adjust USER-QTB examples to match more closely with LAMMPS' style. add log files.
This commit is contained in:
Axel Kohlmeyer
@ -1,15 +1,15 @@
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#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.
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#Pair Potentials
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pair_style hybrid/overlay buck/coul/long ${cut_off} table linear 39901
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pair_coeff 1 1 buck/coul/long 0.0 1.0 0.0 #No interactions between Si atoms
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pair_coeff 1 2 buck/coul/long 18003.757200 0.205205 133.538100
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pair_coeff 2 2 buck/coul/long 1388.773000 0.362319 175.000000 #BKS interaction in PRL 64 1955 (1990)
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pair_modify shift yes
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pair_coeff 1 2 table potential_SiO2.TPF Si-O ${cut_off}
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pair_coeff 2 2 table potential_SiO2.TPF O-O ${cut_off} #See the potential file for more information
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kspace_style pppm 1.0e-4
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pair_style hybrid/overlay buck/coul/long ${cut_off} table linear 39901
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pair_coeff 1 1 buck/coul/long 0.0 1.0 0.0 #No interactions between Si atoms
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pair_coeff 1 2 buck/coul/long 18003.757200 0.205205 133.538100
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pair_coeff 2 2 buck/coul/long 1388.773000 0.362319 175.000000 #BKS interaction in PRL 64 1955 (1990)
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pair_modify shift yes
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pair_coeff 1 2 table potential_SiO2.TPF Si-O ${cut_off}
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pair_coeff 2 2 table potential_SiO2.TPF O-O ${cut_off} #See the potential file for more information
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kspace_style pppm 1.0e-4
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#Neighbor style
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neighbor 2.0 bin
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neigh_modify check yes every 1 delay 0 page 100000 one 2000
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neighbor 2.0 bin
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neigh_modify check yes every 1 delay 0 page 100000 one 2000
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@ -1,55 +0,0 @@
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## 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
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variable x_rep equal 2 #plot is made with x_rep = 8 #x-direction replication number
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variable y_rep equal 1 #plot is made with y_rep = 5 #y-direction replication number
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variable z_rep equal 4 #plot is made with z_rep = 15 #z-direction replication number
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variable cut_off equal 10.0 #Cut-off distance for the Buckingham term (Angstrom in metal units)
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variable pressure equal 1.03125 #Initial state pressure (bar in metal units)
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variable temperature equal 300.0 #Initial state quantum temperature (K in metal units)
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variable delta_t equal 1.0e-3 #MD timestep length (ps in metal units)
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variable damp_qtb equal 1 #1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
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variable v_msst equal 78.0 #Shock velocity (Angstrom/ps in metal units)
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variable q_msst equal 40.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in metal units)
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variable tscale_msst equal 0.05 #Temperature reduction parameter in the MSST (unitless)
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variable eta_qbmsst equal 1.0 #Coupling constant between the shock and the quantum thermal bath (unitless constant)
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## This part uses fix qtb to prepare alpha-quartz with quantum nuclear correction of the initial state
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include alpha_quartz_qtb.mod
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## This part demonstrates how to retart fix qbmsst during any stage of the shock simulation.
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## PPPM may break down when compression ratio becomes extremely large. One can always use this restart technique to resume the shock simulation.
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#Compression restart 1
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reset_timestep 0
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#Beta is the number of time steps between each update of the quantum bath temperature. Setting a larger beta can reduce thermal flactuations.
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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}
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fix_modify shock energy yes
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variable dhug equal f_shock[1]
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variable dray equal f_shock[2]
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variable lgr_vel equal f_shock[3]
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variable lgr_pos equal f_shock[4]
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variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
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thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
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thermo 100
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timestep ${delta_t}
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run 1000
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write_restart restart.1000
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#Compression restart 2
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#Read restart file and load potential again
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clear
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read_restart restart.1000
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include alpha_quartz_potential.mod
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#Use the same fix id and add no tscale if the system is already compressed
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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}
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fix_modify shock energy yes
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variable dhug equal f_shock[1]
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variable dray equal f_shock[2]
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variable lgr_vel equal f_shock[3]
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variable lgr_pos equal f_shock[4]
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variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
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thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
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thermo 100
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timestep ${delta_t}
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restart 1000 restart
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run 10000 #10 ps
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@ -3,60 +3,60 @@
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## This part defines units, alpha-quartz crystal, and atomic information
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#General
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units metal
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dimension 3
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boundary p p p
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atom_style charge
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units metal
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dimension 3
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boundary p p p
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atom_style charge
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#Lattice
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lattice custom 1.0 &
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a1 4.916000 0.000000 0.000000 &
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a2 -2.45800 4.257381 0.000000 &
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a3 0.000000 0.000000 5.405400 &
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&
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basis 0.469700 0.000000 0.000000 &
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basis 0.000000 0.469700 0.666667 &
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basis 0.530300 0.530300 0.333333 &
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&
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basis 0.413500 0.266900 0.119100 &
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basis 0.266900 0.413500 0.547567 &
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basis 0.733100 0.146600 0.785767 &
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basis 0.586500 0.853400 0.214233 &
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basis 0.853400 0.586500 0.452433 &
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basis 0.146600 0.733100 0.880900 #American Mineralogist 65 920 1980 (Space Group 154)
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lattice custom 1.0 &
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a1 4.916000 0.000000 0.000000 &
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a2 -2.45800 4.257381 0.000000 &
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a3 0.000000 0.000000 5.405400 &
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&
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basis 0.469700 0.000000 0.000000 &
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basis 0.000000 0.469700 0.666667 &
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basis 0.530300 0.530300 0.333333 &
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&
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basis 0.413500 0.266900 0.119100 &
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basis 0.266900 0.413500 0.547567 &
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basis 0.733100 0.146600 0.785767 &
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basis 0.586500 0.853400 0.214233 &
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basis 0.853400 0.586500 0.452433 &
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basis 0.146600 0.733100 0.880900 #American Mineralogist 65 920 1980 (Space Group 154)
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#Computational Cell
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region orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box
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create_box 2 orthorhombic_unit_cell
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create_atoms 1 box &
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basis 1 1 &
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basis 2 1 &
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basis 3 1 &
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basis 4 2 &
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basis 5 2 &
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basis 6 2 &
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basis 7 2 &
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basis 8 2 &
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basis 9 2
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replicate ${x_rep} ${y_rep} ${z_rep}
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region orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box
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create_box 2 orthorhombic_unit_cell
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create_atoms 1 box &
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basis 1 1 &
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basis 2 1 &
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basis 3 1 &
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basis 4 2 &
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basis 5 2 &
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basis 6 2 &
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basis 7 2 &
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basis 8 2 &
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basis 9 2
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replicate ${x_rep} ${y_rep} ${z_rep}
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#Atomic Information
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mass 1 28.085500
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mass 2 15.999400
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set type 1 charge +2.4
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set type 2 charge -1.2
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mass 1 28.085500
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mass 2 15.999400
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set type 1 charge +2.4
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set type 2 charge -1.2
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## This part implements the BKS pair potential with a cut-off distance for the Buckingham term. Long range Coulomb interactions are evaluated with the pppm method.
