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small changes to examples scripts for regression purposes

This commit is contained in:
Steve Plimpton 2020-05-06 15:28:27 -06:00
parent 8e32f623f1
commit 1225f7d1e0
29 changed files with 40 additions and 48 deletions
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6
examples/ASPHERE/line/in.line
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@ -10,7 +10,7 @@ velocity all create 1.44 320984 loop geom
neighbor 0.3 bin neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule all neigh_modify exclude molecule/intra all
pair_style line/lj 2.5 pair_style line/lj 2.5
pair_coeff * * 1.0 1.0 1.0 0.25 2.5 pair_coeff * * 1.0 1.0 1.0 0.25 2.5
@ -33,8 +33,10 @@ compute 2 all ke
compute 3 all pe compute 3 all pe
variable toteng equal (c_1+c_2+c_3)/atoms variable toteng equal (c_1+c_2+c_3)/atoms
compute_modify thermo_temp extra/dof -350
thermo 1000 thermo 1000
thermo_style custom step temp f_2 pe ke c_1 c_2 c_3 v_toteng thermo_style custom step f_2 pe ke c_1 c_2 c_3 v_toteng
run 10000 run 10000

6
examples/ASPHERE/line/in.line.srd
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@ -36,7 +36,7 @@ velocity small create 1.44 87287 loop geom
neighbor 0.3 bin neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule big include big neigh_modify exclude molecule/intra big include big
comm_modify mode multi group big vel yes comm_modify mode multi group big vel yes
neigh_modify include big neigh_modify include big
@ -68,13 +68,15 @@ compute tbig big temp
variable pebig equal pe*atoms/count(big) variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big) variable ebig equal etotal*atoms/count(big)
compute_modify tbig extra/dof -350
compute 1 big erotate/asphere compute 1 big erotate/asphere
compute 2 all ke compute 2 all ke
compute 3 all pe compute 3 all pe
variable toteng equal (c_1+c_2+c_3)/atoms variable toteng equal (c_1+c_2+c_3)/atoms
thermo 1000 thermo 1000
thermo_style custom step temp c_tsmall f_2[9] c_1 etotal & thermo_style custom step c_tsmall f_2[9] c_1 etotal &
v_pebig v_ebig press v_pebig v_ebig press
thermo_modify temp tbig thermo_modify temp tbig

4
examples/ASPHERE/tri/in.tri.srd
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@ -35,7 +35,7 @@ velocity small create 1.44 87287 loop geom
neighbor 0.3 bin neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule big include big neigh_modify exclude molecule/intra big include big
comm_modify mode multi group big vel yes comm_modify mode multi group big vel yes
neigh_modify include big neigh_modify include big
@ -66,6 +66,8 @@ compute tbig big temp
variable pebig equal pe*atoms/count(big) variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big) variable ebig equal etotal*atoms/count(big)
compute_modify tbig extra/dof -4500
compute 1 big erotate/asphere compute 1 big erotate/asphere
compute 2 all ke compute 2 all ke
compute 3 all pe compute 3 all pe

2
examples/USER/dpd/dpd-shardlow/in.dpd-shardlow
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@ -1,5 +1,5 @@
# Input File for DPD fluid under isothermal conditions using the VV-SSA integration scheme # Input File for DPD fluid under isothermal conditions using the VV-SSA integration scheme
log log.dpd-shardlow
boundary p p p boundary p p p
units metal units metal

1
examples/USER/dpd/dpd-vv/in.dpd-vv
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@ -1,6 +1,5 @@
# INPUT FILE FOR DPD_Fluid # INPUT FILE FOR DPD_Fluid
log log.dpd-vv
boundary p p p boundary p p p
units metal # ev, ps units metal # ev, ps

