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anticipate patches from upstream to 12 Aug 2013 version

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This commit is contained in:
Axel Kohlmeyer
2013-07-30 10:12:29 +02:00
parent 39f16dc386
commit dedb247fcd
19 changed files with 193 additions and 69 deletions
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2
doc/Manual.html
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@ -22,7 +22,7 @@
<CENTER><H3>LAMMPS-ICMS Documentation
</H3></CENTER>
<CENTER><H4>9 Aug 2013 version
<CENTER><H4>12 Aug 2013 version
</H4></CENTER>
<H4>Version info:
</H4>

2
doc/Manual.txt
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@ -18,7 +18,7 @@
<H1></H1>
LAMMPS-ICMS Documentation :c,h3
9 Aug 2013 version :c,h4
12 Aug 2013 version :c,h4
Version info: :h4

12
doc/Section_packages.html
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@ -51,10 +51,10 @@ packages, more details are provided.
<TR ALIGN="center"><TD >FLD</TD><TD > Fast Lubrication Dynamics</TD><TD > Kumar & Bybee & Higdon (1)</TD><TD > <A HREF = "pair_lubricateU.html">pair_style lubricateU</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >GPU</TD><TD > GPU-enabled potentials</TD><TD > Mike Brown (ORNL)</TD><TD > <A HREF = "Section_accelerate.html#acc_6">Section accelerate</A></TD><TD > gpu</TD><TD > lib/gpu</TD></TR>
<TR ALIGN="center"><TD >GRANULAR</TD><TD > granular systems</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_6">Section_howto</A></TD><TD > pour</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >KIM</TD><TD > openKIM potentials</TD><TD > Smirichinski & Elliot & Tadmor (3)</TD><TD > <A HREF = "pair_kim.html">pair_style kim</A></TD><TD > kim</TD><TD > lib/kim</TD></TR>
<TR ALIGN="center"><TD >KIM</TD><TD > openKIM potentials</TD><TD > Smirichinski & Elliot & Tadmor (3)</TD><TD > <A HREF = "pair_kim.html">pair_style kim</A></TD><TD > kim</TD><TD > KIM</TD></TR>
<TR ALIGN="center"><TD >KSPACE</TD><TD > long-range Coulombic solvers</TD><TD > -</TD><TD > <A HREF = "kspace_style.html">kspace_style</A></TD><TD > peptide</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >MANYBODY</TD><TD > many-body potentials</TD><TD > -</TD><TD > <A HREF = "pair_tersoff.html">pair_style tersoff</A></TD><TD > shear</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >MEAM</TD><TD > modified EAM potential</TD><TD > Greg Wagner (Sandia)</TD><TD > <A HREF = "pair_meam.html">pair_style meam</A></TD><TD > meam</TD><TD > KIM</TD></TR>
<TR ALIGN="center"><TD >MEAM</TD><TD > modified EAM potential</TD><TD > Greg Wagner (Sandia)</TD><TD > <A HREF = "pair_meam.html">pair_style meam</A></TD><TD > meam</TD><TD > lib/meam</TD></TR>
<TR ALIGN="center"><TD >MC</TD><TD > Monte Carlo options</TD><TD > -</TD><TD > <A HREF = "fix_gcmc.html">fix gcmc</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >MOLECULE</TD><TD > molecular system force fields</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_3">Section_howto</A></TD><TD > peptide</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >OPT</TD><TD > optimized pair potentials</TD><TD > Fischer & Richie & Natoli (2)</TD><TD > <A HREF = "Section_accelerate.html#acc_4">Section accelerate</A></TD><TD > -</TD><TD > -</TD></TR>
@ -97,10 +97,10 @@ lib/package, then the code for the library is under the lib directory
of the LAMMPS distribution. See the lib/package/README file for info
on how to build the library. If it is not listed as lib/package, then
it is a third-party library not included in the LAMMPS distribution.
See the src/package/Makefile.lammps file for info on where to download
the library. <A HREF = "Section_start.html#start_3_3">Section start</A> of the
manual also gives details on how to build LAMMPS with both kinds of
auxiliary libraries.
See the src/package/README or src/package/Makefile.lammps file for
info on where to download the library. <A HREF = "Section_start.html#start_3_3">Section
start</A> of the manual also gives details
on how to build LAMMPS with both kinds of auxiliary libraries.
</P>
<HR>

