diff --git a/examples/PACKAGES/interlayer/aip_water_2dm/COH.DMC.aip.water.2dm b/examples/PACKAGES/interlayer/aip_water_2dm/COH.DMC.aip.water.2dm new file mode 120000 index 0000000000..83fe1fed34 --- /dev/null +++ b/examples/PACKAGES/interlayer/aip_water_2dm/COH.DMC.aip.water.2dm @@ -0,0 +1 @@ +../../../../potentials/COH.DMC.aip.water.2dm \ No newline at end of file diff --git a/examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water b/examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water index 9f8e717a7e..7024a82e07 100644 --- a/examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water +++ b/examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water @@ -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 diff --git a/examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water.opt b/examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water.opt index 8494bfcb3e..0ec86ccd85 100644 --- a/examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water.opt +++ b/examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water.opt @@ -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 diff --git a/examples/PACKAGES/pafi/Fe_mm.eam.fs b/examples/PACKAGES/pafi/Fe_mm.eam.fs new file mode 120000 index 0000000000..833ec1dfeb --- /dev/null +++ b/examples/PACKAGES/pafi/Fe_mm.eam.fs @@ -0,0 +1 @@ +../../../potentials/Fe_mm.eam.fs \ No newline at end of file diff --git a/examples/PACKAGES/ti/Cu_mishin1.eam.alloy b/examples/PACKAGES/ti/Cu_mishin1.eam.alloy new file mode 120000 index 0000000000..96df246acf --- /dev/null +++ b/examples/PACKAGES/ti/Cu_mishin1.eam.alloy @@ -0,0 +1 @@ +../../../potentials/Cu_mishin1.eam.alloy \ No newline at end of file diff --git a/potentials/CBNOH.aip.water.2dm b/potentials/CBNOH.aip.water.2dm old mode 100755 new mode 100644