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Merge branch 'develop' into collected-small-changes

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Axel Kohlmeyer
2023-01-16 21:37:24 -05:00
parent 637e12cd01 0a5f97c327
commit e8be2dfba8
23 changed files with 820 additions and 723 deletions
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2
.gitignore vendored
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@ -55,3 +55,5 @@ out/RelWithDebInfo
out/Release
out/x86
out/x64
src/Makefile.package-e
src/Makefile.package.settings-e

127
doc/src/fix_neb.rst
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@ -18,9 +18,10 @@ Syntax
.. parsed-literal::
*parallel* value = *neigh* or *ideal*
*parallel* value = *neigh* or *ideal* or *equal*
*neigh* = parallel nudging force based on distance to neighbor replicas (Kspring = force/distance units)
*ideal* = parallel nudging force based on interpolated ideal position (Kspring = force units)
*equal* = parallel nudging force based on interpolated ideal position before climbing, then interpolated ideal energy whilst climbing (Kspring = force units)
*perp* value = *Kspring2*
*Kspring2* = spring constant for perpendicular nudging force (force/distance units)
*end* values = estyle Kspring3
@ -59,37 +60,37 @@ replica having the highest energy relaxes toward the saddle point
relaxation is performed.
A key purpose of the nudging forces is to keep the replicas equally
spaced. During the NEB calculation, the 3N-length vector of
interatomic force Fi = -Grad(V) for each replica I is altered. For
all intermediate replicas (i.e. for 1 < I < N, except the climbing
replica) the force vector becomes:
spaced. During the NEB calculation, the :math:`3N`-length vector of
interatomic force :math:`F_i = -\nabla V` for each replica *i* is
altered. For all intermediate replicas (i.e. for :math:`1 < i < N`,
except the climbing replica) the force vector becomes:
.. parsed-literal::
.. math::
Fi = -Grad(V) + (Grad(V) dot T') T' + Fnudge_parallel + Fnudge_perp
F_i = -\nabla V + (\nabla V \cdot T') T' + F_\parallel + F_\perp
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
:ref:`(Henkelman1) <Henkelman1>` paper for details. Ri are 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
distribute the replica unevenly along the path. Fnudge_parallel is an
artificial nudging force which is applied only in the tangent
direction and which maintains the equal spacing between replicas (see
below for more information). Fnudge_perp is an optional artificial
spring which is applied in a direction perpendicular to the tangent
direction and which prevent the paths from forming acute kinks (see
below for more information).
T' is the unit "tangent" vector for replica *i* and is a function of
:math:`R_i, R_{i-1}, R_{i+1}`, and the potential energy of the 3
replicas; it points roughly in the direction of :math:`R_{i+i} -
R_{i-1}`; see the :ref:`(Henkelman1) <Henkelman1>` paper for details.
:math:`R_i` are the atomic coordinates of replica *i*; :math:`R_{i-1}`
and :math:`R_{i+1}` are the coordinates of its neighbor replicas. The
term :math:`\nabla V \cdot T'` is used to remove the component of the
gradient parallel to the path which would tend to distribute the replica
unevenly along the path. :math:`F_\parallel` is an artificial nudging
force which is applied only in the tangent direction and which maintains
the equal spacing between replicas (see below for more information).
:math:`F_\perp` is an optional artificial spring which is applied in a
direction perpendicular to the tangent direction and which prevent the
paths from forming acute kinks (see below for more information).
In the second stage of the NEB calculation, the interatomic force Fi
In the second stage of the NEB calculation, the interatomic force :math:`F_i`
for the climbing replica (the replica of highest energy after the
first stage) is changed to:
.. parsed-literal::
.. math::
Fi = -Grad(V) + 2 (Grad(V) dot T') T' + Fnudge_perp
F_i = -\nabla V + 2 (\nabla V \cdot T') T' + F_\perp
and the relaxation procedure is continued to a new converged MEP.
@ -100,29 +101,56 @@ computed. With a value of *neigh*, the parallel nudging force is
computed as in :ref:`(Henkelman1) <Henkelman1>` by connecting each
intermediate replica with the previous and the next image:
.. parsed-literal::
.. math::
Fnudge_parallel = *Kspring* \* (\|Ri+1 - Ri\| - \|Ri - Ri-1\|)
F_\parallel = Kspring \cdot \left(\left|R_{i+1} - R_i\right| - \left|R_i - R_{i-1}\right|\right)
Note that in this case the specified *Kspring* is in force/distance
units.
Note that in this case the specified *Kspring* is in
force/distance units.
With a value of *ideal*, the spring force is computed as suggested in
ref`(WeinanE) <WeinanE>`
.. parsed-literal::
.. math::
Fnudge_parallel = -\ *Kspring* \* (RD-RDideal) / (2 \* meanDist)
F_\parallel = -Kspring \cdot (RD - RD_{ideal}) / (2 \cdot meanDist)
where RD is the "reaction coordinate" see :doc:`neb <neb>` section, and
RDideal is the ideal RD for which all the images are equally spaced.
I.e. RDideal = (I-1)\*meanDist when the climbing replica is off, where
I is the replica number). The meanDist is the average distance
between replicas. Note that in this case the specified *Kspring* is
in force units.
where *RD* is the "reaction coordinate" see :doc:`neb <neb>` section,
and :math:`RD_{ideal}` is the ideal *RD* for which all the images are
equally spaced. I.e. :math:`RD_{ideal} = (i-1) \cdot meanDist` when the
climbing replica is off, where *i* is the replica number). The
*meanDist* is the average distance between replicas. Note that in this
case the specified *Kspring* is in force units. When the climbing replica
is on, :math:`RD_{ideal}` and :math:`meanDist` are calculated separately
each side of the climbing image. Note that the *ideal* form of nudging
can often be more effective at keeping the replicas equally spaced before
climbing, then equally spaced either side of the climbing image whilst
climbing.
Note that the *ideal* form of nudging can often be more effective at
keeping the replicas equally spaced.
With a value of *equal* the spring force is computed as for *ideal*
when the climbing replica is off, promoting equidistance. When the climbing
replica is on, the spring force is computed to promote equidistant
absolute differences in energy, rather than distance, each side of
the climbing image:
.. math::
F_\parallel = -Kspring \cdot (ED - ED_{ideal}) / (2 \cdot meanEDist)
where *ED* is the cumulative sum of absolute energy differences:
.. math::
ED = \sum_{i<N} \left|E(R_{i+1}) - E(R_i)\right|,
*meanEdist* is the average absolute energy difference between
replicas up to the climbing image or from the climbing image
to the final image, for images before or after the climbing
image respectively. :math:`ED_{ideal}` is the corresponding
cumulative sum of average absolute energy differences in
each case, in close analogy to *ideal*. This form of nudging
is to aid schemes which integrate forces along, or near to,
NEB pathways such as :doc:`fix_pafi <fix_pafi>`.
----------
@ -135,14 +163,16 @@ resolution is poor. I.e. when few replicas are used; see
The perpendicular spring force is given by
.. parsed-literal::
.. math::
Fnudge_perp = *Kspring2* \* F(Ri-1,Ri,Ri+1) (Ri+1 + Ri-1 - 2 Ri)
F_\perp = K_{spring2} \cdot F(R_{i-1},R_i,R_{i+1}) (R_{i+1} + R_{i-1} - 2 R_i)
where *Kspring2* is the specified value. F(Ri-1 Ri R+1) is a smooth
scalar function of the angle Ri-1 Ri Ri+1. It is equal to 0.0 when
the path is straight and is equal to 1 when the angle Ri-1 Ri Ri+1 is
acute. F(Ri-1 Ri R+1) is defined in :ref:`(Jonsson) <Jonsson>`.
where *Kspring2* is the specified value. :math:`F(R_{i-1}, R_i,
R_{i+1})` is a smooth scalar function of the angle :math:`R_{i-1} R_i
R_{i+1}`. It is equal to 0.0 when the path is straight and is equal to
1 when the angle :math:`R_{i-1} R_i R_{i+1}` is acute.
:math:`F(R_{i-1}, R_i, R_{i+1})` is defined in :ref:`(Jonsson)
<Jonsson>`.
If *Kspring2* is set to 0.0 (the default) then no perpendicular spring
force is added.
@ -156,12 +186,13 @@ forces can be applied to the first and/or last replicas, to enable
them to relax toward a MEP while constraining their energy E to the
target energy ETarget.
If ETarget>E, the interatomic force Fi for the specified replica becomes:
If :math:`E_{Target} > E`, the interatomic force :math:`F_i` for the
specified replica becomes:
.. parsed-literal::
.. math::
Fi = -Grad(V) + (Grad(V) dot T' + (E-ETarget)\*Kspring3) T', *when* Grad(V) dot T' < 0
Fi = -Grad(V) + (Grad(V) dot T' + (ETarget- E)\*Kspring3) T', *when* Grad(V) dot T' > 0
F_i & = -\nabla V + (\nabla V \cdot T' + (E - E_{Target}) \cdot K_{spring3}) T', \qquad \textrm{when} \quad \nabla V \cdot T' < 0 \\
F_i & = -\nabla V + (\nabla V \cdot T' + (E_{Target} - E) \cdot K_{spring3}) T', \qquad \textrm{when} \quad \nabla V \cdot T' > 0
The "spring" constant on the difference in energies is the specified
*Kspring3* value.

