From a71eb75caabaddb416d51bdd138dc719926d7119 Mon Sep 17 00:00:00 2001 From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa> Date: Thu, 30 Sep 2010 23:12:46 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4920 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- examples/neb/README | 15 ++++++ examples/neb/final.hop1 | 1 + examples/neb/final.hop2 | 1 + examples/neb/in.neb.hop1 | 62 ++++++++++++++++++++++ examples/neb/in.neb.hop2 | 64 +++++++++++++++++++++++ examples/neb/log.neb.hop1.10Sep10.linux.4 | 10 ++++ examples/neb/log.neb.hop2.10Sep10.linux.4 | 17 ++++++ 7 files changed, 170 insertions(+) create mode 100644 examples/neb/README create mode 100644 examples/neb/final.hop1 create mode 100644 examples/neb/final.hop2 create mode 100644 examples/neb/in.neb.hop1 create mode 100644 examples/neb/in.neb.hop2 create mode 100644 examples/neb/log.neb.hop1.10Sep10.linux.4 create mode 100644 examples/neb/log.neb.hop2.10Sep10.linux.4 diff --git a/examples/neb/README b/examples/neb/README new file mode 100644 index 0000000000..d49f3f1ffd --- /dev/null +++ b/examples/neb/README @@ -0,0 +1,15 @@ +Run these examples as: + +mpirun -np 4 lmp_linux -partition 4x1 -in in.neb.hop1 +mpirun -np 4 lmp_linux -partition 4x1 -in in.neb.hop2 + +Create dump files to do visualization from as: +(see lammps/tools/README for more info on these Python scripts) + +python ~/lammps/tools/python/neb1.py dump.hop1.a 3 tmp.dump.* +python ~/lammps/tools/python/neb2.py dump.hop1.b tmp.dump.* + +dump.hop1.a = series of snapshots for all replicas together + time = progression of NEB calculation +dump.hop1.b = series of snapshots for final state of all replicas + time = replica # diff --git a/examples/neb/final.hop1 b/examples/neb/final.hop1 new file mode 100644 index 0000000000..6465c7596a --- /dev/null +++ b/examples/neb/final.hop1 @@ -0,0 +1 @@ +412 14.0 20.5 0 diff --git a/examples/neb/final.hop2 b/examples/neb/final.hop2 new file mode 100644 index 0000000000..8ca1762a34 --- /dev/null +++ b/examples/neb/final.hop2 @@ -0,0 +1 @@ +421 14.0 20.5 0 diff --git a/examples/neb/in.neb.hop1 b/examples/neb/in.neb.hop1 new file mode 100644 index 0000000000..452e4bb1ce --- /dev/null +++ b/examples/neb/in.neb.hop1 @@ -0,0 +1,62 @@ +# 2d NEB surface simulation, hop from surface to become adatom + +dimension 2 +boundary p s p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 +atom_modify map array sort 0 0.0 + +variable u uloop 20 + +# create geometry with flat surface + +lattice hex 0.9 +region box block 0 20 0 10 -0.25 0.25 +create_box 3 box +create_atoms 1 box + +mass * 1.0 + +# LJ potentials + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 2.5 + +# initial minimization to relax surface + +minimize 1.0e-6 0.001 1000 10000 +reset_timestep 0 + +# define groups + +region 1 block INF INF INF 1.25 INF INF +group lower region 1 +group mobile subtract all lower +set group lower type 2 + +timestep 0.005 + +# group of NEB atoms - either block or single atom ID 412 + +region surround block 10 18 17 20 0 0 units box +group one region surround +#group one id 412 +set group one type 3 + +fix 1 lower setforce 0.0 0.0 0.0 +fix 2 all neb 1.0 +fix 3 all enforce2d + +thermo 100 + +dump 1 all atom 10 tmp.dump.