2
examples/USER/dpd/dpde-shardlow/in.dpde-shardlow
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@ -1,5 +1,5 @@
# Input File for DPD fluid under isoenergetic conditions using the VV-SSA integration scheme # Input File for DPD fluid under isoenergetic conditions using the VV-SSA integration scheme
log log.dpde-shardlow
boundary p p p boundary p p p
units metal # ev, ps units metal # ev, ps

1
examples/USER/dpd/dpde-vv/in.dpde-vv
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@ -1,6 +1,5 @@
# INPUT FILE FOR DPD_Fluid # INPUT FILE FOR DPD_Fluid
log log.dpde-vv
boundary p p p boundary p p p
units metal # ev, ps units metal # ev, ps

2
examples/USER/dpd/dpdh-shardlow/in.dpdh-shardlow
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@ -1,5 +1,5 @@
# Input File for DPD fluid under isoenthalpic conditions using the VV-SSA integration scheme # Input File for DPD fluid under isoenthalpic conditions using the VV-SSA integration scheme
log log.dpdh-shardlow
boundary p p p boundary p p p
units metal # ev, ps units metal # ev, ps

2
examples/USER/dpd/dpdp-shardlow/in.dpdp-shardlow
View File

@ -1,5 +1,5 @@
# Input File for DPD fluid under isobaric conditions using the VV-SSA integration scheme # Input File for DPD fluid under isobaric conditions using the VV-SSA integration scheme
log log.dpdp-shardlow
boundary p p p boundary p p p
units metal units metal

1
examples/USER/dpd/dpdrx-shardlow/in.dpdrx-shardlow
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@ -1,6 +1,5 @@
# Example for running DPD-RX # Example for running DPD-RX
log log.dpdrx-shardlow
boundary p p p boundary p p p
units metal # ev, ps units metal # ev, ps
atom_style dpd atom_style dpd

2
examples/USER/dpd/multi-lucy/in.multi-lucy
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@ -1,5 +1,5 @@
# RDX coarse-grain model # RDX coarse-grain model
log log.multi-lucy
units metal # ev, ps units metal # ev, ps
atom_style dpd atom_style dpd
atom_modify map array atom_modify map array

1
examples/USER/eff/Auger-Adamantane/in.adamantane_ionized.nve
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@ -1,5 +1,4 @@
variable sname index adamantane_ionized variable sname index adamantane_ionized
log ${sname}.nve.log
units electron units electron
newton on newton on

1
examples/USER/eff/Be-solid/in.Be-solid.spe
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@ -1,5 +1,4 @@
variable sname index Be-solid variable sname index Be-solid
log ${sname}.spe.log
units electron units electron
newton on newton on

1
examples/USER/eff/CH4/in.ch4.dynamics
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@ -1,5 +1,4 @@
variable sname index ch4 variable sname index ch4
log ${sname}.nve.log
units electron units electron
newton on newton on

1
examples/USER/eff/CH4/in.ch4.min
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@ -1,5 +1,4 @@
variable sname index ch4 variable sname index ch4
log ${sname}.nve.log
units electron units electron
newton on newton on

2
examples/USER/eff/CH4/in.ch4_ionized.dynamics
View File

@ -1,5 +1,4 @@
variable sname index ch4_ionized variable sname index ch4_ionized
log ${sname}.nvt.log
units electron units electron
newton on newton on
@ -15,6 +14,7 @@ pair_coeff * *
comm_modify vel yes comm_modify vel yes
# minimize # minimize
min_style cg min_style cg
min_modify line quadratic min_modify line quadratic
minimize 0 1.0e-6 10000 100000 minimize 0 1.0e-6 10000 100000

1
examples/USER/eff/H/in.h_atom.spe.ang
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@ -1,5 +1,4 @@
variable sname index h_atom.ang variable sname index h_atom.ang
log ${sname}.spe.log
units real units real
newton on newton on

1
examples/USER/eff/H/in.h_atom.spe.bohr
View File

@ -1,5 +1,4 @@
variable sname index h_atom.bohr variable sname index h_atom.bohr
log ${sname}.spe.log
units electron units electron
newton on newton on

