From 1225f7d1e015b2b518eb0d81146b7722df049c76 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 6 May 2020 15:28:27 -0600 Subject: [PATCH] small changes to examples scripts for regression purposes --- examples/ASPHERE/line/in.line | 6 ++++-- examples/ASPHERE/line/in.line.srd | 6 ++++-- examples/ASPHERE/tri/in.tri.srd | 4 +++- examples/USER/dpd/dpd-shardlow/in.dpd-shardlow | 2 +- examples/USER/dpd/dpd-vv/in.dpd-vv | 1 - examples/USER/dpd/dpde-shardlow/in.dpde-shardlow | 2 +- examples/USER/dpd/dpde-vv/in.dpde-vv | 1 - examples/USER/dpd/dpdh-shardlow/in.dpdh-shardlow | 2 +- examples/USER/dpd/dpdp-shardlow/in.dpdp-shardlow | 2 +- examples/USER/dpd/dpdrx-shardlow/in.dpdrx-shardlow | 1 - examples/USER/dpd/multi-lucy/in.multi-lucy | 2 +- .../USER/eff/Auger-Adamantane/in.adamantane_ionized.nve | 1 - examples/USER/eff/Be-solid/in.Be-solid.spe | 1 - examples/USER/eff/CH4/in.ch4.dynamics | 1 - examples/USER/eff/CH4/in.ch4.min | 1 - examples/USER/eff/CH4/in.ch4_ionized.dynamics | 2 +- examples/USER/eff/H/in.h_atom.spe.ang | 1 - examples/USER/eff/H/in.h_atom.spe.bohr | 1 - examples/USER/eff/H2/in.h2 | 3 +-- examples/USER/eff/H_plasma/in.h2bulk.npt | 4 ++-- examples/USER/eff/H_plasma/in.h2bulk.nve | 7 +++---- examples/USER/eff/H_plasma/in.h2bulk.nve.ang | 7 +++---- examples/USER/eff/Li-dendritic/in.Li-dendritic.min | 5 ++--- examples/USER/eff/Li-dendritic/in.Li-dendritic.nvt | 5 ++--- examples/USER/eff/Li-solid/in.Li.ang | 7 +++---- examples/USER/eff/Li-solid/in.Li.bohr | 7 +++---- examples/granular/in.pour.drum | 2 ++ examples/qeq/in.qeq.buck | 2 +- examples/streitz/in.streitz.wolf | 2 +- 29 files changed, 40 insertions(+), 48 deletions(-) diff --git a/examples/ASPHERE/line/in.line b/examples/ASPHERE/line/in.line index cd7fed1639..815eacfa35 100644 --- a/examples/ASPHERE/line/in.line +++ b/examples/ASPHERE/line/in.line @@ -10,7 +10,7 @@ velocity all create 1.44 320984 loop geom neighbor 0.3 bin 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_coeff * * 1.0 1.0 1.0 0.25 2.5 @@ -33,8 +33,10 @@ compute 2 all ke compute 3 all pe variable toteng equal (c_1+c_2+c_3)/atoms +compute_modify thermo_temp extra/dof -350 + 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 diff --git a/examples/ASPHERE/line/in.line.srd b/examples/ASPHERE/line/in.line.srd index 4b89b14b4b..6ec1998d31 100644 --- a/examples/ASPHERE/line/in.line.srd +++ b/examples/ASPHERE/line/in.line.srd @@ -36,7 +36,7 @@ velocity small create 1.44 87287 loop geom neighbor 0.3 bin 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 neigh_modify include big @@ -68,13 +68,15 @@ compute tbig big temp variable pebig equal pe*atoms/count(big) variable ebig equal etotal*atoms/count(big) +compute_modify tbig extra/dof -350 + compute 1 big erotate/asphere compute 2 all ke compute 3 all pe variable toteng equal (c_1+c_2+c_3)/atoms 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 thermo_modify temp tbig diff --git a/examples/ASPHERE/tri/in.tri.srd b/examples/ASPHERE/tri/in.tri.srd index caff7f60dd..e7ef6ef59a 100644 --- a/examples/ASPHERE/tri/in.tri.srd +++ b/examples/ASPHERE/tri/in.tri.srd @@ -35,7 +35,7 @@ velocity small create 1.44 87287 loop geom neighbor 0.3 bin 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 neigh_modify include big @@ -66,6 +66,8 @@ compute tbig big temp variable pebig equal pe*atoms/count(big) variable ebig equal etotal*atoms/count(big) +compute_modify tbig extra/dof -4500 + compute 1 big erotate/asphere compute 2 all ke compute 3 all pe diff --git a/examples/USER/dpd/dpd-shardlow/in.dpd-shardlow b/examples/USER/dpd/dpd-shardlow/in.dpd-shardlow index e6e46bc38c..6251623374 