forked from lijiext/lammps
update example inputs and logfile for fix_modify energy yes/no changes, where needed
This commit is contained in:
Axel Kohlmeyer
parent
d26c744e54
commit
5646714470
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@ -1,6 +1,6 @@
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# fcc nickel in a 3d periodic box
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clear
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clear
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units metal
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atom_style spin
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@ -8,7 +8,7 @@ dimension 3
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boundary p p p
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# necessary for the serial algorithm (sametag)
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atom_modify map array
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atom_modify map array
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lattice fcc 3.524
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region box block 0.0 5.0 0.0 5.0 0.0 5.0
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@ -20,7 +20,7 @@ create_atoms 1 box
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mass 1 58.69
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set group all spin/random 31 0.63
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#set group all spin 0.63 0.0 0.0 1.0
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#set group all spin 0.63 0.0 0.0 1.0
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velocity all create 100 4928459 rot yes dist gaussian
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pair_style hybrid/overlay eam/alloy spin/exchange 4.0
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@ -31,7 +31,7 @@ neighbor 0.1 bin
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neigh_modify every 10 check yes delay 20
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fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
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fix_modify 1 energy yes
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fix_modify 1 energy yes
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fix 2 all langevin/spin 0.0 0.0 21
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fix 3 all nve/spin lattice moving
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@ -1,60 +1,60 @@
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# fcc nickel in a 3d periodic box
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clear
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units metal
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atom_style spin
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clear
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units metal
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atom_style spin
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dimension 3
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boundary p p p
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dimension 3
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boundary p p p
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# necessary for the serial algorithm (sametag)
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atom_modify map array
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atom_modify map array
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lattice fcc 3.524
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region box block 0.0 5.0 0.0 5.0 0.0 5.0
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create_box 1 box
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create_atoms 1 box
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lattice fcc 3.524
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region box block 0.0 5.0 0.0 5.0 0.0 5.0
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create_box 1 box
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create_atoms 1 box
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# setting mass, mag. moments, and interactions for cobalt
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mass 1 58.69
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mass 1 58.69
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set group all spin/random 31 0.63
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#set group all spin 0.63 0.0 0.0 1.0
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velocity all create 100 4928459 rot yes dist gaussian
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set group all spin/random 31 0.63
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#set group all spin 0.63 0.0 0.0 1.0
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velocity all create 100 4928459 rot yes dist gaussian
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pair_style hybrid/overlay eam/alloy spin/exchange 4.0
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pair_coeff * * eam/alloy Ni99.eam.alloy Ni
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pair_coeff * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
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pair_style hybrid/overlay eam/alloy spin/exchange 4.0
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pair_coeff * * eam/alloy Ni99.eam.alloy Ni
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pair_coeff * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
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neighbor 0.1 bin
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neigh_modify every 10 check yes delay 20
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neighbor 0.1 bin
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neigh_modify every 10 check yes delay 20
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fix 1 all precession/spin cubic -0.0001 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 &
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zeeman 0.0 0.0 0.0 1.0
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fix_modify 1 energy yes
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fix 2 all langevin/spin 0.0 0.0 21
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fix 1 all precession/spin cubic -0.0001 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 &
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zeeman 0.0 0.0 0.0 1.0
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fix_modify 1 energy yes
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fix 2 all langevin/spin 0.0 0.0 21
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fix 3 all nve/spin lattice moving
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timestep 0.0001
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fix 3 all nve/spin lattice moving
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timestep 0.0001
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# compute and output options
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compute out_mag all spin
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compute out_pe all pe
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compute out_ke all ke
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compute out_temp all temp
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compute out_mag all spin
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compute out_pe all pe
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compute out_ke all ke
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compute out_temp all temp
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variable magz equal c_out_mag[3]
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variable magnorm equal c_out_mag[4]
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variable emag equal c_out_mag[5]
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variable tmag equal c_out_mag[6]
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variable magz equal c_out_mag[3]
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variable magnorm equal c_out_mag[4]
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variable emag equal c_out_mag[5]
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variable tmag equal c_out_mag[6]
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thermo_style custom step time v_magnorm pe v_emag temp v_tmag etotal
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thermo 50
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compute outsp all property/atom spx spy spz sp fmx fmy fmz
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dump 1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
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compute outsp all property/atom spx spy spz sp fmx fmy fmz
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dump 1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
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run 1000
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run 1000
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@ -1,12 +1,12 @@
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units real
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atom_style full
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units real
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atom_style full
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pair_style lj/cut/tip4p/long 1 2 1 1 0.14714951 8
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bond_style class2
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angle_style harmonic
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kspace_style pppm/tip4p 0.0001
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pair_style lj/cut/tip4p/long 1 2 1 1 0.14714951 8
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bond_style class2
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angle_style harmonic
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kspace_style pppm/tip4p 0.0001
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read_data data.h2o-quantum
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read_data data.h2o-quantum
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pair_coeff * 2 0.0 0.0
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pair_coeff 1 1 0.1852 3.1589022
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@ -15,7 +15,7 @@ pair_coeff 1 1 0.1852 3.1589022
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bond_coeff 1 0.9419 607.19354 -1388.6516 1852.577
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angle_coeff 1 43.93 107.4
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timestep 0.5
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timestep 0.5
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# mean velocity is higher than target T because of zero point energy
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velocity all create 800.0 1112 dist gaussian mom yes
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@ -24,18 +24,17 @@ thermo 100
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thermo_style custom step temp pe ke etotal
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# some problem
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fix 1 all gle 6 300.0 300.0 31415 qt-300k.A noneq qt-300k.C
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fix_modify 1 energy no
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fix 1 all gle 6 300.0 300.0 31415 qt-300k.A noneq qt-300k.C
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#dump 1 all atom 100 h2o-smart.lammpstrj
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#dump 1 all atom 100 h2o-smart.lammpstrj
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#dump 2 all image 1000 h2o-smart.*.jpg element element &
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# zoom 1.4
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#dump_modify 2 pad 5 element O H
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#dump 2 all image 1000 h2o-smart.*.jpg element element &
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# zoom 1.4
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#dump_modify 2 pad 5 element O H
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#dump 3 all movie 100 movie.mp4 element element &
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# zoom 1.4
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#dump_modify 3 pad 5 element O H
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#dump 3 all movie 100 movie.mp4 element element &
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# zoom 1.4
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#dump_modify 3 pad 5 element O H
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run 10000
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run 10000
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@ -1,12 +1,12 @@
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units real
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atom_style full
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units real
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atom_style full
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pair_style lj/cut/tip4p/long 1 2 1 1 0.14714951 8
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bond_style class2
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angle_style harmonic
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kspace_style pppm/tip4p 0.0001
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pair_style lj/cut/tip4p/long 1 2 1 1 0.14714951 8
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bond_style class2
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angle_style harmonic
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kspace_style pppm/tip4p 0.0001
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read_data data.h2o-smart
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read_data data.h2o-smart
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pair_coeff * 2 0.0 0.0
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pair_coeff 1 1 0.1852 3.1589022
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@ -15,27 +15,26 @@ pair_coeff 1 1 0.1852 3.1589022
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bond_coeff 1 0.9419 607.19354 -1388.6516 1852.577
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angle_coeff 1 43.93 107.4
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timestep 0.5
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timestep 0.5
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velocity all create 300.0 1112 dist gaussian mom yes
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velocity all create 300.0 1112 dist gaussian mom yes
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thermo 100
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thermo_style custom step temp pe ke etotal
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# smart sampling with GLE: best efficiency on slow diffusive modes,
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# and as good as possible on higher-frequency modes
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fix 1 all gle 6 300.0 300.0 31415 smart.A
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fix_modify 1 energy no
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fix 1 all gle 6 300.0 300.0 31415 smart.A
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#dump 1 all atom 100 h2o-smart.lammpstrj
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#dump 1 all atom 100 h2o-smart.lammpstrj
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#dump 2 all image 1000 h2o-smart.*.jpg element element &
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# zoom 1.4
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#dump_modify 2 pad 5 element O H
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#dump 2 all image 1000 h2o-smart.*.jpg element element &
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# zoom 1.4
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#dump_modify 2 pad 5 element O H
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#dump 3 all movie 100 movie.mp4 element element &
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# zoom 1.4
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#dump_modify 3 pad 5 element O H
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#dump 3 all movie 100 movie.mp4 element element &
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# zoom 1.4
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#dump_modify 3 pad 5 element O H
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run 10000
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run 10000
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@ -23,13 +23,12 @@ include alpha_quartz_qtb.mod
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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_style custom step v_T_qm press econserve 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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@ -42,14 +41,14 @@ 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_style custom step v_T_qm press econserve 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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#restart 1000 restart
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run 10000 #10 ps
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shell rm restart.1000
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@ -1,4 +1,4 @@
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LAMMPS (15 Jun 2020)
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LAMMPS (24 Dec 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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@ -29,12 +29,12 @@ atom_style charge
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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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Lattice spacing in x,y,z = 7.3740000 4.2573810 5.4054000
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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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Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (4.9160000 8.5147620 5.4054000)
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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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@ -43,17 +43,20 @@ 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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Replicating atoms ...
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orthogonal box = (0.0000000 0.0000000 0.0000000) to (9.8320000 8.5147620 21.621600)
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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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replicate CPU = 0.001 seconds
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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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Setting atom values ...
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48 settings made for charge
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set type 2 charge -1.2
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Setting atom values ...
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96 settings made for charge
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@ -72,8 +75,8 @@ 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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WARNING: 1 of 39901 force values in table O-O are inconsistent with -dE/dr.
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Should only be flagged at inflection points (src/pair_table.cpp:461)
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kspace_style pppm 1.0e-4
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#Neighbor style
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@ -96,12 +99,12 @@ thermo_style custom step temp press etotal vol lx ly lz pxx pyy pzz p
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thermo 200
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run 2000 # 2 ps
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
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G vector (1/distance) = 0.301598
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using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
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G vector (1/distance) = 0.30159814
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grid = 9 8 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.00117056
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estimated relative force accuracy = 8.12908e-05
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estimated absolute RMS force accuracy = 0.0011705589
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estimated relative force accuracy = 8.1290814e-05
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using double precision FFTW3
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3d grid and FFT values/proc = 5280 1080
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Neighbor list info ...
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@ -123,42 +126,42 @@ Neighbor list info ...
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 80.09 | 80.09 | 80.09 Mbytes
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Step Temp Press TotEng Volume Lx Ly Lz Pxx Pyy Pzz Pxy Pyz Pxz
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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
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0 0 -34026.791 -2793.6042 1810.0985 9.832 8.514762 21.6216 -37470.578 -37470.432 -27139.363 3.7975984e-11 0.94245783 8.5085457e-11
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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
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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
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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
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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
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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
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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
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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
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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
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1800 447.7623 -8344.6306 -2780.1071 1858.4925 9.9188518 8.5899779 21.812596 -17549.498 3336.8135 -10821.208 1643.4226 -644.56065 -8935.9666
|
||||
2000 438.1306 -6691.4691 -2780.7407 1871.3547 9.9416812 8.6097487 21.862801 -6959.2196 -8486.8466 -4628.341 -1019.9006 443.03694 -2751.917
|
||||
Loop time of 2.46815 on 1 procs for 2000 steps with 144 atoms
|
||||
400 258.09921 -28257.8 -2788.3487 1856.1432 9.9146707 8.5863569 21.803402 -19478.873 -29571.375 -35723.151 4633.9025 8487.8103 -626.12008
|
||||
600 277.77032 -22751.351 -2786.2715 1866.9783 9.9339253 8.6030319 21.845744 -21727.333 -29200.028 -17326.691 -4327.8577 -8218.4994 252.30614
|
||||
800 349.8665 30508.004 -2784.2204 1873.4953 9.9454706 8.6130304 21.871134 29929.053 33562.675 28032.284 -3188.5636 12329.485 7558.5604
|
||||
1000 373.67652 -18839.562 -2783.2178 1855.5937 9.9136922 8.5855095 21.80125 -18063.481 -22288.32 -16166.887 -416.09489 -10368.975 9030.4151
|
||||
1200 423.34739 6846.9842 -2781.9271 1896.2131 9.9855083 8.6477041 21.959181 2147.3919 11765.847 6627.7141 -7627.6762 -1297.649 -4758.4757
|
||||
1400 418.54526 -6416.7547 -2781.4358 1834.2719 9.8755745 8.5524986 21.717425 5693.0508 -19487.901 -5455.4139 827.66188 -523.1469 -3890.9904
|
||||
1600 429.42798 3939.889 -2780.5861 1895.8859 9.984934 8.6472068 21.957918 3755.6972 -1326.4252 9390.395 1948.1084 4489.8536 1466.083
|
||||
1800 447.76215 -8344.6447 -2780.1071 1858.4925 9.9188519 8.5899779 21.812596 -17549.502 3336.8092 -10821.241 1643.4315 -644.54621 -8935.98
|
||||
2000 438.1305 -6691.4324 -2780.7407 1871.3547 9.9416812 8.6097487 21.8628 -6959.1834 -8486.8262 -4628.2877 -1019.8998 443.04638 -2751.9173
|
||||
Loop time of 11.2763 on 1 procs for 2000 steps with 144 atoms
|
||||
|
||||
Performance: 70.012 ns/day, 0.343 hours/ns, 810.323 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 15.324 ns/day, 1.566 hours/ns, 177.363 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.0003 | 2.0003 | 2.0003 | 0.0 | 81.04
|
||||
Kspace | 0.20006 | 0.20006 | 0.20006 | 0.0 | 8.11
|
||||
Pair | 7.9085 | 7.9085 | 7.9085 | 0.0 | 70.13
|
||||
Kspace | 2.0339 | 2.0339 | 2.0339 | 0.0 | 18.04
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.023753 | 0.023753 | 0.023753 | 0.0 | 0.96
|
||||
Output | 0.0001986 | 0.0001986 | 0.0001986 | 0.0 | 0.01
|
||||
Modify | 0.23896 | 0.23896 | 0.23896 | 0.0 | 9.68
|
||||
Other | | 0.004907 | | | 0.20
|
||||
Comm | 0.15276 | 0.15276 | 0.15276 | 0.0 | 1.35
|
||||
Output | 0.00036049 | 0.00036049 | 0.00036049 | 0.0 | 0.00
|
||||
Modify | 1.1706 | 1.1706 | 1.1706 | 0.0 | 10.38
|
||||
Other | | 0.01023 | | | 0.09
|
||||
|
||||
Nlocal: 144 ave 144 max 144 min
|
||||
Nlocal: 144.000 ave 144 max 144 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3943 ave 3943 max 3943 min
|
||||
Nghost: 3943.00 ave 3943 max 3943 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 41952 ave 41952 max 41952 min
|
||||
Neighs: 41952.0 ave 41952 max 41952 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 41952
|
||||
Ave neighs/atom = 291.333
|
||||
Ave neighs/atom = 291.33333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
unfix quartz_qtb
|
||||
|
|
@ -185,24 +188,23 @@ QBMSST parameters:
|
|||
Initial pressure calculated on first step
|
||||
Initial volume calculated on first step
|
||||
Initial energy calculated on first step
|
||||
fix_modify shock energy yes
|
||||
variable dhug equal f_shock[1]
|
||||
variable dray equal f_shock[2]
|
||||
variable lgr_vel equal f_shock[3]
|
||||
variable lgr_pos equal f_shock[4]
|
||||
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
|
||||
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo_style custom step v_T_qm press econserve vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo 200
|
||||
timestep ${delta_t}
|
||||
timestep 0.001
|
||||
run 1000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.303132
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
|
||||
G vector (1/distance) = 0.30313178
|
||||
grid = 9 8 16
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00104699
|
||||
estimated relative force accuracy = 7.27093e-05
|
||||
estimated absolute RMS force accuracy = 0.0010469888
|
||||
estimated relative force accuracy = 7.2709348e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 5520 1152
|
||||
Neighbor list info ...
