From 35705217f4bb2c88c1f9f0b8ae0b17d5e078387a Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Tue, 27 Sep 2016 15:34:08 -0600
Subject: [PATCH] enable multi-processor NEB replicas
---
doc/src/Manual.txt | 4 +-
doc/src/neb.txt | 9 -
examples/neb/README | 18 +-
examples/neb/in.neb.hop1 | 9 +-
examples/neb/in.neb.hop2 | 11 +-
examples/neb/in.neb.sivac | 18 +-
examples/neb/initial.hop1 | 860 ++++++++++++++
examples/neb/initial.hop2 | 862 ++++++++++++++
examples/neb/initial.sivac | 1042 +++++++++++++++++
....hop1.g++.4 => log.28Sep16.neb.hop1.g++.4} | 2 +-
examples/neb/log.28Sep16.neb.hop1.g++.8 | 10 +
....hop2.g++.4 => log.28Sep16.neb.hop2.g++.4} | 2 +-
examples/neb/log.28Sep16.neb.hop2.g++.8 | 18 +
examples/neb/log.28Sep16.neb.sivac.g++.3 | 14 +
examples/neb/log.28Sep16.neb.sivac.g++.6 | 14 +
...ivac.g++.3 => log.28Sep16.neb.sivac.g++.9} | 10 +-
examples/snap/Ta06A_pot.snap | 6 +-
src/REPLICA/fix_neb.cpp | 352 +++++-
src/REPLICA/fix_neb.h | 23 +-
src/REPLICA/neb.cpp | 7 +-
src/version.h | 2 +-
21 files changed, 3204 insertions(+), 89 deletions(-)
create mode 100644 examples/neb/initial.hop1
create mode 100644 examples/neb/initial.hop2
create mode 100644 examples/neb/initial.sivac
rename examples/neb/{log.15Feb16.neb.hop1.g++.4 => log.28Sep16.neb.hop1.g++.4} (98%)
create mode 100644 examples/neb/log.28Sep16.neb.hop1.g++.8
rename examples/neb/{log.15Feb16.neb.hop2.g++.4 => log.28Sep16.neb.hop2.g++.4} (99%)
create mode 100644 examples/neb/log.28Sep16.neb.hop2.g++.8
create mode 100644 examples/neb/log.28Sep16.neb.sivac.g++.3
create mode 100644 examples/neb/log.28Sep16.neb.sivac.g++.6
rename examples/neb/{log.15Feb16.neb.sivac.g++.3 => log.28Sep16.neb.sivac.g++.9} (60%)
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index fc728afd61..f8f7644e5b 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="27 Sep 2016 version">
+<META NAME="docnumber" CONTENT="28 Sep 2016 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@@ -21,7 +21,7 @@
<H1></H1>
LAMMPS Documentation :c,h3
-27 Sep 2016 version :c,h4
+28 Sep 2016 version :c,h4
Version info: :h4
diff --git a/doc/src/neb.txt b/doc/src/neb.txt
index f7cae7919a..59e6db966b 100644
--- a/doc/src/neb.txt
+++ b/doc/src/neb.txt
@@ -57,9 +57,6 @@ would see with one or more physical processors per replica. See
"Section 6.5"_Section_howto.html#howto_5 of the manual for further
discussion.
-NOTE: The current NEB implementation in LAMMPS only allows there to be
-one processor per replica.
-
NOTE: As explained below, a NEB calculation perfoms a damped dynamics
minimization across all the replicas. The mimimizer uses whatever
timestep you have defined in your input script, via the
@@ -255,12 +252,6 @@ An atom map must be defined which it is not by default for "atom_style
atomic"_atom_style.html problems. The "atom_modify
map"_atom_modify.html command can be used to do this.
-The "atom_modify sort 0 0.0" command should be used to turn off atom
-sorting.
-
-NOTE: This sorting restriction will be removed in a future version of
-NEB in LAMMPS.