12
doc/Section_packages.txt
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@ -46,10 +46,10 @@ DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dip
FLD, Fast Lubrication Dynamics, Kumar & Bybee & Higdon (1), "pair_style lubricateU"_pair_lubricateU.html, -, -
GPU, GPU-enabled potentials, Mike Brown (ORNL), "Section accelerate"_Section_accelerate.html#acc_6, gpu, lib/gpu
GRANULAR, granular systems, -, "Section_howto"_Section_howto.html#howto_6, pour, -
KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), "pair_style kim"_pair_kim.html, kim, lib/kim
KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), "pair_style kim"_pair_kim.html, kim, KIM
KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, -
MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, -
MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, KIM
MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam
MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, -
MOLECULE, molecular system force fields, -, "Section_howto"_Section_howto.html#howto_3, peptide, -
OPT, optimized pair potentials, Fischer & Richie & Natoli (2), "Section accelerate"_Section_accelerate.html#acc_4, -, -
@ -91,10 +91,10 @@ lib/package, then the code for the library is under the lib directory
of the LAMMPS distribution. See the lib/package/README file for info
on how to build the library. If it is not listed as lib/package, then
it is a third-party library not included in the LAMMPS distribution.
See the src/package/Makefile.lammps file for info on where to download
the library. "Section start"_Section_start.html#start_3_3 of the
manual also gives details on how to build LAMMPS with both kinds of
auxiliary libraries.
See the src/package/README or src/package/Makefile.lammps file for
info on where to download the library. "Section
start"_Section_start.html#start_3_3 of the manual also gives details
on how to build LAMMPS with both kinds of auxiliary libraries.
:line
:line

65
doc/fix_external.html
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@ -47,7 +47,7 @@ script</A>.
<HR>
<P>If mode is <I>pf/callback</I> then the fix will make a callback every
<I>Ncall</I> timesteps or minimization iteration to the external program.
<I>Ncall</I> timesteps or minimization iterations to the external program.
The external program computes forces on atoms by setting values in an
array owned by the fix. The fix then adds these forces to each atom
in the group, once every <I>Napply</I> steps, similar to the way the <A HREF = "fix_addforce.html">fix
@ -89,29 +89,70 @@ array. The fix adds these forces to each atom in the group, once
every <I>Napply</I> steps, similar to the way the <A HREF = "fix_addforce.html">fix
addforce</A> command works.
</P>
<P>The name of the public force array provided by the FixExternal
class is
</P>
<PRE>double **fexternal;
</PRE>
<P>It is allocated by the FixExternal class as an (N,3) array where N is
the number of atoms owned by a processor. The 3 corresponds to the
fx, fy, fz components of force.
</P>
<P>It is up to the external program to set the values in this array to
the desired quantities, as often as desired. For example, the driver
program might perform an MD run in stages of 1000 timesteps each. In
between calls to the LAMMPS <A HREF = "run.html">run</A> command, it could retrieve
atom coordinates from LAMMPS, compute forces, set values in the fix
external array, etc.
atom coordinates from LAMMPS, compute forces, set values in fexternal,
etc.
</P>
<HR>
<P>To use this fix during energy minimization, the energy corresponding
to the added forces must also be set so as to be consistent with the
added forces. Otherwise the minimization will not converge correctly.
</P>
<P>This can be done from the external driver by calling this public
method of the FixExternal class:
</P>
<PRE>void set_energy(double eng);
</PRE>
<P>where eng is the potential energy. Eng is an extensive quantity,
meaning it should be the sum over per-atom energies of all affected
atoms. It should also be provided in <A HREF = "units.html">energy units</A>
consistent with the simulation. See the details below for how to
insure this energy setting is used appropriately in a minimization.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. No parameter of this fix can
be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
files</A>.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the potential "energy" set by the external driver to the
system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>. This is a fictitious quantity but is
needed so that the <A HREF = "minimize.html">minimize</A> command can include the
forces added by this fix in a consistent manner. I.e. there is a
decrease in potential energy when atoms move in the direction of the
added force.
</P>
<P>This fix computes a global scalar which can be accessed by various
<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
potential energy discussed above. The scalar stored by this fix
is "extensive".
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command.
</P>
<P>The forces due to this fix are imposed during an energy minimization,
invoked by the <A HREF = "minimize.html">minimize</A> command. However, LAMMPS
knows nothing about the energy associated with these forces. So you
should perform the minimization based on a force tolerance, not an
energy tolerance.
invoked by the <A HREF = "minimize.html">minimize</A> command.
</P>
<P>IMPORTANT NOTE: If you want the fictitious potential energy associated
with the added forces to be included in the total potential energy of
the system (the quantity being minimized), you MUST enable the
<A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for this fix.
</P>
<P><B>Restrictions:</B> none
</P>