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doc/src/neb.rst
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@ -8,7 +8,7 @@ Syntax
.. parsed-literal::
neb etol ftol N1 N2 Nevery file-style arg keyword
neb etol ftol N1 N2 Nevery file-style arg keyword values
* etol = stopping tolerance for energy (energy units)
* ftol = stopping tolerance for force (force units)
@ -29,7 +29,15 @@ Syntax
*none* arg = no argument all replicas assumed to already have
their initial coords
keyword = *verbose*
* zero or more keyword/value pairs may be appended
* keyword = *verbosity*
.. parsed-literal::
*verbosity* value = *verbose* or *default* or *terse*
*verbose* = very detailed per-replica output
*default* = some per-replica output
*terse* = only global state output
Examples
""""""""
@ -47,19 +55,21 @@ Perform a nudged elastic band (NEB) calculation using multiple
replicas of a system. Two or more replicas must be used; the first
and last are the end points of the transition path.
NEB is a method for finding both the atomic configurations and height
of the energy barrier associated with a transition state, e.g. for an
atom to perform a diffusive hop from one energy basin to another in a
NEB is a method for finding both the atomic configurations and height of
the energy barrier associated with a transition state, e.g. for an atom
to perform a diffusive hop from one energy basin to another in a
coordinated fashion with its neighbors. The implementation in LAMMPS
follows the discussion in these 4 papers: :ref:`(HenkelmanA) <HenkelmanA>`,
:ref:`(HenkelmanB) <HenkelmanB>`, :ref:`(Nakano) <Nakano3>` and :ref:`(Maras) <Maras2>`.
follows the discussion in these 4 papers: :ref:`(HenkelmanA)
<HenkelmanA>`, :ref:`(HenkelmanB) <HenkelmanB>`, :ref:`(Nakano)
<Nakano3>` and :ref:`(Maras) <Maras2>`.
Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the :doc:`-partition command-line switch <Run_options>`. Note that if you have MPI installed, you
can run a multi-replica simulation with more replicas (partitions)
than you have physical processors, e.g you can run a 10-replica
simulation on just one or two processors. You will simply not get the
performance speed-up you would see with one or more physical
partitions are defined at run-time using the :doc:`-partition
command-line switch <Run_options>`. Note that if you have MPI
installed, you can run a multi-replica simulation with more replicas
(partitions) than you have physical processors, e.g you can run a
10-replica simulation on just one or two processors. You will simply
not get the performance speed-up you would see with one or more physical
processors per replica. See the :doc:`Howto replica <Howto_replica>`
doc page for further discussion.
@ -302,12 +312,26 @@ and restart files.
When running with multiple partitions (each of which is a replica in
this case), the print-out to the screen and master log.lammps file
contains a line of output, printed once every *Nevery* timesteps. It
contains the timestep, the maximum force per replica, the maximum
force per atom (in any replica), potential gradients in the initial,
final, and climbing replicas, the forward and backward energy
barriers, the total reaction coordinate (RDT), and the normalized
reaction coordinate and potential energy of each replica.
contains a line of output, printed once every *Nevery* timesteps. The
amount of information printed in this line can be selected with the
*verbosity* keyword. Available options are *terse*, *default*, and
*verbose*.
With the *terse* setting, it contains the timestep, the maximum force of
a replica, the maximum force per atom (in any replica), potential
gradients in the initial, final, and climbing replicas, the forward and
backward energy barriers, the total reaction coordinate (RDT).
With the *default* setting, additionally the normalized
reaction coordinate and potential energy of each replica are printed.
With the *verbose* setting, additional per-replica properties are
printed: the "path angle" (pathangle), the angle between the 3N-length
tangent vector and the 3N-length force vector at image *i*
(angletangrad), the angle between the 3N-length energy gradient vector
of replica *i* and that of replica *i*\ +1 (anglegrad), the norm of the
energy gradient (gradV), the the two-norm of the 3N-length force vector
(RepForce), and the maximum force component of any atom (MaxAtomForce).
The "maximum force per replica" is the two-norm of the 3N-length force
vector for the atoms in each replica, maximized across replicas, which
@ -330,22 +354,21 @@ the fix neb command.
The forward (reverse) energy barrier is the potential energy of the
highest replica minus the energy of the first (last) replica.
Supplementary information for all replicas can be printed out to the
screen and master log.lammps file by adding the verbose keyword. This
information include the following. The "path angle" (pathangle) for
the replica i which is the angle between the 3N-length vectors (Ri-1 -
Ri) and (Ri+1 - Ri) (where Ri is the atomic coordinates of replica
i). A "path angle" of 180 indicates that replicas i-1, i and i+1 are
aligned. "angletangrad" is the angle between the 3N-length tangent
vector and the 3N-length force vector at image i. The tangent vector
is calculated as in :ref:`(HenkelmanA) <HenkelmanA>` for all intermediate
replicas and at R2 - R1 and RM - RM-1 for the first and last replica,
respectively. "anglegrad" is the angle between the 3N-length energy
gradient vector of replica i and that of replica i+1. It is not
defined for the final replica and reads nan. gradV is the norm of the
energy gradient of image i. ReplicaForce is the two-norm of the
3N-length force vector (including nudging forces) for replica i.
MaxAtomForce is the maximum force component of any atom in replica i.
The "path angle" (pathangle) for the replica i which is the angle
between the 3N-length vectors :math:`(R_{i-1} - R_i)` and
:math:`(R_{i+1} - R_i)` (where :math:`R_i` is the atomic coordinates of
replica *i*). A "path angle" of 180 indicates that replicas *i*\ -1, *i*
and *i*\ +1 are aligned. "angletangrad" is the angle between the
3N-length tangent vector and the 3N-length force vector at image
*i*. The tangent vector is calculated as in :ref:`(HenkelmanA)
<HenkelmanA>` for all intermediate replicas and at R2 - R1 and RM - RM-1
for the first and last replica, respectively. "anglegrad" is the angle
between the 3N-length energy gradient vector of replica *i* and that of
replica *i*\ +1. It is not defined for the final replica and reads nan.
gradV is the norm of the energy gradient of image *i* (:math:`\nabla
V`). ReplicaForce is the two-norm of the 3N-length force vector
(including nudging forces) for replica *i*. MaxAtomForce is the maximum
force component of any atom in replica *i*.
When a NEB calculation does not converge properly, the supplementary
information can help understanding what is going wrong. For instance
@ -427,7 +450,7 @@ Related commands
Default
"""""""
none
*verbosity* = *default*
----------

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@ -0,0 +1,11 @@
LAMMPS (22 Dec 2022)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4
0 229.26196 21515.76 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 0.0072949206 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 0.0056973977 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 RD3 PE3 RD4 PE4
130 0.37838747 0.12267051 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 0.14827532 0.015635771 3.1230352 0.0083310795 0.14070676 0.0018353858 0.0022776729 1.769345 0 -3.0483349 0.39530832 -3.0464995 0.64330942 -3.046694 1 -3.0487772
279 0.099842536 0.0074295981 3.1400424 0.0068603912 0.095180758 0.0018424455 0.0022860594 1.7685036 0 -3.0483338 0.41228692 -3.0464914 0.65522525 -3.0467282 1 -3.0487775