-
The minimizers in LAMMPS operate on all atoms in your system, even
non-NEB atoms, as defined above. To prevent non-NEB atoms from moving
during the minimization, you should use the "fix
diff --git a/examples/neb/README b/examples/neb/README
index 137c42a068..130d0fd2e3 100644
--- a/examples/neb/README
+++ b/examples/neb/README
@@ -1,12 +1,18 @@
Run these examples as:
-mpirun -np 4 lmp_linux -partition 4x1 -in in.neb.hop1
-mpirun -np 4 lmp_linux -partition 4x1 -in in.neb.hop2
-mpirun -np 3 lmp_linux -partition 3x1 -in in.neb.sivac
+mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1
+mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop2
+mpirun -np 3 lmp_g++ -partition 3x1 -in in.neb.sivac
-Create dump files to do visualization from via Python tools:
-(see lammps/tools/README and lammps/tools/python/README
-for more info on these Python scripts)
+mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1
+mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop2
+mpirun -np 6 lmp_g++ -partition 3x2 -in in.neb.sivac
+mpirun -np 9 lmp_g++ -partition 3x3 -in in.neb.sivac
+
+If you uncomment the dump command lines in the input scripts, you can
+create dump files to do visualization from via Python tools: (see
+lammps/tools/README and lammps/tools/python/README for more info on
+these Python scripts)
python ~/lammps/tools/python/neb_combine.py -o dump.hop1.combine
-b dump.nonneb.1
diff --git a/examples/neb/in.neb.hop1 b/examples/neb/in.neb.hop1
index a5dea35721..9a3d7579f3 100644
--- a/examples/neb/in.neb.hop1
+++ b/examples/neb/in.neb.hop1
@@ -14,10 +14,13 @@ variable u uloop 20
lattice hex 0.9
region box block 0 20 0 10 -0.25 0.25
-create_box 3 box
-create_atoms 1 box
-mass * 1.0
+#create_box 3 box
+#create_atoms 1 box
+#mass * 1.0
+#write_data initial.hop1
+
+read_data initial.hop1
# LJ potentials
diff --git a/examples/neb/in.neb.hop2 b/examples/neb/in.neb.hop2
index 1ce1f6f82d..3eb16248e1 100644
--- a/examples/neb/in.neb.hop2
+++ b/examples/neb/in.neb.hop2
@@ -15,11 +15,14 @@ variable u uloop 20
lattice hex 0.9
region box block 0 20 0 11 -0.25 0.25
region box1 block 0 20 0 10 -0.25 0.25
-create_box 3 box
-create_atoms 1 region box1
-create_atoms 1 single 11.5 10.5 0
-mass * 1.0
+#create_box 3 box
+#create_atoms 1 region box1
+#create_atoms 1 single 11.5 10.5 0
+#mass * 1.0
+#write_data initial.hop2
+
+read_data initial.hop2
# LJ potentials
diff --git a/examples/neb/in.neb.sivac b/examples/neb/in.neb.sivac
index baf87bf215..566a380627 100644
--- a/examples/neb/in.neb.sivac
+++ b/examples/neb/in.neb.sivac
@@ -30,17 +30,20 @@ lattice custom $a &
region myreg block 0 4 &
0 4 &
0 4
-create_box 1 myreg
-create_atoms 1 region myreg
-mass 1 28.06
+#create_box 1 myreg
+#create_atoms 1 region myreg
+#mass 1 28.06
+#write_data initial.sivac
-group Si type 1
+read_data initial.sivac
# make a vacancy
+group Si type 1
+
group del id 300
-delete_atoms group del
+delete_atoms group del compress no
group vacneigh id 174 175 301 304 306 331 337
# choose potential
@@ -54,7 +57,7 @@ variable u uloop 20
# only output atoms near vacancy
-dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z
+#dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z
# initial minimization to relax vacancy
@@ -72,5 +75,4 @@ thermo 100
timestep 0.01
min_style quickmin
-neb 0.0 0.01 50 100 10 final final.sivac
-
+neb 0.0 0.01 100 100 10 final final.sivac
diff --git a/examples/neb/initial.hop1 b/examples/neb/initial.hop1
new file mode 100644
index 0000000000..228708c314
--- /dev/null
+++ b/examples/neb/initial.hop1
@@ -0,0 +1,860 @@
+LAMMPS data file via write_data, version 27 Sep 2016, timestep = 0