|
||||
|
|
@ -223,52 +225,53 @@ Neighbor list info ...
|
|||
stencil: none
|
||||
bin: none
|
||||
Fix QBMSST v0 = 1.87135e+03
|
||||
Fix QBMSST p0 = -4.62948e+03
|
||||
Fix QBMSST p0 = -4.62942e+03
|
||||
Fix QBMSST e0 = to be -2.78074e+03
|
||||
Fix QBMSST initial strain rate of -4.01096e-01 established by reducing temperature by factor of 5.00000e-02
|
||||
Per MPI rank memory allocation (min/avg/max) = 80.1 | 80.1 | 80.1 Mbytes
|
||||
Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
0 300 -6922.9433 -2780.7394 1871.3547 9.9416812 8.6097487 21.862801 -4819.9907 10.953265 -190.51273 0 0
|
||||
200 294.95797 54876.416 -2779.2988 1723.7621 9.9416812 8.6097487 20.138495 108897.19 -29.773973 -9271.7281 6.1518102 -15.057867
|
||||
400 288.3711 139521.03 -2778.7321 1628.5574 9.9416812 8.6097487 19.026231 222107.71 8.0682073 24727.575 10.120041 -28.714693
|
||||
600 280.56521 98070.281 -2779.8934 1687.2434 9.9416812 8.6097487 19.711852 164558.51 2.6076928 16005.656 7.6739491 -42.705007
|
||||
800 274.94701 106060.26 -2779.2916 1651.0723 9.9416812 8.6097487 19.289269 176842.6 -39.645354 -1804.9466 9.1815975 -56.628078
|
||||
1000 268.47106 189695.34 -2779.4951 1492.6355 9.9416812 8.6097487 17.438272 277351.5 -84.834482 -33116.996 15.785409 -69.870519
|
||||
Loop time of 2.05219 on 1 procs for 1000 steps with 144 atoms
|
||||
Fix QBMSST initial strain rate of -4.01095e-01 established by reducing temperature by factor of 5.00000e-02
|
||||
Per MPI rank memory allocation (min/avg/max) = 80.10 | 80.10 | 80.10 Mbytes
|
||||
Step v_T_qm Press Econserve Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
0 300 -6922.9066 -2780.7394 1871.3547 9.9416812 8.6097487 21.8628 -4819.9374 10.953262 -190.5127 0 0
|
||||
200 294.95802 54876.628 -2779.2988 1723.7617 9.9416812 8.6097487 20.13849 108897.62 -29.773363 -9271.7016 6.1518278 -15.057866
|
||||
400 288.37122 139520.66 -2778.7321 1628.5573 9.9416812 8.6097487 19.02623 222107.14 8.0673735 24726.892 10.120044 -28.714689
|
||||
600 280.56538 98072.818 -2779.8934 1687.2396 9.9416812 8.6097487 19.711808 164562.57 2.6099747 16006.563 7.6741039 -42.704989
|
||||
800 274.9472 106058.35 -2779.2916 1651.0755 9.9416812 8.6097487 19.289307 176839.13 -39.647552 -1805.8176 9.1814643 -56.628046
|
||||
1000 268.4714 189679.65 -2779.4952 1492.6558 9.9416812 8.6097487 17.43851 277332.66 -84.846841 -33118.917 15.784559 -69.870561
|
||||
Loop time of 8.7779 on 1 procs for 1000 steps with 144 atoms
|
||||
|
||||
Performance: 42.101 ns/day, 0.570 hours/ns, 487.284 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 9.843 ns/day, 2.438 hours/ns, 113.922 timesteps/s
|
||||
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.6815 | 1.6815 | 1.6815 | 0.0 | 81.94
|
||||
Kspace | 0.10373 | 0.10373 | 0.10373 | 0.0 | 5.05
|
||||
Neigh | 0.0061183 | 0.0061183 | 0.0061183 | 0.0 | 0.30
|
||||
Comm | 0.012444 | 0.012444 | 0.012444 | 0.0 | 0.61
|
||||
Output | 0.00014687 | 0.00014687 | 0.00014687 | 0.0 | 0.01
|
||||
Modify | 0.24529 | 0.24529 | 0.24529 | 0.0 | 11.95
|
||||
Other | | 0.002948 | | | 0.14
|
||||
Pair | 6.8031 | 6.8031 | 6.8031 | 0.0 | 77.50
|
||||
Kspace | 1.0505 | 1.0505 | 1.0505 | 0.0 | 11.97
|
||||
Neigh | 0.024976 | 0.024976 | 0.024976 | 0.0 | 0.28
|
||||
Comm | 0.082612 | 0.082612 | 0.082612 | 0.0 | 0.94
|
||||
Output | 0.00032592 | 0.00032592 | 0.00032592 | 0.0 | 0.00
|
||||
Modify | 0.8108 | 0.8108 | 0.8108 | 0.0 | 9.24
|
||||
Other | | 0.005632 | | | 0.06
|
||||
|
||||
Nlocal: 144 ave 144 max 144 min
|
||||
Nlocal: 144.000 ave 144 max 144 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4243 ave 4243 max 4243 min
|
||||
Nghost: 4243.00 ave 4243 max 4243 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 48210 ave 48210 max 48210 min
|
||||
Neighs: 48210.0 ave 48210 max 48210 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 48210
|
||||
Ave neighs/atom = 334.792
|
||||
Ave neighs/atom = 334.79167
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
write_restart restart.1000
|
||||
System init for write_restart ...
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.306435
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
|
||||
G vector (1/distance) = 0.30643517
|
||||
grid = 9 8 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000955688
|
||||
estimated relative force accuracy = 6.63689e-05
|
||||
estimated absolute RMS force accuracy = 0.0009556927
|
||||
estimated relative force accuracy = 6.6369185e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 5280 1080
|
||||
Neighbor list info ...
|
||||
|
|
@ -294,12 +297,14 @@ Neighbor list info ...
|
|||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.1000
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style charge from restart
|
||||
orthogonal box = (-0.05484062286382799 -0.04749337384227555 2.0916641327653274) to (9.886840622863804 8.562255373842252 19.52993586723476)
|
||||
orthogonal box = (-0.054840605 -0.047493358 2.0915450) to (9.8868406 8.5622554 19.530055)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
restoring pair style hybrid/overlay from restart
|
||||
144 atoms
|
||||
read_restart CPU = 0.0002563 secs
|
||||
read_restart CPU = 0.001 seconds
|
||||
include alpha_quartz_potential.mod
|
||||
#This script implements the BKS pair potential for various silicon dioxide compounds. Inner part is fixed with a harmonic potential. Long range Coulomb interactions are evaluated with the pppm method.
|
||||
|
||||
|
|
@ -314,8 +319,8 @@ pair_coeff 1 2 table potential_SiO2.TPF Si-O ${cut_off}
|
|||
pair_coeff 1 2 table potential_SiO2.TPF Si-O 10
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O ${cut_off} #See the potential file for more information
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O 10
|
||||
WARNING: 1 of 39901 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:471)
|
||||
WARNING: 1 of 39901 force values in table O-O are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:461)
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
#Neighbor style
|
||||
|
|
@ -338,25 +343,24 @@ QBMSST parameters:
|
|||
Initial energy calculated on first step
|
||||
Resetting global fix info from restart file:
|
||||
fix style: qbmsst, fix ID: shock
|
||||
fix_modify shock energy yes
|
||||
variable dhug equal f_shock[1]
|
||||
variable dray equal f_shock[2]
|
||||
variable lgr_vel equal f_shock[3]
|
||||
variable lgr_pos equal f_shock[4]
|
||||
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
|
||||
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo_style custom step v_T_qm press econserve vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo 500
|
||||
timestep ${delta_t}
|
||||
timestep 0.001
|
||||
restart 1000 restart
|
||||
#restart 1000 restart
|
||||
run 10000 #10 ps
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.306435
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
|
||||
G vector (1/distance) = 0.30643517
|
||||
grid = 9 8 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000955688
|
||||
estimated relative force accuracy = 6.63689e-05
|
||||
estimated absolute RMS force accuracy = 0.0009556927
|
||||
estimated relative force accuracy = 6.6369185e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 5280 1080
|
||||
All restart file global fix info was re-assigned
|
||||
|
|
@ -378,53 +382,54 @@ Neighbor list info ...