65
doc/fix_external.txt
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@ -40,7 +40,7 @@ script"_Section_python.html.
:line
If mode is {pf/callback} then the fix will make a callback every
{Ncall} timesteps or minimization iteration to the external program.
{Ncall} timesteps or minimization iterations to the external program.
The external program computes forces on atoms by setting values in an
array owned by the fix. The fix then adds these forces to each atom
in the group, once every {Napply} steps, similar to the way the "fix
@ -82,29 +82,70 @@ array. The fix adds these forces to each atom in the group, once
every {Napply} steps, similar to the way the "fix
addforce"_fix_addforce.html command works.
The name of the public force array provided by the FixExternal
class is
double **fexternal; :pre
It is allocated by the FixExternal class as an (N,3) array where N is
the number of atoms owned by a processor. The 3 corresponds to the
fx, fy, fz components of force.
It is up to the external program to set the values in this array to
the desired quantities, as often as desired. For example, the driver
program might perform an MD run in stages of 1000 timesteps each. In
between calls to the LAMMPS "run"_run.html command, it could retrieve
atom coordinates from LAMMPS, compute forces, set values in the fix
external array, etc.
atom coordinates from LAMMPS, compute forces, set values in fexternal,
etc.
:line
To use this fix during energy minimization, the energy corresponding
to the added forces must also be set so as to be consistent with the
added forces. Otherwise the minimization will not converge correctly.
This can be done from the external driver by calling this public
method of the FixExternal class:
void set_energy(double eng); :pre
where eng is the potential energy. Eng is an extensive quantity,
meaning it should be the sum over per-atom energies of all affected
atoms. It should also be provided in "energy units"_units.html
consistent with the simulation. See the details below for how to
insure this energy setting is used appropriately in a minimization.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#howto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
files"_restart.html.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the potential "energy" set by the external driver to the
system's potential energy as part of "thermodynamic
output"_thermo_style.html. This is a fictitious quantity but is
needed so that the "minimize"_minimize.html command can include the
forces added by this fix in a consistent manner. I.e. there is a
decrease in potential energy when atoms move in the direction of the
added force.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
potential energy discussed above. The scalar stored by this fix
is "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command. However, LAMMPS
knows nothing about the energy associated with these forces. So you
should perform the minimization based on a force tolerance, not an
energy tolerance.
invoked by the "minimize"_minimize.html command.
IMPORTANT NOTE: If you want the fictitious potential energy associated
with the added forces to be included in the total potential energy of
the system (the quantity being minimized), you MUST enable the
"fix_modify"_fix_modify.html {energy} option for this fix.
[Restrictions:] none

4
doc/fix_qeq_reax.html
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@ -100,7 +100,7 @@ be used for periodic cell dimensions less than 10 angstroms.
</P>
<A NAME = "Aktulga"></A>
<P><B>(Aktulga)</B> Aktulga, Fogarty, Pandit, Grama, Parallel Computing, to
appear (2011).
<P>(Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38,
245-259 (2012).
</P>
</HTML>

4
doc/fix_qeq_reax.txt
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@ -94,5 +94,5 @@ be used for periodic cell dimensions less than 10 angstroms.
[(Nakano)] Nakano, Computer Physics Communications, 104, 59-69 (1997).
:link(Aktulga)
[(Aktulga)] Aktulga, Fogarty, Pandit, Grama, Parallel Computing, to
appear (2011).
(Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38,
245-259 (2012).