+
+420 atoms
+3 atom types
+
+0.0000000000000000e+00 2.2653923264628304e+01 xlo xhi
+-1.9618873042551413e-03 1.9620834929855668e+01 ylo yhi
+-2.8317404080785380e-01 2.8317404080785380e-01 zlo zhi
+
+Masses
+
+1 1
+2 1
+3 1
+
+Atoms # atomic
+
+1 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
+2 1 5.6634808161570760e-01 9.8094365212757073e-01 0.0000000000000000e+00 0 0 0
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diff --git a/examples/neb/initial.hop2 b/examples/neb/initial.hop2
new file mode 100644
index 0000000000..5683b18309
--- /dev/null
+++ b/examples/neb/initial.hop2
@@ -0,0 +1,862 @@
+LAMMPS data file via write_data, version 27 Sep 2016, timestep = 0
+
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+-2.1580760346806556e-03 2.0601974770713667e+01 ylo yhi
+-2.8317404080785380e-01 2.8317404080785380e-01 zlo zhi
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diff --git a/examples/neb/initial.sivac b/examples/neb/initial.sivac
new file mode 100644
index 0000000000..5664b6c39a
--- /dev/null
+++ b/examples/neb/initial.sivac
@@ -0,0 +1,1042 @@
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diff --git a/examples/neb/log.15Feb16.neb.hop1.g++.4 b/examples/neb/log.28Sep16.neb.hop1.g++.4
similarity index 98%
rename from examples/neb/log.15Feb16.neb.hop1.g++.4
rename to examples/neb/log.28Sep16.neb.hop1.g++.4
index c6d97c389a..61809ea123 100644
--- a/examples/neb/log.15Feb16.neb.hop1.g++.4
+++ b/examples/neb/log.28Sep16.neb.hop1.g++.4
@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (27 Sep 2016)
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
diff --git a/examples/neb/log.28Sep16.neb.hop1.g++.8 b/examples/neb/log.28Sep16.neb.hop1.g++.8
new file mode 100644
index 0000000000..4ad460e8c6
--- /dev/null
+++ b/examples/neb/log.28Sep16.neb.hop1.g++.8
@@ -0,0 +1,10 @@
+LAMMPS (27 Sep 2016)
+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
+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
diff --git a/examples/neb/log.15Feb16.neb.hop2.g++.4 b/examples/neb/log.28Sep16.neb.hop2.g++.4
similarity index 99%
rename from examples/neb/log.15Feb16.neb.hop2.g++.4
rename to examples/neb/log.28Sep16.neb.hop2.g++.4
index 5ff6468fa4..418717387b 100644
--- a/examples/neb/log.15Feb16.neb.hop2.g++.4
+++ b/examples/neb/log.28Sep16.neb.hop2.g++.4
@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (27 Sep 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
diff --git a/examples/neb/log.28Sep16.neb.hop2.g++.8 b/examples/neb/log.28Sep16.neb.hop2.g++.8
new file mode 100644
index 0000000000..418717387b
--- /dev/null
+++ b/examples/neb/log.28Sep16.neb.hop2.g++.8
@@ -0,0 +1,18 @@
+LAMMPS (27 Sep 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
diff --git a/examples/neb/log.28Sep16.neb.sivac.g++.3 b/examples/neb/log.28Sep16.neb.sivac.g++.3
new file mode 100644
index 0000000000..e9406754d6
--- /dev/null
+++ b/examples/neb/log.28Sep16.neb.sivac.g++.3
@@ -0,0 +1,14 @@
+LAMMPS (27 Sep 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
diff --git a/examples/neb/log.28Sep16.neb.sivac.g++.6 b/examples/neb/log.28Sep16.neb.sivac.g++.6
new file mode 100644
index 0000000000..eac33a8863
--- /dev/null
+++ b/examples/neb/log.28Sep16.neb.sivac.g++.6
@@ -0,0 +1,14 @@
+LAMMPS (27 Sep 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
diff --git a/examples/neb/log.15Feb16.neb.sivac.g++.3 b/examples/neb/log.28Sep16.neb.sivac.g++.9
similarity index 60%
rename from examples/neb/log.15Feb16.neb.sivac.g++.3
rename to examples/neb/log.28Sep16.neb.sivac.g++.9
index dbc2f08929..1b7f46b656 100644
