From 00db690e64376dfa1df9213785a8324dcbcb4e08 Mon Sep 17 00:00:00 2001
From: stamoor <stamoor@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Tue, 10 Jun 2014 16:07:24 +0000
Subject: [PATCH] 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
--
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