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added some documentation and reference example

This commit is contained in:
vishalkenchan 2017-10-20 12:03:22 +02:00
parent 71c4edda51
commit e284545c5b
5 changed files with 474 additions and 7 deletions
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21
doc/src/pair_cs.txt
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@ -9,12 +9,13 @@
pair_style born/coul/long/cs command :h3
pair_style buck/coul/long/cs command :h3
pair_style born/coul/dsf/cs command :h3
pair_style born/coul/wolf/cs command :h3
[Syntax:]
pair_style style args :pre
style = {born/coul/long/cs} or {buck/coul/long/cs} or {born/coul/dsf/cs}
style = {born/coul/long/cs} or {buck/coul/long/cs} or {born/coul/dsf/cs} or {born/coul/wolf/cs}
args = list of arguments for a particular style :ul
{born/coul/long/cs} args = cutoff (cutoff2)
cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
@ -26,6 +27,10 @@ args = list of arguments for a particular style :ul
alpha = damping parameter (inverse distance units)
cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (distance units) :pre
{born/coul/wolf/cs} args = alpha cutoff (cutoff2)
alpha = damping parameter (inverse distance units)
cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
[Examples:]
@ -41,6 +46,10 @@ pair_style born/coul/dsf/cs 0.1 10.0 12.0
pair_coeff * * 0.0 1.00 0.00 0.00 0.00
pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre
pair_style born/coul/wolf/cs 0.25 10.0 12.0
pair_coeff * * 0.0 1.00 0.00 0.00 0.00
pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre
[Description:]
These pair styles are designed to be used with the adiabatic
@ -73,13 +82,21 @@ the core and shell, epsilon is the dielectric constant and r_min is the
minimal distance.
The pair style {born/coul/dsf/cs} is identical to the
"pair_style born/coul/dsf"_pair_born.html style, which uses the
"pair_style born/coul/dsf"_pair_born.html style, which uses
the damped shifted force model as in "coul/dsf"_pair_coul.html
to compute the Coulomb contribution. This approach does not require
a long-range solver, thus the only correction is the addition of a
minimal distance to avoid the possible r = 0.0 case for a
core/shell pair.
The pair style {born/coul/wolf/cs} is identical to the
"pair_style born/coul/wolf"_pair_born.html style, which uses
the Wolf summation as in "coul/wolf"_pair_coul.html to compute
the Coulomb contribution. This approach does not require
a long-range solver, thus the only correction is the addition of a
minimal distance to avoid the possible r = 0.0 case for a
core/shell pair.
[Restrictions:]
These pair styles are part of the CORESHELL package. They are only

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examples/coreshell/in.coreshell.wolf Normal file
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# Testsystem for core-shell model compared to Mitchel and Finchham
# Shamelessly copied from in.coreshell.dsf but this script uses Wolf summation.
# ------------------------ INITIALIZATION ----------------------------
units metal
dimension 3
boundary p p p
atom_style full
# ----------------------- ATOM DEFINITION ----------------------------
fix csinfo all property/atom i_CSID
read_data data.coreshell fix csinfo NULL CS-Info
group cores type 1 2
group shells type 3 4
neighbor 2.0 bin
comm_modify vel yes
# ------------------------ FORCE FIELDS ------------------------------
pair_style born/coul/wolf/cs 0.1 20.0 20.0 # A, rho, sigma=0, C, D
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
bond_style harmonic
bond_coeff 1 63.014 0.0
bond_coeff 2 25.724 0.0
# ------------------------ Equilibration Run -------------------------------
reset_timestep 0
thermo 50
thermo_style custom step etotal pe ke temp press &
epair evdwl ecoul elong ebond fnorm fmax vol
compute CSequ all temp/cs cores shells
# output via chunk method
#compute prop all property/atom i_CSID
#compute cs_chunk all chunk/atom c_prop
#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
thermo_modify temp CSequ
# velocity bias option
velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
velocity all scale 1427 temp CSequ
fix thermoberendsen all temp/berendsen 1427 1427 0.4
fix nve all nve
fix_modify thermoberendsen temp CSequ
# 2 fmsec timestep
timestep 0.002
run 500
unfix thermoberendsen
# ------------------------ Dynamic Run -------------------------------
run 1000

190
examples/coreshell/log.22Sep17.coreshell.wolf.g++.1 Normal file
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@ -0,0 +1,190 @@
LAMMPS (22 Sep 2017)
