ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Updating USER-EFF examples to use compute property/atom

Browse Source 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12109 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
stamoor
2014-06-10 16:07:24 +00:00
parent e9bcfbbaea
commit 00db690e64
21 changed files with 54 additions and 32 deletions
Download Patch File Download Diff File Expand all files Collapse all files

5
examples/USER/eff/Auger-Adamantane/in.adamantane_ionized.nve
View File

@ -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

3
examples/USER/eff/Be-solid/in.Be-solid.spe
View File

@ -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

5
examples/USER/eff/CH4/in.ch4.dynamics
View File

@ -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

3
examples/USER/eff/CH4/in.ch4.min
View File

@ -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

3
examples/USER/eff/CH4/in.ch4_ionized.dynamics
View File

@ -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

3
examples/USER/eff/ECP/Si2H6/in.Si2H6
View File

@ -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

5
examples/USER/eff/ECP/Si2H6/in.Si2H6.ang
View File

@ -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

5
examples/USER/eff/ECP/SiC/bulk/in.SiC
View File

@ -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

3
examples/USER/eff/ECP/SiH4/in.SiH4
View File

@ -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

3
examples/USER/eff/ECP/SiH4/in.SiH4.ang
View File

@ -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

3
examples/USER/eff/H2/in.h2
View File

@ -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

3
examples/USER/eff/H_plasma/in.h2bulk.npt
View File

@ -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

3
examples/USER/eff/H_plasma/in.h2bulk.nve
View File

@ -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

3
examples/USER/eff/H_plasma/in.h2bulk.nve.ang
View File

@ -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

3
examples/USER/eff/Li-dendritic/in.Li-dendritic.min
View File

@ -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

6
examples/USER/eff/Li-dendritic/in.Li-dendritic.nvt
View File

@ -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

3
examples/USER/eff/Li-solid/in.Li.ang
View File

@ -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

7
examples/USER/eff/fixed-core/C2H6/in.C2H6fc.ang
View File

@ -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

7
examples/USER/eff/fixed-core/C2H6/in.C2H6fc.bohr
View File

@ -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

5
examples/USER/eff/fixed-core/CH4/in.CH4fc.ang
View File

@ -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

5
examples/USER/eff/fixed-core/CH4/in.CH4fc.bohr
View File

@ -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