Merge pull request #533 from lammps/user-intel

Updates for USER-INTEL package and NEB command flags/docs updates and issues

doc/src/Section_commands.txt

@@ -964,7 +964,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "lj/expand (gko)"_pair_lj_expand.html,
 "lj/gromacs (gko)"_pair_gromacs.html,
 "lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
-"lj/long/coul/long (o)"_pair_lj_long.html,
+"lj/long/coul/long (io)"_pair_lj_long.html,
 "lj/long/dipole/long"_pair_dipole.html,
 "lj/long/tip4p/long"_pair_lj_long.html,
 "lj/smooth (o)"_pair_lj_smooth.html,
@@ -1225,7 +1225,7 @@ USER-OMP, t = OPT.
 "msm/cg (o)"_kspace_style.html,
 "pppm (go)"_kspace_style.html,
 "pppm/cg (o)"_kspace_style.html,
-"pppm/disp"_kspace_style.html,
+"pppm/disp (i)"_kspace_style.html,
 "pppm/disp/tip4p"_kspace_style.html,
 "pppm/stagger"_kspace_style.html,
 "pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)

doc/src/accelerate_intel.txt

@@ -30,8 +30,8 @@ Dihedral Styles: charmm, harmonic, opls :l
 Fixes: nve, npt, nvt, nvt/sllod :l
 Improper Styles: cvff, harmonic :l
 Pair Styles: buck/coul/cut, buck/coul/long, buck, eam, gayberne,
-charmm/coul/long, lj/cut, lj/cut/coul/long, sw, tersoff :l
-K-Space Styles: pppm :l
+charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, sw, tersoff :l
+K-Space Styles: pppm, pppm/disp :l
 :ule
 
 [Speed-ups to expect:]
@@ -42,62 +42,88 @@ precision mode. Performance improvements are shown compared to
 LAMMPS {without using other acceleration packages} as these are
 under active development (and subject to performance changes). The
 measurements were performed using the input files available in
-the src/USER-INTEL/TEST directory. These are scalable in size; the
-results given are with 512K particles (524K for Liquid Crystal).
-Most of the simulations are standard LAMMPS benchmarks (indicated
-by the filename extension in parenthesis) with modifications to the
-run length and to add a warmup run (for use with offload
-benchmarks).
+the src/USER-INTEL/TEST directory with the provided run script. 
+These are scalable in size; the results given are with 512K 
+particles (524K for Liquid Crystal). Most of the simulations are 
+standard LAMMPS benchmarks (indicated by the filename extension in
+parenthesis) with modifications to the run length and to add a 
+warmup run (for use with offload benchmarks).
 
 :c,image(JPG/user_intel.png)
 
 Results are speedups obtained on Intel Xeon E5-2697v4 processors
 (code-named Broadwell) and Intel Xeon Phi 7250 processors
-(code-named Knights Landing) with "18 Jun 2016" LAMMPS built with
-Intel Parallel Studio 2016 update 3. Results are with 1 MPI task
+(code-named Knights Landing) with "June 2017" LAMMPS built with
+Intel Parallel Studio 2017 update 2. Results are with 1 MPI task
 per physical core. See {src/USER-INTEL/TEST/README} for the raw
 simulation rates and instructions to reproduce.
 
 :line
 
+[Accuracy and order of operations:]
+
+In most molecular dynamics software, parallelization parameters
+(# of MPI, OpenMP, and vectorization) can change the results due
+to changing the order of operations with finite-precision 
+calculations. The USER-INTEL package is deterministic. This means
+that the results should be reproducible from run to run with the
+{same} parallel configurations and when using determinstic 
+libraries or library settings (MPI, OpenMP, FFT). However, there
+are differences in the USER-INTEL package that can change the
+order of operations compared to LAMMPS without acceleration:
+
+Neighbor lists can be created in a different order :ulb,l
+Bins used for sorting atoms can be oriented differently :l
+The default stencil order for PPPM is 7. By default, LAMMPS will 
+calculate other PPPM parameters to fit the desired acuracy with 
+this order :l
+The {newton} setting applies to all atoms, not just atoms shared
+between MPI tasks :l
+Vectorization can change the order for adding pairwise forces :l
+:ule
+
+The precision mode (described below) used with the USER-INTEL 
+package can change the {accuracy} of the calculations. For the 
+default {mixed} precision option, calculations between pairs or 
+triplets of atoms are performed in single precision, intended to 
+be within the inherent error of MD simulations. All accumulation
+is performed in double precision to prevent the error from growing 
+with the number of atoms in the simulation. {Single} precision
+mode should not be used without appropriate validation.
+
+:line
+
 [Quick Start for Experienced Users:]
 