3
examples/USER/eff/H2/in.h2
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@ -1,5 +1,4 @@
variable sname index h2 variable sname index h2
log ${sname}.spe.log
units electron units electron
newton on newton on
@ -47,4 +46,4 @@ unfix 3
#fix 1 all nve/eff #fix 1 all nve/eff
run 100000 run 10000

4
examples/USER/eff/H_plasma/in.h2bulk.npt
View File

@ -1,5 +1,4 @@
variable sname index h2bulk variable sname index h2bulk
log ${sname}.npt.log
units electron units electron
newton on newton on
@ -41,7 +40,8 @@ dump 2 all xyz 10000 ${sname}.npt.xyz
compute 1 all property/atom 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] dump 3 all custom 10000 ${sname}.npt.lammpstrj id type x y z c_1[1] c_1[2]
run 10000000 thermo 1
run 10
unfix 1 unfix 1
undump 2 undump 2

7
examples/USER/eff/H_plasma/in.h2bulk.nve
View File

@ -1,5 +1,4 @@
variable sname index h2bulk variable sname index h2bulk
log ${sname}.nve.log
units electron units electron
newton on newton on
@ -18,13 +17,13 @@ comm_modify vel yes
compute effTemp all temp/eff compute effTemp all temp/eff
thermo 1000 thermo 10
thermo_style custom step pe temp press thermo_style custom step pe temp press
thermo_modify temp effTemp thermo_modify temp effTemp
# structure minimization # structure minimization
min_style cg min_style cg
minimize 0 1.0e-4 1000 10000 minimize 0 1.0e-4 10 10
timestep 0.001 timestep 0.001
@ -41,7 +40,7 @@ dump 2 all xyz 1000 ${sname}.nve.xyz
compute 1 all property/atom spin eradius 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 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 run 10
unfix 1 unfix 1
#unfix 2 #unfix 2

7
examples/USER/eff/H_plasma/in.h2bulk.nve.ang
View File

@ -1,5 +1,4 @@
variable sname index h2bulk.ang variable sname index h2bulk.ang
log ${sname}.nve.log
units real units real
newton on newton on
@ -29,13 +28,13 @@ variable epauli equal c_energies[2]
variable ecoul equal c_energies[3] variable ecoul equal c_energies[3]
variable erres equal c_energies[4] variable erres equal c_energies[4]
thermo 100 thermo 10
thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres press v_press temp thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres press v_press temp
thermo_modify temp effTemp press effPress flush yes thermo_modify temp effTemp press effPress flush yes
# structure minimization # structure minimization
min_style cg min_style cg
minimize 0 1.0e-4 1000 10000 minimize 0 1.0e-4 10 10
timestep 0.001 timestep 0.001
@ -52,7 +51,7 @@ dump 2 all xyz 1000 ${sname}.nve.xyz
compute 1 all property/atom spin eradius 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 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 run 10
unfix 1 unfix 1
#unfix 2 #unfix 2

5
examples/USER/eff/Li-dendritic/in.Li-dendritic.min
View File

@ -1,5 +1,4 @@
variable sname index Li-dendritic variable sname index Li-dendritic
log ${sname}.min.log
units electron units electron
newton on newton on
@ -7,8 +6,8 @@ boundary p p p
atom_style electron atom_style electron
#read_data data.${sname} read_data data.${sname}
read_restart ${sname}.min.restart2 #read_restart ${sname}.min.restart2
pair_style eff/cut 50.112 pair_style eff/cut 50.112
pair_coeff * * pair_coeff * *