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@ -0,0 +1,10 @@
LAMMPS (22 Dec 2022)
Running on 8 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4 RD5 PE5 RD6 PE6 RD7 PE7 RD8 PE8
0 353.31221 52709.758 2.9774577 4.4127369 354.16808 0.035499368 0.034660125 1.4763579 0 -3.048332 0.14285714 -3.0450092 0.28571429 -3.0318848 0.42857143 -3.0128327 0.57142857 -3.0157894 0.71428571 -3.0354827 0.85714286 -3.0458819 1 -3.0474928
100 0.18371802 0.016897952 3.0181603 0.026618267 0.11111596 0.0018567895 0.0022827846 1.8009397 0 -3.0483491 0.13062498 -3.0471842 0.26462893 -3.0466755 0.40763124 -3.0464923 0.53986455 -3.0465208 0.68351825 -3.0468184 0.81489539 -3.0476023 1 -3.0487751
182 0.099603091 0.0039050116 3.0068142 0.010832038 0.074630455 0.001848721 0.0022882994 1.8108868 0 -3.0483371 0.13698322 -3.0471393 0.27599082 -3.0466464 0.41841798 -3.0464884 0.55670019 -3.046546 0.69926219 -3.0469046 0.83686246 -3.0478727 1 -3.0487767
Climbing replica = 4
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4 RD5 PE5 RD6 PE6 RD7 PE7 RD8 PE8
182 0.093479786 0.0046539741 3.0068142 0.010832038 0.074630455 0.001848721 0.0022882994 1.8108868 0 -3.0483371 0.13698322 -3.0471393 0.27599082 -3.0466464 0.41841798 -3.0464884 0.55670019 -3.046546 0.69926219 -3.0469046 0.83686246 -3.0478727 1 -3.0487767
183 0.093479786 0.0046539741 3.0068142 0.010832038 0.074630455 0.001848721 0.0022882994 1.8108868 0 -3.0483371 0.13698322 -3.0471393 0.27599082 -3.0466464 0.41841798 -3.0464884 0.55670019 -3.046546 0.69926219 -3.0469046 0.83686246 -3.0478727 1 -3.0487767

9
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@ -0,0 +1,9 @@
LAMMPS (22 Dec 2022)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4
0 4327.2753 7542371.4 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 0.0027794936 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 RD3 PE3 RD4 PE4
87 0.14137277 0.012340886 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 0.0073851506 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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@ -0,0 +1,10 @@
LAMMPS (22 Dec 2022)
Running on 8 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4 RD5 PE5 RD6 PE6 RD7 PE7 RD8 PE8
0 12172.47 48315818 0.082169072 4.9967651 12254.987 1.1034547 1.0973568 1.8941131 0 -3.0535948 0.14285714 -3.0398884 0.28571429 -2.8426874 0.42857143 -1.9501401 0.57142857 -2.1439119 0.71428571 -2.9187789 0.85714286 -3.0422538 1 -3.0474969
100 0.14433533 0.0056834028 0.0051714625 0.047051976 0.11774619 0.0071018066 0.002280994 2.3772214 0 -3.0535967 0.12651739 -3.0512933 0.26516133 -3.0480936 0.41814034 -3.0467867 0.55534109 -3.0464949 0.69779433 -3.0465932 0.83399724 -3.0472934 1 -3.0487759
147 0.098667494 0.0031400895 0.0040851637 0.017209593 0.096695061 0.007103925 0.002284434 2.3892288 0 -3.0535968 0.13266908 -3.051146 0.27206276 -3.0479976 0.42113052 -3.046774 0.55968697 -3.0464929 0.7017833 -3.0466074 0.8397451 -3.0473745 1 -3.0487774
Climbing replica = 5
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4 RD5 PE5 RD6 PE6 RD7 PE7 RD8 PE8
147 0.10065405 0.0077673218 0.0040851637 0.017209593 0.096695061 0.007103925 0.002284434 2.3892288 0 -3.0535968 0.13266908 -3.051146 0.27206276 -3.0479976 0.42113052 -3.046774 0.55968697 -3.0464929 0.7017833 -3.0466074 0.8397451 -3.0473745 1 -3.0487774
150 0.099859382 0.0075603521 0.0040615957 0.016809825 0.096007238 0.0071040699 0.0022845963 2.3894645 0 -3.0535969 0.13277764 -3.0511437 0.27216411 -3.0479964 0.42112067 -3.0467741 0.55997348 -3.0464928 0.70181216 -3.0466076 0.83985415 -3.0473761 1 -3.0487774

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@ -0,0 +1,9 @@
LAMMPS (22 Dec 2022)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4
0 14.104748 108.56876 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
46 0.049691778 0.001449144 0.0041836599 0.0070455894 0.94610709 0.0014279446 0.0014276971 1.1698782 0 -3.0514942 0.3026746 -3.0502925 0.63457326 -3.0500662 1 -3.0514939
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4
46 0.94646532 0.8692782 0.0041836599 0.0070455894 0.94610709 0.0014279446 0.0014276971 1.1698782 0 -3.0514942 0.3026746 -3.0502925 0.63457326 -3.0500662 1 -3.0514939
88 0.042941386 0.00046017358 0.0021155242 0.0031463438 0.0095074767 0.0016016953 0.0016016258 1.1725045 0 -3.0514943 0.26292929 -3.0504854 0.50610293 -3.0498926 1 -3.0514943

9
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LAMMPS (22 Dec 2022)
Running on 8 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4 RD5 PE5 RD6 PE6 RD7 PE7 RD8 PE8
0 15.805883 137.15721 0.1227071 4.999238 15.828539 0.0021830032 0.00099588309 0.98401186 0 -3.0514921 0.14285714 -3.0509383 0.28571429 -3.049949 0.42857143 -3.0493091 0.57142857 -3.0493602 0.71428571 -3.0498345 0.85714286 -3.0502192 1 -3.050305
73 0.049714315 0.0011853232 0.0036385263 0.0057874304 0.079285231 0.0016005788 0.001600399 1.2115403 0 -3.0514942 0.13043211 -3.0512538 0.25481496 -3.0505642 0.37535798 -3.0500676 0.49844851 -3.0498936 0.63571599 -3.0500698 0.80272589 -3.0508376 1 -3.051494
Climbing replica = 5
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4 RD5 PE5 RD6 PE6 RD7 PE7 RD8 PE8
73 0.079737673 0.0060506501 0.0036385263 0.0057874304 0.079285231 0.0016005788 0.001600399 1.2115403 0 -3.0514942 0.13043211 -3.0512538 0.25481496 -3.0505642 0.37535798 -3.0500676 0.49844851 -3.0498936 0.63571599 -3.0500698 0.80272589 -3.0508376 1 -3.051494
82 0.046923812 0.00207513 0.0033938491 0.0054082765 0.046102157 0.0016015266 0.0016013694 1.2125153 0 -3.0514942 0.13012408 -3.0512565 0.25462869 -3.0505663 0.37576663 -3.0500667 0.50363184 -3.0498927 0.63838032 -3.0500776 0.80516707 -3.0508541 1 -3.0514941

18
examples/neb/log.14Jan23.neb.sivac.g++.4 Normal file
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LAMMPS (22 Dec 2022)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4
0 7.5525391 2.671788 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 0.0013324036 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 0.00026889621 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 0.094973706 6.994258e-05 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 1.9827557e-05 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 0.019429351 9.0662903e-06 0.0087135562 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 0.018992557 2.6317454e-06 0.005342608 0.0086165759 0.777596 0.38936859 0.38933361 1.7610433 0 -2213.3374 0.33187549 -2212.9523 0.66497619 -2212.948 1 -2213.3373
63 0.0097571737 1.6189866e-06 0.0047788465 0.0076143824 0.77864965 0.38888882 0.3888615 1.7615283 0 -2213.3374 0.33212054 -2212.952 0.66525325 -2212.9485 1 -2213.3373
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4
63 0.77864965 0.096633568 0.0047788465 0.0076143824 0.77864965 0.38888882 0.3888615 1.7615283 0 -2213.3374 0.33212054 -2212.952 0.66525325 -2212.9485 1 -2213.3373
73 0.098863403 0.0011310488 0.0027890076 0.0042744972 0.036283915 0.5102483 0.51023975 1.76072 0 -2213.3374 0.2757098 -2213.0417 0.50430234 -2212.8271 1 -2213.3374
83 0.031748825 0.00015683838 0.0020809514 0.0031533485 0.0099572603 0.51014575 0.51014111 1.7602531 0 -2213.3374 0.26034606 -2213.0674 0.50354802 -2212.8272 1 -2213.3374
93 0.011560904 6.778749e-06 0.0013983005 0.0020949841 0.0052524482 0.51011026 0.51010823 1.7601164 0 -2213.3374 0.2537964 -2213.0786 0.50388122 -2212.8273 1 -2213.3374
96 0.0080547159 4.4226058e-06 0.001318412 0.0019726613 0.0048040798 0.510108 0.5101062 1.7601158 0 -2213.3374 0.25347618 -2213.0792 0.50393582 -2212.8273 1 -2213.3374