# Testsystem for core-shell model compared to Mitchel and Finchham
# Shamelessly copied from in.coreshell.dsf but this script uses Wolf summation.
# ------------------------ INITIALIZATION ----------------------------
units metal
dimension 3
boundary p p p
atom_style full
# ----------------------- ATOM DEFINITION ----------------------------
fix csinfo all property/atom i_CSID
read_data data.coreshell fix csinfo NULL CS-Info
orthogonal box = (0 0 0) to (24.096 24.096 24.096)
1 by 1 by 1 MPI processor grid
reading atoms ...
432 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
216 bonds
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
group cores type 1 2
216 atoms in group cores
group shells type 3 4
216 atoms in group shells
neighbor 2.0 bin
comm_modify vel yes
# ------------------------ FORCE FIELDS ------------------------------
pair_style born/coul/wolf/cs 0.1 20.0 20.0 # A, rho, sigma=0, C, D
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
bond_style harmonic
bond_coeff 1 63.014 0.0
bond_coeff 2 25.724 0.0
# ------------------------ Equilibration Run -------------------------------
reset_timestep 0
thermo 50
thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol
compute CSequ all temp/cs cores shells
# output via chunk method
#compute prop all property/atom i_CSID
#compute cs_chunk all chunk/atom c_prop
#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
thermo_modify temp CSequ
# velocity bias option
velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 22
ghost atom cutoff = 22
binsize = 11, bins = 3 3 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair born/coul/wolf/cs, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
velocity all scale 1427 temp CSequ
fix thermoberendsen all temp/berendsen 1427 1427 0.4
fix nve all nve
fix_modify thermoberendsen temp CSequ
# 2 fmsec timestep
timestep 0.002
run 500
Per MPI rank memory allocation (min/avg/max) = 8.59 | 8.59 | 8.59 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
0 -637.41039 -677.06805 39.657659 1427 -21302.622 -677.06805 1.6320365 -678.70009 0 0 1.2935454e-14 3.3306691e-15 13990.5
50 -635.62711 -667.67134 32.044236 1153.0465 -4533.0717 -669.45724 37.76997 -707.22721 0 1.7858939 9.6844521 2.2001656 13990.5
100 -632.76337 -662.83035 30.066977 1081.8989 -3492.8736 -664.98454 39.197093 -704.18164 0 2.1541967 11.063962 2.1543406 13990.5
150 -630.82538 -663.70056 32.875182 1182.9464 -74.330324 -666.12202 46.263665 -712.38569 0 2.4214607 11.739683 2.7558416 13990.5
200 -629.1541 -664.54637 35.39227 1273.5187 -1707.5508 -666.87772 41.796197 -708.67391 0 2.3313445 10.594804 3.0025376 13990.5
250 -627.86587 -662.60879 34.742918 1250.1531 -1258.7537 -665.21416 43.017024 -708.23118 0 2.6053655 10.576999 1.8400986 13990.5
300 -627.10755 -664.12897 37.021419 1332.1403 -1891.3466 -666.39618 40.769593 -707.16577 0 2.2672094 9.412943 1.2434258 13990.5
350 -626.27558 -665.04303 38.767448 1394.9676 -1436.8514 -667.47081 41.854746 -709.32556 0 2.4277827 10.304721 1.977594 13990.5
400 -625.55098 -661.86388 36.312896 1306.6455 -331.92076 -664.4632 44.426542 -708.88975 0 2.599325 11.081635 2.1734468 13990.5
450 -624.88626 -661.07359 36.187328 1302.1272 -2325.834 -663.6031 39.662697 -703.26579 0 2.5295037 9.9810051 1.3068929 13990.5
500 -623.87093 -660.24145 36.370525 1308.7192 410.85324 -662.86944 45.869201 -708.73864 0 2.6279856 10.592785 1.8162326 13990.5
