Merge branch 'master' into charge_regulation2
This commit is contained in:
Axel Kohlmeyer
0
examples/USER/dpd/dpdrx-shardlow/kinetics.dpdrx
Executable file → Normal file
0
examples/USER/dpd/dpdrx-shardlow/kinetics.dpdrx
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examples/USER/dpd/dpdrx-shardlow/params.exp6
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examples/USER/dpd/dpdrx-shardlow/params.exp6
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examples/USER/dpd/dpdrx-shardlow/table.eos
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examples/USER/dpd/dpdrx-shardlow/table.eos
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examples/USER/dpd/dpdrx-shardlow/thermo.dpdrx
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examples/USER/dpd/dpdrx-shardlow/thermo.dpdrx
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@ -1,17 +0,0 @@
|
||||
# rx heats of formation for various molecules
|
||||
# multiple entries can be added to this file, LAMMPS reads the ones it needs
|
||||
# the entries are in LAMMPS "metal" units (eV)
|
||||
# Be sure the units are consistent with your input file
|
||||
|
||||
# format of a single entry (one or more lines):
|
||||
# species DeltaHformation
|
||||
|
||||
rdx 1.989907438211819
|
||||
hcn 1.400635733970104
|
||||
no2 0.343004076201018
|
||||
no 0.935781955892458
|
||||
h2o -2.506184777415379
|
||||
n2 0.000000000000000
|
||||
h2 0.000000000000000
|
||||
co -1.145533746031845
|
||||
co2 -4.078501848437456
|
||||
0
examples/USER/lb/confined_colloid/results64.out
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examples/USER/lb/confined_colloid/results64.out
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examples/USER/lb/dragforce/data.one_radius16d2
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examples/USER/lb/dragforce/data.one_radius16d2
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examples/USER/lb/dragforce/defaultgamma_drag.out
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examples/USER/lb/dragforce/defaultgamma_drag.out
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examples/USER/lb/dragforce/setgamma13d0_drag.out
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examples/USER/lb/dragforce/setgamma13d0_drag.out
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examples/USER/lb/fourspheres/data.four
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examples/USER/lb/fourspheres/data.four
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examples/USER/lb/fourspheres/fourspheres_velocity0d0001_defaultgamma.out
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examples/USER/lb/fourspheres/fourspheres_velocity0d0001_defaultgamma.out
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examples/USER/lb/fourspheres/fourspheres_velocity0d0001_setgamma.out
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examples/USER/lb/fourspheres/fourspheres_velocity0d0001_setgamma.out
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examples/USER/lb/microrheology/data.two
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examples/USER/lb/microrheology/data.two
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examples/USER/lb/microrheology/microrheology_defaultgamma.out
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examples/USER/lb/microrheology/microrheology_defaultgamma.out
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examples/USER/lb/microrheology/microrheology_setgamma.out
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examples/USER/lb/microrheology/microrheology_setgamma.out
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0
examples/USER/lb/planewall/data.one_radius16d2
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examples/USER/lb/planewall/data.one_radius16d2
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examples/USER/lb/planewall/wall_defaultgamma.out
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examples/USER/lb/planewall/wall_defaultgamma.out
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examples/USER/lb/planewall/wall_setgamma.out
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examples/USER/lb/planewall/wall_setgamma.out
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@ -1,12 +1,12 @@
|
||||
units real
|
||||
atom_style full
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/cut/tip4p/long 1 2 1 1 0.14714951 8
|
||||
bond_style class2
|
||||
angle_style harmonic
|
||||
kspace_style pppm/tip4p 0.0001
|
||||
pair_style lj/cut/tip4p/long 1 2 1 1 0.14714951 8
|
||||
bond_style class2
|
||||
angle_style harmonic
|
||||
kspace_style pppm/tip4p 0.0001
|
||||
|
||||
read_data data.h2o-quantum
|
||||
read_data data.h2o-quantum
|
||||
|
||||
pair_coeff * 2 0.0 0.0
|
||||
pair_coeff 1 1 0.1852 3.1589022
|
||||
@ -15,7 +15,7 @@ pair_coeff 1 1 0.1852 3.1589022
|
||||
bond_coeff 1 0.9419 607.19354 -1388.6516 1852.577
|
||||
angle_coeff 1 43.93 107.4
|
||||
|
||||
timestep 0.5
|
||||
timestep 0.5
|
||||
|
||||
# mean velocity is higher than target T because of zero point energy
|
||||
velocity all create 800.0 1112 dist gaussian mom yes
|
||||
@ -24,18 +24,17 @@ thermo 100
|
||||
thermo_style custom step temp pe ke etotal
|
||||
|
||||
# some problem
|
||||
fix 1 all gle 6 300.0 300.0 31415 qt-300k.A noneq qt-300k.C
|
||||
fix_modify 1 energy no
|
||||
fix 1 all gle 6 300.0 300.0 31415 qt-300k.A noneq qt-300k.C
|
||||
|
||||
#dump 1 all atom 100 h2o-smart.lammpstrj
|
||||
#dump 1 all atom 100 h2o-smart.lammpstrj
|
||||
|
||||
#dump 2 all image 1000 h2o-smart.*.jpg element element &
|
||||
# zoom 1.4
|
||||
#dump_modify 2 pad 5 element O H
|
||||
#dump 2 all image 1000 h2o-smart.*.jpg element element &
|
||||
# zoom 1.4
|
||||
#dump_modify 2 pad 5 element O H
|
||||
|
||||
#dump 3 all movie 100 movie.mp4 element element &
|
||||
# zoom 1.4
|
||||
#dump_modify 3 pad 5 element O H
|
||||
#dump 3 all movie 100 movie.mp4 element element &
|
||||
# zoom 1.4
|
||||
#dump_modify 3 pad 5 element O H
|
||||
|
||||
run 10000
|
||||
run 10000
|
||||
|
||||
|
||||
@ -1,12 +1,12 @@
|
||||
units real
|
||||
atom_style full
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/cut/tip4p/long 1 2 1 1 0.14714951 8
|
||||
bond_style class2
|
||||
angle_style harmonic
|
||||
kspace_style pppm/tip4p 0.0001
|
||||
pair_style lj/cut/tip4p/long 1 2 1 1 0.14714951 8
|
||||
bond_style class2
|
||||
angle_style harmonic
|
||||
kspace_style pppm/tip4p 0.0001
|
||||
|
||||
read_data data.h2o-smart
|
||||
read_data data.h2o-smart
|
||||
|
||||
pair_coeff * 2 0.0 0.0
|
||||
pair_coeff 1 1 0.1852 3.1589022
|
||||
@ -15,27 +15,26 @@ pair_coeff 1 1 0.1852 3.1589022
|
||||
bond_coeff 1 0.9419 607.19354 -1388.6516 1852.577
|
||||
angle_coeff 1 43.93 107.4
|
||||
|
||||
timestep 0.5
|
||||
timestep 0.5
|
||||
|
||||
velocity all create 300.0 1112 dist gaussian mom yes
|
||||
velocity all create 300.0 1112 dist gaussian mom yes
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step temp pe ke etotal
|
||||
|
||||
# smart sampling with GLE: best efficiency on slow diffusive modes,
|
||||
# and as good as possible on higher-frequency modes
|
||||
fix 1 all gle 6 300.0 300.0 31415 smart.A
|
||||
fix_modify 1 energy no
|
||||
fix 1 all gle 6 300.0 300.0 31415 smart.A
|
||||
|
||||
#dump 1 all atom 100 h2o-smart.lammpstrj
|
||||
#dump 1 all atom 100 h2o-smart.lammpstrj
|
||||
|
||||
#dump 2 all image 1000 h2o-smart.*.jpg element element &
|
||||
# zoom 1.4
|
||||
#dump_modify 2 pad 5 element O H
|
||||
#dump 2 all image 1000 h2o-smart.*.jpg element element &
|
||||
# zoom 1.4
|
||||
#dump_modify 2 pad 5 element O H
|
||||
|
||||
#dump 3 all movie 100 movie.mp4 element element &
|
||||
# zoom 1.4
|
||||
#dump_modify 3 pad 5 element O H
|
||||
#dump 3 all movie 100 movie.mp4 element element &
|
||||
# zoom 1.4
|
||||
#dump_modify 3 pad 5 element O H
|
||||
|
||||
run 10000
|
||||
run 10000
|
||||
|
||||
|
||||
0
examples/USER/phonon/dynamical_matrix_command/Silicon/ff-silicon.lmp
Executable file → Normal file
0
examples/USER/phonon/dynamical_matrix_command/Silicon/ff-silicon.lmp
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0
examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/amorphous_silicon.lmp
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0
examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/amorphous_silicon.lmp
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0
examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_216.lmp
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0
examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_216.lmp
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0
examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_512.lmp
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0
examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_512.lmp
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0
examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_8.lmp
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0
examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_8.lmp
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0
examples/USER/phonon/dynamical_matrix_command/Silicon/silicon_input_file.lmp
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0
examples/USER/phonon/dynamical_matrix_command/Silicon/silicon_input_file.lmp
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@ -23,13 +23,12 @@ include alpha_quartz_qtb.mod
|
||||
reset_timestep 0
|
||||
#Beta is the number of time steps between each update of the quantum bath temperature. Setting a larger beta can reduce thermal flactuations.
|
||||
fix shock all qbmsst z ${v_msst} q ${q_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix_modify shock energy yes
|
||||
variable dhug equal f_shock[1]
|
||||
variable dray equal f_shock[2]
|
||||
variable lgr_vel equal f_shock[3]
|
||||
variable lgr_pos equal f_shock[4]
|
||||
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
|
||||
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo_style custom step v_T_qm press econserve vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo 200
|
||||
timestep ${delta_t}
|
||||
run 1000
|
||||
@ -42,14 +41,14 @@ read_restart restart.1000
|
||||
include alpha_quartz_potential.mod
|
||||
#Use the same fix id and add no tscale if the system is already compressed
|
||||
fix shock all qbmsst z ${v_msst} q ${q_msst} tscale 0.0 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix_modify shock energy yes
|
||||
variable dhug equal f_shock[1]
|
||||
variable dray equal f_shock[2]
|
||||
variable lgr_vel equal f_shock[3]
|
||||
variable lgr_pos equal f_shock[4]
|
||||
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
|
||||
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo_style custom step v_T_qm press econserve vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo 500
|
||||
timestep ${delta_t}
|
||||
restart 1000 restart
|
||||
#restart 1000 restart
|
||||
run 10000 #10 ps
|
||||
shell rm restart.1000
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Jun 2020)
|
||||
LAMMPS (24 Dec 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
## This script first uses fix qtb to equilibrate alpha quartz structure to an initial state with quantum nuclear correction and then simulate shock induced phase transition through the quantum thermal bath multi-scale shock technique
|
||||
variable x_rep equal 2 #plot is made with x_rep = 8 #x-direction replication number
|
||||
@ -29,12 +29,12 @@ atom_style charge
|
||||
|
||||
#Lattice
|
||||
lattice custom 1.0 a1 4.916000 0.000000 0.000000 a2 -2.45800 4.257381 0.000000 a3 0.000000 0.000000 5.405400 basis 0.469700 0.000000 0.000000 basis 0.000000 0.469700 0.666667 basis 0.530300 0.530300 0.333333 basis 0.413500 0.266900 0.119100 basis 0.266900 0.413500 0.547567 basis 0.733100 0.146600 0.785767 basis 0.586500 0.853400 0.214233 basis 0.853400 0.586500 0.452433 basis 0.146600 0.733100 0.880900 #American Mineralogist 65 920 1980 (Space Group 154)
|
||||
Lattice spacing in x,y,z = 7.374 4.25738 5.4054
|
||||
Lattice spacing in x,y,z = 7.3740000 4.2573810 5.4054000
|
||||
|
||||
#Computational Cell
|
||||
region orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box
|
||||
create_box 2 orthorhombic_unit_cell
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (4.916 8.514762 5.4054)
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (4.9160000 8.5147620 5.4054000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 2 basis 5 2 basis 6 2 basis 7 2 basis 8 2 basis 9 2
|
||||
Created 18 atoms
|
||||
@ -43,17 +43,20 @@ replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
replicate 2 ${y_rep} ${z_rep}
|
||||
replicate 2 1 ${z_rep}
|
||||
replicate 2 1 4
|
||||
orthogonal box = (0.0 0.0 0.0) to (9.832 8.514762 21.6216)
|
||||
Replicating atoms ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (9.8320000 8.5147620 21.621600)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
144 atoms
|
||||
replicate CPU = 0.000271082 secs
|
||||
replicate CPU = 0.001 seconds
|
||||
|
||||
#Atomic Information
|
||||
mass 1 28.085500
|
||||
mass 2 15.999400
|
||||
set type 1 charge +2.4
|
||||
Setting atom values ...
|
||||
48 settings made for charge
|
||||
set type 2 charge -1.2
|
||||
Setting atom values ...
|
||||
96 settings made for charge
|
||||
|
||||
|
||||
@ -72,8 +75,8 @@ pair_coeff 1 2 table potential_SiO2.TPF Si-O ${cut_off}
|
||||
pair_coeff 1 2 table potential_SiO2.TPF Si-O 10
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O ${cut_off} #See the potential file for more information
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O 10
|
||||
WARNING: 1 of 39901 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:471)
|
||||
WARNING: 1 of 39901 force values in table O-O are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:461)
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
#Neighbor style
|
||||
@ -96,12 +99,12 @@ thermo_style custom step temp press etotal vol lx ly lz pxx pyy pzz p
|
||||
thermo 200
|
||||
run 2000 # 2 ps
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.301598
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
|
||||
G vector (1/distance) = 0.30159814
|
||||
grid = 9 8 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00117056
|
||||
estimated relative force accuracy = 8.12908e-05
|
||||
estimated absolute RMS force accuracy = 0.0011705589
|
||||
estimated relative force accuracy = 8.1290814e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 5280 1080
|
||||
Neighbor list info ...
|
||||
@ -123,42 +126,42 @@ Neighbor list info ...
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 80.09 | 80.09 | 80.09 Mbytes
|
||||
Step Temp Press TotEng Volume Lx Ly Lz Pxx Pyy Pzz Pxy Pyz Pxz
|
||||
0 0 -34026.791 -2793.6042 1810.0985 9.832 8.514762 21.6216 -37470.578 -37470.432 -27139.363 -6.4345368e-12 0.94245783 4.2212262e-10
|
||||
0 0 -34026.791 -2793.6042 1810.0985 9.832 8.514762 21.6216 -37470.578 -37470.432 -27139.363 3.7975984e-11 0.94245783 8.5085457e-11
|
||||
200 170.7381 43248.332 -2790.8398 1879.164 9.9554912 8.6217086 21.89317 39337.624 42979.126 47428.246 324.91326 454.85872 -2034.6053
|
||||
400 258.09921 -28257.8 -2788.3487 1856.1432 9.9146707 8.5863569 21.803402 -19478.873 -29571.375 -35723.152 4633.9026 8487.8103 -626.12005
|
||||
600 277.77032 -22751.351 -2786.2715 1866.9783 9.9339253 8.6030319 21.845744 -21727.335 -29200.027 -17326.692 -4327.8571 -8218.4965 252.30681
|
||||
800 349.8665 30508.003 -2784.2204 1873.4953 9.9454706 8.6130304 21.871134 29929.055 33562.672 28032.281 -3188.5605 12329.482 7558.5678
|
||||
1000 373.67651 -18839.569 -2783.2178 1855.5937 9.9136922 8.5855095 21.80125 -18063.486 -22288.321 -16166.902 -416.09547 -10368.975 9030.4208
|
||||
1200 423.3474 6846.9905 -2781.9271 1896.2131 9.9855083 8.6477041 21.959181 2147.3938 11765.857 6627.7202 -7627.6782 -1297.6517 -4758.4746
|
||||
1400 418.54527 -6416.7506 -2781.4358 1834.2719 9.8755745 8.5524986 21.717425 5693.0543 -19487.901 -5455.405 827.66513 -523.1508 -3890.9919
|
||||
1600 429.42796 3939.8836 -2780.5861 1895.8859 9.984934 8.6472068 21.957918 3755.6959 -1326.4343 9390.3893 1948.1153 4489.8629 1466.0914
|
||||
1800 447.7623 -8344.6306 -2780.1071 1858.4925 9.9188518 8.5899779 21.812596 -17549.498 3336.8135 -10821.208 1643.4226 -644.56065 -8935.9666
|
||||
2000 438.1306 -6691.4691 -2780.7407 1871.3547 9.9416812 8.6097487 21.862801 -6959.2196 -8486.8466 -4628.341 -1019.9006 443.03694 -2751.917
|
||||
Loop time of 2.46815 on 1 procs for 2000 steps with 144 atoms
|
||||
400 258.09921 -28257.8 -2788.3487 1856.1432 9.9146707 8.5863569 21.803402 -19478.873 -29571.375 -35723.151 4633.9025 8487.8103 -626.12008
|
||||
600 277.77032 -22751.351 -2786.2715 1866.9783 9.9339253 8.6030319 21.845744 -21727.333 -29200.028 -17326.691 -4327.8577 -8218.4994 252.30614
|
||||
800 349.8665 30508.004 -2784.2204 1873.4953 9.9454706 8.6130304 21.871134 29929.053 33562.675 28032.284 -3188.5636 12329.485 7558.5604
|
||||
1000 373.67652 -18839.562 -2783.2178 1855.5937 9.9136922 8.5855095 21.80125 -18063.481 -22288.32 -16166.887 -416.09489 -10368.975 9030.4151
|
||||
1200 423.34739 6846.9842 -2781.9271 1896.2131 9.9855083 8.6477041 21.959181 2147.3919 11765.847 6627.7141 -7627.6762 -1297.649 -4758.4757
|
||||
1400 418.54526 -6416.7547 -2781.4358 1834.2719 9.8755745 8.5524986 21.717425 5693.0508 -19487.901 -5455.4139 827.66188 -523.1469 -3890.9904
|
||||
1600 429.42798 3939.889 -2780.5861 1895.8859 9.984934 8.6472068 21.957918 3755.6972 -1326.4252 9390.395 1948.1084 4489.8536 1466.083
|
||||
1800 447.76215 -8344.6447 -2780.1071 1858.4925 9.9188519 8.5899779 21.812596 -17549.502 3336.8092 -10821.241 1643.4315 -644.54621 -8935.98
|
||||
2000 438.1305 -6691.4324 -2780.7407 1871.3547 9.9416812 8.6097487 21.8628 -6959.1834 -8486.8262 -4628.2877 -1019.8998 443.04638 -2751.9173
|
||||
Loop time of 11.2763 on 1 procs for 2000 steps with 144 atoms
|
||||
|
||||
Performance: 70.012 ns/day, 0.343 hours/ns, 810.323 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 15.324 ns/day, 1.566 hours/ns, 177.363 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.0003 | 2.0003 | 2.0003 | 0.0 | 81.04
|
||||
Kspace | 0.20006 | 0.20006 | 0.20006 | 0.0 | 8.11
|
||||
Pair | 7.9085 | 7.9085 | 7.9085 | 0.0 | 70.13
|
||||
Kspace | 2.0339 | 2.0339 | 2.0339 | 0.0 | 18.04
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.023753 | 0.023753 | 0.023753 | 0.0 | 0.96
|
||||
Output | 0.0001986 | 0.0001986 | 0.0001986 | 0.0 | 0.01
|
||||
Modify | 0.23896 | 0.23896 | 0.23896 | 0.0 | 9.68
|
||||
Other | | 0.004907 | | | 0.20
|
||||
Comm | 0.15276 | 0.15276 | 0.15276 | 0.0 | 1.35
|
||||
Output | 0.00036049 | 0.00036049 | 0.00036049 | 0.0 | 0.00
|
||||
Modify | 1.1706 | 1.1706 | 1.1706 | 0.0 | 10.38
|
||||
Other | | 0.01023 | | | 0.09
|
||||
|
||||
Nlocal: 144 ave 144 max 144 min
|
||||
Nlocal: 144.000 ave 144 max 144 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3943 ave 3943 max 3943 min
|
||||
Nghost: 3943.00 ave 3943 max 3943 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 41952 ave 41952 max 41952 min
|
||||
Neighs: 41952.0 ave 41952 max 41952 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 41952
|
||||
Ave neighs/atom = 291.333
|
||||
Ave neighs/atom = 291.33333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
unfix quartz_qtb
|
||||
@ -185,24 +188,23 @@ QBMSST parameters:
|
||||
Initial pressure calculated on first step
|
||||
Initial volume calculated on first step
|
||||
Initial energy calculated on first step
|
||||
fix_modify shock energy yes
|
||||
variable dhug equal f_shock[1]
|
||||
variable dray equal f_shock[2]
|
||||
variable lgr_vel equal f_shock[3]
|
||||
variable lgr_pos equal f_shock[4]
|
||||
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
|
||||
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo_style custom step v_T_qm press econserve vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo 200
|
||||
timestep ${delta_t}
|
||||
timestep 0.001
|
||||
run 1000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.303132
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
|
||||
G vector (1/distance) = 0.30313178
|
||||
grid = 9 8 16
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00104699
|
||||
estimated relative force accuracy = 7.27093e-05
|
||||
estimated absolute RMS force accuracy = 0.0010469888
|
||||
estimated relative force accuracy = 7.2709348e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 5520 1152
|
||||
Neighbor list info ...