20
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LAMMPS (22 Dec 2022)
Running on 8 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4 RD5 PE5 RD6 PE6 RD7 PE7 RD8 PE8
0 7.5525391 2.671788 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.14285714 -2213.1848 0.28571429 -2212.8577 0.42857143 -2212.5353 0.57142857 -2212.3131 0.71428571 -2212.192 0.85714286 -2212.0797 1 -2211.7959
10 0.45237221 0.0038899054 0.043713415 0.45237221 0.33984237 0.50434364 0.47974444 1.681593 0 -2213.3362 0.145972 -2213.2393 0.28963267 -2213.0224 0.43234899 -2212.8512 0.57436617 -2212.8319 0.71564291 -2212.9699 0.85294239 -2213.1766 1 -2213.3116
20 0.17466055 0.00038449492 0.027733064 0.16054263 0.29142661 0.49877454 0.49547267 1.7524163 0 -2213.3369 0.14387205 -2213.2456 0.28439667 -2213.0291 0.42233932 -2212.8573 0.5588361 -2212.8381 0.69513708 -2212.9781 0.83702043 -2213.2011 1 -2213.3336
30 0.045422642 0.00010721083 0.01818213 0.045422642 0.28112975 0.49759387 0.49675173 1.7746784 0 -2213.3371 0.14290957 -2213.2488 0.28281709 -2213.0326 0.41989281 -2212.859 0.55582211 -2212.8395 0.69368801 -2212.9853 0.83973606 -2213.2161 1 -2213.3363
40 0.038021578 6.0627173e-05 0.013142053 0.027303941 0.28657705 0.49667648 0.49635337 1.7848045 0 -2213.3372 0.1420496 -2213.2509 0.28169834 -2213.0351 0.41895631 -2212.8598 0.55576002 -2212.8406 0.69554601 -2212.9918 0.84293215 -2213.2247 1 -2213.3369
50 0.023478387 2.5440651e-05 0.0094370881 0.017117841 0.2948129 0.4956627 0.49552819 1.7913648 0 -2213.3373 0.14130551 -2213.2524 0.28080367 -2213.0371 0.41862494 -2212.8601 0.55666336 -2212.8417 0.69796419 -2212.9977 0.84561062 -2213.2308 1 -2213.3372
60 0.015568348 1.3385057e-05 0.0065356733 0.010880239 0.30476692 0.49454143 0.49448589 1.7961707 0 -2213.3374 0.14069048 -2213.2537 0.28018046 -2213.0385 0.41875119 -2212.86 0.55806463 -2212.8428 0.70047903 -2213.0032 0.84789117 -2213.2356 1 -2213.3373
70 0.011117036 8.589416e-06 0.0046665959 0.0074340441 0.31343723 0.4935777 0.49355166 1.7991441 0 -2213.3374 0.14033265 -2213.2544 0.27992696 -2213.0392 0.41915513 -2212.8596 0.55940642 -2212.8438 0.7024513 -2213.0073 0.8494878 -2213.2387 1 -2213.3373
77 0.0095032996 6.4872648e-06 0.003778822 0.0059131255 0.31843187 0.49301961 0.49300316 1.8005356 0 -2213.3374 0.14019726 -2213.2547 0.27989276 -2213.0394 0.41949002 -2212.8594 0.56021116 -2212.8444 0.70351827 -2213.0094 0.85030233 -2213.2402 1 -2213.3374
Climbing replica = 5
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 RD3 PE3 RD4 PE4 RD5 PE5 RD6 PE6 RD7 PE7 RD8 PE8
77 0.31843187 0.016533023 0.003778822 0.0059131255 0.31843187 0.49301961 0.49300316 1.8005356 0 -2213.3374 0.14019726 -2213.2547 0.27989276 -2213.0394 0.41949002 -2212.8594 0.56021116 -2212.8444 0.70351827 -2213.0094 0.85030233 -2213.2402 1 -2213.3374
87 0.068521294 0.00041696849 0.002590902 0.0039658354 0.024993269 0.51001428 0.51000692 1.8017659 0 -2213.3374 0.13988527 -2213.2554 0.27815879 -2213.0427 0.4060317 -2212.8709 0.50551576 -2212.8274 0.69112296 -2212.99 0.84991798 -2213.2398 1 -2213.3374
97 0.031487615 0.00015286198 0.0020335677 0.0030841188 0.0070128682 0.51009653 0.51009209 1.8020354 0 -2213.3374 0.13898618 -2213.2569 0.27382107 -2213.0504 0.39686059 -2212.8798 0.50256203 -2212.8273 0.68247072 -2212.9764 0.84621774 -2213.2346 1 -2213.3374
107 0.016814587 4.4986184e-05 0.0013659976 0.0020482331 0.0024996635 0.51009833 0.51009639 1.8028763 0 -2213.3374 0.13616152 -2213.2608 0.26706798 -2213.0624 0.38875801 -2212.8885 0.50194006 -2212.8273 0.67498881 -2212.9648 0.84072701 -2213.2269 1 -2213.3374
117 0.013420011 2.244148e-05 0.00091637825 0.0013624439 0.0016781664 0.51009641 0.51009556 1.8036672 0 -2213.3374 0.13322116 -2213.2647 0.26208966 -2213.0712 0.38454183 -2212.8933 0.50207828 -2212.8273 0.67150999 -2212.9596 0.83745606 -2213.2222 1 -2213.3374
127 0.0091080864 1.3208992e-05 0.00070311367 0.0010407514 0.0013146017 0.5100957 0.5100952 1.804094 0 -2213.3374 0.13160053 -2213.2667 0.25966338 -2213.0755 0.38274006 -2212.8954 0.50217662 -2212.8273 0.6702885 -2212.9577 0.83622287 -2213.2204 1 -2213.3374

11
examples/neb/log.19Jun17.neb.hop1.end.g++.4
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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.19Jun17.neb.hop1.end.g++.8
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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

9
examples/neb/log.19Jun17.neb.hop1.g++.4
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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

9
examples/neb/log.19Jun17.neb.hop1.g++.8
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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

12
examples/neb/log.19Jun17.neb.hop2.g++.4
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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.19Jun17.neb.hop2.g++.8
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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.19Jun17.neb.sivac.g++.4
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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.19Jun17.neb.sivac.g++.8
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@ -1,18 +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 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

717
src/REPLICA/fix_neb.cpp
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File diff suppressed because it is too large Load Diff

9
src/REPLICA/fix_neb.h
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@ -37,9 +37,9 @@ class FixNEB : public Fix {
void min_post_force(int) override;
private:
int me, nprocs, nprocs_universe;
double kspring, kspringIni, kspringFinal, kspringPerp, EIniIni, EFinalIni;
bool StandardNEB, NEBLongRange, PerpSpring, FreeEndIni, FreeEndFinal;
int me, nprocs, nprocs_universe, neb_mode;
double kspring, kspringIni, kspringFinal, kspringPerp, EIniIni, EFinalIni, idealPos, actualPos;
bool PerpSpring, FreeEndIni, FreeEndFinal;
bool FreeEndFinalWithRespToEIni, FinalAndInterWithRespToEIni;
int ireplica, nreplica;
int procnext, procprev;
@ -53,7 +53,7 @@ class FixNEB : public Fix {
int nebatoms;
int ntotal; // total # of atoms, NEB or not
int maxlocal; // size of xprev,xnext,tangent arrays
double *nlenall;
double *nlenall, *vengall;
double **xprev, **xnext, **fnext, **springF;
double **tangent;
double **xsend, **xrecv; // coords to send/recv to/from other replica
@ -68,6 +68,7 @@ class FixNEB : public Fix {
int *counts, *displacements; // used for MPI_Gather
void inter_replica_comm();
void calculate_ideal_positions();
void reallocate();
};