|
|||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 80.12 | 80.12 | 80.12 Mbytes
|
||||
Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
1000 268.47106 189686.77 -2781.5194 1492.6355 9.9416812 8.6097487 17.438272 277378.37 -84.692548 -33090.129 15.785409 0
|
||||
1500 362.13476 692245.96 -2800.9352 1011.2037 9.9416812 8.6097487 11.813766 661095.53 188.71833 -49928.712 35.851981 -24.11484
|
||||
2000 860.78914 714816.8 -2830.893 997.64749 9.9416812 8.6097487 11.65539 653537.64 852.68158 -68765.537 36.41702 -44.978484
|
||||
2500 1620.8281 709511.19 -2840.8217 1000.3425 9.9416812 8.6097487 11.686875 660030.01 1184.3105 -60030.892 36.304689 -65.69966
|
||||
3000 2395.6824 649526.84 -2832.6859 995.56591 9.9416812 8.6097487 11.631071 660984.37 939.07209 -63050.693 36.503782 -86.383242
|
||||
3500 3034.6774 715794.56 -2822.6098 995.8622 9.9416812 8.6097487 11.634532 712849.74 1055.7295 -10938.816 36.491433 -106.99315
|
||||
4000 3487.9039 736791.25 -2804.1216 994.13867 9.9416812 8.6097487 11.614397 765817.85 943.15747 40595.305 36.563271 -127.76315
|
||||
4500 3718.6279 813775.8 -2788.1942 995.82514 9.9416812 8.6097487 11.634099 881961.06 1370.5559 158141.68 36.492977 -148.68649
|
||||
5000 3691.4947 750146.58 -2770.5541 1018.4785 9.9416812 8.6097487 11.898756 770500.36 196.2793 65528.786 35.548762 -169.8589
|
||||
5500 3585.8602 831522.51 -2766.0198 1005.6834 9.9416812 8.6097487 11.749273 916093.67 1088.1987 200476.48 36.082073 -190.89436
|
||||
6000 3431.6405 749891.94 -2771.6404 1011.9077 9.9416812 8.6097487 11.82199 781321.11 268.24344 70882.55 35.82264 -212.20913
|
||||
6500 3350.2876 666113.16 -2780.4124 1028.8353 9.9416812 8.6097487 12.019753 749294.32 371.38231 52939.676 35.117081 -233.59556
|
||||
7000 3339.2397 675783.2 -2782.7559 1022.6541 9.9416812 8.6097487 11.947539 690109.39 -26.949124 -11388.054 35.374719 -254.95868
|
||||
7500 3395.582 726601.74 -2784.7652 1018.1439 9.9416812 8.6097487 11.894846 759167.86 506.5811 53917.852 35.56271 -276.24361
|
||||
8000 3393.2372 625141.93 -2771.6398 1035.4915 9.9416812 8.6097487 12.097517 598674.46 -895.80046 -92142.112 34.839641 -297.61681
|
||||
8500 3272.9752 659367.77 -2776.608 1031.8188 9.9416812 8.6097487 12.054609 688358.42 -142.30814 -5513.8593 34.992722 -318.94541
|
||||
9000 3277.8848 724828.76 -2777.6502 1017.6314 9.9416812 8.6097487 11.888859 724452.11 58.574942 18775.738 35.58407 -340.1718
|
||||
9500 3273.7854 620652.38 -2780.0794 1023.5922 9.9416812 8.6097487 11.958499 747175.42 317.3826 46458.505 35.335617 -361.41643
|
||||
10000 3329.1766 668606.38 -2786.3493 1022.9534 9.9416812 8.6097487 11.951035 703351.81 168.14538 2103.38 35.362244 -382.64609
|
||||
10500 3398.9956 642919.16 -2784.2833 1016.2587 9.9416812 8.6097487 11.872822 661298.16 -230.03577 -45520.34 35.641287 -403.78721
|
||||
11000 3418.7053 675754.06 -2782.6318 1005.7483 9.9416812 8.6097487 11.75003 689789.84 -136.97148 -25773.422 36.079372 -424.97556
|
||||
Loop time of 32.4277 on 1 procs for 10000 steps with 144 atoms
|
||||
Step v_T_qm Press Econserve Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
1000 268.4714 189671.09 -2781.5189 1492.6558 9.9416812 8.6097487 17.43851 277359.52 -84.704915 -33092.054 15.784559 0
|
||||
1500 362.24943 690690.88 -2801.3189 1013.1871 9.9416812 8.6097487 11.836938 660912.81 210.15736 -48461.278 35.76931 -24.117097
|
||||
2000 851.29288 687202.75 -2829.28 998.92158 9.9416812 8.6097487 11.670275 702779.72 1177.175 -18463.457 36.363914 -45.102068
|
||||
2500 1584.7231 702373.6 -2840.9926 998.47448 9.9416812 8.6097487 11.665052 685551.65 1366.7769 -36063.512 36.382549 -65.966813
|
||||
3000 2369.1915 765783.04 -2835.3495 994.53954 9.9416812 8.6097487 11.61908 742616.98 1609.2532 17727.912 36.546562 -86.541922
|
||||
3500 3092.3052 829161.44 -2827.8974 977.82563 9.9416812 8.6097487 11.423814 768559.05 1500.9858 29763.85 37.243215 -107.10048
|
||||
4000 3627.1538 773057.81 -2813.687 988.31955 9.9416812 8.6097487 11.546413 738541.81 959.39292 8477.6525 36.805818 -127.75274
|
||||
4500 3910.5455 753799.74 -2790.7863 1002.749 9.9416812 8.6097487 11.71499 763069.75 602.0127 45010.991 36.204385 -148.51594
|
||||
5000 3976.7913 761978.62 -2782.0448 998.85434 9.9416812 8.6097487 11.669489 780709.6 482.34112 59410.482 36.366717 -169.42341
|
||||
5500 3928.0113 702739.91 -2765.8379 1008.695 9.9416812 8.6097487 11.784456 632171.28 -991.2791 -80940.344 35.956549 -190.30951
|
||||
6000 3731.5486 654300.14 -2763.1253 1032.1476 9.9416812 8.6097487 12.05845 642590.19 -832.8417 -51008.602 34.979018 -211.41573
|
||||
6500 3505.5984 713092.19 -2767.3169 1010.6873 9.9416812 8.6097487 11.807732 735218.98 -176.4579 23764.995 35.873507 -232.57305
|
||||
7000 3348.5047 762624.48 -2769.0996 1010.8032 9.9416812 8.6097487 11.809086 662703.98 -667.90587 -48653.562 35.868676 -253.64668
|
||||
7500 3197.2839 689038.79 -2770.7583 1036.994 9.9416812 8.6097487 12.11507 679188.92 -330.37222 -10377.635 34.777016 -275.06425
|
||||
8000 3117.1867 765531.79 -2775.0143 1023.9741 9.9416812 8.6097487 11.96296 681640.02 -288.82226 -18759.215 35.319699 -296.38453
|
||||
8500 3053.5599 667992.24 -2772.057 1027.6458 9.9416812 8.6097487 12.005857 657921.43 -507.92809 -39422.884 35.166657 -317.64367
|
||||
9000 2997.4957 704542.99 -2780.9279 1020.074 9.9416812 8.6097487 11.917396 647510.98 -398.1601 -56133.168 35.482259 -338.8598
|
||||
9500 2990.5818 810181.5 -2783.2413 1002.8927 9.9416812 8.6097487 11.716669 859476.58 1107.5241 141537.42 36.198393 -359.85577
|
||||
10000 3055.8298 792271.02 -2786.5277 991.62826 9.9416812 8.6097487 11.585068 847298.17 1051.5369 119986.89 36.667907 -380.83279
|
||||
10500 3159.7134 706528.08 -2793.5555 1009.9173 9.9416812 8.6097487 11.798737 673106.83 67.67511 -38987.761 35.905599 -401.74903
|
||||
11000 3261.7609 748345.85 -2783.0699 1017.8806 9.9416812 8.6097487 11.891771 656140.32 -267.8786 -49328.779 35.573683 -422.65593
|
||||
Loop time of 130.289 on 1 procs for 10000 steps with 144 atoms
|
||||
|
||||
Performance: 26.644 ns/day, 0.901 hours/ns, 308.378 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 6.631 ns/day, 3.619 hours/ns, 76.752 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 28.397 | 28.397 | 28.397 | 0.0 | 87.57
|
||||
Kspace | 1.0225 | 1.0225 | 1.0225 | 0.0 | 3.15
|
||||
Neigh | 0.27594 | 0.27594 | 0.27594 | 0.0 | 0.85
|
||||
Comm | 0.1797 | 0.1797 | 0.1797 | 0.0 | 0.55
|
||||
Output | 0.10409 | 0.10409 | 0.10409 | 0.0 | 0.32
|
||||
Modify | 2.4112 | 2.4112 | 2.4112 | 0.0 | 7.44
|
||||
Other | | 0.03707 | | | 0.11
|
||||
Pair | 109.8 | 109.8 | 109.8 | 0.0 | 84.27
|
||||
Kspace | 10.328 | 10.328 | 10.328 | 0.0 | 7.93
|
||||
Neigh | 1.0855 | 1.0855 | 1.0855 | 0.0 | 0.83
|
||||
Comm | 1.2041 | 1.2041 | 1.2041 | 0.0 | 0.92
|
||||
Output | 0.0012848 | 0.0012848 | 0.0012848 | 0.0 | 0.00
|
||||
Modify | 7.8094 | 7.8094 | 7.8094 | 0.0 | 5.99
|
||||
Other | | 0.06511 | | | 0.05
|
||||
|
||||
Nlocal: 144 ave 144 max 144 min
|
||||
Nlocal: 144.000 ave 144 max 144 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5541 ave 5541 max 5541 min
|
||||
Nghost: 5430.00 ave 5430 max 5430 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 74662 ave 74662 max 74662 min
|
||||
Neighs: 72807.0 ave 72807 max 72807 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 74662
|
||||
Ave neighs/atom = 518.486
|
||||
Neighbor list builds = 207
|
||||
Total # of neighbors = 72807
|
||||
Ave neighs/atom = 505.60417
|
||||
Neighbor list builds = 206
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:37
|
||||
shell rm restart.1000
|
||||
Total wall time: 0:02:32
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (15 Jun 2020)
|
||||
LAMMPS (24 Dec 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
## This script first uses fix qtb to equilibrate alpha quartz structure to an initial state with quantum nuclear correction and then simulate shock induced phase transition through the quantum thermal bath multi-scale shock technique
|
||||
variable x_rep equal 2 #plot is made with x_rep = 8 #x-direction replication number
|
||||
|
|
@ -29,12 +29,12 @@ atom_style charge
|
|||
|
||||
#Lattice
|
||||
lattice custom 1.0 a1 4.916000 0.000000 0.000000 a2 -2.45800 4.257381 0.000000 a3 0.000000 0.000000 5.405400 basis 0.469700 0.000000 0.000000 basis 0.000000 0.469700 0.666667 basis 0.530300 0.530300 0.333333 basis 0.413500 0.266900 0.119100 basis 0.266900 0.413500 0.547567 basis 0.733100 0.146600 0.785767 basis 0.586500 0.853400 0.214233 basis 0.853400 0.586500 0.452433 basis 0.146600 0.733100 0.880900 #American Mineralogist 65 920 1980 (Space Group 154)
|
||||
Lattice spacing in x,y,z = 7.374 4.25738 5.4054
|
||||
Lattice spacing in x,y,z = 7.3740000 4.2573810 5.4054000
|
||||
|
||||
#Computational Cell
|
||||
region orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box
|
||||
create_box 2 orthorhombic_unit_cell
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (4.916 8.514762 5.4054)
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (4.9160000 8.5147620 5.4054000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 2 basis 5 2 basis 6 2 basis 7 2 basis 8 2 basis 9 2
|
||||
Created 18 atoms
|
||||
|
|
@ -43,17 +43,20 @@ replicate ${x_rep} ${y_rep} ${z_rep}
|
|||
replicate 2 ${y_rep} ${z_rep}
|
||||
replicate 2 1 ${z_rep}
|
||||
replicate 2 1 4
|
||||
orthogonal box = (0.0 0.0 0.0) to (9.832 8.514762 21.6216)
|
||||
Replicating atoms ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (9.8320000 8.5147620 21.621600)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
144 atoms
|
||||
replicate CPU = 0.000225782 secs
|
||||
replicate CPU = 0.001 seconds
|
||||
|
||||
#Atomic Information
|
||||
mass 1 28.085500
|
||||
mass 2 15.999400
|
||||
set type 1 charge +2.4
|
||||
Setting atom values ...
|
||||
48 settings made for charge
|
||||
set type 2 charge -1.2
|
||||
Setting atom values ...
|
||||
96 settings made for charge
|
||||
|
||||
|
||||
|
|
@ -72,8 +75,8 @@ pair_coeff 1 2 table potential_SiO2.TPF Si-O ${cut_off}
|
|||
pair_coeff 1 2 table potential_SiO2.TPF Si-O 10
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O ${cut_off} #See the potential file for more information
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O 10
|
||||
WARNING: 1 of 39901 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:471)
|
||||
WARNING: 1 of 39901 force values in table O-O are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:461)
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
#Neighbor style
|
||||
|
|
@ -96,12 +99,12 @@ thermo_style custom step temp press etotal vol lx ly lz pxx pyy pzz p
|
|||
thermo 200
|
||||
run 2000 # 2 ps
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.301598
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
|
||||
G vector (1/distance) = 0.30159814
|
||||
grid = 9 8 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00117056
|
||||
estimated relative force accuracy = 8.12908e-05
|
||||
estimated absolute RMS force accuracy = 0.0011705589
|
||||
estimated relative force accuracy = 8.1290814e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 2400 288
|
||||
Neighbor list info ...
|
||||
|
|
@ -121,44 +124,44 @@ Neighbor list info ...