Loop time of 11.7065 on 1 procs for 500 steps with 432 atoms
Performance: 7.381 ns/day, 3.252 hours/ns, 42.711 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.535 | 11.535 | 11.535 | 0.0 | 98.54
Bond | 0.001443 | 0.001443 | 0.001443 | 0.0 | 0.01
Neigh | 0.10952 | 0.10952 | 0.10952 | 0.0 | 0.94
Comm | 0.048796 | 0.048796 | 0.048796 | 0.0 | 0.42
Output | 0.00038695 | 0.00038695 | 0.00038695 | 0.0 | 0.00
Modify | 0.0067511 | 0.0067511 | 0.0067511 | 0.0 | 0.06
Other | | 0.004243 | | | 0.04
Nlocal: 432 ave 432 max 432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9328 ave 9328 max 9328 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 297280 ave 297280 max 297280 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 297280
Ave neighs/atom = 688.148
Ave special neighs/atom = 1
Neighbor list builds = 21
Dangerous builds = 0
unfix thermoberendsen
# ------------------------ Dynamic Run -------------------------------
run 1000
Per MPI rank memory allocation (min/avg/max) = 8.59 | 8.59 | 8.59 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
500 -623.87093 -660.24145 36.370525 1308.7192 410.85324 -662.86944 45.869201 -708.73864 0 2.6279856 10.592785 1.8162326 13990.5
550 -623.95762 -659.99899 36.041371 1296.8752 -442.62446 -662.68699 44.004419 -706.69141 0 2.6879934 10.936057 1.7358509 13990.5
600 -624.04214 -661.21748 37.175332 1337.6785 47.615854 -663.76133 45.009742 -708.77107 0 2.5438549 11.431366 2.1185464 13990.5
650 -623.98279 -661.85255 37.86976 1362.6661 -1708.3823 -664.31138 40.933446 -705.24482 0 2.4588298 9.7960191 1.4159904 13990.5
700 -624.02941 -661.57484 37.54543 1350.9958 -124.09512 -663.95322 44.666402 -708.61962 0 2.3783801 10.518712 2.0854584 13990.5
750 -624.03935 -661.11619 37.076837 1334.1344 -1163.2721 -663.82553 42.1219 -705.94743 0 2.7093404 10.634859 1.9381654 13990.5
800 -623.98709 -659.43647 35.44938 1275.5737 -285.65702 -662.23782 44.650233 -706.88805 0 2.8013482 11.83459 3.4506407 13990.5
850 -623.96081 -661.77923 37.818422 1360.8188 -814.33212 -664.38161 42.860208 -707.24181 0 2.6023728 10.766451 2.9211132 13990.5
900 -623.96136 -662.98419 39.022831 1404.157 308.13105 -665.65877 45.053188 -710.71195 0 2.6745786 11.028799 1.8494322 13990.5
950 -623.91048 -660.63828 36.7278 1321.575 -445.31526 -663.79806 43.94833 -707.74639 0 3.1597729 11.852051 1.8238458 13990.5
1000 -623.90541 -661.03474 37.129332 1336.0233 522.57958 -663.50212 45.863261 -709.36538 0 2.4673781 10.949291 1.8614095 13990.5
1050 -624.01134 -660.99076 36.979422 1330.6291 -1710.2829 -663.67762 41.056102 -704.73372 0 2.6868521 10.86533 2.2154165 13990.5
1100 -624.02639 -660.86661 36.840225 1325.6204 1151.0236 -663.5066 47.207185 -710.71378 0 2.6399847 11.298044 1.8900703 13990.5
1150 -624.04418 -661.29819 37.254006 1340.5094 161.09847 -663.73735 45.222561 -708.95991 0 2.4391651 11.261119 2.2245673 13990.5
1200 -624.08628 -662.39932 38.313043 1378.6168 -1405.0927 -664.93121 41.728112 -706.65933 0 2.5318927 10.458041 2.1153159 13990.5
1250 -624.03036 -661.25661 37.226248 1339.5106 63.407721 -663.72719 45.086961 -708.81415 0 2.4705832 11.766021 2.2297809 13990.5
1300 -623.97475 -661.55998 37.585229 1352.4278 -763.66781 -663.80645 42.870244 -706.6767 0 2.2464703 10.098322 1.7614596 13990.5
1350 -623.93123 -660.30786 36.376631 1308.9389 -2389.8052 -663.04725 39.749029 -702.79628 0 2.7393936 10.879364 2.6622521 13990.5