398
src/REPLICA/neb.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -41,6 +40,8 @@ using namespace MathConst;
#define CHUNK 1024
#define ATTRIBUTE_PERLINE 4
enum { DEFAULT, TERSE, VERBOSE };
/* ---------------------------------------------------------------------- */
NEB::NEB(LAMMPS *lmp) : Command(lmp), all(nullptr), rdist(nullptr) {}
@ -49,18 +50,18 @@ NEB::NEB(LAMMPS *lmp) : Command(lmp), all(nullptr), rdist(nullptr) {}
internal NEB constructor, called from TAD
------------------------------------------------------------------------- */
NEB::NEB(LAMMPS *lmp, double etol_in, double ftol_in, int n1steps_in,
int n2steps_in, int nevery_in, double *buf_init, double *buf_final)
: Command(lmp), fp(nullptr), all(nullptr), rdist(nullptr)
NEB::NEB(LAMMPS *lmp, double etol_in, double ftol_in, int n1steps_in, int n2steps_in, int nevery_in,
double *buf_init, double *buf_final) :
Command(lmp),
fp(nullptr), all(nullptr), rdist(nullptr)
{
double delx,dely,delz;
double delx, dely, delz;
etol = etol_in;
ftol = ftol_in;
n1steps = n1steps_in;
n2steps = n2steps_in;
nevery = nevery_in;
verbose = false;
// replica info
@ -68,22 +69,22 @@ NEB::NEB(LAMMPS *lmp, double etol_in, double ftol_in, int n1steps_in,
ireplica = universe->iworld;
me_universe = universe->me;
uworld = universe->uworld;
MPI_Comm_rank(world,&me);
MPI_Comm_rank(world, &me);
// generate linear interpolate replica
double fraction = ireplica/(nreplica-1.0);
double fraction = ireplica / (nreplica - 1.0);
double **x = atom->x;
int nlocal = atom->nlocal;
int ii = 0;
for (int i = 0; i < nlocal; i++) {
delx = buf_final[ii] - buf_init[ii];
dely = buf_final[ii+1] - buf_init[ii+1];
delz = buf_final[ii+2] - buf_init[ii+2];
domain->minimum_image(delx,dely,delz);
x[i][0] = buf_init[ii] + fraction*delx;
x[i][1] = buf_init[ii+1] + fraction*dely;
x[i][2] = buf_init[ii+2] + fraction*delz;
dely = buf_final[ii + 1] - buf_init[ii + 1];
delz = buf_final[ii + 2] - buf_init[ii + 2];
domain->minimum_image(delx, dely, delz);
x[i][0] = buf_init[ii] + fraction * delx;
x[i][1] = buf_init[ii + 1] + fraction * dely;
x[i][2] = buf_init[ii + 2] + fraction * delz;
ii += 3;
}
}
@ -96,8 +97,10 @@ NEB::~NEB()
memory->destroy(all);
delete[] rdist;
if (fp) {
if (compressed) platform::pclose(fp);
else fclose(fp);
if (compressed)
platform::pclose(fp);
else
fclose(fp);
}
}
@ -108,22 +111,22 @@ NEB::~NEB()
void NEB::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->universe_all(FLERR,"NEB command before simulation box is defined");
error->universe_all(FLERR, "NEB command before simulation box is defined");
if (narg < 6) error->universe_all(FLERR,"Illegal NEB command: missing argument(s)");
if (narg < 6) error->universe_all(FLERR, "Illegal NEB command: missing argument(s)");
etol = utils::numeric(FLERR,arg[0],false,lmp);
ftol = utils::numeric(FLERR,arg[1],false,lmp);
n1steps = utils::inumeric(FLERR,arg[2],false,lmp);
n2steps = utils::inumeric(FLERR,arg[3],false,lmp);
nevery = utils::inumeric(FLERR,arg[4],false,lmp);
etol = utils::numeric(FLERR, arg[0], false, lmp);
ftol = utils::numeric(FLERR, arg[1], false, lmp);
n1steps = utils::inumeric(FLERR, arg[2], false, lmp);
n2steps = utils::inumeric(FLERR, arg[3], false, lmp);
nevery = utils::inumeric(FLERR, arg[4], false, lmp);
// error checks
if (etol < 0.0) error->universe_all(FLERR, fmt::format("Illegal NEB energy tolerance: {}", etol));
if (ftol < 0.0) error->universe_all(FLERR, fmt::format("Illegal NEB force tolerance: {}", ftol));
if (nevery <= 0)
error->universe_all(FLERR,fmt::format("Illegal NEB command every parameter: {}", nevery));
error->universe_all(FLERR, fmt::format("Illegal NEB command every parameter: {}", nevery));
if (n1steps % nevery)
error->all(FLERR, fmt::format("NEB N1 value {} incompatible with every {}", n1steps, nevery));
if (n2steps % nevery)
@ -135,38 +138,50 @@ void NEB::command(int narg, char **arg)
ireplica = universe->iworld;
me_universe = universe->me;
uworld = universe->uworld;
MPI_Comm_rank(world,&me);
MPI_Comm_rank(world, &me);
// error checks
if (nreplica == 1) error->universe_all(FLERR,"Cannot use NEB with a single replica");
if (nreplica == 1) error->universe_all(FLERR, "Cannot use NEB with a single replica");
if (atom->map_style == Atom::MAP_NONE)
error->universe_all(FLERR,"Cannot use NEB without an atom map");
error->universe_all(FLERR, "Cannot use NEB without an atom map");
// process file-style setting to setup initial configs for all replicas
int iarg = 5;
int filecmd = 0;
verbose=false;
print_mode = DEFAULT;
while (iarg < narg) {
if (strcmp(arg[iarg],"final") == 0) {
if (iarg + 2 > narg) error->universe_all(FLERR,"Illegal NEB command: missing arguments");
inpfile = arg[iarg+1];
readfile(inpfile,0);
if (strcmp(arg[iarg], "final") == 0) {
if (iarg + 2 > narg)
error->universe_all(FLERR, "Illegal NEB final command: missing arguments");
inpfile = arg[iarg + 1];
readfile(inpfile, 0);
filecmd = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"each") == 0) {
if (iarg + 2 > narg) error->universe_all(FLERR,"Illegal NEB command: missing arguments");
inpfile = arg[iarg+1];
readfile(inpfile,1);
} else if (strcmp(arg[iarg], "each") == 0) {
if (iarg + 2 > narg)
error->universe_all(FLERR, "Illegal NEB each command: missing arguments");
inpfile = arg[iarg + 1];
readfile(inpfile, 1);
filecmd = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"none") == 0) {
} else if (strcmp(arg[iarg], "none") == 0) {
filecmd = 1;
++iarg;
} else if (strcmp(arg[iarg],"verbose") == 0) {
verbose=true;
++iarg;
} else error->universe_all(FLERR,fmt::format("Unknown NEB command keyword: {}", arg[iarg]));
} else if (strcmp(arg[iarg], "verbosity") == 0) {
if (iarg + 2 > narg)
error->universe_all(FLERR, "Illegal NEB verbosity command: missing arguments");
if (strcmp(arg[iarg+1], "verbose") == 0)
print_mode = VERBOSE;
else if (strcmp(arg[iarg+1], "default") == 0)
print_mode = DEFAULT;
else if (strcmp(arg[iarg+1], "terse") == 0)
print_mode = TERSE;
else
error->universe_all(FLERR, fmt::format("Unknown NEB verbosity option {}", arg[iarg+1]));
iarg += 2;
} else
error->universe_all(FLERR, fmt::format("Unknown NEB command keyword: {}", arg[iarg]));
}
if (!filecmd) error->universe_all(FLERR, "NEB is missing 'final', 'each', or 'none' keyword");
@ -185,18 +200,22 @@ void NEB::run()
