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Merge remote-tracking branch 'lammps-ro/master' into lammps-icms

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Resolved Conflicts:
	doc/Manual.html
	doc/Manual.txt
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Axel Kohlmeyer
2014-11-06 11:03:09 -05:00
parent 176facc1fa 79034a7dcf
commit 8014e5cf0d
9 changed files with 180 additions and 14 deletions
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doc/Manual.html
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@ -1,7 +1,7 @@
<HTML>
<HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="30 Oct 2014 version">
<META NAME="docnumber" CONTENT="5 Nov 2014 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>
@ -22,7 +22,7 @@
<CENTER><H3>LAMMPS-ICMS Documentation
</H3></CENTER>
<CENTER><H4>30 Oct 2014 version
<CENTER><H4>5 Nov 2014 version
</H4></CENTER>
<H4>Version info:
</H4>

4
doc/Manual.txt
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@ -1,7 +1,7 @@
<HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="30 Oct 2014 version">
<META NAME="docnumber" CONTENT="5 Nov 2014 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>
@ -19,7 +19,7 @@
<H1></H1>
LAMMPS-ICMS Documentation :c,h3
30 Oct 2014 version :c,h4
5 Nov 2014 version :c,h4
Version info: :h4

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examples/COUPLE/simple/README
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@ -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

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examples/MC/README
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@ -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.

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src/USER-INTEL/TEST/README Normal file
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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
+++++++++++++++++++++++

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src/USER-INTEL/TEST/in.intel.lc Normal file
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# 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

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src/USER-INTEL/TEST/in.intel.rhodo Normal file
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# 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

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src/fix_temp_csvr.cpp
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@ -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]) {

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src/version.h
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@ -1 +1 @@
#define LAMMPS_VERSION "30 Oct 2014"
#define LAMMPS_VERSION "5 Nov 2014"