4
doc/pair_reax_c.html
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@ -316,8 +316,8 @@ Journal of Physical Chemistry A, 112, 1040-1053 (2008).
</P>
<A NAME = "Aktulga"></A>
<P><B>(Aktulga)</B> Aktulga, Fogarty, Pandit, Grama, Parallel Computing, to
appear (2011).
<P>(Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38,
245-259 (2012).
</P>
<A NAME = "Liu_2011"></A>

4
doc/pair_reax_c.txt
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@ -308,8 +308,8 @@ mincap = 50.
Journal of Physical Chemistry A, 112, 1040-1053 (2008).
:link(Aktulga)
[(Aktulga)] Aktulga, Fogarty, Pandit, Grama, Parallel Computing, to
appear (2011).
(Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38,
245-259 (2012).
:link(Liu_2011)
[(Liu)] L. Liu, Y. Liu, S. V. Zybin, H. Sun and W. A. Goddard, Journal

3
examples/voronoi/in.voronoi
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@ -92,7 +92,7 @@ undump d1
#
# TEST 4: Edge histogram tests
#
compute v1 type2 voronoi/atom edge_histo 6
compute v1 type2 voronoi/atom edge_histo 8
thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
run 1
variable t4a equal (abs(c_v1[4]-12000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[6]+c_v1[7])/120
@ -150,6 +150,5 @@ uncompute v1
uncompute r0
undump d1
# All tests done
print TEST_DONE

7
src/dump_image.cpp
View File

@ -47,11 +47,12 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
{
if (binary || multiproc) error->all(FLERR,"Invalid dump image filename");
// set filetype based on filename suffix
// _and_ turn on the binary flag so we don't get corrupted
// output on windows.
// force binary flag on to avoid corrupted output on Windows
binary = 1;
// set filetype based on filename suffix
int n = strlen(filename);
if (strlen(filename) > 4 && strcmp(&filename[n-4],".jpg") == 0)
filetype = JPG;

24
src/fix_external.cpp
View File

@ -33,6 +33,10 @@ FixExternal::FixExternal(LAMMPS *lmp, int narg, char **arg) :
{
if (narg < 4) error->all(FLERR,"Illegal fix external command");
scalar_flag = 1;
global_freq = 1;
extscalar = 1;
if (strcmp(arg[3],"pf/callback") == 0) {
if (narg != 6) error->all(FLERR,"Illegal fix external command");
mode = PF_CALLBACK;
@ -55,6 +59,8 @@ FixExternal::FixExternal(LAMMPS *lmp, int narg, char **arg) :
fexternal = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
user_energy = 0.0;
}
/* ---------------------------------------------------------------------- */
@ -75,6 +81,7 @@ int FixExternal::setmask()
int mask = 0;
if (mode == PF_CALLBACK || mode == PF_ARRAY) {
mask |= POST_FORCE;
mask |= THERMO_ENERGY;
mask |= MIN_POST_FORCE;
}
return mask;
@ -138,6 +145,23 @@ void FixExternal::min_post_force(int vflag)
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixExternal::set_energy(double eng)
{
user_energy = eng;
}
/* ----------------------------------------------------------------------
potential energy of added force
up to user to set it via set_energy()
------------------------------------------------------------------------- */
double FixExternal::compute_scalar()
{
return user_energy;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */

7
src/fix_external.h
View File

@ -26,6 +26,8 @@ namespace LAMMPS_NS {
class FixExternal : public Fix {
public:
double **fexternal;
FixExternal(class LAMMPS *, int, char **);
~FixExternal();
int setmask();
@ -34,6 +36,9 @@ class FixExternal : public Fix {
void min_setup(int);
void post_force(int);
void min_post_force(int);
double compute_scalar();
void set_energy(double eng);
double memory_usage();
void grow_arrays(int);
@ -48,7 +53,7 @@ class FixExternal : public Fix {
int mode,ncall,napply;
FnPtr callback;
void *ptr_caller;
double **fexternal;
double user_energy;
};
}