// create MPI communicator for root proc from each world
int color;
if (me == 0) color = 0;
else color = 1;
MPI_Comm_split(uworld,color,0,&roots);
if (me == 0)
color = 0;
else
color = 1;
MPI_Comm_split(uworld, color, 0, &roots);
auto fixes = modify->get_fix_by_style("^neb$");
if (fixes.size() != 1)
error->universe_all(FLERR,"NEB requires use of exactly one fix neb instance");
error->universe_all(FLERR, "NEB requires use of exactly one fix neb instance");
fneb = dynamic_cast<FixNEB *>(fixes[0]);
if (verbose) numall =7;
else numall = 4;
memory->create(all,nreplica,numall,"neb:all");
if (print_mode == VERBOSE)
numall = 7;
else
numall = 4;
memory->create(all, nreplica, numall, "neb:all");
rdist = new double[nreplica];
// initialize LAMMPS
@ -209,56 +228,65 @@ void NEB::run()
lmp->init();
if (update->minimize->searchflag)
error->universe_all(FLERR,"NEB requires a damped dynamics minimizer");
error->universe_all(FLERR, "NEB requires a damped dynamics minimizer");
// setup regular NEB minimization
FILE *uscreen = universe->uscreen;
FILE *ulogfile = universe->ulogfile;
if (me_universe == 0 && uscreen)
fprintf(uscreen,"Setting up regular NEB ...\n");
if (me_universe == 0 && uscreen) fprintf(uscreen, "Setting up regular NEB ...\n");
update->beginstep = update->firststep = update->ntimestep;
update->endstep = update->laststep = update->firststep + n1steps;
update->nsteps = n1steps;
update->max_eval = n1steps;
if (update->laststep < 0) error->universe_all(FLERR,"Too many timesteps for NEB");
if (update->laststep < 0) error->universe_all(FLERR, "Too many timesteps for NEB");
update->minimize->setup();
if (me_universe == 0) {
if (uscreen) {
fmt::print(uscreen," Step {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} ",
"MaxReplicaForce", "MaxAtomForce", "GradV0","GradV1","GradVc","EBF", "EBR", "RDT");
for (int i = 1; i <= nreplica; ++i)
fmt::print(uscreen, "{:^14} {:^14} ", "RD"+std::to_string(i), "PE"+std::to_string(i));
fmt::print(uscreen, " Step {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} ",
"MaxReplicaForce", "MaxAtomForce", "GradV0", "GradV1", "GradVc", "EBF", "EBR",
"RDT");
if (verbose) {
if (print_mode != TERSE) {
for (int i = 1; i <= nreplica; ++i)
fmt::print(uscreen, "{:^14} {:^14} ", "RD" + std::to_string(i), "PE" + std::to_string(i));
}
if (print_mode == VERBOSE) {
for (int i = 1; i <= nreplica; ++i) {
auto idx = std::to_string(i);
fmt::print(uscreen, "{:^12}{:^12}{:^12} {:^12} {:^12}{:^12} ",
"pathangle"+idx, "angletangrad"+idx, "anglegrad"+idx, "gradV"+idx,
"RepForce"+idx, "MaxAtomForce"+idx);
fmt::print(uscreen, "{:^12}{:^12}{:^12} {:^12} {:^12}{:^12} ", "pathangle" + idx,
"angletangrad" + idx, "anglegrad" + idx, "gradV" + idx, "RepForce" + idx,
"MaxAtomForce" + idx);
}
}
fprintf(uscreen,"\n");
fprintf(uscreen, "\n");
}
if (ulogfile) {
fmt::print(ulogfile," Step {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} ",
"MaxReplicaForce", "MaxAtomForce", "GradV0","GradV1","GradVc","EBF", "EBR", "RDT");
for (int i = 1; i <= nreplica; ++i)
fmt::print(ulogfile, "{:^14} {:^14} ", "RD"+std::to_string(i), "PE"+std::to_string(i));
fmt::print(ulogfile, " Step {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} ",
"MaxReplicaForce", "MaxAtomForce", "GradV0", "GradV1", "GradVc", "EBF", "EBR",
"RDT");
if (verbose) {
if (print_mode != TERSE) {
for (int i = 1; i <= nreplica; ++i)
fmt::print(ulogfile, "{:^14} {:^14} ", "RD" + std::to_string(i),
"PE" + std::to_string(i));
}
if (print_mode == VERBOSE) {
for (int i = 1; i <= nreplica; ++i) {
auto idx = std::to_string(i);
fmt::print(ulogfile, "{:^12}{:^12}{:^12} {:^12} {:^12}{:^12} ",
"pathangle"+idx, "angletangrad"+idx, "anglegrad"+idx, "gradV"+idx,
"RepForce"+idx, "MaxAtomForce"+idx);
fmt::print(ulogfile, "{:^12}{:^12}{:^12} {:^12} {:^12}{:^12} ", "pathangle" + idx,
"angletangrad" + idx, "anglegrad" + idx, "gradV" + idx, "RepForce" + idx,
"MaxAtomForce" + idx);
}
}
fprintf(ulogfile,"\n");
fprintf(ulogfile, "\n");
}
}
print_status();
@ -298,21 +326,18 @@ void NEB::run()
// setup climbing NEB minimization
// must reinitialize minimizer so it re-creates its fix MINIMIZE
if (me_universe == 0 && uscreen)
fprintf(uscreen,"Setting up climbing ...\n");
if (me_universe == 0 && uscreen) fprintf(uscreen, "Setting up climbing ...\n");
if (me_universe == 0) {
if (uscreen)
fprintf(uscreen,"Climbing replica = %d\n",top+1);
if (ulogfile)
fprintf(ulogfile,"Climbing replica = %d\n",top+1);
if (uscreen) fprintf(uscreen, "Climbing replica = %d\n", top + 1);
if (ulogfile) fprintf(ulogfile, "Climbing replica = %d\n", top + 1);
}
update->beginstep = update->firststep = update->ntimestep;
update->endstep = update->laststep = update->firststep + n2steps;
update->nsteps = n2steps;
update->max_eval = n2steps;
if (update->laststep < 0) error->universe_all(FLERR,"Too many timesteps");
if (update->laststep < 0) error->universe_all(FLERR, "Too many timesteps");
update->minimize->init();
fneb->rclimber = top;
@ -320,37 +345,46 @@ void NEB::run()
if (me_universe == 0) {
if (uscreen) {
fmt::print(uscreen," Step {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} ",
"MaxReplicaForce", "MaxAtomForce", "GradV0","GradV1","GradVc","EBF", "EBR", "RDT");
for (int i = 1; i <= nreplica; ++i)
fmt::print(uscreen, "{:^14} {:^14} ", "RD"+std::to_string(i), "PE"+std::to_string(i));
fmt::print(uscreen, " Step {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} ",
"MaxReplicaForce", "MaxAtomForce", "GradV0", "GradV1", "GradVc", "EBF", "EBR",
"RDT");
if (verbose) {
if (print_mode != TERSE) {
for (int i = 1; i <= nreplica; ++i)
fmt::print(uscreen, "{:^14} {:^14} ", "RD" + std::to_string(i), "PE" + std::to_string(i));
}
if (print_mode == VERBOSE) {
for (int i = 1; i <= nreplica; ++i) {
auto idx = std::to_string(i);
fmt::print(uscreen, "{:^12}{:^12}{:^12} {:^12} {:^12}{:^12} ",
"pathangle"+idx, "angletangrad"+idx, "anglegrad"+idx, "gradV"+idx,
"RepForce"+idx, "MaxAtomForce"+idx);
fmt::print(uscreen, "{:^12}{:^12}{:^12} {:^12} {:^12}{:^12} ", "pathangle" + idx,
"angletangrad" + idx, "anglegrad" + idx, "gradV" + idx, "RepForce" + idx,
"MaxAtomForce" + idx);
}
}
fprintf(uscreen,"\n");
fprintf(uscreen, "\n");
}
if (ulogfile) {
fmt::print(ulogfile," Step {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} ",
"MaxReplicaForce", "MaxAtomForce", "GradV0","GradV1","GradVc","EBF", "EBR", "RDT");
