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minor cleanup in docs and updated log files for kolmogorov/crespi/full
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akohlmey committed Mar 23, 2018
1 parent 78e09e1 commit 5a341be
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42 changes: 0 additions & 42 deletions doc/src/Eqs/pair_ilp_gr_hBN.tex

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1 change: 1 addition & 0 deletions examples/USER/misc/kolmogorov_crespi_full/CC.KC-full
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LAMMPS (8 Mar 2018)
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)
1 by 1 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 etotal pe ke v_REBO v_KC temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify line one format float %.10f
thermo_modify flush yes norm no lost warn #ignore

#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes

###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair rebo, perpetual, 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) = 16.96 | 16.96 | 16.96 Mbytes
Step TotEng PotEng KinEng v_REBO v_KC Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
0 -5025.3867722725 -5040.0767391239 14.6899668514 -5011.2636297759 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108
100 -5025.3962433293 -5041.3829775585 15.9867342292 -5012.5109377234 -28.8720398351 91.0071804888 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069014
200 -5025.3942568861 -5041.9638220670 16.5695651809 -5012.7804299195 -29.1833921475 94.3250439654 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265577
300 -5025.3919463074 -5040.9705419367 15.5785956293 -5012.0510295102 -28.9195124265 88.6837826830 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745908
400 -5025.3965376948 -5041.6929964127 16.2964587179 -5012.6418090677 -29.0511873450 92.7703393702 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704496
500 -5025.4050172900 -5042.1712310053 16.7662137153 -5013.1850218645 -28.9862091408 95.4444989087 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066
600 -5025.3985715734 -5041.2158947893 15.8173232159 -5012.4875319345 -28.7283628548 90.0427797270 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001093
700 -5025.3997561572 -5041.6276721306 16.2279159734 -5012.7093581188 -28.9183140118 92.3801482386 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311564
800 -5025.3967603736 -5042.3401685987 16.9434082251 -5013.3044877099 -29.0356808888 96.4532085367 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492925
900 -5025.3984542801 -5042.2820667481 16.8836124680 -5013.4066841442 -28.8753826039 96.1128111061 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648638
1000 -5025.3988185618 -5041.9160822433 16.5172636815 -5012.8147737982 -29.1013084450 94.0273088606 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119
Loop time of 156.142 on 1 procs for 1000 steps with 1360 atoms

Performance: 0.553 ns/day, 43.373 hours/ns, 6.404 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 155.99 | 155.99 | 155.99 | 0.0 | 99.90
Bond | 0.00075769 | 0.00075769 | 0.00075769 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.084217 | 0.084217 | 0.084217 | 0.0 | 0.05
Output | 0.0016122 | 0.0016122 | 0.0016122 | 0.0 | 0.00
Modify | 0.034797 | 0.034797 | 0.034797 | 0.0 | 0.02
Other | | 0.02838 | | | 0.02

Nlocal: 1360 ave 1360 max 1360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7964 ave 7964 max 7964 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 265206 ave 265206 max 265206 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 265206
Ave neighs/atom = 195.004
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:02:36
Original file line number Diff line number Diff line change
@@ -0,0 +1,136 @@
LAMMPS (8 Mar 2018)
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 etotal pe ke v_REBO v_KC temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify line one format float %.10f
thermo_modify flush yes norm no lost warn #ignore

#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes

###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair rebo, perpetual, 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) = 11.13 | 11.13 | 11.13 Mbytes
Step TotEng PotEng KinEng v_REBO v_KC Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
0 -5025.3867722725 -5040.0767391239 14.6899668514 -5011.2636297759 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108
100 -5025.3962433293 -5041.3829775585 15.9867342292 -5012.5109377234 -28.8720398351 91.0071804888 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069014
200 -5025.3942568861 -5041.9638220670 16.5695651809 -5012.7804299195 -29.1833921475 94.3250439654 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265577
300 -5025.3919463074 -5040.9705419367 15.5785956293 -5012.0510295103 -28.9195124265 88.6837826830 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745908
400 -5025.3965376948 -5041.6929964127 16.2964587179 -5012.6418090677 -29.0511873450 92.7703393702 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704496
500 -5025.4050172900 -5042.1712310053 16.7662137153 -5013.1850218645 -28.9862091408 95.4444989088 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066
600 -5025.3985715734 -5041.2158947893 15.8173232159 -5012.4875319345 -28.7283628548 90.0427797270 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001093
700 -5025.3997561572 -5041.6276721306 16.2279159734 -5012.7093581188 -28.9183140118 92.3801482386 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311564
800 -5025.3967603736 -5042.3401685987 16.9434082251 -5013.3044877099 -29.0356808888 96.4532085367 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492925
900 -5025.3984542801 -5042.2820667481 16.8836124680 -5013.4066841442 -28.8753826039 96.1128111061 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648638
1000 -5025.3988185618 -5041.9160822433 16.5172636815 -5012.8147737983 -29.1013084450 94.0273088606 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119
Loop time of 42.5422 on 4 procs for 1000 steps with 1360 atoms

Performance: 2.031 ns/day, 11.817 hours/ns, 23.506 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 39.928 | 40.992 | 42.377 | 15.8 | 96.36
Bond | 0.0003643 | 0.00043392 | 0.00048113 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.12253 | 1.5076 | 2.5698 | 82.1 | 3.54
Output | 0.0012577 | 0.0013637 | 0.0016453 | 0.4 | 0.00
Modify | 0.010833 | 0.012247 | 0.013317 | 0.9 | 0.03
Other | | 0.02864 | | | 0.07

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: 0:00:42
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