--- a/examples/neb/log.15Feb16.neb.sivac.g++.3
+++ b/examples/neb/log.28Sep16.neb.sivac.g++.9
@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (27 Sep 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
@@ -6,9 +6,9 @@ Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 P
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 0.025904252 0.0022808801 0.008105847 0.025904252 0.016908971 0.5101712 0.51008591 1.7391431 0 -2213.3373 0.49923347 -2212.8272 1 -2213.3373
+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
-50 0.025904252 0.0044134315 0.008105847 0.025904252 0.016908971 0.5101712 0.51008591 1.7391431 0 -2213.3373 0.49923347 -2212.8272 1 -2213.3373
-60 0.011518317 0.0013089596 0.0054472815 0.011518317 0.0091629734 0.51014415 0.51010903 1.7406815 0 -2213.3374 0.50065207 -2212.8272 1 -2213.3373
-61 0.0089525108 0.0012703829 0.0052524345 0.0088142351 0.0089525108 0.51014321 0.51010962 1.7407173 0 -2213.3374 0.50065779 -2212.8272 1 -2213.3373
+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
diff --git a/examples/snap/Ta06A_pot.snap b/examples/snap/Ta06A_pot.snap
index edcc002524..7c86c24641 100644
--- a/examples/snap/Ta06A_pot.snap
+++ b/examples/snap/Ta06A_pot.snap
@@ -9,9 +9,9 @@ variable zblz equal 73
# Specify hybrid with SNAP, ZBL
-pair_style hybrid/overlay &
-zbl ${zblcutinner} ${zblcutouter} &
-snap
+pair_style hybrid/overlay snap &
+zbl ${zblcutinner} ${zblcutouter}
+
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp
index c66fa2dd04..5b426465e3 100644
--- a/src/REPLICA/fix_neb.cpp
+++ b/src/REPLICA/fix_neb.cpp
@@ -18,10 +18,12 @@
#include "fix_neb.h"
#include "universe.h"
#include "update.h"
+#include "atom.h"
#include "domain.h"
+#include "comm.h"
#include "modify.h"
#include "compute.h"
-#include "atom.h"
+#include "group.h"
#include "memory.h"
#include "error.h"
#include "force.h"
@@ -29,6 +31,8 @@
using namespace LAMMPS_NS;
using namespace FixConst;
+enum{SINGLE_PROC_DIRECT,SINGLE_PROC_MAP,MULTI_PROC};
+
/* ---------------------------------------------------------------------- */
FixNEB::FixNEB(LAMMPS *lmp, int narg, char **arg) :
@@ -41,8 +45,13 @@ FixNEB::FixNEB(LAMMPS *lmp, int narg, char **arg) :
// nreplica = number of partitions
// ireplica = which world I am in universe
+ // nprocs_universe = # of procs in all replicase
// procprev,procnext = root proc in adjacent replicas
+ me = comm->me;
+ nprocs = comm->nprocs;
+
+ nprocs_universe = universe->nprocs;
nreplica = universe->nworlds;
ireplica = universe->iworld;
@@ -67,7 +76,17 @@ FixNEB::FixNEB(LAMMPS *lmp, int narg, char **arg) :
modify->add_compute(3,newarg);
delete [] newarg;
+ // initialize local storage
+
+ maxlocal = 0;
+ ntotal = 0;
+
xprev = xnext = tangent = NULL;
+ xsend = xrecv = NULL;
+ tagsend = tagrecv = NULL;
+ xsendall = xrecvall = NULL;
+ tagsendall = tagrecvall = NULL;
+ counts = displacements = NULL;
}
/* ---------------------------------------------------------------------- */
@@ -80,6 +99,19 @@ FixNEB::~FixNEB()
memory->destroy(xprev);
memory->destroy(xnext);
memory->destroy(tangent);
+
+ memory->destroy(xsend);
+ memory->destroy(xrecv);
+ memory->destroy(tagsend);
+ memory->destroy(tagrecv);
+
+ memory->destroy(xsendall);
+ memory->destroy(xrecvall);
+ memory->destroy(tagsendall);
+ memory->destroy(tagrecvall);
+
+ memory->destroy(counts);
+ memory->destroy(displacements);
}
/* ---------------------------------------------------------------------- */
@@ -104,15 +136,35 @@ void FixNEB::init()
rclimber = -1;
- // setup xprev and xnext arrays
+ // nebatoms = # of atoms in fix group = atoms with inter-replica forces
- memory->destroy(xprev);
