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modified the documentation, first and last freeend can have different spring constants

This commit is contained in:
Emile Maras 2017-06-19 16:30:42 +02:00
parent c97415aefa
commit 8988b692a3
18 changed files with 121 additions and 114 deletions
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23
doc/src/fix_neb.txt
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@ -34,7 +34,7 @@ keyword = {nudge} or {perp} or {ends} :l
fix 1 active neb 10.0
fix 2 all neb 1.0 perp 1.0 end last
fix 2 all neb 1.0 perp 1.0 end first end last
fix 2 all neb 1.0 perp 1.0 end first 1.0 end last 1.0
fix 1 all neb 1.0 nudge ideal end last/efirst 1 :pre
[Description:]
@ -64,7 +64,7 @@ Fi = -Grad(V) + (Grad(V) dot T') T' + Fnudge_parallel + Fspring_perp :pre
T' is the unit "tangent" vector for replica I and is a function of Ri,
Ri-1, Ri+1, and the potential energy of the 3 replicas; it points
roughly in the direction of (Ri+i - Ri-1); see the
"(Henkelman1)"_#Henkelman1 paper for details. Ri are the atomic
"(Henkelman1)"_#Henkelman1 paper for details. Ri gives the atomic
coordinates of replica I; Ri-1 and Ri+1 are the coordinates of its
neighbor replicas. The term (Grad(V) dot T') is used to remove the
component of the gradient parallel to the path which would tend to
@ -114,7 +114,7 @@ keeping the replicas equally spaced.
:line
The keyword {perp} adds a spring force perpendicular to the path in
order to prevent the path from becoming too kinky, with magnitude It
order to prevent the path from becoming too kinky. It
can significantly improve the convergence of the NEB calculation when
the resolution is poor. I.e. when too few replicas are used; see
"(Maras)"_#Maras1 for details.
@ -133,11 +133,11 @@ force is added.
:line
By default, no forces act on the first and last replicas during the
NEB relaxation, so these replicas simply relax toward their respective
local minima. By using the key word {end}, additional forces can be
applied to the first or last replica, to enable them to relax toward a
MEP while constraining their energy.
By default, no nudging forces act on the first and last replicas during
the NEB relaxation, so these replicas simply relax toward their
respective local minima. By using the key word {end}, additional forces
can be applied to the first or last replica, to enable them to relax
toward a MEP while constraining their energy.
The interatomic force Fi for the specified replica becomes:
@ -177,10 +177,9 @@ only be done if a particular intermediate replica has a lower energy
than the first replica. This should effectively prevent the
intermediate replicas from over-relaxing.
After converging a NEB calculation using an {estyle} of {last/efirst},
you should check that all intermediate replicas have a larger energy
than the first replica. If not, then repeat the calculation with an
{estyle} of {last/efirst/middle}.
After converging a NEB calculation using an {estyle} of {last/efirst/middle},
you should check that all intermediate replicas have a larger energy than the
first replica. If this is not the case, the path is probably not a MEP.
Finally, note that if the last replica converges toward a local
minimum which has a larger energy than the energy of the first

4
examples/neb/README
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@ -2,12 +2,12 @@ Run these examples as:
mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1
mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop2
mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1freeend
mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1.end
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.hop1freeend
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

2
examples/neb/in.neb.hop2
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@ -65,4 +65,4 @@ thermo 100
min_style fire
neb 0.0 0.01 1000 1000 100 final final.hop2
neb 0.0 0.05 1000 1000 100 final final.hop2