11
src/fix_langevin.cpp
View File

@ -534,15 +534,12 @@ void FixLangevin::post_force_untemplated
if (Tp_BIAS) {
temperature->remove_bias(i,v[i]);
fdrag[0] = gamma1*v[i][0];
fdrag[1] = gamma1*v[i][1];
fdrag[2] = gamma1*v[i][2];
fdrag[0] = gamma1*v[i][0];
if (v[i][0] != 0.0) f[i][0] += fdrag[0] + fran[0];
else fran[0] = 0.0;
if (v[i][1] != 0.0) f[i][1] += fdrag[1] + fran[1];
else fran[1] = 0.0;
if (v[i][2] != 0.0) f[i][2] += fdrag[2] + fran[2];
else fran[2] = 0.0;
if (v[i][0] == 0.0) fran[0] = 0.0;
if (v[i][1] == 0.0) fran[1] = 0.0;
if (v[i][2] == 0.0) fran[2] = 0.0;
temperature->restore_bias(i,v[i]);
} else {
fdrag[0] = gamma1*v[i][0];

27
src/fix_shake.cpp
View File

@ -413,9 +413,15 @@ void FixShake::setup(int vflag)
dtv = step_respa[0];
dtf_innerhalf = 0.5 * step_respa[0] * force->ftm2v;
dtf_inner = dtf_innerhalf;
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
// apply correction to all rRESPA levels
for (int ilevel = 0; ilevel < nlevels_respa; ilevel++) {
((Respa *) update->integrate)->copy_flevel_f(ilevel);
post_force_respa(vflag,ilevel,loop_respa[ilevel]-1);
((Respa *) update->integrate)->copy_f_flevel(ilevel);
}
dtf_inner = step_respa[0] * force->ftm2v;
}
}
@ -543,10 +549,12 @@ void FixShake::post_force_respa(int vflag, int ilevel, int iloop)
if (ilevel == nlevels_respa-1 && update->ntimestep == next_output) stats();
// enforce SHAKE constraints on every loop iteration of every rRESPA level
// except last loop iteration of inner levels
// might be OK to skip enforcing SHAKE constraings
// on last iteration of inner levels if pressure not requested
// however, leads to slightly different trajectories
if (ilevel < nlevels_respa-1 && iloop == loop_respa[ilevel]-1) return;
//if (ilevel < nlevels_respa-1 && iloop == loop_respa[ilevel]-1 && !vflag)
// return;
// xshake = unconstrained move with current v,f as function of level
// communicate results if necessary
@ -554,9 +562,12 @@ void FixShake::post_force_respa(int vflag, int ilevel, int iloop)
unconstrained_update_respa(ilevel);
if (nprocs > 1) comm->forward_comm_fix(this);
// virial setup, only need to compute on outermost level
// virial setup only needed on last iteration of innermost level
// and if pressure is requested
// virial accumulation happens at outermost level
if (ilevel == nlevels_respa-1 && vflag) v_setup(vflag);
if (ilevel == 0 && iloop == loop_respa[ilevel] - 1 && vflag) v_setup(vflag);
if (iloop == loop_respa[ilevel]-1) evflag = 1;
else evflag = 0;
// loop over clusters to add constraint forces

4
src/neigh_derive.cpp
View File

@ -439,9 +439,13 @@ void Neighbor::skip_from_respa(NeighList *list)
if (ipage_middle->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
inum++;
}
list->inum = inum;
listinner->inum = inum;
if (respamiddle) listmiddle->inum = inum;
}
/* ----------------------------------------------------------------------

3
src/respa.cpp
View File

@ -286,7 +286,8 @@ void Respa::init()
ev_setup();
// detect if fix omp is present and will clear force arrays for us
// detect if fix omp is present and will clear force arrays
int ifix = modify->find_fix("package_omp");
if (ifix >= 0) external_force_clear = 1;

2
src/version.h
View File

@ -1 +1 @@
#define LAMMPS_VERSION "9 Aug 2013"
#define LAMMPS_VERSION "12 Aug 2013"