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include alpha_quartz_potential.mod
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include alpha_quartz_potential.mod
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## This part equilibrates your crystal to a pressure of ${pressure}(unit pressure) and a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
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variable p_damp equal ${delta_t}*1000 #Recommended pressure damping parameter in fix nph
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fix scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp} ptemp ${temperature} #NPH does the time integration
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fix quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 #Change f_max (THz) if your Debye frequency is higher
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thermo_style custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
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thermo 100
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run 2000 # 2 ps
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unfix quartz_qtb
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unfix scapegoat_qtb
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variable p_damp equal ${delta_t}*1000 #Recommended pressure damping parameter in fix nph
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fix scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp} ptemp ${temperature} #NPH does the time integration
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fix quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 #Change f_max (THz) if your Debye frequency is higher
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thermo_style custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
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thermo 200
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run 2000 # 2 ps
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unfix quartz_qtb
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unfix scapegoat_qtb
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55
examples/USER/qtb/alpha_quartz_qbmsst/in.alpha_quartz_qbmsst
Normal file
55
examples/USER/qtb/alpha_quartz_qbmsst/in.alpha_quartz_qbmsst
Normal file
@ -0,0 +1,55 @@
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## 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
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variable x_rep equal 2 #plot is made with x_rep = 8 #x-direction replication number
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variable y_rep equal 1 #plot is made with y_rep = 5 #y-direction replication number
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variable z_rep equal 4 #plot is made with z_rep = 15 #z-direction replication number
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variable cut_off equal 10.0 #Cut-off distance for the Buckingham term (Angstrom in metal units)
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variable pressure equal 1.03125 #Initial state pressure (bar in metal units)
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variable temperature equal 300.0 #Initial state quantum temperature (K in metal units)
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variable delta_t equal 1.0e-3 #MD timestep length (ps in metal units)
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variable damp_qtb equal 1 #1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
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variable v_msst equal 78.0 #Shock velocity (Angstrom/ps in metal units)
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variable q_msst equal 40.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in metal units)
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variable tscale_msst equal 0.05 #Temperature reduction parameter in the MSST (unitless)
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variable eta_qbmsst equal 1.0 #Coupling constant between the shock and the quantum thermal bath (unitless constant)
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## This part uses fix qtb to prepare alpha-quartz with quantum nuclear correction of the initial state
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include alpha_quartz_qtb.mod
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## This part demonstrates how to retart fix qbmsst during any stage of the shock simulation.
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## PPPM may break down when compression ratio becomes extremely large. One can always use this restart technique to resume the shock simulation.
|
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#Compression restart 1
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reset_timestep 0
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#Beta is the number of time steps between each update of the quantum bath temperature. Setting a larger beta can reduce thermal flactuations.
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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}
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fix_modify shock energy yes
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variable dhug equal f_shock[1]
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variable dray equal f_shock[2]
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variable lgr_vel equal f_shock[3]
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variable lgr_pos equal f_shock[4]
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variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
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thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
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thermo 200
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timestep ${delta_t}
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run 1000
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write_restart restart.1000
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#Compression restart 2
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#Read restart file and load potential again
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clear
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read_restart restart.1000
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include alpha_quartz_potential.mod
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#Use the same fix id and add no tscale if the system is already compressed
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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}
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fix_modify shock energy yes
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variable dhug equal f_shock[1]
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variable dray equal f_shock[2]
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variable lgr_vel equal f_shock[3]
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variable lgr_pos equal f_shock[4]
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variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
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thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
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thermo 500
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timestep ${delta_t}
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restart 1000 restart
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run 10000 #10 ps
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@ -0,0 +1,430 @@
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LAMMPS (15 Jun 2020)
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using 1 OpenMP thread(s) per MPI task
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## 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
|
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variable x_rep equal 2 #plot is made with x_rep = 8 #x-direction replication number
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variable y_rep equal 1 #plot is made with y_rep = 5 #y-direction replication number
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variable z_rep equal 4 #plot is made with z_rep = 15 #z-direction replication number
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variable cut_off equal 10.0 #Cut-off distance for the Buckingham term (Angstrom in metal units)
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variable pressure equal 1.03125 #Initial state pressure (bar in metal units)
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variable temperature equal 300.0 #Initial state quantum temperature (K in metal units)
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variable delta_t equal 1.0e-3 #MD timestep length (ps in metal units)
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variable damp_qtb equal 1 #1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
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variable v_msst equal 78.0 #Shock velocity (Angstrom/ps in metal units)
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variable q_msst equal 40.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in metal units)
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variable tscale_msst equal 0.05 #Temperature reduction parameter in the MSST (unitless)
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variable eta_qbmsst equal 1.0 #Coupling constant between the shock and the quantum thermal bath (unitless constant)
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## This part uses fix qtb to prepare alpha-quartz with quantum nuclear correction of the initial state
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include alpha_quartz_qtb.mod
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## This script first constructs an alpha quartz structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
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## This part defines units, alpha-quartz crystal, and atomic information
|
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#General
|
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units metal
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dimension 3
|
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boundary p p p
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atom_style charge
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|
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#Lattice
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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)
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Lattice spacing in x,y,z = 7.374 4.25738 5.4054
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#Computational Cell
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region orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box
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create_box 2 orthorhombic_unit_cell
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Created orthogonal box = (0.0 0.0 0.0) to (4.916 8.514762 5.4054)
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1 by 1 by 1 MPI processor grid
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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
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Created 18 atoms
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create_atoms CPU = 0.000 seconds
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replicate ${x_rep} ${y_rep} ${z_rep}
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replicate 2 ${y_rep} ${z_rep}
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replicate 2 1 ${z_rep}
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replicate 2 1 4
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orthogonal box = (0.0 0.0 0.0) to (9.832 8.514762 21.6216)
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1 by 1 by 1 MPI processor grid
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144 atoms
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replicate CPU = 0.000271082 secs
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#Atomic Information
|
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mass 1 28.085500
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mass 2 15.999400
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set type 1 charge +2.4
|
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48 settings made for charge
|
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set type 2 charge -1.2
|
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96 settings made for charge
|
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|
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|
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## This part implements the BKS pair potential with a cut-off distance for the Buckingham term. Long range Coulomb interactions are evaluated with the pppm method.