11
examples/neb/log.19June17.neb.hop1.end.g++.4 Normal file
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@ -0,0 +1,11 @@
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
0 229.26196 146.68251 2.9774577 4.4127369 233.11559 0.023301843 0.0224626 1.4763579 0 -3.048332 0.33333333 -3.0250302 0.66666667 -3.0291888 1 -3.0474928
100 0.11027532 0.085410308 3.0967938 0.024201563 0.38551033 0.0017583261 0.0021866943 1.7710358 0 -3.0483469 0.31192818 -3.0465886 0.61093022 -3.0466143 1 -3.0487752
130 0.09954083 0.075481108 3.0927626 0.015664388 0.37491833 0.0017573704 0.0021913201 1.7713726 0 -3.048342 0.31428487 -3.0465846 0.61762817 -3.0466296 1 -3.048776
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
130 0.37838747 0.3502435 3.0927626 0.015664388 0.37491833 0.0017573704 0.0021913201 1.7713726 0 -3.048342 0.31428487 -3.0465846 0.61762817 -3.0466296 1 -3.048776
230 0.22757286 0.12027481 3.1250243 0.0081260569 0.14019507 0.0018364585 0.002278918 1.76926 0 -3.0483347 0.39730698 -3.0464983 0.64450769 -3.0466973 1 -3.0487772
278 0.096184498 0.085088496 3.1405655 0.0068164307 0.093861113 0.0018426056 0.002286256 1.7684765 0 -3.0483338 0.41277997 -3.0464912 0.65562984 -3.0467294 1 -3.0487775

11
examples/neb/log.19June17.neb.hop1.end.g++.8 Normal file
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@ -0,0 +1,11 @@
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
0 229.26196 146.68251 2.9774577 4.4127369 233.11559 0.023301843 0.0224626 1.4763579 0 -3.048332 0.33333333 -3.0250302 0.66666667 -3.0291888 1 -3.0474928
100 0.11375359 0.085350745 3.0966418 0.0236765 0.38531777 0.0017582606 0.0021868783 1.7710738 0 -3.0483467 0.31201141 -3.0465884 0.61117406 -3.0466149 1 -3.0487753
119 0.09996986 0.078639268 3.0937691 0.017444108 0.3780308 0.0017574935 0.0021899317 1.7713574 0 -3.0483433 0.31354192 -3.0465858 0.61555533 -3.0466249 1 -3.0487758
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
119 0.3793192 0.35281863 3.0937691 0.017444108 0.3780308 0.0017574935 0.0021899317 1.7713574 0 -3.0483433 0.31354192 -3.0465858 0.61555533 -3.0466249 1 -3.0487758
219 0.20159133 0.12247026 3.1244061 0.0085896057 0.13938632 0.0018362816 0.0022783681 1.7693295 0 -3.048335 0.39646633 -3.0464988 0.64277703 -3.0466925 1 -3.0487771
266 0.099868725 0.086180598 3.1401661 0.0070922949 0.095128081 0.001842608 0.002286044 1.7685191 0 -3.048334 0.41231024 -3.0464914 0.65425179 -3.0467252 1 -3.0487774

12
examples/neb/log.5Oct16.neb.hop1.g++.4 → examples/neb/log.19June17.neb.hop1.g++.4
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@ -1,10 +1,10 @@
LAMMPS (5 Oct 2016)
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 0.3387091 5.0075576 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 0.014588241 0.066178594 0.19602237 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 0.013922973 0.05417562 0.2023467 0.0070871172 0.0022668002 2.3052945 0 -3.0535968 0.31853431 -3.0473633 0.64178871 -3.0465096 1 -3.0487764
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 0.013922973 0.05417562 0.2023467 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 0.01040177 0.023364005 0.096874474 0.0071047642 0.0022856172 2.3122768 0 -3.0535969 0.31577311 -3.0473955 0.61798541 -3.0464922 1 -3.0487778
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

12
examples/neb/log.5Oct16.neb.hop1.g++.8 → examples/neb/log.19June17.neb.hop1.g++.8
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@ -1,10 +1,10 @@
LAMMPS (5 Oct 2016)
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 0.3387091 5.0075576 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 0.014588234 0.066178435 0.19602242 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 0.013922966 0.054175505 0.20234693 0.0070871172 0.0022668002 2.3052946 0 -3.0535968 0.31853431 -3.0473633 0.64178873 -3.0465096 1 -3.0487764
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 0.013922966 0.054175505 0.20234693 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 0.010577358 0.024247224 0.09975409 0.0071042931 0.0022851195 2.312004 0 -3.0535969 0.31607934 -3.0473923 0.618931 -3.0464926 1 -3.0487777
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

