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update example inputs and logs for change in ReaxFF required name

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Axel Kohlmeyer
2023-11-30 07:20:33 -05:00
parent 6ff87f5c39
commit 00be75e084
71 changed files with 4207 additions and 2369 deletions
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## 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
##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_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}
#restart 1000 restart
run 500

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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 1 by 1 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 1 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) = 201.3 | 201.3 | 201.3 Mbytes
Step Temp Press TotEng Volume
0 110 -15717.706 -110869.31 15741.751
20 133.92166 8773.5364 -110569.51 15741.751
40 184.43244 -12136.835 -110378.92 15741.751
60 203.58164 6527.2188 -110190.9 15741.751
80 183.0518 -9667.6163 -110095.24 15741.751
100 236.07378 4393.5089 -109905.8 15741.751
120 226.94599 -5612.6845 -109708.46 15741.751
140 249.34156 988.50573 -109631.88 15741.751
160 255.08331 -1397.98 -109469.09 15741.751
180 281.64743 -1682.598 -109285.53 15741.751
200 303.76929 2594.8345 -109206.84 15741.751
220 311.6547 -4566.4307 -109053.21 15741.751
240 350.68316 5132.0272 -108918.26 15741.751
260 347.11102 -6078.5078 -108828.31 15741.751
280 366.56298 6373.2426 -108694.64 15741.751
300 393.62524 -6438.9321 -108521.5 15741.751
320 403.64821 5946.6873 -108487.83 15741.751
340 406.12883 -5053.5592 -108331.25 15741.751
360 450.60139 4323.0942 -108185.06 15741.751
380 429.46056 -3317.8604 -108146.84 15741.751
400 448.11876 3264.6165 -108048.01 15741.751
420 485.98657 -3047.3542 -107882.88 15741.751
440 463.23761 3088.3325 -107853.09 15741.751
460 504.27223 -1966.5888 -107689.56 15741.751
480 515.66783 2915.6322 -107550.83 15741.751
500 516.26369 -1733.2701 -107498.06 15741.751
Loop time of 41.4818 on 1 procs for 500 steps with 1250 atoms
Performance: 0.260 ns/day, 92.182 hours/ns, 12.053 timesteps/s, 15.067 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 30.707 | 30.707 | 30.707 | 0.0 | 74.03
Neigh | 2.2815 | 2.2815 | 2.2815 | 0.0 | 5.50
Comm | 0.023963 | 0.023963 | 0.023963 | 0.0 | 0.06
Output | 0.00073327 | 0.00073327 | 0.00073327 | 0.0 | 0.00
Modify | 8.4653 | 8.4653 | 8.4653 | 0.0 | 20.41
Other | | 0.00334 | | | 0.01
Nlocal: 1250 ave 1250 max 1250 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8444 ave 8444 max 8444 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 601915 ave 601915 max 601915 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 601915
Ave neighs/atom = 481.532
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 = -3.03801e+03
Fix QBMSST e0 = to be -1.07498e+05
Fix QBMSST initial strain rate of -1.02043e-04 established by reducing temperature by factor of 1.00000e-02
Per MPI rank memory allocation (min/avg/max) = 201.4 | 201.4 | 201.4 Mbytes
Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
0 110 -1789.091 -107498.06 15741.751 19.891812 19.891812 39.783624 -3095.1546 1.9543098e-12 -57.148468 0 0
20 110 313.41128 -107231.57 15733.908 19.891812 19.891812 39.763803 1026.815 -35.805172 3755.1834 6.0783853e-05 -0.60983919
40 110 1248.5771 -107106.23 15726.494 19.891812 19.891812 39.745066 -277.53233 -52.672766 2158.1479 0.00011824041 -1.219383
60 110 -944.55947 -107017.75 15719.482 19.891812 19.891812 39.727345 1006.8843 -64.550247 3165.7346 0.00017258388 -1.8286479