for (int i = 1; i <= nreplica; ++i)
fmt::print(ulogfile, "{:^14} {:^14} ", "RD"+std::to_string(i), "PE"+std::to_string(i));
fmt::print(ulogfile, " Step {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} ",
"MaxReplicaForce", "MaxAtomForce", "GradV0", "GradV1", "GradVc", "EBF", "EBR",
"RDT");
if (verbose) {
if (print_mode != TERSE) {
for (int i = 1; i <= nreplica; ++i)
fmt::print(ulogfile, "{:^14} {:^14} ", "RD" + std::to_string(i),
"PE" + std::to_string(i));
}
if (print_mode == VERBOSE) {
for (int i = 1; i <= nreplica; ++i) {
auto idx = std::to_string(i);
fmt::print(ulogfile, "{:^12}{:^12}{:^12} {:^12} {:^12}{:^12} ",
"pathangle"+idx, "angletangrad"+idx, "anglegrad"+idx, "gradV"+idx,
"RepForce"+idx, "MaxAtomForce"+idx);
fmt::print(ulogfile, "{:^12}{:^12}{:^12} {:^12} {:^12}{:^12} ", "pathangle" + idx,
"angletangrad" + idx, "anglegrad" + idx, "gradV" + idx, "RepForce" + idx,
"MaxAtomForce" + idx);
}
}
fprintf(ulogfile,"\n");
fprintf(ulogfile, "\n");
}
}
print_status();
@ -398,14 +432,14 @@ void NEB::run()
void NEB::readfile(char *file, int flag)
{
int i,nchunk,eofflag,nlines;
int i, nchunk, eofflag, nlines;
tagint tag;
char *eof,*start,*next,*buf;
char *eof, *start, *next, *buf;
char line[MAXLINE];
double delx,dely,delz;
double delx, dely, delz;
if (me_universe == 0 && universe->uscreen)
fprintf(universe->uscreen,"Reading NEB coordinate file(s) ...\n");
fprintf(universe->uscreen, "Reading NEB coordinate file(s) ...\n");
// flag = 0, universe root reads header of file, bcast to universe
// flag = 1, each replica's root reads header of file, bcast to world
@ -415,38 +449,37 @@ void NEB::readfile(char *file, int flag)
if (me_universe == 0) {
open(file);
while (true) {
eof = fgets(line,MAXLINE,fp);
if (eof == nullptr) error->one(FLERR,"Unexpected end of NEB file");
start = &line[strspn(line," \t\n\v\f\r")];
eof = fgets(line, MAXLINE, fp);
if (eof == nullptr) error->one(FLERR, "Unexpected end of NEB file");
start = &line[strspn(line, " \t\n\v\f\r")];
if (*start != '\0' && *start != '#') break;
}
int rv = sscanf(line,"%d",&nlines);
int rv = sscanf(line, "%d", &nlines);
if (rv != 1) nlines = -1;
}
MPI_Bcast(&nlines,1,MPI_INT,0,uworld);
if (nlines < 0)
error->universe_all(FLERR,"Incorrectly formatted NEB file");
MPI_Bcast(&nlines, 1, MPI_INT, 0, uworld);
if (nlines < 0) error->universe_all(FLERR, "Incorrectly formatted NEB file");
} else {
if (me == 0) {
if (ireplica) {
open(file);
while (true) {
eof = fgets(line,MAXLINE,fp);
if (eof == nullptr) error->one(FLERR,"Unexpected end of NEB file");
start = &line[strspn(line," \t\n\v\f\r")];
eof = fgets(line, MAXLINE, fp);
if (eof == nullptr) error->one(FLERR, "Unexpected end of NEB file");
start = &line[strspn(line, " \t\n\v\f\r")];
if (*start != '\0' && *start != '#') break;
}
int rv = sscanf(line,"%d",&nlines);
int rv = sscanf(line, "%d", &nlines);
if (rv != 1) nlines = -1;
} else nlines = 0;
} else
nlines = 0;
}
MPI_Bcast(&nlines,1,MPI_INT,0,world);
if (nlines < 0)
error->universe_all(FLERR,"Incorrectly formatted NEB file");
MPI_Bcast(&nlines, 1, MPI_INT, 0, world);
if (nlines < 0) error->universe_all(FLERR, "Incorrectly formatted NEB file");
}
auto buffer = new char[CHUNK*MAXLINE];
double fraction = ireplica/(nreplica-1.0);
auto buffer = new char[CHUNK * MAXLINE];
double fraction = ireplica / (nreplica - 1.0);
double **x = atom->x;
int nlocal = atom->nlocal;
@ -456,32 +489,31 @@ void NEB::readfile(char *file, int flag)
int ncount = 0, nread = 0;
while (nread < nlines) {
nchunk = MIN(nlines-nread,CHUNK);
nchunk = MIN(nlines - nread, CHUNK);
if (flag == 0)
eofflag = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,
universe->me,universe->uworld);
eofflag =
utils::read_lines_from_file(fp, nchunk, MAXLINE, buffer, universe->me, universe->uworld);
else
eofflag = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
if (eofflag) error->all(FLERR,"Unexpected end of NEB file");
eofflag = utils::read_lines_from_file(fp, nchunk, MAXLINE, buffer, me, world);
if (eofflag) error->all(FLERR, "Unexpected end of NEB file");
buf = buffer;
next = strchr(buf,'\n');
next = strchr(buf, '\n');
*next = '\0';
int nwords = utils::count_words(utils::trim_comment(buf));
*next = '\n';
if (nwords != ATTRIBUTE_PERLINE)
error->all(FLERR,"Incorrect atom format in NEB file");
if (nwords != ATTRIBUTE_PERLINE) error->all(FLERR, "Incorrect atom format in NEB file");
// loop over lines of atom coords
// tokenize the line into values
for (i = 0; i < nchunk; i++) {
next = strchr(buf,'\n');
next = strchr(buf, '\n');
*next = '\0';
try {
ValueTokenizer values(buf," \t\n\r\f");
ValueTokenizer values(buf, " \t\n\r\f");
// adjust atom coord based on replica fraction
// for flag = 0, interpolate for intermediate and final replicas
@ -502,12 +534,12 @@ void NEB::readfile(char *file, int flag)
dely = values.next_double() - x[m][1];
delz = values.next_double() - x[m][2];
domain->minimum_image(delx,dely,delz);
domain->minimum_image(delx, dely, delz);
if (flag == 0) {
x[m][0] += fraction*delx;
x[m][1] += fraction*dely;
x[m][2] += fraction*delz;
x[m][0] += fraction * delx;
x[m][1] += fraction * dely;
x[m][2] += fraction * delz;
} else {
x[m][0] += delx;
x[m][1] += dely;
@ -515,7 +547,7 @@ void NEB::readfile(char *file, int flag)
}
}
} catch (std::exception &e) {
error->universe_one(FLERR,"Incorrectly formatted NEB file: " + std::string(e.what()));
error->universe_one(FLERR, "Incorrectly formatted NEB file: " + std::string(e.what()));
}
buf = next + 1;
}
@ -526,14 +558,12 @@ void NEB::readfile(char *file, int flag)
if (flag == 0) {
int ntotal;
MPI_Allreduce(&ncount,&ntotal,1,MPI_INT,MPI_SUM,uworld);
if (ntotal != nreplica*nlines)
error->universe_all(FLERR,"Invalid atom IDs in NEB file");
MPI_Allreduce(&ncount, &ntotal, 1, MPI_INT, MPI_SUM, uworld);
if (ntotal != nreplica * nlines) error->universe_all(FLERR, "Invalid atom IDs in NEB file");
} else {
int ntotal;
MPI_Allreduce(&ncount,&ntotal,1,MPI_INT,MPI_SUM,world);
if (ntotal != nlines)
error->all(FLERR,"Invalid atom IDs in NEB file");
MPI_Allreduce(&ncount, &ntotal, 1, MPI_INT, MPI_SUM, world);
if (ntotal != nlines) error->all(FLERR, "Invalid atom IDs in NEB file");
}
// clean up
@ -541,13 +571,17 @@ void NEB::readfile(char *file, int flag)
if (flag == 0) {
if (me_universe == 0) {
