diff --git a/examples/colloid/in.colloid b/examples/colloid/in.colloid index 4ab4e5909d..589b4478e3 100644 --- a/examples/colloid/in.colloid +++ b/examples/colloid/in.colloid @@ -29,7 +29,7 @@ pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5 pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0 pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5 -fix 1 all npt 2.0 2.0 1.0 xyz 0.0 1.0 10.0 drag 1.0 +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 fix 2 all enforce2d dump 1 all atom 200 dump.colloid diff --git a/examples/ellipse/in.ellipse.gayberne b/examples/ellipse/in.ellipse.gayberne index 61e38c015d..870c7bfe2b 100644 --- a/examples/ellipse/in.ellipse.gayberne +++ b/examples/ellipse/in.ellipse.gayberne @@ -47,7 +47,7 @@ dump 1 all custom 100 dump.ellipse.gayberne & #dump 1 all custom 100 dump.ellipse.resquared & # id type x y z quatw quati quatj quatk -fix 1 all npt/asphere 2.0 2.0 0.1 xyz 0.0 1.0 1.0 +fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 fix 2 all enforce2d compute_modify 1_temp extra ${dof} diff --git a/examples/ellipse/in.ellipse.resquared b/examples/ellipse/in.ellipse.resquared index 2bd270a88a..2843dfd701 100644 --- a/examples/ellipse/in.ellipse.resquared +++ b/examples/ellipse/in.ellipse.resquared @@ -47,7 +47,7 @@ timestep 0.002 dump 1 all custom 100 dump.ellipse.resquared & id type x y z quatw quati quatj quatk -fix 1 all npt/asphere 2.0 2.0 0.1 xyz 0.0 1.0 1.0 +fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 fix 2 all enforce2d compute_modify 1_temp extra ${dof} diff --git a/examples/min/in.min.box b/examples/min/in.min.box new file mode 100644 index 0000000000..9850309034 --- /dev/null +++ b/examples/min/in.min.box @@ -0,0 +1,44 @@ +# 2d Lennard-Jones melt and subsequent energy minimization + +units lj +dimension 2 +atom_style atomic + +lattice sq2 0.8442 +region box block 0 20 0 20 -0.1 0.1 +create_box 1 box +create_atoms 1 box +mass 1 1.0 + +velocity all create 5.0 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 +pair_modify shift yes + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +fix 2 all enforce2d + +dump 1 all atom 100 dump.min + +thermo 100 + +run 1000 + +neigh_modify delay 0 every 1 check yes + + +velocity all create 0.0 1 +dump_modify 1 every 25 +thermo 50 +minimize 1.0e-6 0.001 1000 10000 + +fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-4 nreset 1000 + +thermo_style custom step temp pe pxx pyy pxy + +min_modify line quadratic +minimize 0.0 1.0e-3 10000 100000 diff --git a/examples/nemd/in.nemd b/examples/nemd/in.nemd index f0df5f31f5..07cf0f0ab3 100644 --- a/examples/nemd/in.nemd +++ b/examples/nemd/in.nemd @@ -21,7 +21,7 @@ pair_coeff * * 1.0 1.0 1.0 neighbor 0.3 bin neigh_modify delay 0 every 1 -fix 1 all nvt/sllod 1.0 1.0 1.0 +fix 1 all nvt/sllod temp 1.0 1.0 1.0 fix 2 all deform 1 xy erate 0.01 remap v dump 1 all custom 500 dump.nemd id type x y z diff --git a/examples/peptide/in.peptide b/examples/peptide/in.peptide index 6b46439203..0acdb7a214 100644 --- a/examples/peptide/in.peptide +++ b/examples/peptide/in.peptide @@ -20,7 +20,7 @@ timestep 2.0 thermo_style multi thermo 50 -fix 1 all nvt 275.0 275.0 100.0 +fix 1 all nvt temp 275.0 275.0 100.0 fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 group peptide type <= 12 diff --git a/examples/prd/in.prd b/examples/prd/in.prd index 0e88ad8195..e6e1ed6bf5 100644 --- a/examples/prd/in.prd +++ b/examples/prd/in.prd @@ -64,7 +64,7 @@ pair_coeff * * Si.sw Si thermo 10 -fix 1 all nvt $t $t 0.1 +fix 1 all nvt temp $t $t 0.1 timestep 1.0e-3 neighbor 1.0 bin