80 110 2164.646 -107053.82 15712.848 19.891812 19.891812 39.710579 686.99949 -59.728513 2583.9345 0.00022399951 -2.4376489
100 110 -332.40946 -106996.04 15706.579 19.891812 19.891812 39.694734 1555.274 -67.472889 3204.6947 0.00027258815 -3.0464001
120 110 2556.8172 -106828.33 15700.655 19.891812 19.891812 39.679765 -1406.2492 -90.123866 9.330762 0.00031849257 -3.6549157
140 110 -649.1633 -106851.95 15695.029 19.891812 19.891812 39.665545 3704.8784 -86.742267 4898.3193 0.00036209988 -4.2632077
160 110 2301.4774 -106787.04 15689.738 19.891812 19.891812 39.652174 -893.31294 -95.690383 91.247096 0.00040310452 -4.8712886
180 110 -701.59672 -106639.61 15684.711 19.891812 19.891812 39.63947 3211.2065 -115.27944 3997.3199 0.00044206086 -5.47917
200 110 3857.6228 -106696.51 15679.975 19.891812 19.891812 39.627501 -1722.9124 -107.93584 -1123.778 0.00047876602 -6.0868625
220 110 -1057.1346 -106590.95 15675.462 19.891812 19.891812 39.616094 3285.0876 -121.80821 3706.0326 0.00051374575 -6.6943761
240 110 2748.5299 -106428.9 15671.216 19.891812 19.891812 39.605364 172.15717 -143.78629 425.48974 0.00054664912 -7.3017201
260 110 64.99143 -106442.23 15667.188 19.891812 19.891812 39.595183 981.21139 -141.94851 1075.4979 0.00057787086 -7.9089043
280 110 1612.9607 -106412.77 15663.362 19.891812 19.891812 39.585514 662.48897 -145.93658 605.73218 0.00060752164 -8.5159364
300 110 1435.9566 -106307.06 15659.725 19.891812 19.891812 39.576323 759.46794 -160.13403 559.12791 0.00063570794 -9.1228243
320 110 -890.72712 -106332.6 15656.258 19.891812 19.891812 39.56756 234.14376 -156.75496 -103.07714 0.00066257852 -9.7295747
340 110 4270.0983 -106252.72 15652.976 19.891812 19.891812 39.559265 5411.2268 -167.0427 4944.423 0.00068801647 -10.336194
360 110 -2801.0763 -106105.96 15649.905 19.891812 19.891812 39.551504 -3276.3824 -187.5258 -3864.4213 0.00071181569 -10.942691
380 110 5566.9116 -106139.88 15646.926 19.891812 19.891812 39.543977 2737.1121 -182.43141 2031.4929 0.00073489745 -11.549071
400 110 -4432.9416 -106074.79 15644.09 19.891812 19.891812 39.536808 -4946.1908 -191.90759 -5763.8068 0.00075688314 -12.155339
420 52.599535 5582.8126 -105959.96 15641.311 19.891812 19.891812 39.529786 7869.5301 -206.09135 6942.2136 0.00077841805 -12.761497
440 52.599535 -2861.6332 -106017.66 15638.758 19.891812 19.891812 39.523335 -1820.4742 -199.30721 -2848.5648 0.00079820063 -13.367553
460 52.599535 3942.7505 -105984.45 15636.294 19.891812 19.891812 39.517106 3327.0393 -203.24794 2201.6559 0.00081729985 -13.973511
480 52.599535 419.18442 -105827.32 15633.955 19.891812 19.891812 39.511194 -1910.6109 -224.9021 -3128.3482 0.00083542949 -14.579377
500 52.599535 117.60016 -105904.83 15631.655 19.891812 19.891812 39.505383 -603.40365 -214.36236 -1911.9203 0.00085325005 -15.185153
Loop time of 41.8312 on 1 procs for 500 steps with 1250 atoms
Performance: 0.258 ns/day, 92.958 hours/ns, 11.953 timesteps/s, 14.941 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 31.016 | 31.016 | 31.016 | 0.0 | 74.15
Neigh | 2.2849 | 2.2849 | 2.2849 | 0.0 | 5.46
Comm | 0.020391 | 0.020391 | 0.020391 | 0.0 | 0.05
Output | 0.0019403 | 0.0019403 | 0.0019403 | 0.0 | 0.00
Modify | 8.505 | 8.505 | 8.505 | 0.0 | 20.33
Other | | 0.003238 | | | 0.01
Nlocal: 1250 ave 1250 max 1250 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8489 ave 8489 max 8489 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 606382 ave 606382 max 606382 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 606382
Ave neighs/atom = 485.1056
Neighbor list builds = 50
Dangerous builds not checked
Total wall time: 0:01:23