|
|||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 79.7 | 79.7 | 79.7 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 79.70 | 79.70 | 79.70 Mbytes
|
||||
Step Temp Press TotEng Volume Lx Ly Lz Pxx Pyy Pzz Pxy Pyz Pxz
|
||||
0 0 -34026.791 -2793.6042 1810.0985 9.832 8.514762 21.6216 -37470.578 -37470.432 -27139.363 1.0530512e-10 0.94245783 4.0087238e-10
|
||||
0 0 -34026.791 -2793.6042 1810.0985 9.832 8.514762 21.6216 -37470.578 -37470.432 -27139.363 -3.2012455e-11 0.94245783 1.6892124e-10
|
||||
200 153.57631 45538.205 -2790.8177 1873.0866 9.9447472 8.612404 21.869543 41721.016 44095.248 50798.351 -3961.4596 1223.325 2871.656
|
||||
400 234.74785 -34404.175 -2789.0189 1850.2127 9.9041 8.5772024 21.780156 -28329.333 -39376.313 -35506.88 -1154.5043 -5411.1071 2246.6749
|
||||
600 265.24833 -20905.145 -2786.2727 1874.9981 9.948129 8.6153326 21.87698 -22753.886 -21091.083 -18870.468 -4645.5548 2968.2945 1415.0311
|
||||
800 297.79035 32990.58 -2784.8247 1853.6946 9.910309 8.5825796 21.79381 30061.364 35359.18 33551.195 -3092.2971 1525.52 -6461.0249
|
||||
1000 367.71884 -27539.239 -2783.0102 1864.7161 9.9299114 8.5995557 21.836917 -20273.387 -38720.429 -23623.901 7639.0334 -866.35665 543.52723
|
||||
1200 399.77109 3807.7814 -2781.511 1893.4978 9.9807399 8.6435745 21.948695 1625.8226 7441.2236 2356.298 -4057.1674 3814.9305 1528.4567
|
||||
1400 466.57962 -4148.235 -2780.1546 1851.5925 9.9065614 8.5793341 21.785568 -10883.19 1816.768 -3378.2828 896.25296 -7208.541 -42.253127
|
||||
1600 497.86539 14505.31 -2778.9409 1882.2616 9.9609584 8.6264432 21.905193 8268.1103 20614.738 14633.082 -2690.5669 6807.3187 11995.878
|
||||
1800 557.31182 -108.04462 -2778.1875 1875.514 9.9490413 8.6161228 21.878986 948.68308 -1929.7575 656.94053 -1628.2172 -6594.5909 -4423.4368
|
||||
2000 480.39449 -8852.2243 -2778.4963 1862.9552 9.9267847 8.596848 21.830042 -18274.307 3038.8369 -11321.203 -5002.1016 12023.282 6845.2769
|
||||
Loop time of 1.42181 on 4 procs for 2000 steps with 144 atoms
|
||||
600 265.24834 -20905.145 -2786.2727 1874.9981 9.948129 8.6153326 21.87698 -22753.885 -21091.083 -18870.467 -4645.5539 2968.2936 1415.0335
|
||||
800 297.79036 32990.577 -2784.8247 1853.6946 9.910309 8.5825796 21.79381 30061.366 35359.175 33551.191 -3092.2938 1525.518 -6461.029
|
||||
1000 367.71885 -27539.237 -2783.0102 1864.7161 9.9299114 8.5995557 21.836917 -20273.384 -38720.43 -23623.895 7639.0325 -866.34777 543.5312
|
||||
1200 399.7711 3807.785 -2781.511 1893.4978 9.9807399 8.6435745 21.948695 1625.8297 7441.2317 2356.2937 -4057.1659 3814.9292 1528.4637
|
||||
1400 466.57958 -4148.2231 -2780.1546 1851.5925 9.9065614 8.5793341 21.785568 -10883.182 1816.778 -3378.2653 896.24645 -7208.5417 -42.262464
|
||||
1600 497.86536 14505.308 -2778.9409 1882.2616 9.9609584 8.6264432 21.905193 8268.1088 20614.74 14633.075 -2690.5703 6807.3188 11995.875
|
||||
1800 557.31178 -108.02787 -2778.1875 1875.514 9.9490413 8.6161228 21.878986 948.70277 -1929.753 656.96663 -1628.2124 -6594.6026 -4423.4256
|
||||
2000 480.39444 -8852.2282 -2778.4963 1862.9552 9.9267847 8.596848 21.830042 -18274.302 3038.8276 -11321.21 -5002.1095 12023.298 6845.2631
|
||||
Loop time of 4.1373 on 4 procs for 2000 steps with 144 atoms
|
||||
|
||||
Performance: 121.535 ns/day, 0.197 hours/ns, 1406.656 timesteps/s
|
||||
87.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 41.766 ns/day, 0.575 hours/ns, 483.407 timesteps/s
|
||||
96.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.72578 | 0.80093 | 0.87518 | 6.1 | 56.33
|
||||
Kspace | 0.33737 | 0.41245 | 0.48642 | 8.4 | 29.01
|
||||
Pair | 2.2821 | 2.4503 | 2.7881 | 12.7 | 59.22
|
||||
Kspace | 0.81032 | 1.1413 | 1.306 | 18.2 | 27.59
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.066098 | 0.071334 | 0.076039 | 1.6 | 5.02
|
||||
Output | 0.00021172 | 0.00039291 | 0.00093484 | 0.0 | 0.03
|
||||
Modify | 0.090105 | 0.1077 | 0.11384 | 3.1 | 7.58
|
||||
Other | | 0.029 | | | 2.04
|
||||
Comm | 0.16143 | 0.16964 | 0.17659 | 1.3 | 4.10
|
||||
Output | 0.00026584 | 0.00061899 | 0.0016773 | 0.0 | 0.01
|
||||
Modify | 0.29943 | 0.33639 | 0.34927 | 3.7 | 8.13
|
||||
Other | | 0.03911 | | | 0.95
|
||||
|
||||
Nlocal: 36 ave 36 max 36 min
|
||||
Nlocal: 36.0000 ave 36 max 36 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2614 ave 2614 max 2614 min
|
||||
Nghost: 2614.00 ave 2614 max 2614 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 10488 ave 11326 max 9404 min
|
||||
Neighs: 10488.0 ave 11326 max 9404 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
|
||||
Total # of neighbors = 41952
|
||||
Ave neighs/atom = 291.333
|
||||
Ave neighs/atom = 291.33333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
unfix quartz_qtb
|
||||
|
|
@ -185,24 +188,23 @@ QBMSST parameters:
|
|||
Initial pressure calculated on first step
|
||||
Initial volume calculated on first step
|
||||
Initial energy calculated on first step
|
||||
fix_modify shock energy yes
|
||||
variable dhug equal f_shock[1]
|
||||
variable dray equal f_shock[2]
|
||||
variable lgr_vel equal f_shock[3]
|
||||
variable lgr_pos equal f_shock[4]
|
||||
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
|
||||
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo_style custom step v_T_qm press econserve vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo 200
|
||||
timestep ${delta_t}
|
||||
timestep 0.001
|
||||
run 1000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.30088
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
|
||||
G vector (1/distance) = 0.30087967
|
||||
grid = 9 8 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00120534
|
||||
estimated relative force accuracy = 8.37062e-05
|
||||
estimated absolute RMS force accuracy = 0.0012053392
|
||||
estimated relative force accuracy = 8.3706174e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 2400 288
|
||||
Neighbor list info ...
|
||||
|
|
@ -225,50 +227,51 @@ Neighbor list info ...
|
|||
Fix QBMSST v0 = 1.86296e+03
|
||||
Fix QBMSST p0 = -1.13219e+04
|
||||
Fix QBMSST e0 = to be -2.77850e+03
|
||||
Fix QBMSST initial strain rate of -4.21890e-01 established by reducing temperature by factor of 5.00000e-02
|
||||
Per MPI rank memory allocation (min/avg/max) = 79.7 | 79.7 | 79.7 Mbytes
|
||||
Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
0 300 -9106.318 -2778.4963 1862.9552 9.9267847 8.596848 21.830042 -11562.002 12.009862 -240.0699 0 0
|
||||
200 296.47213 25984.111 -2777.5178 1770.2164 9.9267847 8.596848 20.743332 64970.204 -25.305765 -1564.7673 3.8828772 -15.16768
|
||||
400 291.06707 69977.517 -2777.6325 1684.893 9.9267847 8.596848 19.743515 144833.82 -12.184734 6667.384 7.4552796 -29.607028
|
||||
600 287.21118 39706.699 -2778.0322 1716.9533 9.9267847 8.596848 20.119196 87971.152 -38.593844 -23279.741 6.1129484 -43.751298
|
||||
800 284.33611 18833.281 -2778.1637 1792.7576 9.9267847 8.596848 21.007468 43725.433 -8.1267799 -3885.5802 2.9391022 -58.454556
|
||||
1000 281.98328 -6030.6935 -2778.3314 1881.8369 9.9267847 8.596848 22.051297 -14118.602 1.3183874 13055.078 -0.79055793 -73.780965
|
||||
Loop time of 1.25215 on 4 procs for 1000 steps with 144 atoms
|
||||
Fix QBMSST initial strain rate of -4.21889e-01 established by reducing temperature by factor of 5.00000e-02
|
||||
Per MPI rank memory allocation (min/avg/max) = 79.70 | 79.70 | 79.70 Mbytes
|
||||
Step v_T_qm Press Econserve Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
0 300 -9106.3219 -2778.4963 1862.9552 9.9267847 8.596848 21.830042 -11562.009 12.009861 -240.06987 0 0
|
||||
200 296.47212 25984.099 -2777.5178 1770.2165 9.9267847 8.596848 20.743332 64970.178 -25.305804 -1564.7427 3.8828751 -15.16768
|
||||
400 291.06704 69977.415 -2777.6325 1684.8932 9.9267847 8.596848 19.743517 144833.61 -12.18477 6667.3264 7.4552723 -29.607029
|
||||
600 287.21114 39706.769 -2778.0322 1716.9533 9.9267847 8.596848 20.119196 87971.211 -38.594057 -23279.705 6.1129499 -43.7513
|
||||
800 284.33606 18833.325 -2778.1637 1792.7575 9.9267847 8.596848 21.007467 43725.516 -8.1270751 -3885.5508 2.9391052 -58.454557
|
||||
1000 281.98323 -6030.7047 -2778.3314 1881.8368 9.9267847 8.596848 22.051295 -14118.589 1.3182589 13054.989 -0.79055248 -73.780966
|
||||
Loop time of 3.32539 on 4 procs for 1000 steps with 144 atoms
|
||||
|
||||
Performance: 69.001 ns/day, 0.348 hours/ns, 798.628 timesteps/s
|
||||
90.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 25.982 ns/day, 0.924 hours/ns, 300.717 timesteps/s
|
||||
97.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.67979 | 0.73665 | 0.8091 | 5.4 | 58.83
|
||||
Kspace | 0.18687 | 0.25893 | 0.31544 | 9.1 | 20.68
|
||||
Neigh | 0.0011306 | 0.0012404 | 0.0013735 | 0.3 | 0.10
|
||||
Comm | 0.040339 | 0.041345 | 0.042296 | 0.4 | 3.30
|
||||
Output | 0.00020051 | 0.00035506 | 0.00081801 | 0.0 | 0.03
|
||||
Modify | 0.19595 | 0.2007 | 0.20253 | 0.6 | 16.03
|
||||
Other | | 0.01292 | | | 1.03
|
||||
Pair | 1.9626 | 2.0842 | 2.2541 | 7.9 | 62.68
|
||||
Kspace | 0.44255 | 0.61231 | 0.73369 | 14.5 | 18.41
|
||||
Neigh | 0.0050733 | 0.0052404 | 0.0053804 | 0.2 | 0.16
|
||||
Comm | 0.077084 | 0.077385 | 0.077714 | 0.1 | 2.33
|
||||
Output | 0.00029039 | 0.00046909 | 0.0010037 | 0.0 | 0.01
|
||||
Modify | 0.50853 | 0.52962 | 0.53724 | 1.7 | 15.93
|
||||
Other | | 0.01615 | | | 0.49
|
||||
|
||||
Nlocal: 36 ave 38 max 34 min
|
||||
Nlocal: 36.0000 ave 38 max 34 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Nghost: 2527.75 ave 2547 max 2518 min
|
||||
Nghost: 2527.75 ave 2547 max 2518 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 10194.8 ave 11177 max 9437 min
|
||||
Neighs: 10194.8 ave 11177 max 9437 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 40779
|
||||
Ave neighs/atom = 283.188
|
||||
Ave neighs/atom = 283.18750
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
write_restart restart.1000
|
||||
System init for write_restart ...
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.302953
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
|
||||
G vector (1/distance) = 0.30295266
|
||||
grid = 9 8 16
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00105569
|
||||
estimated relative force accuracy = 7.33134e-05
|
||||
estimated absolute RMS force accuracy = 0.0010556863
|
||||
estimated relative force accuracy = 7.3313358e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 2640 288
|
||||
Neighbor list info ...
|
||||
|
|
@ -294,12 +297,14 @@ Neighbor list info ...
|
|||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.1000
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style charge from restart
|
||||
orthogonal box = (-0.04739235907204603 -0.041042988010289584 -0.21484841641189512) to (9.879392359072014 8.555804988010294 21.83644841641206)
|
||||
orthogonal box = (-0.047392358 -0.041042987 -0.21484765) to (9.8793924 8.5558050 21.836448)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
restoring pair style hybrid/overlay from restart
|
||||
144 atoms
|
||||
read_restart CPU = 0.000472307 secs
|
||||
read_restart CPU = 0.009 seconds
|
||||
include alpha_quartz_potential.mod
|
||||
#This script implements the BKS pair potential for various silicon dioxide compounds. Inner part is fixed with a harmonic potential. Long range Coulomb interactions are evaluated with the pppm method.
|
||||
|
||||
|
|
@ -314,8 +319,8 @@ pair_coeff 1 2 table potential_SiO2.TPF Si-O ${cut_off}
|
|||
pair_coeff 1 2 table potential_SiO2.TPF Si-O 10
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O ${cut_off} #See the potential file for more information
|
||||
pair_coeff 2 2 table potential_SiO2.TPF O-O 10
|
||||
WARNING: 1 of 39901 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:471)
|
||||
WARNING: 1 of 39901 force values in table O-O are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:461)
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
#Neighbor style
|
||||
|
|
@ -338,25 +343,24 @@ QBMSST parameters:
|
|||
Initial energy calculated on first step
|
||||
Resetting global fix info from restart file:
|
||||
fix style: qbmsst, fix ID: shock
|
||||
fix_modify shock energy yes
|
||||
variable dhug equal f_shock[1]
|
||||
variable dray equal f_shock[2]
|
||||
variable lgr_vel equal f_shock[3]
|
||||
variable lgr_pos equal f_shock[4]
|
||||
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
|
||||
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo_style custom step v_T_qm press econserve vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo 500
|
||||
timestep ${delta_t}
|
||||
timestep 0.001
|
||||
restart 1000 restart
|
||||
#restart 1000 restart
|
||||
run 10000 #10 ps
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
|
||||
G vector (1/distance) = 0.302953
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
|
||||
G vector (1/distance) = 0.30295266
|
||||
grid = 9 8 16
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00105569
|
||||
estimated relative force accuracy = 7.33134e-05
|
||||
estimated absolute RMS force accuracy = 0.0010556863
|
||||
estimated relative force accuracy = 7.3313358e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 2640 288
|
||||
All restart file global fix info was re-assigned
|
||||
|
|
@ -378,53 +382,54 @@ Neighbor list info ...