12
examples/neb/log.19June17.neb.hop2.g++.4 Normal file
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@ -0,0 +1,12 @@
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 14.104748 10.419633 0.1227071 4.999238 8.2087606 0.0018276223 0.00064050211 0.98401186 0 -3.0514921 0.33333333 -3.0496673 0.66666667 -3.0496645 1 -3.050305
100 0.24646695 0.10792196 0.0077146918 0.058733261 0.63504706 0.001516756 0.0015151635 1.165391 0 -3.0514939 0.2890334 -3.0503533 0.59718494 -3.0499771 1 -3.0514923
200 0.061777741 0.050288749 0.0047486883 0.0095236035 0.88698597 0.0014465772 0.0014462528 1.1692938 0 -3.0514941 0.29975094 -3.0503052 0.62768286 -3.0500476 1 -3.0514938
261 0.048699591 0.038138604 0.0040083594 0.0074854409 0.95722712 0.0014243579 0.0014241377 1.1696848 0 -3.0514942 0.30525481 -3.0502812 0.6357998 -3.0500698 1 -3.051494
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
261 0.95753855 0.94297239 0.0040083594 0.0074854409 0.95722712 0.0014243579 0.0014241377 1.1696848 0 -3.0514942 0.30525481 -3.0502812 0.6357998 -3.0500698 1 -3.051494
361 0.072509627 0.06580631 0.0027545765 0.0044749366 0.016746483 0.0016018879 0.0016017805 1.1704611 0 -3.0514943 0.28176307 -3.0503855 0.50355454 -3.0498924 1 -3.0514942
381 0.04884836 0.040787876 0.0023445904 0.0035162935 0.017959209 0.0016017716 0.0016016898 1.1713862 0 -3.0514943 0.27120138 -3.0504399 0.50428218 -3.0498925 1 -3.0514942

12
examples/neb/log.19June17.neb.hop2.g++.8 Normal file
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@ -0,0 +1,12 @@
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 14.104748 10.419633 0.1227071 4.999238 8.2087606 0.0018276223 0.00064050211 0.98401186 0 -3.0514921 0.33333333 -3.0496673 0.66666667 -3.0496645 1 -3.050305
100 0.24646695 0.10792196 0.0077146918 0.058733261 0.63504706 0.001516756 0.0015151635 1.165391 0 -3.0514939 0.2890334 -3.0503533 0.59718494 -3.0499771 1 -3.0514923
200 0.061777741 0.050288749 0.0047486883 0.0095236035 0.88698597 0.0014465772 0.0014462528 1.1692938 0 -3.0514941 0.29975094 -3.0503052 0.62768286 -3.0500476 1 -3.0514938
261 0.048699591 0.038138604 0.0040083594 0.0074854409 0.95722712 0.0014243579 0.0014241377 1.1696848 0 -3.0514942 0.30525481 -3.0502812 0.6357998 -3.0500698 1 -3.051494
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
261 0.95753855 0.94297239 0.0040083594 0.0074854409 0.95722712 0.0014243579 0.0014241377 1.1696848 0 -3.0514942 0.30525481 -3.0502812 0.6357998 -3.0500698 1 -3.051494
361 0.072509627 0.06580631 0.0027545765 0.0044749366 0.016746483 0.0016018879 0.0016017805 1.1704611 0 -3.0514943 0.28176307 -3.0503855 0.50355454 -3.0498924 1 -3.0514942
381 0.04884836 0.040787876 0.0023445904 0.0035162935 0.017959209 0.0016017716 0.0016016898 1.1713862 0 -3.0514943 0.27120138 -3.0504399 0.50428218 -3.0498925 1 -3.0514942

