From 28b9fa3754086ab2d0cd45d12d3b1cf362c87bb3 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 10 Jun 2014 15:03:41 +0000 Subject: [PATCH 01/11] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12107 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- examples/USER/eff/Li-solid/in.Li.bohr | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/examples/USER/eff/Li-solid/in.Li.bohr b/examples/USER/eff/Li-solid/in.Li.bohr index a02d524d01..7d61cfd4c1 100644 --- a/examples/USER/eff/Li-solid/in.Li.bohr +++ b/examples/USER/eff/Li-solid/in.Li.bohr @@ -35,12 +35,15 @@ thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain thermo_modify temp effTemp press effPress min_style cg -minimize 0 1e-6 100 2000 +minimize 0 1e-6 10 10 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 -run 1000 +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 10 From e9bcfbbaea5513bdc74a9b1abe9f9d67e8710a74 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 10 Jun 2014 15:45:27 +0000 Subject: [PATCH 02/11] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12108 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/fix_ave_spatial.cpp | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/src/fix_ave_spatial.cpp b/src/fix_ave_spatial.cpp index c55ffd0e7f..c6606d9252 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) { From 00db690e64376dfa1df9213785a8324dcbcb4e08 Mon Sep 17 00:00:00 2001 From: stamoor Date: Tue, 10 Jun 2014 16:07:24 +0000 Subject: [PATCH 03/11] Updating USER-EFF examples to use compute property/atom git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12109 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- .../USER/eff/Auger-Adamantane/in.adamantane_ionized.nve | 5 +++-- examples/USER/eff/Be-solid/in.Be-solid.spe | 3 ++- examples/USER/eff/CH4/in.ch4.dynamics | 5 +++-- examples/USER/eff/CH4/in.ch4.min | 3 ++- examples/USER/eff/CH4/in.ch4_ionized.dynamics | 3 ++- examples/USER/eff/ECP/Si2H6/in.Si2H6 | 3 ++- examples/USER/eff/ECP/Si2H6/in.Si2H6.ang | 5 +++-- examples/USER/eff/ECP/SiC/bulk/in.SiC | 5 +++-- examples/USER/eff/ECP/SiH4/in.SiH4 | 3 ++- examples/USER/eff/ECP/SiH4/in.SiH4.ang | 3 ++- examples/USER/eff/H2/in.h2 | 3 ++- examples/USER/eff/H_plasma/in.h2bulk.npt | 3 ++- examples/USER/eff/H_plasma/in.h2bulk.nve | 3 ++- examples/USER/eff/H_plasma/in.h2bulk.nve.ang | 3 ++- examples/USER/eff/Li-dendritic/in.Li-dendritic.min | 3 ++- examples/USER/eff/Li-dendritic/in.Li-dendritic.nvt | 6 ++++-- examples/USER/eff/Li-solid/in.Li.ang | 3 ++- examples/USER/eff/fixed-core/C2H6/in.C2H6fc.ang | 7 ++++--- examples/USER/eff/fixed-core/C2H6/in.C2H6fc.bohr | 7 ++++--- examples/USER/eff/fixed-core/CH4/in.CH4fc.ang | 5 +++-- examples/USER/eff/fixed-core/CH4/in.CH4fc.bohr | 5 +++-- 21 files changed, 54 insertions(+), 32 deletions(-) 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..fd2be9db58 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 902ec6d861..09d667bd2c 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 728446ef29..63f44e6809 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 7ae283e9fc..7bd04d7ba2 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 a73133a717..8b0a709fb9 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 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/fixed-core/C2H6/in.C2H6fc.ang b/examples/USER/eff/fixed-core/C2H6/in.C2H6fc.ang index 8c4c98ac9e..74ced0db88 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 dd42e48fb9..69395eb041 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 3720d84440..fbad1ce83c 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 05246740a0..6e337998b7 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 From fcb81d2b48e501a75e4dfe7142ebc1a3b859d685 Mon Sep 17 00:00:00 2001 From: stamoor Date: Tue, 10 Jun 2014 17:00:33 +0000 Subject: [PATCH 04/11] Fixing broken USER-EFF examples git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12110 