tx258/lammps-gran-kokkos
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

symlink potentials

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files

1
examples/PACKAGES/interlayer/aip_water_2dm/COH.DMC.aip.water.2dm Symbolic link
View File

@ -0,0 +1 @@
../../../../potentials/COH.DMC.aip.water.2dm

46
examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water
View File

@ -4,26 +4,26 @@ boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
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 3 1.008 # hydrogen mass (g/mole)
mass 3 1.008 # hydrogen mass (g/mole)
# Separate atom groups
group gr molecule 1
group water molecule 2
group gr molecule 1
group water molecule 2
######################## Potential defition ##############################
# 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_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 * * aip/water/2dm COH.aip.water.2dm C Ow Hw # C-H2O
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 * * aip/water/2dm COH.DMC.aip.water.2dm C Ow Hw # C-H2O
# bond and angle
bond_style harmonic
bond_coeff 1 0.0 0.9572
angle_style harmonic
angle_coeff 1 0.0 104.52
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
@ -31,21 +31,21 @@ 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 aip/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
compute 1 all pair lj/cut/tip4p/long
compute 2 all pair aip/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
fix subf gr setforce 0.0 0.0 0.0
fix 1 water shake 0.0001 20 100 b 1 a 1
timestep 1e-3
velocity water create 300.0 12345 dist gaussian mom yes rot yes
fix 2 water nve
run 1000
timestep 1e-3
velocity water create 300.0 12345 dist gaussian mom yes rot yes
fix 2 water nve
run 1000

46
examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water.opt
View File

@ -4,26 +4,26 @@ boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
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 3 1.008 # hydrogen mass (g/mole)
mass 3 1.008 # hydrogen mass (g/mole)
# Separate atom groups
group gr molecule 1
group water molecule 2
group gr molecule 1
group water molecule 2
######################## Potential defition ##############################
# 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_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 * * aip/water/2dm/opt COH.aip.water.2dm C Ow Hw # C-H2O
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 * * aip/water/2dm/opt COH.DMC.aip.water.2dm C Ow Hw # C-H2O
# bond and angle
bond_style harmonic
bond_coeff 1 0.0 0.9572
angle_style harmonic
angle_coeff 1 0.0 104.52
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
@ -31,21 +31,21 @@ 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 aip/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
compute 1 all pair lj/cut/tip4p/long
compute 2 all pair aip/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
fix subf gr setforce 0.0 0.0 0.0
fix 1 water shake 0.0001 20 100 b 1 a 1
timestep 1e-3
velocity water create 300.0 12345 dist gaussian mom yes rot yes
fix 2 water nve
run 1000
timestep 1e-3
velocity water create 300.0 12345 dist gaussian mom yes rot yes
fix 2 water nve
run 1000

1
examples/PACKAGES/pafi/Fe_mm.eam.fs Symbolic link
View File

@ -0,0 +1 @@
../../../potentials/Fe_mm.eam.fs

1
examples/PACKAGES/ti/Cu_mishin1.eam.alloy Symbolic link
View File

@ -0,0 +1 @@
../../../potentials/Cu_mishin1.eam.alloy

0
potentials/CBNOH.aip.water.2dm Executable file → Normal file
View File