17
examples/neb/log.19June17.neb.sivac.g++.4 Normal file
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@ -0,0 +1,17 @@
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 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.33333333 -2212.7428 0.66666667 -2212.2247 1 -2211.7959
10 0.24005275 0.036502104 0.036483049 0.24005275 0.68351722 0.42916118 0.41794425 1.6989349 0 -2213.3365 0.32909183 -2212.9587 0.65386736 -2212.9073 1 -2213.3253
20 0.07940898 0.016398055 0.024706844 0.07940898 0.71637784 0.41387872 0.41157886 1.7343662 0 -2213.3369 0.32478734 -2212.9621 0.65348766 -2212.923 1 -2213.3346
30 0.094973707 0.0083631681 0.015145947 0.035267404 0.7535772 0.40072717 0.40024605 1.7504612 0 -2213.3372 0.32705584 -2212.9584 0.65894506 -2212.9365 1 -2213.3367
40 0.027727472 0.0044528145 0.011618173 0.022562656 0.76133752 0.39614635 0.39591731 1.7547519 0 -2213.3373 0.32873163 -2212.9562 0.66124255 -2212.9411 1 -2213.337
50 0.019429348 0.0030110281 0.0087135563 0.015391975 0.76952681 0.39274846 0.3926388 1.7578616 0 -2213.3373 0.33022595 -2212.9543 0.66307279 -2212.9446 1 -2213.3372
60 0.019009471 0.0016234562 0.0053426307 0.0086166186 0.77759617 0.38936861 0.38933364 1.7610433 0 -2213.3374 0.33187548 -2212.9523 0.66497617 -2212.948 1 -2213.3373
63 0.0097365134 0.0012734598 0.004777604 0.0076121987 0.77865149 0.38888778 0.38886047 1.7615294 0 -2213.3374 0.33212107 -2212.952 0.66525385 -2212.9485 1 -2213.3373
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
63 0.77865149 0.31085821 0.004777604 0.0076121987 0.77865149 0.38888778 0.38886047 1.7615294 0 -2213.3374 0.33212107 -2212.952 0.66525385 -2212.9485 1 -2213.3373
73 0.098175496 0.033609035 0.0027886955 0.0042742148 0.036594003 0.51024838 0.51023983 1.7607181 0 -2213.3374 0.27574151 -2213.0416 0.50432348 -2212.8271 1 -2213.3374
83 0.03341862 0.012760857 0.0020868177 0.0031625649 0.010189924 0.51014634 0.51014168 1.7602562 0 -2213.3374 0.26045338 -2213.0672 0.50355193 -2212.8272 1 -2213.3374
93 0.0097374358 0.0028416114 0.0014003718 0.0020986584 0.0053485291 0.51011052 0.51010848 1.7601202 0 -2213.3374 0.25397887 -2213.0783 0.50388111 -2212.8273 1 -2213.3374

18
examples/neb/log.19June17.neb.sivac.g++.8 Normal file
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@ -0,0 +1,18 @@
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 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.33333333 -2212.7428 0.66666667 -2212.2247 1 -2211.7959
10 0.24005275 0.036502104 0.036483049 0.24005275 0.68351722 0.42916118 0.41794425 1.6989349 0 -2213.3365 0.32909183 -2212.9587 0.65386736 -2212.9073 1 -2213.3253
20 0.07940898 0.016398055 0.024706844 0.07940898 0.71637784 0.41387872 0.41157886 1.7343662 0 -2213.3369 0.32478734 -2212.9621 0.65348766 -2212.923 1 -2213.3346
30 0.094973708 0.0083631681 0.015145947 0.035267404 0.7535772 0.40072717 0.40024605 1.7504612 0 -2213.3372 0.32705584 -2212.9584 0.65894506 -2212.9365 1 -2213.3367
40 0.027727472 0.0044528144 0.011618173 0.022562656 0.76133752 0.39614635 0.39591731 1.7547519 0 -2213.3373 0.32873163 -2212.9562 0.66124255 -2212.9411 1 -2213.337
50 0.019429341 0.0030110281 0.0087135565 0.015391975 0.7695268 0.39274846 0.3926388 1.7578616 0 -2213.3373 0.33022595 -2212.9543 0.66307279 -2212.9446 1 -2213.3372
60 0.019048963 0.0016262345 0.0053426844 0.0086167196 0.77759655 0.38936867 0.3893337 1.7610433 0 -2213.3374 0.33187545 -2212.9523 0.66497615 -2212.948 1 -2213.3373
63 0.0097037048 0.0012761841 0.0047749367 0.0076075138 0.77865545 0.38888554 0.38885827 1.7615318 0 -2213.3374 0.33212221 -2212.952 0.66525512 -2212.9485 1 -2213.3373
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
63 0.77865545 0.3108551 0.0047749367 0.0076075138 0.77865545 0.38888554 0.38885827 1.7615318 0 -2213.3374 0.33212221 -2212.952 0.66525512 -2212.9485 1 -2213.3373
73 0.098595989 0.033659485 0.0027927196 0.0042813387 0.038224344 0.51024759 0.51023901 1.7607156 0 -2213.3374 0.27595612 -2213.0413 0.50453988 -2212.8271 1 -2213.3374
83 0.033344977 0.012868685 0.0020880608 0.0031645847 0.010250413 0.51014677 0.5101421 1.7602601 0 -2213.3374 0.26053624 -2213.067 0.50358775 -2212.8272 1 -2213.3374
93 0.013254873 0.0038176141 0.0014928226 0.0022407967 0.0058577818 0.51011371 0.51011138 1.7601272 0 -2213.3374 0.25452741 -2213.0774 0.50382161 -2212.8273 1 -2213.3374
95 0.0099964951 0.0031053214 0.0014131665 0.0021184362 0.0053683638 0.51011105 0.51010897 1.7601232 0 -2213.3374 0.2540975 -2213.0781 0.50387313 -2212.8273 1 -2213.3374

