IMPORTANT NOTE: If your input script changes settings between 2 runs (e.g. adds a fix or dump or -compute or changes a neighbor list -parameter), then the initial setup must be performed. LAMMPS does not -check for this, but it would be an error to use the pre no option in -this case. +compute, changes a neighbor list +parameter, writes a restart file which can migrate atoms between +processors), then the initial setup must be performed. LAMMPS has no +easy way to check for this, but it would be an error to use the pre +no option in this case.
If post is specified as "no", the full timing summary is skipped; only a one-line summary timing is printed. diff --git a/doc/run.txt b/doc/run.txt index 79dabffa30..c38ea06236 100644 --- a/doc/run.txt +++ b/doc/run.txt @@ -97,10 +97,11 @@ must be done. IMPORTANT NOTE: If your input script changes settings between 2 runs (e.g. adds a "fix"_fix.html or "dump"_dump.html or -"compute"_compute.html or changes a "neighbor"_neigh_modify.html list -parameter), then the initial setup must be performed. LAMMPS does not -check for this, but it would be an error to use the {pre no} option in -this case. +"compute"_compute.html, changes a "neighbor"_neigh_modify.html list +parameter, writes a restart file which can migrate atoms between +processors), then the initial setup must be performed. LAMMPS has no +easy way to check for this, but it would be an error to use the {pre +no} option in this case. If {post} is specified as "no", the full timing summary is skipped; only a one-line summary timing is printed. diff --git a/examples/USER/eff/Auger-Adamantane/in.adamantane_ionized.nve b/examples/USER/eff/Auger-Adamantane/in.adamantane_ionized.nve index a465ed122f..77c7b0d465 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 967f450982..e7245cabbc 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 2a85262796..2536fa8f48 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 17df27892c..69b7c15bd4 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 762dcd2d0a..14f214296f 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 da289af992..c419b11144 100644 --- a/examples/USER/eff/ECP/Si2H6/in.Si2H6 +++ b/examples/USER/eff/ECP/Si2H6/in.Si2H6 @@ -23,7 +23,7 @@ variable epauli equal c_energies[2] variable estatics equal c_energies[3] variable errestrain equal c_energies[4] -communicate single vel yes +comm_modify vel yes compute peratom all stress/atom NULL compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3] @@ -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 902ec6d861..e33f77b57e 100644 --- a/examples/USER/eff/ECP/Si2H6/in.Si2H6.ang +++ b/examples/USER/eff/ECP/Si2H6/in.Si2H6.ang @@ -23,7 +23,7 @@ variable epauli equal c_energies[2] variable estatics equal c_energies[3] variable errestrain equal c_energies[4] -communicate single vel yes +comm_modify vel yes compute peratom all stress/atom NULL compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3] @@ -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 728446ef29..fff1112b41 100644 --- a/examples/USER/eff/ECP/SiC/bulk/in.SiC +++ b/examples/USER/eff/ECP/SiC/bulk/in.SiC @@ -14,7 +14,7 @@ pair_coeff * * pair_coeff 1 s 0.320852 2.283269 0.814857 pair_coeff 2 p 22.721015 0.728733 1.103199 17.695345 6.693621 -communicate single vel yes +comm_modify vel yes neigh_modify one 4000 page 40000 @@ -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 7ae283e9fc..ff474c9907 100644 --- a/examples/USER/eff/ECP/SiH4/in.SiH4 +++ b/examples/USER/eff/ECP/SiH4/in.SiH4 @@ -24,7 +24,7 @@ variable epauli equal c_energies[2] variable estatics equal c_energies[3] variable errestrain equal c_energies[4] -communicate single vel yes +comm_modify vel yes compute peratom all stress/atom NULL compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3] @@ -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 a73133a717..e483f486f0 100644 --- a/examples/USER/eff/ECP/SiH4/in.SiH4.ang +++ b/examples/USER/eff/ECP/SiH4/in.SiH4.ang @@ -23,7 +23,7 @@ variable epauli equal c_energies[2] variable estatics equal c_energies[3] variable errestrain equal c_energies[4] -communicate single vel yes +comm_modify vel yes compute peratom all stress/atom NULL compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3] @@ -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/H/in.h_atom.spe.ang b/examples/USER/eff/H/in.h_atom.spe.ang index 3d4897461e..2493e273c4 100644 --- a/examples/USER/eff/H/in.h_atom.spe.ang +++ b/examples/USER/eff/H/in.h_atom.spe.ang @@ -13,6 +13,7 @@ pair_style eff/cut 0.529177249 pair_coeff * * comm_modify vel yes +timestep 0.0001 compute energies all