 LAMMPS should be built with the USER-INTEL package installed.
 Simulations should be run with 1 MPI task per physical {core},
 not {hardware thread}.
 
-For Intel Xeon CPUs:
-
 Edit src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi as necessary. :ulb,l
-If using {kspace_style pppm} in the input script, add "neigh_modify binsize cutoff" and "kspace_modify diff ad" to the input script for better
-performance.  Cutoff should be roughly the neighbor list cutoff.  By
-default the binsize is half the neighbor list cutoff.  :l
-"-pk intel 0 omp 2 -sf intel" added to LAMMPS command-line :l
+Set the environment variable KMP_BLOCKTIME=0 :l
+"-pk intel 0 omp $t -sf intel" added to LAMMPS command-line :l
+$t should be 2 for Intel Xeon CPUs and 2 or 4 for Intel Xeon Phi :l
+For some of the simple 2-body potentials without long-range
+electrostatics, performance and scalability can be better with
+the "newton off" setting added to the input script :l
+If using {kspace_style pppm} in the input script, add 
+"kspace_modify diff ad" for better performance :l
 :ule
 
-For Intel Xeon Phi CPUs for simulations without {kspace_style
-pppm} in the input script :
+For Intel Xeon Phi CPUs:
 
-Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l
-Runs should be performed using MCDRAM. :l
-"-pk intel 0 omp 2 -sf intel" {or} "-pk intel 0 omp 4 -sf intel"
-should be added to the LAMMPS command-line. Choice for best
-performance will depend on the simulation. :l
+Runs should be performed using MCDRAM. :ulb,l
 :ule
 
-For Intel Xeon Phi CPUs for simulations with {kspace_style
-pppm} in the input script:
-
-Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l
-Runs should be performed using MCDRAM. :l
-Add "neigh_modify binsize 3" to the input script for better
-performance. :l
-Add "kspace_modify diff ad" to the input script for better
-performance. :l
-export KMP_AFFINITY=none :l
-"-pk intel 0 omp 3 lrt yes -sf intel" or "-pk intel 0 omp 1 lrt yes
--sf intel" added to LAMMPS command-line. Choice for best performance
-will depend on the simulation. :l
+For simulations using {kspace_style pppm} on Intel CPUs 
+supporting AVX-512:
+
+Add "kspace_modify diff ad" to the input script :ulb,l
+The command-line option should be changed to 
+"-pk intel 0 omp $r lrt yes -sf intel" where $r is the number of 
+threads minus 1. :l
+Do not use thread affinity (set KMP_AFFINITY=none) :l
+The "newton off" setting may provide better scalability :l
 :ule
 
 For Intel Xeon Phi coprocessors (Offload):
@@ -169,6 +195,10 @@ cat /proc/cpuinfo :pre
 
 [Building LAMMPS with the USER-INTEL package:]
 
+NOTE: See the src/USER-INTEL/README file for additional flags that
+might be needed for best performance on Intel server processors
+code-named "Skylake".
+
 The USER-INTEL package must be installed into the source directory:
 
 make yes-user-intel :pre
@@ -322,8 +352,8 @@ follow in the input script.
 
 NOTE: The USER-INTEL package will perform better with modifications
 to the input script when "PPPM"_kspace_style.html is used:
-"kspace_modify diff ad"_kspace_modify.html and "neigh_modify binsize
-3"_neigh_modify.html should be added to the input script.
+"kspace_modify diff ad"_kspace_modify.html should be added to the 
+input script.
 
 Long-Range Thread (LRT) mode is an option to the "package
 intel"_package.html command that can improve performance when using
@@ -342,6 +372,10 @@ would normally perform best with "-pk intel 0 omp 4", instead use
 environment variable "KMP_AFFINITY=none". LRT mode is not supported
 when using offload.
 