|
|||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 79.71 | 79.71 | 79.71 Mbytes
|
||||
Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
1000 281.98328 -6031.2395 -2778.6227 1881.8369 9.9267847 8.596848 22.051297 -14113.621 1.3373278 13060.059 -0.79055793 0
|
||||
1500 266.12746 44405.573 -2777.9815 1739.6543 9.9267847 8.596848 20.385206 92590.239 -12.06041 397.47049 5.1624821 -37.823748
|
||||
2000 255.79411 17620.408 -2777.9685 1785.7619 9.9267847 8.596848 20.925494 48670.364 -16.082827 -4813.6764 3.2320016 -73.974437
|
||||
2500 256.8887 40153.833 -2778.4337 1752.9461 9.9267847 8.596848 20.540959 79665.002 7.7413878 -1368.8927 4.6059671 -112.35254
|
||||
3000 261.55251 5315.4799 -2779.0755 1834.3375 9.9267847 8.596848 21.4947 15896.368 22.588205 3192.882 1.1981949 -148.36068
|
||||
3500 261.57101 57911.809 -2778.1223 1713.3956 9.9267847 8.596848 20.077507 110996.8 -9.4471543 -3240.9018 6.2619064 -186.41261
|
||||
4000 254.88665 13952.95 -2778.4816 1818.2782 9.9267847 8.596848 21.306518 26833.588 2.2818412 647.88057 1.8705799 -222.72504
|
||||
4500 240.08908 73322.997 -2776.7382 1668.6666 9.9267847 8.596848 19.553375 151978.11 -43.917346 189.1572 8.1346613 -260.52885
|
||||
5000 214.49084 1925.2557 -2777.0657 1890.0985 9.9267847 8.596848 22.148106 -5218.7292 -44.5537 28890.787 -1.1364617 -297.26329
|
||||
5500 194.6515 71804.842 -2777.3417 1669.7297 9.9267847 8.596848 19.565832 146911.42 -34.911593 -3985.0635 8.0901523 -334.1879
|
||||
6000 186.23814 10196.007 -2777.1394 1837.3793 9.9267847 8.596848 21.530344 23550.907 -18.381207 13401.096 1.0708382 -371.9208
|
||||
6500 172.53603 5474.3725 -2777.4502 1818.0038 9.9267847 8.596848 21.303303 18389.825 -22.65951 -8026.2088 1.8820667 -407.83084
|
||||
7000 160.91186 107908.64 -2777.6746 1621.7378 9.9267847 8.596848 19.003464 196841.27 -8.6606903 5654.1938 10.099523 -444.9925
|
||||
7500 146.01905 147030.69 -2777.2543 1539.7536 9.9267847 8.596848 18.042777 253089.02 -43.928324 -6926.1018 13.532114 -478.63113
|
||||
8000 207.17758 837859.1 -2796.8957 989.32874 9.9267847 8.596848 11.592918 811765.11 1172.3778 89652.363 36.577833 -503.41923
|
||||
8500 725.15657 853732.89 -2832.3144 974.18299 9.9267847 8.596848 11.415441 773926.64 1749.5702 39098.598 37.21197 -524.17835
|
||||
9000 1554.6089 807867.74 -2843.0063 990.10922 9.9267847 8.596848 11.602064 749697.22 1959.0322 28239.71 36.545155 -544.77354
|
||||
9500 2440.1194 748145.05 -2839.2364 992.38871 9.9267847 8.596848 11.628775 691503.58 1437.0708 -28040.223 36.449715 -565.41198
|
||||
10000 3112.1817 823862.43 -2820.0495 982.35471 9.9267847 8.596848 11.511197 754954.89 1330.6807 26987.244 36.869828 -586.12357
|
||||
10500 3550.0273 868916.79 -2803.7678 983.70386 9.9267847 8.596848 11.527006 867368.45 1727.9058 140533.46 36.813341 -607.00946
|
||||
11000 3839.7527 830581.55 -2795.3804 995.31485 9.9267847 8.596848 11.663063 811740 1150.0462 94652.768 36.327201 -628.02229
|
||||
Loop time of 15.1476 on 4 procs for 10000 steps with 144 atoms
|
||||
Step v_T_qm Press Econserve Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
1000 281.98323 -6031.2507 -2778.6227 1881.8368 9.9267847 8.596848 22.051295 -14113.608 1.3371988 13059.97 -0.79055248 0
|
||||
1500 266.12743 44405.252 -2777.9815 1739.6551 9.9267847 8.596848 20.385215 92589.619 -12.060756 397.55607 5.1624473 -37.823753
|
||||
2000 255.79412 17620.89 -2777.9685 1785.7605 9.9267847 8.596848 20.925477 48671.42 -16.082485 -4813.8454 3.2320631 -73.974438
|
||||
2500 257.13592 39692.462 -2778.6986 1751.4095 9.9267847 8.596848 20.522952 80667.315 15.746345 -1656.6275 4.6703047 -112.35088
|
||||
3000 248.95332 9617.5633 -2778.937 1830.5557 9.9267847 8.596848 21.450385 25275.769 19.730704 9397.3972 1.3565331 -148.37113
|
||||
3500 247.70025 100159.87 -2778.0604 1610.8047 9.9267847 8.596848 18.875351 189849.69 -33.726976 -10516.027 10.557281 -185.61862
|
||||
4000 266.07224 848367.31 -2787.9052 992.46097 9.9267847 8.596848 11.629622 880163.37 1477.3994 160680.23 36.44669 -213.83067
|
||||
4500 645.86948 789169.63 -2822.9559 992.40405 9.9267847 8.596848 11.628955 696879.41 1039.4139 -22651.518 36.449073 -234.79958
|
||||
5000 1369.4257 735014.89 -2838.4571 1002.6048 9.9267847 8.596848 11.748487 648785.76 1170.3517 -62181.314 36.021977 -255.55776
|
||||
5500 2156.7632 768865.28 -2835.9297 995.94989 9.9267847 8.596848 11.670505 678013.94 1271.734 -38540.152 36.300612 -276.42588
|
||||
6000 2864.2837 773631.53 -2828.0627 993.01727 9.9267847 8.596848 11.63614 749067.81 1567.7659 30051.708 36.423398 -297.26898
|
||||
6500 3422.632 861319.73 -2810.1415 985.48363 9.9267847 8.596848 11.547861 816792.18 1535.8348 91451.363 36.738824 -318.12934
|
||||
7000 3798.2073 791521.73 -2801.7757 993.1961 9.9267847 8.596848 11.638236 677215.78 330.09854 -41650.204 36.415911 -338.86015
|
||||
7500 4060.7728 836165.25 -2789.6215 984.13658 9.9267847 8.596848 11.532077 780101.5 698.84908 53629.791 36.795223 -359.64284
|
||||
8000 4122.5641 754871.86 -2776.0049 1006.6266 9.9267847 8.596848 11.795613 699610.84 -124.86381 -7979.8848 35.853592 -380.58907
|
||||
8500 4087.3529 769727.63 -2775.3629 1018.2197 9.9267847 8.596848 11.931461 767853.09 415.9984 69995.141 35.368199 -401.90058
|
||||
9000 3958.4459 615996.33 -2758.7864 1058.0696 9.9267847 8.596848 12.398422 641295.34 -689.82578 -23107.426 33.699723 -423.43203
|
||||
9500 3746.2013 643366.31 -2767.1851 1043.1232 9.9267847 8.596848 12.22328 610176.19 -767.67823 -66774.534 34.325515 -445.14544
|
||||
10000 3723.8623 659730.11 -2781.6634 1034.0441 9.9267847 8.596848 12.116891 671355.25 0.037615796 -13217.642 34.705647 -466.9448
|
||||
10500 3705.48 637406.18 -2776.4898 1041.5851 9.9267847 8.596848 12.205256 725619.7 274.78304 47377.665 34.389914 -488.75102
|
||||
11000 3678.0139 648116.35 -2779.0968 1049.9523 9.9267847 8.596848 12.303303 723144.21 382.51198 51926.71 34.039587 -510.63944
|
||||
Loop time of 51.3151 on 4 procs for 10000 steps with 144 atoms
|
||||
|
||||
Performance: 57.039 ns/day, 0.421 hours/ns, 660.171 timesteps/s
|
||||
91.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 16.837 ns/day, 1.425 hours/ns, 194.874 timesteps/s
|
||||
94.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.7228 | 9.085 | 10.626 | 36.0 | 59.98
|
||||
Kspace | 1.6343 | 3.1795 | 4.5467 | 61.0 | 20.99
|
||||
Neigh | 0.02063 | 0.027076 | 0.034395 | 3.1 | 0.18
|
||||
Comm | 0.54719 | 0.57781 | 0.60468 | 2.8 | 3.81
|
||||
Output | 0.10128 | 0.1019 | 0.10373 | 0.3 | 0.67
|
||||
Modify | 2.0819 | 2.1159 | 2.1495 | 1.8 | 13.97
|
||||
Other | | 0.06035 | | | 0.40
|
||||
Pair | 26.662 | 32.362 | 38.05 | 70.9 | 63.07
|
||||
Kspace | 5.8733 | 11.582 | 17.302 | 118.9 | 22.57
|
||||
Neigh | 0.18541 | 0.22229 | 0.25113 | 5.0 | 0.43
|
||||
Comm | 1.4273 | 1.4501 | 1.483 | 1.9 | 2.83
|
||||
Output | 0.0011935 | 0.0018681 | 0.003891 | 2.7 | 0.00
|
||||
Modify | 5.4539 | 5.5056 | 5.5294 | 1.3 | 10.73
|
||||
Other | | 0.1916 | | | 0.37
|
||||
|
||||
Nlocal: 36 ave 38 max 33 min
|
||||
Nlocal: 36.0000 ave 37 max 35 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 4159.50 ave 4171 max 4140 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 4267 ave 4304 max 4239 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Neighs: 18859.2 ave 25108 max 12333 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 17967.8 ave 20291 max 15710 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 75437
|
||||
Ave neighs/atom = 523.868
|
||||
Neighbor list builds = 95
|
||||
Total # of neighbors = 71871
|
||||
Ave neighs/atom = 499.10417
|
||||
Neighbor list builds = 161
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:17
|
||||
shell rm restart.1000
|
||||
Total wall time: 0:01:01
|
||||
|
|
@ -23,9 +23,9 @@ neigh_modify delay 0
|
|||
neigh_modify check yes
|
||||
|
||||
#### Simulation settings ####
|
||||
timestep 0.001
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix thermostat all nve
|
||||
timestep 0.001
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix thermostat all nve
|
||||
|
||||
############# Output ###############
|
||||
thermo 100
|
||||
|
|
@ -34,4 +34,4 @@ thermo_style custom step etotal pe ke temp
|
|||
thermo_modify line one format float %20.16g lost warn
|
||||
|
||||
###### Run molecular dynamics ######
|
||||
run 1000
|
||||
run 1000
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@ units metal
|
|||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
|
|
@ -35,45 +35,45 @@ region myreg block 0 4 &
|
|||
|
||||
create_box 8 myreg
|
||||
create_atoms 1 region myreg &
|
||||
basis 1 1 &
|
||||
basis 2 2 &
|
||||
basis 3 3 &
|
||||
basis 4 4 &
|
||||
basis 5 5 &
|
||||
basis 6 6 &
|
||||
basis 7 7 &
|
||||
basis 8 8
|
||||
basis 1 1 &
|
||||
basis 2 2 &
|
||||
basis 3 3 &
|
||||
basis 4 4 &
|
||||
basis 5 5 &
|
||||
basis 6 6 &
|
||||
basis 7 7 &
|
||||
basis 8 8
|
||||
|
||||
mass * 28.06
|
||||
|
||||
velocity all create $t 5287287 loop geom
|
||||
velocity all create $t 5287287 loop geom
|
||||
|
||||
# Equilibrate using Tersoff model for silicon
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * Si.tersoff Si Si Si Si Si Si Si Si
|
||||
pair_coeff * * Si.tersoff Si Si Si Si Si Si Si Si
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
|
||||
write_restart restart.equil
|
||||
write_restart restart.equil
|
||||
|
||||
# Test Tersoff/Mod model for Si
|
||||
|
||||
clear
|
||||
read_restart restart.equil
|
||||
read_restart restart.equil
|
||||
|
||||
pair_style tersoff/mod
|
||||
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
|
||||
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
|
@ -82,14 +82,14 @@ run 100
|
|||
# Test Tersoff/Mod/C model for Si
|
||||
|
||||
clear
|
||||
read_restart restart.equil
|
||||
read_restart restart.equil
|
||||
newton on on
|
||||
pair_style tersoff/mod/c
|
||||
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
|
||||
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
|
@ -98,17 +98,17 @@ run 100
|
|||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
read_restart restart.equil
|
||||
read_restart restart.equil
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
|
@ -117,19 +117,20 @@ run 100
|
|||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
read_restart restart.equil
|
||||
read_restart restart.equil
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
|
||||
pair_style tersoff shift 0.05
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
|
||||
shell rm restart.equil
|
||||
|
|
|
|||
|
|
@ -1,5 +1,4 @@
|
|||
LAMMPS (24 Dec 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple regression tests for Tersoff potentials
|
||||
|
||||
|
|
@ -10,7 +9,7 @@ units metal
|
|||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
|
|
@ -28,26 +27,26 @@ region myreg block 0 4 0 4
|
|||
create_box 8 myreg
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
|
||||
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
|
||||
Created 512 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
mass * 28.06
|
||||
|
||||
velocity all create $t 5287287 loop geom
|
||||
velocity all create 1800 5287287 loop geom
|
||||
velocity all create $t 5287287 loop geom
|
||||
velocity all create 1800 5287287 loop geom
|
||||
|
||||
# Equilibrate using Tersoff model for silicon
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * Si.tersoff Si Si Si Si Si Si Si Si
|
||||
pair_coeff * * Si.tersoff Si Si Si Si Si Si Si Si
|
||||
Reading tersoff potential file Si.tersoff with DATE: 2007-10-25
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
|
@ -65,32 +64,32 @@ Neighbor list info ...
