09800000 -1888.67012436 -1894.61056767 180.22458605 -0.05973444 3.35973444
|
||||
990 0.09900000 -1888.67010608 -1894.58107659 179.33042338 -0.06049672 3.36049672
|
||||
1000 0.10000000 -1888.67003981 -1894.34773305 172.25312330 -0.06125581 3.36125581
|
||||
Loop time of 2.21183 on 4 procs for 1000 steps with 256 atoms
|
||||
|
||||
Performance: 3.906 ns/day, 6.144 hours/ns, 452.115 timesteps/s
|
||||
120.2% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.9363 | 1.9928 | 2.0303 | 2.5 | 90.10
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.16714 | 0.20465 | 0.26123 | 7.8 | 9.25
|
||||
Output | 0.002469 | 0.0028505 | 0.003949 | 1.2 | 0.13
|
||||
Modify | 0.002423 | 0.0026275 | 0.002853 | 0.4 | 0.12
|
||||
Other | | 0.008904 | | | 0.40
|
||||
|
||||
Nlocal: 64 ave 64 max 64 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1265 ave 1265 max 1265 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 11824 ave 11824 max 11824 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 23648 ave 23648 max 23648 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 94592
|
||||
Ave neighs/atom = 369.5
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
Loading…
Reference in New Issue