diff --git a/doc/Manual.html b/doc/Manual.html index 7e4625722c..730cf5c067 100644 --- a/doc/Manual.html +++ b/doc/Manual.html @@ -1,7 +1,7 @@ LAMMPS-ICMS Users Manual - + @@ -22,7 +22,7 @@

LAMMPS-ICMS Documentation

-

30 Oct 2014 version +

5 Nov 2014 version

Version info:

diff --git a/doc/Manual.txt b/doc/Manual.txt index 69f33b47e1..e50f7f6f28 100644 --- a/doc/Manual.txt +++ b/doc/Manual.txt @@ -1,7 +1,7 @@ LAMMPS-ICMS Users Manual LAMMPS Users Manual - + @@ -19,7 +19,7 @@

LAMMPS-ICMS Documentation :c,h3 -30 Oct 2014 version :c,h4 +5 Nov 2014 version :c,h4 Version info: :h4 diff --git a/examples/COUPLE/simple/README b/examples/COUPLE/simple/README index b79c9f3fed..d40aaa6246 100644 --- a/examples/COUPLE/simple/README +++ b/examples/COUPLE/simple/README @@ -12,10 +12,11 @@ libfwrapper.c is the Fortran-to-C wrapper The 3 codes do the same thing, so you can compare them to see how to drive LAMMPS in this manner. The C driver is similar in spirit to what -one could use to write a scripting language interface. The Fortran -driver in addition requires a wrapper library that interfaces the C -interface of the LAMMPS library to Fortran and also translates the MPI -communicator from Fortran to C. +one could use to write a scripting language interface. See +python/examples/simple.py for an example of using Python as a wrapper +in that way. The Fortran driver in addition requires a wrapper +library that interfaces the C interface of the LAMMPS library to +Fortran and also translates the MPI communicator from Fortran to C. First, you must build LAMMPS as a library, either static or shared. See http://lammps.sandia.gov/doc/Section_start.html#start_5 for diff --git a/examples/MC/README b/examples/MC/README index adbd13c420..7c38b65478 100644 --- a/examples/MC/README +++ b/examples/MC/README @@ -26,8 +26,5 @@ are printed. Dump file snapshots or images or a movie of the MC relaxation can be produced by uncommenting the appropriate dump lines in the script. -At some point, we will add a Python script to the python/examples -directory that performs the same operation as this script. It will -invoke LAMMPS as a library and use Python to implement the MC -accept/reject logic more cleanly than the LAMMPS input script can do -it. +See the Python script mc.py in python/examples for similar +functionality encoded in a script that invokes LAMMPS as a library. diff --git a/src/USER-INTEL/TEST/README b/src/USER-INTEL/TEST/README new file mode 100644 index 0000000000..62b8a58188 --- /dev/null +++ b/src/USER-INTEL/TEST/README @@ -0,0 +1,67 @@ +If you run in another directory, please edit the read_data line to point to +the data.rhodo file. This is included in the LAMMPS distribution in the +'bench' directory. + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +Expected times are the expected LOOP times based on runs using dual-socket +Intel Xeon processor E5-2697 V2 with Intel Xeon Phi coprocessor 7120P. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + + +TO RUN WITHOUT A PACKAGE: +----------------------------------------------------------------------------- +mpirun -np 48 ../../../src/lmp_YOUR_MACHINE -in in.intel.rhodo -log none -v b 0 -v s off +mpirun -np 48 ../../../src/lmp_YOUR_MACHINE -in in.intel.lc -log none -v b 0 -v s off + + +TO RUN WITH OMP PACKAGE +----------------------------------------------------------------------------- +env OMP_NUM_THREADS=2 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.rhodo -log none -v b 0 -v s omp ++++++++++++++++++++++++ ++ EXPECTED TIME: 20.33s ++++++++++++++++++++++++ + +env OMP_NUM_THREADS=1 mpirun -np 48 ../../../src/lmp_YOUR_MACHINE -in in.intel.lc -log none -v b 0 -v s omp ++++++++++++++++++++++++ ++ EXPECTED TIME: 19.92s ++++++++++++++++++++++++ + + +TO RUN WITH INTEL+OMP PACKAGE WITHOUT OFFLOAD: +----------------------------------------------------------------------------- +env OMP_NUM_THREADS=2 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.rhodo -log none -v b 0 -v s intel ++++++++++++++++++++++++ ++ EXPECTED TIME: 16.94s ++++++++++++++++++++++++ + +env OMP_NUM_THREADS=2 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.lc -log none -v b 0 -v s intel ++++++++++++++++++++++++ ++ EXPECTED TIME: 5.80s ++++++++++++++++++++++++ + + +TO RUN WITH INTEL+OMP PACKAGE WITH OFFLOAD TO XEON PHI (AUTO-BALANCED): +----------------------------------------------------------------------------- +env OMP_NUM_THREADS=1 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.rhodo -log none -v b -1 -v s intel ++++++++++++++++++++++++ ++ EXPECTED TIME: 12.31s ++++++++++++++++++++++++ + +env OMP_NUM_THREADS=1 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.lc -log none -v b -1 -v s intel ++++++++++++++++++++++++ ++ EXPECTED TIME: 4.00s ++++++++++++++++++++++++ + + +TO RUN WITH INTEL+OMP PACKAGE WITH OFFLOAD TO XEON PHI (FIXED BALANCE): +----------------------------------------------------------------------------- +env OMP_NUM_THREADS=1 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.rhodo -log none -v b 0.68 -v s intel ++++++++++++++++++++++++ ++ EXPECTED TIME: 11.40s ++++++++++++++++++++++++ + +env OMP_NUM_THREADS=1 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.lc -log none -v b 0.53 -v s intel ++++++++++++++++++++++++ ++ EXPECTED TIME: 3.93s ++++++++++++++++++++++++ + diff --git a/src/USER-INTEL/TEST/in.intel.lc b/src/USER-INTEL/TEST/in.intel.lc new file mode 100644 index 0000000000..646065f6f9 --- /dev/null +++ b/src/USER-INTEL/TEST/in.intel.lc @@ -0,0 +1,61 @@ +# Gay-Berne benchmark +# biaxial ellipsoid mesogens in isotropic phase +# shape: 2 1.5 1 +# cutoff 4.0 with skin 0.8 +# NPT, T=2.4, P=8.0 + +package intel 1 mode mixed balance $b +package omp 0 +suffix $s +processors * * * grid numa + +variable x index 4 +variable y index 2 +variable z index 2 + +variable i equal $x*32 +variable j equal $y*32 +variable k equal $z*32 + +units lj +atom_style ellipsoid + +# creation +lattice sc 0.22 +region box block 0 $i 0 $j 0 $k +create_box 1 box +create_atoms 1 box + +# read_data data.gb + +set type 1 mass 1.5 +set type 1 shape 1 1.5 2 +set group all quat/random 982381 + +compute rot all temp/asphere +group spheroid type 1 +variable dof equal count(spheroid)+3 +compute_modify rot extra ${dof} + +velocity all create 2.4 41787 loop geom + +pair_style gayberne 1.0 3.0 1.0 4.0 +pair_coeff 1 1 1.0 1.0 1.0 0.5 0.2 1.0 0.5 0.2 + +neighbor 0.8 bin + +timestep 0.002 +thermo 300 + +# equilibration run +fix 1 all npt/asphere temp 2.4 2.4 0.1 iso 5.0 8.0 0.1 +compute_modify 1_temp extra ${dof} +run 210 +thermo 100 + +reset_timestep 0 +unfix 1 +fix 1 all nve/asphere +run 10 +run 50 + diff --git a/src/USER-INTEL/TEST/in.intel.rhodo b/src/USER-INTEL/TEST/in.intel.rhodo new file mode 100644 index 0000000000..4b227b3d1e --- /dev/null +++ b/src/USER-INTEL/TEST/in.intel.rhodo @@ -0,0 +1,39 @@ +# Rhodopsin model + +package intel 1 mode mixed balance $b +package omp 0 +suffix $s + +variable x index 4 +variable y index 2 +variable z index 2 + +units real +neigh_modify delay 5 every 1 + +atom_style full +atom_modify map hash +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +pair_style lj/charmm/coul/long 8.0 10.0 +pair_modify mix arithmetic +kspace_style pppm 1e-4 + +read_data ../../../bench/data.rhodo + +replicate $x $y $z + +fix 1 all shake 0.0001 5 0 m 1.0 a 232 +fix 2 all npt temp 300.0 300.0 100.0 & + z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1 + +special_bonds charmm + +thermo 50 +thermo_style multi +timestep 2.0 + +run 10 +run 100 diff --git a/src/fix_temp_csvr.cpp b/src/fix_temp_csvr.cpp index 6f5ee12d05..636250ab05 100644 --- a/src/fix_temp_csvr.cpp +++ b/src/fix_temp_csvr.cpp @@ -49,6 +49,7 @@ FixTempCSVR::FixTempCSVR(LAMMPS *lmp, int narg, char **arg) : nevery = 1; global_freq = nevery; + dynamic_group_allow = 1; tstr = NULL; if (strstr(arg[3],"v_") == arg[3]) { diff --git a/src/version.h b/src/version.h index b9da07334e..65016e33ba 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "30 Oct 2014" +#define LAMMPS_VERSION "5 Nov 2014"