+NOTE: Changing the "newton"_newton.html setting to off can improve
+performance and/or scalability for simple 2-body potentials such as
+lj/cut or when using LRT mode on processors supporting AVX-512.
+
 Not all styles are supported in the USER-INTEL package. You can mix
 the USER-INTEL package with styles from the "OPT"_accelerate_opt.html
 package or the "USER-OMP package"_accelerate_omp.html. Of course,
@@ -467,7 +501,7 @@ supported.
 
 Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l
 
-Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. 2016 International Conference for High Performance Computing. In press. :l
+Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. "Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency."_http://dl.acm.org/citation.cfm?id=3014915 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95). :l
 
 Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101. :l
 :ule

doc/src/fix_neb.txt

@@ -14,152 +14,177 @@ fix ID group-ID neb Kspring keyword value :pre
 
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 neb = style name of this fix command :l
-Kspring = parallel spring constant (force/distance units or force units) :l
+Kspring = parallel spring constant (force/distance units or force units, see nudge keyword) :l
 zero or more keyword/value pairs may be appended :l
-keyword = {nudg_style} or {perp} or {freend} or {freend_k_spring} :l
-  {nudg_style} value = {neigh} or {idealpos}
-    {neigh} = the parallel nudging force is calculated from the distances to neighbouring replicas (in this case, Kspring is in force/distance units)
-    {idealpos} = the parallel nudging force is proportional to the distance between the replica and its interpolated ideal position (in this case Kspring is in force units)
-  {perp} value {none} or kspring2
-    {none} = no perpendicular spring force is applied
-    {kspring2} = spring constant for the perpendicular nudging force (in force/distance units)
-  {freeend} value = {none} or {ini} or {final} or {finaleini} or {final2eini}
-    {none} = no nudging force is applied to the first and last replicas
-    {ini} = set the first replica to be a free end 
-    {final} = set the last replica to be a free end
-    {finaleini} = set the last replica to be a free end and set its target energy as that of the first replica
-    {final2eini} = same as {finaleini} plus prevent intermediate replicas to have a lower energy than the first replica
-  {freeend_kspring}  value = kspring3
-    kspring3 = spring constant of the perpendicular spring force (per distance units)    
-   :pre
+keyword = {nudge} or {perp} or {ends} :l
+  {nudge} value = {neigh} or {ideal}
+    {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)
+  {perp} value = {Kspring2}
+    {Kspring2} = spring constant for perpendicular nudging force (force/distance units)
+  {end} values = estyle Kspring3
+    {estyle} = {first} or {last} or {last/efirst} or {last/efirst/middle}
+      {first} = apply force to first replica
+      {last} = apply force to last replica
+      {last/efirst} = apply force to last replica and set its target energy to that of first replica
+      {last/efirst/middle} = same as {last/efirst} plus prevent middle replicas having lower energy than first replica
+    {Kspring3} = spring constant for target energy term (1/distance units) :pre
 
 [Examples:]
 
 fix 1 active neb 10.0
-fix 2 all neb 1.0 perp 1.0 freeend final
-fix 1 all neb 1.0 nudg_style idealpos freeend final2eini freend_kspring 1:pre
+fix 2 all neb 1.0 perp 1.0 end last
+fix 2 all neb 1.0 perp 1.0 end first 1.0 end last 1.0
+fix 1 all neb 1.0 nudge ideal end last/efirst 1 :pre
 
 [Description:]
 