100644 --- a/examples/USER/dpd/dpd-shardlow/in.dpd-shardlow +++ b/examples/USER/dpd/dpd-shardlow/in.dpd-shardlow @@ -1,5 +1,5 @@ # Input File for DPD fluid under isothermal conditions using the VV-SSA integration scheme -log log.dpd-shardlow + boundary p p p units metal diff --git a/examples/USER/dpd/dpd-vv/in.dpd-vv b/examples/USER/dpd/dpd-vv/in.dpd-vv index 5360ca2431..6890c881d4 100644 --- a/examples/USER/dpd/dpd-vv/in.dpd-vv +++ b/examples/USER/dpd/dpd-vv/in.dpd-vv @@ -1,6 +1,5 @@ # INPUT FILE FOR DPD_Fluid -log log.dpd-vv boundary p p p units metal # ev, ps diff --git a/examples/USER/dpd/dpde-shardlow/in.dpde-shardlow b/examples/USER/dpd/dpde-shardlow/in.dpde-shardlow index 68361adfa5..c639bef9f2 100644 --- a/examples/USER/dpd/dpde-shardlow/in.dpde-shardlow +++ b/examples/USER/dpd/dpde-shardlow/in.dpde-shardlow @@ -1,5 +1,5 @@ # Input File for DPD fluid under isoenergetic conditions using the VV-SSA integration scheme -log log.dpde-shardlow + boundary p p p units metal # ev, ps diff --git a/examples/USER/dpd/dpde-vv/in.dpde-vv b/examples/USER/dpd/dpde-vv/in.dpde-vv index 3ffcf0ec07..52309682c3 100644 --- a/examples/USER/dpd/dpde-vv/in.dpde-vv +++ b/examples/USER/dpd/dpde-vv/in.dpde-vv @@ -1,6 +1,5 @@ # INPUT FILE FOR DPD_Fluid -log log.dpde-vv boundary p p p units metal # ev, ps diff --git a/examples/USER/dpd/dpdh-shardlow/in.dpdh-shardlow b/examples/USER/dpd/dpdh-shardlow/in.dpdh-shardlow index e403175e7a..5353085359 100644 --- a/examples/USER/dpd/dpdh-shardlow/in.dpdh-shardlow +++ b/examples/USER/dpd/dpdh-shardlow/in.dpdh-shardlow @@ -1,5 +1,5 @@ # Input File for DPD fluid under isoenthalpic conditions using the VV-SSA integration scheme -log log.dpdh-shardlow + boundary p p p units metal # ev, ps diff --git a/examples/USER/dpd/dpdp-shardlow/in.dpdp-shardlow b/examples/USER/dpd/dpdp-shardlow/in.dpdp-shardlow index 1d5eb5dd7d..93f26bd946 100644 --- a/examples/USER/dpd/dpdp-shardlow/in.dpdp-shardlow +++ b/examples/USER/dpd/dpdp-shardlow/in.dpdp-shardlow @@ -1,5 +1,5 @@ # Input File for DPD fluid under isobaric conditions using the VV-SSA integration scheme -log log.dpdp-shardlow + boundary p p p units metal diff --git a/examples/USER/dpd/dpdrx-shardlow/in.dpdrx-shardlow b/examples/USER/dpd/dpdrx-shardlow/in.dpdrx-shardlow index 815c974741..f93b316e14 100755 --- a/examples/USER/dpd/dpdrx-shardlow/in.dpdrx-shardlow +++ b/examples/USER/dpd/dpdrx-shardlow/in.dpdrx-shardlow @@ -1,6 +1,5 @@ # Example for running DPD-RX -log log.dpdrx-shardlow boundary p p p units metal # ev, ps atom_style dpd diff --git a/examples/USER/dpd/multi-lucy/in.multi-lucy b/examples/USER/dpd/multi-lucy/in.multi-lucy index 26d21f66ea..bb223e0a25 100644 --- a/examples/USER/dpd/multi-lucy/in.multi-lucy +++ b/examples/USER/dpd/multi-lucy/in.multi-lucy @@ -1,5 +1,5 @@ # RDX coarse-grain model -log log.multi-lucy + units metal # ev, ps atom_style dpd atom_modify map array diff --git a/examples/USER/eff/Auger-Adamantane/in.adamantane_ionized.nve b/examples/USER/eff/Auger-Adamantane/in.adamantane_ionized.nve index 77c7b0d465..edbe76beef 100644 --- a/examples/USER/eff/Auger-Adamantane/in.adamantane_ionized.nve +++ b/examples/USER/eff/Auger-Adamantane/in.adamantane_ionized.nve @@ -1,5 +1,4 @@ variable sname index adamantane_ionized -log ${sname}.nve.log units electron newton on diff --git a/examples/USER/eff/Be-solid/in.Be-solid.spe b/examples/USER/eff/Be-solid/in.Be-solid.spe index e7245cabbc..ce61a21f8c 100644 --- a/examples/USER/eff/Be-solid/in.Be-solid.spe +++ b/examples/USER/eff/Be-solid/in.Be-solid.spe @@ -1,5 +1,4 @@ variable sname index Be-solid -log ${sname}.spe.log units