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- examples/USER/eff/ECP/Si2H6/in.Si2H6 | 2 +- examples/USER/eff/ECP/Si2H6/in.Si2H6.ang | 2 +- examples/USER/eff/ECP/SiC/bulk/in.SiC | 2 +- examples/USER/eff/ECP/SiH4/in.SiH4 | 2 +- examples/USER/eff/ECP/SiH4/in.SiH4.ang | 2 +- examples/USER/eff/Li-solid/in.Li.bohr | 4 ++-- examples/USER/eff/fixed-core/C2H6/in.C2H6fc.ang | 2 +- examples/USER/eff/fixed-core/C2H6/in.C2H6fc.bohr | 2 +- examples/USER/eff/fixed-core/CH4/in.CH4fc.ang | 2 +- examples/USER/eff/fixed-core/CH4/in.CH4fc.bohr | 2 +- examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.ang | 2 +- examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.bohr | 2 +- 12 files changed, 13 insertions(+), 13 deletions(-) diff --git a/examples/USER/eff/ECP/Si2H6/in.Si2H6 b/examples/USER/eff/ECP/Si2H6/in.Si2H6 index fd2be9db58..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] diff --git a/examples/USER/eff/ECP/Si2H6/in.Si2H6.ang b/examples/USER/eff/ECP/Si2H6/in.Si2H6.ang index 09d667bd2c..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] diff --git a/examples/USER/eff/ECP/SiC/bulk/in.SiC b/examples/USER/eff/ECP/SiC/bulk/in.SiC index 63f44e6809..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 diff --git a/examples/USER/eff/ECP/SiH4/in.SiH4 b/examples/USER/eff/ECP/SiH4/in.SiH4 index 7bd04d7ba2..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] diff --git a/examples/USER/eff/ECP/SiH4/in.SiH4.ang b/examples/USER/eff/ECP/SiH4/in.SiH4.ang index 8b0a709fb9..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] diff --git a/examples/USER/eff/Li-solid/in.Li.bohr b/examples/USER/eff/Li-solid/in.Li.bohr index 7d61cfd4c1..2843d3ca6a 100644 --- a/examples/USER/eff/Li-solid/in.Li.bohr +++ b/examples/USER/eff/Li-solid/in.Li.bohr @@ -35,7 +35,7 @@ thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain thermo_modify temp effTemp press effPress min_style cg -minimize 0 1e-6 10 10 +minimize 0 1e-6 100 2000 fix 0 all temp/rescale/eff 1 0.0 3000.0 0.02 0.5 @@ -45,5 +45,5 @@ 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 10 +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 74ced0db88..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] diff --git a/examples/USER/eff/fixed-core/C2H6/in.C2H6fc.bohr b/examples/USER/eff/fixed-core/C2H6/in.C2H6fc.bohr index 69395eb041..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] diff --git a/examples/USER/eff/fixed-core/CH4/in.CH4fc.ang b/examples/USER/eff/fixed-core/CH4/in.CH4fc.ang index fbad1ce83c..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] diff --git a/examples/USER/eff/fixed-core/CH4/in.CH4fc.bohr b/examples/USER/eff/fixed-core/CH4/in.CH4fc.bohr index 6e337998b7..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] 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..234aae74ea 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 +21,7 @@ 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/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] From d37745fa1b9c9e42449075e5aeb21f75044824d6 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 10 Jun 2014 17:37:48 +0000 Subject: [PATCH 05/11] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12111 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/neigh_request.cpp | 5 ++++- src/neighbor.cpp | 3 ++- 2 files changed, 6 insertions(+), 2 deletions(-) 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; From 2642b7d3a55f723d80c8754748babce0372944b1 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 10 Jun 2014 17:40:44 +0000 Subject: [PATCH 06/11] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12112 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/run.html | 9 +++++---- doc/run.txt | 9 +++++---- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/doc/run.html b/doc/run.html index 49fb6e34a7..768659757a 100644 --- a/doc/run.html +++ b/doc/run.html @@ -104,10 +104,11 @@ must be done.