-Add a nudging force to atoms in the group for a multi-replica
+Add nudging forces to atoms in the group for a multi-replica
 simulation run via the "neb"_neb.html command to perform a nudged
 elastic band (NEB) calculation for finding the transition state.
 Hi-level explanations of NEB are given with the "neb"_neb.html command
 and in "Section_howto 5"_Section_howto.html#howto_5 of the manual.
 The fix neb command must be used with the "neb" command and defines
-how nudging inter-replica forces are computed.  A NEB calculation is
+how inter-replica nudging forces are computed.  A NEB calculation is
 divided in two stages. In the first stage n replicas are relaxed
-toward a MEP and in a second stage, the climbing image scheme (see
-"(Henkelman2)"_#Henkelman2) is turned on so that the replica having
-the highest energy relaxes toward the saddle point (i.e. the point of
-highest energy along the MEP).
-
-One purpose of the nudging forces is to keep the replicas equally
-spaced.  During the NEB, the 3N-length vector of interatomic force Fi
-= -Grad(V) of replicas i is altered. For all intermediate replicas
-(i.e. for 1<i<n) but the climbing replica the force vector
-becomes:
-
-Fi = -Grad(V) + (Grad(V) dot That) That + Fnudgparallel + Fspringperp :pre
-
-That is the unit "tangent" vector for replica i and is a function of
-Ri, Ri-1, Ri+1, and the potential energy of the 3 replicas; it points
-roughly in the direction of (Ri+i - Ri-1) (see the
-"(Henkelman1)"_#Henkelman1 paper for details).  Ri are the atomic
-coordinates of replica i; Ri-1 and Ri+1 are the coordinates of its
-neighbor replicas.  The term (Grad(V) dot That) is used to remove the
+toward a MEP until convergence.  In the second stage, the climbing
+image scheme (see "(Henkelman2)"_#Henkelman2) is enabled, so that the
+replica having the highest energy relaxes toward the saddle point
+(i.e. the point of highest energy along the MEP), and a second
+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:
+
+Fi = -Grad(V) + (Grad(V) dot T') T' + Fnudge_parallel + Fspring_perp :pre
+
+T' is the unit "tangent" vector for replica I and is a function of Ri,
+Ri-1, Ri+1, and the potential energy of the 3 replicas; it points
+roughly in the direction of (Ri+i - Ri-1); see the
+"(Henkelman1)"_#Henkelman1 paper for details.  Ri gives the atomic
+coordinates of replica I; Ri-1 and Ri+1 are the coordinates of its
+neighbor replicas.  The term (Grad(V) dot T') is used to remove the
 component of the gradient parallel to the path which would tend to
-distribute the replica unevenly along the path.  Fnudgparallel is an
-artificial nudging force which is applied only in the tangent direction
-and which maintains the replicas equally spaced (see below for more
-information).  Fspringperp is an optinal artificial spring which is
-applied only perpendicular to the tangent and which prevent the paths
-from forming too acute kinks (see below for more information).
-
-The keyword {nudg_style} allow to specify how to parallel
-nudging force is computed. With a value of idealpos, the spring 
-force is computed as suggested in "(E)"_#E :
-   
-Fnudgparallel=-{Kspring}* (RD-RDideal)/(2 meanDist) :pre
-
-where RD is the "reaction coordinate" see "neb"_neb.html section, and
-RDideal is the ideal RD for which all the images are equally spaced
-(i.e. RDideal = (i-1)*meanDist when the climbing image is off, where i
-is the replica number). The meanDist is the average distance between
-replicas.
+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).  Fspring_perp is an optional artificial
+spring which is applied only perpendicular to the tangent and which
+prevent the paths from forming acute kinks (see below for more
+information).
 
-When {nudg_style} has a value of neigh (or by default), the parallel 
-nudging force is computed as in "(Henkelman1)"_#Henkelman1 by 
-connecting each intermediate replica with the previous and the next 
-image:
+In the second stage of the NEB calculation, the interatomic force Fi
+for the climbing replica (the replica of highest energy after the
+first stage) is changed to:
 
-Fnudgparallel= {Kspring}* (|Ri+1 - Ri| - |Ri - Ri-1|) :pre
+Fi = -Grad(V) + 2 (Grad(V) dot T') T' :pre
 
-The parallel nudging force associated with the key word idealpos should
-usually be more efficient at keeping the images equally spaced.
+and the relaxation procedure is continued to a new converged MEP.
 
