281 lines
19 KiB
Groff
281 lines
19 KiB
Groff
LAMMPS (21 Nov 2023)
|
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
## This script first uses fix qtb to equilibrate liquid methane to an initial state with quantum nuclear correction and then simulate shock induced chemical reactions through the quantum thermal bath multi-scale shock technique
|
|
#The default system size may take a while to run you can change to a smaller size
|
|
variable x_rep equal 5 #x-direction replication number
|
|
variable y_rep equal 5 #y-direction replication number
|
|
variable z_rep equal 10 #z-direction replication number
|
|
variable temperature equal 110.0 #Target quantum temperature (K in real units)
|
|
variable delta_t equal 0.25 #MD timestep length (fs in real units)
|
|
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
|
|
variable v_msst equal 0.122 #Shock velocity (Angstrom/fs in metal units)
|
|
variable q_msst equal 25.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in real units)
|
|
variable mu_msst equal 0.9 #Artificial viscosity in the MSST (mass/length/time, where mass=grams/mole, length=Angstrom and time=fs in real units)
|
|
variable tscale_msst equal 0.01 #Temperature reduction parameter in the MSST (unitless)
|
|
variable eta_qbmsst equal 1.0 #Coupling constant between the shock and the quantum thermal bath (unitless constant)
|
|
|
|
|
|
##The included part first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
|
include methane_qtb.mod
|
|
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
|
|
|
|
|
## This part defines units, methane structure, and atomic information
|
|
#General
|
|
units real
|
|
dimension 3
|
|
boundary p p p
|
|
atom_style charge
|
|
|
|
#Lattice
|
|
lattice custom 1.0 a1 3.9783624 0 0 a2 0 3.9783624 0 a3 0 0 3.9783624 basis 0.5 0.5 0.5 basis 0.663 0.663 0.663 basis 0.337 0.337 0.663 basis 0.663 0.337 0.337 basis 0.337 0.663 0.337
|
|
Lattice spacing in x,y,z = 3.9783624 3.9783624 3.9783624
|
|
|
|
#Computational Cell
|
|
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
|
|
create_box 2 simbox
|
|
Created orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
|
|
1 by 2 by 2 MPI processor grid
|
|
create_atoms 1 box basis 1 1 basis 2 2 basis 3 2 basis 4 2 basis 5 2
|
|
Created 5 atoms
|
|
using lattice units in orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
|
|
create_atoms CPU = 0.000 seconds
|
|
replicate ${x_rep} ${y_rep} ${z_rep}
|
|
replicate 5 ${y_rep} ${z_rep}
|
|
replicate 5 5 ${z_rep}
|
|
replicate 5 5 10
|
|
Replication is creating a 5x5x10 = 250 times larger system...
|
|
orthogonal box = (0 0 0) to (19.891812 19.891812 39.783624)
|
|
1 by 1 by 4 MPI processor grid
|
|
1250 atoms
|
|
replicate CPU = 0.000 seconds
|
|
|
|
#Atomic Information
|
|
mass 1 12.011150
|
|
mass 2 1.007970
|
|
|
|
|
|
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
|
|
#Pair Potentials
|
|
pair_style reaxff NULL
|
|
pair_coeff * * ffield.reax C H
|
|
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
|
|
|
|
#Neighbor Style
|
|
neighbor 2.5 bin
|
|
neigh_modify every 10 delay 0 check no
|
|
|
|
|
|
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
|
#Initialization
|
|
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
|
|
velocity all create 110 93 dist gaussian sum no mom yes rot yes loop all
|
|
|
|
#Setup output
|
|
thermo_style custom step temp press etotal vol
|
|
thermo 20
|
|
|
|
#Colored thermal bath
|
|
fix scapegoat_qtb all nve #NVE does the time integration
|
|
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
|
|
fix methane_qtb all qtb temp 110 damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50
|
|
fix methane_qtb all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 50
|
|
timestep ${delta_t}
|
|
timestep 0.25
|
|
run 500 #500 fs
|
|
|
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
|
|
|
Your simulation uses code contributions which should be cited:
|
|
|
|
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
|
|
|
@Article{Aktulga12,
|
|
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
|
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
|
journal = {Parallel Computing},
|
|
year = 2012,
|
|
volume = 38,
|
|
number = {4--5},
|
|
pages = {245--259}
|
|
}
|
|
|
|
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
|
|
|
@Article{Aktulga12,
|
|
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
|
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
|
journal = {Parallel Computing},
|
|
year = 2012,
|
|
volume = 38,
|
|
pages = {245--259}
|
|
}
|
|
|
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
|
|
|
Neighbor list info ...
