mv examples/gcmc to mc, add 2 scripts for fix mol/swap
This commit is contained in:
Steve Plimpton
44
examples/mc/CO2.txt
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44
examples/mc/CO2.txt
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# CO2 molecule file. TraPPE model.
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3 atoms
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2 bonds
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1 angles
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Coords
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1 0.0 0.0 0.0
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2 -1.16 0.0 0.0
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3 1.16 0.0 0.0
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Types
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1 1
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2 2
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3 2
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Charges
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1 0.7
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2 -0.35
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3 -0.35
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Bonds
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1 1 1 2
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2 1 1 3
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Angles
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1 1 2 1 3
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Special Bond Counts
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1 2 0 0
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2 1 1 0
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3 1 1 0
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Special Bonds
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1 2 3
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2 1 3
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3 1 2
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62
examples/mc/H2O.txt
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62
examples/mc/H2O.txt
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@ -0,0 +1,62 @@
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# Water molecule. SPC/E model.
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3 atoms
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2 bonds
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1 angles
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Coords
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1 1.12456 0.09298 1.27452
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2 1.53683 0.75606 1.89928
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3 0.49482 0.56390 0.65678
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Types
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1 1
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2 2
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3 2
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Charges
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1 -0.8472
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2 0.4236
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3 0.4236
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Bonds
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1 1 1 2
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2 1 1 3
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Angles
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1 1 2 1 3
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Shake Flags
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1 1
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2 1
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3 1
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Shake Atoms
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1 1 2 3
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2 1 2 3
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3 1 2 3
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Shake Bond Types
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1 1 1 1
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2 1 1 1
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3 1 1 1
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Special Bond Counts
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1 2 0 0
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2 1 1 0
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3 1 1 0
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Special Bonds
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1 2 3
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2 1 3
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3 1 2
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11733
examples/mc/data.bead
Executable file
11733
examples/mc/data.bead
Executable file
File diff suppressed because it is too large
Load Diff
17322
examples/mc/data.spce
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17322
examples/mc/data.spce
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File diff suppressed because it is too large
Load Diff
2019
examples/mc/data.widom.lj
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2019
examples/mc/data.widom.lj
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File diff suppressed because it is too large
Load Diff
97
examples/mc/in.gcmc.co2
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97
examples/mc/in.gcmc.co2
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@ -0,0 +1,97 @@
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# GCMC for CO2 molecular fluid, rigid/small dynamics
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# Rigid CO2 TraPPE model
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# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
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# mixtures containing alkanes, carbon dioxide and
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# nitrogen AIChE J., 47,1676-1682 (2001)].
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# variables available on command line
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variable mu index -8.1
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variable disp index 0.5
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variable temp index 338.0
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variable lbox index 10.0
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variable spacing index 5.0
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# global model settings
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units real
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atom_style full
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boundary p p p
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pair_style lj/cut/coul/long 14
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pair_modify mix arithmetic tail yes
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kspace_style ewald 0.0001
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bond_style harmonic
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angle_style harmonic
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# box, start molecules on simple cubic lattice
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lattice sc ${spacing}
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region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
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create_box 2 box &
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bond/types 1 &
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angle/types 1 &
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extra/bond/per/atom 2 &
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extra/angle/per/atom 1 &
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extra/special/per/atom 2
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molecule co2mol CO2.txt
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create_atoms 0 box mol co2mol 464563 units box
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# rigid CO2 TraPPE model
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pair_coeff 1 1 0.053649 2.8
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pair_coeff 2 2 0.156973 3.05
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bond_coeff 1 0 1.16
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angle_coeff 1 0 180
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# masses
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mass 1 12.0107
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mass 2 15.9994
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# MD settings
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group co2 type 1 2
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neighbor 2.0 bin
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neigh_modify every 1 delay 10 check yes
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velocity all create ${temp} 54654
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timestep 1.0
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# rigid constraints with thermostat
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fix myrigid co2 rigid/small molecule mol co2mol
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# dynamically update fix rigid/nvt/small temperature ndof
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fix_modify myrigid dynamic/dof yes
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# gcmc
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variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
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fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
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co2mol tfac_insert ${tfac} group co2 rigid myrigid
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# atom counts
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variable carbon atom "type==1"
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variable oxygen atom "type==2"
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group carbon dynamic co2 var carbon
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group oxygen dynamic co2 var oxygen
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variable nC equal count(carbon)
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variable nO equal count(oxygen)
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# output
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variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
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variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
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variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
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variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
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# dynamically update default temperature ndof
