Additional input script requirements to run styles with a cuda suffix are as follows:
-make yes-kokkos # install the KOKKOS package make g++ OMP=yes # build with OpenMP, no CUDA-
mpirun -np 12 lmp_g++ -k off < in.lj # MPI-only mode with no Kokkos -mpirun -np 12 lmp_g++ -sf kk < in.lj # MPI-only mode with Kokkos +mpirun -np 12 lmp_g++ < in.lj # MPI-only mode with no Kokkos +mpirun -np 12 lmp_g++ -k on -sf kk < in.lj # MPI-only mode with Kokkos mpirun -np 1 lmp_g++ -k on t 12 -sf kk < in.lj # one MPI task, 12 threads mpirun -np 2 lmp_g++ -k on t 6 -sf kk < in.lj # two MPI tasks, 6 threads/task@@ -825,8 +828,7 @@ section of the manual.Here are common options to use:
-
-cuda on/off
Explicitly enable or disable CUDA support, as provided by the -USER-CUDA package. If LAMMPS is built with this package, as described -above in Section 2.3, then by default LAMMPS will run in -CUDA mode. If this switch is set to "off", then it will not, even if -it was built with the USER-CUDA package, which means you can run -standard LAMMPS or with the GPU package for testing or benchmarking -purposes. The only reason to set the switch to "on", is to check if -LAMMPS was built with the USER-CUDA package, since an error will be -generated if it was not. +USER-CUDA package. Even if LAMMPS is built with this package, as +described above in Section 2.3, this switch must be set to +enable running with the CUDA-enabled styles the package provides. If +the switch is not set (the default), LAMMPS will operate as if the +USER-CUDA package were not installed; i.e. you can run standard LAMMPS +or with the GPU package, for testing or benchmarking purposes.
-echo style@@ -1204,16 +1202,14 @@ used.
-kokkos on/off keyword/value ...-
Explicitly enable or disable Kokkos support, as provided by the KOKKOS -package. If LAMMPS is built with this package, as described above in -Section 2.3, then by default LAMMPS will run in Kokkos -mode. If this switch is set to "off", then it will not, even if it -was built with the KOKKOS package, which means you can run standard -LAMMPS styles or use styles enhanced by other acceleration packages, -such as the GPU or USER-CUDA or USER-OMP packages, for testing or -benchmarking purposes. The only reason to set the switch to "on", is -to check if LAMMPS was built with the KOKKOS package, since an error -will be generated if it was not. +
Explicitly enable or disable KOKKOS support, as provided by the KOKKOS +package. Even if LAMMPS is built with this package, as described +above in Section 2.3, this switch must be set to enable +running with the KOKKOS-enabled styles the package provides. If the +switch is not set (the default), LAMMPS will operate as if the KOKKOS +package were not installed; i.e. you can run standard LAMMPS or with +the GPU or USER-CUDA or USER-OMP packages, for testing or benchmarking +purposes.
Additional optional keyword/value pairs can be specified which determine how Kokkos will use the underlying hardware on your diff --git a/doc/Section_start.txt b/doc/Section_start.txt index 2e8d786809..e4b75a34f2 100644 --- a/doc/Section_start.txt +++ b/doc/Section_start.txt @@ -1157,14 +1157,12 @@ Here are the details on the options: -cuda on/off :pre Explicitly enable or disable CUDA support, as provided by the -USER-CUDA package. If LAMMPS is built with this package, as described -above in "Section 2.3"_#start_3, then by default LAMMPS will run in -CUDA mode. If this switch is set to "off", then it will not, even if -it was built with the USER-CUDA package, which means you can run -standard LAMMPS or with the GPU package for testing or benchmarking -purposes. The only reason to set the switch to "on", is to check if -LAMMPS was built with the USER-CUDA package, since an error will be -generated if it was not. +USER-CUDA package. Even if LAMMPS is built with this package, as +described above in "Section 2.3"_#start_3, this switch must be set to +enable running with the CUDA-enabled styles the package provides. If +the switch is not set (the default), LAMMPS will operate as if the +USER-CUDA package were not installed; i.e. you can run standard LAMMPS +or with the GPU package, for testing or benchmarking purposes. -echo style :pre @@ -1198,16 +1196,14 @@ used. -kokkos on/off keyword/value ... :pre -Explicitly enable or disable Kokkos support, as provided by the KOKKOS -package. If LAMMPS is built with this package, as described above in -"Section 2.3"_#start_3, then by default LAMMPS will run in Kokkos -mode. If this switch is set to "off", then it will not, even if it -was built with the KOKKOS package, which means you can run standard -LAMMPS styles or use styles enhanced by other acceleration packages, -such as the GPU or USER-CUDA or USER-OMP packages, for testing or -benchmarking purposes. The only reason to set the switch to "on", is -to check if LAMMPS was built with the KOKKOS package, since an error -will be generated if it was not. +Explicitly enable or disable KOKKOS support, as provided by the KOKKOS +package. Even if LAMMPS is built with this package, as described +above in "Section 2.3"_#start_3, this switch must be set to enable +running with the KOKKOS-enabled styles the package provides. If the +switch is not set (the default), LAMMPS will operate as if the KOKKOS +package were not installed; i.e. you can run standard LAMMPS or with +the GPU or USER-CUDA or USER-OMP packages, for testing or benchmarking +purposes. Additional optional keyword/value pairs can be specified which determine how Kokkos will use the underlying hardware on your diff --git a/doc/compute_property_atom.html b/doc/compute_property_atom.html index bbf71ff36d..62a7e04da9 100644 --- a/doc/compute_property_atom.html +++ b/doc/compute_property_atom.html @@ -29,12 +29,14 @@ angmomx, angmomy, angmomz, shapex,shapey, shapez, quatw, quati, quatj, quatk, tqx, tqy, tqz, - spin, eradius, ervel, erforce end1x, end1y, end1z, end2x, end2y, end2z, corner1x, corner1y, corner1z, corner2x, corner2y, corner2z, corner3x, corner3y, corner3z, nbonds, + vfrac, s0, + spin, eradius, ervel, erforce, + rho, drho, e, de, cv, i_name, d_name
id = atom ID
@@ -56,13 +58,28 @@
shapex,shapey,shapez = 3 diameters of aspherical particle
quatw,quati,quatj,quatk = quaternion components for aspherical or body particles
tqx,tqy,tqz = torque on finite-size particles
+ end12x, end12y, end12z = end points of line segment
+ corner123x, corner123y, corner123z = corner points of triangle
+ nbonds = number of bonds
+
+PERI package per-atom properties: + vfrac = ??? + s0 = ??? ++
USER-EFF and USER-AWPMD package per-atom properties:
spin = electron spin
eradius = electron radius
ervel = electron radial velocity
- erforce = electron radial force
- end12x, end12y, end12z = end points of line segment
- corner123x, corner123y, corner123z = corner points of triangle
- nbonds = number of bonds
+ erforce = electron radial force
+
+USER-SPH package per-atom properties: + rho = ??? + drho = ??? + e = ??? + de = ??? + cv = ??? ++
fix property/atom per-atom properties: i_name = custom integer vector with name d_name = custom integer vector with namediff --git a/doc/compute_property_atom.txt b/doc/compute_property_atom.txt index 0ae271ad25..b6c1cc2f03 100644 --- a/doc/compute_property_atom.txt +++ b/doc/compute_property_atom.txt @@ -23,12 +23,14 @@ input = one or more atom attributes :l angmomx, angmomy, angmomz, shapex,shapey, shapez, quatw, quati, quatj, quatk, tqx, tqy, tqz, - spin, eradius, ervel, erforce end1x, end1y, end1z, end2x, end2y, end2z, corner1x, corner1y, corner1z, corner2x, corner2y, corner2z, corner3x, corner3y, corner3z, nbonds, + vfrac, s0, + spin, eradius, ervel, erforce, + rho, drho, e, de, cv, i_name, d_name :pre id = atom ID mol = molecule ID @@ -49,13 +51,28 @@ input = one or more atom attributes :l shapex,shapey,shapez = 3 diameters of aspherical particle quatw,quati,quatj,quatk = quaternion components for aspherical or body particles tqx,tqy,tqz = torque on finite-size particles + end12x, end12y, end12z = end points of line segment + corner123x, corner123y, corner123z = corner points of triangle + nbonds = number of bonds :pre + + PERI package per-atom properties: + vfrac = ??? + s0 = ??? :pre + + USER-EFF and USER-AWPMD package per-atom properties: spin = electron spin eradius = electron radius ervel = electron radial velocity - erforce = electron radial force - end12x, end12y, end12z = end points of line segment - corner123x, corner123y, corner123z = corner points of triangle - nbonds = number of bonds + erforce = electron radial force :pre + + USER-SPH package per-atom properties: + rho = ??? + drho = ??? + e = ??? + de = ??? + cv = ??? :pre + + "fix property/atom"_fix_property_atom.html per-atom properties: i_name = custom integer vector with name d_name = custom integer vector with name :pre :ule diff --git a/doc/dump.html b/doc/dump.html index 8b63b05e2a..5527540cc4 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -64,7 +64,6 @@ q, mux, muy, muz, mu, radius, diameter, omegax, omegay, omegaz, angmomx, angmomy, angmomz, tqx, tqy, tqz, - spin, eradius, ervel, erforce, c_ID, c_ID[N], f_ID, f_ID[N], v_name
id = atom ID
@@ -86,10 +85,6 @@
omegax,omegay,omegaz = angular velocity of spherical particle