|
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include alpha_quartz_potential.mod
|
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#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.
|
||||
|
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#Pair Potentials
|
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pair_style hybrid/overlay buck/coul/long ${cut_off} table linear 39901
|
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pair_style hybrid/overlay buck/coul/long 10 table linear 39901
|
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pair_coeff 1 1 buck/coul/long 0.0 1.0 0.0 #No interactions between Si atoms
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||||
pair_coeff 1 2 buck/coul/long 18003.757200 0.205205 133.538100
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pair_coeff 2 2 buck/coul/long 1388.773000 0.362319 175.000000 #BKS interaction in PRL 64 1955 (1990)
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pair_modify shift yes
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pair_coeff 1 2 table potential_SiO2.TPF Si-O ${cut_off}
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pair_coeff 1 2 table potential_SiO2.TPF Si-O 10
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pair_coeff 2 2 table potential_SiO2.TPF O-O ${cut_off} #See the potential file for more information
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pair_coeff 2 2 table potential_SiO2.TPF O-O 10
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WARNING: 1 of 39901 force values in table are inconsistent with -dE/dr.
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Should only be flagged at inflection points (src/pair_table.cpp:471)
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kspace_style pppm 1.0e-4
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#Neighbor style
|
||||
neighbor 2.0 bin
|
||||
neigh_modify check yes every 1 delay 0 page 100000 one 2000
|
||||
|
||||
|
||||
## This part equilibrates your crystal to a pressure of ${pressure}(unit pressure) and a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
variable p_damp equal ${delta_t}*1000 #Recommended pressure damping parameter in fix nph
|
||||
variable p_damp equal 0.001*1000
|
||||
fix scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp} ptemp ${temperature} #NPH does the time integration
|
||||
fix scapegoat_qtb all nph iso 1.03125 ${pressure} ${p_damp} ptemp ${temperature}
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fix scapegoat_qtb all nph iso 1.03125 1.03125 ${p_damp} ptemp ${temperature}
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fix scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp ${temperature}
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fix scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp 300
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fix quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 #Change f_max (THz) if your Debye frequency is higher
|
||||
fix quartz_qtb all qtb temp 300 damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100
|
||||
fix quartz_qtb all qtb temp 300 damp 1 seed 35082 f_max 120.00 N_f 100
|
||||
thermo_style custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
|
||||
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
|
||||
grid = 9 8 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00117056
|
||||
estimated relative force accuracy = 8.12908e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 5280 1080
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 2 2 4
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair buck/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair table, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
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
|
||||
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
|
||||
|
||||
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
|
||||
|
||||
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
|
||||
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
|
||||
|
||||
Nlocal: 144 ave 144 max 144 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3943 ave 3943 max 3943 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 41952 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
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
unfix quartz_qtb
|
||||
unfix scapegoat_qtb
|
||||
|
||||
|
||||
## This part demonstrates how to retart fix qbmsst during any stage of the shock simulation.
|
||||
## PPPM may break down when compression ratio becomes extremely large. One can always use this restart technique to resume the shock simulation.
|
||||
#Compression restart 1
|
||||
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 shock all qbmsst z 78 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 shock all qbmsst z 78 q 40 tscale ${tscale_msst} damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.05 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.05 damp 1 f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.05 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.05 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init 300
|
||||
QBMSST parameters:
|
||||
Shock in z direction
|
||||
Cell mass-like parameter qmass (units of mass^2/length^4) = 4.00000e+01
|
||||
Shock velocity = 7.80000e+01
|
||||
Artificial viscosity (units of mass/length/time) = 0.00000e+00
|
||||
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 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
|
||||
grid = 9 8 16
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00104699
|
||||
estimated relative force accuracy = 7.27093e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 5520 1152
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 2 2 4
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair buck/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair table, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Fix QBMSST v0 = 1.87135e+03
|
||||
Fix QBMSST p0 = -4.62948e+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
|
||||
|
||||
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
|
||||
|
||||
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
|
||||
|
||||
Nlocal: 144 ave 144 max 144 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4243 ave 4243 max 4243 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 48210 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
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
write_restart restart.1000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.306435
|
||||
grid = 9 8 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000955688
|
||||
estimated relative force accuracy = 6.63689e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 5280 1080
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 2 2 3
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair buck/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair table, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
|
||||
#Compression restart 2
|
||||
#Read restart file and load potential again
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.1000
|
||||
restoring atom style charge from restart
|
||||
orthogonal box = (-0.05484062286382799 -0.04749337384227555 2.0916641327653274) to (9.886840622863804 8.562255373842252 19.52993586723476)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
restoring pair style hybrid/overlay from restart
|
||||
144 atoms
|
||||
read_restart CPU = 0.0002563 secs
|
||||
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.