|
|
update: every = 10 steps, delay = 0 steps, check = no
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 12.5
|
|
ghost atom cutoff = 12.5
|
|
binsize = 6.25, bins = 4 4 7
|
|
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
|
(1) pair reaxff, perpetual
|
|
attributes: half, newton off, ghost
|
|
pair build: half/bin/newtoff/ghost
|
|
stencil: full/ghost/bin/3d
|
|
bin: standard
|
|
(2) fix qeq/reax, perpetual, copy from (1)
|
|
attributes: half, newton off
|
|
pair build: copy
|
|
stencil: none
|
|
bin: none
|
|
Per MPI rank memory allocation (min/avg/max) = 125.2 | 125.3 | 125.4 Mbytes
|
|
Step Temp Press TotEng Volume
|
|
0 110 -15717.706 -110869.31 15741.751
|
|
20 133.92621 9503.0083 -110548.47 15741.751
|
|
40 188.1524 -13687.131 -110344.93 15741.751
|
|
60 205.85747 8421.3906 -110165.58 15741.751
|
|
80 185.08989 -11337.006 -110026.24 15741.751
|
|
100 245.36524 5805.0694 -109841.66 15741.751
|
|
120 218.83661 -7740.8838 -109674.15 15741.751
|
|
140 254.6075 3396.3936 -109589.89 15741.751
|
|
160 262.20963 -3574.2575 -109413.81 15741.751
|
|
180 297.89271 917.40867 -109204.79 15741.751
|
|
200 315.54026 -371.17448 -109129.45 15741.751
|
|
220 323.90745 -2811.4367 -108988.12 15741.751
|
|
240 358.28478 3972.8358 -108848.95 15741.751
|
|
260 359.12673 -6289.689 -108788.08 15741.751
|
|
280 376.47656 6851.3186 -108664.07 15741.751
|
|
300 404.30975 -7805.7238 -108482.75 15741.751
|
|
320 410.9097 7696.2518 -108421.87 15741.751
|
|
340 406.19092 -8175.1703 -108311.84 15741.751
|
|
360 460.37085 7630.6182 -108139.6 15741.751
|
|
380 413.96355 -7515.2307 -108150.73 15741.751
|
|
400 452.17428 7148.0954 -108027.39 15741.751
|
|
420 467.1725 -6662.4113 -107842.71 15741.751
|
|
440 481.03775 6117.6862 -107759.03 15741.751
|
|
460 509.03937 -4095.0215 -107648.46 15741.751
|
|
480 533.22373 2211.9169 -107481.89 15741.751
|
|
500 517.71195 -214.23969 -107489.48 15741.751
|
|
Loop time of 22.2711 on 4 procs for 500 steps with 1250 atoms
|
|
|
|
Performance: 0.485 ns/day, 49.491 hours/ns, 22.451 timesteps/s, 28.063 katom-step/s
|
|
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 13.689 | 15.195 | 16.732 | 27.7 | 68.23
|
|
Neigh | 1.5325 | 1.5496 | 1.5658 | 1.0 | 6.96
|
|
Comm | 0.073366 | 1.6105 | 3.116 | 85.1 | 7.23
|
|
Output | 0.00052192 | 0.00057642 | 0.00073657 | 0.0 | 0.00
|
|
Modify | 3.896 | 3.9129 | 3.9306 | 0.6 | 17.57
|
|
Other | | 0.00241 | | | 0.01
|
|
|
|
Nlocal: 312.5 ave 317 max 308 min
|
|
Histogram: 1 0 0 1 0 0 1 0 0 1
|
|
Nghost: 4982 ave 4995 max 4967 min
|
|
Histogram: 1 0 0 0 0 1 1 0 0 1
|
|
Neighs: 172509 ave 174182 max 170676 min
|
|
Histogram: 1 0 0 1 0 0 0 1 0 1
|
|
|
|
Total # of neighbors = 690037
|
|
Ave neighs/atom = 552.0296
|
|
Neighbor list builds = 50
|
|
Dangerous builds not checked
|
|
unfix methane_qtb
|
|
unfix scapegoat_qtb
|
|
|
|