angmomx,angmomy,angmomz = angular momentum of aspherical particle
tqx,tqy,tqz = torque on finite-size particles
- spin = electron spin
- eradius = electron radius
- ervel = electron radial velocity
- erforce = electron radial force
c_ID = per-atom vector calculated by a compute with ID
c_ID[N] = Nth column of per-atom array calculated by a compute with ID
f_ID = per-atom vector calculated by a fix with ID
@@ -108,8 +103,7 @@ dump 4a all custom 100 dump.myforce.* id type x y vx fx
dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]
-dump 1 all xtc 1000 file.xtc
-dump e_data all custom 100 dump.eff id type x y z spin eradius fx fy fz eforce
+dump 1 all xtc 1000 file.xtc
Description:
@@ -523,12 +517,6 @@ the ellipsoid atom style defines this quantity. can sustain a rotational torque due to interactions with other particles. -The spin, eradius, ervel, and erforce attributes are for -particles that represent nuclei and electrons modeled with the -electronic force field (EFF). See atom_style -electron and pair_style eff for more -details. -
The c_ID and c_ID[N] attributes allow per-atom vectors or arrays calculated by a compute to be output. The ID in the attribute should be replaced by the actual ID of the compute that has diff --git a/doc/dump.txt b/doc/dump.txt index a7d7e68b92..5d1be5881d 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -51,7 +51,6 @@ args = list of arguments for a particular style :l q, mux, muy, muz, mu, radius, diameter, omegax, omegay, omegaz, angmomx, angmomy, angmomz, tqx, tqy, tqz, - spin, eradius, ervel, erforce, c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre id = atom ID @@ -73,10 +72,6 @@ args = list of arguments for a particular style :l omegax,omegay,omegaz = angular velocity of spherical particle angmomx,angmomy,angmomz = angular momentum of aspherical particle tqx,tqy,tqz = torque on finite-size particles - spin = electron spin - eradius = electron radius - ervel = electron radial velocity - erforce = electron radial force c_ID = per-atom vector calculated by a compute with ID c_ID\[N\] = Nth column of per-atom array calculated by a compute with ID f_ID = per-atom vector calculated by a fix with ID @@ -94,8 +89,7 @@ dump 4a all custom 100 dump.myforce.* id type x y vx fx dump 4b flow custom 100 dump.%.myforce id type c_myF\[3\] v_ke dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress\[2\] -dump 1 all xtc 1000 file.xtc -dump e_data all custom 100 dump.eff id type x y z spin eradius fx fy fz eforce :pre +dump 1 all xtc 1000 file.xtc :pre [Description:] @@ -508,12 +502,6 @@ The {tqx}, {tqy}, {tqz} attributes are for finite-size particles that can sustain a rotational torque due to interactions with other particles. -The {spin}, {eradius}, {ervel}, and {erforce} attributes are for -particles that represent nuclei and electrons modeled with the -electronic force field (EFF). See "atom_style -electron"_atom_style.html and "pair_style eff"_pair_eff.html for more -details. - The {c_ID} and {c_ID\[N\]} attributes allow per-atom vectors or arrays calculated by a "compute"_compute.html to be output. The ID in the attribute should be replaced by the actual ID of the compute that has diff --git a/doc/pair_buck_long.html b/doc/pair_buck_long.html index 2316d7d534..7c41f28ee9 100644 --- a/doc/pair_buck_long.html +++ b/doc/pair_buck_long.html @@ -35,7 +35,7 @@
pair_style buck/long/coul/long cut off 2.5 pair_style buck/long/coul/long cut long 2.5 4.0 -pair_style buck/long/coul/long long long 2.5 4.0 +pair_style buck/long/coul/long long long 4.0 pair_coeff * * 1 1 pair_coeff 1 1 1 3 4diff --git a/doc/pair_buck_long.txt b/doc/pair_buck_long.txt index b8e96214c2..4555c8e351 100644 --- a/doc/pair_buck_long.txt +++ b/doc/pair_buck_long.txt @@ -26,7 +26,7 @@ cutoff2 = global cutoff for Coulombic (optional) (distance units) :l,ule pair_style buck/long/coul/long cut off 2.5 pair_style buck/long/coul/long cut long 2.5 4.0 -pair_style buck/long/coul/long long long 2.5 4.0 +pair_style buck/long/coul/long long long 4.0 pair_coeff * * 1 1 pair_coeff 1 1 1 3 4 :pre diff --git a/doc/pair_dpd.html b/doc/pair_dpd.html index 096ef612b8..6a75343b6f 100644 --- a/doc/pair_dpd.html +++ b/doc/pair_dpd.html @@ -175,8 +175,8 @@ number of "dangerous" reneighborings (printed at the end of a simulation), you should experiment with forcing reneighboring more often and see if system energies/trajectories change. -
These pair styles requires you to use the communicate vel -yes option so that velocites are stored by ghost +
These pair styles requires you to use the comm_modify vel +yes command so that velocites are stored by ghost atoms.