pair eff/cut variable eke equal c_energies[1] diff --git a/examples/USER/eff/H2/in.h2 b/examples/USER/eff/H2/in.h2 index 0c42a9c83e..8f4a63cc84 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 4e925c2473..6d9fc5d55f 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 94c2e6ce1d..9786ff476f 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 d4b952b7a0..4935e39be3 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 5411da21a6..f791544e44 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 eee8eafe6a..143e23cbc1 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 44a932000a..c9a726b88c 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/Li-solid/in.Li.bohr b/examples/USER/eff/Li-solid/in.Li.bohr index a02d524d01..2843d3ca6a 100644 --- a/examples/USER/eff/Li-solid/in.Li.bohr +++ b/examples/USER/eff/Li-solid/in.Li.bohr @@ -40,7 +40,10 @@ minimize 0 1e-6 100 2000 fix 0 all temp/rescale/eff 1 0.0 3000.0 0.02 0.5 fix 1 all npt/eff temp 3000.0 3000.0 0.1 iso 1e7 1e7 1.0 -dump 1 all custom 100 ${sname}.spe.lammpstrj id type q spin eradius x y z + +compute 1 all property/atom spin eradius +dump 1 all custom 1 ${sname}.spe.lammpstrj & + id type q c_1[1] c_1[2] x y z run 1000 diff --git a/examples/USER/eff/fixed-core/C2H6/in.C2H6fc.ang b/examples/USER/eff/fixed-core/C2H6/in.C2H6fc.ang index 8c4c98ac9e..e0275a6562 100644 --- a/examples/USER/eff/fixed-core/C2H6/in.C2H6fc.ang +++ b/examples/USER/eff/fixed-core/C2H6/in.C2H6fc.ang @@ -22,7 +22,7 @@ variable epauli equal c_energies[2] variable estatics equal c_energies[3] variable errestrain equal c_energies[4] -communicate single vel yes +comm_modify vel yes compute peratom all stress/atom NULL compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3] @@ -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 dd42e48fb9..399944cf8d 100644 --- a/examples/USER/eff/fixed-core/C2H6/in.C2H6fc.bohr +++ b/examples/USER/eff/fixed-core/C2H6/in.C2H6fc.bohr @@ -22,7 +22,7 @@ variable epauli equal c_energies[2] variable estatics equal c_energies[3] variable errestrain equal c_energies[4] -communicate single vel yes +comm_modify vel yes compute peratom all stress/atom NULL compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3] @@ -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 3720d84440..55c05ad6fa 100644 --- a/examples/USER/eff/fixed-core/CH4/in.CH4fc.ang +++ b/examples/USER/eff/fixed-core/CH4/in.CH4fc.ang @@ -21,7 +21,7 @@ variable epauli equal c_energies[2] variable estatics equal c_energies[3] variable errestrain equal c_energies[4] -communicate single vel yes +comm_modify vel yes compute peratom all stress/atom NULL compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3] @@ -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 05246740a0..8a20fa0c8c 100644 --- a/examples/USER/eff/fixed-core/CH4/in.CH4fc.bohr +++ b/examples/USER/eff/fixed-core/CH4/in.CH4fc.bohr @@ -21,7 +21,7 @@ variable epauli equal c_energies[2] variable estatics equal c_energies[3] variable errestrain equal c_energies[4] -communicate single vel yes +comm_modify vel yes compute peratom all stress/atom NULL compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3] @@ -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 diff --git a/examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.ang b/examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.ang index 1b5e1e4abd..2db361feb5 100644 --- a/examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.ang +++ b/examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.ang @@ -21,7 +21,8 @@ variable epauli equal c_energies[2] variable estatics equal c_energies[3] variable errestrain equal c_energies[4] -communicate single vel yes +comm_modify vel yes +timestep 0.0001 compute peratom all stress/atom NULL compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3] diff --git a/examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.bohr b/examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.bohr index f59c6ad5c6..e3d0121ac2 100644 --- a/examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.bohr +++ b/examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.bohr @@ -21,7 +21,7 @@ variable epauli equal c_energies[2] variable estatics equal c_energies[3] variable errestrain equal c_energies[4] -communicate single vel yes +comm_modify vel yes compute peratom all stress/atom NULL compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3] diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp index 2883cb06e3..5f5d1542bd 100644 --- a/src/KOKKOS/verlet_kokkos.cpp +++ b/src/KOKKOS/verlet_kokkos.cpp @@ -370,9 +370,7 @@ void