 :line
 
-The keyword {perp} allows to add a spring force perpendicular to the
-path in order to prevent the path from becoming too kinky. It can
-improve significantly the convergence of the NEB when the resolution
-is poor (i.e. when too few images are used) (see "(Maras)"_#Maras1).
-The perpendicular spring force is given by
+The keyword {nudge} specifies how the parallel nudging force is
+computed.  With a value of {neigh}, the parallel nudging force is
+computed as in "(Henkelman1)"_#Henkelman1 by connecting each
+intermediate replica with the previous and the next image:
+
+Fnudge_parallel = {Kspring} * (|Ri+1 - Ri| - |Ri - Ri-1|) :pre
+
+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
+"(WeinenE)"_#WeinenE :
+   
+Fnudge_parallel = -{Kspring} * (RD-RDideal) / (2 * meanDist) :pre
 
-Fspringperp = {Kspringperp} * f(Ri-1,Ri,Ri+1) (Ri+1 + Ri-1 - 2 Ri) :pre
+where RD is the "reaction coordinate" see "neb"_neb.html 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.
 
-f(Ri-1 Ri R+1) is a smooth scalar function of the angle Ri-1 Ri
-Ri+1. It is equal to 0 when the path is straight and is equal to 1
-when the angle Ri-1 Ri Ri+1 is accute. f(Ri-1 Ri R+1) is defined in
-"(Jonsson)"_#Jonsson
+Note that the {ideal} form of nudging can often be more effective at
+keeping the replicas equally spaced.
 
 :line
 
-By default, the force acting on the first and last replicas is not
-altered so that during the NEB relaxation, these ending replicas relax
-toward local minima. However it is possible to use the key word
-{freeend} to allow either the initial or the final replica to relax
-toward a MEP while constraining its energy.  The interatomic force Fi
-for the free end image becomes :
+The keyword {perp} adds a spring force perpendicular to the path in
+order to prevent the path from becoming too kinky. It
+can significantly improve the convergence of the NEB calculation when
+the resolution is poor.  I.e. when too few replicas are used; see
+"(Maras)"_#Maras1 for details.
 
-Fi = -Grad(V)+ (Grad(V) dot That + (E-ETarget)*kspring3) That,  {when} Grad(V) dot That < 0
-Fi = -Grad(V)+ (Grad(V) dot That + (ETarget- E)*kspring3) That, {when} Grad(V) dot That > 0
-:pre
+The perpendicular spring force is given by
 
-where E is the energy of the free end replica and ETarget is the
-target energy.
-
-When the value {ini} ({final}) is used after the keyword {freeend},
-the first (last) replica is considered as a free end. The target
-energy is set to the energy of the replica at starting of the NEB
-calculation. When the value {finaleini} or {final2eini} is used the
-last image is considered as a free end and the target energy is equal
-to the energy of the first replica (which can evolve during the NEB
-relaxation).  With the value {finaleini}, when the initial path is too
-far from the MEP, an intermediate repilica might relax "faster" and
-get a lower energy than the last replica. The benefit of the free end
-is then lost since this intermediate replica will relax toward a local
-minima. This behavior can be prevented by using the value {final2eini}
-which remove entirely the contribution of the gradient for all
-intermediate replica which have a lower energy than the initial one
-thus preventing these replicae to over-relax.  After converging a NEB
-with the {final2eini} value it is recommended to check that all
-intermediate replica have a larger energy than the initial
-replica. Finally note that if the last replica converges toward a
-local minimum with a larger energy than the energy of the first
-replica, a free end neb calculation with the value {finaleini} or
-{final2eini} cannot reach the convergence criteria.
+Fspring_perp = {Kspring2} * F(Ri-1,Ri,Ri+1) (Ri+1 + Ri-1 - 2 Ri) :pre
 
-:line
+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 "(Jonsson)"_#Jonsson.
 
+If {Kspring2} is set to 0.0 (the default) then no perpendicular spring
+force is added.
 
+:line
 
-In the second stage of the NEB, the interatomic force Fi for the
-climbing replica (which is the replica of highest energy) becomes:
+By default, no nudging forces act on the first and last replicas during 
+the NEB relaxation, so these replicas simply relax toward their 
+respective local minima.  By using the key word {end}, additional forces 
+can be applied to the first or last replica, to enable them to relax 
+toward a MEP while constraining their energy.
 