|
||||
|
||||
#Pair Potentials
|
||||
pair_style hybrid/overlay buck/coul/long ${cut_off} table linear 39901
|
||||
pair_style hybrid/overlay buck/coul/long 10 table linear 39901
|
||||
pair_coeff 1 1 buck/coul/long 0.0 1.0 0.0 #No interactions between Si atoms
|
||||
pair_coeff 1 2 buck/coul/long 18003.757200 0.205205 133.538100
|
||||
pair_coeff 2 2 buck/coul/long 1388.773000 0.362319 175.000000 #BKS interaction in PRL 64 1955 (1990)
|
||||
pair_modify shift yes
|
||||
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)
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
#Neighbor style
|
||||
neighbor 2.0 bin
|
||||
neigh_modify check yes every 1 delay 0 page 100000 one 2000
|
||||
#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 shock all qbmsst z 78 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 shock all qbmsst z 78 q 40 tscale 0.0 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.0 damp 1 f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.0 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.0 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init 300
|
||||
QBMSST parameters:
|
||||
Shock in z direction
|
||||
Cell mass-like parameter qmass (units of mass^2/length^4) = 4.00000e+01
|
||||
Shock velocity = 7.80000e+01
|
||||
Artificial viscosity (units of mass/length/time) = 0.00000e+00
|
||||
Initial pressure calculated on first step
|
||||
Initial volume calculated on first step
|
||||
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 500
|
||||
timestep ${delta_t}
|
||||
timestep 0.001
|
||||
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
|
||||
grid = 9 8 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000955688
|
||||
estimated relative force accuracy = 6.63689e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 5280 1080
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 2 2 3
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair buck/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair table, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
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
|
||||
|
||||
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
|
||||
|
||||
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
|
||||
|
||||
Nlocal: 144 ave 144 max 144 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5541 ave 5541 max 5541 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 74662 ave 74662 max 74662 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
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:37
|
||||
@ -0,0 +1,430 @@
|
||||
LAMMPS (15 Jun 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
|
||||
variable y_rep equal 1 #plot is made with y_rep = 5 #y-direction replication number
|
||||
variable z_rep equal 4 #plot is made with z_rep = 15 #z-direction replication number
|
||||
variable cut_off equal 10.0 #Cut-off distance for the Buckingham term (Angstrom in metal units)
|
||||
variable pressure equal 1.03125 #Initial state pressure (bar in metal units)
|
||||
variable temperature equal 300.0 #Initial state quantum temperature (K in metal units)
|
||||
variable delta_t equal 1.0e-3 #MD timestep length (ps in metal units)
|
||||
variable damp_qtb equal 1 #1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
|
||||
variable v_msst equal 78.0 #Shock velocity (Angstrom/ps in metal units)
|
||||
variable q_msst equal 40.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in metal units)
|
||||
variable tscale_msst equal 0.05 #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)
|
||||
|
||||
|
||||
## This part uses fix qtb to prepare alpha-quartz with quantum nuclear correction of the initial state
|
||||
include alpha_quartz_qtb.mod
|
||||
## This script first constructs an alpha quartz 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, alpha-quartz crystal, and atomic information
|
||||
#General
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
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
|
||||
|
||||
#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)
|
||||
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
|
||||
create_atoms CPU = 0.000 seconds
|
||||
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)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
144 atoms
|
||||
replicate CPU = 0.000225782 secs
|
||||
|
||||
#Atomic Information
|
||||
mass 1 28.085500
|
||||
mass 2 15.999400
|
||||
set type 1 charge +2.4
|
||||
48 settings made for charge
|
||||
set type 2 charge -1.2
|
||||
96 settings made for charge
|
||||
|
||||
|
||||
## This part implements the BKS pair potential with a cut-off distance for the Buckingham term. Long range Coulomb interactions are evaluated with the pppm method.
|
||||
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.
|
||||
|
||||
#Pair Potentials
|
||||
pair_style hybrid/overlay buck/coul/long ${cut_off} table linear 39901
|
||||
pair_style hybrid/overlay buck/coul/long 10 table linear 39901
|
||||
pair_coeff 1 1 buck/coul/long 0.0 1.0 0.0 #No interactions between Si atoms
|
||||
pair_coeff 1 2 buck/coul/long 18003.757200 0.205205 133.538100
|
||||
pair_coeff 2 2 buck/coul/long 1388.773000 0.362319 175.000000 #BKS interaction in PRL 64 1955 (1990)
|
||||
pair_modify shift yes
|
||||
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)
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
#Neighbor style
|
||||
neighbor 2.0 bin
|
||||
neigh_modify check yes every 1 delay 0 page 100000 one 2000
|
||||
|
||||
|
||||
## This part equilibrates your crystal to a pressure of ${pressure}(unit pressure) and a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
variable p_damp equal ${delta_t}*1000 #Recommended pressure damping parameter in fix nph
|
||||
variable p_damp equal 0.001*1000
|
||||
fix scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp} ptemp ${temperature} #NPH does the time integration
|
||||
fix scapegoat_qtb all nph iso 1.03125 ${pressure} ${p_damp} ptemp ${temperature}
|
||||
fix scapegoat_qtb all nph iso 1.03125 1.03125 ${p_damp} ptemp ${temperature}
|
||||
fix scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp ${temperature}
|
||||
fix scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp 300
|
||||
fix quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 #Change f_max (THz) if your Debye frequency is higher
|
||||
fix quartz_qtb all qtb temp 300 damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100
|
||||
fix quartz_qtb all qtb temp 300 damp 1 seed 35082 f_max 120.00 N_f 100
|
||||
thermo_style custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
|
||||
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
|
||||
grid = 9 8 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00117056
|
||||
estimated relative force accuracy = 8.12908e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 2400 288
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 2 2 4
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair buck/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair table, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 79.7 | 79.7 | 79.7 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
|
||||
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
|
||||
|
||||
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
|
||||
|
||||
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
|
||||
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
|
||||
|
||||
Nlocal: 36 ave 36 max 36 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2614 ave 2614 max 2614 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 10488 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
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
unfix quartz_qtb
|
||||
unfix scapegoat_qtb
|
||||
|
||||
|
||||
## This part demonstrates how to retart fix qbmsst during any stage of the shock simulation.
|
||||
## PPPM may break down when compression ratio becomes extremely large. One can always use this restart technique to resume the shock simulation.
|
||||
#Compression restart 1
|
||||
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 shock all qbmsst z 78 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 shock all qbmsst z 78 q 40 tscale ${tscale_msst} damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.05 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.05 damp 1 f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.05 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.05 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init 300
|
||||
QBMSST parameters:
|
||||
Shock in z direction
|
||||
Cell mass-like parameter qmass (units of mass^2/length^4) = 4.00000e+01
|
||||
Shock velocity = 7.80000e+01
|
||||
Artificial viscosity (units of mass/length/time) = 0.00000e+00
|
||||
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 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
|
||||
grid = 9 8 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00120534
|
||||
estimated relative force accuracy = 8.37062e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 2400 288
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 2 2 4
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair buck/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair table, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
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
|
||||
|
||||
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
|
||||
|
||||
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
|
||||
|
||||
Nlocal: 36 ave 38 max 34 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
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
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 40779
|
||||
Ave neighs/atom = 283.188
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
write_restart restart.1000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.302953
|
||||
grid = 9 8 16
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00105569
|
||||
estimated relative force accuracy = 7.33134e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 2640 288
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 2 2 4
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair buck/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair table, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
|
||||
#Compression restart 2
|
||||
#Read restart file and load potential again
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.1000
|
||||
restoring atom style charge from restart
|
||||
orthogonal box = (-0.04739235907204603 -0.041042988010289584 -0.21484841641189512) to (9.879392359072014 8.555804988010294 21.83644841641206)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
restoring pair style hybrid/overlay from restart
|
||||
144 atoms
|
||||
read_restart CPU = 0.000472307 secs
|
||||
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.