|
||||
@ -223,52 +225,53 @@ Neighbor list info ...
|
||||
stencil: none
|
||||
bin: none
|
||||
Fix QBMSST v0 = 1.87135e+03
|
||||
Fix QBMSST p0 = -4.62948e+03
|
||||
Fix QBMSST p0 = -4.62942e+03
|
||||
Fix QBMSST e0 = to be -2.78074e+03
|
||||
Fix QBMSST initial strain rate of -4.01096e-01 established by reducing temperature by factor of 5.00000e-02
|
||||
Per MPI rank memory allocation (min/avg/max) = 80.1 | 80.1 | 80.1 Mbytes
|
||||
Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
0 300 -6922.9433 -2780.7394 1871.3547 9.9416812 8.6097487 21.862801 -4819.9907 10.953265 -190.51273 0 0
|
||||
200 294.95797 54876.416 -2779.2988 1723.7621 9.9416812 8.6097487 20.138495 108897.19 -29.773973 -9271.7281 6.1518102 -15.057867
|
||||
400 288.3711 139521.03 -2778.7321 1628.5574 9.9416812 8.6097487 19.026231 222107.71 8.0682073 24727.575 10.120041 -28.714693
|
||||
600 280.56521 98070.281 -2779.8934 1687.2434 9.9416812 8.6097487 19.711852 164558.51 2.6076928 16005.656 7.6739491 -42.705007
|
||||
800 274.94701 106060.26 -2779.2916 1651.0723 9.9416812 8.6097487 19.289269 176842.6 -39.645354 -1804.9466 9.1815975 -56.628078
|
||||
1000 268.47106 189695.34 -2779.4951 1492.6355 9.9416812 8.6097487 17.438272 277351.5 -84.834482 -33116.996 15.785409 -69.870519
|
||||
Loop time of 2.05219 on 1 procs for 1000 steps with 144 atoms
|
||||
Fix QBMSST initial strain rate of -4.01095e-01 established by reducing temperature by factor of 5.00000e-02
|
||||
Per MPI rank memory allocation (min/avg/max) = 80.10 | 80.10 | 80.10 Mbytes
|
||||
Step v_T_qm Press Econserve Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
0 300 -6922.9066 -2780.7394 1871.3547 9.9416812 8.6097487 21.8628 -4819.9374 10.953262 -190.5127 0 0
|
||||
200 294.95802 54876.628 -2779.2988 1723.7617 9.9416812 8.6097487 20.13849 108897.62 -29.773363 -9271.7016 6.1518278 -15.057866
|
||||
400 288.37122 139520.66 -2778.7321 1628.5573 9.9416812 8.6097487 19.02623 222107.14 8.0673735 24726.892 10.120044 -28.714689
|
||||
600 280.56538 98072.818 -2779.8934 1687.2396 9.9416812 8.6097487 19.711808 164562.57 2.6099747 16006.563 7.6741039 -42.704989
|
||||
800 274.9472 106058.35 -2779.2916 1651.0755 9.9416812 8.6097487 19.289307 176839.13 -39.647552 -1805.8176 9.1814643 -56.628046
|
||||
1000 268.4714 189679.65 -2779.4952 1492.6558 9.9416812 8.6097487 17.43851 277332.66 -84.846841 -33118.917 15.784559 -69.870561
|
||||
Loop time of 8.7779 on 1 procs for 1000 steps with 144 atoms
|
||||
|
||||
Performance: 42.101 ns/day, 0.570 hours/ns, 487.284 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 9.843 ns/day, 2.438 hours/ns, 113.922 timesteps/s
|
||||
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.6815 | 1.6815 | 1.6815 | 0.0 | 81.94
|
||||
Kspace | 0.10373 | 0.10373 | 0.10373 | 0.0 | 5.05
|
||||
Neigh | 0.0061183 | 0.0061183 | 0.0061183 | 0.0 | 0.30
|
||||
Comm | 0.012444 | 0.012444 | 0.012444 | 0.0 | 0.61
|
||||
Output | 0.00014687 | 0.00014687 | 0.00014687 | 0.0 | 0.01
|
||||
Modify | 0.24529 | 0.24529 | 0.24529 | 0.0 | 11.95
|
||||
Other | | 0.002948 | | | 0.14
|
||||
Pair | 6.8031 | 6.8031 | 6.8031 | 0.0 | 77.50
|
||||
Kspace | 1.0505 | 1.0505 | 1.0505 | 0.0 | 11.97
|
||||
Neigh | 0.024976 | 0.024976 | 0.024976 | 0.0 | 0.28
|
||||
Comm | 0.082612 | 0.082612 | 0.082612 | 0.0 | 0.94
|
||||
Output | 0.00032592 | 0.00032592 | 0.00032592 | 0.0 | 0.00
|
||||
Modify | 0.8108 | 0.8108 | 0.8108 | 0.0 | 9.24
|
||||
Other | | 0.005632 | | | 0.06
|
||||
|
||||
Nlocal: 144 ave 144 max 144 min
|
||||
Nlocal: 144.000 ave 144 max 144 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4243 ave 4243 max 4243 min
|
||||
Nghost: 4243.00 ave 4243 max 4243 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 48210 ave 48210 max 48210 min
|
||||
Neighs: 48210.0 ave 48210 max 48210 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 48210
|
||||
Ave neighs/atom = 334.792
|
||||
Ave neighs/atom = 334.79167
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
write_restart restart.1000
|
||||
System init for write_restart ...
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.306435
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
|
||||
G vector (1/distance) = 0.30643517
|
||||
grid = 9 8 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000955688
|
||||
estimated relative force accuracy = 6.63689e-05
|
||||
estimated absolute RMS force accuracy = 0.0009556927
|
||||
estimated relative force accuracy = 6.6369185e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 5280 1080
|
||||
Neighbor list info ...
|
||||
@ -294,12 +297,14 @@ Neighbor list info ...
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.1000
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style charge from restart
|
||||
orthogonal box = (-0.05484062286382799 -0.04749337384227555 2.0916641327653274) to (9.886840622863804 8.562255373842252 19.52993586723476)
|
||||
orthogonal box = (-0.054840605 -0.047493358 2.0915450) to (9.8868406 8.5622554 19.530055)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
restoring pair style hybrid/overlay from restart
|
||||
144 atoms
|
||||
read_restart CPU = 0.0002563 secs
|
||||
read_restart CPU = 0.001 seconds
|
||||
include alpha_quartz_potential.mod
|
||||
#This script implements the BKS pair potential for various silicon dioxide compounds. Inner part is fixed with a harmonic potential. Long range Coulomb interactions are evaluated with the pppm method.
|
||||
|
||||
@ -314,8 +319,8 @@ pair_coeff 1 2 table potential_SiO2.TPF Si-O ${cut_off}
|
||||
pair_coeff 1 2 table potential_SiO2.TPF Si-O 10
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O ${cut_off} #See the potential file for more information
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O 10
|
||||
WARNING: 1 of 39901 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:471)
|
||||
WARNING: 1 of 39901 force values in table O-O are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:461)
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
#Neighbor style
|
||||
@ -338,25 +343,24 @@ QBMSST parameters:
|
||||
Initial energy calculated on first step
|
||||
Resetting global fix info from restart file:
|
||||
fix style: qbmsst, fix ID: shock
|
||||
fix_modify shock energy yes
|
||||
variable dhug equal f_shock[1]
|
||||
variable dray equal f_shock[2]
|
||||
variable lgr_vel equal f_shock[3]
|
||||
variable lgr_pos equal f_shock[4]
|
||||
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
|
||||
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo_style custom step v_T_qm press econserve vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo 500
|
||||
timestep ${delta_t}
|
||||
timestep 0.001
|
||||
restart 1000 restart
|
||||
#restart 1000 restart
|
||||
run 10000 #10 ps
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.306435
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
|
||||
G vector (1/distance) = 0.30643517
|
||||
grid = 9 8 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000955688
|
||||
estimated relative force accuracy = 6.63689e-05
|
||||
estimated absolute RMS force accuracy = 0.0009556927
|
||||
estimated relative force accuracy = 6.6369185e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 5280 1080
|
||||
All restart file global fix info was re-assigned
|
||||
@ -378,53 +382,54 @@ Neighbor list info ...
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 80.12 | 80.12 | 80.12 Mbytes
|
||||
Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
1000 268.47106 189686.77 -2781.5194 1492.6355 9.9416812 8.6097487 17.438272 277378.37 -84.692548 -33090.129 15.785409 0
|
||||
1500 362.13476 692245.96 -2800.9352 1011.2037 9.9416812 8.6097487 11.813766 661095.53 188.71833 -49928.712 35.851981 -24.11484
|
||||
2000 860.78914 714816.8 -2830.893 997.64749 9.9416812 8.6097487 11.65539 653537.64 852.68158 -68765.537 36.41702 -44.978484
|
||||
2500 1620.8281 709511.19 -2840.8217 1000.3425 9.9416812 8.6097487 11.686875 660030.01 1184.3105 -60030.892 36.304689 -65.69966
|
||||
3000 2395.6824 649526.84 -2832.6859 995.56591 9.9416812 8.6097487 11.631071 660984.37 939.07209 -63050.693 36.503782 -86.383242
|
||||
3500 3034.6774 715794.56 -2822.6098 995.8622 9.9416812 8.6097487 11.634532 712849.74 1055.7295 -10938.816 36.491433 -106.99315
|
||||
4000 3487.9039 736791.25 -2804.1216 994.13867 9.9416812 8.6097487 11.614397 765817.85 943.15747 40595.305 36.563271 -127.76315
|
||||
4500 3718.6279 813775.8 -2788.1942 995.82514 9.9416812 8.6097487 11.634099 881961.06 1370.5559 158141.68 36.492977 -148.68649
|
||||
5000 3691.4947 750146.58 -2770.5541 1018.4785 9.9416812 8.6097487 11.898756 770500.36 196.2793 65528.786 35.548762 -169.8589
|
||||
5500 3585.8602 831522.51 -2766.0198 1005.6834 9.9416812 8.6097487 11.749273 916093.67 1088.1987 200476.48 36.082073 -190.89436
|
||||
6000 3431.6405 749891.94 -2771.6404 1011.9077 9.9416812 8.6097487 11.82199 781321.11 268.24344 70882.55 35.82264 -212.20913
|
||||
6500 3350.2876 666113.16 -2780.4124 1028.8353 9.9416812 8.6097487 12.019753 749294.32 371.38231 52939.676 35.117081 -233.59556
|
||||
7000 3339.2397 675783.2 -2782.7559 1022.6541 9.9416812 8.6097487 11.947539 690109.39 -26.949124 -11388.054 35.374719 -254.95868
|
||||
7500 3395.582 726601.74 -2784.7652 1018.1439 9.9416812 8.6097487 11.894846 759167.86 506.5811 53917.852 35.56271 -276.24361
|
||||
8000 3393.2372 625141.93 -2771.6398 1035.4915 9.9416812 8.6097487 12.097517 598674.46 -895.80046 -92142.112 34.839641 -297.61681
|
||||
8500 3272.9752 659367.77 -2776.608 1031.8188 9.9416812 8.6097487 12.054609 688358.42 -142.30814 -5513.8593 34.992722 -318.94541
|
||||
9000 3277.8848 724828.76 -2777.6502 1017.6314 9.9416812 8.6097487 11.888859 724452.11 58.574942 18775.738 35.58407 -340.1718
|
||||
9500 3273.7854 620652.38 -2780.0794 1023.5922 9.9416812 8.6097487 11.958499 747175.42 317.3826 46458.505 35.335617 -361.41643
|
||||
10000 3329.1766 668606.38 -2786.3493 1022.9534 9.9416812 8.6097487 11.951035 703351.81 168.14538 2103.38 35.362244 -382.64609
|
||||
10500 3398.9956 642919.16 -2784.2833 1016.2587 9.9416812 8.6097487 11.872822 661298.16 -230.03577 -45520.34 35.641287 -403.78721
|
||||
11000 3418.7053 675754.06 -2782.6318 1005.7483 9.9416812 8.6097487 11.75003 689789.84 -136.97148 -25773.422 36.079372 -424.97556
|
||||
Loop time of 32.4277 on 1 procs for 10000 steps with 144 atoms
|
||||
Step v_T_qm Press Econserve Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
1000 268.4714 189671.09 -2781.5189 1492.6558 9.9416812 8.6097487 17.43851 277359.52 -84.704915 -33092.054 15.784559 0
|
||||
1500 362.24943 690690.88 -2801.3189 1013.1871 9.9416812 8.6097487 11.836938 660912.81 210.15736 -48461.278 35.76931 -24.117097
|
||||
2000 851.29288 687202.75 -2829.28 998.92158 9.9416812 8.6097487 11.670275 702779.72 1177.175 -18463.457 36.363914 -45.102068
|
||||
2500 1584.7231 702373.6 -2840.9926 998.47448 9.9416812 8.6097487 11.665052 685551.65 1366.7769 -36063.512 36.382549 -65.966813
|
||||
3000 2369.1915 765783.04 -2835.3495 994.53954 9.9416812 8.6097487 11.61908 742616.98 1609.2532 17727.912 36.546562 -86.541922
|
||||
3500 3092.3052 829161.44 -2827.8974 977.82563 9.9416812 8.6097487 11.423814 768559.05 1500.9858 29763.85 37.243215 -107.10048
|
||||
4000 3627.1538 773057.81 -2813.687 988.31955 9.9416812 8.6097487 11.546413 738541.81 959.39292 8477.6525 36.805818 -127.75274
|
||||
4500 3910.5455 753799.74 -2790.7863 1002.749 9.9416812 8.6097487 11.71499 763069.75 602.0127 45010.991 36.204385 -148.51594
|
||||
5000 3976.7913 761978.62 -2782.0448 998.85434 9.9416812 8.6097487 11.669489 780709.6 482.34112 59410.482 36.366717 -169.42341
|
||||
5500 3928.0113 702739.91 -2765.8379 1008.695 9.9416812 8.6097487 11.784456 632171.28 -991.2791 -80940.344 35.956549 -190.30951
|
||||
6000 3731.5486 654300.14 -2763.1253 1032.1476 9.9416812 8.6097487 12.05845 642590.19 -832.8417 -51008.602 34.979018 -211.41573
|
||||
6500 3505.5984 713092.19 -2767.3169 1010.6873 9.9416812 8.6097487 11.807732 735218.98 -176.4579 23764.995 35.873507 -232.57305
|
||||
7000 3348.5047 762624.48 -2769.0996 1010.8032 9.9416812 8.6097487 11.809086 662703.98 -667.90587 -48653.562 35.868676 -253.64668
|
||||
7500 3197.2839 689038.79 -2770.7583 1036.994 9.9416812 8.6097487 12.11507 679188.92 -330.37222 -10377.635 34.777016 -275.06425
|
||||
8000 3117.1867 765531.79 -2775.0143 1023.9741 9.9416812 8.6097487 11.96296 681640.02 -288.82226 -18759.215 35.319699 -296.38453
|
||||
8500 3053.5599 667992.24 -2772.057 1027.6458 9.9416812 8.6097487 12.005857 657921.43 -507.92809 -39422.884 35.166657 -317.64367
|
||||
9000 2997.4957 704542.99 -2780.9279 1020.074 9.9416812 8.6097487 11.917396 647510.98 -398.1601 -56133.168 35.482259 -338.8598
|
||||
9500 2990.5818 810181.5 -2783.2413 1002.8927 9.9416812 8.6097487 11.716669 859476.58 1107.5241 141537.42 36.198393 -359.85577
|
||||
10000 3055.8298 792271.02 -2786.5277 991.62826 9.9416812 8.6097487 11.585068 847298.17 1051.5369 119986.89 36.667907 -380.83279
|
||||
10500 3159.7134 706528.08 -2793.5555 1009.9173 9.9416812 8.6097487 11.798737 673106.83 67.67511 -38987.761 35.905599 -401.74903
|
||||
11000 3261.7609 748345.85 -2783.0699 1017.8806 9.9416812 8.6097487 11.891771 656140.32 -267.8786 -49328.779 35.573683 -422.65593
|
||||
Loop time of 130.289 on 1 procs for 10000 steps with 144 atoms
|
||||
|
||||
Performance: 26.644 ns/day, 0.901 hours/ns, 308.378 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 6.631 ns/day, 3.619 hours/ns, 76.752 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 | 28.397 | 28.397 | 28.397 | 0.0 | 87.57
|
||||
Kspace | 1.0225 | 1.0225 | 1.0225 | 0.0 | 3.15
|
||||
Neigh | 0.27594 | 0.27594 | 0.27594 | 0.0 | 0.85
|
||||
Comm | 0.1797 | 0.1797 | 0.1797 | 0.0 | 0.55
|
||||
Output | 0.10409 | 0.10409 | 0.10409 | 0.0 | 0.32
|
||||
Modify | 2.4112 | 2.4112 | 2.4112 | 0.0 | 7.44
|
||||
Other | | 0.03707 | | | 0.11
|
||||
Pair | 109.8 | 109.8 | 109.8 | 0.0 | 84.27
|
||||
Kspace | 10.328 | 10.328 | 10.328 | 0.0 | 7.93
|
||||
Neigh | 1.0855 | 1.0855 | 1.0855 | 0.0 | 0.83
|
||||
Comm | 1.2041 | 1.2041 | 1.2041 | 0.0 | 0.92
|
||||
Output | 0.0012848 | 0.0012848 | 0.0012848 | 0.0 | 0.00
|
||||
Modify | 7.8094 | 7.8094 | 7.8094 | 0.0 | 5.99
|
||||
Other | | 0.06511 | | | 0.05
|
||||
|
||||
Nlocal: 144 ave 144 max 144 min
|
||||
Nlocal: 144.000 ave 144 max 144 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5541 ave 5541 max 5541 min
|
||||
Nghost: 5430.00 ave 5430 max 5430 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 74662 ave 74662 max 74662 min
|
||||
Neighs: 72807.0 ave 72807 max 72807 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 74662
|
||||
Ave neighs/atom = 518.486
|
||||
Neighbor list builds = 207
|
||||
Total # of neighbors = 72807
|
||||
Ave neighs/atom = 505.60417
|
||||
Neighbor list builds = 206
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:37
|
||||
shell rm restart.1000
|
||||
Total wall time: 0:02:32
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (15 Jun 2020)
|
||||
LAMMPS (24 Dec 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
## This script first uses fix qtb to equilibrate alpha quartz structure to an initial state with quantum nuclear correction and then simulate shock induced phase transition through the quantum thermal bath multi-scale shock technique
|
||||
variable x_rep equal 2 #plot is made with x_rep = 8 #x-direction replication number
|
||||
@ -29,12 +29,12 @@ atom_style charge
|
||||
|
||||
#Lattice
|
||||
lattice custom 1.0 a1 4.916000 0.000000 0.000000 a2 -2.45800 4.257381 0.000000 a3 0.000000 0.000000 5.405400 basis 0.469700 0.000000 0.000000 basis 0.000000 0.469700 0.666667 basis 0.530300 0.530300 0.333333 basis 0.413500 0.266900 0.119100 basis 0.266900 0.413500 0.547567 basis 0.733100 0.146600 0.785767 basis 0.586500 0.853400 0.214233 basis 0.853400 0.586500 0.452433 basis 0.146600 0.733100 0.880900 #American Mineralogist 65 920 1980 (Space Group 154)
|
||||
Lattice spacing in x,y,z = 7.374 4.25738 5.4054
|
||||
Lattice spacing in x,y,z = 7.3740000 4.2573810 5.4054000
|
||||
|
||||
#Computational Cell
|
||||
region orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box
|
||||
create_box 2 orthorhombic_unit_cell
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (4.916 8.514762 5.4054)
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (4.9160000 8.5147620 5.4054000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 2 basis 5 2 basis 6 2 basis 7 2 basis 8 2 basis 9 2
|
||||
Created 18 atoms
|
||||
@ -43,17 +43,20 @@ replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
replicate 2 ${y_rep} ${z_rep}
|
||||
replicate 2 1 ${z_rep}
|
||||
replicate 2 1 4
|
||||
orthogonal box = (0.0 0.0 0.0) to (9.832 8.514762 21.6216)
|
||||
Replicating atoms ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (9.8320000 8.5147620 21.621600)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
144 atoms
|
||||
replicate CPU = 0.000225782 secs
|
||||
replicate CPU = 0.001 seconds
|
||||
|
||||
#Atomic Information
|
||||
mass 1 28.085500
|
||||
mass 2 15.999400
|
||||
set type 1 charge +2.4
|
||||
Setting atom values ...
|
||||
48 settings made for charge
|
||||
set type 2 charge -1.2
|
||||
Setting atom values ...
|
||||
96 settings made for charge
|
||||
|
||||
|
||||
@ -72,8 +75,8 @@ pair_coeff 1 2 table potential_SiO2.TPF Si-O ${cut_off}
|
||||
pair_coeff 1 2 table potential_SiO2.TPF Si-O 10
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O ${cut_off} #See the potential file for more information
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O 10
|
||||
WARNING: 1 of 39901 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:471)
|
||||
WARNING: 1 of 39901 force values in table O-O are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:461)
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
#Neighbor style
|
||||
@ -96,12 +99,12 @@ thermo_style custom step temp press etotal vol lx ly lz pxx pyy pzz p
|
||||
thermo 200
|
||||
run 2000 # 2 ps
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.301598
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
|
||||
G vector (1/distance) = 0.30159814
|
||||
grid = 9 8 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00117056
|
||||
estimated relative force accuracy = 8.12908e-05
|
||||
estimated absolute RMS force accuracy = 0.0011705589
|
||||
estimated relative force accuracy = 8.1290814e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 2400 288
|
||||
Neighbor list info ...
|
||||
@ -121,44 +124,44 @@ Neighbor list info ...