electron newton on diff --git a/examples/USER/eff/CH4/in.ch4.dynamics b/examples/USER/eff/CH4/in.ch4.dynamics index 2536fa8f48..cb06a1c8cf 100644 --- a/examples/USER/eff/CH4/in.ch4.dynamics +++ b/examples/USER/eff/CH4/in.ch4.dynamics @@ -1,5 +1,4 @@ variable sname index ch4 -log ${sname}.nve.log units electron newton on diff --git a/examples/USER/eff/CH4/in.ch4.min b/examples/USER/eff/CH4/in.ch4.min index 69b7c15bd4..df052c728e 100644 --- a/examples/USER/eff/CH4/in.ch4.min +++ b/examples/USER/eff/CH4/in.ch4.min @@ -1,5 +1,4 @@ variable sname index ch4 -log ${sname}.nve.log units electron newton on diff --git a/examples/USER/eff/CH4/in.ch4_ionized.dynamics b/examples/USER/eff/CH4/in.ch4_ionized.dynamics index 14f214296f..51ca071fc6 100644 --- a/examples/USER/eff/CH4/in.ch4_ionized.dynamics +++ b/examples/USER/eff/CH4/in.ch4_ionized.dynamics @@ -1,5 +1,4 @@ variable sname index ch4_ionized -log ${sname}.nvt.log units electron newton on @@ -15,6 +14,7 @@ pair_coeff * * comm_modify vel yes # minimize + min_style cg min_modify line quadratic minimize 0 1.0e-6 10000 100000 diff --git a/examples/USER/eff/H/in.h_atom.spe.ang b/examples/USER/eff/H/in.h_atom.spe.ang index 2493e273c4..85bedf5b59 100644 --- a/examples/USER/eff/H/in.h_atom.spe.ang +++ b/examples/USER/eff/H/in.h_atom.spe.ang @@ -1,5 +1,4 @@ variable sname index h_atom.ang -log ${sname}.spe.log units real newton on diff --git a/examples/USER/eff/H/in.h_atom.spe.bohr b/examples/USER/eff/H/in.h_atom.spe.bohr index 2f18ee4e43..91b39a70db 100644 --- a/examples/USER/eff/H/in.h_atom.spe.bohr +++ b/examples/USER/eff/H/in.h_atom.spe.bohr @@ -1,5 +1,4 @@ variable sname index h_atom.bohr -log ${sname}.spe.log units electron newton on diff --git a/examples/USER/eff/H2/in.h2 b/examples/USER/eff/H2/in.h2 index 8f4a63cc84..0c9dd620a3 100644 --- a/examples/USER/eff/H2/in.h2 +++ b/examples/USER/eff/H2/in.h2 @@ -1,5 +1,4 @@ variable sname index h2 -log ${sname}.spe.log units electron newton on @@ -47,4 +46,4 @@ unfix 3 #fix 1 all nve/eff -run 100000 +run 10000 diff --git a/examples/USER/eff/H_plasma/in.h2bulk.npt b/examples/USER/eff/H_plasma/in.h2bulk.npt index 6d9fc5d55f..55c3d9b16f 100644 --- a/examples/USER/eff/H_plasma/in.h2bulk.npt +++ b/examples/USER/eff/H_plasma/in.h2bulk.npt @@ -1,5 +1,4 @@ variable sname index h2bulk -log ${sname}.npt.log units electron newton on @@ -41,7 +40,8 @@ dump 2 all xyz 10000 ${sname}.npt.xyz 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 +thermo 1 +run 10 unfix 1 undump 2 diff --git a/examples/USER/eff/H_plasma/in.h2bulk.nve b/examples/USER/eff/H_plasma/in.h2bulk.nve index 9786ff476f..32b724c539 100644 --- a/examples/USER/eff/H_plasma/in.h2bulk.nve +++ b/examples/USER/eff/H_plasma/in.h2bulk.nve @@ -1,5 +1,4 @@ variable sname index h2bulk -log ${sname}.nve.log units electron newton on @@ -18,13 +17,13 @@ comm_modify vel yes compute effTemp all temp/eff -thermo 1000 +thermo 10 thermo_style custom step pe temp press thermo_modify temp effTemp # structure minimization min_style cg -minimize 0 1.0e-4 1000 10000 +minimize 0 1.0e-4 10 10 timestep 0.001 @@ -41,7 +40,7 @@ dump 2 all xyz 1000 ${sname}.nve.xyz 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 +run 10 unfix 1 #unfix 2 diff --git a/examples/USER/eff/H_plasma/in.h2bulk.nve.ang b/examples/USER/eff/H_plasma/in.h2bulk.nve.ang index 4935e39be3..3377d63580 100644 --- a/examples/USER/eff/H_plasma/in.h2bulk.nve.ang +++ b/examples/USER/eff/H_plasma/in.h2bulk.nve.ang @@ -1,5 +1,4 @@ variable sname index h2bulk.ang -log ${sname}.nve.log units real newton on @@ -29,13 +28,13 @@ variable epauli equal c_energies[2] variable ecoul