|
||||
|
||||
#Pair Potentials
|
||||
pair_style hybrid/overlay buck/coul/long ${cut_off} table linear 39901
|
||||
pair_style hybrid/overlay buck/coul/long 10 table linear 39901
|
||||
pair_coeff 1 1 buck/coul/long 0.0 1.0 0.0 #No interactions between Si atoms
|
||||
pair_coeff 1 2 buck/coul/long 18003.757200 0.205205 133.538100
|
||||
pair_coeff 2 2 buck/coul/long 1388.773000 0.362319 175.000000 #BKS interaction in PRL 64 1955 (1990)
|
||||
pair_modify shift yes
|
||||
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)
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
#Neighbor style
|
||||
neighbor 2.0 bin
|
||||
neigh_modify check yes every 1 delay 0 page 100000 one 2000
|
||||
#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 shock all qbmsst z 78 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 shock all qbmsst z 78 q 40 tscale 0.0 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.0 damp 1 f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.0 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init ${temperature}
|
||||
fix shock all qbmsst z 78 q 40 tscale 0.0 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init 300
|
||||
QBMSST parameters:
|
||||
Shock in z direction
|
||||
Cell mass-like parameter qmass (units of mass^2/length^4) = 4.00000e+01
|
||||
Shock velocity = 7.80000e+01
|
||||
Artificial viscosity (units of mass/length/time) = 0.00000e+00
|
||||
Initial pressure calculated on first step
|
||||
Initial volume calculated on first step
|
||||
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 500
|
||||
timestep ${delta_t}
|
||||
timestep 0.001
|
||||
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
|
||||
grid = 9 8 16
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00105569
|
||||
estimated relative force accuracy = 7.33134e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 2640 288
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 2 2 4
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair buck/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair table, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
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
|
||||
|
||||
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
|
||||
|
||||
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
|
||||
|
||||
Nlocal: 36 ave 38 max 33 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
|
||||
|
||||
Total # of neighbors = 75437
|
||||
Ave neighs/atom = 523.868
|
||||
Neighbor list builds = 95
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:17
|
||||
2
examples/USER/qtb/alpha_quartz_qbmsst/potential_SiO2.TPF
Executable file → Normal file
2
examples/USER/qtb/alpha_quartz_qbmsst/potential_SiO2.TPF
Executable file → Normal file
@ -1,4 +1,4 @@
|
||||
#Potential between O,Si atoms. r ranges from 0.1 to 20.0. This file+BKS(with no shift)=alpha*(r-rs)^2(0.1<r<rs);BKS(20.0>r>rs). alpha=100, rsOO=1.43869, rsSiO=1.19362. All with metal units.
|
||||
#Potential between O,Si atoms. UNITS: metal r ranges from 0.1 to 20.0. This file+BKS(with no shift)=alpha*(r-rs)^2(0.1<r<rs);BKS(20.0>r>rs). alpha=100, rsOO=1.43869, rsSiO=1.19362. All with metal units.
|
||||
|
||||
Si-O
|
||||
N 39901
|
||||
|
||||
@ -1,79 +0,0 @@
|
||||
## This script first constructs an alpha quartz 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 cut_off equal 10.0 #Cut-off distance for the Buckingham term (Angstrom in metal units)
|
||||
variable pressure equal 1.03125 #Initial state pressure (bar in metal units)
|
||||
variable temperature equal 300.0 #Initial state quantum temperature (K in metal units)
|
||||
variable delta_t equal 1.0e-3 #MD timestep length (ps in metal units)
|
||||
variable damp_qtb equal 1 #1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
|
||||
|
||||
## This part defines units, alpha-quartz crystal, and atomic information
|
||||
#General
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
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)
|
||||
|
||||
#Computational Cell
|
||||
region orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box
|
||||
create_box 2 orthorhombic_unit_cell
|
||||
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
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
|
||||
#Atomic Information
|
||||
mass 1 28.085500
|
||||
mass 2 15.999400
|
||||
set type 1 charge +2.4
|
||||
set type 2 charge -1.2
|
||||
|
||||
|
||||
## This part implements the BKS pair potential with a cut-off distance for the Buckingham term. Long range Coulomb interactions are evaluated with the pppm method.
|
||||
#Pair Potentials
|
||||
pair_style buck/coul/long ${cut_off} #BKS interaction, PRL 64 1955 (1990)
|
||||
pair_coeff 1 1 0.0 1.0 0.0
|
||||
pair_coeff 1 2 18003.757200 0.205205 133.538100
|
||||
pair_coeff 2 2 1388.773000 0.362319 175.000000
|
||||
pair_modify shift yes
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
#Neighbor style
|
||||
neighbor 2.0 bin
|
||||
neigh_modify check yes every 1 delay 0 page 100000 one 2000
|
||||
|
||||
|
||||
## This part equilibrates your crystal to a pressure of ${pressure}(unit pressure) and a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
variable p_damp equal ${delta_t}*1000 #Recommended pressure damping parameter in fix nph
|
||||
fix scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp} ptemp ${temperature} #NPH does the time integration
|
||||
fix quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 #Change f_max (THz) if your Debye frequency is higher
|
||||
thermo_style custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
|
||||
thermo 100
|
||||
run 20000 # 20 ps
|
||||
unfix quartz_qtb
|
||||
unfix scapegoat_qtb
|
||||
79
examples/USER/qtb/alpha_quartz_qtb/in.alpha_quartz_qtb
Normal file
79
examples/USER/qtb/alpha_quartz_qtb/in.alpha_quartz_qtb
Normal file
@ -0,0 +1,79 @@
|
||||
## This script first constructs an alpha quartz 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 cut_off equal 10.0 #Cut-off distance for the Buckingham term (Angstrom in metal units)
|
||||
variable pressure equal 1.03125 #Initial state pressure (bar in metal units)
|
||||
variable temperature equal 300.0 #Initial state quantum temperature (K in metal units)
|
||||
variable delta_t equal 1.0e-3 #MD timestep length (ps in metal units)
|
||||
variable damp_qtb equal 1 #1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
|
||||
|
||||
## This part defines units, alpha-quartz crystal, and atomic information
|
||||
#General
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
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)
|
||||
|
||||
#Computational Cell
|
||||
region orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box
|
||||
create_box 2 orthorhombic_unit_cell
|
||||
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
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
|
||||
#Atomic Information
|
||||
mass 1 28.085500
|
||||
mass 2 15.999400
|
||||
set type 1 charge +2.4
|
||||
set type 2 charge -1.2
|
||||
|
||||
|
||||
## This part implements the BKS pair potential with a cut-off distance for the Buckingham term. Long range Coulomb interactions are evaluated with the pppm method.