5
examples/USER/eff/Li-dendritic/in.Li-dendritic.nvt
View File

@ -1,5 +1,4 @@
variable sname index Li-dendritic variable sname index Li-dendritic
log ${sname}.min.log
units electron units electron
newton on newton on
@ -29,7 +28,7 @@ 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 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 #dump 2 all xyz 100 ${sname}.min.xyz
min_modify line quadratic dmax 0.05 min_modify line quadratic dmax 0.05
minimize 0 1.0e-7 1000 2000 minimize 0 1.0e-7 100 100
write_restart ${sname}.min.restart write_restart ${sname}.min.restart
@ -46,7 +45,7 @@ dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1
dump 2 all xyz 100 ${sname}.nvt.xyz dump 2 all xyz 100 ${sname}.nvt.xyz
restart 100 ${sname}.nvt.restart1 ${sname}.nvt.restart2 restart 100 ${sname}.nvt.restart1 ${sname}.nvt.restart2
run 10000 run 100
undump 1 undump 1
undump 2 undump 2

7
examples/USER/eff/Li-solid/in.Li.ang
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@ -1,5 +1,4 @@
variable sname index Li.ang variable sname index Li.ang
log ${sname}.spe.log
units real units real
newton on newton on
@ -46,13 +45,13 @@ fix 0 all temp/rescale/eff 1 10.0 3000.0 0.05 1.0
#fix 0 all langevin/eff 3000.0 3000.0 10.0 699483 #fix 0 all langevin/eff 3000.0 3000.0 10.0 699483
fix 1 all nve/eff fix 1 all nve/eff
run 1000 run 200
unfix 0 unfix 0
unfix 1 unfix 1
fix 1 all nvt/eff temp 3000.0 3000.0 100.0 fix 1 all nvt/eff temp 3000.0 3000.0 100.0
compute 1 all property/atom spin eradius 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] dump 1 all custom 500 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z vx vy vz c_1[3]
run 100000 run 500

7
examples/USER/eff/Li-solid/in.Li.bohr
View File

@ -1,5 +1,4 @@
variable sname index Li.bohr variable sname index Li.bohr
log ${sname}.spe.log
units electron units electron
newton off newton off
@ -35,15 +34,15 @@ thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain
thermo_modify temp effTemp press effPress thermo_modify temp effTemp press effPress
min_style cg min_style cg
minimize 0 1e-6 100 2000 minimize 0 1e-6 100 200
fix 0 all temp/rescale/eff 1 0.0 3000.0 0.02 0.5 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 fix 1 all npt/eff temp 3000.0 3000.0 0.1 iso 1e7 1e7 1.0
compute 1 all property/atom spin eradius compute 1 all property/atom spin eradius
dump 1 all custom 1 ${sname}.spe.lammpstrj & dump 1 all custom 100 ${sname}.spe.lammpstrj &
id type q c_1[1] c_1[2] x y z id type q c_1[1] c_1[2] x y z
run 1000 run 100

2
examples/granular/in.pour.drum
View File

@ -92,6 +92,8 @@ fix 5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindl
# 'Turn' drum by switching the direction of gravity # 'Turn' drum by switching the direction of gravity
unfix grav unfix grav
unfix ins1
unfix ins2
fix grav all gravity 10 vector 0 -1 0 fix grav all gravity 10 vector 0 -1 0
variable theta equal 2*PI*elapsed/20000.0 variable theta equal 2*PI*elapsed/20000.0

2
examples/qeq/in.qeq.buck
View File

@ -24,7 +24,7 @@ compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2 compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2 variable qtot equal count(type1)*c_q1+count(type2)*c_q2
thermo_style custom step pe c_q1 c_q2 v_qtot spcpu thermo_style custom step pe c_q1 c_q2 v_qtot
thermo 10 thermo 10
timestep 0.0001 timestep 0.0001

2
examples/streitz/in.streitz.wolf
View File

@ -39,7 +39,7 @@ neigh_modify every 10 delay 0 check yes
timestep 0.0004 timestep 0.0004
thermo_style custom step temp etotal pe evdwl ecoul elong & thermo_style custom step temp etotal pe evdwl ecoul elong &
c_q1 c_q2 v_qsum press spcpu c_q1 c_q2 v_qsum press
thermo_modify norm yes thermo_modify norm yes
thermo 10 thermo 10