1400 -623.86468 -658.44644 34.581765 1244.3543 2262.7586 -660.95368 50.10608 -711.05976 0 2.5072434 11.528291 1.7861906 13990.5
1450 -623.85494 -661.47216 37.617217 1353.5789 -1435.0174 -664.13587 41.701767 -705.83764 0 2.6637191 11.297444 2.0038345 13990.5
1500 -623.79928 -659.70124 35.901959 1291.8588 -198.39562 -662.57415 44.358482 -706.93263 0 2.872907 11.075746 2.2821286 13990.5
Loop time of 23.4119 on 1 procs for 1000 steps with 432 atoms
Performance: 7.381 ns/day, 3.252 hours/ns, 42.713 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 23.069 | 23.069 | 23.069 | 0.0 | 98.54
Bond | 0.0029275 | 0.0029275 | 0.0029275 | 0.0 | 0.01
Neigh | 0.22821 | 0.22821 | 0.22821 | 0.0 | 0.97
Comm | 0.097941 | 0.097941 | 0.097941 | 0.0 | 0.42
Output | 0.00074033 | 0.00074033 | 0.00074033 | 0.0 | 0.00
Modify | 0.0042015 | 0.0042015 | 0.0042015 | 0.0 | 0.02
Other | | 0.00865 | | | 0.04
Nlocal: 432 ave 432 max 432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9388 ave 9388 max 9388 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 297212 ave 297212 max 297212 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 297212
Ave neighs/atom = 687.991
Ave special neighs/atom = 1
Neighbor list builds = 45
Dangerous builds = 0
Total wall time: 0:00:35

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examples/coreshell/log.22Sep17.coreshell.wolf.g++.4 Normal file
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LAMMPS (22 Sep 2017)
# Testsystem for core-shell model compared to Mitchel and Finchham
# Shamelessly copied from in.coreshell.dsf but this script uses Wolf summation.
# ------------------------ INITIALIZATION ----------------------------
units metal
dimension 3
boundary p p p
atom_style full
# ----------------------- ATOM DEFINITION ----------------------------
fix csinfo all property/atom i_CSID
read_data data.coreshell fix csinfo NULL CS-Info
orthogonal box = (0 0 0) to (24.096 24.096 24.096)
1 by 2 by 2 MPI processor grid
reading atoms ...
432 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
216 bonds
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
group cores type 1 2
216 atoms in group cores
group shells type 3 4
216 atoms in group shells
neighbor 2.0 bin
comm_modify vel yes
# ------------------------ FORCE FIELDS ------------------------------
pair_style born/coul/wolf/cs 0.1 20.0 20.0 # A, rho, sigma=0, C, D
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
bond_style harmonic
bond_coeff 1 63.014 0.0
bond_coeff 2 25.724 0.0
# ------------------------ Equilibration Run -------------------------------
reset_timestep 0
thermo 50
thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol
compute CSequ all temp/cs cores shells
# output via chunk method
#compute prop all property/atom i_CSID
#compute cs_chunk all chunk/atom c_prop
#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
thermo_modify temp CSequ
# velocity bias option
velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 22
ghost atom cutoff = 22
binsize = 11, bins = 3 3 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair born/coul/wolf/cs, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
velocity all scale 1427 temp CSequ
fix thermoberendsen all temp/berendsen 1427 1427 0.4
fix nve all nve
fix_modify thermoberendsen temp CSequ
# 2 fmsec timestep
timestep 0.002
run 500
Per MPI rank memory allocation (min/avg/max) = 6.881 | 6.881 | 6.881 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
