diff --git a/examples/USER/eff/Auger-Adamantane/in.adamantane_ionized.nve b/examples/USER/eff/Auger-Adamantane/in.adamantane_ionized.nve index a465ed122f4ef8415b12c3f362a707356c8929e7..77c7b0d4654259fca8c2e551577dad213da044f6 100644 --- a/examples/USER/eff/Auger-Adamantane/in.adamantane_ionized.nve +++ b/examples/USER/eff/Auger-Adamantane/in.adamantane_ionized.nve @@ -23,7 +23,8 @@ thermo_modify temp effTemp # Minimization min_style cg dump 1 all xyz 500 ${sname}.min.xyz -dump 2 all custom 500 ${sname}.min.lammpstrj id type x y z spin eradius fx fy fz erforce +compute 1 all property/atom spin eradius erforce +dump 2 all custom 500 ${sname}.min.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3] min_modify line quadratic minimize 0.0 1.0e-5 10000 100000 @@ -40,7 +41,7 @@ timestep 0.001 fix 1 all nve/eff dump 1 all xyz 1000 ${sname}.nve.xyz -dump 2 all custom 1000 ${sname}.nve.lammpstrj id type x y z spin eradius fx fy fz erforce +dump 2 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3] #restart 1000 ${sname}.nve.restart1 ${sname}.nve.restart2 run 200000 diff --git a/examples/USER/eff/Be-solid/in.Be-solid.spe b/examples/USER/eff/Be-solid/in.Be-solid.spe index 967f4509824594439a83ec020c85f1abcb323ef5..e7245cabbc29d030538ffc055dc53994a6ff2e12 100644 --- a/examples/USER/eff/Be-solid/in.Be-solid.spe +++ b/examples/USER/eff/Be-solid/in.Be-solid.spe @@ -22,7 +22,8 @@ thermo 10 thermo_style custom step etotal pe ke temp press thermo_modify temp effTemp -dump 1 all custom 1 ${sname}.spe.lammpstrj id type x y z spin eradius +compute 1 all property/atom spin eradius +dump 1 all custom 1 ${sname}.spe.lammpstrj id type x y z c_1[1] c_1[2] fix 1 all nve/eff diff --git a/examples/USER/eff/CH4/in.ch4.dynamics b/examples/USER/eff/CH4/in.ch4.dynamics index 2a85262796e81bbcdfd4077cf230c888890233f1..2536fa8f4817aaff8fbc1d8b3dcdefa05f6df8c5 100644 --- a/examples/USER/eff/CH4/in.ch4.dynamics +++ b/examples/USER/eff/CH4/in.ch4.dynamics @@ -16,7 +16,8 @@ comm_modify vel yes # Minimize min_style cg -dump 1 all custom 1 ${sname}.min.lammpstrj id type q spin eradius x y z +compute 1 all property/atom spin eradius +dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z min_modify line quadratic dmax 0.1 minimize 0 1.0e-6 1000 10000 @@ -34,7 +35,7 @@ timestep 0.005 fix 1 all nve/eff # the custom dump includes the radii -dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q spin eradius x y z +dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z dump 3 all xyz 1000 ${sname}.nve.xyz run 100000 diff --git a/examples/USER/eff/CH4/in.ch4.min b/examples/USER/eff/CH4/in.ch4.min index 17df27892ce484293f7546488da4ac2a504f5ce0..69b7c15bd4f6065b445d3ed2740a7ad932647bdb 100644 --- a/examples/USER/eff/CH4/in.ch4.min +++ b/examples/USER/eff/CH4/in.ch4.min @@ -26,6 +26,7 @@ thermo 1 thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres min_style cg -dump 2 all custom 10 ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce +compute 1 all property/atom spin eradius erforce +dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3] minimize 0 1e-6 2000 4000 diff --git a/examples/USER/eff/CH4/in.ch4_ionized.dynamics b/examples/USER/eff/CH4/in.ch4_ionized.dynamics index 762dcd2d0a62b0b4da7348910a6e5871f27b9f04..14f214296fb65c750e43a0012f913e8e48bc2671 