18
examples/neb/log.5Oct16.neb.hop2.g++.4
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@ -1,18 +0,0 @@
LAMMPS (5 Oct 2016)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 14.104748 10.419633 0.24852044 5.0039071 8.2116049 0.0018276223 0.00064050211 0.98401186 0 -3.0514921 0.33333333 -3.0496673 0.66666667 -3.0496645 1 -3.050305
100 0.24646695 0.10792196 0.01781018 0.098854684 0.63725646 0.001516756 0.0015151635 1.165391 0 -3.0514939 0.2890334 -3.0503533 0.59718494 -3.0499771 1 -3.0514923
200 0.061777741 0.050288749 0.012466513 0.020420207 0.88741041 0.0014465772 0.0014462528 1.1692938 0 -3.0514941 0.29975094 -3.0503052 0.62768286 -3.0500476 1 -3.0514938
300 0.056346766 0.030000618 0.0093152917 0.013765031 1.0101529 0.0014069751 0.0014068154 1.1699608 0 -3.0514942 0.30992449 -3.0502613 0.64174291 -3.0500873 1 -3.0514941
400 0.025589489 0.015671005 0.0061287063 0.008588518 1.1136424 0.001370987 0.0013709154 1.1704204 0 -3.0514943 0.32016645 -3.0502198 0.65324019 -3.0501233 1 -3.0514943
500 0.014778626 0.0092108366 0.0042668521 0.0059963914 1.1636579 0.0013527466 0.0013527072 1.1706283 0 -3.0514944 0.32550275 -3.0501993 0.65875414 -3.0501416 1 -3.0514943
600 0.08786211 0.020876327 0.0031421548 0.0051657363 1.1898894 0.0013430848 0.0013430599 1.1707681 0 -3.0514944 0.32831927 -3.0501889 0.66160681 -3.0501513 1 -3.0514944
633 0.0098132678 0.0055392541 0.0030063464 0.0043091323 1.1924486 0.0013420127 0.0013419893 1.1707818 0 -3.0514944 0.32862625 -3.0501878 0.66191769 -3.0501524 1 -3.0514944
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
633 1.1924486 1.1648685 0.0030063464 0.0043091323 1.1924486 0.0013420127 0.0013419893 1.1707818 0 -3.0514944 0.32862625 -3.0501878 0.66191769 -3.0501524 1 -3.0514944
733 0.095331134 0.089136608 0.0021551441 0.0031844438 0.043042998 0.0016022317 0.0016022168 1.170789 0 -3.0514944 0.29157063 -3.0503375 0.50358402 -3.0498922 1 -3.0514944
833 0.10539135 0.030724373 0.0013749699 0.002221013 0.10539135 0.0016019798 0.001601971 1.1732118 0 -3.0514944 0.26249002 -3.0504848 0.50415223 -3.0498924 1 -3.0514944
933 0.01883894 0.011496399 0.0011058925 0.0018178041 0.014621806 0.0016018934 0.0016018865 1.173866 0 -3.0514944 0.25788763 -3.0505113 0.50466375 -3.0498925 1 -3.0514944
996 0.0082457876 0.0036336551 0.00077325986 0.0013910671 0.0068823708 0.0016018293 0.0016018244 1.174511 0 -3.0514944 0.2544553 -3.0505324 0.50520462 -3.0498926 1 -3.0514944