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 79.7 | 79.7 | 79.7 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 79.70 | 79.70 | 79.70 Mbytes
|
||||
Step Temp Press TotEng Volume Lx Ly Lz Pxx Pyy Pzz Pxy Pyz Pxz
|
||||
0 0 -34026.791 -2793.6042 1810.0985 9.832 8.514762 21.6216 -37470.578 -37470.432 -27139.363 1.0530512e-10 0.94245783 4.0087238e-10
|
||||
0 0 -34026.791 -2793.6042 1810.0985 9.832 8.514762 21.6216 -37470.578 -37470.432 -27139.363 -3.2012455e-11 0.94245783 1.6892124e-10
|
||||
200 153.57631 45538.205 -2790.8177 1873.0866 9.9447472 8.612404 21.869543 41721.016 44095.248 50798.351 -3961.4596 1223.325 2871.656
|
||||
400 234.74785 -34404.175 -2789.0189 1850.2127 9.9041 8.5772024 21.780156 -28329.333 -39376.313 -35506.88 -1154.5043 -5411.1071 2246.6749
|
||||
600 265.24833 -20905.145 -2786.2727 1874.9981 9.948129 8.6153326 21.87698 -22753.886 -21091.083 -18870.468 -4645.5548 2968.2945 1415.0311
|
||||
800 297.79035 32990.58 -2784.8247 1853.6946 9.910309 8.5825796 21.79381 30061.364 35359.18 33551.195 -3092.2971 1525.52 -6461.0249
|
||||
1000 367.71884 -27539.239 -2783.0102 1864.7161 9.9299114 8.5995557 21.836917 -20273.387 -38720.429 -23623.901 7639.0334 -866.35665 543.52723
|
||||
1200 399.77109 3807.7814 -2781.511 1893.4978 9.9807399 8.6435745 21.948695 1625.8226 7441.2236 2356.298 -4057.1674 3814.9305 1528.4567
|
||||
1400 466.57962 -4148.235 -2780.1546 1851.5925 9.9065614 8.5793341 21.785568 -10883.19 1816.768 -3378.2828 896.25296 -7208.541 -42.253127
|
||||
1600 497.86539 14505.31 -2778.9409 1882.2616 9.9609584 8.6264432 21.905193 8268.1103 20614.738 14633.082 -2690.5669 6807.3187 11995.878
|
||||
1800 557.31182 -108.04462 -2778.1875 1875.514 9.9490413 8.6161228 21.878986 948.68308 -1929.7575 656.94053 -1628.2172 -6594.5909 -4423.4368
|
||||
2000 480.39449 -8852.2243 -2778.4963 1862.9552 9.9267847 8.596848 21.830042 -18274.307 3038.8369 -11321.203 -5002.1016 12023.282 6845.2769
|
||||
Loop time of 1.42181 on 4 procs for 2000 steps with 144 atoms
|
||||
600 265.24834 -20905.145 -2786.2727 1874.9981 9.948129 8.6153326 21.87698 -22753.885 -21091.083 -18870.467 -4645.5539 2968.2936 1415.0335
|
||||
800 297.79036 32990.577 -2784.8247 1853.6946 9.910309 8.5825796 21.79381 30061.366 35359.175 33551.191 -3092.2938 1525.518 -6461.029
|
||||
1000 367.71885 -27539.237 -2783.0102 1864.7161 9.9299114 8.5995557 21.836917 -20273.384 -38720.43 -23623.895 7639.0325 -866.34777 543.5312
|
||||
1200 399.7711 3807.785 -2781.511 1893.4978 9.9807399 8.6435745 21.948695 1625.8297 7441.2317 2356.2937 -4057.1659 3814.9292 1528.4637
|
||||
1400 466.57958 -4148.2231 -2780.1546 1851.5925 9.9065614 8.5793341 21.785568 -10883.182 1816.778 -3378.2653 896.24645 -7208.5417 -42.262464
|
||||
1600 497.86536 14505.308 -2778.9409 1882.2616 9.9609584 8.6264432 21.905193 8268.1088 20614.74 14633.075 -2690.5703 6807.3188 11995.875
|
||||
1800 557.31178 -108.02787 -2778.1875 1875.514 9.9490413 8.6161228 21.878986 948.70277 -1929.753 656.96663 -1628.2124 -6594.6026 -4423.4256
|
||||
2000 480.39444 -8852.2282 -2778.4963 1862.9552 9.9267847 8.596848 21.830042 -18274.302 3038.8276 -11321.21 -5002.1095 12023.298 6845.2631
|
||||
Loop time of 4.1373 on 4 procs for 2000 steps with 144 atoms
|
||||
|
||||
Performance: 121.535 ns/day, 0.197 hours/ns, 1406.656 timesteps/s
|
||||
87.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 41.766 ns/day, 0.575 hours/ns, 483.407 timesteps/s
|
||||
96.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.72578 | 0.80093 | 0.87518 | 6.1 | 56.33
|
||||
Kspace | 0.33737 | 0.41245 | 0.48642 | 8.4 | 29.01
|
||||
Pair | 2.2821 | 2.4503 | 2.7881 | 12.7 | 59.22
|
||||
Kspace | 0.81032 | 1.1413 | 1.306 | 18.2 | 27.59
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.066098 | 0.071334 | 0.076039 | 1.6 | 5.02
|
||||
Output | 0.00021172 | 0.00039291 | 0.00093484 | 0.0 | 0.03
|
||||
Modify | 0.090105 | 0.1077 | 0.11384 | 3.1 | 7.58
|
||||
Other | | 0.029 | | | 2.04
|
||||
Comm | 0.16143 | 0.16964 | 0.17659 | 1.3 | 4.10
|
||||
Output | 0.00026584 | 0.00061899 | 0.0016773 | 0.0 | 0.01
|
||||
Modify | 0.29943 | 0.33639 | 0.34927 | 3.7 | 8.13
|
||||
Other | | 0.03911 | | | 0.95
|
||||
|
||||
Nlocal: 36 ave 36 max 36 min
|
||||
Nlocal: 36.0000 ave 36 max 36 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2614 ave 2614 max 2614 min
|
||||
Nghost: 2614.00 ave 2614 max 2614 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 10488 ave 11326 max 9404 min
|
||||
Neighs: 10488.0 ave 11326 max 9404 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
|
||||
Total # of neighbors = 41952
|
||||
Ave neighs/atom = 291.333
|
||||
Ave neighs/atom = 291.33333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
unfix quartz_qtb
|
||||
@ -185,24 +188,23 @@ QBMSST parameters:
|
||||
Initial pressure calculated on first step
|
||||
Initial volume calculated on first step
|
||||
Initial energy calculated on first step
|
||||
fix_modify shock energy yes
|
||||
variable dhug equal f_shock[1]
|
||||
variable dray equal f_shock[2]
|
||||
variable lgr_vel equal f_shock[3]
|
||||
variable lgr_pos equal f_shock[4]
|
||||
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
|
||||
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo_style custom step v_T_qm press econserve vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo 200
|
||||
timestep ${delta_t}
|
||||
timestep 0.001
|
||||
run 1000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.30088
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
|
||||
G vector (1/distance) = 0.30087967
|
||||
grid = 9 8 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00120534
|
||||
estimated relative force accuracy = 8.37062e-05
|
||||
estimated absolute RMS force accuracy = 0.0012053392
|
||||
estimated relative force accuracy = 8.3706174e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 2400 288
|
||||
Neighbor list info ...
|
||||
@ -225,50 +227,51 @@ Neighbor list info ...
|
||||
Fix QBMSST v0 = 1.86296e+03
|
||||
Fix QBMSST p0 = -1.13219e+04
|
||||
Fix QBMSST e0 = to be -2.77850e+03
|
||||
Fix QBMSST initial strain rate of -4.21890e-01 established by reducing temperature by factor of 5.00000e-02
|
||||
Per MPI rank memory allocation (min/avg/max) = 79.7 | 79.7 | 79.7 Mbytes
|
||||
Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
0 300 -9106.318 -2778.4963 1862.9552 9.9267847 8.596848 21.830042 -11562.002 12.009862 -240.0699 0 0
|
||||
200 296.47213 25984.111 -2777.5178 1770.2164 9.9267847 8.596848 20.743332 64970.204 -25.305765 -1564.7673 3.8828772 -15.16768
|
||||
400 291.06707 69977.517 -2777.6325 1684.893 9.9267847 8.596848 19.743515 144833.82 -12.184734 6667.384 7.4552796 -29.607028
|
||||
600 287.21118 39706.699 -2778.0322 1716.9533 9.9267847 8.596848 20.119196 87971.152 -38.593844 -23279.741 6.1129484 -43.751298
|
||||
800 284.33611 18833.281 -2778.1637 1792.7576 9.9267847 8.596848 21.007468 43725.433 -8.1267799 -3885.5802 2.9391022 -58.454556
|
||||
1000 281.98328 -6030.6935 -2778.3314 1881.8369 9.9267847 8.596848 22.051297 -14118.602 1.3183874 13055.078 -0.79055793 -73.780965
|
||||
Loop time of 1.25215 on 4 procs for 1000 steps with 144 atoms
|
||||
Fix QBMSST initial strain rate of -4.21889e-01 established by reducing temperature by factor of 5.00000e-02
|
||||
Per MPI rank memory allocation (min/avg/max) = 79.70 | 79.70 | 79.70 Mbytes
|
||||
Step v_T_qm Press Econserve Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
0 300 -9106.3219 -2778.4963 1862.9552 9.9267847 8.596848 21.830042 -11562.009 12.009861 -240.06987 0 0
|
||||
200 296.47212 25984.099 -2777.5178 1770.2165 9.9267847 8.596848 20.743332 64970.178 -25.305804 -1564.7427 3.8828751 -15.16768
|
||||
400 291.06704 69977.415 -2777.6325 1684.8932 9.9267847 8.596848 19.743517 144833.61 -12.18477 6667.3264 7.4552723 -29.607029
|
||||
600 287.21114 39706.769 -2778.0322 1716.9533 9.9267847 8.596848 20.119196 87971.211 -38.594057 -23279.705 6.1129499 -43.7513
|
||||
800 284.33606 18833.325 -2778.1637 1792.7575 9.9267847 8.596848 21.007467 43725.516 -8.1270751 -3885.5508 2.9391052 -58.454557
|
||||
1000 281.98323 -6030.7047 -2778.3314 1881.8368 9.9267847 8.596848 22.051295 -14118.589 1.3182589 13054.989 -0.79055248 -73.780966
|
||||
Loop time of 3.32539 on 4 procs for 1000 steps with 144 atoms
|
||||
|
||||
Performance: 69.001 ns/day, 0.348 hours/ns, 798.628 timesteps/s
|
||||
90.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 25.982 ns/day, 0.924 hours/ns, 300.717 timesteps/s
|
||||
97.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.67979 | 0.73665 | 0.8091 | 5.4 | 58.83
|
||||
Kspace | 0.18687 | 0.25893 | 0.31544 | 9.1 | 20.68
|
||||
Neigh | 0.0011306 | 0.0012404 | 0.0013735 | 0.3 | 0.10
|
||||
Comm | 0.040339 | 0.041345 | 0.042296 | 0.4 | 3.30
|
||||
Output | 0.00020051 | 0.00035506 | 0.00081801 | 0.0 | 0.03
|
||||
Modify | 0.19595 | 0.2007 | 0.20253 | 0.6 | 16.03
|
||||
Other | | 0.01292 | | | 1.03
|
||||
Pair | 1.9626 | 2.0842 | 2.2541 | 7.9 | 62.68
|
||||
Kspace | 0.44255 | 0.61231 | 0.73369 | 14.5 | 18.41
|
||||
Neigh | 0.0050733 | 0.0052404 | 0.0053804 | 0.2 | 0.16
|
||||
Comm | 0.077084 | 0.077385 | 0.077714 | 0.1 | 2.33
|
||||
Output | 0.00029039 | 0.00046909 | 0.0010037 | 0.0 | 0.01
|
||||
Modify | 0.50853 | 0.52962 | 0.53724 | 1.7 | 15.93
|
||||
Other | | 0.01615 | | | 0.49
|
||||
|
||||
Nlocal: 36 ave 38 max 34 min
|
||||
Nlocal: 36.0000 ave 38 max 34 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Nghost: 2527.75 ave 2547 max 2518 min
|
||||
Nghost: 2527.75 ave 2547 max 2518 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 10194.8 ave 11177 max 9437 min
|
||||
Neighs: 10194.8 ave 11177 max 9437 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 40779
|
||||
Ave neighs/atom = 283.188
|
||||
Ave neighs/atom = 283.18750
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
write_restart restart.1000
|
||||
System init for write_restart ...
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.302953
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
|
||||
G vector (1/distance) = 0.30295266
|
||||
grid = 9 8 16
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00105569
|
||||
estimated relative force accuracy = 7.33134e-05
|
||||
estimated absolute RMS force accuracy = 0.0010556863
|
||||
estimated relative force accuracy = 7.3313358e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 2640 288
|
||||
Neighbor list info ...
|
||||
@ -294,12 +297,14 @@ Neighbor list info ...
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.1000
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style charge from restart
|
||||
orthogonal box = (-0.04739235907204603 -0.041042988010289584 -0.21484841641189512) to (9.879392359072014 8.555804988010294 21.83644841641206)
|
||||
orthogonal box = (-0.047392358 -0.041042987 -0.21484765) to (9.8793924 8.5558050 21.836448)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
restoring pair style hybrid/overlay from restart
|
||||
144 atoms
|
||||
read_restart CPU = 0.000472307 secs
|
||||
read_restart CPU = 0.009 seconds
|
||||
include alpha_quartz_potential.mod
|
||||
#This script implements the BKS pair potential for various silicon dioxide compounds. Inner part is fixed with a harmonic potential. Long range Coulomb interactions are evaluated with the pppm method.
|
||||
|
||||
@ -314,8 +319,8 @@ pair_coeff 1 2 table potential_SiO2.TPF Si-O ${cut_off}
|
||||
pair_coeff 1 2 table potential_SiO2.TPF Si-O 10
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O ${cut_off} #See the potential file for more information
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O 10
|
||||
WARNING: 1 of 39901 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:471)
|
||||
WARNING: 1 of 39901 force values in table O-O are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:461)
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
#Neighbor style
|
||||
@ -338,25 +343,24 @@ QBMSST parameters:
|
||||
Initial energy calculated on first step
|
||||
Resetting global fix info from restart file:
|
||||
fix style: qbmsst, fix ID: shock
|
||||
fix_modify shock energy yes
|
||||
variable dhug equal f_shock[1]
|
||||
variable dray equal f_shock[2]
|
||||
variable lgr_vel equal f_shock[3]
|
||||
variable lgr_pos equal f_shock[4]
|
||||
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
|
||||
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo_style custom step v_T_qm press econserve vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo 500
|
||||
timestep ${delta_t}
|
||||
timestep 0.001
|
||||
restart 1000 restart
|
||||
#restart 1000 restart
|
||||
run 10000 #10 ps
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.302953
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
|
||||
G vector (1/distance) = 0.30295266
|
||||
grid = 9 8 16
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00105569
|
||||
estimated relative force accuracy = 7.33134e-05
|
||||
estimated absolute RMS force accuracy = 0.0010556863
|
||||
estimated relative force accuracy = 7.3313358e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 2640 288
|
||||
All restart file global fix info was re-assigned
|
||||
@ -378,53 +382,54 @@ Neighbor list info ...