|
||||
#Pair Potentials
|
||||
pair_style buck/coul/long ${cut_off} #BKS interaction, PRL 64 1955 (1990)
|
||||
pair_coeff 1 1 0.0 1.0 0.0
|
||||
pair_coeff 1 2 18003.757200 0.205205 133.538100
|
||||
pair_coeff 2 2 1388.773000 0.362319 175.000000
|
||||
pair_modify shift yes
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
#Neighbor style
|
||||
neighbor 2.0 bin
|
||||
neigh_modify check yes every 1 delay 0 page 100000 one 2000
|
||||
|
||||
|
||||
## This part equilibrates your crystal to a pressure of ${pressure}(unit pressure) and a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
variable p_damp equal ${delta_t}*1000 #Recommended pressure damping parameter in fix nph
|
||||
fix scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp} ptemp ${temperature} #NPH does the time integration
|
||||
fix quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 #Change f_max (THz) if your Debye frequency is higher
|
||||
thermo_style custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
|
||||
thermo 500
|
||||
run 10000 # 20 ps
|
||||
unfix quartz_qtb
|
||||
unfix scapegoat_qtb
|
||||
@ -0,0 +1,152 @@
|
||||
LAMMPS (15 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
## This script first constructs an alpha quartz 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 cut_off equal 10.0 #Cut-off distance for the Buckingham term (Angstrom in metal units)
|
||||
variable pressure equal 1.03125 #Initial state pressure (bar in metal units)
|
||||
variable temperature equal 300.0 #Initial state quantum temperature (K in metal units)
|
||||
variable delta_t equal 1.0e-3 #MD timestep length (ps in metal units)
|
||||
variable damp_qtb equal 1 #1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
|
||||
|
||||
## This part defines units, alpha-quartz crystal, and atomic information
|
||||
#General
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
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
|
||||
|
||||
#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)
|
||||
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
|
||||
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
|
||||
orthogonal box = (0.0 0.0 0.0) to (9.832 17.029524 10.8108)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
144 atoms
|
||||
replicate CPU = 0.000219584 secs
|
||||
|
||||
#Atomic Information
|
||||
mass 1 28.085500
|
||||
mass 2 15.999400
|
||||
set type 1 charge +2.4
|
||||
48 settings made for charge
|
||||
set type 2 charge -1.2
|
||||
96 settings made for charge
|
||||
|
||||
|
||||
## This part implements the BKS pair potential with a cut-off distance for the Buckingham term. Long range Coulomb interactions are evaluated with the pppm method.
|
||||
#Pair Potentials
|
||||
pair_style buck/coul/long ${cut_off} #BKS interaction, PRL 64 1955 (1990)
|
||||
pair_style buck/coul/long 10
|
||||
pair_coeff 1 1 0.0 1.0 0.0
|
||||
pair_coeff 1 2 18003.757200 0.205205 133.538100
|
||||
pair_coeff 2 2 1388.773000 0.362319 175.000000
|
||||
pair_modify shift yes
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
#Neighbor style
|
||||
neighbor 2.0 bin
|
||||
neigh_modify check yes every 1 delay 0 page 100000 one 2000
|
||||
|
||||
|
||||
## This part equilibrates your crystal to a pressure of ${pressure}(unit pressure) and a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
variable p_damp equal ${delta_t}*1000 #Recommended pressure damping parameter in fix nph
|
||||
variable p_damp equal 0.001*1000
|
||||
fix scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp} ptemp ${temperature} #NPH does the time integration
|
||||
fix scapegoat_qtb all nph iso 1.03125 ${pressure} ${p_damp} ptemp ${temperature}
|
||||
fix scapegoat_qtb all nph iso 1.03125 1.03125 ${p_damp} ptemp ${temperature}
|
||||
fix scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp ${temperature}
|
||||
fix scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp 300
|
||||
fix quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 #Change f_max (THz) if your Debye frequency is higher
|
||||
fix quartz_qtb all qtb temp 300 damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100
|
||||
fix quartz_qtb all qtb temp 300 damp 1 seed 35082 f_max 120.00 N_f 100
|
||||
thermo_style custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
|
||||
thermo 500
|
||||
run 10000 # 20 ps
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.307414
|
||||
grid = 9 15 10
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000822922
|
||||
estimated relative force accuracy = 5.71487e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 5984 1350
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 2 3 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair buck/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 79.54 | 79.54 | 79.54 Mbytes
|
||||
Step Temp Press TotEng Volume Lx Ly Lz Pxx Pyy Pzz Pxy Pyz Pxz
|
||||
0 0 -34025.794 -2793.6041 1810.0985 9.832 17.029524 10.8108 -37478.502 -37477.413 -27121.466 -1.3649088e-10 1.3388978 5.8209479e-10
|
||||
500 281.29079 -40385.348 -2786.6755 1844.5575 9.893999 17.136909 10.878971 -44649.574 -45631.516 -30874.953 -5970.3691 3630.1324 5208.8966
|
||||