|
|
##Shock compression with quantum nuclear corrections
|
|
reset_timestep 0
|
|
fix shock all qbmsst z ${v_msst} q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
|
fix shock all qbmsst z 0.122 q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
|
fix shock all qbmsst z 0.122 q 25 mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
|
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
|
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
|
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
|
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta 1 beta 400 T_init ${temperature}
|
|
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta 1 beta 400 T_init 110
|
|
QBMSST parameters:
|
|
Shock in z direction
|
|
Cell mass-like parameter qmass (units of mass^2/length^4) = 2.50000e+01
|
|
Shock velocity = 1.22000e-01
|
|
Artificial viscosity (units of mass/length/time) = 9.00000e-01
|
|
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 20
|
|
timestep ${delta_t}
|
|
timestep 0.25
|
|
#restart 1000 restart
|
|
run 500
|
|
Fix QBMSST v0 = 1.57418e+04
|
|
Fix QBMSST p0 = -5.88788e+01
|
|
Fix QBMSST e0 = to be -1.07489e+05
|
|
Fix QBMSST initial strain rate of -1.02186e-04 established by reducing temperature by factor of 1.00000e-02
|
|
Per MPI rank memory allocation (min/avg/max) = 126.1 | 126.1 | 126.1 Mbytes
|
|
Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
|
0 110 -270.21489 -107489.48 15741.751 19.891812 19.891812 39.783624 -118.93551 0 -60.056661 0 0
|
|
20 110 -2180.5877 -107208.2 15733.847 19.891812 19.891812 39.763648 223.47326 -37.773571 -29.703539 6.1258507e-05 -0.60983836
|
|
40 110 5004.864 -107109.95 15726.306 19.891812 19.891812 39.744592 3335.6341 -50.920246 2784.77 0.00011969641 -1.2193771
|
|
60 110 -4549.1199 -106949.22 15719.136 19.891812 19.891812 39.72647 -4461.4212 -72.656651 -5295.3675 0.00017526726 -1.8286321
|
|
80 110 6695.6833 -106942.12 15712.214 19.891812 19.891812 39.708976 5333.2741 -73.356417 4226.043 0.00022891479 -2.4376137
|
|
100 110 -5337.7671 -106930.78 15705.644 19.891812 19.891812 39.692373 -2682.4224 -75.129348 -4049.0157 0.00027982924 -3.0463347
|
|
120 110 6526.5587 -106736.15 15699.334 19.891812 19.891812 39.676424 7038.2375 -100.8809 5422.5046 0.00032873694 -3.6548061
|
|
140 110 -3284.0472 -106761.36 15693.36 19.891812 19.891812 39.661329 -3999.8116 -97.977739 -5851.3636 0.00037502973 -4.2630401
|
|
160 110 4792.0537 -106662.24 15687.56 19.891812 19.891812 39.64667 4484.6905 -110.86184 2404.1579 0.00041998006 -4.8710464
|
|
180 110 -1253.5849 -106532.38 15682.037 19.891812 19.891812 39.632711 -723.78287 -128.58314 -3022.3825 0.00046278801 -5.4788331
|
|
200 110 3276.2225 -106488.13 15676.725 19.891812 19.891812 39.619286 5117.4749 -134.15782 2609.1518 0.00050395806 -6.0864105
|
|
