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symlink potentials

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This commit is contained in:
Axel Kohlmeyer
2024-08-12 21:58:51 -04:00
parent a4bff8988b
commit 5bcfed5fce
6 changed files with 49 additions and 46 deletions
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1
examples/PACKAGES/interlayer/aip_water_2dm/COH.DMC.aip.water.2dm Symbolic link
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../../../../potentials/COH.DMC.aip.water.2dm

46
examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water
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@ -4,26 +4,26 @@ boundary p p p
atom_style full atom_style full
processors * * 1 # domain decomposition over x and y processors * * 1 # domain decomposition over x and y
read_data ./gra_water.data read_data ./gra_water.data
mass 1 12.0107 # carbon mass (g/mole) mass 1 12.0107 # carbon mass (g/mole)
mass 2 15.9994 # oxygen mass (g/mole) mass 2 15.9994 # oxygen mass (g/mole)
mass 3 1.008 # hydrogen mass (g/mole) mass 3 1.008 # hydrogen mass (g/mole)
# Separate atom groups # Separate atom groups
group gr molecule 1 group gr molecule 1
group water molecule 2 group water molecule 2
######################## Potential defition ############################## ######################## Potential defition ##############################
# Interlayer potential # Interlayer potential
pair_style hybrid/overlay aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5 pair_style hybrid/overlay aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
#################################################################### ####################################################################
pair_coeff 1 1 none pair_coeff 1 1 none
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O 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 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 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
pair_coeff * * aip/water/2dm COH.aip.water.2dm C Ow Hw # C-H2O pair_coeff * * aip/water/2dm COH.DMC.aip.water.2dm C Ow Hw # C-H2O
# bond and angle # bond and angle
bond_style harmonic bond_style harmonic
bond_coeff 1 0.0 0.9572 bond_coeff 1 0.0 0.9572
angle_style harmonic angle_style harmonic
angle_coeff 1 0.0 104.52 angle_coeff 1 0.0 104.52
# define kspace calculation # define kspace calculation
kspace_style pppm/tip4p 1E-5 kspace_style pppm/tip4p 1E-5
# Neighbor update settings # Neighbor update settings
@ -31,21 +31,21 @@ neighbor 2.0 bin
neigh_modify every 1 delay 5 check yes page 1000000 one 100000 neigh_modify every 1 delay 5 check yes page 1000000 one 100000
#################################################################### ####################################################################
# Calculate pair energy # Calculate pair energy
compute 1 all pair lj/cut/tip4p/long compute 1 all pair lj/cut/tip4p/long
compute 2 all pair aip/water/2dm compute 2 all pair aip/water/2dm
compute wt water temp compute wt water temp
variable TIP4P equal c_1 variable TIP4P equal c_1
variable EILP equal c_2 # total interlayer energy variable EILP equal c_2 # total interlayer energy
variable temp_wt equal c_wt variable temp_wt equal c_wt
############# Output ############## ############# Output ##############
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
thermo 100 thermo 100
thermo_modify lost error thermo_modify lost error
fix subf gr setforce 0.0 0.0 0.0 fix subf gr setforce 0.0 0.0 0.0
fix 1 water shake 0.0001 20 100 b 1 a 1 fix 1 water shake 0.0001 20 100 b 1 a 1
timestep 1e-3 timestep 1e-3
velocity water create 300.0 12345 dist gaussian mom yes rot yes velocity water create 300.0 12345 dist gaussian mom yes rot yes
fix 2 water nve fix 2 water nve
run 1000 run 1000

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examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water.opt
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@ -4,26 +4,26 @@ boundary p p p
atom_style full atom_style full
processors * * 1 # domain decomposition over x and y processors * * 1 # domain decomposition over x and y
read_data ./gra_water.data read_data ./gra_water.data
mass 1 12.0107 # carbon mass (g/mole) mass 1 12.0107 # carbon mass (g/mole)
mass 2 15.9994 # oxygen mass (g/mole) mass 2 15.9994 # oxygen mass (g/mole)
mass 3 1.008 # hydrogen mass (g/mole) mass 3 1.008 # hydrogen mass (g/mole)
# Separate atom groups # Separate atom groups
group gr molecule 1 group gr molecule 1
group water molecule 2 group water molecule 2
######################## Potential defition ############################## ######################## Potential defition ##############################
# Interlayer potential # Interlayer potential
pair_style hybrid/overlay aip/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5 pair_style hybrid/overlay aip/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 1 1 none
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O 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 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 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
pair_coeff * * aip/water/2dm/opt COH.aip.water.2dm C Ow Hw # C-H2O pair_coeff * * aip/water/2dm/opt COH.DMC.aip.water.2dm C Ow Hw # C-H2O
# bond and angle # bond and angle
bond_style harmonic bond_style harmonic
bond_coeff 1 0.0 0.9572 bond_coeff 1 0.0 0.9572
angle_style harmonic angle_style harmonic
angle_coeff 1 0.0 104.52 angle_coeff 1 0.0 104.52
# define kspace calculation # define kspace calculation
kspace_style pppm/tip4p 1E-5 kspace_style pppm/tip4p 1E-5
# Neighbor update settings # Neighbor update settings
@ -31,21 +31,21 @@ neighbor 2.0 bin
neigh_modify every 1 delay 5 check yes page 1000000 one 100000 neigh_modify every 1 delay 5 check yes page 1000000 one 100000
#################################################################### ####################################################################
# Calculate pair energy # Calculate pair energy
compute 1 all pair lj/cut/tip4p/long compute 1 all pair lj/cut/tip4p/long
compute 2 all pair aip/water/2dm/opt compute 2 all pair aip/water/2dm/opt
compute wt water temp compute wt water temp
variable TIP4P equal c_1 variable TIP4P equal c_1
variable EILP equal c_2 # total interlayer energy variable EILP equal c_2 # total interlayer energy
variable temp_wt equal c_wt variable temp_wt equal c_wt
############# Output ############## ############# Output ##############
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
thermo 100 thermo 100
thermo_modify lost error thermo_modify lost error
fix subf gr setforce 0.0 0.0 0.0 fix subf gr setforce 0.0 0.0 0.0
fix 1 water shake 0.0001 20 100 b 1 a 1 fix 1 water shake 0.0001 20 100 b 1 a 1
timestep 1e-3 timestep 1e-3
velocity water create 300.0 12345 dist gaussian mom yes rot yes velocity water create 300.0 12345 dist gaussian mom yes rot yes
fix 2 water nve fix 2 water nve
run 1000 run 1000

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examples/PACKAGES/pafi/Fe_mm.eam.fs Symbolic link
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../../../potentials/Fe_mm.eam.fs

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examples/PACKAGES/ti/Cu_mishin1.eam.alloy Symbolic link
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../../../potentials/Cu_mishin1.eam.alloy

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potentials/CBNOH.aip.water.2dm Executable file → Normal file
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