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minor changes to NEB doc pages and examples

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This commit is contained in:
Steve Plimpton
2017-06-20 08:19:23 -06:00
parent 326a8a1289
commit d2610d9e7c
17 changed files with 57 additions and 62 deletions
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4
examples/neb/README
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@ -8,9 +8,7 @@ mpirun -np 3 lmp_g++ -partition 3x1 -in in.neb.sivac
mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1
mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop2
mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1.end
mpirun -np 6 lmp_g++ -partition 3x2 -in in.neb.sivac
mpirun -np 9 lmp_g++ -partition 3x3 -in in.neb.sivac
mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.sivac
Note that more than 4 replicas should be used for a precise estimate
of the activation energy corresponding to a transition.

2
examples/neb/in.neb.hop1
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@ -51,7 +51,7 @@ set group nebatoms type 3
group nonneb subtract all nebatoms
fix 1 lower setforce 0.0 0.0 0.0
fix 2 nebatoms neb 1.0 #nudge ideal
fix 2 nebatoms neb 1.0 parallel ideal
fix 3 all enforce2d
thermo 100

2
examples/neb/in.neb.hop1.end
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@ -41,7 +41,7 @@ set group nebatoms type 3
group nonneb subtract all nebatoms
fix 1 lower setforce 0.0 0.0 0.0
fix 2 nebatoms neb 1.0 nudge ideal end first 1.0
fix 2 nebatoms neb 1.0 parallel ideal end first 1.0
fix 3 all enforce2d
thermo 100

0
examples/neb/log.19June17.neb.hop1.end.g++.4 → examples/neb/log.19Jun17.neb.hop1.end.g++.4
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examples/neb/log.19June17.neb.hop1.end.g++.8 → examples/neb/log.19Jun17.neb.hop1.end.g++.8
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examples/neb/log.19Jun17.neb.hop1.g++.4 Normal file
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@ -0,0 +1,9 @@
LAMMPS (19 May 2017)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 4327.2753 2746.3378 0.082169072 4.9967651 4514.5424 0.42933428 0.42323635 1.8941131 0 -3.0535948 0.33333333 -2.6242605 0.66666667 -2.7623811 1 -3.0474969
87 0.095951502 0.052720903 0.005588927 0.065110105 0.12467831 0.0071014928 0.0022798007 2.3003372 0 -3.0535967 0.32435271 -3.0473127 0.62805027 -3.0464952 1 -3.048775
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
87 0.14137277 0.11108954 0.005588927 0.065110105 0.12467831 0.0071014928 0.0022798007 2.3003372 0 -3.0535967 0.32435271 -3.0473127 0.62805027 -3.0464952 1 -3.048775
124 0.099583263 0.085936899 0.0044220372 0.023873795 0.091308308 0.0071061754 0.0022863931 2.308121 0 -3.0535968 0.32223905 -3.0473329 0.61673898 -3.0464906 1 -3.048777

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examples/neb/log.19Jun17.neb.hop1.g++.8 Normal file
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@ -0,0 +1,9 @@
LAMMPS (19 May 2017)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 4327.2753 2746.3378 0.082169072 4.9967651 4514.5424 0.42933428 0.42323635 1.8941131 0 -3.0535948 0.33333333 -2.6242605 0.66666667 -2.7623811 1 -3.0474969
87 0.095951792 0.052720902 0.0055889267 0.065110091 0.12467831 0.0071014928 0.0022798007 2.3003372 0 -3.0535967 0.32435271 -3.0473127 0.62805027 -3.0464952 1 -3.048775
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
87 0.14137297 0.11108954 0.0055889267 0.065110091 0.12467831 0.0071014928 0.0022798007 2.3003372 0 -3.0535967 0.32435271 -3.0473127 0.62805027 -3.0464952 1 -3.048775
124 0.099582186 0.08593683 0.0044220345 0.023873731 0.091308197 0.0071061754 0.0022863931 2.3081211 0 -3.0535968 0.32223904 -3.0473329 0.61673896 -3.0464906 1 -3.048777

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examples/neb/log.19June17.neb.hop2.g++.4 → examples/neb/log.19Jun17.neb.hop2.g++.4
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examples/neb/log.19June17.neb.hop2.g++.8 → examples/neb/log.19Jun17.neb.hop2.g++.8
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examples/neb/log.19June17.neb.sivac.g++.4 → examples/neb/log.19Jun17.neb.sivac.g++.4
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examples/neb/log.19June17.neb.sivac.g++.8 → examples/neb/log.19Jun17.neb.sivac.g++.8
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examples/neb/log.19June17.neb.hop1.g++.4
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@ -1,10 +0,0 @@
LAMMPS (19 May 2017)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 4327.2753 2746.3378 0.082169072 4.9967651 4514.5424 0.42933428 0.42323635 1.8941131 0 -3.0535948 0.33333333 -2.6242605 0.66666667 -2.7623811 1 -3.0474969
100 0.10482184 0.085218486 0.0051952047 0.04785954 0.19041553 0.0070900402 0.0022691875 2.3031875 0 -3.0535967 0.31839181 -3.0473647 0.63987598 -3.0465067 1 -3.0487759
111 0.096708467 0.07803707 0.0048656875 0.03613038 0.19671332 0.0070871172 0.0022668002 2.3052945 0 -3.0535968 0.31853431 -3.0473633 0.64178871 -3.0465096 1 -3.0487764
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
111 0.2023467 0.1777038 0.0048656875 0.03613038 0.19671332 0.0070871172 0.0022668002 2.3052945 0 -3.0535968 0.31853431 -3.0473633 0.64178871 -3.0465096 1 -3.0487764
179 0.096874474 0.090676856 0.0034851031 0.0094134782 0.093630619 0.0071047642 0.0022856172 2.3122768 0 -3.0535969 0.31577311 -3.0473955 0.61798541 -3.0464922 1 -3.0487778

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examples/neb/log.19June17.neb.hop1.g++.8
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@ -1,10 +0,0 @@
LAMMPS (19 May 2017)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 4327.2753 2746.3378 0.082169072 4.9967651 4514.5424 0.42933428 0.42323635 1.8941131 0 -3.0535948 0.33333333 -2.6242605 0.66666667 -2.7623811 1 -3.0474969
100 0.10482171 0.085218406 0.0051952008 0.047859379 0.1904156 0.0070900401 0.0022691875 2.3031875 0 -3.0535967 0.31839181 -3.0473647 0.639876 -3.0465067 1 -3.0487759
111 0.096708718 0.078036984 0.0048656841 0.036130268 0.1967134 0.0070871172 0.0022668002 2.3052946 0 -3.0535968 0.31853431 -3.0473633 0.64178873 -3.0465096 1 -3.0487764
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
111 0.20234693 0.17770387 0.0048656841 0.036130268 0.1967134 0.0070871172 0.0022668002 2.3052946 0 -3.0535968 0.31853431 -3.0473633 0.64178873 -3.0465096 1 -3.0487764
178 0.09975409 0.093814031 0.0035463662 0.010006594 0.096949208 0.0071042931 0.0022851195 2.312004 0 -3.0535969 0.31607934 -3.0473923 0.618931 -3.0464926 1 -3.0487777