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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

33
examples/PACKAGES/qtb/methane_qbmsst/methane_qbmsst.in
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@ -1,33 +0,0 @@
## 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
##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_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 100
timestep ${delta_t}
restart 1000 restart
run 5000

78
examples/PACKAGES/qtb/methane_qbmsst/methane_qtb.mod
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@ -3,62 +3,62 @@
## This part defines units, methane structure, and atomic information
#General
units real
dimension 3
boundary p p p
atom_style charge
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 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
#Computational Cell
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
create_box 2 simbox
create_atoms 1 box &
basis 1 1 &
basis 2 2 &
basis 3 2 &
basis 4 2 &
basis 5 2
replicate ${x_rep} ${y_rep} ${z_rep}
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
create_box 2 simbox
create_atoms 1 box &
basis 1 1 &
basis 2 2 &
basis 3 2 &
basis 4 2 &
basis 5 2
replicate ${x_rep} ${y_rep} ${z_rep}
#Atomic Information
mass 1 12.011150
mass 2 1.007970
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 reax/c NULL
pair_coeff * * ffield.reax C H
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
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
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 ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
#Setup output
thermo_style custom step temp press etotal vol
thermo 100
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
timestep ${delta_t}
run 2000 #500 fs
unfix methane_qtb
unfix scapegoat_qtb
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
timestep ${delta_t}
run 500 #500 fs
unfix methane_qtb
unfix scapegoat_qtb

70
examples/PACKAGES/qtb/methane_qtb/in.methane_qtb Normal file
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@ -0,0 +1,70 @@
## 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.
variable x_rep equal 2 #x-direction replication number
variable y_rep equal 2 #y-direction replication number
variable z_rep equal 2 #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)
## 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
#Computational Cell
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
create_box 2 simbox
create_atoms 1 box &
basis 1 1 &
basis 2 2 &
basis 3 2 &
basis 4 2 &
basis 5 2
replicate ${x_rep} ${y_rep} ${z_rep}
#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
#Setup output
thermo_style custom step temp press etotal vol
thermo 50
#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
timestep ${delta_t}
run 1000
unfix methane_qtb
unfix scapegoat_qtb

174
examples/PACKAGES/qtb/methane_qtb/log.30Nov23.methane_qtb.g++.1 Normal file
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@ -0,0 +1,174 @@
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 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.
variable x_rep equal 2 #x-direction replication number
variable y_rep equal 2 #y-direction replication number
variable z_rep equal 2 #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)
## 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 1 by 1 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 2 ${y_rep} ${z_rep}
replicate 2 2 ${z_rep}
replicate 2 2 2
Replication is creating a 2x2x2 = 8 times larger system...
orthogonal box = (0 0 0) to (7.9567248 7.9567248 7.9567248)
1 by 1 by 1 MPI processor grid
40 atoms
replicate CPU = 0.001 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 50
#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 1000
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 = 2 2 2
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) = 82.45 | 82.45 | 82.45 Mbytes
Step Temp Press TotEng Volume
0 110 -15746.508 -3548.1354 503.73603
50 191.27715 -7523.7503 -3530.4179 503.73603
100 214.09982 12016.892 -3517.4544 503.73603
150 317.38272 3098.2254 -3499.5793 503.73603
200 338.76362 -4484.9241 -3490.3649 503.73603
250 402.05826 3973.0488 -3474.81 503.73603
300 340.80076 11193.4 -3470.8029 503.73603
350 556.19747 8086.3266 -3451.5937 503.73603
400 566.8737 5499.5505 -3439.2335 503.73603
450 643.2883 -8270.5736 -3426.0767 503.73603
500 613.09742 -12406.229 -3419.8547 503.73603
550 669.28891 -9757.601 -3410.7281 503.73603
600 600.66922 10407.403 -3408.3776 503.73603
650 573.1485 30971.977 -3405.0744 503.73603
700 726.22146 29573.798 -3386.3167 503.73603
750 777.22659 13265.88 -3378.8462 503.73603
800 652.46476 -9231.9331 -3388.7229 503.73603
850 679.18414 -19802.254 -3384.6321 503.73603
900 711.60594 -18792.396 -3373.2944 503.73603
950 865.79013 -2837.6042 -3363.2971 503.73603
1000 884.14995 6160.4875 -3360.6295 503.73603
Loop time of 7.87 on 1 procs for 1000 steps with 40 atoms
Performance: 2.745 ns/day, 8.744 hours/ns, 127.065 timesteps/s, 5.083 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.3662 | 6.3662 | 6.3662 | 0.0 | 80.89
Neigh | 0.97757 | 0.97757 | 0.97757 | 0.0 | 12.42
Comm | 0.013653 | 0.013653 | 0.013653 | 0.0 | 0.17
Output | 0.00042319 | 0.00042319 | 0.00042319 | 0.0 | 0.01
Modify | 0.50971 | 0.50971 | 0.50971 | 0.0 | 6.48
Other | | 0.00248 | | | 0.03
Nlocal: 40 ave 40 max 40 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2552 ave 2552 max 2552 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 25110 ave 25110 max 25110 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 25110
Ave neighs/atom = 627.75
Neighbor list builds = 100
Dangerous builds not checked
unfix methane_qtb
unfix scapegoat_qtb
Total wall time: 0:00:07

