10 Aug 2015 version
+19 Aug 2015 version
Version info:
diff --git a/doc/doc2/Section_commands.html b/doc/doc2/Section_commands.html
index bb0a097c9b..1a2161566b 100644
--- a/doc/doc2/Section_commands.html
+++ b/doc/doc2/Section_commands.html
@@ -478,7 +478,7 @@ package.
meso_rho/atom meso_t/atom saed smd/contact/radius smd/damage smd/hourglass/error smd/internal/energy smd/plastic/strain smd/plastic/strain/rate smd/rho smd/tlsph/defgrad smd/tlsph/dt smd/tlsph/num/neighs smd/tlsph/shape smd/tlsph/strain smd/tlsph/strain/rate smd/tlsph/stress smd/triangle/mesh/vertices smd/ulsph/num/neighs smd/ulsph/strain smd/ulsph/strain/rate smd/ulpsh/stress smd/vol temp/drude smd/ulsph/num/neighs smd/ulsph/strain smd/ulsph/strain/rate smd/ulsph/stress smd/vol temp/drude temp/eff temp/deform/eff temp/region/eff temp/rotate xrd
cd indent
cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
-lmp_linux < in.indent # run the problem
+lmp_linux -in in.indent # run the problem
19 Aug 2015 version
Running the simulation produces the files dump.indent and log.lammps. You can visualize the dump file as follows: diff --git a/doc/doc2/Section_python.html b/doc/doc2/Section_python.html index 2921bc4c3f..518e5de5cc 100644 --- a/doc/doc2/Section_python.html +++ b/doc/doc2/Section_python.html @@ -412,7 +412,7 @@ interactively from the bench directory: on a single processor appear on the screen, the same as if you had typed something like:
-lmp_g++ < in.lj +lmp_g++ -in in.ljTest LAMMPS and Python in parallel:
@@ -433,7 +433,7 @@ pypar.finalize()
and you should see the same output as if you had typed
-% mpirun -np 4 lmp_g++ < in.lj +% mpirun -np 4 lmp_g++ -in in.ljNote that if you leave out the 3 lines from test.py that specify Pypar commands you will instantiate and run LAMMPS independently on each of diff --git a/doc/doc2/Section_start.html b/doc/doc2/Section_start.html index acc1beac4d..9553f05b28 100644 --- a/doc/doc2/Section_start.html +++ b/doc/doc2/Section_start.html @@ -1213,7 +1213,7 @@ Linux box, using mpirun to launch a parallel job: make linux cp lmp_linux ../bench cd ../bench -mpirun -np 4 lmp_linux < in.lj +mpirun -np 4 lmp_linux -in in.lj
See this page for timings for this and the other benchmarks on various platforms. Note that some of the example scripts require @@ -1329,8 +1329,8 @@ letter abbreviation can be used:
For example, lmp_ibm might be launched as follows:
-mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none < in.alloy -mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none < in.alloy +mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none -in in.alloy +mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none -in in.alloyHere are the details on the options:
diff --git a/doc/doc2/delete_atoms.html b/doc/doc2/delete_atoms.html index c0dc0590d8..9e2a0eadb1 100644 --- a/doc/doc2/delete_atoms.html +++ b/doc/doc2/delete_atoms.html @@ -140,7 +140,7 @@ deletion by the overlap styles. You probably don't want to be deleting one atom in a bonded pair anyway.The bond yes option cannot be used with molecular systems defined -using molecule template files via the molecule and +using molecule template files via the molecule and atom_style template commands.
Related commands: diff --git a/doc/doc2/package.html b/doc/doc2/package.html index d4b2a4fa52..757facece6 100644 --- a/doc/doc2/package.html +++ b/doc/doc2/package.html @@ -320,6 +320,13 @@ large cutoffs or with a small number of particles per GPU, increasing the value can improve performance. The number of threads per atom must be a power of 2 and currently cannot be greater than 32.
+The blocksize keyword allows to tweak the number of threads used +per thread block. This number should be a multiple of 32 (for GPUs) +and its maximum depends on the specific GPU hardware. Typical choices +are 64, 128, or 256. A larger blocksize increases occupancy of individual +GPU cores, but reduces the total number of thread blocks, thus may lead +to load imbalance. +
The device keyword can be used to tune parameters optimized for a specific accelerator, when using OpenCL. For CUDA, the device keyword is ignored. Currently, the device type is limited to NVIDIA diff --git a/doc/doc2/pair_lj_cubic.html b/doc/doc2/pair_lj_cubic.html index e173da74a1..6e450e0c20 100644 --- a/doc/doc2/pair_lj_cubic.html +++ b/doc/doc2/pair_lj_cubic.html @@ -26,16 +26,15 @@ pair_coeff * * 1.0 0.8908987
Description:
-The lj/cubic style computes a truncated LJ interaction potential whose -energy and force are continuous everywhere. -Inside the inflection point the interaction is identical to the -standard 12/6 Lennard-Jones potential. -The LJ function outside the inflection point is replaced -with a cubic function of distance. The energy, force, and second -derivative are continuous at the inflection point. -The cubic coefficient A3 is chosen so -that both energy and force go to zero at the cutoff distance. -Outside the cutoff distance the energy and force are zero. +
The lj/cubic style computes a truncated LJ interaction potential +whose energy and force are continuous everywhere. Inside the +inflection point the interaction is identical to the standard 12/6 +Lennard-Jones potential. The LJ function outside the +inflection point is replaced with a cubic function of distance. The +energy, force, and second derivative are continuous at the inflection +point. The cubic coefficient A3 is chosen so that both energy and +force go to zero at the cutoff distance. Outside the cutoff distance +the energy and force are zero.
This potential is commonly used to study the shock mechanics -of FCC solids, as in Ravelo et al. (Ravelo). +
This potential is commonly used to study the shock mechanics of FCC +solids, as in Ravelo et al. (Ravelo).
-The following coefficients must be defined for each pair of atom -types via the pair_coeff command as in the example -above, or in the data file or restart files read by the +
The following coefficients must be defined for each pair of atom types +via the pair_coeff command as in the example above, +or in the data file or restart files read by the read_data or read_restart commands, or by mixing as described below:
@@ -60,9 +59,9 @@ commands, or by mixing as described below:Note that sigma is defined in the LJ formula as the zero-crossing -distance for the potential, not as the energy minimum, which -is located at rmin = 2^(1/6)*sigma. In the above example, sigma = 0.8908987, -so rmin = 1. +distance for the potential, not as the energy minimum, which is +located at rmin = 2^(1/6)*sigma. In the above example, sigma = +0.8908987, so rmin = 1.