diff --git a/examples/neb/README b/examples/neb/README index d49f3f1ffd..c512726727 100644 --- a/examples/neb/README +++ b/examples/neb/README @@ -3,13 +3,20 @@ 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) +Create dump files to do visualization from via Python tools: +(see lammps/tools/README and lammps/tools/python/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.* +python ~/lammps/tools/python/neb_combine.py -o dump.hop1.combine + -b dump.nonneb.1 + -r dump.neb.* +python ~/lammps/tools/python/neb_final.py -o dump.hop1.final + -b dump.nonneb.1 + -r dump.neb.* -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 # +produces: + +dump.hop1.combine = series of snapshots for all replicas together + time = progression of NEB calculation +dump.hop1.final = series of snapshots for final state of all replicas + time = replica # diff --git a/examples/neb/in.neb.hop1 b/examples/neb/in.neb.hop1 index 452e4bb1ce..ca1a67ae8b 100644 --- a/examples/neb/in.neb.hop1 +++ b/examples/neb/in.neb.hop1 @@ -26,7 +26,7 @@ pair_coeff * * 1.0 1.0 2.5 # initial minimization to relax surface -minimize 1.0e-6 0.001 1000 10000 +minimize 1.0e-6 1.0e-4 1000 10000 reset_timestep 0 # define groups @@ -41,18 +41,19 @@ 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 +group nebatoms region surround +#group nebatoms id 412 +set group nebatoms type 3 +group nonneb subtract all nebatoms fix 1 lower setforce 0.0 0.0 0.0 -fix 2 all neb 1.0 +fix 2 nebatoms neb 1.0 fix 3 all enforce2d thermo 100 -dump 1 all atom 10 tmp.dump.$u -dump_modify 1 scale no +dump 1 nebatoms atom 10 dump.neb.$u +dump 2 nonneb atom 10 dump.nonneb.$u # run NEB for 2000 steps or to force tolerance diff --git a/examples/neb/in.neb.hop2 b/examples/neb/in.neb.hop2 index be87e7dafc..cd961827b0 100644 --- a/examples/neb/in.neb.hop2 +++ b/examples/neb/in.neb.hop2 @@ -28,7 +28,7 @@ pair_coeff * * 1.0 1.0 2.5 # initial minimization to relax surface -minimize 1.0e-6 0.001 1000 10000 +minimize 1.0e-6 1.0e-4 1000 10000 reset_timestep 0 # define groups @@ -43,18 +43,19 @@ timestep 0.005 # group of NEB atoms - either block or single atom ID 421 region surround block 10 18 17 21 0 0 units box -group one region surround -#group one id 421 -set group one type 3 +group nebatoms region surround +#group nebatoms id 421 +set group nebatoms type 3 +group nonneb subtract all nebatoms fix 1 lower setforce 0.0 0.0 0.0 -fix 2 one neb 1.0 +fix 2 nebatoms neb 1.0 fix 3 all enforce2d -thermo 10 +thermo 100 -dump 1 all atom 10 tmp.dump.$u -dump_modify 1 scale no +dump 1 nebatoms atom 10 dump.neb.$u +dump 2 nonneb atom 10 dump.nonneb.$u # run NEB for 2000 steps or to force tolerance diff --git a/examples/neb/log.neb.hop1.10Sep10.linux.4 b/examples/neb/log.neb.hop1.10Sep10.linux.4 index 727aefb099..8098fd1eda 100644 --- a/examples/neb/log.neb.hop1.10Sep10.linux.4 +++ b/examples/neb/log.neb.hop1.10Sep10.linux.4 @@ -1,10 +1,11 @@ -LAMMPS (29 Sep 2010) +LAMMPS (7 Oct 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 +Step MaxReplicaForce MaxAtomForce RD1 PE1 RD2 PE2 ... RDN PEN +0 4394.41 2794.68 0 -3.19266 0.333333 -2.75656 0.666667 -2.88382 1 -3.18641 +100 0.232633 0.1346 0 -3.19267 0.324324 -3.18618 0.627598 -3.18537 1 -3.18765 +179 0.099568 0.0739454 0 -3.19267 0.320641 -3.18622 0.644159 -3.18536 1 -3.18766 +Climbing replica = 3 +Step MaxReplicaForce MaxAtomForce RD1 PE1 RD2 PE2 ... RDN PEN +179 0.215761 0.186274 0 -3.19267 0.320641 -3.18622 0.644159 -3.18536 1 -3.18766 +279 0.190356 0.178099 0 -3.19267 0.320598 -3.18623 0.633941 -3.18535 1 -3.18766 +350 0.0993201 0.0883921 0 -3.19268 0.317736 -3.18626 0.617322 -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 index c4e93ff89d..8e7ac5b638 100644 --- a/examples/neb/log.neb.hop2.10Sep10.linux.4 +++ b/examples/neb/log.neb.hop2.10Sep10.linux.4 @@ -1,17 +1,18 @@ -LAMMPS (29 Sep 2010) +LAMMPS (7 Oct 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 +Step MaxReplicaForce MaxAtomForce RD1 PE1 RD2 PE2 ... RDN PEN +0 14.4706 10.6542 0 -3.19051 0.333333 -3.18866 0.666667 -3.18862 1 -3.18934 +100 0.376157 0.149124 0 -3.19051 0.293005 -3.18936 0.59723 -3.18895 1 -3.19051 +200 0.205029 0.0602429 0 -3.19052 0.300372 -3.18932 0.633185 -3.18904 1 -3.19051 +300 0.290337 0.0762659 0 -3.19052 0.315043 -3.18926 0.644819 -3.18908 1 -3.19052 +400 0.102264 0.0250286 0 -3.19052 0.323255 -3.18923 0.655365 -3.18911 1 -3.19052 +500 0.0245027 0.00963392 0 -3.19052 0.326135 -3.18922 0.658828 -3.18913 1 -3.19052 +600 0.0282936 0.00605774 0 -3.19052 0.328852 -3.18921 0.662529 -3.18914 1 -3.19052 +700 0.0193091 0.00411287 0 -3.19052 0.330378 -3.1892 0.664116 -3.18918 1 -3.19052 +763 0.00925047 0.00239377 0 -3.19052 0.331738 -3.1892 0.664872 -3.18919 1 -3.19052 +Climbing replica = 3 +Step MaxReplicaForce MaxAtomForce RD1 PE1 RD2 PE2 ... RDN PEN +763 1.25625 1.22516 0 -3.19052 0.331738 -3.1892 0.664872 -3.18919 1 -3.19052 +863 0.111473 0.0576821 0 -3.19052 0.278536 -3.18942 0.502167 -3.18884 1 -3.19052 +963 0.0365617 0.0188834 0 -3.19052 0.260586 -3.18952 0.503636 -3.18884 1 -3.19052 +1049 0.00944841 0.00581768 0 -3.19052 0.254838 -3.18955 0.504648 -3.18884 1 -3.19052