100644 --- a/examples/USER/eff/CH4/in.ch4_ionized.dynamics +++ b/examples/USER/eff/CH4/in.ch4_ionized.dynamics @@ -31,7 +31,8 @@ timestep 0.001 fix 1 all nvt/eff temp 300.0 300.0 0.1 # the custom dump includes the radii -dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z spin eradius +compute 1 all property/atom spin eradius +dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1[2] dump 2 all xyz 100 ${sname}.nvt.xyz run 1000000 diff --git a/examples/USER/eff/ECP/Si2H6/in.Si2H6 b/examples/USER/eff/ECP/Si2H6/in.Si2H6 index da289af9925392557e381f118acbb574d1b64feb..fd2be9db58a4c21e1a1ea7d13be7b74c8c280574 100644 --- a/examples/USER/eff/ECP/Si2H6/in.Si2H6 +++ b/examples/USER/eff/ECP/Si2H6/in.Si2H6 @@ -40,7 +40,8 @@ thermo_modify temp effTemp press effPress min_style cg dump 1 all xyz 2 ${sname}.min.xyz -dump 2 all custom 2 ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce +compute 1 all property/atom spin eradius erforce +dump 2 all custom 2 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3] min_modify line quadratic minimize 0 1.0e-5 1000 10000 diff --git a/examples/USER/eff/ECP/Si2H6/in.Si2H6.ang b/examples/USER/eff/ECP/Si2H6/in.Si2H6.ang index 902ec6d8612cb376f6d497f7f60d68543dfbd914..09d667bd2c059f691cee1909725e34307f626fc7 100644 --- a/examples/USER/eff/ECP/Si2H6/in.Si2H6.ang +++ b/examples/USER/eff/ECP/Si2H6/in.Si2H6.ang @@ -40,7 +40,8 @@ thermo_modify temp effTemp press effPress min_style cg dump 1 all xyz 10 ${sname}.min.xyz -dump 2 all custom 10 ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce +compute 1 all property/atom spin eradius erforce +dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3] min_modify line quadratic minimize 0 1.0e-6 2000 10000 @@ -52,7 +53,7 @@ velocity all create 300.0 4928459 rot yes mom yes dist gaussian timestep 0.001 -dump 1 all custom 1000 ${sname}.nvt.lammpstrj id type q spin eradius x y z fx fy fz erforce +dump 1 all custom 1000 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3] #fix 0 all langevin/eff 300.0 300.0 0.1 fix 1 all nvt/eff temp 300.0 300.0 0.1 diff --git a/examples/USER/eff/ECP/SiC/bulk/in.SiC b/examples/USER/eff/ECP/SiC/bulk/in.SiC index 728446ef292ea9a19ed7e7d7e0d8b3f36b027cac..63f44e6809651d76f760d796768ed63b61bb0e44 100644 --- a/examples/USER/eff/ECP/SiC/bulk/in.SiC +++ b/examples/USER/eff/ECP/SiC/bulk/in.SiC @@ -34,8 +34,9 @@ thermo_modify lost warn norm yes flush yes min_style cg dump 1 all xyz ${nstep} ${sname}.min.xyz -dump 2 all custom ${nstep} ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce -dump 3 all custom ${nstep} ${sname}.data.restart id type q spin eradius x y z +compute 1 all property/atom spin eradius erforce +dump 2 all custom ${nstep} ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3] +dump 3 all custom ${nstep} ${sname}.data.restart id type q c_1[1] c_1[2] x y z min_modify line quadratic minimize 0 1e-8 100000 1000000 diff --git a/examples/USER/eff/ECP/SiH4/in.SiH4 b/examples/USER/eff/ECP/SiH4/in.SiH4 index 7ae283e9fc3561e33a7b5c1f3f104c718f810310..7bd04d7ba2cd7677ecca6d7f29cc1b47c4dca9da 100644 --- a/examples/USER/eff/ECP/SiH4/in.SiH4 +++ b/examples/USER/eff/ECP/SiH4/in.SiH4 @@ -41,7 +41,8 @@ thermo_modify temp effTemp press effPress min_style cg dump 1 all xyz 1 ${sname}.min.xyz -dump 