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. From 7e1c6ccfac6fb716a7f134150a8f7f9f6c73248a Mon Sep 17 00:00:00 2001 From: stamoor Date: Tue, 10 Jun 2014 18:17:25 +0000 Subject: [PATCH 07/11] Fixing more broken USER-EFF examples git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12113 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- examples/USER/eff/H/in.h_atom.spe.ang | 1 + examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.ang | 1 + 2 files changed, 2 insertions(+) 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/fixed-core/CH4/in.CH4fc.spe.ang b/examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.ang index 234aae74ea..2db361feb5 100644 --- a/examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.ang +++ b/examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.ang @@ -22,6 +22,7 @@ variable estatics equal c_energies[3] variable errestrain equal c_energies[4] 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] From b9eb6f0afaa8b3a4b3420627551f10be50433508 Mon Sep 17 00:00:00 2001 From: athomps Date: Tue, 10 Jun 2014 19:34:30 +0000 Subject: [PATCH 08/11] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12114 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/KOKKOS/verlet_kokkos.cpp | 33 +-------------------------------- 1 file changed, 1 insertion(+), 32 deletions(-) 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; - } } } } From 5e1cc8e250cfae386c86bcbb5d5bde607de49459 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 10 Jun 2014 23:24:50 +0000 Subject: [PATCH 09/11] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12115 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/MOLECULE/improper_umbrella.cpp | 10 ++++++++++ src/MOLECULE/improper_umbrella.h | 1 + 2 files changed, 11 insertions(+) diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp index a3b7295b3d..812201cbbf 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,k0[i],w0[i]/MY_PI*180.0); +} diff --git a/src/MOLECULE/improper_umbrella.h b/src/MOLECULE/improper_umbrella.h index 3d005aa105..efb29acd54 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; From abf916584832e232bd23259ab5bbe9075de90db2 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 10 Jun 2014 23:25:21 +0000 Subject: [PATCH 10/11] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12116 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/MOLECULE/improper_umbrella.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp index 812201cbbf..0eadf1686a 100644 --- a/src/MOLECULE/improper_umbrella.cpp +++ b/src/MOLECULE/improper_umbrella.cpp @@ -317,5 +317,5 @@ void ImproperUmbrella::read_restart(FILE *fp) void ImproperUmbrella::write_data(FILE *fp) { for (int i = 1; i <= atom->nimpropertypes; i++) - fprintf(fp,"%d %g %g\n",i,k0[i],w0[i]/MY_PI*180.0); + fprintf(fp,"%d %g %g\n",i,kw[i],w0[i]/MY_PI*180.0); } From eabfaf18ec17ff2d09fcd4e0940dde4870aea313 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 10 Jun 2014 23:38:51 +0000 Subject: [PATCH 11/11] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12117 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/pair_style.html | 2 +- doc/pair_style.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/pair_style.html b/doc/pair_style.html index ed0fdee2a5..dbf6e5896c 100644 --- a/doc/pair_style.html +++ b/doc/pair_style.html @@ -177,7 +177,7 @@ in the pair section of this page.

  • pair_style meam - modified embedded atom method (MEAM)
  • pair_style mie/cut - Mie potential
  • pair_style morse - Morse potential -
  • pair_style nb3b/harmonic - nonbonded 3-body harmonic potential +
  • pair_style nb3b/harmonic - nonbonded 3-body harmonic potential
  • pair_style nm/cut - N-M potential
  • pair_style nm/cut/coul/cut - N-M potential with cutoff Coulomb
  • pair_style nm/cut/coul/long - N-M potential with long-range Coulombics diff --git a/doc/pair_style.txt b/doc/pair_style.txt index 5cda9ef681..564142c4e0 100644 --- a/doc/pair_style.txt +++ b/doc/pair_style.txt @@ -174,7 +174,7 @@ in the pair section of "this page"_Section_commands.html#cmd_5. "pair_style meam"_pair_meam.html - modified embedded atom method (MEAM) "pair_style mie/cut"_pair_mie.html - Mie potential "pair_style morse"_pair_morse.html - Morse potential -"pair_style nb3b/harmonic"_pair_nb3d_harmonic.html - nonbonded 3-body harmonic potential +"pair_style nb3b/harmonic"_pair_nb3b_harmonic.html - nonbonded 3-body harmonic potential "pair_style nm/cut"_pair_nm.html - N-M potential "pair_style nm/cut/coul/cut"_pair_nm.html - N-M potential with cutoff Coulomb "pair_style nm/cut/coul/long"_pair_nm.html - N-M potential with long-range Coulombics