|
|||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.985 | 2.985 | 2.985 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1800 -2370.771 0 -2251.8775 12511.419
|
||||
10 1144.7447 -2327.3227 0 -2251.7759 21852.599
|
||||
20 770.19243 -2302.1547 0 -2251.7633 22286.587
|
||||
30 1059.4324 -2320.1988 0 -2251.8159 6242.222
|
||||
40 1000.972 -2314.6531 0 -2251.796 -3069.9273
|
||||
50 803.91758 -2300.1702 0 -2251.7834 -7154.1383
|
||||
60 761.38639 -2296.1731 0 -2251.7928 -14520.921
|
||||
70 750.57677 -2294.3086 0 -2251.7965 -21400.198
|
||||
80 676.66672 -2288.2634 0 -2251.7899 -23480.201
|
||||
90 640.24103 -2284.6678 0 -2251.7848 -20659.983
|
||||
100 742.67188 -2290.0616 0 -2251.7855 -16211.799
|
||||
Loop time of 0.107338 on 1 procs for 100 steps with 512 atoms
|
||||
Step Temp E_pair TotEng Econserve Press
|
||||
0 1800 -2370.771 -2251.8775 -2251.8775 12511.419
|
||||
10 1144.7447 -2327.3227 -2251.7101 -2251.7759 21852.599
|
||||
20 770.19243 -2302.1547 -2251.282 -2251.7633 22286.587
|
||||
30 1059.4324 -2320.1988 -2250.2213 -2251.8159 6242.222
|
||||
40 1000.972 -2314.6531 -2248.5369 -2251.796 -3069.9273
|
||||
50 803.91758 -2300.1702 -2247.0699 -2251.7834 -7154.1383
|
||||
60 761.38639 -2296.1731 -2245.882 -2251.7928 -14520.921
|
||||
70 750.57677 -2294.3086 -2244.7316 -2251.7965 -21400.198
|
||||
80 676.66672 -2288.2634 -2243.5683 -2251.7899 -23480.201
|
||||
90 640.24103 -2284.6678 -2242.3786 -2251.7848 -20659.983
|
||||
100 742.67188 -2290.0616 -2241.0067 -2251.7855 -16211.799
|
||||
Loop time of 0.447105 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 80.493 ns/day, 0.298 hours/ns, 931.637 timesteps/s
|
||||
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 19.324 ns/day, 1.242 hours/ns, 223.661 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.10455 | 0.10455 | 0.10455 | 0.0 | 97.40
|
||||
Neigh | 0.001115 | 0.001115 | 0.001115 | 0.0 | 1.04
|
||||
Comm | 0.000482 | 0.000482 | 0.000482 | 0.0 | 0.45
|
||||
Output | 0.000194 | 0.000194 | 0.000194 | 0.0 | 0.18
|
||||
Modify | 0.000787 | 0.000787 | 0.000787 | 0.0 | 0.73
|
||||
Other | | 0.000209 | | | 0.19
|
||||
Pair | 0.4373 | 0.4373 | 0.4373 | 0.0 | 97.81
|
||||
Neigh | 0.0021279 | 0.0021279 | 0.0021279 | 0.0 | 0.48
|
||||
Comm | 0.0021732 | 0.0021732 | 0.0021732 | 0.0 | 0.49
|
||||
Output | 0.00020552 | 0.00020552 | 0.00020552 | 0.0 | 0.05
|
||||
Modify | 0.0047524 | 0.0047524 | 0.0047524 | 0.0 | 1.06
|
||||
Other | | 0.0005488 | | | 0.12
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
|
@ -106,15 +105,14 @@ Ave neighs/atom = 16.414062
|
|||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
write_restart restart.equil
|
||||
write_restart restart.equil
|
||||
System init for write_restart ...
|
||||
|
||||
# Test Tersoff/Mod model for Si
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
|
|
@ -122,19 +120,19 @@ Reading restart file ...
|
|||
1 by 1 by 1 MPI processor grid
|
||||
pair style tersoff stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.006 seconds
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
pair_style tersoff/mod
|
||||
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
|
||||
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
|
||||
Reading tersoff/mod potential file Si.tersoff.mod with DATE: 2013-07-26
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
|
@ -153,32 +151,32 @@ Neighbor list info ...
|
|||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.979 | 2.979 | 2.979 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 742.67188 -2210.6446 0 -2172.3685 -6444.2163
|
||||
110 1135.5853 -2234.6974 0 -2172.3908 113.80404
|
||||
120 1462.8415 -2253.8186 0 -2172.3853 10922.229
|
||||
130 1755.9617 -2270.5152 0 -2172.3964 18780.707
|
||||
140 1895.1939 -2277.1484 0 -2172.3965 22357.106
|
||||
150 1869.5375 -2273.2734 0 -2172.3851 22616.492
|
||||
160 1824.0448 -2268.4342 0 -2172.393 19254.299
|
||||
170 1637.9038 -2254.5219 0 -2172.3815 15904.928
|
||||
180 1451.9871 -2240.7199 0 -2172.3771 12064.754
|
||||
190 1362.8248 -2233.1942 0 -2172.3789 7970.534
|
||||
200 1341.1467 -2229.8951 0 -2172.3717 6244.8542
|
||||
Loop time of 0.128972 on 1 procs for 100 steps with 512 atoms
|
||||
Step Temp E_pair TotEng Econserve Press
|
||||
100 742.67188 -2210.6446 -2161.5897 -2172.3685 -6444.2163
|
||||
110 1135.5853 -2234.6974 -2159.6898 -2172.3908 113.80404
|
||||
120 1462.8415 -2253.8186 -2157.1951 -2172.3853 10922.229
|
||||
130 1755.9617 -2270.5152 -2154.5306 -2172.3964 18780.707
|
||||
140 1895.1939 -2277.1484 -2151.9672 -2172.3965 22357.106
|
||||
150 1869.5375 -2273.2734 -2149.7868 -2172.3851 22616.492
|
||||
160 1824.0448 -2268.4342 -2147.9525 -2172.393 19254.299
|
||||
170 1637.9038 -2254.5219 -2146.3352 -2172.3815 15904.928
|
||||
180 1451.9871 -2240.7199 -2144.8134 -2172.3771 12064.754
|
||||
190 1362.8248 -2233.1942 -2143.177 -2172.3789 7970.534
|
||||
200 1341.1467 -2229.8951 -2141.3097 -2172.3717 6244.8542
|
||||
Loop time of 0.428851 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 66.991 ns/day, 0.358 hours/ns, 775.362 timesteps/s
|
||||
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 20.147 ns/day, 1.191 hours/ns, 233.181 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.12498 | 0.12498 | 0.12498 | 0.0 | 96.91
|
||||
Neigh | 0.002322 | 0.002322 | 0.002322 | 0.0 | 1.80
|
||||
Comm | 0.000537 | 0.000537 | 0.000537 | 0.0 | 0.42
|
||||
Output | 0.000177 | 0.000177 | 0.000177 | 0.0 | 0.14
|
||||
Modify | 0.000761 | 0.000761 | 0.000761 | 0.0 | 0.59
|
||||
Other | | 0.000192 | | | 0.15
|
||||
Pair | 0.41656 | 0.41656 | 0.41656 | 0.0 | 97.13
|
||||
Neigh | 0.0043387 | 0.0043387 | 0.0043387 | 0.0 | 1.01
|
||||
Comm | 0.0025339 | 0.0025339 | 0.0025339 | 0.0 | 0.59
|
||||
Output | 0.00019503 | 0.00019503 | 0.00019503 | 0.0 | 0.05
|
||||
Modify | 0.0047224 | 0.0047224 | 0.0047224 | 0.0 | 1.10
|
||||
Other | | 0.0004995 | | | 0.12
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
|
@ -197,9 +195,8 @@ Dangerous builds = 0
|
|||
# Test Tersoff/Mod/C model for Si
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
|
|
@ -210,16 +207,16 @@ Reading restart file ...
|
|||
read_restart CPU = 0.001 seconds
|
||||
newton on on
|
||||
pair_style tersoff/mod/c
|
||||
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
|
||||
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
|
||||
Reading tersoff/mod/c potential file Si.tersoff.modc with DATE: 2016-11-09
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
|
@ -238,32 +235,32 @@ Neighbor list info ...
|
|||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.976 | 2.976 | 2.976 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 742.67188 -2221.9308 0 -2183.6547 -11721.269
|
||||
110 1106.895 -2244.1196 0 -2183.6843 -2359.7819
|
||||
120 1327.6674 -2256.3155 0 -2183.6767 7904.6604
|
||||
130 1487.0219 -2264.3656 0 -2183.6707 14660.783
|
||||
140 1709.1746 -2276.4761 0 -2183.6886 19298.791
|
||||
150 1710.6528 -2274.1129 0 -2183.6764 22026.559
|
||||
160 1651.0659 -2267.9877 0 -2183.6699 20916.722
|
||||
170 1632.7705 -2264.7081 0 -2183.6777 17339.031
|
||||
180 1477.693 -2252.4683 0 -2183.6706 12563.594
|
||||
190 1310.8768 -2239.5419 0 -2183.6581 9591.0484
|
||||
200 1356.7172 -2240.5315 0 -2183.668 5584.6734
|
||||
Loop time of 0.133106 on 1 procs for 100 steps with 512 atoms
|
||||
Step Temp E_pair TotEng Econserve Press
|
||||
100 742.67188 -2221.9308 -2172.8759 -2183.6547 -11721.269
|
||||
110 1106.895 -2244.1196 -2171.007 -2183.6843 -2359.7819
|
||||
120 1327.6674 -2256.3155 -2168.6205 -2183.6767 7904.6604
|
||||
130 1487.0219 -2264.3656 -2166.1449 -2183.6707 14660.783
|
||||
140 1709.1746 -2276.4761 -2163.5818 -2183.6886 19298.791
|
||||
150 1710.6528 -2274.1129 -2161.1209 -2183.6764 22026.559
|
||||
160 1651.0659 -2267.9877 -2158.9316 -2183.6699 20916.722
|
||||
170 1632.7705 -2264.7081 -2156.8605 -2183.6777 17339.031
|
||||
180 1477.693 -2252.4683 -2154.8638 -2183.6706 12563.594
|
||||
190 1310.8768 -2239.5419 -2152.9559 -2183.6581 9591.0484
|
||||
200 1356.7172 -2240.5315 -2150.9177 -2183.668 5584.6734
|
||||
Loop time of 0.444872 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 64.911 ns/day, 0.370 hours/ns, 751.281 timesteps/s
|
||||
96.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 19.421 ns/day, 1.236 hours/ns, 224.784 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.1291 | 0.1291 | 0.1291 | 0.0 | 96.99
|
||||
Neigh | 0.002343 | 0.002343 | 0.002343 | 0.0 | 1.76
|
||||
Comm | 0.0005 | 0.0005 | 0.0005 | 0.0 | 0.38
|
||||
Output | 0.000186 | 0.000186 | 0.000186 | 0.0 | 0.14
|
||||
Modify | 0.000786 | 0.000786 | 0.000786 | 0.0 | 0.59
|
||||
Other | | 0.000191 | | | 0.14
|
||||
Pair | 0.43275 | 0.43275 | 0.43275 | 0.0 | 97.28
|
||||
Neigh | 0.0042851 | 0.0042851 | 0.0042851 | 0.0 | 0.96
|
||||
Comm | 0.0024009 | 0.0024009 | 0.0024009 | 0.0 | 0.54
|
||||
Output | 0.00019312 | 0.00019312 | 0.00019312 | 0.0 | 0.04
|
||||
Modify | 0.0047414 | 0.0047414 | 0.0047414 | 0.0 | 1.07
|
||||
Other | | 0.0004966 | | | 0.11
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
|
@ -282,9 +279,8 @@ Dangerous builds = 0
|
|||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
|
|
@ -294,27 +290,27 @@ Reading restart file ...
|
|||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
Changing box ...
|
||||
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
|
@ -333,32 +329,32 @@ Neighbor list info ...