2 all custom 1 ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce +compute 1 all property/atom spin eradius erforce +dump 2 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3] min_modify line quadratic minimize 0 1.0e-5 1000 10000 diff --git a/examples/USER/eff/ECP/SiH4/in.SiH4.ang b/examples/USER/eff/ECP/SiH4/in.SiH4.ang index a73133a7175068617b2d9b1bd4f88bb86a8b51db..8b0a709fb93eed695204c265c8e143ddab15560e 100644 --- a/examples/USER/eff/ECP/SiH4/in.SiH4.ang +++ b/examples/USER/eff/ECP/SiH4/in.SiH4.ang @@ -40,7 +40,8 @@ thermo_modify temp effTemp press effPress min_style cg dump 1 all xyz 1 ${sname}.min.xyz -dump 2 all custom 1 ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce +compute 1 all property/atom spin eradius erforce +dump 2 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3] min_modify line quadratic minimize 0 1.0e-5 1000 10000 diff --git a/examples/USER/eff/H2/in.h2 b/examples/USER/eff/H2/in.h2 index 0c42a9c83e1bcdb97aec085dccc336f980f64fd2..8f4a63cc8439ebdc7ec913934d435861f4610d51 100644 --- a/examples/USER/eff/H2/in.h2 +++ b/examples/USER/eff/H2/in.h2 @@ -41,8 +41,9 @@ fix 1 all nve/eff run 10000 unfix 3 +#compute 1 all property/atom spin eradius #fix 1 all npt/eff temp 3000.0 3000.0 0.1 iso 1e7 1e7 1.0 drag 0.5 -#dump 1 all custom 100 dump.file id type q spin eradius x y z +#dump 1 all custom 100 dump.file id type q c_1[1] c_1[2] x y z #fix 1 all nve/eff diff --git a/examples/USER/eff/H_plasma/in.h2bulk.npt b/examples/USER/eff/H_plasma/in.h2bulk.npt index 4e925c2473752ddc5be0b48a5e1d991fb462f229..6d9fc5d55f7e44a95c952e704744ad040b1375ee 100644 --- a/examples/USER/eff/H_plasma/in.h2bulk.npt +++ b/examples/USER/eff/H_plasma/in.h2bulk.npt @@ -38,7 +38,8 @@ thermo_style custom step pe temp press vol v_density thermo_modify temp effTemp dump 2 all xyz 10000 ${sname}.npt.xyz -dump 3 all custom 10000 ${sname}.npt.lammpstrj id type x y z spin eradius +compute 1 all property/atom spin eradius +dump 3 all custom 10000 ${sname}.npt.lammpstrj id type x y z c_1[1] c_1[2] run 10000000 diff --git a/examples/USER/eff/H_plasma/in.h2bulk.nve b/examples/USER/eff/H_plasma/in.h2bulk.nve index 94c2e6ce1d5880c61c3a373c8a3458556dc9ef62..9786ff476f08efe495f93ff2a2d5f57023c9b22e 100644 --- a/examples/USER/eff/H_plasma/in.h2bulk.nve +++ b/examples/USER/eff/H_plasma/in.h2bulk.nve @@ -38,7 +38,8 @@ compute peatom all pe/atom compute keatom all ke/atom/eff dump 2 all xyz 1000 ${sname}.nve.xyz -dump 3 all custom 1000 ${sname}.nve.lammpstrj id type x y z spin eradius c_peatom c_keatom +compute 1 all property/atom spin eradius +dump 3 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom run 100000 diff --git a/examples/USER/eff/H_plasma/in.h2bulk.nve.ang b/examples/USER/eff/H_plasma/in.h2bulk.nve.ang index d4b952b7a008340d2d7df956923548e7a933e02d..4935e39be3053ce32c10d75d37d164093f54eab6 100644 --- a/examples/USER/eff/H_plasma/in.h2bulk.nve.ang +++ b/examples/USER/eff/H_plasma/in.h2bulk.nve.ang @@ -49,7 +49,8 @@ compute peatom all pe/atom compute keatom all ke/atom/eff dump 2 all xyz 1000 ${sname}.nve.xyz -dump 3 all custom 1000 ${sname}.nve.lammpstrj id type x y z spin eradius c_peatom c_keatom +compute 1 all property/atom spin eradius +dump 3 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom run 100000 