$u +dump_modify 1 scale no + +# run NEB for 2000 steps or to force tolerance + +min_style quickmin + +#neb 0.0 1000 1000 100 final.hop1 +neb 0.1 1000 1000 100 final.hop1 diff --git a/examples/neb/in.neb.hop2 b/examples/neb/in.neb.hop2 new file mode 100644 index 0000000000..be87e7dafc --- /dev/null +++ b/examples/neb/in.neb.hop2 @@ -0,0 +1,64 @@ +# 2d NEB surface simulation, hop of adatom on surface + +dimension 2 +boundary p s p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 +atom_modify map array sort 0 0.0 + +variable u uloop 20 + +# create geometry with adatom + +lattice hex 0.9 +region box block 0 20 0 11 -0.25 0.25 +region box1 block 0 20 0 10 -0.25 0.25 +create_box 3 box +create_atoms 1 region box1 +create_atoms 1 single 11.5 10.5 0 + +mass * 1.0 + +# LJ potentials + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 2.5 + +# initial minimization to relax surface + +minimize 1.0e-6 0.001 1000 10000 +reset_timestep 0 + +# define groups + +region 1 block INF INF INF 1.25 INF INF +group lower region 1 +group mobile subtract all lower +set group lower type 2 + +timestep 0.005 + +# group of NEB atoms - either block or single atom ID 421 + +region surround block 10 18 17 21 0 0 units box +group one region surround +#group one id 421 +set group one type 3 + +fix 1 lower setforce 0.0 0.0 0.0 +fix 2 one neb 1.0 +fix 3 all enforce2d + +thermo 10 + +dump 1 all atom 10 tmp.dump.$u +dump_modify 1 scale no + +# run NEB for 2000 steps or to force tolerance + +min_style fire + +#neb 0.0 1000 1000 100 final.hop2 +neb 0.01 1000 1000 100 final.hop2 diff --git a/examples/neb/log.neb.hop1.10Sep10.linux.4 b/examples/neb/log.neb.hop1.10Sep10.linux.4 new file mode 100644 index 0000000000..727aefb099 --- /dev/null +++ b/examples/neb/log.neb.hop1.10Sep10.linux.4 @@ -0,0 +1,10 @@ +LAMMPS (29 Sep 2010) +Running on 4 partitions of processors +Step RD1 PE1 RD2 PE2 ... RDN PEN +0 0 -3.19266 0.333333 -2.75656 0.666667 -2.88382 1 -3.18641 +100 0 -3.19267 0.325226 -3.18617 0.627987 -3.18537 1 -3.18765 +175 0 -3.19267 0.321396 -3.18621 0.644098 -3.18536 1 -3.18766 +Step RD1 PE1 RD2 PE2 ... RDN PEN +175 0 -3.19267 0.321396 -3.18621 0.644098 -3.18536 1 -3.18766 +275 0 -3.19267 0.321136 -3.18621 0.633855 -3.18535 1 -3.18766 +345 0 -3.19268 0.318221 -3.18625 0.617506 -3.18538 1 -3.18766 diff --git a/examples/neb/log.neb.hop2.10Sep10.linux.4 b/examples/neb/log.neb.hop2.10Sep10.linux.4 new file mode 100644 index 0000000000..c4e93ff89d --- /dev/null +++ b/examples/neb/log.neb.hop2.10Sep10.linux.4 @@ -0,0 +1,17 @@ +LAMMPS (29 Sep 2010) +Running on 4 partitions of processors +Step RD1 PE1 RD2 PE2 ... RDN PEN +0 0 -3.19051 0.333333 -3.18866 0.666667 -3.18862 1 -3.18934 +100 0 -3.19051 0.293005 -3.18936 0.59723 -3.18895 1 -3.19051 +200 0 -3.19052 0.300372 -3.18932 0.633185 -3.18904 1 -3.19051 +300 0 -3.19052 0.315043 -3.18926 0.644819 -3.18908 1 -3.19052 +400 0 -3.19052 0.323255 -3.18923 0.655365 -3.18911 1 -3.19052 +500 0 -3.19052 0.326135 -3.18922 0.658828 -3.18913 1 -3.19052 +600 0 -3.19052 0.328852 -3.18921 0.662529 -3.18914 1 -3.19052 +700 0 -3.19052 0.330378 -3.1892 0.664116 -3.18918 1 -3.19052 +763 0 -3.19052 0.331738 -3.1892 0.664872 -3.18919 1 -3.19052 +Step RD1 PE1 RD2 PE2 ... RDN PEN +763 0 -3.19052 0.331738 -3.1892 0.664872 -3.18919 1 -3.19052 +863 0 -3.19052 0.278536 -3.18942 0.502167 -3.18884 1 -3.19052 +963 0 -3.19052 0.260586 -3.18952 0.503636 -3.18884 1 -3.19052 +1049 0 -3.19052 0.254838 -3.18955 0.504648 -3.18884 1 -3.19052 -- GitLab