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eliminating the discrepancies

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This commit is contained in:
Wengen Ouyang
2021-01-11 08:43:15 +02:00
parent 45fab72fdc
commit 86264c85a5
3 changed files with 202 additions and 2 deletions
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99
examples/USER/misc/tersoff_shift/shift0.05_300K_after_change_corrected2.lmp Normal file
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@ -0,0 +1,99 @@
LAMMPS (30 Nov 2020)
# Initialization
units metal
boundary p p p
atom_style charge
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN-momolayer-5nm.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
1 by 1 by 1 MPI processor grid
reading atoms ...
880 atoms
read_data CPU = 0.008 seconds
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
######################## Potential defition ########################
pair_style tersoff shift 0.05
pair_coeff * * BNC.tersoff B N
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 4928459 loop geom
fix thermostat all nve
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke temp
#thermo_modify lost warn
thermo_modify line one format float %20.16g lost warn
###### 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 = 4.1
ghost atom cutoff = 4.1
binsize = 2.05, bins = 23 24 49
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.670 | 3.670 | 3.670 Mbytes
Step TotEng PotEng KinEng Temp
0 -6570.525999324201 -6604.6118995607 34.0859002365 300
100 -6570.310828576854 -6584.788128201215 14.47729962436111 127.4189579026445
200 -6570.372315728006 -6587.981402302972 17.60908657496559 154.9827329140865
300 -6570.341402414298 -6587.005611017617 16.66420860331855 146.6665849019365
400 -6570.373381655082 -6587.812074340176 17.43869268509345 153.4830463396682
500 -6570.357279692746 -6587.139105628338 16.78182593559257 147.7017695218933
600 -6570.364533408488 -6588.19904338089 17.83450997240154 156.9667503160493
700 -6570.362000654085 -6587.514376495219 17.15237584113411 150.9630878644091
800 -6570.358394689029 -6587.200486866495 16.842092177466 148.232190383205
900 -6570.372035122417 -6588.096861613295 17.72482649087753 156.0013938422904
1000 -6570.355748883552 -6587.399428461644 17.04367957809142 150.0064201898998
Loop time of 1.44364 on 1 procs for 1000 steps with 880 atoms
Performance: 59.849 ns/day, 0.401 hours/ns, 692.693 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.4138 | 1.4138 | 1.4138 | 0.0 | 97.93
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.010364 | 0.010364 | 0.010364 | 0.0 | 0.72
Output | 0.00061329 | 0.00061329 | 0.00061329 | 0.0 | 0.04
Modify | 0.011744 | 0.011744 | 0.011744 | 0.0 | 0.81
Other | | 0.007168 | | | 0.50
Nlocal: 880.000 ave 880 max 880 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1518.00 ave 1518 max 1518 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 15840.0 ave 15840 max 15840 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15840
Ave neighs/atom = 18.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

99
examples/USER/misc/tersoff_shift/shift0.05_300K_before_change.lmp Normal file
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@ -0,0 +1,99 @@
LAMMPS (30 Nov 2020)
# Initialization
units metal
boundary p p p
atom_style charge
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN-momolayer-5nm.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
1 by 1 by 1 MPI processor grid
reading atoms ...
880 atoms
read_data CPU = 0.026 seconds
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
######################## Potential defition ########################
pair_style tersoff shift 0.05
pair_coeff * * BNC.tersoff B N
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 4928459 loop geom
fix thermostat all nve
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke temp
#thermo_modify lost warn
thermo_modify line one format float %20.16g lost warn
###### 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 = 4.1
ghost atom cutoff = 4.1
binsize = 2.05, bins = 23 24 49
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.670 | 3.670 | 3.670 Mbytes
Step TotEng PotEng KinEng Temp
0 -6570.525999324201 -6604.6118995607 34.0859002365 300
100 -6570.310828576859 -6584.788128201219 14.47729962436133 127.4189579026464
200 -6570.372315728009 -6587.981402302975 17.60908657496529 154.9827329140839
300 -6570.341402414291 -6587.005611017611 16.66420860331987 146.6665849019482
400 -6570.373381655075 -6587.812074340168 17.43869268509273 153.4830463396618
500 -6570.357279692751 -6587.139105628346 16.78182593559452 147.7017695219105
600 -6570.364533408485 -6588.199043380885 17.83450997240024 156.9667503160379
700 -6570.36200065409 -6587.514376495224 17.15237584113493 150.9630878644163
800 -6570.358394688987 -6587.200486866453 16.8420921774656 148.2321903832015
900 -6570.372035122419 -6588.096861613297 17.72482649087754 156.0013938422906
1000 -6570.355748883598 -6587.399428461688 17.04367957809044 150.0064201898913
Loop time of 1.34199 on 1 procs for 1000 steps with 880 atoms
Performance: 64.382 ns/day, 0.373 hours/ns, 745.161 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.313 | 1.313 | 1.313 | 0.0 | 97.84
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0098526 | 0.0098526 | 0.0098526 | 0.0 | 0.73
Output | 0.00069011 | 0.00069011 | 0.00069011 | 0.0 | 0.05
Modify | 0.011561 | 0.011561 | 0.011561 | 0.0 | 0.86
Other | | 0.006894 | | | 0.51
Nlocal: 880.000 ave 880 max 880 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1518.00 ave 1518 max 1518 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 15840.0 ave 15840 max 15840 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15840
Ave neighs/atom = 18.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

6
src/MANYBODY/pair_tersoff.cpp
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@ -686,8 +686,10 @@ void PairTersoff::attractive(Param *param, double prefactor,
// correct 1/r for shift in rsq
if (shift_flag == 1) {
rijinv *= sqrt((rsqij + shift*shift + 2*sqrt(rsqij)*shift)/rsqij);
rikinv *= sqrt((rsqik + shift*shift + 2*sqrt(rsqik)*shift)/rsqik);
rijinv = 1.0/(rij - shift);
rikinv = 1.0/(rik - shift);
//rijinv *= sqrt(rsqij/(rsqij + shift*shift - 2*sqrt(rsqij)*shift));
//rikinv *= sqrt(rsqik/(rsqik + shift*shift - 2*sqrt(rsqik)*shift));
}
ters_zetaterm_d(prefactor,rij_hat,rij,rijinv,rik_hat,rik,rikinv,fi,fj,fk,param);