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 79.71 | 79.71 | 79.71 Mbytes
|
||||
Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
1000 281.98328 -6031.2395 -2778.6227 1881.8369 9.9267847 8.596848 22.051297 -14113.621 1.3373278 13060.059 -0.79055793 0
|
||||
1500 266.12746 44405.573 -2777.9815 1739.6543 9.9267847 8.596848 20.385206 92590.239 -12.06041 397.47049 5.1624821 -37.823748
|
||||
2000 255.79411 17620.408 -2777.9685 1785.7619 9.9267847 8.596848 20.925494 48670.364 -16.082827 -4813.6764 3.2320016 -73.974437
|
||||
2500 256.8887 40153.833 -2778.4337 1752.9461 9.9267847 8.596848 20.540959 79665.002 7.7413878 -1368.8927 4.6059671 -112.35254
|
||||
3000 261.55251 5315.4799 -2779.0755 1834.3375 9.9267847 8.596848 21.4947 15896.368 22.588205 3192.882 1.1981949 -148.36068
|
||||
3500 261.57101 57911.809 -2778.1223 1713.3956 9.9267847 8.596848 20.077507 110996.8 -9.4471543 -3240.9018 6.2619064 -186.41261
|
||||
4000 254.88665 13952.95 -2778.4816 1818.2782 9.9267847 8.596848 21.306518 26833.588 2.2818412 647.88057 1.8705799 -222.72504
|
||||
4500 240.08908 73322.997 -2776.7382 1668.6666 9.9267847 8.596848 19.553375 151978.11 -43.917346 189.1572 8.1346613 -260.52885
|
||||
5000 214.49084 1925.2557 -2777.0657 1890.0985 9.9267847 8.596848 22.148106 -5218.7292 -44.5537 28890.787 -1.1364617 -297.26329
|
||||
5500 194.6515 71804.842 -2777.3417 1669.7297 9.9267847 8.596848 19.565832 146911.42 -34.911593 -3985.0635 8.0901523 -334.1879
|
||||
6000 186.23814 10196.007 -2777.1394 1837.3793 9.9267847 8.596848 21.530344 23550.907 -18.381207 13401.096 1.0708382 -371.9208
|
||||
6500 172.53603 5474.3725 -2777.4502 1818.0038 9.9267847 8.596848 21.303303 18389.825 -22.65951 -8026.2088 1.8820667 -407.83084
|
||||
7000 160.91186 107908.64 -2777.6746 1621.7378 9.9267847 8.596848 19.003464 196841.27 -8.6606903 5654.1938 10.099523 -444.9925
|
||||
7500 146.01905 147030.69 -2777.2543 1539.7536 9.9267847 8.596848 18.042777 253089.02 -43.928324 -6926.1018 13.532114 -478.63113
|
||||
8000 207.17758 837859.1 -2796.8957 989.32874 9.9267847 8.596848 11.592918 811765.11 1172.3778 89652.363 36.577833 -503.41923
|
||||
8500 725.15657 853732.89 -2832.3144 974.18299 9.9267847 8.596848 11.415441 773926.64 1749.5702 39098.598 37.21197 -524.17835
|
||||
9000 1554.6089 807867.74 -2843.0063 990.10922 9.9267847 8.596848 11.602064 749697.22 1959.0322 28239.71 36.545155 -544.77354
|
||||
9500 2440.1194 748145.05 -2839.2364 992.38871 9.9267847 8.596848 11.628775 691503.58 1437.0708 -28040.223 36.449715 -565.41198
|
||||
10000 3112.1817 823862.43 -2820.0495 982.35471 9.9267847 8.596848 11.511197 754954.89 1330.6807 26987.244 36.869828 -586.12357
|
||||
10500 3550.0273 868916.79 -2803.7678 983.70386 9.9267847 8.596848 11.527006 867368.45 1727.9058 140533.46 36.813341 -607.00946
|
||||
11000 3839.7527 830581.55 -2795.3804 995.31485 9.9267847 8.596848 11.663063 811740 1150.0462 94652.768 36.327201 -628.02229
|
||||
Loop time of 15.1476 on 4 procs for 10000 steps with 144 atoms
|
||||
Step v_T_qm Press Econserve Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
1000 281.98323 -6031.2507 -2778.6227 1881.8368 9.9267847 8.596848 22.051295 -14113.608 1.3371988 13059.97 -0.79055248 0
|
||||
1500 266.12743 44405.252 -2777.9815 1739.6551 9.9267847 8.596848 20.385215 92589.619 -12.060756 397.55607 5.1624473 -37.823753
|
||||
2000 255.79412 17620.89 -2777.9685 1785.7605 9.9267847 8.596848 20.925477 48671.42 -16.082485 -4813.8454 3.2320631 -73.974438
|
||||
2500 257.13592 39692.462 -2778.6986 1751.4095 9.9267847 8.596848 20.522952 80667.315 15.746345 -1656.6275 4.6703047 -112.35088
|
||||
3000 248.95332 9617.5633 -2778.937 1830.5557 9.9267847 8.596848 21.450385 25275.769 19.730704 9397.3972 1.3565331 -148.37113
|
||||
3500 247.70025 100159.87 -2778.0604 1610.8047 9.9267847 8.596848 18.875351 189849.69 -33.726976 -10516.027 10.557281 -185.61862
|
||||
4000 266.07224 848367.31 -2787.9052 992.46097 9.9267847 8.596848 11.629622 880163.37 1477.3994 160680.23 36.44669 -213.83067
|
||||
4500 645.86948 789169.63 -2822.9559 992.40405 9.9267847 8.596848 11.628955 696879.41 1039.4139 -22651.518 36.449073 -234.79958
|
||||
5000 1369.4257 735014.89 -2838.4571 1002.6048 9.9267847 8.596848 11.748487 648785.76 1170.3517 -62181.314 36.021977 -255.55776
|
||||
5500 2156.7632 768865.28 -2835.9297 995.94989 9.9267847 8.596848 11.670505 678013.94 1271.734 -38540.152 36.300612 -276.42588
|
||||
6000 2864.2837 773631.53 -2828.0627 993.01727 9.9267847 8.596848 11.63614 749067.81 1567.7659 30051.708 36.423398 -297.26898
|
||||
6500 3422.632 861319.73 -2810.1415 985.48363 9.9267847 8.596848 11.547861 816792.18 1535.8348 91451.363 36.738824 -318.12934
|
||||
7000 3798.2073 791521.73 -2801.7757 993.1961 9.9267847 8.596848 11.638236 677215.78 330.09854 -41650.204 36.415911 -338.86015
|
||||
7500 4060.7728 836165.25 -2789.6215 984.13658 9.9267847 8.596848 11.532077 780101.5 698.84908 53629.791 36.795223 -359.64284
|
||||
8000 4122.5641 754871.86 -2776.0049 1006.6266 9.9267847 8.596848 11.795613 699610.84 -124.86381 -7979.8848 35.853592 -380.58907
|
||||
8500 4087.3529 769727.63 -2775.3629 1018.2197 9.9267847 8.596848 11.931461 767853.09 415.9984 69995.141 35.368199 -401.90058
|
||||
9000 3958.4459 615996.33 -2758.7864 1058.0696 9.9267847 8.596848 12.398422 641295.34 -689.82578 -23107.426 33.699723 -423.43203
|
||||
9500 3746.2013 643366.31 -2767.1851 1043.1232 9.9267847 8.596848 12.22328 610176.19 -767.67823 -66774.534 34.325515 -445.14544
|
||||
10000 3723.8623 659730.11 -2781.6634 1034.0441 9.9267847 8.596848 12.116891 671355.25 0.037615796 -13217.642 34.705647 -466.9448
|
||||
10500 3705.48 637406.18 -2776.4898 1041.5851 9.9267847 8.596848 12.205256 725619.7 274.78304 47377.665 34.389914 -488.75102
|
||||
11000 3678.0139 648116.35 -2779.0968 1049.9523 9.9267847 8.596848 12.303303 723144.21 382.51198 51926.71 34.039587 -510.63944
|
||||
Loop time of 51.3151 on 4 procs for 10000 steps with 144 atoms
|
||||
|
||||
Performance: 57.039 ns/day, 0.421 hours/ns, 660.171 timesteps/s
|
||||
91.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 16.837 ns/day, 1.425 hours/ns, 194.874 timesteps/s
|
||||
94.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.7228 | 9.085 | 10.626 | 36.0 | 59.98
|
||||
Kspace | 1.6343 | 3.1795 | 4.5467 | 61.0 | 20.99
|
||||
Neigh | 0.02063 | 0.027076 | 0.034395 | 3.1 | 0.18
|
||||
Comm | 0.54719 | 0.57781 | 0.60468 | 2.8 | 3.81
|
||||
Output | 0.10128 | 0.1019 | 0.10373 | 0.3 | 0.67
|
||||
Modify | 2.0819 | 2.1159 | 2.1495 | 1.8 | 13.97
|
||||
Other | | 0.06035 | | | 0.40
|
||||
Pair | 26.662 | 32.362 | 38.05 | 70.9 | 63.07
|
||||
Kspace | 5.8733 | 11.582 | 17.302 | 118.9 | 22.57
|
||||
Neigh | 0.18541 | 0.22229 | 0.25113 | 5.0 | 0.43
|
||||
Comm | 1.4273 | 1.4501 | 1.483 | 1.9 | 2.83
|
||||
Output | 0.0011935 | 0.0018681 | 0.003891 | 2.7 | 0.00
|
||||
Modify | 5.4539 | 5.5056 | 5.5294 | 1.3 | 10.73
|
||||
Other | | 0.1916 | | | 0.37
|
||||
|
||||
Nlocal: 36 ave 38 max 33 min
|
||||
Nlocal: 36.0000 ave 37 max 35 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 4159.50 ave 4171 max 4140 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 4267 ave 4304 max 4239 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Neighs: 18859.2 ave 25108 max 12333 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 17967.8 ave 20291 max 15710 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 75437
|
||||
Ave neighs/atom = 523.868
|
||||
Neighbor list builds = 95
|
||||
Total # of neighbors = 71871
|
||||
Ave neighs/atom = 499.10417
|
||||
Neighbor list builds = 161
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:17
|
||||
shell rm restart.1000
|
||||
Total wall time: 0:01:01
|
||||
@ -0,0 +1,66 @@
|
||||
map file: styrene growth
|
||||
|
||||
1 edgeIDs
|
||||
30 equivalences
|
||||
16 createIDs
|
||||
|
||||
InitiatorIDs
|
||||
|
||||
4
|
||||
13
|
||||
|
||||
EdgeIDs
|
||||
|
||||
30
|
||||
|
||||
CreateIDs
|
||||
|
||||
1
|
||||
2
|
||||
3
|
||||
4
|
||||
5
|
||||
6
|
||||
7
|
||||
8
|
||||
9
|
||||
10
|
||||
11
|
||||
12
|
||||
13
|
||||
14
|
||||
15
|
||||
16
|
||||
|
||||
Equivalences
|
||||
|
||||
1 45
|
||||
2 46
|
||||
3 44
|
||||
4 43
|
||||
5 42
|
||||
6 41
|
||||
7 40
|
||||
8 39
|
||||
9 38
|
||||
10 37
|
||||
11 36
|
||||
12 35
|
||||
13 34
|
||||
14 33
|
||||
15 32
|
||||
16 31
|
||||
17 17
|
||||
18 18
|
||||
19 19
|
||||
20 20
|
||||
21 21
|
||||
22 22
|
||||
23 23
|
||||
24 24
|
||||
25 25
|
||||
26 26
|
||||
27 27
|
||||
28 28
|
||||
29 29
|
||||
30 30
|
||||
@ -0,0 +1,456 @@
|
||||
molecule template: end of chain plus polymerized styrene
|
||||
|
||||
46 atoms
|
||||
48 bonds
|
||||
81 angles
|
||||
121 dihedrals
|
||||
35 impropers
|
||||
1 fragments
|
||||
|
||||
Fragments
|
||||
|
||||
create_fit 34 44
|
||||
|
||||
Types
|
||||
|
||||
1 1
|
||||
2 2
|
||||
3 1
|
||||
4 5
|
||||
5 1
|
||||
6 2
|
||||
7 1
|
||||
8 2
|
||||
9 1
|
||||
10 2
|
||||
11 1
|
||||
12 2
|
||||
13 2
|
||||
14 6
|
||||
15 2
|
||||
16 2
|
||||
17 1
|
||||
18 2
|
||||
19 1
|
||||
20 5
|
||||
21 1
|
||||
22 2
|
||||
23 1
|
||||
24 2
|
||||
25 1
|
||||
26 2
|
||||
27 1
|
||||
28 2
|
||||
29 2
|
||||
30 6
|
||||
31 1
|
||||
32 2
|
||||
33 1
|
||||
34 5
|
||||
35 1
|
||||
36 2
|
||||
37 1
|
||||
38 2
|
||||
39 1
|
||||
40 2
|
||||
41 1
|
||||
42 2
|
||||
43 2
|
||||
44 6
|
||||
45 2
|
||||
46 2
|
||||
|
||||
Charges
|
||||
|
||||
1 -0.129000
|
||||
2 0.123700
|
||||
3 0.026600
|
||||
4 -0.018200
|
||||
5 -0.129000
|
||||
6 0.123700
|
||||
7 -0.173400
|
||||
8 0.140300
|
||||
9 -0.113400
|
||||
10 0.128800
|
||||
11 -0.173400
|
||||
12 0.140300
|
||||
13 0.051600
|
||||
14 -0.069600
|
||||
15 0.035400
|
||||
16 0.035400
|
||||
17 -0.129000
|
||||
18 0.123700
|
||||
19 0.026600
|
||||
20 -0.018200
|
||||
21 -0.129000
|
||||
22 0.123700
|
||||
23 -0.173400
|
||||
24 0.140300
|
||||
25 -0.113400
|
||||
26 0.128800
|
||||
27 -0.173400
|
||||
28 0.140300
|
||||
29 0.051600
|
||||
30 -0.069600
|
||||
31 -0.129000
|
||||
32 0.123700
|
||||
33 0.026600
|
||||
34 -0.018200
|
||||
35 -0.129000
|
||||
36 0.123700
|
||||
37 -0.173400
|
||||
38 0.140300
|
||||
39 -0.113400
|
||||
40 0.128800
|
||||
41 -0.173400
|
||||
42 0.140300
|
||||
43 0.051600
|
||||
44 -0.069600
|
||||
45 0.035400
|
||||
46 0.035400
|
||||
|
||||
Coords
|
||||
|
||||
1 24.130699 1.043900 -1.309300
|
||||
2 25.062700 1.582900 -1.309300
|
||||
3 22.900700 1.753900 -1.309300
|
||||
4 22.900700 3.253900 -1.309300
|
||||
5 21.670700 1.043900 -1.309300
|
||||
6 20.738701 1.582900 -1.309300
|
||||
7 21.670700 -0.376100 -1.309300
|
||||
8 20.738701 -0.915100 -1.309300
|
||||
9 22.900700 -1.086100 -1.309300
|
||||
10 22.900700 -2.163100 -1.309300
|
||||
11 24.130699 -0.376100 -1.309300
|
||||
12 25.062700 -0.915100 -1.309300
|
||||
13 23.766701 3.658900 -0.952300
|
||||
14 21.622700 3.802900 -1.871300
|
||||
15 21.672701 4.544900 -1.970300
|
||||
16 20.979700 2.979900 -2.165300
|
||||
17 13.465800 0.682500 -1.658900
|
||||
18 14.397800 1.221500 -1.658900
|
||||
19 12.235800 1.392500 -1.658900
|
||||
20 12.235800 2.892500 -1.658900
|
||||
21 11.005800 0.682500 -1.658900
|
||||
22 10.073800 1.221500 -1.658900
|
||||
23 11.005800 -0.737500 -1.658900
|
||||
24 10.073800 -1.276500 -1.658900
|
||||
25 12.235800 -1.447500 -1.658900
|
||||
26 12.235800 -2.524500 -1.658900
|
||||
27 13.465800 -0.737500 -1.658900
|
||||
28 14.397800 -1.276500 -1.658900
|
||||
29 13.101800 3.297500 -1.301900
|
||||
30 10.957800 3.441500 -2.220900
|
||||
31 18.663500 0.855500 -1.372100
|
||||
32 19.595501 1.394500 -1.372100
|
||||
33 17.433500 1.565500 -1.372100
|
||||
34 17.433500 3.065500 -1.372100
|
||||
35 16.203501 0.855500 -1.372100
|
||||
36 15.271500 1.394500 -1.372100
|
||||
37 16.203501 -0.564500 -1.372100
|
||||
38 15.271500 -1.103500 -1.372100
|
||||
39 17.433500 -1.274500 -1.372100
|
||||
40 17.433500 -2.351500 -1.372100
|
||||
41 18.663500 -0.564500 -1.372100
|
||||
42 19.595501 -1.103500 -1.372100
|
||||
43 18.299500 3.470500 -1.015100
|
||||
44 16.155500 3.614500 -1.934100
|
||||
45 16.205500 4.356500 -2.033100
|
||||
46 15.512500 2.791500 -2.228100
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 2 1 3
|
||||
3 2 1 11
|
||||
4 11 3 4
|
||||
5 2 3 5
|
||||
6 12 13 4
|
||||
7 13 4 14
|
||||
8 1 5 6
|
||||
9 2 5 7
|
||||
10 1 7 8
|
||||
11 2 7 9
|
||||
12 1 9 10
|
||||
13 2 9 11
|
||||
14 1 11 12
|
||||
15 10 15 14
|
||||
16 10 16 14
|
||||
17 9 14 34
|
||||
18 1 17 18
|
||||
19 2 17 19
|
||||
20 2 17 27
|
||||
21 7 19 20
|
||||
22 2 19 21
|
||||
23 8 29 20
|
||||
24 9 30 20
|
||||
25 9 44 20
|
||||
26 1 21 22
|
||||
27 2 21 23
|
||||
28 1 23 24
|
||||
29 2 23 25
|
||||
30 1 25 26
|
||||
31 2 25 27
|
||||
32 1 27 28
|
||||
33 1 31 32
|
||||
34 2 31 33
|
||||
35 2 31 41
|
||||
36 7 33 34
|
||||
37 2 33 35
|
||||
38 8 43 34
|
||||
39 9 44 34
|
||||
40 1 35 36
|
||||
41 2 35 37
|
||||
42 1 37 38
|
||||
43 2 37 39
|
||||
44 1 39 40
|
||||
45 2 39 41
|
||||
46 1 41 42
|
||||
47 10 45 44
|
||||
48 10 46 44
|
||||
|
||||
Angles
|
||||
|
||||
1 1 3 1 2
|
||||
2 1 11 1 2
|
||||
3 2 3 1 11
|
||||
4 17 1 3 4
|
||||
5 2 1 3 5
|
||||
6 17 5 3 4
|
||||
7 18 3 4 13
|
||||
8 19 3 4 14
|
||||
9 20 13 4 14
|
||||
10 1 3 5 6
|
||||
11 2 3 5 7
|
||||
12 1 7 5 6
|
||||
13 1 5 7 8
|
||||
14 2 5 7 9
|
||||
15 1 9 7 8
|
||||
16 1 7 9 10
|
||||
17 2 7 9 11
|
||||
18 1 11 9 10
|
||||
19 2 1 11 9
|
||||
20 1 1 11 12
|
||||
21 1 9 11 12
|
||||
22 21 15 14 4
|
||||
23 21 16 14 4
|
||||
24 22 4 14 34
|
||||
25 15 15 14 16
|
||||
26 14 15 14 34
|
||||
27 14 16 14 34
|
||||
28 1 19 17 18
|
||||
29 1 27 17 18
|
||||
30 2 19 17 27
|
||||
31 9 17 19 20
|
||||
32 2 17 19 21
|
||||
33 9 21 19 20
|
||||
34 10 19 20 29
|
||||
35 11 19 20 30
|
||||
36 11 19 20 44
|
||||
37 12 29 20 30
|
||||
38 12 29 20 44
|
||||
39 13 30 20 44
|
||||
40 1 19 21 22
|
||||
41 2 19 21 23
|
||||
42 1 23 21 22
|
||||
43 1 21 23 24
|
||||
44 2 21 23 25
|
||||
45 1 25 23 24
|
||||
46 1 23 25 26
|
||||
47 2 23 25 27
|
||||
48 1 27 25 26
|
||||
49 2 17 27 25
|
||||
50 1 17 27 28
|
||||
51 1 25 27 28
|
||||