These pair styles will not restart exactly when using the diff --git a/doc/pair_dpd.txt b/doc/pair_dpd.txt index 0f75172dfd..e1d837fa0c 100644 --- a/doc/pair_dpd.txt +++ b/doc/pair_dpd.txt @@ -167,8 +167,8 @@ number of "dangerous" reneighborings (printed at the end of a simulation), you should experiment with forcing reneighboring more often and see if system energies/trajectories change. -These pair styles requires you to use the "communicate vel -yes"_communicate.html option so that velocites are stored by ghost +These pair styles requires you to use the "comm_modify vel +yes"_comm_modify.html command so that velocites are stored by ghost atoms. These pair styles will not restart exactly when using the diff --git a/doc/pair_eff.html b/doc/pair_eff.html index c183a434ca..1e3b5391c5 100644 --- a/doc/pair_eff.html +++ b/doc/pair_eff.html @@ -296,8 +296,8 @@ such as radius, radial velocity, and radital force, as defined by the atom_style. The electron atom style does all of this.
-Thes pair styles require you to use the communicate vel -yes option so that velocites are stored by ghost +
Thes pair styles require you to use the comm_modify vel +yes command so that velocites are stored by ghost atoms.
Related commands: diff --git a/doc/pair_eff.txt b/doc/pair_eff.txt index 80adfba5d1..49b0ef8be5 100644 --- a/doc/pair_eff.txt +++ b/doc/pair_eff.txt @@ -289,8 +289,8 @@ such as radius, radial velocity, and radital force, as defined by the "atom_style"_atom_style.html. The {electron} atom style does all of this. -Thes pair styles require you to use the "communicate vel -yes"_communicate.html option so that velocites are stored by ghost +Thes pair styles require you to use the "comm_modify vel +yes"_comm_modify.html command so that velocites are stored by ghost atoms. [Related commands:] diff --git a/doc/pair_gran.html b/doc/pair_gran.html index 37e7cc70e7..6a26c0bb7d 100644 --- a/doc/pair_gran.html +++ b/doc/pair_gran.html @@ -243,8 +243,8 @@ LAMMPS section for more info. require a per-particle radius is stored. The sphere atom style does all of this.
-This pair style requires you to use the communicate vel -yes option so that velocites are stored by ghost +
This pair style requires you to use the comm_modify vel +yes command so that velocites are stored by ghost atoms.
These pair styles will not restart exactly when using the diff --git a/doc/pair_gran.txt b/doc/pair_gran.txt index 1333363e82..da955f14a1 100644 --- a/doc/pair_gran.txt +++ b/doc/pair_gran.txt @@ -229,8 +229,8 @@ These pair styles require that atoms store torque and angular velocity require a per-particle radius is stored. The {sphere} atom style does all of this. -This pair style requires you to use the "communicate vel -yes"_communicate.html option so that velocites are stored by ghost +This pair style requires you to use the "comm_modify vel +yes"_comm_modify.html command so that velocites are stored by ghost atoms. These pair styles will not restart exactly when using the diff --git a/doc/pair_style.html b/doc/pair_style.html index eafbe4c59a..ed0fdee2a5 100644 --- a/doc/pair_style.html +++ b/doc/pair_style.html @@ -117,7 +117,7 @@ in the pair section of this page.
The nbuild and ndanger keywords are useful for monitoring neighbor +list builds during a run. Note that both these values are also +printed with the end-of-run statistics. The nbuild keyword is the +number of re-builds during the current run. The ndanger keyword is +the number of re-builds that LAMMPS considered potentially +"dangerous". If atom movement triggered neighbor list rebuilding (see +the neigh_modify command), then dangerous +reneighborings are those that were triggered on the first timestep +atom movement was checked for. If this count is non-zero you may wish +to reduce the delay factor to insure no force interactions are missed +by atoms moving beyond the neighbor skin distance before a rebuild +takes place. +