-Fi = -Grad(V) + 2 (Grad(V) dot That) That :pre
+The interatomic force Fi for the specified replica becomes:
 
+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
+:pre
 
+where E is the current energy of the replica and ETarget is the target
+energy.  The "spring" constant on the difference in energies is the
+specified {Kspring3} value.
+
+When {estyle} is specified as {first}, the force is applied to the
+first replica.  When {estyle} is specified as {last}, the force is
+applied to the last replica.  Note that the {end} keyword can be used
+twice to add forces to both the first and last replicas.
+
+For both these {estyle} settings, the target energy {ETarget} is set
+to the initial energy of the replica (at the start of the NEB
+calculation).
+
+If the {estyle} is specified as {last/efirst} or {last/efirst/middle},
+force is applied to the last replica, but the target energy {ETarget}
+is continuously set to the energy of the first replica, as it evolves
+during the NEB relaxation.
+
+The difference between these two {estyle} options is as follows.  When
+{estyle} is specified as {last/efirst}, no change is made to the
+inter-replica force applied to the intermediate replicas (neither
+first or last).  If the initial path is too far from the MEP, an
+intermediate repilica may relax "faster" and reach a lower energy than
+the last replica.  In this case the intermediate replica will be
+relaxing toward its own local minima.  This behavior can be prevented
+by specifying {estyle} as {last/efirst/middle} which will alter the
+inter-replica force applied to intermediate replicas by removing the
+contribution of the gradient to the inter-replica force.  This will
+only be done if a particular intermediate replica has a lower energy
+than the first replica.  This should effectively prevent the
+intermediate replicas from over-relaxing.
+
+After converging a NEB calculation using an {estyle} of {last/efirst/middle},
+you should check that all intermediate replicas have a larger energy than the
+first replica. If this is not the case, the path is probably not a MEP.
+
+Finally, note that if the last replica converges toward a local
+minimum which has a larger energy than the energy of the first
+replica, a NEB calculation using an {estyle} of {last/efirst} or
+{last/efirst/middle} cannot reach final convergence.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
@@ -186,7 +211,8 @@ for more info on packages.
 
 [Default:]
 
-The option defaults are nudg_style = neigh, perp = none, freeend = none and freend_kspring = 1.
+The option defaults are nudge = neigh, perp = 0.0, ends is not
+specified (no inter-replica force on the end replicas).
 
 :line
 
@@ -197,14 +223,14 @@ The option defaults are nudg_style = neigh, perp = none, freeend = none and free
 [(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
 9901-9904 (2000).
 
-:link(E)
-[(E)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002)
+:link(WeinenE)
+[(WeinenE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).
 
 :link(Jonsson)
 [(Jonsson)] Jonsson, Mills and Jacobsen, in Classical and Quantum
-Dynamics in Condensed Phase Simulations, edited by Berne, Ciccotti, and Coker
-World Scientific, Singapore, 1998, p. 385
+Dynamics in Condensed Phase Simulations, edited by Berne, Ciccotti,
+and Coker World Scientific, Singapore, 1998, p 385.
 
 :link(Maras1)
 [(Maras)] Maras, Trushin, Stukowski, Ala-Nissila, Jonsson,
-Comp Phys Comm, 205, 13-21 (2016)
+Comp Phys Comm, 205, 13-21 (2016).

doc/src/kspace_modify.txt

@@ -308,7 +308,8 @@ The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp =
 gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust =
 yes (MSM), pressure/scalar = yes (MSM), fftbench = yes (PPPM), diff = ik
 (PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace = -1.0,
-split = 0, tol = 1.0e-6, and disp/auto = no.
+split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel, order =
+order/disp = 7.
 
 :line
 

doc/src/kspace_style.txt

@@ -33,12 +33,16 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg}
     accuracy = desired relative error in forces
   {pppm/gpu} value = accuracy
     accuracy = desired relative error in forces
+  {pppm/intel} value = accuracy
+    accuracy = desired relative error in forces
   {pppm/kk} value = accuracy
     accuracy = desired relative error in forces
   {pppm/omp} value = accuracy
     accuracy = desired relative error in forces
   {pppm/cg/omp} value = accuracy
     accuracy = desired relative error in forces
+  {pppm/disp/intel} value = accuracy
+    accuracy = desired relative error in forces
   {pppm/tip4p/omp} value = accuracy
     accuracy = desired relative error in forces
   {pppm/stagger} value = accuracy

doc/src/pair_lj_long.txt

@@ -7,6 +7,7 @@
 :line
 
 pair_style lj/long/coul/long command :h3
+pair_style lj/long/coul/long/intel command :h3
 pair_style lj/long/coul/long/omp command :h3
 pair_style lj/long/coul/long/opt command :h3
 pair_style lj/long/tip4p/long command :h3

doc/src/pair_lj_smooth_linear.txt

@@ -104,3 +104,8 @@ This pair style can only be used via the {pair} keyword of the
 "pair_coeff"_pair_coeff.html, "pair lj/smooth"_pair_lj_smooth.html
 