- memory->destroy(xnext);
- memory->destroy(tangent);
- nebatoms = atom->nlocal;
- memory->create(xprev,nebatoms,3,"neb:xprev");
- memory->create(xnext,nebatoms,3,"neb:xnext");
- memory->create(tangent,nebatoms,3,"neb:tangent");
+ bigint count = group->count(igroup);
+ if (count > MAXSMALLINT) error->all(FLERR,"Too many active NEB atoms");
+ nebatoms = count;
+
+ // comm style for inter-replica exchange of coords
+
+ if (nreplica == nprocs_universe &&
+ nebatoms == atom->natoms && atom->sortfreq == 0)
+ cmode = SINGLE_PROC_DIRECT;
+ else if (nreplica == nprocs_universe) cmode = SINGLE_PROC_MAP;
+ else cmode = MULTI_PROC;
+
+ // ntotal = total # of atoms in system, NEB atoms or not
+
+ if (atom->natoms > MAXSMALLINT) error->all(FLERR,"Too many atoms for NEB");
+ ntotal = atom->natoms;
+
+ if (atom->nlocal > maxlocal) reallocate();
+
+ if (MULTI_PROC && counts == NULL) {
+ memory->create(xsendall,ntotal,3,"neb:xsendall");
+ memory->create(xrecvall,ntotal,3,"neb:xrecvall");
+ memory->create(tagsendall,ntotal,"neb:tagsendall");
+ memory->create(tagrecvall,ntotal,"neb:tagrecvall");
+ memory->create(counts,nprocs,"neb:counts");
+ memory->create(displacements,nprocs,"neb:displacements");
+ }
}
/* ---------------------------------------------------------------------- */
@@ -133,40 +185,31 @@ void FixNEB::min_post_force(int vflag)
double vprev,vnext,vmax,vmin;
double delx,dely,delz;
double delta1[3],delta2[3];
- MPI_Request request;
// veng = PE of this replica
// vprev,vnext = PEs of adjacent replicas
+ // only proc 0 in each replica communicates
vprev = vnext = veng = pe->compute_scalar();
- if (ireplica < nreplica-1) MPI_Send(&veng,1,MPI_DOUBLE,procnext,0,uworld);
- if (ireplica > 0) MPI_Recv(&vprev,1,MPI_DOUBLE,procprev,0,uworld,MPI_STATUS_IGNORE);
+ if (ireplica < nreplica-1 && me == 0)
+ MPI_Send(&veng,1,MPI_DOUBLE,procnext,0,uworld);
+ if (ireplica > 0 && me == 0)
+ MPI_Recv(&vprev,1,MPI_DOUBLE,procprev,0,uworld,MPI_STATUS_IGNORE);
- if (ireplica > 0) MPI_Send(&veng,1,MPI_DOUBLE,procprev,0,uworld);
- if (ireplica < nreplica-1)
+ if (ireplica > 0 && me == 0)
+ MPI_Send(&veng,1,MPI_DOUBLE,procprev,0,uworld);
+ if (ireplica < nreplica-1 && me == 0)
MPI_Recv(&vnext,1,MPI_DOUBLE,procnext,0,uworld,MPI_STATUS_IGNORE);
- // xprev,xnext = atom coords of adjacent replicas
- // assume order of atoms in all replicas is the same
- // check that number of atoms hasn't changed
-
- double **x = atom->x;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
- if (nlocal != nebatoms) error->one(FLERR,"Atom count changed in fix neb");
+ if (cmode == MULTI_PROC) {
+ MPI_Bcast(&vprev,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&vnext,1,MPI_DOUBLE,0,world);
+ }
- if (ireplica > 0)
- MPI_Irecv(xprev[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld,&request);
- if (ireplica < nreplica-1)
- MPI_Send(x[0],3*nlocal,MPI_DOUBLE,procnext,0,uworld);
- if (ireplica > 0) MPI_Wait(&request,MPI_STATUS_IGNORE);
+ // communicate atoms to/from adjacent replicas to fill xprev,xnext
- if (ireplica < nreplica-1)
- MPI_Irecv(xnext[0],3*nlocal,MPI_DOUBLE,procnext,0,uworld,&request);
- if (ireplica > 0)
- MPI_Send(x[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld);
- if (ireplica < nreplica-1) MPI_Wait(&request,MPI_STATUS_IGNORE);
+ inter_replica_comm();
// trigger potential energy computation on next timestep
@@ -175,11 +218,13 @@ void FixNEB::min_post_force(int vflag)
// compute norm of GradV for log output
double **f = atom->f;
+ int nlocal = atom->nlocal;
+
double fsq = 0.0;
for (int i = 0; i < nlocal; i++)
fsq += f[i][0]*f[i][0] + f[i][1]*f[i][1] + f[i][2]*f[i][2];