|
|||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.985 | 2.985 | 2.985 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 742.67188 -2973.8527 0 -2935.5766 3438975.9
|
||||
110 4061.1085 -3183.2489 0 -2930.1208 2211712.7
|
||||
120 4120.3231 -3187.0108 0 -2928.3047 2166764.3
|
||||
130 3602.7602 -3158.5939 0 -2926.6167 2244475.7
|
||||
140 3222.7773 -3141.7275 0 -2925.5369 2161607
|
||||
150 3487.4703 -3163.7495 0 -2921.2462 2222150.2
|
||||
160 3436.3009 -3169.4234 0 -2920.8775 2144368.7
|
||||
170 3308.1796 -3170.3773 0 -2920.8967 2223612.9
|
||||
180 3304.3776 -3178.7805 0 -2920.102 2072546.6
|
||||
190 3217.3561 -3180.7963 0 -2918.4548 2118776.2
|
||||
200 3041.6832 -3176.1794 0 -2916.5787 2130124.6
|
||||
Loop time of 0.134621 on 1 procs for 100 steps with 512 atoms
|
||||
Step Temp E_pair TotEng Econserve Press
|
||||
100 742.67188 -2973.8527 -2924.7978 -2935.5766 3438975.9
|
||||
110 4061.1085 -3183.2489 -2915.0049 -2930.1208 2211712.7
|
||||
120 4120.3231 -3187.0108 -2914.8555 -2928.3047 2166764.3
|
||||
130 3602.7602 -3158.5939 -2920.6246 -2926.6167 2244475.7
|
||||
140 3222.7773 -3141.7275 -2928.8568 -2925.5369 2161607
|
||||
150 3487.4703 -3163.7495 -2933.3954 -2921.2462 2222150.2
|
||||
160 3436.3009 -3169.4234 -2942.449 -2920.8775 2144368.7
|
||||
170 3308.1796 -3170.3773 -2951.8656 -2920.8967 2223612.9
|
||||
180 3304.3776 -3178.7805 -2960.52 -2920.102 2072546.6
|
||||
190 3217.3561 -3180.7963 -2968.2837 -2918.4548 2118776.2
|
||||
200 3041.6832 -3176.1794 -2975.2703 -2916.5787 2130124.6
|
||||
Loop time of 0.55964 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 64.180 ns/day, 0.374 hours/ns, 742.826 timesteps/s
|
||||
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 15.438 ns/day, 1.555 hours/ns, 178.686 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.12837 | 0.12837 | 0.12837 | 0.0 | 95.35
|
||||
Neigh | 0.004553 | 0.004553 | 0.004553 | 0.0 | 3.38
|
||||
Comm | 0.000601 | 0.000601 | 0.000601 | 0.0 | 0.45
|
||||
Output | 0.000177 | 0.000177 | 0.000177 | 0.0 | 0.13
|
||||
Modify | 0.000742 | 0.000742 | 0.000742 | 0.0 | 0.55
|
||||
Other | | 0.000181 | | | 0.13
|
||||
Pair | 0.54187 | 0.54187 | 0.54187 | 0.0 | 96.83
|
||||
Neigh | 0.0087171 | 0.0087171 | 0.0087171 | 0.0 | 1.56
|
||||
Comm | 0.0036685 | 0.0036685 | 0.0036685 | 0.0 | 0.66
|
||||
Output | 0.00019526 | 0.00019526 | 0.00019526 | 0.0 | 0.03
|
||||
Modify | 0.0047348 | 0.0047348 | 0.0047348 | 0.0 | 0.85
|
||||
Other | | 0.0004504 | | | 0.08
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
|
@ -377,9 +373,8 @@ Dangerous builds = 0
|
|||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
|
|
@ -389,27 +384,27 @@ Reading restart file ...
|
|||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
Changing box ...
|
||||
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
|
||||
|
||||
pair_style tersoff shift 0.05
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
|
@ -428,32 +423,32 @@ Neighbor list info ...
|
|||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.985 | 2.985 | 2.985 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 742.67188 -3294.0266 0 -3255.7505 1615779.4
|
||||
110 2870.7114 -3432.8485 0 -3257.629 1053310.6
|
||||
120 2898.0798 -3431.4968 0 -3256.6851 1223402.3
|
||||
130 2708.4483 -3419.0142 0 -3256.436 1105893.8
|
||||
140 2307.8661 -3394.1268 0 -3256.1686 1148075.8
|
||||
150 2215.3423 -3390.1427 0 -3255.8733 1138540
|
||||
160 2515.488 -3412.6704 0 -3255.1731 1122902.8
|
||||
170 2485.7109 -3415.0402 0 -3255.3787 1097748.5
|
||||
180 2327.476 -3408.2463 0 -3254.6537 1061602.6
|
||||
190 2339.5966 -3413.3961 0 -3254.7496 1088059
|
||||
200 2260.5961 -3411.477 0 -3254.0771 1104581.5
|
||||
Loop time of 0.120764 on 1 procs for 100 steps with 512 atoms
|
||||
Step Temp E_pair TotEng Econserve Press
|
||||
100 742.67188 -3294.0266 -3244.9717 -3255.7505 1615779.4
|
||||
110 2870.7114 -3432.8485 -3243.2324 -3257.629 1053310.6
|
||||
120 2898.0798 -3431.4968 -3240.0731 -3256.6851 1223402.3
|
||||
130 2708.4483 -3419.0142 -3240.1159 -3256.436 1105893.8
|
||||
140 2307.8661 -3394.1268 -3241.6877 -3256.1686 1148075.8
|
||||
150 2215.3423 -3390.1427 -3243.8151 -3255.8733 1138540
|
||||
160 2515.488 -3412.6704 -3246.5175 -3255.1731 1122902.8
|
||||
170 2485.7109 -3415.0402 -3250.8542 -3255.3787 1097748.5
|
||||
180 2327.476 -3408.2463 -3254.512 -3254.6537 1061602.6
|
||||
190 2339.5966 -3413.3961 -3258.8612 -3254.7496 1088059
|
||||
200 2260.5961 -3411.477 -3262.1603 -3254.0771 1104581.5
|
||||
Loop time of 0.511812 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 71.545 ns/day, 0.335 hours/ns, 828.061 timesteps/s
|
||||
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 16.881 ns/day, 1.422 hours/ns, 195.384 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.11521 | 0.11521 | 0.11521 | 0.0 | 95.40
|
||||
Neigh | 0.003874 | 0.003874 | 0.003874 | 0.0 | 3.21
|
||||
Comm | 0.000542 | 0.000542 | 0.000542 | 0.0 | 0.45
|
||||
Output | 0.000177 | 0.000177 | 0.000177 | 0.0 | 0.15
|
||||
Modify | 0.000774 | 0.000774 | 0.000774 | 0.0 | 0.64
|
||||
Other | | 0.00019 | | | 0.16
|
||||
Pair | 0.49628 | 0.49628 | 0.49628 | 0.0 | 96.96
|
||||
Neigh | 0.0072167 | 0.0072167 | 0.0072167 | 0.0 | 1.41
|
||||
Comm | 0.0029061 | 0.0029061 | 0.0029061 | 0.0 | 0.57
|
||||
Output | 0.00019026 | 0.00019026 | 0.00019026 | 0.0 | 0.04
|
||||
Modify | 0.0047674 | 0.0047674 | 0.0047674 | 0.0 | 0.93
|
||||
Other | | 0.0004566 | | | 0.09
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
|
@ -469,4 +464,4 @@ Ave neighs/atom = 28.664062
|
|||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
Total wall time: 0:00:02
|
||||
|
|
@ -1,5 +1,4 @@
|
|||
LAMMPS (24 Dec 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple regression tests for Tersoff potentials
|
||||
|
||||
|
|
@ -10,7 +9,7 @@ units metal
|
|||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
|
|
@ -28,26 +27,26 @@ region myreg block 0 4 0 4
|
|||
create_box 8 myreg
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
|
||||
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
|
||||
Created 512 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
mass * 28.06
|
||||
|
||||
velocity all create $t 5287287 loop geom
|
||||
velocity all create 1800 5287287 loop geom
|
||||
velocity all create $t 5287287 loop geom
|
||||
velocity all create 1800 5287287 loop geom
|
||||
|
||||
# Equilibrate using Tersoff model for silicon
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * Si.tersoff Si Si Si Si Si Si Si Si
|
||||
pair_coeff * * Si.tersoff Si Si Si Si Si Si Si Si
|
||||
Reading tersoff potential file Si.tersoff with DATE: 2007-10-25
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
|
@ -65,32 +64,32 @@ Neighbor list info ...
|
|||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.958 | 2.958 | 2.958 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1800 -2370.771 0 -2251.8775 12511.419
|
||||
10 1144.7447 -2327.3227 0 -2251.7759 21852.599
|
||||
20 770.19243 -2302.1547 0 -2251.7633 22286.587
|
||||
30 1059.4324 -2320.1988 0 -2251.8159 6242.222
|
||||
40 1000.972 -2314.6531 0 -2251.796 -3069.9273
|
||||
50 803.91758 -2300.1702 0 -2251.7834 -7154.1383
|
||||
60 761.38639 -2296.1731 0 -2251.7928 -14520.921
|
||||
70 750.57677 -2294.3086 0 -2251.7965 -21400.198
|
||||
80 676.66672 -2288.2634 0 -2251.7899 -23480.201
|
||||
90 640.24103 -2284.6678 0 -2251.7848 -20659.983
|
||||
100 742.67188 -2290.0616 0 -2251.7855 -16211.799
|
||||
Loop time of 0.0321762 on 4 procs for 100 steps with 512 atoms
|
||||
Step Temp E_pair TotEng Econserve Press
|
||||
0 1800 -2370.771 -2251.8775 -2251.8775 12511.419
|
||||
10 1144.7447 -2327.3227 -2251.7101 -2251.7759 21852.599
|
||||
20 770.19243 -2302.1547 -2251.282 -2251.7633 22286.587
|
||||
30 1059.4324 -2320.1988 -2250.2213 -2251.8159 6242.222
|
||||
40 1000.972 -2314.6531 -2248.5369 -2251.796 -3069.9273
|
||||
50 803.91758 -2300.1702 -2247.0699 -2251.7834 -7154.1383
|
||||
60 761.38639 -2296.1731 -2245.882 -2251.7928 -14520.921
|
||||
70 750.57677 -2294.3086 -2244.7316 -2251.7965 -21400.198
|
||||
80 676.66672 -2288.2634 -2243.5683 -2251.7899 -23480.201
|
||||
90 640.24103 -2284.6678 -2242.3786 -2251.7848 -20659.983
|
||||
100 742.67188 -2290.0616 -2241.0067 -2251.7855 -16211.799
|
||||
Loop time of 0.130429 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 268.521 ns/day, 0.089 hours/ns, 3107.882 timesteps/s
|
||||
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 66.243 ns/day, 0.362 hours/ns, 766.701 timesteps/s
|
||||
96.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.026599 | 0.02712 | 0.027602 | 0.2 | 84.28
|
||||
Neigh | 0.000285 | 0.00028875 | 0.000294 | 0.0 | 0.90
|
||||
Comm | 0.003471 | 0.0039375 | 0.004446 | 0.6 | 12.24
|
||||
Output | 0.000112 | 0.00013675 | 0.000203 | 0.0 | 0.43
|
||||
Modify | 0.000443 | 0.0004555 | 0.000471 | 0.0 | 1.42
|
||||
Other | | 0.000238 | | | 0.74
|
||||
Pair | 0.10994 | 0.11386 | 0.11991 | 1.1 | 87.30
|
||||
Neigh | 0.0005877 | 0.00059474 | 0.00059915 | 0.0 | 0.46
|
||||
Comm | 0.0072911 | 0.013476 | 0.017439 | 3.4 | 10.33
|
||||
Output | 0.00014305 | 0.00022113 | 0.00045156 | 0.0 | 0.17
|
||||
Modify | 0.0015786 | 0.0016485 | 0.0017092 | 0.1 | 1.26
|
||||
Other | | 0.0006239 | | | 0.48
|
||||
|
||||
Nlocal: 128.000 ave 131 max 126 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
|
@ -106,15 +105,14 @@ Ave neighs/atom = 16.414062
|
|||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
write_restart restart.equil
|
||||
write_restart restart.equil
|
||||
System init for write_restart ...
|
||||
|
||||
# Test Tersoff/Mod model for Si
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
|
|
@ -122,19 +120,19 @@ Reading restart file ...
|
|||
1 by 2 by 2 MPI processor grid
|
||||
pair style tersoff stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.002 seconds
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
pair_style tersoff/mod
|
||||
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
|
||||
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
|
||||
Reading tersoff/mod potential file Si.tersoff.mod with DATE: 2013-07-26
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
|
@ -153,32 +151,32 @@ Neighbor list info ...
|
|||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.949 | 2.950 | 2.950 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 742.67188 -2210.6446 0 -2172.3685 -6444.2163
|
||||
110 1135.5853 -2234.6974 0 -2172.3908 113.80404
|
||||
120 1462.8415 -2253.8186 0 -2172.3853 10922.229
|
||||
130 1755.9617 -2270.5152 0 -2172.3964 18780.707
|
||||
140 1895.1939 -2277.1484 0 -2172.3965 22357.106
|
||||
150 1869.5375 -2273.2734 0 -2172.3851 22616.492
|
||||
160 1824.0448 -2268.4342 0 -2172.393 19254.299
|
||||
170 1637.9038 -2254.5219 0 -2172.3815 15904.928
|
||||
180 1451.9871 -2240.7199 0 -2172.3771 12064.754
|
||||
190 1362.8248 -2233.1942 0 -2172.3789 7970.534
|
||||
200 1341.1467 -2229.8951 0 -2172.3717 6244.8542
|
||||
Loop time of 0.0389003 on 4 procs for 100 steps with 512 atoms
|
||||
Step Temp E_pair TotEng Econserve Press
|
||||
100 742.67188 -2210.6446 -2161.5897 -2172.3685 -6444.2163
|
||||
110 1135.5853 -2234.6974 -2159.6898 -2172.3908 113.80404
|
||||
120 1462.8415 -2253.8186 -2157.1951 -2172.3853 10922.229
|
||||
130 1755.9617 -2270.5152 -2154.5306 -2172.3964 18780.707
|
||||
140 1895.1939 -2277.1484 -2151.9672 -2172.3965 22357.106
|
||||
150 1869.5375 -2273.2734 -2149.7868 -2172.3851 22616.492
|
||||
160 1824.0448 -2268.4342 -2147.9525 -2172.393 19254.299
|
||||
170 1637.9038 -2254.5219 -2146.3352 -2172.3815 15904.928
|
||||
180 1451.9871 -2240.7199 -2144.8134 -2172.3771 12064.754
|
||||
190 1362.8248 -2233.1942 -2143.177 -2172.3789 7970.534
|
||||
200 1341.1467 -2229.8951 -2141.3097 -2172.3717 6244.8542
|
||||
Loop time of 0.128801 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 222.107 ns/day, 0.108 hours/ns, 2570.678 timesteps/s
|
||||
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 67.080 ns/day, 0.358 hours/ns, 776.389 timesteps/s
|
||||
97.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.031362 | 0.032656 | 0.033605 | 0.5 | 83.95
|
||||
Neigh | 0.000575 | 0.000599 | 0.000613 | 0.0 | 1.54
|
||||
Comm | 0.003768 | 0.004733 | 0.006014 | 1.2 | 12.17
|
||||
Output | 0.000207 | 0.00022525 | 0.000276 | 0.0 | 0.58
|
||||
Modify | 0.000445 | 0.00047975 | 0.0005 | 0.0 | 1.23
|
||||
Other | | 0.0002077 | | | 0.53
|
||||
Pair | 0.10866 | 0.11135 | 0.1163 | 0.9 | 86.45
|
||||
Neigh | 0.0011961 | 0.001219 | 0.0012498 | 0.1 | 0.95
|
||||
Comm | 0.0087612 | 0.013886 | 0.016597 | 2.6 | 10.78
|
||||
Output | 0.00013447 | 0.00028586 | 0.000736 | 0.0 | 0.22
|
||||
Modify | 0.0014391 | 0.0015088 | 0.0015388 | 0.1 | 1.17
|
||||
Other | | 0.0005538 | | | 0.43
|
||||
|
||||
Nlocal: 128.000 ave 135 max 123 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
|
|
@ -197,9 +195,8 @@ Dangerous builds = 0
|
|||
# Test Tersoff/Mod/C model for Si
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
|
|
@ -210,16 +207,16 @@ Reading restart file ...