 [Default:] none
+
+:line
+
+:link(Toxvaerd)
+[(Toxvaerd)] Toxvaerd, Dyre, J Chem Phys, 134, 081102 (2011).

examples/neb/README

@@ -2,12 +2,12 @@ Run these examples as:
 
 mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1
 mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop2
-mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1freeend
+mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1.end
 mpirun -np 3 lmp_g++ -partition 3x1 -in in.neb.sivac
 
 mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1
 mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop2
-mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1freeend
+mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1.end
 mpirun -np 6 lmp_g++ -partition 3x2 -in in.neb.sivac
 mpirun -np 9 lmp_g++ -partition 3x3 -in in.neb.sivac
 

examples/neb/in.neb.hop1

@@ -51,7 +51,7 @@ set		group nebatoms type 3
 group		nonneb subtract all nebatoms
 
 fix		1 lower setforce 0.0 0.0 0.0
-fix		2 nebatoms neb 1.0 nudg_style idealpos
+fix		2 nebatoms neb 1.0 #nudge ideal
 fix		3 all enforce2d
 
 thermo		100

examples/neb/in.neb.hop1freeend → examples/neb/in.neb.hop1.end

@@ -15,7 +15,7 @@ variable	u uloop 20
 lattice		hex 0.9
 region		box block 0 20 0 10 -0.25 0.25
 
-read_data        initial.hop1freeend
+read_data        initial.hop1.end
 
 # LJ potentials
 
@@ -41,7 +41,7 @@ set		group nebatoms type 3
 group		nonneb subtract all nebatoms
 
 fix		1 lower setforce 0.0 0.0 0.0
-fix		2 nebatoms neb 1.0 nudg_style idealpos freeend ini
+fix		2 nebatoms neb 1.0 nudge ideal end first 1.0
 fix		3 all enforce2d
 
 thermo		100

examples/neb/in.neb.hop2

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

examples/neb/log.19June17.neb.hop1.end.g++.4

+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 

examples/neb/log.19June17.neb.hop1.end.g++.8

+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 

examples/neb/log.5Oct16.neb.hop1.g++.4 → examples/neb/log.19June17.neb.hop1.g++.4

-LAMMPS (5 Oct 2016)
+LAMMPS (19 May 2017)
 Running on 4 partitions of processors
 Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
-0    4327.2753    2746.3378    0.3387091    5.0075576    4514.5424   0.42933428   0.42323635    1.8941131            0   -3.0535948   0.33333333   -2.6242605   0.66666667   -2.7623811            1   -3.0474969 
-100   0.10482184  0.085218486  0.014588241  0.066178594   0.19602237 0.0070900402 0.0022691875    2.3031875            0   -3.0535967   0.31839181   -3.0473647   0.63987598   -3.0465067            1   -3.0487759 
-111  0.096708467   0.07803707  0.013922973   0.05417562    0.2023467 0.0070871172 0.0022668002    2.3052945            0   -3.0535968   0.31853431   -3.0473633   0.64178871   -3.0465096            1   -3.0487764 
+0    4327.2753    2746.3378  0.082169072    4.9967651    4514.5424   0.42933428   0.42323635    1.8941131            0   -3.0535948   0.33333333   -2.6242605   0.66666667   -2.7623811            1   -3.0474969 
+100   0.10482184  0.085218486 0.0051952047   0.04785954   0.19041553 0.0070900402 0.0022691875    2.3031875            0   -3.0535967   0.31839181   -3.0473647   0.63987598   -3.0465067            1   -3.0487759 
+111  0.096708467   0.07803707 0.0048656875   0.03613038   0.19671332 0.0070871172 0.0022668002    2.3052945            0   -3.0535968   0.31853431   -3.0473633   0.64178871   -3.0465096            1   -3.0487764 
 Climbing replica = 3
 Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
-111    0.2023467    0.1777038  0.013922973   0.05417562    0.2023467 0.0070871172 0.0022668002    2.3052945            0   -3.0535968   0.31853431   -3.0473633   0.64178871   -3.0465096            1   -3.0487764 
-179  0.096874474  0.090676856   0.01040177  0.023364005  0.096874474 0.0071047642 0.0022856172    2.3122768            0   -3.0535969   0.31577311   -3.0473955   0.61798541   -3.0464922            1   -3.0487778 
+111    0.2023467    0.1777038 0.0048656875   0.03613038   0.19671332 0.0070871172 0.0022668002    2.3052945            0   -3.0535968   0.31853431   -3.0473633   0.64178871   -3.0465096            1   -3.0487764 
+179  0.096874474  0.090676856 0.0034851031 0.0094134782  0.093630619 0.0071047642 0.0022856172    2.3122768            0   -3.0535969   0.31577311   -3.0473955   0.61798541   -3.0464922            1   -3.0487778 