1000 405.39848 -15491.657 -2783.3315 1874.0851 9.9465141 17.227868 10.936714 -7770.4561 -21469.887 -17234.627 -4706.5632 -8313.9522 -5109.7918
|
||||
1500 428.98568 -12118.951 -2781.3232 1874.1627 9.9466513 17.228106 10.936865 -11239.135 -11740.052 -13377.666 -3778.9317 -6220.1431 12775.412
|
||||
2000 522.11905 -6687.482 -2779.2181 1855.9626 9.914349 17.172157 10.901347 -8016.0133 -10737.23 -1309.2028 -4980.3805 5270.2674 5848.5479
|
||||
2500 496.74376 4264.2623 -2778.9979 1849.3244 9.9025147 17.151659 10.888335 -477.1374 3487.19 9782.7343 -4961.2016 2380.6522 4736.0758
|
||||
3000 456.49628 2320.781 -2779.3844 1853.2925 9.9095923 17.163918 10.896117 5479.6232 -2954.3023 4437.022 3719.9287 4445.0723 -3278.5058
|
||||
3500 485.20722 -7480.1789 -2778.6062 1859.6305 9.920876 17.183462 10.908524 -9340.6334 -6129.8494 -6970.0541 -7379.3507 1772.8159 334.33057
|
||||
4000 527.61216 -13499.73 -2777.3433 1889.9405 9.9744857 17.276316 10.96747 -16483.038 -7465.2297 -16550.923 -2517.02 -1863.063 3314.927
|
||||
4500 519.94117 721.60614 -2777.8506 1879.6562 9.9563603 17.244922 10.947541 -913.2791 -1765.7541 4843.8516 4466.5704 -14141.087 -6439.5669
|
||||
5000 505.27757 -6278.3805 -2777.3641 1881.2931 9.9592497 17.249927 10.950718 -14254.233 -2653.6233 -1927.2858 1838.1568 5767.9267 597.47761
|
||||
5500 500.70903 11303.821 -2777.8881 1871.0076 9.9410666 17.218433 10.930724 -6452.7947 24876.967 15487.29 522.01171 10473.257 9780.893
|
||||
6000 526.65329 7991.2419 -2777.172 1856.9227 9.9160583 17.175117 10.903227 -68.823156 11005.468 13037.081 1253.9214 10039.559 1053.0486
|
||||
6500 485.30026 12811.546 -2777.5866 1845.31 9.8953442 17.139239 10.88045 10063.921 20215.037 8155.6798 -3886.954 2249.2807 4855.0011
|
||||
7000 507.85472 2649.7919 -2777.3359 1861.2877 9.923822 17.188564 10.911763 -4214.7779 6995.1472 5169.0064 -2188.489 6157.0955 533.65478
|
||||
7500 528.5729 3161.4629 -2779.0851 1855.7946 9.9140499 17.171639 10.901018 2935.365 -2873.1363 9422.1601 771.1885 -4360.9131 4939.8209
|
||||
8000 533.77283 4534.849 -2777.6538 1858.4772 9.9188246 17.179909 10.906268 -1187.9433 15739.396 -946.90551 -5187.8588 2446.5059 8079.2032
|
||||
8500 518.71765 1108.9877 -2777.7019 1866.6125 9.9332765 17.20494 10.922159 8720.4976 -8234.9325 2841.3979 5148.5004 -2125.3524 -4127.7468
|
||||
9000 536.71495 -496.88283 -2778.0262 1877.7099 9.9529227 17.238968 10.943761 -3481.5874 -4611.6246 6602.5634 -2788.5111 -13323.148 4338.813
|
||||
9500 527.06773 -236.09043 -2778.1125 1895.9227 9.9849986 17.294525 10.97903 -12233.409 7578.0514 3947.0863 -6399.0254 995.22838 8590.7109
|
||||
10000 526.77335 -4480.6866 -2777.7171 1886.8998 9.9691335 17.267046 10.961585 -3139.961 1336.993 -11639.092 13496.371 -11543.676 -6180.9262
|
||||
Loop time of 8.86837 on 1 procs for 10000 steps with 144 atoms
|
||||
|
||||
Performance: 97.425 ns/day, 0.246 hours/ns, 1127.603 timesteps/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 | 6.1503 | 6.1503 | 6.1503 | 0.0 | 69.35
|
||||
Kspace | 1.1522 | 1.1522 | 1.1522 | 0.0 | 12.99
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.11705 | 0.11705 | 0.11705 | 0.0 | 1.32
|
||||
Output | 0.00035834 | 0.00035834 | 0.00035834 | 0.0 | 0.00
|
||||
Modify | 1.4245 | 1.4245 | 1.4245 | 0.0 | 16.06
|
||||
Other | | 0.02397 | | | 0.27
|
||||
|
||||
Nlocal: 144 ave 144 max 144 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3804 ave 3804 max 3804 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 41952 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
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
unfix quartz_qtb
|
||||
unfix scapegoat_qtb
|
||||
Total wall time: 0:00:08
|
||||
@ -0,0 +1,152 @@
|
||||
LAMMPS (15 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
## This script first constructs an alpha quartz 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 cut_off equal 10.0 #Cut-off distance for the Buckingham term (Angstrom in metal units)
|
||||
variable pressure equal 1.03125 #Initial state pressure (bar in metal units)
|
||||
variable temperature equal 300.0 #Initial state quantum temperature (K in metal units)
|
||||
variable delta_t equal 1.0e-3 #MD timestep length (ps in metal units)
|
||||
variable damp_qtb equal 1 #1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
|
||||
|
||||
## This part defines units, alpha-quartz crystal, and atomic information
|
||||
#General
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
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
|
||||
|
||||
#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)
|
||||
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
|
||||
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
|
||||
orthogonal box = (0.0 0.0 0.0) to (9.832 17.029524 10.8108)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
144 atoms
|
||||
replicate CPU = 0.000231981 secs
|
||||
|
||||
#Atomic Information
|
||||
mass 1 28.085500
|
||||
mass 2 15.999400
|
||||
set type 1 charge +2.4
|
||||
48 settings made for charge
|
||||
set type 2 charge -1.2
|
||||
96 settings made for charge
|
||||
|
||||
|
||||
## This part implements the BKS pair potential with a cut-off distance for the Buckingham term. Long range Coulomb interactions are evaluated with the pppm method.