18
examples/neb/log.5Oct16.neb.hop2.g++.8
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@ -1,18 +0,0 @@
LAMMPS (5 Oct 2016)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 14.104748 10.419633 0.24852044 5.0039071 8.2116049 0.0018276223 0.00064050211 0.98401186 0 -3.0514921 0.33333333 -3.0496673 0.66666667 -3.0496645 1 -3.050305
100 0.24646695 0.10792196 0.01781018 0.098854684 0.63725646 0.001516756 0.0015151635 1.165391 0 -3.0514939 0.2890334 -3.0503533 0.59718494 -3.0499771 1 -3.0514923
200 0.061777741 0.050288749 0.012466513 0.020420207 0.88741041 0.0014465772 0.0014462528 1.1692938 0 -3.0514941 0.29975094 -3.0503052 0.62768286 -3.0500476 1 -3.0514938
300 0.056346766 0.030000618 0.0093152917 0.013765031 1.0101529 0.0014069751 0.0014068154 1.1699608 0 -3.0514942 0.30992449 -3.0502613 0.64174291 -3.0500873 1 -3.0514941
400 0.025589489 0.015671005 0.0061287063 0.008588518 1.1136424 0.001370987 0.0013709154 1.1704204 0 -3.0514943 0.32016645 -3.0502198 0.65324019 -3.0501233 1 -3.0514943
500 0.014778626 0.0092108366 0.0042668521 0.0059963914 1.1636579 0.0013527466 0.0013527072 1.1706283 0 -3.0514944 0.32550275 -3.0501993 0.65875414 -3.0501416 1 -3.0514943
600 0.08786211 0.020876327 0.0031421548 0.0051657363 1.1898894 0.0013430848 0.0013430599 1.1707681 0 -3.0514944 0.32831927 -3.0501889 0.66160681 -3.0501513 1 -3.0514944
633 0.0098132678 0.0055392541 0.0030063464 0.0043091323 1.1924486 0.0013420127 0.0013419893 1.1707818 0 -3.0514944 0.32862625 -3.0501878 0.66191769 -3.0501524 1 -3.0514944
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
633 1.1924486 1.1648685 0.0030063464 0.0043091323 1.1924486 0.0013420127 0.0013419893 1.1707818 0 -3.0514944 0.32862625 -3.0501878 0.66191769 -3.0501524 1 -3.0514944
733 0.095331134 0.089136608 0.0021551441 0.0031844438 0.043042998 0.0016022317 0.0016022168 1.170789 0 -3.0514944 0.29157063 -3.0503375 0.50358402 -3.0498922 1 -3.0514944
833 0.10539135 0.030724373 0.0013749699 0.002221013 0.10539135 0.0016019798 0.001601971 1.1732118 0 -3.0514944 0.26249002 -3.0504848 0.50415223 -3.0498924 1 -3.0514944
933 0.01883894 0.011496399 0.0011058925 0.0018178041 0.014621806 0.0016018934 0.0016018865 1.173866 0 -3.0514944 0.25788763 -3.0505113 0.50466375 -3.0498925 1 -3.0514944
996 0.0082457876 0.0036336551 0.00077325986 0.0013910671 0.0068823708 0.0016018293 0.0016018244 1.174511 0 -3.0514944 0.2544553 -3.0505324 0.50520462 -3.0498926 1 -3.0514944