220 110 -553.17982 -106421.17 15671.675 19.891812 19.891812 39.606524 -1360.8796 -143.56979 -4068.5641 0.00054309397 -6.6937871
|
|
240 110 1329.8793 -106309.56 15666.794 19.891812 19.891812 39.594187 775.35326 -158.40869 -2125.0508 0.00058092605 -7.300972
|
|
260 110 1809.8974 -106360.42 15662.075 19.891812 19.891812 39.582262 3075.2725 -151.39659 -11.4097 0.00061749364 -7.9079706
|
|
280 110 24.534819 -106310.46 15657.56 19.891812 19.891812 39.570852 1043.8352 -158.25965 -2221.0935 0.00065248454 -8.5147908
|
|
300 110 2854.2862 -106150.2 15653.217 19.891812 19.891812 39.559874 3727.6844 -179.54521 291.27132 0.00068614803 -9.1214393
|
|
320 110 -776.61228 -106199.04 15649.041 19.891812 19.891812 39.549322 -1285.3999 -173.42703 -4886.655 0.00071850756 -9.7279234
|
|
340 110 3778.2238 -106201.03 15644.958 19.891812 19.891812 39.539001 3694.462 -172.6926 -68.017561 0.00075015694 -10.334247
|
|
360 110 -1505.9413 -106025.15 15641.031 19.891812 19.891812 39.529078 -1491.3768 -196.81063 -5408.8787 0.00078058882 -10.940416
|
|
380 110 3414.9599 -106071.49 15637.176 19.891812 19.891812 39.519335 4956.6752 -189.93327 886.98409 0.00081046454 -11.546435
|
|
400 110 -947.2273 -106003.34 15633.49 19.891812 19.891812 39.510021 726.91825 -199.51619 -3488.2795 0.0008390284 -12.152307
|
|
420 46.681884 1610.2414 -105884.37 15629.905 19.891812 19.891812 39.500961 -1377.8364 -215.72223 -5734.5653 0.00086681188 -12.758039
|
|
440 46.681884 2290.4653 -105923.83 15626.371 19.891812 19.891812 39.492029 6296.7177 -209.55961 1800.4591 0.00089420243 -13.363632
|
|
460 46.681884 -2068.0472 -105879.44 15622.969 19.891812 19.891812 39.483432 -5629.8405 -216.88862 -10260.4 0.00092056659 -13.969092
|
|
480 46.681884 5011.06 -105748.92 15619.556 19.891812 19.891812 39.474805 8649.5097 -232.72756 3884.1859 0.00094702163 -14.574419
|
|
500 46.681884 -3314.8335 -105829.23 15616.305 19.891812 19.891812 39.46659 -5120.4784 -223.60669 -10014.132 0.00097221364 -15.179618
|
|
Loop time of 26.5748 on 4 procs for 500 steps with 1250 atoms
|
|
|
|
Performance: 0.406 ns/day, 59.055 hours/ns, 18.815 timesteps/s, 23.519 katom-step/s
|
|
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 16.259 | 18.109 | 19.999 | 31.1 | 68.14
|
|
Neigh | 1.8265 | 1.8477 | 1.8638 | 1.0 | 6.95
|
|
Comm | 0.045073 | 1.9349 | 3.7845 | 95.1 | 7.28
|
|
Output | 0.0019058 | 0.0019666 | 0.0021202 | 0.2 | 0.01
|
|
Modify | 4.6619 | 4.6782 | 4.699 | 0.6 | 17.60
|
|
Other | | 0.002774 | | | 0.01
|
|
|
|
Nlocal: 312.5 ave 318 max 307 min
|
|
Histogram: 1 0 0 0 1 1 0 0 0 1
|
|
Nghost: 5059 ave 5080 max 5039 min
|
|
Histogram: 1 0 1 0 0 0 1 0 0 1
|
|
Neighs: 173854 ave 176807 max 170839 min
|
|
Histogram: 1 0 0 1 0 0 1 0 0 1
|
|
|
|
Total # of neighbors = 695414
|
|
Ave neighs/atom = 556.3312
|
|
Neighbor list builds = 50
|
|
Dangerous builds not checked
|
|
Total wall time: 0:00:49
|