diff --git a/examples/USER/eff/Li-dendritic/in.Li-dendritic.min b/examples/USER/eff/Li-dendritic/in.Li-dendritic.min index 5411da21a6ef09eb94a2273f4f085e1c604b15e8..f791544e4406a9477e11bb2d9dd2ce69fc8e1985 100644 --- a/examples/USER/eff/Li-dendritic/in.Li-dendritic.min +++ b/examples/USER/eff/Li-dendritic/in.Li-dendritic.min @@ -21,7 +21,8 @@ thermo 10 thermo_style custom step etotal pe ke temp press thermo_modify temp effTemp -dump 1 all custom 10 ${sname}.min.lammpstrj id type q spin eradius x y z +compute 1 all property/atom spin eradius +dump 1 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z dump 2 all xyz 10 ${sname}.min.xyz restart 10 ${sname}.nve.restart1 ${sname}.nve.restart2 diff --git a/examples/USER/eff/Li-dendritic/in.Li-dendritic.nvt b/examples/USER/eff/Li-dendritic/in.Li-dendritic.nvt index eee8eafe6a3122b456787e8f1fc72af4857102bb..143e23cbc1c3cc176780b2f34761b84243e4c414 100644 --- a/examples/USER/eff/Li-dendritic/in.Li-dendritic.nvt +++ b/examples/USER/eff/Li-dendritic/in.Li-dendritic.nvt @@ -24,7 +24,9 @@ thermo_modify temp effTemp press effPress print "Starting minimizer" min_style cg -#dump 1 all custom 100 ${sname}.min.lammpstrj id type x y z q spin eradius + +compute 1 all property/atom spin eradius +#dump 1 all custom 100 ${sname}.min.lammpstrj id type x y z q c_1[1] c_1[2] #dump 2 all xyz 100 ${sname}.min.xyz min_modify line quadratic dmax 0.05 minimize 0 1.0e-7 1000 2000 @@ -40,7 +42,7 @@ timestep 0.005 print "Starting nvt" fix 1 all nvt/eff temp 300.0 300.0 0.1 -dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z spin eradius +dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1[2] dump 2 all xyz 100 ${sname}.nvt.xyz restart 100 ${sname}.nvt.restart1 ${sname}.nvt.restart2 diff --git a/examples/USER/eff/Li-solid/in.Li.ang b/examples/USER/eff/Li-solid/in.Li.ang index 44a932000a7300f6d5e4a79710e9e600f60f3b86..c9a726b88c191c6504a2a2d75217dedb4bb34baa 100644 --- a/examples/USER/eff/Li-solid/in.Li.ang +++ b/examples/USER/eff/Li-solid/in.Li.ang @@ -51,7 +51,8 @@ unfix 0 unfix 1 fix 1 all nvt/eff temp 3000.0 3000.0 100.0 -dump 1 all custom 1000 ${sname}.nvt.lammpstrj id type q spin eradius x y z vx vy vz ervel +compute 1 all property/atom spin eradius ervel +dump 1 all custom 1000 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z vx vy vz c_1[3] run 100000 diff --git a/examples/USER/eff/fixed-core/C2H6/in.C2H6fc.ang b/examples/USER/eff/fixed-core/C2H6/in.C2H6fc.ang index 8c4c98ac9eb02f800d17d7399df73b894e25309a..74ced0db88c69262621b443c9f8d340340860acb 100644 --- a/examples/USER/eff/fixed-core/C2H6/in.C2H6fc.ang +++ b/examples/USER/eff/fixed-core/C2H6/in.C2H6fc.ang @@ -39,8 +39,9 @@ thermo_modify temp effTemp press effPress min_style cg dump 1 all xyz 100 ${sname}.min.xyz -dump 2 all custom 100 ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce -dump 3 all custom 100 data.${sname}.restart id type q spin eradius x y z +compute 1 all property/atom spin eradius erforce +dump 2 all custom 100 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3] +dump 3 all custom 100 data.