52 1 33 31 32
|
||||
53 1 41 31 32
|
||||
54 2 33 31 41
|
||||
55 9 31 33 34
|
||||
56 2 31 33 35
|
||||
57 9 35 33 34
|
||||
58 11 33 34 14
|
||||
59 12 43 34 14
|
||||
60 13 14 34 44
|
||||
61 10 33 34 43
|
||||
62 11 33 34 44
|
||||
63 12 43 34 44
|
||||
64 1 33 35 36
|
||||
65 2 33 35 37
|
||||
66 1 37 35 36
|
||||
67 1 35 37 38
|
||||
68 2 35 37 39
|
||||
69 1 39 37 38
|
||||
70 1 37 39 40
|
||||
71 2 37 39 41
|
||||
72 1 41 39 40
|
||||
73 2 31 41 39
|
||||
74 1 31 41 42
|
||||
75 1 39 41 42
|
||||
76 16 20 44 34
|
||||
77 14 45 44 20
|
||||
78 14 46 44 20
|
||||
79 14 45 44 34
|
||||
80 14 46 44 34
|
||||
81 15 45 44 46
|
||||
|
||||
Dihedrals
|
||||
|
||||
1 20 2 1 3 4
|
||||
2 2 5 3 1 2
|
||||
3 21 11 1 3 4
|
||||
4 4 11 1 3 5
|
||||
5 2 9 11 1 2
|
||||
6 5 2 1 11 12
|
||||
7 4 3 1 11 9
|
||||
8 2 3 1 11 12
|
||||
9 22 1 3 4 13
|
||||
10 23 1 3 4 14
|
||||
11 22 5 3 4 13
|
||||
12 23 5 3 4 14
|
||||
13 2 1 3 5 6
|
||||
14 4 1 3 5 7
|
||||
15 20 6 5 3 4
|
||||
16 21 7 5 3 4
|
||||
17 24 3 4 14 15
|
||||
18 24 3 4 14 16
|
||||
19 25 3 4 14 34
|
||||
20 26 13 4 14 15
|
||||
21 26 13 4 14 16
|
||||
22 27 13 4 14 34
|
||||
23 2 3 5 7 8
|
||||
24 4 3 5 7 9
|
||||
25 5 6 5 7 8
|
||||
26 2 9 7 5 6
|
||||
27 2 5 7 9 10
|
||||
28 4 5 7 9 11
|
||||
29 5 8 7 9 10
|
||||
30 2 11 9 7 8
|
||||
31 4 7 9 11 1
|
||||
32 2 7 9 11 12
|
||||
33 2 1 11 9 10
|
||||
34 5 10 9 11 12
|
||||
35 28 4 14 34 33
|
||||
36 29 4 14 34 43
|
||||
37 30 4 14 34 44
|
||||
38 31 15 14 34 33
|
||||
39 32 15 14 34 43
|
||||
40 33 15 14 34 44
|
||||
41 31 16 14 34 33
|
||||
42 32 16 14 34 43
|
||||
43 33 16 14 34 44
|
||||
44 10 18 17 19 20
|
||||
45 2 21 19 17 18
|
||||
46 11 27 17 19 20
|
||||
47 4 27 17 19 21
|
||||
48 2 25 27 17 18
|
||||
49 5 18 17 27 28
|
||||
50 4 19 17 27 25
|
||||
51 2 19 17 27 28
|
||||
52 12 17 19 20 29
|
||||
53 13 17 19 20 30
|
||||
54 13 17 19 20 44
|
||||
55 12 21 19 20 29
|
||||
56 13 21 19 20 30
|
||||
57 13 21 19 20 44
|
||||
58 2 17 19 21 22
|
||||
59 4 17 19 21 23
|
||||
60 10 22 21 19 20
|
||||
61 11 23 21 19 20
|
||||
62 34 34 44 20 19
|
||||
63 31 45 44 20 19
|
||||
64 31 46 44 20 19
|
||||
65 35 34 44 20 29
|
||||
66 32 45 44 20 29
|
||||
67 32 46 44 20 29
|
||||
68 36 34 44 20 30
|
||||
69 33 45 44 20 30
|
||||
70 33 46 44 20 30
|
||||
71 2 19 21 23 24
|
||||
72 4 19 21 23 25
|
||||
73 5 22 21 23 24
|
||||
74 2 25 23 21 22
|
||||
75 2 21 23 25 26
|
||||
76 4 21 23 25 27
|
||||
77 5 24 23 25 26
|
||||
78 2 27 25 23 24
|
||||
79 4 23 25 27 17
|
||||
80 2 23 25 27 28
|
||||
81 2 17 27 25 26
|
||||
82 5 26 25 27 28
|
||||
83 10 32 31 33 34
|
||||
84 2 35 33 31 32
|
||||
85 11 41 31 33 34
|
||||
86 4 41 31 33 35
|
||||
87 2 39 41 31 32
|
||||
88 5 32 31 41 42
|
||||
89 4 33 31 41 39
|
||||
90 2 33 31 41 42
|
||||
91 13 31 33 34 14
|
||||
92 12 31 33 34 43
|
||||
93 13 31 33 34 44
|
||||
94 13 35 33 34 14
|
||||
95 12 35 33 34 43
|
||||
96 13 35 33 34 44
|
||||
97 2 31 33 35 36
|
||||
98 4 31 33 35 37
|
||||
99 10 36 35 33 34
|
||||
100 11 37 35 33 34
|
||||
101 36 20 44 34 14
|
||||
102 33 45 44 34 14
|
||||
103 33 46 44 34 14
|
||||
104 34 20 44 34 33
|
||||
105 31 45 44 34 33
|
||||
106 31 46 44 34 33
|
||||
107 35 20 44 34 43
|
||||
108 32 45 44 34 43
|
||||
109 32 46 44 34 43
|
||||
110 2 33 35 37 38
|
||||
111 4 33 35 37 39
|
||||
112 5 36 35 37 38
|
||||
113 2 39 37 35 36
|
||||
114 2 35 37 39 40
|
||||
115 4 35 37 39 41
|
||||
116 5 38 37 39 40
|
||||
117 2 41 39 37 38
|
||||
118 4 37 39 41 31
|
||||
119 2 37 39 41 42
|
||||
120 2 31 41 39 40
|
||||
121 5 40 39 41 42
|
||||
|
||||
Impropers
|
||||
|
||||
1 1 3 1 11 2
|
||||
2 8 1 3 5 4
|
||||
3 9 3 4 13 14
|
||||
4 1 3 5 7 6
|
||||
5 1 5 7 9 8
|
||||
6 1 7 9 11 10
|
||||
7 1 1 11 9 12
|
||||
8 1 19 17 27 18
|
||||
9 5 17 19 21 20
|
||||
10 1 19 21 23 22
|
||||
11 1 21 23 25 24
|
||||
12 1 23 25 27 26
|
||||
13 1 17 27 25 28
|
||||
14 1 33 31 41 32
|
||||
15 5 31 33 35 34
|
||||
16 1 33 35 37 36
|
||||
17 1 35 37 39 38
|
||||
18 1 37 39 41 40
|
||||
19 1 31 41 39 42
|
||||
20 1 15 14 16 4
|
||||
21 1 15 14 4 34
|
||||
22 1 16 14 4 34
|
||||
23 1 15 14 16 34
|
||||
24 1 19 20 29 30
|
||||
25 1 19 20 29 44
|
||||
26 1 19 20 30 44
|
||||
27 1 29 20 30 44
|
||||
28 1 33 34 43 14
|
||||
29 1 33 34 14 44
|
||||
30 1 43 34 14 44
|
||||
31 1 33 34 43 44
|
||||
32 1 45 44 34 20
|
||||
33 1 46 44 34 20
|
||||
34 1 45 44 46 20
|
||||
35 1 45 44 46 34
|
||||
@ -0,0 +1,294 @@
|
||||
molecule template: end of styrene chain
|
||||
|
||||
30 atoms
|
||||
31 bonds
|
||||
51 angles
|
||||
73 dihedrals
|
||||
21 impropers
|
||||
|
||||
Types
|
||||
|
||||
1 2
|
||||
2 2
|
||||
3 6
|
||||
4 2
|
||||
5 2
|
||||
6 1
|
||||
7 2
|
||||
8 1
|
||||
9 2
|
||||
10 1
|
||||
11 2
|
||||
12 1
|
||||
13 5
|
||||
14 1
|
||||
15 2
|
||||
16 1
|
||||
17 1
|
||||
18 2
|
||||
19 1
|
||||
20 5
|
||||
21 1
|
||||
22 2
|
||||
23 1
|
||||
24 2
|
||||
25 1
|
||||
26 2
|
||||
27 1
|
||||
28 2
|
||||
29 2
|
||||
30 6
|
||||
|
||||
Coords
|
||||
|
||||
1 59.89981112372972 62.733697275315585 59.09884284578856
|
||||
2 61.41970248324232 63.42116581894993 59.52874545893742
|
||||
3 60.864754970096406 62.91724243011892 59.559720865992695
|
||||
4 62.139819000186826 61.41011937002877 60.81065044071466
|
||||
5 60.036455711425084 57.160029629288026 60.31958663310848
|
||||
6 59.734195751174056 58.18706337912225 60.20562410798949
|
||||
7 57.64574781117771 57.712432799329 59.860109977091554
|
||||
8 58.37408644866664 58.50134169314242 59.94422053768215
|
||||
9 56.94300092269842 60.093170109004795 59.5955638127831
|
||||
10 57.974275786582744 59.85577775892068 59.793714995577716
|
||||
11 58.63231375134033 61.922969938852454 59.79065033121885
|
||||
12 58.934573711591355 60.89593618901822 59.904612856337835
|
||||
13 61.30908151524225 61.68041745837013 60.28316188676589
|
||||
14 60.29468229868386 60.58165855333751 60.16601625920239
|
||||
15 61.725768540066994 58.98982945913568 60.51467315154424
|
||||
16 60.69449367618267 59.2272218092198 60.31652196874961
|
||||
17 56.90935800040509 62.609851248143706 59.150831390216375
|
||||
18 57.940632148874506 62.37245957639904 59.3489824055682
|
||||
19 56.509546622906285 63.96428799226142 59.00032568066915
|
||||
20 57.52394583946467 65.06304689729403 59.11747130823266
|
||||
21 55.14943732039887 64.27856630628159 58.738922110361806
|
||||
22 54.84717807556275 65.30559937777636 58.62495975268562
|
||||
23 54.18913939539026 63.23840787618404 58.62802424960169
|
||||
24 53.15786524692084 63.4757995479287 58.42987323424986
|
||||
25 54.58895077288906 61.88397113206633 58.77852995914891
|
||||
26 53.86061213540014 61.09506223825291 58.69441939855832
|
||||
27 55.94906007539648 61.56969281804616 59.039933529456256
|
||||
28 56.2513193202326 60.54265974655139 59.15389588713244
|
||||
29 58.35468332440925 64.79274880895268 59.64495986218142
|
||||
30 57.07961929431883 66.29987186904283 58.394030287459465
|
||||
|
||||
Charges
|
||||
|
||||
1 0.0354
|
||||
2 0.0354
|
||||
3 -0.0696
|
||||
4 0.0516
|
||||
5 0.1403
|
||||
6 -0.1734
|
||||
7 0.1288
|
||||
8 -0.1134
|
||||
9 0.1403
|
||||
10 -0.1734
|
||||
11 0.1237
|
||||
12 -0.129
|
||||
13 -0.0182
|
||||
14 0.0266
|
||||
15 0.1237
|
||||
16 -0.129
|
||||
17 -0.129
|
||||
18 0.1237
|
||||
19 0.0266
|
||||
20 -0.0182
|
||||
21 -0.129
|
||||
22 0.1237
|
||||
23 -0.1734
|
||||
24 0.1403
|
||||
25 -0.1134
|
||||
26 0.1288
|
||||
27 -0.1734
|
||||
28 0.1403
|
||||
29 0.0516
|
||||
30 -0.0696
|
||||
|
||||
Bonds
|
||||
|
||||
1 10 1 3
|
||||
2 10 2 3
|
||||
3 8 4 13
|
||||
4 1 6 5
|
||||
5 1 8 7
|
||||
6 2 8 6
|
||||
7 1 10 9
|
||||
8 2 10 8
|
||||
9 1 12 11
|
||||
10 2 12 10
|
||||
11 9 13 3
|
||||
12 7 14 13
|
||||
13 2 14 12
|
||||
14 1 16 15
|
||||
15 2 16 14
|
||||
16 2 16 6
|
||||
17 1 17 18
|
||||
18 2 17 19
|
||||
19 2 17 27
|
||||
20 7 19 20
|
||||
21 2 19 21
|
||||
22 9 20 30
|
||||
23 9 20 3
|
||||
24 1 21 22
|
||||
25 2 21 23
|
||||
26 1 23 24
|
||||
27 2 23 25
|
||||
28 1 25 26
|
||||
29 2 25 27
|
||||
30 1 27 28
|
||||
31 8 29 20
|
||||
|
||||
Angles
|
||||
|
||||
1 16 20 3 13
|
||||
2 14 2 3 20
|
||||
3 14 1 3 20
|
||||
4 14 2 3 13
|
||||
5 14 1 3 13
|
||||
6 15 2 3 1
|
||||
7 2 16 6 8
|
||||
8 1 16 6 5
|
||||
9 1 8 6 5
|
||||
10 1 10 8 7
|
||||
11 2 10 8 6
|
||||
12 1 6 8 7
|
||||
13 1 12 10 9
|
||||
14 2 12 10 8
|
||||
15 1 8 10 9
|
||||
16 1 14 12 11
|
||||
17 2 14 12 10
|
||||
18 1 10 12 11
|
||||
19 10 14 13 4
|
||||
20 11 14 13 3
|
||||
21 12 4 13 3
|
||||
22 9 16 14 13
|
||||
23 2 16 14 12
|
||||
24 9 12 14 13
|
||||
25 1 14 16 15
|
||||
26 1 6 16 15
|
||||
27 2 14 16 6
|
||||
28 1 19 17 18
|
||||
29 1 27 17 18
|
||||
30 2 19 17 27
|
||||
31 9 17 19 20
|
||||
32 2 17 19 21
|
||||
33 9 21 19 20
|
||||
34 10 19 20 29
|
||||
35 11 19 20 30
|
||||
36 11 19 20 3
|
||||
37 12 29 20 30
|
||||
38 12 29 20 3
|
||||
39 13 30 20 3
|
||||
40 1 19 21 22
|
||||
41 2 19 21 23
|
||||
42 1 23 21 22
|
||||
43 1 21 23 24
|
||||
44 2 21 23 25
|
||||
45 1 25 23 24
|
||||
46 1 23 25 26
|
||||
47 2 23 25 27
|
||||
48 1 27 25 26
|
||||
49 2 17 27 25
|
||||
50 1 17 27 28
|
||||
51 1 25 27 28
|
||||
|
||||
Dihedrals
|
||||
|
||||
1 2 8 6 16 15
|
||||
2 2 16 6 8 7
|
||||
3 2 6 8 10 9
|
||||
4 4 10 8 6 16
|
||||
5 2 10 8 6 5
|
||||
6 5 7 8 6 5
|
||||
7 2 8 10 12 11
|
||||
8 2 12 10 8 7
|
||||
9 4 12 10 8 6
|
||||
10 5 9 10 8 7
|
||||
11 10 11 12 14 13
|
||||
12 11 10 12 14 13
|
||||
13 2 14 12 10 9
|
||||
14 4 14 12 10 8
|
||||
15 5 11 12 10 9
|
||||
16 17 14 13 3 20
|
||||
17 14 14 13 3 2
|
||||
18 14 14 13 3 1
|
||||
19 18 4 13 3 20
|
||||
20 15 4 13 3 2
|
||||
21 15 4 13 3 1
|
||||
22 2 12 14 16 15
|
||||
23 12 16 14 13 4
|
||||
24 13 16 14 13 3
|
||||
25 12 12 14 13 4
|
||||
26 13 12 14 13 3
|
||||
27 2 16 14 12 11
|
||||
28 4 16 14 12 10
|
||||
29 10 15 16 14 13
|
||||
30 11 6 16 14 13
|
||||
31 4 6 16 14 12
|
||||
32 5 15 16 6 5
|
||||
33 4 14 16 6 8
|
||||
34 2 14 16 6 5
|
||||
35 10 18 17 19 20
|
||||
36 11 27 17 19 20
|
||||
37 4 27 17 19 21
|
||||
38 5 18 17 27 28
|
||||
39 4 19 17 27 25
|
||||
40 2 19 17 27 28
|
||||
41 2 21 19 17 18
|
||||
42 12 17 19 20 29
|
||||
43 13 17 19 20 30
|
||||
44 13 17 19 20 3
|
||||
45 12 21 19 20 29
|
||||
46 13 21 19 20 30
|
||||
47 13 21 19 20 3
|
||||
48 2 17 19 21 22
|
||||
49 4 17 19 21 23
|
||||
50 17 19 20 3 13
|
||||
51 14 19 20 3 2
|
||||
52 14 19 20 3 1
|
||||
53 18 29 20 3 13
|
||||
54 15 29 20 3 2
|
||||
55 15 29 20 3 1
|
||||
56 19 30 20 3 13
|
||||
57 16 30 20 3 2
|
||||
58 16 30 20 3 1
|
||||
59 10 22 21 19 20
|
||||
60 11 23 21 19 20
|
||||
61 2 19 21 23 24
|
||||
62 4 19 21 23 25
|
||||
63 5 22 21 23 24
|
||||
64 2 25 23 21 22
|
||||
65 2 21 23 25 26
|
||||
66 4 21 23 25 27
|
||||
67 5 24 23 25 26
|
||||
68 2 27 25 23 24
|
||||
69 4 23 25 27 17
|
||||
70 2 23 25 27 28
|
||||
71 5 26 25 27 28
|
||||
72 2 25 27 17 18
|
||||
73 2 17 27 25 26
|
||||
|
||||
Impropers
|
||||
|
||||
1 1 2 3 13 20
|
||||
2 1 1 3 13 20
|
||||
3 1 2 3 1 20
|
||||
4 1 2 3 1 13
|
||||
5 1 16 6 8 5
|
||||
6 1 10 8 6 7
|
||||
7 1 12 10 8 9
|
||||
8 1 14 12 10 11
|
||||
9 7 14 13 4 3
|
||||
10 5 16 14 12 13
|
||||
11 1 14 16 6 15
|
||||
12 1 19 17 27 18
|
||||
13 5 17 19 21 20
|
||||
14 1 19 20 29 30
|
||||
15 1 19 20 29 3
|
||||
16 1 19 20 30 3
|
||||
17 1 29 20 30 3
|
||||
18 1 19 21 23 22
|
||||
19 1 21 23 25 24
|
||||
20 1 23 25 27 26
|
||||
21 1 17 27 25 28
|
||||
@ -0,0 +1,48 @@
|
||||
# use bond/react 'create atoms' feature to add 30 new styrene monomers to chain
|
||||
|
||||
units real
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
pair_style lj/class2/coul/long 8.5
|
||||
|
||||
angle_style class2
|
||||
|
||||
bond_style class2
|
||||
|
||||
dihedral_style class2
|
||||
|
||||
improper_style class2
|
||||
|
||||
variable T equal 530
|
||||
|
||||
read_data trimer.data &
|
||||
extra/bond/per/atom 5 &
|
||||
extra/angle/per/atom 15 &
|
||||
extra/dihedral/per/atom 15 &
|
||||
extra/improper/per/atom 25 &
|
||||
extra/special/per/atom 25
|
||||
|
||||
molecule mol1 grow_styrene_pre.data_template
|
||||
molecule mol2 grow_styrene_post.data_template
|
||||
|
||||
fix myrxns all bond/react stabilization yes statted_grp .03 &
|
||||
react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map &
|
||||
modify_create fit create_fit overlap 2.0 &
|
||||
stabilize_steps 100 max_rxn 30
|
||||
|
||||
fix 1 statted_grp_REACT nvt temp $T $T 100
|
||||
|
||||
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
|
||||
|
||||
thermo_style custom step temp press density f_myrxns[1]
|
||||
|
||||
thermo 100
|
||||
|
||||
run 8000
|
||||
|
||||
# write_data final.data nofix
|
||||
@ -0,0 +1,196 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
Reading data file ...
|
||||
orthogonal box = (50.000000 50.000000 50.000000) to (250.00000 250.00000 250.00000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
48 atoms
|
||||
reading velocities ...
|
||||
48 velocities
|
||||
scanning bonds ...
|
||||
8 = max bonds/atom
|
||||
scanning angles ...
|
||||
21 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
33 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
29 = max impropers/atom
|
||||
reading bonds ...
|
||||
50 bonds
|
||||
reading angles ...
|
||||
84 angles
|
||||
reading dihedrals ...
|
||||
127 dihedrals
|
||||
reading impropers ...
|
||||
36 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
8 = max # of 1-3 neighbors
|
||||
17 = max # of 1-4 neighbors
|
||||
46 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.077 seconds
|
||||
Read molecule template mol1:
|
||||
1 molecules
|
||||
30 atoms with max type 6
|
||||
31 bonds with max type 10
|
||||
51 angles with max type 16
|
||||
73 dihedrals with max type 19
|
||||
21 impropers with max type 7
|
||||
Read molecule template mol2:
|
||||
1 molecules
|
||||
46 atoms with max type 6
|
||||
48 bonds with max type 13
|
||||
81 angles with max type 22
|
||||
121 dihedrals with max type 36
|
||||
35 impropers with max type 9
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
dynamic group statted_grp_REACT defined
|
||||
PPPM initialization ...