if (compressed) platform::pclose(fp);
else fclose(fp);
if (compressed)
platform::pclose(fp);
else
fclose(fp);
}
} else {
if (me == 0 && ireplica) {
if (compressed) platform::pclose(fp);
else fclose(fp);
if (compressed)
platform::pclose(fp);
else
fclose(fp);
}
}
fp = nullptr;
@ -564,11 +598,11 @@ void NEB::open(char *file)
if (platform::has_compress_extension(file)) {
compressed = 1;
fp = platform::compressed_read(file);
if (!fp) error->one(FLERR,"Cannot open compressed file {}: {}", file, utils::getsyserror());
} else fp = fopen(file,"r");
if (!fp) error->one(FLERR, "Cannot open compressed file {}: {}", file, utils::getsyserror());
} else
fp = fopen(file, "r");
if (fp == nullptr)
error->one(FLERR,"Cannot open file {}: {}", file, utils::getsyserror());
if (fp == nullptr) error->one(FLERR, "Cannot open file {}: {}", file, utils::getsyserror());
}
/* ----------------------------------------------------------------------
@ -580,16 +614,16 @@ void NEB::print_status()
{
double fnorm2 = sqrt(update->minimize->fnorm_sqr());
double fmaxreplica;
MPI_Allreduce(&fnorm2,&fmaxreplica,1,MPI_DOUBLE,MPI_MAX,roots);
MPI_Allreduce(&fnorm2, &fmaxreplica, 1, MPI_DOUBLE, MPI_MAX, roots);
double fnorminf = update->minimize->fnorm_inf();
double fmaxatom;
MPI_Allreduce(&fnorminf,&fmaxatom,1,MPI_DOUBLE,MPI_MAX,roots);
MPI_Allreduce(&fnorminf, &fmaxatom, 1, MPI_DOUBLE, MPI_MAX, roots);
if (verbose) {
if (print_mode == VERBOSE) {
freplica = new double[nreplica];
MPI_Allgather(&fnorm2,1,MPI_DOUBLE,&freplica[0],1,MPI_DOUBLE,roots);
MPI_Allgather(&fnorm2, 1, MPI_DOUBLE, &freplica[0], 1, MPI_DOUBLE, roots);
fmaxatomInRepl = new double[nreplica];
MPI_Allgather(&fnorminf,1,MPI_DOUBLE,&fmaxatomInRepl[0],1,MPI_DOUBLE,roots);
MPI_Allgather(&fnorminf, 1, MPI_DOUBLE, &fmaxatomInRepl[0], 1, MPI_DOUBLE, roots);
}
double one[7];
@ -598,23 +632,20 @@ void NEB::print_status()
one[2] = fneb->nlen;
one[3] = fneb->gradlen;
if (verbose) {
if (print_mode == VERBOSE) {
one[4] = fneb->dotpath;
one[5] = fneb->dottangrad;
one[6] = fneb->dotgrad;
}
if (output->thermo->normflag) one[0] /= atom->natoms;
if (me == 0)
MPI_Allgather(one,numall,MPI_DOUBLE,&all[0][0],numall,MPI_DOUBLE,roots);
MPI_Bcast(&all[0][0],numall*nreplica,MPI_DOUBLE,0,world);
if (me == 0) MPI_Allgather(one, numall, MPI_DOUBLE, &all[0][0], numall, MPI_DOUBLE, roots);
MPI_Bcast(&all[0][0], numall * nreplica, MPI_DOUBLE, 0, world);
rdist[0] = 0.0;
for (int i = 1; i < nreplica; i++)
rdist[i] = rdist[i-1] + all[i][1];
double endpt = rdist[nreplica-1] = rdist[nreplica-2] + all[nreplica-2][2];
for (int i = 1; i < nreplica; i++)
rdist[i] /= endpt;
for (int i = 1; i < nreplica; i++) rdist[i] = rdist[i - 1] + all[i][1];
double endpt = rdist[nreplica - 1] = rdist[nreplica - 2] + all[nreplica - 2][2];
for (int i = 1; i < nreplica; i++) rdist[i] /= endpt;
// look up GradV for the initial, final, and climbing replicas
// these are identical to fnorm2, but to be safe we
@ -625,13 +656,13 @@ void NEB::print_status()
int irep;
irep = 0;
gradvnorm0 = all[irep][3];
irep = nreplica-1;
irep = nreplica - 1;
gradvnorm1 = all[irep][3];
irep = fneb->rclimber;
if (irep > -1) {
gradvnormc = all[irep][3];
ebf = all[irep][0]-all[0][0];
ebr = all[irep][0]-all[nreplica-1][0];
ebf = all[irep][0] - all[0][0];
ebr = all[irep][0] - all[nreplica - 1][0];
} else {
double vmax = all[0][0];
int top = 0;
@ -642,27 +673,32 @@ void NEB::print_status()
}
irep = top;
gradvnormc = all[irep][3];
ebf = all[irep][0]-all[0][0];
ebr = all[irep][0]-all[nreplica-1][0];
ebf = all[irep][0] - all[0][0];
ebr = all[irep][0] - all[nreplica - 1][0];
}
if (me_universe == 0) {
constexpr double todeg=180.0/MY_PI;
std::string mesg = fmt::format("{:10} {:<14.8g} {:<14.8g} ",update->ntimestep,fmaxreplica,fmaxatom);
mesg += fmt::format("{:<14.8g} {:<14.8g} {:<14.8g} ",gradvnorm0,gradvnorm1,gradvnormc);
mesg += fmt::format("{:<14.8g} {:<14.8g} {:<14.8g} ",ebf,ebr,endpt);
for (int i = 0; i < nreplica; i++) mesg += fmt::format("{:<14.8g} {:<14.8g} ",rdist[i],all[i][0]);
if (verbose) {
mesg += fmt::format("{:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g}",
NAN,180-acos(all[0][5])*todeg,180-acos(all[0][6])*todeg,
all[0][3],freplica[0],fmaxatomInRepl[0]);
for (int i = 1; i < nreplica-1; i++)
mesg += fmt::format("{:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g}",
180-acos(all[i][4])*todeg,180-acos(all[i][5])*todeg,
180-acos(all[i][6])*todeg,all[i][3],freplica[i],fmaxatomInRepl[i]);
mesg += fmt::format("{:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g}",
NAN,180-acos(all[nreplica-1][5])*todeg,NAN,all[nreplica-1][3],
freplica[nreplica-1],fmaxatomInRepl[nreplica-1]);
constexpr double todeg = 180.0 / MY_PI;
std::string mesg =
fmt::format("{:10} {:<14.8g} {:<14.8g} ", update->ntimestep, fmaxreplica, fmaxatom);
mesg += fmt::format("{:<14.8g} {:<14.8g} {:<14.8g} ", gradvnorm0, gradvnorm1, gradvnormc);
mesg += fmt::format("{:<14.8g} {:<14.8g} {:<14.8g} ", ebf, ebr, endpt);
if (print_mode != TERSE) {
for (int i = 0; i < nreplica; i++)
mesg += fmt::format("{:<14.8g} {:<14.8g} ", rdist[i], all[i][0]);
}
if (print_mode == VERBOSE) {
mesg += fmt::format("{:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g}", NAN,
180 - acos(all[0][5]) * todeg, 180 - acos(all[0][6]) * todeg, all[0][3],
freplica[0], fmaxatomInRepl[0]);
for (int i = 1; i < nreplica - 1; i++)
mesg +=
fmt::format("{:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g}",
180 - acos(all[i][4]) * todeg, 180 - acos(all[i][5]) * todeg,
180 - acos(all[i][6]) * todeg, all[i][3], freplica[i], fmaxatomInRepl[i]);
mesg += fmt::format("{:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g}", NAN,
180 - acos(all[nreplica - 1][5]) * todeg, NAN, all[nreplica - 1][3],
freplica[nreplica - 1], fmaxatomInRepl[nreplica - 1]);
}
mesg += "\n";
@ -672,7 +708,7 @@ void NEB::print_status()
fflush(universe->ulogfile);
}
}
if (verbose) {
if (print_mode == VERBOSE) {
delete[] freplica;
delete[] fmaxatomInRepl;
}

2
src/REPLICA/neb.h
View File

@ -35,9 +35,9 @@ class NEB : public Command {
double ebf, ebr; // forward and reverse energy barriers
private:
int print_mode; // output verbosity
int me, me_universe; // my proc ID in world and universe
int ireplica, nreplica;
bool verbose;
MPI_Comm uworld;
MPI_Comm roots; // MPI comm with 1 root proc from each world
FILE *fp;