${sname}.restart id type q c_1[1] c_1[2] x y z min_modify line quadratic minimize 0 1e-6 1000 2000 @@ -54,7 +55,7 @@ velocity all create 1.0 4928459 rot yes mom yes dist gaussian timestep 0.001 fix 1 all nvt/eff temp 1.0 10000.0 1.0 -dump 2 all custom 100 ${sname}.nvt.lammpstrj id type q spin eradius x y z fx fy fz erforce +dump 2 all custom 100 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3] run 100000 diff --git a/examples/USER/eff/fixed-core/C2H6/in.C2H6fc.bohr b/examples/USER/eff/fixed-core/C2H6/in.C2H6fc.bohr index dd42e48fb959ec78e1890436d8e40b43c714c478..69395eb041dc862e62a547e2012afb74fe652c40 100644 --- a/examples/USER/eff/fixed-core/C2H6/in.C2H6fc.bohr +++ b/examples/USER/eff/fixed-core/C2H6/in.C2H6fc.bohr @@ -38,8 +38,9 @@ thermo_modify temp effTemp press effPress min_style cg dump 1 all xyz 10 ${sname}.min.xyz -dump 2 all custom 10 ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce -dump 3 all custom 10 data.${sname}.restart id type q spin eradius x y z +compute 1 all property/atom spin eradius erforce +dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3] +dump 3 all custom 10 data.${sname}.restart id type q c_1[1] c_1[2] x y z min_modify line quadratic minimize 0 1e-6 1000 2000 @@ -48,6 +49,6 @@ undump 2 undump 3 fix 1 all nvt/eff 1 2000 1.0 -dump 2 all custom 10 ${sname}.nvt.lammpstrj id type q spin eradius x y z fx fy fz erforce +dump 2 all custom 10 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3] run 10000 diff --git a/examples/USER/eff/fixed-core/CH4/in.CH4fc.ang b/examples/USER/eff/fixed-core/CH4/in.CH4fc.ang index 3720d844404c5d84b4950ff1f3d3cad1ecdd1b82..fbad1ce83cfb22190e40b197d03655c36bdf68e7 100644 --- a/examples/USER/eff/fixed-core/CH4/in.CH4fc.ang +++ b/examples/USER/eff/fixed-core/CH4/in.CH4fc.ang @@ -37,7 +37,8 @@ thermo_modify temp effTemp min_style cg dump 1 all xyz 10 ${sname}.min.xyz -dump 2 all custom 10 ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce +compute 1 all property/atom spin eradius erforce +dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3] #min_modify line quadratic minimize 0 1.0e-6 1000 10000 @@ -49,7 +50,7 @@ velocity all create 10.0 4928459 rot yes mom yes dist gaussian timestep 0.0005 -dump 1 all custom 1000 ${sname}.nvt.lammpstrj id type q spin eradius x y z fx fy fz erforce +dump 1 all custom 1000 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3] #fix 0 all langevin/eff 300.0 300.0 0.1 fix 1 all nvt/eff temp 10.0 10000.0 0.1 diff --git a/examples/USER/eff/fixed-core/CH4/in.CH4fc.bohr b/examples/USER/eff/fixed-core/CH4/in.CH4fc.bohr index 05246740a0735c18e5f12969a52158f78a3dc0c7..6e337998b751f909a3dcc45f7672453874c7d155 100644 --- a/examples/USER/eff/fixed-core/CH4/in.CH4fc.bohr +++ b/examples/USER/eff/fixed-core/CH4/in.CH4fc.bohr @@ -38,7 +38,8 @@ thermo_modify temp effTemp press effPress min_style cg dump 1 all xyz 10 ${sname}.min.xyz -dump 2 all custom 10 ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce +compute 1 all property/atom spin eradius erforce +dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3] min_modify line quadratic minimize 0 1.0e-6 1000 10000 @@ -50,7 +51,7 @@ velocity all create 10000.0 4928459 rot yes mom yes dist gaussian timestep 0.001 -dump 1 all custom 1000 ${sname}.nvt.lammpstrj id type q spin eradius x y z fx fy fz erforce +dump 1 all custom 1000 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3] #fix 0 all langevin/eff 300.0 300.0 0.1 fix 1 all nvt/eff temp 10000.0 10000.0 0.1