|
||||
WARNING: System is not charge neutral, net charge = -0.00060000000 (../kspace.cpp:324)
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:339)
|
||||
G vector (1/distance) = 0.20144813
|
||||
grid = 45 45 45
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00053712952
|
||||
estimated relative force accuracy = 1.6175496e-06
|
||||
using double precision KISS FFT
|
||||
3d grid and FFT values/proc = 125000 91125
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 39 39 39
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) pair lj/class2/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) fix bond/react, occasional, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 48.02 | 48.02 | 48.02 Mbytes
|
||||
Step Temp Press Density f_myrxns[1]
|
||||
0 496.23742 0.9983211 6.4856516e-05 0
|
||||
100 534.05394 -0.76952227 6.4856516e-05 0
|
||||
200 552.2225 -0.55375493 6.4856516e-05 0
|
||||
300 857.52834 -0.4272061 8.6475354e-05 1
|
||||
400 714.10681 1.5004615 8.6475354e-05 1
|
||||
500 678.19171 0.21965471 8.6475354e-05 1
|
||||
600 572.3234 0.87879933 8.6475354e-05 1
|
||||
700 996.17398 -0.24269717 0.00010809419 2
|
||||
800 904.50395 1.3662054 0.00010809419 2
|
||||
900 1097.1568 -2.2909907 0.00012971303 3
|
||||
1000 954.08892 1.7705672 0.00012971303 3
|
||||
1100 1102.0377 -1.7018446 0.00015133187 4
|
||||
1200 1239.785 -0.30442903 0.00015133187 4
|
||||
1300 1388.4127 1.3301175 0.00017295071 5
|
||||
1400 1559.3853 1.6709729 0.00017295071 5
|
||||
1500 1471.8623 0.8268427 0.00017295071 5
|
||||
1600 1543.6793 2.1987908 0.00019456955 6
|
||||
1700 1694.5595 0.48852817 0.00019456955 6
|
||||
1800 1632.7737 -1.4617692 0.00021618839 7
|
||||
1900 1922.6502 1.1664257 0.00021618839 7
|
||||
2000 2223.503 -0.95799878 0.00023780722 8
|
||||
2100 2142.6035 0.88444463 0.00025942606 9
|
||||
2200 2298.8636 3.4239313 0.00025942606 9
|
||||
2300 2252.4355 0.82167302 0.00025942606 9
|
||||
2400 2321.0788 1.7499714 0.00025942606 9
|
||||
2500 2095.6715 0.55288444 0.00025942606 9
|
||||
2600 2136.0316 -3.833114 0.00025942606 9
|
||||
2700 2466.3134 -2.2519511 0.00025942606 9
|
||||
2800 2294.3454 1.0637304 0.00025942606 9
|
||||
2900 2340.3891 1.3997049 0.0002810449 10
|
||||
3000 2272.0013 -0.27591886 0.0002810449 10
|
||||
3100 2333.9696 -0.11772138 0.0002810449 10
|
||||
3200 2409.0946 -1.025473 0.0002810449 10
|
||||
3300 2148.023 1.6752329 0.0002810449 10
|
||||
3400 2267.636 -0.45297583 0.0002810449 10
|
||||
3500 2457.622 0.35627297 0.0002810449 10
|
||||
3600 2288.008 -15.516626 0.00030266374 11
|
||||
3700 2458.2681 1.4571773 0.00030266374 11
|
||||
3800 2566.7623 -29.140553 0.00032428258 12
|
||||
3900 2839.4062 0.64583638 0.00032428258 12
|
||||
4000 2893.9852 -52.954497 0.00034590142 13
|
||||
4100 3021.3611 -65.03731 0.00036752025 14
|
||||
4200 3002.7136 1.5750081 0.00036752025 14
|
||||
4300 3218.6248 -120.74039 0.00038913909 15
|
||||
4400 3345.1482 -0.96545269 0.00038913909 15
|
||||
4500 3603.2429 1.2438833 0.00038913909 15
|
||||
4600 3129.8814 -249.91806 0.00041075793 16
|
||||
4700 3769.052 -289.24351 0.00043237677 17
|
||||
4800 3560.4714 -3.1655406 0.00043237677 17
|
||||
4900 3452.2717 -2.1270765 0.00043237677 17
|
||||
5000 3594.3247 -523.48506 0.00045399561 18
|
||||
5100 3578.4199 1.0009097 0.00045399561 18
|
||||
5200 3822.1566 1.0526914 0.00047561445 19
|
||||
5300 3901.8883 -0.14607602 0.00047561445 19
|
||||
5400 4059.3644 -1.7789927 0.00049723329 20
|
||||
5500 4163.6847 1.0240127 0.00049723329 20
|
||||
5600 4109.1649 0.80199787 0.00049723329 20
|
||||
5700 4391.2091 2.8730036 0.00049723329 20
|
||||
5800 4279.6579 -0.36499822 0.00051885212 21
|
||||
5900 4296.2695 -1.3064528 0.00051885212 21
|
||||
6000 4065.3758 -2.0483224 0.00051885212 21
|
||||
6100 4772.5362 -2.6814694 0.00054047096 22
|
||||
6200 4627.029 2.999215 0.0005620898 23
|
||||
6300 5120.7881 0.65372968 0.00058370864 24
|
||||
6400 4588.9559 3.7570705 0.00058370864 24
|
||||
6500 5008.7814 2.3595833 0.00060532748 25
|
||||
6600 5195.0053 1.4641612 0.00060532748 25
|
||||
6700 5622.293 -0.33396047 0.00062694632 26
|
||||
6800 5515.1957 -4.234874 0.00062694632 26
|
||||
6900 5156.7455 0.40171954 0.00064856516 27
|
||||
7000 5120.1639 -1.6065245 0.00064856516 27
|
||||
7100 5650.0327 0.94436323 0.00067018399 28
|
||||
7200 5985.1115 -3.8940347 0.00069180283 29
|
||||
7300 5983.197 0.5293568 0.00069180283 29
|
||||
7400 6001.1559 -0.13712834 0.00071342167 30
|
||||
7500 5889.2134 0.17230892 0.00071342167 30
|
||||
7600 5797.31 2.0920058 0.00071342167 30
|
||||
7700 5865.2783 -0.18556395 0.00071342167 30
|
||||
7800 6207.0659 -5.6237083 0.00071342167 30
|
||||
7900 5627.5108 -2.3718942 0.00071342167 30
|
||||
8000 5823.9502 -0.85418578 0.00071342167 30
|
||||
Loop time of 184.87 on 1 procs for 8000 steps with 528 atoms
|
||||
|
||||
Performance: 3.739 ns/day, 6.419 hours/ns, 43.274 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 | 3.3043 | 3.3043 | 3.3043 | 0.0 | 1.79
|
||||
Bond | 8.0003 | 8.0003 | 8.0003 | 0.0 | 4.33
|
||||
Kspace | 168.33 | 168.33 | 168.33 | 0.0 | 91.05
|
||||
Neigh | 4.6322 | 4.6322 | 4.6322 | 0.0 | 2.51
|
||||
Comm | 0.077927 | 0.077927 | 0.077927 | 0.0 | 0.04
|
||||
Output | 0.0020548 | 0.0020548 | 0.0020548 | 0.0 | 0.00
|
||||
Modify | 0.5005 | 0.5005 | 0.5005 | 0.0 | 0.27
|
||||
Other | | 0.02483 | | | 0.01
|
||||
|
||||
Nlocal: 528.000 ave 528 max 528 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 341.000 ave 341 max 341 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 35111.0 ave 35111 max 35111 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 35111
|
||||
Ave neighs/atom = 66.498106
|
||||
Ave special neighs/atom = 11.409091
|
||||
Neighbor list builds = 8000
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:03:05
|
||||
@ -0,0 +1,196 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
Reading data file ...
|
||||
orthogonal box = (50.000000 50.000000 50.000000) to (250.00000 250.00000 250.00000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
48 atoms
|
||||
reading velocities ...
|
||||
48 velocities
|
||||
scanning bonds ...
|
||||
8 = max bonds/atom
|
||||
scanning angles ...
|
||||
21 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
33 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
29 = max impropers/atom
|
||||
reading bonds ...
|
||||
50 bonds
|
||||
reading angles ...
|
||||
84 angles
|
||||
reading dihedrals ...
|
||||
127 dihedrals
|
||||
reading impropers ...
|
||||
36 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
8 = max # of 1-3 neighbors
|
||||
17 = max # of 1-4 neighbors
|
||||
46 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.007 seconds
|
||||
Read molecule template mol1:
|
||||
1 molecules
|
||||
30 atoms with max type 6
|
||||
31 bonds with max type 10
|
||||
51 angles with max type 16
|
||||
73 dihedrals with max type 19
|
||||
21 impropers with max type 7
|
||||
Read molecule template mol2:
|
||||
1 molecules
|
||||
46 atoms with max type 6
|
||||
48 bonds with max type 13
|
||||
81 angles with max type 22
|
||||
121 dihedrals with max type 36
|
||||
35 impropers with max type 9
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
dynamic group statted_grp_REACT defined
|
||||
PPPM initialization ...
|
||||
WARNING: System is not charge neutral, net charge = -0.00060000000 (../kspace.cpp:324)
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:339)
|
||||
G vector (1/distance) = 0.20144813
|
||||
grid = 45 45 45
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00053712952
|
||||
estimated relative force accuracy = 1.6175496e-06
|
||||
using double precision KISS FFT
|
||||
3d grid and FFT values/proc = 39200 24300
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 39 39 39
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) pair lj/class2/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) fix bond/react, occasional, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 38.70 | 38.92 | 39.43 Mbytes
|
||||
Step Temp Press Density f_myrxns[1]
|
||||
0 496.23742 0.9983211 6.4856516e-05 0
|
||||
100 534.05394 -0.76952227 6.4856516e-05 0
|
||||
200 552.2225 -0.55375493 6.4856516e-05 0
|
||||
300 857.52834 -0.4272061 8.6475354e-05 1
|
||||
400 714.10681 1.5004615 8.6475354e-05 1
|
||||
500 678.19171 0.21965471 8.6475354e-05 1
|
||||
600 572.3234 0.87879933 8.6475354e-05 1
|
||||
700 996.17398 -0.24269717 0.00010809419 2
|
||||
800 904.50395 1.3662054 0.00010809419 2
|
||||
900 1097.1568 -2.2909907 0.00012971303 3
|
||||
1000 954.08892 1.7705672 0.00012971303 3
|
||||
1100 1102.0377 -1.7018446 0.00015133187 4
|
||||
1200 1239.785 -0.30442903 0.00015133187 4
|
||||
1300 1388.4127 1.3301175 0.00017295071 5
|
||||
1400 1559.3853 1.6709729 0.00017295071 5
|
||||
1500 1471.8623 0.8268427 0.00017295071 5
|
||||
1600 1543.6793 2.1987908 0.00019456955 6
|
||||
1700 1694.5595 0.48852817 0.00019456955 6
|
||||
1800 1632.7737 -1.4617692 0.00021618839 7
|
||||
1900 1922.6502 1.1664257 0.00021618839 7
|
||||
2000 2223.503 -0.95799878 0.00023780722 8
|
||||
2100 2142.6035 0.88444463 0.00025942606 9
|
||||
2200 2298.8636 3.4239313 0.00025942606 9
|
||||
2300 2252.4355 0.82167302 0.00025942606 9
|
||||
2400 2321.0788 1.7499714 0.00025942606 9
|
||||
2500 2095.6715 0.55288444 0.00025942606 9
|
||||
2600 2136.0316 -3.833114 0.00025942606 9
|
||||
2700 2466.3134 -2.2519511 0.00025942606 9
|
||||
2800 2294.3454 1.0637304 0.00025942606 9
|
||||
2900 2340.3891 1.3997049 0.0002810449 10
|
||||
3000 2272.0013 -0.27591886 0.0002810449 10
|
||||
3100 2333.9696 -0.11772138 0.0002810449 10
|
||||
3200 2409.0946 -1.025473 0.0002810449 10
|
||||
3300 2148.023 1.6752329 0.0002810449 10
|
||||
3400 2267.636 -0.45297583 0.0002810449 10
|
||||
3500 2457.622 0.35627297 0.0002810449 10
|
||||
3600 2288.008 -15.516626 0.00030266374 11
|
||||
3700 2458.2681 1.4571773 0.00030266374 11
|
||||
3800 2566.7623 -29.140553 0.00032428258 12
|
||||
3900 2839.4062 0.64583638 0.00032428258 12
|
||||
4000 2893.2204 -53.187892 0.00034590142 13
|
||||
4100 3024.6375 -65.068146 0.00036752025 14
|
||||
4200 3004.6784 1.4155214 0.00036752025 14
|
||||
4300 3033.1895 1.8572273 0.00036752025 14
|
||||
4400 3157.2542 -0.92462977 0.00036752025 14
|
||||
4500 3557.7137 -194.46498 0.00038913909 15
|
||||
4600 3096.485 -1.830492 0.00038913909 15
|
||||
4700 3488.088 -286.81055 0.00041075793 16
|
||||
4800 3390.5493 -372.77818 0.00043237677 17
|
||||
4900 3773.7226 -446.58574 0.00045399561 18
|
||||
5000 3703.0159 -0.81188551 0.00045399561 18
|
||||
5100 4051.3067 1.2567439 0.00045399561 18
|
||||
5200 3813.3682 0.92945737 0.00047561445 19
|
||||
5300 4036.0078 -2.5336258 0.00049723329 20
|
||||
5400 4219.803 -0.96928261 0.00049723329 20
|
||||
5500 4433.7447 -0.026762463 0.00051885212 21
|
||||
5600 4477.4505 -1.417316 0.00054047096 22
|
||||
5700 4500.0306 -1.0551443 0.00054047096 22
|
||||
5800 4600.3507 -4.9580056 0.00054047096 22
|
||||
5900 4765.4978 -2.2546941 0.0005620898 23
|
||||
6000 5442.6193 0.91161284 0.00058370864 24
|
||||
6100 5086.8047 -0.9875332 0.00060532748 25
|
||||
6200 5485.3437 -2.8296626 0.00062694632 26
|
||||
6300 4988.0396 -0.15179023 0.00064856516 27
|
||||
6400 5597.3703 4.2941885 0.00067018399 28
|
||||
6500 5677.0263 -2.8611595 0.00069180283 29
|
||||
6600 6058.0009 1.4111778 0.00071342167 30
|
||||
6700 5859.0817 -2.5782466 0.00071342167 30
|
||||
6800 5879.3941 -4.5681807 0.00071342167 30
|
||||
6900 6398.288 2.5259412 0.00071342167 30
|
||||
7000 6250.1096 -2.6049627 0.00071342167 30
|
||||
7100 5849.651 -0.44062578 0.00071342167 30
|
||||
7200 5778.6532 -0.27299118 0.00071342167 30
|
||||
7300 5977.6661 4.2483639 0.00071342167 30
|
||||
7400 5862.4231 1.0289519 0.00071342167 30
|
||||
7500 6482.376 7.5412373 0.00071342167 30
|
||||
7600 5810.4325 1.0343075 0.00071342167 30
|
||||
7700 5916.7304 2.304302 0.00071342167 30
|
||||
7800 5869.9504 -0.5946555 0.00071342167 30
|
||||
7900 5804.0522 -4.1207689 0.00071342167 30
|
||||
8000 6077.1704 0.52211243 0.00071342167 30
|
||||
Loop time of 60.5603 on 4 procs for 8000 steps with 528 atoms
|
||||
|
||||
Performance: 11.413 ns/day, 2.103 hours/ns, 132.100 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0041695 | 0.90113 | 2.3423 | 102.8 | 1.49
|
||||
Bond | 0.011606 | 2.1188 | 5.8107 | 163.9 | 3.50
|
||||
Kspace | 47.987 | 52.817 | 55.679 | 43.7 | 87.21
|
||||
Neigh | 3.5961 | 3.6262 | 3.6496 | 1.2 | 5.99
|
||||
Comm | 0.11097 | 0.16569 | 0.26369 | 15.3 | 0.27
|
||||
Output | 0.0020366 | 0.0023427 | 0.0032469 | 1.1 | 0.00
|
||||
Modify | 0.62302 | 0.91659 | 1.1227 | 21.5 | 1.51
|
||||
Other | | 0.0126 | | | 0.02
|
||||
|
||||
Nlocal: 132.000 ave 295 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 133.000 ave 349 max 0 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 8383.50 ave 20143 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 33534
|
||||
Ave neighs/atom = 63.511364
|
||||
Ave special neighs/atom = 11.409091
|
||||
Neighbor list builds = 8000
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:01:00
|
||||
796
examples/USER/reaction/create_atoms_polystyrene/trimer.data
Normal file
796
examples/USER/reaction/create_atoms_polystyrene/trimer.data
Normal file
@ -0,0 +1,796 @@
|
||||
polystyrene trimer
|
||||
|
||||
48 atoms
|
||||
7 atom types
|
||||
50 bonds
|
||||
13 bond types
|
||||
84 angles
|
||||
22 angle types
|
||||
127 dihedrals
|
||||
36 dihedral types
|
||||
36 impropers
|
||||
9 improper types
|
||||
|
||||
50 250 xlo xhi
|
||||
50 250 ylo yhi
|
||||
50 250 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 12.0112
|
||||
2 1.00797
|
||||
3 12.0112
|
||||
4 12.0112
|
||||
5 12.0112
|
||||
6 12.0112
|
||||
7 12.0112
|
||||
|
||||
Pair Coeffs # lj/class2/coul/long
|
||||
|
||||
1 0.064 4.01