- MPI_Allreduce(&fsq,&gradvnorm,1,MPI_DOUBLE,MPI_MAX,world);
+ MPI_Allreduce(&fsq,&gradvnorm,1,MPI_DOUBLE,MPI_SUM,world);
gradvnorm = sqrt(gradvnorm);
// first or last replica has no change to forces, just return
@@ -195,6 +240,9 @@ void FixNEB::min_post_force(int vflag)
// depending on relative PEs of 3 replicas
// see Henkelman & Jonsson 2000 paper, eqs 8-11
+ double **x = atom->x;
+ int *mask = atom->mask;
+
if (vnext > veng && veng > vprev) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
@@ -260,9 +308,15 @@ void FixNEB::min_post_force(int vflag)
nlen += delx*delx + dely*dely + delz*delz;
}
- tlen = sqrt(tlen);
- plen = sqrt(plen);
- nlen = sqrt(nlen);
+ double lenall;
+ MPI_Allreduce(&tlen,&lenall,1,MPI_DOUBLE,MPI_SUM,world);
+ tlen = sqrt(lenall);
+
+ MPI_Allreduce(&plen,&lenall,1,MPI_DOUBLE,MPI_SUM,world);
+ plen = sqrt(lenall);
+
+ MPI_Allreduce(&nlen,&lenall,1,MPI_DOUBLE,MPI_SUM,world);
+ nlen = sqrt(lenall);
// normalize tangent vector
@@ -295,9 +349,12 @@ void FixNEB::min_post_force(int vflag)
f[i][2]*tangent[i][2];
}
+ double dotall;
+ MPI_Allreduce(&dot,&dotall,1,MPI_DOUBLE,MPI_SUM,world);
+
double prefactor;
- if (ireplica == rclimber) prefactor = -2.0*dot;
- else prefactor = -dot + kspring*(nlen-plen);
+ if (ireplica == rclimber) prefactor = -2.0*dotall;
+ else prefactor = -dotall + kspring*(nlen-plen);
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
@@ -306,3 +363,222 @@ void FixNEB::min_post_force(int vflag)
f[i][2] += prefactor*tangent[i][2];
}
}
+
+/* ----------------------------------------------------------------------
+ send/recv NEB atoms to/from adjacent replicas
+ received atoms matching my local atoms are stored in xprev,xnext
+ replicas 0 and N-1 send but do not receive any atoms
+------------------------------------------------------------------------- */
+
+void FixNEB::inter_replica_comm()
+{
+ int i,m;
+ MPI_Request request;
+ MPI_Request requests[2];
+ MPI_Status statuses[2];
+
+ // reallocate memory if necessary
+
+ if (atom->nlocal > maxlocal) reallocate();
+
+ double **x = atom->x;
+ tagint *tag = atom->tag;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ // -----------------------------------------------------
+ // 3 cases: two for single proc per replica
+ // one for multiple procs per replica
+ // -----------------------------------------------------
+
+ // single proc per replica
+ // all atoms are NEB atoms and no atom sorting is enabled
+ // direct comm of x -> xprev and x -> xnext
+
+ if (cmode == SINGLE_PROC_DIRECT) {
+ if (ireplica > 0)
+ MPI_Irecv(xprev[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld,&request);
+ if (ireplica < nreplica-1)
+ MPI_Send(x[0],3*nlocal,MPI_DOUBLE,procnext,0,uworld);
+ if (ireplica > 0) MPI_Wait(&request,MPI_STATUS_IGNORE);
+
+ if (ireplica < nreplica-1)
+ MPI_Irecv(xnext[0],3*nlocal,MPI_DOUBLE,procnext,0,uworld,&request);
+ if (ireplica > 0)
+ MPI_Send(x[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld);
+ if (ireplica < nreplica-1) MPI_Wait(&request,MPI_STATUS_IGNORE);
+
+ return;
+ }
+
+ // single proc per replica
+ // but only some atoms are NEB atoms or atom sorting is enabled
+ // send atom IDs and coords of only NEB atoms to prev/next proc
+ // recv proc uses atom->map() to match received coords to owned atoms
+
+ if (cmode == SINGLE_PROC_MAP) {
+ m = 0;
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) {
+ tagsend[m] = tag[i];
+ xsend[m][0] = x[i][0];
+ xsend[m][1] = x[i][1];
+ xsend[m][2] = x[i][2];
+ m++;
+ }
+
+ if (ireplica > 0) {
+ MPI_Irecv(xrecv[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld,&requests[0]);
+ MPI_Irecv(tagrecv,nebatoms,MPI_LMP_TAGINT,procprev,0,uworld,&requests[1]);
+ }
+ if (ireplica < nreplica-1) {
+ MPI_Send(xsend[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld);
+ MPI_Send(tagsend,nebatoms,MPI_LMP_TAGINT,procnext,0,uworld);
+ }
+
+ if (ireplica > 0) {
+ MPI_Waitall(2,requests,statuses);
+ for (i = 0; i < nebatoms; i++) {
+ m = atom->map(tagrecv[i]);
+ xprev[m][0] = xrecv[i][0];
+ xprev[m][1] = xrecv[i][1];
+ xprev[m][2] = xrecv[i][2];
+ }
+ }
+
+ if (ireplica < nreplica-1) {
+ MPI_Irecv(xrecv[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld,&requests[0]);
+ MPI_Irecv(tagrecv,nebatoms,MPI_LMP_TAGINT,procnext,0,uworld,&requests[1]);
+ }
+ if (ireplica > 0) {
+ MPI_Send(xsend[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld);
+ MPI_Send(tagsend,nebatoms,MPI_LMP_TAGINT,procprev,0,uworld);
+ }
+
+ if (ireplica < nreplica-1) {
+ MPI_Waitall(2,requests,statuses);
+ for (i = 0; i < nebatoms; i++) {
+ m = atom->map(tagrecv[i]);
+ xnext[m][0] = xrecv[i][0];
+ xnext[m][1] = xrecv[i][1];
+ xnext[m][2] = xrecv[i][2];
+ }
+ }
+
+ return;
+ }
+
+ // multiple procs per replica
+ // MPI_Gather all coords and atom IDs to root proc of each replica
+ // send to root of adjacent replicas
+ // bcast within each replica
+ // each proc extracts info for atoms it owns via atom->map()
+
+ m = 0;
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) {
+ tagsend[m] = tag[i];
+ xsend[m][0] = x[i][0];
+ xsend[m][1] = x[i][1];
+ xsend[m][2] = x[i][2];
+ m++;
+ }
+
+ MPI_Gather(&m,1,MPI_INT,counts,1,MPI_INT,0,world);
+ displacements[0] = 0;
+ for (i = 0; i < nprocs-1; i++)
+ displacements[i+1] = displacements[i] + counts[i];
+ MPI_Gatherv(tagsend,m,MPI_LMP_TAGINT,
+ tagsendall,counts,displacements,MPI_LMP_TAGINT,0,world);
+ for (i = 0; i < nprocs; i++) counts[i] *= 3;
+ for (i = 0; i < nprocs-1; i++)
+ displacements[i+1] = displacements[i] + counts[i];
+ if (xsend)
+ MPI_Gatherv(xsend[0],3*m,MPI_DOUBLE,
+ xsendall[0],counts,displacements,MPI_DOUBLE,0,world);
+ else
+ MPI_Gatherv(NULL,3*m,MPI_DOUBLE,
+ xsendall[0],counts,displacements,MPI_DOUBLE,0,world);
+
+ if (ireplica > 0 && me == 0) {
+ MPI_Irecv(xrecvall[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld,&requests[0]);
+ MPI_Irecv(tagrecvall,nebatoms,MPI_LMP_TAGINT,procprev,0,uworld,
+ &requests[1]);
+ }
+ if (ireplica < nreplica-1 && me == 0) {
+ MPI_Send(xsendall[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld);
+ MPI_Send(tagsendall,nebatoms,MPI_LMP_TAGINT,procnext,0,uworld);
+ }
+
+ if (ireplica > 0) {
+ if (me == 0) MPI_Waitall(2,requests,statuses);
+
+ MPI_Bcast(tagrecvall,nebatoms,MPI_INT,0,world);
+ MPI_Bcast(xrecvall[0],3*nebatoms,MPI_DOUBLE,0,world);
+
+ for (i = 0; i < nebatoms; i++) {
+ m = atom->map(tagrecvall[i]);
+ if (m < 0 || m >= nlocal) continue;
+ xprev[m][0] = xrecvall[i][0];
+ xprev[m][1] = xrecvall[i][1];
+ xprev[m][2] = xrecvall[i][2];
+ }
+ }
+
+ if (ireplica < nreplica-1 && me == 0) {
+ MPI_Irecv(xrecvall[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld,&requests[0]);
+ MPI_Irecv(tagrecvall,nebatoms,MPI_LMP_TAGINT,procnext,0,uworld,
+ &requests[1]);
+ }
+ if (ireplica > 0 && me == 0) {
+ MPI_Send(xsendall[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld);
+ MPI_Send(tagsendall,nebatoms,MPI_LMP_TAGINT,procprev,0,uworld);
+ }
+
+ if (ireplica < nreplica-1) {
+ if (me == 0) MPI_Waitall(2,requests,statuses);
+
+ MPI_Bcast(tagrecvall,nebatoms,MPI_INT,0,world);
+ MPI_Bcast(xrecvall[0],3*nebatoms,MPI_DOUBLE,0,world);
+
+ for (i = 0; i < nebatoms; i++) {
+ m = atom->map(tagrecvall[i]);
+ if (m < 0 || m >= nlocal) continue;