|
|||
read_restart CPU = 0.001 seconds
|
||||
newton on on
|
||||
pair_style tersoff/mod/c
|
||||
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
|
||||
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
|
||||
Reading tersoff/mod/c potential file Si.tersoff.modc with DATE: 2016-11-09
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
|
@ -238,32 +235,32 @@ Neighbor list info ...
|
|||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.949 | 2.949 | 2.949 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 742.67188 -2221.9308 0 -2183.6547 -11721.269
|
||||
110 1106.895 -2244.1196 0 -2183.6843 -2359.7819
|
||||
120 1327.6674 -2256.3155 0 -2183.6767 7904.6604
|
||||
130 1487.0219 -2264.3656 0 -2183.6707 14660.783
|
||||
140 1709.1746 -2276.4761 0 -2183.6886 19298.791
|
||||
150 1710.6528 -2274.1129 0 -2183.6764 22026.559
|
||||
160 1651.0659 -2267.9877 0 -2183.6699 20916.722
|
||||
170 1632.7705 -2264.7081 0 -2183.6777 17339.031
|
||||
180 1477.693 -2252.4683 0 -2183.6706 12563.594
|
||||
190 1310.8768 -2239.5419 0 -2183.6581 9591.0484
|
||||
200 1356.7172 -2240.5315 0 -2183.668 5584.6734
|
||||
Loop time of 0.039244 on 4 procs for 100 steps with 512 atoms
|
||||
Step Temp E_pair TotEng Econserve Press
|
||||
100 742.67188 -2221.9308 -2172.8759 -2183.6547 -11721.269
|
||||
110 1106.895 -2244.1196 -2171.007 -2183.6843 -2359.7819
|
||||
120 1327.6674 -2256.3155 -2168.6205 -2183.6767 7904.6604
|
||||
130 1487.0219 -2264.3656 -2166.1449 -2183.6707 14660.783
|
||||
140 1709.1746 -2276.4761 -2163.5818 -2183.6886 19298.791
|
||||
150 1710.6528 -2274.1129 -2161.1209 -2183.6764 22026.559
|
||||
160 1651.0659 -2267.9877 -2158.9316 -2183.6699 20916.722
|
||||
170 1632.7705 -2264.7081 -2156.8605 -2183.6777 17339.031
|
||||
180 1477.693 -2252.4683 -2154.8638 -2183.6706 12563.594
|
||||
190 1310.8768 -2239.5419 -2152.9559 -2183.6581 9591.0484
|
||||
200 1356.7172 -2240.5315 -2150.9177 -2183.668 5584.6734
|
||||
Loop time of 0.131975 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 220.161 ns/day, 0.109 hours/ns, 2548.160 timesteps/s
|
||||
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 65.467 ns/day, 0.367 hours/ns, 757.717 timesteps/s
|
||||
97.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.03126 | 0.032782 | 0.033915 | 0.5 | 83.53
|
||||
Neigh | 0.000599 | 0.000707 | 0.000821 | 0.0 | 1.80
|
||||
Comm | 0.00363 | 0.004893 | 0.006493 | 1.5 | 12.47
|
||||
Output | 0.000122 | 0.0001425 | 0.000192 | 0.0 | 0.36
|
||||
Modify | 0.000497 | 0.00050925 | 0.000522 | 0.0 | 1.30
|
||||
Other | | 0.0002105 | | | 0.54
|
||||
Pair | 0.11186 | 0.11507 | 0.11812 | 0.7 | 87.19
|
||||
Neigh | 0.0011823 | 0.0011939 | 0.0012088 | 0.0 | 0.90
|
||||
Comm | 0.010214 | 0.0134 | 0.016663 | 2.0 | 10.15
|
||||
Output | 0.000139 | 0.000296 | 0.00076294 | 0.0 | 0.22
|
||||
Modify | 0.0014501 | 0.0014552 | 0.0014606 | 0.0 | 1.10
|
||||
Other | | 0.0005632 | | | 0.43
|
||||
|
||||
Nlocal: 128.000 ave 133 max 124 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
|
|
@ -282,9 +279,8 @@ Dangerous builds = 0
|
|||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
|
|
@ -292,29 +288,29 @@ Reading restart file ...
|
|||
1 by 2 by 2 MPI processor grid
|
||||
pair style tersoff stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
read_restart CPU = 0.007 seconds
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
Changing box ...
|
||||
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
|
@ -333,32 +329,32 @@ Neighbor list info ...
|
|||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.952 | 2.952 | 2.952 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 742.67188 -2973.8527 0 -2935.5766 3438975.9
|
||||
110 4061.1085 -3183.2489 0 -2930.1208 2211712.7
|
||||
120 4120.3231 -3187.0108 0 -2928.3047 2166764.3
|
||||
130 3602.7602 -3158.5939 0 -2926.6167 2244475.7
|
||||
140 3222.7773 -3141.7275 0 -2925.5369 2161607
|
||||
150 3487.4703 -3163.7495 0 -2921.2462 2222150.2
|
||||
160 3436.3009 -3169.4234 0 -2920.8775 2144368.7
|
||||
170 3308.1796 -3170.3773 0 -2920.8967 2223612.9
|
||||
180 3304.3776 -3178.7805 0 -2920.102 2072546.6
|
||||
190 3217.3561 -3180.7963 0 -2918.4548 2118776.2
|
||||
200 3041.6832 -3176.1794 0 -2916.5787 2130124.6
|
||||
Loop time of 0.0488862 on 4 procs for 100 steps with 512 atoms
|
||||
Step Temp E_pair TotEng Econserve Press
|
||||
100 742.67188 -2973.8527 -2924.7978 -2935.5766 3438975.9
|
||||
110 4061.1085 -3183.2489 -2915.0049 -2930.1208 2211712.7
|
||||
120 4120.3231 -3187.0108 -2914.8555 -2928.3047 2166764.3
|
||||
130 3602.7602 -3158.5939 -2920.6246 -2926.6167 2244475.7
|
||||
140 3222.7773 -3141.7275 -2928.8568 -2925.5369 2161607
|
||||
150 3487.4703 -3163.7495 -2933.3954 -2921.2462 2222150.2
|
||||
160 3436.3009 -3169.4234 -2942.449 -2920.8775 2144368.7
|
||||
170 3308.1796 -3170.3773 -2951.8656 -2920.8967 2223612.9
|
||||
180 3304.3776 -3178.7805 -2960.52 -2920.102 2072546.6
|
||||
190 3217.3561 -3180.7963 -2968.2837 -2918.4548 2118776.2
|
||||
200 3041.6832 -3176.1794 -2975.2703 -2916.5787 2130124.6
|
||||
Loop time of 0.171186 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 176.737 ns/day, 0.136 hours/ns, 2045.565 timesteps/s
|
||||
93.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 50.471 ns/day, 0.476 hours/ns, 584.160 timesteps/s
|
||||
96.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.037364 | 0.039346 | 0.041066 | 0.8 | 80.49
|
||||
Neigh | 0.001207 | 0.0012568 | 0.00136 | 0.2 | 2.57
|
||||
Comm | 0.005218 | 0.007064 | 0.009117 | 1.9 | 14.45
|
||||
Output | 0.000173 | 0.00020325 | 0.000277 | 0.0 | 0.42
|
||||
Modify | 0.000709 | 0.000715 | 0.000723 | 0.0 | 1.46
|
||||
Other | | 0.0003008 | | | 0.62
|
||||
Pair | 0.14009 | 0.14402 | 0.15181 | 1.2 | 84.13
|
||||
Neigh | 0.0023134 | 0.0024782 | 0.0026977 | 0.3 | 1.45
|
||||
Comm | 0.013972 | 0.02211 | 0.026362 | 3.3 | 12.92
|
||||
Output | 0.00015235 | 0.0003258 | 0.00084186 | 0.0 | 0.19
|
||||
Modify | 0.0016432 | 0.0017257 | 0.0018435 | 0.2 | 1.01
|
||||
Other | | 0.0005236 | | | 0.31
|
||||
|
||||
Nlocal: 128.000 ave 132 max 123 min
|
||||
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||
|
|
@ -377,9 +373,8 @@ Dangerous builds = 0
|
|||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
|
|
@ -389,27 +384,27 @@ Reading restart file ...
|
|||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
Changing box ...
|
||||
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
|
||||
|
||||
pair_style tersoff shift 0.05
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
|
@ -428,32 +423,32 @@ Neighbor list info ...
|
|||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.952 | 2.952 | 2.952 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 742.67188 -3294.0266 0 -3255.7505 1615779.4
|
||||
110 2870.7114 -3432.8485 0 -3257.629 1053310.6
|
||||
120 2898.0798 -3431.4968 0 -3256.6851 1223402.3
|
||||
130 2708.4483 -3419.0142 0 -3256.436 1105893.8
|
||||
140 2307.8661 -3394.1268 0 -3256.1686 1148075.8
|
||||
150 2215.3423 -3390.1427 0 -3255.8733 1138540
|
||||
160 2515.488 -3412.6704 0 -3255.1731 1122902.8
|
||||
170 2485.7109 -3415.0402 0 -3255.3787 1097748.5
|
||||
180 2327.476 -3408.2463 0 -3254.6537 1061602.6
|
||||
190 2339.5966 -3413.3961 0 -3254.7496 1088059
|
||||
200 2260.5961 -3411.477 0 -3254.0771 1104581.5
|
||||
Loop time of 0.0409132 on 4 procs for 100 steps with 512 atoms
|
||||
Step Temp E_pair TotEng Econserve Press
|
||||
100 742.67188 -3294.0266 -3244.9717 -3255.7505 1615779.4
|
||||
110 2870.7114 -3432.8485 -3243.2324 -3257.629 1053310.6
|
||||
120 2898.0798 -3431.4968 -3240.0731 -3256.6851 1223402.3
|
||||
130 2708.4483 -3419.0142 -3240.1159 -3256.436 1105893.8
|
||||
140 2307.8661 -3394.1268 -3241.6877 -3256.1686 1148075.8
|
||||
150 2215.3423 -3390.1427 -3243.8151 -3255.8733 1138540
|
||||
160 2515.488 -3412.6704 -3246.5175 -3255.1731 1122902.8
|
||||
170 2485.7109 -3415.0402 -3250.8542 -3255.3787 1097748.5
|
||||
180 2327.476 -3408.2463 -3254.512 -3254.6537 1061602.6
|
||||
190 2339.5966 -3413.3961 -3258.8612 -3254.7496 1088059
|
||||
200 2260.5961 -3411.477 -3262.1603 -3254.0771 1104581.5
|
||||
Loop time of 0.15156 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 211.179 ns/day, 0.114 hours/ns, 2444.196 timesteps/s
|
||||
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 57.007 ns/day, 0.421 hours/ns, 659.806 timesteps/s
|
||||
96.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.03285 | 0.033327 | 0.03406 | 0.3 | 81.46
|
||||
Neigh | 0.000975 | 0.0010677 | 0.001184 | 0.2 | 2.61
|
||||
Comm | 0.004915 | 0.005528 | 0.006044 | 0.7 | 13.51
|
||||
Output | 0.000129 | 0.0001535 | 0.000226 | 0.0 | 0.38
|
||||
Modify | 0.000564 | 0.0005885 | 0.000604 | 0.0 | 1.44
|
||||
Other | | 0.0002483 | | | 0.61
|
||||
Pair | 0.12637 | 0.13067 | 0.13398 | 0.8 | 86.22
|
||||
Neigh | 0.0019262 | 0.0020029 | 0.0021148 | 0.2 | 1.32
|
||||
Comm | 0.012843 | 0.01629 | 0.020752 | 2.2 | 10.75
|
||||
Output | 0.00014877 | 0.00030798 | 0.00078011 | 0.0 | 0.20
|
||||
Modify | 0.0015197 | 0.0016043 | 0.0017824 | 0.3 | 1.06
|
||||
Other | | 0.0006804 | | | 0.45
|
||||
|
||||
Nlocal: 128.000 ave 133 max 123 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
Loading…
Reference in New Issue