0 -637.41039 -677.06805 39.657659 1427 -21302.622 -677.06805 1.6320365 -678.70009 0 0 1.3530839e-14 3.6429193e-15 13990.5
50 -635.62704 -667.67108 32.044047 1153.0397 -4532.6842 -669.45828 37.771018 -707.2293 0 1.787201 9.6848095 2.2028349 13990.5
100 -632.76343 -662.83014 30.066711 1081.8893 -3493.0827 -664.98212 39.195967 -704.17809 0 2.151977 11.060773 2.1578583 13990.5
150 -630.82533 -663.70172 32.876385 1182.9897 -75.706974 -666.12608 46.261038 -712.38712 0 2.4243598 11.746728 2.7663319 13990.5
200 -629.15463 -664.55009 35.395466 1273.6337 -1707.9185 -666.88117 41.794868 -708.67604 0 2.331082 10.596229 3.0031523 13990.5
250 -627.86625 -662.60876 34.742511 1250.1384 -1263.5726 -665.214 43.005742 -708.21974 0 2.6052329 10.572641 1.841604 13990.5
300 -627.10829 -664.12159 37.013298 1331.8481 -1884.8587 -666.39136 40.786141 -707.1775 0 2.2697693 9.4160685 1.2472271 13990.5
350 -626.2729 -665.01858 38.745682 1394.1844 -1433.1302 -667.44315 41.864785 -709.30793 0 2.4245625 10.312641 1.9815612 13990.5
400 -625.54274 -661.84438 36.301638 1306.2404 -355.45544 -664.4483 44.370671 -708.81897 0 2.6039276 11.076154 2.1819703 13990.5
450 -624.88802 -661.12299 36.234964 1303.8413 -2356.6101 -663.6463 39.57847 -703.22477 0 2.523314 9.8995886 1.3113549 13990.5
500 -623.86344 -660.20235 36.338906 1307.5814 462.72862 -662.8515 45.983055 -708.83455 0 2.6491489 10.523732 1.6709561 13990.5
Loop time of 4.63313 on 4 procs for 500 steps with 432 atoms
Performance: 18.648 ns/day, 1.287 hours/ns, 107.919 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.8133 | 3.5934 | 4.4255 | 36.3 | 77.56
Bond | 0.00042245 | 0.00050305 | 0.00059825 | 0.0 | 0.01
Neigh | 0.0411 | 0.041561 | 0.04202 | 0.2 | 0.90
Comm | 0.15622 | 0.9884 | 1.7686 | 69.2 | 21.33
Output | 0.00028311 | 0.00031345 | 0.00040011 | 0.0 | 0.01
Modify | 0.0039899 | 0.00403 | 0.0040654 | 0.0 | 0.09
Other | | 0.004911 | | | 0.11
Nlocal: 108 ave 112 max 106 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 6531.75 ave 6611 max 6460 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 74316.2 ave 75641 max 72780 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 297265
Ave neighs/atom = 688.113
Ave special neighs/atom = 1
Neighbor list builds = 21
Dangerous builds = 0
unfix thermoberendsen
# ------------------------ Dynamic Run -------------------------------
run 1000
Per MPI rank memory allocation (min/avg/max) = 6.884 | 7.01 | 7.138 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
500 -623.86344 -660.20235 36.338906 1307.5814 462.72862 -662.8515 45.983055 -708.83455 0 2.6491489 10.523732 1.6709561 13990.5
550 -623.95339 -660.07946 36.126069 1299.9229 -362.67288 -662.8047 44.180832 -706.98553 0 2.725239 11.07199 2.0461377 13990.5
600 -624.04508 -661.27298 37.227902 1339.5701 110.39823 -663.90927 45.166569 -709.07584 0 2.6362911 11.747923 2.1846828 13990.5
650 -623.9608 -661.50573 37.544934 1350.9779 -1594.4701 -663.91531 41.226571 -705.14188 0 2.4095736 10.022027 1.6264014 13990.5
700 -624.00658 -663.55636 39.549777 1423.1181 -588.9804 -665.88666 43.124023 -709.01068 0 2.3302979 9.924587 2.1027837 13990.5
750 -623.99813 -659.97695 35.978816 1294.6243 -364.1415 -662.75959 43.973556 -706.73315 0 2.782646 11.487832 1.8799695 13990.5
800 -624.01235 -661.04908 37.036728 1332.6911 -85.655852 -663.49204 44.570117 -708.06215 0 2.4429547 11.213149 1.6792926 13990.5