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compute_modify thermo_temp dynamic/dof yes
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thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
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thermo 1000
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# run
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run 20000
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100
examples/mc/in.gcmc.h2o
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100
examples/mc/in.gcmc.h2o
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@ -0,0 +1,100 @@
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# fix gcmc example with fix shake
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# variables available on command line
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variable mu index -8.1
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variable disp index 0.5
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variable temp index 338.0
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variable lbox index 10.0
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variable spacing index 5.0
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# global model settings
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units real
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atom_style full
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boundary p p p
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pair_style lj/cut/coul/long 14
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pair_modify mix arithmetic tail yes
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kspace_style ewald 0.0001
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bond_style harmonic
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angle_style harmonic
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# box, start molecules on simple cubic lattice
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lattice sc ${spacing}
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region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
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create_box 2 box &
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bond/types 1 &
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angle/types 1 &
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extra/bond/per/atom 2 &
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extra/angle/per/atom 1 &
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extra/special/per/atom 2
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molecule h2omol H2O.txt
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create_atoms 0 box mol h2omol 464563 units box
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# rigid SPC/E water model
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pair_coeff 1 1 0.15535 3.166
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pair_coeff * 2 0.0000 0.0000
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bond_coeff 1 1000 1.0
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angle_coeff 1 100 109.47
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# masses
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mass 1 15.9994
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mass 2 1.0
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# MD settings
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group h2o type 1 2
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neighbor 2.0 bin
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neigh_modify every 1 delay 1 check yes
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velocity all create ${temp} 54654
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timestep 1.0
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minimize 0.0 0.0 100 1000
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reset_timestep 0
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# rigid constraints with thermostat
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fix mynvt h2o nvt temp ${temp} ${temp} 100
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fix wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol
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# important to make temperature dofs dynamic
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compute_modify thermo_temp dynamic/dof yes
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compute_modify mynvt_temp dynamic/dof yes
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run 1000
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reset_timestep 0
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# gcmc
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variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
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fix mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
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h2omol tfac_insert ${tfac} group h2o shake wshake
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# atom counts
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variable oxygen atom "type==1"
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variable hydrogen atom "type==2"
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group oxygen dynamic all var oxygen
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group hydrogen dynamic all var hydrogen
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variable nO equal count(oxygen)
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variable nH equal count(hydrogen)
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# output
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variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
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variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
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variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
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variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
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thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
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thermo 1000
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# run
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run 20000
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70
examples/mc/in.gcmc.lj
Normal file
70
examples/mc/in.gcmc.lj
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@ -0,0 +1,70 @@
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# GCMC for LJ simple fluid, no dynamics
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# T = 2.0
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# rho ~ 0.5
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# p ~ 1.5
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# mu_ex ~ 0.0
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# comparable to Frenkel and Smit GCMC Case Study, Figure 5.8
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# variables modifiable using -var command line switch
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variable mu index -1.25
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variable temp index 2.0
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variable disp index 1.0
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variable lbox index 5.0
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# global model settings
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units lj
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atom_style atomic
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pair_style lj/cut 3.0
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pair_modify tail no # turn of to avoid triggering full_energy
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# box
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region box block 0 ${lbox} 0 ${lbox} 0 ${lbox}
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create_box 1 box
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# lj parameters
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pair_coeff * * 1.0 1.0
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mass * 1.0
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# we recommend setting up a dedicated group for gcmc
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group gcmcgroup type 1
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# gcmc
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fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
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# atom count
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variable type1 atom "type==1"
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group type1 dynamic gcmcgroup var type1
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variable n1 equal count(type1)
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# averaging
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variable rho equal density
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variable p equal press
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variable nugget equal 1.0e-8
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variable lambda equal 1.0
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variable muex equal ${mu}-${temp}*ln(density*${lambda}+${nugget})
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fix ave all ave/time 10 100 1000 v_rho v_p v_muex v_n1 ave one file rho_vs_p.dat
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variable rhoav equal f_ave[1]
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variable pav equal f_ave[2]
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variable muexav equal f_ave[3]
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variable n1av equal f_ave[4]
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# output
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variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+${nugget})
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variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+${nugget})
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variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
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compute_modify thermo_temp dynamic yes
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thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
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thermo 1000
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# run
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run 10000
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44
examples/mc/in.mixed
Executable file
44
examples/mc/in.mixed
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@ -0,0 +1,44 @@
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# test script for fix mol/swap
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# initial system is 50/50 chains of type 1 and type 2
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# b/c epsilon12 is set to 1.02 (weakly same as 1/1 or 1/2) the
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# system will stay in equilibrium as a mix of both chain types
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# fix mol/swap helps this happen quickly
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# see the last 2 columns of thermo output for counts of 2 chain types
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units lj
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atom_style angle
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neighbor 0.36 bin
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neigh_modify delay 0
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pair_style lj/cut 1.1224620483
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bond_style fene
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angle_style cosine
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special_bonds lj 0.0 1.0 1.0
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read_data data.bead
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pair_coeff * * 1.0 1.0 1.1224620483
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pair_coeff 1 2 1.02 1.0 1.1224620483
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bond_coeff 1 30.0 1.5 1.0 1.0
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angle_coeff 1 1.500
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pair_modify shift yes
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variable vt1 atom type==1
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variable vt2 atom type==2
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group g1 dynamic all var vt1 every 100
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group g2 dynamic all var vt2 every 100
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variable count1 equal count(g1)
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variable count2 equal count(g2)
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timestep 0.010
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fix 1 all langevin 1.0 1.0 100.0 702547
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fix 2 all nve
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fix 3 all mol/swap 100 1 1 2 482794 1.0
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compute p all pressure thermo_temp
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thermo 1000
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thermo_style custom step temp etotal press f_3[1] f_3[2] v_count1 v_count2
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run 50000
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44
examples/mc/in.pure
Executable file
44
examples/mc/in.pure
Executable file
@ -0,0 +1,44 @@
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# test script for fix mol/swap
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# initial system is 50/50 chains of type 1 and type 2
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# b/c epsilon12 is set to 1.1 (stronger than 1/1 or 2/2) the
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# system will go to equilibrium as mostly one type or the other
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# fix mol/swap helps this happen quickly
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# see the last 2 columns of thermo output for counts of 2 chain types
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units lj
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atom_style angle
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neighbor 0.36 bin
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neigh_modify delay 0
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pair_style lj/cut 1.1224620483
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bond_style fene
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angle_style cosine
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special_bonds lj 0.0 1.0 1.0
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read_data data.bead
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pair_coeff * * 1.0 1.0 1.1224620483
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pair_coeff 1 2 1.1 1.0 1.1224620483
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bond_coeff 1 30.0 1.5 1.0 1.0
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angle_coeff 1 1.500
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pair_modify shift yes
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variable vt1 atom type==1
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variable vt2 atom type==2
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group g1 dynamic all var vt1 every 100
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group g2 dynamic all var vt2 every 100
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variable count1 equal count(g1)
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variable count2 equal count(g2)
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timestep 0.010
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fix 1 all langevin 1.0 1.0 100.0 702547
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fix 2 all nve
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fix 3 all mol/swap 100 1 1 2 482794 1.0
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compute p all pressure thermo_temp
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thermo 1000
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thermo_style custom step temp etotal press f_3[1] f_3[2] v_count1 v_count2
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run 50000
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28
examples/mc/in.widom.lj
Normal file
28
examples/mc/in.widom.lj
Normal file
@ -0,0 +1,28 @@
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# Kob and Andersen model Phys. Rev. E 51, 4626 (1995)
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units lj
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atom_style atomic
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pair_style lj/cut 2.5
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pair_modify shift yes
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read_data data.widom.lj
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pair_coeff 1 1 1.0 1.0 2.5
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pair_coeff 1 2 1.5 0.8 2.0
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pair_coeff 2 2 0.5 0.88 2.2
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neighbor 0.3 bin
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neigh_modify delay 0 every 5 check yes
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fix mywidom all widom 10 100000 2 29494 0.75
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fix 1 all langevin 0.75 0.75 0.1 48279 zero yes
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fix 2 all nve
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timestep 0.002
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thermo_style custom step temp pe etotal press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
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thermo 10
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run 100
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38
examples/mc/in.widom.spce
Normal file
38
examples/mc/in.widom.spce
Normal file
@ -0,0 +1,38 @@
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units real
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||||
dimension 3
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boundary p p p
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||||
atom_style full
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||||
|
||||
pair_style lj/cut/coul/long 10.0
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||||
bond_style harmonic
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||||
angle_style harmonic
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||||
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||||
read_data data.spce
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||||
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||||
molecule h2omol H2O.txt
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||||
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||||
### Flexible SPC/E Potential Parameters ###
|
||||
### Zhang et al., Fluid Phase Equilibria, 262 (2007) 210-216 ###
|
||||
pair_coeff 1 1 0.1502629 3.1169
|
||||
pair_coeff 1 2 0.0341116368 2.04845
|
||||
pair_coeff 2 2 0.00774378 0.98
|
||||
|
||||
bond_coeff 1 176.864 0.9611
|
||||
angle_coeff 1 42.1845 109.4712
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
fix mywidom all widom 10 20 0 29494 298 mol h2omol
|
||||
|
||||
fix 2 all nvt temp 298.0 298.0 100.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 10 every 2 check yes
|
||||
|
||||
|
||||
#run variables
|
||||
timestep 0.5
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal pe temp press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
|
||||
|
||||
run 100
|
||||
164
examples/mc/log.13Oct21.mixed.g++.4
Normal file
164
examples/mc/log.13Oct21.mixed.g++.4
Normal file
@ -0,0 +1,164 @@
|
||||
LAMMPS (29 Sep 2021)
|
||||
# test script for fix mol/swap
|
||||
# initial system is 50/50 chains of type 1 and type 2
|
||||
# b/c epsilon12 is set to 1.02 (weakly same as 1/1 or 1/2) the
|
||||
# system will stay in equilibrium as a mix of both chain types
|
||||
# fix mol/swap helps this happen quickly
|
||||
# see the last 2 columns of thermo output for counts of 2 chain types
|
||||
|
||||
units lj
|
||||
atom_style angle
|
||||
neighbor 0.36 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
pair_style lj/cut 1.1224620483
|
||||
bond_style fene
|
||||
angle_style cosine
|
||||
special_bonds lj 0.0 1.0 1.0
|
||||
|
||||
read_data data.bead
|
||||
Reading data file ...
|
||||
orthogonal box = (-8.2115700 -8.2115700 -8.2115700) to (8.2115700 8.2115700 8.2115700)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
4000 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
3900 bonds
|
||||
reading angles ...
|
||||
3800 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.028 seconds
|
||||
|
||||
pair_coeff * * 1.0 1.0 1.1224620483
|
||||
pair_coeff 1 2 1.02 1.0 1.1224620483
|
||||
bond_coeff 1 30.0 1.5 1.0 1.0
|
||||
angle_coeff 1 1.500
|
||||
pair_modify shift yes
|
||||
|
||||
variable vt1 atom type==1
|
||||
variable vt2 atom type==2
|
||||
group g1 dynamic all var vt1 every 100
|
||||
dynamic group g1 defined
|
||||
group g2 dynamic all var vt2 every 100
|
||||
dynamic group g2 defined
|
||||
variable count1 equal count(g1)
|
||||
variable count2 equal count(g2)
|
||||
|
||||
timestep 0.010
|
||||
|
||||
fix 1 all langevin 1.0 1.0 100.0 702547
|
||||
fix 2 all nve
|
||||
fix 3 all mol/swap 100 1 1 2 482794 1.0
|
||||
|
||||
compute p all pressure thermo_temp
|
||||
thermo 1000
|
||||
thermo_style custom step temp etotal press f_3[1] f_3[2] v_count1 v_count2
|
||||
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.482462
|
||||
ghost atom cutoff = 1.482462
|
||||
binsize = 0.74123102, bins = 23 23 23
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
WARNING: Communication cutoff 1.4824620483 is shorter than a bond length based estimate of 1.815. This may lead to errors. (../comm.cpp:728)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.313 | 5.314 | 5.314 Mbytes
|
||||
Step Temp TotEng Press f_3[1] f_3[2] v_count1 v_count2
|
||||
0 0 21.451627 5.079399 0 0 2000 2000
|
||||
1000 0.49011138 21.59359 4.2337989 10 10 2000 2000
|
||||
2000 0.55288866 21.724374 4.4596786 20 20 2080 1920
|
||||
3000 0.59299724 21.844178 4.6112243 30 29 2280 1720
|
||||
4000 0.64746348 21.964318 4.9463669 40 39 2280 1720
|
||||
5000 0.67853936 22.053147 5.1950218 50 48 2320 1680
|
||||
6000 0.70751144 22.147453 5.0636869 60 58 2240 1760
|
||||
7000 0.73570064 22.233705 5.4872622 70 68 2160 1840
|
||||
8000 0.7677554 22.312938 5.4283736 80 77 2360 1640
|
||||
9000 0.78493237 22.383155 5.8547233 90 87 2440 1560
|
||||
10000 0.80634514 22.449402 5.8785731 100 96 2400 1600
|
||||
11000 0.82563194 22.475286 5.8193738 110 104 2400 1600
|
||||
12000 0.81684024 22.527492 6.0323967 120 114 2320 1680
|
||||
13000 0.84497155 22.567888 6.0488755 130 122 2240 1760
|
||||
14000 0.85452242 22.606908 6.1983634 140 132 2080 1920
|
||||
15000 0.88109242 22.654336 6.1408279 150 141 1960 2040
|
||||
16000 0.88925915 22.707597 6.1560975 160 150 2000 2000
|
||||
17000 0.91598439 22.762791 6.1071728 170 160 2000 2000
|
||||
18000 0.92453211 22.778304 6.3330693 180 170 2240 1760
|
||||
19000 0.92839551 22.797316 6.2917909 190 180 2000 2000
|
||||
20000 0.93054033 22.819289 6.091701 200 189 2200 1800
|
||||
21000 0.93955351 22.844135 6.5833013 210 198 2000 2000
|
||||
22000 0.94454858 22.856272 6.5661753 220 207 2200 1800
|
||||
23000 0.95446407 22.878735 6.5957294 230 216 2160 1840
|
||||
24000 0.94748257 22.894539 6.6187447 240 226 1920 2080
|
||||
25000 0.95732202 22.912292 6.4795471 250 236 1680 2320
|
||||
26000 0.96970172 22.908988 6.537366 260 245 1720 2280
|
||||
27000 0.96032166 22.924899 6.6238248 270 255 1960 2040
|
||||
28000 0.96197769 22.9358 6.8926097 280 264 1920 2080
|
||||
29000 0.98745595 22.964694 6.5839025 290 271 2040 1960
|
||||
30000 0.99264869 22.947884 6.3893499 300 280 1920 2080
|
||||
31000 0.96953069 22.957927 6.6616047 310 289 1800 2200
|
||||
32000 0.99955117 22.963979 6.5958456 320 298 1680 2320
|
||||
33000 0.97090103 22.969029 6.9087296 330 307 1800 2200
|
||||
34000 0.99818457 22.988477 6.6471994 340 316 1920 2080
|
||||
35000 0.9965288 22.992883 6.9691785 350 325 2040 1960
|
||||
36000 0.99533174 22.983774 6.6585089 360 334 2000 2000
|
||||
37000 0.98819278 22.995387 6.618802 370 344 2080 1920
|
||||
38000 0.99598576 22.991892 6.7536669 380 354 2080 1920
|
||||
39000 0.99312702 22.989239 6.4028165 390 364 2080 1920
|
||||
40000 1.0035821 23.001944 6.9307671 400 374 1920 2080
|
||||
41000 0.99914733 23.00134 6.6251677 410 383 1880 2120
|
||||
42000 0.98054536 22.981781 6.5918554 420 393 1880 2120
|
||||
43000 0.99413829 23.008 6.7390795 430 403 1720 2280
|
||||
44000 0.98867961 23.00521 6.8505543 440 412 1600 2400
|
||||
45000 0.99626811 23.019995 6.827741 450 421 1640 2360
|
||||
46000 1.0186043 23.020759 6.6195562 460 430 1680 2320
|
||||
47000 1.0121335 23.019271 6.6022102 470 439 1800 2200
|
||||
48000 0.99883756 23.013973 6.5255522 480 448 1920 2080
|
||||
49000 0.99425223 23.022708 6.609746 490 458 2240 1760
|
||||
50000 0.99505489 23.012641 6.4592863 500 468 2240 1760
|
||||
Loop time of 19.4175 on 4 procs for 50000 steps with 4000 atoms
|
||||
|
||||
Performance: 2224796.830 tau/day, 2574.996 timesteps/s
|
||||
95.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.5467 | 2.6684 | 2.7896 | 6.3 | 13.74
|
||||
Bond | 2.3037 | 2.4117 | 2.5085 | 5.3 | 12.42
|
||||
Neigh | 7.3597 | 7.3633 | 7.3673 | 0.1 | 37.92
|
||||
Comm | 3.0482 | 3.2694 | 3.4997 | 10.2 | 16.84
|
||||
Output | 0.0014609 | 0.0017069 | 0.0021793 | 0.7 | 0.01
|
||||
Modify | 2.9624 | 3.0581 | 3.1424 | 4.7 | 15.75
|
||||
Other | | 0.6447 | | | 3.32
|
||||
|
||||
Nlocal: 1000.00 ave 1013 max 986 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
Nghost: 1186.25 ave 1198 max 1178 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Neighs: 4927.00 ave 5028 max 4790 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
|
||||
Total # of neighbors = 19708
|
||||
Ave neighs/atom = 4.9270000
|
||||
Ave special neighs/atom = 5.7000000
|
||||
Neighbor list builds = 10721
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:19
|
||||
164
examples/mc/log.13Oct21.pure.g++.4
Normal file
164
examples/mc/log.13Oct21.pure.g++.4
Normal file
@ -0,0 +1,164 @@
|
||||
LAMMPS (29 Sep 2021)
|
||||
# test script for fix mol/swap
|
||||
# initial system is 50/50 chains of type 1 and type 2
|
||||
# b/c epsilon12 is set to 1.1 (stronger than 1/1 or 2/2) the
|
||||
# system will go to equilibrium as mostly one type or the other
|
||||
# fix mol/swap helps this happen quickly
|
||||
# see the last 2 columns of thermo output for counts of 2 chain types
|
||||
|
||||
units lj
|
||||
atom_style angle
|
||||
neighbor 0.36 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
pair_style lj/cut 1.1224620483
|
||||
bond_style fene
|
||||
angle_style cosine
|
||||
special_bonds lj 0.0 1.0 1.0
|
||||
|
||||
read_data data.bead
|
||||
Reading data file ...
|
||||
orthogonal box = (-8.2115700 -8.2115700 -8.2115700) to (8.2115700 8.2115700 8.2115700)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
4000 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
3900 bonds
|
||||
reading angles ...
|
||||
3800 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.034 seconds
|
||||
|
||||
pair_coeff * * 1.0 1.0 1.1224620483
|
||||
pair_coeff 1 2 1.1 1.0 1.1224620483
|
||||
bond_coeff 1 30.0 1.5 1.0 1.0
|
||||
angle_coeff 1 1.500
|
||||
pair_modify shift yes
|
||||
|
||||
variable vt1 atom type==1
|
||||
variable vt2 atom type==2
|
||||
group g1 dynamic all var vt1 every 100
|
||||
dynamic group g1 defined
|
||||
group g2 dynamic all var vt2 every 100
|
||||
dynamic group g2 defined
|
||||
variable count1 equal count(g1)
|
||||
variable count2 equal count(g2)
|
||||
|
||||
timestep 0.010
|
||||
|
||||
fix 1 all langevin 1.0 1.0 100.0 702547
|
||||
fix 2 all nve
|
||||
fix 3 all mol/swap 100 1 1 2 482794 1.0
|
||||
|
||||
compute p all pressure thermo_temp
|
||||
thermo 1000
|
||||
thermo_style custom step temp etotal press f_3[1] f_3[2] v_count1 v_count2
|
||||
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.482462
|
||||
ghost atom cutoff = 1.482462
|
||||
binsize = 0.74123102, bins = 23 23 23
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
WARNING: Communication cutoff 1.4824620483 is shorter than a bond length based estimate of 1.815. This may lead to errors. (../comm.cpp:728)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.313 | 5.314 | 5.314 Mbytes
|
||||
Step Temp TotEng Press f_3[1] f_3[2] v_count1 v_count2
|
||||
0 0 21.4699 5.230121 0 0 2000 2000
|
||||
1000 0.50228459 21.61044 4.3659303 10 9 1960 2040
|
||||
2000 0.55721903 21.75955 4.5695439 20 17 1960 2040
|
||||
3000 0.61139287 21.892943 4.6514755 30 26 2240 1760
|
||||
4000 0.65767189 22.002303 5.1854503 40 33 2280 1720
|
||||
5000 0.69383416 22.110271 5.3803498 50 41 2280 1720
|
||||
6000 0.72692038 22.205887 5.1756569 60 49 2280 1720
|
||||
7000 0.77151336 22.306777 5.5743555 70 56 2240 1760
|
||||
8000 0.78606858 22.37036 5.7745208 80 64 2560 1440
|
||||
9000 0.79363653 22.420931 5.7369418 90 71 2680 1320
|
||||
10000 0.82352629 22.488759 6.0238896 100 76 2720 1280
|
||||
11000 0.83867685 22.534887 6.1263771 110 82 2800 1200
|
||||
12000 0.85335127 22.590281 6.1499954 120 86 2800 1200
|
||||
13000 0.86430985 22.632068 6.1654016 130 89 2760 1240
|
||||
14000 0.88057592 22.680253 6.2162735 140 94 2800 1200
|
||||
15000 0.89326694 22.719731 6.4789839 150 97 2760 1240
|
||||
16000 0.90667644 22.737367 6.214481 160 101 2760 1240
|
||||
17000 0.91190336 22.758572 6.2293336 170 105 2600 1400
|
||||
18000 0.93182455 22.782019 6.2865382 180 111 2680 1320
|
||||
19000 0.93002139 22.797048 6.5579988 190 117 2600 1400
|
||||
20000 0.92396243 22.796108 6.6207461 200 122 2800 1200
|
||||
21000 0.92949808 22.802813 6.3753268 210 125 2920 1080
|
||||
22000 0.93415719 22.807112 6.4696121 220 130 3040 960
|
||||
23000 0.9214833 22.82116 6.4146288 230 131 3080 920
|
||||
24000 0.95693685 22.839738 6.4035728 240 135 2920 1080
|
||||
25000 0.95421851 22.865199 6.4510751 250 138 2880 1120
|
||||
26000 0.95476555 22.878082 6.4652888 260 145 3000 1000
|
||||
27000 0.95773535 22.880671 6.757952 270 149 3000 1000
|
||||
28000 0.95405332 22.896053 6.7425175 280 155 3080 920
|
||||
29000 0.95955713 22.904144 6.6672832 290 161 3240 760
|
||||
30000 0.95521498 22.886699 6.6197941 300 164 3360 640
|
||||
31000 0.96431176 22.91094 6.6373887 310 168 3440 560
|
||||
32000 0.96592495 22.903679 6.4245884 320 172 3520 480
|
||||
33000 0.96457971 22.922681 6.6987987 330 175 3480 520
|
||||
34000 0.96541889 22.92116 6.5992755 340 178 3600 400
|
||||
35000 0.96892691 22.923361 6.7973298 350 178 3600 400
|
||||
36000 0.97267726 22.923431 6.6577403 360 179 3640 360
|
||||
37000 0.97514714 22.939979 6.4028068 370 183 3640 360
|
||||
38000 0.98638599 22.952022 6.6518868 380 183 3640 360
|
||||
39000 0.97864891 22.962534 6.3906837 390 184 3680 320
|
||||
40000 0.9933016 22.975785 6.6819613 400 185 3720 280
|
||||
41000 0.9861477 22.977271 6.6747347 410 187 3800 200
|
||||
42000 0.98157369 22.963129 6.830028 420 187 3800 200
|
||||
43000 0.98202452 22.966947 6.5257905 430 187 3800 200
|
||||
44000 0.99540503 22.971262 6.5546513 440 187 3800 200
|
||||
45000 0.98433653 22.978028 6.4316725 450 189 3800 200
|
||||
46000 0.97912775 22.981328 6.9139851 460 189 3800 200
|
||||
47000 0.9791927 22.981131 6.6417971 470 190 3840 160
|
||||
48000 0.99601024 22.998536 6.6756953 480 191 3880 120
|
||||
49000 0.99589958 22.998489 6.9262843 490 191 3880 120
|
||||
50000 0.99294715 23.00399 6.6976013 500 192 3920 80
|
||||
Loop time of 19.5161 on 4 procs for 50000 steps with 4000 atoms
|
||||
|
||||
Performance: 2213556.537 tau/day, 2561.987 timesteps/s
|
||||
95.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.6256 | 2.7183 | 2.8265 | 5.2 | 13.93
|
||||
Bond | 2.3363 | 2.4406 | 2.5197 | 4.8 | 12.51
|
||||
Neigh | 7.382 | 7.3884 | 7.3936 | 0.2 | 37.86
|
||||
Comm | 3.014 | 3.2136 | 3.3994 | 9.4 | 16.47
|
||||
Output | 0.0014574 | 0.0017086 | 0.0020613 | 0.5 | 0.01
|
||||
Modify | 3.0282 | 3.1295 | 3.2034 | 4.1 | 16.04
|
||||
Other | | 0.624 | | | 3.20
|
||||
|
||||
Nlocal: 1000.00 ave 1011 max 993 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Nghost: 1187.25 ave 1202 max 1179 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 4939.25 ave 5067 max 4850 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 19757
|
||||
Ave neighs/atom = 4.9392500
|
||||
Ave special neighs/atom = 5.7000000
|
||||
Neighbor list builds = 10714
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:19
|
||||
290
examples/mc/log.27Nov18.gcmc.h2o.g++.1
Normal file
290
examples/mc/log.27Nov18.gcmc.h2o.g++.1
Normal file
@ -0,0 +1,290 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# fix gcmc example with fix shake
|
||||
|
||||
# variables available on command line
|
||||
|
||||
variable mu index -8.1
|
||||
variable disp index 0.5
|
||||
variable temp index 338.0
|
||||
variable lbox index 10.0
|
||||
variable spacing index 5.0
|
||||
|
||||
# global model settings
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
boundary p p p
|
||||
pair_style lj/cut/coul/long 14
|
||||
pair_modify mix arithmetic tail yes
|
||||
kspace_style ewald 0.0001
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
# box, start molecules on simple cubic lattice
|
||||
|
||||
lattice sc ${spacing}
|
||||
lattice sc 5.0
|
||||
Lattice spacing in x,y,z = 5 5 5
|
||||
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
|
||||
region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
|
||||
region box block 0 10.0 0 10.0 0 ${lbox} units box
|
||||
region box block 0 10.0 0 10.0 0 10.0 units box
|
||||
create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
|
||||
Created orthogonal box = (0 0 0) to (10 10 10)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
molecule h2omol H2O.txt
|
||||
Read molecule h2omol:
|
||||
3 atoms with max type 2
|
||||
2 bonds with max type 1
|
||||
1 angles with max type 1
|
||||
0 dihedrals with max type 0
|
||||
0 impropers with max type 0
|
||||
create_atoms 0 box mol h2omol 464563 units box
|
||||
Created 24 atoms
|
||||
Time spent = 0.00128841 secs
|
||||
|
||||
# rigid SPC/E water model
|
||||
|
||||
pair_coeff 1 1 0.15535 3.166
|
||||
pair_coeff * 2 0.0000 0.0000
|
||||
|
||||
bond_coeff 1 1000 1.0
|
||||
angle_coeff 1 100 109.47
|
||||
|
||||
# masses
|
||||
|
||||
mass 1 15.9994
|
||||
mass 2 1.0
|
||||
|
||||
# MD settings
|
||||
|
||||
group h2o type 1 2
|
||||
24 atoms in group h2o
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
velocity all create ${temp} 54654
|
||||
velocity all create 338.0 54654
|
||||
timestep 1.0
|
||||
|
||||
minimize 0.0 0.0 100 1000
|
||||
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
|
||||
Ewald initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.170448
|
||||
estimated absolute RMS force accuracy = 0.0332064
|
||||
estimated relative force accuracy = 0.0001
|
||||
KSpace vectors: actual max1d max3d = 16 2 62
|
||||
kxmax kymax kzmax = 2 2 2
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 16
|
||||
ghost atom cutoff = 16
|
||||
binsize = 8, bins = 2 2 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.88 | 11.88 | 11.88 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 338 -4.1890564 9.2628112e-06 18.98377 739.06991
|
||||
100 338 -36.122455 0.67828405 -12.271354 573.22675
|
||||
Loop time of 0.0461962 on 1 procs for 100 steps with 24 atoms
|
||||
|
||||
98.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
-4.18904713252 -34.586018764 -35.4441713339
|
||||
Force two-norm initial, final = 18.0027 42.115
|
||||
Force max component initial, final = 5.8993 15.4907
|
||||
Final line search alpha, max atom move = 0.00127226 0.0197082
|
||||
Iterations, force evaluations = 100 239
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.038526 | 0.038526 | 0.038526 | 0.0 | 83.40
|
||||
Bond | 0.00031209 | 0.00031209 | 0.00031209 | 0.0 | 0.68
|
||||
Kspace | 0.0019636 | 0.0019636 | 0.0019636 | 0.0 | 4.25
|
||||
Neigh | 0.00055456 | 0.00055456 | 0.00055456 | 0.0 | 1.20
|
||||
Comm | 0.0040288 | 0.0040288 | 0.0040288 | 0.0 | 8.72
|
||||
Output | 1.5259e-05 | 1.5259e-05 | 1.5259e-05 | 0.0 | 0.03
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.0007958 | | | 1.72
|
||||
|
||||
Nlocal: 24 ave 24 max 24 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2011 ave 2011 max 2011 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 4921 ave 4921 max 4921 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 4921
|
||||
Ave neighs/atom = 205.042
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
|
||||
# rigid constraints with thermostat
|
||||
|
||||
fix mynvt h2o nvt temp ${temp} ${temp} 100
|
||||
fix mynvt h2o nvt temp 338.0 ${temp} 100
|
||||
fix mynvt h2o nvt temp 338.0 338.0 100
|
||||
fix wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
8 = # of frozen angles
|
||||
|
||||
# important to make temperature dofs dynamic
|
||||
|
||||
compute_modify thermo_temp dynamic/dof yes
|
||||
compute_modify mynvt_temp dynamic/dof yes
|
||||
|
||||
run 1000
|
||||
Ewald initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.170448
|
||||
estimated absolute RMS force accuracy = 0.0332064
|
||||
estimated relative force accuracy = 0.0001
|
||||
KSpace vectors: actual max1d max3d = 16 2 62
|
||||
kxmax kymax kzmax = 2 2 2
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 518.26667 -36.122455 0 -12.949638 703.43827
|
||||
1000 260.39219 -55.141232 0 -43.498537 -1698.672
|
||||
Loop time of 0.140376 on 1 procs for 1000 steps with 24 atoms
|
||||
|
||||
Performance: 615.489 ns/day, 0.039 hours/ns, 7123.720 timesteps/s
|
||||
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.10434 | 0.10434 | 0.10434 | 0.0 | 74.33
|
||||
Bond | 0.00013041 | 0.00013041 | 0.00013041 | 0.0 | 0.09
|
||||
Kspace | 0.008199 | 0.008199 | 0.008199 | 0.0 | 5.84
|
||||
Neigh | 0.0061581 | 0.0061581 | 0.0061581 | 0.0 | 4.39
|
||||
Comm | 0.015352 | 0.015352 | 0.015352 | 0.0 | 10.94
|
||||
Output | 1.4305e-05 | 1.4305e-05 | 1.4305e-05 | 0.0 | 0.01
|
||||
Modify | 0.004544 | 0.004544 | 0.004544 | 0.0 | 3.24
|
||||
Other | | 0.001639 | | | 1.17
|
||||
|
||||
Nlocal: 24 ave 24 max 24 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1776 ave 1776 max 1776 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 5073 ave 5073 max 5073 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 5073
|
||||
Ave neighs/atom = 211.375
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 27
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
|
||||
# gcmc
|
||||
|
||||
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
|
||||
fix mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
|
||||
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
|
||||
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
|
||||
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake
|
||||
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake
|
||||
|
||||
# atom counts
|
||||
|
||||
variable oxygen atom "type==1"
|
||||
variable hydrogen atom "type==2"
|
||||
group oxygen dynamic all var oxygen
|
||||
dynamic group oxygen defined
|
||||
group hydrogen dynamic all var hydrogen
|
||||
dynamic group hydrogen defined
|
||||
variable nO equal count(oxygen)
|
||||
variable nH equal count(hydrogen)
|
||||
|
||||
# output
|
||||
|
||||
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
|
||||
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
|
||||
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
|
||||
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
|
||||
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
|
||||
thermo 1000
|
||||
|
||||
# run
|
||||
|
||||
run 20000
|
||||
Ewald initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.170448
|
||||
estimated absolute RMS force accuracy = 0.0332064
|
||||
estimated relative force accuracy = 0.0001
|
||||
KSpace vectors: actual max1d max3d = 16 2 62
|
||||
kxmax kymax kzmax = 2 2 2
|
||||
WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:487)
|
||||
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
|
||||
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
|
||||
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:471)
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes
|
||||
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
|
||||
0 260.39219 -1699.3643 -55.141232 11.642695 0.23910963 24 0 0 0 0 8 16
|
||||
1000 340.44409 -2560.1501 -280.70157 53.784356 0.80699501 81 0.054205983 0.015933081 0 0 27 54
|
||||
2000 302.57602 592.41718 -310.37771 53.213377 0.89666113 90 0.030546787 0.0078577743 0 0 30 60
|
||||
3000 270.18045 -817.18659 -346.75773 50.737466 0.95643854 96 0.021969243 0.0060076096 0 0 32 64
|
||||
4000 334.17192 1153.3017 -335.25519 62.75449 0.95643854 96 0.016400775 0.0045269353 0 0 32 64
|
||||
5000 360.36872 -647.99689 -336.2928 67.674015 0.95643854 96 0.012996731 0.0036569014 0 0 32 64
|
||||
6000 282.37822 -986.51765 -341.91848 53.028098 0.95643854 96 0.010941282 0.0030159847 0 0 32 64
|
||||
7000 363.01448 2952.0391 -358.72963 70.335018 0.98632724 99 0.0098923151 0.0028884203 0 0 33 66
|
||||
8000 331.70391 323.34886 -382.04165 68.223498 1.0461046 105 0.0092083323 0.0025112378 0 0 35 70
|
||||
9000 337.2032 -3637.5257 -390.66472 69.35457 1.0461046 105 0.0081585853 0.0022395915 0 0 35 70
|
||||
10000 373.67063 3081.3271 -380.5107 76.855041 1.0461046 105 0.0073396679 0.0020164949 0 0 35 70
|
||||
11000 336.64665 5535.9451 -405.21548 71.247059 1.0759934 108 0.0068442571 0.0018355023 0 0 36 72
|
||||
12000 306.51164 1448.1757 -410.3655 64.869362 1.0759934 108 0.0062798499 0.0016809265 0 0 36 72
|
||||
13000 319.03497 177.44405 -406.17113 67.519768 1.0759934 108 0.0057952448 0.0015520479 0 0 36 72
|
||||
14000 309.89701 -1022.6798 -384.20239 65.585833 1.0759934 108 0.005391524 0.0014384143 0 0 36 72
|
||||
15000 398.91559 2058.9251 -404.32604 84.425503 1.0759934 108 0.0050257238 0.0013442486 0 0 36 72
|
||||
16000 318.98778 873.46142 -392.13338 67.50978 1.0759934 108 0.0047204383 0.0012578458 0 0 36 72
|
||||
17000 333.16025 2347.0215 -387.73943 70.509206 1.0759934 108 0.0044407568 0.0011843991 0 0 36 72
|
||||
18000 353.23789 -2305.787 -382.1633 74.758389 1.0759934 108 0.0042016342 0.0011165574 0 0 36 72
|
||||
19000 322.70939 5619.9631 -381.81328 68.297412 1.0759934 108 0.0039877848 0.0010558436 0 0 36 72
|
||||
20000 371.07261 3916.1113 -389.76357 78.532884 1.0759934 108 0.0037874635 0.0010033009 0 0 36 72
|
||||
Loop time of 242.59 on 1 procs for 20000 steps with 108 atoms
|
||||
|
||||
Performance: 7.123 ns/day, 3.369 hours/ns, 82.444 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 38.279 | 38.279 | 38.279 | 0.0 | 15.78
|
||||
Bond | 0.055672 | 0.055672 | 0.055672 | 0.0 | 0.02
|
||||
Kspace | 0.60623 | 0.60623 | 0.60623 | 0.0 | 0.25
|
||||
Neigh | 4.4189 | 4.4189 | 4.4189 | 0.0 | 1.82
|
||||
Comm | 1.2719 | 1.2719 | 1.2719 | 0.0 | 0.52
|
||||
Output | 0.00096583 | 0.00096583 | 0.00096583 | 0.0 | 0.00
|
||||
Modify | 197.85 | 197.85 | 197.85 | 0.0 | 81.56
|
||||
Other | | 0.1098 | | | 0.05
|
||||
|
||||
Nlocal: 108 ave 108 max 108 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 8000 ave 8000 max 8000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 100006 ave 100006 max 100006 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 100006
|
||||
Ave neighs/atom = 925.981
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 20903
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:04:02
|
||||
141
examples/mc/log.27Nov18.gcmc.lj.g++.1
Normal file
141
examples/mc/log.27Nov18.gcmc.lj.g++.1
Normal file
@ -0,0 +1,141 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# GCMC for LJ simple fluid, no dynamics
|
||||
# T = 2.0
|
||||
# rho ~ 0.5
|
||||
# p ~ 1.5
|
||||
# mu_ex ~ 0.0
|
||||
# comparable to Frenkel and Smit GCMC Case Study, Figure 5.8
|
||||
|
||||
# variables modifiable using -var command line switch
|
||||
|
||||
variable mu index -1.25
|
||||
variable temp index 2.0
|
||||
variable disp index 1.0
|
||||
variable lbox index 5.0
|
||||
|
||||
# global model settings
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
pair_style lj/cut 3.0
|
||||
pair_modify tail no # turn of to avoid triggering full_energy
|
||||
|
||||
# box
|
||||
|
||||
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox}
|
||||
region box block 0 5.0 0 ${lbox} 0 ${lbox}
|
||||
region box block 0 5.0 0 5.0 0 ${lbox}
|
||||
region box block 0 5.0 0 5.0 0 5.0
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (5 5 5)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
# lj parameters
|
||||
|
||||
pair_coeff * * 1.0 1.0
|
||||
mass * 1.0
|
||||
|
||||
# we recommend setting up a dedicated group for gcmc
|
||||
|
||||
group gcmcgroup type 1
|
||||
0 atoms in group gcmcgroup
|
||||
|
||||
# gcmc
|
||||
|
||||
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
|
||||
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
|
||||
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
|
||||
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 1.0
|
||||
|
||||
# atom count
|
||||
|
||||
variable type1 atom "type==1"
|
||||
group type1 dynamic gcmcgroup var type1
|
||||
dynamic group type1 defined
|
||||
variable n1 equal count(type1)
|
||||
|
||||
# averaging
|
||||
|
||||
variable rho equal density
|
||||
variable p equal press
|
||||
variable nugget equal 1.0e-8
|
||||
variable lambda equal 1.0
|
||||
variable muex equal ${mu}-${temp}*ln(density*${lambda}+${nugget})
|
||||
variable muex equal -1.25-${temp}*ln(density*${lambda}+${nugget})
|
||||
variable muex equal -1.25-2.0*ln(density*${lambda}+${nugget})
|
||||
variable muex equal -1.25-2.0*ln(density*1+${nugget})
|
||||
variable muex equal -1.25-2.0*ln(density*1+1e-08)
|
||||
fix ave all ave/time 10 100 1000 v_rho v_p v_muex v_n1 ave one file rho_vs_p.dat
|
||||
variable rhoav equal f_ave[1]
|
||||
variable pav equal f_ave[2]
|
||||
variable muexav equal f_ave[3]
|
||||
variable n1av equal f_ave[4]
|
||||
|
||||
# output
|
||||
|
||||
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+${nugget})
|
||||
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+1e-08)
|
||||
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+${nugget})
|
||||
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+1e-08)
|
||||
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
|
||||
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+1e-08)
|
||||
compute_modify thermo_temp dynamic yes
|
||||
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
|
||||
thermo 1000
|
||||
|
||||
# run
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
binsize = 1.65, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 0.433 | 0.433 | 0.433 Mbytes
|
||||
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
|
||||
0 0 0 0 -0 0 0 0 0 0 0 0 0 0
|
||||
1000 2.0603874 2.9024736 -3.2576986 3.0482443 0.584 73 0.069266074 0.066959582 0.11158434 0.53624 1.3978532 0.0014407586 64.19
|
||||
2000 2.1586837 1.5581387 -2.8420766 3.1857993 0.496 62 0.068487803 0.067570935 0.1126652 0.53128 1.3713694 0.020274019 63.41
|
||||
3000 2.4664064 0.65471138 -3.3428236 3.6435549 0.528 66 0.068182273 0.067547792 0.11226502 0.53472 1.3892234 0.0070204504 63.68
|
||||
4000 1.8880496 1.4802782 -2.7846019 2.785647 0.488 61 0.068250075 0.067843541 0.11299989 0.52744 1.299496 0.033918563 63.1
|
||||
5000 2.0578649 1.3204331 -3.5571862 3.0433213 0.568 71 0.067858571 0.067732262 0.11271981 0.5364 1.4237505 0.00065741209 64
|
||||
6000 2.3627973 0.97064566 -3.1107668 3.4879388 0.504 63 0.067846204 0.06757018 0.11272207 0.5332 1.3945131 0.014216594 63.7
|
||||
7000 1.6629817 0.98138972 -2.7780297 2.4514644 0.464 58 0.067451389 0.067269791 0.11263692 0.53688 1.4207486 -0.0012887793 63.82
|
||||
8000 2.2135488 2.0878792 -3.0471089 3.2707661 0.536 67 0.067926473 0.067738312 0.1135594 0.52736 1.4348314 0.034380623 62.43
|
||||
9000 1.8904287 0.52639383 -3.3548657 2.7920177 0.52 65 0.06818197 0.068003094 0.11356319 0.53072 1.4528143 0.021683615 63.23
|
||||
10000 2.2353281 0.73275312 -3.2197702 3.3006016 0.512 64 0.068465059 0.068208485 0.11414748 0.52712 1.4143492 0.03497858 62.44
|
||||
Loop time of 27.8547 on 1 procs for 10000 steps with 64 atoms
|
||||
|
||||
Performance: 155090.656 tau/day, 359.006 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 | 0.43892 | 0.43892 | 0.43892 | 0.0 | 1.58
|
||||
Neigh | 1.278 | 1.278 | 1.278 | 0.0 | 4.59
|
||||
Comm | 0.24105 | 0.24105 | 0.24105 | 0.0 | 0.87
|
||||
Output | 0.00032067 | 0.00032067 | 0.00032067 | 0.0 | 0.00
|
||||
Modify | 25.88 | 25.88 | 25.88 | 0.0 | 92.91
|
||||
Other | | 0.01693 | | | 0.06
|
||||
|
||||
Nlocal: 64 ave 64 max 64 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 714 ave 714 max 714 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2423 ave 2423 max 2423 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2423
|
||||
Ave neighs/atom = 37.8594
|
||||
Neighbor list builds = 10000
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:27
|
||||
141
examples/mc/log.27Nov18.gcmc.lj.g++.4
Normal file
141
examples/mc/log.27Nov18.gcmc.lj.g++.4
Normal file
@ -0,0 +1,141 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# GCMC for LJ simple fluid, no dynamics
|
||||
# T = 2.0
|
||||
# rho ~ 0.5
|
||||
# p ~ 1.5
|
||||
# mu_ex ~ 0.0
|
||||
# comparable to Frenkel and Smit GCMC Case Study, Figure 5.8
|
||||
|
||||
# variables modifiable using -var command line switch
|
||||
|
||||
variable mu index -1.25
|
||||
variable temp index 2.0
|
||||
variable disp index 1.0
|
||||
variable lbox index 5.0
|
||||
|
||||
# global model settings
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
pair_style lj/cut 3.0
|
||||
pair_modify tail no # turn of to avoid triggering full_energy
|
||||
|
||||
# box
|
||||
|
||||
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox}
|
||||
region box block 0 5.0 0 ${lbox} 0 ${lbox}
|
||||
region box block 0 5.0 0 5.0 0 ${lbox}
|
||||
region box block 0 5.0 0 5.0 0 5.0
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (5 5 5)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
|
||||
# lj parameters
|
||||
|
||||
pair_coeff * * 1.0 1.0
|
||||
mass * 1.0
|
||||
|
||||
# we recommend setting up a dedicated group for gcmc
|
||||
|
||||
group gcmcgroup type 1
|
||||
0 atoms in group gcmcgroup
|
||||
|
||||
# gcmc
|
||||
|
||||
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
|
||||
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
|
||||
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
|
||||
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 1.0
|
||||
|
||||
# atom count
|
||||
|
||||
variable type1 atom "type==1"
|
||||
group type1 dynamic gcmcgroup var type1
|
||||
dynamic group type1 defined
|
||||
variable n1 equal count(type1)
|
||||
|
||||
# averaging
|
||||
|
||||
variable rho equal density
|
||||
variable p equal press
|
||||
variable nugget equal 1.0e-8
|
||||
variable lambda equal 1.0
|
||||
variable muex equal ${mu}-${temp}*ln(density*${lambda}+${nugget})
|
||||
variable muex equal -1.25-${temp}*ln(density*${lambda}+${nugget})
|
||||
variable muex equal -1.25-2.0*ln(density*${lambda}+${nugget})
|
||||
variable muex equal -1.25-2.0*ln(density*1+${nugget})
|
||||
variable muex equal -1.25-2.0*ln(density*1+1e-08)
|
||||
fix ave all ave/time 10 100 1000 v_rho v_p v_muex v_n1 ave one file rho_vs_p.dat
|
||||
variable rhoav equal f_ave[1]
|
||||
variable pav equal f_ave[2]
|
||||
variable muexav equal f_ave[3]
|
||||
variable n1av equal f_ave[4]
|
||||
|
||||
# output
|
||||
|
||||
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+${nugget})
|
||||
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+1e-08)
|
||||
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+${nugget})
|
||||
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+1e-08)
|
||||
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
|
||||
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+1e-08)
|
||||
compute_modify thermo_temp dynamic yes
|
||||
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
|
||||
thermo 1000
|
||||
|
||||
# run
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
binsize = 1.65, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 0.4477 | 0.4477 | 0.4477 Mbytes
|
||||
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
|
||||
0 0 0 0 -0 0 0 0 0 0 0 0 0 0
|
||||
1000 2.4378552 1.9014939 -3.23439 3.6030066 0.544 68 0.073050445 0.070796636 0.11934255 0.52552 1.3006333 0.04152087 62.56
|
||||
2000 1.9339159 1.0360287 -3.5001391 2.8594327 0.56 70 0.069588893 0.068587488 0.11319584 0.542 1.4012888 -0.020696665 64.56
|
||||
3000 1.8891807 2.2857708 -3.3755633 2.7954769 0.592 74 0.068329031 0.067640916 0.11187803 0.53536 1.3380926 0.0062359288 64.21
|
||||
4000 2.0436517 1.7600211 -3.4067452 3.0229014 0.576 72 0.067464211 0.067003868 0.11060324 0.54144 1.4484907 -0.016246603 64.75
|
||||
5000 2.1512268 1.0811095 -3.2418366 3.1786785 0.536 67 0.066830654 0.066717982 0.1094094 0.54368 1.4962073 -0.025791643 65.04
|
||||
6000 2.128931 1.5444487 -3.1904474 3.1450116 0.528 66 0.067479197 0.067193531 0.1104464 0.53112 1.4247377 0.019908014 63.01
|
||||
7000 1.8194311 0.72981963 -3.6601329 2.6912418 0.576 72 0.068131849 0.067910074 0.11182024 0.51968 1.4517098 0.063444774 61.72
|
||||
8000 1.947817 0.74570466 -3.0935809 2.8753489 0.504 63 0.068034071 0.067855883 0.11217045 0.53304 1.4924302 0.012298733 63.45
|
||||
9000 1.8942389 1.3367401 -2.8925016 2.7962574 0.504 63 0.068117479 0.067943081 0.11236152 0.536 1.4091106 0.0011494886 63.73
|
||||
10000 2.2092799 0.95517153 -2.9117781 3.2586879 0.48 60 0.068264792 0.068016591 0.11310789 0.52272 1.4774174 0.051284873 62.04
|
||||
Loop time of 26.0069 on 4 procs for 10000 steps with 60 atoms
|
||||
|
||||
Performance: 166109.741 tau/day, 384.513 timesteps/s
|
||||
95.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.10309 | 0.115 | 0.1225 | 2.2 | 0.44
|
||||
Neigh | 0.3907 | 0.40447 | 0.41957 | 1.7 | 1.56
|
||||
Comm | 0.44236 | 0.46678 | 0.49472 | 2.8 | 1.79
|
||||
Output | 0.0011411 | 0.0062903 | 0.0080109 | 3.7 | 0.02
|
||||
Modify | 25 | 25.002 | 25.005 | 0.0 | 96.14
|
||||
Other | | 0.01231 | | | 0.05
|
||||
|
||||
Nlocal: 15 ave 16 max 14 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 437 ave 446 max 431 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Neighs: 529 ave 595 max 437 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 2116
|
||||
Ave neighs/atom = 35.2667
|
||||
Neighbor list builds = 10000
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:26
|
||||
89
examples/mc/log.30Jun20.widom.lj.g++.1
Normal file
89
examples/mc/log.30Jun20.widom.lj.g++.1
Normal file
@ -0,0 +1,89 @@
|
||||
LAMMPS (30 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Kob and Andersen model Phys. Rev. E 51, 4626 (1995)
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_modify shift yes
|
||||
|
||||
read_data data.widom.lj
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (9.4000000 9.4000000 9.4000000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1000 atoms
|
||||
reading velocities ...
|
||||
1000 velocities
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.5 0.8 2.0
|
||||
pair_coeff 2 2 0.5 0.88 2.2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 5 check yes
|
||||
|
||||
fix mywidom all widom 10 100000 2 29494 0.75
|
||||
|
||||
fix 1 all langevin 0.75 0.75 0.1 48279 zero yes
|
||||
fix 2 all nve
|
||||
|
||||
timestep 0.002
|
||||
|
||||
thermo_style custom step temp pe etotal press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
|
||||
thermo 10
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 5 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.181 | 3.181 | 3.181 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3]
|
||||
0 0.75021245 -6.4204308 -5.2962374 7.2962696 830.584 1.2039721 0 0 830.584
|
||||
10 0.7358936 -6.4405082 -5.3377717 7.1699962 830.584 1.2039721 -3.8577501 171.3429 830.584
|
||||
20 0.75426414 -6.4267946 -5.2965298 7.2833985 830.584 1.2039721 -4.0708206 227.63895 830.584
|
||||
30 0.72947489 -6.4064078 -5.3132896 7.3872583 830.584 1.2039721 -4.4304803 367.7146 830.584
|
||||
40 0.73504751 -6.4248725 -5.3234038 7.2927069 830.584 1.2039721 -4.1904189 266.99373 830.584
|
||||
50 0.76497439 -6.4352472 -5.2889331 7.3046861 830.584 1.2039721 -3.8628472 172.51133 830.584
|
||||
60 0.75752861 -6.4147051 -5.2795485 7.4416 830.584 1.2039721 -3.5355467 111.5042 830.584
|
||||
70 0.77775078 -6.4210798 -5.2556202 7.4473703 830.584 1.2039721 -3.4754802 102.92223 830.584
|
||||
80 0.80937104 -6.4320008 -5.2191583 7.4121087 830.584 1.2039721 -3.9287513 188.35625 830.584
|
||||
90 0.76321255 -6.4203633 -5.2766893 7.4307727 830.584 1.2039721 -4.2257529 279.87337 830.584
|
||||
100 0.74561743 -6.4010576 -5.2837499 7.52907 830.584 1.2039721 -3.6817835 135.5099 830.584
|
||||
Loop time of 25.8264 on 1 procs for 100 steps with 1000 atoms
|
||||
|
||||
Performance: 669.082 tau/day, 3.872 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.08186 | 0.08186 | 0.08186 | 0.0 | 0.32
|
||||
Neigh | 0.023613 | 0.023613 | 0.023613 | 0.0 | 0.09
|
||||
Comm | 0.0053532 | 0.0053532 | 0.0053532 | 0.0 | 0.02
|
||||
Output | 0.00037837 | 0.00037837 | 0.00037837 | 0.0 | 0.00
|
||||
Modify | 25.715 | 25.715 | 25.715 | 0.0 | 99.57
|
||||
Other | | 0.0005643 | | | 0.00
|
||||
|
||||
Nlocal: 1000.00 ave 1000 max 1000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3049.00 ave 3049 max 3049 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 46176.0 ave 46176 max 46176 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 46176
|
||||
Ave neighs/atom = 46.176000
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:25
|
||||
89
examples/mc/log.30Jun20.widom.lj.g++.4
Normal file
89
examples/mc/log.30Jun20.widom.lj.g++.4
Normal file
@ -0,0 +1,89 @@
|
||||
LAMMPS (30 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Kob and Andersen model Phys. Rev. E 51, 4626 (1995)
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_modify shift yes
|
||||
|
||||
read_data data.widom.lj
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (9.4000000 9.4000000 9.4000000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
1000 atoms
|
||||
reading velocities ...
|
||||
1000 velocities
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.5 0.8 2.0
|
||||
pair_coeff 2 2 0.5 0.88 2.2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 5 check yes
|
||||
|
||||
fix mywidom all widom 10 100000 2 29494 0.75
|
||||
|
||||
fix 1 all langevin 0.75 0.75 0.1 48279 zero yes
|
||||
fix 2 all nve
|
||||
|
||||
timestep 0.002
|
||||
|
||||
thermo_style custom step temp pe etotal press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
|
||||
thermo 10
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 5 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.13 | 3.13 | 3.131 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3]
|
||||
0 0.75021245 -6.4204308 -5.2962374 7.2962696 830.584 1.2039721 0 0 830.584
|
||||
10 0.74279259 -6.4332442 -5.3201696 7.2071344 830.584 1.2039721 -3.4462258 98.984938 830.584
|
||||
20 0.73016272 -6.4222911 -5.3281423 7.2714238 830.584 1.2039721 -4.4887329 397.41346 830.584
|
||||
30 0.74416342 -6.429139 -5.3140101 7.2713375 830.584 1.2039721 -4.3313574 322.19056 830.584
|
||||
40 0.73295457 -6.4370942 -5.3387618 7.227091 830.584 1.2039721 -4.7419281 557.00309 830.584
|
||||
50 0.76914235 -6.4473959 -5.2948361 7.2179148 830.584 1.2039721 -3.1794069 69.352982 830.584
|
||||
60 0.74099083 -6.4433012 -5.3329265 7.204973 830.584 1.2039721 -3.5231065 109.66994 830.584
|
||||
70 0.74514671 -6.4288463 -5.312244 7.2771269 830.584 1.2039721 -1.0154832 3.8727995 830.584
|
||||
80 0.72787097 -6.4457574 -5.3550427 7.1130709 830.584 1.2039721 -3.6691709 133.2501 830.584
|
||||
90 0.78452846 -6.5034376 -5.3278217 6.8238659 830.584 1.2039721 -2.0798339 16.008373 830.584
|
||||
100 0.77188499 -6.487313 -5.3306433 6.9133194 830.584 1.2039721 -2.066579 15.727938 830.584
|
||||
Loop time of 3.37748 on 4 procs for 100 steps with 1000 atoms
|
||||
|
||||
Performance: 5116.239 tau/day, 29.608 timesteps/s
|
||||
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.02025 | 0.020952 | 0.021322 | 0.3 | 0.62
|
||||
Neigh | 0.0059071 | 0.0060568 | 0.0061543 | 0.1 | 0.18
|
||||
Comm | 0.016558 | 0.059554 | 0.094282 | 12.2 | 1.76
|
||||
Output | 0.00022173 | 0.00042927 | 0.0010471 | 0.0 | 0.01
|
||||
Modify | 3.2552 | 3.2902 | 3.3335 | 1.7 | 97.42
|
||||
Other | | 0.0003003 | | | 0.01
|
||||
|
||||
Nlocal: 250.000 ave 256 max 242 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Nghost: 1666.00 ave 1670 max 1659 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Neighs: 11538.0 ave 11832 max 11091 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
|
||||
Total # of neighbors = 46152
|
||||
Ave neighs/atom = 46.152000
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
133
examples/mc/log.30Jun20.widom.spce.g++.1
Normal file
133
examples/mc/log.30Jun20.widom.spce.g++.1
Normal file
@ -0,0 +1,133 @@
|
||||
LAMMPS (30 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style full
|
||||
|
||||
pair_style lj/cut/coul/long 10.0
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
read_data data.spce
|
||||
orthogonal box = (-0.031613 -0.023523 -0.085255) to (43.234352 44.939753 42.306533)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
8640 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
5760 bonds
|
||||
reading angles ...
|
||||
2880 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.008 seconds
|
||||
read_data CPU = 0.028 seconds
|
||||
|
||||
molecule h2omol H2O.txt
|
||||
Read molecule template h2omol:
|
||||
1 molecules
|
||||
3 atoms with max type 2
|
||||
2 bonds with max type 1
|
||||
1 angles with max type 1
|
||||
0 dihedrals with max type 0
|
||||
0 impropers with max type 0
|
||||
|
||||
### Flexible SPC/E Potential Parameters ###
|
||||
### Zhang et al., Fluid Phase Equilibria, 262 (2007) 210-216 ###
|
||||
pair_coeff 1 1 0.1502629 3.1169
|
||||
pair_coeff 1 2 0.0341116368 2.04845
|
||||
pair_coeff 2 2 0.00774378 0.98
|
||||
|
||||
bond_coeff 1 176.864 0.9611
|
||||
angle_coeff 1 42.1845 109.4712
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
fix mywidom all widom 10 20 0 29494 298 mol h2omol
|
||||
|
||||
fix 2 all nvt temp 298.0 298.0 100.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 10 every 2 check yes
|
||||
|
||||
|
||||
#run variables
|
||||
timestep 0.5
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal pe temp press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:330)
|
||||
G vector (1/distance) = 0.2690183
|
||||
grid = 24 24 24
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.024843102
|
||||
estimated relative force accuracy = 7.4814263e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 29791 13824
|
||||
WARNING: Fix Widom using full_energy option (src/MC/fix_widom.cpp:297)
|
||||
0 atoms in group FixWidom:widom_exclusion_group:mywidom
|
||||
0 atoms in group FixWidom:rotation_gas_atoms:mywidom
|
||||
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:487)
|
||||
Neighbor list info ...
|
||||
update every 2 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 29.66 | 29.66 | 29.66 Mbytes
|
||||
Step TotEng PotEng Temp Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3]
|
||||
0 -29703.973 -29703.973 0 -4764.5901 82468.116 1.9140713 0 0 82468.116
|
||||
10 -29712.131 -31110.041 54.285179 -3154.4423 82468.116 1.9140713 241.93348 3.7366217e-178 82468.116
|
||||
20 -29711.939 -32614.429 112.71273 -4216.1592 82468.116 1.9140713 16.095006 1.5716469e-12 82468.116
|
||||
30 -29688.142 -32368.506 104.08688 -4093.6515 82468.116 1.9140713 5.7862327 5.7086352e-05 82468.116
|
||||
40 -29662.343 -32252.144 100.57005 -1458.5339 82468.116 1.9140713 126.68071 1.2467216e-93 82468.116
|
||||
50 -29646.78 -32837.635 123.91081 -4607.1155 82468.116 1.9140713 74.622397 1.8790479e-55 82468.116
|
||||
60 -29628.968 -33001.229 130.9554 -4589.5296 82468.116 1.9140713 3.6575433 0.0020780497 82468.116
|
||||
70 -29602.78 -32816.28 124.79023 -3082.1133 82468.116 1.9140713 13.983097 5.561247e-11 82468.116
|
||||
80 -29577.552 -33141.454 138.39742 -6332.8138 82468.116 1.9140713 41.98931 1.6075608e-31 82468.116
|
||||
90 -29550.865 -33792.115 164.70094 -4607.6419 82468.116 1.9140713 68.690681 4.2082269e-51 82468.116
|
||||
100 -29515.107 -34052.782 176.21207 -3609.5709 82468.116 1.9140713 41.090597 7.3326206e-31 82468.116
|
||||
Loop time of 163.407 on 1 procs for 100 steps with 8640 atoms
|
||||
|
||||
Performance: 0.026 ns/day, 907.819 hours/ns, 0.612 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 8.5495 | 8.5495 | 8.5495 | 0.0 | 5.23
|
||||
Bond | 0.031981 | 0.031981 | 0.031981 | 0.0 | 0.02
|
||||
Kspace | 2.3995 | 2.3995 | 2.3995 | 0.0 | 1.47
|
||||
Neigh | 5.0542 | 5.0542 | 5.0542 | 0.0 | 3.09
|
||||
Comm | 0.051965 | 0.051965 | 0.051965 | 0.0 | 0.03
|
||||
Output | 0.0018802 | 0.0018802 | 0.0018802 | 0.0 | 0.00
|
||||
Modify | 147.31 | 147.31 | 147.31 | 0.0 | 90.15
|
||||
Other | | 0.003614 | | | 0.00
|
||||
|
||||
Nlocal: 8640.00 ave 8640 max 8640 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 23499.0 ave 23499 max 23499 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3.27380e+06 ave 3.2738e+06 max 3.2738e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3273800
|
||||
Ave neighs/atom = 378.91204
|
||||
Ave special neighs/atom = 2.0000000
|
||||
Neighbor list builds = 220
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:02:44
|
||||
196
examples/mc/log.31Mar21.gcmc.co2.g++.1
Normal file
196
examples/mc/log.31Mar21.gcmc.co2.g++.1
Normal file
@ -0,0 +1,196 @@
|
||||
LAMMPS (10 Mar 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# GCMC for CO2 molecular fluid, rigid/small dynamics
|
||||
# Rigid CO2 TraPPE model
|
||||
# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
|
||||
# mixtures containing alkanes, carbon dioxide and
|
||||
# nitrogen AIChE J., 47,1676-1682 (2001)].
|
||||
|
||||
# variables available on command line
|
||||
|
||||
variable mu index -8.1
|
||||
variable disp index 0.5
|
||||
variable temp index 338.0
|
||||
variable lbox index 10.0
|
||||
variable spacing index 5.0
|
||||
|
||||
# global model settings
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
boundary p p p
|
||||
pair_style lj/cut/coul/long 14
|
||||
pair_modify mix arithmetic tail yes
|
||||
kspace_style ewald 0.0001
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
# box, start molecules on simple cubic lattice
|
||||
|
||||
lattice sc ${spacing}
|
||||
lattice sc 5.0
|
||||
Lattice spacing in x,y,z = 5.0000000 5.0000000 5.0000000
|
||||
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
|
||||
region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
|
||||
region box block 0 10.0 0 10.0 0 ${lbox} units box
|
||||
region box block 0 10.0 0 10.0 0 10.0 units box
|
||||
create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.000000 10.000000 10.000000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
molecule co2mol CO2.txt
|
||||
Read molecule template co2mol:
|
||||
1 molecules
|
||||
3 atoms with max type 2
|
||||
2 bonds with max type 1
|
||||
1 angles with max type 1
|
||||
0 dihedrals with max type 0
|
||||
0 impropers with max type 0
|
||||
create_atoms 0 box mol co2mol 464563 units box
|
||||
Created 24 atoms
|
||||
create_atoms CPU = 0.002 seconds
|
||||
|
||||
# rigid CO2 TraPPE model
|
||||
|
||||
pair_coeff 1 1 0.053649 2.8
|
||||
pair_coeff 2 2 0.156973 3.05
|
||||
bond_coeff 1 0 1.16
|
||||
angle_coeff 1 0 180
|
||||
|
||||
# masses
|
||||
|
||||
mass 1 12.0107
|
||||
mass 2 15.9994
|
||||
|
||||
# MD settings
|
||||
|
||||
group co2 type 1 2
|
||||
24 atoms in group co2
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
velocity all create ${temp} 54654
|
||||
velocity all create 338.0 54654
|
||||
timestep 1.0
|
||||
|
||||
# rigid constraints with thermostat
|
||||
|
||||
fix myrigid co2 rigid/small molecule mol co2mol
|
||||
create bodies CPU = 0.000 seconds
|
||||
8 rigid bodies with 24 atoms
|
||||
1.1600000 = max distance from body owner to body atom
|
||||
|
||||
# dynamically update fix rigid/nvt/small temperature ndof
|
||||
fix_modify myrigid dynamic/dof yes
|
||||
|
||||
# gcmc
|
||||
|
||||
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
|
||||
fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigid
|
||||
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigid
|
||||
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigid
|
||||
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigid
|
||||
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigid
|
||||
|
||||
# atom counts
|
||||
|
||||
variable carbon atom "type==1"
|
||||
variable oxygen atom "type==2"
|
||||
group carbon dynamic co2 var carbon
|
||||
dynamic group carbon defined
|
||||
group oxygen dynamic co2 var oxygen
|
||||
dynamic group oxygen defined
|
||||
variable nC equal count(carbon)
|
||||
variable nO equal count(oxygen)
|
||||
|
||||
# output
|
||||
|
||||
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
|
||||
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
|
||||
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
|
||||
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
|
||||
|
||||
# dynamically update default temperature ndof
|
||||
compute_modify thermo_temp dynamic/dof yes
|
||||
|
||||
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
|
||||
thermo 1000
|
||||
|
||||
# run
|
||||
|
||||
run 20000
|
||||
Ewald initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
|
||||
G vector (1/distance) = 0.16463644
|
||||
estimated absolute RMS force accuracy = 0.033206372
|
||||
estimated relative force accuracy = 0.0001
|
||||
KSpace vectors: actual max1d max3d = 16 2 62
|
||||
kxmax kymax kzmax = 2 2 2
|
||||
WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:482)
|
||||
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
|
||||
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
|
||||
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 16
|
||||
ghost atom cutoff = 16
|
||||
binsize = 8, bins = 2 2 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.62 | 15.62 | 15.62 Mbytes
|
||||
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
|
||||
0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0 8 16
|
||||
1000 261.50949 -204.60974 -9.6459249 8.3147747 0.51155641 21 0.096366192 0.097590121 0 0 7 14
|
||||
2000 479.39697 231.28436 -7.0089345 10.47927 0.36539744 15 0.085531005 0.085453295 0 0 5 10
|
||||
3000 318.31766 -433.17133 -7.3680951 8.5396005 0.43847693 18 0.078556687 0.080101462 0 0 6 12
|
||||
4000 357.40776 -186.78 -16.453111 14.915105 0.65771539 27 0.082003877 0.08249082 0 0 9 18
|
||||
5000 399.94731 1524.2909 -16.624678 18.677282 0.73079488 30 0.071285101 0.072731705 0 0 10 20
|
||||
6000 354.71736 60.134827 -18.988979 16.565073 0.73079488 30 0.071615663 0.071713414 0 0 10 20
|
||||
7000 483.32057 966.32174 -5.7393251 10.565037 0.36539744 15 0.087027775 0.089855826 0 0 5 10
|
||||
8000 547.68562 494.96891 -4.125626 11.97201 0.36539744 15 0.11738082 0.11937373 0 0 5 10
|
||||
9000 433.76488 390.91467 -0.85312985 5.1718828 0.21923846 9 0.13265238 0.13513212 0 0 3 6
|
||||
10000 330.01685 -862.07457 -26.494645 18.690633 0.87695385 36 0.13775034 0.13905403 0 0 12 24
|
||||
11000 334.26318 -578.48274 -13.236965 12.288625 0.5846359 24 0.13713936 0.13960485 0 0 8 16
|
||||
12000 243.68657 -1244.7156 -25.757644 12.590645 0.80387436 33 0.1339588 0.13588739 0 0 11 22
|
||||
13000 307.66758 -429.66928 -17.864639 14.367878 0.73079488 30 0.12604721 0.1278094 0 0 10 20
|
||||
14000 330.91434 495.97112 -15.374248 13.809499 0.65771539 27 0.12011756 0.12145865 0 0 9 18
|
||||
15000 564.87966 982.72332 -14.810525 26.379517 0.73079488 30 0.12164324 0.12343521 0 0 10 20
|
||||
16000 342.63867 -54.776299 -2.2580523 5.7875978 0.29231795 12 0.13535812 0.13790758 0 0 4 8
|
||||
17000 461.07005 -2.4317694 -1.145154 3.2068452 0.14615898 6 0.1444739 0.14730804 0 0 2 4
|
||||
18000 197.21207 -40.124433 -7.0857418 5.2906654 0.43847693 18 0.14403997 0.14574329 0 0 6 12
|
||||
19000 393.36395 -420.49802 -11.172739 14.461366 0.5846359 24 0.15005606 0.15142063 0 0 8 16
|
||||
20000 356.48539 56.071962 -1.7861789 4.2504609 0.21923846 9 0.15422732 0.15627984 0 0 3 6
|
||||
Loop time of 19.5982 on 1 procs for 20000 steps with 9 atoms
|
||||
|
||||
Performance: 88.171 ns/day, 0.272 hours/ns, 1020.502 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 | 2.3404 | 2.3404 | 2.3404 | 0.0 | 11.94
|
||||
Bond | 0.033919 | 0.033919 | 0.033919 | 0.0 | 0.17
|
||||
Kspace | 0.19974 | 0.19974 | 0.19974 | 0.0 | 1.02
|
||||
Neigh | 0.11478 | 0.11478 | 0.11478 | 0.0 | 0.59
|
||||
Comm | 0.22538 | 0.22538 | 0.22538 | 0.0 | 1.15
|
||||
Output | 0.00096536 | 0.00096536 | 0.00096536 | 0.0 | 0.00
|
||||
Modify | 16.627 | 16.627 | 16.627 | 0.0 | 84.84
|
||||
Other | | 0.05594 | | | 0.29
|
||||
|
||||
Nlocal: 9.00000 ave 9 max 9 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 703.000 ave 703 max 703 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 719.000 ave 719 max 719 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 719
|
||||
Ave neighs/atom = 79.888889
|
||||
Ave special neighs/atom = 2.0000000
|
||||
Neighbor list builds = 20196
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:19
|
||||
Reference in New Issue
Block a user