+ xnext[m][0] = xrecvall[i][0];
+ xnext[m][1] = xrecvall[i][1];
+ xnext[m][2] = xrecvall[i][2];
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ reallocate xprev,xnext,tangent arrays if necessary
+ reallocate communication arrays if necessary
+------------------------------------------------------------------------- */
+
+void FixNEB::reallocate()
+{
+ memory->destroy(xprev);
+ memory->destroy(xnext);
+ memory->destroy(tangent);
+
+ if (cmode != SINGLE_PROC_DIRECT) {
+ memory->destroy(xsend);
+ memory->destroy(xrecv);
+ memory->destroy(tagsend);
+ memory->destroy(tagrecv);
+ }
+
+ maxlocal = atom->nmax;
+
+ memory->create(xprev,maxlocal,3,"neb:xprev");
+ memory->create(xnext,maxlocal,3,"neb:xnext");
+ memory->create(tangent,maxlocal,3,"neb:tangent");
+
+ if (cmode != SINGLE_PROC_DIRECT) {
+ memory->create(xsend,maxlocal,3,"neb:xsend");
+ memory->create(xrecv,maxlocal,3,"neb:xrecv");
+ memory->create(tagsend,maxlocal,"neb:tagsend");
+ memory->create(tagrecv,maxlocal,"neb:tagrecv");
+ }
+}
diff --git a/src/REPLICA/fix_neb.h b/src/REPLICA/fix_neb.h
index 39bb5dc81f..4026f84f15 100644
--- a/src/REPLICA/fix_neb.h
+++ b/src/REPLICA/fix_neb.h
@@ -38,17 +38,34 @@ class FixNEB : public Fix {
void min_post_force(int);
private:
+ int me,nprocs,nprocs_universe;
double kspring;
int ireplica,nreplica;
int procnext,procprev;
+ int cmode;
MPI_Comm uworld;
char *id_pe;
class Compute *pe;
- int nebatoms;
- double **xprev,**xnext;
- double **tangent;
+ int nebatoms; // # of active NEB atoms
+ int ntotal; // total # of atoms, NEB or not
+ int maxlocal; // size of xprev,xnext,tangent arrays
+
+ double **xprev,**xnext; // coords of my owned atoms in neighbor replicas
+ double **tangent; // work vector for inter-replica forces
+
+ double **xsend,**xrecv; // coords to send/recv to/from other replica
+ tagint *tagsend,*tagrecv; // ditto for atom IDs
+
+ // info gathered from all procs in my replica
+ double **xsendall,**xrecvall; // coords to send/recv to/from other replica
+ tagint *tagsendall,*tagrecvall; // ditto for atom IDs
+
+ int *counts,*displacements; // used for MPI_Gather
+
+ void inter_replica_comm();
+ void reallocate();
};
}
diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp
index 3677c834a6..03bd0b61e1 100644
--- a/src/REPLICA/neb.cpp
+++ b/src/REPLICA/neb.cpp
@@ -137,10 +137,6 @@ void NEB::command(int narg, char **arg)
// error checks
if (nreplica == 1) error->all(FLERR,"Cannot use NEB with a single replica");
- if (nreplica != universe->nprocs)
- error->all(FLERR,"Can only use NEB with 1-processor replicas");
- if (atom->sortfreq > 0)
- error->all(FLERR,"Cannot use NEB with atom_modify sort enabled");
if (atom->map_style == 0)
error->all(FLERR,"Cannot use NEB unless atom map exists");
@@ -531,7 +527,7 @@ void NEB::open(char *file)
/* ----------------------------------------------------------------------
query fix NEB for info on each replica
- proc 0 prints current NEB status
+ universe proc 0 prints current NEB status
------------------------------------------------------------------------- */
void NEB::print_status()
@@ -552,6 +548,7 @@ void NEB::print_status()
if (output->thermo->normflag) one[0] /= atom->natoms;
if (me == 0)
MPI_Allgather(one,nall,MPI_DOUBLE,&all[0][0],nall,MPI_DOUBLE,roots);
+ MPI_Bcast(&all[0][0],nall*nreplica,MPI_DOUBLE,0,world);
rdist[0] = 0.0;
for (int i = 1; i < nreplica; i++)
diff --git a/src/version.h b/src/version.h
index 62ae64bc16..40ef405c35 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "27 Sep 2016"
+#define LAMMPS_VERSION "28 Sep 2016"
--
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