|
||||
2 0.02 2.7
|
||||
3 0.064 4.01
|
||||
4 0.064 3.9
|
||||
5 0.054 4.01
|
||||
6 0.054 4.01
|
||||
7 0.054 4.01
|
||||
|
||||
Bond Coeffs # class2
|
||||
|
||||
1 1.0982 372.825 -803.453 894.317
|
||||
2 1.417 470.836 -627.618 1327.63
|
||||
3 1.501 321.902 -521.821 572.163
|
||||
4 1.0883 365.768 -725.54 781.662
|
||||
5 1.34 543.99 -1238.2 1644.03
|
||||
6 1.0883 365.768 -725.54 781.662
|
||||
7 1.501 321.902 -521.821 572.163
|
||||
8 1.101 345 -691.89 844.6
|
||||
9 1.53 299.67 -501.77 679.81
|
||||
10 1.101 345 -691.89 844.6
|
||||
11 1.501 321.902 -521.821 572.163
|
||||
12 1.101 345 -691.89 844.6
|
||||
13 1.53 299.67 -501.77 679.81
|
||||
|
||||
Angle Coeffs # class2
|
||||
|
||||
1 117.94 35.1558 -12.4682 0
|
||||
2 118.9 61.0226 -34.9931 0
|
||||
3 120.05 44.7148 -22.7352 0
|
||||
4 111 44.3234 -9.4454 0
|
||||
5 108.4 43.9594 -8.3924 -9.3379
|
||||
6 124.88 35.2766 -17.774 -1.6215
|
||||
7 124.88 35.2766 -17.774 -1.6215
|
||||
8 115.49 29.6363 -12.4853 -6.2218
|
||||
9 120.05 44.7148 -22.7352 0
|
||||
10 111 44.3234 -9.4454 0
|
||||
11 108.4 43.9594 -8.3924 -9.3379
|
||||
12 110.77 41.453 -10.604 5.129
|
||||
13 112.67 39.516 -7.443 -9.5583
|
||||
14 110.77 41.453 -10.604 5.129
|
||||
15 107.66 39.641 -12.921 -2.4318
|
||||
16 112.67 39.516 -7.443 -9.5583
|
||||
17 120.05 44.7148 -22.7352 0
|
||||
18 111 44.3234 -9.4454 0
|
||||
19 108.4 43.9594 -8.3924 -9.3379
|
||||
20 110.77 41.453 -10.604 5.129
|
||||
21 110.77 41.453 -10.604 5.129
|
||||
22 112.67 39.516 -7.443 -9.5583
|
||||
|
||||
BondBond Coeffs
|
||||
|
||||
1 1.0795 1.417 1.0982
|
||||
2 68.2856 1.417 1.417
|
||||
3 12.0676 1.417 1.501
|
||||
4 2.9168 1.501 1.0883
|
||||
5 0 1.501 1.34
|
||||
6 10.1047 1.0883 1.34
|
||||
7 10.1047 1.0883 1.34
|
||||
8 4.8506 1.0883 1.0883
|
||||
9 12.0676 1.417 1.501
|
||||
10 2.9168 1.501 1.101
|
||||
11 0 1.501 1.53
|
||||
12 3.3872 1.101 1.53
|
||||
13 0 1.53 1.53
|
||||
14 3.3872 1.101 1.53
|
||||
15 5.3316 1.101 1.101
|
||||
16 0 1.53 1.53
|
||||
17 12.0676 1.417 1.501
|
||||
18 2.9168 1.501 1.101
|
||||
19 0 1.501 1.53
|
||||
20 3.3872 1.101 1.53
|
||||
21 3.3872 1.101 1.53
|
||||
22 0 1.53 1.53
|
||||
|
||||
BondAngle Coeffs
|
||||
|
||||
1 20.0033 24.2183 1.417 1.0982
|
||||
2 28.8708 28.8708 1.417 1.417
|
||||
3 31.0771 47.0579 1.417 1.501
|
||||
4 26.4608 11.7717 1.501 1.0883
|
||||
5 0 0 1.501 1.34
|
||||
6 19.0592 23.3588 1.0883 1.34
|
||||
7 19.0592 23.3588 1.0883 1.34
|
||||
8 17.9795 17.9795 1.0883 1.0883
|
||||
9 31.0771 47.0579 1.417 1.501
|
||||
10 26.4608 11.7717 1.501 1.101
|
||||
11 0 0 1.501 1.53
|
||||
12 11.421 20.754 1.101 1.53
|
||||
13 8.016 8.016 1.53 1.53
|
||||
14 11.421 20.754 1.101 1.53
|
||||
15 18.103 18.103 1.101 1.101
|
||||
16 8.016 8.016 1.53 1.53
|
||||
17 31.0771 47.0579 1.417 1.501
|
||||
18 26.4608 11.7717 1.501 1.101
|
||||
19 0 0 1.501 1.53
|
||||
20 11.421 20.754 1.101 1.53
|
||||
21 11.421 20.754 1.101 1.53
|
||||
22 8.016 8.016 1.53 1.53
|
||||
|
||||
Dihedral Coeffs # class2
|
||||
|
||||
1 0 0 1.559 0 0 0
|
||||
2 0 0 3.9661 0 0 0
|
||||
3 0 0 4.4072 0 0 0
|
||||
4 8.3667 0 1.1932 0 0 0
|
||||
5 0 0 1.8769 0 0 0
|
||||
6 0 0 0 0 0 0
|
||||
7 0 0 0 0 0 0
|
||||
8 0 0 0 0 0 0
|
||||
9 0 0 4.8974 0 0 0
|
||||
10 0 0 1.559 0 0 0
|
||||
11 0 0 4.4072 0 0 0
|
||||
12 -0.2801 0 -0.0678 0 -0.0122 0
|
||||
13 -0.2802 0 -0.0678 0 -0.0122 0
|
||||
14 -0.0228 0 0.028 0 -0.1863 0
|
||||
15 -0.1432 0 0.0617 0 -0.1083 0
|
||||
16 0 0 0.0316 0 -0.1681 0
|
||||
17 0 0 0 0 0 0
|
||||
18 0 0 0.0316 0 -0.1681 0
|
||||
19 0 0 0.0514 0 -0.143 0
|
||||
20 0 0 1.559 0 0 0
|
||||
21 0 0 4.4072 0 0 0
|
||||
22 -0.2801 0 -0.0678 0 -0.0122 0
|
||||
23 -0.2802 0 -0.0678 0 -0.0122 0
|
||||
24 -0.0228 0 0.028 0 -0.1863 0
|
||||
25 0 0 0 0 0 0
|
||||
26 -0.1432 0 0.0617 0 -0.1083 0
|
||||
27 0 0 0.0316 0 -0.1681 0
|
||||
28 0 0 0 0 0 0
|
||||
29 0 0 0.0316 0 -0.1681 0
|
||||
30 0 0 0.0514 0 -0.143 0
|
||||
31 -0.0228 0 0.028 0 -0.1863 0
|
||||
32 -0.1432 0 0.0617 0 -0.1083 0
|
||||
33 0 0 0.0316 0 -0.1681 0
|
||||
34 0 0 0 0 0 0
|
||||
35 0 0 0.0316 0 -0.1681 0
|
||||
36 0 0 0.0514 0 -0.143 0
|
||||
|
||||
AngleAngleTorsion Coeffs
|
||||
|
||||
1 4.4444 117.94 120.05
|
||||
2 -4.8141 118.9 117.94
|
||||
3 -14.4097 118.9 120.05
|
||||
4 0 118.9 118.9
|
||||
5 0.3598 117.94 117.94
|
||||
6 0 120.05 111
|
||||
7 0 120.05 108.4
|
||||
8 0 108.4 124.88
|
||||
9 -7.0058 124.88 124.88
|
||||
10 4.4444 117.94 120.05
|
||||
11 -14.4097 118.9 120.05
|
||||
12 -5.8888 120.05 111
|
||||
13 0 120.05 108.4
|
||||
14 0 108.4 110.77
|
||||
15 -12.564 110.77 110.77
|
||||
16 -16.164 112.67 110.77
|
||||
17 0 108.4 112.67
|
||||
18 -16.164 110.77 112.67
|
||||
19 -22.045 112.67 112.67
|
||||
20 4.4444 117.94 120.05
|
||||
21 -14.4097 118.9 120.05
|
||||
22 -5.8888 120.05 111
|
||||
23 0 120.05 108.4
|
||||
24 0 108.4 110.77
|
||||
25 0 108.4 112.67
|
||||
26 -12.564 110.77 110.77
|
||||
27 -16.164 110.77 112.67
|
||||
28 0 112.67 108.4
|
||||
29 -16.164 112.67 110.77
|
||||
30 -22.045 112.67 112.67
|
||||
31 0 110.77 108.4
|
||||
32 -12.564 110.77 110.77
|
||||
33 -16.164 110.77 112.67
|
||||
34 0 112.67 108.4
|
||||
35 -16.164 112.67 110.77
|
||||
36 -22.045 112.67 112.67
|
||||
|
||||
EndBondTorsion Coeffs
|
||||
|
||||
1 0 -0.4879 0 0 -1.797 0 1.0982 1.501
|
||||
2 0 -6.8958 0 0 -0.4669 0 1.417 1.0982
|
||||
3 0 -0.6918 0 0 0.2421 0 1.417 1.501
|
||||
4 -0.1185 6.3204 0 -0.1185 6.3204 0 1.417 1.417
|
||||
5 0 -0.689 0 0 -0.689 0 1.0982 1.0982
|
||||
6 0 0 0 0 0 0 1.417 1.0883
|
||||
7 0 0 0 0 0 0 1.417 1.34
|
||||
8 0 0 0 0 0 0 1.501 1.0883
|
||||
9 0.7129 0.5161 0 0.7129 0.5161 0 1.0883 1.0883
|
||||
10 0 -0.4879 0 0 -1.797 0 1.0982 1.501
|
||||
11 0 -0.6918 0 0 0.2421 0 1.417 1.501
|
||||
12 -0.5835 1.122 0.3978 1.3997 0.7756 0 1.417 1.101
|
||||
13 0 0 0 0 0 0 1.417 1.53
|
||||
14 0 0 0 0 0 0 1.501 1.101
|
||||
15 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
|
||||
16 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
|
||||
17 0 0 0 0 0 0 1.501 1.53
|
||||
18 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.101 1.53
|
||||
19 -0.0732 0 0 -0.0732 0 0 1.53 1.53
|
||||
20 0 -0.4879 0 0 -1.797 0 1.0982 1.501
|
||||
21 0 -0.6918 0 0 0.2421 0 1.417 1.501
|
||||
22 -0.5835 1.122 0.3978 1.3997 0.7756 0 1.417 1.101
|
||||
23 0 0 0 0 0 0 1.417 1.53
|
||||
24 0 0 0 0 0 0 1.501 1.101
|
||||
25 0 0 0 0 0 0 1.501 1.53
|
||||
26 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
|
||||
27 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.101 1.53
|
||||
28 0 0 0 0 0 0 1.53 1.501
|
||||
29 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
|
||||
30 -0.0732 0 0 -0.0732 0 0 1.53 1.53
|
||||
31 0 0 0 0 0 0 1.101 1.501
|
||||
32 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
|
||||
33 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.101 1.53
|
||||
34 0 0 0 0 0 0 1.53 1.501
|
||||
35 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
|
||||
36 -0.0732 0 0 -0.0732 0 0 1.53 1.53
|
||||
|
||||
MiddleBondTorsion Coeffs
|
||||
|
||||
1 0 3.9421 0 1.417
|
||||
2 0 -1.1521 0 1.417
|
||||
3 0 9.1792 0 1.417
|
||||
4 27.5989 -2.312 0 1.417
|
||||
5 0 4.8228 0 1.417
|
||||
6 0 0 0 1.501
|
||||
7 0 0 0 1.501
|
||||
8 0 0 0 1.34
|
||||
9 0.8558 6.3911 0 1.34
|
||||
10 0 3.9421 0 1.417
|
||||
11 0 9.1792 0 1.417
|
||||
12 -5.5679 1.4083 0.301 1.501
|
||||
13 0 0 0 1.501
|
||||
14 0 0 0 1.53
|
||||
15 -14.261 -0.5322 -0.4864 1.53
|
||||
16 -14.879 -3.6581 -0.3138 1.53
|
||||
17 0 0 0 1.53
|
||||
18 -14.879 -3.6581 -0.3138 1.53
|
||||
19 -17.787 -7.1877 0 1.53
|
||||
20 0 3.9421 0 1.417
|
||||
21 0 9.1792 0 1.417
|
||||
22 -5.5679 1.4083 0.301 1.501
|
||||
23 0 0 0 1.501
|
||||
24 0 0 0 1.53
|
||||
25 0 0 0 1.53
|
||||
26 -14.261 -0.5322 -0.4864 1.53
|
||||
27 -14.879 -3.6581 -0.3138 1.53
|
||||
28 0 0 0 1.53
|
||||
29 -14.879 -3.6581 -0.3138 1.53
|
||||
30 -17.787 -7.1877 0 1.53
|
||||
31 0 0 0 1.53
|
||||
32 -14.261 -0.5322 -0.4864 1.53
|
||||
33 -14.879 -3.6581 -0.3138 1.53
|
||||
34 0 0 0 1.53
|
||||
35 -14.879 -3.6581 -0.3138 1.53
|
||||
36 -17.787 -7.1877 0 1.53
|
||||
|
||||
BondBond13 Coeffs
|
||||
|
||||
1 0.8743 1.0982 1.501
|
||||
2 -6.2741 1.417 1.0982
|
||||
3 2.5085 1.417 1.501
|
||||
4 53 1.417 1.417
|
||||
5 -1.7077 1.0982 1.0982
|
||||
6 0 1.417 1.0883
|
||||
7 0 1.417 1.34
|
||||
8 0 1.501 1.0883
|
||||
9 0 1.0883 1.0883
|
||||
10 0.8743 1.0982 1.501
|
||||
11 2.5085 1.417 1.501
|
||||
12 -3.4826 1.417 1.101
|
||||
13 0 1.417 1.53
|
||||
14 0 1.501 1.101
|
||||
15 0 1.101 1.101
|
||||
16 0 1.53 1.101
|
||||
17 0 1.501 1.53
|
||||
18 0 1.101 1.53
|
||||
19 0 1.53 1.53
|
||||
20 0.8743 1.0982 1.501
|
||||
21 2.5085 1.417 1.501
|
||||
22 -3.4826 1.417 1.101
|
||||
23 0 1.417 1.53
|
||||
24 0 1.501 1.101
|
||||
25 0 1.501 1.53
|
||||
26 0 1.101 1.101
|
||||
27 0 1.101 1.53
|
||||
28 0 1.53 1.501
|
||||
29 0 1.53 1.101
|
||||
30 0 1.53 1.53
|
||||
31 0 1.101 1.501
|
||||
32 0 1.101 1.101
|
||||
33 0 1.101 1.53
|
||||
34 0 1.53 1.501
|
||||
35 0 1.53 1.101
|
||||
36 0 1.53 1.53
|
||||
|
||||
AngleTorsion Coeffs
|
||||
|
||||
1 0 3.4601 0 0 -0.1242 0 117.94 120.05
|
||||
2 0 2.5014 0 0 2.7147 0 118.9 117.94
|
||||
3 0 3.8987 0 0 -4.4683 0 118.9 120.05
|
||||
4 1.9767 1.0239 0 1.9767 1.0239 0 118.9 118.9
|
||||
5 0 2.4501 0 0 2.4501 0 117.94 117.94
|
||||
6 0 0 0 0 0 0 120.05 111
|
||||
7 0 0 0 0 0 0 120.05 108.4
|
||||
8 0 0 0 0 0 0 108.4 124.88
|
||||
9 -1.8911 3.254 0 -1.8911 3.254 0 124.88 124.88
|
||||
10 0 3.4601 0 0 -0.1242 0 117.94 120.05
|
||||
11 0 3.8987 0 0 -4.4683 0 118.9 120.05
|
||||
12 0.2251 0.6548 0.1237 4.6266 0.1632 0.0461 120.05 111
|
||||
13 0 0 0 0 0 0 120.05 108.4
|
||||
14 0 0 0 0 0 0 108.4 110.77
|
||||
15 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
|
||||
16 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
|
||||
17 0 0 0 0 0 0 108.4 112.67
|
||||
18 0.3113 0.4516 -0.1988 -0.2454 0 -0.1136 110.77 112.67
|
||||
19 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
|
||||
20 0 3.4601 0 0 -0.1242 0 117.94 120.05
|
||||
21 0 3.8987 0 0 -4.4683 0 118.9 120.05
|
||||
22 0.2251 0.6548 0.1237 4.6266 0.1632 0.0461 120.05 111
|
||||
23 0 0 0 0 0 0 120.05 108.4
|
||||
24 0 0 0 0 0 0 108.4 110.77
|
||||
25 0 0 0 0 0 0 108.4 112.67
|
||||
26 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
|
||||
27 0.3113 0.4516 -0.1988 -0.2454 0 -0.1136 110.77 112.67
|
||||
28 0 0 0 0 0 0 112.67 108.4
|
||||
29 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
|
||||
30 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
|
||||
31 0 0 0 0 0 0 110.77 108.4
|
||||
32 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
|
||||
33 0.3113 0.4516 -0.1988 -0.2454 0 -0.1136 110.77 112.67
|
||||
34 0 0 0 0 0 0 112.67 108.4
|
||||
35 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
|
||||
36 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
|
||||
|
||||
Improper Coeffs # class2
|
||||
|
||||
1 4.8912 0
|
||||
2 7.8153 0
|
||||
3 0 0
|
||||
4 2.8561 0
|
||||
5 7.8153 0
|
||||
6 0 0
|
||||
7 0 0
|
||||
8 7.8153 0
|
||||
9 0 0
|
||||
|
||||
AngleAngle Coeffs
|
||||
|
||||
1 0 0 0 118.9 117.94 117.94
|
||||
2 0 0 0 118.9 120.05 120.05
|
||||
3 0 0 0 111 124.88 108.4
|
||||
4 0 0 0 115.49 124.88 124.88
|
||||
5 0 0 0 118.9 120.05 120.05
|
||||
6 0 0 0 107.66 110.77 110.77
|
||||
7 0 0 0 111 110.77 108.4
|
||||
8 0 0 0 118.9 120.05 120.05
|
||||
9 0 0 0 111 110.77 108.4
|
||||
|
||||
Atoms # full
|
||||
|
||||
44 1 2 3.5400000000000001e-02 6.1476397222913839e+01 8.2376490601205234e+01 6.0906939115836181e+01
|
||||
45 1276 2 3.5400000000000001e-02 5.8398688202244472e+01 8.0172948526664996e+01 6.2115536813582672e+01
|
||||
46 1276 6 -6.9599999999999995e-02 5.9489073989392523e+01 8.0264057167571636e+01 6.1984002598976552e+01
|
||||
48 1276 2 3.5400000000000001e-02 5.9675170230342431e+01 8.0048052449390738e+01 6.0920159395372401e+01
|
||||
47 1276 2 1.2370000000000000e-01 5.9297455513100488e+01 8.3187777608476154e+01 5.9645157256520122e+01
|
||||
18 1 5 -1.8200000000000001e-02 6.2426251430535707e+01 8.2055473568260709e+01 6.2971661388612958e+01
|
||||
19 1 6 -6.9599999999999995e-02 6.1399255844467369e+01 8.1794665295860213e+01 6.1821819828185660e+01
|
||||
21 1 1 -1.2900000000000000e-01 6.4032918371445831e+01 8.0190179089286701e+01 6.3021564712316334e+01
|
||||
22 1 1 2.6599999999999999e-02 6.3672975135915053e+01 8.1418558650051665e+01 6.2448012627881994e+01
|
||||
23 1 2 3.5400000000000001e-02 6.1545198223694939e+01 8.0836309422842305e+01 6.1349823957467130e+01
|
||||
27 1276 2 5.1600000000000000e-02 5.9809503696580933e+01 8.1831265916389881e+01 6.3253745193271065e+01
|
||||
28 1276 5 -1.8200000000000001e-02 5.9900307947967441e+01 8.1677453781363639e+01 6.2190757403657820e+01
|
||||
31 1276 2 1.2370000000000000e-01 5.8050043823867973e+01 8.2698312265456622e+01 6.3667111329534436e+01
|
||||
38 1 2 1.2370000000000000e-01 6.3754126973935612e+01 7.9931147303963002e+01 6.4022259163067275e+01
|
||||
20 1 2 1.2370000000000000e-01 6.4070158368422781e+01 8.2950071388392274e+01 6.1042631212883315e+01
|
||||
24 1 1 -1.2900000000000000e-01 6.4337973861569580e+01 8.1916618276489871e+01 6.1387866780102470e+01
|
||||
37 1 2 1.4030000000000001e-01 6.5360115866618415e+01 7.8586112104863830e+01 6.3004997314380716e+01
|
||||
39 1 1 -1.7340000000000000e-01 6.5018338085325610e+01 7.9478260591306125e+01 6.2440745569712817e+01
|
||||
40 1 1 -1.1340000000000000e-01 6.5628759887796605e+01 7.9941156332165264e+01 6.1248476296558067e+01
|
||||
41 1 1 -1.7340000000000000e-01 6.5247995680260402e+01 8.1172439250598345e+01 6.0753045571239831e+01
|
||||
42 1 2 1.2880000000000000e-01 6.6569600059599281e+01 7.9514748976494360e+01 6.0810611807135601e+01
|
||||
43 1 2 1.4030000000000001e-01 6.5780165393063371e+01 8.1570974991007958e+01 5.9850915261812396e+01