|
||||
#Pair Potentials
|
||||
pair_style buck/coul/long ${cut_off} #BKS interaction, PRL 64 1955 (1990)
|
||||
pair_style buck/coul/long 10
|
||||
pair_coeff 1 1 0.0 1.0 0.0
|
||||
pair_coeff 1 2 18003.757200 0.205205 133.538100
|
||||
pair_coeff 2 2 1388.773000 0.362319 175.000000
|
||||
pair_modify shift yes
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
#Neighbor style
|
||||
neighbor 2.0 bin
|
||||
neigh_modify check yes every 1 delay 0 page 100000 one 2000
|
||||
|
||||
|
||||
## This part equilibrates your crystal to a pressure of ${pressure}(unit pressure) and a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
variable p_damp equal ${delta_t}*1000 #Recommended pressure damping parameter in fix nph
|
||||
variable p_damp equal 0.001*1000
|
||||
fix scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp} ptemp ${temperature} #NPH does the time integration
|
||||
fix scapegoat_qtb all nph iso 1.03125 ${pressure} ${p_damp} ptemp ${temperature}
|
||||
fix scapegoat_qtb all nph iso 1.03125 1.03125 ${p_damp} ptemp ${temperature}
|
||||
fix scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp ${temperature}
|
||||
fix scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp 300
|
||||
fix quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 #Change f_max (THz) if your Debye frequency is higher
|
||||
fix quartz_qtb all qtb temp 300 damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100
|
||||
fix quartz_qtb all qtb temp 300 damp 1 seed 35082 f_max 120.00 N_f 100
|
||||
thermo_style custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
|
||||
thermo 500
|
||||
run 10000 # 20 ps
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.307414
|
||||
grid = 9 15 10
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000822922
|
||||
estimated relative force accuracy = 5.71487e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 2688 405
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 2 3 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair buck/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 79.08 | 79.08 | 79.09 Mbytes
|
||||
Step Temp Press TotEng Volume Lx Ly Lz Pxx Pyy Pzz Pxy Pyz Pxz
|
||||
0 0 -34025.794 -2793.6041 1810.0985 9.832 17.029524 10.8108 -37478.502 -37477.413 -27121.466 -5.9958847e-10 1.3388978 7.2750373e-10
|
||||
500 222.04947 -50221.579 -2787.6677 1851.5661 9.9065143 17.158586 10.892732 -61493.697 -53512.432 -35658.61 4973.9976 7095.5481 -2041.6341
|
||||
1000 361.92367 -14345.85 -2783.1509 1861.0579 9.9234137 17.187857 10.911314 -4145.4149 -28701.195 -10190.939 7896.3934 -3901.2874 -490.57107
|
||||
1500 457.97039 -4934.8727 -2779.8321 1860.2254 9.9219337 17.185294 10.909687 -3680.7192 -3045.0707 -8078.8283 456.70383 -4705.3346 -2175.8144
|
||||
2000 523.52684 -9516.755 -2778.5181 1866.3577 9.9328244 17.204157 10.921662 -11042.489 -7777.5634 -9730.2127 -2016.3336 6027.001 -4150.3656
|
||||
2500 489.58881 -4968.5157 -2777.3948 1864.0745 9.9287723 17.197139 10.917206 -13652.344 -2823.514 1570.3111 -7481.9537 -1150.3548 10502.368
|
||||
3000 559.52782 -2882.7076 -2777.5527 1883.2223 9.9626528 17.255821 10.95446 3061.1755 -10570.656 -1138.642 -12045.354 -856.20951 16292.443
|
||||
3500 521.67929 9974.5929 -2776.7752 1880.5936 9.9580152 17.247789 10.94936 15358.559 7855.8683 6709.3509 7292.9372 -9848.9204 -523.61056
|
||||
4000 497.90872 -2012.9259 -2776.5554 1862.1703 9.9253904 17.191281 10.913488 -1154.5123 4270.0275 -9154.2927 971.94826 -10157.618 4694.0509
|
||||
4500 533.64016 -7218.9278 -2775.8789 1883.3041 9.962797 17.256071 10.954618 -18299.547 -5497.566 2140.3296 -1335.6063 -10353.21 5703.7506
|
||||
5000 551.61416 1590.9702 -2777.6093 1866.2047 9.9325531 17.203687 10.921363 -4600.02 6535.3 2837.6306 3412.3383 9492.18 1017.5742
|
||||
5500 499.36075 188.82067 -2777.9872 1863.2925 9.9273838 17.194734 10.91568 -3238.914 1143.013 2662.363 4193.7623 -11565.423 2575.9361
|
||||
6000 478.563 4064.8319 -2778.946 1867.7185 9.935238 17.208337 10.924316 1947.7246 3346.7411 6900.0301 -6339.9554 4133.6942 -4555.406
|
||||
6500 512.63865 10227.461 -2778.8476 1855.5323 9.9135828 17.17083 10.900505 7423.8967 7558.2024 15700.285 -621.4585 -2620.4837 -3256.7524
|
||||
7000 489.9889 13037.303 -2778.8793 1856.2469 9.9148553 17.173034 10.901904 10690.345 16770.786 11650.779 -4056.5527 -5023.8847 469.21909
|
||||
7500 495.52187 1320.5068 -2778.1189 1871.7467 9.9423755 17.2207 10.932164 1978.2905 738.78041 1244.4496 1826.0923 -7829.3563 1873.2713
|
||||
8000 474.60945 -4203.2068 -2778.8915 1866.5966 9.9332482 17.204891 10.922128 -1480.6896 -12516.261 1387.3306 2731.4462 -1292.9741 10743.939
|
||||
8500 473.16225 -6266.1992 -2778.594 1872.9075 9.9444304 17.224259 10.934423 -12680.492 -2832.6603 -3285.4455 7226.9632 3762.6841 -5834.9064
|
||||
9000 486.6579 2843.7947 -2778.0388 1877.3735 9.9523282 17.237939 10.943107 805.23659 6213.7247 1512.4228 2685.2063 -3517.5266 -17054.035
|
||||
9500 549.35112 -1028.3899 -2776.8124 1880.7965 9.9583733 17.248409 10.949754 -1817.8413 2754.8459 -4022.1743 -3101.1463 8397.2345 -8608.1342
|
||||
10000 562.27081 12885.53 -2775.7435 1850.2864 9.9042316 17.154633 10.890222 15758.218 9989.5121 12908.859 -25.724137 -16691.374 267.85371
|
||||
Loop time of 3.80648 on 4 procs for 10000 steps with 144 atoms
|
||||
|
||||
Performance: 226.981 ns/day, 0.106 hours/ns, 2627.100 timesteps/s
|
||||
94.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.3526 | 1.6581 | 1.9634 | 21.3 | 43.56
|
||||
Kspace | 0.92143 | 1.2222 | 1.5232 | 24.7 | 32.11
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.31886 | 0.32256 | 0.32604 | 0.5 | 8.47
|
||||
Output | 0.0003643 | 0.00083923 | 0.0022533 | 0.0 | 0.02
|
||||
Modify | 0.39166 | 0.45985 | 0.52607 | 8.9 | 12.08
|
||||
Other | | 0.143 | | | 3.76
|
||||
|
||||
Nlocal: 36 ave 36 max 36 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2614 ave 2614 max 2614 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 10488 ave 12570 max 8406 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 41952
|
||||
Ave neighs/atom = 291.333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
unfix quartz_qtb
|
||||
unfix scapegoat_qtb
|
||||
Total wall time: 0:00:03
|
||||
Reference in New Issue
Block a user