174
examples/PACKAGES/qtb/methane_qtb/log.30Nov23.methane_qtb.g++.4 Normal file
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@ -0,0 +1,174 @@
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 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.
variable x_rep equal 2 #x-direction replication number
variable y_rep equal 2 #y-direction replication number
variable z_rep equal 2 #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)
## 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 2 ${y_rep} ${z_rep}
replicate 2 2 ${z_rep}
replicate 2 2 2
Replication is creating a 2x2x2 = 8 times larger system...
orthogonal box = (0 0 0) to (7.9567248 7.9567248 7.9567248)
1 by 2 by 2 MPI processor grid
40 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 50
#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 1000
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 = 2 2 2
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) = 72.47 | 72.47 | 72.47 Mbytes
Step Temp Press TotEng Volume
0 110 -15746.508 -3548.1354 503.73603
50 183.74482 -917.59204 -3534.8518 503.73603
100 200.96363 16464.403 -3517.1456 503.73603
150 255.33305 14801.963 -3507.7299 503.73603
200 328.11626 5119.3618 -3498.0388 503.73603
250 356.88626 -11306.151 -3485.1746 503.73603
300 284.7363 -25276.091 -3479.4732 503.73603
350 434.79382 -23326.29 -3471.7491 503.73603
400 414.69602 2800.9047 -3465.7225 503.73603
450 464.61242 20775.398 -3449.1675 503.73603
500 671.43369 15272.581 -3433.9453 503.73603
550 534.01157 -8545.4173 -3427.6672 503.73603
600 512.69648 -15904.052 -3417.8071 503.73603
650 604.62051 -1777.9242 -3419.4324 503.73603
700 650.2196 20108.199 -3415.8902 503.73603
750 677.45644 21721.335 -3409.1253 503.73603
800 707.98295 171.53756 -3413.4048 503.73603
850 740.68522 -23846.627 -3384.7024 503.73603
900 739.55514 -22742.841 -3377.091 503.73603
950 769.44821 -7060.9388 -3389.817 503.73603
1000 987.6246 -0.47618437 -3373.9263 503.73603
Loop time of 6.80367 on 4 procs for 1000 steps with 40 atoms
Performance: 3.175 ns/day, 7.560 hours/ns, 146.980 timesteps/s, 5.879 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 | 5.1801 | 5.3491 | 5.5417 | 6.1 | 78.62
Neigh | 0.76934 | 0.77281 | 0.77567 | 0.3 | 11.36
Comm | 0.072213 | 0.26492 | 0.4339 | 27.2 | 3.89
Output | 0.00032365 | 0.00035547 | 0.00044739 | 0.0 | 0.01
Modify | 0.41139 | 0.41424 | 0.4179 | 0.4 | 6.09
Other | | 0.00226 | | | 0.03
Nlocal: 10 ave 10 max 10 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1950 ave 1950 max 1950 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 6434.5 ave 6447 max 6427 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 25738
Ave neighs/atom = 643.45
Neighbor list builds = 100
Dangerous builds not checked
unfix methane_qtb
unfix scapegoat_qtb
Total wall time: 0:00:06

70
examples/PACKAGES/qtb/methane_qtb/methane_qtb.in
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@ -1,70 +0,0 @@
## 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.
variable x_rep equal 2 #x-direction replication number
variable y_rep equal 2 #y-direction replication number
variable z_rep equal 2 #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)
## 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
#Computational Cell
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
create_box 2 simbox
create_atoms 1 box &
basis 1 1 &
basis 2 2 &
basis 3 2 &
basis 4 2 &
basis 5 2
replicate ${x_rep} ${y_rep} ${z_rep}
#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 reax/c NULL
pair_coeff * * ffield.reax C H
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
#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
#Setup output
thermo_style custom step temp press etotal vol
thermo 100
#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
timestep ${delta_t}
run 3000 #750 fs
unfix methane_qtb
unfix scapegoat_qtb