examples/neb/log.5Oct16.neb.hop1.g++.8 → examples/neb/log.19June17.neb.hop1.g++.8

-LAMMPS (5 Oct 2016)
+LAMMPS (19 May 2017)
 Running on 4 partitions of processors
 Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
-0    4327.2753    2746.3378    0.3387091    5.0075576    4514.5424   0.42933428   0.42323635    1.8941131            0   -3.0535948   0.33333333   -2.6242605   0.66666667   -2.7623811            1   -3.0474969 
-100   0.10482171  0.085218406  0.014588234  0.066178435   0.19602242 0.0070900401 0.0022691875    2.3031875            0   -3.0535967   0.31839181   -3.0473647     0.639876   -3.0465067            1   -3.0487759 
-111  0.096708718  0.078036984  0.013922966  0.054175505   0.20234693 0.0070871172 0.0022668002    2.3052946            0   -3.0535968   0.31853431   -3.0473633   0.64178873   -3.0465096            1   -3.0487764 
+0    4327.2753    2746.3378  0.082169072    4.9967651    4514.5424   0.42933428   0.42323635    1.8941131            0   -3.0535948   0.33333333   -2.6242605   0.66666667   -2.7623811            1   -3.0474969 
+100   0.10482171  0.085218406 0.0051952008  0.047859379    0.1904156 0.0070900401 0.0022691875    2.3031875            0   -3.0535967   0.31839181   -3.0473647     0.639876   -3.0465067            1   -3.0487759 
+111  0.096708718  0.078036984 0.0048656841  0.036130268    0.1967134 0.0070871172 0.0022668002    2.3052946            0   -3.0535968   0.31853431   -3.0473633   0.64178873   -3.0465096            1   -3.0487764 
 Climbing replica = 3
 Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
-111   0.20234693   0.17770387  0.013922966  0.054175505   0.20234693 0.0070871172 0.0022668002    2.3052946            0   -3.0535968   0.31853431   -3.0473633   0.64178873   -3.0465096            1   -3.0487764 
-178   0.09975409  0.093814031  0.010577358  0.024247224   0.09975409 0.0071042931 0.0022851195     2.312004            0   -3.0535969   0.31607934   -3.0473923     0.618931   -3.0464926            1   -3.0487777 
+111   0.20234693   0.17770387 0.0048656841  0.036130268    0.1967134 0.0070871172 0.0022668002    2.3052946            0   -3.0535968   0.31853431   -3.0473633   0.64178873   -3.0465096            1   -3.0487764 
+178   0.09975409  0.093814031 0.0035463662  0.010006594  0.096949208 0.0071042931 0.0022851195     2.312004            0   -3.0535969   0.31607934   -3.0473923     0.618931   -3.0464926            1   -3.0487777 

examples/neb/log.19June17.neb.hop2.g++.4

+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 

examples/neb/log.19June17.neb.hop2.g++.8

+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 

examples/neb/log.19June17.neb.sivac.g++.4

+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