|
||||
9 1276 2 1.2880000000000000e-01 5.5651795605743445e+01 8.5074472139235127e+01 6.1094480497979262e+01
|
||||
30 1276 2 1.4030000000000001e-01 5.6082982679196888e+01 8.3912863624076010e+01 6.3351889697403472e+01
|
||||
33 1276 1 -1.7340000000000000e-01 5.6718133911388506e+01 8.3758479063002000e+01 6.2493293749545209e+01
|
||||
34 1276 1 -1.1340000000000000e-01 5.6498352105218459e+01 8.4426576393179090e+01 6.1290147608586011e+01
|
||||
6 3822 1 -1.7340000000000000e-01 6.3308103537340351e+01 8.7713509787622499e+01 6.4643082313868433e+01
|
||||
7 3822 1 -1.2900000000000000e-01 6.3010291684764312e+01 8.6423650045069493e+01 6.4252844241495922e+01
|
||||
8 3822 2 1.2370000000000000e-01 6.2089199187020355e+01 8.6309198636296912e+01 6.3711263099850854e+01
|
||||
10 1276 2 1.4030000000000001e-01 5.7266131308654970e+01 8.4599328362003035e+01 5.9281511478144402e+01
|
||||
11 3822 2 3.5400000000000001e-02 6.1694306618059791e+01 8.3823470438280594e+01 6.3778953909925114e+01
|
||||
12 3822 5 -1.8200000000000001e-02 6.3814926998838651e+01 8.3900077798460728e+01 6.4108991789590448e+01
|
||||
13 3822 6 -6.9599999999999995e-02 6.2604540882379787e+01 8.3491998603381077e+01 6.3249610918984622e+01
|
||||
14 3822 2 1.2370000000000000e-01 6.5739253131027880e+01 8.4813736128157771e+01 6.5351692111169555e+01
|
||||
15 3822 1 -1.2900000000000000e-01 6.5071144269009466e+01 8.5646783550482454e+01 6.5086813218945636e+01
|
||||
16 3822 1 2.6599999999999999e-02 6.3957099792282079e+01 8.5375816595044753e+01 6.4385073943729708e+01
|
||||
17 1 2 5.1600000000000000e-02 6.2256484483973310e+01 8.1576962161157596e+01 6.3963984654065122e+01
|
||||
26 3822 2 5.1600000000000000e-02 6.4196825763126355e+01 8.3291442832977836e+01 6.4907094488854057e+01
|
||||
29 1276 1 2.6599999999999999e-02 5.8784742332505303e+01 8.2766055380197670e+01 6.1667239692876961e+01
|
||||
32 1276 1 -1.2900000000000000e-01 5.7836199787435064e+01 8.3005060229118428e+01 6.2669788306756018e+01
|
||||
35 1276 1 -1.2900000000000000e-01 5.8572661840325132e+01 8.3404075689965083e+01 6.0443288532625175e+01
|
||||
36 1276 1 -1.7340000000000000e-01 5.7380616699226330e+01 8.4134680429976896e+01 6.0248710539932475e+01
|
||||
25 3822 2 3.5400000000000001e-02 6.2750675036816460e+01 8.3891633300878468e+01 6.2249429178485677e+01
|
||||
5 3822 2 1.4030000000000001e-01 6.2626160082050376e+01 8.8416565740835182e+01 6.4093918967496805e+01
|
||||
1 3822 2 1.2880000000000000e-01 6.4863557606529355e+01 8.9096029197548390e+01 6.5342927535537825e+01
|
||||
2 3822 1 -1.1340000000000000e-01 6.4627442641031166e+01 8.8047381925321190e+01 6.5138073202291650e+01
|
||||
3 3822 2 1.4030000000000001e-01 6.6470254992065406e+01 8.6991893750821745e+01 6.5857474890608984e+01
|
||||
4 3822 1 -1.7340000000000000e-01 6.5416488888088338e+01 8.6963894801200169e+01 6.5357641085394278e+01
|
||||
|
||||
Velocities
|
||||
|
||||
44 -1.1274099342391698e-02 2.8614364731871914e-02 7.8116535486555949e-03
|
||||
45 2.3164382404151666e-03 3.9815732957733160e-03 -2.9971878581527899e-02
|
||||
46 -7.1653099619954563e-03 4.5491360587300133e-04 4.9898614093692017e-03
|
||||
48 9.8069086061434527e-03 4.0008139512159270e-03 6.2934259772882122e-03
|
||||
47 2.2646445306743783e-03 1.3029071608409702e-03 4.2232440120174040e-02
|
||||
18 7.0040064100195757e-03 3.2877451206009701e-03 -3.5376010407568422e-04
|
||||
19 -1.3998188760009689e-02 7.2238210565990146e-03 7.7956220633332383e-03
|
||||
21 3.1954292320462373e-03 -2.9717583309420764e-03 -3.1753395094325522e-03
|
||||
22 5.2997643939121201e-03 -2.9646963088534335e-03 -4.1351926198204894e-03
|
||||
23 7.6443400078766528e-03 4.0358953976530103e-02 -2.6684706183248367e-02
|
||||
27 1.9261652416455359e-03 -1.1632914130150688e-02 1.0061732021630769e-02
|
||||
28 -8.2251676802878315e-03 -1.5111873066969876e-04 1.3808893565582731e-02
|
||||
31 5.2475840572179860e-03 1.8266996572138715e-02 2.3453280610166885e-03
|
||||
38 -2.0343905130199073e-02 3.2815536859276281e-02 3.6511922534330152e-03
|
||||
20 2.2914549087537126e-02 1.4424503744223915e-02 2.1708279654645496e-03
|
||||
24 -2.4717233344142471e-03 1.2966123098719246e-02 8.1261459853411936e-03
|
||||
37 -2.4547379584186218e-02 -3.0213966592845171e-02 -3.1437442951939183e-02
|
||||
39 2.5476117829076835e-03 1.2743160680987653e-03 1.8775880208113892e-03
|
||||
40 -6.9216508143939990e-03 1.0986173624795060e-02 8.4543093049661480e-03
|
||||
41 -6.9641432145561661e-03 3.4497795547843439e-03 -6.5914679936187716e-03
|
||||
42 -1.6682931637687005e-02 -7.9952140358728052e-03 -5.4993265930488526e-02
|
||||
43 -1.2747392921213267e-03 -8.9033092043203244e-03 -1.4285400545629027e-02
|
||||
9 -4.6235166357676289e-03 -1.3071850427027999e-02 -1.4097407987100977e-02
|
||||
30 -1.0949617396609294e-02 2.8255703113196974e-03 1.7171748232322353e-02
|
||||
33 -6.1375812469323665e-03 -2.4748644899411924e-03 -9.4761978149296138e-03
|
||||
34 1.3676079846441525e-03 5.6076140293943458e-03 4.3217204641336267e-03
|
||||
6 -1.0264635053701928e-02 6.5278337056107680e-03 7.0056151148588212e-04
|
||||
7 -8.7519451205145676e-03 -4.6476440106580945e-03 2.5970484253527112e-03
|
||||
8 2.1377395557690311e-02 -3.3261274153819453e-03 -1.0112266596677577e-02
|
||||
10 -3.5793767912309253e-02 -4.7139872292323019e-02 -1.6709528481405608e-02
|
||||
11 8.5071485795589590e-03 9.9402848610678270e-03 -3.8088596341056854e-03
|
||||
12 -7.1678159384257103e-04 -6.9164463557228907e-04 -6.4073519808107186e-03
|
||||
13 -4.8443902657902991e-03 -1.1919190682985097e-03 6.3946846087726637e-03
|
||||
14 1.4810157483257907e-02 1.9829623839419017e-03 -2.7393844990063056e-02
|
||||
15 2.4171850935506777e-03 8.5003135180758520e-03 -1.4373227798951704e-03
|
||||
16 2.7567342910947553e-03 4.7168484476890456e-03 -5.5131873288712992e-03
|
||||
17 -3.8456662730386774e-02 2.0220106671151108e-02 -1.3822049134399602e-02
|
||||
26 2.7415414728694614e-02 1.4392155257037418e-03 -6.7281635499082748e-03
|
||||
29 2.8284983560440745e-03 2.8809942505517976e-03 -9.0489583066552114e-04
|
||||
32 -3.8543634697614316e-03 4.6751647301899795e-03 4.2171867397204537e-03
|
||||
35 -8.6957974827209118e-03 -4.4615282666186267e-04 -2.6571026120482824e-03
|
||||
36 9.4881057996863086e-04 -7.5665878069688429e-03 2.0333670960646154e-03
|
||||
25 1.8105924111310519e-02 -8.6933495274689535e-03 -1.9695291360338044e-04
|
||||
5 -5.0447438383189585e-03 -4.5665146331657552e-02 1.0653751333175230e-02
|
||||
1 -1.7372868398038824e-02 -2.3625357536259349e-03 1.2220266128368908e-02
|
||||
2 3.7050246021929395e-03 -1.0236943515935205e-03 7.2206774682170580e-03
|
||||
3 2.3669435799326944e-02 2.7891427939155597e-02 -6.7091036888174346e-03
|
||||
4 3.4910623999263577e-03 2.6370880132825258e-03 -6.4694788112864129e-03
|
||||
|
||||
Bonds
|
||||
|
||||
1 10 44 19
|
||||
2 10 45 46
|
||||
3 10 48 46
|
||||
4 9 19 18
|
||||
5 1 21 38
|
||||
6 2 21 22
|
||||
7 2 21 39
|
||||
8 7 22 18
|
||||
9 2 22 24
|
||||
10 10 23 19
|
||||
11 8 27 28
|
||||
12 9 28 46
|
||||
13 9 28 19
|
||||
14 1 24 20
|
||||
15 2 24 41
|
||||
16 1 39 37
|
||||
17 1 40 42
|
||||
18 2 40 39
|
||||
19 1 41 43
|
||||
20 2 41 40
|
||||
21 1 33 30
|
||||
22 1 34 9
|
||||
23 2 34 33
|
||||
24 1 6 5
|
||||
25 2 6 2
|
||||
26 1 7 8
|
||||
27 2 7 6
|
||||
28 10 11 13
|
||||
29 13 12 13
|
||||
30 9 13 18
|
||||
31 1 15 14
|
||||
32 2 15 16
|
||||
33 2 15 4
|
||||
34 11 16 12
|
||||
35 2 16 7
|
||||
36 8 17 18
|
||||
37 12 26 12
|
||||
38 7 29 28
|
||||
39 2 29 35
|
||||
40 1 32 31
|
||||
41 2 32 29
|
||||
42 2 32 33
|
||||
43 1 35 47
|
||||
44 2 35 36
|
||||
45 1 36 10
|
||||
46 2 36 34
|
||||
47 10 25 13
|
||||
48 1 2 1
|
||||
49 2 2 4
|
||||
50 1 4 3
|
||||
|
||||
Angles
|
||||
|
||||
1 14 45 46 28
|
||||
2 14 48 46 28
|
||||
3 15 45 46 48
|
||||
4 11 22 18 13
|
||||
5 12 17 18 13
|
||||
6 13 13 18 19
|
||||
7 10 22 18 17
|
||||
8 11 22 18 19
|
||||
9 12 17 18 19
|
||||
10 16 28 19 18
|
||||
11 14 44 19 28
|
||||
12 14 23 19 28
|
||||
13 14 44 19 18
|
||||
14 14 23 19 18
|
||||
15 15 44 19 23
|
||||
16 1 22 21 38
|
||||
17 1 39 21 38
|
||||
18 2 22 21 39
|
||||
19 9 21 22 18
|
||||
20 2 21 22 24
|
||||
21 9 24 22 18
|
||||
22 10 29 28 27
|
||||
23 11 29 28 46
|
||||
24 11 29 28 19
|
||||
25 12 27 28 46
|
||||
26 12 27 28 19
|
||||
27 13 46 28 19
|
||||
28 1 22 24 20
|
||||
29 2 22 24 41
|
||||
30 1 41 24 20
|
||||
31 2 21 39 40
|
||||
32 1 21 39 37
|
||||
33 1 40 39 37
|
||||
34 1 41 40 42
|
||||
35 2 41 40 39
|
||||
36 1 39 40 42
|
||||
37 1 24 41 43
|
||||
38 2 24 41 40
|
||||
39 1 40 41 43
|
||||
40 2 32 33 34
|
||||
41 1 32 33 30
|
||||
42 1 34 33 30
|
||||
43 1 36 34 9
|
||||
44 2 36 34 33
|
||||
45 1 33 34 9
|
||||
46 1 7 6 5
|
||||
47 2 7 6 2
|
||||
48 1 2 6 5
|
||||
49 1 16 7 8
|
||||
50 2 16 7 6
|
||||
51 1 6 7 8
|
||||
52 18 16 12 26
|
||||
53 19 16 12 13
|
||||
54 20 26 12 13
|
||||
55 21 25 13 12
|
||||
56 21 11 13 12
|
||||
57 22 12 13 18
|
||||
58 15 25 13 11
|
||||
59 14 25 13 18
|
||||
60 14 11 13 18
|
||||
61 1 16 15 14
|
||||
62 1 4 15 14
|
||||
63 2 16 15 4
|
||||
64 17 15 16 12
|
||||
65 2 15 16 7
|
||||
66 17 7 16 12
|
||||
67 9 32 29 28
|
||||
68 2 32 29 35
|
||||
69 9 35 29 28
|
||||
70 1 29 32 31
|
||||
71 1 33 32 31
|
||||
72 2 29 32 33
|
||||
73 1 29 35 47
|
||||
74 2 29 35 36
|
||||
75 1 36 35 47
|
||||
76 1 35 36 10
|
||||
77 2 35 36 34
|
||||
78 1 34 36 10
|
||||
79 1 6 2 1
|
||||
80 2 6 2 4
|
||||
81 1 4 2 1
|
||||
82 2 15 4 2
|
||||
83 1 15 4 3
|
||||
84 1 2 4 3
|
||||
|
||||
Dihedrals
|
||||
|
||||
1 34 18 19 28 29
|
||||
2 31 44 19 28 29
|
||||
3 31 23 19 28 29
|
||||
4 35 18 19 28 27
|
||||
5 32 44 19 28 27
|
||||
6 32 23 19 28 27
|
||||
7 36 18 19 28 46
|
||||
8 33 44 19 28 46
|
||||
9 33 23 19 28 46
|
||||
10 36 28 19 18 13
|
||||
11 33 44 19 18 13
|
||||
12 33 23 19 18 13
|
||||
13 34 28 19 18 22
|
||||
14 31 44 19 18 22
|
||||
15 31 23 19 18 22
|
||||
16 35 28 19 18 17
|
||||
17 32 44 19 18 17
|
||||
18 32 23 19 18 17
|
||||
19 10 38 21 22 18
|
||||
20 11 39 21 22 18
|
||||
21 4 39 21 22 24
|
||||
22 5 38 21 39 37
|
||||
23 4 22 21 39 40
|
||||
24 2 22 21 39 37
|
||||
25 2 24 22 21 38
|
||||
26 13 21 22 18 13
|
||||
27 12 21 22 18 17
|
||||
28 13 21 22 18 19
|
||||
29 13 24 22 18 13
|
||||
30 12 24 22 18 17
|
||||
31 13 24 22 18 19
|
||||
32 2 21 22 24 20
|
||||
33 4 21 22 24 41
|
||||
34 14 29 28 46 45
|
||||
35 14 29 28 46 48
|
||||
36 15 27 28 46 45
|
||||
37 15 27 28 46 48
|
||||
38 16 19 28 46 45
|
||||
39 16 19 28 46 48
|
||||
40 10 20 24 22 18
|
||||
41 11 41 24 22 18
|
||||
42 2 22 24 41 43
|
||||
43 4 22 24 41 40
|
||||
44 5 20 24 41 43
|
||||
45 2 40 39 21 38
|
||||
46 2 21 39 40 42
|
||||
47 2 39 40 41 43
|
||||
48 4 41 40 39 21
|
||||
49 2 41 40 39 37
|
||||
50 5 42 40 39 37
|
||||
51 2 40 41 24 20
|
||||
52 2 24 41 40 42
|
||||
53 4 24 41 40 39
|
||||
54 5 43 41 40 42
|
||||
55 2 34 33 32 31
|
||||
56 2 32 33 34 9
|
||||
57 2 33 34 36 10
|
||||
58 4 36 34 33 32
|
||||
59 2 36 34 33 30
|
||||
60 5 9 34 33 30
|
||||
61 2 2 6 7 8
|
||||
62 2 7 6 2 1
|
||||
63 4 7 6 2 4
|
||||
64 5 5 6 2 1
|
||||
65 20 8 7 16 12
|
||||
66 21 6 7 16 12
|
||||
67 2 16 7 6 5
|
||||
68 4 16 7 6 2
|
||||
69 5 8 7 6 5
|
||||
70 24 16 12 13 25
|
||||
71 24 16 12 13 11
|
||||
72 25 16 12 13 18
|
||||
73 26 26 12 13 25
|
||||
74 26 26 12 13 11
|
||||
75 27 26 12 13 18
|
||||
76 28 12 13 18 22
|
||||
77 29 12 13 18 17
|
||||
78 30 12 13 18 19
|
||||
79 31 25 13 18 22
|
||||
80 32 25 13 18 17
|
||||
81 33 25 13 18 19
|
||||
82 31 11 13 18 22
|
||||
83 32 11 13 18 17
|
||||
84 33 11 13 18 19
|
||||
85 20 14 15 16 12
|
||||
86 21 4 15 16 12
|
||||
87 4 4 15 16 7
|
||||
88 5 14 15 4 3
|
||||
89 4 16 15 4 2
|
||||
90 2 16 15 4 3
|
||||
91 2 7 16 15 14
|
||||
92 22 15 16 12 26
|
||||
93 23 15 16 12 13
|
||||
94 22 7 16 12 26
|
||||
95 23 7 16 12 13
|
||||
96 2 15 16 7 8
|
||||
97 4 15 16 7 6
|
||||
98 2 35 29 32 31
|
||||
99 12 32 29 28 27
|
||||
100 13 32 29 28 46
|
||||
101 13 32 29 28 19
|
||||
102 12 35 29 28 27
|
||||
103 13 35 29 28 46
|
||||
104 13 35 29 28 19
|
||||
105 2 32 29 35 47
|
||||
106 4 32 29 35 36
|
||||
107 10 31 32 29 28
|
||||
108 11 33 32 29 28
|
||||
109 4 33 32 29 35
|
||||
110 5 31 32 33 30
|
||||
111 4 29 32 33 34
|
||||
112 2 29 32 33 30
|
||||
113 10 47 35 29 28
|
||||
114 11 36 35 29 28
|
||||
115 2 29 35 36 10
|
||||
116 4 29 35 36 34
|
||||
117 5 47 35 36 10
|
||||
118 2 34 36 35 47
|
||||
119 2 35 36 34 9
|
||||
120 4 35 36 34 33
|
||||
121 5 10 36 34 9
|
||||
122 2 4 2 6 5
|
||||
123 4 6 2 4 15
|
||||
124 2 6 2 4 3
|
||||
125 5 1 2 4 3
|
||||
126 2 2 4 15 14
|
||||
127 2 15 4 2 1
|
||||
|
||||
Impropers
|
||||
|
||||
1 6 45 46 48 28
|
||||
2 1 22 18 17 13
|
||||
3 1 22 18 13 19
|
||||
4 1 17 18 13 19
|
||||
5 1 22 18 17 19
|
||||
6 1 44 19 18 28
|
||||
7 1 23 19 18 28
|
||||
8 1 44 19 23 28
|
||||
9 1 44 19 23 18
|
||||
10 1 22 21 39 38
|
||||
11 5 21 22 24 18
|
||||
12 1 29 28 27 46
|
||||
13 1 29 28 27 19
|
||||
14 1 29 28 46 19
|
||||
15 1 27 28 46 19
|
||||
16 1 22 24 41 20
|
||||
17 1 21 39 40 37
|
||||
18 1 41 40 39 42
|
||||
19 1 24 41 40 43
|
||||
20 1 32 33 34 30
|
||||
21 1 36 34 33 9
|
||||
22 1 7 6 2 5
|
||||
23 1 16 7 6 8
|
||||
24 9 16 12 26 13
|
||||
25 1 25 13 11 12
|
||||
26 1 25 13 12 18
|
||||
27 1 11 13 12 18
|
||||
28 1 25 13 11 18
|
||||
29 1 16 15 4 14
|
||||
30 8 15 16 7 12
|
||||
31 5 32 29 35 28
|
||||
32 1 29 32 33 31
|
||||
33 1 29 35 36 47
|
||||
34 1 35 36 34 10
|
||||
35 1 6 2 4 1
|
||||
36 1 15 4 2 3
|
||||
0
examples/USER/sph/shock_tube/exact_solution.dat
Executable file → Normal file
0
examples/USER/sph/shock_tube/exact_solution.dat
Executable file → Normal file
0
examples/USER/sph/shock_tube/shock2d.lmp
Executable file → Normal file
0
examples/USER/sph/shock_tube/shock2d.lmp
Executable file → Normal file
Reference in New Issue
Block a user