850 -624.02581 -659.39933 35.373519 1272.844 -1090.9179 -662.11969 42.375064 -704.49476 0 2.7203673 11.214629 2.2907474 13990.5
900 -624.09244 -663.33386 39.241421 1412.0225 303.76207 -666.00593 45.332458 -711.33839 0 2.6720667 11.897188 2.0599033 13990.5
950 -624.04544 -661.11578 37.070341 1333.9007 1637.6438 -663.61305 48.65892 -712.27197 0 2.49727 12.343774 2.429225 13990.5
1000 -623.95457 -661.51816 37.563586 1351.6491 -851.77182 -663.83594 42.813468 -706.64941 0 2.317782 10.251422 1.6922864 13990.5
1050 -623.98731 -662.01988 38.032562 1368.5242 -2123.9075 -664.72609 39.917382 -704.64348 0 2.706218 9.600838 1.7365559 13990.5
1100 -623.9653 -659.32023 35.354929 1272.1751 -436.90576 -662.14454 44.057776 -706.20232 0 2.8243167 11.267546 2.6807602 13990.5
1150 -624.02273 -665.13902 41.116293 1479.486 -128.13268 -667.4769 44.013761 -711.49066 0 2.3378768 10.406604 1.5102324 13990.5
1200 -623.97328 -663.08042 39.107135 1407.1905 -539.63284 -665.67946 43.319308 -708.99877 0 2.599042 10.632657 1.4608707 13990.5
1250 -623.92529 -661.81902 37.893723 1363.5284 1708.0621 -664.63624 48.396874 -713.03311 0 2.8172251 11.369352 1.8836979 13990.5
1300 -623.99283 -662.19734 38.204509 1374.7114 -820.77291 -664.34556 42.656202 -707.00176 0 2.1482151 10.186898 1.7081329 13990.5
1350 -623.99798 -658.70752 34.709535 1248.9519 776.28486 -662.01647 46.925412 -708.94188 0 3.3089536 12.457581 2.5027978 13990.5
1400 -623.96941 -662.15959 38.190183 1374.1959 880.21756 -664.90452 46.628183 -711.5327 0 2.7449282 11.918894 3.0466188 13990.5
1450 -623.95068 -662.25435 38.303671 1378.2795 -391.56711 -664.7631 43.644066 -708.40716 0 2.5087493 10.465803 1.8744864 13990.5
1500 -624.00637 -661.48756 37.481185 1348.684 430.69453 -664.32151 45.704366 -710.02587 0 2.8339501 11.650821 2.0752813 13990.5
Loop time of 6.7003 on 4 procs for 1000 steps with 432 atoms
Performance: 25.790 ns/day, 0.931 hours/ns, 149.247 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.9613 | 6.0752 | 6.2064 | 4.1 | 90.67
Bond | 0.00087095 | 0.00088993 | 0.00091671 | 0.0 | 0.01
Neigh | 0.06494 | 0.064964 | 0.064987 | 0.0 | 0.97
Comm | 0.41743 | 0.54863 | 0.6626 | 13.8 | 8.19
Output | 0.00053867 | 0.00059268 | 0.00074867 | 0.0 | 0.01
Modify | 0.0013288 | 0.0013592 | 0.0013841 | 0.1 | 0.02
Other | | 0.008613 | | | 0.13
Nlocal: 108 ave 116 max 102 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 6504.5 ave 6624 max 6380 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 74267 ave 79230 max 70993 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 297068
Ave neighs/atom = 687.657
Ave special neighs/atom = 1
Neighbor list builds = 45
Dangerous builds = 0
Total wall time: 0:00:11

9
src/CORESHELL/pair_born_coul_wolf_cs.cpp
View File

@ -70,8 +70,7 @@ void PairBornCoulWolfCS::compute(int eflag, int vflag)
e_self = v_sh = 0.0;
e_shift = erfc(alf*cut_coul)/cut_coul;
f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) /
cut_coul;
f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) / cut_coul;
inum = list->inum;
ilist = list->ilist;
@ -107,9 +106,9 @@ void PairBornCoulWolfCS::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
rsq += EPSILON;
// Add EPISLON for case: r = 0; Interaction must be removed
// by special bond
rsq += EPSILON;
// Add EPISLON for case: r = 0; Interaction must be removed
// by special bond
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {