add examples
This commit is contained in:
oywg11
1
examples/PACKAGES/interlayer/ilp_water_2dm/COH.ILP
Symbolic link
1
examples/PACKAGES/interlayer/ilp_water_2dm/COH.ILP
Symbolic link
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../../../../potentials/COH.ILP
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2040
examples/PACKAGES/interlayer/ilp_water_2dm/gra_water.data
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2040
examples/PACKAGES/interlayer/ilp_water_2dm/gra_water.data
Normal file
File diff suppressed because it is too large
Load Diff
51
examples/PACKAGES/interlayer/ilp_water_2dm/in.gr_water
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51
examples/PACKAGES/interlayer/ilp_water_2dm/in.gr_water
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# Initialization
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units metal
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boundary p p p
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atom_style full
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processors * * 1 # domain decomposition over x and y
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read_data ./gra_water.data
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mass 1 12.0107 # carbon mass (g/mole)
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mass 2 15.9994 # oxygen mass (g/mole)
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mass 3 1.008 # hydrogen mass (g/mole)
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# Separate atom groups
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group gr molecule 1
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group water molecule 2
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######################## Potential defition ##############################
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# Interlayer potential
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pair_style hybrid/overlay ilp/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
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####################################################################
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pair_coeff 1 1 none
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pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
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pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
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pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
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pair_coeff * * ilp/water/2dm COH.ILP C Ow Hw # C-water
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# bond and angle
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bond_style harmonic
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bond_coeff 1 0.0 0.9572
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angle_style harmonic
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angle_coeff 1 0.0 104.52
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# define kspace calculation
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kspace_style pppm/tip4p 1E-5
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# Neighbor update settings
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neighbor 2.0 bin
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neigh_modify every 1 delay 5 check yes page 1000000 one 100000
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####################################################################
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# Calculate pair energy
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compute 1 all pair lj/cut/tip4p/long
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compute 2 all pair ilp/water/2dm
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compute wt water temp
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variable TIP4P equal c_1
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variable EILP equal c_2 # total interlayer energy
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variable temp_wt equal c_wt
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############# Output ##############
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thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
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thermo 100
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thermo_modify lost error
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fix subf gr setforce 0.0 0.0 0.0
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fix 1 water shake 0.0001 20 100 b 1 a 1
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timestep 1e-3
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velocity water create 300.0 12345 dist gaussian mom yes rot yes
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fix 2 water nve
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run 1000
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51
examples/PACKAGES/interlayer/ilp_water_2dm/in.gr_water.opt
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51
examples/PACKAGES/interlayer/ilp_water_2dm/in.gr_water.opt
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# Initialization
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units metal
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boundary p p p
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atom_style full
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processors * * 1 # domain decomposition over x and y
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read_data ./gra_water.data
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mass 1 12.0107 # carbon mass (g/mole)
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mass 2 15.9994 # oxygen mass (g/mole)
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mass 3 1.008 # hydrogen mass (g/mole)
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# Separate atom groups
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group gr molecule 1
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group water molecule 2
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######################## Potential defition ##############################
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# Interlayer potential
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pair_style hybrid/overlay ilp/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
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####################################################################
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pair_coeff 1 1 none
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pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
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pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
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pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
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pair_coeff * * ilp/water/2dm/opt COH.ILP C Ow Hw # C-water
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# bond and angle
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bond_style harmonic
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bond_coeff 1 0.0 0.9572
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angle_style harmonic
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angle_coeff 1 0.0 104.52
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# define kspace calculation
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kspace_style pppm/tip4p 1E-5
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# Neighbor update settings
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neighbor 2.0 bin
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neigh_modify every 1 delay 5 check yes page 1000000 one 100000
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####################################################################
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# Calculate pair energy
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compute 1 all pair lj/cut/tip4p/long
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compute 2 all pair ilp/water/2dm/opt
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compute wt water temp
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variable TIP4P equal c_1
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variable EILP equal c_2 # total interlayer energy
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variable temp_wt equal c_wt
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############# Output ##############
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thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
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thermo 100
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thermo_modify lost error
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fix subf gr setforce 0.0 0.0 0.0
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fix 1 water shake 0.0001 20 100 b 1 a 1
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timestep 1e-3
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velocity water create 300.0 12345 dist gaussian mom yes rot yes
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fix 2 water nve
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run 1000
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@ -0,0 +1,234 @@
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LAMMPS (23 Jun 2022)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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# Initialization
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units metal
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boundary p p p
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atom_style full
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processors * * 1 # domain decomposition over x and y
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read_data ./gra_water.data
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Reading data file ...
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orthogonal box = (0 0 0) to (46.92336 44.331078 200)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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936 atoms
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reading velocities ...
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936 velocities
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scanning bonds ...
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2 = max bonds/atom
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scanning angles ...
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1 = max angles/atom
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reading bonds ...
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96 bonds
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reading angles ...
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48 angles
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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special bonds CPU = 0.005 seconds
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read_data CPU = 0.020 seconds
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mass 1 12.0107 # carbon mass (g/mole)
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mass 2 15.9994 # oxygen mass (g/mole)
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mass 3 1.008 # hydrogen mass (g/mole)
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# Separate atom groups
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group gr molecule 1
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792 atoms in group gr
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group water molecule 2
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144 atoms in group water
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######################## Potential defition ##############################
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# Interlayer potential
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||||||
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pair_style hybrid/overlay ilp/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
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####################################################################
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pair_coeff 1 1 none
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pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
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pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
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pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
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pair_coeff * * ilp/water/2dm COH.ILP C Ow Hw # C-water
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Reading ilp/water/2dm potential file COH.ILP with DATE: 2023-05-17
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# bond and angle
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bond_style harmonic
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bond_coeff 1 0.0 0.9572
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angle_style harmonic
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||||||
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angle_coeff 1 0.0 104.52
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# define kspace calculation
|
||||||
|
kspace_style pppm/tip4p 1E-5
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||||||
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# Neighbor update settings
|
||||||
|
neighbor 2.0 bin
|
||||||
|
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
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||||||
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####################################################################
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||||||
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# Calculate pair energy
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||||||
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compute 1 all pair lj/cut/tip4p/long
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||||||
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compute 2 all pair ilp/water/2dm
|
||||||
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compute wt water temp
|
||||||
|
variable TIP4P equal c_1
|
||||||
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variable EILP equal c_2 # total interlayer energy
|
||||||
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variable temp_wt equal c_wt
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||||||
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############# Output ##############
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||||||
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thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
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||||||
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thermo 100
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||||||
|
thermo_modify lost error
|
||||||
|
|
||||||
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fix subf gr setforce 0.0 0.0 0.0
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fix 1 water shake 0.0001 20 100 b 1 a 1
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0 = # of size 2 clusters
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0 = # of size 3 clusters
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0 = # of size 4 clusters
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48 = # of frozen angles
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find clusters CPU = 0.001 seconds
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timestep 1e-3
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velocity water create 300.0 12345 dist gaussian mom yes rot yes
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fix 2 water nve
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run 1000
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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|
|
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Your simulation uses code contributions which should be cited:
|
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|
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- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
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@Article{Ouyang2018
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author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
|
||||||
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title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
|
||||||
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journal = {Nano Letters},
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||||||
|
volume = 18,
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||||||
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pages = {6009}
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year = 2018,
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}
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- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
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@Article{Ouyang2021
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||||||
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author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},
|
||||||
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title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide},
|
||||||
|
journal = {J. Chem. Theory Comput.},
|
||||||
|
volume = 17,
|
||||||
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pages = {7237–7245}
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year = 2021,
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}
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- ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
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@Article{Feng2023
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author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},
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title = {Registry-Dependent Potential for Interfaces of Water with Graphene},
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journal = {J. Phys. Chem. C},
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volume = 127,
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pages = {8704-8713}
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year = 2023,
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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PPPM initialization ...
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extracting TIP4P info from pair style
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using 12-bit tables for long-range coulomb (../kspace.cpp:342)
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G vector (1/distance) = 0.28684806
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grid = 25 24 80
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0001640931
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estimated relative force accuracy = 1.1395635e-05
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using single precision MKL FFT
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3d grid and FFT values/proc = 84320 48000
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WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
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Neighbor list info ...
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update every 1 steps, delay 5 steps, check yes
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max neighbors/atom: 100000, page size: 1000000
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master list distance cutoff = 18
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ghost atom cutoff = 18
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binsize = 9, bins = 6 5 23
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3 neighbor lists, perpetual/occasional/extra = 3 0 0
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(1) pair ilp/water/2dm, perpetual
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attributes: full, newton on, ghost
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pair build: full/bin/ghost
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stencil: full/ghost/bin/3d
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bin: standard
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(2) pair lj/cut/tip4p/long, perpetual, skip from (3)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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(3) neighbor class addition, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d
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bin: standard
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SHAKE stats (type/ave/delta/count) on step 0
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Bond: 1 0.957201 2.19705e-06 96
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Angle: 1 104.52 0.000203056 48
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Per MPI rank memory allocation (min/avg/max) = 33.53 | 33.53 | 33.53 Mbytes
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Step TotEng PotEng KinEng v_TIP4P v_EILP v_temp_wt
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0 -16.131263 -19.815178 3.6839141 189.37246 -1.903543 300
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SHAKE stats (type/ave/delta/count) on step 100
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Bond: 1 0.9572 9.54949e-07 96
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Angle: 1 104.52 6.01522e-05 48
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100 -17.494868 -20.796993 3.3021253 188.4955 -1.8981262 268.90898
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SHAKE stats (type/ave/delta/count) on step 200
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Bond: 1 0.9572 9.63922e-07 96
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Angle: 1 104.52 7.7021e-05 48
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||||||
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200 -17.486271 -21.194892 3.7086213 188.14561 -1.9871708 302.01203
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SHAKE stats (type/ave/delta/count) on step 300
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||||||
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Bond: 1 0.9572 1.4264e-06 96
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Angle: 1 104.52 6.48393e-05 48
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300 -17.502844 -20.993704 3.49086 188.23268 -1.8457229 284.27861
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SHAKE stats (type/ave/delta/count) on step 400
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Bond: 1 0.9572 1.33728e-06 96
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Angle: 1 104.52 7.6239e-05 48
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||||||
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400 -17.495287 -20.828353 3.3330658 188.48002 -1.8429075 271.42862
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SHAKE stats (type/ave/delta/count) on step 500
|
||||||
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Bond: 1 0.9572 1.14685e-06 96
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Angle: 1 104.52 8.58621e-05 48
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||||||
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500 -17.491435 -20.443044 2.9516084 188.7589 -1.8566335 240.36459
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SHAKE stats (type/ave/delta/count) on step 600
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Bond: 1 0.9572 9.17601e-07 96
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Angle: 1 104.52 8.24516e-05 48
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600 -17.505684 -20.608457 3.1027731 188.72078 -1.9560796 252.67471
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SHAKE stats (type/ave/delta/count) on step 700
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Bond: 1 0.9572 9.50422e-07 96
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Angle: 1 104.52 5.62423e-05 48
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700 -17.496703 -21.072663 3.5759596 188.2777 -1.9833956 291.20871
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SHAKE stats (type/ave/delta/count) on step 800
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Bond: 1 0.9572 1.15262e-06 96
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Angle: 1 104.52 7.02157e-05 48
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800 -17.478623 -20.819504 3.3408809 188.37868 -1.9112996 272.06505
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SHAKE stats (type/ave/delta/count) on step 900
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Bond: 1 0.9572 9.14138e-07 96
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Angle: 1 104.52 6.98742e-05 48
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900 -17.48086 -20.728495 3.2476349 188.59022 -1.8922102 264.47155
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SHAKE stats (type/ave/delta/count) on step 1000
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Bond: 1 0.9572 1.00586e-06 96
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Angle: 1 104.52 0.000111712 48
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||||||
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1000 -17.498465 -20.331545 2.8330804 188.87473 -1.812177 230.71225
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Loop time of 20.801 on 1 procs for 1000 steps with 936 atoms
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||||||
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|
||||||
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Performance: 4.154 ns/day, 5.778 hours/ns, 48.075 timesteps/s
|
||||||
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99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
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|
||||||
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MPI task timing breakdown:
|
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Section | min time | avg time | max time |%varavg| %total
|
||||||
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---------------------------------------------------------------
|
||||||
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Pair | 16.429 | 16.429 | 16.429 | 0.0 | 78.98
|
||||||
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Bond | 0.0010991 | 0.0010991 | 0.0010991 | 0.0 | 0.01
|
||||||
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Kspace | 3.4769 | 3.4769 | 3.4769 | 0.0 | 16.72
|
||||||
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Neigh | 0.83359 | 0.83359 | 0.83359 | 0.0 | 4.01
|
||||||
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Comm | 0.028825 | 0.028825 | 0.028825 | 0.0 | 0.14
|
||||||
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Output | 0.00046349 | 0.00046349 | 0.00046349 | 0.0 | 0.00
|
||||||
|
Modify | 0.01943 | 0.01943 | 0.01943 | 0.0 | 0.09
|
||||||
|
Other | | 0.01154 | | | 0.06
|
||||||
|
|
||||||
|
Nlocal: 936 ave 936 max 936 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 5242 ave 5242 max 5242 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 431382 ave 431382 max 431382 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 431382
|
||||||
|
Ave neighs/atom = 460.87821
|
||||||
|
Ave special neighs/atom = 0.30769231
|
||||||
|
Neighbor list builds = 28
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:21
|
||||||
@ -0,0 +1,234 @@
|
|||||||
|
LAMMPS (23 Jun 2022)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Initialization
|
||||||
|
units metal
|
||||||
|
boundary p p p
|
||||||
|
atom_style full
|
||||||
|
processors * * 1 # domain decomposition over x and y
|
||||||
|
read_data ./gra_water.data
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (46.92336 44.331078 200)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
936 atoms
|
||||||
|
reading velocities ...
|
||||||
|
936 velocities
|
||||||
|
scanning bonds ...
|
||||||
|
2 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
1 = max angles/atom
|
||||||
|
reading bonds ...
|
||||||
|
96 bonds
|
||||||
|
reading angles ...
|
||||||
|
48 angles
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
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 = 0.003 seconds
|
||||||
|
read_data CPU = 0.018 seconds
|
||||||
|
mass 1 12.0107 # carbon mass (g/mole)
|
||||||
|
mass 2 15.9994 # oxygen mass (g/mole)
|
||||||
|
mass 3 1.008 # hydrogen mass (g/mole)
|
||||||
|
# Separate atom groups
|
||||||
|
group gr molecule 1
|
||||||
|
792 atoms in group gr
|
||||||
|
group water molecule 2
|
||||||
|
144 atoms in group water
|
||||||
|
######################## Potential defition ##############################
|
||||||
|
# Interlayer potential
|
||||||
|
pair_style hybrid/overlay ilp/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
|
||||||
|
####################################################################
|
||||||
|
pair_coeff 1 1 none
|
||||||
|
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
|
||||||
|
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
||||||
|
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
||||||
|
pair_coeff * * ilp/water/2dm COH.ILP C Ow Hw # C-water
|
||||||
|
Reading ilp/water/2dm potential file COH.ILP with DATE: 2023-05-17
|
||||||
|
# bond and angle
|
||||||
|
bond_style harmonic
|
||||||
|
bond_coeff 1 0.0 0.9572
|
||||||
|
angle_style harmonic
|
||||||
|
angle_coeff 1 0.0 104.52
|
||||||
|
# define kspace calculation
|
||||||
|
kspace_style pppm/tip4p 1E-5
|
||||||
|
# Neighbor update settings
|
||||||
|
neighbor 2.0 bin
|
||||||
|
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
|
||||||
|
####################################################################
|
||||||
|
# Calculate pair energy
|
||||||
|
compute 1 all pair lj/cut/tip4p/long
|
||||||
|
compute 2 all pair ilp/water/2dm
|
||||||
|
compute wt water temp
|
||||||
|
variable TIP4P equal c_1
|
||||||
|
variable EILP equal c_2 # total interlayer energy
|
||||||
|
variable temp_wt equal c_wt
|
||||||
|
############# Output ##############
|
||||||
|
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
|
||||||
|
thermo 100
|
||||||
|
thermo_modify lost error
|
||||||
|
|
||||||
|
fix subf gr setforce 0.0 0.0 0.0
|
||||||
|
fix 1 water shake 0.0001 20 100 b 1 a 1
|
||||||
|
0 = # of size 2 clusters
|
||||||
|
0 = # of size 3 clusters
|
||||||
|
0 = # of size 4 clusters
|
||||||
|
48 = # of frozen angles
|
||||||
|
find clusters CPU = 0.001 seconds
|
||||||
|
|
||||||
|
timestep 1e-3
|
||||||
|
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
||||||
|
fix 2 water nve
|
||||||
|
run 1000
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
|
||||||
|
@Article{Ouyang2018
|
||||||
|
author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
|
||||||
|
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
|
||||||
|
journal = {Nano Letters},
|
||||||
|
volume = 18,
|
||||||
|
pages = {6009}
|
||||||
|
year = 2018,
|
||||||
|
}
|
||||||
|
|
||||||
|
- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
|
||||||
|
@Article{Ouyang2021
|
||||||
|
author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},
|
||||||
|
title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide},
|
||||||
|
journal = {J. Chem. Theory Comput.},
|
||||||
|
volume = 17,
|
||||||
|
pages = {7237–7245}
|
||||||
|
year = 2021,
|
||||||
|
}
|
||||||
|
|
||||||
|
- ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
|
||||||
|
@Article{Feng2023
|
||||||
|
author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},
|
||||||
|
title = {Registry-Dependent Potential for Interfaces of Water with Graphene},
|
||||||
|
journal = {J. Phys. Chem. C},
|
||||||
|
volume = 127,
|
||||||
|
pages = {8704-8713}
|
||||||
|
year = 2023,
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
PPPM initialization ...
|
||||||
|
extracting TIP4P info from pair style
|
||||||
|
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
|
||||||
|
G vector (1/distance) = 0.28684806
|
||||||
|
grid = 25 24 80
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 0.0001640931
|
||||||
|
estimated relative force accuracy = 1.1395635e-05
|
||||||
|
using single precision MKL FFT
|
||||||
|
3d grid and FFT values/proc = 30685 12480
|
||||||
|
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 5 steps, check yes
|
||||||
|
max neighbors/atom: 100000, page size: 1000000
|
||||||
|
master list distance cutoff = 18
|
||||||
|
ghost atom cutoff = 18
|
||||||
|
binsize = 9, bins = 6 5 23
|
||||||
|
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||||
|
(1) pair ilp/water/2dm, perpetual
|
||||||
|
attributes: full, newton on, ghost
|
||||||
|
pair build: full/bin/ghost
|
||||||
|
stencil: full/ghost/bin/3d
|
||||||
|
bin: standard
|
||||||
|
(2) pair lj/cut/tip4p/long, perpetual, skip from (3)
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: skip
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(3) neighbor class addition, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 0
|
||||||
|
Bond: 1 0.957201 2.19705e-06 96
|
||||||
|
Angle: 1 104.52 0.000203056 48
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 25.84 | 25.88 | 25.92 Mbytes
|
||||||
|
Step TotEng PotEng KinEng v_TIP4P v_EILP v_temp_wt
|
||||||
|
0 -16.131263 -19.815178 3.6839141 189.37246 -1.903543 300
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 100
|
||||||
|
Bond: 1 0.9572 9.54949e-07 96
|
||||||
|
Angle: 1 104.52 6.01522e-05 48
|
||||||
|
100 -17.494869 -20.796995 3.3021253 188.4955 -1.8981262 268.90898
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 200
|
||||||
|
Bond: 1 0.9572 9.63922e-07 96
|
||||||
|
Angle: 1 104.52 7.7021e-05 48
|
||||||
|
200 -17.48627 -21.194892 3.7086213 188.14561 -1.9871708 302.01203
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 300
|
||||||
|
Bond: 1 0.9572 1.4264e-06 96
|
||||||
|
Angle: 1 104.52 6.48393e-05 48
|
||||||
|
300 -17.502843 -20.993703 3.4908599 188.23268 -1.8457229 284.27861
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 400
|
||||||
|
Bond: 1 0.9572 1.33728e-06 96
|
||||||
|
Angle: 1 104.52 7.6239e-05 48
|
||||||
|
400 -17.495285 -20.82835 3.333065 188.48003 -1.8429074 271.42856
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 500
|
||||||
|
Bond: 1 0.9572 1.14685e-06 96
|
||||||
|
Angle: 1 104.52 8.58621e-05 48
|
||||||
|
500 -17.491436 -20.443043 2.9516075 188.7589 -1.8566335 240.36452
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 600
|
||||||
|
Bond: 1 0.9572 9.17601e-07 96
|
||||||
|
Angle: 1 104.52 8.24517e-05 48
|
||||||
|
600 -17.505683 -20.608456 3.1027734 188.72078 -1.9560795 252.67474
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 700
|
||||||
|
Bond: 1 0.9572 9.50425e-07 96
|
||||||
|
Angle: 1 104.52 5.62422e-05 48
|
||||||
|
700 -17.496706 -21.072664 3.575958 188.2777 -1.9833951 291.20858
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 800
|
||||||
|
Bond: 1 0.9572 1.15256e-06 96
|
||||||
|
Angle: 1 104.52 7.02177e-05 48
|
||||||
|
800 -17.478628 -20.819507 3.340879 188.37868 -1.9113009 272.06489
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 900
|
||||||
|
Bond: 1 0.9572 9.14163e-07 96
|
||||||
|
Angle: 1 104.52 6.98849e-05 48
|
||||||
|
900 -17.480865 -20.728504 3.2476386 188.5902 -1.8922108 264.47185
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 1000
|
||||||
|
Bond: 1 0.9572 1.00568e-06 96
|
||||||
|
Angle: 1 104.52 0.000111707 48
|
||||||
|
1000 -17.498474 -20.331607 2.833133 188.87466 -1.8121689 230.71654
|
||||||
|
Loop time of 9.42273 on 4 procs for 1000 steps with 936 atoms
|
||||||
|
|
||||||
|
Performance: 9.169 ns/day, 2.617 hours/ns, 106.126 timesteps/s
|
||||||
|
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 2.2328 | 4.3228 | 7.5931 | 103.1 | 45.88
|
||||||
|
Bond | 0.00084131 | 0.00088983 | 0.00095229 | 0.0 | 0.01
|
||||||
|
Kspace | 1.3979 | 4.6476 | 6.7252 | 98.8 | 49.32
|
||||||
|
Neigh | 0.34367 | 0.34371 | 0.34376 | 0.0 | 3.65
|
||||||
|
Comm | 0.042806 | 0.062908 | 0.075887 | 5.4 | 0.67
|
||||||
|
Output | 0.00037677 | 0.00041431 | 0.0004619 | 0.0 | 0.00
|
||||||
|
Modify | 0.028432 | 0.031138 | 0.034528 | 1.3 | 0.33
|
||||||
|
Other | | 0.01321 | | | 0.14
|
||||||
|
|
||||||
|
Nlocal: 234 ave 302 max 198 min
|
||||||
|
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||||
|
Nghost: 2876.5 ave 3122 max 2632 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 107846 ave 150684 max 82181 min
|
||||||
|
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 431382
|
||||||
|
Ave neighs/atom = 460.87821
|
||||||
|
Ave special neighs/atom = 0.30769231
|
||||||
|
Neighbor list builds = 28
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:09
|
||||||
@ -0,0 +1,251 @@
|
|||||||
|
LAMMPS (23 Jun 2022)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Initialization
|
||||||
|
units metal
|
||||||
|
boundary p p p
|
||||||
|
atom_style full
|
||||||
|
processors * * 1 # domain decomposition over x and y
|
||||||
|
read_data ./gra_water.data
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (46.92336 44.331078 200)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
936 atoms
|
||||||
|
reading velocities ...
|
||||||
|
936 velocities
|
||||||
|
scanning bonds ...
|
||||||
|
2 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
1 = max angles/atom
|
||||||
|
reading bonds ...
|
||||||
|
96 bonds
|
||||||
|
reading angles ...
|
||||||
|
48 angles
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
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 = 0.005 seconds
|
||||||
|
read_data CPU = 0.020 seconds
|
||||||
|
mass 1 12.0107 # carbon mass (g/mole)
|
||||||
|
mass 2 15.9994 # oxygen mass (g/mole)
|
||||||
|
mass 3 1.008 # hydrogen mass (g/mole)
|
||||||
|
# Separate atom groups
|
||||||
|
group gr molecule 1
|
||||||
|
792 atoms in group gr
|
||||||
|
group water molecule 2
|
||||||
|
144 atoms in group water
|
||||||
|
######################## Potential defition ##############################
|
||||||
|
# Interlayer potential
|
||||||
|
pair_style hybrid/overlay ilp/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
|
||||||
|
####################################################################
|
||||||
|
pair_coeff 1 1 none
|
||||||
|
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
|
||||||
|
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
||||||
|
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
||||||
|
pair_coeff * * ilp/water/2dm/opt COH.ILP C Ow Hw # C-water
|
||||||
|
Reading ilp/water/2dm potential file COH.ILP with DATE: 2023-05-17
|
||||||
|
# bond and angle
|
||||||
|
bond_style harmonic
|
||||||
|
bond_coeff 1 0.0 0.9572
|
||||||
|
angle_style harmonic
|
||||||
|
angle_coeff 1 0.0 104.52
|
||||||
|
# define kspace calculation
|
||||||
|
kspace_style pppm/tip4p 1E-5
|
||||||
|
# Neighbor update settings
|
||||||
|
neighbor 2.0 bin
|
||||||
|
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
|
||||||
|
####################################################################
|
||||||
|
# Calculate pair energy
|
||||||
|
compute 1 all pair lj/cut/tip4p/long
|
||||||
|
compute 2 all pair ilp/water/2dm/opt
|
||||||
|
compute wt water temp
|
||||||
|
variable TIP4P equal c_1
|
||||||
|
variable EILP equal c_2 # total interlayer energy
|
||||||
|
variable temp_wt equal c_wt
|
||||||
|
############# Output ##############
|
||||||
|
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
|
||||||
|
thermo 100
|
||||||
|
thermo_modify lost error
|
||||||
|
|
||||||
|
fix subf gr setforce 0.0 0.0 0.0
|
||||||
|
fix 1 water shake 0.0001 20 100 b 1 a 1
|
||||||
|
0 = # of size 2 clusters
|
||||||
|
0 = # of size 3 clusters
|
||||||
|
0 = # of size 4 clusters
|
||||||
|
48 = # of frozen angles
|
||||||
|
find clusters CPU = 0.001 seconds
|
||||||
|
|
||||||
|
timestep 1e-3
|
||||||
|
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
||||||
|
fix 2 water nve
|
||||||
|
run 1000
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
|
||||||
|
@Article{Ouyang2018
|
||||||
|
author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
|
||||||
|
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
|
||||||
|
journal = {Nano Letters},
|
||||||
|
volume = 18,
|
||||||
|
pages = {6009}
|
||||||
|
year = 2018,
|
||||||
|
}
|
||||||
|
|
||||||
|
- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
|
||||||
|
@Article{Ouyang2021
|
||||||
|
author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},
|
||||||
|
title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide},
|
||||||
|
journal = {J. Chem. Theory Comput.},
|
||||||
|
volume = 17,
|
||||||
|
pages = {7237–7245}
|
||||||
|
year = 2021,
|
||||||
|
}
|
||||||
|
|
||||||
|
- ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
|
||||||
|
@Article{Feng2023
|
||||||
|
author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},
|
||||||
|
title = {Registry-Dependent Potential for Interfaces of Water with Graphene},
|
||||||
|
journal = {J. Phys. Chem. C},
|
||||||
|
volume = 127,
|
||||||
|
pages = {8704-8713}
|
||||||
|
year = 2023,
|
||||||
|
}
|
||||||
|
|
||||||
|
- ilp/graphene/hbn/opt potential doi:10.1145/3458817.3476137
|
||||||
|
@inproceedings{gao2021lmff
|
||||||
|
author = {Gao, Ping and Duan, Xiaohui and Others},
|
||||||
|
title = {LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors},
|
||||||
|
year = {2021},
|
||||||
|
isbn = {9781450384421},
|
||||||
|
publisher = {Association for Computing Machinery},
|
||||||
|
address = {New York, NY, USA},
|
||||||
|
url = {https://doi.org/10.1145/3458817.3476137},
|
||||||
|
doi = {10.1145/3458817.3476137},
|
||||||
|
booktitle = {Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis},
|
||||||
|
articleno = {42},
|
||||||
|
numpages = {14},
|
||||||
|
location = {St. Louis, Missouri},
|
||||||
|
series = {SC'21},
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
PPPM initialization ...
|
||||||
|
extracting TIP4P info from pair style
|
||||||
|
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
|
||||||
|
G vector (1/distance) = 0.28684806
|
||||||
|
grid = 25 24 80
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 0.0001640931
|
||||||
|
estimated relative force accuracy = 1.1395635e-05
|
||||||
|
using single precision MKL FFT
|
||||||
|
3d grid and FFT values/proc = 84320 48000
|
||||||
|
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 5 steps, check yes
|
||||||
|
max neighbors/atom: 100000, page size: 1000000
|
||||||
|
master list distance cutoff = 18
|
||||||
|
ghost atom cutoff = 18
|
||||||
|
binsize = 9, bins = 6 5 23
|
||||||
|
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||||
|
(1) pair ilp/water/2dm/opt, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
(2) pair lj/cut/tip4p/long, perpetual, skip from (3)
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: skip
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(3) neighbor class addition, perpetual, half/full from (1)
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: halffull/newton
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 0
|
||||||
|
Bond: 1 0.957201 2.19705e-06 96
|
||||||
|
Angle: 1 104.52 0.000203056 48
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 25.89 | 25.89 | 25.89 Mbytes
|
||||||
|
Step TotEng PotEng KinEng v_TIP4P v_EILP v_temp_wt
|
||||||
|
0 -16.131263 -19.815178 3.6839141 189.37246 -1.903543 300
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 100
|
||||||
|
Bond: 1 0.9572 9.54949e-07 96
|
||||||
|
Angle: 1 104.52 6.01522e-05 48
|
||||||
|
100 -17.494868 -20.796993 3.3021253 188.4955 -1.8981262 268.90898
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 200
|
||||||
|
Bond: 1 0.9572 9.63922e-07 96
|
||||||
|
Angle: 1 104.52 7.7021e-05 48
|
||||||
|
200 -17.486271 -21.194892 3.7086213 188.14561 -1.9871708 302.01203
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 300
|
||||||
|
Bond: 1 0.9572 1.4264e-06 96
|
||||||
|
Angle: 1 104.52 6.48393e-05 48
|
||||||
|
300 -17.502844 -20.993704 3.49086 188.23268 -1.8457229 284.27861
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 400
|
||||||
|
Bond: 1 0.9572 1.33728e-06 96
|
||||||
|
Angle: 1 104.52 7.6239e-05 48
|
||||||
|
400 -17.495287 -20.828353 3.3330658 188.48002 -1.8429075 271.42862
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 500
|
||||||
|
Bond: 1 0.9572 1.14685e-06 96
|
||||||
|
Angle: 1 104.52 8.58621e-05 48
|
||||||
|
500 -17.491436 -20.443044 2.9516084 188.7589 -1.8566335 240.36459
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 600
|
||||||
|
Bond: 1 0.9572 9.17601e-07 96
|
||||||
|
Angle: 1 104.52 8.24516e-05 48
|
||||||
|
600 -17.505684 -20.608457 3.1027731 188.72078 -1.9560796 252.67471
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 700
|
||||||
|
Bond: 1 0.9572 9.50422e-07 96
|
||||||
|
Angle: 1 104.52 5.62423e-05 48
|
||||||
|
700 -17.496701 -21.07266 3.5759595 188.2777 -1.9833956 291.20871
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 800
|
||||||
|
Bond: 1 0.9572 1.15262e-06 96
|
||||||
|
Angle: 1 104.52 7.02158e-05 48
|
||||||
|
800 -17.478623 -20.819504 3.340881 188.37868 -1.9112996 272.06506
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 900
|
||||||
|
Bond: 1 0.9572 9.14138e-07 96
|
||||||
|
Angle: 1 104.52 6.98742e-05 48
|
||||||
|
900 -17.480864 -20.728498 3.2476343 188.59022 -1.8922102 264.4715
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 1000
|
||||||
|
Bond: 1 0.9572 1.00586e-06 96
|
||||||
|
Angle: 1 104.52 0.000111711 48
|
||||||
|
1000 -17.498466 -20.331547 2.8330808 188.87473 -1.8121768 230.71228
|
||||||
|
Loop time of 8.95265 on 1 procs for 1000 steps with 936 atoms
|
||||||
|
|
||||||
|
Performance: 9.651 ns/day, 2.487 hours/ns, 111.699 timesteps/s
|
||||||
|
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 5.2127 | 5.2127 | 5.2127 | 0.0 | 58.23
|
||||||
|
Bond | 0.00083377 | 0.00083377 | 0.00083377 | 0.0 | 0.01
|
||||||
|
Kspace | 3.5005 | 3.5005 | 3.5005 | 0.0 | 39.10
|
||||||
|
Neigh | 0.17946 | 0.17946 | 0.17946 | 0.0 | 2.00
|
||||||
|
Comm | 0.028553 | 0.028553 | 0.028553 | 0.0 | 0.32
|
||||||
|
Output | 0.00035446 | 0.00035446 | 0.00035446 | 0.0 | 0.00
|
||||||
|
Modify | 0.01889 | 0.01889 | 0.01889 | 0.0 | 0.21
|
||||||
|
Other | | 0.01135 | | | 0.13
|
||||||
|
|
||||||
|
Nlocal: 936 ave 936 max 936 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 5242 ave 5242 max 5242 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 431382 ave 431382 max 431382 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 431382
|
||||||
|
Ave neighs/atom = 460.87821
|
||||||
|
Ave special neighs/atom = 0.30769231
|
||||||
|
Neighbor list builds = 28
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:09
|
||||||
@ -0,0 +1,251 @@
|
|||||||
|
LAMMPS (23 Jun 2022)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Initialization
|
||||||
|
units metal
|
||||||
|
boundary p p p
|
||||||
|
atom_style full
|
||||||
|
processors * * 1 # domain decomposition over x and y
|
||||||
|
read_data ./gra_water.data
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (46.92336 44.331078 200)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
936 atoms
|
||||||
|
reading velocities ...
|
||||||
|
936 velocities
|
||||||
|
scanning bonds ...
|
||||||
|
2 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
1 = max angles/atom
|
||||||
|
reading bonds ...
|
||||||
|
96 bonds
|
||||||
|
reading angles ...
|
||||||
|
48 angles
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
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 = 0.003 seconds
|
||||||
|
read_data CPU = 0.017 seconds
|
||||||
|
mass 1 12.0107 # carbon mass (g/mole)
|
||||||
|
mass 2 15.9994 # oxygen mass (g/mole)
|
||||||
|
mass 3 1.008 # hydrogen mass (g/mole)
|
||||||
|
# Separate atom groups
|
||||||
|
group gr molecule 1
|
||||||
|
792 atoms in group gr
|
||||||
|
group water molecule 2
|
||||||
|
144 atoms in group water
|
||||||
|
######################## Potential defition ##############################
|
||||||
|
# Interlayer potential
|
||||||
|
pair_style hybrid/overlay ilp/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
|
||||||
|
####################################################################
|
||||||
|
pair_coeff 1 1 none
|
||||||
|
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
|
||||||
|
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
||||||
|
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
||||||
|
pair_coeff * * ilp/water/2dm/opt COH.ILP C Ow Hw # C-water
|
||||||
|
Reading ilp/water/2dm potential file COH.ILP with DATE: 2023-05-17
|
||||||
|
# bond and angle
|
||||||
|
bond_style harmonic
|
||||||
|
bond_coeff 1 0.0 0.9572
|
||||||
|
angle_style harmonic
|
||||||
|
angle_coeff 1 0.0 104.52
|
||||||
|
# define kspace calculation
|
||||||
|
kspace_style pppm/tip4p 1E-5
|
||||||
|
# Neighbor update settings
|
||||||
|
neighbor 2.0 bin
|
||||||
|
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
|
||||||
|
####################################################################
|
||||||
|
# Calculate pair energy
|
||||||
|
compute 1 all pair lj/cut/tip4p/long
|
||||||
|
compute 2 all pair ilp/water/2dm/opt
|
||||||
|
compute wt water temp
|
||||||
|
variable TIP4P equal c_1
|
||||||
|
variable EILP equal c_2 # total interlayer energy
|
||||||
|
variable temp_wt equal c_wt
|
||||||
|
############# Output ##############
|
||||||
|
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
|
||||||
|
thermo 100
|
||||||
|
thermo_modify lost error
|
||||||
|
|
||||||
|
fix subf gr setforce 0.0 0.0 0.0
|
||||||
|
fix 1 water shake 0.0001 20 100 b 1 a 1
|
||||||
|
0 = # of size 2 clusters
|
||||||
|
0 = # of size 3 clusters
|
||||||
|
0 = # of size 4 clusters
|
||||||
|
48 = # of frozen angles
|
||||||
|
find clusters CPU = 0.001 seconds
|
||||||
|
|
||||||
|
timestep 1e-3
|
||||||
|
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
||||||
|
fix 2 water nve
|
||||||
|
run 1000
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
|
||||||
|
@Article{Ouyang2018
|
||||||
|
author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
|
||||||
|
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
|
||||||
|
journal = {Nano Letters},
|
||||||
|
volume = 18,
|
||||||
|
pages = {6009}
|
||||||
|
year = 2018,
|
||||||
|
}
|
||||||
|
|
||||||
|
- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
|
||||||
|
@Article{Ouyang2021
|
||||||
|
author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},
|
||||||
|
title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide},
|
||||||
|
journal = {J. Chem. Theory Comput.},
|
||||||
|
volume = 17,
|
||||||
|
pages = {7237–7245}
|
||||||
|
year = 2021,
|
||||||
|
}
|
||||||
|
|
||||||
|
- ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
|
||||||
|
@Article{Feng2023
|
||||||
|
author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},
|
||||||
|
title = {Registry-Dependent Potential for Interfaces of Water with Graphene},
|
||||||
|
journal = {J. Phys. Chem. C},
|
||||||
|
volume = 127,
|
||||||
|
pages = {8704-8713}
|
||||||
|
year = 2023,
|
||||||
|
}
|
||||||
|
|
||||||
|
- ilp/graphene/hbn/opt potential doi:10.1145/3458817.3476137
|
||||||
|
@inproceedings{gao2021lmff
|
||||||
|
author = {Gao, Ping and Duan, Xiaohui and Others},
|
||||||
|
title = {LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors},
|
||||||
|
year = {2021},
|
||||||
|
isbn = {9781450384421},
|
||||||
|
publisher = {Association for Computing Machinery},
|
||||||
|
address = {New York, NY, USA},
|
||||||
|
url = {https://doi.org/10.1145/3458817.3476137},
|
||||||
|
doi = {10.1145/3458817.3476137},
|
||||||
|
booktitle = {Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis},
|
||||||
|
articleno = {42},
|
||||||
|
numpages = {14},
|
||||||
|
location = {St. Louis, Missouri},
|
||||||
|
series = {SC'21},
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
PPPM initialization ...