14
examples/neb/log.5Oct16.neb.sivac.g++.3
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@ -1,14 +0,0 @@
LAMMPS (5 Oct 2016)
Running on 3 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.5 -2212.4096 1 -2211.7959
10 0.27332818 0.040944923 0.039164338 0.27332818 0.17804882 0.51235911 0.497084 1.6790474 0 -2213.3364 0.49024121 -2212.824 1 -2213.3211
20 0.1820396 0.018049916 0.024428411 0.1820396 0.08601739 0.51038174 0.5080746 1.7224961 0 -2213.337 0.49199582 -2212.8266 1 -2213.3347
30 0.043288796 0.0068108825 0.017372479 0.043288796 0.049466709 0.51032316 0.5095943 1.7304745 0 -2213.3371 0.49553568 -2212.8268 1 -2213.3364
40 0.0421393 0.0037035761 0.01173707 0.0421393 0.026104735 0.51022733 0.5100163 1.7366752 0 -2213.3373 0.49838067 -2212.8271 1 -2213.3371
50 0.025897844 0.0022804241 0.0081056535 0.025897844 0.016908913 0.5101712 0.51008591 1.739143 0 -2213.3373 0.49923344 -2212.8272 1 -2213.3373
59 0.00962839 0.0012946076 0.005657505 0.009365729 0.012040803 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955698 -2212.8272 1 -2213.3373
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
59 0.012040803 0.0031505502 0.005657505 0.009365729 0.012040803 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955698 -2212.8272 1 -2213.3373
63 0.009152118 0.0016692472 0.0049645771 0.0081967836 0.009152118 0.51013743 0.51010776 1.7409028 0 -2213.3374 0.50022239 -2212.8272 1 -2213.3373

14
examples/neb/log.5Oct16.neb.sivac.g++.6
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@ -1,14 +0,0 @@
LAMMPS (5 Oct 2016)
Running on 3 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.5 -2212.4096 1 -2211.7959
10 0.27332818 0.040944923 0.039164338 0.27332818 0.17804882 0.51235911 0.497084 1.6790474 0 -2213.3364 0.49024121 -2212.824 1 -2213.3211
20 0.1820396 0.018049916 0.024428411 0.1820396 0.08601739 0.51038174 0.5080746 1.7224961 0 -2213.337 0.49199582 -2212.8266 1 -2213.3347
30 0.043288796 0.0068108825 0.017372479 0.043288796 0.049466709 0.51032316 0.5095943 1.7304745 0 -2213.3371 0.49553568 -2212.8268 1 -2213.3364
40 0.042139305 0.0037035764 0.01173707 0.042139305 0.026104735 0.51022733 0.5100163 1.7366752 0 -2213.3373 0.49838067 -2212.8271 1 -2213.3371
50 0.025899631 0.0022805513 0.0081057075 0.025899631 0.016908929 0.5101712 0.51008591 1.739143 0 -2213.3373 0.49923345 -2212.8272 1 -2213.3373
59 0.0096285044 0.0012946258 0.0056576061 0.0093678253 0.012040919 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955698 -2212.8272 1 -2213.3373
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
59 0.012040919 0.0031505771 0.0056576061 0.0093678253 0.012040919 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955698 -2212.8272 1 -2213.3373
63 0.0091523813 0.0016692845 0.0049647607 0.0081998372 0.0091523813 0.51013743 0.51010775 1.7409028 0 -2213.3374 0.50022236 -2212.8272 1 -2213.3373

14
examples/neb/log.5Oct16.neb.sivac.g++.9
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@ -1,14 +0,0 @@
LAMMPS (5 Oct 2016)
Running on 3 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.5 -2212.4096 1 -2211.7959
10 0.27332818 0.040944923 0.039164338 0.27332818 0.17804882 0.51235911 0.497084 1.6790474 0 -2213.3364 0.49024121 -2212.824 1 -2213.3211
20 0.1820396 0.018049916 0.024428411 0.1820396 0.08601739 0.51038174 0.5080746 1.7224961 0 -2213.337 0.49199582 -2212.8266 1 -2213.3347
30 0.043288796 0.0068108825 0.017372479 0.043288796 0.049466709 0.51032316 0.5095943 1.7304745 0 -2213.3371 0.49553568 -2212.8268 1 -2213.3364
40 0.042139318 0.0037035773 0.011737071 0.042139318 0.026104737 0.51022733 0.5100163 1.7366752 0 -2213.3373 0.49838067 -2212.8271 1 -2213.3371
50 0.025904121 0.0022808707 0.0081058431 0.025904121 0.016908969 0.5101712 0.51008591 1.7391431 0 -2213.3373 0.49923346 -2212.8272 1 -2213.3373
59 0.0096287928 0.0012946716 0.005657861 0.0093731008 0.01204121 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955696 -2212.8272 1 -2213.3373
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
59 0.01204121 0.0031506449 0.005657861 0.0093731008 0.01204121 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955696 -2212.8272 1 -2213.3373
63 0.0091530442 0.0016693787 0.0049652227 0.0082075097 0.0091530442 0.51013743 0.51010775 1.7409027 0 -2213.3374 0.50022228 -2212.8272 1 -2213.3373

