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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4991 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2010-10-06 23:33:17 +00:00
parent a4ef8e330f
commit f1fee8d3e0
5 changed files with 59 additions and 48 deletions
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23
examples/neb/README
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@ -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 #

15
examples/neb/in.neb.hop1
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@ -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

17
examples/neb/in.neb.hop2
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@ -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

19
examples/neb/log.neb.hop1.10Sep10.linux.4
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@ -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

33
examples/neb/log.neb.hop2.10Sep10.linux.4
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@ -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