equal c_energies[3] 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_modify temp effTemp press effPress flush yes # structure minimization min_style cg -minimize 0 1.0e-4 1000 10000 +minimize 0 1.0e-4 10 10 timestep 0.001 @@ -52,7 +51,7 @@ dump 2 all xyz 1000 ${sname}.nve.xyz 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 +run 10 unfix 1 #unfix 2 diff --git a/examples/USER/eff/Li-dendritic/in.Li-dendritic.min b/examples/USER/eff/Li-dendritic/in.Li-dendritic.min index f791544e44..5dfa85e52c 100644 --- a/examples/USER/eff/Li-dendritic/in.Li-dendritic.min +++ b/examples/USER/eff/Li-dendritic/in.Li-dendritic.min @@ -1,5 +1,4 @@ variable sname index Li-dendritic -log ${sname}.min.log units electron newton on @@ -7,8 +6,8 @@ boundary p p p atom_style electron -#read_data data.${sname} -read_restart ${sname}.min.restart2 +read_data data.${sname} +#read_restart ${sname}.min.restart2 pair_style eff/cut 50.112 pair_coeff * * diff --git a/examples/USER/eff/Li-dendritic/in.Li-dendritic.nvt b/examples/USER/eff/Li-dendritic/in.Li-dendritic.nvt index 143e23cbc1..4203b50dde 100644 --- a/examples/USER/eff/Li-dendritic/in.Li-dendritic.nvt +++ b/examples/USER/eff/Li-dendritic/in.Li-dendritic.nvt @@ -1,5 +1,4 @@ variable sname index Li-dendritic -log ${sname}.min.log units electron 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 2 all xyz 100 ${sname}.min.xyz 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 @@ -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 restart 100 ${sname}.nvt.restart1 ${sname}.nvt.restart2 -run 10000 +run 100 undump 1 undump 2 diff --git a/examples/USER/eff/Li-solid/in.Li.ang b/examples/USER/eff/Li-solid/in.Li.ang index c9a726b88c..e4f5614c56 100644 --- a/examples/USER/eff/Li-solid/in.Li.ang +++ b/examples/USER/eff/Li-solid/in.Li.ang @@ -1,5 +1,4 @@ variable sname index Li.ang -log ${sname}.spe.log units real 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 1 all nve/eff -run 1000 +run 200 unfix 0 unfix 1 fix 1 all nvt/eff temp 3000.0 3000.0 100.0 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 diff --git a/examples/USER/eff/Li-solid/in.Li.bohr b/examples/USER/eff/Li-solid/in.Li.bohr index 2843d3ca6a..2ff8b661d5 100644 --- a/examples/USER/eff/Li-solid/in.Li.bohr +++ b/examples/USER/eff/Li-solid/in.Li.bohr @@ -1,5 +1,4 @@ variable sname index Li.bohr -log ${sname}.spe.log units electron 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 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 1 all npt/eff temp 3000.0 3000.0 0.1 iso 1e7 1e7 1.0 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 -run 1000 +run 100 diff --git a/examples/granular/in.pour.drum b/examples/granular/in.pour.drum index c30f30b377..54372cd391 100644 --- a/examples/granular/in.pour.drum +++ b/examples/granular/in.pour.drum @@ -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 unfix grav +unfix ins1 +unfix ins2 fix grav all gravity 10 vector 0 -1 0 variable theta equal 2*PI*elapsed/20000.0 diff --git a/examples/qeq/in.qeq.buck b/examples/qeq/in.qeq.buck index f7ec2bb808..2258a9e2ae 100644 --- a/examples/qeq/in.qeq.buck +++ b/examples/qeq/in.qeq.buck @@ -24,7 +24,7 @@ compute charge2 type2 property/atom q compute q2 type2 reduce ave c_charge2 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 timestep 0.0001 diff --git a/examples/streitz/in.streitz.wolf b/examples/streitz/in.streitz.wolf index ff4479448e..cdf7cf33c9 100644 --- a/examples/streitz/in.streitz.wolf +++ b/examples/streitz/in.streitz.wolf @@ -39,7 +39,7 @@ neigh_modify every 10 delay 0 check yes timestep 0.0004 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 10