VerletKokkos::force_clear() atomKK->modified(Device,F_MASK); } if (torqueflag) memset(&(atomKK->torque[0][0]),0,3*nbytes); - if (erforceflag) memset(&(atomKK->erforce[0]), 0, nbytes); - if (e_flag) memset(&(atomKK->de[0]), 0, nbytes); - if (rho_flag) memset(&(atomKK->drho[0]), 0, nbytes); + } // neighbor includegroup flag is set @@ -397,21 +395,6 @@ void VerletKokkos::force_clear() } } - if (erforceflag) { - double *erforce = atomKK->erforce; - for (i = 0; i < nall; i++) erforce[i] = 0.0; - } - - if (e_flag) { - double *de = atomKK->de; - for (i = 0; i < nall; i++) de[i] = 0.0; - } - - if (rho_flag) { - double *drho = atomKK->drho; - for (i = 0; i < nall; i++) drho[i] = 0.0; - } - if (force->newton) { nall = atomKK->nlocal + atomKK->nghost; @@ -424,20 +407,6 @@ void VerletKokkos::force_clear() } } - if (erforceflag) { - double *erforce = atomKK->erforce; - for (i = atomKK->nlocal; i < nall; i++) erforce[i] = 0.0; - } - - if (e_flag) { - double *de = atomKK->de; - for (i = 0; i < nall; i++) de[i] = 0.0; - } - - if (rho_flag) { - double *drho = atomKK->drho; - for (i = 0; i < nall; i++) drho[i] = 0.0; - } } } } diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp index a3b7295b3d..0eadf1686a 100644 --- a/src/MOLECULE/improper_umbrella.cpp +++ b/src/MOLECULE/improper_umbrella.cpp @@ -309,3 +309,13 @@ void ImproperUmbrella::read_restart(FILE *fp) for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1; } + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void ImproperUmbrella::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->nimpropertypes; i++) + fprintf(fp,"%d %g %g\n",i,kw[i],w0[i]/MY_PI*180.0); +} diff --git a/src/MOLECULE/improper_umbrella.h b/src/MOLECULE/improper_umbrella.h index 94820e6339..1103303747 100644 --- a/src/MOLECULE/improper_umbrella.h +++ b/src/MOLECULE/improper_umbrella.h @@ -33,6 +33,7 @@ class ImproperUmbrella : public Improper { void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); + void write_data(FILE *); protected: double *kw, *w0, *C; diff --git a/src/fix_ave_spatial.cpp b/src/fix_ave_spatial.cpp index 67e1b6a48c..bb139071c7 100644 --- a/src/fix_ave_spatial.cpp +++ b/src/fix_ave_spatial.cpp @@ -42,7 +42,6 @@ enum{BOX,LATTICE,REDUCED}; enum{ONE,RUNNING,WINDOW}; #define INVOKED_PERATOM 8 -#define BIG 1000000000 /* ---------------------------------------------------------------------- */ @@ -329,9 +328,9 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) : delete [] title3; // this fix produces a global array + // size_array_rows set by setup_bins() array_flag = 1; - size_array_rows = BIG; size_array_cols = 1 + ndim + nvalues; extarray = 0; @@ -362,6 +361,8 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) : } // initializations + // invoke setup_bins() now to set size_array_rows + // will be reset in setup(), but needed now so Thermo custom can access it irepeat = 0; iwindow = window_limit = 0; @@ -380,6 +381,8 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) : values_one = values_many = values_sum = values_total = NULL; values_list = NULL; + setup_bins(); + // nvalid = next step on which end_of_step does something // add nvalid to all computes that store invocation times // since don't know a priori which are invoked by this fix @@ -897,6 +900,8 @@ void FixAveSpatial::setup_bins() bin_volume *= delta[m]/prd[dim[m]]; } + size_array_rows = nbins; + // reallocate bin arrays if needed if (nbins > maxbin) { diff --git a/src/neigh_request.cpp b/src/neigh_request.cpp index 5937a9e31b..643d11b3bb 100644 --- a/src/neigh_request.cpp +++ b/src/neigh_request.cpp @@ -98,7 +98,10 @@ int NeighRequest::identical(NeighRequest *other) { int same = 1; - if (unprocessed) same = 0; + // set same = 0 if old list was never processed + + if (other->unprocessed) same = 0; + if (requestor != other->requestor) same = 0; if (id != other->id) same = 0; diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 0d1601a86e..705887ba03 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -490,7 +490,6 @@ void Neighbor::init() // wait to allocate initial pages until copy lists are detected for (i = 0; i < nrequest; i++) { - requests[i]->unprocessed = 0; if (requests[i]->kokkos_host || requests[i]->kokkos_device) continue; lists[i] = new NeighList(lmp); lists[i]->index = i; @@ -757,9 +756,11 @@ void Neighbor::init() #endif } + // mark all current requests as processed // delete old requests // copy current requests and style to old for next run + for (i = 0; i < nrequest; i++) requests[i]->unprocessed = 0; for (i = 0; i < old_nrequest; i++) delete old_requests[i]; memory->sfree(old_requests); old_nrequest = nrequest;