|
||||||
|
extracting TIP4P info from pair style
|
||||||
|
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
|
||||||
|
G vector (1/distance) = 0.28684806
|
||||||
|
grid = 25 24 80
|
||||||
|
stencil order = 5
|
||||||
|
estimated absolute RMS force accuracy = 0.0001640931
|
||||||
|
estimated relative force accuracy = 1.1395635e-05
|
||||||
|
using single precision MKL FFT
|
||||||
|
3d grid and FFT values/proc = 30685 12480
|
||||||
|
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 5 steps, check yes
|
||||||
|
max neighbors/atom: 100000, page size: 1000000
|
||||||
|
master list distance cutoff = 18
|
||||||
|
ghost atom cutoff = 18
|
||||||
|
binsize = 9, bins = 6 5 23
|
||||||
|
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||||
|
(1) pair ilp/water/2dm/opt, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
(2) pair lj/cut/tip4p/long, perpetual, skip from (3)
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: skip
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
(3) neighbor class addition, perpetual, half/full from (1)
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: halffull/newton
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 0
|
||||||
|
Bond: 1 0.957201 2.19705e-06 96
|
||||||
|
Angle: 1 104.52 0.000203056 48
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 22.03 | 22.06 | 22.1 Mbytes
|
||||||
|
Step TotEng PotEng KinEng v_TIP4P v_EILP v_temp_wt
|
||||||
|
0 -16.131263 -19.815178 3.6839141 189.37246 -1.903543 300
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 100
|
||||||
|
Bond: 1 0.9572 9.54949e-07 96
|
||||||
|
Angle: 1 104.52 6.01522e-05 48
|
||||||
|
100 -17.494869 -20.796995 3.3021253 188.4955 -1.8981262 268.90898
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 200
|
||||||
|
Bond: 1 0.9572 9.63922e-07 96
|
||||||
|
Angle: 1 104.52 7.7021e-05 48
|
||||||
|
200 -17.48627 -21.194892 3.7086213 188.14561 -1.9871708 302.01203
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 300
|
||||||
|
Bond: 1 0.9572 1.4264e-06 96
|
||||||
|
Angle: 1 104.52 6.48393e-05 48
|
||||||
|
300 -17.502843 -20.993703 3.4908599 188.23268 -1.8457229 284.27861
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 400
|
||||||
|
Bond: 1 0.9572 1.33728e-06 96
|
||||||
|
Angle: 1 104.52 7.6239e-05 48
|
||||||
|
400 -17.495285 -20.82835 3.333065 188.48003 -1.8429074 271.42856
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 500
|
||||||
|
Bond: 1 0.9572 1.14685e-06 96
|
||||||
|
Angle: 1 104.52 8.58621e-05 48
|
||||||
|
500 -17.491436 -20.443043 2.9516075 188.7589 -1.8566335 240.36452
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 600
|
||||||
|
Bond: 1 0.9572 9.17601e-07 96
|
||||||
|
Angle: 1 104.52 8.24517e-05 48
|
||||||
|
600 -17.505682 -20.608456 3.1027734 188.72078 -1.9560795 252.67474
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 700
|
||||||
|
Bond: 1 0.9572 9.50425e-07 96
|
||||||
|
Angle: 1 104.52 5.62423e-05 48
|
||||||
|
700 -17.496706 -21.072664 3.575958 188.2777 -1.9833951 291.20858
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 800
|
||||||
|
Bond: 1 0.9572 1.15256e-06 96
|
||||||
|
Angle: 1 104.52 7.02177e-05 48
|
||||||
|
800 -17.478628 -20.819507 3.340879 188.37868 -1.9113009 272.0649
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 900
|
||||||
|
Bond: 1 0.9572 9.14163e-07 96
|
||||||
|
Angle: 1 104.52 6.98849e-05 48
|
||||||
|
900 -17.480868 -20.728506 3.2476383 188.5902 -1.8922108 264.47182
|
||||||
|
SHAKE stats (type/ave/delta/count) on step 1000
|
||||||
|
Bond: 1 0.9572 1.00568e-06 96
|
||||||
|
Angle: 1 104.52 0.000111707 48
|
||||||
|
1000 -17.498472 -20.331605 2.8331335 188.87466 -1.8121689 230.71657
|
||||||
|
Loop time of 4.7828 on 4 procs for 1000 steps with 936 atoms
|
||||||
|
|
||||||
|
Performance: 18.065 ns/day, 1.329 hours/ns, 209.082 timesteps/s
|
||||||
|
96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.26735 | 1.3839 | 3.2059 | 99.7 | 28.93
|
||||||
|
Bond | 0.00079377 | 0.00086039 | 0.00093529 | 0.0 | 0.02
|
||||||
|
Kspace | 1.4248 | 3.2254 | 4.3332 | 64.6 | 67.44
|
||||||
|
Neigh | 0.061885 | 0.061916 | 0.061951 | 0.0 | 1.29
|
||||||
|
Comm | 0.044281 | 0.065185 | 0.078628 | 5.1 | 1.36
|
||||||
|
Output | 0.0003482 | 0.0003787 | 0.00040746 | 0.0 | 0.01
|
||||||
|
Modify | 0.028727 | 0.031529 | 0.034914 | 1.3 | 0.66
|
||||||
|
Other | | 0.01367 | | | 0.29
|
||||||
|
|
||||||
|
Nlocal: 234 ave 302 max 198 min
|
||||||
|
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||||
|
Nghost: 2876.5 ave 3122 max 2632 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 107846 ave 150684 max 82181 min
|
||||||
|
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 431382
|
||||||
|
Ave neighs/atom = 460.87821
|
||||||
|
Ave special neighs/atom = 0.30769231
|
||||||
|
Neighbor list builds = 28
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:04
|
||||||
Reference in New Issue
Block a user