21
src/REPLICA/fix_neb.cpp
View File

@ -63,7 +63,8 @@ FixNEB::FixNEB(LAMMPS *lmp, int narg, char **arg) :
PerpSpring = FreeEndIni = FreeEndFinal = false;
FreeEndFinalWithRespToEIni = FinalAndInterWithRespToEIni = false;
kspringPerp = 0.0;
kspring2 = 1.0;
kspringIni = 1.0;
kspringFinal = 1.0;
int iarg = 4;
while (iarg < narg) {
@ -90,20 +91,24 @@ FixNEB::FixNEB(LAMMPS *lmp, int narg, char **arg) :
if (iarg+3 > narg) error->all(FLERR,"Illegal fix neb command");
if (strcmp(arg[iarg+1],"first") == 0) {
FreeEndIni = true;
kspringIni = force->numeric(FLERR,arg[iarg+2]);
} else if (strcmp(arg[iarg+1],"last") == 0) {
FreeEndFinal = true;
FinalAndInterWithRespToEIni = false;
FreeEndFinalWithRespToEIni = false;
kspringFinal = force->numeric(FLERR,arg[iarg+2]);
} else if (strcmp(arg[iarg+1],"last/efirst") == 0) {
FreeEndFinal = false;
FinalAndInterWithRespToEIni = false;
FreeEndFinalWithRespToEIni = true;
kspringFinal = force->numeric(FLERR,arg[iarg+2]);
} else if (strcmp(arg[iarg+1],"last/efirst/middle") == 0) {
FreeEndFinal = false;
FinalAndInterWithRespToEIni = true;
FreeEndFinalWithRespToEIni = true;
kspringFinal = force->numeric(FLERR,arg[iarg+2]);
} else error->all(FLERR,"Illegal fix neb command");
kspring2 = force->numeric(FLERR,arg[iarg+2]);
iarg += 3;
} else error->all(FLERR,"Illegal fix neb command");
@ -488,8 +493,8 @@ void FixNEB::min_post_force(int vflag)
MPI_Allreduce(&dot,&dotall,1,MPI_DOUBLE,MPI_SUM,world);
dot=dotall/tlen;
if (dot<0) prefactor = -dot - kspring2*(veng-EIniIni);
else prefactor = -dot + kspring2*(veng-EIniIni);
if (dot<0) prefactor = -dot - kspringIni*(veng-EIniIni);
else prefactor = -dot + kspringIni*(veng-EIniIni);
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
@ -506,8 +511,8 @@ void FixNEB::min_post_force(int vflag)
MPI_Allreduce(&dot,&dotall,1,MPI_DOUBLE,MPI_SUM,world);
dot=dotall/tlen;
if (dot<0) prefactor = -dot - kspring2*(veng-EFinalIni);
else prefactor = -dot + kspring2*(veng-EFinalIni);
if (dot<0) prefactor = -dot - kspringFinal*(veng-EFinalIni);
else prefactor = -dot + kspringFinal*(veng-EFinalIni);
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
@ -524,8 +529,8 @@ void FixNEB::min_post_force(int vflag)
MPI_Allreduce(&dot,&dotall,1,MPI_DOUBLE,MPI_SUM,world);
dot=dotall/tlen;
if (dot<0) prefactor = -dot - kspring2*(veng-vIni);
else prefactor = -dot + kspring2*(veng-vIni);
if (dot<0) prefactor = -dot - kspringFinal*(veng-vIni);
else prefactor = -dot + kspringFinal*(veng-vIni);
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {

2
src/REPLICA/fix_neb.h
View File

@ -38,7 +38,7 @@ class FixNEB : public Fix {
private:
int me,nprocs,nprocs_universe;
double kspring,kspring2,kspringPerp,EIniIni,EFinalIni;
double kspring,kspringIni,kspringFinal,kspringPerp,EIniIni,EFinalIni;
bool StandardNEB,NEBLongRange,PerpSpring,FreeEndIni,FreeEndFinal;
bool FreeEndFinalWithRespToEIni,FinalAndInterWithRespToEIni;
int ireplica,nreplica;